BLASTP 2.2.22 [Sep-27-2009]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.


Reference for composition-based statistics starting in round 2:
Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
Eugene V. Koonin, and Stephen F. Altschul (2001), 
"Improving the accuracy of PSI-BLAST protein database searches with 
composition-based statistics and other refinements",  Nucleic Acids Res. 29:2994-3005.

Query= gi|254780237|ref|YP_003064650.1| DNA-directed RNA polymerase
subunit alpha [Candidatus Liberibacter asiaticus str. psy62]
         (340 letters)

Database: nr 
           13,984,884 sequences; 4,792,584,752 total letters

Searching..................................................done


Results from round 1


>gi|254780237|ref|YP_003064650.1| DNA-directed RNA polymerase subunit alpha [Candidatus Liberibacter
           asiaticus str. psy62]
 gi|254039914|gb|ACT56710.1| DNA-directed RNA polymerase subunit alpha [Candidatus Liberibacter
           asiaticus str. psy62]
          Length = 340

 Score =  696 bits (1796), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 340/340 (100%), Positives = 340/340 (100%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI
Sbjct: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ
Sbjct: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI
Sbjct: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE
Sbjct: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR
Sbjct: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
           KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC
Sbjct: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340


>gi|315122794|ref|YP_004063283.1| DNA-directed RNA polymerase subunit alpha [Candidatus Liberibacter
           solanacearum CLso-ZC1]
 gi|313496196|gb|ADR52795.1| DNA-directed RNA polymerase subunit alpha [Candidatus Liberibacter
           solanacearum CLso-ZC1]
          Length = 340

 Score =  625 bits (1611), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 299/340 (87%), Positives = 321/340 (94%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPNNIE+ VLG EEENRT+++AEP PRGFAHTLGNALRRVL+SSLRGAAI
Sbjct: 1   MIQKNWQELIKPNNIEFTVLGHEEENRTMVVAEPFPRGFAHTLGNALRRVLLSSLRGAAI 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHEISSIKGV ED+TDIILNIKGINLKMS DS KRVTI+KRGPGVVTAGDIQ
Sbjct: 61  TAVQIDGVLHEISSIKGVREDITDIILNIKGINLKMSSDSSKRVTIYKRGPGVVTAGDIQ 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TVNDIE+LNPDHVICNLDVDAVVRMELTVSKG GYVPAKHHRTENDPIGLITIDALYSPI
Sbjct: 121 TVNDIEILNPDHVICNLDVDAVVRMELTVSKGQGYVPAKHHRTENDPIGLITIDALYSPI 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VESAREGQ+LDYDKL+M IDTDGSI GED+VA ASRILQDQL +FINF+EP KE
Sbjct: 181 KKVSYKVESAREGQILDYDKLNMIIDTDGSIGGEDAVAFASRILQDQLNVFINFDEPTKE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            KED++V  LPFNPALLKKVEELELSVRS NCLRG+NI+Y+GDLIQ+TEA+MLR ANFGR
Sbjct: 241 EKEDMDVDRLPFNPALLKKVEELELSVRSANCLRGDNIIYIGDLIQKTEAEMLRTANFGR 300

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
           KSL+EIKGVL TMGLFLGMNLPDWPPESIE+LAKKYEDKC
Sbjct: 301 KSLLEIKGVLATMGLFLGMNLPDWPPESIEDLAKKYEDKC 340


>gi|222085699|ref|YP_002544229.1| DNA-directed RNA polymerase, alpha subunit [Agrobacterium
           radiobacter K84]
 gi|254765239|sp|B9JDV2|RPOA_AGRRK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|221723147|gb|ACM26303.1| DNA-directed RNA polymerase, alpha subunit [Agrobacterium
           radiobacter K84]
          Length = 336

 Score =  495 bits (1274), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 238/339 (70%), Positives = 285/339 (84%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+   G+    +  ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVEFTSSGR---TKATLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I +KM GD  KR+ + K+GPGVVTAGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIKMDGDDAKRMVVRKQGPGVVTAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDIEILNPEHVICTLDEGAEIRMEFTVNNGKGYVPAERNRAEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQVLDYDKLSM+I+TDGSITGED+VA A+RILQDQLG+F+NF+EP+KE
Sbjct: 178 KKVSYKVENTREGQVLDYDKLSMSIETDGSITGEDAVAFAARILQDQLGVFVNFDEPQKE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 238 AEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 297 KSLNEIKEVLASMGLHLGMEVPAWPPENIEDLAKRYEDQ 335


>gi|86357329|ref|YP_469221.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli CFN 42]
 gi|116251564|ref|YP_767402.1| DNA-directed RNA polymerase subunit alpha [Rhizobium leguminosarum
           bv. viciae 3841]
 gi|190891379|ref|YP_001977921.1| DNA-directed RNA polymerase protein, alpha subunit [Rhizobium etli
           CIAT 652]
 gi|209548959|ref|YP_002280876.1| DNA-directed RNA polymerase subunit alpha [Rhizobium leguminosarum
           bv. trifolii WSM2304]
 gi|218516292|ref|ZP_03513132.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli 8C-3]
 gi|241204189|ref|YP_002975285.1| DNA-directed RNA polymerase subunit alpha [Rhizobium leguminosarum
           bv. trifolii WSM1325]
 gi|119366712|sp|Q2K9J2|RPOA_RHIEC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366713|sp|Q1MIB7|RPOA_RHIL3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238057757|sp|B5ZZ57|RPOA_RHILW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238692528|sp|B3PWU5|RPOA_RHIE6 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|86281431|gb|ABC90494.1| DNA-directed RNA polymerase alpha chain protein [Rhizobium etli CFN
           42]
 gi|115256212|emb|CAK07293.1| putative DNA-directed RNA polymerase alpha chain [Rhizobium
           leguminosarum bv. viciae 3841]
 gi|190696658|gb|ACE90743.1| DNA-directed RNA polymerase protein, alpha subunit [Rhizobium etli
           CIAT 652]
 gi|209534715|gb|ACI54650.1| DNA-directed RNA polymerase, alpha subunit [Rhizobium leguminosarum
           bv. trifolii WSM2304]
 gi|240858079|gb|ACS55746.1| DNA-directed RNA polymerase, alpha subunit [Rhizobium leguminosarum
           bv. trifolii WSM1325]
 gi|327189694|gb|EGE56841.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli CNPAF512]
          Length = 336

 Score =  494 bits (1273), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 238/339 (70%), Positives = 283/339 (83%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+         R  ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVEF---SSSSRTRATLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I +KM GD  KR+ + K+GPGVVTAGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIKMDGDDAKRMVVRKQGPGVVTAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDIEILNPEHVICTLDEGAEIRMEFTVNNGKGYVPAERNRAEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQVLDYDKL+MTI+TDGSITGED+VA A+RILQDQLG+F+NF+EP+KE
Sbjct: 178 KKVSYKVENTREGQVLDYDKLNMTIETDGSITGEDAVAFAARILQDQLGVFVNFDEPQKE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 238 TEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 297 KSLNEIKEVLASMGLHLGMEVPAWPPENIEDLAKRYEDQ 335


>gi|110634006|ref|YP_674214.1| DNA-directed RNA polymerase subunit alpha [Mesorhizobium sp. BNC1]
 gi|119366696|sp|Q11HS6|RPOA_MESSB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|110284990|gb|ABG63049.1| DNA-directed RNA polymerase subunit alpha [Chelativorans sp. BNC1]
          Length = 336

 Score =  494 bits (1271), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 237/339 (69%), Positives = 284/339 (83%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP+ IE+   G+ + N   ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPSKIEFTSKGRTQTN---LVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M GD  KR+ + K+GPG VTAGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIAGVREDVTDIVLNIKEIAIRMEGDGPKRMVLRKQGPGAVTAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDVEILNPEHVICTLDQGAEIRMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQVLDYDKL+MTI+TDGS+TGED+VA A+RILQDQLG+F+NFEEP+KE
Sbjct: 178 KKVSYKVENTREGQVLDYDKLTMTIETDGSVTGEDAVAFAARILQDQLGLFVNFEEPQKE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V  +  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 238 VPAE-QVTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +PDWPP++IEELAK+YED+
Sbjct: 297 KSLNEIKEVLASMGLHLGMEVPDWPPDNIEELAKRYEDQ 335


>gi|319783344|ref|YP_004142820.1| DNA-directed RNA polymerase subunit alpha [Mesorhizobium ciceri
           biovar biserrulae WSM1271]
 gi|317169232|gb|ADV12770.1| DNA-directed RNA polymerase, alpha subunit [Mesorhizobium ciceri
           biovar biserrulae WSM1271]
          Length = 336

 Score =  491 bits (1265), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 237/339 (69%), Positives = 281/339 (82%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN IE+     +++  T ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKIEF---SSKKKTLTTLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M GD  KR+ + K+GPG V AGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIAGVREDVTDIVLNIKEIAIRMEGDGPKRMVVRKQGPGAVLAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNPDHVIC LD  A +RME TV  G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDVEILNPDHVICTLDEGAEIRMEFTVDTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQVLDYDKL+MTI+TDGSITGED+VA A+RILQDQLG+F+NF+EP+KE
Sbjct: 178 KKVSYKVENTREGQVLDYDKLTMTIETDGSITGEDAVAFAARILQDQLGLFVNFDEPQKE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V  +  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 238 VAAEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +PDWPPE+IE+LAK+YED+
Sbjct: 297 KSLNEIKEVLAAMGLHLGMEVPDWPPENIEDLAKRYEDQ 335


>gi|13470575|ref|NP_102144.1| DNA-directed RNA polymerase subunit alpha [Mesorhizobium loti
           MAFF303099]
 gi|260468530|ref|ZP_05813697.1| DNA-directed RNA polymerase, alpha subunit [Mesorhizobium
           opportunistum WSM2075]
 gi|20139638|sp|Q98N33|RPOA_RHILO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|14021317|dbj|BAB47930.1| DNA-directed RNA polymerase alpha subunit [Mesorhizobium loti
           MAFF303099]
 gi|259028686|gb|EEW29995.1| DNA-directed RNA polymerase, alpha subunit [Mesorhizobium
           opportunistum WSM2075]
          Length = 336

 Score =  491 bits (1264), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 236/339 (69%), Positives = 282/339 (83%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN IE+     +++  T ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKIEF---SSKKKTLTTLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M GD  KR+ + K+GPG V AGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIAGVREDVTDIVLNIKEIAIRMEGDGPKRMVVRKQGPGAVLAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNPDHVIC LD  A +RME TV  G GYVPA+ +R E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDVEILNPDHVICTLDEGAEIRMEFTVDTGKGYVPAERNRAEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQVLDYDKL+MTI+TDGSI+GED+VA A+RILQDQLG+F+NF+EP+KE
Sbjct: 178 KKVSYKVENTREGQVLDYDKLTMTIETDGSISGEDAVAFAARILQDQLGLFVNFDEPQKE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V  +  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 238 VAAEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +PDWPPE+IE+LAK+YED+
Sbjct: 297 KSLNEIKEVLAAMGLHLGMEVPDWPPENIEDLAKRYEDQ 335


>gi|15965133|ref|NP_385486.1| DNA-directed RNA polymerase subunit alpha [Sinorhizobium meliloti
           1021]
 gi|150396231|ref|YP_001326698.1| DNA-directed RNA polymerase subunit alpha [Sinorhizobium medicae
           WSM419]
 gi|307314383|ref|ZP_07593989.1| DNA-directed RNA polymerase, alpha subunit [Sinorhizobium meliloti
           BL225C]
 gi|307322095|ref|ZP_07601471.1| DNA-directed RNA polymerase, alpha subunit [Sinorhizobium meliloti
           AK83]
 gi|20139518|sp|Q925Z2|RPOA_RHIME RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|166229280|sp|A6U883|RPOA_SINMW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|15074313|emb|CAC45959.1| DNA-directed RNA polymerase, alpha subunit [Sinorhizobium meliloti
           1021]
 gi|16588802|gb|AAL26901.1| RNA polymerase alpha-subunit [Sinorhizobium meliloti]
 gi|150027746|gb|ABR59863.1| DNA-directed RNA polymerase, alpha subunit [Sinorhizobium medicae
           WSM419]
 gi|306892277|gb|EFN23087.1| DNA-directed RNA polymerase, alpha subunit [Sinorhizobium meliloti
           AK83]
 gi|306899081|gb|EFN29723.1| DNA-directed RNA polymerase, alpha subunit [Sinorhizobium meliloti
           BL225C]
          Length = 336

 Score =  490 bits (1262), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 234/339 (69%), Positives = 284/339 (83%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+   G+    +  ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVEFASSGR---TKATLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I +KM GD  KR+ + K+GPGVVTAGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIKMDGDDAKRMVVRKQGPGVVTAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA  +R+E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDIEILNPNHVICTLDEGAEIRMEFTVNNGKGYVPADRNRSEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQVLDYDKL+M+I+TDGS+TGED++A A+RILQDQL +F+NF+EP+KE
Sbjct: 178 KKVSYKVENTREGQVLDYDKLTMSIETDGSVTGEDAIAFAARILQDQLSVFVNFDEPQKE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 238 TEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 297 KSLNEIKEVLASMGLHLGMEVPSWPPENIEDLAKRYEDQ 335


>gi|227821779|ref|YP_002825749.1| DNA-directed RNA polymerase subunit alpha [Sinorhizobium fredii
           NGR234]
 gi|254765259|sp|C3MB03|RPOA_RHISN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|227340778|gb|ACP24996.1| DNA-directed RNA polymerase alpha chain [Sinorhizobium fredii
           NGR234]
          Length = 336

 Score =  490 bits (1261), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 233/339 (68%), Positives = 285/339 (84%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++   G+    +  ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFTSSGR---TKATLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I +KM GD  KR+ + K+GPGVVTAGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIKMDGDDSKRMVVRKQGPGVVTAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +R+E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDIEILNPNHVICTLDEGAEIRMEFTVNNGKGYVPAERNRSEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQVLDYDKL+M+I+TDGS+TGED++A A+RILQDQL +F+NF+EP+KE
Sbjct: 178 KKVSYKVENTREGQVLDYDKLTMSIETDGSVTGEDAIAFAARILQDQLSVFVNFDEPQKE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 238 AEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 297 KSLNEIKEVLASMGLHLGMEVPSWPPENIEDLAKRYEDQ 335


>gi|15889218|ref|NP_354899.1| DNA-directed RNA polymerase subunit alpha [Agrobacterium
           tumefaciens str. C58]
 gi|325293312|ref|YP_004279176.1| DNA-directed RNA polymerase subunit alpha [Agrobacterium sp. H13-3]
 gi|61234197|sp|P0A4E3|RPOA_AGRT5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61234204|sp|P0A4E4|RPOA_RHIRD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|5712306|gb|AAD47422.1|AF111855_1 RNA polymerase alpha subunit [Agrobacterium tumefaciens]
 gi|15157043|gb|AAK87684.1| DNA-directed RNA polymerase alpha subunit [Agrobacterium
           tumefaciens str. C58]
 gi|325061165|gb|ADY64856.1| DNA-directed RNA polymerase subunit alpha [Agrobacterium sp. H13-3]
          Length = 336

 Score =  488 bits (1257), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 234/339 (69%), Positives = 282/339 (83%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+         +  ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVEFT---SSSRTKATLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I +KM GD  KR+ + K+GPG VTAGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIKMDGDDSKRMVVRKQGPGSVTAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIE+LNPDHVIC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDIEILNPDHVICTLDEGAEIRMEFTVNNGKGYVPAERNRAEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQVLDYDKL MTI+T+GS++GED+VA A+RILQDQLG+F+NF+EP+KE
Sbjct: 178 KKVSYKVENTREGQVLDYDKLIMTIETNGSVSGEDAVAFAARILQDQLGVFVNFDEPQKE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E+ +V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 238 AEEE-SVTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 297 KSLNEIKEVLASMGLHLGMEVPAWPPENIEDLAKRYEDQ 335


>gi|222148390|ref|YP_002549347.1| DNA-directed RNA polymerase subunit alpha [Agrobacterium vitis S4]
 gi|254765240|sp|B9JVR1|RPOA_AGRVS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|221735378|gb|ACM36341.1| DNA-directed RNA polymerase alpha subunit [Agrobacterium vitis S4]
          Length = 336

 Score =  487 bits (1254), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 234/339 (69%), Positives = 282/339 (83%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+   G+    +  ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVEFSSSGR---TKATLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I +KM GD  KR+ + K+GPGVVTAGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIKMDGDDAKRMVVRKQGPGVVTAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIE+LNP HVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDIEILNPHHVICTLDEGAEIRMEFTVNNGKGYVPADRNRAEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQVLDYDKL+MTI+TDGS++GED+VA A+RILQDQL +F+NF+EP++E
Sbjct: 178 KKVSYKVENTREGQVLDYDKLTMTIETDGSVSGEDAVAFAARILQDQLSVFVNFDEPQRE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 238 AEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 297 KSLNEIKEVLASMGLHLGMEVPAWPPENIEDLAKRYEDQ 335


>gi|62290120|ref|YP_221913.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 1
           str. 9-941]
 gi|82700043|ref|YP_414617.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis
           biovar Abortus 2308]
 gi|189024358|ref|YP_001935126.1| RNA polymerase, alpha chain, bacterial and organelle [Brucella
           abortus S19]
 gi|225627680|ref|ZP_03785717.1| DNA-directed RNA polymerase, alpha subunit [Brucella ceti str.
           Cudo]
 gi|237815628|ref|ZP_04594625.1| DNA-directed RNA polymerase, alpha subunit [Brucella abortus str.
           2308 A]
 gi|254689429|ref|ZP_05152683.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 6
           str. 870]
 gi|254693914|ref|ZP_05155742.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 3
           str. Tulya]
 gi|254697564|ref|ZP_05159392.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 2
           str. 86/8/59]
 gi|254710280|ref|ZP_05172091.1| DNA-directed RNA polymerase subunit alpha [Brucella pinnipedialis
           B2/94]
 gi|254714277|ref|ZP_05176088.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti M644/93/1]
 gi|254717714|ref|ZP_05179525.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti M13/05/1]
 gi|254730458|ref|ZP_05189036.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 4
           str. 292]
 gi|256031774|ref|ZP_05445388.1| DNA-directed RNA polymerase subunit alpha [Brucella pinnipedialis
           M292/94/1]
 gi|256159944|ref|ZP_05457662.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti M490/95/1]
 gi|256255175|ref|ZP_05460711.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti B1/94]
 gi|256257675|ref|ZP_05463211.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 9
           str. C68]
 gi|256369633|ref|YP_003107143.1| DNA-directed RNA polymerase alpha subunit [Brucella microti CCM
           4915]
 gi|260168908|ref|ZP_05755719.1| DNA-directed RNA polymerase subunit alpha [Brucella sp. F5/99]
 gi|260546668|ref|ZP_05822407.1| RNA polymerase [Brucella abortus NCTC 8038]
 gi|260754952|ref|ZP_05867300.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 6
           str. 870]
 gi|260758168|ref|ZP_05870516.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 4
           str. 292]
 gi|260761994|ref|ZP_05874337.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 2
           str. 86/8/59]
 gi|260883961|ref|ZP_05895575.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 9
           str. C68]
 gi|261214205|ref|ZP_05928486.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 3
           str. Tulya]
 gi|261219556|ref|ZP_05933837.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti M13/05/1]
 gi|261222371|ref|ZP_05936652.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti B1/94]
 gi|261317842|ref|ZP_05957039.1| DNA-directed RNA polymerase subunit alpha [Brucella pinnipedialis
           B2/94]
 gi|261322051|ref|ZP_05961248.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti M644/93/1]
 gi|261758400|ref|ZP_06002109.1| RNA polymerase [Brucella sp. F5/99]
 gi|265988872|ref|ZP_06101429.1| DNA-directed RNA polymerase subunit alpha [Brucella pinnipedialis
           M292/94/1]
 gi|265998336|ref|ZP_06110893.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti M490/95/1]
 gi|297248515|ref|ZP_06932233.1| DNA-directed RNA polymerase, alpha subunit [Brucella abortus bv. 5
           str. B3196]
 gi|306840325|ref|ZP_07473097.1| DNA-directed RNA polymerase, alpha subunit [Brucella sp. BO2]
 gi|306844112|ref|ZP_07476706.1| DNA-directed RNA polymerase, alpha subunit [Brucella sp. BO1]
 gi|75496695|sp|Q57CT2|RPOA_BRUAB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366668|sp|Q2YRU0|RPOA_BRUA2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238689381|sp|B2S655|RPOA_BRUA1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|62196252|gb|AAX74552.1| RpoA, DNA-directed RNA polymerase, alpha subunit [Brucella abortus
           bv. 1 str. 9-941]
 gi|82616144|emb|CAJ11187.1| RNA polymerase, alpha chain, bacterial and organelle [Brucella
           melitensis biovar Abortus 2308]
 gi|189019930|gb|ACD72652.1| RNA polymerase, alpha chain, bacterial and organelle [Brucella
           abortus S19]
 gi|225617685|gb|EEH14730.1| DNA-directed RNA polymerase, alpha subunit [Brucella ceti str.
           Cudo]
 gi|237788926|gb|EEP63137.1| DNA-directed RNA polymerase, alpha subunit [Brucella abortus str.
           2308 A]
 gi|255999795|gb|ACU48194.1| DNA-directed RNA polymerase alpha subunit [Brucella microti CCM
           4915]
 gi|260095718|gb|EEW79595.1| RNA polymerase [Brucella abortus NCTC 8038]
 gi|260668486|gb|EEX55426.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 4
           str. 292]
 gi|260672426|gb|EEX59247.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 2
           str. 86/8/59]
 gi|260675060|gb|EEX61881.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 6
           str. 870]
 gi|260873489|gb|EEX80558.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 9
           str. C68]
 gi|260915812|gb|EEX82673.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 3
           str. Tulya]
 gi|260920955|gb|EEX87608.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti B1/94]
 gi|260924645|gb|EEX91213.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti M13/05/1]
 gi|261294741|gb|EEX98237.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti M644/93/1]
 gi|261297065|gb|EEY00562.1| DNA-directed RNA polymerase subunit alpha [Brucella pinnipedialis
           B2/94]
 gi|261738384|gb|EEY26380.1| RNA polymerase [Brucella sp. F5/99]
 gi|262552804|gb|EEZ08794.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti M490/95/1]
 gi|264661069|gb|EEZ31330.1| DNA-directed RNA polymerase subunit alpha [Brucella pinnipedialis
           M292/94/1]
 gi|297175684|gb|EFH35031.1| DNA-directed RNA polymerase, alpha subunit [Brucella abortus bv. 5
           str. B3196]
 gi|306275555|gb|EFM57287.1| DNA-directed RNA polymerase, alpha subunit [Brucella sp. BO1]
 gi|306289724|gb|EFM60913.1| DNA-directed RNA polymerase, alpha subunit [Brucella sp. BO2]
          Length = 337

 Score =  478 bits (1229), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 228/339 (67%), Positives = 279/339 (82%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFITHGSR--THATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K GPGVVTAGDIQ
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKEGPGVVTAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 119 TVGDVEILNPEHVICTLDEGAEIRMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY +E+ REGQVLDYDKL++ I+T+GS+TGED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKIENTREGQVLDYDKLTLNIETNGSVTGEDAVAYAARILQDQLSIFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 APQE-QVAELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 298 KSLNEIKEVLASMGLHLGMEIPAWPPENIEDLAKRYEDQ 336


>gi|153009310|ref|YP_001370525.1| DNA-directed RNA polymerase subunit alpha [Ochrobactrum anthropi
           ATCC 49188]
 gi|239832098|ref|ZP_04680427.1| DNA-directed RNA polymerase, alpha subunit [Ochrobactrum
           intermedium LMG 3301]
 gi|166229274|sp|A6X0E2|RPOA_OCHA4 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|151561198|gb|ABS14696.1| DNA-directed RNA polymerase, alpha subunit [Ochrobactrum anthropi
           ATCC 49188]
 gi|239824365|gb|EEQ95933.1| DNA-directed RNA polymerase, alpha subunit [Ochrobactrum
           intermedium LMG 3301]
          Length = 337

 Score =  478 bits (1229), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 226/339 (66%), Positives = 279/339 (82%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFITNGSR--THATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGVLHE SSI GV ED+TDI+LN+K I ++M G+  KR+ + K GPGVVTAGDIQ
Sbjct: 59  TAIQIDGVLHEFSSIPGVREDVTDIVLNVKEIAIRMEGEGPKRMVVRKEGPGVVTAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNPDHVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 119 TVGDVEILNPDHVICTLDEGAEIRMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY +E+ REGQVLDYDKL++ I+T+GS++GED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKIENTREGQVLDYDKLTLNIETNGSVSGEDAVAYAARILQDQLAIFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 APQE-QVAELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 298 KSLNEIKEVLASMGLHLGMEIPSWPPENIEDLAKRYEDQ 336


>gi|23502086|ref|NP_698213.1| DNA-directed RNA polymerase subunit alpha [Brucella suis 1330]
 gi|163843474|ref|YP_001627878.1| DNA-directed RNA polymerase subunit alpha [Brucella suis ATCC
           23445]
 gi|254704494|ref|ZP_05166322.1| DNA-directed RNA polymerase subunit alpha [Brucella suis bv. 3 str.
           686]
 gi|260566262|ref|ZP_05836732.1| DNA-directed RNA polymerase subunit alpha [Brucella suis bv. 4 str.
           40]
 gi|261755176|ref|ZP_05998885.1| DNA-directed RNA polymerase subunit alpha [Brucella suis bv. 3 str.
           686]
 gi|38258599|sp|Q8G094|RPOA_BRUSU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|189043832|sp|B0CH07|RPOA_BRUSI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|23348045|gb|AAN30128.1| DNA-directed RNA polymerase, alpha subunit [Brucella suis 1330]
 gi|163674197|gb|ABY38308.1| DNA-directed RNA polymerase, alpha subunit [Brucella suis ATCC
           23445]
 gi|260155780|gb|EEW90860.1| DNA-directed RNA polymerase subunit alpha [Brucella suis bv. 4 str.
           40]
 gi|261744929|gb|EEY32855.1| DNA-directed RNA polymerase subunit alpha [Brucella suis bv. 3 str.
           686]
          Length = 337

 Score =  478 bits (1229), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 228/339 (67%), Positives = 279/339 (82%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFITHGSR--THATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K GPGVVTAGDIQ
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKEGPGVVTAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 119 TVGDVEILNPEHVICTLDEGAEIRMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY +E+ REGQVLDYDKL++ I+T+GS+TGED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKIENTREGQVLDYDKLTLNIETNGSVTGEDAVAYAARILQDQLSIFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 APQE-QVAELAFNPALLKKVDELELSVRSANCLKTDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 298 KSLNEIKEVLASMGLHLGMEIPAWPPENIEDLAKRYEDQ 336


>gi|256061289|ref|ZP_05451439.1| DNA-directed RNA polymerase subunit alpha [Brucella neotomae 5K33]
 gi|261325296|ref|ZP_05964493.1| DNA-directed RNA polymerase subunit alpha [Brucella neotomae 5K33]
 gi|261301276|gb|EEY04773.1| DNA-directed RNA polymerase subunit alpha [Brucella neotomae 5K33]
          Length = 337

 Score =  477 bits (1228), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 228/339 (67%), Positives = 279/339 (82%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFITHGSR--THATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K GPGVVTAGDIQ
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIVIRMEGEGPKRMVVRKEGPGVVTAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 119 TVGDVEILNPEHVICTLDEGAEIRMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY +E+ REGQVLDYDKL++ I+T+GS+TGED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKIENTREGQVLDYDKLTLNIETNGSVTGEDAVAYAARILQDQLSIFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 APQE-QVAELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 298 KSLNEIKEVLASMGLHLGMEIPAWPPENIEDLAKRYEDQ 336


>gi|17987064|ref|NP_539698.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           1 str. 16M]
 gi|225852705|ref|YP_002732938.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis ATCC
           23457]
 gi|256044859|ref|ZP_05447763.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           1 str. Rev.1]
 gi|256113763|ref|ZP_05454567.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           3 str. Ether]
 gi|256263804|ref|ZP_05466336.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           2 str. 63/9]
 gi|260565539|ref|ZP_05836023.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           1 str. 16M]
 gi|265991286|ref|ZP_06103843.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           1 str. Rev.1]
 gi|265995123|ref|ZP_06107680.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           3 str. Ether]
 gi|20139479|sp|Q8YHL6|RPOA_BRUME RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|254765245|sp|C0RJH6|RPOA_BRUMB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|17982721|gb|AAL51962.1| DNA-directed RNA polymerase alpha chain [Brucella melitensis bv. 1
           str. 16M]
 gi|225641070|gb|ACO00984.1| DNA-directed RNA polymerase, alpha subunit [Brucella melitensis
           ATCC 23457]
 gi|260151607|gb|EEW86701.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           1 str. 16M]
 gi|262766236|gb|EEZ12025.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           3 str. Ether]
 gi|263002070|gb|EEZ14645.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           1 str. Rev.1]
 gi|263093932|gb|EEZ17866.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           2 str. 63/9]
 gi|326409230|gb|ADZ66295.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis M28]
 gi|326538938|gb|ADZ87153.1| DNA-directed RNA polymerase, alpha subunit [Brucella melitensis
           M5-90]
          Length = 337

 Score =  477 bits (1227), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 228/339 (67%), Positives = 279/339 (82%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFITHGSR--THATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K GPGVVTAGDIQ
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVHKEGPGVVTAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 119 TVGDVEILNPEHVICTLDEGAEIRMEFTVNTGKGYVPADCNRAEDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY +E+ REGQVLDYDKL++ I+T+GS+TGED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKIENTREGQVLDYDKLTLNIETNGSVTGEDAVAYAARILQDQLSIFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 APQE-QVAELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 298 KSLNEIKEVLASMGLHLGMEIPAWPPENIEDLAKRYEDQ 336


>gi|163760824|ref|ZP_02167903.1| putative DNA-directed RNA polymerase alpha chain [Hoeflea
           phototrophica DFL-43]
 gi|162281868|gb|EDQ32160.1| putative DNA-directed RNA polymerase alpha chain [Hoeflea
           phototrophica DFL-43]
          Length = 336

 Score =  477 bits (1227), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 227/339 (66%), Positives = 280/339 (82%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP+ +E+     +   +  ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPSKVEF---STQSRTKASVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDIILNIK I ++M GD  KR+ + K+GPGVVTAGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIPGVREDVTDIILNIKEIAIRMEGDEAKRMVVRKQGPGVVTAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIE+LNP+H +C LD  A +RME TV+ G GYV A  +R E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDIEILNPEHALCTLDEGAEIRMEFTVNNGKGYVAADRNRAEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KK SY VE+ REGQVLDYDKL+++++TDGS++GED+VA A+RILQDQLG+F+NF+EP+KE
Sbjct: 178 KKCSYKVENTREGQVLDYDKLTLSLETDGSVSGEDAVAYAARILQDQLGVFVNFDEPQKE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V E+  V  L FNP+LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 238 VHEE-TVAELAFNPSLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 297 KSLNEIKEVLASMGLHLGMEVPSWPPENIEDLAKRYEDQ 335


>gi|254719267|ref|ZP_05181078.1| DNA-directed RNA polymerase subunit alpha [Brucella sp. 83/13]
 gi|265984266|ref|ZP_06097001.1| DNA-directed RNA polymerase subunit alpha [Brucella sp. 83/13]
 gi|306838018|ref|ZP_07470876.1| DNA-directed RNA polymerase, alpha subunit [Brucella sp. NF 2653]
 gi|264662858|gb|EEZ33119.1| DNA-directed RNA polymerase subunit alpha [Brucella sp. 83/13]
 gi|306406942|gb|EFM63163.1| DNA-directed RNA polymerase, alpha subunit [Brucella sp. NF 2653]
          Length = 337

 Score =  476 bits (1226), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 227/339 (66%), Positives = 278/339 (82%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFITHGSR--THATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K GPGVVT GDIQ
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKEGPGVVTTGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 119 TVGDVEILNPEHVICTLDEGAEIRMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY +E+ REGQVLDYDKL++ I+T+GS+TGED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKIENTREGQVLDYDKLTLNIETNGSVTGEDAVAYAARILQDQLSIFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 APQE-QVAELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 298 KSLNEIKEVLASMGLHLGMEIPAWPPENIEDLAKRYEDQ 336


>gi|161619164|ref|YP_001593051.1| DNA-directed RNA polymerase subunit alpha [Brucella canis ATCC
           23365]
 gi|189043831|sp|A9M5M5|RPOA_BRUC2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|161335975|gb|ABX62280.1| DNA-directed RNA polymerase, alpha subunit [Brucella canis ATCC
           23365]
          Length = 337

 Score =  476 bits (1224), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 227/339 (66%), Positives = 278/339 (82%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFITHGSR--THATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K GPGVVTAGDIQ
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKEGPGVVTAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 119 TVGDVEILNPEHVICTLDEGAEIRMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY +E+ REGQVLDYDKL++ I+T+GS+TGED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKIENTREGQVLDYDKLTLNIETNGSVTGEDAVAYAARILQDQLSIFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++  V  L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 APQE-QVAELAFNPVLLKKVDELELSVRSANCLKTDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 298 KSLNEIKEVLASMGLHLGMEIPAWPPENIEDLAKRYEDQ 336


>gi|294852544|ref|ZP_06793217.1| DNA-directed RNA polymerase [Brucella sp. NVSL 07-0026]
 gi|294821133|gb|EFG38132.1| DNA-directed RNA polymerase [Brucella sp. NVSL 07-0026]
          Length = 337

 Score =  474 bits (1221), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 227/339 (66%), Positives = 278/339 (82%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFITHGSR--THATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K GPGVVTAGDIQ
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKEGPGVVTAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 119 TVGDVEILNPEHVICTLDEGAEIRMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY +E+ REGQVLDYDKL++ I+T+GS+TGED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKIENTREGQVLDYDKLTLNIETNGSVTGEDAVAYAARILQDQLSIFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++  V  L FN ALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 APQE-QVAELAFNAALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 298 KSLNEIKEVLASMGLHLGMEIPAWPPENIEDLAKRYEDQ 336


>gi|254706610|ref|ZP_05168438.1| DNA-directed RNA polymerase subunit alpha [Brucella pinnipedialis
           M163/99/10]
 gi|261314070|ref|ZP_05953267.1| DNA-directed RNA polymerase subunit alpha [Brucella pinnipedialis
           M163/99/10]
 gi|261303096|gb|EEY06593.1| DNA-directed RNA polymerase subunit alpha [Brucella pinnipedialis
           M163/99/10]
          Length = 337

 Score =  473 bits (1218), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 227/339 (66%), Positives = 278/339 (82%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFITHGSR--THATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K GPGVVTAGDIQ
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKEGPGVVTAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 119 TVGDVEILNPEHVICTLDEGAEIRMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY +E+ REGQVLDYDKL++ I+T+GS+TGED+VA A+RILQDQL +F+NFEE +KE
Sbjct: 179 RKVSYKIENTREGQVLDYDKLTLNIETNGSVTGEDAVAYAARILQDQLSIFVNFEELQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 APQE-QVAELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 298 KSLNEIKEVLASMGLHLGMEIPAWPPENIEDLAKRYEDQ 336


>gi|148560545|ref|YP_001259129.1| DNA-directed RNA polymerase subunit alpha [Brucella ovis ATCC
           25840]
 gi|166229260|sp|A5VQY2|RPOA_BRUO2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|148371802|gb|ABQ61781.1| DNA-directed RNA polymerase, alpha subunit [Brucella ovis ATCC
           25840]
          Length = 337

 Score =  473 bits (1216), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 226/339 (66%), Positives = 277/339 (81%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFITHGSRA--HATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K GPGVVTAGDIQ
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKEGPGVVTAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+H IC LD  A + ME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 119 TVGDVEILNPEHAICTLDEGAEICMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY +E+ REGQVLDYDKL++ I+T+GS+TGED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKIENTREGQVLDYDKLTLNIETNGSVTGEDAVAYAARILQDQLSIFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 APQE-QVAELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 298 KSLNEIKEVLASMGLHLGMEIPAWPPENIEDLAKRYEDQ 336


>gi|240850811|ref|YP_002972211.1| DNA-directed RNA polymerase subunit alpha [Bartonella grahamii
           as4aup]
 gi|240267934|gb|ACS51522.1| DNA-directed RNA polymerase subunit alpha [Bartonella grahamii
           as4aup]
          Length = 337

 Score =  461 bits (1186), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 228/339 (67%), Positives = 273/339 (80%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E      +  N   +IAEPL RGF  TLGNALRRVL+SSLRGAAI
Sbjct: 1   MIQKNWQELIKPNKVES--CAHDNPNVISVIAEPLERGFGLTLGNALRRVLLSSLRGAAI 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDIILNIK I L+M  +  KRV ++K GPGVV AGDI 
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIILNIKEIALRMEEEGPKRVVVYKEGPGVVKAGDIS 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNPDHVIC LD DA +RME  V+ G GYVP+  +  ++  IGLI ID+LYSPI
Sbjct: 119 TVGDMEILNPDHVICTLDEDAEIRMEFIVNTGKGYVPSDRNCVDDARIGLIPIDSLYSPI 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQVLDYDKL++TI+T+G++ GED+VA A+RILQDQL +FINFEEP+KE
Sbjct: 179 RKVSYKVENTREGQVLDYDKLTLTIETNGAVNGEDAVAFAARILQDQLSLFINFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E+ +   L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE++MLR  NFGR
Sbjct: 239 PVEEAD-SELSFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPPE+I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEIPAWPPENIDDLAKRYEDQ 336


>gi|298291462|ref|YP_003693401.1| DNA-directed RNA polymerase, subunit alpha [Starkeya novella DSM
           506]
 gi|296927973|gb|ADH88782.1| DNA-directed RNA polymerase, alpha subunit [Starkeya novella DSM
           506]
          Length = 338

 Score =  461 bits (1186), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 220/338 (65%), Positives = 278/338 (82%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP  +E + +G + +    ++AEPL RGF  TLGNALRR+L+SSL+GAA+
Sbjct: 1   MIQKNWQELIKPEKLE-VAVGSDPKRLATVVAEPLERGFGQTLGNALRRILLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V IDGVLHE SSI GV ED+TDI+LNIK I +KM+GD  KR+ + K+GPG+VTAGDIQ
Sbjct: 60  TSVHIDGVLHEFSSIPGVREDVTDIVLNIKDIAIKMAGDGPKRMVVKKQGPGIVTAGDIQ 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D++VLNP+ V+C LD  A +RME TV  G GYV  + +R E+ PIGLI +D+LYSP+
Sbjct: 120 TVGDVQVLNPELVLCTLDDGAEIRMEFTVDTGKGYVAGERNRPEDAPIGLIPVDSLYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQ+LDYDKL+MTI+T+GS++ ED++A A+RILQDQL +F+NFEEPK+E
Sbjct: 180 KKVSYKVENTREGQILDYDKLTMTIETNGSVSPEDALAFAARILQDQLEIFVNFEEPKRE 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E   ++ LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 T-ESPAMQELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK++ED
Sbjct: 299 KSLNEIKEVLASMGLHLGMEVPGWPPENIEDLAKRFED 336


>gi|163868626|ref|YP_001609835.1| DNA-directed RNA polymerase subunit alpha [Bartonella tribocorum
           CIP 105476]
 gi|189043830|sp|A9IVZ5|RPOA_BART1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|161018282|emb|CAK01840.1| DNA-directed RNA polymerase alpha subunit [Bartonella tribocorum
           CIP 105476]
          Length = 337

 Score =  459 bits (1182), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 227/339 (66%), Positives = 273/339 (80%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E      +  N   +IAEPL RGF  TLGNALRRVL+SSLRGAAI
Sbjct: 1   MIQKNWQELIKPNKVESFT--HDNSNIISVIAEPLERGFGLTLGNALRRVLLSSLRGAAI 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDIILNIK I L+M  +  KR+ ++K GPGVV AGDI 
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIILNIKEIALRMEEEGPKRLVVYKEGPGVVRAGDIN 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNPDHVIC LD DA +RME  V+ G GYVP+  +  ++  IGLI ID+LYSPI
Sbjct: 119 TVGDMEILNPDHVICTLDEDAEIRMEFIVNTGKGYVPSDRNCVDDGRIGLIPIDSLYSPI 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQVLDYDKL++TI+T+G++ GED+VA A+RILQDQL +FINFEEP+KE
Sbjct: 179 RKVSYKVENTREGQVLDYDKLTLTIETNGAVNGEDAVAFAARILQDQLSLFINFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E+ +   L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE++MLR  NFGR
Sbjct: 239 PVEEAD-SELSFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPPE+I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEIPAWPPENIDDLAKRYEDQ 336


>gi|254470353|ref|ZP_05083757.1| DNA-directed RNA polymerase, alpha subunit [Pseudovibrio sp. JE062]
 gi|211960664|gb|EEA95860.1| DNA-directed RNA polymerase, alpha subunit [Pseudovibrio sp. JE062]
          Length = 340

 Score =  458 bits (1179), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 225/337 (66%), Positives = 275/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELIKP  ++ I  G +   +  +IAEPL RG+  TLGNALRRVL+SSL+GAA+T
Sbjct: 3   IQKNWQELIKPTKLD-IRAGDDARFKASVIAEPLERGYGLTLGNALRRVLLSSLQGAAVT 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           AVQIDGVLHE SSI GV ED+TDIILNIK + L+M G+  KR+ + K+GPG V AGDI+T
Sbjct: 62  AVQIDGVLHEFSSIPGVREDVTDIILNIKEVALRMEGEGPKRMVLRKQGPGAVYAGDIET 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V DIEVLNP  ++CNLD  A VR+E TV+ G GYVPA  +R E+ PIGLI +D+LYSP+K
Sbjct: 122 VGDIEVLNPGLLLCNLDEGAEVRIEFTVNTGKGYVPAAANRPEDAPIGLIPVDSLYSPVK 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQVLDYDKL++T++TDGS+  ED+VA A+RILQDQL +F+NFEEP++EV
Sbjct: 182 KVSYKVENTREGQVLDYDKLTLTVETDGSVIPEDAVAFAARILQDQLSIFVNFEEPQREV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +ED  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGRK
Sbjct: 242 QED-TVAELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM + +WPPE+I+ELAK+YED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVANWPPENIDELAKRYED 337


>gi|328543382|ref|YP_004303491.1| DNA-directed RNA polymerase subunit alpha [Polymorphum gilvum
           SL003B-26A1]
 gi|326413127|gb|ADZ70190.1| DNA-directed RNA polymerase subunit alpha [Polymorphum gilvum
           SL003B-26A1]
          Length = 353

 Score =  457 bits (1177), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 221/337 (65%), Positives = 278/337 (82%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELIKP  ++ +  G++      ++AEPL RG+  TLGNALRR+L+SSL+GAA+T
Sbjct: 16  IQKNWQELIKPTKLD-VKPGEDPRFVATVVAEPLERGYGLTLGNALRRILLSSLQGAAVT 74

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           AVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K+GPG+VTAGDIQT
Sbjct: 75  AVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKQGPGLVTAGDIQT 134

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V D+EVLNP+ V+C LD  A +RME TV+ G GYVP+  +R E+ PIGLI +D+LYSP+K
Sbjct: 135 VGDVEVLNPELVLCTLDEGAEIRMEFTVNTGKGYVPSDRNRPEDAPIGLIPVDSLYSPVK 194

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQVLDYDKL++T++TDGS+  +D+VA A+RILQDQL +F+NFEEPK+EV
Sbjct: 195 KVSYKVEATREGQVLDYDKLTLTVETDGSVKPDDAVAYAARILQDQLSIFVNFEEPKREV 254

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ED +V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGRK
Sbjct: 255 AED-HVPELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRK 313

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM++ +WPPE+IE+LAK+YED
Sbjct: 314 SLNEIKEVLAQMGLHLGMDVANWPPENIEDLAKRYED 350


>gi|304391480|ref|ZP_07373422.1| DNA-directed RNA polymerase, alpha subunit [Ahrensia sp. R2A130]
 gi|303295709|gb|EFL90067.1| DNA-directed RNA polymerase, alpha subunit [Ahrensia sp. R2A130]
          Length = 335

 Score =  456 bits (1174), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 222/339 (65%), Positives = 272/339 (80%), Gaps = 5/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI +NWQELIKP  ++    G     +  ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIHRNWQELIKPTKLDVSSNG----TKGTLVAEPLERGFGLTLGNALRRVLLSSLQGAAV 56

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDIILNIK + ++M G+  KR+ + K G GVVTAGDIQ
Sbjct: 57  TAVQIDGVLHEFSSIPGVREDVTDIILNIKELAIRMEGEGPKRMVVRKEGAGVVTAGDIQ 116

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HV+C LD DA +RME TV  G GYV A  +R E+ PIGLI +DAL+SP+
Sbjct: 117 TVGDLEILNPEHVLCTLDEDAEIRMEFTVDTGKGYVAADRNRPEDAPIGLIPVDALFSPV 176

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY  E+ REGQVLDYDKL+MTI+TDGS+T ED+VA  +RILQDQL +F+NFEEP+KE
Sbjct: 177 RKVSYKTENTREGQVLDYDKLTMTIETDGSVTPEDAVAYGARILQDQLSIFVNFEEPQKE 236

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V ++  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE +MLR  NFGR
Sbjct: 237 VVQE-QVTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEGEMLRTPNFGR 295

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL TMGL LGM +P WPPE+I++LAK+YED+
Sbjct: 296 KSLNEIKEVLATMGLHLGMEIPAWPPENIDDLAKRYEDQ 334


>gi|91977628|ref|YP_570287.1| DNA-directed RNA polymerase subunit alpha [Rhodopseudomonas
           palustris BisB5]
 gi|119366717|sp|Q134V3|RPOA_RHOPS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|91684084|gb|ABE40386.1| DNA-directed RNA polymerase, alpha subunit [Rhodopseudomonas
           palustris BisB5]
          Length = 339

 Score =  456 bits (1173), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 218/337 (64%), Positives = 275/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +  G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQ-VSPGSDATRFATLVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +VQIDGVLHE SSI GV ED+TDI+LNIK I+LKM G+  KR+ + K+GPGVVTAGDIQT
Sbjct: 62  SVQIDGVLHEFSSIAGVREDVTDIVLNIKDISLKMQGEGPKRMVVKKQGPGVVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V DI VLNPD  IC LD  A +RME TV+ G GYV A+ +R E+ PIGLI +D+LYSP++
Sbjct: 122 VGDIVVLNPDLQICTLDEGAEIRMEFTVNTGKGYVAAERNRPEDAPIGLIPVDSLYSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+MT++T+G++T +D+VA A+RILQDQL +F+NFEEP+KEV
Sbjct: 182 KVSYKVENTREGQILDYDKLTMTVETNGALTPDDAVAFAARILQDQLNVFVNFEEPRKEV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 242 TQEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 337


>gi|27380487|ref|NP_772016.1| DNA-directed RNA polymerase subunit alpha [Bradyrhizobium japonicum
           USDA 110]
 gi|41688696|sp|Q89JA7|RPOA_BRAJA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|27353651|dbj|BAC50641.1| DNA-directed RNA polymerase alpha subunit [Bradyrhizobium japonicum
           USDA 110]
          Length = 343

 Score =  455 bits (1171), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 217/337 (64%), Positives = 275/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +  G +      ++AEPL RGF  TLGNALRR+L+SSL+GAA+ 
Sbjct: 7   IQKNWQELIRPNKLQ-VTPGSDPARFATIVAEPLERGFGQTLGNALRRILLSSLQGAAVQ 65

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I++KM G+  KR+ + K+GPGVVTAGDIQT
Sbjct: 66  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDISIKMQGEGPKRMVVKKQGPGVVTAGDIQT 125

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V D+ VLNPD  IC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +D+LYSP++
Sbjct: 126 VGDVVVLNPDLQICTLDEGAEIRMEFTVATGKGYVPAERNRPEDAPIGLIPVDSLYSPVR 185

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+MTI+T+G+I+ +DSVA A+RILQDQL +F+NFEEP+KEV
Sbjct: 186 KVSYKVENTREGQILDYDKLTMTIETNGAISPDDSVAYAARILQDQLNVFVNFEEPRKEV 245

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 246 AQEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 304

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 305 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 341


>gi|316933551|ref|YP_004108533.1| DNA-directed RNA polymerase subunit alpha [Rhodopseudomonas
           palustris DX-1]
 gi|315601265|gb|ADU43800.1| DNA-directed RNA polymerase, alpha subunit [Rhodopseudomonas
           palustris DX-1]
          Length = 339

 Score =  455 bits (1170), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 219/337 (64%), Positives = 273/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +  G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQ-VTAGSDATRFATLVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I+LKM G+  KR+ I K GPGVVTAGDIQT
Sbjct: 62  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDISLKMQGEGPKRMVIKKSGPGVVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V DI VLNPD  +C LD  A +RME TV+ G GYV A+ +R E+ PIGLI +D+LYSP++
Sbjct: 122 VGDIVVLNPDLQLCTLDDGAEIRMEFTVNTGKGYVAAERNRPEDAPIGLIPVDSLYSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+MT++T+G+IT ED+VA A+RILQDQL +F+NFEEP+KEV
Sbjct: 182 KVSYKVENTREGQILDYDKLTMTVETNGAITPEDAVAYAARILQDQLNVFVNFEEPRKEV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 242 TQEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 337


>gi|319405874|emb|CBI79506.1| DNA-directed RNA polymerase alpha subunit [Bartonella sp. AR 15-3]
          Length = 337

 Score =  455 bits (1170), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 220/339 (64%), Positives = 275/339 (81%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+      + N   ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVEF--HAHNDPNIVSVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID +LHE SSI GV ED+TDIILNIK I ++M  +  KRV + K GPGVV AGDIQ
Sbjct: 59  TAVQIDSILHEFSSIPGVREDVTDIILNIKEIAIRMEEEGPKRVILCKEGPGVVKAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T+ D+ +LNP+HVIC LD D  VRMEL V+ G GYVPA+ + T + PIGLI +D+LYSP+
Sbjct: 119 TIGDMAILNPEHVICTLDEDVEVRMELIVNTGKGYVPAERNCTNDTPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQ+LDYDKL++T++T+G++ GED++A A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKVENTREGQILDYDKLTLTVETNGAVNGEDAIAFAARILQDQLLVFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           + E+ +   L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 LIEEPD-PELSFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPPE+I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEIPAWPPENIDDLAKRYEDQ 336


>gi|86749439|ref|YP_485935.1| DNA-directed RNA polymerase subunit alpha [Rhodopseudomonas
           palustris HaA2]
 gi|119366715|sp|Q2IXN6|RPOA_RHOP2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|86572467|gb|ABD07024.1| DNA-directed RNA polymerase, alpha subunit [Rhodopseudomonas
           palustris HaA2]
          Length = 339

 Score =  455 bits (1170), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 217/337 (64%), Positives = 274/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +  G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQ-VTAGSDATRFATLVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I+LKM G+  KR+ + K+GPGVVTAGDIQT
Sbjct: 62  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDISLKMQGEGPKRMVVKKQGPGVVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V DI VLNPD  IC LD  A +RME TV+ G GYV A+ +R E+ PIGLI +D+LYSP++
Sbjct: 122 VGDIVVLNPDLQICTLDEGAEIRMEFTVNTGKGYVAAERNRPEDAPIGLIPVDSLYSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+MT++T+G++T +D+VA A+RILQDQL +F+NFEEP+KEV
Sbjct: 182 KVSYKVENTREGQILDYDKLTMTVETNGALTPDDAVAFAARILQDQLNVFVNFEEPRKEV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 242 TQEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 337


>gi|118591156|ref|ZP_01548555.1| DNA-directed RNA polymerase subunit alpha [Stappia aggregata IAM
           12614]
 gi|118436232|gb|EAV42874.1| DNA-directed RNA polymerase subunit alpha [Stappia aggregata IAM
           12614]
          Length = 340

 Score =  453 bits (1166), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 221/337 (65%), Positives = 275/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELIKP  +E I  G++      ++AEPL RG+  TLGNALRR+L+SSL+GAA+T
Sbjct: 3   IQKNWQELIKPTKLE-IKPGEDPRFLATVVAEPLERGYGLTLGNALRRILLSSLQGAAVT 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           AVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K+GPGVVTAGDIQT
Sbjct: 62  AVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKQGPGVVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V D+EVLNP+ V+C LD  A +RME TV+ G GY  +  +R E+ PIGLI +D+LYSP+K
Sbjct: 122 VGDVEVLNPELVLCTLDEGAEIRMEFTVNTGKGYHSSDRNRPEDAPIGLIPVDSLYSPVK 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQVLDYDKL++T++TDGS+  ED+VA A+RILQDQL +F+NFEEP++EV
Sbjct: 182 KVSYKVENTREGQVLDYDKLTLTVETDGSVKPEDAVAFAARILQDQLSIFVNFEEPQREV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ED +V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGRK
Sbjct: 242 AED-SVPELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM + +WPPE+I++LAK+YED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVANWPPENIDDLAKRYED 337


>gi|307946311|ref|ZP_07661646.1| DNA-directed RNA polymerase, alpha subunit [Roseibium sp.
           TrichSKD4]
 gi|307769975|gb|EFO29201.1| DNA-directed RNA polymerase, alpha subunit [Roseibium sp.
           TrichSKD4]
          Length = 340

 Score =  453 bits (1166), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 220/337 (65%), Positives = 274/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELIKP  +E +  G +      ++AEPL RG+  TLGNALRR+L+SSL+GAA+T
Sbjct: 3   IQKNWQELIKPTKLE-VKPGDDPRFLATVVAEPLERGYGLTLGNALRRILLSSLQGAAVT 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           AVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K+GPGVVTAGDIQT
Sbjct: 62  AVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKQGPGVVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V D+EVLNP+ V+C LD  A +RME TV+ G GYV +  +R E+ PIGLI +D+LYSP+K
Sbjct: 122 VGDVEVLNPELVLCTLDEGAEIRMEFTVNTGKGYVASDRNRPEDAPIGLIPVDSLYSPVK 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQVLDYDKL++T++TDGS+  +D+VA A+RILQDQL +F+NFEEP++EV
Sbjct: 182 KVSYKVENTREGQVLDYDKLTLTVETDGSVKPDDAVAFAARILQDQLSIFVNFEEPQREV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ED  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGRK
Sbjct: 242 AED-TVPELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM + +WPPE+I++LAK+YED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVANWPPENIDDLAKRYED 337


>gi|146340081|ref|YP_001205129.1| DNA-directed RNA polymerase subunit alpha [Bradyrhizobium sp.
           ORS278]
 gi|148256368|ref|YP_001240953.1| DNA-directed RNA polymerase subunit alpha [Bradyrhizobium sp.
           BTAi1]
 gi|158513287|sp|A5ELK3|RPOA_BRASB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158514218|sp|A4YSL6|RPOA_BRASO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|146192887|emb|CAL76892.1| DNA-directed RNA polymerase alpha chain [Bradyrhizobium sp. ORS278]
 gi|146408541|gb|ABQ37047.1| DNA-directed RNA polymerase subunit alpha [Bradyrhizobium sp.
           BTAi1]
          Length = 343

 Score =  453 bits (1166), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 216/337 (64%), Positives = 274/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +  G +      ++AEPL RGF  TLGNALRR+L+SSL+GAA+ 
Sbjct: 7   IQKNWQELIRPNKLQ-VTPGSDATRFATVVAEPLERGFGQTLGNALRRILLSSLQGAAVQ 65

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I++KM G+  KR+ + K+GPG VTAGDIQT
Sbjct: 66  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDISIKMQGEGPKRMVVKKQGPGAVTAGDIQT 125

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V DI VLNPD  +C LD  A +RME TV+ G GYVPA+ +R E+ PIGLI ID+L+SP++
Sbjct: 126 VGDIVVLNPDLQLCTLDEGAEIRMEFTVATGKGYVPAERNRPEDAPIGLIPIDSLFSPVR 185

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+MTI+T+G+I+ ED+VA A+RILQDQL +F+NFEEP+KEV
Sbjct: 186 KVSYKVENTREGQILDYDKLTMTIETNGAISPEDAVAYAARILQDQLNVFVNFEEPRKEV 245

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 246 AQEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 304

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 305 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 341


>gi|158424154|ref|YP_001525446.1| DNA-directed RNA polymerase subunit alpha [Azorhizobium caulinodans
           ORS 571]
 gi|172047974|sp|A8IAN5|RPOA_AZOC5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158331043|dbj|BAF88528.1| DNA-directed RNA polymerase alpha subunit [Azorhizobium caulinodans
           ORS 571]
          Length = 341

 Score =  453 bits (1165), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 218/338 (64%), Positives = 272/338 (80%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKP  ++ +  G + +    ++AEPL RGF  TLGN+LRR+L+SSL+GAA+
Sbjct: 4   VIQKNWQELIKPEKLQ-VTAGADPKRLATVVAEPLERGFGMTLGNSLRRILLSSLQGAAV 62

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V IDGVLHE SSI GV ED+TDIILNIK I +KM GD  KR+   K GPGV+ AGDIQ
Sbjct: 63  TSVHIDGVLHEFSSIPGVREDVTDIILNIKDIAIKMQGDGPKRLVAKKNGPGVLVAGDIQ 122

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DI++LNP  V+C LD  A +RME TV  G GYVPA+ +R E+ PIGLI ID+LYSP+
Sbjct: 123 TVGDIQILNPHLVLCTLDEGAELRMEFTVDTGKGYVPAERNRPEDAPIGLIPIDSLYSPV 182

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQ+LDYDKL+M I+TDGS++ ED++A A+RILQDQL +F+NFEEPK+E
Sbjct: 183 RKVSYKVENTREGQILDYDKLTMQIETDGSVSAEDALAYAARILQDQLEIFVNFEEPKRE 242

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E   ++ LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++E +MLR  NFGR
Sbjct: 243 -SETAAIQELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSETEMLRTPNFGR 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL +MGL LGM +P WPPE+IEELAK++ED
Sbjct: 302 KSLNEIKEVLASMGLHLGMEVPGWPPENIEELAKRFED 339


>gi|49474380|ref|YP_032422.1| DNA-directed RNA polymerase subunit alpha [Bartonella quintana str.
           Toulouse]
 gi|61215920|sp|Q6FZE6|RPOA_BARQU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|49239884|emb|CAF26282.1| DNA-directed RNA polymerase alpha chain [Bartonella quintana str.
           Toulouse]
          Length = 337

 Score =  453 bits (1165), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 221/339 (65%), Positives = 273/339 (80%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+     +  N + +I EPL RGF  TLGNALRRVL+SSLRGAAI
Sbjct: 1   MIQKNWQELIKPNKVEFCT--HDNPNISSVIVEPLERGFGLTLGNALRRVLLSSLRGAAI 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDIILNIK I L+M  +  KRV + K GPGVV AGDI 
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIILNIKEIALRMQEEGPKRVVVCKEGPGVVRAGDIN 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME  V+ G GY+P+  +  ++  IGLI +D+LYSPI
Sbjct: 119 TVGDMEILNPEHVICTLDEGAEIRMEFIVNTGKGYIPSDRNCVDDGRIGLIPVDSLYSPI 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQVLDYDKL++TI+T+G++ GED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKVENTREGQVLDYDKLTLTIETNGAVNGEDAVAFAARILQDQLSLFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           + ++ +   L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE++MLR  NFGR
Sbjct: 239 IVDESD-SELTFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPPE+I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEIPTWPPENIDDLAKRYEDQ 336


>gi|319899075|ref|YP_004159168.1| DNA-directed RNA polymerase alpha subunit [Bartonella clarridgeiae
           73]
 gi|319403039|emb|CBI76594.1| DNA-directed RNA polymerase alpha subunit [Bartonella clarridgeiae
           73]
          Length = 337

 Score =  453 bits (1165), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 219/339 (64%), Positives = 275/339 (81%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP+ +E+      + N   ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPSKVEFHT--HNDPNIVSVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID +LHE SSI GV ED+TDIILNIK I ++M  +  KR+ + K GPGVV AGDIQ
Sbjct: 59  TAVQIDSILHEFSSIPGVREDVTDIILNIKEIAIRMEEEGPKRIILCKEGPGVVKAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+ +LNP+HVIC LD DA VRMEL V+ G GYVP++ +  ++ PIGLI +D+LYSP+
Sbjct: 119 TVGDMAILNPEHVICTLDEDAEVRMELIVNTGKGYVPSERNCVDDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQ+LDYDKL++TI+T+G++ GED++A A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKVENTREGQILDYDKLTLTIETNGAVNGEDAIAFAARILQDQLLVFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           + E+     L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 LIEE-PASELTFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPPE+I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEIPAWPPENIDDLAKRYEDQ 336


>gi|254501022|ref|ZP_05113173.1| DNA-directed RNA polymerase, alpha subunit [Labrenzia alexandrii
           DFL-11]
 gi|222437093|gb|EEE43772.1| DNA-directed RNA polymerase, alpha subunit [Labrenzia alexandrii
           DFL-11]
          Length = 340

 Score =  452 bits (1164), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 221/337 (65%), Positives = 273/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELIKP  +E I  G +      ++AEPL RG+  TLGNALRR+L+SSL+GAA+T
Sbjct: 3   IQKNWQELIKPTKLE-IKPGDDPRFLATVVAEPLERGYGLTLGNALRRILLSSLQGAAVT 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           AVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K+GPGVVTAGDIQT
Sbjct: 62  AVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKQGPGVVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V D+EVLNPD V+C LD  A +RME TV+ G GY  +  +R E+ PIGLI +D+LYSP+K
Sbjct: 122 VGDVEVLNPDLVLCTLDEGAEIRMEFTVNTGKGYHSSDRNRPEDAPIGLIPVDSLYSPVK 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQVLDYDKL++T++TDGS+  +D+VA A+RILQDQL +F+NFEEP++EV
Sbjct: 182 KVSYKVENTREGQVLDYDKLTLTVETDGSVKPDDAVAFAARILQDQLSIFVNFEEPQREV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ED  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGRK
Sbjct: 242 AED-TVPELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM + +WPPE+I++LAK+YED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVANWPPENIDDLAKRYED 337


>gi|319404401|emb|CBI78004.1| DNA-directed RNA polymerase alpha subunit [Bartonella rochalimae
           ATCC BAA-1498]
          Length = 337

 Score =  452 bits (1163), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 219/339 (64%), Positives = 276/339 (81%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP+ +E+      + N   ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPSKVEF--HAHNDPNIVSVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID +LHE SSI GV ED+TDIILNIK I ++M  +  KRV + K GPGVV AGDIQ
Sbjct: 59  TAVQIDSILHEFSSIPGVREDVTDIILNIKEIAIRMEEEGPKRVILCKEGPGVVKAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+ +LNP+HVIC LD DA VRMEL V+ G GYVP++ +  ++ PIGLI +D+LYSP+
Sbjct: 119 TVGDMAILNPEHVICTLDEDAEVRMELIVNTGKGYVPSERNCIDDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQ+LDYDKL++TI+T+G++ GED++A A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKVENTREGQILDYDKLTLTIETNGAVNGEDAIAFAARILQDQLLVFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           + E+ +   L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 LVEEPD-SELSFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPP++I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEIPAWPPDNIDDLAKRYEDQ 336


>gi|49475770|ref|YP_033811.1| DNA-directed RNA polymerase subunit alpha [Bartonella henselae str.
           Houston-1]
 gi|51704335|sp|Q9FDC7|RPOA_BARHE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|49238577|emb|CAF27818.1| DNA-directed RNA polymerase alpha chain [Bartonella henselae str.
           Houston-1]
          Length = 337

 Score =  452 bits (1163), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 221/339 (65%), Positives = 272/339 (80%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+     +  N + +I EPL RGF  TLGNALRRVL+SSLRGAAI
Sbjct: 1   MIQKNWQELIKPNKVEFS--KHDNPNISSVIVEPLERGFGLTLGNALRRVLLSSLRGAAI 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDIILNIK I L+M  +  KR+ + K GPGV+ AGDI 
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIILNIKEIALRMREEGPKRIVVCKEGPGVLRAGDIS 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNPDHVIC LD DA +RME  V+ G GYVP+  +  ++  IGLI +D+LYSPI
Sbjct: 119 TVGDMEILNPDHVICTLDEDAEIRMEFIVNTGKGYVPSDRNCIDDARIGLIPVDSLYSPI 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQVLDYDKL++T++T+G++ GED++A A+RILQDQL +FINF+EP+K 
Sbjct: 179 RKVSYKVENTREGQVLDYDKLTLTVETNGAVNGEDALAFAARILQDQLALFINFKEPEKP 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E+ N   L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE++MLR  NFGR
Sbjct: 239 TVEESN-SELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPPE+I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEVPTWPPENIDDLAKRYEDQ 336


>gi|39936289|ref|NP_948565.1| DNA-directed RNA polymerase subunit alpha [Rhodopseudomonas
           palustris CGA009]
 gi|192292012|ref|YP_001992617.1| DNA-directed RNA polymerase subunit alpha [Rhodopseudomonas
           palustris TIE-1]
 gi|61215951|sp|Q6N4V7|RPOA_RHOPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|229564256|sp|B3QBV5|RPOA_RHOPT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|39650144|emb|CAE28667.1| DNA-directed RNA polymerase alpha subunit [Rhodopseudomonas
           palustris CGA009]
 gi|192285761|gb|ACF02142.1| DNA-directed RNA polymerase, alpha subunit [Rhodopseudomonas
           palustris TIE-1]
          Length = 339

 Score =  452 bits (1163), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 216/337 (64%), Positives = 273/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +  G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQ-VTPGSDATRFATLVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I+LKM G+  KR+ + K+GPG VTAGDIQT
Sbjct: 62  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDISLKMQGEGPKRMVVKKQGPGAVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V DI VLNPD  +C LD  A +RME TV+ G GYV A+ +R E+ PIGLI +D+LYSP++
Sbjct: 122 VGDIVVLNPDLQLCTLDDGAEIRMEFTVNTGKGYVAAERNRPEDAPIGLIPVDSLYSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+MT++T+G+I+ ED+VA A+RILQDQL +F+NFEEP+KEV
Sbjct: 182 KVSYKVENTREGQILDYDKLTMTVETNGAISPEDAVAFAARILQDQLNVFVNFEEPRKEV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 242 TQEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 337


>gi|85715106|ref|ZP_01046090.1| DNA-directed RNA polymerase alpha subunit [Nitrobacter sp. Nb-311A]
 gi|85698021|gb|EAQ35894.1| DNA-directed RNA polymerase alpha subunit [Nitrobacter sp. Nb-311A]
          Length = 343

 Score =  451 bits (1160), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 216/337 (64%), Positives = 271/337 (80%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +V G +      ++AEPL RGF  TLGNALRR+L+SSL+GAA+ 
Sbjct: 7   IQKNWQELIRPNKLQ-VVPGSDPSRFATLVAEPLERGFGQTLGNALRRILLSSLQGAAVQ 65

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I +KM G+  KR+ + K+GPG VTAGDIQT
Sbjct: 66  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDIAIKMQGEGPKRMVVKKQGPGSVTAGDIQT 125

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V DI VLNPD  IC LD  A +RME TV+ G GY+ A+ +R E+ PIGLI +D+LYSP++
Sbjct: 126 VGDIVVLNPDLQICTLDDGAEIRMEFTVAAGKGYIAAERNRPEDAPIGLIPVDSLYSPVR 185

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+MTI+T+G +T ED+VA A+RILQDQL +F+NFEEP+KEV
Sbjct: 186 KVSYKVENTREGQILDYDKLTMTIETNGGVTPEDAVAFAARILQDQLNVFVNFEEPRKEV 245

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
             +I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 246 ATEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 304

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 305 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 341


>gi|319407401|emb|CBI81052.1| DNA-directed RNA polymerase alpha subunit [Bartonella sp. 1-1C]
          Length = 337

 Score =  451 bits (1159), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 217/339 (64%), Positives = 276/339 (81%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP+ +E+      + N   ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPSKVEF--HAHNDPNIVSVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID +LHE SSI GV ED+TDIILNIK I ++M  +  KRV + K GPGVV AGDIQ
Sbjct: 59  TAVQIDSILHEFSSIPGVREDVTDIILNIKEIAIRMEEEGPKRVILCKEGPGVVKAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+ +LNP+HVIC LD DA VRMEL ++ G GYVP++ +  ++ PIGLI +D+LYSP+
Sbjct: 119 TVGDMAILNPEHVICTLDEDAEVRMELIINTGKGYVPSERNCIDDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY VE+ REGQ+LDYDKL++TI+T+G++ GED++A A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RRVSYKVENTREGQILDYDKLTLTIETNGAVNGEDAIAFAARILQDQLLVFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           + E+ +   L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 LVEEPD-SELSFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPP++I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEIPAWPPDNIDDLAKRYEDQ 336


>gi|75675580|ref|YP_318001.1| DNA-directed RNA polymerase subunit alpha [Nitrobacter winogradskyi
           Nb-255]
 gi|90110853|sp|Q3SSU2|RPOA_NITWN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|74420450|gb|ABA04649.1| DNA-directed RNA polymerase subunit alpha [Nitrobacter winogradskyi
           Nb-255]
          Length = 339

 Score =  451 bits (1159), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 216/337 (64%), Positives = 271/337 (80%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +V G +      +IAEPL RGF  TLGNALRR+L+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQ-VVPGSDPSRFATLIAEPLERGFGQTLGNALRRILLSSLQGAAVQ 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K+GPG VTAGDIQT
Sbjct: 62  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDIAIRMQGEGPKRMVVKKQGPGTVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V D+ VLNPD  IC LD  A +RME TV+ G GYV A+ +R E+ PIGLI +D+LYSP++
Sbjct: 122 VGDVVVLNPDLQICTLDDGAEIRMEFTVASGKGYVAAERNRPEDAPIGLIPVDSLYSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+MTI+T+G +T ED+VA A+RILQDQL +F+NFEEP+KEV
Sbjct: 182 KVSYKVENTREGQILDYDKLTMTIETNGGVTPEDAVAFAARILQDQLNVFVNFEEPRKEV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
             +I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 242 TTEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 337


>gi|115525561|ref|YP_782472.1| DNA-directed RNA polymerase subunit alpha [Rhodopseudomonas
           palustris BisA53]
 gi|122295431|sp|Q07KP2|RPOA_RHOP5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|115519508|gb|ABJ07492.1| DNA-directed RNA polymerase, alpha subunit [Rhodopseudomonas
           palustris BisA53]
          Length = 339

 Score =  449 bits (1156), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 216/337 (64%), Positives = 273/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +  G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQ-VTPGSDSGRFATLVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I++KM G+  KR+ + K+GPG VTAGDIQT
Sbjct: 62  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDISIKMQGEGPKRMVVKKQGPGTVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V DI VLNPD  IC LD  A +RME TV+ G GYV A+ +R E+ PIGLI +D+L+SP++
Sbjct: 122 VGDIVVLNPDLQICTLDDGAEIRMEFTVNTGKGYVAAERNRPEDAPIGLIPVDSLFSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+MTI+T+G+IT +D+VA A+RILQDQL +F+NFEEP+KEV
Sbjct: 182 KVSYKVENTREGQILDYDKLTMTIETNGAITPDDAVAYAARILQDQLNVFVNFEEPRKEV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 242 TQEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 337


>gi|92117122|ref|YP_576851.1| DNA-directed RNA polymerase subunit alpha [Nitrobacter hamburgensis
           X14]
 gi|119366703|sp|Q1QN06|RPOA_NITHX RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|91800016|gb|ABE62391.1| DNA-directed RNA polymerase subunit alpha [Nitrobacter hamburgensis
           X14]
          Length = 339

 Score =  449 bits (1155), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 216/337 (64%), Positives = 270/337 (80%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN + ++V G +      +IAEPL RGF  TLGNALRR+L+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKL-HVVPGSDPSRFATLIAEPLERGFGQTLGNALRRILLSSLQGAAVQ 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I++KM G+  KR+ + K+GPG VTAGDIQT
Sbjct: 62  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDISIKMQGEGPKRMVVKKQGPGTVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V DI VLNPD  IC LD  A +RME TV+ G GYV A+ +R E+ PIGLI +D+LYSP++
Sbjct: 122 VGDIVVLNPDLPICTLDDGAEIRMEFTVASGKGYVAAERNRPEDAPIGLIPVDSLYSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+M I+T+G +T ED+VA A+RILQDQL +F+NFEEP+KEV
Sbjct: 182 KVSYKVENTREGQILDYDKLTMMIETNGGVTPEDAVAFAARILQDQLNVFVNFEEPRKEV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
             +I +  L FNP  LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 242 ATEI-IPDLAFNPGFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 337


>gi|319408741|emb|CBI82398.1| DNA-directed RNA polymerase alpha subunit [Bartonella
           schoenbuchensis R1]
          Length = 337

 Score =  448 bits (1152), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 222/339 (65%), Positives = 271/339 (79%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+   G    N   ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVEFHADGNS--NVVSVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDIILNIK I ++M  +  K V I K GPGVV AGDI+
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIILNIKEIAIRMEEEGPKHVIICKEGPGVVRAGDIR 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME  V+ G GYVP+  +  ++  IGLI ID+LYSP+
Sbjct: 119 TVGDMEILNPEHVICTLDEGAEIRMEFIVNTGKGYVPSDRNCVDDAVIGLIPIDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQVLDYDKL++TI+T+G++ GED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKVENTREGQVLDYDKLTLTIETNGAVNGEDAVAFAARILQDQLSVFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           + E+     L FN ALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 LVEE-PASELSFNLALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPPE+I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEIPAWPPENIDDLAKRYEDQ 336


>gi|9837272|gb|AAG00506.1|AF285111_1 RNA polymerase alpha subunit [Bartonella henselae]
          Length = 337

 Score =  447 bits (1150), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 219/339 (64%), Positives = 270/339 (79%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELI PN +E+     +  N + +I EPL RGF  TLGNALRRVL+S LRGAAI
Sbjct: 1   MIQKNWQELINPNKVEFS--KHDNPNISSVIVEPLERGFGLTLGNALRRVLLSYLRGAAI 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDIILNIK I L+M  +  KR+ + K GPGV+ AGDI 
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIILNIKEIALRMREEGPKRIVVCKEGPGVLRAGDIS 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNPDHVIC LD DA +RME  V+ G GYVP+  +  ++  IGLI +D+LYSPI
Sbjct: 119 TVGDMEILNPDHVICTLDEDAEIRMEFIVNTGKGYVPSDRNCIDDARIGLIPVDSLYSPI 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQVLDYDKL++T++T+G++ GED++A A+RILQDQL +FINF+EP+K 
Sbjct: 179 RKVSYKVENTREGQVLDYDKLTLTVETNGAVNGEDALAFAARILQDQLALFINFKEPEKP 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E+ N   L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE++MLR  NFGR
Sbjct: 239 TVEESN-SELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPPE+I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEVPTWPPENIDDLAKRYEDQ 336


>gi|90417743|ref|ZP_01225655.1| DNA-directed RNA polymerase, alpha subunit [Aurantimonas
           manganoxydans SI85-9A1]
 gi|90337415|gb|EAS51066.1| DNA-directed RNA polymerase, alpha subunit [Aurantimonas
           manganoxydans SI85-9A1]
          Length = 342

 Score =  447 bits (1150), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 217/343 (63%), Positives = 272/343 (79%), Gaps = 6/343 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI  NWQ+L KPN + +   G    ++  + AEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIASNWQDLTKPNQVVFKNGGSR--SKASLTAEPLERGFGLTLGNALRRVLLSSLQGAAI 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGVLHE SSI GV ED+TDI+LN+K IN+ M G+  KR+ + K+GPG+V AGDIQ
Sbjct: 59  TAIQIDGVLHEFSSIPGVREDVTDIVLNVKEINIGMQGEGPKRMVVRKQGPGIVRAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIEVLNP+H IC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+L+SP+
Sbjct: 119 TVGDIEVLNPEHEICTLDEGAEIRMEFTVNTGKGYVPADQNRAEDAPIGLIPVDSLFSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQ L+ DKL+M I+TDGSI+GED+VA A+RILQDQL +F+NFEEP+++
Sbjct: 179 KKVSYKVEATREGQDLNKDKLTMQIETDGSISGEDAVAYAARILQDQLSVFVNFEEPQRD 238

Query: 241 VK----EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +     +  +  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  
Sbjct: 239 QRAPAGAEEQMAELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTP 298

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           NFGRKSL EIK VL +MGL LGM + DWPPE+I++LAK+YED+
Sbjct: 299 NFGRKSLNEIKEVLASMGLHLGMEVSDWPPENIDDLAKRYEDQ 341


>gi|90424913|ref|YP_533283.1| DNA-directed RNA polymerase subunit alpha [Rhodopseudomonas
           palustris BisB18]
 gi|119366716|sp|Q211H2|RPOA_RHOPB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|90106927|gb|ABD88964.1| DNA-directed RNA polymerase, alpha subunit [Rhodopseudomonas
           palustris BisB18]
          Length = 339

 Score =  447 bits (1149), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 214/337 (63%), Positives = 272/337 (80%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN +  +  G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKL-VVTPGSDPTRFATLVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I++KM G+  KR+ + K+GPG VTAGDIQT
Sbjct: 62  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDISIKMQGEGPKRMVVKKQGPGTVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V D+ VLNPD  IC LD  A +RME TV+ G GYV A+ +R E+ PIGLI +D+L+SP++
Sbjct: 122 VGDVVVLNPDLQICTLDEGAEIRMEFTVAGGKGYVAAERNRPEDAPIGLIPVDSLFSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+MTI+T+G+I+ +D+VA A+RILQDQL +F+NFEEP+KEV
Sbjct: 182 KVSYKVENTREGQILDYDKLTMTIETNGAISPDDAVAYAARILQDQLNVFVNFEEPRKEV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 242 TQEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 337


>gi|323136111|ref|ZP_08071194.1| DNA-directed RNA polymerase, alpha subunit [Methylocystis sp. ATCC
           49242]
 gi|322399202|gb|EFY01721.1| DNA-directed RNA polymerase, alpha subunit [Methylocystis sp. ATCC
           49242]
          Length = 339

 Score =  446 bits (1146), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 215/337 (63%), Positives = 270/337 (80%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELIKPN +E +  G +       +AEPL RGF  TLGNALRR+L+SSL+GAAIT
Sbjct: 3   IQKNWQELIKPNKLE-VTAGDDPRRVATAVAEPLERGFGVTLGNALRRILLSSLQGAAIT 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           ++ IDGVLHE SSI GV ED+TDI+LNIK I +K  G+  KR+T+ K GPG VTAGDIQ 
Sbjct: 62  SIHIDGVLHEFSSIPGVREDVTDIVLNIKDIAIKYQGEGVKRLTLKKTGPGAVTAGDIQA 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
             D++VLNPD VIC LD  A +R+E TVS G GYVPA  +R E+ PIGLI +D+LYSP+K
Sbjct: 122 TGDVQVLNPDLVICTLDEGAEIRIEFTVSTGKGYVPADRNRAEDAPIGLIPVDSLYSPVK 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQVLDYDKL++TI+T+G+IT ED++A ++RILQDQL +F+NFEEP++E 
Sbjct: 182 KVSYRVENTREGQVLDYDKLTLTIETNGAITPEDALAFSARILQDQLNVFVNFEEPRRE- 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +   ++  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++EA+MLR  NFGRK
Sbjct: 241 EAAPSIPQLAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I++LAK++E+
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDDLAKRFEE 337


>gi|220921923|ref|YP_002497224.1| DNA-directed RNA polymerase subunit alpha [Methylobacterium
           nodulans ORS 2060]
 gi|254765257|sp|B8IT35|RPOA_METNO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|219946529|gb|ACL56921.1| DNA-directed RNA polymerase, alpha subunit [Methylobacterium
           nodulans ORS 2060]
          Length = 339

 Score =  445 bits (1145), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 213/338 (63%), Positives = 273/338 (80%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN +E +  G + +    ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 2   VIQKNWQELIKPNKLE-VAPGHDPKRIATVVAEPLERGFGTTLGNALRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V IDGVLHE SSI GV ED+TDI+LNIK I ++ S D+ KR+T+ K GPG+VTAGDI 
Sbjct: 61  TSVHIDGVLHEFSSIPGVREDVTDIVLNIKTIAIRSSSDTPKRMTLRKTGPGLVTAGDIS 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T+ DI++LNPD V+C LD  A +RME TV+ G GYVPA  +R E+ PIGLI +DAL+SP+
Sbjct: 121 TIGDIQILNPDLVLCTLDEGAEIRMEFTVATGKGYVPADRNRPEDAPIGLIPVDALFSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY +E+ REGQ LD DKL+MT++T+G+++ ED++A A+RI+QDQL +F+NFEEP+KE
Sbjct: 181 TKVSYRIENTREGQDLDKDKLTMTVETNGAVSPEDALAYAARIIQDQLQIFVNFEEPRKE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
               +    LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 241 EAAPL-APQLPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++P WPPE+IE+LAK++E+
Sbjct: 300 KSLNEIKEVLAAMGLHLGMDVPGWPPENIEDLAKRFEE 337


>gi|170738679|ref|YP_001767334.1| DNA-directed RNA polymerase subunit alpha [Methylobacterium sp.
           4-46]
 gi|226699356|sp|B0UHU5|RPOA_METS4 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|168192953|gb|ACA14900.1| DNA-directed RNA polymerase, alpha subunit [Methylobacterium sp.
           4-46]
          Length = 339

 Score =  445 bits (1144), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 213/338 (63%), Positives = 274/338 (81%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN +E +V G + +    ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 2   VIQKNWQELIKPNKLE-VVPGHDPKRVATVVAEPLERGFGTTLGNALRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V IDGVLHE SSI GV ED+TDI+LNIK I ++ + D+ KR+T+ K GPG+VTAGDI 
Sbjct: 61  TSVHIDGVLHEFSSIPGVREDVTDIVLNIKTIAIRSNSDAPKRMTLRKTGPGLVTAGDIS 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T+ DI++LNPD V+C LD  A +RME TV+ G GYVPA  +R E+ PIGLI +DAL+SP+
Sbjct: 121 TIGDIQILNPDLVLCTLDEGAEIRMEFTVATGKGYVPADRNRPEDAPIGLIPVDALFSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY +E+ REGQ LD DKL+MT++T+G+++ ED++A A+RI+QDQL +F+NFEEP+KE
Sbjct: 181 TKVSYRIENTREGQDLDKDKLTMTVETNGAVSPEDALAYAARIIQDQLQIFVNFEEPRKE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
               +    LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 241 EAAPL-APQLPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++P WPPE+IE+LAK++E+
Sbjct: 300 KSLNEIKEVLAAMGLHLGMDVPGWPPENIEDLAKRFEE 337


>gi|209884837|ref|YP_002288694.1| DNA-directed RNA polymerase, alpha subunit [Oligotropha
           carboxidovorans OM5]
 gi|229564255|sp|B6JEY9|RPOA_OLICO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|209873033|gb|ACI92829.1| DNA-directed RNA polymerase, alpha subunit [Oligotropha
           carboxidovorans OM5]
          Length = 339

 Score =  445 bits (1144), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 213/337 (63%), Positives = 272/337 (80%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +  G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQ-VTPGSDPSRFATLVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I++KM G+  KR+ I K+GPGVVTAGDIQT
Sbjct: 62  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDISIKMQGEGPKRMVIKKQGPGVVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V D+ VLNP+  +C LD  A +RME TV  G GYV A  +R E+ PIGLI +D+L+SP++
Sbjct: 122 VGDVVVLNPELQLCTLDDGAEIRMEFTVDTGKGYVAADRNRPEDAPIGLIPVDSLFSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL++TI+T+G+IT ED++A ++RILQDQL +F+NFEEP+KEV
Sbjct: 182 KVSYKVENTREGQILDYDKLTLTIETNGAITPEDALAYSARILQDQLNVFVNFEEPRKEV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 242 VQEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 337


>gi|121601834|ref|YP_989021.1| DNA-directed RNA polymerase subunit alpha [Bartonella bacilliformis
           KC583]
 gi|158513082|sp|A1USR8|RPOA_BARBK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|120614011|gb|ABM44612.1| DNA-directed RNA polymerase, alpha subunit [Bartonella
           bacilliformis KC583]
          Length = 337

 Score =  443 bits (1139), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 216/339 (63%), Positives = 269/339 (79%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN IE+        N   ++AEPL RGF  TLGNALRR+L+SSLRGAAI
Sbjct: 1   MIQKNWQELIKPNKIEF--HAHSNPNVLSVVAEPLERGFGLTLGNALRRILLSSLRGAAI 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQ++GVLHE SSI GV ED+ DIILNIK I ++M  +  KR+ + K GPG+V AGDI+
Sbjct: 59  TAVQVEGVLHEFSSIPGVREDVADIILNIKEIAIRMEEEGPKRIVVCKEGPGIVKAGDIR 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME  V+ G GYVP+  +  ++ PIGLI ID+LYSPI
Sbjct: 119 TVGDMEILNPEHVICTLDEGAEIRMEFIVNTGKGYVPSDRNCFDDAPIGLIPIDSLYSPI 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY VE+ REGQVLDYDKL++TI+T+G++ G+D+VA A+RILQDQL +F+NF+EP+KE
Sbjct: 179 NKVSYKVENTREGQVLDYDKLTLTIETNGAVNGKDAVAFAARILQDQLSVFVNFKEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           + E+     L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE++MLR  NFGR
Sbjct: 239 LVEE-QTSELSFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +  WPPE+I++LAK YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEISAWPPENIDDLAKHYEDQ 336


>gi|114704508|ref|ZP_01437416.1| DNA-directed RNA polymerase alpha subunit [Fulvimarina pelagi
           HTCC2506]
 gi|114539293|gb|EAU42413.1| DNA-directed RNA polymerase alpha subunit [Fulvimarina pelagi
           HTCC2506]
          Length = 350

 Score =  443 bits (1139), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 219/352 (62%), Positives = 271/352 (76%), Gaps = 16/352 (4%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI  NWQ+L KPN + +   G+    +  + AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIASNWQDLSKPNQVVFKGSGR---TKASLTAEPLERGFGLTLGNALRRVLLSSLQGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK IN+ M G+  KR+ + K+GPGVV AGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEINIGMQGEGPKRMVVRKQGPGVVRAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIEVLNPDH IC LD  A +RME TV+ G GY+PA  +R E+ PIGLI IDAL+SP+
Sbjct: 118 TVGDIEVLNPDHEICTLDEGAEIRMEFTVNTGKGYIPADQNRAEDAPIGLIPIDALFSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQ L+ DKL+M I+TDGSI+GED+VA A+RI+QDQL +F+NFEEP+++
Sbjct: 178 KKVSYKVENTREGQDLNKDKLTMQIETDGSISGEDAVAYAARIIQDQLSVFVNFEEPQRD 237

Query: 241 VKEDIN-------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
            +                 ++ L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+
Sbjct: 238 QRGMAIGAGVGGGAAAEEPMQELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQK 297

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           TEA+MLR  NFGRKSL EIK VL +MGL LGM +  WPPE+I++LAK+YED+
Sbjct: 298 TEAEMLRTPNFGRKSLNEIKEVLASMGLHLGMEVQAWPPENIDDLAKRYEDQ 349


>gi|299135233|ref|ZP_07028424.1| DNA-directed RNA polymerase, alpha subunit [Afipia sp. 1NLS2]
 gi|298590210|gb|EFI50414.1| DNA-directed RNA polymerase, alpha subunit [Afipia sp. 1NLS2]
          Length = 339

 Score =  442 bits (1137), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 211/337 (62%), Positives = 273/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +  G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQ-VTPGADATRFATVVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I++KM G+  KR+ I K+GPGVVTAGDIQT
Sbjct: 62  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDISVKMQGEGPKRMVIKKQGPGVVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V D+ VLNP+  +C LD  A +RME T++ G GYV A  +R E+ PIGLI +D+L+SP++
Sbjct: 122 VGDVVVLNPELQLCTLDDGAEIRMEFTINTGKGYVAADRNRPEDAPIGLIPVDSLFSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL++TI+T+G+I+ ED++A ++RILQDQL +F+NFEEP+KEV
Sbjct: 182 KVSYKVENTREGQILDYDKLTLTIETNGAISPEDALAYSARILQDQLNVFVNFEEPRKEV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 242 VQEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 337


>gi|254418751|ref|ZP_05032475.1| DNA-directed RNA polymerase, alpha subunit [Brevundimonas sp. BAL3]
 gi|196184928|gb|EDX79904.1| DNA-directed RNA polymerase, alpha subunit [Brevundimonas sp. BAL3]
          Length = 339

 Score =  441 bits (1134), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 212/339 (62%), Positives = 269/339 (79%), Gaps = 1/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI++NWQELI+P   + I +G + + +  ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIERNWQELIRPEKPQ-IEIGSDAQRKARLVAEPLERGFGVTLGNALRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGV+HE SS++GV ED+ DI+LNIK + L+M  +  KR+T+   GPG VTAG I 
Sbjct: 60  TAIQIDGVVHEFSSLEGVREDVVDIVLNIKQLALRMHAEGPKRMTLRATGPGAVTAGQID 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DIEVLNPDHVIC LD  A VRMELTV  G GYV A+ +R E+ PIGLI +DALYSP+
Sbjct: 120 VSADIEVLNPDHVICTLDDGASVRMELTVQNGKGYVAAELNRPEDAPIGLIAVDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V+Y VE  R+GQ LDYDKL + ++T+G++T  D+VA A+RILQDQL +FI FEEPKK 
Sbjct: 180 KRVAYRVEPTRQGQSLDYDKLLLEVETNGAVTPVDAVAYAARILQDQLQIFITFEEPKKA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V++      LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE +MLR  NFGR
Sbjct: 240 VEQSDGKPDLPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEGEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL TMGL LGM++P+WPPE+IE+LAKK++D+
Sbjct: 300 KSLNEIKEVLATMGLSLGMDVPNWPPENIEDLAKKFDDQ 338


>gi|171769752|sp|A7HWT5|RPOA_PARL1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 338

 Score =  441 bits (1134), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 218/339 (64%), Positives = 273/339 (80%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNW+ELIKPN +E I  G + +    ++AEPL RGF  TLGNALRRVLMSSL+GAA+
Sbjct: 1   MIQKNWEELIKPNKLE-INPGHDAQRFATVVAEPLERGFGLTLGNALRRVLMSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDIILNIK + L++  +  KR+++ K+GPGVVTAGDI 
Sbjct: 60  TAVQIDGVLHEFSSIAGVREDVTDIILNIKQLALRLHAEGPKRMSLSKKGPGVVTAGDIT 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DIEVLNPD V+C LD  A +RME TV+ G GYV +  +R E+ PIGL+ +D+LYSP+
Sbjct: 120 AGADIEVLNPDLVLCTLDEGAEIRMEFTVALGKGYVASDRNRPEDAPIGLMPVDSLYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VSY VE+ REGQVLDYDKL++ I+T+G+IT +D+VA A+RILQDQL  F+NFEEP+++
Sbjct: 180 KRVSYKVENTREGQVLDYDKLTLQIETNGAITPDDAVAYAARILQDQLQTFVNFEEPEQK 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E+ +   L FN ALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE++MLR  NFGR
Sbjct: 240 HVEE-SRPELEFNAALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P+WPPE+IEELAK+YED+
Sbjct: 299 KSLNEIKEVLAQMGLHLGMEVPNWPPENIEELAKRYEDQ 337


>gi|163851599|ref|YP_001639642.1| DNA-directed RNA polymerase subunit alpha [Methylobacterium
           extorquens PA1]
 gi|163663204|gb|ABY30571.1| DNA-directed RNA polymerase, alpha subunit [Methylobacterium
           extorquens PA1]
          Length = 365

 Score =  440 bits (1131), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 212/338 (62%), Positives = 271/338 (80%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN ++ +  G + +    ++AEPL RGF  TLGN+LRRVL+SSL+GAA+
Sbjct: 28  VIQKNWQELIKPNKLQ-VTAGDDPKRVATVVAEPLERGFGTTLGNSLRRVLLSSLQGAAV 86

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQIDGVLHE SSI GV ED+TDI+LNIK I ++   D  KR+T+ K GPG+VTAGDI 
Sbjct: 87  TSVQIDGVLHEFSSIPGVREDVTDIVLNIKTIAIRSQTDQPKRMTLRKTGPGLVTAGDIG 146

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
            V DI++LNPD VIC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +DALYSP+
Sbjct: 147 AVGDIQILNPDLVICTLDDGAEIRMEFTVATGKGYVPAERNRPEDAPIGLIPVDALYSPV 206

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY VE+ REGQ LD DKL+MT++T+G+++ ED++A A+RI+QDQL +F+NFEEP+KE
Sbjct: 207 TKVSYRVETTREGQDLDKDKLTMTLETNGAVSPEDALAYAARIIQDQLQVFVNFEEPRKE 266

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
               +    LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++E +MLR  NFGR
Sbjct: 267 EAAPL-APQLPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSEGEMLRTPNFGR 325

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++P WPPE+IE+LAK++E+
Sbjct: 326 KSLNEIKEVLAGMGLHLGMDVPGWPPENIEDLAKRFEE 363


>gi|154253201|ref|YP_001414025.1| DNA-directed RNA polymerase subunit alpha [Parvibaculum
           lavamentivorans DS-1]
 gi|154157151|gb|ABS64368.1| DNA-directed RNA polymerase, alpha subunit [Parvibaculum
           lavamentivorans DS-1]
          Length = 357

 Score =  440 bits (1131), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 217/339 (64%), Positives = 273/339 (80%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNW+ELIKPN +E I  G + +    ++AEPL RGF  TLGNALRRVLMSSL+GAA+
Sbjct: 20  LIQKNWEELIKPNKLE-INPGHDAQRFATVVAEPLERGFGLTLGNALRRVLMSSLQGAAV 78

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDIILNIK + L++  +  KR+++ K+GPGVVTAGDI 
Sbjct: 79  TAVQIDGVLHEFSSIAGVREDVTDIILNIKQLALRLHAEGPKRMSLSKKGPGVVTAGDIT 138

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DIEVLNPD V+C LD  A +RME TV+ G GYV +  +R E+ PIGL+ +D+LYSP+
Sbjct: 139 AGADIEVLNPDLVLCTLDEGAEIRMEFTVALGKGYVASDRNRPEDAPIGLMPVDSLYSPV 198

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VSY VE+ REGQVLDYDKL++ I+T+G+IT +D+VA A+RILQDQL  F+NFEEP+++
Sbjct: 199 KRVSYKVENTREGQVLDYDKLTLQIETNGAITPDDAVAYAARILQDQLQTFVNFEEPEQK 258

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E+ +   L FN ALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE++MLR  NFGR
Sbjct: 259 HVEE-SRPELEFNAALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 317

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P+WPPE+IEELAK+YED+
Sbjct: 318 KSLNEIKEVLAQMGLHLGMEVPNWPPENIEELAKRYEDQ 356


>gi|170748609|ref|YP_001754869.1| DNA-directed RNA polymerase subunit alpha [Methylobacterium
           radiotolerans JCM 2831]
 gi|226699355|sp|B1LWP9|RPOA_METRJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|170655131|gb|ACB24186.1| DNA-directed RNA polymerase, alpha subunit [Methylobacterium
           radiotolerans JCM 2831]
          Length = 339

 Score =  440 bits (1131), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 211/338 (62%), Positives = 273/338 (80%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN ++ +  G + +    ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 2   VIQKNWQELIKPNKLQ-VTTGDDPKRVATVVAEPLERGFGTTLGNALRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQIDGVLHE SSI GV ED+TDI+LNIK I ++   D+ KR+T+ K GPG+VTAGDI 
Sbjct: 61  TSVQIDGVLHEFSSIPGVREDVTDIVLNIKTIAIRSQTDAPKRMTLRKTGPGLVTAGDIG 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DI++LNPD VIC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +D+L+SP+
Sbjct: 121 TVGDIQILNPDLVICTLDDGAEIRMEFTVATGKGYVPAERNRPEDAPIGLIPVDSLFSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY VE+ REGQ LD DKL+MT++T+G+++ ED++A A+RI+QDQL +F+NFE+P+KE
Sbjct: 181 TKVSYRVETTREGQDLDKDKLTMTVETNGAVSPEDALAYAARIIQDQLQVFVNFEDPRKE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
               +    LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++E +MLR  NFGR
Sbjct: 241 EAAPL-APQLPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSEGEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++P WPPE+IE+LAK++E+
Sbjct: 300 KSLNEIKEVLAGMGLHLGMDIPGWPPENIEDLAKRFEE 337


>gi|23010819|ref|ZP_00051380.1| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Magnetospirillum magnetotacticum MS-1]
          Length = 339

 Score =  440 bits (1131), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 212/338 (62%), Positives = 271/338 (80%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN ++ +  G + +    ++AEPL RGF  TLGN+LRRVL+SSL+GAA+
Sbjct: 2   VIQKNWQELIKPNKLQ-VTAGDDPKRVATVVAEPLERGFGTTLGNSLRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQIDGVLHE SSI GV ED+TDI+LNIK I ++   D  KR+T+ K GPG+VTAGDI 
Sbjct: 61  TSVQIDGVLHEFSSIPGVREDVTDIVLNIKTIAIRSQTDQPKRLTLRKTGPGLVTAGDIG 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
            V DI++LNPD VIC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +DALYSP+
Sbjct: 121 AVGDIQILNPDLVICTLDDGAEIRMEFTVATGKGYVPAERNRPEDAPIGLIPVDALYSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY VE+ REGQ LD DKL+MT++T+G+++ ED++A A+RI+QDQL +F+NFEEP+KE
Sbjct: 181 TKVSYRVETTREGQDLDKDKLTMTVETNGAVSPEDALAYAARIIQDQLQVFVNFEEPRKE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
               +    LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++E +MLR  NFGR
Sbjct: 241 EAAPL-APQLPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSEGEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++P WPPE+IE+LAK++E+
Sbjct: 300 KSLNEIKEVLAGMGLHLGMDVPGWPPENIEDLAKRFEE 337


>gi|240138767|ref|YP_002963239.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           (Transcriptase alpha chain) (RNA polymerase alpha
           subunit) [Methylobacterium extorquens AM1]
 gi|254561367|ref|YP_003068462.1| DNA-directed RNA polymerase alpha chain [Methylobacterium
           extorquens DM4]
 gi|240008736|gb|ACS39962.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           (Transcriptase alpha chain) (RNA polymerase alpha
           subunit) [Methylobacterium extorquens AM1]
 gi|254268645|emb|CAX24604.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           (Transcriptase alpha chain) (RNA polymerase alpha
           subunit) [Methylobacterium extorquens DM4]
          Length = 339

 Score =  439 bits (1130), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 212/338 (62%), Positives = 271/338 (80%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN ++ +  G + +    ++AEPL RGF  TLGN+LRRVL+SSL+GAA+
Sbjct: 2   VIQKNWQELIKPNKLQ-VTAGDDPKRVATVVAEPLERGFGTTLGNSLRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQIDGVLHE SSI GV ED+TDI+LNIK I ++   D  KR+T+ K GPG+VTAGDI 
Sbjct: 61  TSVQIDGVLHEFSSIPGVREDVTDIVLNIKTIAIRSQTDQPKRMTLRKTGPGLVTAGDIG 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
            V DI++LNPD VIC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +DALYSP+
Sbjct: 121 AVGDIQILNPDLVICTLDDGAEIRMEFTVATGKGYVPAERNRPEDAPIGLIPVDALYSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY VE+ REGQ LD DKL+MT++T+G+++ ED++A A+RI+QDQL +F+NFEEP+KE
Sbjct: 181 TKVSYRVETTREGQDLDKDKLTMTLETNGAVSPEDALAYAARIIQDQLQVFVNFEEPRKE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
               +    LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++E +MLR  NFGR
Sbjct: 241 EAAPL-APQLPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSEGEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++P WPPE+IE+LAK++E+
Sbjct: 300 KSLNEIKEVLAGMGLHLGMDVPGWPPENIEDLAKRFEE 337


>gi|260577155|ref|ZP_05845132.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacter sp. SW2]
 gi|259020629|gb|EEW23948.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacter sp. SW2]
          Length = 338

 Score =  438 bits (1126), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 218/339 (64%), Positives = 269/339 (79%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +  +  G +      +IAEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQL-VVKPGPDASRTATVIAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG++LKM  +  KR++I  +GPGVVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKGVSLKMEVEGPKRLSISAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             N IEVLN DHVIC+LD  A V MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ESNGIEVLNKDHVICHLDDGADVFMELTVNTGKGYVAADKNKPEDAPIGLIAIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M I+TDGS+T +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 KKVSYEVQPTREGQVLDYDKLTMKIETDGSLTPDDAVAYAARILQDQLSVFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           ++ D++   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 LRHDVD-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPPE+IE+LAK++ED+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPENIEDLAKRFEDQ 337


>gi|154248691|ref|YP_001419649.1| DNA-directed RNA polymerase subunit alpha [Xanthobacter
           autotrophicus Py2]
 gi|254765264|sp|A7IPP6|RPOA_XANP2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|154162776|gb|ABS69992.1| DNA-directed RNA polymerase, alpha subunit [Xanthobacter
           autotrophicus Py2]
          Length = 338

 Score =  438 bits (1126), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 211/338 (62%), Positives = 270/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP  ++ +  G + +    +IAEPL RGF  TLGNALRR+L+SSL+GAA+
Sbjct: 1   MIQKNWQELIKPEKLQ-VNPGHDPKRFATVIAEPLERGFGMTLGNALRRILLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T++ IDGVLHE SSI GV ED+TDIILN+K + ++M GD  KR+   K GPGV+ AGDIQ
Sbjct: 60  TSIHIDGVLHEFSSIPGVREDVTDIILNVKDVAIRMQGDGPKRMVAKKTGPGVLLAGDIQ 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+ +LNP+  IC LD  A +R+E TV  G GYV A  +R E+ PIGLI ID+LYSP+
Sbjct: 120 TVGDVAILNPNLPICTLDEGAELRIEFTVDTGKGYVAADRNRPEDAPIGLIPIDSLYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQ+LDYDKL++ I+T+GSIT ED++A A+RILQDQL +F+NFEEPK+E
Sbjct: 180 RKVSYKVENTREGQILDYDKLTLQIETNGSITAEDALAYAARILQDQLEIFVNFEEPKRE 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E   +++LPF+PALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++E +MLR  NFGR
Sbjct: 240 -SETTAIQTLPFSPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSETEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL ++GL LGM +P WPPE+IEELAK++E+
Sbjct: 299 KSLNEIKEVLASLGLHLGMEVPGWPPENIEELAKRFEE 336


>gi|218530408|ref|YP_002421224.1| DNA-directed RNA polymerase subunit alpha [Methylobacterium
           chloromethanicum CM4]
 gi|254765256|sp|B7L0S5|RPOA_METC4 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|218522711|gb|ACK83296.1| DNA-directed RNA polymerase, alpha subunit [Methylobacterium
           chloromethanicum CM4]
          Length = 339

 Score =  437 bits (1125), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 211/338 (62%), Positives = 271/338 (80%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN ++ +  G + +    ++AEPL RGF  TLGN+LRRVL+SSL+GAA+
Sbjct: 2   VIQKNWQELIKPNKLQ-VTAGDDPKRVATVVAEPLERGFGTTLGNSLRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQIDGVLHE SSI GV ED+TDI+LNIK I ++   D  KR+T+ K GPG+VTAGDI 
Sbjct: 61  TSVQIDGVLHEFSSIPGVREDVTDIVLNIKTIAIRSQTDQPKRMTLRKTGPGLVTAGDIG 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
            V DI++LNPD VIC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +DALYSP+
Sbjct: 121 AVGDIQILNPDLVICTLDDGAEIRMEFTVATGKGYVPAERNRPEDAPIGLIPVDALYSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY VE+ REGQ LD DKL++T++T+G+++ ED++A A+RI+QDQL +F+NFEEP+KE
Sbjct: 181 TKVSYRVETTREGQDLDKDKLTITLETNGAVSPEDALAYAARIIQDQLQVFVNFEEPRKE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
               +    LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++E +MLR  NFGR
Sbjct: 241 EAAPL-APQLPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSEGEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++P WPPE+IE+LAK++E+
Sbjct: 300 KSLNEIKEVLAGMGLHLGMDVPGWPPENIEDLAKRFEE 337


>gi|188581391|ref|YP_001924836.1| DNA-directed RNA polymerase subunit alpha [Methylobacterium populi
           BJ001]
 gi|226699354|sp|B1Z768|RPOA_METPB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|179344889|gb|ACB80301.1| DNA-directed RNA polymerase, alpha subunit [Methylobacterium populi
           BJ001]
          Length = 339

 Score =  437 bits (1125), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 211/338 (62%), Positives = 270/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN ++ +  G + +    ++AEPL RGF  TLGN+LRRVL+SSL+GAA+
Sbjct: 2   VIQKNWQELIKPNKLQ-VSAGDDPKRVATVVAEPLERGFGTTLGNSLRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQIDGVLHE SSI GV ED+TDI+LNIK I ++   D  KR+T+ K GPG+VTAGDI 
Sbjct: 61  TSVQIDGVLHEFSSIPGVREDVTDIVLNIKTIAIRSQTDQPKRMTLRKTGPGLVTAGDIG 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
            V DI++LNPD VIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +DAL+SP+
Sbjct: 121 AVGDIQILNPDLVICTLDDGAEIRMEFTVATGKGYVPADRNRPEDAPIGLIPVDALFSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY VE+ REGQ LD DKL+MT++T+G+++ ED++A A+RI+QDQL +F+NFEEP+KE
Sbjct: 181 TKVSYRVETTREGQDLDKDKLTMTVETNGAVSPEDALAYAARIIQDQLQVFVNFEEPRKE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
               +    LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++E +MLR  NFGR
Sbjct: 241 EAAPL-APQLPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSEGEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++P WPPE+IE+LAK++E+
Sbjct: 300 KSLNEIKEVLAGMGLHLGMDVPGWPPENIEDLAKRFEE 337


>gi|300022565|ref|YP_003755176.1| DNA-directed RNA polymerase, subunit alpha [Hyphomicrobium
           denitrificans ATCC 51888]
 gi|299524386|gb|ADJ22855.1| DNA-directed RNA polymerase, alpha subunit [Hyphomicrobium
           denitrificans ATCC 51888]
          Length = 340

 Score =  437 bits (1123), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 214/339 (63%), Positives = 270/339 (79%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++QKNWQ+LIKP+ +E I  G++      ++AEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 3   VLQKNWQDLIKPSKLE-IQTGRDRSRIATVVAEPLERGFGMTLGNALRRVLLSSLQGAAI 61

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
             VQIDGVLHE SS+ GV ED+T+IILNIK I L++  +  KR+ + K G G VTAGDI+
Sbjct: 62  KTVQIDGVLHEFSSVPGVREDVTNIILNIKEIALRIHSEGVKRMVLKKEGAGPVTAGDIE 121

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             +++EVLNPDHVIC+LD  A +RME T   G GYV +  +R E+ PIGLI +D+LYSP+
Sbjct: 122 ASSEVEVLNPDHVICHLDQGASIRMEFTADMGKGYVASDRNRPEDAPIGLIPVDSLYSPV 181

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQ+LDYDKL+M ++TDGS+  ED+VALA+RILQDQL +FINFEEPKK 
Sbjct: 182 KKVSYKVENTREGQILDYDKLTMVVETDGSVRPEDAVALAARILQDQLAVFINFEEPKK- 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E+     L FN ALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 241 AQEEQRHPELAFNAALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 300

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL TMGL LGM +P+WPP++I+ELAK++ED+
Sbjct: 301 KSLNEIKEVLATMGLHLGMEVPNWPPDNIDELAKRFEDQ 339


>gi|296445047|ref|ZP_06887008.1| DNA-directed RNA polymerase, alpha subunit [Methylosinus
           trichosporium OB3b]
 gi|296257468|gb|EFH04534.1| DNA-directed RNA polymerase, alpha subunit [Methylosinus
           trichosporium OB3b]
          Length = 339

 Score =  436 bits (1122), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 212/337 (62%), Positives = 270/337 (80%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELIKP+ +E +  G +     + +AEPL RGF  TLGNALRR+L+SSL+G+AIT
Sbjct: 3   IQKNWQELIKPSKLE-VTAGDDPRRVAVAVAEPLERGFGVTLGNALRRILLSSLQGSAIT 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           ++ IDGVLHE SSI GV ED+TDI+LNIK I +K   +  KR+T+ K GPG VTAGDIQT
Sbjct: 62  SIHIDGVLHEFSSIPGVREDVTDIVLNIKDIAIKNHAEGVKRMTLKKTGPGPVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
             D+++LNPD VIC LD  A +R+E TV+ G GYVPA  +R E+ PIGLI ID+LYSP+K
Sbjct: 122 PGDVQILNPDLVICTLDEGAEIRVEFTVATGKGYVPADRNRAEDAPIGLIPIDSLYSPVK 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ R GQVLDYDKL++TI+T+G+I+ EDS+A A+RILQDQL +F+NFEEP++E 
Sbjct: 182 KVSYRVENTRAGQVLDYDKLTLTIETNGAISPEDSLAYAARILQDQLSVFVNFEEPRRE- 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +   ++  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++EA+MLR  NFGRK
Sbjct: 241 ETAPSIPQLAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I++LAK++E+
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDDLAKRFEE 337


>gi|294675883|ref|YP_003576498.1| DNA-directed RNA polymerase subunit alpha [Rhodobacter capsulatus
           SB 1003]
 gi|294474703|gb|ADE84091.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacter capsulatus
           SB 1003]
          Length = 338

 Score =  436 bits (1122), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 221/339 (65%), Positives = 266/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E I  G + + +  +IAEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLE-IKAGNDPQRQATVIAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KGI+LKM  +  KR++I  +GP VVT  DI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGISLKMDVEGPKRLSISAKGPRVVTGADIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A V MELTV+ G GYV A  +R E+ PIGLI IDA+YSP+
Sbjct: 120 ESMGIEVLNKDHVICHLDDGADVFMELTVNTGKGYVAADKNRPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKV+Y V+  REGQVLDYDKL+M I+TDGS+T ED+VA A+RILQDQL +F+NFEEP+  
Sbjct: 180 KKVAYDVQPTREGQVLDYDKLTMKIETDGSLTPEDAVAYAARILQDQLSIFVNFEEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            K D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SKTDAD-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM + DWPPE+IE+LAK++ED+
Sbjct: 299 KSLNEIKEVLSSMGLHLGMEVEDWPPENIEDLAKRFEDQ 337


>gi|304321464|ref|YP_003855107.1| DNA-directed RNA polymerase subunit alpha [Parvularcula bermudensis
           HTCC2503]
 gi|303300366|gb|ADM09965.1| DNA-directed RNA polymerase alpha subunit [Parvularcula bermudensis
           HTCC2503]
          Length = 338

 Score =  436 bits (1120), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 207/339 (61%), Positives = 276/339 (81%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M++KNWQELIKP  +E +V   + + +  ++A+PL RGF  TLGN+LRR+LMSSL+GAA+
Sbjct: 1   MLEKNWQELIKPQKLE-VVSSYDPQRKATIVAQPLERGFGLTLGNSLRRILMSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGV+HE SSI GV ED+T I+LNIK + L+M  D  +R+T+ K+GPG+VTAGDIQ
Sbjct: 60  TAIQIDGVVHEFSSIPGVREDVTIIVLNIKQLALRMHVDGPRRLTLKKQGPGIVTAGDIQ 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DIE+L+ DHVIC LD  A +RME+TV  G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 120 ETADIEILDKDHVICTLDEGADLRMEITVQTGKGYVPADRNRPEDAPIGLIPVDSLYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY+VE+ REGQVLDYDKL + ++T+G++T ED+ A A+RILQDQL +F+NF+EPK++
Sbjct: 180 RRVSYSVENTREGQVLDYDKLILEVETNGAVTPEDAAAFAARILQDQLQIFVNFDEPKRD 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +   + + L FN ALL+KV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 DQGGAD-EELLFNAALLRKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL T+GL LGM++PDWPP++IEELA+K+ED+
Sbjct: 299 KSLNEIKEVLATLGLHLGMDVPDWPPDNIEELARKFEDQ 337


>gi|167645602|ref|YP_001683265.1| DNA-directed RNA polymerase subunit alpha [Caulobacter sp. K31]
 gi|189043833|sp|B0T2E6|RPOA_CAUSK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|167348032|gb|ABZ70767.1| DNA-directed RNA polymerase, alpha subunit [Caulobacter sp. K31]
          Length = 338

 Score =  436 bits (1120), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 209/339 (61%), Positives = 269/339 (79%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI++NW ELI+P   + I  G +   +  ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIERNWNELIRPEKPQ-IETGADATRKARIVAEPLERGFGVTLGNALRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGV+HE SS++GV ED+ DI+LNIK + ++M  +  KR+T+   GPGVVTAG I+
Sbjct: 60  TAIQIDGVVHEFSSLEGVREDVVDIVLNIKQLAVRMHAEGPKRMTLRATGPGVVTAGQIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIE+LNPDHV+C LD  A VRME TV+ G GYVPA  +R E+ PIGLI +DALYSP+
Sbjct: 120 TPSDIEILNPDHVLCTLDDGASVRMEFTVNTGKGYVPADKNRPEDAPIGLIAVDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V+Y VE  R+GQ LDYDKL + ++T+G++T  D+VA A+RILQDQL +FI FEEPK +
Sbjct: 180 KRVAYRVEPTRQGQSLDYDKLILEVETNGAVTPVDAVAYAARILQDQLQIFITFEEPKAK 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++     LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 TADEAK-PELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++P+WPPE+IE+LAKK+ED+
Sbjct: 299 KSLNEIKEVLAGMGLHLGMDVPNWPPENIEDLAKKFEDQ 337


>gi|254488277|ref|ZP_05101482.1| DNA-directed RNA polymerase, alpha subunit [Roseobacter sp. GAI101]
 gi|214045146|gb|EEB85784.1| DNA-directed RNA polymerase, alpha subunit [Roseobacter sp. GAI101]
          Length = 338

 Score =  435 bits (1118), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 215/338 (63%), Positives = 269/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++ +  G +   +  ++AEPL RGF  T+GNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPQQLD-VKPGNDPARQATVVAEPLERGFGLTMGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KG++L+M  +  KR++I  +GPGVVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGVSLRMEVEGPKRLSISAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD  A V MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ESAGIEILNRDHVICHLDDGADVYMELTVNTGKGYVAADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGSIT +D+VA A+RILQDQLG+F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSITPDDAVAFAARILQDQLGIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SRQDDD-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|83854948|ref|ZP_00948478.1| DNA-directed RNA polymerase alpha subunit [Sulfitobacter sp.
           NAS-14.1]
 gi|83941471|ref|ZP_00953933.1| DNA-directed RNA polymerase alpha subunit [Sulfitobacter sp. EE-36]
 gi|83842791|gb|EAP81958.1| DNA-directed RNA polymerase alpha subunit [Sulfitobacter sp.
           NAS-14.1]
 gi|83847291|gb|EAP85166.1| DNA-directed RNA polymerase alpha subunit [Sulfitobacter sp. EE-36]
          Length = 338

 Score =  434 bits (1117), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 214/338 (63%), Positives = 270/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++ +  G +   +  +IAEPL RGF  T+GNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPQQLD-VKPGNDPARQATVIAEPLERGFGLTMGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG++L+M  +  KR++I  +GPGVVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKGVSLRMEVEGPKRLSISAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD +A V MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ESAGIEILNRDHVICHLDDNADVYMELTVNTGKGYVAADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGSI+ +D+VA A+RILQDQLG+F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSISPDDAVAFAARILQDQLGIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SRQDDD-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|302382643|ref|YP_003818466.1| DNA-directed RNA polymerase subunit alpha [Brevundimonas
           subvibrioides ATCC 15264]
 gi|302193271|gb|ADL00843.1| DNA-directed RNA polymerase, alpha subunit [Brevundimonas
           subvibrioides ATCC 15264]
          Length = 339

 Score =  434 bits (1117), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 208/339 (61%), Positives = 271/339 (79%), Gaps = 1/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI++NWQELI+P   + I LG + + +  ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIERNWQELIRPEKPQ-IELGSDAQRKARLVAEPLERGFGVTLGNALRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGV+HE SS++GV ED+ DI+LNIK + L+M  +  KR+T+   GPG VTAG I+
Sbjct: 60  TAIQIDGVVHEFSSLEGVREDVVDIVLNIKQLALRMHAEGPKRMTLRATGPGPVTAGQIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             +DIEVLNP+HVIC LD  A +RMELTV  G GYV ++ +R E+ PIGLI +DALYSP+
Sbjct: 120 VPSDIEVLNPNHVICTLDDGASIRMELTVQNGKGYVASEFNRPEDAPIGLIAVDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V+Y VE  R+GQ LDYDKL + ++T+G+++  D+VA ASRILQDQL +FI F+EPKK 
Sbjct: 180 KRVAYRVEPTRQGQSLDYDKLVLEVETNGAVSPVDAVAYASRILQDQLQIFITFDEPKKA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V++      LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE +MLR  NFGR
Sbjct: 240 VEQVDGKPDLPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEGEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM++P+WPPE+IE+LAKK++D+
Sbjct: 300 KSLNEIKEVLTSMGLSLGMDVPNWPPENIEDLAKKFDDQ 338


>gi|182679004|ref|YP_001833150.1| DNA-directed RNA polymerase subunit alpha [Beijerinckia indica
           subsp. indica ATCC 9039]
 gi|226699352|sp|B2IF96|RPOA_BEII9 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|182634887|gb|ACB95661.1| DNA-directed RNA polymerase, alpha subunit [Beijerinckia indica
           subsp. indica ATCC 9039]
          Length = 338

 Score =  434 bits (1117), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 212/338 (62%), Positives = 270/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP+ ++ +  G + +    +IAEPL RGF  TLGNALRR+L+SSL+GAAI
Sbjct: 1   MIQKNWQELIKPSKLD-VTPGDDSKRFATIIAEPLERGFGLTLGNALRRILLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V IDGVLHE SSI GV ED+TDIILNIK I +KM G+  KR+ + K+GPG V AGDI 
Sbjct: 60  TSVHIDGVLHEFSSIPGVREDVTDIILNIKDIAIKMQGEGPKRMVLKKQGPGKVLAGDIG 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
            V D+++LNP+ VIC LD  A +RME TV+ G GYV A  +R E+ PIGLI +D+LYSP+
Sbjct: 120 AVGDVQILNPNLVICTLDEGAEIRMEFTVNTGKGYVAADRNRAEDAPIGLIPVDSLYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQ+LDYDKL++ I+T+GS+T ED+VA ++RILQDQL +F+NFEEP++E
Sbjct: 180 KKVSYKVENTREGQILDYDKLTLQIETNGSLTPEDAVAFSARILQDQLNVFVNFEEPRRE 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +   ++  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 -EATPSIPELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM +  WPP++I+ELAK++E+
Sbjct: 299 KSLNEIKEVLAQMGLHLGMEVTGWPPDNIDELAKRFEE 336


>gi|163745568|ref|ZP_02152928.1| DNA-directed RNA polymerase subunit alpha [Oceanibulbus indolifex
           HEL-45]
 gi|161382386|gb|EDQ06795.1| DNA-directed RNA polymerase subunit alpha [Oceanibulbus indolifex
           HEL-45]
          Length = 338

 Score =  434 bits (1115), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 216/338 (63%), Positives = 269/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++ +  G +   +  ++AEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPQQLD-VKPGNDPARQATVMAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KG++L+M  +  KR++I  +GPGVVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGVSLRMEVEGPKRLSISAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN +HVIC+LD  A V MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ESAGIEILNREHVICHLDDGADVYMELTVNTGKGYVSADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGSIT +D+VA A+RILQDQLG+F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSITPDDAVAFAARILQDQLGIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SRQDDD-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPPE+IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPENIEDLAKKFED 336


>gi|146278544|ref|YP_001168703.1| DNA-directed RNA polymerase subunit alpha [Rhodobacter sphaeroides
           ATCC 17025]
 gi|166229275|sp|A4WVI4|RPOA_RHOS5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|145556785|gb|ABP71398.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacter sphaeroides
           ATCC 17025]
          Length = 338

 Score =  433 bits (1113), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 216/339 (63%), Positives = 265/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +  +  G +      +IAEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQL-VVKPGADPARVATVIAEPLERGFGLTLGNALRRVLLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG+++KM  +  KR++I  +GPGVVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKGVSIKMDVEGPKRLSISAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             N IE+LN DHVIC+LD  A V MELTV+ G GYV A  +R E+ PIGLI IDA+YSP+
Sbjct: 120 ESNGIEILNKDHVICHLDEGADVFMELTVNTGKGYVAADKNRPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V   REGQVLDYDKL+M ++TDG +T ED+VA A+RILQDQL +F+NFEEP+  
Sbjct: 180 KKVSYEVTPTREGQVLDYDKLTMRVETDGGLTPEDAVAYAARILQDQLSIFVNFEEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            + D+    L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 TRHDVE-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPPE+IE+LAK++ED+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPENIEDLAKRFEDQ 337


>gi|163733783|ref|ZP_02141225.1| DNA-directed RNA polymerase subunit alpha [Roseobacter litoralis
           Och 149]
 gi|161392894|gb|EDQ17221.1| DNA-directed RNA polymerase subunit alpha [Roseobacter litoralis
           Och 149]
          Length = 338

 Score =  432 bits (1112), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 214/338 (63%), Positives = 269/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++ +  G +   +  + AEPL RGF  T+GNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPQQLD-VKPGNDPARQATVTAEPLERGFGLTMGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KG++++M  +  KR++I  +GPGVVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGVSIRMEVEGPKRLSISAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD  A V MELTV++G GYV A+ ++ E+ PIGLI IDA+YSP+
Sbjct: 120 DSAGIEILNRDHVICHLDDGADVYMELTVNQGKGYVSAEKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGS+T +D+VA A+RILQDQLG+F+NFEEP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSLTPDDAVAFAARILQDQLGIFVNFEEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            + D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SRADED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|295688930|ref|YP_003592623.1| DNA-directed RNA polymerase subunit alpha [Caulobacter segnis ATCC
           21756]
 gi|295430833|gb|ADG10005.1| DNA-directed RNA polymerase, alpha subunit [Caulobacter segnis ATCC
           21756]
          Length = 338

 Score =  432 bits (1112), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 209/339 (61%), Positives = 267/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI++NW ELI+P   + I  G +   +  ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIERNWNELIRPEKPQ-IETGADASRKARIVAEPLERGFGVTLGNALRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGV+HE SS++GV ED+ DI+LNIK + ++M  +  KR+T+   GPG VTAG I+
Sbjct: 60  TAIQIDGVVHEFSSLEGVREDVVDIVLNIKQLAVRMHAEGPKRMTLRATGPGPVTAGQIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T  DIE+LNPDHV+C LD  A VRME TV+ G GYVPA  +R E+ PIGLI +DALYSP+
Sbjct: 120 TPADIEILNPDHVLCTLDDGASVRMEFTVNTGKGYVPADRNRPEDAPIGLIAVDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V+Y VE  R+GQ LDYDKL + ++T+G++T  D+VA A+RILQDQL +FI FEEPK +
Sbjct: 180 KRVAYRVEPTRQGQSLDYDKLILEVETNGAVTPVDAVAYAARILQDQLQIFITFEEPKAK 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
              D +   LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 -SADESKPELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++P+WPPE+IE+LAKK+ED+
Sbjct: 299 KSLNEIKEVLAGMGLHLGMDVPNWPPENIEDLAKKFEDQ 337


>gi|77462283|ref|YP_351787.1| DNA-directed RNA polymerase subunit alpha [Rhodobacter sphaeroides
           2.4.1]
 gi|126461159|ref|YP_001042273.1| DNA-directed RNA polymerase subunit alpha [Rhodobacter sphaeroides
           ATCC 17029]
 gi|221638137|ref|YP_002524399.1| DNA-directed RNA polymerase subunit alpha [Rhodobacter sphaeroides
           KD131]
 gi|90110864|sp|Q3J5P8|RPOA_RHOS4 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158513430|sp|A3PGN5|RPOA_RHOS1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|254765260|sp|B9KLB5|RPOA_RHOSK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|77386701|gb|ABA77886.1| RNA polymerase, alpha chain [Rhodobacter sphaeroides 2.4.1]
 gi|126102823|gb|ABN75501.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacter sphaeroides
           ATCC 17029]
 gi|221158918|gb|ACL99897.1| DNA-directed RNA polymerase subunit alpha [Rhodobacter sphaeroides
           KD131]
          Length = 338

 Score =  432 bits (1111), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 216/339 (63%), Positives = 265/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +  +  G +      +IAEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQL-VVKPGADPARVATVIAEPLERGFGLTLGNALRRVLLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG+++KM  +  KR++I  +GPGVVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKGVSIKMEVEGPKRLSISAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             N IE+LN DHVIC+LD  A V MELTV+ G GYV A  +R E+ PIGLI IDA+YSP+
Sbjct: 120 ESNGIEILNKDHVICHLDEGADVFMELTVNTGKGYVAADKNRPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V   REGQVLDYDKL+M I+TDG +T +D+VA A+RILQDQL +F+NFEEP+  
Sbjct: 180 KKVSYEVTPTREGQVLDYDKLTMRIETDGGLTPDDAVAYAARILQDQLSIFVNFEEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            + D+    L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 TRHDVE-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPPE+IE+LAK++ED+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPENIEDLAKRFEDQ 337


>gi|16125521|ref|NP_420085.1| DNA-directed RNA polymerase subunit alpha [Caulobacter crescentus
           CB15]
 gi|221234267|ref|YP_002516703.1| DNA-directed RNA polymerase subunit alpha [Caulobacter crescentus
           NA1000]
 gi|20139678|sp|Q9A8S9|RPOA_CAUCR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|254765246|sp|B8H4F8|RPOA_CAUCN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|13422605|gb|AAK23253.1| DNA-directed RNA polymerase, alpha subunit [Caulobacter crescentus
           CB15]
 gi|220963439|gb|ACL94795.1| DNA-directed RNA polymerase alpha chain [Caulobacter crescentus
           NA1000]
          Length = 338

 Score =  432 bits (1111), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 209/339 (61%), Positives = 267/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI++NW ELI+P   + I  G +   +  ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIERNWNELIRPEKPQ-IETGADATRKARIVAEPLERGFGVTLGNALRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGV+HE SS++GV ED+ DI+LNIK + ++M  +  KR+T+   GPG VTAG I+
Sbjct: 60  TAIQIDGVVHEFSSLEGVREDVVDIVLNIKQLAVRMHAEGPKRMTLRATGPGPVTAGQIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T  DIE+LNPDHV+C LD  A VRME TV+ G GYVPA  +R E+ PIGLI +DALYSP+
Sbjct: 120 TPADIEILNPDHVLCTLDDGASVRMEFTVNNGKGYVPADRNRPEDAPIGLIAVDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V+Y VE  R+GQ LDYDKL + ++T+G++T  D+VA A+RILQDQL +FI FEEPK +
Sbjct: 180 KRVAYRVEPTRQGQSLDYDKLILEVETNGAVTPVDAVAYAARILQDQLQIFITFEEPKAK 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
              D +   LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 -SADESKPELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++P+WPPE+IE+LAKK+ED+
Sbjct: 299 KSLNEIKEVLAGMGLHLGMDVPNWPPENIEDLAKKFEDQ 337


>gi|119366721|sp|Q16AB8|RPOA_ROSDO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 338

 Score =  431 bits (1109), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 213/338 (63%), Positives = 269/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++ +  G +   +  + AEPL RGF  T+GNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPQQLD-VKPGNDPARQATVTAEPLERGFGLTMGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KG++++M  +  KR++I  +GPGVVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGVSIRMEVEGPKRLSISAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD  A V MELTV++G GYV A+ ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ESAGIEILNRDHVICHLDDGADVYMELTVNQGKGYVSAEKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGS+T +D+VA A+RILQDQLG+F+NFEEP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSLTPDDAVAFAARILQDQLGIFVNFEEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            + D +   L FNP LLKKV++LELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SRADED-DGLEFNPLLLKKVDDLELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|110678754|ref|YP_681761.1| DNA-directed RNA polymerase subunit alpha [Roseobacter
           denitrificans OCh 114]
 gi|109454870|gb|ABG31075.1| DNA-directed RNA polymerase, alpha subunit [Roseobacter
           denitrificans OCh 114]
          Length = 342

 Score =  431 bits (1109), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 213/338 (63%), Positives = 269/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++ +  G +   +  + AEPL RGF  T+GNALRRVLMSSL+GAAI
Sbjct: 5   MIHKNWAELIKPQQLD-VKPGNDPARQATVTAEPLERGFGLTMGNALRRVLMSSLQGAAI 63

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KG++++M  +  KR++I  +GPGVVTAGDI 
Sbjct: 64  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGVSIRMEVEGPKRLSISAKGPGVVTAGDIS 123

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD  A V MELTV++G GYV A+ ++ E+ PIGLI IDA+YSP+
Sbjct: 124 ESAGIEILNRDHVICHLDDGADVYMELTVNQGKGYVSAEKNKPEDAPIGLIPIDAIYSPV 183

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGS+T +D+VA A+RILQDQLG+F+NFEEP+  
Sbjct: 184 KKVSYDVQPTREGQVLDYDKLTMKVETDGSLTPDDAVAFAARILQDQLGIFVNFEEPESA 243

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            + D +   L FNP LLKKV++LELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 244 SRADED-DGLEFNPLLLKKVDDLELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 302

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 303 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 340


>gi|89053108|ref|YP_508559.1| DNA-directed RNA polymerase subunit alpha [Jannaschia sp. CCS1]
 gi|119366690|sp|Q28US8|RPOA_JANSC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|88862657|gb|ABD53534.1| DNA-directed RNA polymerase subunit alpha [Jannaschia sp. CCS1]
          Length = 338

 Score =  429 bits (1103), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 211/338 (62%), Positives = 267/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNWQELIKP  +  +  G +   +  ++AEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWQELIKPTQL-VVQPGTDPARKATVVAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQIDGVLHE SS+ GV ED+TDI+LN+KG+ ++M  +  KRV+I  +GP VVTAGDI 
Sbjct: 60  TSVQIDGVLHEFSSVAGVREDVTDIVLNLKGVAIRMDAEGPKRVSISAKGPRVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               I+VLN DHVIC+LD  A + +ELTV+ G GYV A  +R E+ PIGL+ IDA+YSP+
Sbjct: 120 ESAGIDVLNKDHVICHLDDGADLYIELTVNTGKGYVAADKNRPEDAPIGLMPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL++ ++TDGS++ +D+VA A+RI+QDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTLKLETDGSLSPDDAVAYAARIIQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 TRQD-DEDDLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IEELAKKYED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDIVDWPPDNIEELAKKYED 336


>gi|254463868|ref|ZP_05077279.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacterales
           bacterium Y4I]
 gi|206684776|gb|EDZ45258.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacterales
           bacterium Y4I]
          Length = 338

 Score =  429 bits (1103), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 215/338 (63%), Positives = 267/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E +  G +   +  ++AEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPAQLE-VKPGNDPARQATVVAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+K ++L+M  +  KR++I  +GP VVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKQVSLRMEVEGPKRLSINAKGPAVVTAGDIA 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ETAGIEVLNRDHVICHLDDGADLFMELTVNTGKGYVSADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGSIT +D+VA A+RILQDQLG+F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSITPDDAVAFAARILQDQLGIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 GRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|85706695|ref|ZP_01037787.1| DNA-directed RNA polymerase alpha subunit [Roseovarius sp. 217]
 gi|85668753|gb|EAQ23622.1| DNA-directed RNA polymerase alpha subunit [Roseovarius sp. 217]
          Length = 338

 Score =  429 bits (1102), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 213/338 (63%), Positives = 268/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++ +  G +   + ++IAEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLD-VKPGNDPLRQAVLIAEPLERGFGLTLGNALRRVLLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID VLHE SS+ GV ED+TDI+LN+KG+ ++M  +  KR+++  +GPGVVTAGDI 
Sbjct: 60  TAVQIDNVLHEFSSVAGVREDVTDIVLNLKGVAIRMEVEGPKRLSVNAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD  A + MELTV++G GYV A  ++ E+ PIGLI IDA+YSPI
Sbjct: 120 DSAGIEILNKDHVICHLDEGADLFMELTVNQGKGYVSADKNKPEDAPIGLIPIDAIYSPI 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY V+  REGQVLDYDKL+M I+TDGSIT +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 SKVSYEVQPTREGQVLDYDKLTMKIETDGSITPDDAVAYAARILQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SRQDDD-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|149202868|ref|ZP_01879839.1| DNA-directed RNA polymerase subunit alpha [Roseovarius sp. TM1035]
 gi|149143414|gb|EDM31450.1| DNA-directed RNA polymerase subunit alpha [Roseovarius sp. TM1035]
          Length = 338

 Score =  429 bits (1102), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 213/338 (63%), Positives = 268/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E +  G +   + ++IAEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLE-VKPGNDPLRQAVLIAEPLERGFGLTLGNALRRVLLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID VLHE SS+ GV ED+TDI+LN+KG+ ++M  +  KR+++  +GPGVVTAGDI 
Sbjct: 60  TAVQIDNVLHEFSSVAGVREDVTDIVLNLKGVAIRMEVEGPKRLSVNAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD  A + MELTV++G GYV A  ++ E+ PIGLI IDA+YSPI
Sbjct: 120 DSAGIEILNKDHVICHLDEGADLFMELTVNQGKGYVSADKNKPEDAPIGLIPIDAIYSPI 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            +VSY V+  REGQVLDYDKL+M I+TDGSIT +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 SRVSYEVQPTREGQVLDYDKLTMKIETDGSITPDDAVAYAARILQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SRQDDD-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|315497997|ref|YP_004086801.1| DNA-directed RNA polymerase, alpha subunit [Asticcacaulis
           excentricus CB 48]
 gi|315416009|gb|ADU12650.1| DNA-directed RNA polymerase, alpha subunit [Asticcacaulis
           excentricus CB 48]
          Length = 338

 Score =  428 bits (1101), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 210/339 (61%), Positives = 264/339 (77%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI++NWQ+LI+P   + I  GQ+ + +  ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIERNWQQLIRPEKPQ-IESGQDSQRKMRLVAEPLERGFGVTLGNALRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGV+HE SSI+GV ED+ DIILNIK + L+M  +  KR+ +     G VTAG I 
Sbjct: 60  TAVQIDGVVHEFSSIEGVREDVVDIILNIKQLALRMHAEGPKRMVLRASSAGPVTAGMID 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             +DIEVLNPDHVIC LD  A VRME TV  G GYVPA   R E+ PIGLI +DALYSP+
Sbjct: 120 VPSDIEVLNPDHVICTLDEGASVRMEFTVQTGKGYVPADRLRPEDAPIGLIAVDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKV+Y VE  R+GQ LDYDKL + ++T+ ++T  D+VA A+RILQDQL +FI FEEPK  
Sbjct: 180 KKVAYRVEPTRQGQSLDYDKLVLDVETNAAVTPVDAVAYAARILQDQLQIFITFEEPKPA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           + E+     LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE++MLR  NFGR
Sbjct: 240 IVEE-GKPELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM++P+WPPE++E+LAKK+ED+
Sbjct: 299 KSLNEIKEVLQSMGLSLGMDVPNWPPENVEDLAKKFEDQ 337


>gi|254477240|ref|ZP_05090626.1| DNA-directed RNA polymerase, alpha subunit [Ruegeria sp. R11]
 gi|214031483|gb|EEB72318.1| DNA-directed RNA polymerase, alpha subunit [Ruegeria sp. R11]
          Length = 338

 Score =  428 bits (1101), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 214/338 (63%), Positives = 267/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++ +  G +   +  ++AEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLD-VKPGNDPARQATVVAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KG++L+M  +  KR++I  +GP VVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGVSLRMEVEGPKRLSINAKGPAVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN +HVIC+LD  A + MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ESAGIEVLNREHVICHLDDGADLFMELTVNTGKGYVSADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGSIT ED+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSITPEDAVAFAARILQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 GRQDDD-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|84499816|ref|ZP_00998104.1| DNA-directed RNA polymerase alpha subunit [Oceanicola batsensis
           HTCC2597]
 gi|84392960|gb|EAQ05171.1| DNA-directed RNA polymerase alpha subunit [Oceanicola batsensis
           HTCC2597]
          Length = 338

 Score =  428 bits (1101), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 212/339 (62%), Positives = 269/339 (79%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++ +  G +   +  ++AEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLD-VKPGFDPSRQATVVAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SSI GV ED+TD++LN+KG++L+M  +  KR++I  +GPGVVTA +I 
Sbjct: 60  TSVQIDNVLHEFSSIAGVREDVTDVVLNLKGVSLRMDVEGPKRLSINAKGPGVVTAAEIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN +HVIC+LD  A + MELTV+ G GYVPA  ++ E+ PIGLI IDA+YSPI
Sbjct: 120 ESAGIEVLNKNHVICHLDEGASLFMELTVNTGKGYVPADRNKPEDAPIGLIPIDAIYSPI 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGS+T +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSVTPDDAVAYAARILQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 GRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFEDQ 337


>gi|197104720|ref|YP_002130097.1| DNA-directed RNA polymerase alpha subunit [Phenylobacterium
           zucineum HLK1]
 gi|238690127|sp|B4R8P1|RPOA_PHEZH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|196478140|gb|ACG77668.1| DNA-directed RNA polymerase alpha subunit [Phenylobacterium
           zucineum HLK1]
          Length = 338

 Score =  428 bits (1100), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 207/339 (61%), Positives = 266/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI++NW ELI+P   + I  G +   +  ++AEPL RGF  TLGN+LRRVL+SSL+GAA+
Sbjct: 1   MIERNWNELIRPEKPQ-IETGADASRKARLVAEPLERGFGVTLGNSLRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGV+HE SS++GV ED+ DI+LNIK + L+M  +  KR+T+   GPG VTA  I+
Sbjct: 60  TAVQIDGVVHEFSSLEGVREDVVDIVLNIKQLALRMHAEGPKRMTLRATGPGAVTASQIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DIE+LN DHV+C LD  A VRME TV  G GYVPA+ +R E+ PIGLI +D+L+SP+
Sbjct: 120 APADIEILNGDHVLCTLDDGASVRMEFTVQTGKGYVPAEMNRPEDAPIGLIAVDSLFSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V+Y VE  R+GQ LDYDKL M ++T+G+++  D+VA A+RILQDQL +FI FEEPKK+
Sbjct: 180 KRVAYRVEPTRQGQSLDYDKLIMEVETNGAVSPVDAVAYAARILQDQLQIFITFEEPKKK 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V+ +     LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 VEGEAK-PELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++P+WPPE+IEELAKK+ED+
Sbjct: 299 KSLNEIKEVLAGMGLHLGMDVPNWPPENIEELAKKFEDQ 337


>gi|114570321|ref|YP_757001.1| DNA-directed RNA polymerase subunit alpha [Maricaulis maris MCS10]
 gi|119366695|sp|Q0ANS4|RPOA_MARMM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|114340783|gb|ABI66063.1| DNA-directed RNA polymerase subunit alpha [Maricaulis maris MCS10]
          Length = 339

 Score =  428 bits (1100), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 208/338 (61%), Positives = 264/338 (78%), Gaps = 1/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI+KNWQELI+P   E I  G +   +  ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIEKNWQELIRPMKPE-IEPGHDPARQAKIVAEPLERGFGMTLGNALRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T V IDGV+HE SSI GV ED+TDI+LNIK I L+M G+  KRV + K GPG+VTAGDI+
Sbjct: 60  TNVHIDGVVHEFSSIDGVREDVTDIVLNIKQIALRMHGEGPKRVVLKKSGPGIVTAGDIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              D+E++N D  +C LD  A +RME T++ G GYVP++ +R E+ PIGLI +DALYSP+
Sbjct: 120 ETADVEIVNKDLALCTLDEGAEIRMEFTINTGKGYVPSERNRPEDAPIGLIGVDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VSY VE+ REGQVLDYDKL++ ++TDG++T EDSVA A+RILQDQ  +FINFEE  + 
Sbjct: 180 KRVSYKVENTREGQVLDYDKLTLEVETDGTVTPEDSVAFAARILQDQFQIFINFEEAVEA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
              + +   L FNPALL+KV+ELELSVRS NCL+ +NIVY+GDLIQ++EA+MLR  NFGR
Sbjct: 240 RPAEDDKPELDFNPALLRKVDELELSVRSANCLKNDNIVYIGDLIQKSEAEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM  P+WPPE+IE+LAK++ED
Sbjct: 300 KSLNEIKEVLAQMGLHLGMEAPNWPPENIEDLAKRFED 337


>gi|99080120|ref|YP_612274.1| DNA-directed RNA polymerase subunit alpha [Ruegeria sp. TM1040]
 gi|119366729|sp|Q1GK04|RPOA_SILST RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|99036400|gb|ABF63012.1| DNA-directed RNA polymerase alpha subunit [Ruegeria sp. TM1040]
          Length = 338

 Score =  428 bits (1100), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 213/338 (63%), Positives = 267/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E +  G +   +  ++AEPL RGF  TLGNALRR+LMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLE-VKPGNDPARQATLVAEPLERGFGLTLGNALRRILMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+K ++L+M  +  KR++I  +GP VVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKQVSLRMEVEGPKRLSINAKGPAVVTAGDIA 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN +HVIC+LD  A + MELTV+ G GYV A+ ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ETAGIEVLNREHVICHLDDGADLFMELTVNTGKGYVSAEKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL++ +DTDGSIT ED++A A+RILQDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTLKVDTDGSITPEDALAFAARILQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 GRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IEELAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEELAKKFED 336


>gi|312115711|ref|YP_004013307.1| DNA-directed RNA polymerase, subunit alpha [Rhodomicrobium
           vannielii ATCC 17100]
 gi|311220840|gb|ADP72208.1| DNA-directed RNA polymerase, alpha subunit [Rhodomicrobium
           vannielii ATCC 17100]
          Length = 346

 Score =  427 bits (1099), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 205/338 (60%), Positives = 267/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++ KNWQ+LIKP  I  +V G   +    ++AEPL RGF  TLGNALRRVL+SSL+G A+
Sbjct: 9   VLNKNWQDLIKPGKIN-VVPGANPKYVASIVAEPLERGFGLTLGNALRRVLLSSLQGGAV 67

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T + IDGVLHE SSI GV ED+TDI+LN+K + L++  +  KR+ + K GPGV  A DI+
Sbjct: 68  TTIHIDGVLHEFSSIPGVREDVTDIVLNVKEVALRIHSEGVKRMVLRKEGPGVARARDIE 127

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              D+E+LNPDHV+C LD  A VRMELT + G GYVPA+ +R ++ PIGLI +D+LYSP+
Sbjct: 128 AGPDVEILNPDHVLCTLDEGATVRMELTAAIGKGYVPAERNRPDDAPIGLIPVDSLYSPV 187

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY + + REGQ+LDYDKL++ ++T+G+++ ED+VALA+RI+QDQL +F+NFEEP+KE
Sbjct: 188 KKVSYRIANTREGQILDYDKLTLDVETNGAVSPEDAVALAARIIQDQLSIFVNFEEPRKE 247

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V E+  +  L FN ALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 248 VAEE-RIPQLEFNAALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 306

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM +P+WPPE+IEELAK++ED
Sbjct: 307 KSLNEIKEVLAGMGLHLGMEVPNWPPENIEELAKRFED 344


>gi|114771243|ref|ZP_01448663.1| DNA-directed RNA polymerase alpha subunit [alpha proteobacterium
           HTCC2255]
 gi|114548168|gb|EAU51055.1| DNA-directed RNA polymerase alpha subunit [alpha proteobacterium
           HTCC2255]
          Length = 338

 Score =  427 bits (1099), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 214/339 (63%), Positives = 261/339 (76%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNWQELIKP  +E I  G +      +IAEPL RGF  TLGNALRRVL+SSL+G+AI
Sbjct: 1   MIHKNWQELIKPTQLE-IKPGADPLRMATVIAEPLERGFGLTLGNALRRVLLSSLQGSAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TD++LN+KG+ + M  +  KRV+I  +GP +VTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDMVLNLKGVAIAMEVEGPKRVSISAKGPTIVTAGDIA 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DH+IC+LD  A + MELTV  G GYV A  +R E+ PIGLI IDALYSP+
Sbjct: 120 ETAGIEVLNKDHIICHLDDGASLFMELTVDTGKGYVAADQNRPEDAPIGLIPIDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY V+  REGQVLDYD+L+M I+TDGS++ ED+VA A+RILQDQL  F+NF EP+  
Sbjct: 180 LKVSYDVQPTREGQVLDYDQLTMKIETDGSVSAEDAVAFAARILQDQLATFVNFNEPEAA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D     L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 QRQD-EEDDLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPPE+IEELAKK+ED+
Sbjct: 299 KSLNEIKEVLTVMGLHLGMDIVDWPPENIEELAKKFEDQ 337


>gi|329889151|ref|ZP_08267494.1| DNA-directed RNA polymerase, alpha subunit [Brevundimonas diminuta
           ATCC 11568]
 gi|328844452|gb|EGF94016.1| DNA-directed RNA polymerase, alpha subunit [Brevundimonas diminuta
           ATCC 11568]
          Length = 339

 Score =  427 bits (1099), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 206/339 (60%), Positives = 267/339 (78%), Gaps = 1/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI++NWQELI+P   + +  G + +++  +IAEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIERNWQELIRPEKPQ-VEGGSDPQHKARLIAEPLERGFGVTLGNALRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGV+HE SS++GV ED+ DI+LNIK + L+M  +  KR+T+   GPG VTA  I 
Sbjct: 60  TAIQIDGVVHEFSSLEGVREDVVDIVLNIKQLALRMHAEGPKRMTLRATGPGPVTAAQID 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DIEVLNPDHVIC LD  A VRMELTV  G GYV A+ +R E+ PIGLI +DALYSP+
Sbjct: 120 LPADIEVLNPDHVICTLDDGASVRMELTVQNGKGYVAAELNRPEDAPIGLIAVDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V+Y VE  R+GQ LDYDKL + ++T+G+++  D+VA A+RILQDQL +FI F+EP K 
Sbjct: 180 KRVAYRVEPTRQGQSLDYDKLILEVETNGAVSPVDAVAYAARILQDQLQIFITFDEPTKA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V++      LPFNP+LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE +MLR  NFGR
Sbjct: 240 VEQSDGKPELPFNPSLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEGEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM++P+WPPE+IE+LAKK++D+
Sbjct: 300 KSLNEIKEVLASMGLSLGMDVPNWPPENIEDLAKKFDDQ 338


>gi|126737032|ref|ZP_01752767.1| DNA-directed RNA polymerase subunit alpha [Roseobacter sp.
           SK209-2-6]
 gi|126721617|gb|EBA18320.1| DNA-directed RNA polymerase subunit alpha [Roseobacter sp.
           SK209-2-6]
          Length = 338

 Score =  427 bits (1099), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 215/338 (63%), Positives = 266/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E    G +   +  +IAEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLEAKP-GNDPARQATIIAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KG++L+M  +  KR++I  +GP VVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGVSLRMEVEGPKRLSINAKGPAVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ESAGIEVLNRDHVICHLDDGADLFMELTVNTGKGYVSADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL++ I+TDGS+T +D++A A+RILQDQL +F+NFEEP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTLKIETDGSVTPDDALAYAARILQDQLSIFVNFEEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 NRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|254460512|ref|ZP_05073928.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacterales
           bacterium HTCC2083]
 gi|206677101|gb|EDZ41588.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacteraceae
           bacterium HTCC2083]
          Length = 342

 Score =  427 bits (1098), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 212/338 (62%), Positives = 268/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++ +  G +   +  ++AEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 5   MIHKNWAELIKPTQLD-VKPGNDAGRQATVVAEPLERGFGLTLGNALRRVLMSSLQGAAI 63

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG++L+M  +  KR++I  +GPG+VTAGDI 
Sbjct: 64  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKGVSLRMEVEGPKRLSINAKGPGIVTAGDIS 123

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN +HVIC+LD  A V MELTV+ G GYV A+ ++ E+ PIGLI IDA+YSP+
Sbjct: 124 DSAGIEVLNREHVICHLDDGADVYMELTVNTGKGYVAAEKNKPEDAPIGLIPIDAIYSPV 183

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGS+T +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 184 KKVSYDVQPTREGQVLDYDKLTMKVETDGSLTPDDAVAYAARILQDQLSIFVNFDEPESA 243

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             +D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 244 SAKDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 302

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 303 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 340


>gi|259416700|ref|ZP_05740620.1| DNA-directed RNA polymerase, alpha subunit [Silicibacter sp.
           TrichCH4B]
 gi|259348139|gb|EEW59916.1| DNA-directed RNA polymerase, alpha subunit [Silicibacter sp.
           TrichCH4B]
          Length = 338

 Score =  427 bits (1098), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 213/338 (63%), Positives = 266/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E +  G +   +  ++AEPL RGF  TLGNALRR+LMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLE-VKPGNDPARQATLVAEPLERGFGLTLGNALRRILMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+K ++L+M  +  KR++I  +GP VVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKQVSLRMEVEGPKRLSINAKGPAVVTAGDIA 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN +HVIC+LD  A + MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ETAGIEVLNREHVICHLDDGADLFMELTVNTGKGYVSADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL++ +DTDGSIT ED++A A+RILQDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTLKVDTDGSITPEDALAFAARILQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 GRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IEELAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEELAKKFED 336


>gi|254510629|ref|ZP_05122696.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacteraceae
           bacterium KLH11]
 gi|221534340|gb|EEE37328.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacteraceae
           bacterium KLH11]
          Length = 348

 Score =  427 bits (1098), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 214/338 (63%), Positives = 267/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   +  ++AEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 11  MIHKNWAELIKPTQLDGKP-GNDPARQATLVAEPLERGFGLTLGNALRRVLMSSLQGAAI 69

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KG++L+M  +  KR++I  +GP VVTAGDI 
Sbjct: 70  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGVSLRMEVEGPKRLSINAKGPAVVTAGDIS 129

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + MELTV+ G GYV A+ ++ E+ PIGLI IDA+YSP+
Sbjct: 130 ESAGIEVLNRDHVICHLDDGADLFMELTVNTGKGYVSAEKNKPEDAPIGLIPIDAIYSPV 189

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKV+Y V+  REGQVLDYDKL++ IDTDGSIT ED++A A+RILQDQL +F+NF+EP+  
Sbjct: 190 KKVAYDVQPTREGQVLDYDKLTLKIDTDGSITPEDALAFAARILQDQLSIFVNFDEPESA 249

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 250 GRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 308

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 309 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 346


>gi|56695425|ref|YP_165773.1| DNA-directed RNA polymerase subunit alpha [Ruegeria pomeroyi DSS-3]
 gi|62287367|sp|Q5LW32|RPOA_SILPO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|56677162|gb|AAV93828.1| DNA-directed RNA polymerase, alpha subunit [Ruegeria pomeroyi
           DSS-3]
          Length = 338

 Score =  426 bits (1095), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 213/338 (63%), Positives = 266/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E +  G +   +  +IAEPL RGF  TLGNALRR+LMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLE-VKPGNDPARQATVIAEPLERGFGLTLGNALRRILMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           ++VQID VLHE SS+ GV ED+TDIILN+K ++L+M  +  KR+++  +GP VVTAGDI 
Sbjct: 60  SSVQIDNVLHEFSSVAGVREDVTDIILNLKQVSLRMDVEGPKRLSVNAKGPAVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + MELTV+ G GYV A  +R E+ PIGLI IDA+YSP+
Sbjct: 120 ESAGIEVLNRDHVICHLDDGADLFMELTVNTGKGYVSADKNRPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKV+Y V+  REGQVLDYDKL+M I+TDGSIT +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 KKVAYDVQPTREGQVLDYDKLTMKIETDGSITPDDAVAFAARILQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 GRQDDD-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|163796895|ref|ZP_02190852.1| lipoyltransferase [alpha proteobacterium BAL199]
 gi|159177884|gb|EDP62433.1| lipoyltransferase [alpha proteobacterium BAL199]
          Length = 338

 Score =  426 bits (1095), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 206/338 (60%), Positives = 264/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQ LIKP+ ++ I  G + +    ++AEPL RGF  TLGNALRR+L+SSL+GAAI
Sbjct: 1   MIQKNWQALIKPSKLD-IQAGYDPKRTATVVAEPLERGFGLTLGNALRRILLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           +A+QIDGVLHE SS+ GV ED+TDI+LNIK + ++M G+  K++ +   GPG VTAG I+
Sbjct: 60  SAIQIDGVLHEFSSVPGVREDVTDIVLNIKSVAIRMHGEGPKKMRLKAEGPGEVTAGMIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIE++NP HVIC LD DA + MELTV  G GYV A  +R E+ PIGLI +D++YSP+
Sbjct: 120 TVGDIEIMNPKHVICTLDRDATLSMELTVETGKGYVAASANRPEDAPIGLIPVDSIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY VE+ R GQV DYDKLSMT++TDGS+T ED+VA A+RILQDQL +F+NFEEP   
Sbjct: 180 RQVSYKVENTRVGQVTDYDKLSMTLETDGSMTPEDAVAYAARILQDQLQLFVNFEEPTHR 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            + +     LPFN  LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q+TE +MLR  NFGR
Sbjct: 240 AEAE-EAHDLPFNKNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKTEPEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL +MGL LGM + +WPPE+IEELAK+ E+
Sbjct: 299 KSLNEIKEVLASMGLSLGMEITNWPPENIEELAKRLEE 336


>gi|163739473|ref|ZP_02146883.1| DNA-directed RNA polymerase subunit alpha [Phaeobacter
           gallaeciensis BS107]
 gi|163740266|ref|ZP_02147660.1| DNA-directed RNA polymerase subunit alpha [Phaeobacter
           gallaeciensis 2.10]
 gi|161386124|gb|EDQ10499.1| DNA-directed RNA polymerase subunit alpha [Phaeobacter
           gallaeciensis 2.10]
 gi|161387226|gb|EDQ11585.1| DNA-directed RNA polymerase subunit alpha [Phaeobacter
           gallaeciensis BS107]
          Length = 338

 Score =  426 bits (1094), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 213/338 (63%), Positives = 267/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++ +  G +   +  ++AEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLD-VKPGNDPARQATVVAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KG++L+M  +  KR++I  +GP VVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGVSLRMEVEGPKRLSINAKGPAVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN +HVIC+LD  A + MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ESAGIEVLNREHVICHLDDGADLFMELTVNTGKGYVSADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M I+TDGSIT +D+VA A+RI+QDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKIETDGSITPDDAVAYAARIVQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 NRQDDD-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|86135793|ref|ZP_01054372.1| DNA-directed RNA polymerase alpha subunit [Roseobacter sp. MED193]
 gi|85826667|gb|EAQ46863.1| DNA-directed RNA polymerase alpha subunit [Roseobacter sp. MED193]
          Length = 338

 Score =  426 bits (1094), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 214/338 (63%), Positives = 266/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E    G +   +  +IAEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLEAKP-GNDPARQATIIAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KG++L+M  +  KR++I  +GP VVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGVSLRMEVEGPKRLSINAKGPAVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN +HVIC+LD  A + MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ESAGIEVLNREHVICHLDDGADLFMELTVNTGKGYVSADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL++ I+TDGS+T +D++A A+RILQDQL +F+NFEEP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTLKIETDGSVTPDDALAYAARILQDQLSIFVNFEEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 NRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|260427855|ref|ZP_05781834.1| DNA-directed RNA polymerase, alpha subunit [Citreicella sp. SE45]
 gi|260422347|gb|EEX15598.1| DNA-directed RNA polymerase, alpha subunit [Citreicella sp. SE45]
          Length = 338

 Score =  426 bits (1094), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 209/339 (61%), Positives = 268/339 (79%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E +  G +      ++AEPL RGF  T+GNALRR+L+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLE-VRPGADPSRVATVVAEPLERGFGLTMGNALRRILLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG++L+M  +  KR++I  +GPGVVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKGVSLRMEVEGPKRLSINAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + +ELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ETAGIEVLNKDHVICHLDDGADLYVELTVNTGKGYVSADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VSY V+  REGQVLDYDKL+M ++TDGS+T +D++A A+RILQDQL +F+NFEEP+  
Sbjct: 180 KRVSYEVQPTREGQVLDYDKLTMKVETDGSVTPDDAIAFAARILQDQLSIFVNFEEPEAA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 GRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM++ DWPP++IE+LAKK ED+
Sbjct: 299 KSLNEIKEVLSSMGLHLGMDVEDWPPDNIEDLAKKLEDQ 337


>gi|149915869|ref|ZP_01904393.1| DNA-directed RNA polymerase subunit alpha [Roseobacter sp. AzwK-3b]
 gi|149810192|gb|EDM70038.1| DNA-directed RNA polymerase subunit alpha [Roseobacter sp. AzwK-3b]
          Length = 338

 Score =  425 bits (1092), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 212/339 (62%), Positives = 268/339 (79%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++ +  G +   +  +IAEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLD-VKPGNDPMRQATVIAEPLERGFGLTLGNALRRVLLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG++L+M  +  KR++I  +GP +VTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKGVSLRMEVEGPKRLSISAKGPAIVTAGDIT 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 DSAGIEVLNKDHVICHLDDGADLFMELTVNTGKGYVAADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL++ ++TDGSIT +D+VA A+RILQDQL +F+NFEEP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTLKLETDGSITPDDAVAYAARILQDQLSIFVNFEEPEAA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E  + + L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 GRESED-EGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFEDQ 337


>gi|126728199|ref|ZP_01744015.1| DNA-directed RNA polymerase subunit alpha [Sagittula stellata E-37]
 gi|126711164|gb|EBA10214.1| DNA-directed RNA polymerase subunit alpha [Sagittula stellata E-37]
          Length = 338

 Score =  424 bits (1091), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 211/338 (62%), Positives = 262/338 (77%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E I  G +   +   +AEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLE-IKPGADPSKQATCVAEPLERGFGLTLGNALRRVLLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+K + LKM  +  KR+++  +GPGVV AGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKQVALKMEVEGPKRLSVSAKGPGVVKAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC++D  A V ME TV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ESAGIEILNRDHVICHVDEGAEVYMEFTVNTGKGYVSADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKV+Y V+  REGQVLDYDKL+M ++TDGS+T ED++A A+RILQDQL +F+NFEEP+  
Sbjct: 180 KKVAYDVQPTREGQVLDYDKLTMKVETDGSVTPEDAIAYAARILQDQLSIFVNFEEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 TRQDDD-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKLED 336


>gi|310816986|ref|YP_003964950.1| DNA-directed RNA polymerase alpha subunit [Ketogulonicigenium
           vulgare Y25]
 gi|308755721|gb|ADO43650.1| DNA-directed RNA polymerase alpha subunit [Ketogulonicigenium
           vulgare Y25]
          Length = 338

 Score =  424 bits (1091), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 210/339 (61%), Positives = 265/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI +NW ELIKP  ++ +  G +   +  ++AEPL RGF  TLGNALRR+L+SSL+GAAI
Sbjct: 1   MIHRNWSELIKPTQLD-VRPGADAARQATIVAEPLERGFGLTLGNALRRILLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID VLHE SSI GV ED+TDI+LN+KG+ ++M  +  +RV+I  +GP VVTAGDI 
Sbjct: 60  TAVQIDNVLHEFSSITGVREDVTDIVLNLKGVAIRMDVEGPRRVSIQVKGPAVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             N IE+LN DHVIC+LD  A + MELTV+ G GYV A  ++ E+ PIGLI IDALYSP+
Sbjct: 120 ESNGIEILNKDHVICHLDDGASLYMELTVNTGKGYVAADRNKPEDAPIGLIAIDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYD+L+M I+T+G ++ ED+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDRLTMKIETNGGLSPEDAVAYAARILQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           +    +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 LGGAAD-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ +WPPE+IEELAKKYED+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEEWPPENIEELAKKYEDQ 337


>gi|84685391|ref|ZP_01013289.1| DNA-directed RNA polymerase alpha subunit [Maritimibacter
           alkaliphilus HTCC2654]
 gi|84666548|gb|EAQ13020.1| DNA-directed RNA polymerase alpha subunit [Rhodobacterales
           bacterium HTCC2654]
          Length = 338

 Score =  424 bits (1091), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 209/339 (61%), Positives = 268/339 (79%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++ +  G +   +  +IAEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLD-VKPGNDPSRQATVIAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG++++M  +  KR++I  +GP VVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKGVSIRMEVEGPKRLSISAKGPMVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD  A + MELTV+ G GYV A  ++ E+ PIGLI +DA+YSP+
Sbjct: 120 ESAGIEILNKDHVICHLDDGADLFMELTVNTGKGYVSADKNKPEDAPIGLIPVDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL++ ++TDGSIT +D+VA A+RI+QDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTLKVETDGSITPDDAVAFAARIIQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SRQDDD-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ +WPPE+IE+LAKK+ED+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEEWPPENIEDLAKKFEDQ 337


>gi|126736630|ref|ZP_01752370.1| DNA-directed RNA polymerase alpha subunit [Roseobacter sp. CCS2]
 gi|126713943|gb|EBA10814.1| DNA-directed RNA polymerase alpha subunit [Roseobacter sp. CCS2]
          Length = 338

 Score =  424 bits (1091), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 208/339 (61%), Positives = 266/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E +  G +   +  +IAEPL RGF  TLGNALRR+LMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLE-VKPGNDPARQATVIAEPLERGFGLTLGNALRRILMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID VLHE SS+ GV ED+TDI+LN+KG+ ++M  +  KR+++  +GPGVVTA DI 
Sbjct: 60  TAVQIDNVLHEFSSVSGVREDVTDIVLNLKGVAIRMEVEGPKRLSVQAKGPGVVTAADIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + MELTV+ G GYV A  ++ E+ PIG++++DA+YSP+
Sbjct: 120 ETAGIEVLNKDHVICHLDDGADLYMELTVNTGKGYVSADKNKPEDAPIGMMSVDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGS+T +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSLTPDDAVAYAARILQDQLSIFVNFDEPES- 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +   +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 AQAGQDDDGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFEDQ 337


>gi|89070528|ref|ZP_01157817.1| DNA-directed RNA polymerase alpha subunit [Oceanicola granulosus
           HTCC2516]
 gi|89043835|gb|EAR50033.1| DNA-directed RNA polymerase alpha subunit [Oceanicola granulosus
           HTCC2516]
          Length = 338

 Score =  424 bits (1091), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 209/339 (61%), Positives = 265/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E +  G +   +  +IAEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLE-VKPGNDPMRQATVIAEPLERGFGLTLGNALRRVLLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID VLHE SS+ GV ED+TDI+LN+KG+ ++M  +  KR+T+  +GPGVVTAGDI 
Sbjct: 60  TAVQIDNVLHEFSSVSGVREDVTDIVLNLKGVAIRMEVEGPKRLTVNAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD  A + MELTV+ G GYV A  ++ E+ PIG++ IDA+YSP+
Sbjct: 120 ESAGIEILNKDHVICHLDEGADLYMELTVNTGKGYVSADKNKPEDAPIGMMAIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGS++ +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSLSPDDAVAYAARILQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 TSTSDD-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFEDQ 337


>gi|254437251|ref|ZP_05050745.1| DNA-directed RNA polymerase, alpha subunit [Octadecabacter
           antarcticus 307]
 gi|198252697|gb|EDY77011.1| DNA-directed RNA polymerase, alpha subunit [Octadecabacter
           antarcticus 307]
          Length = 342

 Score =  424 bits (1090), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 208/338 (61%), Positives = 265/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++ +  G +   +  +IAEPL RGF  TLGNALRR+LMSSL+GAAI
Sbjct: 5   MIHKNWAELIKPTQLD-VQPGNDPSRQATVIAEPLERGFGLTLGNALRRILMSSLQGAAI 63

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID VLHE SSI GV ED+TD++LN+KG+ ++M  +  KR+ +  +GPGVVTAGDI 
Sbjct: 64  TAVQIDNVLHEFSSISGVREDVTDVVLNLKGVAIRMEVEGPKRLQVQAKGPGVVTAGDIS 123

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHV+C+LD  A + MELTV+ G+GYV A  ++ E+ PIG++ IDA+YSP+
Sbjct: 124 ESAGIEILNKDHVLCHLDEGAELYMELTVNTGNGYVAADKNKPEDAPIGMMAIDAIYSPV 183

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGSIT +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 184 KKVSYDVQPTREGQVLDYDKLTMKVETDGSITPDDAVAFAARILQDQLSIFVNFDEPES- 242

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +   +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 243 AQTASDDDGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 302

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 303 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 340


>gi|255264362|ref|ZP_05343704.1| DNA-directed RNA polymerase, alpha subunit [Thalassiobium sp.
           R2A62]
 gi|255106697|gb|EET49371.1| DNA-directed RNA polymerase, alpha subunit [Thalassiobium sp.
           R2A62]
          Length = 342

 Score =  424 bits (1090), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 209/341 (61%), Positives = 269/341 (78%), Gaps = 6/341 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++ +  G +   +  ++AEPL RGF  T+GNALRRVLMSSL+GAAI
Sbjct: 5   MIHKNWAELIKPTQLD-VKPGNDPSRQATVVAEPLERGFGLTMGNALRRVLMSSLQGAAI 63

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID VLHE SS+ G+ ED+TDI+LN+KG+ ++M  +  KR++I  +GPGVVTAGDI 
Sbjct: 64  TAVQIDNVLHEFSSVSGLREDVTDIVLNLKGVAIRMEVEGPKRLSIQAKGPGVVTAGDIS 123

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN +HVIC+LD  A + MELTV+ G GYV A+ ++ E+ PIG+++IDA+YSP+
Sbjct: 124 ESAGIEILNKEHVICHLDDGADLFMELTVNTGKGYVSAEKNKPEDAPIGMMSIDAIYSPV 183

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGSIT +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 184 KKVSYDVQPTREGQVLDYDKLTMKVETDGSITPDDAVAFAARILQDQLSIFVNFDEPESA 243

Query: 241 --VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              +ED     L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NF
Sbjct: 244 STAQED---DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNF 300

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           GRKSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED+
Sbjct: 301 GRKSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFEDQ 341


>gi|126724892|ref|ZP_01740735.1| DNA-directed RNA polymerase subunit alpha [Rhodobacterales
           bacterium HTCC2150]
 gi|126706056|gb|EBA05146.1| DNA-directed RNA polymerase subunit alpha [Rhodobacterales
           bacterium HTCC2150]
          Length = 338

 Score =  424 bits (1089), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 209/338 (61%), Positives = 266/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNWQELIKPN ++ +  G +   +  +IAEPL RGF  T+GNALRR+LMSSL+GAAI
Sbjct: 1   MIHKNWQELIKPNQLK-VQPGNDPSRQATVIAEPLERGFGLTMGNALRRILMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+K + ++M  +  KR++I  +GPGVVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKSVAIRMEVEGPKRLSIAAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD  A V MELTV+ G GYV A+ ++ E+ PIGLI IDA++SP+
Sbjct: 120 DSAGIEILNKDHVICHLDDGADVFMELTVNTGKGYVSAEKNKPEDAPIGLIPIDAIFSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL++ ++TDGS+T +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTLKLETDGSLTPDDAVAFAARILQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            + D     L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SRAD-EEDELEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK +D
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDIVDWPPDNIEDLAKKLDD 336


>gi|159042865|ref|YP_001531659.1| DNA-directed RNA polymerase subunit alpha [Dinoroseobacter shibae
           DFL 12]
 gi|157910625|gb|ABV92058.1| DNA-directed RNA polymerase, alpha subunit [Dinoroseobacter shibae
           DFL 12]
          Length = 343

 Score =  423 bits (1088), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 214/342 (62%), Positives = 266/342 (77%), Gaps = 8/342 (2%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNWQELIKP  +E +  G E   +  ++AEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 6   MIHKNWQELIKPTQLE-VKPGNEPARQATVVAEPLERGFGLTLGNALRRVLMSSLQGAAI 64

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+K + ++M  +  KRV+I  +GP VVTAGDI 
Sbjct: 65  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKQVAIRMEVEGPKRVSISAKGPRVVTAGDIS 124

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + MEL V+ G GYV A  +R E+ PIGLI IDA++SP+
Sbjct: 125 ESAGIEVLNRDHVICHLDEGADLFMELIVNTGKGYVSADKNRPEDAPIGLIPIDAIFSPV 184

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP--- 237
           KKVSY V+  REGQVLDYDKL++ ++TDGS+T +D+VA A+RILQDQL +F+NF+EP   
Sbjct: 185 KKVSYDVQPTREGQVLDYDKLTLKLETDGSVTPDDAVAYAARILQDQLSVFVNFDEPEAA 244

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           + + +ED     L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  N
Sbjct: 245 RSQSEED----DLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPN 300

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           FGRKSL EIK VL  MGL LGM++ DWPPE+IE+LAKK+ED+
Sbjct: 301 FGRKSLNEIKEVLSGMGLHLGMDILDWPPENIEDLAKKFEDQ 342


>gi|114767226|ref|ZP_01446091.1| DNA-directed RNA polymerase alpha subunit [Pelagibaca bermudensis
           HTCC2601]
 gi|114540636|gb|EAU43707.1| DNA-directed RNA polymerase alpha subunit [Roseovarius sp.
           HTCC2601]
          Length = 338

 Score =  423 bits (1087), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 209/339 (61%), Positives = 266/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E +  G +      ++AEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLE-VRPGADPSRVATVVAEPLERGFGLTLGNALRRVLLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG++L+M  +  KR++I   GPG VTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKGVSLRMEVEGPKRLSINATGPGAVTAGDIA 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + +ELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ETAGIEVLNKDHVICHLDDGADLYVELTVNTGKGYVSADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V+Y V+  REGQVLDYDKL+M ++TDGS+T ED++A A+RILQDQL +F+NF+EP+  
Sbjct: 180 KRVAYEVQPTREGQVLDYDKLTMKVETDGSVTPEDAIAFAARILQDQLSIFVNFDEPEAA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 GRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM++ DWPP++IE+LAKK ED+
Sbjct: 299 KSLNEIKEVLSSMGLHLGMDVEDWPPDNIEDLAKKLEDQ 337


>gi|83312207|ref|YP_422471.1| DNA-directed RNA polymerase subunit alpha [Magnetospirillum
           magneticum AMB-1]
 gi|119366694|sp|Q2W2L3|RPOA_MAGSA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|82947048|dbj|BAE51912.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Magnetospirillum magneticum AMB-1]
          Length = 338

 Score =  422 bits (1086), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 207/338 (61%), Positives = 267/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN + ++  G + +   +++AEPL RGF  TLGN+LRRVL+SSL+GAA+
Sbjct: 1   MIQKNWQELIKPNKL-HVEPGADPQRTAIVVAEPLERGFGMTLGNSLRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGVLHE SSI GV ED+TDIILNIK + L+M G+  KR+ +   GPG VTAG I+
Sbjct: 60  TAIQIDGVLHEFSSIPGVREDVTDIILNIKTLGLRMHGEGPKRMHLRAVGPGEVTAGLIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             +DIE+++P+ V+C LD  A + +E TV  G GYVPA  +R E+ PIGLI IDA++SP+
Sbjct: 120 VGHDIEIMDPELVLCTLDEGAKLNIEFTVETGKGYVPASQNRPEDSPIGLIPIDAIFSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KV+Y VE+ R GQV DYDKLSMT++T+G++T +D+VALA+RILQDQL +FINFEEP   
Sbjct: 180 RKVAYKVENTRVGQVTDYDKLSMTVETNGAVTPDDAVALAARILQDQLQLFINFEEPTAV 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V+E+     LPFN  LL+KV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+MLR  NFGR
Sbjct: 240 VEEE-KKDELPFNKNLLRKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM + +WPPE+IEELAKK E+
Sbjct: 299 KSLNEIKEVLAQMGLHLGMEIANWPPENIEELAKKLEE 336


>gi|260432472|ref|ZP_05786443.1| DNA-directed RNA polymerase, alpha subunit [Silicibacter
           lacuscaerulensis ITI-1157]
 gi|260416300|gb|EEX09559.1| DNA-directed RNA polymerase, alpha subunit [Silicibacter
           lacuscaerulensis ITI-1157]
          Length = 372

 Score =  422 bits (1086), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 213/338 (63%), Positives = 265/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   +  ++AEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 35  MIHKNWAELIKPTQLDGKP-GNDPARQATIVAEPLERGFGLTLGNALRRVLMSSLQGAAI 93

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+K + L+M  +  KR++I  +GP VVTAGDI 
Sbjct: 94  TSVQIDNVLHEFSSVAGVREDVTDIILNLKQVALRMEVEGPKRLSINAKGPAVVTAGDIS 153

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + MELTV+ G GYV A+ ++ E+ PIGLI IDA+YSP+
Sbjct: 154 ESAGIEVLNRDHVICHLDDGAELFMELTVNTGKGYVSAEKNKPEDAPIGLIPIDAIYSPV 213

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKV+Y V+  REGQVLDYDKL+M I+TDGSIT ED++A A+RILQDQL +F+NF+EP+  
Sbjct: 214 KKVAYDVQPTREGQVLDYDKLTMKIETDGSITPEDALAFAARILQDQLSIFVNFDEPESA 273

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 274 GRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 332

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 333 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 370


>gi|288958717|ref|YP_003449058.1| DNA-directed RNA polymerase subunit alpha [Azospirillum sp. B510]
 gi|288911025|dbj|BAI72514.1| DNA-directed RNA polymerase subunit alpha [Azospirillum sp. B510]
          Length = 338

 Score =  422 bits (1086), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 208/338 (61%), Positives = 267/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M+QKNWQELIKP+ +E I  G + +    ++AEPL RGF  TLGNALRR+L+SSL+GAA+
Sbjct: 1   MLQKNWQELIKPSKLE-IQPGDDADRFATVVAEPLERGFGLTLGNALRRILLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T++ IDGVLHE SSI GV ED+TDI+LNIK + L+M GD  KR+ +   GPG V AG I+
Sbjct: 60  TSIHIDGVLHEFSSIPGVREDVTDIVLNIKTMGLRMGGDGPKRMRLRAEGPGEVKAGMIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T  DI+V++P+ VIC LD  A + MELTV  G GYVPA  +R E+ PIGLI IDAL+SP+
Sbjct: 120 TGPDIQVMDPELVICTLDNGARLNMELTVETGKGYVPASQNRPEDAPIGLIPIDALFSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY V++AR GQV DYD+LSMT++T+GS+  +D+VALA+RI+QDQL +FINFEEP   
Sbjct: 180 RKVSYKVDNARVGQVTDYDRLSMTVETNGSVKPDDAVALAARIMQDQLQLFINFEEPTHA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V E+ + + +PFN  LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q+TEA+MLR  NFGR
Sbjct: 240 VSEEKH-EEVPFNKNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM +P+WPPE+IEELAK+ E+
Sbjct: 299 KSLNEIKEVLSQMGLHLGMEIPNWPPENIEELAKRLEE 336


>gi|119383536|ref|YP_914592.1| DNA-directed RNA polymerase subunit alpha [Paracoccus denitrificans
           PD1222]
 gi|158512588|sp|A1B052|RPOA_PARDP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119373303|gb|ABL68896.1| DNA-directed RNA polymerase subunit alpha [Paracoccus denitrificans
           PD1222]
          Length = 338

 Score =  422 bits (1085), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 209/339 (61%), Positives = 262/339 (77%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E I  G +      ++AEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLE-IKPGADSSRVATVVAEPLERGFGLTLGNALRRVLLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG+ LKM  D+ KR+T+  +GPG V AGDIQ
Sbjct: 60  TSVQIDNVLHEFSSVPGVREDVTDIVLNLKGVTLKMDVDAPKRLTLSAKGPGEVKAGDIQ 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               I +LN DHVIC+LD  A + MEL V+ G GYV A  +R E+ PIGLI IDA++SP+
Sbjct: 120 ESAGITILNRDHVICHLDEGAELHMELAVANGKGYVAADKNRPEDAPIGLIPIDAIFSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VSY V   REGQVLDYDKL+M ++TDGS+T ED+VA A+RI+QDQL +F+NF+EP+  
Sbjct: 180 KRVSYEVTPTREGQVLDYDKLTMKVETDGSLTPEDAVAYAARIIQDQLSVFVNFDEPETA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            + D     L F+P LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 TRSDAE-DGLEFDPRLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPPE+IE+LAK+++D+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVVDWPPENIEDLAKRFDDQ 337


>gi|217979117|ref|YP_002363264.1| DNA-directed RNA polymerase subunit alpha [Methylocella silvestris
           BL2]
 gi|254765258|sp|B8EIT5|RPOA_METSB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|217504493|gb|ACK51902.1| DNA-directed RNA polymerase, alpha subunit [Methylocella silvestris
           BL2]
          Length = 338

 Score =  422 bits (1084), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 208/338 (61%), Positives = 264/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQEL KPN +E ++ G + +    ++A PL  GF  TLGN+LRR+L+SSL+GAAI
Sbjct: 1   MIQKNWQELTKPNKLE-VISGDDPKRFATIVAGPLELGFGLTLGNSLRRILLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V IDGVLHE SSI GV ED+TDI+LNIK I +KM GD  KR+ + K+GPG VTAGDIQ
Sbjct: 60  TSVHIDGVLHEFSSIPGVREDVTDIVLNIKDIAIKMPGDGPKRLVLKKQGPGKVTAGDIQ 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T  DI +LNP  VIC LD  A +RME TV  G GYV A  +R E+ PIGLI ID+LYSP+
Sbjct: 120 TSGDISILNPGLVICTLDEGAEIRMEFTVHTGKGYVAADRNRAEDAPIGLIPIDSLYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQ LD DKL++ ++T+G++T ED+VA A+RILQDQL +F+NFEEP++ 
Sbjct: 180 KKVSYRVENTREGQNLDLDKLTLQVETNGALTPEDAVAFAARILQDQLNVFVNFEEPRR- 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V+   ++  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++E +MLR  NFGR
Sbjct: 239 VEATPSIPELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSEGEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM +  WPP++I++LAK++E+
Sbjct: 299 KSLNEIKEVLAQMGLHLGMEVNGWPPDNIDDLAKRFEE 336


>gi|83949763|ref|ZP_00958496.1| DNA-directed RNA polymerase alpha subunit [Roseovarius nubinhibens
           ISM]
 gi|83837662|gb|EAP76958.1| DNA-directed RNA polymerase alpha subunit [Roseovarius nubinhibens
           ISM]
          Length = 338

 Score =  422 bits (1084), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 208/338 (61%), Positives = 266/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++ +  G +   +  ++AEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLD-VKPGNDPLRQATVVAEPLERGFGLTLGNALRRVLLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG+ L+M  +  KR++I  +GPGVVTA DI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKGVALRMDVEGPKRLSISAKGPGVVTAADIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + +ELTV+ G GYV A  ++ E+ PIG+I +DA+YSP+
Sbjct: 120 ETAGIEVLNRDHVICHLDEGADLYVELTVNTGKGYVAADKNKPEDAPIGMIPVDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY V+  REGQVLDYDKL+M I+TDGSIT +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 RRVSYDVQPTREGQVLDYDKLTMKIETDGSITPDDAVAFAARILQDQLSIFVNFDEPEAA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 GRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|84515660|ref|ZP_01003021.1| DNA-directed RNA polymerase alpha subunit [Loktanella vestfoldensis
           SKA53]
 gi|84510102|gb|EAQ06558.1| DNA-directed RNA polymerase alpha subunit [Loktanella vestfoldensis
           SKA53]
          Length = 338

 Score =  419 bits (1078), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 206/339 (60%), Positives = 264/339 (77%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++ +  G +   +  M+AEPL RGF  TLGNALRR+LMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPMQLD-VKPGNDPMRQATMVAEPLERGFGLTLGNALRRILMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID VLHE SS+ GV ED+TDI+LN+KG+ ++M  +  KR+++  +GPGVVTA DI 
Sbjct: 60  TAVQIDNVLHEFSSVPGVREDVTDIVLNLKGVAIRMEVEGPKRLSVQAKGPGVVTAADIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD  A + MELTV+ G GYV A  ++ E+ PIG+I IDA++SP+
Sbjct: 120 ETAGIEILNKDHVICHLDDGADLYMELTVNTGKGYVAADKNKPEDAPIGMIVIDAIFSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGS++ +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSLSPDDAVAYAARILQDQLSIFVNFDEPES- 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 ASAGSDDDGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFEDQ 337


>gi|329850231|ref|ZP_08265076.1| DNA-directed RNA polymerase, alpha subunit [Asticcacaulis
           biprosthecum C19]
 gi|328840546|gb|EGF90117.1| DNA-directed RNA polymerase, alpha subunit [Asticcacaulis
           biprosthecum C19]
          Length = 338

 Score =  419 bits (1078), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 206/339 (60%), Positives = 259/339 (76%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI++NWQ+LI+P   + +  G +   +  ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIERNWQQLIRPEKPQ-VEAGTDASRKMRLVAEPLERGFGVTLGNALRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQIDGV+HE SSI+GV ED+ DIILNIK + L+M  +  KR+ +   G G VTAG I 
Sbjct: 60  TSVQIDGVVHEFSSIEGVREDVVDIILNIKQLALRMHAEGPKRMVLRASGAGPVTAGQID 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DIEVLNPDHVIC LD  A VRME TV  G GYV A   R E+ PIGLI +DALYSP+
Sbjct: 120 VPADIEVLNPDHVICTLDEGASVRMEFTVQNGKGYVAADRLRPEDAPIGLIAVDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKV+Y VE  R+GQ LDYDKL + ++T+ ++T  D+VA A+RILQDQL +FI FEEPK  
Sbjct: 180 KKVAYRVEPTRQGQSLDYDKLILDVETNAAVTPVDAVAFAARILQDQLQIFITFEEPKAP 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V E+     LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLI +TE++MLR  NFGR
Sbjct: 240 VVEE-GKPELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLILKTESEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +M L LGM++P+WPPE++E+LAKK+ED+
Sbjct: 299 KSLNEIKEVLASMNLSLGMDIPNWPPENVEDLAKKFEDQ 337


>gi|83593996|ref|YP_427748.1| DNA-directed RNA polymerase subunit alpha [Rhodospirillum rubrum
           ATCC 11170]
 gi|119366718|sp|Q2RQY4|RPOA_RHORT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|83576910|gb|ABC23461.1| DNA-directed RNA polymerase, alpha subunit [Rhodospirillum rubrum
           ATCC 11170]
          Length = 340

 Score =  418 bits (1075), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 207/338 (61%), Positives = 264/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN +   ++G  ++  T+ +AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 3   VIQKNWQELIKPNKLMIELVGGSKKVATV-VAEPLERGFGLTLGNALRRVLLSSLQGAAV 61

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QI+GVLHE SSI GV ED+TD+ILNIKG+ L M  +  +R+T+   GPG VTA  I+
Sbjct: 62  TAIQIEGVLHEFSSIPGVREDVTDVILNIKGLALLMHSEGPRRMTLKASGPGEVTAAQIE 121

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             +DIE++NPD VIC+LD  A + ME TV  G GYVP+  +R E+ PIG I ID+++SP+
Sbjct: 122 MGSDIEIMNPDLVICHLDEGATLSMEFTVGMGKGYVPSTQNRPEDAPIGYIPIDSIFSPV 181

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY VE++R GQV DYDKLSM ++TDGS+  ED+VALA+RILQDQL +FINFEEP+  
Sbjct: 182 TKVSYRVENSRVGQVTDYDKLSMVVETDGSVGPEDAVALAARILQDQLQLFINFEEPQA- 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V E+     LPFN  LL+KV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+MLR  NFGR
Sbjct: 241 VSEEKKDDELPFNKNLLRKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEMLRTPNFGR 300

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM + +WPPE+IE+LAKK E+
Sbjct: 301 KSLNEIKEVLAQMGLHLGMEISNWPPENIEDLAKKLEE 338


>gi|144900908|emb|CAM77772.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           [Magnetospirillum gryphiswaldense MSR-1]
          Length = 338

 Score =  417 bits (1073), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 204/338 (60%), Positives = 265/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP+ ++ +  G +      +IAEPL RGF  TLGN+LRR+L+SSL+GAA+
Sbjct: 1   MIQKNWQELIKPSKLQ-VEPGADAARVATVIAEPLERGFGMTLGNSLRRILLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QI+GVLHE SS+ GV ED+TDIILNIK + L+M G+  KR+ +   GPG V AG I+
Sbjct: 60  TAIQIEGVLHEFSSVPGVREDVTDIILNIKNLGLRMHGEGPKRMQLRASGPGEVKAGMIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             +DIE+++PD V+C LD  A + +E TV  G GYVPA  +RTE+ PIGLI IDA++SP+
Sbjct: 120 AGHDIEIMDPDLVLCTLDQGAKLNIEFTVETGKGYVPASQNRTEDSPIGLIPIDAIFSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKV+Y VE+ R GQV DYDKLSM ++T+G++T +D+VALA+RILQDQL +FINF+EP   
Sbjct: 180 KKVAYKVENTRVGQVTDYDKLSMVLETNGAVTPDDAVALAARILQDQLQLFINFDEPTHV 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V+E+     LPFN  LL+KV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+MLR  NFGR
Sbjct: 240 VEEE-KKDELPFNKNLLRKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM +P+WPPE+IE+LAKK E+
Sbjct: 299 KSLNEIKEVLSHMGLHLGMEIPNWPPENIEDLAKKLEE 336


>gi|296116709|ref|ZP_06835319.1| DNA-directed RNA polymerase subunit alpha [Gluconacetobacter
           hansenii ATCC 23769]
 gi|295976921|gb|EFG83689.1| DNA-directed RNA polymerase subunit alpha [Gluconacetobacter
           hansenii ATCC 23769]
          Length = 339

 Score =  416 bits (1070), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 205/338 (60%), Positives = 260/338 (76%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++QKNWQ LIKP  +E +  G E      ++AEPL RGF  TLGNA+RRVL+SSL+GAA+
Sbjct: 2   VLQKNWQSLIKPEKLE-VEPGAEPSRTATVVAEPLERGFGMTLGNAIRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGVLHE SS+ GV ED+TDI+LNIK + L+M G+  KR+ +   GPG V AG IQ
Sbjct: 61  TAIQIDGVLHEFSSVAGVREDVTDIVLNIKQLALRMHGEGPKRMVLTATGPGEVRAGQIQ 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIEV+NPD VIC LD      ME TV+ G GYVPA  +R E+ PIGLI IDA+YSP+
Sbjct: 121 TGHDIEVMNPDLVICTLDEGVKFGMEFTVNMGKGYVPAAANRPEDAPIGLIPIDAIYSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY VE  R GQV DYD+L +T++T+G++T EDSVALA+RILQDQL +FINF+EP+  
Sbjct: 181 RRVSYKVEQTRVGQVTDYDRLLLTVETNGAVTPEDSVALAARILQDQLQLFINFDEPRA- 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V+ +     LPFN  LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q+TE +MLR  NFGR
Sbjct: 240 VRTEEPQDDLPFNRNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKTEQEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGMN+P WPPE+IE+LAK+ ++
Sbjct: 300 KSLNEIKEVLTAMGLSLGMNVPAWPPENIEDLAKRLDE 337


>gi|254294416|ref|YP_003060439.1| DNA-directed RNA polymerase subunit alpha [Hirschia baltica ATCC
           49814]
 gi|254042947|gb|ACT59742.1| DNA-directed RNA polymerase, alpha subunit [Hirschia baltica ATCC
           49814]
          Length = 341

 Score =  415 bits (1066), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 202/337 (59%), Positives = 262/337 (77%), Gaps = 6/337 (1%)

Query: 4   KNWQELIKPNN--IEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           KNW+ELI+P+   +E+     +   +  +I EPL RGF  TLG++LRR+L+SSL+GAAIT
Sbjct: 9   KNWKELIRPSRPVVEHDF---DAGRKASLIVEPLERGFGTTLGSSLRRILLSSLQGAAIT 65

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            VQIDGV+HE SSI GV ED+TDI+LN+K + + M  ++ KR+T+   GPGVVTAG I+ 
Sbjct: 66  GVQIDGVVHEFSSIPGVREDVTDIVLNLKRVAISMVSETSKRMTLSASGPGVVTAGQIEL 125

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
             D+E+LNPDHVIC LD  A +RME TV+ G GYVPA  +R ++ P+G I +DA++SP++
Sbjct: 126 PGDMEILNPDHVICTLDDGANIRMEFTVASGKGYVPADRNRPDDAPLGFIPVDAIFSPVE 185

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +V + V+  REGQVLDYDKL++T++TDGS+T ED+VA A+RILQDQL + INF+EP  E 
Sbjct: 186 RVGFKVDDTREGQVLDYDKLTLTVETDGSVTPEDAVAYAARILQDQLQLLINFDEPVVE- 244

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +E      L FNP LLKKV+ELELSVRS NCLR +NIVY+GDLIQ++EA+MLR  NFGRK
Sbjct: 245 QEAEQEPDLGFNPVLLKKVDELELSVRSANCLRNDNIVYIGDLIQKSEAEMLRTPNFGRK 304

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL TMGL LGM++P WPPE+IE+LAKKYED
Sbjct: 305 SLNEIKEVLATMGLHLGMDVPSWPPENIEDLAKKYED 341


>gi|330993873|ref|ZP_08317805.1| DNA-directed RNA polymerase subunit alpha [Gluconacetobacter sp.
           SXCC-1]
 gi|329759141|gb|EGG75653.1| DNA-directed RNA polymerase subunit alpha [Gluconacetobacter sp.
           SXCC-1]
          Length = 339

 Score =  414 bits (1063), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 203/338 (60%), Positives = 260/338 (76%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++QKNWQ LIKP  +E +  G E      ++AEPL RGF  TLGNA+RRVL+SSL+GAA+
Sbjct: 2   VLQKNWQSLIKPEKLE-VEPGAEPSRIATVVAEPLERGFGMTLGNAIRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGVLHE SS+ GV ED+TDI+LNIK + L+M G+  KR+ +   GPG V AG IQ
Sbjct: 61  TAIQIDGVLHEFSSVAGVREDVTDIVLNIKQLALRMHGEGPKRMVLTATGPGEVRAGQIQ 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIEV+NPD VIC LD      ME TV+ G GYVPA  +R E+ PIGLI +DA+YSP+
Sbjct: 121 TGHDIEVMNPDLVICTLDEGVKFGMEFTVNMGKGYVPAAANRPEDAPIGLIPVDAIYSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY VE  R GQV DYD+L +T++T+G++T ED+VALA+RILQDQL +FINF+EP+  
Sbjct: 181 RRVSYKVEQTRVGQVTDYDRLLLTVETNGAVTPEDAVALAARILQDQLQLFINFDEPRT- 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V+ +     LPFN  LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q+TE +MLR  NFGR
Sbjct: 240 VRTEEPQDDLPFNRNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKTEQEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGMN+P WPPE+IE+LAK+ ++
Sbjct: 300 KSLNEIKEVLTAMGLSLGMNVPAWPPENIEDLAKRLDE 337


>gi|114327242|ref|YP_744399.1| DNA-directed RNA polymerase subunit alpha [Granulibacter
           bethesdensis CGDNIH1]
 gi|119366685|sp|Q0BUM6|RPOA_GRABC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|114315416|gb|ABI61476.1| DNA-directed RNA polymerase alpha chain [Granulibacter bethesdensis
           CGDNIH1]
          Length = 339

 Score =  414 bits (1063), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 203/338 (60%), Positives = 261/338 (77%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQ+NWQ LIKP  ++ +  G E      ++AEPL RGF  TLGNA+RR+L+SSL+GAA+
Sbjct: 2   VIQRNWQSLIKPEKLD-VEPGNEPSRIATIVAEPLERGFGMTLGNAIRRILLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SS+ GV ED+TDI+LNIK + L+M G+  KR+ +   GPG VTAG IQ
Sbjct: 61  TAVQIDGVLHEFSSVAGVREDVTDIVLNIKQLALRMHGEGPKRMMLTATGPGEVTAGQIQ 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             +DIE++NPD V+C LD    + ME TV+ G GYVPA  +R E+ PIGLI IDA+YSP+
Sbjct: 121 AGHDIEIMNPDLVLCTLDDGVKLGMEFTVNLGKGYVPASQNRQEDSPIGLIPIDAIYSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY VE  R GQV DYDKL +T++T+G++T EDSVALA+RILQDQL +FINFEEP ++
Sbjct: 181 RRVSYKVEPTRVGQVTDYDKLLLTVETNGAVTPEDSVALAARILQDQLQLFINFEEP-QQ 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V+ D     LPFN  LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q++E +MLR  NFGR
Sbjct: 240 VRHDEPQDDLPFNRNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKSEQEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++  WPPE+IE+LAK+ E+
Sbjct: 300 KSLNEIKEVLANMGLSLGMSVSGWPPENIEDLAKRLEE 337


>gi|162149150|ref|YP_001603611.1| DNA-directed RNA polymerase subunit alpha [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|209545106|ref|YP_002277335.1| DNA-directed RNA polymerase subunit alpha [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|189043839|sp|A9H3I9|RPOA_GLUDA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|161787727|emb|CAP57323.1| DNA-directed RNA polymerase alpha chain [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|209532783|gb|ACI52720.1| DNA-directed RNA polymerase, alpha subunit [Gluconacetobacter
           diazotrophicus PAl 5]
          Length = 339

 Score =  412 bits (1058), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 202/338 (59%), Positives = 261/338 (77%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++QKNWQ LIKP  +E +  G E      ++AEPL RGF  TLGNA+RRVL+SSL+GAA+
Sbjct: 2   VLQKNWQSLIKPEKLE-VEPGGEPLRTATVVAEPLERGFGMTLGNAIRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGVLHE SS+ GV ED+TDI+LN+K + L+M G+  KR+ +   GPG V AG IQ
Sbjct: 61  TAIQIDGVLHEFSSVAGVREDVTDIVLNVKQLALRMHGEGPKRMVLTATGPGEVRAGQIQ 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIEV+NPD VIC LD      ME TV+ G GYVPA  +R E+ PIGLI +DA+YSP+
Sbjct: 121 TGHDIEVMNPDLVICTLDEGVKFGMEFTVNLGKGYVPAAANRPEDAPIGLIPVDAIYSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY VE  R GQV DYD+L +T++T+G++T ED+VALA+RILQDQL +FINF+EP+  
Sbjct: 181 RRVSYKVEPTRVGQVTDYDRLLLTVETNGAVTPEDAVALAARILQDQLQLFINFDEPRP- 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V+ +     LPFN  LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q+TE +MLR  NFGR
Sbjct: 240 VRTEEPQDDLPFNRNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKTEQEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL +MGL LGMN+P WPPE+IE+LAK+ ++
Sbjct: 300 KSLNEIKEVLTSMGLSLGMNVPAWPPENIEDLAKRLDE 337


>gi|209964064|ref|YP_002296979.1| DNA-directed RNA polymerase subunit alpha [Rhodospirillum centenum
           SW]
 gi|259494170|sp|B6IRT0|RPOA_RHOCS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|209957530|gb|ACI98166.1| DNA-directed RNA polymerase, alpha subunit [Rhodospirillum centenum
           SW]
          Length = 338

 Score =  411 bits (1056), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 200/338 (59%), Positives = 259/338 (76%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQ L KP+ ++ I  G + +    ++A PL RGF  TLGNA+RRVL+SSL+GAA+
Sbjct: 1   MIQKNWQTLEKPSKLD-ITPGSDPKREATIVAGPLERGFGLTLGNAIRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T++ IDGVLHE SSI GV ED+TDI+LNIK + LKM  +  +R+ +   GP  VTAG I+
Sbjct: 60  TSIHIDGVLHEFSSIPGVREDVTDIVLNIKAMALKMGAEGPRRMRLRAEGPCEVTAGMIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T  DIEVL+P HVIC LD  A + MELTV+ G GYVPA  +R E+ PIGLI +DA++SP+
Sbjct: 120 TGADIEVLDPGHVICTLDSGARLNMELTVAMGKGYVPASQNRPEDAPIGLIPVDAIFSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KV+Y VE+ R GQ  DYDKL + ++T+G+++ ED+VA+A+RILQDQL MFINFEEP+  
Sbjct: 180 RKVAYKVENTRVGQTTDYDKLLLNVETNGAVSPEDAVAIAARILQDQLQMFINFEEPQAA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V E      +PFN  LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q+TEA+MLR  NFGR
Sbjct: 240 VAE-TKADEIPFNKNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM +P+WPPE+IE+LAK+ E+
Sbjct: 299 KSLNEIKEVLAQMGLHLGMEIPNWPPENIEDLAKRLEE 336


>gi|148260915|ref|YP_001235042.1| DNA-directed RNA polymerase subunit alpha [Acidiphilium cryptum
           JF-5]
 gi|172047769|sp|A5FZU1|RPOA_ACICJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|146402596|gb|ABQ31123.1| DNA-directed RNA polymerase subunit alpha [Acidiphilium cryptum
           JF-5]
          Length = 345

 Score =  410 bits (1055), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 205/337 (60%), Positives = 259/337 (76%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q+NWQ L KP  ++ I  G ++     +IAEPL RGF  TLGNALRRVL+SSL GAA+T
Sbjct: 9   LQRNWQSLRKPEKLD-IEPGADDTRVATIIAEPLERGFGLTLGNALRRVLLSSLHGAAVT 67

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+IDGVLHE SSI GV ED+TDI+LNIK I ++M GD  KR+T+   GP  VTAG IQT
Sbjct: 68  SVRIDGVLHEFSSIAGVREDVTDIVLNIKQIAVRMHGDGPKRMTVSATGPCEVTAGMIQT 127

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +DIEV+NP+ VIC LD  A + ME TV  G GYVPA  +R E+ PIGLI +D++YSP++
Sbjct: 128 GHDIEVMNPELVICTLDDGATLGMEFTVESGRGYVPAAANRPEDAPIGLIPVDSIYSPVR 187

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +VSY VE  R GQV DYD+L + I+T+G++T ED+VALA+RILQDQLGMFINFEEP++  
Sbjct: 188 RVSYRVEPTRVGQVTDYDRLILNIETNGAVTPEDAVALAARILQDQLGMFINFEEPQRLR 247

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+     LPFNP LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q++E +MLR  NFGRK
Sbjct: 248 AEEPR-PELPFNPNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKSEQEMLRTPNFGRK 306

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM + DWPPE+IEEL K+ ++
Sbjct: 307 SLNEIKEVLSAMGLGLGMVVQDWPPENIEELVKRSDN 343


>gi|258542051|ref|YP_003187484.1| DNA-directed RNA polymerase subunit alpha [Acetobacter pasteurianus
           IFO 3283-01]
 gi|329114194|ref|ZP_08242956.1| DNA-directed RNA polymerase subunit alpha [Acetobacter pomorum
           DM001]
 gi|256633129|dbj|BAH99104.1| DNA-directed RNA polymerase alpha subunit [Acetobacter pasteurianus
           IFO 3283-01]
 gi|256639241|dbj|BAI05203.1| DNA-directed RNA polymerase alpha subunit [Acetobacter pasteurianus
           IFO 3283-07]
 gi|256642295|dbj|BAI08250.1| DNA-directed RNA polymerase alpha subunit [Acetobacter pasteurianus
           IFO 3283-22]
 gi|256648405|dbj|BAI14346.1| DNA-directed RNA polymerase alpha subunit [Acetobacter pasteurianus
           IFO 3283-32]
 gi|256651458|dbj|BAI17392.1| DNA-directed RNA polymerase alpha subunit [Acetobacter pasteurianus
           IFO 3283-01-42C]
 gi|256654449|dbj|BAI20376.1| DNA-directed RNA polymerase alpha subunit [Acetobacter pasteurianus
           IFO 3283-12]
 gi|326696270|gb|EGE47949.1| DNA-directed RNA polymerase subunit alpha [Acetobacter pomorum
           DM001]
          Length = 339

 Score =  409 bits (1052), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 203/338 (60%), Positives = 260/338 (76%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++QKNWQ LIKP  +E +  G E      ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 2   VLQKNWQSLIKPEKLE-VESGVEPARIATVVAEPLERGFGMTLGNALRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SS+ GV ED+TDI+LNIK + L+M G+  KR+ +   GPG V A  IQ
Sbjct: 61  TAVQIDGVLHEFSSVAGVREDVTDIVLNIKQLALRMHGEGPKRMMLTATGPGEVRARQIQ 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIE++NPD VIC LD    + ME  V+ G GYVPA  +R E+ PIGLI +DA+YSP+
Sbjct: 121 TGHDIEIMNPDLVICTLDDGVKLGMEFIVNMGKGYVPAAANRPEDAPIGLIPVDAIYSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VSY VE  R GQV DYDKL +T++T+G++T ED+VALA+RILQDQL +FINF+EP+  
Sbjct: 181 KRVSYKVEPTRVGQVTDYDKLLLTVETNGAVTPEDAVALAARILQDQLQLFINFDEPRP- 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V+ +     LPFN  LL+KV+ELELSVRS NCL+ +NI+Y+GDL+Q++E +MLR  NFGR
Sbjct: 240 VQAEEPEDDLPFNRNLLRKVDELELSVRSANCLKNDNIIYIGDLVQKSEQEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL +MGL LGMN+P WPPE+IEELAK+ ++
Sbjct: 300 KSLNEIKEVLTSMGLSLGMNVPAWPPENIEELAKRLDE 337


>gi|326404313|ref|YP_004284395.1| DNA-directed RNA polymerase subunit alpha [Acidiphilium multivorum
           AIU301]
 gi|325051175|dbj|BAJ81513.1| DNA-directed RNA polymerase subunit alpha [Acidiphilium multivorum
           AIU301]
          Length = 339

 Score =  409 bits (1051), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 204/337 (60%), Positives = 259/337 (76%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q+NWQ L KP  ++ I  G ++     +IAEPL RGF  TLGNALRRVL+SSL GAA+T
Sbjct: 3   LQRNWQSLRKPEKLD-IEPGADDTRVATIIAEPLERGFGLTLGNALRRVLLSSLHGAAVT 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+IDGVLHE SSI GV ED+TDI+LNIK I ++M GD  KR+T+   GP  VTAG IQT
Sbjct: 62  SVRIDGVLHEFSSIAGVREDVTDIVLNIKQIAVRMHGDGPKRMTVSATGPCEVTAGMIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +DIEV+NP+ VIC LD  A + ME TV  G GY+PA  +R E+ PIGLI +D++YSP++
Sbjct: 122 GHDIEVMNPELVICTLDDGATLGMEFTVESGRGYLPAAANRPEDAPIGLIPVDSIYSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +VSY VE  R GQV DYD+L + I+T+G++T ED+VALA+RILQDQLGMFINFEEP++  
Sbjct: 182 RVSYRVEPTRVGQVTDYDRLILNIETNGAVTPEDAVALAARILQDQLGMFINFEEPQRLR 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+     LPFNP LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q++E +MLR  NFGRK
Sbjct: 242 AEEPR-PELPFNPNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKSEQEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM + DWPPE+IEEL K+ ++
Sbjct: 301 SLNEIKEVLSAMGLGLGMVVQDWPPENIEELVKRSDN 337


>gi|114798821|ref|YP_761505.1| DNA-directed RNA polymerase subunit alpha [Hyphomonas neptunium
           ATCC 15444]
 gi|119366689|sp|Q0BYD8|RPOA_HYPNA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|114738995|gb|ABI77120.1| DNA-directed RNA polymerase, alpha subunit [Hyphomonas neptunium
           ATCC 15444]
          Length = 342

 Score =  408 bits (1049), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 200/335 (59%), Positives = 252/335 (75%), Gaps = 1/335 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW+ LI+PN    +  G + + +  ++ EPL RG+  TLGNALRRVL+SSL+GAAI  V
Sbjct: 7   RNWKVLIRPNR-PVVQAGYDAKRKAKLVVEPLERGYGTTLGNALRRVLLSSLQGAAIIGV 65

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           QIDGV+HE S+I GV ED+T I+LN+K + + M  D+ KR+ +  +GPG V AG I+T  
Sbjct: 66  QIDGVVHEFSAIPGVREDVTTIVLNLKQVAIFMESDTPKRMVLRAKGPGEVKAGQIETPG 125

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           D+++LNPD VIC LD  + VRME TV+ G GYV A+ HR E+ PIG I IDA+YSP+++V
Sbjct: 126 DVKILNPDLVICTLDGGSEVRMEFTVATGKGYVAAEAHRPEDAPIGYIPIDAIYSPVRRV 185

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
            Y VE  REG VLDYDKL++ I+TDGS++ EDSVA A+RILQDQL +FINFEEP  E   
Sbjct: 186 GYQVEDTREGTVLDYDKLTLDIETDGSLSPEDSVAYAARILQDQLQLFINFEEPTLETGG 245

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++EA+MLR  NFGRKSL
Sbjct: 246 AADETDLGFNPVLLKKVDELELSVRSANCLKNDNIVYIGDLIQKSEAEMLRTPNFGRKSL 305

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
            EIK VL  MGL LGM +PDWPPE IE LAKKY+D
Sbjct: 306 NEIKEVLAGMGLHLGMEVPDWPPEDIEGLAKKYDD 340


>gi|296534011|ref|ZP_06896527.1| DNA-directed RNA polymerase subunit alpha [Roseomonas cervicalis
           ATCC 49957]
 gi|296265677|gb|EFH11786.1| DNA-directed RNA polymerase subunit alpha [Roseomonas cervicalis
           ATCC 49957]
          Length = 338

 Score =  408 bits (1049), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 195/338 (57%), Positives = 260/338 (76%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M+++NW+ LI+P  ++ +  G +     +++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MLERNWRSLIRPEKLD-VEPGADPSRVAVVVAEPLERGFGMTLGNALRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA++IDG LHE SS++GV ED+TDI+LNIK + ++M  +  KR+ +   GPG VTAG IQ
Sbjct: 60  TAIRIDGALHEFSSLQGVREDVTDIVLNIKRLAIRMQSEGPKRLQLTATGPGEVTAGQIQ 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T  DIE+ NP+ VIC LD  A + MELTV  G GYVPA  +R E+ PIGLI +DA+YSP+
Sbjct: 120 TTGDIEIANPELVICTLDDGAKLSMELTVDVGKGYVPASENRPEDAPIGLIPVDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++V+Y V+  R GQ  DYDKL +T++TDG++  ED+VALA+RILQDQL +FINF+EP++ 
Sbjct: 180 RRVAYQVQPTRVGQRTDYDKLVLTVETDGTVAPEDAVALAARILQDQLQLFINFDEPRER 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E++    LPFN  LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q+TE +MLR  NFGR
Sbjct: 240 KVEEVQ-DDLPFNRNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKTEQEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL +MGL LGM +P WPPE+IE+LAKK E+
Sbjct: 299 KSLNEIKEVLASMGLSLGMTVPGWPPENIEDLAKKIEE 336


>gi|256636186|dbj|BAI02155.1| DNA-directed RNA polymerase alpha subunit (variant) [Acetobacter
           pasteurianus IFO 3283-03]
 gi|256645350|dbj|BAI11298.1| DNA-directed RNA polymerase alpha subunit (variant) [Acetobacter
           pasteurianus IFO 3283-26]
          Length = 339

 Score =  407 bits (1046), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 202/338 (59%), Positives = 259/338 (76%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++QKNWQ LIKP  +E +  G E      ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 2   VLQKNWQSLIKPEKLE-VESGVEPARIATVVAEPLERGFGMTLGNALRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SS+ GV ED+TDI+LNIK + L+M G+  KR+ +   GPG V A  IQ
Sbjct: 61  TAVQIDGVLHEFSSVAGVREDVTDIVLNIKQLALRMHGEGPKRMMLTATGPGEVRARQIQ 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIE++NPD VIC LD    + ME  V+ G GYVPA  +R E+ PIGLI +DA+YSP+
Sbjct: 121 TGHDIEIMNPDLVICTLDDGVKLGMEFIVNMGKGYVPAAANRPEDAPIGLIPVDAIYSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VSY VE  R GQV DYDKL +T++T+G++T ED+VALA+RILQDQL +FINF+EP+  
Sbjct: 181 KRVSYKVEPTRVGQVTDYDKLLLTVETNGAVTPEDAVALAARILQDQLQLFINFDEPRP- 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V+ +      PFN  LL+KV+ELELSVRS NCL+ +NI+Y+GDL+Q++E +MLR  NFGR
Sbjct: 240 VQAEEPEDDQPFNRNLLRKVDELELSVRSANCLKNDNIIYIGDLVQKSEQEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL +MGL LGMN+P WPPE+IEELAK+ ++
Sbjct: 300 KSLNEIKEVLTSMGLSLGMNVPAWPPENIEELAKRLDE 337


>gi|254449927|ref|ZP_05063364.1| DNA-directed RNA polymerase, alpha subunit [Octadecabacter
           antarcticus 238]
 gi|198264333|gb|EDY88603.1| DNA-directed RNA polymerase, alpha subunit [Octadecabacter
           antarcticus 238]
          Length = 322

 Score =  407 bits (1045), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 197/318 (61%), Positives = 252/318 (79%), Gaps = 1/318 (0%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
           G +   +  ++AEPL RGF  TLGNALRR+LMSSL+GAAITAVQID VLHE SSI GV E
Sbjct: 4   GNDPSRQATVVAEPLERGFGLTLGNALRRILMSSLQGAAITAVQIDNVLHEFSSISGVRE 63

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+TD++LN+KG+ ++M  +  KR+ +  +GPGVVTAGDI     IE+LN DHV+C+LD  
Sbjct: 64  DVTDVVLNLKGVAIRMEVEGPKRLQVQAKGPGVVTAGDISESAGIEILNKDHVLCHLDEG 123

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
           A + MELTV+ G GYV A+ ++ E+ PIG++ IDA+YSP+KKVSY V+  REGQVLDYDK
Sbjct: 124 AELYMELTVNTGKGYVAAEKNKPEDAPIGMMAIDAIYSPVKKVSYDVQPTREGQVLDYDK 183

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L+M ++TDGSIT +D+VA A+RILQDQL +F+NF+EP+     + +   L FNP LLKKV
Sbjct: 184 LTMKVETDGSITPDDAVAFAARILQDQLSIFVNFDEPESAQAANDD-DGLEFNPLLLKKV 242

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           +ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGRKSL EIK VL  MGL LGM+
Sbjct: 243 DELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRKSLNEIKEVLSGMGLHLGMD 302

Query: 321 LPDWPPESIEELAKKYED 338
           + DWPP++IE+LAKK+ED
Sbjct: 303 VEDWPPDNIEDLAKKFED 320


>gi|58038831|ref|YP_190795.1| DNA-directed RNA polymerase subunit alpha [Gluconobacter oxydans
           621H]
 gi|81557187|sp|Q5FU07|RPOA_GLUOX RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|58001245|gb|AAW60139.1| DNA-directed RNA polymerase alpha chain [Gluconobacter oxydans
           621H]
          Length = 339

 Score =  402 bits (1033), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 197/338 (58%), Positives = 259/338 (76%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++QKNWQ LIKP  +E +  G        ++AEPL RGF  TLGNALRR+L+SSL+GAA+
Sbjct: 2   VLQKNWQSLIKPEKLE-VEPGPVASRIATVVAEPLERGFGMTLGNALRRILLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGVLHE S++ GV ED+TDI+LN+K + L+M G+  KR+ +   GPG VTAG IQ
Sbjct: 61  TAIQIDGVLHEFSAVPGVREDVTDIVLNVKQLALRMHGEGPKRMILTATGPGEVTAGQIQ 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             +DIE++NPD VIC LD    + ME TV+ G GYV A  +R E+ PIGLI IDA+YSP+
Sbjct: 121 AGHDIEIMNPDLVICTLDDGVKLGMEFTVNMGKGYVAAAANRPEDAPIGLIPIDAIYSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY +E  R GQV DYDKL +T++T+G++T EDS+ALA+RILQDQL +FINF+EP+  
Sbjct: 181 RRVSYKIEQTRVGQVTDYDKLLLTVETNGAVTPEDSLALAARILQDQLQLFINFDEPRP- 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V+ +     LPFN  LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q++E +MLR  NFGR
Sbjct: 240 VQHEEPQDDLPFNRNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKSEQEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++P WPPE+IE+LAK+ ++
Sbjct: 300 KSLNEIKEVLTGMGLSLGMSVPAWPPENIEDLAKRLDE 337


>gi|296282607|ref|ZP_06860605.1| DNA-directed RNA polymerase subunit alpha [Citromicrobium
           bathyomarinum JL354]
          Length = 352

 Score =  399 bits (1026), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 200/342 (58%), Positives = 254/342 (74%), Gaps = 8/342 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KP ++E    G +++ +   +AEPL RGF  TLGNALRRVL+SSL+GAAIT++
Sbjct: 6   KNWQELKKPTSLELKDTGADKKRKATFVAEPLERGFGLTLGNALRRVLLSSLQGAAITSI 65

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LN+K I LKM G+  KR+ +   GPG V AGDI    
Sbjct: 66  KIENVLHEFSSLAGVREDVTDIVLNVKQIALKMEGEGPKRLQLSATGPGAVKAGDIAVSG 125

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIE+LN D VIC LD  A + MELT   G GYVPA  +R  + PIGLI +D+LYSPIK+V
Sbjct: 126 DIEILNKDLVICQLDEGATLNMELTADTGKGYVPAVQNRPADAPIGLIPVDSLYSPIKQV 185

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE--PKKE- 240
           SY VE+AR GQ LDYDKL++TI+TDG++T ED+VA A+RILQDQL +F++FE+  P+   
Sbjct: 186 SYKVENARVGQELDYDKLNLTIETDGTVTPEDAVAYAARILQDQLTLFVHFEDGIPQPSS 245

Query: 241 -----VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
                  E     +   N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+MLR 
Sbjct: 246 PMIGMAAEPQESDANQLNRYLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEMLRT 305

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
            NFGRKSL EIK VL +MGL LGM++P WPPE+IEE+AKK E
Sbjct: 306 PNFGRKSLNEIKEVLSSMGLRLGMDIPGWPPENIEEMAKKLE 347


>gi|262277117|ref|ZP_06054910.1| DNA-directed RNA polymerase, alpha subunit [alpha proteobacterium
           HIMB114]
 gi|262224220|gb|EEY74679.1| DNA-directed RNA polymerase, alpha subunit [alpha proteobacterium
           HIMB114]
          Length = 338

 Score =  398 bits (1022), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 189/340 (55%), Positives = 262/340 (77%), Gaps = 5/340 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI+KNW+EL+KP+ ++  V   ++++   +  EPL +GFA TLGNALRR+L+SS++G A+
Sbjct: 1   MIEKNWKELVKPSKLD--VQTNDDKSYAKITIEPLEKGFALTLGNALRRILLSSIQGTAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGV+HE SSI GV ED+TDI+LNIK ++LK+     K++ +  +GPG + A D++
Sbjct: 59  TAIQIDGVVHEFSSINGVREDVTDIVLNIKALSLKLKNPGPKKLVLDAQGPGEIKAKDLK 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DIE+LNP+ VICNLD +  + MELTV+ G GYV A+ +R ++ P+GLI +D++YSP+
Sbjct: 119 ESADIEILNPEQVICNLDDNTKIYMELTVNTGKGYVSAEKNREKDSPLGLIPVDSVYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VSY V   REG  +DYDKL+M ++T+GS+  ED VA A+RILQDQLGMFINFEEPK+ 
Sbjct: 179 KRVSYNVSETREGLSIDYDKLTMEVETNGSVEAEDCVAYAARILQDQLGMFINFEEPKEA 238

Query: 241 VKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           V +    KS P FN  LL++V+ELELSVRS NCL+ +NI+Y+GDL+Q+TE +MLR  NFG
Sbjct: 239 VAQ--QTKSEPEFNKNLLRRVDELELSVRSMNCLKNDNIIYIGDLVQKTEGEMLRTPNFG 296

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           RKSL EIK VL  M L+LG+ +P+WPPE+I EL+KK E++
Sbjct: 297 RKSLNEIKEVLSGMSLYLGIEIPNWPPENIAELSKKLEEE 336


>gi|85709029|ref|ZP_01040095.1| DNA-directed RNA polymerase alpha subunit [Erythrobacter sp. NAP1]
 gi|85690563|gb|EAQ30566.1| DNA-directed RNA polymerase alpha subunit [Erythrobacter sp. NAP1]
          Length = 351

 Score =  396 bits (1017), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 201/345 (58%), Positives = 258/345 (74%), Gaps = 15/345 (4%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN +E I  G +++ +T  +AEPL RGF  TLGNALRRVL+SSL+GAAIT++
Sbjct: 6   KNWQELKKPNALE-IKEGGDKQRKTTFVAEPLERGFGLTLGNALRRVLLSSLQGAAITSI 64

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LN+K I LKM G+  KR+ +   GP  VTAGDI    
Sbjct: 65  KIENVLHEFSSLAGVREDVTDIVLNVKQIALKMEGEGPKRLQLSMTGPAEVTAGDIAVTG 124

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+N D V+C+LD  A + MELT   G GY PA  +R  + PIGLI +D+LYSP+++V
Sbjct: 125 DIEVMNKDLVLCHLDEGATLNMELTADVGKGYSPAVQNRPADAPIGLIPVDSLYSPVRQV 184

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKK 239
           SY VE+AR GQ LDYDKLS+TI+TDG++T ED+VA A+RILQDQL +F++FE    +P+ 
Sbjct: 185 SYKVENARVGQELDYDKLSLTIETDGTVTPEDAVAYAARILQDQLTLFVHFEDGIPQPQS 244

Query: 240 EVKEDINVKSLP-------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            +   I   + P        N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+M
Sbjct: 245 AM---IGQAATPQEDDANQLNRYLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEM 301

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
           LR  NFGRKSL EIK VL +MGL LGM++P WPPE+IEE+AKK E
Sbjct: 302 LRTPNFGRKSLNEIKEVLSSMGLRLGMDIPGWPPENIEEMAKKLE 346


>gi|87200540|ref|YP_497797.1| DNA-directed RNA polymerase subunit alpha [Novosphingobium
           aromaticivorans DSM 12444]
 gi|119366705|sp|Q2G5B0|RPOA_NOVAD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|87136221|gb|ABD26963.1| DNA-directed RNA polymerase subunit alpha [Novosphingobium
           aromaticivorans DSM 12444]
          Length = 353

 Score =  395 bits (1016), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 201/347 (57%), Positives = 258/347 (74%), Gaps = 13/347 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPNN+E I  G + + R   +AEPL RGF  TLGNALRRVL+SSL+GAA+T++
Sbjct: 6   KNWQELKKPNNLE-IKPGNDSKRRATFVAEPLERGFGLTLGNALRRVLLSSLQGAAVTSI 64

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LN+K I LKM G+  KR+ +   GPG V AGDI    
Sbjct: 65  KIENVLHEFSSLAGVREDVTDIVLNVKQIALKMQGEGPKRLQLSATGPGEVKAGDIAVTG 124

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+N D VIC+LD  A   MELTV  G GYVPA  +R  + PIGLI +D+LYSP+++V
Sbjct: 125 DIEVMNKDLVICHLDEGATFNMELTVDTGKGYVPAVSNRPVDAPIGLIPVDSLYSPVRQV 184

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VE+AR GQ LDYDKL++T++TDG++T ED+VA A+RILQDQL +F++F++ +  V  
Sbjct: 185 SYKVENARIGQELDYDKLNLTVETDGTVTPEDAVAYAARILQDQLALFVHFDD-QVPVGH 243

Query: 244 DINVKSLP-----------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
              V  +P            N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+M
Sbjct: 244 VPMVAGVPAHAPEESDANQLNRYLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEM 303

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           LR  NFGRKSL EIK VL +MGL LGM++P WPPE+IEE+AKK E +
Sbjct: 304 LRTPNFGRKSLNEIKEVLSSMGLRLGMDIPGWPPENIEEMAKKLEQE 350


>gi|94496225|ref|ZP_01302803.1| DNA-directed RNA polymerase, alpha subunit [Sphingomonas sp. SKA58]
 gi|94424404|gb|EAT09427.1| DNA-directed RNA polymerase, alpha subunit [Sphingomonas sp. SKA58]
          Length = 350

 Score =  394 bits (1013), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 200/349 (57%), Positives = 255/349 (73%), Gaps = 20/349 (5%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN++E    G  +   T  +AEPL RGF  TLGNALRRVL+SSL+GAA+T++
Sbjct: 2   KNWQELKKPNSLEIKASGDGKRKATF-VAEPLERGFGLTLGNALRRVLLSSLQGAAVTSI 60

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LNIK + LKM G+  KR+ +   GP VV AGDI  V 
Sbjct: 61  KIENVLHEFSSLTGVREDVTDIVLNIKQVALKMEGEGPKRLQLSATGPAVVKAGDISVVG 120

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+NPD VIC+LD  A + MELT   G GYVPA  +R  + PIGLI +DALYSP+++V
Sbjct: 121 DIEVMNPDLVICHLDQGATLNMELTADVGKGYVPAVANRPADAPIGLIPVDALYSPVRQV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP------ 237
           +Y V++ R GQ LDYDKLS+T++TDG++T ED+VA A+RILQDQL +F++FE+       
Sbjct: 181 AYKVDNTRVGQELDYDKLSLTLETDGTVTPEDAVAYAARILQDQLQLFVHFEDALPAAAP 240

Query: 238 ---------KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
                      E + D N      N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+T
Sbjct: 241 ATGHAAGAAASEGESDAN----QINRYLLKKVDELELSVRSANCLKNDNIIYIGDLVQKT 296

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
           EA+MLR  NFGRKSL EIK VL +MGL LGM++P WPPE+IEE+AKK E
Sbjct: 297 EAEMLRTPNFGRKSLNEIKEVLSSMGLRLGMDIPGWPPENIEEMAKKLE 345


>gi|71083781|ref|YP_266501.1| DNA-directed RNA polymerase subunit alpha [Candidatus Pelagibacter
           ubique HTCC1062]
 gi|91763183|ref|ZP_01265147.1| DNA-directed RNA polymerase alpha subunit [Candidatus Pelagibacter
           ubique HTCC1002]
 gi|90110855|sp|Q4FLP1|RPOA_PELUB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|71062894|gb|AAZ21897.1| DNA-directed RNA polymerase [Candidatus Pelagibacter ubique
           HTCC1062]
 gi|91717596|gb|EAS84247.1| DNA-directed RNA polymerase alpha subunit [Candidatus Pelagibacter
           ubique HTCC1002]
          Length = 342

 Score =  394 bits (1012), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 190/338 (56%), Positives = 260/338 (76%), Gaps = 7/338 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNW+ LIKP  ++  +   ++++   +IAEPL +G+  TLGN+LRR+L+SS+RGAA+T++
Sbjct: 9   KNWKALIKPAQLDVKI--SDDKSHAKIIAEPLEKGYGLTLGNSLRRILLSSIRGAAVTSI 66

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           QIDGVLHE +SIKGV ED+TDI+LN+K + LK S ++ K++ +  +GPG + A DI  V 
Sbjct: 67  QIDGVLHEFTSIKGVREDVTDIVLNVKSLALKSSSETTKKLILDAKGPGEIKASDIAPVA 126

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIE+LNPD VICNLD +    ME+ V  G GYVPA  ++ E  P+GLI ID+LYSP+KKV
Sbjct: 127 DIEILNPDLVICNLDENTHFHMEMNVGTGKGYVPAVMNKPEEPPLGLIAIDSLYSPVKKV 186

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP-KKEVK 242
           SY++ +AREG+ LDYDKL M ++T+GSI+ ED+VA ++RI QDQL MF+NF+EP +  VK
Sbjct: 187 SYSISTAREGKALDYDKLIMEVETNGSISAEDAVAYSARIFQDQLNMFVNFDEPVEVPVK 246

Query: 243 EDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           E   V S P FN  LL+KV+ELELSVRS NCL+ +NI+Y+GDL+Q++E +MLR  NFGRK
Sbjct: 247 E---VSSEPEFNKNLLRKVDELELSVRSMNCLKNDNIIYIGDLVQKSEGEMLRTPNFGRK 303

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           SL EIK VL  M L+LGM +P+WPPE+I E++KK E++
Sbjct: 304 SLNEIKEVLTGMSLYLGMEIPNWPPENIAEMSKKLEEQ 341


>gi|330814176|ref|YP_004358415.1| DNA-directed RNA polymerase alpha subunit [Candidatus Pelagibacter
           sp. IMCC9063]
 gi|327487271|gb|AEA81676.1| DNA-directed RNA polymerase alpha subunit [Candidatus Pelagibacter
           sp. IMCC9063]
          Length = 338

 Score =  394 bits (1011), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 190/340 (55%), Positives = 260/340 (76%), Gaps = 5/340 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW+ELIKP+ I+  +   E++    ++ EPL RGFA TLGNALRRVL+SS++G A+
Sbjct: 1   MIDKNWKELIKPSKID--IQASEDKKFAKIVVEPLERGFALTLGNALRRVLLSSIQGTAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGVLHE SSI GV ED+TDI+LNIK ++LK++ +  K++ +  +GPG +TA  I 
Sbjct: 59  TAIQIDGVLHEFSSINGVREDVTDIVLNIKSLSLKLNTNGPKKLILDAKGPGEITAKMIN 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DIE+LNPD VICNLD ++ V ME  V+ G GYV A  +R ++ P+GLI ID++YSP+
Sbjct: 119 PNPDIEILNPDQVICNLDENSKVYMEFVVNTGKGYVSADKNREKDSPLGLIPIDSVYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VSY V + REG  +DYDKL+M I+T+GS+  +D +A A+RILQDQL +F+NF+EPK+ 
Sbjct: 179 KRVSYNVSNTREGLSIDYDKLTMEIETNGSVASDDCLAFAARILQDQLSLFVNFDEPKEV 238

Query: 241 VKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           V +    +S P FN  LL++V+ELELSVRS NCL+ +NI+Y+GDL+Q+TE +MLR  NFG
Sbjct: 239 VVQP--TQSEPEFNKNLLRRVDELELSVRSMNCLKNDNIIYIGDLVQKTEGEMLRTPNFG 296

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           RKSL EIK V+  M L+LG+ +P+WPPE+I EL+KK ED+
Sbjct: 297 RKSLNEIKEVISGMSLYLGIEIPNWPPENISELSKKLEDE 336


>gi|294010565|ref|YP_003544025.1| DNA-directed RNA polymerase alpha subunit [Sphingobium japonicum
           UT26S]
 gi|292673895|dbj|BAI95413.1| DNA-directed RNA polymerase alpha subunit [Sphingobium japonicum
           UT26S]
          Length = 354

 Score =  393 bits (1010), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 198/345 (57%), Positives = 253/345 (73%), Gaps = 12/345 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN++E  V G      T  +AEPL RGF  TLGNALRRVL+SSL+GAA+T++
Sbjct: 6   KNWQELKKPNSLEIKVAGDGRRKATF-VAEPLERGFGLTLGNALRRVLLSSLQGAAVTSI 64

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LNIK + L+M GD  +R+ +   GP  V AGDI TV 
Sbjct: 65  KIENVLHEFSSLAGVREDVTDIVLNIKQVALRMEGDGPRRLQLSATGPAEVRAGDITTVG 124

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+NPD VIC+LD  A + MELT   G GYVPA  +R  + PIGLI IDALYSP+++V
Sbjct: 125 DIEVMNPDLVICHLDQGATLNMELTADVGKGYVPAVANRPADAPIGLIPIDALYSPVRQV 184

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP------ 237
           +Y V++ R GQ LDYDKLS+T++TDG++T ED+VA A+RILQDQL +F++FE+       
Sbjct: 185 AYKVDNTRVGQELDYDKLSLTVETDGTVTPEDAVAYAARILQDQLQLFVHFEDALPAAAP 244

Query: 238 -----KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                      +    +   N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+M
Sbjct: 245 AAGAAAGGSASEGESDANQINRYLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEM 304

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
           LR  NFGRKSL EIK VL +MGL LGM++P WPPE+IEE+AKK E
Sbjct: 305 LRTPNFGRKSLNEIKEVLSSMGLRLGMDIPGWPPENIEEMAKKLE 349


>gi|103486058|ref|YP_615619.1| DNA-directed RNA polymerase subunit alpha [Sphingopyxis alaskensis
           RB2256]
 gi|119366731|sp|Q1GVN6|RPOA_SPHAL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|98976135|gb|ABF52286.1| DNA-directed RNA polymerase, alpha subunit [Sphingopyxis alaskensis
           RB2256]
          Length = 352

 Score =  393 bits (1009), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 197/347 (56%), Positives = 257/347 (74%), Gaps = 18/347 (5%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NWQEL KP+N+E I  G + + +   +AEPL RGF  TLGNALRRVL+SSL+GAAIT++
Sbjct: 6   RNWQELKKPSNLE-IKTGGDGKRKATFVAEPLERGFGLTLGNALRRVLLSSLQGAAITSI 64

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LN+K I LKM G+  KR+ +   GP  V AGDI    
Sbjct: 65  KIENVLHEFSSLAGVREDVTDIVLNVKQIALKMEGEGPKRLQLSATGPATVKAGDIMVSG 124

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DI+V+NP+HVIC+LD  A + MEL    G GYVPA  +R  + PIGLI +D+LYSP+++V
Sbjct: 125 DIKVMNPNHVICHLDEGATLNMELVADTGKGYVPATANRPADAPIGLIPVDSLYSPVRQV 184

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE------- 236
           +Y V++AR GQ LDYDKL++T++TDG++T ED+VA A+RILQDQL +F++FEE       
Sbjct: 185 AYKVDNARIGQELDYDKLNLTVETDGTVTPEDAVAYAARILQDQLQVFVHFEEAMSDSGL 244

Query: 237 -----PKKEVKE-DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
                P     E D+N      N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA
Sbjct: 245 IGMAAPSAASDESDVN----QLNRFLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEA 300

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
           +MLR  NFGRKSL EIK VL +MGL LGM++P WPPE+IEE+AKK E
Sbjct: 301 EMLRTPNFGRKSLNEIKEVLSSMGLRLGMDIPGWPPENIEEMAKKLE 347


>gi|307294931|ref|ZP_07574773.1| DNA-directed RNA polymerase, alpha subunit [Sphingobium
           chlorophenolicum L-1]
 gi|306879405|gb|EFN10623.1| DNA-directed RNA polymerase, alpha subunit [Sphingobium
           chlorophenolicum L-1]
          Length = 354

 Score =  393 bits (1009), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 198/345 (57%), Positives = 253/345 (73%), Gaps = 12/345 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN++E  V G      T  +AEPL RGF  TLGNALRRVL+SSL+GAA+T++
Sbjct: 6   KNWQELKKPNSLEIKVSGDGRRKATF-VAEPLERGFGLTLGNALRRVLLSSLQGAAVTSI 64

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LNIK + L+M GD  +R+ +   GP  V AGDI TV 
Sbjct: 65  KIENVLHEFSSLAGVREDVTDIVLNIKQVALRMEGDGPRRLQLSATGPAEVRAGDITTVG 124

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+NPD VIC+LD  A + MELT   G GYVPA  +R  + PIGLI IDALYSP+++V
Sbjct: 125 DIEVMNPDLVICHLDQGATLNMELTADVGKGYVPAVANRPADAPIGLIPIDALYSPVRQV 184

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP------ 237
           +Y V++ R GQ LDYDKLS+T++TDG++T ED+VA A+RILQDQL +F++FE+       
Sbjct: 185 AYKVDNTRVGQELDYDKLSLTVETDGTVTPEDAVAYAARILQDQLQLFVHFEDALPAAAP 244

Query: 238 -----KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                      +    +   N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+M
Sbjct: 245 AAGAAAGGSASEGESDANQINRYLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEM 304

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
           LR  NFGRKSL EIK VL +MGL LGM++P WPPE+IEE+AKK E
Sbjct: 305 LRTPNFGRKSLNEIKEVLSSMGLRLGMDIPGWPPENIEEMAKKLE 349


>gi|326387079|ref|ZP_08208689.1| DNA-directed RNA polymerase subunit alpha [Novosphingobium
           nitrogenifigens DSM 19370]
 gi|326208260|gb|EGD59067.1| DNA-directed RNA polymerase subunit alpha [Novosphingobium
           nitrogenifigens DSM 19370]
          Length = 353

 Score =  391 bits (1005), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 200/348 (57%), Positives = 258/348 (74%), Gaps = 15/348 (4%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN++E +  G + + R   IAEPL RGF  TLGNALRRVL+SSL+GAA+T++
Sbjct: 6   KNWQELKKPNSLE-VKPGNDPQRRATFIAEPLERGFGLTLGNALRRVLLSSLQGAAVTSI 64

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LN+K I LKM G+  KR+ +   GPG V AGDI    
Sbjct: 65  RIENVLHEFSSLAGVREDVTDIVLNVKQIALKMQGEGPKRLQLSATGPGEVRAGDIAVTG 124

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+N D VIC+LD  A   MELT   G GYVPA  +R  + PIGLI ID+LYSP+++V
Sbjct: 125 DIEVMNKDLVICHLDEGATFNMELTADTGKGYVPAVSNRPIDAPIGLIPIDSLYSPVRQV 184

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE--PKKEV 241
           SY V++AR GQ LDYDKL++T++TDG++T ED+VA A+RILQDQL +F++F++  P   V
Sbjct: 185 SYKVDNARIGQELDYDKLNLTVETDGTVTPEDAVAYAARILQDQLSLFVHFDDQLPTGHV 244

Query: 242 K----------EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
                      E+ +   L  N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+
Sbjct: 245 AVVSGLATHAPEESDANQL--NRYLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAE 302

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           MLR  NFGRKSL EIK VL +MGL LGM++P WPPE+IEE+AKK E +
Sbjct: 303 MLRTPNFGRKSLNEIKEVLSSMGLRLGMDIPGWPPENIEEMAKKLEQE 350


>gi|149184338|ref|ZP_01862656.1| DNA-directed RNA polymerase subunit alpha [Erythrobacter sp. SD-21]
 gi|148831658|gb|EDL50091.1| DNA-directed RNA polymerase subunit alpha [Erythrobacter sp. SD-21]
          Length = 351

 Score =  390 bits (1003), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 199/342 (58%), Positives = 255/342 (74%), Gaps = 9/342 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN ++ I  G ++  +   +AEPL RGF  TLGNALRRVL+SSL+GAAIT++
Sbjct: 6   KNWQELKKPNTLD-IKDGGDKGRKATFVAEPLERGFGLTLGNALRRVLLSSLQGAAITSI 64

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LN+K I LKM G+  KR+ +   GPG V AGDI    
Sbjct: 65  KIENVLHEFSSLAGVREDVTDIVLNVKQIALKMEGEGLKRLQLSATGPGEVKAGDIAVTG 124

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+N D VIC+LD  A + MELT   G GY PA  +R  + PIGLI +D+LYSP+++V
Sbjct: 125 DIEVMNKDLVICHLDEGATLNMELTADSGKGYRPAVMNRPVDAPIGLIPVDSLYSPVRQV 184

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE--PKK-- 239
           SY VE+AR GQ LDYDKLS+TI+TDG++T ED+VA A+RILQDQL +F++FE+  P+   
Sbjct: 185 SYKVENARVGQELDYDKLSLTIETDGTVTPEDAVAYAARILQDQLTLFVHFEDGIPQPSS 244

Query: 240 ----EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
               +  E     +   N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+MLR 
Sbjct: 245 AMIGQAAEPQESDTNQLNRYLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEMLRT 304

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
            NFGRKSL EIK VL +MGL LGM++P WPPE+IEE+AKK E
Sbjct: 305 PNFGRKSLNEIKEVLSSMGLRLGMDIPGWPPENIEEMAKKLE 346


>gi|254455604|ref|ZP_05069033.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Pelagibacter
           sp. HTCC7211]
 gi|207082606|gb|EDZ60032.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Pelagibacter
           sp. HTCC7211]
          Length = 342

 Score =  389 bits (999), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 185/337 (54%), Positives = 259/337 (76%), Gaps = 7/337 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNW+ LIKP+ ++  +   ++     +IAEPL +G+  TLGN+LRR+L+SS+RGAA+T++
Sbjct: 9   KNWKSLIKPSKLDVQI--SDDLTHAKIIAEPLEKGYGLTLGNSLRRILLSSIRGAAVTSI 66

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           QIDGVLHE +SIKGV ED+TDI+LN+K + LK + +  K++ +  +GPG + A DI  V 
Sbjct: 67  QIDGVLHEFTSIKGVREDVTDIVLNVKSLALKSNSEGTKKLVLDAKGPGEIKASDIAPVA 126

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           D+E+LNPD VICNLD +    ME+ V+ G GYVPA  ++ E  P+GLI ID+LYSP+KKV
Sbjct: 127 DVEILNPDLVICNLDENTNFHMEMNVNTGKGYVPADLNKPEEPPLGLIAIDSLYSPVKKV 186

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP-KKEVK 242
           SY++ +AREG+ LDYDKL+M ++T+G+I+ ED+VA ++RI QDQL MF+NF+EP +  VK
Sbjct: 187 SYSISTAREGKALDYDKLTMEVETNGAISAEDAVAYSARIFQDQLKMFVNFDEPVEAPVK 246

Query: 243 EDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           E   V + P FN  LL+KV+ELELSVRS NCL+ +NI+Y+GDL+Q++E +MLR  NFGRK
Sbjct: 247 E---VSTEPEFNKNLLRKVDELELSVRSMNCLKNDNIIYIGDLVQKSEGEMLRTPNFGRK 303

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  M L+LGM +P+WPP++I E++KK E+
Sbjct: 304 SLNEIKEVLTGMSLYLGMEIPNWPPDNIAEMSKKLEE 340


>gi|56551437|ref|YP_162276.1| DNA-directed RNA polymerase subunit alpha [Zymomonas mobilis subsp.
           mobilis ZM4]
 gi|241761084|ref|ZP_04759173.1| DNA-directed RNA polymerase, alpha subunit [Zymomonas mobilis
           subsp. mobilis ATCC 10988]
 gi|260752950|ref|YP_003225843.1| DNA-directed RNA polymerase subunit alpha [Zymomonas mobilis subsp.
           mobilis NCIMB 11163]
 gi|61215794|sp|Q5NQ40|RPOA_ZYMMO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|56543011|gb|AAV89165.1| DNA-directed RNA polymerase, alpha subunit [Zymomonas mobilis
           subsp. mobilis ZM4]
 gi|241374703|gb|EER64164.1| DNA-directed RNA polymerase, alpha subunit [Zymomonas mobilis
           subsp. mobilis ATCC 10988]
 gi|258552313|gb|ACV75259.1| DNA-directed RNA polymerase, alpha subunit [Zymomonas mobilis
           subsp. mobilis NCIMB 11163]
          Length = 353

 Score =  389 bits (999), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 199/348 (57%), Positives = 255/348 (73%), Gaps = 13/348 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN +E    G  +   T  +AEPL RGF  TLGNALRRVL+SSL+GAAITA+
Sbjct: 6   KNWQELKKPNALEKKASGNGKCKATF-VAEPLERGFGLTLGNALRRVLLSSLQGAAITAI 64

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LNIK + +KM GD  +R+ I + GPGVVTAGDI    
Sbjct: 65  KIENVLHEFSSLNGVREDVTDIVLNIKQVAIKMQGDGSRRLHISRTGPGVVTAGDIAVSG 124

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+NP+ VIC+LD  AV   ELTV  G GYV A  +R  + PIGLI +DALYSP+++V
Sbjct: 125 DIEVMNPELVICHLDQGAVFNAELTVDTGKGYVAAVANRPADAPIGLIPVDALYSPVRQV 184

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE----PKK 239
           +Y VE+AR GQ LDYDKL +TI+TDG+I+ ED++A ++RILQDQL +F++F++    P  
Sbjct: 185 AYKVENARVGQELDYDKLLLTIETDGTISPEDAIAYSARILQDQLQLFVHFDDGLAPPTS 244

Query: 240 EVKE--------DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
            + +        +    +   N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+
Sbjct: 245 AIGQSSLPSSSSEAENSANQLNRNLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAE 304

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           MLR  NFGRKSL EIK VL  MGL LGM +P WPPE+IEE+AKK E +
Sbjct: 305 MLRTPNFGRKSLNEIKEVLSGMGLRLGMEIPGWPPENIEEMAKKLEQE 352


>gi|85374439|ref|YP_458501.1| DNA-directed RNA polymerase subunit alpha [Erythrobacter litoralis
           HTCC2594]
 gi|123099515|sp|Q2N9D7|RPOA_ERYLH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|84787522|gb|ABC63704.1| DNA-directed RNA polymerase alpha subunit [Erythrobacter litoralis
           HTCC2594]
          Length = 351

 Score =  387 bits (994), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 197/345 (57%), Positives = 254/345 (73%), Gaps = 15/345 (4%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KP  ++ +    ++  +   IAEPL RG+  TLGNALRRVL++SL+GAAIT++
Sbjct: 6   KNWQELKKPTQLD-VKESSDKARKATFIAEPLERGYGLTLGNALRRVLLASLQGAAITSI 64

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LN+K I LKM G+  KR+ +   GP  V AGDI    
Sbjct: 65  KIENVLHEFSSLAGVREDVTDIVLNVKQIALKMEGEGPKRLQLSATGPAEVKAGDIAVSG 124

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+N D VIC+LD  A + MELT   G GYVPA  +R  + PIGLI +D+LYSPI++V
Sbjct: 125 DIEVMNKDLVICHLDEGATLNMELTADIGSGYVPAVQNRPADAPIGLIPVDSLYSPIRQV 184

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKK 239
           SY VE AR GQ LD+DKLS+TI+TDG++T ED+VA A+RILQDQL +F++FE    +P+ 
Sbjct: 185 SYKVEKARVGQELDFDKLSLTIETDGTVTPEDAVAYAARILQDQLTLFVHFEDGIPQPQS 244

Query: 240 EVKEDINVKSLP-------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            +   I V + P        N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+M
Sbjct: 245 AM---IGVAAEPQQDDANQLNRYLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEM 301

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
           LR  NFGRKSL EIK VL +MGL LGM++P WPPE+IEE+AKK E
Sbjct: 302 LRTPNFGRKSLNEIKEVLSSMGLRLGMDIPGWPPENIEEMAKKLE 346


>gi|332186889|ref|ZP_08388631.1| DNA-directed RNA polymerase, alpha subunit [Sphingomonas sp. S17]
 gi|332013222|gb|EGI55285.1| DNA-directed RNA polymerase, alpha subunit [Sphingomonas sp. S17]
          Length = 354

 Score =  381 bits (978), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 188/346 (54%), Positives = 249/346 (71%), Gaps = 14/346 (4%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN +E    G + + +   +AEPL RGF  TLGNALRRVL+SSL+GAA+T++
Sbjct: 6   KNWQELKKPNALEK--KGGDGKRKATFVAEPLERGFGLTLGNALRRVLLSSLQGAAVTSI 63

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LN+K + ++M G+  KR+ +   GP  V AGDI    
Sbjct: 64  KIENVLHEFSSLAGVREDVTDIVLNVKQLAIRMQGEGPKRLQLSATGPTTVKAGDIAVSG 123

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+N D VIC+LD  A + MELT   G GYVPA  +R  + PIGLI +DALYSP+++V
Sbjct: 124 DIEVMNKDLVICHLDEGATLNMELTADIGKGYVPAASNRPADAPIGLIPVDALYSPVRQV 183

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY V+  R GQ LDYDKL+++++TDG++T ED+VA A+RILQDQL +F++F++       
Sbjct: 184 SYKVDPTRVGQDLDYDKLTLSVETDGTVTPEDAVAYAARILQDQLALFVHFDDSALTRAA 243

Query: 244 DINVKSLP------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
            +   ++P             N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+ +TEA+
Sbjct: 244 PVGQAAIPAAGGEPQSDAQQINRYLLKKVDELELSVRSANCLKNDNIIYIGDLVGKTEAE 303

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
           MLR  NFGRKSL EIK VL +MGL LGM +P WPPE+IEE+AKK E
Sbjct: 304 MLRTPNFGRKSLNEIKEVLSSMGLRLGMEIPGWPPENIEEMAKKLE 349


>gi|294085982|ref|YP_003552742.1| DNA-directed RNA polymerase subunit alpha [Candidatus
           Puniceispirillum marinum IMCC1322]
 gi|292665557|gb|ADE40658.1| DNA-directed RNA polymerase, alpha subunit [Candidatus
           Puniceispirillum marinum IMCC1322]
          Length = 338

 Score =  380 bits (975), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 187/338 (55%), Positives = 256/338 (75%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI+KNW +L KP+ +E I + +   ++ ++   P  RGF  T+GNALRRVL+SSL+G+AI
Sbjct: 1   MIEKNWLDLKKPDELE-IKVSEYNPSQAVVAVGPFERGFGVTIGNALRRVLLSSLQGSAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQI GV+HE SSI GV ED+TD++LN+KG+ ++   +  KR+ +   GP  VTAG I 
Sbjct: 60  TAVQIQGVVHEFSSIPGVREDVTDLVLNLKGVAVRKDEEGSKRLRLSAEGPLAVTAGMIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               +E++NPDHV+C+LD  A + MELTV+ G GYVPA  +R+E+ PIGLI IDA++SP+
Sbjct: 120 ESAGVEIMNPDHVLCHLDKGASLAMELTVASGKGYVPAVANRSEDSPIGLIPIDAIFSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            +V+Y VE+AR GQ+ DYDKL +T++TDGS+T ED+VA A+RILQ+QL  FINFEEPK  
Sbjct: 180 LQVAYKVENARVGQITDYDKLLLTLETDGSVTPEDAVAYAARILQEQLQTFINFEEPKSN 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             +D +   LPF+  LL+KV+ELELSVRS NCL+ +NIVY+GDL+ +TE +MLR  NFGR
Sbjct: 240 T-QDEDPDPLPFSRNLLRKVDELELSVRSANCLKNDNIVYIGDLVLKTEHEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  M L LGM++ +WPPE++EELA++ ++
Sbjct: 299 KSLNEIKEVLKGMELELGMDIANWPPENVEELARRLDE 336


>gi|254701949|ref|ZP_05163777.1| DNA-directed RNA polymerase subunit alpha [Brucella suis bv. 5 str.
           513]
          Length = 267

 Score =  378 bits (971), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 178/267 (66%), Positives = 222/267 (83%), Gaps = 1/267 (0%)

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           SSI GV ED+TDI+LNIK I ++M G+  KR+ + K GPGVVTAGDIQTV D+E+LNP+H
Sbjct: 1   SSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKEGPGVVTAGDIQTVGDVEILNPEH 60

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           VIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP++KVSY +E+ RE
Sbjct: 61  VICTLDEGAEIRMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPVRKVSYKIENTRE 120

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           GQVLDYDKL++ I+T+GS+TGED+VA A+RILQDQL +F+NFEEP+KE  ++  V  L F
Sbjct: 121 GQVLDYDKLTLNIETNGSVTGEDAVAYAARILQDQLSIFVNFEEPQKEAPQE-QVAELAF 179

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           NPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGRKSL EIK VL +
Sbjct: 180 NPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRKSLNEIKEVLAS 239

Query: 313 MGLFLGMNLPDWPPESIEELAKKYEDK 339
           MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 240 MGLHLGMEIPAWPPENIEDLAKRYEDQ 266


>gi|157804011|ref|YP_001492560.1| DNA-directed RNA polymerase subunit alpha [Rickettsia canadensis
           str. McKiel]
 gi|166229278|sp|A8EZJ2|RPOA_RICCK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|157785274|gb|ABV73775.1| DNA-directed RNA polymerase subunit alpha [Rickettsia canadensis
           str. McKiel]
          Length = 340

 Score =  377 bits (968), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 187/339 (55%), Positives = 252/339 (74%), Gaps = 7/339 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y  +  E  N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNALIKPNKVAYENVS-ETNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE S+I GV ED++++ILNIKGI +KM     + + +   GP VVTAG I+T
Sbjct: 63  SIKIPAIEHEFSAIPGVKEDVSEMILNIKGIEVKMYVAEKRIIKLKAIGPCVVTAGMIET 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNPDHVICNL  +  + MELT   G GYV + +   +N PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPDHVICNLAKNKQLEMELTCKVGKGYVLSTNSYADNLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK--K 239
            V+Y VE+ R GQV DYDKL M ++T+G +  E +V LA+RILQ+QL +FI+FEE +  K
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDLLPEMAVGLAARILQEQLQLFISFEEQEEDK 242

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           +VK D    +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTEADMLR  NFG
Sbjct: 243 QVKTD----ALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTEADMLRTPNFG 298

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           RKSL EIK +L  + L  GM++PDWPPE+I+EL+K+YED
Sbjct: 299 RKSLNEIKEILAKLNLRFGMDVPDWPPENIQELSKRYED 337


>gi|157828836|ref|YP_001495078.1| DNA-directed RNA polymerase subunit alpha [Rickettsia rickettsii
           str. 'Sheila Smith']
 gi|165933563|ref|YP_001650352.1| DNA-directed RNA polymerase subunit alpha [Rickettsia rickettsii
           str. Iowa]
 gi|166229279|sp|A8GT45|RPOA_RICRS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|189043844|sp|B0BUN6|RPOA_RICRO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|157801317|gb|ABV76570.1| DNA-directed RNA polymerase subunit alpha [Rickettsia rickettsii
           str. 'Sheila Smith']
 gi|165908650|gb|ABY72946.1| DNA-directed RNA polymerase alpha chain [Rickettsia rickettsii str.
           Iowa]
          Length = 340

 Score =  377 bits (967), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 187/339 (55%), Positives = 252/339 (74%), Gaps = 7/339 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y     E  N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNKVAYENF-PETNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE SSI GV ED++++ILNIKGI +KM     + + +   GP VVTAG I+T
Sbjct: 63  SIKIPAIEHEFSSIPGVKEDVSEVILNIKGIEVKMHVAEKRIMKLKATGPCVVTAGMIET 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNPDHVIC+L  D  + MELT   G GYV + ++  +N PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPDHVICDLAKDKQLEMELTCKVGKGYVLSTNNYEDNLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK--K 239
            V+Y VE+ R GQV DYDKL M ++T+G++  E +V LA+RILQ+QL +FI+FEE +  K
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGAVLPEMAVGLAARILQEQLQLFISFEEQEEDK 242

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           +VK D    +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTEADMLR  NFG
Sbjct: 243 QVKTD----ALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTEADMLRTPNFG 298

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           RKSL EIK +L    L  GM++PDWPPE+++EL+K+YED
Sbjct: 299 RKSLNEIKEILAKFNLRFGMDVPDWPPENMQELSKRYED 337


>gi|15604481|ref|NP_220999.1| DNA-directed RNA polymerase subunit alpha [Rickettsia prowazekii
           str. Madrid E]
 gi|6226040|sp|Q9ZCS9|RPOA_RICPR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|3861175|emb|CAA15075.1| DNA-DIRECTED RNA POLYMERASE ALPHA CHAIN (rpoA) [Rickettsia
           prowazekii]
 gi|292572263|gb|ADE30178.1| DNA-directed RNA polymerase alpha chain [Rickettsia prowazekii
           Rp22]
          Length = 340

 Score =  377 bits (967), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 189/339 (55%), Positives = 248/339 (73%), Gaps = 7/339 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y     E  N+  +I EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNRVTYENF-PETNNKAKIIVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE SSI GV ED++++ILNIKGI +KM     + + +   GP VVTAG I T
Sbjct: 63  SIKIPAIEHEFSSIPGVQEDVSEVILNIKGIEVKMHVSEKRIIKLKAMGPCVVTAGMIDT 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNPDHVICNL  +  + MELT   G GYV + +   +N PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPDHVICNLAKNKQLEMELTCKVGKGYVLSTNSYEDNLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK--K 239
            V+Y VE+ R GQV DYDKL M ++T+G +  E +V LA+RILQ+QL +FI FEE +  K
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDVLPEMAVGLAARILQEQLQLFIAFEEQEEDK 242

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           +VK D    SLPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFG
Sbjct: 243 QVKTD----SLPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFG 298

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           RKSL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 299 RKSLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>gi|34581393|ref|ZP_00142873.1| DNA-directed RNA polymerase alpha chain [Rickettsia sibirica 246]
 gi|28262778|gb|EAA26282.1| DNA-directed RNA polymerase alpha chain [Rickettsia sibirica 246]
          Length = 340

 Score =  375 bits (964), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 187/339 (55%), Positives = 251/339 (74%), Gaps = 7/339 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y  +  E  N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNKVAYENV-PETNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE SSI GV ED++++ILNIKGI +KM     + + +   GP VVTAG I+T
Sbjct: 63  SIKIPAIEHEFSSIPGVKEDVSEVILNIKGIEVKMYVAEKRIMKLKATGPCVVTAGMIET 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNPDHVIC+L  D  + MELT   G GYV + +   +N PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPDHVICDLAKDKQLEMELTCKVGKGYVLSTNSYEDNLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK--K 239
            V+Y VE+ R GQV DYDKL M ++T+G +  E +V LA+RILQ+QL +FI+FEE +  K
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDVLPEMAVGLAARILQEQLQLFISFEEQEEDK 242

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           +VK D    +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFG
Sbjct: 243 QVKTD----ALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFG 298

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           RKSL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 299 RKSLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>gi|15892905|ref|NP_360619.1| DNA-directed RNA polymerase subunit alpha [Rickettsia conorii str.
           Malish 7]
 gi|20139543|sp|Q92GZ0|RPOA_RICCN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|15620096|gb|AAL03520.1| DNA-directed RNA polymerase alpha chain [Rickettsia conorii str.
           Malish 7]
          Length = 340

 Score =  375 bits (963), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 187/339 (55%), Positives = 250/339 (73%), Gaps = 7/339 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y     E  N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNKVAYENF-PETNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE SSI GV ED++++ILNIKGI +KM     + + +   GP VVTAG I+T
Sbjct: 63  SIKIPAIEHEFSSIPGVKEDVSEVILNIKGIEVKMHVAEKRIMKLKATGPCVVTAGMIET 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNPDHVIC+L  D  + MELT   G GYV + +   +N PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPDHVICDLAKDKQLEMELTCKVGKGYVLSTNSYEDNLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK--K 239
            V+Y VE+ R GQV DYDKL M ++T+G +  E +V LA+RILQ+QL +FI+FEE +  K
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDVLPEMAVGLAARILQEQLQLFISFEEQEEDK 242

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           +VK D    +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFG
Sbjct: 243 QVKTD----TLPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFG 298

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           RKSL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 299 RKSLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>gi|148554247|ref|YP_001261829.1| DNA-directed RNA polymerase subunit alpha [Sphingomonas wittichii
           RW1]
 gi|166229281|sp|A5V5X5|RPOA_SPHWW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|148499437|gb|ABQ67691.1| DNA-directed RNA polymerase, alpha subunit [Sphingomonas wittichii
           RW1]
          Length = 353

 Score =  374 bits (960), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 189/346 (54%), Positives = 248/346 (71%), Gaps = 13/346 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN +E    G + + +   +AEPL RGF  TLGN+LRRVL+SSL+GAA+T++
Sbjct: 6   KNWQELKKPNGLEKKS-GGDGKRKATFVAEPLERGFGLTLGNSLRRVLLSSLQGAAVTSI 64

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LN+K I LKM GD  +R+ +   GP  VTAG I    
Sbjct: 65  KIENVLHEFSSLAGVREDVTDIVLNVKQIALKMQGDGPRRLQLSATGPAEVTAGMIAASG 124

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+N D VIC+LD  A + MELT   G GYV A  +R  + PIGLI +DALYSP+++V
Sbjct: 125 DIEVMNTDLVICHLDDGATLNMELTADVGKGYVTAAANRPVDAPIGLIPVDALYSPVRQV 184

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE------- 236
           +Y VE+ R GQ LDYDKL++TI+TDG++T ED++A ++RILQDQL +F++F++       
Sbjct: 185 AYKVENTRVGQELDYDKLTLTIETDGTVTPEDALAYSARILQDQLQLFVHFDDGMAISAP 244

Query: 237 -----PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
                       +    +   N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+
Sbjct: 245 AAGAGAAGGAAGEPEGDANQLNRYLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAE 304

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
           MLR  NFGRKSL EIK VL +MGL LGM +P WPPE+IEE+AKK E
Sbjct: 305 MLRTPNFGRKSLNEIKEVLASMGLRLGMEIPGWPPENIEEMAKKLE 350


>gi|51473815|ref|YP_067572.1| DNA-directed RNA polymerase subunit alpha [Rickettsia typhi str.
           Wilmington]
 gi|61215890|sp|Q68WA2|RPOA_RICTY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|51460127|gb|AAU04090.1| RNA nucleotidyltransferase (DNA-directed) [Rickettsia typhi str.
           Wilmington]
          Length = 340

 Score =  373 bits (957), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 187/339 (55%), Positives = 248/339 (73%), Gaps = 7/339 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y     E  N+  +I EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNRVTYENF-PETNNKAKIIVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE SSI GV ED++++ILNIKGI +KM     + + +   GP VVTAG I T
Sbjct: 63  SIKIPAIEHEFSSIPGVQEDVSEVILNIKGIEVKMHVSEKRIMKLKATGPCVVTAGMIDT 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNP+HVICNL  +  + MELT   G GYV + +   +N PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPNHVICNLAKNKQLEMELTCKVGKGYVLSTNSYEDNLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK--K 239
            V+Y VE+ R GQV DYDKL + ++T+G +  E +V LA+RILQ+QL +FI FEE +  K
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIIFVETNGDVLPEMAVGLAARILQEQLQLFIAFEEQEEDK 242

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           +VK D    SLPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFG
Sbjct: 243 QVKTD----SLPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFG 298

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           RKSL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 299 RKSLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>gi|67458694|ref|YP_246318.1| DNA-directed RNA polymerase subunit alpha [Rickettsia felis
           URRWXCal2]
 gi|75536844|sp|Q4UMQ5|RPOA_RICFE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|67004227|gb|AAY61153.1| DNA-directed RNA polymerase alpha chain [Rickettsia felis
           URRWXCal2]
          Length = 340

 Score =  372 bits (956), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 185/339 (54%), Positives = 249/339 (73%), Gaps = 7/339 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y     E  N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNKVAYENF-PETNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE SSI GV ED++++ILNIKGI +KM     + + +   GP V+TAG I+T
Sbjct: 63  SIKIPAIEHEFSSIPGVKEDVSEVILNIKGIEVKMHVAEKRIMKLKATGPCVITAGMIET 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNPDHVICNL  +  + MELT   G GYV + +   +N PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPDHVICNLAKNKQLEMELTCKVGKGYVLSTNSYEDNLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK--K 239
            V+Y VE+ R GQV DYDKL M ++T+G +  E +V LA+RILQ+QL +FI+FEE +  K
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDLLPEMAVGLAARILQEQLQLFISFEEQEEDK 242

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           +VK D    +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFG
Sbjct: 243 QVKTD----ALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFG 298

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           RKSL EIK +L    L  GM++PDWPPE+I+EL+ +YED
Sbjct: 299 RKSLNEIKEILAKFNLRFGMDVPDWPPENIQELSNRYED 337


>gi|238650948|ref|YP_002916804.1| DNA-directed RNA polymerase subunit alpha [Rickettsia peacockii
           str. Rustic]
 gi|259494172|sp|C4K2F5|RPOA_RICPU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238625046|gb|ACR47752.1| DNA-directed RNA polymerase subunit alpha [Rickettsia peacockii
           str. Rustic]
          Length = 340

 Score =  372 bits (955), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 186/339 (54%), Positives = 248/339 (73%), Gaps = 7/339 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y     E  N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNKVAYENF-PETNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE SSI GV ED++++ILNIKGI +KM     + + +   GP VV AG I+T
Sbjct: 63  SIKIPAIEHEFSSIPGVKEDVSEVILNIKGIEVKMHVAEKRIMKLKATGPCVVKAGMIET 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNPDHVIC+L  D  + MELT   G GYV + +   +N PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPDHVICDLAKDKQLEMELTCKVGKGYVLSTNSYEDNLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK--K 239
            V+Y VE+ R GQV DYDKL M ++T+G +  E +V LA+RILQ+QL +FI+FEE +  K
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDVLPEMAVGLAARILQEQLQLFISFEEQEEDK 242

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           +VK D    +LPF P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFG
Sbjct: 243 QVKTD----ALPFAPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFG 298

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           RKSL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 299 RKSLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>gi|157826787|ref|YP_001495851.1| DNA-directed RNA polymerase subunit alpha [Rickettsia bellii OSU
           85-389]
 gi|166229277|sp|A8GVD7|RPOA_RICB8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|157802091|gb|ABV78814.1| DNA-directed RNA polymerase subunit alpha [Rickettsia bellii OSU
           85-389]
          Length = 341

 Score =  371 bits (953), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 185/340 (54%), Positives = 249/340 (73%), Gaps = 8/340 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIK + + Y     E  N++ +I EPL RGF  TLGNA+RRVL+SSL+GAA+T
Sbjct: 4   LSKNWNALIKTDKVSYESF-HETNNKSKIIVEPLERGFGLTLGNAMRRVLLSSLQGAAVT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I G+ HE SSI GV ED+++IILN+KGI +KM     + + +   GPG +TAG I+ 
Sbjct: 63  SIKIPGIEHEFSSIPGVKEDISEIILNVKGIEIKMHVAEKRVIRLKATGPGAITAGMIEA 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPI 180
            +D+E+LNPDHVICNL  +    MELT   G GY  + ++  +N+ PIG I IDAL++P+
Sbjct: 123 GHDVEILNPDHVICNLAKNKQFEMELTCKVGKGYTLSTNNNEDNNLPIGEIAIDALFNPV 182

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK-- 238
           K V+Y VE+ R GQV DYDKL M ++T+G I  E +V LA+RILQ+QL +FI+FEE +  
Sbjct: 183 KSVTYKVENTRIGQVTDYDKLIMFVETNGDILPEMAVGLAARILQEQLQLFISFEEQEED 242

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           K+VK D    +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTEADMLR  NF
Sbjct: 243 KQVKTD----ALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTEADMLRTPNF 298

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           GRKSL EIK +L    L  GM++PDWPPE+I EL+K+YED
Sbjct: 299 GRKSLNEIKEILAKFSLRFGMDVPDWPPENIHELSKRYED 338


>gi|239948295|ref|ZP_04700048.1| DNA-directed RNA polymerase, alpha subunit [Rickettsia endosymbiont
           of Ixodes scapularis]
 gi|239922571|gb|EER22595.1| DNA-directed RNA polymerase, alpha subunit [Rickettsia endosymbiont
           of Ixodes scapularis]
          Length = 340

 Score =  371 bits (953), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 185/339 (54%), Positives = 249/339 (73%), Gaps = 7/339 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y     E  N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNKVAYENF-PETNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE S I GV ED++++ILNIKGI +KM     + + +   GP VVTAG I+T
Sbjct: 63  SIKIPAIEHEFSFIPGVKEDVSEVILNIKGIEVKMHVAEKRIMKLKATGPCVVTAGMIET 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNPDHVICN+  +  + MELT   G GYV + +   +N PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPDHVICNIAKNKQLEMELTCKVGKGYVLSTNSYEDNLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK--K 239
            V+Y VE+ R GQV DYDKL M ++T+G +  E +V LA+RILQ+QL +FI+FEE +  K
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDLLPEMAVGLAARILQEQLRLFISFEEQEEDK 242

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           +VK D    +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFG
Sbjct: 243 QVKTD----ALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFG 298

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           RKSL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 299 RKSLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>gi|229586985|ref|YP_002845486.1| DNA-directed RNA polymerase subunit alpha [Rickettsia africae
           ESF-5]
 gi|259494171|sp|C3PP83|RPOA_RICAE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|228022035|gb|ACP53743.1| DNA-directed RNA polymerase alpha chain [Rickettsia africae ESF-5]
          Length = 340

 Score =  371 bits (952), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 186/339 (54%), Positives = 249/339 (73%), Gaps = 7/339 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y     E  N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNKVAYENF-PETNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE SSI GV ED++++ILNIKGI +KM     + + +   GP VVTAG I+T
Sbjct: 63  SIKIPAIEHEFSSIPGVKEDVSEVILNIKGIEVKMHVAEKRIMKLKATGPCVVTAGMIET 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNPDHVIC+L  D  + MELT   G GYV + +   +N PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPDHVICDLAKDKQLEMELTCKVGKGYVLSTNSYEDNLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK--K 239
            V+Y VE+ R GQV DYDKL M ++T+G +  E +V LA+RILQ+QL +FI+FEE +  K
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDVLPEMAVGLAARILQEQLQLFISFEEQEEDK 242

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           +VK D    +L F+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFG
Sbjct: 243 QVKTD----ALLFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFG 298

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           RKSL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 299 RKSLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>gi|157964782|ref|YP_001499606.1| DNA-directed RNA polymerase subunit alpha [Rickettsia massiliae
           MTU5]
 gi|166991522|sp|A8F2C3|RPOA_RICM5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|157844558|gb|ABV85059.1| DNA-directed RNA polymerase alpha chain [Rickettsia massiliae MTU5]
          Length = 340

 Score =  371 bits (952), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 189/340 (55%), Positives = 250/340 (73%), Gaps = 9/340 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y     E  N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNALIKPNKVAYENF-PETNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQ 120
           +++I  + HE SSI GV ED++++ILNIKGI +KM   + KR+   K  GP VVTAG I 
Sbjct: 63  SIKIPAIEHEFSSIPGVKEDVSEVILNIKGIEVKMHV-AEKRIMKLKVTGPCVVTAGMID 121

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +D+E+LNPDHVIC+L  D  + M LT   G GYV + +   +N PIG I IDAL++P+
Sbjct: 122 TGHDVEILNPDHVICDLAKDKQLEMALTCKVGKGYVLSTNSYEDNLPIGEIAIDALFNPV 181

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK-- 238
           K V+Y VE+ R GQV DYDKL M ++T+G +  E +V LA+RILQ+QL +FI+FEE +  
Sbjct: 182 KSVTYKVENTRVGQVTDYDKLIMFVETNGDLLPEMAVGLAARILQEQLQLFISFEEQEED 241

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           K+VK D    +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NF
Sbjct: 242 KQVKTD----ALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNF 297

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           GRKSL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 298 GRKSLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>gi|91205853|ref|YP_538208.1| DNA-directed RNA polymerase subunit alpha [Rickettsia bellii
           RML369-C]
 gi|119366720|sp|Q1RHP5|RPOA_RICBR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|91069397|gb|ABE05119.1| DNA-directed RNA polymerase alpha chain [Rickettsia bellii
           RML369-C]
          Length = 341

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 185/340 (54%), Positives = 249/340 (73%), Gaps = 8/340 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIK + + Y     E  N++ +I EPL RGF  TLGNA+RRVL+SSL+GAA+T
Sbjct: 4   LSKNWNALIKTDKVSYESF-PETNNKSKIIVEPLERGFGLTLGNAMRRVLLSSLQGAAVT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I G+ HE SSI GV ED+++IILN+KGI +KM     + + +   GPG +TAG I+ 
Sbjct: 63  SIKIPGIEHEFSSIPGVKEDISEIILNVKGIEIKMHVAEKRVIRLKATGPGAITAGMIEA 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPI 180
            +D+E+LNPDHVICNL  +    MELT   G GY  + ++  +N+ PIG I IDAL++P+
Sbjct: 123 GHDVEILNPDHVICNLAKNKQFEMELTCKVGKGYTLSTNNNEDNNLPIGEIAIDALFNPV 182

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK-- 238
           K V+Y VE+ R GQV DYDKL M ++T+G I  E +V LA+RILQ+QL +FI+FEE +  
Sbjct: 183 KSVTYKVENTRIGQVTDYDKLIMFVETNGDILPEMAVGLAARILQEQLQLFISFEEQEED 242

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           K+VK D    +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTEADMLR  NF
Sbjct: 243 KQVKTD----ALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTEADMLRTPNF 298

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           GRKSL EIK +L    L  GM++PDWPPE+I EL+K+YED
Sbjct: 299 GRKSLNEIKEILAKFSLRFGMDVPDWPPENIHELSKRYED 338


>gi|157826039|ref|YP_001493759.1| DNA-directed RNA polymerase subunit alpha [Rickettsia akari str.
           Hartford]
 gi|166229276|sp|A8GPC6|RPOA_RICAH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|157799997|gb|ABV75251.1| DNA-directed RNA polymerase subunit alpha [Rickettsia akari str.
           Hartford]
          Length = 340

 Score =  369 bits (947), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 184/339 (54%), Positives = 249/339 (73%), Gaps = 7/339 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y     E  N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNRVAYENF-PEINNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE SSI GV ED++++ILNIKG+ LKM     + + +   GP VVTAG I+T
Sbjct: 63  SIKIPAIEHEFSSIPGVKEDVSEVILNIKGVELKMHVAEKRIMKLKATGPCVVTAGMIET 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNPDH+ICNL  +  + M LT   G GYV + +   ++ PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPDHIICNLAKNKQLEMALTCKVGKGYVLSTNSYEDDLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK--K 239
            V+Y VE+ R GQV DYDKL M ++T+G +  E +V LA+RILQ+QL +FI+FEE +  K
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGGLLPEMAVGLAARILQEQLQLFISFEEHEEDK 242

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           +VK D    +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFG
Sbjct: 243 QVKTD----TLPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFG 298

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           RKSL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 299 RKSLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>gi|218462761|ref|ZP_03502852.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli Kim 5]
          Length = 247

 Score =  365 bits (938), Expect = 4e-99,   Method: Compositional matrix adjust.
 Identities = 173/246 (70%), Positives = 210/246 (85%), Gaps = 1/246 (0%)

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +KM GD  KR+ + K+GPGVVTAGDIQTV DIE+LNP+HVIC LD  A +RME TV+ G 
Sbjct: 2   IKMDGDDAKRMVVRKQGPGVVTAGDIQTVGDIEILNPEHVICTLDEGAEIRMEFTVNNGK 61

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYVPA+ +R E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKL+MTI+TDGSITG
Sbjct: 62  GYVPAERNRAEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLNMTIETDGSITG 121

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCL 273
           ED+VA A+RILQDQLG+F+NF+EP+KE +E+  V  L FNPALLKKV+ELELSVRS NCL
Sbjct: 122 EDAVAFAARILQDQLGVFVNFDEPQKETEEEA-VTELAFNPALLKKVDELELSVRSANCL 180

Query: 274 RGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELA 333
           + +NIVY+GDLIQ+TEA+MLR  NFGRKSL EIK VL +MGL LGM +P WPPE+IE+LA
Sbjct: 181 KNDNIVYIGDLIQKTEAEMLRTPNFGRKSLNEIKEVLASMGLHLGMEVPAWPPENIEDLA 240

Query: 334 KKYEDK 339
           K+YED+
Sbjct: 241 KRYEDQ 246


>gi|297717806|gb|ADI50046.1| DNA-directed RNA polymerase alpha subunit [Candidatus Odyssella
           thessalonicensis L13]
          Length = 338

 Score =  360 bits (924), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 188/338 (55%), Positives = 250/338 (73%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++Q NW+ LIKPN ++ +  G  +     +I EPL RG+  TLGNALRR+L+SSL+GAA 
Sbjct: 1   VLQNNWEALIKPNKLD-VRYGTPDLRHADIIVEPLERGYGLTLGNALRRILLSSLQGAAF 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V+I+GVLHE S+I GV ED+TDIILN+K + ++   +  KRV +   G G V A  I+
Sbjct: 60  TSVKIEGVLHEFSTIPGVMEDVTDIILNLKTVGVRSQVEGVKRVKLVASGKGPVYARQIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+L+ D +IC+LD  A + ME+TV  G GY+PA     E+ PIGLI IDA++SP+
Sbjct: 120 CPAGIEILDEDIIICHLDEGAKLSMEMTVESGKGYIPANSTSHEDKPIGLIPIDAIFSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VSY +E  R GQ  D+DKL M+I TDGS+  +D+VALA+RI+QDQL  FINF+EPK  
Sbjct: 180 KRVSYKIEQTRVGQRTDFDKLIMSISTDGSLKPDDAVALAARIMQDQLYSFINFDEPKTI 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            K++  ++ LPFNP LL+KV+ELELSVRS NCL+ ENI+Y+GDL+Q++E +MLR  NFGR
Sbjct: 240 DKKESKIE-LPFNPNLLRKVDELELSVRSANCLKNENIIYIGDLVQKSEHEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EI+ VL TMGL LGM +P+WPPE+IEEL KK ED
Sbjct: 299 KSLNEIREVLETMGLTLGMIIPNWPPENIEELTKKLED 336


>gi|261752517|ref|ZP_05996226.1| DNA-directed RNA polymerase subunit alpha [Brucella suis bv. 5 str.
           513]
 gi|261742270|gb|EEY30196.1| DNA-directed RNA polymerase subunit alpha [Brucella suis bv. 5 str.
           513]
          Length = 244

 Score =  350 bits (897), Expect = 2e-94,   Method: Compositional matrix adjust.
 Identities = 163/244 (66%), Positives = 203/244 (83%), Gaps = 1/244 (0%)

Query: 96  MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY 155
           M G+  KR+ + K GPGVVTAGDIQTV D+E+LNP+HVIC LD  A +RME TV+ G GY
Sbjct: 1   MEGEGPKRMVVRKEGPGVVTAGDIQTVGDVEILNPEHVICTLDEGAEIRMEFTVNTGKGY 60

Query: 156 VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
           VPA  +R E+ PIGLI +D+LYSP++KVSY +E+ REGQVLDYDKL++ I+T+GS+TGED
Sbjct: 61  VPADRNRAEDAPIGLIPVDSLYSPVRKVSYKIENTREGQVLDYDKLTLNIETNGSVTGED 120

Query: 216 SVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRG 275
           +VA A+RILQDQL +F+NFEEP+KE  ++  V  L FNPALLKKV+ELELSVRS NCL+ 
Sbjct: 121 AVAYAARILQDQLSIFVNFEEPQKEAPQE-QVAELAFNPALLKKVDELELSVRSANCLKN 179

Query: 276 ENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
           +NIVY+GDLIQ+TEA+MLR  NFGRKSL EIK VL +MGL LGM +P WPPE+IE+LAK+
Sbjct: 180 DNIVYIGDLIQKTEAEMLRTPNFGRKSLNEIKEVLASMGLHLGMEIPAWPPENIEDLAKR 239

Query: 336 YEDK 339
           YED+
Sbjct: 240 YEDQ 243


>gi|218674111|ref|ZP_03523780.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli GR56]
          Length = 237

 Score =  348 bits (893), Expect = 6e-94,   Method: Compositional matrix adjust.
 Identities = 166/235 (70%), Positives = 195/235 (82%), Gaps = 3/235 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+         R  ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVEF---SSSSRTRATLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I +KM GD  KR+ + K+GPGVVTAGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIKMDGDDAKRMVVRKQGPGVVTAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDIEILNPEHVICTLDEGAEIRMEFTVNNGKGYVPAERNRAEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           KKVSY VE+ REGQVLDYDKL+MTI+TDGSITGED+VA A+RILQDQLG+F+NFE
Sbjct: 178 KKVSYKVENTREGQVLDYDKLNMTIETDGSITGEDAVAFAARILQDQLGVFVNFE 232


>gi|117924180|ref|YP_864797.1| DNA-directed RNA polymerase subunit alpha [Magnetococcus sp. MC-1]
 gi|158512333|sp|A0L5Z8|RPOA_MAGSM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|117607936|gb|ABK43391.1| DNA-directed RNA polymerase subunit alpha [Magnetococcus sp. MC-1]
          Length = 340

 Score =  341 bits (874), Expect = 9e-92,   Method: Compositional matrix adjust.
 Identities = 182/341 (53%), Positives = 247/341 (72%), Gaps = 10/341 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEE---ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +NW ELIKP+ IE   LG +E   + +  ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 3   RNWTELIKPHTIE---LGGDETEIQRKATLVAEPLERGFGTTLGNALRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           + V+I+GVLHE SS+ GV ED+TDIILNIKG+ L+M     K + +     G VTAG I+
Sbjct: 60  STVRIEGVLHEFSSVPGVIEDVTDIILNIKGLALRMESTGIKNIYLRVDKEGPVTAGMIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT-ENDPIGLITIDALYSP 179
               IE+LNPDH I  L+    + + +TV+ G GYV A+ +R  E+  IG I IDA Y+P
Sbjct: 120 CETGIEILNPDHHIATLNKSGTLDITMTVTTGKGYVRAQLNREDESYAIGDIPIDASYNP 179

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +KKV+Y VE+AR GQ  DYDKL M I+T+G +T ED++ALA++ILQDQL  FINF++   
Sbjct: 180 VKKVAYRVENARVGQQTDYDKLIMDIETNGVVTPEDALALAAKILQDQLNPFINFDDVP- 238

Query: 240 EVKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
               D  ++  P +NP L +KV+ELELSVRS NCL+ ++IVY+GDL+Q++E++ML+  NF
Sbjct: 239 -TAHDHEMEDRPQWNPNLFRKVDELELSVRSANCLKNDDIVYIGDLVQKSESEMLKTPNF 297

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           GRKSL EIK VL  MGL LGM L  WPPE+I++L+K++E++
Sbjct: 298 GRKSLNEIKEVLDEMGLSLGMTLDTWPPENIDDLSKQFEEE 338


>gi|239787588|emb|CAX84056.1| DNA-directed RNA polymerase subunit alpha [uncultured bacterium]
          Length = 339

 Score =  340 bits (873), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 178/342 (52%), Positives = 249/342 (72%), Gaps = 9/342 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +NW ELIKP  +E +  G  +   TL +AEPL RGF  TLGNALRRVL+SSL+GAA++
Sbjct: 1   MYRNWTELIKPRKVELVGEGDSQYKATL-VAEPLERGFGTTLGNALRRVLLSSLQGAAVS 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           AV+I+GVLHE SSI GV ED+TDIILN+KG+ ++M     + +T+     GVVTAGDI  
Sbjct: 60  AVRIEGVLHEFSSIPGVLEDVTDIILNLKGVAIRMRSGVTRTMTLVADKEGVVTAGDIDC 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP--IGLITIDALYSP 179
            +DIE+LNP H I  L+    + M +TV+ G GYV A     ++ P  IG I +D  Y+P
Sbjct: 120 GHDIEILNPGHHIATLNKSGKLNMTMTVTTGKGYVRATTG-ADDQPTNIGDIPLDCSYNP 178

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE-PK 238
           +K+VSY V +AR GQ  DYD+L + I+T+G ++ ED++ALA++ILQDQL +FINF++ P 
Sbjct: 179 VKRVSYKVSNARVGQQTDYDRLVLDIETNGVVSPEDALALAAKILQDQLSLFINFDDIPI 238

Query: 239 KEVKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            E ++D    + P +NP L +KV+ELELSVRS NCL+ ++IVY+GDL+Q+TE++ML+  N
Sbjct: 239 HEGRDD---NATPKWNPNLFRKVDELELSVRSANCLKNDDIVYIGDLVQKTESEMLKTPN 295

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           FGRKSL EIK VL  M L LGM+L  WPPE++E+LA++++++
Sbjct: 296 FGRKSLNEIKEVLEEMDLSLGMHLDGWPPENLEDLARQFDEE 337


>gi|116749017|ref|YP_845704.1| DNA-directed RNA polymerase subunit alpha [Syntrophobacter
           fumaroxidans MPOB]
 gi|158512349|sp|A0LIL7|RPOA_SYNFM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116698081|gb|ABK17269.1| DNA-directed RNA polymerase, alpha subunit [Syntrophobacter
           fumaroxidans MPOB]
          Length = 335

 Score =  337 bits (864), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 181/337 (53%), Positives = 239/337 (70%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q+NW+ELIKP  +E    G           EPL RGF  TLGNALRRVL+SSL+GAAIT
Sbjct: 1   MQRNWRELIKPKRLEVETKGLPNTYGKFE-CEPLERGFGITLGNALRRVLLSSLQGAAIT 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V++DGVLHE S+I GV ED+TD+ILN+K +  KM  D  + V I K G G V AGDIQ 
Sbjct: 60  SVKVDGVLHEFSTIPGVLEDVTDVILNLKEVRFKMHSDGPRLVVIEKDGEGEVAAGDIQG 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              +EVLNP+  IC L+ DA +RMELTV +G GY+PA  +  EN PIG I IDA++SPI+
Sbjct: 120 GPHVEVLNPEQHICTLEKDARLRMELTVKQGKGYLPADRNIEENQPIGTIPIDAIFSPIR 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSYTV  AR  Q+ DYDKL+M I +DGS+  +D++A +++IL+DQL +FINFEE  +  
Sbjct: 180 KVSYTVTQARVAQITDYDKLTMEIWSDGSVKPDDALAYSAKILKDQLTIFINFEEEMETT 239

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +E++  + + FN  L + V+ELELSVRS NCL+  +I Y+G+L+Q+TEA+ML+  NFGRK
Sbjct: 240 EEEVRAEPV-FNDHLFRSVDELELSVRSANCLKNADIRYIGELVQKTEAEMLKTKNFGRK 298

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPP-ESIEELAKKYE 337
           SL EIK +L  MGL LGM L ++P  + IE   K+ E
Sbjct: 299 SLNEIKEILTEMGLSLGMKLENFPSRDDIENRRKEQE 335


>gi|73667205|ref|YP_303221.1| DNA-directed RNA polymerase subunit alpha [Ehrlichia canis str.
           Jake]
 gi|90110840|sp|Q3YRN2|RPOA_EHRCJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|72394346|gb|AAZ68623.1| DNA-directed RNA polymerase subunit alpha [Ehrlichia canis str.
           Jake]
          Length = 372

 Score =  337 bits (864), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 171/342 (50%), Positives = 240/342 (70%), Gaps = 5/342 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +W +L KP++I+    G    N+  +I EPL  GFA TLGNALRRV+MSSLRG A+ 
Sbjct: 32  MSDHWSKLTKPSSIKVESNGASP-NKADLIVEPLESGFALTLGNALRRVMMSSLRGFAVY 90

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+ VLHE +SI GV ED+TDI+LNI  + +K+SG S+K +++  +GP  V +G I  
Sbjct: 91  GVEIENVLHEFTSISGVREDVTDILLNISMMRVKLSGLSNKVLSLRVKGPCEVRSGMIPD 150

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT----ENDPIGLITIDALY 177
            +D  +LN D +IC LD D    +++ V+ G GYVPA   ++     + P+  I  +ALY
Sbjct: 151 TDDCIILNKDLLICTLDQDVDFNIKMYVNSGKGYVPAVKRKSVSKLSDVPVNFIATNALY 210

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPIKK S+ VES+R GQ  DYD+L ++++TDGSI  +++VALA+RILQDQ   FINF+E 
Sbjct: 211 SPIKKASFKVESSRIGQFTDYDRLVLSVETDGSILPDEAVALAARILQDQFQPFINFDET 270

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +  K+     +LP++  LL+KV+ELELSVRS NCL+ +NI Y+GDL+Q+TE+DMLR  N
Sbjct: 271 DEPHKKIDTKDALPYDSNLLRKVDELELSVRSYNCLKNDNITYIGDLVQKTESDMLRTPN 330

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           FGRKSL EI  +L +M L LGM + +WPPESIE L+K+Y ++
Sbjct: 331 FGRKSLNEINELLASMNLHLGMKIANWPPESIESLSKQYSEE 372


>gi|88658298|ref|YP_507250.1| DNA-directed RNA polymerase subunit alpha [Ehrlichia chaffeensis
           str. Arkansas]
 gi|88599755|gb|ABD45224.1| DNA-directed RNA polymerase, alpha subunit [Ehrlichia chaffeensis
           str. Arkansas]
          Length = 341

 Score =  336 bits (862), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 172/342 (50%), Positives = 239/342 (69%), Gaps = 5/342 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +W +L KP++I+ +  G    N+  +I EPL  GFA TLGNALRRV+MSSLRG A+ 
Sbjct: 1   MSDHWSKLTKPSSIKVVPSGASP-NKADLIIEPLESGFALTLGNALRRVMMSSLRGFAVY 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+ VLHE +SI GV ED+TDI+LNI  + +K+SG + K +++  +GP  V +G I  
Sbjct: 60  GVEIENVLHEFTSISGVREDVTDILLNISMMRVKLSGMNSKVLSLKVKGPCEVRSGMIPD 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND----PIGLITIDALY 177
            +D  +LN D +IC LD      +++ V+ G GYVPA   ++ N     PI  I  +ALY
Sbjct: 120 TDDCIILNKDLLICTLDQGVDFNIKMYVNAGKGYVPAVKRKSVNKLGDIPINFIATNALY 179

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPIKK S+ VES+R GQ  DYD+L M+++TDGSI  +++VALA+RILQDQ   FINF+E 
Sbjct: 180 SPIKKASFKVESSRIGQFTDYDRLIMSVETDGSILPDEAVALAARILQDQFQPFINFDET 239

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +  K+     +LP++  LL+KV+ELELSVRS NCL+ +NI Y+GDL+Q+TE+DMLR  N
Sbjct: 240 DEPHKKVDAKDTLPYDSNLLRKVDELELSVRSYNCLKNDNITYIGDLVQKTESDMLRTPN 299

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           FGRKSL EI  +L +M L LGM + +WPPESIE L+K+Y ++
Sbjct: 300 FGRKSLNEINELLASMNLHLGMKIANWPPESIESLSKQYSEE 341


>gi|119366682|sp|Q2GH33|RPOA_EHRCR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 372

 Score =  336 bits (862), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 172/342 (50%), Positives = 239/342 (69%), Gaps = 5/342 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +W +L KP++I+ +  G    N+  +I EPL  GFA TLGNALRRV+MSSLRG A+ 
Sbjct: 32  MSDHWSKLTKPSSIKVVPSGASP-NKADLIIEPLESGFALTLGNALRRVMMSSLRGFAVY 90

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+ VLHE +SI GV ED+TDI+LNI  + +K+SG + K +++  +GP  V +G I  
Sbjct: 91  GVEIENVLHEFTSISGVREDVTDILLNISMMRVKLSGMNSKVLSLKVKGPCEVRSGMIPD 150

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND----PIGLITIDALY 177
            +D  +LN D +IC LD      +++ V+ G GYVPA   ++ N     PI  I  +ALY
Sbjct: 151 TDDCIILNKDLLICTLDQGVDFNIKMYVNAGKGYVPAVKRKSVNKLGDIPINFIATNALY 210

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPIKK S+ VES+R GQ  DYD+L M+++TDGSI  +++VALA+RILQDQ   FINF+E 
Sbjct: 211 SPIKKASFKVESSRIGQFTDYDRLIMSVETDGSILPDEAVALAARILQDQFQPFINFDET 270

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +  K+     +LP++  LL+KV+ELELSVRS NCL+ +NI Y+GDL+Q+TE+DMLR  N
Sbjct: 271 DEPHKKVDAKDTLPYDSNLLRKVDELELSVRSYNCLKNDNITYIGDLVQKTESDMLRTPN 330

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           FGRKSL EI  +L +M L LGM + +WPPESIE L+K+Y ++
Sbjct: 331 FGRKSLNEINELLASMNLHLGMKIANWPPESIESLSKQYSEE 372


>gi|58579279|ref|YP_197491.1| DNA-directed RNA polymerase subunit alpha [Ehrlichia ruminantium
           str. Welgevonden]
 gi|90110841|sp|Q5HAU5|RPOA_EHRRW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|58417905|emb|CAI27109.1| DNA-directed RNA polymerase alpha chain [Ehrlichia ruminantium str.
           Welgevonden]
          Length = 374

 Score =  336 bits (861), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 174/345 (50%), Positives = 239/345 (69%), Gaps = 9/345 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +W +L KP++I+ +  G    N+  +I EPL  GFA TLGNALRRV+MSSLRG A+ 
Sbjct: 32  MSDHWNKLTKPSSIKVVNHGNAL-NKADLIIEPLESGFALTLGNALRRVMMSSLRGFAVY 90

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+ VLHE +SI GV ED+TDI+LNI  I LK+SG  +K +++  +GP  V +G I  
Sbjct: 91  GVEIENVLHEFTSISGVREDVTDILLNISMIRLKLSGMDNKVLSLKVKGPCEVRSGMIAD 150

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND------PIGLITIDA 175
             D  +LN D +IC LD D    +++ V+ G GYVPA   ++ N       P+  I  +A
Sbjct: 151 TPDCTILNKDLLICTLDQDVDFNIKMYVNSGKGYVPAVKRKSINKFGLNDVPVNFIATNA 210

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           LYSPIKK S+ VES+R GQ  DYD+L M+++TD SI  +++VALA+RILQDQ   FINF+
Sbjct: 211 LYSPIKKASFRVESSRIGQFTDYDRLIMSVETDHSILPDEAVALAARILQDQFQQFINFD 270

Query: 236 EPKKEVKEDINVKS-LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           E   E  + ++ K  LP++  LL+KV+ELELSVRS NCL+ +NI Y+GDL+Q+TE+DMLR
Sbjct: 271 E-TDEPHQKVDTKDVLPYDSNLLRKVDELELSVRSYNCLKNDNITYIGDLVQKTESDMLR 329

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             NFGRKSL EI  +L +M L LGM + +WPPESIE L+K+Y ++
Sbjct: 330 TPNFGRKSLNEINELLASMNLHLGMKIANWPPESIESLSKQYSEE 374


>gi|58617333|ref|YP_196532.1| DNA-directed RNA polymerase subunit alpha [Ehrlichia ruminantium
           str. Gardel]
 gi|75432689|sp|Q5FFS1|RPOA_EHRRG RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|58416945|emb|CAI28058.1| DNA-directed RNA polymerase alpha chain [Ehrlichia ruminantium str.
           Gardel]
          Length = 374

 Score =  336 bits (861), Expect = 4e-90,   Method: Compositional matrix adjust.
 Identities = 174/345 (50%), Positives = 239/345 (69%), Gaps = 9/345 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +W +L KP++I+ +  G    N+  +I EPL  GFA TLGNALRRV+MSSLRG A+ 
Sbjct: 32  MSDHWNKLTKPSSIKVVNHGNAL-NKADLIIEPLESGFALTLGNALRRVMMSSLRGFAVY 90

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+ VLHE +SI GV ED+TDI+LNI  I LK+SG  +K +++  +GP  V +G I  
Sbjct: 91  GVEIENVLHEFTSISGVREDVTDILLNISMIRLKLSGMDNKVLSLKVKGPCEVRSGMIAD 150

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND------PIGLITIDA 175
             D  +LN D +IC LD D    +++ V+ G GYVPA   ++ N       P+  I  +A
Sbjct: 151 TPDCTILNKDLLICTLDQDVDFNIKMYVNSGKGYVPAVKRKSINKFGLSDVPVNFIATNA 210

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           LYSPIKK S+ VES+R GQ  DYD+L M+++TD SI  +++VALA+RILQDQ   FINF+
Sbjct: 211 LYSPIKKASFRVESSRIGQFTDYDRLIMSVETDHSILPDEAVALAARILQDQFQQFINFD 270

Query: 236 EPKKEVKEDINVKS-LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           E   E  + ++ K  LP++  LL+KV+ELELSVRS NCL+ +NI Y+GDL+Q+TE+DMLR
Sbjct: 271 E-TDEPHQKVDTKDVLPYDSNLLRKVDELELSVRSYNCLKNDNITYIGDLVQKTESDMLR 329

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             NFGRKSL EI  +L +M L LGM + +WPPESIE L+K+Y ++
Sbjct: 330 TPNFGRKSLNEINELLASMNLHLGMKIANWPPESIESLSKQYSEE 374


>gi|57239313|ref|YP_180449.1| DNA-directed RNA polymerase subunit alpha [Ehrlichia ruminantium
           str. Welgevonden]
 gi|57161392|emb|CAH58316.1| DNA-directed RNA polymerase alpha chain [Ehrlichia ruminantium str.
           Welgevonden]
          Length = 358

 Score =  335 bits (860), Expect = 5e-90,   Method: Compositional matrix adjust.
 Identities = 174/345 (50%), Positives = 239/345 (69%), Gaps = 9/345 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +W +L KP++I+ +  G    N+  +I EPL  GFA TLGNALRRV+MSSLRG A+ 
Sbjct: 16  MSDHWNKLTKPSSIKVVNHGNAL-NKADLIIEPLESGFALTLGNALRRVMMSSLRGFAVY 74

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+ VLHE +SI GV ED+TDI+LNI  I LK+SG  +K +++  +GP  V +G I  
Sbjct: 75  GVEIENVLHEFTSISGVREDVTDILLNISMIRLKLSGMDNKVLSLKVKGPCEVRSGMIAD 134

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND------PIGLITIDA 175
             D  +LN D +IC LD D    +++ V+ G GYVPA   ++ N       P+  I  +A
Sbjct: 135 TPDCTILNKDLLICTLDQDVDFNIKMYVNSGKGYVPAVKRKSINKFGLNDVPVNFIATNA 194

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           LYSPIKK S+ VES+R GQ  DYD+L M+++TD SI  +++VALA+RILQDQ   FINF+
Sbjct: 195 LYSPIKKASFRVESSRIGQFTDYDRLIMSVETDHSILPDEAVALAARILQDQFQQFINFD 254

Query: 236 EPKKEVKEDINVKS-LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           E   E  + ++ K  LP++  LL+KV+ELELSVRS NCL+ +NI Y+GDL+Q+TE+DMLR
Sbjct: 255 E-TDEPHQKVDTKDVLPYDSNLLRKVDELELSVRSYNCLKNDNITYIGDLVQKTESDMLR 313

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             NFGRKSL EI  +L +M L LGM + +WPPESIE L+K+Y ++
Sbjct: 314 TPNFGRKSLNEINELLASMNLHLGMKIANWPPESIESLSKQYSEE 358


>gi|108758094|ref|YP_631525.1| DNA-directed RNA polymerase subunit alpha [Myxococcus xanthus DK
           1622]
 gi|119366701|sp|Q1D748|RPOA_MYXXD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|108461974|gb|ABF87159.1| DNA-directed RNA polymerase, alpha subunit [Myxococcus xanthus DK
           1622]
          Length = 340

 Score =  330 bits (845), Expect = 3e-88,   Method: Compositional matrix adjust.
 Identities = 166/329 (50%), Positives = 228/329 (69%), Gaps = 5/329 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGA 58
            + KNW++LIKP  +E   + Q+    T    +AEPL RGF  TLGN+LRRVL+SSL+GA
Sbjct: 5   FVAKNWRDLIKPRRME---VDQDSATPTYGKFVAEPLERGFGTTLGNSLRRVLLSSLQGA 61

Query: 59  AITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGD 118
           AIT V+I+GV HE ++I  V ED+TD++LN+K + L+M  +  K + I   GP  V AGD
Sbjct: 62  AITTVKIEGVDHEFTTIPEVSEDVTDVVLNLKEVLLRMHTNETKTLRIEAEGPKEVKAGD 121

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           I T  D E+LNP H IC +     +RMELT  +G GY PA  ++    PIG I ID+L+S
Sbjct: 122 IITDPDTEILNPGHHICTISEGGKLRMELTCRRGRGYTPANVNKVAGSPIGTIPIDSLFS 181

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI+KV+Y V +AR GQV D+DKLS+ + TDGS++ +D+VA A++I+++QL +F+NF+E +
Sbjct: 182 PIRKVNYQVTNARVGQVTDFDKLSLEVWTDGSVSPQDAVAYAAKIIKEQLTVFVNFDETE 241

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V  +   +    N  L + V+ELELSVRS NCL+  NI  +GDL+QRTEA+ML+  NF
Sbjct: 242 EPVVAEAPKEEAKLNENLFRSVDELELSVRSANCLQQANIKSIGDLVQRTEAEMLKTKNF 301

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           GRKSL EIK +L  MGL LGM L +WPP+
Sbjct: 302 GRKSLKEIKEILAEMGLSLGMKLENWPPK 330


>gi|162456219|ref|YP_001618586.1| DNA-directed RNA polymerase, alpha subunit [Sorangium cellulosum
           'So ce 56']
 gi|229564257|sp|A9FGB8|RPOA_SORC5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|161166801|emb|CAN98106.1| DNA-directed RNA polymerase, alpha subunit [Sorangium cellulosum
           'So ce 56']
          Length = 346

 Score =  329 bits (843), Expect = 4e-88,   Method: Compositional matrix adjust.
 Identities = 167/329 (50%), Positives = 228/329 (69%), Gaps = 9/329 (2%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIA----EPLPRGFAHTLGNALRRVLMSSLR 56
           MI +NW++LI+P  I       + E+ T   A    EPL RGF  T+GN+LRRVL+SSL+
Sbjct: 10  MIARNWRDLIRPKGISI-----DAESGTQFYAKFTCEPLERGFGITIGNSLRRVLLSSLQ 64

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAA TA++I+G LHE +++  V ED++DIILN+K +  K +      V I + GPG V A
Sbjct: 65  GAAATAIRIEGALHEFTTVPDVVEDVSDIILNVKEVVFKAATPKTYSVRIDREGPGPVYA 124

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
            DIQ V  + VLNPDH+I  LD    + MELTV+ G GYVPA+ ++T   PIG I IDAL
Sbjct: 125 RDIQLVEGLSVLNPDHLIAVLDKKGPLSMELTVNVGRGYVPAERNKTPTMPIGTIPIDAL 184

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +SPI+KV+YTV++AR GQV DYDKL++ + T+GS++  D+VA A++IL++QL +++NFEE
Sbjct: 185 FSPIRKVNYTVQNARVGQVTDYDKLTLEVWTNGSVSPADAVAFAAKILKEQLSIWVNFEE 244

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            ++   + +     P N  L + VEELELSVRS NCL+  NI  +G+L+QRTE DML+  
Sbjct: 245 SEETSYQAVMSDDEPLNENLFRSVEELELSVRSANCLQNANITLIGELVQRTEQDMLKTK 304

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           NFGRKSL EIK +L  MGL LGM + +WP
Sbjct: 305 NFGRKSLKEIKEILANMGLSLGMKIDNWP 333


>gi|189183975|ref|YP_001937760.1| DNA-directed RNA polymerase subunit alpha [Orientia tsutsugamushi
           str. Ikeda]
 gi|238692016|sp|B3CT29|RPOA_ORITI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|189180746|dbj|BAG40526.1| DNA-directed RNA polymerase alpha chain [Orientia tsutsugamushi
           str. Ikeda]
          Length = 342

 Score =  328 bits (842), Expect = 6e-88,   Method: Compositional matrix adjust.
 Identities = 172/341 (50%), Positives = 234/341 (68%), Gaps = 5/341 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
            + KNW  LIKP  ++Y  +      +T M+ EPL RG   TLGN+LRRVL+SSLRGAAI
Sbjct: 4   FLAKNWSSLIKPTKVQYEAVDNNPNIKT-MVVEPLERGLGLTLGNSLRRVLLSSLRGAAI 62

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+++I GV HE+S + GV EDLTDIILNI+ + +KM       + +   GP VVTAG I 
Sbjct: 63  TSIKIPGVEHELSPVSGVKEDLTDIILNIRDVIVKMDSVQKCNLRLEVTGPAVVTAGMIT 122

Query: 121 TVN--DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
             +  D+ +LNP HVICNL     + M+L   +G GYVP       + PIG I +DAL++
Sbjct: 123 VTDKQDVTILNPQHVICNLSKGFNLEMDLICEQGKGYVPTSCLHNSDSPIGAIHLDALFN 182

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY VE++  GQ+ +YDKL +T++T+G +  + ++ LA+RIL DQL +FINF+E +
Sbjct: 183 PVRRVSYKVENSMVGQMTNYDKLIITVETNGVVNPDAALGLAARILLDQLQVFINFQEVE 242

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +E  E + ++++  NP LLKKV ELELSVRS NCL+ ENIVY+GDL+ RTE  ML+ ANF
Sbjct: 243 EEKPEKLELQTI--NPVLLKKVYELELSVRSQNCLKNENIVYVGDLVARTETQMLKTANF 300

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           GRKSL E+K VL    L  GM    WPPE++E LAKK+ED+
Sbjct: 301 GRKSLNELKKVLANFNLEFGMKDIGWPPENLESLAKKHEDQ 341


>gi|77918342|ref|YP_356157.1| DNA-directed RNA polymerase subunit alpha [Pelobacter carbinolicus
           DSM 2380]
 gi|90110854|sp|Q3A6M0|RPOA_PELCD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|77544425|gb|ABA87987.1| DNA-directed RNA polymerase subunit alpha [Pelobacter carbinolicus
           DSM 2380]
          Length = 338

 Score =  328 bits (841), Expect = 6e-88,   Method: Compositional matrix adjust.
 Identities = 174/336 (51%), Positives = 239/336 (71%), Gaps = 2/336 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNW+ELIKP  ++       +     M AEP  RGF  TLGN+LRRVL+SSL+GAAIT+V
Sbjct: 3   KNWRELIKPKRLQVDADSLSDTYGKFM-AEPFERGFGTTLGNSLRRVLLSSLQGAAITSV 61

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I GVLHE S+I GV ED+TDIILN+KG+ LK+ G   + + I K+G GV+TA DI T +
Sbjct: 62  RIKGVLHEFSNIPGVTEDVTDIILNLKGVLLKLHGSDSRNIRIVKKGAGVITAADIITDS 121

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            ++VLNPDH I     DA + +++ V+ G GYVPA+ +R +  P+G I ID+L+SP+KKV
Sbjct: 122 HVDVLNPDHHILTCGKDADIELDMVVAMGKGYVPAERNRDDKAPVGTIPIDSLFSPVKKV 181

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           ++TV +AR GQ+ DYDKL + + TDGS+  +D VA A++IL++QL +FINF+E  + V E
Sbjct: 182 NFTVTNARVGQITDYDKLILEVLTDGSVRPDDGVAYAAKILKEQLQIFINFDEETETVVE 241

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           + + +S   N  L + VEELELSVRS NCL+  NI  +GDL+QR+EA+ML+  NFGRKSL
Sbjct: 242 EESEESRKINENLYRSVEELELSVRSANCLKNANIHLIGDLVQRSEAEMLKTQNFGRKSL 301

Query: 304 VEIKGVLGTMGLFLGMNLPDWP-PESIEELAKKYED 338
            EIK +L  MGL LGM L ++P PE ++ + +  ED
Sbjct: 302 NEIKDILAEMGLSLGMMLENFPDPEYLKMIQEGKED 337


>gi|39997923|ref|NP_953874.1| DNA-directed RNA polymerase subunit alpha [Geobacter sulfurreducens
           PCA]
 gi|61215992|sp|Q749B3|RPOA_GEOSL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|39984868|gb|AAR36224.1| DNA-directed RNA polymerase, alpha subunit [Geobacter
           sulfurreducens PCA]
 gi|298506861|gb|ADI85584.1| DNA-directed RNA polymerase, alpha subunit [Geobacter
           sulfurreducens KN400]
          Length = 340

 Score =  328 bits (840), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 173/346 (50%), Positives = 235/346 (67%), Gaps = 15/346 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTL------MIAEPLPRGFAHTLGNALRRVLMSSL 55
           + +NW++LI P  ++        E+ TL        AEP  RGF  TLGN+LRRVL+SSL
Sbjct: 1   MYRNWRDLISPKKLQV-------ESETLTNKYGKFYAEPFERGFGTTLGNSLRRVLLSSL 53

Query: 56  RGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT 115
           +GA IT+V+I GVLHE SSI GV ED+T+IILN+KG++LKM G   K V I  +G G++T
Sbjct: 54  QGAGITSVRIKGVLHEFSSIPGVTEDVTNIILNLKGVSLKMYGTEPKTVRIIHKGDGIIT 113

Query: 116 AGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDA 175
           AGDI T   +E+LNP+H I     DA + ME+ V  G GYVPA  +R E  P+G I IDA
Sbjct: 114 AGDIITDPQVEILNPEHHIATCSKDANLEMEMVVKVGKGYVPADRNRDEKAPVGTIPIDA 173

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           L+SPI+KV++TV +AR GQ+ DYDKL++ + T+GS+  ED+VA A++IL++QL +FINF+
Sbjct: 174 LFSPIRKVNFTVSNARVGQMTDYDKLTLEVWTNGSVIPEDAVAFAAKILKEQLSIFINFD 233

Query: 236 EPKKEVKE-DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           E  +   E ++     P N  L + V+ELELSVRS NCL+   I  +G+L+ RTEA+ML+
Sbjct: 234 EEAEPSGEAEVGEGESPINENLYRSVDELELSVRSANCLKNAGIKLIGELVSRTEAEMLK 293

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWP-PESIEELAKKYEDK 339
             NFGRKSL EIK +L  MGL LGM L  +P PE +  L  + +D+
Sbjct: 294 TQNFGRKSLNEIKDILAEMGLTLGMKLEGFPDPEVMRRLRGERKDE 339


>gi|148284191|ref|YP_001248281.1| DNA-directed RNA polymerase alpha chain [Orientia tsutsugamushi
           str. Boryong]
 gi|172047207|sp|A5CCI9|RPOA_ORITB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|146739630|emb|CAM79419.1| DNA-directed RNA polymerase alpha chain [Orientia tsutsugamushi
           str. Boryong]
          Length = 342

 Score =  327 bits (838), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 171/341 (50%), Positives = 234/341 (68%), Gaps = 5/341 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
            + KNW  LIKP  ++Y  +      +T M+ EPL RG   TLGN+LRRVL+SSLRGAAI
Sbjct: 4   FLAKNWSSLIKPTKVQYEAVDNNPNIKT-MVVEPLERGLGLTLGNSLRRVLLSSLRGAAI 62

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+++I GV HE+S + GV EDLTDIILNI+ + +KM       + +   GP VVTAG I 
Sbjct: 63  TSIKIPGVEHELSPVSGVKEDLTDIILNIRDVIVKMDSVQKCNLRLEVTGPAVVTAGMIT 122

Query: 121 TVN--DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
             +  D+ +LNP HVICNL     + M+L   +G GYVP       + PIG I +DAL++
Sbjct: 123 VTDKQDVTILNPQHVICNLSKGFNLEMDLICEQGKGYVPTSCLHNSDSPIGAIHLDALFN 182

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY VE++  GQ+ +YDKL +T++T+G +  + ++ LA+RIL DQL +FINF+E +
Sbjct: 183 PVRRVSYKVENSMVGQMTNYDKLIITVETNGVVNPDAALGLAARILLDQLQVFINFQEVE 242

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +E  E + ++++  NP LLKKV ELELSVRS NCL+ ENIVY+GDL+ RTE  ML+ ANF
Sbjct: 243 EEKPEKLELQTI--NPVLLKKVYELELSVRSQNCLKNENIVYVGDLVARTETQMLKTANF 300

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           GRKSL E+K VL    L  GM    WPP+++E LAKK+ED+
Sbjct: 301 GRKSLNELKKVLANFNLEFGMKDIGWPPDNLESLAKKHEDQ 341


>gi|153004800|ref|YP_001379125.1| DNA-directed RNA polymerase subunit alpha [Anaeromyxobacter sp.
           Fw109-5]
 gi|171769306|sp|A7HBP5|RPOA_ANADF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|152028373|gb|ABS26141.1| DNA-directed RNA polymerase, alpha subunit [Anaeromyxobacter sp.
           Fw109-5]
          Length = 339

 Score =  323 bits (827), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 169/337 (50%), Positives = 231/337 (68%), Gaps = 5/337 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGA 58
           ++ KNW++LIKP  +   V+ QE  + T    +AEPL RGF  TLGN+LRRVL+SSL+GA
Sbjct: 5   IVTKNWRDLIKPRGL---VVDQESLSNTYGKFVAEPLERGFGITLGNSLRRVLLSSLQGA 61

Query: 59  AITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGD 118
           AIT+V+I+GV HE  +I  V ED+TDIILN+K + L++  +  K + I   GP  + AGD
Sbjct: 62  AITSVKIEGVEHEFMTIPEVAEDVTDIILNLKEVLLQIHTNEVKTLRIEADGPREIKAGD 121

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           I     +E+LNP H I  +     VRME+T  +G GYVPA  ++    PIG I IDAL+S
Sbjct: 122 IIADGQVEILNPGHHILTISEGGRVRMEMTARRGRGYVPADKNKVPGQPIGTIPIDALFS 181

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI+KV+Y V +AR GQ  DYDKLS+ + TDGS+   D+VA A++I+++QL +FINF+E +
Sbjct: 182 PIRKVNYQVTNARVGQQTDYDKLSLEVWTDGSVAPNDAVAYAAKIVKEQLSIFINFDEAE 241

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +  +E   V+    N  L + V+ELELSVRS NCL+  NI  +GDL+Q+TEA+ML+  NF
Sbjct: 242 EPAEEVKPVEEQKLNENLFRSVDELELSVRSANCLQNANIKTIGDLVQKTEAEMLKTKNF 301

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
           GRKSL EIK +L  MGL LGM L +WPP++  + A K
Sbjct: 302 GRKSLKEIKEILAEMGLSLGMKLENWPPKAAPQGAPK 338


>gi|95930496|ref|ZP_01313232.1| DNA-directed RNA polymerase, alpha subunit [Desulfuromonas
           acetoxidans DSM 684]
 gi|95133536|gb|EAT15199.1| DNA-directed RNA polymerase, alpha subunit [Desulfuromonas
           acetoxidans DSM 684]
          Length = 338

 Score =  322 bits (825), Expect = 5e-86,   Method: Compositional matrix adjust.
 Identities = 166/342 (48%), Positives = 236/342 (69%), Gaps = 14/342 (4%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTL------MIAEPLPRGFAHTLGNALRRVLMSSLRG 57
           KNW++LIKP  ++        ++R+L        AEP  RGF  T+GN+LRR+L+SSL+G
Sbjct: 3   KNWRDLIKPKRLQV-------DSRSLTANYGKFFAEPFERGFGTTIGNSLRRILLSSLQG 55

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
           AAIT+V+I GVLHE S++ GV ED+TDIILN+K + L++ G   + + I K+G GV+TAG
Sbjct: 56  AAITSVRIKGVLHEFSTVPGVTEDVTDIILNLKSVLLRLEGQESRNIRIVKKGAGVITAG 115

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI T +++E+LNPD  I     +A V +++ VS G GYV A+ +R +  P+G I ID+++
Sbjct: 116 DIVTDSNVEILNPDLYIATCTKEADVEIDMVVSMGKGYVTAERNRDDKAPVGTIPIDSIF 175

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPIKKV+Y V +AR GQ+ DYDKL++ + TD S+  ED+VA +++IL++ L MFINF+E 
Sbjct: 176 SPIKKVNYAVTNARVGQITDYDKLTLEVWTDASVKPEDAVAYSAKILKEHLQMFINFDEE 235

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +   +E    +    N  L + VEELELSVRS NCL+   I  +GDL+Q+TEA+ML+  N
Sbjct: 236 QIPEEEPEEEEVQKINENLYRSVEELELSVRSANCLKNARISLIGDLVQKTEAEMLKTQN 295

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWP-PESIEELAKKYED 338
           FGRKSL EIK +L  MGL LGM L ++P PE ++ L K  E+
Sbjct: 296 FGRKSLNEIKDILAEMGLTLGMKLENFPDPEYLKVLQKSREE 337


>gi|269958607|ref|YP_003328394.1| DNA-directed RNA polymerase subunit alpha [Anaplasma centrale str.
           Israel]
 gi|269848436|gb|ACZ49080.1| DNA-directed RNA polymerase subunit alpha [Anaplasma centrale str.
           Israel]
          Length = 368

 Score =  322 bits (825), Expect = 6e-86,   Method: Compositional matrix adjust.
 Identities = 167/350 (47%), Positives = 239/350 (68%), Gaps = 16/350 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTL-MIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           I  +W  L +P++I+  V+G  + +R+  +I EPL  GFA TLGNALRRV+MSSLRG A+
Sbjct: 21  ISDHWDRLTRPSSIK--VVGDGDVSRSAELIVEPLESGFALTLGNALRRVMMSSLRGFAV 78

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
             ++++GV HE++S+ GV ED+ D++LN+  + +K+     + + +  +GPG VTA  I 
Sbjct: 79  YGIEVEGVSHELTSLSGVREDVADLVLNLSMLRVKLLTSESRVLRLVAKGPGEVTAAAIG 138

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--------TENDPIGLIT 172
                 +LN D  IC L  DA   M++ V+ G GYVPA  +R        +E  P G I 
Sbjct: 139 DSEGCVILNKDLHICTLGKDANFSMKIYVNSGKGYVPASEYRAASRSGATSEAGP-GFIA 197

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
            +ALYSP+KKV++ +ES+R GQ  DYDKL ++++TDGSI+ +++VA+++R+LQDQL  FI
Sbjct: 198 TNALYSPVKKVAFRIESSRIGQFTDYDKLVISVETDGSISPDEAVAVSARVLQDQLQAFI 257

Query: 233 NFEEPKKEV----KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
             EE + E     K D    +LP++  LL+KV+ELELSVRS NCL+ +NI Y+GDL+Q+T
Sbjct: 258 GSEEVEGESPVRKKVDKEEGALPYDHNLLRKVDELELSVRSHNCLKNDNITYIGDLVQKT 317

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           E+DMLR  NFGRKSL EI  VL +M L LGM +P+WPPESIE L+K+Y +
Sbjct: 318 ESDMLRTPNFGRKSLNEINEVLASMNLHLGMKVPNWPPESIENLSKQYSE 367


>gi|56416980|ref|YP_154054.1| DNA-directed RNA polymerase subunit alpha [Anaplasma marginale str.
           St. Maries]
 gi|222475348|ref|YP_002563765.1| DNA-directed RNA polymerase alpha chain (rpoA) [Anaplasma marginale
           str. Florida]
 gi|254995156|ref|ZP_05277346.1| DNA-directed RNA polymerase subunit alpha [Anaplasma marginale str.
           Mississippi]
 gi|255003330|ref|ZP_05278294.1| DNA-directed RNA polymerase subunit alpha [Anaplasma marginale str.
           Puerto Rico]
 gi|255004454|ref|ZP_05279255.1| DNA-directed RNA polymerase subunit alpha [Anaplasma marginale str.
           Virginia]
 gi|81599123|sp|Q5PA81|RPOA_ANAMM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|56388212|gb|AAV86799.1| DNA-directed RNA polymerase alpha chain [Anaplasma marginale str.
           St. Maries]
 gi|222419486|gb|ACM49509.1| DNA-directed RNA polymerase alpha chain (rpoA) [Anaplasma marginale
           str. Florida]
          Length = 366

 Score =  320 bits (821), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 163/348 (46%), Positives = 242/348 (69%), Gaps = 14/348 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTL-MIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           I  +W +L +P++I+  V+G  + +R+  +I EPL  GFA TLGNALRRV+MSSLRG A+
Sbjct: 21  ISDHWDKLTRPSSIK--VVGDGDLSRSAELIVEPLESGFALTLGNALRRVMMSSLRGFAV 78

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
             ++++GV HE++S+ GV ED+ D++LN+  + +K+     + + +  +GPG +TA  I 
Sbjct: 79  YGIEVEGVSHELTSLSGVREDVADLVLNLSMLRVKLLTSESRVLRLVAKGPGEITAAAIG 138

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--------TENDPIGLIT 172
                 VLN D  IC L  D    M++ V+ G GYVPA  +R        +E  P G I 
Sbjct: 139 DSEGCVVLNKDLHICTLGKDVDFSMKIYVNSGKGYVPASEYRAASRSGATSEVGP-GFIA 197

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
            +ALYSP+KKV++ +ES+R GQ  DYD+L ++++TDGSI+ +++VA+++R+LQDQL  FI
Sbjct: 198 TNALYSPVKKVAFRIESSRIGQFTDYDRLVISVETDGSISPDEAVAVSARVLQDQLQSFI 257

Query: 233 NFEEPKKEVKEDINVK--SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
             EE + E ++ ++ +  +LP++  LL+KV+ELELSVRS NCL+ +NI Y+GDL+Q+TE+
Sbjct: 258 GSEEVEGESRKKVDKEEGALPYDHNLLRKVDELELSVRSHNCLKNDNITYIGDLVQKTES 317

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           DMLR  NFGRKSL EI  VL +M L LGM +P+WPPESIE L+K+Y +
Sbjct: 318 DMLRTPNFGRKSLNEINEVLASMNLHLGMKVPNWPPESIENLSKQYSE 365


>gi|115376084|ref|ZP_01463329.1| DNA-directed RNA polymerase, alpha subunit [Stigmatella aurantiaca
           DW4/3-1]
 gi|310821022|ref|YP_003953380.1| DNA-directed RNA polymerase subunit alpha [Stigmatella aurantiaca
           DW4/3-1]
 gi|115366899|gb|EAU65889.1| DNA-directed RNA polymerase, alpha subunit [Stigmatella aurantiaca
           DW4/3-1]
 gi|309394094|gb|ADO71553.1| DNA-directed RNA polymerase subunit alpha [Stigmatella aurantiaca
           DW4/3-1]
          Length = 343

 Score =  320 bits (820), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 161/326 (49%), Positives = 227/326 (69%), Gaps = 5/326 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGA 58
            I KNW++LIKP  +E   + Q+  + T    +AEPL RGF  TLGN+LRRVL+SSL+G+
Sbjct: 5   FIAKNWRDLIKPRRLE---VDQDSLSTTYGKFVAEPLERGFGTTLGNSLRRVLLSSLQGS 61

Query: 59  AITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGD 118
           AIT+V+I+ V HE +++  V ED+TDI+LN+K + L+M  +  K + I   GP  + AGD
Sbjct: 62  AITSVKIENVDHEFTTLPEVAEDVTDIVLNLKEVLLRMHTNETKTLRIEAEGPKEIKAGD 121

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           I    D+E+LNP H IC +     VRMEL+  +G GYVPA  ++    P+G I ID+L++
Sbjct: 122 IIADQDVEILNPGHHICTVSEGGKVRMELSCRRGRGYVPASVNKVAGAPLGTIPIDSLFA 181

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI+KV+Y V +AR GQV DYDKL++ + TDGS+T +D+VA A++I+++QL +F+NF+E +
Sbjct: 182 PIRKVNYQVTNARVGQVTDYDKLTLEVWTDGSVTPQDAVAYAAKIIKEQLTVFVNFDETE 241

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V  +   +    N  L + V+ELELSVRS NCL+  NI  +GDL+QRTEA+ML+  NF
Sbjct: 242 EPVVAEAPKEEAKLNENLFRSVDELELSVRSANCLQQANIKSIGDLVQRTEAEMLKTKNF 301

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDW 324
           GRKSL EIK +L  MGL LGM L +W
Sbjct: 302 GRKSLKEIKEILAEMGLSLGMKLENW 327


>gi|225630278|ref|YP_002727069.1| DNA-directed RNA polymerase alpha subunit [Wolbachia sp. wRi]
 gi|225592259|gb|ACN95278.1| DNA-directed RNA polymerase alpha subunit [Wolbachia sp. wRi]
          Length = 355

 Score =  320 bits (820), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 162/345 (46%), Positives = 239/345 (69%), Gaps = 12/345 (3%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           N  +LIKP++++  V+  +   ++ ++ EPL  GFA TLGNALRRV++SSL+G+A+  ++
Sbjct: 12  NLDKLIKPSSVK--VISDDSSEKSDIVLEPLESGFALTLGNALRRVMLSSLKGSAVYGIK 69

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           I+GV HE +SI+GV ED+TDI+LN+  +  K++G S+K + +  +GP  V AG I+T + 
Sbjct: 70  IEGVTHEFTSIQGVREDVTDIVLNMGMLRCKLNGASNKCLNLNAKGPCQVLAGMIETDDQ 129

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--------TENDPIGLITIDAL 176
             ++N D +IC L  +  + M + V+ G GY+P   ++        +E D IG I ++AL
Sbjct: 130 CSIVNKDLLICTLGQNVELNMTIYVASGKGYLPVTKYKENELLKLMSEQDLIGFIPVNAL 189

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI--NF 234
           YSP+ +VSY VE++R GQV D DKL ++I+TDG+I+   +V  A+RILQ+QL  FI  + 
Sbjct: 190 YSPVNRVSYRVENSRVGQVTDKDKLILSIETDGTISPSQAVDSAARILQEQLQPFISSDV 249

Query: 235 EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
              K +V      K L ++P LL+KV+E+ELSVRS NCL+ ENI Y+GDL+Q+TE +MLR
Sbjct: 250 SYKKSQVSSSSGAKDLGYDPVLLRKVDEMELSVRSHNCLKNENITYIGDLVQKTEGEMLR 309

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            ANFGRKSL EIK VL   GL LGMN+ +WPP+ I+ELAK++ D+
Sbjct: 310 TANFGRKSLNEIKAVLTNFGLSLGMNVLNWPPKDIDELAKQHTDE 354


>gi|42520507|ref|NP_966422.1| DNA-directed RNA polymerase subunit alpha [Wolbachia endosymbiont
           of Drosophila melanogaster]
 gi|61215982|sp|Q73HA9|RPOA_WOLPM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|42410246|gb|AAS14356.1| DNA-directed RNA polymerase, alpha subunit [Wolbachia endosymbiont
           of Drosophila melanogaster]
          Length = 355

 Score =  320 bits (820), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 162/345 (46%), Positives = 239/345 (69%), Gaps = 12/345 (3%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           N  +LIKP++++  V+  +   ++ ++ EPL  GFA TLGNALRRV++SSL+G+A+  ++
Sbjct: 12  NLDKLIKPSSVK--VVSDDSSEKSDIVLEPLESGFALTLGNALRRVMLSSLKGSAVYGIK 69

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           I+GV HE +SI+GV ED+TDI+LN+  +  K++G S+K + +  +GP  V AG I+T + 
Sbjct: 70  IEGVTHEFTSIQGVREDVTDIVLNMGMLRCKLNGASNKCLNLNAKGPCQVLAGMIETDDQ 129

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--------TENDPIGLITIDAL 176
             ++N D +IC L  +  + M + V+ G GY+P   ++        +E D IG I ++AL
Sbjct: 130 CSIVNKDLLICTLGQNVELNMTIYVASGKGYLPVTKYKENELLKLMSEQDLIGFIPVNAL 189

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI--NF 234
           YSP+ +VSY VE++R GQV D DKL ++I+TDG+I+   +V  A+RILQ+QL  FI  + 
Sbjct: 190 YSPVNRVSYRVENSRVGQVTDKDKLILSIETDGTISPSQAVDSAARILQEQLQPFISSDV 249

Query: 235 EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
              K +V      K L ++P LL+KV+E+ELSVRS NCL+ ENI Y+GDL+Q+TE +MLR
Sbjct: 250 SYKKSQVSSSSGAKDLGYDPVLLRKVDEMELSVRSHNCLKNENITYIGDLVQKTEGEMLR 309

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            ANFGRKSL EIK VL   GL LGMN+ +WPP+ I+ELAK++ D+
Sbjct: 310 TANFGRKSLNEIKAVLTNFGLSLGMNVLNWPPKDIDELAKQHTDE 354


>gi|262197162|ref|YP_003268371.1| DNA-directed RNA polymerase, subunit alpha [Haliangium ochraceum
           DSM 14365]
 gi|262080509|gb|ACY16478.1| DNA-directed RNA polymerase, alpha subunit [Haliangium ochraceum
           DSM 14365]
          Length = 344

 Score =  320 bits (820), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 164/325 (50%), Positives = 225/325 (69%), Gaps = 4/325 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
            + KNW++LI+P  +E     Q+ +N      EPL RGF  TLGN+LRRVL+SSL+GAA 
Sbjct: 17  FMAKNWRDLIRPRMLE---TEQKTDNYGKFSCEPLERGFGTTLGNSLRRVLLSSLQGAAF 73

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T V+I+  LHE SS+ GV ED+TDIILN+K   LK+  D    V + K G G  TAGDI 
Sbjct: 74  THVKIEHALHEFSSLPGVVEDVTDIILNLKETMLKVEEDRVYTVRLEKEGEGPFTAGDIS 133

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV  + +LNPDHVI +L  D  + MEL +  G GYV A+ H T +  +G + IDALYSPI
Sbjct: 134 TVTGVNILNPDHVIGHLARDGKISMELIIGTGRGYVSAERHTT-SPGVGYVPIDALYSPI 192

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +K ++TV +AR GQ  DYDKL++ + T+G +T +D+VA A++IL++QL +FINFEE  + 
Sbjct: 193 RKANFTVTNARVGQQTDYDKLTLEVWTNGGVTPDDAVAFAAKILKEQLNIFINFEEQAEP 252

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V++ ++ +    N  L + V+ELELSVRS NCL+  NI Y+G+L+Q++E++ML+  NFGR
Sbjct: 253 VEQHVDEEQEKLNENLWRTVDELELSVRSANCLQNANIKYIGELVQKSESEMLKTKNFGR 312

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL EIK +L  MGL LGM L +WP
Sbjct: 313 KSLKEIKEILAEMGLSLGMKLDNWP 337


>gi|193795085|gb|ACF21672.1| RpoA [Rhizobium tropici]
 gi|193795087|gb|ACF21673.1| RpoA [Rhizobium tropici]
          Length = 212

 Score =  318 bits (816), Expect = 5e-85,   Method: Compositional matrix adjust.
 Identities = 152/213 (71%), Positives = 183/213 (85%), Gaps = 1/213 (0%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           KR+ + K+GPGVVTAGDIQTV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +
Sbjct: 1   KRMVVRKQGPGVVTAGDIQTVGDIEILNPEHVICTLDEGAEIRMEFTVNNGKGYVPAERN 60

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKLSM+I+TDGSITGED+VA A+
Sbjct: 61  RAEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLSMSIETDGSITGEDAVAFAA 120

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           RILQDQLG+F+NF+EP+KE +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+
Sbjct: 121 RILQDQLGVFVNFDEPQKEAEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           GDLIQ+TEA+MLR  NFGRKSL EIK VL +MG
Sbjct: 180 GDLIQKTEAEMLRTPNFGRKSLNEIKEVLASMG 212


>gi|68171735|ref|ZP_00545087.1| DNA-directed RNA polymerase [Ehrlichia chaffeensis str. Sapulpa]
 gi|67998846|gb|EAM85546.1| DNA-directed RNA polymerase [Ehrlichia chaffeensis str. Sapulpa]
          Length = 307

 Score =  318 bits (815), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 161/306 (52%), Positives = 219/306 (71%), Gaps = 4/306 (1%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           GFA TLGNALRRV+MSSLRG A+  V+I+ VLHE +SI GV ED+TDI+LNI  + +K+S
Sbjct: 2   GFALTLGNALRRVMMSSLRGFAVYGVEIENVLHEFTSISGVREDVTDILLNISMMRVKLS 61

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
           G + K +++  +GP  V +G I   +D  +LN D +IC LD      +++ V+ G GYVP
Sbjct: 62  GMNSKVLSLKVKGPCEVRSGMIPDTDDCIILNKDLLICTLDQGVDFNIKMYVNAGKGYVP 121

Query: 158 AKHHRTEND----PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           A   ++ N     PI  I  +ALYSPIKK S+ VES+R GQ  DYD+L M+++TDGSI  
Sbjct: 122 AVKRKSVNKLGDIPINFIATNALYSPIKKASFKVESSRIGQFTDYDRLIMSVETDGSILP 181

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCL 273
           +++VALA+RILQDQ   FINF+E  +  K+     +LP++  LL+KV+ELELSVRS NCL
Sbjct: 182 DEAVALAARILQDQFQPFINFDETDEPHKKVDAKDTLPYDSNLLRKVDELELSVRSYNCL 241

Query: 274 RGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELA 333
           + +NI Y+GDL+Q+TE+DMLR  NFGRKSL EI  +L +M L LGM + +WPPESIE L+
Sbjct: 242 KNDNITYIGDLVQKTESDMLRTPNFGRKSLNEINELLASMNLHLGMKIANWPPESIESLS 301

Query: 334 KKYEDK 339
           K+Y ++
Sbjct: 302 KQYSEE 307


>gi|58584576|ref|YP_198149.1| DNA-directed RNA polymerase subunit alpha [Wolbachia endosymbiont
           strain TRS of Brugia malayi]
 gi|75497934|sp|Q5GSW7|RPOA_WOLTR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|58418892|gb|AAW70907.1| DNA-directed RNA polymerase alpha subunit/40 kD subunit, RpoA
           [Wolbachia endosymbiont strain TRS of Brugia malayi]
          Length = 355

 Score =  318 bits (814), Expect = 9e-85,   Method: Compositional matrix adjust.
 Identities = 161/342 (47%), Positives = 236/342 (69%), Gaps = 12/342 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +L KPN+++  V+  +   +  ++ EPL  GFA TLGNALRRV++SSL G+A+  ++IDG
Sbjct: 15  KLTKPNSMK--VVSSDSSEKGDIVLEPLESGFALTLGNALRRVMLSSLIGSAVYGIKIDG 72

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           + HE +SI+GV ED+TDI+LN+  +  K++G S+K +++  +GP  V AG I+T +   +
Sbjct: 73  ITHEFTSIQGVREDVTDIVLNMGMLRCKLNGTSNKCLSLSAKGPCQVLAGMIETDDQCSI 132

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--------TENDPIGLITIDALYSP 179
           +N D +IC L  D  + M + V+ G GY+P   ++         E D I  I ++ALYSP
Sbjct: 133 VNKDLLICTLGQDVELNMTIYVASGKGYLPVTKYKENEFLKPMNEQDLISFIPVNALYSP 192

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI--NFEEP 237
           I +VSY VE++R GQV D DKL ++++TDG+I+   +V  A+RILQ+QL  FI  +    
Sbjct: 193 INRVSYRVENSRVGQVTDKDKLILSVETDGTISPSQAVDSAARILQEQLQPFISSDISYK 252

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           K +V      K L ++P LL+KV+E+ELSVRS NCL+ ENI Y+GDL+Q+TE++MLR AN
Sbjct: 253 KSQVSSPSGYKDLGYDPILLRKVDEMELSVRSHNCLKNENITYIGDLVQKTESEMLRTAN 312

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           FGRKSL EIK VL   GL LGM++PDWPP+ I+ELA+++ D+
Sbjct: 313 FGRKSLNEIKAVLNNFGLSLGMDIPDWPPKDIDELARQHTDE 354


>gi|193795067|gb|ACF21665.1| RpoA [Rhizobium tropici]
          Length = 212

 Score =  317 bits (811), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 151/213 (70%), Positives = 182/213 (85%), Gaps = 1/213 (0%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           KR+ + K+GPGVVTAGDIQTV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +
Sbjct: 1   KRMVVRKQGPGVVTAGDIQTVGDIEILNPEHVICTLDEGAEIRMEFTVNNGKGYVPAERN 60

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKLSM+I+TDGSITGED+VA A+
Sbjct: 61  RAEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLSMSIETDGSITGEDAVAFAA 120

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           RILQDQLG+F+NF+EP+KE +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+
Sbjct: 121 RILQDQLGVFVNFDEPQKEAEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           GDLIQ+TEA+MLR  NFGRKSL EIK VL +M 
Sbjct: 180 GDLIQKTEAEMLRTPNFGRKSLNEIKEVLASMA 212


>gi|78221873|ref|YP_383620.1| DNA-directed RNA polymerase subunit alpha [Geobacter
           metallireducens GS-15]
 gi|119366684|sp|Q39XX9|RPOA_GEOMG RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|78193128|gb|ABB30895.1| DNA-directed RNA polymerase subunit alpha [Geobacter
           metallireducens GS-15]
          Length = 340

 Score =  317 bits (811), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 168/344 (48%), Positives = 236/344 (68%), Gaps = 11/344 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRT----LMIAEPLPRGFAHTLGNALRRVLMSSLRG 57
           + +NW++LI P  ++      E E+ T       AEP  RGF  TLGN+LRRVL+SSL+G
Sbjct: 1   MYRNWRDLISPKKLQV-----ESESLTNTYGKFFAEPFERGFGTTLGNSLRRVLLSSLQG 55

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
           AAI++V+I GVLHE SSI GV ED+T+IILN+KG++LKM G+  + V I  +G G+V AG
Sbjct: 56  AAISSVKIKGVLHEFSSIPGVTEDVTNIILNLKGVSLKMHGNEARTVRIIHKGDGIVKAG 115

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI T  ++E+LNPDH I     DA + ME+ V  G GYVP+  +R E  P+G + IDA++
Sbjct: 116 DIVTDANVEILNPDHHIATCSKDANLEMEMVVKLGKGYVPSDRNRDEKAPVGTMPIDAIF 175

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPIKKV++TV +AR GQ+ DYDKL++ + T+GS+  ED+VA A++IL++QL +FINF+E 
Sbjct: 176 SPIKKVNFTVSNARVGQMTDYDKLTLEVWTNGSVVPEDAVAFAAKILKEQLSIFINFDEE 235

Query: 238 KKEVKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +  +E    +     N  L + V+ELELSVRS NCL+   I  +G+L+ R+EA+ML+  
Sbjct: 236 AEPAEEAETEEERERVNENLYRSVDELELSVRSANCLKNAGIKMIGELVSRSEAEMLKTQ 295

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWP-PESIEELAKKYEDK 339
           NFGRKSL EIK +L  MGL LGM L  +P PE +  +  + +D+
Sbjct: 296 NFGRKSLNEIKDILADMGLTLGMKLDGFPDPEVMRRIRGERKDE 339


>gi|193795092|gb|ACF21675.1| RpoA [Sinorhizobium sp. 206]
          Length = 212

 Score =  316 bits (810), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 150/213 (70%), Positives = 181/213 (84%), Gaps = 1/213 (0%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           KR+ + K+GPG VTAGDIQTV DIE+LNPDHVIC LD  A +RME TV+ G GYVPA  +
Sbjct: 1   KRMVVRKQGPGAVTAGDIQTVGDIEILNPDHVICTLDEGAEIRMEFTVNNGKGYVPADRN 60

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKL+MTI+TDGS+TGED+VA A+
Sbjct: 61  RAEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLTMTIETDGSVTGEDAVAFAA 120

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           RILQDQLG+F+NF+EP+KE +E+ +V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+
Sbjct: 121 RILQDQLGVFVNFDEPQKEAEEE-SVTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           GDLIQ+TEA+MLR  NFGRKSL EIK VL +M 
Sbjct: 180 GDLIQKTEAEMLRTPNFGRKSLNEIKEVLASMA 212


>gi|193795090|gb|ACF21674.1| RpoA [Rhizobium tropici]
          Length = 212

 Score =  316 bits (809), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 151/213 (70%), Positives = 182/213 (85%), Gaps = 1/213 (0%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           KR+ + K+GPGVVTAGDIQTV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +
Sbjct: 1   KRMVVRKQGPGVVTAGDIQTVGDIEILNPEHVICTLDEGAEIRMEFTVNNGKGYVPAERN 60

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKLSM+I+TDGSITGED+VA A+
Sbjct: 61  RAEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLSMSIETDGSITGEDAVAFAA 120

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           RILQDQLG+F+NF+EP+KE +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+
Sbjct: 121 RILQDQLGVFVNFDEPQKEAEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           GDLIQ+TEA+MLR  N GRKSL EIK VL +MG
Sbjct: 180 GDLIQKTEAEMLRTPNLGRKSLNEIKEVLASMG 212


>gi|192362391|ref|YP_001981233.1| DNA-directed RNA polymerase subunit alpha [Cellvibrio japonicus
           Ueda107]
 gi|238692458|sp|B3PK62|RPOA_CELJU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|190688556|gb|ACE86234.1| DNA-directed RNA polymerase, alpha subunit [Cellvibrio japonicus
           Ueda107]
          Length = 328

 Score =  316 bits (809), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 157/332 (47%), Positives = 228/332 (68%), Gaps = 9/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    E + P +I+   + +    R  ++ EPL RGF HTLGNALRR+L+SS+ G AI 
Sbjct: 1   MQTAVNEFLTPRHID---VSEITPTRARVVLEPLERGFGHTLGNALRRILLSSMAGCAIV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ + M G     +T+ K+GPGVVTAGDIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVREDVIEILLNLKGVAVVMHGKDSTVLTLSKKGPGVVTAGDIQV 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E+ NPDHVI N+  +  ++M LT+++G GY PA   R ++D    IG + +DA +S
Sbjct: 118 DHDVEIKNPDHVIANITGNTELKMRLTIARGRGYQPADSRRRDDDESRAIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+K+++Y+VESAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++ E  K
Sbjct: 178 PVKRLAYSVESARVEQRTDLDKLVLDLETNGTIDPEEAIRRAATILQQQLAVFVDLEGEK 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +   E    K    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 QSAPEQ---KEEAIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           G+KSL EIK VL + GL LGM L +WPP S++
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLK 326


>gi|302344329|ref|YP_003808858.1| DNA-directed RNA polymerase, subunit alpha [Desulfarculus baarsii
           DSM 2075]
 gi|301640942|gb|ADK86264.1| DNA-directed RNA polymerase, alpha subunit [Desulfarculus baarsii
           DSM 2075]
          Length = 334

 Score =  315 bits (808), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 166/328 (50%), Positives = 229/328 (69%), Gaps = 10/328 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTL----MIAEPLPRGFAHTLGNALRRVLMSSLRG 57
           +++NW+ELIKP+ ++      +EE  T        EPL RGF HT+GNALRR+L+SSL+G
Sbjct: 1   MERNWRELIKPSRLQI-----DEEIHTSRYGKFSCEPLERGFGHTIGNALRRILISSLQG 55

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
           AA+T ++++GVLHE S+I GV ED+TDIILN+KGI L+  G     +TI  +G GVV AG
Sbjct: 56  AAVTNLRMEGVLHEFSTIPGVLEDVTDIILNLKGIQLRYLGFDSTTMTISAQGEGVVKAG 115

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI+T  D+E+LNP+H I  L  +  +  ELTV  G GYV A+ +++  DPIG I ID+ +
Sbjct: 116 DIKTPPDVEILNPEHHIATLSPEGRLEAELTVRTGKGYVTAERNKSPEDPIGYIAIDSAF 175

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPI KVSY V  AR GQ+ DYDKL++ + T+G++  ED+VA A++IL++QL +FINF E 
Sbjct: 176 SPITKVSYVVTQARVGQITDYDKLTLEVHTNGAVRPEDAVAYAAKILKEQLQIFINFPE- 234

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           + E   +   +    N  L + V+ELELSVRS NCL+  +I Y+G+L+QR+EA+ML+  N
Sbjct: 235 EPEPTHEEEREEPRLNENLFRTVDELELSVRSANCLKNADIKYIGELVQRSEAEMLKTKN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           FGRKSL EIK +L  MGL LGM L  +P
Sbjct: 295 FGRKSLNEIKEMLTDMGLSLGMKLDGFP 322


>gi|193795070|gb|ACF21666.1| RpoA [Rhizobium tropici CIAT 899]
 gi|193795078|gb|ACF21669.1| RpoA [Rhizobium tropici]
          Length = 212

 Score =  315 bits (808), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 150/213 (70%), Positives = 182/213 (85%), Gaps = 1/213 (0%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           KR+ + K+GPGVVTAGDIQTV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +
Sbjct: 1   KRMVVRKQGPGVVTAGDIQTVGDIEILNPEHVICTLDEGAEIRMEFTVNNGKGYVPAERN 60

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKLSM+I+TDGSI+GED+VA A+
Sbjct: 61  RAEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLSMSIETDGSISGEDAVAFAA 120

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           RILQDQLG+F+NF+EP+KE +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+
Sbjct: 121 RILQDQLGVFVNFDEPQKEAEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           GDLIQ+TEA+MLR  NFGRKSL EIK VL +M 
Sbjct: 180 GDLIQKTEAEMLRTPNFGRKSLNEIKEVLASMA 212


>gi|193795075|gb|ACF21668.1| RpoA [Rhizobium tropici]
 gi|193795083|gb|ACF21671.1| RpoA [Rhizobium tropici]
          Length = 212

 Score =  315 bits (808), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 150/213 (70%), Positives = 182/213 (85%), Gaps = 1/213 (0%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           KR+ + K+GPGVVTAGDIQTV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +
Sbjct: 1   KRMVVRKQGPGVVTAGDIQTVGDIEILNPEHVICTLDEGAEIRMEFTVNNGKGYVPAERN 60

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKLSM+I+TDGSI+GED+VA A+
Sbjct: 61  RAEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLSMSIETDGSISGEDAVAFAA 120

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           RILQDQLG+F+NF+EP+KE +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+
Sbjct: 121 RILQDQLGVFVNFDEPQKETEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           GDLIQ+TEA+MLR  NFGRKSL EIK VL +M 
Sbjct: 180 GDLIQKTEAEMLRTPNFGRKSLNEIKEVLASMA 212


>gi|193795081|gb|ACF21670.1| RpoA [Rhizobium gallicum]
          Length = 212

 Score =  315 bits (807), Expect = 6e-84,   Method: Compositional matrix adjust.
 Identities = 149/213 (69%), Positives = 182/213 (85%), Gaps = 1/213 (0%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           KR+ + K+GPGVVTAGDIQTV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +
Sbjct: 1   KRMVVRKQGPGVVTAGDIQTVGDIEILNPEHVICTLDEGAEIRMEFTVNNGKGYVPAERN 60

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKL+MTI+TDGS++GED+VA A+
Sbjct: 61  RAEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLTMTIETDGSVSGEDAVAFAA 120

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           RILQDQLG+F+NF+EP+KE +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+
Sbjct: 121 RILQDQLGVFVNFDEPQKEAEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           GDLIQ+TEA+MLR  NFGRKSL EIK VL +M 
Sbjct: 180 GDLIQKTEAEMLRTPNFGRKSLNEIKEVLASMA 212


>gi|193795063|gb|ACF21663.1| RpoA [Rhizobium giardinii]
          Length = 212

 Score =  314 bits (804), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 150/213 (70%), Positives = 181/213 (84%), Gaps = 1/213 (0%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           KR+ + K+GPGVVTAGDIQTV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA  +
Sbjct: 1   KRMVVRKQGPGVVTAGDIQTVGDIEILNPNHVICTLDEGAEIRMEFTVNNGKGYVPADRN 60

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R+E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKLSM I+TDGS+TGED+VA A+
Sbjct: 61  RSEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLSMQIETDGSVTGEDAVAFAA 120

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           RILQDQLG+F+NF+EP+KE +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+
Sbjct: 121 RILQDQLGVFVNFDEPQKEAEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           GDLIQ+TEA+MLR  N GRKSL EIK VL +MG
Sbjct: 180 GDLIQKTEAEMLRTPNLGRKSLNEIKEVLASMG 212


>gi|51245004|ref|YP_064888.1| DNA-directed RNA polymerase subunit alpha [Desulfotalea
           psychrophila LSv54]
 gi|61215903|sp|Q6AP43|RPOA_DESPS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|50876041|emb|CAG35881.1| probable DNA-directed RNA polymerase, alpha subunit [Desulfotalea
           psychrophila LSv54]
          Length = 343

 Score =  314 bits (804), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 157/324 (48%), Positives = 224/324 (69%), Gaps = 2/324 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +NW ELI+P  +E I      E     I +PL RGFA T+GN+LRR+L+SS++GAAIT
Sbjct: 11  VYRNWHELIRPEKVE-IDQSNHSETYGKFICQPLERGFATTIGNSLRRILLSSIQGAAIT 69

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+G LHE++S+K V ED+++IILN+K + LK++ +  + V I K+GPG V AGDI  
Sbjct: 70  TVKIEGALHELTSMKDVKEDVSEIILNLKQVRLKLNCEESQTVRIEKQGPGPVVAGDIIP 129

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              +E++N DH++CNL  D     ELTV  G GY PA++   ++  +G I IDA+++P+K
Sbjct: 130 SAFVEIMNEDHILCNLTSDMTFCAELTVEWGKGYQPAENQEKDDLTVGQIPIDAIFTPVK 189

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           K+ Y V SAR GQ  DYDKL+  I+TDGS+  ED++A +++IL++QL +FINF+E   E 
Sbjct: 190 KIQYVVSSARVGQQTDYDKLTYEIETDGSVRPEDALAYSAKILKEQLDIFINFDETAVEP 249

Query: 242 -KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            K+ +  +    NP L K VE+LELSVRS NCL+  +I ++GDL+QRT+ +ML+  NFGR
Sbjct: 250 EKKAVETEEKQENPYLDKPVEDLELSVRSANCLKNADINFIGDLVQRTDQEMLKTKNFGR 309

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDW 324
           KSL EIK +L  M L LG+ L  W
Sbjct: 310 KSLNEIKTLLQDMDLTLGVKLEGW 333


>gi|190571569|ref|YP_001975927.1| DNA-directed RNA polymerase, alpha subunit [Wolbachia endosymbiont
           of Culex quinquefasciatus Pel]
 gi|213018971|ref|ZP_03334778.1| DNA-directed RNA polymerase, alpha subunit [Wolbachia endosymbiont
           of Culex quinquefasciatus JHB]
 gi|190357841|emb|CAQ55297.1| DNA-directed RNA polymerase, alpha subunit [Wolbachia endosymbiont
           of Culex quinquefasciatus Pel]
 gi|212995080|gb|EEB55721.1| DNA-directed RNA polymerase, alpha subunit [Wolbachia endosymbiont
           of Culex quinquefasciatus JHB]
          Length = 355

 Score =  313 bits (803), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 160/345 (46%), Positives = 233/345 (67%), Gaps = 12/345 (3%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           N   L KPN I+  V+  +   ++ ++ EPL  GFA TLG+ALRRV++SSLRG+A+  ++
Sbjct: 12  NLDRLTKPNAIK--VISGDSSKKSDIVLEPLESGFALTLGHALRRVMLSSLRGSAVYGIK 69

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           I+GV HE +SI+GV ED+TDI LN+  +  K++  S+K + +  +GP  V AG I+T + 
Sbjct: 70  IEGVNHEFTSIQGVREDITDIALNMGMLRCKLNNTSNKCLNLSAKGPCQVLAGMIETDDQ 129

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--------TENDPIGLITIDAL 176
             ++N D VIC L  D  + + + ++ G GY+    ++         E D IG I ++AL
Sbjct: 130 CSIVNKDLVICTLGQDVELNITIYIASGKGYLSVNKYKENEFLKSMNEQDLIGFIPVNAL 189

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI--NF 234
           YSP+++VSY VE++R GQV D DKL ++I+TDG+I+   +V  A+RILQ+Q   FI  + 
Sbjct: 190 YSPVERVSYRVENSRVGQVTDKDKLILSIETDGTISPSQAVDYAARILQEQFQPFISSDM 249

Query: 235 EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
              K +V      K L ++P LL+KV+E+ELSVRS NCL+ ENI Y+GDL+Q+TE +MLR
Sbjct: 250 SYKKSQVSLSSGAKDLGYDPVLLRKVDEMELSVRSHNCLKNENITYIGDLVQKTEVEMLR 309

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            ANFGRKSL EIK +L   GL LGMN+P+WPP+ I+ELAK++ D+
Sbjct: 310 TANFGRKSLNEIKAILNNSGLSLGMNIPNWPPKDIDELAKQHTDE 354


>gi|254516935|ref|ZP_05128993.1| DNA-directed RNA polymerase, alpha subunit [gamma proteobacterium
           NOR5-3]
 gi|219674440|gb|EED30808.1| DNA-directed RNA polymerase, alpha subunit [gamma proteobacterium
           NOR5-3]
          Length = 334

 Score =  313 bits (803), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 157/331 (47%), Positives = 225/331 (67%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q + +EL+ P  I    + ++ + R  +  EPL RGF HTLGNALRR+L+SS+ G AIT
Sbjct: 1   MQSSVKELLTPRKIN---VAEKSKTRAQVTLEPLERGFGHTLGNALRRILLSSMPGCAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ +I+LN+KG+ L M+G     + + K G G VTA DIQT
Sbjct: 58  EVEIDGVLHEYSAIEGVQEDVIEILLNLKGVALIMNGKDEAELVLSKEGEGPVTAADIQT 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYS 178
            +DIE+ NPDH+IC L+  + V M+LTV++G GY PA   ++   E   IG + +DA +S
Sbjct: 118 DHDIEICNPDHLICTLNSKSAVHMKLTVARGRGYSPADARENPEEETRSIGRLQLDATFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +VSY VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL DQL +F++ +   
Sbjct: 178 PVLRVSYVVEAARVEQRTDLDKLVLDLETNGTIDPEEAIRRAATILNDQLRVFVDLQSET 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V  D   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N 
Sbjct: 238 QAVTSDAEDE---VDPVLLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L  WPP S+
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLESWPPASL 325


>gi|148263165|ref|YP_001229871.1| DNA-directed RNA polymerase subunit alpha [Geobacter uraniireducens
           Rf4]
 gi|146396665|gb|ABQ25298.1| DNA-directed RNA polymerase subunit alpha [Geobacter uraniireducens
           Rf4]
          Length = 340

 Score =  313 bits (803), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 170/337 (50%), Positives = 229/337 (67%), Gaps = 11/337 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRT----LMIAEPLPRGFAHTLGNALRRVLMSSLRG 57
           + +NW++LIKP  ++      E E+ T       AEP  RGF  TLGN+LRRVL+SSL+G
Sbjct: 1   MYRNWRDLIKPKKLQV-----ETESLTNTYGKFYAEPFERGFGTTLGNSLRRVLLSSLQG 55

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
           AAIT+V+  GVLHE S+I GV ED TDIILN+KG+  KM G   + V I ++G G+V AG
Sbjct: 56  AAITSVKAKGVLHEFSAIPGVTEDATDIILNLKGVRFKMHGHESRVVRIVQKGEGLVKAG 115

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI T  ++EVLNP+H I     DA + ME+ V  G GYVPA  +R E  P+G I ID+++
Sbjct: 116 DIITDPNVEVLNPNHHIATCSKDANLEMEMVVKMGKGYVPADRNRDEKAPVGTIPIDSIF 175

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-E 236
           SP+ KV++TV +AR GQ+ DYDKL + I TDGS+  +D++A AS+IL+DQL +FINF+ E
Sbjct: 176 SPLTKVNFTVSNARVGQITDYDKLIIEIWTDGSVKPQDALAYASKILKDQLTIFINFDEE 235

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +   + +   +   FN  L + V+ELELSVRS NCL+   I  +G+L+ RTEA+ML+  
Sbjct: 236 VEPVEEVEPEEERERFNENLYRSVDELELSVRSANCLKNAGIKLIGELVSRTEAEMLKTQ 295

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWP-PESIEEL 332
           NFGRKSL EIK +L  MGL LGM L ++P PE +  L
Sbjct: 296 NFGRKSLNEIKDILVDMGLTLGMRLDNFPDPEIMRRL 332


>gi|83858542|ref|ZP_00952064.1| DNA-directed RNA polymerase alpha subunit [Oceanicaulis alexandrii
           HTCC2633]
 gi|83853365|gb|EAP91217.1| DNA-directed RNA polymerase alpha subunit [Oceanicaulis alexandrii
           HTCC2633]
          Length = 274

 Score =  313 bits (802), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 155/256 (60%), Positives = 198/256 (77%), Gaps = 1/256 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +I+KNWQELI+P   E I  G +   +  +IAEPL RGF  TLGNALRR+L+SSL+GA+I
Sbjct: 20  VIEKNWQELIRPMKPE-IQPGFDPVRQAKIIAEPLERGFGMTLGNALRRILLSSLQGASI 78

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID VLHE SSIKGV ED+TDIILN+K + L+M G+  KR+T+ K+GPG VTAGDI+
Sbjct: 79  TAVQIDSVLHEFSSIKGVREDVTDIILNLKQVALRMHGEGPKRLTLKKQGPGEVTAGDIE 138

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              D+E++N DHVIC LD DA VRM LTV+ G GYVPA  +R E+ PIGLI +DALYSP+
Sbjct: 139 ETADVEIINKDHVICTLDEDADVRMVLTVNTGKGYVPADRNRPEDAPIGLIGVDALYSPV 198

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V+Y VE+ REGQVLDYDKL + ++T+G++T ED+VA A+RILQDQ  +F+NFEEP + 
Sbjct: 199 KRVAYRVENTREGQVLDYDKLILEVETNGAVTPEDAVAYAARILQDQFQIFVNFEEPSEA 258

Query: 241 VKEDINVKSLPFNPAL 256
              + +   L FNPAL
Sbjct: 259 RAAEDDKPELDFNPAL 274


>gi|152998246|ref|YP_001343081.1| DNA-directed RNA polymerase subunit alpha [Marinomonas sp. MWYL1]
 gi|150839170|gb|ABR73146.1| DNA-directed RNA polymerase, alpha subunit [Marinomonas sp. MWYL1]
          Length = 334

 Score =  313 bits (801), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 160/337 (47%), Positives = 232/337 (68%), Gaps = 11/337 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  EL+ P NIE   LG      TL   +PL RGF HTLGNALRR+L+SS+ G AI 
Sbjct: 1   MQRSVSELLTPRNIEVQELGNCRAKVTL---QPLERGFGHTLGNALRRILLSSMPGCAIV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ +I+LN+KG+ + + G     +T+ K+GPG+VTAGDIQ 
Sbjct: 58  EVEIDGVLHEYSAIEGVKEDVIEILLNLKGVAIALHGQDEATLTLSKKGPGIVTAGDIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
           V D E+ NPDH+I +LD  A + M++ V++G GY PA      +D   PIG + +DA +S
Sbjct: 118 VADAEIANPDHIIAHLDDTAELTMQIKVARGRGYEPADARVAGDDETRPIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EP 237
           P+++V+Y+V++AR  Q  D DKL + I+++G+I  E+++  A+ ILQ Q+ +F+  E E 
Sbjct: 178 PVRRVAYSVDNARVEQRTDLDKLVLDIESNGTIDPEEAIRRAATILQQQIAVFVALESES 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +  V E+ +      +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N
Sbjct: 238 EAPVVEEED----EIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
            G+KSL EIK VL   GL LGM L +WPP S+++ +K
Sbjct: 294 LGKKSLTEIKDVLAQRGLSLGMRLENWPPASLKDDSK 330


>gi|222056679|ref|YP_002539041.1| DNA-directed RNA polymerase, alpha subunit [Geobacter sp. FRC-32]
 gi|221565968|gb|ACM21940.1| DNA-directed RNA polymerase, alpha subunit [Geobacter sp. FRC-32]
          Length = 340

 Score =  312 bits (800), Expect = 4e-83,   Method: Compositional matrix adjust.
 Identities = 172/335 (51%), Positives = 230/335 (68%), Gaps = 11/335 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRT----LMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           KNW++LIKP  ++      E E+ T       AEP  RGF  TLGN+LRRVL+SSL+GAA
Sbjct: 3   KNWRDLIKPKKLQV-----ETESLTNTYGKFYAEPFERGFGTTLGNSLRRVLLSSLQGAA 57

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           IT+V+  GVLHE S+I GV ED TDIILN+KG+  KM G   + V I ++G G+V AGDI
Sbjct: 58  ITSVKAKGVLHEFSAIPGVTEDATDIILNLKGVRFKMHGHEPRVVRIAQKGEGIVRAGDI 117

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
            T  +IEVLNP+H I     DA + ME+ V  G GYVPA  +R E  P+G I ID+++SP
Sbjct: 118 ITDPNIEVLNPNHHIATCSKDANLEMEMVVKLGKGYVPADRNRDEKAPVGTIPIDSIFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           + KV++TV +AR GQ+ DYDKL++ + TDGS+  +D+VA AS+IL+DQL +FINF+E  +
Sbjct: 178 LTKVNFTVTNARVGQITDYDKLTIEVWTDGSVKPQDAVAYASKILKDQLTIFINFDEEVE 237

Query: 240 EVKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            V+E   ++     N  L + V+ELELSVRS NCL+   I  +G+L+ R+EA+ML+  NF
Sbjct: 238 PVEEAEPMEERERLNENLYRSVDELELSVRSANCLKNAGIKLIGELVSRSEAEMLKTQNF 297

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWP-PESIEEL 332
           GRKSL EIK +L  MGL LGM L ++P PE +  L
Sbjct: 298 GRKSLNEIKDILVDMGLTLGMKLDNFPDPEIMRRL 332


>gi|193795065|gb|ACF21664.1| RpoA [Sinorhizobium sp. 72]
          Length = 212

 Score =  312 bits (799), Expect = 5e-83,   Method: Compositional matrix adjust.
 Identities = 147/213 (69%), Positives = 182/213 (85%), Gaps = 1/213 (0%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           KR+ + K+GPGVVTAGDIQTV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +
Sbjct: 1   KRMVVRKQGPGVVTAGDIQTVGDIEILNPNHVICTLDEGAEIRMEFTVNNGKGYVPAERN 60

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R+E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKL+M+I+TDGS+TGED++A A+
Sbjct: 61  RSEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLTMSIETDGSVTGEDAIAFAA 120

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           RILQDQL +F+NF+EP+KE +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+
Sbjct: 121 RILQDQLSVFVNFDEPQKEAEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           GDLIQ+TEA+MLR  NFGRKSL EIK VL + G
Sbjct: 180 GDLIQKTEAEMLRTPNFGRKSLNEIKEVLASSG 212


>gi|220935467|ref|YP_002514366.1| DNA-directed RNA polymerase subunit alpha [Thioalkalivibrio sp.
           HL-EbGR7]
 gi|254765261|sp|B8GV33|RPOA_THISH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|219996777|gb|ACL73379.1| DNA-directed RNA polymerase subunit alpha [Thioalkalivibrio sp.
           HL-EbGR7]
          Length = 334

 Score =  311 bits (798), Expect = 7e-83,   Method: Compositional matrix adjust.
 Identities = 155/337 (45%), Positives = 227/337 (67%), Gaps = 9/337 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    EL+KP +IE   +   +     ++ EPL RGF HTLGNALRR+L+SS+ GAA+ 
Sbjct: 1   MQTKVNELLKPRHIEVTSVSDRQAK---VVLEPLERGFGHTLGNALRRILLSSIPGAAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +I+GVLHE +SI+GV ED+ DI+LN+KGI L+M       +T+ K+GPGVVTAGDI  
Sbjct: 58  EAEIEGVLHEYTSIEGVQEDVVDILLNLKGIALRMHNRDEATLTLKKKGPGVVTAGDITL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYS 178
            +D+E++NP+HVI +L  +  + M L + +G GY P    R   +E+ PIG + +DA +S
Sbjct: 118 DHDVEIVNPEHVIAHLTKNGELSMSLKLGRGRGYQPVTARRSSESEDRPIGRLMLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI++V+Y VESAR  Q  D D+L + ++T+G++  +D++  A+ ILQ QL  F+  +  +
Sbjct: 178 PIRRVAYKVESARVEQRTDMDRLVIELETNGTVEADDAIRQAAGILQSQLAAFVELQGDE 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
             V E    K +  +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 STVTES---KQMEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
           G+KSL EIK VL + GL +GM L +WPP  +++  KK
Sbjct: 295 GKKSLTEIKDVLASHGLSMGMRLENWPPPGLKDQDKK 331


>gi|120553677|ref|YP_958028.1| DNA-directed RNA polymerase subunit alpha [Marinobacter aquaeolei
           VT8]
 gi|158513044|sp|A1TYM2|RPOA_MARAV RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|120323526|gb|ABM17841.1| DNA-directed RNA polymerase subunit alpha [Marinobacter aquaeolei
           VT8]
          Length = 334

 Score =  311 bits (797), Expect = 9e-83,   Method: Compositional matrix adjust.
 Identities = 156/331 (47%), Positives = 228/331 (68%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  EL+ P  I+   + +    R  +  EPL RGF HTLG+ALRR+L+SS+ G A+T
Sbjct: 1   MQRSVHELLTPRTID---VKESSATRAKVTLEPLERGFGHTLGSALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             QIDGVLHE S+I+GV ED+ +I+LN+KG+ +KM+G     +T+ K+GPGVVTAGDI+ 
Sbjct: 58  EAQIDGVLHEYSAIEGVQEDVIEILLNLKGVAVKMNGRDDAELTLSKKGPGVVTAGDIKL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E+ NP+HVIC+L  +  V M L V++G GY PA     + D    IG + +DA +S
Sbjct: 118 DHDVEIANPEHVICHLSENGEVNMRLRVARGRGYEPADQRGLDEDETRAIGRLQLDATFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++V+Y VESAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++F+  K
Sbjct: 178 PVRRVAYAVESARVEQRTDLDKLVIDLETNGTIDPEEAIRRAATILQQQLAVFVDFDHEK 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +  +     +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPER---VEEEEEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASL 325


>gi|193795072|gb|ACF21667.1| RpoA [Rhizobium tropici]
          Length = 212

 Score =  311 bits (797), Expect = 9e-83,   Method: Compositional matrix adjust.
 Identities = 149/213 (69%), Positives = 180/213 (84%), Gaps = 1/213 (0%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           KR+ + K+GPGVVTAGDIQTV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +
Sbjct: 1   KRMVVRKQGPGVVTAGDIQTVGDIEILNPEHVICTLDEGAEIRMEFTVNNGKGYVPAERN 60

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKLSM+I+TDGSITGED+VA A+
Sbjct: 61  RAEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLSMSIETDGSITGEDAVAFAA 120

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           RILQDQLG+F+NF+EP+KE +E+  V  L FNPALLKKV+E E SVRS NCL+ +NIVY+
Sbjct: 121 RILQDQLGVFVNFDEPQKEAEEEA-VTELAFNPALLKKVDERERSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           GDLIQ+TEA+MLR  N GRKSL EIK VL +MG
Sbjct: 180 GDLIQKTEAEMLRTPNLGRKSLNEIKEVLASMG 212


>gi|88606699|ref|YP_504915.1| DNA-directed RNA polymerase subunit alpha [Anaplasma
           phagocytophilum HZ]
 gi|119366662|sp|Q2GL36|RPOA_ANAPZ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|88597762|gb|ABD43232.1| DNA-directed RNA polymerase, alpha subunit [Anaplasma
           phagocytophilum HZ]
          Length = 344

 Score =  311 bits (796), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 167/344 (48%), Positives = 236/344 (68%), Gaps = 14/344 (4%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           +W +L +P++I+  V+G +E     ++ EPL  GFA TLGNALRRV+MSSLRG A+  ++
Sbjct: 4   HWNKLTRPSSIK--VVGGKEPCVMELVIEPLESGFALTLGNALRRVMMSSLRGFAVYGIE 61

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           I+G  HE++++ GV ED+ D++LN+  + +K+   + + + +  RGPG VTA  I    D
Sbjct: 62  IEGASHELTALSGVREDVADLVLNLSMLRVKLLNSNQRVLRLVARGPGEVTAASIVDSAD 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP-------IGLITIDALY 177
             VLN D  IC L  D    M++ V+ G GYVPA  +R  +          G I  +ALY
Sbjct: 122 HVVLNKDLHICTLGKDVDFCMKIYVNSGKGYVPATEYRAASRSGGASEVGSGFIATNALY 181

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF--- 234
           SP+KKV+  +ES+R GQ  DYD+L +T++TDGS+  +D+VA+A++ILQDQL  FI+F   
Sbjct: 182 SPVKKVALKIESSRIGQFTDYDRLMLTVETDGSVAPDDAVAVAAKILQDQLQSFISFDEV 241

Query: 235 EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           EE +K V ++  V  LP++  LL+KV+ELELSVRS NCL+ +NI Y+GDL+QRTE+DMLR
Sbjct: 242 EETRKSVDKEEGV--LPYDHNLLRKVDELELSVRSHNCLKNDNITYIGDLVQRTESDMLR 299

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
             NFGRKSL EI  VL +M L LGM +P+WPPESIE L+K+Y +
Sbjct: 300 TPNFGRKSLNEINEVLASMNLHLGMKVPNWPPESIENLSKQYSE 343


>gi|218680479|ref|ZP_03528376.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli CIAT 894]
          Length = 208

 Score =  311 bits (796), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 147/208 (70%), Positives = 178/208 (85%), Gaps = 1/208 (0%)

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
           HVIC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +D+LYSP+KKVSY VE+ R
Sbjct: 1   HVICTLDEGAEIRMEFTVNNGKGYVPAERNRAEDAPIGLIPVDSLYSPVKKVSYKVENTR 60

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           EGQVLDYDKL+MTI+TDGSITGED+VA A+RILQDQLG+F+NF+EP+KE +E+  V  L 
Sbjct: 61  EGQVLDYDKLNMTIETDGSITGEDAVAFAARILQDQLGVFVNFDEPQKETEEEA-VTELA 119

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
           FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGRKSL EIK VL 
Sbjct: 120 FNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRKSLNEIKEVLA 179

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
           +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 180 SMGLHLGMEVPAWPPENIEDLAKRYEDQ 207


>gi|88704351|ref|ZP_01102065.1| DNA-directed RNA polymerase alpha chain [Congregibacter litoralis
           KT71]
 gi|88701402|gb|EAQ98507.1| DNA-directed RNA polymerase alpha chain [Congregibacter litoralis
           KT71]
          Length = 334

 Score =  310 bits (794), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 154/331 (46%), Positives = 225/331 (67%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q + ++L+ P  I    + ++ + R  +  EPL RGF HTLGNALRR+L+SS+ G AIT
Sbjct: 1   MQSSVKDLLTPRKIN---VAEKSKTRAQVTLEPLERGFGHTLGNALRRILLSSMPGCAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ +I+LN+KG+ L M+G     + + K G G VTA DIQT
Sbjct: 58  EVEIDGVLHEYSAIEGVQEDVIEILLNLKGVALIMNGKDEAELVLSKEGEGPVTAADIQT 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYS 178
            +DIE+ NP+H+IC L+  + V M+LT+++G GY PA   ++   E   IG + +DA +S
Sbjct: 118 DHDIEICNPEHLICTLNSKSAVHMKLTIARGRGYSPADARENPEEETRSIGRLQLDATFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +VSY VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL DQL +F++ +   
Sbjct: 178 PVMRVSYVVEAARVEQRTDLDKLVLDLETNGTIDPEEAIRRAATILNDQLRVFVDLQSET 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V  D   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N 
Sbjct: 238 QAVTSDAEDE---VDPVLLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L  WPP S+
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLESWPPASL 325


>gi|158518607|sp|Q6MJ36|RPOA_BDEBA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 343

 Score =  310 bits (793), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 160/323 (49%), Positives = 219/323 (67%), Gaps = 2/323 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           K W+E+IKP   E +      ++    I  PL RGF  TLGN+LRR+L+SS+ G+AITAV
Sbjct: 7   KFWREMIKPKGFE-VDRDSLRDDYAKFIIRPLERGFGVTLGNSLRRILLSSMMGSAITAV 65

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           + +GVLHE ++I  V ED+TDIILN+K +  K        + I K+GPG VTA DIQT +
Sbjct: 66  KFEGVLHEFTTIPDVLEDVTDIILNLKEVRFKQYTADSLTLKISKKGPGKVTAADIQTTD 125

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            IEVLNPD  I  L  +A    E+ VS G GYVP ++  T+  P+G I +DALYSPI+KV
Sbjct: 126 KIEVLNPDLPIATLGANANFNAEIVVSFGRGYVPVENRETDL-PVGFIGVDALYSPIRKV 184

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y V +AR GQ  DYD L++ + TDGS+  E++VAL+S+I+++QL +F+ F+E  +  +E
Sbjct: 185 NYNVSNARVGQRTDYDALTLEVWTDGSLKPEEAVALSSKIMKEQLQIFLTFDETMEPAEE 244

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
              + S   N  L + V++LELSVRS NCL+  NI Y+G+L+ R+EA+ML+  NFGRKSL
Sbjct: 245 ARELGSPTLNENLFRSVDDLELSVRSANCLKNANIRYIGELVVRSEAEMLKTKNFGRKSL 304

Query: 304 VEIKGVLGTMGLFLGMNLPDWPP 326
            EIK +LG MGL LGM +  WPP
Sbjct: 305 NEIKEILGEMGLGLGMKIEGWPP 327


>gi|86158342|ref|YP_465127.1| DNA-directed RNA polymerase subunit alpha [Anaeromyxobacter
           dehalogenans 2CP-C]
 gi|119366661|sp|Q2IJ57|RPOA_ANADE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|85774853|gb|ABC81690.1| DNA-directed RNA polymerase subunit alpha [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 339

 Score =  310 bits (793), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 166/337 (49%), Positives = 232/337 (68%), Gaps = 5/337 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGA 58
           ++ KNW++LIKP  +   V+ Q+  + T    +AEPL RGF  TLGN+LRRVL+SSL+GA
Sbjct: 5   IVTKNWRDLIKPRGL---VVDQDSLSNTYGKFVAEPLERGFGITLGNSLRRVLLSSLQGA 61

Query: 59  AITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGD 118
           AIT+V+++GV HE  +I  V ED+TDIILN+K + L++  +  K + I   GP  + AGD
Sbjct: 62  AITSVKVEGVEHEFMTIPEVAEDVTDIILNLKEVLLQIHTNDVKTIRIEADGPKEIKAGD 121

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           + T   +EVLNP H I  +     VR E+T  +G GYVPA+ ++    PIG I IDAL+S
Sbjct: 122 LITDAQVEVLNPGHHILTISEGGRVRAEMTARRGRGYVPAERNKVPGSPIGTIPIDALFS 181

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI+KV+Y V +AR GQ  DYDKL++ + TDGS+   D+VA A++I+++QL +FINF+E +
Sbjct: 182 PIRKVNYQVTNARVGQQTDYDKLTLEVWTDGSVAPADAVAFAAKIVKEQLSIFINFDEAE 241

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +  +E   V+    N  L + V+ELELSVRS NCL+  NI  +GDL+Q+TEA+ML+  NF
Sbjct: 242 EPAEEIKPVEEQKLNENLFRSVDELELSVRSANCLQNANIKTIGDLVQKTEAEMLKTKNF 301

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
           GRKSL EIK +L  MGL LGM L +WPP++  + A K
Sbjct: 302 GRKSLKEIKEILAEMGLSLGMKLENWPPKAAPQGAPK 338


>gi|110833283|ref|YP_692142.1| DNA-directed RNA polymerase subunit alpha [Alcanivorax borkumensis
           SK2]
 gi|119366659|sp|Q0VSH8|RPOA_ALCBS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|110646394|emb|CAL15870.1| DNA-directed RNA polymerase, alpha subunit [Alcanivorax borkumensis
           SK2]
          Length = 335

 Score =  310 bits (793), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 153/310 (49%), Positives = 217/310 (70%), Gaps = 16/310 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EPL RGF HTLG ALRR+L+SS+ G AIT V+IDGV HE SSI+GV ED+ +I+LN+
Sbjct: 25  VVLEPLERGFGHTLGTALRRILISSMPGCAITEVEIDGVQHEYSSIEGVQEDVINILLNL 84

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM       + + K+GPGVVTA DIQ  + +E++NPDH+IC +  D  +R++L V
Sbjct: 85  KGVALKMEDSEETTLELVKKGPGVVTANDIQRDHSVEIVNPDHLICTITGDTELRVKLKV 144

Query: 150 SKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            KG GYV A   ++E+D    IG + +DA YSP+++V+Y VE+AR  Q  D DKL + ++
Sbjct: 145 QKGRGYVAADSRQSEDDETRGIGRLQLDASYSPVRRVAYVVEAARVEQRTDLDKLVIDLE 204

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFE-----EPKKEVKEDINVKSLPFNPALLKKVE 261
           TDG+I  E+++  A+ ILQ Q+ +F++ E     EPK+E +E         +P LL+ V+
Sbjct: 205 TDGTIEPEEAIRRAATILQQQIAVFVDLEQDAKPEPKQEREE--------IDPILLRPVD 256

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L
Sbjct: 257 DLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASKGLSLGMRL 316

Query: 322 PDWPPESIEE 331
            +WPP S+ +
Sbjct: 317 ENWPPVSLRD 326


>gi|322418391|ref|YP_004197614.1| DNA-directed RNA polymerase subunit alpha [Geobacter sp. M18]
 gi|320124778|gb|ADW12338.1| DNA-directed RNA polymerase, alpha subunit [Geobacter sp. M18]
          Length = 339

 Score =  309 bits (792), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 166/335 (49%), Positives = 230/335 (68%), Gaps = 11/335 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRT----LMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           +NW++LI+P  ++      E E+ T       AEP  RGF  TLG  LRRVL+SSL+GAA
Sbjct: 3   RNWRDLIRPKKLQV-----ETESLTNTYGKFYAEPFERGFGTTLGTGLRRVLISSLQGAA 57

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           I +V+  GVLHE S++ GV ED+TDIILN+KG+ LK+ G+  + + I ++G GVV A DI
Sbjct: 58  IVSVKAKGVLHEFSAVPGVTEDMTDIILNLKGVRLKVHGNESRMIRIVQKGEGVVKAKDI 117

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
            T N++E+LNP+H I     DA + M+L V  G GYVPA  +R E  P+G I IDA++SP
Sbjct: 118 VTDNNVEILNPEHHIATCSKDANLEMDLMVKVGKGYVPADRNRDEKAPVGTIPIDAIFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP-K 238
           + KV++TV +AR GQ+ DYDKL++ + TDGS+  +D+VA AS+IL+DQL +FINF+E  +
Sbjct: 178 VHKVNFTVTNARVGQITDYDKLTIEVWTDGSVKPQDAVAYASKILKDQLSIFINFDEDVE 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            + + +   +   FN  L + V+ELELSVRS NCL+   I  +G+L+ RTEA+ML+  NF
Sbjct: 238 PQEEAEPEEERERFNENLYRSVDELELSVRSANCLKNAGIKLIGELVSRTEAEMLKTQNF 297

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWP-PESIEEL 332
           GRKSL EIK +L  MGL LGM L ++P PE +  L
Sbjct: 298 GRKSLNEIKDILVDMGLTLGMKLENFPDPEIMRRL 332


>gi|332040527|gb|EGI76903.1| DNA-directed RNA polymerase subunit alpha [Hylemonella gracilis
           ATCC 19624]
          Length = 328

 Score =  309 bits (791), Expect = 4e-82,   Method: Compositional matrix adjust.
 Identities = 161/326 (49%), Positives = 217/326 (66%), Gaps = 6/326 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG    NR  +  EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKTINVEQLGP---NRAKVALEPFERGYGHTLGNALRRVLLSSMPGYAATEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE SSI GV ED+ +I+LN+KG+  K+       +++ K G GVVTAGDIQT +D+E++
Sbjct: 62  LHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGVVTAGDIQTPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYSPIKKVSY 185
           NP+HVI  L     + M++ V KG GYVP    +H   ++  IG I +DA YSP+K+VSY
Sbjct: 122 NPEHVIATLSAGGKLDMQIKVEKGRGYVPGTMRRHTDEQSKSIGRIVLDASYSPVKRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL + I+T+G+IT ED+V  +++IL +QL +F   +  +K      
Sbjct: 182 AVESARVEQRTDLDKLVIEIETNGTITAEDAVRASAKILVEQLAVFAQLDGSEKIFDTPS 241

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
              +  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GRKSL E
Sbjct: 242 QRSAGQFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRSENELLKTPNLGRKSLNE 301

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP ++E+
Sbjct: 302 IKEVLASRGLTLGMKLENWPPAALEK 327


>gi|87122790|ref|ZP_01078663.1| DNA-directed RNA polymerase alpha subunit [Marinomonas sp. MED121]
 gi|86161955|gb|EAQ63247.1| DNA-directed RNA polymerase alpha subunit [Marinomonas sp. MED121]
          Length = 334

 Score =  309 bits (791), Expect = 4e-82,   Method: Compositional matrix adjust.
 Identities = 159/336 (47%), Positives = 231/336 (68%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  EL+ P NIE    G+     TL   +PL RGF HTLGNALRR+L+SS+ G AI 
Sbjct: 1   MQRSVSELLTPRNIEVQEAGKTRSKVTL---QPLERGFGHTLGNALRRILLSSMPGCAIV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ +I+LN+KG+ + + G     +T+ K+GPGVVTAGDIQ 
Sbjct: 58  EVEIDGVLHEYSAIEGVKEDVIEILLNLKGVAIALHGQDEATLTLSKKGPGVVTAGDIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
           V D E+ NPDHVI +LD  A + M++ V++G GY PA      +D   PIG + +DA +S
Sbjct: 118 VADAEISNPDHVIAHLDDTAELNMQIKVARGCGYEPADARIASDDETRPIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY+V++AR  Q  D DKL + I+++G+I  E+++  A+ ILQ Q+ +F+     +
Sbjct: 178 PVRRVSYSVDNARVEQRTDLDKLVIDIESNGTIDPEEAIRRAATILQQQIAVFVAL---E 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E ++ +  +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 235 SESEQVVEEEEDEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL   GL LGM L +WPP S+++ +K
Sbjct: 295 GKKSLTEIKDVLAQRGLSLGMRLENWPPASLKDDSK 330


>gi|189424437|ref|YP_001951614.1| DNA-directed RNA polymerase subunit alpha [Geobacter lovleyi SZ]
 gi|189420696|gb|ACD95094.1| DNA-directed RNA polymerase, alpha subunit [Geobacter lovleyi SZ]
          Length = 340

 Score =  308 bits (790), Expect = 6e-82,   Method: Compositional matrix adjust.
 Identities = 160/342 (46%), Positives = 229/342 (66%), Gaps = 11/342 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTL----MIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           KNW++LIKP  ++      E+E  T      +AEP  RGF  TLGN+LRRVL+SSL+GAA
Sbjct: 3   KNWRDLIKPKQLQI-----EKETLTTTYGKFVAEPFERGFGTTLGNSLRRVLLSSLQGAA 57

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           IT+V+I GV HE SSI GV ED+TDIILN+K + L+  G     + I  +G G++ A DI
Sbjct: 58  ITSVRIKGVQHEFSSIPGVTEDVTDIILNLKSVRLRFHGADQATIRIIHKGDGIIKAADI 117

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
              +++E++NP+  I     DAV+ ME+TV  G GYV A  +R E  P+G I IDA++SP
Sbjct: 118 MVPHNVEIMNPEMHIATCGKDAVLEMEMTVKIGKGYVSADRNRDEKAPVGTIPIDAIFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I KV++ V +AR GQ+ DYDKL++ + TDGS+  +D++A A++I+++Q+ +FINF+E  +
Sbjct: 178 IIKVNFVVSNARVGQMTDYDKLTLEVWTDGSVKPDDAIAYAAKIVKEQMSIFINFDEESE 237

Query: 240 EVKEDINVK-SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            + +D   +     N  L + VEELELSVRS NCL+   I  +G+L+ +TEA+ML+  NF
Sbjct: 238 PLFQDEAAEDDSKINENLYRTVEELELSVRSANCLKNAGIKLIGELVSKTEAEMLKTQNF 297

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWP-PESIEELAKKYEDK 339
           GRKSL EIK +L  MGL  GM L  +P PE ++ L  + +D+
Sbjct: 298 GRKSLNEIKDILNEMGLTFGMKLDSFPDPEVVKRLRGEQKDE 339


>gi|253701895|ref|YP_003023084.1| DNA-directed RNA polymerase subunit alpha [Geobacter sp. M21]
 gi|251776745|gb|ACT19326.1| DNA-directed RNA polymerase, alpha subunit [Geobacter sp. M21]
          Length = 339

 Score =  308 bits (789), Expect = 7e-82,   Method: Compositional matrix adjust.
 Identities = 165/335 (49%), Positives = 230/335 (68%), Gaps = 11/335 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRT----LMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           +NW++LI+P  ++      E E+ T       AEP  RGF  TLG  LRRVL+SSL+GAA
Sbjct: 3   RNWRDLIRPKKLQV-----ETESLTNTYGKFFAEPFERGFGTTLGTGLRRVLISSLQGAA 57

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           I +V+  GVLHE S++ GV ED+TDIILN+KG+ LK+ G+  + + I ++G GVV A DI
Sbjct: 58  IVSVKAKGVLHEFSAVPGVTEDMTDIILNLKGVRLKVHGNESRMIRIVQKGEGVVKAKDI 117

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
            T N++E+LNP+H I     DA + M+L V  G GYVPA  +R E  P+G I IDA++SP
Sbjct: 118 ITDNNVEILNPEHHIATCSKDANLEMDLMVKVGKGYVPADRNRDEKAPVGTIPIDAIFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP-K 238
           + KV++TV +AR GQ+ DYDKL++ + TDGS+  +D+VA AS+IL+DQL +FINF+E  +
Sbjct: 178 VHKVNFTVTNARVGQITDYDKLTIELWTDGSVKPQDAVAYASKILKDQLSIFINFDEDVE 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            + + +   +   FN  L + V+ELELSVRS NCL+   I  +G+L+ R+EA+ML+  NF
Sbjct: 238 PQEEAEPEEERERFNENLYRSVDELELSVRSANCLKNAGIKLIGELVSRSEAEMLKTQNF 297

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWP-PESIEEL 332
           GRKSL EIK +L  MGL LGM L ++P PE +  L
Sbjct: 298 GRKSLNEIKDILVDMGLTLGMKLENFPDPEIMRRL 332


>gi|197117350|ref|YP_002137777.1| DNA-directed RNA polymerase subunit alpha [Geobacter bemidjiensis
           Bem]
 gi|197086710|gb|ACH37981.1| DNA-directed RNA polymerase, alpha subunit [Geobacter bemidjiensis
           Bem]
          Length = 339

 Score =  308 bits (789), Expect = 7e-82,   Method: Compositional matrix adjust.
 Identities = 165/335 (49%), Positives = 230/335 (68%), Gaps = 11/335 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRT----LMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           +NW++LI+P  ++      E E+ T       AEP  RGF  TLG  LRRVL+SSL+GAA
Sbjct: 3   RNWRDLIRPKKLQV-----ETESLTNTYGKFFAEPFERGFGTTLGTGLRRVLISSLQGAA 57

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           I +V+  GVLHE S++ GV ED+TDIILN+KG+ LK+ G+  + + I ++G GVV A DI
Sbjct: 58  IVSVKAKGVLHEFSAVPGVTEDMTDIILNLKGVRLKVHGNESRMIRIVQKGEGVVKAKDI 117

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
            T N++E+LNP+H I     DA + M+L V  G GYVPA  +R E  P+G I IDA++SP
Sbjct: 118 ITDNNVEILNPEHHIATCSKDANLEMDLMVKVGKGYVPADRNRDEKAPVGTIPIDAIFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP-K 238
           + KV++TV +AR GQ+ DYDKL++ + TDGS+  +D+VA AS+IL+DQL +FINF+E  +
Sbjct: 178 VHKVNFTVTNARVGQITDYDKLTIEVWTDGSVKPQDAVAYASKILKDQLSIFINFDEDVE 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            + + +   +   FN  L + V+ELELSVRS NCL+   I  +G+L+ R+EA+ML+  NF
Sbjct: 238 PQEEAEPEEERERFNENLYRSVDELELSVRSANCLKNAGIKLIGELVSRSEAEMLKTQNF 297

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWP-PESIEEL 332
           GRKSL EIK +L  MGL LGM L ++P PE +  L
Sbjct: 298 GRKSLNEIKDILVDMGLTLGMKLDNFPDPEIMRRL 332


>gi|303247018|ref|ZP_07333294.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio
           fructosovorans JJ]
 gi|302491725|gb|EFL51608.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio
           fructosovorans JJ]
          Length = 347

 Score =  308 bits (789), Expect = 8e-82,   Method: Compositional matrix adjust.
 Identities = 157/337 (46%), Positives = 225/337 (66%), Gaps = 2/337 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW EL+KP  +E      +   R   + EPL RGF  TLGNALRRVL+SSL+GAAI A 
Sbjct: 13  RNWTELVKPETLERDSASTDTHGR--FVCEPLERGFGTTLGNALRRVLLSSLQGAAIVAA 70

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+GV HE S+I GV ED+T++ILN+K + L M+ +  +R+T+F    G V A  IQ   
Sbjct: 71  RIEGVQHEFSTIPGVIEDVTEVILNLKQVRLAMATEDPQRLTLFANKKGEVLASAIQGNQ 130

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           ++ VL+ D +I  L  D   R+EL V  G GYV A  H   +  IGLI +D+ +SP+KKV
Sbjct: 131 NVTVLSEDVLIATLSEDRDFRIELEVRMGKGYVTADMHEGLDSEIGLILLDSSFSPVKKV 190

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +YT+E AR GQ+ +YDKL + +DTDGSI+ ED+++ +++IL+DQL +FINF+E + E  +
Sbjct: 191 AYTIEQARVGQMTNYDKLVLEVDTDGSISPEDAISYSAKILKDQLTVFINFDEKESEADK 250

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                 +  NP+L K ++ELELSVR+TNCL+  NI  +G+L+Q+TE +ML+  NFG+KSL
Sbjct: 251 ARRRDDIELNPSLFKSIDELELSVRATNCLKSANIQTVGELMQKTENEMLKTKNFGKKSL 310

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
            EI+ VL  MGL  GM + ++  +  E L +K  D+ 
Sbjct: 311 EEIRRVLEDMGLEFGMRIENFEQKYQEWLKRKQVDET 347


>gi|197122366|ref|YP_002134317.1| DNA-directed RNA polymerase subunit alpha [Anaeromyxobacter sp. K]
 gi|220917148|ref|YP_002492452.1| DNA-directed RNA polymerase, alpha subunit [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|238689847|sp|B4UBC6|RPOA_ANASK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|254765241|sp|B8J887|RPOA_ANAD2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|196172215|gb|ACG73188.1| DNA-directed RNA polymerase, alpha subunit [Anaeromyxobacter sp. K]
 gi|219955002|gb|ACL65386.1| DNA-directed RNA polymerase, alpha subunit [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 340

 Score =  308 bits (789), Expect = 9e-82,   Method: Compositional matrix adjust.
 Identities = 164/330 (49%), Positives = 229/330 (69%), Gaps = 5/330 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGA 58
           ++ KNW++LIKP  +   V+ Q+  + T    +AEPL RGF  TLGN+LRRVL+SSL+GA
Sbjct: 5   IVTKNWRDLIKPRGL---VVDQDSLSNTYGKFVAEPLERGFGITLGNSLRRVLLSSLQGA 61

Query: 59  AITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGD 118
           AIT+V+++GV HE  +I  V ED+TDIILN+K + L++  +  K + I   GP  + AGD
Sbjct: 62  AITSVKVEGVEHEFMTIPEVAEDVTDIILNLKEVLLQIHTNDVKTIRIEADGPKEIKAGD 121

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           + T   +EVLNP H I  +     VR E+T  +G GYVPA+ ++    PIG I IDAL+S
Sbjct: 122 LITDAQVEVLNPGHHILTISEGGRVRAEMTARRGRGYVPAERNKIPGSPIGTIPIDALFS 181

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI+KV+Y V +AR GQ  DYDKL++ + TDGS+   D+VA A++I+++QL +FINF+E +
Sbjct: 182 PIRKVNYQVTNARVGQQTDYDKLTLEVWTDGSVAPADAVAFAAKIVKEQLSIFINFDEAE 241

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +  +E   V+    N  L + V+ELELSVRS NCL+  NI  +GDL+Q+TEA+ML+  NF
Sbjct: 242 EPAEEIKPVEEQKLNENLFRSVDELELSVRSANCLQNANIKTIGDLVQKTEAEMLKTKNF 301

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPES 328
           GRKSL EIK +L  MGL LGM L +WPP++
Sbjct: 302 GRKSLKEIKEILAEMGLSLGMKLENWPPKA 331


>gi|90020631|ref|YP_526458.1| DNA-directed RNA polymerase subunit alpha [Saccharophagus degradans
           2-40]
 gi|119366723|sp|Q21M33|RPOA_SACD2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|89950231|gb|ABD80246.1| DNA-directed RNA polymerase, alpha subunit [Saccharophagus
           degradans 2-40]
          Length = 329

 Score =  308 bits (788), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 157/335 (46%), Positives = 225/335 (67%), Gaps = 15/335 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    E + P +I+   LG     R  ++ EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQSAVNEFLTPRHIDVTELGP---TRAKVVLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGV HE S+I+GV ED+ +I+LN+K + + M G     +++ K+GPG VTAGDIQ 
Sbjct: 58  EVEIDGVQHEYSAIEGVQEDVIEILLNLKNVAVVMHGKDQAVLSLSKQGPGAVTAGDIQV 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +DIE+ NP+ VI N+  D  + M LTVS+G GY P     T+ D    IG + +DA +S
Sbjct: 118 DHDIEIKNPELVIANITSDTSLSMRLTVSRGRGYQPVDARATDEDETRAIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--- 235
           P+++++Y+VESAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++ E   
Sbjct: 178 PVRRLAYSVESARVEQRTDLDKLVLDLETNGTIDPEEAIRRAATILQQQLAVFVDLEGEK 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           E + E KED        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+ 
Sbjct: 238 EAEPEQKED------QIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKT 291

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
            N G+KSL EIK +L + GL LGM L +WPP S++
Sbjct: 292 PNLGKKSLTEIKDILASRGLSLGMRLENWPPASLK 326


>gi|326793583|ref|YP_004311403.1| DNA-directed RNA polymerase subunit alpha [Marinomonas mediterranea
           MMB-1]
 gi|326544347|gb|ADZ89567.1| DNA-directed RNA polymerase subunit alpha [Marinomonas mediterranea
           MMB-1]
          Length = 334

 Score =  308 bits (788), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 157/336 (46%), Positives = 229/336 (68%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  EL+ P NIE   +       TL   +PL RGF HTLGNALRR+L+SS+ G AI 
Sbjct: 1   MQRSVSELLTPRNIEVQEISSTRAKVTL---QPLERGFGHTLGNALRRILLSSMPGCAIV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ +I+LN+KG+ + + G     +T+ K+GPGVVTAGDIQ 
Sbjct: 58  EVEIDGVLHEYSAIEGVKEDVIEILLNLKGVAIALHGQDEATLTLSKKGPGVVTAGDIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
           V D E+ NPDHVI +LD  A + M++ V++G GY PA      +D   PIG + +DA +S
Sbjct: 118 VTDSEISNPDHVIAHLDDTAELNMQIKVARGRGYEPADARVASDDETRPIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++V+Y+V++AR  Q  D DKL + I+++G+I  E+++  A+ ILQ Q+ +F+     +
Sbjct: 178 PVRRVAYSVDNARVEQRTDLDKLVLDIESNGTIDPEEAIRRAATILQQQIAVFVAL---E 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E +  +  +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 235 SESEAVVEEEEDEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL   GL LGM L +WPP S+++ +K
Sbjct: 295 GKKSLTEIKDVLAQRGLSLGMRLENWPPASLKDDSK 330


>gi|149376659|ref|ZP_01894418.1| DNA-directed RNA polymerase subunit alpha [Marinobacter algicola
           DG893]
 gi|149359032|gb|EDM47497.1| DNA-directed RNA polymerase subunit alpha [Marinobacter algicola
           DG893]
          Length = 313

 Score =  307 bits (786), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 153/306 (50%), Positives = 215/306 (70%), Gaps = 6/306 (1%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
           R  +  EPL RGF HTLG+ALRR+L+SS+ G AIT  QIDGVLHE S+I+GV ED+ +I+
Sbjct: 2   RAKVTLEPLERGFGHTLGSALRRILLSSMPGCAITEAQIDGVLHEYSAIEGVQEDVIEIL 61

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+KG+ +KM G     VT+ K+GPGVVTAGDI+  +D+E+ NP+HVIC+L  +  V M 
Sbjct: 62  LNLKGVAVKMGGRDDAEVTLSKKGPGVVTAGDIKLDHDVEITNPEHVICHLSANGEVNMR 121

Query: 147 LTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
           L V++G GY PA     + D    IG + +DA +SP+++V+Y VESAR  Q  D DKL +
Sbjct: 122 LKVARGRGYEPADQRGLDEDETRAIGRLQLDATFSPVRRVAYAVESARVEQRTDLDKLVI 181

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T+G+I  E+++  A+ ILQ QL +F++F+  K+  +     +    +P LL+ V++L
Sbjct: 182 DLETNGTIDPEEAIRRAATILQQQLAVFVDFDHEKEPER---VEEEEEIDPILLRPVDDL 238

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           EL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G+KSL EIK VL + GL LGM L +
Sbjct: 239 ELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLDN 298

Query: 324 WPPESI 329
           WPP S+
Sbjct: 299 WPPASL 304


>gi|126666788|ref|ZP_01737765.1| DNA-directed RNA polymerase subunit alpha [Marinobacter sp. ELB17]
 gi|126628833|gb|EAZ99453.1| DNA-directed RNA polymerase subunit alpha [Marinobacter sp. ELB17]
          Length = 334

 Score =  307 bits (786), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 155/331 (46%), Positives = 227/331 (68%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  EL+ P  I+    G      TL   EPL RGF HTLG+ALRR+L+SS+ G A+T
Sbjct: 1   MQRSVHELLTPRTIDVKESGSTRAKVTL---EPLERGFGHTLGSALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             QIDGVLHE S+I+GV ED+ +I+LN+KG+ +KM G     + + K+GPGVVTAGDI+ 
Sbjct: 58  EAQIDGVLHEYSAIEGVQEDVIEILLNLKGVAVKMHGRDDAELMLSKKGPGVVTAGDIKL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E+ NP+HVIC+L  +  V M L++++G GY PA     + D    IG + +DA +S
Sbjct: 118 DHDVEIANPEHVICHLSENGEVNMRLSIARGRGYEPADQRGLDEDETRAIGRLQLDATFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++V+Y+VESAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++F+  K
Sbjct: 178 PVRRVAYSVESARVEQRTDLDKLVIDLETNGTIDPEEAIRRAATILQQQLAVFVDFDHEK 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +  +     +    +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPER---VEEEEEIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASL 325


>gi|254283060|ref|ZP_04958028.1| DNA-directed RNA polymerase, alpha subunit [gamma proteobacterium
           NOR51-B]
 gi|219679263|gb|EED35612.1| DNA-directed RNA polymerase, alpha subunit [gamma proteobacterium
           NOR51-B]
          Length = 334

 Score =  306 bits (785), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 154/332 (46%), Positives = 219/332 (65%), Gaps = 9/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P  I+   + ++   R  +  EPL RGF HTLGNALRR+L+SS+ G AIT
Sbjct: 1   MQSSVNEFLTPRVIK---VDEKSTTRAQVTLEPLERGFGHTLGNALRRILLSSMPGCAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ +I+LN+KG+ L M+G     +++  +GP  VTAGDIQ 
Sbjct: 58  EVEIDGVLHEYSAIEGVQEDVIEILLNLKGVALTMAGKDEAELSLVAKGPCTVTAGDIQV 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+EV NPDHVIC L  D  + + L   +G GY PA       D    IG + +DA +S
Sbjct: 118 DHDVEVSNPDHVICTLTSDQELAVRLVAQRGRGYSPADSREDPEDETRSIGRLHLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI+++SY VESAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++ E   
Sbjct: 178 PIRRISYVVESARVEQRTDLDKLVIDLETNGTIDPEEAIRRAATILQQQLSVFVDLE--- 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E +     +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N 
Sbjct: 235 SEAQTTATEQEDEVDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           G+KSL EIK VL + GL LGM L +WPP S++
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLK 326


>gi|254429260|ref|ZP_05042967.1| DNA-directed RNA polymerase, alpha subunit [Alcanivorax sp. DG881]
 gi|196195429|gb|EDX90388.1| DNA-directed RNA polymerase, alpha subunit [Alcanivorax sp. DG881]
          Length = 335

 Score =  306 bits (785), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 151/310 (48%), Positives = 216/310 (69%), Gaps = 16/310 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EPL RGF HTLG ALRR+L+SS+ G AIT V+IDGV HE SSI+GV ED+ +I+LN+
Sbjct: 25  VVLEPLERGFGHTLGTALRRILISSMPGCAITEVEIDGVQHEYSSIEGVQEDVINILLNL 84

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ L+M       + + K+GPG VTA DIQ  + +E++NPDH+IC +  D  +R++L V
Sbjct: 85  KGVALQMEDREEATLELVKKGPGAVTANDIQRDHSVEIVNPDHLICTITGDTELRVKLKV 144

Query: 150 SKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            KG GYV A   ++E+D    IG + +DA YSP+++V+Y VE+AR  Q  D DKL + ++
Sbjct: 145 QKGRGYVAADSRQSEDDETRGIGRLQLDASYSPVRRVAYVVEAARVEQRTDLDKLVIDLE 204

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFE-----EPKKEVKEDINVKSLPFNPALLKKVE 261
           TDG+I  E+++  A+ ILQ Q+ +F++ E     EPK+E +E         +P LL+ V+
Sbjct: 205 TDGTIDPEEAIRRAATILQQQIAVFVDLEQDAKPEPKQEREE--------IDPILLRPVD 256

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L
Sbjct: 257 DLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASKGLSLGMRL 316

Query: 322 PDWPPESIEE 331
            +WPP S+ +
Sbjct: 317 ENWPPVSLRD 326


>gi|239905884|ref|YP_002952623.1| DNA-directed RNA polymerase alpha subunit [Desulfovibrio magneticus
           RS-1]
 gi|259494168|sp|C4XLK3|RPOA_DESMR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|239795748|dbj|BAH74737.1| DNA-directed RNA polymerase alpha subunit [Desulfovibrio magneticus
           RS-1]
          Length = 347

 Score =  306 bits (783), Expect = 3e-81,   Method: Compositional matrix adjust.
 Identities = 157/337 (46%), Positives = 225/337 (66%), Gaps = 2/337 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW EL+KP  ++      E   R   + EPL RGF  TLGNALRRVL+SSL+GAAI A 
Sbjct: 13  RNWTELVKPEVLDKDPSSTETFGR--FVCEPLERGFGTTLGNALRRVLLSSLQGAAIVAA 70

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+GV HE S+I GV ED+T+IILN+K + L M+ D  +R+T+  +  G V A  IQ  +
Sbjct: 71  RIEGVQHEFSTIPGVIEDVTEIILNLKQVRLAMATDEPQRLTLLAKEKGEVRASAIQGNH 130

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           ++ VL+ D +I  L  D   R++L V  G GYVPA  H      IGLI +DA +SP+KKV
Sbjct: 131 NVSVLSEDVLIATLSEDRDFRIDLEVRMGKGYVPADMHEGLESEIGLILLDASFSPVKKV 190

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +YT+E AR GQ+ +YDKL + + TDGSI  ED+++ +++IL+DQL +FINF+E + E ++
Sbjct: 191 AYTIEQARVGQMTNYDKLVLEVTTDGSIAPEDAISYSAKILKDQLTVFINFDEKESEAEK 250

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +     +  NP+L K ++ELELSVR+TNCL+  NI  +G+L+Q+TE +ML+  NFG+KS 
Sbjct: 251 NRRRDDIELNPSLFKSIDELELSVRATNCLKSANIQTVGELMQKTEHEMLKTKNFGKKSF 310

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
            EI+ VL  MGL  GM + ++  +  E L +K  D+ 
Sbjct: 311 EEIRRVLEDMGLEFGMRIENFDQKYQEWLKRKQTDEA 347


>gi|261400077|ref|ZP_05986202.1| DNA-directed RNA polymerase, alpha subunit [Neisseria lactamica
           ATCC 23970]
 gi|313667466|ref|YP_004047750.1| DNA-directed RNA polymerase alpha chain [Neisseria lactamica
           ST-640]
 gi|269210302|gb|EEZ76757.1| DNA-directed RNA polymerase, alpha subunit [Neisseria lactamica
           ATCC 23970]
 gi|309379134|emb|CBX22265.1| DNA-directed RNA polymerase, alpha subunit [Neisseria lactamica
           Y92-1009]
 gi|313004928|emb|CBN86354.1| DNA-directed RNA polymerase alpha chain [Neisseria lactamica
           020-06]
          Length = 328

 Score =  306 bits (783), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 163/334 (48%), Positives = 219/334 (65%), Gaps = 11/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+          R  +  +P  RGF HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSTAEFLKPRQIDVNTFSA---TRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE S++ GV ED+ DI+LNIKGI  K+ G S  ++ + K G GVV+AGDI+ 
Sbjct: 58  EVAIAGVLHEYSTVDGVQEDVVDILLNIKGIVFKLHGRSQVQLVLKKTGSGVVSAGDIEL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
            +D+E+LNPDHVIC+L  +  + ME+ V +G GY         R EN  IG I +DA +S
Sbjct: 118 PHDVEILNPDHVICHLADNGQIEMEIKVEQGRGYQSVSGRQAVRDENRQIGAIQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EP 237
           PI +VS+ VE AR  Q  D DKL + I+TDGSI  E++V  A+RIL DQ+ +F N +  P
Sbjct: 178 PISRVSFEVEPARVEQRTDLDKLVLDIETDGSIDPEEAVRSAARILIDQMSIFANLQGTP 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +EV+E    K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N
Sbjct: 238 VEEVEE----KAPPIDPVLLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 294 LGRKSLNEIKEVLASKGLTLGSKLEAWPPAGLEK 327


>gi|311693295|gb|ADP96168.1| DNA-directed RNA polymerase subunit alpha [marine bacterium HP15]
          Length = 319

 Score =  305 bits (781), Expect = 6e-81,   Method: Compositional matrix adjust.
 Identities = 151/307 (49%), Positives = 216/307 (70%), Gaps = 6/307 (1%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
            R  +  EPL RGF HTLG+ALRR+L+SS+ G A+T  QIDGVLHE S+I+GV ED+ +I
Sbjct: 7   TRAKVTLEPLERGFGHTLGSALRRILLSSMPGCAVTEAQIDGVLHEYSAIEGVQEDVIEI 66

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           +LN+KG+ +KM+G     +T+ K+GPGVVTAGDI+  +D+E+ NP+HVIC+L  +  V M
Sbjct: 67  LLNLKGVAVKMNGRDDAELTLSKKGPGVVTAGDIKLDHDVEIANPEHVICHLSENGEVNM 126

Query: 146 ELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
            L V++G GY PA     + D    IG + +DA +SP+++V+Y VESAR  Q  D DKL 
Sbjct: 127 RLRVARGRGYEPADQRGLDEDETRAIGRLQLDATFSPVRRVAYAVESARVEQRTDLDKLV 186

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + ++T+G+I  E+++  A+ ILQ QL +F++F+  K+  +     +    +P LL+ V++
Sbjct: 187 IDLETNGTIDPEEAIRRAATILQQQLAVFVDFDHEKEPER---VEEEEEIDPILLRPVDD 243

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G+KSL EIK VL + GL LGM L 
Sbjct: 244 LELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLD 303

Query: 323 DWPPESI 329
           +WPP S+
Sbjct: 304 NWPPASL 310


>gi|221126761|ref|XP_002164946.1| PREDICTED: similar to alpha subunit of RNA polymerase [Hydra
           magnipapillata]
 gi|260222202|emb|CBA31529.1| DNA-directed RNA polymerase subunit alpha [Curvibacter putative
           symbiont of Hydra magnipapillata]
          Length = 329

 Score =  305 bits (781), Expect = 7e-81,   Method: Compositional matrix adjust.
 Identities = 162/333 (48%), Positives = 219/333 (65%), Gaps = 19/333 (5%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP +I    LG    NR  +  EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKSISVEQLGP---NRAKVALEPFERGYGHTLGNALRRVLLSSMPGFAATEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE SSI GV ED+ +I+LN+KG+  K+       +++ K   GVVTA DIQT +D+E++
Sbjct: 62  LHEYSSIDGVQEDVVNILLNLKGVVFKLHNREEVTLSLRKDTEGVVTAADIQTPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NP+HVI NL     + M++ V KG GYVP    R  ++P   IG I +DA +SP+++VSY
Sbjct: 122 NPEHVIANLSHGGKLDMQIKVEKGRGYVPGSMRRYADEPNKSIGRIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVESAR  Q  D DKL + I+T+G++T ED+V  +++IL +QL +F   E        ++
Sbjct: 182 TVESARVEQRTDLDKLVVEIETNGAVTAEDAVRASAKILVEQLAVFAQLE------GSEL 235

Query: 246 NVKSLP-------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +  + P       F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 236 DAFTAPAPRGNTQFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKTPNL 295

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL + GL LGM L  WPP S+E+
Sbjct: 296 GRKSLNEIKEVLASRGLTLGMKLESWPPASLEK 328


>gi|329893624|ref|ZP_08269758.1| DNA-directed RNA polymerase alpha subunit [gamma proteobacterium
           IMCC3088]
 gi|328923551|gb|EGG30863.1| DNA-directed RNA polymerase alpha subunit [gamma proteobacterium
           IMCC3088]
          Length = 334

 Score =  304 bits (779), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 155/332 (46%), Positives = 220/332 (66%), Gaps = 9/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    E + P     I + ++   R L+  EPL RGF HTLGNALRR+L+SS+ G AIT
Sbjct: 1   MQSAVNEFLTP---RVITVDEKSNTRALVTLEPLERGFGHTLGNALRRILLSSMPGCAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            VQIDGVLHE S+I+GV ED+ +I+LN+K + + ++G     +T+ K+ PG VTAGDI  
Sbjct: 58  EVQIDGVLHEYSTIEGVQEDVIEILLNLKDVAVVLNGKDEAELTLSKKEPGPVTAGDITL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E+ NPDHVICN+   + V ++L VS+G GY PA     E D    IG + +DA +S
Sbjct: 118 DHDVEICNPDHVICNVTGGSGVNLKLVVSRGRGYSPADSRGNEEDETRAIGRLQLDATFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI++V+Y VESAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++ E   
Sbjct: 178 PIRRVAYVVESARVEQRTDLDKLVLDLETNGTIDPEEAIRRAATILQQQLAVFVDLESEG 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +        +  P    LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N 
Sbjct: 238 EAEAVVEEDEVDPI---LLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           G+KSL EIK VL + GL LGM L +WPP S++
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLK 326


>gi|118579145|ref|YP_900395.1| DNA-directed RNA polymerase subunit alpha [Pelobacter propionicus
           DSM 2379]
 gi|158512561|sp|A1ALW7|RPOA_PELPD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|118501855|gb|ABK98337.1| DNA-directed RNA polymerase subunit alpha [Pelobacter propionicus
           DSM 2379]
          Length = 340

 Score =  303 bits (777), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 156/335 (46%), Positives = 228/335 (68%), Gaps = 11/335 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRT----LMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           KNW++LI+P  +++     E+E+ +       AEP  RGFA TLGN+LRR+L+SSL+G+A
Sbjct: 3   KNWRDLIRPKQLQF-----EKESLSDTYGKFFAEPFERGFATTLGNSLRRILLSSLQGSA 57

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           IT+V+I GVLHE S+I+GV ED+TDIILN+KG+ LK+       + +   G GVV AGD 
Sbjct: 58  ITSVRIKGVLHEFSAIQGVTEDVTDIILNLKGVRLKLHSVVQATIRVVHTGEGVVKAGDF 117

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
              +++E++NP+H I     DA   M++TV  G GYV A  +R E  P+G I ID+++SP
Sbjct: 118 VVGHNVEIMNPEHHIATCGKDAHFEMDMTVKMGKGYVSADKNRDEKAPVGTIPIDSIFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           IKKV++T+ +AR GQ+ DYDKL++ I TDGS+  +D++A +++I+++QL +FINF+E  +
Sbjct: 178 IKKVNFTISNARVGQMTDYDKLTLEIWTDGSVKPDDALAYSAKIMKEQLSIFINFDEEAE 237

Query: 240 EVKEDINVKSL-PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
               + +   +   N  L + VEELELSVRS NCL+   I  +G+L+ +TEA+ML+  NF
Sbjct: 238 PQAPEESQDEIDKINENLYRTVEELELSVRSANCLKNAGIKLIGELVSKTEAEMLKTQNF 297

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWP-PESIEEL 332
           GRKSL EIK +L  MGL  GM L  +P P+ +  L
Sbjct: 298 GRKSLNEIKDILSDMGLTFGMKLDSFPEPDMLRRL 332


>gi|2896137|gb|AAC03116.1| DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa]
          Length = 358

 Score =  303 bits (777), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 156/336 (46%), Positives = 227/336 (67%), Gaps = 15/336 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+ Q     TL   EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQSSVNEFLTPRHIDVQVVSQTRAKITL---EPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLAKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++N DHVI NL  +  + M+L V++G GY PA   +++ D    IG + +DA +S
Sbjct: 118 DHDVEIINGDHVIANLADNGALNMKLKVARGRGYEPADARQSDEDESRSIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--- 235
           P+++VSY VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRVSYVVENARVEQRTNLDKLVLDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           EP  E +ED        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+ 
Sbjct: 238 EPVVEEQED------EIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKT 291

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL + GL LGM L +WPP S+ E
Sbjct: 292 PNLGKKSLTEIKDVLASRGLSLGMRLDNWPPASLTE 327


>gi|15599434|ref|NP_252928.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas aeruginosa
           PAO1]
 gi|107103754|ref|ZP_01367672.1| hypothetical protein PaerPA_01004825 [Pseudomonas aeruginosa PACS2]
 gi|116054394|ref|YP_788881.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|152984557|ref|YP_001346248.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas aeruginosa
           PA7]
 gi|218889433|ref|YP_002438297.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas aeruginosa
           LESB58]
 gi|254237102|ref|ZP_04930425.1| DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa
           C3719]
 gi|254242909|ref|ZP_04936231.1| DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa
           2192]
 gi|296387205|ref|ZP_06876704.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas aeruginosa
           PAb1]
 gi|313111392|ref|ZP_07797197.1| DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa
           39016]
 gi|12230944|sp|O52760|RPOA_PSEAE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|122261422|sp|Q02T55|RPOA_PSEAB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|171460895|sp|A6UZL3|RPOA_PSEA7 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|9950455|gb|AAG07626.1|AE004841_4 DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa
           PAO1]
 gi|115589615|gb|ABJ15630.1| DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|126169033|gb|EAZ54544.1| DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa
           C3719]
 gi|126196287|gb|EAZ60350.1| DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa
           2192]
 gi|150959715|gb|ABR81740.1| DNA-directed RNA polymerase, alpha subunit [Pseudomonas aeruginosa
           PA7]
 gi|218769656|emb|CAW25416.1| DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa
           LESB58]
 gi|310883699|gb|EFQ42293.1| DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa
           39016]
          Length = 333

 Score =  303 bits (777), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 154/336 (45%), Positives = 228/336 (67%), Gaps = 15/336 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+ Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQSSVNEFLTPRHIDVQVVSQ---TRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLAKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++N DHVI NL  +  + M+L V++G GY PA   +++ D    IG + +DA +S
Sbjct: 118 DHDVEIINGDHVIANLADNGALNMKLKVARGRGYEPADARQSDEDESRSIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--- 235
           P+++VSY VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRVSYVVENARVEQRTNLDKLVLDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           EP  E +ED        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+ 
Sbjct: 238 EPVVEEQED------EIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKT 291

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL + GL LGM L +WPP S+++
Sbjct: 292 PNLGKKSLTEIKDVLASRGLSLGMRLDNWPPASLKK 327


>gi|49087442|gb|AAT51459.1| PA4238 [synthetic construct]
          Length = 334

 Score =  303 bits (777), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 154/336 (45%), Positives = 228/336 (67%), Gaps = 15/336 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+ Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQSSVNEFLTPRHIDVQVVSQ---TRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLAKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++N DHVI NL  +  + M+L V++G GY PA   +++ D    IG + +DA +S
Sbjct: 118 DHDVEIINGDHVIANLADNGALNMKLKVARGRGYEPADARQSDEDESRSIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--- 235
           P+++VSY VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRVSYVVENARVEQRTNLDKLVLDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           EP  E +ED        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+ 
Sbjct: 238 EPVVEEQED------EIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKT 291

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL + GL LGM L +WPP S+++
Sbjct: 292 PNLGKKSLTEIKDVLASRGLSLGMRLDNWPPASLKK 327


>gi|317153932|ref|YP_004121980.1| DNA-directed RNA polymerase subunit alpha [Desulfovibrio
           aespoeensis Aspo-2]
 gi|316944183|gb|ADU63234.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio
           aespoeensis Aspo-2]
          Length = 346

 Score =  303 bits (776), Expect = 3e-80,   Method: Compositional matrix adjust.
 Identities = 153/332 (46%), Positives = 221/332 (66%), Gaps = 3/332 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW EL+KP  +  +  G+        I EPL RG+A T+GNA+RRVL+SS++G AI A 
Sbjct: 13  RNWSELVKPEKL--MRDGKSNIRYGKFICEPLERGYATTIGNAMRRVLLSSMQGCAIVAA 70

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
            I+GV HE +++ GV ED+T+++LN+K + + M+ D  +R+ +     G V AG IQ   
Sbjct: 71  SIEGVQHEFTTLPGVLEDMTEVVLNLKQVRIAMTTDEPQRLVLEADKKGQVIAGMIQENQ 130

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           ++ +LN D +I  L  D  ++MEL V  G GYVPA  H    + IG + +DA YSP+KKV
Sbjct: 131 NVRILNTDQLIATLTEDRPLKMELEVRMGKGYVPADMHEGLTEEIGAVILDASYSPVKKV 190

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+VE AR GQ+ +YDKL + + TDGS+T ED+ A +++IL+DQL +FINF+E   E  E
Sbjct: 191 AYSVEQARVGQMTNYDKLILEVWTDGSVTPEDACAYSAKILKDQLSVFINFDELSSETME 250

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +++  S+  NP L K ++ELELSVR+TNCL+  NI  +G+L+QRTE  ML+  NFGRKSL
Sbjct: 251 EVD-SSIDLNPNLFKSIDELELSVRATNCLKAANIQLVGELVQRTEQAMLKTKNFGRKSL 309

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
            EI+ VL +M L  GM + D+  +  E L +K
Sbjct: 310 DEIRRVLDSMSLKFGMGVEDFDKKYQEWLKRK 341


>gi|283853179|ref|ZP_06370432.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio sp.
           FW1012B]
 gi|283571437|gb|EFC19444.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio sp.
           FW1012B]
          Length = 347

 Score =  303 bits (775), Expect = 3e-80,   Method: Compositional matrix adjust.
 Identities = 156/337 (46%), Positives = 225/337 (66%), Gaps = 2/337 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW EL+KP  +E      +   R   + EPL RGF  TLGNALRRVL+SSL+GAAI A 
Sbjct: 13  RNWTELVKPEKLEKDPGATDTFGR--FVCEPLERGFGTTLGNALRRVLLSSLQGAAIVAA 70

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+GV HE S+I GV ED+T+IILN+K + L M+ +  +R+T+F    G V A  IQ   
Sbjct: 71  RIEGVQHEFSTIPGVIEDVTEIILNLKQVRLAMTTEDPQRLTLFANQKGEVLASAIQGNQ 130

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           ++ VL+ D +I  L  D   R++L V  G GYVPA  H   +  IGLI +D+ +SP+KKV
Sbjct: 131 NVTVLSDDVLIATLSEDRDFRIDLEVRMGKGYVPADMHEGLDSEIGLILLDSSFSPVKKV 190

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +YT+E AR GQ+ +YDKL + + TDGSI+ +D+++ +++IL+DQL +FINF+E + E  +
Sbjct: 191 AYTIEQARVGQMTNYDKLVLEVGTDGSISPDDAISYSAKILKDQLTVFINFDEKESEADK 250

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                 +  NP+L K ++ELELSVR+TNCL+  NI  +G+L+Q+TE +ML+  NFG+KSL
Sbjct: 251 ARRRDDIELNPSLFKSIDELELSVRATNCLKSANIQTVGELMQKTENEMLKTKNFGKKSL 310

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
            EI+ VL  MGL  GM + ++  +  E L +K  D+ 
Sbjct: 311 EEIRRVLEDMGLEFGMRIENFEQKYQEWLKRKQVDET 347


>gi|89902964|ref|YP_525435.1| DNA-directed RNA polymerase subunit alpha [Rhodoferax ferrireducens
           T118]
 gi|119366714|sp|Q21QP9|RPOA_RHOFD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|89347701|gb|ABD71904.1| DNA-directed RNA polymerase, alpha subunit [Rhodoferax
           ferrireducens T118]
          Length = 329

 Score =  302 bits (774), Expect = 4e-80,   Method: Compositional matrix adjust.
 Identities = 160/327 (48%), Positives = 219/327 (66%), Gaps = 7/327 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    +G    NR  +  EP  RG+ HTLGNALRRVL++S+ G A T V I GV
Sbjct: 5   LLKPKAINVEQMGG---NRAKVALEPFERGYGHTLGNALRRVLLASMPGYAATEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE SSI GV ED+ +I+LN+KG+  K+       +++ K G G+VTA DIQT +D+E++
Sbjct: 62  LHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGLVTASDIQTPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NPDHVI +L     + M++ V KG GYVP    R  ++P   IG I +DA +SP+K+VSY
Sbjct: 122 NPDHVIAHLSQGGKLDMQIKVEKGRGYVPGTMRRHGDEPTKSIGRIILDASFSPVKRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVESAR  Q  D DKL + I+T+G+I+ ED+V  +++IL +QL +F   E  +    +  
Sbjct: 182 TVESARVEQRTDLDKLVVDIETNGAISAEDAVRASAKILVEQLAVFAQLEGSELAAFDTP 241

Query: 246 NVK-SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           + + S  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL 
Sbjct: 242 SPRGSTQFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLN 301

Query: 305 EIKGVLGTMGLFLGMNLPDWPPESIEE 331
           EIK VL + GL LGM L  WPP ++E+
Sbjct: 302 EIKEVLASRGLTLGMKLESWPPAALEK 328


>gi|254483442|ref|ZP_05096671.1| DNA-directed RNA polymerase, alpha subunit [marine gamma
           proteobacterium HTCC2148]
 gi|214036316|gb|EEB76994.1| DNA-directed RNA polymerase, alpha subunit [marine gamma
           proteobacterium HTCC2148]
          Length = 334

 Score =  302 bits (774), Expect = 4e-80,   Method: Compositional matrix adjust.
 Identities = 155/332 (46%), Positives = 221/332 (66%), Gaps = 9/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    E + P     I + ++   R  +  EPL RGF HTLGNALRR+L+SS+ G AIT
Sbjct: 1   MQSAVNEFLTP---RVINVDEKNSTRAQVTLEPLERGFGHTLGNALRRILLSSMPGCAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ +I+LN+KG+ L M+G     +T+ K+G G VTA DIQ 
Sbjct: 58  EVEIDGVLHEYSAIEGVQEDVIEILLNLKGVALVMNGKEEAELTLSKKGSGAVTAADIQV 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYS 178
            +DIE+ NPDHVIC+L+  + + M+LTV++G GY PA        E   IG + +DA ++
Sbjct: 118 DHDIEIRNPDHVICHLNGASEINMKLTVARGRGYSPADSRENPEEETRSIGRLQLDATFA 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +VSY VESAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++ E   
Sbjct: 178 PVHRVSYVVESARVEQRTDLDKLVLDLETNGTIDPEEAIRRAATILQQQLAVFVDLESES 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +    +   +  P    LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N 
Sbjct: 238 ESESVEEEDEVDPI---LLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           G+KSL EIK VL + GL LGM L +WPP S++
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLK 326


>gi|26987220|ref|NP_742645.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas putida
           KT2440]
 gi|104779780|ref|YP_606278.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas entomophila
           L48]
 gi|148545764|ref|YP_001265866.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas putida F1]
 gi|167031524|ref|YP_001666755.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas putida GB-1]
 gi|170723881|ref|YP_001751569.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas putida W619]
 gi|325272033|ref|ZP_08138476.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas sp. TJI-51]
 gi|37999653|sp|Q88QL1|RPOA_PSEPK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|123079274|sp|Q1IFU1|RPOA_PSEE4 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172048432|sp|A5VXS2|RPOA_PSEP1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|24981859|gb|AAN66109.1|AE016239_4 DNA-directed RNA polymerase, alpha subunit [Pseudomonas putida
           KT2440]
 gi|95108767|emb|CAK13461.1| RNA polymerase, alpha subunit [Pseudomonas entomophila L48]
 gi|148509822|gb|ABQ76682.1| DNA-directed RNA polymerase, alpha subunit [Pseudomonas putida F1]
 gi|166858012|gb|ABY96419.1| DNA-directed RNA polymerase, alpha subunit [Pseudomonas putida
           GB-1]
 gi|169761884|gb|ACA75200.1| DNA-directed RNA polymerase, alpha subunit [Pseudomonas putida
           W619]
 gi|313496844|gb|ADR58210.1| RpoA [Pseudomonas putida BIRD-1]
 gi|324102837|gb|EGC00241.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas sp. TJI-51]
          Length = 333

 Score =  302 bits (774), Expect = 4e-80,   Method: Compositional matrix adjust.
 Identities = 154/336 (45%), Positives = 228/336 (67%), Gaps = 15/336 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+       TL   EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVVSPTRAKITL---EPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  +  + M+LTV++G GY PA   +T+ D    IG + +DA +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGALNMKLTVARGRGYEPADSRQTDEDESRSIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--- 235
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           EP    +ED        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+ 
Sbjct: 238 EPVVVEQED------EIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKT 291

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL + GL LGM L +WPP S+++
Sbjct: 292 PNLGKKSLTEIKDVLASRGLSLGMRLDNWPPASLKK 327


>gi|328953130|ref|YP_004370464.1| DNA-directed RNA polymerase subunit alpha [Desulfobacca acetoxidans
           DSM 11109]
 gi|328453454|gb|AEB09283.1| DNA-directed RNA polymerase subunit alpha [Desulfobacca acetoxidans
           DSM 11109]
          Length = 336

 Score =  302 bits (773), Expect = 5e-80,   Method: Compositional matrix adjust.
 Identities = 163/327 (49%), Positives = 220/327 (67%), Gaps = 5/327 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           + KNW +LI+P  +E   +  +  NR       EPL RGF  TLGNALRRVL+SSLRG A
Sbjct: 1   MHKNWTDLIRPKKLE---IDPDTHNRFYGKFTCEPLERGFGATLGNALRRVLLSSLRGTA 57

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           IT+V+I G+ HE S I GV ED+T++ILN+K +  KM     K + +  R  G VTAG  
Sbjct: 58  ITSVKIKGIHHEFSPIPGVIEDVTEVILNLKAVRFKMHSQEEKVIYLEAREEGEVTAGAF 117

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
           +T   IE+LNPD  I  L  D  + +E TV  G GY PA+ ++ E   IG I +DA++SP
Sbjct: 118 KTDGTIEILNPDSHIATLARDGELFIEATVKSGKGYRPAEENKQEGQSIGTIPVDAIFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I+KV++ V  AR GQ  DYDKL++ + TDGS++ ED+VALA++IL++QL +FINFEEP +
Sbjct: 178 IRKVNHIVTQARVGQQTDYDKLTLEVWTDGSVSPEDAVALAAKILKEQLTIFINFEEPCE 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           E +E    +    N  L + V ELELSVRS NCL+  NI ++G+L+Q++EA+ML+  NFG
Sbjct: 238 ETEEKPATEISRLNENLFRPVNELELSVRSANCLKNANIRFIGELVQKSEAEMLKTKNFG 297

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           RKSL EIK +L  MGL LGM L ++PP
Sbjct: 298 RKSLNEIKEILSEMGLNLGMKLENFPP 324


>gi|42524352|ref|NP_969732.1| DNA-directed RNA polymerase subunit alpha [Bdellovibrio
           bacteriovorus HD100]
 gi|39576561|emb|CAE80725.1| DNA-directed RNA polymerase, alpha subunit [Bdellovibrio
           bacteriovorus HD100]
          Length = 332

 Score =  301 bits (772), Expect = 7e-80,   Method: Compositional matrix adjust.
 Identities = 157/318 (49%), Positives = 215/318 (67%), Gaps = 2/318 (0%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           +IKP   E +      ++    I  PL RGF  TLGN+LRR+L+SS+ G+AITAV+ +GV
Sbjct: 1   MIKPKGFE-VDRDSLRDDYAKFIIRPLERGFGVTLGNSLRRILLSSMMGSAITAVKFEGV 59

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE ++I  V ED+TDIILN+K +  K        + I K+GPG VTA DIQT + IEVL
Sbjct: 60  LHEFTTIPDVLEDVTDIILNLKEVRFKQYTADSLTLKISKKGPGKVTAADIQTTDKIEVL 119

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NPD  I  L  +A    E+ VS G GYVP ++  T+  P+G I +DALYSPI+KV+Y V 
Sbjct: 120 NPDLPIATLGANANFNAEIVVSFGRGYVPVENRETDL-PVGFIGVDALYSPIRKVNYNVS 178

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +AR GQ  DYD L++ + TDGS+  E++VAL+S+I+++QL +F+ F+E  +  +E   + 
Sbjct: 179 NARVGQRTDYDALTLEVWTDGSLKPEEAVALSSKIMKEQLQIFLTFDETMEPAEEARELG 238

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
           S   N  L + V++LELSVRS NCL+  NI Y+G+L+ R+EA+ML+  NFGRKSL EIK 
Sbjct: 239 SPTLNENLFRSVDDLELSVRSANCLKNANIRYIGELVVRSEAEMLKTKNFGRKSLNEIKE 298

Query: 309 VLGTMGLFLGMNLPDWPP 326
           +LG MGL LGM +  WPP
Sbjct: 299 ILGEMGLGLGMKIEGWPP 316


>gi|297569395|ref|YP_003690739.1| DNA-directed RNA polymerase, alpha subunit [Desulfurivibrio
           alkaliphilus AHT2]
 gi|296925310|gb|ADH86120.1| DNA-directed RNA polymerase, alpha subunit [Desulfurivibrio
           alkaliphilus AHT2]
          Length = 341

 Score =  301 bits (771), Expect = 9e-80,   Method: Compositional matrix adjust.
 Identities = 158/327 (48%), Positives = 221/327 (67%), Gaps = 11/327 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +NW +LI P  +E   + Q+    +    I +PL RGFA T+GN+LRR+L+SS+RGAAIT
Sbjct: 10  RNWHDLIFPEKLE---VDQDTHTASFGKFICQPLERGFATTIGNSLRRILLSSIRGAAIT 66

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+I+GVLHE+S+I G+ ED T+IILN+K + L++     K V I K+  GVVTAGDI  
Sbjct: 67  SVKIEGVLHELSTIPGIKEDATEIILNLKEVRLRLHSGEAKTVRIEKKKKGVVTAGDIIG 126

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              +EV+NP+  IC +  D     EL V  G GYVPA+ ++ E+ PIG+I +D++++PI+
Sbjct: 127 DPQVEVMNPEQHICTITGDGKFDAELEVDWGKGYVPAERNKREDQPIGVIPLDSVFTPIR 186

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE----P 237
            V      AR GQ  DYDKL++ I TDGSI  ED++A A++IL++Q+ +FINF+E    P
Sbjct: 187 NVRVITSQARVGQQTDYDKLTLEITTDGSILPEDALAYAAKILKEQMQVFINFDESAVVP 246

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            K+ KE      L  N  L + VE+LELSVRS NCLR   I ++G+L+Q+TEA+ML+  N
Sbjct: 247 VKKEKESGEQPQL--NENLYRSVEDLELSVRSANCLRNAEIRHIGELVQKTEAEMLKTKN 304

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           FGRKSL EIK +L  M L+LGM +  W
Sbjct: 305 FGRKSLNEIKQLLSEMDLYLGMKIDGW 331


>gi|301057476|ref|ZP_07198572.1| DNA-directed RNA polymerase, alpha subunit [delta proteobacterium
           NaphS2]
 gi|300448404|gb|EFK12073.1| DNA-directed RNA polymerase, alpha subunit [delta proteobacterium
           NaphS2]
          Length = 388

 Score =  301 bits (771), Expect = 9e-80,   Method: Compositional matrix adjust.
 Identities = 162/325 (49%), Positives = 221/325 (68%), Gaps = 5/325 (1%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +NW+ELIKP  IE   + QE    T    + EPL RGF  T+GNALRR+L+SSL+GAAI 
Sbjct: 7   RNWRELIKPKRIE---IDQETNTSTYGKFVCEPLERGFGITIGNALRRILLSSLQGAAIV 63

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+ + V+HE SS+ GV ED+TDIILN+K I LK        + + + G G+VTAGDI+T
Sbjct: 64  SVKFEDVVHEFSSMPGVLEDVTDIILNLKEIKLKTLDVEEAVIKVNREGEGIVTAGDIET 123

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              +EVL P   I  L+ +  + ME+ V  G GYVPA+  + EN PIG+I IDA +S +K
Sbjct: 124 DGSVEVLEPVQHIATLNKEGKLNMEMVVKMGKGYVPAERLKEENTPIGVIAIDATFSCVK 183

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KV+Y V ++R GQV DYDKL++ + TDGS+  ED+VA A++IL++Q+  FINFEE  + V
Sbjct: 184 KVNYVVTNSRVGQVTDYDKLTLEVWTDGSVFPEDAVAFAAKILKEQMNPFINFEEEIEPV 243

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +E+   +    N  L + V +LELSVRS NCL+   I  +G+L+Q+T+A+ML+  NFGRK
Sbjct: 244 EEEEVREDQEVNENLFRPVSDLELSVRSANCLQNAKINLIGELVQKTDAEMLKTKNFGRK 303

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPP 326
           SL EIK +L  MGL LGM L  +PP
Sbjct: 304 SLNEIKAILSDMGLSLGMKLDFFPP 328


>gi|221133740|ref|ZP_03560045.1| DNA-directed RNA polymerase subunit alpha [Glaciecola sp. HTCC2999]
          Length = 326

 Score =  301 bits (770), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 148/308 (48%), Positives = 217/308 (70%), Gaps = 8/308 (2%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
            R  ++ EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I
Sbjct: 21  TRAKVVLEPLERGFGHTLGNALRRILLSSMPGVAVTEVEIDGVLHEYSTKEGVQEDVIEI 80

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           +LN+KG+ +++ G +   +T+ K G G V AGDIQ   D+E++NP+HVIC L  +A V M
Sbjct: 81  LLNLKGLAVRLEGKTEATLTLVKSGAGAVVAGDIQHDGDVEIINPEHVICTLTGEAEVSM 140

Query: 146 ELTVSKGHGYVPAKHHRT--END-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
            + V  G GYVPA   R+  E+D PIG + +DA +SP+++++Y+VESAR  Q  D DKL 
Sbjct: 141 RIKVETGRGYVPASVRRSSEEDDRPIGRLLVDASFSPVERIAYSVESARVEQRTDLDKLI 200

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEE-PKKEVKEDINVKSLPFNPALLKKVE 261
           + ++T+G++  E+++  ++ IL +QL  F++  +  + E KE+       F+P LL+ V+
Sbjct: 201 IDMETNGTLDPEEAIRRSATILAEQLDAFVDLRDVSQPEAKEE----KPEFDPILLRPVD 256

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +LEL+VRS NCL+ E + Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L
Sbjct: 257 DLELTVRSANCLKAEAVQYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRL 316

Query: 322 PDWPPESI 329
            +WPPESI
Sbjct: 317 ENWPPESI 324


>gi|28867879|ref|NP_790498.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           tomato str. DC3000]
 gi|66047751|ref|YP_237592.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           syringae B728a]
 gi|71737175|ref|YP_276681.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|213969239|ref|ZP_03397377.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           tomato T1]
 gi|237797457|ref|ZP_04585918.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           oryzae str. 1_6]
 gi|257483210|ref|ZP_05637251.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           tabaci ATCC 11528]
 gi|289623824|ref|ZP_06456778.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           aesculi str. NCPPB3681]
 gi|289648917|ref|ZP_06480260.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           aesculi str. 2250]
 gi|289675513|ref|ZP_06496403.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           syringae FF5]
 gi|298489071|ref|ZP_07007093.1| DNA-directed RNA polymerase alpha subunit [Pseudomonas savastanoi
           pv. savastanoi NCPPB 3335]
 gi|301381746|ref|ZP_07230164.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           tomato Max13]
 gi|302061054|ref|ZP_07252595.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           tomato K40]
 gi|302130805|ref|ZP_07256795.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           tomato NCPPB 1108]
 gi|302189302|ref|ZP_07265975.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           syringae 642]
 gi|37999595|sp|Q889U6|RPOA_PSESM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|75500423|sp|Q4ZMR8|RPOA_PSEU2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|90110858|sp|Q48D61|RPOA_PSE14 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|28851115|gb|AAO54193.1| DNA-directed RNA polymerase, alpha subunit [Pseudomonas syringae
           pv. tomato str. DC3000]
 gi|63258458|gb|AAY39554.1| DNA-directed RNA polymerase [Pseudomonas syringae pv. syringae
           B728a]
 gi|71557728|gb|AAZ36939.1| DNA-directed RNA polymerase, alpha subunit [Pseudomonas syringae
           pv. phaseolicola 1448A]
 gi|213925917|gb|EEB59474.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           tomato T1]
 gi|298156383|gb|EFH97481.1| DNA-directed RNA polymerase alpha subunit [Pseudomonas savastanoi
           pv. savastanoi NCPPB 3335]
 gi|330869406|gb|EGH04115.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           aesculi str. 0893_23]
 gi|330879417|gb|EGH13566.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
 gi|330899711|gb|EGH31130.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           japonica str. M301072PT]
 gi|330940915|gb|EGH43866.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           pisi str. 1704B]
 gi|330953172|gb|EGH53432.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae Cit
           7]
 gi|330966886|gb|EGH67146.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           actinidiae str. M302091]
 gi|330988257|gb|EGH86360.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           lachrymans str. M301315]
 gi|331012438|gb|EGH92494.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           tabaci ATCC 11528]
 gi|331020307|gb|EGI00364.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           oryzae str. 1_6]
          Length = 333

 Score =  301 bits (770), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 153/336 (45%), Positives = 229/336 (68%), Gaps = 15/336 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+       TL   EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVVSPTRAKITL---EPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  + V+ M+LTV++G GY PA   +++ D    IG + +D+ +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGVLNMKLTVARGRGYEPADSRQSDEDESRSIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--- 235
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           EP    +ED        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+ 
Sbjct: 238 EPVVIEQED------EIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKT 291

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL + GL LGM L +WPP S+++
Sbjct: 292 PNLGKKSLTEIKDVLASRGLSLGMRLDNWPPASLKK 327


>gi|241763535|ref|ZP_04761587.1| DNA-directed RNA polymerase, alpha subunit [Acidovorax delafieldii
           2AN]
 gi|241367266|gb|EER61606.1| DNA-directed RNA polymerase, alpha subunit [Acidovorax delafieldii
           2AN]
          Length = 330

 Score =  301 bits (770), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 162/331 (48%), Positives = 217/331 (65%), Gaps = 14/331 (4%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG    NR  +  EP  RG+ HTLGNA+RRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKAINVEQLGH---NRAKVALEPFERGYGHTLGNAIRRVLLSSMVGYAATEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE SSI GV ED+ +I+LN+KG+  K+       +++ K G GVVTA DIQT +D+E++
Sbjct: 62  LHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGVVTARDIQTPHDVEIV 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSY 185
           NPDHVI NL     + M++ V KG GYVP    R  ++    IG I +DA +SP+K+VSY
Sbjct: 122 NPDHVIANLSAGGKLDMQIKVEKGRGYVPGNLRRYADESTKSIGRIVLDASFSPVKRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVESAR  Q  D DKL + I+T+G+IT ED+V  +++IL +QL +F   E  +       
Sbjct: 182 TVESARVEQRTDLDKLVVEIETNGAITAEDAVRASAKILVEQLAVFAQLEGGELAA---F 238

Query: 246 NVKSLP-----FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           +  + P     F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GR
Sbjct: 239 DAPAGPRGNATFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           KSL EIK VL + GL LGM L +WPP  +++
Sbjct: 299 KSLNEIKEVLASRGLTLGMKLENWPPAGLDK 329


>gi|254449307|ref|ZP_05062752.1| DNA-directed RNA polymerase, alpha subunit [gamma proteobacterium
           HTCC5015]
 gi|198261066|gb|EDY85366.1| DNA-directed RNA polymerase, alpha subunit [gamma proteobacterium
           HTCC5015]
          Length = 330

 Score =  301 bits (770), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 154/328 (46%), Positives = 223/328 (67%), Gaps = 9/328 (2%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           N  E +KP  ++   + Q  + R  ++ EPL RGF HTLGNALRR+L+SS+ GAA+T VQ
Sbjct: 4   NVNEFLKPRLVD---VQQLSDTRAKVVLEPLERGFGHTLGNALRRILLSSMPGAAVTEVQ 60

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           IDGVLHE ++I+GV ED+ +I+LN+K + + ++  +   +++ K+G G V AGDIQ  +D
Sbjct: 61  IDGVLHEYTTIEGVQEDVLEILLNLKNLAIVLNAKNEAVLSLSKKGKGPVKAGDIQADHD 120

Query: 125 IEVLNPDHVICNLDVDAV-VRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIK 181
           +E++NPD VI NL  D+  + M L V KG GY PA   R E +   +G + +DA YSP+ 
Sbjct: 121 VEIVNPDFVIANLTQDSSELSMTLKVKKGRGYEPASQRREEAETAAVGTLQLDASYSPVY 180

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +V+YTV+SAR  Q  D DKL + ++T+G+I  E+S+  A+ ILQ+Q+ +F++ +      
Sbjct: 181 RVAYTVDSARVEQRTDLDKLIIDLETNGTIDPEESIRRAATILQEQISVFVDLQAEDVSE 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +ED    +   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G+K
Sbjct: 241 EED---DASDIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNLGKK 297

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           SL EIK VL   GL LGM L +WPP SI
Sbjct: 298 SLTEIKDVLAQHGLSLGMRLENWPPASI 325


>gi|221064829|ref|ZP_03540934.1| DNA-directed RNA polymerase, alpha subunit [Comamonas testosteroni
           KF-1]
 gi|264680560|ref|YP_003280470.1| DNA-directed RNA polymerase, subunit alpha [Comamonas testosteroni
           CNB-2]
 gi|299532876|ref|ZP_07046263.1| DNA-directed RNA polymerase subunit alpha [Comamonas testosteroni
           S44]
 gi|220709852|gb|EED65220.1| DNA-directed RNA polymerase, alpha subunit [Comamonas testosteroni
           KF-1]
 gi|262211076|gb|ACY35174.1| DNA-directed RNA polymerase, alpha subunit [Comamonas testosteroni
           CNB-2]
 gi|298719100|gb|EFI60070.1| DNA-directed RNA polymerase subunit alpha [Comamonas testosteroni
           S44]
          Length = 332

 Score =  300 bits (769), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 162/330 (49%), Positives = 216/330 (65%), Gaps = 10/330 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG    NR  ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKTINVEQLGH---NRAKVVLEPFERGYGHTLGNALRRVLLSSMVGYAATEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE SSI GV ED+T+I+LN+KG+  K+       +++ K G GVVTA DIQT +D+E++
Sbjct: 62  LHEYSSIDGVQEDVTNILLNLKGVVFKLHNRDEVTLSLRKDGEGVVTARDIQTPHDVEIV 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSY 185
           NPDHVI +L     + M++ V KG GYVP    R  ++    IG I +DA +SP+K+VSY
Sbjct: 122 NPDHVIAHLSQGGKLDMQIKVEKGRGYVPGNVRRYGDESTKSIGRIVLDASFSPVKRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL + I+T+G+IT ED+V  +++IL +QL +F   +        D 
Sbjct: 182 AVESARVEQRTDLDKLVLEIETNGAITAEDAVRASAKILVEQLAVFAQLDGGDIASVFDA 241

Query: 246 NV----KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
                  +  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRK
Sbjct: 242 PAGGRGAATSFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRK 301

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           SL EIK VL + GL LGM L +WPP  +E+
Sbjct: 302 SLNEIKEVLASRGLTLGMKLENWPPAGLEK 331


>gi|301628933|ref|XP_002943603.1| PREDICTED: DNA-directed RNA polymerase subunit alpha-like [Xenopus
           (Silurana) tropicalis]
          Length = 332

 Score =  300 bits (769), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 164/336 (48%), Positives = 220/336 (65%), Gaps = 22/336 (6%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I+   LG    NR  +  EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKTIQVEQLGH---NRAKVELEPFERGYGHTLGNALRRVLLSSMVGYAATEVTIVGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE SSI GV ED+ +I+LN+KG+  K+       +++ K G GVVTA DIQT +D+E++
Sbjct: 62  LHEYSSIDGVQEDVVNILLNLKGVVFKLYNRDEVTLSLRKDGEGVVTARDIQTPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NPDHVI +L   A + M++ V KG GYVP    R  ++P   IG I +DA +SP+K+VSY
Sbjct: 122 NPDHVIAHLSQGAKLDMQIKVEKGRGYVPGNVRRYGDEPTKTIGRIVLDASFSPVKRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVESAR  Q  D DKL + I+T+G+IT E++V  +++IL +QL +F   E        DI
Sbjct: 182 TVESARVEQRTDLDKLVVEIETNGAITAEEAVRASAKILVEQLAVFAQLE------GGDI 235

Query: 246 N----------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           +            +  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+ 
Sbjct: 236 DGMLIGSGASRSSATTFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKT 295

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N GRKSL EIK VL + GL LGM L +WPP  +++
Sbjct: 296 PNLGRKSLNEIKEVLASRGLTLGMKLENWPPAGLDK 331


>gi|320322297|gb|EFW78391.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           glycinea str. B076]
 gi|320331955|gb|EFW87891.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           glycinea str. race 4]
          Length = 333

 Score =  300 bits (769), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 153/336 (45%), Positives = 229/336 (68%), Gaps = 15/336 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+       TL   EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVVSPTRAKITL---EPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  + V+ M+LTV++G GY PA   +++ D    IG + +D+ +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGVLNMKLTVARGRGYEPADSRQSDEDESRSIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--- 235
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDMETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           EP    +ED        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+ 
Sbjct: 238 EPVVIEQED------EIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKT 291

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL + GL LGM L +WPP S+++
Sbjct: 292 PNLGKKSLTEIKDVLASRGLSLGMRLDNWPPASLKK 327


>gi|298370566|ref|ZP_06981881.1| DNA-directed RNA polymerase, alpha subunit [Neisseria sp. oral
           taxon 014 str. F0314]
 gi|298281176|gb|EFI22666.1| DNA-directed RNA polymerase, alpha subunit [Neisseria sp. oral
           taxon 014 str. F0314]
          Length = 328

 Score =  300 bits (769), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 159/334 (47%), Positives = 219/334 (65%), Gaps = 11/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+   L      R  +  +P  RGF HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSTTEFLKPRQIDVDTLST---TRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE S++ GV ED+ DI+LNIKGI  K+ G S  ++T+ K G G V AGDI+ 
Sbjct: 58  EVAIAGVLHEYSTVDGVQEDVVDILLNIKGIVFKLYGRSQVQLTLKKSGTGTVVAGDIEL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYS 178
            +D+E++NP+HVIC+L  +  + ME+ V +G GY      R    EN  IG I +DA +S
Sbjct: 118 PHDVEIINPEHVICHLSDNGQIEMEIKVEQGRGYQSVSGRRVFRDENKQIGAIQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EP 237
           PI +VS+ VE AR  Q  D DKL + I+TDGS+  E++V  A+RIL DQ+ +F + +  P
Sbjct: 178 PISRVSFEVEPARVEQRTDLDKLVLDIETDGSLDPEEAVRSAARILIDQMSIFADLQGTP 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +E++E    K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N
Sbjct: 238 VEEIEE----KAPPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 294 LGRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 327


>gi|160896495|ref|YP_001562077.1| DNA-directed RNA polymerase subunit alpha [Delftia acidovorans
           SPH-1]
 gi|238687179|sp|A9BRX5|RPOA_DELAS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|160362079|gb|ABX33692.1| DNA-directed RNA polymerase, alpha subunit [Delftia acidovorans
           SPH-1]
          Length = 332

 Score =  300 bits (769), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 162/330 (49%), Positives = 215/330 (65%), Gaps = 10/330 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG    NR  ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKTINVEQLGH---NRAKVVLEPFERGYGHTLGNALRRVLLSSMVGYAATEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE SSI GV ED+ +I+LN+KG+  K+       +++ K G GVVTA DIQT +D+E++
Sbjct: 62  LHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGVVTARDIQTPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSY 185
           NPDHVI NL     + M++ V KG GYVP    R  ++    IG I +DA +SP+K+VSY
Sbjct: 122 NPDHVIANLSQGGKLDMQIKVEKGRGYVPGNVRRYGDESTKSIGRIVLDASFSPVKRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL + I+T+G+IT ED+V  +++IL +QL +F   +        D 
Sbjct: 182 AVESARVEQRTDLDKLVVEIETNGAITAEDAVRASAKILVEQLAVFAQLDGGDIASVFDA 241

Query: 246 NV----KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
                  +  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRK
Sbjct: 242 PAGGRGAATAFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRK 301

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           SL EIK VL + GL LGM L +WPP  +E+
Sbjct: 302 SLNEIKEVLASRGLTLGMKLENWPPAGLEK 331


>gi|220903960|ref|YP_002479272.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
 gi|254765250|sp|B8IYL7|RPOA_DESDA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|219868259|gb|ACL48594.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
          Length = 347

 Score =  300 bits (769), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 161/339 (47%), Positives = 225/339 (66%), Gaps = 17/339 (5%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRT----LMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           +NW EL+KP+ I      +EEE  +      + EPL RG+  T+GNA+RRVL++SL+GAA
Sbjct: 13  RNWSELVKPDQIL-----REEETASGTHGKFVCEPLERGYGTTIGNAMRRVLLASLQGAA 67

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
             +V+I GV HE ++I GV ED+TD+ILNIK + L+M  +  +R+T+     G VTA DI
Sbjct: 68  FVSVKIIGVQHEFTTIHGVLEDITDVILNIKQVRLRMDTEEPQRLTLRVERKGPVTAADI 127

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
                +EVLNPD  I  L  D V+ MEL V  G GYVPA  H    D IGLI +D+ +SP
Sbjct: 128 VANQHVEVLNPDLHIATLTEDVVLEMELEVRMGKGYVPADMHEGLADEIGLIKLDSSFSP 187

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           ++KV+YTVE AR GQ+ +YD+L + + TDGS+T ED++A +++I++DQ+ +FINF+E   
Sbjct: 188 VRKVAYTVEQARVGQMTNYDRLLLEVWTDGSLTPEDAIAYSAKIIKDQISVFINFDERVS 247

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
               + + +S   N  L K +++LELSVR+TNCLR  NI  +G+L+QRTEA+ML+  NFG
Sbjct: 248 GDMRNGSGESGEVNEHLFKSIDDLELSVRATNCLRSANIGLVGELVQRTEAEMLKTKNFG 307

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           RKSL EIKGVL  MGL  GM         ++   KKY++
Sbjct: 308 RKSLDEIKGVLLGMGLDFGMK--------VDSFDKKYQE 338


>gi|242278684|ref|YP_002990813.1| DNA-directed RNA polymerase subunit alpha [Desulfovibrio salexigens
           DSM 2638]
 gi|259494166|sp|C6C1B1|RPOA_DESAD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|242121578|gb|ACS79274.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio
           salexigens DSM 2638]
          Length = 346

 Score =  300 bits (767), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 157/337 (46%), Positives = 224/337 (66%), Gaps = 3/337 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW EL+KP  +  +   +  E     I EPL RGF  T+GN+LRRVL+SS++GAA  AV
Sbjct: 13  RNWAELVKPEQL--VRDPKSNELYGKFICEPLERGFGTTIGNSLRRVLLSSMQGAAAVAV 70

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+GV HE ++I+GV ED+T+I+LNIK I   M+ D  + +T+     GVVTA DIQ   
Sbjct: 71  KIEGVQHEFTTIEGVMEDVTEIVLNIKQIRFAMTTDEPQFLTLRVNKQGVVTAADIQENQ 130

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           +++VLNP+ +I  L     + M   +  G GYVPA  H    + IG I +D+ +SPI+KV
Sbjct: 131 NVKVLNPEQIIATLSEKMDMEMTFEIRMGKGYVPADMHEGLVNEIGHIILDSSFSPIRKV 190

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+VE AR GQ+ +YDKL + + TDGS+T ED++A +++IL+DQL +FINF+E   E +E
Sbjct: 191 AYSVEQARVGQMTNYDKLIIEVFTDGSVTPEDAIAYSAKILKDQLSVFINFDEMGSE-QE 249

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +     L  NP L K ++ELELSVR+TNCL+  NI  +G+L+QRTE  ML+  NFGRKSL
Sbjct: 250 ESKESDLDLNPNLFKSIDELELSVRATNCLKAANIRIVGELVQRTEQTMLKTKNFGRKSL 309

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
            EI+ VL +M L  GM L D+  +  E L +K +++ 
Sbjct: 310 DEIRRVLDSMELKFGMVLEDFDKKHQEWLKRKEKNEA 346


>gi|88799194|ref|ZP_01114774.1| DNA-directed RNA polymerase alpha subunit [Reinekea sp. MED297]
 gi|88778177|gb|EAR09372.1| DNA-directed RNA polymerase alpha subunit [Reinekea sp. MED297]
          Length = 333

 Score =  300 bits (767), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 154/332 (46%), Positives = 225/332 (67%), Gaps = 9/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  + + P +I+   + +   NR  +  EPL RGF HTLGNALRR+L+SS+ GAAIT
Sbjct: 1   MQRSANDFLTPRHID---VQEVNANRAKITLEPLERGFGHTLGNALRRILLSSMPGAAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ +I+LN+K + +K+       +T+ K G G +TAGDIQ 
Sbjct: 58  EVEIDGVLHEYSTIEGVQEDVQEILLNLKDVAVKLHEREECTLTLRKSGAGTLTAGDIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            + +EV NPDHVI +L   A V M L V+ G GYVPA+   +E D   PIG + +DA +S
Sbjct: 118 DHGVEVANPDHVIAHLGSSADVNMTLKVALGRGYVPAEARSSEEDESKPIGRLQLDATFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +V+Y+VE+AR  Q  D DKL + ++T+G++  E+++  ++ ILQ Q+  F++ +   
Sbjct: 178 PVVRVAYSVENARVEQRTDLDKLVIELETNGTLDPEEAIRRSATILQQQVAAFVDLDHQA 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V+E    K    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EAVQEKEEDK---IDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           G+KSL EIK VL + GL LGM L  WPP S++
Sbjct: 295 GKKSLTEIKDVLASKGLSLGMVLEAWPPASLK 326


>gi|77461276|ref|YP_350783.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas fluorescens
           Pf0-1]
 gi|330812051|ref|YP_004356513.1| DNA-directed RNA polymerase alpha chain [Pseudomonas brassicacearum
           subsp. brassicacearum NFM421]
 gi|90110861|sp|Q3K612|RPOA_PSEPF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|77385279|gb|ABA76792.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas fluorescens
           Pf0-1]
 gi|327380159|gb|AEA71509.1| DNA-directed RNA polymerase alpha chain [Pseudomonas brassicacearum
           subsp. brassicacearum NFM421]
          Length = 333

 Score =  300 bits (767), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 152/336 (45%), Positives = 228/336 (67%), Gaps = 15/336 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+       TL   EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVVSPTRAKITL---EPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  +  + M+LTV++G GY PA   +++ D    IG + +D+ +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGALNMKLTVARGRGYEPADSRQSDEDESRSIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--- 235
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           EP    +ED        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+ 
Sbjct: 238 EPVVVEQED------EIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKT 291

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL + GL LGM L +WPP S+++
Sbjct: 292 PNLGKKSLTEIKDVLASRGLSLGMRLDNWPPASLKK 327


>gi|15676095|ref|NP_273226.1| DNA-directed RNA polymerase subunit alpha [Neisseria meningitidis
           MC58]
 gi|121634042|ref|YP_974287.1| DNA-directed RNA polymerase subunit alpha [Neisseria meningitidis
           FAM18]
 gi|161871037|ref|YP_001600069.1| DNA-directed RNA polymerase subunit alpha [Neisseria meningitidis
           053442]
 gi|218767142|ref|YP_002341654.1| DNA-directed RNA polymerase subunit alpha [Neisseria meningitidis
           Z2491]
 gi|254805788|ref|YP_003084009.1| DNA-directed RNA polymerase alpha chain [Neisseria meningitidis
           alpha14]
 gi|304388968|ref|ZP_07371015.1| DNA-directed RNA polymerase subunit alpha [Neisseria meningitidis
           ATCC 13091]
 gi|54039275|sp|P66704|RPOA_NEIMB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|54042186|sp|P66703|RPOA_NEIMA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158513130|sp|A1KRJ9|RPOA_NEIMF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|7225386|gb|AAF40625.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           MC58]
 gi|120865748|emb|CAM09477.1| DNA-directed RNA polymerase alpha chain [Neisseria meningitidis
           FAM18]
 gi|121051150|emb|CAM07421.1| DNA-directed RNA polymerase alpha chain [Neisseria meningitidis
           Z2491]
 gi|161596590|gb|ABX74250.1| DNA-directed RNA polymerase alpha chain [Neisseria meningitidis
           053442]
 gi|254669330|emb|CBA08369.1| DNA-directed RNA polymerase alpha chain [Neisseria meningitidis
           alpha14]
 gi|254670763|emb|CBA07039.1| DNA-directed RNA polymerase alpha chain [Neisseria meningitidis
           alpha153]
 gi|254672693|emb|CBA06591.1| DNA-directed RNA polymerase alpha chain [Neisseria meningitidis
           alpha275]
 gi|261391704|emb|CAX49153.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit;
           transcriptase alpha chain; RNA polymerase alpha subunit)
           [Neisseria meningitidis 8013]
 gi|304337102|gb|EFM03289.1| DNA-directed RNA polymerase subunit alpha [Neisseria meningitidis
           ATCC 13091]
 gi|308388384|gb|ADO30704.1| DNA-directed RNA polymerase alpha chain [Neisseria meningitidis
           alpha710]
 gi|316985690|gb|EFV64636.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           H44/76]
 gi|319411348|emb|CBY91759.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit;
           transcriptase alpha chain; RNA polymerase alpha subunit)
           [Neisseria meningitidis WUE 2594]
 gi|325129087|gb|EGC51936.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           N1568]
 gi|325131058|gb|EGC53782.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           OX99.30304]
 gi|325133080|gb|EGC55752.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           M6190]
 gi|325135174|gb|EGC57800.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           M13399]
 gi|325137226|gb|EGC59821.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           M0579]
 gi|325139058|gb|EGC61604.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           ES14902]
 gi|325141181|gb|EGC63681.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           CU385]
 gi|325143258|gb|EGC65597.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           961-5945]
 gi|325145365|gb|EGC67642.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           M01-240013]
 gi|325197455|gb|ADY92911.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           G2136]
 gi|325199381|gb|ADY94836.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           H44/76]
 gi|325202997|gb|ADY98451.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           M01-240149]
 gi|325203288|gb|ADY98741.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           M01-240355]
 gi|325205261|gb|ADZ00714.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           M04-240196]
 gi|325207205|gb|ADZ02657.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           NZ-05/33]
          Length = 328

 Score =  300 bits (767), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 160/334 (47%), Positives = 218/334 (65%), Gaps = 11/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+          R  +  +P  RGF HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSTTEFLKPRQIDVNTFSA---TRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE S++ G+ ED+ DI+LNIKGI  K+ G S  ++ + K G GVV+AGDI+ 
Sbjct: 58  EVAIAGVLHEYSTVDGIQEDVVDILLNIKGIVFKLHGRSQVQLVLKKSGSGVVSAGDIEL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
            +D+E+LNP HVIC+L  +  + ME+ V +G GY         R EN  IG I +DA +S
Sbjct: 118 PHDVEILNPGHVICHLADNGQIEMEIKVEQGRGYQSVSGRQVVRDENRQIGAIQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EP 237
           PI +VS+ VE AR  Q  D DKL + I+TDGSI  E++V  A+RIL DQ+ +F + +  P
Sbjct: 178 PISRVSFEVEPARVEQRTDLDKLVLDIETDGSIDPEEAVRSAARILIDQMSIFADLQGTP 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +EV+E    K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N
Sbjct: 238 VEEVEE----KAPPIDPVLLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 294 LGRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 327


>gi|59802135|ref|YP_208847.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae FA
           1090]
 gi|194099939|ref|YP_002003077.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           NCCP11945]
 gi|239997951|ref|ZP_04717875.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           35/02]
 gi|240015071|ref|ZP_04721984.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           DGI18]
 gi|240017520|ref|ZP_04724060.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           FA6140]
 gi|240081663|ref|ZP_04726206.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           FA19]
 gi|240113941|ref|ZP_04728431.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           MS11]
 gi|240116675|ref|ZP_04730737.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           PID18]
 gi|240118897|ref|ZP_04732959.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           PID1]
 gi|240122143|ref|ZP_04735105.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           PID24-1]
 gi|240124435|ref|ZP_04737391.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           PID332]
 gi|240124696|ref|ZP_04737582.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           SK-92-679]
 gi|240129111|ref|ZP_04741772.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           SK-93-1035]
 gi|254494696|ref|ZP_05107867.1| DNA-directed RNA polymerase subunit alpha chain [Neisseria
           gonorrhoeae 1291]
 gi|260439566|ref|ZP_05793382.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           DGI2]
 gi|268593801|ref|ZP_06127968.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           35/02]
 gi|268597760|ref|ZP_06131927.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           FA19]
 gi|268600005|ref|ZP_06134172.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           MS11]
 gi|268602342|ref|ZP_06136509.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           PID18]
 gi|268604606|ref|ZP_06138773.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           PID1]
 gi|268683063|ref|ZP_06149925.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           PID332]
 gi|268683270|ref|ZP_06150132.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           SK-92-679]
 gi|268687493|ref|ZP_06154355.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           SK-93-1035]
 gi|291042802|ref|ZP_06568543.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           DGI2]
 gi|293398177|ref|ZP_06642382.1| DNA-directed RNA polymerase, alpha subunit [Neisseria gonorrhoeae
           F62]
 gi|75432361|sp|Q5F5V2|RPOA_NEIG1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|59719030|gb|AAW90435.1| putative DNA-directed RNA polymerase alpha chain [Neisseria
           gonorrhoeae FA 1090]
 gi|193935229|gb|ACF31053.1| DNA-directed RNA polymerase alpha subunit [Neisseria gonorrhoeae
           NCCP11945]
 gi|226513736|gb|EEH63081.1| DNA-directed RNA polymerase subunit alpha chain [Neisseria
           gonorrhoeae 1291]
 gi|268547190|gb|EEZ42608.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           35/02]
 gi|268551548|gb|EEZ46567.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           FA19]
 gi|268584136|gb|EEZ48812.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           MS11]
 gi|268586473|gb|EEZ51149.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           PID18]
 gi|268588737|gb|EEZ53413.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           PID1]
 gi|268623347|gb|EEZ55747.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           PID332]
 gi|268623554|gb|EEZ55954.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           SK-92-679]
 gi|268627777|gb|EEZ60177.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           SK-93-1035]
 gi|291013236|gb|EFE05202.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           DGI2]
 gi|291611440|gb|EFF40510.1| DNA-directed RNA polymerase, alpha subunit [Neisseria gonorrhoeae
           F62]
 gi|317165391|gb|ADV08932.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           TCDC-NG08107]
          Length = 328

 Score =  300 bits (767), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 162/334 (48%), Positives = 217/334 (64%), Gaps = 11/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+          R  +  +P  RGF HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSTTEFLKPRQIDVNTFSA---TRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE S++ GV ED+ DI+LNIKGI  K+ G S  ++ + K G GVV+AGDI+ 
Sbjct: 58  EVAIAGVLHEYSTVGGVQEDVVDILLNIKGIVFKLHGRSQVQLVLKKSGSGVVSAGDIEL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
            +D+E+LNP HVIC+L  +  + ME+ V +G GY         R EN  IG I +DA +S
Sbjct: 118 PHDVEILNPGHVICHLADNGQIEMEIKVEQGRGYQSVSGRQVVRDENRQIGAIQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EP 237
           PI +VS+ VE AR  Q  D DKL + I+TDGSI  E++V  A+RIL DQ+ +F + +  P
Sbjct: 178 PISRVSFEVEPARVEQRTDLDKLVLDIETDGSIDPEEAVRSAARILIDQMSIFADLQGTP 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +EV+E    KS P +P LL  V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N
Sbjct: 238 VEEVEE----KSPPIDPVLLHPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 294 LGRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 327


>gi|229592878|ref|YP_002874997.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas fluorescens
           SBW25]
 gi|312963345|ref|ZP_07777828.1| DNA-directed RNA polymerase, alpha subunit [Pseudomonas fluorescens
           WH6]
 gi|229364744|emb|CAY52723.1| DNA-directed RNA polymerase alpha chain [Pseudomonas fluorescens
           SBW25]
 gi|311282425|gb|EFQ61023.1| DNA-directed RNA polymerase, alpha subunit [Pseudomonas fluorescens
           WH6]
 gi|330962500|gb|EGH62760.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 333

 Score =  299 bits (766), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 152/336 (45%), Positives = 228/336 (67%), Gaps = 15/336 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+       TL   EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVVSPTRAKITL---EPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  +  + M+LTV++G GY PA   +++ D    IG + +D+ +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGALNMKLTVARGRGYEPADSRQSDEDESRSIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--- 235
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           EP    +ED        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+ 
Sbjct: 238 EPVVIEQED------EIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKT 291

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL + GL LGM L +WPP S+++
Sbjct: 292 PNLGKKSLTEIKDVLASRGLSLGMRLDNWPPASLKK 327


>gi|239996312|ref|ZP_04716836.1| DNA-directed RNA polymerase subunit alpha [Alteromonas macleodii
           ATCC 27126]
 gi|332142181|ref|YP_004427919.1| DNA-directed RNA polymerase subunit alpha [Alteromonas macleodii
           str. 'Deep ecotype']
 gi|327552203|gb|AEA98921.1| DNA-directed RNA polymerase subunit alpha [Alteromonas macleodii
           str. 'Deep ecotype']
          Length = 328

 Score =  299 bits (766), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 152/327 (46%), Positives = 220/327 (67%), Gaps = 9/327 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +KP  +E   +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDG
Sbjct: 6   EFLKPRLVE---IENVSPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+ +GV ED+ +I+LN+KG+ +++ G +   +T+ K G G V AGDIQ   D+E+
Sbjct: 63  VLHEYSTKEGVQEDVIEILLNLKGLAVRLEGKTEATLTLVKSGAGPVVAGDIQHDGDVEI 122

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--END-PIGLITIDALYSPIKKVS 184
            NPDHVIC L  +A + M + V  G GYVPA   R+  E+D PIG + +DA YSP+++++
Sbjct: 123 TNPDHVICTLTGEAEISMRIKVEMGRGYVPASTRRSSEEDDRPIGRLLVDASYSPVERIA 182

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y+VESAR  Q  D DKL + ++T+G++  E+++  ++ IL +QL  F++  +  +     
Sbjct: 183 YSVESARVEQRTDLDKLIIDMETNGTLDPEEAIRRSATILAEQLDAFVDLRDVSEPEA-- 240

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 241 -KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIQYIGDLVQRTEVELLKTPNLGKKSLT 299

Query: 305 EIKGVLGTMGLFLGMNLPDWPPESIEE 331
           EIK VL + GL LGM L +WPPESI E
Sbjct: 300 EIKDVLASRGLSLGMRLENWPPESIAE 326


>gi|89093590|ref|ZP_01166538.1| DNA-directed RNA polymerase, alpha subunit [Oceanospirillum sp.
           MED92]
 gi|89082280|gb|EAR61504.1| DNA-directed RNA polymerase, alpha subunit [Oceanospirillum sp.
           MED92]
          Length = 334

 Score =  299 bits (766), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 154/332 (46%), Positives = 224/332 (67%), Gaps = 8/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  E + P +I+   + +     TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQRSVNEFLSPRHIDVQEISKTRAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ +I+LN+KGI + +  +    +T+ K   G VTAGDIQ 
Sbjct: 58  EVEIDGVLHEYSTIEGVQEDVIEILLNLKGIAVLLHNNDEAVLTLSKSEAGPVTAGDIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
             D+E+ NPDHVI +L+  A + M+LT+ +G GYVPA        E   IG + +DA +S
Sbjct: 118 NQDVEIANPDHVIAHLNEGASLNMQLTIGRGRGYVPADLRVSDEEETRAIGRLQLDATFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY VESAR  Q  D DKL + I+++G+I  E+++  A+ ILQ QL +F++ E+  
Sbjct: 178 PVRRVSYVVESARVEQRTDLDKLVIDIESNGTIDPEEAIRRAATILQQQLIVFVDLEDGA 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            + K++     +  +P LL+ V++LEL+VRS NCL+ E I Y+GDLIQRTE ++L+  N 
Sbjct: 238 DQAKDEPEEPEI--DPILLRPVDDLELTVRSANCLKAEQIYYIGDLIQRTEVELLKTPNL 295

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           G+KSL EIK VL + GL LGM L +WPP S++
Sbjct: 296 GKKSLTEIKDVLASKGLSLGMRLENWPPASLK 327


>gi|330969796|gb|EGH69862.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           aceris str. M302273PT]
          Length = 333

 Score =  299 bits (766), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 153/336 (45%), Positives = 229/336 (68%), Gaps = 15/336 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+       TL   EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVVSPTRAKITL---EPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  + V+ M+LTV++G GY PA   +++ D    IG + +D+ +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGVLNMKLTVARGRGYEPADSRQSDEDESRSIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--- 235
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           EP    +ED        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+ 
Sbjct: 238 EPVVIEQED------EIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKT 291

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL + GL LGM L +WPP S+++
Sbjct: 292 PNLGKKSLTEIKDVLVSRGLSLGMRLDNWPPASLKK 327


>gi|165977221|ref|YP_001652814.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 3 str. JL03]
 gi|190151139|ref|YP_001969664.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|303250037|ref|ZP_07336239.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|303253211|ref|ZP_07339360.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|165877322|gb|ABY70370.1| RNA polymerase alpha subunit [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|189916270|gb|ACE62522.1| DNA-directed RNA polymerase alpha chain [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|302647893|gb|EFL78100.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|302651100|gb|EFL81254.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
          Length = 329

 Score =  299 bits (766), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 159/337 (47%), Positives = 227/337 (67%), Gaps = 16/337 (4%)

Query: 2   IQKNWQELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           +Q +  E +KP+  NIE     Q       +  EPL RGF HTLGNALRR+L+SS+ G A
Sbjct: 1   MQGSVTEFLKPHLVNIE-----QVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCA 55

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+SG     +T+ K G G VTA DI
Sbjct: 56  VTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVSGKDDIILTLNKSGIGPVTAADI 115

Query: 120 QTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDA 175
               D+E++NP HVIC+L D DA + M + V +G GYVPA    H + E+ PIG + +DA
Sbjct: 116 THDGDVEIVNPHHVICHLTDKDASISMRIRVQRGRGYVPASARVHSQDEDRPIGRLLVDA 175

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
            +SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  
Sbjct: 176 RFSPVDRIAYNVEAARVEQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLR 235

Query: 236 EPKK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           + ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+
Sbjct: 236 DVRQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLK 291

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
             N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 292 TPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|91786411|ref|YP_547363.1| DNA-directed RNA polymerase subunit alpha [Polaromonas sp. JS666]
 gi|119366707|sp|Q12G77|RPOA_POLSJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|91695636|gb|ABE42465.1| DNA-directed RNA polymerase subunit alpha [Polaromonas sp. JS666]
          Length = 329

 Score =  299 bits (765), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 159/327 (48%), Positives = 213/327 (65%), Gaps = 7/327 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG    NR  +  EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKTINVEQLGA---NRAKVTLEPFERGYGHTLGNALRRVLLSSMVGHAATEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE SSI GV ED+ +I+LN+KG+  K+       +++ K G G VTA DIQT +D+E++
Sbjct: 62  LHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGPVTAADIQTPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSY 185
           NP+HVI NL     + M++ V  G GYVP    R  ++    IG I +DA +SP+K+VSY
Sbjct: 122 NPEHVIVNLSHGGKIDMQIKVENGRGYVPGTMRRYGDESPKSIGRIVLDASFSPVKRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK-KEVKED 244
           TVESAR  Q  D DKL + I+T+G++T ED+V  +++IL +QL +F   E  +       
Sbjct: 182 TVESARVEQRTDLDKLVLEIETNGAVTAEDAVRASAKILVEQLAVFAQLEGNELAAFDAP 241

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +   S  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL 
Sbjct: 242 VQRSSQQFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLN 301

Query: 305 EIKGVLGTMGLFLGMNLPDWPPESIEE 331
           EIK VL + GL LGM L  WPP  +++
Sbjct: 302 EIKEVLASRGLTLGMRLESWPPAGLDK 328


>gi|37999710|sp|Q8L2F8|RPOA_PSEPU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|21039415|gb|AAM33636.1|AF506984_1 RpoA [Pseudomonas putida]
          Length = 333

 Score =  299 bits (765), Expect = 5e-79,   Method: Compositional matrix adjust.
 Identities = 151/336 (44%), Positives = 227/336 (67%), Gaps = 15/336 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+       TL   EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQSSVNEFLTPRHIDVQVVSPTRAKITL---EPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  +  + M+L V++G GY PA   +++ D    IG + +D+ +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGALNMKLVVARGRGYEPADSRQSDEDESRSIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--- 235
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           EP    +ED        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+ 
Sbjct: 238 EPVVVEQED------EIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKT 291

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL + GL LGM L +WPP S+++
Sbjct: 292 PNLGKKSLTEIKDVLASRGLSLGMRLDNWPPASLKK 327


>gi|121603260|ref|YP_980589.1| DNA-directed RNA polymerase subunit alpha [Polaromonas
           naphthalenivorans CJ2]
 gi|158513921|sp|A1VJ40|RPOA_POLNA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|120592229|gb|ABM35668.1| DNA-directed RNA polymerase subunit alpha [Polaromonas
           naphthalenivorans CJ2]
          Length = 330

 Score =  299 bits (765), Expect = 5e-79,   Method: Compositional matrix adjust.
 Identities = 160/328 (48%), Positives = 214/328 (65%), Gaps = 8/328 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG    NR  +  EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKTINVEQLGA---NRAKVTLEPFERGYGHTLGNALRRVLLSSMVGHAATEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE SSI GV ED+ +I+LN+KG+  K+       +++ K G G +TA DIQT +D+E++
Sbjct: 62  LHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGPITAADIQTPHDVEIV 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSY 185
           NPDHVI NL     + M++ V  G GYVP    R  ++    IG I +DA +SP+K+VSY
Sbjct: 122 NPDHVIMNLSHGGKIDMQIKVENGRGYVPGNVRRYGDESPKSIGRIVLDASFSPVKRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--EPKKEVKE 243
           TVESAR  Q  D DKL + I+T+G++T ED+V  +++IL +QL +F   E  E    + +
Sbjct: 182 TVESARVEQRTDLDKLVLEIETNGAVTAEDAVRASAKILVEQLAVFAQLEGNELGAIIND 241

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                S  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 242 PAPRSSQQFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 301

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L  WPP  +++
Sbjct: 302 NEIKEVLASRGLTLGMRLESWPPAGLDK 329


>gi|146308898|ref|YP_001189363.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas mendocina
           ymp]
 gi|330505182|ref|YP_004382051.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas mendocina
           NK-01]
 gi|172046039|sp|A4XZ65|RPOA_PSEMY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|145577099|gb|ABP86631.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas mendocina
           ymp]
 gi|328919468|gb|AEB60299.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas mendocina
           NK-01]
          Length = 333

 Score =  298 bits (764), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 152/336 (45%), Positives = 228/336 (67%), Gaps = 15/336 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+   + +    R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHID---VQEVSPTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+GPGVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLAKKGPGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++N DHVI NL  +  + M+LTV++G GY PA   +++ D    IG + +DA +S
Sbjct: 118 DHDVEIVNGDHVIANLAANGSLNMKLTVARGRGYEPADARQSDEDESRSIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--- 235
           P+++V+Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRVAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           EP    +ED        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+ 
Sbjct: 238 EPVVVEQED------EIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKT 291

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL + GL LGM L +WPP S+++
Sbjct: 292 PNLGKKSLTEIKDVLASRGLSLGMRLDNWPPASLKK 327


>gi|120609326|ref|YP_969004.1| DNA-directed RNA polymerase subunit alpha [Acidovorax citrulli
           AAC00-1]
 gi|326315415|ref|YP_004233087.1| DNA-directed RNA polymerase subunit alpha [Acidovorax avenae subsp.
           avenae ATCC 19860]
 gi|158513025|sp|A1TJU2|RPOA_ACIAC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|120587790|gb|ABM31230.1| DNA-directed RNA polymerase subunit alpha [Acidovorax citrulli
           AAC00-1]
 gi|323372251|gb|ADX44520.1| DNA-directed RNA polymerase subunit alpha [Acidovorax avenae subsp.
           avenae ATCC 19860]
          Length = 330

 Score =  298 bits (764), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 161/328 (49%), Positives = 216/328 (65%), Gaps = 8/328 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG    NR  +  EP  RG+ HTLGNA+RRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKTINVEQLGH---NRAKVALEPFERGYGHTLGNAIRRVLLSSMVGYAATEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE SSI GV ED+ +I+LN+KG+  K+       +++ K G GVVTA DIQT +D+E++
Sbjct: 62  LHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGVVTARDIQTPHDVEIV 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSY 185
           NPDHVI +L     + M++ V KG GYVP    R  ++    IG I +DA +SP+K+VSY
Sbjct: 122 NPDHVIAHLSQGGKLDMQIKVEKGRGYVPGNLRRYADESTKSIGRIVLDASFSPVKRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVESAR  Q  D DKL + I+T+G+IT ED+V  +++IL +QL +F   E  +    +  
Sbjct: 182 TVESARVEQRTDLDKLVVEIETNGAITAEDAVRASAKILVEQLAVFAQLEGGELAAFDTP 241

Query: 246 N--VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                S  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 242 AGPRGSATFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 301

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 302 NEIKEVLASRGLTLGMKLENWPPAGLDK 329


>gi|297537556|ref|YP_003673325.1| DNA-directed RNA polymerase subunit alpha [Methylotenera sp. 301]
 gi|297256903|gb|ADI28748.1| DNA-directed RNA polymerase, alpha subunit [Methylotenera sp. 301]
          Length = 328

 Score =  298 bits (764), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 166/334 (49%), Positives = 222/334 (66%), Gaps = 11/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++  VL       TL   EP+ RGF +TLGNALRRVL+SS+ G AIT
Sbjct: 1   MQNSPTEYLKPRVVDVEVLSPLRARVTL---EPMERGFGYTLGNALRRVLLSSIPGFAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGV+HE S++ GV ED+ DI+LN+KG+ LK++  S   + + K   GVVTAGD +T
Sbjct: 58  EVKIDGVVHEYSTLDGVQEDVVDILLNLKGVALKLNTKSETILVLNKSVEGVVTAGDFET 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY--VPAKHHRTENDPI-GLITIDALYS 178
            +D E++NPDHVI +L     + +E+ V+ G GY  VPA+    E D + G I +DA +S
Sbjct: 118 GHDAEIVNPDHVIAHLTKGGKLNLEVKVAMGRGYQPVPARQKANEEDRVLGFIMVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI KVSY VESAR  Q  D DKL M ++T+G I  E ++  A+RIL  QL +F + E   
Sbjct: 178 PINKVSYQVESARVEQRTDLDKLVMDVETNGVIEPEQAIRDAARILMGQLSVFADLEGAP 237

Query: 239 KEVKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            EV+    VKS P  +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N
Sbjct: 238 SEVE----VKSAPQVDPILLRPVDDLELTVRSANCLKAENIFYIGDLIQRTENELLKAPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            GRKSL EIK VL T GL LGM L +WPP  +E+
Sbjct: 294 LGRKSLNEIKDVLATRGLTLGMKLENWPPVGLEK 327


>gi|254785104|ref|YP_003072532.1| DNA-directed RNA polymerase subunit alpha [Teredinibacter turnerae
           T7901]
 gi|237684107|gb|ACR11371.1| DNA-directed RNA polymerase, alpha subunit [Teredinibacter turnerae
           T7901]
          Length = 329

 Score =  298 bits (764), Expect = 7e-79,   Method: Compositional matrix adjust.
 Identities = 152/335 (45%), Positives = 224/335 (66%), Gaps = 15/335 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    E + P +I+   L      R  ++ EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQSAVNEFLTPRHIDVTELAP---TRAKVVLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I GV HE S+I+GV ED+ +I+LNIK + + M G     +++ K+GPGVVT  DIQ 
Sbjct: 58  EVEIAGVQHEYSAIEGVREDVIEILLNIKNLAVVMHGKDTTTLSLVKQGPGVVTGADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E+ NP+ VI N+  D  + M+LT+++G GY P    +++ D    IG + +DA +S
Sbjct: 118 DHDVEIANPELVIANITGDVTLDMKLTIARGRGYQPVDARQSDEDETRAIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--- 235
           P+++++YTVESAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++ E   
Sbjct: 178 PVRRLAYTVESARVEQRTDLDKLVLDLETNGTIDPEEAIRRAATILQQQLAVFVDLEGEK 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           E + E KED        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+ 
Sbjct: 238 EVEPEQKED------QIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKT 291

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
            N G+KSL EIK +L + GL LGM L +WPP S++
Sbjct: 292 PNLGKKSLTEIKDILASRGLSLGMRLENWPPASLK 326


>gi|320352939|ref|YP_004194278.1| DNA-directed RNA polymerase subunit alpha [Desulfobulbus
           propionicus DSM 2032]
 gi|320121441|gb|ADW16987.1| DNA-directed RNA polymerase subunit alpha [Desulfobulbus
           propionicus DSM 2032]
          Length = 346

 Score =  298 bits (763), Expect = 9e-79,   Method: Compositional matrix adjust.
 Identities = 157/333 (47%), Positives = 214/333 (64%), Gaps = 8/333 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNW  LI P  +E +  G         + +PL RGFA T+GN+LRR+++SS+RGAAIT+V
Sbjct: 13  KNWHSLISPEKLE-VDEGTLTSRYGKFVCQPLERGFATTIGNSLRRIMLSSIRGAAITSV 71

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I   LHE ++I GVHED+ +IILN+K + LK+ G   + V + K GPG V AGDI    
Sbjct: 72  RIGNALHEFTTIDGVHEDVAEIILNLKQVRLKLHGPESRTVVLEKNGPGRVLAGDINGGA 131

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            +EV+NP+ VIC +  +   R EL V  G GYVPA+ ++ E   IG+I IDA +SPI +V
Sbjct: 132 YVEVMNPELVICTVTSETNFRAELEVHWGKGYVPAEQNKKEGQSIGVIPIDAAFSPIIRV 191

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE----PKK 239
            Y V  AR GQ  DYD+L+M I+TDGS+  + ++A A++IL++Q+ +FINF E       
Sbjct: 192 QYVVSQARVGQQTDYDRLTMEIETDGSVEPQSALAYAAKILKEQMTIFINFNEEIAKAPD 251

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            +  D + K+ P  P L K VE+LELSVRS NCL+   I Y+G L+ +T+A+ML+  NFG
Sbjct: 252 SLDSDEDGKAYP--PFLDKNVEDLELSVRSANCLKNAQIQYIGQLVNKTDAEMLKTKNFG 309

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDW-PPESIEE 331
           RKSL EIK +L    L LGM    W  PE  EE
Sbjct: 310 RKSLNEIKALLAEHNLTLGMKYEGWVAPEKREE 342


>gi|119947101|ref|YP_944781.1| DNA-directed RNA polymerase subunit alpha [Psychromonas ingrahamii
           37]
 gi|158513126|sp|A1T0B7|RPOA2_PSYIN RecName: Full=DNA-directed RNA polymerase subunit alpha 2;
           Short=RNAP subunit alpha 2; AltName: Full=RNA polymerase
           subunit alpha 2; AltName: Full=Transcriptase subunit
           alpha 2
 gi|119865705|gb|ABM05182.1| DNA-directed RNA polymerase, alpha subunit [Psychromonas ingrahamii
           37]
          Length = 328

 Score =  298 bits (762), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 153/336 (45%), Positives = 228/336 (67%), Gaps = 15/336 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEEN--RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           +Q +  E +KPN     ++G E+ N  R  +   PL RGF HTLGNALRR+L+SS+ G A
Sbjct: 1   MQGSVIEFLKPN-----LVGIEQINATRAKVTLGPLERGFGHTLGNALRRILLSSMPGTA 55

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T V+IDGV HE S+ +GV ED+ +I+LN+KG+ +K+ G  +  V++ K G G VTAGDI
Sbjct: 56  VTEVEIDGVQHEYSTKEGVQEDILEILLNLKGLAVKLEGKDNVLVSLTKSGAGPVTAGDI 115

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              +D+E++NP+HVIC+L  +A + M + +  G GYVPA    H   +  PIG + +DA 
Sbjct: 116 THGSDVEIVNPEHVICHLTGNAEISMRIKIESGRGYVPASSRIHTEEDERPIGRLLVDAT 175

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +SP+++++Y+VESAR  Q  D DKL + ++TDG++  E+++  A+ IL +QL  F++   
Sbjct: 176 FSPVERIAYSVESARVEQRTDLDKLVIDMETDGTLDPEEAIRRAATILAEQLDAFVDL-- 233

Query: 237 PKKEVKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
             ++V E +  +  P F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+ 
Sbjct: 234 --RKVSEPVAKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKT 291

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL + GL LGM L +WPP S+ E
Sbjct: 292 PNLGKKSLTEIKDVLASRGLSLGMRLENWPPASLSE 327


>gi|289209304|ref|YP_003461370.1| DNA-directed RNA polymerase, subunit alpha [Thioalkalivibrio sp.
           K90mix]
 gi|288944935|gb|ADC72634.1| DNA-directed RNA polymerase, alpha subunit [Thioalkalivibrio sp.
           K90mix]
          Length = 328

 Score =  298 bits (762), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 155/327 (47%), Positives = 215/327 (65%), Gaps = 9/327 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           EL+K   IE   +  E  N+  +  EPL RGF HTLGNALRRVL+SS+ GAAI   +I+G
Sbjct: 5   ELVKKQQIE---VEAENRNQAKVALEPLERGFGHTLGNALRRVLLSSIPGAAIVEARIEG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE ++I+GV ED+ DI+LN+KG+ L+M       +++ K+GP VVTAGDI   +D+EV
Sbjct: 62  VLHEYTAIEGVQEDVVDILLNLKGVALRMHSREESTLSLKKKGPCVVTAGDITVDHDVEV 121

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR-TENDP--IGLITIDALYSPIKKVS 184
           +NP+HVI  +  +  + M LT   G GY P    R  E D   IG + +DA +SPI++V+
Sbjct: 122 VNPEHVIATITKNVEIDMTLTARAGRGYEPVSTRRQAEGDETGIGRLLLDASFSPIRRVA 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VESAR  Q  D D+L + ++T+G+I  +D+V  A+ ILQ QL  F++ +E   EV   
Sbjct: 182 YRVESARLAQRTDMDRLVLELETNGAIAPDDAVRQAATILQGQLAPFVDLQEETGEVP-- 239

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
               +   +P LL+ V+ELEL+VRS NCL+ EN+ Y+GDL+QRTE ++LR  N G+KSL 
Sbjct: 240 -GTTAGAIDPILLRPVDELELTVRSANCLKAENLYYIGDLVQRTEVELLRAPNLGKKSLT 298

Query: 305 EIKGVLGTMGLFLGMNLPDWPPESIEE 331
           EIK  L T GL LGM L +WPP  + +
Sbjct: 299 EIKDTLATHGLSLGMRLENWPPPGLRD 325


>gi|70732859|ref|YP_262626.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas fluorescens
           Pf-5]
 gi|90110859|sp|Q4K557|RPOA_PSEF5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|68347158|gb|AAY94764.1| DNA-directed RNA polymerase, alpha subunit [Pseudomonas fluorescens
           Pf-5]
          Length = 333

 Score =  298 bits (762), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 151/336 (44%), Positives = 227/336 (67%), Gaps = 15/336 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+       TL   EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVVSPTRAKITL---EPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  +  + M+L V++G GY PA   +++ D    IG + +D+ +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGALNMKLVVARGRGYEPADSRQSDEDESRSIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--- 235
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           EP    +ED        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+ 
Sbjct: 238 EPVVVEQED------EIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKT 291

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL + GL LGM L +WPP S+++
Sbjct: 292 PNLGKKSLTEIKDVLASRGLSLGMRLDNWPPASLKK 327


>gi|330891907|gb|EGH24568.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           mori str. 301020]
          Length = 333

 Score =  298 bits (762), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 152/336 (45%), Positives = 228/336 (67%), Gaps = 15/336 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+       TL   EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVVSPTRAKITL---EPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +I GVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIGGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  + V+ M+LTV++G GY PA   +++ D    IG + +D+ +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGVLNMKLTVARGRGYEPADSRQSDEDESRSIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--- 235
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           EP    +ED        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+ 
Sbjct: 238 EPVVIEQED------EIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKT 291

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL + GL LGM L +WPP S+++
Sbjct: 292 PNLGKKSLTEIKDVLASRGLSLGMRLDNWPPASLKK 327


>gi|239818003|ref|YP_002946913.1| DNA-directed RNA polymerase subunit alpha [Variovorax paradoxus
           S110]
 gi|319796380|ref|YP_004158020.1| DNA-directed RNA polymerase, alpha subunit [Variovorax paradoxus
           EPS]
 gi|259494174|sp|C5CQ75|RPOA_VARPS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|239804580|gb|ACS21647.1| DNA-directed RNA polymerase, alpha subunit [Variovorax paradoxus
           S110]
 gi|315598843|gb|ADU39909.1| DNA-directed RNA polymerase, alpha subunit [Variovorax paradoxus
           EPS]
          Length = 329

 Score =  298 bits (762), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 158/327 (48%), Positives = 216/327 (66%), Gaps = 7/327 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I+   + Q   N+  +  EP  RG+ HTLGNALRRVL+SS+ G + T V I GV
Sbjct: 5   LLKPKTIQ---VEQLAANKAKVTLEPFERGYGHTLGNALRRVLLSSMVGYSATEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE SSI GV ED+ +I+LN+KG+  K+       +++ K G G V A DIQT +D+E++
Sbjct: 62  LHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGPVLASDIQTPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NPDHVI +L     + M++ V KG GYVP    R  ++P   IG I +DA +SP+K+VSY
Sbjct: 122 NPDHVIAHLSQGGKLDMQIKVEKGRGYVPGTMRRYADEPTKSIGRIVLDASFSPVKRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVESAR  Q  D DKL + I+T+G+IT ED+V  +++IL +QL +F   E  +    +  
Sbjct: 182 TVESARVEQRTDLDKLLVEIETNGAITAEDAVRASAKILVEQLAVFAQLEGGELAAFDAP 241

Query: 246 NVKSL-PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
             +S   F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL 
Sbjct: 242 APRSAQQFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLN 301

Query: 305 EIKGVLGTMGLFLGMNLPDWPPESIEE 331
           EIK VL + GL LGM L  WPP  +++
Sbjct: 302 EIKEVLASRGLTLGMKLESWPPAGLDK 328


>gi|167855325|ref|ZP_02478093.1| DNA-directed RNA polymerase alpha chain [Haemophilus parasuis
           29755]
 gi|219871571|ref|YP_002475946.1| DNA-directed RNA polymerase subunit alpha [Haemophilus parasuis
           SH0165]
 gi|167853583|gb|EDS24829.1| DNA-directed RNA polymerase alpha chain [Haemophilus parasuis
           29755]
 gi|219691775|gb|ACL32998.1| DNA-directed RNA polymerase subunit alpha [Haemophilus parasuis
           SH0165]
          Length = 329

 Score =  298 bits (762), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 156/337 (46%), Positives = 226/337 (67%), Gaps = 16/337 (4%)

Query: 2   IQKNWQELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           +Q +  E +KP+  NIE I           +  EPL RGF HTLGNALRR+L+SS+ G A
Sbjct: 1   MQGSVTEFLKPHLVNIEQI-----SSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCA 55

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G VTA DI
Sbjct: 56  VTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDIILTLTKSGIGPVTAADI 115

Query: 120 QTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDA 175
               D+E++NPDHVICNL D +A + M + V +G GYVPA    H + ++ PIG + +DA
Sbjct: 116 THDGDVEIVNPDHVICNLTDKNASISMRIRVQRGRGYVPASARVHTQDDDRPIGRLLVDA 175

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
            +SP+ +++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  
Sbjct: 176 RFSPVDRIAYNVEAARVEQRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLR 235

Query: 236 EPKK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           + ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+
Sbjct: 236 DVRQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLK 291

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
             N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 292 TPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|307246714|ref|ZP_07528784.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|307248855|ref|ZP_07530868.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
 gi|307251083|ref|ZP_07533007.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
 gi|307253469|ref|ZP_07535340.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|307255699|ref|ZP_07537503.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|307257883|ref|ZP_07539639.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
 gi|307260151|ref|ZP_07541861.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
 gi|307262279|ref|ZP_07543928.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
 gi|307264488|ref|ZP_07546073.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
 gi|306852414|gb|EFM84649.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|306854782|gb|EFM86972.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
 gi|306856913|gb|EFM89045.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
 gi|306859148|gb|EFM91190.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|306861376|gb|EFM93366.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|306863613|gb|EFM95540.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
 gi|306865797|gb|EFM97675.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
 gi|306868042|gb|EFM99869.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
 gi|306870185|gb|EFN01944.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
          Length = 325

 Score =  298 bits (762), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 158/331 (47%), Positives = 224/331 (67%), Gaps = 16/331 (4%)

Query: 8   ELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           E +KP+  NIE     Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I
Sbjct: 3   EFLKPHLVNIE-----QVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEI 57

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGVLHE SS +GV ED+ +++LN+KG+ +K+SG     +T+ K G G VTA DI    D+
Sbjct: 58  DGVLHEYSSKEGVQEDILEVLLNLKGLAVKVSGKDDIILTLNKSGIGPVTAADITHDGDV 117

Query: 126 EVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIK 181
           E++NP HVIC+L D DA + M + V +G GYVPA    H + E+ PIG + +DA +SP+ 
Sbjct: 118 EIVNPHHVICHLTDKDASISMRIRVQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVD 177

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK-E 240
           +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++ E
Sbjct: 178 RIAYNVEAARVEQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQPE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           VKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+
Sbjct: 238 VKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGK 293

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 294 KSLTEIKDVLASRGLSLGMRLENWPPASIAE 324


>gi|29653615|ref|NP_819307.1| DNA-directed RNA polymerase subunit alpha [Coxiella burnetii RSA
           493]
 gi|154706094|ref|YP_001425157.1| DNA-directed RNA polymerase subunit alpha [Coxiella burnetii Dugway
           5J108-111]
 gi|161349357|ref|ZP_02096741.1| DNA-directed RNA polymerase, alpha subunit [Coxiella burnetii 'MSU
           Goat Q177']
 gi|161830881|ref|YP_001596210.1| DNA-directed RNA polymerase subunit alpha [Coxiella burnetii RSA
           331]
 gi|212213225|ref|YP_002304161.1| DNA-directed RNA polymerase subunit alpha [Coxiella burnetii
           CbuG_Q212]
 gi|212218099|ref|YP_002304886.1| DNA-directed RNA polymerase subunit alpha [Coxiella burnetii
           CbuK_Q154]
 gi|41688670|sp|Q83EQ2|RPOA_COXBU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|189043837|sp|A9KD06|RPOA_COXBN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|189043838|sp|A9NAZ5|RPOA_COXBR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238057755|sp|B6J5F7|RPOA_COXB1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238057756|sp|B6J238|RPOA_COXB2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|29540877|gb|AAO89821.1| DNA-directed RNA polymerase alpha chain [Coxiella burnetii RSA 493]
 gi|154355380|gb|ABS76842.1| DNA-directed RNA polymerase alpha chain [Coxiella burnetii Dugway
           5J108-111]
 gi|161762748|gb|ABX78390.1| DNA-directed RNA polymerase, alpha subunit [Coxiella burnetii RSA
           331]
 gi|164601573|gb|EDQ95164.1| DNA-directed RNA polymerase, alpha subunit [Coxiella burnetii 'MSU
           Goat Q177']
 gi|212011635|gb|ACJ19016.1| DNA-directed RNA polymerase alpha chain [Coxiella burnetii
           CbuG_Q212]
 gi|212012361|gb|ACJ19741.1| DNA-directed RNA polymerase alpha chain [Coxiella burnetii
           CbuK_Q154]
          Length = 327

 Score =  297 bits (761), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 149/332 (44%), Positives = 221/332 (66%), Gaps = 8/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q   +  + P NI+   +         ++ EPL RGF HTLGNALRR+L+SS+ GAAI 
Sbjct: 1   MQNVLKSFLTPKNIQVQTI---SPCHFRILLEPLERGFGHTLGNALRRILLSSMPGAAIV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE SSI+GV ED+ D++LN+KG+ +K+ G    ++T+ K+G G VTAGDIQT
Sbjct: 58  QAEIDGVLHEYSSIEGVREDVVDVLLNLKGVAIKLEGREDAKLTLHKKGAGTVTAGDIQT 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSP 179
            + ++++NPDHVI ++  D  + M L  + G GY P+    T  ++  +GL+ +DA YSP
Sbjct: 118 ESGVKIVNPDHVIAHITKDGEINMTLKAAMGRGYEPSSARSTGDQSRSVGLLLLDASYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I++V+Y+VE+AR  +  D DKL + ++TDG++  E+++  A+ +LQ QL  F++    K+
Sbjct: 178 IRRVTYSVENARVEKRTDLDKLIIDLETDGTLDPEEAIRFAAAVLQHQLAAFVDL---KQ 234

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           E   D   K    NP LL+ VE+LEL+VR+ NCL+ E+I Y+GDL+Q TE D+L+  N G
Sbjct: 235 ESDRDGGGKEGKVNPLLLRPVEDLELTVRAANCLKAESINYIGDLVQCTENDLLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +KSL+EIK VL   GL LGM+L  WPP  + +
Sbjct: 295 KKSLLEIKSVLAQKGLSLGMDLKGWPPADLTD 326


>gi|319639574|ref|ZP_07994321.1| DNA-directed RNA polymerase subunit alpha [Neisseria mucosa C102]
 gi|317399145|gb|EFV79819.1| DNA-directed RNA polymerase subunit alpha [Neisseria mucosa C102]
          Length = 328

 Score =  297 bits (761), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 159/334 (47%), Positives = 218/334 (65%), Gaps = 11/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+   L      R  +  +P  RGF HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSTTEFLKPRQIDVDTLSS---TRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE S+I GV ED+ D++LNIKGI  K+ G +  ++T+ K G G V AGDI  
Sbjct: 58  EVVISGVLHEYSTIDGVQEDVVDVLLNIKGIVFKLHGRNQVQLTLKKAGAGAVVAGDIDL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYS 178
            +D+E++NP+HVIC+L  +  + ME+ V +G GY      R    EN  IG I +DA +S
Sbjct: 118 PHDVEIINPEHVICHLSDNGQIDMEIKVEQGRGYQSVSGRRVLRDENKQIGAIQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EP 237
           PI +VS+ VE AR  Q  D DKL + I+T+GSI  E++V  A+RIL DQ+ +F + +  P
Sbjct: 178 PISRVSFEVEPARVEQRTDLDKLVLDIETNGSIDPEEAVRSAARILIDQMSIFADLQGTP 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +EV+E    K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N
Sbjct: 238 VEEVEE----KAPPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 294 LGRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 327


>gi|330879400|gb|EGH13549.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           glycinea str. race 4]
          Length = 333

 Score =  297 bits (761), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 152/336 (45%), Positives = 228/336 (67%), Gaps = 15/336 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+       TL   EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVVSPTRAKITL---EPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GV TA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVGTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  + V+ M+LTV++G GY PA   +++ D    IG + +D+ +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGVLNMKLTVARGRGYEPADSRQSDEDESRSIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--- 235
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDMETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           EP    +ED        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+ 
Sbjct: 238 EPVVIEQED------EIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKT 291

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL + GL LGM L +WPP S+++
Sbjct: 292 PNLGKKSLTEIKDVLASRGLSLGMRLDNWPPASLKK 327


>gi|331018185|gb|EGH98241.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           lachrymans str. M302278PT]
          Length = 333

 Score =  297 bits (761), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 152/336 (45%), Positives = 227/336 (67%), Gaps = 15/336 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+       TL   EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVVSPTRAKITL---EPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  + V+ M+LTV++G GY PA   +++ D    IG + +D+ +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGVLNMKLTVARGRGYEPADSRQSDEDESRSIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--- 235
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           EP    +ED        +P LL+ V +LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+ 
Sbjct: 238 EPVVIEQED------EIDPILLRPVYDLELTVRSANCLKAENIYYIGDLIQRTEVELLKT 291

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL +  L LGM L +WPP S+++
Sbjct: 292 PNLGKKSLTEIKDVLASRSLSLGMRLDNWPPASLKK 327


>gi|292492446|ref|YP_003527885.1| DNA-directed RNA polymerase, subunit alpha [Nitrosococcus
           halophilus Nc4]
 gi|291581041|gb|ADE15498.1| DNA-directed RNA polymerase, alpha subunit [Nitrosococcus
           halophilus Nc4]
          Length = 332

 Score =  297 bits (760), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 146/302 (48%), Positives = 206/302 (68%), Gaps = 6/302 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G AI   QIDGVLHE ++ +GV ED+T+I+LN+KG+
Sbjct: 27  EPLERGFGHTLGNALRRILLSSMPGCAIVEAQIDGVLHEYTTKEGVQEDMTEILLNLKGV 86

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K+ G     + +  +GPG VTAG+IQ  +D+E++NP+HVI +L     + + + V +G
Sbjct: 87  AIKLHGRDEVTLALNSKGPGAVTAGEIQLEHDVEIINPEHVIAHLTKSGELNITMKVVRG 146

Query: 153 HGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            GY PA        E  PIG + +DA +SPI++V+Y V+SAR  Q  D DKL + I+T+G
Sbjct: 147 RGYQPASVRIPKEEEERPIGYLILDASFSPIRRVTYEVDSARVEQRTDLDKLIIEIETNG 206

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  +++V  A+ ILQDQL  F+  E   +  KE    K+   +P LL+ +++LEL+VRS
Sbjct: 207 TIASDEAVRKAATILQDQLTAFVELEGKTETAKEK---KTAEIDPVLLQPIDDLELTVRS 263

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            NCL+ ENI Y+GDLIQRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP  +
Sbjct: 264 ANCLKAENIYYIGDLIQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPAGL 323

Query: 330 EE 331
            E
Sbjct: 324 HE 325


>gi|88861469|ref|ZP_01136095.1| DNA-directed RNA polymerase alpha chain [Pseudoalteromonas tunicata
           D2]
 gi|88816517|gb|EAR26346.1| DNA-directed RNA polymerase alpha chain [Pseudoalteromonas tunicata
           D2]
          Length = 328

 Score =  297 bits (760), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 151/335 (45%), Positives = 226/335 (67%), Gaps = 12/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  +E   +      R+ ++ EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVEIDAVSP---TRSKVVLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DIQ 
Sbjct: 58  EVEIDGVLHEYSAKEGVQEDIIEILLNLKGLAVTLEGKDEVFLTLTKSGVGPVTAADIQH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALY 177
             D+ + NPDHVIC+L   ++ + M + V +G GYVPA +  + +D   PIG + +DA +
Sbjct: 118 DGDVTICNPDHVICHLTTANSSISMRIRVERGRGYVPASNRLSSDDDERPIGRLLLDASF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y+VESAR  Q  D DKL + ++T+G++  E+++  AS IL +QL  F++    
Sbjct: 178 SPVERIAYSVESARVEQRTDLDKLIIDMETNGTLDPEEAIRRASTILAEQLDAFVDL--- 234

Query: 238 KKEVKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            ++V E +  +  P F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 235 -RDVTEPVAKEEKPEFDPILLRPVDDLELTVRSANCLKAEQIQYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP S+ E
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASLAE 328


>gi|223042028|ref|ZP_03612209.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus minor
           202]
 gi|198246530|gb|ACH82222.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus minor
           202]
          Length = 329

 Score =  297 bits (760), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 157/337 (46%), Positives = 227/337 (67%), Gaps = 16/337 (4%)

Query: 2   IQKNWQELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           +Q +  E +KP+  NIE I           +  EPL RGF HTLGNALRR+L+SS+ G A
Sbjct: 1   MQGSVTEFLKPHLVNIEQI-----SSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCA 55

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G VTAGDI
Sbjct: 56  VTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQSKDDVVLTLNKSGIGPVTAGDI 115

Query: 120 QTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDA 175
               D+E++NPDHVIC+L D +A + M + V +G GYVPA    H + ++ PIG + +DA
Sbjct: 116 THDGDVEIVNPDHVICHLTDKNASINMRIRVQRGRGYVPASARIHAQDDDRPIGRLLVDA 175

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
            +SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  
Sbjct: 176 RFSPVDRIAYNVEAARVEQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLR 235

Query: 236 EPKK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           + ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+
Sbjct: 236 DVRQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLK 291

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
             N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 292 TPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|121592838|ref|YP_984734.1| DNA-directed RNA polymerase subunit alpha [Acidovorax sp. JS42]
 gi|222109618|ref|YP_002551882.1| DNA-directed RNA polymerase subunit alpha [Acidovorax ebreus TPSY]
 gi|158513895|sp|A1W333|RPOA_ACISJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|254765252|sp|B9MBW2|RPOA_ACIET RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|120604918|gb|ABM40658.1| DNA-directed RNA polymerase subunit alpha [Acidovorax sp. JS42]
 gi|221729062|gb|ACM31882.1| DNA-directed RNA polymerase, alpha subunit [Acidovorax ebreus TPSY]
          Length = 330

 Score =  297 bits (760), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 160/328 (48%), Positives = 215/328 (65%), Gaps = 8/328 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG    NR  +  EP  RG+ HTLGNA+RRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKAINVEQLGP---NRAKVALEPFERGYGHTLGNAIRRVLLSSMVGYAATEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE SSI GV ED+ +I+LN+KG+  K+       +++ K G GVVTA DIQT +D+E++
Sbjct: 62  LHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGVVTARDIQTPHDVEIV 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NP+HVI  L     + M++ V KG GYVP    R  ++    IG I +DA +SP+K+VSY
Sbjct: 122 NPEHVIATLSAGGKLDMQIKVEKGRGYVPGNLRRYADEATKSIGRIVLDASFSPVKRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--EPKKEVKE 243
           TVESAR  Q  D DKL + I+T+G+IT ED+V  +++IL +QL +F   E  E       
Sbjct: 182 TVESARVEQRTDLDKLVVEIETNGAITAEDAVRASAKILVEQLAVFAQLEGGELAAFDAP 241

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             +  +  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 242 ASSRGAATFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 301

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 302 NEIKEVLASRGLTLGMKLENWPPAGLDK 329


>gi|260579894|ref|ZP_05847724.1| DNA-directed RNA polymerase, alpha subunit [Haemophilus influenzae
           RdAW]
 gi|260093178|gb|EEW77111.1| DNA-directed RNA polymerase, alpha subunit [Haemophilus influenzae
           RdAW]
          Length = 328

 Score =  296 bits (759), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 153/334 (45%), Positives = 225/334 (67%), Gaps = 11/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVILTLNKSGIGPVVAADITY 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYS 178
             D+E++NPDHVIC+L D +A + M + V +G GYVPA  + H  E  PIG + +DA YS
Sbjct: 118 DGDVEIVNPDHVICHLTDENASISMRIRVQRGRGYVPASSRTHTQEERPIGRLLVDACYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +
Sbjct: 178 PVERIAYNVEAARVEQRTDLDKLVIELETNGALEPEEAIRRAATILAEQLDAFVDLRDVR 237

Query: 239 K-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           + E+KE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 QPEIKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 294 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 327


>gi|119502948|ref|ZP_01625033.1| DNA-directed RNA polymerase subunit alpha [marine gamma
           proteobacterium HTCC2080]
 gi|119461294|gb|EAW42384.1| DNA-directed RNA polymerase subunit alpha [marine gamma
           proteobacterium HTCC2080]
          Length = 334

 Score =  296 bits (759), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 147/331 (44%), Positives = 219/331 (66%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  N  E + P  I+   + ++   R  +  EPL RGF HTLGNALRR+L+SS+ G AIT
Sbjct: 1   MSTNVNEFLTPRVIK---VDEKSPTRAQVTLEPLERGFGHTLGNALRRILLSSMPGCAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGV HE S+++G  ED+ +I+LN+KG+ L M+G     +++  +GP  VTA +IQT
Sbjct: 58  EVEIDGVQHEYSAVEGAQEDVIEILLNLKGVALSMTGKDEAELSLVAKGPCTVTAAEIQT 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
            +D+++ NPDHVIC+L  D  + M + V +G GY PA        E   IG + +DA +S
Sbjct: 118 DHDVQIGNPDHVICHLTADQELVMRVVVERGRGYSPADSRINPEEETRSIGKLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY V+SAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++ E   
Sbjct: 178 PVRRVSYVVDSARVEQRTDLDKLIIDLETNGTIDPEEAIRRAATILQQQLLVFVDLESEA 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +   ++ + +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N 
Sbjct: 238 QATAQEADDE---VDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASL 325


>gi|126209248|ref|YP_001054473.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae L20]
 gi|158513517|sp|A3N382|RPOA_ACTP2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|126098040|gb|ABN74868.1| DNA-directed RNA polymerase alpha chain [Actinobacillus
           pleuropneumoniae serovar 5b str. L20]
          Length = 329

 Score =  296 bits (759), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 159/337 (47%), Positives = 226/337 (67%), Gaps = 16/337 (4%)

Query: 2   IQKNWQELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           +Q +  E +KP+  NIE     Q       +  EPL RGF HTLGNALRR+L+SS+ G A
Sbjct: 1   MQGSVTEFLKPHLVNIE-----QVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCA 55

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+SG     +T+ K G G VTA DI
Sbjct: 56  VTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVSGKDDIILTLNKSGIGPVTAADI 115

Query: 120 QTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDA 175
               D+E++NP HVIC+L D DA + M + V +G GYVPA    H + E+ PIG + +DA
Sbjct: 116 THDGDVEIVNPHHVICHLTDKDASISMRIRVQRGRGYVPASARVHSQDEDRPIGRLLVDA 175

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
            +SP+ +++Y VESAR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  
Sbjct: 176 RFSPVDRIAYNVESARVEQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLR 235

Query: 236 EPKK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           + ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+ DL+QRTE ++L+
Sbjct: 236 DVRQPEVKEE----KPEFDPILLRPVDDLELTVRSHNCLKAETIHYICDLVQRTEVELLK 291

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
             N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 292 TPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|260581619|ref|ZP_05849416.1| DNA-directed RNA polymerase, alpha subunit [Haemophilus influenzae
           NT127]
 gi|260095212|gb|EEW79103.1| DNA-directed RNA polymerase, alpha subunit [Haemophilus influenzae
           NT127]
          Length = 328

 Score =  296 bits (759), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 153/334 (45%), Positives = 225/334 (67%), Gaps = 11/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVILTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYS 178
             D+E++NPDHVIC+L D +A + M + V +G GYVPA  + H  E  PIG + +DA YS
Sbjct: 118 DGDVEIVNPDHVICHLTDENASISMRIRVQRGRGYVPASSRTHTQEERPIGRLLVDACYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +
Sbjct: 178 PVERITYNVEAARVEQRTDLDKLVIELETNGALEPEEAIRRAATILAEQLDAFVDLRDVR 237

Query: 239 K-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           + E+KE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 QPEIKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 294 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 327


>gi|241759603|ref|ZP_04757704.1| DNA-directed RNA polymerase, alpha subunit [Neisseria flavescens
           SK114]
 gi|261380584|ref|ZP_05985157.1| DNA-directed RNA polymerase, alpha subunit [Neisseria subflava
           NJ9703]
 gi|241319975|gb|EER56356.1| DNA-directed RNA polymerase, alpha subunit [Neisseria flavescens
           SK114]
 gi|284796552|gb|EFC51899.1| DNA-directed RNA polymerase, alpha subunit [Neisseria subflava
           NJ9703]
          Length = 328

 Score =  296 bits (759), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 159/334 (47%), Positives = 218/334 (65%), Gaps = 11/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+   L      R  +  +P  RGF HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSTTEFLKPRQIDVDTLSS---TRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE S+I GV ED+ D++LNIKGI  K+ G +  ++T+ K G G V AGDI  
Sbjct: 58  EVVISGVLHEYSTIDGVQEDVVDVLLNIKGIVFKLHGRNQVQLTLKKTGAGAVVAGDIDL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYS 178
            +D+E++NP+HVIC+L  +  + ME+ V +G GY      R    EN  IG I +DA +S
Sbjct: 118 PHDVEIINPEHVICHLADNGQIDMEIKVEQGRGYQSVSGRRVLRDENKQIGAIQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EP 237
           PI +VS+ VE AR  Q  D DKL + I+T+GSI  E++V  A+RIL DQ+ +F + +  P
Sbjct: 178 PISRVSFEVEPARVEQRTDLDKLVLDIETNGSIDPEEAVRSAARILIDQMSIFADLQGTP 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +EV+E    K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N
Sbjct: 238 VEEVEE----KAPPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 294 LGRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 327


>gi|68249398|ref|YP_248510.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           86-028NP]
 gi|145628303|ref|ZP_01784104.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           22.1-21]
 gi|145638396|ref|ZP_01794006.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           PittII]
 gi|148827991|ref|YP_001292744.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           PittGG]
 gi|81336175|sp|Q4QM97|RPOA_HAEI8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172048058|sp|A5UHV5|RPOA_HAEIG RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|68057597|gb|AAX87850.1| DNA-directed RNA polymerase alpha chain [Haemophilus influenzae
           86-028NP]
 gi|144980078|gb|EDJ89737.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           22.1-21]
 gi|145272725|gb|EDK12632.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           PittII]
 gi|148719233|gb|ABR00361.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           PittGG]
 gi|301169521|emb|CBW29122.1| RNA polymerase, alpha subunit [Haemophilus influenzae 10810]
 gi|309751536|gb|ADO81520.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           R2866]
          Length = 328

 Score =  296 bits (759), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 153/334 (45%), Positives = 225/334 (67%), Gaps = 11/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVILTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYS 178
             D+E++NPDHVIC+L D +A + M + V +G GYVPA  + H  E  PIG + +DA YS
Sbjct: 118 DGDVEIVNPDHVICHLTDENASISMRIRVQRGRGYVPASSRTHTQEERPIGRLLVDACYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +
Sbjct: 178 PVERIAYNVEAARVEQRTDLDKLVIELETNGALEPEEAIRRAATILAEQLDAFVDLRDVR 237

Query: 239 K-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           + E+KE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 QPEIKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 294 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 327


>gi|149922187|ref|ZP_01910625.1| DNA-directed RNA polymerase subunit alpha [Plesiocystis pacifica
           SIR-1]
 gi|149816927|gb|EDM76412.1| DNA-directed RNA polymerase subunit alpha [Plesiocystis pacifica
           SIR-1]
          Length = 337

 Score =  296 bits (758), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 158/337 (46%), Positives = 221/337 (65%), Gaps = 16/337 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTL------MIAEPLPRGFAHTLGNALRRVLMSSL 55
           I +NW++LI+P  ++        +N +L         EPL RG+  T+GN+LRRVL+SSL
Sbjct: 7   IARNWRDLIRPKKLDV-------DNDSLTDSYGKFTCEPLERGYGITIGNSLRRVLLSSL 59

Query: 56  RGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT 115
           +GAA+T V+I+G LHE +SI  V ED+TDIILNIK + L M   + + + I K G G VT
Sbjct: 60  QGAAVTTVRIEGALHEFTSIPAVVEDVTDIILNIKALRLSMDDATPRTLLISKTGEGPVT 119

Query: 116 AGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDA 175
           A DIQ  + + VL+P   I  L     ++ME+T + G GY  A  ++TE  PIG+I ID+
Sbjct: 120 AADIQAPSGVHVLDPSQHIATLSKGGRLQMEMTCAMGRGYATADQNKTEGMPIGVIPIDS 179

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           L+SPI+KV+Y V +AR G   DYD+L + + TDGS+  +D++A A++I+++QL +FIN E
Sbjct: 180 LFSPIRKVNYRVTNARVGHRTDYDRLILQVWTDGSVKPDDALAYAAKIVKEQLSIFINHE 239

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           E  +E +     +    N  L + V+ELELSVRS NCL+  NI Y+GDL+QRTEA+ML+ 
Sbjct: 240 E-IEETQAPSQSEQDKLNDVLWRSVDELELSVRSANCLQNANIHYIGDLVQRTEAEMLKT 298

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDW--PPESIE 330
            NFGRKSL EIK +L  MGL LGM +  W  PP + E
Sbjct: 299 KNFGRKSLKEIKEILAQMGLSLGMKIEGWQGPPPNRE 335


>gi|171060593|ref|YP_001792942.1| DNA-directed RNA polymerase subunit alpha [Leptothrix cholodnii
           SP-6]
 gi|238689121|sp|B1Y7M9|RPOA_LEPCP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|170778038|gb|ACB36177.1| DNA-directed RNA polymerase, alpha subunit [Leptothrix cholodnii
           SP-6]
          Length = 328

 Score =  296 bits (758), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 156/326 (47%), Positives = 213/326 (65%), Gaps = 6/326 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG      TL   EP  RGF HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKAINVDPLGGHRAKVTL---EPFERGFGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S++ GV ED+  I+LN+KG+  ++       + + K G G V A DIQT +D+E++
Sbjct: 62  LHEYSTVDGVQEDVVHIMLNLKGVVFRLHNRDEVTLVLRKEGEGPVKASDIQTPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NPDHVI +L     + M++ V KG GYVP    R  ++P   IG I +DA +SP+K+VSY
Sbjct: 122 NPDHVIAHLAQGGKLDMQIKVEKGRGYVPGSMRRYADEPTKSIGRIVLDASFSPLKRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVESAR  Q  D DKL M I+T+G+I+ E+++  +++IL +QL +F   E     + E  
Sbjct: 182 TVESARVEQRTDLDKLVMEIETNGAISPEEAIRASAKILVEQLAVFAQLEGSDLAIFEAP 241

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 242 APRAQHFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTETELLKTPNLGRKSLNE 301

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LG  L +WPP+ +++
Sbjct: 302 IKEVLASRGLTLGARLENWPPQGLDK 327


>gi|53803448|ref|YP_114763.1| DNA-directed RNA polymerase subunit alpha [Methylococcus capsulatus
           str. Bath]
 gi|61215838|sp|Q605D7|RPOA_METCA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|53757209|gb|AAU91500.1| DNA-directed RNA polymerase, alpha subunit [Methylococcus
           capsulatus str. Bath]
          Length = 328

 Score =  296 bits (758), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 156/332 (46%), Positives = 219/332 (65%), Gaps = 7/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +  ELIKP  +E +  G        ++ EPL RGF HTLGNALRRVL+S++ GAA+T
Sbjct: 1   MHNSLAELIKPRTVEVVPHGSHSAR---VVIEPLERGFGHTLGNALRRVLLSAIPGAAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V IDGVLHE S+I+GV ED+ D++LN+K + ++++G     + + K GPG V AGDI+ 
Sbjct: 58  DVVIDGVLHEYSTIEGVQEDVIDVLLNLKNLAIRLNGPHDVYLNVDKHGPGPVLAGDIEA 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPI 180
            +D+EVLNP+ +I +++ +  +RM L V KG GY P  +   E D  IG + +DA +SPI
Sbjct: 118 SHDVEVLNPELLIAHINGNGRLRMTLHVQKGRGYQPVANRAIEGDSAIGTLHLDASFSPI 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VESAR  Q  D D+L + + T+G++  E++V  A+ IL   L + ++    K E
Sbjct: 178 KKVSYVVESARVEQRTDLDRLVIELQTNGTVQPEEAVKHAANILNQHLAILVDL---KGE 234

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                      F+P LL  V++LEL+VRS NCL+ ENI Y+GDLIQR+EAD+L+  N G+
Sbjct: 235 DLPLFGEDGPQFDPLLLHPVDDLELTVRSANCLKAENIFYIGDLIQRSEADLLKTPNLGK 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEEL 332
           KSL EIK VL T GL LGM L +WPPE +++L
Sbjct: 295 KSLTEIKDVLATKGLSLGMRLENWPPEGLKKL 326


>gi|16272744|ref|NP_438962.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           Rd KW20]
 gi|1173145|sp|P43737|RPOA_HAEIN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|1573813|gb|AAC22461.1| DNA-directed RNA polymerase, alpha chain (rpoA) [Haemophilus
           influenzae Rd KW20]
          Length = 328

 Score =  296 bits (758), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 153/334 (45%), Positives = 224/334 (67%), Gaps = 11/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVILTLNKSGIGPVVAADITY 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYS 178
             D+E++NPDHVIC+L D +A + M + V +G GYVPA  + H  E  PIG + +DA YS
Sbjct: 118 DGDVEIVNPDHVICHLTDENASISMRIRVQRGRGYVPASSRTHTQEERPIGRLLVDACYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +
Sbjct: 178 PVERIAYNVEAARVEQRTDLDKLVIELETNGALEPEEAIRRAATILAEQLDAFVDLRDVR 237

Query: 239 K-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           + E+KE+       F P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 QPEIKEE----KPEFXPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 294 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 327


>gi|145630549|ref|ZP_01786329.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           R3021]
 gi|144983939|gb|EDJ91381.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           R3021]
          Length = 328

 Score =  296 bits (757), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 153/334 (45%), Positives = 224/334 (67%), Gaps = 11/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVILTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYS 178
             D+E++NPDHVIC+L D +A + M + V +G GYVPA  + H  E  PIG + +DA YS
Sbjct: 118 DGDVEIVNPDHVICHLTDENASISMRIRVQRGRGYVPASSRTHTQEERPIGRLLVDACYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  D DKL + ++T+G +  E+++  A+ IL +QL  F++  + +
Sbjct: 178 PVERIAYNVEAARVEQRTDLDKLVIELETNGELEPEEAIRRAATILAEQLDAFVDLRDVR 237

Query: 239 K-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           + E+KE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 QPEIKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 294 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 327


>gi|322515610|ref|ZP_08068589.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus ureae
           ATCC 25976]
 gi|322118320|gb|EFX90595.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus ureae
           ATCC 25976]
          Length = 329

 Score =  296 bits (757), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 157/337 (46%), Positives = 227/337 (67%), Gaps = 16/337 (4%)

Query: 2   IQKNWQELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           +Q +  E +KP+  NIE I           +  EPL RGF HTLGNALRR+L+SS+ G A
Sbjct: 1   MQGSVTEFLKPHLVNIEQI-----SSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCA 55

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T V+IDGVLHE SS +G+ ED+ +++LN+KG+ +K+S      +T+ K G G VTA DI
Sbjct: 56  VTEVKIDGVLHEYSSKEGIQEDILEVLLNLKGLAVKVSNKDDIILTLNKSGIGPVTAADI 115

Query: 120 QTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDA 175
               D+E++NPDHVIC+L D +A + M + V +G GYVPA    H + E+ PIG + +DA
Sbjct: 116 THDGDVEIVNPDHVICHLTDKNASINMCIRVQRGRGYVPASARVHSQDEDRPIGRLLVDA 175

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
            +SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  
Sbjct: 176 RFSPVDRIAYNVEAARVEQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLR 235

Query: 236 EPKK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           + ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+
Sbjct: 236 DVRQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLK 291

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
             N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 292 TPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|315633479|ref|ZP_07888769.1| DNA-directed RNA polymerase subunit alpha [Aggregatibacter segnis
           ATCC 33393]
 gi|315477521|gb|EFU68263.1| DNA-directed RNA polymerase subunit alpha [Aggregatibacter segnis
           ATCC 33393]
          Length = 329

 Score =  296 bits (757), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 154/335 (45%), Positives = 226/335 (67%), Gaps = 12/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    +  +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTQAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A +I  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDIIEVLLNLKGLAVKVQNKDDVLLTLSKSGIGPVVAANITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++NP+HVIC+L D +A + M + V +G GYVPA     ++ E+ PIG + +DA Y
Sbjct: 118 DGDVEIVNPEHVICHLTDENASINMRIRVQRGRGYVPASARTQNQDEDRPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPI +++Y VE+AR  Q  D DKL + ++T+G+I  ED++  A+ IL +QL  F++  + 
Sbjct: 178 SPIDRIAYNVEAARVEQRTDLDKLVIELETNGTIDPEDAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|33152929|ref|NP_874282.1| DNA-directed RNA polymerase subunit alpha [Haemophilus ducreyi
           35000HP]
 gi|41688646|sp|Q7VKF8|RPOA_HAEDU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|33149154|gb|AAP96671.1| RNA polymerase alpha subunit [Haemophilus ducreyi 35000HP]
          Length = 329

 Score =  296 bits (757), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 156/337 (46%), Positives = 227/337 (67%), Gaps = 16/337 (4%)

Query: 2   IQKNWQELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           +Q +  E +KP+  NIE I           +  EPL RGF HTLGNALRR+L+SS+ G A
Sbjct: 1   MQGSVIEFLKPHLVNIEQI-----SSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCA 55

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +  V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+SG +   +T+ K G G V A DI
Sbjct: 56  VAEVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVSGKNDVTLTLNKSGIGPVLAADI 115

Query: 120 QTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDA 175
               D+E++NP+HVIC+L D DA + M + V +G GYVPA    H + E+ PIG + +DA
Sbjct: 116 THDGDVEIINPNHVICHLTDKDASINMRIYVQRGRGYVPASARVHSQDEDRPIGRLLVDA 175

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
            +SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  
Sbjct: 176 RFSPVDRIAYNVEAARVEQRTDLDKLIIDMETNGTIDPEEAIRRAATILAEQLDAFVDLR 235

Query: 236 EPKK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           + ++ E+KE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+
Sbjct: 236 DVRQPEIKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLK 291

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
             N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 292 TPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|325577151|ref|ZP_08147635.1| DNA-directed RNA polymerase subunit alpha [Haemophilus
           parainfluenzae ATCC 33392]
 gi|301155355|emb|CBW14821.1| RNA polymerase, alpha subunit [Haemophilus parainfluenzae T3T1]
 gi|325160733|gb|EGC72854.1| DNA-directed RNA polymerase subunit alpha [Haemophilus
           parainfluenzae ATCC 33392]
          Length = 329

 Score =  296 bits (757), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 154/335 (45%), Positives = 224/335 (66%), Gaps = 12/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVILTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++NP HVIC+L D +A + M + V +G GYVPA    H + E+ PIG + +DA Y
Sbjct: 118 DGDVEIVNPSHVICHLTDENASINMRIRVQRGRGYVPASARTHSQNEDRPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|224827042|ref|ZP_03700139.1| DNA-directed RNA polymerase, alpha subunit [Lutiella nitroferrum
           2002]
 gi|224600708|gb|EEG06894.1| DNA-directed RNA polymerase, alpha subunit [Lutiella nitroferrum
           2002]
          Length = 327

 Score =  296 bits (757), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 156/332 (46%), Positives = 220/332 (66%), Gaps = 8/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+   +       ++   EP  RG+AHTLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSASEFLKPRLIDVQPVSATHARVSM---EPFERGYAHTLGNALRRILLSSMPGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE S++ GV ED+ DI+LN+KG+ LK+ G     +T+ K G G V AGDI+ 
Sbjct: 58  EVTIAGVLHEYSALDGVREDVVDILLNLKGVVLKLHGRDSVVLTLKKEGEGAVLAGDIEL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP--AKHHRTENDPIGLITIDALYSP 179
            +D+EV+NPDHVIC+L     + +E+ V KG GY P   + ++ +N  IG I +DA +SP
Sbjct: 118 PHDVEVINPDHVICHLAAGGKIDLEVKVEKGRGYQPVSVRVNQDDNRAIGTIQLDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +++VS+ VESAR  Q  D D+L + I+T+G I  E +V  A+RIL DQL +F + +    
Sbjct: 178 VRRVSFGVESARVEQRTDLDRLVLDIETNGVIEPEQAVRNAARILMDQLSIFADLQ---G 234

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
              E++  K+ P +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G
Sbjct: 235 TAVEEVVEKAPPIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTETELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           RKSL EIK VL + GL LGM L +WPP  +E+
Sbjct: 295 RKSLNEIKEVLASKGLTLGMKLENWPPAGLEK 326


>gi|225076420|ref|ZP_03719619.1| hypothetical protein NEIFLAOT_01465 [Neisseria flavescens
           NRL30031/H210]
 gi|224952268|gb|EEG33477.1| hypothetical protein NEIFLAOT_01465 [Neisseria flavescens
           NRL30031/H210]
          Length = 328

 Score =  296 bits (757), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 158/334 (47%), Positives = 218/334 (65%), Gaps = 11/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+   L      R  +  +P  RGF HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSTTEFLKPRQIDVDTLSS---TRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE S+I GV ED+ D++LNIKGI  K+ G +  ++T+ K G G V AGDI  
Sbjct: 58  EVVISGVLHEYSTIDGVQEDVVDVLLNIKGIVFKLHGRNQVQLTLKKTGAGAVVAGDIDL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYS 178
            +D+E++NP+HVIC+L  +  + ME+ V +G GY      R    +N  IG I +DA +S
Sbjct: 118 PHDVEIINPEHVICHLSDNGQIDMEIKVEQGRGYQSVSGRRVLRDDNKQIGAIQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EP 237
           PI +VS+ VE AR  Q  D DKL + I+T+GSI  E++V  A+RIL DQ+ +F + +  P
Sbjct: 178 PISRVSFEVEPARVEQRTDLDKLVLDIETNGSIDPEEAVRSAARILIDQMSIFADLQGTP 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +EV+E    K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N
Sbjct: 238 VEEVEE----KAPPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 294 LGRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 327


>gi|319764614|ref|YP_004128551.1| DNA-directed RNA polymerase, alpha subunit [Alicycliphilus
           denitrificans BC]
 gi|330826871|ref|YP_004390174.1| DNA-directed RNA polymerase subunit alpha [Alicycliphilus
           denitrificans K601]
 gi|317119175|gb|ADV01664.1| DNA-directed RNA polymerase, alpha subunit [Alicycliphilus
           denitrificans BC]
 gi|329312243|gb|AEB86658.1| DNA-directed RNA polymerase, alpha subunit [Alicycliphilus
           denitrificans K601]
          Length = 331

 Score =  296 bits (757), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 157/329 (47%), Positives = 216/329 (65%), Gaps = 9/329 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG    NR  +  EP  RG+ HTLGNA+RRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKAINVEQLGH---NRAKVELEPFERGYGHTLGNAIRRVLLSSMVGYAATEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE SSI GV ED+ +I+LN+KG+  K+       +++ K G GVVTA DIQT +D+E++
Sbjct: 62  LHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGVVTARDIQTPHDVEIV 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSY 185
           NPDHVI  L     + M++ V KG GYVP    R  ++    IG I +DA +SP+K+VSY
Sbjct: 122 NPDHVIATLSAGGKLDMQIKVEKGRGYVPGNLRRFADESTKSIGRIVLDASFSPVKRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVESAR  Q  D DKL + I+T+G+I+ E++V  +++IL +QL +F   +  +    +  
Sbjct: 182 TVESARVEQRTDLDKLVLEIETNGAISAEEAVRASAKILVEQLAVFAQLDGGEIFESQAT 241

Query: 246 NVKSLP---FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
             ++     F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKS
Sbjct: 242 GARAASGATFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKS 301

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           L EIK VL + GL LGM L +WPP  +++
Sbjct: 302 LNEIKEVLASRGLTLGMKLENWPPAGLDK 330


>gi|94987424|ref|YP_595357.1| DNA-directed RNA polymerase subunit alpha [Lawsonia intracellularis
           PHE/MN1-00]
 gi|119366693|sp|Q1MPP1|RPOA_LAWIP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|94731673|emb|CAJ55036.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Lawsonia
           intracellularis PHE/MN1-00]
          Length = 347

 Score =  296 bits (757), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 156/338 (46%), Positives = 220/338 (65%), Gaps = 15/338 (4%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTL---MIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +NW +L++P      V+   E N T       EPL RG+  T+GNALRRVL+SSL+GAA 
Sbjct: 13  RNWAKLVRPE----AVINNMESNTTTYGRFEYEPLERGYGITIGNALRRVLLSSLQGAAF 68

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
            +V+I GV HE ++I G+ ED+TDIILN+K + L M  D  + +++F    G+VTA DIQ
Sbjct: 69  VSVKILGVQHEFTTIPGILEDVTDIILNLKQVRLAMDTDEPQHLSLFVSKKGIVTAADIQ 128

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T   +EVLNP+  I  L  D  +RME  V  G GYVPA+ H   ++ IGLI +D+ +SPI
Sbjct: 129 TNQHVEVLNPEQHIATLTEDIELRMEFEVRMGKGYVPAEMHEDLHEEIGLIKLDSSFSPI 188

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           + V+Y VE AR GQ+ +YDKL + + TDGS++ ED++A +++I++DQ+ +FINF+E    
Sbjct: 189 RNVTYVVEQARVGQMTNYDKLVLEVWTDGSVSPEDAIAYSAKIIKDQISVFINFDERISG 248

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
              +    S   N  L K ++ELELSVR+TNCLR  NI  +G+L+Q+ EADML+  NFG+
Sbjct: 249 SGGNEGSGSSDLNDNLFKGIDELELSVRATNCLRSANISTVGELVQKAEADMLKTKNFGK 308

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK +L +MGL  GM         I+   KKY++
Sbjct: 309 KSLDEIKALLTSMGLDFGM--------KIDGFEKKYQE 338


>gi|251793851|ref|YP_003008583.1| DNA-directed RNA polymerase subunit alpha [Aggregatibacter
           aphrophilus NJ8700]
 gi|247535250|gb|ACS98496.1| DNA-directed RNA polymerase, alpha subunit [Aggregatibacter
           aphrophilus NJ8700]
          Length = 329

 Score =  295 bits (756), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 152/335 (45%), Positives = 226/335 (67%), Gaps = 12/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    +  ++ EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTQAKVVLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVLLTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++NP+HVIC+L D +A + M + V +G GYVPA     ++ E+ PIG + +DA Y
Sbjct: 118 DGDVEIVNPEHVICHLTDENASINMRIRVQRGRGYVPASARAQNQDEDRPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  ED++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLVIELETNGTIDPEDAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ E+KE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEIKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|240948150|ref|ZP_04752553.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus minor
           NM305]
 gi|240297503|gb|EER48010.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus minor
           NM305]
          Length = 329

 Score =  295 bits (756), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 154/336 (45%), Positives = 225/336 (66%), Gaps = 14/336 (4%)

Query: 2   IQKNWQELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           +Q +  E +KP+  NIE I           +  EPL RGF HTLGNALRR+L+SS+ G A
Sbjct: 1   MQGSVTEFLKPHLVNIEQI-----SSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCA 55

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G VTAGDI
Sbjct: 56  VTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQSKDDVVLTLNKSGIGPVTAGDI 115

Query: 120 QTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDA 175
               D+E++NPDHVIC+L D +A + M + V +G GYVPA    H + ++ PIG + +DA
Sbjct: 116 THDGDVEIVNPDHVICHLTDKNASINMRIRVQRGRGYVPASARVHTQDDDRPIGRLLVDA 175

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
            +SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  
Sbjct: 176 RFSPVDRIAYNVEAARVEQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLR 235

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           + ++ V   +  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+ 
Sbjct: 236 DVRQPV---VKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKT 292

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 293 PNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|119899680|ref|YP_934893.1| DNA-directed RNA polymerase subunit alpha [Azoarcus sp. BH72]
 gi|158512916|sp|A1KB01|RPOA_AZOSB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119672093|emb|CAL96007.1| DNA-directed RNA polymerase [Azoarcus sp. BH72]
          Length = 326

 Score =  295 bits (756), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 157/328 (47%), Positives = 220/328 (67%), Gaps = 10/328 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I+   +   +   T+   EP  RGF HTLGNALRR+L+SSL G A T V I+GV
Sbjct: 6   LLKPRIIDVQSISPVQARVTM---EPFERGFGHTLGNALRRILLSSLPGHAPTEVSIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S++ G+ ED+ D++LN+KG+ LK+   S   +T+ K G GVVTA DI+  +D+E++
Sbjct: 63  LHEYSTLDGMREDIVDLLLNLKGVVLKLHNRSEAMLTLSKSGEGVVTARDIEGGHDVEII 122

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVP--AKHHRTENDPIGLITIDALYSPIKKVSYT 186
           NPDHVI +L     + M++ V +G GYVP  A+    EN  IG I +DA +SP+++VSY 
Sbjct: 123 NPDHVIAHLAPGGKLEMQIKVEQGRGYVPGNARPVSAENKTIGRIVLDASFSPVRRVSYL 182

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EPKKEVKEDI 245
           VESAR  Q  D D+L + I+T+G++  E+++  A+R+L DQL +F + E  P   V E  
Sbjct: 183 VESARVEQRTDLDRLVIDIETNGAVDPEEAIRYAARVLMDQLSVFADLEGTPVAVVPE-- 240

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             K+   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 241 --KTPSIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTETELLKTPNLGRKSLNE 298

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEELA 333
           IK VL + GL LGM L +WPP  +E+L 
Sbjct: 299 IKEVLASRGLTLGMKLENWPPAGLEKLG 326


>gi|52426078|ref|YP_089215.1| DNA-directed RNA polymerase subunit alpha [Mannheimia
           succiniciproducens MBEL55E]
 gi|61215866|sp|Q65QY0|RPOA_MANSM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|52308130|gb|AAU38630.1| RpoA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 329

 Score =  295 bits (756), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 154/335 (45%), Positives = 225/335 (67%), Gaps = 12/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVD---IEQVSPTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVFLTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++NP+HVIC+L D +A + M + V +G GYVPA    H + E  PIG + +DA Y
Sbjct: 118 DGDVEIVNPEHVICHLTDENASINMRIRVQRGRGYVPASARVHAQDEERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLVIELETNGAIDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|92112579|ref|YP_572507.1| DNA-directed RNA polymerase subunit alpha [Chromohalobacter
           salexigens DSM 3043]
 gi|119366673|sp|Q1R0F0|RPOA_CHRSD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|91795669|gb|ABE57808.1| DNA-directed RNA polymerase subunit alpha [Chromohalobacter
           salexigens DSM 3043]
          Length = 333

 Score =  295 bits (756), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 150/334 (44%), Positives = 230/334 (68%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  E ++P +I+   + +   N   ++ EP  RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQRSVTEFLRPRDIK---VEEINANHAKIVLEPFERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV-TIFKRGPGVVTAGDIQ 120
             +I+GVLHE S+I+GV ED+ +I+LN+K + +KM G+  + V  + K+GP VVTAGDI 
Sbjct: 58  EAEIEGVLHEYSAIEGVQEDVIEILLNLKDVAVKMHGNRDEVVLALSKQGPSVVTAGDIA 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALY 177
             +D+E++NPDHVI +L+    ++M+L V +G GY PA    +E D    IG + +DA +
Sbjct: 118 VDHDVEIVNPDHVIAHLNDSGELKMQLKVVRGRGYEPADTRASEEDESRAIGRLQLDATF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++VSY+VE+AR  Q  D DKL + ++TDG++  E+++  ++ ILQ+QL  F++ E  
Sbjct: 178 SPVRRVSYSVEAARVEQRTDLDKLIIDLETDGTLDPEEAIRRSATILQEQLAAFVDLEAD 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           K++  E+   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N
Sbjct: 238 KEQEVEEEEDQ---IDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL   GL LGM L +WPP S+++
Sbjct: 295 LGKKSLNEIKDVLAARGLSLGMRLENWPPASLKD 328


>gi|294789219|ref|ZP_06754458.1| DNA-directed RNA polymerase, alpha subunit [Simonsiella muelleri
           ATCC 29453]
 gi|294482960|gb|EFG30648.1| DNA-directed RNA polymerase, alpha subunit [Simonsiella muelleri
           ATCC 29453]
          Length = 327

 Score =  295 bits (755), Expect = 6e-78,   Method: Compositional matrix adjust.
 Identities = 154/332 (46%), Positives = 217/332 (65%), Gaps = 8/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+   L      R  +  +P  RGF HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSTTEFLKPRQIDVDTLSA---TRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I  VLHE S++ GV ED+ DI+LNIKGI  K+   +   V++ K G GVV AGDI+ 
Sbjct: 58  EVSIANVLHEYSTLDGVQEDVVDILLNIKGIVFKLHNRTEVTVSLKKSGAGVVRAGDIEL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY--VPAKHHRTENDPIGLITIDALYSP 179
            +D+E++NPDHV+C+L  +  + ME+ V +G GY  V  +    E + IG I +DA +SP
Sbjct: 118 SHDVEIINPDHVLCHLAENGNIEMEIKVEQGRGYQSVSGRRQGKEQNKIGAIQLDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I +VS+ VE+AR  Q  D D L + I+T+G+I  E++V  A+RIL DQ+ +F + +    
Sbjct: 178 ISRVSFDVEAARVEQRTDLDSLILDIETNGAIDPEEAVRAAARILIDQMSIFADLQGTPV 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           EV+E+   K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N G
Sbjct: 238 EVEEE---KAPPIDPVLLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           RKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 295 RKSLNEIKEVLASKGLTLGSKLEAWPPAGLEK 326


>gi|260914656|ref|ZP_05921122.1| DNA-directed RNA polymerase subunit alpha [Pasteurella dagmatis
           ATCC 43325]
 gi|260631255|gb|EEX49440.1| DNA-directed RNA polymerase subunit alpha [Pasteurella dagmatis
           ATCC 43325]
          Length = 329

 Score =  295 bits (755), Expect = 6e-78,   Method: Compositional matrix adjust.
 Identities = 154/335 (45%), Positives = 224/335 (66%), Gaps = 12/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVFLTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++NP+HVIC+L D +A + M + V +G GYVPA    H + E  PIG + +DA Y
Sbjct: 118 DGDVEIVNPEHVICHLTDENASINMRIRVQRGRGYVPASARVHAQDEERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|332175074|gb|AEE24328.1| DNA-directed RNA polymerase, alpha subunit [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 329

 Score =  295 bits (755), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 153/327 (46%), Positives = 221/327 (67%), Gaps = 9/327 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +KP  +E   +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDG
Sbjct: 7   EFLKPRLVE---IDNVSPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDG 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+ +GV ED+ +I+LN+KG+ +++ G +   +T+ K G G V AGDIQ   D+E+
Sbjct: 64  VLHEYSTKEGVQEDVIEILLNLKGLAVRLEGKTEATLTLVKSGAGPVLAGDIQHDGDVEI 123

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--END-PIGLITIDALYSPIKKVS 184
           +NP HV+C L  +A + M + V  G GYVPA   R+  E+D PIG + +DA +SPI ++S
Sbjct: 124 VNPSHVLCTLTGEAELSMRIKVEMGRGYVPASTRRSSEEDDRPIGRLLVDASFSPISRIS 183

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VESAR  Q  D DKL + ++T+G+I  E+++  ++ IL +QL  F+   +  + V+++
Sbjct: 184 YNVESARVEQRTDLDKLIIDMETNGTIDPEEAIRRSATILAEQLDAFVELRDMSEPVEKE 243

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 244 EKPE---FDPILLRPVDDLELTVRSANCLKAEAIQYIGDLVQRTEVELLKTPNLGKKSLT 300

Query: 305 EIKGVLGTMGLFLGMNLPDWPPESIEE 331
           EIK VL + GL LGM L +WPPESI E
Sbjct: 301 EIKDVLASRGLSLGMRLENWPPESIAE 327


>gi|15603255|ref|NP_246329.1| DNA-directed RNA polymerase subunit alpha [Pasteurella multocida
           subsp. multocida str. Pm70]
 gi|13431846|sp|P57941|RPOA_PASMU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|12721765|gb|AAK03474.1| RpoA [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 329

 Score =  295 bits (755), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 154/335 (45%), Positives = 223/335 (66%), Gaps = 12/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVFLTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++NP+HVIC+L D  A + M + V +G GYVPA    H + E  PIG + +DA Y
Sbjct: 118 DGDVEIVNPEHVICHLTDESASINMRIRVQRGRGYVPASARVHAQDEERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|254362772|ref|ZP_04978854.1| DNA-directed RNA polymerase subunit alpha [Mannheimia haemolytica
           PHL213]
 gi|261492717|ref|ZP_05989265.1| DNA-directed RNA polymerase subunit alpha [Mannheimia haemolytica
           serotype A2 str. BOVINE]
 gi|261495668|ref|ZP_05992114.1| DNA-directed RNA polymerase subunit alpha [Mannheimia haemolytica
           serotype A2 str. OVINE]
 gi|153094401|gb|EDN75250.1| DNA-directed RNA polymerase subunit alpha [Mannheimia haemolytica
           PHL213]
 gi|261308775|gb|EEY10032.1| DNA-directed RNA polymerase subunit alpha [Mannheimia haemolytica
           serotype A2 str. OVINE]
 gi|261311570|gb|EEY12725.1| DNA-directed RNA polymerase subunit alpha [Mannheimia haemolytica
           serotype A2 str. BOVINE]
          Length = 329

 Score =  295 bits (755), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 155/337 (45%), Positives = 226/337 (67%), Gaps = 16/337 (4%)

Query: 2   IQKNWQELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           +Q +  E +KP+  NIE     Q       +  EPL RGF HTLGNALRR+L+SS+ G A
Sbjct: 1   MQGSVTEFLKPHLVNIE-----QVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCA 55

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G VTA DI
Sbjct: 56  VTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDIILTLNKSGIGPVTAADI 115

Query: 120 QTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDA 175
               D+E++NPDHVIC+L D +A + M + V +G GYVPA    H + ++ PIG + +DA
Sbjct: 116 THDGDVEIVNPDHVICHLTDKNASINMRIRVQRGRGYVPASARLHTQNDDRPIGRLLVDA 175

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
            +SP+ +++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  
Sbjct: 176 RFSPVDRIAYNVEAARVEQRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLR 235

Query: 236 EPKK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           + ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+
Sbjct: 236 DVRQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLK 291

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
             N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 292 TPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|212704609|ref|ZP_03312737.1| hypothetical protein DESPIG_02671 [Desulfovibrio piger ATCC 29098]
 gi|212672008|gb|EEB32491.1| hypothetical protein DESPIG_02671 [Desulfovibrio piger ATCC 29098]
          Length = 347

 Score =  295 bits (755), Expect = 8e-78,   Method: Compositional matrix adjust.
 Identities = 155/338 (45%), Positives = 218/338 (64%), Gaps = 15/338 (4%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTL---MIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +NW EL+KP+ I    L  E+   +     + EPL RG+  T+GNA+RRVL++SL+GAA 
Sbjct: 13  RNWNELVKPDQI----LRDEDTASSTHGKFVCEPLERGYGTTIGNAMRRVLLASLQGAAF 68

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
            +V+I GV HE ++I GV ED+TD++LNIK + L+M  D  +R+T+     G VTA  IQ
Sbjct: 69  VSVKITGVQHEFTTIHGVLEDVTDVVLNIKQVRLRMDTDEPQRLTLRVDSKGPVTAAQIQ 128

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               + VLNP+  I  L  D V+ ME  V  G GYVPA  H    D IGLI +D+ +SP+
Sbjct: 129 ANQHVTVLNPEQHIATLTEDVVLEMEFEVRMGKGYVPADMHEGLADEIGLIKLDSSFSPV 188

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KV+Y VE AR GQ+ +YD+L + + TDGS+T ED++A +++I++DQ+ +FINF+E    
Sbjct: 189 RKVAYAVEQARVGQMTNYDRLILEVWTDGSLTPEDAIAYSAKIIKDQISVFINFDERVSG 248

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                +  S   N  L K +++LELSVR+TNCLR  NI  +G+L+QR+EA+ML+  NFGR
Sbjct: 249 DMRHGSSDSGETNEHLFKSIDDLELSVRATNCLRSANIALVGELVQRSEAEMLKTKNFGR 308

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL  GM         ++   KKY+D
Sbjct: 309 KSLDEIKEVLHDMGLDFGMK--------VDGFEKKYQD 338


>gi|319787901|ref|YP_004147376.1| DNA-directed RNA polymerase subunit alpha [Pseudoxanthomonas
           suwonensis 11-1]
 gi|317466413|gb|ADV28145.1| DNA-directed RNA polymerase, alpha subunit [Pseudoxanthomonas
           suwonensis 11-1]
          Length = 332

 Score =  295 bits (754), Expect = 8e-78,   Method: Compositional matrix adjust.
 Identities = 143/307 (46%), Positives = 211/307 (68%), Gaps = 6/307 (1%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           NR  ++ EPL RG+ HTLGNALRRVL+SS+ G AIT V+IDGVLHE ++++G+ ED+ ++
Sbjct: 22  NRAKIVIEPLERGYGHTLGNALRRVLLSSIPGFAITEVEIDGVLHEYTTVEGLQEDVLEV 81

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           +LN+K + ++M       +++ K+GPGVVTAGDI+T + +E+LNP+HVIC+L  D  + M
Sbjct: 82  LLNLKDVAIRMHTGESATLSLAKQGPGVVTAGDIKTDHSVEILNPEHVICHLTKDTALNM 141

Query: 146 ELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
            L + +G GY PA   R    E   IG + +DA +SP+++V+Y+VE+AR  Q  D DKL 
Sbjct: 142 RLKIERGFGYQPATSRRRPDEETRAIGRLMLDASFSPVRRVAYSVEAARVEQRTDLDKLV 201

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + I+T+G+I  E++V  A+ IL DQL +F +F    +   +         +P LL+ +++
Sbjct: 202 IDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPAQAG---VDPVLLRPIDD 258

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KSL EIK VL   GL LGM L 
Sbjct: 259 LELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSLTEIKEVLAQRGLSLGMKLE 318

Query: 323 DWPPESI 329
           +WPP  +
Sbjct: 319 NWPPAGV 325


>gi|145632161|ref|ZP_01787896.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           3655]
 gi|145634786|ref|ZP_01790494.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           PittAA]
 gi|145636639|ref|ZP_01792306.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           PittHH]
 gi|145640901|ref|ZP_01796483.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           R3021]
 gi|229844670|ref|ZP_04464809.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           6P18H1]
 gi|229845853|ref|ZP_04465965.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           7P49H1]
 gi|144987068|gb|EDJ93598.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           3655]
 gi|145267952|gb|EDK07948.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           PittAA]
 gi|145270165|gb|EDK10101.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           PittHH]
 gi|145274415|gb|EDK14279.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           22.4-21]
 gi|229810857|gb|EEP46574.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           7P49H1]
 gi|229812384|gb|EEP48074.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           6P18H1]
 gi|309973706|gb|ADO96907.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           R2846]
          Length = 328

 Score =  295 bits (754), Expect = 8e-78,   Method: Compositional matrix adjust.
 Identities = 152/334 (45%), Positives = 225/334 (67%), Gaps = 11/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVILTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYS 178
             ++E++NPDHVIC+L D +A + M + V +G GYVPA  + H  E  PIG + +DA YS
Sbjct: 118 DGNVEIVNPDHVICHLTDENASISMRIRVQRGRGYVPASSRTHTQEERPIGRLLVDACYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +
Sbjct: 178 PVERIAYNVEAARVEQRTDLDKLVIELETNGALEPEEAIRRAATILAEQLDAFVDLRDVR 237

Query: 239 K-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           + E+KE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 QPEIKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 294 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 327


>gi|152978166|ref|YP_001343795.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           succinogenes 130Z]
 gi|171704199|sp|A6VLL3|RPOA_ACTSZ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|150839889|gb|ABR73860.1| DNA-directed RNA polymerase, alpha subunit [Actinobacillus
           succinogenes 130Z]
          Length = 329

 Score =  295 bits (754), Expect = 9e-78,   Method: Compositional matrix adjust.
 Identities = 153/335 (45%), Positives = 226/335 (67%), Gaps = 12/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V AGDI  
Sbjct: 58  EVEIEGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVFLTLNKSGIGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++NP+HVIC+L D +A + M + V +G GYVPA    H + E  PIG + +DA Y
Sbjct: 118 DGDVEIVNPEHVICHLTDENASISMRIRVQRGRGYVPASARAHSQDEERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLVIELETNGTLDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLDNWPPASIAE 328


>gi|109897339|ref|YP_660594.1| DNA-directed RNA polymerase subunit alpha [Pseudoalteromonas
           atlantica T6c]
 gi|119366709|sp|Q15X48|RPOA_PSEA6 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|109699620|gb|ABG39540.1| DNA-directed RNA polymerase subunit alpha [Pseudoalteromonas
           atlantica T6c]
          Length = 329

 Score =  295 bits (754), Expect = 9e-78,   Method: Compositional matrix adjust.
 Identities = 152/327 (46%), Positives = 221/327 (67%), Gaps = 9/327 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +KP  +E   +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDG
Sbjct: 7   EFLKPRLVE---IDNVSPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDG 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+ +GV ED+ +I+LN+KG+ +++ G +   +T+ K G G V AGDIQ   D+E+
Sbjct: 64  VLHEYSTKEGVQEDVIEILLNLKGLAVRLEGKTEATLTLVKSGAGPVLAGDIQHDGDVEI 123

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--END-PIGLITIDALYSPIKKVS 184
           +NP HV+C L  +A + M + V  G GYVPA   R+  E+D PIG + +DA +SP+ ++S
Sbjct: 124 VNPSHVLCTLTGEAELSMRIKVEMGRGYVPASTRRSSEEDDRPIGRLLVDASFSPVSRIS 183

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VESAR  Q  D DKL + ++T+G+I  E+++  ++ IL +QL  F+   +  + V+++
Sbjct: 184 YNVESARVEQRTDLDKLIIDMETNGTIDPEEAIRRSATILAEQLDAFVELRDMSEPVEKE 243

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 244 EKPE---FDPILLRPVDDLELTVRSANCLKAEAIQYIGDLVQRTEVELLKTPNLGKKSLT 300

Query: 305 EIKGVLGTMGLFLGMNLPDWPPESIEE 331
           EIK VL + GL LGM L +WPPESI E
Sbjct: 301 EIKDVLASRGLSLGMRLENWPPESIAE 327


>gi|91774660|ref|YP_544416.1| DNA-directed RNA polymerase subunit alpha [Methylobacillus
           flagellatus KT]
 gi|119366697|sp|Q1H4L2|RPOA_METFK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|91708647|gb|ABE48575.1| DNA-directed RNA polymerase subunit alpha [Methylobacillus
           flagellatus KT]
          Length = 328

 Score =  294 bits (753), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 161/335 (48%), Positives = 217/335 (64%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++  V+       TL   EP+ RGF +TLGNALRRVL+SS+ G AIT
Sbjct: 1   MQNSPTEYLKPRVVDVDVISPVRARVTL---EPMERGFGYTLGNALRRVLLSSIPGFAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGV+HE S++ GV ED+ DI+LN+KG+ LK++  +   +T+ K   GVVTAGD  T
Sbjct: 58  EVKIDGVVHEYSTLDGVQEDVVDILLNLKGVALKLNSKNEATLTLNKSTEGVVTAGDFDT 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYS 178
            +D E+ NPDHVI +L     + +E+ V  G GY P    R   D    +G I +DA +S
Sbjct: 118 GHDAEIANPDHVIAHLTKGGKLNLEVKVEMGRGYQPVPQRRKTEDEDRVLGFIQVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI KVSY VESAR  Q  D DKL M ++T+G I  E ++  A+RIL  QL +F + E   
Sbjct: 178 PISKVSYQVESARVEQRTDLDKLIMDVETNGIIEPEQAIRDAARILMGQLSVFADLEGAP 237

Query: 239 KEVKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            EV+    VK  P  +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N
Sbjct: 238 SEVE----VKQAPQVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKAPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEEL 332
            GRKSL EIK VL + GL LGM L +WPP  +E++
Sbjct: 294 LGRKSLNEIKDVLASKGLTLGMKLENWPPAGLEKV 328


>gi|226939212|ref|YP_002794283.1| DNA-directed RNA polymerase subunit alpha [Laribacter hongkongensis
           HLHK9]
 gi|254765253|sp|C1DAU3|RPOA_LARHH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|226714136|gb|ACO73274.1| RpoA [Laribacter hongkongensis HLHK9]
          Length = 327

 Score =  294 bits (753), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 158/332 (47%), Positives = 220/332 (66%), Gaps = 8/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+   +   +  R  M  EP  RG+A+TLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSASEFLKPRLIDVQPVSATQA-RVAM--EPFERGYAYTLGNALRRILLSSMPGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE S++ GV ED+ DI+LN+KG+  K+ G     +T+ K G G V A DI  
Sbjct: 58  EVSIAGVLHEYSALDGVREDVVDILLNLKGVVFKLHGRDSVLLTLKKEGEGAVRASDIDL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY--VPAKHHRTENDPIGLITIDALYSP 179
            +D+EV+NPDHVIC+L     + ME+ V KG GY   PA+  + +N  IG I +DA +SP
Sbjct: 118 PHDVEVVNPDHVICHLAAGGKIDMEIKVEKGRGYQPAPARVKQDDNRQIGTILLDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +++VS++VESAR  Q  D D+L M I+T+G I  E++V  A+RIL DQL +F + +    
Sbjct: 178 LRRVSFSVESARVEQRTDLDRLVMDIETNGVIEPEEAVRSAARILIDQLSIFADLQGTTV 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           EV E+   ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G
Sbjct: 238 EVVEE---RAPQVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTETELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           RKSL EIK VL + GL LGM L +WPP  +E+
Sbjct: 295 RKSLNEIKEVLASKGLTLGMKLENWPPAGLEK 326


>gi|146281195|ref|YP_001171348.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas stutzeri
           A1501]
 gi|158514171|sp|A4VHQ5|RPOA_PSEU5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|145569400|gb|ABP78506.1| DNA-directed RNA polymerase alpha chain [Pseudomonas stutzeri
           A1501]
 gi|327479348|gb|AEA82658.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas stutzeri DSM
           4166]
          Length = 333

 Score =  294 bits (753), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 150/336 (44%), Positives = 225/336 (66%), Gaps = 15/336 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+       TL   EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQSSVNEFLTPRHIDVQVVSPTRAKITL---EPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KGI +K+ G     +++ K+G G VTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGIAIKLHGRDEVTLSLVKKGAGAVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++N DH+I NL  +  + M+L V++G GY PA   +++ D    IG + +DA +S
Sbjct: 118 DHDVEIVNGDHLIANLAANGSLNMKLKVARGRGYEPADARQSDEDESRSIGRLQLDATFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--- 235
           P+++V+Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRVAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           EP    +ED        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+ 
Sbjct: 238 EPVVVEQED------EIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKT 291

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL + GL LGM L +WPP S+++
Sbjct: 292 PNLGKKSLTEIKDVLASRGLSLGMRLDNWPPASLKK 327


>gi|238921419|ref|YP_002934934.1| DNA-directed RNA polymerase subunit alpha [Edwardsiella ictaluri
           93-146]
 gi|269140549|ref|YP_003297250.1| DNA-directed RNA polymerase subunit alpha [Edwardsiella tarda
           EIB202]
 gi|294638029|ref|ZP_06716289.1| DNA-directed RNA polymerase, alpha subunit [Edwardsiella tarda ATCC
           23685]
 gi|238870988|gb|ACR70699.1| DNA-directed RNA polymerase subunit alpha, putative [Edwardsiella
           ictaluri 93-146]
 gi|267986210|gb|ACY86039.1| DNA-directed RNA polymerase subunit alpha [Edwardsiella tarda
           EIB202]
 gi|291088821|gb|EFE21382.1| DNA-directed RNA polymerase, alpha subunit [Edwardsiella tarda ATCC
           23685]
 gi|304560334|gb|ADM42998.1| DNA-directed RNA polymerase alpha subunit [Edwardsiella tarda
           FL6-60]
          Length = 329

 Score =  294 bits (753), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 155/333 (46%), Positives = 222/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   L       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQLSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPHHVICHLTDENASINMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+S+  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEESIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|113460233|ref|YP_718291.1| DNA-directed RNA polymerase subunit alpha [Haemophilus somnus
           129PT]
 gi|170718274|ref|YP_001785292.1| DNA-directed RNA polymerase subunit alpha [Haemophilus somnus 2336]
 gi|119366686|sp|Q0I137|RPOA_HAES1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|112822276|gb|ABI24365.1| DNA-directed RNA polymerase subunit alpha [Haemophilus somnus
           129PT]
 gi|168826403|gb|ACA31774.1| DNA-directed RNA polymerase, alpha subunit [Haemophilus somnus
           2336]
          Length = 329

 Score =  294 bits (752), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 154/335 (45%), Positives = 224/335 (66%), Gaps = 12/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGYAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+    +  +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDIIEVLLNLKGLAVKVQNKDNVFLTLSKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++NPDHVIC+L D +A + M + V +G GYVPA    H   E  PIG + +DA Y
Sbjct: 118 DGDVEIVNPDHVICHLTDENASINMRIRVQRGRGYVPASSRVHSLDEERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y V++AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVQAARVEQRTDLDKLVIELETNGTIEPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 294 NLGKKSLTEIKDVLVSRGLSLGMRLENWPPASIAE 328


>gi|317494317|ref|ZP_07952731.1| DNA-directed RNA polymerase [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316917567|gb|EFV38912.1| DNA-directed RNA polymerase [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 329

 Score =  294 bits (752), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 154/333 (46%), Positives = 222/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   L       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQLSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + + +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKIQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+S+  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEESIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|83648827|ref|YP_437262.1| DNA-directed RNA polymerase subunit alpha [Hahella chejuensis KCTC
           2396]
 gi|119366687|sp|Q2S937|RPOA_HAHCH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|83636870|gb|ABC32837.1| DNA-directed RNA polymerase, alpha subunit [Hahella chejuensis KCTC
           2396]
          Length = 334

 Score =  294 bits (752), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 150/331 (45%), Positives = 221/331 (66%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  E + P  IE   +       TL   EPL RGF HTLG+ALRR+L+SS+ G A+ 
Sbjct: 1   MQRSLNEFLTPRTIEVNQINATHAKVTL---EPLERGFGHTLGSALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+++GV ED+ +I+LN+K + +KM       +++ K+G G V A DIQ 
Sbjct: 58  EVEIDGVLHEYSTVEGVQEDVIEILLNLKNLAIKMHNRDEATLSLNKKGAGPVLASDIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E+ NPD VICNL+ +  V+M+L V++G GY PA    + +D    IG + +D+ +S
Sbjct: 118 DHDVEIANPDMVICNLNSNGDVKMKLKVARGRGYEPADQRNSADDETRAIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +V+Y VESAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++F++  
Sbjct: 178 PVLRVAYNVESARVEQRTDLDKLVIDLETNGTIDPEEAIRRAATILQQQLAVFVDFDQQN 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +  K     +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPEKV---EEQEEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASI 325


>gi|237653970|ref|YP_002890284.1| DNA-directed RNA polymerase subunit alpha [Thauera sp. MZ1T]
 gi|237625217|gb|ACR01907.1| DNA-directed RNA polymerase, alpha subunit [Thauera sp. MZ1T]
          Length = 326

 Score =  293 bits (751), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 147/303 (48%), Positives = 207/303 (68%), Gaps = 5/303 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EP  RGF HTLGNALRR+L+SSL G A T V I+GVLHE S++ GV ED+ D++LN+KG+
Sbjct: 27  EPFERGFGHTLGNALRRILLSSLPGHAPTEVTIEGVLHEYSTLDGVREDIVDLLLNLKGV 86

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
             K++G S   V + K G GVVTA DI+  +D+E++NPDHVI +L     + M++ V +G
Sbjct: 87  VFKLNGRSEVTVRLAKAGEGVVTAADIEVGHDVEIINPDHVIAHLAPGGKLDMQIKVEEG 146

Query: 153 HGYVP--AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            GYVP  ++    E+  IG + +DA + P+++VSY VESAR  Q  D D+L + I+T+G+
Sbjct: 147 RGYVPGNSRPENAESKSIGRVVLDASFGPVRRVSYLVESARVEQRTDLDRLIIDIETNGA 206

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           +  E+++  A+R+L DQL +F + E       E +   S   +P LL+ V++LEL+VRS 
Sbjct: 207 VDPEEAIRYAARVLMDQLSVFADLE---GTAPERVEAASPTIDPVLLRPVDDLELTVRSA 263

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL EIK VL + GL LGM L +WPP  +E
Sbjct: 264 NCLKAENIYYIGDLIQRTETELLKTPNLGRKSLNEIKEVLASRGLTLGMKLENWPPAGLE 323

Query: 331 ELA 333
           +L 
Sbjct: 324 KLG 326


>gi|149912289|ref|ZP_01900860.1| DNA-directed RNA polymerase alpha subunit [Moritella sp. PE36]
 gi|149804634|gb|EDM64693.1| DNA-directed RNA polymerase alpha subunit [Moritella sp. PE36]
          Length = 328

 Score =  293 bits (751), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 149/331 (45%), Positives = 219/331 (66%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E ++P  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLRPRLVD---IEQISSTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDVLEILLNLKGLAIKLEGKDEALLTLTKSGTGPVLAGDITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
             D+E++NP+HVICNL   A + M + V+KG GYVPA      +D   PIG + +DA +S
Sbjct: 118 DGDVEIINPEHVICNLTGQADISMRIRVAKGRGYVPASTRIQSDDEERPIGRLLVDAAFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  + DKL + ++TDG++  E+++  A+ IL +QL  F++    +
Sbjct: 178 PVSRIAYNVEAARVEQRTNLDKLVIDMETDGTLDPEEAIRRAATILAEQLDAFVDL---R 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              + +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 235 DVTEPEQKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASI 325


>gi|329298509|ref|ZP_08255845.1| DNA-directed RNA polymerase subunit alpha [Plautia stali symbiont]
          Length = 329

 Score =  293 bits (751), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 154/333 (46%), Positives = 222/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ L++ G     +T+ + G G VTAGDI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLALRVQGKDEVILTLNQSGIGPVTAGDITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  AS IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRASTILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|329122808|ref|ZP_08251380.1| DNA-directed RNA polymerase subunit alpha [Haemophilus aegyptius
           ATCC 11116]
 gi|327472072|gb|EGF17510.1| DNA-directed RNA polymerase subunit alpha [Haemophilus aegyptius
           ATCC 11116]
          Length = 328

 Score =  293 bits (751), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 152/334 (45%), Positives = 224/334 (67%), Gaps = 11/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS  GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKGGVQEDILEVLLNLKGLAVKVQNKDDVILTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYS 178
             ++E++NPDHVIC+L D +A + M + V +G GYVPA  + H  E  PIG + +DA YS
Sbjct: 118 DGNVEIVNPDHVICHLTDENASISMRIRVQRGRGYVPASSRTHTQEERPIGRLLVDACYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +
Sbjct: 178 PVERIAYNVEAARVEQRTDLDKLVIELETNGALEPEEAIRRAATILAEQLDAFVDLRDVR 237

Query: 239 K-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           + E+KE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 QPEIKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 294 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 327


>gi|85858173|ref|YP_460375.1| DNA-directed RNA polymerase subunit alpha [Syntrophus
           aciditrophicus SB]
 gi|119366739|sp|Q2LQC9|RPOA_SYNAS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|85721264|gb|ABC76207.1| DNA-directed RNA polymerase alpha chain [Syntrophus aciditrophicus
           SB]
          Length = 345

 Score =  293 bits (751), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 164/345 (47%), Positives = 223/345 (64%), Gaps = 13/345 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +NW  LI+P  IE   + +    R     + +PL RGF  TLGNALRRVL+SS++GAAI 
Sbjct: 3   RNWCSLIRPRRIE---IDESTHTRFYGEFVCQPLERGFGITLGNALRRVLLSSIQGAAIV 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+ID VLHE S++ GV ED+TDIILN+KG+ LK+  D  + + I  +  GV+TA DI T
Sbjct: 60  SVKIDNVLHEFSTVPGVKEDITDIILNLKGVRLKLLSDGPRVIRIDTKKEGVITAADIIT 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              +EVLN DH I +L  D   RME+ V+ G GYV AK  +  + P G I IDALYSPIK
Sbjct: 120 DGTVEVLNEDHYIASLSGDMPFRMEMVVNSGRGYVQAKKEKDVDQPEGTINIDALYSPIK 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE------ 235
           KV+YTV  AR GQ+ DYDKLS+ + TDG++  ED+VA A++IL+ QL +F+         
Sbjct: 180 KVNYTVTHARVGQIADYDKLSLEVWTDGNVLPEDAVAFAAKILKKQLQVFVGLHTVIGTE 239

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           E ++E + +   +    N  LL+ VE+LELSVRS NCL+   I  +G+L+Q++EA+ML+ 
Sbjct: 240 EVEEEEEGEAVSEKENLNDILLRHVEDLELSVRSANCLKNAGINLIGELVQKSEAEMLKT 299

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNL--PDWPPESIEELAKKYED 338
            NFGRKSL EIK +L   GL  GM L    W  +  EE+ +  E+
Sbjct: 300 KNFGRKSLSEIKEILAEYGLTFGMKLEFTPWNKDVREEMGEIQEE 344


>gi|62181920|ref|YP_218337.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Choleraesuis str. SC-B67]
 gi|75480371|sp|Q57J56|RPOA_SALCH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|62129553|gb|AAX67256.1| DNA-directed RNA polymerase alpha chain [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|322716406|gb|EFZ07977.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Choleraesuis str. A50]
          Length = 329

 Score =  293 bits (750), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 153/333 (45%), Positives = 222/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L DWPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLEDWPPASI 326


>gi|319775263|ref|YP_004137751.1| RNA polymerase subunit alpha [Haemophilus influenzae F3047]
 gi|319897703|ref|YP_004135900.1| RNA polymerase, alpha subunit [Haemophilus influenzae F3031]
 gi|317433209|emb|CBY81584.1| RNA polymerase, alpha subunit [Haemophilus influenzae F3031]
 gi|317449854|emb|CBY86065.1| RNA polymerase, alpha subunit [Haemophilus influenzae F3047]
          Length = 328

 Score =  293 bits (750), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 152/334 (45%), Positives = 224/334 (67%), Gaps = 11/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVILTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYS 178
             ++E++NPDHVIC+L D +A + M + V +G GYVPA  + H  E  PIG + +DA YS
Sbjct: 118 DGNVEIVNPDHVICHLTDENASISMRIRVQRGRGYVPASSRTHTQEERPIGRLLVDACYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL  QL  F++  + +
Sbjct: 178 PVERIAYNVEAARVEQRTDLDKLVIELETNGALEPEEAIRRAATILAGQLDAFVDLRDVR 237

Query: 239 K-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           + E+KE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 QPEIKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 294 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 327


>gi|34499615|ref|NP_903830.1| DNA-directed RNA polymerase subunit alpha [Chromobacterium
           violaceum ATCC 12472]
 gi|41688632|sp|Q7NQH7|RPOA_CHRVO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|34105466|gb|AAQ61821.1| DNA-directed RNA polymerase (alpha subunit) [Chromobacterium
           violaceum ATCC 12472]
          Length = 327

 Score =  293 bits (750), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 154/332 (46%), Positives = 218/332 (65%), Gaps = 8/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+   +       ++   EP  RG+AHTLGN+LRR+L+SS+ G A T
Sbjct: 1   MQNSASEFLKPRLIDVQPVSATHARVSM---EPFERGYAHTLGNSLRRILLSSMPGYAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE S++ GV ED+ DI+LN+KG+ LK+ G     +T+ K G G V A DI+ 
Sbjct: 58  EVTIAGVLHEYSALDGVREDVVDILLNLKGVVLKLHGRDSVVLTLKKEGEGAVLASDIEL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP--AKHHRTENDPIGLITIDALYSP 179
            +D+EV+NP+HVIC++     + ME+ V KG GY P  A+    +N  IG I +DA +SP
Sbjct: 118 PHDVEVINPEHVICHISSGGKIDMEVKVEKGRGYQPVSARTSHDDNRSIGTIQLDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +++VS+ VESAR  Q  D D+L + I+T+G I  E +V  A+RIL DQL +F + +    
Sbjct: 178 VRRVSFAVESARVEQRTDLDRLVLDIETNGVIEPEQAVRNAARILMDQLSIFADLQ---G 234

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
              E++  K+ P +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G
Sbjct: 235 TAVEEVVEKAPPIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTETELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           RKSL EIK VL + GL LGM L +WPP  +E+
Sbjct: 295 RKSLNEIKEVLASKGLTLGMKLENWPPAGLEK 326


>gi|293390660|ref|ZP_06634994.1| DNA-directed RNA polymerase, alpha subunit [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290951194|gb|EFE01313.1| DNA-directed RNA polymerase, alpha subunit [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 329

 Score =  293 bits (749), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 154/335 (45%), Positives = 223/335 (66%), Gaps = 12/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    E +KP  ++   + Q    +  +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGAVTEFLKPRLVD---IEQVSSTQAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVLLTLSKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+EV+NP+HVIC+L D  + + M + V +G GYVPA      + E  PIG + +DA Y
Sbjct: 118 DGDVEVINPEHVICHLTDESSSISMRIRVRRGRGYVPASVRAQIQDEERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPI++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPIERIAYNVEAARVEQRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|323700832|ref|ZP_08112744.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio sp.
           ND132]
 gi|323460764|gb|EGB16629.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio
           desulfuricans ND132]
          Length = 346

 Score =  293 bits (749), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 151/332 (45%), Positives = 221/332 (66%), Gaps = 3/332 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW +L+KP  +  +   +  +     I EPL RG+A T+GNA+RRVL+SS++G AI + 
Sbjct: 13  RNWSQLVKPEAL--VRDSKSSKTYGKFICEPLERGYATTIGNAMRRVLLSSMQGCAIVSA 70

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
            I+GV HE +++ GV ED+T+++LN+K + + M+ D  +R+ +     G VTAG IQ   
Sbjct: 71  SIEGVQHEFTTLPGVLEDMTEVVLNLKQVRIAMTTDEPQRLVLEANKKGQVTAGMIQENQ 130

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           ++ +LN D +I  L  +  ++MEL V  G GYVPA  H    D IG + +DA YSP+KKV
Sbjct: 131 NVTILNKDQLIATLTENRPLKMELEVRMGKGYVPADMHEGLTDEIGSMVLDASYSPVKKV 190

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+VE AR GQ+ +YDKL + + TDGS+T ED+ A +++IL+DQL +FINF+E   E  E
Sbjct: 191 AYSVEQARVGQMTNYDKLILEVWTDGSVTPEDACAYSAKILKDQLSVFINFDESSSETHE 250

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           + +  S+  NP L K ++ELELSVR+TNCL+  NI  +G+L+QRTE  ML+  NFGRKSL
Sbjct: 251 EED-NSIDLNPNLFKSIDELELSVRATNCLKAANIQLVGELVQRTEQTMLKTKNFGRKSL 309

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
            EI+ VL  M L  GM++ D+  +  E L +K
Sbjct: 310 DEIRRVLDGMALKFGMSVEDFDKKYQEWLKRK 341


>gi|332107893|gb|EGJ09117.1| DNA-directed RNA polymerase subunit alpha [Rubrivivax
           benzoatilyticus JA2]
          Length = 328

 Score =  293 bits (749), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 154/326 (47%), Positives = 213/326 (65%), Gaps = 6/326 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG     R   + EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKAIHVEPLGG---YRAKAVLEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+I GV ED+  I+LN+KG+  ++       + + K G G VTA DIQT +D+E++
Sbjct: 62  LHEYSAIDGVQEDVVHIMLNLKGVVFRLHNRDEVTLVLRKEGEGAVTAADIQTPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NPDHVI +L     + M++ V KG GYVP    R  ++    IG I +DA +SP+K+VSY
Sbjct: 122 NPDHVIAHLSQGGKLDMQIKVEKGRGYVPGNLRRYGDEATKAIGRIVLDASFSPVKRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+AR  Q  D DKL M I+T+G+IT E+++  +++IL +QL +F   E    ++ E  
Sbjct: 182 AVENARVEQRTDLDKLVMEIETNGAITPEEAIRQSAKILVEQLAVFAQLEGQVSDIFEPQ 241

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 242 PQRTPNFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTETELLKTPNLGRKSLNE 301

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LG  L +WPP+ +++
Sbjct: 302 IKEVLASRGLTLGARLENWPPQGLDK 327


>gi|149926592|ref|ZP_01914852.1| DNA-directed RNA polymerase subunit alpha [Limnobacter sp. MED105]
 gi|149824521|gb|EDM83737.1| DNA-directed RNA polymerase subunit alpha [Limnobacter sp. MED105]
          Length = 326

 Score =  293 bits (749), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 153/326 (46%), Positives = 217/326 (66%), Gaps = 9/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  +E   +     N   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 6   LLKPRIVEVETVAP---NSAKVVMEPFERGYGHTLGNALRRVLLSSMIGYAPTEVSIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S++ GV ED+ D++LN+KGI  K+       VT+ +   GVVTAGDI+  +D+E++
Sbjct: 63  VHEYSTLDGVQEDVVDLLLNLKGIVFKLESRDVVTVTLKREVEGVVTAGDIELPHDVEII 122

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NPDHVI +L     + M++ V KG GYVP    R  ++P   IG I +DA +SP+K+VSY
Sbjct: 123 NPDHVIAHLSQGGKLDMQIKVEKGRGYVPGSVRRFPDEPSKAIGRIVLDASFSPVKRVSY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D D+L M+I+T+G ++ E+S+ LA+RIL +QL +F   E      + ++
Sbjct: 183 AVESARVEQRTDLDRLVMSIETNGVLSPEESIRLAARILVEQLSVFAALE---NTAEPEV 239

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           + ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 240 SQRAPQVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 299

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL   GL LGM L +WPP  +++
Sbjct: 300 IKEVLAARGLTLGMKLENWPPAGLDK 325


>gi|253995744|ref|YP_003047808.1| DNA-directed RNA polymerase subunit alpha [Methylotenera mobilis
           JLW8]
 gi|253982423|gb|ACT47281.1| DNA-directed RNA polymerase, alpha subunit [Methylotenera mobilis
           JLW8]
          Length = 328

 Score =  293 bits (749), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 162/334 (48%), Positives = 218/334 (65%), Gaps = 11/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++  VL       TL   EP+ RGF +TLGNALRRVL+SS+ G AIT
Sbjct: 1   MQNSPTEYLKPRVVDVEVLSPLRARVTL---EPMERGFGYTLGNALRRVLLSSIPGFAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGV+HE S++ GV ED+ DI+LN+KG+ LK++  S   + + K   GVVTA D +T
Sbjct: 58  EVKIDGVVHEYSTLDGVQEDVVDILLNLKGVALKLNSKSETILKLNKSVEGVVTAADFET 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYS 178
            +D E++NPDHVI +L     + +E+ V  G GY P    +  ND    +G I +DA +S
Sbjct: 118 GHDAEIVNPDHVIAHLTKGGKLNLEVKVEIGRGYQPVPVRQKSNDEDRVLGFIMVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI KVSY V+SAR  Q  D DKL M ++T+G I  E ++  A+RIL  QL +F + E   
Sbjct: 178 PINKVSYYVDSARVEQRTDLDKLVMDVETNGVIEPEQAIRDAARILMGQLSVFADLEGAP 237

Query: 239 KEVKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            EV+    VKS P  +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N
Sbjct: 238 SEVE----VKSAPQVDPVLLRPVDDLELTVRSANCLKAENIFYIGDLIQRTENELLKAPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            GRKSL EIK VL T GL LGM L +WPP  +E+
Sbjct: 294 LGRKSLNEIKDVLATRGLTLGMKLENWPPVGLEK 327


>gi|258406159|ref|YP_003198901.1| DNA-directed RNA polymerase subunit alpha [Desulfohalobium
           retbaense DSM 5692]
 gi|257798386|gb|ACV69323.1| DNA-directed RNA polymerase, alpha subunit [Desulfohalobium
           retbaense DSM 5692]
          Length = 347

 Score =  293 bits (749), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 154/336 (45%), Positives = 215/336 (63%), Gaps = 7/336 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW  L+ P  +E        EN      EPL RGF  TLGNALRRVL+SSL+GAAI AV
Sbjct: 13  RNWSTLVHPETLERD--EDSTENYGKFSCEPLERGFGTTLGNALRRVLLSSLQGAAIVAV 70

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I G+ HE ++I GV ED+TDI+LN+K + L+M+ D  +R+ +     G VTA   QT  
Sbjct: 71  RIKGIQHEFTTIPGVMEDITDIVLNLKQLRLRMNTDEPQRIELNVNTKGAVTASAFQTTQ 130

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           ++E+LNPD  I  L  D    +E  V  G GYVPA+ H    + IGLI++DA +SPI+KV
Sbjct: 131 NLEILNPDLHIATLSEDIEFGIEAEVRMGKGYVPAEMHEGLEEEIGLISMDASFSPIRKV 190

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE AR GQ+ +YDKL M + TDGS+  ED+VA +++IL++QL +FINF E    V E
Sbjct: 191 AYRVEQARVGQMTNYDKLVMEVWTDGSVLPEDAVAYSAKILKEQLAVFINFNEDSANVCE 250

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                +   N  L K +++LEL VR++NCL+  NI  +G+L+Q+TE +ML+  NFGRKSL
Sbjct: 251 SKGAGTESLNSNLFKHIDDLELPVRASNCLKSANINLVGELVQKTEGEMLKTKNFGRKSL 310

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +I+ V+  +GL  GM L     +  EE  KK+ ++
Sbjct: 311 EDIRKVIHELGLDFGMKL-----DGFEEQYKKWRER 341


>gi|121609260|ref|YP_997067.1| DNA-directed RNA polymerase subunit alpha [Verminephrobacter
           eiseniae EF01-2]
 gi|158514002|sp|A1WK92|RPOA_VEREI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|121553900|gb|ABM58049.1| DNA-directed RNA polymerase, alpha subunit [Verminephrobacter
           eiseniae EF01-2]
          Length = 330

 Score =  293 bits (749), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 158/331 (47%), Positives = 215/331 (64%), Gaps = 14/331 (4%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG       L   EP  RG+ HTLGNA+RRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKAINVEQLGHHHAKVAL---EPFERGYGHTLGNAIRRVLLSSMVGYAATEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE SSI GV ED+ +I+LN+KG+  K+       +++ K G G+VTA DIQT +D+E++
Sbjct: 62  LHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGMVTARDIQTPHDVEIV 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSY 185
           NPDHVI NL     + M++ V KG GY+P    R  ++    IG I +DA +SP+++VSY
Sbjct: 122 NPDHVIANLSQGGKLDMQIKVEKGRGYMPGNLRRYADEVTKSIGRIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVESAR  Q  D DKL + I+T+G+IT ED+V  +++IL +QL +F   E  +       
Sbjct: 182 TVESARVEQRTDLDKLVVEIETNGAITAEDAVRASAKILVEQLAVFAQLEGGELAA---F 238

Query: 246 NVKSLP-----FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           +  + P     F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GR
Sbjct: 239 DAPTGPRGNASFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           KSL EIK VL + GL LGM L +WPP  +++
Sbjct: 299 KSLNEIKEVLASRGLTLGMKLENWPPAGLDK 329


>gi|148826553|ref|YP_001291306.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           PittEE]
 gi|172048050|sp|A5UDS2|RPOA_HAEIE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|148716713|gb|ABQ98923.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           PittEE]
          Length = 328

 Score =  292 bits (748), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 151/334 (45%), Positives = 224/334 (67%), Gaps = 11/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       + + K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVILILNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYS 178
             ++E++NPDHVIC+L D +A + M + V +G GYVPA  + H  E  PIG + +DA YS
Sbjct: 118 DGNVEIVNPDHVICHLTDENASISMRIRVQRGRGYVPASSRTHTQEERPIGRLLVDACYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +
Sbjct: 178 PVERIAYNVEAARVEQRTDLDKLVIELETNGALEPEEAIRRAATILAEQLDAFVDLRDVR 237

Query: 239 K-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           + E+KE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 QPEIKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 294 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 327


>gi|197287093|ref|YP_002152965.1| DNA-directed RNA polymerase subunit alpha [Proteus mirabilis
           HI4320]
 gi|227354911|ref|ZP_03839325.1| DNA-directed RNA polymerase alpha chain [Proteus mirabilis ATCC
           29906]
 gi|194684580|emb|CAR46430.1| DNA-directed RNA polymerase alpha chain [Proteus mirabilis HI4320]
 gi|227164993|gb|EEI49832.1| DNA-directed RNA polymerase alpha chain [Proteus mirabilis ATCC
           29906]
          Length = 329

 Score =  292 bits (748), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 154/333 (46%), Positives = 222/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVHGKDEVILTLSKSGIGPVIAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASINMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++YTVE+AR  Q  D DKL + ++T+G+I  E+S+  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYTVEAARVEQRTDLDKLVIEMETNGTIDPEESIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|304310040|ref|YP_003809638.1| DNA-directed RNA polymerase alpha subunit [gamma proteobacterium
           HdN1]
 gi|301795773|emb|CBL43972.1| DNA-directed RNA polymerase alpha subunit [gamma proteobacterium
           HdN1]
          Length = 334

 Score =  292 bits (748), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 149/337 (44%), Positives = 222/337 (65%), Gaps = 18/337 (5%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  E + P +I    +   +   TL   EPL RGF HTLGNALRR+L+SS+ GAAI 
Sbjct: 1   MQRSVSEFLTPKSIAVQQVTATQAKVTL---EPLERGFGHTLGNALRRILLSSMPGAAIV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ D++LN+K + +KM       ++I K GPG+VTAGDI+ 
Sbjct: 58  EVEIDGVLHEYSTIEGVQEDVLDVLLNLKNVAVKMQDRDEAFLSISKEGPGLVTAGDIKC 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSP 179
              ++++N  H+I NL     + M + V +G GY PA+      E+  IG + +DA +SP
Sbjct: 118 DASVDIVNKAHIIANLSAGTKLNMRVKVVRGRGYCPAEAQLEADESKTIGRLMLDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE---- 235
           +++V+Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++ E    
Sbjct: 178 VRRVAYVVENARVEQRTDLDKLVIDLETNGTIDPEEAIRRAATILQQQLSIFVDLEKESL 237

Query: 236 -EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
            EP +E +E         +P LL+ V++LEL+VRS NCL+ EN+ Y+GDL+QRTE ++L+
Sbjct: 238 PEPVEEREE--------IDPILLRPVDDLELTVRSANCLKAENVYYIGDLVQRTEVELLK 289

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
             N G+KSL EIK VL + GL LGM L +WPP S+++
Sbjct: 290 TPNLGKKSLTEIKDVLASKGLSLGMRLENWPPASLKD 326


>gi|261867279|ref|YP_003255201.1| DNA-directed RNA polymerase subunit alpha [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261412611|gb|ACX81982.1| DNA-directed RNA polymerase, alpha subunit [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 329

 Score =  292 bits (748), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 155/335 (46%), Positives = 223/335 (66%), Gaps = 12/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    E +KP  ++   + Q    +  +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGAVTEFLKPRLVD---IEQISSTQAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVLLTLSKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+EV+NP+HVIC+L D +A + M + V +G GYVPA      + E  PIG + +DA Y
Sbjct: 118 DGDVEVINPEHVICHLTDENASISMRIRVRRGRGYVPASVRAQIQDEERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPI++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPIERIAYNVEAARVEQRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL  V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLLPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|300718680|ref|YP_003743483.1| DNA-directed RNA polymerase subunit alpha [Erwinia billingiae
           Eb661]
 gi|299064516|emb|CAX61636.1| DNA-directed RNA polymerase subunit alpha [Erwinia billingiae
           Eb661]
          Length = 329

 Score =  292 bits (748), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 222/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+EV+ P HVIC+L D +A + M + + +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEVVKPQHVICHLTDENAAISMRIKIQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|146313360|ref|YP_001178434.1| DNA-directed RNA polymerase subunit alpha [Enterobacter sp. 638]
 gi|152972203|ref|YP_001337349.1| DNA-directed RNA polymerase subunit alpha [Klebsiella pneumoniae
           subsp. pneumoniae MGH 78578]
 gi|157372752|ref|YP_001480741.1| DNA-directed RNA polymerase subunit alpha [Serratia proteamaculans
           568]
 gi|206579035|ref|YP_002236303.1| DNA-directed RNA polymerase, alpha subunit [Klebsiella pneumoniae
           342]
 gi|238896792|ref|YP_002921537.1| DNA-directed RNA polymerase subunit alpha [Klebsiella pneumoniae
           NTUH-K2044]
 gi|259909975|ref|YP_002650331.1| DNA-directed RNA polymerase subunit alpha [Erwinia pyrifoliae
           Ep1/96]
 gi|261342765|ref|ZP_05970623.1| DNA-directed RNA polymerase, alpha subunit [Enterobacter
           cancerogenus ATCC 35316]
 gi|262045154|ref|ZP_06018181.1| DNA-directed RNA polymerase subunit alpha [Klebsiella pneumoniae
           subsp. rhinoscleromatis ATCC 13884]
 gi|270264348|ref|ZP_06192614.1| DNA-directed RNA polymerase subunit alpha [Serratia odorifera
           4Rx13]
 gi|288933291|ref|YP_003437350.1| DNA-directed RNA polymerase, subunit alpha [Klebsiella variicola
           At-22]
 gi|290512093|ref|ZP_06551461.1| DNA-directed RNA polymerase, alpha subunit [Klebsiella sp. 1_1_55]
 gi|292489824|ref|YP_003532714.1| DNA-directed RNA polymerase subunit alpha [Erwinia amylovora
           CFBP1430]
 gi|292900866|ref|YP_003540235.1| DNA-directed RNA polymerase subunit alpha [Erwinia amylovora ATCC
           49946]
 gi|296105003|ref|YP_003615149.1| DNA-directed RNA polymerase subunit alpha [Enterobacter cloacae
           subsp. cloacae ATCC 13047]
 gi|322831097|ref|YP_004211124.1| DNA-directed RNA polymerase, subunit alpha [Rahnella sp. Y9602]
 gi|330002270|ref|ZP_08304264.1| DNA-directed RNA polymerase, alpha subunit [Klebsiella sp. MS 92-3]
 gi|172046001|sp|A4WFA3|RPOA_ENT38 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172047787|sp|A8GKH3|RPOA_SERP5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172052443|sp|A6TEU8|RPOA_KLEP7 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|145320236|gb|ABP62383.1| DNA-directed RNA polymerase subunit alpha [Enterobacter sp. 638]
 gi|150957052|gb|ABR79082.1| DNA-directed RNA polymerase alpha subunit [Klebsiella pneumoniae
           subsp. pneumoniae MGH 78578]
 gi|157324516|gb|ABV43613.1| DNA-directed RNA polymerase, alpha subunit [Serratia proteamaculans
           568]
 gi|190341369|gb|ACE74761.1| RpoA [Enterobacter sp. 638]
 gi|206568093|gb|ACI09869.1| DNA-directed RNA polymerase, alpha subunit [Klebsiella pneumoniae
           342]
 gi|224965597|emb|CAX57129.1| DNA-directed RNA polymerase subunit alpha [Erwinia pyrifoliae
           Ep1/96]
 gi|238549119|dbj|BAH65470.1| DNA-directed RNA polymerase alpha subunit [Klebsiella pneumoniae
           subsp. pneumoniae NTUH-K2044]
 gi|259037474|gb|EEW38718.1| DNA-directed RNA polymerase subunit alpha [Klebsiella pneumoniae
           subsp. rhinoscleromatis ATCC 13884]
 gi|270041484|gb|EFA14582.1| DNA-directed RNA polymerase subunit alpha [Serratia odorifera
           4Rx13]
 gi|283480074|emb|CAY75990.1| DNA-directed RNA polymerase alpha chain [Erwinia pyrifoliae DSM
           12163]
 gi|288314944|gb|EFC53882.1| DNA-directed RNA polymerase, alpha subunit [Enterobacter
           cancerogenus ATCC 35316]
 gi|288888020|gb|ADC56338.1| DNA-directed RNA polymerase, alpha subunit [Klebsiella variicola
           At-22]
 gi|289775883|gb|EFD83883.1| DNA-directed RNA polymerase, alpha subunit [Klebsiella sp. 1_1_55]
 gi|291200714|emb|CBJ47847.1| DNA-directed RNA polymerase alpha chain [Erwinia amylovora ATCC
           49946]
 gi|291555261|emb|CBA23539.1| DNA-directed RNA polymerase alpha chain [Erwinia amylovora
           CFBP1430]
 gi|295059462|gb|ADF64200.1| DNA-directed RNA polymerase subunit alpha [Enterobacter cloacae
           subsp. cloacae ATCC 13047]
 gi|295096939|emb|CBK86029.1| DNA-directed RNA polymerase subunit alpha [Enterobacter cloacae
           subsp. cloacae NCTC 9394]
 gi|310765573|gb|ADP10523.1| DNA-directed RNA polymerase subunit alpha [Erwinia sp. Ejp617]
 gi|312174006|emb|CBX82259.1| DNA-directed RNA polymerase alpha chain [Erwinia amylovora ATCC
           BAA-2158]
 gi|321166298|gb|ADW71997.1| DNA-directed RNA polymerase, alpha subunit [Rahnella sp. Y9602]
 gi|328537343|gb|EGF63593.1| DNA-directed RNA polymerase, alpha subunit [Klebsiella sp. MS 92-3]
          Length = 329

 Score =  292 bits (748), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 222/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENAAISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|301168432|emb|CBW28022.1| DNA-directed RNA polymerase alpha chain [Bacteriovorax marinus SJ]
          Length = 337

 Score =  292 bits (748), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 148/324 (45%), Positives = 219/324 (67%), Gaps = 4/324 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
            + KNW  +I+P ++E      +  N    +A+PL RG+  TLGN+LRR L+SSL+GA I
Sbjct: 4   FVAKNWTNMIRPVSLEADNESMKA-NYGKFVAKPLERGYGQTLGNSLRRALLSSLQGAGI 62

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
            A++I+GV HE  +I  V E++++IILN+K +  K+ G     +T+ K G G VTAGDI 
Sbjct: 63  VAIRIEGVEHEFGTINNVKEEVSEIILNLKEVFFKLKGKEDTVLTLEKSGEGPVTAGDIS 122

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALYSP 179
               +EVLNP+HVICN+     +++EL V++G GYV A  ++ E D P+G I +D L+SP
Sbjct: 123 ESASLEVLNPEHVICNISSGGSIKVELKVARGKGYVTASENKEEYDLPVGWIYVDTLFSP 182

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           + +V++TV ++R G+  D+DKL++ + T+  I  +D+VA +++IL+DQL +F+NFE+ ++
Sbjct: 183 VHRVNFTVTNSRVGKRTDFDKLTLEVWTNAGIQPQDAVAFSAKILRDQLAVFLNFEDEEE 242

Query: 240 EVK--EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            V+  +     S P N ALLK V ELELSVRS NCL+  NI Y+ +L+ +TE +MLR  N
Sbjct: 243 VVRLEKAPAQASSPANSALLKPVSELELSVRSANCLQNANIKYIYELVSKTEGEMLRTKN 302

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNL 321
           FGRKSL EIK +L  MGL LGM +
Sbjct: 303 FGRKSLNEIKEILSNMGLGLGMKV 326


>gi|161523455|ref|YP_001578467.1| DNA-directed RNA polymerase subunit alpha [Burkholderia multivorans
           ATCC 17616]
 gi|189351772|ref|YP_001947400.1| DNA-directed RNA polymerase subunit alpha [Burkholderia multivorans
           ATCC 17616]
 gi|221201591|ref|ZP_03574629.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           multivorans CGD2M]
 gi|221207334|ref|ZP_03580344.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           multivorans CGD2]
 gi|221213472|ref|ZP_03586447.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           multivorans CGD1]
 gi|238687015|sp|A9ADL9|RPOA_BURM1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|160340884|gb|ABX13970.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           multivorans ATCC 17616]
 gi|189335794|dbj|BAG44864.1| DNA-directed RNA polymerase subunit alpha [Burkholderia multivorans
           ATCC 17616]
 gi|221166924|gb|EED99395.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           multivorans CGD1]
 gi|221172922|gb|EEE05359.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           multivorans CGD2]
 gi|221178407|gb|EEE10816.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           multivorans CGD2M]
          Length = 325

 Score =  292 bits (747), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 157/326 (48%), Positives = 212/326 (65%), Gaps = 8/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG   EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVESLG---ENHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVVTAGDI+  +D EV+
Sbjct: 62  VHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVTAGDIELAHDCEVI 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NPDHVI +L     + +++ V KG GYVP    R   D    IG I +DA +SP+++VSY
Sbjct: 122 NPDHVIAHLSKGGKLDVQIKVEKGRGYVPGNVRRYGEDTAKIIGRIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T G IT E+++  ++RIL DQL +F   E    E   + 
Sbjct: 182 AVESARVEQRTDLDKLVMNIETTGVITPEEAIRQSARILVDQLSVFAALE--GTETAAEA 239

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 240 PSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 299

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +++
Sbjct: 300 IKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|218779736|ref|YP_002431054.1| DNA-directed RNA polymerase subunit alpha [Desulfatibacillum
           alkenivorans AK-01]
 gi|218761120|gb|ACL03586.1| DNA-directed RNA polymerase, alpha subunit [Desulfatibacillum
           alkenivorans AK-01]
          Length = 343

 Score =  292 bits (747), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 155/335 (46%), Positives = 226/335 (67%), Gaps = 8/335 (2%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++  NW+ELIKP  ++     +        I EPL RGF  TLGNALRR+++SSL GAAI
Sbjct: 6   LMYMNWRELIKPQRVQV----ESSPTHGKFITEPLERGFGLTLGNALRRIILSSLHGAAI 61

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
            +V+ D V+HE S+I GV ED++++ILN+K + L M+      + + K+GPGVVTAGD+ 
Sbjct: 62  VSVKFDNVMHEFSAIPGVLEDVSELILNLKEVRLTMTETGPCPLNLEKQGPGVVTAGDLI 121

Query: 121 TVN-DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
           + N  ++VLNPD  I  +  D+V RME+    G GY  A+ ++ E+DP+G I ID+++SP
Sbjct: 122 SPNGKVQVLNPDLYIATISDDSVFRMEMQCQVGKGYAMAEANKNEDDPVGTIPIDSVFSP 181

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--EP 237
           I++V+Y V +AR GQ  DYDKL++ + TDGS+T ED+VA A++IL++Q+ +FINF+    
Sbjct: 182 IRRVNYVVGNARVGQRTDYDKLTLEVWTDGSLTPEDAVAYAAKILKEQISIFINFDEEME 241

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            ++  E     +  FN  L + V+ELELSVRS NCL+  +I  + +L+++TE++ML+  N
Sbjct: 242 PEQEVEAEETDAPEFNENLYRSVDELELSVRSANCLKNASIHKIFELVRKTESEMLKTKN 301

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDW-PPESIEE 331
           FGRKSL EIK VL  MGL  GM L  + PPE  +E
Sbjct: 302 FGRKSLNEIKEVLSEMGLSFGMKLEGFQPPEESDE 336


>gi|119478107|ref|ZP_01618186.1| DNA-directed RNA polymerase alpha subunit [marine gamma
           proteobacterium HTCC2143]
 gi|119448813|gb|EAW30056.1| DNA-directed RNA polymerase alpha subunit [marine gamma
           proteobacterium HTCC2143]
          Length = 334

 Score =  292 bits (747), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 151/332 (45%), Positives = 221/332 (66%), Gaps = 9/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    E + P  I+   + +    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQSAVNEFLTPRVID---VDEVSSTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V IDGVLHE S+I+GV ED+ +I+LN+KG+++ M G     +T+ K G G VTAGDIQ 
Sbjct: 58  EVAIDGVLHEYSAIEGVQEDVIEILLNLKGVSILMHGKDEAVLTLSKSGAGPVTAGDIQV 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +DIE+ NPDH+I  L+    + M LT+ +G GYVPA   +++++    IG + +DA +S
Sbjct: 118 DHDIEISNPDHLIATLNEAGSLNMTLTIGRGRGYVPADARQSDDEETRSIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +V+Y VESAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++ E  K
Sbjct: 178 PVHRVAYVVESARVEQRTDLDKLVLDLETNGTIDPEEAIRRAATILQQQLSVFVDLESEK 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +        +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N 
Sbjct: 238 EAEP---EEEEDEVDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           G+KSL EIK VL + GL LG+ L +WPP S++
Sbjct: 295 GKKSLTEIKDVLASRGLSLGLRLDNWPPASLK 326


>gi|74316448|ref|YP_314188.1| DNA-directed RNA polymerase subunit alpha [Thiobacillus
           denitrificans ATCC 25259]
 gi|90110875|sp|Q3SLM4|RPOA_THIDA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|74055943|gb|AAZ96383.1| DNA-directed RNA polymerase, alpha subunit [Thiobacillus
           denitrificans ATCC 25259]
          Length = 326

 Score =  292 bits (747), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 154/329 (46%), Positives = 215/329 (65%), Gaps = 8/329 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           ++  E +KP  +E   + +       +I EP  RG+ HTLGNALRR+L+SS+ G A T V
Sbjct: 2   QSATEFLKPRIVE---VDRASPLHAKVIMEPFERGYGHTLGNALRRILLSSMVGYAPTEV 58

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
            I GV+HE S+I+GV ED+ DI+LN+KGI  KM G +   + + K G GVVTAGDI+  +
Sbjct: 59  AISGVVHEYSTIEGVQEDVVDILLNLKGIAFKMHGKAEAILKVSKSGEGVVTAGDIEVGH 118

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIK 181
           DIEVLNPDHVI +L     + ME+ +  G GY PA   +   E   +G I +DA +SP++
Sbjct: 119 DIEVLNPDHVIAHLTKGGKLDMEIKIEAGRGYQPATARKVSEETRAVGSILVDASFSPVR 178

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +V+Y VESAR  Q  D D+L + I+T+G +  E++V  A+RIL  QL +F + E    E 
Sbjct: 179 RVAYAVESARVEQRTDLDRLVIDIETNGVVEPEEAVRTAARILVSQLSVFADLEGTPAES 238

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +   + +S   +P LL+ V++LEL+VRS NCL+ ENI ++GDLIQR+E ++LR  N GRK
Sbjct: 239 E---SPRSPQVDPLLLRPVDDLELTVRSANCLKAENIYFIGDLIQRSETELLRTPNLGRK 295

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           SL EIK VL + GL LGM L +WPP  +E
Sbjct: 296 SLNEIKDVLASKGLSLGMKLENWPPAGLE 324


>gi|156932260|ref|YP_001436176.1| DNA-directed RNA polymerase subunit alpha [Cronobacter sakazakii
           ATCC BAA-894]
 gi|260599615|ref|YP_003212186.1| DNA-directed RNA polymerase subunit alpha [Cronobacter turicensis
           z3032]
 gi|171769808|sp|A7MPF8|RPOA_ENTS8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|156530514|gb|ABU75340.1| hypothetical protein ESA_00031 [Cronobacter sakazakii ATCC BAA-894]
 gi|260218792|emb|CBA34140.1| DNA-directed RNA polymerase subunit alpha [Cronobacter turicensis
           z3032]
          Length = 329

 Score =  292 bits (747), Expect = 6e-77,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 222/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVVLTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|317485796|ref|ZP_07944660.1| DNA-directed RNA polymerase [Bilophila wadsworthia 3_1_6]
 gi|316922902|gb|EFV44124.1| DNA-directed RNA polymerase [Bilophila wadsworthia 3_1_6]
          Length = 347

 Score =  292 bits (747), Expect = 6e-77,   Method: Compositional matrix adjust.
 Identities = 160/340 (47%), Positives = 220/340 (64%), Gaps = 19/340 (5%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTL---MIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +NW +L++P  I    +   + N T+      EPL RG+  T+GNALRRVL+SSL+GAA 
Sbjct: 13  RNWAKLVRPEQI----VCDSDPNDTMYGKFTYEPLERGYGVTIGNALRRVLLSSLQGAAF 68

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGD 118
            AV+I GV HE ++I GV ED+TD+ILNIK + L M+ D   H  +++ K+GP  VTA D
Sbjct: 69  VAVKISGVQHEFTTIPGVLEDITDVILNIKQVRLGMTTDEPQHLTLSVSKKGP--VTAAD 126

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           I T  ++EVLNP+  I  L  D  + ME  V  G GYVPA  H    D IGLI +DA +S
Sbjct: 127 IMTNANVEVLNPELHIATLTEDMELSMEFEVRMGKGYVPADMHEGLPDTIGLIKLDASFS 186

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P++KV+YTVE AR GQ+ +YDKL + + TDGS+  ED++A +++I++DQ+ +FI+F+E  
Sbjct: 187 PVRKVAYTVEQARVGQMTNYDKLILEVWTDGSVLPEDAIAYSAKIIKDQISVFISFDERI 246

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                     S   N  L K ++ELELSVR+TNCLR  NI  +G+L+QR EA+ML+  NF
Sbjct: 247 SGESGGEGGGSADINDNLFKGIDELELSVRATNCLRSANIATVGELVQRPEAEMLKTKNF 306

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           G+KSL EIK VL +MGL  GM         I+   KKY++
Sbjct: 307 GKKSLDEIKAVLESMGLDFGM--------KIDNFEKKYQE 338


>gi|261346910|ref|ZP_05974554.1| DNA-directed RNA polymerase, alpha subunit [Providencia rustigianii
           DSM 4541]
 gi|282564976|gb|EFB70511.1| DNA-directed RNA polymerase, alpha subunit [Providencia rustigianii
           DSM 4541]
          Length = 329

 Score =  292 bits (747), Expect = 6e-77,   Method: Compositional matrix adjust.
 Identities = 154/333 (46%), Positives = 222/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVQGKDEVILTLNKSGIGPVTAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A V M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASVNMRIKVQRGRGYVPASARVHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|238754197|ref|ZP_04615555.1| DNA-directed RNA polymerase subunit alpha [Yersinia ruckeri ATCC
           29473]
 gi|238758785|ref|ZP_04619959.1| DNA-directed RNA polymerase subunit alpha [Yersinia aldovae ATCC
           35236]
 gi|238783188|ref|ZP_04627214.1| DNA-directed RNA polymerase subunit alpha [Yersinia bercovieri ATCC
           43970]
 gi|238792960|ref|ZP_04636590.1| DNA-directed RNA polymerase subunit alpha [Yersinia intermedia ATCC
           29909]
 gi|238703082|gb|EEP95625.1| DNA-directed RNA polymerase subunit alpha [Yersinia aldovae ATCC
           35236]
 gi|238707693|gb|EEQ00053.1| DNA-directed RNA polymerase subunit alpha [Yersinia ruckeri ATCC
           29473]
 gi|238715984|gb|EEQ07970.1| DNA-directed RNA polymerase subunit alpha [Yersinia bercovieri ATCC
           43970]
 gi|238727814|gb|EEQ19338.1| DNA-directed RNA polymerase subunit alpha [Yersinia intermedia ATCC
           29909]
          Length = 329

 Score =  291 bits (746), Expect = 7e-77,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 222/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|123444073|ref|YP_001008043.1| DNA-directed RNA polymerase subunit alpha [Yersinia enterocolitica
           subsp. enterocolitica 8081]
 gi|238752666|ref|ZP_04614137.1| DNA-directed RNA polymerase subunit alpha [Yersinia rohdei ATCC
           43380]
 gi|238788887|ref|ZP_04632677.1| DNA-directed RNA polymerase subunit alpha [Yersinia frederiksenii
           ATCC 33641]
 gi|332163236|ref|YP_004299813.1| DNA-directed RNA polymerase subunit alpha [Yersinia enterocolitica
           subsp. palearctica 105.5R(r)]
 gi|158512898|sp|A1JS01|RPOA_YERE8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|122091034|emb|CAL13917.1| DNA-directed RNA polymerase alpha chain [Yersinia enterocolitica
           subsp. enterocolitica 8081]
 gi|238709093|gb|EEQ01340.1| DNA-directed RNA polymerase subunit alpha [Yersinia rohdei ATCC
           43380]
 gi|238722914|gb|EEQ14564.1| DNA-directed RNA polymerase subunit alpha [Yersinia frederiksenii
           ATCC 33641]
 gi|318607720|emb|CBY29218.1| DNA-directed RNA polymerase alpha subunit [Yersinia enterocolitica
           subsp. palearctica Y11]
 gi|325667466|gb|ADZ44110.1| DNA-directed RNA polymerase subunit alpha [Yersinia enterocolitica
           subsp. palearctica 105.5R(r)]
 gi|330861829|emb|CBX72000.1| DNA-directed RNA polymerase subunit alpha [Yersinia enterocolitica
           W22703]
          Length = 330

 Score =  291 bits (746), Expect = 7e-77,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 222/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|22127885|ref|NP_671308.1| DNA-directed RNA polymerase subunit alpha [Yersinia pestis KIM 10]
 gi|45440092|ref|NP_991631.1| DNA-directed RNA polymerase subunit alpha [Yersinia pestis biovar
           Microtus str. 91001]
 gi|51597963|ref|YP_072154.1| DNA-directed RNA polymerase subunit alpha [Yersinia
           pseudotuberculosis IP 32953]
 gi|108809230|ref|YP_653146.1| DNA-directed RNA polymerase subunit alpha [Yersinia pestis Antiqua]
 gi|108813995|ref|YP_649762.1| DNA-directed RNA polymerase subunit alpha [Yersinia pestis
           Nepal516]
 gi|145597475|ref|YP_001161550.1| DNA-directed RNA polymerase subunit alpha [Yersinia pestis
           Pestoides F]
 gi|150260718|ref|ZP_01917446.1| DNA-directed RNA polymerase alpha chain [Yersinia pestis CA88-4125]
 gi|153948087|ref|YP_001402838.1| DNA-directed RNA polymerase subunit alpha [Yersinia
           pseudotuberculosis IP 31758]
 gi|162420536|ref|YP_001605197.1| DNA-directed RNA polymerase subunit alpha [Yersinia pestis Angola]
 gi|165927880|ref|ZP_02223712.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Orientalis str. F1991016]
 gi|165936419|ref|ZP_02224987.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Orientalis str. IP275]
 gi|166010435|ref|ZP_02231333.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Antiqua str. E1979001]
 gi|166213170|ref|ZP_02239205.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Antiqua str. B42003004]
 gi|167398622|ref|ZP_02304146.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Antiqua str. UG05-0454]
 gi|167419336|ref|ZP_02311089.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Orientalis str. MG05-1020]
 gi|167425603|ref|ZP_02317356.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Mediaevalis str. K1973002]
 gi|170022569|ref|YP_001719074.1| DNA-directed RNA polymerase subunit alpha [Yersinia
           pseudotuberculosis YPIII]
 gi|186897159|ref|YP_001874271.1| DNA-directed RNA polymerase subunit alpha [Yersinia
           pseudotuberculosis PB1/+]
 gi|218927440|ref|YP_002345315.1| DNA-directed RNA polymerase subunit alpha [Yersinia pestis CO92]
 gi|229836284|ref|ZP_04456451.1| RNA polymerase, alpha subunit [Yersinia pestis Pestoides A]
 gi|229840092|ref|ZP_04460251.1| RNA polymerase, alpha subunit [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229842174|ref|ZP_04462329.1| RNA polymerase, alpha subunit [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229904526|ref|ZP_04519637.1| RNA polymerase, alpha subunit [Yersinia pestis Nepal516]
 gi|270488256|ref|ZP_06205330.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis KIM
           D27]
 gi|294502309|ref|YP_003566371.1| DNA-directed RNA polymerase alpha subunit [Yersinia pestis Z176003]
 gi|311277750|ref|YP_003939981.1| DNA-directed RNA polymerase, alpha subunit [Enterobacter cloacae
           SCF1]
 gi|20139507|sp|Q8ZJ87|RPOA_YERPE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61215876|sp|Q664U6|RPOA_YERPS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366751|sp|Q1C2X1|RPOA_YERPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366752|sp|Q1CCW8|RPOA_YERPN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158514063|sp|A4TH15|RPOA_YERPP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|171769159|sp|A7FNL0|RPOA_YERP3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|21961021|gb|AAM87559.1|AE014003_17 RNA polymerase, alpha subunit [Yersinia pestis KIM 10]
 gi|45434947|gb|AAS60508.1| DNA-directed RNA polymerase alpha chain [Yersinia pestis biovar
           Microtus str. 91001]
 gi|51591245|emb|CAH22911.1| DNA-directed RNA polymerase alpha chain [Yersinia
           pseudotuberculosis IP 32953]
 gi|108777643|gb|ABG20162.1| DNA-directed RNA polymerase alpha chain [Yersinia pestis Nepal516]
 gi|108781143|gb|ABG15201.1| DNA-directed RNA polymerase alpha chain [Yersinia pestis Antiqua]
 gi|115346051|emb|CAL18917.1| DNA-directed RNA polymerase alpha chain [Yersinia pestis CO92]
 gi|145209171|gb|ABP38578.1| DNA-directed RNA polymerase alpha chain [Yersinia pestis Pestoides
           F]
 gi|149290126|gb|EDM40203.1| DNA-directed RNA polymerase alpha chain [Yersinia pestis CA88-4125]
 gi|152959582|gb|ABS47043.1| DNA-directed RNA polymerase, alpha subunit [Yersinia
           pseudotuberculosis IP 31758]
 gi|162353351|gb|ABX87299.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis Angola]
 gi|165915535|gb|EDR34144.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Orientalis str. IP275]
 gi|165920156|gb|EDR37457.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Orientalis str. F1991016]
 gi|165990525|gb|EDR42826.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Antiqua str. E1979001]
 gi|166205468|gb|EDR49948.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Antiqua str. B42003004]
 gi|166963330|gb|EDR59351.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Orientalis str. MG05-1020]
 gi|167051126|gb|EDR62534.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Antiqua str. UG05-0454]
 gi|167055293|gb|EDR65087.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Mediaevalis str. K1973002]
 gi|169749103|gb|ACA66621.1| DNA-directed RNA polymerase, alpha subunit [Yersinia
           pseudotuberculosis YPIII]
 gi|186700185|gb|ACC90814.1| DNA-directed RNA polymerase, alpha subunit [Yersinia
           pseudotuberculosis PB1/+]
 gi|229678644|gb|EEO74749.1| RNA polymerase, alpha subunit [Yersinia pestis Nepal516]
 gi|229690484|gb|EEO82538.1| RNA polymerase, alpha subunit [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229696458|gb|EEO86505.1| RNA polymerase, alpha subunit [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229706352|gb|EEO92359.1| RNA polymerase, alpha subunit [Yersinia pestis Pestoides A]
 gi|262360389|gb|ACY57110.1| DNA-directed RNA polymerase alpha subunit [Yersinia pestis D106004]
 gi|262364339|gb|ACY60896.1| DNA-directed RNA polymerase alpha subunit [Yersinia pestis D182038]
 gi|270336760|gb|EFA47537.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis KIM
           D27]
 gi|294352768|gb|ADE63109.1| DNA-directed RNA polymerase alpha subunit [Yersinia pestis Z176003]
 gi|308746945|gb|ADO46697.1| DNA-directed RNA polymerase, alpha subunit [Enterobacter cloacae
           SCF1]
 gi|320013367|gb|ADV96938.1| RNA polymerase, alpha subunit [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 329

 Score =  291 bits (746), Expect = 7e-77,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 222/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASINMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|304399265|ref|ZP_07381131.1| DNA-directed RNA polymerase, alpha subunit [Pantoea sp. aB]
 gi|308188331|ref|YP_003932462.1| DNA-directed RNA polymerase alpha chain [Pantoea vagans C9-1]
 gi|304353191|gb|EFM17572.1| DNA-directed RNA polymerase, alpha subunit [Pantoea sp. aB]
 gi|308058841|gb|ADO11013.1| DNA-directed RNA polymerase alpha chain [Pantoea vagans C9-1]
          Length = 329

 Score =  291 bits (746), Expect = 8e-77,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 221/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENAAISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|238797219|ref|ZP_04640720.1| DNA-directed RNA polymerase subunit alpha [Yersinia mollaretii ATCC
           43969]
 gi|238718856|gb|EEQ10671.1| DNA-directed RNA polymerase subunit alpha [Yersinia mollaretii ATCC
           43969]
          Length = 329

 Score =  291 bits (746), Expect = 8e-77,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 222/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRVKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|53720795|ref|YP_109781.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei K96243]
 gi|53723828|ref|YP_104140.1| DNA-directed RNA polymerase subunit alpha [Burkholderia mallei ATCC
           23344]
 gi|76808919|ref|YP_335114.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei 1710b]
 gi|121599305|ref|YP_994430.1| DNA-directed RNA polymerase subunit alpha [Burkholderia mallei
           SAVP1]
 gi|124385479|ref|YP_001027921.1| DNA-directed RNA polymerase subunit alpha [Burkholderia mallei NCTC
           10229]
 gi|126440174|ref|YP_001060724.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei 668]
 gi|126450024|ref|YP_001083016.1| DNA-directed RNA polymerase subunit alpha [Burkholderia mallei NCTC
           10247]
 gi|126453965|ref|YP_001068008.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei 1106a]
 gi|134283239|ref|ZP_01769940.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 305]
 gi|167001673|ref|ZP_02267465.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           PRL-20]
 gi|167721551|ref|ZP_02404787.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei DM98]
 gi|167740525|ref|ZP_02413299.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei 14]
 gi|167817730|ref|ZP_02449410.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei 91]
 gi|167826127|ref|ZP_02457598.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei 9]
 gi|167847639|ref|ZP_02473147.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei B7210]
 gi|167896211|ref|ZP_02483613.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei 7894]
 gi|167904593|ref|ZP_02491798.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei NCTC 13177]
 gi|167912858|ref|ZP_02499949.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei 112]
 gi|167920817|ref|ZP_02507908.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei BCC215]
 gi|217424731|ref|ZP_03456228.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 576]
 gi|226198177|ref|ZP_03793748.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei Pakistan 9]
 gi|237814119|ref|YP_002898570.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei MSHR346]
 gi|238562959|ref|ZP_00439640.2| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei GB8
           horse 4]
 gi|242316674|ref|ZP_04815690.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 1106b]
 gi|254174996|ref|ZP_04881657.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           ATCC 10399]
 gi|254180365|ref|ZP_04886963.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 1655]
 gi|254190328|ref|ZP_04896836.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei Pasteur 52237]
 gi|254198455|ref|ZP_04904876.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei S13]
 gi|254201213|ref|ZP_04907577.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           FMH]
 gi|254206554|ref|ZP_04912905.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           JHU]
 gi|254260470|ref|ZP_04951524.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 1710a]
 gi|254300602|ref|ZP_04968047.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 406e]
 gi|254357093|ref|ZP_04973367.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           2002721280]
 gi|61215842|sp|Q62GN1|RPOA_BURMA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61215856|sp|Q63Q37|RPOA_BURPS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|90101574|sp|Q3JMT9|RPOA_BURP1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158513536|sp|A3P087|RPOA_BURP0 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|166229261|sp|A3MRY0|RPOA_BURM7 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|166229262|sp|A2S7K2|RPOA_BURM9 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|166229263|sp|A1V877|RPOA_BURMS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|166229264|sp|A3NEF3|RPOA_BURP6 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|52211209|emb|CAH37198.1| DNA-directed RNA polymerase alpha chain [Burkholderia pseudomallei
           K96243]
 gi|52427251|gb|AAU47844.1| dna-directed rna polymerase alpha chain [Burkholderia mallei ATCC
           23344]
 gi|76578372|gb|ABA47847.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 1710b]
 gi|121228115|gb|ABM50633.1| DNA-directed rna polymerase, alpha subunit [Burkholderia mallei
           SAVP1]
 gi|124293499|gb|ABN02768.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           NCTC 10229]
 gi|126219667|gb|ABN83173.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 668]
 gi|126227607|gb|ABN91147.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 1106a]
 gi|126242894|gb|ABO05987.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           NCTC 10247]
 gi|134245434|gb|EBA45527.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 305]
 gi|147747107|gb|EDK54183.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           FMH]
 gi|147752096|gb|EDK59162.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           JHU]
 gi|148026157|gb|EDK84242.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           2002721280]
 gi|157810631|gb|EDO87801.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 406e]
 gi|157938004|gb|EDO93674.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei Pasteur 52237]
 gi|160696041|gb|EDP86011.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           ATCC 10399]
 gi|169655195|gb|EDS87888.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei S13]
 gi|184210904|gb|EDU07947.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 1655]
 gi|217392187|gb|EEC32212.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 576]
 gi|225929697|gb|EEH25713.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei Pakistan 9]
 gi|237503877|gb|ACQ96195.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei MSHR346]
 gi|238521642|gb|EEP85092.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei GB8
           horse 4]
 gi|242139913|gb|EES26315.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 1106b]
 gi|243062570|gb|EES44756.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           PRL-20]
 gi|254219159|gb|EET08543.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 1710a]
          Length = 325

 Score =  291 bits (746), Expect = 8e-77,   Method: Compositional matrix adjust.
 Identities = 156/326 (47%), Positives = 214/326 (65%), Gaps = 8/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG   EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVESLG---ENHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVVTAGDI+  +D EV+
Sbjct: 62  VHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVTAGDIELAHDCEVI 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NP+HVI +L     + +++ V KG GYVP    R  ++    IG I +DA +SP+++VSY
Sbjct: 122 NPNHVIAHLSKGGKLDVQIKVEKGRGYVPGNVRRYGDETAKIIGRIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVESAR  Q  D DKL M I+T G IT E+++  ++RIL DQL +F   E    E   + 
Sbjct: 182 TVESARVEQRTDLDKLVMNIETSGVITPEEAIRQSARILVDQLSVFAALE--GTETAAEA 239

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 240 PSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 299

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +++
Sbjct: 300 IKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|303328068|ref|ZP_07358507.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio sp.
           3_1_syn3]
 gi|302861894|gb|EFL84829.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio sp.
           3_1_syn3]
          Length = 347

 Score =  291 bits (746), Expect = 8e-77,   Method: Compositional matrix adjust.
 Identities = 157/344 (45%), Positives = 227/344 (65%), Gaps = 16/344 (4%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRT----LMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           +NW EL+KP+ I      +EEE  +      I EPL RG+  T+GNA+RRVL++SL+GAA
Sbjct: 13  RNWSELVKPDQIL-----REEETASGTHGKFICEPLERGYGTTIGNAMRRVLLASLQGAA 67

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
             +V+I GV HE ++I GV ED+TD+ILN+K + L++  D  +R+ +     G VTA  I
Sbjct: 68  FVSVKITGVQHEFTTIHGVLEDVTDVILNLKQVRLRLDTDEPQRLILRVDRKGPVTAAQI 127

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
           QT   +EVLNP+  I  L  D V+ MEL    G GYVPA  H   ++ IGLI +D+ +SP
Sbjct: 128 QTNQHVEVLNPELHIATLTEDVVLEMELEARMGKGYVPADMHEGLSEEIGLIKLDSSFSP 187

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           ++KV+YTVE AR GQ+ +YD+L + + TDGS+T ED++A +++I++DQ+ +FINF+E   
Sbjct: 188 VRKVAYTVEQARVGQMTNYDRLLLEVWTDGSLTPEDAIAYSAKIIKDQISVFINFDE--- 244

Query: 240 EVKEDINVKSL---PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            V  D+ + S      N  L K +++LELSVR+TNCLR  NI  +G+L+QR+E +ML+  
Sbjct: 245 RVSGDMRLGSSDGGEVNEHLFKSIDDLELSVRATNCLRSANIALVGELVQRSEGEMLKTK 304

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
           NFGRKSL EIK VL  MGL  GM + D   +  +E  +K +++ 
Sbjct: 305 NFGRKSLDEIKSVLLDMGLDFGMKV-DGFDKKYQEWKRKQQNEA 347


>gi|170769532|ref|ZP_02903985.1| DNA-directed RNA polymerase, alpha subunit [Escherichia albertii
           TW07627]
 gi|170121589|gb|EDS90520.1| DNA-directed RNA polymerase, alpha subunit [Escherichia albertii
           TW07627]
          Length = 329

 Score =  291 bits (746), Expect = 8e-77,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 222/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASSRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|15803822|ref|NP_289856.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O157:H7
           EDL933]
 gi|15833414|ref|NP_312187.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O157:H7
           str. Sakai]
 gi|16131174|ref|NP_417754.1| RNA polymerase, alpha subunit [Escherichia coli str. K-12 substr.
           MG1655]
 gi|16762868|ref|NP_458485.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. CT18]
 gi|16766704|ref|NP_462319.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhimurium str. LT2]
 gi|24114573|ref|NP_709083.1| DNA-directed RNA polymerase subunit alpha [Shigella flexneri 2a
           str. 301]
 gi|26249880|ref|NP_755920.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli CFT073]
 gi|29144355|ref|NP_807697.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. Ty2]
 gi|30065404|ref|NP_839575.1| DNA-directed RNA polymerase subunit alpha [Shigella flexneri 2a
           str. 2457T]
 gi|56415334|ref|YP_152409.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Paratyphi A str. ATCC 9150]
 gi|74313814|ref|YP_312233.1| DNA-directed RNA polymerase subunit alpha [Shigella sonnei Ss046]
 gi|82545658|ref|YP_409605.1| DNA-directed RNA polymerase subunit alpha [Shigella boydii Sb227]
 gi|89110715|ref|AP_004495.1| RNA polymerase, alpha subunit [Escherichia coli str. K-12 substr.
           W3110]
 gi|91212722|ref|YP_542708.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli UTI89]
 gi|110643534|ref|YP_671264.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli 536]
 gi|110807143|ref|YP_690663.1| DNA-directed RNA polymerase subunit alpha [Shigella flexneri 5 str.
           8401]
 gi|117625577|ref|YP_858900.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli APEC
           O1]
 gi|157148870|ref|YP_001456189.1| DNA-directed RNA polymerase subunit alpha [Citrobacter koseri ATCC
           BAA-895]
 gi|157157450|ref|YP_001464763.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli
           E24377A]
 gi|157162769|ref|YP_001460087.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli HS]
 gi|161506032|ref|YP_001573144.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|161616440|ref|YP_001590405.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Paratyphi B str. SPB7]
 gi|168264704|ref|ZP_02686677.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Hadar str. RI_05P066]
 gi|168468028|ref|ZP_02701865.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Newport str. SL317]
 gi|168752256|ref|ZP_02777278.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4113]
 gi|168758523|ref|ZP_02783530.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4401]
 gi|168764978|ref|ZP_02789985.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4501]
 gi|168769157|ref|ZP_02794164.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4486]
 gi|168777847|ref|ZP_02802854.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4196]
 gi|168786185|ref|ZP_02811192.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC869]
 gi|168802724|ref|ZP_02827731.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC508]
 gi|170018469|ref|YP_001723423.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli ATCC
           8739]
 gi|170082815|ref|YP_001732135.1| RNA polymerase, alpha subunit [Escherichia coli str. K-12 substr.
           DH10B]
 gi|170683426|ref|YP_001745557.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli
           SMS-3-5]
 gi|187731728|ref|YP_001881980.1| DNA-directed RNA polymerase subunit alpha [Shigella boydii CDC
           3083-94]
 gi|188495000|ref|ZP_03002270.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli 53638]
 gi|191169307|ref|ZP_03031056.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli B7A]
 gi|193066493|ref|ZP_03047537.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli E22]
 gi|193071560|ref|ZP_03052469.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           E110019]
 gi|194430287|ref|ZP_03062782.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli B171]
 gi|194440020|ref|ZP_03072078.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli 101-1]
 gi|194442652|ref|YP_002042666.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Newport str. SL254]
 gi|194447380|ref|YP_002047439.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Heidelberg str. SL476]
 gi|194469288|ref|ZP_03075272.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Kentucky str. CVM29188]
 gi|194735121|ref|YP_002116358.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Schwarzengrund str. CVM19633]
 gi|195939843|ref|ZP_03085225.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O157:H7
           str. EC4024]
 gi|197248562|ref|YP_002148335.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Agona str. SL483]
 gi|197262940|ref|ZP_03163014.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Saintpaul str. SARA23]
 gi|197364264|ref|YP_002143901.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Paratyphi A str. AKU_12601]
 gi|198244932|ref|YP_002217378.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Dublin str. CT_02021853]
 gi|200387689|ref|ZP_03214301.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Virchow str. SL491]
 gi|204931405|ref|ZP_03222074.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Javiana str. GA_MM04042433]
 gi|205354957|ref|YP_002228758.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Gallinarum str. 287/91]
 gi|207858657|ref|YP_002245308.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Enteritidis str. P125109]
 gi|208806531|ref|ZP_03248868.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4206]
 gi|208813497|ref|ZP_03254826.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4045]
 gi|208818909|ref|ZP_03259229.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4042]
 gi|209396788|ref|YP_002272751.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4115]
 gi|209920761|ref|YP_002294845.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli SE11]
 gi|213027592|ref|ZP_03342039.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. 404ty]
 gi|213052883|ref|ZP_03345761.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E00-7866]
 gi|213425776|ref|ZP_03358526.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E02-1180]
 gi|213647329|ref|ZP_03377382.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. J185]
 gi|213859911|ref|ZP_03385615.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. M223]
 gi|215488595|ref|YP_002331026.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O127:H6
           str. E2348/69]
 gi|217324841|ref|ZP_03440925.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. TW14588]
 gi|218550571|ref|YP_002384362.1| DNA-directed RNA polymerase subunit alpha [Escherichia fergusonii
           ATCC 35469]
 gi|218555853|ref|YP_002388766.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli IAI1]
 gi|218560357|ref|YP_002393270.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli S88]
 gi|218691582|ref|YP_002399794.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli ED1a]
 gi|218696988|ref|YP_002404655.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli 55989]
 gi|218702058|ref|YP_002409687.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli IAI39]
 gi|218706903|ref|YP_002414422.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli UMN026]
 gi|237703025|ref|ZP_04533506.1| RNA polymerase [Escherichia sp. 3_2_53FAA]
 gi|238902386|ref|YP_002928182.1| RNA polymerase, alpha subunit [Escherichia coli BW2952]
 gi|238913870|ref|ZP_04657707.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Tennessee str. CDC07-0191]
 gi|253771881|ref|YP_003034712.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254038456|ref|ZP_04872512.1| DNA-directed RNA polymerase [Escherichia sp. 1_1_43]
 gi|254163223|ref|YP_003046331.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli B str.
           REL606]
 gi|254795232|ref|YP_003080069.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O157:H7
           str. TW14359]
 gi|256020654|ref|ZP_05434519.1| DNA-directed RNA polymerase subunit alpha [Shigella sp. D9]
 gi|256025977|ref|ZP_05439842.1| DNA-directed RNA polymerase subunit alpha [Escherichia sp. 4_1_40B]
 gi|260846093|ref|YP_003223871.1| RNA polymerase, alpha subunit [Escherichia coli O103:H2 str. 12009]
 gi|260857416|ref|YP_003231307.1| RNA polymerase, alpha subunit [Escherichia coli O26:H11 str. 11368]
 gi|260870038|ref|YP_003236440.1| RNA polymerase, alpha subunit [Escherichia coli O111:H- str. 11128]
 gi|261224600|ref|ZP_05938881.1| RNA polymerase, alpha subunit [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261254506|ref|ZP_05947039.1| RNA polymerase, alpha subunit [Escherichia coli O157:H7 str.
           FRIK966]
 gi|283788069|ref|YP_003367934.1| DNA-directed RNA polymerase alpha chain [Citrobacter rodentium
           ICC168]
 gi|289824200|ref|ZP_06543795.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E98-3139]
 gi|291284653|ref|YP_003501471.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O55:H7
           str. CB9615]
 gi|293406892|ref|ZP_06650816.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli
           FVEC1412]
 gi|293412714|ref|ZP_06655382.1| DNA-directed RNA polymerase [Escherichia coli B354]
 gi|293416714|ref|ZP_06659351.1| DNA-directed RNA polymerase [Escherichia coli B185]
 gi|293453614|ref|ZP_06664033.1| DNA-directed RNA polymerase [Escherichia coli B088]
 gi|297517819|ref|ZP_06936205.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli OP50]
 gi|298382633|ref|ZP_06992228.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli
           FVEC1302]
 gi|300815494|ref|ZP_07095719.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           107-1]
 gi|300822901|ref|ZP_07103037.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           119-7]
 gi|300896644|ref|ZP_07115160.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           198-1]
 gi|300903544|ref|ZP_07121466.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           84-1]
 gi|300918270|ref|ZP_07134874.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           115-1]
 gi|300921895|ref|ZP_07138051.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           182-1]
 gi|300932189|ref|ZP_07147468.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           187-1]
 gi|300935294|ref|ZP_07150304.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           21-1]
 gi|300946518|ref|ZP_07160783.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           116-1]
 gi|300954830|ref|ZP_07167256.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           175-1]
 gi|300973975|ref|ZP_07172382.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           200-1]
 gi|300979868|ref|ZP_07174744.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           45-1]
 gi|301018839|ref|ZP_07183083.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           69-1]
 gi|301021165|ref|ZP_07185203.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           196-1]
 gi|301046067|ref|ZP_07193245.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           185-1]
 gi|301305505|ref|ZP_07211597.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           124-1]
 gi|301325137|ref|ZP_07218671.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           78-1]
 gi|301643884|ref|ZP_07243915.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           146-1]
 gi|306816362|ref|ZP_07450500.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli NC101]
 gi|307139978|ref|ZP_07499334.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli H736]
 gi|307315126|ref|ZP_07594709.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli W]
 gi|309794571|ref|ZP_07688993.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           145-7]
 gi|312972444|ref|ZP_07786618.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           1827-70]
 gi|331643991|ref|ZP_08345120.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli H736]
 gi|331649092|ref|ZP_08350178.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli M605]
 gi|331659585|ref|ZP_08360523.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli TA206]
 gi|331664908|ref|ZP_08365809.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli TA143]
 gi|331670124|ref|ZP_08370963.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli TA271]
 gi|331674801|ref|ZP_08375558.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli TA280]
 gi|331679364|ref|ZP_08380034.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli H591]
 gi|331684937|ref|ZP_08385523.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli H299]
 gi|62287386|sp|Q5PK10|RPOA_SALPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|62288914|sp|P0A7Z4|RPOA_ECOLI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|62288915|sp|P0A7Z5|RPOA_ECOL6 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|62288916|sp|P0A7Z6|RPOA_ECO57 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|62288917|sp|P0A7Z7|RPOA_SALTY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|62288918|sp|P0A7Z8|RPOA_SALTI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|62288919|sp|P0A7Z9|RPOA_SHIFL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|90110865|sp|Q31VY1|RPOA_SHIBS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|90110867|sp|Q3YWW4|RPOA_SHISS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366680|sp|Q0TCG6|RPOA_ECOL5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366681|sp|Q1R637|RPOA_ECOUT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|123342435|sp|Q0T007|RPOA_SHIF8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158512617|sp|A1AGI6|RPOA_ECOK1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|171855221|sp|A7ZSI4|RPOA_ECO24 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172044360|sp|A8A5A0|RPOA_ECOHS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172045613|sp|A8AQJ0|RPOA_CITK8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|25288369|pir||AB1009 DNA-directed RNA polymerase (EC 2.7.7.6) alpha chain [imported] -
           Salmonella enterica subsp. enterica serovar Typhi
           (strain CT18)
 gi|266618715|pdb|3IYD|A Chain A, Three-Dimensional Em Structure Of An Intact Activator-
           Dependent Transcription Initiation Complex
 gi|266618716|pdb|3IYD|B Chain B, Three-Dimensional Em Structure Of An Intact Activator-
           Dependent Transcription Initiation Complex
 gi|307776495|pdb|3LU0|A Chain A, Molecular Model Of Escherichia Coli Core Rna Polymerase
 gi|307776496|pdb|3LU0|B Chain B, Molecular Model Of Escherichia Coli Core Rna Polymerase
 gi|12517924|gb|AAG58416.1|AE005556_9 RNA polymerase, alpha subunit [Escherichia coli O157:H7 str.
           EDL933]
 gi|26110308|gb|AAN82494.1|AE016767_254 DNA-directed RNA polymerase alpha chain [Escherichia coli CFT073]
 gi|42807|emb|CAA25337.1| unnamed protein product [Escherichia coli]
 gi|147715|gb|AAA24577.1| RNA polymerase alpha subunit [Escherichia coli]
 gi|154353|gb|AAA27214.1| RNA polymerase alpha-subunit [Salmonella enterica subsp. enterica
           serovar Typhimurium]
 gi|606229|gb|AAA58092.1| CG Site No. 234 [Escherichia coli str. K-12 substr. MG1655]
 gi|1789690|gb|AAC76320.1| RNA polymerase, alpha subunit [Escherichia coli str. K-12 substr.
           MG1655]
 gi|13363633|dbj|BAB37583.1| RNA polymerase, alpha subunit [Escherichia coli O157:H7 str. Sakai]
 gi|16421971|gb|AAL22278.1| RNA polymerase, alpha subunit [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|16505175|emb|CAD09171.1| DNA-directed RNA polymerase alpha chain [Salmonella enterica subsp.
           enterica serovar Typhi]
 gi|22774035|gb|AAN07185.1| RNA polymerase alpha subunit [Cloning vector pIA423]
 gi|24053769|gb|AAN44790.1| RNA polymerase, alpha subunit [Shigella flexneri 2a str. 301]
 gi|29139993|gb|AAO71557.1| DNA-directed RNA polymerase alpha chain [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|30043666|gb|AAP19386.1| RNA polymerase, alpha subunit [Shigella flexneri 2a str. 2457T]
 gi|56129591|gb|AAV79097.1| DNA-directed RNA polymerase alpha chain [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|73857291|gb|AAZ89998.1| RNA polymerase, alpha subunit [Shigella sonnei Ss046]
 gi|81247069|gb|ABB67777.1| RNA polymerase alpha subunit [Shigella boydii Sb227]
 gi|85676746|dbj|BAE77996.1| RNA polymerase, alpha subunit [Escherichia coli str. K12 substr.
           W3110]
 gi|91074296|gb|ABE09177.1| RNA polymerase, alpha subunit [Escherichia coli UTI89]
 gi|110345126|gb|ABG71363.1| DNA-directed RNA polymerase alpha chain [Escherichia coli 536]
 gi|110616691|gb|ABF05358.1| RNA polymerase, alpha subunit [Shigella flexneri 5 str. 8401]
 gi|115514701|gb|ABJ02776.1| RNA polymerase, alpha subunit [Escherichia coli APEC O1]
 gi|157068449|gb|ABV07704.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli HS]
 gi|157079480|gb|ABV19188.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           E24377A]
 gi|157086075|gb|ABV15753.1| hypothetical protein CKO_04708 [Citrobacter koseri ATCC BAA-895]
 gi|160867379|gb|ABX24002.1| hypothetical protein SARI_04213 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
 gi|161365804|gb|ABX69572.1| hypothetical protein SPAB_04255 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|169753397|gb|ACA76096.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli ATCC
           8739]
 gi|169890650|gb|ACB04357.1| RNA polymerase, alpha subunit [Escherichia coli str. K-12 substr.
           DH10B]
 gi|170521144|gb|ACB19322.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           SMS-3-5]
 gi|187428720|gb|ACD07994.1| DNA-directed RNA polymerase, alpha subunit [Shigella boydii CDC
           3083-94]
 gi|187766995|gb|EDU30839.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4196]
 gi|188013845|gb|EDU51967.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4113]
 gi|188490199|gb|EDU65302.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli 53638]
 gi|189354678|gb|EDU73097.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4401]
 gi|189361767|gb|EDU80186.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4486]
 gi|189365126|gb|EDU83542.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4501]
 gi|189374058|gb|EDU92474.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC869]
 gi|189375355|gb|EDU93771.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC508]
 gi|190900662|gb|EDV60462.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli B7A]
 gi|192925874|gb|EDV80524.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli E22]
 gi|192955148|gb|EDV85642.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           E110019]
 gi|194401315|gb|ACF61537.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Newport str. SL254]
 gi|194405684|gb|ACF65903.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Heidelberg str. SL476]
 gi|194411676|gb|EDX28003.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli B171]
 gi|194421072|gb|EDX37101.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli 101-1]
 gi|194455652|gb|EDX44491.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Kentucky str. CVM29188]
 gi|194710623|gb|ACF89844.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Schwarzengrund str. CVM19633]
 gi|195628904|gb|EDX48314.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Newport str. SL317]
 gi|197095741|emb|CAR61311.1| DNA-directed RNA polymerase alpha chain [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|197212265|gb|ACH49662.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Agona str. SL483]
 gi|197241195|gb|EDY23815.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Saintpaul str. SARA23]
 gi|197939448|gb|ACH76781.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Dublin str. CT_02021853]
 gi|199604787|gb|EDZ03332.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Virchow str. SL491]
 gi|204319833|gb|EDZ05043.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Javiana str. GA_MM04042433]
 gi|205274738|emb|CAR39794.1| DNA-directed RNA polymerase alpha chain [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205346884|gb|EDZ33515.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Hadar str. RI_05P066]
 gi|206710460|emb|CAR34818.1| DNA-directed RNA polymerase alpha chain [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|208726332|gb|EDZ75933.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4206]
 gi|208734774|gb|EDZ83461.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4045]
 gi|208739032|gb|EDZ86714.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4042]
 gi|209158188|gb|ACI35621.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4115]
 gi|209757288|gb|ACI76956.1| RNA polymerase, alpha subunit [Escherichia coli]
 gi|209757290|gb|ACI76957.1| RNA polymerase, alpha subunit [Escherichia coli]
 gi|209757292|gb|ACI76958.1| RNA polymerase, alpha subunit [Escherichia coli]
 gi|209757294|gb|ACI76959.1| RNA polymerase, alpha subunit [Escherichia coli]
 gi|209757296|gb|ACI76960.1| RNA polymerase, alpha subunit [Escherichia coli]
 gi|209914020|dbj|BAG79094.1| RNA polymerase alpha subunit [Escherichia coli SE11]
 gi|215266667|emb|CAS11106.1| RNA polymerase, alpha subunit [Escherichia coli O127:H6 str.
           E2348/69]
 gi|217321062|gb|EEC29486.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. TW14588]
 gi|218353720|emb|CAU99996.1| RNA polymerase, alpha subunit [Escherichia coli 55989]
 gi|218358112|emb|CAQ90759.1| RNA polymerase, alpha subunit [Escherichia fergusonii ATCC 35469]
 gi|218362621|emb|CAR00247.1| RNA polymerase, alpha subunit [Escherichia coli IAI1]
 gi|218367126|emb|CAR04900.1| RNA polymerase, alpha subunit [Escherichia coli S88]
 gi|218372044|emb|CAR19904.1| RNA polymerase, alpha subunit [Escherichia coli IAI39]
 gi|218429146|emb|CAR10098.2| RNA polymerase, alpha subunit [Escherichia coli ED1a]
 gi|218434000|emb|CAR14917.1| RNA polymerase, alpha subunit [Escherichia coli UMN026]
 gi|222035004|emb|CAP77747.1| DNA-directed RNA polymerase alpha chain [Escherichia coli LF82]
 gi|226838962|gb|EEH70985.1| DNA-directed RNA polymerase [Escherichia sp. 1_1_43]
 gi|226902289|gb|EEH88548.1| RNA polymerase [Escherichia sp. 3_2_53FAA]
 gi|238863493|gb|ACR65491.1| RNA polymerase, alpha subunit [Escherichia coli BW2952]
 gi|242378822|emb|CAQ33614.1| RNA polymerase, alpha subunit, subunit of RNA polymerase, core
           enzyme, RNA polymerase sigma 70, RNA polymerase sigma
           54, RNA polymerase sigma 32, RNA polymerase sigma 38,
           RNA polymerase sigma 28, RNA polymerase sigma 19 and RNA
           polymerase sigma 24 [Escherichia coli BL21(DE3)]
 gi|253322925|gb|ACT27527.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253975124|gb|ACT40795.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli B str.
           REL606]
 gi|253979280|gb|ACT44950.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli
           BL21(DE3)]
 gi|254594632|gb|ACT73993.1| RNA polymerase, alpha subunit [Escherichia coli O157:H7 str.
           TW14359]
 gi|257756065|dbj|BAI27567.1| RNA polymerase, alpha subunit [Escherichia coli O26:H11 str. 11368]
 gi|257761240|dbj|BAI32737.1| RNA polymerase, alpha subunit [Escherichia coli O103:H2 str. 12009]
 gi|257766394|dbj|BAI37889.1| RNA polymerase, alpha subunit [Escherichia coli O111:H- str. 11128]
 gi|260447686|gb|ACX38108.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli DH1]
 gi|261248572|emb|CBG26410.1| DNA-directed RNA polymerase alpha chain [Salmonella enterica subsp.
           enterica serovar Typhimurium str. D23580]
 gi|267995624|gb|ACY90509.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhimurium str. 14028S]
 gi|281180330|dbj|BAI56660.1| RNA polymerase alpha subunit [Escherichia coli SE15]
 gi|281602660|gb|ADA75644.1| DNA-directed RNA polymerase subunit alpha [Shigella flexneri
           2002017]
 gi|282951523|emb|CBG91222.1| DNA-directed RNA polymerase alpha chain [Citrobacter rodentium
           ICC168]
 gi|284923301|emb|CBG36395.1| DNA-directed RNA polymerase alpha chain [Escherichia coli 042]
 gi|290764526|gb|ADD58487.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O55:H7
           str. CB9615]
 gi|291321740|gb|EFE61171.1| DNA-directed RNA polymerase [Escherichia coli B088]
 gi|291425703|gb|EFE98737.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli
           FVEC1412]
 gi|291431290|gb|EFF04275.1| DNA-directed RNA polymerase [Escherichia coli B185]
 gi|291468361|gb|EFF10854.1| DNA-directed RNA polymerase [Escherichia coli B354]
 gi|294490097|gb|ADE88853.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           IHE3034]
 gi|298276469|gb|EFI17987.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli
           FVEC1302]
 gi|299881641|gb|EFI89852.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           196-1]
 gi|300301893|gb|EFJ58278.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           185-1]
 gi|300308985|gb|EFJ63505.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           200-1]
 gi|300318230|gb|EFJ68014.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           175-1]
 gi|300359475|gb|EFJ75345.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           198-1]
 gi|300399549|gb|EFJ83087.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           69-1]
 gi|300404417|gb|EFJ87955.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           84-1]
 gi|300409379|gb|EFJ92917.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           45-1]
 gi|300414531|gb|EFJ97841.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           115-1]
 gi|300421743|gb|EFK05054.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           182-1]
 gi|300453764|gb|EFK17384.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           116-1]
 gi|300459450|gb|EFK22943.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           21-1]
 gi|300460013|gb|EFK23506.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           187-1]
 gi|300524667|gb|EFK45736.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           119-7]
 gi|300532386|gb|EFK53448.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           107-1]
 gi|300839200|gb|EFK66960.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           124-1]
 gi|300848016|gb|EFK75776.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           78-1]
 gi|301077787|gb|EFK92593.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           146-1]
 gi|301159958|emb|CBW19477.1| DNA-directed RNA polymerase alpha chain [Salmonella enterica subsp.
           enterica serovar Typhimurium str. SL1344]
 gi|305850758|gb|EFM51215.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli NC101]
 gi|306905475|gb|EFN36010.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli W]
 gi|307555383|gb|ADN48158.1| DNA-directed RNA polymerase alpha chain [Escherichia coli ABU
           83972]
 gi|307628330|gb|ADN72634.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli UM146]
 gi|308121621|gb|EFO58883.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           145-7]
 gi|309703707|emb|CBJ03048.1| DNA-directed RNA polymerase alpha chain [Escherichia coli ETEC
           H10407]
 gi|310334821|gb|EFQ01026.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           1827-70]
 gi|312914438|dbj|BAJ38412.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhimurium str. T000240]
 gi|312947846|gb|ADR28673.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O83:H1
           str. NRG 857C]
 gi|313647395|gb|EFS11847.1| DNA-directed RNA polymerase, alpha subunit [Shigella flexneri 2a
           str. 2457T]
 gi|315062587|gb|ADT76914.1| RNA polymerase, alpha subunit [Escherichia coli W]
 gi|315137870|dbj|BAJ45029.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli DH1]
 gi|315255879|gb|EFU35847.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           85-1]
 gi|315284629|gb|EFU44074.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           110-3]
 gi|315292387|gb|EFU51739.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           153-1]
 gi|315298594|gb|EFU57849.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           16-3]
 gi|315617097|gb|EFU97707.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli 3431]
 gi|320087860|emb|CBY97623.1| DNA-directed RNA polymerase alpha chain [Salmonella enterica subsp.
           enterica serovar Weltevreden str. 2007-60-3289-1]
 gi|320173939|gb|EFW49115.1| DNA-directed RNA polymerase alpha subunit [Shigella dysenteriae CDC
           74-1112]
 gi|320182707|gb|EFW57593.1| DNA-directed RNA polymerase alpha subunit [Shigella boydii ATCC
           9905]
 gi|320187016|gb|EFW61728.1| DNA-directed RNA polymerase alpha subunit [Shigella flexneri CDC
           796-83]
 gi|320191671|gb|EFW66321.1| DNA-directed RNA polymerase alpha subunit [Escherichia coli O157:H7
           str. EC1212]
 gi|320195387|gb|EFW70014.1| DNA-directed RNA polymerase alpha subunit [Escherichia coli
           WV_060327]
 gi|320199482|gb|EFW74072.1| DNA-directed RNA polymerase alpha subunit [Escherichia coli
           EC4100B]
 gi|320639600|gb|EFX09194.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O157:H7
           str. G5101]
 gi|320645098|gb|EFX14114.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O157:H-
           str. 493-89]
 gi|320650409|gb|EFX18875.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O157:H-
           str. H 2687]
 gi|320655934|gb|EFX23854.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O55:H7
           str. 3256-97 TW 07815]
 gi|320661386|gb|EFX28801.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O55:H7
           str. USDA 5905]
 gi|320666408|gb|EFX33391.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O157:H7
           str. LSU-61]
 gi|321226466|gb|EFX51516.1| DNA-directed RNA polymerase alpha subunit [Salmonella enterica
           subsp. enterica serovar Typhimurium str. TN061786]
 gi|322615044|gb|EFY11968.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 315996572]
 gi|322617331|gb|EFY14232.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 495297-1]
 gi|322625553|gb|EFY22378.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 495297-3]
 gi|322626395|gb|EFY23204.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 495297-4]
 gi|322632093|gb|EFY28846.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 515920-1]
 gi|322635028|gb|EFY31751.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 515920-2]
 gi|322643271|gb|EFY39838.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 531954]
 gi|322646645|gb|EFY43152.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str.
           NC_MB110209-0054]
 gi|322649991|gb|EFY46410.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. OH_2009072675]
 gi|322652708|gb|EFY49048.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str.
           CASC_09SCPH15965]
 gi|322665523|gb|EFY61710.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 81038-01]
 gi|322670417|gb|EFY66556.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. MD_MDA09249507]
 gi|322670490|gb|EFY66624.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 414877]
 gi|322675066|gb|EFY71149.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 366867]
 gi|322681603|gb|EFY77632.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 413180]
 gi|322685947|gb|EFY81936.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 446600]
 gi|323131773|gb|ADX19203.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhimurium str. 4/74]
 gi|323154133|gb|EFZ40336.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           EPECa14]
 gi|323162974|gb|EFZ48809.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           E128010]
 gi|323164859|gb|EFZ50650.1| DNA-directed RNA polymerase, alpha subunit [Shigella sonnei 53G]
 gi|323173931|gb|EFZ59559.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli LT-68]
 gi|323179169|gb|EFZ64743.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli 1180]
 gi|323182773|gb|EFZ68174.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli 1357]
 gi|323189100|gb|EFZ74384.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           RN587/1]
 gi|323195817|gb|EFZ80990.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 609458-1]
 gi|323196427|gb|EFZ81578.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 556150-1]
 gi|323202334|gb|EFZ87379.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 609460]
 gi|323207317|gb|EFZ92267.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 507440-20]
 gi|323211247|gb|EFZ96092.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 556152]
 gi|323216044|gb|EGA00775.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. MB101509-0077]
 gi|323223465|gb|EGA07793.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. MB102109-0047]
 gi|323226805|gb|EGA10995.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. MB110209-0055]
 gi|323231833|gb|EGA15943.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. MB111609-0052]
 gi|323233214|gb|EGA17309.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 2009083312]
 gi|323237281|gb|EGA21346.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 2009085258]
 gi|323245516|gb|EGA29515.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 315731156]
 gi|323249022|gb|EGA32944.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. IA_2009159199]
 gi|323250645|gb|EGA34526.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. IA_2010008282]
 gi|323256874|gb|EGA40588.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. IA_2010008283]
 gi|323263023|gb|EGA46570.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. IA_2010008284]
 gi|323266023|gb|EGA49518.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. IA_2010008285]
 gi|323272780|gb|EGA56183.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. IA_2010008287]
 gi|323376826|gb|ADX49094.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli KO11]
 gi|323934506|gb|EGB30914.1| DNA-directed RNA polymerase [Escherichia coli E1520]
 gi|323939283|gb|EGB35495.1| DNA-directed RNA polymerase [Escherichia coli E482]
 gi|323944284|gb|EGB40360.1| DNA-directed RNA polymerase [Escherichia coli H120]
 gi|323950209|gb|EGB46091.1| DNA-directed RNA polymerase [Escherichia coli H252]
 gi|323954582|gb|EGB50365.1| DNA-directed RNA polymerase [Escherichia coli H263]
 gi|323959554|gb|EGB55207.1| DNA-directed RNA polymerase [Escherichia coli H489]
 gi|323966257|gb|EGB61692.1| DNA-directed RNA polymerase [Escherichia coli M863]
 gi|323970099|gb|EGB65373.1| DNA-directed RNA polymerase [Escherichia coli TA007]
 gi|323974752|gb|EGB69865.1| DNA-directed RNA polymerase [Escherichia coli TW10509]
 gi|324009030|gb|EGB78249.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           57-2]
 gi|324014912|gb|EGB84131.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           60-1]
 gi|324017886|gb|EGB87105.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           117-3]
 gi|324111974|gb|EGC05953.1| DNA-directed RNA polymerase [Escherichia fergusonii B253]
 gi|324116315|gb|EGC10235.1| DNA-directed RNA polymerase [Escherichia coli E1167]
 gi|325498864|gb|EGC96723.1| DNA-directed RNA polymerase subunit alpha [Escherichia fergusonii
           ECD227]
 gi|326342543|gb|EGD66317.1| DNA-directed RNA polymerase alpha subunit [Escherichia coli O157:H7
           str. 1044]
 gi|326344530|gb|EGD68279.1| DNA-directed RNA polymerase alpha subunit [Escherichia coli O157:H7
           str. 1125]
 gi|326625159|gb|EGE31504.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Dublin str. 3246]
 gi|326630106|gb|EGE36449.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Gallinarum str. 9]
 gi|330909339|gb|EGH37853.1| DNA-directed RNA polymerase alpha subunit [Escherichia coli AA86]
 gi|331036285|gb|EGI08511.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli H736]
 gi|331041590|gb|EGI13734.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli M605]
 gi|331052800|gb|EGI24833.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli TA206]
 gi|331057418|gb|EGI29404.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli TA143]
 gi|331062186|gb|EGI34106.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli TA271]
 gi|331067710|gb|EGI39108.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli TA280]
 gi|331072536|gb|EGI43861.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli H591]
 gi|331077308|gb|EGI48520.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli H299]
 gi|332085444|gb|EGI90610.1| DNA-directed RNA polymerase, alpha subunit [Shigella boydii
           5216-82]
 gi|332104202|gb|EGJ07548.1| RNA polymerase alpha subunit [Shigella sp. D9]
          Length = 329

 Score =  291 bits (745), Expect = 8e-77,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 222/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|331654888|ref|ZP_08355887.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli M718]
 gi|331046903|gb|EGI18981.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli M718]
          Length = 329

 Score =  291 bits (745), Expect = 9e-77,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 222/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDAYY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|300721391|ref|YP_003710662.1| RNA polymerase subunit alpha [Xenorhabdus nematophila ATCC 19061]
 gi|297627879|emb|CBJ88425.1| RNA polymerase, alpha subunit [Xenorhabdus nematophila ATCC 19061]
          Length = 329

 Score =  291 bits (745), Expect = 9e-77,   Method: Compositional matrix adjust.
 Identities = 153/333 (45%), Positives = 221/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVQGKDEVILTVNKSGIGPVTAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D  A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDESASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|124268601|ref|YP_001022605.1| DNA-directed RNA polymerase subunit alpha [Methylibium
           petroleiphilum PM1]
 gi|158512865|sp|A2SLD1|RPOA_METPP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|124261376|gb|ABM96370.1| DNA-directed RNA polymerase [Methylibium petroleiphilum PM1]
          Length = 333

 Score =  291 bits (745), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 154/328 (46%), Positives = 216/328 (65%), Gaps = 5/328 (1%)

Query: 9   LIKPNNIEYIVLGQEE-ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           L+KP  I    L   +  +R  +  EP  RG+ HTLGNALRRVL+SS+ G A T V I G
Sbjct: 5   LLKPKAINVEPLSAAKGAHRAKVTLEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAG 64

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+  ++LN+KG+  ++       + + K G G V AGDIQT +D+E+
Sbjct: 65  VLHEYSAIDGVQEDVVHVMLNLKGVVFRLHNRDEVTLVLRKEGEGPVKAGDIQTPHDVEI 124

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVS 184
           +NPDHVI +L     + M++ V KG GYVP    R  ++P   IG I +DA +SP+++VS
Sbjct: 125 INPDHVITHLSQGGKLDMQIKVEKGRGYVPGTMRRFGDEPTKSIGRIVLDASFSPVRRVS 184

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           YTVESAR  Q  D DKL M I+T+G+IT E+++  +++IL +QL +F   E    ++ + 
Sbjct: 185 YTVESARVEQRTDLDKLVMEIETNGAITPEEAIRASAKILVEQLAVFAQLEGQINDIFDA 244

Query: 245 INV-KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +S  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 245 QPAQRSTQFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTETELLKTPNLGRKSL 304

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LG  L +WPP+ +++
Sbjct: 305 NEIKEVLASRGLTLGGRLENWPPQGLDK 332


>gi|298531060|ref|ZP_07018461.1| DNA-directed RNA polymerase, alpha subunit [Desulfonatronospira
           thiodismutans ASO3-1]
 gi|298509083|gb|EFI32988.1| DNA-directed RNA polymerase, alpha subunit [Desulfonatronospira
           thiodismutans ASO3-1]
          Length = 347

 Score =  291 bits (745), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 157/343 (45%), Positives = 222/343 (64%), Gaps = 14/343 (4%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW  L+KP+ ++      E+  +     EPL RGF +T GNALRR+L+SSL+GAAI A+
Sbjct: 13  RNWSSLVKPDQVQRDEKSTEQYGK--FSCEPLERGFGNTFGNALRRILLSSLQGAAIVAI 70

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +ID   HE ++I GV ED+TDI+LN+K +  KMS D  +++ +     G VTA  IQT  
Sbjct: 71  KIDNAPHEFATITGVVEDVTDIVLNLKQVRFKMSRDEPQKLKLVANEKGQVTAKAIQTNQ 130

Query: 124 DIEVLNPDHVICNL--DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           +I VLNPD  I  L  D+D V+ +E  V  G GYVP++ H   ++ IGLI +DA +SPI+
Sbjct: 131 NIAVLNPDQHIATLSQDIDLVINIE--VRMGKGYVPSEQHEDLDEEIGLIPMDATFSPIR 188

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSYTVE AR GQ+ +YDKL + I TDGS+  ED++A +++IL+DQL +FINF+E +   
Sbjct: 189 KVSYTVEQARVGQMTNYDKLILEIHTDGSVLPEDALAYSAKILKDQLSVFINFDESQT-- 246

Query: 242 KEDINV----KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
             DINV         +P L K +EELEL VR+ NCLR   I  +G+LIQ++E D+LR  N
Sbjct: 247 --DINVIDTNSDEGLDPKLFKTIEELELPVRAGNCLRNAGIRLVGELIQQSENDLLRTKN 304

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
           FGRKSL +I+ V+  MG      + ++  +  E L +K +D+ 
Sbjct: 305 FGRKSLEDIRRVIEQMGYDFNTQIDNFDQKYQEWLKRKEDDEA 347


>gi|183600727|ref|ZP_02962220.1| hypothetical protein PROSTU_04323 [Providencia stuartii ATCC 25827]
 gi|188019707|gb|EDU57747.1| hypothetical protein PROSTU_04323 [Providencia stuartii ATCC 25827]
          Length = 329

 Score =  291 bits (745), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 153/333 (45%), Positives = 221/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVQGKDEVILTLNKSGIGPVTAADIVH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D  A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDESASINMRIKVQRGRGYVPASARVHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|330430070|gb|AEC21404.1| DNA-directed RNA polymerase alpha chain [Pusillimonas sp. T7-7]
          Length = 329

 Score =  291 bits (745), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 150/327 (45%), Positives = 213/327 (65%), Gaps = 6/327 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           Q  +KP +IE   +G+   N   ++ EP  RG+ HTLGNALRR+L+SS+ G A T VQ+ 
Sbjct: 4   QGFLKPRSIEVEPVGK---NHARVVMEPFERGYGHTLGNALRRILLSSMTGYAPTEVQMT 60

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S++ GV ED+ DI+LN+KG+  K+       + + K+G GVV A DI+  +D+E
Sbjct: 61  GVVHEYSTVAGVREDVVDILLNLKGVVFKLHNREEVTLVLRKQGAGVVLASDIELPHDVE 120

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKV 183
           ++NPDHVI NL     + M++ V +G GYVP       +D    IG I +DA YSP+++V
Sbjct: 121 IINPDHVIANLTDAGKLEMQIKVEQGRGYVPGNVRALSDDRTHTIGRIVLDASYSPVRRV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VESAR  Q  D DKL + I+T+G ++ E++V  ++RIL DQ+ +F   E      ++
Sbjct: 181 SYAVESARVEQRTDLDKLVLDIETNGVVSPEEAVRQSARILMDQISVFAALEGAGDSYED 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             +  +   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 241 APSRAAQQIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 300

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIE 330
            EIK VL   GL LGM L +WPP  +E
Sbjct: 301 NEIKEVLAARGLTLGMKLENWPPLGLE 327


>gi|242237884|ref|YP_002986065.1| DNA-directed RNA polymerase subunit alpha [Dickeya dadantii Ech703]
 gi|242129941|gb|ACS84243.1| DNA-directed RNA polymerase, alpha subunit [Dickeya dadantii
           Ech703]
          Length = 329

 Score =  291 bits (745), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 222/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASINMRIKVQRGRGYVPASARIHTEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|322659535|gb|EFY55779.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 19N]
          Length = 329

 Score =  291 bits (745), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 221/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICRLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|251787996|ref|YP_003002717.1| DNA-directed RNA polymerase subunit alpha [Dickeya zeae Ech1591]
 gi|271502221|ref|YP_003335247.1| DNA-directed RNA polymerase subunit alpha [Dickeya dadantii Ech586]
 gi|307132814|ref|YP_003884830.1| DNA-directed RNA polymerase subunit alpha [Dickeya dadantii 3937]
 gi|247536617|gb|ACT05238.1| DNA-directed RNA polymerase, alpha subunit [Dickeya zeae Ech1591]
 gi|270345776|gb|ACZ78541.1| DNA-directed RNA polymerase, alpha subunit [Dickeya dadantii
           Ech586]
 gi|306530343|gb|ADN00274.1| DNA-directed RNA polymerase alpha subunit [Dickeya dadantii 3937]
          Length = 329

 Score =  291 bits (745), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 222/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASINMRIKVQRGRGYVPASARIHTEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|284006138|emb|CBA71380.1| DNA-directed RNA polymerase alpha chain [Arsenophonus nasoniae]
          Length = 329

 Score =  291 bits (745), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 153/333 (45%), Positives = 220/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVHGKDEVILTLNKSGIGPVTAADITP 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
            +DIE++ P HVIC+L D  A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 NDDIEIVKPQHVICHLTDESAAINMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE- 236
           SP+++++Y VE+ R  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEATRVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            K EVK++       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 AKVEVKDE----KPEFDPILLRAVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|330432099|gb|AEC17158.1| DNA-directed RNA polymerase subunit alpha [Gallibacterium anatis
           UMN179]
          Length = 327

 Score =  291 bits (744), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 151/333 (45%), Positives = 222/333 (66%), Gaps = 10/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVDIEQISPTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVFLTLTKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHH-RTENDPIGLITIDALYSP 179
             D+E++NPDH+IC+L D +A + M + V +G GY+PA      E  PIG + +DA YSP
Sbjct: 118 DGDVEIVNPDHIICHLTDENASINMRIRVQRGRGYIPASSRTHDEERPIGRLLVDACYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           + +++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++
Sbjct: 178 VDRIAYNVEAARVEQRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRQ 237

Query: 240 -EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 PEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNL 293

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 294 GKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 326


>gi|188535253|ref|YP_001909050.1| DNA-directed RNA polymerase subunit alpha [Erwinia tasmaniensis
           Et1/99]
 gi|188030295|emb|CAO98184.1| DNA-directed RNA polymerase alpha chain [Erwinia tasmaniensis
           Et1/99]
          Length = 329

 Score =  291 bits (744), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 151/333 (45%), Positives = 221/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P H IC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHAICHLTDENAAISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|82778591|ref|YP_404940.1| DNA-directed RNA polymerase subunit alpha [Shigella dysenteriae
           Sd197]
 gi|90110866|sp|Q32B56|RPOA_SHIDS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|81242739|gb|ABB63449.1| RNA polymerase, alpha subunit [Shigella dysenteriae Sd197]
          Length = 329

 Score =  291 bits (744), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 222/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVRRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|294341216|emb|CAZ89617.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           (Transcriptase alpha chain) (RNA polymerase alpha
           subunit) [Thiomonas sp. 3As]
          Length = 328

 Score =  291 bits (744), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 151/326 (46%), Positives = 215/326 (65%), Gaps = 6/326 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L++P +I+   LG    NR+ ++ EP  RG+ HTLGNALRRV++SSL G A T V I+GV
Sbjct: 5   LLRPKSIQVESLGH---NRSKVVLEPFERGYGHTLGNALRRVMLSSLVGYAPTEVSINGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S + G+ ED+  ++LN+KG+ LK+       +++ K G GVVTA DIQT +D+E++
Sbjct: 62  LHEYSVVDGLQEDVIGVLLNLKGVVLKLHNRDEVTLSLRKEGEGVVTAADIQTPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSY 185
           NPDHVI +L     + M++ V KG GYVP        +    IG I +DA +SP+++VSY
Sbjct: 122 NPDHVIAHLSQGGKLDMQIKVEKGRGYVPGTLRNFGEEGGKSIGHIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL +QL +F + E  +     + 
Sbjct: 182 AVESARVEQRTDLDKLVMEIETNGVISAEEAIRSSARILVEQLSVFASLEGAETTEAAEA 241

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                 ++P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GRKSL E
Sbjct: 242 AAGGQTYDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRSETELLKTPNLGRKSLNE 301

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL   GL LGM L +WPP  +++
Sbjct: 302 IKEVLAARGLTLGMKLDNWPPSGLDK 327


>gi|261854974|ref|YP_003262257.1| DNA-directed RNA polymerase, subunit alpha [Halothiobacillus
           neapolitanus c2]
 gi|261835443|gb|ACX95210.1| DNA-directed RNA polymerase, alpha subunit [Halothiobacillus
           neapolitanus c2]
          Length = 331

 Score =  291 bits (744), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 149/334 (44%), Positives = 222/334 (66%), Gaps = 7/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    EL+KP  ++  VL   +  R  ++ EPL RGF +TLGNALRR+L+SS+ G A+T
Sbjct: 1   MQLGSTELLKPRLVDVQVL---DATRARVVLEPLERGFGYTLGNALRRILLSSIPGVAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +I+GV+HE ++I+GVHED+ +I+LN+KG+++ + G     ++I K G G +TA DI+ 
Sbjct: 58  EAEIEGVVHEYTTIEGVHEDVLEILLNLKGLSVMLHGRDEAMLSIKKTGAGAITAADIKA 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSPI 180
            + +E++NP+H I  L+    + M   V++G GYVPA   R E    IG + +DA +SP+
Sbjct: 118 DHAVEIINPEHHIATLNDQGSLVMTFKVTRGKGYVPASARREEAGGQIGRLLVDASFSPL 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY+VE AR  Q  D D L + I+T+GSI+ ED++  A+ IL DQL +F++    K E
Sbjct: 178 RRVSYSVERARVEQRTDLDSLVLDIETNGSISAEDAIRQAAGILVDQLSVFVDL---KAE 234

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E +  ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G+
Sbjct: 235 KVEPVVEQAPAVDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEIELLKTPNLGK 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           KSL EIK VL   GL LG  L +WPP  +  LA+
Sbjct: 295 KSLTEIKDVLAKQGLSLGQRLENWPPAELLNLAE 328


>gi|237728630|ref|ZP_04559111.1| RNA polymerase [Citrobacter sp. 30_2]
 gi|283835712|ref|ZP_06355453.1| hypothetical protein CIT292_10105 [Citrobacter youngae ATCC 29220]
 gi|226909252|gb|EEH95170.1| RNA polymerase [Citrobacter sp. 30_2]
 gi|291068392|gb|EFE06501.1| DNA-directed RNA polymerase, alpha subunit [Citrobacter youngae
           ATCC 29220]
          Length = 329

 Score =  291 bits (744), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 222/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDDVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|212709004|ref|ZP_03317132.1| hypothetical protein PROVALCAL_00036 [Providencia alcalifaciens DSM
           30120]
 gi|212688370|gb|EEB47898.1| hypothetical protein PROVALCAL_00036 [Providencia alcalifaciens DSM
           30120]
          Length = 329

 Score =  291 bits (744), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 153/333 (45%), Positives = 221/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVQGKDEVILTLNKSGIGPVTAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D  A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDESASINMRIKVQRGRGYVPASARVHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|291619150|ref|YP_003521892.1| RpoA [Pantoea ananatis LMG 20103]
 gi|317049815|ref|YP_004117463.1| DNA-directed RNA polymerase subunit alpha [Pantoea sp. At-9b]
 gi|291154180|gb|ADD78764.1| RpoA [Pantoea ananatis LMG 20103]
 gi|316951432|gb|ADU70907.1| DNA-directed RNA polymerase, alpha subunit [Pantoea sp. At-9b]
 gi|327395479|dbj|BAK12901.1| DNA-directed RNA polymerase alpha chain RpoA [Pantoea ananatis
           AJ13355]
          Length = 329

 Score =  291 bits (744), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 221/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|46579740|ref|YP_010548.1| DNA-directed RNA polymerase subunit alpha [Desulfovibrio vulgaris
           str. Hildenborough]
 gi|120602783|ref|YP_967183.1| DNA-directed RNA polymerase subunit alpha [Desulfovibrio vulgaris
           DP4]
 gi|61215968|sp|Q72CF4|RPOA_DESVH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158513912|sp|A1VE90|RPOA_DESVV RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|46449155|gb|AAS95807.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio vulgaris
           str. Hildenborough]
 gi|120563012|gb|ABM28756.1| DNA-directed RNA polymerase subunit alpha [Desulfovibrio vulgaris
           DP4]
 gi|311233531|gb|ADP86385.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio vulgaris
           RCH1]
          Length = 347

 Score =  291 bits (744), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 152/338 (44%), Positives = 220/338 (65%), Gaps = 15/338 (4%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTL---MIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +NW EL+KP  I        E + T+    + EPL RG+A T+GNA+RRVL+SSL+GAA 
Sbjct: 13  RNWSELVKPEQISR----DGEVSDTMYGKFVCEPLERGYATTIGNAMRRVLLSSLQGAAF 68

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
            AV+I GV HE ++I GV ED+TD++LN+K + L M  +  + + +     G +TAGD++
Sbjct: 69  VAVKISGVQHEFTTIPGVLEDVTDVVLNLKQVRLAMDTEEPQYLELKVDKRGAITAGDVR 128

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T   + VLNPD  I  L  D  +  EL V  G GYVPA  H   ++ IGLI +DA +SP+
Sbjct: 129 TNQHVMVLNPDQHIATLTEDIELTFELEVRMGKGYVPADMHEGLSEEIGLIKLDASFSPV 188

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KV+YTVE AR GQ+ +YDKL + + TDGS++ ED++A +++I++DQ+ +FINF+E    
Sbjct: 189 RKVAYTVEQARVGQMTNYDKLILEVWTDGSVSPEDAIAYSAKIIKDQISVFINFDERISG 248

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
              + +  S  FN  L K ++ELELSVR+TNCL+  NI  +G+L+Q++E +ML+  NFGR
Sbjct: 249 ENSNGSADSGEFNEHLFKSIDELELSVRATNCLKSANIALVGELVQKSENEMLKTKNFGR 308

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EI+ VLG MGL  G          ++   KKY++
Sbjct: 309 KSLDEIRRVLGDMGLDFGTK--------VDGFEKKYQE 338


>gi|296137039|ref|YP_003644281.1| DNA-directed RNA polymerase, alpha subunit [Thiomonas intermedia
           K12]
 gi|295797161|gb|ADG31951.1| DNA-directed RNA polymerase, alpha subunit [Thiomonas intermedia
           K12]
          Length = 328

 Score =  291 bits (744), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 151/326 (46%), Positives = 215/326 (65%), Gaps = 6/326 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L++P +I+   LG    NR+ ++ EP  RG+ HTLGNALRRV++SSL G A T V I+GV
Sbjct: 5   LLRPKSIQVESLGH---NRSKVVLEPFERGYGHTLGNALRRVMLSSLVGYAPTEVSINGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S + G+ ED+  ++LN+KG+ LK+       +++ K G GVVTA DIQT +D+E++
Sbjct: 62  LHEYSVVDGLQEDVIGVLLNLKGVVLKLHNRDEVTLSLRKEGEGVVTAADIQTPHDVEIV 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSY 185
           NPDHVI +L     + M++ V KG GYVP        +    IG I +DA +SP+++VSY
Sbjct: 122 NPDHVIAHLSQGGKLDMQIKVEKGRGYVPGTLRNFGEEGGKSIGHIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL +QL +F + E  +     + 
Sbjct: 182 AVESARVEQRTDLDKLVMEIETNGVISAEEAIRSSARILVEQLSVFASLEGAETTEAAEA 241

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                 ++P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GRKSL E
Sbjct: 242 AAGGQTYDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRSETELLKTPNLGRKSLNE 301

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL   GL LGM L +WPP  +++
Sbjct: 302 IKEVLAARGLTLGMKLDNWPPSGLDK 327


>gi|315127931|ref|YP_004069934.1| DNA-directed RNA polymerase subunit alpha [Pseudoalteromonas sp.
           SM9913]
 gi|315016445|gb|ADT69783.1| DNA-directed RNA polymerase subunit alpha [Pseudoalteromonas sp.
           SM9913]
          Length = 328

 Score =  291 bits (744), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 148/334 (44%), Positives = 222/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +      R+ ++ EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIDAINP---TRSKVVLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DIQ 
Sbjct: 58  EVEIDGVLHEYSAKEGVQEDIIEILLNLKGLAVTLEGKDEVFLTLTKSGVGPVTAADIQH 117

Query: 122 VNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALY 177
             D+ + NPDHVICNL   ++ + M + V +G GYVPA    + +D   PIG + +DA +
Sbjct: 118 DGDVTIANPDHVICNLTTNNSEISMRIRVERGRGYVPASSRLSSDDDERPIGRLLLDASF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y+VESAR  Q  D DKL + ++T+G++  E+++  AS IL +QL  F++    
Sbjct: 178 SPVERIAYSVESARVEQRTDLDKLIIDMETNGTLDPEEAIRRASTILAEQLDAFVDL--- 234

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +   + +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 235 RDVTEPEEKEEKPEFDPILLRPVDDLELTVRSANCLKAEQIQYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP S+ E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASLAE 328


>gi|256821687|ref|YP_003145650.1| DNA-directed RNA polymerase subunit alpha [Kangiella koreensis DSM
           16069]
 gi|256795226|gb|ACV25882.1| DNA-directed RNA polymerase, alpha subunit [Kangiella koreensis DSM
           16069]
          Length = 326

 Score =  290 bits (743), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 151/330 (45%), Positives = 218/330 (66%), Gaps = 19/330 (5%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E + P  I+   +   E  +  ++ EP  RGF HTLGN+LRR+L+SS+ GAA+T V+IDG
Sbjct: 5   EFLTPRQIK---VESSEGTKARVVLEPFERGFGHTLGNSLRRILLSSMPGAAVTEVEIDG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+ DI+LN+KG+ +++       +T+ K+G GVVTA DI+ V+  EV
Sbjct: 62  VLHEYSAIEGVQEDVIDILLNLKGLAVRLEDKEVATLTLQKKGEGVVTAADIEEVSGTEV 121

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYSPIKKVS 184
           +N DH I  L+    + M + +  G GY  +   K    E+  IG++ +DA +SP+KKVS
Sbjct: 122 VNKDHYIATLNKGGALNMRIKIRLGRGYEASNTRKQPEGEDKAIGVLQVDASFSPMKKVS 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-----EPKK 239
           YTVESAR  Q  D DKL + ++T+G+I  E+++  ++ ILQ+QL  F++ +     EP+K
Sbjct: 182 YTVESARVEQRTDLDKLVLDLETNGTIDPEEAIRRSATILQEQLAAFVDLKDEKQAEPEK 241

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           E  E         +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G
Sbjct: 242 EEPE--------IDPILLRPVDDLELTVRSANCLKTENIHYIGDLVQRTEVELLKTPNLG 293

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 KKSLTEIKDVLASRGLSLGMRLENWPPSSI 323


>gi|42799|emb|CAA26395.1| unnamed protein product [Escherichia coli]
          Length = 329

 Score =  290 bits (743), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 221/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETTGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|54307566|ref|YP_128586.1| DNA-directed RNA polymerase subunit alpha [Photobacterium profundum
           SS9]
 gi|61215937|sp|Q6LV91|RPOA_PHOPR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|46911986|emb|CAG18784.1| putative DNA-directed RNA polymerase, alpha subunit [Photobacterium
           profundum SS9]
          Length = 329

 Score =  290 bits (743), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 151/334 (45%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GVHED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI  
Sbjct: 58  EVEIDGVLHEYSTKEGVHEDILEILLNLKGLAIKVEGKDEVILTLNKSGAGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E+ NP+HVIC+L D  A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIANPEHVICHLTDDHAEISMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|224585210|ref|YP_002639009.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Paratyphi C strain RKS4594]
 gi|224469738|gb|ACN47568.1| DNA-directed RNA polymerase alpha subunit [Salmonella enterica
           subsp. enterica serovar Paratyphi C strain RKS4594]
          Length = 304

 Score =  290 bits (743), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 147/305 (48%), Positives = 211/305 (69%), Gaps = 9/305 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           M  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+
Sbjct: 1   MTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELT 148
           KG+ +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + 
Sbjct: 61  KGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIK 120

Query: 149 VSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           V +G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + +
Sbjct: 121 VQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEM 180

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELE 264
           +T+G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LE
Sbjct: 181 ETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLE 236

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +W
Sbjct: 237 LTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENW 296

Query: 325 PPESI 329
           PP SI
Sbjct: 297 PPASI 301


>gi|332037268|gb|EGI73723.1| DNA-directed RNA polymerase alpha subunit [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 328

 Score =  290 bits (743), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 148/334 (44%), Positives = 222/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +      R+ ++ EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIDAINP---TRSKIVLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DIQ 
Sbjct: 58  EVEIDGVLHEYSAKEGVQEDIIEILLNLKGLAVTLEGKDEVFLTLTKSGVGPVTAADIQH 117

Query: 122 VNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALY 177
             D+ + NPDHVICNL   ++ + M + V +G GYVPA    + +D   PIG + +DA +
Sbjct: 118 DGDVTIANPDHVICNLTTNNSEISMRIRVERGRGYVPASSRLSSDDDERPIGRLLLDASF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y+VESAR  Q  D DKL + ++T+G++  E+++  AS IL +QL  F++    
Sbjct: 178 SPVERIAYSVESARVEQRTDLDKLIIDMETNGTLDPEEAIRRASTILAEQLDAFVDL--- 234

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +   + +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 235 RDVTEPEEKEEKPEFDPILLRPVDDLELTVRSANCLKAEQIQYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP S+ E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASLAE 328


>gi|77361710|ref|YP_341285.1| DNA-directed RNA polymerase subunit alpha [Pseudoalteromonas
           haloplanktis TAC125]
 gi|90110860|sp|Q3IJI6|RPOA_PSEHT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|76876621|emb|CAI87843.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           (Transcriptase alpha chain) (RNA polymerase alpha
           subunit) [Pseudoalteromonas haloplanktis TAC125]
          Length = 328

 Score =  290 bits (743), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 148/334 (44%), Positives = 222/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +      R+ ++ EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIDAINP---TRSKIVLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DIQ 
Sbjct: 58  EVEIDGVLHEYSAKEGVQEDIIEILLNLKGLAVTLEGKDEVFLTLAKSGVGPVTASDIQH 117

Query: 122 VNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALY 177
             D+ + NPDHVICNL   ++ + M + V +G GYVPA    + +D   PIG + +DA +
Sbjct: 118 DGDVTIANPDHVICNLTTNNSEISMRIRVERGRGYVPASSRLSSDDDERPIGRLLLDASF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y+VESAR  Q  D DKL + ++T+G++  E+++  AS IL +QL  F++    
Sbjct: 178 SPVERIAYSVESARVEQRTDLDKLIIDMETNGTLDPEEAIRRASTILAEQLDAFVDL--- 234

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +   + +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 235 RDVTEPEEKEEKPEFDPILLRPVDDLELTVRSANCLKAEQIQYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP S+ E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASLAE 328


>gi|78064950|ref|YP_367719.1| DNA-directed RNA polymerase subunit alpha [Burkholderia sp. 383]
 gi|107024277|ref|YP_622604.1| DNA-directed RNA polymerase subunit alpha [Burkholderia cenocepacia
           AU 1054]
 gi|115350348|ref|YP_772187.1| DNA-directed RNA polymerase subunit alpha [Burkholderia ambifaria
           AMMD]
 gi|116688398|ref|YP_834021.1| DNA-directed RNA polymerase subunit alpha [Burkholderia cenocepacia
           HI2424]
 gi|134294469|ref|YP_001118204.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           vietnamiensis G4]
 gi|170700720|ref|ZP_02891715.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia ambifaria
           IOP40-10]
 gi|170731708|ref|YP_001763655.1| DNA-directed RNA polymerase subunit alpha [Burkholderia cenocepacia
           MC0-3]
 gi|171318374|ref|ZP_02907532.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia ambifaria
           MEX-5]
 gi|172059367|ref|YP_001807019.1| DNA-directed RNA polymerase subunit alpha [Burkholderia ambifaria
           MC40-6]
 gi|206558667|ref|YP_002229427.1| DNA-directed RNA polymerase subunit alpha [Burkholderia cenocepacia
           J2315]
 gi|254246577|ref|ZP_04939898.1| DNA-directed RNA polymerase [Burkholderia cenocepacia PC184]
 gi|90101525|sp|Q39KE1|RPOA_BURS3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366669|sp|Q1BRX4|RPOA_BURCA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|122324240|sp|Q0BJ20|RPOA_BURCM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158512278|sp|A0K3Q1|RPOA_BURCH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|166229265|sp|A4JAR6|RPOA_BURVG RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238688546|sp|B1JU48|RPOA_BURCC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238689152|sp|B1YRQ5|RPOA_BURA4 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238693061|sp|B4E5E6|RPOA_BURCJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|77965695|gb|ABB07075.1| DNA-directed RNA polymerase subunit alpha [Burkholderia sp. 383]
 gi|105894466|gb|ABF77631.1| DNA-directed RNA polymerase subunit alpha [Burkholderia cenocepacia
           AU 1054]
 gi|115280336|gb|ABI85853.1| DNA-directed RNA polymerase subunit alpha [Burkholderia ambifaria
           AMMD]
 gi|116646487|gb|ABK07128.1| DNA-directed RNA polymerase subunit alpha [Burkholderia cenocepacia
           HI2424]
 gi|124871353|gb|EAY63069.1| DNA-directed RNA polymerase [Burkholderia cenocepacia PC184]
 gi|134137626|gb|ABO53369.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           vietnamiensis G4]
 gi|169814950|gb|ACA89533.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           cenocepacia MC0-3]
 gi|170134390|gb|EDT02723.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia ambifaria
           IOP40-10]
 gi|171096452|gb|EDT41351.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia ambifaria
           MEX-5]
 gi|171991884|gb|ACB62803.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia ambifaria
           MC40-6]
 gi|198034704|emb|CAR50571.1| DNA-directed RNA polymerase alpha chain [Burkholderia cenocepacia
           J2315]
          Length = 325

 Score =  290 bits (743), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 155/326 (47%), Positives = 212/326 (65%), Gaps = 8/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG   EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVESLG---ENHARVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVVTAGDI+  +D EV+
Sbjct: 62  VHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVTAGDIELAHDCEVI 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NP+HVI +L     + +++ + KG GYVP    R   D    IG I +DA +SP+++VSY
Sbjct: 122 NPNHVIAHLSKGGKLDVQIKIEKGRGYVPGNVRRYGEDTAKIIGRIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T G IT E+++  ++RIL DQL +F   E    E   + 
Sbjct: 182 AVESARVEQRTDLDKLVMNIETSGVITPEEAIRQSARILVDQLSVFAALE--GTETAAEA 239

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 240 PSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 299

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +++
Sbjct: 300 IKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|85060231|ref|YP_455933.1| DNA-directed RNA polymerase subunit alpha [Sodalis glossinidius
           str. 'morsitans']
 gi|119366730|sp|Q2NQP7|RPOA_SODGM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|84780751|dbj|BAE75528.1| RNA polymerase alpha chain [Sodalis glossinidius str. 'morsitans']
          Length = 329

 Score =  290 bits (743), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 221/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVQGKDDVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HV+C+L D +A + M + V +G GYVPA    H      PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVLCHLTDENAAISMRIKVQRGRGYVPASARIHSEEYERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|212634854|ref|YP_002311379.1| DNA-directed RNA polymerase subunit alpha [Shewanella piezotolerans
           WP3]
 gi|212556338|gb|ACJ28792.1| DNA-directed RNA polymerase [Shewanella piezotolerans WP3]
          Length = 329

 Score =  290 bits (742), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 152/332 (45%), Positives = 220/332 (66%), Gaps = 11/332 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVNPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVVIEGKDEAMLTLSKSGAGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-HHRTEND--PIGLITIDALYS 178
             D+ V+NPDHVIC+L  +  V M + V +G GYVPA    +TE+D  PIG + +D+ +S
Sbjct: 118 DGDVTVMNPDHVICHLTGNNEVSMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+      
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFVEL---- 233

Query: 239 KEVKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++V E   V+  P F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 234 RDVTEAAPVEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            G+KSL EIK VL + GL LGM L +WPP S+
Sbjct: 294 LGKKSLTEIKDVLASRGLSLGMRLENWPPASL 325


>gi|254253494|ref|ZP_04946812.1| DNA-directed RNA polymerase [Burkholderia dolosa AUO158]
 gi|124896103|gb|EAY69983.1| DNA-directed RNA polymerase [Burkholderia dolosa AUO158]
 gi|325529704|gb|EGD06567.1| DNA-directed RNA polymerase subunit alpha [Burkholderia sp. TJI49]
          Length = 325

 Score =  290 bits (742), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 155/326 (47%), Positives = 212/326 (65%), Gaps = 8/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG   EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVESLG---ENHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVVTAGDI+  +D EV+
Sbjct: 62  VHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVTAGDIELAHDCEVI 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NP+HVI +L     + +++ + KG GYVP    R   D    IG I +DA +SP+++VSY
Sbjct: 122 NPNHVIAHLSKGGKLDVQIKIEKGRGYVPGNVRRYGEDTAKIIGRIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T G IT E+++  ++RIL DQL +F   E    E   + 
Sbjct: 182 AVESARVEQRTDLDKLVMNIETSGVITPEEAIRQSARILVDQLSVFAALE--GTETAAEA 239

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 240 PSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 299

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +++
Sbjct: 300 IKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|290477168|ref|YP_003470083.1| RNA polymerase subunit alpha [Xenorhabdus bovienii SS-2004]
 gi|289176516|emb|CBJ83325.1| RNA polymerase, alpha subunit [Xenorhabdus bovienii SS-2004]
          Length = 329

 Score =  290 bits (742), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 153/333 (45%), Positives = 221/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVQGKDEVILTLNKSGIGPVTAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D  A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDGSASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|309785617|ref|ZP_07680248.1| DNA-directed RNA polymerase, alpha subunit [Shigella dysenteriae
           1617]
 gi|308926737|gb|EFP72213.1| DNA-directed RNA polymerase, alpha subunit [Shigella dysenteriae
           1617]
          Length = 304

 Score =  290 bits (742), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 147/305 (48%), Positives = 211/305 (69%), Gaps = 9/305 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           M  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+
Sbjct: 1   MTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELT 148
           KG+ +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + 
Sbjct: 61  KGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIK 120

Query: 149 VSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           V +G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + +
Sbjct: 121 VRRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEM 180

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELE 264
           +T+G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LE
Sbjct: 181 ETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLE 236

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +W
Sbjct: 237 LTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENW 296

Query: 325 PPESI 329
           PP SI
Sbjct: 297 PPASI 301


>gi|114561361|ref|YP_748874.1| DNA-directed RNA polymerase subunit alpha [Shewanella frigidimarina
           NCIMB 400]
 gi|119366726|sp|Q089M9|RPOA_SHEFN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|114332654|gb|ABI70036.1| DNA-directed RNA polymerase, alpha subunit [Shewanella
           frigidimarina NCIMB 400]
          Length = 329

 Score =  290 bits (742), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 151/332 (45%), Positives = 220/332 (66%), Gaps = 11/332 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVNSTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVTIEGKDEALLTLSKSGTGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-HHRTEND--PIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  + M + V +G GYVPA    +TE+D  PIG + +DA +S
Sbjct: 118 DGDVTIVNPDHVICHLTGNNDISMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+      
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFVEL---- 233

Query: 239 KEVKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++V E   V+  P F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 234 RDVTEQAVVEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            G+KSL EIK VL + GL LGM L +WPP S+
Sbjct: 294 LGKKSLTEIKDVLASRGLSLGMRLENWPPASL 325


>gi|289669368|ref|ZP_06490443.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas campestris
           pv. musacearum NCPPB4381]
          Length = 332

 Score =  290 bits (742), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 145/311 (46%), Positives = 215/311 (69%), Gaps = 8/311 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR  ++ EPL RG+ HTLGNALRRVL+SS+ G AIT V+IDGVLHE ++++G+ ED+ D
Sbjct: 21  DNRAKVVIEPLKRGYGHTLGNALRRVLLSSIPGFAITEVEIDGVLHEYTTVEGLQEDVLD 80

Query: 85  IILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           ++LN+K + ++M SGDS   +++ K+GPG VTA DI+T +++E++N DHVIC+L  D  +
Sbjct: 81  VLLNLKDVAIRMHSGDSAT-LSLSKQGPGTVTAADIRTDHNVEIINGDHVICHLTKDTAL 139

Query: 144 RMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
            M L + +G GY PA   R    E   IG + +DA +SP+++V+Y VE+AR  Q  D DK
Sbjct: 140 NMRLKIERGFGYQPAAARRRPDEETRTIGRLMLDASFSPVRRVAYAVEAARVEQRTDLDK 199

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + I+T+G+I  E++V  A+ IL DQL +F +F    +   +     +   +P LL+ +
Sbjct: 200 LVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKP---AASGVDPVLLRPI 256

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           ++LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KSL EIK VL   GL LGM 
Sbjct: 257 DDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSLTEIKEVLAQRGLALGMK 316

Query: 321 LPDWPPESIEE 331
           L +WPP  + +
Sbjct: 317 LENWPPAGVAQ 327


>gi|226329506|ref|ZP_03805024.1| hypothetical protein PROPEN_03415 [Proteus penneri ATCC 35198]
 gi|225202692|gb|EEG85046.1| hypothetical protein PROPEN_03415 [Proteus penneri ATCC 35198]
          Length = 329

 Score =  290 bits (742), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 153/333 (45%), Positives = 221/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVHGKDEVILTLSKSGIGPVIAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASINMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+S+  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEESIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|268593566|ref|ZP_06127787.1| DNA-directed RNA polymerase, alpha subunit [Providencia rettgeri
           DSM 1131]
 gi|291310843|gb|EFE51296.1| DNA-directed RNA polymerase, alpha subunit [Providencia rettgeri
           DSM 1131]
          Length = 329

 Score =  290 bits (742), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 221/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVQGKDEVILTLNKSGIGPVTAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P H+IC+L D  A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHIICHLTDESASINMRIKVQRGRGYVPASARVHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|21230388|ref|NP_636305.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas campestris
           pv. campestris str. ATCC 33913]
 gi|21241761|ref|NP_641343.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas axonopodis
           pv. citri str. 306]
 gi|58583181|ref|YP_202197.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas oryzae pv.
           oryzae KACC10331]
 gi|66769618|ref|YP_244380.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas campestris
           pv. campestris str. 8004]
 gi|78046579|ref|YP_362754.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas campestris
           pv. vesicatoria str. 85-10]
 gi|84625020|ref|YP_452392.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas oryzae pv.
           oryzae MAFF 311018]
 gi|166710857|ref|ZP_02242064.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas oryzae pv.
           oryzicola BLS256]
 gi|188575514|ref|YP_001912443.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas oryzae pv.
           oryzae PXO99A]
 gi|188992830|ref|YP_001904840.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas campestris
           pv. campestris str. B100]
 gi|289665161|ref|ZP_06486742.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas campestris
           pv. vasculorum NCPPB702]
 gi|294627862|ref|ZP_06706441.1| DNA-directed RNA polymerase alpha subunit [Xanthomonas fuscans
           subsp. aurantifolii str. ICPB 11122]
 gi|294664167|ref|ZP_06729553.1| DNA-directed RNA polymerase alpha subunit [Xanthomonas fuscans
           subsp. aurantifolii str. ICPB 10535]
 gi|325916511|ref|ZP_08178780.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas vesicatoria
           ATCC 35937]
 gi|325921505|ref|ZP_08183360.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas gardneri
           ATCC 19865]
 gi|325925363|ref|ZP_08186765.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas perforans
           91-118]
 gi|59800197|sp|P0A0Y1|RPOA_XANCP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|59800198|sp|P0A0Y2|RPOA_XANAC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|75434358|sp|Q5GWV9|RPOA_XANOR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|81304427|sp|Q4URG3|RPOA_XANC8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|90110876|sp|Q3BWV9|RPOA_XANC5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366750|sp|Q2P009|RPOA_XANOM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|229564281|sp|B0RU58|RPOA_XANCB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238689542|sp|B2SQT4|RPOA_XANOP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|7709421|gb|AAD00325.2| RNA polymerase ALPHA subunit [Xanthomonas campestris pv.
           campestris]
 gi|21107133|gb|AAM35879.1| RNA polymerase alpha subunit [Xanthomonas axonopodis pv. citri str.
           306]
 gi|21111945|gb|AAM40229.1| RNA polymerase alpha subunit [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|58427775|gb|AAW76812.1| RNA polymerase alpha subunit [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|66574950|gb|AAY50360.1| RNA polymerase alpha subunit [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|78035009|emb|CAJ22654.1| DNA directed RNA polymerase (alpha subunit) [Xanthomonas campestris
           pv. vesicatoria str. 85-10]
 gi|84368960|dbj|BAE70118.1| RNA polymerase alpha subunit [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|167734590|emb|CAP52800.1| DNA directed RNA polymerase (alpha subunit) [Xanthomonas campestris
           pv. campestris]
 gi|188519966|gb|ACD57911.1| DNA-directed RNA polymerase, alpha subunit [Xanthomonas oryzae pv.
           oryzae PXO99A]
 gi|292597776|gb|EFF41934.1| DNA-directed RNA polymerase alpha subunit [Xanthomonas fuscans
           subsp. aurantifolii str. ICPB 11122]
 gi|292606070|gb|EFF49335.1| DNA-directed RNA polymerase alpha subunit [Xanthomonas fuscans
           subsp. aurantifolii str. ICPB 10535]
 gi|325537300|gb|EGD09027.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas vesicatoria
           ATCC 35937]
 gi|325544241|gb|EGD15622.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas perforans
           91-118]
 gi|325548052|gb|EGD19051.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas gardneri
           ATCC 19865]
          Length = 332

 Score =  290 bits (742), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 145/311 (46%), Positives = 215/311 (69%), Gaps = 8/311 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR  ++ EPL RG+ HTLGNALRRVL+SS+ G AIT V+IDGVLHE ++++G+ ED+ D
Sbjct: 21  DNRAKVVIEPLERGYGHTLGNALRRVLLSSIPGFAITEVEIDGVLHEYTTVEGLQEDVLD 80

Query: 85  IILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           ++LN+K + ++M SGDS   +++ K+GPG VTA DI+T +++E++N DHVIC+L  D  +
Sbjct: 81  VLLNLKDVAIRMHSGDSAT-LSLSKQGPGTVTAADIRTDHNVEIINGDHVICHLTKDTAL 139

Query: 144 RMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
            M L + +G GY PA   R    E   IG + +DA +SP+++V+Y VE+AR  Q  D DK
Sbjct: 140 NMRLKIERGFGYQPAAARRRPDEETRTIGRLMLDASFSPVRRVAYAVEAARVEQRTDLDK 199

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + I+T+G+I  E++V  A+ IL DQL +F +F    +   +     +   +P LL+ +
Sbjct: 200 LVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKP---AASGVDPVLLRPI 256

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           ++LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KSL EIK VL   GL LGM 
Sbjct: 257 DDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSLTEIKEVLAQRGLALGMK 316

Query: 321 LPDWPPESIEE 331
           L +WPP  + +
Sbjct: 317 LENWPPAGVAQ 327


>gi|37528519|ref|NP_931864.1| DNA-directed RNA polymerase subunit alpha [Photorhabdus luminescens
           subsp. laumondii TTO1]
 gi|253991664|ref|YP_003043020.1| DNA-directed RNA polymerase subunit alpha [Photorhabdus asymbiotica
           subsp. asymbiotica ATCC 43949]
 gi|41688627|sp|Q7MYH5|RPOA_PHOLL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|36787957|emb|CAE17074.1| RNA polymerase alpha subunit [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|253783114|emb|CAQ86279.1| DNA-directed RNA polymerase alpha chain [Photorhabdus asymbiotica]
          Length = 329

 Score =  290 bits (742), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 221/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D  A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDETASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|71276504|ref|ZP_00652779.1| DNA-directed RNA polymerase [Xylella fastidiosa Dixon]
 gi|71900585|ref|ZP_00682712.1| DNA-directed RNA polymerase [Xylella fastidiosa Ann-1]
 gi|170729724|ref|YP_001775157.1| DNA-directed RNA polymerase subunit alpha [Xylella fastidiosa M12]
 gi|238687957|sp|B0U5M3|RPOA_XYLFM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|71162681|gb|EAO12408.1| DNA-directed RNA polymerase [Xylella fastidiosa Dixon]
 gi|71729642|gb|EAO31746.1| DNA-directed RNA polymerase [Xylella fastidiosa Ann-1]
 gi|167964517|gb|ACA11527.1| DNA-directed RNA polymerase [Xylella fastidiosa M12]
          Length = 332

 Score =  290 bits (742), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 143/310 (46%), Positives = 215/310 (69%), Gaps = 6/310 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ENR  ++ EPL RG+AHTLGNALRRVL+SS+ G+AIT V+IDGVLHE ++++G+ ED+ +
Sbjct: 21  ENRAKVVLEPLGRGYAHTLGNALRRVLLSSIPGSAITQVEIDGVLHEYTTVEGLQEDVLE 80

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           ++LN+K + +++       +++FK+G GVVTA DI+T +++E++N  HVIC+L  D  + 
Sbjct: 81  VLLNLKDVAIRIHSGDTATLSLFKQGAGVVTAADIKTDHNVEIINDGHVICHLTKDTTIN 140

Query: 145 MELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           M L V +G GY PA   R    EN  IG + +DA +SP+++V+Y VE+AR  Q  D DKL
Sbjct: 141 MRLKVERGFGYQPAVVRRRPDDENRTIGRLILDASFSPVRRVAYVVEAARVEQRTDLDKL 200

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + I+T+G+I  E+++  A+ IL DQL +F +F    +     +   S   +P LL+ ++
Sbjct: 201 IIDIETNGTIDAEEALRTAADILTDQLSVFGDFTHRDRGT---VKPASSGVDPVLLRPID 257

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KSL EIK VLG  GL LG+ L
Sbjct: 258 DLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSLTEIKEVLGQRGLGLGVKL 317

Query: 322 PDWPPESIEE 331
            +WPP  + +
Sbjct: 318 ENWPPPGVSQ 327


>gi|238763709|ref|ZP_04624668.1| DNA-directed RNA polymerase subunit alpha [Yersinia kristensenii
           ATCC 33638]
 gi|238698011|gb|EEP90769.1| DNA-directed RNA polymerase subunit alpha [Yersinia kristensenii
           ATCC 33638]
          Length = 330

 Score =  290 bits (741), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 152/333 (45%), Positives = 221/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFVPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|71279611|ref|YP_267376.1| DNA-directed RNA polymerase subunit alpha [Colwellia
           psychrerythraea 34H]
 gi|90110833|sp|Q488Y8|RPOA_COLP3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|71145351|gb|AAZ25824.1| DNA-directed RNA polymerase, alpha subunit [Colwellia
           psychrerythraea 34H]
          Length = 329

 Score =  290 bits (741), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 151/332 (45%), Positives = 216/332 (65%), Gaps = 11/332 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E ++P  +    +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLRPRLVGIETVSPRRAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G +   +T+ K G G VTA DIQ 
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDIIEILLNLKGLAVILEGKNEAVLTVTKSGEGPVTAADIQH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYS 178
             D+ + NPDHVIC L  +  + M + V  G GYVPA   R    E+  IG + +DA +S
Sbjct: 118 DGDVTIANPDHVICTLTGEGSISMRIKVEMGRGYVPASARRDAEEEDRAIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y V+SAR  Q  D DKL + ++T+G++  E+++  AS IL +QL  F+      
Sbjct: 178 PVVRIAYDVDSARVEQRTDLDKLVLDMETNGTLDPEEAIRRASTILAEQLDAFVEL---- 233

Query: 239 KEVKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +++KE   V+  P F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QR E ++L+  N
Sbjct: 234 RDIKEVEQVEEKPLFDPILLRPVDDLELTVRSANCLKAEAIQYIGDLVQRAEVELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            G+KSL EIK VL + GL LGM L +WPPESI
Sbjct: 294 LGKKSLTEIKDVLASRGLSLGMRLENWPPESI 325


>gi|312968380|ref|ZP_07782590.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           2362-75]
 gi|312287205|gb|EFR15115.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           2362-75]
 gi|327250943|gb|EGE62636.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           STEC_7v]
 gi|332090427|gb|EGI95525.1| DNA-directed RNA polymerase, alpha subunit [Shigella boydii
           3594-74]
          Length = 325

 Score =  290 bits (741), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 151/327 (46%), Positives = 219/327 (66%), Gaps = 12/327 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T V+IDG
Sbjct: 3   EFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDG 59

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI    D+E+
Sbjct: 60  VLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEI 119

Query: 128 LNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
           + P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP++++
Sbjct: 120 VKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERI 179

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK-EVK 242
           +Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++ EVK
Sbjct: 180 AYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVK 239

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           E+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KS
Sbjct: 240 EE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKS 295

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESI 329
           L EIK VL + GL LGM L +WPP SI
Sbjct: 296 LTEIKDVLASRGLSLGMRLENWPPASI 322


>gi|167626015|ref|YP_001676309.1| DNA-directed RNA polymerase subunit alpha [Shewanella halifaxensis
           HAW-EB4]
 gi|167356037|gb|ABZ78650.1| DNA-directed RNA polymerase, alpha subunit [Shewanella halifaxensis
           HAW-EB4]
          Length = 329

 Score =  290 bits (741), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 151/332 (45%), Positives = 220/332 (66%), Gaps = 11/332 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVNPTRARVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVVIEGKDEAMLTLSKSGAGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-HHRTEND--PIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  V M + V +G GYVPA    +TE+D  PIG + +D+ +S
Sbjct: 118 DGDVTIMNPDHVICHLTGNNDVSMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+      
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFVEL---- 233

Query: 239 KEVKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++V E   V+  P F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 234 RDVTETAPVEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            G+KSL EIK VL + GL LGM L +WPP S+
Sbjct: 294 LGKKSLTEIKDVLASRGLSLGMRLENWPPASL 325


>gi|83720584|ref|YP_443546.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           thailandensis E264]
 gi|167564390|ref|ZP_02357306.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           oklahomensis EO147]
 gi|167571537|ref|ZP_02364411.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           oklahomensis C6786]
 gi|167582597|ref|ZP_02375471.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           thailandensis TXDOH]
 gi|167620711|ref|ZP_02389342.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           thailandensis Bt4]
 gi|167838186|ref|ZP_02465045.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           thailandensis MSMB43]
 gi|257137668|ref|ZP_05585930.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           thailandensis E264]
 gi|119366670|sp|Q2SU53|RPOA_BURTA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|83654409|gb|ABC38472.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           thailandensis E264]
          Length = 325

 Score =  290 bits (741), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 155/326 (47%), Positives = 213/326 (65%), Gaps = 8/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG   EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVESLG---ENHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVVTAGDI+  +D EV+
Sbjct: 62  VHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVTAGDIELAHDCEVI 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NP+HVI +L     + +++ V KG GYVP    R  ++    IG I +DA +SP+++VSY
Sbjct: 122 NPNHVIAHLSKGGKLDVQIKVEKGRGYVPGNVRRYGDETAKIIGRIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T G IT E+++  ++RIL DQL +F   E    E   + 
Sbjct: 182 AVESARVEQRTDLDKLVMNIETSGVITPEEAIRQSARILVDQLSVFAALE--GTETAAEA 239

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 240 PSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 299

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +++
Sbjct: 300 IKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|157960038|ref|YP_001500072.1| DNA-directed RNA polymerase subunit alpha [Shewanella pealeana ATCC
           700345]
 gi|157845038|gb|ABV85537.1| DNA-directed RNA polymerase, alpha subunit [Shewanella pealeana
           ATCC 700345]
          Length = 329

 Score =  290 bits (741), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 151/332 (45%), Positives = 220/332 (66%), Gaps = 11/332 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVNPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVVIEGKDEAMLTLSKSGAGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-HHRTEND--PIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  V M + V +G GYVPA    +TE+D  PIG + +D+ +S
Sbjct: 118 DGDVTIMNPDHVICHLTGNNEVSMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+      
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFVEL---- 233

Query: 239 KEVKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++V E   V+  P F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 234 RDVTETAPVEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            G+KSL EIK VL + GL LGM L +WPP S+
Sbjct: 294 LGKKSLTEIKDVLASRGLSLGMRLENWPPASL 325


>gi|71901056|ref|ZP_00683166.1| DNA-directed RNA polymerase [Xylella fastidiosa Ann-1]
 gi|71729183|gb|EAO31304.1| DNA-directed RNA polymerase [Xylella fastidiosa Ann-1]
          Length = 332

 Score =  290 bits (741), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 143/310 (46%), Positives = 214/310 (69%), Gaps = 6/310 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ENR  ++ EPL RG+AHTLGNALRRVL+SS+ G AIT V+IDGVLHE ++++G+ ED+ +
Sbjct: 21  ENRAKVVLEPLGRGYAHTLGNALRRVLLSSIPGFAITEVEIDGVLHEYTTVEGLQEDVLE 80

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           ++LN+K + +++       +++FK+G GVVTA DI+T +++E++N  HVIC+L  D  + 
Sbjct: 81  VLLNLKDVAIRIHSGDTATLSLFKQGAGVVTAADIKTDHNVEIINDGHVICHLTKDTTIN 140

Query: 145 MELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           M L + +G GY PA   R    EN  IG + +DA +SP+++V+Y VE+AR  Q  D DKL
Sbjct: 141 MRLKIERGFGYQPAVVRRRPDDENRTIGRLILDASFSPVRRVAYVVEAARVEQRTDLDKL 200

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + I+T+G+I  E+++  A+ IL DQL +F NF    +     +   S   +P LL+ ++
Sbjct: 201 IIDIETNGTIDAEEALRTAADILTDQLSVFGNFTHRDRGT---VKPASSGVDPVLLRPID 257

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KSL EIK VLG  GL LG+ L
Sbjct: 258 DLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSLTEIKEVLGQRGLGLGVKL 317

Query: 322 PDWPPESIEE 331
            +WPP  + +
Sbjct: 318 ENWPPPGVSQ 327


>gi|7388086|sp|P74963|RPOA_SHESP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|1565189|dbj|BAA11840.1| RNA polymerase alpha subunit [Shewanella sp. DB6705]
          Length = 328

 Score =  290 bits (741), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 149/331 (45%), Positives = 219/331 (66%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E ++P  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLRPRLVD---IEQISSTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SSI+GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI  
Sbjct: 58  EVEIDGVLHEYSSIEGVQEDVLEILLNLKGLAIKLEGKDEALLTLTKSGTGPVLAGDITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
             D+E++NP+HVI NL   A + M + V+KG GYVPA      +D   PIG + +DA +S
Sbjct: 118 DGDVEIINPEHVIRNLTGQADISMRIRVAKGRGYVPASTRIQSDDEERPIGRLLVDAAFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VESAR  Q  + DKL + ++T+G++  E+++  A+ IL +QL  F++    +
Sbjct: 178 PVSRIAYNVESARVEQRTNLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDL---R 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              + +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 235 DVTEPEQKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASI 325


>gi|330827907|ref|YP_004390859.1| DNA-directed RNA polymerase subunit alpha [Aeromonas veronii B565]
 gi|328803043|gb|AEB48242.1| DNA-directed RNA polymerase subunit alpha [Aeromonas veronii B565]
          Length = 304

 Score =  290 bits (741), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 148/308 (48%), Positives = 212/308 (68%), Gaps = 15/308 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           M  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +I+LN+
Sbjct: 1   MTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEILLNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVVRMELT 148
           KGI +K+ G     +++ K G G VTAGDI   +++E++NP+HVIC+L   +A + M L 
Sbjct: 61  KGIAVKLEGKDEVTLSLTKSGTGPVTAGDITYGDEVEIVNPEHVICHLTGANAEISMRLK 120

Query: 149 VSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           V +G GYVPA    H+  E  PIG + +D+ +SPI +++Y VE+AR  Q  D DKL + +
Sbjct: 121 VQRGRGYVPASARVHNDDEERPIGRLLLDSAFSPIVRIAYNVEAARVEQRTDLDKLVIDM 180

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEE----PKKEVKEDINVKSLPFNPALLKKVE 261
           +T+G++  E+++  ++ IL +QL  F++  +     KKE K +       F+P LL+ V+
Sbjct: 181 ETNGTLDPEEAIRRSATILAEQLEAFVDLRDVSVPEKKEEKPE-------FDPILLRPVD 233

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L
Sbjct: 234 DLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRL 293

Query: 322 PDWPPESI 329
            +WPP SI
Sbjct: 294 ENWPPASI 301


>gi|237747390|ref|ZP_04577870.1| RNA polymerase [Oxalobacter formigenes HOxBLS]
 gi|229378741|gb|EEO28832.1| RNA polymerase [Oxalobacter formigenes HOxBLS]
          Length = 325

 Score =  289 bits (740), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 156/333 (46%), Positives = 218/333 (65%), Gaps = 11/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N+   +KP  I    LG     R+++  EP  RG+ HTLGNALRRVL+SS+ G A T
Sbjct: 1   MQNNF---LKPRIINVESLGG---GRSIVEMEPFERGYGHTLGNALRRVLLSSMTGYAPT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GV+HE S++ GV ED+ D++LN+KG+  K+       +T+ K GPG+VTA DI+ 
Sbjct: 55  EVTIAGVVHEYSTLDGVQEDVVDLLLNLKGVVFKLHNRDVITLTLKKSGPGIVTAADIEL 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYS 178
            +D+E++NPDHVI NL  +  + M++ V KG GYVP    R   D    IG I +DA +S
Sbjct: 115 PHDVEIINPDHVIANLADNGKLDMQIKVEKGRGYVPGNVRRLSEDANKTIGRIILDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY VESAR  Q  D DKL + I+T+G IT E+++  ++RIL DQL +F   E  +
Sbjct: 175 PVRRVSYAVESARVEQRTDLDKLIINIETNGVITAEEAIRQSARILVDQLSVFAALEGTE 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              +    V ++  +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N 
Sbjct: 235 TTSEALTQVPAV--DPILLRPVDDLELTVRSANCLKAENINYIGDLIQRSENELLKTPNL 292

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL + GL LGM L +WPP   E+
Sbjct: 293 GRKSLNEIKEVLASRGLTLGMRLDNWPPAGFEK 325


>gi|194364558|ref|YP_002027168.1| DNA-directed RNA polymerase subunit alpha [Stenotrophomonas
           maltophilia R551-3]
 gi|254523842|ref|ZP_05135897.1| DNA-directed RNA polymerase, alpha subunit [Stenotrophomonas sp.
           SKA14]
 gi|238693448|sp|B4SLH5|RPOA_STRM5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|194347362|gb|ACF50485.1| DNA-directed RNA polymerase, alpha subunit [Stenotrophomonas
           maltophilia R551-3]
 gi|219721433|gb|EED39958.1| DNA-directed RNA polymerase, alpha subunit [Stenotrophomonas sp.
           SKA14]
          Length = 332

 Score =  289 bits (740), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 146/309 (47%), Positives = 213/309 (68%), Gaps = 8/309 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           + R  ++ EPL RG+ HTLGNALRRVL+SS+ G AIT V+IDGVLHE ++++G+ ED+ +
Sbjct: 21  DTRAKVVIEPLERGYGHTLGNALRRVLLSSIPGFAITEVEIDGVLHEYTTVEGLQEDVLE 80

Query: 85  IILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           ++LN+K + ++M SGDS   +++ K+GPGVVTA DI+  +++E+LN DHVIC+L  D  V
Sbjct: 81  VLLNLKDVAIRMHSGDSAT-LSLSKQGPGVVTAADIKVDHNVEILNGDHVICHLTKDTAV 139

Query: 144 RMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
            M L + +G GY PA   R    E   IG + +DA +SP+++V+Y VE+AR  Q  D DK
Sbjct: 140 NMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLDK 199

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ +
Sbjct: 200 LVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNG---VDPVLLRPI 256

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           ++LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KSL EIK VL   GL LGM 
Sbjct: 257 DDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSLTEIKEVLAQRGLSLGMK 316

Query: 321 LPDWPPESI 329
           L +WPP  +
Sbjct: 317 LENWPPAGV 325


>gi|330815274|ref|YP_004358979.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia gladioli
           BSR3]
 gi|327367667|gb|AEA59023.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia gladioli
           BSR3]
          Length = 325

 Score =  289 bits (740), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 154/326 (47%), Positives = 212/326 (65%), Gaps = 8/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG   EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVESLG---ENHAKVVMEPFERGYGHTLGNALRRVLLSSMIGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S++ GV ED+ +++LN+KG+  K+       VT+ K G G+VTAGDI+  +D EV+
Sbjct: 62  VHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGIVTAGDIELAHDCEVI 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NPDHVI +L     + +++ + KG GYVP    R   +    IG I +DA +SP+++VSY
Sbjct: 122 NPDHVIAHLTKGGKLDVQIKIEKGRGYVPGNVRRYGEESAKIIGRIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T G IT E+++  ++RIL DQL +F   E    E   + 
Sbjct: 182 AVESARVEQRTDLDKLVMNIETSGVITPEEAIRQSARILVDQLSVFAALE--GTETAAEA 239

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 240 PSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 299

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +++
Sbjct: 300 IKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|238025958|ref|YP_002910189.1| DNA-directed RNA polymerase subunit alpha [Burkholderia glumae
           BGR1]
 gi|237875152|gb|ACR27485.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia glumae
           BGR1]
          Length = 325

 Score =  289 bits (740), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 154/326 (47%), Positives = 212/326 (65%), Gaps = 8/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG   EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVESLG---ENHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S++ GV ED+ +++LN+KG+  K+       VT+ K G G+VTAGDI+  +D EV+
Sbjct: 62  VHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGIVTAGDIELAHDCEVI 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NPDHVI +L     + +++ + KG GYVP    R   +    IG I +DA +SP+++VSY
Sbjct: 122 NPDHVIAHLTKGGKLDVQIKIEKGRGYVPGNVRRYGEETAKIIGRIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T G IT E+++  ++RIL DQL +F   E    E   + 
Sbjct: 182 AVESARVEQRTDLDKLVMNIETSGVITPEEAIRQSARILVDQLSVFAALE--GTETAAEA 239

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 240 PSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 299

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +++
Sbjct: 300 IKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|253998041|ref|YP_003050104.1| DNA-directed RNA polymerase subunit alpha [Methylovorus sp. SIP3-4]
 gi|313200106|ref|YP_004038764.1| DNA-directed RNA polymerase subunit alpha [Methylovorus sp. MP688]
 gi|253984720|gb|ACT49577.1| DNA-directed RNA polymerase, alpha subunit [Methylovorus sp.
           SIP3-4]
 gi|312439422|gb|ADQ83528.1| DNA-directed RNA polymerase, alpha subunit [Methylovorus sp. MP688]
          Length = 327

 Score =  289 bits (739), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 160/333 (48%), Positives = 217/333 (65%), Gaps = 10/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++  V+       TL   EP+ RGF +TLGNALRRVL+SS+ G AIT
Sbjct: 1   MQNSPTEYLKPRVVDVEVISPVRARVTL---EPMERGFGYTLGNALRRVLLSSIPGFAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGV+HE S++ GV ED+ DI+LN+KG+ LK++  S   +T+ K   GVVTAGD  T
Sbjct: 58  EVKIDGVVHEYSTLDGVQEDVVDILLNLKGVALKLNSKSETTLTLKKSVEGVVTAGDFDT 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY--VPAKHHRTENDPIGLITIDALYSP 179
            +D E+ NP HVI +L     + +E+ V  G GY  VPA+    E+  +G I +DA +SP
Sbjct: 118 GHDAEIANPGHVIAHLTKGGKIDLEVKVEMGRGYQPVPARQKTDEDRVLGFIMVDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I KVSY VESAR  Q  D DKL M ++T+G +  E ++  A+RIL  QL +F + E    
Sbjct: 178 INKVSYHVESARVEQRTDLDKLIMDVETNGVVEPEQAIRDAARILMGQLSVFADLEGAPT 237

Query: 240 EVKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           EV+    VK  P  +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQR E ++L+  N 
Sbjct: 238 EVE----VKHTPQVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRGENELLKAPNL 293

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL + GL LGM L +WPP  +E+
Sbjct: 294 GRKSLNEIKDVLASKGLTLGMKLENWPPVGLEK 326


>gi|50122926|ref|YP_052093.1| DNA-directed RNA polymerase subunit alpha [Pectobacterium
           atrosepticum SCRI1043]
 gi|227115247|ref|ZP_03828903.1| DNA-directed RNA polymerase subunit alpha [Pectobacterium
           carotovorum subsp. brasiliensis PBR1692]
 gi|227328924|ref|ZP_03832948.1| DNA-directed RNA polymerase subunit alpha [Pectobacterium
           carotovorum subsp. carotovorum WPP14]
 gi|253690158|ref|YP_003019348.1| DNA-directed RNA polymerase, alpha subunit [Pectobacterium
           carotovorum subsp. carotovorum PC1]
 gi|261823207|ref|YP_003261313.1| DNA-directed RNA polymerase subunit alpha [Pectobacterium wasabiae
           WPP163]
 gi|61215910|sp|Q6CZZ5|RPOA_ERWCT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|49613452|emb|CAG76903.1| DNA-directed RNA polymerase alpha chain [Pectobacterium
           atrosepticum SCRI1043]
 gi|251756736|gb|ACT14812.1| DNA-directed RNA polymerase, alpha subunit [Pectobacterium
           carotovorum subsp. carotovorum PC1]
 gi|261607220|gb|ACX89706.1| DNA-directed RNA polymerase, alpha subunit [Pectobacterium wasabiae
           WPP163]
          Length = 329

 Score =  289 bits (739), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 151/333 (45%), Positives = 222/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P H+IC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHLICHLTDENASISMRIKVQRGRGYVPASARIHTEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|194435073|ref|ZP_03067311.1| DNA-directed RNA polymerase, alpha subunit [Shigella dysenteriae
           1012]
 gi|194416680|gb|EDX32811.1| DNA-directed RNA polymerase, alpha subunit [Shigella dysenteriae
           1012]
          Length = 329

 Score =  289 bits (739), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 151/333 (45%), Positives = 221/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVI 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|291286339|ref|YP_003503155.1| DNA-directed RNA polymerase, alpha subunit [Denitrovibrio
           acetiphilus DSM 12809]
 gi|290883499|gb|ADD67199.1| DNA-directed RNA polymerase, alpha subunit [Denitrovibrio
           acetiphilus DSM 12809]
          Length = 335

 Score =  289 bits (739), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 150/326 (46%), Positives = 223/326 (68%), Gaps = 10/326 (3%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M+  N+ E+IKP  IE +  G+  +     +AEP  +GF  T+GNALRRVL++++ G A+
Sbjct: 1   MVIMNFHEIIKPRKIEAV--GEVTDRYGEYVAEPYEKGFGITIGNALRRVLLATIEGTAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
             V+IDGV +E ++++GV+ED+ DI++NIK ++LK+     +RV I K G G VTAGDI 
Sbjct: 59  VGVKIDGVSNEFATLEGVYEDVVDILMNIKMLDLKLHTHETRRVYIKKTGEGPVTAGDIT 118

Query: 121 TVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
               +E+L PD  IC + D +  + ME  V +G GYVPA+    + D I ++++DA+++P
Sbjct: 119 GDTMVEILTPDQHICTITDPNKELNMEFVVQRGIGYVPAEELEKDYDEIDMLSVDAVFTP 178

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           IKKV+Y V++AR GQ  DYD+L++ ++TDGSI  ED++  A++I++DQ+ +FINF+EP  
Sbjct: 179 IKKVNYHVDNARVGQSTDYDRLTLEVETDGSINPEDAIGFAAKIIKDQMNLFINFDEPVV 238

Query: 240 EVKEDINVKSLPFNPALL----KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           EVK+D   +    N  LL    K +EELELSVR+ NCL+  NI  + +L  +T+A+ML+ 
Sbjct: 239 EVKQD---EEENQNDQLLDLLDKSIEELELSVRAYNCLKNANIKTLAELCMKTDAEMLKT 295

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNL 321
            NFGRKSL EIK VL  +GL LGM+L
Sbjct: 296 KNFGRKSLEEIKKVLQELGLSLGMDL 321


>gi|94266328|ref|ZP_01290030.1| DNA-directed RNA polymerase, alpha subunit [delta proteobacterium
           MLMS-1]
 gi|93453082|gb|EAT03561.1| DNA-directed RNA polymerase, alpha subunit [delta proteobacterium
           MLMS-1]
          Length = 365

 Score =  289 bits (739), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 154/333 (46%), Positives = 221/333 (66%), Gaps = 9/333 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +NW +LI P ++E   + QE  +      + +PL RGFA T+GN+LRR+L+SS++G AIT
Sbjct: 33  RNWHDLIIPESLE---VDQENHSERFGKFVCQPLERGFATTIGNSLRRILLSSIQGVAIT 89

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           + +IDGVLHE+S+I GV ED T+IILN+K + L++  +  + V I K+  GV+TA DI  
Sbjct: 90  SAKIDGVLHELSTIPGVKEDATEIILNLKEVRLRLHSEKPRMVKIDKKKKGVITAADI-V 148

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            + +EV+NP+  IC +  D     EL V  G GYV A+ +++E   IG+I +DA+++PI+
Sbjct: 149 GDQVEVMNPEQHICTITGDGHFVAELEVRWGKGYVSAERNKSEEQTIGVIALDAIFTPIR 208

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK-KE 240
            V      AR GQ  DYDKL + I TDGSI  ED++A  ++IL++QL +FINF+E +   
Sbjct: 209 NVKVITSQARVGQQTDYDKLILEITTDGSIRPEDALAYGAKILKEQLQVFINFDEERVVP 268

Query: 241 VKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           VK D      P  N  L + VE+LELSVRS NCLR   I ++G+L+Q++EA+ML+  NFG
Sbjct: 269 VKSDSEPGEKPKLNENLYRSVEDLELSVRSANCLRNAEINHIGELVQKSEAEMLKTKNFG 328

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDW-PPESIEE 331
           RKSL EIK +L  M L+LGM +  W PP + E+
Sbjct: 329 RKSLNEIKQLLAEMDLYLGMKIDGWEPPPAAEQ 361


>gi|285017344|ref|YP_003375055.1| DNA-directed RNA polymerase alpha chain (RNA polymerase alpha
           subunit) protein [Xanthomonas albilineans GPE PC73]
 gi|283472562|emb|CBA15067.1| probable dna-directed rna polymerase alpha chain (rna polymerase
           alpha subunit) protein [Xanthomonas albilineans]
          Length = 332

 Score =  289 bits (739), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 142/310 (45%), Positives = 210/310 (67%), Gaps = 6/310 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR  ++ EPL RG+ HTLGNALRRVL+SS+ G AIT V+ID VLHE ++++G+ ED+ +
Sbjct: 21  DNRAKVVIEPLERGYGHTLGNALRRVLLSSIPGFAITEVEIDNVLHEYTTVEGLQEDVLE 80

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           ++LN+K + ++M       +++ K+GPG VTA DI+T +++E+LN DHVIC+L  D  + 
Sbjct: 81  VLLNLKDVAIRMHTGDSATLSLSKQGPGTVTATDIKTDHNVEILNSDHVICHLTKDTALN 140

Query: 145 MELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           M L + +G GY PA   R    E   IG + +DA +SP+++V+Y VESAR  Q  D DKL
Sbjct: 141 MRLKIERGFGYQPAAARRRPDEETRTIGRLVLDASFSPVRRVAYAVESARVEQRTDLDKL 200

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + I+T+G+I  E++V  A+ IL DQL +F +F    +     +   S   +P LL+ ++
Sbjct: 201 VLDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGA---VKPASNGVDPVLLRPID 257

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KSL EIK VL   GL LGM L
Sbjct: 258 DLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSLTEIKEVLAQRGLSLGMKL 317

Query: 322 PDWPPESIEE 331
            +WPP  + +
Sbjct: 318 ENWPPAGVAQ 327


>gi|78357274|ref|YP_388723.1| DNA-directed RNA polymerase subunit alpha [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
 gi|90110839|sp|Q30Z68|RPOA_DESDG RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|78219679|gb|ABB39028.1| DNA-directed RNA polymerase subunit alpha [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
          Length = 348

 Score =  288 bits (738), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 150/340 (44%), Positives = 219/340 (64%), Gaps = 7/340 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTL---MIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +NW EL+KP+ I        E   T+    + EPL RG+  T+GNA+RRVL++SL+GAA 
Sbjct: 13  RNWSELVKPDQISRA----SESADTMYGKFVCEPLERGYGTTIGNAMRRVLLASLQGAAF 68

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
            AV+I GV HE ++I GV ED+TDI+LN+K + L M  +  + + +     G V AGDI+
Sbjct: 69  VAVKISGVQHEFTTIPGVLEDVTDIVLNLKQVRLAMDTEEPQHLELHVNKSGEVKAGDIK 128

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               + VLN D  +  L  D  +  EL V  G GYVPA  H   +D IGLI +DA +SP+
Sbjct: 129 CNQHVMVLNADQHLMTLTEDVELTFELEVRMGKGYVPADMHEGLSDEIGLIALDASFSPV 188

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KV+YTVE AR GQ+ +YDKL + + TDGSI+ ED++A +++I++DQ+ +FINF+E   E
Sbjct: 189 RKVAYTVEQARVGQMTNYDKLILEVWTDGSISPEDAIAYSAKIIKDQISVFINFDERISE 248

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            + +    +   N  L K ++ELELSVR+TNCL+  NI  +G+L+Q++E +ML+  NFGR
Sbjct: 249 QENEGRSSASDVNENLFKGIDELELSVRATNCLKSANISLVGELVQKSEGEMLKTKNFGR 308

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
           KSL EI+ VLG M L  GM +  +  +  E L +K +++ 
Sbjct: 309 KSLDEIRRVLGEMSLDFGMKVDGFEKKYQEWLKRKQQNEA 348


>gi|134096296|ref|YP_001101371.1| DNA-directed RNA polymerase subunit alpha [Herminiimonas
           arsenicoxydans]
 gi|158513574|sp|A4G9R3|RPOA_HERAR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|133740199|emb|CAL63250.1| RNA polymerase, alpha subunit [Herminiimonas arsenicoxydans]
          Length = 325

 Score =  288 bits (738), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 154/326 (47%), Positives = 211/326 (64%), Gaps = 8/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  IE  VLG        ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPRIIEVEVLGA---GHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE SS+ GV ED+ D++LN+KG+  K+       +T+ K G G V A DI+  +D+E++
Sbjct: 62  VHEYSSLDGVQEDVVDLLLNLKGVVFKLHNRDDVTLTLKKEGEGAVLASDIELPHDVELV 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSY 185
           NPDHVI +L     + M++ V KG GYVP    R   D    IG I +DA +SP+++VSY
Sbjct: 122 NPDHVIAHLTAGGKLDMQIKVEKGRGYVPGNVRRLSEDTNKTIGRIILDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL + I+T+G IT E+++  ++R+L DQL +F   E    E   D 
Sbjct: 182 AVESARVEQRTDLDKLVINIETNGVITPEEAIRQSARVLVDQLNVFAALE--GTEAPADA 239

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GRKSL E
Sbjct: 240 PSRAPAVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRSENELLKTPNLGRKSLNE 299

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +E+
Sbjct: 300 IKEVLASRGLTLGMKLENWPPAGLEK 325


>gi|190572968|ref|YP_001970813.1| DNA-directed RNA polymerase subunit alpha [Stenotrophomonas
           maltophilia K279a]
 gi|229564258|sp|B2FQK8|RPOA_STRMK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|190010890|emb|CAQ44499.1| putative DNA-directed RNA polymerase alpha chain [Stenotrophomonas
           maltophilia K279a]
          Length = 332

 Score =  288 bits (738), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 145/309 (46%), Positives = 213/309 (68%), Gaps = 8/309 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           + R  ++ EPL RG+ HTLGNALRRVL+SS+ G AIT V+IDGVLHE ++++G+ ED+ +
Sbjct: 21  DTRAKVVIEPLERGYGHTLGNALRRVLLSSIPGFAITEVEIDGVLHEYTTVEGLQEDVLE 80

Query: 85  IILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           ++LN+K + ++M SGDS   +++ K+GPGVVTA DI+  +++E+LN DHVIC+L  D  +
Sbjct: 81  VLLNLKDVAIRMHSGDSAT-LSLSKQGPGVVTAADIKVDHNVEILNGDHVICHLTKDTAI 139

Query: 144 RMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
            M L + +G GY PA   R    E   IG + +DA +SP+++V+Y VE+AR  Q  D DK
Sbjct: 140 NMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLDK 199

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ +
Sbjct: 200 LVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNG---VDPVLLRPI 256

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           ++LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KSL EIK VL   GL LGM 
Sbjct: 257 DDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSLTEIKEVLAQRGLSLGMK 316

Query: 321 LPDWPPESI 329
           L +WPP  +
Sbjct: 317 LENWPPAGV 325


>gi|149675708|dbj|BAF64734.1| DNA-directed RNA polymerase alpha subunit [Shewanella
           livingstonensis]
          Length = 329

 Score =  288 bits (738), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 150/334 (44%), Positives = 221/334 (66%), Gaps = 11/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVNSTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVTIEGKDEALLTLSKSGTGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-HHRTEND--PIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  + M + V +G GYVPA    +TE+D  PIG + +DA +S
Sbjct: 118 DGDVTIVNPDHVICHLTGNNDISMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+      
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFVEL---- 233

Query: 239 KEVKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++V E   V+  P F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 234 RDVTEQAVVEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL +IK VL + GL LGM L +WPP S+ +
Sbjct: 294 LGKKSLTDIKDVLASRGLSLGMRLENWPPASLAD 327


>gi|307823466|ref|ZP_07653695.1| DNA-directed RNA polymerase, alpha subunit [Methylobacter
           tundripaludum SV96]
 gi|307735451|gb|EFO06299.1| DNA-directed RNA polymerase, alpha subunit [Methylobacter
           tundripaludum SV96]
          Length = 337

 Score =  288 bits (738), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 145/333 (43%), Positives = 222/333 (66%), Gaps = 6/333 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +   L+KP  +E +    +  N + ++ EPL RGF H++GNALRRVL+S++ G A+T
Sbjct: 1   MQNSISGLLKPRLVEVV---SKTPNHSKIVIEPLERGFGHSIGNALRRVLLSTIPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GVLHE ++I+GV ED+ DI+LN+K + + +       +T+ K G G VTA DI  
Sbjct: 58  DVEIEGVLHEYTTIEGVQEDVIDILLNLKKLAVVLHSKDEVELTLSKHGAGCVTAADIIL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYS 178
            +D+E++NPD VI NL    V+ M++ V +G GY P    +  ++    +G + +DA YS
Sbjct: 118 PHDVEIINPDLVIANLTQVGVLNMKIRVRRGRGYEPVSVRKLNSEHSLVVGALQLDASYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI KV+Y VES R  Q  + DKL + ++T+G++  E+++ LA+ IL DQL +F++FE+  
Sbjct: 178 PIVKVAYQVESTRVEQRTNLDKLVIELETNGTVDPEETIKLAATILHDQLSVFVDFEKVN 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            ++ E+       F+P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 DQLAEEEVEVEEIFDPVLLRPVDDLELTVRSANCLKAENIFYIGDLIQRTEVELLKTPNL 297

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK +L   GL LGM L +WPPE++ +
Sbjct: 298 GKKSLTEIKDILALKGLSLGMRLENWPPENLAD 330


>gi|325981830|ref|YP_004294232.1| DNA-directed RNA polymerase, alpha subunit [Nitrosomonas sp. AL212]
 gi|325531349|gb|ADZ26070.1| DNA-directed RNA polymerase, alpha subunit [Nitrosomonas sp. AL212]
          Length = 335

 Score =  288 bits (738), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 146/312 (46%), Positives = 217/312 (69%), Gaps = 12/312 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EP  RG+ HTLGNALRR+L+SS+ G A T ++I GVLHE S++ GV ED+ DI++NI
Sbjct: 24  VVMEPFERGYGHTLGNALRRILLSSMTGYAPTEIKIAGVLHEYSALDGVQEDVVDILMNI 83

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KGI LK+  +    +++ K G G+VTA DI+  +D+E++NP+HVI +L  +  + ++L V
Sbjct: 84  KGIVLKLHNNDEVILSLKKSGKGIVTAADIELSHDVEIINPEHVIAHLTSEGKIDVQLKV 143

Query: 150 SKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            KG GY PA   ++   E + IG I +DA +SPI++VSY+VESAR  Q  D DKL + I+
Sbjct: 144 EKGRGYAPANIRKSGINEKNSIGTILLDASFSPIRRVSYSVESARVEQRTDLDKLIVDIE 203

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEE---PKKEVKEDINVKSLPFNPALLKKVEEL 263
           T+G++  E+++  A+R+L  QL +F + E    PK++       ++   +P LL+ V++L
Sbjct: 204 TNGAVEPEEAIRFAARVLVQQLSVFADLESTPLPKEK------PQAPQIDPILLRPVDDL 257

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           EL+VRS NCL+ ENI Y+GDLIQRTEA++LR  N GRKSL EIK VL +  L LGM L +
Sbjct: 258 ELTVRSANCLKVENIYYIGDLIQRTEAELLRTPNLGRKSLNEIKEVLASRELTLGMKLDN 317

Query: 324 WPPESIEELAKK 335
           WPP +++ ++K+
Sbjct: 318 WPPANLDSVSKE 329


>gi|295677906|ref|YP_003606430.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia sp.
           CCGE1002]
 gi|295437749|gb|ADG16919.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia sp.
           CCGE1002]
          Length = 325

 Score =  288 bits (737), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 154/326 (47%), Positives = 213/326 (65%), Gaps = 8/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG   E+   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVESLG---ESHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVVTAGDI+  +D EV+
Sbjct: 62  VHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVTAGDIELAHDCEVI 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NPDHVI +L     + +++ V KG GYVP    R   +    IG I +DA +SP+++VSY
Sbjct: 122 NPDHVIAHLSKGGKLDVQIKVEKGRGYVPGNVRRYGEESSKIIGRIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL DQL +F   E    E   + 
Sbjct: 182 AVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALE--GTEAAAET 239

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 240 PSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 299

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +++
Sbjct: 300 IKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|186477561|ref|YP_001859031.1| DNA-directed RNA polymerase subunit alpha [Burkholderia phymatum
           STM815]
 gi|209521360|ref|ZP_03270073.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia sp. H160]
 gi|238691303|sp|B2JI39|RPOA_BURP8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|184194020|gb|ACC71985.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia phymatum
           STM815]
 gi|209498180|gb|EDZ98322.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia sp. H160]
          Length = 325

 Score =  288 bits (737), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 154/326 (47%), Positives = 213/326 (65%), Gaps = 8/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG   E+   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVESLG---ESHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVVTAGDI+  +D EV+
Sbjct: 62  VHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVTAGDIELAHDCEVI 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NPDHVI +L     + +++ V KG GYVP    R   +    IG I +DA +SP+++VSY
Sbjct: 122 NPDHVIAHLSKGGKLDVQIKVEKGRGYVPGNVRRYGEESAKIIGRIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL DQL +F   E    E   + 
Sbjct: 182 AVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALE--GTEAAAEA 239

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 240 PSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 299

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +++
Sbjct: 300 IKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|225024813|ref|ZP_03714005.1| hypothetical protein EIKCOROL_01700 [Eikenella corrodens ATCC
           23834]
 gi|224942416|gb|EEG23625.1| hypothetical protein EIKCOROL_01700 [Eikenella corrodens ATCC
           23834]
          Length = 325

 Score =  288 bits (737), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 151/326 (46%), Positives = 213/326 (65%), Gaps = 8/326 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+   L      R  +  EP  RGF +TLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSTYEFLKPRQIDVDALSA---TRAKVFMEPFERGFGYTLGNALRRILLSSMNGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V IDG LHE S++ GV ED+ DI+LNIKG+  K+ G    +V++ K G GVVTA D++ 
Sbjct: 58  EVVIDGALHEYSTLDGVQEDVVDILLNIKGVVFKLQGRDSVQVSLNKSGSGVVTAADLEL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+EV+NP+HVIC L  +  + + +TV KG GY        ++  IG I +DA +SP+ 
Sbjct: 118 PHDVEVINPEHVICRLSDNGKIELTITVEKGRGYQTVSSRNDDHKQIGAIHLDANFSPVH 177

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EPKKE 240
           +VS+ V++AR  Q  D D L + I+T+G+I  E++V  A+RIL DQ+ +F + E  P +E
Sbjct: 178 RVSFEVQAARVEQRTDLDCLVLDIETNGAIDPEEAVRRAARILIDQMSVFADLEGTPVEE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            KE+    + P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N GR
Sbjct: 238 SKEE----APPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPNLGR 293

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPP 326
           KSL EIK VL + GL LG  L  WPP
Sbjct: 294 KSLNEIKEVLASKGLTLGSKLDVWPP 319


>gi|332086261|gb|EGI91417.1| DNA-directed RNA polymerase, alpha subunit [Shigella dysenteriae
           155-74]
          Length = 304

 Score =  288 bits (737), Expect = 8e-76,   Method: Compositional matrix adjust.
 Identities = 146/305 (47%), Positives = 210/305 (68%), Gaps = 9/305 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           M  EPL RGF HTLGNALRR+L+SS+ G A+  V+IDGVLHE S+ +GV ED+ +I+LN+
Sbjct: 1   MTLEPLERGFGHTLGNALRRILLSSMPGCAVIEVEIDGVLHEYSTKEGVQEDILEILLNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELT 148
           KG+ +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + 
Sbjct: 61  KGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIK 120

Query: 149 VSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           V +G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + +
Sbjct: 121 VQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEM 180

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELE 264
           +T+G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LE
Sbjct: 181 ETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLE 236

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +W
Sbjct: 237 LTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENW 296

Query: 325 PPESI 329
           PP SI
Sbjct: 297 PPASI 301


>gi|167587746|ref|ZP_02380134.1| DNA-directed RNA polymerase subunit alpha [Burkholderia ubonensis
           Bu]
          Length = 325

 Score =  288 bits (737), Expect = 8e-76,   Method: Compositional matrix adjust.
 Identities = 154/326 (47%), Positives = 211/326 (64%), Gaps = 8/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG   EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVESLG---ENHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVVTA DI+  +D EV+
Sbjct: 62  VHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVTAADIELAHDCEVI 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NP+HVI +L     + +++ + KG GYVP    R   D    IG I +DA +SP+++VSY
Sbjct: 122 NPNHVIAHLSKGGKLDVQIKIEKGRGYVPGNVRRYGEDTAKIIGRIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T G IT E+++  ++RIL DQL +F   E    E   + 
Sbjct: 182 AVESARVEQRTDLDKLVMNIETSGVITPEEAIRQSARILVDQLSVFAALE--GTETAAEA 239

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 240 PSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 299

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +++
Sbjct: 300 IKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|42810|emb|CAA37839.1| unnamed protein product [Escherichia coli]
          Length = 329

 Score =  288 bits (737), Expect = 8e-76,   Method: Compositional matrix adjust.
 Identities = 151/333 (45%), Positives = 221/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+A   Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAACVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|42812|emb|CAA37838.1| unnamed protein product [Escherichia coli]
          Length = 329

 Score =  288 bits (737), Expect = 8e-76,   Method: Compositional matrix adjust.
 Identities = 151/333 (45%), Positives = 221/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALR +L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRCILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|117619246|ref|YP_854867.1| DNA-directed RNA polymerase subunit alpha [Aeromonas hydrophila
           subsp. hydrophila ATCC 7966]
 gi|145300910|ref|YP_001143751.1| DNA-directed RNA polymerase subunit alpha [Aeromonas salmonicida
           subsp. salmonicida A449]
 gi|158512292|sp|A0KF45|RPOA_AERHH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158514057|sp|A4SSY1|RPOA_AERS4 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|117560653|gb|ABK37601.1| DNA-directed RNA polymerase, alpha subunit [Aeromonas hydrophila
           subsp. hydrophila ATCC 7966]
 gi|142853682|gb|ABO92003.1| DNA-directed RNA polymerase, alpha subunit [Aeromonas salmonicida
           subsp. salmonicida A449]
          Length = 329

 Score =  288 bits (737), Expect = 8e-76,   Method: Compositional matrix adjust.
 Identities = 147/305 (48%), Positives = 211/305 (69%), Gaps = 15/305 (4%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +I+LN+KGI
Sbjct: 29  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEILLNLKGI 88

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVVRMELTVSK 151
            +K+ G     +++ K G G VTAGDI   +++E++NP+HVIC+L   +A + M L V +
Sbjct: 89  AVKLEGKDEVTLSLTKSGTGPVTAGDITHGDEVEIVNPEHVICHLTGANAEISMRLKVQR 148

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H+  E  PIG + +D+ +SPI +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 149 GRGYVPASARVHNDDEERPIGRLLLDSAFSPIVRIAYNVEAARVEQRTDLDKLVIDMETN 208

Query: 209 GSITGEDSVALASRILQDQLGMFINFEE----PKKEVKEDINVKSLPFNPALLKKVEELE 264
           G++  E+++  ++ IL +QL  F++  +     KKE K +       F+P LL+ V++LE
Sbjct: 209 GTLDPEEAIRRSATILAEQLEAFVDLRDVSVPEKKEEKPE-------FDPILLRPVDDLE 261

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +W
Sbjct: 262 LTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENW 321

Query: 325 PPESI 329
           PP SI
Sbjct: 322 PPASI 326


>gi|163859245|ref|YP_001633543.1| DNA-directed RNA polymerase subunit alpha [Bordetella petrii DSM
           12804]
 gi|229564247|sp|A9IHR6|RPOA_BORPD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|163262973|emb|CAP45276.1| DNA-directed RNA polymerase alpha chain [Bordetella petrii]
          Length = 328

 Score =  288 bits (737), Expect = 9e-76,   Method: Compositional matrix adjust.
 Identities = 153/328 (46%), Positives = 209/328 (63%), Gaps = 9/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           Q  +KP +IE   +G        ++ EP  RG+ HTLGNALRR+L+SS+ G A T VQ+ 
Sbjct: 4   QGFLKPRSIEVEPVGTHHAK---IVMEPFERGYGHTLGNALRRILLSSMTGYAPTEVQMT 60

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S+I GV ED+ DI+LN+KG+  K+       + + K G G V A DI+  +D+E
Sbjct: 61  GVVHEYSTIPGVREDVVDILLNLKGVVFKLHNRDEVTLVLRKNGAGTVVASDIELPHDVE 120

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKV 183
           ++NPDH+ICNL     V M++ V KG GYVP        D    IG I +DA +SP+++V
Sbjct: 121 IINPDHLICNLTEAGKVEMQIKVEKGRGYVPGNVRALSEDRTHTIGRIVLDASFSPVRRV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VESAR  Q  D DKL + I+T+G I+ E++V  ++RIL DQ+ +F   E        
Sbjct: 181 SYAVESARVEQRTDLDKLVLDIETNGVISPEEAVRQSARILMDQISVFAALEGAGDSY-- 238

Query: 244 DINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           +  V+  P  +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKS
Sbjct: 239 EAPVRGTPQIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKS 298

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           L EIK VL   GL LGM L +WPP  +E
Sbjct: 299 LNEIKEVLAARGLTLGMKLENWPPLGLE 326


>gi|56477619|ref|YP_159208.1| DNA-directed RNA polymerase subunit alpha [Aromatoleum aromaticum
           EbN1]
 gi|81598738|sp|Q5P307|RPOA_AZOSE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|56313662|emb|CAI08307.1| DNA-directed RNA polymerase (alpha subunit) [Aromatoleum aromaticum
           EbN1]
          Length = 326

 Score =  288 bits (737), Expect = 9e-76,   Method: Compositional matrix adjust.
 Identities = 151/327 (46%), Positives = 215/327 (65%), Gaps = 8/327 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I+   +   +   T+   EP  RGF HTLGNALRR+L+SSL G A T V I+GV
Sbjct: 6   LLKPRIIDVQSVSPVQARVTM---EPFERGFGHTLGNALRRILLSSLPGYAPTEVSIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S++ GV ED+ D++LN+KG+ LK+   S   + + K G GVVTA DI+  +D+E++
Sbjct: 63  LHEYSTLDGVREDIVDLLLNLKGVVLKLHSRSEATLRLAKSGDGVVTARDIEVGHDVEII 122

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYT 186
           NPDHVI +L     + M++ V +G GYVP        D   IG + +DA +SP+++VSY 
Sbjct: 123 NPDHVIAHLAPGGKLDMQIKVEEGRGYVPGNVRPAAGDTKTIGRVVLDASFSPVRRVSYL 182

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VESAR  Q  D D+L + I+T+G++  E+++  A+R+L DQL +F + E     V++   
Sbjct: 183 VESARVEQRTDLDRLVIDIETNGAVDPEEAIRYAARVLMDQLSVFADLEGTAPVVEQS-- 240

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
             +   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL EI
Sbjct: 241 -AAQTIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTETELLKTPNLGRKSLNEI 299

Query: 307 KGVLGTMGLFLGMNLPDWPPESIEELA 333
           K VL + GL LGM L +WPP  +E+L 
Sbjct: 300 KEVLASRGLTLGMKLENWPPAGLEKLG 326


>gi|59710869|ref|YP_203645.1| DNA-directed RNA polymerase subunit alpha [Vibrio fischeri ES114]
 gi|197334008|ref|YP_002155021.1| DNA-directed RNA polymerase, alpha subunit [Vibrio fischeri MJ11]
 gi|75431853|sp|Q5E889|RPOA_VIBF1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238690301|sp|B5FGE1|RPOA_VIBFM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|59478970|gb|AAW84757.1| RNA polymerase, alpha subunit [Vibrio fischeri ES114]
 gi|197315498|gb|ACH64945.1| DNA-directed RNA polymerase, alpha subunit [Vibrio fischeri MJ11]
          Length = 329

 Score =  288 bits (737), Expect = 9e-76,   Method: Compositional matrix adjust.
 Identities = 152/334 (45%), Positives = 222/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI  
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVIITLNKSGAGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVP--AKHHRTEND-PIGLITIDALY 177
             D+E+ NP+HVIC+L D +A + M + V +G GYVP  A+ H  E++ PIG + +DA Y
Sbjct: 118 DGDVEIANPEHVICHLTDDNAEISMRIKVERGRGYVPSTARIHTEEDERPIGRLLVDATY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ K+SY VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDKISYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|33594507|ref|NP_882151.1| DNA-directed RNA polymerase subunit alpha [Bordetella pertussis
           Tohama I]
 gi|33594778|ref|NP_882421.1| DNA-directed RNA polymerase subunit alpha [Bordetella parapertussis
           12822]
 gi|33599050|ref|NP_886610.1| DNA-directed RNA polymerase subunit alpha [Bordetella
           bronchiseptica RB50]
 gi|61234210|sp|P0A4E5|RPOA_BORPE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61234215|sp|P0A4E6|RPOA_BORBR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61234219|sp|P0A4E7|RPOA_BORPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|406284|emb|CAA81390.1| RNA polymerase alpha subunit [Bordetella pertussis Tohama I]
 gi|33564583|emb|CAE43899.1| DNA-directed RNA polymerase alpha chain [Bordetella pertussis
           Tohama I]
 gi|33564854|emb|CAE39798.1| DNA-directed RNA polymerase alpha chain [Bordetella parapertussis]
 gi|33575096|emb|CAE30559.1| DNA-directed RNA polymerase alpha chain [Bordetella bronchiseptica
           RB50]
          Length = 328

 Score =  288 bits (737), Expect = 9e-76,   Method: Compositional matrix adjust.
 Identities = 153/328 (46%), Positives = 209/328 (63%), Gaps = 9/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           Q  +KP +IE   +G        ++ EP  RG+ HTLGNALRR+L+SS+ G A T VQ+ 
Sbjct: 4   QGFLKPRSIEVEPVGAHHAK---IVMEPFERGYGHTLGNALRRILLSSMTGYAPTEVQMT 60

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S+I GV ED+ DI+LN+KG+  K+       + + K G G V A DI+  +D+E
Sbjct: 61  GVVHEYSTIAGVREDVVDILLNLKGVVFKLHNRDEVTLVLRKNGAGAVVASDIELPHDVE 120

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKV 183
           ++NPDH+ICNL     + M++ V KG GYVP        D    IG I +DA +SP+++V
Sbjct: 121 IINPDHLICNLTDAGKIEMQVKVEKGRGYVPGNVRALSEDRTHTIGRIVLDASFSPVRRV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VESAR  Q  D DKL + I+T+G I+ E++V  A+RIL DQ+ +F   E      + 
Sbjct: 181 SYAVESARVEQRTDLDKLVLDIETNGVISPEEAVRQAARILMDQISVFAALEGAGDAYEP 240

Query: 244 DINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              V+  P  +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKS
Sbjct: 241 P--VRGTPQIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKS 298

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           L EIK VL   GL LGM L +WPP  +E
Sbjct: 299 LNEIKEVLAARGLTLGMKLENWPPLGLE 326


>gi|209693948|ref|YP_002261876.1| DNA-directed RNA polymerase subunit alpha [Aliivibrio salmonicida
           LFI1238]
 gi|238057754|sp|B6EPU9|RPOA_ALISL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|208007899|emb|CAQ78029.1| RNA polymerase alpha-subunit [Aliivibrio salmonicida LFI1238]
          Length = 329

 Score =  288 bits (736), Expect = 9e-76,   Method: Compositional matrix adjust.
 Identities = 153/336 (45%), Positives = 224/336 (66%), Gaps = 14/336 (4%)

Query: 2   IQKNWQELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           +Q +  E +KP   +IE + L   +     +  EPL RGF HTLGNALRR+L+SS+ G A
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSLTHAK-----VTLEPLERGFGHTLGNALRRILLSSMPGCA 55

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI
Sbjct: 56  VTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVIITLNKSGAGPVVAGDI 115

Query: 120 QTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVP--AKHHRTEND-PIGLITIDA 175
               D+E+ NP+HVIC+L D +A + M + V +G GYVP  A+ H  E++ PIG + +DA
Sbjct: 116 THDGDVEIANPEHVICHLTDDNAEISMRIKVERGRGYVPSTARIHTEEDERPIGRLLVDA 175

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
            YSP+ K+SY VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  
Sbjct: 176 TYSPVDKISYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLR 235

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+ 
Sbjct: 236 DVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKT 292

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 293 PNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|15837778|ref|NP_298466.1| DNA-directed RNA polymerase subunit alpha [Xylella fastidiosa 9a5c]
 gi|28198377|ref|NP_778691.1| DNA-directed RNA polymerase subunit alpha [Xylella fastidiosa
           Temecula1]
 gi|182681018|ref|YP_001829178.1| DNA-directed RNA polymerase subunit alpha [Xylella fastidiosa M23]
 gi|54039280|sp|P66713|RPOA_XYLFT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|54042190|sp|P66712|RPOA_XYLFA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238691090|sp|B2I8J3|RPOA_XYLF2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|9106142|gb|AAF83986.1|AE003951_11 RNA polymerase alpha subunit [Xylella fastidiosa 9a5c]
 gi|28056447|gb|AAO28340.1| RNA polymerase, alpha subunit [Xylella fastidiosa Temecula1]
 gi|182631128|gb|ACB91904.1| DNA-directed RNA polymerase, alpha subunit [Xylella fastidiosa M23]
 gi|307579487|gb|ADN63456.1| DNA-directed RNA polymerase subunit alpha [Xylella fastidiosa
           subsp. fastidiosa GB514]
          Length = 332

 Score =  288 bits (736), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 142/310 (45%), Positives = 214/310 (69%), Gaps = 6/310 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ENR  ++ EPL RG+AHTLGNALRRVL+SS+ G AIT V+IDGVLHE ++++G+ ED+ +
Sbjct: 21  ENRAKVVLEPLGRGYAHTLGNALRRVLLSSIPGFAITEVEIDGVLHEYTTVEGLQEDVLE 80

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           ++LN+K + +++       +++FK+G GVVTA DI+T +++E++N  HVIC+L  D  + 
Sbjct: 81  VLLNLKDVAIRIHSGDTATLSLFKQGAGVVTAADIKTDHNVEIINDGHVICHLTKDTTIN 140

Query: 145 MELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           M L + +G GY PA   R    EN  IG + +DA +SP+++V+Y VE+AR  Q  D DKL
Sbjct: 141 MRLKIERGFGYQPAVVRRRPDDENRTIGRLILDASFSPVRRVAYVVEAARVEQRTDLDKL 200

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + I+T+G+I  E+++  A+ IL DQL +F +F    +     +   S   +P LL+ ++
Sbjct: 201 IIDIETNGTIDAEEALRTAADILTDQLSVFGDFTHRDRGT---VKPASSGVDPVLLRPID 257

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KSL EIK VLG  GL LG+ L
Sbjct: 258 DLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSLTEIKEVLGQRGLGLGVKL 317

Query: 322 PDWPPESIEE 331
            +WPP  + +
Sbjct: 318 ENWPPPGVSQ 327


>gi|91785439|ref|YP_560645.1| DNA-directed RNA polymerase subunit alpha [Burkholderia xenovorans
           LB400]
 gi|170695707|ref|ZP_02886849.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia graminis
           C4D1M]
 gi|187925590|ref|YP_001897232.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           phytofirmans PsJN]
 gi|296163295|ref|ZP_06846056.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia sp. Ch1-1]
 gi|323527576|ref|YP_004229729.1| DNA-directed RNA polymerase subunit alpha [Burkholderia sp.
           CCGE1001]
 gi|119366671|sp|Q13TJ6|RPOA_BURXL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238689619|sp|B2T725|RPOA_BURPP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|91689393|gb|ABE32593.1| DNA-directed RNA polymerase subunit alpha [Burkholderia xenovorans
           LB400]
 gi|170139312|gb|EDT07498.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia graminis
           C4D1M]
 gi|187716784|gb|ACD18008.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           phytofirmans PsJN]
 gi|295886434|gb|EFG66291.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia sp. Ch1-1]
 gi|323384578|gb|ADX56669.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia sp.
           CCGE1001]
          Length = 325

 Score =  288 bits (736), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 154/326 (47%), Positives = 213/326 (65%), Gaps = 8/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG   E+   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVESLG---ESHAKVVMEPFERGYGHTLGNALRRVLLSSMIGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVVTAGDI+  +D EV+
Sbjct: 62  VHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVTAGDIELAHDCEVI 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NPDHVI +L     + +++ V KG GYVP    R   +    IG I +DA +SP+++VSY
Sbjct: 122 NPDHVIAHLSKGGKLDVQIKVEKGRGYVPGNVRRYGEESAKIIGRIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL DQL +F   E    E   + 
Sbjct: 182 AVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALE--GTEATAEA 239

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 240 PSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 299

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +++
Sbjct: 300 IKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|158520750|ref|YP_001528620.1| DNA-directed RNA polymerase, alpha subunit [Desulfococcus
           oleovorans Hxd3]
 gi|238686889|sp|A8ZV82|RPOA_DESOH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158509576|gb|ABW66543.1| DNA-directed RNA polymerase, alpha subunit [Desulfococcus
           oleovorans Hxd3]
          Length = 339

 Score =  288 bits (736), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 152/326 (46%), Positives = 224/326 (68%), Gaps = 8/326 (2%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           NWQE+I+P+ I+   +          I EPL RGF  T+GNALRR+++SSL GAAIT+V+
Sbjct: 9   NWQEMIQPDKIQ---VEAATPFYGKFICEPLGRGFGITIGNALRRIIISSLHGAAITSVK 65

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           ID V+HE S+++GV ED+++IILN+K + LK S  + K + I   GPGVVTAGDI + + 
Sbjct: 66  IDNVMHEYSTVEGVLEDVSEIILNLKEVRLKTSTAAAKTIRIDAAGPGVVTAGDIASPDG 125

Query: 125 -IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            +E+LNP+  I  L   A ++ME+TV  G GY  A+ ++ E  P+  I IDA++SPI++V
Sbjct: 126 RVEILNPESHIATLSEGATLKMEMTVKVGRGYALAEANKDEETPVNTIPIDAMFSPIRRV 185

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE---EPKKE 240
           +Y V ++R  Q  D+DKL++ + TDGS+  ED+VA A++I+++Q+ +FINF+   EP+  
Sbjct: 186 NYVVGNSRVKQKTDFDKLTLEVWTDGSVLPEDAVAFAAKIMKEQMNVFINFDESAEPEHA 245

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   + FN  L + V ELELSVRS+NCL+   I  +  L+Q+TE++ML+  NFGR
Sbjct: 246 GRKDDSGGKV-FNENLYRSVNELELSVRSSNCLKNAEIDKLYQLVQKTESEMLKTKNFGR 304

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPP 326
           KSL EIK +L  MGL LGM+L  + P
Sbjct: 305 KSLNEIKELLAEMGLSLGMDLEGFVP 330


>gi|90416841|ref|ZP_01224770.1| DNA-directed RNA polymerase alpha chain [marine gamma
           proteobacterium HTCC2207]
 gi|90331188|gb|EAS46432.1| DNA-directed RNA polymerase alpha chain [marine gamma
           proteobacterium HTCC2207]
          Length = 331

 Score =  287 bits (735), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 150/331 (45%), Positives = 217/331 (65%), Gaps = 8/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P NI+   +         ++ EPL RGF HTLGNALRR+L+SS+ G AI 
Sbjct: 1   MQNSANEFLTPRNID---VTSYSPTHAKVVLEPLERGFGHTLGNALRRILLSSMSGCAIV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GV HE S+I+GVHED+  I+LN+KG+ + M G     V++  +GP VVTAGDI+ 
Sbjct: 58  EVEIEGVEHEYSAIEGVHEDVMGILLNLKGVAVVMEGRDETTVSLSVKGPCVVTAGDIEV 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP--AKHHRTENDPIGLITIDALYSP 179
            + +EV+NPDHVI  +     + ++L + +G GY P  A+    +N  IG + +DA +SP
Sbjct: 118 DSHVEVINPDHVIATISDKCTLNIQLRIERGRGYQPSDARISDEDNRTIGRLQLDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I KVSY+VE+AR     D DKL + ++T+G+I  E+S+  A+ ILQ Q+ +F+N E    
Sbjct: 178 IHKVSYSVENARVENRTDLDKLVLELETNGTIDPEESIRRAATILQQQMAVFVNLE---G 234

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           E   +   K    +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N G
Sbjct: 235 ETAAEPEEKEEEIDPILLRPVDDLELTVRSANCLKAESIYYIGDLIQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           +KSL EIK VL + GL LGM L +WPP S++
Sbjct: 295 KKSLTEIKDVLASRGLSLGMRLENWPPASLK 325


>gi|89076299|ref|ZP_01162640.1| DNA-directed RNA polymerase alpha subunit [Photobacterium sp.
           SKA34]
 gi|89048003|gb|EAR53592.1| DNA-directed RNA polymerase alpha subunit [Photobacterium sp.
           SKA34]
          Length = 329

 Score =  287 bits (735), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 149/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVILTLNKSGAGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E+ NP+HVIC++ D +A + M + V +G GYVPA    H   +  PIG + +DA+Y
Sbjct: 118 DGDVEIANPEHVICHITDDNAELSMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAIY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|90414981|ref|ZP_01222943.1| DNA-directed RNA polymerase alpha subunit [Photobacterium profundum
           3TCK]
 gi|90323920|gb|EAS40520.1| DNA-directed RNA polymerase alpha subunit [Photobacterium profundum
           3TCK]
          Length = 329

 Score =  287 bits (734), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 150/334 (44%), Positives = 218/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVILTLNKSGAGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E+ NP+HVIC+L D  A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIANPEHVICHLTDDHAEISMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|227883427|ref|ZP_04001232.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli 83972]
 gi|227839571|gb|EEJ50037.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli 83972]
          Length = 329

 Score =  286 bits (733), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 151/333 (45%), Positives = 221/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L + PP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENCPPASI 326


>gi|152980446|ref|YP_001355075.1| DNA-directed RNA polymerase subunit alpha [Janthinobacterium sp.
           Marseille]
 gi|166229272|sp|A6T3H8|RPOA_JANMA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|151280523|gb|ABR88933.1| DNA-directed RNA polymerase subunit alpha [Janthinobacterium sp.
           Marseille]
          Length = 325

 Score =  286 bits (733), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 153/326 (46%), Positives = 211/326 (64%), Gaps = 8/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  IE  VLG        ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPRIIEVEVLGA---GHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE SS+ GV ED+ D++LN+KG+  K+       +T+ K G G V A DI+  +D+E++
Sbjct: 62  VHEYSSLDGVQEDVVDLLLNLKGVVFKLHNRDDVTLTLKKDGEGAVLASDIELPHDVELV 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSY 185
           NPDHVI +L     + M++ V KG GYVP    R   D    IG I +DA +SP+++VSY
Sbjct: 122 NPDHVIAHLTAGGKLDMQIKVEKGRGYVPGNVRRLSEDTNKTIGRIILDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL + I+T+G I+ E+++  ++R+L DQL +F   E    E   D 
Sbjct: 182 AVESARVEQRTDLDKLVINIETNGVISPEEAIRQSARVLVDQLNVFAALE--GTEAPADA 239

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GRKSL E
Sbjct: 240 PSRAPAVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRSENELLKTPNLGRKSLNE 299

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +E+
Sbjct: 300 IKEVLASRGLTLGMKLENWPPAGLEK 325


>gi|307731229|ref|YP_003908453.1| DNA-directed RNA polymerase subunit alpha [Burkholderia sp.
           CCGE1003]
 gi|307585764|gb|ADN59162.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia sp.
           CCGE1003]
          Length = 325

 Score =  286 bits (733), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 153/326 (46%), Positives = 213/326 (65%), Gaps = 8/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG   E+   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVESLG---ESHAKVVMEPFERGYGHTLGNALRRVLLSSMIGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVVTAG+I+  +D EV+
Sbjct: 62  VHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVTAGEIELAHDCEVI 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NPDHVI +L     + +++ V KG GYVP    R   +    IG I +DA +SP+++VSY
Sbjct: 122 NPDHVIAHLSKGGKLDVQIKVEKGRGYVPGNVRRYGEESAKIIGRIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL DQL +F   E    E   + 
Sbjct: 182 AVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALE--GTEATAEA 239

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 240 PSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 299

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +++
Sbjct: 300 IKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|226942803|ref|YP_002797876.1| DNA-directed RNA polymerase subunit alpha [Azotobacter vinelandii
           DJ]
 gi|226717730|gb|ACO76901.1| DNA-directed RNA polymerase, alpha subunit [Azotobacter vinelandii
           DJ]
          Length = 333

 Score =  286 bits (732), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 147/336 (43%), Positives = 222/336 (66%), Gaps = 15/336 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQSSVNEFLTPRHIDVQAVSPTRAKITL---EPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +++ K+G G VTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLSLSKKGSGAVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++N  HVI NL  +  + M+L V++G GY PA   +++ D    IG + +DA +S
Sbjct: 118 DHDVEIVNGGHVIANLADNGALNMKLKVARGRGYEPADARQSDEDESRSIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++V+Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRVAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDT 237

Query: 239 KEV---KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
             V   +ED        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+ 
Sbjct: 238 APVVVEQED------EIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKT 291

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL + GL LGM L +WPP S+++
Sbjct: 292 PNLGKKSLTEIKDVLASRGLSLGMRLDNWPPASLKK 327


>gi|90581703|ref|ZP_01237491.1| DNA-directed RNA polymerase alpha subunit [Vibrio angustum S14]
 gi|330447012|ref|ZP_08310662.1| DNA-directed RNA polymerase, alpha subunit [Photobacterium
           leiognathi subsp. mandapamensis svers.1.1.]
 gi|90437118|gb|EAS62321.1| DNA-directed RNA polymerase alpha subunit [Vibrio angustum S14]
 gi|328491203|dbj|GAA05159.1| DNA-directed RNA polymerase, alpha subunit [Photobacterium
           leiognathi subsp. mandapamensis svers.1.1.]
          Length = 329

 Score =  286 bits (732), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 149/334 (44%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVILTLNKSGAGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E+ NP+HVIC++ D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIANPEHVICHITDDNAELSMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|300309482|ref|YP_003773574.1| DNA-directed RNA polymerase subunit alpha [Herbaspirillum
           seropedicae SmR1]
 gi|124483590|emb|CAM32668.1| probable DNA-directed RNA polymerase (alpha chain) protein
           [Herbaspirillum seropedicae]
 gi|300072267|gb|ADJ61666.1| DNA-directed RNA polymerase alpha chain protein [Herbaspirillum
           seropedicae SmR1]
          Length = 325

 Score =  286 bits (732), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 153/326 (46%), Positives = 208/326 (63%), Gaps = 8/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  IE   L         ++ EP  RG+ HTLGNALRRVL+S++ G A T V I GV
Sbjct: 5   LLKPRIIEVETLAP---GHAKVVMEPFERGYGHTLGNALRRVLLSTMSGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE SS+ GV ED+ DI+LN+KG+  K+       +T+ K G G V A DI   +D+E++
Sbjct: 62  VHEYSSLDGVQEDVVDILLNLKGVVFKLHNRDEVTLTLKKEGEGAVLASDIDLPHDVELI 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSY 185
           NPDHVI NL     + M++ V KG GYVP    R   D    IG I +DA +SP+++VSY
Sbjct: 122 NPDHVIANLTGGGKLDMQIKVEKGRGYVPGNVRRLSEDTNKTIGRIILDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T+G IT E+++  ++R+L DQL +F   E    E   + 
Sbjct: 182 AVESARVEQRTDLDKLVMNIETNGVITPEEAIRQSARVLVDQLNVFAALE--GTEATAEA 239

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GRKSL E
Sbjct: 240 PSRAPQVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRSENELLKTPNLGRKSLNE 299

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +E+
Sbjct: 300 IKEVLASRGLTLGMKLENWPPAGLEK 325


>gi|295698626|ref|YP_003603281.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Riesia
           pediculicola USDA]
 gi|291157272|gb|ADD79717.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Riesia
           pediculicola USDA]
          Length = 344

 Score =  286 bits (732), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 147/328 (44%), Positives = 223/328 (67%), Gaps = 11/328 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E IKP   +   + + +   TL   EPL RGF HT+GNALRR+L+SS+ G A+T V+IDG
Sbjct: 22  EFIKPKLADIQKISKTQARITL---EPLERGFGHTIGNALRRILLSSMPGFAVTEVEIDG 78

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           +LHE S+  GV ED+ +I+LN+K + +++ G     +++ K+G   VTA DI+   ++E+
Sbjct: 79  ILHEYSTKDGVQEDIVEILLNLKELGVRIYGKEEIVLSLVKKGICTVTAQDIERNENVEI 138

Query: 128 LNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVS 184
           +NP+HVIC++ D + V++M + ++KG GYVP     +E  N  IG + +DA YSP+++VS
Sbjct: 139 INPEHVICHITDENTVIKMRIKINKGRGYVPVSSRSSEEQNRSIGRLLVDACYSPVERVS 198

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EPKKEVKE 243
           Y VE+ R  Q  D DKL + I+T+G+I  ++++  ++ IL +QL  F+  + E KKEV+E
Sbjct: 199 YKVEATRVEQRTDLDKLIIEIETNGTIDPKEAIHKSATILANQLESFVELQNEDKKEVQE 258

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           D       F+P LLK V++LEL+VRS NCL+ E+I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 259 D----HPKFDPMLLKTVDDLELTVRSANCLKTESIHYIGDLVQRTEVELLKTPNLGKKSL 314

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +EIK +L + GL LGM L +WPP   +E
Sbjct: 315 MEIKDILASRGLSLGMKLENWPPSKKDE 342


>gi|330722390|gb|EGH00238.1| DNA-directed RNA polymerase alpha subunit [gamma proteobacterium
           IMCC2047]
          Length = 335

 Score =  286 bits (732), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 151/325 (46%), Positives = 209/325 (64%), Gaps = 8/325 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E + P +I+   +G    N   ++ EP  RGF HTLGN+LRR+L+SS+ GAAI  V IDG
Sbjct: 7   EFLTPKHIQVEEVGV---NHAKVVLEPFERGFGHTLGNSLRRILLSSMPGAAIVEVSIDG 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE S+I+GV ED+ DI+LN+KG+ + M+G     +T+ K   G V AGDIQ  +DIE+
Sbjct: 64  VQHEYSAIEGVQEDVIDILLNLKGVAVAMNGRDEATLTLNKTEAGPVLAGDIQLDHDIEI 123

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
            NP+HVI NL+    + M + VS G GY  A+      E   IG + +DA YSP+ +V+Y
Sbjct: 124 ANPEHVIANLNAKGKLNMSIKVSSGRGYESAESRDLDGETRSIGTLQLDATYSPVTRVAY 183

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL + I+++G+I  E+ +  A+ ILQ QL  F++ E  K+  +   
Sbjct: 184 VVESARVEQRTDLDKLVLDIESNGTIDPEECIRRAATILQQQLTAFVDLEADKEPEQ--- 240

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                  +P LL+ V++LEL+VRS NCL+ EN+ Y+GDLIQRTE D+L+  N G+KSL E
Sbjct: 241 QEDEDEVDPILLRPVDDLELTVRSANCLKAENLYYIGDLIQRTEVDLLKTPNLGKKSLTE 300

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIE 330
           IK VL + GL LGM L  WPP S++
Sbjct: 301 IKDVLASKGLSLGMRLEKWPPASLK 325


>gi|145588267|ref|YP_001154864.1| DNA-directed RNA polymerase subunit alpha [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
 gi|189043841|sp|A4SUY6|RPOA_POLSQ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|145046673|gb|ABP33300.1| DNA-directed RNA polymerase subunit alpha [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
          Length = 326

 Score =  286 bits (731), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 156/328 (47%), Positives = 213/328 (64%), Gaps = 11/328 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    L     N+  ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIISVEAL---TANQAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVAIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S++ GV ED+ +++LN+KGI  K+       + + K GPGVVTA DI   +D+E++
Sbjct: 62  VHEYSTLDGVQEDVVNLLLNLKGIVFKLQSRDEVTINLRKEGPGVVTAKDIDLPHDVEIM 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP----IGLITIDALYSPIKKVS 184
           NPDHVI +L     + M++ V KG GYVP  + R  ND     IG I +DA +SP+ +VS
Sbjct: 122 NPDHVIAHLSAGGKLDMQIKVEKGRGYVPG-NVRQYNDETTKIIGRIVLDASFSPVSRVS 180

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VESAR  Q  D D+L MTI+T+G ++ E+++  A+ IL DQL +F   E    EV  D
Sbjct: 181 YAVESARVEQRTDLDRLVMTIETNGVLSPEEAIRQAASILVDQLVVFAALE--SSEVSGD 238

Query: 245 IN-VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +S   +P L++ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 239 LAPSRSSMVDPMLMRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 298

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL   GL LGM L  WPP ++E+
Sbjct: 299 NEIKDVLAARGLSLGMKLESWPPANLEK 326


>gi|319778699|ref|YP_004129612.1| DNA-directed RNA polymerase alpha subunit [Taylorella equigenitalis
           MCE9]
 gi|317108723|gb|ADU91469.1| DNA-directed RNA polymerase alpha subunit [Taylorella equigenitalis
           MCE9]
          Length = 327

 Score =  285 bits (730), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 153/328 (46%), Positives = 210/328 (64%), Gaps = 17/328 (5%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           +  +KP  I   V+    E    ++ EP  RGF HTLGNALRR+L+SS+ G A T VQI 
Sbjct: 3   EAFLKPRTI---VVNPITEFHAKVVMEPFERGFGHTLGNALRRILLSSMTGYAATEVQIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE +SI+GV ED+ DI+LN+KG+  K+ G     +T+ K  PG + A DI+  +D+E
Sbjct: 60  GVVHEYASIQGVQEDVVDILLNLKGVVFKLHGREEVTLTLSKSEPGEIRASDIELPHDVE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--------KHHRTENDPIGLITIDALYS 178
           ++NP+HVI NL     + M + V +G GYVP         +HH      IG I +DA YS
Sbjct: 120 IINPNHVIANLQEGGRLDMHIKVEQGRGYVPGNVRALREDRHHS-----IGRIILDASYS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI++VSY VE+AR GQ  D DKL + I+T+G +T ED+V  A+RIL DQ+ +F + E   
Sbjct: 175 PIRRVSYEVENARVGQRTDQDKLILDIETNGVLTPEDAVRQAARILMDQISVFASLEG-S 233

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
             + E     +   +P LL+ V++LEL+VRS NCL+ EN+ Y+GDLIQ+TE ++L+  N 
Sbjct: 234 PNMYEAPARGTPQIDPVLLRSVDDLELTVRSANCLKAENVFYIGDLIQKTENELLKTPNL 293

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           GRKSL EIK VL   GL LGM L +WPP
Sbjct: 294 GRKSLNEIKDVLTARGLSLGMKLENWPP 321


>gi|269104037|ref|ZP_06156734.1| DNA-directed RNA polymerase alpha subunit [Photobacterium damselae
           subsp. damselae CIP 102761]
 gi|268163935|gb|EEZ42431.1| DNA-directed RNA polymerase alpha subunit [Photobacterium damselae
           subsp. damselae CIP 102761]
          Length = 329

 Score =  285 bits (730), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 149/334 (44%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVNSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVILTLNKSGAGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E+ NP+HVIC++ D +A + M + V +G GYVPA    H   +  PIG + +DA +
Sbjct: 118 DGDVEIANPEHVICHITDDNAELSMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ ++SY VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRISYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|113869405|ref|YP_727894.1| DNA-directed RNA polymerase subunit alpha [Ralstonia eutropha H16]
 gi|194290997|ref|YP_002006904.1| DNA-directed RNA polymerase subunit alpha [Cupriavidus taiwanensis
           LMG 19424]
 gi|123328832|sp|Q0K645|RPOA_RALEH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238692784|sp|B3R7E3|RPOA_CUPTR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|57506670|dbj|BAD86667.1| RNA polymerase alpha subunit [Cupriavidus necator]
 gi|113528181|emb|CAJ94526.1| DNA-directed RNA polymerase alpha subunit [Ralstonia eutropha H16]
 gi|193224832|emb|CAQ70843.1| RNA polymerase, alpha subunit; RNA polymerase alpha chain family
           [Cupriavidus taiwanensis LMG 19424]
          Length = 326

 Score =  285 bits (730), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 151/326 (46%), Positives = 215/326 (65%), Gaps = 7/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG   ++   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVEPLG---DHHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S+I GV ED+ +++LN+KG+  K+       V++ K G GVVTA DI+  +D+E++
Sbjct: 62  VHEYSTIDGVQEDVVNLLLNLKGVVFKLHNRDEVTVSLRKDGEGVVTAADIELPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NP+HVI +L     + M++ V +G GYVP    +  ++    IG I +DA +SP+++VSY
Sbjct: 122 NPNHVIAHLSAGGKLDMQIKVEQGRGYVPGNVRKFGDESGKVIGRIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+TDG I+ E+++  ++RIL DQL +F    E  +   E  
Sbjct: 182 AVESARVEQRTDLDKLVMNIETDGVISPEEAIRQSARILVDQLSVFAAL-EGTESAAEAA 240

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           + ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 241 SSRTPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 300

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +E+
Sbjct: 301 IKEVLASRGLTLGMKLENWPPAGLEK 326


>gi|325267151|ref|ZP_08133819.1| DNA-directed RNA polymerase subunit alpha [Kingella denitrificans
           ATCC 33394]
 gi|324981389|gb|EGC17033.1| DNA-directed RNA polymerase subunit alpha [Kingella denitrificans
           ATCC 33394]
          Length = 327

 Score =  285 bits (730), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 150/332 (45%), Positives = 215/332 (64%), Gaps = 8/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+   L      R  +  +P  RGF HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSTSEFLKPRQIDVDTLSA---TRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR-GPGVVTAGDIQ 120
            + I GVLHE S++ GV ED+ DI+LN+K +  K+ G+  + V   K+ G G V A D +
Sbjct: 58  EITIAGVLHEYSTLDGVQEDVVDILLNVKSVVFKLHGNRTEAVLSLKKTGAGPVYASDFE 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR-TENDPIGLITIDALYSP 179
             +D+E++NP  VIC+L  +  + ME+ V +G GY      R T+++ IG I +DA +SP
Sbjct: 118 LPHDVEIINPKQVICHLSDNGSIDMEVKVEQGRGYQTVSGRRVTKDNKIGAIQLDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I +VS+ VE+AR  Q  D D L + I+T+GSI  E++V +A+RIL DQ+ +F + E    
Sbjct: 178 ITRVSFDVEAARVEQRTDLDSLILDIETNGSIDPEEAVRMAARILIDQMSIFADLEGTPA 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           EV+E+   K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N G
Sbjct: 238 EVEEE---KAPPIDPVLLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           RKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 295 RKSLNEIKEVLASKGLTLGSRLESWPPAGLEK 326


>gi|229524552|ref|ZP_04413957.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae bv.
           albensis VL426]
 gi|229338133|gb|EEO03150.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae bv.
           albensis VL426]
          Length = 330

 Score =  285 bits (729), Expect = 6e-75,   Method: Compositional matrix adjust.
 Identities = 148/335 (44%), Positives = 222/335 (66%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E++NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIVNPEHVICHLTSDNAAIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +SP+ K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL +F++  +
Sbjct: 178 FSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDVFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|171462905|ref|YP_001797018.1| DNA-directed RNA polymerase, alpha subunit [Polynucleobacter
           necessarius subsp. necessarius STIR1]
 gi|238692836|sp|B1XSS7|RPOA_POLNS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|171192443|gb|ACB43404.1| DNA-directed RNA polymerase, alpha subunit [Polynucleobacter
           necessarius subsp. necessarius STIR1]
          Length = 326

 Score =  284 bits (727), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 156/328 (47%), Positives = 213/328 (64%), Gaps = 11/328 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    L     N+  ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIISVEAL---TANQAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVAIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S++ GV ED+ +++LN+KGI  K+       + + K GPGVVTA DI   +D+E++
Sbjct: 62  VHEYSTLDGVQEDVVNLLLNLKGIVFKLQSRDEVIINLRKEGPGVVTAKDIDLPHDVEIM 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP----IGLITIDALYSPIKKVS 184
           NPDHVI +L     + M++ V KG GYVP  + R  ND     IG I +DA +SP+ +VS
Sbjct: 122 NPDHVIAHLSAGGKLDMQIKVEKGRGYVPG-NVRQYNDEATKIIGHIVLDASFSPVSRVS 180

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VESAR  Q  D D+L MTI+T+G ++ E+++  A+ IL DQL +F   E    EV  D
Sbjct: 181 YAVESARVEQRTDLDRLVMTIETNGVLSPEEAIRQAASILVDQLVVFAALE--SSEVSGD 238

Query: 245 IN-VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +S   +P L++ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 239 LAPSRSSMVDPMLMRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 298

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL   GL LGM L  WPP ++E+
Sbjct: 299 NEIKDVLAARGLSLGMKLESWPPANLEK 326


>gi|28897056|ref|NP_796661.1| DNA-directed RNA polymerase subunit alpha [Vibrio parahaemolyticus
           RIMD 2210633]
 gi|153840230|ref|ZP_01992897.1| DNA-directed RNA polymerase, alpha subunit [Vibrio parahaemolyticus
           AQ3810]
 gi|260877974|ref|ZP_05890329.1| DNA-directed RNA polymerase, alpha subunit [Vibrio parahaemolyticus
           AN-5034]
 gi|262392491|ref|YP_003284345.1| DNA-directed RNA polymerase subunit alpha [Vibrio sp. Ex25]
 gi|269959713|ref|ZP_06174093.1| DNA-directed RNA polymerase alpha subunit [Vibrio harveyi 1DA3]
 gi|269964712|ref|ZP_06178950.1| DNA-directed RNA polymerase alpha subunit [Vibrio alginolyticus
           40B]
 gi|31076905|sp|Q87SZ0|RPOA_VIBPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|28805264|dbj|BAC58545.1| DNA-directed RNA polymerase, alpha subunit [Vibrio parahaemolyticus
           RIMD 2210633]
 gi|149746107|gb|EDM57237.1| DNA-directed RNA polymerase, alpha subunit [Vibrio parahaemolyticus
           AQ3810]
 gi|262336085|gb|ACY49880.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. Ex25]
 gi|269830611|gb|EEZ84832.1| DNA-directed RNA polymerase alpha subunit [Vibrio alginolyticus
           40B]
 gi|269835636|gb|EEZ89715.1| DNA-directed RNA polymerase alpha subunit [Vibrio harveyi 1DA3]
 gi|308089902|gb|EFO39597.1| DNA-directed RNA polymerase, alpha subunit [Vibrio parahaemolyticus
           AN-5034]
 gi|328471859|gb|EGF42736.1| DNA-directed RNA polymerase subunit alpha [Vibrio parahaemolyticus
           10329]
          Length = 330

 Score =  284 bits (727), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 149/335 (44%), Positives = 221/335 (65%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H+  +  PIG + +DA 
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHNEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|15642566|ref|NP_232199.1| DNA-directed RNA polymerase subunit alpha [Vibrio cholerae O1
           biovar El Tor str. N16961]
 gi|121730283|ref|ZP_01682657.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae V52]
 gi|147674278|ref|YP_001218065.1| DNA-directed RNA polymerase subunit alpha [Vibrio cholerae O395]
 gi|153824205|ref|ZP_01976872.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae B33]
 gi|227082688|ref|YP_002811239.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae M66-2]
 gi|229507377|ref|ZP_04396882.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae BX
           330286]
 gi|229509699|ref|ZP_04399180.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae B33]
 gi|229513494|ref|ZP_04402958.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae TMA 21]
 gi|229516824|ref|ZP_04406270.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae RC9]
 gi|229521637|ref|ZP_04411055.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae TM
           11079-80]
 gi|229527499|ref|ZP_04416891.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae
           12129(1)]
 gi|229606883|ref|YP_002877531.1| DNA-directed RNA polymerase subunit alpha [Vibrio cholerae MJ-1236]
 gi|254292242|ref|ZP_04963005.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae
           AM-19226]
 gi|254851111|ref|ZP_05240461.1| DNA-directed RNA polymerase subunit alpha [Vibrio cholerae MO10]
 gi|255744460|ref|ZP_05418412.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholera CIRS 101]
 gi|258622737|ref|ZP_05717755.1| DNA-directed RNA polymerase alpha subunit [Vibrio mimicus VM573]
 gi|258625765|ref|ZP_05720644.1| DNA-directed RNA polymerase alpha subunit [Vibrio mimicus VM603]
 gi|261211126|ref|ZP_05925415.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. RC341]
 gi|262166592|ref|ZP_06034329.1| DNA-directed RNA polymerase alpha subunit [Vibrio mimicus VM223]
 gi|262170492|ref|ZP_06038170.1| DNA-directed RNA polymerase alpha subunit [Vibrio mimicus MB-451]
 gi|262401858|ref|ZP_06078423.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. RC586]
 gi|297581413|ref|ZP_06943336.1| DNA-directed RNA polymerase subunit alpha [Vibrio cholerae RC385]
 gi|12230593|sp|Q9KP08|RPOA_VIBCH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172047565|sp|A5F572|RPOA_VIBC3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|254765262|sp|C3LRN3|RPOA_VIBCM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|9657157|gb|AAF95712.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae O1
           biovar El Tor str. N16961]
 gi|121627963|gb|EAX60526.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae V52]
 gi|126518273|gb|EAZ75498.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae B33]
 gi|146316161|gb|ABQ20700.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae O395]
 gi|150421844|gb|EDN13828.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae
           AM-19226]
 gi|227010576|gb|ACP06788.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae M66-2]
 gi|227014460|gb|ACP10670.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae O395]
 gi|229335131|gb|EEO00616.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae
           12129(1)]
 gi|229341231|gb|EEO06235.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae TM
           11079-80]
 gi|229345887|gb|EEO10859.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae RC9]
 gi|229349371|gb|EEO14327.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae TMA 21]
 gi|229353173|gb|EEO18112.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae B33]
 gi|229354882|gb|EEO19803.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae BX
           330286]
 gi|229369538|gb|ACQ59961.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae MJ-1236]
 gi|254846816|gb|EET25230.1| DNA-directed RNA polymerase subunit alpha [Vibrio cholerae MO10]
 gi|255737985|gb|EET93378.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholera CIRS 101]
 gi|258582003|gb|EEW06873.1| DNA-directed RNA polymerase alpha subunit [Vibrio mimicus VM603]
 gi|258584925|gb|EEW09656.1| DNA-directed RNA polymerase alpha subunit [Vibrio mimicus VM573]
 gi|260839627|gb|EEX66238.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. RC341]
 gi|261891568|gb|EEY37554.1| DNA-directed RNA polymerase alpha subunit [Vibrio mimicus MB-451]
 gi|262026308|gb|EEY44976.1| DNA-directed RNA polymerase alpha subunit [Vibrio mimicus VM223]
 gi|262351830|gb|EEZ00961.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. RC586]
 gi|297534251|gb|EFH73089.1| DNA-directed RNA polymerase subunit alpha [Vibrio cholerae RC385]
 gi|327485053|gb|AEA79460.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae
           LMA3894-4]
          Length = 330

 Score =  284 bits (727), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 148/335 (44%), Positives = 221/335 (65%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E++NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIVNPEHVICHLTSDNAAIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +SP+ K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 FSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|298500605|ref|ZP_07010409.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae MAK
           757]
 gi|297540774|gb|EFH76831.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae MAK
           757]
          Length = 329

 Score =  284 bits (727), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 148/335 (44%), Positives = 221/335 (65%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E++NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIVNPEHVICHLTSDNAAIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +SP+ K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 FSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|312795804|ref|YP_004028726.1| DNA-directed RNA polymerase alpha chain [Burkholderia rhizoxinica
           HKI 454]
 gi|312167579|emb|CBW74582.1| DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) [Burkholderia
           rhizoxinica HKI 454]
          Length = 325

 Score =  284 bits (727), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 152/326 (46%), Positives = 213/326 (65%), Gaps = 8/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG   +N   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVDSLG---DNHAKVVMEPFERGYGHTLGNALRRVLLSSMIGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVV AGDI+  +D EV+
Sbjct: 62  VHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVIAGDIEVPHDCEVI 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NP+HVI +L     + +++ V KG GYVP    R  ++    IG I +DA +SP+++VSY
Sbjct: 122 NPEHVIAHLSKGGKLDVQIKVEKGRGYVPGNVRRYGDESAKVIGRIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL DQL +F   E    E   + 
Sbjct: 182 AVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALE--GTETTAEA 239

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 240 PSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 299

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +++
Sbjct: 300 IKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|114319644|ref|YP_741327.1| DNA-directed RNA polymerase subunit alpha [Alkalilimnicola
           ehrlichii MLHE-1]
 gi|119366660|sp|Q0ABF0|RPOA_ALHEH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|114226038|gb|ABI55837.1| DNA-directed RNA polymerase subunit alpha [Alkalilimnicola
           ehrlichii MLHE-1]
          Length = 331

 Score =  284 bits (727), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 145/331 (43%), Positives = 222/331 (67%), Gaps = 6/331 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q  +++ +KP  ++   + ++ E R  ++ EPL RGF HTLGNALRRVL+SS+ G+A+ 
Sbjct: 1   MQGTFRDFLKPRTVD---IQEQGERRAKIVLEPLERGFGHTLGNALRRVLLSSMPGSAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +I+GV HE SS++GV ED+ DI+LN+K + ++M       +T+  +GPG VTAGDIQT
Sbjct: 58  QAEIEGVEHEYSSMEGVQEDVVDILLNLKSLAVRMHDRDEAELTVSVQGPGPVTAGDIQT 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP-IGLITIDALYSPI 180
            +D+EV NP+ +IC L        +L V++G GY  A     + D  IG + +DA YSP+
Sbjct: 118 AHDVEVKNPELLICTLTKAVAFNAKLMVARGRGYEAATQRDGDEDRVIGRLQLDASYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V+YTVESAR  Q  + DKL + ++T+G +  E++V  A+ +L+DQL +F++ E  + E
Sbjct: 178 KRVAYTVESARVEQRTNLDKLVLDVETNGVLEPEEAVRFAAGLLRDQLSVFVDLEGGEFE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +++     +  +P LL+ ++ELEL+VRS NCL+ E+I Y+GDL+QRTE ++L+  N G+
Sbjct: 238 AEQEEQEPDV--DPILLRPIDELELTVRSANCLKAESIHYVGDLVQRTEVELLKTPNLGK 295

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           KSL EIK  L + GL LGM L +WPP  + E
Sbjct: 296 KSLTEIKETLASHGLSLGMRLENWPPAGLGE 326


>gi|320540586|ref|ZP_08040236.1| RNA polymerase, alpha subunit [Serratia symbiotica str. Tucson]
 gi|320029517|gb|EFW11546.1| RNA polymerase, alpha subunit [Serratia symbiotica str. Tucson]
          Length = 329

 Score =  284 bits (727), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 150/333 (45%), Positives = 220/333 (66%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++   HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA +
Sbjct: 118 DGDVEIVKSQHVICHLTDENAAISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLIIEMETNGAIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL  V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLCPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 294 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 326


>gi|307543850|ref|YP_003896329.1| DNA-directed RNA polymerase subunit alpha [Halomonas elongata DSM
           2581]
 gi|307215874|emb|CBV41144.1| DNA-directed RNA polymerase subunit alpha [Halomonas elongata DSM
           2581]
          Length = 332

 Score =  284 bits (726), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 143/333 (42%), Positives = 226/333 (67%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  E ++P +I+   + +   +   ++ EP  RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQRSVTEFLRPRDIK---VEEISAHHAKIVLEPFERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +I GV HE S+I+G+ ED+ +I+LN+K + +KM       +++ K+GP VVTAGDI  
Sbjct: 58  EAEIAGVDHEYSAIEGIQEDVIEILLNLKDVAIKMHSRDEAVLSLNKQGPAVVTAGDIAL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+EV+NP+HVI +++  A ++M+L +++G GY PA      +D    IG + +DA +S
Sbjct: 118 DHDVEVVNPEHVIAHVNEGAELKMQLKIARGRGYEPADVRGDADDESRAIGRLQLDATFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY+VE+AR  Q  D DKL + ++TDG++  E+++  ++ ILQ+QL  F++ E  K
Sbjct: 178 PVRRVSYSVEAARVEQRTDLDKLIIDLETDGTLDPEEAIRRSATILQEQLAAFVDLEADK 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           ++  E+        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EQEVEEEEDH---IDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL   GL LGM L +WPP S+++
Sbjct: 295 GKKSLNEIKDVLAARGLSLGMRLENWPPASLKD 327


>gi|91791564|ref|YP_561215.1| DNA-directed RNA polymerase subunit alpha [Shewanella denitrificans
           OS217]
 gi|119366725|sp|Q12ST4|RPOA_SHEDO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|91713566|gb|ABE53492.1| DNA-directed RNA polymerase, alpha subunit [Shewanella
           denitrificans OS217]
          Length = 329

 Score =  284 bits (726), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 148/331 (44%), Positives = 218/331 (65%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVNPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVTIEGKDEAMLTLSKSGTGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-HHRTEND--PIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  + M + V +G GYVPA    +TE+D  PIG + +DA +S
Sbjct: 118 DGDVTIMNPDHVICHLTGNNDISMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   E +
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFV---ELR 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              + +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 235 DVTEPEQKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASL 325


>gi|329907624|ref|ZP_08274694.1| DNA-directed RNA polymerase alpha subunit [Oxalobacteraceae
           bacterium IMCC9480]
 gi|327546929|gb|EGF31838.1| DNA-directed RNA polymerase alpha subunit [Oxalobacteraceae
           bacterium IMCC9480]
          Length = 325

 Score =  284 bits (726), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 151/326 (46%), Positives = 210/326 (64%), Gaps = 8/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  IE   LG        ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPRIIEVETLGA---GHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE SS+ GV ED+ D++LN+KG+  K+       +T+ K G G V A DI   +D+E++
Sbjct: 62  VHEYSSLDGVQEDVVDMLLNLKGVVFKLHNRDEVTLTLKKDGEGAVLASDIDLPHDVELI 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NPDHVI +L     + M++ V KG GYVP    R   D    IG I +DA +SP+++VSY
Sbjct: 122 NPDHVIAHLTAGGKLDMQIKVEKGRGYVPGNVRRLAEDANKTIGRIILDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           +VESAR  Q  D DKL + I+T+G I+ E+++  ++R+L DQL +F   E    E   + 
Sbjct: 182 SVESARVEQRTDLDKLVINIETNGVISPEEAIRQSARVLVDQLNVFAALE--GTEAAAEA 239

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GRKSL E
Sbjct: 240 PSRAPSVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRSENELLKTPNLGRKSLNE 299

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +E+
Sbjct: 300 IKEVLASRGLTLGMKLENWPPAGLEK 325


>gi|237806900|ref|YP_002891340.1| DNA-directed RNA polymerase subunit alpha [Tolumonas auensis DSM
           9187]
 gi|259494173|sp|C4L7V5|RPOA_TOLAT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|237499161|gb|ACQ91754.1| DNA-directed RNA polymerase, alpha subunit [Tolumonas auensis DSM
           9187]
          Length = 329

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 152/331 (45%), Positives = 220/331 (66%), Gaps = 16/331 (4%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           + +KP  ++   L       TL   EPL RGF HTLGNALRR+L+SS+ G A+  V+IDG
Sbjct: 7   DFLKPRLVDIEQLSPTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVAEVEIDG 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE SS +GV ED+ +I+LN+KGI +K+ G     +++ K G G VTAGDI   +D+ +
Sbjct: 64  VLHEYSSKEGVQEDILEILLNLKGIAVKLEGKDEVILSLTKSGAGPVTAGDIIHGDDVVI 123

Query: 128 LNPDHVICNLD-VDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
           +NP+HVIC+L   +A + M L V +G GYVPA    H   E+ PIG + +DA +SP+ ++
Sbjct: 124 VNPEHVICHLTGANAEISMRLRVQRGRGYVPASARLHTDDEDRPIGRLLLDAAFSPVVRI 183

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE---PKKE 240
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +   P+K 
Sbjct: 184 AYNVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVSVPEK- 242

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            KED       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+
Sbjct: 243 -KED----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGK 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 298 KSLTEIKDVLASRGLSLGMRLENWPPASLAD 328


>gi|27364190|ref|NP_759718.1| DNA-directed RNA polymerase subunit alpha [Vibrio vulnificus CMCP6]
 gi|37678583|ref|NP_933192.1| DNA-directed RNA polymerase subunit alpha [Vibrio vulnificus YJ016]
 gi|320157576|ref|YP_004189955.1| DNA-directed RNA polymerase subunit alpha [Vibrio vulnificus
           MO6-24/O]
 gi|29611853|sp|Q8DE63|RPOA_VIBVU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|41688623|sp|Q7MPG4|RPOA_VIBVY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|27360308|gb|AAO09245.1| DNA-directed RNA polymerase, alpha subunit [Vibrio vulnificus
           CMCP6]
 gi|37197323|dbj|BAC93163.1| DNA-directed RNA polymerase, alpha subunit [Vibrio vulnificus
           YJ016]
 gi|319932888|gb|ADV87752.1| DNA-directed RNA polymerase alpha subunit [Vibrio vulnificus
           MO6-24/O]
          Length = 330

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 149/335 (44%), Positives = 220/335 (65%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|260779478|ref|ZP_05888368.1| DNA-directed RNA polymerase alpha subunit [Vibrio coralliilyticus
           ATCC BAA-450]
 gi|261250392|ref|ZP_05942967.1| DNA-directed RNA polymerase alpha subunit [Vibrio orientalis CIP
           102891]
 gi|323492144|ref|ZP_08097306.1| DNA-directed RNA polymerase subunit alpha [Vibrio brasiliensis LMG
           20546]
 gi|323495529|ref|ZP_08100603.1| DNA-directed RNA polymerase subunit alpha [Vibrio sinaloensis DSM
           21326]
 gi|260604287|gb|EEX30591.1| DNA-directed RNA polymerase alpha subunit [Vibrio coralliilyticus
           ATCC BAA-450]
 gi|260938961|gb|EEX94948.1| DNA-directed RNA polymerase alpha subunit [Vibrio orientalis CIP
           102891]
 gi|323313705|gb|EGA66807.1| DNA-directed RNA polymerase subunit alpha [Vibrio brasiliensis LMG
           20546]
 gi|323319410|gb|EGA72347.1| DNA-directed RNA polymerase subunit alpha [Vibrio sinaloensis DSM
           21326]
          Length = 330

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 149/335 (44%), Positives = 221/335 (65%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|32491317|ref|NP_871571.1| DNA-directed RNA polymerase subunit alpha [Wigglesworthia
           glossinidia endosymbiont of Glossina brevipalpis]
 gi|30173252|sp|Q8D1Y8|RPOA_WIGBR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|25166524|dbj|BAC24714.1| rpoA [Wigglesworthia glossinidia endosymbiont of Glossina
           brevipalpis]
          Length = 328

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 151/331 (45%), Positives = 220/331 (66%), Gaps = 10/331 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +  E +KP  ++   + +     TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MHNSATEFLKPRLVDIEQISKTHAKITL---EPLERGFGHTLGNALRRILLSSMPGYAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDG+LHE SS +GV ED+ +I+LN+K + L + G     +++FK G G VTA DI  
Sbjct: 58  EVEIDGILHEYSSKEGVQEDIVEILLNLKELALIIKGKDIAVLSLFKSGIGKVTASDIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA-KHHRTENDPIGLITIDALYSP 179
             ++E+ +P+HV+CNL   ++ + M + V KG GYVPA      E+ PIG + +DA YSP
Sbjct: 118 DGNVEICHPEHVLCNLTHENSSINMRIKVQKGRGYVPAISRMHIEDRPIGRLLLDACYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I+++SY VE+AR  Q  D DKL + ++T+G+I  E ++  A+ IL +QL  FI+  + +K
Sbjct: 178 IERISYNVEAARVEQRTDLDKLIIEMETNGTIDPESAIRRAATILSEQLEAFIDLRDIRK 237

Query: 240 -EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E+KE+       F+P LL+ V++LEL+VRS NCL+ E+I Y+GDL+QRTE ++L+  N 
Sbjct: 238 PEIKEE----KPEFDPVLLRPVDDLELTVRSANCLKAESIHYIGDLVQRTEVELLKTPNL 293

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL T  L LGM + +WPP SI
Sbjct: 294 GKKSLTEIKDVLSTRNLTLGMRIENWPPVSI 324


>gi|187476574|ref|YP_784598.1| DNA-directed RNA polymerase subunit alpha [Bordetella avium 197N]
 gi|119366666|sp|Q2L238|RPOA_BORA1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|115421160|emb|CAJ47644.1| DNA-directed RNA polymerase alpha chain [Bordetella avium 197N]
          Length = 328

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 152/328 (46%), Positives = 210/328 (64%), Gaps = 9/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           Q  +KP +IE   +G    N   ++ EP  RG+ HTLGNALRR+L+SS+ G A T VQ+ 
Sbjct: 4   QGFLKPRSIEVEPVGP---NHAKIVMEPFERGYGHTLGNALRRILLSSMTGYAPTEVQMT 60

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S+I GV ED+ DI+LN+KG+  K+       + + K G G+V A DI+  +D+E
Sbjct: 61  GVVHEYSTIPGVREDVVDILLNLKGVVFKLHNRDEVTLILRKNGSGLVLASDIELPHDVE 120

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKV 183
           ++NP+H ICNL     + M++ V KG GYVP        D    IG I +DA +SP+++V
Sbjct: 121 IVNPEHPICNLTDAGKLEMQIKVEKGRGYVPGNVRALSEDRTHTIGRIILDASFSPVRRV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VESAR  Q  D DKL + I+T+G I+ E++V  ++RIL DQ+ +F   E      + 
Sbjct: 181 SYAVESARVEQRTDLDKLVLDIETNGVISPEEAVRQSARILMDQISVFAALEGAGDSYEA 240

Query: 244 DINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              V+  P  +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKS
Sbjct: 241 P--VRGTPQIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKS 298

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           L EIK VL   GL LGM L +WPP  +E
Sbjct: 299 LNEIKEVLAARGLTLGMKLENWPPLGLE 326


>gi|82701925|ref|YP_411491.1| DNA-directed RNA polymerase subunit alpha [Nitrosospira multiformis
           ATCC 25196]
 gi|119366704|sp|Q2YAX2|RPOA_NITMU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|82409990|gb|ABB74099.1| DNA-directed RNA polymerase subunit alpha [Nitrosospira multiformis
           ATCC 25196]
          Length = 334

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 145/302 (48%), Positives = 207/302 (68%), Gaps = 7/302 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EP  RG+ HTLGNALRR+L+SS+ G A T VQI GV+HE S++ GV ED+ DI+LN+KGI
Sbjct: 27  EPFERGYGHTLGNALRRILLSSMPGFAPTEVQISGVVHEYSALDGVQEDVVDILLNLKGI 86

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LK+   +   +T+ K+G G VTAGDI+  +D+E++NPDHV+ +L     + M++ V  G
Sbjct: 87  VLKLHNRTEALLTLSKKGEGTVTAGDIEGGHDVEIINPDHVVAHLTSGGKLDMQIKVEMG 146

Query: 153 HGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            GYVP   +    E+  IG I +DA +SP+++VSY VESAR  Q  D DKL M I+T+G 
Sbjct: 147 RGYVPGTVRQLAHESRAIGSILLDASFSPVRRVSYAVESARVEQRTDLDKLVMDIETNGV 206

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-FNPALLKKVEELELSVRS 269
           +  E+++  A+++L +QL +F + +     V++      LP  +P LL+ V++LEL+VRS
Sbjct: 207 VDPEEAIRYAAKVLVEQLSVFADLKGTPLPVEQ----PKLPQIDPVLLRPVDDLELTVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL EIK VL + GL LGM L  WPP ++
Sbjct: 263 ANCLKAENIYYIGDLIQRTETELLKTPNLGRKSLNEIKEVLASRGLTLGMKLESWPPSNL 322

Query: 330 EE 331
           ++
Sbjct: 323 DK 324


>gi|119773379|ref|YP_926119.1| DNA-directed RNA polymerase subunit alpha [Shewanella amazonensis
           SB2B]
 gi|158513008|sp|A1S243|RPOA_SHEAM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119765879|gb|ABL98449.1| DNA-directed RNA polymerase [Shewanella amazonensis SB2B]
          Length = 329

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 149/336 (44%), Positives = 213/336 (63%), Gaps = 19/336 (5%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVILEGKDEAMLTLSKSGAGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
             D+ + NPDHVIC+L  +  + M + V +G GYVPA       D   PIG + +DA +S
Sbjct: 118 DGDVTIANPDHVICHLTGNHDISMRIRVERGRGYVPASARAQNEDDDRPIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--- 235
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+      
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFVELRDVS 237

Query: 236 --EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
             E K+E  E        F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L
Sbjct: 238 VPEQKEEKPE--------FDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELL 289

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +  N G+KSL EIK VL + GL LGM L +WPP S+
Sbjct: 290 KTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASL 325


>gi|163752127|ref|ZP_02159332.1| DNA-directed RNA polymerase alpha subunit [Shewanella benthica
           KT99]
 gi|161327962|gb|EDP99137.1| DNA-directed RNA polymerase alpha subunit [Shewanella benthica
           KT99]
          Length = 329

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 149/333 (44%), Positives = 219/333 (65%), Gaps = 13/333 (3%)

Query: 2   IQKNWQELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           +Q +  E ++P   NIE     Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A
Sbjct: 1   MQGSVTEFLRPRLVNIE-----QVNPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCA 55

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI
Sbjct: 56  VTEVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVVIEGKDEAMLTLSKSGAGPVTAADI 115

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-HHRTEND--PIGLITIDAL 176
               D+ ++NP+H+IC+L  +  + M + V +G GYVPA    +TE+D  PIG + +DA 
Sbjct: 116 THDGDVTIMNPEHIICHLTGNNEISMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDAS 175

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +SP+ +++YTVE+AR  Q  D DKL + + T+G++  E+++  A+ IL +QL  F+   E
Sbjct: 176 FSPVARIAYTVEAARVEQRTDLDKLVIDMTTNGTLDPEEAIRRAATILAEQLDAFV---E 232

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +   + +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 233 LRDVTEPEQKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 292

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LGM L +WPP S+
Sbjct: 293 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASL 325


>gi|331004894|ref|ZP_08328310.1| DNA-directed RNA polymerase alpha subunit [gamma proteobacterium
           IMCC1989]
 gi|330421281|gb|EGG95531.1| DNA-directed RNA polymerase alpha subunit [gamma proteobacterium
           IMCC1989]
          Length = 331

 Score =  283 bits (724), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 145/333 (43%), Positives = 222/333 (66%), Gaps = 11/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    E + P +I+   + +       ++ EPL RGF HTLGNALRR+L+SS+ G AI 
Sbjct: 1   MQSAVNEFLTPRHID---VTEHSPTHAKVVLEPLERGFGHTLGNALRRILLSSMPGCAII 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI 119
             +I+GV HE S+++GV ED+ +I+LN+KG+ + M     SH  +++ K+GPGVVTA DI
Sbjct: 58  EAEIEGVEHEYSALEGVQEDIIEILLNLKGVAVVMHDQEKSHAMLSLKKKGPGVVTAADI 117

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDAL 176
              +++E+ NPDHVI  +  D  + M L++++G GY PA   R+++D    IG + +DA 
Sbjct: 118 VVDHEVEIKNPDHVIATITGDVELNMSLSIARGRGYQPADARRSDDDETRAIGRLQLDAS 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +SP+K+++Y+VESAR  Q  D DKL + ++T+G+I  E+++  ++ ILQ QL +F++   
Sbjct: 178 FSPVKRLAYSVESARVEQRTDLDKLVLDLETNGTIDPEEAIRRSATILQQQLAVFVDL-- 235

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            + E   +   K    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  
Sbjct: 236 -ESEKSSEPEEKEEDVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LG+ L +WPP S+
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGLRLENWPPASL 327


>gi|84394603|ref|ZP_00993305.1| DNA-directed RNA polymerase alpha subunit [Vibrio splendidus 12B01]
 gi|218710724|ref|YP_002418345.1| DNA-directed RNA polymerase subunit alpha [Vibrio splendidus LGP32]
 gi|254765263|sp|B7VLD2|RPOA_VIBSL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|84374777|gb|EAP91722.1| DNA-directed RNA polymerase alpha subunit [Vibrio splendidus 12B01]
 gi|218323743|emb|CAV20097.1| DNA-directed RNA polymerase, alpha subunit [Vibrio splendidus
           LGP32]
          Length = 330

 Score =  283 bits (724), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 149/335 (44%), Positives = 220/335 (65%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQINTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|312884678|ref|ZP_07744379.1| DNA-directed RNA polymerase subunit alpha [Vibrio caribbenthicus
           ATCC BAA-2122]
 gi|309367591|gb|EFP95142.1| DNA-directed RNA polymerase subunit alpha [Vibrio caribbenthicus
           ATCC BAA-2122]
          Length = 330

 Score =  283 bits (724), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 148/335 (44%), Positives = 221/335 (65%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +++LN+KG+ ++++ G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEVLLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|56460991|ref|YP_156272.1| DNA-directed RNA polymerase subunit alpha [Idiomarina loihiensis
           L2TR]
 gi|61215803|sp|Q5QXV8|RPOA_IDILO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|56180001|gb|AAV82723.1| DNA-directed RNA polymerase alpha subunit [Idiomarina loihiensis
           L2TR]
          Length = 329

 Score =  283 bits (724), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 143/331 (43%), Positives = 219/331 (66%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF +TLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISPTHAKVTL---EPLERGFGYTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ + + G     +T+ K G G VTAGD   
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDVIEVLLNLKGLAVSVEGKDEATLTLNKSGAGPVTAGDFTH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
             D+E++NP+HVIC+L  D  + M + V +G GYVPA   ++ +D   PIG + +DA +S
Sbjct: 118 DGDVEIVNPEHVICHLTGDYELVMRVKVERGRGYVPAASRQSADDDERPIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F+   +  
Sbjct: 178 PVERIAYSVDAARVEQRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLDAFVELRDIS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +  +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 EPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIQYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASL 325


>gi|114778797|ref|ZP_01453604.1| DNA-directed RNA polymerase, alpha subunit [Mariprofundus
           ferrooxydans PV-1]
 gi|114550928|gb|EAU53492.1| DNA-directed RNA polymerase, alpha subunit [Mariprofundus
           ferrooxydans PV-1]
          Length = 325

 Score =  283 bits (723), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 145/315 (46%), Positives = 217/315 (68%), Gaps = 17/315 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EPL RG+  T+GN+LRR+L+SSL GAA+T+V +DGV HE  SIKGV ED+ DIIL++
Sbjct: 22  IVFEPLERGYGTTIGNSLRRMLLSSLPGAAVTSVLMDGVAHEYDSIKGVREDVMDIILSL 81

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K ++L+M GD    +++  +G  +VTA DI+    + VLNP+ ++ +L+ DA +++E  V
Sbjct: 82  KELDLRMEGDEAATISLEIKGSAIVTAADIKCPAGLSVLNPELILAHLNDDAHLKIEAVV 141

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GY PA     +   +G + +DA YSPI++VS  VE+AR GQ  +YDKL M I+T+G
Sbjct: 142 EKGRGYEPATDREVDERAVGSLLVDASYSPIRRVSTRVEAARVGQRTNYDKLIMEIETNG 201

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP------ALLKKVEEL 263
           S++ E+++  A++IL+ QL +F++F        E++++ S P  P       L++ +E L
Sbjct: 202 SLSPEEALNSAAKILEAQLAVFVDF--------ENVSIVSEPEGPDDTLDNLLIQPIEHL 253

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +LSVRS NCL+ +++  +GDL+QR+E +MLR  NFGRKSL EIK VL  MGL LGM+LP+
Sbjct: 254 DLSVRSMNCLKSDDVFRVGDLVQRSEQEMLRTPNFGRKSLNEIKEVLENMGLELGMDLPN 313

Query: 324 WPPESIEELAKKYED 338
           WPP   +E A+  ED
Sbjct: 314 WPP---QEDAEALED 325


>gi|293602598|ref|ZP_06685041.1| DNA-directed RNA polymerase subunit alpha [Achromobacter piechaudii
           ATCC 43553]
 gi|311109576|ref|YP_003982429.1| DNA-directed RNA polymerase subunit alpha [Achromobacter
           xylosoxidans A8]
 gi|292818970|gb|EFF78008.1| DNA-directed RNA polymerase subunit alpha [Achromobacter piechaudii
           ATCC 43553]
 gi|310764265|gb|ADP19714.1| DNA-directed RNA polymerase, alpha subunit [Achromobacter
           xylosoxidans A8]
 gi|317401574|gb|EFV82203.1| DNA-directed RNA polymerase subunit alpha [Achromobacter
           xylosoxidans C54]
          Length = 328

 Score =  283 bits (723), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 151/328 (46%), Positives = 207/328 (63%), Gaps = 9/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           Q  +KP +IE   +G        ++ EP  RG+ HTLGNALRR+L+SS+ G A T VQ+ 
Sbjct: 4   QGFLKPRSIEVEPVGTHHAK---IVMEPFERGYGHTLGNALRRILLSSMTGYAPTEVQMT 60

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S+I GV ED+ DI+LN+KG+  K+       + + K G G V A DI+  +D+E
Sbjct: 61  GVVHEYSTIPGVREDVVDILLNLKGVVFKLHNRDEVTLVLRKTGAGTVLASDIELPHDVE 120

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKV 183
           ++NP H ICNL     + M++ V KG GYVP        D    IG I +DA +SP+++V
Sbjct: 121 IINPGHAICNLTDAGKLEMQIKVEKGRGYVPGNVRALSEDRTHTIGRIVLDASFSPVRRV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VESAR  Q  D DKL + I+T+G I+ E++V  ++RIL DQ+ +F   E        
Sbjct: 181 SYAVESARVEQRTDLDKLVLDIETNGVISPEEAVRQSARILMDQISVFAALEGAGDSY-- 238

Query: 244 DINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           +  V+  P  +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKS
Sbjct: 239 EAPVRGTPQIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKS 298

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           L EIK VL   GL LGM L +WPP  +E
Sbjct: 299 LNEIKEVLAARGLTLGMKLENWPPLGLE 326


>gi|120597014|ref|YP_961588.1| DNA-directed RNA polymerase subunit alpha [Shewanella sp. W3-18-1]
 gi|146294816|ref|YP_001185240.1| DNA-directed RNA polymerase subunit alpha [Shewanella putrefaciens
           CN-32]
 gi|158512973|sp|A1RED9|RPOA_SHESW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172046873|sp|A4YBV8|RPOA_SHEPC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|120557107|gb|ABM23034.1| DNA-directed RNA polymerase, alpha subunit [Shewanella sp. W3-18-1]
 gi|145566506|gb|ABP77441.1| DNA-directed RNA polymerase, alpha subunit [Shewanella putrefaciens
           CN-32]
 gi|319424605|gb|ADV52679.1| DNA-directed RNA polymerase, alpha subunit [Shewanella putrefaciens
           200]
          Length = 329

 Score =  282 bits (722), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 147/333 (44%), Positives = 219/333 (65%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVNSTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVTIEGKDEAMLTLSKSGAGPVIAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-HHRTEND--PIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  + M + V +G GYVPA    +TE+D  PIG + +DA +S
Sbjct: 118 DGDVTIVNPDHVICHLTGNNDISMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   E +
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFV---ELR 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              + ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 235 DVTEPELKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>gi|24371854|ref|NP_715896.1| DNA-directed RNA polymerase subunit alpha [Shewanella oneidensis
           MR-1]
 gi|113968569|ref|YP_732362.1| DNA-directed RNA polymerase subunit alpha [Shewanella sp. MR-4]
 gi|114045732|ref|YP_736282.1| DNA-directed RNA polymerase subunit alpha [Shewanella sp. MR-7]
 gi|117918682|ref|YP_867874.1| DNA-directed RNA polymerase subunit alpha [Shewanella sp. ANA-3]
 gi|41688704|sp|Q8EK47|RPOA_SHEON RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366727|sp|Q0HNR2|RPOA_SHESM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366728|sp|Q0I080|RPOA_SHESR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158512311|sp|A0KRP9|RPOA_SHESA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|24345671|gb|AAN53341.1|AE015474_4 DNA-directed RNA polymerase, alpha subunit [Shewanella oneidensis
           MR-1]
 gi|113883253|gb|ABI37305.1| DNA-directed RNA polymerase, alpha subunit [Shewanella sp. MR-4]
 gi|113887174|gb|ABI41225.1| DNA-directed RNA polymerase, alpha subunit [Shewanella sp. MR-7]
 gi|117611014|gb|ABK46468.1| DNA-directed RNA polymerase, alpha subunit [Shewanella sp. ANA-3]
          Length = 329

 Score =  282 bits (722), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 147/333 (44%), Positives = 219/333 (65%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVNSTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVTIEGKDEAMLTLSKSGAGPVIAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-HHRTEND--PIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  + M + V +G GYVPA    +TE+D  PIG + +DA +S
Sbjct: 118 DGDVTIVNPDHVICHLTGNNDISMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   E +
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFV---ELR 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              + ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 235 DVTEPEMKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>gi|110812362|gb|ABG91718.1| DNA-directed RNA polymerase, alpha subunit [Shewanella putrefaciens
           200]
          Length = 336

 Score =  282 bits (722), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 147/333 (44%), Positives = 219/333 (65%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 8   MQGSVTEFLKPRLVD---IEQVNSTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 64

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G V A DI  
Sbjct: 65  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVTIEGKDEAMLTLSKSGAGPVIAADITH 124

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-HHRTEND--PIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  + M + V +G GYVPA    +TE+D  PIG + +DA +S
Sbjct: 125 DGDVTIVNPDHVICHLTGNNDISMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDASFS 184

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   E +
Sbjct: 185 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFV---ELR 241

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              + ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 242 DVTEPELKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 301

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 302 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 334


>gi|157377426|ref|YP_001476026.1| DNA-directed RNA polymerase subunit alpha [Shewanella sediminis
           HAW-EB3]
 gi|157319800|gb|ABV38898.1| DNA-directed RNA polymerase, alpha subunit [Shewanella sediminis
           HAW-EB3]
          Length = 329

 Score =  282 bits (722), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 147/333 (44%), Positives = 219/333 (65%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E ++P  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLRPRLVD---IEQVNPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVVIEGKDEAMLTLSKSGAGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-HHRTEND--PIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  V M + V +G GYVPA    +TE+D  PIG + +D+ +S
Sbjct: 118 DGDVTIMNPDHVICHLTGNNDVSMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   E +
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFV---ELR 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              + +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 235 DVTEPEQKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>gi|156973075|ref|YP_001443982.1| DNA-directed RNA polymerase subunit alpha [Vibrio harveyi ATCC
           BAA-1116]
 gi|166229282|sp|A7N0H8|RPOA_VIBHB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|156524669|gb|ABU69755.1| hypothetical protein VIBHAR_00754 [Vibrio harveyi ATCC BAA-1116]
          Length = 330

 Score =  282 bits (722), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 148/335 (44%), Positives = 220/335 (65%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQGSVTEFLKPRLVDIEQISSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVI 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H+  +  PIG + +DA 
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHNEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|300114711|ref|YP_003761286.1| DNA-directed RNA polymerase subunit alpha [Nitrosococcus watsonii
           C-113]
 gi|299540648|gb|ADJ28965.1| DNA-directed RNA polymerase, alpha subunit [Nitrosococcus watsonii
           C-113]
          Length = 332

 Score =  282 bits (722), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 144/307 (46%), Positives = 205/307 (66%), Gaps = 6/307 (1%)

Query: 28  TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIIL 87
           T +  EPL RGF HTLGNALRR+L+SS+ G AI   QIDGVLHE ++ +GV ED+T+I+L
Sbjct: 22  TKVTLEPLERGFGHTLGNALRRILLSSMPGCAIIEAQIDGVLHEYTTKEGVQEDMTEILL 81

Query: 88  NIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           N+KG+ +K+ G     +++  +GP  VTAGDIQ  +D+EV+NP HVI +L     + + +
Sbjct: 82  NLKGVAIKLHGRDEVTLSLSSKGPVTVTAGDIQLEHDVEVINPKHVIAHLTKSGELNLTM 141

Query: 148 TVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
            V +G GY PA        +   IG + +DA +SPI++V+Y V+SAR  Q  D DKL + 
Sbjct: 142 KVVRGRGYQPASVRIPKEEDERSIGHLILDASFSPIRRVTYEVDSARVEQRTDLDKLIIE 201

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           I+T+G+I  +++V  A+ ILQDQL  F+  E   +  KE    K+   +P LL+ +++LE
Sbjct: 202 IETNGTIAPDEAVRKAATILQDQLTAFVELEGRIETAKEK---KAAEIDPVLLQPIDDLE 258

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L+VRS NCL+ ENI Y+GDLIQ+TE ++L+  N G+KSL EIK VL   GL LG+ L +W
Sbjct: 259 LTVRSANCLKAENIYYIGDLIQKTEVELLKTPNLGKKSLTEIKDVLTLRGLSLGIRLENW 318

Query: 325 PPESIEE 331
           PP  + E
Sbjct: 319 PPAGLRE 325


>gi|127511117|ref|YP_001092314.1| DNA-directed RNA polymerase subunit alpha [Shewanella loihica PV-4]
 gi|158513465|sp|A3Q9A7|RPOA_SHELP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|126636412|gb|ABO22055.1| DNA-directed RNA polymerase, alpha subunit [Shewanella loihica
           PV-4]
          Length = 329

 Score =  282 bits (721), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 147/333 (44%), Positives = 219/333 (65%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVNPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVVIEGKDEAMLTLSKSGAGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-HHRTEND--PIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  + M + V +G GYVPA    +TE+D  PIG + +D+ +S
Sbjct: 118 DGDVTIMNPDHVICHLTGNNDISMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   E +
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFV---ELR 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              + +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 235 DVTEPEQKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>gi|237749540|ref|ZP_04580020.1| DNA-directed RNA polymerase subunit alpha [Oxalobacter formigenes
           OXCC13]
 gi|229380902|gb|EEO30993.1| DNA-directed RNA polymerase subunit alpha [Oxalobacter formigenes
           OXCC13]
          Length = 325

 Score =  282 bits (721), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 151/326 (46%), Positives = 212/326 (65%), Gaps = 8/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  I    LG     R+++  EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   FLKPRIINVESLGA---GRSVVEMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S++ GV ED+ D++LN+KG+  K+       +T+ K G GVV A DI+  +D+E++
Sbjct: 62  VHEYSTLDGVQEDVVDLLLNLKGVVFKLHNRDSITLTLKKSGAGVVLASDIELPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NP+HVI NL  +  + M++ V KG GYVP    R   D    IG I +DA +SP+++VSY
Sbjct: 122 NPEHVIANLTDNGKLDMQIKVEKGRGYVPGNVRRLSEDANKTIGRIILDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL + I+T+G I+ E+++  ++RIL DQL +F   E  +   +   
Sbjct: 182 AVESARVEQRTDLDKLIINIETNGVISAEEAIRQSARILVDQLSVFAALEGTETTSEALT 241

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            V ++  +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GRKSL E
Sbjct: 242 QVPAV--DPILLRPVDDLELTVRSANCLKAENINYIGDLIQRSENELLKTPNLGRKSLNE 299

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP   E+
Sbjct: 300 IKEVLASRGLTLGMRLDNWPPAGFEK 325


>gi|260770938|ref|ZP_05879867.1| DNA-directed RNA polymerase alpha subunit [Vibrio furnissii CIP
           102972]
 gi|260614175|gb|EEX39365.1| DNA-directed RNA polymerase alpha subunit [Vibrio furnissii CIP
           102972]
 gi|315178983|gb|ADT85897.1| DNA-directed RNA polymerase subunit alpha - rpoA [Vibrio furnissii
           NCTC 11218]
          Length = 330

 Score =  282 bits (721), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 147/335 (43%), Positives = 222/335 (66%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E++NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIVNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +SP+ K++Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 FSPVDKIAYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|170728984|ref|YP_001763010.1| DNA-directed RNA polymerase subunit alpha [Shewanella woodyi ATCC
           51908]
 gi|169814331|gb|ACA88915.1| DNA-directed RNA polymerase, alpha subunit [Shewanella woodyi ATCC
           51908]
          Length = 329

 Score =  282 bits (721), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 147/333 (44%), Positives = 220/333 (66%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E ++P  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLRPRLVD---IEQVNPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDVLEILLNLKGLAVVVEGKDEAMLTLSKSGAGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-HHRTEND--PIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  V M + V +G GYVPA    +TE+D  PIG + +D+ +S
Sbjct: 118 DGDVTIMNPDHVICHLTGNNDVSMRIRVERGRGYVPASARAQTEDDERPIGRLLVDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   E +
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFV---ELR 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              + ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 235 DVTEPELKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>gi|308272953|emb|CBX29557.1| DNA-directed RNA polymerase subunit alpha [uncultured
           Desulfobacterium sp.]
          Length = 340

 Score =  282 bits (721), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 150/323 (46%), Positives = 218/323 (67%), Gaps = 6/323 (1%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           NWQE+I P+ ++   +     N    + EPL RGF  T+GNALRR+++SSL GAAI +V+
Sbjct: 10  NWQEMIMPDKVQ---VTTNMPNYDKFVCEPLERGFGLTIGNALRRIMLSSLYGAAIVSVK 66

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN- 123
           ID V HE S I GV ED+++IILN+K +  K + D  K V I   G   +TA DI + + 
Sbjct: 67  IDSVFHEFSVIPGVLEDVSEIILNLKCVRFKTADDEPKTVRIDATGECEITARDIISDDG 126

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
             EVLNPD  I +L  DAV++  +TV  G GY  ++ ++ E+DP+G I ID+++SP+K+V
Sbjct: 127 KCEVLNPDIHIASLSKDAVLKANMTVKVGKGYSLSESNKNEDDPVGTIPIDSVFSPVKRV 186

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP-KKEVK 242
           +Y V +AR GQ  DYDKL++ + TDGS++  ++++ +++I+++Q+ +FINF+E  + EV+
Sbjct: 187 NYVVGNARVGQRTDYDKLTIEVWTDGSLSPVEALSYSAKIIKEQMSIFINFDEKLEPEVE 246

Query: 243 EDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +    +  P FN  L + VEELELSVRS NCL+  NI  +  L+ +TEA+MLR  NFGRK
Sbjct: 247 KKSEKRQKPQFNENLYRSVEELELSVRSANCLKNANIFKIYQLVNKTEAEMLRTKNFGRK 306

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL EIK VL  MGL LGM L ++
Sbjct: 307 SLNEIKEVLSEMGLSLGMKLEEF 329


>gi|114330598|ref|YP_746820.1| DNA-directed RNA polymerase subunit alpha [Nitrosomonas eutropha
           C91]
 gi|122314408|sp|Q0AIH1|RPOA_NITEC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|114307612|gb|ABI58855.1| DNA-directed RNA polymerase subunit alpha [Nitrosomonas eutropha
           C91]
          Length = 335

 Score =  281 bits (720), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 141/312 (45%), Positives = 212/312 (67%), Gaps = 6/312 (1%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
           R  ++ EP  RGF +TLGNALRRVL+SS+ G A T + I GV+HE S+I G+ ED+ D+I
Sbjct: 21  RAKVVMEPFERGFGYTLGNALRRVLLSSIPGCAPTKISISGVVHEYSTIDGLQEDIVDLI 80

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+KG+ LK+   +   +++ K   G+VTAGDI++ +D+E++NP+HVI ++     +  +
Sbjct: 81  LNLKGVVLKLHSKNSTVLSLKKDTEGIVTAGDIESSHDVEIVNPEHVIAHITSGGRIEAQ 140

Query: 147 LTVSKGHGYVPAKHHRTEN---DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
           +TV KG GY+P+ +   E+     IG I +DA +SP+++VSYT+E+AR  Q  D DKL +
Sbjct: 141 ITVEKGRGYLPSVNRSREDKSLSSIGDILLDASFSPVRRVSYTIENARVEQRTDLDKLII 200

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            I+T+GS+  E+++  A+R+L +Q   F + E      ++    ++   +P LL+ V++L
Sbjct: 201 DIETNGSVDPEEAIRYAARVLVEQFSFFADLESTLLPTEQP---RAPAIDPILLRPVDDL 257

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           EL+VRS NCL+ ENI Y+GDLIQRTEA++LR  N GRKSL EIK VL +  L LGM L +
Sbjct: 258 ELTVRSANCLKVENIFYIGDLIQRTEAELLRTPNLGRKSLNEIKEVLASRDLSLGMKLEN 317

Query: 324 WPPESIEELAKK 335
           WPP ++E   K+
Sbjct: 318 WPPANLENYVKE 329


>gi|126176330|ref|YP_001052479.1| DNA-directed RNA polymerase subunit alpha [Shewanella baltica
           OS155]
 gi|152998774|ref|YP_001364455.1| DNA-directed RNA polymerase subunit alpha [Shewanella baltica
           OS185]
 gi|160873350|ref|YP_001552666.1| DNA-directed RNA polymerase subunit alpha [Shewanella baltica
           OS195]
 gi|217975176|ref|YP_002359927.1| DNA-directed RNA polymerase subunit alpha [Shewanella baltica
           OS223]
 gi|304412789|ref|ZP_07394391.1| DNA-directed RNA polymerase, alpha subunit [Shewanella baltica
           OS183]
 gi|307307453|ref|ZP_07587188.1| DNA-directed RNA polymerase, alpha subunit [Shewanella baltica
           BA175]
 gi|171704509|sp|A6WHV3|RPOA_SHEB8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|171769979|sp|A3DA47|RPOA_SHEB5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|125999535|gb|ABN63610.1| DNA-directed RNA polymerase, alpha subunit [Shewanella baltica
           OS155]
 gi|151363392|gb|ABS06392.1| DNA-directed RNA polymerase, alpha subunit [Shewanella baltica
           OS185]
 gi|160858872|gb|ABX47406.1| DNA-directed RNA polymerase, alpha subunit [Shewanella baltica
           OS195]
 gi|217500311|gb|ACK48504.1| DNA-directed RNA polymerase, alpha subunit [Shewanella baltica
           OS223]
 gi|304348869|gb|EFM13285.1| DNA-directed RNA polymerase, alpha subunit [Shewanella baltica
           OS183]
 gi|306910241|gb|EFN40674.1| DNA-directed RNA polymerase, alpha subunit [Shewanella baltica
           BA175]
 gi|315265578|gb|ADT92431.1| DNA-directed RNA polymerase, alpha subunit [Shewanella baltica
           OS678]
          Length = 329

 Score =  281 bits (720), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 146/333 (43%), Positives = 219/333 (65%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVNSTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVTIEGKDEAMLTLSKSGAGPVIAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-HHRTEND--PIGLITIDALYS 178
             D+ ++NPDH+IC+L  +  + M + V +G GYVPA    +TE+D  PIG + +DA +S
Sbjct: 118 DGDVTIVNPDHIICHLTGNNDISMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   E +
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFV---ELR 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              + ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 235 DVTEPELKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>gi|77165763|ref|YP_344288.1| DNA-directed RNA polymerase subunit alpha [Nitrosococcus oceani
           ATCC 19707]
 gi|254434921|ref|ZP_05048429.1| DNA-directed RNA polymerase, alpha subunit [Nitrosococcus oceani
           AFC27]
 gi|90110852|sp|Q3J8T8|RPOA_NITOC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|76884077|gb|ABA58758.1| DNA-directed RNA polymerase subunit alpha [Nitrosococcus oceani
           ATCC 19707]
 gi|207091254|gb|EDZ68525.1| DNA-directed RNA polymerase, alpha subunit [Nitrosococcus oceani
           AFC27]
          Length = 332

 Score =  281 bits (720), Expect = 8e-74,   Method: Compositional matrix adjust.
 Identities = 145/307 (47%), Positives = 207/307 (67%), Gaps = 6/307 (1%)

Query: 28  TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIIL 87
           T +  EPL RGF HTLGNALRR+L+SS+ G AI   QIDGVLHE ++ +GV ED+T+I+L
Sbjct: 22  TKVTLEPLERGFGHTLGNALRRILLSSMPGCAIIEAQIDGVLHEYTTKEGVQEDMTEILL 81

Query: 88  NIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           N+KG+ +K+ G     + +  +GP  VTAGDIQ  +D+EV+NP+HVI +L     + + +
Sbjct: 82  NLKGVAVKLHGRDEVTLNLSSKGPVTVTAGDIQLEHDVEVINPEHVIAHLTKSGELNLTM 141

Query: 148 TVSKGHGYVPAKHH--RTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
            V +G GY  A     + E++  IG + +DA +SPI++V+Y V+SAR  Q  D DKL + 
Sbjct: 142 KVVRGRGYQSASMRIPKEEDERSIGHLILDASFSPIRRVTYEVDSARVEQRTDLDKLIIE 201

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           I+T+G+I  +++V  A+ ILQDQL  F+  E   +  KE    K+   +P LL+ +++LE
Sbjct: 202 IETNGTIAPDEAVRKAATILQDQLTAFVELEGKIETAKEK---KAAEIDPVLLQPIDDLE 258

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L+VRS NCL+ ENI Y+GDLIQ+TE ++L+  N G+KSL EIK VL   GL LGM L +W
Sbjct: 259 LTVRSANCLKAENIYYIGDLIQKTEVELLKTPNLGKKSLTEIKDVLTLRGLSLGMRLENW 318

Query: 325 PPESIEE 331
           PP  + E
Sbjct: 319 PPAGLRE 325


>gi|238898902|ref|YP_002924584.1| RNA polymerase, alpha subunit [Candidatus Hamiltonella defensa 5AT
           (Acyrthosiphon pisum)]
 gi|229466662|gb|ACQ68436.1| RNA polymerase, alpha subunit [Candidatus Hamiltonella defensa 5AT
           (Acyrthosiphon pisum)]
          Length = 330

 Score =  281 bits (720), Expect = 8e-74,   Method: Compositional matrix adjust.
 Identities = 148/337 (43%), Positives = 221/337 (65%), Gaps = 16/337 (4%)

Query: 2   IQKNWQELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           +Q +  E +KP   NIE I       +   +  EPL RGF HTLGNALRR+L+SS++G A
Sbjct: 1   MQGSEIEFLKPRLVNIEQI-----SPSHAKITLEPLERGFGHTLGNALRRILLSSMQGYA 55

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T V+IDGVLHE S+ +GV ED+ +++LN+KG+ +K+ G +   VT+ K G G V A DI
Sbjct: 56  VTEVEIDGVLHEYSTKEGVQEDILEVLLNLKGLKVKVQGKNEVTVTLNKSGIGPVLAADI 115

Query: 120 QTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDA 175
               D+E++ P HVIC L D +A + M++ + +G GYVPA        +  PIG + +DA
Sbjct: 116 THNGDVEIVKPQHVICYLTDENASISMKIKIQRGRGYVPASSRMNLEEDERPIGRLLVDA 175

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
            YSP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  ++ IL  QL  FI+  
Sbjct: 176 CYSPVERIAYVVEAARVEQRTDLDKLVIDMETNGTINPEEAIRFSATILAKQLEAFIDLH 235

Query: 236 EPKK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
             ++ E+KE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+
Sbjct: 236 HVRQPELKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLK 291

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
             N G+KSL EIK VL +  L LGM L +WPP ++ +
Sbjct: 292 TPNLGKKSLTEIKDVLASRALSLGMRLENWPPANLSD 328


>gi|288942047|ref|YP_003444287.1| DNA-directed RNA polymerase subunit alpha [Allochromatium vinosum
           DSM 180]
 gi|288897419|gb|ADC63255.1| DNA-directed RNA polymerase, alpha subunit [Allochromatium vinosum
           DSM 180]
          Length = 337

 Score =  281 bits (720), Expect = 9e-74,   Method: Compositional matrix adjust.
 Identities = 143/305 (46%), Positives = 202/305 (66%), Gaps = 4/305 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I GVLHE ++++GV ED+ +I+LN K +
Sbjct: 31  EPLERGFGHTLGNALRRILLSSMDGYAVTEVEIQGVLHEYTTLEGVQEDVLEILLNFKQL 90

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            + + G       + KRGPG VTA DI   +  E+ NP+ VI NL     + M LTV +G
Sbjct: 91  AIVLQGKDEATFALSKRGPGPVTAADIAIDHTAEIANPELVIANLTTGGELSMTLTVRRG 150

Query: 153 HGYVPAKHHR---TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            GY PA        E+ PIG + IDA +SP+++V+  V+SAR  Q  D D+L + ++T+G
Sbjct: 151 RGYEPASQRELEGAEDRPIGKLPIDASFSPVRRVAIEVQSARVEQRTDLDRLVIDLETNG 210

Query: 210 SITGEDSVALASRILQDQLGMFINFE-EPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           +I  ++++  A+ IL+DQL  F+  E     E +   +    P++P LL+ V++LEL+VR
Sbjct: 211 TIDPKETIQRAATILRDQLSSFVALEGTAPAETQVQESRDESPYDPILLRPVDDLELTVR 270

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPES 328
           S NCL+ ENI  +GDLIQRTE ++L+  N G+KSL EIK VL T GL LGM L +WPPE+
Sbjct: 271 SANCLKAENIYLIGDLIQRTEVELLKTPNLGKKSLTEIKDVLATRGLSLGMRLENWPPEN 330

Query: 329 IEELA 333
           I EL+
Sbjct: 331 IAELS 335


>gi|148361030|ref|YP_001252237.1| DNA-directed RNA polymerase subunit alpha RpoA [Legionella
           pneumophila str. Corby]
 gi|296105902|ref|YP_003617602.1| DNA-directed RNA polymerase subunit alpha [Legionella pneumophila
           2300/99 Alcoy]
 gi|166229273|sp|A5IHP1|RPOA_LEGPC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|148282803|gb|ABQ56891.1| DNA-directed RNA polymerase alpha subunit RpoA [Legionella
           pneumophila str. Corby]
 gi|295647803|gb|ADG23650.1| DNA-directed RNA polymerase subunit alpha [Legionella pneumophila
           2300/99 Alcoy]
          Length = 330

 Score =  281 bits (719), Expect = 9e-74,   Method: Compositional matrix adjust.
 Identities = 144/310 (46%), Positives = 212/310 (68%), Gaps = 13/310 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EPL RGF HTLGNALRR+L+SS+ G+AIT   IDGVLHE S+I+GV ED+ D++LN+
Sbjct: 26  IVLEPLERGFGHTLGNALRRILLSSMPGSAITEASIDGVLHEYSTIEGVQEDVVDLLLNL 85

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + +K++  +  +VT+ K GP  VTAGDIQ  +  E++NP+ VI NL+    + M L V
Sbjct: 86  KSVAIKLTVGNEAQVTLNKEGPCQVTAGDIQLTHGQEIINPELVIANLNEKGKLNMTLKV 145

Query: 150 SKGHGY----VPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +G G+       ++H    E   +G + ID  +SP+KKV+Y V+SAR     D DKL++
Sbjct: 146 ERGIGFHNTDAFVRYHEDEIEKKTVGKLKIDNSFSPVKKVAYFVDSARVENRTDLDKLTI 205

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFIN--FEEPKKEVKEDINVKSLPFNPALLKKVE 261
            ++T+G+I  E+++ +++ ILQ QL  F++  FEE + + KE  +     F+P LL+ V+
Sbjct: 206 ELETNGTIDAEEAIRISASILQRQLHAFVDMKFEESRADNKERND-----FDPVLLRSVD 260

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +LEL+VRS NCL+ ENI Y+GDL+QRTE+++L+  N G+KSL EIK VL +  L LGM L
Sbjct: 261 DLELTVRSANCLKAENIHYIGDLVQRTESELLKTPNLGKKSLTEIKDVLASRSLSLGMKL 320

Query: 322 PDWPPESIEE 331
            +WPP S+ E
Sbjct: 321 ENWPPASLGE 330


>gi|308048016|ref|YP_003911582.1| DNA-directed RNA polymerase subunit alpha [Ferrimonas balearica DSM
           9799]
 gi|307630206|gb|ADN74508.1| DNA-directed RNA polymerase subunit alpha [Ferrimonas balearica DSM
           9799]
          Length = 330

 Score =  281 bits (719), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 147/332 (44%), Positives = 217/332 (65%), Gaps = 10/332 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IDQVSPYRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDVLEILLNLKGLAVKLEGKDEAILTLSKSGAGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAK-HHRTEND--PIGLITIDALY 177
             D+E++NP+H+IC L   DA + M + V  G GY+PA    + E D  PIG + +DA +
Sbjct: 118 DGDVEIVNPEHLICTLTGADAEISMRIKVELGRGYIPASARAQVEEDERPIGRLLVDASF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + + TDG++  E+++  ++ IL +QL  F++  + 
Sbjct: 178 SPVVRIAYNVEAARVEQRTDLDKLIIDMHTDGTLDPEEAIRRSATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +  +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 SEPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            G+KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASL 326


>gi|54296390|ref|YP_122759.1| DNA-directed RNA polymerase subunit alpha [Legionella pneumophila
           str. Paris]
 gi|61215818|sp|Q5X834|RPOA_LEGPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|53750175|emb|CAH11567.1| DNA-directed RNA polymerase alpha chain [Legionella pneumophila
           str. Paris]
          Length = 330

 Score =  281 bits (718), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 144/310 (46%), Positives = 212/310 (68%), Gaps = 13/310 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EPL RGF HTLGNALRR+L+SS+ G+AIT   IDGVLHE S+I+GV ED+ D++LN+
Sbjct: 26  IVLEPLERGFGHTLGNALRRILLSSMPGSAITEASIDGVLHEYSTIEGVQEDVVDLLLNL 85

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + +K++  +  +VT+ K GP  VTAGDIQ  +  E++NP+ VI NL+    + M L V
Sbjct: 86  KSVAIKLTVGNEAQVTLNKEGPCQVTAGDIQLTHGQEIINPELVIANLNEKGKLNMTLKV 145

Query: 150 SKGHGY----VPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +G G+       ++H    E   +G + ID  +SP+KKV+Y V+SAR     D DKL++
Sbjct: 146 ERGIGFHNTDAFVRYHDDEIEKKTVGKLKIDNSFSPVKKVAYFVDSARVENRTDLDKLTI 205

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFIN--FEEPKKEVKEDINVKSLPFNPALLKKVE 261
            ++T+G+I  E+++ +++ ILQ QL  F++  FEE + + KE  +     F+P LL+ V+
Sbjct: 206 ELETNGTIDAEEAIRISASILQRQLHAFVDMKFEESRADNKERND-----FDPVLLRSVD 260

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +LEL+VRS NCL+ ENI Y+GDL+QRTE+++L+  N G+KSL EIK VL +  L LGM L
Sbjct: 261 DLELTVRSANCLKAENIHYIGDLVQRTESELLKTPNLGKKSLTEIKDVLASRSLSLGMKL 320

Query: 322 PDWPPESIEE 331
            +WPP S+ E
Sbjct: 321 ENWPPASLGE 330


>gi|294142908|ref|YP_003558886.1| DNA-directed RNA polymerase subunit alpha [Shewanella violacea
           DSS12]
 gi|12230609|sp|Q9S0Q8|RPOA_SHEVD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|5913932|dbj|BAA84525.1| RNA polymerase alpha subunit [Shewanella violacea]
 gi|293329377|dbj|BAJ04108.1| DNA-directed RNA polymerase, alpha subunit [Shewanella violacea
           DSS12]
          Length = 329

 Score =  281 bits (718), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 145/331 (43%), Positives = 218/331 (65%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E ++P  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLRPRLVD---IEQVNPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVVIEGKDEAMLTLSKSGAGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-HHRTEND--PIGLITIDALYS 178
             D+ ++NP+HV+C+L  +  + M + V +G GYVPA    +TE+D  PIG + +DA +S
Sbjct: 118 DGDVTIMNPEHVVCHLTGNNEISMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G++  E+++  A+ IL +QL  F+   E +
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTLDPEEAIRRAATILAEQLDAFV---ELR 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              + +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 235 DVTEPEQKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASL 325


>gi|52840599|ref|YP_094398.1| DNA-directed RNA polymerase subunit alpha [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
 gi|54293346|ref|YP_125761.1| DNA-directed RNA polymerase subunit alpha [Legionella pneumophila
           str. Lens]
 gi|61215814|sp|Q5WZI7|RPOA_LEGPL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61215830|sp|Q5ZYL8|RPOA_LEGPH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|52627710|gb|AAU26451.1| DNA-directed RNA polymerase alpha subunit RpoA [Legionella
           pneumophila subsp. pneumophila str. Philadelphia 1]
 gi|53753178|emb|CAH14625.1| DNA-directed RNA polymerase alpha chain [Legionella pneumophila
           str. Lens]
 gi|307609162|emb|CBW98618.1| DNA-directed RNA polymerase alpha chain [Legionella pneumophila
           130b]
          Length = 330

 Score =  281 bits (718), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 143/310 (46%), Positives = 212/310 (68%), Gaps = 13/310 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EPL RGF HTLGNALRR+L+SS+ G+AIT   IDGVLHE S+I+GV ED+ D++LN+
Sbjct: 26  IVLEPLERGFGHTLGNALRRILLSSMPGSAITEASIDGVLHEYSTIEGVQEDVVDLLLNL 85

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + +K++  +  ++T+ K GP  VTAGDIQ  +  E++NP+ VI NL+    + M L V
Sbjct: 86  KSVAIKLTVGNEAQITLNKEGPCQVTAGDIQLTHGQEIINPELVIANLNEKGKLNMTLKV 145

Query: 150 SKGHGY----VPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +G G+       ++H    E   +G + ID  +SP+KKV+Y V+SAR     D DKL++
Sbjct: 146 ERGIGFHNTDAFVRYHDDEIEKKTVGKLKIDNSFSPVKKVAYFVDSARVENRTDLDKLTI 205

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFIN--FEEPKKEVKEDINVKSLPFNPALLKKVE 261
            ++T+G+I  E+++ +++ ILQ QL  F++  FEE + + KE  +     F+P LL+ V+
Sbjct: 206 ELETNGTIDAEEAIRISASILQRQLHAFVDMKFEESRADNKERND-----FDPVLLRSVD 260

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +LEL+VRS NCL+ ENI Y+GDL+QRTE+++L+  N G+KSL EIK VL +  L LGM L
Sbjct: 261 DLELTVRSANCLKAENIHYIGDLVQRTESELLKTPNLGKKSLTEIKDVLASRSLSLGMKL 320

Query: 322 PDWPPESIEE 331
            +WPP S+ E
Sbjct: 321 ENWPPASLGE 330


>gi|94968283|ref|YP_590331.1| DNA-directed RNA polymerase subunit alpha [Candidatus Koribacter
           versatilis Ellin345]
 gi|119366658|sp|Q1IS93|RPOA_ACIBL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|94550333|gb|ABF40257.1| DNA-directed RNA polymerase subunit alpha [Candidatus Koribacter
           versatilis Ellin345]
          Length = 368

 Score =  281 bits (718), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 145/290 (50%), Positives = 205/290 (70%), Gaps = 1/290 (0%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
           A+P  RGF  T+GNALRRVL+SS+ GAAITAV+I+GVLHE  SI GV ED TDIILN+K 
Sbjct: 28  AQPFERGFGTTIGNALRRVLLSSIEGAAITAVKIEGVLHEFQSIPGVVEDATDIILNLKQ 87

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           I  +++GD+ K + +    PG+VT+G I+T  D+E+L+ D  I  +     + ME+ + K
Sbjct: 88  IPFRLNGDAPKAIYLRAEQPGIVTSGMIETDADVEILDKDVYIATISEGGKLDMEMRLKK 147

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GYV A  +  E+  +G I ID+++SP++K +Y+VE+AR GQ+ DYDKLS+ + T+GS+
Sbjct: 148 GRGYVSADKNFDEDLGLGFIPIDSVHSPVRKCNYSVEAARLGQITDYDKLSIELWTNGSV 207

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTN 271
              D++ LA+++L+D + +FINFEE + E     + K    N  L + VEELELSVRS N
Sbjct: 208 NPADALGLAAKLLKDHMNIFINFEE-EIEASHAEDRKPEIRNENLNRSVEELELSVRSYN 266

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           CL+  NI  +G+L+Q+TEA+ML+  NFGRKSL EIK +L +MGL LGM +
Sbjct: 267 CLKNANIQTIGELVQKTEAEMLKTKNFGRKSLNEIKEILASMGLSLGMKI 316


>gi|30248443|ref|NP_840513.1| DNA-directed RNA polymerase subunit alpha [Nitrosomonas europaea
           ATCC 19718]
 gi|41688666|sp|Q82X69|RPOA_NITEU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|30138329|emb|CAD84337.1| Bacterial RNA polymerase, alpha chain [Nitrosomonas europaea ATCC
           19718]
          Length = 336

 Score =  280 bits (717), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 146/313 (46%), Positives = 209/313 (66%), Gaps = 13/313 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EP   GF +TLGNALRRVL+SS+ G A T V I GV+HE S+I G+ ED+ D+ILN+
Sbjct: 24  VVMEPFEHGFGYTLGNALRRVLLSSIPGCAPTKVSISGVVHEYSTIDGLQEDVVDLILNL 83

Query: 90  KGINLKMSGDSHKRV-TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           KG+ LK+  +  + V T+ K   G+VTAGDI+  +D+E++NPDHVI ++     +  ++T
Sbjct: 84  KGVVLKLHNNKTQSVLTLKKSSEGIVTAGDIEATHDVEIVNPDHVIAHITSGGKIEAQIT 143

Query: 149 VSKGHGYVPAKHHRTEN---DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           V KG GY P+ +   E+     IG I +DA +SPI++VSY VESAR  Q  D DKL + I
Sbjct: 144 VEKGRGYWPSANRSKEDKSSSSIGDILLDASFSPIRRVSYAVESARVEQRTDLDKLIIDI 203

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEE---PKKEVKEDINVKSLPFNPALLKKVEE 262
           +T+GS+  E+++  A+++L +Q   F + E    P ++ K  +       +P LL+ V++
Sbjct: 204 ETNGSVDPEEAIRYAAKVLVEQFSFFADLESTPLPTEQPKAPV------IDPILLRPVDD 257

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           LEL+VRS NCL+ ENI Y+GDLIQRTEA++LR  N GRKSL EIK VL +  L LGM L 
Sbjct: 258 LELTVRSANCLKVENIFYIGDLIQRTEAELLRTPNLGRKSLNEIKEVLASRDLSLGMKLE 317

Query: 323 DWPPESIEELAKK 335
           +WPP ++E   K+
Sbjct: 318 NWPPANLENYIKE 330


>gi|94500967|ref|ZP_01307492.1| DNA-directed RNA polymerase alpha subunit [Oceanobacter sp. RED65]
 gi|94426907|gb|EAT11890.1| DNA-directed RNA polymerase alpha subunit [Oceanobacter sp. RED65]
          Length = 333

 Score =  280 bits (716), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 146/333 (43%), Positives = 220/333 (66%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  E + P +I+   +   +   TL   EPL RGF HTLG ALRR+L+SS+ GAAI 
Sbjct: 1   MQRSVNEFLTPRHIQVEQVSNTQAKVTL---EPLERGFGHTLGAALRRILLSSMPGAAIV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ +I+LN+KG+ +++       +T+ K G G VTA DIQ 
Sbjct: 58  EVEIDGVLHEYSTIEGVQEDVIEILLNLKGVAVRLHERDEAFLTLHKTGAGQVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
            + +E+ NP+HVI NL     ++M + V+ G GY   +    +  E   IG + +DA YS
Sbjct: 118 DHGVEIANPEHVIANLSDKGELKMTIKVAAGRGYETVESRNQNEEETKAIGKLQLDATYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+K+V+Y VE+AR  Q  D DKL + ++T+G+I  E+++  ++ ILQ QL +F++    +
Sbjct: 178 PVKRVAYGVENARVEQRTDLDKLVIDLETNGTIEPEEAIRRSATILQQQLAVFVDL---E 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E + +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 235 NEAEPEPEEQEDEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM+L +WPP S+++
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMHLENWPPASLKK 327


>gi|299138174|ref|ZP_07031354.1| DNA-directed RNA polymerase, alpha subunit [Acidobacterium sp.
           MP5ACTX8]
 gi|298600104|gb|EFI56262.1| DNA-directed RNA polymerase, alpha subunit [Acidobacterium sp.
           MP5ACTX8]
          Length = 359

 Score =  280 bits (716), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 148/318 (46%), Positives = 209/318 (65%), Gaps = 5/318 (1%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           W+   KP  +    + QE    T     A+P  RGF  T+GNALRR L+SS+ GAA+TAV
Sbjct: 3   WRGFQKPKRL---AVDQETLTPTFGKFSAQPFERGFGTTIGNALRRTLLSSIEGAAVTAV 59

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+GVLHE  SI GV ED TDIILN+K I  K++GD  K + +     GVVT+G I+  +
Sbjct: 60  KIEGVLHEFQSIAGVVEDATDIILNLKQIPFKLNGDGPKTLYLRADAAGVVTSGSIEADS 119

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           D+E+L+P   IC +     + ME+ + +G GYV A  +   +  IG I +D+++SP++KV
Sbjct: 120 DVEILDPSVYICTISEGGRIDMEMRLKRGRGYVSADKNFDSDLGIGFIPVDSVHSPVRKV 179

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR GQ+ DYDKL++ I T+G+I   D++ L++++L+D + +FINFEE  +    
Sbjct: 180 NYLVEAARLGQITDYDKLTLEIWTNGTILPADALGLSAKLLKDHMTIFINFEEEMEAGAS 239

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             +   L  N  L + VEELELSVRS NCL+  NI  +G+LIQ+TEA+ML+  NFGRKSL
Sbjct: 240 GDHDGPLLRNENLNRSVEELELSVRSYNCLKNANIATIGELIQKTEAEMLKTKNFGRKSL 299

Query: 304 VEIKGVLGTMGLFLGMNL 321
            EIK +L  MGL LGM +
Sbjct: 300 NEIKEILAQMGLSLGMKI 317


>gi|187930338|ref|YP_001900825.1| DNA-directed RNA polymerase subunit alpha [Ralstonia pickettii 12J]
 gi|241664506|ref|YP_002982866.1| DNA-directed RNA polymerase subunit alpha [Ralstonia pickettii 12D]
 gi|309782860|ref|ZP_07677580.1| DNA-directed RNA polymerase, alpha subunit [Ralstonia sp.
           5_7_47FAA]
 gi|238691836|sp|B2UEJ3|RPOA_RALPJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|187727228|gb|ACD28393.1| DNA-directed RNA polymerase, alpha subunit [Ralstonia pickettii
           12J]
 gi|240866533|gb|ACS64194.1| DNA-directed RNA polymerase, alpha subunit [Ralstonia pickettii
           12D]
 gi|308918284|gb|EFP63961.1| DNA-directed RNA polymerase, alpha subunit [Ralstonia sp.
           5_7_47FAA]
          Length = 326

 Score =  280 bits (715), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 151/327 (46%), Positives = 212/327 (64%), Gaps = 9/327 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG   ++   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVEPLG---DHHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S+I GV ED+ +++LN+KG+  K+       V++ K G GVVTA DI+  +D+E++
Sbjct: 62  VHEYSTIDGVQEDVVNLLLNLKGVVFKLHNRDEVTVSLRKEGEGVVTAADIELPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NP HVI NL     + ++L V +G GYVP    +  ++    IG I +DA ++P+++VSY
Sbjct: 122 NPGHVIANLSAGGKLDLQLKVEQGRGYVPGNVRKFGDESSKVIGRIVLDASFAPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL DQL +F   E    E   + 
Sbjct: 182 AVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALE--GTESAAEA 239

Query: 246 NVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
                P  +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL 
Sbjct: 240 AAARAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLN 299

Query: 305 EIKGVLGTMGLFLGMNLPDWPPESIEE 331
           EIK VL + GL LGM L +WPP  +E+
Sbjct: 300 EIKEVLASRGLTLGMKLENWPPAGLEK 326


>gi|224713514|gb|ACN62064.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus minor]
          Length = 309

 Score =  280 bits (715), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 143/294 (48%), Positives = 207/294 (70%), Gaps = 9/294 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 20  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 79

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+       +T+ K G G VTAGDI    D+E++NPDHVIC+L D +A + M + V +
Sbjct: 80  AVKVQSKDDVVLTLNKSGIGPVTAGDITHDGDVEIVNPDHVICHLTDKNASINMRIRVQR 139

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 140 GRGYVPASARIHAQDDDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLIIEMETN 199

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 200 GTIDPEEAIRRAATILAEQLDAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 255

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L
Sbjct: 256 RSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRL 309


>gi|260772121|ref|ZP_05881038.1| DNA-directed RNA polymerase alpha subunit [Vibrio metschnikovii CIP
           69.14]
 gi|260612988|gb|EEX38190.1| DNA-directed RNA polymerase alpha subunit [Vibrio metschnikovii CIP
           69.14]
          Length = 330

 Score =  280 bits (715), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 146/335 (43%), Positives = 222/335 (66%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  +  +  +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRLGENKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E++NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIVNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +SP+ K++Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 FSPVDKIAYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|118595310|ref|ZP_01552657.1| DNA-directed RNA polymerase subunit alpha [Methylophilales
           bacterium HTCC2181]
 gi|118441088|gb|EAV47715.1| DNA-directed RNA polymerase subunit alpha [Methylophilales
           bacterium HTCC2181]
          Length = 328

 Score =  279 bits (714), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 149/335 (44%), Positives = 214/335 (63%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  +   ++  +   R  ++ EP+ RGF  TLGNALRRVL+SS+ G AIT
Sbjct: 1   MQNSPTEYLKPRIVNVDIVNSQ---RAKVVLEPMERGFGFTLGNALRRVLLSSIPGYAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGV+HE S+++GV ED+ D++LN+K + LK+   +   + + K   G VT  D   
Sbjct: 58  EVKIDGVVHEYSTLEGVQEDVVDVLLNLKKVALKIHEGTEATIRLSKSEEGPVTVADFDV 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYS 178
            +D+EV+NP+HVI +L+    + +E  V  G GY P    R    E+  IG I IDA +S
Sbjct: 118 GHDVEVVNPEHVIAHLNKGGKLNIEAKVEMGRGYQPVPQRRKGPQEDSTIGYIMIDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI KVSY VESAR  Q  D D+L + ++T+G +  E ++  A+RIL  QL +F N E   
Sbjct: 178 PINKVSYFVESARVEQRTDLDRLILDVETNGVVDAEQAIRDAARILMGQLSVFANLESEL 237

Query: 239 KEVKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            EV+    V+  P  +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQR E+D+L+  N
Sbjct: 238 TEVE----VQQAPQIDPVLLRPVDDLELTVRSANCLKAESIYYIGDLIQRNESDLLKAPN 293

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEEL 332
            GRKSL EIK +L T GL LGM + +WPP  +E++
Sbjct: 294 LGRKSLNEIKDILATKGLSLGMKVENWPPAGVEKV 328


>gi|71905987|ref|YP_283574.1| DNA-directed RNA polymerase subunit alpha [Dechloromonas aromatica
           RCB]
 gi|90110836|sp|Q47J77|RPOA_DECAR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|71845608|gb|AAZ45104.1| DNA-directed RNA polymerase subunit alpha [Dechloromonas aromatica
           RCB]
          Length = 324

 Score =  279 bits (713), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 144/305 (47%), Positives = 202/305 (66%), Gaps = 8/305 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EP  RG+ HTLGNALRR+L+SS+ G A T V IDGVLHE S++ GV ED+ DI+LN+
Sbjct: 24  VVMEPFERGYGHTLGNALRRILLSSMVGYAPTEVGIDGVLHEYSTVDGVQEDVVDILLNL 83

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+  K+       + + K G G V AGDI+  +D+E++NP+HVI +L     + ME+ V
Sbjct: 84  KGVVFKLHNRDVVNLKLVKEGEGAVRAGDIELPHDVEIINPEHVIAHLSPGGKLAMEIKV 143

Query: 150 SKGHGYVPAK-HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
            KG GYVP    +  +   IG + +DA +SPI++V+Y VESAR  Q  D DKL + I+T+
Sbjct: 144 EKGRGYVPGNVRNLGDAKTIGKLVLDASFSPIRRVAYAVESARVEQRTDLDKLIVDIETN 203

Query: 209 GSITGEDSVALASRILQDQLGMFINFE--EPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           G +  E+++  A+R+L +QL +F + E   P  E  +   V     +P LL+ V++LEL+
Sbjct: 204 GVVEPEEAIRYAARVLMEQLSVFADLEGTAPVAEASKPAQV-----DPVLLRPVDDLELT 258

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL EIK VL   GL LGM L +WPP
Sbjct: 259 VRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNEIKEVLAARGLTLGMKLENWPP 318

Query: 327 ESIEE 331
             +E+
Sbjct: 319 AGLEK 323


>gi|254468410|ref|ZP_05081816.1| DNA-directed RNA polymerase, alpha subunit [beta proteobacterium
           KB13]
 gi|207087220|gb|EDZ64503.1| DNA-directed RNA polymerase, alpha subunit [beta proteobacterium
           KB13]
          Length = 327

 Score =  279 bits (713), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 152/332 (45%), Positives = 216/332 (65%), Gaps = 10/332 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  +E  ++     NR  ++ EP+ RGF  TLGNALRRVL+SS+ G AIT
Sbjct: 1   MQNSPTEYLKPRIVEVDLINP---NRAKVVLEPMERGFGFTLGNALRRVLLSSIPGFAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGV+HE S+I GV ED+ DI+LN+K + LK+   +   + + K   G VTA D + 
Sbjct: 58  EVKIDGVVHEYSTIDGVQEDVVDILLNLKKVALKIHDGAEATINLKKDSEGEVTAADFEL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY--VPAKHHRTENDPIGLITIDALYSP 179
            +++E++N D VI N++    + +E  V  G GY  VP + ++ +++ IG + IDA +SP
Sbjct: 118 PHNVEIVNKDLVIANVNKGGNLNIEAKVEMGRGYQPVPQRVNKDQDNVIGHLMIDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I KVSY VESAR  Q  D DKL M ++T+G +  E ++  A+RIL  QL +F N E    
Sbjct: 178 IFKVSYVVESARVEQRTDLDKLIMDVETNGVVDAEQAIRDAARILMGQLSVFANLESELT 237

Query: 240 EVKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           EV+    V+  P  +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQR E D+L+  N 
Sbjct: 238 EVE----VQQAPQIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRHENDLLKAPNL 293

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           GRKSL EIK +L T GL LGM + +WPP+ +E
Sbjct: 294 GRKSLNEIKDILATKGLSLGMKVDNWPPQGVE 325


>gi|78484664|ref|YP_390589.1| DNA-directed RNA polymerase subunit alpha [Thiomicrospira crunogena
           XCL-2]
 gi|119366747|sp|Q31IV8|RPOA_THICR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|78362950|gb|ABB40915.1| DNA-directed RNA polymerase, alpha subunit [Thiomicrospira
           crunogena XCL-2]
          Length = 329

 Score =  279 bits (713), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 143/298 (47%), Positives = 204/298 (68%), Gaps = 4/298 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ GAAI   QIDGVLHE S+I+GV ED+ +I+LN+K +
Sbjct: 29  EPLERGFGHTLGNALRRILLSSMPGAAIVEAQIDGVLHEYSAIEGVREDVLEIMLNLKEV 88

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K++  S   +T+ K+GP VVTA DIQ  +D E++NPD VI +L   A + M+L V KG
Sbjct: 89  AIKLNETSEAELTLSKKGPAVVTAADIQLNHDTEIMNPDLVIAHLGEGAELSMKLKVEKG 148

Query: 153 HGYVPA-KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
            GY  A +   +E+  IG++ +DA +SP+K VSY V++AR  Q  D DKL + + TDG++
Sbjct: 149 IGYRAAVQSSDSESANIGVLKLDASFSPVKTVSYEVQNARVEQRTDLDKLILNVVTDGTL 208

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTN 271
             ED++  A+ +L  QL  F++ +  +  V+E+   +   F+P  L+ V++LEL+VRS N
Sbjct: 209 DPEDAIKQAATVLHYQLIAFVDLKHKEIVVQEE---EENEFDPIFLQPVDDLELTVRSAN 265

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           CL+ E I Y+GDL+QR E+ +L+  N G+KSL EIK VL   GL LG  L +WPP S+
Sbjct: 266 CLKAEQIYYIGDLVQRAESSLLKTPNLGKKSLQEIKDVLAQRGLGLGTKLENWPPSSL 323


>gi|300690186|ref|YP_003751181.1| RNA polymerase, alpha subunit; RNA polymerase alpha chain family
           [Ralstonia solanacearum PSI07]
 gi|299077246|emb|CBJ49872.1| RNA polymerase, alpha subunit; RNA polymerase alpha chain family
           [Ralstonia solanacearum PSI07]
          Length = 326

 Score =  279 bits (713), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 150/327 (45%), Positives = 212/327 (64%), Gaps = 9/327 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG   ++   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVEPLG---DHHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYASTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S+I GV ED+ +++LN+KG+  K+       V++ K G GVVTA DI+  +D+E++
Sbjct: 62  VHEYSTIDGVQEDVVNLLLNLKGVVFKLHNRDEVTVSLRKEGEGVVTAADIELPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NP HVI +L     + M++ V +G GYVP    +  ++    IG I +DA ++P+++VSY
Sbjct: 122 NPGHVIASLSAGGKLDMQIKVEQGRGYVPGNVRKFGDESSKVIGRIVLDASFAPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL DQL +F   E    E   + 
Sbjct: 182 AVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALE--GTESAAEA 239

Query: 246 NVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
                P  +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL 
Sbjct: 240 AAARAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLN 299

Query: 305 EIKGVLGTMGLFLGMNLPDWPPESIEE 331
           EIK VL + GL LGM L +WPP  +E+
Sbjct: 300 EIKEVLASRGLTLGMKLENWPPAGLEK 326


>gi|94312222|ref|YP_585432.1| DNA-directed RNA polymerase subunit alpha [Cupriavidus
           metallidurans CH34]
 gi|119366711|sp|Q1LI63|RPOA_RALME RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|93356074|gb|ABF10163.1| RNA polymerase, alpha subunit [Cupriavidus metallidurans CH34]
          Length = 326

 Score =  278 bits (712), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 150/326 (46%), Positives = 212/326 (65%), Gaps = 7/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG   ++   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVEPLG---DHHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S+I GV ED+ +++LN+KG+  K+       V++ K G GVVTA DI+  +D+E++
Sbjct: 62  VHEYSTIDGVQEDVVNLLLNLKGVVFKLHNRDEVTVSLRKDGEGVVTAADIELPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NP HVI +L     + M++ V +G GYVP    +  ++    IG I +DA +SP+++VSY
Sbjct: 122 NPGHVIAHLSAGGKLDMQIKVEQGRGYVPGNVRKFGDEASKVIGRIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+TDG I+ E+++  ++RIL DQL +F   E  +   +   
Sbjct: 182 AVESARVEQRTDLDKLVMNIETDGVISPEEAIRQSARILVDQLSVFAALEGTESAAEAAS 241

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           +      +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 242 SRAP-QIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 300

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +E+
Sbjct: 301 IKEVLASRGLTLGMKLENWPPAGLEK 326


>gi|218885213|ref|YP_002434534.1| DNA-directed RNA polymerase subunit alpha [Desulfovibrio vulgaris
           str. 'Miyazaki F']
 gi|226699353|sp|B8DNK9|RPOA_DESVM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|218756167|gb|ACL07066.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio vulgaris
           str. 'Miyazaki F']
          Length = 347

 Score =  278 bits (712), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 149/337 (44%), Positives = 213/337 (63%), Gaps = 13/337 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +NW EL+KP   E I    +  +      + EPL RG+  T+GNALRRVL+SSL+GAA  
Sbjct: 13  RNWSELVKP---EQITRDSDPADAMYGKFVCEPLERGYGTTIGNALRRVLLSSLQGAAFV 69

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V++ GV HE ++I GV ED+TDI+LN+K + L M  D  + + +     G V AGDI+T
Sbjct: 70  SVKVSGVQHEFTTIPGVLEDVTDIVLNLKQVRLAMDTDEPQFLELSVNKKGAVKAGDIKT 129

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              + VLNPD  I  L  D  +  E  V  G GYVPA  H   ++ IGLI +D+ ++P++
Sbjct: 130 NQHVMVLNPDLHIATLTEDLELTFEFEVRMGKGYVPADMHEGLSEEIGLIKLDSSFAPVR 189

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KV+YTVE AR GQ+ +YDKL + + TDGS+T ED++A +++I++DQ+ +FINF+E     
Sbjct: 190 KVAYTVEQARVGQMTNYDKLIIEVWTDGSVTPEDAIAYSAKIIKDQISVFINFDERISGE 249

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
               +  S   N  L K ++ELELSVR+TNCL+  NI  +G+L+Q++E +ML+  NFGRK
Sbjct: 250 SSGNSSGSSDVNENLFKGIDELELSVRATNCLKSANITLVGELVQKSENEMLKTKNFGRK 309

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  M L  GM         ++   KKY++
Sbjct: 310 SLDEIKRVLCDMSLDFGM--------KVDGFEKKYQE 338


>gi|17547712|ref|NP_521114.1| DNA-directed RNA polymerase subunit alpha [Ralstonia solanacearum
           GMI1000]
 gi|20139458|sp|Q8XV38|RPOA_RALSO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|17430017|emb|CAD16702.1| probable dna-directed rna polymerase alpha chain (rnap
           alphasubunit) (transcriptase alpha chain) (rna
           polymerase alpha subunit) protein [Ralstonia
           solanacearum GMI1000]
 gi|299065441|emb|CBJ36610.1| RNA polymerase, alpha subunit; RNA polymerase alpha chain family
           [Ralstonia solanacearum CMR15]
          Length = 326

 Score =  278 bits (712), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 150/327 (45%), Positives = 212/327 (64%), Gaps = 9/327 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG   ++   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVEPLG---DHHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S+I GV ED+ +++LN+KG+  K+       V++ K G GVVTA DI+  +D+E++
Sbjct: 62  VHEYSTIDGVQEDVVNLLLNLKGVVFKLHNRDEVTVSLRKEGEGVVTAADIELPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NP HVI +L     + M++ V +G GYVP    +  ++    IG I +DA ++P+++VSY
Sbjct: 122 NPGHVIASLSAGGKLDMQIKVEQGRGYVPGNVRKFGDESSKVIGRIVLDASFAPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL DQL +F   E    E   + 
Sbjct: 182 AVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALE--GTESAAEA 239

Query: 246 NVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
                P  +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL 
Sbjct: 240 AAARAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLN 299

Query: 305 EIKGVLGTMGLFLGMNLPDWPPESIEE 331
           EIK VL + GL LGM L +WPP  +E+
Sbjct: 300 EIKEVLASRGLTLGMKLENWPPAGLEK 326


>gi|119946252|ref|YP_943932.1| DNA-directed RNA polymerase subunit alpha [Psychromonas ingrahamii
           37]
 gi|158513118|sp|A1SXW8|RPOA1_PSYIN RecName: Full=DNA-directed RNA polymerase subunit alpha 1;
           Short=RNAP subunit alpha 1; AltName: Full=RNA polymerase
           subunit alpha 1; AltName: Full=Transcriptase subunit
           alpha 1
 gi|119864856|gb|ABM04333.1| DNA-directed RNA polymerase, alpha subunit [Psychromonas ingrahamii
           37]
          Length = 328

 Score =  278 bits (711), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 147/336 (43%), Positives = 224/336 (66%), Gaps = 15/336 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEEN--RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           +Q   ++ +KPN     ++G E+ N  R  +  EPL RGF HTLGNALRR+L+SS+ GAA
Sbjct: 1   MQGFVKDFLKPN-----LVGIEQINATRAKVTLEPLERGFGHTLGNALRRILLSSMPGAA 55

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           IT V+IDGV +E S  +GV E++ +I+LN+KG+ +K+ G +   V++ K G G V A DI
Sbjct: 56  ITEVEIDGVQNEYSIKEGVQEEILEILLNLKGLAVKLEGKNEVLVSLTKSGAGPVIAADI 115

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              +D+E++NP+HVIC+L  +  + M + +  G GYVPA    H   +    G + +DA 
Sbjct: 116 THDSDLEIVNPEHVICHLTGNTEISMRIKIELGRGYVPASSRIHSEEDKSANGRLFVDAT 175

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +SP+++++Y+VESAR  Q  + DKL + ++TDG++  E+++  A+ IL  QL  F++   
Sbjct: 176 FSPVERIAYSVESARVEQRTNLDKLVIDMETDGTLEPEEAIRQAAMILAGQLDEFVD--- 232

Query: 237 PKKEVKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
            ++ +   + V+  P F+P LL+ V +LEL+VRS NCL+ E+I Y+GDL+QRTE ++L+M
Sbjct: 233 -ERIISAPVEVEEKPEFDPILLRPVNDLELTVRSANCLKAESIYYIGDLVQRTEVELLKM 291

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N GRKSL EIK  L + GL+LGM L +WPP S+ E
Sbjct: 292 PNLGRKSLTEIKDDLVSRGLYLGMRLENWPPASLIE 327


>gi|257095015|ref|YP_003168656.1| DNA-directed RNA polymerase subunit alpha [Candidatus
           Accumulibacter phosphatis clade IIA str. UW-1]
 gi|257047539|gb|ACV36727.1| DNA-directed RNA polymerase, alpha subunit [Candidatus
           Accumulibacter phosphatis clade IIA str. UW-1]
          Length = 324

 Score =  278 bits (710), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 145/305 (47%), Positives = 203/305 (66%), Gaps = 7/305 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EP  RG+ HTLGNALRR+L+SS+ G A T V IDGVLHE S+I GV ED+ DI+LN+
Sbjct: 24  VVMEPFERGYGHTLGNALRRILLSSMPGYAPTEVSIDGVLHEYSTIDGVQEDVVDILLNL 83

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+  K+       + + K G GVV A DI+  +D+E++NP+H+I +L     + MEL V
Sbjct: 84  KGVVFKLHNREEVVLHLRKEGKGVVRAADIEVSHDVEIINPEHIIAHLSAGGKLAMELKV 143

Query: 150 SKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            K  GY+ A + R   D    IG + +DA +SP+++VSY VESAR  Q  D DKL M I+
Sbjct: 144 EKSRGYL-AGNLREFGDGGKSIGKLVLDASFSPVRRVSYAVESARVEQRTDLDKLIMDIE 202

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+G+I  E+++  A+RIL +QL +F +       ++     K++  +P LL+ V++LEL+
Sbjct: 203 TNGAIEPEEAIRTAARILMEQLSVFADLAGTAMPIEYQ---KTVQVDPLLLRPVDDLELT 259

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL EIK VL   GL LGM L +WPP
Sbjct: 260 VRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNEIKEVLAARGLTLGMKLENWPP 319

Query: 327 ESIEE 331
             +E+
Sbjct: 320 AGLEK 324


>gi|15617093|ref|NP_240306.1| DNA-directed RNA polymerase subunit alpha [Buchnera aphidicola str.
           APS (Acyrthosiphon pisum)]
 gi|219682400|ref|YP_002468784.1| DNA-directed RNA polymerase alpha subunit [Buchnera aphidicola str.
           Tuc7 (Acyrthosiphon pisum)]
 gi|11134569|sp|P57566|RPOA_BUCAI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|25288361|pir||H84987 DNA-directed RNA polymerase (EC 2.7.7.6) alpha chain [imported] -
           Buchnera sp. (strain APS)
 gi|10039158|dbj|BAB13192.1| DNA-directed RNA polymerase alpha chain [Buchnera aphidicola str.
           APS (Acyrthosiphon pisum)]
 gi|219622133|gb|ACL30289.1| DNA-directed RNA polymerase alpha subunit [Buchnera aphidicola str.
           Tuc7 (Acyrthosiphon pisum)]
 gi|311086221|gb|ADP66303.1| DNA-directed RNA polymerase subunit alpha [Buchnera aphidicola str.
           LL01 (Acyrthosiphon pisum)]
 gi|311086798|gb|ADP66879.1| DNA-directed RNA polymerase subunit alpha [Buchnera aphidicola str.
           TLW03 (Acyrthosiphon pisum)]
 gi|311087385|gb|ADP67465.1| DNA-directed RNA polymerase subunit alpha [Buchnera aphidicola str.
           JF99 (Acyrthosiphon pisum)]
 gi|311087882|gb|ADP67961.1| DNA-directed RNA polymerase subunit alpha [Buchnera aphidicola str.
           JF98 (Acyrthosiphon pisum)]
          Length = 329

 Score =  278 bits (710), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 144/332 (43%), Positives = 218/332 (65%), Gaps = 10/332 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  + ++P  ++   + Q     T +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQNSIMDFLRPRLVD---IEQISATHTKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+K + +K+ G     +T+ K G G +TA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDVLEILLNLKALAVKVYGKDETLLTLHKSGIGSITAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A ++M + V +G GY+PA    H   ++ PIG + +DA Y
Sbjct: 118 DGDVEIIKPQHVICHLTDENASIKMRIKVQRGRGYIPASSRVHLEEDSRPIGCLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPI ++SY VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPINRISYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDI 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++   ++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 REPEFKEEKPEFEPI---LLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            G+KSL EIK VL +  L LGM L +WPP SI
Sbjct: 295 LGKKSLTEIKDVLASRSLSLGMRLENWPPSSI 326


>gi|83748175|ref|ZP_00945202.1| DNA-directed RNA polymerase alpha chain [Ralstonia solanacearum
           UW551]
 gi|300702806|ref|YP_003744407.1| RNA polymerase subunit alpha; RNA polymerase alpha chain family
           [Ralstonia solanacearum CFBP2957]
 gi|83725143|gb|EAP72294.1| DNA-directed RNA polymerase alpha chain [Ralstonia solanacearum
           UW551]
 gi|299070468|emb|CBJ41763.1| RNA polymerase, alpha subunit; RNA polymerase alpha chain family
           [Ralstonia solanacearum CFBP2957]
          Length = 326

 Score =  278 bits (710), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 149/327 (45%), Positives = 212/327 (64%), Gaps = 9/327 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG   ++   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVEPLG---DHHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S+I GV ED+ +++LN+KG+  K+       V++ K G GVVTA DI+  +D+E++
Sbjct: 62  VHEYSTIDGVQEDVVNLLLNLKGVVFKLHNRDEVTVSLRKEGEGVVTAADIELPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NP HVI +L     + M++ V +G GYVP    +  ++    IG + +DA ++P+++VSY
Sbjct: 122 NPGHVIASLSAGGKLDMQIKVEQGRGYVPGNVRKFGDESSKVIGRVVLDASFAPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL DQL +F   E    E   + 
Sbjct: 182 AVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALE--GTESAAEA 239

Query: 246 NVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
                P  +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL 
Sbjct: 240 AAARAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLN 299

Query: 305 EIKGVLGTMGLFLGMNLPDWPPESIEE 331
           EIK VL + GL LGM L +WPP  +E+
Sbjct: 300 EIKEVLASRGLTLGMKLENWPPAGLEK 326


>gi|73542838|ref|YP_297358.1| DNA-directed RNA polymerase subunit alpha [Ralstonia eutropha
           JMP134]
 gi|90110863|sp|Q46WG9|RPOA_RALEJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|72120251|gb|AAZ62514.1| DNA-directed RNA polymerase, alpha subunit [Ralstonia eutropha
           JMP134]
          Length = 326

 Score =  278 bits (710), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 148/326 (45%), Positives = 213/326 (65%), Gaps = 7/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG   ++   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVEPLG---DHHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S+I GV ED+ +++LN+KG+  K+       V++ K G G+VTA DI+  +D+E++
Sbjct: 62  VHEYSTIDGVQEDVVNLLLNLKGVVFKLHNRDEVTVSLRKDGEGIVTAADIELPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NP+HVI +L     + M++ V +G GYVP    +  ++    IG I +DA +SP+++VSY
Sbjct: 122 NPNHVIAHLSAGGKLDMQIKVEQGRGYVPGNVRKFGDESSKVIGRIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+TDG I+ E+++  ++RIL DQL +F   E  +   +   
Sbjct: 182 AVESARVEQRTDLDKLVMNIETDGVISPEEAIRQSARILVDQLSVFAALEGTESAAEAAS 241

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           +      +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 242 SRAP-QIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 300

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +++
Sbjct: 301 IKEVLASRGLTLGMKLENWPPAGLDK 326


>gi|219681845|ref|YP_002468231.1| DNA-directed RNA polymerase alpha subunit [Buchnera aphidicola str.
           5A (Acyrthosiphon pisum)]
 gi|219624688|gb|ACL30843.1| DNA-directed RNA polymerase alpha subunit [Buchnera aphidicola str.
           5A (Acyrthosiphon pisum)]
          Length = 329

 Score =  277 bits (708), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 144/332 (43%), Positives = 217/332 (65%), Gaps = 10/332 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  + ++P  ++   + Q     T +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQNSIMDFLRPRLVD---IEQISATHTKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+K + +K+ G     +T+ K G G +TA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDVLEILLNLKALAVKVYGKDETLLTLHKSGIGSITAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A ++M + V +G GY+PA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIIKPQHVICHLTDENASIKMRIKVQRGRGYIPASSRVHLEEDARPIGCLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPI ++SY VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPINRISYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDI 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++   ++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 REPEFKEEKPEFEPI---LLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            G+KSL EIK VL +  L LGM L +WPP SI
Sbjct: 295 LGKKSLTEIKDVLASRSLSLGMRLENWPPSSI 326


>gi|88812732|ref|ZP_01127978.1| DNA-directed RNA polymerase, alpha subunit [Nitrococcus mobilis
           Nb-231]
 gi|88789970|gb|EAR21091.1| DNA-directed RNA polymerase, alpha subunit [Nitrococcus mobilis
           Nb-231]
          Length = 333

 Score =  276 bits (707), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 144/340 (42%), Positives = 218/340 (64%), Gaps = 14/340 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q  +++ ++P  +    L    +   ++  EPL RGF HTLGNALRRVL+SS+ G A+ 
Sbjct: 1   MQGQFKDFLRPRLVGVEALS---DRHAMITLEPLERGFGHTLGNALRRVLLSSMPGYAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GVLHE ++I+GV ED+ DI+LN+K + +++       + + K+GPG+VTA DI  
Sbjct: 58  EVEIEGVLHEYTAIEGVQEDVVDILLNLKNLAVRLHSKDTATLHLSKQGPGLVTAADIGI 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP--AKHHRTENDPIGLITIDALYSP 179
            +D+E+ NP+  I NL   + + M L +++G GY P   +    E  PIG + +DA YSP
Sbjct: 118 DHDVEIKNPELAIANLTKASEINMTLHIARGRGYEPVTTRGEHDEERPIGRLQLDASYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +++V+Y VESAR  Q  D DKL M I+T+G +  E++V  A+ +L+DQL +F++ E    
Sbjct: 178 VRRVAYNVESARVEQRTDLDKLVMDIETNGVLEPEEAVRFAAGLLRDQLSVFVDLE--GG 235

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           E  ED    +   +P LL+ +++LEL+VRS NCL+ ENI  +GDL+Q+TE ++L+  N G
Sbjct: 236 EEAEDQERTAPEVDPVLLRSIDDLELTVRSANCLKAENIHCVGDLVQKTEVELLKTPNLG 295

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           +KSL EIK VL   GL LGM L +WPP       + Y+DK
Sbjct: 296 KKSLNEIKEVLAQHGLALGMRLENWPP-------RGYDDK 328


>gi|291613262|ref|YP_003523419.1| DNA-directed RNA polymerase subunit alpha [Sideroxydans
           lithotrophicus ES-1]
 gi|291583374|gb|ADE11032.1| DNA-directed RNA polymerase, alpha subunit [Sideroxydans
           lithotrophicus ES-1]
          Length = 323

 Score =  276 bits (707), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 151/318 (47%), Positives = 205/318 (64%), Gaps = 8/318 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I+   + +    +  ++ EP  RG+ HTLGNALRRVL+SS+ G A+T V+I GV
Sbjct: 6   LLKPRIID---VQRSSATQARVVMEPFERGYGHTLGNALRRVLLSSMPGYAVTEVKIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE SSI GV ED+ +I+LN+KG+ LK+       + + K G GVVTA DI+   D EV+
Sbjct: 63  LHEYSSIDGVQEDVVEILLNLKGLVLKLHNSREATLHLRKSGAGVVTAADIEVGADTEVI 122

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYT 186
           NP+HVI +L     + ME+ V +G GYV A  +       P+G I +DA +SPI +VSY 
Sbjct: 123 NPNHVIAHLAAGGKLDMEIKVEQGRGYVSAISRMQPGATRPVGHIALDASFSPISRVSYA 182

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VESAR  Q  D DKL M I+T+ +I  E+++  A+RIL DQL +F   E     V++   
Sbjct: 183 VESARVEQRTDLDKLIMDIETNSAIDPEEAIRYAARILMDQLSVFAALEGTPAPVEKPQT 242

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            K    +P LL+ V++LEL+ RS+NCL+ ++I Y+GDLIQ TEAD+LR  N GRKSL EI
Sbjct: 243 PK---VDPMLLRPVDDLELTPRSSNCLKAQSIHYIGDLIQNTEADLLRTPNLGRKSLNEI 299

Query: 307 KGVLGTMGLFLGMNLPDW 324
           K VL   GL LGM L +W
Sbjct: 300 KQVLAEHGLSLGMKLENW 317


>gi|90193996|gb|ABD92559.1| RpoA [Volucribacter psittacicida]
          Length = 302

 Score =  276 bits (707), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 142/293 (48%), Positives = 205/293 (69%), Gaps = 9/293 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +I EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+
Sbjct: 14  VILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNL 73

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELT 148
           KG+ +K+       +T+ K G G V AGDI    D+E++NP+HVIC+L D +A ++M + 
Sbjct: 74  KGLAVKVQNKDDVLLTLSKSGIGPVVAGDIIHDGDVEIVNPEHVICHLTDENASIQMRIR 133

Query: 149 VSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           V +G GYVPA    H + E  PIG + +DA YSP+ +++Y VE+AR  Q  D DKL + +
Sbjct: 134 VQRGRGYVPASARVHAQDEERPIGRLLVDACYSPVDRIAYNVEAARVEQRTDLDKLVIEL 193

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELE 264
           +T+G+I  ED++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LE
Sbjct: 194 ETNGTIDPEDAIRRAATILAEQLDAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLE 249

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 250 LTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|90194024|gb|ABD92573.1| RpoA [Actinobacillus genomosp. 1]
          Length = 303

 Score =  276 bits (707), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 142/290 (48%), Positives = 204/290 (70%), Gaps = 9/290 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 76

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+SG     +T+ K G G VTA DI    D+E++NP HVIC+L D DA + M + V +
Sbjct: 77  AVKVSGKDDIILTLNKSGIGPVTAADITHDGDVEIVNPHHVICHLTDKDAAISMRIRVQR 136

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 137 GRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLIIEMETN 196

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 197 GTIDPEEAIRRAATILAEQLDAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 252

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 253 RSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|224713516|gb|ACN62065.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus minor]
          Length = 307

 Score =  276 bits (706), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 139/291 (47%), Positives = 204/291 (70%), Gaps = 7/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 20  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 79

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+       +T+ K G G VTAGDI    D+E++NPDHVIC+L D +A + M + V +
Sbjct: 80  AVKVQSKDDVVLTLNKSGIGPVTAGDITHDGDVEIVNPDHVICHLTDKNASINMRIRVQR 139

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 140 GRGYVPASARVHTQDDDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLIIEMETN 199

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G+I  E+++  A+ IL +QL  F++  + ++ V   +  +   F+P LL+ V++LEL+VR
Sbjct: 200 GTIDPEEAIRRAATILAEQLDAFVDLRDVRQPV---VKEEKPEFDPILLRPVDDLELTVR 256

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM
Sbjct: 257 SANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGM 307


>gi|21672745|ref|NP_660812.1| DNA-directed RNA polymerase subunit alpha [Buchnera aphidicola str.
           Sg (Schizaphis graminum)]
 gi|22654275|sp|O69232|RPOA_BUCAP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|21623391|gb|AAM68023.1| DNA-directed RNA polymerase alpha chain [Buchnera aphidicola str.
           Sg (Schizaphis graminum)]
          Length = 329

 Score =  276 bits (706), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 147/327 (44%), Positives = 212/327 (64%), Gaps = 10/327 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  +E   + Q     T +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 8   FLKPRLVE---IEQITATHTKVTLEPLERGFGHTLGNALRRILLSSMPGYAVTEVEIDGV 64

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+K + +K+ G     +++ K G G VTA DI    D+E++
Sbjct: 65  LHEYSTKEGVQEDILEILLNLKELAVKVHGKDEVFMSLNKSGIGSVTASDIIHDGDVEII 124

Query: 129 NPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
            PDH+IC+L D +A ++M + V +G GY+PA    H   +  PIG + +DA YSPI ++S
Sbjct: 125 KPDHLICHLTDENASIQMRIKVQRGRGYIPASSRIHMEDDLRPIGCLLVDACYSPINRIS 184

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + + T+G+I  E+++  A+ IL +QL  F++  + K+     
Sbjct: 185 YNVEAARVEQRTDLDKLIIEMKTNGTIDPEEAIRRAATILSEQLEAFVDLRDVKEPEI-- 242

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F P LL+ V++LEL+VRS NCL+ E+I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 243 -KEEKPEFEPILLRPVDDLELTVRSANCLKAESIHYIGDLVQRTEVELLKTPNLGKKSLT 301

Query: 305 EIKGVLGTMGLFLGMNLPDWPPESIEE 331
           EIK +L    L LGM L  WPP SI E
Sbjct: 302 EIKDILAARNLSLGMKLEKWPPSSILE 328


>gi|157100341|emb|CAP03336.1| RpoA protein [Vibrio aestuarianus]
          Length = 323

 Score =  276 bits (705), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 144/329 (43%), Positives = 217/329 (65%), Gaps = 11/329 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISTTHAKVTL---EPLERGFGHTLGNALRRILLSSMAGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEITNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           N G+KSL EIK VL + GL LGM L +WP
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWP 323


>gi|302036693|ref|YP_003797015.1| DNA-directed RNA polymerase subunit alpha [Candidatus Nitrospira
           defluvii]
 gi|300604757|emb|CBK41089.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Nitrospira
           defluvii]
          Length = 333

 Score =  276 bits (705), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 142/298 (47%), Positives = 202/298 (67%), Gaps = 3/298 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
              E   RGF  T+GN+LRRVL+SSL GAA+T V+I+GVLHE S+I GV ED+T IILN+
Sbjct: 28  FTTEAFERGFGTTVGNSLRRVLLSSLTGAAVTTVKIEGVLHEFSTIPGVTEDVTSIILNV 87

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L + GD  K + + K+GPG     DI    D+ +L PD  I  LD DA + +E+T+
Sbjct: 88  KSLRLALQGDKPKTIRLKKKGPGEAKGSDITHDGDVTILTPDLHIATLDKDASLDLEMTI 147

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G G+VPA+ ++ E  PIG+I +D+++SPIK+V++ VE+AR G++ DYDKL++ I TDG
Sbjct: 148 KHGRGFVPAERNKEEGLPIGVIAVDSIFSPIKRVNFHVENARVGRMTDYDKLTLEIWTDG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP--FNPALLKKVEELELSV 267
           +I+  D+++ A+ IL++ L +FIN EE + + K     + L    N  L + V ELELSV
Sbjct: 208 TISPRDALSNAAGILREHLDIFINPEE-RSDAKPAAGSEDLSDEVNKNLYRSVNELELSV 266

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           R+ NCL+  NI  + DL+Q+TEA+ML+  NFG+KSL EIK +L  MGL LGM +   P
Sbjct: 267 RAANCLKNANIKTIADLVQKTEAEMLKTKNFGKKSLNEIKEILTEMGLSLGMKVDALP 324


>gi|90194032|gb|ABD92577.1| RpoA [Actinobacillus lignieresii]
          Length = 302

 Score =  276 bits (705), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 142/290 (48%), Positives = 204/290 (70%), Gaps = 9/290 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 76

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+SG     +T+ K G G VTA DI    D+E++NP HVIC+L D DA + M + V +
Sbjct: 77  AVKVSGKDDIILTLNKSGIGPVTAADITHDGDVEIVNPHHVICHLTDKDASISMRIRVQR 136

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 137 GRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLIIEMETN 196

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 197 GTIDPEEAIRRAATILAEQLDAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 252

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 253 RSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|304413170|ref|ZP_07394643.1| RNA polymerase alpha subunit [Candidatus Regiella insecticola LSR1]
 gi|304284013|gb|EFL92406.1| RNA polymerase alpha subunit [Candidatus Regiella insecticola LSR1]
          Length = 335

 Score =  276 bits (705), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 146/333 (43%), Positives = 214/333 (64%), Gaps = 11/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q + +E +KP+ I   +     +    +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVKEFLKPSLISEKI----SQTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 56

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV-TIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+  I+LN+K + +K+    ++ + T+ K G G VTA DI 
Sbjct: 57  EVEIEGVLHEYSTKEGVKEDILSILLNLKELAVKVQEKENEVILTLEKSGIGPVTAADIT 116

Query: 121 TVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
           + + IE++ P+HVIC+L D  A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 117 SDSKIEIIKPEHVICHLTDKSASINMRIKVQRGRGYVPASTRVHGEEDERPIGRLLVDAC 176

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSPI++++Y VE+ R     D DKL + ++T+G+I  E+++  AS IL +QL  F++   
Sbjct: 177 YSPIERIAYNVEATRYQDRTDLDKLIIEMETNGTIDPEEAIRHASTILSEQLTAFVDISH 236

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
                K  +     P  P LL+ V++LEL+VRS NCL+ E I ++GDL+QRTE ++L+  
Sbjct: 237 NVNTCKTSVEAPDFP--PILLRPVDDLELTVRSANCLKAEAIHFIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL   GL LGM L +WPP SI
Sbjct: 295 NLGKKSLTEIKDVLAVHGLSLGMRLENWPPASI 327


>gi|94676571|ref|YP_588801.1| DNA-directed RNA polymerase subunit alpha [Baumannia
           cicadellinicola str. Hc (Homalodisca coagulata)]
 gi|119366665|sp|Q1LTB3|RPOA_BAUCH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|94219721|gb|ABF13880.1| DNA-directed RNA polymerase, alpha subunit [Baumannia
           cicadellinicola str. Hc (Homalodisca coagulata)]
          Length = 327

 Score =  275 bits (704), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 146/330 (44%), Positives = 221/330 (66%), Gaps = 14/330 (4%)

Query: 2   IQKNWQELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           +Q +  E +KP   +IE + L   +     +I EPL RGF HTLGNALRR+L+SS+ G A
Sbjct: 1   MQGSVTEFLKPRLVDIEQLSLTHAK-----VILEPLERGFGHTLGNALRRILLSSIPGYA 55

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T V+IDG+LHE S+ +G+ ED+ +I+LN+K + +K+    +  +T+ K G G VTA +I
Sbjct: 56  VTEVEIDGILHEYSTKEGIREDIIEILLNLKELAVKVQSKDNVILTLNKSGLGPVTAANI 115

Query: 120 QTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALY 177
              +D++++ P H++C+L + +A + M + V +G GYVPA     + D PIG + +DA Y
Sbjct: 116 IHDSDVQIIKPQHILCHLTEENASINMRIKVQRGRGYVPASARIHKYDRPIGRLLVDACY 175

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE- 236
           SP++ +SY VE+AR  Q  D DKL + I+T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 176 SPVENISYNVEAARVEQRTDLDKLILEIETNGTIDPEEAIRRAATILAEQLEAFVDLRDI 235

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            + EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 236 SQPEVKEE----KPEFDPVLLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 291

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           N G+KSL EIK VL + GL LGM L +WPP
Sbjct: 292 NLGKKSLTEIKDVLASRGLSLGMRLENWPP 321


>gi|257471550|ref|ZP_05635549.1| DNA-directed RNA polymerase subunit alpha [Buchnera aphidicola str.
           LSR1 (Acyrthosiphon pisum)]
          Length = 324

 Score =  275 bits (703), Expect = 6e-72,   Method: Compositional matrix adjust.
 Identities = 142/312 (45%), Positives = 207/312 (66%), Gaps = 7/312 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           Q     T +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED
Sbjct: 13  QISATHTKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQED 72

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVD 140
           + +I+LN+K + +K+ G     +T+ K G G +TA DI    D+E++ P HVIC+L D +
Sbjct: 73  VLEILLNLKALAVKVYGKDETLLTLHKSGIGSITAADIIHDGDVEIIKPQHVICHLTDEN 132

Query: 141 AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           A ++M + V +G GY+PA    H   +  PIG + +DA YSPI ++SY VE+AR  Q  D
Sbjct: 133 ASIKMRIKVQRGRGYIPASSRVHLEEDARPIGCLLVDACYSPINRISYNVEAARVEQRTD 192

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
            DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++   ++   +  P    LL
Sbjct: 193 LDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDIREPEFKEEKPEFEPI---LL 249

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +  L L
Sbjct: 250 RPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRSLSL 309

Query: 318 GMNLPDWPPESI 329
           GM L +WPP SI
Sbjct: 310 GMRLENWPPSSI 321


>gi|157100343|emb|CAP03337.1| RpoA protein [Vibrio aestuarianus]
          Length = 323

 Score =  275 bits (703), Expect = 7e-72,   Method: Compositional matrix adjust.
 Identities = 144/329 (43%), Positives = 217/329 (65%), Gaps = 11/329 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEITNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           N G+KSL EIK VL + GL LGM L +WP
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWP 323


>gi|121997624|ref|YP_001002411.1| DNA-directed RNA polymerase subunit alpha [Halorhodospira halophila
           SL1]
 gi|158514009|sp|A1WV97|RPOA_HALHL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|121589029|gb|ABM61609.1| DNA-directed RNA polymerase subunit alpha [Halorhodospira halophila
           SL1]
          Length = 332

 Score =  275 bits (703), Expect = 7e-72,   Method: Compositional matrix adjust.
 Identities = 138/329 (41%), Positives = 219/329 (66%), Gaps = 6/329 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           ++ +KP ++E   L    +NR  ++ EPL RGF HTLGNALRR+L+SS+ G A+T V+I+
Sbjct: 6   KDFLKPRSVEIEPLS---DNRAKVVLEPLERGFGHTLGNALRRLLLSSMPGTAVTEVEIE 62

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV HE ++++G+HED  DI+LN+K + ++++      +++ K+GPG VTA DI T +D+E
Sbjct: 63  GVQHEYTAVEGIHEDTVDILLNLKDLAVRLNERDSVTLSVEKQGPGSVTAADIATDHDVE 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSY 185
           + NPD  I  +  +   +  L + +G GY+P      E+   IG + +DA +SP+++VSY
Sbjct: 123 IQNPDLHIATITHEQPFKASLKIERGRGYLPVTAREEEDTRTIGHLALDASFSPVRRVSY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL + ++T+G +T E++V  A+ +L+DQL +F++ E    E  ++ 
Sbjct: 183 AVESARVEQRTDLDKLVLDVETNGVVTPEEAVKFAASLLRDQLSVFVDLEGGLLEGGDEQ 242

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
               +  +P LL+ +++LEL+VRS NCL+ E+I ++GDL+QRTE ++L+  N G+KSL E
Sbjct: 243 EEPEI--DPVLLRPIDDLELTVRSANCLKAESIHFVGDLVQRTEVELLKTPNLGKKSLNE 300

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           IK  L   GL LGM L +WPP S+ + A+
Sbjct: 301 IKDTLAEHGLSLGMQLDNWPPPSLGDRAR 329


>gi|308171330|gb|ADO15984.1| RpoA [Vibrio brasiliensis LMG 20546]
          Length = 318

 Score =  275 bits (703), Expect = 8e-72,   Method: Compositional matrix adjust.
 Identities = 144/323 (44%), Positives = 214/323 (66%), Gaps = 11/323 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T V+I+G
Sbjct: 2   EFLKPRLVDIEQVSTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           VLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI    D+E
Sbjct: 59  VLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVE 118

Query: 127 VLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKK 182
           + NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K
Sbjct: 119 IANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDK 178

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           ++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   +
Sbjct: 179 IAYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE 238

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KS
Sbjct: 239 ---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKS 295

Query: 303 LVEIKGVLGTMGLFLGMNLPDWP 325
           L EIK VL + GL LGM L +WP
Sbjct: 296 LTEIKDVLASRGLSLGMRLENWP 318


>gi|90194034|gb|ABD92578.1| RpoA [Actinobacillus pleuropneumoniae serovar 1]
 gi|90194036|gb|ABD92579.1| RpoA [Actinobacillus pleuropneumoniae serovar 2 str. S1536]
 gi|90194038|gb|ABD92580.1| RpoA [Actinobacillus pleuropneumoniae]
 gi|90194040|gb|ABD92581.1| RpoA [Actinobacillus pleuropneumoniae serovar 4 str. M62]
 gi|90194042|gb|ABD92582.1| RpoA [Actinobacillus pleuropneumoniae]
 gi|90194044|gb|ABD92583.1| RpoA [Actinobacillus pleuropneumoniae serovar 8 str. 405]
          Length = 301

 Score =  275 bits (702), Expect = 9e-72,   Method: Compositional matrix adjust.
 Identities = 141/288 (48%), Positives = 203/288 (70%), Gaps = 9/288 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 76

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+SG     +T+ K G G VTA DI    D+E++NP HVIC+L D DA + M + V +
Sbjct: 77  AVKVSGKDDIILTLNKSGIGPVTAADITHDGDVEIVNPHHVICHLTDKDASISMRIRVQR 136

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 137 GRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLIIEMETN 196

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 197 GTIDPEEAIRRAATILAEQLDAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 252

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL
Sbjct: 253 RSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGL 300


>gi|90194014|gb|ABD92568.1| RpoA [Actinobacillus genomosp. 2]
          Length = 303

 Score =  275 bits (702), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 140/290 (48%), Positives = 204/290 (70%), Gaps = 9/290 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 76

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+SG     +T+ K G G VTA DI    D+E++NP HVIC+L D DA + M + + +
Sbjct: 77  AVKVSGKDDIILTLNKSGIGPVTAADITHDGDVEIVNPHHVICHLTDKDASISMRIRIQR 136

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 137 GRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLIIEMETN 196

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ E+KE+       F+P LL+ V++LEL+V
Sbjct: 197 GTIDPEEAIRRAATILAEQLDAFVDLRDVRQPEIKEE----KPEFDPILLRPVDDLELTV 252

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 253 RSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|71891999|ref|YP_277729.1| DNA-directed RNA polymerase subunit alpha [Candidatus Blochmannia
           pennsylvanicus str. BPEN]
 gi|90101573|sp|Q493I4|RPOA_BLOPB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|71796105|gb|AAZ40856.1| RNA polymerase, alpha subunit [Candidatus Blochmannia
           pennsylvanicus str. BPEN]
          Length = 330

 Score =  275 bits (702), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 147/334 (44%), Positives = 221/334 (66%), Gaps = 13/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q  E R  +  EPL RGF HTLGNALRR+L+SS+ G AIT
Sbjct: 1   MQNSVIEFLKPRLVD---IEQITETRAKVTLEPLERGFGHTLGNALRRILLSSMPGYAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI-Q 120
            V+IDGVLHE S+ +G+ ED+ +I+LN+K + +++ G     +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSTKEGIQEDVLEILLNLKKLAIRIEGKDSVTLTLKKSGIGPVIANDILY 117

Query: 121 TVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
             N ++++ P+H+IC++ D +  + M + V +G GYVPA    H  ++  PIG + +DA 
Sbjct: 118 DSNSVKIVTPNHIICHITDKNTSISMSIKVQRGRGYVPASSRFHSESDILPIGRLLLDAC 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP++++SY VE+AR  Q  D DKL + ++TDG+I  E+++  A+ IL +QL  FI+  +
Sbjct: 178 YSPVERISYNVEAARVEQRTDLDKLIIDMETDGTIEPEEAIRRAATILSEQLEAFIDLRD 237

Query: 237 -PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
             + E KE+       F+P LL+ V++LEL+VRS NCL+ E+I Y+GDL+QRTE ++L+ 
Sbjct: 238 IHQPEHKEE----KPEFDPILLRLVDDLELTVRSANCLKAESIHYIGDLVQRTEIELLKT 293

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            N G+KSL EIK VL + GL LG  L +WPP +I
Sbjct: 294 PNLGKKSLTEIKDVLASRGLSLGTRLENWPPTNI 327


>gi|322436518|ref|YP_004218730.1| DNA-directed RNA polymerase, alpha subunit [Acidobacterium sp.
           MP5ACTX9]
 gi|321164245|gb|ADW69950.1| DNA-directed RNA polymerase, alpha subunit [Acidobacterium sp.
           MP5ACTX9]
          Length = 367

 Score =  274 bits (701), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 138/290 (47%), Positives = 201/290 (69%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
           A+P  RGF  T+GNALRR L+SS+ GAA+TAV+I+GVLHE  SI GV ED TDIILN+K 
Sbjct: 28  AQPFERGFGTTIGNALRRTLLSSIEGAAVTAVRIEGVLHEFQSITGVVEDATDIILNLKQ 87

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           I  K++GD  K + +     GV+T+G I+   D+E+L+P+  IC +     + ME+ + +
Sbjct: 88  IPFKLAGDGPKALYLRSDAAGVITSGMIEADADVEILDPNVYICTISEGGKIDMEMRLKR 147

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GY+ A  +   +  +G I +D+++SP++KV+Y VE+AR GQ+ DYDKLS+ I T+G++
Sbjct: 148 GRGYISADKNFDGDLGLGFIPVDSVHSPVRKVNYVVEAARLGQITDYDKLSIEIWTNGTV 207

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTN 271
              D++ L++++L+D + +FINFEE  +   ++ +      N  L + VEELELSVRS N
Sbjct: 208 LPADALGLSAKLLKDHMTIFINFEEEMEAGHDNGHDGPAMRNENLNRSVEELELSVRSYN 267

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           CL+  NI  +G+LIQ+TEA+ML+  NFGRKSL EIK +L  MGL LGM +
Sbjct: 268 CLKNANIATIGELIQKTEAEMLKTKNFGRKSLNEIKEILAQMGLSLGMKI 317


>gi|190341453|gb|ACE74803.1| RpoA [Cronobacter sakazakii]
          Length = 308

 Score =  274 bits (701), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 140/291 (48%), Positives = 202/291 (69%), Gaps = 9/291 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + V +
Sbjct: 82  AVRVQGKDEVVLTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQR 141

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPASARIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 202 GTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 257

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I YMGDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 258 RSANCLKAEAIHYMGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|90194062|gb|ABD92592.1| RpoA [Pasteurella multocida subsp. septica]
          Length = 304

 Score =  274 bits (701), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 141/294 (47%), Positives = 203/294 (69%), Gaps = 9/294 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +I EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+
Sbjct: 15  VILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNL 74

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELT 148
           KG+ +K+       +T+ K G G V A DI    D+E++NP+HVIC+L D  A + M + 
Sbjct: 75  KGLAVKVQNKDDVFLTLNKSGIGPVVAADITHDGDVEIVNPEHVICHLTDESASINMRIR 134

Query: 149 VSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           V +G GYVPA    H + E  PIG + +DA YSP+ +++Y VE+AR  Q  D DKL + +
Sbjct: 135 VQRGRGYVPASARVHAQDEERPIGRLLVDACYSPVDRIAYNVEAARVEQRTDLDKLVIEL 194

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELE 264
           +T+G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LE
Sbjct: 195 ETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLE 250

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           L+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 251 LTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 304


>gi|90194054|gb|ABD92588.1| RpoA [Mannheimia varigena]
          Length = 302

 Score =  274 bits (701), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 139/290 (47%), Positives = 204/290 (70%), Gaps = 9/290 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTDVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 76

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+       +T+ K G G VTA DI    D+E++NPDHVICNL D +A + M + V +
Sbjct: 77  AVKVQNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPDHVICNLTDKNASINMRIRVQR 136

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H ++++ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 137 GRGYVPASARLHTQSDDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLVIEMETN 196

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G++  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 197 GTLDPEEAIRRAATILAEQLAAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 252

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 253 RSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|308171338|gb|ADO15988.1| RpoA [Vibrio caribbenthicus]
          Length = 323

 Score =  274 bits (701), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 143/323 (44%), Positives = 214/323 (66%), Gaps = 11/323 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T V+I+G
Sbjct: 7   EFLKPRLVDIEQVSTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEG 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           VLHE S+ +GV ED+ +++LN+KG+ ++++ G     +T+ K G G V AGDI    D+E
Sbjct: 64  VLHEYSTKEGVQEDILEVLLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVE 123

Query: 127 VLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKK 182
           + NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K
Sbjct: 124 IANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDK 183

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           ++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   +
Sbjct: 184 IAYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KS
Sbjct: 244 ---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKS 300

Query: 303 LVEIKGVLGTMGLFLGMNLPDWP 325
           L EIK VL + GL LGM L +WP
Sbjct: 301 LTEIKDVLASRGLSLGMRLENWP 323


>gi|270157886|ref|ZP_06186543.1| DNA-directed RNA polymerase alpha subunit [Legionella longbeachae
           D-4968]
 gi|289163855|ref|YP_003453993.1| DNA-directed RNA polymerase alpha chain [Legionella longbeachae
           NSW150]
 gi|269989911|gb|EEZ96165.1| DNA-directed RNA polymerase alpha subunit [Legionella longbeachae
           D-4968]
 gi|288857028|emb|CBJ10842.1| DNA-directed RNA polymerase alpha chain [Legionella longbeachae
           NSW150]
          Length = 330

 Score =  274 bits (701), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 145/332 (43%), Positives = 217/332 (65%), Gaps = 16/332 (4%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E++ PN ++   +  E   +  ++ EPL RGF HTLGNALRR+L+SS+ G+ IT   I+G
Sbjct: 7   EMLTPNVLK---VQAESPFKAKIVLEPLERGFGHTLGNALRRILLSSMPGSVITEASIEG 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+ DI+LN+K + +KM+      +T+ K+GP  VTAGDIQ  + +EV
Sbjct: 64  VLHEYSTIEGVQEDVVDILLNLKLVAIKMTVGEEALITLNKQGPCQVTAGDIQLSHGLEV 123

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH------RTENDPIGLITIDALYSPIK 181
           +NPD VI NL+    + M + V +G G+              E   +G + ID  +SP++
Sbjct: 124 VNPDLVIANLNEKGKLNMTMKVERGIGFHSTDSFIGHFDDEVERKSVGKLKIDNSFSPVR 183

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN--FEEPKK 239
           KV+Y V+SAR     D DKL++ ++T+G+I  E+++ +++ ILQ QL  F++  FEE + 
Sbjct: 184 KVAYYVDSARVENRTDLDKLTIELETNGTIDSEEAIRISASILQRQLHAFVDMRFEESRS 243

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           + KE  +     F+P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G
Sbjct: 244 DQKERND-----FDPILLRSVDDLELTVRSANCLKAENIHYIGDLVQRTENELLKTPNLG 298

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +KSL EIK VL +  L LGM L +WPP ++ E
Sbjct: 299 KKSLTEIKDVLASRSLSLGMKLENWPPANLGE 330


>gi|302877827|ref|YP_003846391.1| DNA-directed RNA polymerase, alpha subunit [Gallionella
           capsiferriformans ES-2]
 gi|302580616|gb|ADL54627.1| DNA-directed RNA polymerase, alpha subunit [Gallionella
           capsiferriformans ES-2]
          Length = 322

 Score =  274 bits (701), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 152/322 (47%), Positives = 210/322 (65%), Gaps = 12/322 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           + +KP  IE   + +  E +  ++ EP  RGF HTLGNALRR+L+SS+ GAA T V++ G
Sbjct: 5   DFLKPRIIE---VQKISETQAKVVMEPFERGFGHTLGNALRRILLSSMAGAAPTEVKMSG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE ++I GV ED+ DI+LN+KG+ L++ G     +T+ K G GVVTA DI    ++EV
Sbjct: 62  VLHEYATIDGVQEDVVDILLNLKGVVLRLHGVKEVVLTLKKEGFGVVTAADISANAEVEV 121

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSY 185
           LNP+HVI +L     + M++ V +G GYV A   +  N+   +G I +DA +SP+ +VSY
Sbjct: 122 LNPEHVIAHLTAGGKLDMQIKVEQGRGYVSAISRQLPNETRAVGHIALDASFSPVSRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--EPKKEVKE 243
            VESAR  Q  D DKL MTI+T+G+I  E ++  A+RIL DQ  +F   E  EP  E KE
Sbjct: 182 AVESARVEQRTDLDKLIMTIETNGAIDPEQAIRNAARILVDQFSVFAALEGTEPVVE-KE 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +       +P LL+ V++LEL+ RS+NCL+ ++I Y+GDLIQ +E D+LR  N GRKSL
Sbjct: 241 HVP----QVDPILLRPVDDLELTPRSSNCLKAQSIHYIGDLIQYSENDLLRTPNLGRKSL 296

Query: 304 VEIKGVLGTMGLFLGMNLPDWP 325
            EIK VL    L LGM L +WP
Sbjct: 297 NEIKQVLAEHNLSLGMKLENWP 318


>gi|90194008|gb|ABD92565.1| RpoA [Bibersteinia trehalosi]
          Length = 302

 Score =  274 bits (701), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 139/290 (47%), Positives = 203/290 (70%), Gaps = 9/290 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 76

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+       +T+ K G G VTA DI    D+E++NPDHVIC+L D +A + M + V +
Sbjct: 77  AVKVQNKDDIILTLTKSGIGPVTAADITADADVEIVNPDHVICHLTDKNASISMRIRVQR 136

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 137 GRGYVPASARVHSQHEDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLVIEMETN 196

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G++  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 197 GTLDPEEAIRRAATILAEQLAAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 252

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 253 RSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|291280121|ref|YP_003496956.1| DNA-directed RNA polymerase subunit alpha [Deferribacter
           desulfuricans SSM1]
 gi|290754823|dbj|BAI81200.1| DNA-directed RNA polymerase, alpha subunit [Deferribacter
           desulfuricans SSM1]
          Length = 338

 Score =  274 bits (700), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 151/323 (46%), Positives = 217/323 (67%), Gaps = 4/323 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M+  ++++++KP  IE I  G+  +     + EP  RGF  T+GN+LRRVL+S++ G A+
Sbjct: 1   MVLMDFRKVMKPKKIEQI--GEATDRYAKFVIEPYERGFGITIGNSLRRVLLSTIEGTAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
             V+IDGV HE  +I GV ED+ DIILNIK + L +   + KRV I K+G G +TA DIQ
Sbjct: 59  VGVKIDGVHHEYDTINGVLEDVVDIILNIKQLELNLLEHTLKRVYIHKKGEGRITANDIQ 118

Query: 121 TVNDIEVLNPD-HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
           +   + VLNPD H+    + +  V MEL V +G GYVP++  + + D I +I +DA+Y+P
Sbjct: 119 SDGSVVVLNPDQHIATITNPETEVYMELYVERGIGYVPSEEIKDKFDDIDVIPVDAIYTP 178

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           IKKV+Y VE+AR GQ  DYDKL   ++TDGSI   D++A A++I++DQ+  FINF+EP  
Sbjct: 179 IKKVNYVVENARVGQSTDYDKLIFELETDGSIKPVDAIAFAAKIIKDQMEFFINFDEPVY 238

Query: 240 EVKEDINVKSLPFNPALL-KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           E  E+   +   +   LL K +EELELSVR+ NCL+  NI  + DL ++T+A++L+  NF
Sbjct: 239 EEVEEEEKEDNSYILELLDKSIEELELSVRAYNCLKNANIKTLADLCEKTDAELLKTKNF 298

Query: 299 GRKSLVEIKGVLGTMGLFLGMNL 321
           GR+SL EIK VL  +GL LGM+L
Sbjct: 299 GRRSLEEIKKVLAELGLSLGMDL 321


>gi|90194056|gb|ABD92589.1| RpoA [Mannheimia ruminalis]
          Length = 302

 Score =  274 bits (700), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 140/301 (46%), Positives = 206/301 (68%), Gaps = 9/301 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED
Sbjct: 6   QVSSTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQED 65

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVD 140
           + +++LN+KG+ +K+       +T+ K G G VTA DI    D+E++NPDH+IC+L D +
Sbjct: 66  ILEVLLNLKGLAVKVQNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPDHIICHLTDKN 125

Query: 141 AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           A + M + V +G GYVPA    H + ++ PIG + +DA YSP+ +++Y VE+AR  Q  D
Sbjct: 126 ASISMRIRVQRGRGYVPASARLHTQNDDRPIGRLLVDARYSPVDRIAYNVEAARVEQRTD 185

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPAL 256
            DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P L
Sbjct: 186 LDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDVRQPEVKEE----KPEFDPIL 241

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
           L+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL 
Sbjct: 242 LRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLS 301

Query: 317 L 317
           L
Sbjct: 302 L 302


>gi|90194020|gb|ABD92571.1| RpoA [Actinobacillus arthritidis]
          Length = 303

 Score =  274 bits (700), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 139/290 (47%), Positives = 204/290 (70%), Gaps = 9/290 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 76

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+SG     +T+ K G G VTA DI    D+E++NP H+IC+L D DA + M + + +
Sbjct: 77  AVKVSGKDDIILTLNKSGIGPVTAADITHDGDVEIVNPHHIICHLTDKDASISMRIRIQR 136

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 137 GRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLIIEMETN 196

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ E+KE+       F+P LL+ V++LEL+V
Sbjct: 197 GTIDPEEAIRRAATILAEQLDAFVDLRDVRQPEIKEE----KPEFDPILLRPVDDLELTV 252

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 253 RSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|90194046|gb|ABD92584.1| RpoA [Actinobacillus indolicus]
          Length = 303

 Score =  274 bits (700), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 139/290 (47%), Positives = 203/290 (70%), Gaps = 9/290 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 76

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+       +T+ K G G VTA DI    D+E++NPDHVICNL D +A + M + V +
Sbjct: 77  AVKVQNKDDIILTLTKSGIGPVTAADITHDGDVEIVNPDHVICNLTDKNASINMRIRVQR 136

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 137 GRGYVPASARVHTQDDDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLVIEMETN 196

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G++  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 197 GTLDPEEAIRRAATILAEQLAAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 252

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 253 RSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|90194012|gb|ABD92567.1| RpoA [Actinobacillus porcitonsillarum]
          Length = 303

 Score =  274 bits (700), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 140/290 (48%), Positives = 204/290 (70%), Gaps = 9/290 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 76

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+       +T+ K G G VTAGDI    D+E++NPDHVIC+L D +A + M + V +
Sbjct: 77  AVKVQSKDDVVLTLNKSGIGPVTAGDITHDGDVEIVNPDHVICHLTDKNASINMRIRVQR 136

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 137 GRGYVPASARVHAQDDDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLIIEMETN 196

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 197 GTIDPEEAIRRAATILAEQLDAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 252

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 253 RSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|308171332|gb|ADO15985.1| RpoA [Vibrio ichthyoenteri ATCC 700023]
          Length = 323

 Score =  273 bits (699), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 143/323 (44%), Positives = 214/323 (66%), Gaps = 11/323 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T V+I+G
Sbjct: 7   EFLKPRLVDIEQISTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEG 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           VLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI    D+E
Sbjct: 64  VLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVE 123

Query: 127 VLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKK 182
           + NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K
Sbjct: 124 ITNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDK 183

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           ++Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   +
Sbjct: 184 IAYSVDAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KS
Sbjct: 244 ---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKS 300

Query: 303 LVEIKGVLGTMGLFLGMNLPDWP 325
           L EIK VL + GL LGM L +WP
Sbjct: 301 LTEIKDVLASRGLSLGMRLENWP 323


>gi|256830513|ref|YP_003159241.1| DNA-directed RNA polymerase, alpha subunit [Desulfomicrobium
           baculatum DSM 4028]
 gi|256579689|gb|ACU90825.1| DNA-directed RNA polymerase, alpha subunit [Desulfomicrobium
           baculatum DSM 4028]
          Length = 348

 Score =  273 bits (699), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 144/337 (42%), Positives = 218/337 (64%), Gaps = 2/337 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW EL++P  +E      +   R   + EPL RGF  T+GNALRRVL+SSL+GAA  +V
Sbjct: 14  RNWAELVRPEQLEKDPKCNDMYGR--FVCEPLERGFGTTIGNALRRVLLSSLQGAAPVSV 71

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
            I G+ HE ++I GV ED+TDI+LN+K + + M+    +RV +     G VTA  I    
Sbjct: 72  NIQGIQHEFTTIPGVTEDITDIVLNLKQLRVAMNTPEPQRVQLIANAKGEVTASAIVENQ 131

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            I++LNP+  I  L  D  + M L    G GYVPA+ H   ++ IG+IT+D+ +SPI+KV
Sbjct: 132 HIKILNPELHIATLSEDIDLVMNLEFRMGKGYVPAEMHEDLDNEIGVITLDSSFSPIRKV 191

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE AR GQ+ +YDKL + + TDGSIT +D++A +++IL++QL +FINF+E   ++++
Sbjct: 192 AYAVEQARVGQMTNYDKLIIEVWTDGSITPDDALAFSAKILKEQLTVFINFDEGSADIEK 251

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             +      N  L K +E+LEL VR++NCL+   I  +G+L+Q+TEAD+L+  NFGRKSL
Sbjct: 252 AKSKPQDKINENLFKNIEDLELPVRASNCLKSAGIHIVGELVQKTEADLLKTKNFGRKSL 311

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
            +I+ VL +MGL  G+ + ++     + L +  ED+ 
Sbjct: 312 EDIRRVLESMGLDFGIRVDNFDELYQDWLKRNEEDEA 348


>gi|157100339|emb|CAP03335.1| RpoA protein [Vibrio aestuarianus]
          Length = 323

 Score =  273 bits (699), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 143/329 (43%), Positives = 216/329 (65%), Gaps = 11/329 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGN LRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISTTHAKVTL---EPLERGFGHTLGNXLRRILLSSMXGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEITNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           N G+KSL EIK VL + GL LGM L +WP
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWP 323


>gi|308171334|gb|ADO15986.1| RpoA [Vibrio scophthalmi LMG 19158]
          Length = 321

 Score =  273 bits (698), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 143/323 (44%), Positives = 214/323 (66%), Gaps = 11/323 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T V+I+G
Sbjct: 5   EFLKPRLVDIEQISTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           VLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI    D+E
Sbjct: 62  VLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVE 121

Query: 127 VLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKK 182
           + NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K
Sbjct: 122 ITNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDK 181

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           ++Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   +
Sbjct: 182 IAYSVDAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE 241

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KS
Sbjct: 242 ---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKS 298

Query: 303 LVEIKGVLGTMGLFLGMNLPDWP 325
           L EIK VL + GL LGM L +WP
Sbjct: 299 LTEIKDVLASRGLSLGMRLENWP 321


>gi|158319572|ref|YP_001512079.1| DNA-directed RNA polymerase, alpha subunit [Alkaliphilus oremlandii
           OhILAs]
 gi|172048250|sp|A8MLG9|RPOA_ALKOO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158139771|gb|ABW18083.1| DNA-directed RNA polymerase, alpha subunit [Alkaliphilus oremlandii
           OhILAs]
          Length = 317

 Score =  273 bits (698), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 136/285 (47%), Positives = 204/285 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+++SSL GAA+T+V+IDGVLHE S+I GV ED+ +II+N+KG+
Sbjct: 28  EPLERGYGTTLGNSLRRIMLSSLPGAAVTSVKIDGVLHEFSTIPGVKEDVAEIIINLKGL 87

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
           +++M G+  K V I  +G GV+TAGDI    D+E+L+PD  I  LD DAV+ MELT++KG
Sbjct: 88  SIRMHGNEPKTVRIEAKGEGVITAGDIIADADVEILSPDTHIATLDTDAVLNMELTIAKG 147

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYVPA++++T   PIG++ ID++++P+ KVSY VE+ R GQV DYDKL + + TDGSI 
Sbjct: 148 RGYVPAENNKTPGMPIGVLPIDSIFTPVTKVSYHVENTRVGQVTDYDKLVIEVFTDGSIV 207

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
            +++++LA++I+ + L +FI   +   +V+  +  +       L   +EEL+LSVRS NC
Sbjct: 208 PDEAISLAAKIMNEHLNLFITLTDHVNDVEIMVQKEEDKKEKVLEMTIEELDLSVRSYNC 267

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+   I  + +L Q++E DM+++ N GRKSL E++  L  +GL L
Sbjct: 268 LKRAGINTVDELAQKSEEDMMKVRNLGRKSLEEVQKKLEELGLGL 312


>gi|90194004|gb|ABD92563.1| RpoA [Lonepinella koalarum]
          Length = 302

 Score =  273 bits (698), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 141/293 (48%), Positives = 203/293 (69%), Gaps = 9/293 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +I EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE SS +GV ED+ +++LN+
Sbjct: 14  VILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSSKEGVQEDILEVLLNL 73

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELT 148
           KG+ +K+       +T+ K G G V A DI    D+E++NPDHVIC+L D +A V M + 
Sbjct: 74  KGLAVKVQNKDDVFLTLNKSGIGPVVAADITHDGDVEIVNPDHVICHLTDENASVNMRIR 133

Query: 149 VSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           V +G GYVPA    H + E  PIG + +DA YSP+ +++Y VE+AR  Q  D DKL + +
Sbjct: 134 VQRGRGYVPASARVHTQDEERPIGRLLVDACYSPVDRIAYNVEAARVEQRTDLDKLVIEL 193

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELE 264
           +T+G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LE
Sbjct: 194 ETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLE 249

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 250 LTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|190341313|gb|ACE74733.1| RpoA [Enterobacter amnigenus]
          Length = 308

 Score =  273 bits (698), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 139/291 (47%), Positives = 202/291 (69%), Gaps = 9/291 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + V +
Sbjct: 82  AVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENAAISMRIKVQR 141

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPASARIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 202 GTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 257

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 258 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|190341315|gb|ACE74734.1| RpoA [Enterobacter asburiae]
 gi|190341317|gb|ACE74735.1| RpoA [Enterobacter asburiae]
 gi|190341319|gb|ACE74736.1| RpoA [Enterobacter cancerogenus]
 gi|190341321|gb|ACE74737.1| RpoA [Enterobacter cancerogenus]
 gi|190341323|gb|ACE74738.1| RpoA [Enterobacter cloacae]
 gi|190341349|gb|ACE74751.1| RpoA [Enterobacter hormaechei ATCC 49162]
 gi|190341351|gb|ACE74752.1| RpoA [Enterobacter kobei]
 gi|190341353|gb|ACE74753.1| RpoA [Enterobacter ludwigii]
 gi|190341371|gb|ACE74762.1| RpoA [Enterobacter sp. KM877_04]
 gi|190341373|gb|ACE74763.1| RpoA [Enterobacter sp. OD1121_04]
 gi|190341381|gb|ACE74767.1| RpoA [Escherichia vulneris]
 gi|190341383|gb|ACE74768.1| RpoA [Leclercia adecarboxylata ATCC 23216]
 gi|190341385|gb|ACE74769.1| RpoA [Leclercia adecarboxylata]
          Length = 308

 Score =  273 bits (697), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 139/291 (47%), Positives = 202/291 (69%), Gaps = 9/291 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + V +
Sbjct: 82  AVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENAAISMRIKVQR 141

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPASARIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 202 GTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 257

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 258 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|90194022|gb|ABD92572.1| RpoA [Actinobacillus suis ATCC 33415]
          Length = 302

 Score =  273 bits (697), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 140/290 (48%), Positives = 204/290 (70%), Gaps = 9/290 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 76

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+S      +T+ K G G VTA DI    D+E++NP+HVIC+L D +A + M + V +
Sbjct: 77  AVKVSNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPNHVICHLTDKNASINMRIRVQR 136

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 137 GRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLIIEMETN 196

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 197 GTIDPEEAIRRAATILAEQLDAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 252

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 253 RSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|90194016|gb|ABD92569.1| RpoA [Actinobacillus hominis]
          Length = 302

 Score =  273 bits (697), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 140/290 (48%), Positives = 204/290 (70%), Gaps = 9/290 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 76

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+S      +T+ K G G VTA DI    D+E++NP+HVIC+L D +A + M + V +
Sbjct: 77  AVKVSNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPNHVICHLTDKNASINMRIRVQR 136

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 137 GRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLIIEMETN 196

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 197 GTIDPEEAIRRAATILAEQLDAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 252

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 253 RSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|190341325|gb|ACE74739.1| RpoA [Enterobacter cowanii]
          Length = 308

 Score =  273 bits (697), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 139/291 (47%), Positives = 202/291 (69%), Gaps = 9/291 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + V +
Sbjct: 82  AVRVQGKDEVILTLSKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASINMRIKVQR 141

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPASARIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 202 GTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 257

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 258 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|90194030|gb|ABD92576.1| RpoA [Actinobacillus equuli subsp. haemolyticus]
          Length = 303

 Score =  273 bits (697), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 140/290 (48%), Positives = 204/290 (70%), Gaps = 9/290 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 76

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+S      +T+ K G G VTA DI    D+E++NP+HVIC+L D +A + M + V +
Sbjct: 77  AVKVSNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPNHVICHLTDKNASINMRIRVQR 136

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 137 GRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLIIEMETN 196

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 197 GTIDPEEAIRRAATILAEQLDAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 252

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 253 RSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|90194018|gb|ABD92570.1| RpoA [Actinobacillus ureae ATCC 25976]
          Length = 302

 Score =  273 bits (697), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 140/290 (48%), Positives = 204/290 (70%), Gaps = 9/290 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G+ ED+ +++LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVKIDGVLHEYSSKEGIQEDILEVLLNLKGL 76

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+S      +T+ K G G VTA DI    D+E++NPDHVIC+L D +A + M + V +
Sbjct: 77  AVKVSNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPDHVICHLTDKNASINMCIRVQR 136

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 137 GRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLIIEMETN 196

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 197 GTIDPEEAIRRAATILAEQLDAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 252

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 253 RSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|190341335|gb|ACE74744.1| RpoA [Enterobacter helveticus]
          Length = 307

 Score =  272 bits (696), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 139/291 (47%), Positives = 202/291 (69%), Gaps = 9/291 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 21  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 80

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + V +
Sbjct: 81  AVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQR 140

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + ++T+
Sbjct: 141 GRGYVPASARIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETN 200

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 201 GTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 256

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 257 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 307


>gi|190341399|gb|ACE74776.1| RpoA [Cronobacter genomosp. 1]
          Length = 308

 Score =  272 bits (696), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 139/291 (47%), Positives = 202/291 (69%), Gaps = 9/291 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + V +
Sbjct: 82  AVRVQGKDEVVLTLNKSGIGPVTAADINHDGDVEIVKPQHVICHLTDENASISMRIKVQR 141

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPASARIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 202 GTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 257

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 258 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|190341461|gb|ACE74807.1| RpoA [Cronobacter sakazakii]
          Length = 301

 Score =  272 bits (696), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 139/291 (47%), Positives = 202/291 (69%), Gaps = 9/291 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 15  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 74

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + V +
Sbjct: 75  AVRVQGKDEVVLTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQR 134

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + ++T+
Sbjct: 135 GRGYVPASARIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETN 194

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 195 GTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 250

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 251 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 301


>gi|190341311|gb|ACE74732.1| RpoA [Enterobacter aerogenes]
 gi|190341327|gb|ACE74740.1| RpoA [Enterobacter helveticus]
 gi|190341329|gb|ACE74741.1| RpoA [Enterobacter helveticus]
 gi|190341331|gb|ACE74742.1| RpoA [Enterobacter helveticus]
 gi|190341333|gb|ACE74743.1| RpoA [Enterobacter helveticus]
 gi|190341337|gb|ACE74745.1| RpoA [Enterobacter helveticus]
 gi|190341339|gb|ACE74746.1| RpoA [Enterobacter helveticus]
 gi|190341341|gb|ACE74747.1| RpoA [Enterobacter helveticus]
 gi|190341343|gb|ACE74748.1| RpoA [Enterobacter helveticus]
 gi|190341345|gb|ACE74749.1| RpoA [Enterobacter helveticus]
 gi|190341347|gb|ACE74750.1| RpoA [Enterobacter helveticus]
 gi|190341355|gb|ACE74754.1| RpoA [Enterobacter pulveris]
 gi|190341357|gb|ACE74755.1| RpoA [Enterobacter pulveris]
 gi|190341359|gb|ACE74756.1| RpoA [Enterobacter pulveris]
 gi|190341361|gb|ACE74757.1| RpoA [Enterobacter pulveris]
 gi|190341363|gb|ACE74758.1| RpoA [Enterobacter pulveris]
 gi|190341365|gb|ACE74759.1| RpoA [Enterobacter pulveris]
 gi|190341375|gb|ACE74764.1| RpoA [Escherichia hermannii]
 gi|190341377|gb|ACE74765.1| RpoA [Escherichia hermannii]
          Length = 308

 Score =  272 bits (696), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 139/291 (47%), Positives = 202/291 (69%), Gaps = 9/291 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + V +
Sbjct: 82  AVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQR 141

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPASARIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 202 GTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 257

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 258 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|190341389|gb|ACE74771.1| RpoA [Cronobacter dublinensis]
 gi|190341391|gb|ACE74772.1| RpoA [Cronobacter dublinensis]
 gi|190341393|gb|ACE74773.1| RpoA [Cronobacter dublinensis]
 gi|190341395|gb|ACE74774.1| RpoA [Cronobacter dublinensis]
 gi|190341397|gb|ACE74775.1| RpoA [Cronobacter dublinensis]
 gi|190341401|gb|ACE74777.1| RpoA [Cronobacter genomosp. 1]
 gi|190341403|gb|ACE74778.1| RpoA [Cronobacter malonaticus]
 gi|190341405|gb|ACE74779.1| RpoA [Cronobacter malonaticus]
 gi|190341407|gb|ACE74780.1| RpoA [Cronobacter malonaticus]
 gi|190341409|gb|ACE74781.1| RpoA [Cronobacter malonaticus]
 gi|190341411|gb|ACE74782.1| RpoA [Cronobacter malonaticus]
 gi|190341413|gb|ACE74783.1| RpoA [Cronobacter malonaticus]
 gi|190341415|gb|ACE74784.1| RpoA [Cronobacter malonaticus]
 gi|190341417|gb|ACE74785.1| RpoA [Cronobacter muytjensii]
 gi|190341419|gb|ACE74786.1| RpoA [Cronobacter muytjensii]
 gi|190341421|gb|ACE74787.1| RpoA [Cronobacter muytjensii]
 gi|190341423|gb|ACE74788.1| RpoA [Cronobacter muytjensii]
 gi|190341425|gb|ACE74789.1| RpoA [Cronobacter muytjensii]
 gi|190341427|gb|ACE74790.1| RpoA [Cronobacter sakazakii]
 gi|190341429|gb|ACE74791.1| RpoA [Cronobacter sakazakii]
 gi|190341431|gb|ACE74792.1| RpoA [Cronobacter sakazakii]
 gi|190341433|gb|ACE74793.1| RpoA [Cronobacter sakazakii]
 gi|190341435|gb|ACE74794.1| RpoA [Cronobacter sakazakii]
 gi|190341437|gb|ACE74795.1| RpoA [Cronobacter sakazakii]
 gi|190341439|gb|ACE74796.1| RpoA [Cronobacter sakazakii]
 gi|190341441|gb|ACE74797.1| RpoA [Cronobacter sakazakii]
 gi|190341443|gb|ACE74798.1| RpoA [Cronobacter sakazakii]
 gi|190341445|gb|ACE74799.1| RpoA [Cronobacter sakazakii]
 gi|190341447|gb|ACE74800.1| RpoA [Cronobacter sakazakii]
 gi|190341449|gb|ACE74801.1| RpoA [Cronobacter sakazakii]
 gi|190341451|gb|ACE74802.1| RpoA [Cronobacter sakazakii]
 gi|190341455|gb|ACE74804.1| RpoA [Cronobacter sakazakii]
 gi|190341457|gb|ACE74805.1| RpoA [Cronobacter sakazakii]
 gi|190341459|gb|ACE74806.1| RpoA [Cronobacter sakazakii]
 gi|190341463|gb|ACE74808.1| RpoA [Cronobacter sakazakii]
 gi|190341465|gb|ACE74809.1| RpoA [Cronobacter sakazakii]
 gi|190341467|gb|ACE74810.1| RpoA [Cronobacter sakazakii]
 gi|190341469|gb|ACE74811.1| RpoA [Cronobacter sakazakii]
 gi|190341471|gb|ACE74812.1| RpoA [Cronobacter sakazakii]
 gi|190341473|gb|ACE74813.1| RpoA [Cronobacter sakazakii]
 gi|190341475|gb|ACE74814.1| RpoA [Cronobacter sakazakii]
 gi|190341477|gb|ACE74815.1| RpoA [Cronobacter turicensis]
 gi|190341479|gb|ACE74816.1| RpoA [Cronobacter turicensis]
 gi|190341481|gb|ACE74817.1| RpoA [Cronobacter turicensis]
 gi|190341483|gb|ACE74818.1| RpoA [Cronobacter turicensis]
          Length = 308

 Score =  272 bits (696), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 139/291 (47%), Positives = 202/291 (69%), Gaps = 9/291 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + V +
Sbjct: 82  AVRVQGKDEVVLTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQR 141

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPASARIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 202 GTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 257

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 258 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|90193998|gb|ABD92560.1| RpoA [Avibacterium gallinarum]
          Length = 302

 Score =  272 bits (696), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 139/293 (47%), Positives = 204/293 (69%), Gaps = 9/293 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +I EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+
Sbjct: 14  VILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNL 73

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELT 148
           KG+ +K+    +  +T+ K G G V A DI    D+E++NP+HVIC+L D +A + M + 
Sbjct: 74  KGLAVKVQNKDNVFLTLSKSGIGPVVAADITYDGDVEIVNPEHVICHLTDENASINMCIR 133

Query: 149 VSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           V +G GYVPA    H + E  PIG + +DA YSP+++++Y VE+ R  Q  D DKL + +
Sbjct: 134 VQRGRGYVPASARVHSQDEERPIGRLLVDACYSPVQRIAYNVEATRVEQRTDLDKLVIEL 193

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELE 264
           +T+G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LE
Sbjct: 194 ETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLE 249

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 250 LTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|255020793|ref|ZP_05292851.1| DNA-directed RNA polymerase alpha subunit [Acidithiobacillus caldus
           ATCC 51756]
 gi|254969789|gb|EET27293.1| DNA-directed RNA polymerase alpha subunit [Acidithiobacillus caldus
           ATCC 51756]
          Length = 339

 Score =  272 bits (696), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 148/323 (45%), Positives = 207/323 (64%), Gaps = 5/323 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +L++P + +  VL      R  +   PL RGF HTLGNALRRVL+SSL+GAA+T V+I+G
Sbjct: 6   DLLRPEHYDLEVLSP---RRARISLGPLERGFGHTLGNALRRVLLSSLKGAAVTEVEIEG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE SSI+GV ED+ DI+LN+K + ++  G +   VT+ KRGPG+VT  DI   + IEV
Sbjct: 63  VLHEYSSIEGVQEDVVDILLNLKQLAVRAQGRNEVMVTLRKRGPGLVTGADIIAEHGIEV 122

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP-IGLITIDALYSPIKKVSYT 186
            NP+ VI  L  D  + M L    G GY PA   R  ++  IG++ +DA YSP+ +VS+ 
Sbjct: 123 ANPEQVIATLTRDVELVMHLRFDTGRGYEPAATRRQSHEKRIGVLALDASYSPVHRVSFQ 182

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VESAR  Q  D D+L + ++T+G +    +V  A+RIL+ QL +F   E   +       
Sbjct: 183 VESARVEQRTDLDRLVLDVETNGVVEPLWAVQEAARILRQQLAVFGGAEAATEREAHAAP 242

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           V      P L + V++LEL+VRS NCL+ E+I Y+GDL+Q+TE ++L+  N GRKSL EI
Sbjct: 243 VHE-DLLPLLARPVDDLELTVRSANCLKAEDIFYIGDLVQKTEQELLKAPNLGRKSLTEI 301

Query: 307 KGVLGTMGLFLGMNLPDWPPESI 329
           K VL   GL LGM + +WPPE++
Sbjct: 302 KEVLDKNGLTLGMRIENWPPENL 324


>gi|190341307|gb|ACE74730.1| RpoA [Citrobacter koseri]
 gi|190341309|gb|ACE74731.1| RpoA [Citrobacter koseri]
          Length = 308

 Score =  272 bits (696), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 139/291 (47%), Positives = 202/291 (69%), Gaps = 9/291 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + V +
Sbjct: 82  AVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQR 141

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 202 GTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 257

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 258 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|303256475|ref|ZP_07342489.1| DNA-directed RNA polymerase, alpha subunit [Burkholderiales
           bacterium 1_1_47]
 gi|302859966|gb|EFL83043.1| DNA-directed RNA polymerase, alpha subunit [Burkholderiales
           bacterium 1_1_47]
          Length = 346

 Score =  272 bits (696), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 154/338 (45%), Positives = 207/338 (61%), Gaps = 22/338 (6%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP +IE +   +       +  EP   G+AHTLGNALRRVL+SS+ G A T  QI GV
Sbjct: 6   LLKPRSIE-VETAEGNPYSATVTMEPFETGYAHTLGNALRRVLLSSMVGFAPTEAQIAGV 64

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S I GV ED+ DI+LN+KGI  K+       +T+ K G GVVTA D    +D+++L
Sbjct: 65  VHEYSQIDGVKEDVVDILLNVKGIIFKLENRDEVTITLRKEGEGVVTAADFDLPHDVQIL 124

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND----PIGLITIDALYSPIKKVS 184
           NP+HVI NL     + M+L + KG GY P      ++D     IG I +DA +SPI +V+
Sbjct: 125 NPEHVIANLS-GGKLDMQLKIEKGRGYQPGDMRALKDDYSKGTIGRIIMDASFSPILRVA 183

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF-----INFE---- 235
           Y VE+AR  Q  D DKL M I+T+G+I  E+++  A+ ILQDQL +F     I  E    
Sbjct: 184 YRVENARVEQRTDLDKLVMNIETNGAILPEEALRQAAHILQDQLSVFGGLPTIGLEPVAP 243

Query: 236 -------EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
                  +P+  V+  +     P +P L + V++LEL+VRS NCL+ ENI Y+GDLIQRT
Sbjct: 244 QPAFGAMQPQAPVEAPMAKPQPPVDPILRRPVDDLELTVRSANCLKAENIYYIGDLIQRT 303

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           E ++L+  N GRKSL EIK VL   GL LGM L +WPP
Sbjct: 304 ENELLKTPNLGRKSLNEIKEVLAAHGLTLGMKLENWPP 341


>gi|90193990|gb|ABD92556.1| RpoA [Pasteurella multocida]
 gi|90194060|gb|ABD92591.1| RpoA [Pasteurella multocida subsp. gallicida]
          Length = 302

 Score =  272 bits (696), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 140/293 (47%), Positives = 202/293 (68%), Gaps = 9/293 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +I EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+
Sbjct: 14  VILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNL 73

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELT 148
           KG+ +K+       +T+ K G G V A DI    D+E++NP+HVIC+L D  A + M + 
Sbjct: 74  KGLAVKVQNKDDVFLTLNKSGIGPVVAADITHDGDVEIVNPEHVICHLTDESASINMRIR 133

Query: 149 VSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           V +G GYVPA    H + E  PIG + +DA YSP+ +++Y VE+AR  Q  D DKL + +
Sbjct: 134 VQRGRGYVPASARVHAQDEERPIGRLLVDACYSPVDRIAYNVEAARVEQRTDLDKLVIEL 193

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELE 264
           +T+G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LE
Sbjct: 194 ETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLE 249

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 250 LTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|331000670|ref|ZP_08324323.1| DNA-directed RNA polymerase, alpha subunit [Parasutterella
           excrementihominis YIT 11859]
 gi|329570882|gb|EGG52593.1| DNA-directed RNA polymerase, alpha subunit [Parasutterella
           excrementihominis YIT 11859]
          Length = 346

 Score =  272 bits (695), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 154/338 (45%), Positives = 207/338 (61%), Gaps = 22/338 (6%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP +IE +   +       +  EP   G+AHTLGNALRRVL+SS+ G A T  QI GV
Sbjct: 6   LLKPRSIE-VETAEGNPYSATVTMEPFETGYAHTLGNALRRVLLSSMVGFAPTEAQIAGV 64

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S I GV ED+ DI+LN+KGI  K+       +T+ K G GVVTA D    +D+++L
Sbjct: 65  VHEYSQIDGVKEDVVDILLNVKGIIFKLENRDEVTITLRKEGEGVVTAADFDLPHDVQIL 124

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND----PIGLITIDALYSPIKKVS 184
           NP+HVI NL     + M+L + KG GY P      ++D     IG I +DA +SPI +V+
Sbjct: 125 NPEHVIANLS-GGKLDMQLKIEKGRGYQPGDMRALKDDYSKGTIGRIIMDASFSPILRVA 183

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF-----INFE---- 235
           Y VE+AR  Q  D DKL M I+T+G+I  E+++  A+ ILQDQL +F     I  E    
Sbjct: 184 YRVENARVEQRTDLDKLVMNIETNGAILPEEALRQAAHILQDQLSVFGGLPTIGLEPVAP 243

Query: 236 -------EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
                  +P+  V+  +     P +P L + V++LEL+VRS NCL+ ENI Y+GDLIQRT
Sbjct: 244 QPAFGAMQPQAPVEAPMAKPQPPVDPILRRPVDDLELTVRSANCLKAENIYYIGDLIQRT 303

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           E ++L+  N GRKSL EIK VL   GL LGM L +WPP
Sbjct: 304 ENELLKTPNLGRKSLNEIKEVLAAHGLTLGMKLENWPP 341


>gi|190341387|gb|ACE74770.1| RpoA [Pantoea sp. E147]
          Length = 308

 Score =  272 bits (695), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 139/291 (47%), Positives = 201/291 (69%), Gaps = 9/291 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + V +
Sbjct: 82  AVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENAAISMRIKVQR 141

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPASARIHSEEDERPIGRLLVDACYSPVDRIAYNVEAARVEQRTDLDKLVIEMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 202 GTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 257

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 258 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|90194028|gb|ABD92575.1| RpoA [Actinobacillus equuli subsp. equuli]
          Length = 300

 Score =  272 bits (695), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 140/290 (48%), Positives = 204/290 (70%), Gaps = 9/290 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 14  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 73

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+S      +T+ K G G VTA DI    D+E++NP+HVIC+L D +A + M + V +
Sbjct: 74  AVKVSNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPNHVICHLTDKNASINMRIRVQR 133

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 134 GRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLIIEMETN 193

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 194 GTIDPEEAIRRAATILAEQLDAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 249

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 250 RSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 299


>gi|33519683|ref|NP_878515.1| DNA-directed RNA polymerase subunit alpha [Candidatus Blochmannia
           floridanus]
 gi|41688649|sp|Q7VQC3|RPOA_BLOFL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|33517346|emb|CAD83731.1| DNA-directed RNA polymerase alpha chain [Candidatus Blochmannia
           floridanus]
          Length = 331

 Score =  272 bits (695), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 149/337 (44%), Positives = 222/337 (65%), Gaps = 14/337 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q   +E +KP +I    + +     TL   EPL RGF HTLGNALRR+L+SS+ G AIT
Sbjct: 1   MQSFEKEFLKPRSINIEKISEIHSKITL---EPLERGFGHTLGNALRRILLSSMPGCAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GVLHE  + +GV ED+ +I+LN+K + + M       +T+ K G G V A DI+ 
Sbjct: 58  EVEIEGVLHEYGTKEGVREDVLEILLNLKTLAINMYVKDSIVLTLKKTGIGPVIASDIEY 117

Query: 122 VNDI-EVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHHRTEND----PIGLITIDA 175
            + I  ++NP+H+IC + D D  + M + V +G GYVPA    + +D    PIG + +DA
Sbjct: 118 DSSIISIVNPNHIICCITDQDTSIIMRIKVQRGRGYVPAFSRFSSDDQHDLPIGRLLLDA 177

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
            YSP++++SYTVE+AR  +  D DKL + ++T+G+I  E+++  A+ IL DQL  FI+ +
Sbjct: 178 CYSPVERISYTVEAARVEKRTDLDKLIIDMETNGTIDPEEAIRRAATILSDQLSSFIDLK 237

Query: 236 EPKK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           +  + EVKE+       F+P+LL  V++LEL+VRS NCL+ E+I Y+GDL+Q+TE ++L+
Sbjct: 238 DVHQPEVKEE----KPEFDPSLLNLVDDLELTVRSANCLKAESIHYIGDLVQKTEVELLK 293

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
             N G+KSL EIK VL + GL LGM L +WPP+ + E
Sbjct: 294 TPNLGKKSLTEIKDVLASRGLSLGMRLDNWPPKHLSE 330


>gi|90194010|gb|ABD92566.1| RpoA [Actinobacillus minor NM305]
          Length = 303

 Score =  272 bits (695), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 137/289 (47%), Positives = 202/289 (69%), Gaps = 7/289 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 76

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+       +T+ K G G VTAGDI    D+E++NPDHVIC+L D +A + M + V +
Sbjct: 77  AVKVQSKDDVVLTLNKSGIGPVTAGDITHDGDVEIVNPDHVICHLTDKNASINMRIRVQR 136

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 137 GRGYVPASARVHTQDDDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLIIEMETN 196

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G+I  E+++  A+ IL +QL  F++  + ++ V   +  +   F+P LL+ V++LEL+VR
Sbjct: 197 GTIDPEEAIRRAATILAEQLDAFVDLRDVRQPV---VKEEKPEFDPILLRPVDDLELTVR 253

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 254 SANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|225873050|ref|YP_002754509.1| DNA-directed RNA polymerase, alpha subunit [Acidobacterium
           capsulatum ATCC 51196]
 gi|225794173|gb|ACO34263.1| DNA-directed RNA polymerase, alpha subunit [Acidobacterium
           capsulatum ATCC 51196]
          Length = 363

 Score =  272 bits (695), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 138/290 (47%), Positives = 198/290 (68%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
           A+P  RGF  T+GNALRR L+SS+ GAA+TAV+I+GVLHE  SI GV ED TDIILN+K 
Sbjct: 28  AQPFERGFGTTIGNALRRTLLSSIEGAAVTAVKIEGVLHEFQSIPGVVEDATDIILNLKQ 87

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           +  K++GD  K + +    PGVVT+G I+   D+E+L+ D  I  +     + ME+ + +
Sbjct: 88  VPFKLNGDGPKALYVRADQPGVVTSGMIEADADVEILDKDIYIATVSEGGKLEMEMRLKR 147

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G G+V A  +   +  IG I +D+++SP++KV+Y VE+AR GQ+ DYDKL++ + T+G++
Sbjct: 148 GRGFVSADKNHDNDLGIGFIPVDSVHSPVRKVNYFVEAARLGQITDYDKLTLEVMTNGTV 207

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTN 271
              D+V LA+++L+D + +FINFEE  +        +    N  L + VEELELSVRS N
Sbjct: 208 LPADAVGLAAKLLKDHMSIFINFEEEIEAESHSEEGRVQLRNENLNRSVEELELSVRSYN 267

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           CL+  NI  +G+L+Q+TEA+ML+  NFGRKSL EIK +L  MGL LGM +
Sbjct: 268 CLKNANIQTIGELVQKTEAEMLKTKNFGRKSLNEIKEILAQMGLSLGMKI 317


>gi|308171336|gb|ADO15987.1| RpoA [Vibrio sinaloensis DSM 21326]
          Length = 321

 Score =  272 bits (695), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 143/322 (44%), Positives = 213/322 (66%), Gaps = 11/322 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T V+I+G
Sbjct: 6   EFLKPRLVDIEQVSTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           VLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI    D+E
Sbjct: 63  VLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVE 122

Query: 127 VLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKK 182
           + NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K
Sbjct: 123 IANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDK 182

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           ++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   +
Sbjct: 183 IAYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE 242

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KS
Sbjct: 243 ---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKS 299

Query: 303 LVEIKGVLGTMGLFLGMNLPDW 324
           L EIK VL + GL LGM L +W
Sbjct: 300 LTEIKDVLASRGLSLGMRLENW 321


>gi|90194006|gb|ABD92564.1| RpoA [Mannheimia haemolytica]
          Length = 302

 Score =  272 bits (695), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 138/290 (47%), Positives = 203/290 (70%), Gaps = 9/290 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 76

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+       +T+ K G G VTA DI    D+E++NPDHVIC+L D +A + M + V +
Sbjct: 77  AVKVQNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPDHVICHLTDKNASINMRIRVQR 136

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 137 GRGYVPASARLHTQNDDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLVIEMETN 196

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G++  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 197 GTLDPEEAIRRAATILAEQLAAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 252

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 253 RSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|90194064|gb|ABD92593.1| RpoA [Pasteurella canis]
          Length = 302

 Score =  271 bits (694), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 139/293 (47%), Positives = 203/293 (69%), Gaps = 9/293 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +I EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+
Sbjct: 14  VILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNL 73

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELT 148
           KG+ +K+       +T+ K G G V A DI    D+E++NP+H+IC+L D +A + M + 
Sbjct: 74  KGLAVKVQNKDDVFLTLNKSGIGPVVAADITHDGDVEIVNPEHIICHLTDDNASINMRIR 133

Query: 149 VSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           V +G GYVPA    H + E  PIG + +DA YSP+ +++Y VE+AR  Q  D DKL + +
Sbjct: 134 VQRGRGYVPASARVHAQDEERPIGRLLVDACYSPVDRIAYNVEAARVEQRTDLDKLVIEL 193

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELE 264
           +T+G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LE
Sbjct: 194 ETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLE 249

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 250 LTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|190341367|gb|ACE74760.1| RpoA [Enterobacter radicincitans]
          Length = 308

 Score =  271 bits (694), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 139/291 (47%), Positives = 202/291 (69%), Gaps = 9/291 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + V +
Sbjct: 82  AVRVQGKDDVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASINMRIKVQR 141

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPASARIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 202 GTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 257

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 258 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|190341299|gb|ACE74726.1| RpoA [Citrobacter freundii]
 gi|190341301|gb|ACE74727.1| RpoA [Citrobacter sp. NZ3872_90]
 gi|190341303|gb|ACE74728.1| RpoA [Citrobacter sp. OD1158_06]
          Length = 308

 Score =  271 bits (694), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 139/291 (47%), Positives = 202/291 (69%), Gaps = 9/291 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + V +
Sbjct: 82  AVRVQGKDDVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQR 141

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 202 GTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 257

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 258 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|90194048|gb|ABD92585.1| RpoA [Actinobacillus porcinus]
          Length = 303

 Score =  271 bits (694), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 139/293 (47%), Positives = 203/293 (69%), Gaps = 9/293 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +I EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE SS +GV ED+ +++LN+
Sbjct: 14  VILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSSKEGVQEDILEVLLNL 73

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELT 148
           KG+ +K+       +T+ K G G V A DI    D+E++NPDHV+C+L D +A + M + 
Sbjct: 74  KGLAVKVQNKDDVFLTLNKSGIGPVVAADITHDGDVEIVNPDHVLCHLTDENASINMRIR 133

Query: 149 VSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           V +G GYVPA    H + E  PIG + +DA YSP+ +++Y VE+AR  Q  D DKL + +
Sbjct: 134 VQRGRGYVPASARAHTQDEERPIGRLLVDACYSPVDRIAYNVEAARVEQRTDLDKLVIEL 193

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELE 264
           +T+G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LE
Sbjct: 194 ETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLE 249

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 250 LTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|207744550|ref|YP_002260942.1| dna-directed rna polymerase alpha chain (rnap alphasubunit)
           (transcriptase alpha chain) (rna polymerase alpha
           subunit) protein [Ralstonia solanacearum IPO1609]
 gi|206595956|emb|CAQ62883.1| dna-directed rna polymerase alpha chain (rnap alphasubunit)
           (transcriptase alpha chain) (rna polymerase alpha
           subunit) protein [Ralstonia solanacearum IPO1609]
          Length = 302

 Score =  271 bits (694), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 142/303 (46%), Positives = 200/303 (66%), Gaps = 6/303 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EP  RG+ HTLGNALRRVL+SS+ G A T V I GV+HE S+I GV ED+ +++LN+KG+
Sbjct: 2   EPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGVVHEYSTIDGVQEDVVNLLLNLKGV 61

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
             K+       V++ K G GVVTA DI+  +D+E++NP HVI +L     + M++ V +G
Sbjct: 62  VFKLHNRDEVTVSLRKEGEGVVTAADIELPHDVEIINPGHVIASLSAGGKLDMQIKVEQG 121

Query: 153 HGYVPAKHHRTENDP---IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            GYVP    +  ++    IG + +DA ++P+++VSY VESAR  Q  D DKL M I+T+G
Sbjct: 122 RGYVPGNVRKFGDESSKVIGRVVLDASFAPVRRVSYAVESARVEQRTDLDKLVMNIETNG 181

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-FNPALLKKVEELELSVR 268
            I+ E+++  ++RIL DQL +F   E    E   +      P  +P LL+ V++LEL+VR
Sbjct: 182 VISPEEAIRQSARILVDQLSVFAALE--GTESAAEAAAARAPQIDPILLRPVDDLELTVR 239

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPES 328
           S NCL+ ENI Y+GDLIQ TE ++L+  N GRKSL EIK VL + GL LGM L +WPP  
Sbjct: 240 SANCLKAENIYYIGDLIQLTENELLKTPNLGRKSLNEIKEVLASRGLTLGMKLENWPPAG 299

Query: 329 IEE 331
           +E+
Sbjct: 300 LEK 302


>gi|90194052|gb|ABD92587.1| RpoA [Mannheimia glucosida]
          Length = 304

 Score =  271 bits (694), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 138/290 (47%), Positives = 203/290 (70%), Gaps = 9/290 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 76

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+       +T+ K G G VTA DI    D+E++NPDHVIC+L D +A + M + V +
Sbjct: 77  AVKVQNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPDHVICHLTDKNASINMRIRVQR 136

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 137 GRGYVPASARLHTQNDDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLVIEMETN 196

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G++  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 197 GTLDPEEAIRRAATILAEQLAAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 252

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 253 RSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|319942198|ref|ZP_08016514.1| DNA-directed RNA polymerase subunit alpha [Sutterella
           wadsworthensis 3_1_45B]
 gi|319804251|gb|EFW01143.1| DNA-directed RNA polymerase subunit alpha [Sutterella
           wadsworthensis 3_1_45B]
          Length = 335

 Score =  271 bits (694), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 149/328 (45%), Positives = 209/328 (63%), Gaps = 9/328 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP +++ + + +   NR ++  EP  RG+ HTLGNALRR+L+SS+ G A T  QI G+
Sbjct: 6   LLKPTSVD-VSVDESNPNRAVITLEPFERGYGHTLGNALRRILLSSMVGFAPTEAQITGI 64

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S I GV ED+ DI+LN+KG+  K+       + + K G GVVTA D    +D+ VL
Sbjct: 65  VHEYSQIDGVLEDVVDILLNLKGVVFKLEKRDEVTIMLRKDGDGVVTAADFDLPHDVTVL 124

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND----PIGLITIDALYSPIKKVS 184
           NPDHVI +L     + M++ + KG GY P       +D     IG I +DA +SPI +V+
Sbjct: 125 NPDHVIAHLS-GGRLEMQVKIEKGRGYQPGDVRAFRDDYSKSSIGRIIMDASFSPILRVA 183

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVK 242
           Y V +AR  Q  D DKL MTI+T+G+I  E+++  + RILQDQL +F  I+ E+    +K
Sbjct: 184 YQVMAARVAQRTDLDKLEMTIETNGAIGPEEALRESVRILQDQLAVFGAIHPEQGTDGIK 243

Query: 243 -EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ED      P +P LL+ V++LEL+VRS NCL+ E+I ++GDLIQRTE ++L+  N GRK
Sbjct: 244 PEDAANNPPPLDPILLRPVDDLELTVRSANCLKAESIYFIGDLIQRTENELLKTPNLGRK 303

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           SL EIK VL   GL LG  L +WPP  +
Sbjct: 304 SLNEIKEVLAAHGLTLGSKLENWPPAGV 331


>gi|190341305|gb|ACE74729.1| RpoA [Citrobacter koseri]
          Length = 308

 Score =  271 bits (693), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 139/291 (47%), Positives = 201/291 (69%), Gaps = 9/291 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + V +
Sbjct: 82  AVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQR 141

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F P LL+ V++LEL+V
Sbjct: 202 GTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEE----KPEFAPILLRPVDDLELTV 257

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 258 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|126643071|ref|YP_001086055.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter baumannii
           ATCC 17978]
          Length = 310

 Score =  271 bits (692), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 138/302 (45%), Positives = 215/302 (71%), Gaps = 5/302 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           MI EPL RGF HTLGNALRR+L+SSL GAA+  V+I+GV HE S+++G+ +D+ +++LN+
Sbjct: 1   MILEPLERGFGHTLGNALRRILLSSLPGAAVVEVEIEGVEHEYSTLEGLQQDIVELLLNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+++K+   +   +T+ K+GPG +TA D++  +++EV+NP+H+I  L     ++M L V
Sbjct: 61  KGLSIKLFDQNEAYLTLEKQGPGDITAADLRLPHNVEVVNPEHLIGTLSATGSLKMRLKV 120

Query: 150 SKGHGY--VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           S+G GY    ++    E  P+G + +DA YSPIK+VSYTVE+AR  Q  D DKL + ++T
Sbjct: 121 SQGRGYETSDSRFPEGETRPVGRLQLDASYSPIKRVSYTVENARVEQRTDLDKLVIDLET 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ ILQ Q+ +F++ ++ +  V ++   +    +P LL+ V++LEL+V
Sbjct: 181 NGTVDPEEAIRKAATILQQQIAIFVDLQKDQTPVAQEPREE---VDPILLRPVDDLELTV 237

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           RS NCL+ ENI Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP 
Sbjct: 238 RSANCLKAENIYYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASKGLQLGMRLENWPPA 297

Query: 328 SI 329
           S+
Sbjct: 298 SL 299


>gi|50086190|ref|YP_047700.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter sp. ADP1]
 gi|61215915|sp|Q6F7T7|RPOA_ACIAD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|49532166|emb|CAG69878.1| RNA polymerase, alpha subunit [Acinetobacter sp. ADP1]
          Length = 335

 Score =  271 bits (692), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 137/302 (45%), Positives = 215/302 (71%), Gaps = 5/302 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +I EPL RGF HTLGNALRR+L+SSL GAA+  V+I+GV HE S+++G+ +D+ +++LN+
Sbjct: 26  VILEPLERGFGHTLGNALRRILLSSLPGAAVVEVEIEGVEHEYSTLEGLQQDIVELLLNL 85

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+++K+   +   +T+ K+GPG +TA D++  +++EV+NP+H+I  L     ++M L V
Sbjct: 86  KGLSIKLFDQNEAYLTLEKQGPGDITAADLRLPHNVEVVNPEHLIGTLSASGSIKMRLKV 145

Query: 150 SKGHGY--VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           S+G GY    ++    E  P+G + +DA YSPIK+VSYTVE+AR  Q  D DKL + ++T
Sbjct: 146 SQGRGYETSDSRFPEGETRPVGRLQLDASYSPIKRVSYTVENARVEQRTDLDKLVIDLET 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ ILQ Q+ +F++ ++ +  V ++   +    +P LL+ V++LEL+V
Sbjct: 206 NGTVDPEEAIRKAATILQQQIAIFVDLQKDQAPVAQEPREE---VDPILLRPVDDLELTV 262

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           RS NCL+ ENI Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP 
Sbjct: 263 RSANCLKAENIYYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASKGLQLGMRLENWPPA 322

Query: 328 SI 329
           S+
Sbjct: 323 SL 324


>gi|90193992|gb|ABD92557.1| RpoA [Histophilus somni]
          Length = 302

 Score =  271 bits (692), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 140/293 (47%), Positives = 203/293 (69%), Gaps = 9/293 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +I EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+
Sbjct: 14  VILEPLERGFGHTLGNALRRILLSSMPGYAVTEVEIDGVLHEYSSKEGVQEDIIEVLLNL 73

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELT 148
           KG+ +K+    +  +T+ K G G V A DI    D+E++NPDHVIC+L D +A + M + 
Sbjct: 74  KGLAVKVQNKDNVFLTLSKSGIGPVVAADITHDGDVEIVNPDHVICHLTDENASINMRIR 133

Query: 149 VSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           V +G GYVPA    H   E  PIG + +DA YSP+ +++Y V++AR  Q  D DKL + +
Sbjct: 134 VQRGRGYVPASSRVHSLDEERPIGRLLVDACYSPVDRIAYNVQAARVEQRTDLDKLVIEL 193

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELE 264
           +T+G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LE
Sbjct: 194 ETNGTIEPEEAIRRAATILAEQLDAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLE 249

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 250 LTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLVSRGLSL 302


>gi|262370553|ref|ZP_06063878.1| RNA polymerase [Acinetobacter johnsonii SH046]
 gi|262314353|gb|EEY95395.1| RNA polymerase [Acinetobacter johnsonii SH046]
          Length = 335

 Score =  271 bits (692), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 138/302 (45%), Positives = 215/302 (71%), Gaps = 5/302 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +I EPL RGF HTLGNALRR+L+SSL GAA+  V+I+GV HE S+++G+ +D+ +++LN+
Sbjct: 26  VILEPLERGFGHTLGNALRRILLSSLPGAAVVEVEIEGVEHEYSTLEGLQQDIVELLLNL 85

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+++K+   +   +T+ K+GPG VTA D++  +++EV+NP+H+I  L     ++M L V
Sbjct: 86  KGLSIKLFDQNEAYLTLEKQGPGDVTAADLRLPHNVEVVNPEHLIGTLSASGSLKMRLKV 145

Query: 150 SKGHGY--VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           S+G GY    ++    E  P+G + +DA YSPIK+VSYTVE+AR  Q  D DKL + ++T
Sbjct: 146 SQGRGYETSDSRFPEGETRPVGRLQLDASYSPIKRVSYTVENARVEQRTDLDKLVIDLET 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ ILQ Q+ +F++ ++ +  V ++   +    +P LL+ V++LEL+V
Sbjct: 206 NGTVDPEEAIRKAATILQQQIAIFVDLQKDQAPVAQEPREE---VDPILLRPVDDLELTV 262

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           RS NCL+ ENI Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP 
Sbjct: 263 RSANCLKAENIYYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASKGLQLGMRLENWPPA 322

Query: 328 SI 329
           S+
Sbjct: 323 SL 324


>gi|260549815|ref|ZP_05824031.1| RNA polymerase alpha subunit [Acinetobacter sp. RUH2624]
 gi|260407065|gb|EEX00542.1| RNA polymerase alpha subunit [Acinetobacter sp. RUH2624]
          Length = 335

 Score =  271 bits (692), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 137/302 (45%), Positives = 215/302 (71%), Gaps = 5/302 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +I EPL RGF HTLGNALRR+L+SSL GAA+  V+I+GV HE S+++G+ +D+ +++LN+
Sbjct: 26  VILEPLERGFGHTLGNALRRILLSSLPGAAVVEVEIEGVEHEYSTLEGLQQDIVELLLNL 85

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+++K+   +   +T+ K+GPG +TA D++  +++EV+NPDH+I  L     ++M L V
Sbjct: 86  KGLSIKLFDQNEAYLTLEKQGPGDITAADLRLPHNVEVVNPDHLIGTLSASGSLKMRLKV 145

Query: 150 SKGHGY--VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           ++G GY    ++    E  P+G + +DA YSPIK+VSYTVE+AR  Q  D DKL + ++T
Sbjct: 146 AQGRGYETSDSRFPEGETRPVGRLQLDASYSPIKRVSYTVENARVEQRTDLDKLVIDLET 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ ILQ Q+ +F++ ++ +  V ++   +    +P LL+ V++LEL+V
Sbjct: 206 NGTVDPEEAIRKAATILQQQIAIFVDLQKDQTPVAQEPREE---VDPILLRPVDDLELTV 262

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           RS NCL+ ENI Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP 
Sbjct: 263 RSANCLKAENIYYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASKGLQLGMRLENWPPA 322

Query: 328 SI 329
           S+
Sbjct: 323 SL 324


>gi|90194002|gb|ABD92562.1| RpoA [Phocoenobacter uteri]
          Length = 302

 Score =  270 bits (691), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 137/290 (47%), Positives = 203/290 (70%), Gaps = 9/290 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 76

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+       +T+ K G G V A DI    D+E++NP+HVIC+L D DA + M + V +
Sbjct: 77  AVKVQNKDDIVLTLNKSGIGPVIAADITHDGDVEIVNPEHVICHLTDKDASINMRIRVQR 136

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H ++++ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 137 GRGYVPASARVHSQSDDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLIIEMETN 196

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G++  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 197 GTLDPEEAIRRAATILAEQLAAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 252

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 253 RSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|268316435|ref|YP_003290154.1| DNA-directed RNA polymerase, alpha subunit [Rhodothermus marinus
           DSM 4252]
 gi|262333969|gb|ACY47766.1| DNA-directed RNA polymerase, alpha subunit [Rhodothermus marinus
           DSM 4252]
          Length = 323

 Score =  270 bits (691), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 141/307 (45%), Positives = 206/307 (67%), Gaps = 5/307 (1%)

Query: 23  EEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
           EE   T    + +PL RG+  T+GNALRRVL+SSL G AITAV+IDGV HE S+I GV E
Sbjct: 11  EEATETFGRFVVQPLERGYGVTIGNALRRVLLSSLPGVAITAVRIDGVQHEFSTIPGVTE 70

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDV 139
           D+ +IILN+KG+  K    +   + +  +GP V TA DI +  +  EVLNPDH I  L  
Sbjct: 71  DVAEIILNLKGVRFKAKDTTDANIRLSLKGPHVWTARDIGEATSHYEVLNPDHYIATLAE 130

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
            A V +EL + +G GYVPA+ ++  +DPIG+I IDA+++PIK V YT++  R GQ ++Y+
Sbjct: 131 GAEVNLELRMGRGRGYVPAEENKLPDDPIGVIAIDAIFTPIKNVRYTIKPTRVGQKIEYE 190

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EPKKEV-KEDINVKSLPFNPALL 257
           +L + I TDGS++ E+++  A+ IL+D + +FI  E EP+ EV K++++ +       L 
Sbjct: 191 RLELEITTDGSVSPEEALVQAATILRDHINLFITMESEPQPEVKKKEVDAEVQRIRELLS 250

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + V+EL+LSVR+ NCL+  NI  +GDL++R E++ML+  NFGRKSL E+  VL   GL  
Sbjct: 251 QPVDELDLSVRAQNCLKAANIRTIGDLVRRQESEMLKFRNFGRKSLQELIAVLEERGLHF 310

Query: 318 GMNLPDW 324
           GM++  +
Sbjct: 311 GMDVDKY 317


>gi|258591343|emb|CBE67642.1| DNA-directed RNA polymerase alpha chain [NC10 bacterium 'Dutch
           sediment']
          Length = 342

 Score =  270 bits (691), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 150/336 (44%), Positives = 213/336 (63%), Gaps = 24/336 (7%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQK ++ + KP  +E   L           AEP  RGF  T+GNALRR L+S++ GAA+
Sbjct: 1   MIQK-FKGIQKPKRLE-CELESLTSTYGKFFAEPFERGFGLTIGNALRRTLLSAIEGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAV+I G LHE S+I GV ED+TDIILN+KG+ L++  D  K + +     G V A  I 
Sbjct: 59  TAVRITGALHEFSTIPGVKEDVTDIILNLKGLRLRLHVDHPKTLYLKAFSEGEVRAEHIV 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           +  D+EVLNPD  I  L+ D  + +EL V  G GYVPA+ ++ E  P+ +I ID+++SPI
Sbjct: 119 SDPDVEVLNPDLRIATLEQDGKLELELEVRLGRGYVPAERNKREGQPVDVIAIDSIFSPI 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF------ 234
           +KV++ VE  R GQV DY+KL++ + TDGS+   D++A A++IL+D L +F NF      
Sbjct: 179 RKVNFRVEDTRVGQVTDYNKLTLEVWTDGSVLPRDAIAYAAKILKDHLSIFTNFEEEPEG 238

Query: 235 -----EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
                +E +K++ +++N           + V+ELELSVRS NCL+  +I Y+ +L+ R+E
Sbjct: 239 EGVVVDEARKQLLDNLN-----------RSVDELELSVRSANCLKHSDIRYIYELVVRSE 287

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           A+ML+  NFGRKSL EIK +L  MGL LGM L   P
Sbjct: 288 AEMLKTKNFGRKSLNEIKEILTGMGLTLGMKLEGLP 323


>gi|179184854|gb|ACB78162.1| RNA polymerase alpha subunit [Aliivibrio finisterrensis]
          Length = 306

 Score =  270 bits (691), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 140/291 (48%), Positives = 203/291 (69%), Gaps = 7/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 19  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 78

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +
Sbjct: 79  AVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNAEISMRIRVER 138

Query: 152 GHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVP  A+ H  E++ PIG + IDA YSP+ K+SY+VE+AR  Q  D DKL + ++T+
Sbjct: 139 GRGYVPSTARIHTEEDERPIGRLLIDATYSPVDKISYSVEAARVEQRTDLDKLVIDMETN 198

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 199 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 255

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM
Sbjct: 256 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGM 306


>gi|197288305|gb|ACH57435.1| RpoA [Aliivibrio finisterrensis]
          Length = 313

 Score =  270 bits (690), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 140/291 (48%), Positives = 203/291 (69%), Gaps = 7/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 25  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 84

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +
Sbjct: 85  AVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNAEISMRIRVER 144

Query: 152 GHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVP  A+ H  E++ PIG + IDA YSP+ K+SY+VE+AR  Q  D DKL + ++T+
Sbjct: 145 GRGYVPSTARIHTEEDERPIGRLLIDATYSPVDKISYSVEAARVEQRTDLDKLVIDMETN 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 205 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 261

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM
Sbjct: 262 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGM 312


>gi|118602238|ref|YP_903453.1| DNA-directed RNA polymerase subunit alpha [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
 gi|158512574|sp|A1AVM5|RPOA_RUTMC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|118567177|gb|ABL01982.1| DNA-directed RNA polymerase subunit alpha [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
          Length = 326

 Score =  270 bits (690), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 147/330 (44%), Positives = 212/330 (64%), Gaps = 15/330 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q + +  +KP  +E     Q   N   +I EPL RGF HTLGNALRR L+SS+ G+A+T
Sbjct: 1   MQGSARNFLKPKLVES---SQTGVNEFKVILEPLERGFGHTLGNALRRTLLSSMTGSAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V IDGV+HE S+I+GV ED+ DI+LN+K +++ ++     +V I K+GP  +T  DI+ 
Sbjct: 58  EVAIDGVMHEFSTIEGVQEDVLDILLNLKEVSVMLNTAETAQVVIEKKGPCEITVADIEA 117

Query: 122 VN-DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DI   NPD VI  ++ ++ +RM L +S G GY  A     E   IG + +DA +SPI
Sbjct: 118 NGIDITAFNPDKVIATINDESHMRMTLKISTGIGYDTATSRTDEASSIGGMQLDASFSPI 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VS+TV++AR  Q ++ DKL++TI+T+GS+  E ++  A+ ILQ+QL  F        E
Sbjct: 178 RRVSFTVDAARVKQKVNLDKLNITIETNGSVNAEVAIKRAAIILQEQLSSF-------VE 230

Query: 241 VKEDINVKSLP----FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++     ++LP    F+P LL  V+ELEL+VRS NCL+ E I Y+GDLIQ++E D+LR  
Sbjct: 231 LELVEEEEALPTSEDFDPQLLAAVDELELTVRSANCLKAEQIYYIGDLIQKSEQDLLRTP 290

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           N GRKSL EIK VL   GL L  ++ +WPP
Sbjct: 291 NLGRKSLNEIKEVLTEKGLNLATSIENWPP 320


>gi|32423696|gb|AAP81239.1| RNA polymerase alpha subunit [Candidatus Portiera aleyrodidarum]
          Length = 329

 Score =  270 bits (689), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 143/323 (44%), Positives = 207/323 (64%), Gaps = 7/323 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E ++P+ I    +     N  ++  EPL RGF HTLGNALRR+L+S + G A+   +I G
Sbjct: 6   EFVRPSKINVEAISN---NHAIISLEPLERGFGHTLGNALRRILLSYMPGCAVVEAEIKG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE S I G+ ED+ +IILNIK I +K+ G     + + K G GVV AGDI+   D+EV
Sbjct: 63  VQHEYSVIDGIKEDVIEIILNIKEIAIKLYGIDEIELELKKIGSGVVKAGDIKARQDVEV 122

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDHVI +L+    + M+L   +G GY PA      +   G I IDA +SP+K+V+Y V
Sbjct: 123 INPDHVIAHLNDHGELNMKLRFVRGRGYEPAYLRNKSDKNYGRIQIDAKFSPVKRVAYFV 182

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EPKKEVKEDI- 245
           ESAR  Q  D+DKL + ++T+G++  E+++  +++IL++QL  F++   E KK V+ ++ 
Sbjct: 183 ESARVEQKTDFDKLIIELETNGTLDPEEAIRTSAKILRNQLDFFVDLSCENKKHVENEVE 242

Query: 246 --NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                    + ALL  VE+LEL+VRS NCL+ ENI Y+GDL++RTE ++L+  N G+KSL
Sbjct: 243 HDRRTDTKIDKALLLPVEDLELTVRSANCLKAENIFYIGDLVKRTEGELLKTPNLGKKSL 302

Query: 304 VEIKGVLGTMGLFLGMNLPDWPP 326
            EIK VL   GL LGM++  WPP
Sbjct: 303 NEIKKVLKVRGLALGMHIDLWPP 325


>gi|319944770|ref|ZP_08019034.1| DNA-directed RNA polymerase subunit alpha [Lautropia mirabilis ATCC
           51599]
 gi|319742019|gb|EFV94442.1| DNA-directed RNA polymerase subunit alpha [Lautropia mirabilis ATCC
           51599]
          Length = 359

 Score =  270 bits (689), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 152/354 (42%), Positives = 216/354 (61%), Gaps = 34/354 (9%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           ++KP  +E   +      R +M  EP  RG+ HTLGNALRRVL+SS+ G A T VQI GV
Sbjct: 5   MLKPRLVEVQEISGPSHARVVM--EPFERGYGHTLGNALRRVLLSSMVGYAPTEVQIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S++ G+ ED+ D++LN+KG+  K+ G S   +T+ K  PG V A DI+  +D+E++
Sbjct: 63  VHEYSTVDGLREDVVDLLLNLKGVVFKLRGRSEVFLTLRKEVPGPVKASDIELPHDVEII 122

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAK-HHRTENDPIGLITIDALYSPIKKVSYTV 187
           NPDHVI  L     + M++ V +G GYVP    +  ++  IG I +DA +SP+++VSY V
Sbjct: 123 NPDHVIATLTEGGKLDMQIKVEQGRGYVPGNMRNLGDSKTIGRIVLDASFSPVRRVSYAV 182

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--EPKKEVKEDI 245
           ESAR  Q  D D+L + I+T+G+I  E++V  ++ IL DQL +F + E  +P   +    
Sbjct: 183 ESARVEQRTDLDRLLIDIETNGAIAPEEAVRKSAAILVDQLQVFASIEGNDPAVPIGGSQ 242

Query: 246 ---------NVKSLP--------------------FNPALLKKVEELELSVRSTNCLRGE 276
                    +V S+P                     +P LL+ V++LEL+VRS NCL+ E
Sbjct: 243 TPMGATIGGHVSSVPSGVEGLGAGGAAGFGASTGTIDPILLRPVDDLELTVRSANCLKAE 302

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           NI Y+GDLIQRTE ++L+  N GRKSL EIK VL + GL LGM L DWPP  +E
Sbjct: 303 NIYYIGDLIQRTENELLKTPNLGRKSLNEIKEVLASRGLTLGMRLDDWPPAGLE 356


>gi|294497011|ref|YP_003560711.1| DNA-directed RNA polymerase subunit alpha [Bacillus megaterium QM
           B1551]
 gi|295702376|ref|YP_003595451.1| DNA-directed RNA polymerase subunit alpha [Bacillus megaterium DSM
           319]
 gi|294346948|gb|ADE67277.1| DNA-directed RNA polymerase, alpha subunit [Bacillus megaterium QM
           B1551]
 gi|294800035|gb|ADF37101.1| DNA-directed RNA polymerase, alpha subunit [Bacillus megaterium DSM
           319]
          Length = 314

 Score =  270 bits (689), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 137/288 (47%), Positives = 196/288 (68%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QI+GVLHE S++ GV ED+T+IILN+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIEGVLHEFSTVPGVVEDVTNIILNV 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +GPG VTA DIQ  +DIEVLNPD  I  L+ DA  RM LT 
Sbjct: 83  KKLALKIYSDEEKTLEIDVKGPGTVTAADIQADSDIEVLNPDLHIATLESDAHFRMRLTA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GY PA  ++ E+ PIG++ ID++Y+P+ +VSY VE+ R GQ+ +YDKL++ + TDG
Sbjct: 143 RTGRGYNPADANKREDQPIGVLPIDSIYTPVTRVSYYVENTRVGQMTNYDKLTLDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  E +VAL ++IL + L +F+N  +  ++ +  +  +       L   +EEL+LSVRS
Sbjct: 203 SIEPEKAVALGAKILTEHLNIFVNLTDEAQKAEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGL 310


>gi|169632375|ref|YP_001706111.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter baumannii
           SDF]
 gi|169794619|ref|YP_001712412.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter baumannii
           AYE]
 gi|184159573|ref|YP_001847912.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter baumannii
           ACICU]
 gi|213158810|ref|YP_002320808.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter baumannii
           AB0057]
 gi|215482208|ref|YP_002324390.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter baumannii
           AB307-0294]
 gi|239503209|ref|ZP_04662519.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter baumannii
           AB900]
 gi|260557052|ref|ZP_05829269.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter baumannii
           ATCC 19606]
 gi|294839722|ref|ZP_06784405.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter sp.
           6013113]
 gi|294860400|ref|ZP_06798169.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter sp.
           6013150]
 gi|301345035|ref|ZP_07225776.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter baumannii
           AB056]
 gi|301512034|ref|ZP_07237271.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter baumannii
           AB058]
 gi|301595209|ref|ZP_07240217.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter baumannii
           AB059]
 gi|158513671|sp|A3M959|RPOA_ACIBT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|226699350|sp|B7GW27|RPOA_ACIB3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|226699351|sp|B7IA14|RPOA_ACIB5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238688116|sp|B0V6U7|RPOA_ACIBY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238688241|sp|B0VQU3|RPOA_ACIBS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238691002|sp|B2HZ83|RPOA_ACIBC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|169147546|emb|CAM85407.1| RNA polymerase, alpha subunit [Acinetobacter baumannii AYE]
 gi|169151167|emb|CAO99839.1| RNA polymerase, alpha subunit [Acinetobacter baumannii]
 gi|183211167|gb|ACC58565.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Acinetobacter baumannii ACICU]
 gi|193078462|gb|ABO13453.2| RNA polymerase alpha subunit [Acinetobacter baumannii ATCC 17978]
 gi|213057970|gb|ACJ42872.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter baumannii
           AB0057]
 gi|213988894|gb|ACJ59193.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter baumannii
           AB307-0294]
 gi|260409658|gb|EEX02959.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter baumannii
           ATCC 19606]
 gi|322509483|gb|ADX04937.1| RNA polymerase, alpha subunit [Acinetobacter baumannii 1656-2]
 gi|323519504|gb|ADX93885.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter baumannii
           TCDC-AB0715]
          Length = 335

 Score =  270 bits (689), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 137/302 (45%), Positives = 215/302 (71%), Gaps = 5/302 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +I EPL RGF HTLGNALRR+L+SSL GAA+  V+I+GV HE S+++G+ +D+ +++LN+
Sbjct: 26  VILEPLERGFGHTLGNALRRILLSSLPGAAVVEVEIEGVEHEYSTLEGLQQDIVELLLNL 85

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+++K+   +   +T+ K+GPG +TA D++  +++EV+NP+H+I  L     ++M L V
Sbjct: 86  KGLSIKLFDQNEAYLTLEKQGPGDITAADLRLPHNVEVVNPEHLIGTLSATGSLKMRLKV 145

Query: 150 SKGHGY--VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           S+G GY    ++    E  P+G + +DA YSPIK+VSYTVE+AR  Q  D DKL + ++T
Sbjct: 146 SQGRGYETSDSRFPEGETRPVGRLQLDASYSPIKRVSYTVENARVEQRTDLDKLVIDLET 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ ILQ Q+ +F++ ++ +  V ++   +    +P LL+ V++LEL+V
Sbjct: 206 NGTVDPEEAIRKAATILQQQIAIFVDLQKDQTPVAQEPREE---VDPILLRPVDDLELTV 262

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           RS NCL+ ENI Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP 
Sbjct: 263 RSANCLKAENIYYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASKGLQLGMRLENWPPA 322

Query: 328 SI 329
           S+
Sbjct: 323 SL 324


>gi|294842678|ref|ZP_06787361.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter sp.
           6014059]
          Length = 335

 Score =  270 bits (689), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 137/302 (45%), Positives = 215/302 (71%), Gaps = 5/302 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +I EPL RGF HTLGNALRR+L+SSL GAA+  V+I+GV HE S+++G+ +D+ +++LN+
Sbjct: 26  VILEPLERGFGHTLGNALRRILLSSLPGAAVVEVEIEGVEHEYSTLEGLQQDIVELLLNL 85

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+++K+   +   +T+ K+GPG +TA D++  +++EV+NP+H+I  L     ++M L V
Sbjct: 86  KGLSIKLFDQNEAYLTLEKQGPGDITAADLRLPHNVEVVNPEHLIGTLSATGSLKMRLKV 145

Query: 150 SKGHGY--VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           S+G GY    ++    E  P+G + +DA YSPIK+VSYTVE+AR  Q  D DKL + ++T
Sbjct: 146 SQGRGYETSDSRFPEGETRPVGRLQLDASYSPIKRVSYTVENARVEQRTDLDKLVIDLET 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ ILQ Q+ +F++ ++ +  V ++   +    +P LL+ V++LEL+V
Sbjct: 206 NGTVDPEEAIRKAATILQQQIAIFVDLQKDQTPVAQEPREE---VDPILLRPVDDLELTV 262

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           RS NCL+ ENI Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP 
Sbjct: 263 RSANCLKAENIYYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASKGLQLGMRLENWPPA 322

Query: 328 SI 329
           S+
Sbjct: 323 SL 324


>gi|164608420|gb|ABY62513.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio sp. ATCC
           33715]
 gi|164608422|gb|ABY62514.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. cann.1.1]
 gi|164608424|gb|ABY62515.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. cann.1.2]
 gi|164608426|gb|ABY62516.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. cann.1.3]
 gi|164608428|gb|ABY62517.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. cann.1.4]
 gi|164608430|gb|ABY62518.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. cann.2.1]
 gi|164608432|gb|ABY62519.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. cann.2.2]
 gi|164608434|gb|ABY62520.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. cann.2.3]
 gi|164608436|gb|ABY62521.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. cann.2.4]
 gi|164608438|gb|ABY62522.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. cann.2.5]
 gi|164608440|gb|ABY62523.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. cann.2.6]
          Length = 308

 Score =  269 bits (688), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 144/314 (45%), Positives = 211/314 (67%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q     TL   EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQVSQTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ 
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIA 117

Query: 129 NPDHVICNL-DVDAVVRMELTVSKGHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVS 184
           NP+HVIC+L D +A + M + V +G GYVP  A+ H  E++ PIG + IDA YSP+ K+S
Sbjct: 118 NPEHVICHLTDDNAEISMRIKVERGRGYVPSTARIHTEEDERPIGRLLIDATYSPVDKIS 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   +  
Sbjct: 178 YSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE-- 235

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 236 -KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|262280200|ref|ZP_06057984.1| RNA polymerase [Acinetobacter calcoaceticus RUH2202]
 gi|299768691|ref|YP_003730717.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter sp. DR1]
 gi|262257978|gb|EEY76712.1| RNA polymerase [Acinetobacter calcoaceticus RUH2202]
 gi|298698779|gb|ADI89344.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter sp. DR1]
          Length = 335

 Score =  269 bits (688), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 136/302 (45%), Positives = 215/302 (71%), Gaps = 5/302 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +I EPL RGF HTLGNALRR+L+SSL GAA+  V+I+GV HE S+++G+ +D+ +++LN+
Sbjct: 26  VILEPLERGFGHTLGNALRRILLSSLPGAAVVEVEIEGVEHEYSTLEGLQQDIVELLLNL 85

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+++K+   +   +T+ K+GPG +TA D++  +++EV+NP+H+I  L     ++M L V
Sbjct: 86  KGLSIKLFDQNEAYLTLEKQGPGEITAADLRLPHNVEVVNPEHLIGTLSASGSLKMRLKV 145

Query: 150 SKGHGY--VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           ++G GY    ++    E  P+G + +DA YSPIK+VSYTVE+AR  Q  D DKL + ++T
Sbjct: 146 AQGRGYETSDSRFPEGETRPVGRLQLDASYSPIKRVSYTVENARVEQRTDLDKLVIDLET 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ ILQ Q+ +F++ ++ +  V ++   +    +P LL+ V++LEL+V
Sbjct: 206 NGTVDPEEAIRKAATILQQQIAIFVDLQKDQTPVAQEPREE---VDPILLRPVDDLELTV 262

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           RS NCL+ ENI Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP 
Sbjct: 263 RSANCLKAENIYYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASKGLQLGMRLENWPPA 322

Query: 328 SI 329
           S+
Sbjct: 323 SL 324


>gi|190341379|gb|ACE74766.1| RpoA [Escherichia vulneris]
          Length = 308

 Score =  269 bits (688), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 138/290 (47%), Positives = 201/290 (69%), Gaps = 9/290 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + V +
Sbjct: 82  AVRVQGKDDVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQR 141

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPASARIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 202 GTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 257

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 258 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 307


>gi|164608442|gb|ABY62524.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. MdR7]
 gi|164608444|gb|ABY62525.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. SA5]
 gi|164608446|gb|ABY62526.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. SA6]
          Length = 308

 Score =  269 bits (688), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 144/314 (45%), Positives = 211/314 (67%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q     TL   EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQVSQTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ 
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIA 117

Query: 129 NPDHVICNL-DVDAVVRMELTVSKGHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVS 184
           NP+HVIC+L D +A + M + V +G GYVP  A+ H  E++ PIG + IDA YSP+ K+S
Sbjct: 118 NPEHVICHLTDGNAEISMRIKVERGRGYVPSTARIHTEEDERPIGRLLIDATYSPVDKIS 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   +  
Sbjct: 178 YSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE-- 235

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 236 -KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|164608414|gb|ABY62510.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio wodanis]
          Length = 308

 Score =  269 bits (687), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 144/314 (45%), Positives = 210/314 (66%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q     TL   EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQVSQTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ 
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIA 117

Query: 129 NPDHVICNL-DVDAVVRMELTVSKGHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVS 184
           NP+HVIC+L D +A + M + V +G GYVP  A+ H  E++ PIG + IDA YSP+ K+S
Sbjct: 118 NPEHVICHLTDDNAEISMRIKVERGRGYVPSTARIHSEEDERPIGRLLIDATYSPVDKIS 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   +  
Sbjct: 178 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE-- 235

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 236 -KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|164608416|gb|ABY62511.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio wodanis]
 gi|164608418|gb|ABY62512.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio wodanis]
          Length = 308

 Score =  269 bits (687), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 142/314 (45%), Positives = 208/314 (66%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q     TL   EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQVSQTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ 
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIA 117

Query: 129 NPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
           NP+HVIC+L D +A + M + V +G GYVP+    H+  +  PIG + IDA YSP+ K+S
Sbjct: 118 NPEHVICHLTDDNAEISMRIKVERGRGYVPSTARIHNEEDERPIGRLLIDATYSPVDKIS 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   +  
Sbjct: 178 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE-- 235

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 236 -KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|58416108|emb|CAH57468.1| RNA polymerase alpha-subunit [Aliivibrio wodanis]
 gi|58416110|emb|CAH57469.1| RNA polymerase alpha-subunit [Aliivibrio wodanis]
 gi|148536422|gb|ABQ85763.1| RNA polymerase alpha-subunit [Aliivibrio wodanis]
          Length = 308

 Score =  269 bits (687), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 144/314 (45%), Positives = 210/314 (66%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q     TL   EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQVSQTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ 
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIA 117

Query: 129 NPDHVICNL-DVDAVVRMELTVSKGHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVS 184
           NP+HVIC+L D +A + M + V +G GYVP  A+ H  E++ PIG + IDA YSP+ K+S
Sbjct: 118 NPEHVICHLTDDNAEISMRIKVERGRGYVPSTARIHTEEDERPIGRLLIDATYSPVDKIS 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   +  
Sbjct: 178 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE-- 235

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 236 -KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|239825720|ref|YP_002948344.1| DNA-directed RNA polymerase subunit alpha [Geobacillus sp. WCH70]
 gi|239806013|gb|ACS23078.1| DNA-directed RNA polymerase, alpha subunit [Geobacillus sp. WCH70]
          Length = 314

 Score =  269 bits (687), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 137/288 (47%), Positives = 196/288 (68%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDGVLHE S+I GV ED+T IILNI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDGVLHEFSTIDGVVEDVTAIILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +G GVVTA DI   +D+E+LNPD  I  L     +RM +T 
Sbjct: 83  KKLALKIYSDEEKTLEIDAQGEGVVTAADITHDSDVEILNPDLHIATLAEGGRLRMRMTA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYVPA+ ++ E+ PIG+I ID++Y+P+ +VSY VE+ R GQV DYDKL++ + TDG
Sbjct: 143 KRGRGYVPAEANKREDQPIGVIPIDSIYTPVSRVSYQVENTRVGQVTDYDKLTIDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  ++++AL ++IL + L +F++  +  +  +  +  +       L   +EEL+LSVRS
Sbjct: 203 SIGPKEAIALGAKILTEHLNIFVSLTDEAQNAEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L Q+TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELTQKTEEDMMKVRNLGRKSLEEVKAKLAELGLSL 310


>gi|293610849|ref|ZP_06693149.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292827193|gb|EFF85558.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|325123579|gb|ADY83102.1| RNA polymerase, alpha subunit [Acinetobacter calcoaceticus PHEA-2]
          Length = 335

 Score =  269 bits (687), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 136/302 (45%), Positives = 215/302 (71%), Gaps = 5/302 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +I EPL RGF HTLGNALRR+L+SSL GAA+  V+I+GV HE S+++G+ +D+ +++LN+
Sbjct: 26  VILEPLERGFGHTLGNALRRILLSSLPGAAVVEVEIEGVEHEYSTLEGLQQDIVELLLNL 85

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+++K+   +   +T+ K+GPG +TA D++  +++EV+NP+H+I  L     ++M L V
Sbjct: 86  KGLSIKLFDQNEAYLTLEKQGPGDITAADLRLPHNVEVVNPEHLIGTLSASGSLKMRLKV 145

Query: 150 SKGHGY--VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           ++G GY    ++    E  P+G + +DA YSPIK+VSYTVE+AR  Q  D DKL + ++T
Sbjct: 146 AQGRGYETSDSRFPEGETRPVGRLQLDASYSPIKRVSYTVENARVEQRTDLDKLVIDLET 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ ILQ Q+ +F++ ++ +  V ++   +    +P LL+ V++LEL+V
Sbjct: 206 NGTVDPEEAIRKAATILQQQIAIFVDLQKDQTPVAQEPREE---VDPILLRPVDDLELTV 262

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           RS NCL+ ENI Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP 
Sbjct: 263 RSANCLKAENIYYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASKGLQLGMRLENWPPA 322

Query: 328 SI 329
           S+
Sbjct: 323 SL 324


>gi|90193994|gb|ABD92558.1| RpoA [Gallibacterium anatis]
          Length = 300

 Score =  269 bits (687), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 137/288 (47%), Positives = 199/288 (69%), Gaps = 7/288 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 76

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+       +T+ K G G V A DI    D+E++NPDH+IC+L D +A + M + V +
Sbjct: 77  AVKVQNKDDVFLTLTKSGIGPVVAADITHDGDVEIVNPDHIICHLTDENASINMRIRVQR 136

Query: 152 GHGYVPAKHH-RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           G GYVPA      E  PIG + +DA YSP+ +++Y VE+AR  Q  D DKL + ++T+G+
Sbjct: 137 GRGYVPASSRTHDEERPIGRLLVDACYSPVDRIAYNVEAARVEQRTDLDKLVIEMETNGT 196

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+VRS
Sbjct: 197 LDPEEAIRRAATILAEQLDAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTVRS 252

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 253 ANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 300


>gi|90194026|gb|ABD92574.1| RpoA [Actinobacillus capsulatus]
          Length = 303

 Score =  268 bits (686), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 139/290 (47%), Positives = 202/290 (69%), Gaps = 9/290 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 76

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+S      +T+ K G G VTA DI    D+E++NP+HVIC+L D  A + M + V +
Sbjct: 77  AVKVSNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPNHVICHLTDKSASINMRIRVQR 136

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYV A    H + E+ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 137 GRGYVSASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLIIEMETN 196

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 197 GTIDPEEAIRRAATILAEQLDAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 252

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 253 RSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|90194000|gb|ABD92561.1| RpoA [Nicoletella semolina]
          Length = 302

 Score =  268 bits (686), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 138/290 (47%), Positives = 202/290 (69%), Gaps = 9/290 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 76

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+       +T+ K G G V A DI    D+E++NP+HVIC+L D +A + M + V +
Sbjct: 77  AVKVQNKDDVILTLTKSGIGPVIAADIVHDGDVEIVNPNHVICHLTDNNASINMRIRVRR 136

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H + +N PIG + +DA +SP+ ++SY VE+AR  Q  D DKL + ++T+
Sbjct: 137 GRGYVPASALVHTQDDNRPIGRLLVDARFSPVDRISYNVEAARVEQRTDLDKLVIEMETN 196

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G++  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 197 GTLDPEEAIRRAATILAEQLAAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 252

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 253 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 302


>gi|90194050|gb|ABD92586.1| RpoA [Haemophilus parasuis]
          Length = 302

 Score =  268 bits (686), Expect = 7e-70,   Method: Compositional matrix adjust.
 Identities = 136/287 (47%), Positives = 200/287 (69%), Gaps = 9/287 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 16  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 75

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+       +T+ K G G VTA DI    D+E++NPDHVICNL D +A + M + V +
Sbjct: 76  AVKVQNKDDIILTLTKSGIGPVTAADITHDGDVEIVNPDHVICNLTDKNASISMRIRVQR 135

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 136 GRGYVPASARVHTQDDDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLVIEMETN 195

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G++  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 196 GTLDPEEAIRRAATILAEQLAAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 251

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL  + 
Sbjct: 252 RSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLALVA 298


>gi|116515234|ref|YP_802863.1| DNA-directed RNA polymerase subunit alpha [Buchnera aphidicola str.
           Cc (Cinara cedri)]
 gi|122285370|sp|Q057C9|RPOA_BUCCC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116257088|gb|ABJ90770.1| RNA polymerase, a subunit [Buchnera aphidicola str. Cc (Cinara
           cedri)]
          Length = 329

 Score =  268 bits (686), Expect = 7e-70,   Method: Compositional matrix adjust.
 Identities = 144/334 (43%), Positives = 212/334 (63%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q   ++ +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGFVEDFLKPRLVDIQQISATHAKITL---EPLERGFGHTLGNALRRILLSSISGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDG+LHE    +GV ED+ DI+LN+KG+++K+ G     + + K G G V A DI  
Sbjct: 58  EVEIDGILHEYMHKEGVKEDILDILLNLKGLSIKLFGKDEVTLYLKKSGIGPVLAKDINH 117

Query: 122 VNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALY 177
            N  E++N  H+ICNL   DA + + + V++G GY+ AK  +   D    IG + +D  Y
Sbjct: 118 DNSTEIINNKHIICNLTCSDASIDIRMKVTRGRGYITAKSRKENYDNEHIIGKLFLDVTY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPI+++ YTVESAR  Q  D DKL + ++T+G+I  ED++  A+ IL  QL  F++    
Sbjct: 178 SPIERIMYTVESARVEQRTDLDKLIIEMETNGTIDPEDAIRKAATILAQQLEAFVDLRGV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++        +   F P LL+ V++LEL+VRS NCL+ E+I Y+GDL+Q+TE ++L+  N
Sbjct: 238 REPEI---KEEKPEFEPVLLRPVDDLELTVRSANCLKAESIHYIGDLVQKTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP+S+ E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMKLDNWPPKSLLE 328


>gi|255319790|ref|ZP_05360995.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter
           radioresistens SK82]
 gi|262380323|ref|ZP_06073477.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter
           radioresistens SH164]
 gi|255303109|gb|EET82321.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter
           radioresistens SK82]
 gi|262297769|gb|EEY85684.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter
           radioresistens SH164]
          Length = 335

 Score =  268 bits (686), Expect = 7e-70,   Method: Compositional matrix adjust.
 Identities = 135/302 (44%), Positives = 215/302 (71%), Gaps = 5/302 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +I EPL RGF HTLGNALRR+L+SSL GAA+  V+I+GV HE S+++G+ +D+ +++LN+
Sbjct: 26  VILEPLERGFGHTLGNALRRILLSSLPGAAVVEVEIEGVEHEYSTLEGLQQDIVELLLNL 85

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+++K+   +   +T+ K+GPG +TA D++  +++EV+NP+H+I  L     ++M L V
Sbjct: 86  KGLSIKLFDQNEAYLTLEKQGPGDITAADLRLPHNVEVVNPEHLIGTLSASGSIKMRLKV 145

Query: 150 SKGHGY--VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           ++G GY    ++    E  P+G + +DA YSPI++VSYTVE+AR  Q  D DKL + ++T
Sbjct: 146 AQGRGYETSDSRFPEGETRPVGRLQLDASYSPIQRVSYTVENARVEQRTDLDKLIIDLET 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ ILQ Q+ +F++ ++ +  V ++   +    +P LL+ V++LEL+V
Sbjct: 206 NGTVDPEEAIRKAATILQQQIAIFVDLQKDQAPVAQEPREE---VDPILLRPVDDLELTV 262

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           RS NCL+ ENI Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP 
Sbjct: 263 RSANCLKAENIYYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASKGLQLGMRLENWPPA 322

Query: 328 SI 329
           S+
Sbjct: 323 SL 324


>gi|58384667|gb|AAW72682.1| DNA-directed RNA polymerase alpha chain [Buchnera aphidicola
           (Cinara cedri)]
          Length = 329

 Score =  268 bits (686), Expect = 8e-70,   Method: Compositional matrix adjust.
 Identities = 144/334 (43%), Positives = 212/334 (63%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q   ++ +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGFVEDFLKPGLVDIQQISATHAKITL---EPLERGFGHTLGNALRRILLSSISGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDG+LHE    +GV ED+ DI+LN+KG+++K+ G     + + K G G V A DI  
Sbjct: 58  EVEIDGILHEYMHKEGVKEDILDILLNLKGLSIKLFGKDEVTLYLKKSGIGPVLAKDINH 117

Query: 122 VNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALY 177
            N  E++N  H+ICNL   DA + + + V++G GY+ AK  +   D    IG + +D  Y
Sbjct: 118 DNSTEIINNKHIICNLTCSDASIDIRMKVTRGRGYITAKSRKENYDNEHIIGKLFLDVTY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPI+++ YTVESAR  Q  D DKL + ++T+G+I  ED++  A+ IL  QL  F++    
Sbjct: 178 SPIERIMYTVESARVEQRTDLDKLIIEMETNGTIDPEDAIRKAATILAQQLEAFVDLRGV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++        +   F P LL+ V++LEL+VRS NCL+ E+I Y+GDL+Q+TE ++L+  N
Sbjct: 238 REPEI---KEEKPEFEPVLLRPVDDLELTVRSANCLKAESIHYIGDLVQKTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP+S+ E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMKLDNWPPKSLLE 328


>gi|295401893|ref|ZP_06811856.1| DNA-directed RNA polymerase, alpha subunit [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312109288|ref|YP_003987604.1| DNA-directed RNA polymerase, subunit alpha [Geobacillus sp.
           Y4.1MC1]
 gi|294976023|gb|EFG51638.1| DNA-directed RNA polymerase, alpha subunit [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311214389|gb|ADP72993.1| DNA-directed RNA polymerase, alpha subunit [Geobacillus sp.
           Y4.1MC1]
          Length = 314

 Score =  268 bits (685), Expect = 9e-70,   Method: Compositional matrix adjust.
 Identities = 136/288 (47%), Positives = 196/288 (68%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDGVLHE S+I GV ED+T IILNI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDGVLHEFSTIDGVVEDVTAIILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +G GVVTA DI   +D+E+LNPD  I  L     +RM +T 
Sbjct: 83  KKLALKIYSDEEKTLEIDAQGEGVVTAADITHDSDVEILNPDLHIATLAEGGRLRMRMTA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYVPA+ ++ E+ PIG+I ID++Y+P+ +V+Y VE+ R GQV DYDKL++ + TDG
Sbjct: 143 KRGRGYVPAEANKREDQPIGVIPIDSIYTPVSRVAYQVENTRVGQVTDYDKLTIDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  ++++AL ++IL + L +F++  +  +  +  +  +       L   +EEL+LSVRS
Sbjct: 203 SIGPKEAIALGAKILTEHLNIFVSLTDEAQNAEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L Q+TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELTQKTEEDMMKVRNLGRKSLEEVKAKLAELGLSL 310


>gi|58416068|emb|CAH57448.1| RNA polymerase alpha-subunit [Vibrio sp. R-23695]
          Length = 308

 Score =  268 bits (685), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 139/290 (47%), Positives = 202/290 (69%), Gaps = 7/290 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +
Sbjct: 82  AVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNAEISMRIKVER 141

Query: 152 GHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVP  A+ H  E++ PIG + IDA YSP+ K+SY+VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPSTARIHTEEDERPIGRLLIDATYSPVDKISYSVEAARVEQRTDLDKLVIDMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 202 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 258

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|148244354|ref|YP_001219048.1| DNA-directed RNA polymerase subunit alpha [Candidatus
           Vesicomyosocius okutanii HA]
 gi|158514275|sp|A5CXI9|RPOA_VESOH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|146326181|dbj|BAF61324.1| DNA-directed RNA polymerase alpha subunit [Candidatus
           Vesicomyosocius okutanii HA]
          Length = 326

 Score =  268 bits (684), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 147/326 (45%), Positives = 209/326 (64%), Gaps = 7/326 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q + ++ +KP  +E     Q   N   +I EPL RGF HTLGNA+RR L+SS+ G A+T
Sbjct: 1   MQGSARDFLKPKLVES---SQTGVNEFKVILEPLERGFGHTLGNAIRRTLLSSMTGFAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V IDGV+HE S+I GV ED+ DI+LN+K +++ ++     +V I K+GP  +T  DI+T
Sbjct: 58  EVVIDGVMHEFSTIDGVQEDVLDILLNLKEVSVVLNTVETAQVVIDKKGPCEITVADIET 117

Query: 122 VN-DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DI   NPD VI  ++ +  +RM L ++ G GY  A     E   IG + +DA +SPI
Sbjct: 118 NGIDITTFNPDKVIATINDEGHMRMTLKITAGIGYDAAASRTDEASSIGGMQLDASFSPI 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VS+TV++AR  Q ++ DKL++ I+T+GS+  E ++   + ILQ+QL    +F E +  
Sbjct: 178 KRVSFTVDAARVKQKVNLDKLNIMIETNGSVNAEVAIKRVATILQEQLS---SFVELELV 234

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E     S  F+P LL  V+ELEL+VRS NCL+ E I Y+GDLIQ++E D+LR  N GR
Sbjct: 235 EEEVSLPTSEDFDPQLLAAVDELELTVRSANCLKAEQIYYIGDLIQKSEQDLLRTPNLGR 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPP 326
           KSL EIK VL   GL LG N+ +WPP
Sbjct: 295 KSLNEIKEVLTEKGLSLGTNIENWPP 320


>gi|226953896|ref|ZP_03824360.1| RNA polymerase, alpha subunit [Acinetobacter sp. ATCC 27244]
 gi|294651609|ref|ZP_06728913.1| DNA-directed RNA polymerase [Acinetobacter haemolyticus ATCC 19194]
 gi|226835379|gb|EEH67762.1| RNA polymerase, alpha subunit [Acinetobacter sp. ATCC 27244]
 gi|292822458|gb|EFF81357.1| DNA-directed RNA polymerase [Acinetobacter haemolyticus ATCC 19194]
          Length = 335

 Score =  268 bits (684), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 137/302 (45%), Positives = 214/302 (70%), Gaps = 5/302 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +I EPL RGF HTLGNALRR+L+SSL GAA+  V+I+GV HE S+++G+ +D+ +++LN+
Sbjct: 26  VILEPLERGFGHTLGNALRRILLSSLPGAAVVEVEIEGVEHEYSTLEGLQQDIVELLLNL 85

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+++K+   +   +T+ K+G G VTA D++  +++EV+NPDH+I  L     ++M L V
Sbjct: 86  KGLSIKLFDQNEAYLTLEKQGAGDVTAADLRLPHNVEVVNPDHLIGTLSASGSLKMRLKV 145

Query: 150 SKGHGY--VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           ++G GY    ++    E  P+G + +DA YSPIK+VSYTVE+AR  Q  D DKL + ++T
Sbjct: 146 AQGRGYETSDSRFPEGETRPVGRLQLDASYSPIKRVSYTVENARVEQRTDLDKLVIDLET 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ ILQ Q+ +F++ ++ +  V ++   +    +P LL+ V++LEL+V
Sbjct: 206 NGTVDPEEAIRKAATILQQQIAIFVDLQKDQTPVAQEPREE---VDPILLRPVDDLELTV 262

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           RS NCL+ ENI Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP 
Sbjct: 263 RSANCLKAENIYYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASKGLQLGMRLENWPPA 322

Query: 328 SI 329
           S+
Sbjct: 323 SL 324


>gi|198282664|ref|YP_002218985.1| DNA-directed RNA polymerase subunit alpha [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218666577|ref|YP_002424857.1| DNA-directed RNA polymerase, alpha subunit [Acidithiobacillus
           ferrooxidans ATCC 23270]
 gi|198247185|gb|ACH82778.1| DNA-directed RNA polymerase, alpha subunit [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218518790|gb|ACK79376.1| DNA-directed RNA polymerase, alpha subunit [Acidithiobacillus
           ferrooxidans ATCC 23270]
          Length = 339

 Score =  268 bits (684), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 145/333 (43%), Positives = 213/333 (63%), Gaps = 7/333 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           EL++P  ++  V+      R  +   PL RGF HTLG+ LRRVL+SSL+GAA+T V+I+G
Sbjct: 6   ELLRPQGVDVEVISA---RRARLALGPLERGFGHTLGSGLRRVLLSSLKGAAVTEVEIEG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE SSI+GV ED+ DI+LN+K + ++  G     VT+ KRGPG +T  DI + + IEV
Sbjct: 63  VLHEYSSIEGVQEDVVDILLNLKMLAVRAHGRGDAVVTLRKRGPGQMTGADIVSEHGIEV 122

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP-IGLITIDALYSPIKKVSYT 186
            NP+ VI  L  D  + + L + +G GY  A   R  ++  IG++ +DA +SP+ +VSY 
Sbjct: 123 ANPEQVIATLTRDVELVLRLRIDEGRGYDAAATRRQSHEKRIGVMALDASFSPVLRVSYL 182

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+AR  Q  D D+L + ++T+G +    +V  A+RI + QLG+    E   +E+ E   
Sbjct: 183 VENARVEQRTDLDRLILDVETNGVVDPVWAVQEAARIFRSQLGVLAGAE--TREIPEASQ 240

Query: 247 VK-SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           V+ S    P L++ V++LEL+VRS NCL+ E+I Y+GDL+Q++E ++L+  N GRKSL E
Sbjct: 241 VQVSQSLTPLLIRPVDDLELTVRSANCLKAEDIFYIGDLVQKSEQELLKAPNLGRKSLNE 300

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           IK VL   GL LGM L  WPPE++  +  +  D
Sbjct: 301 IKEVLVAHGLTLGMRLDSWPPENLPPVPGRAAD 333


>gi|148793282|gb|ABR12705.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           kishitanii]
          Length = 308

 Score =  268 bits (684), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 137/293 (46%), Positives = 200/293 (68%), Gaps = 7/293 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +I EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+
Sbjct: 19  VILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNL 78

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELT 148
           KG+ +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + 
Sbjct: 79  KGLAVKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNAELSMRIK 138

Query: 149 VSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           V +G GYVPA    H   +  PIG + +DA YSP+ +++Y VE+AR  Q  D DKL + +
Sbjct: 139 VERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDRIAYAVEAARVEQRTDLDKLVIDM 198

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
           +T+G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL
Sbjct: 199 ETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLEL 255

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           +VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 256 TVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|319760354|ref|YP_004124292.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Blochmannia
           vafer str. BVAF]
 gi|318039068|gb|ADV33618.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Blochmannia
           vafer str. BVAF]
          Length = 334

 Score =  268 bits (684), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 155/342 (45%), Positives = 220/342 (64%), Gaps = 25/342 (7%)

Query: 2   IQKNWQELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           +Q   +E +KP   NIE I      E    +  EPL RGF HTLGNALRRVL+SS+ G A
Sbjct: 1   MQSPEKEFLKPRLINIEKI-----SEVHAKITLEPLERGFGHTLGNALRRVLLSSMPGCA 55

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T V+IDGVLHE    +G+ ED+ +I+LN+K + + + G     +++ K G G V A DI
Sbjct: 56  VTEVEIDGVLHEYGIKEGIREDVLEILLNLKTLAIAIEGKDSMILSLKKSGVGPVVASDI 115

Query: 120 QTVNDI-EVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPA--KHHRTEND-----PIGL 170
              + I +++NP HVIC +  D A++ M + V +G GYVPA  K +   ++     PIG 
Sbjct: 116 LYDSSIVKIVNPAHVICVITDDHAILSMRIKVQRGRGYVPAFSKFNSILDEQQTAIPIGR 175

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           + +DA YSP+++VSYTVE+AR  +  D DKL + ++T+G+I  E+++  A+ IL DQL  
Sbjct: 176 LVLDACYSPVERVSYTVEAARVEKRTDLDKLIIDMETNGTIDPEEAIRRAATILSDQLST 235

Query: 231 FI---NFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
           FI   N  +P  E+KED       F+PALL  V++LEL+VRS NCL+ E+I Y+GDL+Q+
Sbjct: 236 FIDLNNVYQP--EIKED----KPEFDPALLHLVDDLELTVRSANCLKAESIHYIGDLVQK 289

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           TE ++L+  N G+KSL EIK VL + GL LGM L  WPP+S 
Sbjct: 290 TEVELLKTPNLGKKSLTEIKDVLASRGLSLGMCLEKWPPKSF 331


>gi|42518455|ref|NP_964385.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus johnsonii
           NCC 533]
 gi|227888827|ref|ZP_04006632.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus johnsonii
           ATCC 33200]
 gi|61215995|sp|Q74L64|RPOA_LACJO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|41582740|gb|AAS08351.1| DNA-directed RNA polymerase alpha chain [Lactobacillus johnsonii
           NCC 533]
 gi|227850664|gb|EEJ60750.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus johnsonii
           ATCC 33200]
 gi|329666718|gb|AEB92666.1| DNA-directed RNA polymerase alpha chain [Lactobacillus johnsonii
           DPC 6026]
          Length = 312

 Score =  268 bits (684), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 146/316 (46%), Positives = 205/316 (64%), Gaps = 16/316 (5%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +EE     + EPL RGF  TLGN+LRRVL++S+ G A++ +QIDG
Sbjct: 3   EFEKPN----ITVVDQEEAYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTALSYIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILN+K + LK   D  K   I   GP +VTA D++  +DIEV
Sbjct: 59  VLHEFSTIPGVREDVTKIILNLKKLELKSLSDEEKIAEIDVTGPAIVTAADLKVDSDIEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC++     + M + +  G GYVPA  ++T++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICSIADGGHLHMNVAIKTGRGYVPASENKTDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN------FEEPKKEV 241
           ESAR G+  DYDKL++ I TDGSIT  D+++ A++IL +   +F++      F++   E 
Sbjct: 179 ESARVGKRDDYDKLTLEIWTDGSITPNDALSFAAKILVEHFKVFMSTDMDAQFDDVMVEK 238

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           ++D N K L         +EEL+LSVRS NCL+   I  + +L  ++EADM+R+ N GRK
Sbjct: 239 EDDKNEKKLEMT------IEELDLSVRSYNCLKRAGINTVQELTDKSEADMMRVRNLGRK 292

Query: 302 SLVEIKGVLGTMGLFL 317
           SL E+K  L  +GL L
Sbjct: 293 SLEEVKNKLADLGLSL 308


>gi|300362364|ref|ZP_07058540.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus gasseri
           JV-V03]
 gi|300353355|gb|EFJ69227.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus gasseri
           JV-V03]
          Length = 312

 Score =  267 bits (683), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 146/316 (46%), Positives = 205/316 (64%), Gaps = 16/316 (5%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +EE     + EPL RGF  TLGN+LRRVL++S+ G A++ +QIDG
Sbjct: 3   EFEKPN----ITVVDQEEAYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTALSYIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILN+K + LK   D  K   I   GP +VTA D++  +DIEV
Sbjct: 59  VLHEFSTIPGVREDVTKIILNLKKLELKSLSDEEKIAEIDVTGPAIVTAADLKVDSDIEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC++     + M + +  G GYVPA  ++T++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICSIADGGHLHMNVAIKNGRGYVPASENKTDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN------FEEPKKEV 241
           ESAR G+  DYDKL++ I TDGSIT  D+++ A++IL +   +F++      F++   E 
Sbjct: 179 ESARVGKRDDYDKLTLEIWTDGSITPNDALSFAAKILVEHFKVFMSTDMDAQFDDVMVEK 238

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           ++D N K L         +EEL+LSVRS NCL+   I  + +L  ++EADM+R+ N GRK
Sbjct: 239 EDDKNEKKLEMT------IEELDLSVRSYNCLKRAGINTVQELTDKSEADMMRVRNLGRK 292

Query: 302 SLVEIKGVLGTMGLFL 317
           SL E+K  L  +GL L
Sbjct: 293 SLEEVKNKLAELGLSL 308


>gi|179184384|gb|ACB78145.1| RNA polymerase alpha subunit [Aliivibrio finisterrensis]
 gi|179184823|gb|ACB78161.1| RNA polymerase alpha subunit [Aliivibrio finisterrensis]
          Length = 313

 Score =  267 bits (683), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 144/319 (45%), Positives = 212/319 (66%), Gaps = 10/319 (3%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T 
Sbjct: 1   QGSVTEFLKPRLVDIEQVSMTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVTE 57

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI   
Sbjct: 58  VEIEGVLHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVIITLNKSGAGPVVAGDITHD 117

Query: 123 NDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVP--AKHHRTEND-PIGLITIDALYS 178
            D+E+ NP+HVIC+L D +A + M + V +G GYVP  A+ H  E++ PIG + IDA YS
Sbjct: 118 GDVEIANPEHVICHLTDDNAEISMRIRVERGRGYVPSTARIHTEEDERPIGRLLIDATYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ K+SY+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +
Sbjct: 178 PVDKISYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVR 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 VPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFL 317
           G+KSL EIK VL + GL L
Sbjct: 295 GKKSLTEIKDVLASRGLSL 313


>gi|27904917|ref|NP_778043.1| DNA-directed RNA polymerase subunit alpha [Buchnera aphidicola str.
           Bp (Baizongia pistaciae)]
 gi|29427637|sp|P59455|RPOA_BUCBP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|27904315|gb|AAO27148.1| DNA-directed RNA polymerase alpha chain [Buchnera aphidicola str.
           Bp (Baizongia pistaciae)]
          Length = 331

 Score =  267 bits (683), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 135/303 (44%), Positives = 203/303 (66%), Gaps = 9/303 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDG+LHE S+ +GV ED+ +I+LN+KG+
Sbjct: 29  EPLERGFGHTLGNALRRILLSSMPGFAVTEVEIDGILHEYSTKEGVQEDIIEILLNLKGL 88

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV-DAVVRMELTVSK 151
            +++ G     +T+ K G GVVTA DI   ND+E++N DH+IC L   +A + M + V  
Sbjct: 89  AIRVYGKDQVYLTLVKTGIGVVTAADINHGNDVEIINLDHIICTLTCKNASISMRIKVQC 148

Query: 152 GHGYVPAKHHR-----TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           G GYVP           + + +G + +DA YSP++++ Y VE+AR  +  D DKL + ++
Sbjct: 149 GRGYVPVISRTNVISDNKENYVGKLLVDACYSPVERMIYKVEAARVEKRTDLDKLVIEME 208

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+G++  E+++  A+ IL +QL  F+   + ++   +    +   F+P LL+ V++LEL+
Sbjct: 209 TNGTLDPEEAIRRAATILSNQLESFVYLRDIREPEIK---EEKPEFDPILLRPVDDLELT 265

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           VRS NCL+ E I Y+GDL+Q+TE ++LR  N G+KSL EIK VL    L LGMNL +WPP
Sbjct: 266 VRSANCLKAEMIHYIGDLVQKTEVELLRTPNLGKKSLTEIKDVLAAKNLSLGMNLENWPP 325

Query: 327 ESI 329
           ++I
Sbjct: 326 DNI 328


>gi|58415830|emb|CAH57329.1| RNA polymerase alpha-subunit [Vibrio ezurae]
 gi|58415832|emb|CAH57330.1| RNA polymerase alpha-subunit [Vibrio ezurae]
 gi|58415834|emb|CAH57331.1| RNA polymerase alpha-subunit [Vibrio ezurae]
          Length = 309

 Score =  267 bits (683), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 139/291 (47%), Positives = 202/291 (69%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNADIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +  V+E I  K   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVR--VQEPIEEKP-EFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|58415862|emb|CAH57345.1| RNA polymerase alpha-subunit [Vibrio gazogenes]
          Length = 309

 Score =  267 bits (682), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 140/291 (48%), Positives = 204/291 (70%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L D +A V M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLNDDNAEVAMRIKVQ 141

Query: 151 KGHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVP  A+ H  E+D PIG + +DA YSP+ K++YTVE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTDEDDRPIGRLLVDATYSPVDKIAYTVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G+I  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTIEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|262373496|ref|ZP_06066774.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter junii
           SH205]
 gi|262311249|gb|EEY92335.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter junii
           SH205]
          Length = 335

 Score =  267 bits (682), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 137/302 (45%), Positives = 214/302 (70%), Gaps = 5/302 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +I EPL RGF HTLGNALRR+L+SSL GAA+  V+I+GV HE S+++G+ +D+ +++LN+
Sbjct: 26  VILEPLERGFGHTLGNALRRILLSSLPGAAVVEVEIEGVEHEYSTLEGLQQDIVELLLNL 85

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+++K+   +   +T+ K+G G VTA D++  +++EV+NPDH+I  L     ++M L V
Sbjct: 86  KGLSIKLFDQNEAYLTLEKQGAGDVTAADLRLPHNVEVVNPDHLIGTLSSSGSLKMRLKV 145

Query: 150 SKGHGY--VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           ++G GY    ++    E  P+G + +DA YSPIK+VSYTVE+AR  Q  D DKL + ++T
Sbjct: 146 AQGRGYETSDSRFPEGETRPVGRLQLDASYSPIKRVSYTVENARVEQRTDLDKLVIDLET 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ ILQ Q+ +F++ ++ +  V ++   +    +P LL+ V++LEL+V
Sbjct: 206 NGTVDPEEAIRKAATILQQQIAIFVDLQKDQTPVAQEPREE---VDPILLRPVDDLELTV 262

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           RS NCL+ ENI Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP 
Sbjct: 263 RSANCLKAENIYYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASKGLQLGMRLENWPPA 322

Query: 328 SI 329
           S+
Sbjct: 323 SL 324


>gi|116628988|ref|YP_814160.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus gasseri
           ATCC 33323]
 gi|238853457|ref|ZP_04643835.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus gasseri
           202-4]
 gi|282852675|ref|ZP_06262017.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus gasseri
           224-1]
 gi|311111214|ref|ZP_07712611.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus gasseri
           MV-22]
 gi|122274014|sp|Q046A0|RPOA_LACGA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116094570|gb|ABJ59722.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus gasseri
           ATCC 33323]
 gi|238833897|gb|EEQ26156.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus gasseri
           202-4]
 gi|282556417|gb|EFB62037.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus gasseri
           224-1]
 gi|311066368|gb|EFQ46708.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus gasseri
           MV-22]
          Length = 312

 Score =  267 bits (682), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 145/316 (45%), Positives = 205/316 (64%), Gaps = 16/316 (5%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +EE     + EPL RGF  TLGN+LRRVL++S+ G A++ +QIDG
Sbjct: 3   EFEKPN----ITVVDQEEAYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTALSYIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK   D  K   I   GP +VTA D++  +DIEV
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSLSDEEKIAEIDVTGPAIVTAADLKVDSDIEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC++     + M + +  G GYVPA  ++T++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICSIADGGHLHMNVAIKNGRGYVPASENKTDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN------FEEPKKEV 241
           ESAR G+  DYDKL++ I TDGSIT  D+++ A++IL +   +F++      F++   E 
Sbjct: 179 ESARVGKRDDYDKLTLEIWTDGSITPNDALSFAAKILVEHFKVFMSTDMDAQFDDVMVEK 238

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           ++D N K L         +EEL+LSVRS NCL+   I  + +L  ++EADM+R+ N GRK
Sbjct: 239 EDDKNEKKLEMT------IEELDLSVRSYNCLKRAGINTVQELTDKSEADMMRVRNLGRK 292

Query: 302 SLVEIKGVLGTMGLFL 317
           SL E+K  L  +GL L
Sbjct: 293 SLEEVKNKLAELGLSL 308


>gi|58415836|emb|CAH57332.1| RNA polymerase alpha-subunit [Aliivibrio fischeri]
 gi|58415838|emb|CAH57333.1| RNA polymerase alpha-subunit [Aliivibrio fischeri]
 gi|148536414|gb|ABQ85759.1| RNA polymerase alpha-subunit [Aliivibrio fischeri]
 gi|148536416|gb|ABQ85760.1| RNA polymerase alpha-subunit [Aliivibrio fischeri]
 gi|148536418|gb|ABQ85761.1| RNA polymerase alpha-subunit [Aliivibrio fischeri]
 gi|148793252|gb|ABR12690.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio fischeri]
 gi|164608402|gb|ABY62504.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio fischeri]
          Length = 308

 Score =  267 bits (682), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 138/290 (47%), Positives = 201/290 (69%), Gaps = 7/290 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +
Sbjct: 82  AVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNAEISMRIKVER 141

Query: 152 GHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVP  A+ H  E++ PIG + +DA YSP+ K+SY VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPSTARIHTEEDERPIGRLLVDATYSPVDKISYAVEAARVEQRTDLDKLVIDMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 202 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 258

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|58415916|emb|CAH57372.1| RNA polymerase alpha-subunit [Aliivibrio logei]
 gi|148536420|gb|ABQ85762.1| RNA polymerase alpha-subunit [Aliivibrio salmonicida]
 gi|164608404|gb|ABY62505.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio logei]
 gi|164608406|gb|ABY62506.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio logei]
 gi|164608408|gb|ABY62507.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio logei]
 gi|164608410|gb|ABY62508.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio salmonicida]
 gi|164608412|gb|ABY62509.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio salmonicida]
          Length = 308

 Score =  267 bits (682), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 138/290 (47%), Positives = 201/290 (69%), Gaps = 7/290 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +
Sbjct: 82  AVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNAEISMRIKVER 141

Query: 152 GHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVP  A+ H  E++ PIG + +DA YSP+ K+SY VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPSTARIHTEEDERPIGRLLVDATYSPVDKISYAVEAARVEQRTDLDKLVIDMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 202 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 258

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|58415866|emb|CAH57347.1| RNA polymerase alpha-subunit [Vibrio halioticoli]
 gi|58415868|emb|CAH57348.1| RNA polymerase alpha-subunit [Vibrio halioticoli]
 gi|58415870|emb|CAH57349.1| RNA polymerase alpha-subunit [Vibrio halioticoli]
 gi|58415950|emb|CAH57389.1| RNA polymerase alpha-subunit [Vibrio neonatus]
 gi|58415952|emb|CAH57390.1| RNA polymerase alpha-subunit [Vibrio neonatus]
 gi|58415954|emb|CAH57391.1| RNA polymerase alpha-subunit [Vibrio neonatus]
          Length = 309

 Score =  267 bits (682), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 139/291 (47%), Positives = 202/291 (69%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDDVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNADIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +  V+E I  K   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVR--VQEPIEEKP-EFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|90194058|gb|ABD92590.1| RpoA [Mannheimia granulomatis]
          Length = 303

 Score =  266 bits (681), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 135/282 (47%), Positives = 198/282 (70%), Gaps = 9/282 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGL 76

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+       +T+ K G G VTA DI    D+E++NPDHVICNL D +A + M + V +
Sbjct: 77  AVKVQNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPDHVICNLTDKNASINMRIRVQR 136

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 137 GRGYVPASARLHTQNDDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLDKLVIEMETN 196

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSV 267
           G++  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+V
Sbjct: 197 GTLDPEEAIRRAATILAEQLAAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTV 252

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK V
Sbjct: 253 RSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDV 294


>gi|212637981|ref|YP_002314501.1| DNA-directed RNA polymerase subunit alpha [Anoxybacillus
           flavithermus WK1]
 gi|212559461|gb|ACJ32516.1| DNA-directed RNA polymerase alpha subunit [Anoxybacillus
           flavithermus WK1]
          Length = 314

 Score =  266 bits (681), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 136/288 (47%), Positives = 195/288 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDGVLHE S+I GV ED+T IILNI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDGVLHEFSTIDGVVEDVTTIILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +G GVVTA DI   +D+E+LNPD  I  L  D  +RM +T 
Sbjct: 83  KKLALKIYSDEEKTLEIDVQGEGVVTAADITHDSDVEILNPDLQIATLAKDGRLRMRMTA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY PA  ++ E+ PIG+I ID++Y+P+ +VSY VE+ R GQ+ +YDKL++ + TDG
Sbjct: 143 KRGRGYTPADANKREDQPIGVIPIDSIYTPVSRVSYQVENTRVGQMTNYDKLTIDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  +++++L ++IL + L +F+N  +  +  +  I  +       L   +EEL+LSVRS
Sbjct: 203 SIGPKEAISLGAKILTEHLNIFVNLTDEAQHAEIMIEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L Q+TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELAQKTEEDMMKVRNLGRKSLEEVKAKLEELGLSL 310


>gi|319827250|gb|ADV74824.1| RNA polymerase subunit A [Vibrio neptunius]
 gi|319827252|gb|ADV74825.1| RNA polymerase subunit A [Vibrio coralliilyticus]
          Length = 305

 Score =  266 bits (680), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 137/294 (46%), Positives = 202/294 (68%), Gaps = 8/294 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 15  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 74

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 75  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 134

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 135 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMET 194

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 195 NGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 251

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L
Sbjct: 252 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRL 305


>gi|317050555|ref|YP_004111671.1| DNA-directed RNA polymerase subunit alpha [Desulfurispirillum
           indicum S5]
 gi|316945639|gb|ADU65115.1| DNA-directed RNA polymerase, alpha subunit [Desulfurispirillum
           indicum S5]
          Length = 354

 Score =  266 bits (680), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 149/319 (46%), Positives = 208/319 (65%), Gaps = 3/319 (0%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           NW E+I+P  +         ++    IAEPL RGF  TLGNALRRVL+SSL GAA+TA++
Sbjct: 4   NWNEVIRPRAL-VCDTKTATDSYGKFIAEPLERGFGITLGNALRRVLLSSLEGAAVTAIR 62

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           ID VLHE S++ GV ED+TDIILN+K +  K+     K +T+     G VTA  ++   D
Sbjct: 63  IDNVLHEFSTVSGVVEDVTDIILNVKQLRFKLLSPGEKVLTLKASSVGPVTAASLECPPD 122

Query: 125 IEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           ++VLN D VI  L   DA + MEL V  G  Y  A+ ++  +D I +I +D+L++P+ KV
Sbjct: 123 VKVLNSDCVIATLGREDAELNMELRVDIGRAYRLAEENKKADDVIDMIPVDSLFNPVVKV 182

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK- 242
           +YTVE AR  Q  ++DKL + + TDGS+  ED+VA A++I++DQL +FINFE+ ++ V  
Sbjct: 183 NYTVEQARVVQDTNFDKLILEVWTDGSVKPEDAVAFAAKIIKDQLAIFINFEDVEEPVAL 242

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           E +   S      L K VEELELSVRS NCL   +I  + DL+ R+E ++L+  NFG+KS
Sbjct: 243 ESVEDGSEELFALLSKSVEELELSVRSYNCLNNIDIRTIADLVARSENELLKTKNFGKKS 302

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           L+EIK +L  M L LGM+L
Sbjct: 303 LLEIKEILKEMNLTLGMDL 321


>gi|58415724|emb|CAH57276.1| RNA polymerase alpha-subunit [Photobacterium iliopiscarium]
 gi|58415732|emb|CAH57280.1| RNA polymerase alpha-subunit [Photobacterium phosphoreum]
 gi|148536424|gb|ABQ85764.1| RNA polymerase alpha-subunit [Photobacterium iliopiscarium]
 gi|148793266|gb|ABR12697.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           phosphoreum]
 gi|148793268|gb|ABR12698.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           phosphoreum]
 gi|148793270|gb|ABR12699.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           iliopiscarium]
 gi|148793276|gb|ABR12702.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           kishitanii]
 gi|148793278|gb|ABR12703.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           kishitanii]
          Length = 308

 Score =  266 bits (680), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 136/290 (46%), Positives = 198/290 (68%), Gaps = 7/290 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +
Sbjct: 82  AVKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNAELSMRIKVER 141

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPASARIHTEEDERPIGRLLVDATYSPVDRIAYAVEAARVEQRTDLDKLVIDMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 202 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 258

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|116624174|ref|YP_826330.1| DNA-directed RNA polymerase subunit alpha [Candidatus Solibacter
           usitatus Ellin6076]
 gi|122253110|sp|Q01WC0|RPOA_SOLUE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116227336|gb|ABJ86045.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Solibacter
           usitatus Ellin6076]
          Length = 347

 Score =  266 bits (680), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 144/319 (45%), Positives = 205/319 (64%), Gaps = 16/319 (5%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E   +  A+P  RGF  T+GN+LRRVL+SS+ GAAITAV+I+GV HE S I GV ED TD
Sbjct: 20  ERYGMFTAQPFQRGFGTTIGNSLRRVLLSSIEGAAITAVRIEGVEHEFSPIPGVVEDATD 79

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+K I  K+S D  K V +     G V +G I+T  D+EVL+ D  +  +     + 
Sbjct: 80  IILNLKQIPFKISSDGIKTVRLSVDSHGDVRSGQIETDADVEVLDRDVHVATVSEGGKLN 139

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +E+ +  G GYV A  +  E+  +G I ID+++SP++KV++ VE+AR GQ+ DYDKL++ 
Sbjct: 140 IEMRLKSGRGYVSADKNFDEDLALGYIPIDSVHSPVRKVNFAVEAARLGQMTDYDKLTLE 199

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           + T+G+++ +DS+  A+++L+D + +FINFEE  ++ +E         N  L + VEELE
Sbjct: 200 VWTNGAVSPQDSIGYAAKLLKDHMTIFINFEEVPEQTEEISERGMDKMNEVLNRSVEELE 259

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL--- 321
           LSVRS NCL+  NI  +G+L+Q+TEA+MLR  NFGRKSL EIK +L  MGL LGM +   
Sbjct: 260 LSVRSYNCLKNANIQSIGELVQKTEAEMLRTKNFGRKSLNEIKEILANMGLSLGMRIDQH 319

Query: 322 -------------PDWPPE 327
                        PD+ PE
Sbjct: 320 GRLVAPPPSAGGGPDFGPE 338


>gi|197288307|gb|ACH57436.1| RpoA [Vibrio gallaecicus]
          Length = 311

 Score =  266 bits (680), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 137/294 (46%), Positives = 201/294 (68%), Gaps = 8/294 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 21  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 80

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 81  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 140

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 141 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 200

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 201 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 257

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L
Sbjct: 258 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRL 311


>gi|268318877|ref|YP_003292533.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus johnsonii
           FI9785]
 gi|262397252|emb|CAX66266.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus johnsonii
           FI9785]
          Length = 312

 Score =  266 bits (680), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 145/316 (45%), Positives = 205/316 (64%), Gaps = 16/316 (5%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +EE     + EPL RGF  TLGN+LRRVL++S+ G A++ +QIDG
Sbjct: 3   EFEKPN----ITVVDQEEAYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTALSYIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK   D  K   I   GP +VTA D++  +DIEV
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSLSDEEKIAEIDVTGPAIVTAADLKVDSDIEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC++     + M + +  G GYVPA  ++T++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICSIADGGHLHMNVAIKTGRGYVPASENKTDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN------FEEPKKEV 241
           ESAR G+  DYDKL++ I TDGSIT  D+++ A++IL +   +F++      F++   E 
Sbjct: 179 ESARVGKRDDYDKLTLEIWTDGSITPNDALSFAAKILVEHFKVFMSTDMDAQFDDVMVEK 238

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           ++D N K L         +EEL+LSVRS NCL+   I  + +L  ++EADM+R+ N GRK
Sbjct: 239 EDDKNEKKLEMT------IEELDLSVRSYNCLKRAGINTVQELTDKSEADMMRVRNLGRK 292

Query: 302 SLVEIKGVLGTMGLFL 317
           SL E+K  L  +GL L
Sbjct: 293 SLEEVKNKLTDLGLSL 308


>gi|58415734|emb|CAH57281.1| RNA polymerase alpha-subunit [Salinivibrio costicola subsp.
           costicola]
          Length = 308

 Score =  266 bits (680), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 136/290 (46%), Positives = 200/290 (68%), Gaps = 7/290 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+ G     +T+ K G G V AGDI     +E+ NP+HVIC+L D +A + M + V +
Sbjct: 82  AVKVEGKDEVILTLTKSGAGPVVAGDITHDGGVEIANPEHVICHLTDANAEISMRIKVER 141

Query: 152 GHGYVPAKHH-RTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA     +E+D  PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPASARIDSEDDERPIGRLLVDATFSPVDRIAYNVEAARVEQRTDLDKLVIDMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 202 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 258

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GLFLG
Sbjct: 259 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLFLG 308


>gi|313673440|ref|YP_004051551.1| DNA-directed RNA polymerase subunit alpha [Calditerrivibrio
           nitroreducens DSM 19672]
 gi|312940196|gb|ADR19388.1| DNA-directed RNA polymerase subunit alpha [Calditerrivibrio
           nitroreducens DSM 19672]
          Length = 336

 Score =  266 bits (680), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 145/323 (44%), Positives = 211/323 (65%), Gaps = 4/323 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI  N++ LIKP  +E        +   + +AEPL RGF  T+GN+LRR+L+SS+ G A+
Sbjct: 1   MILMNFKSLIKPKKLE--TSPDNTDRFGVFVAEPLERGFGITIGNSLRRILLSSIEGTAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
             V+I+ V HE ++I GV ED+ +IILNIK + L ++    KRV I K+G GVV A DI 
Sbjct: 59  VGVKINDVTHEYTTIPGVLEDVVEIILNIKMLELNLNTHEQKRVYIKKKGEGVVKASDIF 118

Query: 121 TVNDIEVLNPD-HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
               ++VLNPD H+    D +A + +EL V +G GYVP++  + +   I +I +DA+++P
Sbjct: 119 GDPLVQVLNPDQHIATITDPNAELNIELYVERGIGYVPSEDMKGKFSDIHIIPVDAIFTP 178

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK- 238
           IK+ ++ VE+AR GQ  DYDKL + ++TDGSI  ED++  +++IL+D L +FINF+EP  
Sbjct: 179 IKRANFRVENARVGQSTDYDKLILEVETDGSIAPEDAIGFSAKILKDHLDLFINFDEPDY 238

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E  E   +++      L K +EELELSVR+ NCL+   I  + +L  +T+ DML+  NF
Sbjct: 239 SEEAEKNEIRNDQILELLDKSIEELELSVRAYNCLKNAEIKTLAELCSKTDNDMLKTKNF 298

Query: 299 GRKSLVEIKGVLGTMGLFLGMNL 321
           GRKSL EIK VL  +GL LGM+L
Sbjct: 299 GRKSLEEIKKVLSELGLSLGMDL 321


>gi|262377287|ref|ZP_06070511.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter lwoffii
           SH145]
 gi|262307740|gb|EEY88879.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter lwoffii
           SH145]
          Length = 335

 Score =  266 bits (679), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 136/302 (45%), Positives = 214/302 (70%), Gaps = 5/302 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +I EPL RGF HTLGNALRR+L+SSL GAA+  V+I+GV HE S+++G+ +D+ +++LN+
Sbjct: 26  VILEPLERGFGHTLGNALRRILLSSLPGAAVVEVEIEGVEHEYSTLEGLQQDIVELLLNL 85

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+++K+   +   +T+ K+G G VTA D++  +++EV+NP+H+I  L     ++M L V
Sbjct: 86  KGLSIKLFDQNEAYLTLEKQGAGDVTAADLRLPHNVEVVNPEHLIGTLSASGSLKMRLKV 145

Query: 150 SKGHGY--VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           ++G GY    ++    E  P+G + +DA YSPIK+VSYTVE+AR  Q  D DKL + ++T
Sbjct: 146 AQGRGYETSDSRFPEGETRPVGRLQLDASYSPIKRVSYTVENARVEQRTDLDKLIIDLET 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ ILQ Q+ +F++ ++ +  V ++   +    +P LL+ V++LEL+V
Sbjct: 206 NGTVDPEEAIRKAATILQQQIAIFVDLQKDQAPVAQEPREE---VDPILLRPVDDLELTV 262

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           RS NCL+ ENI Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP 
Sbjct: 263 RSANCLKAENIYYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASKGLQLGMRLENWPPA 322

Query: 328 SI 329
           S+
Sbjct: 323 SL 324


>gi|295315349|gb|ADF97760.1| RpoA [Vibrio sp. KTW-12]
          Length = 311

 Score =  266 bits (679), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 135/291 (46%), Positives = 199/291 (68%), Gaps = 7/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 23  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 82

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +
Sbjct: 83  AVKVEGKDEVILTLSKSGAGPVKAGDITHDGDVEIANPEHVICHLTDDNAEISMRIKVER 142

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 143 GRGYVPASARIHTDDDERPIGRLLVDATFSPVDRIAYAVEAARVEQRTDLDKLVIEMETN 202

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 203 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 259

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           S NCL+ E I Y+GDL+QRT+ ++L+  N G+KSL EIK VL + GL LGM
Sbjct: 260 SANCLKAEAIHYIGDLVQRTDVELLKTPNLGKKSLTEIKDVLASRGLSLGM 310


>gi|320108368|ref|YP_004183958.1| DNA-directed RNA polymerase subunit alpha [Terriglobus saanensis
           SP1PR4]
 gi|319926889|gb|ADV83964.1| DNA-directed RNA polymerase, alpha subunit [Terriglobus saanensis
           SP1PR4]
          Length = 366

 Score =  266 bits (679), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 143/317 (45%), Positives = 208/317 (65%), Gaps = 3/317 (0%)

Query: 6   WQELIKPNNIEYIVLGQE-EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           W+   KP  +   V G+   E      A+P  RGF  T+GN LRR L+SS+ GAA+TAV+
Sbjct: 3   WRGFQKPKRLA--VEGETLTEKYGKFSAQPFERGFGTTIGNGLRRTLLSSIEGAAVTAVR 60

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           ++GVLHE  SI GV ED TDIILN+K I  K++G+  K + +    PGVVT+G I+   D
Sbjct: 61  LEGVLHEFQSITGVVEDATDIILNLKQIPFKLNGEGPKALYLRVDQPGVVTSGMIEADGD 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           +E+L+ D  I  +     + ME+ + +G GYV A  +   +  IG I +D+++SP++KV+
Sbjct: 121 VEILDKDVYIATVSEGGKMDMEMRLKRGRGYVSADKNFDPDLGIGFIPVDSVHSPVRKVN 180

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           YTV++AR GQ+ DYDKL++ I T+G++   D++ L++++L+D + +FINFEE  +   + 
Sbjct: 181 YTVDAARLGQITDYDKLTIEIWTNGTVLPADALGLSAKLLKDHMTIFINFEEEMEAGLDG 240

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
            +      N  L + VEELELSVRS NCL+  NI  +G+LIQ+TEA+ML+  NFGRKSL 
Sbjct: 241 SHDGPAMRNDNLNRSVEELELSVRSYNCLKNANIATIGELIQKTEAEMLKTKNFGRKSLN 300

Query: 305 EIKGVLGTMGLFLGMNL 321
           EIK +L  MGL LGM +
Sbjct: 301 EIKEILAQMGLSLGMKI 317


>gi|138893810|ref|YP_001124263.1| DNA-directed RNA polymerase subunit alpha [Geobacillus
           thermodenitrificans NG80-2]
 gi|196250997|ref|ZP_03149679.1| DNA-directed RNA polymerase, alpha subunit [Geobacillus sp.
           G11MC16]
 gi|158513827|sp|A4IJL4|RPOA_GEOTN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|134265323|gb|ABO65518.1| DNA-directed RNA polymerase alpha chain [Geobacillus
           thermodenitrificans NG80-2]
 gi|196209469|gb|EDY04246.1| DNA-directed RNA polymerase, alpha subunit [Geobacillus sp.
           G11MC16]
          Length = 314

 Score =  266 bits (679), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 135/288 (46%), Positives = 196/288 (68%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDGVLHE S+I+GV ED+T IILN+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDGVLHEFSTIEGVVEDVTAIILNV 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +G GVVTA DI   +D+E+LNPD  I  L     +RM +T 
Sbjct: 83  KKLALKIYSDEEKTLEIDVQGEGVVTAADITHDSDVEILNPDLHIATLAEGGRLRMRMTA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYVPA+ ++ E+ PIG+I ID++Y+P+ +VSY VE+ R GQV DYDKL++ + TDG
Sbjct: 143 RRGRGYVPAEANKREDQPIGVIPIDSIYTPVSRVSYQVENTRVGQVTDYDKLTIDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  +++++L ++IL + L +F+   +  +  +  +  +       L   +EEL+LSVRS
Sbjct: 203 SIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEKEDDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L Q+TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELTQKTEEDMMKVRNLGRKSLEEVKAKLAELGLSL 310


>gi|56418668|ref|YP_145986.1| DNA-directed RNA polymerase subunit alpha [Geobacillus kaustophilus
           HTA426]
 gi|261417634|ref|YP_003251316.1| DNA-directed RNA polymerase subunit alpha [Geobacillus sp.
           Y412MC61]
 gi|297528509|ref|YP_003669784.1| DNA-directed RNA polymerase subunit alpha [Geobacillus sp. C56-T3]
 gi|319765292|ref|YP_004130793.1| DNA-directed RNA polymerase, subunit alpha [Geobacillus sp.
           Y412MC52]
 gi|61215780|sp|Q5L3R2|RPOA_GEOKA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|56378510|dbj|BAD74418.1| DNA-directed RNA polymerase alpha subunit [Geobacillus kaustophilus
           HTA426]
 gi|261374091|gb|ACX76834.1| DNA-directed RNA polymerase, alpha subunit [Geobacillus sp.
           Y412MC61]
 gi|297251761|gb|ADI25207.1| DNA-directed RNA polymerase, alpha subunit [Geobacillus sp. C56-T3]
 gi|317110158|gb|ADU92650.1| DNA-directed RNA polymerase, alpha subunit [Geobacillus sp.
           Y412MC52]
          Length = 314

 Score =  266 bits (679), Expect = 5e-69,   Method: Compositional matrix adjust.
 Identities = 136/288 (47%), Positives = 195/288 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDGVLHE S+I GV ED+T IILNI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDGVLHEFSTIDGVVEDVTAIILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +G GVVTA DI   +D+E+LNPD  I  L     +RM +T 
Sbjct: 83  KKLALKIYSDEEKTLEIDVQGEGVVTAADITHDSDVEILNPDLHIATLAEGGRLRMRMTA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYVPA+ ++ E+ PIG+I ID++Y+P+ +VSY VE+ R GQV DYDKL++ + TDG
Sbjct: 143 KRGRGYVPAEANKREDQPIGVIPIDSIYTPVSRVSYQVENTRVGQVTDYDKLTIDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  +++++L ++IL + L +F+   +  +  +  +  +       L   +EEL+LSVRS
Sbjct: 203 SIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEKEDDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L Q+TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELTQKTEEDMMKVRNLGRKSLEEVKAKLAELGLSL 310


>gi|58415706|emb|CAH57267.1| RNA polymerase alpha-subunit [Photobacterium angustum]
 gi|58415726|emb|CAH57277.1| RNA polymerase alpha-subunit [Photobacterium leiognathi subsp.
           leiognathi]
 gi|58415730|emb|CAH57279.1| RNA polymerase alpha-subunit [Photobacterium leiognathi subsp.
           leiognathi]
 gi|148793254|gb|ABR12691.1| DNA-directed RNA polymerase alpha subunit [Photobacterium angustum]
 gi|148793256|gb|ABR12692.1| DNA-directed RNA polymerase alpha subunit [Photobacterium angustum]
 gi|148793258|gb|ABR12693.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           leiognathi]
 gi|148793260|gb|ABR12694.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           leiognathi]
 gi|148793262|gb|ABR12695.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           leiognathi subsp. mandapamensis]
 gi|148793264|gb|ABR12696.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           leiognathi subsp. mandapamensis]
          Length = 308

 Score =  265 bits (678), Expect = 5e-69,   Method: Compositional matrix adjust.
 Identities = 135/290 (46%), Positives = 198/290 (68%), Gaps = 7/290 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC++ D +A + M + V +
Sbjct: 82  AVKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIANPEHVICHITDDNAELSMRIKVER 141

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPASARIHTEEDERPIGRLLVDATYSPVDRIAYAVEAARVEQRTDLDKLVIDMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 202 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 258

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|58415728|emb|CAH57278.1| RNA polymerase alpha-subunit [Photobacterium leiognathi subsp.
           leiognathi]
          Length = 292

 Score =  265 bits (678), Expect = 6e-69,   Method: Compositional matrix adjust.
 Identities = 135/290 (46%), Positives = 198/290 (68%), Gaps = 7/290 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 6   EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 65

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC++ D +A + M + V +
Sbjct: 66  AVKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIANPEHVICHITDDNAELSMRIKVER 125

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 126 GRGYVPASARIHTEEDERPIGRLLVDATYSPVDRIAYAVEAARVEQRTDLDKLVIDMETN 185

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 186 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 242

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 243 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 292


>gi|58415714|emb|CAH57271.1| RNA polymerase alpha-subunit [Photobacterium rosenbergii]
 gi|58415716|emb|CAH57272.1| RNA polymerase alpha-subunit [Photobacterium rosenbergii]
 gi|58415718|emb|CAH57273.1| RNA polymerase alpha-subunit [Photobacterium rosenbergii]
 gi|58415720|emb|CAH57274.1| RNA polymerase alpha-subunit [Photobacterium rosenbergii]
 gi|58415722|emb|CAH57275.1| RNA polymerase alpha-subunit [Photobacterium rosenbergii]
          Length = 308

 Score =  265 bits (677), Expect = 7e-69,   Method: Compositional matrix adjust.
 Identities = 135/290 (46%), Positives = 198/290 (68%), Gaps = 7/290 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +
Sbjct: 82  AVKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNADISMRIKVER 141

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPASARIHTEEDERPIGRLLVDATFSPVDRIAYAVEAARVEQRTDLDKLVIDMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 202 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 258

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|28377858|ref|NP_784750.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus plantarum
           WCFS1]
 gi|254556043|ref|YP_003062460.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus plantarum
           JDM1]
 gi|300767846|ref|ZP_07077756.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus plantarum
           subsp. plantarum ATCC 14917]
 gi|308180036|ref|YP_003924164.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus plantarum
           subsp. plantarum ST-III]
 gi|38258532|sp|Q88XW0|RPOA_LACPL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|28270691|emb|CAD63597.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus plantarum
           WCFS1]
 gi|254044970|gb|ACT61763.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus plantarum
           JDM1]
 gi|300494831|gb|EFK29989.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus plantarum
           subsp. plantarum ATCC 14917]
 gi|308045527|gb|ADN98070.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus plantarum
           subsp. plantarum ST-III]
          Length = 314

 Score =  265 bits (677), Expect = 7e-69,   Method: Compositional matrix adjust.
 Identities = 145/312 (46%), Positives = 204/312 (65%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN I  I    E +N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EFEKPN-IHKI---DENDNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EV
Sbjct: 59  VLHEFSTIEGVTEDVTAIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAK--HHRTENDPIGLITIDALYSPIKKVSY 185
           LNPD  IC +   A   M +T + G GYV A+   HR ++ PIG++ +D+LYSPI++V+Y
Sbjct: 119 LNPDLPICTVADGAHFHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R GQ  D+DKL++ + T+GSIT  ++++L+++IL D L +F+N  +  K     +
Sbjct: 179 QVENTRVGQRDDFDKLTLDVWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   +EEL+LSVRS NCL+   I  + +L  +TEADM+++ N GRKSL E
Sbjct: 239 EKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTNKTEADMMKVRNLGRKSLEE 298

Query: 306 IKGVLGTMGLFL 317
           +K  L  +GL L
Sbjct: 299 VKAKLADLGLSL 310


>gi|148793272|gb|ABR12700.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           kishitanii]
 gi|148793274|gb|ABR12701.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           kishitanii]
 gi|148793280|gb|ABR12704.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           kishitanii]
          Length = 308

 Score =  265 bits (676), Expect = 9e-69,   Method: Compositional matrix adjust.
 Identities = 135/290 (46%), Positives = 198/290 (68%), Gaps = 7/290 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +
Sbjct: 82  AVKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNAELSMRIKVER 141

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPASARIHTEEDERPIGRLLVDATFSPVDRIAYAVEAARVEQRTDLDKLVIDMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 202 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 258

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|326203867|ref|ZP_08193729.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           papyrosolvens DSM 2782]
 gi|325985965|gb|EGD46799.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           papyrosolvens DSM 2782]
          Length = 315

 Score =  265 bits (676), Expect = 9e-69,   Method: Compositional matrix adjust.
 Identities = 133/289 (46%), Positives = 195/289 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAA+ +++IDGVLHE S++ GV ED+T+IILNI
Sbjct: 23  FIVEPLERGYGITLGNSLRRILLSSLPGAAVNSIKIDGVLHEFSTVPGVVEDVTEIILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K ++L + G+  K + I   G G +TAGDI T  D+E+LNPD  I  L+ D    ME+ +
Sbjct: 83  KSLSLLIHGEGSKVIYIDANGEGPITAGDIITDQDVEILNPDLHIATLNGDHRFYMEMVI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           SKG GYV A  ++    PIG++ +D++Y+P+KKV+YTVE+ R GQ+ DYDKL++ + TDG
Sbjct: 143 SKGRGYVSADKNKQAGQPIGVVPVDSIYTPVKKVNYTVENTRVGQITDYDKLTLEVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  +++++L ++IL + L +F++  +  K  +  +  +       L   +EEL+LSVRS
Sbjct: 203 SINPDEAISLGAKILSEHLNLFVDLSDQAKHTEIMVEKEETKKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            NCL+   I  + DL  RTE DM+++ N GRKSL E+   L  +GLFL 
Sbjct: 263 YNCLKRAGINTVEDLTNRTEEDMMKVRNLGRKSLEEVLQKLQALGLFLA 311


>gi|58415708|emb|CAH57268.1| RNA polymerase alpha-subunit [Photobacterium damselae subsp.
           damselae]
 gi|58415710|emb|CAH57269.1| RNA polymerase alpha-subunit [Photobacterium damselae subsp.
           damselae]
 gi|58415712|emb|CAH57270.1| RNA polymerase alpha-subunit [Photobacterium damselae subsp.
           damselae]
          Length = 308

 Score =  265 bits (676), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 135/290 (46%), Positives = 198/290 (68%), Gaps = 7/290 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC++ D +A + M + V +
Sbjct: 82  AVKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIANPEHVICHITDDNAELSMRIKVER 141

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA +SP+ ++SY VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPASARIHTEEDERPIGRLLVDATFSPVDRISYAVEAARVEQRTDLDKLVIDMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 202 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 258

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|58415864|emb|CAH57346.1| RNA polymerase alpha-subunit [Vibrio halioticoli]
          Length = 309

 Score =  265 bits (676), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 138/291 (47%), Positives = 202/291 (69%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDDVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNADIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +  V+E I  K   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVR--VQEPIEEKP-EFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  + G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPSLGKKSLTEIKDVLASRGLSLG 309


>gi|304405589|ref|ZP_07387248.1| DNA-directed RNA polymerase, alpha subunit [Paenibacillus
           curdlanolyticus YK9]
 gi|304345628|gb|EFM11463.1| DNA-directed RNA polymerase, alpha subunit [Paenibacillus
           curdlanolyticus YK9]
          Length = 314

 Score =  265 bits (676), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 135/290 (46%), Positives = 200/290 (68%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDGVLHE S++ GV ED+T+IILN+
Sbjct: 23  FVIEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDGVLHEFSTVPGVIEDVTEIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG++LK+  D  K + I   G G VTAGDI+  +D+E+LNPD  I  L   A + M +  
Sbjct: 83  KGLSLKIHSDEEKVLEIDAEGEGNVTAGDIRADSDVEILNPDLHIATLASGARLHMRVFA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           ++G GYVPA  ++ E+ PIG+I +D++Y+PI +V+Y+VE+ R GQV +YDKL++ + TDG
Sbjct: 143 NRGRGYVPADRNKKEDQPIGVIPVDSIYTPITRVNYSVENTRVGQVTNYDKLTLEVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  E++V+L ++IL + L +F+   +  K+ +  +  +       L   +EEL+LSVRS
Sbjct: 203 SIRPEEAVSLGAKILTEHLDLFVGLTDEAKDAEIMVEKEEDKKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
            NCL+   I  + +LI +TE DM+++ N GRKSL E++  L  +GL L M
Sbjct: 263 YNCLKRAGINTVQELITKTEEDMMKVRNLGRKSLEEVQEKLEELGLGLRM 312


>gi|206890328|ref|YP_002249220.1| DNA-directed RNA polymerase, alpha subunit [Thermodesulfovibrio
           yellowstonii DSM 11347]
 gi|206742266|gb|ACI21323.1| DNA-directed RNA polymerase, alpha subunit [Thermodesulfovibrio
           yellowstonii DSM 11347]
          Length = 343

 Score =  265 bits (676), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 154/344 (44%), Positives = 217/344 (63%), Gaps = 22/344 (6%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           ++E   P  +E+    QE    T   ++ EPL RG+  TLGN+LRRVL+SSL G A+ A+
Sbjct: 4   YKEFQMPKKVEF---DQESLTDTYGKLVIEPLERGYGITLGNSLRRVLLSSLDGVAVYAI 60

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFK-RGPGVVTAGDIQT 121
           +I+  LHE SSIKGV ED+ DIILN+K +  K  + DS K++   K +GP  VTA  IQT
Sbjct: 61  RINDALHEFSSIKGVKEDILDIILNVKKLRFKYYAQDSDKKIATIKIKGPADVTAESIQT 120

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
               EVLN    IC+LD DA + M L + KG GYVP++  + +  P+  IT+DA++SP+K
Sbjct: 121 DGTYEVLNKSQYICSLDQDAQMEMVLYIRKGRGYVPSEAIKDDELPVDAITVDAIFSPVK 180

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK--- 238
           KV++ VE  R G++ DYD+L + I TDGSIT E +++ AS IL       I F+E +   
Sbjct: 181 KVNFRVEKTRVGELTDYDRLILEIWTDGSITPERAISDASSILIKHFEYLIFFKEAELQN 240

Query: 239 KEV-------KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           KE+       +ED+N   L  N  +LK +E+LELSVR+ NCL+   I  + +L+QRTE +
Sbjct: 241 KEIHETVPNPEEDLNFDLL--NENILKPIEDLELSVRAYNCLKSAGINTIAELVQRTEGE 298

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
           +++  NFGR+SL EIK VL  MGL LGM +    PE +E+  +K
Sbjct: 299 LMKTKNFGRRSLEEIKEVLTNMGLKLGMRI---NPELLEKFKEK 339


>gi|58415736|emb|CAH57282.1| RNA polymerase alpha-subunit [Vibrio aerogenes]
          Length = 293

 Score =  265 bits (676), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 135/291 (46%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 6   EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 65

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L D +A + M + V 
Sbjct: 66  AVRVAEGKDEVFITLHKSGSGPVVAGDITHDGDVEIVNPEHVICHLTDDNAEIAMRIKVE 125

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 126 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 185

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G+I  E+++  A+ +L +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 186 NGTIEPEEAIRRAATVLAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 242

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 243 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 293


>gi|179184358|gb|ACB78144.1| RNA polymerase alpha subunit [Vibrio gallaecicus]
          Length = 315

 Score =  264 bits (675), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 141/321 (43%), Positives = 210/321 (65%), Gaps = 11/321 (3%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T 
Sbjct: 1   QGSVTEFLKPRLVDIEQINTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVTE 57

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQT 121
           V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI  
Sbjct: 58  VEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLG 318
            G+KSL EIK VL + GL LG
Sbjct: 295 LGKKSLTEIKDVLASRGLSLG 315


>gi|220928236|ref|YP_002505145.1| DNA-directed RNA polymerase subunit alpha [Clostridium
           cellulolyticum H10]
 gi|254765248|sp|B8I808|RPOA_CLOCE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|219998564|gb|ACL75165.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           cellulolyticum H10]
          Length = 315

 Score =  264 bits (675), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 133/289 (46%), Positives = 195/289 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL G+A+ +++IDGVLHE S++ GV ED+T+IILNI
Sbjct: 23  FIVEPLERGYGITLGNSLRRILLSSLPGSAVNSIKIDGVLHEFSTVPGVVEDVTEIILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K ++L + G+  K + I   G G +TAGDI T  D+E+LNPD  I  L+ D    ME+ +
Sbjct: 83  KSLSLLVHGEGSKVIYIDANGEGPITAGDIITDQDVEILNPDLHIATLNGDHRFYMEMVI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           SKG GYV A  ++    PIG+I +D++Y+P+KKV+YTVE+ R GQ+ DYDKL++ + TDG
Sbjct: 143 SKGRGYVSADKNKQAGQPIGVIPVDSIYTPVKKVNYTVENTRVGQITDYDKLTLEVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  +++++L ++IL + L +F++  +  K  +  +  +       L   +EEL+LSVRS
Sbjct: 203 SINPDEAISLGAKILSEHLNLFVDLSDQAKHTEIMVEKEETKKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            NCL+   I  + DL  RTE DM+++ N GRKSL E+   L  +GLFL 
Sbjct: 263 YNCLKRAGINTVEDLTNRTEEDMMKVRNLGRKSLEEVLQKLQALGLFLA 311


>gi|179184639|gb|ACB78155.1| RNA polymerase alpha subunit [Vibrio comitans]
          Length = 304

 Score =  264 bits (675), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 136/291 (46%), Positives = 200/291 (68%), Gaps = 9/291 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 18  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 77

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 78  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNADIAMRIKVE 137

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 138 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMET 197

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   KE    +   F+P LL+ V++LEL+V
Sbjct: 198 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEKE----REPRFDPILLRPVDDLELTV 253

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + G  LG
Sbjct: 254 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGWSLG 304


>gi|58416032|emb|CAH57430.1| RNA polymerase alpha-subunit [Vibrio sp. R-21419]
          Length = 308

 Score =  264 bits (675), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 135/290 (46%), Positives = 197/290 (67%), Gaps = 7/290 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDVLEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +
Sbjct: 82  AVKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNADISMRIKVER 141

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + + T+
Sbjct: 142 GRGYVPASARIHTEEDERPIGRLLVDATFSPVDRIAYAVEAARVEQRTDLDKLVIDMQTN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 202 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 258

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|58415758|emb|CAH57293.1| RNA polymerase alpha-subunit [Vibrio campbellii]
          Length = 309

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 135/291 (46%), Positives = 201/291 (69%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
           +++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  SVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H+  +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHNEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|164608448|gb|ABY62527.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 309

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 134/291 (46%), Positives = 201/291 (69%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL +F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDVFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|58415996|emb|CAH57412.1| RNA polymerase alpha-subunit [Vibrio penaeicida]
          Length = 309

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 136/291 (46%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            +K++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVKVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++YTVE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDKIAYTVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  ++ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLDPEEAIRRSATILAEQLDAFVDLRDIRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|179184696|gb|ACB78157.1| RNA polymerase alpha subunit [Vibrio inusitatus]
          Length = 294

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 137/290 (47%), Positives = 201/290 (69%), Gaps = 8/290 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 8   EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 67

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 68  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDGNADIAMRIKVE 127

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 128 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMET 187

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +  V+E I  K   F+P LL+ V++LEL+V
Sbjct: 188 NGTLEPEEAIRRAATILAEQLDAFVDLRDVR--VQEPIEEKP-EFDPILLRPVDDLELTV 244

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + G  L
Sbjct: 245 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGXSL 294


>gi|179184326|gb|ACB78143.1| RNA polymerase alpha subunit [Vibrio breoganii]
          Length = 311

 Score =  263 bits (672), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 141/316 (44%), Positives = 209/316 (66%), Gaps = 11/316 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T V+I+G
Sbjct: 2   EFLKPRLVDIEQINTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           VLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI    D+E
Sbjct: 59  VLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVE 118

Query: 127 VLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKK 182
           + NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K
Sbjct: 119 IANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDK 178

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           ++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   K
Sbjct: 179 IAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEK 238

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KS
Sbjct: 239 ---EEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKS 295

Query: 303 LVEIKGVLGTMGLFLG 318
           L EIK VL + GL LG
Sbjct: 296 LTEIKDVLASRGLSLG 311


>gi|58415964|emb|CAH57396.1| RNA polymerase alpha-subunit [Vibrio nigripulchritudo]
          Length = 309

 Score =  263 bits (672), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 136/291 (46%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            +K++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVKVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++YTVE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDKIAYTVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  ++ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLDPEEAIRRSATILAEQLDAFVDLRDIRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|179184592|gb|ACB78153.1| RNA polymerase alpha subunit [Vibrio breoganii]
          Length = 314

 Score =  263 bits (672), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 141/316 (44%), Positives = 209/316 (66%), Gaps = 11/316 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T V+I+G
Sbjct: 5   EFLKPRLVDIEQINTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           VLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI    D+E
Sbjct: 62  VLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVE 121

Query: 127 VLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKK 182
           + NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K
Sbjct: 122 IANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDK 181

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           ++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   K
Sbjct: 182 IAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEK 241

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KS
Sbjct: 242 ---EEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKS 298

Query: 303 LVEIKGVLGTMGLFLG 318
           L EIK VL + GL LG
Sbjct: 299 LTEIKDVLASRGLSLG 314


>gi|58415740|emb|CAH57284.1| RNA polymerase alpha-subunit [Vibrio alginolyticus]
 gi|58415742|emb|CAH57285.1| RNA polymerase alpha-subunit [Vibrio alginolyticus]
 gi|58415746|emb|CAH57287.1| RNA polymerase alpha-subunit [Vibrio alginolyticus]
 gi|58415748|emb|CAH57288.1| RNA polymerase alpha-subunit [Vibrio alginolyticus]
 gi|58415760|emb|CAH57294.1| RNA polymerase alpha-subunit [Vibrio campbellii]
 gi|58415762|emb|CAH57295.1| RNA polymerase alpha-subunit [Vibrio campbellii]
 gi|58415764|emb|CAH57296.1| RNA polymerase alpha-subunit [Vibrio campbellii]
 gi|58415766|emb|CAH57297.1| RNA polymerase alpha-subunit [Vibrio campbellii]
 gi|58415768|emb|CAH57298.1| RNA polymerase alpha-subunit [Vibrio campbellii]
 gi|58415818|emb|CAH57323.1| RNA polymerase alpha-subunit [Vibrio diabolicus]
 gi|58415872|emb|CAH57350.1| RNA polymerase alpha-subunit [Vibrio harveyi]
 gi|58415874|emb|CAH57351.1| RNA polymerase alpha-subunit [Vibrio harveyi]
 gi|58415876|emb|CAH57352.1| RNA polymerase alpha-subunit [Vibrio harveyi]
 gi|58415878|emb|CAH57353.1| RNA polymerase alpha-subunit [Vibrio harveyi]
 gi|58415880|emb|CAH57354.1| RNA polymerase alpha-subunit [Vibrio communis]
 gi|58415882|emb|CAH57355.1| RNA polymerase alpha-subunit [Vibrio harveyi]
 gi|58415884|emb|CAH57356.1| RNA polymerase alpha-subunit [Vibrio harveyi]
 gi|58415886|emb|CAH57357.1| RNA polymerase alpha-subunit [Vibrio harveyi]
 gi|58415888|emb|CAH57358.1| RNA polymerase alpha-subunit [Vibrio harveyi]
 gi|58415890|emb|CAH57359.1| RNA polymerase alpha-subunit [Vibrio harveyi]
 gi|58415982|emb|CAH57405.1| RNA polymerase alpha-subunit [Vibrio parahaemolyticus]
 gi|58415984|emb|CAH57406.1| RNA polymerase alpha-subunit [Vibrio parahaemolyticus]
 gi|58416024|emb|CAH57426.1| RNA polymerase alpha-subunit [Vibrio sp. R-21410]
 gi|58416026|emb|CAH57427.1| RNA polymerase alpha-subunit [Vibrio sp. R-21413]
 gi|58416036|emb|CAH57432.1| RNA polymerase alpha-subunit [Vibrio sp. R-21426]
 gi|58416038|emb|CAH57433.1| RNA polymerase alpha-subunit [Vibrio sp. R-21427]
 gi|58416066|emb|CAH57447.1| RNA polymerase alpha-subunit [Vibrio sp. R-23694]
          Length = 309

 Score =  263 bits (672), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 135/291 (46%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H+  +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHNEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|58415776|emb|CAH57302.1| RNA polymerase alpha-subunit [Vibrio cholerae]
 gi|58415778|emb|CAH57303.1| RNA polymerase alpha-subunit [Vibrio cholerae]
 gi|58415780|emb|CAH57304.1| RNA polymerase alpha-subunit [Vibrio cholerae]
 gi|58415782|emb|CAH57305.1| RNA polymerase alpha-subunit [Vibrio cholerae]
 gi|58415784|emb|CAH57306.1| RNA polymerase alpha-subunit [Vibrio cholerae]
 gi|58415786|emb|CAH57307.1| RNA polymerase alpha-subunit [Vibrio cholerae]
 gi|58415788|emb|CAH57308.1| RNA polymerase alpha-subunit [Vibrio cholerae]
 gi|58415790|emb|CAH57309.1| RNA polymerase alpha-subunit [Vibrio cholerae]
 gi|58415792|emb|CAH57310.1| RNA polymerase alpha-subunit [Vibrio cholerae]
 gi|58415936|emb|CAH57382.1| RNA polymerase alpha-subunit [Vibrio mimicus]
 gi|58415938|emb|CAH57383.1| RNA polymerase alpha-subunit [Vibrio mimicus]
 gi|58415940|emb|CAH57384.1| RNA polymerase alpha-subunit [Vibrio mimicus]
 gi|58415942|emb|CAH57385.1| RNA polymerase alpha-subunit [Vibrio mimicus]
          Length = 309

 Score =  263 bits (672), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 134/291 (46%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|58415744|emb|CAH57286.1| RNA polymerase alpha-subunit [Vibrio alginolyticus]
          Length = 309

 Score =  263 bits (672), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 134/291 (46%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +++LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEVLLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H+  +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHNEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASCGLSLG 309


>gi|58415690|emb|CAH57259.1| RNA polymerase alpha-subunit [Enterovibrio coralii]
 gi|58415692|emb|CAH57260.1| RNA polymerase alpha-subunit [Enterovibrio norvegicus]
 gi|58415694|emb|CAH57261.1| RNA polymerase alpha-subunit [Enterovibrio norvegicus]
 gi|58415696|emb|CAH57262.1| RNA polymerase alpha-subunit [Enterovibrio norvegicus]
 gi|58415698|emb|CAH57263.1| RNA polymerase alpha-subunit [Enterovibrio norvegicus]
 gi|58415700|emb|CAH57264.1| RNA polymerase alpha-subunit [Grimontia hollisae]
 gi|58415702|emb|CAH57265.1| RNA polymerase alpha-subunit [Grimontia hollisae]
 gi|58415704|emb|CAH57266.1| RNA polymerase alpha-subunit [Grimontia hollisae]
          Length = 308

 Score =  263 bits (671), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 134/290 (46%), Positives = 197/290 (67%), Gaps = 7/290 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+ G     +T+ K G G V AGDI     +E+ NP+HVIC+L D +A + M + V +
Sbjct: 82  AVKVEGKDEVILTLNKSGAGPVVAGDITHDGGVEIANPEHVICHLTDSNAEISMRIKVER 141

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+
Sbjct: 142 GRGYVPASARIHTEEDERPIGRLLVDATFSPVDRIAYNVEAARVEQRTDLDKLVIDMETN 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 202 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 258

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 308


>gi|58415860|emb|CAH57344.1| RNA polymerase alpha-subunit [Vibrio gallicus]
 gi|58416084|emb|CAH57456.1| RNA polymerase alpha-subunit [Vibrio superstes]
 gi|179184721|gb|ACB78158.1| RNA polymerase alpha subunit [Vibrio superstes]
 gi|179184755|gb|ACB78159.1| RNA polymerase alpha subunit [Vibrio gallicus]
          Length = 309

 Score =  263 bits (671), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 136/291 (46%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   K     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEK---EEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|179184612|gb|ACB78154.1| RNA polymerase alpha subunit [Vibrio breoganii]
          Length = 314

 Score =  263 bits (671), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 141/320 (44%), Positives = 210/320 (65%), Gaps = 11/320 (3%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T 
Sbjct: 1   QGSVTEFLKPRLVDIEQINTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVTE 57

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQT 121
           V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI  
Sbjct: 58  VEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +   K     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPEK---EEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFL 317
            G+KSL EIK VL + GL L
Sbjct: 295 LGKKSLTEIKDVLASRGLSL 314


>gi|58416002|emb|CAH57415.1| RNA polymerase alpha-subunit [Vibrio proteolyticus]
 gi|58416004|emb|CAH57416.1| RNA polymerase alpha-subunit [Vibrio proteolyticus]
          Length = 309

 Score =  263 bits (671), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 135/291 (46%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|58415754|emb|CAH57291.1| RNA polymerase alpha-subunit [Vibrio brasiliensis]
 gi|58415756|emb|CAH57292.1| RNA polymerase alpha-subunit [Vibrio brasiliensis LMG 20546]
 gi|58415798|emb|CAH57313.1| RNA polymerase alpha-subunit [Vibrio coralliilyticus]
 gi|58415800|emb|CAH57314.1| RNA polymerase alpha-subunit [Vibrio coralliilyticus]
 gi|58415802|emb|CAH57315.1| RNA polymerase alpha-subunit [Vibrio coralliilyticus]
 gi|58415804|emb|CAH57316.1| RNA polymerase alpha-subunit [Vibrio coralliilyticus ATCC BAA-450]
 gi|58415806|emb|CAH57317.1| RNA polymerase alpha-subunit [Vibrio coralliilyticus]
 gi|58415808|emb|CAH57318.1| RNA polymerase alpha-subunit [Vibrio coralliilyticus]
 gi|58415810|emb|CAH57319.1| RNA polymerase alpha-subunit [Vibrio coralliilyticus]
 gi|58415892|emb|CAH57360.1| RNA polymerase alpha-subunit [Vibrio hepatarius]
 gi|58415956|emb|CAH57392.1| RNA polymerase alpha-subunit [Vibrio neptunius]
 gi|58415958|emb|CAH57393.1| RNA polymerase alpha-subunit [Vibrio neptunius]
 gi|58415960|emb|CAH57394.1| RNA polymerase alpha-subunit [Vibrio neptunius]
 gi|58415974|emb|CAH57401.1| RNA polymerase alpha-subunit [Vibrio orientalis]
 gi|58416052|emb|CAH57440.1| RNA polymerase alpha-subunit [Vibrio sp. R-23286]
 gi|58416070|emb|CAH57449.1| RNA polymerase alpha-subunit [Vibrio sp. R-23696]
 gi|58416098|emb|CAH57463.1| RNA polymerase alpha-subunit [Vibrio tubiashii]
 gi|58416100|emb|CAH57464.1| RNA polymerase alpha-subunit [Vibrio tubiashii]
 gi|58416102|emb|CAH57465.1| RNA polymerase alpha-subunit [Vibrio tubiashii]
 gi|58416112|emb|CAH57470.1| RNA polymerase alpha-subunit [Vibrio xuii]
 gi|58416114|emb|CAH57471.1| RNA polymerase alpha-subunit [Vibrio xuii]
 gi|58416116|emb|CAH57472.1| RNA polymerase alpha-subunit [Vibrio xuii]
          Length = 309

 Score =  263 bits (671), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 135/291 (46%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|189308771|gb|ACD87087.1| RpoA [Vibrio sp. PP-200]
          Length = 302

 Score =  263 bits (671), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 135/291 (46%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 15  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 74

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 75  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEITNPEHVICHLTDGNAEIAMRIKVE 134

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 135 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMET 194

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 195 NGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 251

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 252 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 302


>gi|58416062|emb|CAH57445.1| RNA polymerase alpha-subunit [Vibrio sp. R-23692]
          Length = 309

 Score =  262 bits (670), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 134/291 (46%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +++LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEVLLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H+  +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHNEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|58415986|emb|CAH57407.1| RNA polymerase alpha-subunit [Vibrio pectenicida]
 gi|58415988|emb|CAH57408.1| RNA polymerase alpha-subunit [Vibrio pectenicida]
 gi|58415990|emb|CAH57409.1| RNA polymerase alpha-subunit [Vibrio pectenicida]
          Length = 309

 Score =  262 bits (670), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 135/291 (46%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEITNPEHVICHLTDGNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|300244653|gb|ADJ93835.1| RNA polymerase alpha subunit [Vibrio sp. G21]
          Length = 309

 Score =  262 bits (670), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 134/291 (46%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVYITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ +L +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATVLAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|58415918|emb|CAH57373.1| RNA polymerase alpha-subunit [Vibrio mediterranei]
 gi|58415920|emb|CAH57374.1| RNA polymerase alpha-subunit [Vibrio mediterranei]
 gi|58415922|emb|CAH57375.1| RNA polymerase alpha-subunit [Vibrio mediterranei]
 gi|58415924|emb|CAH57376.1| RNA polymerase alpha-subunit [Vibrio mediterranei]
 gi|58415926|emb|CAH57377.1| RNA polymerase alpha-subunit [Vibrio mediterranei]
 gi|58415928|emb|CAH57378.1| RNA polymerase alpha-subunit [Vibrio mediterranei]
 gi|58416020|emb|CAH57424.1| RNA polymerase alpha-subunit [Vibrio shilonii AK1]
 gi|58416072|emb|CAH57450.1| RNA polymerase alpha-subunit [Vibrio sp. R-23697]
          Length = 309

 Score =  262 bits (670), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 135/291 (46%), Positives = 199/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEISMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|58415770|emb|CAH57299.1| RNA polymerase alpha-subunit [Vibrio chagasii]
 gi|58415772|emb|CAH57300.1| RNA polymerase alpha-subunit [Vibrio chagasii]
 gi|58415774|emb|CAH57301.1| RNA polymerase alpha-subunit [Vibrio chagasii]
 gi|58415812|emb|CAH57320.1| RNA polymerase alpha-subunit [Vibrio cyclitrophicus]
 gi|58415814|emb|CAH57321.1| RNA polymerase alpha-subunit [Vibrio cyclitrophicus]
 gi|58415816|emb|CAH57322.1| RNA polymerase alpha-subunit [Vibrio cyclitrophicus]
 gi|58415846|emb|CAH57337.1| RNA polymerase alpha-subunit [Vibrio fortis]
 gi|58415848|emb|CAH57338.1| RNA polymerase alpha-subunit [Vibrio fortis]
 gi|58415850|emb|CAH57339.1| RNA polymerase alpha-subunit [Vibrio fortis]
 gi|58415904|emb|CAH57366.1| RNA polymerase alpha-subunit [Vibrio kanaloae]
 gi|58415906|emb|CAH57367.1| RNA polymerase alpha-subunit [Vibrio kanaloae]
 gi|58415908|emb|CAH57368.1| RNA polymerase alpha-subunit [Vibrio lentus]
 gi|58415910|emb|CAH57369.1| RNA polymerase alpha-subunit [Vibrio lentus]
 gi|58415912|emb|CAH57370.1| RNA polymerase alpha-subunit [Vibrio lentus]
 gi|58415914|emb|CAH57371.1| RNA polymerase alpha-subunit [Vibrio lentus]
 gi|58415992|emb|CAH57410.1| RNA polymerase alpha-subunit [Listonella pelagia]
 gi|58415994|emb|CAH57411.1| RNA polymerase alpha-subunit [Listonella pelagia]
 gi|58415998|emb|CAH57413.1| RNA polymerase alpha-subunit [Vibrio pomeroyi]
 gi|58416000|emb|CAH57414.1| RNA polymerase alpha-subunit [Vibrio pomeroyi]
 gi|58416022|emb|CAH57425.1| RNA polymerase alpha-subunit [Vibrio sp. R-21409]
 gi|58416040|emb|CAH57434.1| RNA polymerase alpha-subunit [Vibrio sp. R-21431]
 gi|58416054|emb|CAH57441.1| RNA polymerase alpha-subunit [Vibrio sp. R-23685]
 gi|58416056|emb|CAH57442.1| RNA polymerase alpha-subunit [Vibrio sp. R-23689]
 gi|58416058|emb|CAH57443.1| RNA polymerase alpha-subunit [Vibrio sp. R-23690]
 gi|58416060|emb|CAH57444.1| RNA polymerase alpha-subunit [Vibrio sp. R-23691]
 gi|58416064|emb|CAH57446.1| RNA polymerase alpha-subunit [Vibrio sp. R-23693]
 gi|58416074|emb|CAH57451.1| RNA polymerase alpha-subunit [Vibrio splendidus]
 gi|58416076|emb|CAH57452.1| RNA polymerase alpha-subunit [Vibrio splendidus]
 gi|58416078|emb|CAH57453.1| RNA polymerase alpha-subunit [Vibrio splendidus]
 gi|58416080|emb|CAH57454.1| RNA polymerase alpha-subunit [Vibrio splendidus]
 gi|58416082|emb|CAH57455.1| RNA polymerase alpha-subunit [Vibrio splendidus]
 gi|58416092|emb|CAH57460.1| RNA polymerase alpha-subunit [Vibrio tasmaniensis]
 gi|58416094|emb|CAH57461.1| RNA polymerase alpha-subunit [Vibrio tasmaniensis]
 gi|58416096|emb|CAH57462.1| RNA polymerase alpha-subunit [Vibrio tasmaniensis]
 gi|179184408|gb|ACB78146.1| RNA polymerase alpha subunit [Vibrio sp. CECT 7226]
 gi|179184453|gb|ACB78148.1| RNA polymerase alpha subunit [Vibrio sp. CECT 7224]
 gi|179184476|gb|ACB78149.1| RNA polymerase alpha subunit [Vibrio sp. CECT 7225]
          Length = 309

 Score =  262 bits (670), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 135/291 (46%), Positives = 199/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|179184509|gb|ACB78150.1| RNA polymerase alpha subunit [Vibrio sp. RD 9.17]
          Length = 303

 Score =  262 bits (670), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 135/291 (46%), Positives = 199/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 16  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 75

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 76  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 135

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 136 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 195

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 196 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 252

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 253 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 303


>gi|58416028|emb|CAH57428.1| RNA polymerase alpha-subunit [Vibrio sp. R-21415]
          Length = 309

 Score =  262 bits (670), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 135/291 (46%), Positives = 199/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEISMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|322381101|ref|ZP_08055104.1| DNA-directed RNA polymerase subunit alpha-like protein
           [Paenibacillus larvae subsp. larvae B-3650]
 gi|321154677|gb|EFX46948.1| DNA-directed RNA polymerase subunit alpha-like protein
           [Paenibacillus larvae subsp. larvae B-3650]
          Length = 314

 Score =  262 bits (670), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 134/288 (46%), Positives = 198/288 (68%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDGVLHE S+I GV ED+T+IILN+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDGVLHEFSTIPGVIEDVTEIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG++LK+  D  K + I   G G V AGDI+  +D+E+LNPD  I  L  DA + M +  
Sbjct: 83  KGLSLKIHSDEEKILEIDVEGEGRVVAGDIRADSDVEILNPDLHIATLSSDARLHMRIHA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYV A  +++E+ PIG+I +D++Y+PI +V+Y+VE+ R GQV +YDKL++ + TDG
Sbjct: 143 GRGRGYVQADKNKSEDQPIGVIPVDSIYTPITRVNYSVENTRVGQVTNYDKLTLEVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  E++V+L ++IL + L +F+   +  K+ +  +  +       L   +EEL+LSVRS
Sbjct: 203 SIRPEEAVSLGAKILTEHLMLFVGLTDEAKDAEIMVEKEEDKKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +LI +TE DM+++ N GRKSL E++  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELITKTEEDMMKVRNLGRKSLEEVQEKLEELGLGL 310


>gi|58416006|emb|CAH57417.1| RNA polymerase alpha-subunit [Vibrio rotiferianus]
 gi|58416008|emb|CAH57418.1| RNA polymerase alpha-subunit [Vibrio rotiferianus]
 gi|58416030|emb|CAH57429.1| RNA polymerase alpha-subunit [Vibrio sp. R-21416]
 gi|58416034|emb|CAH57431.1| RNA polymerase alpha-subunit [Vibrio sp. R-21422]
 gi|58416104|emb|CAH57466.1| RNA polymerase alpha-subunit [Vibrio vulnificus]
 gi|58416106|emb|CAH57467.1| RNA polymerase alpha-subunit [Vibrio vulnificus]
          Length = 309

 Score =  262 bits (670), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 135/291 (46%), Positives = 199/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|179184786|gb|ACB78160.1| RNA polymerase alpha subunit [Vibrio gallaecicus]
          Length = 306

 Score =  262 bits (670), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 135/291 (46%), Positives = 199/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 19  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 78

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 79  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 138

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 139 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 198

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 199 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 255

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 256 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 306


>gi|58415750|emb|CAH57289.1| RNA polymerase alpha-subunit [Listonella anguillarum]
 gi|58415752|emb|CAH57290.1| RNA polymerase alpha-subunit [Listonella anguillarum]
 gi|58415966|emb|CAH57397.1| RNA polymerase alpha-subunit [Vibrio ordalii]
 gi|58415968|emb|CAH57398.1| RNA polymerase alpha-subunit [Vibrio ordalii]
 gi|58415970|emb|CAH57399.1| RNA polymerase alpha-subunit [Vibrio ordalii]
 gi|58415972|emb|CAH57400.1| RNA polymerase alpha-subunit [Vibrio ordalii]
          Length = 309

 Score =  262 bits (670), Expect = 5e-68,   Method: Compositional matrix adjust.
 Identities = 134/291 (46%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +G+ ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGIQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEITNPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|179184539|gb|ACB78151.1| RNA polymerase alpha subunit [Vibrio gigantis]
          Length = 314

 Score =  262 bits (669), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 140/320 (43%), Positives = 209/320 (65%), Gaps = 11/320 (3%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T 
Sbjct: 1   QGSVTEFLKPRLVDIEQINTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVTE 57

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQT 121
           V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI  
Sbjct: 58  VEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFL 317
            G+KSL EIK VL + GL L
Sbjct: 295 LGKKSLTEIKDVLASRGLSL 314


>gi|58415962|emb|CAH57395.1| RNA polymerase alpha-subunit [Vibrio nereis]
          Length = 309

 Score =  262 bits (669), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 134/291 (46%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +++LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEVLLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|179184569|gb|ACB78152.1| RNA polymerase alpha subunit [Vibrio crassostreae]
          Length = 315

 Score =  262 bits (669), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 140/321 (43%), Positives = 209/321 (65%), Gaps = 11/321 (3%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T 
Sbjct: 1   QGSVTEFLKPRLVDXEQINTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVTE 57

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQT 121
           V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI  
Sbjct: 58  VEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+  ++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDXIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLG 318
            G+KSL EIK VL + GL LG
Sbjct: 295 LGKKSLTEIKDVLASRGLSLG 315


>gi|303240944|ref|ZP_07327455.1| DNA-directed RNA polymerase, alpha subunit [Acetivibrio
           cellulolyticus CD2]
 gi|302591530|gb|EFL61267.1| DNA-directed RNA polymerase, alpha subunit [Acetivibrio
           cellulolyticus CD2]
          Length = 315

 Score =  262 bits (669), Expect = 7e-68,   Method: Compositional matrix adjust.
 Identities = 134/300 (44%), Positives = 198/300 (66%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
           V+  E+      + EPL RG+  TLGN+LRR+L+SSL G A+T+++IDGVLHE S++ GV
Sbjct: 12  VISSEDNTYGKFVVEPLERGYGITLGNSLRRILLSSLPGIAVTSIKIDGVLHEFSTVPGV 71

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+IILN+KG+ L + GD  K V I   G G VTA DI+   D+E+LNP+H I  L 
Sbjct: 72  VEDVTEIILNVKGLALNLHGDGPKVVYIDADGEGEVTAADIKADADVEILNPEHKIATLS 131

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  + MEL++ KG GYV A+ ++    PIG+I +D++Y+P+ KV+YTVE+ R GQV DY
Sbjct: 132 GDHKLYMELSLDKGRGYVSAEKNKHPGQPIGVIPVDSIYTPVSKVNYTVENTRVGQVTDY 191

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL++ + T+GSI  +++++L ++I+ + L +FI+  +  K  +  +  +       L  
Sbjct: 192 DKLTLEVWTNGSIKPDEAISLGAKIMSEHLNLFIDLSDNAKNAEIMVEKEETKKEKVLEM 251

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +EEL+LSVRS NCL+   I  + DL  RTE DM+++ N GRKSL E+   L  +GL L 
Sbjct: 252 TIEELDLSVRSYNCLKRAGINTVEDLTNRTEEDMMKVRNLGRKSLEEVFNKLKALGLALA 311


>gi|269213694|ref|ZP_05982639.2| DNA-directed RNA polymerase, alpha subunit [Neisseria cinerea ATCC
           14685]
 gi|269145516|gb|EEZ71934.1| DNA-directed RNA polymerase, alpha subunit [Neisseria cinerea ATCC
           14685]
          Length = 278

 Score =  261 bits (668), Expect = 7e-68,   Method: Compositional matrix adjust.
 Identities = 139/281 (49%), Positives = 190/281 (67%), Gaps = 8/281 (2%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           + G A T V I GVLHE S++ GV ED+ DI+LN+KGI  K+ G S  ++T+ K G GVV
Sbjct: 1   MNGFAPTEVAITGVLHEYSTLDGVQEDVVDILLNVKGIVFKLHGRSQVQLTLKKSGSGVV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLI 171
           +AGDI+  +D+E+LNPDH+IC+L  +  + ME+ V +G GY         R EN  IG I
Sbjct: 61  SAGDIELPHDVEILNPDHIICHLADNGQIEMEIKVEQGRGYQSVSGRQVVRDENRQIGSI 120

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA +SPI +VS+ VE AR  Q  D DKL + I+TDGSI  E++V  A+RIL DQ+ +F
Sbjct: 121 QLDASFSPISRVSFEVEPARVEQRTDLDKLVLDIETDGSIDPEEAVRSAARILIDQMSIF 180

Query: 232 INFE-EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
            + +  P +EV+E    K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE 
Sbjct: 181 ADLQGTPVEEVEE----KAPPIDPVLLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTET 236

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           ++L+  N GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 237 ELLKTPNLGRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 277


>gi|58415946|emb|CAH57387.1| RNA polymerase alpha-subunit [Vibrio natriegens]
          Length = 309

 Score =  261 bits (668), Expect = 8e-68,   Method: Compositional matrix adjust.
 Identities = 134/291 (46%), Positives = 199/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GY+PA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYIPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|58416086|emb|CAH57457.1| RNA polymerase alpha-subunit [Vibrio tapetis]
 gi|58416088|emb|CAH57458.1| RNA polymerase alpha-subunit [Vibrio tapetis]
 gi|58416090|emb|CAH57459.1| RNA polymerase alpha-subunit [Vibrio tapetis]
          Length = 309

 Score =  261 bits (668), Expect = 8e-68,   Method: Compositional matrix adjust.
 Identities = 135/291 (46%), Positives = 199/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            +K++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVKVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  ++ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLDPEEAIRRSATILAEQLDAFVDLRDIRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|58415738|emb|CAH57283.1| RNA polymerase alpha-subunit [Vibrio aestuarianus]
          Length = 309

 Score =  261 bits (667), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 134/291 (46%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEITNPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+V++AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVDAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|58415898|emb|CAH57363.1| RNA polymerase alpha-subunit [Vibrio ichthyoenteri]
 gi|58415900|emb|CAH57364.1| RNA polymerase alpha-subunit [Vibrio ichthyoenteri]
 gi|58415902|emb|CAH57365.1| RNA polymerase alpha-subunit [Vibrio ichthyoenteri]
 gi|58416014|emb|CAH57421.1| RNA polymerase alpha-subunit [Vibrio scophthalmi LMG 19158]
 gi|58416016|emb|CAH57422.1| RNA polymerase alpha-subunit [Vibrio scophthalmi]
 gi|58416018|emb|CAH57423.1| RNA polymerase alpha-subunit [Vibrio scophthalmi]
          Length = 309

 Score =  261 bits (667), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 134/291 (46%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEITNPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+V++AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVDAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|15612725|ref|NP_241028.1| DNA-directed RNA polymerase subunit alpha [Bacillus halodurans
           C-125]
 gi|6094120|sp|O50634|RPOA_BACHD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|2760185|dbj|BAA24194.1| RNA polymerase alpha subunit [Bacillus halodurans]
 gi|4512431|dbj|BAA75298.1| rpoA homologue (identity of 85% to B. subtilis ) [Bacillus
           halodurans]
 gi|10172774|dbj|BAB03881.1| DNA-directed RNA polymerase alpha subunit [Bacillus halodurans
           C-125]
          Length = 314

 Score =  261 bits (667), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 133/288 (46%), Positives = 198/288 (68%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDGVLHE S+I+GV ED+T I+LN+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDGVLHEFSTIEGVVEDVTTIVLNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +G GVVTAGD+   +D++VLNPD  I  L   A +RM +T 
Sbjct: 83  KQLALKIYSDEDKTLEIDTQGEGVVTAGDLTHDSDVDVLNPDLHIATLTTGAHLRMRITA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYVPA+ ++++   IG+I ID++Y+P+ +V+Y VE+ R GQV +YDKL++ + TDG
Sbjct: 143 KRGRGYVPAEGNKSDELAIGVIPIDSIYTPVSRVNYQVENTRVGQVTNYDKLTLDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  E++V+L ++IL + L +F+   +  +  +  +  +       L   +EEL+LSVRS
Sbjct: 203 SIRPEEAVSLGAKILTEHLNIFVGLTDQAQNAEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L Q+TE DM+++ N GRKSL E++  LG +GL L
Sbjct: 263 YNCLKRAGINTVQELTQKTEEDMMKVRNLGRKSLEEVQEKLGELGLGL 310


>gi|58415896|emb|CAH57362.1| RNA polymerase alpha-subunit [Vibrio ichthyoenteri ATCC 700023]
          Length = 297

 Score =  261 bits (667), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 134/291 (46%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 10  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 69

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 70  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEITNPEHVICHLTDDNAEIAMRIKVE 129

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+V++AR  Q  D DKL + ++T
Sbjct: 130 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVDAARVEQRTDLDKLVIDMET 189

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 190 NGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 246

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 247 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 297


>gi|125743179|gb|ABN54790.1| RpoA [Vibrio sp. RLUH-CZ]
          Length = 307

 Score =  261 bits (667), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 134/291 (46%), Positives = 199/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T  +I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 20  EPLERGFGHTLGNALRRILLSSMPGCAVTEXEIEGVLHEYSTKEGVQEDILEILLNLKGL 79

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 80  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 139

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 140 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMET 199

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 200 NGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 256

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 257 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 307


>gi|58415948|emb|CAH57388.1| RNA polymerase alpha-subunit [Vibrio navarrensis]
          Length = 309

 Score =  261 bits (666), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 134/291 (46%), Positives = 199/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYAVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|296840731|ref|ZP_06863331.2| DNA-directed RNA polymerase, alpha subunit [Neisseria polysaccharea
           ATCC 43768]
 gi|296840100|gb|EFH24038.1| DNA-directed RNA polymerase, alpha subunit [Neisseria polysaccharea
           ATCC 43768]
          Length = 278

 Score =  261 bits (666), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 140/281 (49%), Positives = 188/281 (66%), Gaps = 8/281 (2%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           + G A T V I GVLHE S++ GV ED+ DI+LNIKGI  K+ G S  ++ + K G GVV
Sbjct: 1   MNGFAPTEVAIAGVLHEYSTVDGVQEDVVDILLNIKGIVFKLHGRSQVQLVLKKSGSGVV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLI 171
           +AGDI+  +D+E+LNP HVIC+L  +  + ME+ V +G GY         R EN  IG I
Sbjct: 61  SAGDIELPHDVEILNPGHVICHLADNGQIEMEIKVEQGRGYQSVSGRQVVRDENRQIGAI 120

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA +SPI +VS+ VE AR  Q  D DKL + I+TDGSI  E++V  A+RIL DQ+ +F
Sbjct: 121 QLDASFSPISRVSFEVEPARVEQRTDLDKLVLDIETDGSIDPEEAVRSAARILIDQMSIF 180

Query: 232 INFE-EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
            N +  P +EV+E    K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE 
Sbjct: 181 ANLQGTPVEEVEE----KAPPIDPVLLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTET 236

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           ++L+  N GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 237 ELLKTPNLGRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 277


>gi|58415976|emb|CAH57402.1| RNA polymerase alpha-subunit [Vibrio pacinii]
 gi|58415978|emb|CAH57403.1| RNA polymerase alpha-subunit [Vibrio pacinii]
 gi|58415980|emb|CAH57404.1| RNA polymerase alpha-subunit [Vibrio pacinii]
          Length = 309

 Score =  261 bits (666), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 135/291 (46%), Positives = 198/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVS 150
            + ++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L  D A + M + V 
Sbjct: 82  AVHVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTNDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|296131864|ref|YP_003639111.1| DNA-directed RNA polymerase, alpha subunit [Thermincola sp. JR]
 gi|296030442|gb|ADG81210.1| DNA-directed RNA polymerase, alpha subunit [Thermincola potens JR]
          Length = 315

 Score =  260 bits (665), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 133/288 (46%), Positives = 199/288 (69%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T+V+IDGVLHE S++ GV+ED+TDIILN+
Sbjct: 23  FVVEPLERGYGITLGNSLRRILLSSLPGAAVTSVKIDGVLHEFSTVPGVYEDVTDIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM  D  K + I   GPG V AG+I T  D+E+LNP+  I  L  DA + ME+ V
Sbjct: 83  KELCLKMYTDEEKVLRIESEGPGEVKAGNIITDADVEILNPELHIATLSDDARLVMEINV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GYVPA+ ++ ++  IG+I +D+ +SP+++V+Y +E  R GQ+ DYDKL++ + T+G
Sbjct: 143 AKGRGYVPAERNKKDDHVIGIIPVDSAFSPVRRVNYYIEDTRVGQITDYDKLTLEVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  +++ +L+++IL + L +FI   E  K+V+  +  +    +  L   +EEL+LSVRS
Sbjct: 203 SIRPDEATSLSAKILSEHLRLFIGLTENIKDVEIMVEKEEEEKDKILEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L QRTE DM+++ N G+KSL E+   L  +GL L
Sbjct: 263 YNCLKRAGINTVEELTQRTEEDMIKVRNLGKKSLEEVINKLAELGLSL 310


>gi|58415840|emb|CAH57334.1| RNA polymerase alpha-subunit [Vibrio fluvialis]
 gi|58415842|emb|CAH57335.1| RNA polymerase alpha-subunit [Vibrio fluvialis]
 gi|58415852|emb|CAH57340.1| RNA polymerase alpha-subunit [Vibrio furnissii]
 gi|58415854|emb|CAH57341.1| RNA polymerase alpha-subunit [Vibrio furnissii]
 gi|58415856|emb|CAH57342.1| RNA polymerase alpha-subunit [Vibrio furnissii]
 gi|58415858|emb|CAH57343.1| RNA polymerase alpha-subunit [Vibrio furnissii]
          Length = 309

 Score =  260 bits (665), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 133/291 (45%), Positives = 201/291 (69%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+V++AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVDAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|116334243|ref|YP_795770.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus brevis
           ATCC 367]
 gi|122269075|sp|Q03PY3|RPOA_LACBA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116099590|gb|ABJ64739.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Lactobacillus brevis ATCC 367]
          Length = 316

 Score =  260 bits (665), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 142/314 (45%), Positives = 204/314 (64%), Gaps = 8/314 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN I  I    E  N    I EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EFEKPN-IHKI---DESNNYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE S+++GV ED+T IILN+K I LK++G  D  + + I  +GP  +TAGDI    D+
Sbjct: 59  VLHEFSTVEGVVEDVTQIILNVKKIALKLNGSDDQEETMEINVKGPAQITAGDIVAGADV 118

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKV 183
           ++LNPD  I  +   A   M +T  KG GYV A  ++T N   PIG++ +D++Y+PI++V
Sbjct: 119 DILNPDLYIATVADGATFHMRMTADKGRGYVSADENKTRNTDMPIGVLAVDSIYTPIERV 178

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR GQ  DYDKL++ + T+GSI   +++ALA++IL + L MF++  +  K  + 
Sbjct: 179 NYQVENARVGQRADYDKLTLDVWTNGSINPSEAIALAAKILTEHLAMFVDLTDEAKNAEI 238

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  +       L   +EEL+LSVRS NCL+   I  + +L  +TEADM+++ N GRKSL
Sbjct: 239 MVEKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELNNKTEADMMKVRNLGRKSL 298

Query: 304 VEIKGVLGTMGLFL 317
            E+K  L  +GL L
Sbjct: 299 EEVKAKLADLGLSL 312


>gi|58415796|emb|CAH57312.1| RNA polymerase alpha-subunit [Vibrio coralliilyticus]
          Length = 287

 Score =  260 bits (665), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 134/290 (46%), Positives = 199/290 (68%), Gaps = 8/290 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ 
Sbjct: 1   PLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLA 60

Query: 94  LKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
           ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +
Sbjct: 61  VRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVER 120

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T+
Sbjct: 121 GRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMETN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 181 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 237

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 238 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 287


>gi|152973983|ref|YP_001373500.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus subsp.
           cytotoxis NVH 391-98]
 gi|171769269|sp|A7GK47|RPOA_BACCN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|152022735|gb|ABS20505.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cytotoxicus
           NVH 391-98]
          Length = 314

 Score =  260 bits (665), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 138/310 (44%), Positives = 206/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L ++ +    +I EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDG
Sbjct: 3   EIEKPK-IETVELNEDAKYGKFVI-EPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K + LK+  D  K + I  +G G+VTA DI   +D+E+
Sbjct: 61  VLHEFSTVEGVVEDVTTIILNLKKLALKIYSDEEKTLEIDVQGEGIVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  DA  R+ LT  +G GY PA  +++E+ PIG+I ID++Y+P+ +V+Y V
Sbjct: 121 LNPDLYIATLAKDAHFRVRLTAKRGRGYTPADANKSEDQPIGVIPIDSIYTPVSRVTYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R GQV +YDKL++ + TDGSI  +++++L ++IL + L +F+   +  +  +  +  
Sbjct: 181 EKTRVGQVANYDKLTLDVWTDGSIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 HKLEELGLGL 310


>gi|58415820|emb|CAH57324.1| RNA polymerase alpha-subunit [Vibrio diazotrophicus]
 gi|58415824|emb|CAH57326.1| RNA polymerase alpha-subunit [Vibrio diazotrophicus]
          Length = 309

 Score =  260 bits (665), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 133/291 (45%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDSNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+V++AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVDAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|146742342|gb|ABQ42692.1| RNA polymerase alpha subunit [Vibrio porteresiae]
 gi|156106873|gb|ABU49636.1| RNA polymerase alpha subunit [Vibrio porteresiae]
          Length = 307

 Score =  260 bits (665), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 133/292 (45%), Positives = 200/292 (68%), Gaps = 8/292 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T  +I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 19  EPLERGFGHTLGNALRRILLSSMPGCAVTEAEIEGVLHEYSTKEGVQEDILEILLNLKGL 78

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L D +A + M + V 
Sbjct: 79  AVRVADGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTDDNAEIAMRIKVQ 138

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+V +AR  Q  D DKL + ++T
Sbjct: 139 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVAAARVEQRTDLDKLVIDMET 198

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 199 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 255

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM
Sbjct: 256 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGM 307


>gi|124514416|gb|EAY55929.1| DNA-directed RNA polymerase, alpha subunit [Leptospirillum rubarum]
          Length = 324

 Score =  260 bits (664), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 145/304 (47%), Positives = 203/304 (66%), Gaps = 22/304 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +IAEP  RG+  TLGN+LRR+L+SS++GAAITAV+  GV HE S+I GV ED++DIILN+
Sbjct: 27  VIAEPFERGYGTTLGNSLRRILLSSIKGAAITAVRFRGVFHEFSNIPGVLEDVSDIILNL 86

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + +K        V +   G   VTAGDI T   I++L+P H I  LD  A + M+L +
Sbjct: 87  KEVRVKSHEPEPHWVHLKVSGQKYVTAGDISTGGVIDILDPGHHIATLDKGASLEMDLRI 146

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A+ ++TE+  +G+I IDA+++P+KKV++TV+S R G++ DYDKL++ I+TDG
Sbjct: 147 ETGRGYVSAERNKTESLEVGVIPIDAVFTPLKKVNFTVDSTRVGRMTDYDKLTLDIETDG 206

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE------- 262
           S+T E++++ A++IL+D L MF         V ED +   +P +P    KVEE       
Sbjct: 207 SLTPEEALSQAAQILKDHLDMF---------VIEDTD-HLIPDSPKPTMKVEEIGDDLLT 256

Query: 263 -----LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
                LELSVR++NCL+   I  +GDLIQ+TE ++L+  NFGRKSL EIK VL  MGL L
Sbjct: 257 RNVLDLELSVRASNCLKNAEIKTVGDLIQKTENELLKTKNFGRKSLNEIKTVLSNMGLTL 316

Query: 318 GMNL 321
           GM L
Sbjct: 317 GMEL 320


>gi|257870543|ref|ZP_05650196.1| DNA directed RNA polymerase [Enterococcus gallinarum EG2]
 gi|257804707|gb|EEV33529.1| DNA directed RNA polymerase [Enterococcus gallinarum EG2]
          Length = 312

 Score =  260 bits (664), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 136/295 (46%), Positives = 196/295 (66%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+
Sbjct: 14  EEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDV 73

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             IILNIKG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  ICN+   A 
Sbjct: 74  AQIILNIKGLALKMYGDEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICNVSEGAS 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
               LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+
Sbjct: 134 FHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLT 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           M I TDGSI   ++++LA++I+ + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 194 MEIWTDGSIEPLEAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEE 253

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E+K  L  +GL L
Sbjct: 254 LDLSVRSYNCLKRAGINTVQELTNKSEPEMIKVRNLGRKSLEEVKVKLHDLGLGL 308


>gi|251799614|ref|YP_003014345.1| DNA-directed RNA polymerase subunit alpha [Paenibacillus sp. JDR-2]
 gi|247547240|gb|ACT04259.1| DNA-directed RNA polymerase, alpha subunit [Paenibacillus sp.
           JDR-2]
          Length = 314

 Score =  260 bits (664), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 131/290 (45%), Positives = 200/290 (68%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDGVLHE S++ GV ED+T+IILN+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDGVLHEFSTVPGVIEDVTEIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG++LK+  D  K + I   G G+VTAGDI+  +D+E+LNPD  I  L   A + + +  
Sbjct: 83  KGLSLKIHSDEEKVLEIDAEGEGIVTAGDIRADSDVEILNPDLHIATLASGARLHLRIFA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           ++G GYV A  ++ ++ PIG+I +D++Y+PI +V+Y+VE+ R GQV +YDKL++ + TDG
Sbjct: 143 NRGRGYVQADRNKRDDQPIGVIPVDSIYTPITRVNYSVENTRVGQVTNYDKLTLEVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  E++V+L ++IL + L +F+   +  K+ +  +  +       L   +EEL+LSVRS
Sbjct: 203 SIRPEEAVSLGAKILTEHLDLFVGLTDEAKDAEIMVEKEEDKKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
            NCL+   I  + +LI ++E DM+++ N GRKSL E++  L  +GL L M
Sbjct: 263 YNCLKRAGINTVQELITKSEEDMMKVRNLGRKSLEEVQEKLEELGLGLRM 312


>gi|179184433|gb|ACB78147.1| RNA polymerase alpha subunit [Vibrio sp. CECT 7223]
          Length = 308

 Score =  260 bits (664), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 134/290 (46%), Positives = 198/290 (68%), Gaps = 8/290 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 308


>gi|58415844|emb|CAH57336.1| RNA polymerase alpha-subunit [Vibrio fluvialis]
          Length = 309

 Score =  259 bits (663), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 133/291 (45%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+V++AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVDAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFGPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|45644721|gb|AAS73109.1| predicted DNA-directed RNA polymerase alpha subunit [uncultured
           marine gamma proteobacterium EBAC20E09]
          Length = 321

 Score =  259 bits (663), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 136/296 (45%), Positives = 199/296 (67%), Gaps = 7/296 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ GAA+T V I+G+ HE S+I+GV ED+ DI+LNIK +
Sbjct: 29  EPLERGFGHTLGNALRRILLSSMPGAAVTDVAIEGISHEYSTIEGVREDVIDILLNIKDM 88

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV-VRMELTVSK 151
            +K+       + +   GP  V A       ++E+++ D  I  + VD V ++M LTV  
Sbjct: 89  PIKLIEGDAAEIILDVTGPCDVLASSFAAPGNLELVDQDFHIATI-VDKVNLKMTLTVKT 147

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GY PA     E+  +G + +DA YSP+++VSYTV++AR G+  D DKL + ++TDG++
Sbjct: 148 GRGYEPADLREDEDRAVGALKVDASYSPVRRVSYTVDNARSGKRTDLDKLVIELETDGTL 207

Query: 212 TGEDSVALASRILQDQLGMFINFEE-PKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
             + ++  ++ ILQ QLG F++ +   ++E K+D N     F+P LL+ +EELEL+VRST
Sbjct: 208 DPKMAIEHSATILQQQLGAFVDLDAIAEQEAKKDQN----DFDPILLRSIEELELTVRST 263

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           NCL+ E+I  +GDLI R+E D+L+  N G+KSL EIK VL +  L LGMN+ +WPP
Sbjct: 264 NCLKAESIFLIGDLIHRSEFDLLKTPNLGKKSLNEIKDVLASKNLSLGMNVENWPP 319


>gi|206602703|gb|EDZ39184.1| DNA-directed RNA polymerase, alpha subunit [Leptospirillum sp.
           Group II '5-way CG']
          Length = 324

 Score =  259 bits (663), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 142/300 (47%), Positives = 205/300 (68%), Gaps = 14/300 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +IAEP  RG+  TLGN+LRR+L+SS++GAAITAV+  GV HE S+I GV ED++DIILN+
Sbjct: 27  VIAEPFERGYGTTLGNSLRRILLSSIKGAAITAVRFRGVFHEFSNIPGVLEDVSDIILNL 86

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + +K        V +   G   VTAGDI T   I++L+P H I  LD  A + M+L +
Sbjct: 87  KEVRVKSHESEPHWVHLKVSGQKYVTAGDISTGGVIDILDPGHHIATLDKGASLEMDLRI 146

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A+ +++E+  +G+I IDA+++P+KKV++TV+S R G++ DYDKL++ I+TDG
Sbjct: 147 ETGRGYVSAERNKSESLEVGVIPIDAVFTPLKKVNFTVDSTRVGRMTDYDKLTLDIETDG 206

Query: 210 SITGEDSVALASRILQDQLGMFINF-------EEPKKEVK-EDINVKSLPFNPALLKKVE 261
           S+T E++++ A++IL+D L MF+         + PK  +K E+I       +  L + V 
Sbjct: 207 SLTPEEALSQAAQILKDHLDMFVIEDTDHLIPDSPKPTMKVEEIG------DDLLTRNVL 260

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +LELSVR++NCL+   I  +GDLIQ+TE ++L+  NFGRKSL EIK VL  MGL LGM L
Sbjct: 261 DLELSVRASNCLKNAEIKTVGDLIQKTENELLKTKNFGRKSLNEIKTVLSNMGLTLGMEL 320


>gi|58415822|emb|CAH57325.1| RNA polymerase alpha-subunit [Vibrio diazotrophicus]
          Length = 309

 Score =  259 bits (662), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 133/291 (45%), Positives = 199/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDSNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+V+ AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVDPARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|255067433|ref|ZP_05319288.1| DNA-directed RNA polymerase, alpha subunit [Neisseria sicca ATCC
           29256]
 gi|255048228|gb|EET43692.1| DNA-directed RNA polymerase, alpha subunit [Neisseria sicca ATCC
           29256]
          Length = 278

 Score =  259 bits (662), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 137/281 (48%), Positives = 188/281 (66%), Gaps = 8/281 (2%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           + G A T V I GVLHE S++ GV ED+ DI+LN+KGI  K+ G    ++T+ K G GVV
Sbjct: 1   MNGFAPTEVAISGVLHEYSTVDGVQEDVVDILLNVKGIVFKLHGRGQVQLTLRKSGAGVV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLI 171
            AGDI+  +D+E+LNP+H+IC+L  +  + ME+ V +G GY      R    EN  IG I
Sbjct: 61  VAGDIELPHDVEILNPEHIICHLAENGQIEMEIKVEQGRGYQSVSGRRVVRDENRQIGAI 120

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA +SPI +VS+ VE AR  Q  D DKL + I+TDGSI  E++V  A+RIL DQ+ +F
Sbjct: 121 QLDASFSPISRVSFEVEPARVEQRTDLDKLVLDIETDGSIDPEEAVRSAARILIDQMSIF 180

Query: 232 INFE-EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
            + +  P +EV+E    K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE 
Sbjct: 181 ADLQGTPVEEVEE----KAPPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTET 236

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           ++L+  N GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 237 ELLKTPNLGRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 277


>gi|58415894|emb|CAH57361.1| RNA polymerase alpha-subunit [Vibrio hispanicus]
          Length = 309

 Score =  259 bits (662), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 132/291 (45%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D ++ + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDSNSEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+V++AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVDAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|58416010|emb|CAH57419.1| RNA polymerase alpha-subunit [Vibrio rumoiensis]
 gi|58416012|emb|CAH57420.1| RNA polymerase alpha-subunit [Vibrio rumoiensis]
          Length = 309

 Score =  259 bits (661), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 136/291 (46%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            + ++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D  A + M + V 
Sbjct: 82  AVSVAEGKDEVFITLKKSGSGPVVAGDIIHDGDVEIANPEHVICHLTDDKAEIAMRIKVQ 141

Query: 151 KGHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVP  A+ H  E++ PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPSSARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|69247195|ref|ZP_00604257.1| DNA-directed RNA polymerase [Enterococcus faecium DO]
 gi|227550745|ref|ZP_03980794.1| DNA-directed RNA polymerase [Enterococcus faecium TX1330]
 gi|257878750|ref|ZP_05658403.1| DNA directed RNA polymerase [Enterococcus faecium 1,230,933]
 gi|257881392|ref|ZP_05661045.1| DNA directed RNA polymerase [Enterococcus faecium 1,231,502]
 gi|257885659|ref|ZP_05665312.1| DNA directed RNA polymerase [Enterococcus faecium 1,231,501]
 gi|257887996|ref|ZP_05667649.1| DNA directed RNA polymerase [Enterococcus faecium 1,141,733]
 gi|257890609|ref|ZP_05670262.1| DNA directed RNA polymerase [Enterococcus faecium 1,231,410]
 gi|257893200|ref|ZP_05672853.1| DNA directed RNA polymerase [Enterococcus faecium 1,231,408]
 gi|257896385|ref|ZP_05676038.1| DNA directed RNA polymerase [Enterococcus faecium Com12]
 gi|257899360|ref|ZP_05679013.1| DNA directed RNA polymerase [Enterococcus faecium Com15]
 gi|258615185|ref|ZP_05712955.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecium DO]
 gi|260558313|ref|ZP_05830509.1| DNA directed RNA polymerase [Enterococcus faecium C68]
 gi|261207018|ref|ZP_05921707.1| DNA directed RNA polymerase [Enterococcus faecium TC 6]
 gi|289565347|ref|ZP_06445797.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           D344SRF]
 gi|293379471|ref|ZP_06625615.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           PC4.1]
 gi|293553904|ref|ZP_06674510.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E1039]
 gi|293562972|ref|ZP_06677439.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E1162]
 gi|293567906|ref|ZP_06679247.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E1071]
 gi|293570709|ref|ZP_06681759.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E980]
 gi|294615368|ref|ZP_06695241.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E1636]
 gi|294618294|ref|ZP_06697875.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E1679]
 gi|294621104|ref|ZP_06700295.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           U0317]
 gi|314937634|ref|ZP_07844960.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0133a04]
 gi|314942867|ref|ZP_07849680.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0133C]
 gi|314947997|ref|ZP_07851401.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0082]
 gi|314950914|ref|ZP_07853983.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0133A]
 gi|314991438|ref|ZP_07856915.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0133B]
 gi|314995041|ref|ZP_07860161.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0133a01]
 gi|68194960|gb|EAN09428.1| DNA-directed RNA polymerase [Enterococcus faecium DO]
 gi|227180206|gb|EEI61178.1| DNA-directed RNA polymerase [Enterococcus faecium TX1330]
 gi|257812978|gb|EEV41736.1| DNA directed RNA polymerase [Enterococcus faecium 1,230,933]
 gi|257817050|gb|EEV44378.1| DNA directed RNA polymerase [Enterococcus faecium 1,231,502]
 gi|257821515|gb|EEV48645.1| DNA directed RNA polymerase [Enterococcus faecium 1,231,501]
 gi|257824050|gb|EEV50982.1| DNA directed RNA polymerase [Enterococcus faecium 1,141,733]
 gi|257826969|gb|EEV53595.1| DNA directed RNA polymerase [Enterococcus faecium 1,231,410]
 gi|257829579|gb|EEV56186.1| DNA directed RNA polymerase [Enterococcus faecium 1,231,408]
 gi|257832950|gb|EEV59371.1| DNA directed RNA polymerase [Enterococcus faecium Com12]
 gi|257837272|gb|EEV62346.1| DNA directed RNA polymerase [Enterococcus faecium Com15]
 gi|260075487|gb|EEW63793.1| DNA directed RNA polymerase [Enterococcus faecium C68]
 gi|260078646|gb|EEW66348.1| DNA directed RNA polymerase [Enterococcus faecium TC 6]
 gi|289162837|gb|EFD10687.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           D344SRF]
 gi|291589491|gb|EFF21298.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E1071]
 gi|291591742|gb|EFF23378.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E1636]
 gi|291595388|gb|EFF26700.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E1679]
 gi|291599340|gb|EFF30366.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           U0317]
 gi|291601956|gb|EFF32202.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E1039]
 gi|291605098|gb|EFF34565.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E1162]
 gi|291609181|gb|EFF38453.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E980]
 gi|292641994|gb|EFF60160.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           PC4.1]
 gi|313590767|gb|EFR69612.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0133a01]
 gi|313593918|gb|EFR72763.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0133B]
 gi|313596923|gb|EFR75768.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0133A]
 gi|313598339|gb|EFR77184.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0133C]
 gi|313643011|gb|EFS07591.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0133a04]
 gi|313645595|gb|EFS10175.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0082]
          Length = 312

 Score =  259 bits (661), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 135/295 (45%), Positives = 195/295 (66%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+
Sbjct: 14  EEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDV 73

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILNIKG+ LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A 
Sbjct: 74  TQIILNIKGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGAT 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
               LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+
Sbjct: 134 FHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLT 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           M I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 194 MEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEE 253

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E+K  L  +GL L
Sbjct: 254 LDLSVRSYNCLKRAGINTVQELTNKSEPEMIKVRNLGRKSLEEVKAKLHDLGLGL 308


>gi|312622073|ref|YP_004023686.1| DNA-directed RNA polymerase subunit alpha [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312202540|gb|ADQ45867.1| DNA-directed RNA polymerase, alpha subunit [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 324

 Score =  259 bits (661), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 138/301 (45%), Positives = 202/301 (67%), Gaps = 2/301 (0%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  T+GNALRR L+SSL GAA+TAV+IDGVLHE S+I GV ED+ +IILN+K
Sbjct: 24  VIEPLERGYGITVGNALRRTLLSSLPGAAVTAVKIDGVLHEFSTIPGVLEDVPEIILNLK 83

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           G+ +KMS    K + I  +G   V A DI+   DIE+ NPDH I  L+ DA + ME+TVS
Sbjct: 84  GLAIKMSSPGPKVMYIEAQGECEVKAKDIKADADIEICNPDHHIATLNSDARLFMEITVS 143

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           +G GYVPA+ ++  N PIG+I +D++Y+P+ KV+Y VE+ R GQV DYDKL+M I T+G+
Sbjct: 144 QGKGYVPAERNKQPNQPIGVIPVDSIYTPVVKVNYKVENTRVGQVTDYDKLTMEIWTNGT 203

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I  ++++ +A++IL +   +F +      +++  +  +    N  L   +EELELSVRS 
Sbjct: 204 IRPDEALTVAAKILIEHFNLFTDLSNIPTKIETVVKQEPPKRNKLLDMTIEELELSVRSY 263

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           NCL+   I  + DL+ +TE +M+++ N G+KSL E+   L ++GL L  +  D  P+  E
Sbjct: 264 NCLKRAGINTVEDLVNKTEEEMMKVRNLGKKSLEEVIQKLHSLGLSLKKS--DSTPKEEE 321

Query: 331 E 331
           E
Sbjct: 322 E 322


>gi|51894182|ref|YP_076873.1| DNA-directed RNA polymerase subunit alpha [Symbiobacterium
           thermophilum IAM 14863]
 gi|61215885|sp|Q67JX1|RPOA_SYMTH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|51857871|dbj|BAD42029.1| RNA polymerase alpha subunit [Symbiobacterium thermophilum IAM
           14863]
          Length = 315

 Score =  259 bits (661), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 137/307 (44%), Positives = 207/307 (67%), Gaps = 2/307 (0%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KP  IE +VL  E+ +    + EPL RG+  TLGN+LRR+L+SSL GAA+T+V+IDGVLH
Sbjct: 6   KPK-IETVVLA-EDNSYGKFVVEPLERGYGITLGNSLRRILLSSLPGAAVTSVKIDGVLH 63

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+TDIILN+K ++L+M  D  K + +   G G VTAGDI T  D+E+LNP
Sbjct: 64  EFSTLPGVVEDVTDIILNLKQLSLRMHSDEPKVLRLHAEGEGEVTAGDIHTDADVEILNP 123

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  LD    +  E+TVSKG GYVPA  ++T + PIG+I +D+++SPI++V+YT+E  
Sbjct: 124 DLHIATLDKGGRLIAEITVSKGRGYVPADQNKTPDMPIGVIPVDSIFSPIRRVNYTIEHT 183

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R G   +YDKL++ + T+G+I  +++ + A++IL++ L +FI+  E   E++     +  
Sbjct: 184 RVGNKTNYDKLTLEVWTNGAIRPDEACSWAAKILKEHLELFISLTEDADEIEVMQEKEDD 243

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             N  +   +EEL+LSVRS NCL+   I  + +L+ +T+ +M+++ N G+KSL E+K  L
Sbjct: 244 ERNKLMEMTIEELDLSVRSYNCLKRAGINTIAELVSKTDEEMMKVRNLGKKSLEEVKTKL 303

Query: 311 GTMGLFL 317
              GL L
Sbjct: 304 AAFGLSL 310


>gi|319654896|ref|ZP_08008971.1| DNA-directed RNA polymerase subunit alpha [Bacillus sp. 2_A_57_CT2]
 gi|317393459|gb|EFV74222.1| DNA-directed RNA polymerase subunit alpha [Bacillus sp. 2_A_57_CT2]
          Length = 314

 Score =  259 bits (661), Expect = 6e-67,   Method: Compositional matrix adjust.
 Identities = 132/288 (45%), Positives = 192/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTSIILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +G GVV A D+   +D+E+LNPD  I  L  +A +RM LT 
Sbjct: 83  KKLALKIYSDEEKTLEIDVQGEGVVKAADVTHDSDVEILNPDLHIATLGSNAHLRMRLTA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY PA  ++ E+ PIG+I ID++Y+P+ ++SY VE+ R GQ+ +YDKL+  + TDG
Sbjct: 143 RRGRGYTPADQNKREDQPIGVIPIDSIYTPVSRISYQVENTRVGQMTNYDKLTFDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           S   +D+VAL ++IL + L +F+   +  +  +  +  +       L   +EEL+LSVRS
Sbjct: 203 STGPQDAVALGAKILTEHLNIFVGLTDEAQNAEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKHKLEDLGLGL 310


>gi|304315969|ref|YP_003851114.1| DNA-directed RNA polymerase, subunit alpha [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302777471|gb|ADL68030.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 316

 Score =  258 bits (660), Expect = 7e-67,   Method: Compositional matrix adjust.
 Identities = 130/288 (45%), Positives = 197/288 (68%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA   ++IDGVLHE S++ GV ED+T+IILN+
Sbjct: 24  FVIEPLERGYGITLGNSLRRMLLSSLPGAAAKTIKIDGVLHEFSTVPGVKEDVTEIILNL 83

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + +K+  D  K V I   G G VTAGDI +  D+E++NPD  I  L  +  + ME+ +
Sbjct: 84  KELAVKLYTDEPKIVRIEAEGKGEVTAGDIISDGDVEIMNPDLHIATLSDNGKLNMEIEL 143

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYVP+  ++  N PIG+I +D++++P+KKVSY VE+ R GQV DYDKL+M + T+G
Sbjct: 144 VKGKGYVPSDKNKEPNQPIGIIPVDSIFTPVKKVSYNVENTRVGQVTDYDKLTMEVWTNG 203

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I+ +++++LA++IL D   +F +F E   +++  +       +  L   +EEL+LSVRS
Sbjct: 204 TISPKEAISLAAKILIDHFNLFTSFAENYNDMEVLVEKSEKKTDKPLDMTIEELDLSVRS 263

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL+Q+TE +M+++ N G+KSLVE++  L  +GL L
Sbjct: 264 YNCLKRAGINTVQDLVQKTEEEMMKVRNLGKKSLVEVEQKLKALGLSL 311


>gi|228989345|ref|ZP_04149336.1| DNA-directed RNA polymerase subunit alpha [Bacillus pseudomycoides
           DSM 12442]
 gi|228995528|ref|ZP_04155196.1| DNA-directed RNA polymerase subunit alpha [Bacillus mycoides
           Rock3-17]
 gi|229003153|ref|ZP_04160999.1| DNA-directed RNA polymerase subunit alpha [Bacillus mycoides
           Rock1-4]
 gi|229083457|ref|ZP_04215805.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock3-44]
 gi|228699890|gb|EEL52527.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock3-44]
 gi|228758116|gb|EEM07315.1| DNA-directed RNA polymerase subunit alpha [Bacillus mycoides
           Rock1-4]
 gi|228764257|gb|EEM13136.1| DNA-directed RNA polymerase subunit alpha [Bacillus mycoides
           Rock3-17]
 gi|228770423|gb|EEM18996.1| DNA-directed RNA polymerase subunit alpha [Bacillus pseudomycoides
           DSM 12442]
          Length = 314

 Score =  258 bits (660), Expect = 7e-67,   Method: Compositional matrix adjust.
 Identities = 137/310 (44%), Positives = 206/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L ++ +    +I EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDG
Sbjct: 3   EIEKPK-IETVELNEDAKYGKFVI-EPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K + LK+  +  K + I  +G G+VTA DI   +D+E+
Sbjct: 61  VLHEFSTVEGVVEDVTTIILNLKKLALKIYSEEEKTLEIDVQGEGIVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  DA  R+ LT  +G GY PA  +++E+ PIG+I ID++Y+P+ +V+Y V
Sbjct: 121 LNPDLYIATLAKDAHFRVRLTAKRGRGYTPADANKSEDQPIGVIPIDSIYTPVSRVTYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R GQV +YDKL++ + TDGSI  +++++L ++IL + L +F+   +  +  +  +  
Sbjct: 181 EKTRVGQVANYDKLTLDVWTDGSIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 HKLEELGLGL 310


>gi|58415930|emb|CAH57379.1| RNA polymerase alpha-subunit [Vibrio metschnikovii]
 gi|58415932|emb|CAH57380.1| RNA polymerase alpha-subunit [Vibrio metschnikovii]
 gi|58415934|emb|CAH57381.1| RNA polymerase alpha-subunit [Vibrio metschnikovii]
          Length = 309

 Score =  258 bits (660), Expect = 7e-67,   Method: Compositional matrix adjust.
 Identities = 132/291 (45%), Positives = 201/291 (69%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            +++  +  +  +T+ K G G V AGDI    D+E++NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRLGENKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+V++AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVDAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|163938145|ref|YP_001643029.1| DNA-directed RNA polymerase subunit alpha [Bacillus
           weihenstephanensis KBAB4]
 gi|229131145|ref|ZP_04260057.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           BDRD-ST196]
 gi|163860342|gb|ABY41401.1| DNA-directed RNA polymerase, alpha subunit [Bacillus
           weihenstephanensis KBAB4]
 gi|228652358|gb|EEL08283.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           BDRD-ST196]
          Length = 314

 Score =  258 bits (660), Expect = 8e-67,   Method: Compositional matrix adjust.
 Identities = 137/310 (44%), Positives = 206/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L ++ +    +I EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDG
Sbjct: 3   EIEKPK-IETVELNEDAKYGKFVI-EPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T +ILN+K + LK+  D  K + I  +G G+VTA DI   +D+E+
Sbjct: 61  VLHEFSTVEGVVEDVTTMILNLKKLALKIYSDEEKTLEIDVQGEGIVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  +A  RM LT  +G GY PA  +++E+ PIG+I ID++Y+P+ +V+Y V
Sbjct: 121 LNPDLHIATLAKNAHFRMRLTAKRGRGYTPADANKSEDQPIGVIPIDSIYTPVSRVTYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R GQV +YDKL++ + TDGSI  +++++L ++IL + L +F+   +  +  +  +  
Sbjct: 181 EKTRVGQVANYDKLTLDVWTDGSIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 HKLEELGLGL 310


>gi|229542177|ref|ZP_04431237.1| DNA-directed RNA polymerase, alpha subunit [Bacillus coagulans
           36D1]
 gi|229326597|gb|EEN92272.1| DNA-directed RNA polymerase, alpha subunit [Bacillus coagulans
           36D1]
          Length = 314

 Score =  258 bits (660), Expect = 8e-67,   Method: Compositional matrix adjust.
 Identities = 128/288 (44%), Positives = 196/288 (68%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGV+HE S+++GV ED+T IILN+
Sbjct: 23  FVIEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVMHEFSTVEGVVEDVTSIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +G G VTA DI   +D+E+LNPD  I  +  +  +RM +T 
Sbjct: 83  KKLALKIYSDEEKTLEIDVQGEGAVTAADITHDSDVEILNPDLYIATVAENGHLRMRMTA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           ++G GYVPA  ++ E+ PIG+I ID++Y+P+++V+Y VE+ R GQ+ +YDKLS+ + TDG
Sbjct: 143 NQGRGYVPADQNKREDHPIGVIPIDSIYTPVQRVNYQVENTRVGQISNYDKLSLDVTTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  ++++AL ++IL + L +F+   +  +  +  +  +       L   +EEL+LSVRS
Sbjct: 203 SIGPKEAIALGAKILTEHLNIFVGLTDEAQNAEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEDLGLGL 310


>gi|58415794|emb|CAH57311.1| RNA polymerase alpha-subunit [Vibrio cincinnatiensis]
          Length = 309

 Score =  258 bits (659), Expect = 8e-67,   Method: Compositional matrix adjust.
 Identities = 132/291 (45%), Positives = 200/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVS 150
            +++  +  +  +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V 
Sbjct: 82  AVRLGENKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+V++AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVDAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|83591247|ref|YP_431256.1| DNA-directed RNA polymerase subunit alpha [Moorella thermoacetica
           ATCC 39073]
 gi|119366698|sp|Q2RFS6|RPOA_MOOTA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|83574161|gb|ABC20713.1| DNA-directed RNA polymerase subunit alpha [Moorella thermoacetica
           ATCC 39073]
          Length = 313

 Score =  258 bits (659), Expect = 8e-67,   Method: Compositional matrix adjust.
 Identities = 134/288 (46%), Positives = 196/288 (68%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T+V+I+GVLHE S+I GV ED TDIILNI
Sbjct: 21  FVVEPLERGYGITLGNSLRRMLLSSLPGAAVTSVKIEGVLHEFSTIPGVVEDTTDIILNI 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  + + I     GVVTAGDI T  D+E+LNP+ VI  ++    + ME+TV
Sbjct: 81  KSLALKLHSDEPRVIRIEADDEGVVTAGDIITGADVEILNPEQVIATVEKGGRLYMEMTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYV A  ++ E+ PIG+I +D+L+SPI KV+YTVE+ R GQ+ DYDKL++ + TDG
Sbjct: 141 EKGRGYVSADKNKKEDQPIGIIPVDSLFSPIHKVNYTVENTRVGQITDYDKLTLEVWTDG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  +++V+ A++IL + + +F+   E   +    +  +    +  +   +EEL+LSVRS
Sbjct: 201 SIAPDEAVSSAAKILIEHMRLFLGLTERVSDEVTMVEKEEETRDRLMDMSIEELDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L+QR+E DM+++ N G+KSL E+   L  +GL L
Sbjct: 261 YNCLKRAGINTVAELLQRSEEDMMKVRNLGKKSLEEVTQKLSELGLSL 308


>gi|323340399|ref|ZP_08080656.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus ruminis
           ATCC 25644]
 gi|323092175|gb|EFZ34790.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus ruminis
           ATCC 25644]
          Length = 314

 Score =  258 bits (659), Expect = 9e-67,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 198/298 (66%), Gaps = 2/298 (0%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E  N    + EPL RG+  TLGN+LRR+L+SSL GAAIT VQIDGVLHE S++KGV ED
Sbjct: 13  EESNNHGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAITDVQIDGVLHEFSTVKGVLED 72

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T+IILN+K + LK++ +  + +     GP  VTAGDI T +D+E+LNPD  IC +   A
Sbjct: 73  VTEIILNLKKVALKLNSEEPQSLEFDIVGPKEVTAGDISTNSDVEILNPDLYICTVADGA 132

Query: 142 VVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
                +T +KG GYV A  ++ + D  PIG++ ID++Y+PI++V+Y VE  R GQ  DYD
Sbjct: 133 SFHARMTANKGRGYVSANENKAKADDMPIGVLAIDSIYTPIERVNYQVEKTRVGQKNDYD 192

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL++ + T+GSIT  ++++L+++IL + L +F+N  +  K  +  +  +       L   
Sbjct: 193 KLTLDVWTNGSITPSEAISLSAKILTEHLALFVNLTDEAKNAEIMVEKEETHKEKMLEMT 252

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +EEL+LSVRS NCL+  +I  +  L  ++E+DM+++ N GRKSL E+K  L  +GL L
Sbjct: 253 IEELDLSVRSYNCLKRASINTVQALTNKSESDMMKVRNLGRKSLEEVKAKLADLGLSL 310


>gi|116495921|ref|YP_807655.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus casei ATCC
           334]
 gi|191639403|ref|YP_001988569.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus casei
           BL23]
 gi|227533985|ref|ZP_03964034.1| DNA-directed RNA polymerase [Lactobacillus paracasei subsp.
           paracasei ATCC 25302]
 gi|239630326|ref|ZP_04673357.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus paracasei
           subsp. paracasei 8700:2]
 gi|301067478|ref|YP_003789501.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus casei str.
           Zhang]
 gi|122262679|sp|Q035A9|RPOA_LACC3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238693011|sp|B3WAJ2|RPOA_LACCB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116106071|gb|ABJ71213.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus casei ATCC
           334]
 gi|190713705|emb|CAQ67711.1| DNA-directed RNA polymerase subunit alpha (RNAP subunit alpha)
           (Transcriptase subunit alpha) (RNA polymerase subunit
           alpha) [Lactobacillus casei BL23]
 gi|227188362|gb|EEI68429.1| DNA-directed RNA polymerase [Lactobacillus paracasei subsp.
           paracasei ATCC 25302]
 gi|239527938|gb|EEQ66939.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus paracasei
           subsp. paracasei 8700:2]
 gi|300439885|gb|ADK19651.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Lactobacillus casei str. Zhang]
 gi|327383491|gb|AEA54967.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus casei
           LC2W]
 gi|327386684|gb|AEA58158.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus casei
           BD-II]
          Length = 312

 Score =  258 bits (659), Expect = 9e-67,   Method: Compositional matrix adjust.
 Identities = 138/310 (44%), Positives = 200/310 (64%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E  N    + EPL RG+  TLGN+LRR+L+SSL GAAI+++QIDG
Sbjct: 3   EFEKPN----ITKVDESTNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAISSIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILNIK + LKM+ D  K + I   GP  VTA DI    D+EV
Sbjct: 59  VLHEFSTIDGVLEDVTQIILNIKKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  IC +       + +TV KG GYV A  +++++ PIG++ ID++++PI +V+Y V
Sbjct: 119 LNPEQYICTVADGGHFHVRMTVKKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL++ + T+GSI+  ++++LA++IL + L +F+N  +  K  +  +  
Sbjct: 179 ESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TEADM+++ N GRKSL E+K
Sbjct: 239 EETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTNKTEADMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLADLGLGL 308


>gi|226309835|ref|YP_002769729.1| DNA-directed RNA polymerase subunit alpha [Brevibacillus brevis
           NBRC 100599]
 gi|254765244|sp|C0ZIK7|RPOA_BREBN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|226092783|dbj|BAH41225.1| DNA-directed RNA polymerase alpha chain [Brevibacillus brevis NBRC
           100599]
          Length = 314

 Score =  258 bits (659), Expect = 9e-67,   Method: Compositional matrix adjust.
 Identities = 131/288 (45%), Positives = 197/288 (68%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGVLHE S+++GV ED+T+IILNI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVRTVQIDGVLHEFSTVEGVVEDVTEIILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+  D  K + I   G GVV AGDI+  +D+EVLNPD  I  L     + + +T 
Sbjct: 83  KGLALKIHSDEEKVIEIDAEGEGVVKAGDIRADSDVEVLNPDLHIATLANGGRLHIRMTA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYV +  +++E+ PIG+I ID++Y+PIK+V+Y VE+ R GQ+ +YDKL++ + T+G
Sbjct: 143 GRGRGYVQSDGNKSEDLPIGVIPIDSIYTPIKRVNYQVENTRVGQMTNYDKLTLEVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI+ E++V+L ++I+ + L +F+   +  K+ +  +  +       L   +EEL+LSVRS
Sbjct: 203 SISPEEAVSLGAKIMTEHLNLFVGLTDEAKDAEIMVEKEEDKKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L Q+TE DM+++ N GRKSL E++  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELTQKTEEDMMKVRNLGRKSLEEVQEKLAELGLSL 310


>gi|58415826|emb|CAH57327.1| RNA polymerase alpha-subunit [Vibrio diazotrophicus]
          Length = 309

 Score =  258 bits (658), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 132/291 (45%), Positives = 199/291 (68%), Gaps = 8/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNAL R+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALHRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDSNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+V++AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVDAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 309


>gi|288575869|ref|ZP_05977763.2| DNA-directed RNA polymerase, alpha subunit [Neisseria mucosa ATCC
           25996]
 gi|288566928|gb|EFC88488.1| DNA-directed RNA polymerase, alpha subunit [Neisseria mucosa ATCC
           25996]
          Length = 278

 Score =  258 bits (658), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 136/281 (48%), Positives = 187/281 (66%), Gaps = 8/281 (2%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           + G A T V I GVLHE S++ GV ED+ DI+LN+KGI  K+ G    ++T+ K G G V
Sbjct: 1   MNGFAPTEVAISGVLHEYSTVDGVQEDVVDILLNVKGIVFKLHGRGQVQLTLKKSGAGAV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLI 171
            AGDI+  +D+E+LNP+H+IC+L  +  + ME+ V +G GY      R    EN  IG I
Sbjct: 61  VAGDIELPHDVEILNPEHIICHLAENGQIEMEIKVEQGRGYQSVSGRRVVRDENRQIGAI 120

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA +SPI +VS+ VE AR  Q  D DKL + I+TDGSI  E++V  A+RIL DQ+ +F
Sbjct: 121 QLDASFSPISRVSFEVEPARVEQRTDLDKLVLDIETDGSIDPEEAVRSAARILIDQMSIF 180

Query: 232 INFE-EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
            + +  P +EV+E    K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE 
Sbjct: 181 ADLQGTPVEEVEE----KAPPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTET 236

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           ++L+  N GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 237 ELLKTPNLGRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 277


>gi|46143635|ref|ZP_00134832.2| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Actinobacillus pleuropneumoniae serovar 1 str. 4074]
          Length = 279

 Score =  258 bits (658), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 133/280 (47%), Positives = 193/280 (68%), Gaps = 9/280 (3%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+SG     +T+ K G G VTA
Sbjct: 3   GCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVSGKDDIILTLNKSGIGPVTA 62

Query: 117 GDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLIT 172
            DI    D+E++NP HVIC+L D DA + M + V +G GYVPA    H + E+ PIG + 
Sbjct: 63  ADITHDGDVEIVNPHHVICHLTDKDASISMRIRVQRGRGYVPASARVHSQDEDRPIGRLL 122

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F+
Sbjct: 123 VDARFSPVDRIAYNVEAARVEQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFV 182

Query: 233 NFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           +  + ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE +
Sbjct: 183 DLRDVRQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVE 238

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +L+  N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 239 LLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 278


>gi|261409493|ref|YP_003245734.1| DNA-directed RNA polymerase subunit alpha [Paenibacillus sp.
           Y412MC10]
 gi|315649671|ref|ZP_07902755.1| DNA-directed RNA polymerase subunit alpha [Paenibacillus vortex
           V453]
 gi|329922053|ref|ZP_08277846.1| DNA-directed RNA polymerase, alpha subunit [Paenibacillus sp. HGF5]
 gi|261285956|gb|ACX67927.1| DNA-directed RNA polymerase, alpha subunit [Paenibacillus sp.
           Y412MC10]
 gi|315274859|gb|EFU38235.1| DNA-directed RNA polymerase subunit alpha [Paenibacillus vortex
           V453]
 gi|328942436|gb|EGG38700.1| DNA-directed RNA polymerase, alpha subunit [Paenibacillus sp. HGF5]
          Length = 314

 Score =  258 bits (658), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 134/295 (45%), Positives = 197/295 (66%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           EE      + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I GV ED+
Sbjct: 16  EEGTYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIPGVMEDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T++ILN+K ++LK+  D  K   I   G GVVTAGDI+  +D+E+LNPD  I  L   A 
Sbjct: 76  TEVILNLKALSLKIHSDEEKVFEIDAEGEGVVTAGDIRADSDVEILNPDLHIATLGPGAR 135

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + M +  S+G GYV A  ++ ++ PIG+I +D++Y+PI +V+Y VE+ R GQV +YDKL+
Sbjct: 136 LHMRIFASRGRGYVQADRNKRDDQPIGVIPVDSIYTPISRVNYGVENTRVGQVTNYDKLT 195

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + I TDGSI  E++V+L ++IL + L +F+   +  K+ +  +  +       L   +EE
Sbjct: 196 LEIWTDGSIRPEEAVSLGAKILTEHLFLFVGLTDEAKDAEIMVEKEEDKKEKVLEMTIEE 255

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E++  L  +GL L
Sbjct: 256 LDLSVRSYNCLKRAGINTVQELTTKTEEDMMKVRNLGRKSLEEVQEKLEELGLGL 310


>gi|205372042|ref|ZP_03224859.1| DNA-directed RNA polymerase subunit alpha [Bacillus coahuilensis
           m4-4]
          Length = 314

 Score =  258 bits (658), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 131/288 (45%), Positives = 194/288 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T +ILNI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTSMILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +G GVVTA DI   +D+E+LNPD  I  L  D+ +RM L  
Sbjct: 83  KKLALKIYSDEEKTLEIDIKGNGVVTAADITHDSDVEILNPDLHIATLSGDSHLRMRLNA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY PA  ++ E+ PIG+I ID++Y+P+ +V+Y VE+ R GQ+ +YDKLS+ + TDG
Sbjct: 143 QRGRGYTPADQNKREDLPIGVIPIDSIYTPVSRVNYQVENTRVGQLTNYDKLSLDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  +++++L ++IL + L +F+   +  +  +  +  +       L   +EEL+LSVRS
Sbjct: 203 SIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLDELGLGL 310


>gi|78044042|ref|YP_361090.1| DNA-directed RNA polymerase subunit alpha [Carboxydothermus
           hydrogenoformans Z-2901]
 gi|90110830|sp|Q3A9U4|RPOA_CARHZ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|77996157|gb|ABB15056.1| DNA-directed RNA polymerase, alpha subunit [Carboxydothermus
           hydrogenoformans Z-2901]
          Length = 313

 Score =  258 bits (658), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 134/293 (45%), Positives = 203/293 (69%), Gaps = 10/293 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN++RR+L+SSL GAA+T+++I+GVLHE S++ GV ED+T+IILNI
Sbjct: 21  FVIEPLERGYGITLGNSMRRILLSSLPGAAVTSIKIEGVLHEFSTVPGVVEDVTEIILNI 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+ GD  + + I   G GV+TA DI    ++E+LNPD VI ++     + ME+TV
Sbjct: 81  KNLTLKLHGDEEQVLRIEAEGEGVITAKDIIAPPEVEILNPDLVIAHIAEGGRLFMEMTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           ++G GYVPA+ ++     IG+I +D+++SP+ KV++ VE+ R GQ+ DYDKL++ + TDG
Sbjct: 141 ARGRGYVPAERNKKGEHVIGVIPVDSIFSPVLKVNFQVENTRVGQITDYDKLTLEVWTDG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEV-----KEDINVKSLPFNPALLKKVEELE 264
           SI  +++V+LA+RI+ + L +F+N  E    V     KE+   + L   P     +E+L+
Sbjct: 201 SIRPDEAVSLAARIMVEHLQLFVNLNERATGVEIMVEKEEDAKEKLAEMP-----IEDLD 255

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LSVRS NCL+   I  +G+LIQ+TEADM+++ N G+KSL E+   L +MGL L
Sbjct: 256 LSVRSYNCLKRAGINTVGELIQKTEADMMKVRNLGKKSLEEVISKLNSMGLSL 308


>gi|229015538|ref|ZP_04172535.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH1273]
 gi|229027985|ref|ZP_04184138.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH1271]
 gi|229170988|ref|ZP_04298589.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus MM3]
 gi|228612528|gb|EEK69749.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus MM3]
 gi|228733373|gb|EEL84202.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH1271]
 gi|228745761|gb|EEL95766.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH1273]
          Length = 314

 Score =  258 bits (658), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 137/310 (44%), Positives = 206/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L ++ +    +I EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDG
Sbjct: 3   EIEKPK-IETVELNEDAKYGKFVI-EPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K + LK+  +  K + I  +G G+VTA DI   +D+E+
Sbjct: 61  VLHEFSTVEGVVEDVTTIILNLKKLALKIYSEEEKTLEIDVQGEGIVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  +A  RM LT  +G GY PA  +++E+ PIG+I ID++Y+P+ +V+Y V
Sbjct: 121 LNPDLHIATLAKNAHFRMRLTAKRGRGYTPADANKSEDQPIGVIPIDSIYTPVSRVTYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R GQV +YDKL++ + TDGSI  +++++L ++IL + L +F+   +  +  +  +  
Sbjct: 181 EKTRVGQVANYDKLTLDVWTDGSIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 HKLEELGLGL 310


>gi|199598858|ref|ZP_03212269.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus rhamnosus
           HN001]
 gi|229552733|ref|ZP_04441458.1| DNA-directed RNA polymerase [Lactobacillus rhamnosus LMS2-1]
 gi|258509456|ref|YP_003172207.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus rhamnosus
           GG]
 gi|258540654|ref|YP_003175153.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus rhamnosus
           Lc 705]
 gi|199590270|gb|EDY98365.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus rhamnosus
           HN001]
 gi|229313939|gb|EEN79912.1| DNA-directed RNA polymerase [Lactobacillus rhamnosus LMS2-1]
 gi|257149383|emb|CAR88356.1| DNA-directed RNA polymerase, subunit alpha [Lactobacillus rhamnosus
           GG]
 gi|257152330|emb|CAR91302.1| DNA-directed RNA polymerase, subunit alpha [Lactobacillus rhamnosus
           Lc 705]
 gi|259650735|dbj|BAI42897.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus rhamnosus
           GG]
          Length = 312

 Score =  258 bits (658), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 137/310 (44%), Positives = 200/310 (64%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E  N    + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDG
Sbjct: 3   EFEKPN----ITKVDESTNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILNIK + LKM+ D  K + I   GP  VTA DI    D+EV
Sbjct: 59  VLHEFSTIDGVLEDVTQIILNIKKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  IC +       + +TV KG GYV A  +++++ PIG++ ID++++PI +V+Y V
Sbjct: 119 LNPEQYICTVADGGHFHVRMTVKKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL++ + T+GSI+  ++++LA++IL + L +F+N  +  K  +  +  
Sbjct: 179 ESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TEADM+++ N GRKSL E+K
Sbjct: 239 EETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTNKTEADMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLADLGLGL 308


>gi|323706479|ref|ZP_08118040.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacterium
           xylanolyticum LX-11]
 gi|323534199|gb|EGB23989.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacterium
           xylanolyticum LX-11]
          Length = 316

 Score =  258 bits (658), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 129/288 (44%), Positives = 198/288 (68%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA   ++IDGVLHE S++ GV ED+T+IILN+
Sbjct: 24  FVIEPLERGYGITLGNSLRRMLLSSLPGAAAKTIKIDGVLHEFSTVPGVKEDVTEIILNL 83

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + +K+  D  K V I   G G VTAGDI +  D+E++NPD  I  L  +  + ME+ +
Sbjct: 84  KELAVKLYTDEPKIVRIEAEGKGEVTAGDIISDGDVEIMNPDLHIATLSDNGKLNMEIEL 143

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYVP+  ++  N PIG+I +D++++P+KKVSY+VE+ R GQV DYDKL+M + T+G
Sbjct: 144 VKGKGYVPSDKNKEPNQPIGIIPVDSIFTPVKKVSYSVENTRVGQVTDYDKLTMEVWTNG 203

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I+ +++++LA++IL D   +F +F +   +++  +       +  L   +EEL+LSVRS
Sbjct: 204 TISPKEAISLAAKILIDHFNLFTSFADNYNDMEVLVEKSEKKTDKPLDMTIEELDLSVRS 263

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL+Q+TE +M+++ N G+KSLVE++  L  +GL L
Sbjct: 264 YNCLKRAGINTVQDLVQKTEEEMMKVRNLGKKSLVEVEQKLKALGLSL 311


>gi|30018406|ref|NP_830037.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus ATCC
           14579]
 gi|30260328|ref|NP_842705.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           Ames]
 gi|42779218|ref|NP_976465.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus ATCC
           10987]
 gi|47525393|ref|YP_016742.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           'Ames Ancestor']
 gi|47570249|ref|ZP_00240900.1| DNA-directed RNA polymerase alpha chain [Bacillus cereus G9241]
 gi|49183171|ref|YP_026423.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           Sterne]
 gi|49481737|ref|YP_034488.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar konkukian str. 97-27]
 gi|52145083|ref|YP_081747.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus E33L]
 gi|65317583|ref|ZP_00390542.1| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Bacillus anthracis str. A2012]
 gi|118475905|ref|YP_893056.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           str. Al Hakam]
 gi|167642075|ref|ZP_02400299.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           A0193]
 gi|170689688|ref|ZP_02880866.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           A0465]
 gi|177656195|ref|ZP_02937176.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           A0174]
 gi|190567453|ref|ZP_03020367.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis
           Tsiankovskii-I]
 gi|196041162|ref|ZP_03108458.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus
           NVH0597-99]
 gi|206972214|ref|ZP_03233161.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus AH1134]
 gi|217957712|ref|YP_002336256.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH187]
 gi|218232273|ref|YP_002364986.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus B4264]
 gi|218895272|ref|YP_002443683.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus G9842]
 gi|218901342|ref|YP_002449176.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus AH820]
 gi|222093907|ref|YP_002527957.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus Q1]
 gi|225862189|ref|YP_002747567.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus
           03BB102]
 gi|227812810|ref|YP_002812819.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           CDC 684]
 gi|228898890|ref|ZP_04063172.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           IBL 4222]
 gi|228905934|ref|ZP_04069831.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           IBL 200]
 gi|228912876|ref|ZP_04076523.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar pulsiensis BGSC 4CC1]
 gi|228919087|ref|ZP_04082466.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar huazhongensis BGSC 4BD1]
 gi|228925390|ref|ZP_04088486.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar pondicheriensis BGSC 4BA1]
 gi|228931639|ref|ZP_04094545.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar andalousiensis BGSC 4AW1]
 gi|228937440|ref|ZP_04100086.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar berliner ATCC 10792]
 gi|228943942|ref|ZP_04106327.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar monterrey BGSC 4AJ1]
 gi|228950685|ref|ZP_04112819.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar kurstaki str. T03a001]
 gi|228956578|ref|ZP_04118374.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar pakistani str. T13001]
 gi|228963237|ref|ZP_04124406.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar sotto str. T04001]
 gi|228970326|ref|ZP_04130985.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar thuringiensis str. T01001]
 gi|228976896|ref|ZP_04137308.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           Bt407]
 gi|228983392|ref|ZP_04143605.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar tochigiensis BGSC 4Y1]
 gi|229041042|ref|ZP_04189805.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH676]
 gi|229067902|ref|ZP_04201219.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus F65185]
 gi|229074198|ref|ZP_04207244.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock4-18]
 gi|229089268|ref|ZP_04220549.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock3-42]
 gi|229094859|ref|ZP_04225864.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock3-29]
 gi|229100936|ref|ZP_04231740.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock3-28]
 gi|229107823|ref|ZP_04237459.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock1-15]
 gi|229113813|ref|ZP_04243248.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus Rock1-3]
 gi|229119799|ref|ZP_04249060.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus 95/8201]
 gi|229125654|ref|ZP_04254686.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           BDRD-Cer4]
 gi|229136983|ref|ZP_04265610.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           BDRD-ST26]
 gi|229142943|ref|ZP_04271384.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           BDRD-ST24]
 gi|229148546|ref|ZP_04276802.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus m1550]
 gi|229153915|ref|ZP_04282045.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus ATCC
           4342]
 gi|229159310|ref|ZP_04287334.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus R309803]
 gi|229176737|ref|ZP_04304141.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus 172560W]
 gi|229182531|ref|ZP_04309782.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus BGSC
           6E1]
 gi|229188422|ref|ZP_04315470.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus ATCC
           10876]
 gi|229194527|ref|ZP_04321330.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus m1293]
 gi|229602997|ref|YP_002864788.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           A0248]
 gi|254686636|ref|ZP_05150495.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           CNEVA-9066]
 gi|254726284|ref|ZP_05188066.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           A1055]
 gi|254735289|ref|ZP_05192997.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           Western North America USA6153]
 gi|254739481|ref|ZP_05197179.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           Kruger B]
 gi|254756844|ref|ZP_05208872.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           Australia 94]
 gi|296500970|ref|YP_003662670.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           BMB171]
 gi|300119550|ref|ZP_07057094.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus SJ1]
 gi|301051874|ref|YP_003790085.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis CI]
 gi|33301600|sp|Q81J18|RPOA_BACCR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|33301605|sp|Q81VQ4|RPOA_BACAN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61215852|sp|Q63H64|RPOA_BACCZ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61215930|sp|Q6HPN2|RPOA_BACHK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61215979|sp|Q73F69|RPOA_BACC1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158512483|sp|A0R8K6|RPOA_BACAH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|29893946|gb|AAP07238.1| DNA-directed RNA polymerase alpha chain [Bacillus cereus ATCC
           14579]
 gi|30253649|gb|AAP24191.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           Ames]
 gi|42735133|gb|AAS39073.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus ATCC
           10987]
 gi|47500541|gb|AAT29217.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           'Ames Ancestor']
 gi|47553073|gb|EAL11473.1| DNA-directed RNA polymerase alpha chain [Bacillus cereus G9241]
 gi|49177098|gb|AAT52474.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           Sterne]
 gi|49333293|gb|AAT63939.1| DNA-directed RNA polymerase [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|51978552|gb|AAU20102.1| DNA-directed RNA polymerase [Bacillus cereus E33L]
 gi|118415130|gb|ABK83549.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           str. Al Hakam]
 gi|167509962|gb|EDR85384.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           A0193]
 gi|170666359|gb|EDT17144.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           A0465]
 gi|172079843|gb|EDT64957.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           A0174]
 gi|190561580|gb|EDV15551.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis
           Tsiankovskii-I]
 gi|196028097|gb|EDX66708.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus
           NVH0597-99]
 gi|206732788|gb|EDZ49963.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus AH1134]
 gi|217066667|gb|ACJ80917.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus AH187]
 gi|218160230|gb|ACK60222.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus B4264]
 gi|218539881|gb|ACK92279.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus AH820]
 gi|218541781|gb|ACK94175.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus G9842]
 gi|221237955|gb|ACM10665.1| DNA-directed RNA polymerase [Bacillus cereus Q1]
 gi|225788641|gb|ACO28858.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus
           03BB102]
 gi|227006086|gb|ACP15829.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           CDC 684]
 gi|228588993|gb|EEK47008.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus m1293]
 gi|228595096|gb|EEK52867.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus ATCC
           10876]
 gi|228600986|gb|EEK58555.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus BGSC
           6E1]
 gi|228606780|gb|EEK64197.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus 172560W]
 gi|228624202|gb|EEK81004.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus R309803]
 gi|228629596|gb|EEK86293.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus ATCC
           4342]
 gi|228634962|gb|EEK91535.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus m1550]
 gi|228640564|gb|EEK96953.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           BDRD-ST24]
 gi|228646521|gb|EEL02728.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           BDRD-ST26]
 gi|228657846|gb|EEL13652.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           BDRD-Cer4]
 gi|228663700|gb|EEL19279.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus 95/8201]
 gi|228669684|gb|EEL25091.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus Rock1-3]
 gi|228675672|gb|EEL30880.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock1-15]
 gi|228682515|gb|EEL36588.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock3-28]
 gi|228688602|gb|EEL42475.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock3-29]
 gi|228694107|gb|EEL47789.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock3-42]
 gi|228708968|gb|EEL61095.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock4-18]
 gi|228715261|gb|EEL67120.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus F65185]
 gi|228727339|gb|EEL78533.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH676]
 gi|228776382|gb|EEM24735.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar tochigiensis BGSC 4Y1]
 gi|228782866|gb|EEM31032.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           Bt407]
 gi|228789435|gb|EEM37355.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar thuringiensis str. T01001]
 gi|228796495|gb|EEM43934.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar sotto str. T04001]
 gi|228803143|gb|EEM49965.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar pakistani str. T13001]
 gi|228809036|gb|EEM55521.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar kurstaki str. T03a001]
 gi|228815775|gb|EEM62011.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar monterrey BGSC 4AJ1]
 gi|228822273|gb|EEM68255.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar berliner ATCC 10792]
 gi|228828067|gb|EEM73795.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar andalousiensis BGSC 4AW1]
 gi|228834312|gb|EEM79853.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar pondicheriensis BGSC 4BA1]
 gi|228840612|gb|EEM85874.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar huazhongensis BGSC 4BD1]
 gi|228846812|gb|EEM91817.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar pulsiensis BGSC 4CC1]
 gi|228853749|gb|EEM98509.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           IBL 200]
 gi|228860790|gb|EEN05168.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           IBL 4222]
 gi|229267405|gb|ACQ49042.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           A0248]
 gi|296322022|gb|ADH04950.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           BMB171]
 gi|298723022|gb|EFI63920.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus SJ1]
 gi|300374043|gb|ADK02947.1| DNA-directed RNA polymerase alpha subunit [Bacillus cereus biovar
           anthracis str. CI]
 gi|324324128|gb|ADY19388.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar finitimus YBT-020]
 gi|326937932|gb|AEA13828.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar chinensis CT-43]
          Length = 314

 Score =  257 bits (657), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 137/310 (44%), Positives = 206/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L ++ +    +I EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDG
Sbjct: 3   EIEKPK-IETVELNEDAKYGKFVI-EPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K + LK+  +  K + I  +G G+VTA DI   +D+E+
Sbjct: 61  VLHEFSTVEGVVEDVTTIILNLKKLALKIYSEEEKTLEIDVQGEGIVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  DA  R+ LT  +G GY PA  +++E+ PIG+I ID++Y+P+ +V+Y V
Sbjct: 121 LNPDLHIATLAKDAHFRVRLTAKRGRGYTPADANKSEDQPIGVIPIDSIYTPVSRVTYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R GQV +YDKL++ + TDGSI  +++++L ++IL + L +F+   +  +  +  +  
Sbjct: 181 EKTRVGQVANYDKLTLDVWTDGSIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 HKLEELGLGL 310


>gi|312127254|ref|YP_003992128.1| DNA-directed RNA polymerase subunit alpha [Caldicellulosiruptor
           hydrothermalis 108]
 gi|312793911|ref|YP_004026834.1| DNA-directed RNA polymerase subunit alpha [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312877393|ref|ZP_07737358.1| DNA-directed RNA polymerase, alpha subunit [Caldicellulosiruptor
           lactoaceticus 6A]
 gi|311777273|gb|ADQ06759.1| DNA-directed RNA polymerase, alpha subunit [Caldicellulosiruptor
           hydrothermalis 108]
 gi|311795867|gb|EFR12231.1| DNA-directed RNA polymerase, alpha subunit [Caldicellulosiruptor
           lactoaceticus 6A]
 gi|312181051|gb|ADQ41221.1| DNA-directed RNA polymerase, alpha subunit [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 324

 Score =  257 bits (657), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 137/301 (45%), Positives = 202/301 (67%), Gaps = 2/301 (0%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  T+GNALRR L+SSL GAA+TAV+IDGVLHE S+I GV ED+ +IILN+K
Sbjct: 24  VIEPLERGYGITVGNALRRTLLSSLPGAAVTAVKIDGVLHEFSTIPGVLEDVPEIILNLK 83

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           G+ +KMS    K + I  +G   V A DI+   DIE+ NPDH I  L+ DA + ME+TV+
Sbjct: 84  GLAIKMSSPGPKVMYIEAQGECEVKAKDIKADADIEICNPDHHIATLNSDARLFMEITVN 143

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           +G GYVPA+ ++  N PIG+I +D++Y+P+ KV+Y VE+ R GQV DYDKL+M I T+G+
Sbjct: 144 QGKGYVPAERNKQPNQPIGVIPVDSIYTPVVKVNYKVENTRVGQVTDYDKLTMEIWTNGT 203

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I  ++++ +A++IL +   +F +      +++  +  +    N  L   +EELELSVRS 
Sbjct: 204 IRPDEALTVAAKILIEHFNLFTDLSNIPTKIETVVKQEPPKRNKLLDMTIEELELSVRSY 263

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           NCL+   I  + DL+ +TE +M+++ N G+KSL E+   L ++GL L  +  D  P+  E
Sbjct: 264 NCLKRAGINTVEDLVNKTEEEMMKVRNLGKKSLEEVIQKLHSLGLSLKKS--DSTPKEEE 321

Query: 331 E 331
           E
Sbjct: 322 E 322


>gi|256005300|ref|ZP_05430266.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           thermocellum DSM 2360]
 gi|281419375|ref|ZP_06250390.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           thermocellum JW20]
 gi|255990736|gb|EEU00852.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           thermocellum DSM 2360]
 gi|281406995|gb|EFB37258.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           thermocellum JW20]
 gi|316939529|gb|ADU73563.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           thermocellum DSM 1313]
          Length = 315

 Score =  257 bits (657), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 140/312 (44%), Positives = 205/312 (65%), Gaps = 4/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRT-LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           E+ KP  IE +V    E+NR    + EPL RG+  TLGN+LRR+L+SSL G A+T+++ID
Sbjct: 3   EIEKPK-IECVVCS--EDNRYGKFVVEPLERGYGITLGNSLRRILLSSLPGVAVTSIKID 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE S+I GV ED+T+IILNIK ++L   G+  K + I   G G V A DI+   D+E
Sbjct: 60  GVLHEFSTIPGVIEDVTEIILNIKELSLNFHGEGPKVIYIDAEGEGEVKAKDIKADADVE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +LNP+H I  L  D  + ME+T+ KG GYV A+ ++    PIG+I +D++++P+ KV+YT
Sbjct: 120 ILNPEHKIATLSGDHRLYMEMTIDKGRGYVSAEKNKHPGQPIGVIPVDSIFTPVHKVNYT 179

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+ R GQV DYDKL++ + T+GSI  +++++L ++IL + L +FI+  +  K  +  + 
Sbjct: 180 VENTRVGQVTDYDKLTLEVWTNGSIKPDEAISLGAKILSEHLNLFIDLSDNAKNAEIMVE 239

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L   +EEL+LSVRS NCL+   I  + DLI RTE DM+++ N GRKSL E+
Sbjct: 240 KEETKKEKVLEMTIEELDLSVRSYNCLKRAGINTVEDLISRTEEDMMKVRNLGRKSLEEV 299

Query: 307 KGVLGTMGLFLG 318
              L  +GL L 
Sbjct: 300 VNKLKALGLSLA 311


>gi|331702054|ref|YP_004399013.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus buchneri
           NRRL B-30929]
 gi|329129397|gb|AEB73950.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus buchneri
           NRRL B-30929]
          Length = 319

 Score =  257 bits (657), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 147/314 (46%), Positives = 204/314 (64%), Gaps = 8/314 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN I  I   +E  N   ++ EPL RG+  TLGN+LRR L+SSL GAA+T++QID 
Sbjct: 6   EFEKPN-IHKI---EETNNFGEVVVEPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDD 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE S+IKGV ED+T IILN+K I+LK+ G  D  + + I   GP  VTAGDIQ  +D+
Sbjct: 62  VLHEFSTIKGVVEDVTQIILNVKKISLKLDGPEDEEENLEIDVIGPADVTAGDIQADSDV 121

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKV 183
            VLNPD  I  +   A   M LT +KG GYV A     R+   PIG++ +D++Y+PI++V
Sbjct: 122 TVLNPDLHIATVAEGATFHMRLTANKGRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERV 181

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VES R GQ  D+DKL++ I TDGSIT  ++V+LA++IL + L MF++  +  K  + 
Sbjct: 182 NYQVESTRVGQRDDFDKLTLDIWTDGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEI 241

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  +       L   +EEL+LSVRS NCL+   I  + +L ++TEADM+++ N GRKSL
Sbjct: 242 MVEKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTEKTEADMMKVRNLGRKSL 301

Query: 304 VEIKGVLGTMGLFL 317
            E+K  L  +GL L
Sbjct: 302 EEVKEKLAALGLSL 315


>gi|145577845|gb|ABP87373.1| RpoA [Vibrio ruber]
          Length = 294

 Score =  257 bits (657), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 134/280 (47%), Positives = 197/280 (70%), Gaps = 8/280 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 18  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 77

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L D +A V M + V 
Sbjct: 78  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTDGNAEVAMRIKVQ 137

Query: 151 KGHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVP  A+ H  E+D PIG + +DA YSP+ K++YTVE+AR  Q  D DKL + ++T
Sbjct: 138 RGRGYVPASARIHTDEDDRPIGRLLVDATYSPVDKIAYTVEAARVEQRTDLDKLVIDMET 197

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G+I  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 198 NGTIEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 254

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK
Sbjct: 255 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIK 294


>gi|89100320|ref|ZP_01173185.1| DNA-directed RNA polymerase alpha subunit [Bacillus sp. NRRL
           B-14911]
 gi|89084941|gb|EAR64077.1| DNA-directed RNA polymerase alpha subunit [Bacillus sp. NRRL
           B-14911]
          Length = 314

 Score =  257 bits (657), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 130/288 (45%), Positives = 191/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T +ILNI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTSVILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +G G VTA D+   +D+E+LNPD  I  L  +  +RM LT 
Sbjct: 83  KKLALKIYSDDEKTLEIDIQGEGAVTAADVTHDSDVEILNPDLHIATLGSNGHLRMRLTA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY PA  ++ E+ PIG+I ID++Y+P+ ++SY VE+ R GQ+ +YDKL+  + TDG
Sbjct: 143 KRGRGYTPADQNKREDQPIGVIPIDSIYTPVSRISYQVENTRVGQMTNYDKLTFDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           S   +D+VAL ++IL + L +F+   +  +  +  +  +       L   +EEL+LSVRS
Sbjct: 203 STGPQDAVALGAKILTEHLNIFVGLTDEAQNAEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKHKLEELGLGL 310


>gi|157783870|gb|ABV72700.1| RNA polymerase alpha-subunit [Vibrio mangrovi]
 gi|163962991|gb|ABY50538.1| RNA polymerase alpha-subunit [Vibrio sp. MSSRF39]
          Length = 297

 Score =  257 bits (657), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 134/280 (47%), Positives = 197/280 (70%), Gaps = 8/280 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 76

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L D +A V M + V 
Sbjct: 77  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTDDNAEVAMRIKVQ 136

Query: 151 KGHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVP  A+ H  E+D PIG + +DA YSP+ K++YTVE+AR  Q  D DKL + ++T
Sbjct: 137 RGRGYVPASARIHTDEDDRPIGRLLVDATYSPVDKIAYTVEAARVEQRTDLDKLVIDMET 196

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G+I  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 197 NGTIEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 253

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK
Sbjct: 254 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIK 293


>gi|315640136|ref|ZP_07895258.1| DNA-directed RNA polymerase subunit alpha [Enterococcus italicus
           DSM 15952]
 gi|315484113|gb|EFU74587.1| DNA-directed RNA polymerase subunit alpha [Enterococcus italicus
           DSM 15952]
          Length = 312

 Score =  257 bits (656), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 134/295 (45%), Positives = 194/295 (65%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+
Sbjct: 14  EEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDV 73

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             IILNIKG+ LK+ G+  K + I   GP  VTAGDI   +D+E+LN D  IC +   A 
Sbjct: 74  AQIILNIKGLALKLYGEDEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGAT 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
               LTV  G GYV A  ++ ++ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+
Sbjct: 134 FHARLTVKPGRGYVQADENKKDDMPIGVLPVDSIYTPVRRVNYQVENTRVGHRDDFDKLT 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           M I TDGSI   D+++LA++I+ + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 194 MEIWTDGSIEPLDAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEE 253

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E+K  L  +GL L
Sbjct: 254 LDLSVRSYNCLKRAGINTVQELTNKSEPEMIKVRNLGRKSLEEVKAKLHDLGLGL 308


>gi|256847789|ref|ZP_05553234.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus
           coleohominis 101-4-CHN]
 gi|256715478|gb|EEU30454.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus
           coleohominis 101-4-CHN]
          Length = 313

 Score =  257 bits (656), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 137/309 (44%), Positives = 205/309 (66%), Gaps = 5/309 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E +N    + EPL RG+  TLGN+LRRV+++SL GAAIT++ IDG
Sbjct: 3   EFEKPN----IHKVEETDNYGKFVVEPLERGYGTTLGNSLRRVMLASLPGAAITSINIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K ++L++  +  K + +  +GP  VTAGDIQ   D+ V
Sbjct: 59  VLHEFSTVEGVTEDVTQIILNLKKVSLRIDSEDQKNLELDVKGPAEVTAGDIQGDGDVTV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYT 186
           LNPD  I  +   A + +++T  KGHGY  A  ++T  D  IG++ ID++Y+PI++V+YT
Sbjct: 119 LNPDLHIATVADGAELHIQMTADKGHGYSSADDNKTRMDLAIGVLPIDSIYTPIERVNYT 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+ R GQ  DYDKL++ + T+GS+T  ++V+LA++IL   L MF+N  E  +  +  + 
Sbjct: 179 VENTRVGQNNDYDKLTLDVWTNGSLTPTEAVSLAAKILTSHLAMFVNLTEEAQSAQVMVE 238

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L K +EE +LSVRS NCL+  +I  + DL ++TEADM+++ N G+KSL EI
Sbjct: 239 REESHQEKVLDKTIEEFDLSVRSYNCLKRADIQTVKDLTEKTEADMMKVRNLGQKSLDEI 298

Query: 307 KGVLGTMGL 315
           K  L  +G+
Sbjct: 299 KIKLNELGV 307


>gi|289435872|ref|YP_003465744.1| DNA-directed RNA polymerase subunit alpha [Listeria seeligeri
           serovar 1/2b str. SLCC3954]
 gi|315304917|ref|ZP_07875021.1| DNA-directed RNA polymerase, alpha subunit [Listeria ivanovii FSL
           F6-596]
 gi|289172116|emb|CBH28662.1| DNA-directed RNA polymerase subunit alpha [Listeria seeligeri
           serovar 1/2b str. SLCC3954]
 gi|313626708|gb|EFR95737.1| DNA-directed RNA polymerase, alpha subunit [Listeria ivanovii FSL
           F6-596]
 gi|313631790|gb|EFR98970.1| DNA-directed RNA polymerase, alpha subunit [Listeria seeligeri FSL
           N1-067]
 gi|313636142|gb|EFS02005.1| DNA-directed RNA polymerase, alpha subunit [Listeria seeligeri FSL
           S4-171]
          Length = 314

 Score =  257 bits (656), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 130/288 (45%), Positives = 194/288 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG LHE S I+GV ED+T +ILNI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGALHEFSVIEGVVEDVTTMILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +GPGVVTA DI   +D+E+LNPD  I  L  +A   + L  
Sbjct: 83  KKLALKIYSDEEKTLEIDMQGPGVVTAADINYDSDVEILNPDLHIATLSDNAKFHVRLNA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           ++G GY PA  ++ EN PIG++ +D+++SP+ +V+Y VE+ R GQ+ +YDKL+  + TDG
Sbjct: 143 TRGRGYTPADQNKRENMPIGVLPVDSIFSPVIRVNYQVENTRVGQLTNYDKLTFDVLTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI+ E++V+L ++IL + L +F+N  +  ++ +  I  +       L   +EEL+LSVRS
Sbjct: 203 SISPEEAVSLGAKILSEHLSIFVNLTDEAQKAEIMIEKEESHKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++E DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELADKSEDDMMKVRNLGRKSLEEVKVKLADLGLSL 310


>gi|312135468|ref|YP_004002806.1| DNA-directed RNA polymerase subunit alpha [Caldicellulosiruptor
           owensensis OL]
 gi|311775519|gb|ADQ05006.1| DNA-directed RNA polymerase, alpha subunit [Caldicellulosiruptor
           owensensis OL]
          Length = 324

 Score =  257 bits (656), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 137/301 (45%), Positives = 202/301 (67%), Gaps = 2/301 (0%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  T+GNALRR L+SSL GAA+TAV+IDGVLHE S+I GV ED+ +IILN+K
Sbjct: 24  VIEPLERGYGITVGNALRRTLLSSLPGAAVTAVKIDGVLHEFSTIPGVLEDVPEIILNLK 83

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           G+ +KMS    K + I  +G   V A DI+   DIE+ NPDH I  L+ DA + ME+TV+
Sbjct: 84  GLAIKMSSPGPKIMYIEAQGECEVKAKDIKADADIEICNPDHHIATLNQDARLFMEITVN 143

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           +G GYVPA+ ++  N PIG+I +D++Y+P+ KV+Y VE+ R GQV DYDKL+M I T+G+
Sbjct: 144 QGKGYVPAERNKQPNQPIGVIPVDSIYTPVVKVNYKVENTRVGQVTDYDKLTMEIWTNGT 203

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I  ++++ +A++IL +   +F +      +++  +  +    N  L   +EELELSVRS 
Sbjct: 204 IRPDEALTVAAKILIEHFSLFTDLSNIPTKIETVVKQEPPKRNKLLDMTIEELELSVRSY 263

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           NCL+   I  + DL+ +TE +M+++ N G+KSL E+   L ++GL L  +  D  P+  E
Sbjct: 264 NCLKRAGINTVEDLVNKTEEEMMKVRNLGKKSLEEVIQKLHSLGLSLKKS--DSTPKEEE 321

Query: 331 E 331
           E
Sbjct: 322 E 322


>gi|256852062|ref|ZP_05557449.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           27-2-CHN]
 gi|260661369|ref|ZP_05862282.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           115-3-CHN]
 gi|282932823|ref|ZP_06338223.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           208-1]
 gi|297205063|ref|ZP_06922459.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus jensenii
           JV-V16]
 gi|256615474|gb|EEU20664.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           27-2-CHN]
 gi|260547824|gb|EEX23801.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           115-3-CHN]
 gi|281303052|gb|EFA95254.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           208-1]
 gi|297149641|gb|EFH29938.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus jensenii
           JV-V16]
          Length = 313

 Score =  257 bits (656), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 138/312 (44%), Positives = 201/312 (64%), Gaps = 7/312 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +E+     + EPL RGF  TLGN+LRRVL++S+ G A++ +QIDG
Sbjct: 3   EFEKPN----ITVVDQEDAYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTALSYIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T I+LN+K + LK   D  K V +   GP  VTAGD++  +++ V
Sbjct: 59  VLHEFSTIPGVREDVTKIVLNLKKLELKSVADEEKIVELDVEGPATVTAGDLKVDSEVTV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + M++ V  G GYVPA  ++T++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTVAEGGHLHMQIAVKNGRGYVPASENKTDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  DYDKL++ + TDGSIT  D+++ AS+IL +   +F  F + + +   ++ V
Sbjct: 179 ESTRVGKRDDYDKLTLEVWTDGSITPSDALSFASKILIEHFKVF-KFSDAQTDFGGEVMV 237

Query: 248 KSLPFNP--ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           +         L   +EEL+LSVRS NCL+   I  + +L  ++E+DM+R+ N GRKSL E
Sbjct: 238 EKEDDKKERQLEMTIEELDLSVRSYNCLKRAGINTLQELTDKSESDMMRVRNLGRKSLEE 297

Query: 306 IKGVLGTMGLFL 317
           +K  L  +GL L
Sbjct: 298 VKNKLADLGLSL 309


>gi|125975413|ref|YP_001039323.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           thermocellum ATCC 27405]
 gi|158513382|sp|A3DJK1|RPOA_CLOTH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|125715638|gb|ABN54130.1| DNA-directed RNA polymerase subunit alpha [Clostridium thermocellum
           ATCC 27405]
          Length = 315

 Score =  257 bits (656), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 139/312 (44%), Positives = 205/312 (65%), Gaps = 4/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRT-LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           E+ KP  IE +V    E+NR    + EPL RG+  TLGN+LRR+L+SSL G A+T+++ID
Sbjct: 3   EIEKPK-IECVVCS--EDNRYGKFVVEPLERGYGITLGNSLRRILLSSLPGVAVTSIKID 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           G+LHE S+I GV ED+T+IILNIK ++L   G+  K + I   G G V A DI+   D+E
Sbjct: 60  GILHEFSTIPGVIEDVTEIILNIKELSLNFHGEGPKVIYIDAEGEGEVKAKDIKADADVE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +LNP+H I  L  D  + ME+T+ KG GYV A+ ++    PIG+I +D++++P+ KV+YT
Sbjct: 120 ILNPEHKIATLSGDHRLYMEMTIDKGRGYVSAEKNKHPGQPIGVIPVDSIFTPVHKVNYT 179

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+ R GQV DYDKL++ + T+GSI  +++++L ++IL + L +FI+  +  K  +  + 
Sbjct: 180 VENTRVGQVTDYDKLTLEVWTNGSIKPDEAISLGAKILSEHLNLFIDLSDNAKNAEIMVE 239

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L   +EEL+LSVRS NCL+   I  + DLI RTE DM+++ N GRKSL E+
Sbjct: 240 KEETKKEKVLEMTIEELDLSVRSYNCLKRAGINTVEDLISRTEEDMMKVRNLGRKSLEEV 299

Query: 307 KGVLGTMGLFLG 318
              L  +GL L 
Sbjct: 300 VNKLKALGLSLA 311


>gi|302871526|ref|YP_003840162.1| DNA-directed RNA polymerase, alpha subunit [Caldicellulosiruptor
           obsidiansis OB47]
 gi|302574385|gb|ADL42176.1| DNA-directed RNA polymerase, alpha subunit [Caldicellulosiruptor
           obsidiansis OB47]
          Length = 324

 Score =  256 bits (655), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 136/301 (45%), Positives = 202/301 (67%), Gaps = 2/301 (0%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  T+GNALRR L+SSL GAA+TAV+IDGVLHE S+I GV ED+ +IILN+K
Sbjct: 24  VIEPLERGYGITVGNALRRTLLSSLPGAAVTAVKIDGVLHEFSTIPGVLEDVPEIILNLK 83

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           G+ +KMS    K + I  +G   V A DI+   DIE+ NPDH I  L+ DA + ME+TV+
Sbjct: 84  GLAIKMSSPGPKIMYIEAQGECEVKAKDIKADADIEICNPDHHIATLNQDARLFMEITVN 143

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           +G GY+PA+ ++  N PIG+I +D++Y+P+ KV+Y VE+ R GQV DYDKL+M I T+G+
Sbjct: 144 QGKGYIPAERNKQPNQPIGVIPVDSIYTPVVKVNYKVENTRVGQVTDYDKLTMEIWTNGT 203

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I  ++++ +A++IL +   +F +      +++  +  +    N  L   +EELELSVRS 
Sbjct: 204 IRPDEALTIAAKILIEHFNLFTDLSNIPTKIETVVKQEPPKRNKLLDMTIEELELSVRSY 263

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           NCL+   I  + DL+ +TE +M+++ N G+KSL E+   L ++GL L  +  D  P+  E
Sbjct: 264 NCLKRAGINTVEDLVNKTEEEMMKVRNLGKKSLEEVIQKLHSLGLSLKKS--DSTPKEEE 321

Query: 331 E 331
           E
Sbjct: 322 E 322


>gi|146297257|ref|YP_001181028.1| DNA-directed RNA polymerase, alpha subunit [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|166229266|sp|A4XLQ2|RPOA_CALS8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|145410833|gb|ABP67837.1| DNA-directed RNA polymerase subunit alpha [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 324

 Score =  256 bits (655), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 136/301 (45%), Positives = 202/301 (67%), Gaps = 2/301 (0%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  T+GNALRR L+SSL GAA+TAV+IDGVLHE S+I GV ED+ +IILN+K
Sbjct: 24  VIEPLERGYGITIGNALRRTLLSSLPGAAVTAVKIDGVLHEFSTIPGVLEDVPEIILNLK 83

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           G+ +KMS    K + I  +G   V A DI+   DIE+ NP+H I  L+ DA + ME+TV+
Sbjct: 84  GLAIKMSSPGPKVMYIEAQGECEVKAKDIKADADIEICNPEHHIATLNEDARLFMEITVN 143

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           +G GYVPA+ ++  N PIG+I +D++Y+P+ KV+Y VE+ R GQV DYDKL+M I T+G+
Sbjct: 144 QGKGYVPAERNKQSNQPIGVIPVDSIYTPVTKVNYKVENTRVGQVTDYDKLTMEIWTNGT 203

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I  ++++ +A++IL +   +F +      +++  +  +    N  L   +EELELSVRS 
Sbjct: 204 IRPDEALTVAAKILIEHFNLFTDLSNIPTKIETVVKQEPPKRNKLLDMTIEELELSVRSY 263

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           NCL+   I  + DL+ +TE +M+++ N G+KSL E+   L ++GL L  +  D  P+  E
Sbjct: 264 NCLKRAGINTVEDLVNKTEEEMMKVRNLGKKSLEEVIQKLHSLGLSLKKS--DSTPKGEE 321

Query: 331 E 331
           E
Sbjct: 322 E 322


>gi|229009646|ref|ZP_04166872.1| DNA-directed RNA polymerase subunit alpha [Bacillus mycoides DSM
           2048]
 gi|229053983|ref|ZP_04195417.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH603]
 gi|229165125|ref|ZP_04292920.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH621]
 gi|228618388|gb|EEK75418.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH621]
 gi|228721401|gb|EEL72922.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH603]
 gi|228751668|gb|EEM01468.1| DNA-directed RNA polymerase subunit alpha [Bacillus mycoides DSM
           2048]
          Length = 314

 Score =  256 bits (655), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 136/310 (43%), Positives = 206/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L ++ +    +I EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDG
Sbjct: 3   EIEKPK-IETVELNEDAKYGKFVI-EPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T +ILN+K + LK+  +  K + I  +G G+VTA DI   +D+E+
Sbjct: 61  VLHEFSTVEGVVEDVTTMILNLKKLALKIYSEEEKTLEIDVQGEGIVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  +A  RM LT  +G GY PA  +++E+ PIG+I ID++Y+P+ +V+Y V
Sbjct: 121 LNPDLHIATLAKNAHFRMRLTAKRGRGYTPADANKSEDQPIGVIPIDSIYTPVSRVTYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R GQV +YDKL++ + TDGSI  +++++L ++IL + L +F+   +  +  +  +  
Sbjct: 181 EKTRVGQVANYDKLTLDVWTDGSIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 HKLEELGLGL 310


>gi|299820982|ref|ZP_07052871.1| DNA-directed RNA polymerase subunit alpha [Listeria grayi DSM
           20601]
 gi|299818003|gb|EFI85238.1| DNA-directed RNA polymerase subunit alpha [Listeria grayi DSM
           20601]
          Length = 314

 Score =  256 bits (654), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 132/288 (45%), Positives = 193/288 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG LHE S I GV ED+T +ILNI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGALHEFSVIDGVVEDVTTMILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +GPGVVTAGDI   +D+E+LNPD  I  L  +A   + L  
Sbjct: 83  KKLALKIYSDDEKTLEIDVQGPGVVTAGDINYDSDVEILNPDLHIATLSDNAKFHVRLNA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           ++G GY PA  ++ EN PIG++ +D+++SP+ +V+Y VE+ R GQ  +YDKLS  + TDG
Sbjct: 143 TRGRGYTPADLNKHENMPIGVLPVDSIFSPVIRVNYQVENTRVGQSTNYDKLSFDVLTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI+ E++V+L ++IL + L +F+N  +  ++ +  I  +       L   +EEL+LSVRS
Sbjct: 203 SISPEEAVSLGAKILSEHLSIFVNLTDEAQKAEIMIEKEESHKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++E DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELADKSEDDMMKVRNLGRKSLEEVKVKLADLGLSL 310


>gi|169830464|ref|YP_001716446.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Desulforudis
           audaxviator MP104C]
 gi|238688212|sp|B1I1B3|RPOA_DESAP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|169637308|gb|ACA58814.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Desulforudis
           audaxviator MP104C]
          Length = 315

 Score =  256 bits (654), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 133/288 (46%), Positives = 197/288 (68%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + +PL RG+  TLGN+LRRVL++SL GAA+TAV+IDGVLHE SSI GV ED+T++ILN+
Sbjct: 23  FVVDPLERGYGITLGNSLRRVLLASLPGAAVTAVKIDGVLHEFSSIPGVREDVTELILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+ G+  + + I   G G +TAGDI T  D+E+LNPD  I  L+ DA + MELTV
Sbjct: 83  KSLRLKLYGEEDRLMRIEAEGEGRITAGDIITSPDVEILNPDLHIATLEPDARLYMELTV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYVPA+ ++  N  IG+I +D++++P+ KV++TV+  R G   D+DKL+M + TDG
Sbjct: 143 GRGRGYVPAEKNKRGNHVIGVIPVDSIFTPVTKVNFTVDKTRVGHDTDFDKLTMEVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           S+  +++++LA+RI  + L +F+   E    V+  +  +    N  L   +EEL+LSVRS
Sbjct: 203 SLRPDEALSLAARITTEHLRLFVGLTESVNNVEIMVTKEEEKKNKLLEMPIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +LIQR E +M+++ N G+KSL E+   LG +GL L
Sbjct: 263 YNCLKRAGINTVEELIQRNEEEMMKVRNLGKKSLEEVVRKLGELGLDL 310


>gi|16801816|ref|NP_472084.1| DNA-directed RNA polymerase subunit alpha [Listeria innocua
           Clip11262]
 gi|16804644|ref|NP_466129.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           EGD-e]
 gi|46908778|ref|YP_015167.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           str. 4b F2365]
 gi|47093972|ref|ZP_00231706.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           str. 4b H7858]
 gi|47097177|ref|ZP_00234742.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           str. 1/2a F6854]
 gi|116873972|ref|YP_850753.1| DNA-directed RNA polymerase subunit alpha [Listeria welshimeri
           serovar 6b str. SLCC5334]
 gi|217966195|ref|YP_002351873.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           HCC23]
 gi|224499278|ref|ZP_03667627.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           Finland 1988]
 gi|224503600|ref|ZP_03671907.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL R2-561]
 gi|226225152|ref|YP_002759259.1| RNA polymerase (alpha subunit) [Listeria monocytogenes Clip81459]
 gi|254825033|ref|ZP_05230034.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL J1-194]
 gi|254829055|ref|ZP_05233742.1| rpoA [Listeria monocytogenes FSL N3-165]
 gi|254830963|ref|ZP_05235618.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           10403S]
 gi|254854189|ref|ZP_05243537.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL R2-503]
 gi|254899943|ref|ZP_05259867.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           J0161]
 gi|254912851|ref|ZP_05262863.1| rpoA [Listeria monocytogenes J2818]
 gi|254931124|ref|ZP_05264483.1| rpoA [Listeria monocytogenes HPB2262]
 gi|254937231|ref|ZP_05268928.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           F6900]
 gi|254992726|ref|ZP_05274916.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL J2-064]
 gi|255520569|ref|ZP_05387806.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL J1-175]
 gi|284800508|ref|YP_003412373.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           08-5578]
 gi|284993694|ref|YP_003415462.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           08-5923]
 gi|290891791|ref|ZP_06554788.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL J2-071]
 gi|300763643|ref|ZP_07073641.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           FSL N1-017]
 gi|54039273|sp|P66700|RPOA_LISIN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|54042184|sp|P66699|RPOA_LISMO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61215961|sp|Q71WH2|RPOA_LISMF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|123461447|sp|A0ALU2|RPOA_LISW6 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|254765254|sp|B8DB34|RPOA_LISMH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|259494169|sp|C1KZF5|RPOA_LISMC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|16412094|emb|CAD00684.1| rpoA [Listeria monocytogenes EGD-e]
 gi|16415291|emb|CAC97981.1| rpoA [Listeria innocua Clip11262]
 gi|46882051|gb|AAT05344.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           serotype 4b str. F2365]
 gi|47014436|gb|EAL05404.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           str. 1/2a F6854]
 gi|47017633|gb|EAL08432.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           str. 4b H7858]
 gi|116742850|emb|CAK21974.1| DNA-directed RNA polymerase, alpha subunit [Listeria welshimeri
           serovar 6b str. SLCC5334]
 gi|217335465|gb|ACK41259.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           HCC23]
 gi|225877614|emb|CAS06328.1| Putative RNA polymerase (alpha subunit) [Listeria monocytogenes
           serotype 4b str. CLIP 80459]
 gi|258601464|gb|EEW14789.1| rpoA [Listeria monocytogenes FSL N3-165]
 gi|258607581|gb|EEW20189.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL R2-503]
 gi|258609836|gb|EEW22444.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           F6900]
 gi|284056070|gb|ADB67011.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           08-5578]
 gi|284059161|gb|ADB70100.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           08-5923]
 gi|290558385|gb|EFD91902.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL J2-071]
 gi|293582672|gb|EFF94704.1| rpoA [Listeria monocytogenes HPB2262]
 gi|293590849|gb|EFF99183.1| rpoA [Listeria monocytogenes J2818]
 gi|293594275|gb|EFG02036.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL J1-194]
 gi|300515920|gb|EFK42969.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           FSL N1-017]
 gi|307572195|emb|CAR85374.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           L99]
 gi|328468090|gb|EGF39096.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           1816]
 gi|328469778|gb|EGF40695.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           220]
          Length = 314

 Score =  256 bits (654), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 130/288 (45%), Positives = 193/288 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG LHE S I+GV ED+T +ILNI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGALHEFSVIEGVVEDVTTMILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +GPGVVTA DI   +D+E+LNPD  I  L  +A   + L  
Sbjct: 83  KKLALKIYSDEEKTLEIDMQGPGVVTAADINYDSDVEILNPDLHIATLSDNAKFHVRLNA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           ++G GY PA  ++ EN PIG++ +D+++SP+ +V+Y VE+ R GQ  +YDKL+  + TDG
Sbjct: 143 TRGRGYTPADQNKRENMPIGVLPVDSIFSPVIRVNYQVENTRVGQSTNYDKLTFDVLTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI+ E++V+L ++IL + L +F+N  +  ++ +  I  +       L   +EEL+LSVRS
Sbjct: 203 SISPEEAVSLGAKILSEHLSIFVNLTDEAQKAEIMIEKEESHKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++E DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELADKSEDDMMKVRNLGRKSLEEVKVKLADLGLSL 310


>gi|288870169|ref|ZP_06113169.2| DNA-directed RNA polymerase, alpha subunit [Clostridium hathewayi
           DSM 13479]
 gi|288868138|gb|EFD00437.1| DNA-directed RNA polymerase, alpha subunit [Clostridium hathewayi
           DSM 13479]
          Length = 347

 Score =  256 bits (654), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 132/292 (45%), Positives = 198/292 (67%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDGVLHE SSI GV ED+T+II+NI
Sbjct: 48  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDGVLHEFSSIPGVKEDVTEIIMNI 107

Query: 90  KGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K + D++  K   I   G GVVTA DIQ   DIE++NPD VI  L    D+   M
Sbjct: 108 KSLAIKNNSDTNEAKVAYIEFEGEGVVTAADIQADPDIEIMNPDQVIATLSGGTDSKFYM 167

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++KG GYV A  +++E+ PIG+I +D++Y+P+++V+ TV++ R GQV D+DKL++ +
Sbjct: 168 ELTITKGRGYVSADKNKSEDLPIGVIAVDSIYTPVERVNMTVQNTRVGQVTDFDKLTLDV 227

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            TDG++  +++V+LA+++L + L +FI+  E  K  +  +  +       L   ++ELEL
Sbjct: 228 YTDGTLAPDEAVSLAAKVLSEHLNLFIDLSENAKTAEVMVEKEDNEKEKVLEMNIDELEL 287

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L
Sbjct: 288 SVRSYNCLKRAGINTVEELCNRTSEDMMKVRNLGRKSLEEVLAKLKELGLQL 339


>gi|189308773|gb|ACD87088.1| RpoA [Vibrio sp. PP-204]
          Length = 295

 Score =  256 bits (654), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 131/284 (46%), Positives = 195/284 (68%), Gaps = 8/284 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 15  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 74

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 75  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEITNPEHVICHLTDGNAEIAMRIKVE 134

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 135 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMET 194

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 195 NGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 251

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL 
Sbjct: 252 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKNVLA 295


>gi|257454071|ref|ZP_05619345.1| DNA-directed RNA polymerase, alpha subunit [Enhydrobacter
           aerosaccus SK60]
 gi|257448549|gb|EEV23518.1| DNA-directed RNA polymerase, alpha subunit [Enhydrobacter
           aerosaccus SK60]
          Length = 335

 Score =  256 bits (654), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 144/332 (43%), Positives = 215/332 (64%), Gaps = 18/332 (5%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           N  E + PN I    + +     TL   EPL RGF HTLGNALRR+L+SSL GAA+   +
Sbjct: 4   NATEFLTPNAIHVDTVNETHAKVTL---EPLERGFGHTLGNALRRILLSSLPGAAVIEAE 60

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           I+GV HE S+++G+ ED+ D++LN+KG+ +++   +   +T+ K+GPG V A DI+  ++
Sbjct: 61  IEGVDHEYSTLEGLQEDVLDLLLNLKGLAIQLHDQNEVFLTLDKQGPGTVLASDIELPHN 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKK 182
           +E++NPD V+  L     ++M L V+ G GY PA  +    +N  IG + +DA YSPI +
Sbjct: 121 VEIINPDLVLGTLSDRGHLKMRLRVAVGRGYEPANVRKDSGDNKVIGRLKLDASYSPILR 180

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-----EP 237
           V+Y VE+AR  Q  D D+L + ++T+G+I  E+++  A+ ILQ Q+ +F++ E     EP
Sbjct: 181 VAYQVENARVEQRTDLDRLVIELETNGTIDPEEAIRKAATILQQQIAVFVDLEAEATPEP 240

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            KE +E         +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N
Sbjct: 241 VKEKEE--------VDPVLLRPVDDLELTVRSANCLKAENIYYIGDLVQRTETELLKTPN 292

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            G+KSL EIK VL +  L LGM L +WPP  +
Sbjct: 293 LGKKSLTEIKDVLASKDLELGMRLENWPPADL 324


>gi|227530231|ref|ZP_03960280.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus vaginalis
           ATCC 49540]
 gi|227349906|gb|EEJ40197.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus vaginalis
           ATCC 49540]
          Length = 314

 Score =  256 bits (654), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 139/310 (44%), Positives = 205/310 (66%), Gaps = 6/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E ++    + EPL RG+  TLGN+LRRVL++SL GAAIT++QIDG
Sbjct: 3   EFEKPN----IHKVEETDSYGKFVVEPLERGYGTTLGNSLRRVLLASLPGAAITSIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K ++LK+  +  K + I  +GP  VTAGDIQ   ++EV
Sbjct: 59  VLHEFSTVEGVTEDVTQIILNLKKVSLKLDSEEQKDLEIDVKGPAEVTAGDIQGDGEVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSY 185
           LNPD  I  +   A + +++T  KG GY+ A  ++   D   IG++ ID++Y+PI++V+Y
Sbjct: 119 LNPDLYIATVADGAELHIKMTADKGRGYLSANDNKARMDDLAIGVLPIDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVE+AR GQ  DYDKL++ + TDGS+T  ++V+L ++IL + L MF+N  E  +  +  +
Sbjct: 179 TVENARVGQRNDYDKLTLDVWTDGSLTPTEAVSLGAKILTEHLAMFVNLTEEAQNAQVMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   +EEL+LSVRS NCL+   I  + +L  RTEADM+++ N G+KSL E
Sbjct: 239 EKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVKELTDRTEADMMKVRNLGQKSLEE 298

Query: 306 IKGVLGTMGL 315
           IK  L  +G+
Sbjct: 299 IKLKLNDLGV 308


>gi|208659512|gb|ACI31186.1| RpoA [Vibrio breoganii]
 gi|208659514|gb|ACI31187.1| RpoA [Vibrio breoganii]
 gi|208659516|gb|ACI31188.1| RpoA [Vibrio breoganii]
          Length = 302

 Score =  256 bits (654), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 132/284 (46%), Positives = 195/284 (68%), Gaps = 8/284 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   K     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEK---EEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL 
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLA 302


>gi|238855094|ref|ZP_04645422.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           269-3]
 gi|260664879|ref|ZP_05865730.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           SJ-7A-US]
 gi|282931913|ref|ZP_06337385.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           208-1]
 gi|313472571|ref|ZP_07813060.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           1153]
 gi|238832338|gb|EEQ24647.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           269-3]
 gi|239530011|gb|EEQ69012.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           1153]
 gi|260561362|gb|EEX27335.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           SJ-7A-US]
 gi|281303965|gb|EFA96095.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           208-1]
          Length = 313

 Score =  256 bits (653), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 137/312 (43%), Positives = 201/312 (64%), Gaps = 7/312 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +E+     + EPL RGF  TLGN+LRRVL++S+ G A++ +QIDG
Sbjct: 3   EFEKPN----ITVVDQEDAYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTALSYIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T I+LN+K + LK   D  K V +   GP  VTAGD++  +++ V
Sbjct: 59  VLHEFSTVPGVREDVTKIVLNLKKLELKSIADEEKIVELDVEGPATVTAGDLKVDSEVTV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + M++ V  G GYVPA  ++T++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTVAEGGHLHMQIAVKNGRGYVPASENKTDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  DYDKL++ + TDGSIT  D+++ AS+IL +   +F  F + + +   ++ V
Sbjct: 179 ESTRVGKKDDYDKLTLEVWTDGSITPSDALSFASKILIEHFKVF-KFSDAQTDFGGEVMV 237

Query: 248 KSLPFNP--ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           +         L   +EEL+LSVRS NCL+   I  + +L  ++E+DM+R+ N GRKSL E
Sbjct: 238 EKEDDKKERQLEMTIEELDLSVRSYNCLKRAGINTLQELTDKSESDMMRVRNLGRKSLEE 297

Query: 306 IKGVLGTMGLFL 317
           +K  L  +GL L
Sbjct: 298 VKNKLADLGLSL 309


>gi|179184670|gb|ACB78156.1| RNA polymerase alpha subunit [Vibrio rarus]
          Length = 301

 Score =  256 bits (653), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 134/290 (46%), Positives = 198/290 (68%), Gaps = 8/290 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I  VLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 15  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIGSVLHEYSTKEGVQEDILEILLNLKGL 74

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 75  AVRVAEGKDDVLITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNADIAMRIKVE 134

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ +++Y+V +AR  Q  D DKL + ++T
Sbjct: 135 RGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDQIAYSVAAARVEQRTDLDKLVIDMET 194

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +  V+E I  K   F+P LL+ V++LEL+V
Sbjct: 195 NGTLEPEEAIRRAATILAEQLDAFVDLRDVR--VQEPIEEKP-EFDPILLRPVDDLELTV 251

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + G  L
Sbjct: 252 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGXSL 301


>gi|52078637|ref|YP_077428.1| DNA-directed RNA polymerase subunit alpha [Bacillus licheniformis
           ATCC 14580]
 gi|52783999|ref|YP_089828.1| DNA-directed RNA polymerase subunit alpha [Bacillus licheniformis
           ATCC 14580]
 gi|319649088|ref|ZP_08003296.1| DNA-directed RNA polymerase subunit alpha [Bacillus sp. BT1B_CT2]
 gi|81667225|sp|Q65P79|RPOA_BACLD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|52001848|gb|AAU21790.1| RNA polymerase (alpha subunit) [Bacillus licheniformis ATCC 14580]
 gi|52346501|gb|AAU39135.1| RpoA [Bacillus licheniformis ATCC 14580]
 gi|317388788|gb|EFV69607.1| DNA-directed RNA polymerase subunit alpha [Bacillus sp. BT1B_CT2]
          Length = 314

 Score =  256 bits (653), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 130/288 (45%), Positives = 193/288 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTTIILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  +G GVVTA DI   +D+E+LNPD  I  L  +A  R+ LT 
Sbjct: 83  KKLALKIYSEEEKTLEIDVQGEGVVTAADITHDSDVEILNPDLHIATLGQNASFRVRLTA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY PA  ++ ++ PIG+I ID++++P+ +VSY VE+ R GQ+ +YDKL++ + TDG
Sbjct: 143 QRGRGYTPADANKRDDQPIGVIPIDSIFTPVSRVSYQVENTRVGQITNYDKLTLDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           S   ++++AL S+IL + L +F+   +  +  +  +  +       L   +EEL+LSVRS
Sbjct: 203 STGPKEAIALGSKILTEHLNIFVGLTDEAQHAEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGL 310


>gi|313606573|gb|EFR83374.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           FSL F2-208]
          Length = 314

 Score =  256 bits (653), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 129/288 (44%), Positives = 193/288 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG LHE S I+GV ED+T +ILNI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGALHEFSVIEGVVEDVTTMILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +GPG+VTA DI   +D+E+LNPD  I  L  +A   + L  
Sbjct: 83  KKLALKIYSDEEKTLEIDMQGPGIVTAADINYDSDVEILNPDLHIATLSDNAKFHVRLNA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           ++G GY PA  ++ EN PIG++ +D+++SP+ +V+Y VE+ R GQ  +YDKL+  + TDG
Sbjct: 143 TRGRGYTPADQNKRENMPIGVLPVDSIFSPVIRVNYQVENTRVGQSTNYDKLTFDVLTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI+ E++V+L ++IL + L +F+N  +  ++ +  I  +       L   +EEL+LSVRS
Sbjct: 203 SISPEEAVSLGAKILSEHLSIFVNLTDEAQKAEIMIEKEESHKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++E DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELADKSEDDMMKVRNLGRKSLEEVKVKLADLGLSL 310


>gi|257876158|ref|ZP_05655811.1| DNA directed RNA polymerase [Enterococcus casseliflavus EC20]
 gi|257810324|gb|EEV39144.1| DNA directed RNA polymerase [Enterococcus casseliflavus EC20]
          Length = 312

 Score =  255 bits (652), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 133/295 (45%), Positives = 195/295 (66%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E+++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+
Sbjct: 14  EDKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDV 73

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             IILNIKG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  IC +   A 
Sbjct: 74  AQIILNIKGLALKMYGDEEKTLEIDISGPATVTAGDIIVDSDVEILNKDMYICTVSEGAT 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
               LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+
Sbjct: 134 FHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLT 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           M I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 194 MEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEE 253

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E+K  L  +GL L
Sbjct: 254 LDLSVRSYNCLKRAGINTVQELTNKSEPEMIKVRNLGRKSLEEVKVKLHDLGLGL 308


>gi|293393287|ref|ZP_06637601.1| DNA-directed RNA polymerase subunit alpha [Serratia odorifera DSM
           4582]
 gi|291424197|gb|EFE97412.1| DNA-directed RNA polymerase subunit alpha [Serratia odorifera DSM
           4582]
          Length = 334

 Score =  255 bits (652), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 135/311 (43%), Positives = 204/311 (65%), Gaps = 12/311 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENAAISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 293

Query: 297 NFGRKSLVEIK 307
           N G+  L  +K
Sbjct: 294 NLGKNLLPRLK 304


>gi|225376438|ref|ZP_03753659.1| hypothetical protein ROSEINA2194_02080 [Roseburia inulinivorans DSM
           16841]
 gi|225211814|gb|EEG94168.1| hypothetical protein ROSEINA2194_02080 [Roseburia inulinivorans DSM
           16841]
          Length = 319

 Score =  255 bits (652), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 132/292 (45%), Positives = 198/292 (67%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDGVLHE SSI GV ED+T+II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDGVLHEFSSIPGVKEDVTEIIMNI 82

Query: 90  KGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + ++   S D  K   I   G GVVTA DIQ  +DI++LNPD VI NL+   D  + M
Sbjct: 83  KELAIRNNSSSDEPKVAYIEFEGEGVVTAADIQVDSDIQILNPDLVIANLNGGADCKLYM 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++KG GYV +  ++TE+ PIG+I ID++Y+P+++V+ ++E+ R GQ+ DYDKL++ +
Sbjct: 143 ELTITKGRGYVSSDKNKTEDTPIGVIAIDSIYTPVERVNLSIENTRVGQITDYDKLTLDV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L +FI+  E  ++    I          L   ++ELEL
Sbjct: 203 YTNGTLEPDEAVSLAAKVLSEHLNLFIDLSEAAQQADVMIEKADDAKEKVLEMNIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L
Sbjct: 263 SVRSFNCLKRAGINTVEELTNRTPEDMMKVRNLGRKSLEEVLAKLKELGLQL 314


>gi|167629496|ref|YP_001679995.1| DNA-directed RNA polymerase, alpha subunit [Heliobacterium
           modesticaldum Ice1]
 gi|238687877|sp|B0TC85|RPOA_HELMI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|167592236|gb|ABZ83984.1| DNA-directed RNA polymerase, alpha subunit [Heliobacterium
           modesticaldum Ice1]
          Length = 314

 Score =  255 bits (652), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 130/288 (45%), Positives = 191/288 (66%), Gaps = 1/288 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L++SL GAA+T+V+I+GVLHE S+I GV ED TDIILN+
Sbjct: 23  FVVEPLERGYGVTLGNSLRRILLTSLFGAAVTSVKIEGVLHEFSTIPGVVEDTTDIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + +KM  +  + + +   G GVVTA DI T  D+E+LNPD VI  +D   +  ME+TV
Sbjct: 83  KQLAIKMHTEESRTIRVEFEGEGVVTAADILTDADVEILNPDQVIATVDKGRLF-MEITV 141

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            K  GY+ A  HR     IG+I IDA +SP++KV+Y VE  R GQ+ +YD+L + + T+G
Sbjct: 142 EKSRGYITATKHRKSEHAIGVIPIDANFSPVRKVNYRVEDTRVGQITNYDRLILEVWTNG 201

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           S+T E++++ +++I+ D L +F+   E  + V+  +  +  P +  L   +EEL+LSVRS
Sbjct: 202 SLTPEEAISWSAKIMNDYLKLFVALTENTENVEIMVETEERPQDKILEMTIEELDLSVRS 261

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL  +TE DM+++ N GRKSL E+   L  +GL L
Sbjct: 262 YNCLKRAGINTVKDLTNKTEEDMIKVRNLGRKSLEEVDAKLAALGLSL 309


>gi|189308769|gb|ACD87086.1| RpoA [Vibrio sp. PP-203]
          Length = 295

 Score =  255 bits (652), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 131/283 (46%), Positives = 195/283 (68%), Gaps = 8/283 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 16  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 75

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 76  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEITNPEHVICHLTDGNAEIAMRIKVE 135

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 136 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMET 195

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 196 NGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 252

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL
Sbjct: 253 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVL 295


>gi|16077211|ref|NP_388024.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|221307956|ref|ZP_03589803.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|221312277|ref|ZP_03594082.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis subsp.
           subtilis str. NCIB 3610]
 gi|221317211|ref|ZP_03598505.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis subsp.
           subtilis str. JH642]
 gi|221321474|ref|ZP_03602768.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis subsp.
           subtilis str. SMY]
 gi|296333140|ref|ZP_06875594.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305672843|ref|YP_003864514.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|321313815|ref|YP_004206102.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis BSn5]
 gi|133395|sp|P20429|RPOA_BACSU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|142463|gb|AAA22217.1| RNA polymerase alpha-core-subunit [Bacillus subtilis]
 gi|1044991|gb|AAB06826.1| RNA polymerase alpha-core-subunit [Bacillus subtilis]
 gi|2632410|emb|CAB11919.1| RNA polymerase (alpha subunit) [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|116733896|gb|ABK20007.1| DNA-directed RNA polymerase alpha subunit [synthetic construct]
 gi|291482515|dbj|BAI83590.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis subsp.
           natto BEST195]
 gi|296149756|gb|EFG90651.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305411086|gb|ADM36204.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|320020089|gb|ADV95075.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis BSn5]
          Length = 314

 Score =  255 bits (652), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 131/288 (45%), Positives = 192/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IIL+I
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTTIILHI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +G G VTA DI   +D+E+LNPD  I  L  +A  R+ LT 
Sbjct: 83  KKLALKIYSDEEKTLEIDVQGEGTVTAADITHDSDVEILNPDLHIATLGENASFRVRLTA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY PA  ++ ++ PIG+I ID++Y+P+ +VSY VE+ R GQV +YDKL++ + TDG
Sbjct: 143 QRGRGYTPADANKRDDQPIGVIPIDSIYTPVSRVSYQVENTRVGQVANYDKLTLDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           S   ++++AL S+IL + L +F+   +  +  +  +  +       L   +EEL+LSVRS
Sbjct: 203 STGPKEAIALGSKILTEHLNIFVGLTDEAQHAEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGL 310


>gi|223933080|ref|ZP_03625073.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus suis
           89/1591]
 gi|223898267|gb|EEF64635.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus suis
           89/1591]
          Length = 312

 Score =  255 bits (652), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 133/290 (45%), Positives = 199/290 (68%), Gaps = 4/290 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL++SL GAA+T+++IDGVLHE  ++ GV ED+  IILNI
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNI 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KGI +K   +  K++ +   GP  VTAGDI T +DIE++NPDH +  +   A  +  LTV
Sbjct: 81  KGIAVKSYVEDEKKIELDVVGPAEVTAGDILTDSDIEIVNPDHYLFTIADGATFKAVLTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           + G GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I+T+G
Sbjct: 141 NSGRGYVPAEDNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTLEINTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK--EVKEDINVKSLPFNPALLKKVEELELSV 267
           +I  ED++ L++RIL + LG+F +  E  K  EV ++  V S   +  L + +EEL+LSV
Sbjct: 201 TIVPEDTLGLSARILMEHLGLFTDLTEVAKSAEVMKEAEVAS--DDRMLDRTIEELDLSV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+   I  + DL ++TE +M+++ N GRKSL E+K  L  +GL L
Sbjct: 259 RSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVKVKLADLGLGL 308


>gi|330831946|ref|YP_004400771.1| DNA-directed RNA polymerase subunit alpha [Streptococcus suis ST3]
 gi|329306169|gb|AEB80585.1| DNA-directed RNA polymerase subunit alpha [Streptococcus suis ST3]
          Length = 312

 Score =  255 bits (652), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 133/290 (45%), Positives = 199/290 (68%), Gaps = 4/290 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL++SL GAA+T+++IDGVLHE  ++ GV ED+  IILNI
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNI 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KGI +K   +  K++ +   GP  VTAGDI T +DIE++NPDH +  +   A  +  LTV
Sbjct: 81  KGIAVKSYVEDEKKIELDVVGPAEVTAGDILTDSDIEIVNPDHYLFTIADGATFKAVLTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           + G GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I+T+G
Sbjct: 141 NSGRGYVPAEDNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTLEINTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK--EVKEDINVKSLPFNPALLKKVEELELSV 267
           +I  ED++ L++RIL + LG+F +  E  K  EV ++  V S   +  L + +EEL+LSV
Sbjct: 201 TIVPEDALGLSARILMEHLGLFTDLTEVAKSAEVMKEAEVAS--DDRMLDRTIEELDLSV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+   I  + DL ++TE +M+++ N GRKSL E+K  L  +GL L
Sbjct: 259 RSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVKVKLADLGLGL 308


>gi|288554753|ref|YP_003426688.1| DNA-directed RNA polymerase subunit alpha [Bacillus pseudofirmus
           OF4]
 gi|288545913|gb|ADC49796.1| DNA-directed RNA polymerase subunit alpha [Bacillus pseudofirmus
           OF4]
          Length = 314

 Score =  255 bits (651), Expect = 7e-66,   Method: Compositional matrix adjust.
 Identities = 138/310 (44%), Positives = 205/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KPN IE + +  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQID 
Sbjct: 3   EIEKPN-IETVEVS-EDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDS 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IILN+K + LK+  D  K + +  +G GVVTAGD+   +DIEV
Sbjct: 61  VLHEFSTIEGVVEDVTTIILNLKKLALKIYSDEEKTLEVDVQGEGVVTAGDLTHDSDIEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L   A   M LT  +G GY  A+ ++ ++ PIG++ ID++Y+P+ +V+Y V
Sbjct: 121 LNPDLHIATLAKGAHFHMRLTAKRGRGYALAEGNKNDDQPIGVLPIDSIYTPVSRVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV +YDKL++ + TDGSI  E++V+L ++IL + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQVTNYDKLTLDVWTDGSIRPEEAVSLGAKILTEHLNIFVGLTDQAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L Q++E DM+++ N GRKSL E++
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTQKSEEDMMKVRNLGRKSLEEVQ 300

Query: 308 GVLGTMGLFL 317
             LG +GL L
Sbjct: 301 EKLGELGLGL 310


>gi|146317755|ref|YP_001197467.1| DNA-directed RNA polymerase subunit alpha [Streptococcus suis
           05ZYH33]
 gi|146319946|ref|YP_001199657.1| DNA-directed RNA polymerase subunit alpha [Streptococcus suis
           98HAH33]
 gi|253751015|ref|YP_003024156.1| DNA-directed RNA polymerase alpha chain [Streptococcus suis SC84]
 gi|253752915|ref|YP_003026055.1| DNA-directed RNA polymerase alpha chain [Streptococcus suis P1/7]
 gi|253754740|ref|YP_003027880.1| DNA-directed RNA polymerase alpha chain [Streptococcus suis BM407]
 gi|158514125|sp|A4VSH8|RPOA_STRSY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158514142|sp|A4VYR8|RPOA_STRS2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|145688561|gb|ABP89067.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Streptococcus suis 05ZYH33]
 gi|145690752|gb|ABP91257.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Streptococcus suis 98HAH33]
 gi|251815304|emb|CAZ50872.1| DNA-directed RNA polymerase alpha chain [Streptococcus suis SC84]
 gi|251817204|emb|CAZ54927.1| DNA-directed RNA polymerase alpha chain [Streptococcus suis BM407]
 gi|251819160|emb|CAR44293.1| DNA-directed RNA polymerase alpha chain [Streptococcus suis P1/7]
 gi|292557557|gb|ADE30558.1| DNA-directed RNA polymerase alpha subunit [Streptococcus suis GZ1]
 gi|319757266|gb|ADV69208.1| DNA-directed RNA polymerase subunit alpha [Streptococcus suis JS14]
          Length = 312

 Score =  255 bits (651), Expect = 7e-66,   Method: Compositional matrix adjust.
 Identities = 133/290 (45%), Positives = 199/290 (68%), Gaps = 4/290 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL++SL GAA+T+++IDGVLHE  ++ GV ED+  IILNI
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNI 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KGI +K   +  K++ +   GP  VTAGDI T +DIE++NPDH +  +   A  +  LTV
Sbjct: 81  KGIAVKSYVEDEKKIELDVVGPAEVTAGDILTDSDIEIVNPDHYLFTIADGATFKAVLTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           + G GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I+T+G
Sbjct: 141 NSGRGYVPAEDNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTLEINTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK--EVKEDINVKSLPFNPALLKKVEELELSV 267
           +I  ED++ L++RIL + LG+F +  E  K  EV ++  V S   +  L + +EEL+LSV
Sbjct: 201 TIIPEDALGLSARILMEHLGLFTDLTEVAKSAEVMKEAEVAS--DDRMLDRTIEELDLSV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+   I  + DL ++TE +M+++ N GRKSL E+K  L  +GL L
Sbjct: 259 RSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVKVKLADLGLGL 308


>gi|40063201|gb|AAR38038.1| DNA-directed RNA polymerase, alpha subunit [uncultured marine
           bacterium 562]
          Length = 321

 Score =  255 bits (651), Expect = 8e-66,   Method: Compositional matrix adjust.
 Identities = 136/303 (44%), Positives = 201/303 (66%), Gaps = 7/303 (2%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           N + +  EPL RGF HTLGNALRR+L+SS+ GAA+T V IDG+ HE S+I+GV ED+ DI
Sbjct: 22  NLSKITLEPLERGFGHTLGNALRRILLSSMPGAAVTDVAIDGISHEYSTIEGVREDVIDI 81

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV-VR 144
           +LNIK + + +   +   +T+   GP  V A       ++E++N D  +  + VD V ++
Sbjct: 82  LLNIKDMPVNIIEGNTAEITLDVTGPCDVLASSFDVPGNVELVNQDFHVATI-VDKVNLK 140

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           M LTV  G GY PA     E+  +G + +DA YSP+++VSYTV++AR  +  D DKL + 
Sbjct: 141 MTLTVQTGRGYEPADTRDDEDRVVGALKVDASYSPVRRVSYTVDNARFEKRTDLDKLVIE 200

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEE-PKKEVKEDINVKSLPFNPALLKKVEEL 263
           ++TDG++  + ++  ++ ILQ QL  F++ +   ++E K+D N     F+P LL+ +EEL
Sbjct: 201 LETDGTLDPKMAIEHSATILQQQLSSFVDLDAIAEQEAKKDQN----DFDPFLLRSIEEL 256

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           EL+VRSTNCL+ E+I  +GDLI R+E D+L+  N G+KSL EIK VL +  L LGMN+ +
Sbjct: 257 ELTVRSTNCLKAESIFLIGDLIHRSEFDLLKTPNLGKKSLNEIKDVLASKELSLGMNVDN 316

Query: 324 WPP 326
           WPP
Sbjct: 317 WPP 319


>gi|227520018|ref|ZP_03950067.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           TX0104]
 gi|227555879|ref|ZP_03985926.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           HH22]
 gi|229546938|ref|ZP_04435663.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           TX1322]
 gi|229550527|ref|ZP_04439252.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           ATCC 29200]
 gi|255971735|ref|ZP_05422321.1| DNA-directed RNA polymerase [Enterococcus faecalis T1]
 gi|255974735|ref|ZP_05425321.1| DNA-directed RNA polymerase [Enterococcus faecalis T2]
 gi|256762030|ref|ZP_05502610.1| DNA-directed RNA polymerase [Enterococcus faecalis T3]
 gi|256855189|ref|ZP_05560550.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           T8]
 gi|256956836|ref|ZP_05561007.1| DNA-directed RNA polymerase [Enterococcus faecalis DS5]
 gi|256960643|ref|ZP_05564814.1| DNA-directed RNA polymerase [Enterococcus faecalis Merz96]
 gi|256964158|ref|ZP_05568329.1| DNA-directed RNA polymerase [Enterococcus faecalis HIP11704]
 gi|257078506|ref|ZP_05572867.1| DNA-directed RNA polymerase [Enterococcus faecalis JH1]
 gi|257081523|ref|ZP_05575884.1| DNA-directed RNA polymerase [Enterococcus faecalis E1Sol]
 gi|257084171|ref|ZP_05578532.1| DNA-directed RNA polymerase [Enterococcus faecalis Fly1]
 gi|257087998|ref|ZP_05582359.1| DNA-directed RNA polymerase [Enterococcus faecalis D6]
 gi|257088675|ref|ZP_05583036.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           CH188]
 gi|257417601|ref|ZP_05594595.1| DNA-directed RNA polymerase [Enterococcus faecalis AR01/DG]
 gi|257418673|ref|ZP_05595667.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           T11]
 gi|257421525|ref|ZP_05598515.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           X98]
 gi|293382732|ref|ZP_06628657.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           R712]
 gi|293388085|ref|ZP_06632613.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           S613]
 gi|294781077|ref|ZP_06746428.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           PC1.1]
 gi|300861766|ref|ZP_07107846.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TUSoD Ef11]
 gi|307269113|ref|ZP_07550474.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX4248]
 gi|307274197|ref|ZP_07555405.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0855]
 gi|307276422|ref|ZP_07557545.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX2134]
 gi|307278632|ref|ZP_07559702.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0860]
 gi|307286988|ref|ZP_07567063.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0109]
 gi|307291671|ref|ZP_07571546.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0411]
 gi|312901096|ref|ZP_07760384.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0470]
 gi|312904658|ref|ZP_07763813.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0635]
 gi|312908627|ref|ZP_07767569.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           DAPTO 512]
 gi|312909225|ref|ZP_07768082.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           DAPTO 516]
 gi|312952633|ref|ZP_07771497.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0102]
 gi|227072566|gb|EEI10529.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           TX0104]
 gi|227175046|gb|EEI56018.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           HH22]
 gi|229304246|gb|EEN70242.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           ATCC 29200]
 gi|229307866|gb|EEN73853.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           TX1322]
 gi|255962753|gb|EET95229.1| DNA-directed RNA polymerase [Enterococcus faecalis T1]
 gi|255967607|gb|EET98229.1| DNA-directed RNA polymerase [Enterococcus faecalis T2]
 gi|256683281|gb|EEU22976.1| DNA-directed RNA polymerase [Enterococcus faecalis T3]
 gi|256709702|gb|EEU24749.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           T8]
 gi|256947332|gb|EEU63964.1| DNA-directed RNA polymerase [Enterococcus faecalis DS5]
 gi|256951139|gb|EEU67771.1| DNA-directed RNA polymerase [Enterococcus faecalis Merz96]
 gi|256954654|gb|EEU71286.1| DNA-directed RNA polymerase [Enterococcus faecalis HIP11704]
 gi|256986536|gb|EEU73838.1| DNA-directed RNA polymerase [Enterococcus faecalis JH1]
 gi|256989553|gb|EEU76855.1| DNA-directed RNA polymerase [Enterococcus faecalis E1Sol]
 gi|256992201|gb|EEU79503.1| DNA-directed RNA polymerase [Enterococcus faecalis Fly1]
 gi|256996028|gb|EEU83330.1| DNA-directed RNA polymerase [Enterococcus faecalis D6]
 gi|256997487|gb|EEU84007.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           CH188]
 gi|257159429|gb|EEU89389.1| DNA-directed RNA polymerase [Enterococcus faecalis ARO1/DG]
 gi|257160501|gb|EEU90461.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           T11]
 gi|257163349|gb|EEU93309.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           X98]
 gi|291079892|gb|EFE17256.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           R712]
 gi|291082536|gb|EFE19499.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           S613]
 gi|294451880|gb|EFG20331.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           PC1.1]
 gi|295112524|emb|CBL31161.1| DNA-directed RNA polymerase subunit alpha [Enterococcus sp. 7L76]
 gi|300848291|gb|EFK76048.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TUSoD Ef11]
 gi|306497290|gb|EFM66832.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0411]
 gi|306501934|gb|EFM71223.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0109]
 gi|306504692|gb|EFM73892.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0860]
 gi|306506902|gb|EFM76049.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX2134]
 gi|306509159|gb|EFM78221.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0855]
 gi|306514593|gb|EFM83147.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX4248]
 gi|310625414|gb|EFQ08697.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           DAPTO 512]
 gi|310629421|gb|EFQ12704.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0102]
 gi|310632010|gb|EFQ15293.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0635]
 gi|311290467|gb|EFQ69023.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           DAPTO 516]
 gi|311291768|gb|EFQ70324.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0470]
 gi|315026809|gb|EFT38741.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX2137]
 gi|315028850|gb|EFT40782.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX4000]
 gi|315031165|gb|EFT43097.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0017]
 gi|315035989|gb|EFT47921.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0027]
 gi|315145362|gb|EFT89378.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX2141]
 gi|315147145|gb|EFT91161.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX4244]
 gi|315151097|gb|EFT95113.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0012]
 gi|315153583|gb|EFT97599.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0031]
 gi|315156237|gb|EFU00254.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0043]
 gi|315158618|gb|EFU02635.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0312]
 gi|315160753|gb|EFU04770.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0645]
 gi|315165876|gb|EFU09893.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX1302]
 gi|315168126|gb|EFU12143.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX1341]
 gi|315171434|gb|EFU15451.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX1342]
 gi|315172668|gb|EFU16685.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX1346]
 gi|315573540|gb|EFU85731.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0309B]
 gi|315579352|gb|EFU91543.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0630]
 gi|315582112|gb|EFU94303.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0309A]
 gi|323479448|gb|ADX78887.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           62]
 gi|327534030|gb|AEA92864.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           OG1RF]
 gi|329577723|gb|EGG59149.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX1467]
          Length = 312

 Score =  254 bits (650), Expect = 9e-66,   Method: Compositional matrix adjust.
 Identities = 134/296 (45%), Positives = 197/296 (66%), Gaps = 2/296 (0%)

Query: 24  EENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +ENR     + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+I GV ED
Sbjct: 13  DENRDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIPGVRED 72

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILNIKG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D VIC++   A
Sbjct: 73  VTQIILNIKGLALKLYAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLVICSVAEGA 132

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
                LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL
Sbjct: 133 TFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKL 192

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           +M I TDGSI  +++++LA++I+ + L +F+N  +  K  +  +  +       L   +E
Sbjct: 193 TMEIWTDGSIIPQEALSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIE 252

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           EL+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E+K  L  +GL L
Sbjct: 253 ELDLSVRSYNCLKRAGINTVQELTNKSEPEMIKVRNLGRKSLEEVKLKLHDLGLGL 308


>gi|256618354|ref|ZP_05475200.1| DNA-directed RNA polymerase [Enterococcus faecalis ATCC 4200]
 gi|256597881|gb|EEU17057.1| DNA-directed RNA polymerase [Enterococcus faecalis ATCC 4200]
          Length = 312

 Score =  254 bits (650), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 134/296 (45%), Positives = 197/296 (66%), Gaps = 2/296 (0%)

Query: 24  EENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +ENR     + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+I GV ED
Sbjct: 13  DENRDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIPGVRED 72

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILNIKG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D VIC++   A
Sbjct: 73  VTQIILNIKGLALKLYAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLVICSVAEGA 132

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
                LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL
Sbjct: 133 TFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKL 192

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           +M I TDGSI  +++++LA++I+ + L +F+N  +  K  +  +  +       L   +E
Sbjct: 193 TMEIWTDGSIIPQEALSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIE 252

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           EL+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E+K  L  +GL L
Sbjct: 253 ELDLSVRSYNCLKRAGINTVQELTNKSEPEMIKVRNLGRKSLEEVKLNLHDLGLGL 308


>gi|224370665|ref|YP_002604829.1| DNA-directed RNA polymerase subunit alpha [Desulfobacterium
           autotrophicum HRM2]
 gi|259494167|sp|C0Q9U7|RPOA_DESAH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|223693382|gb|ACN16665.1| RpoA [Desulfobacterium autotrophicum HRM2]
          Length = 340

 Score =  254 bits (650), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 140/331 (42%), Positives = 209/331 (63%), Gaps = 8/331 (2%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++  NW+E+I P  +               + EPL +G+  T+GN+LRR+++SSL GAAI
Sbjct: 6   LVYMNWREIIMPEKVAVTTTS----TYGKFVCEPLEKGYGITIGNSLRRIILSSLYGAAI 61

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
            +V+    LHE S +  V ED+++II+N+K + LK+     K +TI  +G   VTA DI 
Sbjct: 62  VSVKFSEALHEYSVVSDVREDVSEIIMNLKEVKLKLDDPGDKILTINVKGEKFVTAADII 121

Query: 121 TVND-IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
           + +  +E+LNP+  I  +     + M + V  G GY  A  ++    P+G I ID+++SP
Sbjct: 122 SGDGRVEILNPEQHIATVSKGGELMMTMLVKTGKGYALAASNKDPEAPVGTIPIDSVFSP 181

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE--P 237
           IK+V Y V ++R GQ  DYDKL+M I TDGS+T EDSVA A++IL++Q+  FINF+E   
Sbjct: 182 IKRVKYVVGASRIGQKTDYDKLTMEIWTDGSVTPEDSVAYAAKILKEQMNPFINFDEDIE 241

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            + V+++    +  FN  L + V+ELELSVRS+NCL+   I+ +  L+Q+T+ +ML+  N
Sbjct: 242 PELVEKEHEGAAKNFNENLYRSVDELELSVRSSNCLKNAQILKIYQLVQKTDNEMLKTKN 301

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDW-PPE 327
           FGRKSL EIK VL +M L LGM+L  + PPE
Sbjct: 302 FGRKSLNEIKEVLTSMDLSLGMDLEGFEPPE 332


>gi|302388059|ref|YP_003823881.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           saccharolyticum WM1]
 gi|302198687|gb|ADL06258.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           saccharolyticum WM1]
          Length = 322

 Score =  254 bits (650), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 131/292 (44%), Positives = 198/292 (67%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDGVLHE SSI GV ED+T+II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDGVLHEFSSIPGVKEDVTEIIMNI 82

Query: 90  KGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K +++K + D++  K   I   G GV+TA DIQ   DIE++NP+ VI  L    D+   M
Sbjct: 83  KSLSIKNNSDTNEAKVAYIEFEGEGVITAADIQADPDIEIMNPEQVIATLSGGTDSKFYM 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++KG GYV A  +++E+ PIG+I +D++Y+P+++V+ TVE+ R GQV DYDKL++ +
Sbjct: 143 ELTITKGRGYVSADKNKSEDLPIGVIAVDSIYTPVERVNMTVENTRVGQVTDYDKLTLDV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G+   +++V+LA+++L + L +FI+  E  K  +  +  +       L   ++ELEL
Sbjct: 203 FTNGTSAPDEAVSLAAKVLSEHLNLFIDLSENAKTAEVMVEKEDNEKEKVLEMNIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L
Sbjct: 263 SVRSYNCLKRAGINTVEELCNRTSEDMMKVRNLGRKSLEEVLAKLKELGLQL 314


>gi|150392131|ref|YP_001322180.1| DNA-directed RNA polymerase, alpha subunit [Alkaliphilus
           metalliredigens QYMF]
 gi|166991520|sp|A6TWF3|RPOA_ALKMQ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|149951993|gb|ABR50521.1| DNA-directed RNA polymerase, alpha subunit [Alkaliphilus
           metalliredigens QYMF]
          Length = 315

 Score =  254 bits (649), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 127/288 (44%), Positives = 199/288 (69%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAA+T+V+I+G+LHE S+I GV ED+T+IILN+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAVTSVKIEGILHEFSTIPGVKEDVTEIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K +++ + G+  K + I   GPG VTAGDI    D+EVLNPD  I  LD ++ + ME+ +
Sbjct: 83  KDLSIGIDGNEPKTLRIEMEGPGTVTAGDIIADADVEVLNPDMYIATLDDNSKLNMEINI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GYV A++++T   PIG+I +D++++P++KVSY V + R GQV DYDKL + + TDG
Sbjct: 143 AKGRGYVSAENNKTAGMPIGVIPVDSIFTPVRKVSYFVGNTRVGQVTDYDKLEIEVFTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  +++++LA++++ + L +FI  +E   +V+  +  +       L   +EEL+LSVRS
Sbjct: 203 SIKPDEAISLAAKVMSEHLNLFITLKEDVSDVEIMVQKEEDKKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++E DM+++ N G+KSL E+   L  +GL L
Sbjct: 263 YNCLKRAGINTVEELSLKSEEDMMKVRNLGKKSLEEVDKKLEELGLGL 310


>gi|188584865|ref|YP_001916410.1| DNA-directed RNA polymerase, alpha subunit [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|229564254|sp|B2A4Q0|RPOA_NATTJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|179349552|gb|ACB83822.1| DNA-directed RNA polymerase, alpha subunit [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 315

 Score =  254 bits (649), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 128/295 (43%), Positives = 199/295 (67%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           EE      + EPL RG+  TLGN+LRR+L+SSL GAA+T+V+IDGVLHE SSI GV ED 
Sbjct: 16  EESTYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTSVKIDGVLHEFSSIPGVVEDT 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T+I+LN+K + LK+  D ++ +T+ K G G VTAGDIQ  +D++V+NP+  I  L  D  
Sbjct: 76  TEIVLNLKRLALKIHSDENQVLTLEKEGKGPVTAGDIQAGSDVDVINPELHIATLSEDTR 135

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + ME+T   G GYV A+ ++    PIGLI +D++++P+ K ++ V+  R GQV DYD+L+
Sbjct: 136 LYMEITAKNGRGYVRAERNKEPEQPIGLIPVDSVFTPVTKANFYVDDTRVGQVTDYDRLT 195

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + + TDGS+  +++V+++++I+Q+ L +FIN  E   +++  +  +       +   ++E
Sbjct: 196 LEVWTDGSLKPDEAVSMSAKIMQEHLDLFINLTEKATDMEVMVEKEEDNKEKIMELSIDE 255

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+LSVRS NCL+   I  +G+L Q+T  DM+++ N G+KSL E+K  L  +GL L
Sbjct: 256 LDLSVRSYNCLKRAGINTIGELTQKTPEDMMKVRNLGKKSLEEVKNKLTELGLSL 310


>gi|148652262|ref|YP_001279355.1| DNA-directed RNA polymerase subunit alpha [Psychrobacter sp.
           PRwf-1]
 gi|172048491|sp|A5WCL4|RPOA_PSYWF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|148571346|gb|ABQ93405.1| DNA-directed RNA polymerase, alpha subunit [Psychrobacter sp.
           PRwf-1]
          Length = 335

 Score =  254 bits (649), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 141/329 (42%), Positives = 214/329 (65%), Gaps = 18/329 (5%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           N  E + PN I    + +     TL   EPL RGF HTLGNALRR+L+SSL GAA+   +
Sbjct: 4   NATEFLTPNAINVDAVDETNAKVTL---EPLERGFGHTLGNALRRILLSSLPGAAVIEAE 60

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           I+GV HE S+++G+ ED+ D++LN+KG+ + M   +   +T+ K+GPG++TA DI+  ++
Sbjct: 61  IEGVDHEYSTLEGLQEDVLDLLLNLKGLAITMHDQNEVFLTLDKKGPGIITAADIELPHN 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKK 182
           ++++NP+ V+  L     ++M L V  G GY PA   R + D   IG + +DA +SP+ +
Sbjct: 121 VDIVNPELVLGTLGDRGHLKMRLRVVMGRGYEPANLRREDGDTKAIGRLKLDASFSPVSR 180

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-----EP 237
           V+Y VE+AR  Q  D D+L + ++T+G+I  E+++  A+ ILQ Q+ +F++ E     EP
Sbjct: 181 VAYQVENARVEQRTDLDRLIIELETNGTIDPEEAIRKAATILQQQISIFVDLEAEEAPEP 240

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            KE +E         +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QR+E ++L+  N
Sbjct: 241 VKEKEE--------VDPVLLRPVDDLELTVRSANCLKAENIYYIGDLVQRSETELLKTPN 292

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
            G+KSL EIK VL + GL L M L +WPP
Sbjct: 293 LGKKSLTEIKDVLASKGLELDMRLENWPP 321


>gi|326562118|gb|EGE12446.1| DNA-directed RNA polymerase subunit alpha [Moraxella catarrhalis
           7169]
 gi|326565701|gb|EGE15864.1| DNA-directed RNA polymerase subunit alpha [Moraxella catarrhalis
           12P80B1]
 gi|326566269|gb|EGE16421.1| DNA-directed RNA polymerase subunit alpha [Moraxella catarrhalis
           103P14B1]
 gi|326567079|gb|EGE17201.1| DNA-directed RNA polymerase subunit alpha [Moraxella catarrhalis
           BC1]
 gi|326568343|gb|EGE18423.1| DNA-directed RNA polymerase subunit alpha [Moraxella catarrhalis
           BC7]
 gi|326574842|gb|EGE24772.1| DNA-directed RNA polymerase subunit alpha [Moraxella catarrhalis
           101P30B1]
 gi|326576166|gb|EGE26081.1| DNA-directed RNA polymerase subunit alpha [Moraxella catarrhalis
           CO72]
          Length = 334

 Score =  254 bits (649), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 144/332 (43%), Positives = 214/332 (64%), Gaps = 18/332 (5%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           N  E + P+ I    + +     TL   EPL RGF HTLGNALRR+L+SSL GAA+   +
Sbjct: 3   NATEFLTPSAINVDTVNETTAKVTL---EPLERGFGHTLGNALRRILLSSLSGAAVVEAE 59

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           I+GV HE S+++G+ ED+ D++LN+K + + +   +   +T+ KRG GVVTA D++  ++
Sbjct: 60  IEGVDHEYSTLEGLQEDVLDLLLNLKSLAIILHDQNEAYLTLDKRGAGVVTAADLELPHN 119

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP--IGLITIDALYSPIKK 182
           +E+ NPD V+  L     ++M L V  G GY PA   R + +   IG + +DA +SPI +
Sbjct: 120 VEIANPDLVLGTLSERGHLKMRLHVVTGRGYEPANQRREDANSKIIGRLKLDASFSPIIR 179

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-----EP 237
           V+Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ ILQ Q+ +F++ E     EP
Sbjct: 180 VAYDVENARVEQRTDLDKLIIELETNGTIDPEEAIRKAATILQQQIAIFVDLEAEEAPEP 239

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            KE KE+I       +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QR+E ++L+  N
Sbjct: 240 IKE-KEEI-------DPVLLRPVDDLELTVRSANCLKAENIYYIGDLVQRSETELLKTPN 291

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            G+KSL EIK VL +  L LGM L +WPP  +
Sbjct: 292 LGKKSLTEIKDVLASKNLELGMRLDNWPPSDL 323


>gi|270265489|emb|CBI68381.1| RNA polymerase alpha-subunit [Vibrio tapetis]
 gi|270265491|emb|CBI68382.1| RNA polymerase alpha-subunit [Vibrio tapetis]
          Length = 299

 Score =  254 bits (649), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 131/285 (45%), Positives = 194/285 (68%), Gaps = 8/285 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 18  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 77

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            +K++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 78  AVKVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 137

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 138 RGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 197

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  ++ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 198 NGTLDPEEAIRRSATILAEQLDAFVDLRDIRVPEE---KEEKPEFDPILLRPVDDLELTV 254

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           RS NCL+ E I Y+GDL+QRTE ++L+  N G KSL EIK VL +
Sbjct: 255 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGNKSLTEIKDVLAS 299


>gi|315925227|ref|ZP_07921441.1| DNA-directed RNA polymerase subunit alpha [Pseudoramibacter
           alactolyticus ATCC 23263]
 gi|315621461|gb|EFV01428.1| DNA-directed RNA polymerase subunit alpha [Pseudoramibacter
           alactolyticus ATCC 23263]
          Length = 318

 Score =  254 bits (648), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 134/303 (44%), Positives = 196/303 (64%), Gaps = 2/303 (0%)

Query: 17  YIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS 74
           +I L    E+ T      EPL RG+  TLGN+LRR+++SSL G AIT V+IDGVLHE S+
Sbjct: 8   FIKLVDRSEDNTYGKFTVEPLERGYGTTLGNSLRRIMLSSLPGVAITTVKIDGVLHEFST 67

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           I G+ ED+ +I+LN+KG+   M  D  + V I  +G G VTAGDI    ++E+LNPD  I
Sbjct: 68  IPGIKEDVIEILLNLKGLCAVMHTDELQTVRIEAKGAGEVTAGDIIAGPEVEILNPDMHI 127

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
           C +  DA + ME+ +  G GY P++ ++ +  PIG + +D+++SPI+KV + VE  R GQ
Sbjct: 128 CTMAGDAELTMEMALEVGRGYRPSEKNKYDGMPIGTLPMDSIFSPIRKVIFRVEDTRVGQ 187

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
           V D+DKL++ I TDG+ + E++++L+++++ D L +FI+  E    V+  +  +      
Sbjct: 188 VTDFDKLTLEIWTDGTTSPEEALSLSAKVMNDHLRLFIDLTEEAGSVETIVEKEETERER 247

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +EELELSVRS+NCLR  NI  +  L Q+TE DM+++ N GRKSL EIK  L  MG
Sbjct: 248 IREMSIEELELSVRSSNCLRRANIDTVEKLTQKTEEDMMKVRNLGRKSLNEIKHKLAEMG 307

Query: 315 LFL 317
           L L
Sbjct: 308 LSL 310


>gi|257866554|ref|ZP_05646207.1| DNA directed RNA polymerase [Enterococcus casseliflavus EC30]
 gi|257872930|ref|ZP_05652583.1| DNA directed RNA polymerase [Enterococcus casseliflavus EC10]
 gi|257800512|gb|EEV29540.1| DNA directed RNA polymerase [Enterococcus casseliflavus EC30]
 gi|257807094|gb|EEV35916.1| DNA directed RNA polymerase [Enterococcus casseliflavus EC10]
          Length = 312

 Score =  254 bits (648), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 132/295 (44%), Positives = 195/295 (66%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E+++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+
Sbjct: 14  EDKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDV 73

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             IILNIKG+ LKM G+  K + I   GP  VTAGDI   +D+E+LN D  IC +   A 
Sbjct: 74  AQIILNIKGLALKMYGNEEKTLEIDISGPATVTAGDIIVDSDVEILNKDMYICTVSEGAT 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
               LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+
Sbjct: 134 FHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLT 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           M I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 194 MEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEE 253

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E+K  L  +GL L
Sbjct: 254 LDLSVRSYNCLKRAGINTVQELTNKSEPEMIKVRNLGRKSLEEVKVKLHDLGLGL 308


>gi|145577855|gb|ABP87378.1| RpoA [Vibrio sp. MSSRF10]
          Length = 286

 Score =  254 bits (648), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 132/278 (47%), Positives = 195/278 (70%), Gaps = 8/278 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 12  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 71

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L D +A V M + V 
Sbjct: 72  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTDGNAEVAMRIKVQ 131

Query: 151 KGHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVP  A+ H  E+D PIG + +DA YSP+ K++YTVE+AR  Q  D DKL + ++T
Sbjct: 132 RGRGYVPASARIHTDEDDRPIGRLLVDATYSPVDKIAYTVEAARVEQRTDLDKLVIDMET 191

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G+I  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 192 NGTIEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 248

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 249 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 286


>gi|315222793|ref|ZP_07864679.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus anginosus
           F0211]
 gi|315188096|gb|EFU21825.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus anginosus
           F0211]
          Length = 312

 Score =  254 bits (648), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 133/310 (42%), Positives = 200/310 (64%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E +N  + + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKNYGIFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILN+KGI +K   +  K + +   GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNVKGIAVKSYVEDEKTIELDVEGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A ++  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIGEGASLKAIMTVNTGRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I TDG+I  ED++ L++RIL + L +F N  E  K        
Sbjct: 179 EPARVGSNDGFDKLTLEIMTDGTIIPEDALGLSARILTEHLDLFTNLTEVAKSTDVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +  +  L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 EKVSDDRVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 VKLADLGLGL 308


>gi|145577841|gb|ABP87371.1| RpoA [Vibrio rhizosphaerae]
 gi|162955840|gb|ABY25295.1| RNA polymerase alpha subunit [Vibrio sp. MSSRF6]
          Length = 286

 Score =  254 bits (648), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 132/278 (47%), Positives = 195/278 (70%), Gaps = 8/278 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 12  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 71

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L D +A V M + V 
Sbjct: 72  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLNDDNAEVAMRIKVQ 131

Query: 151 KGHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVP  A+ H  E+D PIG + +DA YSP+ K++YTVE+AR  Q  D DKL + ++T
Sbjct: 132 RGRGYVPASARIHTDEDDRPIGRLLVDATYSPVDKIAYTVEAARVEQRTDLDKLVIDMET 191

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G+I  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 192 NGTIEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 248

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 249 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 286


>gi|325567351|ref|ZP_08144018.1| DNA-directed RNA polymerase subunit alpha [Enterococcus
           casseliflavus ATCC 12755]
 gi|325158784|gb|EGC70930.1| DNA-directed RNA polymerase subunit alpha [Enterococcus
           casseliflavus ATCC 12755]
          Length = 312

 Score =  254 bits (648), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 132/295 (44%), Positives = 195/295 (66%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E+++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVL+E S++KGV ED+
Sbjct: 14  EDKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLYEFSTVKGVREDV 73

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             IILNIKG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  IC +   A 
Sbjct: 74  AQIILNIKGLALKMYGDEEKTLEIDISGPATVTAGDIIVDSDVEILNKDMYICTVSEGAT 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
               LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+
Sbjct: 134 FHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLT 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           M I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 194 MEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEE 253

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E+K  L  +GL L
Sbjct: 254 LDLSVRSYNCLKRAGINTVQELTNKSEPEMIKVRNLGRKSLEEVKVKLHDLGLGL 308


>gi|325560586|gb|ADZ31263.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus sp.
           SL1108]
          Length = 298

 Score =  253 bits (647), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 128/292 (43%), Positives = 194/292 (66%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E  N    + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGV+HE S+I GV ED+
Sbjct: 7   EGTNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVVHEFSTIDGVLEDV 66

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILN+K + LK+ GD  K V I  +GP  VTA DI   +D+EVLNP+  IC +     
Sbjct: 67  TQIILNVKELALKIEGDEDKTVEIDVQGPATVTAADIVADSDVEVLNPEQYICTVAEGGH 126

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
             + +T+ KG GYV A  ++ ++ PIG++ ID++++PI +V+Y VES R G+  D+DKL+
Sbjct: 127 FHVRMTIKKGRGYVAADQNKVDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLT 186

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + + T+GSI+  ++++LA++IL + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 187 LDVWTNGSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEE 246

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           L+LSVRS NCL+   I  + +L  +TEADM+++ N GRKSL E+K  L  +G
Sbjct: 247 LDLSVRSYNCLKRAGINTVQELTNKTEADMMKVRNLGRKSLEEVKNKLSDLG 298


>gi|56961959|ref|YP_173681.1| DNA-directed RNA polymerase subunit alpha [Bacillus clausii
           KSM-K16]
 gi|61215810|sp|Q5WLN5|RPOA_BACSK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|56908193|dbj|BAD62720.1| DNA-directed RNA polymerase alpha subunit [Bacillus clausii
           KSM-K16]
          Length = 314

 Score =  253 bits (647), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 138/310 (44%), Positives = 203/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KPN IE + +  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDG
Sbjct: 3   EIEKPN-IETVEVS-EDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IILN+K + LK+  D  K + I  +G G VTAGD+   +D+EV
Sbjct: 61  VLHEFSTIEGVVEDVTTIILNLKKLALKIYSDEEKTLEIDVQGEGNVTAGDLTHDSDVEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L   A  RM L   +G GYV A+ ++ ++ PIG++ ID++Y+P+ +V+Y V
Sbjct: 121 LNPDLHIATLTKGASFRMRLQAKRGRGYVLAEGNKNDDQPIGVLPIDSIYTPVARVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV +YDKL++ + TDGS   E++V+L  +IL + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQVTNYDKLTLDVWTDGSTRPEEAVSLGVKILTEHLNIFVGLTDQAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E++
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTHKTEEDMMKVRNLGRKSLEEVQ 300

Query: 308 GVLGTMGLFL 317
             LG +GL L
Sbjct: 301 EKLGELGLGL 310


>gi|311070791|ref|YP_003975714.1| DNA-directed RNA polymerase subunit alpha [Bacillus atrophaeus
           1942]
 gi|310871308|gb|ADP34783.1| DNA-directed RNA polymerase subunit alpha [Bacillus atrophaeus
           1942]
          Length = 314

 Score =  253 bits (647), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 130/288 (45%), Positives = 192/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IIL+I
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTTIILHI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +G G VTA DI   +DIE+LNPD  I  L  +A  R+ LT 
Sbjct: 83  KKLALKIYSDEEKTLEIDVQGEGTVTAADITHDSDIEILNPDLHIATLGENASFRVRLTA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY PA  ++ ++ PIG+I ID++++P+ ++SY VE+ R GQV +YDKL++ + TDG
Sbjct: 143 QRGRGYTPADSNKRDDQPIGVIPIDSIFTPVSRLSYQVENTRVGQVANYDKLTLDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           S   ++++AL S+IL + L +F+   +  +  +  +  +       L   +EEL+LSVRS
Sbjct: 203 STGPKEAIALGSKILTEHLNIFVGLTDEAQHAEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGL 310


>gi|310829556|ref|YP_003961913.1| DNA-directed RNA polymerase [Eubacterium limosum KIST612]
 gi|308741290|gb|ADO38950.1| DNA-directed RNA polymerase [Eubacterium limosum KIST612]
          Length = 319

 Score =  253 bits (646), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 134/303 (44%), Positives = 201/303 (66%), Gaps = 4/303 (1%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           IV   E+E     + EPL RG+  TLGN+LRR+++SSL G A+T+V+IDGVLHE S+I G
Sbjct: 11  IVEKSEDETYGKFVVEPLERGYGTTLGNSLRRIMLSSLPGVAVTSVKIDGVLHEFSTIPG 70

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +I+LN+KG+  ++  D  K V I   G G +TAGDI T  D+E+LNPD  I  L
Sbjct: 71  VREDVVEILLNMKGLAAEIFSDEPKTVRIEAEGEGEITAGDIITDADVEILNPDMHIATL 130

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
              A + ME+ + KG GYV +  ++    PIG + +D+++SPI+KV++ VE+ R GQ+ D
Sbjct: 131 AKGATLNMEMRLEKGRGYVASDKNKYPGMPIGTLPVDSIFSPIRKVNFLVENTRVGQITD 190

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL++ + TDG+ T E++++L++++L + L +FI+  +    V  +I V+        +
Sbjct: 191 FDKLTLEVWTDGTTTPEEALSLSAKVLNEHLNLFIDLTDHANSV--EIMVEKEENEKERI 248

Query: 258 KK--VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           ++  +EELELSVRS+NCLR  NI  +  L Q+TE DM+++ N GRKSL EIK  L  +GL
Sbjct: 249 REMSIEELELSVRSSNCLRRANIDTVEKLTQKTEEDMIKVRNLGRKSLNEIKHKLAEIGL 308

Query: 316 FLG 318
            L 
Sbjct: 309 SLS 311


>gi|153952889|ref|YP_001393654.1| DNA-directed RNA polymerase subunit alpha [Clostridium kluyveri DSM
           555]
 gi|219853554|ref|YP_002470676.1| hypothetical protein CKR_0211 [Clostridium kluyveri NBRC 12016]
 gi|189043836|sp|A5N4S5|RPOA_CLOK5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|254765249|sp|B9DYD7|RPOA_CLOK1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|146345770|gb|EDK32306.1| RpoA [Clostridium kluyveri DSM 555]
 gi|219567278|dbj|BAH05262.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 315

 Score =  253 bits (646), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 130/299 (43%), Positives = 202/299 (67%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E+ N    + EPL RG+  TLGNALRR+L+SSL G A + V+IDGVLHE S+++GV ED
Sbjct: 15  SEDGNYGKFVVEPLERGYGTTLGNALRRILLSSLPGVAASHVKIDGVLHEFSTVRGVKED 74

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           ++++ILNIK + LKM+GD  K + I  +GPG V AGDI+T  D+E++N +  I  LD ++
Sbjct: 75  VSELILNIKELALKMNGDGTKTIYIDAQGPGEVVAGDIKTDGDVEIINGELHIATLDENS 134

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ME+TV+ G GYV  + ++ E+ PIG I +D++Y+PIK+V++ VE+ R GQ+ DYDKL
Sbjct: 135 RLYMEITVNGGRGYVSQRRNKFEDMPIGTIPVDSIYTPIKRVNFNVENTRVGQITDYDKL 194

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           S+ + T+G+I  +++V+L+++IL +   +F+   +    V+  +  +       L   +E
Sbjct: 195 SLEVWTNGTILPDEAVSLSAKILIEHFKLFMTLTDHANNVEIMVEKEEDKKEKVLEMAIE 254

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           EL+LSVRS NCL+   I  + +L +RT  DM+++ N G+KSL E++  L T+GL L  N
Sbjct: 255 ELDLSVRSYNCLKRAGINTVQELTERTMDDMMKVRNLGKKSLEEVEQKLDTLGLSLKQN 313


>gi|157493235|gb|ABV57983.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493237|gb|ABV57984.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 289

 Score =  253 bits (646), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 128/280 (45%), Positives = 193/280 (68%), Gaps = 8/280 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 11  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 70

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V 
Sbjct: 71  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVE 130

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 131 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMET 190

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 191 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 247

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK
Sbjct: 248 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIK 287


>gi|227509956|ref|ZP_03940005.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus brevis
           subsp. gravesensis ATCC 27305]
 gi|227190562|gb|EEI70629.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus brevis
           subsp. gravesensis ATCC 27305]
          Length = 319

 Score =  253 bits (646), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 145/314 (46%), Positives = 204/314 (64%), Gaps = 8/314 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN I  I   +E +N   ++ EPL RG+  TLGN+LRR L+SSL GAA+T++QID 
Sbjct: 6   EFEKPN-IHKI---EETKNFGEVVVEPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDD 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE S+IKGV ED+T IILN+K I+LK+ G  D  + + I   GP  VTAGDIQ  +D+
Sbjct: 62  VLHEFSTIKGVVEDVTQIILNVKKISLKLDGPEDEEENLEIDVIGPADVTAGDIQGDSDV 121

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKV 183
            VLNPD  I  +   A   M LT ++G GYV A     R    PIG++ +D++Y+PI++V
Sbjct: 122 TVLNPDLHIATVAEGATFHMRLTANRGRGYVSAVENKKRATEMPIGVLPVDSIYTPIERV 181

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VES R GQ  D+DKL++ I T+GSIT  ++V+LA++IL + L MF++  +  K  + 
Sbjct: 182 NYQVESTRVGQRDDFDKLTLDIWTNGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEI 241

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  +       L   +EEL+LSVRS NCL+   I  + +L ++TEADM+++ N GRKSL
Sbjct: 242 MVEKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTEKTEADMMKVRNLGRKSL 301

Query: 304 VEIKGVLGTMGLFL 317
            E+K  L  +GL L
Sbjct: 302 EEVKEKLAALGLSL 315


>gi|259502556|ref|ZP_05745458.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus antri DSM
           16041]
 gi|259169508|gb|EEW54003.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus antri DSM
           16041]
          Length = 314

 Score =  253 bits (646), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 139/310 (44%), Positives = 205/310 (66%), Gaps = 6/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E +N    + EPL RG+  TLGN+LRRVL++SL GAAIT +QIDG
Sbjct: 3   EFEKPN----IHKVEETDNYGKFVVEPLERGYGTTLGNSLRRVLIASLPGAAITTMQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++KGV ED+T IILN+K ++LK++ +  K + +  +GP  VTAGDIQ  +++ V
Sbjct: 59  VLHEFSTVKGVTEDVTQIILNLKKVSLKINSEDQKDLELDVKGPAEVTAGDIQGDSEVSV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSY 185
           LNPD  I  +   A + +++T  KG GY+ A  +  R E+  IG++ ID++Y+PI++V+Y
Sbjct: 119 LNPDLHIATVADGAELHIKMTADKGRGYLSANDNKARMEDLAIGVLPIDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVE+AR GQ  DYDKL++ + TDGSIT  ++V+L ++IL + L MF+N  E  +  +  +
Sbjct: 179 TVENARVGQRSDYDKLTLDVWTDGSITPTEAVSLGAKILTEHLAMFVNLTETAQNAQVMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   +EEL+LSVRS NCL+   I  + +L  RT +DM+++ N G+KSL E
Sbjct: 239 EKEETHKEKTLEMTIEELDLSVRSYNCLKRAGINTVKELTDRTVSDMMKVRNLGQKSLEE 298

Query: 306 IKGVLGTMGL 315
           IK  L  +G+
Sbjct: 299 IKLKLNDLGV 308


>gi|222529702|ref|YP_002573584.1| DNA-directed RNA polymerase subunit alpha [Caldicellulosiruptor
           bescii DSM 6725]
 gi|254765242|sp|B9MKF3|RPOA_ANATD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|222456549|gb|ACM60811.1| DNA-directed RNA polymerase, alpha subunit [Caldicellulosiruptor
           bescii DSM 6725]
          Length = 324

 Score =  253 bits (646), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 136/301 (45%), Positives = 201/301 (66%), Gaps = 2/301 (0%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  T+GNALRR L+SSL GAA+TAV+IDGVLHE S+I GV ED+ +IILN+K
Sbjct: 24  VIEPLERGYGITVGNALRRTLLSSLPGAAVTAVKIDGVLHEFSTIPGVLEDVPEIILNLK 83

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           G+ +KMS    K + I  +G   V A DI+   DIE+ NPDH I  L+ DA + ME+TV+
Sbjct: 84  GLAIKMSSPGPKVMYIEAQGECEVKAKDIKADADIEICNPDHHIATLNQDARLFMEITVN 143

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           +G GYV A+ ++  N PIG+I +D++Y+P+ KV+Y VE+ R GQV DYDKL+M I T+G+
Sbjct: 144 QGKGYVLAERNKQPNQPIGVIPVDSIYTPVVKVNYKVENTRVGQVTDYDKLTMEIWTNGT 203

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I  ++++ +A++IL +   +F +      +++  +  +    N  L   +EELELSVRS 
Sbjct: 204 IRPDEALTVAAKILIEHFNLFTDLSNIPTKIETVVKQEPPKRNKLLDMTIEELELSVRSY 263

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           NCL+   I  + DL+ +TE +M+++ N G+KSL E+   L ++GL L  +  D  P+  E
Sbjct: 264 NCLKRAGINTVEDLVNKTEEEMMKVRNLGKKSLEEVIQKLHSLGLSLKKS--DSTPKEEE 321

Query: 331 E 331
           E
Sbjct: 322 E 322


>gi|154684661|ref|YP_001419822.1| DNA-directed RNA polymerase subunit alpha [Bacillus
           amyloliquefaciens FZB42]
 gi|308172034|ref|YP_003918739.1| RNA polymerase subunit alpha [Bacillus amyloliquefaciens DSM 7]
 gi|171854997|sp|A7Z0R5|RPOA_BACA2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|52313146|emb|CAH55603.1| DNA-directed RNA polymerase alpha chain [Bacillus amyloliquefaciens
           FZB42]
 gi|154350512|gb|ABS72591.1| RpoA [Bacillus amyloliquefaciens FZB42]
 gi|307604898|emb|CBI41269.1| RNA polymerase (alpha subunit) [Bacillus amyloliquefaciens DSM 7]
 gi|328551844|gb|AEB22336.1| DNA-directed RNA polymerase subunit alpha [Bacillus
           amyloliquefaciens TA208]
 gi|328910100|gb|AEB61696.1| DNA-directed RNA polymerase subunit alpha [Bacillus
           amyloliquefaciens LL3]
          Length = 314

 Score =  253 bits (645), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 129/288 (44%), Positives = 192/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IIL+I
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTTIILHI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +G G VTA DI   +D+E+LNPD  I  L  +A  R+ LT 
Sbjct: 83  KKLALKIYSDEEKTLEIDVQGEGTVTAADITHDSDVEILNPDLHIATLGENASFRVRLTA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY PA  ++ ++ PIG+I ID++++P+ ++SY VE+ R GQV +YDKL++ + TDG
Sbjct: 143 QRGRGYTPADSNKRDDQPIGVIPIDSIFTPVSRLSYQVENTRVGQVANYDKLTLDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           S   ++++AL S+IL + L +F+   +  +  +  +  +       L   +EEL+LSVRS
Sbjct: 203 STGPKEAIALGSKILTEHLNIFVGLTDEAQHAEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGL 310


>gi|270291108|ref|ZP_06197331.1| DNA-directed RNA polymerase, alpha subunit [Pediococcus
           acidilactici 7_4]
 gi|270280504|gb|EFA26339.1| DNA-directed RNA polymerase, alpha subunit [Pediococcus
           acidilactici 7_4]
          Length = 314

 Score =  253 bits (645), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 137/295 (46%), Positives = 190/295 (64%), Gaps = 2/295 (0%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E +N    + EPL RG+  TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+
Sbjct: 14  ENDNYGRFVIEPLERGYGTTLGNSLRRILLSSLPGAAITSVQIDNVLHEFSTIEGVVEDV 73

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ VLNPD  IC +     
Sbjct: 74  TQIILNLKKVSLKIESDDEKTLDINVVGPANVTAGDIMGDGDVTVLNPDSPICTVAEGTT 133

Query: 143 VRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
               LT   G GY  A  +  R  + PIG++ ID++Y+PI++V+Y VE  R GQ  DYDK
Sbjct: 134 FHAVLTADTGRGYTSADENKARKADMPIGVLPIDSIYTPIERVNYQVEKTRVGQRDDYDK 193

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L++ I TDGSIT  ++ +L+++IL + L +F+N  +  KE +  +  +       L   +
Sbjct: 194 LTLDIWTDGSITPSEATSLSAKILTEHLAIFVNLNDQAKETEIMVEKEETHKEKMLEMTI 253

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           EEL+LSVRS NCL+   I  + +L  RTEA M+++ N GRKSLVEI+  L ++GL
Sbjct: 254 EELDLSVRSYNCLKRAGINSVQELTDRTEAQMMKVRNLGRKSLVEIQEKLNSLGL 308


>gi|253577207|ref|ZP_04854527.1| DNA-directed RNA polymerase, alpha subunit [Paenibacillus sp. oral
           taxon 786 str. D14]
 gi|251843451|gb|EES71479.1| DNA-directed RNA polymerase, alpha subunit [Paenibacillus sp. oral
           taxon 786 str. D14]
          Length = 314

 Score =  253 bits (645), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 128/288 (44%), Positives = 195/288 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDGVLHE +++ GV ED+T+IILN+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDGVLHEFATVPGVMEDVTEIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K ++LK+  D  K + I   G GVVTAGDI+  +D+E+LN D  I  L+  + + M +  
Sbjct: 83  KALSLKIHSDEEKILEIDAEGEGVVTAGDIRADSDVEILNTDLHIATLEPGSRLHMRIYA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYV A  ++ ++ PIG+I +D++Y+PI +V+Y VE+ R GQV +YDKL++ + TDG
Sbjct: 143 GRGRGYVQADRNKRDDQPIGVIPVDSIYTPITRVNYVVENTRVGQVTNYDKLTLEVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  E++V+L ++IL + L +F+   +  K+ +  +  +       L   +EEL+LSVRS
Sbjct: 203 SIRPEEAVSLGAKILTEHLFLFVGLTDEAKDAEIMVEKEEDKKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  +TE DM+++ N GRKSL E++  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELTTKTEEDMMKVRNLGRKSLEEVQEKLQELGLGL 310


>gi|29374877|ref|NP_814030.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           V583]
 gi|41688668|sp|Q839D9|RPOA_ENTFA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|29342335|gb|AAO80101.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           V583]
          Length = 312

 Score =  253 bits (645), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 134/296 (45%), Positives = 196/296 (66%), Gaps = 2/296 (0%)

Query: 24  EENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +ENR     + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+I GV ED
Sbjct: 13  DENRDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIPGVRED 72

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILNIKG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D VIC++   A
Sbjct: 73  VTQIILNIKGLALKLYAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLVICSVAEGA 132

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
                LTV  G GYV A  ++ E+ PIG++ +D++Y+P+ +V+Y VE+ R G+  D+DKL
Sbjct: 133 TFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVLRVNYQVENTRVGRRDDFDKL 192

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           +M I TDGSI  +++++LA++I+ + L +F+N  +  K  +  +  +       L   +E
Sbjct: 193 TMEIWTDGSIIPQEALSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIE 252

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           EL+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E+K  L  +GL L
Sbjct: 253 ELDLSVRSYNCLKRAGINTVQELTNKSEPEMIKVRNLGRKSLEEVKLKLHDLGLGL 308


>gi|227512889|ref|ZP_03942938.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus buchneri
           ATCC 11577]
 gi|227523017|ref|ZP_03953066.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus hilgardii
           ATCC 8290]
 gi|227083889|gb|EEI19201.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus buchneri
           ATCC 11577]
 gi|227089835|gb|EEI25147.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus hilgardii
           ATCC 8290]
          Length = 319

 Score =  253 bits (645), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 145/314 (46%), Positives = 204/314 (64%), Gaps = 8/314 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN I  I   +E +N   ++ EPL RG+  TLGN+LRR L+SSL GAA+T++QID 
Sbjct: 6   EFEKPN-IHKI---EETKNFGEVVVEPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDD 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE S+IKGV ED+T IILN+K I+LK+ G  D  + + I   GP  VTAGDIQ  +D+
Sbjct: 62  VLHEFSTIKGVVEDVTQIILNVKKISLKLDGPEDEDENLEIDVIGPADVTAGDIQGDSDV 121

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKV 183
            VLNPD  I  +   A   M LT ++G GYV A     R    PIG++ +D++Y+PI++V
Sbjct: 122 TVLNPDLHIATVAEGATFHMRLTANRGRGYVSAVENKKRATEMPIGVLPVDSIYTPIERV 181

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VES R GQ  D+DKL++ I T+GSIT  ++V+LA++IL + L MF++  +  K  + 
Sbjct: 182 NYQVESTRVGQRDDFDKLTLDIWTNGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEI 241

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  +       L   +EEL+LSVRS NCL+   I  + +L ++TEADM+++ N GRKSL
Sbjct: 242 MVEKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTEKTEADMMKVRNLGRKSL 301

Query: 304 VEIKGVLGTMGLFL 317
            E+K  L  +GL L
Sbjct: 302 EEVKEKLAALGLSL 315


>gi|71065084|ref|YP_263811.1| DNA-directed RNA polymerase subunit alpha [Psychrobacter arcticus
           273-4]
 gi|93005339|ref|YP_579776.1| DNA-directed RNA polymerase subunit alpha [Psychrobacter
           cryohalolentis K5]
 gi|90110862|sp|Q4FUD1|RPOA_PSYA2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366710|sp|Q1QDG1|RPOA_PSYCK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|71038069|gb|AAZ18377.1| DNA-directed RNA polymerase, 30-40 kDa subunit:RNA polymerase,
           alpha chain, bacterial and organelle [Psychrobacter
           arcticus 273-4]
 gi|92393017|gb|ABE74292.1| DNA-directed RNA polymerase, alpha subunit [Psychrobacter
           cryohalolentis K5]
          Length = 335

 Score =  253 bits (645), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 141/332 (42%), Positives = 213/332 (64%), Gaps = 18/332 (5%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           N  E + PN I    + +     TL   EPL RGF HTLGNALRR+L+SSL GAA+   +
Sbjct: 4   NATEFLTPNAINVDTVNETIAKVTL---EPLERGFGHTLGNALRRILLSSLPGAAVIEAE 60

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           IDGV HE S+++G+ ED+ D++LN+KG+ + +   +   +T+ K+GPG +TA DI   ++
Sbjct: 61  IDGVDHEYSTLEGLQEDVLDLLLNLKGLAITLHDQNEVFLTLDKQGPGTITAADITLPHN 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKK 182
           ++++NP+ V+  L     ++M L V  G GY PA   R + D   IG + +DA +SP+ +
Sbjct: 121 VDIINPELVLGTLSDRGHLKMRLRVVMGRGYEPANQRREDGDTKAIGRLKLDASFSPVLR 180

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-----EP 237
           V+Y VE+AR  Q  D D+L + ++T+G+I  E+++  A+ ILQ Q+ +F++ E     EP
Sbjct: 181 VAYQVENARVEQRTDLDRLIIELETNGTIDPEEAIRKAATILQQQISIFVDLEAEEAPEP 240

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            KE +E         +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QR+E ++L+  N
Sbjct: 241 VKEKEE--------VDPVLLRPVDDLELTVRSANCLKAENIYYIGDLVQRSETELLKTPN 292

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            G+KSL EIK VL +  L LGM L +WPP  +
Sbjct: 293 LGKKSLTEIKDVLASKDLELGMRLDNWPPADL 324


>gi|90962380|ref|YP_536296.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus salivarius
           UCC118]
 gi|227891570|ref|ZP_04009375.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus salivarius
           ATCC 11741]
 gi|119366692|sp|Q1WSB6|RPOA_LACS1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|90821574|gb|ABE00213.1| DNA-directed RNA polymerase alpha chain [Lactobacillus salivarius
           UCC118]
 gi|227866717|gb|EEJ74138.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus salivarius
           ATCC 11741]
 gi|300215021|gb|ADJ79437.1| DNA-directed RNA polymerase subunit alpha (RNAP subunit alpha)
           (Transcriptase subunit alpha) (RNA polymerase subunit
           alpha) [Lactobacillus salivarius CECT 5713]
          Length = 314

 Score =  253 bits (645), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 197/298 (66%), Gaps = 2/298 (0%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E+ N    + EPL RG+  TLGN+LRR+L+SSL GAAIT VQIDGVLHE S+I GV ED
Sbjct: 13  EEDNNYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAITDVQIDGVLHEFSTIPGVLED 72

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILN+K + L M  +  + + I   GP  VTAGDIQ+ +D+EVLNP+  IC +   A
Sbjct: 73  VTLIILNLKKVALSMESEDSQALEINVTGPMEVTAGDIQSNSDVEVLNPEQYICTVADGA 132

Query: 142 VVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
            + + +  +KG GYV A  ++   D  PIG++ ID++Y+PI++V+Y VE  R GQ  DYD
Sbjct: 133 ELHVRMNANKGRGYVSANDNKALADDMPIGVLPIDSIYTPIERVNYQVEKTRVGQKNDYD 192

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL++ + T+GSIT  ++++L+++IL + L +F++  +  K  +  +  +       L   
Sbjct: 193 KLTLDVWTNGSITPSEAISLSAKILTEHLALFVDLTDEAKNAEIMVEKEETHKEKMLEMT 252

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +EEL+LSVRS NCL+   I  + +L  ++EADM+++ N GRKSL E+K  L  +GL L
Sbjct: 253 IEELDLSVRSYNCLKRAGINTVQELTNKSEADMMKVRNLGRKSLDEVKAKLADLGLSL 310


>gi|311029077|ref|ZP_07707167.1| DNA-directed RNA polymerase subunit alpha [Bacillus sp. m3-13]
          Length = 314

 Score =  253 bits (645), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 132/295 (44%), Positives = 195/295 (66%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           ++ N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+
Sbjct: 16  DDANYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T +ILN+K + LK+  D  K + I  +G G VTA DI   +D+EVLNPD  I  L  DA 
Sbjct: 76  TTVILNVKKLALKIYSDDEKTLEIDVQGEGAVTAADITHDSDVEVLNPDLHIATLAKDAH 135

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           +R+  T  +G GYV A  ++ E+ PIG+I ID++++P+ +VSY VE+ R GQV +YDKL+
Sbjct: 136 LRIRFTAKRGRGYVTADGNKREDQPIGVIPIDSIFTPVSRVSYYVENTRVGQVSNYDKLT 195

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + + TDGS   +++VAL ++IL + L +F+   +  +  +  +  +       L   +EE
Sbjct: 196 LDVWTDGSNGPQEAVALGAKILTEHLNIFVGLTDEAQNAEIMVEKEEDQKEKVLEMTIEE 255

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 256 LDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKHKLEELGLGL 310


>gi|304385388|ref|ZP_07367733.1| DNA-directed RNA polymerase subunit alpha [Pediococcus acidilactici
           DSM 20284]
 gi|304328595|gb|EFL95816.1| DNA-directed RNA polymerase subunit alpha [Pediococcus acidilactici
           DSM 20284]
          Length = 314

 Score =  252 bits (644), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 137/295 (46%), Positives = 189/295 (64%), Gaps = 2/295 (0%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E +N    + EPL RG+  TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+
Sbjct: 14  ENDNYGRFVIEPLERGYGTTLGNSLRRILLSSLPGAAITSVQIDNVLHEFSTIEGVVEDV 73

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ VLNPD  IC +     
Sbjct: 74  TQIILNLKKVSLKIESDDEKTLDINVVGPANVTAGDIMGDGDVTVLNPDSPICTVAEGTT 133

Query: 143 VRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
               LT   G GY  A  +  R  + PIG++ ID++Y+PI++V+Y VE  R GQ  DYDK
Sbjct: 134 FHAVLTADTGRGYTSADENKARKADMPIGVLPIDSIYTPIERVNYQVEKTRVGQRDDYDK 193

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L++ I TDGSIT  ++ +L+++IL + L +F+N  +  KE +  +  +       L   +
Sbjct: 194 LTLDIWTDGSITPSEATSLSAKILTEHLAIFVNLNDQAKETEIMVEKEETHKEKMLEMTI 253

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           EEL+LSVRS NCL+   I  + +L  RTEA M+++ N GRKSLVEI+  L  +GL
Sbjct: 254 EELDLSVRSYNCLKRAGINSVQELTDRTEAQMMKVRNLGRKSLVEIQEKLNALGL 308


>gi|296113773|ref|YP_003627711.1| DNA-directed RNA polymerase alpha subunit [Moraxella catarrhalis
           RH4]
 gi|295921467|gb|ADG61818.1| DNA-directed RNA polymerase alpha subunit [Moraxella catarrhalis
           RH4]
 gi|326564517|gb|EGE14743.1| DNA-directed RNA polymerase subunit alpha [Moraxella catarrhalis
           46P47B1]
 gi|326572244|gb|EGE22239.1| DNA-directed RNA polymerase subunit alpha [Moraxella catarrhalis
           BC8]
 gi|326574586|gb|EGE24526.1| DNA-directed RNA polymerase subunit alpha [Moraxella catarrhalis
           O35E]
          Length = 334

 Score =  252 bits (644), Expect = 5e-65,   Method: Compositional matrix adjust.
 Identities = 143/332 (43%), Positives = 214/332 (64%), Gaps = 18/332 (5%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           N  E + P+ I    + +     TL   EPL RGF HTLGNALRR+L+SSL GAA+   +
Sbjct: 3   NATEFLTPSAINVDTVNETTAKVTL---EPLERGFGHTLGNALRRILLSSLSGAAVVEAE 59

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           I+GV HE S+++G+ ED+ D++LN+K + + +   +   +T+ K+G GVVTA D++  ++
Sbjct: 60  IEGVDHEYSTLEGLQEDVLDLLLNLKSLAIILHDQNEAYLTLDKQGAGVVTAADLELPHN 119

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP--IGLITIDALYSPIKK 182
           +E+ NPD V+  L     ++M L V  G GY PA   R + +   IG + +DA +SPI +
Sbjct: 120 VEIANPDLVLGTLSERGHLKMRLHVVTGRGYEPANQRREDANSKIIGRLKLDASFSPIIR 179

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-----EP 237
           V+Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ ILQ Q+ +F++ E     EP
Sbjct: 180 VAYDVENARVEQRTDLDKLIIELETNGTIDPEEAIRKAATILQQQIAIFVDLEAEEAPEP 239

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            KE KE+I       +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QR+E ++L+  N
Sbjct: 240 IKE-KEEI-------DPVLLRPVDDLELTVRSANCLKAENIYYIGDLVQRSETELLKTPN 291

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            G+KSL EIK VL +  L LGM L +WPP  +
Sbjct: 292 LGKKSLTEIKDVLASKNLELGMRLDNWPPSDL 323


>gi|208659518|gb|ACI31189.1| RpoA [Vibrio breoganii]
          Length = 302

 Score =  252 bits (644), Expect = 5e-65,   Method: Compositional matrix adjust.
 Identities = 130/284 (45%), Positives = 194/284 (68%), Gaps = 8/284 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC++ D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHITDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   K     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEK---EEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
           RS NCL+ E I Y+GD +QRTE ++L+  N G+KSL EIK VL 
Sbjct: 259 RSANCLKAEAIHYIGDXVQRTEVELLKTPNLGKKSLTEIKDVLA 302


>gi|283796525|ref|ZP_06345678.1| DNA-directed RNA polymerase, alpha subunit [Clostridium sp. M62/1]
 gi|291075939|gb|EFE13303.1| DNA-directed RNA polymerase, alpha subunit [Clostridium sp. M62/1]
          Length = 319

 Score =  252 bits (644), Expect = 5e-65,   Method: Compositional matrix adjust.
 Identities = 128/292 (43%), Positives = 199/292 (68%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDGVLHE SSI GV ED+T+II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDGVLHEFSSIPGVKEDVTEIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K S ++++  T +    G GVVTA DI   +DIE+LNPD VI  L    D+   M
Sbjct: 83  KSLAIKNSSETNEPKTAYIEFEGEGVVTAADINADSDIEILNPDQVIATLSGGADSKFYM 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++KG GY+ A  +++++ PIG+I +D++Y+P+++V+ +VE+ R GQV DYDKL++ +
Sbjct: 143 ELTITKGRGYISADKNKSDDLPIGVIAVDSIYTPVERVNMSVENTRVGQVTDYDKLTLDV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L +FI+  E  +  +  +  +       L   ++ELEL
Sbjct: 203 FTNGTLAPDEAVSLAAKVLSEHLNLFIDLSENARTAEVMVEKEDNEKEKVLEMNIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L
Sbjct: 263 SVRSYNCLKRAGINTVEELCNRTPEDMMKVRNLGRKSLEEVLAKLKELGLQL 314


>gi|319940035|ref|ZP_08014389.1| DNA-directed RNA polymerase subunit alpha [Streptococcus anginosus
           1_2_62CV]
 gi|319810749|gb|EFW07076.1| DNA-directed RNA polymerase subunit alpha [Streptococcus anginosus
           1_2_62CV]
          Length = 312

 Score =  252 bits (643), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 132/310 (42%), Positives = 200/310 (64%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++  + + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKDYGIFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILN+KGI +K   +  K + +   GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNVKGIAVKSYVEDEKTIELDVEGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A ++  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIGEGASLKAIMTVNTGRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I TDG+I  ED++ L++RIL + L +F N  E  K        
Sbjct: 179 EPARVGSNDGFDKLTLEIMTDGTIIPEDALGLSARILTEHLDLFTNLTEVAKSTDVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +  +  L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 EKVSDDRVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 VKLADLGLGL 308


>gi|147676684|ref|YP_001210899.1| DNA-directed RNA polymerase subunit alpha [Pelotomaculum
           thermopropionicum SI]
 gi|146272781|dbj|BAF58530.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 315

 Score =  252 bits (643), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 132/288 (45%), Positives = 197/288 (68%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T+V+IDGVLHE S+I GV ED+TDIILN+
Sbjct: 23  FVVEPLERGYGITLGNSLRRILLSSLPGAAVTSVKIDGVLHEFSTIPGVVEDVTDIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+ GD  K + +     GVV A DI    D+E++NPD  I  L  +A + ME+TV
Sbjct: 83  KNLCLKIYGDEEKVLRVEASTEGVVKAKDIIHDADVEIMNPDLTIATLAENARLYMEITV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GYV A+ ++  +  IG+I +D++++P++KV+YTVE+ R GQ+ DYDKL++ + TDG
Sbjct: 143 AKGRGYVSAERNKKGDHIIGVIPVDSVFTPVRKVNYTVENTRVGQITDYDKLTLEVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  +++ +L+++IL + L +FI   E   +V+  +  +    +  L   +EEL+LSVRS
Sbjct: 203 SIRPDEATSLSAKILSEHLRLFIGLTETVSDVEIMVEKEEEHKDRVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +LIQR E DM+++ N G+KSL E+   L  +GL L
Sbjct: 263 YNCLKRAGINTVEELIQRNEEDMMKVRNLGKKSLEEVINKLHELGLSL 310


>gi|238922857|ref|YP_002936370.1| DNA-directed RNA polymerase, alpha subunit [Eubacterium rectale
           ATCC 33656]
 gi|238874529|gb|ACR74236.1| DNA-directed RNA polymerase, alpha subunit [Eubacterium rectale
           ATCC 33656]
          Length = 319

 Score =  252 bits (643), Expect = 7e-65,   Method: Compositional matrix adjust.
 Identities = 129/292 (44%), Positives = 202/292 (69%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDGVLHE SSI GV ED+T+II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDGVLHEFSSIPGVKEDVTEIIMNI 82

Query: 90  KGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + ++ +  ++  K   I   G GVVTA DIQ  +DIE+LNP+  I +L+   D+ + M
Sbjct: 83  KNLAIRNNSSTNEPKVAYIEFEGEGVVTAADIQVDSDIEILNPELEIAHLNGGADSKLYM 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++ G GYV A+ ++ E+ PIG++ +D++Y+P+++V+ TVE+ R GQV DYDKL++ +
Sbjct: 143 ELTITNGRGYVGAEKNKNEDTPIGVLAVDSIYTPVERVNLTVENTRVGQVTDYDKLTLDV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L +FI+  E  ++V   +  ++      L   ++ELEL
Sbjct: 203 FTNGTLEPDEAVSLAAKVLSEHLNLFIDLSEAAQQVDVMVEKENDAQEKVLEMNIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + +LI RT  DM+++ N GRKSL E+   L  +GL L
Sbjct: 263 SVRSYNCLKRAGINTVAELINRTPEDMMKVRNLGRKSLEEVLAKLKELGLEL 314


>gi|226323042|ref|ZP_03798560.1| hypothetical protein COPCOM_00814 [Coprococcus comes ATCC 27758]
 gi|225208609|gb|EEG90963.1| hypothetical protein COPCOM_00814 [Coprococcus comes ATCC 27758]
          Length = 319

 Score =  252 bits (643), Expect = 7e-65,   Method: Compositional matrix adjust.
 Identities = 131/292 (44%), Positives = 199/292 (68%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAAI+ ++IDGVLHE SSI GV ED+T+II+N+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAISQIKIDGVLHEFSSIPGVKEDVTEIIMNL 82

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K S   D  K   I   G GVVTA DIQ  +DIE++NP+ VI  L+   D+ + M
Sbjct: 83  KTLAIKNSSETDEPKTAYIEFEGEGVVTAADIQADSDIEIMNPETVIATLNGGADSKLYM 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++KG GYV +  ++TE+ PIG+I ID++Y+P+++V+ TV++ R GQ+ DYDKL++ +
Sbjct: 143 ELTITKGRGYVGSDKNKTEDMPIGVIPIDSIYTPVERVNLTVQNTRVGQITDYDKLTLDV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L +FI+  E  +  +  I  +       L   ++ELEL
Sbjct: 203 YTNGTLAPDEAVSLAAKVLNEHLKLFIDLSEVAQSAEVMIEKEDDEKEKVLEMSIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L
Sbjct: 263 SVRSYNCLKRAGINTVEELTNRTSEDMMKVRNLGRKSLEEVLAKLKELGLEL 314


>gi|295425627|ref|ZP_06818314.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           amylolyticus DSM 11664]
 gi|295064643|gb|EFG55564.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           amylolyticus DSM 11664]
          Length = 312

 Score =  251 bits (642), Expect = 9e-65,   Method: Compositional matrix adjust.
 Identities = 135/310 (43%), Positives = 196/310 (63%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDG
Sbjct: 3   EFEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK + D  K + +   GP  VTA D++  +D+EV
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSNSDEQKVIELDVEGPATVTADDLKVDSDVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + M++ V  G GYV A  +++E+ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMQIAVKNGRGYVAASDNKSEDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL+  I TDGSI   D+++ A+ IL +   +F + +   K  +  +  
Sbjct: 179 ESTRVGKRDDFDKLTFEIWTDGSINPNDALSFAANILVEHFKVFESADADNKFSEVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+R+ N GRKSL E+K
Sbjct: 239 EDNKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELTDKSEADMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLADLGLSL 308


>gi|325663034|ref|ZP_08151484.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae
           bacterium 4_1_37FAA]
 gi|331086641|ref|ZP_08335718.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae
           bacterium 9_1_43BFAA]
 gi|325470488|gb|EGC73718.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae
           bacterium 4_1_37FAA]
 gi|330409807|gb|EGG89242.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae
           bacterium 9_1_43BFAA]
          Length = 319

 Score =  251 bits (642), Expect = 9e-65,   Method: Compositional matrix adjust.
 Identities = 133/293 (45%), Positives = 196/293 (66%), Gaps = 4/293 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAAI+ V+IDGVLHE SSI GV ED+T+II+N+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAISHVKIDGVLHEFSSIPGVKEDVTEIIMNL 82

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K S   D  K   I   G GVVTA DIQ   DIE++NPD VI  L+   D+ + M
Sbjct: 83  KSLAIKNSSETDEPKTAYIEFEGEGVVTAADIQVDPDIEIMNPDAVIATLNGGADSKLYM 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++KG GY+ A  ++ E  PIG+I ID++Y+P+++V+ TVE+ R GQ+ DYDKL++ +
Sbjct: 143 ELTITKGRGYISADKNKNEELPIGVIPIDSIYTPVERVNLTVENTRVGQITDYDKLTLDV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L +FI+  E  +  +  I  +       L   ++ELEL
Sbjct: 203 YTNGTLLPDEAVSLAAKVLNEHLKLFIDLSEVAQAAEVMIEKEDDEKEKVLEMSIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           SVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L 
Sbjct: 263 SVRSYNCLKRAGINTVEELTNRTPEDMMKVRNLGRKSLEEVLAKLKELGLELS 315


>gi|160872598|ref|ZP_02062730.1| DNA-directed RNA polymerase, alpha subunit [Rickettsiella grylli]
 gi|159121397|gb|EDP46735.1| DNA-directed RNA polymerase, alpha subunit [Rickettsiella grylli]
          Length = 348

 Score =  251 bits (641), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 134/321 (41%), Positives = 201/321 (62%), Gaps = 9/321 (2%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           N ++ + P  IE   +     NR+L+  +P   GF HTLGNALRRVL+SS+ G A+   +
Sbjct: 4   NVKKFLTPQTIEVQTIAP---NRSLITLQPFEAGFGHTLGNALRRVLLSSMPGCAVVEAK 60

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           I+GVLHE SS++GV ED+ DI+LN+KG+  +M G     + + K   G V AGDI   +D
Sbjct: 61  IEGVLHEYSSLEGVQEDIIDILLNLKGVAFQMHGKEEVTLELIKNTVGPVCAGDITLPSD 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN---DPIGLITIDALYSPIK 181
           IEV NPD VI +L      +M L V++G GY PA   + +      +G + +DA ++PI 
Sbjct: 121 IEVKNPDFVIAHLTKPKEFKMTLKVARGRGYQPASLRKADERFVSEVGALQLDARFNPIL 180

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           + +Y+VE+AR  Q  D DKL + ++T+G+I  E+++  A+ I+Q+QL  F+   E K E 
Sbjct: 181 RATYSVENARVEQRTDLDKLVIDLETNGTIDPEEAIRRAATIIQEQLRTFV---ELKHET 237

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +E++  + +  NP LL  V+ELEL+VR+ NCL+ E+I  + DL+ +TE+++L   N G+ 
Sbjct: 238 EEEVVDEFVDINPMLLLPVDELELTVRAANCLKAEHIYRIADLVTKTESELLSTPNLGKV 297

Query: 302 SLVEIKGVLGTMGLFLGMNLP 322
           SL EIK  L   GL LGM +P
Sbjct: 298 SLWEIKTALQKRGLSLGMEVP 318


>gi|260589249|ref|ZP_05855162.1| DNA-directed RNA polymerase, alpha subunit [Blautia hansenii DSM
           20583]
 gi|331082657|ref|ZP_08331780.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae
           bacterium 6_1_63FAA]
 gi|260540330|gb|EEX20899.1| DNA-directed RNA polymerase, alpha subunit [Blautia hansenii DSM
           20583]
 gi|330400276|gb|EGG79918.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae
           bacterium 6_1_63FAA]
          Length = 319

 Score =  251 bits (641), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 131/292 (44%), Positives = 194/292 (66%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDGVLHE SSI GV ED+T+II+N+
Sbjct: 23  FVVEPLERGYGITLGNSLRRIMLSSLPGAAVSQVKIDGVLHEFSSIPGVKEDVTEIIMNL 82

Query: 90  KGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K   DS++  T +    G GVVT  DIQ   D+E+LNPD VI  L+   D     
Sbjct: 83  KNLAIKNVSDSNEPKTAYIEFEGEGVVTGADIQVDQDLEILNPDLVIATLNGGADCKFNA 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++KG GYV A   +T++ PIG+I +D++Y+P+++V+  VE+ R GQV DYDKL++ I
Sbjct: 143 ELTITKGRGYVSADKGKTDDMPIGMIAVDSIYTPVERVNMAVENTRVGQVTDYDKLTLDI 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L +FI+  E  K  +  I  +       L   ++ELEL
Sbjct: 203 YTNGTLDADEAVSLAAKVLSEHLSLFIDLSESAKTAEVMIEKEDNEKEKVLEMNIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L
Sbjct: 263 SVRSYNCLKRAGINTVEELCNRTSEDMMKVRNLGRKSLEEVLAKLKELGLQL 314


>gi|295103950|emb|CBL01494.1| DNA-directed RNA polymerase subunit alpha [Faecalibacterium
           prausnitzii SL3/3]
          Length = 318

 Score =  251 bits (641), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 131/291 (45%), Positives = 195/291 (67%), Gaps = 3/291 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +AEPL RGF  TLGN+LRRVL+SSL G A+T+V+IDGV+HE S+I+GV ED+T+I+LN+
Sbjct: 23  FVAEPLERGFGITLGNSLRRVLLSSLPGVAVTSVKIDGVVHEFSTIEGVKEDVTEIVLNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KGI  K+  D  K V +   GP  VTA +I+  +DIE+LNP+  I  L   A + MELT 
Sbjct: 83  KGIAAKLYTDGPKTVRVEAVGPCEVTADNIKQGDDIEILNPEWHIATLGEGAKLVMELTF 142

Query: 150 SKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            KG GYVPA+ ++    E + I  + +D++Y+P+ KV+Y VES R GQ +DYDKL++ + 
Sbjct: 143 DKGRGYVPAERNKQAIIEKNDINTLPVDSIYTPVLKVNYNVESTRVGQAIDYDKLTIEVW 202

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           TDG+I  +++V+LA+R+L + L +F+N  +     +  +   +     AL   +EEL+LS
Sbjct: 203 TDGTINAQEAVSLAARVLTEHLNLFVNLSDEAAGAEIMVEKTNDDKEKALEMTIEELDLS 262

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           VRS NCL+   I  + DL+ ++E +M+++ N GRKSL E+   L ++G  L
Sbjct: 263 VRSFNCLKRAGINTVEDLVSKSEDEMMKVRNLGRKSLEEVMAKLDSLGFKL 313


>gi|302023188|ref|ZP_07248399.1| DNA-directed RNA polymerase subunit alpha [Streptococcus suis
           05HAS68]
          Length = 300

 Score =  251 bits (641), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 129/280 (46%), Positives = 194/280 (69%), Gaps = 4/280 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL++SL GAA+T+++IDGVLHE  ++ GV ED+  IILNI
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNI 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KGI +K   +  K++ +   GP  VTAGDI T +DIE++NPDH +  +   A  +  LTV
Sbjct: 81  KGIAVKSYVEDEKKIELDVVGPAEVTAGDILTDSDIEIVNPDHYLFTIADGATFKAVLTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           + G GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I+T+G
Sbjct: 141 NSGRGYVPAEDNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTLEINTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK--EVKEDINVKSLPFNPALLKKVEELELSV 267
           +I  ED++ L++RIL + LG+F +  E  K  EV ++  V S   +  L + +EEL+LSV
Sbjct: 201 TIVPEDALGLSARILMEHLGLFTDLTEVAKSAEVMKEAEVAS--DDRMLDRTIEELDLSV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           RS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 259 RSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVK 298


>gi|157493247|gb|ABV57989.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 286

 Score =  251 bits (641), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 127/279 (45%), Positives = 192/279 (68%), Gaps = 8/279 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 11  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 70

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V 
Sbjct: 71  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVE 130

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 131 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMET 190

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 191 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 247

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EI
Sbjct: 248 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEI 286


>gi|28212154|ref|NP_783098.1| DNA-directed RNA polymerase subunit alpha [Clostridium tetani E88]
 gi|41688695|sp|Q890R0|RPOA_CLOTE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|28204598|gb|AAO37035.1| DNA-directed RNA polymerase alpha chain [Clostridium tetani E88]
          Length = 315

 Score =  251 bits (641), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 127/288 (44%), Positives = 196/288 (68%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGNALRR+L+SSL G A+ +++I+ VLHE S++KGV ED+T+IILNI
Sbjct: 23  FVVEPLERGYGITLGNALRRILLSSLPGVAVNSIKIENVLHEFSTVKGVKEDVTEIILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM+G+  K + I  +GPGVVTA DI+T +D+E++N D  I  LD D  + +E+TV
Sbjct: 83  KLLALKMTGEGPKTIYIDAKGPGVVTAADIKTDSDVEIINKDLHIATLDDDGKLYIEMTV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYV    ++ E  PIG I ID++Y+P+K+V++TV + R GQ+ DYDKL++ I T+G
Sbjct: 143 DRGRGYVSQNRNKVEGMPIGTIPIDSIYTPVKRVNFTVANTRVGQITDYDKLTLEIWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  +D+++L+++IL +   +F+   +   +V+  +  +       L   +EEL+LSVRS
Sbjct: 203 TIMPDDAISLSAKILIEHFKLFMTLTDHADDVEIMVEKEEDKKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L +RT  DM+++ N GRKSL E++  L  + L L
Sbjct: 263 YNCLKRAGINTVQELTERTVEDMMKVRNLGRKSLEEVEQKLEALELGL 310


>gi|157690927|ref|YP_001485389.1| DNA-directed RNA polymerase subunit alpha [Bacillus pumilus
           SAFR-032]
 gi|194017476|ref|ZP_03056087.1| DNA-directed RNA polymerase, alpha subunit [Bacillus pumilus ATCC
           7061]
 gi|172045997|sp|A8F9B2|RPOA_BACP2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|157679685|gb|ABV60829.1| DNA-directed RNA polymerase subunit alpha [Bacillus pumilus
           SAFR-032]
 gi|194010748|gb|EDW20319.1| DNA-directed RNA polymerase, alpha subunit [Bacillus pumilus ATCC
           7061]
          Length = 314

 Score =  251 bits (641), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 129/288 (44%), Positives = 191/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTTIILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  +  G VTA DI   +DIE+LNPD  I  L  +A  R+ LT 
Sbjct: 83  KKLALKIYSEEEKTLEIDVQDEGTVTAADITHDSDIEILNPDLHIATLGKNASFRVRLTA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY PA  ++ ++ PIG+I ID++Y+P+ +V+Y VE+ R GQ+ +YDKL++ + TDG
Sbjct: 143 QRGRGYNPADANKRDDQPIGVIPIDSIYTPVSRVTYQVENTRVGQITNYDKLTLDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           S   ++++AL S+IL + L +F+   +  +  +  +  +       L   +EEL+LSVRS
Sbjct: 203 STGPKEAIALGSKILTEHLNIFVGLTDEAQHAEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGL 310


>gi|160942870|ref|ZP_02090109.1| hypothetical protein FAEPRAM212_00346 [Faecalibacterium prausnitzii
           M21/2]
 gi|158445771|gb|EDP22774.1| hypothetical protein FAEPRAM212_00346 [Faecalibacterium prausnitzii
           M21/2]
          Length = 332

 Score =  251 bits (641), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 131/291 (45%), Positives = 195/291 (67%), Gaps = 3/291 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +AEPL RGF  TLGN+LRRVL+SSL G A+T+V+IDGV+HE S+I+GV ED+T+I+LN+
Sbjct: 37  FVAEPLERGFGITLGNSLRRVLLSSLPGVAVTSVKIDGVVHEFSTIEGVKEDVTEIVLNL 96

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KGI  K+  D  K V +   GP  VTA +I+  +DIE+LNP+  I  L   A + MELT 
Sbjct: 97  KGIAAKLYTDGPKTVRVEAVGPCEVTADNIKQGDDIEILNPEWHIATLGEGAKLVMELTF 156

Query: 150 SKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            KG GYVPA+ ++    E + I  + +D++Y+P+ KV+Y VES R GQ +DYDKL++ + 
Sbjct: 157 DKGRGYVPAERNKQAIIEKNDINTLPVDSIYTPVLKVNYNVESTRVGQAIDYDKLTIEVW 216

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           TDG+I  +++V+LA+R+L + L +F+N  +     +  +   +     AL   +EEL+LS
Sbjct: 217 TDGTINAQEAVSLAARVLTEHLNLFVNLSDEAAGAEIMVEKTNDDKEKALEMTIEELDLS 276

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           VRS NCL+   I  + DL+ ++E +M+++ N GRKSL E+   L ++G  L
Sbjct: 277 VRSFNCLKRAGINTVEDLVSKSEDEMMKVRNLGRKSLEEVMAKLDSLGFKL 327


>gi|238021616|ref|ZP_04602042.1| hypothetical protein GCWU000324_01516 [Kingella oralis ATCC 51147]
 gi|237866230|gb|EEP67272.1| hypothetical protein GCWU000324_01516 [Kingella oralis ATCC 51147]
          Length = 278

 Score =  251 bits (641), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 133/280 (47%), Positives = 186/280 (66%), Gaps = 6/280 (2%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV-TIFKRGPGV 113
           + G A T V I GVLHE S++ GV ED+ DI+LNIKG+  K+ G S + V T+ K G GV
Sbjct: 1   MNGFAPTEVTIAGVLHEYSTLDGVQEDIVDILLNIKGVVFKLHGGSTEAVITLKKEGSGV 60

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY--VPAKHHRTENDPIGLI 171
           VTA D +  +D+E++NP+ VIC+L  +  + ME+ V +G GY  V  +    E   IG I
Sbjct: 61  VTAADFELPHDVEIINPEQVICHLAANGNIDMEVKVEQGRGYQSVAGRKAAKEQTKIGSI 120

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +D+ +SPI +VS+ VE+AR  Q  D D L + I+T+GSI  E++V  A+RIL DQ+ +F
Sbjct: 121 QLDSSFSPISRVSFEVEAARVEQRTDLDSLVLDIETNGSIEPEEAVRAAARILIDQMSIF 180

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
            + E    EV+E+   K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE +
Sbjct: 181 ADLEGTPIEVEEE---KAPPIDPVLLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETE 237

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +L+  N GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 238 LLKTPNLGRKSLNEIKEVLASKGLTLGSKLESWPPAGLEK 277


>gi|240145849|ref|ZP_04744450.1| DNA-directed RNA polymerase, alpha subunit [Roseburia intestinalis
           L1-82]
 gi|257201997|gb|EEV00282.1| DNA-directed RNA polymerase, alpha subunit [Roseburia intestinalis
           L1-82]
          Length = 319

 Score =  251 bits (640), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 130/292 (44%), Positives = 198/292 (67%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDGVLHE SSI GV ED+T+II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDGVLHEFSSIPGVKEDVTEIIMNI 82

Query: 90  KGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + ++ +  ++  K   I   G GVVTA DIQ  +DI++LNPD VI NL+   D  + M
Sbjct: 83  KNLAIRNNSSTNEPKVAYIEFEGEGVVTAADIQVDSDIQILNPDLVIANLNGGPDCKLYM 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++ G GYV A  ++TE+ PIG+I ID++Y+P+++V+  +E+ R GQ+ DYDKL++ +
Sbjct: 143 ELTITNGRGYVSADKNKTEDIPIGVIAIDSIYTPVERVNLLIENTRVGQITDYDKLTLDV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L +FI+  E  ++    I  +       L   ++ELEL
Sbjct: 203 YTNGTLEPDEAVSLAAKVLSEHLSLFIDLSEAAQQADVMIEKEDNAKEKVLEMNIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L
Sbjct: 263 SVRSYNCLKRAGINTVEELTNRTPEDMMKVRNLGRKSLEEVLAKLKELGLQL 314


>gi|223936403|ref|ZP_03628315.1| DNA-directed RNA polymerase, alpha subunit [bacterium Ellin514]
 gi|223894921|gb|EEF61370.1| DNA-directed RNA polymerase, alpha subunit [bacterium Ellin514]
          Length = 333

 Score =  251 bits (640), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 131/309 (42%), Positives = 192/309 (62%), Gaps = 6/309 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E     +AEP   G+ HT+GN+LRRVL+SSL GAAI++++IDG +HE +++ GV ED+TD
Sbjct: 14  ETYAKFVAEPFETGYGHTIGNSLRRVLLSSLEGAAISSIKIDGAMHEFTTVDGVVEDVTD 73

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           I+LN+K +  K      + + +     G VTA DIQ   +IE++NP   IC LD      
Sbjct: 74  IVLNLKKVLFKAHNREPQTLLLSANKDGEVTAADIQVNQNIELVNPKQHICTLDKKKKFE 133

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +EL V  G G+ P   ++  N  IG+I ID+L+SP+ +V Y VESAR GQ  DYD+L + 
Sbjct: 134 IELEVKVGRGFCPGDENKKPNQAIGVIAIDSLFSPVTRVRYAVESARVGQRTDYDRLILE 193

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK---SLPFNPALLKKVE 261
           + TDG I+ +D++  AS ILQ  L +F+ +++   E +E ++ +          L   V 
Sbjct: 194 VWTDGRISPDDALTQASAILQHHLDVFVGYDKNAVEFEEVVDKQDEEKTKLKKLLGMSVN 253

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           E+ELSVR+ NCL   NI  +G L  +TEA+ML+  NFG+KSL EIK  L  +GL LGM+ 
Sbjct: 254 EIELSVRAANCLNNANITTVGQLAMKTEAEMLKYRNFGKKSLNEIKEKLTALGLSLGMS- 312

Query: 322 PDWPPESIE 330
             + PE+++
Sbjct: 313 --FDPEALD 319


>gi|302669991|ref|YP_003829951.1| DNA-directed RNA polymerase alpha subunit RpoA [Butyrivibrio
           proteoclasticus B316]
 gi|302394464|gb|ADL33369.1| DNA-directed RNA polymerase alpha subunit RpoA [Butyrivibrio
           proteoclasticus B316]
          Length = 319

 Score =  251 bits (640), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 130/291 (44%), Positives = 198/291 (68%), Gaps = 3/291 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAA++ V+I+GVLHE SSI GV ED+T+II+NI
Sbjct: 23  FVVEPLERGYGITLGNSLRRIMLSSLPGAAVSQVKIEGVLHEFSSIPGVKEDVTEIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVVRME 146
           K +++K S D+++  T +    G GVV A DIQ   DIE++NPD VI  L   DA + ME
Sbjct: 83  KNLSIKNSSDTNEPKTAYIEYSGEGVVRASDIQVDQDIEIMNPDQVIATLSGKDAKLYME 142

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           LT++KG GYV +  ++  + PIG+I ID++Y+P+++V+ TVE+ R GQV D+DKL++ + 
Sbjct: 143 LTITKGRGYVSSDKNKGGDLPIGVIAIDSIYTPVERVNVTVENTRVGQVTDFDKLTLDVH 202

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           TDG++  +++V+LA+++L + L +FI+  E  K  +  +  +       L   ++ELELS
Sbjct: 203 TDGTLAPDEAVSLAAKVLSEHLSLFIDLSENAKTAEVMVEKEDDEKGKVLEMSIDELELS 262

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           VRS NCL+   I  + +L  +T  DM+++ N GRKSL E+   L  +GL L
Sbjct: 263 VRSFNCLKRAGINTVQELANKTSDDMMKVRNLGRKSLEEVLAKLDELGLSL 313


>gi|301300224|ref|ZP_07206436.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus
           salivarius ACS-116-V-Col5a]
 gi|300852165|gb|EFK79837.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus
           salivarius ACS-116-V-Col5a]
          Length = 314

 Score =  251 bits (640), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 132/298 (44%), Positives = 197/298 (66%), Gaps = 2/298 (0%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E+ N    + EPL RG+  TLGN+LRR+L+SSL GAAIT VQIDGVLHE S+I GV ED
Sbjct: 13  EEDNNYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAITDVQIDGVLHEFSTIPGVLED 72

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILN+K + L +  +  + + I   GP  VTAGDIQ+ +D+EVLNP+  IC +   A
Sbjct: 73  VTLIILNLKKVALSIESEDSQALEINVTGPMEVTAGDIQSNSDVEVLNPEQYICTVADGA 132

Query: 142 VVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
            + + +  +KG GYV A  ++   D  PIG++ ID++Y+PI++V+Y VE  R GQ  DYD
Sbjct: 133 ELHVRMNANKGRGYVSANDNKALADDMPIGVLPIDSIYTPIERVNYQVEKTRVGQKNDYD 192

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL++ + T+GSIT  ++++L+++IL + L +F++  +  K  +  +  +       L   
Sbjct: 193 KLTLDVWTNGSITPSEAISLSAKILTEHLALFVDLTDEAKNAEIMVEKEETHKEKMLEMT 252

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +EEL+LSVRS NCL+   I  + +L  ++EADM+++ N GRKSL E+K  L  +GL L
Sbjct: 253 IEELDLSVRSYNCLKRAGINTVQELTNKSEADMMKVRNLGRKSLDEVKAKLADLGLSL 310


>gi|189219450|ref|YP_001940091.1| DNA-directed RNA polymerase, alpha subunit [Methylacidiphilum
           infernorum V4]
 gi|189186308|gb|ACD83493.1| DNA-directed RNA polymerase, alpha subunit [Methylacidiphilum
           infernorum V4]
          Length = 337

 Score =  250 bits (639), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 134/300 (44%), Positives = 194/300 (64%), Gaps = 15/300 (5%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           I EP   G+ HTLGN+LRR+L+SSL GAAI++V+I+GV+HE ++++GV ED+ DI+LN+K
Sbjct: 29  IIEPFESGYGHTLGNSLRRILLSSLEGAAISSVKIEGVMHEFTTMEGVVEDVVDIVLNLK 88

Query: 91  GINLKMSGDSHK--RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
            + +KM     +  RV +FK G   VTAGDIQ    +E++NP+ +IC LD    + MEL 
Sbjct: 89  KVLIKMPDRQTRVFRVDVFKEG--AVTAGDIQVDPGVEIVNPEQLICTLDKKQRLLMELE 146

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V  G G++  ++++ ++  IG+I ID L+SP++ V YTVE+ R GQ  DYD+L   I TD
Sbjct: 147 VKVGRGFLLGEYNKKQDQSIGVIPIDCLFSPVRHVKYTVENTRVGQRTDYDRLIFEIWTD 206

Query: 209 GSITGEDSVALASRILQDQLGMFIN-------FEEPKKEVKEDINVKSLPFNPALLKKVE 261
           G I  ++++  ++ ILQ  L +F+        FE+PK  +KE+ N         L   V 
Sbjct: 207 GRIGPDEALVQSAAILQHHLDIFVQYGKEPVEFEKPKPPIKEEEN----RLRKILNMSVN 262

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           E+ELSVR+ NCL   NI  +G L  +TEA+ML+  NFG+KSL EIK  L ++GL LGM  
Sbjct: 263 EIELSVRAANCLNNANITTVGQLAMKTEAEMLKYRNFGKKSLNEIKEKLASLGLSLGMKF 322


>gi|227894546|ref|ZP_04012351.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus ultunensis
           DSM 16047]
 gi|227863705|gb|EEJ71126.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus ultunensis
           DSM 16047]
          Length = 312

 Score =  250 bits (639), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 135/310 (43%), Positives = 195/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDG
Sbjct: 3   EFEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++V
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMELAVKNGRGYVTASDNKSDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   K  +  +  
Sbjct: 179 ESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADANTKFSEVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE+DM+R+ N GRKSL E+K
Sbjct: 239 EDDKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELTDKTESDMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLADLGLSL 308


>gi|218289978|ref|ZP_03494155.1| DNA-directed RNA polymerase, alpha subunit [Alicyclobacillus
           acidocaldarius LAA1]
 gi|258512642|ref|YP_003186076.1| DNA-directed RNA polymerase, alpha subunit [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|218239963|gb|EED07150.1| DNA-directed RNA polymerase, alpha subunit [Alicyclobacillus
           acidocaldarius LAA1]
 gi|257479368|gb|ACV59687.1| DNA-directed RNA polymerase, alpha subunit [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 312

 Score =  250 bits (639), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 126/288 (43%), Positives = 196/288 (68%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SS+ GAA+ +V+I+GVLHE S+I GV ED+T+IILN+
Sbjct: 21  FVCEPLERGYGTTLGNSLRRILLSSIPGAAVRSVKIEGVLHEFSTIPGVVEDVTEIILNL 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K ++LK+  D  K + I   GPGVVTAGDI+  +D++++NPD  I  L   A + ME+  
Sbjct: 81  KRLSLKIHSDEEKTLIIDAVGPGVVTAGDIRADSDVDIMNPDLHIATLTEGARIYMEMRA 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYVPA  ++ E   IGLI ID+LYSPI +V+++VE+ R GQ+ DYDKL++ + TDG
Sbjct: 141 GRGRGYVPAHRNKPEEQEIGLIPIDSLYSPISRVNFSVENTRVGQITDYDKLTLEVWTDG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           S+  +++V++ ++IL + L +F+   +  ++    +  ++   +  L   +EEL+LSVRS
Sbjct: 201 SVAPDEAVSIGAKILTEHLMLFVGLTDRARDTDLMVEKENAHNDKILDMPIEELDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++E +M+++ N GRKSL E+   L  +GL L
Sbjct: 261 YNCLKRAGINTVAELCAKSEEEMMKVRNLGRKSLEEVVEKLHALGLSL 308


>gi|184155965|ref|YP_001844305.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus fermentum
           IFO 3956]
 gi|227515513|ref|ZP_03945562.1| DNA-directed RNA polymerase [Lactobacillus fermentum ATCC 14931]
 gi|260662778|ref|ZP_05863672.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus fermentum
           28-3-CHN]
 gi|183227309|dbj|BAG27825.1| DNA-directed RNA polymerase alpha subunit [Lactobacillus fermentum
           IFO 3956]
 gi|227086126|gb|EEI21438.1| DNA-directed RNA polymerase [Lactobacillus fermentum ATCC 14931]
 gi|260552859|gb|EEX25858.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus fermentum
           28-3-CHN]
 gi|299783528|gb|ADJ41526.1| DNA-directed RNA polymerase alpha subunit [Lactobacillus fermentum
           CECT 5716]
          Length = 314

 Score =  250 bits (639), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 137/310 (44%), Positives = 203/310 (65%), Gaps = 6/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E +N    + EPL RG+  TLGN+LRRV+++SL GAAIT++QIDG
Sbjct: 3   EFEKPN----IHKVEETDNYGKFVVEPLERGYGTTLGNSLRRVMLASLPGAAITSIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K + LK+  +  K + I  +GP  VTA DIQ   D+ +
Sbjct: 59  VLHEFSTVQGVTEDVTQIILNLKQVALKIDSEDAKDLEIDVKGPAEVTAADIQGDGDVTI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
           LN D  I  +   A + +++T  KG GY  A  ++T  E   IG++ ID++Y+PI++V+Y
Sbjct: 119 LNSDLHIATVSDGAELHVKMTADKGRGYSSADDNKTRMEGLAIGVLPIDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVE+ R GQ  DYDKL++ + T+GS+T  ++++LA++IL + L MF+N  E  +  +  +
Sbjct: 179 TVENTRVGQSNDYDKLTLDVWTNGSLTPTEAISLAAKILTEHLTMFVNLTEEAQVTQVMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L K +EEL+LSVRS NCL+  +I  + DL +RTEADM+++ N G KSL E
Sbjct: 239 EREETHQEKVLDKTIEELDLSVRSYNCLKRADIQTVKDLTERTEADMMKVRNLGTKSLDE 298

Query: 306 IKGVLGTMGL 315
           IK  L  +G+
Sbjct: 299 IKLKLAELGV 308


>gi|308070947|ref|YP_003872552.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           [Paenibacillus polymyxa E681]
 gi|305860226|gb|ADM72014.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           [Paenibacillus polymyxa E681]
          Length = 314

 Score =  250 bits (638), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 126/288 (43%), Positives = 195/288 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDGVLHE +++ GV ED+T+IILN+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDGVLHEFATVPGVKEDVTEIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K ++LK+  D  K + I   G GVVTAGDI+  +D+E+LNPD  I  L   + + M +  
Sbjct: 83  KALSLKIHSDEEKVLEIDAEGEGVVTAGDIRADSDVEILNPDLHIATLGPGSRLHMRIFA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           ++G GYV    ++ ++ PIG+I +D++Y+PI +V+Y VE+ R GQV +YDKL++ + TDG
Sbjct: 143 NRGRGYVKQDRNKRDDQPIGVIPVDSIYTPIARVNYGVENTRVGQVTNYDKLTLEVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  E++V+L ++IL + + +F+   +  K+ +  +  +       L   +EEL+LSVRS
Sbjct: 203 SIRPEEAVSLGAKILTEHVMLFVGLTDEAKDAEIMVEKEEDKKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++E DM+++ N GRKSL E++  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELTTKSEEDMMKVRNLGRKSLEEVQEKLEELGLGL 310


>gi|312870507|ref|ZP_07730626.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus oris
           PB013-T2-3]
 gi|311093969|gb|EFQ52294.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus oris
           PB013-T2-3]
          Length = 314

 Score =  250 bits (638), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 137/310 (44%), Positives = 205/310 (66%), Gaps = 6/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E +N    + EPL RG+  TLGN+LRRVL++SL G+AIT +QIDG
Sbjct: 3   EFEKPN----IHKVEETDNYGKFVVEPLERGYGTTLGNSLRRVLIASLPGSAITTMQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++KGV ED+T IILN+K ++LK++ +  K + +  +GP  VTAGDIQ  +++ V
Sbjct: 59  VLHEFSTVKGVTEDVTQIILNLKKVSLKINSEDQKDLELDVKGPAKVTAGDIQGDSEVSV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSY 185
           LNPD  I  +   A + +++T  KG GY+ A  +  R E+  IG++ ID++Y+PI++V+Y
Sbjct: 119 LNPDLHIATVADGAELHIKMTADKGRGYLSANDNKARMEDLAIGVLPIDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVE+AR GQ  D+DKL++ + TDGSIT  ++V+L ++IL + L MF+N  E  +  +  +
Sbjct: 179 TVENARVGQRSDFDKLTLDVWTDGSITPTEAVSLGAKILTEHLAMFVNLTETAQNAQVMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   +EEL+LSVRS NCL+   I  + +L  RT +DM+++ N G+KSL E
Sbjct: 239 EKEETHKEKTLEMTIEELDLSVRSYNCLKRAGINTVKELTDRTVSDMMKVRNLGQKSLEE 298

Query: 306 IKGVLGTMGL 315
           IK  L  +G+
Sbjct: 299 IKLKLNDLGV 308


>gi|261415794|ref|YP_003249477.1| DNA-directed RNA polymerase, alpha subunit [Fibrobacter
           succinogenes subsp. succinogenes S85]
 gi|261372250|gb|ACX74995.1| DNA-directed RNA polymerase, alpha subunit [Fibrobacter
           succinogenes subsp. succinogenes S85]
          Length = 324

 Score =  250 bits (638), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 140/322 (43%), Positives = 208/322 (64%), Gaps = 6/322 (1%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           W+ L  P + + +  G E+      + E L RG+  TLGNALRRVL+SSL+GAAI +V+I
Sbjct: 3   WKSLQMPRSFQKVETG-EDGRYAKFVVEALERGWGITLGNALRRVLLSSLQGAAIVSVKI 61

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           +GV  E S+I GV ED+TDIILN+K I +K+  D  + + +   G G VTA D     ++
Sbjct: 62  EGVDKEFSTIPGVKEDVTDIILNLKSIRVKLLSDHDETLHLDMSGDGEVTAKDFMDNPNV 121

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
            +L PD  I  L+ +A + M++ +S G GYV A   + ++ PIG+I +DA ++P++KV+ 
Sbjct: 122 TILTPDVHIATLNGNASLSMDVKISCGRGYVVADELKDKDAPIGVIAMDANFNPVQKVAM 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE---EPKKEVK 242
            +   R GQ  DY++L + I TDGSI  ED++A A+++L D L +FINFE   E  +E++
Sbjct: 182 HISDTRVGQKTDYNRLELEITTDGSIDPEDALAYAAKLLVDHLEIFINFEGDLESPEELE 241

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
            D   + +     L  +V++LELSVRS+NCLR  NI  +G+L++  E DML+  NFGRKS
Sbjct: 242 MDEERQRIA--NLLRMRVDDLELSVRSSNCLRMANIHTIGELVRNKENDMLKYKNFGRKS 299

Query: 303 LVEIKGVLGTMGLFLGMNLPDW 324
           LVE+  VL +MGL  GM++ D+
Sbjct: 300 LVELNEVLTSMGLSFGMDVDDY 321


>gi|260656836|gb|ACX47808.1| RNA polymerase alpha-subunit [Vibrio casei]
          Length = 295

 Score =  250 bits (638), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 131/282 (46%), Positives = 194/282 (68%), Gaps = 8/282 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 17  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 76

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            + ++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D  A + M + V 
Sbjct: 77  AVSVAEGKDEVFITLKKSGSGPVVAGDIIHDGDVEIANPEHVICHLTDDKAEIAMRIKVQ 136

Query: 151 KGHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVP  A+ H  E++ PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 137 RGRGYVPSSARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 196

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 197 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 253

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK V
Sbjct: 254 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDV 295


>gi|317126889|ref|YP_004093171.1| DNA-directed RNA polymerase, subunit alpha [Bacillus
           cellulosilyticus DSM 2522]
 gi|315471837|gb|ADU28440.1| DNA-directed RNA polymerase, alpha subunit [Bacillus
           cellulosilyticus DSM 2522]
          Length = 314

 Score =  250 bits (638), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 126/288 (43%), Positives = 191/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL G+A+T+VQ DGVLHE S+I+GV ED+T IILN+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGSAVTSVQFDGVLHEFSTIEGVVEDITSIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I   G GVVTA D    +D+EVLNPD  I  L   A   M++  
Sbjct: 83  KKLALKIYSDEEKTLEIEATGEGVVTAADFMHDSDVEVLNPDLHIATLSKGAQFHMKVAA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           ++G GYVPA+ +++E  PIG+I +D++Y+P+ +V+Y VE+ R GQ+ +YDKL++ + TDG
Sbjct: 143 NRGRGYVPAEGNKSEELPIGVIPVDSIYTPVARVNYQVENTRVGQITNYDKLTLDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           S   E++V+L ++IL + L +F+   +  +  +  +  +       L   +EEL+LSVRS
Sbjct: 203 STRPEEAVSLGAKILTEHLNIFVGLTDQAQHAEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++E DM+++ N GRKSL E++  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELTHKSEEDMMKVRNLGRKSLEEVQEKLAELGLGL 310


>gi|182412026|ref|YP_001817092.1| DNA-directed RNA polymerase subunit alpha [Opitutus terrae PB90-1]
 gi|177839240|gb|ACB73492.1| DNA-directed RNA polymerase, alpha subunit [Opitutus terrae PB90-1]
          Length = 333

 Score =  250 bits (638), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 133/299 (44%), Positives = 183/299 (61%), Gaps = 11/299 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            IAEP   G+ HT+GN+LRRVL+SS+ GAAI++++IDGV HE  SI GV ED+TDI+LN+
Sbjct: 28  FIAEPFEAGYGHTIGNSLRRVLLSSIEGAAISSIKIDGVNHEFQSIDGVVEDVTDIVLNL 87

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L         + I     G+VTA DIQ   +I+V+NP+ VIC LD       E+ +
Sbjct: 88  KKVLLVSQKRESINLAIRVNKAGIVTAADIQPDPNIQVINPEQVICTLDAKKTFDAEIEI 147

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GY P + ++ E   IG+I ID+L+SP++ V Y VE+ R GQ+ DYDKL + + TDG
Sbjct: 148 KTGRGYCPGEANKKEEQAIGVIPIDSLFSPVRLVKYAVEATRVGQITDYDKLVLEVWTDG 207

Query: 210 SITGEDSVALASRILQDQLGMF-------INFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
            IT +D++  A+ IL+  L +F         FE  + EV E+ N         L   V E
Sbjct: 208 RITPDDALKQAASILKHHLDVFDRVSEETYEFENQQSEVSEEQN----KLRKLLNMSVNE 263

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +ELSVR+ NCL   NI  +G+L  +TE +ML+  NFG+KSL EIK  L  +GL LGM  
Sbjct: 264 IELSVRAANCLNNANITTVGELAMKTEQEMLKYRNFGKKSLNEIKEKLEALGLSLGMKF 322


>gi|307694123|ref|ZP_07636360.1| DNA-directed RNA polymerase subunit alpha [Ruminococcaceae
           bacterium D16]
          Length = 316

 Score =  250 bits (638), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 128/288 (44%), Positives = 186/288 (64%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRR+L+SSL G A+T+++I GV HE S+I G+ ED+T+I+LNIK
Sbjct: 24  VVEPLERGYGTTLGNSLRRILLSSLPGTAVTSIKIAGVQHEFSTIPGIKEDVTEIVLNIK 83

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            I  K+  + +K V I   G   VTAGDI+   D+E+LNP+  I  L  DA + MELT+S
Sbjct: 84  SIIAKLHCEENKTVHIEASGECEVTAGDIKCDADVEILNPELHIATLGPDATLSMELTLS 143

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            G GYVPA  ++     IGLI +D++Y+P++KV+YTVE+ R G   DYDKL++ + TDG+
Sbjct: 144 HGRGYVPADRNKPAQTIIGLIPVDSIYTPVRKVNYTVENTRVGDATDYDKLTLEVWTDGT 203

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I   D+V+L +RIL D   +F +  E        +       +  +   +++++LSVRS 
Sbjct: 204 IDARDAVSLGARILCDHFALFTDLSETMGSRSTVVEKAETQRDKVMEMTIDDMDLSVRSY 263

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           NCL+  NI  + DLI +TE +M+++ N GRKSL E+   L  MGL L 
Sbjct: 264 NCLKRANINTVEDLISKTEEEMMKVRNLGRKSLEEVINKLAMMGLSLA 311


>gi|157493231|gb|ABV57981.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493233|gb|ABV57982.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493239|gb|ABV57985.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493241|gb|ABV57986.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493245|gb|ABV57988.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493249|gb|ABV57990.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493251|gb|ABV57991.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493253|gb|ABV57992.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493257|gb|ABV57994.1| RNA polymerase alpha subunit [Vibrio mimicus]
 gi|157493259|gb|ABV57995.1| RNA polymerase alpha subunit [Vibrio mimicus]
 gi|157493261|gb|ABV57996.1| RNA polymerase alpha subunit [Vibrio mimicus]
 gi|157493265|gb|ABV57998.1| RNA polymerase alpha subunit [Vibrio mimicus]
 gi|157493269|gb|ABV58000.1| RNA polymerase alpha subunit [Vibrio mimicus VM603]
 gi|157493271|gb|ABV58001.1| RNA polymerase alpha subunit [Vibrio mimicus]
 gi|157493289|gb|ABV58010.1| RNA polymerase alpha subunit [Vibrio mimicus]
 gi|157493291|gb|ABV58011.1| RNA polymerase alpha subunit [Vibrio mimicus]
 gi|157493293|gb|ABV58012.1| RNA polymerase alpha subunit [Vibrio mimicus]
          Length = 285

 Score =  250 bits (638), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 126/278 (45%), Positives = 191/278 (68%), Gaps = 8/278 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 11  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 70

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V 
Sbjct: 71  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVE 130

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 131 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMET 190

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 191 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 247

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 248 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 285


>gi|157493243|gb|ABV57987.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 286

 Score =  250 bits (638), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 126/278 (45%), Positives = 191/278 (68%), Gaps = 8/278 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 12  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 71

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V 
Sbjct: 72  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVE 131

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 132 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMET 191

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 192 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 248

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 249 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 286


>gi|27262232|gb|AAN87397.1| DNA-directed RNA polymerase alpha chain [Heliobacillus mobilis]
          Length = 315

 Score =  250 bits (638), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 129/288 (44%), Positives = 190/288 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T+V+I+GVLHE S+I GV ED TDIILN+
Sbjct: 23  FVVEPLERGYGVTLGNSLRRILLSSLPGAAVTSVKIEGVLHEFSTIPGVVEDTTDIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K +++KM  D  + + +   G GVVT  DI    D+E+LNPD  I  LD    + MELTV
Sbjct: 83  KLLSIKMYTDEPRIIRVEAEGEGVVTGKDIICDADVEILNPDQPIATLDKGGRLFMELTV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            K  GY+ A  H+     IG+I +DA +SP++KV+Y VE  R GQ+ +YD+L + + ++G
Sbjct: 143 EKDRGYMTATKHKKSEHVIGVIPVDANFSPVRKVNYRVEDTRVGQITNYDRLILEVWSNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           S+T E++++L+++I+ D L +F+   E  + V+  +  +  P +  L   +EEL+LSVRS
Sbjct: 203 SLTPEEAISLSAKIMNDHLKLFVGLTESTENVEIMVEKEERPQDKVLDMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL  +TE DM+++ N GRKSL E+   L  +GL L
Sbjct: 263 YNCLKRAGINSVRDLTLKTEEDMIKVRNLGRKSLEEVDAKLNALGLSL 310


>gi|308522652|dbj|BAJ22937.1| RNA polymerase alpha subunit [Aliivibrio sp. LC2-088]
          Length = 271

 Score =  249 bits (637), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 128/273 (46%), Positives = 191/273 (69%), Gaps = 7/273 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 2   EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 61

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +
Sbjct: 62  AVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNAEISMRIRVER 121

Query: 152 GHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVP  A+ H  E++ PIG + IDA YSP+ K+SY+VE+AR  Q  D DKL + ++T+
Sbjct: 122 GRGYVPSTARIHTEEDERPIGRLLIDATYSPVDKISYSVEAARVEQRTDLDKLVIDMETN 181

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL +F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 182 GTLDPEEAIRRAATILAEQLDVFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 238

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           S NCL+ E I Y+GDL+QRTE ++L+  N G+K
Sbjct: 239 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKK 271


>gi|58336655|ref|YP_193240.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           acidophilus NCFM]
 gi|227903213|ref|ZP_04021018.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           acidophilus ATCC 4796]
 gi|75433035|sp|Q5FM65|RPOA_LACAC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|58253972|gb|AAV42209.1| RNA-polymerase DNA-directed [Lactobacillus acidophilus NCFM]
 gi|227869018|gb|EEJ76439.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           acidophilus ATCC 4796]
          Length = 312

 Score =  249 bits (637), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 135/310 (43%), Positives = 195/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDG
Sbjct: 3   EFEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++V
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMELAVKNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   K  +  +  
Sbjct: 179 ESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADANTKFSEVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE+DM+R+ N GRKSL E+K
Sbjct: 239 EDDKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELTDKTESDMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLTDLGLSL 308


>gi|89893245|ref|YP_516732.1| DNA-directed RNA polymerase subunit alpha [Desulfitobacterium
           hafniense Y51]
 gi|219666518|ref|YP_002456953.1| DNA-directed RNA polymerase subunit alpha [Desulfitobacterium
           hafniense DCB-2]
 gi|119366679|sp|Q250K4|RPOA_DESHY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|254765251|sp|B8G1Z4|RPOA_DESHD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|89332693|dbj|BAE82288.1| hypothetical protein [Desulfitobacterium hafniense Y51]
 gi|219536778|gb|ACL18517.1| DNA-directed RNA polymerase, alpha subunit [Desulfitobacterium
           hafniense DCB-2]
          Length = 315

 Score =  249 bits (637), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 131/286 (45%), Positives = 191/286 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL G A+T+V+I+GVLHE S++ GV ED+TDIILN+
Sbjct: 23  FVVEPLERGYGITLGNSLRRILLSSLPGTAVTSVKIEGVLHEFSTVPGVLEDVTDIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK   D  K + +   G GV+ AGDI T  DIE+LNPD  I  LD D  + ME+T 
Sbjct: 83  KSLALKGHTDEPKVLRLEAEGEGVIKAGDIITDADIEILNPDLKIATLDKDGRLFMEMTA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYV A  ++  +  IG+I ID++++PI KV+YTVE  R G V DYDKL++ + ++G
Sbjct: 143 ERGRGYVSADKNKKPDQAIGIIPIDSIFAPIYKVNYTVEDTRVGMVTDYDKLTLEVWSNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SIT E++ +LA++IL + L +FI   +    V+  +  +    +  L   +E+L+LSVRS
Sbjct: 203 SITPEEATSLAAKILSEHLRLFIGLTDKLNNVEIMVEKEEEAKDKILEMTIEDLDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
            NCL+   I  + +L Q+TE DM+++ N GRKSL E++  L  +GL
Sbjct: 263 YNCLKRAGINSVEELTQKTEEDMIKVRNLGRKSLEEVESKLKELGL 308


>gi|151400011|gb|ABS11121.1| RpoA [Vibrio cholerae]
 gi|151400013|gb|ABS11122.1| RpoA [Vibrio cholerae]
 gi|151400015|gb|ABS11123.1| RpoA [Vibrio cholerae]
 gi|151400017|gb|ABS11124.1| RpoA [Vibrio cholerae]
 gi|151400019|gb|ABS11125.1| RpoA [Vibrio cholerae]
 gi|151400021|gb|ABS11126.1| RpoA [Vibrio cholerae]
 gi|151400023|gb|ABS11127.1| RpoA [Vibrio mimicus]
          Length = 283

 Score =  249 bits (637), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 126/278 (45%), Positives = 191/278 (68%), Gaps = 8/278 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 9   EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 68

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V 
Sbjct: 69  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVE 128

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 129 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMET 188

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 189 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 245

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 246 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 283


>gi|308522648|dbj|BAJ22935.1| RNA polymerase alpha subunit [Aliivibrio sifiae]
 gi|308522650|dbj|BAJ22936.1| RNA polymerase alpha subunit [Aliivibrio sifiae]
 gi|308522654|dbj|BAJ22938.1| RNA polymerase alpha subunit [Aliivibrio sp. ATCC 33715]
          Length = 271

 Score =  249 bits (637), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 128/273 (46%), Positives = 190/273 (69%), Gaps = 7/273 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 2   EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 61

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +
Sbjct: 62  AVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNAEISMRIKVER 121

Query: 152 GHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVP  A+ H  E++ PIG + IDA YSP+ K+SY+VE+AR  Q  D DKL + ++T+
Sbjct: 122 GRGYVPSTARIHTEEDERPIGRLLIDATYSPVDKISYSVEAARVEQRTDLDKLVIDMETN 181

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 182 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 238

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           S NCL+ E I Y+GDL+QRTE ++L+  N G+K
Sbjct: 239 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKK 271


>gi|295101439|emb|CBK98984.1| DNA-directed RNA polymerase subunit alpha [Faecalibacterium
           prausnitzii L2-6]
          Length = 318

 Score =  249 bits (636), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 130/291 (44%), Positives = 194/291 (66%), Gaps = 3/291 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +AEPL RGF  TLGN+LRRVL+SSL G A+T+V+IDGV+HE S+I+GV ED+T+I+LN+
Sbjct: 23  FVAEPLERGFGITLGNSLRRVLLSSLPGVAVTSVKIDGVVHEFSTIEGVKEDVTEIVLNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KGI  K+  D  K V +   GP  VTA +I+  +DIE+LNP+  I  L     + MELT 
Sbjct: 83  KGIAAKLYTDGPKTVRVEAVGPCEVTADNIKQGDDIEILNPEWHIATLGEGGKLVMELTF 142

Query: 150 SKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            KG GYVPA+ ++    E + I  + +D++Y+P+ KV+Y VES R GQ +DYDKL++ + 
Sbjct: 143 DKGRGYVPAERNKQAIIEKNDINTLPVDSIYTPVLKVNYNVESTRVGQAIDYDKLTIEVW 202

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           TDG+I  +++V+LA+R+L + L +F+N  +     +  +   +     AL   +EEL+LS
Sbjct: 203 TDGTINAQEAVSLAARVLTEHLNLFVNLSDEAAGAEIMVEKTNDDKEKALEMTIEELDLS 262

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           VRS NCL+   I  + DL+ ++E +M+++ N GRKSL E+   L ++G  L
Sbjct: 263 VRSFNCLKRAGINTVEDLVSKSEDEMMKVRNLGRKSLEEVMAKLDSLGFKL 313


>gi|149197867|ref|ZP_01874916.1| DNA-directed RNA polymerase subunit alpha [Lentisphaera araneosa
           HTCC2155]
 gi|149139088|gb|EDM27492.1| DNA-directed RNA polymerase subunit alpha [Lentisphaera araneosa
           HTCC2155]
          Length = 341

 Score =  249 bits (636), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 187/298 (62%), Gaps = 8/298 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            IAEP  +GF HTLGN LRRVL+ SL G A+T ++IDGVLHE +    V ED+T+I+LN 
Sbjct: 28  FIAEPFEKGFGHTLGNGLRRVLLHSLEGVAVTWIKIDGVLHEYAQAADVVEDVTEIVLNF 87

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K +     GD  +++ +     G VTA DI T    +V+NP+  IC LD D  +R+E  V
Sbjct: 88  KNVRFTAEGDLPRKLELRANTKGPVTAADIVTDGVTQVVNPEQYICTLDKDTPLRIEFEV 147

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           + G G+  A  ++    PIGLI +D+L+SPI++VSY V   R GQ+ DYDKL + I TDG
Sbjct: 148 ASGRGWKSADDNKPSEAPIGLIPVDSLFSPIERVSYDVSDTRVGQMTDYDKLELEIWTDG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK----VEELEL 265
            I+ ED++  ++ IL+D L +F + + P+      I     P + A+L K    V  +EL
Sbjct: 208 RISPEDALRKSAIILRDHLCVFTD-DNPEDSTASLIQT---PEDEAILSKMLIPVTSVEL 263

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           SVR+ NCLR   I Y+G+LIQ++E++ML+  NFG+KSL EIK  +  MG+ L M L D
Sbjct: 264 SVRAQNCLRNAEIKYLGELIQKSESEMLKYRNFGKKSLDEIKDKMLEMGITLNMKLKD 321


>gi|227879268|ref|ZP_03997138.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus crispatus
           JV-V01]
 gi|256844455|ref|ZP_05549941.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus crispatus
           125-2-CHN]
 gi|256849157|ref|ZP_05554590.1| RNA-polymerase DNA-directed [Lactobacillus crispatus MV-1A-US]
 gi|262047173|ref|ZP_06020131.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus crispatus
           MV-3A-US]
 gi|295692185|ref|YP_003600795.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus crispatus
           ST1]
 gi|227861162|gb|EEJ68811.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus crispatus
           JV-V01]
 gi|256613533|gb|EEU18736.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus crispatus
           125-2-CHN]
 gi|256713933|gb|EEU28921.1| RNA-polymerase DNA-directed [Lactobacillus crispatus MV-1A-US]
 gi|260572418|gb|EEX28980.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus crispatus
           MV-3A-US]
 gi|295030291|emb|CBL49770.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus crispatus
           ST1]
          Length = 312

 Score =  249 bits (636), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 135/310 (43%), Positives = 195/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDG
Sbjct: 3   EFEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++V
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDIEGPATVTADDLKVDADVQV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMELAVKNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   K  +  +  
Sbjct: 179 ESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADANAKFSEVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE+DM+R+ N GRKSL E+K
Sbjct: 239 EDDKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELTDKTESDMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLTDLGLSL 308


>gi|210611154|ref|ZP_03288768.1| hypothetical protein CLONEX_00958 [Clostridium nexile DSM 1787]
 gi|210152141|gb|EEA83148.1| hypothetical protein CLONEX_00958 [Clostridium nexile DSM 1787]
          Length = 319

 Score =  249 bits (636), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 131/293 (44%), Positives = 196/293 (66%), Gaps = 4/293 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAAI+ V+IDGVLHE SSI GV ED+T+I++N+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAISQVKIDGVLHEFSSIPGVKEDVTEIVMNL 82

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K +   D  K   I   G GVVTA DIQ   DIE++NPD VI  L+   D+ + M
Sbjct: 83  KSLAIKNTSETDEPKTAYIEFEGEGVVTAADIQVDPDIEIMNPDAVIATLNGGADSKLYM 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++KG GYV A  ++ E+ PI +I ID++Y+P+++V+ TVE+ R GQ+ DYDKL++ +
Sbjct: 143 ELTITKGRGYVSADKNKKEDLPIAVIPIDSIYTPVERVNLTVENTRVGQITDYDKLTLDV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L +FI+  E  +  +  I  +       L   ++ELEL
Sbjct: 203 YTNGTLLPDEAVSLAAKVLNEHLKLFIDLSEVAQAAEVMIEKEDDEKEKVLEMSIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           SVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L 
Sbjct: 263 SVRSYNCLKRAGINTVEELTNRTPEDMMKVRNLGRKSLEEVLAKLKELGLELS 315


>gi|312866534|ref|ZP_07726751.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus downei
           F0415]
 gi|311097965|gb|EFQ56192.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus downei
           F0415]
          Length = 312

 Score =  249 bits (636), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 126/288 (43%), Positives = 194/288 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNI
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNI 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV
Sbjct: 81  KGLAVKSYVEDEKTIELDVTGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGHTLKATMTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 141 AKNRGYVPAEGNKNDSAPVGTLAVDSIYTPVKKVNYQVEPARVGSNAGFDKLTIEIMTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  ED++ L++R+L + L +F +  E  K  +     +S+  +  L + +EE++LSVRS
Sbjct: 201 TIIPEDALGLSARVLIEHLNLFTDLTEIAKTTEVMKETESVSNDQVLDRTIEEIDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL ++TE +M+++ N GRKSL E+K  L  +GL L
Sbjct: 261 YNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVKVKLAELGLGL 308


>gi|253580648|ref|ZP_04857912.1| DNA-directed RNA polymerase [Ruminococcus sp. 5_1_39B_FAA]
 gi|251848019|gb|EES75985.1| DNA-directed RNA polymerase [Ruminococcus sp. 5_1_39BFAA]
          Length = 319

 Score =  249 bits (636), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 129/292 (44%), Positives = 195/292 (66%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDGVLHE SSI GV ED++DII+N+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDGVLHEFSSIPGVKEDVSDIIMNL 82

Query: 90  KGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K   + +  K   I   G GVVTA DIQ   DIE++NPD VI  L+   D  + M
Sbjct: 83  KSLAIKNHSTDNEPKTAYIECEGKGVVTAADIQADQDIEIMNPDQVIATLNGGKDCRLAM 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++KG GY+ A   ++++ PIG++ +DA+Y+P+ +V+ TVE+ R GQV DYDKL++ +
Sbjct: 143 ELTITKGRGYISADKGKSDDMPIGVLAVDAIYTPVDRVNMTVENTRVGQVTDYDKLTLDV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L +FI+  E  K  +  I  +       L   ++ELEL
Sbjct: 203 YTNGTLDPDEAVSLAAKVLSEHLSLFIDLSENAKTAEVMIEKEDNEKEKVLEMSIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + +L  +T  DM+++ N GRKSL E+   L  +GL L
Sbjct: 263 SVRSYNCLKRAGINTVEELCNKTSDDMMKVRNLGRKSLEEVLAKLKELGLQL 314


>gi|257440240|ref|ZP_05615995.1| DNA-directed RNA polymerase, alpha subunit [Faecalibacterium
           prausnitzii A2-165]
 gi|257197274|gb|EEU95558.1| DNA-directed RNA polymerase, alpha subunit [Faecalibacterium
           prausnitzii A2-165]
          Length = 332

 Score =  249 bits (636), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 130/291 (44%), Positives = 194/291 (66%), Gaps = 3/291 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +AEPL RGF  TLGN+LRRVL+SSL G A+T+V+IDGV+HE S+I+GV ED+T+I+LN+
Sbjct: 37  FVAEPLERGFGITLGNSLRRVLLSSLPGVAVTSVKIDGVVHEFSTIEGVKEDVTEIVLNL 96

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KGI  K+  D  K V +   GP  VTA +I+  +DIE+LNP+  I  L     + MELT 
Sbjct: 97  KGIAAKLYTDGPKTVRVEAVGPCEVTADNIKQGDDIEILNPEWHIATLGEGGKLVMELTF 156

Query: 150 SKGHGYVPAKHHR---TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            KG GYVPA+ ++    E + I  + +D++Y+P+ KV+Y VES R GQ +DYDKL++ + 
Sbjct: 157 DKGRGYVPAERNKQAIVEKNDINTLPVDSIYTPVLKVNYNVESTRVGQAIDYDKLTIEVW 216

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           TDG+I  +++V+LA+R+L + L +F+N  +     +  +   +     AL   +EEL+LS
Sbjct: 217 TDGTINAQEAVSLAARVLTEHLNLFVNLSDEAAGTEIMVEKTNDDKEKALEMTIEELDLS 276

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           VRS NCL+   I  + DL+ ++E +M+++ N GRKSL E+   L ++G  L
Sbjct: 277 VRSFNCLKRAGINTVEDLVSKSEDEMMKVRNLGRKSLEEVMAKLDSLGFKL 327


>gi|310644172|ref|YP_003948931.1| DNA-directed RNA polymerase subunit alpha [Paenibacillus polymyxa
           SC2]
 gi|309249123|gb|ADO58690.1| DNA-directed RNA polymerase subunit alpha [Paenibacillus polymyxa
           SC2]
          Length = 314

 Score =  249 bits (636), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 125/288 (43%), Positives = 195/288 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDGVLHE +++ GV ED+T+IILN+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDGVLHEFATVPGVKEDVTEIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K ++LK+  D  K + I   G GVVTAGDI+  +D+E+LNPD  I  L   + + M +  
Sbjct: 83  KALSLKIHSDEEKVLEIDAEGEGVVTAGDIRADSDVEILNPDLHIATLGPGSRLHMRIFA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           ++G GYV    ++ ++ PIG+I +D++Y+PI +V+Y VE+ R GQV +YDKL++ + TDG
Sbjct: 143 NRGRGYVKQDRNKRDDQPIGVIPVDSIYTPIARVNYGVENTRVGQVTNYDKLTLEVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  E++V+L ++IL + + +F+   +  K+ +  +  +       L   +EEL+LSVRS
Sbjct: 203 TIRPEEAVSLGAKILTEHVMLFVGLTDEAKDAEIMVEKEEDKKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++E DM+++ N GRKSL E++  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELTTKSEEDMMKVRNLGRKSLEEVQEKLEELGLGL 310


>gi|300857219|ref|YP_003782203.1| DNA-directed RNA polymerase subunit alpha [Clostridium ljungdahlii
           DSM 13528]
 gi|300437334|gb|ADK17101.1| DNA-directed RNA polymerase alpha chain [Clostridium ljungdahlii
           DSM 13528]
          Length = 315

 Score =  249 bits (635), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 128/296 (43%), Positives = 197/296 (66%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E+ N    + EPL RG+  TLGNALRR+L+SSL G A   ++IDGVLHE S+I+GV ED
Sbjct: 15  SEDGNYGKFVVEPLERGYGITLGNALRRILLSSLPGVAANHIKIDGVLHEFSTIRGVKED 74

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + ++ILNIK + LKM+G+  K + I  +GPG V AGDI+T  D+E++N D  I  LD D 
Sbjct: 75  VAELILNIKELALKMNGEGPKTIYIDAQGPGEVVAGDIKTDGDVEIINKDLHIATLDDDG 134

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ME+ V+ G GYV  + +++E+ PIG I +D++Y+PIK+V++ VE+ R GQ+ DYDKL
Sbjct: 135 KLYMEIAVNGGRGYVSQRKNKSEDMPIGTIPVDSIYTPIKRVNFAVENTRVGQITDYDKL 194

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           S+ + T+G+I  +++V+L+++IL +   +F+   +    V+  +  +       L   +E
Sbjct: 195 SLEVWTNGTILPDEAVSLSAKILIEHFKLFMTLTDHANNVEIMVEKEEDKKEKVLEMTIE 254

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           EL+LSVRS NCL+   I  + +L +RT  DM+++ N G+KSL E++  L  +GL L
Sbjct: 255 ELDLSVRSYNCLKRAGINTVQELTERTMDDMMKVRNLGKKSLEEVEQKLDALGLSL 310


>gi|315037556|ref|YP_004031124.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus amylovorus
           GRL 1112]
 gi|325956029|ref|YP_004286639.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           acidophilus 30SC]
 gi|312275689|gb|ADQ58329.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus amylovorus
           GRL 1112]
 gi|325332594|gb|ADZ06502.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           acidophilus 30SC]
 gi|327182852|gb|AEA31299.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus amylovorus
           GRL 1118]
          Length = 312

 Score =  249 bits (635), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 134/310 (43%), Positives = 195/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDG
Sbjct: 3   EFEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++V
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMELAVKNGRGYVTASDNKSDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   +  +  +  
Sbjct: 179 ESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADANTQFSEVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE+DM+R+ N GRKSL E+K
Sbjct: 239 EDDKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELTDKTESDMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLADLGLSL 308


>gi|300521220|gb|ADK25829.1| RpoA [Vibrio vulnificus]
 gi|300521222|gb|ADK25830.1| RpoA [Vibrio vulnificus]
 gi|300521224|gb|ADK25831.1| RpoA [Vibrio vulnificus]
 gi|300521226|gb|ADK25832.1| RpoA [Vibrio vulnificus]
 gi|300521228|gb|ADK25833.1| RpoA [Vibrio vulnificus]
 gi|300521230|gb|ADK25834.1| RpoA [Vibrio vulnificus]
 gi|300521232|gb|ADK25835.1| RpoA [Vibrio vulnificus]
 gi|300521234|gb|ADK25836.1| RpoA [Vibrio vulnificus]
 gi|300521236|gb|ADK25837.1| RpoA [Vibrio vulnificus]
 gi|300521238|gb|ADK25838.1| RpoA [Vibrio vulnificus]
 gi|300521240|gb|ADK25839.1| RpoA [Vibrio vulnificus]
          Length = 286

 Score =  249 bits (635), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 127/278 (45%), Positives = 190/278 (68%), Gaps = 8/278 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 12  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 71

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 72  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 131

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 132 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 191

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 192 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 248

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 249 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 286


>gi|322391224|ref|ZP_08064696.1| DNA-directed RNA polymerase subunit alpha [Streptococcus peroris
           ATCC 700780]
 gi|321145977|gb|EFX41366.1| DNA-directed RNA polymerase subunit alpha [Streptococcus peroris
           ATCC 700780]
          Length = 311

 Score =  249 bits (635), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 138/312 (44%), Positives = 202/312 (64%), Gaps = 8/312 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSIDIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILNIKGI +K      K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNIKGIAVKSYVKDEKTIELDVEGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A  +  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGASFKATMTVNTGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK--EVKEDI 245
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  K  EV ++ 
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSTEVMKEA 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           + +S   +  L + +EEL+LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E
Sbjct: 239 DTES--DDRILERTIEELDLSVRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEE 296

Query: 306 IKGVLGTMGLFL 317
           +K  L  +GL L
Sbjct: 297 VKLKLIDLGLGL 308


>gi|322388376|ref|ZP_08061979.1| DNA-directed RNA polymerase subunit alpha [Streptococcus infantis
           ATCC 700779]
 gi|321140689|gb|EFX36191.1| DNA-directed RNA polymerase subunit alpha [Streptococcus infantis
           ATCC 700779]
          Length = 311

 Score =  249 bits (635), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 138/312 (44%), Positives = 202/312 (64%), Gaps = 8/312 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSIDIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILNIKGI +K      K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNIKGIAVKSYVKDEKTIELDVEGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A  +  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGASFKATMTVNTGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK--EVKEDI 245
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  K  EV ++ 
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSAEVMKEA 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           + +S   +  L + +EEL+LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E
Sbjct: 239 DTES--DDRILERTIEELDLSVRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEE 296

Query: 306 IKGVLGTMGLFL 317
           +K  L  +GL L
Sbjct: 297 VKLKLIDLGLGL 308


>gi|260895674|ref|ZP_05904170.1| DNA-directed RNA polymerase, alpha subunit [Vibrio parahaemolyticus
           Peru-466]
 gi|308089502|gb|EFO39197.1| DNA-directed RNA polymerase, alpha subunit [Vibrio parahaemolyticus
           Peru-466]
          Length = 318

 Score =  249 bits (635), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 132/314 (42%), Positives = 204/314 (64%), Gaps = 11/314 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H+  +  PIG + +DA 
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHNEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVL 310
           N G+  L+ +K  L
Sbjct: 295 NLGKNLLLRLKTYL 308


>gi|225026391|ref|ZP_03715583.1| hypothetical protein EUBHAL_00640 [Eubacterium hallii DSM 3353]
 gi|224956280|gb|EEG37489.1| hypothetical protein EUBHAL_00640 [Eubacterium hallii DSM 3353]
          Length = 319

 Score =  249 bits (635), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 127/292 (43%), Positives = 198/292 (67%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAA++AV+I GVLHE SSI GV ED+T+II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSAVKIKGVLHEFSSIPGVKEDVTEIIMNI 82

Query: 90  KGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K +  S+  KR  I   G GVVTA DIQ  +DIE++NPD VI  L    D+    
Sbjct: 83  KELAIKNNSSSNEPKRAFIEFSGEGVVTAADIQVDSDIEIINPDLVIATLSGGADSHFEA 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++KG GYV A  +++E+  I +I +D++Y+P+++V+ TV++ R GQ+ D+DKL++ +
Sbjct: 143 ELTITKGRGYVGADKNKSEDQSIDVIAVDSIYTPVERVNLTVQNTRVGQITDFDKLTLDV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L +FI+  E  ++ +  +     P +  L   ++ELEL
Sbjct: 203 FTNGTLAPDEAVSLAAKVLSEHLNLFIDLSENAQKAEVMVETAQDPVDKVLEMNIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + +L  +T  DM+++ N GRKSL E+   L  +GL L
Sbjct: 263 SVRSYNCLKRAGINTVEELTNKTPEDMMKVRNLGRKSLEEVLAKLKELGLSL 314


>gi|81429352|ref|YP_396353.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus sakei
           subsp. sakei 23K]
 gi|90110847|sp|Q38UT7|RPOA_LACSS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|78610995|emb|CAI56047.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus sakei
           subsp. sakei 23K]
          Length = 312

 Score =  249 bits (635), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 132/310 (42%), Positives = 199/310 (64%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E  N    + EPL RG+  TLGN+LRR+L++SL G A+T +QIDG
Sbjct: 3   EFEKPN----ITKVDESTNYGKFVVEPLERGYGTTLGNSLRRILLASLPGTAVTDIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILNIK + LK+  +  K + I  +GP  VTA DI + +D+EV
Sbjct: 59  VLHEFSTIDGVLEDVTQIILNIKKLALKLHVEEDKTIEIDVKGPATVTAADIISDDDVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D  IC +       + +TV KG GYV A  +++++ PIG++ ID++Y+PI +V+Y V
Sbjct: 119 LNTDQYICTVAEGGNFHVRMTVKKGRGYVAAVQNKSDDMPIGVLPIDSIYTPISRVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL++ + T+GSI+  ++++LA++I+ + L +F++  +  K  +  +  
Sbjct: 179 ESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKIMTEHLAIFVDLTDEAKNAEIMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+++ N GRKSL E+K
Sbjct: 239 EETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTDKSEADMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLFDLGLGL 308


>gi|313112850|ref|ZP_07798496.1| DNA-directed RNA polymerase, alpha subunit [Faecalibacterium cf.
           prausnitzii KLE1255]
 gi|310624755|gb|EFQ08064.1| DNA-directed RNA polymerase, alpha subunit [Faecalibacterium cf.
           prausnitzii KLE1255]
          Length = 333

 Score =  249 bits (635), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 130/291 (44%), Positives = 194/291 (66%), Gaps = 3/291 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +AEPL RGF  TLGN+LRRVL+SSL G A+T+V+IDGV+HE S+I+GV ED+T+I+LN+
Sbjct: 37  FVAEPLERGFGITLGNSLRRVLLSSLPGVAVTSVKIDGVVHEFSTIEGVKEDVTEIVLNL 96

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KGI  K+  D  K V +   GP  VTA +I+  +DIE+LNP+  I  L     + MELT 
Sbjct: 97  KGIAAKLYTDGPKTVRVEAVGPCEVTADNIKQGDDIEILNPEWHIATLGEGGKLVMELTF 156

Query: 150 SKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            KG GYVPA+ ++    E + I  + +D++Y+P+ KV+Y VES R GQ +DYDKL++ + 
Sbjct: 157 DKGRGYVPAERNKQAIIEKNDINTLPVDSIYTPVLKVNYNVESTRVGQAIDYDKLTIEVW 216

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           TDG+I  +++V+LA+R+L + L +F+N  +     +  +   +     AL   +EEL+LS
Sbjct: 217 TDGTINAQEAVSLAARVLTEHLNLFVNLSDEAAGAEIMVEKTNDDKEKALEMTIEELDLS 276

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           VRS NCL+   I  + DL+ ++E +M+++ N GRKSL E+   L ++G  L
Sbjct: 277 VRSFNCLKRAGINTVEDLVSKSEDEMMKVRNLGRKSLEEVMAKLDSLGFKL 327


>gi|255526607|ref|ZP_05393514.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           carboxidivorans P7]
 gi|296187296|ref|ZP_06855692.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           carboxidivorans P7]
 gi|255509715|gb|EET86048.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           carboxidivorans P7]
 gi|296048167|gb|EFG87605.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           carboxidivorans P7]
          Length = 315

 Score =  249 bits (635), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 126/288 (43%), Positives = 193/288 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGNALRR+L+SSL G A   ++IDGVLHE S+++GV ED+ +++LNI
Sbjct: 23  FVVEPLERGYGITLGNALRRILLSSLPGVAANHIKIDGVLHEFSTVRGVKEDVAELVLNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM+G+  K + I  +GPG V AGDI+T  DIE++N D  I  LD D  + ME+ V
Sbjct: 83  KCLALKMNGEGPKTIYIDAQGPGEVVAGDIKTDGDIEIINKDLHIATLDDDGKLYMEIQV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           + G GYV    +++E+ PIG I ID++Y+PIK+V++ VE+ R GQ+ DYDKLS+ + T+G
Sbjct: 143 NTGRGYVSQTKNKSEDMPIGTIAIDSIYTPIKRVNFVVENTRVGQITDYDKLSLEVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  E++++L+++IL +   +F+   +    V+  +  +       L   +EEL+LSVRS
Sbjct: 203 TIMPEEAISLSAKILIEHFKLFMTLTDHANNVEIMVEKEEDKKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L +RT  DM+++ N G+KSL E++  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELTERTMDDMMKVRNLGKKSLEEVEQKLEALGLSL 310


>gi|293380402|ref|ZP_06626473.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus crispatus
           214-1]
 gi|290923085|gb|EFE00017.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus crispatus
           214-1]
          Length = 312

 Score =  248 bits (634), Expect = 7e-64,   Method: Compositional matrix adjust.
 Identities = 134/310 (43%), Positives = 195/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDG
Sbjct: 3   EFEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++V
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDIEGPATVTADDLKVDADVQV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPI+KV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMELAVKNGRGYVAASDNKSDDMPIGVIPVDSLFSPIRKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   K  +  +  
Sbjct: 179 ESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADANAKFSEVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE+DM+R+ N GRKSL E+K
Sbjct: 239 EDDKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELTDKTESDMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLTDLGLSL 308


>gi|254517499|ref|ZP_05129555.1| RNA polymerase subunit alpha [Clostridium sp. 7_2_43FAA]
 gi|226911248|gb|EEH96449.1| RNA polymerase subunit alpha [Clostridium sp. 7_2_43FAA]
          Length = 315

 Score =  248 bits (633), Expect = 8e-64,   Method: Compositional matrix adjust.
 Identities = 128/290 (44%), Positives = 202/290 (69%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGNALRR+L+SSL GAA T+V+IDGVLHE S+++GV ED+T+IILNIK
Sbjct: 24  VIEPLERGYGITLGNALRRILLSSLPGAAPTSVKIDGVLHEFSTVQGVKEDVTEIILNIK 83

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            + L M+G+  K + I  +GPGVVT  DI+T  D+EV++ D  I  LD +A + ME+TV+
Sbjct: 84  SLALIMNGEGPKTIYIDAQGPGVVTGADIKTDGDVEVVSKDLHIATLDDNAKLYMEITVN 143

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           +G GYV    +++E+ P+  I +D++Y+P+K+V++TVE+ R GQ+ DYDKL++ I T+G+
Sbjct: 144 RGRGYVTQNKNKSEDLPLSAIAVDSIYTPVKRVNFTVENTRVGQITDYDKLTLEIWTNGT 203

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I  +++++L+++IL +   +F++  +   +V+  I  +       L   VEEL+LSVRS 
Sbjct: 204 IKIDEAISLSAKILIEHFKLFMSLGDSTNDVEIMIEKEEDKKEKVLEMTVEELDLSVRSY 263

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           NCL+   I  + +L  ++  DM+++ N G+KSL E++  L  +GL L +N
Sbjct: 264 NCLKRAGINTVQELAGKSMDDMMKVRNLGKKSLEEVERKLKELGLGLRLN 313


>gi|225387210|ref|ZP_03756974.1| hypothetical protein CLOSTASPAR_00962 [Clostridium asparagiforme
           DSM 15981]
 gi|225046689|gb|EEG56935.1| hypothetical protein CLOSTASPAR_00962 [Clostridium asparagiforme
           DSM 15981]
          Length = 330

 Score =  248 bits (633), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 128/292 (43%), Positives = 193/292 (66%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDGVLHE SSI GV ED+T+II+NI
Sbjct: 33  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDGVLHEFSSIAGVKEDVTEIIMNI 92

Query: 90  KGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K + D+   K   I   G GV+TA DIQ   DIE++NPD +I  L    D+   M
Sbjct: 93  KSLAIKNNSDTDEPKVAYIEFEGEGVITAADIQADADIEIMNPDQIIATLSGGTDSKFYM 152

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++KG GYV A  ++ ++ PIG+I +D++Y+P+++V+  V + R GQ  DYDKL++ I
Sbjct: 153 ELTITKGRGYVSADKNKNDDLPIGVIAVDSIYTPVERVNMAVANTRVGQQTDYDKLTLEI 212

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L +FI+  E  K  +  +  +       L   ++ELEL
Sbjct: 213 YTNGTLAPDEAVSLAAKVLSEHLNLFIDLSENAKTAEIMVEKEDNEKEKVLEMNIDELEL 272

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L
Sbjct: 273 SVRSYNCLKRAGINTVEELCNRTSEDMMKVRNLGRKSLEEVLAKLKELGLQL 324


>gi|323703520|ref|ZP_08115166.1| DNA-directed RNA polymerase, alpha subunit [Desulfotomaculum
           nigrificans DSM 574]
 gi|323531511|gb|EGB21404.1| DNA-directed RNA polymerase, alpha subunit [Desulfotomaculum
           nigrificans DSM 574]
          Length = 315

 Score =  248 bits (633), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 131/300 (43%), Positives = 197/300 (65%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           IV   E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+V+I+GVLHE S++ G
Sbjct: 11  IVEQSEDNTYGKFVVEPLERGYGITLGNSLRRILLSSLPGAAVTSVKIEGVLHEFSTVPG 70

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+TDIILN+K + LK+  D  K + I     G VTAGDI    D+E+LNPD  +  L
Sbjct: 71  VREDVTDIILNLKNLCLKIHSDEEKVLRIEADTEGPVTAGDIIHDADVEILNPDLHLATL 130

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           D    + ME+T +KG GYV A+ ++     IG+I +D++Y+P++KV+Y VE+ R GQ+ D
Sbjct: 131 DAGGRLYMEITANKGRGYVSAEKNKKGEHIIGVIPVDSIYTPVRKVNYNVENTRVGQITD 190

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           YDKL++ + T+GSI  +++ +L+++IL + L +FI   E   +V+  +  +    +  + 
Sbjct: 191 YDKLTLEVWTNGSIRPDEATSLSAKILSEHLRLFIGLTETVNDVEIMVEKEEEQKDKIME 250

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +EEL+LSVRS NCL+   I  + +LIQR E DM+++ N G+KSL E+   L  +GL L
Sbjct: 251 MTIEELDLSVRSYNCLKRAGINTVEELIQRNEEDMMKVRNLGKKSLEEVMNKLAELGLSL 310


>gi|148544670|ref|YP_001272040.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus reuteri
           DSM 20016]
 gi|184154023|ref|YP_001842364.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus reuteri
           JCM 1112]
 gi|194466927|ref|ZP_03072914.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus reuteri
           100-23]
 gi|227363793|ref|ZP_03847900.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus reuteri
           MM2-3]
 gi|227543597|ref|ZP_03973646.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus reuteri
           CF48-3A]
 gi|300909374|ref|ZP_07126835.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus reuteri
           SD2112]
 gi|325683004|ref|ZP_08162520.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus reuteri
           MM4-1A]
 gi|166991521|sp|A5VLH9|RPOA_LACRD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|229564249|sp|B2G8V2|RPOA_LACRJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|148531704|gb|ABQ83703.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus reuteri
           DSM 20016]
 gi|183225367|dbj|BAG25884.1| DNA-directed RNA polymerase alpha subunit [Lactobacillus reuteri
           JCM 1112]
 gi|194453963|gb|EDX42860.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus reuteri
           100-23]
 gi|227071150|gb|EEI09466.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus reuteri
           MM2-3]
 gi|227186437|gb|EEI66508.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus reuteri
           CF48-3A]
 gi|300893239|gb|EFK86598.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus reuteri
           SD2112]
 gi|324977354|gb|EGC14305.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus reuteri
           MM4-1A]
          Length = 314

 Score =  248 bits (633), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 135/310 (43%), Positives = 203/310 (65%), Gaps = 6/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E +N    + EPL RG+  TLGN+LRRVL++SL GAAIT++QIDG
Sbjct: 3   EFEKPN----IHKVEETDNYGKFVVEPLERGYGTTLGNSLRRVLIASLPGAAITSMQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K ++LK+  +  K + +  +GP  VTA DIQ  N++ +
Sbjct: 59  VLHEFSTVEGVTEDVTQIILNLKKVSLKLDSEDQKNLELDVKGPAEVTASDIQGDNEVTI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSY 185
           LNPD  I  +   A + ++LT  KG GY+ A  ++   D   IG++ ID++Y+PI++V+Y
Sbjct: 119 LNPDLHIATVADGAELHIKLTADKGRGYLSANDNKARMDDLAIGVLPIDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVE+AR GQ  DYDKL++ + TDGS+T  ++V+L ++IL + L MF++  E  +  +  +
Sbjct: 179 TVENARVGQRNDYDKLTLDVWTDGSLTPTEAVSLGAKILTEHLAMFVDLTETAQNAQVMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   +EEL+LSVRS NCL+   I  + +L  RT +DM+++ N G+KSL E
Sbjct: 239 EKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVKELTDRTVSDMMKVRNLGQKSLEE 298

Query: 306 IKGVLGTMGL 315
           IK  L  +G+
Sbjct: 299 IKLKLNDLGV 308


>gi|157493267|gb|ABV57999.1| RNA polymerase alpha subunit [Vibrio mimicus]
          Length = 283

 Score =  248 bits (633), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 125/276 (45%), Positives = 190/276 (68%), Gaps = 8/276 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 11  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 70

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V 
Sbjct: 71  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVE 130

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 131 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMET 190

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 191 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 247

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 248 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 283


>gi|254444876|ref|ZP_05058352.1| DNA-directed RNA polymerase, alpha subunit [Verrucomicrobiae
           bacterium DG1235]
 gi|198259184|gb|EDY83492.1| DNA-directed RNA polymerase, alpha subunit [Verrucomicrobiae
           bacterium DG1235]
          Length = 307

 Score =  248 bits (633), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 133/308 (43%), Positives = 191/308 (62%), Gaps = 11/308 (3%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
           AEP   G+ HT+GN+LRR+L+SS+ GAAI++V+I+GV HE  S+ G+ ED+TDI+LN+K 
Sbjct: 4   AEPFEAGYGHTIGNSLRRILLSSIEGAAISSVKIEGVSHEFQSVDGIVEDITDIVLNLKK 63

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           + L        ++ I     G +TA DIQ  +++EV+NPD +IC LD +     EL +  
Sbjct: 64  VLLVCHKREGVKLMINTNRSGAITAADIQPDSNVEVINPDQIICTLDREMPFTAELEIKV 123

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GY P   ++ E DPIG+I ID+L+SP+  V Y VE+   GQ+ DYDKL + + TDG I
Sbjct: 124 GRGYCPGDDNKDEEDPIGVIAIDSLFSPVSLVKYAVEATLVGQITDYDKLLLEVWTDGRI 183

Query: 212 TGEDSVALASRILQDQLGMFIN-------FEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           T +D++  A+ IL+  L +F N       FE+   EV E+ N         L   V E+E
Sbjct: 184 TPDDALKQAAAILKHHLDVFDNVSDENYEFEDEGGEVSEEQN----KLRKLLNMSVNEIE 239

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           LSVR+ NCL   NI  +G+L  ++E +ML+  NFG+KSL EIK  L ++GL LGM   + 
Sbjct: 240 LSVRAANCLNNANITTVGELAMKSEQEMLKYRNFGKKSLNEIKDKLESLGLSLGMKFDER 299

Query: 325 PPESIEEL 332
             +S +EL
Sbjct: 300 LLDSKKEL 307


>gi|302388740|ref|YP_003824561.1| DNA-directed RNA polymerase subunit alpha [Thermosediminibacter
           oceani DSM 16646]
 gi|302199368|gb|ADL06938.1| DNA-directed RNA polymerase subunit alpha [Thermosediminibacter
           oceani DSM 16646]
          Length = 316

 Score =  248 bits (632), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 131/288 (45%), Positives = 190/288 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EPL RG+  TLGN+LRRVL+SSL GAAIT+V+IDGV HE S+I GV ED  +II+NI
Sbjct: 23  IVIEPLERGYGTTLGNSLRRVLLSSLPGAAITSVKIDGVQHEFSTIPGVLEDTVEIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +KM  D  K + I  +G G VTA DI    D+E++N DH I  LD D  +  ELT+
Sbjct: 83  KGLAIKMHSDEPKLLRIEAQGEGEVTAKDIICDADVEIINKDHHIATLDKDGRLFAELTL 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYV A+ ++    PIG+I ID++++P+ K +YTVE  R GQV DYDKL++ + T+G
Sbjct: 143 EKGKGYVTAEKNKKPGQPIGIIPIDSIFTPVIKANYTVEHTRVGQVTDYDKLTLEVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  +++V+ A++IL D   +F       K+V+  +  +       L   +EEL+LSVRS
Sbjct: 203 TIKPDEAVSAAAKILIDYFNLFTGLTTAVKKVEAPVEKEKDERERILEMPIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  +G+LIQ+T  +M+++ N G+KSL E++  L  + L L
Sbjct: 263 YNCLKRAGINTIGELIQKTPEEMMKVRNLGKKSLEEVEEKLAALNLSL 310


>gi|269997192|gb|ACZ57818.1| RNA polymerase alpha subunit [Vibrio owensii]
 gi|269997194|gb|ACZ57819.1| RNA polymerase alpha subunit [Vibrio owensii]
 gi|269997196|gb|ACZ57820.1| RNA polymerase alpha subunit [Vibrio sp. CAIM 994]
          Length = 294

 Score =  248 bits (632), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 126/276 (45%), Positives = 190/276 (68%), Gaps = 8/276 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H+  +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHNEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294


>gi|322377205|ref|ZP_08051697.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus sp. M334]
 gi|321281918|gb|EFX58926.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus sp. M334]
          Length = 311

 Score =  248 bits (632), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 136/312 (43%), Positives = 204/312 (65%), Gaps = 8/312 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK--EVKEDI 245
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  K  EV ++ 
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSTEVMKEA 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           + +S   +  L + +EEL+LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E
Sbjct: 239 DTES--DDRILDRTIEELDLSVRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEE 296

Query: 306 IKGVLGTMGLFL 317
           +K  L  +GL L
Sbjct: 297 VKFKLIDLGLGL 308


>gi|302379835|ref|ZP_07268319.1| DNA-directed RNA polymerase, alpha subunit [Finegoldia magna
           ACS-171-V-Col3]
 gi|302312423|gb|EFK94420.1| DNA-directed RNA polymerase, alpha subunit [Finegoldia magna
           ACS-171-V-Col3]
          Length = 317

 Score =  248 bits (632), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 133/306 (43%), Positives = 197/306 (64%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           IV   E+ N    +  PL RG+  TLGN+LRRVL+SSL GAAI+ + I GV HE+S+IKG
Sbjct: 11  IVELDEQNNYGKFVIMPLERGYGTTLGNSLRRVLLSSLPGAAISKINIQGVAHEMSTIKG 70

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +IILN+KGI +K   +    + +  +GP V+TA DI    D+EV NPDH I  L
Sbjct: 71  VKEDVPEIILNLKGIAVKKYNEEPISLNVDIKGPCVLTAKDILVDTDLEVKNPDHYIATL 130

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + DA + M++TV  G GY  ++ ++TE D IG I ID+L+SP+KKV++TV++AR GQV+D
Sbjct: 131 NEDASLEMQITVINGKGYKISEFNKTEEDIIGDIAIDSLFSPVKKVNFTVDNARVGQVID 190

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           YDKL++ + T+G+I  +D+++  S IL + L +F      +     D           ++
Sbjct: 191 YDKLTIEVWTNGTIRPQDALSEGSNILINCLELFSELPNYECNTNSDDEDNQKDKETQMV 250

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +EEL+ S+RS NCL+  NI  +GD++  T+ADM+++ NFG+KSL E++  L  MGL  
Sbjct: 251 INIEELDFSLRSFNCLKRANINTVGDIVSHTKADMMKIKNFGKKSLDEVEEKLQEMGLAF 310

Query: 318 GMNLPD 323
              + D
Sbjct: 311 KQEIKD 316


>gi|126654446|ref|ZP_01726183.1| DNA-directed RNA polymerase subunit alpha [Bacillus sp. B14905]
 gi|169830005|ref|YP_001700163.1| DNA-directed RNA polymerase subunit alpha [Lysinibacillus
           sphaericus C3-41]
 gi|299541958|ref|ZP_07052281.1| DNA-directed RNA polymerase subunit alpha [Lysinibacillus
           fusiformis ZC1]
 gi|126589096|gb|EAZ83300.1| DNA-directed RNA polymerase subunit alpha [Bacillus sp. B14905]
 gi|168994493|gb|ACA42033.1| DNA-directed RNA polymerase alpha chain [Lysinibacillus sphaericus
           C3-41]
 gi|298725696|gb|EFI66337.1| DNA-directed RNA polymerase subunit alpha [Lysinibacillus
           fusiformis ZC1]
          Length = 314

 Score =  248 bits (632), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 124/288 (43%), Positives = 191/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+ +TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+  IILN+
Sbjct: 23  FVVEPLERGYGNTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVASIILNV 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +G G VTA DI   +D+E+LNPD  I  +  +  +RM +  
Sbjct: 83  KKLALKIYSDEEKVIEIDVKGDGTVTAADITHDSDVEILNPDLYIATIAKNGHLRMRMYA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY PA  ++ E+ PIG+I ID++Y+P+ +V++ VE+ R GQ  DYDKLS+ + TDG
Sbjct: 143 QRGRGYTPADQNKREDLPIGVIPIDSIYTPVSRVNFQVENTRVGQSSDYDKLSLDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  +++++L ++IL + L +F+   +  +  +  +  +       L   +EEL+LSVRS
Sbjct: 203 SIGPKEAISLGAKILTEHLNIFVGMTDEAQTAEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++E DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVLELANKSEDDMMKVRNLGRKSLEEVKAKLEELGLGL 310


>gi|163790168|ref|ZP_02184602.1| DNA-directed RNA polymerase subunit alpha [Carnobacterium sp. AT7]
 gi|328958703|ref|YP_004376089.1| DNA-directed RNA polymerase subunit alpha [Carnobacterium sp. 17-4]
 gi|159874659|gb|EDP68729.1| DNA-directed RNA polymerase subunit alpha [Carnobacterium sp. AT7]
 gi|328675027|gb|AEB31073.1| DNA-directed RNA polymerase subunit alpha [Carnobacterium sp. 17-4]
          Length = 314

 Score =  248 bits (632), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 127/288 (44%), Positives = 191/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T +QIDGVLHE S++ GV ED+T IILNI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTTIQIDGVLHEFSTVDGVVEDVTSIILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+     K + I  +GP VVTA DI   +D+E+LNPD  IC +   A   + +T 
Sbjct: 83  KKLALKLYSGEDKTIEIDVKGPAVVTAADIIYDSDVEILNPDLYICTVAEGARFHVRMTA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A+H++ ++ PIG++ ID++Y+P+ +V+Y VE+ R GQ    DKL++ +  DG
Sbjct: 143 KSGRGYVRAEHNKQDDMPIGVLPIDSIYTPVSRVNYQVENTRVGQKNISDKLTLDVWADG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI+ E++V+LA++IL + L +F+N  +  ++ +  +  +       L   +EEL+LSVRS
Sbjct: 203 SISPEEAVSLAAKILTEHLNVFVNLTDEARKAEIMVEKEETHKEKMLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  +TEA+M+++ N GRKSL E+K  L  + L L
Sbjct: 263 YNCLKRAGINSVQELTDKTEAEMIKVRNLGRKSLEEVKFKLAELDLNL 310


>gi|157493255|gb|ABV57993.1| RNA polymerase alpha subunit [Vibrio mimicus]
          Length = 285

 Score =  248 bits (632), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 125/278 (44%), Positives = 190/278 (68%), Gaps = 8/278 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G  +T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 11  EPLERGFGHTLGNALRRILLSSMPGCVVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 70

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V 
Sbjct: 71  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVE 130

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 131 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMET 190

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 191 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 247

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 248 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 285


>gi|218135253|ref|ZP_03464057.1| hypothetical protein BACPEC_03158 [Bacteroides pectinophilus ATCC
           43243]
 gi|217990638|gb|EEC56649.1| hypothetical protein BACPEC_03158 [Bacteroides pectinophilus ATCC
           43243]
          Length = 319

 Score =  248 bits (632), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 128/295 (43%), Positives = 199/295 (67%), Gaps = 4/295 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAA++ V+I+GVLHE SSI GV ED+T+II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIEGVLHEFSSIPGVKEDVTEIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD--AVVRM 145
           K + +K + DS +  T +    G GVV A DIQT  DIE++NPD VI +L+      + M
Sbjct: 83  KNLAIKNNSDSDEPKTAYIEFEGEGVVKASDIQTDGDIEIINPDLVIAHLNGGDGCKLSM 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++KG GYV +  ++TE+ P+G+I +D++Y+P+++V+  V++ R GQV DYDKL++ +
Sbjct: 143 ELTITKGRGYVSSDKNKTEDTPVGVIAVDSIYTPVERVNMAVQNTRVGQVTDYDKLTLDV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L +FI+  E  K  +  +   +      L   ++ELEL
Sbjct: 203 YTNGTLAPDEAVSLAAKVLSEHLNLFIDLSENAKTAEIMVEESTDEHEKVLEMTIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           SVRS NCL+   I  + +L  +T  DM+++ N GRKSL E+   L  +GL L  N
Sbjct: 263 SVRSYNCLKRAGINTVEELCNKTPDDMMKVRNLGRKSLEEVLAKLKELGLQLSPN 317


>gi|87306331|ref|ZP_01088478.1| DNA-directed RNA polymerase alpha subunit [Blastopirellula marina
           DSM 3645]
 gi|87290510|gb|EAQ82397.1| DNA-directed RNA polymerase alpha subunit [Blastopirellula marina
           DSM 3645]
          Length = 328

 Score =  247 bits (631), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 128/300 (42%), Positives = 185/300 (61%), Gaps = 4/300 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            IAEP  RGF  T+GN+LRR+L+SSL GAA+T +++ G  HE +SI GV ED+T+I+LN 
Sbjct: 28  FIAEPFERGFGVTIGNSLRRILLSSLEGAAVTQIKVRGAQHEFTSIPGVVEDMTEIVLNT 87

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I +K   +  K VTI K+GP  +T  DIQ   +++++N D  IC +  D    ME+ V
Sbjct: 88  KAIVVKKHSEMTKVVTIEKQGPCTITGADIQCDPEVDIINKDIHICTITGDIPFMMEMVV 147

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GY+PA  H T    IG+I +DA+YSP+ +V Y VE  R GQ  +YDKL++ I TDG
Sbjct: 148 ESGRGYIPATEHSTAEHEIGIIPVDAVYSPVTRVRYEVEETRVGQKTNYDKLTLEIWTDG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE----ELEL 265
           SI  E S+  A++IL+  L  F+ + E   ++      +S   +P L  K+     E+ L
Sbjct: 208 SIHPEYSLVEAAKILRKHLNPFVQYNELGSKISIPSRTQSSGLDPVLESKLNMSLAEMHL 267

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           SVR++NCL  ENI  + DL++RTE  ++ + NFG  +L E++  L  +GL LGM +   P
Sbjct: 268 SVRASNCLESENINTVRDLVRRTEDQLMEVRNFGETTLTEVREKLKELGLHLGMRVQSAP 327


>gi|58416044|emb|CAH57436.1| RNA polymerase alpha-subunit [Vibrio sp. R-21433]
          Length = 294

 Score =  247 bits (631), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 126/276 (45%), Positives = 189/276 (68%), Gaps = 8/276 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294


>gi|193214826|ref|YP_001996025.1| DNA-directed RNA polymerase subunit alpha [Chloroherpeton
           thalassium ATCC 35110]
 gi|238692721|sp|B3QYF0|RPOA_CHLT3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|193088303|gb|ACF13578.1| DNA-directed RNA polymerase, alpha subunit [Chloroherpeton
           thalassium ATCC 35110]
          Length = 328

 Score =  247 bits (631), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 130/305 (42%), Positives = 201/305 (65%), Gaps = 15/305 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            IA+PL RG+  T+GNA+RRVL+SSL G AIT ++I+GVLHE S+I GV ED+ DI+LN+
Sbjct: 25  FIAQPLERGYGVTIGNAIRRVLLSSLPGTAITGIKIEGVLHEFSTIDGVKEDVPDIVLNL 84

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV-NDIEVLNPDHVICNLDVDAVVRMELT 148
           K I  +     +  VT+  RGP    AGDI +   D EVLNP+H I  L+ DA ++++++
Sbjct: 85  KQIRFRSISKRNAVVTLVLRGPKDFVAGDIVSPEGDFEVLNPEHHIATLNEDATLKIDVS 144

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V +G GY+PA+ ++ E  PIG I++D++++PI+ V Y+VE+ R GQ  DY+KLS+ ++TD
Sbjct: 145 VGRGRGYMPAEDNKPETMPIGYISVDSIFTPIRNVKYSVENTRVGQRTDYEKLSLEVETD 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEP---------KKEVKEDINVKSLPFNPALLKK 259
           GSI  +++V++A +I+ D + +F  F            ++E +E  N++ L     L+ +
Sbjct: 205 GSIAPDEAVSMAGKIINDHVRLFSLFSPTQEEEVEEEVQQEDEEFENMRKL-----LMTR 259

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +E+LELSVRS NCLR   I  +G L+ + E ++L   NFG+KSL E+K +L +  L  GM
Sbjct: 260 IEDLELSVRSHNCLRSAEIDTLGQLVSKREDELLGYKNFGKKSLAELKELLESKNLSFGM 319

Query: 320 NLPDW 324
            +  +
Sbjct: 320 EVTKY 324


>gi|121534660|ref|ZP_01666481.1| DNA-directed RNA polymerase, alpha subunit [Thermosinus
           carboxydivorans Nor1]
 gi|121306680|gb|EAX47601.1| DNA-directed RNA polymerase, alpha subunit [Thermosinus
           carboxydivorans Nor1]
          Length = 319

 Score =  247 bits (631), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 139/306 (45%), Positives = 197/306 (64%), Gaps = 17/306 (5%)

Query: 24  EENRT-LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E+NR   ++ EPL RGF  TLGN+LRRVL+SSL GAA+T+V+IDGVLHE S+I GV ED+
Sbjct: 16  EDNRYGKIVWEPLERGFGITLGNSLRRVLLSSLPGAAVTSVKIDGVLHEFSTIPGVREDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           TDIILN+K + LKM  D  K + I  +G   V AGDI T  D+E+LNP+  I  LD    
Sbjct: 76  TDIILNLKELCLKMHSDEPKVLRIEAQGERDVKAGDIITDADVEILNPELHIATLDASGS 135

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           ++ME+TV +G GYVPA  ++  +  IG+I +D+++SP+ +V+YTV   R G V DYDKL+
Sbjct: 136 LKMEITVERGRGYVPADKNKKPDHVIGVIPVDSIFSPVLRVNYTVTDTRVGNVTDYDKLT 195

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINF----------EEPKKEVKEDINVKSLPF 252
           + + TDGS+  E++V+ A+ IL   L +F N           + P  E  E+   K++  
Sbjct: 196 LEVWTDGSMRPEEAVSKAAGILVAHLKLFQNITGTPAEDEAGDGPFAETPEETGPKTMEM 255

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                  +E+L+LSVRS NCL+   I  + +L Q+TE +M+++ N GRKSL E+K  L  
Sbjct: 256 T------IEDLDLSVRSYNCLKRAGINTVAELTQKTEEEMMKVRNLGRKSLEEVKKKLEE 309

Query: 313 MGLFLG 318
           +GL L 
Sbjct: 310 LGLSLA 315


>gi|189501184|ref|YP_001960654.1| DNA-directed RNA polymerase subunit alpha [Chlorobium
           phaeobacteroides BS1]
 gi|238692283|sp|B3EP34|RPOA_CHLPB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|189496625|gb|ACE05173.1| DNA-directed RNA polymerase, alpha subunit [Chlorobium
           phaeobacteroides BS1]
          Length = 328

 Score =  247 bits (631), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 130/314 (41%), Positives = 199/314 (63%), Gaps = 15/314 (4%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
           G   +   + IA+PL RG+  TLGNA+RRVL++SL G AIT ++IDGV HE S+I GV E
Sbjct: 16  GTHNDKNGIFIAQPLERGYGVTLGNAMRRVLLASLPGTAITGIKIDGVFHEFSAIDGVRE 75

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDV 139
           D+ DIILN+K +  + S     + T+   GP  VTAGDI     + EVLN D  I  ++ 
Sbjct: 76  DVPDIILNLKKVRFRSSTKRSCKTTVTVDGPADVTAGDIVAQEGEFEVLNTDLHIATVNE 135

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
            + + M++ + +G GYVPA+ +R +  P+G I ID++++PIK V ++VE+ R GQ  DY+
Sbjct: 136 GSRLSMDVYIGRGRGYVPAEDNRGDGMPLGFIAIDSIFTPIKNVKFSVENTRVGQRTDYE 195

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINF---------EEPKKEVKEDINVKSL 250
           K+ + ++TDGS++ +DS++LA +I+ + + +F NF         EE K++  E  N++ +
Sbjct: 196 KMILDVETDGSVSPDDSISLAGKIINEHVSLFANFSPTDEEFTEEEYKQQDDEFENMRKM 255

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                LL ++E+L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL E+K  L
Sbjct: 256 -----LLTRIEDLDLSVRSHNCLRLAEIDTLGDLVSRKEDELLTYKNFGKKSLTELKEQL 310

Query: 311 GTMGLFLGMNLPDW 324
               L  GM++  +
Sbjct: 311 EKFELKFGMDITKY 324


>gi|260102381|ref|ZP_05752618.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus helveticus
           DSM 20075]
 gi|260083825|gb|EEW67945.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus helveticus
           DSM 20075]
 gi|328463390|gb|EGF35063.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus helveticus
           MTCC 5463]
          Length = 312

 Score =  247 bits (631), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 134/310 (43%), Positives = 194/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDG
Sbjct: 3   EFEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++V
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSLSDERKVIELDVEGPATVTADDLKVDADVQV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + ME+ V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMEIAVQNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   K  +  +  
Sbjct: 179 ESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFATKILVEHFKVFESADADTKFSEVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L   TE+DM+R+ N GRKSL E+K
Sbjct: 239 EDDKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELTDMTESDMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLTDLGLSL 308


>gi|261367774|ref|ZP_05980657.1| DNA-directed RNA polymerase, alpha subunit [Subdoligranulum
           variabile DSM 15176]
 gi|282570572|gb|EFB76107.1| DNA-directed RNA polymerase, alpha subunit [Subdoligranulum
           variabile DSM 15176]
          Length = 319

 Score =  247 bits (631), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 128/291 (43%), Positives = 194/291 (66%), Gaps = 3/291 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN+LRRVL+SSL G A+T+V+IDGV+HE S+I+GV ED+T+I+LN+
Sbjct: 23  FVVEPLERGFGTTLGNSLRRVLLSSLPGVAVTSVKIDGVVHEFSTIEGVREDVTEIVLNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KGI  K+ G+S K V +   GP  + AG I+  +D+E+LNP+  I  L   A + MELT 
Sbjct: 83  KGIAAKIYGESPKTVRVEAVGPCELIAGSIKGGDDLEILNPEWHIATLGEGAKLVMELTF 142

Query: 150 SKGHGYVPAKHHR---TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            KG GYVPA+ ++    E + I  + +D++Y+P+ K +YTV+  R GQ+ DYDKL + + 
Sbjct: 143 DKGRGYVPAERNKLALIEKNDISTLPVDSIYTPVLKANYTVDHTRVGQITDYDKLIIEVW 202

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           TDG+   +++++LA+R+L + L +F+N  +   E +  ++        AL   +EEL+LS
Sbjct: 203 TDGTCNAQEALSLAARVLTEHLNLFVNLCDETGETEIMVDNDDQGREKALEMTIEELDLS 262

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           VRS NCL+   I  +GDLI ++E +M+++ N GRKSL E+   L ++G  L
Sbjct: 263 VRSFNCLKRAGINTVGDLINKSEDEMMKVRNLGRKSLEEVMAKLDSLGFSL 313


>gi|161506898|ref|YP_001576852.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus helveticus
           DPC 4571]
 gi|172048388|sp|A8YXN0|RPOA_LACH4 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|160347887|gb|ABX26561.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus
           helveticus DPC 4571]
          Length = 312

 Score =  247 bits (631), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 134/310 (43%), Positives = 194/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDG
Sbjct: 3   EFEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++V
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSLSDERKVIELDVEGPATVTADDLKVDADVQV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + ME+ V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMEIAVQNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   K  +  +  
Sbjct: 179 ESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADADTKFSEVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L   TE+DM+R+ N GRKSL E+K
Sbjct: 239 EDDKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELTDMTESDMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLTDLGLSL 308


>gi|154498913|ref|ZP_02037291.1| hypothetical protein BACCAP_02905 [Bacteroides capillosus ATCC
           29799]
 gi|150271753|gb|EDM98979.1| hypothetical protein BACCAP_02905 [Bacteroides capillosus ATCC
           29799]
          Length = 315

 Score =  247 bits (631), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 131/288 (45%), Positives = 185/288 (64%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRR+L+SSL G A+T+++I GV HE  SI GV ED+T+I+LN+K
Sbjct: 24  VVEPLERGYGTTLGNSLRRILLSSLPGTAVTSIKIAGVQHEFCSIPGVKEDVTEIVLNVK 83

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            I  K+  +  K V I   G   VTAGDI+   ++EVLNPD  I  L  DA + MELT+S
Sbjct: 84  SIIAKLHCEGVKTVYIEASGECEVTAGDIKADGEVEVLNPDLHIATLGPDASLNMELTLS 143

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            G GYVPA  ++   + IG+I +D++Y+P++KV+YTVE  R G   D+DKL++ + T+G+
Sbjct: 144 HGRGYVPADRNKPAQNIIGVIPVDSVYTPVRKVNYTVEPTRVGDQTDFDKLTLEVWTNGT 203

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           IT  D+V+L +RIL D   +F +  E        +       +  L   +EEL+LSVRS 
Sbjct: 204 ITARDAVSLGARILCDHFVLFTDLSETMGNKSTVVEKAEAQRDKVLEMTIEELDLSVRSF 263

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           NCL+  NI  + DLI +TE +M+++ N GRKSL E+   L  MGL L 
Sbjct: 264 NCLKRANINTVEDLISKTEDEMMKVRNLGRKSLEEVVNKLAMMGLSLA 311


>gi|58415828|emb|CAH57328.1| RNA polymerase alpha-subunit [Vibrio diazotrophicus]
          Length = 285

 Score =  247 bits (631), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 125/278 (44%), Positives = 191/278 (68%), Gaps = 8/278 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 11  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 70

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 71  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDSNAEIAMRIKVE 130

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+V++AR  Q  D DKL + ++T
Sbjct: 131 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVDAARVEQRTDLDKLVIDMET 190

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 191 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 247

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 248 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 285


>gi|241895163|ref|ZP_04782459.1| DNA-directed RNA polymerase alpha chain [Weissella
           paramesenteroides ATCC 33313]
 gi|241871469|gb|EER75220.1| DNA-directed RNA polymerase alpha chain [Weissella
           paramesenteroides ATCC 33313]
          Length = 331

 Score =  247 bits (631), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 132/300 (44%), Positives = 195/300 (65%), Gaps = 2/300 (0%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I+L +E+ N    + EPL RG+  TLGN+LRRVL+SSL GAAI +VQIDGVLHE S+++G
Sbjct: 26  IMLVEEDSNYGKFVVEPLERGYGTTLGNSLRRVLLSSLPGAAINSVQIDGVLHEFSTVEG 85

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+T IILN+K +++++  D  K + +   GP  VTAGDI   +D+E+LN D  I  +
Sbjct: 86  VVEDVTQIILNLKKVSMRIDSDDEKTLEVNVTGPADVTAGDIAGDSDVEILNGDLHIATV 145

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQV 195
              A + M LT  +G GYV    ++  +D  PIG++ ID++++PI++V+Y VE+ R GQ 
Sbjct: 146 AAGATLHMTLTAVRGRGYVSGDQNKELHDEMPIGVLAIDSIFTPIERVNYQVENTRVGQR 205

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            D+DKL++ + TDGS+T  ++V+LA+RI+ D L  FI+  E     +   + +  P    
Sbjct: 206 DDFDKLTLDVWTDGSLTATEAVSLAARIMSDHLNAFIDMSERAITAQVMADKEEEPTTKH 265

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
               +EEL+LSVRS NCL+   I  + +L +RTE  M+ + N GRKSL EI+  L  +GL
Sbjct: 266 ADTPIEELDLSVRSYNCLKRAGINSVQELTERTETQMMSVRNLGRKSLDEIQDKLKLLGL 325


>gi|323465848|gb|ADX69535.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus helveticus
           H10]
          Length = 312

 Score =  247 bits (631), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 134/310 (43%), Positives = 194/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDG
Sbjct: 3   EFEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++V
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSLSDERKVIELDFEGPATVTADDLKVDADVQV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + ME+ V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMEIAVQNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   K  +  +  
Sbjct: 179 ESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADADTKFSEVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L   TE+DM+R+ N GRKSL E+K
Sbjct: 239 EDDKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELTDMTESDMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLTDLGLSL 308


>gi|323141382|ref|ZP_08076273.1| DNA-directed RNA polymerase, alpha subunit [Phascolarctobacterium
           sp. YIT 12067]
 gi|322414131|gb|EFY04959.1| DNA-directed RNA polymerase, alpha subunit [Phascolarctobacterium
           sp. YIT 12067]
          Length = 321

 Score =  247 bits (631), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 139/298 (46%), Positives = 190/298 (63%), Gaps = 9/298 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T V+IDGVLHE ++I GV ED+ DIILNI
Sbjct: 23  FVWEPLERGYGITLGNSLRRVLLSSLPGAAVTYVKIDGVLHEFATIPGVREDVADIILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM G+  K + I   G   VTA +I   +D+E+LNP+  I  LD DAV  ME+ +
Sbjct: 83  KALCLKMEGEGEKILRIECSGEQEVTAANIIADSDVEILNPELHIATLDKDAVFNMEIHI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYVPA  ++  + PIG+I +D++YSPI +V + V   R G V +YDKL++ + TDG
Sbjct: 143 DKGRGYVPADKNKQPDQPIGVIPVDSIYSPITRVKFAVNDTRVGNVTNYDKLTLEVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK-------VEE 262
           SI  +++V +AS IL D L +F   +     +   +   S P  P   K+       +++
Sbjct: 203 SIKPDEAVDMASTILIDYLKLFQTSDGKGSVIT--VAGGSEPEAPEPSKQEGQNTMSIDD 260

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           L+LSVRS NCLR   I  + +LIQ+TEADM+++ N G KSL EIK  L  MGL    N
Sbjct: 261 LDLSVRSNNCLRRAGINTVEELIQKTEADMIKVRNLGSKSLEEIKKKLEDMGLHFRKN 318


>gi|15900172|ref|NP_344776.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           TIGR4]
 gi|15902259|ref|NP_357809.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           R6]
 gi|111658776|ref|ZP_01409407.1| hypothetical protein SpneT_02000073 [Streptococcus pneumoniae
           TIGR4]
 gi|116516293|ref|YP_815737.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           D39]
 gi|148983635|ref|ZP_01816954.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP3-BS71]
 gi|148987973|ref|ZP_01819436.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP6-BS73]
 gi|148992813|ref|ZP_01822456.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP9-BS68]
 gi|148996658|ref|ZP_01824376.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP11-BS70]
 gi|149001657|ref|ZP_01826630.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae SP14-BS69]
 gi|149005987|ref|ZP_01829716.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP18-BS74]
 gi|149011106|ref|ZP_01832411.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP19-BS75]
 gi|149017926|ref|ZP_01834385.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP23-BS72]
 gi|168483873|ref|ZP_02708825.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae CDC1873-00]
 gi|168485997|ref|ZP_02710505.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae CDC1087-00]
 gi|168489713|ref|ZP_02713912.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae SP195]
 gi|168492190|ref|ZP_02716333.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae CDC0288-04]
 gi|168493930|ref|ZP_02718073.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae CDC3059-06]
 gi|168576337|ref|ZP_02722220.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae MLV-016]
 gi|169834017|ref|YP_001693767.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           Hungary19A-6]
 gi|182683213|ref|YP_001834960.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           CGSP14]
 gi|194396717|ref|YP_002036935.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           G54]
 gi|221231138|ref|YP_002510290.1| DNA-directed RNA polymerase alpha chain [Streptococcus pneumoniae
           ATCC 700669]
 gi|225853841|ref|YP_002735353.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           JJA]
 gi|225856000|ref|YP_002737511.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           P1031]
 gi|225858089|ref|YP_002739599.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           70585]
 gi|225860277|ref|YP_002741786.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           Taiwan19F-14]
 gi|289168706|ref|YP_003446975.1| DNA-dependent RNA polymerase, alpha subunit [Streptococcus mitis
           B6]
 gi|298230392|ref|ZP_06964073.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           str. Canada MDR_19F]
 gi|298256013|ref|ZP_06979599.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           str. Canada MDR_19A]
 gi|298502049|ref|YP_003723989.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           TCH8431/19A]
 gi|303255069|ref|ZP_07341145.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           BS455]
 gi|303259287|ref|ZP_07345265.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           SP-BS293]
 gi|303261042|ref|ZP_07346991.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           SP14-BS292]
 gi|303263370|ref|ZP_07349293.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           BS397]
 gi|303265535|ref|ZP_07351435.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           BS457]
 gi|303267907|ref|ZP_07353709.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           BS458]
 gi|307066913|ref|YP_003875879.1| DNA-directed RNA polymerase subunit alpha/40 kD subunit
           [Streptococcus pneumoniae AP200]
 gi|307126454|ref|YP_003878485.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           670-6B]
 gi|307704090|ref|ZP_07641019.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus mitis
           SK597]
 gi|307708085|ref|ZP_07644553.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus mitis
           NCTC 12261]
 gi|307709936|ref|ZP_07646383.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus mitis
           SK564]
 gi|307711030|ref|ZP_07647452.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus mitis
           SK321]
 gi|54039278|sp|P66709|RPOA_STRR6 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|54042188|sp|P66708|RPOA_STRPN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|122279377|sp|Q04ML1|RPOA_STRP2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|14971705|gb|AAK74416.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae TIGR4]
 gi|15457760|gb|AAK99019.1| RNA polymerase alpha subunit [Streptococcus pneumoniae R6]
 gi|116076869|gb|ABJ54589.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae D39]
 gi|147757233|gb|EDK64272.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP11-BS70]
 gi|147760115|gb|EDK67104.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae SP14-BS69]
 gi|147762343|gb|EDK69304.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP18-BS74]
 gi|147764742|gb|EDK71672.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP19-BS75]
 gi|147923782|gb|EDK74894.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP3-BS71]
 gi|147926437|gb|EDK77510.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP6-BS73]
 gi|147928539|gb|EDK79554.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP9-BS68]
 gi|147931490|gb|EDK82468.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP23-BS72]
 gi|168996519|gb|ACA37131.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae Hungary19A-6]
 gi|172042844|gb|EDT50890.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae CDC1873-00]
 gi|182628547|gb|ACB89495.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           CGSP14]
 gi|183570913|gb|EDT91441.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae CDC1087-00]
 gi|183571834|gb|EDT92362.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae SP195]
 gi|183573577|gb|EDT94105.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae CDC0288-04]
 gi|183576079|gb|EDT96607.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae CDC3059-06]
 gi|183577825|gb|EDT98353.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae MLV-016]
 gi|194356384|gb|ACF54832.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae G54]
 gi|220673598|emb|CAR68084.1| DNA-directed RNA polymerase alpha chain [Streptococcus pneumoniae
           ATCC 700669]
 gi|225720212|gb|ACO16066.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae 70585]
 gi|225723399|gb|ACO19252.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae JJA]
 gi|225725259|gb|ACO21111.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae P1031]
 gi|225726707|gb|ACO22558.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae Taiwan19F-14]
 gi|288908273|emb|CBJ23115.1| DNA-dependent RNA polymerase, alpha subunit [Streptococcus mitis
           B6]
 gi|298237644|gb|ADI68775.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           TCH8431/19A]
 gi|301793507|emb|CBW35880.1| DNA-directed RNA polymerase alpha chain [Streptococcus pneumoniae
           INV104]
 gi|301799383|emb|CBW31918.1| DNA-directed RNA polymerase alpha chain [Streptococcus pneumoniae
           OXC141]
 gi|301801178|emb|CBW33851.1| DNA-directed RNA polymerase alpha chain [Streptococcus pneumoniae
           INV200]
 gi|302597899|gb|EFL64969.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           BS455]
 gi|302637879|gb|EFL68365.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           SP14-BS292]
 gi|302639705|gb|EFL70162.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           SP-BS293]
 gi|302642603|gb|EFL72948.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           BS458]
 gi|302644975|gb|EFL75222.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           BS457]
 gi|302647143|gb|EFL77367.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           BS397]
 gi|306408450|gb|ADM83877.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Streptococcus pneumoniae AP200]
 gi|306483516|gb|ADM90385.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae 670-6B]
 gi|307615870|gb|EFN95075.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus mitis
           NCTC 12261]
 gi|307616992|gb|EFN96170.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus mitis
           SK321]
 gi|307619307|gb|EFN98436.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus mitis
           SK564]
 gi|307622380|gb|EFO01388.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus mitis
           SK597]
 gi|327390653|gb|EGE88993.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae GA04375]
 gi|332075900|gb|EGI86367.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae GA17570]
 gi|332076680|gb|EGI87142.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae GA17545]
          Length = 311

 Score =  247 bits (631), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 136/312 (43%), Positives = 204/312 (65%), Gaps = 8/312 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK--EVKEDI 245
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  K  EV ++ 
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSTEVMKEA 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           + +S   +  L + +EEL+LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E
Sbjct: 239 DTES--DDRILDRTIEELDLSVRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEE 296

Query: 306 IKGVLGTMGLFL 317
           +K  L  +GL L
Sbjct: 297 VKLKLIDLGLGL 308


>gi|260584442|ref|ZP_05852189.1| DNA-directed RNA polymerase, alpha subunit [Granulicatella elegans
           ATCC 700633]
 gi|260157960|gb|EEW93029.1| DNA-directed RNA polymerase, alpha subunit [Granulicatella elegans
           ATCC 700633]
          Length = 314

 Score =  247 bits (631), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 131/288 (45%), Positives = 191/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL G A+T +Q+DGVLHE S+I GV ED+  IILNI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGTAVTDIQMDGVLHEFSTIDGVVEDVAAIILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK   +  K + I   GP VVTAGDI+  +DIE+LNPD  IC +       + +  
Sbjct: 83  KKIALKSFSEDDKVLEIDIVGPAVVTAGDIKHDSDIEILNPDLYICTVAEGHRFHVRMNA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A +++++N PIG+I ID++Y+PI KV+Y VE+ R GQ   YDKL++ + TDG
Sbjct: 143 KNGRGYVRADYNKSDNMPIGVIPIDSIYTPISKVNYQVENTRIGQKNIYDKLTLDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI+ E++++LA+RIL + L +F+N  +  ++V+  +  +       L   +EEL+LSVRS
Sbjct: 203 SISPEEAISLAARILTEHLNIFVNLTDETRQVEIMVEKEETQKEKMLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++EA+M+++ N GRKSL E+K  L  + L L
Sbjct: 263 YNCLKRAGINTVQELTNKSEAEMIKVRNLGRKSLEEVKHKLIELNLDL 310


>gi|300089409|gb|ADJ67856.1| RNA polymerase alpha-subunit [Photobacterium jeanii]
          Length = 274

 Score =  247 bits (631), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 125/274 (45%), Positives = 186/274 (67%), Gaps = 7/274 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 4   EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDVLEILLNLKGL 63

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +
Sbjct: 64  AVKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNADISMRIKVER 123

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + + T+
Sbjct: 124 GRGYVPASARIHTEEDERPIGRLLVDATFSPVDRIAYAVEAARVEQRTDLDKLVIDMQTN 183

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 184 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 240

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KS
Sbjct: 241 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKS 274


>gi|323483272|ref|ZP_08088662.1| hypothetical protein HMPREF9474_00411 [Clostridium symbiosum
           WAL-14163]
 gi|323691229|ref|ZP_08105505.1| DNA-directed RNA polymerase [Clostridium symbiosum WAL-14673]
 gi|323403370|gb|EGA95678.1| hypothetical protein HMPREF9474_00411 [Clostridium symbiosum
           WAL-14163]
 gi|323504748|gb|EGB20534.1| DNA-directed RNA polymerase [Clostridium symbiosum WAL-14673]
          Length = 320

 Score =  247 bits (630), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 126/292 (43%), Positives = 196/292 (67%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDGVLHE SSI GV ED+T+II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDGVLHEFSSIPGVKEDVTEIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K   ++++  T +    G GVVTA DIQ  +DIE+LNP+ VI  L    D+   M
Sbjct: 83  KSLAIKNLSETNEPKTAYIEFEGEGVVTAADIQVDSDIEILNPEQVIATLSGGTDSKFYM 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           EL ++KG GY+ A  ++ +  PIG+I +D++Y+P+++V+ TVE+ R GQV D+DKL++ +
Sbjct: 143 ELNITKGRGYISADKNKNDELPIGMIAVDSIYTPVERVNMTVENTRVGQVTDFDKLTLDV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L +FI+  E  +  +  +  +       L   ++ELEL
Sbjct: 203 FTNGTLAPDEAVSLAAKVLSEHLNLFIDLSENARTAEVMVEKEDNEKEKVLEMNIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L
Sbjct: 263 SVRSYNCLKRAGINTVEELCNRTPEDMMKVRNLGRKSLEEVLAKLKELGLQL 314


>gi|294669850|ref|ZP_06734909.1| hypothetical protein NEIELOOT_01743 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291308243|gb|EFE49486.1| hypothetical protein NEIELOOT_01743 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 277

 Score =  247 bits (630), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 135/281 (48%), Positives = 189/281 (67%), Gaps = 9/281 (3%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           + G A T V I GVLHE S++ G+ ED+ D++LNIKGI  K+ G +  R+ + K G GVV
Sbjct: 1   MDGFAPTEVSITGVLHEYSTLDGIQEDVVDVLLNIKGIIFKLHGRNEVRLRLKKSGSGVV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY---VPAKHHRTENDPIGLI 171
            A DI+  +D EV+NP+H+IC+L  +A + ME+ V KG GY   V  K    EN+ IG I
Sbjct: 61  LASDIELPHDAEVINPNHIICHLSDNADIEMEIKVEKGRGYQSVVGRKKSGNENN-IGSI 119

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA +SPI +VS+ VE AR  Q  D D+L + I+TDGS+  E++V  A+RIL DQ+ +F
Sbjct: 120 QLDASFSPIARVSFDVEPARVEQRTDLDRLVLDIETDGSLEPEEAVRSAARILIDQMAVF 179

Query: 232 INFE-EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
            + +  P +EV+E     + P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE 
Sbjct: 180 ADLQGTPVEEVEE----VAPPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTET 235

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           ++L+  N GRKSL EIK VL + GL LG  L  WPP ++E+
Sbjct: 236 ELLKTPNLGRKSLNEIKEVLASKGLTLGSKLEAWPPVNLEK 276


>gi|251772518|gb|EES53084.1| DNA-directed RNA polymerase, alpha subunit [Leptospirillum
           ferrodiazotrophum]
          Length = 322

 Score =  247 bits (630), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 134/297 (45%), Positives = 194/297 (65%), Gaps = 8/297 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EP  RGF  T+GNALRRVL+SS+ G AITA++   V HE S+I GV ED+TDIILN+
Sbjct: 25  VVVEPFERGFGITVGNALRRVLLSSIPGVAITAIRAKNVFHEFSNIPGVVEDVTDIILNL 84

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + +K        + +  +GP +V A DI TV  +E+++PDHVI  LD    + M+L  
Sbjct: 85  KSLRMKPLLQGEHWLHLKVKGPRIVKASDIDTVGAVEMMDPDHVIATLDEGGHLDMDLKT 144

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYVPA H R+    +G+I IDA+++PI KV+Y VES R G++ DYD+L   I+TDG
Sbjct: 145 EFGRGYVPADHSRSTETEVGIIPIDAIFTPINKVNYFVESTRVGRITDYDRLIFEIETDG 204

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA-----LLKKVEELE 264
           SIT  ++++ A++IL+  L +F++ +     +  D +  SL  N +     + K V ELE
Sbjct: 205 SITPGEALSEAAKILRTHLDLFVSSD---LHLANDSSPLSLESNSSKEETIMDKSVNELE 261

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           LSVR+ NCL+  +I  +G+L+ RTE ++L+  NFG+KSL EIK  L  +GL LGM+L
Sbjct: 262 LSVRAANCLKSSDIKKIGELVIRTEDELLQTKNFGKKSLDEIKEALENIGLSLGMDL 318


>gi|294507076|ref|YP_003571134.1| DNA-directed RNA polymerase alpha chain [Salinibacter ruber M8]
 gi|158518577|sp|Q2S3N9|RPOA_SALRD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|294343404|emb|CBH24182.1| DNA-directed RNA polymerase alpha chain [Salinibacter ruber M8]
          Length = 328

 Score =  247 bits (630), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 137/297 (46%), Positives = 195/297 (65%), Gaps = 3/297 (1%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  T+GNALRRVL+SSLRG AITAV+IDGV HE S+I GV ED+ D+ILN+K + 
Sbjct: 28  PLERGYGVTIGNALRRVLLSSLRGLAITAVKIDGVQHEFSTIPGVTEDVADLILNLKEVR 87

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            K        + +   GPG  TA DI +   + +VLNPD  +  L  DAVV ++L V  G
Sbjct: 88  FKADEMQEGHLHLNLEGPGNWTAADIDEATAEYDVLNPDQHVATLAEDAVVNVDLRVGYG 147

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYVP++ ++ E+DPIG+I ID++++PIK V+Y V+  R GQ +DY++L + ++TDGS+T
Sbjct: 148 RGYVPSEENKREDDPIGVIAIDSIFTPIKNVNYEVKPTRVGQKIDYEELLLDVETDGSLT 207

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP--FNPALLKKVEELELSVRST 270
            E+++   + IL+D +  FI  EE  + V E+  V          L + V+EL+LSVRS 
Sbjct: 208 PEEAITQGASILRDHVSFFIQLEEEPEPVVEEQEVDEEVKRIRELLAQPVDELDLSVRSH 267

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           NCL+  NI  +GDL++R E +ML+  NFGRKSL E+  VL   GL  GM++ ++  E
Sbjct: 268 NCLKAANIKTIGDLVRREEDEMLKFRNFGRKSLQELVEVLDERGLQFGMDVEEYLEE 324


>gi|83815189|ref|YP_445192.1| DNA-directed RNA polymerase subunit alpha [Salinibacter ruber DSM
           13855]
 gi|83756583|gb|ABC44696.1| DNA-directed RNA polymerase, alpha subunit [Salinibacter ruber DSM
           13855]
          Length = 321

 Score =  247 bits (630), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 137/297 (46%), Positives = 195/297 (65%), Gaps = 3/297 (1%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  T+GNALRRVL+SSLRG AITAV+IDGV HE S+I GV ED+ D+ILN+K + 
Sbjct: 21  PLERGYGVTIGNALRRVLLSSLRGLAITAVKIDGVQHEFSTIPGVTEDVADLILNLKEVR 80

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            K        + +   GPG  TA DI +   + +VLNPD  +  L  DAVV ++L V  G
Sbjct: 81  FKADEMQEGHLHLNLEGPGNWTAADIDEATAEYDVLNPDQHVATLAEDAVVNVDLRVGYG 140

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYVP++ ++ E+DPIG+I ID++++PIK V+Y V+  R GQ +DY++L + ++TDGS+T
Sbjct: 141 RGYVPSEENKREDDPIGVIAIDSIFTPIKNVNYEVKPTRVGQKIDYEELLLDVETDGSLT 200

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP--FNPALLKKVEELELSVRST 270
            E+++   + IL+D +  FI  EE  + V E+  V          L + V+EL+LSVRS 
Sbjct: 201 PEEAITQGASILRDHVSFFIQLEEEPEPVVEEQEVDEEVKRIRELLAQPVDELDLSVRSH 260

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           NCL+  NI  +GDL++R E +ML+  NFGRKSL E+  VL   GL  GM++ ++  E
Sbjct: 261 NCLKAANIKTIGDLVRREEDEMLKFRNFGRKSLQELVEVLDERGLQFGMDVEEYLEE 317


>gi|15896355|ref|NP_349704.1| DNA-directed RNA polymerase subunit alpha [Clostridium
           acetobutylicum ATCC 824]
 gi|20139603|sp|Q97EK6|RPOA_CLOAB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|15026170|gb|AAK81044.1|AE007807_2 DNA-dependent RNA polymerase alpha subunit [Clostridium
           acetobutylicum ATCC 824]
 gi|325510511|gb|ADZ22147.1| DNA-directed RNA polymerase subunit alpha [Clostridium
           acetobutylicum EA 2018]
          Length = 315

 Score =  247 bits (630), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 126/291 (43%), Positives = 193/291 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL G A  +V+I+GVLHE S++KGV ED+T++ILNI
Sbjct: 23  FVVEPLERGYGITLGNSLRRILLSSLPGVAANSVRIEGVLHEFSTVKGVKEDVTELILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM G+  K + I   GPG VT  DI+T   +EV+N D  I  LD D  + ME+ V
Sbjct: 83  KALCLKMEGEDSKVIYIDAHGPGEVTGADIRTDGSVEVINKDLHIATLDEDGKLYMEIEV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           ++G GYV    ++ ++ PIG I +D++YSPIK+V++TVE+ R  Q+ DYDKL++ +  +G
Sbjct: 143 NRGRGYVTQNKNKRDDMPIGTIAVDSIYSPIKRVNFTVENTRVAQITDYDKLTIEVWGNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  E++++LA++IL +   +F+   +   +V+  +  +       L   +EEL+LSVRS
Sbjct: 203 TIRPEEAISLAAKILIEHFKLFMTLTDHADDVEIMVEKEEDKKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
            NCL+   I  + +L QR+  DM+++ N GRKSL E++  L  +GL L +N
Sbjct: 263 YNCLKRAGINTVQELTQRSMEDMMKVRNLGRKSLEEVEQKLKALGLSLKLN 313


>gi|260656834|gb|ACX47807.1| RNA polymerase alpha-subunit [Vibrio litoralis]
          Length = 276

 Score =  247 bits (630), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 129/279 (46%), Positives = 192/279 (68%), Gaps = 8/279 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ 
Sbjct: 1   PLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLA 60

Query: 94  LKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
           + ++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D  A + M + V +
Sbjct: 61  VSVAEGKDEVFITLKKSGSGPVVAGDIIHDGDVEIANPEHVICHLTDDKAEIAMRIKVQR 120

Query: 152 GHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVP  A+ H  E++ PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+
Sbjct: 121 GRGYVPSSARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 181 GTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 237

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK
Sbjct: 238 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIK 276


>gi|296875379|ref|ZP_06899453.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           parasanguinis ATCC 15912]
 gi|312867033|ref|ZP_07727244.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           parasanguinis F0405]
 gi|322390685|ref|ZP_08064199.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           parasanguinis ATCC 903]
 gi|296433572|gb|EFH19345.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           parasanguinis ATCC 15912]
 gi|311097515|gb|EFQ55748.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           parasanguinis F0405]
 gi|321142658|gb|EFX38122.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           parasanguinis ATCC 903]
          Length = 312

 Score =  247 bits (630), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 135/312 (43%), Positives = 200/312 (64%), Gaps = 8/312 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++  + + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKDYGVFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILN+KGI +K      K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNVKGIAVKSYVQDEKIIELDVEGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A ++  LTV+ G GYVPA  ++ ++ P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGASLKATLTVNSGRGYVPADQNKKDDAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E          V
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLFTNLTEIAIATDVMKEV 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLR--GENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            +   +  L + +EEL+LSVRS NCL+  G N VY  DL +++EA+M+++ N GRKSL E
Sbjct: 239 DTTSDDRILERTIEELDLSVRSYNCLKRAGINTVY--DLTEKSEAEMMKVRNLGRKSLEE 296

Query: 306 IKGVLGTMGLFL 317
           +K  L  +GL L
Sbjct: 297 VKIKLADLGLGL 308


>gi|313884601|ref|ZP_07818362.1| DNA-directed RNA polymerase, alpha subunit [Eremococcus coleocola
           ACS-139-V-Col8]
 gi|312620385|gb|EFR31813.1| DNA-directed RNA polymerase, alpha subunit [Eremococcus coleocola
           ACS-139-V-Col8]
          Length = 314

 Score =  247 bits (630), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 128/288 (44%), Positives = 196/288 (68%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGV+HE ++I GV ED+  IILNI
Sbjct: 23  IVIEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVVHEFATIDGVVEDVPTIILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + +   GP +VTA DI   ND+++LNP+  IC L   A ++M L  
Sbjct: 83  KNLALKLYTEEDKVLELNAVGPKIVTAADIIHDNDVQILNPELEICTLAEGAEIKMLLNA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           S G GYV +  +++++  IG++ ID++Y+P+KKV+Y VE+ R GQ    DKL++ I TDG
Sbjct: 143 STGRGYVRSDFNKSDDTTIGVLPIDSIYTPVKKVNYQVENTRIGQQNICDKLTLDIWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI+ E S++LA++IL + L +F++  E  ++V+  +  +       L+  +EEL+LSVRS
Sbjct: 203 SISPEKSLSLAAKILIEYLNVFVDLNEEARDVEIMVEKEETEKEKVLVMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  +TEA+M+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTIQELTNKTEAEMMKVRNLGRKSLTEVKNKLNDLGLGL 310


>gi|154505141|ref|ZP_02041879.1| hypothetical protein RUMGNA_02654 [Ruminococcus gnavus ATCC 29149]
 gi|153794620|gb|EDN77040.1| hypothetical protein RUMGNA_02654 [Ruminococcus gnavus ATCC 29149]
          Length = 319

 Score =  247 bits (630), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 129/292 (44%), Positives = 198/292 (67%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAAI++V+IDGVLHE SSI GV ED+T+II+N+
Sbjct: 23  FVVEPLERGYGITLGNSLRRIMLSSLPGAAISSVKIDGVLHEFSSIPGVKEDVTEIIMNL 82

Query: 90  KGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K + +S   K   I   G G+VT  DIQT +DIE++NP+ VI  L    D+ + M
Sbjct: 83  KSLAIKNTSESDEVKTAYIEFEGEGIVTGADIQTDSDIEIMNPEQVIATLSGGKDSKLYM 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++KG GYV A  +++E+ PIG+I ID++Y+P+++V+ TV++ R GQV DYDKL++ +
Sbjct: 143 ELTITKGRGYVSADKNKSEDMPIGVIPIDSIYTPVERVNMTVQNTRVGQVTDYDKLTLDV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T G++  +++V+LA+++L + L +FI+  E  +  +  I  +       L   ++ELEL
Sbjct: 203 WTKGTLLPDEAVSLAAKVLSEHLKLFIDLSEVAQSAEVMIEKEDDEKEKVLEMSIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + +L  +T  DM+++ N GRKSL E+   L  + L L
Sbjct: 263 SVRSYNCLKRAGINTVEELTNKTPEDMMKVRNLGRKSLEEVLAKLKELNLEL 314


>gi|58415944|emb|CAH57386.1| RNA polymerase alpha-subunit [Vibrio mytili]
          Length = 294

 Score =  247 bits (630), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 125/276 (45%), Positives = 189/276 (68%), Gaps = 8/276 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GY+PA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYIPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294


>gi|306832573|ref|ZP_07465713.1| DNA-directed RNA polymerase subunit alpha [Streptococcus bovis ATCC
           700338]
 gi|304425331|gb|EFM28457.1| DNA-directed RNA polymerase subunit alpha [Streptococcus bovis ATCC
           700338]
          Length = 312

 Score =  246 bits (629), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 126/288 (43%), Positives = 191/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNI
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNI 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   D  K + +   GP  VTAGDI T +D+E++NPDH +  +     ++  +T+
Sbjct: 81  KGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDSDVEIVNPDHYLFTIAEGHSLKATMTI 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ E+ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 141 AKNRGYVPAEGNKKEDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTLEIMTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  ED++ L++R+L + L +F +  E  K        + +     L + +EEL+LSVRS
Sbjct: 201 TIIPEDALGLSARVLIEHLNLFTDLTEVAKNTDVMKETEKVNDEKVLDRTIEELDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL ++TE +M+++ N GRKSL E+K  L  +GL L
Sbjct: 261 YNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVKVKLADLGLGL 308


>gi|293364322|ref|ZP_06611048.1| DNA-directed RNA polymerase subunit alpha [Streptococcus oralis
           ATCC 35037]
 gi|291317168|gb|EFE57595.1| DNA-directed RNA polymerase subunit alpha [Streptococcus oralis
           ATCC 35037]
          Length = 311

 Score =  246 bits (629), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 135/312 (43%), Positives = 204/312 (65%), Gaps = 8/312 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK--EVKEDI 245
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  K  EV ++ 
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSTEVMKEA 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           + +S   +  L + +EEL+LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E
Sbjct: 239 DTES--DDRILDRTIEELDLSVRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEE 296

Query: 306 IKGVLGTMGLFL 317
           +K  L  +GL L
Sbjct: 297 VKLKLIDLGLGL 308


>gi|225574733|ref|ZP_03783343.1| hypothetical protein RUMHYD_02810 [Blautia hydrogenotrophica DSM
           10507]
 gi|225038062|gb|EEG48308.1| hypothetical protein RUMHYD_02810 [Blautia hydrogenotrophica DSM
           10507]
          Length = 319

 Score =  246 bits (629), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 130/292 (44%), Positives = 195/292 (66%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDGVLHE SSI GV ED+++II+N+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDGVLHEFSSIPGVKEDVSEIIMNL 82

Query: 90  KGINLK-MSGDSH-KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K  S DS  K   I   G GVVTA DIQ   DIE++NP+ VI  L+   D  + M
Sbjct: 83  KSLAIKNKSNDSEPKTAYIECEGKGVVTAADIQADQDIEIMNPEQVIATLNGGKDCRLAM 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++KG GYV A   ++++ PIG+I +DA+Y+P+ +V+  VE+ R GQ+ D+DKL++ +
Sbjct: 143 ELTITKGRGYVSADKGKSDDMPIGVIAVDAIYTPVDRVNLVVENTRVGQITDFDKLTLDV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L +FI+  E  K  +  I  +       L   ++ELEL
Sbjct: 203 YTNGTLDPDEAVSLAAKVLSEHLSLFIDLSENAKTAEVMIEKEDNEKEKVLEMSIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L
Sbjct: 263 SVRSYNCLKRAGINTVEELCNRTSDDMMKVRNLGRKSLEEVLAKLKELGLQL 314


>gi|325261521|ref|ZP_08128259.1| DNA-directed RNA polymerase, alpha subunit [Clostridium sp. D5]
 gi|324032975|gb|EGB94252.1| DNA-directed RNA polymerase, alpha subunit [Clostridium sp. D5]
          Length = 319

 Score =  246 bits (629), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 130/292 (44%), Positives = 196/292 (67%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAAI++V+IDGVLHE SSI GV ED+T+II+N+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAISSVKIDGVLHEFSSIPGVKEDVTEIIMNL 82

Query: 90  KGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K + +S   K   I   G GVVT  DIQ  +DIE++NPD VI  L    D+ + M
Sbjct: 83  KSLAIKNTSESDEVKTAYIEFEGEGVVTGADIQADSDIEIMNPDQVIATLSGGKDSKLYM 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++KG GYV A  ++ E+ PIG+I ID++Y+P+++V+ TVE+ R GQ+ DYDKL++ +
Sbjct: 143 ELTITKGRGYVSADKNKNEDLPIGVIPIDSIYTPVERVNLTVENTRVGQITDYDKLTLDV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T G++  +++V+LA+++L + L +FI+  E  +  +  I  +       L   ++ELEL
Sbjct: 203 WTKGTLLPDEAVSLAAKVLSEHLKLFIDLSEVAQAAEVMIEKEDDEKEKVLEMSIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + +L  +T  DM+++ N GRKSL E+   L  + L L
Sbjct: 263 SVRSYNCLKRAGINTVEELTNKTPEDMMKVRNLGRKSLEEVLAKLKELDLEL 314


>gi|24380343|ref|NP_722298.1| DNA-directed RNA polymerase subunit alpha [Streptococcus mutans
           UA159]
 gi|290581264|ref|YP_003485656.1| DNA-directed RNA polymerase subunit alpha [Streptococcus mutans
           NN2025]
 gi|41688701|sp|Q8DS36|RPOA_STRMU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|24378361|gb|AAN59604.1|AE015023_5 DNA-directed RNA polymerase, alpha subunit [Streptococcus mutans
           UA159]
 gi|254998163|dbj|BAH88764.1| DNA-directed RNA polymerase alpha subunit [Streptococcus mutans
           NN2025]
          Length = 312

 Score =  246 bits (629), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 126/288 (43%), Positives = 193/288 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNI
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNI 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K V +   GP  +TAGDI T +DIE++NPDH +  +   A ++  +TV
Sbjct: 81  KGLAVKSYVEEEKIVELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIAEGANLKATMTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +   GYVPA+ ++ ++ P+G + ID++Y+P+KKV+Y VE AR G   ++DKL++ I T+G
Sbjct: 141 ATNRGYVPAEKNKRDDAPVGTLAIDSIYTPVKKVNYQVEPARVGSNDNFDKLTIEIMTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  ED++ L++R+L + L +F +  E  K        + +     L + +EEL+LSVRS
Sbjct: 201 TIIPEDALGLSARVLIEHLNLFTDLTEVAKATDVMKETEQVSDEKVLDRTIEELDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL +++E++M+++ N GRKSL E+K  L  +GL L
Sbjct: 261 YNCLKRAGINTVYDLTEKSESEMMKVRNLGRKSLEEVKVKLADLGLGL 308


>gi|160941042|ref|ZP_02088380.1| hypothetical protein CLOBOL_05935 [Clostridium bolteae ATCC
           BAA-613]
 gi|158435991|gb|EDP13758.1| hypothetical protein CLOBOL_05935 [Clostridium bolteae ATCC
           BAA-613]
          Length = 320

 Score =  246 bits (629), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 127/292 (43%), Positives = 193/292 (66%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDGVLHE SSI GV ED+T+II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDGVLHEFSSIPGVKEDVTEIIMNI 82

Query: 90  KGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K + D+   K   I   G GV+TA DIQ   DIE++NPD +I  L    D+   M
Sbjct: 83  KSLAIKNNSDTDEPKVAYIEFEGEGVITAADIQADADIEIMNPDQIIATLSGGTDSKFYM 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++KG GY+ A  ++ ++ PIG+I +D++Y+P+++V+  V + R GQ  DYDKL++ I
Sbjct: 143 ELTITKGRGYISADKNKNDDLPIGVIAVDSIYTPVERVNMAVANTRVGQQTDYDKLTLEI 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L +FI+  E  K  +  +  +       L   ++ELEL
Sbjct: 203 YTNGTLAPDEAVSLAAKVLSEHLNLFIDLSENAKTAEIMVEKEDNEKEKVLEMNIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L
Sbjct: 263 SVRSYNCLKRAGINTVEELCNRTSEDMMKVRNLGRKSLEEVLAKLKELGLQL 314


>gi|220930993|ref|YP_002507901.1| DNA-directed RNA polymerase, alpha subunit [Halothermothrix orenii
           H 168]
 gi|219992303|gb|ACL68906.1| DNA-directed RNA polymerase, alpha subunit [Halothermothrix orenii
           H 168]
          Length = 314

 Score =  246 bits (629), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 131/285 (45%), Positives = 197/285 (69%), Gaps = 1/285 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRVL+SSL GAAIT+V+I+GV HE S+I GV ED++++ILN+KG+ 
Sbjct: 25  PLERGYGITLGNSLRRVLLSSLPGAAITSVKIEGVRHEFSTIPGVVEDVSEVILNLKGVV 84

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK  G+  +++T+   G G VTAGD +T  DIEV+NPDH I  L     +++E TV  G 
Sbjct: 85  LKYKGEDIEKITLNCEGEGEVTAGDFKTSGDIEVINPDHHIATLAEGGKLQLEATVEFGR 144

Query: 154 GYVPAKHHRTENDP-IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           GYV A+ ++   D  IGLI ID+ +SPI++ ++ VE+ R GQV DYD+L + + T+GSI+
Sbjct: 145 GYVTAEENKEHFDRVIGLIPIDSSFSPIERANFKVENTRVGQVTDYDRLVLEVYTNGSIS 204

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
            ED+++LA++I+ + L +F+N  +   +V+  +  +    +  L   +EEL+LSVRS+NC
Sbjct: 205 PEDAISLAAKIMVEHLELFLNLTDEVTDVEIMVEKEEEEKDKILDTTIEELDLSVRSSNC 264

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+   I  +G+LI +TE D++++ N G+KSL EIK  L  + L L
Sbjct: 265 LKRAGINTVGELINKTEDDLMKVRNLGKKSLQEIKEKLNELDLKL 309


>gi|116493137|ref|YP_804872.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Pediococcus pentosaceus ATCC 25745]
 gi|122265399|sp|Q03EE2|RPOA_PEDPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116103287|gb|ABJ68430.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus
           ATCC 25745]
          Length = 314

 Score =  246 bits (629), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 134/295 (45%), Positives = 190/295 (64%), Gaps = 2/295 (0%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E +N    + EPL RG+  TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+
Sbjct: 14  ENDNYGRFVIEPLERGYGTTLGNSLRRILLSSLPGAAITSVQIDSVLHEFSTIEGVVEDV 73

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  IC +     
Sbjct: 74  TQIILNLKKVSLKIESDEDKTLEINVAGPANVTAGDIMGDGDVVILNPELPICTVAEGTT 133

Query: 143 VRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
               LT   G GY  A  +  R  + PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDK
Sbjct: 134 FHAVLTADTGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDK 193

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L++ I TDGSIT  ++ +L+++IL + L +F+N  +  KE +  +  +       L   +
Sbjct: 194 LTLDIWTDGSITPSEATSLSAKILTEHLAIFVNLNDQAKETEIMVEKEETHKEKMLEMTI 253

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           EEL+LSVRS NCL+   I  + +L  RT+A M+++ N GRKSLVEI+  L  +GL
Sbjct: 254 EELDLSVRSYNCLKRAGINSVQELTDRTDAQMMKVRNLGRKSLVEIQEKLSLLGL 308


>gi|169823878|ref|YP_001691489.1| DNA-directed RNA polymerase subunit alpha [Finegoldia magna ATCC
           29328]
 gi|303234800|ref|ZP_07321426.1| DNA-directed RNA polymerase, alpha subunit [Finegoldia magna
           BVS033A4]
 gi|167830683|dbj|BAG07599.1| DNA-directed RNA polymerase alpha subunit [Finegoldia magna ATCC
           29328]
 gi|302494141|gb|EFL53921.1| DNA-directed RNA polymerase, alpha subunit [Finegoldia magna
           BVS033A4]
          Length = 317

 Score =  246 bits (629), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 132/306 (43%), Positives = 197/306 (64%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           IV   E+ N    +  PL RG+  TLGN+LRRVL+SSL GAAI+ + I GV HE+S+IKG
Sbjct: 11  IVELDEQNNYGKFVIMPLERGYGTTLGNSLRRVLLSSLPGAAISKINIQGVAHEMSTIKG 70

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +IILN+KGI +K   +    + +  +GP V+TA DI    D+EV NPDH I  L
Sbjct: 71  VKEDVPEIILNLKGIAVKKYNEEPISLNVDIKGPCVLTAKDILVDTDLEVKNPDHYIATL 130

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + DA + M++TV  G GY  ++ ++T+ D IG I ID+L+SP+KKV++TV++AR GQV+D
Sbjct: 131 NEDASLEMQITVINGKGYKISEFNKTDEDIIGDIAIDSLFSPVKKVNFTVDNARVGQVID 190

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           YDKL++ + T+G+I  +D+++  S IL + L +F      +     D           ++
Sbjct: 191 YDKLTIEVWTNGTIRPQDALSEGSNILINCLELFSELPNYECNTNSDDEDNQKDKETQMV 250

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +EEL+ S+RS NCL+  NI  +GD++  T+ADM+++ NFG+KSL E++  L  MGL  
Sbjct: 251 INIEELDFSLRSFNCLKRANINTVGDIVSHTKADMMKIKNFGKKSLDEVEEKLQEMGLAF 310

Query: 318 GMNLPD 323
              + D
Sbjct: 311 KQEIKD 316


>gi|288904299|ref|YP_003429520.1| RNA polymerase (alpha subunit) [Streptococcus gallolyticus UCN34]
 gi|306830328|ref|ZP_07463499.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325977278|ref|YP_004286994.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
 gi|288731024|emb|CBI12568.1| RNA polymerase (alpha subunit) [Streptococcus gallolyticus UCN34]
 gi|304427575|gb|EFM30676.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325177206|emb|CBZ47250.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
          Length = 312

 Score =  246 bits (628), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 127/288 (44%), Positives = 191/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNI
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNI 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   D  K + +   GP  VTAGDI T +D+E++NPDH +  +     ++  +TV
Sbjct: 81  KGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDSDVEIVNPDHYLFTIAEGHSLKATMTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ E+ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 141 AKKRGYVPAEGNKKEDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  ED++ L++R+L + L +F +  E  K        + +     L + +EEL+LSVRS
Sbjct: 201 TIIPEDALGLSARVLIEHLNLFTDLTEVAKNTDVMKETEKVNDEKVLDRTIEELDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL ++TE +M+++ N GRKSL E+K  L  +GL L
Sbjct: 261 YNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVKVKLADLGLGL 308


>gi|166031630|ref|ZP_02234459.1| hypothetical protein DORFOR_01330 [Dorea formicigenerans ATCC
           27755]
 gi|166028607|gb|EDR47364.1| hypothetical protein DORFOR_01330 [Dorea formicigenerans ATCC
           27755]
          Length = 322

 Score =  246 bits (628), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 128/293 (43%), Positives = 196/293 (66%), Gaps = 4/293 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL G+AI+ V+IDGVLHE SSI GV ED+T+II+N+
Sbjct: 26  FVVEPLERGYGTTLGNSLRRIMLSSLPGSAISQVKIDGVLHEFSSIPGVKEDVTEIIMNL 85

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K +   D  K   I   G GVVTA DIQ   DIE++NP+ VI  L+   D+ + M
Sbjct: 86  KSLAIKNTSETDEPKTAYIEFEGEGVVTAADIQVDQDIEIMNPETVIATLNGGADSKLYM 145

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++KG GYV A+ ++ +  PI +I ID++Y+P+++V+ TVE+ R GQ+ D+DKL++ +
Sbjct: 146 ELTITKGRGYVSAEKNKNDELPIAVIPIDSIYTPVERVNLTVENTRVGQITDFDKLTLDV 205

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L +FI+  E  +  +  I  +       L   ++ELEL
Sbjct: 206 YTNGTLLPDEAVSLAAKVLSEHLKLFIDLSEVAQAAEVMIEKEDDEKEKVLEMSIDELEL 265

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           SVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L 
Sbjct: 266 SVRSYNCLKRAGINTVEELTNRTSEDMMKVRNLGRKSLEEVLAKLDELGLSLS 318


>gi|308522660|dbj|BAJ22941.1| RNA polymerase alpha subunit [Vibrio sagamiensis]
 gi|308522662|dbj|BAJ22942.1| RNA polymerase alpha subunit [Vibrio sagamiensis]
          Length = 282

 Score =  246 bits (628), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 126/276 (45%), Positives = 189/276 (68%), Gaps = 8/276 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 10  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 69

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
           +++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D  A + M + V 
Sbjct: 70  SVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDSADIAMRIKVE 129

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 130 RGRGYVPASARIHTDEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 189

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 190 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 246

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 247 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 282


>gi|58416046|emb|CAH57437.1| RNA polymerase alpha-subunit [Vibrio sp. R-21434]
 gi|58416048|emb|CAH57438.1| RNA polymerase alpha-subunit [Vibrio sp. R-21435]
 gi|58416050|emb|CAH57439.1| RNA polymerase alpha-subunit [Vibrio sp. R-21439]
          Length = 293

 Score =  246 bits (628), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 125/275 (45%), Positives = 189/275 (68%), Gaps = 8/275 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H+  +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHNEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+KS
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKS 293


>gi|332077536|gb|EGI87997.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae GA41301]
          Length = 311

 Score =  246 bits (628), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 135/312 (43%), Positives = 204/312 (65%), Gaps = 8/312 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK--EVKEDI 245
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  +  EV ++ 
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIARSTEVMKEA 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           + +S   +  L + +EEL+LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E
Sbjct: 239 DTES--DDRILDRTIEELDLSVRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEE 296

Query: 306 IKGVLGTMGLFL 317
           +K  L  +GL L
Sbjct: 297 VKLKLIDLGLGL 308


>gi|183221322|ref|YP_001839318.1| DNA-directed RNA polymerase subunit alpha [Leptospira biflexa
           serovar Patoc strain 'Patoc 1 (Paris)']
 gi|189911413|ref|YP_001962968.1| DNA-directed RNA polymerase subunit alpha [Leptospira biflexa
           serovar Patoc strain 'Patoc 1 (Ames)']
 gi|238687771|sp|B0SA20|RPOA_LEPBA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238687824|sp|B0SSF2|RPOA_LEPBP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|167776089|gb|ABZ94390.1| DNA-directed RNA polymerase, alpha subunit [Leptospira biflexa
           serovar Patoc strain 'Patoc 1 (Ames)']
 gi|167779744|gb|ABZ98042.1| DNA-directed RNA polymerase alpha chain [Leptospira biflexa serovar
           Patoc strain 'Patoc 1 (Paris)']
          Length = 325

 Score =  246 bits (628), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 136/312 (43%), Positives = 203/312 (65%), Gaps = 4/312 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P  IE+        N    +AEP  RG   T+GN+LRR LMSS+ GAAI+A++I+GV H
Sbjct: 12  RPKKIEFTT-DVNTPNYGKFVAEPFERGIGTTIGNSLRRTLMSSIEGAAISAIRIEGVSH 70

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMS---GDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           E S I+GV ED+T IILN+K + +K      ++ K + +  +G G   A D+   + IE+
Sbjct: 71  EFSYIEGVAEDVTRIILNLKQVRIKYEPEDKEASKVIHLELKGAGYFRAADLAVDSSIEI 130

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPD  I  L+ DA + M+L + +G GYVPA+  + + + +G I ID+++SPI+KV + V
Sbjct: 131 MNPDLHIATLNEDANLIMDLEIQRGRGYVPAEDKKKDIEVLGTIPIDSIFSPIQKVLFEV 190

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
              R  Q  DY+KL+M + TDGS++ ED+VA A++IL+D L +FINFEE  +E +E+++ 
Sbjct: 191 SETRVAQRSDYEKLTMEVWTDGSVSPEDAVAQAAKILKDHLTVFINFEEEIEEEEEELDE 250

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                  AL K VEELELSVRSTN LR   I ++G+L++R+E +M +  +F  +SL+E+K
Sbjct: 251 ADEKLKAALSKHVEELELSVRSTNVLRSLEIDFIGELVKRSEDEMTKSKHFSEQSLLELK 310

Query: 308 GVLGTMGLFLGM 319
             L +MGL  GM
Sbjct: 311 AKLSSMGLSFGM 322


>gi|317131398|ref|YP_004090712.1| DNA-directed RNA polymerase, alpha subunit [Ethanoligenens
           harbinense YUAN-3]
 gi|315469377|gb|ADU25981.1| DNA-directed RNA polymerase, alpha subunit [Ethanoligenens
           harbinense YUAN-3]
          Length = 316

 Score =  246 bits (628), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 132/291 (45%), Positives = 194/291 (66%), Gaps = 5/291 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL G A+T V+IDGV HE S++ GV ED+T+IILNI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRVLLSSLPGVAVTQVKIDGVQHEFSTVPGVKEDVTEIILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+  K+  D  K V I   G   VTAGDI+T +++E+L+P+  I  L   A + ME+T+
Sbjct: 83  KGLTAKLHSDGPKVVYIDAEGECKVTAGDIKTDSEVEILDPNMHIATLAAGAKLYMEITL 142

Query: 150 SKGHGYVPAKHHRTENDP-IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
            KG GYV A+ ++    P IG+I +D++Y+P+ KV+Y VE+ R GQ+ DYDKL++ + TD
Sbjct: 143 DKGRGYVAAERNKQNLQPAIGVIPVDSIYTPVLKVNYAVENTRVGQITDYDKLTLEVWTD 202

Query: 209 GSITGEDSVALASRILQDQLGMFINF--EEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
            +I+ +++V++ ++IL + LG+F+    E    E+  + + KS      L   +EEL+LS
Sbjct: 203 ATISAKEAVSIGAKILNEHLGLFVALCAETQSTEIMVEKDDKS--KEKVLEMTIEELDLS 260

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           VRS NCL+   I  + DLI RTE DM+++ N GRKSL E+   L ++G  L
Sbjct: 261 VRSFNCLKRAGINTVEDLINRTEDDMMKVRNLGRKSLEEVISKLNSLGFSL 311


>gi|329118621|ref|ZP_08247325.1| DNA-directed RNA polymerase subunit alpha [Neisseria bacilliformis
           ATCC BAA-1200]
 gi|327465356|gb|EGF11637.1| DNA-directed RNA polymerase subunit alpha [Neisseria bacilliformis
           ATCC BAA-1200]
          Length = 277

 Score =  246 bits (628), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 130/279 (46%), Positives = 184/279 (65%), Gaps = 7/279 (2%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           + G A T V I GVLHE S++ GV ED+ DI+LN+KG+  K+ G    R+ + K G G V
Sbjct: 1   MNGFAPTEVSISGVLHEYSTLDGVQEDVVDILLNLKGVVFKLHGREEIRLKLKKAGNGPV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY--VPAKHHRTENDPIGLIT 172
           TA DI   +D++V+NP HVICNL  +  + ME+ V +G GY  V  +     +  IG+I 
Sbjct: 61  TAADIDLPHDVDVINPKHVICNLANNGSIEMEIVVEQGRGYQSVSGRRDVRSDTGIGVIQ 120

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           +DA +SPI +VS+ VE AR  Q  D D+L + ++T+GS+  E++V  A+RIL DQ+ +F 
Sbjct: 121 LDASFSPISRVSFEVEPARVEQRTDLDRLVLDVETNGSLDPEEAVRSAARILIDQMSVFA 180

Query: 233 NFE-EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           + +  P +EV+E    K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE +
Sbjct: 181 DLQGTPVEEVEE----KTPPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETE 236

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           +L+  N GRKSL EIK VL + GL LG  L  WPP  +E
Sbjct: 237 LLKTPNLGRKSLNEIKEVLASKGLTLGSKLEAWPPAGLE 275


>gi|187933966|ref|YP_001884502.1| DNA-directed RNA polymerase subunit alpha [Clostridium botulinum B
           str. Eklund 17B]
 gi|188589874|ref|YP_001919701.1| DNA-directed RNA polymerase subunit alpha [Clostridium botulinum E3
           str. Alaska E43]
 gi|251778696|ref|ZP_04821616.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           E1 str. 'BoNT E Beluga']
 gi|238689634|sp|B2UYD9|RPOA_CLOBA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238691607|sp|B2TIK4|RPOA_CLOBB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|187722119|gb|ACD23340.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum B
           str. Eklund 17B]
 gi|188500155|gb|ACD53291.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           E3 str. Alaska E43]
 gi|243083011|gb|EES48901.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           E1 str. 'BoNT E Beluga']
          Length = 315

 Score =  246 bits (627), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 126/290 (43%), Positives = 198/290 (68%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGNALRR+L+SSL G A ++V+IDGVLHE S+++GV ED+T++ILNIK
Sbjct: 24  VVEPLERGYGITLGNALRRILLSSLPGVATSSVKIDGVLHEFSTVQGVKEDVTELILNIK 83

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            + L+M+G+  K + I  +GPG VT  DI+T  D+EV+N D  I  LD +  + MELTV+
Sbjct: 84  SLALRMNGEGPKVIYIDAKGPGEVTGADIKTDGDVEVVNKDLHIATLDDNGRLYMELTVN 143

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           +G GYV    ++++  PI  I ID++Y+P+KKV++TV++ R GQ+ DYDKL++ I T+G+
Sbjct: 144 RGRGYVTQNKNKSDELPISSIAIDSIYTPVKKVNFTVDNTRVGQITDYDKLTLEIWTNGT 203

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I  +++++L+++IL +   +F++      +V+  I  +       L   VEEL+LSVRS 
Sbjct: 204 IKIDEAISLSAKILIEHFKLFMSLTNNTNDVEIMIEKEEDKKEKVLEMTVEELDLSVRSY 263

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           NCL+   I  + +L  ++  DM+++ N G+KSL E++  L  +GL L +N
Sbjct: 264 NCLKRAGINTVQELATKSMDDMMKVRNLGKKSLEEVERKLKELGLCLKLN 313


>gi|331268442|ref|YP_004394934.1| DNA-directed RNA polymerase subunit alpha [Clostridium botulinum
           BKT015925]
 gi|329124992|gb|AEB74937.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           BKT015925]
          Length = 315

 Score =  246 bits (627), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 124/288 (43%), Positives = 193/288 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL G A  +++IDGVLHE S++ GV ED+T++ILNI
Sbjct: 23  FVIEPLERGYGITLGNSLRRILLSSLPGVAANSIKIDGVLHEFSTVTGVKEDVTELILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM+G+    + I  +GPG VTA DI +  +IEV+N D  I  LD D  + ME+ +
Sbjct: 83  KGLALKMNGEGPSTIYIEAQGPGEVTAADIISDGNIEVMNKDMHIATLDDDGKLYMEINI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYV    ++ E+ PIG I +D++Y+P+K+V++TVE+ R GQ+ DYDKLS+ + T+G
Sbjct: 143 DRGRGYVTQNKNKKEDLPIGTIPVDSIYTPVKRVNFTVENTRVGQITDYDKLSIEVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  E++++L+++IL +   +F+   +    V+  +  +       L   +EEL+LSVRS
Sbjct: 203 TIQPEEAISLSAKILIEHFKLFMTLTDHADNVEIMVEKEEDKKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L +RT  DM+++ N G+KSL E++  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELTERTIDDMMKVRNLGKKSLEEVQEKLAALGLGL 310


>gi|325912373|ref|ZP_08174769.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           UPII 143-D]
 gi|325475844|gb|EGC79014.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           UPII 143-D]
          Length = 312

 Score =  246 bits (627), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 136/308 (44%), Positives = 200/308 (64%), Gaps = 4/308 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +EE+    + EPL RGF  TLGN+LRRVL++S+ G A++ + IDG
Sbjct: 3   EFEKPN----ITVIDQEESYGKFVVEPLERGFGTTLGNSLRRVLLTSISGTALSYIMIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILN+K + LK+  D  K V I   GP VVTA D++   D+E+
Sbjct: 59  VLHEFSTIPGVREDVTKIILNLKKLELKLLVDEEKMVEIDVEGPAVVTAADLKVDADVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + M + +  G GY+PA  +++++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMSIAIKSGRGYIPASENKSDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+AR G+  DYDKL++ + TDGSIT  D+++ A++IL++   +F++ +   +     I  
Sbjct: 179 ENARVGKRDDYDKLTLELWTDGSITPNDALSFAAKILEEHFKVFMSADMSDQFANVMIEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+R+ N GRKSL E+K
Sbjct: 239 EDKSNEKKLEMTIEELDLSVRSYNCLKRAGINTVQELNNKSEADMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGL 315
             L  +GL
Sbjct: 299 NKLTELGL 306


>gi|182418825|ref|ZP_02950090.1| DNA-directed RNA polymerase, alpha subunit [Clostridium butyricum
           5521]
 gi|237666885|ref|ZP_04526870.1| DNA-directed RNA polymerase, alpha subunit [Clostridium butyricum
           E4 str. BoNT E BL5262]
 gi|182377322|gb|EDT74883.1| DNA-directed RNA polymerase, alpha subunit [Clostridium butyricum
           5521]
 gi|237658084|gb|EEP55639.1| DNA-directed RNA polymerase, alpha subunit [Clostridium butyricum
           E4 str. BoNT E BL5262]
          Length = 315

 Score =  246 bits (627), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 124/290 (42%), Positives = 199/290 (68%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGNALRR+L+SSL G A T+V+IDGVLHE S+++GV ED+T++ILNIK
Sbjct: 24  VVEPLERGYGITLGNALRRILLSSLPGVAPTSVKIDGVLHEFSTVQGVKEDVTELILNIK 83

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            + LKM+G+  K + I  +GPG VT  DI+T  D+EV+N D  I  LD D  + MELTV+
Sbjct: 84  SLALKMNGEGPKVIYIDAKGPGEVTGADIKTDGDVEVVNKDLHIATLDSDGRLYMELTVN 143

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            G GYV    +++++ PI  I +D++Y+P+K+V++TV++ R GQ+ DYDKL++ I T+G+
Sbjct: 144 NGRGYVTQNKNKSDDLPISSIAVDSIYTPVKRVNFTVDNTRVGQITDYDKLTLEIWTNGT 203

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I  +++++L+++IL +   +F++  +   +++  +  +       L   VEEL+LSVRS 
Sbjct: 204 IRIDEAISLSAKILIEHFKLFMSLTDNTNDIEVMVEKEEDKKEKVLEMTVEELDLSVRSY 263

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           NCL+   I  + +L  ++  DM+++ N G+KSL E++  L  +GL L ++
Sbjct: 264 NCLKRAGINTVQELATKSMDDMMKVRNLGKKSLEEVERKLKELGLCLKLS 313


>gi|157493285|gb|ABV58008.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 272

 Score =  246 bits (627), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 124/275 (45%), Positives = 189/275 (68%), Gaps = 8/275 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ 
Sbjct: 1   PLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLA 60

Query: 94  LKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSK 151
           ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V +
Sbjct: 61  VRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVER 120

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T+
Sbjct: 121 GRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMETN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 181 GTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 237

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 272


>gi|239623375|ref|ZP_04666406.1| DNA-directed RNA polymerase [Clostridiales bacterium 1_7_47_FAA]
 gi|239522341|gb|EEQ62207.1| DNA-directed RNA polymerase [Clostridiales bacterium 1_7_47FAA]
          Length = 320

 Score =  246 bits (627), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 127/292 (43%), Positives = 193/292 (66%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDGVLHE SSI GV ED+T+II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDGVLHEFSSIPGVKEDVTEIIMNI 82

Query: 90  KGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K + D+   K   I   G GV+TA DIQ   DIE++NPD VI  L    D+   M
Sbjct: 83  KSLAIKNNSDTDEPKVAYIEFEGEGVITAADIQADADIEIMNPDQVIATLSGGTDSKFYM 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++KG GY+ A  ++ ++ PIG+I +D++Y+P+++V+  V + R GQ  D+DKL++ I
Sbjct: 143 ELTITKGRGYISADKNKNDDLPIGVIAVDSIYTPVERVNMAVTNTRVGQQTDFDKLTLEI 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L +FI+  E  K  +  +  +       L   ++ELEL
Sbjct: 203 YTNGTLAPDEAVSLAAKVLSEHLNLFIDLSENAKTAEIMVEKEDNEKEKVLEMNIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L
Sbjct: 263 SVRSYNCLKRAGINTVEELCNRTSEDMMKVRNLGRKSLEEVLAKLKELGLQL 314


>gi|258513668|ref|YP_003189890.1| DNA-directed RNA polymerase subunit alpha [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257777373|gb|ACV61267.1| DNA-directed RNA polymerase, alpha subunit [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 315

 Score =  246 bits (627), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 129/289 (44%), Positives = 197/289 (68%), Gaps = 1/289 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL G A+T+V+IDGVLHE S++ GV ED+TDIILN+
Sbjct: 22  FIVEPLERGYGITLGNSLRRILLSSLPGVAVTSVKIDGVLHEFSTVPGVREDVTDIILNL 81

Query: 90  KGINLKMSGDSHKRV-TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           K + LKM G++ +++  I  +G G V AGDI   +D+E+LNPD  I  L  +  + M++T
Sbjct: 82  KSLRLKMHGEADEKILRIEAQGEGEVRAGDIVPDSDVEILNPDMYIATLAANGRLSMDIT 141

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           +++G GY  A+ ++     IG+I ID++++P+ KV+Y+VE+ R GQ  DYDKLS+ I TD
Sbjct: 142 IARGRGYFSAERNKKGEPIIGVIPIDSIFTPVYKVNYSVENTRVGQRTDYDKLSIEIWTD 201

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           GSI  +++ +LA++I+ + L +FI   E  K+V+  +  +    +  +   +EEL+LSVR
Sbjct: 202 GSIHPDEAASLAAKIMSEHLQLFIGLTEETKDVEIMVEKEEEKKDKIMEMTIEELDLSVR 261

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           S NCL+   I  + +LIQR E DM+++ N G+KSL E+   L  +G+ L
Sbjct: 262 SYNCLKRACINTVEELIQRNEEDMMKVRNLGKKSLEEVIQKLNELGVSL 310


>gi|23097600|ref|NP_691066.1| DNA-directed RNA polymerase subunit alpha [Oceanobacillus iheyensis
           HTE831]
 gi|33301658|sp|Q8ETV9|RPOA_OCEIH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|22775823|dbj|BAC12101.1| DNA-directed RNA polymerase alpha subunit [Oceanobacillus iheyensis
           HTE831]
          Length = 314

 Score =  245 bits (626), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 126/295 (42%), Positives = 193/295 (65%), Gaps = 2/295 (0%)

Query: 25  ENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           EN T    + EPL RG+  TLGN+LRR+L+SSL GAA+T VQIDG LHE S++ GV ED+
Sbjct: 16  ENATFGKFVVEPLERGYGATLGNSLRRILLSSLPGAAVTTVQIDGALHEFSTVDGVVEDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILN+K + LK+  +  K + I  +G G VTA D+   +D+EV+NPD  I  L+    
Sbjct: 76  TTIILNLKKLALKIYSEEPKTLEIDVQGEGAVTAADLTYDSDVEVMNPDLHIATLNSKGN 135

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + M+L   +G GY PA+ ++ ++ PIG+I ID++++P+ +V+Y VE+ R GQV +YDKL+
Sbjct: 136 LHMKLIAERGRGYRPAEENKNDDQPIGVIPIDSIFTPVSRVTYQVENTRVGQVANYDKLT 195

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           M + TDGSI  E++V+L ++I+ + L +F+   +  +  +  +  +       +   +EE
Sbjct: 196 MDVSTDGSIRPEEAVSLGAKIITEHLNIFVGLTDEAQNAEIMVEKEEDQKEKVMEMTIEE 255

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+LSVRS NCL+   I  + +L  ++E DM+++ N GRKSL E+K  L  +GL L
Sbjct: 256 LDLSVRSYNCLKRAGINTVQELANKSEEDMMKVRNLGRKSLEEVKVKLEDLGLGL 310


>gi|259500918|ref|ZP_05743820.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus iners DSM
           13335]
 gi|302190629|ref|ZP_07266883.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus iners
           AB-1]
 gi|309803637|ref|ZP_07697727.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LactinV 11V1-d]
 gi|309804964|ref|ZP_07699022.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LactinV 09V1-c]
 gi|309806715|ref|ZP_07700710.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LactinV 03V1-b]
 gi|309808436|ref|ZP_07702335.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LactinV 01V1-a]
 gi|309809144|ref|ZP_07703017.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           SPIN 2503V10-D]
 gi|312871172|ref|ZP_07731270.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LEAF 3008A-a]
 gi|312872807|ref|ZP_07732872.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LEAF 2062A-h1]
 gi|312874040|ref|ZP_07734075.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LEAF 2052A-d]
 gi|312874841|ref|ZP_07734860.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LEAF 2053A-b]
 gi|315654000|ref|ZP_07906916.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus iners ATCC
           55195]
 gi|325913233|ref|ZP_08175602.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           UPII 60-B]
 gi|329920643|ref|ZP_08277330.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           SPIN 1401G]
 gi|259167612|gb|EEW52107.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus iners DSM
           13335]
 gi|308164235|gb|EFO66492.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LactinV 11V1-d]
 gi|308165724|gb|EFO67949.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LactinV 09V1-c]
 gi|308166895|gb|EFO69079.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LactinV 03V1-b]
 gi|308168264|gb|EFO70383.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LactinV 01V1-a]
 gi|308170589|gb|EFO72609.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           SPIN 2503V10-D]
 gi|311089586|gb|EFQ48011.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LEAF 2053A-b]
 gi|311090380|gb|EFQ48789.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LEAF 2052A-d]
 gi|311091849|gb|EFQ50228.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LEAF 2062A-h1]
 gi|311093186|gb|EFQ51532.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LEAF 3008A-a]
 gi|315488696|gb|EFU78342.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus iners ATCC
           55195]
 gi|325477497|gb|EGC80640.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           UPII 60-B]
 gi|328935901|gb|EGG32361.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           SPIN 1401G]
          Length = 312

 Score =  245 bits (626), Expect = 6e-63,   Method: Compositional matrix adjust.
 Identities = 136/308 (44%), Positives = 200/308 (64%), Gaps = 4/308 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +EE+    + EPL RGF  TLGN+LRRVL++S+ G A++ + IDG
Sbjct: 3   EFEKPN----ITVIDQEESYGKFVVEPLERGFGTTLGNSLRRVLLTSISGTALSYIMIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILN+K + LK+  D  K V I   GP VVTA D++   D+E+
Sbjct: 59  VLHEFSTIPGVREDVTKIILNLKKLELKLLVDEEKMVEIDVEGPAVVTAADLKVDADVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + M + +  G GY+PA  +++++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMSIAIKNGRGYIPASENKSDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+AR G+  DYDKL++ + TDGSIT  D+++ A++IL++   +F++ +   +     I  
Sbjct: 179 ENARVGKRDDYDKLTLELWTDGSITPNDALSFAAKILEEHFKVFMSADMSDQFANVMIEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+R+ N GRKSL E+K
Sbjct: 239 EDKSNEKKLEMTIEELDLSVRSYNCLKRAGINTVQELNNKSEADMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGL 315
             L  +GL
Sbjct: 299 NKLTELGL 306


>gi|300089407|gb|ADJ67855.1| RNA polymerase alpha-subunit [Photobacterium jeanii]
          Length = 270

 Score =  245 bits (626), Expect = 6e-63,   Method: Compositional matrix adjust.
 Identities = 124/273 (45%), Positives = 185/273 (67%), Gaps = 7/273 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+ 
Sbjct: 1   PLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDVLEILLNLKGLA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKG 152
           +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +G
Sbjct: 61  VKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNADISMRIKVERG 120

Query: 153 HGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            GYVPA    H   +  PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + + T+G
Sbjct: 121 RGYVPASARIHTEEDERPIGRLLVDATFSPVDRIAYAVEAARVEQRTDLDKLVIDMQTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           ++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VRS
Sbjct: 181 TLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRS 237

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
            NCL+ E I Y+GDL+QRTE ++L+  N G+KS
Sbjct: 238 ANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKS 270


>gi|302876505|ref|YP_003845138.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           cellulovorans 743B]
 gi|307687177|ref|ZP_07629623.1| DNA-directed RNA polymerase subunit alpha [Clostridium
           cellulovorans 743B]
 gi|302579362|gb|ADL53374.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           cellulovorans 743B]
          Length = 315

 Score =  245 bits (626), Expect = 6e-63,   Method: Compositional matrix adjust.
 Identities = 125/291 (42%), Positives = 196/291 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL G A  +++IDGVLHE S++KGV ED+T++ILN+
Sbjct: 23  FVIEPLERGYGITLGNSLRRILLSSLPGVAANSIKIDGVLHEFSTVKGVKEDVTELILNV 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM+G+  K + I  +GP VVTA DI T + +EV++ D  I  LD D  ++ME+ V
Sbjct: 83  KPLALKMNGEGPKTIYIDAQGPAVVTAADIITDDSVEVISKDLHIATLDEDGRLQMEIEV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           + G GYV    ++ ++ PIG I ID++Y+PI +V++TVE+ R GQ+ DYDKL++ + T+G
Sbjct: 143 NSGRGYVTQNKNKRDDMPIGTIAIDSIYTPITRVNFTVENTRVGQITDYDKLTLEVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  E++++L+S+IL + L +F+   +    V+  +  +       L   +EEL+LSVRS
Sbjct: 203 TIRPEEAISLSSKILIEHLKLFMTLTDNADNVEIMVEKEEDKKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
            NCL+   I  + +L +R+  DM+++ N G+KSL E+   L  +GL L +N
Sbjct: 263 YNCLKRAGINTVQELTERSMDDMMKVRNLGKKSLEEVDQKLTALGLGLKLN 313


>gi|197303839|ref|ZP_03168875.1| hypothetical protein RUMLAC_02578 [Ruminococcus lactaris ATCC
           29176]
 gi|197297132|gb|EDY31696.1| hypothetical protein RUMLAC_02578 [Ruminococcus lactaris ATCC
           29176]
          Length = 319

 Score =  245 bits (626), Expect = 6e-63,   Method: Compositional matrix adjust.
 Identities = 128/292 (43%), Positives = 197/292 (67%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAAI++V+IDGVLHE SSI GV ED+T+II+N+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAISSVKIDGVLHEFSSIPGVKEDVTEIIMNL 82

Query: 90  KGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K + +S   K   I   G GVVT  DIQ  +DIE++NP+ VI  L    D+ + M
Sbjct: 83  KSLAIKNTSESDEVKTAYIEYEGEGVVTGADIQADSDIEIVNPEQVIATLSGGKDSKLYM 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++KG GYV +  ++TE+ PIG++ ID++Y+PI +V+ TV++ R GQ+ DYDKL++ +
Sbjct: 143 ELTITKGRGYVSSDKNKTEDMPIGVLPIDSIYTPIDRVNLTVQNTRVGQITDYDKLTLDV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T G++  +++V+LA+++L + L +FI+  E  ++ +  I  +       L   ++ELEL
Sbjct: 203 WTKGTMAPDEAVSLAAKVLSEHLKLFIDLSEVAQQAEVMIEKEDDEKEKVLEMSIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + +L  +T  DM+++ N GRKSL E+   L  + L L
Sbjct: 263 SVRSYNCLKRAGINTVEELTNKTPEDMMKVRNLGRKSLEEVLAKLKELNLEL 314


>gi|171778401|ref|ZP_02919580.1| hypothetical protein STRINF_00431 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171282932|gb|EDT48356.1| hypothetical protein STRINF_00431 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 312

 Score =  245 bits (626), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 127/288 (44%), Positives = 191/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNI
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNI 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   D  K + +   GP  VTAGDI T +D+E++NPDH +  +     ++  +TV
Sbjct: 81  KGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDSDVEIVNPDHYLFTIAEGHSLKAIMTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ E+ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 141 AKKRGYVPAEGNKKEDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  ED++ L++R+L + L +F +  E  K        + +     L + +EEL+LSVRS
Sbjct: 201 TIIPEDALGLSARVLIEHLNLFTDLTEVAKNTDVMKETEKVNDEKVLDRTIEELDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL ++TE +M+++ N GRKSL E+K  L  +GL L
Sbjct: 261 YNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVKVKLADLGLGL 308


>gi|55821879|ref|YP_140321.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           thermophilus LMG 18311]
 gi|55823795|ref|YP_142236.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           thermophilus CNRZ1066]
 gi|116628572|ref|YP_821191.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           thermophilus LMD-9]
 gi|81558875|sp|Q5LXT7|RPOA_STRT1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|81560062|sp|Q5M2D9|RPOA_STRT2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|122266834|sp|Q03IH7|RPOA_STRTD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|55737864|gb|AAV61506.1| DNA-directed RNA polymerase alpha subunit [Streptococcus
           thermophilus LMG 18311]
 gi|55739780|gb|AAV63421.1| DNA-directed RNA polymerase alpha subunit [Streptococcus
           thermophilus CNRZ1066]
 gi|116101849|gb|ABJ66995.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Streptococcus thermophilus LMD-9]
 gi|312279233|gb|ADQ63890.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           thermophilus ND03]
          Length = 312

 Score =  245 bits (626), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 126/288 (43%), Positives = 191/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILNI
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNI 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +  +GP  VTAGDI T +DIE++NPDH +  +   A  +  +TV
Sbjct: 81  KGLAVKSYVEDEKTIELDVQGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGASFQATMTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           S   GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 141 STNRGYVPAEENKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIVTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  ED++ L++RIL + L +F +  +  K        + +     L + +EEL+LSVRS
Sbjct: 201 TIIPEDALGLSARILIEHLNLFTDLTDVAKATDVMKETEKVNDEKLLDRTIEELDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL ++TE +M+++ N GRKSL E+K  L  +GL L
Sbjct: 261 YNCLKRAGINTVHDLTEKTEPEMMKVRNLGRKSLEEVKVKLADLGLGL 308


>gi|306825961|ref|ZP_07459297.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sp. oral
           taxon 071 str. 73H25AP]
 gi|304431677|gb|EFM34657.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sp. oral
           taxon 071 str. 73H25AP]
          Length = 311

 Score =  245 bits (626), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 134/312 (42%), Positives = 204/312 (65%), Gaps = 8/312 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK--EVKEDI 245
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  K  EV ++ 
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSTEVMKEA 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           + +S   +  L + +EEL+LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E
Sbjct: 239 DTES--DDRILDRTIEELDLSVRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEE 296

Query: 306 IKGVLGTMGLFL 317
           +K  L  +GL L
Sbjct: 297 VKFKLIDLGLGL 308


>gi|312862356|ref|ZP_07722599.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           vestibularis F0396]
 gi|322515893|ref|ZP_08068835.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           vestibularis ATCC 49124]
 gi|311101999|gb|EFQ60199.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           vestibularis F0396]
 gi|322125680|gb|EFX97007.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           vestibularis ATCC 49124]
          Length = 312

 Score =  245 bits (625), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 124/288 (43%), Positives = 191/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILNI
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNI 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +  +GP  VTAGDI T +DIE++NPDH +  +   A ++  +TV
Sbjct: 81  KGLAVKSYVEDEKTIELDVQGPAEVTAGDILTDSDIEIVNPDHYLFTISEGASLKATMTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +   GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 141 ATNRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  ED++ L++R+L + L +F +  +  K        + +     L + +EEL+LSVRS
Sbjct: 201 TIIPEDALGLSARVLIEHLNLFTDLTDVAKATDVMKETEKVNDEKVLDRTIEELDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL ++TE +M+++ N GRKSL E+K  L  +GL L
Sbjct: 261 YNCLKRAGINTVHDLTEKTEPEMMKVRNLGRKSLEEVKVKLADLGLGL 308


>gi|327438303|dbj|BAK14668.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Solibacillus silvestris StLB046]
          Length = 314

 Score =  245 bits (625), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 124/288 (43%), Positives = 190/288 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+ +TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+  IILN+
Sbjct: 23  FVVEPLERGYGNTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVASIILNV 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +G G VTA DI   +D+E+LNPD  I  +  +  +RM +  
Sbjct: 83  KKLALKIYSDEEKVIEIDVKGDGTVTAADITHDSDVEILNPDLYIATIAKNGHLRMRMYA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY PA  ++ E+ PIG+I ID++Y+P+ +V++ VE+ R GQ  DYDKLS+ + TDG
Sbjct: 143 QRGRGYTPADQNKREDLPIGVIPIDSIYTPVSRVNFQVENTRVGQNSDYDKLSLDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  +++++L ++IL + L +F+      +  +  +  +       L   +EEL+LSVRS
Sbjct: 203 SIGPKEAISLGAKILTEHLNIFVGMTNEAQTAEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++E DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVLELANKSEDDMMKVRNLGRKSLEEVKHKLEELGLGL 310


>gi|150015072|ref|YP_001307326.1| DNA-directed RNA polymerase subunit alpha [Clostridium beijerinckii
           NCIMB 8052]
 gi|189043835|sp|A6LPU0|RPOA_CLOB8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|149901537|gb|ABR32370.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           beijerinckii NCIMB 8052]
          Length = 315

 Score =  245 bits (625), Expect = 8e-63,   Method: Compositional matrix adjust.
 Identities = 125/289 (43%), Positives = 198/289 (68%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGNALRR+L+SSL G A T+V+IDGVLHE S+++GV ED+T++ILNIK
Sbjct: 24  VVEPLERGYGITLGNALRRILLSSLPGVATTSVKIDGVLHEFSTVQGVKEDVTELILNIK 83

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            + L+M+G+  K + I  +GPG VT  DI+T  D+EV+N +  I  LD D  + MELTV+
Sbjct: 84  SLALRMNGEGPKVIYIDAKGPGEVTGADIKTDGDVEVVNKNLHIATLDNDGRLYMELTVN 143

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYV    ++++  PI  I +D++Y+P+K+V++TV++ R GQ+ DYDKL++ I T+G+
Sbjct: 144 KGRGYVTQNKNKSDELPISAIAVDSIYTPVKRVNFTVDNTRVGQITDYDKLTLEIWTNGT 203

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I  +++++L+++IL +   +F++  +   +V+  I  +       L   VEEL+LSVRS 
Sbjct: 204 IKIDEAISLSAKILIEHFKLFMSLTDNTNDVEIMIEKEDDKKEKVLEMTVEELDLSVRSY 263

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           NCL+   I  + +L  ++  DM+++ N G+KSL E++  L  +GL L +
Sbjct: 264 NCLKRAGINTVQELATKSMDDMMKVRNLGKKSLEEVERKLKELGLALKL 312


>gi|270292026|ref|ZP_06198241.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus sp. M143]
 gi|306828808|ref|ZP_07462000.1| DNA-directed RNA polymerase subunit alpha [Streptococcus mitis ATCC
           6249]
 gi|315612357|ref|ZP_07887270.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           ATCC 49296]
 gi|322375014|ref|ZP_08049528.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus sp. C300]
 gi|331267109|ref|YP_004326739.1| DNA-dependent RNA polymerase, alpha subunit [Streptococcus oralis
           Uo5]
 gi|270279554|gb|EFA25396.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus sp. M143]
 gi|304428986|gb|EFM32074.1| DNA-directed RNA polymerase subunit alpha [Streptococcus mitis ATCC
           6249]
 gi|315315338|gb|EFU63377.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           ATCC 49296]
 gi|321280514|gb|EFX57553.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus sp. C300]
 gi|326683781|emb|CBZ01399.1| DNA-dependent RNA polymerase, alpha subunit [Streptococcus oralis
           Uo5]
          Length = 311

 Score =  245 bits (625), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 134/312 (42%), Positives = 204/312 (65%), Gaps = 8/312 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK--EVKEDI 245
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  K  EV ++ 
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSTEVMKEA 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           + +S   +  L + +EEL+LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E
Sbjct: 239 DTES--DDRILDRTIEELDLSVRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEE 296

Query: 306 IKGVLGTMGLFL 317
           +K  L  +GL L
Sbjct: 297 VKLKLIDLGLGL 308


>gi|325104841|ref|YP_004274495.1| DNA-directed RNA polymerase subunit alpha [Pedobacter saltans DSM
           12145]
 gi|324973689|gb|ADY52673.1| DNA-directed RNA polymerase subunit alpha [Pedobacter saltans DSM
           12145]
          Length = 330

 Score =  244 bits (624), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 128/298 (42%), Positives = 191/298 (64%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AIT+V+  GV HE S+IKGV ED+ DIILN+K + 
Sbjct: 28  PLEPGFGVTIGNALRRILLSSLEGYAITSVRFSGVSHEFSTIKGVAEDVVDIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQTV-NDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K +G+S   +++ +   G     AGDI    N+ EVLNPD V+CN++    + +ELT++
Sbjct: 88  FKKTGESGDSEKIFVIINGQESFKAGDITKFSNNFEVLNPDFVVCNMESSVTLEIELTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYV A+ ++  +  +G+I ID++Y+PIK V YT+E+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVAAEENKNADAAVGVIAIDSIYTPIKNVKYTIENYRVEQKTDYEKLLLDISTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ED++  A++IL     +F +     E   KE  ++++ + L     L  ++ +L+LS
Sbjct: 208 IHPEDALKEAAKILIQHFMLFSDENLILESQAKEETKEVDEEVLHMRKILKTELVDLDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  +I  + DL+    ADML+  NFG+KSL EI+ ++ + GL  GMNL  +
Sbjct: 268 VRALNCLKAADIRSLADLVSYDVADMLKFRNFGKKSLTEIQELVKSKGLSFGMNLSKY 325


>gi|18311358|ref|NP_563292.1| DNA-directed RNA polymerase subunit alpha [Clostridium perfringens
           str. 13]
 gi|110799041|ref|YP_697065.1| DNA-directed RNA polymerase subunit alpha [Clostridium perfringens
           ATCC 13124]
 gi|110802435|ref|YP_699634.1| DNA-directed RNA polymerase subunit alpha [Clostridium perfringens
           SM101]
 gi|168205205|ref|ZP_02631210.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           E str. JGS1987]
 gi|168211876|ref|ZP_02637501.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           B str. ATCC 3626]
 gi|168215205|ref|ZP_02640830.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           CPE str. F4969]
 gi|168216660|ref|ZP_02642285.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           NCTC 8239]
 gi|169347112|ref|ZP_02866054.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           C str. JGS1495]
 gi|182626919|ref|ZP_02954652.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           D str. JGS1721]
 gi|119366675|sp|Q0TMS5|RPOA_CLOP1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366676|sp|Q0SQH3|RPOA_CLOPS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|124053359|sp|P0C2E6|RPOA_CLOPE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|7707686|dbj|BAA95357.1| RNA polymerase alpha subunit [Clostridium perfringens]
 gi|18146042|dbj|BAB82082.1| RNA polymerase alpha subunit [Clostridium perfringens str. 13]
 gi|110673688|gb|ABG82675.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           ATCC 13124]
 gi|110682936|gb|ABG86306.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           SM101]
 gi|169296795|gb|EDS78924.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           C str. JGS1495]
 gi|170663306|gb|EDT15989.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           E str. JGS1987]
 gi|170710183|gb|EDT22365.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           B str. ATCC 3626]
 gi|170713403|gb|EDT25585.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           CPE str. F4969]
 gi|177907709|gb|EDT70324.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           D str. JGS1721]
 gi|182381168|gb|EDT78647.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           NCTC 8239]
          Length = 315

 Score =  244 bits (624), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 127/288 (44%), Positives = 195/288 (67%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGNALRR+L+SSL G A T+V+ID VLHE S+I GV ED+T+IILN+K +
Sbjct: 26  EPLERGYGITLGNALRRILLSSLPGVAPTSVKIDSVLHEFSTITGVKEDVTEIILNLKML 85

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            L M G+  K + I  +GPGVVT  DI+T  D+EV+N D  I  LD D  + ME+ V++G
Sbjct: 86  ALTMEGEGPKTIYIDAQGPGVVTGADIKTDGDVEVVNKDLHIATLDNDGKLYMEIVVNRG 145

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV    ++TE+ P+  I ID++Y+P+K+V+++V++ R GQ+ DYDKL++ I T+G+I 
Sbjct: 146 RGYVTQNKNKTEDLPLSAIAIDSIYTPVKRVNFSVQNTRVGQITDYDKLTLEIWTNGTIR 205

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
            E++++L+++IL +   +F+   +   +V+  I  +      AL   +EEL+LSVRS NC
Sbjct: 206 IEEAISLSAKILIEHFKLFMTLTDNANDVEIMIEKEEDKKEKALEMTIEELDLSVRSYNC 265

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           L+   I  + +L  ++  DM+++ N G+KSL E++  L  +GL L +N
Sbjct: 266 LKRAGINTVQELAGKSMDDMMKVRNLGKKSLEEVERKLNELGLNLRLN 313


>gi|313903124|ref|ZP_07836518.1| DNA-directed RNA polymerase subunit alpha [Thermaerobacter
           subterraneus DSM 13965]
 gi|313466626|gb|EFR62146.1| DNA-directed RNA polymerase subunit alpha [Thermaerobacter
           subterraneus DSM 13965]
          Length = 315

 Score =  244 bits (624), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 126/294 (42%), Positives = 198/294 (67%), Gaps = 12/294 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGNALRRVL+SSL GAA+T+V+I+GVLHE S++ GV ED T+IILN+
Sbjct: 23  FVVEPLERGYGITLGNALRRVLLSSLPGAAVTSVRIEGVLHEFSTLPGVVEDTTEIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + +KM  D  + + I  +G G V A DI T  D+E++N DH+I  L+ D  + ME+TV
Sbjct: 83  KELAIKMYTDEPQVLRIEAQGEGEVRAADIITPPDVEIVNGDHLIATLEPDGRLFMEMTV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYVPA  ++  +  IG+I +D++++PI+KV++ VE+ R G+V DYD+L++ + T+G
Sbjct: 143 QRGRGYVPADRNKDPDRSIGVIPVDSIFTPIRKVNFQVENTRVGKVTDYDRLTLEVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK------EVKEDINVKSLPFNPALLKKVEEL 263
           +I  +++ + A++IL D L +F+   +  +      E ++D   K L  +      ++EL
Sbjct: 203 TIAPDEAASQAAQILTDHLALFLTLTDQARGTGTAVEKEDDARAKLLEMS------IDEL 256

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +LSVRS NCL+   I  +G+L+++T  DM+R+ N G+KSL E++  L  +GL L
Sbjct: 257 DLSVRSYNCLKRAGINTIGELVEKTPEDMMRVRNLGKKSLEEVEEKLAALGLSL 310


>gi|167759833|ref|ZP_02431960.1| hypothetical protein CLOSCI_02196 [Clostridium scindens ATCC 35704]
 gi|167662452|gb|EDS06582.1| hypothetical protein CLOSCI_02196 [Clostridium scindens ATCC 35704]
          Length = 322

 Score =  244 bits (624), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 128/293 (43%), Positives = 195/293 (66%), Gaps = 4/293 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAAI+ V+IDGVLHE SSI GV ED+T+II+N+
Sbjct: 26  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAISQVKIDGVLHEFSSIPGVKEDVTEIIMNL 85

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K +   D  K   I   G GVVTA DIQ   DIE++NP+ VI  L+   D+ + M
Sbjct: 86  KSLAIKNTSETDEPKTAYIEFEGEGVVTAADIQVDQDIEIMNPETVIATLNGGADSKLYM 145

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT+++G GYV A  ++ +  PI +I ID++Y+P+++V+ TVE+ R GQ+ D+DKL++ +
Sbjct: 146 ELTITRGRGYVSADKNKNDELPIAVIPIDSIYTPVERVNLTVENTRVGQITDFDKLTLDV 205

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L +FI+  E  +  +  I  +       L   ++ELEL
Sbjct: 206 YTNGTLLPDEAVSLAAKVLSEHLKLFIDLSEVAQAAEVMIEKEDDEKEKVLEMSIDELEL 265

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           SVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L 
Sbjct: 266 SVRSYNCLKRAGINTVEELTNRTPEDMMKVRNLGRKSLEEVLAKLDELGLSLS 318


>gi|295694866|ref|YP_003588104.1| DNA-directed RNA polymerase, alpha subunit [Bacillus tusciae DSM
           2912]
 gi|295410468|gb|ADG04960.1| DNA-directed RNA polymerase, alpha subunit [Bacillus tusciae DSM
           2912]
          Length = 314

 Score =  244 bits (623), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 125/288 (43%), Positives = 187/288 (64%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGNALRR+L+SSL GAA T+V+IDGVLHE S+I GV ED T+IILN+
Sbjct: 23  FVIEPLERGYGTTLGNALRRILLSSLPGAACTSVKIDGVLHEFSTIPGVVEDTTEIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L++  D  K + I   G G + AGDIQ  +D+++LNP+  I  L   A +  E+  
Sbjct: 83  KHLALRIHSDEEKTLIIDAEGEGEIKAGDIQADSDVDILNPELHIATLAEGARLYAEIKA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           ++G GYVPA  ++ E  PIG+I +D++++PI +V+Y++E+ R GQV DYDKL+  + TDG
Sbjct: 143 ARGRGYVPADRNKNEEQPIGVIPMDSIFTPISRVNYSIENTRVGQVTDYDKLTFEVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  +++V+  +RIL + L +F+   +  +     +          L   +EEL+LSVRS
Sbjct: 203 SIRPDEAVSYGARILTEHLTLFLGLTDQPRAGDVLVERDEQRREKVLDMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  +TE +M+++ N GRKSL E++  L  +GL L
Sbjct: 263 YNCLKRAGINTVAELCSKTEEEMMKVRNLGRKSLEEVQEKLAELGLAL 310


>gi|297588218|ref|ZP_06946862.1| DNA-directed RNA polymerase subunit alpha [Finegoldia magna ATCC
           53516]
 gi|297574907|gb|EFH93627.1| DNA-directed RNA polymerase subunit alpha [Finegoldia magna ATCC
           53516]
          Length = 317

 Score =  244 bits (623), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 137/309 (44%), Positives = 201/309 (65%), Gaps = 6/309 (1%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           IV   E+ N    +  PL RG+  TLGN+LRRVL+SSL GAAI+ + I GV HE+S+IKG
Sbjct: 11  IVELDEQNNYGKFVIMPLERGYGTTLGNSLRRVLLSSLPGAAISKINIQGVAHEMSTIKG 70

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +IILN+KGI +K   +    + +  +GP V+TA DI    D+EV NPDH I  L
Sbjct: 71  VKEDVPEIILNLKGIAVKKYNEEPISLNVDIKGPCVLTAKDILVDTDLEVKNPDHYIATL 130

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + DA + M++TV  G GY  ++ ++T+ D IG I ID+L+SP+KKV++TV++AR GQV+D
Sbjct: 131 NEDASLEMQITVINGKGYKISEFNKTDEDIIGDIAIDSLFSPVKKVNFTVDNARVGQVID 190

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI---NFEEPKKEVKEDINVKSLPFNP 254
           YDKL++ + T+G+I  +D+++  S IL + L +F    N+E       ED N K      
Sbjct: 191 YDKLTIEVWTNGTIRPQDALSEGSNILINCLELFSELPNYECNTNSDDED-NQKDKETQM 249

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
            +   +EEL+ S+RS NCL+  NI  +GD++  T+ADM+++ NFG+KSL E++  L  MG
Sbjct: 250 GI--NIEELDFSLRSFNCLKRANINTVGDIVSHTKADMMKIKNFGKKSLDEVEEKLQEMG 307

Query: 315 LFLGMNLPD 323
           L     + D
Sbjct: 308 LAFKEEIKD 316


>gi|228478065|ref|ZP_04062676.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           salivarius SK126]
 gi|228250245|gb|EEK09498.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           salivarius SK126]
          Length = 312

 Score =  244 bits (623), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 124/288 (43%), Positives = 191/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILNI
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNI 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +  +GP  VTAGDI T +DIE++NPDH +  +   A ++  +TV
Sbjct: 81  KGLAVKSYVEDEKTIELDVQGPAEVTAGDILTDSDIEIVNPDHYLFTIADGASLKATMTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +   GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 141 ATNRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  ED++ L++R+L + L +F +  +  K        + +     L + +EEL+LSVRS
Sbjct: 201 TIIPEDALGLSARVLIEHLNLFTDLTDVAKATDVMKETEKVNDEKVLDRTIEELDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL ++TE +M+++ N GRKSL E+K  L  +GL L
Sbjct: 261 YNCLKRAGINTVHDLTEKTEPEMMKVRNLGRKSLEEVKVKLADLGLGL 308


>gi|289579114|ref|YP_003477741.1| DNA-directed RNA polymerase subunit alpha [Thermoanaerobacter
           italicus Ab9]
 gi|297545301|ref|YP_003677603.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           mathranii subsp. mathranii str. A3]
 gi|289528827|gb|ADD03179.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           italicus Ab9]
 gi|296843076|gb|ADH61592.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           mathranii subsp. mathranii str. A3]
          Length = 315

 Score =  244 bits (623), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 138/310 (44%), Positives = 197/310 (63%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+I+P  IE IV   E+      + EPL RG+  TLGN+LRRVL+SSL GAA  +V+IDG
Sbjct: 3   EIIEPK-IE-IVEQAEDGTYGKFVVEPLERGYGITLGNSLRRVLLSSLPGAAPKSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+ +IILN+K I +K+  D      I   G G VTAG I+   DIE+
Sbjct: 61  VLHEFSTLPGVKEDVVEIILNLKEIAVKLHSDEPVVGRIDVEGKGEVTAGHIKGSADIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPDH I  L  D  + ME+   KG GYVP+  ++  N PIG+I +D++++P+KKVSY V
Sbjct: 121 LNPDHHIATLSDDGKLHMEIVFVKGKGYVPSDKNKEPNQPIGVIPVDSIFTPVKKVSYNV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G V DYDKL++ + T+G+IT ++++++AS +L      FI+F    K     ++ 
Sbjct: 181 ENTRVGNVTDYDKLTLEVWTNGTITPKEAISMASDMLIRYFQKFISFSGEYKSSDIFVDK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                   L   +EEL+LSVRS NCL+   I  + +L Q+TE +M+++ N G+KSL E+K
Sbjct: 241 PDKKIEKPLDMTIEELDLSVRSYNCLKRAGINTVQELTQKTEEEMMKVRNLGKKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 QKLQALGLSL 310


>gi|291542059|emb|CBL15169.1| DNA-directed RNA polymerase subunit alpha [Ruminococcus bromii
           L2-63]
          Length = 317

 Score =  244 bits (623), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 123/290 (42%), Positives = 194/290 (66%), Gaps = 2/290 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF +TLGN+LRRVL+SSL G A+T+++IDGVLHE S+I GV ED+T+I+LN+
Sbjct: 23  FVVEPLERGFGNTLGNSLRRVLLSSLEGCAVTSIKIDGVLHEFSTIPGVKEDVTEIVLNM 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K +  K+   S K + I   GP  V A DI+  +++E+LNP+  I  L   A + ME+TV
Sbjct: 83  KSLVAKLHETSPKVIEIAAEGPCEVKAADIKCDDEVEILNPELHIATLGEGAKLNMEITV 142

Query: 150 SKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GY+P++ ++  + N+ IG++ ID++Y+P+ KV+YTV++ R GQ+ DYDKL++ + T
Sbjct: 143 DKGRGYIPSERNKQLSGNNVIGVLPIDSIYTPVLKVNYTVDNTRVGQITDYDKLTLDVWT 202

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G I  +++V+LA+++L + L +F+N  +     +  +          L   +E+L+LSV
Sbjct: 203 NGVINAQEAVSLAAKVLTEHLNLFVNLSDKASSAEVMVEKDDKGKEKILEMTIEDLDLSV 262

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+   I  + DLI ++E DM+++ N GRKSL E+   L ++G  L
Sbjct: 263 RSFNCLKRAGINTVEDLINKSEEDMMKVRNLGRKSLEEVVQKLNSLGFSL 312


>gi|229829398|ref|ZP_04455467.1| hypothetical protein GCWU000342_01488 [Shuttleworthia satelles DSM
           14600]
 gi|229791829|gb|EEP27943.1| hypothetical protein GCWU000342_01488 [Shuttleworthia satelles DSM
           14600]
          Length = 320

 Score =  244 bits (623), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 128/294 (43%), Positives = 201/294 (68%), Gaps = 8/294 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SS+ G A+T ++I+GVLHE SSI GV ED+T+I+LNI
Sbjct: 23  FVVEPLERGYGITLGNSLRRIMLSSMPGVAVTQIKIEGVLHEFSSIPGVKEDVTEIVLNI 82

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + ++ +   D  K   I   G G VTA DIQ  +DIE++NPD VI +L+   D+ + M
Sbjct: 83  KQLAIRSNSQTDEPKVAYIEYEGEGTVTAADIQVDSDIEIVNPDLVIAHLNGGSDSKLYM 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT+SKG GYV +  ++T++ PIG+I +D++Y+P+++V+  VE+ R GQV D+DKL++ +
Sbjct: 143 ELTISKGRGYVSSDKNKTDDTPIGVIAVDSIYTPVERVNMNVENTRVGQVTDFDKLTLEV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK--KVEEL 263
            T+G+I  +++ +LA+++L + L +FI+  E  +    +I V+    + A +K   ++EL
Sbjct: 203 WTNGTIGPDEAASLAAKVLSEHLNLFIDLSENARNT--EIMVEKPSADTASMKMMNIDEL 260

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           ELSVRS NCL+   I  + +L+ +T  DM+++ N GRKSL E+   L  MGL L
Sbjct: 261 ELSVRSYNCLKRAGINTVEELVNKTPEDMMKVRNLGRKSLEEVLQKLQEMGLSL 314


>gi|118443967|ref|YP_877227.1| DNA-directed RNA polymerase subunit alpha [Clostridium novyi NT]
 gi|168187785|ref|ZP_02622420.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum C
           str. Eklund]
 gi|158512402|sp|A0PXX5|RPOA_CLONN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|118134423|gb|ABK61467.1| DNA-directed RNA polymerase, alpha subunit [Clostridium novyi NT]
 gi|169294320|gb|EDS76453.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum C
           str. Eklund]
          Length = 315

 Score =  244 bits (623), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 123/288 (42%), Positives = 192/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL G A  +++IDGVLHE S++ GV ED+T++ILNI
Sbjct: 23  FVIEPLERGYGITLGNSLRRILLSSLPGGAANSIKIDGVLHEFSTVTGVKEDVTELILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM+G+    + I  +GPG VTA DI +  ++E++N D  I  LD D  + ME+ V
Sbjct: 83  KGLALKMNGEGPSTIYIDAQGPGEVTAADIISDGNVEIMNKDMHIATLDDDGKLYMEINV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV    ++ E+ PIG I +D++Y+P+K+V++TVE+ R GQ+ DYDKLS+ + T+G
Sbjct: 143 DNGRGYVTQNKNKKEDLPIGTIPVDSIYTPVKRVNFTVENTRVGQITDYDKLSIEVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  E++++L+++IL +   +F+   +    V+  +  +       L   +EEL+LSVRS
Sbjct: 203 TIQPEEAISLSAKILIEHFKLFMTLTDHADNVEIMVEKEEDKKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L +RT  DM+++ N G+KSL E++  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELTERTIDDMMKVRNLGKKSLEEVQEKLAALGLGL 310


>gi|253682321|ref|ZP_04863118.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum D
           str. 1873]
 gi|253562033|gb|EES91485.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum D
           str. 1873]
          Length = 315

 Score =  244 bits (623), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 123/288 (42%), Positives = 193/288 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL G A  +++IDGVLHE S++ GV ED+T++ILNI
Sbjct: 23  FVIEPLERGYGITLGNSLRRILLSSLPGVAANSIKIDGVLHEFSTVTGVKEDVTELILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM+G+    + I  +GPG VTA DI +  +IEV+N D  I  LD D  + ME+ +
Sbjct: 83  KGLALKMNGEGPSTIYIEAQGPGEVTAADIISDGNIEVMNKDMHIATLDDDGKLYMEINI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYV    ++ ++ PIG I +D++Y+P+K+V++TVE+ R GQ+ DYDKLS+ + T+G
Sbjct: 143 DRGRGYVTQNKNKKDDLPIGTIPVDSIYTPVKRVNFTVENTRVGQITDYDKLSIEVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  E++++L+++IL +   +F+   +    V+  +  +       L   +EEL+LSVRS
Sbjct: 203 TIQPEEAISLSAKILIEHFKLFMTLTDHADNVEIMVEKEEDKKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L +RT  DM+++ N G+KSL E++  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELTERTIDDMMKVRNLGKKSLEEVQEKLAALGLGL 310


>gi|32477618|ref|NP_870612.1| DNA-directed RNA polymerase subunit alpha [Rhodopirellula baltica
           SH 1]
 gi|41688636|sp|Q7UIC5|RPOA_RHOBA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|32448172|emb|CAD77689.1| DNA-directed RNA polymerase alpha chain [Rhodopirellula baltica SH
           1]
 gi|327538948|gb|EGF25586.1| DNA-directed RNA polymerase subunit alpha [Rhodopirellula baltica
           WH47]
          Length = 331

 Score =  244 bits (623), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 125/298 (41%), Positives = 186/298 (62%), Gaps = 4/298 (1%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
           AEP  RGF  ++GN++RRVL+SSL G+A+T ++I G  HE ++I GV ED+TDI+LN+K 
Sbjct: 32  AEPFERGFGASIGNSMRRVLLSSLVGSAVTQIKIRGAQHEFTTIPGVLEDVTDIVLNVKS 91

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           + +  + DS + +T+ +   GVVT  D+QT  D+E++N DHVIC L  D    ME+ V  
Sbjct: 92  LIVNSNTDSTRVITVERNTAGVVTGADVQTDADVEIINKDHVICTLTDDVPFMMEMVVET 151

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GYVP+  H + +  IG+I IDA++SPI +V Y VE+ R GQ  +YD+L++ I TDG+I
Sbjct: 152 GRGYVPSTEHSSVDHEIGIIPIDAVFSPIVRVRYEVEATRVGQKTNYDRLNLEIWTDGTI 211

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEV----KEDINVKSLPFNPALLKKVEELELSV 267
             E ++  A++IL+  L  F+ + E    +    +             L   + +L LSV
Sbjct: 212 NPEMALTEAAKILRKHLNPFVQYRELGPSIFSAARGGAGSPEAQLEAKLNMTLADLRLSV 271

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           R+ NCL  ENI+ + DL+QRTE  +L + NFG  +L E++  L   GL LGM +P+ P
Sbjct: 272 RANNCLESENIMTVRDLVQRTEDSLLEVRNFGDTTLNEVREKLSQYGLHLGMRVPNQP 329


>gi|258543844|ref|ZP_05704078.1| DNA-directed RNA polymerase, alpha subunit [Cardiobacterium hominis
           ATCC 15826]
 gi|258520933|gb|EEV89792.1| DNA-directed RNA polymerase, alpha subunit [Cardiobacterium hominis
           ATCC 15826]
          Length = 322

 Score =  244 bits (623), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 135/319 (42%), Positives = 198/319 (62%), Gaps = 7/319 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            EL+ P  ++   +G      TL   EPL RGF +TLG ALRRVL+SS+ GAA+T  +ID
Sbjct: 4   SELLTPRIVKIQEMGLNTSRVTL---EPLERGFGYTLGTALRRVLLSSIEGAAVTECEID 60

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE S I+GV ED+ D++LN+KG+ L +       + +     G V A D    +++E
Sbjct: 61  GVLHEYSGIEGVSEDVIDVLLNLKGLALILHEGERAEMRLSVNKAGEVKASDFSAPSNVE 120

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGY-VPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           + NPDHVI +L  D    M + V KG GY V  +   T      ++ +DA +SPIK+++Y
Sbjct: 121 ICNPDHVIAHLTQDVSFSMTVVVEKGRGYRVATQEIDTATHAPNVLRVDASFSPIKRIAY 180

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+AR  Q  D DKL + I+++G+I  E ++  A+ IL  Q+ +F+N E  + E +   
Sbjct: 181 RVEAARVEQHTDLDKLVIDIESNGTIDPEQAIREAATILHKQIAVFVNLESTEVEAE--- 237

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             + +  +P LL+ V++LEL+VRS NCL+ ENI  +GDL++RTE ++L+  N G+KSL E
Sbjct: 238 YEEEVQVDPVLLRPVDDLELTVRSANCLKAENINNIGDLVRRTEVELLKTPNLGKKSLNE 297

Query: 306 IKGVLGTMGLFLGMNLPDW 324
           IK VL   GL LGM+L +W
Sbjct: 298 IKEVLAAHGLELGMDLENW 316


>gi|225571582|ref|ZP_03780578.1| hypothetical protein CLOHYLEM_07680 [Clostridium hylemonae DSM
           15053]
 gi|225159659|gb|EEG72278.1| hypothetical protein CLOHYLEM_07680 [Clostridium hylemonae DSM
           15053]
          Length = 322

 Score =  244 bits (623), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 127/293 (43%), Positives = 195/293 (66%), Gaps = 4/293 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL G+AI+ V+IDGVLHE SSI GV ED+T+I++N+
Sbjct: 26  FVVEPLERGYGTTLGNSLRRIMLSSLPGSAISQVKIDGVLHEFSSIPGVKEDVTEIVMNL 85

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K +   D  K   I   G GVVTA DIQ   DIE++NP+ VI  L+   D+ + M
Sbjct: 86  KSLAIKNTSETDEPKTAYIEFEGEGVVTAADIQVDQDIEIMNPETVIATLNGGADSKLYM 145

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++KG GYV A  ++ +  PI +I ID++Y+P+++V+ TVE+ R GQ+ D+DKL++ +
Sbjct: 146 ELTITKGRGYVSADKNKNDELPIAVIPIDSIYTPVERVNLTVENTRVGQITDFDKLTLDV 205

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L +FI+  E  +  +  I  +       L   ++ELEL
Sbjct: 206 YTNGTLLPDEAVSLAAKVLSEHLKLFIDLSEVAQAAEVMIEKEDDEKEKVLEMSIDELEL 265

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           SVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L 
Sbjct: 266 SVRSYNCLKRAGINTVEELTNRTPEDMMKVRNLGRKSLEEVLAKLDELGLCLS 318


>gi|169335657|ref|ZP_02862850.1| hypothetical protein ANASTE_02077 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258395|gb|EDS72361.1| hypothetical protein ANASTE_02077 [Anaerofustis stercorihominis DSM
           17244]
          Length = 315

 Score =  244 bits (622), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 134/314 (42%), Positives = 205/314 (65%), Gaps = 14/314 (4%)

Query: 8   ELIKPNNIEYIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           E  KPN    I + +   +RT    + EPL RG+  T+GN+LRR+++SSL GAA+T V+I
Sbjct: 3   EFQKPN----IEIAEISADRTYGKFVVEPLERGYGTTIGNSLRRIMLSSLPGAAVTNVKI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           + VLHE ++I GV ED+  IILN+K +++K+  D    V I   G G VTAGDI   +D+
Sbjct: 59  ENVLHEFATIDGVAEDVLQIILNLKDLSVKLHSDGPVDVHIHSEGEGEVTAGDIICDSDV 118

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++NPD  I +L  DAV+ M +T+  G GYVP++ ++ E+ PIG + +D++++P+KK ++
Sbjct: 119 EIVNPDLHIASLMADAVLDMTITIDGGTGYVPSEKNKKEDMPIGTLPVDSIFTPVKKANF 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI----NFEEPKKEV 241
            VE+ R G V DYDKL++ + TDG+I+ E++V+LA++++ D L +FI    N       V
Sbjct: 179 AVENTRVGNVTDYDKLTIEVWTDGTISPEEAVSLAAKVINDHLQLFIDMNANLPNASLMV 238

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           + + N K       L   ++ELELSVRS+NCL+  +I  + +LI R+E DM ++ N G+K
Sbjct: 239 EREENEKE----KVLEMSIDELELSVRSSNCLKRTSINTVEELISRSEEDMSKVRNLGKK 294

Query: 302 SLVEIKGVLGTMGL 315
           SL EIK  L  +GL
Sbjct: 295 SLNEIKKKLAEIGL 308


>gi|255659529|ref|ZP_05404938.1| DNA-directed RNA polymerase, alpha subunit [Mitsuokella multacida
           DSM 20544]
 gi|260848082|gb|EEX68089.1| DNA-directed RNA polymerase, alpha subunit [Mitsuokella multacida
           DSM 20544]
          Length = 319

 Score =  244 bits (622), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 137/302 (45%), Positives = 203/302 (67%), Gaps = 5/302 (1%)

Query: 24  EENRT-LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E+NR    I EPL RG+  T GN+LRR+L+SSL GAAIT+++IDGVLHE S+I GV +D+
Sbjct: 16  EDNRYGKFICEPLERGYGTTFGNSLRRMLLSSLEGAAITSIRIDGVLHEFSTIPGVRDDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T+I+LN+K + LKM+G+  + + I   G   VTA DI    DIE+LNPD  I  ++ D  
Sbjct: 76  TNIVLNLKELCLKMAGNEPRIIRIDVEGEKEVTAADIICDADIEILNPDLHIATVNEDGK 135

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           +++E+TV +G GYVPA  ++  +D IG+I ID+++SP+K+V+YTV+  R G V DYD+L 
Sbjct: 136 LKIEMTVERGRGYVPADKNKKPDDTIGVIPIDSIFSPVKRVNYTVQDTRVGNVTDYDRLI 195

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEE-PKKEVKEDINVKSLPFNPA---LLK 258
           + + TDGS+  E++V+ A+ IL   L +F N +  P++E +E+        + +   L  
Sbjct: 196 LEVWTDGSLRPEEAVSKAAGILVMHLKLFQNMDGLPEEEEEEEATFPEEEEDDSSKVLDM 255

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L+LSVRS NCL+  NI  + DL ++TE DM+++ N GRKSL E+K  L  +GL L 
Sbjct: 256 TIEDLDLSVRSFNCLKRANINTVADLAEKTEDDMMKVRNLGRKSLEEVKKKLEELGLTLK 315

Query: 319 MN 320
            N
Sbjct: 316 QN 317


>gi|326407604|gb|ADZ64675.1| DNA-directed RNA polymerase subunit alpha [Lactococcus lactis
           subsp. lactis CV56]
          Length = 312

 Score =  244 bits (622), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 124/295 (42%), Positives = 194/295 (65%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E EN    + EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+
Sbjct: 14  ESENYGKFVVEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDV 73

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             I+L +KGI +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     
Sbjct: 74  IQIVLAVKGIAIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHS 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           +R  +TV KG+GYVPA  ++ +  PIG I +D++Y+P+ KV+Y VE AR G    YDKL+
Sbjct: 134 IRAVMTVKKGYGYVPADENKVDGAPIGTIAVDSIYTPVSKVNYQVEPARVGGDSSYDKLT 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + I T+G+I  +++++L+++IL D L +F++  E   E +  +    +     L K +EE
Sbjct: 194 LEITTNGTIVSDEALSLSAKILTDHLNLFVDLSEVASEAETLVVKDEVKTERVLDKIIEE 253

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           ++ SVR+ N L+   I  + D+++ +EADM+++ N G KS+ E+K  L  +GL L
Sbjct: 254 MDFSVRAYNGLKRAGINTVADIVEMSEADMIKVKNLGHKSVEEVKVKLTELGLSL 308


>gi|326803058|ref|YP_004320876.1| DNA-directed RNA polymerase, alpha subunit [Aerococcus urinae
           ACS-120-V-Col10a]
 gi|326651415|gb|AEA01598.1| DNA-directed RNA polymerase, alpha subunit [Aerococcus urinae
           ACS-120-V-Col10a]
          Length = 314

 Score =  244 bits (622), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 136/311 (43%), Positives = 205/311 (65%), Gaps = 4/311 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIA-EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           E+ KPN IE I     E+N+    A EPL RG+  TLGN+LRRVL+SSL G A+T+++I+
Sbjct: 3   EIEKPN-IETI--ETSEDNKFGKFAVEPLERGYGTTLGNSLRRVLLSSLPGTAVTSIKIE 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
            VLHE S+I GV ED+T I+LNIK + LK+     K + +   GP  VTA DI    D +
Sbjct: 60  NVLHEFSTIPGVREDVTQIVLNIKQLALKLYDVDEKDIELDITGPAEVTAADITADADFD 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           VLNP   IC+L   A + M + V  G G+V A++++T++ PIG+I +D++Y+PIKKV+Y 
Sbjct: 120 VLNPYLHICSLAEGAKIHMLMHVKNGRGFVRAENNKTDDMPIGVIPVDSIYTPIKKVNYQ 179

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+ R G+V +YDKL+  I TDG+I  +++++LA+++L + L +F++  +  +E +  + 
Sbjct: 180 VENTRIGEVNEYDKLTFDIWTDGTIAPKEALSLAAKVLTEHLAIFVSLTDEAQEAEIMVE 239

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L   +EEL+LSVRS NCL+   I  + +L Q+TEA+M+++ N GRKSL E+
Sbjct: 240 KEETQKEKMLEMTIEELDLSVRSYNCLKRAGINTVEELTQKTEAEMMKVRNLGRKSLDEV 299

Query: 307 KGVLGTMGLFL 317
           KG L  + L L
Sbjct: 300 KGKLDALDLSL 310


>gi|319945810|ref|ZP_08020060.1| DNA-directed RNA polymerase subunit alpha [Streptococcus australis
           ATCC 700641]
 gi|319747875|gb|EFW00119.1| DNA-directed RNA polymerase subunit alpha [Streptococcus australis
           ATCC 700641]
          Length = 312

 Score =  244 bits (622), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 130/310 (41%), Positives = 196/310 (63%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++  + + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKDYGVFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILN+KGI +K      K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNVKGIAVKSYVQDEKIIELDVEGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   +  +  LTV+ G GYVPA  ++ ++ P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGSSFKATLTVNSGRGYVPADQNKKDDAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E          V
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLFTNLTEIAIATDVMKEV 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            +   +  L + +EEL+LSVRS NCL+   I  + DL +++E +M+++ N GRKSL E+K
Sbjct: 239 DTASDDRVLERTIEELDLSVRSYNCLKRAGINTVYDLTEKSEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 VKLADLGLGL 308


>gi|297618355|ref|YP_003703514.1| DNA-directed RNA polymerase, subunit alpha [Syntrophothermus
           lipocalidus DSM 12680]
 gi|297146192|gb|ADI02949.1| DNA-directed RNA polymerase, alpha subunit [Syntrophothermus
           lipocalidus DSM 12680]
          Length = 315

 Score =  244 bits (622), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 132/286 (46%), Positives = 193/286 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN+LRRVL+SSL GAAI+ ++IDGVLHE S+I GV ED T+IILN+
Sbjct: 23  FVIEPLERGFGITLGNSLRRVLLSSLPGAAISTIKIDGVLHEFSTIPGVVEDTTEIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L+   D  K V + +RGP  V AGDI    +IE+LNP+  I  L+ D  + ME+TV
Sbjct: 83  KQVVLRYDYDQPKTVFVEQRGPKEVKAGDIIRDAEIEILNPELHIATLNEDGRLAMEMTV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYV A   + + + IGLI ID++++PI KV++TVE+AR G+V DYD+L + + T+G
Sbjct: 143 ERGRGYVSADQKKKDENVIGLIPIDSIFTPINKVNFTVENARVGRVTDYDRLMLEVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI+ E++V+L++ IL D L +F    +    V+  +  +    +  L   +EELELSVR+
Sbjct: 203 SISPEEAVSLSAHILIDHLKLFTEINDSYSPVEILVEKEEDQKDKILDMSIEELELSVRA 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           +N L+  NI  +GDL+++T  +M ++ N G+KSL EI+  L  +GL
Sbjct: 263 SNGLKRANINTVGDLVEKTREEMSKIRNLGQKSLDEIERKLKELGL 308


>gi|322374071|ref|ZP_08048605.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus sp. C150]
 gi|321277037|gb|EFX54108.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus sp. C150]
          Length = 312

 Score =  243 bits (621), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 123/288 (42%), Positives = 191/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILN+
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNV 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +  +GP  VTAGDI T +DIE++NPDH +  +   A ++  +TV
Sbjct: 81  KGLAVKSYVEDEKTIELDVQGPAEVTAGDILTDSDIEIVNPDHYLFTIADGASLKATMTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +   GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 141 ATNRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  ED++ L++R+L + L +F +  +  K        + +     L + +EEL+LSVRS
Sbjct: 201 TIIPEDALGLSARVLIEHLNLFTDLTDVAKATDVMKETEKVNDEKVLDRTIEELDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL ++TE +M+++ N GRKSL E+K  L  +GL L
Sbjct: 261 YNCLKRAGINTVHDLTEKTEPEMMKVRNLGRKSLEEVKVKLADLGLGL 308


>gi|21909602|ref|NP_663870.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           MGAS315]
 gi|28894980|ref|NP_801330.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           SSI-1]
 gi|25009138|sp|Q8K8W9|RPOA_STRP3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|21903783|gb|AAM78673.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pyogenes
           MGAS315]
 gi|28810225|dbj|BAC63163.1| putative DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pyogenes SSI-1]
          Length = 312

 Score =  243 bits (621), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 125/288 (43%), Positives = 192/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNV 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     +R  +TV
Sbjct: 81  KGLAVKSYVEDEKIIELEVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLRATMTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 141 AKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  ED++ L++R+L + L +F +  E  K  +     + +     L + +EEL+LSVRS
Sbjct: 201 TIIPEDALGLSARVLIEHLNLFTDLTEVAKSTEVMKETEKVNDEKVLDRTIEELDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL +++E +M+++ N GRKSL E+K  L  +GL L
Sbjct: 261 YNCLKRAGINTVFDLTEKSEPEMMKVRNLGRKSLEEVKVKLADLGLGL 308


>gi|22536269|ref|NP_687120.1| DNA-directed RNA polymerase subunit alpha [Streptococcus agalactiae
           2603V/R]
 gi|25010159|ref|NP_734554.1| DNA-directed RNA polymerase subunit alpha [Streptococcus agalactiae
           NEM316]
 gi|76798216|ref|ZP_00780466.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae 18RS21]
 gi|77412562|ref|ZP_00788854.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae CJB111]
 gi|77414960|ref|ZP_00791053.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae 515]
 gi|41688699|sp|Q8CX32|RPOA_STRA3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|41688702|sp|Q8E2B1|RPOA_STRA5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|22533090|gb|AAM98992.1|AE014195_11 DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae 2603V/R]
 gi|23094510|emb|CAD45729.1| RNA polymerase (alpha subunit) [Streptococcus agalactiae NEM316]
 gi|76586425|gb|EAO62933.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae 18RS21]
 gi|77158989|gb|EAO70207.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae 515]
 gi|77161385|gb|EAO72404.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae CJB111]
 gi|319743969|gb|EFV96349.1| DNA-directed RNA polymerase subunit alpha [Streptococcus agalactiae
           ATCC 13813]
          Length = 312

 Score =  243 bits (621), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 124/288 (43%), Positives = 192/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNV 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +   GP  +TAGDI T +DIE++NPDH +  +     ++  +TV
Sbjct: 81  KGLAVKSYVEDEKIIELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIAEGHSLKATMTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 141 AKNRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  ED++ L++R+L + L +F +  E  K  +     + +     L + +EEL+LSVRS
Sbjct: 201 TIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKETEKVNDEKVLDRTIEELDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL ++TE +M+++ N GRKSL E+K  L  +GL L
Sbjct: 261 YNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVKIKLADLGLGL 308


>gi|255530541|ref|YP_003090913.1| DNA-directed RNA polymerase subunit alpha [Pedobacter heparinus DSM
           2366]
 gi|255343525|gb|ACU02851.1| DNA-directed RNA polymerase, alpha subunit [Pedobacter heparinus
           DSM 2366]
          Length = 330

 Score =  243 bits (621), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 129/298 (43%), Positives = 192/298 (64%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AIT+++  GV HE S+IKGV EDLT+IILN+K + 
Sbjct: 28  PLEPGFGVTIGNALRRILLSSLEGYAITSIRFSGVSHEFSTIKGVVEDLTEIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQTV-NDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K SGD+   ++V I   G     AGDI    N+ EVLNPD VICN++    + +ELT++
Sbjct: 88  FKKSGDAGDSEKVFILVNGQEQFVAGDITKFSNNFEVLNPDFVICNMEKSVTLEVELTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++  +  +G+I ID++++P+K V YT+E+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPAEENKINDAVVGVIAIDSIFTPMKNVKYTIENYRVEQKTDYEKLILDISTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  E+++  A++IL     +F +     E   KE  ++++ + L     L  ++ +L+LS
Sbjct: 208 IHPEEALKEAAKILIQHFMLFSDENLVLESQAKEETKEVDEEILHMRKILKTELVDLDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  +I  + DL+    ADML+  NFG+KSL EI+ ++ +  L  GMNL  +
Sbjct: 268 VRALNCLKAADIRTLADLVSYDVADMLKFRNFGKKSLTEIQELVKSKSLSFGMNLSKF 325


>gi|260438188|ref|ZP_05792004.1| DNA-directed RNA polymerase, alpha subunit [Butyrivibrio crossotus
           DSM 2876]
 gi|292809378|gb|EFF68583.1| DNA-directed RNA polymerase, alpha subunit [Butyrivibrio crossotus
           DSM 2876]
          Length = 321

 Score =  243 bits (621), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 130/300 (43%), Positives = 202/300 (67%), Gaps = 18/300 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL G+A++ V+IDGVLHE S I GV ED++DII+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGSAVSQVKIDGVLHEFSPIPGVKEDVSDIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRG---PGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVR 144
           K + +K S DS++    +       GVVTAGDI T +DIE++NPD  I  L+   D  + 
Sbjct: 83  KNLAIKNSSDSNEPKIAYIECDGREGVVTAGDIHTDSDIEIMNPDLPIATLNGGNDCKLF 142

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MELT++ G GYV A+ ++ E+ PIG+++ID++Y+P+++V+ TV++ R GQV D+DKL++ 
Sbjct: 143 MELTITNGRGYVSAEKNKHEDTPIGVLSIDSIYTPVERVNMTVQNTRVGQVTDFDKLTLE 202

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV-------KEDINVKSLPFNPALL 257
           + T+G++  +D+V+LA+++L + L +F++  +  K+V        ED  VK+   N    
Sbjct: 203 VYTNGTLAPDDAVSLAAKVLCEHLNLFVDLSDNTKDVVGTFIEKPEDEKVKTGAIN---- 258

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             ++ELELSVRS NCL+   I  + +L  +T  DM+++ N GRKSL E+   L  +GL L
Sbjct: 259 --IDELELSVRSYNCLKRAGINTVEELCSKTAEDMMKVRNLGRKSLEEVLAKLKELGLEL 316


>gi|15674313|ref|NP_268486.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           M1 GAS]
 gi|19745267|ref|NP_606403.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           MGAS8232]
 gi|50913465|ref|YP_059437.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           MGAS10394]
 gi|71902735|ref|YP_279538.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           MGAS6180]
 gi|71909884|ref|YP_281434.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           MGAS5005]
 gi|94987701|ref|YP_595802.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           MGAS9429]
 gi|94989582|ref|YP_597682.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           MGAS10270]
 gi|94991570|ref|YP_599669.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           MGAS2096]
 gi|94993470|ref|YP_601568.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           MGAS10750]
 gi|139472953|ref|YP_001127668.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           str. Manfredo]
 gi|209558653|ref|YP_002285125.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           NZ131]
 gi|306828235|ref|ZP_07461495.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           ATCC 10782]
 gi|54039279|sp|P66711|RPOA_STRP8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|54042189|sp|P66710|RPOA_STRP1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61215821|sp|Q5XEA9|RPOA_STRP6 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|90110873|sp|Q48VS3|RPOA_STRPM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366735|sp|Q1JE33|RPOA_STRPB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366736|sp|Q1JNZ1|RPOA_STRPC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366737|sp|Q1JJ35|RPOA_STRPD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366738|sp|Q1J8Y7|RPOA_STRPF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158512769|sp|A2RC40|RPOA_STRPG RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|13621394|gb|AAK33208.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pyogenes
           M1 GAS]
 gi|19747362|gb|AAL96902.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pyogenes
           MGAS8232]
 gi|50902539|gb|AAT86254.1| DNA-directed RNA polymerase alpha chain [Streptococcus pyogenes
           MGAS10394]
 gi|71801830|gb|AAX71183.1| DNA-directed RNA polymerase alpha chain [Streptococcus pyogenes
           MGAS6180]
 gi|71852666|gb|AAZ50689.1| DNA-directed RNA polymerase alpha chain [Streptococcus pyogenes
           MGAS5005]
 gi|94541209|gb|ABF31258.1| DNA-directed RNA polymerase alpha chain [Streptococcus pyogenes
           MGAS9429]
 gi|94543090|gb|ABF33138.1| DNA-directed RNA polymerase alpha chain [Streptococcus pyogenes
           MGAS10270]
 gi|94545078|gb|ABF35125.1| DNA-directed RNA polymerase alpha chain [Streptococcus pyogenes
           MGAS2096]
 gi|94546978|gb|ABF37024.1| DNA-directed RNA polymerase alpha chain [Streptococcus pyogenes
           MGAS10750]
 gi|134271199|emb|CAM29412.1| DNA-directed RNA polymerase alpha chain [Streptococcus pyogenes
           str. Manfredo]
 gi|209539854|gb|ACI60430.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pyogenes
           NZ131]
 gi|304429546|gb|EFM32595.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           ATCC 10782]
          Length = 312

 Score =  243 bits (621), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 125/288 (43%), Positives = 192/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNV 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     +R  +TV
Sbjct: 81  KGLAVKSYVEDEKIIELEVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLRATMTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 141 AKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  ED++ L++R+L + L +F +  E  K  +     + +     L + +EEL+LSVRS
Sbjct: 201 TIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKETEKVNDEKVLDRTIEELDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL +++E +M+++ N GRKSL E+K  L  +GL L
Sbjct: 261 YNCLKRAGINTVFDLTEKSEPEMMKVRNLGRKSLEEVKVKLADLGLGL 308


>gi|325678576|ref|ZP_08158186.1| RNA polymerase, alpha subunit C-terminal domain protein
           [Ruminococcus albus 8]
 gi|324109626|gb|EGC03832.1| RNA polymerase, alpha subunit C-terminal domain protein
           [Ruminococcus albus 8]
          Length = 326

 Score =  243 bits (621), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 124/290 (42%), Positives = 197/290 (67%), Gaps = 2/290 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRRVL+SSL G A+T+V+IDGV HE+S+I GV ED+T+IILN+
Sbjct: 31  FILEPLERGYGITLGNSLRRVLLSSLPGVAVTSVKIDGVHHELSTIPGVKEDVTEIILNL 90

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+  K+ G+  K + I   G  VVTAGDI+  +++++L PD  I  L   A + ME+T+
Sbjct: 91  KGLTAKLYGEGPKTIYIEAEGECVVTAGDIKADSEVDILVPDMHIATLGAGAKLYMEITI 150

Query: 150 SKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            +G GYV A+ +++  +N PIG+I +D++YSP+ KV+YTV++ R G + D+DKL++ + T
Sbjct: 151 DRGRGYVSAEKNKSLMQNAPIGIIAVDSIYSPVLKVNYTVDNTRVGHITDFDKLTLEVWT 210

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           DG+I+ +++V++A+++L + L  F++  E    V+  +          L   +EEL+LSV
Sbjct: 211 DGTISAKEAVSMAAKLLNEHLNPFVDLSEEANVVEIMVEKDDQSQAKVLEMTIEELDLSV 270

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+   I  + DLI+++  +M+++ N G+KS  E+K  L ++G  L
Sbjct: 271 RSFNCLKRAGINTVNDLIEKSAEEMMKVRNLGKKSFDEVKEKLHSLGYEL 320


>gi|312889340|ref|ZP_07748894.1| DNA-directed RNA polymerase subunit alpha [Mucilaginibacter paludis
           DSM 18603]
 gi|311298217|gb|EFQ75332.1| DNA-directed RNA polymerase subunit alpha [Mucilaginibacter paludis
           DSM 18603]
          Length = 330

 Score =  243 bits (620), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 129/298 (43%), Positives = 193/298 (64%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AIT+V+  GV HE S+IKGV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGITIGNALRRILLSSLEGYAITSVRFSGVNHEFSTIKGVVEDVTEIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQTV-NDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +K SG+S   +++ +   G    +AGDI    N+  VLNPD VICN+D    + +E+TV 
Sbjct: 88  MKKSGESGDSEKIFVIINGQDTFSAGDITKFSNNFTVLNPDLVICNMDSSVTLEIEITVG 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVP++ ++  +  +G+I ID++Y+PIK V YT+E+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPSEENKNPDAMVGVIAIDSIYTPIKNVKYTIENYRVEQKTDYEKLVLDIATDGS 207

Query: 211 ITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           +  ED++  A++IL     +F +     E   KE  ++++ + L     L  ++ +L+LS
Sbjct: 208 VHPEDALKEAAKILIQHFMLFSDENMMLEAQAKEETKEVDEEILHMRKILKTELVDLDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  +I  + DL+    ADML+  NFG+KSL EI+ ++ + GL  GMNL  +
Sbjct: 268 VRALNCLKAADIRSLADLVSYDVADMLKFRNFGKKSLTEIQDLVKSKGLSFGMNLSKF 325


>gi|116327251|ref|YP_796971.1| DNA-directed RNA polymerase subunit alpha [Leptospira
           borgpetersenii serovar Hardjo-bovis L550]
 gi|116327291|ref|YP_797011.1| DNA-directed RNA polymerase subunit alpha [Leptospira
           borgpetersenii serovar Hardjo-bovis L550]
 gi|116332095|ref|YP_801813.1| DNA-directed RNA polymerase subunit alpha [Leptospira
           borgpetersenii serovar Hardjo-bovis JB197]
 gi|122280175|sp|Q04PW5|RPOA_LEPBJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|122284902|sp|Q055B7|RPOA_LEPBL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116119995|gb|ABJ78038.1| DNA-directed RNA polymerase, alpha subunit [Leptospira
           borgpetersenii serovar Hardjo-bovis L550]
 gi|116120035|gb|ABJ78078.1| DNA-directed RNA polymerase, alpha subunit [Leptospira
           borgpetersenii serovar Hardjo-bovis L550]
 gi|116125784|gb|ABJ77055.1| DNA-directed RNA polymerase, alpha subunit [Leptospira
           borgpetersenii serovar Hardjo-bovis JB197]
          Length = 325

 Score =  243 bits (620), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 132/312 (42%), Positives = 202/312 (64%), Gaps = 4/312 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P  IE+        N    +AEP  RGFA T+GN+LRR LMSS+ GAAI+A++I+GV H
Sbjct: 12  RPKKIEFNTEASTP-NYGKFVAEPFERGFATTIGNSLRRTLMSSIEGAAISAIRIEGVNH 70

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMS---GDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           E S I+GV ED+T IILN+K + +K      D  K + +  +G G   AGD+   + IE+
Sbjct: 71  EFSFIEGVAEDVTRIILNLKQVRIKYEPEEKDQSKIIHLELKGAGYFRAGDLAVDSSIEI 130

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPD  I  L+ DA + M+L + +G GYVPA+  + + + +G I +D+++SP++KV + V
Sbjct: 131 MNPDLHIATLNEDANLVMDLEIQRGRGYVPAEEKKKDIEVLGTIPVDSIFSPVQKVVFEV 190

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
              R  Q  DY+KL++ + TDGS++ +D+VA A++IL++ L +FINFEE  +E  ++++ 
Sbjct: 191 SETRVAQRSDYEKLTLEVWTDGSVSPDDAVAQAAKILKEHLTVFINFEEELEEEDDELDE 250

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                  +L K VEELELSVRS N LR   I ++GDL++R+E +M +  ++  + L E+K
Sbjct: 251 ADEKLKASLSKHVEELELSVRSLNVLRSLEIDFIGDLVKRSEEEMSKSKHYSDQCLQELK 310

Query: 308 GVLGTMGLFLGM 319
           G L T+GL  GM
Sbjct: 311 GKLSTLGLSFGM 322


>gi|134298121|ref|YP_001111617.1| DNA-directed RNA polymerase subunit alpha [Desulfotomaculum
           reducens MI-1]
 gi|172044239|sp|A4J139|RPOA_DESRM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|134050821|gb|ABO48792.1| DNA-directed RNA polymerase subunit alpha [Desulfotomaculum
           reducens MI-1]
          Length = 315

 Score =  243 bits (620), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 128/300 (42%), Positives = 198/300 (66%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           IV   E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+V+I+GVLHE +++ G
Sbjct: 11  IVEQSEDNTYGKFVVEPLERGYGITLGNSLRRILLSSLPGAAVTSVKIEGVLHEFATVPG 70

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+TDIILN+K + LK+  D  K + +  +  G VTAGDI    D+E+LNPD  +  L
Sbjct: 71  VQEDVTDIILNLKNLCLKIHSDEEKVLRVEAQTEGPVTAGDIIHDADVEILNPDLHLATL 130

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           D    + ME++V+KG GY  A+ ++     IG+I ID++Y+P+++V+Y VE+ R GQ+ D
Sbjct: 131 DTGGRLFMEISVNKGRGYSSAEKNKKGEHIIGVIPIDSIYTPVRRVNYNVENTRVGQITD 190

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           YDKL++ + T+GSI  +++ +L+++IL + L +FI   E   +V+  +  +    +  L 
Sbjct: 191 YDKLTLEVWTNGSIRPDEATSLSAKILSEHLRLFIGLTETVNDVEIMVEKEEEQKDKILE 250

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +EEL++SVRS NCL+   I  + +LIQR E DM+++ N G+KSL E+   L  +GL L
Sbjct: 251 MTIEELDMSVRSYNCLKRAGINTVEELIQRNEEDMMKVRNLGKKSLEEVINKLHELGLSL 310


>gi|317123070|ref|YP_004103073.1| DNA-directed RNA polymerase subunit alpha [Thermaerobacter
           marianensis DSM 12885]
 gi|315593050|gb|ADU52346.1| DNA-directed RNA polymerase subunit alpha [Thermaerobacter
           marianensis DSM 12885]
          Length = 315

 Score =  243 bits (620), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 126/294 (42%), Positives = 197/294 (67%), Gaps = 12/294 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGNALRRVL+SSL GAA+T+V+I+GVLHE S+I GV ED T+IILN+
Sbjct: 23  FVVEPLERGYGITLGNALRRVLLSSLPGAAVTSVRIEGVLHEFSTIPGVVEDTTEIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + +KM  D  + + +  +G G V A DI    ++E++N DH+I  L+ D  + ME+TV
Sbjct: 83  KELAIKMHTDEPQILRVEAQGEGEVRAADIIAPPEVEIVNGDHLIATLEHDGRLFMEMTV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYVPA  ++  +  IGLI +D++++PI+KV++ VE+ R G+V DYD+L++ I T+G
Sbjct: 143 QRGRGYVPADRNKGPDRSIGLIPVDSIFTPIRKVNFQVENTRVGKVTDYDRLTLEIWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK------EVKEDINVKSLPFNPALLKKVEEL 263
           ++  +++ + A+RIL D L +F+   +  +      E ++D   K L  +      ++EL
Sbjct: 203 TVAPDEAASQAARILTDHLALFLTLTDQTRGAGTAAEKEDDARAKLLEMS------IDEL 256

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +LSVRS NCL+   I  +G+L+++T  DM+R+ N G+KSL E++  L  +GL L
Sbjct: 257 DLSVRSYNCLKRAGINTIGELVEKTPEDMMRVRNLGKKSLEEVEEKLAALGLSL 310


>gi|262283556|ref|ZP_06061321.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sp.
           2_1_36FAA]
 gi|262260613|gb|EEY79314.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sp.
           2_1_36FAA]
          Length = 312

 Score =  243 bits (620), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 132/310 (42%), Positives = 195/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILNIKGI +K      K + +   GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNIKGIAVKSYVQDEKMIELDVEGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A  +  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGARFKAVMTVNSGRGYVPADQNKRDDAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F +  E  K       V
Sbjct: 179 EPARVGSNDGFDKLTLEIMTNGTIIPEDALGLSARILTEHLDLFTDLTEVAKATDVMKEV 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                +  L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 DKSSDDHVLERTIEELDLSVRSYNCLKRAGINTVYDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 VKLTDLGLGL 308


>gi|281492732|ref|YP_003354712.1| DNA-directed RNA polymerase subunit alpha [Lactococcus lactis
           subsp. lactis KF147]
 gi|281376384|gb|ABX75652.2| DNA-directed RNA polymerase, alpha chain [Lactococcus lactis subsp.
           lactis KF147]
          Length = 312

 Score =  243 bits (620), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 124/295 (42%), Positives = 194/295 (65%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E EN    + EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+
Sbjct: 14  ESENYGKFVVEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDV 73

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             I+L +KGI +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     
Sbjct: 74  IQIVLAVKGIAIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHS 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           +R  +TV KG+GYVPA  ++ +  PIG I +D++Y+P+ KV+Y VE AR G    YDKL+
Sbjct: 134 MRAVMTVKKGYGYVPADENKVDGAPIGTIAVDSIYTPVSKVNYQVEPARVGGDSSYDKLT 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + I T+G+I  +++++L+++IL D L +F++  E   E +  +    +     L K +EE
Sbjct: 194 LEITTNGTIVSDEALSLSAKILTDHLNLFVDLSEVAAEAETLVVKDEVKTERVLDKIIEE 253

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           ++ SVR+ N L+   I  + D+++ +EADM+++ N G KS+ E+K  L  +GL L
Sbjct: 254 MDFSVRAYNGLKRAGINTVADIVEMSEADMIKVKNLGHKSVEEVKVKLTELGLSL 308


>gi|125625115|ref|YP_001033598.1| DNA-directed RNA polymerase subunit alpha [Lactococcus lactis
           subsp. cremoris MG1363]
 gi|158512804|sp|A2RNM7|RPOA_LACLM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|124493923|emb|CAL98918.1| RNA polymerase alpha subunit [Lactococcus lactis subsp. cremoris
           MG1363]
 gi|300071923|gb|ADJ61323.1| DNA-directed RNA polymerase subunit alpha [Lactococcus lactis
           subsp. cremoris NZ9000]
          Length = 312

 Score =  243 bits (620), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 124/295 (42%), Positives = 194/295 (65%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E EN    + EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+
Sbjct: 14  ESENYGKFVVEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDV 73

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             I+L +KGI +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     
Sbjct: 74  IQIVLAVKGIAIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHS 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           +R  +TV KG+GYVPA  ++ +  PIG I +D++Y+P+ KV+Y VE AR G    YDKL+
Sbjct: 134 MRAVMTVKKGYGYVPADENKVDGAPIGTIAVDSIYTPVSKVNYQVEPARVGGDSSYDKLT 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + I T+G+I  +++++L+++IL D L +F++  E   E +  +    +     L K +EE
Sbjct: 194 LEITTNGTIVSDEALSLSAKILTDHLNLFVDLSEVAAEAETLVVKDEVKTERVLDKIIEE 253

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           ++ SVR+ N L+   I  + D+++ +EADM+++ N G KS+ E+K  L  +GL L
Sbjct: 254 MDFSVRTYNGLKRAGINTVADIVEMSEADMIKVKNLGHKSVEEVKVKLTELGLSL 308


>gi|307266986|ref|ZP_07548502.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           wiegelii Rt8.B1]
 gi|326390633|ref|ZP_08212188.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           ethanolicus JW 200]
 gi|306917971|gb|EFN48229.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           wiegelii Rt8.B1]
 gi|325993311|gb|EGD51748.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 315

 Score =  243 bits (620), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 137/321 (42%), Positives = 205/321 (63%), Gaps = 24/321 (7%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+I+P  IE IV   E+      + EPL RG+  TLGN+LRRVL+SSL GAA  +V+IDG
Sbjct: 3   EMIEPK-IE-IVEQSEDGTYGKFVVEPLERGYGITLGNSLRRVLLSSLPGAAPKSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+ +IILN+K + +K+  D      I   G G VTAG I+   DIE+
Sbjct: 61  VLHEFSTLPGVKEDVVEIILNLKEVAVKLHSDEPVVGRIDVEGKGEVTAGHIKGSADIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPDH I  L  D  + ME+   KG GYVP+  ++  N PIG+I +D++++P+K+VSY V
Sbjct: 121 LNPDHHIATLSDDGKLHMEIVFVKGKGYVPSDKNKEPNQPIGVIPVDSIFTPVKRVSYNV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF-----------EE 236
           E+ R G V DYDKL++ + T+G+IT ++++++AS +L      FI+F           ++
Sbjct: 181 ENTRVGHVTDYDKLTLEVWTNGTITPKEAISMASDMLIKYFQKFISFTGEYKSSDIFVDK 240

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           P+K+V++ +++            +EEL+LSVRS NCL+   I  + +L Q+TE +M+++ 
Sbjct: 241 PEKKVEKPLDM-----------TIEELDLSVRSYNCLKRAGINTVQELTQKTEEEMMKVR 289

Query: 297 NFGRKSLVEIKGVLGTMGLFL 317
           N G+KSL E+K  L  +GL L
Sbjct: 290 NLGKKSLEEVKQKLEALGLSL 310


>gi|259047529|ref|ZP_05737930.1| DNA-directed RNA polymerase, alpha subunit [Granulicatella adiacens
           ATCC 49175]
 gi|259035720|gb|EEW36975.1| DNA-directed RNA polymerase, alpha subunit [Granulicatella adiacens
           ATCC 49175]
          Length = 315

 Score =  243 bits (620), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 132/289 (45%), Positives = 190/289 (65%), Gaps = 1/289 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL G A+T +Q+DGVLHE S+I GV ED+  IILNI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGTAVTDIQMDGVLHEFSTIDGVVEDVAAIILNI 82

Query: 90  KGINLK-MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           K I LK  S D +K + I  +GP VVTAGDI+  +DI+VLNPD  IC +       + + 
Sbjct: 83  KKIALKSFSEDENKVLEIDVKGPAVVTAGDIKHDSDIQVLNPDLYICTVAEGHHFHVRMN 142

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
              G GYV + ++++EN PIG+I ID++Y+PI KV+Y VE+ R GQ   YDKL++ + TD
Sbjct: 143 AKNGRGYVRSDYNKSENMPIGVIPIDSIYTPISKVNYQVENTRIGQKNVYDKLTLDVWTD 202

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           GSI  +D+++LA+RIL + L +F+N       ++  +  +       L   +EEL+LSVR
Sbjct: 203 GSIAPQDAISLAARILTEHLNIFVNLTNEALPMEIMVEKEETQKERLLEMTIEELDLSVR 262

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           S NCL+   I  + +L  ++EA+M+++ N GRKSL E+K  L  + L L
Sbjct: 263 SYNCLKRAGINTVHELTSKSEAEMIKVRNLGRKSLEEVKQKLIDLNLDL 311


>gi|320548029|ref|ZP_08042309.1| DNA-directed RNA polymerase subunit alpha [Streptococcus equinus
           ATCC 9812]
 gi|320447271|gb|EFW88034.1| DNA-directed RNA polymerase subunit alpha [Streptococcus equinus
           ATCC 9812]
          Length = 312

 Score =  243 bits (620), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 126/288 (43%), Positives = 190/288 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNI
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNI 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   D  K + +   GP  VTAGDI T +D+E++N DH +  +     ++  +TV
Sbjct: 81  KGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDSDVEIVNTDHYLFTIAEGHSLKATMTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ E+ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 141 AKKRGYVPAEGNKKEDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  ED++ L++R+L + L +F +  E  K        + +     L + +EEL+LSVRS
Sbjct: 201 TIIPEDALGLSARVLIEHLNLFTDLTEVAKNTDVMKEAEKVNDEKVLDRTIEELDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL ++TE +M+++ N GRKSL E+K  L  +GL L
Sbjct: 261 YNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVKVKLADLGLGL 308


>gi|255994834|ref|ZP_05427969.1| DNA-directed RNA polymerase, alpha subunit [Eubacterium saphenum
           ATCC 49989]
 gi|255993547|gb|EEU03636.1| DNA-directed RNA polymerase, alpha subunit [Eubacterium saphenum
           ATCC 49989]
          Length = 316

 Score =  243 bits (619), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 123/289 (42%), Positives = 186/289 (64%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+S+L GAA+T+++IDG+LHE S+I GV ED+T+IILNI
Sbjct: 23  FVIEPLERGYGITLGNSLRRVLLSTLPGAAVTSIRIDGILHEFSTIPGVTEDVTEIILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + ++   +     TI   GP  +TA DI   +++++ N DH I  LD DA + MEL +
Sbjct: 83  KRLAIRAWSEEPIVATIKASGPCEITAADIDCGSEVKIFNEDHHIATLDKDAELDMELVI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY  A+ ++ ++DPI  I ID+++SP++K ++ V   R GQV D+DKL + + TDG
Sbjct: 143 DRGRGYSSAEQNKGKDDPISTIAIDSIFSPVEKANFIVSDTRVGQVTDFDKLELEVRTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI+  D+VA+A+RI+Q+ L +F+   E   E    +  + +     L K +E+LEL+VRS
Sbjct: 203 SISANDAVAVAARIMQEHLALFVELSEEATEYSIMLEHEDIEQTRVLEKNIEDLELTVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            N L    I  + DL+  TE ++  + N G+KSL EIK  +  +GL L 
Sbjct: 263 LNALTQAGIDTVSDLVSMTEGELNSVKNLGKKSLSEIKDKIRELGLSLS 311


>gi|21674971|ref|NP_663036.1| DNA-directed RNA polymerase subunit alpha [Chlorobium tepidum TLS]
 gi|25009133|sp|Q8KAJ8|RPOA_CHLTE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|21648203|gb|AAM73378.1| DNA-directed RNA polymerase, alpha subunit [Chlorobium tepidum TLS]
          Length = 328

 Score =  243 bits (619), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 130/301 (43%), Positives = 189/301 (62%), Gaps = 7/301 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            IA+PL RG+  TLGNA+RRVL++SL G AIT ++IDGV HE S+I GV ED+ +I+LN+
Sbjct: 25  FIAQPLERGYGVTLGNAMRRVLLASLPGTAITGIKIDGVFHEFSTIDGVREDVPEIVLNL 84

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           K +  K +     + T+   GP    AGDI     + EVLN D  I  ++ +A V +++ 
Sbjct: 85  KKVRFKSNCKRSCKTTLTLAGPKDFLAGDIVAQEGEFEVLNKDLHIATINSEATVTIDIY 144

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           + +G GYVPA+ +R++  PIG I ID++Y+PIK V  TVE+ R GQ  DY+K+ + ++TD
Sbjct: 145 IGRGRGYVPAEENRSDGMPIGFIAIDSIYTPIKNVKLTVENTRVGQKTDYEKMILDVETD 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL-----PFNPALLKKVEEL 263
           GSIT +D+++LA +I+ D +  F NF  P +E   +   K L          L  K+E+L
Sbjct: 205 GSITPDDAISLAGKIINDHITFFANF-SPTEEEFSEEEYKQLDDEFESMRKLLQTKIEDL 263

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL E+K  L    L  GM++  
Sbjct: 264 DLSVRSHNCLRLAEIDSLGDLVSRREEELLNYKNFGKKSLTELKEQLEKFNLKFGMDITR 323

Query: 324 W 324
           +
Sbjct: 324 Y 324


>gi|157150884|ref|YP_001451209.1| DNA-directed RNA polymerase subunit alpha [Streptococcus gordonii
           str. Challis substr. CH1]
 gi|172045615|sp|A8AZJ9|RPOA_STRGC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|157075678|gb|ABV10361.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus gordonii
           str. Challis substr. CH1]
          Length = 312

 Score =  243 bits (619), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 132/310 (42%), Positives = 195/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILNIKGI +K      K + +   GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNIKGIAVKSYVQDEKMIELDVEGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A  +  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGARFKAVMTVNSGRGYVPADQNKRDDAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F +  E  K       V
Sbjct: 179 EPARVGSNDGFDKLTLEIMTNGTIIPEDALGLSARILTEHLDLFTDLTEVAKATDVMKEV 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                +  L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 DKSSDDHVLERTIEELDLSVRSYNCLKRAGINTVYDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 IKLTDLGLGL 308


>gi|237649697|ref|ZP_04523949.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           CCRI 1974]
 gi|237821395|ref|ZP_04597240.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           CCRI 1974M2]
          Length = 311

 Score =  243 bits (619), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 135/312 (43%), Positives = 203/312 (65%), Gaps = 8/312 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K   +  K + +   G   VTAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGLAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK--EVKEDI 245
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  K  EV ++ 
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSTEVMKEA 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           + +S   +  L + +EEL+LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E
Sbjct: 239 DTES--DDRILDRTIEELDLSVRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEE 296

Query: 306 IKGVLGTMGLFL 317
           +K  L  +GL L
Sbjct: 297 VKLKLIDLGLGL 308


>gi|262273354|ref|ZP_06051168.1| DNA-directed RNA polymerase alpha subunit [Grimontia hollisae CIP
           101886]
 gi|262222332|gb|EEY73643.1| DNA-directed RNA polymerase alpha subunit [Grimontia hollisae CIP
           101886]
          Length = 279

 Score =  243 bits (619), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 124/279 (44%), Positives = 185/279 (66%), Gaps = 7/279 (2%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V A
Sbjct: 3   GCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVILTLNKSGAGPVVA 62

Query: 117 GDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLIT 172
           GDI     +E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + 
Sbjct: 63  GDITHDGGVEIANPEHVICHLTDSNAEISMRIKVERGRGYVPASARIHTEEDERPIGRLL 122

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F+
Sbjct: 123 VDATFSPVDRIAYNVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFV 182

Query: 233 NFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++
Sbjct: 183 DLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVEL 239

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           L+  N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 240 LKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 278


>gi|20808632|ref|NP_623803.1| DNA-directed RNA polymerase subunit alpha [Thermoanaerobacter
           tengcongensis MB4]
 gi|22257018|sp|Q8R7Y2|RPOA_THETN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|20517265|gb|AAM25407.1| DNA-directed RNA polymerase alpha subunit/40 kD subunit
           [Thermoanaerobacter tengcongensis MB4]
          Length = 315

 Score =  243 bits (619), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 135/311 (43%), Positives = 201/311 (64%), Gaps = 4/311 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRT-LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           E+I+P  IE  ++ Q E+ R    + EPL RG+  TLGN+LRRVL+SS+ GAA  +V+ID
Sbjct: 3   EIIEPK-IE--IVEQSEDGRYGKFVVEPLERGYGITLGNSLRRVLLSSIPGAAPKSVKID 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE S++ GV ED+ +IILN+K + +K+  D      I   G G VTAG I+   ++E
Sbjct: 60  GVLHEFSTLPGVKEDVVEIILNLKEVAVKLHSDEPVIGRIDVEGKGEVTAGHIKGGPELE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +LNPDH I  L  D  + ME+   KG GYVPA+ ++  N PIG+I +D++++PI+KV+YT
Sbjct: 120 ILNPDHHIATLSDDGKIHMEIVFVKGKGYVPAEKNKEPNQPIGVIPVDSIFTPIRKVNYT 179

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+ R G V DYDKL++ + T+G+IT +++V++A+ +L      FI+F    K     + 
Sbjct: 180 VENTRVGHVTDYDKLTLEVWTNGTITPKEAVSMAADMLIKYFQKFISFTGEYKSPDVFVE 239

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L   +EEL+LSVRS NCL+   I  + +L Q+TE +M+++ N G+KSL E+
Sbjct: 240 KQEKKVEKPLDMTIEELDLSVRSYNCLKRAGINTVQELTQKTEEEMMKIRNLGKKSLEEV 299

Query: 307 KGVLGTMGLFL 317
           K  L  +GL L
Sbjct: 300 KQKLAALGLSL 310


>gi|167748457|ref|ZP_02420584.1| hypothetical protein ANACAC_03201 [Anaerostipes caccae DSM 14662]
 gi|317472010|ref|ZP_07931342.1| DNA-directed RNA polymerase [Anaerostipes sp. 3_2_56FAA]
 gi|167652449|gb|EDR96578.1| hypothetical protein ANACAC_03201 [Anaerostipes caccae DSM 14662]
 gi|316900414|gb|EFV22396.1| DNA-directed RNA polymerase [Anaerostipes sp. 3_2_56FAA]
          Length = 318

 Score =  243 bits (619), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 133/298 (44%), Positives = 197/298 (66%), Gaps = 4/298 (1%)

Query: 24  EENR-TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E+NR    + EPL RG+  TLGN+LRR+++SSL GAA++AV+I GVLHE SS+ GV ED+
Sbjct: 16  EDNRFGRFVVEPLVRGYGTTLGNSLRRIMLSSLPGAAVSAVKIKGVLHEFSSVPGVKEDV 75

Query: 83  TDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
            +II+NIK + +K   S D  K+  I   G GVVTAGDI+  +DIE+LNPD VI  L  D
Sbjct: 76  PEIIMNIKSLAIKNNSSTDEPKQAFIECSGSGVVTAGDIKADSDIEILNPDMVIATLSGD 135

Query: 141 -AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
            A + MELT++KG GYV A     E + I  I +DA+Y+P+++V+  VE+ R GQV DYD
Sbjct: 136 DAHLDMELTITKGRGYVGADKADKEGNSIDEIAVDAIYTPVERVNLKVENTRVGQVTDYD 195

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL++ + T+G+++ +++V+LA+++L + L +F++  E  K  +  +  +       L   
Sbjct: 196 KLTLDVFTNGTLSPDEAVSLAAKVLCEHLNLFVDLSENAKTAEVMVEKEDDEKEKVLEMS 255

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           ++ELELSVRS NCL+   I  + +L  +T  DM+++ N GRKSL E+   L  +GL L
Sbjct: 256 IDELELSVRSYNCLKRAGINTVEELTNKTSEDMMKVRNLGRKSLEEVLAKLNELGLAL 313


>gi|149279637|ref|ZP_01885766.1| DNA-directed RNA polymerase subunit alpha [Pedobacter sp. BAL39]
 gi|149229673|gb|EDM35063.1| DNA-directed RNA polymerase subunit alpha [Pedobacter sp. BAL39]
          Length = 330

 Score =  242 bits (618), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 129/298 (43%), Positives = 192/298 (64%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AIT+++  GV HE S++KGV EDLT+IILN+K + 
Sbjct: 28  PLEPGFGVTIGNALRRILLSSLEGYAITSIRFSGVSHEFSTMKGVVEDLTEIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQTV-NDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K  GDS   ++V I   G    TAGDI    N+ EVLNPD VICN++    + +ELT++
Sbjct: 88  FKKVGDSGDSEKVFILVNGQDQFTAGDITKFSNNFEVLNPDFVICNMEKTVTLEVELTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++  +  +G+I ID++++P+K V YT+E+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPAEENKINDAVVGVIAIDSIFTPMKNVKYTIENYRVEQKTDYEKLILDISTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  E+++  A++IL     +F +     E   KE  ++++ + L     L  ++ +L+LS
Sbjct: 208 IHPEEALKEAAKILIQHFMLFSDENLVLESQAKEETKEVDEEILHMRKILKTELVDLDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  +I  + DL+    ADML+  NFG+KSL EI+ ++ +  L  GMNL  +
Sbjct: 268 VRALNCLKAADIRTLADLVSYDVADMLKFRNFGKKSLTEIQELVKSKSLSFGMNLSKF 325


>gi|76787566|ref|YP_328809.1| DNA-directed RNA polymerase subunit alpha [Streptococcus agalactiae
           A909]
 gi|90110872|sp|Q3K3U4|RPOA_STRA1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|76562623|gb|ABA45207.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae A909]
          Length = 312

 Score =  242 bits (618), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 124/288 (43%), Positives = 192/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNV 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +   GP  +TAGDI T +DIE++NPDH +  +     ++  +TV
Sbjct: 81  KGLAVKSYVEDEKIIELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIAEGHSLKATMTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 141 AKNRGYVPAEGNKKDDVPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  ED++ L++R+L + L +F +  E  K  +     + +     L + +EEL+LSVRS
Sbjct: 201 TIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKETEKVNDEKVLDRTIEELDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL ++TE +M+++ N GRKSL E+K  L  +GL L
Sbjct: 261 YNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVKIKLADLGLGL 308


>gi|313889541|ref|ZP_07823186.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pseudoporcinus SPIN 20026]
 gi|313122050|gb|EFR45144.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pseudoporcinus SPIN 20026]
          Length = 312

 Score =  242 bits (618), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 125/288 (43%), Positives = 191/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNI
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNI 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV
Sbjct: 81  KGLAVKSYVEDEKMIELDVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLKATMTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 141 AKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  ED++ L++R+L + L +F +  E  K        + +     L + +EEL+LSVRS
Sbjct: 201 TIIPEDALGLSARVLIEHLNLFTDLTEVAKATDVMKETEKVNDEKVLDRTIEELDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL +++E +M+++ N GRKSL E+K  L  +GL L
Sbjct: 261 YNCLKRAGINTVFDLTEKSEPEMMKVRNLGRKSLEEVKVKLADLGLGL 308


>gi|116513027|ref|YP_811934.1| DNA-directed RNA polymerase subunit alpha [Lactococcus lactis
           subsp. cremoris SK11]
 gi|122939924|sp|Q02W51|RPOA_LACLS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116108681|gb|ABJ73821.1| DNA-directed RNA polymerase subunit alpha [Lactococcus lactis
           subsp. cremoris SK11]
          Length = 312

 Score =  242 bits (618), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 124/295 (42%), Positives = 194/295 (65%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E EN    + EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+
Sbjct: 14  ESENYGKFVVEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDV 73

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             I+L +KGI +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     
Sbjct: 74  IQIVLAVKGIAIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHS 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           +R  +TV KG+GYVPA  ++ +  PIG I +D++Y+P+ KV+Y VE AR G    YDKL+
Sbjct: 134 MRAVMTVKKGYGYVPADENKVDGAPIGTIAVDSIYTPVSKVNYQVEPARVGGDSSYDKLT 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + I T+G+I  +++++L+++IL D L +F++  E   E +  +    +     L K +EE
Sbjct: 194 LEITTNGTIVSDEALSLSAKILTDHLNLFVDLSEVAAEAETLVVKDEVKTERVLDKIIEE 253

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           ++ SVR+ N L+   I  + D+++ +EADM+++ N G KS+ E+K  L  +GL L
Sbjct: 254 MDFSVRAYNGLKRAGINTVTDIVEMSEADMIKVKNLGHKSVEEVKVKLTELGLSL 308


>gi|251781544|ref|YP_002995845.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
 gi|242390172|dbj|BAH80631.1| DNA-directed RNA polymerase alpha subunit [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
 gi|322410884|gb|EFY01792.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           dysgalactiae subsp. dysgalactiae ATCC 27957]
          Length = 312

 Score =  242 bits (617), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 124/288 (43%), Positives = 192/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNV 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     +R  +TV
Sbjct: 81  KGLAVKSYVEDEKIIELEVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLRATMTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 141 AKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  ED++ L++R+L + L +F +  +  K  +     + +     L + +EEL+LSVRS
Sbjct: 201 TIIPEDALGLSARVLIEHLNLFTDLTDVAKATEVMKETEKVNDEKVLDRTIEELDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL +++E +M+++ N GRKSL E+K  L  +GL L
Sbjct: 261 YNCLKRAGINTVFDLTEKSEPEMMKVRNLGRKSLEEVKVKLADLGLGL 308


>gi|125717012|ref|YP_001034145.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK36]
 gi|323350965|ref|ZP_08086623.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           VMC66]
 gi|158513356|sp|A3CK90|RPOA_STRSV RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|125496929|gb|ABN43595.1| DNA-directed RNA polymerase, alpha chain, putative [Streptococcus
           sanguinis SK36]
 gi|322122947|gb|EFX94653.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           VMC66]
 gi|324989977|gb|EGC21918.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK353]
 gi|324991840|gb|EGC23765.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK405]
 gi|324996270|gb|EGC28178.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK678]
 gi|325686430|gb|EGD28460.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK72]
 gi|325689206|gb|EGD31212.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK115]
 gi|325695785|gb|EGD37682.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK150]
 gi|325698001|gb|EGD39884.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK160]
 gi|327458456|gb|EGF04812.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK1]
 gi|327463697|gb|EGF10013.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK1057]
 gi|327467360|gb|EGF12860.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK330]
 gi|327471717|gb|EGF17158.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK408]
 gi|327490438|gb|EGF22220.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK1058]
 gi|328945192|gb|EGG39346.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK1087]
          Length = 312

 Score =  242 bits (617), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 130/310 (41%), Positives = 194/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILN+KGI +K      K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTISGVREDVMQIILNVKGIAVKSYVQDEKIIELDVEGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A  +  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+ KV+Y V
Sbjct: 119 INPDHYLFTIGEGASFKATMTVNSGRGYVPADENKKDDAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E           
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLFTNLTEVAIAADVMKEA 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    +  L + +EEL+LSVRS NCL+   I  + DL +++E +M+++ N GRKSL E+K
Sbjct: 239 EKTSDDRILERTIEELDLSVRSYNCLKRAGINTVFDLTEKSEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 VKLADLGLGL 308


>gi|193211878|ref|YP_001997831.1| DNA-directed RNA polymerase subunit alpha [Chlorobaculum parvum
           NCIB 8327]
 gi|238692676|sp|B3QR98|RPOA_CHLP8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|193085355|gb|ACF10631.1| DNA-directed RNA polymerase, alpha subunit [Chlorobaculum parvum
           NCIB 8327]
          Length = 328

 Score =  242 bits (617), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 129/301 (42%), Positives = 189/301 (62%), Gaps = 7/301 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            IA+PL RG+  TLGNA+RRVL++SL G AIT ++IDGV HE S+I GV ED+ +I+LN+
Sbjct: 25  FIAQPLERGYGVTLGNAMRRVLLASLPGTAITGIKIDGVFHEFSTIDGVREDVPEIVLNL 84

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           K +  K +     + T+   GP    AGDI     + EVLN D  I  ++ +A V +++ 
Sbjct: 85  KKVRFKSNCKRSCKTTLTLAGPKDFLAGDIVAQEGEFEVLNKDLHIATINSEAAVTIDIY 144

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           + +G GYVPA+ +R++  PIG I ID++Y+PIK V  TVE+ R GQ  DY+K+ + ++TD
Sbjct: 145 IGRGRGYVPAEENRSDGMPIGFIAIDSIYTPIKNVKLTVENTRVGQKTDYEKMILDVETD 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-----FNPALLKKVEEL 263
           GSI+ +D+++LA RI+ D +  F NF  P +E   +   K L          L  K+E+L
Sbjct: 205 GSISPDDAISLAGRIINDHVTFFANF-SPTEEEYAEEEYKQLDEEFENMRKKLQTKIEDL 263

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +LSVRS NCLR   I  + DL+ R E ++L   NFG+KSL E++  L   GL  GM++  
Sbjct: 264 DLSVRSHNCLRLAEIDTLADLVSRREDELLNYKNFGKKSLTELREALEKEGLKFGMDITR 323

Query: 324 W 324
           +
Sbjct: 324 Y 324


>gi|317054795|ref|YP_004103262.1| DNA-directed RNA polymerase subunit alpha [Ruminococcus albus 7]
 gi|315447064|gb|ADU20628.1| DNA-directed RNA polymerase, alpha subunit [Ruminococcus albus 7]
          Length = 319

 Score =  241 bits (616), Expect = 8e-62,   Method: Compositional matrix adjust.
 Identities = 123/290 (42%), Positives = 197/290 (67%), Gaps = 2/290 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRRVL+SSL G A+T+V+IDGV HE+S+I GV ED+T+IILN+
Sbjct: 24  FILEPLERGYGITLGNSLRRVLLSSLPGVAVTSVKIDGVHHELSTIPGVKEDVTEIILNL 83

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+  K+ G+  K + I   G  VVTAGDI+  +++++L PD  I  L   A + ME+T+
Sbjct: 84  KGLTAKLYGEGPKTIYIEAEGECVVTAGDIKADSEVDILVPDMHIATLGAGAKLYMEITI 143

Query: 150 SKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            +G GYV A+ +++  +N PIG+I +D++YSP+ KV+YTV++ R G + D+DKL++ + T
Sbjct: 144 DRGRGYVSAEKNKSLMQNAPIGIIAVDSIYSPVLKVNYTVDNTRVGHITDFDKLTLEVWT 203

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           DG+I+ +++V++A+++L + L  F++  E    V+  +          L   +EEL+LSV
Sbjct: 204 DGTISAKEAVSMAAKLLNEHLNPFVDLSEETNVVELIVEKDDQGKEKILEMTIEELDLSV 263

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+   I  + DLI+++  +M+++ N G+KS  E++  L ++G  L
Sbjct: 264 RSFNCLKRAGINTVNDLIEKSAEEMMKVRNLGKKSFDEVREKLHSLGYEL 313


>gi|309799084|ref|ZP_07693337.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus infantis
           SK1302]
 gi|308117319|gb|EFO54742.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus infantis
           SK1302]
          Length = 311

 Score =  241 bits (616), Expect = 8e-62,   Method: Compositional matrix adjust.
 Identities = 133/312 (42%), Positives = 203/312 (65%), Gaps = 8/312 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K      K + +  +GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVKDEKIIELDVQGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NP H +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPGHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK--EVKEDI 245
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  K  EV ++ 
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSAEVMKEA 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           + +S   +  L + +EEL+LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E
Sbjct: 239 DTES--DDRILERTIEELDLSVRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEE 296

Query: 306 IKGVLGTMGLFL 317
           +K  L  +GL L
Sbjct: 297 VKVKLIDLGLGL 308


>gi|157493273|gb|ABV58002.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493275|gb|ABV58003.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 270

 Score =  241 bits (616), Expect = 8e-62,   Method: Compositional matrix adjust.
 Identities = 122/272 (44%), Positives = 186/272 (68%), Gaps = 8/272 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 2   EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 61

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V 
Sbjct: 62  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVE 121

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 122 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMET 181

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 182 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 238

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           RS NCL+ E I Y+GDL+QRTE ++L+  N G
Sbjct: 239 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLG 270


>gi|25027128|ref|NP_737182.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           efficiens YS-314]
 gi|259506741|ref|ZP_05749641.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           efficiens YS-314]
 gi|41688706|sp|Q8FS33|RPOA_COREF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|23492408|dbj|BAC17382.1| putative DNA-directed RNA polymerase alpha chain [Corynebacterium
           efficiens YS-314]
 gi|259165682|gb|EEW50236.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           efficiens YS-314]
          Length = 338

 Score =  241 bits (616), Expect = 9e-62,   Method: Compositional matrix adjust.
 Identities = 132/307 (42%), Positives = 196/307 (63%), Gaps = 1/307 (0%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           + +R+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+V+IDGVLHE ++I G+ ED++
Sbjct: 15  DSSRSKFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVKIDGVLHEFTTINGIKEDVS 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           DIILNIKG+ L    D    + + K GPGVVTAGDI+   D+E+ NPD  I  L+ +A +
Sbjct: 75  DIILNIKGLVLSSDSDEPVIMHLSKEGPGVVTAGDIEPPADVEIHNPDLHIATLNENAKL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +EL V +G GYVPA    T  D IG I +D +YSP+ KVSY VE+ R  Q  D+DKL +
Sbjct: 135 DIELIVERGRGYVPATMTATGGD-IGRIPVDQIYSPVLKVSYKVEATRVEQRTDFDKLII 193

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T  SI+  D++A A + L +  G+        + ++   + +   +  A    +E+L
Sbjct: 194 DVETKNSISARDALASAGKTLVELFGLARELNVAAEGIEIGPSPQETEYIAAYSMPIEDL 253

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           + SVRS NCL+ E+I  +G+L +R E+D+L + NFG+KS+ E+K  L  +GL L     D
Sbjct: 254 DFSVRSYNCLKREDIHTVGELAERAESDLLDIRNFGQKSINEVKIKLAGLGLTLKDAPED 313

Query: 324 WPPESIE 330
           + P ++E
Sbjct: 314 FDPSTLE 320


>gi|322386328|ref|ZP_08059958.1| DNA-directed RNA polymerase subunit alpha [Streptococcus cristatus
           ATCC 51100]
 gi|321269552|gb|EFX52482.1| DNA-directed RNA polymerase subunit alpha [Streptococcus cristatus
           ATCC 51100]
          Length = 312

 Score =  241 bits (616), Expect = 9e-62,   Method: Compositional matrix adjust.
 Identities = 130/310 (41%), Positives = 194/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E +N    + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKNYGKFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILNIKGI +K      K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTISGVREDVMQIILNIKGIAVKSYVQDEKMIELDVEGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A  + ++ V+ G GYVPA  ++ ++ P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTISEGARFKAKMAVNSGRGYVPADENKKDDAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F +  E           
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLFTDLTEVAISTDVMKEA 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    +  L + +EEL+LSVRS NCL+   I  + DL +++E +M+++ N GRKSL E+K
Sbjct: 239 EKSSDDRILERTIEELDLSVRSYNCLKRAGINTVFDLTEKSEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 VKLADLGLGL 308


>gi|300775039|ref|ZP_07084902.1| DNA-directed RNA polymerase subunit alpha [Chryseobacterium gleum
           ATCC 35910]
 gi|300506854|gb|EFK37989.1| DNA-directed RNA polymerase subunit alpha [Chryseobacterium gleum
           ATCC 35910]
          Length = 331

 Score =  241 bits (616), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 125/324 (38%), Positives = 208/324 (64%), Gaps = 10/324 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           + IKP+ +   +L   +E +      PL  GF  T+GNALRRVL+SSL G AI++++I+G
Sbjct: 5   QFIKPDKV---ILLNSDEFKGQFEFRPLEPGFGLTIGNALRRVLLSSLEGYAISSIKIEG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMS--GDSHKRVTIFKRGPGVVTAGDI-QTVND 124
           V HE S+I GV ED+T+IILN+K + LK +  G ++++V     G  V+TAGD+ +++N 
Sbjct: 62  VEHEFSTIPGVIEDVTEIILNLKQVRLKAAAEGQANEQVVAKVSGQTVITAGDLGKSING 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            EVLNPD VICNL+ D    +   + KG GYVP++ +++ N P+G I ID++++PIKKV 
Sbjct: 122 FEVLNPDLVICNLNTDVTFEITFNIEKGRGYVPSEQNKSNNAPVGTIAIDSIFTPIKKVQ 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y++E+ R  Q  DY+KL + I+TDGSI+ ++++  AS+IL     +F    I  E    +
Sbjct: 182 YSIENYRVEQKTDYEKLVLDIETDGSISPQNALTEASKILIYHFMLFSDERITLETEAVK 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                + ++L     L  K+ +++LSVR+ NCL+   +  +G+L+  +++D+++  NFG+
Sbjct: 242 ASIQYDEETLHTRQLLKSKLADMDLSVRALNCLKAAEVETLGELVSYSKSDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDW 324
           KSL E++ ++ + GL  G ++  +
Sbjct: 302 KSLTELEELVHSKGLNFGFDVAKY 325


>gi|167771239|ref|ZP_02443292.1| hypothetical protein ANACOL_02597 [Anaerotruncus colihominis DSM
           17241]
 gi|167666490|gb|EDS10620.1| hypothetical protein ANACOL_02597 [Anaerotruncus colihominis DSM
           17241]
          Length = 319

 Score =  241 bits (616), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 132/296 (44%), Positives = 193/296 (65%), Gaps = 13/296 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +AEPL RGF  TLGN+LRRVL+SSL G A+ +V+IDG+ HE S+I GV ED+T+IILNI
Sbjct: 23  FVAEPLDRGFGTTLGNSLRRVLLSSLPGVAVISVKIDGIQHEFSTIPGVKEDVTEIILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+  K+  D  K V I  +G   VTAG I+  +++E+L+P   I  LD  A + ME+T+
Sbjct: 83  KGLTAKLYCDEPKTVRIDAQGECEVTAGSIECDSEVEILDPSMHIATLDTGAKLAMEITL 142

Query: 150 SKGHGYVPA---KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            KG GYV A   KH   E  P+G I +D++Y+P+ KV+YTVE+ R  Q+ DYDKL++ + 
Sbjct: 143 KKGQGYVSADRNKHTELEKAPVGTIAVDSIYTPVLKVNYTVENTRVEQITDYDKLTLEVW 202

Query: 207 TDGSITGEDSVALASRILQDQLGMFINF--EEPKKEV---KEDINVKSLPFNPALLKKVE 261
           TDG+I+ +++V+LA++IL  QL  F++   E    E+   KED     L     L   +E
Sbjct: 203 TDGTISAKEAVSLAAKILNRQLNHFVDLSDEVSATEIMDKKEDTGKDKL-----LEMTIE 257

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           EL+LSVR+ NCL+   +  + DLI ++  +M+++ N G+KSL E+   L ++G  L
Sbjct: 258 ELDLSVRAFNCLKRAGVNTVADLINKSPDEMMKVRNLGKKSLEEVIWKLQSLGFDL 313


>gi|225016257|ref|ZP_03705449.1| hypothetical protein CLOSTMETH_00160 [Clostridium methylpentosum
           DSM 5476]
 gi|224950932|gb|EEG32141.1| hypothetical protein CLOSTMETH_00160 [Clostridium methylpentosum
           DSM 5476]
          Length = 316

 Score =  241 bits (615), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 135/293 (46%), Positives = 196/293 (66%), Gaps = 9/293 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RGF  TLGN+LRRVL+SSL G A+T+++IDGV HE S+I GV ED+T+I+LNI
Sbjct: 23  FILEPLERGFGTTLGNSLRRVLLSSLPGVAVTSIKIDGVQHEFSTIPGVKEDVTEIVLNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+  K+ GD  K V I   G   VTAGDI+  +++E+L+P   I  LD  A + MEL +
Sbjct: 83  KGLIAKVHGDVPKTVYIEAEGECEVTAGDIKADSEVEILDPGMHIATLDEGAKLYMELVI 142

Query: 150 SKGHGYVPAKHHRTENDP-IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
            +G GYV +  ++    P IG+I ID++Y+P+ KV+Y+VE+ R GQ+ DYDKL++ I TD
Sbjct: 143 DRGRGYVSSDRNKQIMQPVIGVIPIDSIYTPVLKVNYSVENTRVGQITDYDKLTLEIWTD 202

Query: 209 GSITGEDSVALASRILQDQLGMFINF-EEPKKE---VKEDINVKSLPFNPALLKKVEELE 264
           G+I+ +++V+LA+++L + L +F++  EE   E   V++D   K       L   +EEL+
Sbjct: 203 GTISAKEAVSLAAKVLNEHLNLFVDLSEEGYTEQIMVEKDDKCK----EKVLEMTIEELD 258

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LSVRS NCL+   I  + DL  +TE DM+++ N GRKSL E+   L ++G  L
Sbjct: 259 LSVRSFNCLKRAGINTVEDLTNKTEEDMMKVRNLGRKSLDEVVLKLKSLGYDL 311


>gi|167036829|ref|YP_001664407.1| DNA-directed RNA polymerase subunit alpha [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|167039548|ref|YP_001662533.1| DNA-directed RNA polymerase subunit alpha [Thermoanaerobacter sp.
           X514]
 gi|256752660|ref|ZP_05493512.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300915201|ref|ZP_07132516.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter sp.
           X561]
 gi|307725125|ref|YP_003904876.1| DNA-directed RNA polymerase subunit alpha [Thermoanaerobacter sp.
           X513]
 gi|320115251|ref|YP_004185410.1| DNA-directed RNA polymerase subunit alpha [Thermoanaerobacter
           brockii subsp. finnii Ako-1]
 gi|238687620|sp|B0K5S1|RPOA_THEPX RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238687717|sp|B0KCM8|RPOA_THEP3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|166853788|gb|ABY92197.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter sp.
           X514]
 gi|166855663|gb|ABY94071.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|256748480|gb|EEU61532.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300888925|gb|EFK84072.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter sp.
           X561]
 gi|307582186|gb|ADN55585.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter sp.
           X513]
 gi|319928342|gb|ADV79027.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           brockii subsp. finnii Ako-1]
          Length = 315

 Score =  241 bits (615), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 134/310 (43%), Positives = 197/310 (63%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+I+P  IE I+   E+      + EPL RG+  TLGN+LRRVL+SSL GAA  +V+IDG
Sbjct: 3   EMIEPK-IE-IIEQSEDGTYGKFVVEPLERGYGITLGNSLRRVLLSSLPGAAPKSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+ +IILN+K + +K+  D      I   G G VTAG I+   DIE+
Sbjct: 61  VLHEFSTLPGVKEDVVEIILNLKEVAVKLHSDEPVVGRIDVEGRGEVTAGHIKGSADIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPDH I  L  D  + ME+   KG GYVP+  ++  N PIG+I +D++++P+K+VSY V
Sbjct: 121 LNPDHHIATLSDDGKLHMEIVFVKGKGYVPSDKNKEPNQPIGVIPVDSIFTPVKRVSYNV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G V DYDKL++ + T+G++T ++++++AS +L      FI+F    K     ++ 
Sbjct: 181 ENTRVGHVTDYDKLTLEVWTNGAVTPKEAISMASDMLIKYFQKFISFTGEYKSSDIFVDK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                   L   +EEL+LSVRS NCL+   I  + +L Q+TE +M+++ N G+KSL E+K
Sbjct: 241 PEKKVEKPLDMTIEELDLSVRSYNCLKRAGINTVQELTQKTEEEMMKVRNLGKKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 QKLEALGLSL 310


>gi|331091639|ref|ZP_08340473.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae
           bacterium 2_1_46FAA]
 gi|330403396|gb|EGG82955.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae
           bacterium 2_1_46FAA]
          Length = 319

 Score =  241 bits (615), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 125/292 (42%), Positives = 194/292 (66%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL G+AI+ V+IDGVLHE SSI GV ED+T+I++N+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGSAISYVKIDGVLHEFSSIPGVKEDVTEIVMNL 82

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K +   D  K   I   G GVVT  DIQ  +DIE++NP+ VI  L+   D+ + M
Sbjct: 83  KSLAIKNTSETDEPKTAYIEFEGEGVVTGADIQVDSDIEIMNPETVIATLNGGADSKLYM 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++ G GYV A  +++   PI +I ID++Y+P+++V+ TVE+ R GQ+ D+DKL++ +
Sbjct: 143 ELTITNGRGYVSADKNKSSELPIAVIPIDSIYTPVERVNLTVENTRVGQITDFDKLTLDV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L +FI+  E  +  +  I  +       L   ++ELEL
Sbjct: 203 YTNGTLAPDEAVSLAAKVLNEHLKLFIDLSEVAQAAEVMIEKEDDEKEKVLEMSIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L
Sbjct: 263 SVRSYNCLKRAGINTVEELTNRTSEDMMKVRNLGRKSLEEVLAKLKELGLEL 314


>gi|172056167|ref|YP_001812627.1| DNA-directed RNA polymerase subunit alpha [Exiguobacterium
           sibiricum 255-15]
 gi|171988688|gb|ACB59610.1| DNA-directed RNA polymerase, alpha subunit [Exiguobacterium
           sibiricum 255-15]
          Length = 314

 Score =  241 bits (615), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 132/294 (44%), Positives = 192/294 (65%), Gaps = 12/294 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN+LRR+L+SSL GAA+TAVQIDGVLHE S+I GV ED+T IILN+
Sbjct: 23  FVVEPLERGFGTTLGNSLRRILLSSLPGAAVTAVQIDGVLHEFSTIDGVVEDVTQIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  +G GVVTA +I   +D+E+LNP+  I  L   A + M LT 
Sbjct: 83  KKLALKVYSEEEKTLEIDIQGAGVVTAANITHDSDVEILNPELHIATLAEGASLHMRLTA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYV A+ ++ ++ PIG+I ID++Y+PI++V+Y VE  R GQ   +DKL++ + TDG
Sbjct: 143 RRGRGYVQAEDNKRDDMPIGVIPIDSIYTPIQRVNYQVEKTRVGQDASFDKLTLDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINF------EEPKKEVKEDINVKSLPFNPALLKKVEEL 263
           SI  E++V+L ++I+ + L +F+         E   E +ED   K L         +EEL
Sbjct: 203 SIRPEEAVSLGAKIMTEHLNIFVGLTDEALHAEIMVEKEEDQKEKVLEMT------IEEL 256

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E++  L  +GL L
Sbjct: 257 DLSVRSYNCLKRAGINTVQELANKSEDEMMKVRNLGRKSLEEVQAKLDELGLGL 310


>gi|229823511|ref|ZP_04449580.1| hypothetical protein GCWU000282_00809 [Catonella morbi ATCC 51271]
 gi|229786955|gb|EEP23069.1| hypothetical protein GCWU000282_00809 [Catonella morbi ATCC 51271]
          Length = 314

 Score =  241 bits (615), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 128/288 (44%), Positives = 198/288 (68%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EPL RG+  TLGN+LRR+L+SSL G+A+T++QIDGVLHE ++++G+ ED+  IILN+
Sbjct: 23  IVVEPLERGYGTTLGNSLRRILLSSLPGSAVTSIQIDGVLHEFATVEGIVEDVPTIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+     K + +   GP VVTA DI   ND+++LNP+  IC L   A ++M L V
Sbjct: 83  KKLALKLHTQESKVIELNVTGPKVVTAADIMHDNDVQILNPELYICTLADGAELKMRLNV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           + G GYV ++H++ E+ PIG++ ID++Y+PIKKV+Y VE+ R GQ   YDKL++ I TDG
Sbjct: 143 ANGRGYVRSEHNKREDMPIGVLPIDSIYTPIKKVNYQVENTRIGQKNVYDKLTLDIWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI+ E S++LA++IL + L +F+N  +  ++ +  +  +       L+  +EEL+LSVRS
Sbjct: 203 SISPEKSLSLAAKILTEHLNIFVNLNDEARQTEIMVEKEEAEKEKMLIMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++EA+M+++ N GRKSL E+K  L  + L L
Sbjct: 263 YNCLKRAGINTIQELTNKSEAEMIKVRNLGRKSLEEVKQKLANLELSL 310


>gi|227497208|ref|ZP_03927456.1| DNA-directed RNA polymerase [Actinomyces urogenitalis DSM 15434]
 gi|226833339|gb|EEH65722.1| DNA-directed RNA polymerase [Actinomyces urogenitalis DSM 15434]
          Length = 333

 Score =  241 bits (615), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 137/308 (44%), Positives = 192/308 (62%), Gaps = 12/308 (3%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           EE+ R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+IDGV HE  +I GV ED+
Sbjct: 15  EEDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRIDGVPHEFRTIAGVKEDV 74

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILNIK I L    D    + + K GPGVVTAGDI     +E+ NPD VI NL+    
Sbjct: 75  TQIILNIKEIVLSSENDEPVVMYLRKSGPGVVTAGDITPPAGVEIHNPDLVIANLNEKGK 134

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +ELTV +G GYV A  ++  N  I  I +D++YSP+KKVSY VE+ R  Q  D+D+L 
Sbjct: 135 LEIELTVERGRGYVSANQNKDPNGEISRIPVDSIYSPVKKVSYAVEATRVEQRTDFDRLV 194

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKK- 259
           + ++T  SIT  D++A A + L +  G+   +N E       E I V   P + AL +  
Sbjct: 195 VDVETKASITPRDALASAGKTLVELFGLARELNVE------AEGIEVGPSPMDQALQQDL 248

Query: 260 ---VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              ++EL+L  RS+N L+ E I  +G+L+ R+EAD+L + NFG KS+ EIK  L  +GL 
Sbjct: 249 ALMIDELDLQARSSNALKREGIHTVGELVARSEADLLDIRNFGAKSISEIKEKLAELGLS 308

Query: 317 LGMNLPDW 324
           L  +  D+
Sbjct: 309 LKGSSVDY 316


>gi|157493263|gb|ABV57997.1| RNA polymerase alpha subunit [Vibrio mimicus]
          Length = 270

 Score =  241 bits (615), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 122/273 (44%), Positives = 187/273 (68%), Gaps = 8/273 (2%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           GF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++
Sbjct: 1   GFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVA 60

Query: 98  -GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGY 155
            G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V +G GY
Sbjct: 61  EGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVERGRGY 120

Query: 156 VPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           VPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T+G++ 
Sbjct: 121 VPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLE 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
            E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VRS NC
Sbjct: 181 PEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANC 237

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           L+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 238 LKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 270


>gi|295398314|ref|ZP_06808356.1| DNA-directed RNA polymerase subunit alpha [Aerococcus viridans ATCC
           11563]
 gi|294973453|gb|EFG49238.1| DNA-directed RNA polymerase subunit alpha [Aerococcus viridans ATCC
           11563]
          Length = 314

 Score =  241 bits (615), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 129/310 (41%), Positives = 204/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KPN IE I +  + +    ++ EPL RG+  TLGN+LRR+L+SSL G A+T++QID 
Sbjct: 3   EIEKPN-IETIEINDDSKFGKFVV-EPLERGYGTTLGNSLRRILLSSLPGTAVTSIQIDD 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T+I+LN+K ++LK+     K+V I   GP  VTA DI    D +V
Sbjct: 61  VLHEYSTVPGVREDVTEIVLNVKQLSLKLYDVEEKQVEIDITGPADVTAADIIADADFDV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPD  IC L   A   M + V  G G+V +++++ ++ PIG I +D++Y+PI KV+Y V
Sbjct: 121 MNPDLHICTLAEGARFHMIMNVKNGRGFVRSENNKVDSMPIGEIPVDSIYTPISKVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G++ +YDKL+M I TDG+I+ E++++LA++I+ + L +F+N  +  ++V+  +  
Sbjct: 181 ENTRIGEINEYDKLTMDIWTDGTISPEEALSLAAKIMTEHLEVFVNLTDEARQVEVMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E+K
Sbjct: 241 EETQKEKMLEMTIEELDLSVRSYNCLKRAGINTVEELTNKSEPEMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  + L L
Sbjct: 301 NKLAALDLSL 310


>gi|195977234|ref|YP_002122478.1| DNA-directed RNA polymerase subunit alpha [Streptococcus equi
           subsp. zooepidemicus MGCS10565]
 gi|225867691|ref|YP_002743639.1| DNA-directed RNA polymerase alpha chain [Streptococcus equi subsp.
           zooepidemicus]
 gi|225869562|ref|YP_002745509.1| DNA-directed RNA polymerase alpha chain [Streptococcus equi subsp.
           equi 4047]
 gi|195973939|gb|ACG61465.1| DNA-directed RNA polymerase alpha chain [Streptococcus equi subsp.
           zooepidemicus MGCS10565]
 gi|225698966|emb|CAW92015.1| DNA-directed RNA polymerase alpha chain [Streptococcus equi subsp.
           equi 4047]
 gi|225700967|emb|CAW97690.1| DNA-directed RNA polymerase alpha chain [Streptococcus equi subsp.
           zooepidemicus]
          Length = 312

 Score =  241 bits (614), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 123/288 (42%), Positives = 192/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIRIDGVLHEFDTIPGVREDVMQIILNV 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV
Sbjct: 81  KGLAVKSYVEDEKIIELDVEGPAEVTAGDILTDSDIELVNPDHYLFTIADGYTLKASMTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 141 AKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  ED++ L++R+L + L +F +  +  K  +     + +     L + +EEL+LSVRS
Sbjct: 201 TIIPEDALGLSARVLIEHLNLFTDLTDVAKATEVMKEAEKVNDEKVLDRTIEELDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL +++E +M+++ N GRKSL E+K  L  +GL L
Sbjct: 261 YNCLKRAGINTVFDLTEKSEPEMMKVRNLGRKSLEEVKVKLADLGLGL 308


>gi|222152291|ref|YP_002561466.1| DNA-directed RNA polymerase subunit alpha [Streptococcus uberis
           0140J]
 gi|222113102|emb|CAR40486.1| DNA-directed RNA polymerase alpha chain [Streptococcus uberis
           0140J]
          Length = 312

 Score =  241 bits (614), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 124/288 (43%), Positives = 190/288 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++ DGVLHE  +I GV ED+  IILNI
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKFDGVLHEFDTIPGVREDVMQIILNI 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV
Sbjct: 81  KGLAVKSYVEDEKMIELEVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLKATMTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 141 AKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  ED++ L++R+L + L +F +  E  K        + +     L + +EEL+LSVRS
Sbjct: 201 TIIPEDALGLSARVLIEHLNLFTDLTEVAKATDVMKETEKVNDEKVLDRTIEELDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL +++E +M+++ N GRKSL E+K  L  +GL L
Sbjct: 261 YNCLKRAGINTVFDLTEKSEPEMMKVRNLGRKSLEEVKVKLADLGLGL 308


>gi|325288605|ref|YP_004264786.1| DNA-directed RNA polymerase subunit alpha [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324964006|gb|ADY54785.1| DNA-directed RNA polymerase subunit alpha [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 315

 Score =  241 bits (614), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 137/316 (43%), Positives = 204/316 (64%), Gaps = 4/316 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KPN IE  V   E+      + EPL RG+  TLGN+LRR+L+SSL G+A+T+V+I+G
Sbjct: 3   EIEKPN-IE-CVERSEDNTYAKFVIEPLERGYGITLGNSLRRILLSSLPGSAVTSVKIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T++ILNIK + LK   D  + + +   G GVVTAGDI T  DIE+
Sbjct: 61  VLHEFSTIPGVLEDVTEVILNIKSLALKGYTDESRVLRLEYEGEGVVTAGDIITGPDIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  LD D  + ME+TV +  GYV A+ ++     IG+I ID++++PI KV+Y V
Sbjct: 121 LNPDLKIATLDKDGRLFMEMTVDRSRGYVSAEKNKKPEHAIGVIPIDSIFAPIYKVNYAV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R G + D+D+L++ + ++GSIT E++ +LA++IL + L +FI   +    V+  +  
Sbjct: 181 EDTRVGMMTDFDRLTLEVWSNGSITPEEATSLAAKILSEHLRLFIGLTDNLGNVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    +  L   +EEL+LSVRS NCL+   I  + +L Q+TE +M+++ N GRKSL E++
Sbjct: 241 EEEAKDKILEMTIEELDLSVRSYNCLKRAGINTVEELTQKTEEEMIKVRNLGRKSLEEVE 300

Query: 308 GVLGTMGLFLGMNLPD 323
             L  +   LG   P+
Sbjct: 301 NKLKELS--LGFRSPE 314


>gi|160881757|ref|YP_001560725.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           phytofermentans ISDg]
 gi|160430423|gb|ABX43986.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           phytofermentans ISDg]
          Length = 319

 Score =  241 bits (614), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 123/295 (41%), Positives = 199/295 (67%), Gaps = 4/295 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDGV+HE S I GV ED+T+II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDGVVHEFSPIPGVKEDVTEIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K + ++++  T +    G GVV AGDIQ   DIE+LNP+ VI  L    D+ + +
Sbjct: 83  KNLAIKNTSETNEPKTAYIEFEGEGVVRAGDIQADPDIEILNPELVIATLSGGADSKLYI 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++KG GY+ A  ++ ++ PIG+I +D++Y+P+++V+ +VE+ R GQ+ D+DKL++ +
Sbjct: 143 ELTITKGRGYISADKNKNDDLPIGVIAVDSIYTPVERVNLSVENTRVGQITDFDKLTLDV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L  FI+  E  K  +  +  +       L   ++ELEL
Sbjct: 203 FTNGTLGPDEAVSLAAKVLSEHLNSFIDLSENAKTAEVMVEKEDNEKEKVLEMNIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           SVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L ++
Sbjct: 263 SVRSYNCLKRAGINTVEELCNRTSEDMMKVRNLGRKSLEEVLAKLKELGLSLNLS 317


>gi|270265495|emb|CBI68384.1| RNA polymerase alpha-subunit [Vibrio tapetis]
          Length = 286

 Score =  241 bits (614), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 123/272 (45%), Positives = 185/272 (68%), Gaps = 8/272 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 18  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 77

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            +K++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 78  AVKVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 137

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 138 RGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 197

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  ++ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 198 NGTLDPEEAIRRSATILAEQLDAFVDLRDIRVPEE---KEEKPEFDPILLRPVDDLELTV 254

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           RS NCL+ E I Y+GDL+QRTE ++L+  N G
Sbjct: 255 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLG 286


>gi|110598114|ref|ZP_01386392.1| DNA-directed RNA polymerase, alpha subunit [Chlorobium ferrooxidans
           DSM 13031]
 gi|110340246|gb|EAT58743.1| DNA-directed RNA polymerase, alpha subunit [Chlorobium ferrooxidans
           DSM 13031]
          Length = 327

 Score =  241 bits (614), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 130/305 (42%), Positives = 192/305 (62%), Gaps = 15/305 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            IA+PL RG+  TLGN +RRVL++SL G AIT ++IDGV HE +++ GV ED+ +I+LN+
Sbjct: 25  FIAQPLERGYGVTLGNVMRRVLLASLPGTAITGLKIDGVFHEFAAVDGVREDVPEIVLNL 84

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           K +  K +   + + T+   GP   TAGDI     + EVLN D  I  ++  A ++++L 
Sbjct: 85  KRVRFKSTCKRNCKTTLAIVGPKEFTAGDIIAQEGEFEVLNKDMHIATVNAGATLKIDLY 144

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V +G GYVPA+ +R E  PIG I IDA+Y+PI+ V +TVE+ R GQ  DY+K+ + ++TD
Sbjct: 145 VGRGRGYVPAEENRPEGMPIGYIAIDAIYTPIRNVRFTVENTRVGQRTDYEKMILDVETD 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFE---------EPKKEVKEDINVKSLPFNPALLKK 259
           GS+T +DS++LA +I+ D +  F NF          E K++  E   ++ L     L  K
Sbjct: 205 GSVTPDDSISLAGKIITDHVTFFANFSPTEEEFTEEEFKQQDDEFETMRRL-----LHTK 259

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +E+L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL E+K  L    L  GM
Sbjct: 260 IEDLDLSVRSHNCLRLAEIDTIGDLVSRKEDELLNYKNFGKKSLTELKEQLEKFDLKFGM 319

Query: 320 NLPDW 324
           ++  +
Sbjct: 320 DITKY 324


>gi|19551799|ref|NP_599801.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           glutamicum ATCC 13032]
 gi|62389454|ref|YP_224856.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           glutamicum ATCC 13032]
 gi|23822074|sp|Q8NSV2|RPOA_CORGL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|21323330|dbj|BAB97958.1| DNA-directed RNA polymerase alpha subunit/40 kD subunit
           [Corynebacterium glutamicum ATCC 13032]
 gi|41324788|emb|CAF19270.1| DNA-DIRECTED RNA POLYMERASE ALPHA SUBUNIT [Corynebacterium
           glutamicum ATCC 13032]
          Length = 338

 Score =  241 bits (614), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 137/312 (43%), Positives = 194/312 (62%), Gaps = 17/312 (5%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
           R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+IDGVLHE ++I GV ED++DII
Sbjct: 18  RSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVKIDGVLHEFTTISGVKEDVSDII 77

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LNIKG+ L    D    + + K GPGVVTAGDIQ    +E+ NPD  I  L+  A + +E
Sbjct: 78  LNIKGLVLSSDSDEPVVMQLVKEGPGVVTAGDIQPPAGVEIHNPDLHIATLNETAKIEIE 137

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           L V +G GYVPA    T  + IG I +D +YSP+ KVSY VE+ R  Q  D+DKL + ++
Sbjct: 138 LIVERGRGYVPATVTATGGE-IGRIPVDQIYSPVLKVSYKVEATRVEQRTDFDKLVIDVE 196

Query: 207 TDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNPALLK 258
           T  SIT  D++A A + L +  G+   +N         P  +  E I   S+P       
Sbjct: 197 TKNSITARDALASAGKTLVELFGLARELNIAAEGIEIGPSPQETEYIAAYSMP------- 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L+ SVRS NCL+ E+I  +G+L +R E+D+L + NFG+KS+ E+K  L  +GL L 
Sbjct: 250 -IEDLDFSVRSYNCLKREDIHTVGELAERAESDLLDIRNFGQKSINEVKIKLAGLGLTLK 308

Query: 319 MNLPDWPPESIE 330
               D+ P ++E
Sbjct: 309 DAPEDFDPSTLE 320


>gi|329116068|ref|ZP_08244785.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           parauberis NCFD 2020]
 gi|326906473|gb|EGE53387.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           parauberis NCFD 2020]
          Length = 312

 Score =  241 bits (614), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 123/288 (42%), Positives = 191/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNV 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV
Sbjct: 81  KGLAVKSYVEDEKMIELDVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLKATMTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GY+PA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 141 AKKRGYIPAEGNKQDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  ED++ L++R+L + L +F +  E  K        + +     L + +EEL+LSVRS
Sbjct: 201 TIIPEDALGLSARVLIEHLNLFTDLTEVAKTTDVMKETEKVNDEKILDRTIEELDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL +++E +M+++ N GRKSL E+K  L  +GL L
Sbjct: 261 YNCLKRAGINTVFDLTEKSEPEMMKVRNLGRKSLEEVKVKLADLGLGL 308


>gi|145294735|ref|YP_001137556.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           glutamicum R]
 gi|158513584|sp|A4QBQ7|RPOA_CORGB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|140844655|dbj|BAF53654.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 338

 Score =  241 bits (614), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 132/304 (43%), Positives = 192/304 (63%), Gaps = 1/304 (0%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
           R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+IDGVLHE ++I GV ED++DII
Sbjct: 18  RSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVKIDGVLHEFTTISGVKEDVSDII 77

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LNIKG+ L    D    + + K GPGVVTAGDIQ    +E+ NPD  I  L+  A + +E
Sbjct: 78  LNIKGLVLSSDSDEPVVMQLVKEGPGVVTAGDIQPPAGVEIHNPDLHIATLNETAKIEIE 137

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           L V +G GYVPA    T  + IG I +D +YSP+ KVSY VE+ R  Q  D+DKL + ++
Sbjct: 138 LIVERGRGYVPATVTATGGE-IGRIPVDQIYSPVLKVSYKVEATRVEQRTDFDKLVIDVE 196

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T  SIT  D++A A + L +  G+        + ++   + +   +  A    +E+L+ S
Sbjct: 197 TKNSITARDALASAGKTLVELFGLARELNIAAEGIEIGPSPQETEYIAAYSMPIEDLDFS 256

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           VRS NCL+ E+I  +G+L +R E+D+L + NFG+KS+ E+K  L  +GL L     D+ P
Sbjct: 257 VRSYNCLKREDIHTVGELAERAESDLLDIRNFGQKSINEVKIKLAGLGLTLKDAPEDFDP 316

Query: 327 ESIE 330
            ++E
Sbjct: 317 STLE 320


>gi|296120769|ref|YP_003628547.1| DNA-directed RNA polymerase, subunit alpha [Planctomyces
           limnophilus DSM 3776]
 gi|296013109|gb|ADG66348.1| DNA-directed RNA polymerase, alpha subunit [Planctomyces
           limnophilus DSM 3776]
          Length = 336

 Score =  241 bits (614), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 125/302 (41%), Positives = 191/302 (63%), Gaps = 11/302 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EP  RGF  T+GN+LRR+L+SSL G+++T+V+I GV HE ++I G+ ED+T+I+LN+K I
Sbjct: 31  EPFERGFGSTIGNSLRRILLSSLEGSSVTSVKIQGVQHEFTTIPGIVEDVTEIVLNLKAI 90

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K    S K + I K   GVVTAGDI T + +E+LN D VI  +  D  + +E+TV  G
Sbjct: 91  IVKNHSPSTKTLRIEKTSRGVVTAGDIITDDQVEILNRDLVIATMTDDVPLYLEMTVENG 150

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GY+PA  H      +G+I +DA++SP+ +V Y +E  R GQ  +YD+L + I T+G++T
Sbjct: 151 RGYIPAADHHGPEQELGVIPLDAIFSPVVRVRYLIEETRVGQRTNYDRLILEIWTNGTVT 210

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS-----------LPFNPALLKKVE 261
            E ++  +++IL+  L  FI + EP  E+  +  +++           L     L + + 
Sbjct: 211 PESALVESAKILRKHLNPFITYREPGPEMFPEGGLRNMLEATGYAPVDLELEEKLGQSLA 270

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           EL LSVR+TNCL  E I ++ DL+ RTE  +L++ NFG  +L E++  LG +GL LGM L
Sbjct: 271 ELNLSVRATNCLESEGINFVRDLVTRTEDQLLQVRNFGETTLTEVRERLGLIGLRLGMKL 330

Query: 322 PD 323
           P+
Sbjct: 331 PN 332


>gi|15674050|ref|NP_268225.1| DNA-directed RNA polymerase subunit alpha [Lactococcus lactis
           subsp. lactis Il1403]
 gi|13878751|sp|Q9CDY3|RPOA_LACLA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|12725120|gb|AAK06166.1|AE006436_15 DNA-directed RNA polymerase alpha chain [Lactococcus lactis subsp.
           lactis Il1403]
          Length = 312

 Score =  240 bits (613), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 123/295 (41%), Positives = 193/295 (65%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E EN    + EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+
Sbjct: 14  ESENYGKFVVEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDV 73

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             I+L +KGI +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     
Sbjct: 74  IQIVLAVKGIAIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHS 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           +R  +TV KG+GYVP   ++ +  PIG I +D++Y+P+ KV+Y VE AR G    YDKL+
Sbjct: 134 MRAVMTVKKGYGYVPDDENKVDGAPIGTIAVDSIYTPVSKVNYQVEPARVGGDSSYDKLT 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + I T+G+I  +++++L+++IL D L +F++  E   E +  +    +     L K +EE
Sbjct: 194 LEITTNGTIVSDEALSLSAKILTDHLNLFVDLSEVAAEAETLVVKDEVKTERVLDKIIEE 253

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           ++ SVR+ N L+   I  + D+++ +EADM+++ N G KS+ E+K  L  +GL L
Sbjct: 254 MDFSVRAYNGLKRAGINTVADIVEMSEADMIKVKNLGHKSVEEVKVKLTELGLSL 308


>gi|171911662|ref|ZP_02927132.1| DNA-directed RNA polymerase subunit alpha [Verrucomicrobium
           spinosum DSM 4136]
          Length = 371

 Score =  240 bits (613), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 130/303 (42%), Positives = 191/303 (63%), Gaps = 18/303 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +AEP  RG+ HT+GN+LRRVL+SSL GA+IT+V+I G  HE +++ GV ED+T I+LN+
Sbjct: 28  FVAEPFDRGYGHTIGNSLRRVLLSSLEGASITSVRIKGAEHEFTTLPGVLEDVTQIVLNL 87

Query: 90  KGINLKMSGDSHKR---VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           K +  +   +   R   V++ K G  VVTAGDI+     +V+N D VIC LD       E
Sbjct: 88  KKVKFRHFENKETRLLQVSVDKEG--VVTAGDIKDDTSYQVINKDQVICTLDRKGKFEAE 145

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           L V  G G+   + ++  + PIG+I ID+++SP+ +V Y VE+ R GQ  DYDKL + + 
Sbjct: 146 LEVKVGRGFATNEDNKRPDMPIGVIPIDSIFSPVTRVKYGVEATRVGQNTDYDKLLIDVW 205

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEE--------PKKEVKEDINVKSLPFNPALLK 258
           TDG IT +D++  +S IL+  L +F+N+++        P+ + +E++ ++ L     L  
Sbjct: 206 TDGRITPQDALLQSSAILRKHLDVFVNYDDNQVEFEVAPEAQSEENLELRKL-----LNM 260

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            V E+ELSVR+ NCL   NI  +G L  ++EA+MLR  NFG+KSL EIK  L  +GL LG
Sbjct: 261 SVNEIELSVRAANCLNNANITSVGQLAMKSEAEMLRYRNFGKKSLTEIKEKLSELGLTLG 320

Query: 319 MNL 321
           M L
Sbjct: 321 MKL 323


>gi|323490649|ref|ZP_08095854.1| DNA-directed RNA polymerase subunit alpha [Planococcus donghaensis
           MPA1U2]
 gi|323395741|gb|EGA88582.1| DNA-directed RNA polymerase subunit alpha [Planococcus donghaensis
           MPA1U2]
          Length = 314

 Score =  240 bits (612), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 122/288 (42%), Positives = 189/288 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+  IILNI
Sbjct: 23  FVIEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVEEDVATIILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +G G VTA DI   +D+E+LNPD  I  +  +  +RM +  
Sbjct: 83  KKLALKIYSDEEKVIEIDVKGDGTVTAADITHDSDVEILNPDLYIATIAKNGHLRMRMYA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           ++G GY  A  ++ E+ PIG+I ID++Y+P+ +V++ VE+ R GQ+  +DKLS+ + TDG
Sbjct: 143 NRGRGYARADQNKREDLPIGVIPIDSIYTPVSRVNFQVENTRVGQLAHFDKLSLDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  ++++AL ++I  + L +F+   +  +  +  +  +       L   +EEL+LSVRS
Sbjct: 203 SIGPKEAIALGAKIFTEHLNIFVGLTDEAQTAEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++E DM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVHELASKSEDDMMKVRNLGRKSLEEVKVKLEDLGLGL 310


>gi|194334834|ref|YP_002016694.1| DNA-directed RNA polymerase subunit alpha [Prosthecochloris
           aestuarii DSM 271]
 gi|238693316|sp|B4S5A1|RPOA_PROA2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|194312652|gb|ACF47047.1| DNA-directed RNA polymerase, alpha subunit [Prosthecochloris
           aestuarii DSM 271]
          Length = 328

 Score =  240 bits (612), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 126/309 (40%), Positives = 194/309 (62%), Gaps = 15/309 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +A+PL RG+  TLGNA+RRVL++SL G AIT ++IDGV HE S+I GV ED+ +I+LN+
Sbjct: 25  FVAQPLERGYGVTLGNAMRRVLLASLPGTAITGIKIDGVFHEFSTIDGVREDVPEIVLNL 84

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           K +  K +     + ++   GP    AGDI     + EVLN D  I  L+ DA + +++ 
Sbjct: 85  KKVRFKSTTKRSCKTSLSIEGPADFKAGDIVAQEGEFEVLNKDMHIATLNGDAKLNIDIY 144

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           + +G GYVPA+ +R E  PIG I ID++++PIK V ++VE+ R GQ  DY+K+ + ++TD
Sbjct: 145 IGRGRGYVPAEENRGEGMPIGFIAIDSIFTPIKNVKFSVENTRVGQRTDYEKMILDVETD 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEP---------KKEVKEDINVKSLPFNPALLKK 259
           GSI+ +DS++LA +++ + + +F NF            K++  E  N++ L     L  +
Sbjct: 205 GSISPDDSISLAGKVINEHVSLFANFSPTEEEFAEEEYKQQDDEFENMRKL-----LQTR 259

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +E+L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL E+K  L    L  GM
Sbjct: 260 IEDLDLSVRSHNCLRLAEIDTLGDLVSRKEDELLTYKNFGKKSLTELKEQLDKCELKFGM 319

Query: 320 NLPDWPPES 328
           ++  +  +S
Sbjct: 320 DITKYQMKS 328


>gi|225165487|ref|ZP_03727313.1| DNA-directed RNA polymerase, alpha subunit [Opitutaceae bacterium
           TAV2]
 gi|224800264|gb|EEG18668.1| DNA-directed RNA polymerase, alpha subunit [Opitutaceae bacterium
           TAV2]
          Length = 334

 Score =  240 bits (612), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 129/299 (43%), Positives = 183/299 (61%), Gaps = 11/299 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            IAEP   G+ HT+GN+LRRVL+SS+ G+AI++++I+GV HE  SI GV ED+TDI+LN+
Sbjct: 28  FIAEPFEAGYGHTIGNSLRRVLLSSIEGSAISSIKIEGVNHEFQSIDGVVEDVTDIVLNL 87

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L  +      + I     G VTA DIQ  +++ V+NP+ VIC LD       E+ +
Sbjct: 88  KKVLLISTKRDPITLQIRVNREGPVTAADIQADSNVTVVNPNQVICTLDRARPFNAEIEI 147

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GY P + ++ E   IG+I ID+L+SP+  V Y VE+ R GQ+ DYDKL++ I TDG
Sbjct: 148 KTGRGYYPGEQNKKEEQAIGVIAIDSLFSPVTLVKYAVENTRVGQITDYDKLNLEIWTDG 207

Query: 210 SITGEDSVALASRILQDQLGMF-------INFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
            IT +D++  ++ IL+  + +F         FE  + EV E+ N         L   V E
Sbjct: 208 RITPDDALKQSAAILKHHIDVFDRVSGENYEFENQQSEVSEEQN----KLRKLLNMSVNE 263

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +ELSVR+ NCL   NI  +G+L  +TE +ML+  NFG+KSL EIK  L  +GL LGM  
Sbjct: 264 IELSVRAANCLNNANITTVGELAMKTEQEMLKYRNFGKKSLNEIKDKLEALGLSLGMKF 322


>gi|297582477|ref|YP_003698257.1| DNA-directed RNA polymerase subunit alpha [Bacillus
           selenitireducens MLS10]
 gi|297140934|gb|ADH97691.1| DNA-directed RNA polymerase, alpha subunit [Bacillus
           selenitireducens MLS10]
          Length = 314

 Score =  240 bits (612), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 120/288 (41%), Positives = 194/288 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L++SL G+A+T+VQ + VLHE S+I+GV ED+T IILN+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLNSLPGSAVTSVQFNNVLHEFSTIEGVVEDVTTIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K ++LK+  +  K + I  +G GV+TA D+   +D+EVLNPD  I  L   A V+M++T 
Sbjct: 83  KKLSLKIFSEEEKTLEIEAQGEGVITARDLTHDSDVEVLNPDLHIATLSKGAQVQMKVTA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYVPA+ + T++ PIG+I +D++++P+ +V+Y VE+ R GQ+ ++DKL++ + TDG
Sbjct: 143 KRGRGYVPAEGNNTDDLPIGVIPVDSIFTPVSRVNYQVENTRVGQITNFDKLTLDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  E++ +L ++IL + L +F+   +  +  +  +  +       L   +EEL+LSVRS
Sbjct: 203 SIRPEEATSLGAKILNEHLNIFVGLTDQAQHAEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++E DM+++ N GRKSL E++  L  + L L
Sbjct: 263 YNCLKRAGINTVQELTHKSEEDMMKVRNLGRKSLEEVQEKLHELSLGL 310


>gi|254495738|ref|ZP_05108652.1| DNA-directed RNA polymerase subunit alpha [Legionella drancourtii
           LLAP12]
 gi|254355016|gb|EET13637.1| DNA-directed RNA polymerase subunit alpha [Legionella drancourtii
           LLAP12]
          Length = 280

 Score =  239 bits (611), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 126/283 (44%), Positives = 188/283 (66%), Gaps = 13/283 (4%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           G+AIT   IDGVLHE S+I+GV ED+ D++LN+K + +K++     +VT+ K+GP  VTA
Sbjct: 3   GSAITEASIDGVLHEYSTIEGVQEDVVDLLLNLKLVAIKLTTGEEAQVTLSKQGPCQVTA 62

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA----KHH--RTENDPIGL 170
           GDIQ  + ++V+NP+ VI NL+    + M L V +G G+       +H     E   +G 
Sbjct: 63  GDIQLTHGVDVVNPELVIANLNEKGKLNMTLKVERGIGFHSTDSFIRHFDDEVERKSVGK 122

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           + ID  +SP+KKV+Y V+SAR     D DKL++ ++T+G+I  E+++ +++ ILQ QL  
Sbjct: 123 LKIDNSFSPVKKVAYYVDSARVENRTDLDKLTIELETNGTIDAEEAIRISASILQRQLHA 182

Query: 231 FIN--FEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
           F++  FEE + + KE  +     F+P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRT
Sbjct: 183 FVDMKFEESRSDNKERND-----FDPVLLRSVDDLELTVRSANCLKAENIHYIGDLVQRT 237

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           E ++L+  N G+KSL EIK VL +  L LGM L +WPP S+ E
Sbjct: 238 ENELLKTPNLGKKSLTEIKDVLASRSLSLGMKLENWPPASLGE 280


>gi|255038116|ref|YP_003088737.1| DNA-directed RNA polymerase subunit alpha [Dyadobacter fermentans
           DSM 18053]
 gi|254950872|gb|ACT95572.1| DNA-directed RNA polymerase, alpha subunit [Dyadobacter fermentans
           DSM 18053]
          Length = 322

 Score =  239 bits (611), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 128/313 (40%), Positives = 194/313 (61%), Gaps = 6/313 (1%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +V+ + ++   L   +PL +G+  T+GNALRR+L+SSL G AIT+V+  GVLHE SSI+G
Sbjct: 5   VVMEKADDFHGLFEFKPLEKGYGVTIGNALRRILLSSLEGYAITSVKFPGVLHEFSSIEG 64

Query: 78  VHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVIC 135
           + ED+T+IILN+K +  K   D S  R+ +  +   V+TAGDI +  +  EVLNPD VIC
Sbjct: 65  IVEDVTEIILNLKMVRFKKVSDLSESRIVVNLKNVSVITAGDIGKFTSAFEVLNPDQVIC 124

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
           ++D      MEL + KG GYVPA   R    P G I +D++Y+PIK V Y+VE+ R  Q 
Sbjct: 125 HIDDQKEFEMELLLDKGRGYVPADEPRANELPFGYIAVDSIYTPIKNVKYSVENTRVEQR 184

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLP 251
            DY++L + I TDGSI  ED++  A+ IL     +F    + FE+ K E    ++ + L 
Sbjct: 185 TDYERLLIDIQTDGSIHPEDALKGAANILIQHFMLFSDQTMTFEKQKAEEDNQVDEEMLR 244

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L   + EL+LSVR+ NCL+  ++  +GDL++   +DM++  NFG+KSL E++ ++ 
Sbjct: 245 MRKLLKTSLSELDLSVRAYNCLKSADVKTLGDLVRLEISDMMKFRNFGKKSLTELEQLVA 304

Query: 312 TMGLFLGMNLPDW 324
              L  GM++  +
Sbjct: 305 DKQLTFGMDVSKY 317


>gi|313904923|ref|ZP_07838294.1| DNA-directed RNA polymerase, alpha subunit [Eubacterium
           cellulosolvens 6]
 gi|313470180|gb|EFR65511.1| DNA-directed RNA polymerase, alpha subunit [Eubacterium
           cellulosolvens 6]
          Length = 320

 Score =  239 bits (611), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 125/292 (42%), Positives = 194/292 (66%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL G+A++ V+I+GVLHE SSI GV ED+T+II+N+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGSAVSQVKIEGVLHEFSSIPGVKEDVTEIIMNL 82

Query: 90  KGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K +++K   S D  K   I   G G+V A DIQ   DIE++NPD +I +L+   D  + M
Sbjct: 83  KNLSIKNNSSSDEPKVAYIEYDGEGIVRASDIQVDQDIEIMNPDQIIAHLNGGPDCKLYM 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++ G GYV A   + E+ PIG+I +DA+Y+P+++V+ TVE+ R GQ+ D+DKL++ +
Sbjct: 143 ELTITNGRGYVGADKGKPEDLPIGVIAVDAIYTPVERVNMTVENTRVGQITDFDKLTLDV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+ ++  +++V+LA+++L + L +FI+  E  K  +  I  +       L   ++ELEL
Sbjct: 203 YTNKTLGPDEAVSLAAKVLSEHLKLFIDLSENAKTAEVMIEHQDDEKEKVLEMNIDELEL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + +L  +T  DM+++ N GRKSL E+   L  +GL L
Sbjct: 263 SVRSYNCLKRAGINTVEELCNKTSEDMMKVRNLGRKSLEEVLAKLNELGLSL 314


>gi|157493279|gb|ABV58005.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493281|gb|ABV58006.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 268

 Score =  239 bits (610), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 121/271 (44%), Positives = 185/271 (68%), Gaps = 8/271 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 1   EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 60

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V 
Sbjct: 61  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVE 120

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 121 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMET 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 181 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 237

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           RS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 RSANCLKAEAIHYIGDLVQRTEVELLKTPNL 268


>gi|157493277|gb|ABV58004.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 269

 Score =  239 bits (610), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 121/271 (44%), Positives = 185/271 (68%), Gaps = 8/271 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 2   EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 61

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V 
Sbjct: 62  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVE 121

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 122 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMET 181

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 182 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 238

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           RS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 239 RSANCLKAEAIHYIGDLVQRTEVELLKTPNL 269


>gi|24213465|ref|NP_710946.1| RNA polymerase subunit alpha [Leptospira interrogans serovar Lai
           str. 56601]
 gi|45658676|ref|YP_002762.1| DNA-directed RNA polymerase subunit alpha [Leptospira interrogans
           serovar Copenhageni str. Fiocruz L1-130]
 gi|26454665|sp|Q9XD09|RPOA_LEPIN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|59798772|sp|Q72NI8|RPOA_LEPIC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|24194237|gb|AAN47964.1| RNA polymerase alpha subunit [Leptospira interrogans serovar Lai
           str. 56601]
 gi|45601920|gb|AAS71399.1| DNA-directed RNA polymerase alpha chain [Leptospira interrogans
           serovar Copenhageni str. Fiocruz L1-130]
          Length = 325

 Score =  239 bits (610), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 131/312 (41%), Positives = 201/312 (64%), Gaps = 4/312 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P  IE+        N    +AEP  RGFA T+GN+LRR LMSS+ GAAI+A++I+GV H
Sbjct: 12  RPKKIEFNTEANTP-NYGKFVAEPFERGFATTIGNSLRRTLMSSIEGAAISAIRIEGVNH 70

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMS---GDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           E S I+GV ED+T IILN+K + +K      D  K + +  +G G   AGD+   + IE+
Sbjct: 71  EFSFIEGVAEDVTRIILNLKQVRIKYEPEEKDQSKIIHLELKGAGYFRAGDLAVDSSIEI 130

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPD  I  L+ DA + M+L + +G GYVPA+  + + + +G I +D+++SP++KV + V
Sbjct: 131 MNPDLHIATLNEDANLVMDLEIQRGRGYVPAEEKKKDIEVLGTIPVDSIFSPVQKVVFEV 190

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
              R  Q  DY+KL++ + TDGS++ +D+VA A++IL++ L +FINFEE  +E  ++++ 
Sbjct: 191 SETRVAQRSDYEKLTLEVWTDGSVSPDDAVAQAAKILKEHLTVFINFEEELEEEDDELDE 250

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                  +L K VEELELSVRS N LR   I ++GDL++R+E +M +  ++  + L E+K
Sbjct: 251 ADEKLKASLSKHVEELELSVRSLNVLRSLEIDFIGDLVKRSEEEMSKSKHYSDQCLQELK 310

Query: 308 GVLGTMGLFLGM 319
             L T+GL  GM
Sbjct: 311 VKLSTLGLSFGM 322


>gi|187735995|ref|YP_001878107.1| DNA-directed RNA polymerase, alpha subunit [Akkermansia muciniphila
           ATCC BAA-835]
 gi|187426047|gb|ACD05326.1| DNA-directed RNA polymerase, alpha subunit [Akkermansia muciniphila
           ATCC BAA-835]
          Length = 374

 Score =  239 bits (610), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 127/305 (41%), Positives = 186/305 (60%), Gaps = 10/305 (3%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           + N    +AEP   G+ HTLGN+LRRVL+ SL GAAIT+V+I G  HE SS+ GV ED+T
Sbjct: 34  DANHLTFVAEPFENGYGHTLGNSLRRVLLGSLEGAAITSVRIAGAQHEFSSLPGVVEDVT 93

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           +I+LN+K +  K +G   + +++     GVVTA DI      +V+NPD +IC LD D + 
Sbjct: 94  EIVLNLKKVKFKHNGKEPRLLSLRVHKQGVVTAADIADDTVYQVVNPDQIICTLDQDTMF 153

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
             E  V  G G+     ++  + PIG+I ID+++SP+ +V Y+V++ R GQ+ DYDKL +
Sbjct: 154 ECEFQVRVGRGFATGDENKVPDMPIGVIPIDSIFSPVTRVKYSVQNTRVGQMTDYDKLIL 213

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMF-------INFEEPKKEVKEDINVKSLPFNPAL 256
            + TDG I   D++  AS IL+  L +F       +NFEE    V+++   +       L
Sbjct: 214 EVWTDGRIAPADAMLQASAILRHHLDVFVNYDDKQVNFEEAPSAVQDEETAR---LRKLL 270

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              V E+ELSVR+ NCL   NI  +G L  ++E++ML+  NFG+KSL EIK  L  +GL 
Sbjct: 271 NMSVNEIELSVRAANCLNNANITTVGQLAMKSESEMLKYRNFGKKSLNEIKDKLLELGLS 330

Query: 317 LGMNL 321
           LG+ +
Sbjct: 331 LGVQV 335


>gi|160932172|ref|ZP_02079563.1| hypothetical protein CLOLEP_01007 [Clostridium leptum DSM 753]
 gi|156868774|gb|EDO62146.1| hypothetical protein CLOLEP_01007 [Clostridium leptum DSM 753]
          Length = 317

 Score =  239 bits (610), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 123/290 (42%), Positives = 192/290 (66%), Gaps = 2/290 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN+LRRVL+SSL G A+T+++IDGVLHE S+I GV ED+T+I+LN+
Sbjct: 23  FVVEPLERGFGTTLGNSLRRVLLSSLPGVAVTSIKIDGVLHEFSTIPGVKEDVTEIVLNM 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+  K+  D  K V I   GP  VTA  I+  +++E+LNP+  I  L   A + ME+T+
Sbjct: 83  KGLTAKLHCDGAKTVEISAEGPCEVTADSIKCDSEVEILNPEMHIATLGDGARLYMEITL 142

Query: 150 SKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GY+ A+ ++   +N+ IG++ ID++Y+P+ KV++ VE+ R GQ+ DYDKL++ + T
Sbjct: 143 DKGRGYISAERNKANMQNNVIGILPIDSIYTPVLKVNFGVENTRVGQITDYDKLTLEVWT 202

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G I  +++V+LA+++L + L +F++  +     +  +          L   +EEL+LSV
Sbjct: 203 NGVINAQEAVSLAAKVLTEHLNLFVDLSDKGYNTEIMVEKDDKGKEKVLEMTIEELDLSV 262

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+   I  + DLI ++E DM+++ N GRKSL E+   L ++G  L
Sbjct: 263 RSFNCLKRAGINTVEDLINKSEDDMMKVRNLGRKSLEEVVYKLNSLGFSL 312


>gi|324985144|gb|ADY69170.1| RNA polymerase subunit A [Photobacterium halotolerans]
          Length = 270

 Score =  239 bits (609), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 121/265 (45%), Positives = 182/265 (68%), Gaps = 7/265 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 9   EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDVLEILLNLKGL 68

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +
Sbjct: 69  AVKVEGKDEVILTLSKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNADISMRIKVER 128

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA +SP+ +++Y+VE+AR  Q  D DKL + ++T+
Sbjct: 129 GRGYVPASARIHSDEDERPIGRLLVDATFSPVDRIAYSVEAARVEQRTDLDKLVIDMETN 188

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 189 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 245

Query: 269 STNCLRGENIVYMGDLIQRTEADML 293
           S NCL+ E I Y+GDL+QRTE ++L
Sbjct: 246 SANCLKAEAIHYIGDLVQRTEVELL 270


>gi|299143167|ref|ZP_07036247.1| DNA-directed RNA polymerase, alpha subunit [Peptoniphilus sp. oral
           taxon 386 str. F0131]
 gi|298517652|gb|EFI41391.1| DNA-directed RNA polymerase, alpha subunit [Peptoniphilus sp. oral
           taxon 386 str. F0131]
          Length = 315

 Score =  239 bits (609), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 130/288 (45%), Positives = 187/288 (64%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL  G+  T+GN+LRRVL+SSL GAAI+ + I GV HE ++I GV ED+  IILNI
Sbjct: 23  FVVEPLESGYGITIGNSLRRVLLSSLPGAAISFINIRGVEHEFATIPGVLEDVPQIILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KGI LK + D   +V I K+G G + A DIQT  D+E++N DH I  L+ DA V +ELT+
Sbjct: 83  KGIVLKTNEDEPVKVIIEKKGEGEILASDIQTGGDVEIINLDHHIATLNEDADVYIELTI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY P++  + E   IG+I ID+ Y+PIKKV++ VE+ R G   DYD+L + + TDG
Sbjct: 143 ERGRGYEPSELKKDEITEIGVIPIDSNYTPIKKVNWKVENTRVGNRTDYDRLILEVTTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           S+  +++ +LA++IL + L +FI   E    V   +  +       L   VEEL+LSVRS
Sbjct: 203 SMKADEATSLAAKILTEHLNLFIGLTEHVNNVNIMVEKEEDQKEKVLEMTVEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+  NI  + +L Q++E DM+++ N G+KSL E++  L  +GL L
Sbjct: 263 FNCLKRANINTVEELTQKSEDDMMKVRNLGKKSLEEVENKLAELGLGL 310


>gi|210623215|ref|ZP_03293654.1| hypothetical protein CLOHIR_01604 [Clostridium hiranonis DSM 13275]
 gi|210153752|gb|EEA84758.1| hypothetical protein CLOHIR_01604 [Clostridium hiranonis DSM 13275]
          Length = 315

 Score =  238 bits (608), Expect = 7e-61,   Method: Compositional matrix adjust.
 Identities = 123/291 (42%), Positives = 193/291 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  T+GNALRR+L+SSL G A+ AV+I+GVLHE S+I GV ED+T+IIL +
Sbjct: 23  FVVEPLERGYGITIGNALRRILLSSLPGVAVNAVKIEGVLHEFSTIPGVKEDVTEIILTL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K ++  + G+ ++ + I  +GP  VT  DI    D+E++N D  I  LD  + + M++ V
Sbjct: 83  KELSATIDGEGNRTLKIEAQGPCTVTGADIICPPDVEIINKDLKIATLDEGSKLNMDIHV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYVPA+ ++TEN PIG++ +D++Y+P++KV+Y VE+ R GQ  DYDKL++ + T+G
Sbjct: 143 DKGRGYVPAEENKTENMPIGVLPVDSIYTPVEKVNYHVENTRVGQKSDYDKLTLEVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  ++ ++LA+++L + L +FI+  E    V+  +  +       L   +EEL+LSVRS
Sbjct: 203 SINPQEGISLAAKVLVEHLKLFIDLTEHVSNVEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
            NCL+   I  + +L  ++E DM+++ N G+KSL E+   L  +GL L  N
Sbjct: 263 YNCLKRAGINTVEELANKSEDDMMKVRNLGKKSLEEVIQKLDELGLGLKPN 313


>gi|255654191|ref|ZP_05399600.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           QCD-23m63]
 gi|296449770|ref|ZP_06891539.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           NAP08]
 gi|296261368|gb|EFH08194.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           NAP08]
          Length = 315

 Score =  238 bits (608), Expect = 7e-61,   Method: Compositional matrix adjust.
 Identities = 123/288 (42%), Positives = 190/288 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  T+GNALRR+L+SSL G A+ A++IDGVLHE S+I GV ED+T+IIL +
Sbjct: 23  FVIEPLERGYGITIGNALRRILLSSLPGVAVNAIKIDGVLHEFSTIPGVKEDVTEIILTL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K ++  + G+  + + I  +GP  +T  DI    D+E+L+ D  I  LD +A + ME+ V
Sbjct: 83  KELSATIDGEGSRTLKIEAQGPCSITGADIICSPDVEILSKDLAIATLDDNAKLNMEIFV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYV A+ ++TEN PIG++ +D++Y+P++KVSY VE+ R GQ  DYDKL + + T+G
Sbjct: 143 DKGRGYVSAEENKTENVPIGVLPVDSIYTPVEKVSYHVENTRVGQKTDYDKLVLEVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  ++ ++LA+++L + L +FI+  E    V+  +  +       L   +EEL+LSVRS
Sbjct: 203 SINPQEGISLAAKVLVEHLNLFIDLTEHVSSVEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++E DM+++ N G+KSL E+   L  +GL L
Sbjct: 263 YNCLKRAGINTVEELANKSEDDMMKVRNLGKKSLEEVIQKLEELGLGL 310


>gi|229917331|ref|YP_002885977.1| DNA-directed RNA polymerase subunit alpha [Exiguobacterium sp.
           AT1b]
 gi|229468760|gb|ACQ70532.1| DNA-directed RNA polymerase, alpha subunit [Exiguobacterium sp.
           AT1b]
          Length = 314

 Score =  238 bits (608), Expect = 8e-61,   Method: Compositional matrix adjust.
 Identities = 130/294 (44%), Positives = 190/294 (64%), Gaps = 12/294 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+TAVQIDGVLHE S+I GV ED+T I+LN+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTAVQIDGVLHEFSTIDGVVEDVTQIVLNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I     G VTA DI   +D+E+LNP+  I  L  +A +RM LT 
Sbjct: 83  KKLALKVYSEEEKTLEINVSSAGAVTAADITHDSDVEILNPELHIATLADNATLRMRLTA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYV A+ ++ ++ PIG+I ID++Y+PI++V+Y V+  R GQ   +DKL + + TDG
Sbjct: 143 RRGRGYVQAEDNKRDDMPIGVIPIDSIYTPIQRVNYEVDKTRVGQDASFDKLLLDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINF------EEPKKEVKEDINVKSLPFNPALLKKVEEL 263
           SI  E++V+L ++IL + L +F+         E   E +ED   K L         +EEL
Sbjct: 203 SIRPEEAVSLGAKILTEHLNIFVGLTDEALNAEIMVEKEEDQKEKVLEMT------IEEL 256

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E++  L  +GL L
Sbjct: 257 DLSVRSYNCLKRAGINTVQELANKSEEEMMKVRNLGRKSLEEVQHKLDELGLGL 310


>gi|283780399|ref|YP_003371154.1| DNA-directed RNA polymerase subunit alpha [Pirellula staleyi DSM
           6068]
 gi|283438852|gb|ADB17294.1| DNA-directed RNA polymerase, alpha subunit [Pirellula staleyi DSM
           6068]
          Length = 330

 Score =  238 bits (608), Expect = 8e-61,   Method: Compositional matrix adjust.
 Identities = 124/297 (41%), Positives = 188/297 (63%), Gaps = 4/297 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +AEP  RGF  T+GN+LRR+L+SSL G+AIT ++I G  HE ++I GV ED+TDI+LN+
Sbjct: 28  FVAEPFERGFGTTIGNSLRRILLSSLEGSAITQIKIRGAQHEFTTIPGVLEDVTDIVLNV 87

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + +K   +S + +T+ K   G++T  D+Q  +D+E++N +HV+  L  +    ME+ V
Sbjct: 88  KSLVVKNHSESTRVITVEKNTTGLITGADVQVDSDVEIINKNHVLATLTDNVPFMMEMVV 147

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GY+PA  H T +  IG+I IDA++SPI +V Y VE  R GQ  +YD+L++ I T+G
Sbjct: 148 ENGRGYIPATEHSTGDHEIGIIPIDAVFSPITRVRYEVEETRVGQKTNYDRLTLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK----VEELEL 265
           SI  E ++  +++IL+  L  F+ + E    V       S   + AL  K    + EL+L
Sbjct: 208 SIHPEMALVESAKILRKHLNPFVQYSELGPRVHAPSRGGSPVVDGALDGKLAMSLAELKL 267

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           SVR+ NCL  ENI  + DL+Q+TE  +L + NFG  +L E+K  L  +G++LGM +P
Sbjct: 268 SVRAMNCLESENIHTVRDLVQKTEDQLLEVRNFGETTLNEVKDKLHDLGMYLGMRVP 324


>gi|310659474|ref|YP_003937195.1| RNA polymerase subunit alpha [Clostridium sticklandii DSM 519]
 gi|308826252|emb|CBH22290.1| RNA polymerase, alpha subunit [Clostridium sticklandii]
          Length = 313

 Score =  238 bits (607), Expect = 9e-61,   Method: Compositional matrix adjust.
 Identities = 125/294 (42%), Positives = 193/294 (65%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           +EN      EPL RGF  T+GN+LRRVL+SSL G A+T++++DGVLHE S+I GV ED+T
Sbjct: 15  KENYGKFALEPLERGFGITVGNSLRRVLLSSLPGVAVTSIKVDGVLHEFSTIPGVKEDVT 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           ++IL +K +++KM  D  + + I   G GV+ AGDI    D+E+LN D  I  L  DA +
Sbjct: 75  ELILTLKELSMKMDSDGARTLKIEHTGEGVIKAGDIICPPDVEILNKDLHIATLSEDAKL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            ME+ V KG GYV A+++++++ PIG+I +D++Y+P+ KVSY  E+ R G   D+++L +
Sbjct: 135 YMEINVDKGRGYVSAENNKSDDMPIGVIPVDSIYTPVHKVSYLTENTRVGTRTDFERLVL 194

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            + TDGSI  ++ V+L ++IL + L +FI+  +   EV+  +  +      AL   +EEL
Sbjct: 195 EVWTDGSIGAQEGVSLGAKILVEHLNLFIDLTDHLGEVELMVEKEEDKKEKALEMTIEEL 254

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +LSVRS NCL+   I  + +L ++TE DM+++ N G+KSL E+   L  +G  L
Sbjct: 255 DLSVRSYNCLKRAGINTVEELTEKTEDDMMKVRNLGKKSLEEVIQKLEELGFSL 308


>gi|323126337|gb|ADX23634.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           dysgalactiae subsp. equisimilis ATCC 12394]
          Length = 312

 Score =  238 bits (607), Expect = 9e-61,   Method: Compositional matrix adjust.
 Identities = 123/288 (42%), Positives = 191/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+
Sbjct: 21  FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNV 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     +R  +TV
Sbjct: 81  KGLAVKSYVEDEKILELEVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLRATMTV 140

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 141 AKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 200

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  ED++ L++R+L + L +F +  +  K  +     + +     L + +E L+LSVRS
Sbjct: 201 TIIPEDALGLSARVLIEHLNLFTDLTDVAKATEVMKETEKVNDEKVLDRTIEVLDLSVRS 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + DL +++E +M+++ N GRKSL E+K  L  +GL L
Sbjct: 261 YNCLKRAGINTVFDLTEKSEPEMMKVRNLGRKSLEEVKVKLADLGLGL 308


>gi|5163231|gb|AAD40610.1|AF115283_29 RNA polymerase alpha-subunit [Leptospira interrogans]
          Length = 325

 Score =  238 bits (607), Expect = 9e-61,   Method: Compositional matrix adjust.
 Identities = 130/312 (41%), Positives = 200/312 (64%), Gaps = 4/312 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P  IE+        N    +AEP  RGFA T+GN+LRR LMSS+ GAAI+A++I+GV H
Sbjct: 12  RPKKIEFNTEANTP-NYGKFVAEPFERGFATTIGNSLRRTLMSSIEGAAISAIRIEGVNH 70

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMS---GDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           E S I+GV ED+T IILN+K + +K      D  K + +  +G G   AGD+   + IE+
Sbjct: 71  EFSFIEGVAEDVTRIILNLKQVRIKYEPEEKDQSKIIHLELKGAGYFRAGDLAVDSSIEI 130

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPD  I  L+ DA + M+L + +G GYVPA+  + + + +G I +D+++SP++KV + V
Sbjct: 131 MNPDLHIATLNEDANLVMDLEIQRGRGYVPAEEKKKDIEVLGTIPVDSIFSPVQKVVFEV 190

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
              R  Q  DY+KL++ + TDGS++ +D+VA A++IL++ L +FINFEE  +E  ++++ 
Sbjct: 191 SETRVAQRSDYEKLTLEVWTDGSVSPDDAVAQAAKILKEHLTVFINFEEELEEEDDELDE 250

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                  +L K VEELELS RS N LR   I ++GDL++R+E +M +  ++  + L E+K
Sbjct: 251 ADEKLKASLSKHVEELELSARSLNVLRSLEIDFIGDLVKRSEEEMSKSKHYSDQCLQELK 310

Query: 308 GVLGTMGLFLGM 319
             L T+GL  GM
Sbjct: 311 VKLSTLGLSFGM 322


>gi|196234320|ref|ZP_03133149.1| DNA-directed RNA polymerase, alpha subunit [Chthoniobacter flavus
           Ellin428]
 gi|196221587|gb|EDY16128.1| DNA-directed RNA polymerase, alpha subunit [Chthoniobacter flavus
           Ellin428]
          Length = 329

 Score =  238 bits (607), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 128/300 (42%), Positives = 181/300 (60%), Gaps = 13/300 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +AEP   G+ +T+GN+LRRVL+SSL GAAIT+V+I G  HE  ++  V +D+TDI+LN+
Sbjct: 19  FVAEPFEAGYGNTIGNSLRRVLLSSLEGAAITSVKITGAQHEFQTLPHVVDDVTDIVLNL 78

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K +  K +    + +TI     G VTAGDI+  +  EVLN D +IC LD       EL V
Sbjct: 79  KKVKFKANDHEIRNLTINVNKEGAVTAGDIEDSSQCEVLNKDQIICTLDKKTKFEAELEV 138

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G G+     ++  + PIG+I ID+++SP+ +V YTV + R GQ  DYDKL + I TDG
Sbjct: 139 KVGRGFSTGDENKHPDQPIGVIAIDSIFSPVTRVKYTVGNTRVGQRTDYDKLELEIWTDG 198

Query: 210 SITGEDSVALASRILQDQLGMFINFEE--------PKKEVKEDINVKSLPFNPALLKKVE 261
            +T E+++  AS IL+     F  ++E        P+ + +E+  +K L     L   V 
Sbjct: 199 RLTPEEALVQASSILKKHFEPFYAYDENAVQFDETPQAQSQENQKMKKL-----LNMSVN 253

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           E+ELSVR+ NCL   NI  +G L  +TEA+ML+  NFG+KSL EIK  L  +GL LGM  
Sbjct: 254 EIELSVRAANCLNNANITTVGQLAMKTEAEMLKYRNFGKKSLNEIKDKLTQLGLSLGMKF 313


>gi|126697669|ref|YP_001086566.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           630]
 gi|254973760|ref|ZP_05270232.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           QCD-66c26]
 gi|255091150|ref|ZP_05320628.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           CIP 107932]
 gi|255099261|ref|ZP_05328238.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           QCD-63q42]
 gi|255305044|ref|ZP_05349216.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           ATCC 43255]
 gi|255312804|ref|ZP_05354387.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           QCD-76w55]
 gi|255515563|ref|ZP_05383239.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           QCD-97b34]
 gi|255648658|ref|ZP_05395560.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           QCD-37x79]
 gi|260681875|ref|YP_003213160.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           CD196]
 gi|260685473|ref|YP_003216606.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           R20291]
 gi|306518780|ref|ZP_07405127.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           QCD-32g58]
 gi|119366674|sp|Q18CI5|RPOA_CLOD6 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|115249106|emb|CAJ66917.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile]
 gi|260208038|emb|CBA60238.1| DNA-directed RNA polymerase alpha chain [Clostridium difficile
           CD196]
 gi|260211489|emb|CBE01629.1| DNA-directed RNA polymerase alpha chain [Clostridium difficile
           R20291]
          Length = 315

 Score =  238 bits (607), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 123/288 (42%), Positives = 190/288 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  T+GNALRR+L+SSL G A+ A++IDGVLHE S+I GV ED+T+IIL +
Sbjct: 23  FVIEPLERGYGITIGNALRRILLSSLPGVAVNAIKIDGVLHEFSTIPGVKEDVTEIILTL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K ++  + G+  + + I  +GP  +T  DI    D+E+L+ D  I  LD +A + ME+ V
Sbjct: 83  KELSATIDGEGSRTLKIEAQGPCSITGADIICPPDVEILSKDLAIATLDDNAKLNMEIFV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYV A+ ++TEN PIG++ +D++Y+P++KVSY VE+ R GQ  DYDKL + + T+G
Sbjct: 143 DKGRGYVSAEENKTENVPIGVLPVDSIYTPVEKVSYHVENTRVGQKTDYDKLVLEVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  ++ ++LA+++L + L +FI+  E    V+  +  +       L   +EEL+LSVRS
Sbjct: 203 SINPQEGISLAAKVLVEHLNLFIDLTEHVSSVEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++E DM+++ N G+KSL E+   L  +GL L
Sbjct: 263 YNCLKRAGINTVEELANKSEDDMMKVRNLGKKSLEEVIQKLEELGLGL 310


>gi|317501801|ref|ZP_07959987.1| DNA-directed RNA polymerase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331088678|ref|ZP_08337588.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae
           bacterium 3_1_46FAA]
 gi|316896834|gb|EFV18919.1| DNA-directed RNA polymerase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330407201|gb|EGG86704.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae
           bacterium 3_1_46FAA]
          Length = 320

 Score =  238 bits (606), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 129/293 (44%), Positives = 196/293 (66%), Gaps = 5/293 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL G+AI++V+IDGVLHE SSI GV ED+T+II+N+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGSAISSVKIDGVLHEFSSIPGVKEDVTEIIMNL 82

Query: 90  KGINLK-MS-GDSHKRVTIFKRGPGVVTAGDIQTVN-DIEVLNPDHVICNLD--VDAVVR 144
           K + ++ MS  D  K V I   G GVVT  DI   + DIE++NPD VI  L    D  + 
Sbjct: 83  KSLAIRNMSESDEPKTVYIEFEGEGVVTGADININDPDIEIVNPDQVIATLSGGKDCRLN 142

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MELT++KG GYV +  ++TE+ PIG+I ID++Y+P+++V+ TVE+ R GQ+ DYDKL++ 
Sbjct: 143 MELTITKGRGYVSSDKNKTEDMPIGVIAIDSIYTPVERVNLTVENTRVGQITDYDKLTLD 202

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           + T G++  +++V+LA+++L + L +F++  E  +  +  I  +       L   ++ELE
Sbjct: 203 VWTKGTMLPDEAVSLAAKVLSEHLKLFVDLSEVAQVAEVMIEKEDDEKEKVLEMSIDELE 262

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LSVRS NCL+   I  + +L  +T  DM+++ N GRKSL E+   L  + L L
Sbjct: 263 LSVRSYNCLKRAGINTVEELTNKTPEDMMKVRNLGRKSLEEVLAKLKELNLEL 315


>gi|313895218|ref|ZP_07828775.1| DNA-directed RNA polymerase, alpha subunit [Selenomonas sp. oral
           taxon 137 str. F0430]
 gi|320529823|ref|ZP_08030900.1| DNA-directed RNA polymerase, alpha subunit [Selenomonas artemidis
           F0399]
 gi|312976113|gb|EFR41571.1| DNA-directed RNA polymerase, alpha subunit [Selenomonas sp. oral
           taxon 137 str. F0430]
 gi|320137841|gb|EFW29746.1| DNA-directed RNA polymerase, alpha subunit [Selenomonas artemidis
           F0399]
          Length = 319

 Score =  238 bits (606), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 131/300 (43%), Positives = 189/300 (63%), Gaps = 20/300 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL  G+  T GN+LRR+L+SSL GAA+T++QIDGVLHE S+I GV +D+T I+LNI
Sbjct: 23  FVCEPLEPGYGTTFGNSLRRMLLSSLEGAAVTSIQIDGVLHEFSTIPGVRDDVTSIVLNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM G     + I   G   VTA DI+  +DIE+LNP+  I  L+    +++E+TV
Sbjct: 83  KQLCLKMQGSDPHTIRIDVAGEREVTAADIECGSDIEILNPELHIATLNATGKLKIEMTV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYVPA  ++  +D IG+I ID+++SP+ +V+YTVE  R G V DYD+L + + T+G
Sbjct: 143 ERGRGYVPADKNKKPDDSIGVIPIDSIFSPVHRVNYTVEDTRVGNVTDYDRLILDVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEE------------PKKEVKEDINVKSLPFNPALL 257
           SI  E++V+ A+ IL   L +F N +             P +EV +   V        L 
Sbjct: 203 SIRPEEAVSKAAAILVMHLRLFQNMDGNVVEEEEEVANFPPEEVDDSAKV--------LE 254

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +++L+LSVRS NCL+   I  + DL Q+TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 255 MTIDDLDLSVRSFNCLKRAGINSVADLTQKTEEDMMKVRNLGRKSLDEVKKKLEELGLSL 314


>gi|320103642|ref|YP_004179233.1| DNA-directed RNA polymerase subunit alpha [Isosphaera pallida ATCC
           43644]
 gi|319750924|gb|ADV62684.1| DNA-directed RNA polymerase subunit alpha [Isosphaera pallida ATCC
           43644]
          Length = 335

 Score =  238 bits (606), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 128/300 (42%), Positives = 186/300 (62%), Gaps = 10/300 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EP  RGF HT+GN+LRR+L+SSL G+A+T ++I+GV HE SSI G+ ED+TD++LN+
Sbjct: 28  FVIEPFERGFGHTVGNSLRRILLSSLEGSAVTRIKIEGVQHEFSSIPGMVEDITDLVLNL 87

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   D  K + I +   G+VTA DI     IEV+NPDH++C L  DA + M +TV
Sbjct: 88  KGLIVKNHSDQPKTIVIERDREGIVTAADIVHDETIEVVNPDHILCTLSGDARLHMRMTV 147

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GY PA    TE+   G I IDA++SP+++V Y VE  R GQ  ++DKL M I T G
Sbjct: 148 ENGRGYRPAAEGHTEDLEPGAIPIDAIFSPVQRVEYRVEETRVGQKTNFDKLIMRIWTTG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEV------KEDINVKSLPFNPALLKKVE-- 261
           +I  + ++  A++IL+  L  F+ + EP   +        DI     P +  L +K+   
Sbjct: 208 TIRPDMALVEAAKILRKHLNPFVQYFEPGPGLPAEGSGPADIGRGLEPHDAELERKLNMS 267

Query: 262 --ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
             ELELSVR+TNCL  E I  + +L+ R+E  +L + NFG  +L E++  L  +G+ LGM
Sbjct: 268 LAELELSVRATNCLESEGITTIRELVSRSEEQLLTVRNFGETTLKEVRSKLNDLGIDLGM 327


>gi|302336353|ref|YP_003801560.1| DNA-directed RNA polymerase subunit alpha [Olsenella uli DSM 7084]
 gi|301320193|gb|ADK68680.1| DNA-directed RNA polymerase subunit alpha [Olsenella uli DSM 7084]
          Length = 313

 Score =  238 bits (606), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 131/317 (41%), Positives = 197/317 (62%), Gaps = 11/317 (3%)

Query: 6   WQELIKPN-NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
             E I+P  ++E I      EN   + AEPL RG+  TLGN+LRRVL+SSL GAA+ A+Q
Sbjct: 1   MSEFIRPQVSVEEI-----SENLARVSAEPLERGYGDTLGNSLRRVLLSSLEGAAVEAIQ 55

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLK-MSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           IDGV HE ++++GV+ED+TDI+LN+KG+  + M        +I   GP  VT GD +   
Sbjct: 56  IDGVQHEFTTVEGVYEDVTDIVLNVKGLVFRSMGTGDEATASISIDGPCTVTGGDFKVPA 115

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           + E++N D VIC L   A + M++ +  G GYV    +  + DPIG+I +D+LYSP+++ 
Sbjct: 116 EFELVNEDQVICTLGEGAHLSMQMRIGTGRGYVAGDDNERDGDPIGIIHVDSLYSPVRRC 175

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +  VE  R GQ  +YD+L + ++TDGSIT  D+V  A+ I+   +  F+   + ++ V E
Sbjct: 176 AKAVEPCRVGQHTNYDRLVLEVETDGSITPRDAVVDAANIVNQHMSAFMALADEEEPV-E 234

Query: 244 DINVKSLPF---NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           D ++ +      N  L K++E+L+LSVRS NCL+   I  +  L++ +E D+L + NFG 
Sbjct: 235 DASIFATGVEEDNTELDKQIEDLDLSVRSYNCLKRAGIHSVRQLVEFSENDLLNIRNFGV 294

Query: 301 KSLVEIKGVLGTMGLFL 317
           KS+ E+K  L TMGL L
Sbjct: 295 KSIEEVKDKLETMGLGL 311


>gi|255283705|ref|ZP_05348260.1| DNA-directed RNA polymerase, alpha subunit [Bryantella
           formatexigens DSM 14469]
 gi|255265770|gb|EET58975.1| DNA-directed RNA polymerase, alpha subunit [Bryantella
           formatexigens DSM 14469]
          Length = 375

 Score =  237 bits (605), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 124/292 (42%), Positives = 193/292 (66%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL GAA++ V+I+GVLHE SSI GV ED+++II+N+
Sbjct: 79  FVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIEGVLHEFSSIPGVKEDVSEIIMNL 138

Query: 90  KGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           K + +K +  ++  K   I   G GVVTA DIQ   DIE+LN D +I  L    D+ + M
Sbjct: 139 KSLAIKNTSKTNEPKVAYIEYDGEGVVTAADIQVDQDIEILNKDQIIATLSGGPDSKLYM 198

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           E+T++KG GY+ A   +T + PIG+I +D++Y+P+++V+ TVE+ R  Q  D+DKL++ +
Sbjct: 199 EITITKGRGYISADEGKTPDMPIGVIAVDSIYTPVERVNMTVENTRVAQATDFDKLTLDV 258

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  +++V+LA+++L + L +FI+  E  K  +  I  +       L   ++ELEL
Sbjct: 259 YTNGTLAPDEAVSLAAKVLSEHLSLFIDLSESAKTAEIMIEKEDNEKEKVLEMNIDELEL 318

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L
Sbjct: 319 SVRSYNCLKRAGINTVEELCNRTPEDMMKVRNLGRKSLEEVLAKLKELGLQL 370


>gi|146329031|ref|YP_001210127.1| DNA-directed RNA polymerase, alpha subunit [Dichelobacter nodosus
           VCS1703A]
 gi|158513303|sp|A5EX94|RPOA_DICNV RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|146232501|gb|ABQ13479.1| DNA-directed RNA polymerase, alpha subunit [Dichelobacter nodosus
           VCS1703A]
          Length = 320

 Score =  237 bits (605), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 133/320 (41%), Positives = 200/320 (62%), Gaps = 8/320 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           EL+ P  ++   +G      TL   EPL RGF +TLG ALRRVL+SS+ GAAIT  QIDG
Sbjct: 5   ELLTPRIVQIKEIGSNTSRVTL---EPLERGFGYTLGTALRRVLLSSIEGAAITECQIDG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE S+I+GV ED+ D++LN+K I L M       + +     G +TAGD +    +E+
Sbjct: 62  VSHEYSAIEGVKEDVIDVLLNLKNIALLMPDLERAEIRLSVTEKGAITAGDFELPAGVEI 121

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGY--VPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +NPD VI +L  D    +   V KG GY   P     +E+    ++ +DA +SP+++++Y
Sbjct: 122 VNPDCVIAHLTRDIPFSLTAVVEKGRGYRVAPQADDNSESTRSNVLRLDASFSPVRRIAY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE AR  Q  D DKL + I+++G+I  E ++  A+ IL +Q+ +F++ E  ++E +E+ 
Sbjct: 182 RVEQARVEQRTDLDKLIIEIESNGTIDPEQAIRDAATILHNQIKVFVDLESTEEETEEEE 241

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            +     +P LL+ V++LEL+VRS NCL+ ENI  +GDL++RTE ++L+  N G+KSL E
Sbjct: 242 EIY---IDPVLLRPVDDLELTVRSANCLKAENINNIGDLVRRTEVELLKTPNLGKKSLNE 298

Query: 306 IKGVLGTMGLFLGMNLPDWP 325
           IK VL    L LGM++ +WP
Sbjct: 299 IKEVLAAHNLELGMDIENWP 318


>gi|291532118|emb|CBK97703.1| DNA-directed RNA polymerase subunit alpha [Eubacterium siraeum
           70/3]
 gi|291558142|emb|CBL35259.1| DNA-directed RNA polymerase subunit alpha [Eubacterium siraeum
           V10Sc8a]
          Length = 319

 Score =  237 bits (605), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 132/294 (44%), Positives = 197/294 (67%), Gaps = 7/294 (2%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
           +   EPL  G+ +TLGN+LRRVL+SSL G A+T+V+IDGV HE S+I GV ED+T+IILN
Sbjct: 23  MFTLEPLECGYGNTLGNSLRRVLLSSLPGVAVTSVKIDGVQHEFSTIPGVKEDVTEIILN 82

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           IKG+  KM G+  K V I   G   VTAGDI+T ++IE+L+P   I  L   A + ME+T
Sbjct: 83  IKGLIAKMYGECPKTVYIEAEGECDVTAGDIKTDSEIEILDPGMHIATLGPGAKLYMEIT 142

Query: 149 VSKGHGYVPAKHHRTENDP-IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           + KG GYV A+ ++ +  P IG+I +D++Y+P+ KV+YTVE+ R GQ  DYDKL + + T
Sbjct: 143 LDKGRGYVSAEKNKQQLQPVIGIIAVDSIYTPVLKVNYTVENTRVGQRTDYDKLILEVWT 202

Query: 208 DGSITGEDSVALASRILQDQLGMFINF--EEPKKEVKEDINVKSLPFNPALLK-KVEELE 264
           DG+I+ +++V+ A+++L D L  F+    E  + E+  D   KS      LL+  +++L+
Sbjct: 203 DGTISAKEAVSYAAKLLVDHLQPFVELSDEAIQPELMAD---KSESGKDKLLEMTIDDLD 259

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LSVRS NCL+  NI  + DLI +++ DM+++ N G+KS  E++  L ++G  L 
Sbjct: 260 LSVRSFNCLKRANINTVDDLINKSQGDMMKVRNLGKKSFEEVRAKLQSLGFDLA 313


>gi|289449938|ref|YP_003475756.1| DNA-directed RNA polymerase subunit alpha [Clostridiales genomosp.
           BVAB3 str. UPII9-5]
 gi|289184485|gb|ADC90910.1| DNA-directed RNA polymerase, alpha subunit [Clostridiales genomosp.
           BVAB3 str. UPII9-5]
          Length = 321

 Score =  237 bits (605), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 124/291 (42%), Positives = 192/291 (65%), Gaps = 2/291 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+TA++++G  HE S+++GV ED+T+IILN+
Sbjct: 23  FVVEPLDRGYGVTLGNSLRRVLLSSLPGAAVTAIRVEGAFHEFSTVEGVIEDMTEIILNV 82

Query: 90  KGINLKMSGDSHKRVTI-FKRG-PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K I +K++ D  K + +  + G  GVVTAGDI T  +++++NP+  I  L+ DA + MEL
Sbjct: 83  KCIRVKLNADGPKTIYLNTEEGRTGVVTAGDIVTDEEVQIMNPEQPIATLNGDARLFMEL 142

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           TV  G GY  A+ ++  N PIG+I +D++++P+KKV+Y+VE+ R GQ  D+DKL++ + T
Sbjct: 143 TVCSGIGYNSAERNKWPNQPIGVIPVDSIFTPVKKVNYSVENTRVGQFTDFDKLTLEVWT 202

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           D +I  + +V+ A+ IL D L  F++ +             S   N  L   +E++  SV
Sbjct: 203 DRTIAADTAVSNAANILMDHLQYFVDLQGGPTGTGTRSYDGSGESNELLETAIEDMNFSV 262

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           R+ NCL+   I  +GDL+ R+E DM+++ N G+KSL E+  +L  MGL L 
Sbjct: 263 RTYNCLKRAGINVIGDLVIRSEDDMMKVRNLGKKSLEEVIQILDEMGLSLA 313


>gi|300770225|ref|ZP_07080104.1| DNA-directed RNA polymerase subunit alpha [Sphingobacterium
           spiritivorum ATCC 33861]
 gi|300762701|gb|EFK59518.1| DNA-directed RNA polymerase subunit alpha [Sphingobacterium
           spiritivorum ATCC 33861]
          Length = 330

 Score =  237 bits (605), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 127/298 (42%), Positives = 190/298 (63%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AIT+++  GV HE S+IKGV ED+T+IILN+K I 
Sbjct: 28  PLEPGFGVTIGNALRRILLSSLEGYAITSIRFSGVSHEFSTIKGVVEDVTEIILNLKQIR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQTV-NDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K +G+    +++ +   G     AGDI    N+  VLNPD V+CN+D    + +EL+V+
Sbjct: 88  FKKTGEQGDSEKIFVVINGQEQFLAGDITKFSNNFTVLNPDFVVCNMDSSVTIEVELSVA 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYV A+ ++  + P+GLI ID++++PIK V YT+E+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVNAEENKVTDGPVGLIAIDSIFTPIKNVKYTIENYRVEQKTDYEKLLLDITTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ED++  A++IL     +F +     E   KE  + ++ + L     L  ++ +L+LS
Sbjct: 208 IHPEDALKEAAKILIQHFMLFSDENMLLESQTKEETKVVDEEILHMRKILKTELVDLDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  +I  + +L+    ADML+  NFG+KSL EI+ ++ + GL  GMNL  +
Sbjct: 268 VRALNCLKAADIRTLAELVTYDVADMLKFRNFGKKSLSEIQELVKSKGLSFGMNLSKF 325


>gi|225175646|ref|ZP_03729640.1| DNA-directed RNA polymerase, alpha subunit [Dethiobacter
           alkaliphilus AHT 1]
 gi|225168975|gb|EEG77775.1| DNA-directed RNA polymerase, alpha subunit [Dethiobacter
           alkaliphilus AHT 1]
          Length = 314

 Score =  237 bits (605), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 140/319 (43%), Positives = 206/319 (64%), Gaps = 14/319 (4%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE +   ++  + T +I EPL RG+  TLGNALRR+L+SSL GAA+T V+I+ 
Sbjct: 3   EIEKPR-IERVDSNEDNTHGTFVI-EPLERGYGITLGNALRRILLSSLPGAAVTNVKIEN 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED T+IILN+K + +K+  D  + + +   G GVVTAGDI+   D+EV
Sbjct: 61  VLHEFSTIPGVLEDTTEIILNLKQLAMKIHSDEPQTLVVVAAGQGVVTAGDIKLPADVEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L+    + MELT   G GYVPA+ ++    PIG+I +D+L++PI++V+Y V
Sbjct: 121 LNPDMHIATLEEGGRLYMELTAVNGRGYVPAERNKEPGQPIGVIAVDSLFAPIQRVNYKV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK----- 242
           E+ R GQ  DYDKL+M + TDGSI  +++++L ++IL   LG+F+N  E   EV+     
Sbjct: 181 ENTRVGQHTDYDKLTMDVWTDGSIRPDEAISLGAKILSKHLGLFVNLTEKVDEVEILDEK 240

Query: 243 -EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ED   K +         +EEL+LSVRS NCL+   I  + +L+ ++E +M+++ N G+K
Sbjct: 241 DEDDKTKVMEMT------IEELDLSVRSYNCLKRAGINTVQELVNKSEDEMMKVRNLGKK 294

Query: 302 SLVEIKGVLGTMGLFLGMN 320
           SL E++  L  + L L  N
Sbjct: 295 SLEEVQHKLEELQLNLRDN 313


>gi|224477194|ref|YP_002634800.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus carnosus
           subsp. carnosus TM300]
 gi|222421801|emb|CAL28615.1| DNA-directed RNA polymerase alpha chain [Staphylococcus carnosus
           subsp. carnosus TM300]
          Length = 314

 Score =  237 bits (604), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 125/288 (43%), Positives = 190/288 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+GVLHE S+I  V ED++ II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEGVLHEFSAIDNVVEDVSTIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  +  G VTA DI   +D+E+LNP+  I  +     +++ L  
Sbjct: 83  KELALKIYSEEDKTLEIDVKDEGEVTAADITHDSDVEILNPELKIATVSKGGHLKIRLVA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTVE+ R GQ  D+DKL++ + TDG
Sbjct: 143 NKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTVENTRVGQSSDFDKLTLDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SIT ++SV+LA++IL + L +F+   +  K  +  I  +       L   +EEL+LSVRS
Sbjct: 203 SITPQESVSLAAKILTEHLNIFVGLTDEAKNAEIMIEKEEDQKEKVLEMSIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++EADM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELADKSEADMMKVRNLGRKSLEEVKYKLEDLGLGL 310


>gi|325108639|ref|YP_004269707.1| DNA-directed RNA polymerase subunit alpha [Planctomyces
           brasiliensis DSM 5305]
 gi|324968907|gb|ADY59685.1| DNA-directed RNA polymerase subunit alpha [Planctomyces
           brasiliensis DSM 5305]
          Length = 338

 Score =  237 bits (604), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 128/328 (39%), Positives = 199/328 (60%), Gaps = 12/328 (3%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           W+ L  PN + +I       N    +AEP  RGF  T+GN+LRR+L+SSL G+++T V+I
Sbjct: 5   WRGLELPNRL-FIDRETATPNYGKFVAEPFERGFGSTIGNSLRRILLSSLEGSSVTRVKI 63

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
            G  HE ++I GV ED+TDI LN+K + +K      K + I K   GVVT  D+   + +
Sbjct: 64  QGAQHEFTTIPGVVEDVTDICLNLKSLIVKSYAAGPKTIRIEKHTRGVVTGADVIADDQV 123

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EV+N D VI  +  D  + +ELTV  G GY+PA  H   +  +G+I +DALYSP+++V++
Sbjct: 124 EVINKDMVIATMTDDVPLSLELTVENGRGYIPASEHFDRDPEVGVIPLDALYSPVERVNF 183

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE  R GQ  +YDKL + I T+G+++ E ++  +++I++  L  FI + EP  EV  D 
Sbjct: 184 QVEETRVGQRTNYDKLILEIWTNGTVSPEMALVESAKIMRKHLNPFITYREPGPEVSPDG 243

Query: 246 NVKSL-------PFNPALLKKVE----ELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
            ++ +       P +  L +K+     EL LSVR+TNCL  E IV + DL+ ++E  +L+
Sbjct: 244 GLQGMAEATGHSPIDLELEEKLNQSLAELNLSVRATNCLESEGIVTVRDLVSKSEDQLLQ 303

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           + NFG  +L E++  L ++GL +GM +P
Sbjct: 304 VRNFGETTLQEVRERLSSIGLRMGMKMP 331


>gi|58416042|emb|CAH57435.1| RNA polymerase alpha-subunit [Vibrio sp. R-21432]
          Length = 287

 Score =  237 bits (604), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 121/267 (45%), Positives = 184/267 (68%), Gaps = 8/267 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 22  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 81

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 82  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 141

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 142 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMET 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 202 NGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 258

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLR 294
           RS NCL+ E I Y+GDL+QRTE ++L+
Sbjct: 259 RSANCLKAEAIHYIGDLVQRTEVELLK 285


>gi|238916292|ref|YP_002929809.1| DNA-directed RNA polymerase subunit alpha [Eubacterium eligens ATCC
           27750]
 gi|238871652|gb|ACR71362.1| DNA-directed RNA polymerase subunit alpha [Eubacterium eligens ATCC
           27750]
          Length = 322

 Score =  237 bits (604), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 125/294 (42%), Positives = 200/294 (68%), Gaps = 3/294 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL G A+++++I+GVLHE SSI GV ED+T+I++NI
Sbjct: 27  FVVEPLERGYGLTLGNSLRRIMLSSLVGTAVSSIKIEGVLHEFSSIPGVKEDVTEIVMNI 86

Query: 90  KGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVVRME 146
           K +++K +G+S   K   I   G GVV A DIQ   DIE++NPD VI +L+  D+ + ME
Sbjct: 87  KQLSIKNNGNSVEPKEAHIDFVGEGVVRASDIQVDPDIEIINPDLVIAHLNGADSKLTME 146

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           LT++ G GYV ++ ++ ++ P G+I ID++Y+P+++V+  V++ R GQ  D+DKL++ I 
Sbjct: 147 LTITNGRGYVSSEKNKRDDQPAGVIAIDSIYTPVERVNMAVQNTRVGQDTDFDKLTLDIF 206

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+G+I  +++++LA+++L + L  FIN  E  ++V+  +  +       L   +E+LELS
Sbjct: 207 TNGTIEPDEALSLAAKVLSEHLKGFINLSENAQKVEIMVEQEEDETTKVLSMSIEDLELS 266

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           VRS+NCLR   I  + +L  +T  DM+++ N G+KSL E+   L  MGL L  N
Sbjct: 267 VRSSNCLRRAGINTVEELCNKTSDDMMKVRNLGKKSLDEVLLKLKEMGLHLRPN 320


>gi|329768299|ref|ZP_08259800.1| DNA-directed RNA polymerase subunit alpha [Gemella haemolysans
           M341]
 gi|328837498|gb|EGF87127.1| DNA-directed RNA polymerase subunit alpha [Gemella haemolysans
           M341]
          Length = 313

 Score =  237 bits (604), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 127/284 (44%), Positives = 181/284 (63%), Gaps = 12/284 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA  ++ I+GV HE  +IKGV ED+T+II+N+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRMLISSLPGAAARSIDIEGVQHEFQAIKGVVEDVTEIIMNV 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I   +  +  K+V+I  +GP VVTA DI   +DIEV+N D  I  +       M + V
Sbjct: 83  KNIAFVVHSEEEKQVSISVKGPAVVTAADIAIDSDIEVVNTDQHIATVSEGGQFEMIIYV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG G+VPA  ++  + PIG+I ID++Y+P+ KV+YTVE  R GQ  D+DKL + + T+G
Sbjct: 143 GKGRGFVPADGNKKRDLPIGVIPIDSIYTPVSKVNYTVEKTRVGQSTDFDKLILDVTTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEV------KEDINVKSLPFNPALLKKVEEL 263
           SIT  D++ALAS+IL   L +F+   E  K        +ED  V+ L         +EEL
Sbjct: 203 SITANDALALASKILISHLELFMEMSEEAKAAEILVAKEEDNKVQMLEMT------IEEL 256

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +LSVRS NCL+   I  + +L  +TE +M+++ N GRKSL E+K
Sbjct: 257 DLSVRSYNCLKRAGINTVQELASKTEQEMIKVRNLGRKSLEEVK 300


>gi|170017919|ref|YP_001728838.1| DNA-directed RNA polymerase alpha chain [Leuconostoc citreum KM20]
 gi|169804776|gb|ACA83394.1| DNA-directed RNA polymerase alpha chain [Leuconostoc citreum KM20]
          Length = 314

 Score =  237 bits (604), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 133/312 (42%), Positives = 193/312 (61%), Gaps = 10/312 (3%)

Query: 8   ELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           E  KPN  NIE      E+ +    + EPL RG+  TLGN+LRR+L+SSL GAA+  VQI
Sbjct: 3   EFEKPNIHNIE------EDAHYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGV+HE S++ GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+Q   D+
Sbjct: 57  DGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDVQGPADVTAADLQAGADV 116

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKV 183
           EVLNPD  I  +     + M +T  KG GY  A  ++   D  PIG++ +D++Y+PI++V
Sbjct: 117 EVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSADENKQLRDEMPIGVLAVDSIYTPIERV 176

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+ R G   DYDKL+  I T+GSI   D+++L S+IL + L +F++      E   
Sbjct: 177 NYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSLGSKILAEHLNLFMDISPVAAEANV 236

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  + +  + +    +E+L+LSVRS NCL+   I  + +L  RTEADM+++ N GRKSL
Sbjct: 237 MVEAEPVAASASDSAPIEDLDLSVRSYNCLKRAGINTIVELTDRTEADMMKVRNLGRKSL 296

Query: 304 VEIKGVLGTMGL 315
            EI+  L  MGL
Sbjct: 297 DEIQEKLTEMGL 308


>gi|241888925|ref|ZP_04776229.1| DNA-directed RNA polymerase, alpha subunit [Gemella haemolysans
           ATCC 10379]
 gi|241864174|gb|EER68552.1| DNA-directed RNA polymerase, alpha subunit [Gemella haemolysans
           ATCC 10379]
          Length = 313

 Score =  237 bits (604), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 127/284 (44%), Positives = 181/284 (63%), Gaps = 12/284 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA  ++ I+GV HE  +IKGV ED+T+II+N+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRMLISSLPGAAARSIDIEGVQHEFQAIKGVVEDVTEIIMNV 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I   +  +  K+V+I  +GP VVTA DI   +DIEV+N D  I  +       M + V
Sbjct: 83  KNIAFVVHSEEEKQVSISVKGPAVVTAADIAIDSDIEVVNTDQHIATVSEGGQFEMIIYV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG G+VPA  ++  + PIG+I ID++Y+P+ KV+YTVE  R GQ  D+DKL + + T+G
Sbjct: 143 GKGRGFVPADGNKKRDLPIGVIPIDSIYTPVSKVNYTVEKTRVGQSTDFDKLILDVTTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEV------KEDINVKSLPFNPALLKKVEEL 263
           SIT  D++ALAS+IL   L +F+   E  K        +ED  V+ L         +EEL
Sbjct: 203 SITANDALALASKILISHLELFMEMSEEAKAAEILVAKEEDNKVQMLEMT------IEEL 256

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +LSVRS NCL+   I  + +L  +TE +M+++ N GRKSL E+K
Sbjct: 257 DLSVRSYNCLKRAGINTVQELANKTEQEMIKVRNLGRKSLEEVK 300


>gi|164686554|ref|ZP_02210582.1| hypothetical protein CLOBAR_00121 [Clostridium bartlettii DSM
           16795]
 gi|164604423|gb|EDQ97888.1| hypothetical protein CLOBAR_00121 [Clostridium bartlettii DSM
           16795]
          Length = 315

 Score =  236 bits (603), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 121/288 (42%), Positives = 192/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  T+GNALRR+L+SSL G A+ +++IDGVLHE S+I GV ED+T+IIL++
Sbjct: 23  FVVEPLERGYGITIGNALRRILLSSLPGVAVNSIKIDGVLHEFSTIPGVKEDVTEIILSL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K ++  + G+  + + I  +GP  +   DI    D+E+L+ D  I  LD +A + ME+ V
Sbjct: 83  KELSATIDGEGSRTLKIEAQGPCSIKGSDIICPPDVEILSKDLHIATLDDNAKLNMEIYV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYVPA+ ++T+N PIG++ +D++Y+P++KVSY VE+ R GQ  DYDKL++ + T+G
Sbjct: 143 DKGRGYVPAEENKTDNMPIGVLPVDSIYTPVEKVSYHVENTRVGQKSDYDKLTLEVMTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  ++ ++LA+++L + L +FI+  E    V+  +  +       L   +EEL+LSVRS
Sbjct: 203 SINPQEGISLAAKVLVEHLNLFIDLTEHVSNVEIMVEKEEDQKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++E DM+++ N G+KSL E+   L  +GL L
Sbjct: 263 YNCLKRAGINTVEELANKSEDDMMKVRNLGKKSLEEVIQKLEELGLGL 310


>gi|326799155|ref|YP_004316974.1| DNA-directed RNA polymerase subunit alpha [Sphingobacterium sp. 21]
 gi|326549919|gb|ADZ78304.1| DNA-directed RNA polymerase subunit alpha [Sphingobacterium sp. 21]
          Length = 330

 Score =  236 bits (603), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 128/298 (42%), Positives = 191/298 (64%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AIT+V+  GV HE S+I GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGVTIGNALRRILLSSLEGYAITSVRFSGVSHEFSTITGVVEDVTEIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K +G+S   +++ +   G     AGDI +  N+  VLNPD VICN++    + +ELTV+
Sbjct: 88  FKKTGESGDSEKIFVVINGQDQFKAGDITSHSNNFTVLNPDLVICNMESSVTLEVELTVN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYV A+ ++  +  +G+I ID++Y+PIK V YT+E+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVNAEENKVADAAVGVIAIDSIYTPIKNVKYTIENFRVEQKTDYEKLLLDISTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ED++  A++IL     +F    I  E   KE  ++++ + L     L  ++ +L+LS
Sbjct: 208 IHPEDALKEAAKILIHHFMLFSDENILLESQTKEETKEVDEEILHMRKILKTELVDLDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  +I  + +L+    ADML+  NFG+KSL EI+ ++ + GL  GMNL  +
Sbjct: 268 VRALNCLKAADIRSLAELVSYDVADMLKFRNFGKKSLTEIQELVKSKGLSFGMNLSKY 325


>gi|296111454|ref|YP_003621836.1| DNA-directed RNA polymerase alpha subunit [Leuconostoc kimchii
           IMSNU 11154]
 gi|295832986|gb|ADG40867.1| DNA-directed RNA polymerase alpha subunit [Leuconostoc kimchii
           IMSNU 11154]
          Length = 314

 Score =  236 bits (603), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 131/312 (41%), Positives = 193/312 (61%), Gaps = 10/312 (3%)

Query: 8   ELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           E  KPN  NIE      E++     + EPL RG+  TLGN+LRR+L+SSL GAA+  VQI
Sbjct: 3   EFEKPNIHNIE------EDDRYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGV+HE S++ GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+Q   D+
Sbjct: 57  DGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDVQGPADVTAADLQAGADV 116

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKV 183
           E+LNPD  +  +     + M +T  KG GY  A  ++   D  PIG++ +D++Y+PI++V
Sbjct: 117 EILNPDLHLATVAAGKSLHMTVTAVKGRGYSSADENKQLRDEMPIGVLAVDSIYTPIERV 176

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+ R G   DYDKL+  I T+GSI   D+++L S+IL + L +F++      E   
Sbjct: 177 NYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSLGSKILAEHLNLFMDISPVAAEASV 236

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  + +  N +    +E+L+LSVRS NCL+   I  + +L  RTEADM+++ N GRKSL
Sbjct: 237 MVEAEPVATNASDSAPIEDLDLSVRSYNCLKRAGINTIVELTDRTEADMMKVRNLGRKSL 296

Query: 304 VEIKGVLGTMGL 315
            EI+  L  MG+
Sbjct: 297 DEIQEKLTEMGI 308


>gi|227538692|ref|ZP_03968741.1| DNA-directed RNA polymerase [Sphingobacterium spiritivorum ATCC
           33300]
 gi|227241611|gb|EEI91626.1| DNA-directed RNA polymerase [Sphingobacterium spiritivorum ATCC
           33300]
          Length = 330

 Score =  236 bits (603), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 126/298 (42%), Positives = 190/298 (63%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AIT+++  GV HE S+IKGV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGVTIGNALRRILLSSLEGYAITSIRFSGVSHEFSTIKGVVEDVTEIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQTV-NDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K +G+    +++ +   G     AGDI    N+  VLNPD V+CN+D    + +EL+V+
Sbjct: 88  FKKTGEQGDSEKIFVVINGQEQFLAGDITKFSNNFTVLNPDFVVCNMDSSVTIEVELSVA 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYV A+ ++  + P+GLI ID++++PIK V YT+E+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVNAEENKVTDGPVGLIAIDSIFTPIKNVKYTIENYRVEQKTDYEKLLLDITTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ED++  A++IL     +F +     E   KE  + ++ + L     L  ++ +L+LS
Sbjct: 208 IHPEDALKEAAKILIQHFMLFSDENMLLESQTKEETKVVDEEILHMRKILKTELVDLDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  +I  + +L+    ADML+  NFG+KSL EI+ ++ + GL  GMNL  +
Sbjct: 268 VRALNCLKAADIRTLAELVTYDVADMLKFRNFGKKSLSEIQELVKSKGLSFGMNLSKF 325


>gi|116490683|ref|YP_810227.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Oenococcus oeni PSU-1]
 gi|290890098|ref|ZP_06553181.1| hypothetical protein AWRIB429_0571 [Oenococcus oeni AWRIB429]
 gi|122277133|sp|Q04G60|RPOA_OENOB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116091408|gb|ABJ56562.1| DNA-directed RNA polymerase subunit alpha [Oenococcus oeni PSU-1]
 gi|290480289|gb|EFD88930.1| hypothetical protein AWRIB429_0571 [Oenococcus oeni AWRIB429]
          Length = 314

 Score =  236 bits (602), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 132/288 (45%), Positives = 190/288 (65%), Gaps = 6/288 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E EN    +AEPL RG+  TLGN+LRRVL+SSL GAAI +VQIDGVLHE ++I GV ED
Sbjct: 13  EESENYGKFVAEPLERGYGTTLGNSLRRVLLSSLPGAAINSVQIDGVLHEFTTIDGVTED 72

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILN+K + +++  D  K + +   G G +TAGDI++  D+E+LNPD  I  +    
Sbjct: 73  VTQIILNLKKVAMRIDSDEQKTLEVDFSGAGELTAGDIKSDGDVEILNPDLHIATVSAGK 132

Query: 142 VVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
            + M LT  +G GY  A+ ++ + +  IG++ ID++Y+PI KV+YTVE  R G   DYDK
Sbjct: 133 SLHMALTAVRGRGYDSAEENKAKMELGIGVLAIDSIYTPISKVNYTVEKTRVGHRDDYDK 192

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP-KKEVKEDIN-VKSLPFNPALLK 258
           L++ + TDGS++  +S++L S+IL + L +FI+     KKE+  D + V+++  N    +
Sbjct: 193 LTLEVWTDGSVSPSESLSLGSKILSEHLALFIDLSNAGKKEMMLDPDAVETVMENK---E 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +EELELSVRS NCL+   I  + DL  +T  DM  + N GRKSL EI
Sbjct: 250 PIEELELSVRSFNCLKRAGINTIEDLTDKTLHDMGEVRNLGRKSLEEI 297


>gi|167749410|ref|ZP_02421537.1| hypothetical protein EUBSIR_00364 [Eubacterium siraeum DSM 15702]
 gi|167657582|gb|EDS01712.1| hypothetical protein EUBSIR_00364 [Eubacterium siraeum DSM 15702]
          Length = 319

 Score =  236 bits (602), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 131/294 (44%), Positives = 197/294 (67%), Gaps = 7/294 (2%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
           +   EPL  G+ +TLGN+LRRVL+SSL G A+T+V+IDGV HE S+I GV ED+T+IILN
Sbjct: 23  MFTLEPLECGYGNTLGNSLRRVLLSSLPGVAVTSVKIDGVQHEFSTIPGVKEDVTEIILN 82

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           IKG+  KM G+  + V I   G   VTAGDI+T ++IE+L+P   I  L   A + ME+T
Sbjct: 83  IKGLIAKMYGECPQTVYIEAEGECDVTAGDIKTDSEIEILDPGMHIATLGPGAKLYMEIT 142

Query: 149 VSKGHGYVPAKHHRTENDP-IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           + KG GYV A+ ++ +  P IG+I +D++Y+P+ KV+YTVE+ R GQ  DYDKL + + T
Sbjct: 143 LDKGRGYVSAEKNKQQLQPVIGIIAVDSIYTPVLKVNYTVENTRVGQRTDYDKLILEVWT 202

Query: 208 DGSITGEDSVALASRILQDQLGMFINF--EEPKKEVKEDINVKSLPFNPALLK-KVEELE 264
           DG+I+ +++V+ A+++L D L  F+    E  + E+  D   KS      LL+  +++L+
Sbjct: 203 DGTISAKEAVSYAAKLLVDHLQPFVELSDEAIQPELMAD---KSESGKDKLLEMTIDDLD 259

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LSVRS NCL+  NI  + DLI +++ DM+++ N G+KS  E++  L ++G  L 
Sbjct: 260 LSVRSFNCLKRANINTVDDLINKSQGDMMKVRNLGKKSFEEVRAKLQSLGFDLA 313


>gi|291334082|gb|ADD93755.1| DNA directed RNA polymerase alpha subunit [uncultured marine
           bacterium MedDCM-OCT-S05-C114]
          Length = 332

 Score =  236 bits (602), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 129/299 (43%), Positives = 182/299 (60%), Gaps = 11/299 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            IA+P   G+ HT+GNA RRVL+SS+ GAAI+++++DGV HE  SI GV ED+TDI+LN+
Sbjct: 28  FIADPFESGYGHTIGNAFRRVLLSSIEGAAISSLKLDGVQHEFQSIDGVVEDVTDIVLNL 87

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + +         +TI     G VTAGDI     IE++NP+ +I   D    V  E+ V
Sbjct: 88  KKVLVISHKADPVTLTIDVEKDGEVTAGDISPAEGIEIINPEQIILTTDRKLQVTGEMIV 147

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           + G G+   +  +++  PIG+I +DALYSP+K V Y V++ R GQ+ DYDKL + + TDG
Sbjct: 148 TVGRGFCLGEDSKSDEQPIGMINVDALYSPVKLVKYEVQNTRVGQMTDYDKLLLEVTTDG 207

Query: 210 SITGEDSVALASRILQDQLGMF-------INFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
            IT +D++  ++ IL+  L +F       I FE   KEV E+ N         L   V E
Sbjct: 208 RITPDDALKQSAAILRHHLDVFDQISEEQIEFESHTKEVSEEQN----RLRNLLSMSVNE 263

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +ELSVR+ NCL   NI  +G+L  ++E +ML+  NFG+KSL EIK  L  +GL LGM  
Sbjct: 264 IELSVRAANCLNNANITTVGELATKSEPEMLKYRNFGKKSLNEIKAKLEQLGLSLGMKF 322


>gi|70725829|ref|YP_252743.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           haemolyticus JCSC1435]
 gi|90110870|sp|Q4L888|RPOA_STAHJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|68446553|dbj|BAE04137.1| DNA-directed RNA polymerase alpha chain [Staphylococcus
           haemolyticus JCSC1435]
          Length = 314

 Score =  236 bits (602), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 125/288 (43%), Positives = 190/288 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+GVLHE S+I  V ED++ II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEGVLHEFSAIDNVVEDVSTIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  R  G VTA DI   +D+EVLNP+  I  +     +++ L  
Sbjct: 83  KKLALKIYSEEDKTLEIDVRDEGEVTASDITHDSDVEVLNPELKIATVSKGGHLKIRLVA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTVE+ R GQ  D+DKL++ + T+G
Sbjct: 143 NKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTVENTRVGQSSDFDKLTLDVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SIT ++SV+LA++IL + L +F+   +  +  +  I  +       L   +EEL+LSVRS
Sbjct: 203 SITPQESVSLAAKILTEHLNIFVGLTDEAQNAEIMIEKEEDQKEKVLEMSIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++EADM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVKYKLEDLGLGL 310


>gi|291166852|gb|EFE28898.1| DNA-directed RNA polymerase, alpha subunit [Filifactor alocis ATCC
           35896]
          Length = 315

 Score =  236 bits (602), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 123/287 (42%), Positives = 193/287 (67%), Gaps = 2/287 (0%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF  T+GN+LRRVL+SSL G A+ +++I+GVLHE S+I GV ED+T+I+L +K +
Sbjct: 24  EPLERGFGITVGNSLRRVLLSSLPGVAVNSIKIEGVLHEFSTIPGVKEDVTEIMLTLKEL 83

Query: 93  NLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            + M+ +  ++ T+   + G G++TAGDI    D+EVLNPD  I     D  + ME+ VS
Sbjct: 84  AMVMNSEESRQRTLIIEQEGEGIITAGDIICPPDVEVLNPDLHIMTCSKDTKLYMEINVS 143

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYV ++ ++TE+ PIG+I +D++Y+P+KKV+YT+E  R G   + +KL+  I T+GS
Sbjct: 144 KGRGYVSSEDNKTEDMPIGVIPMDSIYTPVKKVNYTIEPTRVGARSNLEKLTFEIWTNGS 203

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
              +++V+L S+IL + L +F+N  +   E++  +  +      AL   +EEL+LSVRS 
Sbjct: 204 FEVQEAVSLGSKILIEHLNLFLNLSDKLSEIELMVEKEEGKKEKALEMTIEELDLSVRSY 263

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           NCL+  +I  + +L ++TE DM+++ N G+KSL E+ G L  +G  L
Sbjct: 264 NCLKRASINTVEELTKKTEDDMMKVRNLGKKSLEEVVGKLHDLGFTL 310


>gi|284992846|ref|YP_003411400.1| DNA-directed RNA polymerase subunit alpha [Geodermatophilus
           obscurus DSM 43160]
 gi|284066091|gb|ADB77029.1| DNA-directed RNA polymerase, alpha subunit [Geodermatophilus
           obscurus DSM 43160]
          Length = 358

 Score =  236 bits (601), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 132/323 (40%), Positives = 199/323 (61%), Gaps = 20/323 (6%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++I+G LHE +++ GV ED+T+
Sbjct: 16  EQRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIEGTLHEFTTVPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILN+KG  L +S DS + VT++  K+GPG VTA DI     +EV NP+  I  L+    
Sbjct: 76  IILNLKG--LVVSSDSDEPVTMYLRKQGPGEVTAADIAPPAGVEVHNPELHIATLNGKGR 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D+L 
Sbjct: 134 LEIELVVERGRGYVPAPQNKQPGQEIGRIPVDSIYSPVLKVTYAVEATRVEQRTDFDRLV 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNP 254
           + ++T  SI   D++A A   L +  G+   +N +       P      DI   S+P   
Sbjct: 194 VDVETKPSIAPRDAIASAGSTLVELFGLLRELNIDAEGIEVGPSPAEAADIANFSMP--- 250

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +E+++L+VRS NCL+ E +  +G+L+ R+EAD+L + NFG KS+ E+K  L  MG
Sbjct: 251 -----IEDMDLTVRSYNCLKREGVHTVGELVTRSEADLLDIRNFGAKSIDEVKMKLAAMG 305

Query: 315 LFLGMNLPDWPPESIEELAKKYE 337
           L L  + P + P S+E   + YE
Sbjct: 306 LALKDSPPGFIPTSVESYDEGYE 328


>gi|291544484|emb|CBL17593.1| DNA-directed RNA polymerase subunit alpha [Ruminococcus sp. 18P13]
          Length = 318

 Score =  236 bits (601), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 128/291 (43%), Positives = 195/291 (67%), Gaps = 4/291 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +  PL RG+  TLGN+LRRVL+SSL G A+ +V+IDGV HE+S+I GV ED+T+IIL+I
Sbjct: 24  FVLAPLERGYGITLGNSLRRVLLSSLPGVAVNSVKIDGVHHELSTIPGVKEDVTEIILSI 83

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+  K+ GD  K V I   G   VTAGDI+T +++ +L+P   I  L  DA + ME+T+
Sbjct: 84  KGLTAKLYGDGPKTVYIEATGECEVTAGDIKTDSEVNILDPGMHIATLGKDASLYMEITL 143

Query: 150 SKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GYV A+ ++    N PI +I +D++Y+P+ KV+YTVE  R GQV DYDKL+M + T
Sbjct: 144 DKGRGYVSAERNKQLMPNLPIDVIAVDSIYTPVLKVNYTVEDTRLGQVTDYDKLTMEVWT 203

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK-KVEELELS 266
           DG+I+ +++++ A+ +L + L +F++  E +  + E +  K       +L+  +EEL+LS
Sbjct: 204 DGTISAKEALSQAANLLNEHLKLFVDLSE-EASIAEVLVEKDDKGKEKILEMTIEELDLS 262

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           VRS NCL+   I  + DLI ++E +M+++ N G+KS  E+K  L ++G  L
Sbjct: 263 VRSFNCLKRAGINTVDDLINKSEEEMMKVRNLGKKSFDEVKEKLQSLGFDL 313


>gi|148381392|ref|YP_001255933.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum A
           str. ATCC 3502]
 gi|153932349|ref|YP_001385767.1| DNA-directed RNA polymerase subunit alpha [Clostridium botulinum A
           str. ATCC 19397]
 gi|153936668|ref|YP_001389174.1| DNA-directed RNA polymerase subunit alpha [Clostridium botulinum A
           str. Hall]
 gi|153940858|ref|YP_001392805.1| DNA-directed RNA polymerase subunit alpha [Clostridium botulinum F
           str. Langeland]
 gi|168178861|ref|ZP_02613525.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           NCTC 2916]
 gi|168181893|ref|ZP_02616557.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           Bf]
 gi|170756437|ref|YP_001783092.1| DNA-directed RNA polymerase subunit alpha [Clostridium botulinum B1
           str. Okra]
 gi|170760187|ref|YP_001788792.1| DNA-directed RNA polymerase subunit alpha [Clostridium botulinum A3
           str. Loch Maree]
 gi|187776604|ref|ZP_02993077.1| hypothetical protein CLOSPO_00118 [Clostridium sporogenes ATCC
           15579]
 gi|226950904|ref|YP_002805995.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           A2 str. Kyoto]
 gi|237796913|ref|YP_002864465.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           Ba4 str. 657]
 gi|166229269|sp|A7FZ44|RPOA_CLOB1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|166229270|sp|A5I7H7|RPOA_CLOBH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|166229271|sp|A7GJ45|RPOA_CLOBL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|229564246|sp|B1IGC5|RPOA_CLOBK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238688736|sp|B1KSJ6|RPOA_CLOBM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|254765247|sp|C1FMS2|RPOA_CLOBJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|259494165|sp|C3KVM2|RPOA_CLOB6 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|148290876|emb|CAL85012.1| DNA-directed RNA polymerase alpha chain [Clostridium botulinum A
           str. ATCC 3502]
 gi|152928393|gb|ABS33893.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum A
           str. ATCC 19397]
 gi|152932582|gb|ABS38081.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum A
           str. Hall]
 gi|152936754|gb|ABS42252.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum F
           str. Langeland]
 gi|169121649|gb|ACA45485.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           B1 str. Okra]
 gi|169407176|gb|ACA55587.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           A3 str. Loch Maree]
 gi|182670092|gb|EDT82068.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           NCTC 2916]
 gi|182674826|gb|EDT86787.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           Bf]
 gi|187775263|gb|EDU39065.1| hypothetical protein CLOSPO_00118 [Clostridium sporogenes ATCC
           15579]
 gi|226842850|gb|ACO85516.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           A2 str. Kyoto]
 gi|229260648|gb|ACQ51681.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           Ba4 str. 657]
 gi|295320785|gb|ADG01163.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum F
           str. 230613]
 gi|322807777|emb|CBZ05352.1| DNA-directed RNA polymerase alpha subunit [Clostridium botulinum
           H04402 065]
          Length = 315

 Score =  236 bits (601), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 120/288 (41%), Positives = 194/288 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGNALRR+L+SSL G A   ++ID VLHE S+++GV ED+T++ILNI
Sbjct: 23  FVIEPLERGYGITLGNALRRILLSSLPGVAADHIKIDSVLHEFSTVQGVKEDVTELILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L M+G+  K + I + GP  VTA DI+T  D+EV+N D  I  LD +  + ME+ V
Sbjct: 83  KCLALTMNGEGPKTIYIDEVGPKEVTAADIKTDGDVEVINKDLHIATLDENGKMYMEINV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           ++G GYV    ++T++ PIG I +D++Y+P+K+V+++VE+ R GQ+ DYDKL++ + T+G
Sbjct: 143 NRGRGYVTQNKNKTKDMPIGSIAVDSIYTPVKRVNFSVENTRVGQITDYDKLTIEVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +I  E++V+L+++IL +   +F+   +   +++  +  +       L   +EEL+LSVRS
Sbjct: 203 TIRPEEAVSLSAKILIEHFKLFMTLTDHADDMEIMVEKEEDKKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L +R+  DM+++ N G+KSL E++  L  +GL L
Sbjct: 263 YNCLKRAGINTVQELCERSMDDMMKVRNLGKKSLEEVEQKLEALGLGL 310


>gi|160894727|ref|ZP_02075502.1| hypothetical protein CLOL250_02278 [Clostridium sp. L2-50]
 gi|156863661|gb|EDO57092.1| hypothetical protein CLOL250_02278 [Clostridium sp. L2-50]
          Length = 318

 Score =  235 bits (600), Expect = 6e-60,   Method: Compositional matrix adjust.
 Identities = 130/293 (44%), Positives = 194/293 (66%), Gaps = 7/293 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL G A+T V+I GVLHE SSI GV ED+T+I++NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRIMLSSLPGTAVTHVKIKGVLHEFSSIPGVKEDVTEIVMNI 82

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVVRME 146
           K + +K +   +  K+  I   G  VV A DI    DIE++NPD VI NL   DA + ME
Sbjct: 83  KSLVIKNNSLTNEPKQAYIDVAGDCVVRASDIHVDGDIEIINPDLVIANLSGPDARLEME 142

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           LT+  G GYV +  ++  + PI +I ID++Y+P+++V+ TV++ R GQV DYDKL++ + 
Sbjct: 143 LTIGNGRGYVGSDKNKEADAPIDVIAIDSIYTPVERVNLTVQNTRVGQVTDYDKLTLDVF 202

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP--FNPALLKKVEELE 264
           T+G+I  +++V+LA+R+L + L +F++  E  K V  D+ V+S+       L   ++ELE
Sbjct: 203 TNGAIAPDEAVSLAARVLVEHLNLFVDLSENAKSV--DVMVESVTDEKEKVLEMNIDELE 260

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LSVRS NCL+   I  + +LI +T  DM+++ N GRKSL E+   L  +GL L
Sbjct: 261 LSVRSYNCLKRAGINTVEELINKTPEDMMKVRNLGRKSLDEVLAKLKELGLSL 313


>gi|37912970|gb|AAR05302.1| DNA-directed RNA polymerase alpha subunit [uncultured marine gamma
           proteobacterium EB000-45B06]
          Length = 283

 Score =  235 bits (600), Expect = 6e-60,   Method: Compositional matrix adjust.
 Identities = 126/286 (44%), Positives = 190/286 (66%), Gaps = 7/286 (2%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           +GNALRR+L+SS+ GAA+T V IDG+ HE S+I+GV ED+ DI+LNIK + + +   +  
Sbjct: 1   MGNALRRILLSSMPGAAVTDVAIDGISHEYSTIEGVREDVIDILLNIKDMPVNIIEGNTA 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV-VRMELTVSKGHGYVPAKHH 161
            +T+   GP  V A       ++E++N D  +  + VD V ++M LTV  G GY PA   
Sbjct: 61  EITLDVTGPCDVLASSFDVPGNVELVNQDFHVATI-VDKVNLKMTLTVQTGRGYEPADTR 119

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
             E+  +G + +DA YSP+++VSYTV++AR  +  D DKL + ++TDG++  + ++  ++
Sbjct: 120 DDEDRVVGALKVDASYSPVRRVSYTVDNARFEKRTDLDKLVIELETDGTLDPKMAIEHSA 179

Query: 222 RILQDQLGMFINFEE-PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVY 280
            ILQ QL  F++ +   ++E K+D N     F+P LL+ +EELEL+VRSTNCL+ E+I  
Sbjct: 180 TILQQQLSSFVDLDAIAEQEAKKDQN----DFDPFLLRSIEELELTVRSTNCLKAESIFL 235

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           +GDLI R+E D+L+  N G+KSL EIK VL +  L LGMN+ +WPP
Sbjct: 236 IGDLIHRSEFDLLKTPNLGKKSLNEIKDVLASKELSLGMNVDNWPP 281


>gi|228474561|ref|ZP_04059292.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus hominis
           SK119]
 gi|314935857|ref|ZP_07843209.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus hominis
           subsp. hominis C80]
 gi|228271224|gb|EEK12592.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus hominis
           SK119]
 gi|313656422|gb|EFS20162.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus hominis
           subsp. hominis C80]
          Length = 314

 Score =  235 bits (600), Expect = 7e-60,   Method: Compositional matrix adjust.
 Identities = 124/288 (43%), Positives = 190/288 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+GVLHE S+I  V ED++ II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEGVLHEFSAIDNVVEDVSTIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  R  G VTA DI   +D+EVLNP+  I  +     +++ L  
Sbjct: 83  KKLALKIYSEEDKTLEIDVRDEGEVTASDITHDSDVEVLNPELKIATVSKGGHLKIRLVA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTVE+ R GQ  D+DKL++ + T+G
Sbjct: 143 NKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTVENTRVGQSSDFDKLTLDVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SIT ++SV+LA++I+ + L +F+   +  +  +  I  +       L   +EEL+LSVRS
Sbjct: 203 SITPQESVSLAAKIMTEHLNIFVGLTDEAQNAEIMIEKEEDQKEKVLEMSIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++EADM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVKYKLEDLGLGL 310


>gi|326692212|ref|ZP_08229217.1| DNA-directed RNA polymerase subunit alpha [Leuconostoc argentinum
           KCTC 3773]
          Length = 314

 Score =  235 bits (600), Expect = 7e-60,   Method: Compositional matrix adjust.
 Identities = 132/312 (42%), Positives = 192/312 (61%), Gaps = 10/312 (3%)

Query: 8   ELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           E  KPN  NIE      E+      + EPL RG+  TLGN+LRR+L+SSL GAA+  VQI
Sbjct: 3   EFEKPNIHNIE------EDARYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGV+HE S++ GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+Q   D+
Sbjct: 57  DGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDVQGPAEVTAADLQAGADV 116

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKV 183
           EVLNPD  I  +     + M +T  KG GY  A  ++   E  PIG++ +D++Y+PI++V
Sbjct: 117 EVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSADENKQLREEMPIGVLAVDSIYTPIERV 176

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+ R G   DYDKL+  I T+GSI   D+++L ++IL + L +F++      E   
Sbjct: 177 NYHVENTRVGARDDYDKLTFDIWTNGSIKPSDALSLGAKILAEHLNLFMDISPVAAEANV 236

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  + +  + +    +E+L+LSVRS NCL+   I  + +L  RTEADM+++ N GRKSL
Sbjct: 237 MVEAEPVAVSASDSAPIEDLDLSVRSYNCLKRAGINTIVELTDRTEADMMKVRNLGRKSL 296

Query: 304 VEIKGVLGTMGL 315
            EI+  L  MGL
Sbjct: 297 DEIQEKLTEMGL 308


>gi|82751814|ref|YP_417555.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           RF122]
 gi|119366734|sp|Q2YYM2|RPOA_STAAB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|82657345|emb|CAI81786.1| DNA-directed RNA polymerase alpha chain [Staphylococcus aureus
           RF122]
          Length = 314

 Score =  235 bits (599), Expect = 8e-60,   Method: Compositional matrix adjust.
 Identities = 122/288 (42%), Positives = 190/288 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+GVLHE S++  V ED++ II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLSGAAVKYIEIEGVLHEFSAVDNVVEDVSTIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  R  G VTA DI   +D+E+LNP+  I  +     +++ L  
Sbjct: 83  KQLALKIYSEEDKTLEIDVRDEGEVTASDITHDSDVEILNPELKIATVSKGGHLKIRLVA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTVE+ R GQ  D+DKL++ + T+G
Sbjct: 143 NKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTVENTRVGQSSDFDKLTLDVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SIT ++SV+LA++I+ + L +F+   +  +  +  I  +       L   +EEL+LSVRS
Sbjct: 203 SITPQESVSLAAKIMTEHLNIFVGLTDEAQNAEIMIEKEEDQKEKVLEMSIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++EADM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVKYKLEDLGLGL 310


>gi|260656838|gb|ACX47809.1| RNA polymerase alpha-subunit [Vibrio casei]
          Length = 275

 Score =  235 bits (599), Expect = 8e-60,   Method: Compositional matrix adjust.
 Identities = 123/270 (45%), Positives = 185/270 (68%), Gaps = 8/270 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 9   EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 68

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            + ++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D  A + M + V 
Sbjct: 69  AVSVAEGKDEVFITLKKSGSGPVVAGDIIHDGDVEIANPEHVICHLTDDKAEIAMRIKVQ 128

Query: 151 KGHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVP  A+ H  E++ PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 129 RGRGYVPSSARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 188

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 189 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 245

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           RS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 246 RSANCLKAEAIHYIGDLVQRTEVELLKTPN 275


>gi|313292052|gb|ADR51215.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
 gi|313292054|gb|ADR51216.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
 gi|313292056|gb|ADR51217.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
 gi|313292058|gb|ADR51218.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
 gi|313292060|gb|ADR51219.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
 gi|313292062|gb|ADR51220.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
          Length = 258

 Score =  235 bits (599), Expect = 8e-60,   Method: Compositional matrix adjust.
 Identities = 120/252 (47%), Positives = 170/252 (67%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+
Sbjct: 7   EEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDV 66

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             IILNIKG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  ICN+   A 
Sbjct: 67  AQIILNIKGLALKMYGDEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICNVSEGAS 126

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
               LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+
Sbjct: 127 FHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLT 186

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           M I TDGSI   ++++LA++I+ + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 187 MEIWTDGSIEPLEAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEE 246

Query: 263 LELSVRSTNCLR 274
           L+LSVRS NCL+
Sbjct: 247 LDLSVRSYNCLK 258


>gi|328813991|gb|AEB52111.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 269

 Score =  235 bits (599), Expect = 8e-60,   Method: Compositional matrix adjust.
 Identities = 124/269 (46%), Positives = 178/269 (66%), Gaps = 2/269 (0%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E +N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+
Sbjct: 1   ENDNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDV 60

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A 
Sbjct: 61  TAIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGAH 120

Query: 143 VRMELTVSKGHGYVPAK--HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             M +T + G GYV A+   HR ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DK
Sbjct: 121 FHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDK 180

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L++ + T+GSIT  ++++L+++IL D L +F+N  +  K     +  +       L   +
Sbjct: 181 LTLDVWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEMTI 240

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTE 289
           EEL+LSVRS NCL+   I  + +L  +TE
Sbjct: 241 EELDLSVRSYNCLKRAGINTVQELTNKTE 269


>gi|299767525|gb|ADJ38428.1| RNA polymerase alpha-subunit [Vibrio communis]
 gi|299767527|gb|ADJ38429.1| RNA polymerase alpha-subunit [Vibrio communis]
 gi|299767529|gb|ADJ38430.1| RNA polymerase alpha-subunit [Vibrio communis]
 gi|299767531|gb|ADJ38431.1| RNA polymerase alpha-subunit [Vibrio communis]
 gi|299767533|gb|ADJ38432.1| RNA polymerase alpha-subunit [Vibrio communis]
 gi|299767535|gb|ADJ38433.1| RNA polymerase alpha-subunit [Vibrio communis]
 gi|299767537|gb|ADJ38434.1| RNA polymerase alpha-subunit [Vibrio communis]
          Length = 262

 Score =  235 bits (599), Expect = 9e-60,   Method: Compositional matrix adjust.
 Identities = 120/265 (45%), Positives = 182/265 (68%), Gaps = 8/265 (3%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ 
Sbjct: 1   PLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLA 60

Query: 94  LKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
           ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +
Sbjct: 61  VRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVER 120

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H+  +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+
Sbjct: 121 GRGYVPASARIHNEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 181 GTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 237

Query: 269 STNCLRGENIVYMGDLIQRTEADML 293
           S NCL+ E I Y+GDL+QRTE ++L
Sbjct: 238 SANCLKAEAIHYIGDLVQRTEVELL 262


>gi|116617354|ref|YP_817725.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Leuconostoc mesenteroides subsp. mesenteroides ATCC
           8293]
 gi|122272445|sp|Q03ZM0|RPOA_LEUMM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116096201|gb|ABJ61352.1| DNA-directed RNA polymerase subunit alpha [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
          Length = 314

 Score =  235 bits (599), Expect = 9e-60,   Method: Compositional matrix adjust.
 Identities = 132/312 (42%), Positives = 192/312 (61%), Gaps = 10/312 (3%)

Query: 8   ELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           E  KPN  NIE      E+      + EPL RG+  TLGN+LRR+L+SSL GAA+  VQI
Sbjct: 3   EFEKPNIHNIE------EDARYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGV+HE S++ GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+Q   D+
Sbjct: 57  DGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDIQGPADVTAADLQGGADV 116

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKV 183
           EVLNPD  I  +     + M +T  KG GY  A  ++   D  PIG++ +D++Y+PI++V
Sbjct: 117 EVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSADENKKLRDEMPIGVLAVDSIYTPIERV 176

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+ R G   DYDKL+  I T+GSI   D+++L ++IL + LG+F++      E   
Sbjct: 177 NYQVENTRIGARDDYDKLTFDIWTNGSIKPSDALSLGAKILAEHLGLFMDISPVAAEASV 236

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  + +  + +    +E+L+LSVRS NCL+   I  + +L  RTEADM+++ N GRKSL
Sbjct: 237 MVEAEPVAASASDSAPIEDLDLSVRSYNCLKRAGINTIVELTDRTEADMMKVRNLGRKSL 296

Query: 304 VEIKGVLGTMGL 315
            EI+  L  M L
Sbjct: 297 DEIQEKLTDMNL 308


>gi|330718947|ref|ZP_08313547.1| DNA-directed RNA polymerase subunit alpha [Leuconostoc fallax KCTC
           3537]
          Length = 314

 Score =  235 bits (599), Expect = 9e-60,   Method: Compositional matrix adjust.
 Identities = 132/312 (42%), Positives = 193/312 (61%), Gaps = 10/312 (3%)

Query: 8   ELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           E  KPN  NIE      E+      + EPL RG+  TLGN+LRR+L+SSL GAA+  VQI
Sbjct: 3   EFEKPNIHNIE------EDARYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGV+HE S++ GV ED+T +ILN+K + L +  D  K + I  +GP  VTA D+Q   DI
Sbjct: 57  DGVVHEFSTVDGVVEDVTQLILNLKKVVLAIDSDEEKSLEIDVQGPAEVTAADLQGSADI 116

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKV 183
           EVLNP+  +  +     + M +T  KG GY  A  ++   D  PIG++ +D++Y+PI++V
Sbjct: 117 EVLNPELHLATVAAGKSLHMTVTAVKGRGYSSADENKQLRDEMPIGVLAVDSIYTPIERV 176

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+ R GQ  DYDKL+  I T+GSI   D+++L ++IL + L +F +      E + 
Sbjct: 177 NYQVENTRVGQRDDYDKLTFDIWTNGSIKPSDALSLGAKILSEHLNLFTDISSVAAETEV 236

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            ++V+    +      +E+L+LSVRS NCL+   I  + +L  R+EADM+++ N GRKSL
Sbjct: 237 MVDVEQTVSSVQDSAPIEDLDLSVRSYNCLKRAGINTISELTDRSEADMMKVRNLGRKSL 296

Query: 304 VEIKGVLGTMGL 315
            EI+  L  MGL
Sbjct: 297 DEIQEKLIEMGL 308


>gi|319827247|gb|ADV74823.1| RNA polymerase subunit A [Vibrio neptunius]
          Length = 275

 Score =  234 bits (598), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 120/265 (45%), Positives = 182/265 (68%), Gaps = 8/265 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 14  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 73

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 74  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 133

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 134 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMET 193

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 194 NGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 250

Query: 268 RSTNCLRGENIVYMGDLIQRTEADM 292
           RS NCL+ E I Y+GDL+QRTE ++
Sbjct: 251 RSANCLKAEAIHYIGDLVQRTEVEL 275


>gi|319827245|gb|ADV74822.1| RNA polymerase subunit A [Vibrio coralliilyticus]
          Length = 276

 Score =  234 bits (598), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 120/265 (45%), Positives = 182/265 (68%), Gaps = 8/265 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 15  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 74

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 75  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 134

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 135 RGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMET 194

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 195 NGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 251

Query: 268 RSTNCLRGENIVYMGDLIQRTEADM 292
           RS NCL+ E I Y+GDL+QRTE ++
Sbjct: 252 RSANCLKAEAIHYIGDLVQRTEVEL 276


>gi|73661998|ref|YP_300779.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           saprophyticus subsp. saprophyticus ATCC 15305]
 gi|90110871|sp|Q49ZE2|RPOA_STAS1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|72494513|dbj|BAE17834.1| DNA-directed RNA polymerase alpha chain [Staphylococcus
           saprophyticus subsp. saprophyticus ATCC 15305]
          Length = 314

 Score =  234 bits (598), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 123/288 (42%), Positives = 191/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+GVLHE S+I  V ED++ II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEGVLHEFSAIDNVVEDVSTIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  +  G VTA DI   +D+E+LNP+  I  +     +++ L  
Sbjct: 83  KKLALKIYSEEDKTLEIDVKDEGDVTASDITHDSDVEILNPEIKIATVSKGGHLKIRLVA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GY  A+ ++T + PIG+I +D+LYSP+++V+YTVE+ R GQ  D+DKL++ + T+G
Sbjct: 143 NKGRGYALAEQNKTSDLPIGVIPVDSLYSPVERVNYTVENTRVGQSSDFDKLTLDVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SIT ++SV+LA++IL + L +F+   +  +  +  I  +       L   +EEL+LSVRS
Sbjct: 203 SITPQESVSLAAKILTEHLNIFVGLTDEAQNAEIMIEKEEDQKEKVLEMSIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++EADM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVKYKLEDLGLGL 310


>gi|161511875|emb|CAP16948.1| DNA-directed RNA polymerase subunit alpha [Pediococcus siamensis]
          Length = 275

 Score =  234 bits (598), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 118/254 (46%), Positives = 170/254 (66%), Gaps = 2/254 (0%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E EN    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+
Sbjct: 8   ENENYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDV 67

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILNIK ++LK+  D  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +     
Sbjct: 68  TQIILNIKKVSLKIESDDEKSLEINVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVT 127

Query: 143 VRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
               LT   G GYV A  ++   D  PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDK
Sbjct: 128 FHAVLTADTGRGYVSADENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRNDYDK 187

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L++ + TDGSI+  ++ +L+++IL + L +F+N  +  +E +  +  +       L   +
Sbjct: 188 LTLDVWTDGSISPSEATSLSAKILTEHLALFVNLTDEAQEAEIMVEKEETHKEKMLEMSI 247

Query: 261 EELELSVRSTNCLR 274
           EEL+LSVRS NCL+
Sbjct: 248 EELDLSVRSYNCLK 261


>gi|323144991|ref|ZP_08079551.1| DNA-directed RNA polymerase, alpha subunit [Succinatimonas hippei
           YIT 12066]
 gi|322415270|gb|EFY06044.1| DNA-directed RNA polymerase, alpha subunit [Succinatimonas hippei
           YIT 12066]
          Length = 329

 Score =  234 bits (598), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 139/330 (42%), Positives = 200/330 (60%), Gaps = 16/330 (4%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +L++PN  E + L +   N + +I EP  + +A  LG ALRR+++SS+ G AIT V+IDG
Sbjct: 6   DLLRPNIKEVVTLSR---NVSRVILEPFEQHYAQVLGTALRRIMLSSIPGYAITEVEIDG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGIN-LKMSGDSHKRVT-IFKRGPGVVTAGDIQTVNDI 125
           V+HE S+++GV ED+  I+LN+K +     +   H  V  I K G G VTA DIQ    I
Sbjct: 63  VVHEYSALEGVQEDILLILLNLKEVAVFSATIPQHDPVLEINKSGIGTVTAADIQCPGGI 122

Query: 126 EVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHHR----TENDPIGLITIDALYSPI 180
           E+ NP+ V+C++ D    +RM L V++G GYVPA  H      E+  IG + +DA Y P+
Sbjct: 123 EIRNPELVLCHITDEKTNLRMRLHVTRGRGYVPAVTHPHIEGAEDRFIGRLLLDASYCPV 182

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
             V+       +GQ    ++L + I+T+G+I   D+V  A+ I  DQL  F++       
Sbjct: 183 LNVAVHTAPLNDGQ----EQLILDIETNGTIDPSDAVCSAATIFADQLNSFVDIRNSVAP 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             +D + K L  +P LL  VE+LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+
Sbjct: 239 A-DDASFKPL-IDPKLLCPVEDLELTVRSANCLKAEGIKYIGDLVQRTEVELLKTPNLGK 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           KSL EIK VL   GL LGM L +WPP  +E
Sbjct: 297 KSLTEIKDVLAERGLSLGMRLENWPPADLE 326


>gi|289550169|ref|YP_003471073.1| DNA-directed RNA polymerase alpha subunit [Staphylococcus
           lugdunensis HKU09-01]
 gi|315659201|ref|ZP_07912065.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           lugdunensis M23590]
 gi|289179701|gb|ADC86946.1| DNA-directed RNA polymerase alpha subunit [Staphylococcus
           lugdunensis HKU09-01]
 gi|315495626|gb|EFU83957.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           lugdunensis M23590]
          Length = 314

 Score =  234 bits (597), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 123/288 (42%), Positives = 190/288 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+GVLHE S+I  V ED++ II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEGVLHEFSAIDNVVEDVSTIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  R  G VTA DI   +D+E+LNP+  I  +     +++ L  
Sbjct: 83  KKLALKIYSEEDKTLEIDVRDEGEVTASDITHDSDVEILNPELKIATVSKGGHLKIRLVA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTVE+ R GQ  D+DKL++ + T+G
Sbjct: 143 NKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTVENTRVGQSSDFDKLTLDVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SIT ++SV+LA++I+ + L +F+   +  +  +  I  +       L   +EEL+LSVRS
Sbjct: 203 SITPQESVSLAAKIMTEHLNIFVGLTDEAQNAEIMIEKEEDQKEKVLEMSIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++EADM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVKYKLEDLGLGL 310


>gi|78186095|ref|YP_374138.1| DNA-directed RNA polymerase subunit alpha [Chlorobium luteolum DSM
           273]
 gi|119366706|sp|Q3B6D6|RPOA_PELLD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|78165997|gb|ABB23095.1| DNA-directed RNA polymerase subunit alpha [Chlorobium luteolum DSM
           273]
          Length = 328

 Score =  234 bits (597), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 125/302 (41%), Positives = 190/302 (62%), Gaps = 9/302 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            IA+PL RG+  TLGN +RRVL++SL G AIT +++DGV HE SSI+GV ED+ +I+LN+
Sbjct: 25  FIAQPLERGYGVTLGNMMRRVLLASLPGTAITGIKVDGVFHEFSSIEGVREDVPEIVLNL 84

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           K +  K +     + T+   GP   TAGDI     + EVLN D  I  ++  + + +++ 
Sbjct: 85  KKVRFKSTCKRSCKTTLSIVGPKDFTAGDIVAQEGEFEVLNKDLYIATVNEGSTLNIDVY 144

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           + +G GY PA+  R ++ PIG I IDA+Y+PI+ V + VE+ R GQ  DY+K+ + ++TD
Sbjct: 145 IGRGRGYTPAEESRPDSMPIGYIAIDAIYTPIRNVKFAVENTRVGQRTDYEKMVLDVETD 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEV------KEDINVKSLPFNPALLKKVEE 262
           GSIT +DS++LA RI+ + +  F NF   ++E       ++D   +++     L  K+E+
Sbjct: 205 GSITPDDSISLAGRIINEHVTFFANFSPTEEEFTEEEYKQQDDEFETM--RRLLNTKIED 262

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL E+K  L    L  GM++ 
Sbjct: 263 LDLSVRSHNCLRLAEIDTIGDLVSRKEDELLNYKNFGKKSLTELKEQLEKFELKFGMDIT 322

Query: 323 DW 324
            +
Sbjct: 323 RY 324


>gi|108804947|ref|YP_644884.1| DNA-directed RNA polymerase subunit alpha [Rubrobacter xylanophilus
           DSM 9941]
 gi|119366722|sp|Q1AU56|RPOA_RUBXD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|108766190|gb|ABG05072.1| DNA-directed RNA polymerase, alpha subunit [Rubrobacter
           xylanophilus DSM 9941]
          Length = 313

 Score =  234 bits (597), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 125/303 (41%), Positives = 183/303 (60%), Gaps = 15/303 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E+E   + +AEPLPRG  HTLGNALRRV++S L GAA+T ++I+GV HE S+I+GV ED
Sbjct: 14  EEDERHGIFVAEPLPRGLGHTLGNALRRVMLSGLPGAAVTKLRIEGVQHEFSTIEGVRED 73

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DIILN+K +  ++  D    + I K GPG V   DI+   D+EV+NPD  I +L    
Sbjct: 74  VVDIILNVKQLKFRLERDEPIELQISKDGPGEVRGSDIELKADVEVVNPDAYIASLSEGG 133

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + M LTV +G GYVPA+ ++++ DPIG+I +D+L+SP++KV Y V   R G  +D D L
Sbjct: 134 HLDMTLTVERGQGYVPAEQNKSDADPIGVIAVDSLFSPVEKVQYRVSETRAGARVDLDAL 193

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFIN-------FEEPKKEVKEDINVKSLPFNP 254
           ++ + TDG +   +++  ASR L D  G+F          EEP +     +     P   
Sbjct: 194 TLEVFTDGRLGPREALREASRKLIDFFGLFAEGYQGAGAAEEPGRSGGRPVITDERP--- 250

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +E+LEL+VRS NCL+ E +  +G L   TE +++ + N G KS+ EI+  L   G
Sbjct: 251 -----IEDLELTVRSYNCLKREGVDTIGQLATMTEEELMNIRNLGMKSVDEIRSKLEEYG 305

Query: 315 LFL 317
             L
Sbjct: 306 YTL 308


>gi|227431316|ref|ZP_03913369.1| DNA-directed RNA polymerase, alpha subunit [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
 gi|227352909|gb|EEJ43082.1| DNA-directed RNA polymerase, alpha subunit [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
          Length = 314

 Score =  234 bits (597), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 132/312 (42%), Positives = 192/312 (61%), Gaps = 10/312 (3%)

Query: 8   ELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           E  KPN  NIE      E+      + EPL RG+  TLGN+LRR+L+SSL GAA+  VQI
Sbjct: 3   EFEKPNIHNIE------EDARYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGV+HE S++ GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+Q   D+
Sbjct: 57  DGVVHEFSTVDGVVEDVTQIILNLKKVVLAIESDDERSLEIDIQGPADVTAADLQGGADV 116

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKV 183
           EVLNPD  I  +     + M +T  KG GY  A  ++   D  PIG++ +D++Y+PI++V
Sbjct: 117 EVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSADENKKLRDEMPIGVLAVDSIYTPIERV 176

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+ R G   DYDKL+  I T+GSI   D+++L ++IL + LG+F++      E   
Sbjct: 177 NYQVENTRIGARDDYDKLTFDIWTNGSIKPSDALSLGAKILAEHLGLFMDISPVAAEASV 236

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  + +  + +    +E+L+LSVRS NCL+   I  + +L  RTEADM+++ N GRKSL
Sbjct: 237 MVEAEPVAASESDSAPIEDLDLSVRSYNCLKRAGINTILELTDRTEADMMKVRNLGRKSL 296

Query: 304 VEIKGVLGTMGL 315
            EI+  L  M L
Sbjct: 297 DEIQEKLTDMNL 308


>gi|315652326|ref|ZP_07905318.1| DNA-directed RNA polymerase subunit alpha [Eubacterium saburreum
           DSM 3986]
 gi|315485449|gb|EFU75839.1| DNA-directed RNA polymerase subunit alpha [Eubacterium saburreum
           DSM 3986]
          Length = 330

 Score =  234 bits (597), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 128/296 (43%), Positives = 194/296 (65%), Gaps = 15/296 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+++SSL G+A++ V+IDGVLHE SSI GV ED+T+II+N+
Sbjct: 36  FICEPLERGYGTTLGNSLRRIMLSSLPGSAVSQVKIDGVLHEFSSIPGVKEDVTEIIMNV 95

Query: 90  KGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K + +K S + +  K   I   G GV+TA DIQ    IE++N D VI  +  +    MEL
Sbjct: 96  KSLAIKNSAEDNEPKIAYIDFDGEGVITAEDIQCDPCIEIINKDQVIATVS-EGKFYMEL 154

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           T++ G GYV +  ++ E+ PIG+I ID++Y+P+++V+  VE+ R GQV D+DKL++ + T
Sbjct: 155 TITNGRGYVSSDKNKGEDTPIGVIAIDSIYTPVERVNLRVENTRVGQVTDFDKLTLDVTT 214

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKK------EVKEDINVKSLPFNPALLKKVE 261
           +G++  +++V+LA+++L + L +FI+  +  K      E +ED   K L  N      ++
Sbjct: 215 NGTLEPDEAVSLAAKVLSEHLNLFIDLSDNAKTIDVMVEKEEDDKEKVLEMN------ID 268

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L
Sbjct: 269 ELELSVRSYNCLKRAGINTVEELCSRTSDDMMKVRNLGRKSLEEVLQKLEELGLHL 324


>gi|284042830|ref|YP_003393170.1| DNA-directed RNA polymerase, subunit alpha [Conexibacter woesei DSM
           14684]
 gi|283947051|gb|ADB49795.1| DNA-directed RNA polymerase, alpha subunit [Conexibacter woesei DSM
           14684]
          Length = 333

 Score =  234 bits (597), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 133/317 (41%), Positives = 194/317 (61%), Gaps = 24/317 (7%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           EENR     EPL RGF +T GN+LRRVL+SSL GAA+T+V+I+GV HE S+I GV ED+T
Sbjct: 15  EENRGSFTIEPLDRGFGYTFGNSLRRVLLSSLAGAAVTSVRIEGVAHEFSTIPGVKEDVT 74

Query: 84  DIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           DI+LN+KGI  +M  D+ +    +   GPG +TA DI   + +E+LNPD  I  L+    
Sbjct: 75  DIVLNLKGIVCRMHSDATEIEAPLVVTGPGDITAKDIDLPSGVEILNPDAHIATLEKKTK 134

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + + LT+ +G GY PA+ +++ + PIG+I ID+++SP+++V+Y VE AR GQ  DYDKL+
Sbjct: 135 LEVYLTIGRGRGYRPAEENKSPDQPIGVIPIDSIFSPVRRVAYAVEQARVGQKTDYDKLT 194

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL------------ 250
           + I+TDGSI    ++  A+ IL  QL +F + +    E+++   + +L            
Sbjct: 195 LDIETDGSIDPHAALREAAEILISQLAIFTDADR-VIELRDTGGLGALEPGLAGGGVGGV 253

Query: 251 ----------PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                     P N      +EELEL VRS NCL+   I  +GDLI +TE ++  + NFG+
Sbjct: 254 GGHGAGPGGRPANAMDDILIEELELGVRSYNCLKRAGIQTVGDLISKTENELNAIPNFGK 313

Query: 301 KSLVEIKGVLGTMGLFL 317
           KS+ E+   L   GL L
Sbjct: 314 KSIDEVIETLEGRGLHL 330


>gi|242371871|ref|ZP_04817445.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           epidermidis M23864:W1]
 gi|242350378|gb|EES41979.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           epidermidis M23864:W1]
          Length = 314

 Score =  234 bits (597), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 122/288 (42%), Positives = 190/288 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+GVLHE S++  V ED++ II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEGVLHEFSAVDNVVEDVSTIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  +  G VTA DI   +D+E+LNP+  I  +     +++ L  
Sbjct: 83  KKLALKIYSEEDKTLEIDVKDEGEVTASDITHDSDVEILNPELKIATVSKGGHLKVRLVA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTVE+ R GQ  DYDKL++ + T+G
Sbjct: 143 NKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTVENTRVGQSSDYDKLTLDVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SIT ++SV+LA++I+ + L +F+   +  +  +  I  +       L   +EEL+LSVRS
Sbjct: 203 SITPQESVSLAAKIMTEHLNIFVGLTDEAQNAEIMIEKEEDQKEKVLEMSIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++EADM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVKYKLEDLGLGL 310


>gi|324455908|gb|ADY39246.1| RNA polymerase alpha subunit [Vibrio variabilis]
 gi|324455910|gb|ADY39247.1| RNA polymerase alpha subunit [Vibrio sp. R-40493]
          Length = 262

 Score =  234 bits (597), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 120/265 (45%), Positives = 181/265 (68%), Gaps = 8/265 (3%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ 
Sbjct: 1   PLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLA 60

Query: 94  LKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
           ++++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +
Sbjct: 61  VRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEISMRIKVER 120

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+
Sbjct: 121 GRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 181 GTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 237

Query: 269 STNCLRGENIVYMGDLIQRTEADML 293
           S NCL+ E I Y+GDL+QRTE ++L
Sbjct: 238 SANCLKAEAIHYIGDLVQRTEVELL 262


>gi|15925214|ref|NP_372748.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus Mu50]
 gi|15927804|ref|NP_375337.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus N315]
 gi|21283872|ref|NP_646960.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus MW2]
 gi|49484440|ref|YP_041664.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus MRSA252]
 gi|49487006|ref|YP_044227.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus MSSA476]
 gi|57650808|ref|YP_187023.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus COL]
 gi|87162055|ref|YP_494813.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus USA300_FPR3757]
 gi|88196136|ref|YP_500953.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus NCTC 8325]
 gi|148268664|ref|YP_001247607.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus JH9]
 gi|150394729|ref|YP_001317404.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus JH1]
 gi|151222338|ref|YP_001333160.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus str. Newman]
 gi|156980539|ref|YP_001442798.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus Mu3]
 gi|161510428|ref|YP_001576087.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus USA300_TCH1516]
 gi|221140174|ref|ZP_03564667.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus str. JKD6009]
 gi|253316985|ref|ZP_04840198.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus str. CF-Marseille]
 gi|253729890|ref|ZP_04864055.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus USA300_TCH959]
 gi|253734367|ref|ZP_04868532.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus TCH130]
 gi|255007004|ref|ZP_05145605.2| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus Mu50-omega]
 gi|257423709|ref|ZP_05600138.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus 55/2053]
 gi|257426387|ref|ZP_05602789.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus 65-1322]
 gi|257431673|ref|ZP_05608036.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus E1410]
 gi|257434633|ref|ZP_05610684.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus M876]
 gi|257794570|ref|ZP_05643549.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A9781]
 gi|258408828|ref|ZP_05681112.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A9763]
 gi|258422427|ref|ZP_05685339.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A9719]
 gi|258422671|ref|ZP_05685576.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A9635]
 gi|258439815|ref|ZP_05690561.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A9299]
 gi|258442629|ref|ZP_05691189.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A8115]
 gi|258446673|ref|ZP_05694828.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A6300]
 gi|258450209|ref|ZP_05698301.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A6224]
 gi|258450780|ref|ZP_05698839.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A5948]
 gi|258455419|ref|ZP_05703379.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A5937]
 gi|269203857|ref|YP_003283126.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus ED98]
 gi|282893663|ref|ZP_06301895.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A8117]
 gi|282902127|ref|ZP_06310020.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus C160]
 gi|282906567|ref|ZP_06314415.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus Btn1260]
 gi|282909537|ref|ZP_06317348.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus WW2703/97]
 gi|282911785|ref|ZP_06319581.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus WBG10049]
 gi|282915073|ref|ZP_06322850.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus M899]
 gi|282917569|ref|ZP_06325321.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus D139]
 gi|282920799|ref|ZP_06328517.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus C427]
 gi|282922093|ref|ZP_06329789.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A9765]
 gi|282925704|ref|ZP_06333352.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus C101]
 gi|282926770|ref|ZP_06334397.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A10102]
 gi|283767316|ref|ZP_06340231.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus H19]
 gi|283959002|ref|ZP_06376443.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus A017934/97]
 gi|284025250|ref|ZP_06379648.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus 132]
 gi|293497477|ref|ZP_06665331.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus 58-424]
 gi|293511052|ref|ZP_06669749.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus M809]
 gi|293549658|ref|ZP_06672330.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus M1015]
 gi|294848757|ref|ZP_06789502.1| DNA-directed RNA polymerase [Staphylococcus aureus A9754]
 gi|295404900|ref|ZP_06814713.1| DNA-directed RNA polymerase [Staphylococcus aureus A8819]
 gi|295428807|ref|ZP_06821431.1| DNA-directed RNA polymerase [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|296275985|ref|ZP_06858492.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus MR1]
 gi|297209963|ref|ZP_06926359.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus ATCC 51811]
 gi|297243958|ref|ZP_06927848.1| DNA-directed RNA polymerase [Staphylococcus aureus A8796]
 gi|297589707|ref|ZP_06948348.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus MN8]
 gi|300910975|ref|ZP_07128425.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus TCH70]
 gi|304379408|ref|ZP_07362143.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus ATCC BAA-39]
 gi|54039276|sp|P66706|RPOA_STAAN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|54039277|sp|P66707|RPOA_STAAW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|54042187|sp|P66705|RPOA_STAAM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|56749506|sp|Q6G797|RPOA_STAAS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|56749553|sp|Q6GEK9|RPOA_STAAR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|62287349|sp|Q5HDY4|RPOA_STAAC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366732|sp|Q2FER5|RPOA_STAA3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366733|sp|Q2FW32|RPOA_STAA8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|171769946|sp|A7X5C4|RPOA_STAA1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172049005|sp|A6QJ66|RPOA_STAAE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|13702024|dbj|BAB43316.1| DNA-directed RNA polymerase alpha chain [Staphylococcus aureus
           subsp. aureus N315]
 gi|14247997|dbj|BAB58386.1| DNA-directed RNA polymerase alpha chain [Staphylococcus aureus
           subsp. aureus Mu50]
 gi|21205314|dbj|BAB96008.1| DNA-directed RNA polymerase alpha chain [Staphylococcus aureus
           subsp. aureus MW2]
 gi|49242569|emb|CAG41290.1| DNA-directed RNA polymerase alpha chain [Staphylococcus aureus
           subsp. aureus MRSA252]
 gi|49245449|emb|CAG43926.1| DNA-directed RNA polymerase alpha chain [Staphylococcus aureus
           subsp. aureus MSSA476]
 gi|57284994|gb|AAW37088.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus COL]
 gi|87128029|gb|ABD22543.1| DNA-directed RNA polymerase alpha subunit [Staphylococcus aureus
           subsp. aureus USA300_FPR3757]
 gi|87203694|gb|ABD31504.1| DNA-directed RNA polymerase alpha chain, putative [Staphylococcus
           aureus subsp. aureus NCTC 8325]
 gi|147741733|gb|ABQ50031.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus JH9]
 gi|149947181|gb|ABR53117.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus JH1]
 gi|150375138|dbj|BAF68398.1| DNA-directed RNA polymerase alpha chain [Staphylococcus aureus
           subsp. aureus str. Newman]
 gi|156722674|dbj|BAF79091.1| DNA-directed RNA polymerase alpha chain [Staphylococcus aureus
           subsp. aureus Mu3]
 gi|160369237|gb|ABX30208.1| DNA-directed RNA polymerase alpha subunit [Staphylococcus aureus
           subsp. aureus USA300_TCH1516]
 gi|253726337|gb|EES95066.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus USA300_TCH959]
 gi|253727684|gb|EES96413.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus TCH130]
 gi|257272727|gb|EEV04829.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus 55/2053]
 gi|257276018|gb|EEV07469.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus 65-1322]
 gi|257282552|gb|EEV12684.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus E1410]
 gi|257285229|gb|EEV15345.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus M876]
 gi|257788542|gb|EEV26882.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A9781]
 gi|257840511|gb|EEV64971.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A9763]
 gi|257841858|gb|EEV66295.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A9719]
 gi|257847082|gb|EEV71091.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A9635]
 gi|257847591|gb|EEV71593.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A9299]
 gi|257851750|gb|EEV75684.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A8115]
 gi|257854741|gb|EEV77689.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A6300]
 gi|257856301|gb|EEV79210.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A6224]
 gi|257861563|gb|EEV84365.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A5948]
 gi|257862630|gb|EEV85398.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A5937]
 gi|262076147|gb|ACY12120.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus ED98]
 gi|269941813|emb|CBI50223.1| DNA-directed RNA polymerase alpha chain [Staphylococcus aureus
           subsp. aureus TW20]
 gi|282312533|gb|EFB42937.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus C101]
 gi|282315214|gb|EFB45598.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus C427]
 gi|282318531|gb|EFB48889.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus D139]
 gi|282320794|gb|EFB51128.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus M899]
 gi|282323481|gb|EFB53797.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus WBG10049]
 gi|282326516|gb|EFB56818.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus WW2703/97]
 gi|282329466|gb|EFB58987.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus Btn1260]
 gi|282591221|gb|EFB96294.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A10102]
 gi|282593561|gb|EFB98554.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A9765]
 gi|282596586|gb|EFC01545.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus C160]
 gi|282763721|gb|EFC03849.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A8117]
 gi|283461195|gb|EFC08279.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus H19]
 gi|283471446|emb|CAQ50657.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus ST398]
 gi|283788594|gb|EFC27421.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus A017934/97]
 gi|285817886|gb|ADC38373.1| DNA-directed RNA polymerase alpha subunit [Staphylococcus aureus
           04-02981]
 gi|290918705|gb|EFD95781.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus M1015]
 gi|291096408|gb|EFE26666.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus 58-424]
 gi|291466039|gb|EFF08568.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus M809]
 gi|294824136|gb|EFG40560.1| DNA-directed RNA polymerase [Staphylococcus aureus A9754]
 gi|294969845|gb|EFG45863.1| DNA-directed RNA polymerase [Staphylococcus aureus A8819]
 gi|295127156|gb|EFG56798.1| DNA-directed RNA polymerase [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|296885636|gb|EFH24573.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus ATCC 51811]
 gi|297178736|gb|EFH37981.1| DNA-directed RNA polymerase [Staphylococcus aureus A8796]
 gi|297578218|gb|EFH96931.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus MN8]
 gi|298695481|gb|ADI98703.1| DNA-directed RNA polymerase alpha chain [Staphylococcus aureus
           subsp. aureus ED133]
 gi|300887955|gb|EFK83150.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus TCH70]
 gi|302333860|gb|ADL24053.1| DNA-directed RNA polymerase alpha subunit [Staphylococcus aureus
           subsp. aureus JKD6159]
 gi|302752097|gb|ADL66274.1| DNA-directed RNA polymerase alpha subunit [Staphylococcus aureus
           subsp. aureus str. JKD6008]
 gi|304341940|gb|EFM07844.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus ATCC BAA-39]
 gi|312437365|gb|ADQ76436.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus TCH60]
 gi|312830573|emb|CBX35415.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus ECT-R 2]
 gi|315129696|gb|EFT85687.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus CGS03]
 gi|315193476|gb|EFU23872.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus CGS00]
 gi|315198246|gb|EFU28577.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus CGS01]
 gi|320140238|gb|EFW32097.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus MRSA131]
 gi|320143508|gb|EFW35289.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus MRSA177]
 gi|323440096|gb|EGA97811.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           O11]
 gi|323442770|gb|EGB00396.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           O46]
 gi|329723377|gb|EGG59906.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus 21172]
 gi|329730447|gb|EGG66837.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus 21193]
 gi|329732085|gb|EGG68440.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus 21189]
          Length = 314

 Score =  234 bits (597), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 122/288 (42%), Positives = 190/288 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+GVLHE S++  V ED++ II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEGVLHEFSAVDNVVEDVSTIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  R  G VTA DI   +D+E+LNP+  I  +     +++ L  
Sbjct: 83  KQLALKIYSEEDKTLEIDVRDEGEVTASDITHDSDVEILNPELKIATVSKGGHLKIRLVA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTVE+ R GQ  D+DKL++ + T+G
Sbjct: 143 NKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTVENTRVGQSSDFDKLTLDVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SIT ++SV+LA++I+ + L +F+   +  +  +  I  +       L   +EEL+LSVRS
Sbjct: 203 SITPQESVSLAAKIMTEHLNIFVGLTDEAQNAEIMIEKEEDQKEKVLEMSIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++EADM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVKYKLEDLGLGL 310


>gi|329770014|ref|ZP_08261409.1| DNA-directed RNA polymerase subunit alpha [Gemella sanguinis M325]
 gi|328837325|gb|EGF86955.1| DNA-directed RNA polymerase subunit alpha [Gemella sanguinis M325]
          Length = 313

 Score =  234 bits (597), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 126/284 (44%), Positives = 180/284 (63%), Gaps = 12/284 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA  ++ I GV HE  ++KGV ED+T+II+N+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRMLISSLPGAAARSIDIQGVQHEFQAVKGVVEDVTEIIMNV 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I  K+  +  K V+I  +GP VVTA DI   +DIEV+N D  I  +       M + V
Sbjct: 83  KNIAFKVHSEEEKVVSINVKGPAVVTAEDIAIDSDIEVINTDQHIATVSEGGQFEMLIYV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG G+VPA  ++  + PIG+I ID++Y+P+ KV+YTVE  R GQ  D+DKL + + T+G
Sbjct: 143 GKGRGFVPADGNKKRDLPIGVIPIDSIYTPVSKVNYTVEKTRVGQSTDFDKLILDVTTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEV------KEDINVKSLPFNPALLKKVEEL 263
           +IT  D++ALAS+IL   L +F+   E  K        +ED  V+ L         +EEL
Sbjct: 203 TITANDALALASKILISHLELFMEMSEEAKAADILVAKEEDNKVQMLEMT------IEEL 256

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +LSVRS NCL+   I  + +L  +TE +M+++ N GRKSL E+K
Sbjct: 257 DLSVRSYNCLKRAGINTVQELANKTEQEMIKVRNLGRKSLEEVK 300


>gi|309777158|ref|ZP_07672121.1| DNA-directed RNA polymerase, alpha subunit [Erysipelotrichaceae
           bacterium 3_1_53]
 gi|308915028|gb|EFP60805.1| DNA-directed RNA polymerase, alpha subunit [Erysipelotrichaceae
           bacterium 3_1_53]
          Length = 319

 Score =  234 bits (597), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 130/298 (43%), Positives = 189/298 (63%), Gaps = 5/298 (1%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E ++    + EPL RGF  T+GNALRRVL+SSL GAA+ ++++DGV HE +SI G+ ED+
Sbjct: 16  ESQHYGKFVFEPLERGFGTTIGNALRRVLLSSLPGAAVFSIKVDGVYHEFTSIPGIVEDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILNIK + + +  D    + I K+GPG VT  DI     +EV++ D  IC L+   +
Sbjct: 76  TAIILNIKTLVMSIQDDEIYTLRISKQGPGAVTGADIICPEGVEVISKDLHICTLEEGGM 135

Query: 143 VRMELTVSKGHGYVPA----KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
           + MEL    G GYV A    + ++T N P+G+I  D++Y+PI+KVSY VE  R GQ   Y
Sbjct: 136 LEMELQARIGRGYVSADTNKQLYQTPNQPLGIIYTDSIYTPIEKVSYNVEPTRVGQDAHY 195

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN-VKSLPFNPALL 257
           DK+++ I TD S++  +SVALASRIL D L +  N  E   +++  +   +    N  L+
Sbjct: 196 DKVTLEIWTDSSLSPAESVALASRILIDHLELLTNVHEAVNDMESVMKEAQGEVQNKGLV 255

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
             +E+L+LSVRS NCL+   I  + +L QRTE +M+R+ N G+KSL E+K  +  +GL
Sbjct: 256 MMIEDLDLSVRSYNCLKRAGIQTVEELTQRTEDEMMRVRNLGKKSLKEVKDKIYDLGL 313


>gi|267798457|gb|ACY78909.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 269

 Score =  234 bits (597), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 119/262 (45%), Positives = 180/262 (68%), Gaps = 8/262 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 11  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 70

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V 
Sbjct: 71  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIIVE 130

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 131 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMET 190

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 191 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 247

Query: 268 RSTNCLRGENIVYMGDLIQRTE 289
           RS NCL+ E I Y+GDL+QRTE
Sbjct: 248 RSANCLKAEAIHYIGDLVQRTE 269


>gi|267798443|gb|ACY78902.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798447|gb|ACY78904.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798449|gb|ACY78905.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798451|gb|ACY78906.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798453|gb|ACY78907.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798455|gb|ACY78908.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798459|gb|ACY78910.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798463|gb|ACY78912.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798465|gb|ACY78913.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798467|gb|ACY78914.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798469|gb|ACY78915.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798471|gb|ACY78916.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798473|gb|ACY78917.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798475|gb|ACY78918.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 269

 Score =  234 bits (597), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 119/262 (45%), Positives = 180/262 (68%), Gaps = 8/262 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 11  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 70

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V 
Sbjct: 71  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVE 130

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 131 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMET 190

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 191 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 247

Query: 268 RSTNCLRGENIVYMGDLIQRTE 289
           RS NCL+ E I Y+GDL+QRTE
Sbjct: 248 RSANCLKAEAIHYIGDLVQRTE 269


>gi|163786164|ref|ZP_02180612.1| DNA-directed RNA polymerase alpha subunit [Flavobacteriales
           bacterium ALC-1]
 gi|159878024|gb|EDP72080.1| DNA-directed RNA polymerase alpha subunit [Flavobacteriales
           bacterium ALC-1]
          Length = 330

 Score =  234 bits (596), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 128/298 (42%), Positives = 188/298 (63%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRVL+SSL G AIT+V+I+GV HE S+I GV ED+T++ILN+K +N
Sbjct: 28  PLEPGYGLTVGNALRRVLLSSLEGFAITSVRIEGVDHEFSTISGVVEDVTEMILNLKQVN 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   D   ++ VTI   G   +TAGD Q  ++  +VLN D VICNLD    + MELT+ 
Sbjct: 88  FKRQIDEVDNETVTISISGQEQITAGDFQKFISGFQVLNTDLVICNLDPKVNINMELTIE 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++  + PIG I  D++Y+PIK V Y++E+ R  Q  DY+KL   I TDGS
Sbjct: 148 KGRGYVPAEENKKASAPIGTIFTDSIYTPIKNVKYSIENFRVEQKTDYEKLVFEIQTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++IL     +F    I  E  +    E  + +SL     L  K+ +++LS
Sbjct: 208 INPKDALTEAAKILIHHFMLFSDERITLEADEIAQTETYDEESLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   + D+++  NFG+KSL E++ ++   GL  GM+L  +
Sbjct: 268 VRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKKSLTELEELVNVKGLNFGMDLSKY 325


>gi|267798445|gb|ACY78903.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798461|gb|ACY78911.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 269

 Score =  234 bits (596), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 119/262 (45%), Positives = 180/262 (68%), Gaps = 8/262 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 11  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 70

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V 
Sbjct: 71  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIRVE 130

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 131 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMET 190

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 191 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 247

Query: 268 RSTNCLRGENIVYMGDLIQRTE 289
           RS NCL+ E I Y+GDL+QRTE
Sbjct: 248 RSANCLKAEAIHYIGDLVQRTE 269


>gi|163816005|ref|ZP_02207375.1| hypothetical protein COPEUT_02185 [Coprococcus eutactus ATCC 27759]
 gi|158448815|gb|EDP25810.1| hypothetical protein COPEUT_02185 [Coprococcus eutactus ATCC 27759]
          Length = 318

 Score =  234 bits (596), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 126/294 (42%), Positives = 193/294 (65%), Gaps = 3/294 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL G A++ V+I GVLHE SSI GV ED+T+II+NI
Sbjct: 23  FVIEPLERGYGITLGNSLRRIMLSSLPGTAVSHVKIKGVLHEFSSIPGVKEDVTEIIMNI 82

Query: 90  KGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVVRME 146
           K + +K + D+   K+  I   G  VV AGDI+   DIE++NPD VI NL   DA + ME
Sbjct: 83  KNVVIKNNSDTFEPKQAYIDVVGERVVKAGDIKVDGDIEIVNPDLVIANLSGPDAKLEME 142

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           LT++ G GYV    ++  + PI +I ID++++P+++V+ TV++ R GQV DYDKL++ + 
Sbjct: 143 LTIANGRGYVSLDKNKEADAPIDVIAIDSIFTPVERVNLTVQNTRVGQVTDYDKLTLDVY 202

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+G++  +++V+LA+ +L + L +F++  E  + V   +   +      L   ++ELELS
Sbjct: 203 TNGALAPDEAVSLAANLLVEHLKLFVDLSENARLVDVMVESTTDEKEKVLEMNIDELELS 262

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           VRS NCL+   I  + +LI +T  DM+++ N GRKSL E+   L  +GL L  N
Sbjct: 263 VRSYNCLKRAGINTVQELINKTPEDMMKVRNLGRKSLDEVLAKLKELGLALNQN 316


>gi|312140889|ref|YP_004008225.1| DNA-directed RNA polymerase alpha subunit rpoa [Rhodococcus equi
           103S]
 gi|325675473|ref|ZP_08155157.1| DNA-directed RNA polymerase subunit alpha [Rhodococcus equi ATCC
           33707]
 gi|311890228|emb|CBH49546.1| DNA-directed RNA polymerase alpha subunit RpoA [Rhodococcus equi
           103S]
 gi|325553444|gb|EGD23122.1| DNA-directed RNA polymerase subunit alpha [Rhodococcus equi ATCC
           33707]
          Length = 354

 Score =  233 bits (595), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 129/313 (41%), Positives = 195/313 (62%), Gaps = 16/313 (5%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ENR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+TD
Sbjct: 16  ENRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ +    D    + + K+GPGVVTAGDI     + V NPD  I  L+    + 
Sbjct: 76  IILNLKGLVVSSEEDEPVTMYVRKQGPGVVTAGDIVPPAGVTVNNPDLHIATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D+L + 
Sbjct: 136 IELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDRLILD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNPAL 256
           ++T  SIT  D++A A + L +  G+   +N E       P     + I    LP     
Sbjct: 196 VETKNSITARDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFGLP----- 250

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E+L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L ++GL 
Sbjct: 251 ---IEDLDLTVRSYNCLKREGVHTVGELVGRTESDLLDIRNFGQKSIDEVKVKLHSLGLA 307

Query: 317 LGMNLPDWPPESI 329
           L  +   + P ++
Sbjct: 308 LKDSPASFDPTTV 320


>gi|27468715|ref|NP_765352.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           epidermidis ATCC 12228]
 gi|57867752|ref|YP_189368.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           epidermidis RP62A]
 gi|242243973|ref|ZP_04798416.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           epidermidis W23144]
 gi|251812073|ref|ZP_04826546.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|282875368|ref|ZP_06284241.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus
           epidermidis SK135]
 gi|293368459|ref|ZP_06615083.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|33301647|sp|Q8CRI4|RPOA_STAES RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|71153723|sp|Q5HM25|RPOA_STAEQ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|27316263|gb|AAO05438.1|AE016750_43 DNA-directed RNA polymerase alpha chain [Staphylococcus epidermidis
           ATCC 12228]
 gi|57638410|gb|AAW55198.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus
           epidermidis RP62A]
 gi|242232606|gb|EES34918.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           epidermidis W23144]
 gi|251804407|gb|EES57064.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|281296133|gb|EFA88654.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus
           epidermidis SK135]
 gi|291317417|gb|EFE57839.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|319400599|gb|EFV88824.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus
           epidermidis FRI909]
 gi|329731206|gb|EGG67576.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus
           epidermidis VCU144]
 gi|329736451|gb|EGG72719.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus
           epidermidis VCU028]
 gi|329737076|gb|EGG73331.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus
           epidermidis VCU045]
          Length = 314

 Score =  233 bits (595), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 121/288 (42%), Positives = 191/288 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+GVLHE S++  V ED++ II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEGVLHEFSAVDNVVEDVSTIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  +  G VTA DI   +D+E+LNP+  I  +     +++ L  
Sbjct: 83  KKLALKIYSEEDKTLEIDVKDEGEVTASDITHDSDVEILNPELKIATVSKGGHLKVRLVA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTVE+ R GQ  D+DKL++ + T+G
Sbjct: 143 NKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTVENTRVGQSSDFDKLTLDVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SIT ++SV+LA++I+ + L +F++  +  +  +  I  +       L   +EEL+LSVRS
Sbjct: 203 SITPQESVSLAAKIMTEHLNIFVSLTDEAQNAEIMIEKEEDQKEKVLEMSIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++EADM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVKYKLEDLGLGL 310


>gi|302519632|ref|ZP_07271974.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. SPB78]
 gi|318058101|ref|ZP_07976824.1| DNA-directed RNA polymerase subunit alpha [Streptomyces sp.
           SA3_actG]
 gi|318076046|ref|ZP_07983378.1| DNA-directed RNA polymerase subunit alpha [Streptomyces sp.
           SA3_actF]
 gi|302428527|gb|EFL00343.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. SPB78]
          Length = 340

 Score =  233 bits (595), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 130/318 (40%), Positives = 194/318 (61%), Gaps = 4/318 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPGVVTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGVVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNAKGKLEMELTVERGRGYVSAVQNKQAGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNVDAEGIDMGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPPES 328
             MGL L  + P + P S
Sbjct: 302 AGMGLALKDSPPGFDPTS 319


>gi|328814017|gb|AEB52124.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 263

 Score =  233 bits (594), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 120/260 (46%), Positives = 172/260 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 4   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 63

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV
Sbjct: 64  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTV 123

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 124 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDG 183

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +EEL+LSVRS
Sbjct: 184 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEELDLSVRS 243

Query: 270 TNCLRGENIVYMGDLIQRTE 289
            NCL+   I  + +L  ++E
Sbjct: 244 YNCLKRAGINTVQELTNKSE 263


>gi|300174006|ref|YP_003773172.1| DNA-directed RNA polymerase subunit alpha [Leuconostoc
           gasicomitatum LMG 18811]
 gi|299888385|emb|CBL92353.1| DNA-directed RNA polymerase, alpha subunit [Leuconostoc
           gasicomitatum LMG 18811]
          Length = 314

 Score =  233 bits (594), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 132/312 (42%), Positives = 191/312 (61%), Gaps = 10/312 (3%)

Query: 8   ELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           E  KPN  NIE      E       + EPL RG+  TLGN+LRR+L+SSL GAA+  VQI
Sbjct: 3   EFEKPNIHNIE------EGARYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGV+HE S++ GV ED+T IILN+K + L +  D  + + +  +GP  VTA D+Q   D+
Sbjct: 57  DGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDEERSLEVDIQGPADVTAADLQAGADV 116

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKV 183
           EVLNPD  I  +     + M +T  KG GY  A  ++   D  PIG++ +D++Y+PI++V
Sbjct: 117 EVLNPDLHIATVAAGKSLHMTITAFKGRGYSSADENKQLRDEMPIGVLAVDSIYTPIERV 176

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+ R G   DYDKL+  I T+GSI   D+++L S+IL + L +F++      E   
Sbjct: 177 NYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSLGSKILAEHLNLFMDISPVAAEANV 236

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            + V+ +  + +    +E+L+LSVRS NCL+   I  + +L  RTEADM+++ N GRKSL
Sbjct: 237 MVEVEPVAVSASDSAPIEDLDLSVRSYNCLKRAGINTIVELTDRTEADMMKVRNLGRKSL 296

Query: 304 VEIKGVLGTMGL 315
            EI+  L  M L
Sbjct: 297 DEIQEKLTEMSL 308


>gi|312144220|ref|YP_003995666.1| DNA-directed RNA polymerase, alpha subunit [Halanaerobium sp.
           'sapolanicus']
 gi|311904871|gb|ADQ15312.1| DNA-directed RNA polymerase, alpha subunit [Halanaerobium sp.
           'sapolanicus']
          Length = 314

 Score =  233 bits (594), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 126/285 (44%), Positives = 192/285 (67%), Gaps = 1/285 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAA+T+V+++GV HE S+I GV ED+TD+ILN+K + 
Sbjct: 25  PLERGYGTTLGNSLRRILLSSLPGAALTSVKVEGVKHEFSAISGVVEDMTDLILNLKEVV 84

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +K SG+    + I   G G VTAGD  T  D++V+N DH I  L  D  + +E TV KG 
Sbjct: 85  VKFSGEEQSTIRIEAEGEGEVTAGDFITSGDVQVINKDHHIATLAEDGRLLLEATVEKGR 144

Query: 154 GYVPAKHHRTENDP-IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           GY  A+ ++   D  IGLI ID+ +SPI++ ++ +E+ R GQV DYD+L + + T+GSI 
Sbjct: 145 GYHTAEENKDHFDKVIGLIPIDSSFSPIERANFNIENTRVGQVTDYDRLILEVKTNGSIH 204

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
            +D+++LA++I+ + L +FIN  +  ++V+  + V+    +  L   +EELELSVRS+NC
Sbjct: 205 PDDAISLAAKIMVEHLELFINLTDEIEDVEIMVEVEEEEKDKILDTTIEELELSVRSSNC 264

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+   I  + +L+ +TE D++++ N G+KSL EIK  L  + L L
Sbjct: 265 LKRAGINTVEELVDKTEDDLMKVRNLGKKSLQEIKDKLDELELEL 309


>gi|281357932|ref|ZP_06244417.1| DNA-directed RNA polymerase, alpha subunit [Victivallis vadensis
           ATCC BAA-548]
 gi|281315590|gb|EFA99618.1| DNA-directed RNA polymerase, alpha subunit [Victivallis vadensis
           ATCC BAA-548]
          Length = 338

 Score =  233 bits (594), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 134/302 (44%), Positives = 187/302 (61%), Gaps = 9/302 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E     IA P   GF HTLGN+LRRVL+SSL GAAI +V+IDG  HE  S+  V ED+T+
Sbjct: 22  ETYAKFIAAPFQSGFGHTLGNSLRRVLLSSLEGAAICSVRIDGAKHEFDSLDNVVEDVTE 81

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           I+LN+K + L +  +  K + I K   G VTA DI   + +EVLNPD VIC LD     R
Sbjct: 82  IVLNLKCVRLNLHAEGPKTLEIRKDKAGKVTAADIVCDSTVEVLNPDQVICTLDKSLPFR 141

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
            E+ V KG GY+PA+ + T    IG I +D L+SP+ +V+Y V +AR G+  + D L + 
Sbjct: 142 AEIEVIKGKGYLPAEKN-TAPRSIGTIPVDCLFSPVTRVNYQVGAARVGEETEMDSLELE 200

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV---KEDINVKSLPFNPALLKKVE 261
           I TDG I+ ++++  A+RIL+D L  F+  +  +K+V   +E+  +  L     L   VE
Sbjct: 201 IWTDGRISPQNALEEAARILRDHLQPFMGNQVVEKDVVLTEEETKMFKL-----LSHDVE 255

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
            L+LSVR+ NCL   NI  +G+L  +TE+ ML+  NFG+KSL EIK  +  +GL LGM+ 
Sbjct: 256 ILDLSVRAMNCLNSANIKLIGELCTKTESRMLKYRNFGKKSLDEIKEKIEKLGLELGMSF 315

Query: 322 PD 323
            D
Sbjct: 316 SD 317


>gi|167767776|ref|ZP_02439829.1| hypothetical protein CLOSS21_02311 [Clostridium sp. SS2/1]
 gi|317497067|ref|ZP_07955394.1| DNA-directed RNA polymerase [Lachnospiraceae bacterium 5_1_63FAA]
 gi|167710515|gb|EDS21094.1| hypothetical protein CLOSS21_02311 [Clostridium sp. SS2/1]
 gi|291558883|emb|CBL37683.1| DNA-directed RNA polymerase subunit alpha [butyrate-producing
           bacterium SSC/2]
 gi|316895612|gb|EFV17767.1| DNA-directed RNA polymerase [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 318

 Score =  233 bits (594), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 126/287 (43%), Positives = 190/287 (66%), Gaps = 4/287 (1%)

Query: 24  EENRT-LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E+NR    + EPL RG+  TLGN+LRR+++SSL GAA+++V+I GVLHE SSI GV ED+
Sbjct: 16  EDNRFGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSSVKIKGVLHEFSSIPGVKEDV 75

Query: 83  TDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
            +II+NIK + +K +  S   K+  I   G GVVTAGDI+  +DIE+LNP+ VI  L  D
Sbjct: 76  PEIIMNIKSLAIKNNSSSAETKQAYIEFSGKGVVTAGDIKADSDIEILNPELVIATLSDD 135

Query: 141 AV-VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           +  + MELT++ G GYV A     E   I  I +DA+Y+P+++V+  VE+ R GQ+ DYD
Sbjct: 136 SSKLDMELTITNGRGYVGADKADKEGKAIDEIAVDAIYTPVERVNLKVENTRVGQITDYD 195

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL++ + T+G++T ++SV+LA+++L + L +F++  E  K  +  +  +       L   
Sbjct: 196 KLTLDVFTNGTLTPDESVSLAAKVLCEHLNLFVDLSENAKTAEVMVEKEDDEKEKVLEMS 255

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           ++ELELSVRS NCL+   I  + +L  +T  DM+++ N GRKSL E+
Sbjct: 256 IDELELSVRSYNCLKRAGINTVEELTNKTSEDMMKVRNLGRKSLEEV 302


>gi|194335472|ref|YP_002017266.1| DNA-directed RNA polymerase, alpha subunit [Pelodictyon
           phaeoclathratiforme BU-1]
 gi|238693374|sp|B4SBX4|RPOA_PELPB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|194307949|gb|ACF42649.1| DNA-directed RNA polymerase, alpha subunit [Pelodictyon
           phaeoclathratiforme BU-1]
          Length = 327

 Score =  233 bits (593), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 122/304 (40%), Positives = 189/304 (62%), Gaps = 13/304 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            IA+PL RG+  TLGN +RRVL++SL G AIT ++IDGV HE ++I GV ED+ +I+LN+
Sbjct: 25  FIAQPLERGYGVTLGNVMRRVLLASLPGTAITGIKIDGVFHEFAAIDGVREDVPEIVLNL 84

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           K +  K +   + + ++   GP   TAGDI     + EVLN D  +  ++  A V+++L 
Sbjct: 85  KKVRFKSTCKRNCKTSLTLVGPMDFTAGDIIAQEGEFEVLNKDMHVATINAGATVKIDLY 144

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           + +G GY+PA+ +R E  PIG I +DA+Y+PI+ V +TVE+ R GQ  DY+K+ + ++TD
Sbjct: 145 IGRGRGYMPAEENRPEGMPIGYIAVDAIYTPIRNVKFTVENTRVGQRTDYEKMILDVETD 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFE--------EPKKEVKEDINVKSLPFNPALLKKV 260
           GS++ +DS++LA +I+ D +  F NF         E  K+  ++       F+     K+
Sbjct: 205 GSVSPDDSISLAGKIITDHVTFFANFSPTEEEFTEEEFKQQDDEFETMRRLFH----TKI 260

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           E+L+LSVRS NCLR   I  +G+L+   E ++L   NFG+KSL E+K  L    L  GM+
Sbjct: 261 EDLDLSVRSHNCLRLAEIDTIGELVSHKEDELLNYKNFGKKSLTELKEQLEKFDLKFGMD 320

Query: 321 LPDW 324
           +  +
Sbjct: 321 ITKY 324


>gi|317125840|ref|YP_004099952.1| DNA-directed RNA polymerase subunit alpha [Intrasporangium calvum
           DSM 43043]
 gi|315589928|gb|ADU49225.1| DNA-directed RNA polymerase subunit alpha [Intrasporangium calvum
           DSM 43043]
          Length = 341

 Score =  233 bits (593), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 130/311 (41%), Positives = 197/311 (63%), Gaps = 12/311 (3%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T+
Sbjct: 16  DNRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           +ILNIKG+ +    D    + + K+GPGVVTAGDI     +EV NPD  I  L+    + 
Sbjct: 76  MILNIKGLVVSSEHDEPVVMYLRKQGPGVVTAGDITPPAGVEVHNPDLAIATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MELTV +G GYV A+ +++ +  IG I +D++YSP+  V+Y VE+ R  Q  D+DKL + 
Sbjct: 136 MELTVERGRGYVSAQQNKSGDQEIGRIPVDSIYSPVLAVTYKVEATRVEQRTDFDKLIVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLP----FNPALLK 258
           ++T  S+T  D++A + + L +  G+   +N E       E I++   P        L  
Sbjct: 196 VETKNSMTPRDAMASSGKTLVELFGLARELNVE------AEGIDMGPSPTDAALAADLAL 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  MGL L 
Sbjct: 250 PIEDLDLTVRSYNCLKREGIHTVGELVGRSEADLLDIRNFGAKSIDEVKAKLVGMGLALK 309

Query: 319 MNLPDWPPESI 329
            + P + P ++
Sbjct: 310 DSPPGFDPSAL 320


>gi|238928128|ref|ZP_04659888.1| DNA-directed RNA polymerase [Selenomonas flueggei ATCC 43531]
 gi|238884088|gb|EEQ47726.1| DNA-directed RNA polymerase [Selenomonas flueggei ATCC 43531]
          Length = 319

 Score =  233 bits (593), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 127/294 (43%), Positives = 189/294 (64%), Gaps = 8/294 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL  G+  T GN+LRR+L+SSL GAA+T++QIDGVLHE S+I GV +D+T I+L +
Sbjct: 23  FICEPLEPGYGTTFGNSLRRMLLSSLDGAAVTSIQIDGVLHEFSTIPGVRDDVTSIVLAL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + ++M     + + I   G   VTA DI+  +DIE+LNPD  I  L     +++++TV
Sbjct: 83  KQLCIRMQDSEPRTIRIDAAGACEVTAADIECGSDIEILNPDLHIATLGDTGKLKIDMTV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYVPA  ++  +D IG+I ID+++SP+++V+YTVE  R G V DYD+L + + T+G
Sbjct: 143 ERGRGYVPADRNKKPDDVIGVIPIDSIFSPVQRVNYTVEDTRVGNVTDYDRLILDVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP------FNPALLKKVEEL 263
           SI  E++V+ A+ IL   L +F N +    E +E+  V + P          L   +++L
Sbjct: 203 SIRPEEAVSKAAAILVMHLRLFQNMDGSAAEEEEE--VPNFPPEEVDDSAKVLEMTIDDL 260

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +LSVRS NCL+   I  + DL Q+TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 261 DLSVRSFNCLKRAGINTVADLAQKTEDDMMKVRNLGRKSLDEVKKKLEELGLSL 314


>gi|314934272|ref|ZP_07841631.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus caprae
           C87]
 gi|313652202|gb|EFS15965.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus caprae
           C87]
          Length = 314

 Score =  233 bits (593), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 121/288 (42%), Positives = 190/288 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+GVLHE S++  V ED++ II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEGVLHEFSAVDNVVEDVSTIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  +  G VTA DI   +D+E+LNP+  I  +     +++ L  
Sbjct: 83  KKLALKIYSEEDKTLEIDVKDEGEVTASDITHDSDVEILNPELKIATVSKGGHLKVRLVA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTVE+ R GQ  D+DKL++ + T+G
Sbjct: 143 NKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTVENTRVGQSSDFDKLTLDVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SIT ++SV+LA++I+ + L +F+   +  +  +  I  +       L   +EEL+LSVRS
Sbjct: 203 SITPQESVSLAAKIMTEHLNIFVGLTDEAQNAEIMIEKEEDQKEKVLEMSIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++EADM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVKYKLEDLGLGL 310


>gi|295093661|emb|CBK82752.1| DNA-directed RNA polymerase subunit alpha [Coprococcus sp. ART55/1]
          Length = 318

 Score =  233 bits (593), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 126/294 (42%), Positives = 192/294 (65%), Gaps = 3/294 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+++SSL G A++ V+I GVLHE SSI GV ED+T+II+NI
Sbjct: 23  FVIEPLERGYGITLGNSLRRIMLSSLPGTAVSHVKIKGVLHEFSSIPGVKEDVTEIIMNI 82

Query: 90  KGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVVRME 146
           K + +K + D+   K+  I   G  VV AGDI+   DIE++NPD VI NL   DA + ME
Sbjct: 83  KNVVIKNNSDTFEPKQAYIDVVGERVVKAGDIKVDGDIEIVNPDLVIANLSGPDAKLEME 142

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           LT+  G GYV    ++  + PI +I ID++++P+++V+ TV++ R GQV DYDKL++ + 
Sbjct: 143 LTIVNGRGYVSLDKNKEADAPIDVIAIDSIFTPVERVNLTVQNTRVGQVTDYDKLTLDVY 202

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+G++  +++V+LA+ +L + L +F++  E  + V   +   +      L   ++ELELS
Sbjct: 203 TNGALAPDEAVSLAANLLVEHLKLFVDLSENARLVDVMVESTTDEKEKVLEMNIDELELS 262

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           VRS NCL+   I  + +LI +T  DM+++ N GRKSL E+   L  +GL L  N
Sbjct: 263 VRSYNCLKRAGINTVQELINKTPEDMMKVRNLGRKSLDEVLAKLKELGLSLNQN 316


>gi|328814019|gb|AEB52125.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 263

 Score =  233 bits (593), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 119/252 (47%), Positives = 169/252 (67%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+
Sbjct: 10  EEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDV 69

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILNIKG+ LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A 
Sbjct: 70  TQIILNIKGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGAT 129

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
               LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+
Sbjct: 130 FHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLT 189

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           M I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 190 MEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEE 249

Query: 263 LELSVRSTNCLR 274
           L+LSVRS NCL+
Sbjct: 250 LDLSVRSYNCLK 261


>gi|292669831|ref|ZP_06603257.1| DNA-directed RNA polymerase subunit alpha [Selenomonas noxia ATCC
           43541]
 gi|292648628|gb|EFF66600.1| DNA-directed RNA polymerase subunit alpha [Selenomonas noxia ATCC
           43541]
          Length = 319

 Score =  233 bits (593), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 127/294 (43%), Positives = 188/294 (63%), Gaps = 8/294 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL  G+  T GN+LRR+L+SSL GAA+T++QIDGVLHE S+I GV +D+T I+L +
Sbjct: 23  FVCEPLEPGYGTTFGNSLRRMLLSSLDGAAVTSIQIDGVLHEFSTIPGVRDDVTSIVLAL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + ++M G     + I   G   VTA DI+  +DIE+LNP+  I  L     +++E+TV
Sbjct: 83  KQLCIRMQGSELHTLRIEAEGEREVTAADIECGSDIEILNPELHIATLGATGKLKIEMTV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYVPA  ++   D IG+I ID+++SP+++V+YTVE  R G V DYD+L + + T+G
Sbjct: 143 ERGRGYVPADKNKKSEDSIGVIPIDSIFSPVQRVNYTVEDTRVGNVTDYDRLILDVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP------FNPALLKKVEEL 263
           SI  E++V+ A+ IL   L +F N +    E +E+  V + P          L   +++L
Sbjct: 203 SIRPEEAVSKAAAILVMHLRLFQNMDGTMLEEEEE--VPNFPPEEVDDSAKVLEMTIDDL 260

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +LSVRS NCL+   I  + DL Q+TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 261 DLSVRSFNCLKRAGINTVADLAQKTEDDMMKVRNLGRKSLDEVKKKLEELGLSL 314


>gi|294055196|ref|YP_003548854.1| DNA-directed RNA polymerase, alpha subunit [Coraliomargarita
           akajimensis DSM 45221]
 gi|293614529|gb|ADE54684.1| DNA-directed RNA polymerase, alpha subunit [Coraliomargarita
           akajimensis DSM 45221]
          Length = 333

 Score =  232 bits (592), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 128/297 (43%), Positives = 186/297 (62%), Gaps = 7/297 (2%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
           AEP   G+ HT+GN+LRRVL+SS+ GAAI++++IDGV HE  SI+GV ED+TDI+LN+K 
Sbjct: 30  AEPFEAGYGHTIGNSLRRVLLSSIEGAAISSIKIDGVQHEFQSIEGVVEDVTDIVLNLKK 89

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           + L         + I     G +TA DIQ   +I+V+NPD VIC L+ +     EL V  
Sbjct: 90  VLLVSESRESVNLIIDVTREGAITAADIQEDANIQVVNPDQVICTLEKEQRFFAELEVRV 149

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GY     ++    PIG+I ID+L+SP+K V Y+VE+ R GQ +DYDKL + I TDG I
Sbjct: 150 GRGYCTGDDNKKAEQPIGVIAIDSLFSPVKLVKYSVENTRVGQEMDYDKLVLEITTDGRI 209

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK-----VEELELS 266
           + +D++  ++ IL+  L +F   E  + +++ +   K +      L+K     V E+ELS
Sbjct: 210 SPDDALKQSAAILKHHLDVFD--EVSQDDIEFESESKEISEEQNRLRKLLNMSVNEIELS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           VR+ NCL   NI  +G+L  ++E +ML+  NFG+KSL EIK  L  +GL LGM + +
Sbjct: 268 VRAANCLNNANITTVGELAMKSEQEMLKYRNFGKKSLNEIKDKLEQLGLSLGMKIDE 324


>gi|116513565|ref|YP_812471.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
 gi|122275665|sp|Q04BY9|RPOA_LACDB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116092880|gb|ABJ58033.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
          Length = 312

 Score =  232 bits (592), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 130/316 (41%), Positives = 190/316 (60%), Gaps = 16/316 (5%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +E++    + EPL RGF  TLGN+LRRVL++S+ G  +  V+IDG
Sbjct: 3   EFKKPN----ITVVDQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSVPGTGLVKVKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           +LHE +++ GV ED+T IILN+K + L+   +  K + +   GP  VTA D++   D+EV
Sbjct: 59  ILHEFTTVPGVKEDVTKIILNLKKLELRAYTEEVKTIELDVEGPATVTAEDLKADADVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + M + V  G GYVPA  ++T    IG I +D+L+SPI+KV+Y V
Sbjct: 119 LNPDQYICTIAQGGHLHMWIDVCNGRGYVPASENKTAEMSIGDIPVDSLFSPIEKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK------EV 241
           ES R G+  D+DKL+M I T+GSI   D++  A+R+L +    F + +   +      E 
Sbjct: 179 ESTRVGKREDFDKLTMEIWTNGSIAPNDALNFAARVLVEHFKAFESADAAAEIGEVMVEQ 238

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           + D   K L         +E+L+LSVRS NCL+   I  + DL  ++EA+M+R+ N GRK
Sbjct: 239 ENDQKEKKLEMT------IEDLDLSVRSYNCLKRAGINTLQDLTVKSEAEMMRVRNLGRK 292

Query: 302 SLVEIKGVLGTMGLFL 317
           SL E+K  L  +GL L
Sbjct: 293 SLEEVKNKLADLGLSL 308


>gi|283945407|dbj|BAI66457.1| RNA polymerase alpha-subunit [Vibrio tapetis]
          Length = 260

 Score =  232 bits (592), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 120/262 (45%), Positives = 179/262 (68%), Gaps = 8/262 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 1   EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 60

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            +K++ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V 
Sbjct: 61  AVKVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 120

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 121 RGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  ++ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 181 NGTLDPEEAIRRSATILAEQLDAFVDLRDIRVPEE---KEEKPEFDPILLRPVDDLELTV 237

Query: 268 RSTNCLRGENIVYMGDLIQRTE 289
           RS NCL+ E I Y+GDL+QRTE
Sbjct: 238 RSANCLKAEAIHYIGDLVQRTE 259


>gi|29826981|ref|NP_821615.1| DNA-directed RNA polymerase subunit alpha [Streptomyces avermitilis
           MA-4680]
 gi|41688664|sp|Q82QR5|RPOA2_STRAW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|29604078|dbj|BAC68150.1| putative RNA polymerase alpha subunit [Streptomyces avermitilis
           MA-4680]
          Length = 338

 Score =  232 bits (592), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 131/322 (40%), Positives = 201/322 (62%), Gaps = 16/322 (4%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVK 248
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+   +N +       E I++ 
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNID------AEGIDMG 235

Query: 249 SLPFNPA----LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
             P + A    L+  +EELEL+VRS NCL+ E +  +G+L+ R+EAD+L + NFG KS+ 
Sbjct: 236 PSPVDAALAADLVMPIEELELTVRSYNCLKREGVHSVGELVARSEADLLDIRNFGAKSID 295

Query: 305 EIKGVLGTMGLFLGMNLPDWPP 326
           E+K  L  MGL L  + P + P
Sbjct: 296 EVKAKLAGMGLGLKDSPPGFDP 317


>gi|269217218|ref|ZP_06161072.1| DNA-directed RNA polymerase, alpha subunit [Slackia exigua ATCC
           700122]
 gi|269129355|gb|EEZ60440.1| DNA-directed RNA polymerase, alpha subunit [Slackia exigua ATCC
           700122]
          Length = 317

 Score =  232 bits (592), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 129/305 (42%), Positives = 191/305 (62%), Gaps = 11/305 (3%)

Query: 23  EEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
           EE N T+   I EPL RGF +TLGN +RRVL+SSL GA  TA+QI+GV HE ++ +GV E
Sbjct: 12  EEVNDTIARFIVEPLERGFGYTLGNCMRRVLLSSLDGARATAIQIEGVQHEFTTAEGVIE 71

Query: 81  DLTDIILNIKGINLK-MSGD-SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
           D+TDI LN+KG+  + +S D +    T+   GP  VT  DIQ   +  ++NP+HVIC + 
Sbjct: 72  DVTDIALNVKGLVFQALSEDYTEATATVSVEGPCTVTGADIQVPTEFTLVNPEHVICTVA 131

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + M + +  G GYVPA+ ++   DPIG+I +D+L+SP+++ +  V S R GQ  D+
Sbjct: 132 DGGTLNMTIRIGVGRGYVPAERNKRSEDPIGIIHVDSLFSPVQRCTADVSSTRVGQRTDF 191

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL------PF 252
           DKL + + TDGSIT +++V  A+ I+   +G F+   +   E  ED  + S+        
Sbjct: 192 DKLVLEVATDGSITPDEAVCRAANIINQYMGSFMALADIAGE-DEDGEIPSIFAPEGQES 250

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           N  L K++E+L+LSVRS NCL+   I  +  L++ +E D+L + NFG KS+ E+K  L +
Sbjct: 251 NAELDKQIEDLDLSVRSYNCLKRAGIHSVRQLVEFSENDLLNIRNFGAKSIEEVKDKLIS 310

Query: 313 MGLFL 317
           MGL L
Sbjct: 311 MGLNL 315


>gi|222150471|ref|YP_002559624.1| DNA-directed RNA polymerase alpha chain [Macrococcus caseolyticus
           JCSC5402]
 gi|254765255|sp|B9E9L7|RPOA_MACCJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|222119593|dbj|BAH16928.1| DNA-directed RNA polymerase alpha chain [Macrococcus caseolyticus
           JCSC5402]
          Length = 314

 Score =  232 bits (592), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 120/288 (41%), Positives = 190/288 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+GVLHE S+I+ V ED+T II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVKNIEIEGVLHEFSAIENVVEDVTSIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +  GVVTA DI   +D+E+LNPD  I  +     ++M L  
Sbjct: 83  KKLALKIYSDEDKTLEIDVKDEGVVTAKDIMHDSDVEILNPDLKIATVSKGGHLKMRLIA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           + G GY  A+ + T + PIG+I +D++Y+P+++V+Y VE+ R GQ  ++DKL++ + TDG
Sbjct: 143 NAGRGYTLAEDNNTSDLPIGVIPVDSIYTPVERVNYQVENTRVGQSTNFDKLTLDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SIT +++++L ++I+ + L +F++  +  +  +  I  +       L   +EEL+LSVRS
Sbjct: 203 SITPQEAISLGAKIMTEHLNIFVDLTDEAQNAEIMIEKEEDHKEKVLEMSIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++EADM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVKFKLEDLGLGL 310


>gi|331004149|ref|ZP_08327629.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae oral
           taxon 107 str. F0167]
 gi|330411559|gb|EGG90969.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae oral
           taxon 107 str. F0167]
          Length = 317

 Score =  232 bits (592), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 126/296 (42%), Positives = 193/296 (65%), Gaps = 15/296 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+++SSL G+A++ V+IDGVLHE SSI GV ED+T+II+N+
Sbjct: 23  FICEPLERGYGTTLGNSLRRIMLSSLPGSAVSQVKIDGVLHEFSSIPGVKEDVTEIIMNV 82

Query: 90  KGINLK-MSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K + ++  S D   +V      G GV+TA DIQ    IE++N D VI  +  +    MEL
Sbjct: 83  KSLAIRNTSNDDEPKVAYIDFDGEGVITAEDIQCDPSIEIINKDQVIATVS-EGKFYMEL 141

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           T++ G GYV +  ++ E+ PIG+I ID++Y+P+++V+  VE+ R GQ+ D+DKL++ + T
Sbjct: 142 TITNGRGYVSSDKNKGEDTPIGVIAIDSIYTPVERVNLLVENTRVGQMTDFDKLTLDVTT 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKK------EVKEDINVKSLPFNPALLKKVE 261
           +G++  +++V+LA+++L + L +FI+  +  K      E +ED   K L  N      ++
Sbjct: 202 NGTLEPDEAVSLAAKVLSEHLNLFIDLSDNAKTIDVMIEKEEDDKEKVLEMN------ID 255

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL E+   L  +GL L
Sbjct: 256 ELELSVRSYNCLKRAGINTVEELCSRTSDDMMKVRNLGRKSLEEVLQKLEELGLRL 311


>gi|223042663|ref|ZP_03612712.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus capitis
           SK14]
 gi|222444326|gb|EEE50422.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus capitis
           SK14]
          Length = 314

 Score =  232 bits (591), Expect = 7e-59,   Method: Compositional matrix adjust.
 Identities = 121/288 (42%), Positives = 190/288 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+GVLHE S++  V ED++ II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEGVLHEFSAVDNVVEDVSTIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  +  G VTA DI   +D+E+LNP+  I  +     +++ L  
Sbjct: 83  KKLALKIYSEEDKTLEIDVKDEGEVTASDITHDSDVEILNPELKIATVSKGGHLKVRLVA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTVE+ R GQ  D+DKL++ + T+G
Sbjct: 143 NKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTVENTRVGQSSDFDKLTLDVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SIT ++SV+LA++I+ + L +F+   +  +  +  I  +       L   +EEL+LSVRS
Sbjct: 203 SITPKESVSLAAKIMTEHLNIFVGLTDEAQNAEIMIEKEEDQKEKVLEMSIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++EADM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVKYKLEDLGLGL 310


>gi|295838431|ref|ZP_06825364.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. SPB74]
 gi|197695771|gb|EDY42704.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. SPB74]
          Length = 340

 Score =  232 bits (591), Expect = 7e-59,   Method: Compositional matrix adjust.
 Identities = 129/318 (40%), Positives = 194/318 (61%), Gaps = 4/318 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPGVVTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGVVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + +ELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNAKGKLELELTVERGRGYVSAVQNKQAGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNVDAEGIDMGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPPES 328
             MGL L  + P + P S
Sbjct: 302 AGMGLALKDSPPGFDPTS 319


>gi|313897186|ref|ZP_07830730.1| DNA-directed RNA polymerase, alpha subunit [Clostridium sp. HGF2]
 gi|312957907|gb|EFR39531.1| DNA-directed RNA polymerase, alpha subunit [Clostridium sp. HGF2]
          Length = 319

 Score =  232 bits (591), Expect = 8e-59,   Method: Compositional matrix adjust.
 Identities = 128/298 (42%), Positives = 189/298 (63%), Gaps = 5/298 (1%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E ++    + EPL RGF  T+GNALRRVL+SSL GAA+ ++++DGV HE +SI G+ ED+
Sbjct: 16  ESQHYGKFVFEPLERGFGTTIGNALRRVLLSSLPGAAVFSIKVDGVYHEFTSIPGIVEDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILNIK + + +  D    + I K+GPG VT  DI     +EV++ D  IC L+   +
Sbjct: 76  TAIILNIKTLVMSIQDDEIYTLRISKQGPGAVTGADIICPEGVEVISKDLHICTLEEGGM 135

Query: 143 VRMELTVSKGHGYVPA----KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
           + MEL    G GYV A    + ++T N P+G+I  D++Y+PI+KVSY VE  R GQ   Y
Sbjct: 136 LEMELQARIGRGYVSADTNKQLYQTPNQPLGIIYTDSIYTPIEKVSYNVEPTRVGQDAHY 195

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN-VKSLPFNPALL 257
           DK+++ I TD S++  ++VALAS+IL D L +  N  E   +++  +   +    N  L+
Sbjct: 196 DKVALEIWTDSSLSPAEAVALASKILIDHLELLTNVHEAVNDMESVMKEAQGEVQNKGLV 255

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
             +E+L+LSVRS NCL+   I  + +L QRTE +M+R+ N G+KSL E+K  +  +GL
Sbjct: 256 MMIEDLDLSVRSYNCLKRAGIQTVEELTQRTEDEMMRVRNLGKKSLKEVKDKIYDLGL 313


>gi|255536128|ref|YP_003096499.1| DNA-directed RNA polymerase alpha subunit [Flavobacteriaceae
           bacterium 3519-10]
 gi|255342324|gb|ACU08437.1| DNA-directed RNA polymerase alpha subunit [Flavobacteriaceae
           bacterium 3519-10]
          Length = 331

 Score =  232 bits (591), Expect = 8e-59,   Method: Compositional matrix adjust.
 Identities = 123/323 (38%), Positives = 202/323 (62%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            IKP+ +   +L   ++ +      PL +GF  T+GNALRRVL+SSL G AI++++I+GV
Sbjct: 6   FIKPDKV---ILLNSDDFKGKFEFRPLEQGFGLTIGNALRRVLLSSLEGYAISSIKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR--GPGVVTAGDI-QTVNDI 125
            HE S+I GV ED+T+IILN+K + LK   ++    T+  +  G   VTAGD+ +++   
Sbjct: 63  EHEFSTIPGVIEDVTEIILNLKQLRLKAKSEASAAETVTAKVTGQTTVTAGDLGKSIQGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E+LNPD VICNL+ +    +   + KG GYVP+  ++T + PIG I ID++++PIKKV Y
Sbjct: 123 EILNPDLVICNLNKEVKFELTFNIEKGRGYVPSDQNKTGSAPIGTIAIDSIFTPIKKVQY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           +VE+ R  Q  DY+KL + I+TDGSI+ ++++  AS+IL     +F    I  E    + 
Sbjct: 183 SVENYRVEQKTDYEKLVLDIETDGSISPQNALTEASKILIYHFMLFSDERITLETEAVKA 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
               + ++L     L  K+ +++LSVR+ NCL+   +  +G+L+  T++D+++  NFG+K
Sbjct: 243 SIQYDEETLHTRQLLKSKLTDMDLSVRALNCLKAAEVETLGELVSYTKSDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ ++   GL  G ++  +
Sbjct: 303 SLTELEELVHAKGLNFGFDVAKY 325


>gi|315134694|dbj|BAJ41855.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus ozensis]
          Length = 264

 Score =  231 bits (590), Expect = 8e-59,   Method: Compositional matrix adjust.
 Identities = 120/256 (46%), Positives = 173/256 (67%), Gaps = 4/256 (1%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E +N   ++ EPL RG+  TLGN+LRR+L+SSL GAA+T++QID VLHE S++KGV ED+
Sbjct: 8   ETDNYGEVVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDDVLHEFSTVKGVVEDV 67

Query: 83  TDIILNIKGINLKM--SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
             IILN+K I+LK+  + D  K + I   GP  VTAGDIQ   D+ VLNPD  IC +   
Sbjct: 68  AQIILNVKKISLKLDIADDEEKSMEINVTGPAQVTAGDIQADGDVTVLNPDLKICTVAEG 127

Query: 141 AVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
           A   M +T +KG GYV A  ++  ND  PIG++ +D++Y+PI++V+Y VE+AR GQ  D+
Sbjct: 128 ATFHMRMTANKGRGYVSADENKARNDGMPIGVLPVDSIYTPIERVNYQVENARVGQRADF 187

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL++ + TDGSIT  ++V+LA++IL + L MF++  +  K  +  +  +       L  
Sbjct: 188 DKLTLDVWTDGSITPSEAVSLAAKILSEHLSMFVDLTDEAKNAEVMVEKEETHKEKMLEM 247

Query: 259 KVEELELSVRSTNCLR 274
            +EEL+LSVRS NCL+
Sbjct: 248 TIEELDLSVRSYNCLK 263


>gi|293402527|ref|ZP_06646662.1| DNA-directed RNA polymerase, alpha subunit [Erysipelotrichaceae
           bacterium 5_2_54FAA]
 gi|291304041|gb|EFE45295.1| DNA-directed RNA polymerase, alpha subunit [Erysipelotrichaceae
           bacterium 5_2_54FAA]
          Length = 319

 Score =  231 bits (590), Expect = 9e-59,   Method: Compositional matrix adjust.
 Identities = 125/291 (42%), Positives = 190/291 (65%), Gaps = 5/291 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  T+GNALRRVL+SSL GAA+ ++++DGV HE +SI G+ ED+T +ILNI
Sbjct: 23  FVFEPLERGFGTTIGNALRRVLLSSLPGAAVFSIKVDGVYHEFTSIPGIVEDVTTMILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + +K+  D    + I K+GPG VT  DI     +EVL+ D  IC L+   ++ MEL  
Sbjct: 83  KTLVMKIQDDEIYTLRISKQGPGEVTGADIYCPEGVEVLSKDLHICTLEEGGMLEMELQA 142

Query: 150 SKGHGYVPA----KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
             G GYV A    + ++T N P+G+I  D++Y+PI+KVSY+V+  R GQ  +YDK+++ +
Sbjct: 143 RVGRGYVNADTNKQLYQTPNQPLGIIYTDSIYTPIEKVSYSVDPTRVGQNANYDKVTLEV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN-VKSLPFNPALLKKVEELE 264
            +D SI+  +S+AL+++IL D L +  N +E   +++  +   +    N  L+  +E+L+
Sbjct: 203 WSDSSISPAESLALSAKILIDHLELLTNVDEAVNDMESVMKEAQGEVQNKGLVMMIEDLD 262

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           LSVRS NCL+   I  + +L QRTE +M+R+ N G+KSL E+K  L  +GL
Sbjct: 263 LSVRSYNCLKRAGIQTVEELTQRTEDEMMRVRNLGKKSLKEVKDKLYDLGL 313


>gi|152964684|ref|YP_001360468.1| DNA-directed RNA polymerase subunit alpha [Kineococcus
           radiotolerans SRS30216]
 gi|189043840|sp|A6W5W5|RPOA_KINRD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|151359201|gb|ABS02204.1| DNA-directed RNA polymerase, alpha subunit [Kineococcus
           radiotolerans SRS30216]
          Length = 337

 Score =  231 bits (590), Expect = 9e-59,   Method: Compositional matrix adjust.
 Identities = 131/314 (41%), Positives = 199/314 (63%), Gaps = 16/314 (5%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +S+ GV ED+T
Sbjct: 15  DEYRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSLRIDGVLHEFTSVPGVKEDVT 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +I+LN+K  NL +S +  + V ++  K+GPG VTA DI     +EV NPD  I  L+   
Sbjct: 75  EIVLNVK--NLVVSSEHDEPVVMYLRKQGPGAVTAADIAPPAGVEVHNPDLHIATLNAKG 132

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + +ELTV +G GYV A  ++T    IG I +D++YSP+ KV+Y VE+ R  Q  D+D+L
Sbjct: 133 KLELELTVERGRGYVSAAQNKTGEQEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDRL 192

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLP----FNPA 255
            + ++T  +I+  D+VA A + L +  G+   +N E       E I++   P        
Sbjct: 193 VVDVETKHAISPRDAVASAGKTLTELFGLARELNVE------AEGIDMGPSPTDAALAAD 246

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           L  ++E L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  L  MGL
Sbjct: 247 LALEIEALDLTVRSYNCLKREGIHSVGELVSRSEADLLDIRNFGQKSIDEVKAKLVGMGL 306

Query: 316 FLGMNLPDWPPESI 329
            L  + P + P ++
Sbjct: 307 HLKDSPPGFDPSAV 320


>gi|126662238|ref|ZP_01733237.1| DNA-directed RNA polymerase subunit alpha [Flavobacteria bacterium
           BAL38]
 gi|126625617|gb|EAZ96306.1| DNA-directed RNA polymerase subunit alpha [Flavobacteria bacterium
           BAL38]
          Length = 330

 Score =  231 bits (589), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 125/298 (41%), Positives = 185/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRVL+SSL G AIT+V+I+GV HE S+I GV ED+T+IILN+K + 
Sbjct: 28  PLEPGYGLTVGNALRRVLLSSLEGYAITSVRIEGVEHEFSTISGVVEDVTEIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   ++ V+I   G   +TAGD Q  ++  +VLNPD VICNLD    + MEL++ 
Sbjct: 88  FKRQIEDIDNESVSISLSGKDKITAGDFQKFISGFQVLNPDLVICNLDSKTTLNMELSIE 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++  N PIG I  D++Y+P+K V YT+E+ R  Q  DY+KL   I TDGS
Sbjct: 148 KGRGYVPAEENKKSNAPIGTIYTDSIYTPVKNVKYTIENFRVEQKTDYEKLVFEIITDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++ L     +F    I  E  +    E  + +SL     L  K+ +++LS
Sbjct: 208 IHPKDALTEAAKTLIHHFMLFSDERITLEADEIAQTESYDEESLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   + D+++  NFG+KSL E+  ++    L  GM+L  +
Sbjct: 268 VRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKKSLTELDELVANKNLTFGMDLAKY 325


>gi|111023125|ref|YP_706097.1| DNA-directed RNA polymerase subunit alpha [Rhodococcus jostii RHA1]
 gi|226365624|ref|YP_002783407.1| DNA-directed RNA polymerase subunit alpha [Rhodococcus opacus B4]
 gi|119366719|sp|Q0S3E7|RPOA_RHOSR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|110822655|gb|ABG97939.1| DNA-directed RNA polymerase alpha subunit [Rhodococcus jostii RHA1]
 gi|226244114|dbj|BAH54462.1| DNA-directed RNA polymerase alpha subunit [Rhodococcus opacus B4]
          Length = 353

 Score =  231 bits (589), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 127/313 (40%), Positives = 194/313 (61%), Gaps = 16/313 (5%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+TD
Sbjct: 16  DNRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ +    D    + + K+GPG VTAGDI     + V NPD  I  L+    + 
Sbjct: 76  IILNLKGLVVSSEEDEPVTMYVRKQGPGAVTAGDIVPPAGVTVNNPDLHIATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D+L + 
Sbjct: 136 IELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDRLVLD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNPAL 256
           ++T  SIT  D++A A + L +  G+   +N E       P     + I    LP     
Sbjct: 196 VETKNSITARDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFGLP----- 250

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E+L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L ++GL 
Sbjct: 251 ---IEDLDLTVRSYNCLKREGVHTVGELVGRTESDLLDIRNFGQKSIDEVKVKLHSLGLA 307

Query: 317 LGMNLPDWPPESI 329
           L  +   + P ++
Sbjct: 308 LKDSPASFDPTTV 320


>gi|160914535|ref|ZP_02076750.1| hypothetical protein EUBDOL_00541 [Eubacterium dolichum DSM 3991]
 gi|158433693|gb|EDP11982.1| hypothetical protein EUBDOL_00541 [Eubacterium dolichum DSM 3991]
          Length = 319

 Score =  231 bits (589), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 127/298 (42%), Positives = 189/298 (63%), Gaps = 5/298 (1%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E +N    + EPL RGF  T+GNALRRVL+SSL GAA+ ++++DGV HE +SI G+ ED+
Sbjct: 16  EADNYGKFVFEPLERGFGTTIGNALRRVLLSSLPGAAVFSIKVDGVYHEFTSIPGIVEDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           + +ILNIK + +K+  D    + I K+GPG VT  DI     +EVL+ D  IC L+   +
Sbjct: 76  SAMILNIKTLVMKIQDDEIYTLRISKQGPGEVTGADIICPEGVEVLSKDLHICTLEEGGM 135

Query: 143 VRMELTVSKGHGYVPA----KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
           + MEL    G GYV A    + ++T N P+G+I  D++Y+PI++V+Y  E  R GQ   Y
Sbjct: 136 LEMELQARNGRGYVSADTNKQLYQTPNQPLGIIYTDSIYTPIERVAYNAEPTRVGQNAHY 195

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN-VKSLPFNPALL 257
           DK+++ I TD SI+  +SVALA++IL D L +  N  E   +++  +   +    N  L+
Sbjct: 196 DKVTLEIWTDSSISPAESVALAAKILIDHLELLTNVHEAVNDMESLMKEAQGEVQNKGLV 255

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
             +E+L+LSVRS NCL+   I  + +L QRTE +M+R+ N G+KSL E+K  +  +GL
Sbjct: 256 MMIEDLDLSVRSYNCLKRAGIQTVEELTQRTEDEMMRVRNLGKKSLKEVKDKIYDLGL 313


>gi|228472281|ref|ZP_04057047.1| DNA-directed RNA polymerase, alpha subunit [Capnocytophaga
           gingivalis ATCC 33624]
 gi|228276484|gb|EEK15208.1| DNA-directed RNA polymerase, alpha subunit [Capnocytophaga
           gingivalis ATCC 33624]
          Length = 330

 Score =  231 bits (589), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 125/301 (41%), Positives = 192/301 (63%), Gaps = 7/301 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRV++SSL G AIT+V+ID V HE S+I GV ED+T+IILN+K + 
Sbjct: 28  PLEPGYGLTIGNALRRVMLSSLEGYAITSVKIDSVEHEFSTITGVVEDVTEIILNLKQVR 87

Query: 94  LKMS--GDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K+   G  H++ +I   G   +TAGD Q  +   +VLNPD VICN++ D  ++M++T+ 
Sbjct: 88  FKLQTEGTDHEKASISVTGKKQLTAGDFQKFITGFQVLNPDLVICNMEPDVAIKMDITID 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYV A+ +   N P+G I  DA+++PIK V Y++E+ R  Q  DY+KL   I TDGS
Sbjct: 148 KGMGYVFAEENTKPNMPMGTIPTDAIFTPIKNVKYSIENYRVEQKTDYEKLIFEIKTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMFINFE---EPKKEVK-EDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++ L     +F +     EP++ V+ E  + +SL     L  K+ +++LS
Sbjct: 208 IHPKDALMEAAKTLIHHFMLFSDERITIEPEEVVQPESYDEESLHMRQLLKTKLIDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           VR+ NCL+   +  +GDL+  T+ D+++  NFG+KSL E+  ++ + GL  GM+L  +  
Sbjct: 268 VRALNCLKAAEVDTLGDLVSFTKTDLMKFRNFGKKSLTELDELVESKGLTFGMDLSRYKL 327

Query: 327 E 327
           E
Sbjct: 328 E 328


>gi|227505247|ref|ZP_03935296.1| DNA-directed RNA polymerase [Corynebacterium striatum ATCC 6940]
 gi|227198146|gb|EEI78194.1| DNA-directed RNA polymerase [Corynebacterium striatum ATCC 6940]
          Length = 336

 Score =  231 bits (589), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 130/309 (42%), Positives = 194/309 (62%), Gaps = 7/309 (2%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           + +R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV ED++
Sbjct: 15  DSSRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTINGVKEDVS 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +IILN+KG  L +S DS + V ++  K GPGVVTAGDIQ    +E+ NPD  I +L+  A
Sbjct: 75  EIILNVKG--LVLSSDSDEPVVMYLSKEGPGVVTAGDIQPPAGVEIHNPDLHIASLNDTA 132

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + MEL V +G GYVPA     E   IG I +D +YSP+ +VSY VE+ R  Q  D+DKL
Sbjct: 133 KLDMELVVERGRGYVPAAPTSGE---IGRIPVDQIYSPVLQVSYKVEATRVEQRTDFDKL 189

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + ++T  SI+  D++A A   L +  G+        + ++   + +   +  A    +E
Sbjct: 190 IIDVETKNSISARDALASAGGTLVELFGLARELNNAAEGIEIGPSPQETEYIAAYSMPIE 249

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +L  SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L  +GL L    
Sbjct: 250 DLNFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKIKLANLGLALKDTP 309

Query: 322 PDWPPESIE 330
            D+ P  +E
Sbjct: 310 EDFDPTQLE 318


>gi|313292044|gb|ADR51211.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
 gi|313292046|gb|ADR51212.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
 gi|313292048|gb|ADR51213.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
 gi|313292050|gb|ADR51214.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
          Length = 258

 Score =  231 bits (589), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 118/252 (46%), Positives = 169/252 (67%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+
Sbjct: 7   EEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDV 66

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILNIKG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A 
Sbjct: 67  TQIILNIKGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGAT 126

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
               LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+
Sbjct: 127 FHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLT 186

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           M I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 187 MEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEE 246

Query: 263 LELSVRSTNCLR 274
           L+LSVRS NCL+
Sbjct: 247 LDLSVRSYNCLK 258


>gi|317016847|gb|ADU85964.1| DNA-directed RNA polymerase alpha chain [Lactobacillus sp. 3.1.1]
          Length = 249

 Score =  231 bits (589), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 118/247 (47%), Positives = 169/247 (68%), Gaps = 2/247 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVTEDVTAIILNV 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK+S D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A   M +T 
Sbjct: 61  KKIALKLSSDETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLAICTVADGAHFHMRMTA 120

Query: 150 SKGHGYVPAK--HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           + G GYV A+   HR ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T
Sbjct: 121 NTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +GSIT  ++++L+++IL D L +F+N  +  K     +  +       L   +EEL+LSV
Sbjct: 181 NGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEMTIEELDLSV 240

Query: 268 RSTNCLR 274
           RS NCL+
Sbjct: 241 RSYNCLK 247


>gi|104773568|ref|YP_618548.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC 11842]
 gi|119366691|sp|Q1GBJ2|RPOA_LACDA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|103422649|emb|CAI97257.1| DNA-directed RNA polymerase, alpha chain [Lactobacillus delbrueckii
           subsp. bulgaricus ATCC 11842]
 gi|325125200|gb|ADY84530.1| RNA-polymerase DNA-directed [Lactobacillus delbrueckii subsp.
           bulgaricus 2038]
          Length = 312

 Score =  231 bits (588), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 129/316 (40%), Positives = 190/316 (60%), Gaps = 16/316 (5%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +E++    + EPL RGF  TLGN+LRRVL++S+ G  +  V+IDG
Sbjct: 3   EFKKPN----ITVVDQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSVPGTGLVKVKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           +LHE +++ GV ED+T IILN+K + L+   +  K + +   GP  VTA D++   D+EV
Sbjct: 59  ILHEFTTVPGVKEDVTKIILNLKKLELRAYTEEVKTIELDVEGPATVTAEDLKADADVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + M + V  G GYVPA  ++T    IG I +D+L+SPI+KV+Y V
Sbjct: 119 LNPDQYICTIAQGGHLHMWIDVCNGRGYVPASENKTAEMSIGDIPVDSLFSPIEKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK------EV 241
           ES R G+  D+DKL++ I T+GSI   D++  A+R+L +    F + +   +      E 
Sbjct: 179 ESTRVGKREDFDKLTLEIWTNGSIAPNDALNFAARVLVEHFKAFESADAAAEIGEVMVEQ 238

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           + D   K L         +E+L+LSVRS NCL+   I  + DL  ++EA+M+R+ N GRK
Sbjct: 239 ENDQKEKKLEMT------IEDLDLSVRSYNCLKRAGINTLQDLTVKSEAEMMRVRNLGRK 292

Query: 302 SLVEIKGVLGTMGLFL 317
           SL E+K  L  +GL L
Sbjct: 293 SLEEVKNKLADLGLSL 308


>gi|313292020|gb|ADR51199.1| DNA-directed RNA polymerase alpha chain [Enterococcus viikkiensis]
 gi|313292022|gb|ADR51200.1| DNA-directed RNA polymerase alpha chain [Enterococcus viikkiensis]
 gi|313292024|gb|ADR51201.1| DNA-directed RNA polymerase alpha chain [Enterococcus viikkiensis]
 gi|313292026|gb|ADR51202.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
 gi|313292028|gb|ADR51203.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
 gi|313292030|gb|ADR51204.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
 gi|313292032|gb|ADR51205.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
 gi|313292034|gb|ADR51206.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
 gi|313292036|gb|ADR51207.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
 gi|313292038|gb|ADR51208.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
 gi|313292040|gb|ADR51209.1| DNA-directed RNA polymerase alpha chain [Enterococcus avium]
 gi|313292042|gb|ADR51210.1| DNA-directed RNA polymerase alpha chain [Enterococcus avium]
          Length = 258

 Score =  231 bits (588), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 117/252 (46%), Positives = 168/252 (66%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E+ +    + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+
Sbjct: 7   EDRDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDV 66

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             IILNIKG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A 
Sbjct: 67  VQIILNIKGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGAT 126

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
               LTV  G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+
Sbjct: 127 FHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLT 186

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           M I TDGSI  +++++LA++IL + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 187 MEIWTDGSIIAQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEE 246

Query: 263 LELSVRSTNCLR 274
           L+LSVRS NCL+
Sbjct: 247 LDLSVRSYNCLK 258


>gi|7388098|sp|Q9X4V6|RPOA_STRGT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|4633288|gb|AAD26700.1|AF118449_1 DNA-dependent RNA polymerase alpha subunit [Streptomyces
           granaticolor]
          Length = 340

 Score =  231 bits (588), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 131/325 (40%), Positives = 200/325 (61%), Gaps = 22/325 (6%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNAKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        +E+  +I+ + +
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGL-------AREL--NIDAEGI 232

Query: 251 PFNPA---------LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
              P+         L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG K
Sbjct: 233 DMGPSPTDAALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAK 292

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPP 326
           S+ E+K  L  MGL L  + P + P
Sbjct: 293 SIDEVKAKLAGMGLALKDSPPGFDP 317


>gi|226305370|ref|YP_002765328.1| DNA-directed RNA polymerase alpha chain [Rhodococcus erythropolis
           PR4]
 gi|229489661|ref|ZP_04383524.1| DNA-directed RNA polymerase, alpha subunit [Rhodococcus
           erythropolis SK121]
 gi|226184485|dbj|BAH32589.1| DNA-directed RNA polymerase alpha chain [Rhodococcus erythropolis
           PR4]
 gi|229323758|gb|EEN89516.1| DNA-directed RNA polymerase, alpha subunit [Rhodococcus
           erythropolis SK121]
          Length = 353

 Score =  231 bits (588), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 127/313 (40%), Positives = 194/313 (61%), Gaps = 16/313 (5%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+TD
Sbjct: 16  DNRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ +    D    + + K+GPG VTAGDI     + V NPD  I  L+    + 
Sbjct: 76  IILNLKGLVVNSEEDEPVTMYVRKQGPGAVTAGDIVPPAGVTVNNPDLHIATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D+L + 
Sbjct: 136 IELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDRLVLD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNPAL 256
           ++T  SIT  D++A A + L +  G+   +N E       P     + I    LP     
Sbjct: 196 VETKNSITARDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFGLP----- 250

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E+L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L ++GL 
Sbjct: 251 ---IEDLDLTVRSYNCLKREGVHTVGELVGRTESDLLDIRNFGQKSIDEVKVKLHSLGLS 307

Query: 317 LGMNLPDWPPESI 329
           L  +   + P ++
Sbjct: 308 LKDSPASFDPTTV 320


>gi|313292064|gb|ADR51221.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
 gi|313292066|gb|ADR51222.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
 gi|313292068|gb|ADR51223.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
 gi|313292070|gb|ADR51224.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
 gi|313292072|gb|ADR51225.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
 gi|313292074|gb|ADR51226.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
 gi|313292076|gb|ADR51227.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
          Length = 258

 Score =  231 bits (588), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 117/252 (46%), Positives = 169/252 (67%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E+++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+
Sbjct: 7   EDKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDV 66

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             IILNIKG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  IC +   A 
Sbjct: 67  AQIILNIKGLALKMYGDEEKTLEIDISGPATVTAGDIIVDSDVEILNKDMYICTVSEGAT 126

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
               LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+
Sbjct: 127 FHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLT 186

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           M I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 187 MEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEE 246

Query: 263 LELSVRSTNCLR 274
           L+LSVRS NCL+
Sbjct: 247 LDLSVRSYNCLK 258


>gi|153012268|gb|ABS50355.1| DNA-directed RNA polymerase alpha chain [Enterococcus thailandicus]
          Length = 250

 Score =  231 bits (588), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 117/245 (47%), Positives = 165/245 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 5   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 64

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV
Sbjct: 65  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTV 124

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 125 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDG 184

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +EEL+LSVRS
Sbjct: 185 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEELDLSVRS 244

Query: 270 TNCLR 274
            NCL+
Sbjct: 245 YNCLK 249


>gi|161511763|emb|CAP16892.1| DNA-directed RNA polymerase subunit alpha [Pediococcus parvulus]
          Length = 264

 Score =  231 bits (588), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 116/254 (45%), Positives = 169/254 (66%), Gaps = 2/254 (0%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E  N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+
Sbjct: 10  ENANYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDV 69

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILNIK ++LK+  D  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +     
Sbjct: 70  TQIILNIKKVSLKIESDDEKSLEINVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVT 129

Query: 143 VRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
               LT   G GYV A  ++   D  PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDK
Sbjct: 130 FHAVLTADTGRGYVSADENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDK 189

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L++ + TDGSI+  ++ +L+++IL + L +F+N  +  ++ +  +  +       L   +
Sbjct: 190 LTLDVWTDGSISPSEATSLSAKILTEHLALFVNLTDEAQDAEIMVEKEETHKEKMLEMSI 249

Query: 261 EELELSVRSTNCLR 274
           EEL+LSVRS NCL+
Sbjct: 250 EELDLSVRSYNCLK 263


>gi|319948695|ref|ZP_08022816.1| DNA-directed RNA polymerase subunit alpha [Dietzia cinnamea P4]
 gi|319437597|gb|EFV92596.1| DNA-directed RNA polymerase subunit alpha [Dietzia cinnamea P4]
          Length = 344

 Score =  231 bits (588), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 123/305 (40%), Positives = 192/305 (62%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ENR+  + EPL  GF +T+GN+LRR L+SS+ GAA+T+++I+GVLHE +++ GV ED+TD
Sbjct: 16  ENRSRFVLEPLEPGFGYTIGNSLRRTLLSSIPGAAVTSIRIEGVLHEFTTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ +    D    + + K+GPG VTAGDI     +EV NPD  I  L+    + 
Sbjct: 76  IILNLKGLVVSSVEDEPVTMYLKKQGPGAVTAGDIVPPAGVEVHNPDLHIATLNEKGRLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D+L + 
Sbjct: 136 IELVVERGRGYVPAGLNKDAGHEIGRIPVDSIYSPVLKVTYKVEATRVHQRTDFDRLVLD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           ++T  S+T  D++A A + L +  G+     E  + ++   +        A    +++L+
Sbjct: 196 VETKNSMTARDALASAGKTLVELFGLARELNEEAEGIEIGPSPAEADHIAAYGMPIDDLD 255

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           LSVRS NCL+ E +  +G+L+ R+E+D+L + NFG+KS+ E+K  L  +GL L    P +
Sbjct: 256 LSVRSYNCLKREGVHTVGELVARSESDLLDIRNFGQKSIDEVKVKLVELGLSLKDAPPGF 315

Query: 325 PPESI 329
            P S+
Sbjct: 316 DPASV 320


>gi|54022804|ref|YP_117046.1| DNA-directed RNA polymerase subunit alpha [Nocardia farcinica IFM
           10152]
 gi|61215826|sp|Q5Z1K9|RPOA_NOCFA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|54014312|dbj|BAD55682.1| putative RNA polymerase alpha subunit [Nocardia farcinica IFM
           10152]
          Length = 352

 Score =  231 bits (588), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 128/313 (40%), Positives = 192/313 (61%), Gaps = 16/313 (5%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ENR+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+TD
Sbjct: 16  ENRSKFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ +    D    + + K+GPG VTAGDI     + V NPD  I  L+    + 
Sbjct: 76  IILNLKGLVVSSEEDEPVTMYVRKQGPGTVTAGDIVPPAGVVVHNPDMHIATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D+L + 
Sbjct: 136 IELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDRLILD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNPAL 256
           ++T  SI+  D++A A + L +  G+   +N E       P     + I    LP     
Sbjct: 196 VETKNSISARDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFGLP----- 250

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E+L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL 
Sbjct: 251 ---IEDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKVKLHALGLS 307

Query: 317 LGMNLPDWPPESI 329
           L  +   + P S+
Sbjct: 308 LKDSPASFDPSSV 320


>gi|319893174|ref|YP_004150049.1| DNA-directed RNA polymerase alpha subunit [Staphylococcus
           pseudintermedius HKU10-03]
 gi|317162870|gb|ADV06413.1| DNA-directed RNA polymerase alpha subunit [Staphylococcus
           pseudintermedius HKU10-03]
 gi|323463778|gb|ADX75931.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus
           pseudintermedius ED99]
          Length = 314

 Score =  231 bits (588), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 121/288 (42%), Positives = 188/288 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+GVLHE S+I  V ED++ I++NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEGVLHEFSAIDHVVEDVSTIVMNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  +  G VTA DI   +D+E+LNPD  I  +     +++ L  
Sbjct: 83  KKLALKIYSEEDKTLEIDIKEEGEVTAKDIMHDSDVEILNPDLKIATVSKGGHLKLRLVA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           + G GY  A  + + + PIG+I +D+LYSP+++V+YTVE+ R GQ  D+DKL++ + TDG
Sbjct: 143 NTGRGYALADQNNSSDLPIGVIPVDSLYSPVERVNYTVENTRVGQSSDFDKLTLDVWTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SIT ++SV+LA++I+ + L +F+   +  +  +  I  +       L   +EEL+LSVRS
Sbjct: 203 SITPQESVSLAAKIMTEHLNIFVGLTDEAQNAEIMIEKEEDQKEKVLEMSIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++EADM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVKYKLEDLGLGL 310


>gi|88803724|ref|ZP_01119248.1| DNA-directed RNA polymerase alpha subunit [Polaribacter irgensii
           23-P]
 gi|88780457|gb|EAR11638.1| DNA-directed RNA polymerase alpha subunit [Polaribacter irgensii
           23-P]
          Length = 330

 Score =  230 bits (587), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 124/298 (41%), Positives = 188/298 (63%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRRVL+SSL G AIT++++DGV HE S++ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGLTVGNALRRVLLSSLEGFAITSLRLDGVEHEFSTVSGVVEDVTEIILNLKQVR 87

Query: 94  LKMSGDSHKR--VTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   R  V+I   G    TAGD+Q  ++  +VLNPD VICN+D    +  E+T+ 
Sbjct: 88  FKKQIEETDRETVSISVSGQEQFTAGDLQKFISGFQVLNPDLVICNMDKSVKLNAEITIE 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG G+VPA+ ++  + PIG I  D++Y+PIK V Y VE+ R  Q  DY+KL   IDTDGS
Sbjct: 148 KGRGFVPAEENKKASAPIGTIFTDSIYTPIKNVKYAVENFRVEQKTDYEKLVFDIDTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I+ +D++  A++IL     +F    I  E  +    E  + +SL     L  ++ +++LS
Sbjct: 208 ISPKDALTEAAKILIHHFMLFSDERITLEADEIAQTETYDEESLHMRQLLKTRLIDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   ++D+++  NFG+KSL E++ ++   GL  GM+L  +
Sbjct: 268 VRALNCLKAAEVDTLGDLVSFNKSDLMKFRNFGKKSLTELEELVIVKGLSFGMDLSKY 325


>gi|308233885|ref|ZP_07664622.1| DNA-directed RNA polymerase, alpha subunit [Atopobium vaginae DSM
           15829]
 gi|328943592|ref|ZP_08241057.1| DNA-directed RNA polymerase subunit alpha [Atopobium vaginae DSM
           15829]
 gi|327491561|gb|EGF23335.1| DNA-directed RNA polymerase subunit alpha [Atopobium vaginae DSM
           15829]
          Length = 314

 Score =  230 bits (587), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 123/297 (41%), Positives = 187/297 (62%), Gaps = 4/297 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           EN   +  EPL RG+  TLGN++RRVL+SSL GAA+ A+ IDGV HE S++ GV+ED+TD
Sbjct: 16  ENLARVNVEPLERGYGDTLGNSMRRVLLSSLEGAAVEAISIDGVQHEFSTVDGVYEDVTD 75

Query: 85  IILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           I+LN+KG+    +G       +I   GP  VT GD +   + E++N DHVIC L     +
Sbjct: 76  IVLNVKGLVFHANGSGETAEASISIDGPCTVTGGDFKIPAEFELINKDHVICTLGEGGHL 135

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            M + +  G GYV    +  + DPIG+I +D+LYSP+++ + TVE  R GQ  +YD+L +
Sbjct: 136 AMRMRIGVGRGYVSGDDNERDEDPIGVIHVDSLYSPVRRCAKTVEPCRVGQHTNYDRLIL 195

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS---LPFNPALLKKV 260
            I+T+GSI+  D+V  A+ I+   +  F++  E ++E +ED+++ S      N  L K++
Sbjct: 196 EIETNGSISPRDAVIEAADIINQHMAAFMDLAEDEEEPQEDVSIFSNEEEEENTELDKQI 255

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           E+L+LSVRS NCL+   I  +  L++ +E D+L + NFG KS+ E++  L   GL L
Sbjct: 256 EDLDLSVRSYNCLKRAGIHNVRQLVEFSENDLLNIRNFGVKSIEEVRDKLEDAGLGL 312


>gi|329314907|gb|AEB89320.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus T0131]
          Length = 314

 Score =  230 bits (587), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 121/288 (42%), Positives = 189/288 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+GVLHE S++  V ED++ II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEGVLHEFSAVDNVVEDVSTIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  R  G VTA DI   +D+E+LNP+  I  +     +++ L  
Sbjct: 83  KQLALKIYSEEDKTLEIDVRDEGEVTASDITHDSDVEILNPELKIATVSKGGHLKIRLVA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTVE+   GQ  D+DKL++ + T+G
Sbjct: 143 NKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTVENTCVGQSSDFDKLTLDVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SIT ++SV+LA++I+ + L +F+   +  +  +  I  +       L   +EEL+LSVRS
Sbjct: 203 SITPQESVSLAAKIMTEHLNIFVGLTDEAQNAEIMIEKEEDQKEKVLEMSIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++EADM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVKYKLEDLGLGL 310


>gi|239636207|ref|ZP_04677211.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus warneri
           L37603]
 gi|239598223|gb|EEQ80716.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus warneri
           L37603]
 gi|330685120|gb|EGG96784.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus
           epidermidis VCU121]
          Length = 314

 Score =  230 bits (587), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 120/288 (41%), Positives = 190/288 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL G+A+  ++I+GVLHE S++  V ED++ II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGSAVKYIEIEGVLHEFSAVDNVVEDVSTIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  +  G VTA DI   +D+E+LNP+  I  +     +++ L  
Sbjct: 83  KKLALKIYSEEDKTLEIDVKDEGEVTASDITHDSDVEILNPELKIATVSKGGHLKVRLVA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTVE+ R GQ  D+DKL++ + T+G
Sbjct: 143 NKGRGYALAETNNTSDLPIGVIPVDSLYSPVERVNYTVENTRVGQSSDFDKLTLDVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SIT ++SV+LA++I+ + L +F+   +  +  +  I  +       L   +EEL+LSVRS
Sbjct: 203 SITPQESVSLAAKIMTEHLNIFVGLTDEAQNAEIMIEKEEDQKEKVLEMSIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  ++EADM+++ N GRKSL E+K  L  +GL L
Sbjct: 263 YNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVKYKLEDLGLGL 310


>gi|296141062|ref|YP_003648305.1| DNA-directed RNA polymerase subunit alpha [Tsukamurella
           paurometabola DSM 20162]
 gi|296029196|gb|ADG79966.1| DNA-directed RNA polymerase, alpha subunit [Tsukamurella
           paurometabola DSM 20162]
          Length = 352

 Score =  230 bits (587), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 126/314 (40%), Positives = 193/314 (61%), Gaps = 16/314 (5%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           + R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+TD
Sbjct: 16  DARSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ +    D    + + K+GPG VTAGDI     + V NPD  I  L+    + 
Sbjct: 76  IILNLKGLVVSSEDDEPVTMYVRKQGPGAVTAGDIVPPASVTVHNPDLHIATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D+L + 
Sbjct: 136 IELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDRLILD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNPAL 256
           ++T  S+T  D++A A + L +  G+   +N E       P     + I   SLP     
Sbjct: 196 VETKNSMTARDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIAAFSLP----- 250

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E+L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL 
Sbjct: 251 ---IEDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKVKLHALGLA 307

Query: 317 LGMNLPDWPPESIE 330
           L  +   + P  ++
Sbjct: 308 LKDSPASFDPSQVD 321


>gi|300857809|ref|YP_003782792.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           pseudotuberculosis FRC41]
 gi|300685263|gb|ADK28185.1| DNA-directed RNA polymerase alpha subunit [Corynebacterium
           pseudotuberculosis FRC41]
 gi|302205544|gb|ADL09886.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           pseudotuberculosis C231]
 gi|302330099|gb|ADL20293.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           pseudotuberculosis 1002]
 gi|308275780|gb|ADO25679.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           pseudotuberculosis I19]
          Length = 338

 Score =  230 bits (587), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 130/306 (42%), Positives = 193/306 (63%), Gaps = 5/306 (1%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
           R+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+V+IDGVLHE ++I GV ED++DII
Sbjct: 18  RSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVKIDGVLHEFTTINGVKEDVSDII 77

Query: 87  LNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           LNIKG  L +S DS + V ++  K G GVV+AGDI+    +E+ NPD  I  L+    + 
Sbjct: 78  LNIKG--LVLSSDSDEPVVMYLRKEGAGVVSAGDIEPPAGVEIHNPDLHIATLNEQGRLD 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +E+ V +G GYVPA  +   N+ IG I +D +YSP+ KVSY VE+ R  Q  D+DKL + 
Sbjct: 136 IEMIVERGRGYVPASLYAGTNE-IGRIPVDQIYSPVLKVSYKVEATRVEQRTDFDKLIID 194

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           ++T  SI   D++A A + L +  G+        + ++   + +   +  A    +E+L 
Sbjct: 195 VETKNSIAPSDALASAGKTLVELFGLARELNTAAEGIEIGPSPQETEYIAAYSMPIEDLN 254

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
            SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L  +GLFL  +  D+
Sbjct: 255 FSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKIKLAGLGLFLKDSPEDF 314

Query: 325 PPESIE 330
            P  +E
Sbjct: 315 DPTQLE 320


>gi|254383145|ref|ZP_04998499.1| DNA-directed RNA polymerase alpha subunit [Streptomyces sp. Mg1]
 gi|194342044|gb|EDX23010.1| DNA-directed RNA polymerase alpha subunit [Streptomyces sp. Mg1]
          Length = 340

 Score =  230 bits (587), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 132/325 (40%), Positives = 200/325 (61%), Gaps = 22/325 (6%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVLH
Sbjct: 6   RPSLTEEVV----DEYRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TDIILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDIILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNGKGKLEMELTVERGRGYVSAVQNKQLGQEIGRIPIDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        +E+  +I+ + +
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGL-------AREL--NIDAEGI 232

Query: 251 PFNPA---------LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
              P+         L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG K
Sbjct: 233 DMGPSPTDAALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAK 292

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPP 326
           S+ E+K  L  MGL L  + P + P
Sbjct: 293 SIDEVKAKLAGMGLALKDSPPGFDP 317


>gi|167946610|ref|ZP_02533684.1| DNA-directed RNA polymerase subunit alpha [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 280

 Score =  230 bits (587), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 118/267 (44%), Positives = 176/267 (65%), Gaps = 4/267 (1%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE ++I+GV ED+ +I+LN+K + L M       + + K+GPGVV+AGDI   +DIE+
Sbjct: 11  VLHEYTAIEGVQEDVLEILLNLKQVALVMHSRDEAVLRLQKKGPGVVSAGDITLDHDIEI 70

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVS 184
            NPD  I  L     + M LTV +G GY P+   ++   E+ PIG++ +DA +SP+++V+
Sbjct: 71  ANPDLHIATLTKSGEINMTLTVKRGRGYQPSTARQSSAGEDRPIGMLQLDASFSPVRRVA 130

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y++ESAR  Q  + D+L + + TDG+I  E+++  ++ IL+DQL +F++ E         
Sbjct: 131 YSIESARVEQRTNMDRLVIELQTDGTIDPEEAIRRSAGILRDQLSVFVDLEGGGAAEATA 190

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              + +  +P LL+ V++LEL+VRS NCL+ ENI  +GDLIQRTE ++L+  N G+KSL 
Sbjct: 191 EPEEPM-IDPILLRPVDDLELTVRSANCLKAENIFLIGDLIQRTEVELLKTPNLGKKSLT 249

Query: 305 EIKGVLGTMGLFLGMNLPDWPPESIEE 331
           EIK VL   GL LGM L  WPPESI+E
Sbjct: 250 EIKDVLARRGLSLGMRLEHWPPESIDE 276


>gi|328814003|gb|AEB52117.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 261

 Score =  230 bits (587), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 120/254 (47%), Positives = 171/254 (67%), Gaps = 2/254 (0%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E +N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+
Sbjct: 6   ENDNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDV 65

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A 
Sbjct: 66  TAIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGAH 125

Query: 143 VRMELTVSKGHGYVPAK--HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             M +T + G GYV A+   HR ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DK
Sbjct: 126 FHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDK 185

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L++ + T+GSIT  ++++L+++IL D L +F+N  +  K     +  +       L   +
Sbjct: 186 LTLDVWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEMTI 245

Query: 261 EELELSVRSTNCLR 274
           EEL+LSVRS NCL+
Sbjct: 246 EELDLSVRSYNCLK 259


>gi|254495367|ref|ZP_05108291.1| DNA-directed RNA polymerase, alpha subunit [Polaribacter sp.
           MED152]
 gi|85819721|gb|EAQ40878.1| DNA-directed RNA polymerase, alpha subunit [Polaribacter sp.
           MED152]
          Length = 330

 Score =  230 bits (587), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 123/298 (41%), Positives = 187/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRRVL+SSL G AIT+++IDGV HE S++ G+ ED+T+IILN+K + 
Sbjct: 28  PLEPGFGLTVGNALRRVLLSSLEGFAITSLRIDGVEHEFSTVSGIVEDVTEIILNLKQVR 87

Query: 94  LKMSGDSHKR--VTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   D   R  V++   G    TAGD+Q  ++  +VLNPD VICN+D    +  E+T+ 
Sbjct: 88  FKKQIDETDRETVSVSISGQEQFTAGDLQKFISGFQVLNPDLVICNMDKSVKLNAEITIE 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG G+VPA+ ++  + PIG I  D++Y+PIK V Y +E+ R  Q  DY+KL   IDTDGS
Sbjct: 148 KGRGFVPAEENKKASAPIGTIFTDSIYTPIKNVKYAIENFRVEQKTDYEKLVFDIDTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++IL     +F    I  E  +    E  + +SL     L  ++ +++LS
Sbjct: 208 INPKDALTEAAKILIHHFMLFSDERITLEADEIAQTETYDEESLHMRQLLKTRLIDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   ++D+++  NFG+KSL E++ ++   GL  GM+L  +
Sbjct: 268 VRALNCLKAAEVDTLGDLVSFNKSDLMKFRNFGKKSLTELEELVIVKGLSFGMDLTKY 325


>gi|260893344|ref|YP_003239441.1| DNA-directed RNA polymerase, alpha subunit [Ammonifex degensii KC4]
 gi|260865485|gb|ACX52591.1| DNA-directed RNA polymerase, alpha subunit [Ammonifex degensii KC4]
          Length = 319

 Score =  230 bits (586), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 128/289 (44%), Positives = 187/289 (64%), Gaps = 2/289 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGNALRRVL+SS+ GAA+T V+I+GVLHE S++ GV ED+ +IILN+
Sbjct: 23  FVIEPLVRGYGITLGNALRRVLLSSIPGAAVTMVKIEGVLHEFSTLPGVREDVVEIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           +G+ ++M  D  + + I   G   V A DI    D+E+LNPDH I +L  +  + ME+TV
Sbjct: 83  RGLKIRMHTDEERILRIEAAGEREVRARDIIADADVEILNPDHYIASLAPEGRLFMEMTV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYVPA   R ++  IG I +DA +SP+KKV+Y VE+A  GQ  DYD+L + + T+G
Sbjct: 143 RRGRGYVPADRQRHDH-VIGAIPVDADFSPVKKVNYRVENAWVGQNADYDRLILEVWTNG 201

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK-KVEELELSVR 268
            +  E++V+LA+RIL +   +          +++ +  K       LL+  +EEL+LSVR
Sbjct: 202 CVRPEEAVSLAARILCEHFQLLTGLSTSTGHLEKIMVEKEEDNKNRLLEMPIEELDLSVR 261

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           S NCL+   I  + DL QRTE +M+++ N G+KSL E+K  L  +GL L
Sbjct: 262 SYNCLKRAGINTILDLTQRTEEEMMKVRNLGKKSLEEVKQKLAELGLSL 310


>gi|110589176|gb|ABG77097.1| DNA-directed RNA polymerase alpha subunit [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 303

 Score =  230 bits (586), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 118/267 (44%), Positives = 176/267 (65%), Gaps = 4/267 (1%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE ++I+GV ED+ +I+LN+K + L M       + + K+GPGVV+AGDI   +DIE+
Sbjct: 34  VLHEYTAIEGVQEDVLEILLNLKQVALVMHSRDEAVLRLQKKGPGVVSAGDITLDHDIEI 93

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVS 184
            NPD  I  L     + M LTV +G GY P+   ++   E+ PIG++ +DA +SP+++V+
Sbjct: 94  ANPDLHIATLTKSGEINMTLTVKRGRGYQPSTARQSSAGEDRPIGMLQLDASFSPVRRVA 153

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y++ESAR  Q  + D+L + + TDG+I  E+++  ++ IL+DQL +F++ E         
Sbjct: 154 YSIESARVEQRTNMDRLVIELQTDGTIDPEEAIRRSAGILRDQLSVFVDLEGGGAAEATA 213

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              + +  +P LL+ V++LEL+VRS NCL+ ENI  +GDLIQRTE ++L+  N G+KSL 
Sbjct: 214 EPEEPM-IDPILLRPVDDLELTVRSANCLKAENIFLIGDLIQRTEVELLKTPNLGKKSLT 272

Query: 305 EIKGVLGTMGLFLGMNLPDWPPESIEE 331
           EIK VL   GL LGM L  WPPESI+E
Sbjct: 273 EIKDVLARRGLSLGMRLEHWPPESIDE 299


>gi|328813997|gb|AEB52114.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 270

 Score =  230 bits (586), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 120/254 (47%), Positives = 171/254 (67%), Gaps = 2/254 (0%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E +N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+
Sbjct: 10  ENDNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDV 69

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A 
Sbjct: 70  TAIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGAH 129

Query: 143 VRMELTVSKGHGYVPAK--HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             M +T + G GYV A+   HR ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DK
Sbjct: 130 FHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDK 189

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L++ + T+GSIT  ++++L+++IL D L +F+N  +  K     +  +       L   +
Sbjct: 190 LTLDVWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEMTI 249

Query: 261 EELELSVRSTNCLR 274
           EEL+LSVRS NCL+
Sbjct: 250 EELDLSVRSYNCLK 263


>gi|328814021|gb|AEB52126.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 262

 Score =  230 bits (586), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 117/259 (45%), Positives = 173/259 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+I GV ED+T IILNI
Sbjct: 4   FVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIPGVREDVTQIILNI 63

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D VIC++   A     LTV
Sbjct: 64  KGLALKLYAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLVICSVAEGATFHARLTV 123

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 124 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDG 183

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  +++++LA++I+ + L +F+N  +  K  +  +  +       L   +EEL+LSVRS
Sbjct: 184 SIIPQEALSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEELDLSVRS 243

Query: 270 TNCLRGENIVYMGDLIQRT 288
            NCL+   I  + +L  ++
Sbjct: 244 YNCLKRAGINTVQELTNKS 262


>gi|308178106|ref|YP_003917512.1| DNA-directed RNA polymerase subunit alpha [Arthrobacter
           arilaitensis Re117]
 gi|307745569|emb|CBT76541.1| DNA-directed RNA polymerase alpha chain [Arthrobacter arilaitensis
           Re117]
          Length = 333

 Score =  230 bits (586), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 121/302 (40%), Positives = 189/302 (62%), Gaps = 4/302 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ENR+  + EPL  GF +TLGN+LRR L+SS+ GA++T+++IDGVLHE +++ GV ED+T+
Sbjct: 16  ENRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIRIDGVLHEFTTVAGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           ++LNIK +++    D      + K+GPG+VTA DI     +E  NPD  I  L+ +    
Sbjct: 76  LVLNIKNLSVSSEHDEPVVAYLRKQGPGIVTAADITPPAGVEFHNPDLHIATLNANGKFD 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MELT+ +G GYV A  +++ +  IG I +D++YSP+ KV++ VE+ R  Q  D+D+L + 
Sbjct: 136 MELTIERGRGYVSAAQNKSADGEIGRIPVDSIYSPVLKVTFRVEATRVEQRTDFDRLIVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           ++T  SIT  D+VA A   L +  G+F       + ++   +         +   +E+LE
Sbjct: 196 VETKESITPRDAVASAGTTLVELFGLFRELNTQAEGIEIGPSPTDAAMAADMALPIEDLE 255

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L    + LG+ L D 
Sbjct: 256 LTVRSYNCLKREGIHSVGELVTRSEADLMDIRNFGAKSIDEVKAKL----VELGLALKDS 311

Query: 325 PP 326
           PP
Sbjct: 312 PP 313


>gi|325068059|ref|ZP_08126732.1| DNA-directed RNA polymerase subunit alpha [Actinomyces oris K20]
 gi|326773990|ref|ZP_08233272.1| DNA-directed RNA polymerase, alpha subunit [Actinomyces viscosus
           C505]
 gi|329945757|ref|ZP_08293444.1| DNA-directed RNA polymerase, alpha subunit [Actinomyces sp. oral
           taxon 170 str. F0386]
 gi|326636129|gb|EGE37033.1| DNA-directed RNA polymerase, alpha subunit [Actinomyces viscosus
           C505]
 gi|328528205|gb|EGF55183.1| DNA-directed RNA polymerase, alpha subunit [Actinomyces sp. oral
           taxon 170 str. F0386]
          Length = 333

 Score =  230 bits (586), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 134/320 (41%), Positives = 193/320 (60%), Gaps = 15/320 (4%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V+   E+ R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+IDGV H
Sbjct: 6   RPTLTEEVVV---EDRRSRFVLEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRIDGVPH 62

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E  +I GV ED+  IILNIK I L    D    + + K GP  VTAGDI     +E+ NP
Sbjct: 63  EFRTIPGVKEDVAQIILNIKEIVLSSENDEPVVMYLRKSGPSEVTAGDITPPAGVEIHNP 122

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D VI  L+    + +ELTV +G GYV A  ++  N  I  I +D++YSP+KKVSY+VE+ 
Sbjct: 123 DLVIATLNEKGKLEIELTVERGRGYVSANQNKDPNAEISRIPVDSIYSPVKKVSYSVEAT 182

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVK 248
           R  Q  D+D+L + ++T  SIT  D++A A + L +  G+   +N E       E I V 
Sbjct: 183 RVEQRTDFDRLIVDVETKSSITPRDALASAGKTLVELFGLARELNVE------AEGIEVG 236

Query: 249 SLPFNPALLKK----VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
             P + A  +     ++EL+L  RS+N L+ E I  +G+L+ R+EAD+L + NFG KS+ 
Sbjct: 237 PSPIDEAFQQDLALMIDELDLQARSSNALKREGIHTVGELVSRSEADLLDIRNFGAKSIS 296

Query: 305 EIKGVLGTMGLFLGMNLPDW 324
           EIK  L  +GL L  +  D+
Sbjct: 297 EIKDKLAELGLSLKGSPVDY 316


>gi|261880855|ref|ZP_06007282.1| DNA-directed RNA polymerase subunit alpha [Prevotella bergensis DSM
           17361]
 gi|270332362|gb|EFA43148.1| DNA-directed RNA polymerase subunit alpha [Prevotella bergensis DSM
           17361]
          Length = 330

 Score =  230 bits (586), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 125/298 (41%), Positives = 188/298 (63%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AI  V+IDGV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGVTIGNALRRILLSSLEGYAINTVRIDGVEHEFSSVPGVREDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   +++V+I         AGDI + +   EVLNPD VIC+LD  A ++++LTV+
Sbjct: 88  FKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGFEVLNPDLVICHLDSKASMQIDLTVN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + ++ ID++Y+PI+ V Y+VE  R  Q  DYDKL + I TDGS
Sbjct: 148 KGRGYVPADENRQFCTDVNVLPIDSIYTPIRNVKYSVEPTRVEQKTDYDKLCIEITTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++IL     +F    I  E+P K+  ++ + + L     L  K+ +L LS
Sbjct: 208 IHPKDALNEAAKILIYHFMLFSDEKITLEDPNKDGNQEFDEEVLRMRQLLKTKLLDLNLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKKSLSELDDLLESLNLSFGTDISKY 325


>gi|302536278|ref|ZP_07288620.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. C]
 gi|302445173|gb|EFL16989.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. C]
          Length = 340

 Score =  230 bits (586), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 131/325 (40%), Positives = 200/325 (61%), Gaps = 22/325 (6%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVLH
Sbjct: 6   RPSLTEEVV----DEYRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TDIILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDIILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNGKGKLEMELTVERGRGYVSAVQNKQLGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        +E+  +I+ + +
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGL-------AREL--NIDAEGI 232

Query: 251 PFNPA---------LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
              P+         L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG K
Sbjct: 233 DMGPSPTDAALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAK 292

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPP 326
           S+ E+K  L  MGL L  + P + P
Sbjct: 293 SIDEVKAKLAGMGLALKDSPPGFDP 317


>gi|145219088|ref|YP_001129797.1| DNA-directed RNA polymerase subunit alpha [Prosthecochloris
           vibrioformis DSM 265]
 gi|189043842|sp|A4SCT6|RPOA_PROVI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|145205252|gb|ABP36295.1| DNA-directed RNA polymerase subunit alpha [Chlorobium
           phaeovibrioides DSM 265]
          Length = 328

 Score =  230 bits (586), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 122/302 (40%), Positives = 191/302 (63%), Gaps = 9/302 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +A+PL RG+  TLGN +RRVL++SL G AIT +++DGV HE S+I+GV ED+ +I+LN+
Sbjct: 25  FVAQPLERGYGVTLGNMMRRVLLASLPGTAITGIKVDGVFHEFSAIEGVREDVPEIVLNL 84

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV-NDIEVLNPDHVICNLDVDAVVRMELT 148
           K +  + +     + T+   GP   TAGDI  +  + +VLN D  I  ++  + + +++ 
Sbjct: 85  KKVRFRSTCKRSCKTTLTITGPKDFTAGDIVAMEGEFDVLNKDLHIATVNEGSTLNIDVF 144

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V +G GY PA+ +R E+ PIG I IDA+Y+PI+ V   VE+ R GQ  DY+K+ + ++TD
Sbjct: 145 VGRGRGYTPAEDNRPESMPIGYIAIDAIYTPIRNVKVAVENTRVGQRTDYEKMVLDVETD 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEV------KEDINVKSLPFNPALLKKVEE 262
           GSIT +DS++LA RI+ + +  F +F   ++E       ++D   +++     L  K+E+
Sbjct: 205 GSITPDDSISLAGRIINEHVAFFADFSPTEEEFTEEEFKQQDDEFEAM--RKLLNTKIED 262

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL E+K  L    L  GM++ 
Sbjct: 263 LDLSVRSHNCLRLAEIDSIGDLVSRKEDELLNYKNFGKKSLTELKEQLEKFELKFGMDIT 322

Query: 323 DW 324
            +
Sbjct: 323 KY 324


>gi|326383232|ref|ZP_08204920.1| DNA-directed RNA polymerase subunit alpha [Gordonia neofelifaecis
           NRRL B-59395]
 gi|326197982|gb|EGD55168.1| DNA-directed RNA polymerase subunit alpha [Gordonia neofelifaecis
           NRRL B-59395]
          Length = 350

 Score =  229 bits (585), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 126/313 (40%), Positives = 192/313 (61%), Gaps = 16/313 (5%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ENR+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T+
Sbjct: 16  ENRSKFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTN 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ +    D    + + K+GPG VT  DI     + V NPD  I  L+    + 
Sbjct: 76  IILNLKGLVVSSEEDEPVTMYVRKQGPGAVTGADIVPPAGVTVHNPDLHIATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D+L + 
Sbjct: 136 IELVVERGRGYVPAVQNKATGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDRLVLD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNPAL 256
           ++T  S+T  D++A A + L +  G+   +N E       P  +  + I   SLP     
Sbjct: 196 VETKNSMTARDALASAGKTLVELFGLARELNVEAEGIEIGPSPQEADHIAAFSLP----- 250

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E+LEL+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L ++GL 
Sbjct: 251 ---IEDLELTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKVKLHSLGLA 307

Query: 317 LGMNLPDWPPESI 329
           L  +   + P  +
Sbjct: 308 LKDSPASFDPSQV 320


>gi|327402757|ref|YP_004343595.1| DNA-directed RNA polymerase subunit alpha [Fluviicola taffensis DSM
           16823]
 gi|327318265|gb|AEA42757.1| DNA-directed RNA polymerase subunit alpha [Fluviicola taffensis DSM
           16823]
          Length = 330

 Score =  229 bits (585), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 120/314 (38%), Positives = 199/314 (63%), Gaps = 7/314 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +++ Q +E +      PL  G+  T+GNALRR+L+SSL G AI++V+I+GV HE +++KG
Sbjct: 12  VIMIQSDERKGQFEFRPLEPGYGITVGNALRRILLSSLEGYAISSVRIEGVDHEFATLKG 71

Query: 78  VHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVI 134
           V ED+T+I+LN+K +  K  + G  ++ V +   G   +TAGD+ +  +  +VLNPD VI
Sbjct: 72  VVEDVTEIVLNLKQVRFKQQIEGTDNETVVVSISGQDKLTAGDLGKFTSGFQVLNPDLVI 131

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
           CN++    + +ELT+ KG GY+PA+ +++ N P G I ID++++PI  V YT+E+ R  Q
Sbjct: 132 CNMESSVKLELELTIIKGRGYLPAEENKSGNAPFGTIAIDSIFTPIVNVKYTIENYRVEQ 191

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSL 250
             DY+KL + + TDGSI  +D++  A++IL     +F    I  +   K   E+ +  SL
Sbjct: 192 KTDYEKLVLELTTDGSIHPKDALKEAAKILIHHFMLFSDERITLDSEVKSETEEFDETSL 251

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L  K+ +++LSVR+ NCL+  ++  +GDL+   + D+L+  NFG+KSL E++ ++
Sbjct: 252 HMRQLLKTKLVDMDLSVRALNCLKAADVETLGDLVSYNKNDLLKFRNFGKKSLTELEDLV 311

Query: 311 GTMGLFLGMNLPDW 324
            + GL  GMN+  +
Sbjct: 312 DSKGLNFGMNVAKY 325


>gi|326334519|ref|ZP_08200730.1| DNA-directed RNA polymerase subunit alpha [Capnocytophaga sp. oral
           taxon 338 str. F0234]
 gi|325693288|gb|EGD35216.1| DNA-directed RNA polymerase subunit alpha [Capnocytophaga sp. oral
           taxon 338 str. F0234]
          Length = 330

 Score =  229 bits (585), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 124/301 (41%), Positives = 192/301 (63%), Gaps = 7/301 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRV++SSL G AIT+V+ID V HE S+I GV ED+T+IILN+K + 
Sbjct: 28  PLEPGYGLTIGNALRRVMLSSLEGYAITSVKIDTVEHEFSTIAGVVEDVTEIILNLKQVR 87

Query: 94  LKMS--GDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K+   G  H++ +I   G   +TAGD Q  +   +VLNPD VICN++ +  ++M++T+ 
Sbjct: 88  FKLQTEGTDHEKASISVTGKKQLTAGDFQKFITGFQVLNPDLVICNMEPEVEIKMDITID 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYV A+ +   N P+G I  DA+++PIK V Y++E+ R  Q  DY+KL   I TDGS
Sbjct: 148 KGMGYVSAEENAKPNMPVGTIPTDAIFTPIKNVKYSIENYRVEQKTDYEKLIFEIKTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMFINFE---EPKKEVK-EDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++ L     +F +     EP++ V+ E  + +SL     L  K+ +++LS
Sbjct: 208 IHPKDALMEAAKTLIHHFMLFSDERITIEPEEVVQPESYDEESLHMRQLLKTKLIDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           VR+ NCL+   +  +GDL+  T+ D+++  NFG+KSL E+  ++ + GL  GM+L  +  
Sbjct: 268 VRALNCLKAAEVDTLGDLVSFTKTDLMKFRNFGKKSLTELDELVESKGLTFGMDLSKYKL 327

Query: 327 E 327
           E
Sbjct: 328 E 328


>gi|269955462|ref|YP_003325251.1| DNA-directed RNA polymerase subunit alpha [Xylanimonas
           cellulosilytica DSM 15894]
 gi|269304143|gb|ACZ29693.1| DNA-directed RNA polymerase, alpha subunit [Xylanimonas
           cellulosilytica DSM 15894]
          Length = 334

 Score =  229 bits (585), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 132/308 (42%), Positives = 197/308 (63%), Gaps = 8/308 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ENRT    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T+
Sbjct: 16  ENRTRFAIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILNIK  NL +S ++ + V ++  K+G G VTA DI     +EV NPD  I  L+    
Sbjct: 76  IILNIK--NLVVSSENDEPVVMYLRKQGAGAVTAADIVPPAGVEVHNPDLHIATLNDKGK 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +ELTV +G GYV A  +++ +  IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL 
Sbjct: 134 LEIELTVERGRGYVSAAQNKSLDAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLI 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKV 260
           + ++T  +IT  D++A A + L +  G+   +N E    E+       +L  + AL   +
Sbjct: 194 VDVETKPAITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPTDSALAADLAL--PI 251

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           EEL L++RS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  +GL L  +
Sbjct: 252 EELNLTIRSYNCLKREGIHQVGELVARSEADLLDIRNFGAKSINEVKEKLAELGLALKDS 311

Query: 321 LPDWPPES 328
             D+ P +
Sbjct: 312 PLDFDPSA 319


>gi|300812355|ref|ZP_07092790.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus
           delbrueckii subsp. bulgaricus PB2003/044-T3-4]
 gi|300496660|gb|EFK31747.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus
           delbrueckii subsp. bulgaricus PB2003/044-T3-4]
          Length = 312

 Score =  229 bits (585), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 128/316 (40%), Positives = 190/316 (60%), Gaps = 16/316 (5%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +E++    + EPL RGF  TLGN+LRRVL++S+ G  +  V+IDG
Sbjct: 3   EFKKPN----ITVVDQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSVPGTGLVKVKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           +LHE +++ GV ED+T IILN+K + L+   +  K + +   GP  VTA D++   D+EV
Sbjct: 59  ILHEFTTVPGVKEDVTKIILNLKKLELRAYTEEVKTIELDVEGPATVTAEDLKADADVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + M + V  G GYVPA  +++    IG I +D+L+SPI+KV+Y V
Sbjct: 119 LNPDQYICTIAQGGHLHMWIDVCNGRGYVPASENKSAEMSIGDIPVDSLFSPIEKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK------EV 241
           ES R G+  D+DKL++ I T+GSI   D++  A+R+L +    F + +   +      E 
Sbjct: 179 ESTRVGKREDFDKLTLEIWTNGSIAPNDALNFAARVLVEHFKAFESADAAAEIGEVMVEQ 238

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           + D   K L         +E+L+LSVRS NCL+   I  + DL  ++EA+M+R+ N GRK
Sbjct: 239 ENDQKEKKLEMT------IEDLDLSVRSYNCLKRAGINTLQDLTVKSEAEMMRVRNLGRK 292

Query: 302 SLVEIKGVLGTMGLFL 317
           SL E+K  L  +GL L
Sbjct: 293 SLEEVKNKLADLGLSL 308


>gi|114567812|ref|YP_754966.1| DNA-directed RNA polymerase [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|119366746|sp|Q0AUK9|RPOA_SYNWW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|114338747|gb|ABI69595.1| DNA-directed RNA polymerase [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
          Length = 316

 Score =  229 bits (585), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 125/287 (43%), Positives = 194/287 (67%), Gaps = 1/287 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE S+I GV ED T+IILNI
Sbjct: 23  FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFSTIPGVLEDTTEIILNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L  +G   K + + ++GP  V A DI    ++E+LNPD  + +LD D  V +E+TV
Sbjct: 83  KKLVLSYTGSERKIIRLEQQGPKEVKASDITPDAEVEILNPDLHLASLDEDGKVEIEMTV 142

Query: 150 SKGHGYVPAKHHRTENDPI-GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
            +G GYV +     +ND I GLI ID++++P+ +V+YTVE+AR G+  DYD+L++ + T+
Sbjct: 143 ERGRGYVSSDQQPQKNDDIVGLIPIDSIFTPVSRVNYTVENARVGKRTDYDRLNLEVWTN 202

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           GSI+ E++++L+++IL + L +F   ++   EV+  +  +    +  L   +EELELSVR
Sbjct: 203 GSISPEEAISLSAQILIEYLKLFTEIDDTYAEVEILVEKEEEKKDKILEMSIEELELSVR 262

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           ++N L+  +I  +GDLI +   +M ++ N G+KSL EI+  L  + L
Sbjct: 263 ASNGLKRASINTVGDLIAKNREEMSKIRNLGQKSLEEIERKLKELNL 309


>gi|91200694|emb|CAJ73745.1| strongly similar to DNA-directed RNA polymerase, alpha chain
           [Candidatus Kuenenia stuttgartiensis]
          Length = 338

 Score =  229 bits (585), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 127/312 (40%), Positives = 190/312 (60%), Gaps = 15/312 (4%)

Query: 25  ENRTL------MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
           EN TL       IA P  RGF HT+GN+LRR+L+SSL G+A+ +V+I+GV HE +++ GV
Sbjct: 17  ENETLTDRYGKFIAAPFERGFGHTIGNSLRRILLSSLEGSAVVSVKIEGVAHEFTNVPGV 76

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+ DIILNIK + +KM  D  K + I     G VT  DI T  ++EV+N D  I  L 
Sbjct: 77  IEDVADIILNIKNLIVKMHSDQPKIIKIEANKKGKVTGKDIITDENVEVVNDDLHIATLS 136

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D    +E+ V KG GYV A  +  E+  IGLI++D+ +SP++ V Y  E  R G+  +Y
Sbjct: 137 EDMAFNVEMEVRKGRGYVTADENEAEDQEIGLISVDSFFSPVRNVRYVTEETRVGRRTNY 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE---------DINVKS 249
           D+L + I T+G++T E ++  A+ I +  L  FI + E  +E+++           ++ S
Sbjct: 197 DRLILEIWTNGTVTPEMALVEAAMITRKHLNPFIQYFEIGRELQQIEKNMSAECISDMSS 256

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
             FN  L   + EL+LSVR++NCL   NIV +GDL+ +TE D+L++ NFG+ ++ E+K  
Sbjct: 257 EEFNRTLSMPIAELDLSVRASNCLETVNIVTVGDLVVKTEDDLLQIKNFGKTTMKELKKK 316

Query: 310 LGTMGLFLGMNL 321
           L  + L +GM L
Sbjct: 317 LSQLNLAIGMPL 328


>gi|262203540|ref|YP_003274748.1| DNA-directed RNA polymerase subunit alpha [Gordonia bronchialis DSM
           43247]
 gi|262086887|gb|ACY22855.1| DNA-directed RNA polymerase, alpha subunit [Gordonia bronchialis
           DSM 43247]
          Length = 350

 Score =  229 bits (585), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 127/313 (40%), Positives = 191/313 (61%), Gaps = 16/313 (5%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR+  + EPL  GF +TLGN+LRR L+SS+ GAAIT+++IDGVLHE +++ GV ED+TD
Sbjct: 16  DNRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAITSIRIDGVLHEFTTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ +    D    + + K+GPG VT  DI     + V NPD  I  L+    + 
Sbjct: 76  IILNLKGLVVSSEEDEPVTMYVRKQGPGTVTGADIVPPAGVTVHNPDLHIATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D+L + 
Sbjct: 136 IELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDRLVLD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNPAL 256
           ++T  SI+  D++A A + L +  G+   +N E       P     + I   SLP     
Sbjct: 196 VETKNSISARDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFSLP----- 250

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E+LEL+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL 
Sbjct: 251 ---IEDLELTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKVKLHALGLS 307

Query: 317 LGMNLPDWPPESI 329
           L  +   + P  +
Sbjct: 308 LKDSPASFDPSQV 320


>gi|189347676|ref|YP_001944205.1| DNA-directed RNA polymerase subunit alpha [Chlorobium limicola DSM
           245]
 gi|238692198|sp|B3EGW3|RPOA_CHLL2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|189341823|gb|ACD91226.1| DNA-directed RNA polymerase, alpha subunit [Chlorobium limicola DSM
           245]
          Length = 328

 Score =  229 bits (585), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 123/305 (40%), Positives = 192/305 (62%), Gaps = 15/305 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +A+PL RG+  TLGN +RR L++SL G AIT ++IDGV HE S+I GV ED+ +I+LN+
Sbjct: 25  FVAQPLERGYGVTLGNVMRRALLASLPGTAITGLKIDGVFHEFSTINGVREDVPEIVLNL 84

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           K +  + +   + + ++   G    TAGDI     + EVLN D  I  ++  A +++++ 
Sbjct: 85  KKVRFRSNCKRNCKTSLVLNGQKEFTAGDIIAQEGEFEVLNKDLHIATVNEGATLKIDIF 144

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V +G GY+P++ +R +  PIG I IDA+++PI+ V +TVE+ R GQ  DY+K+ + ++TD
Sbjct: 145 VGRGRGYLPSEENRPDGMPIGFIAIDAIFTPIRNVKFTVENTRVGQRTDYEKMILDVETD 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFE---------EPKKEVKEDINVKSLPFNPALLKK 259
           GSIT +DS++LA +I+ + +  F +F          E K++  E  N++ L FN     K
Sbjct: 205 GSITPDDSISLAGKIINEHVTFFADFSPTEEEFTEEEFKQQDDEFENMRKL-FNT----K 259

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +E+L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL E+K  L    L  GM
Sbjct: 260 IEDLDLSVRSHNCLRLAEIDTIGDLVSRKEDELLNYKNFGKKSLTELKEQLEKFDLKFGM 319

Query: 320 NLPDW 324
           ++  +
Sbjct: 320 DITKY 324


>gi|254391366|ref|ZP_05006569.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           clavuligerus ATCC 27064]
 gi|294814494|ref|ZP_06773137.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           clavuligerus ATCC 27064]
 gi|297192676|ref|ZP_06910074.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           pristinaespiralis ATCC 25486]
 gi|326442883|ref|ZP_08217617.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           clavuligerus ATCC 27064]
 gi|197705056|gb|EDY50868.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           clavuligerus ATCC 27064]
 gi|197721669|gb|EDY65577.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           pristinaespiralis ATCC 25486]
 gi|294327093|gb|EFG08736.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           clavuligerus ATCC 27064]
          Length = 340

 Score =  229 bits (585), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 131/325 (40%), Positives = 200/325 (61%), Gaps = 22/325 (6%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPSLTEEVV----DEYRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        +E+  +I+ + +
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGL-------AREL--NIDAEGI 232

Query: 251 PFNPA---------LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
              P+         L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG K
Sbjct: 233 DMGPSPTDAALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAK 292

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPP 326
           S+ E+K  L  MGL L  + P + P
Sbjct: 293 SIDEVKAKLAGMGLALKDSPPGFDP 317


>gi|213964907|ref|ZP_03393106.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           amycolatum SK46]
 gi|213952443|gb|EEB63826.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           amycolatum SK46]
          Length = 341

 Score =  229 bits (585), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 128/317 (40%), Positives = 189/317 (59%), Gaps = 18/317 (5%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           + +R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV ED++
Sbjct: 15  DSSRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTIPGVKEDVS 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           DIILNIKG+ L    D    V + + G G VTA DI+    +E+ NPDH I  L+    +
Sbjct: 75  DIILNIKGLVLSSEFDEPATVYLRREGAGAVTAADIECPAGVEIHNPDHHIATLNESGRL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +E+ V +G GYVPA  +      IG I +D +YSP+ KVSY VE+ R  Q  D+DKL +
Sbjct: 135 EIEMIVERGRGYVPATPN--SGGEIGRIPMDQIYSPVLKVSYKVEATRVEQRTDFDKLII 192

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEE--------PKKEVKEDINVKSLPFNPA 255
            ++T  SIT  D++A A + L +  G+     E        P     ED+     P    
Sbjct: 193 DVETKNSITARDAMASAGKTLVELFGLARELNEAAEGIEIGPSPREAEDVAAYQTP---- 248

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
               +E+L+ S+RS NCL+ E I  +G+L  RTE+D+L + NFG KS+ E+K  L  +GL
Sbjct: 249 ----IEDLDFSMRSYNCLKREEIHTVGELAARTESDLLDIRNFGDKSINEVKEKLAELGL 304

Query: 316 FLGMNLPDWPPESIEEL 332
            L  +  ++ P ++ +L
Sbjct: 305 ALKDSPNNFDPAAVADL 321


>gi|260886903|ref|ZP_05898166.1| DNA-directed RNA polymerase, alpha subunit [Selenomonas sputigena
           ATCC 35185]
 gi|330839299|ref|YP_004413879.1| DNA-directed RNA polymerase, alpha subunit [Selenomonas sputigena
           ATCC 35185]
 gi|260863502|gb|EEX78002.1| DNA-directed RNA polymerase, alpha subunit [Selenomonas sputigena
           ATCC 35185]
 gi|329747063|gb|AEC00420.1| DNA-directed RNA polymerase, alpha subunit [Selenomonas sputigena
           ATCC 35185]
          Length = 319

 Score =  229 bits (584), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 129/299 (43%), Positives = 191/299 (63%), Gaps = 5/299 (1%)

Query: 24  EENRT-LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E+NR    + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE S+I GV +D+
Sbjct: 16  EDNRYGKFVCEPLERGYGTTLGNSLRRILLSSLPGAAITSIRIDGVLHEFSTIPGVRDDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T+I+LN+K +  KM  +  + + +  +G   +TA DI T  D+E+LNPD  I  L+ D  
Sbjct: 76  TNIVLNLKSLCFKMYSEEPRVLRLDVKGEKEITAADIITDPDVEILNPDLHIATLNEDGE 135

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + ME+ V +G GYV A+ ++  +  IG+I ID+++SPI++V+YTV+  R G V DYDKL 
Sbjct: 136 LHMEMIVERGKGYVAAEKNKKPDHVIGVIPIDSIFSPIQRVNYTVQDTRVGNVTDYDKLI 195

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINF----EEPKKEVKEDINVKSLPFNPALLK 258
           + + TDGSI  E+ V+ A+ IL     +F N     E  ++E       +    +  L  
Sbjct: 196 LDVWTDGSIRPEEGVSRAASILISHFKLFQNMAGIPEIEEEEEIAPPEPEEPDASKVLET 255

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            +++L+LSVRS NCL+  NI  + DL+ +TE DM+++ N GRKSL E+K  L    L L
Sbjct: 256 TIDDLDLSVRSFNCLKRANINTVADLVSKTEEDMMKVRNLGRKSLEEVKKKLEEYDLTL 314


>gi|309389906|gb|ADO77786.1| DNA-directed RNA polymerase subunit alpha [Halanaerobium praevalens
           DSM 2228]
          Length = 315

 Score =  229 bits (584), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 123/289 (42%), Positives = 194/289 (67%), Gaps = 2/289 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAA+T+V+++GV HE S+I GV ED+TD+ILN+K + 
Sbjct: 25  PLERGYGTTLGNSLRRILLSSLPGAALTSVKVEGVKHEFSAIPGVVEDMTDLILNLKEVV 84

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +K SG+    + +   G G +TAGD  +  D+EV+N +H +  L     + +E TV KG 
Sbjct: 85  VKYSGEEQTTIRLEAEGEGEITAGDFISAGDVEVVNKEHHVATLAEGGRLVLEATVDKGR 144

Query: 154 GYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A+ +    EN+ IGLI ID+ YSPI++ ++ +E+ R GQV D+D+L + ++T+GSI
Sbjct: 145 GYHTAEENEKLFENNVIGLIPIDSAYSPIERANFNIENTRVGQVTDFDRLVLEVNTNGSI 204

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTN 271
             +D+++LA++I+ + L +FIN  +  ++V+  + V+    +  L   +EELELSVRS+N
Sbjct: 205 HPDDAISLAAKIMVEHLELFINLTDEIEDVEIMVEVEEEEKDEILDTTIEELELSVRSSN 264

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           CL+   I  + +L+ RTE D++++ N G+KSL EI+  L  + L L  N
Sbjct: 265 CLKRAGINTVEELVSRTEDDLMKVRNLGKKSLKEIEKKLDELELDLKEN 313


>gi|229821593|ref|YP_002883119.1| DNA-directed RNA polymerase, alpha subunit [Beutenbergia cavernae
           DSM 12333]
 gi|259494164|sp|C5C0G1|RPOA_BEUC1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|229567506|gb|ACQ81357.1| DNA-directed RNA polymerase, alpha subunit [Beutenbergia cavernae
           DSM 12333]
          Length = 338

 Score =  229 bits (584), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 122/302 (40%), Positives = 190/302 (62%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T+
Sbjct: 16  DNRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILNIK I +    D    + + K+GPGVVTA DI     +EV NPD  I  ++    + 
Sbjct: 76  IILNIKNIVVSSENDEPVVMYLRKQGPGVVTAADITPPAGVEVHNPDLHIATVNGKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELTV +G GYV A+ ++  +  IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL + 
Sbjct: 136 VELTVERGRGYVSAQQNKAYDTEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLIVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           +++  +I+  D+VA A + L +  G+        + ++   +         L   +E+L+
Sbjct: 196 VESKPAISPRDAVASAGKTLVELFGLARELNTAAEGIEIGPSPTDAALAADLALPIEDLD 255

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L++RS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  +GL L  +  D+
Sbjct: 256 LTIRSYNCLKREGIHQVGELVARSEADLLDIRNFGAKSITEVKEKLAALGLSLKDSPADF 315

Query: 325 PP 326
            P
Sbjct: 316 DP 317


>gi|21223108|ref|NP_628887.1| DNA-directed RNA polymerase subunit alpha [Streptomyces coelicolor
           A3(2)]
 gi|29831496|ref|NP_826130.1| DNA-directed RNA polymerase subunit alpha [Streptomyces avermitilis
           MA-4680]
 gi|182436600|ref|YP_001824319.1| DNA-directed RNA polymerase subunit alpha [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|239929487|ref|ZP_04686440.1| DNA-directed RNA polymerase subunit alpha [Streptomyces ghanaensis
           ATCC 14672]
 gi|239943604|ref|ZP_04695541.1| DNA-directed RNA polymerase subunit alpha [Streptomyces roseosporus
           NRRL 15998]
 gi|239990057|ref|ZP_04710721.1| DNA-directed RNA polymerase subunit alpha [Streptomyces roseosporus
           NRRL 11379]
 gi|256785796|ref|ZP_05524227.1| DNA-directed RNA polymerase subunit alpha [Streptomyces lividans
           TK24]
 gi|282860838|ref|ZP_06269904.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. ACTE]
 gi|289769688|ref|ZP_06529066.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces lividans
           TK24]
 gi|290958124|ref|YP_003489306.1| DNA-directed RNA polymerase subunit alpha [Streptomyces scabiei
           87.22]
 gi|291437812|ref|ZP_06577202.1| RNA polymerase alpha subunit [Streptomyces ghanaensis ATCC 14672]
 gi|291447071|ref|ZP_06586461.1| RNA polymerase alpha subunit [Streptomyces roseosporus NRRL 15998]
 gi|294630920|ref|ZP_06709480.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. e14]
 gi|297201756|ref|ZP_06919153.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sviceus
           ATCC 29083]
 gi|302553569|ref|ZP_07305911.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces
           viridochromogenes DSM 40736]
 gi|302558967|ref|ZP_07311309.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces
           griseoflavus Tu4000]
 gi|326777222|ref|ZP_08236487.1| DNA-directed RNA polymerase subunit alpha [Streptomyces cf. griseus
           XylebKG-1]
 gi|329938205|ref|ZP_08287656.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           griseoaurantiacus M045]
 gi|41692291|sp|P60312|RPOA_STRCO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|41692292|sp|P60313|RPOA1_STRAW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238689027|sp|B1W3Y0|RPOA_STRGG RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|3449241|emb|CAA20385.1| DNA-directed RNA polymerase alpha chain [Streptomyces coelicolor
           A3(2)]
 gi|29608612|dbj|BAC72665.1| RNA polymerase alpha subunit [Streptomyces avermitilis MA-4680]
 gi|178465116|dbj|BAG19636.1| RNA polymerase alpha subunit [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|197710869|gb|EDY54903.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sviceus
           ATCC 29083]
 gi|260647650|emb|CBG70755.1| DNA-directed RNA polymerase alpha chain [Streptomyces scabiei
           87.22]
 gi|282564574|gb|EFB70110.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. ACTE]
 gi|289699887|gb|EFD67316.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces lividans
           TK24]
 gi|291340707|gb|EFE67663.1| RNA polymerase alpha subunit [Streptomyces ghanaensis ATCC 14672]
 gi|291350018|gb|EFE76922.1| RNA polymerase alpha subunit [Streptomyces roseosporus NRRL 15998]
 gi|292834253|gb|EFF92602.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. e14]
 gi|297159625|gb|ADI09337.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           bingchenggensis BCW-1]
 gi|302471187|gb|EFL34280.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces
           viridochromogenes DSM 40736]
 gi|302476585|gb|EFL39678.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces
           griseoflavus Tu4000]
 gi|320009075|gb|ADW03925.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces
           flavogriseus ATCC 33331]
 gi|326657555|gb|EGE42401.1| DNA-directed RNA polymerase subunit alpha [Streptomyces cf. griseus
           XylebKG-1]
 gi|328884454|emb|CCA57693.1| DNA-directed RNA polymerase alpha subunit [Streptomyces venezuelae
           ATCC 10712]
 gi|329302694|gb|EGG46584.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           griseoaurantiacus M045]
          Length = 340

 Score =  229 bits (584), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 131/325 (40%), Positives = 200/325 (61%), Gaps = 22/325 (6%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        +E+  +I+ + +
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGL-------AREL--NIDAEGI 232

Query: 251 PFNPA---------LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
              P+         L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG K
Sbjct: 233 DMGPSPTDAALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAK 292

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPP 326
           S+ E+K  L  MGL L  + P + P
Sbjct: 293 SIDEVKAKLAGMGLALKDSPPGFDP 317


>gi|296168685|ref|ZP_06850434.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           parascrofulaceum ATCC BAA-614]
 gi|295896594|gb|EFG76235.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           parascrofulaceum ATCC BAA-614]
          Length = 347

 Score =  229 bits (584), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 126/313 (40%), Positives = 193/313 (61%), Gaps = 16/313 (5%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T 
Sbjct: 16  DNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVAGVKEDVTA 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ +    D    + + K+GPG VTAGDI     + V NP+  I  L+    + 
Sbjct: 76  IILNLKGLVVSSEEDEPVTMYLRKQGPGAVTAGDIVPPAGVTVHNPEMHIATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL + 
Sbjct: 136 VELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLILD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNPAL 256
           ++T  SIT  D++A A + L +  G+   +N E       P     + I   +LP     
Sbjct: 196 VETKSSITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALP----- 250

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL 
Sbjct: 251 ---IDDLDLTVRSYNCLKREGVHTVGELVSRTESDLLDIRNFGQKSIDEVKVKLHQLGLS 307

Query: 317 LGMNLPDWPPESI 329
           L  + P + P  +
Sbjct: 308 LKDSPPSFDPSQV 320


>gi|120402447|ref|YP_952276.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           vanbaalenii PYR-1]
 gi|158513011|sp|A1T520|RPOA_MYCVP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119955265|gb|ABM12270.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           vanbaalenii PYR-1]
          Length = 350

 Score =  229 bits (584), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 127/307 (41%), Positives = 192/307 (62%), Gaps = 4/307 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ENR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+TD
Sbjct: 16  ENRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ +    D    + + K+GPG VTAGDI     + V NPD  I  L+    + 
Sbjct: 76  IILNLKGLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPDMHIATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL + 
Sbjct: 136 VELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLILD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           ++T  SIT  D++A A + L +  G+   +N E    E+           + AL   +++
Sbjct: 196 VETKNSITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADQAAHFAL--PIDD 253

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  +  
Sbjct: 254 LDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPA 313

Query: 323 DWPPESI 329
            + P  +
Sbjct: 314 SFDPSEV 320


>gi|118469556|ref|YP_885906.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium smegmatis
           str. MC2 155]
 gi|158512464|sp|A0QSL8|RPOA_MYCS2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|118170843|gb|ABK71739.1| DNA-directed RNA polymerase, alpha subunit [Mycobacterium smegmatis
           str. MC2 155]
          Length = 350

 Score =  229 bits (584), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 126/307 (41%), Positives = 193/307 (62%), Gaps = 4/307 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ENR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+TD
Sbjct: 16  ENRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILN+KG  L +S D  + VT++  K+GPGVVTAGDI     + V NPD  I  L+    
Sbjct: 76  IILNLKG--LVVSSDDDEPVTMYLRKQGPGVVTAGDIVPPAGVTVHNPDMHIATLNDKGK 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL 
Sbjct: 134 LEVELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLI 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + ++T  SI+  D++A A   L +  G+        + ++   +        +    +++
Sbjct: 194 IDVETKNSISPRDALASAGGTLVELFGLARELNADSEHIEIGPSPAEADHIASFALPIDD 253

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  +  
Sbjct: 254 LDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPA 313

Query: 323 DWPPESI 329
            + P  +
Sbjct: 314 TFDPSEV 320


>gi|311896536|dbj|BAJ28944.1| putative DNA-directed RNA polymerase subunit alpha [Kitasatospora
           setae KM-6054]
          Length = 340

 Score =  229 bits (584), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 127/316 (40%), Positives = 193/316 (61%), Gaps = 4/316 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPGVVTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGVVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           + V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 ELVLATLNGKGKLEMELTVERGRGYVSAVQNKASGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKPAMRPRDAMASAGKTLVELFGLARELNVDAEGIDMGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEELELTVRSYNCLKREGIHTVGELVARSEADLLDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPP 326
             MGL L  + P + P
Sbjct: 302 AGMGLALKDSPPGFDP 317


>gi|169630849|ref|YP_001704498.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium abscessus
           ATCC 19977]
 gi|169242816|emb|CAM63844.1| DNA-directed RNA polymerase alpha chain RpoA [Mycobacterium
           abscessus]
          Length = 350

 Score =  229 bits (584), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 130/315 (41%), Positives = 197/315 (62%), Gaps = 20/315 (6%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ENR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+TD
Sbjct: 16  ENRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILN+K  +L +S +  + VT++  K+GPG VTAGDI     + V NPD  I  L+    
Sbjct: 76  IILNLK--SLVVSSEEDEPVTMYLRKQGPGAVTAGDIVPPAGVTVHNPDMHIATLNDKGK 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL 
Sbjct: 134 LEIELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYNVEATRVEQRTDFDKLV 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNP 254
           + ++T  SI+  D++A A + L +  G+   +N E       P     + I   +LP   
Sbjct: 194 LDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALP--- 250

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +E+L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +G
Sbjct: 251 -----IEDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLG 305

Query: 315 LFLGMNLPDWPPESI 329
           L L  +   + P  +
Sbjct: 306 LSLKDSPTSFDPSEV 320


>gi|312199992|ref|YP_004020053.1| DNA-directed RNA polymerase, subunit alpha [Frankia sp. EuI1c]
 gi|311231328|gb|ADP84183.1| DNA-directed RNA polymerase, alpha subunit [Frankia sp. EuI1c]
          Length = 350

 Score =  229 bits (584), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 123/302 (40%), Positives = 187/302 (61%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +TLGN+LRR L+SS+ GA++T+++IDGVLHE S++ GV ED+TD
Sbjct: 16  EFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIRIDGVLHEFSTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           +ILN+K + +    D    + + K+GPG VTA DI     +EV NP+  +  ++    + 
Sbjct: 76  VILNLKELVVSSDNDEPTVMYLRKQGPGEVTAADIAPPAGVEVHNPELHLATINDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+ R  Q  D+DKL + 
Sbjct: 136 IELTVERGRGYVSAAQNKQPGQEIGRIPIDSIYSPVLKVTYKVEATRVEQRTDFDKLIVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           ++T  SI+  D++A A + L    G+        + V    + +       L   +EE++
Sbjct: 196 VETKPSISPRDAMASAGKTLVGLFGLAQELNAEAEGVDIGPSAQDAQLAADLALPIEEMD 255

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  LG MGL L  + P +
Sbjct: 256 LTVRSYNCLKREGIHTIGELVSRSEADLLDIRNFGQKSIDEVKTKLGAMGLQLKDSPPGF 315

Query: 325 PP 326
            P
Sbjct: 316 DP 317


>gi|163752891|ref|ZP_02160015.1| DNA-directed RNA polymerase subunit alpha [Kordia algicida OT-1]
 gi|161326623|gb|EDP97948.1| DNA-directed RNA polymerase subunit alpha [Kordia algicida OT-1]
          Length = 330

 Score =  229 bits (583), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 123/298 (41%), Positives = 186/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRVL+SSL G AIT+V+ID V HE S+I GV ED+T+IILN+K + 
Sbjct: 28  PLEPGYGLTIGNALRRVLLSSLEGFAITSVRIDKVDHEFSTISGVVEDVTEIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   D   ++ V+I   G   +TAGD Q  ++  +VLNPD VICN+D    + ME+T+ 
Sbjct: 88  FKRQIDDIDNESVSISVSGKEQLTAGDFQKFISGFQVLNPDLVICNMDASVNINMEITIE 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++  N P+G I  D++Y+P+K V Y++E+ R  Q  DY+KL   I TDGS
Sbjct: 148 KGRGYVPAEENKKSNAPLGTIFTDSIYTPVKNVKYSIENYRVEQKTDYEKLVFEIITDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  A++ L     +F    I  E  +    E  + +SL     L  K+ +++LS
Sbjct: 208 IHPKEALTEAAKTLIHHFMLFSDERITLEADEIAQTETYDEESLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   + D+++  NFG+KSL E++ ++   GL  GM+L  +
Sbjct: 268 VRALNCLKAAEVDTLGDLVSYNKNDLMKFRNFGKKSLTELEELVNVKGLSFGMDLSKY 325


>gi|302543333|ref|ZP_07295675.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces
           hygroscopicus ATCC 53653]
 gi|302460951|gb|EFL24044.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces
           himastatinicus ATCC 53653]
          Length = 340

 Score =  229 bits (583), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 128/316 (40%), Positives = 193/316 (61%), Gaps = 4/316 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNVDAEGIDMGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPP 326
             MGL L  + P + P
Sbjct: 302 AGMGLALKDSPPGFDP 317


>gi|328813993|gb|AEB52112.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 253

 Score =  228 bits (582), Expect = 7e-58,   Method: Compositional matrix adjust.
 Identities = 119/252 (47%), Positives = 170/252 (67%), Gaps = 2/252 (0%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T 
Sbjct: 1   DNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTA 60

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A   
Sbjct: 61  IILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGAHFH 120

Query: 145 MELTVSKGHGYVPAK--HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           M +T + G GYV A+   HR ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL+
Sbjct: 121 MRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLT 180

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + + T+GSIT  ++++L+++IL D L +F+N  +  K     +  +       L   +EE
Sbjct: 181 LDVWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEMTIEE 240

Query: 263 LELSVRSTNCLR 274
           L+LSVRS NCL+
Sbjct: 241 LDLSVRSYNCLK 252


>gi|328813995|gb|AEB52113.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 254

 Score =  228 bits (582), Expect = 7e-58,   Method: Compositional matrix adjust.
 Identities = 118/247 (47%), Positives = 168/247 (68%), Gaps = 2/247 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTAIILNV 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK+  D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A   M +T 
Sbjct: 61  KKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGAHFHMRMTA 120

Query: 150 SKGHGYVPAK--HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           + G GYV A+   HR ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T
Sbjct: 121 NTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +GSIT  ++++L+++IL D L +F+N  +  K     +  +       L   +EEL+LSV
Sbjct: 181 NGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEMTIEELDLSV 240

Query: 268 RSTNCLR 274
           RS NCL+
Sbjct: 241 RSYNCLK 247


>gi|256390173|ref|YP_003111737.1| DNA-directed RNA polymerase subunit alpha [Catenulispora acidiphila
           DSM 44928]
 gi|256356399|gb|ACU69896.1| DNA-directed RNA polymerase, alpha subunit [Catenulispora
           acidiphila DSM 44928]
          Length = 341

 Score =  228 bits (582), Expect = 7e-58,   Method: Compositional matrix adjust.
 Identities = 137/324 (42%), Positives = 200/324 (61%), Gaps = 20/324 (6%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E I+    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLTEEII----DEYRSRFLIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVL 128
           E ++I GV ED+TD+ILNIK   L +S +  + VT++  K+GPG VTA DI     +EV 
Sbjct: 62  EFTTIPGVKEDVTDLILNIK--QLVVSSEIDEPVTMYLRKQGPGTVTAADIAPPAGVEVH 119

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+ +I  L+    + MELTV +G GYV A  ++     IG I ID++YSP+ KV Y VE
Sbjct: 120 NPELIIATLNGKGKLEMELTVERGRGYVSAVQNKQAGQEIGRIPIDSIYSPVLKVKYDVE 179

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDIN 246
           + R  Q  D+D+L + ++T  S+   D+VA A + L +  G+   +N E       E I+
Sbjct: 180 ATRVEQRTDFDRLVLDVETKQSMRPRDAVASAGKTLVELFGLARELNIE------AEGID 233

Query: 247 VKSLP----FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           +   P        L   +E+LEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS
Sbjct: 234 MGPSPTDAALAADLALPIEDLELTVRSYNCLKREGIHTVGELVARSEADLLDIRNFGAKS 293

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPP 326
           + E+K  L +MGL L  + P + P
Sbjct: 294 IDEVKVKLMSMGLALKDSPPGFDP 317


>gi|313123135|ref|YP_004033394.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           delbrueckii subsp. bulgaricus ND02]
 gi|312279698|gb|ADQ60417.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           delbrueckii subsp. bulgaricus ND02]
          Length = 312

 Score =  228 bits (582), Expect = 7e-58,   Method: Compositional matrix adjust.
 Identities = 128/316 (40%), Positives = 190/316 (60%), Gaps = 16/316 (5%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +E++    + EPL RGF  TLGN+LRRVL++S+ G  +  V+IDG
Sbjct: 3   EFKKPN----ITVVDQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSVPGTGLVKVKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           +LHE +++ GV ED+T IILN+K + L+   +  K + +   GP  VTA D++   D+EV
Sbjct: 59  ILHEFTTVPGVKEDVTKIILNLKKLVLRAYTEEVKTIELDVEGPATVTAEDLKADADVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + M + V  G GYVPA  +++    IG I +D+L+SPI+KV+Y V
Sbjct: 119 LNPDQYICTIAQGGHLHMWIDVCNGRGYVPASENKSAEMSIGDIPVDSLFSPIEKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK------EV 241
           ES R G+  D+DKL++ I T+GSI   D++  A+R+L +    F + +   +      E 
Sbjct: 179 ESTRVGKREDFDKLTLEIWTNGSIAPNDALNFAARVLVEHFKAFESADAAAEIGEVMVEQ 238

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           + D   K L         +E+L+LSVRS NCL+   I  + DL  ++EA+M+R+ N GRK
Sbjct: 239 ENDQKEKKLEMT------IEDLDLSVRSYNCLKRAGINTLQDLTVKSEAEMMRVRNLGRK 292

Query: 302 SLVEIKGVLGTMGLFL 317
           SL E+K  L  +GL L
Sbjct: 293 SLEEVKNKLADLGLSL 308


>gi|328813987|gb|AEB52109.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 262

 Score =  228 bits (582), Expect = 7e-58,   Method: Compositional matrix adjust.
 Identities = 119/252 (47%), Positives = 170/252 (67%), Gaps = 2/252 (0%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T 
Sbjct: 5   DNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTA 64

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A   
Sbjct: 65  IILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGAHFH 124

Query: 145 MELTVSKGHGYVPAK--HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           M +T + G GYV A+   HR ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL+
Sbjct: 125 MRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLT 184

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + + T+GSIT  ++++L+++IL D L +F+N  +  K     +  +       L   +EE
Sbjct: 185 LDVWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEMTIEE 244

Query: 263 LELSVRSTNCLR 274
           L+LSVRS NCL+
Sbjct: 245 LDLSVRSYNCLK 256


>gi|331699145|ref|YP_004335384.1| DNA-directed RNA polymerase subunit alpha [Pseudonocardia
           dioxanivorans CB1190]
 gi|326953834|gb|AEA27531.1| DNA-directed RNA polymerase subunit alpha [Pseudonocardia
           dioxanivorans CB1190]
          Length = 347

 Score =  228 bits (582), Expect = 8e-58,   Method: Compositional matrix adjust.
 Identities = 131/314 (41%), Positives = 196/314 (62%), Gaps = 20/314 (6%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+TD
Sbjct: 16  ETRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILN+K   L +S +  + VT++  K+GPG VTAGDI     + V NPD  I  L+    
Sbjct: 76  IILNLK--ELVVSSEEDEPVTMYLRKQGPGPVTAGDIVPPAGVTVHNPDLHIATLNDKGR 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL 
Sbjct: 134 LEVELVVERGRGYVPAMQNKATGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLV 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNP 254
           + ++T  SIT  D++A A + L +  G+   +N +       P  +  + I   ++P   
Sbjct: 194 LDVETKPSITPRDALASAGKTLVELFGLARELNVDAEGIEIGPSPQEADTIAAFAMP--- 250

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +EEL+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  +G
Sbjct: 251 -----IEELDLTVRSYNCLKREGIHTVGELVGRSEADLLDIRNFGAKSIDEVKMKLVGLG 305

Query: 315 LFLGMNLPDWPPES 328
           L L  + P + P +
Sbjct: 306 LALKDSPPGFDPSA 319


>gi|307328058|ref|ZP_07607239.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces
           violaceusniger Tu 4113]
 gi|306886363|gb|EFN17368.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces
           violaceusniger Tu 4113]
          Length = 340

 Score =  228 bits (581), Expect = 9e-58,   Method: Compositional matrix adjust.
 Identities = 127/316 (40%), Positives = 193/316 (61%), Gaps = 4/316 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNVDAEGIDMGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPP 326
             MGL L  + P + P
Sbjct: 302 AGMGLALKDSPPGFDP 317


>gi|327399495|ref|YP_004340364.1| DNA-directed RNA polymerase subunit alpha [Hippea maritima DSM
           10411]
 gi|327182124|gb|AEA34305.1| DNA-directed RNA polymerase subunit alpha [Hippea maritima DSM
           10411]
          Length = 340

 Score =  228 bits (581), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 130/308 (42%), Positives = 194/308 (62%), Gaps = 5/308 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL  G+A T+GNALRRVL+SS+ G A+  V+I+GV HE S+I+GV ED+ +IILN+K +
Sbjct: 29  EPLNEGYATTIGNALRRVLLSSIVGIAVVGVEIEGVEHEFSTIEGVKEDVLNIILNLKQV 88

Query: 93  NLKMSGDSHKR--VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
             K   DS K   V I K GPG V +GDI+ + +IE++N D  I  L   A +  ++ + 
Sbjct: 89  RFKALNDSFKEGEVYIHKEGPGSVVSGDIEALGNIEIVNKDIYIAELMDGAKLDAKIYLQ 148

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           +G GY  A +    N  IG I +DAL+SPI +V+Y  + +      D++KL + I+TDG+
Sbjct: 149 RGIGYKQANYDAV-NREIGFIPVDALFSPIVRVAYHTKKSTMKDYYDFEKLVLEIETDGT 207

Query: 211 ITGEDSVALASRILQDQLGMF-INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           I  +D++  AS IL + + +F  +F+E  ++  E+ N   +  N  LLK VEELEL+VR+
Sbjct: 208 IMPQDALKQASYILGNYISIFSADFKETTQKEPEE-NKIDIQINENLLKPVEELELNVRA 266

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +NCL   NI Y+ +L Q+T+ ++L   NFG++SL EIK  L  +GL LGM       E I
Sbjct: 267 SNCLAAHNIKYIYELTQKTDTELLNTKNFGKQSLKEIKDSLKQLGLELGMKFSQEQLERI 326

Query: 330 EELAKKYE 337
           ++L ++ E
Sbjct: 327 QQLIEEKE 334


>gi|239980029|ref|ZP_04702553.1| DNA-directed RNA polymerase subunit alpha [Streptomyces albus
           J1074]
 gi|291451886|ref|ZP_06591276.1| DNA-directed RNA polymerase subunit alpha [Streptomyces albus
           J1074]
 gi|291354835|gb|EFE81737.1| DNA-directed RNA polymerase subunit alpha [Streptomyces albus
           J1074]
          Length = 340

 Score =  228 bits (581), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 126/316 (39%), Positives = 192/316 (60%), Gaps = 4/316 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG + +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNAKGKLEMELTVERGRGYVSAVQNKQAGQEIGRVPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNVDAEGIDMGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPP 326
             M L L  + P + P
Sbjct: 302 AGMSLALKDSPPGFDP 317


>gi|261876120|gb|ACY04590.1| DNA-directed RNA polymerase [Lactobacillus sp. DCY 50T]
          Length = 251

 Score =  228 bits (581), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 118/249 (47%), Positives = 169/249 (67%), Gaps = 4/249 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNV 60

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K I LK++G  D  + + I  +GP  VTAGDI    D++VLNPD  I  +   A   M +
Sbjct: 61  KKIALKLNGSDDQEETMEINVKGPAQVTAGDIVAGADVDVLNPDLYIATVADGATFHMRM 120

Query: 148 TVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           T  KG GYV A  ++T N   PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ +
Sbjct: 121 TADKGRGYVSADENKTRNTDMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDV 180

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+GSI   +++ALA++IL + L MF++  +  K  +  +  +       L   +EEL+L
Sbjct: 181 WTNGSINPSEAIALAAKILTEHLAMFVDLTDEAKNAEIMVEKEETHKEKMLEMTIEELDL 240

Query: 266 SVRSTNCLR 274
           SVRS NCL+
Sbjct: 241 SVRSYNCLK 249


>gi|145225546|ref|YP_001136224.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium gilvum
           PYR-GCK]
 gi|315445898|ref|YP_004078777.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium sp. Spyr1]
 gi|145218032|gb|ABP47436.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium gilvum
           PYR-GCK]
 gi|315264201|gb|ADU00943.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium sp. Spyr1]
          Length = 354

 Score =  228 bits (581), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 126/307 (41%), Positives = 192/307 (62%), Gaps = 4/307 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ENR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+TD
Sbjct: 16  ENRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ +    D    + + K+GPG VTAGDI     + V NPD  I  L+    + 
Sbjct: 76  IILNLKGLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPDMHIATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL + 
Sbjct: 136 VELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLILD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           ++T  SI+  D++A A + L +  G+   +N E    E+           + AL   +++
Sbjct: 196 VETKNSISPRDALASAGKTLVELFGLARELNIEAEGIEIGPSPAEADQAAHFAL--PIDD 253

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  +  
Sbjct: 254 LDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPA 313

Query: 323 DWPPESI 329
            + P  +
Sbjct: 314 SFDPSEV 320


>gi|317505829|ref|ZP_07963674.1| DNA-directed RNA polymerase [Segniliparus rugosus ATCC BAA-974]
 gi|316255911|gb|EFV15136.1| DNA-directed RNA polymerase [Segniliparus rugosus ATCC BAA-974]
          Length = 350

 Score =  228 bits (581), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 121/306 (39%), Positives = 191/306 (62%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV ED+T+
Sbjct: 16  EYRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTIAGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           I+LN+KG+ +    D    + + K+GPG VTA DI   + + +  PD  I  L+    + 
Sbjct: 76  IVLNVKGLEVSSVEDEPATLYLRKQGPGPVTAADIVAPSGVTITKPDTHIATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MEL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D+L + 
Sbjct: 136 MELVVERGRGYVPAVQNKDSGAEIGRIPVDSIYSPVLKVTYQVEATRVEQRTDFDRLILD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           +++  SIT  D+VA A + L +  G+        + ++      S     +L   +E+L 
Sbjct: 196 VESKSSITPRDAVASAGKTLVELFGLARELNLAAEGIEIGAVAASTNNIASLALPIEDLH 255

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L+VRS NCL+ E +  +G+L+ R+E+D+L + NFG+KS+ E+K  L T+GL L  +  ++
Sbjct: 256 LTVRSYNCLKREGVHTIGELVARSESDLLDIRNFGQKSIDEVKLKLYTLGLALKDSPANF 315

Query: 325 PPESIE 330
            P +I+
Sbjct: 316 DPSNID 321


>gi|158317764|ref|YP_001510272.1| DNA-directed RNA polymerase subunit alpha [Frankia sp. EAN1pec]
 gi|158113169|gb|ABW15366.1| DNA-directed RNA polymerase, alpha subunit [Frankia sp. EAN1pec]
          Length = 375

 Score =  228 bits (581), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 124/302 (41%), Positives = 186/302 (61%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVLHE S++ GV ED+TD
Sbjct: 42  EFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVLHEFSTVPGVKEDVTD 101

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           +ILN+K + +    D    + + K+GPG VTA DI     +EV NPD  +  L+    + 
Sbjct: 102 LILNLKELVVSSDNDEPTVMYLRKQGPGEVTAADIAPPAGVEVHNPDLHLATLNDKGKLE 161

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+ R  Q  D+D+L + 
Sbjct: 162 IELTVERGRGYVSAAQNKQPGQEIGRIPIDSIYSPVLKVTYKVEATRVEQRTDFDRLIVD 221

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           ++T  SI+  D++A A + L    G+        + V    +         L   +EE++
Sbjct: 222 VETKQSISPRDAMASAGKTLVGLFGLAQELNAEAEGVDIGPSAADAALAADLALPIEEMD 281

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  LG MGL L  + P +
Sbjct: 282 LTVRSYNCLKREGIHTIGELVSRSEADLLDIRNFGQKSIDEVKTKLGAMGLQLKDSPPGF 341

Query: 325 PP 326
            P
Sbjct: 342 DP 343


>gi|296268581|ref|YP_003651213.1| DNA-directed RNA polymerase subunit alpha [Thermobispora bispora
           DSM 43833]
 gi|296091368|gb|ADG87320.1| DNA-directed RNA polymerase, alpha subunit [Thermobispora bispora
           DSM 43833]
          Length = 340

 Score =  228 bits (581), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 134/317 (42%), Positives = 192/317 (60%), Gaps = 15/317 (4%)

Query: 22  QEE---ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
           QEE   E R+  I EPL  GF +T+GN+LRR L+SS+ GAA+T+++I+GVLHE S++ GV
Sbjct: 10  QEEPLSEYRSRFILEPLEPGFGYTIGNSLRRTLLSSIPGAAVTSIRIEGVLHEFSTVPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+TDIILN+K + +    D    + + K+GPG VTA DI     +EV NP+  I  L+
Sbjct: 70  KEDVTDIILNLKQLVVSSEHDEPVVMYLRKQGPGEVTAADIAPPAGVEVHNPELHIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
             A + MELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+ R  Q  D+
Sbjct: 130 GKAKLEMELTVERGRGYVSAAQNKQPGQEIGRIPIDSIYSPVLKVTYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLP----F 252
           D+L + ++T  SI   D+VA A + L +  G+   +N E       E I +   P     
Sbjct: 190 DRLILDVETKPSIKPRDAVASAGKTLVELFGLARELNVE------AEGIEIGPSPTDAAL 243

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
              L   +EEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  
Sbjct: 244 AADLALPIEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLDIRNFGAKSIEEVKQKLAE 303

Query: 313 MGLFLGMNLPDWPPESI 329
           MGL L  + P + P ++
Sbjct: 304 MGLTLKDSPPGFDPATV 320


>gi|227832273|ref|YP_002833980.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           aurimucosum ATCC 700975]
 gi|262183871|ref|ZP_06043292.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           aurimucosum ATCC 700975]
 gi|227453289|gb|ACP32042.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           aurimucosum ATCC 700975]
          Length = 336

 Score =  228 bits (581), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 129/309 (41%), Positives = 192/309 (62%), Gaps = 7/309 (2%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           + +R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV ED++
Sbjct: 15  DSSRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTINGVKEDVS 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +IILN+KG  L +S DS + V ++  K GPG VTAGDIQ    +E+ N D  I +L+  A
Sbjct: 75  EIILNVKG--LVLSSDSDEPVVMYLSKEGPGEVTAGDIQPPAGVEIHNSDLHIASLNESA 132

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + MEL V +G GYVPA     E   IG I +D +YSP+ KVSY VE+ R  Q  D+DKL
Sbjct: 133 KLEMELVVERGRGYVPAAATSGE---IGRIPVDQIYSPVLKVSYKVEATRVEQRTDFDKL 189

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + ++T  SI+  D++A A   L +  G+        + ++   + +   +  A    +E
Sbjct: 190 IIDVETKNSISARDALASAGGTLVELFGLARELNTAAEGIEIGPSPQETEYIAAYSMPIE 249

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +L  SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L  +GL L    
Sbjct: 250 DLNFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKIKLANLGLALKDTP 309

Query: 322 PDWPPESIE 330
            D+ P  +E
Sbjct: 310 EDFDPTQLE 318


>gi|320533222|ref|ZP_08033935.1| DNA-directed RNA polymerase, alpha subunit [Actinomyces sp. oral
           taxon 171 str. F0337]
 gi|320134562|gb|EFW26797.1| DNA-directed RNA polymerase, alpha subunit [Actinomyces sp. oral
           taxon 171 str. F0337]
          Length = 353

 Score =  228 bits (581), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 133/320 (41%), Positives = 193/320 (60%), Gaps = 15/320 (4%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V+   E+ R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+IDGV H
Sbjct: 26  RPTLTEEVVV---EDRRSRFVLEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRIDGVPH 82

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E  +I GV ED+  IILNIK I L    D    + + K GP  VTAGDI     +E+ NP
Sbjct: 83  EFRTIPGVKEDVAQIILNIKEIVLSSENDEPVVMYLRKSGPSEVTAGDITPPAGVEIHNP 142

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           + VI  L+    + +ELTV +G GYV A  ++  N  I  I +D++YSP+KKVSY+VE+ 
Sbjct: 143 ELVIATLNEKGKLEIELTVERGRGYVSANQNKDPNAEISRIPVDSIYSPVKKVSYSVEAT 202

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVK 248
           R  Q  D+D+L + ++T  SIT  D++A A + L +  G+   +N E       E I V 
Sbjct: 203 RVEQRTDFDRLIVDVETKSSITPRDALASAGKTLVELFGLARELNVE------AEGIEVG 256

Query: 249 SLPFNPALLKK----VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
             P + A  +     ++EL+L  RS+N L+ E I  +G+L+ R+EAD+L + NFG KS+ 
Sbjct: 257 PSPIDEAFQQDLALMIDELDLQARSSNALKREGIHTVGELVSRSEADLLDIRNFGAKSIS 316

Query: 305 EIKGVLGTMGLFLGMNLPDW 324
           EIK  L  +GL L  +  D+
Sbjct: 317 EIKDKLAELGLSLKGSPVDY 336


>gi|120437149|ref|YP_862835.1| DNA-directed RNA polymerase subunit alpha [Gramella forsetii
           KT0803]
 gi|158512451|sp|A0M573|RPOA_GRAFK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|117579299|emb|CAL67768.1| DNA-directed RNA polymerase alpha subunit [Gramella forsetii
           KT0803]
          Length = 330

 Score =  228 bits (581), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 123/298 (41%), Positives = 187/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRVL+SSL G AIT+V+I+GV HE S+I GV ED+T+IILN+K + 
Sbjct: 28  PLEPGYGLTVGNALRRVLLSSLEGFAITSVRIEGVDHEFSTIAGVVEDVTEIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   D   ++ VTI   G   +TAG  Q  ++  +VLNPD VIC++D    + ME+T+ 
Sbjct: 88  FKRQIDEIDNESVTISVSGEEQLTAGHFQKFISGFQVLNPDQVICHMDKKVSLNMEITIE 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++  N P+G I +D++Y+PIK V Y++E+ R  Q  DY+KL   I +DGS
Sbjct: 148 KGRGYVPAEENKKANAPLGTIFVDSIYTPIKNVKYSIENFRVEQKTDYEKLVFEIISDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++ L     +F    I  E  +    E  + +SL     L  K+ +++LS
Sbjct: 208 IHPKDALTEAAKTLIHHFMLFSDERITLEADEIAQTETYDEESLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   + D+++  NFG+KSL E++ ++   GL  GM+L  +
Sbjct: 268 VRALNCLKAAEVDTLGDLVSYNKNDLMKFRNFGKKSLTELEELVSNKGLNFGMDLSKY 325


>gi|282882483|ref|ZP_06291104.1| DNA-directed RNA polymerase, alpha subunit [Peptoniphilus
           lacrimalis 315-B]
 gi|300814667|ref|ZP_07094918.1| DNA-directed RNA polymerase, alpha subunit [Peptoniphilus sp. oral
           taxon 836 str. F0141]
 gi|281297625|gb|EFA90100.1| DNA-directed RNA polymerase, alpha subunit [Peptoniphilus
           lacrimalis 315-B]
 gi|300511286|gb|EFK38535.1| DNA-directed RNA polymerase, alpha subunit [Peptoniphilus sp. oral
           taxon 836 str. F0141]
          Length = 315

 Score =  228 bits (580), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 128/290 (44%), Positives = 185/290 (63%), Gaps = 4/290 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL  G+  T+GN+LRRVL+SSL GAA++ + I GV HE  +I GV ED+ +IILN+
Sbjct: 23  FIVEPLESGYGITIGNSLRRVLLSSLPGAAVSFINIRGVEHEFDTIPGVLEDVPEIILNV 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I  KM  D   ++ I K G G +TAGDI     + V+NP+H I  L+ DA V +E+TV
Sbjct: 83  KSIVFKMENDEPVKLIIEKSGKGEITAGDIILEPSVSVVNPNHHIATLNEDADVYIEMTV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GY P++  + E   IG+I +D+ YSP++KV++ VE+ R GQ  DYD+L + + TDG
Sbjct: 143 EKGRGYEPSELKKDEVTQIGIIPVDSNYSPVRKVNWKVENTRVGQRTDYDRLILEVTTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK--VEELELSV 267
           S+  +++ +LA++IL + L +FI       EV  +I V+        +K+  VEEL+LSV
Sbjct: 203 SMKADEATSLAAKILTEHLDLFIGLINHVDEV--NIMVEKEEDQSEKVKEMTVEELDLSV 260

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+   I  +G+L  +TE DM+++ N G+KSL E+   L  M L L
Sbjct: 261 RSFNCLKRAGINTVGELTNKTEEDMMKVRNLGKKSLEEVVSKLQEMNLSL 310


>gi|119358164|ref|YP_912808.1| DNA-directed RNA polymerase subunit alpha [Chlorobium
           phaeobacteroides DSM 266]
 gi|158512605|sp|A1BJ07|RPOA_CHLPD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119355513|gb|ABL66384.1| DNA-directed RNA polymerase subunit alpha [Chlorobium
           phaeobacteroides DSM 266]
          Length = 327

 Score =  228 bits (580), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 124/302 (41%), Positives = 190/302 (62%), Gaps = 9/302 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            IA+PL RG+  T+GN +RRVL++SL G AIT V+I+GV HE S+I+GV ED+ +I+LN+
Sbjct: 25  FIAQPLERGYGVTIGNVMRRVLLASLPGTAITGVKIEGVYHEFSAIEGVREDVPEIVLNL 84

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           K +  K +     + ++   G    TAGDI     + EVLN D  I  ++  +V+ +E+ 
Sbjct: 85  KRVRFKSNCKRSCKTSLSIAGTKDFTAGDIIAKEGEFEVLNKDLHIATVNDGSVLNIEIY 144

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           + +G GY+PA+ +  E  PIG I IDA+++PI+ V +TVE+ R GQ  DY+K+ + ++TD
Sbjct: 145 IGRGRGYLPAEENHPEGMPIGFIAIDAIFTPIRNVKFTVENTRVGQRTDYEKMILDVETD 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEV------KEDINVKSLPFNPALLKKVEE 262
           GSI  +DS++LA +I+ D +  F NF   ++E       ++D   +S+     L  K+E+
Sbjct: 205 GSIAPDDSISLAGKIINDHIMYFANFSPTEEEFTEEEFKQQDDEFESM--RKLLHTKIED 262

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL E+K  L    L  GM++ 
Sbjct: 263 LDLSVRSHNCLRLAEIDTIGDLVSRKEDELLNYKNFGKKSLTELKEQLEKFDLKFGMDIT 322

Query: 323 DW 324
            +
Sbjct: 323 RY 324


>gi|256380567|ref|YP_003104227.1| DNA-directed RNA polymerase subunit alpha [Actinosynnema mirum DSM
           43827]
 gi|255924870|gb|ACU40381.1| DNA-directed RNA polymerase, alpha subunit [Actinosynnema mirum DSM
           43827]
          Length = 350

 Score =  228 bits (580), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 130/312 (41%), Positives = 194/312 (62%), Gaps = 16/312 (5%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +TLGN++RR L+SS+ GAA+T+++IDGVLHE +++ GV ED+TD
Sbjct: 16  ETRSRFVIEPLEPGFGYTLGNSIRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILN+K   L +S +  + VT++  K+GPG VTAGDI     + V NPD  I  L+    
Sbjct: 76  IILNLK--ELVVSSEEDEPVTMYLRKQGPGAVTAGDIVPPAGVTVHNPDLHIATLNGKGK 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL 
Sbjct: 134 LEIELVVERGRGYVPAVQNKQAGAEIGRIPVDSIYSPVMKVTYKVEATRVEQRTDFDKLI 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFN----PAL 256
           + +++  SIT  D+VA A + L +  G+   +N +       E I +   P       A 
Sbjct: 194 LDVESKPSITPRDAVASAGKTLVELFGLARELNVD------AEGIEIGPSPAEADTIAAF 247

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  +GL 
Sbjct: 248 AMPIEDLDLTVRSYNCLKREGIHTVGELVSRSEADLLDIRNFGAKSIDEVKMKLVGLGLA 307

Query: 317 LGMNLPDWPPES 328
           L  + P + P +
Sbjct: 308 LKDSPPGFDPSA 319


>gi|269784296|emb|CBH50793.1| alpha subunit of RNA polymerase [Vibrio sp. Cmj 13.4]
          Length = 270

 Score =  228 bits (580), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 119/270 (44%), Positives = 180/270 (66%), Gaps = 8/270 (2%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVT 115
           G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V 
Sbjct: 2   GCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVV 61

Query: 116 AGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLI 171
           AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG +
Sbjct: 62  AGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRL 121

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F
Sbjct: 122 LVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAF 181

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           ++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE +
Sbjct: 182 VDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVE 238

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +L+  N G+KSL EIK VL + GL LGM L
Sbjct: 239 LLKTPNLGKKSLTEIKDVLASRGLSLGMRL 268


>gi|184200289|ref|YP_001854496.1| DNA-directed RNA polymerase subunit alpha [Kocuria rhizophila
           DC2201]
 gi|183580519|dbj|BAG28990.1| DNA-directed RNA polymerase alpha subunit [Kocuria rhizophila
           DC2201]
          Length = 339

 Score =  228 bits (580), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 120/300 (40%), Positives = 189/300 (63%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ENR+  + EPL  GF +TLGN+LRR L+SS+ GA++T+++IDGVLHE S+++GV ED+T+
Sbjct: 16  ENRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIRIDGVLHEFSTVEGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           +ILNIK ++L    D      + K+GPG VTA DI     +EV NP+  I  L+    + 
Sbjct: 76  LILNIKKLSLSSEEDEPVTAWLRKQGPGEVTAADISAPAGVEVHNPELHIATLNSKGQLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELT+ +G GYV A  +++ +  +G I +D++YSP+ KV++ VE+ R  Q  D+DKL + 
Sbjct: 136 IELTIERGRGYVSASQNKSGDAEVGRIPVDSIYSPVLKVTFRVEATRVEQRTDFDKLILD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           ++T  +I+  D+VA A   L +  G+        + ++   +         +   +E+LE
Sbjct: 196 VETKEAISPRDAVASAGTTLVELFGLARELNSSAEGIEIGPSPTDAAAAADMALPIEDLE 255

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           LSVRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  LG +GL L  + P +
Sbjct: 256 LSVRSYNCLKREGIHSVGELVGRSEADLMDIRNFGAKSIDEVKDKLGELGLALKDSPPGY 315


>gi|257054498|ref|YP_003132330.1| DNA-directed RNA polymerase subunit alpha [Saccharomonospora
           viridis DSM 43017]
 gi|256584370|gb|ACU95503.1| DNA-directed RNA polymerase subunit alpha [Saccharomonospora
           viridis DSM 43017]
          Length = 358

 Score =  228 bits (580), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 131/312 (41%), Positives = 195/312 (62%), Gaps = 20/312 (6%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S++ GV ED+T+
Sbjct: 16  ETRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFSTVPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILN+K   L +S +  + VT++  K+GPG VTA DI   + + V NPD  I +L+    
Sbjct: 76  IILNLK--ELVVSSEEDEPVTMYLRKQGPGEVTAADIVPPSGVTVHNPDLHIASLNGKGK 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +EL V +G GYVPA  ++     IG I ID++YSP+ KV+Y VE+ R  Q  D+DKL 
Sbjct: 134 LEIELVVERGRGYVPALQNKQAGAEIGRIPIDSIYSPVLKVTYKVEATRVEQRTDFDKLV 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNP 254
           + ++T  SIT  D+VA A + L +  G+   +N +       P  +  + I   ++P   
Sbjct: 194 LDVETKPSITPRDAVASAGKTLVELFGLARELNVDAEGIEIGPSPQEADTIAAYAMP--- 250

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  +G
Sbjct: 251 -----IEDLDLTVRSYNCLKREGIHTVGELVSRSEADLLDIRNFGAKSIDEVKMKLAGLG 305

Query: 315 LFLGMNLPDWPP 326
           L L  + P + P
Sbjct: 306 LTLKDSPPGFDP 317


>gi|313292016|gb|ADR51197.1| DNA-directed RNA polymerase alpha chain [Enterococcus viikkiensis]
 gi|313292018|gb|ADR51198.1| DNA-directed RNA polymerase alpha chain [Enterococcus viikkiensis]
          Length = 258

 Score =  228 bits (580), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 116/252 (46%), Positives = 167/252 (66%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E+ +    + E L RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+
Sbjct: 7   EDRDYGKFVVESLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDV 66

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             IILNIKG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A 
Sbjct: 67  VQIILNIKGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGAT 126

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
               LTV  G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+
Sbjct: 127 FHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLT 186

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           M I TDGSI  +++++LA++IL + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 187 MEIWTDGSIIAQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEE 246

Query: 263 LELSVRSTNCLR 274
           L+LSVRS NCL+
Sbjct: 247 LDLSVRSYNCLK 258


>gi|328813937|gb|AEB52084.1| DNA-directed RNA polymerase alpha chain [Lactobacillus brevis]
          Length = 263

 Score =  227 bits (579), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 118/263 (44%), Positives = 175/263 (66%), Gaps = 4/263 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVTQIILNV 60

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K I LK++G  D  + + I  +GP  +TAGDI    D+++LNPD  I  +   A   M +
Sbjct: 61  KKIALKLNGSDDQEETMEINVKGPAQITAGDIVAGADVDILNPDLYIATVADGATFHMRM 120

Query: 148 TVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           T  KG GYV A  ++T N   PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ +
Sbjct: 121 TADKGRGYVSADENKTRNTDMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDV 180

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+GSI   +++ALA++IL + L MF++  +  K  +  +  +       L   +EEL+L
Sbjct: 181 WTNGSINPSEAIALAAKILTEHLAMFVDLTDEAKNAEIMVEKEETHKEKMLEMTIEELDL 240

Query: 266 SVRSTNCLRGENIVYMGDLIQRT 288
           SVRS NCL+   I  + +L  +T
Sbjct: 241 SVRSYNCLKRAGINTVQELNNKT 263


>gi|227502699|ref|ZP_03932748.1| DNA-directed RNA polymerase [Corynebacterium accolens ATCC 49725]
 gi|306835270|ref|ZP_07468302.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium accolens
           ATCC 49726]
 gi|227076429|gb|EEI14392.1| DNA-directed RNA polymerase [Corynebacterium accolens ATCC 49725]
 gi|304568863|gb|EFM44396.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium accolens
           ATCC 49726]
          Length = 336

 Score =  227 bits (579), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 129/309 (41%), Positives = 194/309 (62%), Gaps = 7/309 (2%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           + +R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV ED++
Sbjct: 15  DSSRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTINGVKEDVS 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +IILNIK  ++ +S DS + V ++  K GPG VTAGDIQ    +E+ NPD  I +L+  A
Sbjct: 75  EIILNIK--SMVLSSDSDEPVVMYLSKEGPGDVTAGDIQPPAGVEIHNPDLHIASLNDTA 132

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + +EL V +G GYVPA     E   IG I ID +YSP+ KVSY VE+ R  Q  D+DKL
Sbjct: 133 KLDIELVVERGRGYVPAAATSGE---IGRIPIDQIYSPVLKVSYKVEATRVEQRTDFDKL 189

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           ++ ++T  SI+  D++A A   L +  G+        + ++   + +   +  A    +E
Sbjct: 190 TIDVETKNSISARDALASAGGTLVELFGLARELNNAAEGIEIGPSPQETEYIAAYGMPIE 249

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +L  SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L  +GL L    
Sbjct: 250 DLNFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKIKLANLGLALKDTP 309

Query: 322 PDWPPESIE 330
            D+ P  +E
Sbjct: 310 EDFDPTQLE 318


>gi|148273768|ref|YP_001223329.1| DNA-directed RNA polymerase subunit alpha [Clavibacter
           michiganensis subsp. michiganensis NCPPB 382]
 gi|166229268|sp|A5CU80|RPOA_CLAM3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|147831698|emb|CAN02667.1| DNA-directed RNA polymerase alpha chain [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
          Length = 331

 Score =  227 bits (579), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 122/304 (40%), Positives = 186/304 (61%), Gaps = 8/304 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S++ GV ED+T+
Sbjct: 16  EFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFSTVPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILNIKG+ +    D      + K+G G VTA DI     +E+ NP+ VI  L+  A   
Sbjct: 76  IILNIKGLVVSSEHDEPITAYLRKQGAGQVTAADISAPAGVEIHNPELVIATLNEKAKFE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELT+ +G GYV A  +R+E    G I +D++YSP+ KV+Y VE+ R G+  D+D+L + 
Sbjct: 136 LELTIERGRGYVSATQNRSEFSEAGQIPVDSIYSPVLKVTYRVEATRAGERTDFDRLVVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK----V 260
           ++T  +IT  D++A A R L +  G+            E I +   P +  L  +    +
Sbjct: 196 VETKSAITPRDAIASAGRTLTELFGLAREL----NSAAEGIEIGPAPVDAVLSSELSMPI 251

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           E+L+LSVRS NCL+ E I  + +L+  +E  ++ + NFG+KS+ E+K  L  +GL L   
Sbjct: 252 EDLDLSVRSYNCLKREGINNVSELVALSETQLMNIRNFGQKSVDEVKDKLVELGLSLKDA 311

Query: 321 LPDW 324
           +P +
Sbjct: 312 VPGF 315


>gi|119961601|ref|YP_948627.1| DNA-directed RNA polymerase subunit alpha [Arthrobacter aurescens
           TC1]
 gi|158512966|sp|A1R8R5|RPOA_ARTAT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119948460|gb|ABM07371.1| DNA-directed RNA polymerase, alpha subunit [Arthrobacter aurescens
           TC1]
          Length = 336

 Score =  227 bits (579), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 122/302 (40%), Positives = 187/302 (61%), Gaps = 4/302 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ENR+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T+
Sbjct: 16  ENRSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILNIK +++    D      + K+GPGVVTA DI     +E  NPD  I  L+      
Sbjct: 76  IILNIKNLSVSSEHDEPVVAYLRKQGPGVVTAADIAPPAGVEFHNPDLHIATLNSKGKFE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELT+ +G GYV A  +++ +  IG I +D++YSP+ KV++ VE+ R  Q  D+DKL + 
Sbjct: 136 LELTIERGRGYVSAAQNKSGDSEIGRIPVDSIYSPVMKVTFRVEATRVEQRTDFDKLIVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           ++T  +I   D+VA A   L +  G+        + ++   +         +   +E+L+
Sbjct: 196 VETKQAIAPRDAVASAGTTLVELFGLARELNTAAEGIEIGPSPTDAALAADMALPIEDLD 255

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L    + LG++L D 
Sbjct: 256 LTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGAKSIDEVKAKL----VELGLSLKDS 311

Query: 325 PP 326
           PP
Sbjct: 312 PP 313


>gi|328813939|gb|AEB52085.1| DNA-directed RNA polymerase alpha chain [Lactobacillus brevis]
          Length = 265

 Score =  227 bits (579), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 118/263 (44%), Positives = 175/263 (66%), Gaps = 4/263 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+
Sbjct: 3   FIVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVTQIILNV 62

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K I LK++G  D  + + I  +GP  +TAGDI    D+++LNPD  I  +   A   M +
Sbjct: 63  KKIALKLNGSDDQEETMEINVKGPAQITAGDIVAGADVDILNPDLYIATVADGATFHMRM 122

Query: 148 TVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           T  KG GYV A  ++T N   PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ +
Sbjct: 123 TADKGRGYVSADENKTRNTDMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDV 182

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+GSI   +++ALA++IL + L MF++  +  K  +  +  +       L   +EEL+L
Sbjct: 183 WTNGSINPSEAIALAAKILTEHLAMFVDLTDEAKNAEIMVEKEETHKEKMLEMTIEELDL 242

Query: 266 SVRSTNCLRGENIVYMGDLIQRT 288
           SVRS NCL+   I  + +L  +T
Sbjct: 243 SVRSYNCLKRAGINTVQELNNKT 265


>gi|170780766|ref|YP_001709098.1| DNA-directed RNA polymerase subunit alpha [Clavibacter
           michiganensis subsp. sepedonicus]
 gi|189043834|sp|B0RB72|RPOA_CLAMS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|169155334|emb|CAQ00437.1| DNA-directed RNA polymerase alpha chain [Clavibacter michiganensis
           subsp. sepedonicus]
          Length = 331

 Score =  227 bits (579), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 122/304 (40%), Positives = 186/304 (61%), Gaps = 8/304 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S++ GV ED+T+
Sbjct: 16  EFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFSTVPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILNIKG+ +    D      + K+G G VTA DI     +E+ NP+ VI  L+  A   
Sbjct: 76  IILNIKGLVVSSEHDEPITAYLRKQGAGQVTAADISAPAGVEIHNPELVIATLNEKAKFE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELT+ +G GYV A  +R+E    G I +D++YSP+ KV+Y VE+ R G+  D+D+L + 
Sbjct: 136 LELTIERGRGYVSATQNRSEFSEAGQIPVDSIYSPVLKVTYRVEATRAGERTDFDRLVVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK----V 260
           ++T  +IT  D++A A R L +  G+            E I +   P +  L  +    +
Sbjct: 196 VETKSAITPRDAIASAGRTLTELFGLAREL----NSAAEGIEIGPAPVDAVLSSELSMPI 251

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           E+L+LSVRS NCL+ E I  + +L+  +E  ++ + NFG+KS+ E+K  L  +GL L   
Sbjct: 252 EDLDLSVRSYNCLKREGIHNVSELVALSETQLMNIRNFGQKSVDEVKDKLVELGLSLKDA 311

Query: 321 LPDW 324
           +P +
Sbjct: 312 VPGF 315


>gi|240167783|ref|ZP_04746442.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium kansasii
           ATCC 12478]
          Length = 347

 Score =  227 bits (579), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 130/315 (41%), Positives = 196/315 (62%), Gaps = 20/315 (6%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+TD
Sbjct: 16  DNRSQFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILN+K  +L +S +  + VT++  K+GPG VTAGDI     + V NP   I  L+    
Sbjct: 76  IILNLK--SLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIATLNDKGK 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL 
Sbjct: 134 LEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLI 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNP 254
           + ++T  SIT  D++A A + L +  G+   +N E       P     + I   +LP   
Sbjct: 194 LDVETKSSITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALP--- 250

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +G
Sbjct: 251 -----IDDLDLTVRSYNCLKREGVHTVGELVSRTESDLLDIRNFGQKSIDEVKVKLHQLG 305

Query: 315 LFLGMNLPDWPPESI 329
           L L  + P + P  +
Sbjct: 306 LSLKDSPPTFDPSEV 320


>gi|298207753|ref|YP_003715932.1| DNA-directed RNA polymerase alpha subunit [Croceibacter atlanticus
           HTCC2559]
 gi|83850391|gb|EAP88259.1| DNA-directed RNA polymerase alpha subunit [Croceibacter atlanticus
           HTCC2559]
          Length = 317

 Score =  227 bits (579), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 122/298 (40%), Positives = 187/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRVL+SSL G AI++V+++GV HE S+I GV ED+T+IILN+K + 
Sbjct: 15  PLEPGYGLTVGNALRRVLLSSLEGFAISSVRVEGVDHEFSTISGVVEDVTEIILNLKQVR 74

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   D   ++ VT+   G   +TAGD Q  ++  +VLNPD VICN+D    + +E+T+ 
Sbjct: 75  FKRQIDEVDNETVTMNISGQEQLTAGDFQKFISGFQVLNPDMVICNMDKKVNLNIEITIE 134

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++  N PIG I  D++++PIK V Y++E+ R  Q  DY+KL   I TDGS
Sbjct: 135 KGRGYVPAEENKKSNAPIGTIFTDSIFTPIKNVKYSIENYRVEQKTDYEKLVFEIQTDGS 194

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++ L     +F    I  E  +    E  + +SL     L  K+ +++LS
Sbjct: 195 IHPKDALTEAAKTLIHHFMLFSDERITLEADEIAQTETYDEESLHMRQLLKTKLVDMDLS 254

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   + D+++  NFG+KSL E++ ++   GL  GM+L  +
Sbjct: 255 VRALNCLKAAEVDSLGDLVSYNKNDLMKFRNFGKKSLTELEELVNNKGLNFGMDLSKY 312


>gi|313891534|ref|ZP_07825144.1| DNA-directed RNA polymerase, alpha subunit [Dialister
           microaerophilus UPII 345-E]
 gi|329121855|ref|ZP_08250470.1| DNA-directed RNA polymerase subunit alpha [Dialister micraerophilus
           DSM 19965]
 gi|313119993|gb|EFR43175.1| DNA-directed RNA polymerase, alpha subunit [Dialister
           microaerophilus UPII 345-E]
 gi|327467793|gb|EGF13285.1| DNA-directed RNA polymerase subunit alpha [Dialister micraerophilus
           DSM 19965]
          Length = 324

 Score =  227 bits (579), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 133/306 (43%), Positives = 192/306 (62%), Gaps = 23/306 (7%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
            EPL RGF  TLGN+LRRVL+SSL G AIT+++IDGVLHE ++I+GV ED+TD+ILN+K 
Sbjct: 25  CEPLERGFGITLGNSLRRVLLSSLDGVAITSIKIDGVLHEFTTIEGVREDVTDMILNLKK 84

Query: 92  INLKMSGDS----HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           I      ++      R+ I K   G+  AGD+Q  ++I+VLN D  IC LD DA + MEL
Sbjct: 85  IRFIAHDEAVFPIQVRIDIDKE--GIFHAGDMQLPSEIDVLNTDLEICTLDADAHLGMEL 142

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           T+ +GHGYVP   ++ +ND IG+I ID++++P+ K +Y V   R G  +DYDKL++ ++T
Sbjct: 143 TIDRGHGYVPFNKNK-KNDEIGIIPIDSIFTPVVKCNYKVSDTRVGNEMDYDKLTLELET 201

Query: 208 DGSITGEDSVALASRILQDQLGMF----------INFEEPKKEVKEDINVKSLPFNPALL 257
           DGS+  ED+VA A+ IL      F          I+ +E + E++E  +   L   P   
Sbjct: 202 DGSVKVEDAVAQAATILIKYFENFRRLATKQIPEIDVDEIEPEIEEKDDSPDLSVIP--- 258

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +EELELSVR+ NCL+   I  +  L  +TE ++ R+ N G+KS+ EIK  L     + 
Sbjct: 259 --IEELELSVRAFNCLKRAEINMLDQLTDKTEDELTRVRNLGKKSVDEIKEKLAAYKGW- 315

Query: 318 GMNLPD 323
           G++L D
Sbjct: 316 GLHLKD 321


>gi|213584847|ref|ZP_03366673.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E98-0664]
          Length = 253

 Score =  227 bits (578), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 116/257 (45%), Positives = 178/257 (69%), Gaps = 9/257 (3%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           +GNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G    
Sbjct: 1   MGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEV 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK-- 159
            +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + V +G GYVPA   
Sbjct: 61  ILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTR 120

Query: 160 -HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
            H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++ 
Sbjct: 121 IHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIR 180

Query: 219 LASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGEN 277
            A+ IL +QL  F++  + ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E 
Sbjct: 181 RAATILAEQLEAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEA 236

Query: 278 IVYMGDLIQRTEADMLR 294
           I Y+GDL+QRTE ++L+
Sbjct: 237 IHYIGDLVQRTEVELLK 253


>gi|297163220|gb|ADI12932.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           bingchenggensis BCW-1]
          Length = 337

 Score =  227 bits (578), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 123/306 (40%), Positives = 189/306 (61%), Gaps = 12/306 (3%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
           R+  + EPL  GF +TLGN+LRR L+SS+  AA+T+++IDGVLHE +++ GV ED+TD+I
Sbjct: 18  RSRFVIEPLEPGFGYTLGNSLRRTLLSSIPAAAVTSIRIDGVLHEFTTVPGVREDITDLI 77

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+K + +    D    + + K+GPG+ TA DI     +EV NPD V+  L+    + +E
Sbjct: 78  LNLKQLVVSSEHDEPVVMYLRKQGPGLATAADIAPPAGVEVHNPDLVLATLNAKGKLEIE 137

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           LTV +G GYV A  +  +   IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL + ++
Sbjct: 138 LTVERGRGYVSAVQNTQQGQEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLIVDVE 197

Query: 207 TDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLK----KV 260
           T  ++   D++A A + L +  G+   +N +       E I++   P + AL       +
Sbjct: 198 TKPAMHPRDAIASAGKTLVELFGLARGLNID------AEGIDIGPSPTDTALASDLALPI 251

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           EELEL+VRS NCL+ E +  +G+L+ R+EAD+L + NFG KS+ E+K  L  MGL    +
Sbjct: 252 EELELTVRSYNCLKREGVHSVGELVARSEADLLDIRNFGAKSIDEVKAKLAGMGLAFKDS 311

Query: 321 LPDWPP 326
            P + P
Sbjct: 312 PPGFDP 317


>gi|324999252|ref|ZP_08120364.1| DNA-directed RNA polymerase subunit alpha [Pseudonocardia sp. P1]
          Length = 350

 Score =  227 bits (578), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 126/306 (41%), Positives = 193/306 (63%), Gaps = 4/306 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+TD
Sbjct: 16  ETRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILN+K   L +S +  + VT++  K+GPG VTAGDI     + V NPD  I +L+    
Sbjct: 76  IILNLK--ELVVSSEEDEPVTMYLRKQGPGAVTAGDIVPPAGVTVHNPDLHIASLNDKGR 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL 
Sbjct: 134 LEVELVVERGRGYVPAMQNKATGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLV 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + +++  SIT  D++A + + L +  G+        + ++   + +      A    +EE
Sbjct: 194 LDVESKPSITPRDALASSGKTLVELFGLARELNVDAEGIEIGPSPQEADTIAAFAMPIEE 253

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  +GL L  + P
Sbjct: 254 LDLTVRSYNCLKREGIHTVGELVGRSEADLLDIRNFGAKSIDEVKMKLVGLGLALKDSPP 313

Query: 323 DWPPES 328
            + P +
Sbjct: 314 GFDPSA 319


>gi|269128485|ref|YP_003301855.1| DNA-directed RNA polymerase subunit alpha [Thermomonospora curvata
           DSM 43183]
 gi|268313443|gb|ACY99817.1| DNA-directed RNA polymerase, alpha subunit [Thermomonospora curvata
           DSM 43183]
          Length = 337

 Score =  227 bits (578), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 132/311 (42%), Positives = 190/311 (61%), Gaps = 12/311 (3%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           Q +E R+  I EPL  GF +T+GN+LRR L+SS+ GAA+T+++I+GVLHE S+I GV ED
Sbjct: 13  QIDEYRSRFIIEPLEPGFGYTIGNSLRRTLLSSIPGAAVTSIRIEGVLHEFSTIPGVKED 72

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +TDIILN+K + +    D    + + K+GPG VTA DI     +EV NPD  I  L+  A
Sbjct: 73  VTDIILNLKELVVSSEHDEPVVMYLRKQGPGQVTAADIAPPAGVEVHNPDLHIATLNSKA 132

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + MELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+ R  Q  D+D+L
Sbjct: 133 KLEMELTVERGRGYVSAAQNKQPGQEIGRIPIDSIYSPVLKVTYKVEATRVEQRTDFDRL 192

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLP----FNPA 255
            + ++T  ++   D+VA A + L +  G+   +N E       E I++   P        
Sbjct: 193 ILDVETKPAMLPRDAVASAGKTLVELFGLARELNVE------AEGIDMGPSPTDAALAAD 246

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           L   +EEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  MGL
Sbjct: 247 LALPIEELNLTVRSYNCLKREGIHTVGELVARSEQDLLDIRNFGAKSIEEVKQKLADMGL 306

Query: 316 FLGMNLPDWPP 326
            L  + P + P
Sbjct: 307 SLKDSPPGFDP 317


>gi|291442292|ref|ZP_06581682.1| RNA polymerase alpha subunit [Streptomyces ghanaensis ATCC 14672]
 gi|291345187|gb|EFE72143.1| RNA polymerase alpha subunit [Streptomyces ghanaensis ATCC 14672]
          Length = 336

 Score =  227 bits (578), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 129/325 (39%), Positives = 199/325 (61%), Gaps = 22/325 (6%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 5   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 60

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 61  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 120

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 121 DLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEAT 180

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        +E+  +I  + +
Sbjct: 181 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGL-------AREL--NIGAEGI 231

Query: 251 PFNPA---------LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
              P+         L   +EELEL+VRS NCL+ E +  +G+L+ R+EAD+L + NFG K
Sbjct: 232 DMGPSPTDAALAADLALPIEELELTVRSYNCLKREGVHSVGELLARSEADLLDIRNFGAK 291

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPP 326
           S+ E+K  L  +GL L  + P + P
Sbjct: 292 SIDEVKAKLAGLGLALKDSPPGFAP 316


>gi|302524022|ref|ZP_07276364.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. AA4]
 gi|302432917|gb|EFL04733.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. AA4]
          Length = 357

 Score =  227 bits (578), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 133/322 (41%), Positives = 199/322 (61%), Gaps = 22/322 (6%)

Query: 19  VLGQE--EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            LG+E   E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ 
Sbjct: 8   ALGEETVNETRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVP 67

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           GV ED+TDIILN+K   L +S +  + VT++  K+GPG VTA DI     + V NPD  I
Sbjct: 68  GVKEDVTDIILNLK--ELVVSSEEDEPVTMYLRKQGPGEVTAADIVPPAGVTVHNPDLHI 125

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
            +L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q
Sbjct: 126 ASLNGKGKLEIELVVERGRGYVPALQNKQAGAEIGRIPVDSIYSPVLKVTYKVEATRVEQ 185

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDIN 246
             D+DKL + ++T  SIT  D+VA A + L +  G+   +N +       P  +  + I 
Sbjct: 186 RTDFDKLILDVETKPSITARDAVASAGKTLVELFGLARELNVDAEGIEIGPSPQEADTIA 245

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
             ++P        +E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+
Sbjct: 246 AYAMP--------IEDLDLTVRSYNCLKREGIHTVGELVSRSEADLLDIRNFGAKSIDEV 297

Query: 307 KGVLGTMGLFLGMNLPDWPPES 328
           K  L  +GL L  + P + P +
Sbjct: 298 KLKLVGLGLALKDSPPGFDPSA 319


>gi|255324779|ref|ZP_05365893.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           tuberculostearicum SK141]
 gi|311740030|ref|ZP_07713864.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           pseudogenitalium ATCC 33035]
 gi|255298254|gb|EET77557.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           tuberculostearicum SK141]
 gi|311305103|gb|EFQ81172.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           pseudogenitalium ATCC 33035]
          Length = 336

 Score =  227 bits (578), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 128/309 (41%), Positives = 194/309 (62%), Gaps = 7/309 (2%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           + +R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV ED++
Sbjct: 15  DSSRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTINGVKEDVS 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +IILNIK  ++ +S DS + V ++  K GPG VTAGDIQ    +E+ NPD  I +L+  A
Sbjct: 75  EIILNIK--SMVLSSDSDEPVVMYLSKEGPGDVTAGDIQPPAGVEIHNPDLHIASLNDTA 132

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + +EL V +G GYVPA     E   IG I +D +YSP+ KVSY VE+ R  Q  D+DKL
Sbjct: 133 KLDIELVVERGRGYVPAAPTSGE---IGRIPVDQIYSPVLKVSYKVEATRVEQRTDFDKL 189

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           ++ ++T  SI+  D++A A   L +  G+        + ++   + +   +  A    +E
Sbjct: 190 TIDVETKNSISARDALASAGGTLVELFGLARELNNAAEGIEIGPSPQETEYIAAYGMPIE 249

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +L  SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L  +GL L    
Sbjct: 250 DLNFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKIKLANLGLALKDTP 309

Query: 322 PDWPPESIE 330
            D+ P  +E
Sbjct: 310 EDFDPTQLE 318


>gi|61215897|sp|Q6AD21|RPOA_LEIXX RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 332

 Score =  227 bits (578), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 123/304 (40%), Positives = 186/304 (61%), Gaps = 8/304 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S++ GV ED+T+
Sbjct: 16  EFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFSTVPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILNIKG+ +    D      + K G G VTA DI     +E+ NP+ VI  L+  A   
Sbjct: 76  IILNIKGLVVSSEHDEPITAYLRKTGAGQVTAADISAPAGVEIHNPELVIATLNDKAKFE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELT+ +G GYV A+ +R E    G I ID++YSP+ KV+Y VE+ R G+  D+D+L + 
Sbjct: 136 VELTIERGRGYVSAQQNRNEYSEAGQIPIDSIYSPVLKVTYRVEATRAGERTDFDRLVVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK----V 260
           ++T  +I+  D++A A R L +  G+            E I +   P +  L  +    +
Sbjct: 196 VETKPAISPRDAIASAGRTLVELFGLAREL----NSAAEGIEIGPAPVDQVLSSELSMPI 251

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           E+L+LSVRS NCL+ E I  + +L+  +E  ++ + NFG+KS+ E+K  L  MGL L  +
Sbjct: 252 EDLDLSVRSYNCLKREGINTVSELVSLSETQLMNIRNFGQKSVDEVKDKLTEMGLSLKDS 311

Query: 321 LPDW 324
           +P +
Sbjct: 312 VPGF 315


>gi|134103231|ref|YP_001108892.1| DNA-directed RNA polymerase subunit alpha [Saccharopolyspora
           erythraea NRRL 2338]
 gi|291007977|ref|ZP_06565950.1| DNA-directed RNA polymerase subunit alpha [Saccharopolyspora
           erythraea NRRL 2338]
 gi|158513554|sp|A4FPJ2|RPOA_SACEN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|133915854|emb|CAM05967.1| DNA-directed RNA polymerase, alpha subunit [Saccharopolyspora
           erythraea NRRL 2338]
          Length = 359

 Score =  227 bits (578), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 134/310 (43%), Positives = 194/310 (62%), Gaps = 20/310 (6%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV ED+TD
Sbjct: 16  ETRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSLRIDGVLHEFTTIPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           +ILN+K   L +S +  + VT++  K+GPG VTA DI     + V NPD  I  L+    
Sbjct: 76  VILNLK--ELVVSSEEDEPVTMYLRKQGPGEVTAADIVPPAGVTVHNPDLHIATLNGKGK 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL 
Sbjct: 134 LEIELVVERGRGYVPAVQNKQTGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLI 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFN----PAL 256
           + ++T  SIT  D+VA A R L +  G+   +N +       E I +   P       A 
Sbjct: 194 LDVETKPSITPRDAVASAGRTLVELFGLARELNVD------AEGIEIGPSPAEADTIAAY 247

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  +G  
Sbjct: 248 AMPIEDLDLTVRSYNCLKREGIHTVGELVSRSEADLLDIRNFGAKSIDEVK--LKLVG-- 303

Query: 317 LGMNLPDWPP 326
           LG++L D PP
Sbjct: 304 LGLSLKDSPP 313


>gi|190411117|gb|ACE78313.1| RpoA [Vibrio parahaemolyticus]
 gi|190411119|gb|ACE78314.1| RpoA [Vibrio parahaemolyticus]
          Length = 263

 Score =  227 bits (578), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 117/266 (43%), Positives = 181/266 (68%), Gaps = 8/266 (3%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRV 104
           ALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +
Sbjct: 1   ALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---H 160
           T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H
Sbjct: 61  TLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIH 120

Query: 161 HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           +  +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A
Sbjct: 121 NEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRA 180

Query: 221 SRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVY 280
           + IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y
Sbjct: 181 ATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHY 237

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEI 306
           +GDL+QRTE ++L+  N G+KSL EI
Sbjct: 238 IGDLVQRTEVELLKTPNLGKKSLTEI 263


>gi|288919690|ref|ZP_06414017.1| DNA-directed RNA polymerase, alpha subunit [Frankia sp. EUN1f]
 gi|288348879|gb|EFC83129.1| DNA-directed RNA polymerase, alpha subunit [Frankia sp. EUN1f]
          Length = 349

 Score =  226 bits (577), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 123/302 (40%), Positives = 186/302 (61%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +TLGN+LRR L+SS+ GA++T++++DGVLHE S++ GV ED+TD
Sbjct: 16  EFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIRVDGVLHEFSTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           +ILN+K + +    D    + + K+GPG VTA DI     +EV NPD  +  L+    + 
Sbjct: 76  LILNLKELVVSSDNDEPTVMYLRKQGPGDVTAADIAPPAGVEVHNPDLHLATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+ R  Q  D+D+L + 
Sbjct: 136 IELTVERGRGYVSAAQNKQPGQEIGRIPIDSIYSPVLKVTYKVEATRVEQRTDFDRLIVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           ++T  SI+  D++A A + L    G+        + V    +         L   +EE++
Sbjct: 196 VETKQSISPRDAMASAGKTLVGLFGLAQELNAEAEGVDIGPSAADAALAADLALPIEEMD 255

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  LG MGL L  + P +
Sbjct: 256 LTVRSYNCLKREGIHTIGELVSRSEADLLDIRNFGQKSIDEVKTKLGAMGLQLKDSPPGF 315

Query: 325 PP 326
            P
Sbjct: 316 DP 317


>gi|118616625|ref|YP_904957.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium ulcerans
           Agy99]
 gi|183981110|ref|YP_001849401.1| DNA-directed RNA polymerase (alpha chain), RpoA [Mycobacterium
           marinum M]
 gi|158512379|sp|A0PMB7|RPOA_MYCUA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|118568735|gb|ABL03486.1| DNA-directed RNA polymerase (alpha chain), RpoA [Mycobacterium
           ulcerans Agy99]
 gi|183174436|gb|ACC39546.1| DNA-directed RNA polymerase (alpha chain), RpoA [Mycobacterium
           marinum M]
          Length = 347

 Score =  226 bits (577), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 125/313 (39%), Positives = 193/313 (61%), Gaps = 16/313 (5%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ++R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+TD
Sbjct: 16  DSRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+K + +    D    + + K+GPG VTAGDI     + V NP+  I  L+    + 
Sbjct: 76  IILNLKALVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPNMRIATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL + 
Sbjct: 136 VELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLILD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNPAL 256
           ++T  SIT  D++A A + L +  G+   +N E       P     + I   +LP     
Sbjct: 196 VETKNSITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALP----- 250

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL 
Sbjct: 251 ---IDDLDLTVRSYNCLKREGVHTVGELVSRTESDLLDIRNFGQKSIDEVKVKLHQLGLS 307

Query: 317 LGMNLPDWPPESI 329
           L  + P + P  +
Sbjct: 308 LKDSPPSFDPSEV 320


>gi|116671486|ref|YP_832419.1| DNA-directed RNA polymerase subunit alpha [Arthrobacter sp. FB24]
 gi|158512270|sp|A0JZ49|RPOA_ARTS2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116611595|gb|ABK04319.1| DNA-directed RNA polymerase subunit alpha [Arthrobacter sp. FB24]
          Length = 336

 Score =  226 bits (577), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 122/302 (40%), Positives = 187/302 (61%), Gaps = 4/302 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ENR+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T+
Sbjct: 16  ENRSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILNIK +++    D      + K+GPGVVTA DI     +E  NPD  I  L+      
Sbjct: 76  IILNIKNLSVSSEHDEPVVAYLRKQGPGVVTAADIAPPAGVEFHNPDLHIATLNSKGKFE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELT+ +G GYV A  +++ +  IG I +D++YSP+ KV++ VE+ R  Q  D+DKL + 
Sbjct: 136 LELTIERGRGYVSAAQNKSGDSEIGRIPVDSIYSPVLKVTFRVEATRVEQRTDFDKLIVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           ++T  +I   D+VA A   L +  G+        + ++   +         +   +E+L+
Sbjct: 196 VETKQAIAPRDAVASAGTTLVELFGLARELNTAAEGIEIGPSPTDAALAADMALPIEDLD 255

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L    + LG++L D 
Sbjct: 256 LTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGAKSIDEVKAKL----VELGLSLKDS 311

Query: 325 PP 326
           PP
Sbjct: 312 PP 313


>gi|307244752|ref|ZP_07526853.1| DNA-directed RNA polymerase, alpha subunit [Peptostreptococcus
           stomatis DSM 17678]
 gi|306491850|gb|EFM63902.1| DNA-directed RNA polymerase, alpha subunit [Peptostreptococcus
           stomatis DSM 17678]
          Length = 315

 Score =  226 bits (577), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 120/291 (41%), Positives = 191/291 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  T+GNALRR+L+SSL G A+ AV+IDGVLHE S++ GV ED+T++IL++
Sbjct: 23  FVVEPLERGFGITIGNALRRILLSSLPGVAVYAVRIDGVLHEFSTVPGVKEDVTEMILSL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K ++  + G+  K + I   GP  VT  DI    ++E+++ D  I  LD +A + ME+ V
Sbjct: 83  KELSATIDGEESKVLKIQAVGPCEVTGADIICPPEVEIVSKDLHIATLDENAKLNMEIHV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GYV A+ ++ ++ PIG + +D++Y+PI+KVSY VE+ R GQ  D+DKL++ + T+G
Sbjct: 143 NKGRGYVSAEENKNDSMPIGTLPVDSIYTPIEKVSYHVENTRVGQKTDFDKLTLEVLTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  ++ ++LA+++L++ L +FI+  E    V+  +  +       L   +EEL+LSVRS
Sbjct: 203 SINPQEGMSLAAKVLEEHLKLFIDLSEHIGNVEIMVEKEEDKKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
            NCL+   I  + +L  ++E DM+++ N G+KSL E+   L  + L L  N
Sbjct: 263 YNCLKRAGINTVEELSNKSEEDMMKVRNLGKKSLEEVIQKLNELDLKLKPN 313


>gi|50955540|ref|YP_062828.1| DNA-directed RNA polymerase subunit alpha [Leifsonia xyli subsp.
           xyli str. CTCB07]
 gi|50952022|gb|AAT89723.1| DNA-directed RNA polymerase, alpha subunit [Leifsonia xyli subsp.
           xyli str. CTCB07]
          Length = 359

 Score =  226 bits (577), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 123/304 (40%), Positives = 186/304 (61%), Gaps = 8/304 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S++ GV ED+T+
Sbjct: 43  EFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFSTVPGVKEDVTE 102

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILNIKG+ +    D      + K G G VTA DI     +E+ NP+ VI  L+  A   
Sbjct: 103 IILNIKGLVVSSEHDEPITAYLRKTGAGQVTAADISAPAGVEIHNPELVIATLNDKAKFE 162

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELT+ +G GYV A+ +R E    G I ID++YSP+ KV+Y VE+ R G+  D+D+L + 
Sbjct: 163 VELTIERGRGYVSAQQNRNEYSEAGQIPIDSIYSPVLKVTYRVEATRAGERTDFDRLVVD 222

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK----V 260
           ++T  +I+  D++A A R L +  G+            E I +   P +  L  +    +
Sbjct: 223 VETKPAISPRDAIASAGRTLVELFGLAREL----NSAAEGIEIGPAPVDQVLSSELSMPI 278

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           E+L+LSVRS NCL+ E I  + +L+  +E  ++ + NFG+KS+ E+K  L  MGL L  +
Sbjct: 279 EDLDLSVRSYNCLKREGINTVSELVSLSETQLMNIRNFGQKSVDEVKDKLTEMGLSLKDS 338

Query: 321 LPDW 324
           +P +
Sbjct: 339 VPGF 342


>gi|313206369|ref|YP_004045546.1| DNA-directed RNA polymerase subunit alpha [Riemerella anatipestifer
           DSM 15868]
 gi|312445685|gb|ADQ82040.1| DNA-directed RNA polymerase subunit alpha [Riemerella anatipestifer
           DSM 15868]
 gi|315023690|gb|EFT36694.1| DNA-directed RNA polymerase alpha subunit [Riemerella anatipestifer
           RA-YM]
 gi|325336185|gb|ADZ12459.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Riemerella anatipestifer RA-GD]
          Length = 331

 Score =  226 bits (577), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 125/323 (38%), Positives = 204/323 (63%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            IKP+ +   +L    E +      PL  G+  T+G+ALRRVL+SSL G AIT+++I+GV
Sbjct: 6   FIKPDKV---ILLNSTEFQGQFEFRPLEPGYGLTVGHALRRVLLSSLEGYAITSIKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE S+I GV ED+T+IILN+K + LK   ++   ++VT        +TAGD+ + ++  
Sbjct: 63  EHEFSTIPGVIEDVTEIILNLKQLRLKAKSENAPSEQVTAKIANLEQLTAGDLGKFISGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+ VICNL  D  + M  +++KG GYVP++ +++ N PIG I ID++Y+PIKKV Y
Sbjct: 123 EVLNPELVICNLTKDVNLEMNFSINKGRGYVPSEQNKSNNAPIGTIAIDSIYTPIKKVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           +VE+ R  Q  DY+KL + I+TDGSI+ ++++  AS+IL     +F    I  E    + 
Sbjct: 183 SVENYRVEQKTDYEKLILDIETDGSISPQNALIEASKILIYHFMLFSDERITLETEAVKA 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
               + ++L     L  K+ E++LSVR+ NCL+   +  +G+L+  +++D+++  NFG+K
Sbjct: 243 SIQYDEETLHTRQLLKSKLAEMDLSVRALNCLKAAEVETLGELVSYSKSDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ ++ + GL  G ++  +
Sbjct: 303 SLTELEELVHSKGLNFGFDVSKY 325


>gi|313888838|ref|ZP_07822499.1| DNA-directed RNA polymerase, alpha subunit [Peptoniphilus harei
           ACS-146-V-Sch2b]
 gi|312845207|gb|EFR32607.1| DNA-directed RNA polymerase, alpha subunit [Peptoniphilus harei
           ACS-146-V-Sch2b]
          Length = 315

 Score =  226 bits (577), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 119/288 (41%), Positives = 185/288 (64%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL  GF  T+GN+LRRVL+SSL GAA++ + I GV HE  +I GV ED+ +I+LNI
Sbjct: 23  FVVEPLEAGFGITIGNSLRRVLLSSLPGAAVSFINIRGVEHEFDTIPGVLEDVPEIVLNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LKM+ D   ++ I K+G G + A DI+ V  + ++NPD  I  L+ DA   +E+ V
Sbjct: 83  KSIVLKMTEDEPVKLVIEKKGKGEIKASDIELVPHVSIINPDQHIATLNDDADFYLEMMV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GY P++  + E   IG+I +D+ ++P++KV++ VE+ R GQ  D+D+L + + TDG
Sbjct: 143 EKGRGYEPSELKKDEISEIGIIPMDSNFTPVEKVNWKVENTRVGQRTDFDRLILEVTTDG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           S+  +++ +LA++IL + L +FI  +E   E+   +  +       L   VEEL+LSVRS
Sbjct: 203 SMKADEATSLAAKILTEHLELFIGLKEHVSEINLMVEKEEDQKEKVLEMTVEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  + +L  +TE++M+++ N GRKSL+E+   L  +GL L
Sbjct: 263 FNCLKRAGINSVEELTNKTESEMMKVRNLGRKSLLEVTEKLDELGLSL 310


>gi|78189780|ref|YP_380118.1| DNA-directed RNA polymerase subunit alpha [Chlorobium
           chlorochromatii CaD3]
 gi|90110831|sp|Q3APK0|RPOA_CHLCH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|78171979|gb|ABB29075.1| DNA-directed RNA polymerase subunit alpha [Chlorobium
           chlorochromatii CaD3]
          Length = 327

 Score =  226 bits (577), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 120/302 (39%), Positives = 189/302 (62%), Gaps = 9/302 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            IA+PL RG+  TLGN +RRVL++SL G AIT ++I+ V HE S+I+GV ED+ +I+LN+
Sbjct: 25  FIAQPLERGYGVTLGNLMRRVLLASLPGTAITGIKIENVYHEFSTIQGVREDVPEIVLNL 84

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDHVICNLDVDAVVRMELT 148
           K +  +       + T+   GP   TAG IQ    + EVLN D  I  ++    V +++ 
Sbjct: 85  KKVRFRSQCKRSCKTTVTLVGPMEFTAGVIQPQEGEFEVLNKDLHIATINAGTTVTLDIF 144

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           + +G GYVPA+ +R E  P+G I ID++++PI+ V +TVE+ R GQ  DY+K+ + ++TD
Sbjct: 145 IGRGRGYVPAEENRAEGMPLGFIPIDSIFTPIRNVKFTVENTRVGQRTDYEKMILEVETD 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEV------KEDINVKSLPFNPALLKKVEE 262
           GSIT +DS++LA R++ D + +F +F   ++E       ++D   +++     L  K+E+
Sbjct: 205 GSITPDDSISLAGRVISDHVLLFADFSPAEEEYTEEEFKQQDDEFETM--RRLLATKIED 262

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           L+LSVRS NCLR   I  +G+L+   E ++L   NFG+KSL E+K  L    L  GM++ 
Sbjct: 263 LDLSVRSHNCLRLAEIDTLGELVSHKEDELLNYKNFGKKSLTELKEQLDKFDLKFGMDIT 322

Query: 323 DW 324
            +
Sbjct: 323 RY 324


>gi|297204185|ref|ZP_06921582.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sviceus
           ATCC 29083]
 gi|197714127|gb|EDY58161.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sviceus
           ATCC 29083]
          Length = 335

 Score =  226 bits (577), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 130/322 (40%), Positives = 200/322 (62%), Gaps = 20/322 (6%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVK 248
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+   +N +       E I++ 
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNID------AEGIDMG 235

Query: 249 SLPFNPA----LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
             P + A    L+  +E+L+L+VRS NCL+ E +  +G+L+ R+EAD+L + NFG KS+ 
Sbjct: 236 PSPTDAALAADLVMPIEDLDLTVRSYNCLKREGVHSVGELVARSEADLLDIRNFGAKSID 295

Query: 305 EIKGVLGTMGLFLGMNLPDWPP 326
           E+K  L      LG+ L D PP
Sbjct: 296 EVKEKLAG----LGLGLKDSPP 313


>gi|220913400|ref|YP_002488709.1| DNA-directed RNA polymerase subunit alpha [Arthrobacter
           chlorophenolicus A6]
 gi|325964132|ref|YP_004242038.1| DNA-directed RNA polymerase, subunit alpha [Arthrobacter
           phenanthrenivorans Sphe3]
 gi|254765243|sp|B8HCX4|RPOA_ARTCA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|219860278|gb|ACL40620.1| DNA-directed RNA polymerase, alpha subunit [Arthrobacter
           chlorophenolicus A6]
 gi|323470219|gb|ADX73904.1| DNA-directed RNA polymerase, alpha subunit [Arthrobacter
           phenanthrenivorans Sphe3]
          Length = 336

 Score =  226 bits (577), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 122/302 (40%), Positives = 187/302 (61%), Gaps = 4/302 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ENR+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T+
Sbjct: 16  ENRSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILNIK +++    D      + K+GPGVVTA DI     +E  NPD  I  L+      
Sbjct: 76  IILNIKSLSVSSEHDEPVVAYLRKQGPGVVTAADIAPPAGVEFHNPDLHIATLNSKGKFE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELT+ +G GYV A  +++ +  IG I +D++YSP+ KV++ VE+ R  Q  D+DKL + 
Sbjct: 136 LELTIERGRGYVSAAQNKSGDAEIGRIPVDSIYSPVLKVTFRVEATRVEQRTDFDKLIVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           ++T  +I   D+VA A   L +  G+        + ++   +         +   +E+L+
Sbjct: 196 VETKQAIAPRDAVASAGTTLVELFGLARELNTAAEGIEIGPSPTDAALAADMALPIEDLD 255

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L    + LG++L D 
Sbjct: 256 LTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGAKSIDEVKAKL----VELGLSLKDS 311

Query: 325 PP 326
           PP
Sbjct: 312 PP 313


>gi|86739323|ref|YP_479723.1| DNA-directed RNA polymerase subunit alpha [Frankia sp. CcI3]
 gi|119366683|sp|Q2JFE8|RPOA_FRASC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|86566185|gb|ABD09994.1| DNA-directed RNA polymerase subunit alpha [Frankia sp. CcI3]
          Length = 349

 Score =  226 bits (577), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 123/302 (40%), Positives = 186/302 (61%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +TLGN+LRR L+SS+ GA++T+++IDGVLHE S++ GV ED+TD
Sbjct: 16  EFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIRIDGVLHEFSTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           +ILN+K + +    D    + + K+GPG VTA DI     +EV NP+  +  L+    + 
Sbjct: 76  LILNLKELVVSSDNDEPTVMYLRKQGPGEVTAADIAPPAGVEVHNPELRLATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+ R  Q  D+D+L + 
Sbjct: 136 IELTVERGRGYVSAAQNKQAGQEIGRIPIDSIYSPVLKVTYKVEATRVEQRTDFDRLIVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           ++T  SI+  D++A A + L    G+        + V    +         L   +EE++
Sbjct: 196 VETKPSISPRDAMASAGKTLVGLFGLAQELNAEAEGVDIGPSAADAALAADLALPIEEMD 255

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  LG MGL L  + P +
Sbjct: 256 LTVRSYNCLKREGIHTIGELVSRSEADLLDIRNFGQKSIDEVKTKLGAMGLQLKDSPPGF 315

Query: 325 PP 326
            P
Sbjct: 316 DP 317


>gi|330470144|ref|YP_004407887.1| DNA-directed RNA polymerase subunit alpha [Verrucosispora maris
           AB-18-032]
 gi|328813115|gb|AEB47287.1| DNA-directed RNA polymerase subunit alpha [Verrucosispora maris
           AB-18-032]
          Length = 340

 Score =  226 bits (576), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 126/309 (40%), Positives = 189/309 (61%), Gaps = 8/309 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV ED+ +
Sbjct: 16  ETRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTIPGVKEDVVE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           +++NIK + +    D    + + K+GPG VTAGDIQ    + V NPD  +  L+    + 
Sbjct: 76  LVMNIKELCVSSEHDEPVSMYLRKQGPGDVTAGDIQPPAGVSVHNPDLKLATLNGKGRLD 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D+L + 
Sbjct: 136 MELTVERGRGYVTAAQNKQAGAEIGRIPVDSIYSPVLKVTYRVEATRVEQRTDFDRLIID 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK----KV 260
           ++T  S+    ++A A   L +  G+    +    E  E I++   P +  L       +
Sbjct: 196 VETKPSMGPRTALASAGSTLVELFGLARELD----ETAEGIDIGPSPQDAQLAADLALPI 251

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           EEL+L+VRS NCL+ E I  +G+LI RTEAD+L + NFG+KS+ E+K  L  MGL L  +
Sbjct: 252 EELDLTVRSYNCLKREGINSVGELIGRTEADLLDIRNFGQKSIDEVKMKLAGMGLGLKDS 311

Query: 321 LPDWPPESI 329
            P++ P  +
Sbjct: 312 APNFDPAHV 320


>gi|239933876|ref|ZP_04690829.1| DNA-directed RNA polymerase subunit alpha [Streptomyces ghanaensis
           ATCC 14672]
          Length = 329

 Score =  226 bits (576), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 126/312 (40%), Positives = 193/312 (61%), Gaps = 18/312 (5%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T
Sbjct: 7   DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVT 66

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           D+ILNIK + +    D    + + K+GPG+VTA DI     +EV NPD V+  L+    +
Sbjct: 67  DLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNPDLVLATLNGKGKL 126

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL +
Sbjct: 127 EMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLIV 186

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA-------- 255
            ++T  ++   D++A A + L +  G+        +E+  +I  + +   P+        
Sbjct: 187 DVETKQAMRPRDAMASAGKTLVELFGL-------AREL--NIGAEGIDMGPSPTDAALAA 237

Query: 256 -LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
            L   +EELEL+VRS NCL+ E +  +G+L+ R+EAD+L + NFG KS+ E+K  L  +G
Sbjct: 238 DLALPIEELELTVRSYNCLKREGVHSVGELLARSEADLLDIRNFGAKSIDEVKAKLAGLG 297

Query: 315 LFLGMNLPDWPP 326
           L L  + P + P
Sbjct: 298 LALKDSPPGFAP 309


>gi|309812375|ref|ZP_07706130.1| DNA-directed RNA polymerase, alpha subunit [Dermacoccus sp.
           Ellin185]
 gi|308433680|gb|EFP57557.1| DNA-directed RNA polymerase, alpha subunit [Dermacoccus sp.
           Ellin185]
          Length = 339

 Score =  226 bits (576), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 130/308 (42%), Positives = 190/308 (61%), Gaps = 16/308 (5%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E+R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGV HE S+I GV ED+T+
Sbjct: 16  ESRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVQHEFSTIPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           +ILNIKG+ +    D    + + K+G GVVTA DI     +EV NPD  I  L+    + 
Sbjct: 76  VILNIKGLVVSSEHDEPVVMYLRKQGAGVVTAADIAPPAGVEVHNPDLEIATLNDKGSIE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MELTV +G GYV A  +++    IG I +D++YSP+  V+Y VE+ R  Q  D+DKL + 
Sbjct: 136 MELTVERGRGYVSAALNKSAEQEIGRIPVDSIYSPVLAVTYKVEATRVEQRTDFDKLIVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKK--- 259
           ++T  S+   D++A A   L +  G+   +N E       E I++   P + AL +    
Sbjct: 196 VETKNSMAPRDAMASAGSTLVELFGLARELNVE------AEGIDMGPSPTDAALAEDLAL 249

Query: 260 -VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+   L  MGL   
Sbjct: 250 PIEDLDLTVRSYNCLKREGIHTVGELVSRSEADLLDIRNFGSKSIHEVADKLRDMGL--- 306

Query: 319 MNLPDWPP 326
             L D PP
Sbjct: 307 -QLKDSPP 313


>gi|328813955|gb|AEB52093.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 261

 Score =  226 bits (576), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 116/260 (44%), Positives = 173/260 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNI
Sbjct: 2   FVVEPLERGYGTTLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNI 61

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV
Sbjct: 62  KKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTV 121

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+G
Sbjct: 122 KKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNG 181

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI+  ++++LA++IL + L +F+N  +  K  +  +  +       L   +EEL+LSVRS
Sbjct: 182 SISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSVRS 241

Query: 270 TNCLRGENIVYMGDLIQRTE 289
            NCL+   I  + +L  +TE
Sbjct: 242 YNCLKRAGINTVQELTNKTE 261


>gi|326332227|ref|ZP_08198507.1| DNA-directed RNA polymerase, alpha subunit [Nocardioidaceae
           bacterium Broad-1]
 gi|325949933|gb|EGD41993.1| DNA-directed RNA polymerase, alpha subunit [Nocardioidaceae
           bacterium Broad-1]
          Length = 338

 Score =  226 bits (576), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 130/309 (42%), Positives = 189/309 (61%), Gaps = 12/309 (3%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           EE R+  + EPL  GF +TLGN+LRR L+SS+ GA++T+++IDGVLHE S+I+GV ED+T
Sbjct: 15  EEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIKIDGVLHEFSTIEGVKEDVT 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           +IILN+KG+ +    D    + + K G G VTA DI     +EV NPD  I  L     +
Sbjct: 75  EIILNLKGLVVSSEHDEPVTMYLRKSGAGDVTAADIAPPAGVEVHNPDLKIATLSDKGKI 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +EL V +G GYV A  ++   + IG I +D++YSP+ KVSY VE+ R  Q  D+DKL +
Sbjct: 135 ELELVVERGRGYVSAVQNKGAENEIGRIPVDSIYSPVLKVSYKVEATRVEQRTDFDKLVI 194

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLK--- 258
            ++T  SI   D++A A + L +  G+   +N +       E I++   P +  L     
Sbjct: 195 DVETKPSIAPRDAIASAGKTLVELFGLARELNVD------AEGIDIGPSPVDEQLAADLA 248

Query: 259 -KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             VE+L+L+VRS NCL+ E I  +G+LI R+E D+L + NFG KS+ E+K  L  MGL L
Sbjct: 249 LPVEDLQLTVRSYNCLKREGIHTVGELISRSEQDLLDIRNFGAKSIDEVKLKLHEMGLSL 308

Query: 318 GMNLPDWPP 326
             + P + P
Sbjct: 309 KDSAPGFDP 317


>gi|317496164|ref|ZP_07954524.1| DNA-directed RNA polymerase [Gemella moribillum M424]
 gi|316913739|gb|EFV35225.1| DNA-directed RNA polymerase [Gemella moribillum M424]
          Length = 313

 Score =  226 bits (576), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 122/284 (42%), Positives = 179/284 (63%), Gaps = 12/284 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA  ++ I+GV HE  +IKGV ED+T+II+N+
Sbjct: 23  FVVEPLERGYGTTLGNSLRRMLISSLPGAAARSIDIEGVQHEFQAIKGVVEDVTEIIMNV 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I   +  +  K ++I  +GP VVTA DI   +D+EV+N D  I  +       M + V
Sbjct: 83  KNIAFIIHSEEEKVLSINVKGPAVVTAADIAIDSDVEVVNVDQHIATVAEGGHFEMLIYV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G G+VPA  ++  + PIG+I ID++Y+P+ KV+YTVE  R GQ  D+DKL + + T+G
Sbjct: 143 GTGRGFVPADGNKRRDLPIGVIPIDSIYTPVSKVNYTVEKTRVGQSTDFDKLILDVTTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEV------KEDINVKSLPFNPALLKKVEEL 263
           +I+  D++ALAS+IL   L +F+   E  K        +ED  V+ L         +EEL
Sbjct: 203 TISANDALALASKILISHLELFMEMSEQAKAADILVAKEEDNKVQMLEMT------IEEL 256

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +LSVRS NCL+   I  + +L  +TE +M+++ N GRKSL E+K
Sbjct: 257 DLSVRSYNCLKRAGINTVQELASKTEQEMIKVRNLGRKSLEEVK 300


>gi|328813969|gb|AEB52100.1| DNA-directed RNA polymerase alpha chain [Lactobacillus fermentum]
          Length = 275

 Score =  226 bits (576), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 119/270 (44%), Positives = 180/270 (66%), Gaps = 2/270 (0%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E +N    + EPL RG+  TLGN+LRRV+++SL GAAIT++QIDGVLHE S+++GV ED
Sbjct: 6   EETDNYGKFVVEPLERGYGTTLGNSLRRVMLASLPGAAITSIQIDGVLHEFSTVQGVTED 65

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILN+K + LK+  +  K + I  +GP  VTA DIQ   D+ +LN D  I  +   A
Sbjct: 66  VTQIILNLKQVALKIDSEDAKDLEIDVKGPAEVTAADIQGDGDVTILNSDLHIATVSDGA 125

Query: 142 VVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
            + +++T  KG GY  A  ++T  E   IG++ ID++Y+PI++V+YTVE+ R GQ  DYD
Sbjct: 126 ELHVKMTADKGRGYSSADDNKTRMEGLAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYD 185

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL++ + T+GS+T  ++++LA++IL + L MF+N  E  +  +  +  +       L K 
Sbjct: 186 KLTLDVWTNGSLTPTEAISLAAKILTEHLTMFVNLTEEAQVTQVMVEREETHQEKVLDKT 245

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +EEL+LSVRS NCL+  +I  + DL +RTE
Sbjct: 246 IEELDLSVRSYNCLKRADIQTVKDLTERTE 275


>gi|238061094|ref|ZP_04605803.1| DNA-directed RNA polymerase, alpha subunit [Micromonospora sp. ATCC
           39149]
 gi|302869942|ref|YP_003838579.1| DNA-directed RNA polymerase subunit alpha [Micromonospora
           aurantiaca ATCC 27029]
 gi|315501403|ref|YP_004080290.1| DNA-directed RNA polymerase, alpha subunit [Micromonospora sp. L5]
 gi|237882905|gb|EEP71733.1| DNA-directed RNA polymerase, alpha subunit [Micromonospora sp. ATCC
           39149]
 gi|302572801|gb|ADL49003.1| DNA-directed RNA polymerase, alpha subunit [Micromonospora
           aurantiaca ATCC 27029]
 gi|315408022|gb|ADU06139.1| DNA-directed RNA polymerase, alpha subunit [Micromonospora sp. L5]
          Length = 340

 Score =  226 bits (576), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 126/309 (40%), Positives = 189/309 (61%), Gaps = 8/309 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV ED+ +
Sbjct: 16  ETRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTIPGVKEDVVE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           +++NIK + +    D    + + K+GPG VTAGDIQ    + V NPD  +  L+    + 
Sbjct: 76  LVMNIKELCVSSEHDEPVSMYLRKQGPGDVTAGDIQPPAGVSVHNPDLKLATLNGKGRLD 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D+L + 
Sbjct: 136 MELTVERGRGYVTAAQNKQAGAEIGRIPVDSIYSPVLKVTYRVEATRVEQRTDFDRLIID 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK----KV 260
           ++T  S+    ++A A   L +  G+    +    E  E I++   P +  L       +
Sbjct: 196 VETKPSMGPRTALASAGSTLVELFGLARELD----ETAEGIDIGPSPQDAQLAADLALPI 251

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           EEL+L+VRS NCL+ E I  +G+LI RTEAD+L + NFG+KS+ E+K  L  MGL L  +
Sbjct: 252 EELDLTVRSYNCLKREGINSVGELIGRTEADLLDIRNFGQKSIDEVKMKLAGMGLGLKDS 311

Query: 321 LPDWPPESI 329
            P++ P  +
Sbjct: 312 APNFDPAHV 320


>gi|229825289|ref|ZP_04451358.1| hypothetical protein GCWU000182_00643 [Abiotrophia defectiva ATCC
           49176]
 gi|229790661|gb|EEP26775.1| hypothetical protein GCWU000182_00643 [Abiotrophia defectiva ATCC
           49176]
          Length = 319

 Score =  226 bits (576), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 125/303 (41%), Positives = 195/303 (64%), Gaps = 10/303 (3%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E++     + EPL RG+  TLGN+LRR+++SSL GAA+T V+I+G+ HE+SSI GV ED
Sbjct: 15  SEDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVTTVKIEGIKHELSSIPGVKED 74

Query: 82  LTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           +T+II+NIK + ++     D  K   I   G GVVTA +IQ  +DI + NPD VI  L+ 
Sbjct: 75  VTEIIMNIKSLAIRNDSETDEPKTAYIEFEGEGVVTAANIQADSDITITNPDQVIATLNG 134

Query: 140 DAVVR--MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
               R  MEL + +GHGYV A  +++++  I +I ID++Y+P+++V+  +E+ R G + D
Sbjct: 135 GNNCRLYMELNIGRGHGYVSADKNKSDDLAIDVIPIDSIYTPVERVNINIENTRVGHMTD 194

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP--- 254
           YDKL++ + T+G++  +++V+LA+R++ + L  FI+  E  K V  D+ V   P N    
Sbjct: 195 YDKLTLEVYTNGTMGPDEAVSLAARVMSEHLNSFIDLSENAKVV--DVMVAK-PDNERGR 251

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
            L   ++ELELSVR+ NCL+   I  + +L+ +T  DM+++ N G KSL EIK  +  +G
Sbjct: 252 VLEMSIDELELSVRAFNCLKRSGINTVQELVGKTHEDMMKVRNLGNKSLEEIKAKIKALG 311

Query: 315 LFL 317
           L L
Sbjct: 312 LSL 314


>gi|190411121|gb|ACE78315.1| RpoA [Vibrio parahaemolyticus]
          Length = 263

 Score =  226 bits (576), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 117/266 (43%), Positives = 180/266 (67%), Gaps = 8/266 (3%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRV 104
           ALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +
Sbjct: 1   ALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---H 160
           T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H
Sbjct: 61  TLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIH 120

Query: 161 HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           +  +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A
Sbjct: 121 NEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRA 180

Query: 221 SRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVY 280
           + IL +QL  F++  + +   +     +   F+P LL+ V +LEL+VRS NCL+ E I Y
Sbjct: 181 ATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVNDLELTVRSANCLKAEAIHY 237

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEI 306
           +GDL+QRTE ++L+  N G+KSL EI
Sbjct: 238 IGDLVQRTEVELLKTPNLGKKSLTEI 263


>gi|237786334|ref|YP_002907039.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           kroppenstedtii DSM 44385]
 gi|237759246|gb|ACR18496.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           kroppenstedtii DSM 44385]
          Length = 337

 Score =  226 bits (575), Expect = 5e-57,   Method: Compositional matrix adjust.
 Identities = 134/312 (42%), Positives = 187/312 (59%), Gaps = 28/312 (8%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           EYI     + +R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I+GVLHE +++
Sbjct: 12  EYI-----DSSRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRIEGVLHEFTTV 66

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHV 133
            GV ED++DIILNIKG  L +S DS   VT++  K GPG VTAGDI     +E+ NPD  
Sbjct: 67  PGVTEDVSDIILNIKG--LVLSSDSDDPVTMYIRKEGPGEVTAGDIMPPAGVEIHNPDMH 124

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           I  L+    + +EL V +G GYVPA     E   IG I +D +YSP+ KVSY VE+ R  
Sbjct: 125 IATLNEQGKLDIELVVERGRGYVPAAQATGE---IGRIPVDQIYSPVLKVSYKVEATRVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE--------PKKEVKEDI 245
           Q  D+D+L + ++T  SIT  D++A A   L +  G+              P  +  E I
Sbjct: 182 QRTDFDRLVIDVETKNSITARDAMASAGGTLVELFGLARELNTAAEGIEIGPSPQESEHI 241

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
               +P        +E+L  SVRS NCL+ E I  +G+L  RTE+D+L + NFG+KS+ E
Sbjct: 242 QAYGMP--------IEDLNFSVRSYNCLKREEIHTVGELASRTESDLLDIRNFGQKSINE 293

Query: 306 IKGVLGTMGLFL 317
           +K  L  +GL L
Sbjct: 294 VKVKLAGLGLAL 305


>gi|325684745|gb|EGD26899.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 312

 Score =  226 bits (575), Expect = 5e-57,   Method: Compositional matrix adjust.
 Identities = 128/316 (40%), Positives = 189/316 (59%), Gaps = 16/316 (5%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +E++    + EPL R F  TLGN+LRRVL++S+ G  +  V+IDG
Sbjct: 3   EFKKPN----ITVVDQEDSYGKFVVEPLERRFGTTLGNSLRRVLLTSVPGTGLVKVKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           +LHE +++ GV ED+T IILN+K + L+   +  K + +   GP  VTA D++   D+EV
Sbjct: 59  ILHEFTTVPGVKEDVTKIILNLKKLVLRAYTEEVKTIELDVEGPATVTAEDLKADADVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + M + V  G GYVPA  ++T    IG I +D+L+SPI+KV+Y V
Sbjct: 119 LNPDQYICTIAQGGHLHMWIDVCNGRGYVPASENKTAEMFIGDIPVDSLFSPIEKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK------EV 241
           ES R G+  D+DKL++ I T+GSI   D++  A+R+L +    F + +   +      E 
Sbjct: 179 ESTRVGKREDFDKLTLEIWTNGSIAPNDALNFAARVLVEHFKAFESADAAAEIGEVMVEQ 238

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           + D   K L         +E+L+LSVRS NCL+   I  + DL  ++EA+M+R+ N GRK
Sbjct: 239 ENDQKEKKLEMT------IEDLDLSVRSYNCLKRAGINTLQDLTVKSEAEMMRVRNLGRK 292

Query: 302 SLVEIKGVLGTMGLFL 317
           SL E+K  L  +GL L
Sbjct: 293 SLEEVKNKLADLGLSL 308


>gi|289524818|emb|CBJ94465.1| alpha subunit of RNA polymerase [Vibrio sp. Rd 16.2]
          Length = 267

 Score =  226 bits (575), Expect = 5e-57,   Method: Compositional matrix adjust.
 Identities = 118/268 (44%), Positives = 179/268 (66%), Gaps = 8/268 (2%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVT 115
           G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V 
Sbjct: 3   GCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVV 62

Query: 116 AGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLI 171
           AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG +
Sbjct: 63  AGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRL 122

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F
Sbjct: 123 LVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAF 182

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           ++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE +
Sbjct: 183 VDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVE 239

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +L+  N G+KSL EIK VL + GL LGM
Sbjct: 240 LLKTPNLGKKSLTEIKDVLASRGLSLGM 267


>gi|296394890|ref|YP_003659774.1| DNA-directed RNA polymerase subunit alpha [Segniliparus rotundus
           DSM 44985]
 gi|296182037|gb|ADG98943.1| DNA-directed RNA polymerase, alpha subunit [Segniliparus rotundus
           DSM 44985]
          Length = 350

 Score =  226 bits (575), Expect = 5e-57,   Method: Compositional matrix adjust.
 Identities = 125/309 (40%), Positives = 194/309 (62%), Gaps = 6/309 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV ED+T+
Sbjct: 16  EYRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTIAGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           I+LN+KG+ +    D    + + K+GPG VTA DI     + +  P+  I  L+    + 
Sbjct: 76  IVLNVKGLEVSSVEDEPATLYLRKQGPGPVTAADIVAPAGVTITKPETHIATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MEL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D+L + 
Sbjct: 136 MELVVERGRGYVPAVQNKDSGAEIGRIPVDSIYSPVLKVTYQVEATRVEQRTDFDRLILD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLK-KVE 261
           ++T  SIT  D+VA A + L +  G+   +N      E+    +V +   N A L   +E
Sbjct: 196 VETKSSITPRDAVASAGKTLVELFGLARELNLAAEGIEIG---SVAAATNNIASLGLPIE 252

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +L L+VRS NCL+ E +  +G+L+ R+E+D+L + NFG+KS+ E+K  L T+GL L  + 
Sbjct: 253 DLHLTVRSYNCLKREGVHTIGELVARSESDLLDIRNFGQKSIDEVKLKLYTLGLALKDSP 312

Query: 322 PDWPPESIE 330
            ++ P +I+
Sbjct: 313 ANFDPSNID 321


>gi|254776830|ref|ZP_05218346.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium avium
           subsp. avium ATCC 25291]
          Length = 347

 Score =  226 bits (575), Expect = 5e-57,   Method: Compositional matrix adjust.
 Identities = 128/315 (40%), Positives = 197/315 (62%), Gaps = 20/315 (6%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T 
Sbjct: 16  DNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTA 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILN+K  +L +S +  + VT++  K+GPG VTAGDI     + V NP+  I  L+    
Sbjct: 76  IILNLK--SLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPELHIATLNDKGK 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL 
Sbjct: 134 LEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLI 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNP 254
           + ++T  SIT  D++A A + L +  G+   +N E       P     + I   +LP   
Sbjct: 194 LDVETKSSITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPPEADHIASFALP--- 250

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +G
Sbjct: 251 -----IDDLDLTVRSYNCLKREGVHTVGELVSRTESDLLDIRNFGQKSIDEVKVKLHQLG 305

Query: 315 LFLGMNLPDWPPESI 329
           L L  + P + P  +
Sbjct: 306 LSLKDSPPSFDPSQV 320


>gi|41410331|ref|NP_963167.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium avium
           subsp. paratuberculosis K-10]
 gi|118463576|ref|YP_883533.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium avium 104]
 gi|61215987|sp|Q73S43|RPOA_MYCPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158512444|sp|A0QKU5|RPOA_MYCA1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|41399165|gb|AAS06783.1| RpoA [Mycobacterium avium subsp. paratuberculosis K-10]
 gi|118164863|gb|ABK65760.1| DNA-directed RNA polymerase, alpha subunit [Mycobacterium avium
           104]
          Length = 347

 Score =  226 bits (575), Expect = 5e-57,   Method: Compositional matrix adjust.
 Identities = 128/315 (40%), Positives = 197/315 (62%), Gaps = 20/315 (6%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T 
Sbjct: 16  DNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTA 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILN+K  +L +S +  + VT++  K+GPG VTAGDI     + V NP+  I  L+    
Sbjct: 76  IILNLK--SLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPELHIATLNDKGK 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL 
Sbjct: 134 LEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLI 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNP 254
           + ++T  SIT  D++A A + L +  G+   +N E       P     + I   +LP   
Sbjct: 194 LDVETKSSITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALP--- 250

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +G
Sbjct: 251 -----IDDLDLTVRSYNCLKREGVHTVGELVSRTESDLLDIRNFGQKSIDEVKVKLHQLG 305

Query: 315 LFLGMNLPDWPPESI 329
           L L  + P + P  +
Sbjct: 306 LSLKDSPPSFDPSQV 320


>gi|332042695|gb|EGI78895.1| DNA-directed RNA polymerase, alpha subunit [Lacinutrix algicola
           5H-3-7-4]
          Length = 330

 Score =  226 bits (575), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 121/298 (40%), Positives = 187/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRVL+SSL G AIT+++I+GV HE S++ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGYGLTVGNALRRVLLSSLEGFAITSIRIEGVDHEFSTVAGVVEDVTEIILNLKQMR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   ++ V+I   G   +TAGD Q  ++  +VLN D VICNLD    + ME+T+ 
Sbjct: 88  FKRQIEDVDNESVSISISGQDKITAGDFQKFISGFQVLNSDLVICNLDPKVSITMEITIE 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++  + PIG I  D++Y+PIK V Y++E+ R  Q  DY+KL   I +DGS
Sbjct: 148 KGRGYVPAEENKKASAPIGTIFTDSIYTPIKNVKYSIENYRVEQKTDYEKLVFEIQSDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I+ +D++  A++ L     +F    I  E  +    E  + +SL     L  K+ +++LS
Sbjct: 208 ISPQDALTEAAKTLIHHFMLFSDERITLEADEIAQTETYDEESLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   + D+++  NFG+KSL E++ ++   GL  GM+L  +
Sbjct: 268 VRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKKSLTELEELVNVKGLNFGMDLSKY 325


>gi|158148901|dbj|BAF81985.1| RNA polymerase alpha subunit [Lactobacillus parabrevis]
          Length = 246

 Score =  226 bits (575), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 114/245 (46%), Positives = 167/245 (68%), Gaps = 4/245 (1%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+K I 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVTQIILNVKKIA 60

Query: 94  LKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           LK++G  D  + + I  +GP  +TAGDI    D++VLNPD  I  +   A   M +T  K
Sbjct: 61  LKLNGSDDQEETMEINVKGPAQITAGDIVAGADVDVLNPDLYIATVADGATFHMRMTADK 120

Query: 152 GHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           G GYV A  H+ +N   PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ + T+G
Sbjct: 121 GRGYVSADEHKAQNTEMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDVWTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI   +++ALA++IL + L MF++  +  K  +  +  +       L   +EEL+LSVRS
Sbjct: 181 SINPSEAIALAAKILTEHLAMFVDLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSVRS 240

Query: 270 TNCLR 274
            NCL+
Sbjct: 241 YNCLK 245


>gi|68536848|ref|YP_251553.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium jeikeium
           K411]
 gi|260579206|ref|ZP_05847096.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           jeikeium ATCC 43734]
 gi|90110834|sp|Q4JTC2|RPOA_CORJK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|68264447|emb|CAI37935.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           jeikeium K411]
 gi|258602692|gb|EEW15979.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           jeikeium ATCC 43734]
          Length = 337

 Score =  225 bits (574), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 131/304 (43%), Positives = 191/304 (62%), Gaps = 23/304 (7%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           +++R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++I+GVLHE ++I GV ED++
Sbjct: 15  DDSRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSLRIEGVLHEFTTIPGVKEDVS 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           DIILNIK  +L +S DS + V++F  K GPG VT  D++    +EV N D  I  L+   
Sbjct: 75  DIILNIK--SLVLSSDSDEPVSMFIRKEGPGEVTGADVEVPAGVEVHNQDLHIATLNEQG 132

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + +E+TV +G GYVPA    +E   IG I +D +YSP+ KVSY VE+ R  Q  D+DKL
Sbjct: 133 KLEIEMTVERGRGYVPAATASSE---IGRIPVDQIYSPVLKVSYKVEATRVEQRTDFDKL 189

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFN 253
            + ++T  SIT  D++A A + L +  G+   +N E       P  +  E I   S+P  
Sbjct: 190 ILDVETKNSITARDAMASAGKTLVELFGLAQELNHEAEGIEIGPSPQESEHIAAYSMP-- 247

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +E+L  SVRS NCL+ E I  +G+L  RTE+D+L + NFG+KS+ E+K  L  +
Sbjct: 248 ------IEDLNFSVRSYNCLKREEIHTVGELAARTESDLLDIRNFGQKSINEVKVKLAGL 301

Query: 314 GLFL 317
           GL L
Sbjct: 302 GLGL 305


>gi|303233188|ref|ZP_07319861.1| DNA-directed RNA polymerase, alpha subunit [Atopobium vaginae
           PB189-T1-4]
 gi|302480773|gb|EFL43860.1| DNA-directed RNA polymerase, alpha subunit [Atopobium vaginae
           PB189-T1-4]
          Length = 314

 Score =  225 bits (574), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 125/316 (39%), Positives = 191/316 (60%), Gaps = 8/316 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E I+P     +V+    EN   +  EPL RG+  TLGN++RRVL+SSL GAA+ A+ I
Sbjct: 1   MSEFIRPQ----VVVEDISENLARVNVEPLERGYGDTLGNSMRRVLLSSLEGAAVEAISI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVND 124
           DGV HE S+I GV+ED+TDI+LN+KG+  + +G  S    +I   GP  V AGD     +
Sbjct: 57  DGVQHEFSTIPGVYEDVTDIVLNVKGLVFRSNGTGSEAEASISVDGPCTVVAGDFLIPAE 116

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +++N DH IC L   A + M + +  G  YV    +  E+DPIG+I +D+L+SP+ + +
Sbjct: 117 FDLINKDHHICTLCEGAHLSMRMRIGMGRSYVSGDDNEREDDPIGVIHVDSLFSPVTRCA 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
             VE  R GQ  +YD+L + ++T+GSI+  D+V  A+ I+   +  F++  E ++E  ED
Sbjct: 177 KVVEPCRVGQHTNYDRLILEVETNGSISPRDAVIQAADIINQHMCAFMDLAEDEQEPLED 236

Query: 245 INVKSL---PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++ S      N  L K++E+L+LSVRS NCL+   I  +  L++ +E D+L + NFG K
Sbjct: 237 ASIFSTVEEEDNTELDKQIEDLDLSVRSYNCLKRAGIHNVRQLVEFSENDLLNIRNFGVK 296

Query: 302 SLVEIKGVLGTMGLFL 317
           S+ E++  L   GL L
Sbjct: 297 SIEEVREKLEAAGLGL 312


>gi|227549868|ref|ZP_03979917.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           lipophiloflavum DSM 44291]
 gi|227078123|gb|EEI16086.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           lipophiloflavum DSM 44291]
          Length = 337

 Score =  225 bits (574), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 128/315 (40%), Positives = 192/315 (60%), Gaps = 22/315 (6%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I G+ E++++I
Sbjct: 17  NRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTINGIKENVSEI 76

Query: 86  ILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           ILN+K  N+ +S DS + V ++  K GPG VTAGDI+   D+ + NPD  I +L+  A +
Sbjct: 77  ILNVK--NIVLSSDSDEPVVLYLSKEGPGDVTAGDIELTADVAIHNPDLHIASLNDSARL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            MEL V +G GYVPA  +       G I +D +YSP+ +V+Y VE+ R  Q  D+DKL +
Sbjct: 135 EMELVVERGRGYVPAMPYA--GGEAGRIPVDQIYSPVTRVAYKVEATRVEQRTDFDKLII 192

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEE--------PKKEVKEDINVKSLPFNPA 255
            ++T  S+T  D++A A   L +  G+              P  +  E I   +LP    
Sbjct: 193 DVETKNSMTARDALASAGSTLVELFGLARELNTAAEGLEIGPSPQETEYIAAYNLP---- 248

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
               +E+L  SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L ++GL
Sbjct: 249 ----IEDLNFSVRSYNCLKRQEIHSVGELAEYTESDLLDIRNFGQKSINEVKIKLASLGL 304

Query: 316 FLGMNLPDWPPESIE 330
            L     D+ P  IE
Sbjct: 305 TLKDAPEDFDPTQIE 319


>gi|323357346|ref|YP_004223742.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Microbacterium testaceum StLB037]
 gi|323273717|dbj|BAJ73862.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Microbacterium testaceum StLB037]
          Length = 329

 Score =  225 bits (574), Expect = 7e-57,   Method: Compositional matrix adjust.
 Identities = 128/306 (41%), Positives = 186/306 (60%), Gaps = 12/306 (3%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +T+GNALRR L+SS+ GAA+T+++IDGVLHE S+I GV ED+T+
Sbjct: 16  EFRSRFVIEPLEPGFGYTIGNALRRSLLSSIPGAAVTSIRIDGVLHEFSTIPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILNIK + +    D      + K G G VTA DI     +EV NPD VI  L+  A   
Sbjct: 76  IILNIKQLVVSSERDEPITAYLRKTGSGEVTAADISAPAGVEVHNPDLVIATLNDTAKFE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELT+ +G GYV A  +R E    G I ID++YSP+ KVSY VE+ R G+  D+DKL + 
Sbjct: 136 LELTIERGRGYVSATQNRNEYAEAGQIPIDSIYSPVLKVSYRVEATRAGERTDFDKLVLD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKK--- 259
           +++  SI   D+VA A R L +  G+   +N E       E I +   P    L  +   
Sbjct: 196 VESKPSIAPRDAVASAGRTLTELFGLARELNVE------AEGIEIGPAPVETVLSNELSM 249

Query: 260 -VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L+LSVRS NCL+ E I  + +L+  +E  ++ + NFG+KS+ E++  L ++GL L 
Sbjct: 250 PIEDLDLSVRSYNCLKREGINTVSELVALSETQLMNIRNFGQKSVDEVRDKLVSLGLSLK 309

Query: 319 MNLPDW 324
            ++P +
Sbjct: 310 DSVPGF 315


>gi|169788419|emb|CAP58131.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788421|emb|CAP58132.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788423|emb|CAP58133.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788425|emb|CAP58134.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788427|emb|CAP58135.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788429|emb|CAP58136.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788431|emb|CAP58137.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788433|emb|CAP58138.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788435|emb|CAP58139.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788437|emb|CAP58140.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788439|emb|CAP58141.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788441|emb|CAP58142.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788443|emb|CAP58143.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788445|emb|CAP58144.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788449|emb|CAP58146.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788451|emb|CAP58147.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788453|emb|CAP58148.1| RNA polymerase [Lactobacillus rossiae]
          Length = 235

 Score =  225 bits (574), Expect = 7e-57,   Method: Compositional matrix adjust.
 Identities = 114/235 (48%), Positives = 164/235 (69%), Gaps = 2/235 (0%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+K ++LKM
Sbjct: 1   RGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVTQIILNMKKVSLKM 60

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
           + D  K + I  +GP  VTAGDIQT  D+EV+NPD  IC +   A   M LT +KG GYV
Sbjct: 61  ATDEEKGMDIDVKGPATVTAGDIQTDADVEVMNPDLYICTVADGATFHMHLTANKGRGYV 120

Query: 157 PAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A  ++   D  PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSIT  
Sbjct: 121 SADENKARQDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSITPS 180

Query: 215 DSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           ++++LA++IL + L MF++  +  K  +  +  +       L   +EEL+LSVRS
Sbjct: 181 EAISLAAKILTEHLAMFVDLTDTAKNAEIMVEKEETHKEKMLEMTIEELDLSVRS 235


>gi|300932966|ref|ZP_07148222.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           resistens DSM 45100]
          Length = 337

 Score =  225 bits (574), Expect = 7e-57,   Method: Compositional matrix adjust.
 Identities = 133/310 (42%), Positives = 186/310 (60%), Gaps = 24/310 (7%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           EYI     + +R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I+GVLHE ++I
Sbjct: 12  EYI-----DASRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRIEGVLHEFTTI 66

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
            GV ED++DIILNIK + L    D    + + K GPG VT  DI     +EV NPD  I 
Sbjct: 67  PGVKEDVSDIILNIKSLVLSSDSDEPVVMNLHKEGPGAVTGADIMPPAGVEVHNPDLHIA 126

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
            L+    + +EL V +G GYVPA    +E   IG I +D +YSP+ KVSY VE+ R  Q 
Sbjct: 127 TLNEQGKLDIELVVERGRGYVPAATASSE---IGRIPVDQIYSPVLKVSYKVEATRVEQR 183

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINV 247
            D+DKL + ++T  SIT  D++A A + L +  G+   +N E       P  +  E I  
Sbjct: 184 TDFDKLILDVETKNSITARDAMASAGKTLVELFGLAQELNNEAEGIEIGPSPQESEHIAA 243

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            S+P        +E+L  SVRS NCL+ E I  +G+L  RTE+D+L + NFG+KS+ E+K
Sbjct: 244 YSMP--------IEDLNFSVRSYNCLKREEIHTVGELAARTESDLLDIRNFGQKSINEVK 295

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 296 VKLAGLGLGL 305


>gi|300782639|ref|YP_003762930.1| DNA-directed RNA polymerase subunit alpha [Amycolatopsis
           mediterranei U32]
 gi|299792153|gb|ADJ42528.1| DNA-directed RNA polymerase subunit alpha [Amycolatopsis
           mediterranei U32]
          Length = 356

 Score =  225 bits (573), Expect = 8e-57,   Method: Compositional matrix adjust.
 Identities = 135/320 (42%), Positives = 199/320 (62%), Gaps = 26/320 (8%)

Query: 19  VLGQE--EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            LG+E   E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ 
Sbjct: 8   ALGEETVNETRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVP 67

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           GV ED+TDIILN+K   L +S +  + VT++  K+GPG VTA DI     + V NPD  I
Sbjct: 68  GVKEDVTDIILNLK--ELVVSSEEDEPVTMYLRKQGPGEVTAADIVPPAGVTVHNPDLHI 125

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
            +L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q
Sbjct: 126 ASLNGKGKLEIELVVERGRGYVPALQNKQAGAEIGRIPVDSIYSPVLKVTYKVEATRVEQ 185

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDIN 246
             D+DKL + ++T  SIT  D+VA A + L +  G+   +N +       P  +  + I 
Sbjct: 186 RTDFDKLILDVETKPSITPRDAVASAGKTLVELFGLARELNVDAEGIEIGPSPQEADTIA 245

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
             ++P        +E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+
Sbjct: 246 AYAMP--------IEDLDLTVRSYNCLKREGIHTVGELVSRSEADLLDIRNFGAKSIDEV 297

Query: 307 KGVLGTMGLFLGMNLPDWPP 326
           K  L  +G  LG+ L D PP
Sbjct: 298 K--LKLVG--LGLALKDSPP 313


>gi|288801125|ref|ZP_06406581.1| DNA-directed RNA polymerase, alpha subunit [Prevotella sp. oral
           taxon 299 str. F0039]
 gi|288332059|gb|EFC70541.1| DNA-directed RNA polymerase, alpha subunit [Prevotella sp. oral
           taxon 299 str. F0039]
          Length = 330

 Score =  225 bits (573), Expect = 8e-57,   Method: Compositional matrix adjust.
 Identities = 118/298 (39%), Positives = 189/298 (63%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AI  ++I GV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGVTIGNALRRILLSSLEGFAINTIKIGGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   D   +++V+I         AGD+ + +   EVLNPD VIC+LD  A +++++T++
Sbjct: 88  FKQVVDEFENEKVSITVENTTEFKAGDMGKYLTGFEVLNPDLVICHLDAKASMQIDITIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R  +  + ++ ID++Y+PI+ V Y+VE  R  Q  DYDKL + + TDGS
Sbjct: 148 KGRGYVPADENRQYSTDVNVLPIDSIYTPIRNVKYSVEPYRVEQKTDYDKLVLEVTTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I+ +D++  A++IL     +F    I  E P+++  ++ + + L     L  K+ ++ LS
Sbjct: 208 ISPKDALKEAAKILIYHFMLFSDEKITLENPEQDSNDEFDEEVLHMRQLLKTKLVDMNLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKKSLSELDDLLESLNLSFGTDISKY 325


>gi|145596406|ref|YP_001160703.1| DNA-directed RNA polymerase subunit alpha [Salinispora tropica
           CNB-440]
 gi|145305743|gb|ABP56325.1| DNA-directed RNA polymerase, alpha subunit [Salinispora tropica
           CNB-440]
          Length = 354

 Score =  225 bits (573), Expect = 8e-57,   Method: Compositional matrix adjust.
 Identities = 124/309 (40%), Positives = 190/309 (61%), Gaps = 8/309 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV ED+ +
Sbjct: 30  ETRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTIPGVKEDVVE 89

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           +++NIK + +    D    + + K+GPG VTAGDIQ    + V NPD  +  L+    + 
Sbjct: 90  LVMNIKELCVSSEHDEPVSMYLRKQGPGDVTAGDIQPPAGVSVHNPDLKLATLNGKGRLD 149

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MELTV +G GYV A  ++     IG I +D++YSP+ +V+Y VE+ R  Q  D+D+L + 
Sbjct: 150 MELTVERGRGYVTAAQNKQAGAEIGRIPVDSIYSPVLRVTYRVEATRVEQRTDFDRLIID 209

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK----KV 260
           +++  S+    ++A A   L +  G+    +    E  E I++   P +  L       +
Sbjct: 210 VESKPSMGPRTALASAGSTLVELFGLARELD----ETAEGIDIGPSPQDAQLAADLALPI 265

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           EEL+L+VRS NCL+ E I  +G+LI RTEAD+L + NFG+KS+ E+K  L  MGL L  +
Sbjct: 266 EELDLTVRSYNCLKREGINTVGELIGRTEADLLDIRNFGQKSIDEVKMKLAGMGLGLKDS 325

Query: 321 LPDWPPESI 329
            P++ P ++
Sbjct: 326 APNFDPANV 334


>gi|88854650|ref|ZP_01129316.1| DNA-directed RNA polymerase alpha subunit [marine actinobacterium
           PHSC20C1]
 gi|88815811|gb|EAR25667.1| DNA-directed RNA polymerase alpha subunit [marine actinobacterium
           PHSC20C1]
          Length = 331

 Score =  225 bits (573), Expect = 9e-57,   Method: Compositional matrix adjust.
 Identities = 122/306 (39%), Positives = 191/306 (62%), Gaps = 12/306 (3%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +TLGN++RR L+SS+ GAA+T+++IDGVLHE S++ GV ED+T+
Sbjct: 16  EFRSRFVIEPLEPGFGYTLGNSIRRTLLSSIPGAAVTSIRIDGVLHEFSTVAGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           +ILNIK  NL +S +  + +T +  K+G G VTA DI     +E+ NP+ VI  L+  A 
Sbjct: 76  VILNIK--NLVVSSEHDEPITAYLRKQGAGEVTAADISAPAGVEIHNPELVIATLNDKAK 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
             +ELT+ +G GYV A  +R+E    G I +D++YSP+ KV+Y VE+ R G+  D+D+L 
Sbjct: 134 FELELTIERGRGYVTATQNRSEFSEAGQIPVDSIYSPVLKVTYRVEATRAGERTDFDRLV 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK--- 259
           + ++T  +IT  D++A A R L +  G+            E I +   P +  L  +   
Sbjct: 194 VDVETKSAITPRDAIASAGRTLTELFGLAREL----NTAAEGIEIGPAPVDAVLSTELSM 249

Query: 260 -VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L+LSVRS NCL+ E I  + +L+  +E  ++ + NFG+KS+ E++  L  MGL L 
Sbjct: 250 PIEDLDLSVRSYNCLKREGINTVSELVALSETQLMNIRNFGQKSVDEVRDKLVEMGLSLK 309

Query: 319 MNLPDW 324
            ++P +
Sbjct: 310 DSVPGF 315


>gi|86141166|ref|ZP_01059712.1| DNA-directed RNA polymerase alpha subunit [Leeuwenhoekiella
           blandensis MED217]
 gi|85831725|gb|EAQ50180.1| DNA-directed RNA polymerase alpha subunit [Leeuwenhoekiella
           blandensis MED217]
          Length = 317

 Score =  225 bits (573), Expect = 9e-57,   Method: Compositional matrix adjust.
 Identities = 122/298 (40%), Positives = 185/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRVL+SSL G AIT+V+++GV HE S+I GV ED T+IILN+K + 
Sbjct: 15  PLEPGYGLTVGNALRRVLLSSLEGFAITSVRVEGVDHEFSTIAGVVEDFTEIILNLKQVR 74

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   D   ++ VTI       +TAGD Q  ++  ++LNPD VI N++    + ME+TV 
Sbjct: 75  FKRQIDEIDNETVTISVSDKEQLTAGDFQKFISGFQILNPDLVIANMEKSVNINMEITVE 134

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++ +N P+G I  D++Y+PIK V Y++E+ R  Q  DY+KL   I TDGS
Sbjct: 135 KGRGYVPAEENKKQNAPVGTIFTDSIYTPIKNVKYSIENYRVEQKTDYEKLVFEIITDGS 194

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++ L     +F    I  E  +    E  + +SL     L  K+ +++LS
Sbjct: 195 IHPKDALTEAAKTLIHHFMLFSDERITLEADEIAQTETYDEESLHMRQLLKTKLVDMDLS 254

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   + D+++  NFG+KSL E++ ++   GL  GM+L  +
Sbjct: 255 VRALNCLKAAEVETLGDLVSYNKNDLMKFRNFGKKSLTELEELVNVKGLNFGMDLSKY 312


>gi|221195350|ref|ZP_03568405.1| DNA-directed RNA polymerase, alpha subunit [Atopobium rimae ATCC
           49626]
 gi|221184537|gb|EEE16929.1| DNA-directed RNA polymerase, alpha subunit [Atopobium rimae ATCC
           49626]
          Length = 313

 Score =  225 bits (573), Expect = 9e-57,   Method: Compositional matrix adjust.
 Identities = 123/316 (38%), Positives = 193/316 (61%), Gaps = 9/316 (2%)

Query: 6   WQELIKPN-NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
             E I+P+ ++E I       N   + AEPL RG+  TLGN+LRRVL+SSL G+A+ A+Q
Sbjct: 1   MSEFIRPSVSVEEI-----GANAARVSAEPLERGYGDTLGNSLRRVLLSSLEGSAVEAIQ 55

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVN 123
           IDGV HE +++ GV+ED+TDI+LN+K +  +   D      +I   GP VVT  DI    
Sbjct: 56  IDGVQHEFTTVDGVYEDVTDIVLNVKCLVFRSLEDIDEAEASITVDGPKVVTGADIDVPT 115

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
             E++NP+  IC L   A + M L + KG GYV  + +  ++DPIG I++D+++SP+++ 
Sbjct: 116 GFELVNPEQHICTLSDGAHLAMRLRIGKGRGYVSGEDNERDDDPIGFISVDSIFSPVRRC 175

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +  VE  R G+  DYD+L + ++T+G+I+  ++V  A+ I+   +G F+   E  + ++E
Sbjct: 176 AKAVEPCRVGRHTDYDRLVLEVETNGAISPREAVVEAANIINQHMGAFMGLSEVDESLEE 235

Query: 244 D--INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
                 + +  +  L K+VE+L+LSVRS NCL+   I  +  L+  +E D+L + NFG K
Sbjct: 236 TSIFASEDVQDDSELDKQVEDLDLSVRSYNCLKRAGIHSVRQLVDFSENDLLNIRNFGVK 295

Query: 302 SLVEIKGVLGTMGLFL 317
           S+ E+K  L  MGL L
Sbjct: 296 SIEEVKEKLEAMGLSL 311


>gi|159039805|ref|YP_001539058.1| DNA-directed RNA polymerase subunit alpha [Salinispora arenicola
           CNS-205]
 gi|157918640|gb|ABW00068.1| DNA-directed RNA polymerase, alpha subunit [Salinispora arenicola
           CNS-205]
          Length = 340

 Score =  225 bits (573), Expect = 9e-57,   Method: Compositional matrix adjust.
 Identities = 124/309 (40%), Positives = 190/309 (61%), Gaps = 8/309 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV ED+ +
Sbjct: 16  ETRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTIPGVKEDVVE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           +++NIK + +    D    + + K+GPG VTAGDIQ    + V NPD  +  L+    + 
Sbjct: 76  LVMNIKELCVSSEHDEPVSMYLRKQGPGDVTAGDIQPPAGVSVHNPDLKLATLNGKGRLD 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MELTV +G GYV A  ++     IG I +D++YSP+ +V+Y VE+ R  Q  D+D+L + 
Sbjct: 136 MELTVERGRGYVTAAQNKQAGAEIGRIPVDSIYSPVLRVTYRVEATRVEQRTDFDRLIID 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK----KV 260
           +++  S+    ++A A   L +  G+    +    E  E I++   P +  L       +
Sbjct: 196 VESKPSMGPRTALASAGSTLVELFGLARELD----ETAEGIDIGPSPQDAQLAADLALPI 251

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           EEL+L+VRS NCL+ E I  +G+LI RTEAD+L + NFG+KS+ E+K  L  MGL L  +
Sbjct: 252 EELDLTVRSYNCLKREGINSVGELIGRTEADLLDIRNFGQKSIDEVKMKLAGMGLGLKDS 311

Query: 321 LPDWPPESI 329
            P++ P ++
Sbjct: 312 APNFDPANV 320


>gi|84494744|ref|ZP_00993863.1| DNA-directed RNA polymerase alpha subunit [Janibacter sp. HTCC2649]
 gi|84384237|gb|EAQ00117.1| DNA-directed RNA polymerase alpha subunit [Janibacter sp. HTCC2649]
          Length = 346

 Score =  225 bits (573), Expect = 9e-57,   Method: Compositional matrix adjust.
 Identities = 130/321 (40%), Positives = 197/321 (61%), Gaps = 16/321 (4%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E+R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S+I GV ED+T+
Sbjct: 16  EHRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFSTIPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILNIKG+ +    D    + + K+G G VTA DI     +EV+NPD  I  L+    + 
Sbjct: 76  IILNIKGLVVSSEHDEPVVMYLRKQGSGAVTAADIAPPAGVEVINPDLHIATLNDKGSIE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MELTV +G GYV A+ +++ +  IG I +D++YSP+  V+Y VE  R  Q  D++ L + 
Sbjct: 136 MELTVERGRGYVSAQQNKSGDQEIGRIPVDSIYSPVLNVTYKVELTRVEQRTDFNSLVLD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLP----FNPALLK 258
           ++T  ++T  D++A A + L +  G+   +N E       E I++   P        L  
Sbjct: 196 VETKQAVTPRDALASAGKTLVELFGLARELNVE------AEGIDMGPSPTDAALAADLAL 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  L  MGL L 
Sbjct: 250 PIEDLDLTVRSYNCLKREGIHTVGELVGRSEADLLDIRNFGQKSIDEVKAKLHGMGLALK 309

Query: 319 MNLPDWPPESIEELAKKYEDK 339
            +   + P  I      Y+D+
Sbjct: 310 DSPAGFDPSQI----ASYDDE 326


>gi|312130522|ref|YP_003997862.1| DNA-directed RNA polymerase subunit alpha [Leadbetterella
           byssophila DSM 17132]
 gi|311907068|gb|ADQ17509.1| DNA-directed RNA polymerase subunit alpha [Leadbetterella
           byssophila DSM 17132]
          Length = 329

 Score =  225 bits (573), Expect = 9e-57,   Method: Compositional matrix adjust.
 Identities = 122/313 (38%), Positives = 190/313 (60%), Gaps = 6/313 (1%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +V+ + ++       +PL RG+  T+GNALRR+L+SSL G AIT+V+  GVLHE S+I+G
Sbjct: 12  VVMEKADDFHGFFEFKPLERGYGVTIGNALRRILLSSLEGYAITSVRFPGVLHEFSAIEG 71

Query: 78  VHEDLTDIILNIKGINLKMSGDS-HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVIC 135
           V +D+T+I+LN+K +  K   D    ++T+  +    +TAGDI +  +  E+LNPD VI 
Sbjct: 72  VVDDVTEIVLNLKQVRFKKIADYVDNKITVKVKNQTEITAGDIGKYTSSFEILNPDLVIA 131

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
            LD    +  E+ V KG GYVP++  +T + PIG I ID++Y+PIK V Y++E+ R  Q 
Sbjct: 132 RLDSKKELEFEIIVDKGRGYVPSEEQKTADLPIGFIAIDSIYTPIKNVKYSIENTRVEQR 191

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKSLP 251
            DY+KL + I TDGSI  E ++  AS IL      F +    F+    E    ++ + L 
Sbjct: 192 TDYEKLLLEIKTDGSIHPEKALQEASHILIQHFLKFTDENMVFDSKSDEEDNMVDEEFLH 251

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L   +++L+LSVR+ NCL+  +I  +GDL +   ADM++  NFG+KSL E++ ++ 
Sbjct: 252 MRKLLKTPLQDLDLSVRAYNCLKSADIRTLGDLARLEVADMMKFRNFGKKSLTELEQLIA 311

Query: 312 TMGLFLGMNLPDW 324
              L  GM++  +
Sbjct: 312 DKQLHFGMDVSKY 324


>gi|328814015|gb|AEB52123.1| DNA-directed RNA polymerase alpha chain [Lactobacillus rhamnosus]
          Length = 273

 Score =  225 bits (573), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 116/266 (43%), Positives = 174/266 (65%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E  N    + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED+
Sbjct: 8   ESTNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLEDV 67

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILNIK + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +     
Sbjct: 68  TQIILNIKKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGH 127

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
             + +TV KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL+
Sbjct: 128 FHVRMTVKKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLT 187

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + + T+GSI+  ++++LA++IL + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 188 LDVWTNGSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEE 247

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRT 288
           L+LSVRS NCL+   I  + +L  +T
Sbjct: 248 LDLSVRSYNCLKRAGINTVQELTNKT 273


>gi|268609564|ref|ZP_06143291.1| DNA-directed RNA polymerase, alpha subunit [Ruminococcus
           flavefaciens FD-1]
          Length = 321

 Score =  224 bits (572), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 121/293 (41%), Positives = 191/293 (65%), Gaps = 5/293 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG----VLHEISSIKGVHEDLTDI 85
            +  PL RG+  TLGN+LRRVL+SSL G A+T+V++ G    V HE+S+I GV ED+T+I
Sbjct: 24  FVLAPLERGYGITLGNSLRRVLLSSLPGVAVTSVKLSGKDGTVHHELSTIPGVKEDVTEI 83

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           IL+IKG+  K+ G+  K V I   G   +TAGDI+T +++ +L+P   I  L  DA + M
Sbjct: 84  ILSIKGLTAKLYGEGPKTVYIEAEGECEITAGDIKTDSEVNILDPGMHIATLGKDAKLYM 143

Query: 146 ELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           E+T+ +G GYV A+ ++ + N P+ +I +D++Y+P+ KV+YTVE  R GQV DYDKL+M 
Sbjct: 144 EITIDRGRGYVSAERNKKQINLPVDVIAVDSIYTPVLKVNYTVEDTRLGQVTDYDKLTME 203

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           + TDG+I+ +++++ A+ +L + L +FI+  E     +  +          L   +E+L+
Sbjct: 204 VWTDGTISAKEALSQAANLLGEHLKLFIDLSEEAGLAEVLVEKDEKGKEKILEMTIEDLD 263

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LSVRS NCL+   I  + DLI ++E +M+++ N G+KS  E+K  L ++G  L
Sbjct: 264 LSVRSFNCLKRAGINTVDDLINKSEEEMMKVRNLGKKSFDEVKEKLQSLGFDL 316


>gi|156743921|ref|YP_001434050.1| DNA-directed RNA polymerase subunit alpha [Roseiflexus castenholzii
           DSM 13941]
 gi|189043845|sp|A7NR36|RPOA_ROSCS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|156235249|gb|ABU60032.1| DNA-directed RNA polymerase, alpha subunit [Roseiflexus
           castenholzii DSM 13941]
          Length = 323

 Score =  224 bits (572), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 121/289 (41%), Positives = 183/289 (63%), Gaps = 6/289 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           EN      EPL  G+ HTLGNALRRVL+SS+ GAAIT ++IDGV HE S+I G+ ED+T+
Sbjct: 16  ENYGRFKIEPLDPGYGHTLGNALRRVLLSSIPGAAITKIKIDGVFHEFSTISGIKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV-DAVV 143
           I+LNIKG+ L+   +   ++++ KRG G+V A DI   +++E++NP H IC +D  DA++
Sbjct: 76  IVLNIKGVRLRSYAERPVKISLSKRGSGIVRAADIDAPSNVEIVNPFHYICTIDRDDAML 135

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            ME+TV +G GY+PA     +  PIG I IDA+++P+ KV+Y VE+ R GQ  D+D L +
Sbjct: 136 EMEMTVERGRGYLPADQR--DALPIGEIPIDAIFTPVPKVNYVVENIRVGQATDFDSLLI 193

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL--KKVE 261
            I TDG+I   D+++ A+++L        +F     E +       L   PA +    +E
Sbjct: 194 EIWTDGTIKPGDALSHAAQVLVQYSQTIADFNRLSTETESTAAPNGLAI-PADIYDTPIE 252

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           EL+LS R+ NCL+  +I  +G +++  E  +L + N G+KS+ EI+  L
Sbjct: 253 ELDLSTRTYNCLKRADITKVGQVLEMDEKALLSVRNLGQKSMEEIRDKL 301


>gi|304438880|ref|ZP_07398803.1| DNA-directed RNA polymerase subunit alpha [Peptoniphilus duerdenii
           ATCC BAA-1640]
 gi|304372546|gb|EFM26129.1| DNA-directed RNA polymerase subunit alpha [Peptoniphilus duerdenii
           ATCC BAA-1640]
          Length = 315

 Score =  224 bits (572), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 118/295 (40%), Positives = 190/295 (64%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E+  + + + EPL  G+  T+GN+LRRVL+SSL GA+++ V I G  HE ++I GV ED+
Sbjct: 16  EDGKKGIFVVEPLESGYGITIGNSLRRVLLSSLPGASVSFVNIRGAEHEFATIPGVLEDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
            +IILNIK + ++M+      VTI K+GPG +TA DI     + ++NP+  I  L+ DA 
Sbjct: 76  PEIILNIKSVVIQMTEIDEALVTIEKKGPGEITAEDINCPLGVTIVNPEEHIATLNEDAD 135

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           V +E+ + +G GYVP++  + E   IG+I ID+ ++P++ V++ VE+ R GQ  DYD+L 
Sbjct: 136 VYIEMKIERGRGYVPSELKKDEVSTIGVIPIDSNFTPVRHVNWKVENTRVGQRTDYDRLV 195

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + + TDGS+  +++ +LA++IL + L +FI   E   +V   +  +       L   VEE
Sbjct: 196 LDVTTDGSMKADEATSLAAKILTEHLKLFIGLTEHVSDVNIMVEKEEDRKEKVLEMTVEE 255

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+LSVRS NCL+  NI  + +L+ ++EA+M+++ N G+KSL E++  L  +GL L
Sbjct: 256 LDLSVRSFNCLKRANINTVEELVDKSEAEMMKVRNLGKKSLEEVQNKLAELGLGL 310


>gi|224283735|ref|ZP_03647057.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium bifidum
           NCIMB 41171]
 gi|310287998|ref|YP_003939257.1| rpoA DNA-directed RNA polymerase alpha chain [Bifidobacterium
           bifidum S17]
 gi|311064871|ref|YP_003971597.1| DNA-directed RNA polymerase subunit alpha RpoA [Bifidobacterium
           bifidum PRL2010]
 gi|313140891|ref|ZP_07803084.1| DNA-directed RNA polymerase [Bifidobacterium bifidum NCIMB 41171]
 gi|309251935|gb|ADO53683.1| rpoA DNA-directed RNA polymerase alpha chain [Bifidobacterium
           bifidum S17]
 gi|310867191|gb|ADP36560.1| RpoA DNA-directed RNA polymerase alpha chain [Bifidobacterium
           bifidum PRL2010]
 gi|313133401|gb|EFR51018.1| DNA-directed RNA polymerase [Bifidobacterium bifidum NCIMB 41171]
          Length = 331

 Score =  224 bits (572), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 126/298 (42%), Positives = 182/298 (61%), Gaps = 12/298 (4%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
            R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ GV ED+T+I
Sbjct: 17  QRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTTLPGVVEDVTEI 76

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           +LNIKGI L    D    + + K G G VTAGDI     + + NPD  I  L  D  + +
Sbjct: 77  LLNIKGIVLTSEYDEPVVMYLRKSGNGEVTAGDITPPAGVTIANPDQHIATLADDGELEI 136

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           E TV +G GYVPA+ ++ + D IG I +D++YSP+ KVSY VE+ R  Q  D+DKL + +
Sbjct: 137 EFTVERGRGYVPAQMNKQDTDEIGRIPVDSIYSPVLKVSYKVEATRVEQRTDFDKLILDV 196

Query: 206 DTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPF----NPALLKK 259
           +T  +I+  D+VA A   L +  G+   +N +       E + V   P     NP +   
Sbjct: 197 ETKPAISPRDAVASAGSTLVELFGLCRELNVQ------AEGVEVGPAPVAEETNPEMAVP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L +MGL L
Sbjct: 251 IEDLNLTQRSYNCLKREGIHTIGELVAHTEQDLLDIRNFGMKSIDEVKDKLQSMGLSL 308


>gi|111220574|ref|YP_711368.1| DNA-directed RNA polymerase subunit alpha [Frankia alni ACN14a]
 gi|122954575|sp|Q0RRP3|RPOA_FRAAA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|111148106|emb|CAJ59774.1| RNA polymerase, alpha subunit [Frankia alni ACN14a]
          Length = 349

 Score =  224 bits (572), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 122/302 (40%), Positives = 186/302 (61%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +TLGN+LRR L+SS+ GA++T+++IDGVLHE S++ GV ED+TD
Sbjct: 16  EFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIRIDGVLHEFSTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           +ILN+K + +    D    + + K+GPG VTA DI     +EV +P+  +  L+    + 
Sbjct: 76  LILNLKELVVSSDNDEPTVMYLRKQGPGEVTAADIAPPAGVEVHSPELRLATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+ R  Q  D+D+L + 
Sbjct: 136 IELTVERGRGYVSAAQNKQAGQEIGRIPIDSIYSPVLKVTYKVEATRVEQRTDFDRLIVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           ++T  SI+  D++A A + L    G+        + V    +         L   +EE++
Sbjct: 196 VETKPSISPRDAMASAGKTLVGLFGLAQELNAEAEGVDIGPSAADAALAADLALPIEEMD 255

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  LG MGL L  + P +
Sbjct: 256 LTVRSYNCLKREGIHTIGELVSRSEADLLDIRNFGQKSIDEVKTKLGAMGLQLKDSPPGF 315

Query: 325 PP 326
            P
Sbjct: 316 DP 317


>gi|146298135|ref|YP_001192726.1| DNA-directed RNA polymerase subunit alpha [Flavobacterium
           johnsoniae UW101]
 gi|146152553|gb|ABQ03407.1| DNA-directed RNA polymerase, alpha subunit [Flavobacterium
           johnsoniae UW101]
          Length = 330

 Score =  224 bits (571), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 121/298 (40%), Positives = 184/298 (61%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRVL+S+L G AIT+V+I+GV HE S+I GV ED+T+IILN+K + 
Sbjct: 28  PLEPGYGLTVGNALRRVLLSALEGYAITSVRIEGVDHEFSTISGVVEDVTEIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   ++ VTI   G   +TAGD Q  ++  +VLNPD VICNLD    +  +LT+ 
Sbjct: 88  FKRQIEDIDNESVTISVSGKDQLTAGDFQKFISGFQVLNPDLVICNLDSKIKLNFDLTIE 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++ +N  IG I  D++++P+K V Y +E+ R  Q  DY+KL   I TDGS
Sbjct: 148 KGRGYVPAEENKKQNAAIGTIFTDSIFTPVKNVKYAIENFRVEQKTDYEKLVFEIKTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A+++L     +F    I  E  +    E  + +SL     L  K+ +++LS
Sbjct: 208 INPKDALTEAAKVLIHHFMLFSDERITLEADEIAQTESYDEESLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   + D+++  NFG+KSL E+  ++    L  GM+L  +
Sbjct: 268 VRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKKSLTELDELVAVKNLTFGMDLAKY 325


>gi|311748487|ref|ZP_07722272.1| DNA-directed RNA polymerase, alpha subunit [Algoriphagus sp. PR1]
 gi|126577004|gb|EAZ81252.1| DNA-directed RNA polymerase, alpha subunit [Algoriphagus sp. PR1]
          Length = 329

 Score =  224 bits (571), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 122/320 (38%), Positives = 196/320 (61%), Gaps = 16/320 (5%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           E +V+ + ++   L   +PL +G+  T+GNALRR+L+SSL G AIT+++I GVLHE S+I
Sbjct: 10  EKVVMEKADDFHGLFTFKPLEKGYGVTIGNALRRILLSSLEGYAITSIKIPGVLHEFSTI 69

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHV 133
           +GV ED+TDIILN+K +  K   ++   ++T+  +   V TAGDI +  +  E+LNPD V
Sbjct: 70  EGVVEDVTDIILNLKQVRFKKVHEAFDGKITVEIKNQSVFTAGDIAKFTSSFEILNPDLV 129

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           IC++D      +E+TV KG GY+PA+  + +    G I IDA+++PIK V Y+VE+ R  
Sbjct: 130 ICHIDESKNFEIEITVEKGRGYLPAEESKPKEQVFGQIAIDAIFTPIKNVKYSVENTRVE 189

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN---------FEEPKKEVKED 244
           Q  D++KL + + TDGSI  E ++  +++IL     +F +           EP     E 
Sbjct: 190 QKTDFEKLILEVSTDGSIHPEKALQESAKILIQHFMLFSDQTMVLDSTGIAEP-----EP 244

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           I+ + L     L   + +L+LSVR+ NCL+  ++  +GDL +   +DM++  NFG+KSL 
Sbjct: 245 IDEEFLHMRKLLKTSLSDLDLSVRAFNCLKAADVKTLGDLAKLEISDMMKFRNFGKKSLA 304

Query: 305 EIKGVLGTMGLFLGMNLPDW 324
           E++ ++   GL  GM++  +
Sbjct: 305 ELEQLIQEKGLTFGMDISKY 324


>gi|309789643|ref|ZP_07684224.1| DNA-directed RNA polymerase subunit alpha [Oscillochloris
           trichoides DG6]
 gi|308228379|gb|EFO82026.1| DNA-directed RNA polymerase subunit alpha [Oscillochloris
           trichoides DG6]
          Length = 330

 Score =  224 bits (571), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 127/315 (40%), Positives = 193/315 (61%), Gaps = 8/315 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           Q  EN      EPL  G+ HTLGNALRRVL+SS+ G+AIT ++IDGV HE S+I+GV ED
Sbjct: 13  QAAENYGRFKIEPLDPGYGHTLGNALRRVLVSSIPGSAITKIKIDGVFHEFSTIEGVKED 72

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD- 140
           +T+I+LNIKG+ L+   +   +V + KRGPG+VTA DI   ++IE++NP+H IC LD + 
Sbjct: 73  VTEIVLNIKGVRLRSYAERPVKVLLTKRGPGIVTAKDIDVPSNIELVNPNHYICTLDSEV 132

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
           A + +E+TV +G GYV A     +  PIG I +DA+++P+ +V+Y VE+ R GQ  D+D+
Sbjct: 133 ARLEIEMTVERGRGYVSADQR--DILPIGEIPVDAIFTPVPRVNYVVENTRIGQATDFDR 190

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL-KK 259
           L + I TDG++   D+++ A+++L        +F     E +E      L     +    
Sbjct: 191 LLLEIWTDGTVKPGDALSHAAQVLVQYSQTIADFNRLAVEEEESPTPSGLTIPSDIYDTP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +E+L+LS R+ NCL+  +I  +G ++Q  E  +L + N G+KS+ EI+  L   G     
Sbjct: 251 IEDLDLSTRTYNCLKRADITKVGQVLQMDEKALLSVRNLGQKSMEEIRDRLVERGYISRQ 310

Query: 320 ----NLPDWPPESIE 330
               +L D  P +IE
Sbjct: 311 AGNGSLSDSEPVTIE 325


>gi|304438389|ref|ZP_07398330.1| DNA-directed RNA polymerase subunit alpha [Selenomonas sp. oral
           taxon 149 str. 67H29BP]
 gi|304368755|gb|EFM22439.1| DNA-directed RNA polymerase subunit alpha [Selenomonas sp. oral
           taxon 149 str. 67H29BP]
          Length = 319

 Score =  224 bits (571), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 126/298 (42%), Positives = 188/298 (63%), Gaps = 16/298 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL  G+  T GN+LRR+L+SSL GAA+T++QIDGVLHE S+I GV +D+T I+L +
Sbjct: 23  FICEPLEPGYGTTFGNSLRRMLLSSLDGAAVTSIQIDGVLHEFSTIPGVRDDVTSIVLAL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + ++M     + + I   G   VTA DI+  +DIE+LNP+  I  +     +++E+TV
Sbjct: 83  KQLCIRMQDSEPRTIRIEAAGAREVTAADIECGSDIEILNPELHIATMGETGKLKIEMTV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYVPA  ++  +D IG+I ID+++SP+++V+YTVE  R G V DYD+L + + T+G
Sbjct: 143 ERGRGYVPADRNKKPDDVIGVIPIDSIFSPVQRVNYTVEDTRVGNVTDYDRLILEVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKE----------DINVKSLPFNPALLKK 259
           SI  E++V+ A+ IL   L +F N +    E +E          D + K L         
Sbjct: 203 SIRPEEAVSKAAAILVMHLRLFQNMDGSVVEEEEEVPNFPPEEVDDSAKVLEMT------ 256

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +++L+LSVRS NCL+   I  + DL Q+TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 257 IDDLDLSVRSFNCLKRAGINTVADLAQKTEDDMMKVRNLGRKSLDEVKKKLEELGLSL 314


>gi|150008958|ref|YP_001303701.1| DNA-directed RNA polymerase subunit alpha [Parabacteroides
           distasonis ATCC 8503]
 gi|255014788|ref|ZP_05286914.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. 2_1_7]
 gi|256841041|ref|ZP_05546548.1| DNA-directed RNA polymerase, alpha subunit [Parabacteroides sp.
           D13]
 gi|298375809|ref|ZP_06985765.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 3_1_19]
 gi|172048837|sp|A6LEG5|RPOA_PARD8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|149937382|gb|ABR44079.1| DNA-directed RNA polymerase alpha chain [Parabacteroides distasonis
           ATCC 8503]
 gi|256736884|gb|EEU50211.1| DNA-directed RNA polymerase, alpha subunit [Parabacteroides sp.
           D13]
 gi|298266846|gb|EFI08503.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 3_1_19]
          Length = 330

 Score =  224 bits (571), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 122/298 (40%), Positives = 190/298 (63%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRR+L+SSL G AIT+++IDGV HE  +I GV ED+T+IILN+K + 
Sbjct: 28  PLEPGYGITIGNALRRILLSSLEGFAITSIKIDGVDHEFGTIPGVIEDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   D   +++V+I   G  V  AGDI + +   E+LNPD VIC LD  A  ++ELT++
Sbjct: 88  FKHIVDDIENEKVSITVSGSEVFKAGDIGKQLTGFEILNPDLVICRLDPTASFQIELTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R  N  I +I ID++++PI+ V Y++E+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPADENRDPNADIHVIAIDSIFTPIRNVKYSIENFRVEQKTDYEKLVLEIATDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  A++IL     +F    I  E    E  E+ + + L     L  K+ +++LS
Sbjct: 208 IHPKEALKEAAKILIHHFMLFSDEKIAIETADTEGNEEFDEEVLHMRQLLKSKLADMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +G+L++  + D+L+  NFG+KSL E+  +L ++ L  GM++  +
Sbjct: 268 VRALNCLKAADVETLGELVKFNKNDLLKFRNFGKKSLTELDELLESLNLSFGMDITKY 325


>gi|108798085|ref|YP_638282.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium sp. MCS]
 gi|119867181|ref|YP_937133.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium sp. KMS]
 gi|126433745|ref|YP_001069436.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium sp. JLS]
 gi|119366700|sp|Q1BD08|RPOA_MYCSS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158513059|sp|A1UBY5|RPOA_MYCSK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158513450|sp|A3PVL8|RPOA_MYCSJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|108768504|gb|ABG07226.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium sp. MCS]
 gi|119693270|gb|ABL90343.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium sp. KMS]
 gi|126233545|gb|ABN96945.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium sp. JLS]
          Length = 350

 Score =  224 bits (571), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 128/315 (40%), Positives = 197/315 (62%), Gaps = 20/315 (6%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+TD
Sbjct: 16  DNRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILN+K  +L +S +  + VT++  K+GPG VTAGDI     + V NP+  I  L+    
Sbjct: 76  IILNLK--SLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPEMHIATLNDKGK 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL 
Sbjct: 134 LEVELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLI 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNP 254
           + ++T  SIT  D++A A + L +  G+   +N E       P     + I   +LP   
Sbjct: 194 LDVETKNSITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALP--- 250

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +G
Sbjct: 251 -----IDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLG 305

Query: 315 LFLGMNLPDWPPESI 329
           L L  +   + P  +
Sbjct: 306 LSLKDSPATFDPSEV 320


>gi|296119324|ref|ZP_06837892.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           ammoniagenes DSM 20306]
 gi|295967716|gb|EFG80973.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           ammoniagenes DSM 20306]
          Length = 335

 Score =  224 bits (571), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 135/325 (41%), Positives = 195/325 (60%), Gaps = 28/325 (8%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           EYI     + +R+  + EPL  GF +T+GN++RR L+SS+ GAA+T+++IDGVLHE ++I
Sbjct: 12  EYI-----DSSRSRFVFEPLEPGFGYTIGNSMRRTLLSSIPGAAVTSIKIDGVLHEFTTI 66

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHV 133
            GV ED+++IILN+K  NL +S DS + V ++  K GPG VTAGDIQ    +E+ NP+  
Sbjct: 67  SGVKEDVSEIILNVK--NLVLSSDSDEPVVMYLSKEGPGAVTAGDIQPPAGVEIHNPELH 124

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           I  L+  A + MEL V +G GYVPA    T  D IG I ID +YSP+ KVSY VE+ R  
Sbjct: 125 IATLNDTAKLDMELVVERGRGYVPAAP--TSGD-IGRIPIDQIYSPVLKVSYKVEATRVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE--------PKKEVKEDI 245
           Q  D+DKL + ++T  SI+  D++A A   L +  G+              P  +  E I
Sbjct: 182 QRTDFDKLIIDVETKNSISARDALASAGGTLVELFGLARELNTAAEGIEIGPSPQESEYI 241

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
              S+P        +E+L  SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E
Sbjct: 242 AAYSMP--------IEDLNFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINE 293

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIE 330
           +K  L  + L L     D+ P  +E
Sbjct: 294 VKIKLANLNLALKDTPEDFDPTQLE 318


>gi|271962664|ref|YP_003336860.1| RNA polymerase subunit alpha [Streptosporangium roseum DSM 43021]
 gi|270505839|gb|ACZ84117.1| RNA polymerase, alpha chain, N terminal domain protein
           [Streptosporangium roseum DSM 43021]
          Length = 344

 Score =  224 bits (570), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 129/312 (41%), Positives = 189/312 (60%), Gaps = 12/312 (3%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           EE R+  I EPL  GF +T+GN+LRR L+SS+ GAA+T+++I+GVLHE S++ GV ED+T
Sbjct: 21  EETRSKFIIEPLEPGFGYTIGNSLRRTLLSSIPGAAVTSIRIEGVLHEFSTVPGVKEDVT 80

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           DIILN+K + +    D    + + K+GPG VTA DI     +EV NP+  I  L+  A +
Sbjct: 81  DIILNLKELVVSSEHDEPVVMYLRKQGPGEVTAADIAPPAGVEVHNPELRIATLNGKAKL 140

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            MELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+ R  Q  D+D+L +
Sbjct: 141 EMELTVERGRGYVSAAQNKQPGQEIGRIPIDSIYSPVLKVTYKVEATRVEQRTDFDRLIL 200

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLP----FNPALL 257
            ++T   +   D+VA A + L +  G+   +N E       E I++   P        L 
Sbjct: 201 DVETKPCMKPRDAVASAGKTLVELFGLARELNVE------AEGIDIGPSPTDAALAADLA 254

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +EEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  M L L
Sbjct: 255 LPIEELNLTVRSYNCLKREGIHTVGELVARSEQDLLDIRNFGAKSIEEVKQKLHEMTLAL 314

Query: 318 GMNLPDWPPESI 329
             + P + P ++
Sbjct: 315 KDSPPGFDPSAV 326


>gi|149371655|ref|ZP_01891071.1| DNA-directed RNA polymerase subunit alpha [unidentified eubacterium
           SCB49]
 gi|149355282|gb|EDM43842.1| DNA-directed RNA polymerase subunit alpha [unidentified eubacterium
           SCB49]
          Length = 330

 Score =  224 bits (570), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 121/298 (40%), Positives = 186/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRVL+SSL G AIT+++++GV HE S+I GV ED+T+IILN+K + 
Sbjct: 28  PLEPGYGLTIGNALRRVLLSSLEGFAITSLRVEGVDHEFSTIAGVVEDVTEIILNLKQLR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   D   ++ VTI   G   V AGD Q  ++  +VLNPD +ICN+D    + ME+T+ 
Sbjct: 88  FKRQIDEIDNETVTISVSGNDKVVAGDFQKFISGFQVLNPDLIICNMDSKVNLNMEITIE 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++  N P+G I  D++++PIK V Y++E+ R  Q  DY+KL   I +DGS
Sbjct: 148 KGRGYVPAEENKKANAPLGTIFTDSIFTPIKNVKYSIENFRVEQKTDYEKLVFEITSDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++ L     +F    I  E  +    E  + +SL     L  K+ +++LS
Sbjct: 208 IHPKDALTEAAKTLIHHFMLFSDERITLEADEIAQTETYDEESLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   + D+++  NFG+KSL E++ ++   GL  GM+L  +
Sbjct: 268 VRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKKSLTELEELVLVKGLNFGMDLAKY 325


>gi|319952170|ref|YP_004163437.1| DNA-directed RNA polymerase subunit alpha [Cellulophaga algicola
           DSM 14237]
 gi|319420830|gb|ADV47939.1| DNA-directed RNA polymerase subunit alpha [Cellulophaga algicola
           DSM 14237]
          Length = 330

 Score =  224 bits (570), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 119/298 (39%), Positives = 184/298 (61%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRVL+SSL G AIT++++D V HE S I G+ ED+T+IILN+K + 
Sbjct: 28  PLEPGYGLTVGNALRRVLLSSLEGFAITSIRVDKVEHEFSVISGIVEDVTEIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +    + V++   G   +TAGD Q  ++  +VLNPD VICN+D      MEL + 
Sbjct: 88  FKRQIEDVDSETVSVSVSGKNQLTAGDFQKFISGFQVLNPDLVICNMDAKVNFNMELVIE 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++    PIG I ID++++PIK V Y++E+ R  Q  DY+KL   I++DGS
Sbjct: 148 KGRGYVPAEENKKSGAPIGTIAIDSIFTPIKNVKYSIENFRVEQKTDYEKLVFEIESDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           IT +D++   +++L     +F    I  E  +    E  + +SL     L  K+ +++LS
Sbjct: 208 ITPKDALTEGAKVLIHHFMLFSDERITLEADEIAQTETYDEESLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   + D+++  NFG+KSL E++ ++   GL  GM+L  +
Sbjct: 268 VRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKKSLTELEELVINKGLSFGMDLSKY 325


>gi|213420654|ref|ZP_03353720.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E01-6750]
          Length = 271

 Score =  224 bits (570), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 120/278 (43%), Positives = 182/278 (65%), Gaps = 12/278 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLR 274
           ++ EVKE+       F+P LL+ V++LEL+VRS NCL+
Sbjct: 238 RQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLK 271


>gi|163840858|ref|YP_001625263.1| DNA-directed RNA polymerase subunit alpha [Renibacterium
           salmoninarum ATCC 33209]
 gi|189043843|sp|A9WSR1|RPOA_RENSM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|162954334|gb|ABY23849.1| DNA-directed RNA polymerase alpha chain [Renibacterium salmoninarum
           ATCC 33209]
          Length = 336

 Score =  224 bits (570), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 120/302 (39%), Positives = 187/302 (61%), Gaps = 4/302 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T+
Sbjct: 16  DNRSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILNIK +++    D      + K+GPGVVTA DI     +E  NPD  I  L+      
Sbjct: 76  IILNIKNLSVSSEHDEPVVAYLRKQGPGVVTAADIAPPAGVEFHNPDLHIATLNSKGKFE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELT+ +G GYV A  +++ +  IG I +D++YSP+ KV++ VE+ R  Q  D+D+L + 
Sbjct: 136 LELTIERGRGYVSAAQNKSGDAEIGRIPVDSIYSPVLKVTFRVEATRVEQRTDFDRLIVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           ++T  +I   D+VA A   L +  G+        + ++   +         +   +E+L+
Sbjct: 196 VETKQAIAPRDAVASAGTTLVELFGLARELNTAAEGIEIGPSPTDAALAADMALPIEDLD 255

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L    + LG++L D 
Sbjct: 256 LTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGAKSIDEVKAKL----VELGLSLKDS 311

Query: 325 PP 326
           PP
Sbjct: 312 PP 313


>gi|260061923|ref|YP_003195003.1| DNA-directed RNA polymerase subunit alpha [Robiginitalea biformata
           HTCC2501]
 gi|88786056|gb|EAR17225.1| DNA-directed RNA polymerase alpha subunit [Robiginitalea biformata
           HTCC2501]
          Length = 317

 Score =  224 bits (570), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 121/298 (40%), Positives = 187/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRVL++SL G AIT+V+ID V HE S I+GV ED+T+IILN+K I 
Sbjct: 15  PLEPGYGLTVGNALRRVLLASLEGFAITSVRIDKVEHEFSVIEGVVEDVTEIILNLKQIR 74

Query: 94  LKMSGD--SHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   D  + + V+I   G   +TAGD Q  ++  +VLNPD VICN+D    + ME+ + 
Sbjct: 75  FKRQIDDVNEETVSISVSGKEQLTAGDFQKFISGFQVLNPDLVICNMDPKVSINMEIIIE 134

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++  N P+G I +D++++P++ V Y++E+ R  Q  DY+KL   I TDGS
Sbjct: 135 KGRGYVPAEENKKSNAPLGSIAVDSIFTPVRNVKYSIENYRVEQKTDYEKLVFEILTDGS 194

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A+++L     +F    I  E  +    E  + +SL     L  K+ +++LS
Sbjct: 195 IHPKDALTEAAKVLIHHFMLFSDERITLEADEIAQTETYDEESLHMRQLLKTKLVDMDLS 254

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   + D+++  NFG+KSL E++ ++   GL  GM+L  +
Sbjct: 255 VRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKKSLTELEELVINKGLNFGMDLSKY 312


>gi|169788447|emb|CAP58145.1| RNA polymerase [Lactobacillus rossiae]
          Length = 235

 Score =  224 bits (570), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 113/235 (48%), Positives = 163/235 (69%), Gaps = 2/235 (0%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+K ++LKM
Sbjct: 1   RGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVTQIILNMKKVSLKM 60

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
           + D  K + I  +GP  VTAGD QT  D+EV+NPD  IC +   A   M LT +KG GYV
Sbjct: 61  ATDEEKGMDIDVKGPATVTAGDFQTDADVEVMNPDLYICTVADGATFHMHLTANKGRGYV 120

Query: 157 PAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A  ++   D  PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSIT  
Sbjct: 121 SADENKARQDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSITPS 180

Query: 215 DSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           ++++LA++IL + L MF++  +  K  +  +  +       L   +EEL+LSVRS
Sbjct: 181 EAISLAAKILTEHLAMFVDLTDTAKNAEIMVEKEETHKEKMLEMTIEELDLSVRS 235


>gi|157493287|gb|ABV58009.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 259

 Score =  224 bits (570), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 116/265 (43%), Positives = 179/265 (67%), Gaps = 13/265 (4%)

Query: 35  LPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL 94
           L RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +
Sbjct: 1   LERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAV 60

Query: 95  KMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKG 152
           +++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V +G
Sbjct: 61  RVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVERG 120

Query: 153 HGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            GYVPA    H   +  PIG + +DA +SP+ K++Y+VE     Q  D DKL + ++T+G
Sbjct: 121 RGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVE-----QRTDLDKLVIDMETNG 175

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           ++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VRS
Sbjct: 176 TLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRS 232

Query: 270 TNCLRGENIVYMGDLIQRTEADMLR 294
            NCL+ E I Y+GDL+QRTE ++L+
Sbjct: 233 ANCLKAEAIHYIGDLVQRTEVELLK 257


>gi|295135676|ref|YP_003586352.1| DNA-directed RNA polymerase subunit alpha [Zunongwangia profunda
           SM-A87]
 gi|294983691|gb|ADF54156.1| DNA-directed RNA polymerase subunit alpha [Zunongwangia profunda
           SM-A87]
          Length = 330

 Score =  224 bits (570), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 123/298 (41%), Positives = 186/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRVL+SSL G AIT+V+I+GV HE S+I GV ED+T+IILN+K + 
Sbjct: 28  PLEPGYGLTVGNALRRVLLSSLEGFAITSVRIEGVDHEFSTIPGVVEDVTEIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   D   ++ VTI   G   +TAG  Q  ++  +VLNP+ VIC+LD    + ME+T+ 
Sbjct: 88  FKRQIDEIDNEAVTISVSGEEELTAGHFQKFISGFQVLNPELVICHLDSKVNINMEITIE 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++  N P+G I  D++Y+PIK V Y++E+ R  Q  DY+KL   I +DGS
Sbjct: 148 KGRGYVPAEENKKANAPLGTIFTDSIYTPIKNVKYSIENYRVEQKTDYEKLVFEIISDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++ L     +F    I  E  +    E  + +SL     L  K+ +++LS
Sbjct: 208 IHPKDALTEAAKTLIHHFMLFSDERITLEADEIAQTETYDEESLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   + D+++  NFG+KSL E++ ++   GL  GM+L  +
Sbjct: 268 VRALNCLKAAEVDTLGDLVSYNKNDLMKFRNFGKKSLTELEELVSNKGLNFGMDLSKY 325


>gi|328813989|gb|AEB52110.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 264

 Score =  224 bits (570), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 124/266 (46%), Positives = 174/266 (65%), Gaps = 6/266 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN I  I    E +N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EFEKPN-IHKI---DENDNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EV
Sbjct: 59  VLHEFSTIEGVTEDVTAIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAK--HHRTENDPIGLITIDALYSPIKKVSY 185
           LNPD  IC +   A   M +T + G GYV A+   HR ++ PIG++ +D+LYSPI++V+Y
Sbjct: 119 LNPDLPICTVADGAHFHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R GQ  D+DKL++ + T+GSIT  ++++L+++IL D L +F+N  +  K     +
Sbjct: 179 QVENTRVGQRDDFDKLTLDVWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTN 271
             +       L   +EEL+LSVRS N
Sbjct: 239 EKEETHKEKMLEMTIEELDLSVRSYN 264


>gi|300728416|ref|ZP_07061778.1| DNA-directed RNA polymerase, alpha subunit [Prevotella bryantii
           B14]
 gi|299774335|gb|EFI70965.1| DNA-directed RNA polymerase, alpha subunit [Prevotella bryantii
           B14]
          Length = 330

 Score =  224 bits (570), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 122/298 (40%), Positives = 187/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AI  V+I GV HE SS+ GV ED+T+IILN+K I 
Sbjct: 28  PLEPGFGVTVGNALRRMLLSSLEGYAINTVKIAGVEHEFSSVPGVKEDVTNIILNLKQIR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   +++V+I         AGDI + +   EVLNP+ VIC+LD  A +R++LT++
Sbjct: 88  FKQVVEEFENEKVSIIVENSTEFKAGDISKHLTGFEVLNPELVICHLDPKASMRIDLTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y+VE  R  Q  DYDKL++ + TDGS
Sbjct: 148 KGRGYVPADENRQFCTDVNVIPIDSIYTPIRNVKYSVEPYRVEQKTDYDKLTIEVTTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++IL     +F    I  E P ++  ++ + + L     L  K+ ++ LS
Sbjct: 208 IHPKDALKEAAKILIYHFMLFSDEKITLENPDQDGNQEFDEEVLHMRQLLKTKLVDMNLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKKSLSELDDLLESLNLSFGTDISKY 325


>gi|229818214|ref|ZP_04448496.1| hypothetical protein BIFANG_03512 [Bifidobacterium angulatum DSM
           20098]
 gi|229784465|gb|EEP20579.1| hypothetical protein BIFANG_03512 [Bifidobacterium angulatum DSM
           20098]
          Length = 332

 Score =  224 bits (570), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 129/312 (41%), Positives = 187/312 (59%), Gaps = 13/312 (4%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
            R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ GV ED+T+I
Sbjct: 17  QRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTTLPGVQEDVTEI 76

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           +LNIKGI L    D    + + K G G  TAGDI     + + NPD  I  L  D  + +
Sbjct: 77  LLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGVTIANPDKHIATLAEDGELEI 136

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           E TV +G GYVPA  ++ + D IG I +D++YSP+ KVSY VE+ R  Q  D+DKL + +
Sbjct: 137 EFTVERGRGYVPASMNKQDADEIGRIPVDSIYSPVLKVSYKVEATRVEQRTDFDKLILDV 196

Query: 206 DTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPF----NPALLKK 259
           +T  +I+  D+VA A   L +  G+   +N +       E + V S P     NP     
Sbjct: 197 ETKPAISPRDAVASAGSTLVELFGLCRELNVQ------AEGVEVGSAPVVEEANPEHAVP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L ++GL L  
Sbjct: 251 IEDLNLTQRSYNCLKREGIHTIGELVSHTEQDLLDIRNFGMKSIDEVKEKLQSLGLSLKA 310

Query: 320 N-LPDWPPESIE 330
           + L D+ P ++E
Sbjct: 311 SPLGDFDPNNLE 322


>gi|257784935|ref|YP_003180152.1| DNA-directed RNA polymerase, alpha subunit [Atopobium parvulum DSM
           20469]
 gi|257473442|gb|ACV51561.1| DNA-directed RNA polymerase, alpha subunit [Atopobium parvulum DSM
           20469]
          Length = 313

 Score =  224 bits (570), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 125/320 (39%), Positives = 195/320 (60%), Gaps = 17/320 (5%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E I+PN    + + +   N   +  EPL RG+  TLGN+LRRVL+SSL GAA+ A+QI
Sbjct: 1   MSEFIRPN----VSVDEIGANVARVSVEPLERGYGDTLGNSLRRVLLSSLEGAAVEAIQI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVND 124
           DGV HE ++++GV+ED+TDI+LN+KG+  + + +S +   +I   GP  VT  D+     
Sbjct: 57  DGVQHEFTTVEGVYEDVTDIVLNVKGLVFRNTNNSDEAEASISVDGPCTVTGADLDVPMG 116

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            E++NP   IC L   A + M L +  G GYV  + +  ENDPIG I +D+++SP+++ +
Sbjct: 117 YELVNPAQHICALAEGAHLSMRLRIGNGRGYVSGEDNERENDPIGFIHVDSIFSPVRRCA 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI---NFEEPKKE- 240
             VE  R G+  DYD+L + ++T+G+I+  ++V  A+ I+   +  F+   +F+E ++E 
Sbjct: 177 KAVEPCRVGRHTDYDRLVLEVETNGAISPREAVVEAANIINQHMSAFMGLTDFDETQEEA 236

Query: 241 ---VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
               K D+   S      L K+VE+L+LSVRS NCL+   I  +  L+  +E D+L + N
Sbjct: 237 SIFAKADVEDDS-----ELEKQVEDLDLSVRSYNCLKRAGIHSVRQLVDFSENDLLNIRN 291

Query: 298 FGRKSLVEIKGVLGTMGLFL 317
           FG KS+ E+K  L +MGL L
Sbjct: 292 FGVKSIEEVKEKLESMGLSL 311


>gi|260206828|ref|ZP_05774319.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis K85]
 gi|289576193|ref|ZP_06456420.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis K85]
 gi|289540624|gb|EFD45202.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis K85]
          Length = 347

 Score =  223 bits (569), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 127/315 (40%), Positives = 197/315 (62%), Gaps = 20/315 (6%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T+
Sbjct: 16  DNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILN+K  +L +S +  + VT++  K+GPG VTAGDI     + V NP   I  L+    
Sbjct: 76  IILNLK--SLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIATLNDKGK 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL 
Sbjct: 134 LEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLI 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNP 254
           + ++T  SI+  D++A A + L +  G+   +N E       P     + I   +LP   
Sbjct: 194 LDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALP--- 250

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +G
Sbjct: 251 -----IDDLDLTVRSYNCLKREGVHIVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLG 305

Query: 315 LFLGMNLPDWPPESI 329
           L L  + P + P  +
Sbjct: 306 LSLKDSPPSFDPSEV 320


>gi|15610593|ref|NP_217974.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis H37Rv]
 gi|15843052|ref|NP_338089.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis CDC1551]
 gi|31794633|ref|NP_857126.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium bovis
           AF2122/97]
 gi|121639377|ref|YP_979601.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium bovis BCG
           str. Pasteur 1173P2]
 gi|148663322|ref|YP_001284845.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis H37Ra]
 gi|148824667|ref|YP_001289421.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis F11]
 gi|215405496|ref|ZP_03417677.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis 02_1987]
 gi|215413370|ref|ZP_03422055.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis 94_M4241A]
 gi|215428964|ref|ZP_03426883.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis T92]
 gi|215432428|ref|ZP_03430347.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis EAS054]
 gi|215447794|ref|ZP_03434546.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis T85]
 gi|224991873|ref|YP_002646562.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium bovis BCG
           str. Tokyo 172]
 gi|253800502|ref|YP_003033503.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis KZN 1435]
 gi|254234049|ref|ZP_04927374.1| DNA-directed RNA polymerase (alpha chain) rpoA [Mycobacterium
           tuberculosis C]
 gi|260188512|ref|ZP_05765986.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis CPHL_A]
 gi|289449161|ref|ZP_06438905.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis CPHL_A]
 gi|289747290|ref|ZP_06506668.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis 02_1987]
 gi|289752181|ref|ZP_06511559.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis T92]
 gi|289755590|ref|ZP_06514968.1| RNA polymerase subunit alpha [Mycobacterium tuberculosis EAS054]
 gi|289759620|ref|ZP_06518998.1| RNA polymerase subunit alpha [Mycobacterium tuberculosis T85]
 gi|294993005|ref|ZP_06798696.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis 210]
 gi|297636116|ref|ZP_06953896.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis KZN 4207]
 gi|297733116|ref|ZP_06962234.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis KZN R506]
 gi|298526941|ref|ZP_07014350.1| DNA-directed RNA polymerase (alpha chain) rpoA [Mycobacterium
           tuberculosis 94_M4241A]
 gi|306777804|ref|ZP_07416141.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu001]
 gi|306782523|ref|ZP_07420860.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu002]
 gi|306786342|ref|ZP_07424664.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu003]
 gi|306790711|ref|ZP_07429033.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu004]
 gi|306795239|ref|ZP_07433541.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu005]
 gi|306799429|ref|ZP_07437731.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu006]
 gi|306805275|ref|ZP_07441943.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu008]
 gi|306809461|ref|ZP_07446129.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu007]
 gi|306969569|ref|ZP_07482230.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu009]
 gi|306973923|ref|ZP_07486584.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu010]
 gi|307081632|ref|ZP_07490802.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu011]
 gi|307086238|ref|ZP_07495351.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu012]
 gi|313660447|ref|ZP_07817327.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis KZN V2475]
 gi|54039274|sp|P66702|RPOA_MYCBO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|54042185|sp|P66701|RPOA_MYCTU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158512956|sp|A1KPE3|RPOA_MYCBP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172047915|sp|A5U8D3|RPOA_MYCTA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|2104380|emb|CAB08723.1| PROBABLE DNA-DIRECTED RNA POLYMERASE (ALPHA CHAIN) RPOA
           (TRANSCRIPTASE ALPHA CHAIN) (RNA POLYMERASE ALPHA
           SUBUNIT) (DNA-DIRECTED RNA NUCLEOTIDYLTRANSFERASE)
           [Mycobacterium tuberculosis H37Rv]
 gi|13883396|gb|AAK47903.1| DNA-directed RNA polymerase, alpha subunit [Mycobacterium
           tuberculosis CDC1551]
 gi|31620230|emb|CAD95673.1| PROBABLE DNA-DIRECTED RNA POLYMERASE (ALPHA CHAIN) RPOA
           (TRANSCRIPTASE ALPHA CHAIN) (RNA POLYMERASE ALPHA
           SUBUNIT) (DNA-DIRECTED RNA NUCLEOTIDYLTRANSFERASE)
           [Mycobacterium bovis AF2122/97]
 gi|121495025|emb|CAL73511.1| Probable DNA-directed RNA polymerase (alpha chain) rpoA
           [Mycobacterium bovis BCG str. Pasteur 1173P2]
 gi|124599578|gb|EAY58682.1| DNA-directed RNA polymerase (alpha chain) rpoA [Mycobacterium
           tuberculosis C]
 gi|148507474|gb|ABQ75283.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis H37Ra]
 gi|148723194|gb|ABR07819.1| DNA-directed RNA polymerase alpha subunit rpoA [Mycobacterium
           tuberculosis F11]
 gi|224774988|dbj|BAH27794.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium bovis BCG
           str. Tokyo 172]
 gi|253322005|gb|ACT26608.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis KZN 1435]
 gi|289422119|gb|EFD19320.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis CPHL_A]
 gi|289687818|gb|EFD55306.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis 02_1987]
 gi|289692768|gb|EFD60197.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis T92]
 gi|289696177|gb|EFD63606.1| RNA polymerase subunit alpha [Mycobacterium tuberculosis EAS054]
 gi|289715184|gb|EFD79196.1| RNA polymerase subunit alpha [Mycobacterium tuberculosis T85]
 gi|298496735|gb|EFI32029.1| DNA-directed RNA polymerase (alpha chain) rpoA [Mycobacterium
           tuberculosis 94_M4241A]
 gi|308213889|gb|EFO73288.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu001]
 gi|308324840|gb|EFP13691.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu002]
 gi|308329094|gb|EFP17945.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu003]
 gi|308332902|gb|EFP21753.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu004]
 gi|308336562|gb|EFP25413.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu005]
 gi|308340437|gb|EFP29288.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu006]
 gi|308344301|gb|EFP33152.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu007]
 gi|308348192|gb|EFP37043.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu008]
 gi|308352916|gb|EFP41767.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu009]
 gi|308356759|gb|EFP45610.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu010]
 gi|308360704|gb|EFP49555.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu011]
 gi|308364319|gb|EFP53170.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu012]
 gi|323717941|gb|EGB27130.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis CDC1551A]
 gi|328460233|gb|AEB05656.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis KZN 4207]
          Length = 347

 Score =  223 bits (569), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 127/315 (40%), Positives = 197/315 (62%), Gaps = 20/315 (6%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T+
Sbjct: 16  DNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILN+K  +L +S +  + VT++  K+GPG VTAGDI     + V NP   I  L+    
Sbjct: 76  IILNLK--SLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIATLNDKGK 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL 
Sbjct: 134 LEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLI 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNP 254
           + ++T  SI+  D++A A + L +  G+   +N E       P     + I   +LP   
Sbjct: 194 LDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALP--- 250

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +G
Sbjct: 251 -----IDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLG 305

Query: 315 LFLGMNLPDWPPESI 329
           L L  + P + P  +
Sbjct: 306 LSLKDSPPSFDPSEV 320


>gi|289555728|ref|ZP_06444938.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis KZN 605]
 gi|289440360|gb|EFD22853.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis KZN 605]
          Length = 346

 Score =  223 bits (569), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 127/315 (40%), Positives = 197/315 (62%), Gaps = 20/315 (6%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T+
Sbjct: 15  DNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTE 74

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILN+K  +L +S +  + VT++  K+GPG VTAGDI     + V NP   I  L+    
Sbjct: 75  IILNLK--SLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIATLNDKGK 132

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL 
Sbjct: 133 LEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLI 192

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNP 254
           + ++T  SI+  D++A A + L +  G+   +N E       P     + I   +LP   
Sbjct: 193 LDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALP--- 249

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +G
Sbjct: 250 -----IDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLG 304

Query: 315 LFLGMNLPDWPPESI 329
           L L  + P + P  +
Sbjct: 305 LSLKDSPPSFDPSEV 319


>gi|328814007|gb|AEB52119.1| DNA-directed RNA polymerase alpha chain [Lactobacillus rhamnosus]
          Length = 258

 Score =  223 bits (569), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 114/258 (44%), Positives = 172/258 (66%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED+T IILNIK
Sbjct: 1   VVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLEDVTQIILNIK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV 
Sbjct: 61  KLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVK 120

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GS
Sbjct: 121 KGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGS 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I+  ++++LA++IL + L +F+N  +  K  +  +  +       L   +EEL+LSVRS 
Sbjct: 181 ISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSVRSY 240

Query: 271 NCLRGENIVYMGDLIQRT 288
           NCL+   I  + +L  +T
Sbjct: 241 NCLKRAGINTVQELTNKT 258


>gi|269784302|emb|CBH50796.1| alpha subunit of RNA polymerase [Vibrio sp. C 2.4]
 gi|289524814|emb|CBJ94463.1| alpha subunit of RNA polymerase [Vibrio sp. Rd 14.14]
          Length = 266

 Score =  223 bits (569), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 117/267 (43%), Positives = 178/267 (66%), Gaps = 8/267 (2%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVT 115
           G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V 
Sbjct: 3   GCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVV 62

Query: 116 AGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLI 171
           AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG +
Sbjct: 63  AGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRL 122

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F
Sbjct: 123 LVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAF 182

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           ++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE +
Sbjct: 183 VDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVE 239

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLG 318
           +L+  N G+KSL EIK VL + GL LG
Sbjct: 240 LLKTPNLGKKSLTEIKDVLASRGLSLG 266


>gi|226227379|ref|YP_002761485.1| DNA-directed RNA polymerase alpha subunit [Gemmatimonas aurantiaca
           T-27]
 gi|226090570|dbj|BAH39015.1| DNA-directed RNA polymerase alpha subunit [Gemmatimonas aurantiaca
           T-27]
          Length = 357

 Score =  223 bits (569), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 117/293 (39%), Positives = 183/293 (62%), Gaps = 6/293 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           +PL RGF HTLGNA+RR+L+SSLRG+A+ A +IDGV+HE  +I GV ED+  II N+K +
Sbjct: 32  QPLERGFGHTLGNAMRRLLLSSLRGSAVWAFRIDGVVHEHQTIGGVVEDVHQIIGNLKTL 91

Query: 93  NLKMSGDSHKRV-TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
            L +  +  + V  I K GPG VTA DI     + +++P H I  +  +    +EL V+K
Sbjct: 92  TLALPDEVEQTVLRISKSGPGTVTAADIIATGGVRIIDPSHHIFTITGERDFNIELYVNK 151

Query: 152 GHGYVPAKHHRTE-NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           G GY+ +  H  + N  + ++ IDA+YSP+++V++TV   R GQ  DYD+L++T++T+G+
Sbjct: 152 GRGYIESDQHPADKNLSVDVVRIDAIYSPVRRVNFTVAETRVGQRTDYDRLTLTVETNGT 211

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKE----VKEDINVKSLPFNPALLKKVEELELS 266
           ++ E++V+ A+ + Q     F+ F            +  N  ++         +++LELS
Sbjct: 212 MSPEEAVSYAAALAQTHFQYFVGFGSSASAQPGTAGDGANSDAIRLAELFRTPIDDLELS 271

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           VRS N L+  NI  +GDL+++TEA +L++ NFG+KSL EI  +L   GL  GM
Sbjct: 272 VRSVNSLKNSNIRSLGDLVRQTEAQILQVKNFGKKSLQEIAALLEKEGLNFGM 324


>gi|239918173|ref|YP_002957731.1| DNA-directed RNA polymerase, alpha subunit [Micrococcus luteus NCTC
           2665]
 gi|289706559|ref|ZP_06502909.1| DNA-directed RNA polymerase, alpha subunit [Micrococcus luteus
           SK58]
 gi|239839380|gb|ACS31177.1| DNA-directed RNA polymerase, alpha subunit [Micrococcus luteus NCTC
           2665]
 gi|289556694|gb|EFD50035.1| DNA-directed RNA polymerase, alpha subunit [Micrococcus luteus
           SK58]
          Length = 332

 Score =  223 bits (569), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 121/306 (39%), Positives = 194/306 (63%), Gaps = 4/306 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ++R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVLHE S++ GV ED+T+
Sbjct: 16  DHRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVLHEFSTVNGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILNIK +++    D      + K+G GVVTA DI     +E+ NPD  I  L+      
Sbjct: 76  IILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEIHNPDLHIATLNAKGKFD 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MELT+ +G GYV A  +++ +  IG I +D++YSP+ KV++ VE+ R  Q  D+D+L + 
Sbjct: 136 MELTIERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEATRVEQRTDFDRLILD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           ++T  ++   D+VA A   L +  G+   +N E    ++ ++  V  +  +  L + +EE
Sbjct: 196 VETKENMLPRDAVASAGSTLVELFGLARSLNVEAEGIDLGDEPEV--VEGSADLAQPIEE 253

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           LEL+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L  +GL L  +  
Sbjct: 254 LELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEKLQELGLSLKDSPA 313

Query: 323 DWPPES 328
            + P++
Sbjct: 314 GYDPQA 319


>gi|281415637|ref|ZP_06247379.1| DNA-directed RNA polymerase subunit alpha [Micrococcus luteus NCTC
           2665]
          Length = 334

 Score =  223 bits (569), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 121/306 (39%), Positives = 194/306 (63%), Gaps = 4/306 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ++R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVLHE S++ GV ED+T+
Sbjct: 18  DHRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVLHEFSTVNGVKEDVTE 77

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILNIK +++    D      + K+G GVVTA DI     +E+ NPD  I  L+      
Sbjct: 78  IILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEIHNPDLHIATLNAKGKFD 137

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MELT+ +G GYV A  +++ +  IG I +D++YSP+ KV++ VE+ R  Q  D+D+L + 
Sbjct: 138 MELTIERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEATRVEQRTDFDRLILD 197

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           ++T  ++   D+VA A   L +  G+   +N E    ++ ++  V  +  +  L + +EE
Sbjct: 198 VETKENMLPRDAVASAGSTLVELFGLARSLNVEAEGIDLGDEPEV--VEGSADLAQPIEE 255

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           LEL+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L  +GL L  +  
Sbjct: 256 LELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEKLQELGLSLKDSPA 315

Query: 323 DWPPES 328
            + P++
Sbjct: 316 GYDPQA 321


>gi|326905303|gb|EGE52236.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis W-148]
          Length = 348

 Score =  223 bits (569), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 127/314 (40%), Positives = 196/314 (62%), Gaps = 20/314 (6%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T+I
Sbjct: 18  NRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTEI 77

Query: 86  ILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           ILN+K  +L +S +  + VT++  K+GPG VTAGDI     + V NP   I  L+    +
Sbjct: 78  ILNLK--SLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIATLNDKGKL 135

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL +
Sbjct: 136 EVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLIL 195

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNPA 255
            ++T  SI+  D++A A + L +  G+   +N E       P     + I   +LP    
Sbjct: 196 DVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALP---- 251

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
               +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL
Sbjct: 252 ----IDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGL 307

Query: 316 FLGMNLPDWPPESI 329
            L  + P + P  +
Sbjct: 308 SLKDSPPSFDPSEV 321


>gi|163783137|ref|ZP_02178131.1| DNA-directed RNA polymerase alpha subunit [Hydrogenivirga sp.
           128-5-R1-1]
 gi|159881471|gb|EDP74981.1| DNA-directed RNA polymerase alpha subunit [Hydrogenivirga sp.
           128-5-R1-1]
          Length = 316

 Score =  223 bits (568), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 135/317 (42%), Positives = 192/317 (60%), Gaps = 11/317 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E + PN I +    Q+E+N+ + + EPL RGF  TLGNALRRVL+SS+ G A+TAV+I G
Sbjct: 4   EFVFPNKIYW---EQKEDNKGVFVVEPLERGFGTTLGNALRRVLLSSISGTAVTAVKIYG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE SS++GV ED+ +II NIKG+   +     + + + K+G G V AGDI    ++EV
Sbjct: 61  VYHEFSSLEGVAEDVVEIIANIKGVRFTLKDSDVEVLYLKKKGEGEVKAGDISLPPNVEV 120

Query: 128 LNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
            NPD VI  + D +     E+ + +G GYV A+   T  +  G I +DA +SP+K VSY 
Sbjct: 121 ANPDKVIATITDPEVEFNAEIRIERGKGYVLAEEMETIGE-TGWILLDADFSPVKLVSYR 179

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKED 244
           +E  R G+  DY+KL++ + TDG+ + E  V  A  ILQ  L +   I++E P  E  E 
Sbjct: 180 IEQTRVGEKTDYEKLTVEVLTDGTKSPEAVVKEAVDILQRHLSLLEHISYEVPTLE--EP 237

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           I V  L  +  L   +EEL++S R+ N L+   I  +GDL+Q TE ++    N GRK+L 
Sbjct: 238 IPVDEL--SEKLTLSIEELDISQRALNSLKRMGITTIGDLVQMTEEELKSTKNIGRKALA 295

Query: 305 EIKGVLGTMGLFLGMNL 321
           EIK  L  MGL LG+N+
Sbjct: 296 EIKEALKQMGLQLGINI 312


>gi|262383847|ref|ZP_06076983.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp.
           2_1_33B]
 gi|301312005|ref|ZP_07217927.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 20_3]
 gi|262294745|gb|EEY82677.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp.
           2_1_33B]
 gi|300830107|gb|EFK60755.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 20_3]
          Length = 330

 Score =  223 bits (568), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 121/298 (40%), Positives = 190/298 (63%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRR+L+SSL G AIT+++IDGV HE  +I GV ED+T+IILN+K + 
Sbjct: 28  PLEPGYGITIGNALRRILLSSLEGFAITSIKIDGVDHEFGTIPGVIEDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   D   +++V+I   G  V  AGDI + +   E+LNPD VIC LD  A  ++ELT++
Sbjct: 88  FKHIVDDIENEKVSITVSGSEVFKAGDIGKQLTGFEILNPDLVICRLDPTASFQIELTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R  N  + +I ID++++PI+ V Y++E+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPADENRDPNADMHVIAIDSIFTPIRNVKYSIENFRVEQKTDYEKLVLEIATDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  A++IL     +F    I  E    E  E+ + + L     L  K+ +++LS
Sbjct: 208 IHPKEALKEAAKILIHHFMLFSDEKIAIETADTEGNEEFDEEVLHMRQLLKSKLADMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +G+L++  + D+L+  NFG+KSL E+  +L ++ L  GM++  +
Sbjct: 268 VRALNCLKAADVETLGELVKFNKNDLLKFRNFGKKSLTELDELLESLNLSFGMDITKY 325


>gi|291457229|ref|ZP_06596619.1| DNA-directed RNA polymerase, alpha subunit [Bifidobacterium breve
           DSM 20213]
 gi|291381064|gb|EFE88582.1| DNA-directed RNA polymerase, alpha subunit [Bifidobacterium breve
           DSM 20213]
          Length = 331

 Score =  223 bits (568), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 122/296 (41%), Positives = 178/296 (60%), Gaps = 8/296 (2%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
            R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ GV ED+T+I
Sbjct: 17  QRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTTLPGVQEDVTEI 76

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           +LNIKGI L    D    + + K G G  TAGDI   + + + NP+  I  L  D  + +
Sbjct: 77  LLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPSGVTIANPEQHIATLAEDGELEI 136

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           E TV +G GYVPA+ ++ + D IG I +D++YSP+ KVSY VE+ R  Q  D+DKL + +
Sbjct: 137 EFTVERGRGYVPAQMNKQDTDEIGRIPVDSIYSPVLKVSYKVEATRVEQRTDFDKLILDV 196

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF----NPALLKKVE 261
           +T  +I+  D+VA A   L +  G+            E + V   P     NP +   +E
Sbjct: 197 ETKPAISPRDAVASAGSTLVELFGLCREL----NAQAEGVEVGPAPVAEETNPEMAVPIE 252

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +L L+ RS NCL+ E +  +G+L+  TE D+L + NFG KS+ E+K  L T+GL L
Sbjct: 253 DLNLTQRSYNCLKREGVHTIGELVSHTEQDLLDIRNFGMKSIDEVKEKLQTLGLSL 308


>gi|328813965|gb|AEB52098.1| DNA-directed RNA polymerase alpha chain [Lactobacillus farraginis]
          Length = 270

 Score =  223 bits (568), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 122/265 (46%), Positives = 175/265 (66%), Gaps = 4/265 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EPL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+
Sbjct: 6   VVVEPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNV 65

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K I+LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M L
Sbjct: 66  KKISLKLDGPEDEEENLEIDVIGPADVTAGDIQGDSDVTVLNPDLHIATVAEGATFHMRL 125

Query: 148 TVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           T ++G GYV A     R    PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ +
Sbjct: 126 TANRGRGYVSAVENKKRATEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDV 185

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+GSIT  ++V+LA++IL + L MF++  +  K  +  +  +       L   +EEL+L
Sbjct: 186 WTNGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEKEETHKEKMLEMTIEELDL 245

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEA 290
           SVRS NCL+   I  + +L ++TEA
Sbjct: 246 SVRSYNCLKRAGINTVQELTEKTEA 270


>gi|89891130|ref|ZP_01202638.1| DNA-directed RNA polymerase alpha chain [Flavobacteria bacterium
           BBFL7]
 gi|89516774|gb|EAS19433.1| DNA-directed RNA polymerase alpha chain [Flavobacteria bacterium
           BBFL7]
          Length = 330

 Score =  223 bits (568), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 121/298 (40%), Positives = 183/298 (61%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRVL+SSL G AIT+++I+GV HE S+I+GV ED+T+IILN K I 
Sbjct: 28  PLEPGYGLTVGNALRRVLLSSLEGFAITSIRIEGVDHEFSTIEGVVEDVTEIILNFKQIR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            +   D    + V +   G    TAGD+Q  ++  +VLNP+ VICN +    + +ELT+ 
Sbjct: 88  FRRQIDEVDSEVVNVSFSGKDTFTAGDMQKYISGFQVLNPEMVICNTESSVSLNLELTIE 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++  N  IG I ID++++PIK V Y++E+ R  Q  DY+KL   I TDGS
Sbjct: 148 KGRGYVPAEENKNPNAAIGTIAIDSIFTPIKNVKYSIENYRVEQKTDYEKLVFEISTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  + ++  A++ L     +F    I  E  +    E  + +SL     L  K+ ++ELS
Sbjct: 208 IHPKQALTEAAKTLIHHFMLFSDERITLEADEIAQTETYDEESLHMRQLLKTKLVDMELS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   + D+++  NFG+KSL E++ ++   GL  GM+L  +
Sbjct: 268 VRALNCLKAAEVETLGDLVSYNKNDLMKFRNFGKKSLTELEELVNVKGLNFGMDLSKY 325


>gi|91216884|ref|ZP_01253848.1| DNA-directed RNA polymerase alpha subunit [Psychroflexus torquis
           ATCC 700755]
 gi|91185045|gb|EAS71424.1| DNA-directed RNA polymerase alpha subunit [Psychroflexus torquis
           ATCC 700755]
          Length = 330

 Score =  223 bits (568), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 122/298 (40%), Positives = 186/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRVL+SSL G AIT+V+I+GV HE S+I+GV ED+T++ILN+K I 
Sbjct: 28  PLEPGYGLTVGNALRRVLLSSLEGFAITSVRIEGVDHEFSTIEGVVEDVTEMILNLKQIR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   ++ V+I   G   +TAGD Q  +   ++LNPD  IC +D    + +ELTV 
Sbjct: 88  FKKRAEDVDNETVSISFSGNDKMTAGDFQKYLTGFDILNPDLEICTMDKKVSLNLELTVQ 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++T   PIG I  D++++PIK V Y++E+ R  Q  DY+KL   I +DGS
Sbjct: 148 KGRGYVPAEENKTSKAPIGTIFTDSVFTPIKNVKYSIENFRVEQKTDYEKLIFEIISDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++ L     +F    I  E  +    E  + +SL     L  K+ +L+LS
Sbjct: 208 IHPKDALTEAAKTLIHHFMLFSDERITLETEEMSQAETYDEESLHMRQLLKTKLVDLDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   ++D+++  NFG+KSL E++ ++   GL  GM+L  +
Sbjct: 268 VRALNCLKAAEVETLGDLVSHNKSDLMKFRNFGKKSLTELEELVENKGLDFGMDLSKY 325


>gi|172040041|ref|YP_001799755.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           urealyticum DSM 7109]
 gi|171851345|emb|CAQ04321.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           urealyticum DSM 7109]
          Length = 337

 Score =  223 bits (568), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 132/315 (41%), Positives = 194/315 (61%), Gaps = 28/315 (8%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           +++R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED++
Sbjct: 15  DDSRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSLRIDGVLHEFTTVPGVKEDVS 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           DIILNIK  +L +S D  + VT++  K G G VT  DI+T   +EV N D  I  L+   
Sbjct: 75  DIILNIK--SLVLSSDFDEPVTMYLRKEGAGAVTGADIETPAGVEVHNKDLHIATLNEQG 132

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + +EL V +G GYVPA    T  D IG I +D +YSP+ KVSY VE+ R  Q  D+DKL
Sbjct: 133 KLDIELVVERGRGYVPAA---TSTDEIGRIPVDQIYSPVLKVSYKVEATRVEQRTDFDKL 189

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFN 253
            + ++T  S++  D++A A + L +  G+   +N E       P  +  E I   ++P  
Sbjct: 190 ILDVETKSSMSARDAMASAGKTLVELFGLAQELNIEAEGIEIGPSPQESEHIAAYNMP-- 247

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +E+L+ SVRS NCL+ E I  +G+L  RTE+D+L + NFG+KS+ E+K  L  +
Sbjct: 248 ------IEDLDFSVRSYNCLKREEIHTVGELAARTESDLLDIRNFGQKSINEVKVKLAGL 301

Query: 314 GLFL-----GMNLPD 323
           GL L     G +L D
Sbjct: 302 GLALKDSPEGFDLSD 316


>gi|328813947|gb|AEB52089.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 267

 Score =  223 bits (568), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 114/252 (45%), Positives = 168/252 (66%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E  N    + EPL RG+  TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+
Sbjct: 8   ESTNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDV 67

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILNIK + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +     
Sbjct: 68  TQIILNIKKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGH 127

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
             + +TV KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL+
Sbjct: 128 FHVRMTVKKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLT 187

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + + T+GSI+  ++++LA++IL + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 188 LDVWTNGSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEE 247

Query: 263 LELSVRSTNCLR 274
           L+LSVRS NCL+
Sbjct: 248 LDLSVRSYNCLK 259


>gi|260907114|ref|ZP_05915436.1| DNA-directed RNA polymerase subunit alpha [Brevibacterium linens
           BL2]
          Length = 332

 Score =  223 bits (568), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 121/299 (40%), Positives = 185/299 (61%), Gaps = 12/299 (4%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ENR+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S++ GV ED+T+
Sbjct: 16  ENRSRFAIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFSTVPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
            ILN+K + +    D      + K+GPG VTA D+     +E+ NPD  I  L+ +  + 
Sbjct: 76  FILNLKSLVVSSEFDEPVVAYLRKQGPGTVTAADVSAPAGVEIHNPDLHIATLNGEGRLD 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MELT+ +G GYV +  ++  +  IG + +D++YSP+ KV+Y VE+ R  Q  D+D+L + 
Sbjct: 136 MELTIERGRGYVSSAQNKNADAEIGRVPVDSIYSPVLKVTYKVEATRVEQRTDFDRLVLD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPF----NPALLK 258
           I+T  S+T  D++A A + L +  G+   +N E       E I +   P        L  
Sbjct: 196 IETKPSMTPRDAIASAGKTLVELFGLARELNVE------AEGIEIGPSPVDAALAADLAL 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            +E+L+L+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L  +GL L
Sbjct: 250 AIEDLDLTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGSKSIDEVKAKLNELGLSL 308


>gi|119718095|ref|YP_925060.1| DNA-directed RNA polymerase subunit alpha [Nocardioides sp. JS614]
 gi|158513104|sp|A1SNI8|RPOA_NOCSJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119538756|gb|ABL83373.1| DNA-directed RNA polymerase subunit alpha [Nocardioides sp. JS614]
          Length = 338

 Score =  223 bits (568), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 127/309 (41%), Positives = 189/309 (61%), Gaps = 12/309 (3%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           +E R+  + EPL  GF +TLGN+LRR L+SS+ GA++T+++ID VLHE S+I+GV ED+T
Sbjct: 15  DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIKIDNVLHEFSTIEGVKEDVT 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           ++ILN+KG+ +    D    + + K G G VTA DI     +EV NPD  I  L     +
Sbjct: 75  EVILNLKGLVVSSEHDEPVTMYLRKSGAGDVTAADIAPPAGVEVHNPDLKIATLSDKGKL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            MEL V +G GYV A  ++  ++ IG + +D++YSP+ KV+Y VE+ R  Q  D+DKL +
Sbjct: 135 EMELVVERGRGYVSAVQNKGADNEIGRMPVDSIYSPVLKVTYKVEATRVEQRTDFDKLVI 194

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLK--- 258
            ++T  SI   D++A A + L +  G+   +N E       E I++   P +  L     
Sbjct: 195 DVETKPSIRPRDAIASAGKTLVELFGLARELNVE------AEGIDIGPSPVDEQLAADLA 248

Query: 259 -KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             VE+L+L+VRS NCL+ E I  +G+LI R+E D+L + NFG KS+ E+K  L  MGL L
Sbjct: 249 LPVEDLQLTVRSYNCLKREGIHTVGELISRSEQDLLDIRNFGAKSIDEVKAKLVEMGLSL 308

Query: 318 GMNLPDWPP 326
             + P + P
Sbjct: 309 KDSAPGFDP 317


>gi|258646025|ref|ZP_05733494.1| DNA-directed RNA polymerase, alpha subunit [Dialister invisus DSM
           15470]
 gi|260403397|gb|EEW96944.1| DNA-directed RNA polymerase, alpha subunit [Dialister invisus DSM
           15470]
          Length = 326

 Score =  223 bits (567), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 128/309 (41%), Positives = 186/309 (60%), Gaps = 34/309 (11%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRVL+SSL G AIT++ IDGV HE S++ GV ED+TD+ILN+K I 
Sbjct: 27  PLERGYGITLGNSLRRVLLSSLDGVAITSINIDGVEHEFSTVPGVREDVTDMILNLKKIR 86

Query: 94  LKMSGDSH----KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
                ++      RV + K G  V+ AGD+Q  ++I+VLN D  +C LD +A + MELT+
Sbjct: 87  FIAYEEAEFPIKVRVDVTKEG--VLLAGDLQLPSEIDVLNGDLALCTLDTEAHLGMELTI 144

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +GHGYVP   +R E+DPIG I ID++YSP+ K +Y V   R G  +DYDKL++ ++TDG
Sbjct: 145 DRGHGYVPFTKNRREDDPIGSIPIDSIYSPVVKCNYNVSDTRVGNEMDYDKLTLELETDG 204

Query: 210 SITGEDSVALASRILQDQLGMF-----------------INFEEPKKEVKEDINVKSLPF 252
           SI   D+VA A+ IL +   +F                       ++  +E I++  +P 
Sbjct: 205 SIKASDAVATAATILMNCFELFRPLATGPILEARDGSDMARQSSDQQAEEEKIDLSGIP- 263

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                  +EELELSVR+ NCL+   I  +  L ++TE ++ R+ N G+KS+ EI   +  
Sbjct: 264 -------IEELELSVRAFNCLKRAEINTLDQLAEKTEEELGRVRNLGKKSIDEI---IEK 313

Query: 313 MGLFLGMNL 321
           +  F G+ L
Sbjct: 314 LAQFRGLGL 322


>gi|281423812|ref|ZP_06254725.1| DNA-directed RNA polymerase, alpha subunit [Prevotella oris F0302]
 gi|299141174|ref|ZP_07034311.1| DNA-directed RNA polymerase, alpha subunit [Prevotella oris C735]
 gi|281402039|gb|EFB32870.1| DNA-directed RNA polymerase, alpha subunit [Prevotella oris F0302]
 gi|298577134|gb|EFI49003.1| DNA-directed RNA polymerase, alpha subunit [Prevotella oris C735]
          Length = 330

 Score =  223 bits (567), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 120/298 (40%), Positives = 186/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AI  ++I GV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGVTIGNALRRILLSSLEGYAINTIRIAGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   +++V+I         AGDI + +   EVLNPD VIC+LD  A ++++LT++
Sbjct: 88  FKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGFEVLNPDLVICHLDAKASMQIDLTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y+VE  R  Q  DYDKL + + TDGS
Sbjct: 148 KGRGYVPADENREFCTDVNVIPIDSIYTPIRNVKYSVEPYRVEQKTDYDKLVIEVSTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++IL     +F    I  E P ++  ++ + + L     L  K+ ++ LS
Sbjct: 208 IHPKDALKEAAKILIYHFMLFSDEKITLESPDQDGNQEFDEEVLHMRQLLKTKLVDMNLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKKSLSELDDLLESLNLSFGTDISKY 325


>gi|282880974|ref|ZP_06289665.1| DNA-directed RNA polymerase, alpha subunit [Prevotella timonensis
           CRIS 5C-B1]
 gi|281305197|gb|EFA97266.1| DNA-directed RNA polymerase, alpha subunit [Prevotella timonensis
           CRIS 5C-B1]
          Length = 330

 Score =  223 bits (567), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 118/298 (39%), Positives = 187/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GN+LRR+L+SSL G AI  ++I GV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGITIGNSLRRILLSSLEGYAINTMRIAGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   +++V+I         AGDI + +   EVLNPD VIC+LD  A ++++LT++
Sbjct: 88  FKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGFEVLNPDLVICHLDAKASMQIDLTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           +G GYVPA  +R     + ++ ID++Y+PI+ V YTVE  R  Q  DYDKL + + TDGS
Sbjct: 148 QGRGYVPADENRQFCTDVNVLPIDSIYTPIRNVKYTVEPYRVEQKTDYDKLVIEVTTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I+ +D++  A++IL     +F    I  E P ++  ++ + + L     L  K+ ++ LS
Sbjct: 208 ISPKDALKEAAKILIYHFMLFSDEKITLENPDQDTNQEFDEEVLHMRQLLKTKLVDMNLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKKSLSELDDLLESLNLSFGTDISKY 325


>gi|254366058|ref|ZP_04982103.1| DNA-directed RNA polymerase (alpha chain) rpoA [Mycobacterium
           tuberculosis str. Haarlem]
 gi|134151571|gb|EBA43616.1| DNA-directed RNA polymerase (alpha chain) rpoA [Mycobacterium
           tuberculosis str. Haarlem]
          Length = 348

 Score =  223 bits (567), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 127/315 (40%), Positives = 196/315 (62%), Gaps = 20/315 (6%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T+
Sbjct: 17  ETRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTE 76

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILN+K  +L +S +  + VT++  K+GPG VTAGDI     + V NP   I  L+    
Sbjct: 77  IILNLK--SLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIATLNDKGK 134

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL 
Sbjct: 135 LEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLI 194

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNP 254
           + ++T  SI+  D++A A + L +  G+   +N E       P     + I   +LP   
Sbjct: 195 LDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALP--- 251

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +G
Sbjct: 252 -----IDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLG 306

Query: 315 LFLGMNLPDWPPESI 329
           L L  + P + P  +
Sbjct: 307 LSLKDSPPSFDPSEV 321


>gi|23466156|ref|NP_696759.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium longum
           NCC2705]
 gi|46190439|ref|ZP_00121528.2| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Bifidobacterium longum DJO10A]
 gi|189440595|ref|YP_001955676.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium longum
           DJO10A]
 gi|213693062|ref|YP_002323648.1| DNA-directed RNA polymerase, alpha subunit [Bifidobacterium longum
           subsp. infantis ATCC 15697]
 gi|227546502|ref|ZP_03976551.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium longum
           subsp. infantis ATCC 55813]
 gi|239621036|ref|ZP_04664067.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium longum
           subsp. infantis CCUG 52486]
 gi|296454844|ref|YP_003661988.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium longum
           subsp. longum JDM301]
 gi|312133900|ref|YP_004001239.1| rpoa [Bifidobacterium longum subsp. longum BBMN68]
 gi|317483424|ref|ZP_07942414.1| DNA-directed RNA polymerase [Bifidobacterium sp. 12_1_47BFAA]
 gi|322689903|ref|YP_004209637.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium longum
           subsp. infantis 157F]
 gi|322691844|ref|YP_004221414.1| DNA-directed RNA polymerase alpha subunit [Bifidobacterium longum
           subsp. longum JCM 1217]
 gi|41688707|sp|Q8G3Z3|RPOA_BIFLO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|23326893|gb|AAN25395.1| DNA-directed RNA polymerase alpha chain [Bifidobacterium longum
           NCC2705]
 gi|189429030|gb|ACD99178.1| DNA-directed RNA polymerase alpha subunit [Bifidobacterium longum
           DJO10A]
 gi|213524523|gb|ACJ53270.1| DNA-directed RNA polymerase, alpha subunit [Bifidobacterium longum
           subsp. infantis ATCC 15697]
 gi|227213051|gb|EEI80930.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium longum
           subsp. infantis ATCC 55813]
 gi|239516137|gb|EEQ56004.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium longum
           subsp. infantis CCUG 52486]
 gi|296184276|gb|ADH01158.1| DNA-directed RNA polymerase, alpha subunit [Bifidobacterium longum
           subsp. longum JDM301]
 gi|311773194|gb|ADQ02682.1| RpoA [Bifidobacterium longum subsp. longum BBMN68]
 gi|316915110|gb|EFV36542.1| DNA-directed RNA polymerase [Bifidobacterium sp. 12_1_47BFAA]
 gi|320456700|dbj|BAJ67322.1| DNA-directed RNA polymerase alpha subunit [Bifidobacterium longum
           subsp. longum JCM 1217]
 gi|320459240|dbj|BAJ69861.1| DNA-directed RNA polymerase alpha subunit [Bifidobacterium longum
           subsp. infantis ATCC 15697]
 gi|320461239|dbj|BAJ71859.1| DNA-directed RNA polymerase alpha subunit [Bifidobacterium longum
           subsp. infantis 157F]
          Length = 331

 Score =  223 bits (567), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 123/296 (41%), Positives = 177/296 (59%), Gaps = 8/296 (2%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
            R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ GV ED+T+I
Sbjct: 17  QRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTTLPGVQEDVTEI 76

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           +LNIKGI L    D    + + K G G   AGDI     + + NP+  I  L  D  + +
Sbjct: 77  LLNIKGIVLTSEYDEPVVMYLRKSGKGEAVAGDITPPAGVTIANPEQHIATLADDGELEI 136

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           E TV +G GYVPA+ ++ +ND IG I +D++YSP+ KVSY VE+ R  Q  D+DKL + +
Sbjct: 137 EFTVERGRGYVPAQMNKQDNDEIGRIPVDSIYSPVLKVSYKVEATRVEQRTDFDKLILDV 196

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF----NPALLKKVE 261
           +T  +I+  D+VA A   L +  G+            E + V   P     NP +   +E
Sbjct: 197 ETKPAISPRDAVASAGSTLVELFGLCREL----NAQAEGVEVGPAPVAEETNPEMAVPIE 252

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L T+GL L
Sbjct: 253 DLNLTQRSYNCLKREGIHTIGELVSHTEQDLLDIRNFGMKSIDEVKEKLQTLGLSL 308


>gi|225010542|ref|ZP_03701013.1| DNA-directed RNA polymerase, alpha subunit [Flavobacteria bacterium
           MS024-3C]
 gi|225005371|gb|EEG43322.1| DNA-directed RNA polymerase, alpha subunit [Flavobacteria bacterium
           MS024-3C]
          Length = 330

 Score =  223 bits (567), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 120/298 (40%), Positives = 186/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRV++S+L G AIT+V++D V HE S I GV ED+T+IILN+K + 
Sbjct: 28  PLEPGYGLTVGNALRRVMLSALEGFAITSVRMDKVAHEFSVIPGVVEDVTEIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   ++ ++I   G   +TAGD Q  ++  +VLNPD VICN+D    + MELT+ 
Sbjct: 88  FKRQIEDVDNETISIALSGKQQLTAGDFQKFISGFQVLNPDLVICNMDAKVNINMELTIE 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++    PIG I ID++++PIK V Y++E+ R  Q  DY+KL   I +DGS
Sbjct: 148 KGRGYVPAEENKKSGAPIGTIAIDSIFTPIKNVKYSIENFRVEQKTDYEKLVFEIVSDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A+++L     +F    I  E  +    E  + +SL     L  K+ +++LS
Sbjct: 208 IHPKDALTEAAKVLIHHFMLFSDERITLEADEIAQTETYDEESLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   + D+++  NFG+KSL E++ ++   GL  GM+L  +
Sbjct: 268 VRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKKSLTELEELVINKGLSFGMDLSKY 325


>gi|148655310|ref|YP_001275515.1| DNA-directed RNA polymerase subunit alpha [Roseiflexus sp. RS-1]
 gi|172048077|sp|A5USG2|RPOA_ROSS1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|148567420|gb|ABQ89565.1| DNA-directed RNA polymerase, alpha subunit [Roseiflexus sp. RS-1]
          Length = 323

 Score =  223 bits (567), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 122/286 (42%), Positives = 180/286 (62%), Gaps = 6/286 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           EN      EPL  G+ HTLGNALRRVL+SS+ GAAIT ++I+GV HE S+I GV ED+T+
Sbjct: 16  ENYGRFKIEPLDPGYGHTLGNALRRVLLSSIPGAAITKIKIEGVFHEFSTIPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV-DAVV 143
           I+LNIKGI L+   +   ++++ KRG GVV A DI   +++E++NP+H IC +D  DA +
Sbjct: 76  IVLNIKGIRLRSYAERPVKISLSKRGAGVVRAADIDAPSNVEIVNPNHYICTIDRDDAAI 135

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            ME+TV +G GY+PA     +  PIG I IDA+++P+ KV+Y VE  R GQ  D D L +
Sbjct: 136 DMEMTVERGRGYLPADQR--DALPIGEIPIDAIFTPVPKVNYVVEHIRVGQATDIDSLLI 193

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL--KKVE 261
            I TDG+I   D+++ A+++L        +F     E +       L   PA +    +E
Sbjct: 194 EIWTDGTIKPGDALSHAAQVLVQYSQTIADFNRLSTEAEPTTAPNGLAI-PADIYDTPIE 252

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           EL+LS R+ NCL+  +I  +G +++  E  +L + N G+KS+ EI+
Sbjct: 253 ELDLSTRTYNCLKRADITKVGQVLEMDEKALLSVRNLGQKSMEEIR 298


>gi|150025381|ref|YP_001296207.1| DNA-directed RNA polymerase subunit alpha [Flavobacterium
           psychrophilum JIP02/86]
 gi|172048610|sp|A6GZ73|RPOA_FLAPJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|149771922|emb|CAL43396.1| DNA-directed RNA polymerase alpha subunit RpoA [Flavobacterium
           psychrophilum JIP02/86]
          Length = 330

 Score =  223 bits (567), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 119/298 (39%), Positives = 184/298 (61%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRVL+S+L G AIT+++I+GV HE S+I GV ED+T+IIL++K + 
Sbjct: 28  PLEPGYGLTVGNALRRVLLSALEGYAITSIRIEGVDHEFSTIPGVVEDVTEIILSLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   ++ VTI   G   +TAGD Q  ++  +VLNP+ VICNLD      ME+T+ 
Sbjct: 88  FKRQIEDIDNESVTIAISGKNQITAGDFQKYISGFQVLNPELVICNLDSKVNFNMEMTIE 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++ +N  IG I  D++++P+K V Y +E+ R  Q  DY+KL   I TDGS
Sbjct: 148 KGRGYVPAEENKKQNAAIGTIFTDSIFTPVKNVKYAIENFRVEQKTDYEKLVFEIKTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A+++L     +F    I  E  +    E  + +SL     L  K+ +++LS
Sbjct: 208 INPKDALTEAAKVLIHHFMLFSDERITLEADEIAQTESYDEESLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   + D+++  NFG+KSL E+  ++    L  GM+L  +
Sbjct: 268 VRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKKSLTELDELVAIKNLTFGMDLAKY 325


>gi|124003688|ref|ZP_01688536.1| DNA-directed RNA polymerase, alpha subunit [Microscilla marina ATCC
           23134]
 gi|123990743|gb|EAY30210.1| DNA-directed RNA polymerase, alpha subunit [Microscilla marina ATCC
           23134]
          Length = 329

 Score =  223 bits (567), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 125/315 (39%), Positives = 192/315 (60%), Gaps = 6/315 (1%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           E +V+ +  +   +   +PL  GF  T+GNA+RRVL+SSL G AIT ++I GV HE SSI
Sbjct: 10  EKVVMDKTTDFHGMFEFKPLEPGFGVTVGNAIRRVLLSSLEGYAITCIRIPGVQHEFSSI 69

Query: 76  KGVHEDLTDIILNIKGINLK-MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHV 133
           KGV +D+ +IILN+K +  K +S +   ++ +       +TAGDI +  +  E+LNPD V
Sbjct: 70  KGVMQDVAEIILNLKKVRFKKISENVDSKIVVEVSNQETLTAGDIGKFTSSFEILNPDLV 129

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           ICNLD    + +EL + KG GYV ++  +  +  IG I ID++++PIK V Y VE+ R  
Sbjct: 130 ICNLDESVDLEVELYIEKGRGYVSSEDQKLPDAAIGHIPIDSIFTPIKNVRYAVENTRVE 189

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKS 249
           Q  DY+KL + I TDGSI  E+++  A+ IL     +F    I  E  KKE  ++++   
Sbjct: 190 QRTDYEKLLLDIQTDGSIHPEEALKGAANILIQHFMLFSDQNIILETAKKEEVQEVDEHF 249

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           L     L   + +L+LSVR+ NCL+  +I  +GDL++   ADM++  NFG+KSL E++ +
Sbjct: 250 LHMRKLLKTPISDLDLSVRAYNCLKSADIRTLGDLVKLDIADMMKFRNFGKKSLTELEQL 309

Query: 310 LGTMGLFLGMNLPDW 324
           +   GL  GM++  +
Sbjct: 310 VAEKGLSFGMDVSKY 324


>gi|1524340|emb|CAA63080.1| RNA polymerase alpha subunit [Streptomyces coelicolor A3(2)]
          Length = 339

 Score =  223 bits (567), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 130/325 (40%), Positives = 199/325 (61%), Gaps = 23/325 (7%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLSKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNGKGKLEMELTVERGRGYVSAVQNKEVGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++    ++A A + L +  G+        +E+  +I+ + +
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPR-AMASAGKTLVELFGL-------AREL--NIDAEGI 231

Query: 251 PFNPA---------LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
              P+         L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG K
Sbjct: 232 DMGPSPTDAALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAK 291

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPP 326
           S+ E+K  L  MGL L  + P + P
Sbjct: 292 SIDEVKAKLAGMGLALKDSPPGFDP 316


>gi|328813967|gb|AEB52099.1| DNA-directed RNA polymerase alpha chain [Lactobacillus fermentum]
          Length = 271

 Score =  223 bits (567), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 117/268 (43%), Positives = 178/268 (66%), Gaps = 2/268 (0%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E +N    + EPL RG+  TLGN+LRRV+++SL GAAIT++QIDGVLHE S+++GV ED
Sbjct: 4   EETDNYGKFVVEPLERGYGTTLGNSLRRVMLASLPGAAITSIQIDGVLHEFSTVQGVTED 63

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILN+K + LK+  +  K + I  +GP  VTA DIQ   D+ +LN D  I  +   A
Sbjct: 64  VTQIILNLKQVALKIDSEDAKDLEIDVKGPAEVTAADIQGDGDVTILNSDLHIATVSDGA 123

Query: 142 VVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
            + +++T  KG GY  A  ++T  E   IG++ ID++Y+PI++V+YTVE+ R GQ  DYD
Sbjct: 124 ELHVKMTADKGRGYSSADDNKTRMEGLAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYD 183

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL++ + T+GS+T  ++++LA++IL + L MF+N  E  +  +  +  +       L K 
Sbjct: 184 KLTLDVWTNGSLTPTEAISLAAKILTEHLTMFVNLTEEAQVTQVMVEREETHQEKVLDKT 243

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQR 287
           +EEL+LSVRS NCL+  +I  + DL +R
Sbjct: 244 IEELDLSVRSYNCLKRADIQTVKDLTER 271


>gi|294790438|ref|ZP_06755596.1| DNA-directed RNA polymerase, alpha subunit [Scardovia inopinata
           F0304]
 gi|294458335|gb|EFG26688.1| DNA-directed RNA polymerase, alpha subunit [Scardovia inopinata
           F0304]
          Length = 331

 Score =  223 bits (567), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 121/292 (41%), Positives = 179/292 (61%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
            R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ GV ED+T+I
Sbjct: 17  QRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTTLPGVKEDVTEI 76

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           +LNIK + L    D    + + K G G  TA DI     + + NPD  I  L  D  + +
Sbjct: 77  LLNIKELVLTSEYDEPVVMYLRKSGEGEATAADITPPAGVVIANPDLHIATLAEDGELEI 136

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           E TV +G GYVPA+ ++ E D IG I +D++YSP+ KVSY VE+ R  Q  D+DKL + +
Sbjct: 137 EFTVERGRGYVPAQMNKQEGDEIGRIPVDSIYSPVVKVSYKVEATRVEQRTDFDKLIVDV 196

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
           +T  +IT  D+VA A   L +  G+F       + V+      +   +P +   +E+L L
Sbjct: 197 ETKPAITPRDAVASAGSTLVELFGLFHELNNQAEGVEVGPAPVTEEVDPQMEIPIEDLNL 256

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + RS NCL+ E I  +G+L++R+E D+L + NFG+KS+ E+K  L +MGL L
Sbjct: 257 TQRSYNCLKREGIHTIGELVKRSEQDLLDIRNFGQKSIDEVKDKLASMGLSL 308


>gi|328814013|gb|AEB52122.1| DNA-directed RNA polymerase alpha chain [Lactobacillus rhamnosus]
          Length = 260

 Score =  222 bits (566), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 113/252 (44%), Positives = 168/252 (66%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E  N    + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED+
Sbjct: 8   ESTNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLEDV 67

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILNIK + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +     
Sbjct: 68  TQIILNIKKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGH 127

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
             + +TV KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL+
Sbjct: 128 FHVRMTVKKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLT 187

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + + T+GSI+  ++++LA++IL + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 188 LDVWTNGSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEE 247

Query: 263 LELSVRSTNCLR 274
           L+LSVRS NCL+
Sbjct: 248 LDLSVRSYNCLK 259


>gi|310779568|ref|YP_003967901.1| DNA-directed RNA polymerase subunit alpha [Ilyobacter polytropus
           DSM 2926]
 gi|309748891|gb|ADO83553.1| DNA-directed RNA polymerase subunit alpha [Ilyobacter polytropus
           DSM 2926]
          Length = 325

 Score =  222 bits (566), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 121/305 (39%), Positives = 189/305 (61%), Gaps = 6/305 (1%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E + +   I EPL RG+ HT+GNALRRVL+SS+ GAAI  ++IDGVL+E S I+GV E 
Sbjct: 17  KENDFKAQYIVEPLYRGYGHTIGNALRRVLLSSIPGAAIKGLRIDGVLNEFSIIEGVKEA 76

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +TDIILN+K + +K      KR+ +  +GP +VTA DI   +++E++NPD VIC +  + 
Sbjct: 77  VTDIILNVKEVIVKTETSGEKRMNLSVQGPKIVTAADINPDSELEIINPDQVICTVTTEK 136

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ME  V  G G+V A+    ++  +  IT+DA+Y+PIK+VSY+VE    G++ D+DKL
Sbjct: 137 EINMEFLVDTGEGFVVAEDIERKDWSVDYITVDAIYTPIKRVSYSVEDTMVGRMTDFDKL 196

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK------SLPFNPA 255
           ++ ++TDGSI   D+++ A  +L+     F++     + ++ D+  +      S      
Sbjct: 197 TLNVETDGSIVIRDAISYAVELLRLHFDPFLDIGNGMENLRGDLEEEEVEEVDSSKDEDV 256

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           L  K+EEL+L+VRS NCL+   I  +G L   +  ++L++ N GRKSL EI   +  +G 
Sbjct: 257 LNLKIEELDLTVRSFNCLKKAGIEEVGQLAILSLNELLKIKNLGRKSLDEILDKMKELGF 316

Query: 316 FLGMN 320
            L  N
Sbjct: 317 DLSQN 321


>gi|284033971|ref|YP_003383902.1| DNA-directed RNA polymerase subunit alpha [Kribbella flavida DSM
           17836]
 gi|283813264|gb|ADB35103.1| DNA-directed RNA polymerase, alpha subunit [Kribbella flavida DSM
           17836]
          Length = 341

 Score =  222 bits (566), Expect = 6e-56,   Method: Compositional matrix adjust.
 Identities = 128/310 (41%), Positives = 194/310 (62%), Gaps = 20/310 (6%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E+R+  + EPL  GF +TLGN++RR L+SS+ GAA+T++++DGVLHE S++ GV ED T 
Sbjct: 16  EHRSRFVIEPLEPGFGYTLGNSIRRTLLSSIPGAAVTSIKVDGVLHEFSTVAGVKEDATQ 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           +ILN+K  +L +S +  + VT++  K+GPG VTA DI     +EV NPD  I  L+    
Sbjct: 76  LILNLK--DLVVSSEHDEPVTMYLRKQGPGDVTAADIAPPAGVEVHNPDLKIATLNEKGR 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + MEL V +G GYV A  +++ +  IG + +D++YSP+ KV+Y VE+ R  Q  D+D+L 
Sbjct: 134 LEMELVVERGRGYVSAIQNKSADAEIGRMPVDSIYSPVLKVTYKVEATRVEQRTDFDRLV 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLK-- 258
           + ++T  S+   D+VA A + L +  G+   +N E       E I++   P +  +    
Sbjct: 194 VDVETKPSMLPRDAVASAGKTLVELFGLARELNVE------AEGIDIGPSPVDEQMAADL 247

Query: 259 --KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              VE+L+L+VRS NCL+ E I  +G+LI R+E D+L + NFG KS+ E+K  L  MGL 
Sbjct: 248 ALPVEDLQLTVRSYNCLKREGIHTVGELISRSEQDLLDIRNFGSKSIDEVKLKLAEMGL- 306

Query: 317 LGMNLPDWPP 326
              +L D PP
Sbjct: 307 ---SLKDSPP 313


>gi|328813951|gb|AEB52091.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 260

 Score =  222 bits (566), Expect = 6e-56,   Method: Compositional matrix adjust.
 Identities = 112/245 (45%), Positives = 166/245 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNI
Sbjct: 4   FVVEPLERGYGTTLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNI 63

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV
Sbjct: 64  KKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTV 123

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+G
Sbjct: 124 KKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNG 183

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI+  ++++LA++IL + L +F+N  +  K  +  +  +       L   +EEL+LSVRS
Sbjct: 184 SISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSVRS 243

Query: 270 TNCLR 274
            NCL+
Sbjct: 244 YNCLK 248


>gi|300742030|ref|ZP_07072051.1| DNA-directed RNA polymerase, alpha subunit [Rothia dentocariosa
           M567]
 gi|300381215|gb|EFJ77777.1| DNA-directed RNA polymerase, alpha subunit [Rothia dentocariosa
           M567]
          Length = 330

 Score =  222 bits (565), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 125/316 (39%), Positives = 194/316 (61%), Gaps = 9/316 (2%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           NR+    EPL  GF +T+GN+LRR L+SS+ GAA+T+V+IDGVLHE S++ GV ED+T+I
Sbjct: 17  NRSRFTIEPLEPGFGYTMGNSLRRTLLSSIPGAAVTSVRIDGVLHEFSTVPGVTEDVTEI 76

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           ILN+K +++    D      + K+G G +TA DI+    +E+ NP+  I  L+  A    
Sbjct: 77  ILNVKKLSISSENDEPVVAYLRKQGEGELTAADIEVPAGVEIHNPELHIATLNAKANFNA 136

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           EL + +G GYV A  ++T +  IG I +D++YSP+ KV+++V + R  Q  D+D L++ +
Sbjct: 137 ELIIERGRGYVSAAQNKTGDAEIGRIPVDSIYSPVLKVTFSVNATRVEQRTDFDSLTLDV 196

Query: 206 DTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
           +T  +I   D+VA A   L +  G+   +N      EV      +S+  + AL   +E+L
Sbjct: 197 ETKEAIAPRDAVASAGSTLVELFGLARELNVAAEGIEVGPSPADESMAADLAL--PIEDL 254

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            +SVRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L      LG+ L D
Sbjct: 255 SMSVRSYNCLKREGIHTVGELVTRSEADLMDIRNFGAKSIDEVKAKLHE----LGLALKD 310

Query: 324 WPPESIEELAKKYEDK 339
            PP   E +A+ Y+D+
Sbjct: 311 SPP-GFEPVARAYDDE 325


>gi|254819221|ref|ZP_05224222.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           intracellulare ATCC 13950]
          Length = 347

 Score =  222 bits (565), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 127/315 (40%), Positives = 195/315 (61%), Gaps = 20/315 (6%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T 
Sbjct: 16  DNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTA 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILN+K  +L +S +  + VT++  K+GPG VTAGDI     + V NPD  I  L+    
Sbjct: 76  IILNLK--SLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPDLHIATLNDKGK 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL 
Sbjct: 134 LEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLI 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNP 254
           + ++T  SI   D++A A + L +  G+   +N E       P     + I   +LP   
Sbjct: 194 LDVETKSSINPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALP--- 250

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +G
Sbjct: 251 -----IDDLDLTVRSYNCLKREGVHTVGELVSRTESDLLDIRNFGQKSIDEVKVKLHQLG 305

Query: 315 LFLGMNLPDWPPESI 329
           L L  +   + P  +
Sbjct: 306 LSLKDSPASFDPSQV 320


>gi|289641138|ref|ZP_06473306.1| DNA-directed RNA polymerase, alpha subunit [Frankia symbiont of
           Datisca glomerata]
 gi|289509079|gb|EFD30010.1| DNA-directed RNA polymerase, alpha subunit [Frankia symbiont of
           Datisca glomerata]
          Length = 350

 Score =  222 bits (565), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 121/302 (40%), Positives = 184/302 (60%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S++ GV ED+TD
Sbjct: 16  EFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFSTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           +ILN+K + +    D    + + K+GPGVVTA DI     +EV + D  +  L+    + 
Sbjct: 76  LILNLKELVVSSENDEPTVMYLRKQGPGVVTAADIAPPAGVEVHSLDLALATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D+L + 
Sbjct: 136 IELTVERGRGYVSAAQNKQPGQEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDRLIVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           ++T  SI+  D++A A + L    G+        + V    +         L   +EE++
Sbjct: 196 VETKQSISPRDAMASAGKTLVGLFGLAQELNAEAEGVDIGPSAADAALAADLALPIEEMD 255

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  L  M L L  + P +
Sbjct: 256 LTVRSYNCLKREGIHTIGELVSRSEADLLDIRNFGQKSIDEVKTKLAAMALQLKDSPPGF 315

Query: 325 PP 326
            P
Sbjct: 316 DP 317


>gi|328813953|gb|AEB52092.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 250

 Score =  222 bits (565), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 112/245 (45%), Positives = 166/245 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNI
Sbjct: 4   FVVEPLERGYGTTLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNI 63

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV
Sbjct: 64  KKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTV 123

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+G
Sbjct: 124 KKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNG 183

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI+  ++++LA++IL + L +F+N  +  K  +  +  +       L   +EEL+LSVRS
Sbjct: 184 SISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSVRS 243

Query: 270 TNCLR 274
            NCL+
Sbjct: 244 YNCLK 248


>gi|213962766|ref|ZP_03391026.1| DNA-directed RNA polymerase, alpha subunit [Capnocytophaga
           sputigena Capno]
 gi|213954423|gb|EEB65745.1| DNA-directed RNA polymerase, alpha subunit [Capnocytophaga
           sputigena Capno]
          Length = 330

 Score =  222 bits (565), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 120/298 (40%), Positives = 181/298 (60%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRV++SSL G AIT+V+ D V HE S+I GV ED+T+IILN+K + 
Sbjct: 28  PLEPGYGLTIGNALRRVMLSSLEGFAITSVKFDKVDHEFSTIPGVREDVTEIILNLKQVR 87

Query: 94  LKMSGD--SHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +    +  TI   G   +TAGD Q T++  +VLNPD VICN++  A   ME+T+ 
Sbjct: 88  FKRQVEDVEDETATITVSGKKQLTAGDFQKTLSGFQVLNPDLVICNMETSASFTMEITIE 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYV A+ +   N  IG+I  D++++PIK V YT+E+ R  Q  DY+KL   I TDGS
Sbjct: 148 KGRGYVSAEENAKPNAAIGVIATDSIFTPIKNVKYTIENYRVEQKTDYEKLVFEIKTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  + ++  A++ L     +F    I  E  +    +  + +SL     L  K+ +++LS
Sbjct: 208 IHPKQALTEAAKTLIHHFMLFSDERITLEADEVAQTDAYDEESLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   +AD+++  NFG+KSL+E+  ++   GL  GM+   +
Sbjct: 268 VRALNCLKAAEVETLGDLVSFNKADLMKFRNFGKKSLIELDELVANKGLVFGMDTSKY 325


>gi|73913591|gb|AAZ91712.1| RNA polymerase alpha subunit [Corynebacterium stationis]
          Length = 334

 Score =  222 bits (565), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 131/317 (41%), Positives = 192/317 (60%), Gaps = 23/317 (7%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           + +R+  I EPL  GF +T+GN++RR L+SS+ GAA+T+++I+GVLHE +++ GV ED++
Sbjct: 15  DSSRSRFIFEPLEPGFGYTIGNSMRRTLLSSIPGAAVTSIKIEGVLHEFTTVNGVKEDVS 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +IILN+K  +L +S DS + V ++  K GPG VTAGDIQ    +E+ NPD  I  L+  A
Sbjct: 75  EIILNVK--SLVLSSDSDEPVVMYLSKEGPGAVTAGDIQPPAGVEIHNPDLHIATLNDTA 132

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + MEL V +G GYVPA    T  D IG I ID +YSP+ KVSY VE+ R  Q  D+DKL
Sbjct: 133 KLDMELVVERGRGYVPAAP--TSGD-IGRIPIDQIYSPVLKVSYKVEATRVEQRTDFDKL 189

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEE--------PKKEVKEDINVKSLPFN 253
            + ++T  SI+  D++A A   L +  G+              P  +  E I   S+P  
Sbjct: 190 IIDVETKNSISARDALASAGGTLVELFGLARELNTAAEGIEIGPSPQESEYIAAYSMP-- 247

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +E+L  SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L  +
Sbjct: 248 ------IEDLNFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKIKLANL 301

Query: 314 GLFLGMNLPDWPPESIE 330
            L L     D+ P  +E
Sbjct: 302 NLALKDTPEDFDPTQLE 318


>gi|323436177|ref|ZP_01051163.2| DNA-directed RNA polymerase, alpha subunit [Dokdonia donghaensis
           MED134]
 gi|321496492|gb|EAQ37997.2| DNA-directed RNA polymerase, alpha subunit [Dokdonia donghaensis
           MED134]
 gi|332170585|gb|AEE19840.1| DNA-directed RNA polymerase, alpha subunit [Krokinobacter diaphorus
           4H-3-7-5]
          Length = 330

 Score =  222 bits (565), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 121/298 (40%), Positives = 186/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRVL+SSL G AIT+V+I+GV HE S++ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGYGLTVGNALRRVLLSSLEGFAITSVRIEGVDHEFSTLAGVVEDVTEIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   ++ VTI   G   +TAGD Q  ++  +VLNPD VI N+D    + ME+T+ 
Sbjct: 88  FKRQIEEIDNETVTISLSGVDQLTAGDFQKFISGFQVLNPDMVIANMDKKVNLNMEITIE 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++  N P+G I  D++Y+PI+ V Y++E+ R  Q  DY+KL   I TDGS
Sbjct: 148 KGRGYVPAEENKKSNAPLGTIFTDSIYTPIRNVKYSIENYRVEQKTDYEKLVFEIITDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  A++ L     +F    I  E  +    E  + +SL     L  K+ +++LS
Sbjct: 208 IHPKEALTEAAKTLIHHFMLFSDERITLEADEIAQTETYDEESLHMRQLLKTKLIDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   + D+++  NFG+KSL E++ ++   GL  GM+L  +
Sbjct: 268 VRALNCLKAAEVETLGDLVSYNKNDLMKFRNFGKKSLTELEELVNVKGLSFGMDLAKY 325


>gi|227499168|ref|ZP_03929303.1| DNA-directed RNA polymerase [Acidaminococcus sp. D21]
 gi|226904615|gb|EEH90533.1| DNA-directed RNA polymerase [Acidaminococcus sp. D21]
          Length = 323

 Score =  222 bits (565), Expect = 8e-56,   Method: Compositional matrix adjust.
 Identities = 124/295 (42%), Positives = 183/295 (62%), Gaps = 7/295 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL G A+T ++IDGVLHE S+I+GV ED+ DI+LNI
Sbjct: 23  FVWEPLERGYGITLGNSLRRVLLSSLSGMAVTGIKIDGVLHEFSTIEGVREDVADIVLNI 82

Query: 90  KGINLKMSGDSH-----KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           K +  K++ D       K   I K G G VT  DI T  D EVLNP+  I  LD +A + 
Sbjct: 83  KALCFKVNLDDQGTYEPKTFYIKKSGEGEVTGADIITDQDTEVLNPELHIATLDKNANLN 142

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           ME+ V  G GYV A  +++++ PIG I +D++YSPI +V + V   R G V +YD+L++ 
Sbjct: 143 MEIYVDIGRGYVSADKNKSKDQPIGFIPVDSIYSPITRVKFGVTDTRVGNVTNYDRLTLE 202

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV--KSLPFNPALLKKVEE 262
           + TDGS+  +++V  A+ IL + L +F     PK +  E+     +    +  L   +++
Sbjct: 203 VWTDGSLGPDEAVTSAAEILINYLALFKTTNVPKIQGSEESGKPDEEGTKSSVLQMSIDD 262

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+L+VRS NCLR   I  + D+I +TE +++ + N G KSL E+K  +  +GL L
Sbjct: 263 LDLTVRSNNCLRRAGINTVEDIINKTEDELICVRNLGSKSLEEVKNKIEELGLHL 317


>gi|162955838|gb|ABY25294.1| RNA polymerase alpha subunit [Vibrio sp. MSSRF28]
 gi|167077375|gb|ABZ10909.1| RNA polymerase alpha subunit [Vibrio sp. MSSRF2]
          Length = 256

 Score =  222 bits (565), Expect = 8e-56,   Method: Compositional matrix adjust.
 Identities = 118/253 (46%), Positives = 175/253 (69%), Gaps = 8/253 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 7   EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 66

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L D +A V M + V 
Sbjct: 67  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTDGNAEVAMRIKVQ 126

Query: 151 KGHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVP  A+ H  E+D PIG + +DA YSP+ K++YTVE+AR  Q  D DKL + ++T
Sbjct: 127 RGRGYVPASARIHTDEDDRPIGRLLVDATYSPVDKIAYTVEAARVEQRTDLDKLVIDMET 186

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G+I  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 187 NGTIEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 243

Query: 268 RSTNCLRGENIVY 280
           RS NCL+ E I Y
Sbjct: 244 RSANCLKAEAIHY 256


>gi|328814009|gb|AEB52120.1| DNA-directed RNA polymerase alpha chain [Lactobacillus rhamnosus]
          Length = 257

 Score =  222 bits (565), Expect = 8e-56,   Method: Compositional matrix adjust.
 Identities = 113/257 (43%), Positives = 171/257 (66%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED+T IILNIK
Sbjct: 1   VVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLEDVTQIILNIK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV 
Sbjct: 61  KLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVK 120

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GS
Sbjct: 121 KGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGS 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I+  ++++LA++IL + L +F+N  +  K  +  +  +       L   +EEL+LSVRS 
Sbjct: 181 ISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSVRSY 240

Query: 271 NCLRGENIVYMGDLIQR 287
           NCL+   I  + +L  +
Sbjct: 241 NCLKRAGINTVQELTNK 257


>gi|311111944|ref|YP_003983166.1| DNA-directed RNA polymerase subunit alpha [Rothia dentocariosa ATCC
           17931]
 gi|310943438|gb|ADP39732.1| DNA-directed RNA polymerase subunit alpha [Rothia dentocariosa ATCC
           17931]
          Length = 330

 Score =  222 bits (565), Expect = 8e-56,   Method: Compositional matrix adjust.
 Identities = 125/316 (39%), Positives = 194/316 (61%), Gaps = 9/316 (2%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           NR+    EPL  GF +T+GN+LRR L+SS+ GAA+T+V+IDGVLHE S++ GV ED+T+I
Sbjct: 17  NRSRFTIEPLEPGFGYTMGNSLRRTLLSSIPGAAVTSVRIDGVLHEFSTVPGVTEDVTEI 76

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           ILN+K +++    D      + K+G G +TA DI+    +E+ NP+  I  L+  A    
Sbjct: 77  ILNVKKLSISSENDEPVVAYLRKQGEGELTAADIEVPAGVEIHNPELHIATLNAKANFNA 136

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           EL + +G GYV A  ++T +  IG I +D++YSP+ KV+++V + R  Q  D+D L++ +
Sbjct: 137 ELIIERGRGYVSAAQNKTGDAEIGRIPVDSIYSPVLKVTFSVNATRVEQRTDFDSLTLDV 196

Query: 206 DTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
           +T  +I   D+VA A   L +  G+   +N      EV      +S+  + AL   +E+L
Sbjct: 197 ETKEAIAPRDAVASAGSTLVELFGLARELNVAAEGIEVGPSPADESMAADLAL--PIEDL 254

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            +SVRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L      LG+ L D
Sbjct: 255 NMSVRSYNCLKREGIHTVGELVTRSEADLMDIRNFGAKSIDEVKAKLHE----LGLALKD 310

Query: 324 WPPESIEELAKKYEDK 339
            PP   E +A+ Y+D+
Sbjct: 311 SPP-GFEPVARAYDDE 325


>gi|256826600|ref|YP_003150559.1| DNA-directed RNA polymerase subunit alpha [Cryptobacterium curtum
           DSM 15641]
 gi|256582743|gb|ACU93877.1| DNA-directed RNA polymerase subunit alpha [Cryptobacterium curtum
           DSM 15641]
          Length = 316

 Score =  221 bits (564), Expect = 8e-56,   Method: Compositional matrix adjust.
 Identities = 118/294 (40%), Positives = 185/294 (62%), Gaps = 6/294 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + +PL RG+ +TLGN +RRVL++SL GAA TA+QIDGV HE ++ +GV ED+TDI+LN+
Sbjct: 21  FVVDPLERGYGYTLGNTMRRVLLNSLDGAAATAIQIDGVQHEFATAEGVIEDITDIVLNV 80

Query: 90  KGINLKMSGDSHKRVT--IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           KG+   +  +     T  +   GP  VT  D+Q   +  ++NPDHVI  +     + M +
Sbjct: 81  KGLVFSVFAEDAIEATAHVSAEGPCTVTGADLQVPTEFTLVNPDHVIATVADGGQLDMTI 140

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            +  G GYV A+ ++   DPIG+I +D+L+SP+++ + +V   R GQ  DYDKL + ++T
Sbjct: 141 RIGVGRGYVVAERNKRNEDPIGIIHVDSLFSPVRRCALSVTDTRVGQSTDYDKLILEVET 200

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP----FNPALLKKVEEL 263
           DGS+T  D+V  A+ I+   +G F++  E ++E + ++     P     N  L K++E+L
Sbjct: 201 DGSLTPTDAVCQAANIVTQYMGAFLSLNESEEEEEGEVPSIFAPEGEETNAELDKQIEDL 260

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +LSVRS NCL+   I  +  L++ +E D+L + NFG KS+ E+K  L +MGL L
Sbjct: 261 DLSVRSYNCLKRAGIHSVRQLVEYSENDLLNIRNFGAKSIEEVKDKLISMGLNL 314


>gi|284049230|ref|YP_003399569.1| DNA-directed RNA polymerase, alpha subunit [Acidaminococcus
           fermentans DSM 20731]
 gi|283953451|gb|ADB48254.1| DNA-directed RNA polymerase, alpha subunit [Acidaminococcus
           fermentans DSM 20731]
          Length = 323

 Score =  221 bits (564), Expect = 8e-56,   Method: Compositional matrix adjust.
 Identities = 123/295 (41%), Positives = 182/295 (61%), Gaps = 7/295 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL G A+T ++IDGVLHE S+I+GV ED+ DI+LNI
Sbjct: 23  FVWEPLERGYGITLGNSLRRVLLSSLSGMAVTGIKIDGVLHEFSTIEGVREDVADIVLNI 82

Query: 90  KGINLKMSGDSH-----KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           K +  K+  D       K   I K G G VT  D+ T  D EVLNP+  I  LD +  + 
Sbjct: 83  KALCFKVGLDDQASFEPKTFYIKKAGEGEVTGADVITDQDTEVLNPELHIATLDKNGALN 142

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           ME+ V  G GYV A+ +++++ PIG I +D++YSPI +V + V   R G V +YD+L++ 
Sbjct: 143 MEIYVDVGRGYVQAEKNKSKDQPIGFIPVDSIYSPITRVKFGVTDTRVGNVTNYDRLTLE 202

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA--LLKKVEE 262
           + TDGS+  +++V  A+ IL   L +F     P+ +  ED    S   + +  L   +++
Sbjct: 203 VWTDGSLGPDEAVTSAAEILIKYLALFKTTNVPRIQGDEDGTKTSDEGSKSSVLQMSIDD 262

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+L+VRS NCLR   I  + D+I +TE +++ + N G KSL E+K  +  +GL L
Sbjct: 263 LDLTVRSNNCLRRAGINTVEDIINKTEDELICVRNLGSKSLEEVKNKIEELGLHL 317


>gi|15828059|ref|NP_302322.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium leprae TN]
 gi|221230536|ref|YP_002503952.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium leprae
           Br4923]
 gi|7388099|sp|Q9X798|RPOA_MYCLE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|4539112|emb|CAB39833.1| putative DNA-directed RNA polymerase alpha chain [Mycobacterium
           leprae]
 gi|13093612|emb|CAC30912.1| [alpha] subunit of RNA polymerase [Mycobacterium leprae]
 gi|219933643|emb|CAR72054.1| [alpha] subunit of RNA polymerase [Mycobacterium leprae Br4923]
          Length = 347

 Score =  221 bits (564), Expect = 8e-56,   Method: Compositional matrix adjust.
 Identities = 123/301 (40%), Positives = 187/301 (62%), Gaps = 16/301 (5%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T+
Sbjct: 16  DNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ +    D    + + K+GPG VTAGDI     + + NP   I  L+    + 
Sbjct: 76  IILNLKGLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTLHNPGMRIATLNDKGKIE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
            EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL + 
Sbjct: 136 AELVVERGRGYVPAVQNRALGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLILD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNPAL 256
           ++T  SIT  D++A A + L +  G+   +N E       P     + I   +LP     
Sbjct: 196 VETKSSITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALP----- 250

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL 
Sbjct: 251 ---IDDLDLTVRSYNCLKREGVHTVGELVSRTESDLLDIRNFGQKSIDEVKVKLHQLGLS 307

Query: 317 L 317
           L
Sbjct: 308 L 308


>gi|269784256|emb|CBH50773.1| alpha subunit of RNA polymerase [Vibrio sp. Rd 6.8]
 gi|269784258|emb|CBH50774.1| alpha subunit of RNA polymerase [Vibrio sp. Rd2L5]
 gi|269784260|emb|CBH50775.1| alpha subunit of RNA polymerase [Vibrio sp. Rd 16.13]
          Length = 268

 Score =  221 bits (564), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 116/267 (43%), Positives = 177/267 (66%), Gaps = 8/267 (2%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVT 115
           G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V 
Sbjct: 3   GCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVV 62

Query: 116 AGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLI 171
           AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG +
Sbjct: 63  AGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRL 122

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F
Sbjct: 123 LVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAF 182

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           ++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE +
Sbjct: 183 VDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVE 239

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLG 318
           +L+  N G+KSL EIK VL + GL L 
Sbjct: 240 LLKTPNLGKKSLTEIKDVLASRGLSLA 266


>gi|289524822|emb|CBJ94467.1| alpha subunit of RNA polymerase [Vibrio sp. Cmf 5.9]
          Length = 265

 Score =  221 bits (564), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 116/266 (43%), Positives = 177/266 (66%), Gaps = 8/266 (3%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVT 115
           G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V 
Sbjct: 3   GCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVV 62

Query: 116 AGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLI 171
           AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG +
Sbjct: 63  AGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRL 122

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F
Sbjct: 123 LVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAF 182

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           ++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE +
Sbjct: 183 VDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVE 239

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFL 317
           +L+  N G+KSL EIK VL + GL L
Sbjct: 240 LLKTPNLGKKSLTEIKDVLASRGLSL 265


>gi|269122553|ref|YP_003310730.1| DNA-directed RNA polymerase, subunit alpha [Sebaldella termitidis
           ATCC 33386]
 gi|268616431|gb|ACZ10799.1| DNA-directed RNA polymerase, alpha subunit [Sebaldella termitidis
           ATCC 33386]
          Length = 321

 Score =  221 bits (564), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 123/292 (42%), Positives = 184/292 (63%), Gaps = 4/292 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  T+GNALRRVL+SS+ G+AI  V+IDGVL+E S+I+GV E +TDIILNIK I
Sbjct: 28  EPLYRGYGATIGNALRRVLLSSIPGSAIKGVKIDGVLNEFSTIEGVKEAVTDIILNIKEI 87

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            ++      K++++  +GP  +TA DI     ++++NPD VI  +     + ME  V  G
Sbjct: 88  VVESDEPGEKKMSLSVKGPREITARDIILEPGLKIINPDQVIATITTKREINMEFLVDSG 147

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            G+V ++   TEN PIG I +DA+Y+PIKK+SY+VE    G+  DYDKL++ I TDGSI 
Sbjct: 148 EGFVVSEEIETENWPIGYIAVDAIYTPIKKISYSVEDTMVGRATDYDKLTLDITTDGSIE 207

Query: 213 GEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
             D+++ A  ++   L  F N     E+ + E + + +++ +  N     K+EEL+ +VR
Sbjct: 208 IRDALSYAVELISFHLNPFTNIGNSMEKFRSEDEVESSIEVISENNMDDMKIEELDFTVR 267

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           S NCL+   +  +GDL + T A++L++ N GRKSL EI   +  +G  L  N
Sbjct: 268 SYNCLKKAGVNTIGDLGKMTYAELLKIKNLGRKSLNEIIDKMKELGFDLNDN 319


>gi|317503954|ref|ZP_07961962.1| DNA-directed RNA polymerase subunit alpha [Prevotella salivae DSM
           15606]
 gi|315664980|gb|EFV04639.1| DNA-directed RNA polymerase subunit alpha [Prevotella salivae DSM
           15606]
          Length = 330

 Score =  221 bits (563), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 118/298 (39%), Positives = 186/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AI  ++I GV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGVTIGNALRRILLSSLEGYAINTIRIAGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   +++V+I         AGDI + +   EVLNPD VIC+LD  A ++++LT++
Sbjct: 88  FKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGFEVLNPDLVICHLDAKASMQIDLTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GY+PA  +R     + +I ID++Y+PI+ V Y+VE  R  Q  DYDKL + + TDGS
Sbjct: 148 KGRGYIPADENREFCTDVNVIPIDSIYTPIRNVKYSVEPYRVEQKTDYDKLVIEVSTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++IL     +F    I  E P ++  ++ + + L     L  ++ ++ LS
Sbjct: 208 IHPKDALKEAAKILIYHFMLFSDEKITLESPDQDGNQEFDEEVLHMRQLLKTRLVDMNLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKKSLSELDDLLESLNLSFGTDISKY 325


>gi|323344663|ref|ZP_08084887.1| DNA-directed RNA polymerase subunit alpha [Prevotella oralis ATCC
           33269]
 gi|323093933|gb|EFZ36510.1| DNA-directed RNA polymerase subunit alpha [Prevotella oralis ATCC
           33269]
          Length = 330

 Score =  221 bits (563), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 119/298 (39%), Positives = 186/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AI  ++I GV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGVTIGNALRRILLSSLEGYAINTIRIGGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   +++V+I         AGDI + +   EVLNPD VIC+LDV A +++++T++
Sbjct: 88  FKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGFEVLNPDLVICHLDVKASMQIDITIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + ++ ID++Y+PI+ V Y+VE  R  Q  DYDKL + + TDGS
Sbjct: 148 KGRGYVPADENREFCTDVNVLPIDSIYTPIRNVKYSVEPYRVEQKTDYDKLVLEVTTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++IL     +F    I  E   +E  ++ + + L     L  K+ ++ LS
Sbjct: 208 IYPKDALKEAAKILIYHFMLFSDEKITLESSDQENNQEFDEEVLHMRQLLKTKLIDMNLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKKSLSELDDLLESLNLSFGTDISKY 325


>gi|229815743|ref|ZP_04446068.1| hypothetical protein COLINT_02792 [Collinsella intestinalis DSM
           13280]
 gi|229808659|gb|EEP44436.1| hypothetical protein COLINT_02792 [Collinsella intestinalis DSM
           13280]
          Length = 313

 Score =  221 bits (563), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 119/288 (41%), Positives = 182/288 (63%), Gaps = 3/288 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+ A+QIDG  HE ++I  + ED+TDI+LN+KG+
Sbjct: 24  EPLERGYGDTLGNSLRRVLLSSLEGAAVEAIQIDGAQHEFTTIPNMVEDVTDIVLNVKGL 83

Query: 93  NLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
             +  G + +   TI   GP  VT  D    ++ E++NPD  I  L     + M + +  
Sbjct: 84  VFRTLGTTDEGTATISVDGPCEVTGADFFIPSEFELVNPDQHIATLTEGGHLTMSMRIGY 143

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GYV  + ++ +NDPIG+I +D+L+SP+K+ +  VE+ R GQ  DYD+L + I+T+G+I
Sbjct: 144 GRGYVSYEQNKRDNDPIGIIHVDSLFSPVKRCAKLVEACRVGQHTDYDRLVLEIETNGAI 203

Query: 212 TGEDSVALASRILQDQLGMFINF-EEPKKEVKEDINVKSLPF-NPALLKKVEELELSVRS 269
           +  D+V  A+ I+   +  F+   +EP+ E +  I    +   N  L K++E+L+LSVRS
Sbjct: 204 SPRDAVVSAANIINQHMAAFMTLADEPEAEEEVSIFAPEVTSDNAELDKQIEDLDLSVRS 263

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   I  +  L++ +E D+L + NFG KS+ E+K  L +MGL L
Sbjct: 264 YNCLKRAGIHSVRQLVEFSENDLLNIRNFGVKSIEEVKDKLESMGLSL 311


>gi|270284452|ref|ZP_05966137.2| DNA-directed RNA polymerase, alpha subunit [Bifidobacterium
           gallicum DSM 20093]
 gi|270276907|gb|EFA22761.1| DNA-directed RNA polymerase, alpha subunit [Bifidobacterium
           gallicum DSM 20093]
          Length = 351

 Score =  221 bits (562), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 124/294 (42%), Positives = 182/294 (61%), Gaps = 4/294 (1%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
            R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ GV ED+T+I
Sbjct: 37  QRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTALPGVEEDVTEI 96

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           +LNIKGI L    D    + + K G G  TAGDI     I + NP+  I +L  D  + +
Sbjct: 97  LLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGITIANPEMHIASLAEDGELEI 156

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           E TV +G GYVPA+ ++ ++D IG I +D++YSP+ KVSY VE+ R  Q  D+DKL + +
Sbjct: 157 EFTVERGRGYVPAQMNKQDSDEIGRIPVDSIYSPVLKVSYKVEATRVEQRTDFDKLILDV 216

Query: 206 DTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
           +T  +I+  D+VA A   L +  G+   +N +    EV     V+    NP L   +E+L
Sbjct: 217 ETKPAISPRDAVASAGSTLVELFGLCRELNMQAEGVEVGPAPVVEET--NPELAVPIEDL 274

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            L+ RS NCL+ E I  +G+L+   E D+L + NFG KS+ E+K  L ++GL L
Sbjct: 275 NLTQRSYNCLKREGIHTVGELVAHNEQDLLDIRNFGMKSIDEVKEKLQSLGLSL 328


>gi|139438878|ref|ZP_01772338.1| Hypothetical protein COLAER_01342 [Collinsella aerofaciens ATCC
           25986]
 gi|133775589|gb|EBA39409.1| Hypothetical protein COLAER_01342 [Collinsella aerofaciens ATCC
           25986]
          Length = 313

 Score =  221 bits (562), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 126/317 (39%), Positives = 191/317 (60%), Gaps = 11/317 (3%)

Query: 6   WQELIKPN-NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
             E I+P   +E I      E    +  EPL RG+  TLGN+LRRVL+SSL GAA+ A+Q
Sbjct: 1   MSEFIRPQVQVEEI-----NETSARVSVEPLERGYGDTLGNSLRRVLLSSLEGAAVEAIQ 55

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVN 123
           IDG  HE  +I  + ED+TDI+LN+KG+  +  G + +   TI   GP  VT  D    +
Sbjct: 56  IDGAQHEFMTIPNMVEDVTDIVLNVKGLVFRALGTTDEATATISVDGPCEVTGADFFIPS 115

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           + E++NP+  I  L     + M + +  G GYV  + ++ +NDPIG+I +D+LYSP+ + 
Sbjct: 116 EFELVNPEQHIATLTEGGHLTMSMRIGYGRGYVSGEANKRDNDPIGVIHVDSLYSPVSRC 175

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +  VE+ R GQ  DYD+L + I+T+GSI   D+V  A+ I+   +  F+N  E   EV+E
Sbjct: 176 AKLVEACRVGQHTDYDRLVLEIETNGSIAPRDAVVQAANIINQHMAAFMNLAE-TPEVEE 234

Query: 244 DINVKSLPF---NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           + ++ +      N  L K++E+L+LSVRS NCL+  +I  +  L++ +E D+L + NFG 
Sbjct: 235 EASIFAPEVTNDNAELDKQIEDLDLSVRSYNCLKRASIHSVRQLVEFSENDLLNIRNFGV 294

Query: 301 KSLVEIKGVLGTMGLFL 317
           KS+ E+K  L +MGL L
Sbjct: 295 KSIEEVKDKLESMGLSL 311


>gi|153805983|ref|ZP_01958651.1| hypothetical protein BACCAC_00228 [Bacteroides caccae ATCC 43185]
 gi|149130660|gb|EDM21866.1| hypothetical protein BACCAC_00228 [Bacteroides caccae ATCC 43185]
          Length = 330

 Score =  221 bits (562), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 119/298 (39%), Positives = 187/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AIT ++IDGV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGITVGNALRRILLSSLEGFAITTIRIDGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDSHK--RVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +  +  +V+I         AGDI + +   EVLNP+ VIC+LD  A +++++T++
Sbjct: 88  FKQVVEEFESEKVSITVENSSEFKAGDIGKYLTGFEVLNPELVICHLDSKATMQIDITIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y+VE+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKYSVENFRVEQKTDYEKLVLEISTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  A++IL     +F    I  E    +  E+ + + L     L  K+ +++LS
Sbjct: 208 IHPKEALKEAAKILIYHFMLFSDEKITLESNDTDGNEEFDEEVLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKKSLTELDDLLESLNLSFGTDISKY 325


>gi|168701504|ref|ZP_02733781.1| DNA-directed RNA polymerase subunit alpha [Gemmata obscuriglobus
           UQM 2246]
          Length = 336

 Score =  221 bits (562), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 122/303 (40%), Positives = 181/303 (59%), Gaps = 12/303 (3%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
           AEP  +GF  T+GN+LRR+L+SSL G+AIT V+I GV HEIS+I GV ED+TDIILN+K 
Sbjct: 30  AEPFEKGFGMTIGNSLRRILLSSLEGSAITRVKIQGVQHEISTITGVVEDVTDIILNVKS 89

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           + +K   D  K + I K   G V   D+Q    I+++NP+H I  L  D    ME+TV  
Sbjct: 90  LVVKNLSDQPKTIRIQKHEAGAVRGVDVQHDETIQIINPEHHIATLTSDVPFVMEMTVEN 149

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GY  A  +  ++  +G+I +D+ +SP+ +V Y +E  R GQ  +YD+L M I T+G++
Sbjct: 150 GRGYRTADDNAGKDREVGVIPVDSSFSPVVRVKYDIEETRVGQKTNYDRLVMEIWTNGTL 209

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK------------ 259
             + ++  A++IL+  L  F+ + EP  E++ D     +  N ++  +            
Sbjct: 210 APQMAIVEAAKILRKHLNPFVQYTEPGPELQLDDGPIEIGPNASVRDQQDAELERKLNMS 269

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           + EL+LSVR+TNCL  E I  + DL+ RT  ++L + NFG  +L E+K  L   GL LGM
Sbjct: 270 LAELDLSVRATNCLETEGIQTVRDLVIRTSEELLEVRNFGETTLREVKSKLEERGLALGM 329

Query: 320 NLP 322
            LP
Sbjct: 330 RLP 332


>gi|269218963|ref|ZP_06162817.1| DNA-directed RNA polymerase, alpha subunit [Actinomyces sp. oral
           taxon 848 str. F0332]
 gi|269212074|gb|EEZ78414.1| DNA-directed RNA polymerase, alpha subunit [Actinomyces sp. oral
           taxon 848 str. F0332]
          Length = 334

 Score =  221 bits (562), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 125/290 (43%), Positives = 178/290 (61%), Gaps = 8/290 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           Q  E R+  I EPL  GF +TLGN++RR L+SS+ GAA+T+V+IDGVLHE S+I GV ED
Sbjct: 13  QVSEYRSRFILEPLEPGFGYTLGNSMRRTLLSSIPGAAVTSVRIDGVLHEFSTIAGVKED 72

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DIILN+K + +    D    + + K+GPG VTA DI     +E+ NPD  I  L+   
Sbjct: 73  VADIILNLKELVVSSENDEPVLMYLHKQGPGEVTAADITPPAGVEIHNPDLHIATLNDKG 132

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ++LTV +G GYV A  ++ E D IG I ID++YSP+ KVSY VE+ R  Q  D+DKL
Sbjct: 133 KIEIDLTVERGRGYVSAAQNKGEEDEIGRIPIDSIYSPVLKVSYKVEATRVAQRTDFDKL 192

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF----NPALL 257
            + ++   S T  D++A A + L +  G+ +       EV E I +   P     +  L 
Sbjct: 193 VVDVEVKPSTTPRDALASAGKTLVELFGLCVEL---NNEV-EGIELGPPPVVETQSSDLQ 248

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +  L L  RS NCL+ E I  +G+LIQR+EAD+L + NFG KS+ ++K
Sbjct: 249 RPITILNLPARSQNCLQREGIRTIGELIQRSEADLLDIRNFGAKSIEDVK 298


>gi|297625818|ref|YP_003687581.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           (Transcriptase alpha chain) (RNA polymerase subunit
           alpha) [Propionibacterium freudenreichii subsp.
           shermanii CIRM-BIA1]
 gi|296921583|emb|CBL56137.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           (Transcriptase alpha chain) (RNA polymerase subunit
           alpha) [Propionibacterium freudenreichii subsp.
           shermanii CIRM-BIA1]
          Length = 339

 Score =  221 bits (562), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 130/315 (41%), Positives = 190/315 (60%), Gaps = 7/315 (2%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
           R+  + EPL  GF +TLGN+LRR L+SS+ GA+IT+++I+G  HE S++ GV ED+T+II
Sbjct: 18  RSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASITSIKIEGNQHEFSTLPGVVEDVTEII 77

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+KG+ L    D    + + K G G VTA DI     +E+ NPD  I  L  D  + ME
Sbjct: 78  LNLKGLVLSSEEDEPVAMYLRKSGAGEVTAADIAVPTGVEIYNPDLHIATLADDGSIEME 137

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           L V +G GYV +  +   +  IG I +D+LYSP+  VSY VE+ R     D+D+L + ++
Sbjct: 138 LVVERGRGYVSSTLNNNPDAEIGRIAVDSLYSPVLTVSYKVEATRVETRTDFDRLIVDVE 197

Query: 207 TDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           T  SI   D+VA A + L +  G+F  +N E    E+      + L  + AL   VE+L 
Sbjct: 198 TKPSIRPHDAVASAGKTLVELFGLFRELNVEAEGVEMGPSPVDEQLAADMAL--PVEDLN 255

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           LSVRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  LG +GL L  + P +
Sbjct: 256 LSVRSYNCLKREGIHTVGELVSRSEQDLLDIRNFGSKSIDEVKEKLGDLGLTLKDSTPGF 315

Query: 325 PPESIEELAKKYEDK 339
            P +    A ++ED+
Sbjct: 316 DPLAA---ADRFEDE 327


>gi|256831853|ref|YP_003160580.1| DNA-directed RNA polymerase, alpha subunit [Jonesia denitrificans
           DSM 20603]
 gi|256685384|gb|ACV08277.1| DNA-directed RNA polymerase, alpha subunit [Jonesia denitrificans
           DSM 20603]
          Length = 334

 Score =  220 bits (561), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 130/310 (41%), Positives = 194/310 (62%), Gaps = 16/310 (5%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
           R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S+I GV ED+T+II
Sbjct: 18  RSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFSTITGVKEDVTEII 77

Query: 87  LNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           LN+K  NL +S ++ + V ++  K+G GVVTA DI     +EV NPD  I  L+    + 
Sbjct: 78  LNVK--NLVLSSENDEPVVMYLRKQGAGVVTAADIVPPAGVEVHNPDLHIATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELTV +G GYV A+ +++ +  IG I +D++YSP+ KV+Y VE+ R  Q  D+D+L + 
Sbjct: 136 IELTVERGRGYVSAQQNKSMDAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDRLIVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLP----FNPALLK 258
           ++T  SI   D++A A + L +  G+   +N E       E I +   P        L  
Sbjct: 196 VETKSSIVPRDALASAGKTLVELFGLARELNVE------AEGIEIGPSPTDAALAADLAL 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L L++RS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  +GL L 
Sbjct: 250 PIEDLNLTIRSYNCLKREGIHQVGELVARSEADLLDIRNFGAKSINEVKEKLHELGLSLK 309

Query: 319 MNLPDWPPES 328
            +  D+ P S
Sbjct: 310 DSPLDFQPSS 319


>gi|281422225|ref|ZP_06253224.1| DNA-directed RNA polymerase, alpha subunit [Prevotella copri DSM
           18205]
 gi|281403730|gb|EFB34410.1| DNA-directed RNA polymerase, alpha subunit [Prevotella copri DSM
           18205]
          Length = 331

 Score =  220 bits (561), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 118/298 (39%), Positives = 185/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G A+  ++I GV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGVTIGNALRRILLSSLEGYAVNTIRIAGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   +++V+I         AGDI + +   EVLNPD VIC+LD  A ++++LT++
Sbjct: 88  FKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGFEVLNPDLVICHLDAKASMQIDLTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + ++ ID++Y+PI+ V Y VE  R  Q  DYDKL + I TDGS
Sbjct: 148 KGRGYVPADENRQFCTDVNVLPIDSIYTPIRNVKYAVEPYRVEQKTDYDKLVLEITTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I+ +D++  A++IL     +F    I  E   +E  ++ + + L     L  ++ ++ LS
Sbjct: 208 ISPKDALKEAAKILIYHFMLFSDEKITLETQDQESNQEFDEEVLHMRQLLKTRLVDMNLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKKSLSELDDLLESLNLSFGTDISKY 325


>gi|325955023|ref|YP_004238683.1| DNA-directed RNA polymerase subunit alpha [Weeksella virosa DSM
           16922]
 gi|323437641|gb|ADX68105.1| DNA-directed RNA polymerase subunit alpha [Weeksella virosa DSM
           16922]
          Length = 330

 Score =  220 bits (561), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 120/298 (40%), Positives = 186/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRVL+SSL G AIT+++I+GV HE S+I GV ED+T+IILN+K + 
Sbjct: 28  PLEPGYGITVGNALRRVLLSSLEGYAITSIKIEGVEHEFSTIPGVVEDVTEIILNLKKVR 87

Query: 94  LKMSGDSH--KRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   D    + VT    G   +TAGD+ + ++  +VLNP+ VI NLD    + +  T+ 
Sbjct: 88  FKKQIDESDAENVTATISGQDQLTAGDLGKFISGFQVLNPELVIANLDSKVNLTISFTIE 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++  + PIG I ID++Y+PIK V Y +E+ R  Q  DY+KL   I TDGS
Sbjct: 148 KGRGYVPAEENKKASAPIGTIAIDSIYTPIKNVKYAIENYRVEQKTDYEKLVFEITTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I+ +D++  A++IL     +F    I  E  +    E  + ++L     L  K+ +L+LS
Sbjct: 208 ISPQDALTEAAKILIHHFMLFSDERITLEAEEVASGEAYDEEALHMRQLLKTKLVDLDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +G+L+   ++D+++  NFG+KSL E++ ++ + GL  GM+   +
Sbjct: 268 VRALNCLKAAEVETLGELVSFAKSDLMKFRNFGKKSLSELEELVDSKGLSFGMDTSKY 325


>gi|294674744|ref|YP_003575360.1| DNA-directed RNA polymerase subunit alpha [Prevotella ruminicola
           23]
 gi|294472989|gb|ADE82378.1| DNA-directed RNA polymerase, alpha subunit [Prevotella ruminicola
           23]
          Length = 330

 Score =  220 bits (561), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 118/298 (39%), Positives = 186/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AI  ++I GV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGVTIGNALRRILLSSLEGYAINTIRIAGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K  +    +++V+I         AGDI + ++  EVLNPD VIC+LD  A +++++T++
Sbjct: 88  FKQIVEEFENEKVSITVENSTEFKAGDISKYLSGFEVLNPDLVICHLDSKASMQIDITIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y VE  R  Q  DYDKL + + TDGS
Sbjct: 148 KGRGYVPADENREFCTDVNVIAIDSIYTPIRNVKYAVEPYRVEQKTDYDKLVLEVTTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++IL     +F    I+ E  + E  ++ + + L     L  ++ ++ LS
Sbjct: 208 IHPKDALKEAAKILIYHFMLFSDEKISLESSETESNQEFDEEILHMRQLLKTRLVDMNLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKKSLTELDDLLESLNLSFGTDISKY 325


>gi|29348110|ref|NP_811613.1| DNA-directed RNA polymerase subunit alpha [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|253569618|ref|ZP_04847028.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. 1_1_6]
 gi|298386206|ref|ZP_06995763.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 1_1_14]
 gi|41688697|sp|Q8A4A2|RPOA_BACTN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|29340013|gb|AAO77807.1| DNA-directed RNA polymerase alpha chain [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|251841637|gb|EES69718.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. 1_1_6]
 gi|298261434|gb|EFI04301.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 1_1_14]
          Length = 330

 Score =  220 bits (561), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 119/298 (39%), Positives = 186/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AIT ++IDGV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGITVGNALRRILLSSLEGFAITTIRIDGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDSHK--RVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +  +  +V+I         AGDI + +   EVLNP+ VIC+LD  A +++++T++
Sbjct: 88  FKQVVEEFESEKVSITVENSSEFKAGDIGKYLTGFEVLNPELVICHLDSKATMQIDITIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y VE+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKYAVENFRVEQKTDYEKLVLEISTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  A++IL     +F    I  E    +  E+ + + L     L  K+ +++LS
Sbjct: 208 IHPKEALKEAAKILIYHFMLFSDEKITLESNDTDGNEEFDEEVLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKKSLTELDDLLESLNLSFGTDISKY 325


>gi|223983946|ref|ZP_03634106.1| hypothetical protein HOLDEFILI_01387 [Holdemania filiformis DSM
           12042]
 gi|223964138|gb|EEF68490.1| hypothetical protein HOLDEFILI_01387 [Holdemania filiformis DSM
           12042]
          Length = 321

 Score =  220 bits (561), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 128/300 (42%), Positives = 186/300 (62%), Gaps = 9/300 (3%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E ++    + EPL RGF  TLGNALRRVL+SSL GAA+ +++++GV HE +SI GV ED+
Sbjct: 18  ESDHYGKFVVEPLERGFGTTLGNALRRVLLSSLPGAAVYSIKVEGVYHEFTSIPGVEEDV 77

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T +ILNIK + +K+  D    + I  +GP  VTAGDI     +EVLN D  I +L+  A 
Sbjct: 78  TMMILNIKNLIMKIDDDESYTLRIAAKGPMTVTAGDIICPTGVEVLNKDLEIAHLEEGAT 137

Query: 143 VRMELTVSKGHGYVPAKHHRT----ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
           + MEL    G GY+ A  ++      +  IG +  D++Y+PI ++SY VE  R GQ   Y
Sbjct: 138 LEMELKARNGRGYISADGNKALYQGSSQGIGTVYTDSIYTPIDRISYNVEPTRVGQDAKY 197

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP---KKEVKEDINVKSLPFNPA 255
           D+L   I T+GSIT + S+AL S+IL D L +  +  E     + V +D+N +S P N  
Sbjct: 198 DRLIFEIWTNGSITPQMSLALGSKILIDHLDLLTHVNESVADMESVMKDVNGES-PKNMQ 256

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
            +  +E+L+LSVRS NCL+   I  + +L QR+E +M+R+ N G+KSL E+K  +  +GL
Sbjct: 257 SM-AIEDLDLSVRSYNCLKRAGIQTVEELTQRSEEEMMRVRNLGKKSLKEVKDKIYELGL 315


>gi|289524816|emb|CBJ94464.1| alpha subunit of RNA polymerase [Vibrio sp. Rd 14.3]
 gi|289524826|emb|CBJ94469.1| alpha subunit of RNA polymerase [Vibrio sp. Cmf 11.16]
          Length = 267

 Score =  220 bits (560), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 116/268 (43%), Positives = 177/268 (66%), Gaps = 8/268 (2%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVT 115
           G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V 
Sbjct: 3   GCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVV 62

Query: 116 AGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLI 171
           AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG +
Sbjct: 63  AGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRL 122

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F
Sbjct: 123 LVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAF 182

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           ++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE +
Sbjct: 183 VDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVE 239

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +L+  N G+KSL EIK V  + GL L M
Sbjct: 240 LLKTPNLGKKSLTEIKDVHASRGLSLRM 267


>gi|227487074|ref|ZP_03917390.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           glucuronolyticum ATCC 51867]
 gi|227541762|ref|ZP_03971811.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           glucuronolyticum ATCC 51866]
 gi|227093148|gb|EEI28460.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           glucuronolyticum ATCC 51867]
 gi|227182468|gb|EEI63440.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           glucuronolyticum ATCC 51866]
          Length = 338

 Score =  220 bits (560), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 131/312 (41%), Positives = 190/312 (60%), Gaps = 17/312 (5%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
           R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV ED++DI+
Sbjct: 18  RSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTITGVKEDVSDIV 77

Query: 87  LNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           LN+KGI L  S DS + V ++  K G G V AGDIQ    +E+ NPD  +  L+ D  + 
Sbjct: 78  LNVKGIVL--SSDSDEPVVMYLNKEGAGEVKAGDIQPPAGVEIHNPDLHLATLNDDGRLN 135

Query: 145 MELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           MEL V +G GYVPA  +   ND   IG I +D +YSP+ KVSY VE+ R  Q  D+DKL 
Sbjct: 136 MELVVERGRGYVPAAMN---NDVAEIGRIPVDQIYSPVLKVSYKVEATRVEQRTDFDKLV 192

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF----NPALLK 258
           + ++T  SIT  D++A A + L +  G+            E I + + P       +   
Sbjct: 193 IDVETKNSITARDAMASAGKTLVELFGLAREL----NTAAEGIEIGASPLEGDHTASYSM 248

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L+ SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L  +GL L 
Sbjct: 249 PIEDLDFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKVKLAGLGLTLK 308

Query: 319 MNLPDWPPESIE 330
               D+   ++E
Sbjct: 309 DAPEDFDVTTVE 320


>gi|283457576|ref|YP_003362159.1| DNA-directed RNA polymerase subunit alpha [Rothia mucilaginosa
           DY-18]
 gi|283133574|dbj|BAI64339.1| DNA-directed RNA polymerase, alpha subunit [Rothia mucilaginosa
           DY-18]
          Length = 330

 Score =  220 bits (560), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 124/316 (39%), Positives = 193/316 (61%), Gaps = 9/316 (2%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           NR+    EPL  GF +T+GN+LRR L+SS+ GAA+T+V+IDGVLHE S++ GV ED+T+I
Sbjct: 17  NRSRFTIEPLEPGFGYTMGNSLRRTLLSSIPGAAVTSVRIDGVLHEFSTVPGVTEDVTEI 76

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           ILNIK +++    D      + K+G G +TAGDI+    +E+ NP+  +  L+  A    
Sbjct: 77  ILNIKKLSISSENDEPVVAYLRKQGEGELTAGDIEVPAGVEIHNPELHLATLNASANFNA 136

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           EL + +G GYV A  ++  +  IG I +D++YSP+ KV+++V + R  Q  D+D L++ +
Sbjct: 137 ELVIERGRGYVTAAQNKAGDSEIGRIPVDSIYSPVLKVTFSVNATRVEQRTDFDSLTLDV 196

Query: 206 DTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
           +T  +I   D+VA A   L +  G+   +N      EV      +S+  + AL   +E+L
Sbjct: 197 ETKEAIAPRDAVASAGSTLVELFGLARELNIAAEGIEVGPSPADESMAADLAL--PIEDL 254

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            +SVRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L      LG++L D
Sbjct: 255 NMSVRSYNCLKREGIHTVGELVTRSEADLMDIRNFGAKSIDEVKAKLTE----LGLSLKD 310

Query: 324 WPPESIEELAKKYEDK 339
            PP   E  A+  +D+
Sbjct: 311 SPP-GFEPAARPLDDE 325


>gi|269796227|ref|YP_003315682.1| DNA-directed RNA polymerase subunit alpha [Sanguibacter keddieii
           DSM 10542]
 gi|269098412|gb|ACZ22848.1| DNA-directed RNA polymerase subunit alpha [Sanguibacter keddieii
           DSM 10542]
          Length = 334

 Score =  219 bits (559), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 127/310 (40%), Positives = 197/310 (63%), Gaps = 16/310 (5%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E+R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T+
Sbjct: 16  ESRSRFSIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILN+K  NL +S ++ + V ++  K+G GVVTA DI     +EV NPD  I  L+    
Sbjct: 76  IILNVK--NLVVSSENDEPVVMYLRKQGSGVVTAADIVPPAGVEVHNPDLHIATLNDKGK 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +ELTV +G GYV A+ +++ +  IG + +D++YSP+ KV+Y VE+ R  Q  D+DKL 
Sbjct: 134 LEIELTVERGRGYVSAQQNKSFDAEIGRVPVDSIYSPVLKVTYKVEATRVEQRTDFDKLI 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLP----FNPAL 256
           + ++T  +I+  D++A A + L +  G+   +N E       E I +   P        L
Sbjct: 194 VDVETKQAISPRDALASAGKTLVELFGLARELNVE------AEGIEIGPSPTDAALAADL 247

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E+L+L++RS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  +GL 
Sbjct: 248 ALPIEDLQLTIRSYNCLKREGIHAVGELVARSEADLLDIRNFGAKSINEVKDKLAELGLS 307

Query: 317 LGMNLPDWPP 326
           L  +  D+ P
Sbjct: 308 LKDSPLDFDP 317


>gi|183601970|ref|ZP_02963339.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium animalis
           subsp. lactis HN019]
 gi|219682882|ref|YP_002469265.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium animalis
           subsp. lactis AD011]
 gi|241190459|ref|YP_002967853.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium animalis
           subsp. lactis Bl-04]
 gi|241195865|ref|YP_002969420.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium animalis
           subsp. lactis DSM 10140]
 gi|183218855|gb|EDT89497.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium animalis
           subsp. lactis HN019]
 gi|219620532|gb|ACL28689.1| DNA-directed RNA polymerase, alpha subunit [Bifidobacterium
           animalis subsp. lactis AD011]
 gi|240248851|gb|ACS45791.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium animalis
           subsp. lactis Bl-04]
 gi|240250419|gb|ACS47358.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium animalis
           subsp. lactis DSM 10140]
 gi|289178183|gb|ADC85429.1| DNA-directed RNA polymerase alpha chain [Bifidobacterium animalis
           subsp. lactis BB-12]
 gi|295793446|gb|ADG32981.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium animalis
           subsp. lactis V9]
          Length = 331

 Score =  219 bits (559), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 120/292 (41%), Positives = 178/292 (60%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
            R+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ G+ ED+T+I
Sbjct: 17  QRSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTTLPGIEEDVTEI 76

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           +LNIKGI L    D    + + K G G  TAGDI     + + NPD  I  L  D  + +
Sbjct: 77  LLNIKGIVLTSEYDEPVVMYLRKAGSGEATAGDITPPAGVTIANPDLHIATLAEDGELEI 136

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           E TV +G GYVPA+ ++ + D IG I +D++YSP+ KVSY VE+ R  Q  D+DKL + +
Sbjct: 137 EFTVERGRGYVPAQMNKQDGDEIGRIPVDSIYSPVLKVSYKVEATRVEQRTDFDKLILDV 196

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
           +T  +I+  D+VA A   L +  G+        + V+      +   +P +   +E+L L
Sbjct: 197 ETKPAISPRDAVASAGSTLVELFGLCRELNTQAEGVEIGPAPVAEQADPGMSVPIEDLNL 256

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L ++GL L
Sbjct: 257 TQRSYNCLKREGIHTVGELVNHTEQDLLDIRNFGMKSIDEVKEKLQSLGLSL 308


>gi|154494406|ref|ZP_02033726.1| hypothetical protein PARMER_03761 [Parabacteroides merdae ATCC
           43184]
 gi|218262261|ref|ZP_03476784.1| hypothetical protein PRABACTJOHN_02458 [Parabacteroides johnsonii
           DSM 18315]
 gi|154085850|gb|EDN84895.1| hypothetical protein PARMER_03761 [Parabacteroides merdae ATCC
           43184]
 gi|218223484|gb|EEC96134.1| hypothetical protein PRABACTJOHN_02458 [Parabacteroides johnsonii
           DSM 18315]
          Length = 330

 Score =  219 bits (559), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 120/298 (40%), Positives = 191/298 (64%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRR+L+SSL G AIT+++I+GV HE  +I GV ED+T+IILN+K + 
Sbjct: 28  PLEPGYGITIGNALRRILLSSLEGFAITSIKIEGVDHEFGTIPGVIEDVTNIILNLKQVR 87

Query: 94  LKMSGD--SHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   D   +++V+I   G  V  AGDI + +   EVLNP+ VIC LD +A  ++ELT++
Sbjct: 88  FKHIVDDIENEKVSITVSGSEVFKAGDIGKQLTGFEVLNPELVICRLDPNAGFQIELTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R  N  + +I ID++Y+PI+ V Y++E+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPADENRDPNADMHVIAIDSIYTPIRNVKYSIENFRVEQKTDYEKLVLEIATDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  A++IL     +F    I  E    +  E+ + + L     L  K+ +++LS
Sbjct: 208 IHPKEALKEAAKILIHHFMLFSDEKIAIETVDTDGNEEFDEEVLHMRQLLKSKLSDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +G+L++  + D+L+  NFG+KSL E+  +L ++ L  GM++  +
Sbjct: 268 VRALNCLKAADVETLGELVKFNKNDLLKFRNFGKKSLTELDELLESLNLSFGMDITKY 325


>gi|319442995|ref|ZP_07992151.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           variabile DSM 44702]
          Length = 337

 Score =  219 bits (559), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 132/301 (43%), Positives = 185/301 (61%), Gaps = 23/301 (7%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
           R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++I+GVLHE ++I GV ED++DII
Sbjct: 18  RSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIEGVLHEFTTIPGVKEDVSDII 77

Query: 87  LNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           LNIK   L +S DS + VT++  K G G VT  D+     +EV NPD  I  L+    + 
Sbjct: 78  LNIKA--LVISSDSDEPVTMYIRKEGLGEVTGADVVVPAGVEVHNPDLHIATLNEQGKLD 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +EL V +G GYVPA     E   IG I +D +YSP+ KVSY VE+ R  Q  D+DKL + 
Sbjct: 136 IELVVERGRGYVPAAATTGE---IGRIPVDQIYSPVLKVSYKVEATRVEQRTDFDKLVLD 192

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNPAL 256
           ++T  SIT  D++A A   L +  G+   +N E       P  +  E I   SLP     
Sbjct: 193 VETKNSITARDAIASAGGTLVELFGLARELNTEAEGIEIGPSPQETEHIAAYSLP----- 247

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E+L+ SVRS NCL+ E+I  +G+L  RTE+D+L + NFG+KS+ E+K  L  +GL 
Sbjct: 248 ---IEDLDFSVRSYNCLKREDIHTVGELAARTESDLLDIRNFGQKSINEVKVKLAELGLG 304

Query: 317 L 317
           L
Sbjct: 305 L 305


>gi|257064662|ref|YP_003144334.1| DNA-directed RNA polymerase subunit alpha [Slackia
           heliotrinireducens DSM 20476]
 gi|256792315|gb|ACV22985.1| DNA-directed RNA polymerase subunit alpha [Slackia
           heliotrinireducens DSM 20476]
          Length = 316

 Score =  219 bits (559), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 116/294 (39%), Positives = 178/294 (60%), Gaps = 6/294 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF +TLGN +RRVL+SSL GA  TA+QI+GV HE ++ +GV ED+TDI+LN+
Sbjct: 21  FVVEPLERGFGYTLGNCMRRVLLSSLDGARATAIQIEGVQHEFTTAEGVIEDVTDIVLNV 80

Query: 90  KGINLKMSGDSHKRVT--IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           KG+      + +   T  I   GP  VT  DIQ   +  ++NP+HVI  +     + M +
Sbjct: 81  KGLVFAALTEDYTEATATISVEGPCTVTGADIQVPTEFTLINPEHVIATVADGGTLNMSI 140

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            +  G GYV A+ ++   DPIG+I +D+L+SP+++ +  V   R GQ  D+D+L + ++T
Sbjct: 141 RIGVGRGYVSAERNKRTEDPIGIIPVDSLFSPVRRCTLAVNDTRVGQRTDFDQLLLEVET 200

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI----NVKSLPFNPALLKKVEEL 263
           DGSI   ++V  A+ I+   +G F+   +   E + DI      +    N  L K++E+L
Sbjct: 201 DGSIAPNEAVCRAANIINQYMGAFLTLADITDEDEGDIPSIFATEGQESNAELDKQIEDL 260

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +LSVRS NCL+   I  +  L++ +E D+L + NFG KS+ E+K  L +M L L
Sbjct: 261 DLSVRSYNCLKRAGIHSVRQLVEFSENDLLNIRNFGAKSIEEVKDKLISMDLNL 314


>gi|304384302|ref|ZP_07366713.1| DNA-directed RNA polymerase subunit alpha [Prevotella marshii DSM
           16973]
 gi|304334618|gb|EFM00900.1| DNA-directed RNA polymerase subunit alpha [Prevotella marshii DSM
           16973]
          Length = 330

 Score =  219 bits (559), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 121/298 (40%), Positives = 184/298 (61%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AI  ++I  V HE SSI GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGVTIGNALRRILLSSLEGYAINTMRIGSVEHEFSSIPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   +++V+I         AGDI + +   EVLNPD VIC+LD  A ++++LT++
Sbjct: 88  FKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGFEVLNPDLVICHLDAKASMQIDLTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYV A  +R     + +I ID++Y+PI+ V YTVE  R  Q  DYDKL + +DTDGS
Sbjct: 148 KGRGYVTADENREFCTDVNVIPIDSIYTPIRNVKYTVEPYRVEQKTDYDKLVIEVDTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++IL     +F    I  E P  E  ++ + + L     L  ++ ++ LS
Sbjct: 208 IQPKDALKEAAKILIYHFMLFSDEKIALESPDVEGNQEFDEEVLHMRQLLKTRLVDMNLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKKSLSELDDLLESLNLTFGTDISKY 325


>gi|212716586|ref|ZP_03324714.1| hypothetical protein BIFCAT_01515 [Bifidobacterium catenulatum DSM
           16992]
 gi|225351019|ref|ZP_03742042.1| hypothetical protein BIFPSEUDO_02601 [Bifidobacterium
           pseudocatenulatum DSM 20438]
 gi|212660290|gb|EEB20865.1| hypothetical protein BIFCAT_01515 [Bifidobacterium catenulatum DSM
           16992]
 gi|225158475|gb|EEG71717.1| hypothetical protein BIFPSEUDO_02601 [Bifidobacterium
           pseudocatenulatum DSM 20438]
          Length = 332

 Score =  219 bits (559), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 123/296 (41%), Positives = 177/296 (59%), Gaps = 8/296 (2%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
            R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I GV HE +++ GV ED+T+I
Sbjct: 17  QRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGVPHEFTTLPGVEEDVTEI 76

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           +LNIKGI L    D    + + K G G  TAGDI     + + NPD  I  L  D  + +
Sbjct: 77  LLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGVTIANPDMHIATLAEDGELEI 136

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           E TV +G GYVPA+ ++ +N  IG I +D++YSP+ KVSY VE+ R  Q  D+DKL + +
Sbjct: 137 EFTVERGRGYVPAQMNKQDNAEIGRIPVDSIYSPVLKVSYRVEATRVEQRTDFDKLILDV 196

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF----NPALLKKVE 261
           +T  +I+  D+VA A   L +  G+            E + V   P     NP +   +E
Sbjct: 197 ETKPAISPRDAVASAGSTLVELFGLCREL----NTQAEGVEVGPAPVAEETNPEMAVPIE 252

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L ++GL L
Sbjct: 253 DLNLTQRSYNCLKREGIHTIGELVAHTEQDLLDIRNFGMKSIDEVKEKLQSLGLAL 308


>gi|257792534|ref|YP_003183140.1| DNA-directed RNA polymerase, alpha subunit [Eggerthella lenta DSM
           2243]
 gi|317490400|ref|ZP_07948884.1| DNA-directed RNA polymerase [Eggerthella sp. 1_3_56FAA]
 gi|325833640|ref|ZP_08166089.1| DNA-directed RNA polymerase, alpha subunit [Eggerthella sp. HGA1]
 gi|257476431|gb|ACV56751.1| DNA-directed RNA polymerase, alpha subunit [Eggerthella lenta DSM
           2243]
 gi|316910535|gb|EFV32160.1| DNA-directed RNA polymerase [Eggerthella sp. 1_3_56FAA]
 gi|325485564|gb|EGC88033.1| DNA-directed RNA polymerase, alpha subunit [Eggerthella sp. HGA1]
          Length = 316

 Score =  219 bits (559), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 121/305 (39%), Positives = 185/305 (60%), Gaps = 8/305 (2%)

Query: 23  EEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
           EE N T+   I EPL RG+ +TLGN +RRVL+SSL GA  TA+QI+GV HE ++ +GV E
Sbjct: 12  EEVNDTVARFIVEPLERGYGYTLGNCMRRVLLSSLDGAKATAIQIEGVQHEFTTAEGVIE 71

Query: 81  DLTDIILNIKGINLKMSGDSHKRVT--IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
           D+TDI+LN+KG+      D  +  T  +   GP  VT  D+    +  ++NP+HVI  + 
Sbjct: 72  DITDIVLNVKGLVFSALNDDIEEATAHVSAEGPCTVTGADLDIPTEFTLVNPEHVIATVA 131

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + M + +  G GYV A+ ++   DPIG+I +D+L+SP+++ +  V   R GQ  DY
Sbjct: 132 DGGQLDMTVRIGVGRGYVSAERNKRTEDPIGVIHVDSLFSPVRRCTLNVTDTRVGQRTDY 191

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF----EEPKKEVKEDINVKSLPFNP 254
           DKL + ++TDGSIT  ++V  AS I+   +G F++     +E + E+      +    N 
Sbjct: 192 DKLVLEVETDGSITPTEAVCRASNIINQYMGAFLSLSDVVDEEEGEIPSIFAPEGQESNA 251

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
            L K++E+L+LSVRS NCL+   I  +  L++ +E D+L + NFG KS+ E+K  L +M 
Sbjct: 252 ELDKQIEDLDLSVRSYNCLKRAGIHSVRQLVEFSENDLLNIRNFGAKSIEEVKDKLISMD 311

Query: 315 LFLGM 319
           L L +
Sbjct: 312 LNLKL 316


>gi|117927543|ref|YP_872094.1| DNA-directed RNA polymerase subunit alpha [Acidothermus
           cellulolyticus 11B]
 gi|158512363|sp|A0LRP8|RPOA_ACIC1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|117648006|gb|ABK52108.1| DNA-directed RNA polymerase subunit alpha [Acidothermus
           cellulolyticus 11B]
          Length = 341

 Score =  219 bits (559), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 124/308 (40%), Positives = 188/308 (61%), Gaps = 12/308 (3%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           + R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S++ G  ED+T+
Sbjct: 16  DTRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSLRIDGVLHEFSTVPGAKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           +ILNIK + +    D  + + + K+GP  VTA DI     +EV NPD  I  L+    + 
Sbjct: 76  MILNIKELVVSSEHDDPQVIYLRKQGPCEVTAADIVAPAGVEVHNPDLHIATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +E+ V +G GYVPA  ++     IG I ID++YSP+ KV+Y VE+ R  Q  D+D+L M 
Sbjct: 136 IEMVVERGRGYVPAAQNKLPGHEIGRIPIDSIYSPVLKVTYKVEATRVEQRTDFDRLIMD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLP----FNPALLK 258
           ++T  S+   D++A A + L +  G+   +N +       E I++   P        L  
Sbjct: 196 VETKPSMRPRDAMASAGKTLVELFGLVRELNVD------AEGIDIGPSPSDAALAADLAL 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  L  MGL L 
Sbjct: 250 PIEDLNLTVRSYNCLKREGIHTVGELVARSEADLLDIRNFGQKSIEEVKTKLAEMGLSLK 309

Query: 319 MNLPDWPP 326
            + P + P
Sbjct: 310 DSPPGFDP 317


>gi|189501627|ref|YP_001957344.1| DNA-directed RNA polymerase subunit alpha [Candidatus Amoebophilus
           asiaticus 5a2]
 gi|189497068|gb|ACE05615.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Amoebophilus
           asiaticus 5a2]
          Length = 329

 Score =  219 bits (559), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 118/313 (37%), Positives = 190/313 (60%), Gaps = 6/313 (1%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + Q +E   +   +PL RG+  T+GNALRRV++SSL G AIT+++I G+ HE S+I+G
Sbjct: 12  ISVKQADEFHGIFTFKPLERGYGVTIGNALRRVILSSLEGYAITSIRIPGIYHEFSTIEG 71

Query: 78  VHEDLTDIILNIKGINLKMSGDS-HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVIC 135
           V EDL +IILN+K I  K  GD+   ++ I      ++TAGD  Q     E+ NP+ VIC
Sbjct: 72  VTEDLVEIILNLKQIRFKKIGDTTENKIFISINNKKILTAGDFAQATAAFEITNPELVIC 131

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
           ++D  A   +E+TV KG GYVPA+ ++ +    G+I ID++++P+K V Y VE+ R GQ 
Sbjct: 132 HIDESARFEIEVTVEKGRGYVPAEENKIDAQVKGVIPIDSIFTPVKNVKYHVENTRVGQK 191

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKSLP 251
            DY+ L  +++TDG+I  + ++  A+ I+     + I+     E    +  + ++  +L 
Sbjct: 192 TDYESLVFSVETDGTIHPQTAIERAADIMIKHFALLIDRNKMVETKDADEIDVLDESTLQ 251

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L   + E+ LSVR+ NCL+  +I  +GDL+Q   +DM +  NFG+KSL E++ ++ 
Sbjct: 252 MRKLLKTPLSEMGLSVRAFNCLKAADIKTLGDLVQLKVSDMAQFRNFGKKSLKELQDLVA 311

Query: 312 TMGLFLGMNLPDW 324
           +  L  GM+L  +
Sbjct: 312 SKDLTFGMDLSAY 324


>gi|189465444|ref|ZP_03014229.1| hypothetical protein BACINT_01797 [Bacteroides intestinalis DSM
           17393]
 gi|224537843|ref|ZP_03678382.1| hypothetical protein BACCELL_02730 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|189437718|gb|EDV06703.1| hypothetical protein BACINT_01797 [Bacteroides intestinalis DSM
           17393]
 gi|224520529|gb|EEF89634.1| hypothetical protein BACCELL_02730 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 330

 Score =  219 bits (558), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 119/298 (39%), Positives = 185/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AIT ++IDGV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGITVGNALRRILLSSLEGFAITTIKIDGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDSHK--RVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +  +  +V+I         AGDI + +   EVLNP+ VIC+LD  A +++++T++
Sbjct: 88  FKQVVEEFESEKVSITIENSSEFKAGDIGKYLTGFEVLNPELVICHLDSKATMQIDITIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y +E  R  Q  DYDKL + I TDGS
Sbjct: 148 KGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKYQIEPFRVEQKTDYDKLVLEITTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  A++IL     +F    I  E    +  E+ + + L     L  K+ +++LS
Sbjct: 208 IHPKEALKEAAKILIYHFMLFSDEKITLESNDVDGNEEFDEEVLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKKSLTELDDLLESLNLSFGTDISKY 325


>gi|305665111|ref|YP_003861398.1| DNA-directed RNA polymerase subunit alpha [Maribacter sp. HTCC2170]
 gi|88709863|gb|EAR02095.1| DNA-directed RNA polymerase alpha subunit [Maribacter sp. HTCC2170]
          Length = 330

 Score =  219 bits (558), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 120/298 (40%), Positives = 183/298 (61%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRVL+SSL G AIT+V+ID V HE S I GV ED+T+IILN+K + 
Sbjct: 28  PLEPGYGLTVGNALRRVLLSSLEGHAITSVRIDKVEHEFSVIPGVVEDVTEIILNLKQVR 87

Query: 94  LK--MSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K  +     + V+I   G   +TAGD Q  ++  +VLNPD VICN+D    + ME+ + 
Sbjct: 88  FKKQIEDSEAEVVSISVSGKDQLTAGDFQKFISGYQVLNPDLVICNMDSKVSINMEIVID 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++  N  +G I +D++++PIK V Y++E+ R  Q  DY+KL   I TDGS
Sbjct: 148 KGRGYVPAEENKKSNAALGTIAVDSIFTPIKNVKYSIENFRVEQKTDYEKLVFEIVTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++   +++L     +F    I  E  +    E  + +SL     L  K+ +++LS
Sbjct: 208 IHPKDALTEGAKVLIHHFMLFSDERITLEADEIAQTETYDEESLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   + D+++  NFG+KSL E++ ++   GL  GM+L  +
Sbjct: 268 VRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKKSLTELEELVINKGLSFGMDLSKY 325


>gi|148982226|ref|ZP_01816652.1| DNA-directed RNA polymerase subunit alpha [Vibrionales bacterium
           SWAT-3]
 gi|145960588|gb|EDK25941.1| DNA-directed RNA polymerase subunit alpha [Vibrionales bacterium
           SWAT-3]
          Length = 278

 Score =  219 bits (558), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 118/284 (41%), Positives = 181/284 (63%), Gaps = 11/284 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP     + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPR---LVYIEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVY 280
            +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y
Sbjct: 238 VRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHY 278


>gi|326792578|ref|YP_004310399.1| DNA-directed RNA polymerase subunit alpha [Clostridium lentocellum
           DSM 5427]
 gi|326543342|gb|ADZ85201.1| DNA-directed RNA polymerase subunit alpha [Clostridium lentocellum
           DSM 5427]
          Length = 321

 Score =  219 bits (558), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 120/294 (40%), Positives = 188/294 (63%), Gaps = 6/294 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L SSL G+AI++V++DGVLHE SSI GV ED+ +IILN+
Sbjct: 23  FVVEPLERGYGITLGNSLRRILSSSLPGSAISSVKVDGVLHEFSSIPGVKEDVVEIILNL 82

Query: 90  KGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRM 145
           KG+ ++    G   K + I K G G VT  DI+   +IE+LNP+H I  L+   ++ + +
Sbjct: 83  KGLAIRDTSQGTEPKVIYIEKSGEGPVTGADIKCGPEIEILNPEHHIATLNGGANSNLSI 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDAL--YSPIKKVSYTVESAREGQVLDYDKLSM 203
           E+TV+ G GY      +  + PIG+I +DA   Y+P+++V++ VE  R GQ  DYDKL++
Sbjct: 143 EMTVTTGRGYEGVDKLKKTDLPIGVIPVDANANYTPVERVNFIVEDTRVGQQTDYDKLTL 202

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            + T+G++  +++V+LA+++L + L +FI+  E  +  +  +  +       L   +EEL
Sbjct: 203 EVWTNGTLKPDEAVSLAAKVLSEHLNLFIDLSENARTTEIMVTKEDDSKEKTLEMTIEEL 262

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +LSVRS NCL+   I  + DL  +TE +M+++ N GRKSL E+   L  +G  L
Sbjct: 263 DLSVRSFNCLKRAGINTVEDLTNKTEEEMMKVRNLGRKSLEEVFQKLNELGFQL 316


>gi|171741248|ref|ZP_02917055.1| hypothetical protein BIFDEN_00323 [Bifidobacterium dentium ATCC
           27678]
 gi|283455392|ref|YP_003359956.1| polA DNA-directed RNA polymerase subunit alpha [Bifidobacterium
           dentium Bd1]
 gi|306823542|ref|ZP_07456917.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium dentium
           ATCC 27679]
 gi|309802902|ref|ZP_07697003.1| DNA-directed RNA polymerase, alpha subunit [Bifidobacterium dentium
           JCVIHMP022]
 gi|171276862|gb|EDT44523.1| hypothetical protein BIFDEN_00323 [Bifidobacterium dentium ATCC
           27678]
 gi|283102026|gb|ADB09132.1| polA DNA-directed RNA polymerase alpha chain [Bifidobacterium
           dentium Bd1]
 gi|304553249|gb|EFM41161.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium dentium
           ATCC 27679]
 gi|308220369|gb|EFO76680.1| DNA-directed RNA polymerase, alpha subunit [Bifidobacterium dentium
           JCVIHMP022]
          Length = 331

 Score =  219 bits (558), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 123/296 (41%), Positives = 177/296 (59%), Gaps = 8/296 (2%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
            R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I GV HE +++ GV ED+T+I
Sbjct: 17  QRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGVPHEFTTLPGVEEDVTEI 76

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           +LNIKGI L    D    + + K G G  TAGDI     + + NPD  I +L  D  + +
Sbjct: 77  LLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGVTIANPDMHIASLADDGELEI 136

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           E TV +G GYVPA+ ++ +N  IG I +D++YSP+ KVSY VE+ R  Q  D+DKL + +
Sbjct: 137 EFTVERGRGYVPAQMNKQDNAEIGRIPVDSIYSPVLKVSYRVEATRVEQRTDFDKLILDV 196

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF----NPALLKKVE 261
           +T  +I+  D+VA A   L +  G+            E + V   P     NP +   +E
Sbjct: 197 ETKPAISPRDAVASAGSTLVELFGLCREL----NTQAEGVEVGPAPVAEETNPEMAVPIE 252

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L  +GL L
Sbjct: 253 DLNLTQRSYNCLKREGIHTIGELVAHTEQDLLDIRNFGMKSIDEVKEKLQALGLAL 308


>gi|256820008|ref|YP_003141287.1| DNA-directed RNA polymerase subunit alpha [Capnocytophaga ochracea
           DSM 7271]
 gi|256581591|gb|ACU92726.1| DNA-directed RNA polymerase, alpha subunit [Capnocytophaga ochracea
           DSM 7271]
          Length = 330

 Score =  219 bits (558), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 120/298 (40%), Positives = 182/298 (61%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRV++SSL G AIT+V+ D V HE S+I GV ED+T+IILN+K I 
Sbjct: 28  PLEPGYGLTIGNALRRVMLSSLEGFAITSVKFDKVGHEFSTISGVREDVTEIILNLKQIR 87

Query: 94  LKMSGD--SHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   ++  TI   G   +TAGD Q  ++  +VLN D VICN+D  A   +E+T+ 
Sbjct: 88  FKRQIEDIENETATITVSGKRQLTAGDFQKALSGFQVLNTDLVICNMDSSASFTIEITIE 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYV A+ +   N PIG+I  DA+++PIK V Y++E+ R  Q  DY+KL   I TDGS
Sbjct: 148 KGRGYVSAEENAKPNAPIGVIATDAIFTPIKNVKYSIENYRVEQKTDYEKLVFEIKTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  + ++  A++ L     +F    I  E  +    +  + +SL     L  K+ +++LS
Sbjct: 208 IHPKQALTEAAKTLIHHFMLFSDERITLEADEIAQTDTYDEESLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   +AD+++  NFG+KSL+E++ ++   GL  GM+   +
Sbjct: 268 VRALNCLKAAEVETLGDLVSFNKADLMKFRNFGKKSLIELEELVVNKGLVFGMDTSKY 325


>gi|255326871|ref|ZP_05367947.1| DNA-directed RNA polymerase, alpha subunit [Rothia mucilaginosa
           ATCC 25296]
 gi|255296088|gb|EET75429.1| DNA-directed RNA polymerase, alpha subunit [Rothia mucilaginosa
           ATCC 25296]
          Length = 330

 Score =  219 bits (558), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 124/316 (39%), Positives = 193/316 (61%), Gaps = 9/316 (2%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           NR+    EPL  GF +T+GN+LRR L+SS+ GAA+T+V+IDGVLHE S++ GV ED+T+I
Sbjct: 17  NRSRFTIEPLEPGFGYTMGNSLRRTLLSSIPGAAVTSVRIDGVLHEFSTVPGVTEDVTEI 76

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           ILNIK +++    D      + K+G G +TAGDI+    +E+ NP+  +  L+  A    
Sbjct: 77  ILNIKKLSISSENDEPVVAYLRKQGEGELTAGDIEVPAGVEIHNPELHLATLNASANFNA 136

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           EL + +G GYV A  ++  +  IG I +D++YSP+ KV+++V + R  Q  D+D L++ +
Sbjct: 137 ELVIERGRGYVTAAQNKVGDGEIGRIPVDSIYSPVLKVTFSVNATRVEQRTDFDSLTLDV 196

Query: 206 DTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
           +T  +I   D+VA A   L +  G+   +N      EV      +S+  + AL   +E+L
Sbjct: 197 ETKEAIAPRDAVASAGSTLVELFGLARELNIAAEGIEVGPSPADESMAADLAL--PIEDL 254

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            +SVRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L    + LG+ L D
Sbjct: 255 NMSVRSYNCLKREGIHTVGELVTRSEADLMDIRNFGAKSIDEVKAKL----IELGLALKD 310

Query: 324 WPPESIEELAKKYEDK 339
            PP   E  A+  +D+
Sbjct: 311 SPP-GFEPAARPLDDE 325


>gi|294786438|ref|ZP_06751692.1| DNA-directed RNA polymerase, alpha subunit [Parascardovia
           denticolens F0305]
 gi|315226001|ref|ZP_07867789.1| DNA-directed RNA polymerase subunit alpha [Parascardovia
           denticolens DSM 10105]
 gi|294485271|gb|EFG32905.1| DNA-directed RNA polymerase, alpha subunit [Parascardovia
           denticolens F0305]
 gi|315120133|gb|EFT83265.1| DNA-directed RNA polymerase subunit alpha [Parascardovia
           denticolens DSM 10105]
          Length = 331

 Score =  219 bits (558), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 122/296 (41%), Positives = 178/296 (60%), Gaps = 8/296 (2%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
            R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ GV ED+ +I
Sbjct: 17  QRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTALPGVKEDVAEI 76

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           +LNIK + L    D    + + K G G  TA DI     + V NPD  I  L  D  + +
Sbjct: 77  LLNIKELVLTSEYDEPVVMYLRKSGEGEATAADITPPAGVVVANPDLHIATLAEDGELEI 136

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           E TV +G GYVPA+ ++ E D IG I +D++YSP+ KVSY V+  R  Q  D+DKL++ +
Sbjct: 137 EFTVERGRGYVPAQMNKQEGDEIGRIPVDSIYSPVLKVSYKVDPTRVEQRTDFDKLTVDV 196

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP----FNPALLKKVE 261
           +T  SI+  D+VA A   L +  G+F           E + V   P     +P +   +E
Sbjct: 197 ETKPSISPRDAVASAGSTLVELFGLFHEL----NNQAEGVEVGPAPVVEEVDPQMEIPIE 252

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +L L+ RS NCL+ E I  +G+L++R+E D+L + NFG+KS+ E+K  L +MGL L
Sbjct: 253 DLNLTQRSYNCLKREGIHTIGELVKRSEQDLLDIRNFGQKSIDEVKEKLDSMGLSL 308


>gi|160883038|ref|ZP_02064041.1| hypothetical protein BACOVA_01001 [Bacteroides ovatus ATCC 8483]
 gi|237717426|ref|ZP_04547907.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. D1]
 gi|237718716|ref|ZP_04549197.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. 2_2_4]
 gi|255690030|ref|ZP_05413705.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides finegoldii
           DSM 17565]
 gi|260175443|ref|ZP_05761855.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. D2]
 gi|262406191|ref|ZP_06082741.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 2_1_22]
 gi|293372093|ref|ZP_06618484.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides ovatus SD
           CMC 3f]
 gi|294644084|ref|ZP_06721861.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides ovatus SD
           CC 2a]
 gi|294806544|ref|ZP_06765383.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides
           xylanisolvens SD CC 1b]
 gi|298483091|ref|ZP_07001272.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. D22]
 gi|299144597|ref|ZP_07037665.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 3_1_23]
 gi|315923672|ref|ZP_07919912.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. D2]
 gi|156111510|gb|EDO13255.1| hypothetical protein BACOVA_01001 [Bacteroides ovatus ATCC 8483]
 gi|229443409|gb|EEO49200.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. D1]
 gi|229451848|gb|EEO57639.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. 2_2_4]
 gi|260624637|gb|EEX47508.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides finegoldii
           DSM 17565]
 gi|262357066|gb|EEZ06156.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 2_1_22]
 gi|292632885|gb|EFF51472.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides ovatus SD
           CMC 3f]
 gi|292640608|gb|EFF58849.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides ovatus SD
           CC 2a]
 gi|294446239|gb|EFG14867.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides
           xylanisolvens SD CC 1b]
 gi|295085402|emb|CBK66925.1| DNA-directed RNA polymerase subunit alpha [Bacteroides
           xylanisolvens XB1A]
 gi|298270835|gb|EFI12415.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. D22]
 gi|298515088|gb|EFI38969.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 3_1_23]
 gi|313697547|gb|EFS34382.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. D2]
          Length = 330

 Score =  219 bits (558), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 118/298 (39%), Positives = 186/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AIT ++IDGV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGITVGNALRRILLSSLEGFAITTIRIDGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDSHK--RVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +  +  +V+I         AGDI + +   EVLNP+ VIC+LD  + +++++T++
Sbjct: 88  FKQVVEEFESEKVSITVENSSEFKAGDIGKYLTGFEVLNPELVICHLDSKSTMQIDITIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y VE+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKYAVENFRVEQKTDYEKLVLEISTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  A++IL     +F    I  E    +  E+ + + L     L  K+ +++LS
Sbjct: 208 IHPKEALKEAAKILIYHFMLFSDEKITLESNDTDGNEEFDEEVLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKKSLTELDDLLESLNLSFGTDISKY 325


>gi|167755938|ref|ZP_02428065.1| hypothetical protein CLORAM_01458 [Clostridium ramosum DSM 1402]
 gi|237733255|ref|ZP_04563736.1| DNA-directed RNA polymerase [Mollicutes bacterium D7]
 gi|167703930|gb|EDS18509.1| hypothetical protein CLORAM_01458 [Clostridium ramosum DSM 1402]
 gi|229383636|gb|EEO33727.1| DNA-directed RNA polymerase [Coprobacillus sp. D7]
          Length = 314

 Score =  219 bits (558), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 116/293 (39%), Positives = 182/293 (62%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E +N    + EPL RGF  TLGN+LRRVL+SSL G+A+ A+++ G +HE S++ GV ED+
Sbjct: 16  ETDNYGKFVIEPLERGFGTTLGNSLRRVLLSSLPGSAVYAIKVQGAIHEFSAVDGVVEDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILN+K +   +  D    + I   GP  VT  DIQ  +++ +++ D  I ++   A 
Sbjct: 76  TSIILNLKKLVFDVDSDESATMIIDVEGPATVTGADIQCPSEVTMISNDMEIAHVAQGAH 135

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + MEL   K  GYV A  ++ E + IG+I  D++YSP++KVSY VE  R G+   YD+L+
Sbjct: 136 LYMELYAKKDRGYVSADQNKKEINTIGIIPTDSIYSPVEKVSYAVEPTRVGESAKYDQLT 195

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + I+T+G++   ++++LA++IL + L MF+   +    ++     +S   N  L   +EE
Sbjct: 196 LEIETNGALKPYEAISLAAKILVEHLNMFVELTDMAVNMEVMSEAQSDTTNKVLDMTIEE 255

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           L+LSVRS NCL+   I  + DL  ++E DM+++ N G+KSL E+K  L  +GL
Sbjct: 256 LDLSVRSYNCLKRAGIQTVQDLAAKSEDDMIKVRNLGKKSLKEVKEKLVELGL 308


>gi|210631180|ref|ZP_03296791.1| hypothetical protein COLSTE_00676 [Collinsella stercoris DSM 13279]
 gi|210160147|gb|EEA91118.1| hypothetical protein COLSTE_00676 [Collinsella stercoris DSM 13279]
          Length = 313

 Score =  219 bits (557), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 119/290 (41%), Positives = 185/290 (63%), Gaps = 7/290 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+ A+QIDG  HE ++I  + ED+TDI+LN+KG+
Sbjct: 24  EPLERGYGDTLGNSLRRVLLSSLEGAAVEAIQIDGAQHEFTTIPNMVEDVTDIVLNVKGL 83

Query: 93  NLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
             +  G + +   TI   GP  VT  D    ++ E++NP+  I  L     + M + +  
Sbjct: 84  VFRTLGTTDEGTATISVDGPCEVTGADFFIPSEFELVNPEQHIATLTEGGHLTMSMRIGY 143

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GYV  + ++ +NDPIG+I +D+L+SP+K+ +  VE+ R GQ  DYD+L + I+T+G+I
Sbjct: 144 GRGYVSYEQNKRDNDPIGIIHVDSLFSPVKRCAKLVEACRVGQHTDYDRLVLEIETNGAI 203

Query: 212 TGEDSVALASRILQDQLGMFINF-EEPKKEVKEDINVKSLPF---NPALLKKVEELELSV 267
              D+V  A+ I+   +  F+   +EP  E +E+I++ +      N  L K++E+L+LSV
Sbjct: 204 NPRDAVVSAANIINQHMAAFMTLADEP--EAEEEISIFAPEVTSDNAELDKQIEDLDLSV 261

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RS NCL+  +I  +  L++ +E D+L + NFG KS+ E+K  L +MGL L
Sbjct: 262 RSYNCLKRASIHSVRQLVEFSENDLLNIRNFGVKSIEEVKDKLESMGLSL 311


>gi|300779796|ref|ZP_07089652.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           genitalium ATCC 33030]
 gi|300533906|gb|EFK54965.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           genitalium ATCC 33030]
          Length = 337

 Score =  219 bits (557), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 129/317 (40%), Positives = 194/317 (61%), Gaps = 11/317 (3%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           EYI     + NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++I+GVLHE ++I
Sbjct: 12  EYI-----DTNRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIEGVLHEFTTI 66

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHV 133
            GV E++++IILNIK  NL +S DS + V ++   +GP  VTA DI    D+ V NPD  
Sbjct: 67  NGVKENVSEIILNIK--NLVLSSDSDEPVVMYLSAQGPTDVTAADIDLPADVTVHNPDLH 124

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           I +L+  A + MEL V +G GYVPA  +      IG I +D +YSP+ KVSY VE+ R  
Sbjct: 125 IASLNESARLDMELVVERGRGYVPAMTN--SGGEIGRIPVDQIYSPVLKVSYKVEATRVE 182

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D+DKL + ++T  S++  D++A A   L +  G+        + ++   + +   + 
Sbjct: 183 QRTDFDKLIIDVETKNSMSARDALASAGSTLVELFGLARELNTAAEGIEIGPSPQETEYI 242

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
            A    +E+L  SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L ++
Sbjct: 243 AAYNMPIEDLNFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKIKLASL 302

Query: 314 GLFLGMNLPDWPPESIE 330
           GL L     D+ P  IE
Sbjct: 303 GLTLKDAPEDFDPTQIE 319


>gi|288803960|ref|ZP_06409383.1| DNA-directed RNA polymerase, alpha subunit [Prevotella
           melaninogenica D18]
 gi|302345101|ref|YP_003813454.1| DNA-directed RNA polymerase, alpha subunit [Prevotella
           melaninogenica ATCC 25845]
 gi|288333593|gb|EFC72045.1| DNA-directed RNA polymerase, alpha subunit [Prevotella
           melaninogenica D18]
 gi|302149271|gb|ADK95533.1| DNA-directed RNA polymerase, alpha subunit [Prevotella
           melaninogenica ATCC 25845]
          Length = 332

 Score =  219 bits (557), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 121/300 (40%), Positives = 186/300 (62%), Gaps = 9/300 (3%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AI  ++I GV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGVTIGNALRRILLSSLEGFAINTIRIAGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   +++V+I         AGDI + +   EVLNPD VIC+LD  A ++++LT++
Sbjct: 88  FKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGFEVLNPDLVICHLDSKASMQIDLTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ +R     + ++ ID++Y+PI+ V Y VE  R  Q  DYDKL + + TDGS
Sbjct: 148 KGRGYVPAEENREYCTDVNVLPIDSIYTPIRNVKYAVEPYRVEQKTDYDKLVVEVTTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEE--LE 264
           I  +D++  A++IL     +F    I  E P +E  ++ + + L     L  K+ +  L 
Sbjct: 208 IHPKDALKEAAKILIYHFMLFSDEKITLENPDQEGNQEFDEEVLHMRQLLKTKLTDASLN 267

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 LSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKKSLSELDDLLESLNLSFGTDITKY 327


>gi|302390985|ref|YP_003826805.1| DNA-directed RNA polymerase subunit alpha [Acetohalobium arabaticum
           DSM 5501]
 gi|302203062|gb|ADL11740.1| DNA-directed RNA polymerase subunit alpha [Acetohalobium arabaticum
           DSM 5501]
          Length = 314

 Score =  219 bits (557), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 120/285 (42%), Positives = 183/285 (64%), Gaps = 1/285 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+++SSL G A T+V+I+GV HE S+I GV ED+TDI+LN+K + 
Sbjct: 25  PLERGYGITLGNSLRRIMLSSLPGTAPTSVKIEGVEHEFSTISGVVEDVTDIVLNLKELV 84

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+M  +  + + +   G G VTA +     +IE+LNPD  I  L  D  + ME+TV  G 
Sbjct: 85  LRMESEEPEILRLNASGEGEVTADEFTVSGNIEILNPDQHIATLSDDGQLDMEVTVENGR 144

Query: 154 GYVPAKHHR-TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           GYV A+ ++  E   IG+I +D+ +SPIK+V++ VE    G   D DKL + I+TDGS+T
Sbjct: 145 GYVSAEENKDDEEHVIGVIPMDSSFSPIKRVNFDVEDVWVGNRTDLDKLVLEINTDGSLT 204

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
            E++++LA+++L + L + IN  E   +V   +  +    +  L   +EEL+LSVRS+NC
Sbjct: 205 PEEAISLAAKVLDEHLDLLINLNEEITDVDLMVEKEEEEKDKVLETTIEELDLSVRSSNC 264

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+   I  + +L ++TE D++++ N G+KSL EIK  L  + L L
Sbjct: 265 LKRAGIDNVEELTEQTEDDLMKVRNLGKKSLQEIKDKLDELDLSL 309


>gi|284040594|ref|YP_003390524.1| DNA-directed RNA polymerase, subunit alpha [Spirosoma linguale DSM
           74]
 gi|283819887|gb|ADB41725.1| DNA-directed RNA polymerase, alpha subunit [Spirosoma linguale DSM
           74]
          Length = 329

 Score =  219 bits (557), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 122/298 (40%), Positives = 186/298 (62%), Gaps = 6/298 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           +PL +G+  T+GNALRR+L+SSL G AIT+V+  GVLHE SSI+GV ED+T+IILN+K +
Sbjct: 27  KPLEKGYGVTIGNALRRILLSSLEGYAITSVKFPGVLHEFSSIEGVVEDVTEIILNLKMV 86

Query: 93  NLKMSGDS-HKRVTIFKRGPGVVTAGDIQTVN-DIEVLNPDHVICNLDVDAVVRMELTVS 150
             K   D    ++T+  +   V+ AGDI   +   EVLNP+  IC++D    + ME+ V 
Sbjct: 87  RFKKINDMVDNKITVNIKKQSVLKAGDISKFSPSFEVLNPELEICHIDDTRDLEMEIFVE 146

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVP+   R    P G I IDA+Y+PIK V Y+VE+ R  Q  DY++L + I+TDGS
Sbjct: 147 KGRGYVPSDEPRVNELPFGHIPIDAIYTPIKNVKYSVENTRVEQKTDYERLLLDIETDGS 206

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  E+++  A+ IL     +F    + FE  K E +  ++ + L     L   + +L+LS
Sbjct: 207 IHPEEALKGAAYILIQHFMLFSDQTMTFETAKPEEENVVDEEVLHMRKLLKTSLADLDLS 266

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL++   +DM++  NFG+KSL E++ ++    L  GM++  +
Sbjct: 267 VRAYNCLKSADVRTLGDLVRLEISDMMKFRNFGKKSLTELEQLVAEKNLTFGMDVAKY 324


>gi|156752145|gb|ABU93823.1| RNA polymerase subunit A [Vibrio sp. 23023]
          Length = 256

 Score =  219 bits (557), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 113/259 (43%), Positives = 175/259 (67%), Gaps = 8/259 (3%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHK 102
           GNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G    
Sbjct: 1   GNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEV 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK-- 159
            +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA   
Sbjct: 61  FITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEISMRIKVERGRGYVPASAR 120

Query: 160 -HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
            H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++ 
Sbjct: 121 IHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIR 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENI 278
            A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I
Sbjct: 181 RAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAI 237

Query: 279 VYMGDLIQRTEADMLRMAN 297
            Y+GDL+QRTE ++L+  N
Sbjct: 238 HYIGDLVQRTEVELLKTPN 256


>gi|282878784|ref|ZP_06287552.1| DNA-directed RNA polymerase, alpha subunit [Prevotella buccalis
           ATCC 35310]
 gi|281299175|gb|EFA91576.1| DNA-directed RNA polymerase, alpha subunit [Prevotella buccalis
           ATCC 35310]
          Length = 330

 Score =  219 bits (557), Expect = 7e-55,   Method: Compositional matrix adjust.
 Identities = 117/298 (39%), Positives = 185/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GN+LRR+L+SSL G AI  ++I GV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGITIGNSLRRILLSSLEGYAINTIRIAGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   +++V+I         AGDI + +   EVLNPD VIC+LD  A ++++LT++
Sbjct: 88  FKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGFEVLNPDLVICHLDAKASMQIDLTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           +G GYVPA  +R     + ++ ID++Y+PI+ V Y+VE  R  Q  DYDKL + + TDGS
Sbjct: 148 QGRGYVPADENRQFCTDVNVLPIDSIYTPIRNVKYSVEPYRVEQKTDYDKLVIEVTTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           ++ +D++  A++IL     +F    I  E P ++  ++ + + L     L  K+ +L LS
Sbjct: 208 LSPKDALKEAAKILIYHFMLFSDEKITLENPDQDDNQEFDEEVLRMRQLLKTKLIDLNLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G +   +
Sbjct: 268 VRALNCLKAAEVETLGDLVQYNKTDLLKFRNFGKKSLSELDDLLESLNLSFGTDTSKY 325


>gi|302337502|ref|YP_003802708.1| DNA-directed RNA polymerase, subunit alpha [Spirochaeta smaragdinae
           DSM 11293]
 gi|301634687|gb|ADK80114.1| DNA-directed RNA polymerase, alpha subunit [Spirochaeta smaragdinae
           DSM 11293]
          Length = 351

 Score =  218 bits (556), Expect = 7e-55,   Method: Compositional matrix adjust.
 Identities = 125/306 (40%), Positives = 189/306 (61%), Gaps = 10/306 (3%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-----DGVLHEISS---- 74
           + N    +A P  RGF  T+GN LRRVL+SS++G A++AV+I     +G  H +SS    
Sbjct: 24  QSNYGKFVAYPFERGFGTTVGNTLRRVLLSSIQGYAVSAVKITCYNEEGTPHMVSSEFEM 83

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHV 133
           +  V ED  +II N+K + +K+  +  ++  + + +GPG +T  D +  ND+E++N D  
Sbjct: 84  VPEVVEDTPEIIANLKQLQIKLPEEVEQKTLLIECKGPGEITGADFEKDNDVEIINKDWK 143

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           I  +   A   +E+ +  G GYVP++ +    + IG I IDA++SPIK+V+Y +E+ R G
Sbjct: 144 ILTMMEKANFDLEVQIDLGRGYVPSEVNEKYIEEIGTIPIDAVFSPIKRVTYGIENTRVG 203

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  DYDKL+M I TDG+I  ED++A A++I +D   +FINF+E   +  +D++ +     
Sbjct: 204 QRSDYDKLTMEIYTDGTIAPEDALAEAAKIAKDHFTIFINFDEDAIDGDDDVDEEEERVR 263

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
             L   VEELELSVRS NCL+  NI  +GDL ++TE ++ +  NFG+KSL EIK  L   
Sbjct: 264 AVLDTPVEELELSVRSFNCLKSANIRTIGDLTRKTEEEIAKTRNFGKKSLQEIKEKLKEW 323

Query: 314 GLFLGM 319
            L LGM
Sbjct: 324 NLSLGM 329


>gi|158512702|sp|A1A095|RPOA_BIFAA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 332

 Score =  218 bits (556), Expect = 7e-55,   Method: Compositional matrix adjust.
 Identities = 123/296 (41%), Positives = 177/296 (59%), Gaps = 8/296 (2%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
            R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I GV HE +++ GV ED+T+I
Sbjct: 17  QRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGVPHEFTTLPGVEEDVTEI 76

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           +LNIKGI L    D    + + K G G  TAGDI     + + NPD  I  L  D  + +
Sbjct: 77  LLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGVTIANPDMHIATLAEDGELEI 136

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           E TV +G GYVPA+ ++ +N  IG I +D++YSP+ KVSY VE+ R  Q  D+DKL + +
Sbjct: 137 EFTVERGRGYVPAQMNKQDNAEIGRIPVDSIYSPVLKVSYRVEATRVEQRTDFDKLILDV 196

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF----NPALLKKVE 261
           +T  +I+  D+VA A   L +  G+            E + V   P     NP +   +E
Sbjct: 197 ETKPAISPRDAVASAGSTLVELFGLCREL----NTQAEGVEVGPAPVAEETNPEMNIPIE 252

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L ++GL L
Sbjct: 253 DLNLTQRSYNCLKREGIHTIGELVAHTEQDLLDIRNFGMKSIDEVKEKLQSLGLAL 308


>gi|325856023|ref|ZP_08171912.1| DNA-directed RNA polymerase, alpha subunit [Prevotella denticola
           CRIS 18C-A]
 gi|325483695|gb|EGC86659.1| DNA-directed RNA polymerase, alpha subunit [Prevotella denticola
           CRIS 18C-A]
          Length = 332

 Score =  218 bits (556), Expect = 8e-55,   Method: Compositional matrix adjust.
 Identities = 121/300 (40%), Positives = 186/300 (62%), Gaps = 9/300 (3%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AI  ++I GV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGVTIGNALRRILLSSLEGFAINTIRIAGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   +++V+I         AGDI + +   EVLNPD VIC+LD  A ++++LT++
Sbjct: 88  FKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGFEVLNPDLVICHLDSKASMQIDLTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ +R     + ++ ID++Y+PI+ V Y VE  R  Q  DYDKL + + TDGS
Sbjct: 148 KGRGYVPAEENREFCTDVNVLPIDSIYTPIRNVKYAVEPYRVEQKTDYDKLVVEVTTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEE--LE 264
           I  +D++  A++IL     +F    I  E P +E  ++ + + L     L  K+ +  L 
Sbjct: 208 IHPKDALKEAAKILIYHFMLFSDEKITLENPDQEGNQEFDEEVLHMRQLLKTKLTDASLN 267

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 LSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKKSLSELDDLLESLNLSFGTDITKY 327


>gi|260592738|ref|ZP_05858196.1| DNA-directed RNA polymerase, alpha subunit [Prevotella veroralis
           F0319]
 gi|325269508|ref|ZP_08136124.1| DNA-directed RNA polymerase subunit alpha [Prevotella multiformis
           DSM 16608]
 gi|327313217|ref|YP_004328654.1| DNA-directed RNA polymerase subunit alpha [Prevotella denticola
           F0289]
 gi|260535269|gb|EEX17886.1| DNA-directed RNA polymerase, alpha subunit [Prevotella veroralis
           F0319]
 gi|324988127|gb|EGC20094.1| DNA-directed RNA polymerase subunit alpha [Prevotella multiformis
           DSM 16608]
 gi|326945436|gb|AEA21321.1| DNA-directed RNA polymerase, alpha subunit [Prevotella denticola
           F0289]
          Length = 332

 Score =  218 bits (556), Expect = 8e-55,   Method: Compositional matrix adjust.
 Identities = 121/300 (40%), Positives = 186/300 (62%), Gaps = 9/300 (3%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AI  ++I GV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGVTIGNALRRILLSSLEGFAINTIRIAGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   +++V+I         AGDI + +   EVLNPD VIC+LD  A ++++LT++
Sbjct: 88  FKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGFEVLNPDLVICHLDSKASMQIDLTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ +R     + ++ ID++Y+PI+ V Y VE  R  Q  DYDKL + + TDGS
Sbjct: 148 KGRGYVPAEENREFCTDVNVLPIDSIYTPIRNVKYAVEPYRVEQKTDYDKLVVEVTTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEE--LE 264
           I  +D++  A++IL     +F    I  E P +E  ++ + + L     L  K+ +  L 
Sbjct: 208 IHPKDALKEAAKILIYHFMLFSDEKITLENPDQEGNQEFDEEVLHMRQLLKTKLTDASLN 267

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 LSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKKSLSELDDLLESLNLSFGTDITKY 327


>gi|38233158|ref|NP_938925.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           diphtheriae NCTC 13129]
 gi|61215957|sp|Q6NJ63|RPOA_CORDI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|38199417|emb|CAE49060.1| DNA-directed RNA polymerase alpha chain [Corynebacterium
           diphtheriae]
          Length = 338

 Score =  218 bits (556), Expect = 8e-55,   Method: Compositional matrix adjust.
 Identities = 123/306 (40%), Positives = 190/306 (62%), Gaps = 5/306 (1%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
           R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV ED++DII
Sbjct: 18  RSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTINGVKEDVSDII 77

Query: 87  LNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           LNIKG  L +S DS + V ++  K G GV+TAGDI+    +E+ NPD  +  L+    + 
Sbjct: 78  LNIKG--LVLSSDSDEPVVMYLRKEGAGVITAGDIEPPAGVEIHNPDLHLATLNEQGRLD 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +E+ V +G GYVPA  +    + IG I +D +YSP+ KVSY VE+ R  Q  D+DKL + 
Sbjct: 136 IEMIVERGRGYVPATLYSGPAE-IGRIPVDQIYSPVLKVSYKVEATRVEQRTDFDKLIID 194

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           ++T  S+   D++A A + L +  G+        + ++   + +   +  A    +E+L 
Sbjct: 195 VETKNSMAPRDALASAGKTLVELFGLARELNTAAEGIEIGPSPQETEYIAAYGMPIEDLN 254

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
            SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L  +GL L     D+
Sbjct: 255 FSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKIKLAGLGLTLKDAPEDF 314

Query: 325 PPESIE 330
            P  ++
Sbjct: 315 DPTQLD 320


>gi|154486773|ref|ZP_02028180.1| hypothetical protein BIFADO_00598 [Bifidobacterium adolescentis
           L2-32]
 gi|154084636|gb|EDN83681.1| hypothetical protein BIFADO_00598 [Bifidobacterium adolescentis
           L2-32]
          Length = 332

 Score =  218 bits (556), Expect = 8e-55,   Method: Compositional matrix adjust.
 Identities = 123/296 (41%), Positives = 177/296 (59%), Gaps = 8/296 (2%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
            R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I GV HE +++ GV ED+T+I
Sbjct: 17  QRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGVPHEFTTLPGVEEDVTEI 76

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           +LNIKGI L    D    + + K G G  TAGDI     + + NPD  I  L  D  + +
Sbjct: 77  LLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGVTIANPDMHIATLAEDGELEI 136

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           E TV +G GYVPA+ ++ +N  IG I +D++YSP+ KVSY VE+ R  Q  D+DKL + +
Sbjct: 137 EFTVERGRGYVPAQMNKQDNAEIGRIPVDSIYSPVLKVSYRVEATRVEQRTDFDKLILDV 196

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF----NPALLKKVE 261
           +T  +I+  D+VA A   L +  G+            E + V   P     NP +   +E
Sbjct: 197 ETKPAISPRDAVASAGSTLVELFGLCREL----NTQAEGVEVGPAPVAEETNPEMNIPIE 252

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L ++GL L
Sbjct: 253 DLNLTQRSYNCLKREGIHTIGELVAHTEQDLLDIRNFGMKSIDEVKEKLQSLGLAL 308


>gi|156788956|gb|ABU96049.1| RNA polymerase subunit A [Vibrio parahaemolyticus]
          Length = 258

 Score =  218 bits (556), Expect = 9e-55,   Method: Compositional matrix adjust.
 Identities = 112/260 (43%), Positives = 176/260 (67%), Gaps = 8/260 (3%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRV 104
           ALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +
Sbjct: 2   ALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFI 61

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---H 160
           T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H
Sbjct: 62  TLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIH 121

Query: 161 HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           +  +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A
Sbjct: 122 NEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRA 181

Query: 221 SRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVY 280
           + IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y
Sbjct: 182 ATILTEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHY 238

Query: 281 MGDLIQRTEADMLRMANFGR 300
           +GDL+QRTE ++L+  N G+
Sbjct: 239 IGDLVQRTEVELLKTPNLGK 258


>gi|330997338|ref|ZP_08321189.1| DNA-directed RNA polymerase, alpha subunit [Paraprevotella
           xylaniphila YIT 11841]
 gi|329570712|gb|EGG52428.1| DNA-directed RNA polymerase, alpha subunit [Paraprevotella
           xylaniphila YIT 11841]
          Length = 330

 Score =  218 bits (555), Expect = 9e-55,   Method: Compositional matrix adjust.
 Identities = 120/298 (40%), Positives = 185/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AI  ++I GV HE +S+ GV ED+T+IILN+K I 
Sbjct: 28  PLEPGFGITVGNALRRILLSSLEGYAINTMRIAGVEHEFASVPGVKEDVTNIILNLKQIR 87

Query: 94  LK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K  +    +++V+I         AGDI + +   EVLNP+ VIC+LD  A +++EL+++
Sbjct: 88  FKKIVEEFENEKVSITVENTTEFKAGDINKYLTGFEVLNPELVICHLDAKATMQIELSIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y VE+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPADENRIFCTDVNVIPIDSIYTPIRNVKYAVENYRVEQKTDYEKLVLEISTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++IL     +F    I  E    E  E+ + + L     L  K+ +++LS
Sbjct: 208 IHPKDALKEAAKILIYHFMLFSDEKITLENSDGEGNEEFDEEVLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKKSLTELDDLLESLNLSFGTDISKY 325


>gi|315225426|ref|ZP_07867240.1| DNA-directed RNA polymerase subunit alpha [Capnocytophaga ochracea
           F0287]
 gi|314944699|gb|EFS96734.1| DNA-directed RNA polymerase subunit alpha [Capnocytophaga ochracea
           F0287]
          Length = 330

 Score =  218 bits (555), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 120/298 (40%), Positives = 181/298 (60%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRV++SSL G AIT+V+ D V HE S+I GV ED+T+IILN+K I 
Sbjct: 28  PLEPGYGLTIGNALRRVMLSSLEGFAITSVKFDKVGHEFSTISGVREDVTEIILNLKQIR 87

Query: 94  LKMSGD--SHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   ++  TI   G   +TAGD Q  ++  +VLN D VICN+D  A   +E+T+ 
Sbjct: 88  FKRQIEDIENETATITVSGKRQLTAGDFQKALSGFQVLNTDLVICNMDSSASFTIEVTIE 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYV A+ +   N PIG+I  DA+++PIK V Y++E+ R  Q  DY+KL   I TDGS
Sbjct: 148 KGRGYVSAEENAKPNAPIGVIATDAIFTPIKNVKYSIENYRVEQKTDYEKLVFEIKTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  + ++  A++ L     +F    I  E  +    +  + +SL     L  K+ +++LS
Sbjct: 208 IHPKQALTEAAKTLIHHFMLFSDERITLEADEIAQTDTYDEESLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   +AD+++  NFG+KSL+E+  ++   GL  GM+   +
Sbjct: 268 VRALNCLKAAEVETLGDLVSFNKADLMKFRNFGKKSLIELDELVVNKGLVFGMDTSKY 325


>gi|256825858|ref|YP_003149818.1| DNA-directed RNA polymerase subunit alpha [Kytococcus sedentarius
           DSM 20547]
 gi|256689251|gb|ACV07053.1| DNA-directed RNA polymerase subunit alpha [Kytococcus sedentarius
           DSM 20547]
          Length = 340

 Score =  218 bits (555), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 124/307 (40%), Positives = 187/307 (60%), Gaps = 4/307 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S++ GV ED+T+
Sbjct: 16  EARSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFSTVPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           +ILNIK +      D      + K+G G +T  DI     +EV NPD  +  L+ +  + 
Sbjct: 76  LILNIKSLVFSSEHDEPVVAYLRKQGSGEMTGADISCPAGVEVHNPDLYLGALNDEGAID 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELT+ +G GYV A+ ++     IG I +D++YSP+  V+Y VE+ R  Q  D+DKL + 
Sbjct: 136 LELTIERGRGYVSAQQNKGGEQEIGRIPVDSIYSPVLSVTYKVEATRVEQRTDFDKLIVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           ++T  S++  D++A A + L +  G+   +N E    E+       SL  + AL   VEE
Sbjct: 196 VETKNSMSPADAMASAGKTLVELFGLARDLNVEAEGIEMGTVQTDASLAADLAL--PVEE 253

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           L LSVRS NCL+ E I  +G+L+ R++AD+L + NFG KS+ E++  L  +GL L     
Sbjct: 254 LNLSVRSYNCLKREGIHTVGELVARSQADLLDIRNFGNKSIDEVQVELHKLGLALKDTPA 313

Query: 323 DWPPESI 329
           D+ P +I
Sbjct: 314 DFDPSTI 320


>gi|119025365|ref|YP_909210.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium
           adolescentis ATCC 15703]
 gi|118764949|dbj|BAF39128.1| DNA-directed RNA polymerase alpha chain [Bifidobacterium
           adolescentis ATCC 15703]
          Length = 344

 Score =  218 bits (555), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 123/296 (41%), Positives = 177/296 (59%), Gaps = 8/296 (2%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
            R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I GV HE +++ GV ED+T+I
Sbjct: 29  QRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGVPHEFTTLPGVEEDVTEI 88

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           +LNIKGI L    D    + + K G G  TAGDI     + + NPD  I  L  D  + +
Sbjct: 89  LLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGVTIANPDMHIATLAEDGELEI 148

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           E TV +G GYVPA+ ++ +N  IG I +D++YSP+ KVSY VE+ R  Q  D+DKL + +
Sbjct: 149 EFTVERGRGYVPAQMNKQDNAEIGRIPVDSIYSPVLKVSYRVEATRVEQRTDFDKLILDV 208

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF----NPALLKKVE 261
           +T  +I+  D+VA A   L +  G+            E + V   P     NP +   +E
Sbjct: 209 ETKPAISPRDAVASAGSTLVELFGLCREL----NTQAEGVEVGPAPVAEETNPEMNIPIE 264

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L ++GL L
Sbjct: 265 DLNLTQRSYNCLKREGIHTIGELVAHTEQDLLDIRNFGMKSIDEVKEKLQSLGLAL 320


>gi|313292082|gb|ADR51230.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
          Length = 241

 Score =  218 bits (555), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 108/217 (49%), Positives = 152/217 (70%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+
Sbjct: 7   EEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDV 66

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             IILNIKG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  ICN+   A 
Sbjct: 67  AQIILNIKGLALKMYGDEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICNVSEGAS 126

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
               LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+
Sbjct: 127 FHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLT 186

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           M I TDGSI   ++++LA++I+ + L +F+N  +  K
Sbjct: 187 MEIWTDGSIEPLEAMSLAAKIMTEHLDIFVNLTDEAK 223


>gi|254796670|ref|YP_003081506.1| DNA-directed RNA polymerase, alpha subunit [Neorickettsia risticii
           str. Illinois]
 gi|254589917|gb|ACT69279.1| DNA-directed RNA polymerase, alpha subunit [Neorickettsia risticii
           str. Illinois]
          Length = 333

 Score =  218 bits (554), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 128/317 (40%), Positives = 188/317 (59%), Gaps = 19/317 (5%)

Query: 18  IVLGQEEENRTL-MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
           +V  Q  E  +   + EPL  GF  T+GNA+RRVL+SSL G AI+AV I G+ HE S I 
Sbjct: 19  VVFNQIREGYSAEFVVEPLRGGFGLTIGNAMRRVLLSSLSGFAISAVGIKGLTHEFSCIP 78

Query: 77  GVHEDLTDIILNIKGINLK-MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
           GV ED  D+ LN+K + LK +SG +   + +   G G V +  I   +D EV+N D +IC
Sbjct: 79  GVREDFADLALNLKKVVLKSVSGATCGNLHLSVTGGGAVFSNMISPSHDFEVVNADLLIC 138

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRT-ENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
           N+     + ME+ VS G GYV +   R  E D  G + IDA+Y+P++ V++TV+    G 
Sbjct: 139 NVAEGVSLEMEMKVSSGFGYVSSVSVRKDEYDLEGAVPIDAIYNPVRAVNFTVKPTSAGS 198

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
            + +DKL + ++T+G++  + +V  AS+IL  Q   F+N  +P+  V        +P++ 
Sbjct: 199 FVGHDKLILYVETNGAMDPKTAVLEASKILSTQARCFLNIADPEHRVH------GVPYSV 252

Query: 255 A----------LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +          L  +++ L LS R+  CL GENIVY+ DL+ RTEAD+L+  NFGR+SL 
Sbjct: 253 STSDRNDTSDLLSARIDRLYLSARARKCLNGENIVYIRDLVSRTEADLLKAPNFGRRSLE 312

Query: 305 EIKGVLGTMGLFLGMNL 321
           E+K  L + GL LGMNL
Sbjct: 313 EVKKELFSKGLSLGMNL 329


>gi|297242944|ref|ZP_06926882.1| DNA-directed RNA polymerase, alpha subunit [Gardnerella vaginalis
           AMD]
 gi|296889155|gb|EFH27889.1| DNA-directed RNA polymerase, alpha subunit [Gardnerella vaginalis
           AMD]
          Length = 331

 Score =  218 bits (554), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 125/298 (41%), Positives = 178/298 (59%), Gaps = 12/298 (4%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
            R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ GV ED+T+I
Sbjct: 17  QRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTTLPGVEEDVTEI 76

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           +LNIKGI L    D    + + K G G  TAGDI     + + NPD  I  L  D  + +
Sbjct: 77  LLNIKGIVLTSEYDEPVVMYLRKNGKGEATAGDITPPAGVTIANPDLHIATLAEDGELEI 136

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           E TV +G GYVPA+ ++ EN  IG I +D++YSP+ KVSY VE+ R  Q  D+DKL + +
Sbjct: 137 EFTVERGRGYVPAQMNKQENSEIGRIPVDSIYSPVLKVSYKVEATRVEQRTDFDKLILDV 196

Query: 206 DTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLP----FNPALLKK 259
           +T  +IT  D+VA A   L +  G+   +N +       E + V   P     +  L   
Sbjct: 197 ETKPAITPRDAVASAGSTLVELFGLCRELNVD------AEGVEVGPAPTHDEADSQLAIP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +E++  + RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L TMGL L
Sbjct: 251 IEDMNFTQRSYNCLKREGIHTVGELVVHTEQDLLDIRNFGMKSIDEVKEKLQTMGLSL 308


>gi|297564065|ref|YP_003683038.1| DNA-directed RNA polymerase, alpha subunit [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296848514|gb|ADH70532.1| DNA-directed RNA polymerase, alpha subunit [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 340

 Score =  218 bits (554), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 122/313 (38%), Positives = 187/313 (59%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
           R+  + EPL  GF +T+GN+LRR L+SS+ GAA+T+++I+GV HE +++ GV ED+T++I
Sbjct: 18  RSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGAAVTSIRIEGVEHEFTTVPGVKEDVTEMI 77

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+KG+ +    D    + + K+GPGVVTA DI     +EV NPD  I  L+    + ME
Sbjct: 78  LNLKGLVVSSEHDEPVLMYLRKQGPGVVTAADIAPPAGVEVHNPDLHIATLNGKGKLEME 137

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           LTV +G GYV A  ++     IG I ID++YSP+ +V+Y VE+ R  Q  D+D+L + I+
Sbjct: 138 LTVERGRGYVSATQNKQAGQEIGRIPIDSIYSPVLRVTYKVEATRVEQRTDFDRLIVDIE 197

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T  +I   D+VA A + L +  G+        + +    +         L   +E+L L+
Sbjct: 198 TKPAIRPRDAVASAGKTLVELFGLARELNVDAEGIDMGPSPTDAALAADLALPIEDLNLT 257

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  MGL L  + P + P
Sbjct: 258 VRSYNCLKREGIHSVGELVARSEQDLLDIRNFGAKSIDEVKQKLVDMGLSLKDSPPGFDP 317

Query: 327 ESIEELAKKYEDK 339
            S  +     +D+
Sbjct: 318 SSAADSYSSEDDE 330


>gi|328813971|gb|AEB52101.1| DNA-directed RNA polymerase alpha chain [Lactobacillus fermentum]
          Length = 257

 Score =  218 bits (554), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 114/257 (44%), Positives = 172/257 (66%), Gaps = 2/257 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRV+++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+
Sbjct: 1   FVVEPLERGYGTTLGNSLRRVMLASLPGAAITSIQIDGVLHEFSTVQGVTEDVTQIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  +GP  VTA DIQ   D+ +LN D  I  +   A + +++T 
Sbjct: 61  KQVALKIDSEDAKDLEIDVKGPAEVTAADIQGDGDVTILNSDLHIATVSDGAELHVKMTA 120

Query: 150 SKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GY  A  ++T  E   IG++ ID++Y+PI++V+YTVE+ R GQ  DYDKL++ + T
Sbjct: 121 DKGRGYSSADDNKTRMEGLAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +GS+T  ++++LA++IL + L MF+N  E  +  +  +  +       L K +EEL+LSV
Sbjct: 181 NGSLTPTEAISLAAKILTEHLTMFVNLTEEAQVTQVMVEREETHQEKVLDKTIEELDLSV 240

Query: 268 RSTNCLRGENIVYMGDL 284
           RS NCL+  +I  + DL
Sbjct: 241 RSYNCLKRADIQTVKDL 257


>gi|308235469|ref|ZP_07666206.1| DNA-directed RNA polymerase subunit alpha [Gardnerella vaginalis
           ATCC 14018]
 gi|311115142|ref|YP_003986363.1| DNA-directed RNA polymerase subunit alpha [Gardnerella vaginalis
           ATCC 14019]
 gi|310946636|gb|ADP39340.1| DNA-directed RNA polymerase subunit alpha [Gardnerella vaginalis
           ATCC 14019]
          Length = 331

 Score =  218 bits (554), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 124/298 (41%), Positives = 179/298 (60%), Gaps = 12/298 (4%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
            R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ GV ED+T+I
Sbjct: 17  QRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTTLPGVEEDVTEI 76

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           +LNIKGI L    D    + + K G G  TAGDI     + + NP+  I  L  D  + +
Sbjct: 77  LLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGVTIANPEMHIATLAEDGELEI 136

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           E TV +G GYVPA+ ++ EN  IG I +D++YSP+ KVSY VE+ R  Q  D+DKL + +
Sbjct: 137 EFTVERGRGYVPAQMNKQENSEIGRIPVDSIYSPVLKVSYKVEATRVEQRTDFDKLILDV 196

Query: 206 DTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLP----FNPALLKK 259
           +T  +IT  D+VA A   L +  G+   +N +       E + V   P     +  +   
Sbjct: 197 ETKPAITPRDAVASAGSTLVELFGLCRELNVD------AEGVEVGPAPVMGEVDSQMATP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L +MGL L
Sbjct: 251 IEDLNLTQRSYNCLKREGIHTVGELVVHTEQDLLDIRNFGMKSIDEVKEKLQSMGLSL 308


>gi|218131300|ref|ZP_03460104.1| hypothetical protein BACEGG_02911 [Bacteroides eggerthii DSM 20697]
 gi|317476330|ref|ZP_07935579.1| DNA-directed RNA polymerase [Bacteroides eggerthii 1_2_48FAA]
 gi|217986517|gb|EEC52853.1| hypothetical protein BACEGG_02911 [Bacteroides eggerthii DSM 20697]
 gi|316907356|gb|EFV29061.1| DNA-directed RNA polymerase [Bacteroides eggerthii 1_2_48FAA]
          Length = 330

 Score =  218 bits (554), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 118/298 (39%), Positives = 186/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AIT ++IDGV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGITVGNALRRILLSSLEGFAITTIKIDGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDSHK--RVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +  +  +V+I         AGDI + +   EVLNP+ VIC+LD  + +++++T++
Sbjct: 88  FKQVVEEFESEKVSITIENSSEFKAGDIGKYLTGFEVLNPELVICHLDSKSTMQIDITIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y VE+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKYQVENFRVEQKTDYEKLVLEITTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  A++IL     +F    I  E    +  E+ + + L     L  K+ +++LS
Sbjct: 208 IHPKEALKEAAKILIYHFMLFSDEKITLETNDVDGNEEFDEEVLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKKSLTELDDLLESLNLSFGTDISKY 325


>gi|34541514|ref|NP_905993.1| DNA-directed RNA polymerase subunit alpha [Porphyromonas gingivalis
           W83]
 gi|188995705|ref|YP_001929957.1| DNA-directed RNA polymerase subunit alpha [Porphyromonas gingivalis
           ATCC 33277]
 gi|41688626|sp|Q7MTP0|RPOA_PORGI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|34397831|gb|AAQ66892.1| DNA-directed RNA polymerase, alpha subunit [Porphyromonas
           gingivalis W83]
 gi|188595385|dbj|BAG34360.1| DNA-directed RNA polymerase alpha subunit [Porphyromonas gingivalis
           ATCC 33277]
          Length = 330

 Score =  218 bits (554), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 121/300 (40%), Positives = 185/300 (61%), Gaps = 9/300 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           +PL  G+  T+GNALRR+L+SSL G AITA++I+GV HE ++I GV ED+T+IILN+K +
Sbjct: 27  KPLEPGYGITIGNALRRILLSSLEGFAITAIKIEGVEHEFATIPGVLEDVTNIILNLKQV 86

Query: 93  NLKM---SGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELT 148
             K    + D  K  TI      V  AGD+   +++ EVLN + VIC+LD  A + ME +
Sbjct: 87  RFKQIVPNADVEK-ATIVISNSEVFRAGDLNAQLSNFEVLNSNLVICHLDKSATLTMEFS 145

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           ++KG GYV A+ +R E++ +  I ID++Y+PI+ V Y VE+ R  Q  DY+KL M + TD
Sbjct: 146 INKGRGYVSAEENRAEHNELSTIAIDSIYTPIRNVKYAVENFRVEQKTDYEKLLMEVTTD 205

Query: 209 GSITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           GSI   D++  A++IL     +F    I  E       ++ +  SL     L  K+  L+
Sbjct: 206 GSIRPVDALREAAQILISHFSLFAENKIAIEYVDIVDTDEFDEDSLHMRQLLKSKLSGLD 265

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           LSVR+ NCL    +  +GDL+  + +D++++ NFG+KSL E+  +L T+ L  GM++  +
Sbjct: 266 LSVRALNCLNAAGVDTLGDLVSLSRSDLMKIRNFGKKSLTELDELLATLNLSFGMDISKY 325


>gi|224542265|ref|ZP_03682804.1| hypothetical protein CATMIT_01440 [Catenibacterium mitsuokai DSM
           15897]
 gi|224524807|gb|EEF93912.1| hypothetical protein CATMIT_01440 [Catenibacterium mitsuokai DSM
           15897]
          Length = 314

 Score =  218 bits (554), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 119/293 (40%), Positives = 179/293 (61%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E+EN    I EPL RGF  TLGN+LRRVL+SS+ GAA+ AV+I+G +HE S++ GV ED+
Sbjct: 16  EDENYGKFIIEPLERGFGTTLGNSLRRVLLSSMPGAAVFAVKINGAIHEFSAVDGVLEDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILNIK +  ++  D    + I   GP  VT  DIQ  +++++++ D VI ++     
Sbjct: 76  TAIILNIKKLVFELDSDEDVTMVIDVTGPATVTGADIQCPSEVKMISNDLVIAHVAEGQH 135

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
             ME+   K  GY+ A  ++   + IG+I  D+++SP+  V+Y VE  R GQ   YD+L+
Sbjct: 136 FYMEMYAHKDRGYMSADQNKKYVNTIGVIPTDSIFSPVVNVAYLVEPTRVGQSAKYDQLT 195

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           M I TDGSI   + +A+A+++L + L MF+   +    +     V+    N  L   +EE
Sbjct: 196 MEITTDGSIKPHEVLAIAAKVLVEHLNMFVELTDQAMNMDVMSEVQQDTGNKVLDMTIEE 255

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           L+LSVRS NCL+   I  + +L  +TE DM+++ N G+KSL E+K  L  +GL
Sbjct: 256 LDLSVRSYNCLKRAGIQTVQELASKTEDDMIKVRNLGKKSLKEVKEKLNELGL 308


>gi|328813963|gb|AEB52097.1| DNA-directed RNA polymerase alpha chain [Lactobacillus farraginis]
          Length = 264

 Score =  218 bits (554), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 119/262 (45%), Positives = 172/262 (65%), Gaps = 4/262 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EPL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+
Sbjct: 3   VVVEPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNV 62

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K I+LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M L
Sbjct: 63  KKISLKLDGPEDEEENLEIDVIGPADVTAGDIQGDSDVTVLNPDLHIATVAEGATFHMRL 122

Query: 148 TVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           T ++G GYV A     R    PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ +
Sbjct: 123 TANRGRGYVSAVENKKRATEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDV 182

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+GSIT  ++V+LA++IL + L MF++  +  K  +  +  +       L   +EEL+L
Sbjct: 183 WTNGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEKEETHKEKMLEMTIEELDL 242

Query: 266 SVRSTNCLRGENIVYMGDLIQR 287
           SVRS NCL+   I  + +L ++
Sbjct: 243 SVRSYNCLKRAGINTVQELTEK 264


>gi|257069480|ref|YP_003155735.1| DNA-directed RNA polymerase subunit alpha [Brachybacterium faecium
           DSM 4810]
 gi|256560298|gb|ACU86145.1| DNA-directed RNA polymerase subunit alpha [Brachybacterium faecium
           DSM 4810]
          Length = 331

 Score =  218 bits (554), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 125/319 (39%), Positives = 198/319 (62%), Gaps = 8/319 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ENR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S++ GV ED+T+
Sbjct: 16  ENRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFSTVPGVKEDITE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRG--PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           +ILNIK  NL +S ++ + V ++ R    G VTA DI     +E+ NPD  I  L+    
Sbjct: 76  VILNIK--NLVVSSENDEPVVMYLRREEAGRVTAADITPPAGVEIHNPDLHIATLNEKGR 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +EL V +G GYV A  ++  +  IG + +D++YSP+ KV+Y VE+ R  Q  D+DKL 
Sbjct: 134 LEIELIVERGRGYVSAAQNKGVDGEIGRVPVDSIYSPVLKVTYKVEATRVEQRTDFDKLI 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKV 260
           + ++T  +I+  D+VA A + L +  G+   +N E    E+      ++L  + AL   +
Sbjct: 194 VDVETKPAISPRDAVASAGKTLVELFGLAHELNQEAEGIEIGPSPTDQALAADLAL--PI 251

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
            +L L+VRS NCL  E +  +G+L  R+EAD+L + NFG+KS+ E+K  L  +GL L  +
Sbjct: 252 NDLNLTVRSYNCLMREGVHTVGELTARSEADLLDIRNFGQKSIDEVKAKLADLGLSLKDS 311

Query: 321 LPDWPPESIEELAKKYEDK 339
              + P +++  +  + D+
Sbjct: 312 PAGFDPSALDSYSDDFGDQ 330


>gi|293375416|ref|ZP_06621697.1| DNA-directed RNA polymerase, alpha subunit [Turicibacter sanguinis
           PC909]
 gi|325844489|ref|ZP_08168216.1| DNA-directed RNA polymerase, alpha subunit [Turicibacter sp. HGF1]
 gi|292645969|gb|EFF63998.1| DNA-directed RNA polymerase, alpha subunit [Turicibacter sanguinis
           PC909]
 gi|325489163|gb|EGC91547.1| DNA-directed RNA polymerase, alpha subunit [Turicibacter sp. HGF1]
          Length = 314

 Score =  217 bits (553), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 116/289 (40%), Positives = 179/289 (61%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T++ I+GV HE ++I GV ED+T IILN+
Sbjct: 23  FVIEPLKRGYGTTLGNSLRRVLLSSLPGAAVTSISIEGVQHEFTAIDGVVEDVTQIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L +  +  K + I     G VTA DI+   ++ ++NP+  I  L     +RM +  
Sbjct: 83  KNLILSIDTEEVKELRIDVAREGAVTAADIECDEEVTIINPELHIATLSATGRLRMTMKA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G+GYV A  ++   +  G I ID++Y+P+ +VSY VE  R GQ   YDKL++ + T+G
Sbjct: 143 RRGNGYVGADDNKKLLESAGEIAIDSIYTPVTRVSYDVEKTRVGQDASYDKLTLEVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  ++++++AS+IL +   + +N  E  +     +  +    N  L   +EEL+LSVRS
Sbjct: 203 SINPQEAISVASKILVEHFSILVNLNEAGQLASFIVEREDEEKNKVLEMPIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            NCLR   I  + +L + +E DM+++ N G+KSL E+K  L  +GL LG
Sbjct: 263 YNCLRRAGINTVEELARHSEEDMMKVRNLGKKSLKEVKDKLDELGLSLG 311


>gi|76563869|gb|ABA46366.1| RNA polymerase alpha subunit [Photobacterium halotolerans]
          Length = 252

 Score =  217 bits (553), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 111/250 (44%), Positives = 169/250 (67%), Gaps = 7/250 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 5   EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDVLEILLNLKGL 64

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+ G     +++ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +
Sbjct: 65  AVKVEGKDEVILSLSKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNADISMRIKVER 124

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA +SP+ +++Y+VE+AR  Q  D DKL + ++T+
Sbjct: 125 GRGYVPASARIHSDEDERPIGRLLVDATFSPVDRIAYSVEAARVEQRTDLDKLVIDMETN 184

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 185 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 241

Query: 269 STNCLRGENI 278
           S NCL+ E I
Sbjct: 242 SANCLKAEAI 251


>gi|53715439|ref|YP_101431.1| DNA-directed RNA polymerase subunit alpha [Bacteroides fragilis
           YCH46]
 gi|60683411|ref|YP_213555.1| DNA-directed RNA polymerase subunit alpha [Bacteroides fragilis
           NCTC 9343]
 gi|253566697|ref|ZP_04844150.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. 3_2_5]
 gi|255011673|ref|ZP_05283799.1| DNA-directed RNA polymerase subunit alpha [Bacteroides fragilis
           3_1_12]
 gi|265767575|ref|ZP_06095241.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 2_1_16]
 gi|313149509|ref|ZP_07811702.1| RNA polymerase subunit alpha [Bacteroides fragilis 3_1_12]
 gi|61215863|sp|Q64NN5|RPOA_BACFR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|81313537|sp|Q5L8D6|RPOA_BACFN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|52218304|dbj|BAD50897.1| DNA-directed RNA polymerase alpha chain [Bacteroides fragilis
           YCH46]
 gi|60494845|emb|CAH09652.1| putative DNA-directed RNA polymerase alpha chain [Bacteroides
           fragilis NCTC 9343]
 gi|251944869|gb|EES85344.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. 3_2_5]
 gi|263252880|gb|EEZ24392.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 2_1_16]
 gi|301164896|emb|CBW24457.1| putative DNA-directed RNA polymerase alpha chain [Bacteroides
           fragilis 638R]
 gi|313138276|gb|EFR55636.1| RNA polymerase subunit alpha [Bacteroides fragilis 3_1_12]
          Length = 330

 Score =  217 bits (553), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 118/298 (39%), Positives = 186/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AIT ++I+GV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGITVGNALRRILLSSLEGFAITTIRIEGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDSHK--RVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +  +  +V+I         AGDI + +   EVLNP+ VIC+LD  A +++++T++
Sbjct: 88  FKQVVEEFESEKVSITIENSSEFKAGDIGKYLTGFEVLNPELVICHLDSKATMQIDITIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y VE+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKYAVENFRVEQKTDYEKLVLEITTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  A++IL     +F    I  E    +  E+ + + L     L  K+ +++LS
Sbjct: 208 IHPKEALKEAAKILIYHFMLFSDEKITLESNDVDGNEEFDEEVLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKKSLTELDDLLESLNLSFGTDISKY 325


>gi|323342814|ref|ZP_08083046.1| DNA-directed RNA polymerase subunit alpha [Erysipelothrix
           rhusiopathiae ATCC 19414]
 gi|322463926|gb|EFY09120.1| DNA-directed RNA polymerase subunit alpha [Erysipelothrix
           rhusiopathiae ATCC 19414]
          Length = 319

 Score =  217 bits (553), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 122/294 (41%), Positives = 183/294 (62%), Gaps = 11/294 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF +T+GNALRRVL+SSL GAA+ +++I+GV HE +SI GV ED+T I+LN+
Sbjct: 23  FVIEPLERGFGNTIGNALRRVLLSSLPGAAVYSIKIEGVYHEFTSIAGVGEDVTGIVLNV 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L +  +    + I ++GP VVTA DI+   ++E+LN DH+I  L   AV+ MEL  
Sbjct: 83  KDLVLNVQDEEVYTLRISQKGPKVVTAADIECPANVEILNKDHIIATLAEGAVLEMELKA 142

Query: 150 SKGHGYVPAKH----HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
             G GYV +      ++  +  IG I  D++Y+PI++V Y +E  R GQ   YD+L M +
Sbjct: 143 RNGRGYVSSDENKLIYQNASQGIGTIFTDSIYTPIERVKYHIEPTRVGQDSKYDRLIMEV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKE----VKEDINVKSLPFNPALLKKVE 261
            T+GSI  + +++L S+IL D L   +  ++   E    +K D+   S   NP     +E
Sbjct: 203 WTNGSIQPQVALSLGSKILMDHLEQIVAIKDSVYETESVIKPDV---SGVENPMATMMIE 259

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           +L+LSVRS NCL+   I  + +L  +TE +M+R+ N G+KSL E+K  L  +GL
Sbjct: 260 DLDLSVRSYNCLKRAGIQTVEELTLKTEDEMMRIRNLGKKSLKEVKDKLHDLGL 313


>gi|258651412|ref|YP_003200568.1| DNA-directed RNA polymerase subunit alpha [Nakamurella multipartita
           DSM 44233]
 gi|258554637|gb|ACV77579.1| DNA-directed RNA polymerase, alpha subunit [Nakamurella
           multipartita DSM 44233]
          Length = 360

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 125/303 (41%), Positives = 187/303 (61%), Gaps = 20/303 (6%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR+  I EPL  GF +TLGN+LRR L+SS+ GA++T++++DGVLHE +++ GV ED+T+
Sbjct: 16  DNRSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIRVDGVLHEFTTVPGVKEDITE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           +ILN+K   L +S +  + VT++  K+GPG VTA DI     + V N D  +  L     
Sbjct: 76  LILNLK--ELVVSSEDDEPVTMYLRKQGPGDVTAADIAPPAGVTVHNSDLKLATLTKKGK 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL 
Sbjct: 134 LEIELVVERGRGYVPASPNKVVGAEIGRIPVDSIYSPVLKVTYRVEATRVEQRTDFDKLV 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNP 254
           + ++T  SIT  D++A A   L +  G+   +N +       P     + I    LP   
Sbjct: 194 LDVETKPSITPRDALASAGTTLVELFGLARELNVDAEGIEIGPSPAEADHIAAFGLP--- 250

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +EE++L+VRS NCL+ E I  +G+L+ RTEAD+L + NFG+KS+ E+K  L  MG
Sbjct: 251 -----IEEMDLTVRSYNCLKREGIHTVGELVSRTEADLLDIRNFGQKSIDEVKIKLAGMG 305

Query: 315 LFL 317
           L L
Sbjct: 306 LAL 308


>gi|161511759|emb|CAP16890.1| DNA-directed RNA polymerase subunit alpha [Pediococcus damnosus]
          Length = 265

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 113/254 (44%), Positives = 167/254 (65%), Gaps = 2/254 (0%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E+ N    + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDGVLHE S+I+GV ED+
Sbjct: 10  EKSNYGRFVVEPLERGYGTTLGNSLRRILLSSLPGAALTSVQIDGVLHEFSTIEGVVEDV 69

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  IC +     
Sbjct: 70  TQIILNLKKVSLKVESDEEKSLEINVMGPANVTAGDIVGDGDVTILNPELPICTVAEGTT 129

Query: 143 VRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
               LT  KG GY  A  +  R  + PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDK
Sbjct: 130 FHAVLTAEKGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDK 189

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L++ + TDGS+   ++++L+++IL + L +F+N ++  K+ +  +  +       L   +
Sbjct: 190 LTLDVWTDGSLAASEAISLSAKILTEHLTIFVNLDDQAKDTEIMVEKEETHKEKMLEMTI 249

Query: 261 EELELSVRSTNCLR 274
           EEL+LSVRS NCL+
Sbjct: 250 EELDLSVRSYNCLK 263


>gi|296130462|ref|YP_003637712.1| DNA-directed RNA polymerase, alpha subunit [Cellulomonas flavigena
           DSM 20109]
 gi|296022277|gb|ADG75513.1| DNA-directed RNA polymerase, alpha subunit [Cellulomonas flavigena
           DSM 20109]
          Length = 337

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 128/312 (41%), Positives = 195/312 (62%), Gaps = 16/312 (5%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E+R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S+I GV ED+T+
Sbjct: 16  EHRSRFSIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFSTIPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILNIK  NL +S ++ + V ++  K+G G VT  DI     +EV NP+  +  L+    
Sbjct: 76  IILNIK--NLVVSSENDEPVVMYLRKQGAGEVTGADIVPPAGVEVHNPELHLATLNEKGK 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +ELTV +G GYV A  +++ +  IG I ID++YSP+ KV+Y VE+ R  Q  D+DKL 
Sbjct: 134 LEIELTVERGRGYVSANQNKSFDAEIGRIPIDSIYSPVLKVTYKVEATRVEQRTDFDKLI 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLP----FNPAL 256
           + +++  +I+  D++A A R L +  G+   +N E       E I +   P        L
Sbjct: 194 VDVESKPAISPRDALASAGRTLVELFGLARELNVE------AEGIEIGPSPTDAALAADL 247

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E+L+L++RS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  +GL 
Sbjct: 248 ALPIEDLQLTIRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSITEVKEKLAELGLT 307

Query: 317 LGMNLPDWPPES 328
           L  +  D+ P +
Sbjct: 308 LKDSPLDFDPSA 319


>gi|167764346|ref|ZP_02436471.1| hypothetical protein BACSTE_02730 [Bacteroides stercoris ATCC
           43183]
 gi|167697751|gb|EDS14330.1| hypothetical protein BACSTE_02730 [Bacteroides stercoris ATCC
           43183]
          Length = 330

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 117/298 (39%), Positives = 186/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AIT ++I+GV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGITVGNALRRILLSSLEGFAITTIKIEGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDSHK--RVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +  +  +V+I         AGDI + +   EVLNP+ VIC+LD  + +++++T++
Sbjct: 88  FKQVVEEFESEKVSITIENSSEFKAGDIGKYLTGFEVLNPELVICHLDSKSTMQIDITIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y VE+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKYQVENFRVEQKTDYEKLVLEITTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  A++IL     +F    I  E    +  E+ + + L     L  K+ +++LS
Sbjct: 208 IHPKEALKEAAKILIYHFMLFSDEKITLESNDADGNEEFDEEVLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKKSLTELDDLLESLNLSFGTDISKY 325


>gi|269784300|emb|CBH50795.1| alpha subunit of RNA polymerase [Vibrio sp. C 14.7]
          Length = 261

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 113/261 (43%), Positives = 174/261 (66%), Gaps = 8/261 (3%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVT 115
           G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V 
Sbjct: 3   GCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVV 62

Query: 116 AGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLI 171
           AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG +
Sbjct: 63  AGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRL 122

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F
Sbjct: 123 LVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAF 182

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           ++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE +
Sbjct: 183 VDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVE 239

Query: 292 MLRMANFGRKSLVEIKGVLGT 312
           +L+  N G+KSL EIK VL +
Sbjct: 240 LLKTPNLGKKSLTEIKDVLAS 260


>gi|258648132|ref|ZP_05735601.1| DNA-directed RNA polymerase, alpha subunit [Prevotella tannerae
           ATCC 51259]
 gi|260852013|gb|EEX71882.1| DNA-directed RNA polymerase, alpha subunit [Prevotella tannerae
           ATCC 51259]
          Length = 330

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 119/298 (39%), Positives = 184/298 (61%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AI  ++I GV HE +SI GV ED+T+IILN+K + 
Sbjct: 28  PLESGFGVTIGNALRRILLSSLEGFAINTIKIAGVEHEFASIPGVREDVTNIILNLKQVR 87

Query: 94  LK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K  +    +++V++         AGDI + ++  EVLNP+ VI +LD  A + +ELT++
Sbjct: 88  FKHIVEELENEKVSLTISNATEFRAGDIGKHLSGFEVLNPELVIAHLDSKATISIELTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ +R     +  I ID++Y+PI+ V Y VE  R  Q  DYDKL + + TDGS
Sbjct: 148 KGRGYVPAEENRDACVEVTQIPIDSIYTPIRNVKYVVEPFRVEQKTDYDKLVLEVTTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++IL     +F    I  E+  +E  E+ + + L     L +K+ ++ LS
Sbjct: 208 IQPKDALKEAAKILIYHFMLFSDEKITMEDATQEDNEEFDEEVLHMRQVLKQKLSDMNLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L  + L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQFNKNDLLKFRNFGKKSLTELDDLLAGLNLQFGTDISKY 325


>gi|325287074|ref|YP_004262864.1| DNA-directed RNA polymerase subunit alpha [Cellulophaga lytica DSM
           7489]
 gi|324322528|gb|ADY29993.1| DNA-directed RNA polymerase subunit alpha [Cellulophaga lytica DSM
           7489]
          Length = 330

 Score =  217 bits (552), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 118/298 (39%), Positives = 183/298 (61%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRVL+S+L G AIT+V++D V HE S I GV ED+T++ILN+K + 
Sbjct: 28  PLEPGYGLTVGNALRRVLLSALEGFAITSVRMDKVEHEFSVIPGVVEDVTEMILNLKQVR 87

Query: 94  LKMSGD--SHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +    + V+I   G   +TAGD Q  ++  +VLNPD VICN+D    + ME+ + 
Sbjct: 88  FKRQIEDVEAETVSISVSGKNQLTAGDFQKFISGYQVLNPDLVICNMDAKVSINMEIVIE 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++     IG I ID++++PIK V Y++E+ R  Q  DY+KL   I +DGS
Sbjct: 148 KGRGYVPAEENKKPGAAIGTIPIDSIFTPIKNVKYSIENYRVEQKTDYEKLVFEISSDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A+++L     +F    I  E  +    E  + +SL     L  K+ +++LS
Sbjct: 208 INPKDALTEAAKVLIHHFMLFSDERITLEADEIAQTETYDEESLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   + D+++  NFG+KSL E++ ++   GL  GM+L  +
Sbjct: 268 VRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKKSLTELEELVINKGLSFGMDLSKY 325


>gi|328955885|ref|YP_004373218.1| DNA-directed RNA polymerase subunit alpha [Coriobacterium glomerans
           PW2]
 gi|328456209|gb|AEB07403.1| DNA-directed RNA polymerase subunit alpha [Coriobacterium glomerans
           PW2]
          Length = 313

 Score =  217 bits (552), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 120/296 (40%), Positives = 181/296 (61%), Gaps = 19/296 (6%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+ A+QIDG  HE  +I  + ED+TDI+LN+KG+
Sbjct: 24  EPLERGYGDTLGNSLRRVLLSSLEGAAVEAIQIDGAQHEFMTIPNMVEDVTDIVLNVKGL 83

Query: 93  NLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
             +  G + +   TI   GPG VT  D    +D E++NPD  I  L     + M + +  
Sbjct: 84  VFRSLGTTDEATATISVDGPGEVTGADFFVPSDFELVNPDQHIATLTEGGHLTMSMRIGY 143

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GY+  + ++ +NDPIG+I +D+LYSP+++ +  VE+ R GQ  DYD+L + I+T+G++
Sbjct: 144 GRGYISYEANKHDNDPIGIIHVDSLYSPVRRCAKLVEATRVGQHTDYDRLVLEIETNGAL 203

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKK----------EVKEDINVKSLPFNPALLKKVE 261
           +  D+V  A+ I+   +  F+N  E  +          EV  D        N  L K++E
Sbjct: 204 SPRDAVVSAANIINQHMASFMNLAEVPEVEEEVSIFAPEVTSD--------NAELDKQIE 255

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +L+LSVRS NCL+  +I  +  L++ +E D+L + NFG KS+ E+K  L +MGL L
Sbjct: 256 DLDLSVRSYNCLKRASIHSVRQLVEFSENDLLNIRNFGVKSIEEVKDKLESMGLGL 311


>gi|161511757|emb|CAP16889.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 263

 Score =  217 bits (552), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 113/254 (44%), Positives = 167/254 (65%), Gaps = 2/254 (0%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E+ N    + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDGVLHE S+I+GV ED+
Sbjct: 9   EKSNYGRFVVEPLERGYGTTLGNSLRRILLSSLPGAALTSVQIDGVLHEFSTIEGVVEDV 68

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  IC +     
Sbjct: 69  TQIILNLKKVSLKVESDEEKSLEINVMGPANVTAGDIVGDGDVTILNPELPICTVAEGTT 128

Query: 143 VRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
               LT  KG GY  A  +  R  + PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDK
Sbjct: 129 FHAVLTAEKGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDK 188

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L++ + TDGS+   ++++L+++IL + L +F+N ++  K+ +  +  +       L   +
Sbjct: 189 LTLDVWTDGSLAASEAISLSAKILTEHLTIFVNLDDQAKDTEIMVEKEETHKEKMLEMTI 248

Query: 261 EELELSVRSTNCLR 274
           EEL+LSVRS NCL+
Sbjct: 249 EELDLSVRSYNCLK 262


>gi|300089411|gb|ADJ67857.1| RNA polymerase alpha-subunit [Photobacterium jeanii]
          Length = 248

 Score =  216 bits (551), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 111/248 (44%), Positives = 166/248 (66%), Gaps = 7/248 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 4   EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDVLEILLNLKGL 63

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +
Sbjct: 64  AVKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNADISMRIKVER 123

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + + T+
Sbjct: 124 GRGYVPASARIHTEEDERPIGRLLVDATFSPVDRIAYAVEAARVEQRTDLDKLVIDMQTN 183

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VR
Sbjct: 184 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVR 240

Query: 269 STNCLRGE 276
           S NCL+ E
Sbjct: 241 SANCLKAE 248


>gi|198273977|ref|ZP_03206509.1| hypothetical protein BACPLE_00113 [Bacteroides plebeius DSM 17135]
 gi|198273055|gb|EDY97324.1| hypothetical protein BACPLE_00113 [Bacteroides plebeius DSM 17135]
          Length = 330

 Score =  216 bits (551), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 117/298 (39%), Positives = 186/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AI  ++I+GV HE ++I GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGITVGNALRRILLSSLEGYAINTIRIEGVEHEFATIPGVKEDVTNIILNLKQVR 87

Query: 94  LK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K  +    +++V+I         AGDI + +   EVLNP+ VIC+LD  A +++++T++
Sbjct: 88  FKRVVEEFENEKVSITVENSTEFKAGDIGKYLTGFEVLNPELVICHLDSKATMQIDITIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y VE+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPADENREFCTDVNVIPIDSIYTPIRNVKYAVENYRVEQKTDYEKLVLEITTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  A++IL     +F    I  E    E  E+ + + L     L  K+ +++LS
Sbjct: 208 IHPKEALKEAAKILIHHFMLFSDEKITLETSDAEGNEEFDEEVLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKKSLTELDDLLESLNLSFGTDISKY 325


>gi|71056810|emb|CAH58960.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
          Length = 230

 Score =  216 bits (551), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 106/210 (50%), Positives = 148/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  ICN+   A     LTV
Sbjct: 61  KGLALKMYGDEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICNVSEGASFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   ++++LA++I+ + L +F+N  +  K
Sbjct: 181 SIEPLEAMSLAAKIMTEHLDIFVNLTDEAK 210


>gi|157493283|gb|ABV58007.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 249

 Score =  216 bits (550), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 111/251 (44%), Positives = 170/251 (67%), Gaps = 8/251 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 1   EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 60

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V 
Sbjct: 61  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVE 120

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 121 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMET 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+V
Sbjct: 181 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTV 237

Query: 268 RSTNCLRGENI 278
           RS NCL+ E I
Sbjct: 238 RSANCLKAEAI 248


>gi|71056824|emb|CAH58967.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
          Length = 235

 Score =  216 bits (550), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 106/210 (50%), Positives = 148/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNI
Sbjct: 6   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNI 65

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  ICN+   A     LTV
Sbjct: 66  KGLALKMYGDEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICNVSEGASFHARLTV 125

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 126 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDG 185

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   ++++LA++I+ + L +F+N  +  K
Sbjct: 186 SIEPLEAMSLAAKIMTEHLDIFVNLTDEAK 215


>gi|72163017|ref|YP_290674.1| DNA-directed RNA polymerase subunit alpha [Thermobifida fusca YX]
 gi|90110874|sp|Q47LM1|RPOA_THEFY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|71916749|gb|AAZ56651.1| DNA-directed RNA polymerase, alpha subunit [Thermobifida fusca YX]
          Length = 338

 Score =  216 bits (550), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 119/293 (40%), Positives = 178/293 (60%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  I EPL  GF +T+GN+LRR L+SS+ GAA+T+++I+GV HE +++ GV ED+T+
Sbjct: 16  EFRSKFILEPLEPGFGYTIGNSLRRTLLSSIPGAAVTSIRIEGVEHEFTTVPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ +    D    + + K+GPGVVTA DI     +EV NP+  I  L+    + 
Sbjct: 76  IILNLKGLVVSSEHDEPVLMYLRKQGPGVVTAADIAPPAGVEVHNPEMHIATLNSKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           ME+TV +G GYV A  ++     IG I ID++YSP+ +V+Y VE+ R  Q  D+D+L + 
Sbjct: 136 MEMTVERGRGYVSAAQNKQPGQEIGRIPIDSIYSPVMRVTYKVEATRVEQRTDFDRLILD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           + T  +I   D+VA A + L +  G+        + +    +         L   +E+L 
Sbjct: 196 VWTKPAIRPRDAVASAGKTLVELFGLARELNVDAEGIDMGPSPTDAALAADLALPIEDLN 255

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+VRS NCL+ E I  +G+L+ RTE D+L + NFG KS+ E+K  L  MGL L
Sbjct: 256 LTVRSYNCLKREGIHTVGELVARTEQDLLDIRNFGAKSIEEVKQKLSDMGLAL 308


>gi|291298742|ref|YP_003510020.1| DNA-directed RNA polymerase subunit alpha [Stackebrandtia
           nassauensis DSM 44728]
 gi|290567962|gb|ADD40927.1| DNA-directed RNA polymerase, alpha subunit [Stackebrandtia
           nassauensis DSM 44728]
          Length = 345

 Score =  216 bits (550), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 129/320 (40%), Positives = 193/320 (60%), Gaps = 15/320 (4%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           + R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I G  ED+ +
Sbjct: 16  DTRSRFSIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTIPGAKEDVVE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           ++LN+K   L +S +  + VT++  K+GPG VTAGDIQ  + + V NP+  +  L+    
Sbjct: 76  LVLNVK--QLCVSSELDEPVTMYLRKQGPGDVTAGDIQPPSGVTVHNPELKLATLNGKGR 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + MEL V +G GYV A  ++     IG I +D++YSP+ KVSY VE+ R  Q  D+DKL 
Sbjct: 134 LDMELIVERGRGYVSAAQNKQAGAGIGRIPVDSIYSPVVKVSYRVEATRVEQRTDFDKLI 193

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK--- 259
           + ++T  S     ++A A   L +  G++   +       E I+V   P +  L      
Sbjct: 194 IDVETKPSTGPRTALASAGSTLVELFGLYRELD----SAAEGIDVGPSPADAQLAADLAL 249

Query: 260 -VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +EELEL+VRS NCL+ E +  +G+LI RTEAD+L + NFG+KS+ E+K  L  +GL L 
Sbjct: 250 PIEELELTVRSYNCLKREGVDQVGELINRTEADLLDIRNFGQKSIDEVKMKLAGLGLALK 309

Query: 319 MNLPDWPPESIEELAKKYED 338
            +   + P    E A  Y+D
Sbjct: 310 DSPGTFDP---AEAAAAYDD 326


>gi|329956729|ref|ZP_08297302.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides clarus YIT
           12056]
 gi|328524101|gb|EGF51177.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides clarus YIT
           12056]
          Length = 330

 Score =  216 bits (550), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 117/298 (39%), Positives = 186/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AIT ++I+GV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGITVGNALRRILLSSLEGFAITTIKIEGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDSHK--RVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +  +  +V+I         AGDI + +   EVLNP+ VIC+LD  + +++++T++
Sbjct: 88  FKQVVEEFESEKVSITIENSSEFKAGDIGKYLTGFEVLNPELVICHLDSKSTMQIDITIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y VE+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKYQVENFRVEQKTDYEKLVLEITTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  A++IL     +F    I  E    +  E+ + + L     L  K+ +++LS
Sbjct: 208 IHPKEALKEAAKILIYHFMLFSDEKITLESNDVDGNEEFDEEVLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKKSLTELDDLLESLNLSFGTDISKY 325


>gi|153812445|ref|ZP_01965113.1| hypothetical protein RUMOBE_02844 [Ruminococcus obeum ATCC 29174]
 gi|149831370|gb|EDM86458.1| hypothetical protein RUMOBE_02844 [Ruminococcus obeum ATCC 29174]
          Length = 276

 Score =  216 bits (550), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 116/271 (42%), Positives = 179/271 (66%), Gaps = 4/271 (1%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSH-KRVTIFK 108
           ++SSL GAA++ V+IDGVLHE SSI GV ED+++II+N+K + +K  S D+  K   I  
Sbjct: 1   MLSSLPGAAVSQVKIDGVLHEFSSIPGVKEDVSEIIMNLKSLAIKNNSADNEPKTAYIEC 60

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMELTVSKGHGYVPAKHHRTEND 166
            G GVVTA DIQ   DIE++NPD VI  L+   D  + MELT+++G GYV A   +T++ 
Sbjct: 61  EGKGVVTAADIQADQDIEIMNPDQVIATLNGGKDCRLAMELTITRGRGYVSADKGKTDDM 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           PIG++ +DA+Y+P+ +V+  V++ R GQ+ DYDKL++ + T+G++  +++V+LA+++L +
Sbjct: 121 PIGVLAVDAIYTPVDRVNMIVQNTRVGQITDYDKLTLDVYTNGTLDPDEAVSLAAKVLSE 180

Query: 227 QLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQ 286
            L +FI+  E  K  +  I  +       L   ++ELELSVRS NCL+   I  + +L  
Sbjct: 181 HLSLFIDLSENAKTAEVMIEKEDNEKEKVLEMSIDELELSVRSYNCLKRAGINTVEELCN 240

Query: 287 RTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +T  DM+++ N GRKSL E+   L  +GL L
Sbjct: 241 KTSDDMMKVRNLGRKSLEEVLAKLKELGLQL 271


>gi|224023645|ref|ZP_03642011.1| hypothetical protein BACCOPRO_00352 [Bacteroides coprophilus DSM
           18228]
 gi|224016867|gb|EEF74879.1| hypothetical protein BACCOPRO_00352 [Bacteroides coprophilus DSM
           18228]
          Length = 330

 Score =  216 bits (550), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 117/298 (39%), Positives = 184/298 (61%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AI  + IDGV HE ++I GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGITVGNALRRILLSSLEGYAINTIHIDGVEHEFATIPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   +++V+I         AGDI + +   EVLNP+ VIC+LD    ++M++T++
Sbjct: 88  FKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGFEVLNPELVICHLDSKTTMQMDITIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y VE+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKYAVENYRVEQKTDYEKLVLEITTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  A++IL     +F    I  E    +  E+ + + L     L  K+ +++LS
Sbjct: 208 IHPKEALKEAAKILIYHFMLFSDEKITLETSDVDGNEEFDEEVLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKKSLTELDDLLESLNLSFGTDISKY 325


>gi|283782779|ref|YP_003373533.1| DNA-directed RNA polymerase, alpha subunit [Gardnerella vaginalis
           409-05]
 gi|283441001|gb|ADB13467.1| DNA-directed RNA polymerase, alpha subunit [Gardnerella vaginalis
           409-05]
          Length = 331

 Score =  216 bits (550), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 124/298 (41%), Positives = 177/298 (59%), Gaps = 12/298 (4%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
            R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ GV ED+T+I
Sbjct: 17  QRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTTLPGVEEDVTEI 76

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           +LNIKGI L    D    + + K G G  TAGDI     + + NPD  I  L  D  + +
Sbjct: 77  LLNIKGIVLTSEYDEPVVMYLRKNGKGEATAGDITPPAGVTIANPDLHIATLAEDGELEI 136

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           E TV +G GYVPA+ ++ EN  IG I +D++YSP+ KVSY VE+ R  Q  D+DKL + +
Sbjct: 137 EFTVERGRGYVPAQMNKQENSEIGRIPVDSIYSPVLKVSYKVEATRVEQRTDFDKLILDV 196

Query: 206 DTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLP----FNPALLKK 259
           +T  +IT  D+VA A   L +  G+   +N +       E + V   P     +  L   
Sbjct: 197 ETKPAITPRDAVASAGSTLVELFGLCRELNVD------AEGVEVGPAPTHDEADSQLAIP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +E++  + RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L  MGL L
Sbjct: 251 IEDMNFTQRSYNCLKREGIHTVGELVVHTEQDLLDIRNFGMKSIDEVKEKLQAMGLSL 308


>gi|160888372|ref|ZP_02069375.1| hypothetical protein BACUNI_00785 [Bacteroides uniformis ATCC 8492]
 gi|270294725|ref|ZP_06200926.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. D20]
 gi|317477725|ref|ZP_07936918.1| DNA-directed RNA polymerase [Bacteroides sp. 4_1_36]
 gi|156862049|gb|EDO55480.1| hypothetical protein BACUNI_00785 [Bacteroides uniformis ATCC 8492]
 gi|270273972|gb|EFA19833.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. D20]
 gi|316906070|gb|EFV27831.1| DNA-directed RNA polymerase [Bacteroides sp. 4_1_36]
          Length = 330

 Score =  216 bits (550), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 117/298 (39%), Positives = 185/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AIT ++IDGV HE SS+ G  ED+T+IILN+K + 
Sbjct: 28  PLEPGFGITVGNALRRILLSSLEGFAITTIKIDGVEHEFSSVPGAKEDVTNIILNLKQVR 87

Query: 94  LKMSGDSHK--RVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +  +  +V+I         AGDI + +   EVLNP+ VIC+LD  + +++++T++
Sbjct: 88  FKQVVEEFESEKVSITVENSSEFKAGDIGKYLTGFEVLNPELVICHLDSKSTMQIDITIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y VE+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKYQVENFRVEQKTDYEKLVLEITTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  A++IL     +F    I  E    +  E+ + + L     L  K+ +++LS
Sbjct: 208 IHPKEALKEAAKILIYHFMLFSDEKITLETNDVDGNEEFDEEVLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKKSLTELDDLLESLNLSFGTDISKY 325


>gi|190411113|gb|ACE78311.1| RpoA [Vibrio campbellii]
          Length = 257

 Score =  216 bits (550), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 111/260 (42%), Positives = 175/260 (67%), Gaps = 8/260 (3%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRV 104
           ALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +
Sbjct: 1   ALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---H 160
           T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H
Sbjct: 61  TLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIH 120

Query: 161 HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           +  +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A
Sbjct: 121 NEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRA 180

Query: 221 SRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVY 280
           + IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VRS NC + E I Y
Sbjct: 181 ATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCRKAEAIHY 237

Query: 281 MGDLIQRTEADMLRMANFGR 300
           +GDL+QRTE ++L+  N G+
Sbjct: 238 IGDLVQRTEVELLKTPNLGK 257


>gi|156752147|gb|ABU93824.1| RNA polymerase subunit A [Vibrio sp. 09022]
          Length = 256

 Score =  216 bits (550), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 111/259 (42%), Positives = 174/259 (67%), Gaps = 8/259 (3%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVT 105
           LRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T
Sbjct: 1   LRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFIT 60

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HH 161
           + K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H 
Sbjct: 61  LNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHT 120

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
             +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+
Sbjct: 121 EEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAA 180

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
            IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+
Sbjct: 181 TILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYI 237

Query: 282 GDLIQRTEADMLRMANFGR 300
           GDL+QRTE ++L+  N G+
Sbjct: 238 GDLVQRTEVELLKTPNLGK 256


>gi|71056908|emb|CAH59011.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
 gi|71056945|emb|CAH59032.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
          Length = 226

 Score =  216 bits (550), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 106/210 (50%), Positives = 148/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  ICN+   A     LTV
Sbjct: 61  KGLALKMYGDEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICNVSEGASFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   ++++LA++I+ + L +F+N  +  K
Sbjct: 181 SIEPLEAMSLAAKIMTEHLDIFVNLTDEAK 210


>gi|225011672|ref|ZP_03702110.1| DNA-directed RNA polymerase, alpha subunit [Flavobacteria bacterium
           MS024-2A]
 gi|225004175|gb|EEG42147.1| DNA-directed RNA polymerase, alpha subunit [Flavobacteria bacterium
           MS024-2A]
          Length = 330

 Score =  216 bits (550), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 117/298 (39%), Positives = 185/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRVL+SSL G AIT+V+++ V HE S+I GV ED+T+IILN+K + 
Sbjct: 28  PLEPGYGLTVGNALRRVLLSSLEGFAITSVKLENVEHEFSTIPGVVEDVTEIILNLKQVR 87

Query: 94  LK--MSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K  +     ++VT+   G   + A D+Q  ++  +VLNPD VIC+L+    + ME+ + 
Sbjct: 88  FKRQIEDTEEEKVTVIIGGQEQLKAADLQKFISGFQVLNPDLVICHLEKSVQLNMEIAIE 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ ++  N  +G+I ID++++PIK V Y++E+ R  Q  DY+KL   I TDGS
Sbjct: 148 KGRGYVPAEENKKANAELGVIAIDSIFTPIKNVKYSIENFRVEQKTDYEKLVFEIITDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++ L     +F    I  E  +    E  + +SL     L  K+ +++LS
Sbjct: 208 IHPKDALTEAAKTLIHHFLLFSDERITLEADEIAQTETYDEESLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +GDL+   + D+++  NFG+KSL E++ ++   GL  GM+L  +
Sbjct: 268 VRALNCLKAAEVDTLGDLVSYNKNDLMKFRNFGKKSLTELEELVVLKGLSFGMDLAKY 325


>gi|187251794|ref|YP_001876276.1| DNA-directed RNA polymerase subunit alpha [Elusimicrobium minutum
           Pei191]
 gi|186971954|gb|ACC98939.1| DNA-directed RNA polymerase, alpha subunit [Elusimicrobium minutum
           Pei191]
          Length = 329

 Score =  216 bits (550), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 123/306 (40%), Positives = 181/306 (59%), Gaps = 16/306 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +IAEP   G+ HT+GN+LRR+L+S L G+A+TAV++ G +HE S+I  V ED+ +I+LN+
Sbjct: 26  IIAEPYESGYGHTVGNSLRRILLSGLDGSAVTAVRVRGAVHEYSTIPNVKEDVINILLNL 85

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + +K+ G + + V +    PG VTA DI  V+ +E++N D  I NL+    + +E+ +
Sbjct: 86  KKLRVKLEGKNREYVYLTASKPGKVTAKDIAEVSGVEIINKDLEIANLEQGGKLELEIEI 145

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           S+G GYVPA+       P G I +DA++SPI KV Y VE AR GQ  DYD+L + I TDG
Sbjct: 146 SQGKGYVPAEDLSKIQRPAGFIPVDAIFSPILKVHYDVEPARVGQKTDYDRLVIQITTDG 205

Query: 210 SITGEDSVALASRILQDQLGMF------INFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
           ++    ++  A+ +L   L +F      +N   P+ E        S+    A+  KVEEL
Sbjct: 206 TLEPAKALHKAAVLLSQSLHIFTIEGEEVNAAAPETEPLS--TTGSVSGVSAVNSKVEEL 263

Query: 264 --------ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
                   ELS RS NCL+ E +  + DL+ +TE D+  + NFG +SL E+K  L  M L
Sbjct: 264 LNQSVEFIELSSRSINCLKSEGVNTVKDLVSKTEDDLKMIKNFGTRSLDEVKERLAEMNL 323

Query: 316 FLGMNL 321
            LGM  
Sbjct: 324 SLGMKF 329


>gi|295396439|ref|ZP_06806601.1| DNA-directed RNA polymerase subunit alpha [Brevibacterium
           mcbrellneri ATCC 49030]
 gi|294970741|gb|EFG46654.1| DNA-directed RNA polymerase subunit alpha [Brevibacterium
           mcbrellneri ATCC 49030]
          Length = 332

 Score =  216 bits (549), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 121/297 (40%), Positives = 184/297 (61%), Gaps = 12/297 (4%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
           R+  I EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVLHE S++ GV ED+T+ I
Sbjct: 18  RSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVLHEFSTVPGVKEDVTEFI 77

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+K + +    D      + K+GPG VTA DI     +EV NPD  I +L+ +  + +E
Sbjct: 78  LNLKSLVVSSEFDEPVVAYLRKQGPGEVTAADISAPGGVEVHNPDLHIASLNDEGQLDIE 137

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           LT+ +G GYV A  ++  +  IG I +D++YSP+ KV+Y VE+ R  Q  D+D+L + ++
Sbjct: 138 LTIERGRGYVSAAQNKNADAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDRLIIDVE 197

Query: 207 TDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPF----NPALLKKV 260
           T  SI   D+VA A + L +  G+   +N E       E I++   P        L   +
Sbjct: 198 TKPSILPRDAVASAGKTLVELFGLARELNVE------AEGIDIGPSPVDAALAADLALAI 251

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           E+L+L+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L  + L L
Sbjct: 252 EDLDLTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGSKSIDEVKQKLNELNLSL 308


>gi|282855170|ref|ZP_06264502.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           J139]
 gi|289427589|ref|ZP_06429301.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           J165]
 gi|295131352|ref|YP_003582015.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           SK137]
 gi|282581758|gb|EFB87143.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           J139]
 gi|289159080|gb|EFD07272.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           J165]
 gi|291375859|gb|ADD99713.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           SK137]
 gi|313773118|gb|EFS39084.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL074PA1]
 gi|313810401|gb|EFS48115.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL083PA1]
 gi|313812263|gb|EFS49977.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL025PA1]
 gi|313817984|gb|EFS55698.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL046PA2]
 gi|313819897|gb|EFS57611.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL036PA1]
 gi|313823388|gb|EFS61102.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL036PA2]
 gi|313824859|gb|EFS62573.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL063PA1]
 gi|313830101|gb|EFS67815.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL007PA1]
 gi|313832627|gb|EFS70341.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL056PA1]
 gi|314925754|gb|EFS89585.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL036PA3]
 gi|314960834|gb|EFT04935.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL002PA2]
 gi|314964876|gb|EFT08975.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL082PA2]
 gi|314973050|gb|EFT17146.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL053PA1]
 gi|314975546|gb|EFT19641.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL045PA1]
 gi|314979765|gb|EFT23859.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL072PA2]
 gi|314982217|gb|EFT26310.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL110PA3]
 gi|314984829|gb|EFT28921.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL005PA1]
 gi|314986088|gb|EFT30180.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL005PA2]
 gi|314988703|gb|EFT32794.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL005PA3]
 gi|315079863|gb|EFT51839.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL078PA1]
 gi|315083183|gb|EFT55159.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL027PA2]
 gi|315086863|gb|EFT58839.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL002PA3]
 gi|315089955|gb|EFT61931.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL072PA1]
 gi|315090477|gb|EFT62453.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL110PA4]
 gi|315093710|gb|EFT65686.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL060PA1]
 gi|315096723|gb|EFT68699.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL038PA1]
 gi|315104002|gb|EFT75978.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL050PA2]
 gi|327325137|gb|EGE66943.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL096PA3]
 gi|327325234|gb|EGE67039.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL096PA2]
 gi|327325530|gb|EGE67329.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL103PA1]
 gi|327444034|gb|EGE90688.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL043PA1]
 gi|327449338|gb|EGE95992.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL013PA2]
 gi|327449434|gb|EGE96088.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL043PA2]
 gi|328756317|gb|EGF69933.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL020PA1]
 gi|328761349|gb|EGF74876.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL099PA1]
          Length = 338

 Score =  216 bits (549), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 125/308 (40%), Positives = 185/308 (60%), Gaps = 12/308 (3%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV HE S+I+G  ED+T+
Sbjct: 16  EFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQHEFSTIEGCVEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ L    D    + + K G G VTA DI     + + NP+  I  L+ D    
Sbjct: 76  IILNLKGLVLSSEEDEPVAMYLRKSGAGEVTAADINPPAGVTIHNPELHIATLNDDGRFE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MEL V +G GYV +  +   N  IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL + 
Sbjct: 136 MELIVERGRGYVSSALNDDPNAEIGRIAVDSIYSPVLKVTYKVEATRVEQRTDFDKLVVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLP----FNPALLK 258
           ++T  SI   D++A A + L +  G+   +N E       E I + S P    +  +L  
Sbjct: 196 VETKPSILPRDAIASAGKTLVELFGLTRELNAE------AEGIEIGSGPVDEEYAESLGT 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  +GL L 
Sbjct: 250 PVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEKLTELGLALK 309

Query: 319 MNLPDWPP 326
            + P + P
Sbjct: 310 DSAPGFDP 317


>gi|325972636|ref|YP_004248827.1| DNA-directed RNA polymerase subunit alpha [Spirochaeta sp. Buddy]
 gi|324027874|gb|ADY14633.1| DNA-directed RNA polymerase subunit alpha [Spirochaeta sp. Buddy]
          Length = 350

 Score =  216 bits (549), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 125/306 (40%), Positives = 187/306 (61%), Gaps = 11/306 (3%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-----DGVLHEISS---- 74
           E N    IA P  RGF  T+GN LRRVL+SS++G A+TAV+      DGV H ISS    
Sbjct: 24  EPNYGKFIAYPFERGFGTTIGNTLRRVLLSSIQGYAVTAVKFTSFNEDGVPHLISSEYEQ 83

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           + GV ED+ DII  +K + ++M  DS    + I  +GPG+VT  + +  + +E+ N D V
Sbjct: 84  LPGVREDIADIIAALKKLQIRMPEDSEGTNLLIECKGPGIVTGANFER-DQVEITNKDLV 142

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           +  +  DA + ME+ +  G GYVP++ +    + IG I IDA +SP+ +V Y++E  R G
Sbjct: 143 LFTMMDDANIEMEVQIDLGRGYVPSEINEKYVEEIGTIPIDATFSPVTRVKYSIEPTRVG 202

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
              DYDKL++ I TDG+I  ++++A A++I ++   +FINF+E      ++++ +     
Sbjct: 203 YRSDYDKLTLEIYTDGTIAPQNALAEAAKIAKEYFQIFINFDETLISNNDEVDEEEERVR 262

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
             L   VEELEL+VRS+NCL+  NI  +GDL ++TE ++ +  NFG+KSL EIK  L   
Sbjct: 263 KILNTSVEELELTVRSSNCLKNANIRTIGDLTKKTEEEIAKTRNFGKKSLQEIKEKLKEW 322

Query: 314 GLFLGM 319
            L LGM
Sbjct: 323 NLSLGM 328


>gi|311744778|ref|ZP_07718574.1| DNA-directed RNA polymerase subunit alpha [Aeromicrobium marinum
           DSM 15272]
 gi|311311895|gb|EFQ81816.1| DNA-directed RNA polymerase subunit alpha [Aeromicrobium marinum
           DSM 15272]
          Length = 336

 Score =  216 bits (549), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 125/314 (39%), Positives = 193/314 (61%), Gaps = 16/314 (5%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S++ GV ED+T
Sbjct: 15  DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFSTVPGVTEDVT 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRG--PGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +IILN+K  NL +S ++ + V ++ R    GVVT  +I+    +EV NPD  +  L+   
Sbjct: 75  EIILNLK--NLVVSSENDEPVVMYLRADTAGVVTGANIEPPAGVEVHNPDLHVATLNDKG 132

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + +EL V +G GYV A  ++T ++ IG + ID++YSP+ KV+Y VE+ R  Q  D+D+L
Sbjct: 133 RLEIELVVERGRGYVSAVQNKTGDEEIGRMPIDSIYSPVLKVTYKVEATRVEQRTDFDRL 192

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKK 259
            + ++T  SI   D++A A   L +  G+   +N E       E I++   P +  L   
Sbjct: 193 VVDVETKKSILPRDAIASAGSTLVELFGLARELNVE------AEGIDIGPSPVDEQLAAD 246

Query: 260 ----VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
               +E+L  +VRS NCL+ E I  +G+LI R+E D+L + NFG KS+ E+K  L  MGL
Sbjct: 247 LALPIEDLNFTVRSYNCLKREGIHTVGELITRSEQDLLDIRNFGSKSIDEVKAKLAEMGL 306

Query: 316 FLGMNLPDWPPESI 329
            L  +   + P ++
Sbjct: 307 ALKDSPAGFDPSAV 320


>gi|313204944|ref|YP_004043601.1| DNA-directed RNA polymerase subunit alpha [Paludibacter
           propionicigenes WB4]
 gi|312444260|gb|ADQ80616.1| DNA-directed RNA polymerase subunit alpha [Paludibacter
           propionicigenes WB4]
          Length = 330

 Score =  216 bits (549), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 119/298 (39%), Positives = 189/298 (63%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRR+L+SSL G AIT+++I+G+ HE S+I GV +D+T+IILN+K + 
Sbjct: 28  PLEPGYGITIGNALRRILLSSLEGFAITSIKIEGIDHEYSTIPGVIDDVTNIILNLKQVR 87

Query: 94  LK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K  +    +++VTI   G     AGDI +     EVLNP  VIC LD  A  ++++TV+
Sbjct: 88  FKQIVEDIENEKVTINVSGTTSFKAGDIGKYFTGFEVLNPKLVICELDPSASFQIDITVN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GY P++ ++  N  IGLI IDA+++PI+ V Y++E+ R  QV DY+KL + I TDGS
Sbjct: 148 KGRGYAPSEENKPANAEIGLIPIDAIFTPIRNVKYSIENYRVEQVTDYEKLVLEISTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  +++IL     +F    I+ E  + E  ++ + + L     L  K+ +LELS
Sbjct: 208 IHPKEALKESAKILIHHFMLFSDEKISLEVTEGEGSDEFDEEILHMRQLLKTKLTDLELS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +G L    + D+L+  NFG+KSL E++  L ++ L  GM++  +
Sbjct: 268 VRALNCLKAADVDTLGQLAGYHKHDLLKFRNFGKKSLTELEEKLESLNLSFGMDIAKY 325


>gi|313808805|gb|EFS47259.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL087PA2]
          Length = 338

 Score =  216 bits (549), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 125/308 (40%), Positives = 185/308 (60%), Gaps = 12/308 (3%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV HE S+I+G  ED+T+
Sbjct: 16  EFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQHEFSTIEGCVEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ L    D    + + K G G VTA DI     + + NP+  I  L+ D    
Sbjct: 76  IILNLKGLVLSSEEDEPVAMYLRKSGAGEVTAADITPPAGVTIHNPELHIATLNDDGRFE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MEL V +G GYV +  +   N  IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL + 
Sbjct: 136 MELIVERGRGYVSSALNDDPNAEIGRIAVDSIYSPVLKVTYKVEATRVEQRTDFDKLVVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLP----FNPALLK 258
           ++T  SI   D++A A + L +  G+   +N E       E I + S P    +  +L  
Sbjct: 196 VETKPSILPRDAIASAGKTLVELFGLTRELNAE------AEGIEIGSGPVDEEYAESLGT 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  +GL L 
Sbjct: 250 PVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEKLTELGLALK 309

Query: 319 MNLPDWPP 326
            + P + P
Sbjct: 310 DSAPGFDP 317


>gi|289423648|ref|ZP_06425447.1| DNA-directed RNA polymerase, alpha subunit [Peptostreptococcus
           anaerobius 653-L]
 gi|289155898|gb|EFD04564.1| DNA-directed RNA polymerase, alpha subunit [Peptostreptococcus
           anaerobius 653-L]
          Length = 315

 Score =  216 bits (549), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 112/277 (40%), Positives = 182/277 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  T+GNALRR+L+SSL G A+ A++IDGVLHE S++ GV ED+T+IIL++
Sbjct: 23  FVVEPLERGFGITVGNALRRILLSSLPGVAVYAIRIDGVLHEFSTVPGVKEDVTEIILSL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K ++  +  +  K + I   GP  V   DI    ++ +++ D  I  LD  A + ME+ V
Sbjct: 83  KELSATIDDEEPKVLRIQAIGPCEVKGSDIICPPEVNIVSKDLHIATLDEGAKLNMEIYV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GY+ A+ ++ E+ PIG++ +D++Y+P++KVSY VE+ R GQ  D+DKL++ + T+G
Sbjct: 143 NKGRGYISAEENKKESMPIGVLPVDSIYTPVEKVSYHVENTRVGQRSDFDKLTLEVLTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI  ++ ++LA+++L + L +FI+  E    V+  +  +       L   +EEL+LSVRS
Sbjct: 203 SINPQEGISLAAKVLDEHLKLFIDLTEHVGNVEIMVEKEEDKKEKVLEMTIEELDLSVRS 262

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            NCL+   I  + +L  ++E DM+++ N G+KSL E+
Sbjct: 263 YNCLKRAGINTVEELSNKSEDDMMKVRNLGKKSLEEV 299


>gi|150003362|ref|YP_001298106.1| DNA-directed RNA polymerase subunit alpha [Bacteroides vulgatus
           ATCC 8482]
 gi|212695279|ref|ZP_03303407.1| hypothetical protein BACDOR_04819 [Bacteroides dorei DSM 17855]
 gi|237711701|ref|ZP_04542182.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp.
           9_1_42FAA]
 gi|237725858|ref|ZP_04556339.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. D4]
 gi|254881349|ref|ZP_05254059.1| RNA polymerase subunit alpha [Bacteroides sp. 4_3_47FAA]
 gi|265753120|ref|ZP_06088689.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp.
           3_1_33FAA]
 gi|294777846|ref|ZP_06743290.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides vulgatus
           PC510]
 gi|319640350|ref|ZP_07995075.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. 3_1_40A]
 gi|172048639|sp|A6KYH0|RPOA_BACV8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|149931786|gb|ABR38484.1| DNA-directed RNA polymerase alpha chain [Bacteroides vulgatus ATCC
           8482]
 gi|212662189|gb|EEB22763.1| hypothetical protein BACDOR_04819 [Bacteroides dorei DSM 17855]
 gi|229435666|gb|EEO45743.1| DNA-directed RNA polymerase subunit alpha [Bacteroides dorei
           5_1_36/D4]
 gi|229454396|gb|EEO60117.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp.
           9_1_42FAA]
 gi|254834142|gb|EET14451.1| RNA polymerase subunit alpha [Bacteroides sp. 4_3_47FAA]
 gi|263236306|gb|EEZ21801.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp.
           3_1_33FAA]
 gi|294448300|gb|EFG16856.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides vulgatus
           PC510]
 gi|317388125|gb|EFV68979.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. 3_1_40A]
          Length = 330

 Score =  216 bits (549), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 117/298 (39%), Positives = 185/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AI  ++I+GV HE +S+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGITVGNALRRILLSSLEGFAINTIKIEGVEHEFASVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   +++V+I         AGDI + +   EVLNP+ VIC+LD  A ++M++T++
Sbjct: 88  FKQVVEEFENEKVSITVENSSEFKAGDISKYLTGFEVLNPELVICHLDSKATMQMDITIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y VE+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKYQVENFRVEQKTDYEKLVLEITTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  A++IL     +F    I  E    +  E+ + + L     L  K+ +++LS
Sbjct: 208 IHPKEALKEAAKILIYHFMLFSDEKITLETSDVDGNEEFDEEVLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L  + L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKKSLTELDDLLEGLNLSFGTDISKY 325


>gi|288925688|ref|ZP_06419620.1| DNA-directed RNA polymerase, alpha subunit [Prevotella buccae D17]
 gi|315606477|ref|ZP_07881492.1| DNA-directed RNA polymerase subunit alpha [Prevotella buccae ATCC
           33574]
 gi|288337626|gb|EFC75980.1| DNA-directed RNA polymerase, alpha subunit [Prevotella buccae D17]
 gi|315251883|gb|EFU31857.1| DNA-directed RNA polymerase subunit alpha [Prevotella buccae ATCC
           33574]
          Length = 330

 Score =  215 bits (548), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 116/298 (38%), Positives = 183/298 (61%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AI  ++I GV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGVTIGNALRRILLSSLEGYAINTIKIAGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   +++V+I         AGDI + +   EVLNPD VIC+LD  A ++++L ++
Sbjct: 88  FKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGFEVLNPDLVICHLDTKASMQIDLNIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ +R     + ++ ID++Y+PI+ V Y VE  R  Q  DYDKL + + TDGS
Sbjct: 148 KGRGYVPAEENREFCTDVNVLPIDSIYTPIRNVKYAVEPYRVEQKTDYDKLVIEVTTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  +D++  A++ L     +F    I  E P ++  ++ + + L     L  ++ ++ LS
Sbjct: 208 IHPKDALKEAAKTLIYHFMLFSDEKITLENPDQDNNQEFDEEVLHMRQLLKTRLVDMNLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L  + L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKKSLSELDDLLEGLNLSFGTDISKY 325


>gi|161511769|emb|CAP16895.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 262

 Score =  215 bits (548), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 116/254 (45%), Positives = 164/254 (64%), Gaps = 2/254 (0%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E +N    + EPL RG+  TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+
Sbjct: 8   ENDNYGRFVIEPLERGYGTTLGNSLRRILLSSLPGAAITSVQIDSVLHEFSTIEGVVEDV 67

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  IC +     
Sbjct: 68  TQIILNLKKVSLKIESDEDKTLEINVAGPANVTAGDIMGDGDVVILNPELPICTVAEGTT 127

Query: 143 VRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
               LT   G GY  A  +  R  + PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDK
Sbjct: 128 FHAVLTADTGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDK 187

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L++ I TDGSIT  ++ +L+++IL + L +F+N  +  KE +  +  +       L   +
Sbjct: 188 LTLDIWTDGSITPSEATSLSAKILTEHLAIFVNLNDQAKETEIMVEKEETHKEKMLEMTI 247

Query: 261 EELELSVRSTNCLR 274
           EEL+LSVRS NCL+
Sbjct: 248 EELDLSVRSYNCLK 261


>gi|327332743|gb|EGE74477.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL097PA1]
          Length = 338

 Score =  215 bits (548), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 125/308 (40%), Positives = 185/308 (60%), Gaps = 12/308 (3%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV HE S+I+G  ED+T+
Sbjct: 16  EFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQHEFSTIEGCVEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ L    D    + + K G G VTA DI     + + NP+  I  L+ D    
Sbjct: 76  IILNLKGLVLSSEEDEPVAMYLRKTGAGEVTAADINPPAGVTIHNPELHIATLNDDGRFE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MEL V +G GYV +  +   N  IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL + 
Sbjct: 136 MELIVERGRGYVSSALNDDPNAEIGRIAVDSIYSPVLKVTYKVEATRVEQRTDFDKLVVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLP----FNPALLK 258
           ++T  SI   D++A A + L +  G+   +N E       E I + S P    +  +L  
Sbjct: 196 VETKPSILPRDAIASAGKTLVELFGLTRELNAE------AEGIEIGSGPVDEEYAESLGT 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  +GL L 
Sbjct: 250 PVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEKLTELGLALK 309

Query: 319 MNLPDWPP 326
            + P + P
Sbjct: 310 DSAPGFDP 317


>gi|328813943|gb|AEB52087.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 250

 Score =  215 bits (548), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 112/249 (44%), Positives = 167/249 (67%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNIK + LKM+ D  
Sbjct: 2   TLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNTDED 61

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV KG GYV A  +
Sbjct: 62  KNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAADQN 121

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           ++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA+
Sbjct: 122 KSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAA 181

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           +IL + L +F+N  +  K  +  +  +       L   +EEL+LSVRS NCL+   I  +
Sbjct: 182 KILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTV 241

Query: 282 GDLIQRTEA 290
            +L  +TEA
Sbjct: 242 QELTNKTEA 250


>gi|313292080|gb|ADR51229.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 241

 Score =  215 bits (548), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 107/217 (49%), Positives = 151/217 (69%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+
Sbjct: 7   EEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDV 66

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILNIKG+ LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A 
Sbjct: 67  TQIILNIKGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGAT 126

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
               LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+
Sbjct: 127 FHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLT 186

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           M I TDGSI   ++++L+++I+ + L +F+N  +  K
Sbjct: 187 MEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAK 223


>gi|50843283|ref|YP_056510.1| DNA-directed RNA polymerase subunit alpha [Propionibacterium acnes
           KPA171202]
 gi|289424833|ref|ZP_06426615.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           SK187]
 gi|61215892|sp|Q6A6R1|RPOA_PROAC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|50840885|gb|AAT83552.1| DNA-directed RNA polymerase alpha chain [Propionibacterium acnes
           KPA171202]
 gi|289154796|gb|EFD03479.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           SK187]
 gi|313763203|gb|EFS34567.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL013PA1]
 gi|313793292|gb|EFS41350.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL110PA1]
 gi|313801064|gb|EFS42332.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL110PA2]
 gi|313816540|gb|EFS54254.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL059PA1]
 gi|313828399|gb|EFS66113.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL063PA2]
 gi|313837983|gb|EFS75697.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL086PA1]
 gi|314914366|gb|EFS78197.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL005PA4]
 gi|314917686|gb|EFS81517.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL050PA1]
 gi|314919582|gb|EFS83413.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL050PA3]
 gi|314930172|gb|EFS94003.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL067PA1]
 gi|314957155|gb|EFT01259.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL027PA1]
 gi|314957796|gb|EFT01899.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL002PA1]
 gi|314963508|gb|EFT07608.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL082PA1]
 gi|314969909|gb|EFT14007.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL037PA1]
 gi|315077129|gb|EFT49196.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL053PA2]
 gi|315097951|gb|EFT69927.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL059PA2]
 gi|315100594|gb|EFT72570.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL046PA1]
 gi|315106083|gb|EFT78059.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL030PA1]
 gi|327451456|gb|EGE98110.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL087PA3]
 gi|327451856|gb|EGE98510.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL083PA2]
 gi|328752070|gb|EGF65686.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL087PA1]
 gi|328755532|gb|EGF69148.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL025PA2]
          Length = 338

 Score =  215 bits (548), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 124/308 (40%), Positives = 185/308 (60%), Gaps = 12/308 (3%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV HE S+I+G  ED+T+
Sbjct: 16  EFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQHEFSTIEGCVEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ L    D    + + K G G +TA DI     + + NP+  I  L+ D    
Sbjct: 76  IILNLKGLVLSSEEDEPVAMYLRKTGAGEITAADINPPAGVTIHNPELHIATLNDDGRFE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MEL V +G GYV +  +   N  IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL + 
Sbjct: 136 MELIVERGRGYVSSALNDDPNAEIGRIAVDSIYSPVLKVTYKVEATRVEQRTDFDKLVVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLP----FNPALLK 258
           ++T  SI   D++A A + L +  G+   +N E       E I + S P    +  +L  
Sbjct: 196 VETKPSILPRDAIASAGKTLVELFGLTRELNVE------AEGIEIGSGPVDEEYAESLGT 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  +GL L 
Sbjct: 250 PVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEKLTELGLALK 309

Query: 319 MNLPDWPP 326
            + P + P
Sbjct: 310 DSAPGFDP 317


>gi|161511761|emb|CAP16891.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           ethanolidurans]
          Length = 251

 Score =  215 bits (548), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 109/245 (44%), Positives = 161/245 (65%), Gaps = 2/245 (0%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E  N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+
Sbjct: 7   ENANYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDV 66

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILNIK ++LK+  D  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +     
Sbjct: 67  TQIILNIKKVSLKIESDDEKSLEINVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVT 126

Query: 143 VRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
               LT   G GYV A  ++   D  PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDK
Sbjct: 127 FHAVLTADTGRGYVSADENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDK 186

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L++ + TDGSI+  ++ +L+++IL + L +F+N  +  ++ +  +  +       L   +
Sbjct: 187 LTLDVWTDGSISPSEATSLSAKILTEHLALFVNLTDEAQDAEIMVEKEETHKEKMLEMSI 246

Query: 261 EELEL 265
           EEL+L
Sbjct: 247 EELDL 251


>gi|315109197|gb|EFT81173.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL030PA2]
          Length = 338

 Score =  215 bits (547), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 124/308 (40%), Positives = 185/308 (60%), Gaps = 12/308 (3%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV HE S+I+G  ED+T+
Sbjct: 16  EFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQHEFSTIEGCVEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ L    D    + + K G G +TA DI     + + NP+  I  L+ D    
Sbjct: 76  IILNLKGLVLSSEEDEPVAMYLRKTGAGEITAADINPPAGVTIHNPELHIATLNDDGRFE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MEL V +G GYV +  +   N  IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL + 
Sbjct: 136 MELIVERGRGYVSSALNDDPNAEIGRIAVDSIYSPVLKVTYKVEATRVEQRTDFDKLVVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLP----FNPALLK 258
           ++T  SI   D++A A + L +  G+   +N E       E I + S P    +  +L  
Sbjct: 196 VETKPSILPRDAIASAGKTLVELFGLTRELNVE------AEGIEIGSGPVDEEYAESLGT 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  +GL L 
Sbjct: 250 PVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEKLTELGLALK 309

Query: 319 MNLPDWPP 326
            + P + P
Sbjct: 310 DSAPGFDP 317


>gi|295809868|emb|CBL85110.1| alpha subunit of RNA polymerase [Vibrio tapetis]
          Length = 263

 Score =  215 bits (547), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 113/261 (43%), Positives = 173/261 (66%), Gaps = 8/261 (3%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVT 115
           G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +K++ G     +T+ K G G V 
Sbjct: 3   GCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVKVAEGKDEVFITLNKSGSGPVV 62

Query: 116 AGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLI 171
           AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG +
Sbjct: 63  AGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASSRIHTEEDERPIGRL 122

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  ++ IL +QL  F
Sbjct: 123 LVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRSATILAEQLDAF 182

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           ++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE +
Sbjct: 183 VDLRDIRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVE 239

Query: 292 MLRMANFGRKSLVEIKGVLGT 312
           +L+  N G KSL EIK VL +
Sbjct: 240 LLKTPNLGNKSLTEIKDVLAS 260


>gi|328813979|gb|AEB52105.1| DNA-directed RNA polymerase alpha chain [Lactobacillus helveticus]
          Length = 263

 Score =  215 bits (547), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 114/264 (43%), Positives = 167/264 (63%), Gaps = 4/264 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLH
Sbjct: 3   KPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLH 58

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++VLNP
Sbjct: 59  EFSTVPGVREDVTKIILNLKKLELKSLSDERKVIELDVEGPATVTADDLKVDADVQVLNP 118

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  IC +     + ME+ V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES 
Sbjct: 119 DQYICTIAEGGHLHMEIAVQNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVEST 178

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   K  +  +  +  
Sbjct: 179 RVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADADTKFSEVMVEKEDD 238

Query: 251 PFNPALLKKVEELELSVRSTNCLR 274
                L   +EEL+LSVRS NCL+
Sbjct: 239 KKEKKLEMTIEELDLSVRSYNCLK 262


>gi|169350821|ref|ZP_02867759.1| hypothetical protein CLOSPI_01595 [Clostridium spiroforme DSM 1552]
 gi|169292407|gb|EDS74540.1| hypothetical protein CLOSPI_01595 [Clostridium spiroforme DSM 1552]
          Length = 314

 Score =  215 bits (547), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 112/293 (38%), Positives = 183/293 (62%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E +N    + EPL RGF  TLGN+LRRVL+SSL G+A+ A+++ G +HE S++ GV ED+
Sbjct: 16  ETDNYGKFVIEPLERGFGTTLGNSLRRVLLSSLPGSAVYAIKVQGAIHEFSAVDGVVEDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILN+K +   +  D    + I   GP  VT  DIQ  +++ +++ D VI ++   A 
Sbjct: 76  TSIILNLKKLVFDVDSDESATMIIDVEGPATVTGADIQCPSEVTMISNDLVIAHVAQGAH 135

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + MEL   K  GY+ A  ++ + + IG+I  D+++SP+++VSY VE  R G+   YD+L+
Sbjct: 136 LYMELYAKKDRGYISADQNKKDINTIGIIPTDSIFSPVERVSYAVEPTRVGESAKYDQLT 195

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + I+T+G++   ++++LA++IL + L MF+   +    ++     ++   N  L   +EE
Sbjct: 196 LEIETNGALKPYEAISLAAKILVEHLNMFVELTDMAVNMEVMSEAQNDTSNKVLDMTIEE 255

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           L+LSVRS NCL+   I  + DL  ++E DM+++ N G+KSL E+K  L  +GL
Sbjct: 256 LDLSVRSYNCLKRAGIQTVQDLAAKSEDDMIKVRNLGKKSLKEVKEKLVELGL 308


>gi|295809862|emb|CBL85107.1| alpha subunit of RNA polymerase [Vibrio tapetis]
          Length = 260

 Score =  215 bits (547), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 113/261 (43%), Positives = 173/261 (66%), Gaps = 8/261 (3%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVT 115
           G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +K++ G     +T+ K G G V 
Sbjct: 3   GCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVKVAEGKDEVFITLNKSGSGPVV 62

Query: 116 AGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLI 171
           AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG +
Sbjct: 63  AGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASSRIHTEEDERPIGRL 122

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  ++ IL +QL  F
Sbjct: 123 LVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRSATILAEQLDAF 182

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           ++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE +
Sbjct: 183 VDLRDIRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVE 239

Query: 292 MLRMANFGRKSLVEIKGVLGT 312
           +L+  N G KSL EIK VL +
Sbjct: 240 LLKTPNLGNKSLTEIKDVLAS 260


>gi|189460710|ref|ZP_03009495.1| hypothetical protein BACCOP_01357 [Bacteroides coprocola DSM 17136]
 gi|189432669|gb|EDV01654.1| hypothetical protein BACCOP_01357 [Bacteroides coprocola DSM 17136]
          Length = 330

 Score =  215 bits (547), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 116/298 (38%), Positives = 185/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AI  + I+GV HE +++ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGITVGNALRRILLSSLEGYAINTIHIEGVEHEFATVPGVKEDVTNIILNLKQVR 87

Query: 94  LK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K  +    +++V+I         AGDI + +   EVLNP+ VIC+LD  A ++++LT++
Sbjct: 88  FKQIVEEFENEKVSITVENSTEFKAGDIGKYLTGFEVLNPELVICHLDSKATMQIDLTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y VE+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKYAVENYRVEQKTDYEKLVLEITTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  A++IL     +F    I  E    +  E+ + + L     L  K+ +++LS
Sbjct: 208 IHPKEALKEAAKILIYHFMLFSDEKITLETSDADGNEEFDEEVLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKKSLTELDDLLESLNLSFGTDISKY 325


>gi|227494572|ref|ZP_03924888.1| DNA-directed RNA polymerase [Actinomyces coleocanis DSM 15436]
 gi|226832306|gb|EEH64689.1| DNA-directed RNA polymerase [Actinomyces coleocanis DSM 15436]
          Length = 339

 Score =  214 bits (546), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 124/295 (42%), Positives = 180/295 (61%), Gaps = 4/295 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGV HE S++ GV ED+ +
Sbjct: 26  DNRSRFILEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVQHEFSTVPGVKEDVAE 85

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILNIK I L    D    + + K G GVVTAGDI     +E+ NP+  +  L     V 
Sbjct: 86  IILNIKNIVLSSENDEPVVMYLRKTGAGVVTAGDITPPAGVEIHNPELELATLSEKGKVE 145

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELTV +G GYV A  ++  N  I  I ID++YSP+ KV+Y VE+ R  Q  D+D+L + 
Sbjct: 146 IELTVERGRGYVSAMQNKDPNAEISRIPIDSIYSPVLKVTYKVEATRVEQRTDFDRLIVD 205

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           ++T  +IT  D++A A + L +  G+   +N E    E+      ++L  + AL   +E 
Sbjct: 206 VETKPAITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSATDETLAADLAL--PIEN 263

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L L  RS N LR   I+ +G+L+  +EAD+L + NFG KS+ EIK  L  +G+ L
Sbjct: 264 LGLQSRSYNALRRRGILSVGELVAHSEADLLDIRNFGLKSIEEIKEKLAGLGMTL 318


>gi|328813975|gb|AEB52103.1| DNA-directed RNA polymerase alpha chain [Lactobacillus fermentum]
          Length = 248

 Score =  214 bits (546), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 111/246 (45%), Positives = 167/246 (67%), Gaps = 2/246 (0%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRRV+++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K
Sbjct: 1   VVEPLERGYGTTLGNSLRRVMLASLPGAAITSIQIDGVLHEFSTVQGVTEDVTQIILNLK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            + LK+  +  K + I  +GP  VTA DIQ   D+ +LN D  I  +   A + +++T  
Sbjct: 61  QVALKIDSEDAKDLEIDVKGPAEVTAADIQGDGDVTILNSDLHIATVSDGAELHVKMTAD 120

Query: 151 KGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           KG GY  A  ++T  E   IG++ ID++Y+PI++V+YTVE+ R GQ  DYDKL++ + T+
Sbjct: 121 KGRGYSSADDNKTRMEGLAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYDKLTLDVWTN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           GS+T  ++++LA++IL + L MF+N  E  +  +  +  +       L K +EEL+LSVR
Sbjct: 181 GSLTPTEAISLAAKILTEHLTMFVNLTEEAQVTQVMVEREETHQEKVLDKTIEELDLSVR 240

Query: 269 STNCLR 274
           S NCL+
Sbjct: 241 SYNCLK 246


>gi|71056870|emb|CAH58990.1| DNA-directed RNA polymerase alpha chain [Enterococcus malodoratus]
          Length = 231

 Score =  214 bits (546), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV
Sbjct: 61  KGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI  +++++LA++IL + L +F+N  +  K
Sbjct: 181 SIIAQEALSLAAKILTEHLDIFVNLTDEAK 210


>gi|159901451|ref|YP_001547698.1| DNA-directed RNA polymerase subunit alpha [Herpetosiphon
           aurantiacus ATCC 23779]
 gi|238687089|sp|A9B437|RPOA_HERA2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|159894490|gb|ABX07570.1| DNA-directed RNA polymerase, alpha subunit [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 331

 Score =  214 bits (546), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 116/286 (40%), Positives = 183/286 (63%), Gaps = 6/286 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           EN      EPL  G+ HTLGNALRRVL+SS+ GAA+  ++IDG+ HE S I+GV ED T+
Sbjct: 16  ENYGRFKIEPLDPGYGHTLGNALRRVLLSSIPGAAVIKIKIDGIFHEFSPIQGVREDATE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVV 143
           I+LN+KGI L+   +   ++ + K GPGVV A DI+  +++E++NPDH I  LD  DA +
Sbjct: 76  IVLNVKGIRLRSYAERPVKMILSKTGPGVVRASDIECPSNVEIVNPDHYIATLDSSDARL 135

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            MELTV +  GY+PA++   +  PIG I +DA+++P+ KV+Y VE  R G + D+D+L +
Sbjct: 136 DMELTVERHRGYLPAENR--DPVPIGEIPVDAIFTPVHKVNYVVEHTRIGGMTDFDRLLL 193

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE--DINVKSLPFNPALLKKVE 261
            I TDG++   D+++ A+++L     +  +F     E ++  D N   +P +      +E
Sbjct: 194 EIWTDGTVKPGDALSYAAQVLVQYSSIIADFNRFDDEQEQVGDANGLVIP-SEIYDMPIE 252

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +L+LS R+ NCL+  +I  +G +++  E  +L + N G+KS+ EI+
Sbjct: 253 DLDLSTRTYNCLKRADITKVGQVLEMDEKQLLAVRNLGQKSMDEIR 298


>gi|319938481|ref|ZP_08012875.1| DNA-directed RNA polymerase [Coprobacillus sp. 29_1]
 gi|319806397|gb|EFW03064.1| DNA-directed RNA polymerase [Coprobacillus sp. 29_1]
          Length = 314

 Score =  214 bits (546), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 119/299 (39%), Positives = 180/299 (60%), Gaps = 12/299 (4%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E +N    + EPL RGF  TLGN+LRRVL+SS+ G A+ AV++ G +HE S++ GV ED+
Sbjct: 16  ESDNYGKFVIEPLERGFGTTLGNSLRRVLLSSIPGCAVHAVKVQGAIHEFSAVDGVVEDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILNIK +   + GD    + I  +GP VVT  DIQ  +++ +++ D  I ++   A 
Sbjct: 76  TSIILNIKKLVFSIDGDDDVTMIIDVKGPAVVTGADIQCPSNVTMISNDLEIAHVAEGAH 135

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
             ME+   +  GY+ A  ++   + IG+I  D++YSP+ KV+Y  E  R GQ   YD+L+
Sbjct: 136 FYMEMYAHRDRGYMSADQNKKLINTIGVIATDSIYSPVVKVAYATEPTRVGQSAKYDQLT 195

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFE------EPKKEVKEDINVKSLPFNPAL 256
           + I TDGS+   +++ALA++IL + L MF+         E   E +ED +      N  L
Sbjct: 196 LEITTDGSVQPHEALALAAKILVEHLNMFVELTDMAMNMEVMSETEEDTS------NKVL 249

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
              +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N G+KSL E+K  L  +GL
Sbjct: 250 DMTIEELDLSVRSYNCLKRAGIQTVQELAAKSEDDMIKVRNLGKKSLKEVKEKLVELGL 308


>gi|283768437|ref|ZP_06341349.1| DNA-directed RNA polymerase, alpha subunit [Bulleidia extructa
           W1219]
 gi|283104829|gb|EFC06201.1| DNA-directed RNA polymerase, alpha subunit [Bulleidia extructa
           W1219]
          Length = 319

 Score =  214 bits (546), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 125/306 (40%), Positives = 188/306 (61%), Gaps = 11/306 (3%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           EY+    E EN    I  PL RGF  T+GNALRRVL+SSL GAA+ ++++D V HE +SI
Sbjct: 13  EYV----ESENYGRFILTPLERGFGTTIGNALRRVLLSSLPGAAVFSIKVDQVYHEFTSI 68

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
            GV ED++ IILN+K + +K+  D    + I  +GPG V A D+     +E++N D VI 
Sbjct: 69  PGVREDVSMIILNLKQLVMKIEDDEEYTLQISAKGPGTVKAADLIVPAQVEIVNKDLVIA 128

Query: 136 NLDVDAVVRMELTVSKGHGYVPA---KHHRTE-NDPIGLITIDALYSPIKKVSYTVESAR 191
           NL+V A + ME+ V  G GYV A   K  R+  +  IG +  D++Y+P+ KV+Y VE  R
Sbjct: 129 NLEVGASLEMEIKVQNGRGYVSADINKQLRSGVSQGIGTVYTDSIYTPVTKVAYHVEPTR 188

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            G+ + YD+L+M + TDGSI  + +++LA++IL D L +     + +  + + +  +S  
Sbjct: 189 VGENVKYDELTMEVTTDGSINPQKALSLAAKILVDHLEIVAGIND-EVMISDSVIKQSTA 247

Query: 252 FNPALLKK--VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
             P    +  +E+L+LSVRS NCL+   I  + +L Q+TE +M+R+ N G+KSL E+K  
Sbjct: 248 EKPNKGHQMMIEDLDLSVRSYNCLKRAGIQTVDELTQKTEDEMMRVRNLGKKSLKEVKDK 307

Query: 310 LGTMGL 315
           L  MG 
Sbjct: 308 LIEMGF 313


>gi|153854998|ref|ZP_01996211.1| hypothetical protein DORLON_02217 [Dorea longicatena DSM 13814]
 gi|149752495|gb|EDM62426.1| hypothetical protein DORLON_02217 [Dorea longicatena DSM 13814]
          Length = 276

 Score =  214 bits (546), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 114/272 (41%), Positives = 180/272 (66%), Gaps = 4/272 (1%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF--K 108
           ++SSL G+AI+ V+IDGVLHE SSI GV ED+T+II+N+K + +K + +S +  T +   
Sbjct: 1   MLSSLPGSAISQVKIDGVLHEFSSIPGVKEDVTEIIMNLKSLAIKNTSESDEPKTAYIEF 60

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMELTVSKGHGYVPAKHHRTEND 166
            G GVVTA DIQ   DIE++NP+ VI  L+   D+ + MELT++ G GYV A  ++ +  
Sbjct: 61  EGEGVVTAADIQVDQDIEIMNPETVIATLNGGADSKLYMELTITNGRGYVSADKNKNDEL 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           PI +I ID++Y+P+++V+ TVE+ R GQ+ D+DKL++ + T+G++  +++V+LA+++L +
Sbjct: 121 PIAVIPIDSIYTPVERVNLTVENTRVGQITDFDKLTLDVYTNGTLLPDEAVSLAAKVLSE 180

Query: 227 QLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQ 286
            L +FI+  E  +  +  I  +       L   ++ELELSVRS NCL+   I  + +L  
Sbjct: 181 HLKLFIDLSEVAQAAEVMIEKEDDEKEKVLEMSIDELELSVRSYNCLKRAGINTVEELTN 240

Query: 287 RTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RT  DM+++ N GRKSL E+   L  +GL L 
Sbjct: 241 RTPEDMMKVRNLGRKSLEEVLAKLDELGLSLS 272


>gi|88608775|ref|YP_506180.1| DNA-directed RNA polymerase subunit alpha [Neorickettsia sennetsu
           str. Miyayama]
 gi|119366702|sp|Q2GEB6|RPOA_NEOSM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|88600944|gb|ABD46412.1| DNA-directed RNA polymerase, alpha subunit [Neorickettsia sennetsu
           str. Miyayama]
          Length = 333

 Score =  214 bits (546), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 127/298 (42%), Positives = 180/298 (60%), Gaps = 6/298 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL  GF  T+GNA+RRVL+SSL G AI+AV I G+ HE S I GV ED  D+ LN+
Sbjct: 32  FIVEPLRVGFGLTIGNAMRRVLLSSLSGFAISAVGIKGLTHEFSCIPGVREDFADLALNL 91

Query: 90  KGINLK-MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           K + LK +SG +   + +     G V +  I   +D EV+N D +ICN+     + ME+ 
Sbjct: 92  KKVVLKSISGATCGNLHLSVTDGGAVFSNMISPSHDFEVVNGDLLICNVAEGVSLEMEMK 151

Query: 149 VSKGHGYVPAKHHRT-ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           VS G GYV +   R  E D  G + IDA+Y+P++ V++TV+    G    +DKL + ++T
Sbjct: 152 VSSGFGYVSSVSVRKDEYDLEGAVPIDAIYNPVRAVNFTVKPTSAGSFAGHDKLILYVET 211

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE-DINVKSLPFNPA---LLKKVEEL 263
           +G++  + +V  AS+IL  Q   F+N  +P+  V      V +   N A   L  +++ L
Sbjct: 212 NGAMDPKTAVLEASKILSTQARCFLNIADPEHRVHGVPCGVSTSDRNDASDLLSARIDRL 271

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
            LS R+  CL GENIVY+ DL+ RTEAD+L+  NFGR+SL E+K  L + GL LGMNL
Sbjct: 272 YLSARARKCLNGENIVYIRDLVSRTEADLLKAPNFGRRSLEEVKKELFSKGLSLGMNL 329


>gi|325299105|ref|YP_004259022.1| DNA-directed RNA polymerase subunit alpha [Bacteroides salanitronis
           DSM 18170]
 gi|324318658|gb|ADY36549.1| DNA-directed RNA polymerase subunit alpha [Bacteroides salanitronis
           DSM 18170]
          Length = 330

 Score =  214 bits (546), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 116/298 (38%), Positives = 185/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AI  + I+GV HE +++ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGITVGNALRRILLSSLEGYAINTIHIEGVEHEFATVPGVKEDVTNIILNLKQVR 87

Query: 94  LK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K  +    +++V+I         AGDI + +   EVLNP+ VIC+LD  A ++++LT++
Sbjct: 88  FKQIVEEFENEKVSITVENSTEFKAGDIGKYLTGFEVLNPELVICHLDSKATMQIDLTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y VE+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPADENREFCTDVNVIPIDSIYTPIRNVKYAVENYRVEQKTDYEKLVLEITTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  A++IL     +F    I  E    +  E+ + + L     L  K+ +++LS
Sbjct: 208 IHPKEALKEAAKILIYHFMLFSDEKITLETSDADGNEEFDEEVLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKKSLTELDDLLESLNLSFGTDISKY 325


>gi|328813957|gb|AEB52094.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 255

 Score =  214 bits (546), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 111/247 (44%), Positives = 164/247 (66%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E  N    + EPL RG+  TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+
Sbjct: 8   ESTNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDV 67

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILNIK + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +     
Sbjct: 68  TQIILNIKKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGH 127

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
             + +TV KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL+
Sbjct: 128 FHVRMTVKKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLT 187

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + + T+GSI+  ++++LA++IL + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 188 LDVWTNGSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEE 247

Query: 263 LELSVRS 269
           L+LSVRS
Sbjct: 248 LDLSVRS 254


>gi|311990454|gb|ADQ26357.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 260

 Score =  214 bits (546), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 113/260 (43%), Positives = 163/260 (62%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+
Sbjct: 1   FVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK   D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V
Sbjct: 61  KKLELKSLSDERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDG
Sbjct: 121 QNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI   D+++ A++IL +   +F + +   K  +  +  +       L   +EEL+LSVRS
Sbjct: 181 SIKPNDALSFAAKILVEHFKVFESADADTKFSEVMVEKEDDKKEKKLEMTIEELDLSVRS 240

Query: 270 TNCLRGENIVYMGDLIQRTE 289
            NCL+   I  + +L   TE
Sbjct: 241 YNCLKRAGINTLQELTDMTE 260


>gi|71056882|emb|CAH58997.1| DNA-directed RNA polymerase alpha chain [Enterococcus malodoratus]
          Length = 227

 Score =  214 bits (545), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNI
Sbjct: 2   FVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNI 61

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV
Sbjct: 62  KGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTV 121

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 122 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDG 181

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI  +++++LA++IL + L +F+N  +  K
Sbjct: 182 SIIAQEALSLAAKILTEHLDIFVNLTDEAK 211


>gi|225020484|ref|ZP_03709676.1| hypothetical protein CORMATOL_00491 [Corynebacterium matruchotii
           ATCC 33806]
 gi|305679751|ref|ZP_07402561.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           matruchotii ATCC 14266]
 gi|224946873|gb|EEG28082.1| hypothetical protein CORMATOL_00491 [Corynebacterium matruchotii
           ATCC 33806]
 gi|305660371|gb|EFM49868.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           matruchotii ATCC 14266]
          Length = 341

 Score =  214 bits (545), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 132/333 (39%), Positives = 195/333 (58%), Gaps = 27/333 (8%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   EY V    + +R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+IDGVLH
Sbjct: 6   RPRLTEYPV----DNSRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVKIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR--GPGVVTAGDIQTVNDIEVL 128
           E ++I GV ED++DI+LNIKG  L +S DS + V ++ R  G G VTAG I+    +E+ 
Sbjct: 62  EFTTITGVKEDVSDILLNIKG--LAISSDSDEPVVMYLRAEGAGEVTAGTIEPPAGVEIH 119

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYSPIKKVSY 185
           NPD  I  L+    + +E+ V +G GYVP        +    IG I +D +YSP+ KVSY
Sbjct: 120 NPDLHIATLNDQGRLEIEMVVERGRGYVPVSSSTTTNSGTTEIGRIQVDQIYSPVLKVSY 179

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF--INFEE------P 237
            VE+ R  Q  D+DKL++ ++T  SI+  ++ A A + L +  G+   +N         P
Sbjct: 180 NVEATRVEQRTDFDKLTIDVETKNSISPRNAFASAGKTLVELFGLARELNVSAEGIEVGP 239

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
             +  E I    +P        +EEL  SVRS NCL+ + I  +G+L + TE+D+L + N
Sbjct: 240 SPQETEHIAAYGMP--------IEELRFSVRSYNCLKRQEIHTVGELAECTESDLLDIRN 291

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           FG+KS+ E+K  L  +GL L     D+ P  +E
Sbjct: 292 FGQKSINEVKIKLAGLGLTLKDAPEDFDPTQLE 324


>gi|313292084|gb|ADR51231.1| DNA-directed RNA polymerase alpha chain [Enterococcus malodoratus]
          Length = 241

 Score =  214 bits (545), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 105/217 (48%), Positives = 150/217 (69%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E+ +    + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+
Sbjct: 7   EDRDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDV 66

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             IILNIKG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A 
Sbjct: 67  VQIILNIKGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGAT 126

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
               LTV  G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+
Sbjct: 127 FHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLT 186

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           M I TDGSI  +++++LA++IL + L +F+N  +  K
Sbjct: 187 MEIWTDGSIIAQEALSLAAKILTEHLDIFVNLTDEAK 223


>gi|311990462|gb|ADQ26361.1| RNA polymerase alpha subunit [Lactobacillus plantarum]
          Length = 252

 Score =  214 bits (545), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 114/234 (48%), Positives = 160/234 (68%), Gaps = 6/234 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN I  I    E +N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EFEKPN-IHKI---DENDNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EV
Sbjct: 59  VLHEFSTIEGVTEDVTAIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAK--HHRTENDPIGLITIDALYSPIKKVSY 185
           LNPD  IC +   A   M +T + G GYV A+   HR ++ PIG++ +D+LYSPI++V+Y
Sbjct: 119 LNPDLPICTVADGAHFHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
            VE+ R GQ  D+DKL++ + T+GSIT  ++++L+++IL D L +F+N  +  K
Sbjct: 179 QVENTRVGQRDDFDKLTLDVWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAK 232


>gi|319900952|ref|YP_004160680.1| DNA-directed RNA polymerase subunit alpha [Bacteroides helcogenes P
           36-108]
 gi|319415983|gb|ADV43094.1| DNA-directed RNA polymerase subunit alpha [Bacteroides helcogenes P
           36-108]
          Length = 330

 Score =  214 bits (545), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 116/298 (38%), Positives = 185/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AIT ++I+GV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGITVGNALRRILLSSLEGFAITTIKIEGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDSHK--RVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +  +  +V+I         AGDI + +   EVLNP+ VIC+LD  + +++++ ++
Sbjct: 88  FKQVVEEFESEKVSITIENSSEFKAGDIGKYLTGFEVLNPELVICHLDSKSTMQIDIAIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y VE+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKYQVENFRVEQKTDYEKLVLEITTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  A++IL     +F    I  E    +  E+ + + L     L  K+ +++LS
Sbjct: 208 IHPKEALKEAAKILIYHFMLFSDEKITLESNDVDGNEEFDEEVLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 VRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKKSLTELDDLLESLNLSFGTDISKY 325


>gi|71056880|emb|CAH58996.1| DNA-directed RNA polymerase alpha chain [Enterococcus avium]
          Length = 235

 Score =  214 bits (545), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNI
Sbjct: 2   FVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNI 61

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV
Sbjct: 62  KGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTV 121

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 122 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDG 181

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI  +++++LA++IL + L +F+N  +  K
Sbjct: 182 SIIAQEALSLAAKILTEHLDIFVNLTDEAK 211


>gi|71056878|emb|CAH58995.1| DNA-directed RNA polymerase alpha chain [Enterococcus avium]
          Length = 231

 Score =  214 bits (545), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNI
Sbjct: 2   FVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNI 61

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV
Sbjct: 62  KGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTV 121

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 122 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDG 181

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI  +++++LA++IL + L +F+N  +  K
Sbjct: 182 SIIAQEALSLAAKILTEHLDIFVNLTDEAK 211


>gi|71056912|emb|CAH59015.1| DNA-directed RNA polymerase alpha chain [Enterococcus raffinosus]
          Length = 235

 Score =  214 bits (545), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV
Sbjct: 61  KGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI  +++++LA++IL + L +F+N  +  K
Sbjct: 181 SIIAQEALSLAAKILTEHLDIFVNLTDEAK 210


>gi|256420686|ref|YP_003121339.1| DNA-directed RNA polymerase, alpha subunit [Chitinophaga pinensis
           DSM 2588]
 gi|256035594|gb|ACU59138.1| DNA-directed RNA polymerase, alpha subunit [Chitinophaga pinensis
           DSM 2588]
          Length = 331

 Score =  214 bits (545), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 122/325 (37%), Positives = 198/325 (60%), Gaps = 14/325 (4%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           N+Q   KP+ I   VL +  +        PL  G+  T+GNALRRVL+SSL G AI  ++
Sbjct: 5   NFQ---KPDKI---VLQKSTDFEAQFEFRPLEPGYGVTVGNALRRVLLSSLEGYAIVGIK 58

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS---HKRVTIFKRGPGVVTAGDIQT 121
           I+G  HE +++KG+ ED+T+IILN+K +  K   ++   ++++ I  +G     A  I+ 
Sbjct: 59  IEGADHEFATLKGITEDVTEIILNLKQVRFKRIVENEVNNEKIQISIKGKTEFRADMIEK 118

Query: 122 VND-IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
                +++NP+ +IC LD  A + +ELT+ KG GYVPA+ ++ ++   G I ID++++PI
Sbjct: 119 ATSAFQIMNPELLICTLDPSAKLDIELTIGKGRGYVPAEENKPKDAVFGYIAIDSIFTPI 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEE 236
           K V Y++E+ R  Q  DY+KL M + TDG+I  E++V  ASRIL   L +     I+F+ 
Sbjct: 179 KNVKYSIENTRVEQKTDYEKLIMEVITDGTIHPEEAVKQASRILIQHLMIITDENISFDT 238

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
              E ++ ++ ++L     L   +E+L+LSVR+ NCL+   I  + +L+Q  + ++++  
Sbjct: 239 KDTEKEDVVDEQTLQLRKILKTPLEDLDLSVRAFNCLKAAKINSLSELVQYEQEELMKFR 298

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNL 321
           NFG+KSL EI+ VL   GL  GM+L
Sbjct: 299 NFGQKSLSEIEQVLNERGLHFGMDL 323


>gi|330837630|ref|YP_004412271.1| DNA-directed RNA polymerase subunit alpha [Spirochaeta coccoides
           DSM 17374]
 gi|329749533|gb|AEC02889.1| DNA-directed RNA polymerase subunit alpha [Spirochaeta coccoides
           DSM 17374]
          Length = 350

 Score =  214 bits (545), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 121/300 (40%), Positives = 181/300 (60%), Gaps = 11/300 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-----DGVLH----EISSIKGVHE 80
             A P  RGF  T+GN LRR+L+SS++G AITAV+      DGV H    E  S+ GV E
Sbjct: 30  FTAYPFERGFGTTIGNTLRRILLSSIQGYAITAVKFTTFNQDGVPHLVTSEYESLPGVRE 89

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           D++DII  +K + L++  +S     + + +GPG+++    +    +EV+N D  I  +  
Sbjct: 90  DVSDIIAALKKLQLRLPEESESTTLLIECKGPGILSGASFER-GQVEVINKDMEILTMMD 148

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           DA + ME+ +  G GYVPA+ +    + IG I +DA +SP+ +V Y +E  R GQ  DYD
Sbjct: 149 DANIEMEVQIDLGRGYVPAEINEKYVEEIGTIPLDASFSPVTRVKYAIEPTRVGQRSDYD 208

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + + TDG+I+ E ++A A++I +D   +FINF+E      ++I+ +       L   
Sbjct: 209 KLVIEVYTDGTISPESALAEAAKIAKDHFSIFINFDESLINSSDEIDEEEERVRKILNTS 268

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           VEELEL+VRS+NCL+  NI  +GDL ++TE ++ +  NFG+KSL EIK  L    L LGM
Sbjct: 269 VEELELTVRSSNCLKNANIRTIGDLTKKTEEEIAKTRNFGKKSLSEIKAKLAEWNLSLGM 328


>gi|71056852|emb|CAH58981.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
          Length = 232

 Score =  214 bits (545), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV
Sbjct: 61  KGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI  +++++LA++IL + L +F+N  +  K
Sbjct: 181 SIIAQEALSLAAKILTEHLDIFVNLTDEAK 210


>gi|71056822|emb|CAH58966.1| DNA-directed RNA polymerase alpha chain [Enterococcus avium]
          Length = 245

 Score =  214 bits (545), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 105/217 (48%), Positives = 150/217 (69%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E+ +    + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+
Sbjct: 4   EDRDYGQFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDV 63

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             IILNIKG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A 
Sbjct: 64  VQIILNIKGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGAT 123

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
               LTV  G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+
Sbjct: 124 FHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLT 183

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           M I TDGSI  +++++LA++IL + L +F+N  +  K
Sbjct: 184 MEIWTDGSIIAQEALSLAAKILTEHLDIFVNLTDEAK 220


>gi|71056884|emb|CAH58998.1| DNA-directed RNA polymerase alpha chain [Enterococcus pseudoavium]
          Length = 236

 Score =  214 bits (545), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNI
Sbjct: 2   FVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNI 61

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV
Sbjct: 62  KGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTV 121

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 122 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDG 181

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI  +++++LA++IL + L +F+N  +  K
Sbjct: 182 SIIAQEALSLAAKILTEHLDIFVNLTDEAK 211


>gi|328814005|gb|AEB52118.1| DNA-directed RNA polymerase alpha chain [Lactobacillus rhamnosus]
          Length = 250

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 110/247 (44%), Positives = 164/247 (66%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E  N    + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED+
Sbjct: 3   ESTNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLEDV 62

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILNIK + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +     
Sbjct: 63  TQIILNIKKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGH 122

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
             + +TV KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL+
Sbjct: 123 FHVRMTVKKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLT 182

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + + T+GSI+  ++++LA++IL + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 183 LDVWTNGSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEE 242

Query: 263 LELSVRS 269
           L+LSVRS
Sbjct: 243 LDLSVRS 249


>gi|71056830|emb|CAH58970.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
          Length = 243

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 105/217 (48%), Positives = 151/217 (69%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E+++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+
Sbjct: 4   EDKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDV 63

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             IILNIKG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  IC +   A 
Sbjct: 64  AQIILNIKGLALKMYGDEEKTLEIDISGPATVTAGDIIVDSDVEILNKDMYICTVSEGAT 123

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
               LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+
Sbjct: 124 FHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLT 183

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           M I TDGSI   ++++L+++I+ + L +F+N  +  K
Sbjct: 184 MEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAK 220


>gi|71056828|emb|CAH58969.1| DNA-directed RNA polymerase alpha chain [Enterococcus sulfureus]
          Length = 234

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 105/210 (50%), Positives = 146/210 (69%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNI
Sbjct: 2   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNI 61

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G+  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV
Sbjct: 62  KGLALKMYGEDEKTLEIDIAGPATVTAGDILVDSDVEILNKDMYICTVSEGATFNARLTV 121

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 122 RPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHRDDFDKLTMEIWTDG 181

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   D+++LA++I+ + L +F+N  +  K
Sbjct: 182 SIEPLDAMSLAAKIMTEHLDIFVNLTDEAK 211


>gi|71056868|emb|CAH58989.1| DNA-directed RNA polymerase alpha chain [Enterococcus pseudoavium]
          Length = 229

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV
Sbjct: 61  KGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI  +++++LA++IL + L +F+N  +  K
Sbjct: 181 SIIAQEALSLAAKILTEHLDIFVNLTDEAK 210


>gi|71056802|emb|CAH58956.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 234

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 105/210 (50%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 2   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 61

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV
Sbjct: 62  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTV 121

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 122 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDG 181

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   ++++L+++I+ + L +F+N  +  K
Sbjct: 182 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAK 211


>gi|71056818|emb|CAH58964.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 232

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 105/210 (50%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV
Sbjct: 61  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   ++++L+++I+ + L +F+N  +  K
Sbjct: 181 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAK 210


>gi|313292078|gb|ADR51228.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
          Length = 241

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 106/217 (48%), Positives = 151/217 (69%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+
Sbjct: 7   EEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDV 66

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILNIKG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A 
Sbjct: 67  TQIILNIKGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGAT 126

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
               LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+
Sbjct: 127 FHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLT 186

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           M I TDGSI   ++++L+++I+ + L +F+N  +  K
Sbjct: 187 MEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAK 223


>gi|72534409|emb|CAH59041.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 229

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 105/210 (50%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV
Sbjct: 61  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   ++++L+++I+ + L +F+N  +  K
Sbjct: 181 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAK 210


>gi|71056838|emb|CAH58974.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
          Length = 237

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNI
Sbjct: 5   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNI 64

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV
Sbjct: 65  KGLALKMYGDEEKTLEIDISGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTV 124

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 125 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDG 184

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   ++++L+++I+ + L +F+N  +  K
Sbjct: 185 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAK 214


>gi|71056800|emb|CAH58955.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
          Length = 233

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV
Sbjct: 61  KGLALKMYGDEEKTLEIDISGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   ++++L+++I+ + L +F+N  +  K
Sbjct: 181 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAK 210


>gi|313292086|gb|ADR51232.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
          Length = 241

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 105/217 (48%), Positives = 150/217 (69%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E+ +    + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+
Sbjct: 7   EDRDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDV 66

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             IILNIKG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A 
Sbjct: 67  VQIILNIKGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGAT 126

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
               LTV  G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+
Sbjct: 127 FHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLT 186

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           M I TDGSI  +++++LA++IL + L +F+N  +  K
Sbjct: 187 MEIWTDGSIIAQEALSLAAKILTEHLDIFVNLTDEAK 223


>gi|206901886|ref|YP_002250728.1| DNA-directed RNA polymerase, alpha subunit [Dictyoglomus
           thermophilum H-6-12]
 gi|206740989|gb|ACI20047.1| DNA-directed RNA polymerase, alpha subunit [Dictyoglomus
           thermophilum H-6-12]
          Length = 324

 Score =  213 bits (543), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 118/307 (38%), Positives = 193/307 (62%), Gaps = 15/307 (4%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +++ +  E+    + EPL RG+  T+GNALRR+L+SS+ GAA+ +V+IDGV HE+  + G
Sbjct: 8   VIVEKRSEDYGRFVIEPLERGYGWTIGNALRRILLSSIEGAAVVSVKIDGVRHELEVLPG 67

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           + E++ ++++N+K + +K+  ++   + I  RGP VVTA D    ++++++NPD VI  L
Sbjct: 68  LKEEILEVLMNLKKLVVKIEDNNSHILEIDTRGPKVVTAADFIVPSNVKIVNPDLVIATL 127

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D    ME+ V KG GYV A+ ++ +N PIG++ +D+++SP+KKVSYTVE  R G+  D
Sbjct: 128 VEDMPFHMEVEVKKGKGYVSAEENKDQNYPIGVLVLDSIFSPVKKVSYTVEKTRVGRRTD 187

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPA 255
            D+L + I T+GSI+ E++   ASRIL +   +     F+ P +EVK        P N  
Sbjct: 188 LDRLILEIWTNGSISPEEAFREASRILMEYFRLLNEKEFQLPYEEVK--------PENTY 239

Query: 256 LLKK-----VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           L ++     +E+L LS R+ N LR   I  + DL+ +T  +++++ NFG+KSL E++  L
Sbjct: 240 LEEEKKGLTLEDLGLSTRAYNSLRHAGIHTIEDLLSKTREELMKIKNFGQKSLQELEEKL 299

Query: 311 GTMGLFL 317
              GL L
Sbjct: 300 REKGLSL 306


>gi|237736198|ref|ZP_04566679.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium mortiferum
           ATCC 9817]
 gi|229421751|gb|EEO36798.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium mortiferum
           ATCC 9817]
          Length = 325

 Score =  213 bits (543), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 125/306 (40%), Positives = 187/306 (61%), Gaps = 8/306 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E E +   I EPL RG+ HT+GNALRRVL+SS+ GAAI  V+I+GVL E S ++GV E 
Sbjct: 17  KENEFKGQYIVEPLYRGYGHTVGNALRRVLLSSIPGAAIKGVRINGVLSEFSVMEGVKEA 76

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T+IILNIK I +K      +++T+  +GP  VTA DI     IE++NP+ VIC +  D 
Sbjct: 77  VTEIILNIKEIVVKAETSGERKMTLSVKGPKTVTAADIIPDVGIEIVNPEQVICTITTDR 136

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSYT++    G++ D+DKL
Sbjct: 137 ELDMEFLVDTGEGFVVSEDIERKDWPVDYIAVDAIYTPIRKVSYTIQDTMVGRMTDFDKL 196

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINF----EEPKKEV---KEDINVKSLPFNP 254
           ++ I+TDGSI   D+++ A  +L+     F+      E  + EV   +ED    S   N 
Sbjct: 197 TLEIETDGSIEIRDALSYAVELLKLHFDPFLELGNKMENLRAEVEDEEEDSTTHSKDDN- 255

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
            L  K+EEL+L+VRS NCL+   I  +  L + +  ++L++ N GRKSL EI   +  +G
Sbjct: 256 ILNTKIEELDLTVRSFNCLKKAGIEEVSQLAKLSLNELLKIKNLGRKSLDEILEKMKELG 315

Query: 315 LFLGMN 320
             L  N
Sbjct: 316 YDLTQN 321


>gi|328813961|gb|AEB52096.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 248

 Score =  213 bits (543), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 111/248 (44%), Positives = 166/248 (66%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNIK + LKM+ D  
Sbjct: 1   TLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNTDED 60

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV KG GYV A  +
Sbjct: 61  KNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAADQN 120

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           ++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA+
Sbjct: 121 KSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAA 180

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           +IL + L +F+N  +  K  +  +  +       L   +EEL+LSVRS NCL+   I  +
Sbjct: 181 KILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTV 240

Query: 282 GDLIQRTE 289
            +L  +TE
Sbjct: 241 QELTNKTE 248


>gi|307565140|ref|ZP_07627648.1| DNA-directed RNA polymerase, alpha subunit [Prevotella amnii CRIS
           21A-A]
 gi|307346171|gb|EFN91500.1| DNA-directed RNA polymerase, alpha subunit [Prevotella amnii CRIS
           21A-A]
          Length = 332

 Score =  213 bits (543), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 118/300 (39%), Positives = 183/300 (61%), Gaps = 9/300 (3%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AI  ++I GV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGVTIGNALRRILLSSLEGFAINTIRIAGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            +   +   +++V+I         AGDI   +   EVLNPD VIC+LD  A ++++LT++
Sbjct: 88  FRQVVEEFENEKVSITVENSTEFKAGDISNYLTGFEVLNPDLVICHLDSKASMQIDLTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + ++ ID++Y+PI+ V Y+VE  R  Q  DYDKL + + TDGS
Sbjct: 148 KGRGYVPADENREFCTDVNVLPIDSIYTPIRNVKYSVEPYRVEQKTDYDKLIIEVTTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEE--LE 264
           I  ++++  A++ L     +F    I  E P +E  ++ + + L     L  K+ +  L 
Sbjct: 208 IPPKEALKEAAKTLIHHFMLFSDEKITLESPDQENNQEFDEEVLHMRQLLKTKLTDATLN 267

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L  + L  G ++  +
Sbjct: 268 LSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKKSLSELDDLLEGLNLSFGTDITKY 327


>gi|71056919|emb|CAH59018.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
 gi|71056935|emb|CAH59026.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 226

 Score =  213 bits (543), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 105/210 (50%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV
Sbjct: 61  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   ++++L+++I+ + L +F+N  +  K
Sbjct: 181 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAK 210


>gi|71056892|emb|CAH59003.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           phoeniculicola]
 gi|72534418|emb|CAH59045.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           phoeniculicola]
          Length = 230

 Score =  213 bits (543), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 105/210 (50%), Positives = 148/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV
Sbjct: 61  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLYICSVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 121 RPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   ++++LA++I+ + L +F+N  +  +
Sbjct: 181 SIEPLEAMSLAAKIMTEHLDIFVNLTDEAR 210


>gi|72534399|emb|CAH59014.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
          Length = 227

 Score =  213 bits (543), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNI
Sbjct: 2   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNI 61

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV
Sbjct: 62  KGLALKMYGDEEKTLEIDISGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTV 121

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 122 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDG 181

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   ++++L+++I+ + L +F+N  +  K
Sbjct: 182 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAK 211


>gi|71056820|emb|CAH58965.1| DNA-directed RNA polymerase alpha chain [Enterococcus villorum]
 gi|71056844|emb|CAH58977.1| DNA-directed RNA polymerase alpha chain [Enterococcus villorum]
          Length = 230

 Score =  213 bits (543), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV
Sbjct: 61  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHCEDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   ++++L+++I+ + L +F+N  +  K
Sbjct: 181 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAK 210


>gi|58699558|ref|ZP_00374269.1| dna-directed rna polymerase alpha chain [Wolbachia endosymbiont of
           Drosophila ananassae]
 gi|58533923|gb|EAL58211.1| dna-directed rna polymerase alpha chain [Wolbachia endosymbiont of
           Drosophila ananassae]
          Length = 220

 Score =  213 bits (542), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 108/219 (49%), Positives = 150/219 (68%), Gaps = 10/219 (4%)

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--------TENDPIGLITIDALYSPIKK 182
           D +IC L  +  + M + V+ G GY+P   ++        +E D IG I ++ALYSP+ +
Sbjct: 1   DLLICTLGQNVELNMTIYVASGKGYLPVTKYKENELLKLMSEQDLIGFIPVNALYSPVNR 60

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI--NFEEPKKE 240
           VSY VE++R GQV D DKL ++I+TDG+I+   +V  A+RILQ+QL  FI  +    K +
Sbjct: 61  VSYRVENSRVGQVTDKDKLILSIETDGTISPSQAVDSAARILQEQLQPFISSDVSYKKSQ 120

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V      K L ++P LL+KV+E+ELSVRS NCL+ ENI Y+GDL+Q+TE +MLR ANFGR
Sbjct: 121 VSSSSGAKDLGYDPVLLRKVDEMELSVRSHNCLKNENITYIGDLVQKTEGEMLRTANFGR 180

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL   GL LGMN+ +WPP+ I+ELAK++ D+
Sbjct: 181 KSLNEIKAVLTNFGLSLGMNVLNWPPKDIDELAKQHTDE 219


>gi|327451569|gb|EGE98223.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL092PA1]
          Length = 338

 Score =  213 bits (542), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 123/308 (39%), Positives = 184/308 (59%), Gaps = 12/308 (3%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV HE S+I+G  ED+T+
Sbjct: 16  EFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQHEFSTIEGCVEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ L    D    + + K G G + A DI     + + NP+  I  L+ D    
Sbjct: 76  IILNLKGLVLSSEEDEPVAMYLRKTGAGEIPAADINPPAGVTIHNPELHIATLNDDGRFE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MEL V +G GYV +  +   N  IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL + 
Sbjct: 136 MELIVERGRGYVSSALNDDPNAEIGRIAVDSIYSPVLKVTYKVEATRVEQRTDFDKLVVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLP----FNPALLK 258
           ++T  SI   D++A A + L +  G+   +N E       E I + S P    +  +L  
Sbjct: 196 VETKPSILPRDAIASAGKTLVELFGLTRELNVE------AEGIEIGSGPVDEEYAESLGT 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  +GL L 
Sbjct: 250 PVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEKLTELGLALK 309

Query: 319 MNLPDWPP 326
            + P + P
Sbjct: 310 DSAPGFDP 317


>gi|161513438|emb|CAP16862.1| DNA-directed RNA polymerase subunit alpha [Pediococcus damnosus]
          Length = 234

 Score =  213 bits (542), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 102/215 (47%), Positives = 150/215 (69%), Gaps = 2/215 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNI
Sbjct: 3   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNI 62

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K ++LK+  D  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT 
Sbjct: 63  KKVSLKIESDDEKSLEINVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAVLTA 122

Query: 150 SKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             G GYV A  ++   D  PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + T
Sbjct: 123 DTGRGYVSADENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWT 182

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           DGSI+  ++ +L+++IL + L +F+N  +  ++ +
Sbjct: 183 DGSISPSEATSLSAKILTEHLALFVNLTDEAQDAE 217


>gi|71056814|emb|CAH58962.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 243

 Score =  213 bits (542), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 106/218 (48%), Positives = 153/218 (70%), Gaps = 2/218 (0%)

Query: 24  EENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +ENR     + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+I GV ED
Sbjct: 1   DENRDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIPGVRED 60

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILNIKG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D VIC++   A
Sbjct: 61  VTQIILNIKGLALKLYAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLVICSVAEGA 120

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
                LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL
Sbjct: 121 TFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKL 180

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +M I TDGSI  +++++LA++I+ + L +F+N  +  K
Sbjct: 181 TMEIWTDGSIIPQEALSLAAKIMTEHLDIFVNLTDEAK 218


>gi|71056834|emb|CAH58972.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
          Length = 227

 Score =  213 bits (542), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 104/207 (50%), Positives = 146/207 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG+
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNIKGL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G
Sbjct: 61  ALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTVKPG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDGSI 
Sbjct: 121 RGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDGSII 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKK 239
            +++++LA++IL + L +F+N  +  K
Sbjct: 181 AQEALSLAAKILTEHLDIFVNLTDEAK 207


>gi|71056808|emb|CAH58959.1| DNA-directed RNA polymerase alpha chain [Enterococcus raffinosus]
          Length = 228

 Score =  213 bits (542), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 104/207 (50%), Positives = 146/207 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG+
Sbjct: 2   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNIKGL 61

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G
Sbjct: 62  ALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTVKPG 121

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDGSI 
Sbjct: 122 RGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDGSII 181

Query: 213 GEDSVALASRILQDQLGMFINFEEPKK 239
            +++++LA++IL + L +F+N  +  K
Sbjct: 182 AQEALSLAAKILTEHLDIFVNLTDEAK 208


>gi|315655841|ref|ZP_07908739.1| DNA-directed RNA polymerase subunit alpha [Mobiluncus curtisii ATCC
           51333]
 gi|315489905|gb|EFU79532.1| DNA-directed RNA polymerase subunit alpha [Mobiluncus curtisii ATCC
           51333]
          Length = 335

 Score =  213 bits (541), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 123/308 (39%), Positives = 187/308 (60%), Gaps = 8/308 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+    EPL  GF +TLGN+LRR L+SS+ G+A+T+++I+G LHE +++ GV ED+T 
Sbjct: 23  EQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGSAVTSIKIEGALHEFTTLPGVKEDVTQ 82

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           I+LNIK I L    D    + + K G G VT GDI     + + NP+H I  L+ D  + 
Sbjct: 83  IVLNIKEIVLSSDNDEPVVMYLRKTGEGEVTVGDIMPPAGVVIHNPEHHIATLNKDGKLE 142

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELTV +G GYV A  ++     I  I +D++YSP+ KVSY VE+ R  Q  D+D+L + 
Sbjct: 143 IELTVERGRGYVSASQNKDPEAEISRIPVDSIYSPVLKVSYRVEATRVEQRTDFDRLVVD 202

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           ++T  +I   D++A A + L +  G+   +N +    E+    N  +L  + A+   VE+
Sbjct: 203 VETKKAILPRDAMASAGKTLVELFGLARDLNHDAEGIELGPSGNDAALAEDLAM--SVED 260

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           L+L+ R+ NCL  E I  +GDL+ R++AD+L + NFG+KS+ EIK  L  M    GM+L 
Sbjct: 261 LDLTSRALNCLTREGINTVGDLVARSQADLLDIRNFGQKSIDEIKEKLAGM----GMSLK 316

Query: 323 DWPPESIE 330
           D P  ++E
Sbjct: 317 DTPMPAVE 324


>gi|225850763|ref|YP_002730997.1| DNA-directed RNA polymerase subunit alpha [Persephonella marina
           EX-H1]
 gi|225646203|gb|ACO04389.1| DNA-directed RNA polymerase, alpha subunit [Persephonella marina
           EX-H1]
          Length = 324

 Score =  213 bits (541), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 134/318 (42%), Positives = 189/318 (59%), Gaps = 8/318 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           + E I P+ I Y     + E+   +  EPL RG+  TLGNALRRVL+SSL G A+TAV+I
Sbjct: 3   FLEFITPSKI-YWDESSKTESFGRLYVEPLERGYGITLGNALRRVLLSSLEGGAVTAVKI 61

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVN 123
            GV HE ++I+GV ED+++IILN+K I  KM    DS   +  FK G G VTA DI+   
Sbjct: 62  HGVAHEFTTIEGVIEDVSEIILNLKQIKFKMDEGIDSDFAILEFK-GTGEVTAKDIKVPA 120

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            I+++NPD  I  +D +  +RMEL + KG GYV  +      + IG I ID  +SPIKK 
Sbjct: 121 GIKIVNPDVHIATVDKEIELRMELKIEKGRGYVMVEEMEPPTE-IGWIPIDTAFSPIKKC 179

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           ++ VE  R G+  +YDKL + + TDGSIT E+++  A+ IL +   + +N    K EV +
Sbjct: 180 TFYVEPTRVGEKTNYDKLILEVTTDGSITPEEALTKATNILIEHFQLLLNPTVRKVEVIK 239

Query: 244 DINVKSLPFN---PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
               +S+        L   +EELE+S R+TN L+   I  +GDL++ TE D+    + GR
Sbjct: 240 KAEPESIAEKIEADKLSLAIEELEISSRATNTLKKLGIQTIGDLVKMTEEDLKEAKSIGR 299

Query: 301 KSLVEIKGVLGTMGLFLG 318
           K+L EIK  L  +GL L 
Sbjct: 300 KALKEIKEALAELGLELA 317


>gi|71056886|emb|CAH58999.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           saccharolyticus]
          Length = 231

 Score =  213 bits (541), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 146/210 (69%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNI
Sbjct: 2   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNI 61

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G+  K + I   GP  VTAGDI   +D+E+LN D  IC +         LTV
Sbjct: 62  KGLALKMYGEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGTTFHARLTV 121

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 122 RPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDG 181

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   D+++LA++I+ + L +F+N  +  K
Sbjct: 182 SIEPLDAMSLAAKIMTEHLDIFVNLTDEAK 211


>gi|156752143|gb|ABU93822.1| RNA polymerase subunit A [Vibrio sp. 0908]
          Length = 257

 Score =  213 bits (541), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 109/258 (42%), Positives = 175/258 (67%), Gaps = 8/258 (3%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRV 104
           ALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +
Sbjct: 3   ALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFI 62

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---H 160
           T+ K G G V AGDI    D+E++NP+HVIC+L D +A + M + V +G GYVPA    H
Sbjct: 63  TLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIH 122

Query: 161 HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
              +  PIG + +DA +SP+ K++Y+V++AR  Q  D DKL + ++T+G++  E+++  A
Sbjct: 123 TEEDERPIGRLLVDATFSPVDKIAYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRA 182

Query: 221 SRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVY 280
           + IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y
Sbjct: 183 ATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHY 239

Query: 281 MGDLIQRTEADMLRMANF 298
           +GDL+QRTE ++L+  N 
Sbjct: 240 IGDLVQRTEVELLKTPNL 257


>gi|282858348|ref|ZP_06267528.1| DNA-directed RNA polymerase, alpha subunit [Prevotella bivia
           JCVIHMP010]
 gi|282588796|gb|EFB93921.1| DNA-directed RNA polymerase, alpha subunit [Prevotella bivia
           JCVIHMP010]
          Length = 332

 Score =  212 bits (540), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 119/300 (39%), Positives = 182/300 (60%), Gaps = 9/300 (3%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AI  ++I GV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGVTIGNALRRILLSSLEGFAINTIRIAGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            +   +   +++V+I         AGDI   +   EVLNPD VIC+LD  A +++ELT++
Sbjct: 88  FRQVVEEFENEKVSITVENSTEFKAGDISNYLTGFEVLNPDLVICHLDSKASMQIELTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + ++ ID++Y+PI+ V Y+VE  R  Q  DYDKL + + TDGS
Sbjct: 148 KGRGYVPADENREFCTDVNVLPIDSIYTPIRNVKYSVEPYRVEQKTDYDKLVIEVTTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEE--LE 264
           I  +D++  A++ L     +F    I  E   +E  ++ + + L     L  K+ +  L 
Sbjct: 208 IHPKDALKEAAKTLIYHFMLFSDEKITLESSDQENNQEFDEEILHMRQLLKTKLTDASLN 267

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L  + L  G ++  +
Sbjct: 268 LSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKKSLSELDDLLEGLNLSFGTDITKY 327


>gi|71056917|emb|CAH59017.1| DNA-directed RNA polymerase alpha chain [Enterococcus columbae]
          Length = 234

 Score =  212 bits (540), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 148/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QI+GVLHE S+IKGV ED+  IILN+
Sbjct: 2   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIEGVLHEFSTIKGVREDVAQIILNV 61

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+ G   K + I   GP VVTAGDI   +D+E+LN D  IC++   A  R  LTV
Sbjct: 62  KGLALKLYGSEEKTLEIDITGPAVVTAGDILVDSDVEILNKDMYICSVSEGATFRARLTV 121

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+   +DKL+M I TDG
Sbjct: 122 KAGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDVFDKLTMEIWTDG 181

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   D+++LA++I+ + L +F+N  +  K
Sbjct: 182 SIEPLDAMSLAAKIMTEHLDIFVNLTDEAK 211


>gi|71056850|emb|CAH58980.1| DNA-directed RNA polymerase alpha chain [Enterococcus ratti]
 gi|72534395|emb|CAH58994.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 233

 Score =  212 bits (540), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV
Sbjct: 61  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   ++++L+++I+ + L +F+N  +  K
Sbjct: 181 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAK 210


>gi|71056816|emb|CAH58963.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
 gi|71056836|emb|CAH58973.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
 gi|71056872|emb|CAH58991.1| DNA-directed RNA polymerase alpha chain [Enterococcus mundtii]
          Length = 230

 Score =  212 bits (540), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV
Sbjct: 61  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   ++++L+++I+ + L +F+N  +  K
Sbjct: 181 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAK 210


>gi|71056888|emb|CAH59000.1| DNA-directed RNA polymerase alpha chain [Enterococcus mundtii]
          Length = 238

 Score =  212 bits (540), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 6   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 65

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV
Sbjct: 66  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTV 125

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 126 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDG 185

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   ++++L+++I+ + L +F+N  +  K
Sbjct: 186 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAK 215


>gi|71056840|emb|CAH58975.1| DNA-directed RNA polymerase alpha chain [Enterococcus hirae]
          Length = 235

 Score =  212 bits (540), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 6   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 65

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV
Sbjct: 66  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTV 125

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 126 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDG 185

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   ++++L+++I+ + L +F+N  +  K
Sbjct: 186 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAK 215


>gi|303237482|ref|ZP_07324047.1| DNA-directed RNA polymerase, alpha subunit [Prevotella disiens
           FB035-09AN]
 gi|302482302|gb|EFL45332.1| DNA-directed RNA polymerase, alpha subunit [Prevotella disiens
           FB035-09AN]
          Length = 332

 Score =  212 bits (540), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 119/300 (39%), Positives = 184/300 (61%), Gaps = 9/300 (3%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GN+LRR+L+SSL G AI  V+I GV HE S++ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGVTIGNSLRRILLSSLEGYAINTVRIAGVEHEFSTVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   +++V+I         AGDI + +   EVLNPD VIC+LD  A ++++LT++
Sbjct: 88  FKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGFEVLNPDLVICHLDSKASMQIDLTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYV A  +R     + ++ ID++Y+PI+ V Y VE  R  Q  DYDKL + + TDGS
Sbjct: 148 KGRGYVSADENREFCTDVNVLPIDSIYTPIRNVKYAVEPYRVEQKTDYDKLVIEVATDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEE--LE 264
           I  +D++  A++IL     +F    I  E P +E  ++ + + L     L  K+ +  L 
Sbjct: 208 IHPKDALKEAAKILIYHFMLFSDEKIMLESPDQEGNQEFDEEVLHMRQLLKTKLTDSSLN 267

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL E+  +L ++ L  G ++  +
Sbjct: 268 LSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKKSLSELDDLLESLNLTFGTDITKY 327


>gi|71056941|emb|CAH59029.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
 gi|71056947|emb|CAH59033.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 230

 Score =  212 bits (540), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 103/210 (49%), Positives = 149/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+I GV ED+T IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIPGVREDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D VIC++   A     LTV
Sbjct: 61  KGLALKLYAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLVICSVAEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI  +++++LA++I+ + L +F+N  +  K
Sbjct: 181 SIIPQEALSLAAKIMTEHLDIFVNLTDEAK 210


>gi|71056894|emb|CAH59004.1| DNA-directed RNA polymerase alpha chain [Enterococcus italicus]
          Length = 229

 Score =  212 bits (539), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 104/209 (49%), Positives = 147/209 (70%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIK
Sbjct: 1   IVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVAQIILNIK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           G++LK+ G+  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV 
Sbjct: 61  GLSLKLYGEDEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTVK 120

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            G GYV A  ++ ++ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGS
Sbjct: 121 PGRGYVQADENKKDDMPIGVLPVDSIYTPVRRVNYQVENTRVGHRDDFDKLTMEIWTDGS 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKK 239
           I   D+++LA++I+ + L +F+N  +  K
Sbjct: 181 IEPLDAMSLAAKIMTEHLDIFVNLTDEAK 209


>gi|71056812|emb|CAH58961.1| DNA-directed RNA polymerase alpha chain [Enterococcus hirae]
          Length = 237

 Score =  212 bits (539), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 5   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 64

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV
Sbjct: 65  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTV 124

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 125 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDG 184

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   ++++L+++I+ + L +F+N  +  K
Sbjct: 185 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAK 214


>gi|71056910|emb|CAH59012.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
 gi|72534413|emb|CAH59043.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 228

 Score =  212 bits (539), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 104/207 (50%), Positives = 146/207 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+
Sbjct: 2   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGL 61

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV  G
Sbjct: 62  ALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTVKPG 121

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI 
Sbjct: 122 RGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIE 181

Query: 213 GEDSVALASRILQDQLGMFINFEEPKK 239
             ++++L+++I+ + L +F+N  +  K
Sbjct: 182 PLEAMSLSAKIMTEHLDIFVNLTDEAK 208


>gi|72534411|emb|CAH59042.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 224

 Score =  212 bits (539), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 104/207 (50%), Positives = 146/207 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+
Sbjct: 2   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGL 61

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV  G
Sbjct: 62  ALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTVKPG 121

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI 
Sbjct: 122 RGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIE 181

Query: 213 GEDSVALASRILQDQLGMFINFEEPKK 239
             ++++L+++I+ + L +F+N  +  K
Sbjct: 182 PLEAMSLSAKIMTEHLDIFVNLTDEAK 208


>gi|71056921|emb|CAH59019.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
          Length = 226

 Score =  212 bits (539), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDITQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV
Sbjct: 61  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   ++++L+++I+ + L +F+N  +  K
Sbjct: 181 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAK 210


>gi|320094553|ref|ZP_08026319.1| DNA-directed RNA polymerase subunit alpha [Actinomyces sp. oral
           taxon 178 str. F0338]
 gi|319978468|gb|EFW10045.1| DNA-directed RNA polymerase subunit alpha [Actinomyces sp. oral
           taxon 178 str. F0338]
          Length = 331

 Score =  212 bits (539), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 117/291 (40%), Positives = 172/291 (59%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
           R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGV HE  +I+GV ED+ +II
Sbjct: 18  RSRFTLEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVPHEFRTIEGVKEDVAEII 77

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LNIK I L    D    + + K GPG V AGDI     +E+ NPD  +  L+    + +E
Sbjct: 78  LNIKQIVLSSENDEPVVMYLRKAGPGPVVAGDITPPAGVEIHNPDLHLATLNEKGKLEIE 137

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           LTV +G GYV A  ++     I  I ID++YSP+ KV+Y VE+ R  Q  D+D+L + ++
Sbjct: 138 LTVERGRGYVSAAQNKDPQAEISRIPIDSIYSPVVKVTYKVEATRVEQRTDFDRLVIDVE 197

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T  +IT  D++A A + L +  G+     E  + ++   +         L   +E L L 
Sbjct: 198 TKPAITPRDAIASAGKTLVELFGLMRELNEEAEGIEVGPSTTDATLAADLALPIENLNLQ 257

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            RS N LR   I+ +G+L+  +EAD+L + NFG KS+ EIK  L T+G+ L
Sbjct: 258 SRSYNALRRRGILTVGELVAHSEADLLDIRNFGTKSIEEIKESLATLGMTL 308


>gi|71056923|emb|CAH59020.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
          Length = 226

 Score =  212 bits (539), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV
Sbjct: 61  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   ++++L+++I+ + L +F+N  +  K
Sbjct: 181 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAK 210


>gi|320526894|ref|ZP_08028084.1| DNA-directed RNA polymerase, alpha subunit [Solobacterium moorei
           F0204]
 gi|320132862|gb|EFW25402.1| DNA-directed RNA polymerase, alpha subunit [Solobacterium moorei
           F0204]
          Length = 319

 Score =  212 bits (539), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 120/307 (39%), Positives = 186/307 (60%), Gaps = 13/307 (4%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           EY+    E EN    +  PL RGF  T+GNALRRVL+SSL GAA+ ++++DGV HE +SI
Sbjct: 13  EYV----ESENYGKFVLSPLERGFGTTIGNALRRVLLSSLPGAAVFSIKVDGVYHEFTSI 68

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
            GV ED++ IIL +K + +K+  D    + I  +GP  +TAGDI     +EV+N D  I 
Sbjct: 69  PGVREDVSMIILQLKQLVMKIEDDEVYTLQISAKGPCTITAGDIICPAQVEVINKDLEIA 128

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTEN----DPIGLITIDALYSPIKKVSYTVESAR 191
           +L+ D  + MEL    G GY+ A  ++  N      IG +  D++Y+P++KV+Y VE  R
Sbjct: 129 HLEKDVTLEMELKAKNGRGYISADLNKQLNQGSSQGIGTVFTDSIYTPVEKVAYNVEPTR 188

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE---PKKEVKEDINVK 248
            G+ + YD +++ + TDGSI  + ++A+A++IL D L +     +      EV ++ N +
Sbjct: 189 VGEDVKYDAVTLEVWTDGSINPQKAIAMAAKILMDHLDIVAGINDEVLQMDEVLKEGNTE 248

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  ++  +E+L+LSVRS NCL+   I  + +L Q+TE +M+R+ N G+KSL E+K 
Sbjct: 249 QPSKGQQMM--IEDLDLSVRSYNCLKRAGIQTVDELTQKTEDEMMRVRNLGKKSLKEVKD 306

Query: 309 VLGTMGL 315
            L  +GL
Sbjct: 307 KLIELGL 313


>gi|119662309|emb|CAJ33142.1| RNA polymerase alpha subunit [Lactobacillus gasseri]
          Length = 232

 Score =  212 bits (539), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 108/227 (47%), Positives = 155/227 (68%), Gaps = 6/227 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN+LRRVL++S+ G A++ +QIDGVLHE S++ GV ED+T IILN+
Sbjct: 1   FVVEPLERGFGTTLGNSLRRVLLTSIPGTALSYIQIDGVLHEFSTVPGVREDVTKIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK   D  K   I   GP +VTA D++  +DIEVLNPD  IC++     + M + +
Sbjct: 61  KKLELKSLSDEEKIAEIDVTGPAIVTAADLKVDSDIEVLNPDQYICSIADGGHLHMNVAI 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYVPA  ++T++ PIG+I +D+L+SPIKKV+Y VESAR G+  DYDKL++ I TDG
Sbjct: 121 KNGRGYVPASENKTDDMPIGVIPVDSLFSPIKKVNYQVESARVGKRDDYDKLTLEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFIN------FEEPKKEVKEDINVKSL 250
           SIT  D+++ A++IL +   +F++      F++   E ++D N K L
Sbjct: 181 SITPNDALSFAAKILVEHFKVFMSTDMDAQFDDVMVEKEDDKNEKKL 227


>gi|71056925|emb|CAH59021.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
 gi|71056927|emb|CAH59022.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
 gi|71056929|emb|CAH59023.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
 gi|71056931|emb|CAH59024.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 223

 Score =  212 bits (539), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 104/207 (50%), Positives = 146/207 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV  G
Sbjct: 61  ALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTVKPG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI 
Sbjct: 121 RGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIE 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKK 239
             ++++L+++I+ + L +F+N  +  K
Sbjct: 181 PLEAMSLSAKIMTEHLDIFVNLTDEAK 207


>gi|312271196|gb|ADQ57295.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 253

 Score =  212 bits (539), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 110/249 (44%), Positives = 158/249 (63%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+
Sbjct: 5   FVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNL 64

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK   D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V
Sbjct: 65  KKLELKSFSDERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAV 124

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDG
Sbjct: 125 QNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDG 184

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI   D+++ A++IL +   +F + +   K  +  +  +       L   +EEL+LSVRS
Sbjct: 185 SIKPNDALSFAAKILVEHFKVFESADADTKFSEVMVEKEDDKKEKKLEMTIEELDLSVRS 244

Query: 270 TNCLRGENI 278
            NCL+   I
Sbjct: 245 YNCLKRAGI 253


>gi|71056846|emb|CAH58978.1| DNA-directed RNA polymerase alpha chain [Enterococcus moraviensis]
          Length = 225

 Score =  211 bits (538), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 102/206 (49%), Positives = 148/206 (71%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+ 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGLA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK+  +  K + I   GP  VTAGDI   +D+E+LN D +IC++   A     LTV  G 
Sbjct: 61  LKLYAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLIICSVSEGATFHARLTVKPGR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI  
Sbjct: 121 GYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIIP 180

Query: 214 EDSVALASRILQDQLGMFINFEEPKK 239
           +++++LA++I+ + L +F+N  +  K
Sbjct: 181 QEALSLAAKIMTEHLDIFVNLTDEAK 206


>gi|262341038|ref|YP_003283893.1| DNA-directed RNA polymerase subunit alpha [Blattabacterium sp.
           (Blattella germanica) str. Bge]
 gi|262272375|gb|ACY40283.1| DNA-directed RNA polymerase subunit alpha [Blattabacterium sp.
           (Blattella germanica) str. Bge]
          Length = 337

 Score =  211 bits (538), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 123/328 (37%), Positives = 200/328 (60%), Gaps = 16/328 (4%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           + +KP+ I    + +  +N+ +   +PL  G+  TLGNALRRVL+ SL+G A+T+++I G
Sbjct: 5   DFVKPDRI---AMSEFSDNKGIFHLKPLEPGYGITLGNALRRVLLGSLKGFAVTSIRIKG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINL--KMSGDSHKRVTIFKRGPGVVTAGDI-QTVND 124
           V +E S+I+GV ED+T+I+LN K I L  K+SG   + V         VT G + + ++ 
Sbjct: 62  VKYEFSTIEGVVEDVTEIVLNFKKIRLKQKISGIHKETVNASIHHGKQVTGGYLNKFISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP-IGLITIDALYSPIKKV 183
             +LN + VICN D    + +  T+ +G GYVPA+ ++  ND  IG I ID++Y+PI+ V
Sbjct: 122 FHILNENLVICNKDESIPLEISFTIEEGRGYVPAEENKKNNDHLIGTIPIDSIYTPIRNV 181

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
            YT+E+ R GQ  D++ LS+ I TDGSI  + ++  AS+IL     +F + E+  K+ +E
Sbjct: 182 KYTIENCRVGQKTDFENLSLEIQTDGSICPKSALMEASKILIQYFSIF-SHEKIGKKKQE 240

Query: 244 DINVKSLPFNPALLK-------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           +IN K   ++   L+       K+ +++LSVR+ NCL+  +I  + DL+     +ML+M 
Sbjct: 241 EIN-KDKKYDEEFLRMRTLLKSKLSDMDLSVRTKNCLKSASIESIADLVSCNRNNMLKMR 299

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           NFG+KSL E++  +   GL  GM + ++
Sbjct: 300 NFGKKSLDELESKMKEKGLCFGMEISEY 327


>gi|72534405|emb|CAH59039.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 221

 Score =  211 bits (538), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 104/207 (50%), Positives = 146/207 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+
Sbjct: 2   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGL 61

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV  G
Sbjct: 62  ALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTVKPG 121

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI 
Sbjct: 122 RGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIE 181

Query: 213 GEDSVALASRILQDQLGMFINFEEPKK 239
             ++++L+++I+ + L +F+N  +  K
Sbjct: 182 PLEAMSLSAKIMTEHLDIFVNLTDEAK 208


>gi|71056890|emb|CAH59001.1| DNA-directed RNA polymerase alpha chain [Enterococcus cecorum]
          Length = 235

 Score =  211 bits (538), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 104/211 (49%), Positives = 148/211 (70%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
           + I EPL RG+  TLGN+LRR+L+SSL GAAIT++QID V HE S+I GV ED++ IILN
Sbjct: 5   MFIVEPLERGYGTTLGNSLRRILLSSLPGAAITSIQIDTVQHEFSTIVGVREDVSQIILN 64

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           IKG+ LK+ G   K + I   GP VVTAGDI   +D+E+LN D  IC +   A  R  L 
Sbjct: 65  IKGLALKLYGSEEKTLEIDITGPAVVTAGDIIVDSDVEILNKDMYICTVSEGATFRARLK 124

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V  G GYV A  ++TE+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TD
Sbjct: 125 VKAGRGYVQADENKTEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTD 184

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK 239
           GSI   D+++LA++IL + L +F+N  +  +
Sbjct: 185 GSIEPLDAMSLAAKILTEHLDIFVNLTDEAR 215


>gi|71056876|emb|CAH58993.1| DNA-directed RNA polymerase alpha chain [Enterococcus canis]
          Length = 235

 Score =  211 bits (538), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 101/210 (48%), Positives = 146/210 (69%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNI
Sbjct: 2   FVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNI 61

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+     K + I   GP  VTAGDI   +D+E+LN D  +C +   A     LTV
Sbjct: 62  KGLALKLYAQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLYLCTVSEGATFHARLTV 121

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++TE+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 122 KPGRGYVQADENKTEDMPIGVLPVDSIYTPVRRVNYQVENTRVGNRQDFDKLTMEIWTDG 181

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI  +++++L+++IL + L +F+N  +  K
Sbjct: 182 SIIPQEALSLSAKILTEHLDIFVNLTDEAK 211


>gi|328813981|gb|AEB52106.1| DNA-directed RNA polymerase alpha chain [Lactobacillus helveticus]
          Length = 249

 Score =  211 bits (538), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 109/245 (44%), Positives = 157/245 (64%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+
Sbjct: 4   FVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNL 63

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK   D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V
Sbjct: 64  KKLELKSFSDERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAV 123

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDG
Sbjct: 124 QNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDG 183

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI   D+++ A++IL +   +F + +   K  +  +  +       L   +EEL+LSVRS
Sbjct: 184 SIKPNDALSFAAKILVEHFKVFESADADTKFSEVMVEKEDDKKEKKLEMTIEELDLSVRS 243

Query: 270 TNCLR 274
            NCL+
Sbjct: 244 YNCLK 248


>gi|110639509|ref|YP_679718.1| DNA-directed RNA polymerase subunit alpha [Cytophaga hutchinsonii
           ATCC 33406]
 gi|119366677|sp|Q11QD8|RPOA_CYTH3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|110282190|gb|ABG60376.1| DNA-directed RNA polymerase subunit alpha [Cytophaga hutchinsonii
           ATCC 33406]
          Length = 329

 Score =  211 bits (538), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 120/315 (38%), Positives = 193/315 (61%), Gaps = 6/315 (1%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           E +V+ + ++   L   +PL +G+  T+GNALRR+L+SSL G AIT +++ GVLHE S+I
Sbjct: 10  EKVVMEKADDFHGLFEFKPLEKGYGVTIGNALRRILLSSLEGYAITGIKVPGVLHEFSTI 69

Query: 76  KGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHV 133
            GV ED+T+IILN+K +  K   D +  ++ +  +      AGDI +  +  ++LNP+ +
Sbjct: 70  PGVREDVTEIILNLKQVRFKKISDVNENKIVVSIKKQASFKAGDIAKFTSAYQILNPELL 129

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           ICN+D ++   +ELT+ KG GY+PA+ ++      G I IDA+++PIK V Y+VE+ R  
Sbjct: 130 ICNVDSNSNFDIELTLEKGRGYLPAEENKPAEQIFGYIPIDAIFTPIKNVKYSVENTRVE 189

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKS 249
           Q  DY+KL + I TDGSI  ED++  A+ IL     +F    + FE  K E +E ++ + 
Sbjct: 190 QRTDYEKLILEILTDGSIHPEDALKGAANILIKHFMLFSDQTMTFEAVKAEEEETVDEEF 249

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           L     L   + +L+LSVR+ NCL+  +I  +G+L     +DM++  NFG+KSL E++ +
Sbjct: 250 LHMRKLLKTSLADLDLSVRAYNCLKAADIKTLGELATLDISDMMKFRNFGKKSLNELEQL 309

Query: 310 LGTMGLFLGMNLPDW 324
           +    L  GM+   +
Sbjct: 310 IIDKNLSFGMDTAKY 324


>gi|314924147|gb|EFS87978.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL001PA1]
          Length = 338

 Score =  211 bits (538), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 123/308 (39%), Positives = 183/308 (59%), Gaps = 12/308 (3%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV HE S+I+G  ED+T+
Sbjct: 16  EFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQHEFSTIEGCVEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IIL ++G  L    D    + + K G G VTA DI     + + NP+  I  L+ D    
Sbjct: 76  IILTLRGFVLPSEEDEPVAMYLRKSGAGEVTAADINPPAGVTIHNPELHIATLNDDGRFE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MEL V +G GYV +  +   N  IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL + 
Sbjct: 136 MELIVERGRGYVSSALNDDPNAEIGRIAVDSIYSPVLKVTYKVEATRVEQRTDFDKLVVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLP----FNPALLK 258
           ++T  SI   D++A A + L +  G+   +N E       E I + S P    +  +L  
Sbjct: 196 VETKPSILPRDAIASAGKTLVELFGLTRELNAE------AEGIEIGSGPVDEEYAESLGT 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  +GL L 
Sbjct: 250 PVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEKLTELGLALK 309

Query: 319 MNLPDWPP 326
            + P + P
Sbjct: 310 DSAPGFDP 317


>gi|298345434|ref|YP_003718121.1| DNA-directed RNA polymerase subunit alpha [Mobiluncus curtisii ATCC
           43063]
 gi|304390990|ref|ZP_07372942.1| DNA-directed RNA polymerase subunit alpha [Mobiluncus curtisii
           subsp. curtisii ATCC 35241]
 gi|315656234|ref|ZP_07909125.1| DNA-directed RNA polymerase subunit alpha [Mobiluncus curtisii
           subsp. holmesii ATCC 35242]
 gi|298235495|gb|ADI66627.1| DNA-directed RNA polymerase subunit alpha [Mobiluncus curtisii ATCC
           43063]
 gi|304325873|gb|EFL93119.1| DNA-directed RNA polymerase subunit alpha [Mobiluncus curtisii
           subsp. curtisii ATCC 35241]
 gi|315493236|gb|EFU82836.1| DNA-directed RNA polymerase subunit alpha [Mobiluncus curtisii
           subsp. holmesii ATCC 35242]
          Length = 335

 Score =  211 bits (538), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 122/308 (39%), Positives = 187/308 (60%), Gaps = 8/308 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           + R+    EPL  GF +TLGN+LRR L+SS+ G+A+T+++I+G LHE +++ GV ED+T 
Sbjct: 23  DQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGSAVTSIKIEGALHEFTTLPGVKEDVTQ 82

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           I+LNIK I L    D    + + K G G VT GDI     + + NP+H I  L+ D  + 
Sbjct: 83  IVLNIKEIVLSSDNDEPVVMYLRKTGEGEVTVGDIMPPAGVVIHNPEHHIATLNKDGKLE 142

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +ELTV +G GYV A  ++     I  I +D++YSP+ KVSY VE+ R  Q  D+D+L + 
Sbjct: 143 IELTVERGRGYVSASQNKDPEAEISRIPVDSIYSPVLKVSYRVEATRVEQRTDFDRLVVD 202

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           ++T  +I   D++A A + L +  G+   +N +    E+    N  +L  + A+   VE+
Sbjct: 203 VETKKAILPRDAMASAGKTLVELFGLARDLNHDAEGIELGPSGNDAALAEDLAM--SVED 260

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           L+L+ R+ NCL  E I  +GDL+ R++AD+L + NFG+KS+ EIK  L  M    GM+L 
Sbjct: 261 LDLTSRALNCLTREGINTVGDLVARSQADLLDIRNFGQKSIDEIKEKLAGM----GMSLK 316

Query: 323 DWPPESIE 330
           D P  ++E
Sbjct: 317 DTPMPAVE 324


>gi|261749445|ref|YP_003257131.1| DNA-directed RNA polymerase subunit alpha [Blattabacterium sp.
           (Periplaneta americana) str. BPLAN]
 gi|261497538|gb|ACX83988.1| DNA-directed RNA polymerase subunit alpha [Blattabacterium sp.
           (Periplaneta americana) str. BPLAN]
          Length = 332

 Score =  211 bits (538), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 122/328 (37%), Positives = 198/328 (60%), Gaps = 16/328 (4%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           + +KP+ I    + +  + + +   +PL  G+  TLGNALRRVL+ SL+G A+T+++I G
Sbjct: 5   DFVKPDRI---TISEFTDQKGIFHLKPLEPGYGLTLGNALRRVLLGSLKGFAVTSIKIKG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINL--KMSGDSHKRVTIFKRGPGVVTAGDI-QTVND 124
           V +E S+I+GV ED+T+IILN K I    K+ G + + + +  +    VT   + + ++ 
Sbjct: 62  VKYEFSTIEGVVEDVTEIILNFKKIRFHRKIKGVTKETINVLIKNKEKVTGKILNEFISS 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH-RTENDPIGLITIDALYSPIKKV 183
            +VLN D VIC+ +    + M  T+ +G GYVPA+ + +  ND IG I ID++Y+PIK V
Sbjct: 122 FQVLNTDVVICHKEKSIPLEMSFTIEEGRGYVPAEENKKNNNDLIGNIPIDSIYTPIKNV 181

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN-------FEE 236
            YT+E+ R GQ  D++ LS+ I TDGS++ + ++  AS+IL     +F +        EE
Sbjct: 182 KYTIENCRVGQKTDFESLSLEIITDGSMSPKTALMEASQILIKYFSIFSHEKIGKKEHEE 241

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
             KE K D     L     L  K+ +++LSVR+ NCL+  +I  + DL+    ++ML+M 
Sbjct: 242 ISKERKYDEEF--LRMRTLLKSKLTDMDLSVRTKNCLKSASIQSVADLVNCNRSNMLKMR 299

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           NFGRKSL E++  +   GL+ GM++ ++
Sbjct: 300 NFGRKSLEELESQMKEKGLYFGMDISEY 327


>gi|72534416|emb|CAH59044.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 217

 Score =  211 bits (538), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 104/207 (50%), Positives = 146/207 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV  G
Sbjct: 61  ALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTVKPG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI 
Sbjct: 121 RGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIE 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKK 239
             ++++L+++I+ + L +F+N  +  K
Sbjct: 181 PLEAMSLSAKIMTEHLDIFVNLTDEAK 207


>gi|71056806|emb|CAH58958.1| DNA-directed RNA polymerase alpha chain [Enterococcus italicus DSM
           15952]
          Length = 234

 Score =  211 bits (538), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 146/210 (69%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNI
Sbjct: 5   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVAQIILNI 64

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+ G+  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV
Sbjct: 65  KGLALKLYGEDEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTV 124

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ ++ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 125 KPGRGYVQADENKKDDMPIGVLPVDSIYTPVRRVNYQVENTRVGHRDDFDKLTMEIWTDG 184

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   D+++LA++I+ + L +F+N  +  K
Sbjct: 185 SIEPLDAMSLAAKIMTEHLDIFVNLTDEAK 214


>gi|119663520|emb|CAK22331.1| RNA polymerase alpha subunit [Lactobacillus hammesii]
          Length = 227

 Score =  211 bits (537), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 103/214 (48%), Positives = 151/214 (70%), Gaps = 4/214 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVTQIILNV 60

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K I LK++G  D  + + I  +GP  +TAGDI    D++VLNPD  I  +   A   M +
Sbjct: 61  KKIALKLNGSDDQEETMEINVKGPAQITAGDIVAGADVDVLNPDLYIATVADGATFHMRM 120

Query: 148 TVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           T  KG GYV A  H+ +N   PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ +
Sbjct: 121 TADKGRGYVSADEHKAQNTEMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDV 180

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
            T+GSI   +++ALA++IL + L MF++  +  K
Sbjct: 181 WTNGSINPSEAIALAAKILTEHLAMFVDLTDEAK 214


>gi|317016849|gb|ADU85965.1| DNA-directed RNA polymerase alpha chain [Lactobacillus
           fabifermentans]
          Length = 235

 Score =  211 bits (537), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 104/212 (49%), Positives = 151/212 (71%), Gaps = 2/212 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+
Sbjct: 4   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVTEDVTAIILNV 63

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A   M +T 
Sbjct: 64  KKVALKLDSDETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLAICTVADGAHFHMRMTA 123

Query: 150 SKGHGYVPAK--HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           + G GYV A+   HR ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T
Sbjct: 124 NTGRGYVSAEDNKHREDDMPIGVLPVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWT 183

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +GSIT  ++++L+++IL D L +F+N  +  K
Sbjct: 184 NGSITPSEAISLSAKILTDHLSIFVNLTDEAK 215


>gi|298243941|ref|ZP_06967748.1| DNA-directed RNA polymerase, alpha subunit [Ktedonobacter racemifer
           DSM 44963]
 gi|297556995|gb|EFH90859.1| DNA-directed RNA polymerase, alpha subunit [Ktedonobacter racemifer
           DSM 44963]
          Length = 326

 Score =  211 bits (537), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 117/277 (42%), Positives = 175/277 (63%), Gaps = 5/277 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL  G+  TLGNALRRVL+SSL GAA+T+++I+GV HE   + GV ED+TDI+LNIK +
Sbjct: 24  EPLEAGYGQTLGNALRRVLLSSLPGAAVTSIRIEGVQHEFQDVPGVLEDVTDIVLNIKKL 83

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSK 151
            L+   +    + +   G   VTA DI   + +E++NP+  I +LD D A + MEL V  
Sbjct: 84  RLRSFSEHPVTMRLEVNGEREVTAADIVAPSTVEIVNPELHIASLDNDNAHLDMELVVET 143

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G  YVPA     E+ PIG+I +DA+Y+P++KV+YTVE  R GQ+ +YDK+ + + TDG+I
Sbjct: 144 GRSYVPADSK--EDQPIGVIPVDAIYTPVQKVNYTVEHTRVGQMTNYDKIVLEVTTDGTI 201

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL-KKVEELELSVRST 270
           T ++++  ++ +L     +  N+     E  E   + SLP    +    +EEL+LSVR+ 
Sbjct: 202 TPDEALRQSADVLVRHFTLLANYRASLPE-PEKAPLSSLPIPQKIYDTPIEELDLSVRAY 260

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           NCL+  NI  +G ++   E D+L + NFG KSL E++
Sbjct: 261 NCLKRSNITKVGQVLSMNEEDLLGVRNFGEKSLQELR 297


>gi|71056914|emb|CAH59016.1| DNA-directed RNA polymerase alpha chain [Enterococcus cecorum]
          Length = 229

 Score =  211 bits (537), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT++QID V HE S+I GV ED++ IILNI
Sbjct: 2   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITSIQIDTVQHEFSTIVGVREDVSQIILNI 61

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+ G   K + I   GP VVTAGDI   +D+E+LN D  IC +   A  R  L V
Sbjct: 62  KGLALKLYGSEEKTLEIDITGPAVVTAGDIIVDSDVEILNKDMYICTVSEGATFRARLKV 121

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++TE+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 122 KAGRGYVQADENKTEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDG 181

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   D+++LA++IL + L +F+N  +  +
Sbjct: 182 SIEPLDAMSLAAKILTEHLDIFVNLTDEAR 211


>gi|311990466|gb|ADQ26363.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 257

 Score =  211 bits (537), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 112/256 (43%), Positives = 161/256 (62%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K +
Sbjct: 2   EPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKL 61

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LK   D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V  G
Sbjct: 62  ELKSLSDERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNG 121

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI 
Sbjct: 122 RGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIK 181

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
             D+++ A++IL +   +F + +   K  +  +  +       L   +EEL+LSVRS NC
Sbjct: 182 PNDALSFAAKILVEHFKVFESADADTKFSEVMVEKEDDKKEKKLEMTIEELDLSVRSYNC 241

Query: 273 LRGENIVYMGDLIQRT 288
           L+   I  + +L   T
Sbjct: 242 LKRAGINTLQELTDMT 257


>gi|72534397|emb|CAH59002.1| DNA-directed RNA polymerase alpha chain [Enterococcus cecorum]
          Length = 231

 Score =  211 bits (537), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT++QID V HE S+I GV ED++ IILNI
Sbjct: 2   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITSIQIDTVQHEFSTIVGVREDVSQIILNI 61

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+ G   K + I   GP VVTAGDI   +D+E+LN D  IC +   A  R  L V
Sbjct: 62  KGLALKLYGSEEKTLEIDITGPAVVTAGDIIVDSDVEILNKDMYICTVSEGATFRARLKV 121

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++TE+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 122 KAGRGYVQADENKTEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDG 181

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   D+++LA++IL + L +F+N  +  +
Sbjct: 182 SIEPLDAMSLAAKILTEHLDIFVNLTDEAR 211


>gi|71833746|emb|CAH59013.1| DNA-directed RNA polymerase alpha chain [Enterococcus canintestini]
          Length = 233

 Score =  211 bits (537), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 146/210 (69%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT++QIDGVLHE S++KGV ED+  IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITSIQIDGVLHEFSTVKGVREDVAQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM     K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV
Sbjct: 61  KGLALKMYTQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG+I +D++Y+P+ +V+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 121 RPGRGYVQADENKREDMPIGVIPVDSIYTPVNRVNYQVENTRVGRRDDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   ++++LA++I+ + L +F+N  +  K
Sbjct: 181 SIMPMEAMSLAAKIMTEHLDIFVNLTDEAK 210


>gi|71056906|emb|CAH59010.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 228

 Score =  211 bits (537), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 103/207 (49%), Positives = 148/207 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+I GV ED+T IILNIKG+
Sbjct: 2   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIPGVREDVTQIILNIKGL 61

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LK+  +  K + I   GP  VTAGDI   +D+E+LN D VIC++   A     LTV  G
Sbjct: 62  ALKLYAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLVICSVAEGATFHARLTVKPG 121

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI 
Sbjct: 122 RGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSII 181

Query: 213 GEDSVALASRILQDQLGMFINFEEPKK 239
            +++++LA++I+ + L +F+N  +  K
Sbjct: 182 PQEALSLAAKIMTEHLDIFVNLTDEAK 208


>gi|71056953|emb|CAH59037.1| DNA-directed RNA polymerase alpha chain [Enterococcus sp. LMG
           14595]
          Length = 224

 Score =  211 bits (537), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 103/206 (50%), Positives = 145/206 (70%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG+ 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNIKGLA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G 
Sbjct: 61  LKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTVKPGR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDGSI  
Sbjct: 121 GYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDGSIIA 180

Query: 214 EDSVALASRILQDQLGMFINFEEPKK 239
           +++++LA++IL + L +F+N  +  K
Sbjct: 181 QEALSLAAKILTEHLDIFVNLTDEAK 206


>gi|227876167|ref|ZP_03994283.1| DNA-directed RNA polymerase [Mobiluncus mulieris ATCC 35243]
 gi|269976926|ref|ZP_06183900.1| DNA-directed RNA polymerase, alpha subunit [Mobiluncus mulieris
           28-1]
 gi|306819442|ref|ZP_07453149.1| DNA-directed RNA polymerase subunit alpha [Mobiluncus mulieris ATCC
           35239]
 gi|307701655|ref|ZP_07638671.1| DNA-directed RNA polymerase, alpha subunit [Mobiluncus mulieris
           FB024-16]
 gi|227843128|gb|EEJ53321.1| DNA-directed RNA polymerase [Mobiluncus mulieris ATCC 35243]
 gi|269934757|gb|EEZ91317.1| DNA-directed RNA polymerase, alpha subunit [Mobiluncus mulieris
           28-1]
 gi|304647734|gb|EFM45052.1| DNA-directed RNA polymerase subunit alpha [Mobiluncus mulieris ATCC
           35239]
 gi|307613158|gb|EFN92411.1| DNA-directed RNA polymerase, alpha subunit [Mobiluncus mulieris
           FB024-16]
          Length = 327

 Score =  211 bits (536), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 115/291 (39%), Positives = 175/291 (60%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
           R+    EPL  GF +TLGN+LRR L+SS+ G+A+T+++I+G LHE +++ GV ED+T ++
Sbjct: 18  RSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGSAVTSIKIEGALHEFTTLPGVKEDVTQVV 77

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LNIK I L    D    + + K G G VT GDI     + + NP+H I  L+ D  + +E
Sbjct: 78  LNIKEIVLSSDNDEPVVMYLRKTGEGEVTVGDIMPPAGVVIHNPEHHIATLNKDGKLEIE 137

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           LTV +G GYV A  ++     I  I +D++YSP+ KVSY VE+ R  Q  D+D+L + ++
Sbjct: 138 LTVERGRGYVSAAQNKDPEAEISRIPVDSIYSPVLKVSYHVEATRVEQRTDFDRLIVDVE 197

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T  +I+  D++A A + L +  G+        + ++   +         L   VE+LEL+
Sbjct: 198 TKKAISPRDAMASAGKTLVELFGLARALNADAEGIELGSSNTDSALAEDLAMSVEDLELT 257

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            R+ NCL  E I  +GDL+ R++AD+L + NFG KS+ EIK  L TMG+ L
Sbjct: 258 SRALNCLNREGIKTVGDLVARSQADLLDIRNFGHKSIDEIKEKLATMGMSL 308


>gi|328813983|gb|AEB52107.1| DNA-directed RNA polymerase alpha chain [Lactobacillus
           parabuchneri]
          Length = 244

 Score =  211 bits (536), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 115/243 (47%), Positives = 162/243 (66%), Gaps = 4/243 (1%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRR L+SSL G+A+T++QID VLHE S+IKGV ED+T IILN+K
Sbjct: 1   VVEPLERGYGTTLGNSLRRTLLSSLPGSAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVK 60

Query: 91  GINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
            I+LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT
Sbjct: 61  KISLKLDGPEDEEENLEIDVIGPADVTAGDIQADSDVTVLNPDLHIATVAEGATFHMRLT 120

Query: 149 VSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            +KG GYV A     R+   PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ + 
Sbjct: 121 ANKGRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDVW 180

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           TDGSIT  ++V+LA++IL + L MF++  +  K  +  +  +       L   +EEL+LS
Sbjct: 181 TDGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEKEETHKEKMLEMTIEELDLS 240

Query: 267 VRS 269
           VRS
Sbjct: 241 VRS 243


>gi|71056898|emb|CAH59006.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           hermanniensis]
          Length = 234

 Score =  211 bits (536), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 103/210 (49%), Positives = 145/210 (69%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDG LHE S+IKGV ED+  IILNI
Sbjct: 2   FVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGALHEFSTIKGVREDVVQIILNI 61

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV
Sbjct: 62  KGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTV 121

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+ KV+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 122 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVCKVNYQVENTRVGRRDDFDKLTMEIWTDG 181

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI  +++++LA++IL + L +F+N  +  K
Sbjct: 182 SIIAQEALSLAAKILTEHLDIFVNLTDEAK 211


>gi|168334324|ref|ZP_02692511.1| DNA-directed RNA polymerase, alpha subunit [Epulopiscium sp. 'N.t.
           morphotype B']
          Length = 319

 Score =  211 bits (536), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 117/292 (40%), Positives = 182/292 (62%), Gaps = 4/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN LRR+L+S+L G+A++ V+ +GVLHE S+I GV ED+ +IILN+
Sbjct: 23  FVIEPLERGYGMTLGNGLRRILLSTLPGSAVSNVKFEGVLHEFSTIPGVKEDVLEIILNL 82

Query: 90  KGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM-- 145
           KG+ ++ S  +   K   I   G GVVTA DI+    +E+LNP+  I  LD D   ++  
Sbjct: 83  KGLCIRDSSATQEPKIAYIEVTGEGVVTAEDIKCPLGVEILNPEMYIATLDGDKNTKLYA 142

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ELT++ G GY      +     IG+I +DA Y+P+++V++ VE  R GQ  D+D+L++ +
Sbjct: 143 ELTITNGRGYEGISKLKKSELLIGVIPVDASYTPVERVNFKVEDTRVGQQTDFDRLTLEV 202

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T G+I  +++++LA+++L + L +FI+  E  K  +  I  +       L   +EEL+L
Sbjct: 203 FTKGTIRPDEAISLAAKVLSEHLSIFIDLSEHAKRAEIMITKEDDTKEKTLEMTIEELDL 262

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           SVRS NCL+   I  + DL  +TE +M+++ N GRKSL E+   L  +GL L
Sbjct: 263 SVRSFNCLKRAGINNVQDLTNKTEEEMMKVRNLGRKSLEEVFKKLEDLGLSL 314


>gi|124020697|gb|ABM88794.1| DNA-directed RNA polymerase alpha chain [Enterococcus camelliae]
          Length = 223

 Score =  211 bits (536), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 104/210 (49%), Positives = 147/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNI
Sbjct: 5   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVAQIILNI 64

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+ G+  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV
Sbjct: 65  KGLALKLYGEDEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSDGATFHARLTV 124

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ ++ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 125 KPGRGYVQADENKKDDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDG 184

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   D+++LA++I+ + L +F+N  +  K
Sbjct: 185 SIEPLDAMSLAAKIMTEHLDIFVNLTDEAK 214


>gi|312386519|gb|ADQ74778.1| RNA polymerase alpha subunit [Lactobacillus sp. MWBPC 1-3-1]
          Length = 248

 Score =  210 bits (535), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 109/245 (44%), Positives = 157/245 (64%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+
Sbjct: 4   FVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNL 63

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK   D  K + +   GP  VTA D++   D++VLNPD  IC +     + MEL V
Sbjct: 64  KKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMELAV 123

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDG
Sbjct: 124 KNGRGYVTASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDG 183

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI   D+++ A++IL +   +F + +   +  +  +  +       L   +EEL+LSVRS
Sbjct: 184 SIKPNDALSFAAKILVEHFKVFESADANTQFSEVMVEKEDDKKEKKLEMTIEELDLSVRS 243

Query: 270 TNCLR 274
            NCL+
Sbjct: 244 YNCLK 248


>gi|161513430|emb|CAP16858.1| DNA-directed RNA polymerase subunit alpha [Pediococcus parvulus]
          Length = 224

 Score =  210 bits (535), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 101/215 (46%), Positives = 150/215 (69%), Gaps = 2/215 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K ++LK+  +  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT 
Sbjct: 61  KKVSLKIESNDEKSLEINVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAVLTA 120

Query: 150 SKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             G GYV A  ++   D  PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + T
Sbjct: 121 DTGRGYVSADENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           DGSI+  ++ +L+++IL + L +F+N  +  ++ +
Sbjct: 181 DGSISPSEATSLSAKILTEHLALFVNLTDEAQDAE 215


>gi|71056904|emb|CAH59009.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
          Length = 226

 Score =  210 bits (535), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 103/207 (49%), Positives = 146/207 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV  G
Sbjct: 61  ALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTVKPG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI 
Sbjct: 121 RGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIE 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKK 239
             ++++L+++I+ + L +F+N  +  K
Sbjct: 181 PLEAMSLSAKIMTEHLDIFVNLTDEAK 207


>gi|253581360|ref|ZP_04858586.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium varium
           ATCC 27725]
 gi|251836724|gb|EES65258.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium varium
           ATCC 27725]
          Length = 325

 Score =  210 bits (535), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 118/307 (38%), Positives = 185/307 (60%), Gaps = 10/307 (3%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E E +   I EPL RG+ HT+GNALRRVL+SS+ GAAI  V+IDGVL E S ++G+ E 
Sbjct: 17  KESEFKGQYIVEPLYRGYGHTVGNALRRVLLSSIPGAAIKGVRIDGVLSEFSVMEGIKEA 76

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T+I+LNIK I +K      +++T+  +GP +VTA DI     IE++NP+ VIC +  D 
Sbjct: 77  VTEIVLNIKEIVVKAESTGERKMTLSVKGPKIVTAADIIPDVGIEIVNPEQVICTITTDR 136

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ME  V  G G+V ++    ++  +  I +DA+Y+PI+KVSY+V+    G++ D+DKL
Sbjct: 137 ELDMEFLVDTGEGFVVSEEIERKDWAVDYIAVDAIYTPIRKVSYSVQDTMVGRMTDFDKL 196

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA------ 255
           ++ I+TDGSI   D+++ A  +L+     F+      + ++  +  +    NP       
Sbjct: 197 TLDIETDGSIEIRDALSYAVELLKLHFDPFLELGNKMENLR--VEAEEEEENPVSHAKDD 254

Query: 256 --LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
             L  K+EEL+L+VRS NCL+   I  +  L + +  ++L++ N GRKSL EI   +  +
Sbjct: 255 NILNTKIEELDLTVRSFNCLKKAGIEEVSQLAKLSLNELLKIKNLGRKSLDEILEKMKEL 314

Query: 314 GLFLGMN 320
           G  L  N
Sbjct: 315 GYDLSQN 321


>gi|71056902|emb|CAH59008.1| DNA-directed RNA polymerase alpha chain [Enterococcus hirae]
          Length = 224

 Score =  210 bits (535), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 103/207 (49%), Positives = 146/207 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+
Sbjct: 2   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGL 61

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV  G
Sbjct: 62  ALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTVKPG 121

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI 
Sbjct: 122 RGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIE 181

Query: 213 GEDSVALASRILQDQLGMFINFEEPKK 239
             ++++L+++I+ + L +F+N  +  K
Sbjct: 182 PLEAMSLSAKIMTEHLDIFVNLTDEAK 208


>gi|257470860|ref|ZP_05634950.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium ulcerans
           ATCC 49185]
 gi|317065063|ref|ZP_07929548.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium ulcerans
           ATCC 49185]
 gi|313690739|gb|EFS27574.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium ulcerans
           ATCC 49185]
          Length = 325

 Score =  210 bits (535), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 119/307 (38%), Positives = 184/307 (59%), Gaps = 10/307 (3%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E E +   I EPL RG+ HT+GNALRRVL+SS+ GAAI  V+IDGVL E S + G+ E 
Sbjct: 17  KESEFKGQYIVEPLYRGYGHTVGNALRRVLLSSIPGAAIKGVRIDGVLSEFSVMDGIKEA 76

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T+IILNIK I +K      +++T+  +GP +VTA DI     IE++NP+ VIC +  D 
Sbjct: 77  VTEIILNIKEIVVKAESTGERKMTLSVKGPKIVTAADIIPDVGIEIVNPEQVICTITTDR 136

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ME  V  G G+V ++    ++  +  I +DA+Y+PI+KVSY+V+    G++ D+DKL
Sbjct: 137 ELDMEFLVDTGEGFVVSEEIERKDWAVDYIAVDAIYTPIRKVSYSVQDTMVGRMTDFDKL 196

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA------ 255
           ++ I+TDGSI   D+++ A  +L+     F+      + ++  +  +    NP       
Sbjct: 197 TLDIETDGSIEIRDALSYAVELLKLHFDPFLELGNKMENLR--VEAEEEEENPVSHAKDD 254

Query: 256 --LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
             L  K+EEL+L+VRS NCL+   I  +  L + +  ++L++ N GRKSL EI   +  +
Sbjct: 255 NILNTKIEELDLTVRSFNCLKKAGIEEVSQLAKLSLNELLKIKNLGRKSLDEILEKMKEL 314

Query: 314 GLFLGMN 320
           G  L  N
Sbjct: 315 GYDLSQN 321


>gi|71056874|emb|CAH58992.1| DNA-directed RNA polymerase alpha chain [Enterococcus ratti]
          Length = 227

 Score =  210 bits (535), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 103/207 (49%), Positives = 146/207 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV  G
Sbjct: 61  ALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTVKPG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI 
Sbjct: 121 RGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIE 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKK 239
             ++++L+++I+ + L +F+N  +  K
Sbjct: 181 PLEAMSLSAKIMTEHLDIFVNLTDEAK 207


>gi|119663518|emb|CAK22330.1| RNA polymerase alpha subunit [Lactobacillus algidus]
          Length = 230

 Score =  210 bits (535), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 101/210 (48%), Positives = 149/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GA+IT +QIDGVLHE S+I+GV ED+T IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGASITNIQIDGVLHEFSTIEGVLEDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK++ D  + + I  +GP  VTAGDI   +D+EVLNPD  IC +   A   + +  
Sbjct: 61  KKVALKLAADEDQSIEIDVKGPAEVTAGDIIGNSDVEVLNPDLYICTVAEGASFHVRMNA 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           S G GYV A  ++ E+ PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T+G
Sbjct: 121 SNGRGYVSADQNKAEDMPIGVLPIDSIYTPIERVNYQVEKTRVGQKDDYDKLTLDVWTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SIT  ++++L+++IL + L +F++  +  K
Sbjct: 181 SITPSEAISLSAKILTEHLTLFVDLTDEAK 210


>gi|71056943|emb|CAH59030.1| DNA-directed RNA polymerase alpha chain [Enterococcus hirae]
          Length = 225

 Score =  210 bits (535), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 103/207 (49%), Positives = 146/207 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV  G
Sbjct: 61  ALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTVKPG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI 
Sbjct: 121 RGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIE 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKK 239
             ++++L+++I+ + L +F+N  +  K
Sbjct: 181 PLEAMSLSAKIMTEHLDIFVNLTDEAK 207


>gi|262038698|ref|ZP_06012058.1| DNA-directed RNA polymerase, alpha subunit [Leptotrichia
           goodfellowii F0264]
 gi|261747250|gb|EEY34729.1| DNA-directed RNA polymerase, alpha subunit [Leptotrichia
           goodfellowii F0264]
          Length = 322

 Score =  210 bits (535), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 118/295 (40%), Positives = 182/295 (61%), Gaps = 6/295 (2%)

Query: 18  IVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           I L +E+E+R       EPL RG+ +T+GNALRR+L+SS+ G+AI  ++IDGVL+E S+I
Sbjct: 11  IKLTEEKESRYTAKYTLEPLYRGYGNTIGNALRRILLSSIPGSAIKGLRIDGVLNEFSTI 70

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
            GV E +TDIILN+K I +++     K++ +  +GP V+TA DI+    I+++NP+ VI 
Sbjct: 71  PGVKEAVTDIILNVKEIVVELDEPGEKKMVLSVKGPKVITAADIKPDPGIKIINPEQVIA 130

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
            +  D  + ME  V  G G+V +    TE  PIG + +DA+Y+PIK+V+Y+VE    G+V
Sbjct: 131 TVTTDKEINMEFLVDSGEGFVVSDEIDTEGWPIGYLAVDAIYTPIKRVTYSVEDTMVGRV 190

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK----EDINVKSLP 251
            +YDKL + I TDGSI   D+++ A  +L   +  F N      + +    E+ ++ S  
Sbjct: 191 TNYDKLILEISTDGSIEIHDALSYAVELLILHVKPFTNIGNSMSKFRGNEDENSSLNSET 250

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +     K+EEL+ +VRS NCL+   +  + DL   T  ++L++ N GRKSL EI
Sbjct: 251 ESNIEDMKIEELDFTVRSYNCLKKAGVNTISDLTSMTYVELLKIKNLGRKSLNEI 305


>gi|71056842|emb|CAH58976.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 215

 Score =  210 bits (534), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 103/207 (49%), Positives = 148/207 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+I GV ED+T IILNIKG+
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIPGVREDVTQIILNIKGL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LK+  +  K + I   GP  VTAGDI   +D+E+LN D VIC++   A     LTV  G
Sbjct: 61  ALKLYAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLVICSVAEGATFHARLTVKPG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI 
Sbjct: 121 RGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSII 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKK 239
            +++++LA++I+ + L +F+N  +  K
Sbjct: 181 PQEALSLAAKIMTEHLDIFVNLTDEAK 207


>gi|71056798|emb|CAH58954.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
          Length = 224

 Score =  210 bits (534), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 102/206 (49%), Positives = 145/206 (70%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNIKG+ 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNIKGLA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LKM GD  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G 
Sbjct: 61  LKMYGDEEKTLEIDISGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTVKPGR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI  
Sbjct: 121 GYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIEP 180

Query: 214 EDSVALASRILQDQLGMFINFEEPKK 239
            ++++L+++I+ + L +F+N  +  K
Sbjct: 181 LEAMSLSAKIMTEHLDIFVNLTDEAK 206


>gi|190411115|gb|ACE78312.1| RpoA [Vibrio parahaemolyticus]
          Length = 252

 Score =  209 bits (533), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 108/255 (42%), Positives = 171/255 (67%), Gaps = 8/255 (3%)

Query: 49  RVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIF 107
           R+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ 
Sbjct: 1   RILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLN 60

Query: 108 KRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRT 163
           K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H+  
Sbjct: 61  KSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHNEE 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ I
Sbjct: 121 DERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATI 180

Query: 224 LQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGD 283
           L +QL  F++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GD
Sbjct: 181 LAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGD 237

Query: 284 LIQRTEADMLRMANF 298
           L+QRTE ++L+  N 
Sbjct: 238 LVQRTEVELLKTPNL 252


>gi|212697280|ref|ZP_03305408.1| hypothetical protein ANHYDRO_01848 [Anaerococcus hydrogenalis DSM
           7454]
 gi|325848968|ref|ZP_08170478.1| DNA-directed RNA polymerase, alpha subunit [Anaerococcus
           hydrogenalis ACS-025-V-Sch4]
 gi|212675729|gb|EEB35336.1| hypothetical protein ANHYDRO_01848 [Anaerococcus hydrogenalis DSM
           7454]
 gi|325480612|gb|EGC83674.1| DNA-directed RNA polymerase, alpha subunit [Anaerococcus
           hydrogenalis ACS-025-V-Sch4]
          Length = 318

 Score =  209 bits (533), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 120/302 (39%), Positives = 196/302 (64%), Gaps = 9/302 (2%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           EE N    +  PL RG+  T+GN++RR+L+SSL G++++ + IDGVLHE S+I GV ED+
Sbjct: 16  EETNYGKFVLYPLERGYGTTIGNSMRRMLLSSLPGSSVSKILIDGVLHEFSTIPGVVEDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFK--RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
            ++ILNIKGI++K    + + +T+F    GP +VTA DI+T   IEV NPDH +  ++  
Sbjct: 76  PELILNIKGIDIKKH--TKEDLTLFLDIEGPKIVTAKDIKTDAQIEVANPDHYLATVNDK 133

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
           A + + L V+ G GY  A+ ++ + DPIG I ID+ ++P+K V++TVE+ R G+  DYDK
Sbjct: 134 ARLFIALDVTDGKGYRVAELNKKDTDPIGAIAIDSSFTPVKSVNFTVENTRVGESTDYDK 193

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKKEVKEDINVKSLPFNPA- 255
           L + + TDG+IT +++++  + IL + +  F +       P+ E +E   ++    N   
Sbjct: 194 LILEVWTDGTITPQEALSEGASILMEDIRFFKDLPGQQFPPEVEEEEVEEIEEEDDNQVE 253

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           L K +EEL+LS+RS NCL+      +G++I+++EA++  + NFG+KSL E+   + ++GL
Sbjct: 254 LSKTIEELDLSLRSFNCLKRAGYNTVGEIIEKSEAELKDIKNFGKKSLDEVIDKIHSLGL 313

Query: 316 FL 317
            L
Sbjct: 314 SL 315


>gi|313836061|gb|EFS73775.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL037PA2]
 gi|314929597|gb|EFS93428.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL044PA1]
 gi|314970628|gb|EFT14726.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL037PA3]
 gi|328906195|gb|EGG25970.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium sp.
           P08]
          Length = 338

 Score =  209 bits (533), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 122/308 (39%), Positives = 183/308 (59%), Gaps = 12/308 (3%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV HE S+I+G  ED+T+
Sbjct: 16  EFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQHEFSTIEGCVEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ L    D    + + K G G + A DI     + + NP   I  L+ D    
Sbjct: 76  IILNLKGLVLSSEEDEPVAMYLRKSGTGEIIAADINPPAGVTIHNPGLHIATLNDDGRFE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MEL V +G GYV +  +   +  IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL + 
Sbjct: 136 MELVVERGRGYVSSALNDDPSAEIGRIAVDSIYSPVLKVTYKVEATRVEQRTDFDKLVVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLP----FNPALLK 258
           ++T  SI   D+VA A + L +  G+   +N E       E I + + P    +  +L  
Sbjct: 196 VETKPSILPRDAVASAGKTLVELFGLTRELNAE------AEGIEIGAGPVDEEYAESLST 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  +GL L 
Sbjct: 250 PVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEKLTELGLALK 309

Query: 319 MNLPDWPP 326
            + P + P
Sbjct: 310 DSAPGFDP 317


>gi|121591860|ref|ZP_01679032.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae
           2740-80]
 gi|121546275|gb|EAX56569.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae
           2740-80]
          Length = 248

 Score =  209 bits (533), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 107/250 (42%), Positives = 164/250 (65%), Gaps = 8/250 (3%)

Query: 87  LNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVR 144
           +N+KG+ ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + 
Sbjct: 1   MNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIA 60

Query: 145 MELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           M + V +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL
Sbjct: 61  MRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKL 120

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + ++T+G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V+
Sbjct: 121 VIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVD 177

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L
Sbjct: 178 DLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRL 237

Query: 322 PDWPPESIEE 331
            +WPP SI E
Sbjct: 238 ENWPPASIAE 247


>gi|325479152|gb|EGC82249.1| DNA-directed RNA polymerase, alpha subunit [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 318

 Score =  209 bits (533), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 112/300 (37%), Positives = 195/300 (65%), Gaps = 5/300 (1%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           EEEN       PL RG+  T+GN++RRVL+SSL G++++ + I+GVLHE S+I GV ED+
Sbjct: 16  EEENYGKFALYPLERGYGTTIGNSMRRVLLSSLPGSSVSKILIEGVLHEFSTIDGVVEDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
            +I+LNIKG+++    D    + +   GP +VTA DI+  + +++ NPDH I  ++  + 
Sbjct: 76  PEIVLNIKGLDVTKHTDEDVTLFLDVEGPKIVTAKDIKADSLVDIANPDHYIATVNEKSR 135

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + + + V+ G GY  +++++ E+DPIG I ID+ ++P++KV+YTVE+ R G+  DYDKL 
Sbjct: 136 LFIAMDVTDGKGYRISENNKDESDPIGTIAIDSSFTPVEKVNYTVENTRVGESTDYDKLI 195

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK-----KEVKEDINVKSLPFNPALL 257
           + + T+G+I+ +++++L S IL + + +F N  + K     + ++E+ N +    +  L 
Sbjct: 196 LEVWTNGTISPQEALSLGSNILIEDVSLFNNLPDMKFPPEEEIIEEEENNEEEALSEDLS 255

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +EEL+LS+RS NCL+      + D+++ +E+++  + NFG+KSL E+   L  +GL L
Sbjct: 256 MTIEELDLSLRSFNCLKRAGFDKVADIVEVSESELKSIKNFGKKSLTEVMDKLDELGLSL 315


>gi|332144686|dbj|BAK19503.1| RNA polymerase alpha subunit [Lactobacillus camelliae]
          Length = 228

 Score =  209 bits (533), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 103/210 (49%), Positives = 146/210 (69%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA++ +QIDGVLHE S+I GV ED+T IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVSNIQIDGVLHEFSTIDGVLEDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM  D  K V I   GP  VTA DI T  D+EVLNP+  IC +       + +TV
Sbjct: 61  KKLALKMHSDEDKTVEIDVDGPATVTAADIVTDADVEVLNPEQYICTVAEGGHFHVRMTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++TEN PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+G
Sbjct: 121 RTGRGYVAADQNKTENMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI+  ++++LA++IL + L +F+N  +  K
Sbjct: 181 SISPREAISLAAKILTEHLDIFVNLTDSAK 210


>gi|71056896|emb|CAH59005.1| DNA-directed RNA polymerase alpha chain [Enterococcus italicus]
          Length = 223

 Score =  209 bits (533), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 103/207 (49%), Positives = 145/207 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG+
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVAQIILNIKGL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LK+ G+  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G
Sbjct: 61  ALKLYGEDEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTVKPG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ ++ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI 
Sbjct: 121 RGYVQADENKKDDMPIGVLPVDSIYTPVRRVNYQVENTRVGHRDDFDKLTMEIWTDGSIE 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKK 239
             D+++LA++I+ + L +F+N  +  K
Sbjct: 181 PLDAMSLAAKIMTEHLDIFVNLTDEAK 207


>gi|328813941|gb|AEB52086.1| DNA-directed RNA polymerase alpha chain [Lactobacillus brevis]
          Length = 248

 Score =  209 bits (532), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 110/248 (44%), Positives = 165/248 (66%), Gaps = 4/248 (1%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRV 104
           LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+K I LK++G  D  + +
Sbjct: 1   LRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVTQIILNVKKIALKLNGSDDQEETM 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            I  +GP  +TAGDI    D+++LNPD  I  +   A   M +T  KG GYV A  ++T 
Sbjct: 61  EINVKGPAQITAGDIVAGADVDILNPDLYIATVADGATFHMRMTADKGRGYVSADENKTR 120

Query: 165 ND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
           N   PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ + T+GSI   +++ALA++
Sbjct: 121 NTDMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDVWTNGSINPSEAIALAAK 180

Query: 223 ILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMG 282
           IL + L MF++  +  K  +  +  +       L   +EEL+LSVRS NCL+   I  + 
Sbjct: 181 ILTEHLAMFVDLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVQ 240

Query: 283 DLIQRTEA 290
           +L  +TEA
Sbjct: 241 ELNNKTEA 248


>gi|311990460|gb|ADQ26360.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus casei]
 gi|328813945|gb|AEB52088.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 245

 Score =  209 bits (532), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 108/237 (45%), Positives = 160/237 (67%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNIK + LKM+ D  
Sbjct: 2   TLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNTDED 61

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV KG GYV A  +
Sbjct: 62  KNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAADQN 121

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           ++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA+
Sbjct: 122 KSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAA 181

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENI 278
           +IL + L +F+N  +  K  +  +  +       L   +EEL+LSVRS NCL+   I
Sbjct: 182 KILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSVRSYNCLKRAGI 238


>gi|297571895|ref|YP_003697669.1| DNA-directed RNA polymerase, subunit alpha [Arcanobacterium
           haemolyticum DSM 20595]
 gi|296932242|gb|ADH93050.1| DNA-directed RNA polymerase, alpha subunit [Arcanobacterium
           haemolyticum DSM 20595]
          Length = 334

 Score =  209 bits (532), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 119/297 (40%), Positives = 181/297 (60%), Gaps = 8/297 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           + R+     PL  GF +TLGN+LRR L+SS+ GAA+T++ IDGVLHE S+I+GV ED+  
Sbjct: 16  DTRSRFTLNPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIHIDGVLHEFSTIEGVKEDVAQ 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+K + +    D   ++ + K GPG VTA DI     +E+ NP+ +I  L+    + 
Sbjct: 76  IILNLKDLVVTSENDEPVQMYLRKAGPGQVTAEDITPPAGVEIHNPELLIATLNEKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           ++LTV +G GYV A+ + + +  IG I +D++YSP+ KVSY VE+ R GQ  D+DKL + 
Sbjct: 136 IDLTVERGRGYVSAQQNNSPDYEIGRIPVDSIYSPVVKVSYKVEATRVGQRTDFDKLIVD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF----NPALLKKV 260
           ++T  S+   D+ A A + L +  G+     E  +EV E + +K  P     +  L + +
Sbjct: 196 VETKPSMAPRDAFASAGKTLVELFGLTT---ELNQEV-EGLELKEAPVVEQQSSDLQRPI 251

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             L L  RS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ ++K  L  + L L
Sbjct: 252 TILNLPARSQNCLQREGIHTIGELVLRSEADLLDIRNFGAKSIEDVKDELAKLDLRL 308


>gi|256544533|ref|ZP_05471906.1| DNA-directed RNA polymerase, alpha subunit [Anaerococcus vaginalis
           ATCC 51170]
 gi|256399858|gb|EEU13462.1| DNA-directed RNA polymerase, alpha subunit [Anaerococcus vaginalis
           ATCC 51170]
          Length = 317

 Score =  209 bits (532), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 116/301 (38%), Positives = 194/301 (64%), Gaps = 8/301 (2%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           EE N    +  PL RG+  T+GN++RR+L+SSL G++++ + IDGVLHE S+I GV ED+
Sbjct: 16  EETNYGKFVLYPLERGYGTTIGNSMRRMLLSSLPGSSVSKILIDGVLHEFSTIPGVVEDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFK--RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
            ++ILNIKGI++K    + + +T+F    GP +VTA DI+T   I+V NPDH +  ++  
Sbjct: 76  PELILNIKGIDIKKH--TKEDITLFLDIEGPKIVTAKDIKTDAQIDVANPDHYLATVNDK 133

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             + + L V+ G GY  A+ ++ + DPIG I ID+ ++P+K V++TVE+ R G+  DYDK
Sbjct: 134 GRLFIALDVTDGKGYRVAEQNKKDTDPIGAIAIDSSFTPVKSVNFTVENTRVGESTDYDK 193

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKKEVKEDINVKSLPFNPAL 256
           L + + TDG+IT +++++  + IL + +  F +       P+ E +E   ++       L
Sbjct: 194 LILEVWTDGTITPQEALSEGASILMEDIRFFKDLPGQQFPPEDEEEEIEEIEEDNNQMEL 253

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
            K +EEL+LS+RS NCL+      +G++I+++E+++  + NFG+KSL E+   + ++GL 
Sbjct: 254 SKTIEELDLSLRSFNCLKRAGYNTVGEIIEKSESELKDIKNFGKKSLEEVIDKIHSLGLS 313

Query: 317 L 317
           L
Sbjct: 314 L 314


>gi|162446984|ref|YP_001620116.1| DNA-directed RNA polymerase subunit alpha [Acholeplasma laidlawii
           PG-8A]
 gi|161985091|gb|ABX80740.1| DNA-directed RNA polymerase, alpha subunit [Acholeplasma laidlawii
           PG-8A]
          Length = 330

 Score =  209 bits (532), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 118/309 (38%), Positives = 190/309 (61%), Gaps = 11/309 (3%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KP ++E I    +E N    + +PL RG+  TLGNALRRVL+SSL GAAI  V+I+GV H
Sbjct: 8   KPTSVEEI---SQEGNLGRFLIKPLERGYGLTLGNALRRVLLSSLPGAAIVNVKIEGVEH 64

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDS---HKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           E S+I+GV+ED+  I+LN+K +   +        +++ ++  GP V+TAGD    +DIEV
Sbjct: 65  EFSTIEGVYEDVMGIVLNLKKVVFSVDSQDPQYEQQLELYAEGPAVITAGDFNLADDIEV 124

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYT 186
           +N D  I  L   A   M +TV +G GYVPA  ++  +   + +I ID+LY+P+++V Y+
Sbjct: 125 VNKDQHIATLAEGAKFNMTVTVRRGIGYVPADQNKQYSKYELNVIPIDSLYTPVERVIYS 184

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE  R     D D+L++ I+T+G+I  ++++ALAS++L D   + ++  E   E     +
Sbjct: 185 VEKTRG----DLDELTIEIETNGAILAKEALALASKMLVDHFQVLVDISEKASEFDFIRD 240

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           ++  P +     K+E+L+LSVR  N L+   I  +G+L++ +E +++R+ + GRKS  E+
Sbjct: 241 IEEEPASKKSDTKIEQLDLSVRLFNSLKRSGITTVGELLKLSEEEVMRLRSLGRKSFKEL 300

Query: 307 KGVLGTMGL 315
           K  L   GL
Sbjct: 301 KEKLAEHGL 309


>gi|161513428|emb|CAP16857.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           argentinicus]
          Length = 225

 Score =  209 bits (532), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 103/215 (47%), Positives = 148/215 (68%), Gaps = 2/215 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQID VLHE S++KGV ED+T IILN+
Sbjct: 2   FVIEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDDVLHEFSTVKGVVEDVTQIILNL 61

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K ++LK+  D  K + I  +GP  VTAGDI   +D+ +LNPD  IC +   A     LT 
Sbjct: 62  KKVSLKIDSDDEKSMEIDVKGPATVTAGDISADSDVTILNPDLAICTVAEGATFHAHLTA 121

Query: 150 SKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GY  A  +  R  + PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ I T
Sbjct: 122 EKGRGYTSADENKARKADMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDIWT 181

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           DGSIT  ++ +L+++IL + L +F+N  +  K+ +
Sbjct: 182 DGSITPSEATSLSAKILTEHLAIFVNLNDQAKDTE 216


>gi|154507837|ref|ZP_02043479.1| hypothetical protein ACTODO_00319 [Actinomyces odontolyticus ATCC
           17982]
 gi|293190232|ref|ZP_06608728.1| DNA-directed RNA polymerase, alpha subunit [Actinomyces
           odontolyticus F0309]
 gi|153797471|gb|EDN79891.1| hypothetical protein ACTODO_00319 [Actinomyces odontolyticus ATCC
           17982]
 gi|292821048|gb|EFF80001.1| DNA-directed RNA polymerase, alpha subunit [Actinomyces
           odontolyticus F0309]
          Length = 331

 Score =  209 bits (531), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 116/291 (39%), Positives = 171/291 (58%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
           R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGV HE  +I+GV ED+ +II
Sbjct: 18  RSRFTLEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVPHEFRTIEGVKEDVAEII 77

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LNIK I L    D    + + K GPG V AGDI     +E+ NPD  +  L+    + +E
Sbjct: 78  LNIKQIVLSSENDEPVVMYLRKAGPGEVLAGDITPPAGVEIHNPDLHLATLNEKGKLEIE 137

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           LTV +G GYV A  ++     I  I ID++YSP+ KV+Y VE+ R  Q  D+D+L + ++
Sbjct: 138 LTVERGRGYVSAAQNKDPQAEISRIPIDSIYSPVVKVTYKVEATRVQQRTDFDRLVIDVE 197

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T  +IT  D++A A + L +  G+     E  + ++   +         L   +E L L 
Sbjct: 198 TKPAITPRDALASAGKTLVELFGLMRELNEEAEGIEVGPSTTDATLAADLALPIENLNLQ 257

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            RS N LR   I+ +G+L+  +EAD+L + NFG KS+ EIK  L  +G+ L
Sbjct: 258 SRSYNALRRRGILTVGELVAHSEADLLDIRNFGTKSIEEIKESLAALGMTL 308


>gi|153816223|ref|ZP_01968891.1| hypothetical protein RUMTOR_02472 [Ruminococcus torques ATCC 27756]
 gi|145846406|gb|EDK23324.1| hypothetical protein RUMTOR_02472 [Ruminococcus torques ATCC 27756]
          Length = 277

 Score =  209 bits (531), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 117/272 (43%), Positives = 180/272 (66%), Gaps = 5/272 (1%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLK-MS-GDSHKRVTIFK 108
           ++SSL G+AI++V+IDGVLHE SSI GV ED+T+II+N+K + ++ MS  D  K V I  
Sbjct: 1   MLSSLPGSAISSVKIDGVLHEFSSIPGVKEDVTEIIMNLKSLAIRNMSESDEPKTVYIEF 60

Query: 109 RGPGVVTAGDIQTVN-DIEVLNPDHVICNLD--VDAVVRMELTVSKGHGYVPAKHHRTEN 165
            G GVVT  DI   + DIE++NPD VI  L    D  + MELT++KG GYV +  ++TE+
Sbjct: 61  EGEGVVTGADININDPDIEIVNPDQVIATLSGGKDCRLNMELTITKGRGYVSSDKNKTED 120

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
            PIG+I ID++Y+P+++V+ TVE+ R GQ+ DYDKL++ + T G++  +++V+LA+++L 
Sbjct: 121 MPIGVIAIDSIYTPVERVNLTVENTRVGQITDYDKLTLDVWTKGTMLPDEAVSLAAKVLS 180

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLI 285
           + L +F++  E  +  +  I  +       L   ++ELELSVRS NCL+   I  + +L 
Sbjct: 181 EHLKLFVDLSEVAQVAEVMIEKEDDEKEKVLEMSIDELELSVRSYNCLKRAGINTVEELT 240

Query: 286 QRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            +T  DM+++ N GRKSL E+   L  + L L
Sbjct: 241 NKTPEDMMKVRNLGRKSLEEVLAKLKELNLEL 272


>gi|323144989|ref|ZP_08079549.1| DNA-directed RNA polymerase, alpha subunit [Succinatimonas hippei
           YIT 12066]
 gi|322415268|gb|EFY06042.1| DNA-directed RNA polymerase, alpha subunit [Succinatimonas hippei
           YIT 12066]
          Length = 329

 Score =  209 bits (531), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 127/330 (38%), Positives = 192/330 (58%), Gaps = 17/330 (5%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           EL+KP  + +  +     N   ++ EPL RGF +T+G +L  +L+ +L G AI A QIDG
Sbjct: 5   ELLKPKPVSFTEVAP---NCAHIVLEPLERGFGNTIGVSLSGILLKTLPGCAIDAFQIDG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           V  E S    + E + ++I+N+K I +      +S   +++ K G G V A DI   + I
Sbjct: 62  VSDENSVKADMVETVFELIMNLKTIAVASESPLNSPVWLSLVKSGEGEVKASDIVLASGI 121

Query: 126 EVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKH-----HRTENDPIGLITIDALYSP 179
              NPD  IC L    A + M++ VS G GYVPA        ++EN+    I IDA +SP
Sbjct: 122 SFPNPDAHICTLKGAKAALSMKIRVSYGRGYVPASSDAHIPAQSENE----ILIDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +++  Y VESAR  Q  D D+L + I+TDG++  E  +   + +L+D L   ++ EE  +
Sbjct: 178 VRRFVYEVESARVEQRTDLDRLVINIETDGTVAPEAVLMQGADLLRDHLCELVDQEEVSE 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
             +          +P L++ V++LEL+VRS NCL+ E+I+Y+GDL+QRTE ++L+  N G
Sbjct: 238 --RSMAPAAPPMPDPVLMQLVDDLELTVRSANCLKAESIIYIGDLVQRTEVELLKTPNLG 295

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL   GL LGM L +WPP ++
Sbjct: 296 KKSLTEIKDVLAQRGLSLGMRLTNWPPPNL 325


>gi|256371243|ref|YP_003109067.1| DNA-directed RNA polymerase, alpha subunit [Acidimicrobium
           ferrooxidans DSM 10331]
 gi|256007827|gb|ACU53394.1| DNA-directed RNA polymerase, alpha subunit [Acidimicrobium
           ferrooxidans DSM 10331]
          Length = 312

 Score =  209 bits (531), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 124/305 (40%), Positives = 180/305 (59%), Gaps = 15/305 (4%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           LG E +NR      PL  GF H++GNALRRVL+SS+ GAAIT V+ D  LHE ++I GV 
Sbjct: 12  LGDEVDNRQRFAIGPLEPGFGHSIGNALRRVLISSVPGAAITQVRFDDALHEFTTIPGVK 71

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+ DIILN+K I  +   +    V +  RGP  VTAGD    +D+EV+N D  I ++  
Sbjct: 72  EDVIDIILNLKDIVWRSWSEEPVTVRLDVRGPKEVTAGDFMLPSDVEVINRDLHIASVSE 131

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              + ++  V +G GYV A+ ++     IG+I IDA++SP++ V+Y VE  R GQ  D+D
Sbjct: 132 HGRLGLDAVVEQGRGYVSAEGNK-RTTTIGIIAIDAIFSPVRHVNYRVEPVRVGQSTDFD 190

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP------FN 253
           ++ + ++TDGS+T  ++VA A+R L    G+         E+  D+N   +         
Sbjct: 191 QVVLEVETDGSVTPREAVASAARTLTSLFGLV-------AELATDVNALEVAATADDSVR 243

Query: 254 PALLK-KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           PA     +EELEL+ R  NCL+  +I  +GDL++RT  D+L + NFG+KSL E+   L  
Sbjct: 244 PAEYDLPIEELELTERPRNCLKRASINTIGDLVERTPEDLLSITNFGQKSLDEVVERLTQ 303

Query: 313 MGLFL 317
            GL L
Sbjct: 304 RGLEL 308


>gi|328949253|ref|YP_004366590.1| DNA-directed RNA polymerase subunit alpha [Treponema succinifaciens
           DSM 2489]
 gi|328449577|gb|AEB15293.1| DNA-directed RNA polymerase subunit alpha [Treponema succinifaciens
           DSM 2489]
          Length = 348

 Score =  209 bits (531), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 120/304 (39%), Positives = 181/304 (59%), Gaps = 10/304 (3%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-----DGVLHEISS----IK 76
           N     A P   GF  T+GN LRRVL+SS++G AI++V+I     DGV H ISS    I 
Sbjct: 26  NYGKFTAYPFEPGFGTTVGNTLRRVLLSSIQGYAISSVRITSYDADGVPHVISSEFETIP 85

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVIC 135
            + ED  +++ ++K I L++  D  +    ++ +GPG V + D+     +E+++ D  I 
Sbjct: 86  NISEDTLEVLNSLKQIRLRLPRDVEQETFFYEFKGPGTVKSDDLAKEGQLEIMSKDLEIF 145

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
            +   A + +E  V  G GYVPA+ +    + +G I +D +++P+ KV Y++E  R GQ 
Sbjct: 146 TMMEGAHLEIEFQVDLGRGYVPAEVNEHYIEIVGTIAMDCIFTPVPKVKYSIEPCRVGQR 205

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            DYDKL + I TDGSIT ED++A A++I +D   +F+NF E +    ++++         
Sbjct: 206 NDYDKLILEIWTDGSITPEDALAEAAKIAKDYFAIFVNFNESEYSGSDELDEGDEKIRQL 265

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           L   VEELELSVRS+NCL+  NI  +G+L ++TE D+ +  NFG+KSL EIK  L   GL
Sbjct: 266 LNTSVEELELSVRSSNCLKNANIRTIGELTKKTEDDITKTRNFGKKSLEEIKAKLEEHGL 325

Query: 316 FLGM 319
            LGM
Sbjct: 326 TLGM 329


>gi|28493495|ref|NP_787656.1| DNA-directed RNA polymerase subunit alpha [Tropheryma whipplei str.
           Twist]
 gi|28572392|ref|NP_789172.1| DNA-directed RNA polymerase subunit alpha [Tropheryma whipplei
           TW08/27]
 gi|41688659|sp|Q820D4|RPOA_TROWT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|41688662|sp|Q820D8|RPOA_TROW8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|28410523|emb|CAD66909.1| DNA-directed RNA polymerase alpha chain [Tropheryma whipplei
           TW08/27]
 gi|28476537|gb|AAO44625.1| DNA-directed RNA polymerase alpha chain [Tropheryma whipplei str.
           Twist]
          Length = 327

 Score =  209 bits (531), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 117/299 (39%), Positives = 183/299 (61%), Gaps = 1/299 (0%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
           R+  I EPL  GF +TLGN+LRR L+SS+ GAA+T++ I GV+HE S+I GV ED+T+I+
Sbjct: 18  RSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSINIQGVMHEFSTIPGVKEDVTEIV 77

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+K + +    D    V ++K G G V A DI+    IE+ N D VI  L  DAV  M+
Sbjct: 78  LNVKRLVISSEIDEPFTVRLYKTGEGEVLAKDIEVPTGIEIGNGDLVIATLAKDAVFDMQ 137

Query: 147 LTVSKGHGYVPAKHHRTENDPI-GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           LT+ +G GYV A+ +R +   + G I +D++YSP+ KV+Y VE+ R G+  D+D+L + +
Sbjct: 138 LTIERGRGYVSAEQNRNDGMSLAGHIPVDSIYSPVHKVTYRVEATRAGERTDFDRLIIDV 197

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
           +T  SI   D+VA A + L +  G+        + V+  ++      +  L   +E+L L
Sbjct: 198 ETKPSILPRDAVASAGKTLCELFGLARELNSQAEGVEFGVDSMIPESDEDLRIPIEDLGL 257

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           SVRS NCL+ E + Y+ +L+  +E ++L + NFG+KS  E++  L  +G  L  ++P +
Sbjct: 258 SVRSYNCLKREGVNYVSELLGFSEQELLDIRNFGQKSADEVQEKLAELGHSLKGSVPGF 316


>gi|161513424|emb|CAP16855.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           dextrinicus]
          Length = 222

 Score =  209 bits (531), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 100/206 (48%), Positives = 148/206 (71%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL G+A++++QIDGVLHE S+I GV ED+T IILNIK I 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGSAVSSIQIDGVLHEFSTIDGVMEDVTQIILNIKKIA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +K   +  K + I   GP  VTA DI+  +DIEVLNP+  IC++     V M++TVS G 
Sbjct: 61  IKNHSEEQKVIEIDVDGPATVTAADIKADDDIEVLNPEQYICSIAEGGHVHMQMTVSNGR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYVPA  ++  + PIG+I +D++++PI +V+Y VES R G+  D+DKL++ + T+GSI+ 
Sbjct: 121 GYVPADQNKNGDMPIGVIAVDSIFTPINRVNYQVESTRVGKRNDFDKLTLDVWTNGSISP 180

Query: 214 EDSVALASRILQDQLGMFINFEEPKK 239
            ++++LA++IL D L +FI+  +  K
Sbjct: 181 REAISLAAKILSDHLNIFIDLSDEAK 206


>gi|71056832|emb|CAH58971.1| DNA-directed RNA polymerase alpha chain [Enterococcus dispar]
          Length = 226

 Score =  209 bits (531), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 102/207 (49%), Positives = 145/207 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT++QIDGVLHE S++KGV ED+  IILNIKG+
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAITSIQIDGVLHEFSTVKGVREDVAQIILNIKGL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LKM     K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV  G
Sbjct: 61  ALKMYTQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTVRPG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P+ +V+Y VE+ R G+  D+DKL+M I TDGSI 
Sbjct: 121 RGYVQADENKREDMPIGVVPVDSIYTPVNRVNYQVENTRVGRRDDFDKLTMEIWTDGSIM 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKK 239
             ++++LA++I+ + L +F+N  +  K
Sbjct: 181 PMEAMSLAAKIMTEHLDIFVNLTDEAK 207


>gi|269792765|ref|YP_003317669.1| DNA-directed RNA polymerase, alpha subunit [Thermanaerovibrio
           acidaminovorans DSM 6589]
 gi|269100400|gb|ACZ19387.1| DNA-directed RNA polymerase, alpha subunit [Thermanaerovibrio
           acidaminovorans DSM 6589]
          Length = 342

 Score =  209 bits (531), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 124/321 (38%), Positives = 186/321 (57%), Gaps = 18/321 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EPL RG+  TLGNALRRVL+SS+ GA I AV++DGVLHE S+I GV ED+ +++LN+
Sbjct: 20  VVLEPLERGYGTTLGNALRRVLLSSIPGAGIVAVRVDGVLHEFSTIPGVREDVIELLLNL 79

Query: 90  KGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K + +++SG     K + +   GP VV A DIQ   D+E ++P+ VIC LD    V M+L
Sbjct: 80  KHVPVRVSGPGTDVKVLRLEAEGPKVVRAADIQGDADVEFVDPEAVICTLDEGHRVSMDL 139

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            + +G GY P    R    P+  + IDA++SP+K+V Y V+  R GQ  DYD+L + + T
Sbjct: 140 YIERGVGYAPIDRPRPSYLPVDALLIDAIFSPVKRVRYEVQDVRSGQRTDYDRLVLEVWT 199

Query: 208 DGSITGEDSVALASRILQDQL-GMFINFEEPKKEVKED----------INVKSLPF---- 252
           +G ++  D+VA AS IL     G+  +       V              +++ +P     
Sbjct: 200 NGVVSFRDAVAEASSILSGYFRGLSTSLWGQSSAVTAGDEDFFEEKDEEDLQEVPAVCGE 259

Query: 253 -NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +  L + +++LELSVRS NCL    I  +GDL+ R + ++L++ N G+ SL EI+  LG
Sbjct: 260 DDSVLSRPIKDLELSVRSENCLLRGGIHRIGDLVSRPKEELLKIRNLGKISLREIEEKLG 319

Query: 312 TMGLFLGMNLPDWPPESIEEL 332
             GL L    P    +  E+L
Sbjct: 320 KFGLSLKGEEPSGEADQAEDL 340


>gi|315605926|ref|ZP_07880957.1| DNA-directed RNA polymerase subunit alpha [Actinomyces sp. oral
           taxon 180 str. F0310]
 gi|315312208|gb|EFU60294.1| DNA-directed RNA polymerase subunit alpha [Actinomyces sp. oral
           taxon 180 str. F0310]
          Length = 331

 Score =  208 bits (530), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 116/291 (39%), Positives = 171/291 (58%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
           R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGV HE  +I+GV ED+ +II
Sbjct: 18  RSRFTLEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVPHEFRTIEGVKEDVAEII 77

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LNIK I L    D    + + K GPG V AGDI     +E+ NPD  +  L+    + +E
Sbjct: 78  LNIKQIVLSSENDEPVVMYLRKAGPGEVLAGDITPPAGVEIHNPDLHLATLNEKGKLEIE 137

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           LTV +G GYV A  ++     I  I ID++YSP+ KV+Y VE+ R  Q  D+D+L + ++
Sbjct: 138 LTVERGRGYVSAAQNKDPQAEISRIPIDSIYSPVVKVTYKVEATRVEQRTDFDRLVIDVE 197

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T  +IT  D++A A + L +  G+     E  + ++   +         L   +E L L 
Sbjct: 198 TKPAITPRDALASAGKTLVELFGLMRELNEEAEGIEVGPSTTDATLAADLALPIENLNLQ 257

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            RS N LR   I+ +G+L+  +EAD+L + NFG KS+ EIK  L  +G+ L
Sbjct: 258 SRSYNALRRRGILTVGELVAHSEADLLDIRNFGTKSIEEIKESLAALGMTL 308


>gi|229496135|ref|ZP_04389855.1| DNA-directed RNA polymerase, alpha subunit [Porphyromonas
           endodontalis ATCC 35406]
 gi|229316713|gb|EEN82626.1| DNA-directed RNA polymerase, alpha subunit [Porphyromonas
           endodontalis ATCC 35406]
          Length = 343

 Score =  208 bits (530), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 115/302 (38%), Positives = 184/302 (60%), Gaps = 10/302 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           +PL  G+A T+GNALRR+L+SSL G AI +++IDGV HE ++I GV ED+T+IILN+K I
Sbjct: 37  KPLEPGYAKTIGNALRRILLSSLEGYAIASIRIDGVEHEFATIPGVTEDVTNIILNLKKI 96

Query: 93  NLKMSGDS--HKRVTI-FKRGPGVVTAGDIQ-TVNDIEVLNPDHVICNLD--VDAVVRME 146
             K   D+   + VT+ F     V TA D+   + + E+ N D  IC+ D  V + V++E
Sbjct: 97  RFKQKVDNADEEVVTVAFPANKDVFTAEDLNAALGNFEITNLDQHICSFDPQVASNVKIE 156

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
             ++KG GYVP+  +  E DP+  I ID++Y+PI++V    ES R  Q  DY+KL + + 
Sbjct: 157 FRINKGRGYVPSDENAREGDPLNTIAIDSIYTPIRRVMPKEESFRVEQKTDYEKLILEVV 216

Query: 207 TDGSITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           TDG+I  E ++  A++IL D   +F    ++ EE   E  + ++ ++L     L ++++ 
Sbjct: 217 TDGTIEPEMALREAAKILIDLFSLFSDGEMHMEEAGDETGDVMDEETLRIRQMLRQELDS 276

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
             LSVR+ NCLR  N+  + DL++    ++L+  NFG+K+  E++G L  +GL    +L 
Sbjct: 277 FNLSVRARNCLRSNNVFTLADLVKHNRQELLKFRNFGKKTFEELEGFLAEVGLEFATDLS 336

Query: 323 DW 324
            +
Sbjct: 337 KY 338


>gi|332144664|dbj|BAK19492.1| RNA polymerase alpha subunit [Lactobacillus sp. YIT 12363]
          Length = 251

 Score =  208 bits (530), Expect = 9e-52,   Method: Compositional matrix adjust.
 Identities = 106/246 (43%), Positives = 161/246 (65%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E  N    + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE +++ GV ED+
Sbjct: 6   EGTNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFTTVDGVLEDV 65

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILNIK + LK+  D  K V I  +GP  VTA DI    D+EVLNP+  IC +     
Sbjct: 66  TQIILNIKKLALKLLTDDDKTVEIDVQGPATVTAADIVADGDVEVLNPEQYICTVAEGGH 125

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
             + +T+ KG GYV A  ++ ++ PIG++ ID++++PI +V+Y VES R G+  D+DKL+
Sbjct: 126 FHVRMTIKKGRGYVAADQNKVDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLT 185

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + + T+GSI   ++++LA++IL + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 186 LDVWTNGSINPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEE 245

Query: 263 LELSVR 268
           L+LSVR
Sbjct: 246 LDLSVR 251


>gi|329962293|ref|ZP_08300299.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides fluxus YIT
           12057]
 gi|328530401|gb|EGF57278.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides fluxus YIT
           12057]
          Length = 330

 Score =  208 bits (529), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 114/277 (41%), Positives = 175/277 (63%), Gaps = 7/277 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AIT ++IDGV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGITVGNALRRILLSSLEGFAITTIKIDGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDSHK--RVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +  +  +V+I         AGDI + +   EVLNP+ VIC+LD  + +++++T++
Sbjct: 88  FKQVVEEFESEKVSITIENSSEFKAGDIGKYLTGFEVLNPELVICHLDSKSTMQIDITIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y VE+ R  Q  DY+KL + I TDGS
Sbjct: 148 KGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKYQVENFRVEQKTDYEKLVLEIATDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I  ++++  A++IL     +F    I  E    +  E+ + + L     L  K+ +++LS
Sbjct: 208 IHPKEALKEAAKILIYHFMLFSDEKITLESNDVDGNEEFDEEVLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KSL
Sbjct: 268 VRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKKSL 304


>gi|72534407|emb|CAH59040.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
          Length = 219

 Score =  208 bits (529), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 102/203 (50%), Positives = 144/203 (70%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNIKG+ LKM
Sbjct: 1   RGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNIKGLALKM 60

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
            GD  K + I   GP  VTAGDI   +D+E+LN D  ICN+   A     LTV  G GYV
Sbjct: 61  YGDEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICNVSEGASFHARLTVKPGRGYV 120

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
            A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI   ++
Sbjct: 121 QADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIEPLEA 180

Query: 217 VALASRILQDQLGMFINFEEPKK 239
           ++LA++I+ + L +F+N  +  K
Sbjct: 181 MSLAAKIMTEHLDIFVNLTDEAK 203


>gi|119668287|emb|CAK95499.1| RNA polymerase alpha subunit [Lactobacillus brevis]
          Length = 228

 Score =  208 bits (529), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 102/211 (48%), Positives = 150/211 (71%), Gaps = 4/211 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+K I
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVTQIILNVKKI 60

Query: 93  NLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            LK++G  D  + + I  +GP  +TAGDI    D+++LNPD  I  +   A   M +T  
Sbjct: 61  ALKLNGSDDQEETMEINVKGPAQITAGDIVAGADVDILNPDLYIATVADGATFHMRMTAD 120

Query: 151 KGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           KG GYV A  ++T N   PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ + T+
Sbjct: 121 KGRGYVSADENKTRNTDMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDVWTN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK 239
           GSI   +++ALA++IL + L MF++  +  K
Sbjct: 181 GSINPSEAIALAAKILTEHLAMFVDLTDEAK 211


>gi|161367356|gb|ABX71083.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae O1]
          Length = 244

 Score =  208 bits (529), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 107/246 (43%), Positives = 166/246 (67%), Gaps = 8/246 (3%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           GF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++
Sbjct: 1   GFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVA 60

Query: 98  -GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGY 155
            G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V +G GY
Sbjct: 61  EGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVERGRGY 120

Query: 156 VPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           VPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T+G++ 
Sbjct: 121 VPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLE 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
            E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VRS NC
Sbjct: 181 PEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANC 237

Query: 273 LRGENI 278
           L+ E I
Sbjct: 238 LKAEAI 243


>gi|260891349|ref|ZP_05902612.1| DNA-directed RNA polymerase, alpha subunit [Leptotrichia hofstadii
           F0254]
 gi|260858732|gb|EEX73232.1| DNA-directed RNA polymerase, alpha subunit [Leptotrichia hofstadii
           F0254]
          Length = 324

 Score =  208 bits (529), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 118/304 (38%), Positives = 186/304 (61%), Gaps = 5/304 (1%)

Query: 22  QEEENRTLMIA-EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
           ++E+N T     EPL RG+ +T+GNALRR+L+SS+ G AI  ++I+GVL+E S+I+GV E
Sbjct: 16  EKEDNYTAKYTLEPLYRGYGNTIGNALRRILLSSIPGTAIKGIKIEGVLNEFSTIEGVKE 75

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
            +TDIILN+K I ++      K++T+  +GP V+TA DI     + ++NP+ VI  +  D
Sbjct: 76  AVTDIILNVKEIVVEADEPGEKKMTLSVKGPAVITAADIHVEPGLRIINPEQVIMTVTTD 135

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             + +E  V  G G+V +    T+  PIG + +DA+Y+PIK+V+Y+VE    G+V +YDK
Sbjct: 136 RQIDIEFLVDSGEGFVVSDEINTDGWPIGYLAVDAIYTPIKRVNYSVEDTMVGRVTNYDK 195

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK--EDINVKSLPFNPALLK 258
           L + I TDGSI  +D+++ A  +L   L  F N      + +  ED   ++   N   ++
Sbjct: 196 LILEIATDGSIEIKDALSYAVELLTWHLEPFTNIGNSMSKYRDSEDELAEADAENENNIE 255

Query: 259 --KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
             K+EEL+ +VRS NCL+   +  + DL   T  ++L++ N G+KSL EI   +  +G  
Sbjct: 256 DMKIEELDFTVRSYNCLKKAGVNTISDLTSMTYNELLKIKNLGKKSLNEIIDKMKELGYD 315

Query: 317 LGMN 320
           LG N
Sbjct: 316 LGDN 319


>gi|256027710|ref|ZP_05441544.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp. D11]
          Length = 326

 Score =  208 bits (529), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 113/306 (36%), Positives = 186/306 (60%), Gaps = 7/306 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E   ++  I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + GV E 
Sbjct: 17  KESNYKSQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDGVKEA 76

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ +IC +  D 
Sbjct: 77  VTEIILNVKEIVVKAESSGERRMTLSIKGPKVVKAADIVADIGLEIVNPEQIICTVTTDR 136

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D+DKL
Sbjct: 137 TLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTDFDKL 196

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI-NVKSLPFNPALLK-- 258
           ++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI  +   P +  ++   
Sbjct: 197 TLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEIVDEPMDIQVIDDK 256

Query: 259 ----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
               K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +  +G
Sbjct: 257 SHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKMKDLG 316

Query: 315 LFLGMN 320
             L  N
Sbjct: 317 YDLEKN 322


>gi|297621699|ref|YP_003709836.1| DNA-directed RNA polymerase, alpha subunit [Waddlia chondrophila
           WSU 86-1044]
 gi|297377000|gb|ADI38830.1| DNA-directed RNA polymerase, alpha subunit [Waddlia chondrophila
           WSU 86-1044]
          Length = 370

 Score =  208 bits (529), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 133/348 (38%), Positives = 195/348 (56%), Gaps = 32/348 (9%)

Query: 18  IVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           IV+ +E    T    IAEP  RGF HTLGN+LRR++++SL   AI  V+I+GV HE  +I
Sbjct: 14  IVVDEETATGTFARFIAEPFERGFGHTLGNSLRRLMLTSLEAPAIIGVRIEGVAHEYMAI 73

Query: 76  KGVHEDLTDIILNIKGINLKM-----SGDSHKRVTIFK------------RGPGVVTAGD 118
            G+ ED+T+IILNIKG  L+      + ++  +  + K            +G   V  GD
Sbjct: 74  DGIVEDMTNIILNIKGAKLRKLPMEDTPNARNQRLLTKVLEITQEDIDNGKGQYEVRLGD 133

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           I      EV+NP+H I  + V    +++L VS G GYVP++ H   +     I IDA ++
Sbjct: 134 IVEGGIFEVVNPNHHIFTVTVPMQKQVDLRVSFGRGYVPSERHVVNDKSTDEILIDAAFT 193

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF------- 231
           P+K V+Y VE+ R GQ  D+D+L + + TDG +T  ++   AS+I      +F       
Sbjct: 194 PVKLVNYHVENTRVGQDTDFDRLVLEVTTDGRVTPTEAFGFASQIGLKHFEIFKKVQTQM 253

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           ++F+    E+KED +         L  +++E+ELSVRSTNCL G NI  + +L+   E  
Sbjct: 254 VSFD----EIKEDSDSDDDEIMDKLALRIDEIELSVRSTNCLSGANIETIAELVSIPERR 309

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW--PPESIEELAKKYE 337
           ML   NFG+KSL EIK  L  MGL LGM+L  +    E++ E  K+Y+
Sbjct: 310 MLEFRNFGKKSLTEIKAKLQEMGLGLGMDLSRYGITAENVREKIKEYQ 357


>gi|71056804|emb|CAH58957.1| DNA-directed RNA polymerase alpha chain [Enterococcus italicus]
          Length = 224

 Score =  208 bits (529), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 102/206 (49%), Positives = 144/206 (69%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG+ 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVAQIILNIKGLA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK+ G+  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G 
Sbjct: 61  LKLYGEDEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTVKPGR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYV A  ++ ++ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI  
Sbjct: 121 GYVQADENKKDDMPIGVLPVDSIYTPVRRVNYQVENTRVGHRDDFDKLTMEIWTDGSIEP 180

Query: 214 EDSVALASRILQDQLGMFINFEEPKK 239
            D+++LA++I+ + L +F+N  +  K
Sbjct: 181 LDAMSLAAKIMTEHLDIFVNLTDEAK 206


>gi|227501161|ref|ZP_03931210.1| DNA-directed RNA polymerase [Anaerococcus tetradius ATCC 35098]
 gi|227216746|gb|EEI82147.1| DNA-directed RNA polymerase [Anaerococcus tetradius ATCC 35098]
          Length = 318

 Score =  207 bits (528), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 118/301 (39%), Positives = 191/301 (63%), Gaps = 5/301 (1%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            EEE+       PL RG+  T+GN++RRVL+SSL G++++ + I+GVLHE S+I GV ED
Sbjct: 15  NEEEHYGKFALYPLERGYGTTIGNSMRRVLLSSLPGSSVSKILIEGVLHEFSTIDGVVED 74

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + +I+LNIKG+++    D    + +   GP +VTA DI+  + +E+ NPDH I  ++  +
Sbjct: 75  VPEIVLNIKGLDVTKHTDEDVTLFLDIEGPKIVTAKDIKEDSSVEIANPDHYIATVNEKS 134

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + + + V+ G GY  ++ ++ E+DPIG I ID+ ++P+KKV++TVE+ R G+  DYDKL
Sbjct: 135 RLFIAMDVTDGKGYRISEENKKESDPIGAIAIDSSFTPVKKVNFTVENTRVGESTDYDKL 194

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFI-----NFEEPKKEVKEDINVKSLPFNPAL 256
            M + T+G+IT ++++A  S IL D    F       F    +EV+E++N +    N  L
Sbjct: 195 IMEVWTNGTITPQEALAEGSSILIDNFSFFTELPNQQFPPEVEEVEEEVNDEEENLNEDL 254

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +EE++LS+RS NCL+      + D+I+ TE+++  + NFG+KSL E+   L  +GL 
Sbjct: 255 AMTIEEMDLSLRSFNCLKRAGFNRVSDIIEVTESELKAIKNFGKKSLTEVIEKLDELGLS 314

Query: 317 L 317
           L
Sbjct: 315 L 315


>gi|161513440|emb|CAP16863.1| DNA-directed RNA polymerase subunit alpha [Pediococcus inopinatus]
          Length = 229

 Score =  207 bits (528), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 101/210 (48%), Positives = 147/210 (70%), Gaps = 2/210 (0%)

Query: 35  LPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL 94
           L RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNIK ++L
Sbjct: 1   LERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNIKKVSL 60

Query: 95  KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHG 154
           K+  D  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G G
Sbjct: 61  KIESDDEKSLEIDVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAILTADTGRG 120

Query: 155 YVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           YV A  ++   D  PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSI+
Sbjct: 121 YVSADENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSIS 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVK 242
             ++ +L+++IL + L +F+N  +  K+ +
Sbjct: 181 PSEATSLSAKILTEHLALFVNLTDEAKDAE 210


>gi|289765669|ref|ZP_06525047.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp. D11]
 gi|289717224|gb|EFD81236.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp. D11]
          Length = 342

 Score =  207 bits (528), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 113/306 (36%), Positives = 186/306 (60%), Gaps = 7/306 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E   ++  I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + GV E 
Sbjct: 33  KESNYKSQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDGVKEA 92

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ +IC +  D 
Sbjct: 93  VTEIILNVKEIVVKAESSGERRMTLSIKGPKVVKAADIVADIGLEIVNPEQIICTVTTDR 152

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D+DKL
Sbjct: 153 TLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTDFDKL 212

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI-NVKSLPFNPALLK-- 258
           ++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI  +   P +  ++   
Sbjct: 213 TLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEIVDEPMDIQVIDDK 272

Query: 259 ----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
               K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +  +G
Sbjct: 273 SHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKMKDLG 332

Query: 315 LFLGMN 320
             L  N
Sbjct: 333 YDLEKN 338


>gi|86609045|ref|YP_477807.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|119366741|sp|Q2JL74|RPOA_SYNJB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|86557587|gb|ABD02544.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 335

 Score =  207 bits (528), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 119/291 (40%), Positives = 179/291 (61%), Gaps = 12/291 (4%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG   T+GNALRRVL+S+L G A+TAV+I GV HE S++ GV ED+ +I+LN+K + 
Sbjct: 47  PLERGQGITVGNALRRVLLSNLEGTAVTAVRIAGVTHEFSTVPGVREDVMEILLNMKELV 106

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+ S    +   +  +GPG VTA  +Q  +D+EV+NP H I  L   A++ ME  + +GH
Sbjct: 107 LRSSSPETQVGRLVAQGPGEVTAEKLQLPSDVEVINPRHHIATLAEGAILEMEFMIGRGH 166

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY    +  ++   I  + ID+++ P++KV+Y VE+AR GQ L+ D+L + I T+GS+T 
Sbjct: 167 GYRAVDYSDSKAMAIDFLQIDSVFMPVRKVNYAVEAARVGQFLEKDRLVLEIWTNGSLTP 226

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP--FNPALLKKVEELELSVRSTN 271
           +++++ A+RIL   +G+F     P +EV  D  V   P   N      +EEL+LSVR+ N
Sbjct: 227 QEALSQAARIL---VGLFA----PLQEVSFDAPVPPKPDEDNQKNQIPIEELQLSVRAYN 279

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           CL+   I  + DL+  TE D+L + NFG+KS  E+   L       G+ LP
Sbjct: 280 CLKRAQINTVADLLLYTEEDLLEIKNFGQKSAEEVVQALKAR---FGLTLP 327


>gi|307718231|ref|YP_003873763.1| hypothetical protein STHERM_c05210 [Spirochaeta thermophila DSM
           6192]
 gi|306531956|gb|ADN01490.1| hypothetical protein STHERM_c05210 [Spirochaeta thermophila DSM
           6192]
          Length = 363

 Score =  207 bits (528), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 120/301 (39%), Positives = 181/301 (60%), Gaps = 11/301 (3%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-----DGVLHEISS----IKGVHEDL 82
           A P  RG+  T+GN LRR+L+SS++G AI+AV+I      G  H +SS    I GV ED 
Sbjct: 32  AYPFERGYGVTIGNTLRRILLSSIQGYAISAVRITWYDDQGTAHVLSSEYEQIPGVVEDT 91

Query: 83  TDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
            ++  N+K + +++  +   K V +  +GP  VT  D + V+ +EV+N D  +  L  DA
Sbjct: 92  LELFANLKLLRVQLPDEMEQKTVMVEFKGPKEVTGADFE-VDQLEVMNKDFRVMTLMEDA 150

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              ME+ V  G GYVPA+  +   + +G I +DALYSPI++V + VE+ R G   DYDKL
Sbjct: 151 HFEMEMQVDLGRGYVPAEVQKNYIEVVGTIPLDALYSPIQRVRFDVENTRVGHRSDYDKL 210

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + + TDGSI+ ED++  A+++ ++   +FINF+E        ++ +       L   +E
Sbjct: 211 ILEVWTDGSISPEDALGEAAKLAKEHFTVFINFDEDAISHVRQLDHEEEQIRRLLETPIE 270

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           ELELSVRS+NCL+  NI  +GDL+ ++E ++ +  NFG+KSL+EIK  L    L LGM  
Sbjct: 271 ELELSVRSSNCLKNANIRTIGDLVSKSEEELSKTRNFGKKSLLEIKEKLKEWNLSLGMRD 330

Query: 322 P 322
           P
Sbjct: 331 P 331


>gi|257067033|ref|YP_003153289.1| DNA-directed RNA polymerase subunit alpha [Anaerococcus prevotii
           DSM 20548]
 gi|256798913|gb|ACV29568.1| DNA-directed RNA polymerase, alpha subunit [Anaerococcus prevotii
           DSM 20548]
          Length = 318

 Score =  207 bits (528), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 113/300 (37%), Positives = 187/300 (62%), Gaps = 5/300 (1%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           EEEN       PL RG+  T+GN++RRVL+SSL G++++ + I+GVLHE S+I GV ED+
Sbjct: 16  EEENYGKFALYPLERGYGTTIGNSMRRVLLSSLPGSSVSKILIEGVLHEFSTIDGVVEDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
            +I+LNIKG+++    D    + +   GP +VTA DI+  + +++ NPDH I  ++  + 
Sbjct: 76  PEIVLNIKGLDVTKHVDEDVTLFLDIEGPKIVTAKDIKADSSVDIANPDHYIATVNEKSR 135

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + + + V+ G GY  +  ++ E+DPIG I ID+ ++P++KV++TVE+ R G+  DYDKL 
Sbjct: 136 LFIAMDVTDGKGYRVSDDNKKESDPIGAIAIDSSFTPVEKVNFTVENTRVGESTDYDKLV 195

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF-----INFEEPKKEVKEDINVKSLPFNPALL 257
           M + T+G+IT ++++A  S IL +    F       F    +E + +   +    +  L 
Sbjct: 196 MEVWTNGTITPQEALAEGSSILIENFSFFNELPNQQFPPEVEEEEIEEVEEEDSLSEDLA 255

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +EEL+LS+RS NCL+      +GD+I+ +E+++  + NFG+KSL E+   L  +GL L
Sbjct: 256 MTIEELDLSLRSFNCLKRAGFDRVGDIIKVSESELKTIKNFGKKSLTEVIEKLDELGLSL 315


>gi|257126748|ref|YP_003164862.1| DNA-directed RNA polymerase subunit alpha [Leptotrichia buccalis
           C-1013-b]
 gi|257050687|gb|ACV39871.1| DNA-directed RNA polymerase, alpha subunit [Leptotrichia buccalis
           C-1013-b]
          Length = 324

 Score =  207 bits (527), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 117/302 (38%), Positives = 185/302 (61%), Gaps = 5/302 (1%)

Query: 22  QEEENRTLMIA-EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
           ++E+N T     EPL RG+ +T+GNALRR+L+SS+ G AI  ++I+GVL+E S+I+GV E
Sbjct: 16  EKEDNYTAKYTLEPLYRGYGNTIGNALRRILLSSIPGTAIKGIKIEGVLNEFSTIEGVKE 75

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
            +TDIILN+K I ++      K++T+  +GP V+TA DI     ++++NP+ VI  +  D
Sbjct: 76  AVTDIILNVKEIVVESDEPGEKKMTLSVKGPAVITAADIHVEPGLKIINPEQVIMTVTTD 135

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             + +E  V  G G+V +    T+  PIG + +DA+Y+PIK+V+Y+VE    G+V +YDK
Sbjct: 136 KQIDIEFLVDSGEGFVVSDEINTDGWPIGYLAVDAIYTPIKRVNYSVEDTMVGRVTNYDK 195

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK--EDINVKSLPFNPALLK 258
           L + I TDGSI  +D+++ A  +L   L  F N      + +  ED    +   N   ++
Sbjct: 196 LILEIATDGSIEIKDALSYAVELLTWHLEPFTNIGNSMSKYRDSEDELTVTAEENENNIE 255

Query: 259 --KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
             K+EEL+ +VRS NCL+   +  + DL   T  ++L++ N G+KSL EI   +  +G  
Sbjct: 256 DMKIEELDFTVRSYNCLKKAGVNTISDLTSMTYNELLKIKNLGKKSLNEIIDKMKELGYD 315

Query: 317 LG 318
           LG
Sbjct: 316 LG 317


>gi|288929313|ref|ZP_06423158.1| DNA-directed RNA polymerase, alpha subunit [Prevotella sp. oral
           taxon 317 str. F0108]
 gi|288329415|gb|EFC68001.1| DNA-directed RNA polymerase, alpha subunit [Prevotella sp. oral
           taxon 317 str. F0108]
          Length = 330

 Score =  207 bits (527), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 114/276 (41%), Positives = 173/276 (62%), Gaps = 7/276 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GN+LRR+L+SSL G +I  V+I GV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGVTIGNSLRRILLSSLEGFSINTVRIAGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   +++V+I         AGDI + +   EVLNPD VIC+LD  A ++++LT++
Sbjct: 88  FKQVVEEFENEKVSITVENTTEFKAGDIGKYLTGFEVLNPDLVICHLDAKASLQIDLTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y+VE  R  Q  DYDKL + + TDGS
Sbjct: 148 KGRGYVPADENREFCTDVNVIPIDSIYTPIRNVRYSVEPYRVEQKTDYDKLVIDVTTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I+ +D++  A++IL     +F    I  E    +  E+ + + L     L  K+ ++ LS
Sbjct: 208 ISPKDALKEAAKILIYHFMLFSDEKIAVENQDVDTNEEFDEEVLHMRQLLKTKLVDMNLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KS
Sbjct: 268 VRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKKS 303


>gi|283945397|dbj|BAI66454.1| RNA polymerase alpha subunit [Lactobacillus similis]
          Length = 248

 Score =  207 bits (527), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 105/221 (47%), Positives = 154/221 (69%), Gaps = 3/221 (1%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E ++    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED
Sbjct: 9   EESDDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVVED 68

Query: 82  LTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           +T IILN K I+LK+ G  D  + + I  +GP  VTAGDI   +D+ VLNPD  I  +  
Sbjct: 69  VTQIILNTKKISLKLEGPDDEIESMEIDVKGPAQVTAGDITADSDVTVLNPDLYIATVAE 128

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            A   M +T +KG GYV A  ++ + D PIG++ ID++Y+PI++V+Y VE+ R GQ  DY
Sbjct: 129 GATFHMRMTANKGRGYVSADRNKAKEDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDY 188

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           DKL++ + TD SIT  +S++LA++IL + L MF++  +  K
Sbjct: 189 DKLTLDVWTDSSITPSESISLAAKILTEHLAMFVDLTDEAK 229


>gi|283945395|dbj|BAI66453.1| RNA polymerase alpha subunit [Lactobacillus odoratitofui]
          Length = 247

 Score =  207 bits (527), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 105/221 (47%), Positives = 154/221 (69%), Gaps = 3/221 (1%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E ++    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED
Sbjct: 8   EESDDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVED 67

Query: 82  LTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           +T IILN K I+LK+ G  D  + + I  +GP  VTAGDI   +D+ +LNPD  I  +  
Sbjct: 68  VTQIILNTKKISLKLEGPDDEIESMEIDVKGPAQVTAGDITADSDVTILNPDLYIATVAE 127

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            A   M +T +KG GYV A  ++ + D PIG++ ID++Y+PI++V+Y VE+ R GQ  DY
Sbjct: 128 GATFHMRMTANKGRGYVSADRNKAKEDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDY 187

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           DKL++ + TD SIT  +S++LA++IL + L MF++  +  K
Sbjct: 188 DKLTLDVWTDSSITPSESISLAAKILTEHLAMFVDLTDEAK 228


>gi|323925214|gb|ADY11800.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 240

 Score =  207 bits (527), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 103/239 (43%), Positives = 161/239 (67%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +K
Sbjct: 1   VVEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           GI +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV 
Sbjct: 61  GIAIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSIRAVMTVK 120

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG+GYVPA  ++ +  PIG I +D++Y+P+ KV+Y VE AR G    YDKL++ I T+G+
Sbjct: 121 KGYGYVPADENKVDGAPIGTIAVDSIYTPVSKVNYQVEPARVGGDSSYDKLTLEITTNGT 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           I  +++++L+++IL D L +F++  E   E +  +    +     L K +EE++ SVR+
Sbjct: 181 IVSDEALSLSAKILTDHLNLFVDLSEVASEAETLVVKDEVKTERVLDKIIEEMDFSVRA 239


>gi|86438808|emb|CAJ43369.1| RNA polymerase alpha subunit [Lactobacillus casei]
          Length = 233

 Score =  207 bits (527), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 100/210 (47%), Positives = 149/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED+T IILNI
Sbjct: 2   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLEDVTQIILNI 61

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM+ D  K + I   GP  VTA DI T  D+EVLNP+  IC +       + +TV
Sbjct: 62  KKLALKMNTDEDKNIEIDVNGPAKVTAADIVTDPDVEVLNPEQYICTVADGGHFHVRMTV 121

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+G
Sbjct: 122 KKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNG 181

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI+  ++++LA++IL + L +F+N  +  K
Sbjct: 182 SISPREAISLAAKILTEHLDIFVNLTDEAK 211


>gi|260909777|ref|ZP_05916471.1| DNA-directed RNA polymerase subunit alpha [Prevotella sp. oral
           taxon 472 str. F0295]
 gi|260636202|gb|EEX54198.1| DNA-directed RNA polymerase subunit alpha [Prevotella sp. oral
           taxon 472 str. F0295]
          Length = 330

 Score =  207 bits (527), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 114/276 (41%), Positives = 173/276 (62%), Gaps = 7/276 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GN+LRR+L+SSL G +I  V+I GV HE SS+ GV ED+T+IILN+K + 
Sbjct: 28  PLEPGFGVTIGNSLRRILLSSLEGFSINTVRIAGVEHEFSSVPGVKEDVTNIILNLKQVR 87

Query: 94  LKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +   +++V+I         AGDI + +   EVLNPD VIC+LD  A ++++LT++
Sbjct: 88  FKQVVEEFENEKVSITVENTTEFKAGDIGKYLTGFEVLNPDLVICHLDAKASLQIDLTIN 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA  +R     + +I ID++Y+PI+ V Y+VE  R  Q  DYDKL + + TDGS
Sbjct: 148 KGRGYVPADENREFCTDVNVIPIDSIYTPIRNVRYSVEPYRVEQKTDYDKLIIDVTTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I+ +D++  A++IL     +F    I  E    +  E+ + + L     L  K+ ++ LS
Sbjct: 208 ISPKDALKEAAKILIYHFMLFSDEKIAVENQDVDTNEEFDEEVLHMRQLLKTKLVDMNLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           VR+ NCL+  ++  +GDL+Q  + D+L+  NFG+KS
Sbjct: 268 VRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKKS 303


>gi|328813959|gb|AEB52095.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 231

 Score =  207 bits (526), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 100/210 (47%), Positives = 149/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED+T IILNI
Sbjct: 2   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLEDVTQIILNI 61

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM+ D  K + I   GP  VTA DI T  D+EVLNP+  IC +       + +TV
Sbjct: 62  KKLALKMNTDEDKNIEIDVNGPAKVTAADIVTDPDVEVLNPEQYICTVADGGHFHVRMTV 121

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+G
Sbjct: 122 KKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNG 181

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI+  ++++LA++IL + L +F+N  +  K
Sbjct: 182 SISPREAISLAAKILTEHLDIFVNLTDEAK 211


>gi|260494239|ref|ZP_05814370.1| DNA-directed RNA polymerase, alpha subunit [Fusobacterium sp.
           3_1_33]
 gi|260198385|gb|EEW95901.1| DNA-directed RNA polymerase, alpha subunit [Fusobacterium sp.
           3_1_33]
          Length = 332

 Score =  207 bits (526), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 113/306 (36%), Positives = 186/306 (60%), Gaps = 7/306 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E   ++  I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + GV E 
Sbjct: 23  KESNYKSQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDGVKEA 82

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ +IC +  D 
Sbjct: 83  VTEIILNVKEIVVKAESSGERRMTLSIKGPKVVKAADIVADIGLEIVNPEQIICTVTTDR 142

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D+DKL
Sbjct: 143 TLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTDFDKL 202

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI-NVKSLPFNPALLK-- 258
           ++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI  +   P +  ++   
Sbjct: 203 TLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEMVDEPMDIQVIDDK 262

Query: 259 ----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
               K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +  +G
Sbjct: 263 SHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKMKDLG 322

Query: 315 LFLGMN 320
             L  N
Sbjct: 323 YDLEKN 328


>gi|332176606|gb|AEE12296.1| DNA-directed RNA polymerase subunit alpha [Porphyromonas
           asaccharolytica DSM 20707]
          Length = 330

 Score =  207 bits (526), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 116/299 (38%), Positives = 184/299 (61%), Gaps = 7/299 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           +PL  G+A T+GNALRR+L+SSL G AI +++I+GV HE ++I GV ED+T IILN+K I
Sbjct: 27  KPLEPGYAMTIGNALRRILLSSLEGYAIASIRIEGVEHEFATIPGVLEDVTHIILNLKQI 86

Query: 93  NLKMSGD--SHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
             K + +    + +T+   G     AGD+ Q +   +V NPD VICNL  DA   +EL +
Sbjct: 87  RFKAAVEDPQEETITLHVTGRNTFQAGDLNQVLTSYKVQNPDLVICNLAEDADFTIELRI 146

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GYV ++ +R E+DP+  + ID +Y+PI+KV+ T E+ R  Q  DY+KL + I+TDG
Sbjct: 147 NKGRGYVVSEENRREDDPVNTLPIDGIYTPIRKVNQTTEAYRVDQRTDYEKLVLEIETDG 206

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKED----INVKSLPFNPALLKKVEELEL 265
           +I   +++  A+ IL     +F + E   +  +E+    ++ +++     L+  +   +L
Sbjct: 207 TIHPREALRQAATILISHFALFTDKEFEVELPEEEPDQLLDNQTMKVRTQLMTDLATTDL 266

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           SVR+ NCL+   I  + DL+ R   ++L++ NFG+KSLVEI+  L    L   M+L  +
Sbjct: 267 SVRALNCLKAAGISTIADLLSRDRDELLKIKNFGKKSLVEIEQFLADQDLDFDMDLTPY 325


>gi|269925858|ref|YP_003322481.1| DNA-directed RNA polymerase, alpha subunit [Thermobaculum terrenum
           ATCC BAA-798]
 gi|269789518|gb|ACZ41659.1| DNA-directed RNA polymerase, alpha subunit [Thermobaculum terrenum
           ATCC BAA-798]
          Length = 367

 Score =  207 bits (526), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 119/291 (40%), Positives = 178/291 (61%), Gaps = 4/291 (1%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GNALRRVL+SSL GAAIT+VQI+G  HE  ++ GV ED+TDIILNIK I 
Sbjct: 46  PLAPGYGLTIGNALRRVLLSSLEGAAITSVQIEGARHEFMALPGVKEDVTDIILNIKRIR 105

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV-DAVVRMELTVSKG 152
           ++   D    + +   GP VVTA DI+   D+++++ D  I  LD  DA + M+LTV KG
Sbjct: 106 VRSYSDRPVTLRLEATGPKVVTAADIRPHADVDIVSLDQPIATLDSEDATLSMQLTVQKG 165

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYVPA+    +   IG I +DA+YSP+ KV+Y VE  R GQ  DYD L + I TDG+I 
Sbjct: 166 RGYVPAESQ--DFFEIGRIPVDAIYSPVTKVNYVVERTRVGQRTDYDNLIIEIWTDGTIA 223

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
             ++++ A+ IL  Q  +   +   +     ++  +++       + ++EL LS R+ N 
Sbjct: 224 PGEALSQAASILVGQFQIIAAYANAETSFGIELPTETMSVPEVDNRSIDELGLSARTLNS 283

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           L+  +I  +G ++ +T+ D+L + NFG KSL E++  L   G +L  +LP+
Sbjct: 284 LKRAHITTVGQVLSKTKDDLLSIRNFGDKSLHELEAKLKEFG-YLPSDLPE 333


>gi|237744175|ref|ZP_04574656.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp. 7_1]
 gi|229431404|gb|EEO41616.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp. 7_1]
          Length = 342

 Score =  207 bits (526), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 113/306 (36%), Positives = 186/306 (60%), Gaps = 7/306 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E   ++  I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + GV E 
Sbjct: 33  KESNYKSQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDGVKEA 92

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ +IC +  D 
Sbjct: 93  VTEIILNVKEIVVKAESSGERRMTLSIKGPKVVKAADIVADIGLEIVNPEQIICTVTTDR 152

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D+DKL
Sbjct: 153 TLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTDFDKL 212

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI-NVKSLPFNPALLK-- 258
           ++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI  +   P +  ++   
Sbjct: 213 TLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEMVDEPMDIQVIDDK 272

Query: 259 ----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
               K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +  +G
Sbjct: 273 SHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKMKDLG 332

Query: 315 LFLGMN 320
             L  N
Sbjct: 333 YDLEKN 338


>gi|217967396|ref|YP_002352902.1| DNA-directed RNA polymerase, alpha subunit [Dictyoglomus turgidum
           DSM 6724]
 gi|217336495|gb|ACK42288.1| DNA-directed RNA polymerase, alpha subunit [Dictyoglomus turgidum
           DSM 6724]
          Length = 321

 Score =  207 bits (526), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 121/319 (37%), Positives = 200/319 (62%), Gaps = 15/319 (4%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M+++N + +I+  + EY   G+        + EPL RG+  T+GN+LRR+L+SS+ GAA+
Sbjct: 1   MLEENVRVIIEKRSDEY---GR-------FVIEPLERGYGWTIGNSLRRILLSSIEGAAV 50

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
            +V+I+GV HE+  + G+ E++ +I++N+K + +K+  ++   + +  RGP VVTAGD  
Sbjct: 51  VSVKIEGVRHELEVLPGLKEEILEILMNLKKLVVKIEDNNSHILELDVRGPKVVTAGDFI 110

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              ++++LNPD VI  L  D    ME+ V KG GYV A+ ++ ++ PIG++ +D+++SP+
Sbjct: 111 VPANVKILNPDLVIATLVDDIPFHMEVEVRKGKGYVSAEENKDQSYPIGVLVLDSIFSPV 170

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI--NFEEPK 238
           KKVSYTVE  R G+  D D+L + I T+ S+T E++   ASRIL +   +     F+ P 
Sbjct: 171 KKVSYTVEKTRVGRRTDLDRLIIEIWTNKSVTPEEAFREASRILMEYFKLLSEREFQLPH 230

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +EV ++I   SL      L  +E+L LS R+ N LR   I  + DL+ ++  D++++ NF
Sbjct: 231 EEVGQEIT--SLEEEKKGL-TLEDLGLSTRAYNSLRHAGIHTIEDLLSKSREDLMKIKNF 287

Query: 299 GRKSLVEIKGVLGTMGLFL 317
           G+KSL E++  L   GL L
Sbjct: 288 GQKSLQELEEKLREKGLSL 306


>gi|256845557|ref|ZP_05551015.1| DNA-directed RNA polymerase, alpha subunit [Fusobacterium sp.
           3_1_36A2]
 gi|256719116|gb|EEU32671.1| DNA-directed RNA polymerase, alpha subunit [Fusobacterium sp.
           3_1_36A2]
          Length = 332

 Score =  207 bits (526), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 114/306 (37%), Positives = 185/306 (60%), Gaps = 7/306 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E   +   I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + GV E 
Sbjct: 23  KESNYKGQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDGVKEA 82

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ VIC +  D 
Sbjct: 83  VTEIILNVKEIVVKAESSGERRMTLSIKGPKVVKAADIVADIGLEIVNPEQVICTVTTDR 142

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D+DKL
Sbjct: 143 TLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTDFDKL 202

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI-NVKSLPFNPALLK-- 258
           ++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI  +   P +  ++   
Sbjct: 203 TLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEIIEEPMDIQVIDDK 262

Query: 259 ----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
               K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +  +G
Sbjct: 263 SHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKMKDLG 322

Query: 315 LFLGMN 320
             L  N
Sbjct: 323 YDLEKN 328


>gi|72534403|emb|CAH59034.1| DNA-directed RNA polymerase alpha chain [Enterococcus sp. LMG
           13603]
          Length = 226

 Score =  206 bits (525), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 101/203 (49%), Positives = 143/203 (70%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG+ LK+
Sbjct: 1   RGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNIKGLALKL 60

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G GYV
Sbjct: 61  FAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTVKPGRGYV 120

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
            A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDGSI  +++
Sbjct: 121 QADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDGSIIAQEA 180

Query: 217 VALASRILQDQLGMFINFEEPKK 239
           ++LA++IL + L +F+N  +  K
Sbjct: 181 LSLAAKILTEHLDIFVNLTDEAK 203


>gi|119662385|emb|CAJ33181.1| RNA polymerase alpha subunit [Lactobacillus zeae]
          Length = 227

 Score =  206 bits (525), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 100/210 (47%), Positives = 149/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED+T IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLEDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM+ D  K + I   GP  VTA DI T  D+EVLNP+  IC +       + +TV
Sbjct: 61  KKLALKMNTDEDKNIEIDVNGPAKVTAADIVTDPDVEVLNPEQYICTVADGGHFHVRMTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+G
Sbjct: 121 KKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI+  ++++LA++IL + L +F+N  +  K
Sbjct: 181 SISPREAISLAAKILTEHLDIFVNLTDEAK 210


>gi|34763720|ref|ZP_00144641.1| DNA-directed RNA polymerase alpha chain [Fusobacterium nucleatum
           subsp. vincentii ATCC 49256]
 gi|237742278|ref|ZP_04572759.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp.
           4_1_13]
 gi|27886499|gb|EAA23753.1| DNA-directed RNA polymerase alpha chain [Fusobacterium nucleatum
           subsp. vincentii ATCC 49256]
 gi|229429926|gb|EEO40138.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp.
           4_1_13]
          Length = 342

 Score =  206 bits (525), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 114/306 (37%), Positives = 185/306 (60%), Gaps = 7/306 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E   +   I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + GV E 
Sbjct: 33  KESNYKGQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDGVKEA 92

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ VIC +  D 
Sbjct: 93  VTEIILNVKEIVVKAESSGERRMTLSIKGPKVVKAADIVADIGLEIVNPEQVICTVTTDR 152

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D+DKL
Sbjct: 153 TLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTDFDKL 212

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI-NVKSLPFNPALLK-- 258
           ++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI  +   P +  ++   
Sbjct: 213 TLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEIIEEPMDIQVVDDK 272

Query: 259 ----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
               K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +  +G
Sbjct: 273 SHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKMKDLG 332

Query: 315 LFLGMN 320
             L  N
Sbjct: 333 YDLEKN 338


>gi|294785154|ref|ZP_06750442.1| DNA-directed RNA polymerase, alpha subunit [Fusobacterium sp.
           3_1_27]
 gi|294486868|gb|EFG34230.1| DNA-directed RNA polymerase, alpha subunit [Fusobacterium sp.
           3_1_27]
          Length = 332

 Score =  206 bits (525), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 114/306 (37%), Positives = 185/306 (60%), Gaps = 7/306 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E   +   I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + GV E 
Sbjct: 23  KESNYKGQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDGVKEA 82

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ VIC +  D 
Sbjct: 83  VTEIILNVKEIVVKAESSGERRMTLSIKGPKVVKAADIVADIGLEIVNPEQVICTVTTDR 142

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D+DKL
Sbjct: 143 TLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTDFDKL 202

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI-NVKSLPFNPALLK-- 258
           ++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI  +   P +  ++   
Sbjct: 203 TLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEIIEEPMDIQVVDDK 262

Query: 259 ----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
               K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +  +G
Sbjct: 263 SHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKMKDLG 322

Query: 315 LFLGMN 320
             L  N
Sbjct: 323 YDLEKN 328


>gi|323925172|gb|ADY11786.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|323925175|gb|ADY11787.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|323925178|gb|ADY11788.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|323925181|gb|ADY11789.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|323925184|gb|ADY11790.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|323925190|gb|ADY11792.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|323925193|gb|ADY11793.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|323925199|gb|ADY11795.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|323925202|gb|ADY11796.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|323925208|gb|ADY11798.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|323925211|gb|ADY11799.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|323925217|gb|ADY11801.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|323925220|gb|ADY11802.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|323925223|gb|ADY11803.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|323925226|gb|ADY11804.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 240

 Score =  206 bits (525), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 103/239 (43%), Positives = 161/239 (67%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +K
Sbjct: 1   VVEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           GI +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV 
Sbjct: 61  GIAIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVK 120

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG+GYVPA  ++ +  PIG I +D++Y+P+ KV+Y VE AR G    YDKL++ I T+G+
Sbjct: 121 KGYGYVPADENKVDGAPIGTIAVDSIYTPVSKVNYQVEPARVGGDSSYDKLTLEITTNGT 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           I  +++++L+++IL D L +F++  E   E +  +    +     L K +EE++ SVR+
Sbjct: 181 IVSDEALSLSAKILTDHLNLFVDLSEVAAEAETLVVKDEVKTERVLDKIIEEMDFSVRA 239


>gi|323925169|gb|ADY11785.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|323925196|gb|ADY11794.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
          Length = 240

 Score =  206 bits (525), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 103/239 (43%), Positives = 161/239 (67%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +K
Sbjct: 1   VVEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           GI +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV 
Sbjct: 61  GIAIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVK 120

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG+GYVPA  ++ +  PIG I +D++Y+P+ KV+Y VE AR G    YDKL++ I T+G+
Sbjct: 121 KGYGYVPADENKVDGAPIGTIAVDSIYTPVSKVNYQVEPARVGGDSSYDKLTLEITTNGT 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           I  +++++L+++IL D L +F++  E   E +  +    +     L K +EE++ SVR+
Sbjct: 181 IVSDEALSLSAKILTDHLNLFVDLSEVAAEAETLVVKDEVKTERVLDKIIEEMDFSVRT 239


>gi|290968216|ref|ZP_06559759.1| DNA-directed RNA polymerase, alpha subunit [Megasphaera genomosp.
           type_1 str. 28L]
 gi|290781698|gb|EFD94283.1| DNA-directed RNA polymerase, alpha subunit [Megasphaera genomosp.
           type_1 str. 28L]
          Length = 325

 Score =  206 bits (524), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 120/304 (39%), Positives = 187/304 (61%), Gaps = 22/304 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL G AIT+++IDGVLHE S+I+GV ED+++IILN+
Sbjct: 23  FVCEPLDRGYGITLGNSLRRVLLSSLDGVAITSIKIDGVLHEFSTIQGVREDVSEIILNL 82

Query: 90  KGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K + L+ + D  +   +++   G    TA D+   +DIE+LNP+  +  LD DA + M  
Sbjct: 83  KQLRLRFTRDDVNELDISVDVNGECEFTAKDLDVNSDIEILNPELHLATLDADAHIYMTC 142

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            + +G GY+P+  ++ E D IG+I ID+++SP+ +  Y V + R G  +DYD L++ + T
Sbjct: 143 HIERGKGYIPSTKNKKETDMIGVIPIDSIFSPVMRTKYEVGNIRVGNEMDYDSLTLEVKT 202

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL-PFNPALLK-------- 258
           DGSI  E++VA A+ I+   L  F      +K   + +  ++L PF     +        
Sbjct: 203 DGSIAAENAVAKAASIMVSYLDYF------QKIASDPVANEALAPFTTPEGEEPEVEEGP 256

Query: 259 -----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                K++ L+LSVR++NCL+  NI  +GDL++RTE D+ ++ N G+KS+ EI   L   
Sbjct: 257 ELSQVKIDVLDLSVRASNCLKRANIYTLGDLVERTEEDLSKIRNLGKKSVDEIIEKLKDY 316

Query: 314 GLFL 317
           G  L
Sbjct: 317 GFDL 320


>gi|257467163|ref|ZP_05631474.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|315918294|ref|ZP_07914534.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|313692169|gb|EFS29004.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium
           gonidiaformans ATCC 25563]
          Length = 326

 Score =  206 bits (524), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 118/314 (37%), Positives = 184/314 (58%), Gaps = 24/314 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E E +   + EPL RG+ HTLGNALRRVL+SS+ GAAI  ++I+GVL E S + GV E 
Sbjct: 17  RESEFKGQFVVEPLYRGYGHTLGNALRRVLLSSIPGAAIKGIRIEGVLSEFSVMDGVKEA 76

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T+IILN+K I +K      +++T+  +GP VVTA DI     +E++NPD  IC +  D 
Sbjct: 77  VTEIILNVKEIVVKSETAGERKMTLSVKGPKVVTAADIIPDIGLEIINPDQEICTITTDR 136

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + +E  V  G G+V ++    +   +  I +DA+Y+PI+KVSY ++    G++ D+DKL
Sbjct: 137 ELDIEFLVDTGEGFVVSEEIERDGWAVDYIAVDAIYTPIRKVSYDIQDTMVGRMTDFDKL 196

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINF---------------EEPKKEVKEDIN 246
           +++++TDGSI   D+++ A  +L+  L  F+                 E     +K+DIN
Sbjct: 197 TLSVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRVEVEEEVENQSSSIKDDIN 256

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           +           K+EEL+L+VRS NCL+   I  +G L + +  ++L++ N GRKSL EI
Sbjct: 257 LNI---------KIEELDLTVRSFNCLKKAGIEEVGQLSKLSMNELLKIKNLGRKSLDEI 307

Query: 307 KGVLGTMGLFLGMN 320
              +  +G  L  N
Sbjct: 308 LEKMKELGYDLAQN 321


>gi|161513432|emb|CAP16859.1| DNA-directed RNA polymerase subunit alpha [Pediococcus parvulus]
          Length = 224

 Score =  206 bits (524), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 99/208 (47%), Positives = 146/208 (70%), Gaps = 2/208 (0%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNIK ++LK+
Sbjct: 2   RGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNIKKVSLKI 61

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             D  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV
Sbjct: 62  ESDDEKSLEINVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAVLTADTGRGYV 121

Query: 157 PAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A  ++   D  PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSI+  
Sbjct: 122 SADENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSISPS 181

Query: 215 DSVALASRILQDQLGMFINFEEPKKEVK 242
           ++ +L+++IL + L +F+N  +  ++ +
Sbjct: 182 EATSLSAKILTEHLALFVNLTDEAQDAE 209


>gi|313887090|ref|ZP_07820789.1| DNA-directed RNA polymerase, alpha subunit [Porphyromonas
           asaccharolytica PR426713P-I]
 gi|312923501|gb|EFR34311.1| DNA-directed RNA polymerase, alpha subunit [Porphyromonas
           asaccharolytica PR426713P-I]
          Length = 330

 Score =  206 bits (524), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 115/299 (38%), Positives = 184/299 (61%), Gaps = 7/299 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           +PL  G+A T+GNALRR+L+SSL G AI +++I+GV HE ++I GV ED+T IILN+K I
Sbjct: 27  KPLEPGYAMTIGNALRRILLSSLEGYAIASIRIEGVEHEFATIPGVLEDVTHIILNLKQI 86

Query: 93  NLKMSGD--SHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
             K + +    + +T+   G     AGD+ Q +   +V NPD VICNL  DA   +E+ +
Sbjct: 87  RFKAAVEDPQEETITLHVTGRNTFQAGDLNQVLTSYKVQNPDLVICNLAEDADFTIEIRI 146

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GYV ++ +R E+DP+  + ID +Y+PI+KV+ T E+ R  Q  DY+KL + I+TDG
Sbjct: 147 NKGRGYVVSEENRREDDPVNTLPIDGIYTPIRKVNQTTEAYRVDQRTDYEKLVLEIETDG 206

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKED----INVKSLPFNPALLKKVEELEL 265
           +I   +++  A+ IL     +F + E   +  +E+    ++ +++     L+  +   +L
Sbjct: 207 TIHPREALRQAATILISHFALFTDKEFEVELPEEEPDQLLDNQTMKVRTQLMTDLATTDL 266

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           SVR+ NCL+   I  + DL+ R   ++L++ NFG+KSLVEI+  L    L   M+L  +
Sbjct: 267 SVRALNCLKAAGISTIADLLSRDRDELLKIKNFGKKSLVEIEQFLADQDLDFDMDLTPY 325


>gi|306821592|ref|ZP_07455190.1| DNA-directed RNA polymerase subunit alpha [Eubacterium yurii subsp.
           margaretiae ATCC 43715]
 gi|304550337|gb|EFM38330.1| DNA-directed RNA polymerase subunit alpha [Eubacterium yurii subsp.
           margaretiae ATCC 43715]
          Length = 313

 Score =  206 bits (524), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 108/294 (36%), Positives = 186/294 (63%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           EE+      EPL RGFA T+GN+LRRVL+SSL G A+TA++ID V+HE S++KGV ED+T
Sbjct: 15  EEDYGKFALEPLERGFATTVGNSLRRVLLSSLPGVAVTAIKIDKVMHEFSTVKGVKEDVT 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           +++L +K +++ M  +    + I  +G   +TAGDI     +E++N D  I  L  DA +
Sbjct: 75  ELMLTLKELSMNMDSNGEAILRIDAQGECEITAGDIICPAGVEMVNKDLHIATLSEDADL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
           +ME+ ++KG GYV +  ++ +  PIG+I +D++Y+P+KKV++T+E     +   Y++L +
Sbjct: 135 KMEIYINKGRGYVSSDTNKQKGLPIGVIPMDSIYTPVKKVNFTIEEVNVSEDEQYERLVL 194

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            I T  ++  +D++++A++I  + L +FI+  +    ++  +  +       L   +EEL
Sbjct: 195 DIWTKKTVNPKDALSIAAKIFTEHLSLFIDLTDSVNAMEIMVEKEQDEKEKVLEMTIEEL 254

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +LSVRS NCL+  +I  + +L  +TE +M+++ N G+KSL E+   L  +G  L
Sbjct: 255 DLSVRSYNCLKRASINTVQELTSKTEDEMMKVRNLGKKSLEEVIHKLHELGFTL 308


>gi|108792409|emb|CAJ33153.1| RNA polymerase alpha subunit [Lactobacillus murinus]
          Length = 222

 Score =  206 bits (524), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 102/209 (48%), Positives = 148/209 (70%), Gaps = 2/209 (0%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT VQIDGVLHE S++KGV ED+T IILN+K +
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAITDVQIDGVLHEFSTVKGVLEDVTAIILNLKKV 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LK+  +  + +     GP  VTAGDIQ  +D+E+LNPD  IC +   AV    +T +KG
Sbjct: 61  ALKLDSEDSQTLEFDVVGPKEVTAGDIQGSSDVEILNPDQYICTVADGAVFHARMTANKG 120

Query: 153 HGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            GYV A  +  + E+ PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T+GS
Sbjct: 121 RGYVSATENKAKAEDMPIGVLPIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWTNGS 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKK 239
           IT  ++++L+++IL + L +F++  +  K
Sbjct: 181 ITPSEAISLSAKILTEHLTLFVDLTDEAK 209


>gi|311990458|gb|ADQ26359.1| RNA polymerase alpha subunit [Lactobacillus fermentum]
          Length = 242

 Score =  206 bits (524), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 108/241 (44%), Positives = 163/241 (67%), Gaps = 2/241 (0%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRRV+++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K
Sbjct: 1   VVEPLERGYGTTLGNSLRRVMLASLPGAAITSIQIDGVLHEFSTVQGVTEDVTQIILNLK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            + LK+  +  K + I  +GP  VTA DIQ   D+ +LN D  I  +   A + +++T  
Sbjct: 61  QVALKIDSEDAKDLEIDVKGPAEVTAADIQGDGDVTILNSDLHIATVSDGAELHVKMTAD 120

Query: 151 KGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           KG GY  A  ++T  E   IG++ ID++Y+PI++V+YTVE+ R GQ  DYDKL++ + T+
Sbjct: 121 KGRGYSSADDNKTRMEGLAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYDKLTLDVWTN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           GS+T  ++++LA++IL + L MF+N  E  +  +  +  +       L K +EEL+LSVR
Sbjct: 181 GSLTPTEAISLAAKILTEHLTMFVNLTEEAQVTQVMVEREETHQEKVLDKTIEELDLSVR 240

Query: 269 S 269
           S
Sbjct: 241 S 241


>gi|227873400|ref|ZP_03991657.1| DNA-directed RNA polymerase [Oribacterium sinus F0268]
 gi|227840761|gb|EEJ51134.1| DNA-directed RNA polymerase [Oribacterium sinus F0268]
          Length = 312

 Score =  206 bits (524), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 120/298 (40%), Positives = 187/298 (62%), Gaps = 9/298 (3%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           EE+     + + L +G A  LGN+LRR+L+SS+ G+A++ V++D V HE SSI GV ED+
Sbjct: 16  EEQGYARFVCDSLAKGEATVLGNSLRRILLSSMPGSAVSEVKLDSVYHEFSSIPGVKEDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-V 139
           ++II+N+K + L+ +G   + V  +    G GVV A DI+  +++E++NPD V+ +L   
Sbjct: 76  SEIIMNLKNLALRYTGSGEEPVMAYVDYMGEGVVKASDIKVSSEVEIMNPDLVLAHLSGK 135

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           DA + ME+ VSKG GY  A      +  IG+I +DA+YSP+KKV+  VE   +G     +
Sbjct: 136 DAKIYMEMKVSKGKGYDGANTRDHSDLAIGVIAVDAIYSPVKKVNVFVE--EQGNT---E 190

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           +L + + TD ++  E++V+LA+RILQ  L +F++ +   KE    +  +    +  L K 
Sbjct: 191 RLILDVTTDRTMMPEEAVSLAARILQTHLQLFMHMDTSAKEQGAAVANQEAGRDE-LNKS 249

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           ++ELELSVRS NCL+   I  + DL  +T  D++++ N GRKSL EI   L +MGLFL
Sbjct: 250 IDELELSVRSYNCLKRAGINTVEDLCAKTMDDLMKVRNMGRKSLDEILNKLESMGLFL 307


>gi|323925205|gb|ADY11797.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 240

 Score =  206 bits (524), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 103/239 (43%), Positives = 161/239 (67%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +K
Sbjct: 1   VVEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           GI +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV 
Sbjct: 61  GIAIKSYVESEKQIELDVTGPIDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVK 120

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG+GYVPA  ++ +  PIG I +D++Y+P+ KV+Y VE AR G    YDKL++ I T+G+
Sbjct: 121 KGYGYVPADENKVDGAPIGTIAVDSIYTPVSKVNYQVEPARVGGDSSYDKLTLEITTNGT 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           I  +++++L+++IL D L +F++  E   E +  +    +     L K +EE++ SVR+
Sbjct: 181 IVSDEALSLSAKILTDHLNLFVDLSEVAAEAETLVVKDEVKTERVLDKIIEEMDFSVRA 239


>gi|190411125|gb|ACE78317.1| RpoA [Vibrio parahaemolyticus]
          Length = 244

 Score =  206 bits (524), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 107/247 (43%), Positives = 167/247 (67%), Gaps = 8/247 (3%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVT 105
           LRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T
Sbjct: 1   LRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFIT 60

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HH 161
           + K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H+
Sbjct: 61  LNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHN 120

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
             +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+
Sbjct: 121 EEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAA 180

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
            IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+
Sbjct: 181 TILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYI 237

Query: 282 GDLIQRT 288
           GDL+QRT
Sbjct: 238 GDLVQRT 244


>gi|302584003|gb|ADL57236.1| RNA polymerase A [Paralactobacillus selangorensis]
          Length = 222

 Score =  206 bits (523), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 99/206 (48%), Positives = 145/206 (70%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAA+T VQIDGVLHE S+I GV ED+T IILNIK + 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAVTDVQIDGVLHEFSTIDGVVEDVTQIILNIKKLA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +KM G+  + + +   GP  VTA DI T  D+E+LNPD  +C +     +   +TV KG 
Sbjct: 61  IKMEGEEDRTIELDVTGPAKVTAADIHTDADVEILNPDLYLCTVSDGGSIHARMTVKKGR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY   K +++E+ PIG++ ID++Y+PI +V+Y VES R G+  DYDKL++ + T+GSI+ 
Sbjct: 121 GYDSWKENKSEDMPIGVLPIDSIYTPISRVNYQVESTRVGRRSDYDKLTLDVWTNGSISP 180

Query: 214 EDSVALASRILQDQLGMFINFEEPKK 239
            ++++LA++IL + L +F+N  +  K
Sbjct: 181 REAISLAAKILTEHLAIFVNLTDEAK 206


>gi|168805077|gb|ACA28617.1| DNA-directed RNA polymerase subunit alpha [Thiomonas arsenivorans]
          Length = 228

 Score =  206 bits (523), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 100/228 (43%), Positives = 154/228 (67%), Gaps = 3/228 (1%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           G+ ED+  ++LN+KG+  K+       +++ K G GVVTA DIQT +D+E++NP+HVI +
Sbjct: 1   GLQEDVIAVLLNLKGVVFKLHNRDEVTLSLRKEGEGVVTAADIQTPHDVEIINPEHVIAH 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSYTVESAREG 193
           L     + M++ V KG GYVP    R  ++    IG I +DA +SP+++VSY VE+AR  
Sbjct: 61  LSQQGKIDMQIKVEKGRGYVPGNLRRYADEGGKTIGRIVLDASFSPVRRVSYAVENARVE 120

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL M I+T+GSI+ E+++  ++RIL +QL +F + E  +K ++   +  +  F+
Sbjct: 121 QRTDLDKLVMEIETNGSISAEEAIRTSARILVEQLSVFASLEGAEKTLETGGSASAQQFD 180

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GRK
Sbjct: 181 PILLRPVDDLELTVRSANCLKAENIYYIGDLIQRSETELLKTPNLGRK 228


>gi|86606119|ref|YP_474882.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp.
           JA-3-3Ab]
 gi|119366740|sp|Q2JUJ5|RPOA_SYNJA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|86554661|gb|ABC99619.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus sp.
           JA-3-3Ab]
          Length = 331

 Score =  206 bits (523), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 116/295 (39%), Positives = 181/295 (61%), Gaps = 20/295 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG   T+GNALRRVL+S+L G A+TAV+I GV HE S++ GV ED+ +I+LN+K + 
Sbjct: 45  PLERGQGITVGNALRRVLLSNLEGTAVTAVRIAGVTHEFSTVPGVREDVMEILLNMKELV 104

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+ +    +   +  +GPG VTA  +Q  +++EV+NP H I  L   A++ ME  + +G 
Sbjct: 105 LRSNAPDTQVGRLVAQGPGEVTAEKLQLPSEVEVINPRHHIATLAEGAILEMEFMIGRGR 164

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY    +  +++  I  + ID+++ P++KV+YTVE+AR GQ L+ D+L + I T+GS+T 
Sbjct: 165 GYRAVDYSDSKSMAIDFLQIDSVFMPVRKVNYTVEAARVGQSLEKDRLILEIWTNGSLTP 224

Query: 214 EDSVALASRILQDQLGMFINFEE------PKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +++++ A+RIL   +G+F   +E      P+    ED     +P        +EEL+LSV
Sbjct: 225 QEALSQAARIL---VGLFSPLQEVSFDTPPEPRQAEDNQKNQIP--------IEELQLSV 273

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ NCL+   I  + DL+  TE D+L + NFG+KS  E+   L      LG+ LP
Sbjct: 274 RAYNCLKRAQINTVADLLVYTEEDLLEIKNFGQKSAEEVVQALKNR---LGLTLP 325


>gi|328814001|gb|AEB52116.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 232

 Score =  206 bits (523), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 108/231 (46%), Positives = 156/231 (67%), Gaps = 2/231 (0%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK+
Sbjct: 2   RGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTAIILNVKKIALKL 61

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A   M +T + G GYV
Sbjct: 62  ESDETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGAHFHMRMTANTGRGYV 121

Query: 157 PAK--HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A+   HR ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T+GSIT  
Sbjct: 122 SAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWTNGSITPS 181

Query: 215 DSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
           ++++L+++IL D L +F+N  +  K     +  +       L   +EEL+L
Sbjct: 182 EAISLSAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEMTIEELDL 232


>gi|119662337|emb|CAJ33157.1| RNA polymerase alpha subunit [Lactobacillus paracasei subsp.
           tolerans]
          Length = 230

 Score =  205 bits (522), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 100/210 (47%), Positives = 148/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV
Sbjct: 61  KKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+G
Sbjct: 121 KKGRGYVAADQNKSDDVPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI+  ++++LA++IL + L +F+N  +  K
Sbjct: 181 SISPREAISLAAKILTEHLDIFVNLTDEAK 210


>gi|71056951|emb|CAH59036.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
          Length = 219

 Score =  205 bits (522), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 100/203 (49%), Positives = 143/203 (70%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNIKG+ LKM
Sbjct: 1   RGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNIKGLALKM 60

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
            GD  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G GYV
Sbjct: 61  YGDEEKTLEIDISGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTVKPGRGYV 120

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
            A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI   ++
Sbjct: 121 QADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIEPLEA 180

Query: 217 VALASRILQDQLGMFINFEEPKK 239
           ++L+++I+ + L +F+N  +  K
Sbjct: 181 MSLSAKIMTEHLDIFVNLTDEAK 203


>gi|227485498|ref|ZP_03915814.1| DNA-directed RNA polymerase [Anaerococcus lactolyticus ATCC 51172]
 gi|227236497|gb|EEI86512.1| DNA-directed RNA polymerase [Anaerococcus lactolyticus ATCC 51172]
          Length = 316

 Score =  205 bits (522), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 114/307 (37%), Positives = 189/307 (61%), Gaps = 4/307 (1%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
           NIE + + +E+      +  PL RG+  T+GN++RRVL+SSL G++++ + IDGVLHE S
Sbjct: 8   NIEILDINEEDHYGKFALY-PLERGYGTTIGNSMRRVLLSSLPGSSVSKILIDGVLHEFS 66

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
            I GV ED+ +IILNIKG+N+K   D    + +   GP +VTA DI+    +E+ NPDH 
Sbjct: 67  IIDGVVEDVPEIILNIKGLNVKKHSDEDVTLFLEIEGPKIVTAKDIKEDALVEIANPDHY 126

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           I  ++  + + + + V+ G+GY  +  ++ + DPIG I ID+ ++P++KV+YTVE+ R G
Sbjct: 127 IATVNDKSKLLIAMDVTNGNGYRISDDNKDDKDPIGTIAIDSSFTPVEKVNYTVENTRVG 186

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-- 251
           +  D+DKL + + T+G++T ++++A    IL ++   F    + K   +E    + L   
Sbjct: 187 ESTDFDKLIIEVWTNGTVTPQEALAEGLSILMNKFAFFKELPDKKFPPEEIETTEELAAD 246

Query: 252 -FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             N  L + +EEL+LS+RS NCL+      + D+I+  EA++  + NFG+KSL E+   +
Sbjct: 247 DVNEDLERTIEELDLSLRSFNCLKRAGFNTVADIIKVPEAELKIIKNFGKKSLTEVIDKI 306

Query: 311 GTMGLFL 317
             +G  L
Sbjct: 307 HDLGFTL 313


>gi|323925187|gb|ADY11791.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
          Length = 240

 Score =  205 bits (521), Expect = 8e-51,   Method: Compositional matrix adjust.
 Identities = 103/239 (43%), Positives = 160/239 (66%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +K
Sbjct: 1   VVEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           GI +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV 
Sbjct: 61  GIAIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVK 120

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG+GYVPA  ++ +  PIG I +D++Y+P+ KV+Y VE AR G    YDKL++ I T+G+
Sbjct: 121 KGYGYVPADENKVDGAPIGTIAVDSIYTPVSKVNYQVEPARVGGDSSYDKLTLEITTNGT 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           I  +++++L+++IL D L +F +  E   E +  +    +     L K +EE++ SVR+
Sbjct: 181 IVSDEALSLSAKILTDHLNLFXDLSEVAAEAETLVVKDEVKTERVLDKIIEEMDFSVRA 239


>gi|119668363|emb|CAK95475.1| RNA polymerase alpha subunit [Lactobacillus rhamnosus]
          Length = 228

 Score =  205 bits (521), Expect = 9e-51,   Method: Compositional matrix adjust.
 Identities = 99/210 (47%), Positives = 148/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED+T IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLEDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV
Sbjct: 61  KKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+G
Sbjct: 121 KKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI+  ++++LA++IL + L +F+N  +  K
Sbjct: 181 SISPREAISLAAKILTEHLDIFVNLTDEAK 210


>gi|257463991|ref|ZP_05628376.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp. D12]
 gi|317061513|ref|ZP_07925998.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp. D12]
 gi|313687189|gb|EFS24024.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp. D12]
          Length = 314

 Score =  205 bits (521), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 113/283 (39%), Positives = 179/283 (63%), Gaps = 6/283 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+ HTLGNALRRVL+SS+ GAAI  ++I+GVL E S + GV E +T+IILN+
Sbjct: 25  FVVEPLYRGYGHTLGNALRRVLLSSIPGAAIKGIRIEGVLSEFSVMDGVKEAVTEIILNV 84

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I +K      +++T+  +GP VVTA DI     +E++NP+  IC +  D  + +E  V
Sbjct: 85  KEIVVKSETAGERKMTLSVKGPKVVTAADIIPDIGLEIINPEQEICTITTDRSLDIEFLV 144

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G G+V ++    +   +  I +DA+Y+PI+KVSY ++    G++ D+DKL+++++TDG
Sbjct: 145 DTGEGFVVSEEIERDGWVVDYIAVDAIYTPIRKVSYEIQDTMVGRMTDFDKLTLSVETDG 204

Query: 210 SITGEDSVALASRILQDQLGMFI----NFEEPKKEVKEDI--NVKSLPFNPALLKKVEEL 263
           SI   D+++ A  +L+  L  F+      E  + EV+E++     S+  +  L  K+EEL
Sbjct: 205 SIEIRDALSYAVELLKLHLDPFLEIGNKMENLRLEVEEEMENQSSSMKDDINLNIKIEEL 264

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           +L+VRS NCL+   I  +G L + +  ++L++ N GRKSL EI
Sbjct: 265 DLTVRSFNCLKKAGIEEVGQLSKLSMNELLKIKNLGRKSLDEI 307


>gi|332144698|dbj|BAK19509.1| RNA polymerase alpha subunit [Lactobacillus sunkii]
          Length = 235

 Score =  205 bits (521), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 108/214 (50%), Positives = 149/214 (69%), Gaps = 4/214 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EPL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+
Sbjct: 3   VVVEPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNV 62

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K I+LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M L
Sbjct: 63  KKISLKLDGPEDEEENLEIDVIGPADVTAGDIQADSDVTVLNPDLHIATVAEGATFHMRL 122

Query: 148 TVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           T +KG GYV A     R+   PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ I
Sbjct: 123 TANKGRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDI 182

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
            TDGSIT  ++V+LA++IL + L MF++  +  K
Sbjct: 183 WTDGSITPSEAVSLAAKILTEHLEMFVDLTDEAK 216


>gi|23013214|ref|ZP_00053138.1| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Magnetospirillum magnetotacticum MS-1]
          Length = 159

 Score =  204 bits (520), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 99/152 (65%), Positives = 125/152 (82%), Gaps = 1/152 (0%)

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+ R GQV DYDKL+MT++T+G++T +D+VALA+RILQDQL +FINFEEP   V+E+  
Sbjct: 7   VENTRVGQVTDYDKLNMTVETNGAVTPDDAVALAARILQDQLQLFINFEEPTAVVEEE-K 65

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
              LPFN  LL+KV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+MLR  NFGRKSL EI
Sbjct: 66  KDELPFNKNLLRKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEMLRTPNFGRKSLNEI 125

Query: 307 KGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           K VL  MGL LGM + +WPPE+IEELAKK E+
Sbjct: 126 KEVLAQMGLHLGMEIANWPPENIEELAKKLEE 157


>gi|119662349|emb|CAJ33163.1| RNA polymerase alpha subunit [Lactobacillus rhamnosus]
          Length = 223

 Score =  204 bits (520), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 99/210 (47%), Positives = 148/210 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED+T IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLEDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV
Sbjct: 61  KKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+G
Sbjct: 121 KKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI+  ++++LA++IL + L +F+N  +  K
Sbjct: 181 SISPREAISLAAKILTEHLDIFVNLTDEAK 210


>gi|254302866|ref|ZP_04970224.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium nucleatum
           subsp. polymorphum ATCC 10953]
 gi|148323058|gb|EDK88308.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium nucleatum
           subsp. polymorphum ATCC 10953]
          Length = 326

 Score =  204 bits (520), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 112/306 (36%), Positives = 185/306 (60%), Gaps = 7/306 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E   +   I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + GV E 
Sbjct: 17  KESNYKGQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDGVKEA 76

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T+IILN+K I +K      +R+++  +GP VV A DI     +E++NP+ +IC +  D 
Sbjct: 77  VTEIILNVKEIVVKAESSGERRMSLSIKGPKVVKAADIVADIGLEIVNPEQIICTVTTDR 136

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D+DKL
Sbjct: 137 TLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTDFDKL 196

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI-NVKSLPFNPALLK-- 258
           ++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI  +   P +  ++   
Sbjct: 197 TLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEMIEEPMDIQVIDDK 256

Query: 259 ----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
               K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +  +G
Sbjct: 257 SHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKMKDLG 316

Query: 315 LFLGMN 320
             L  N
Sbjct: 317 YDLEKN 322


>gi|153217671|ref|ZP_01951352.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae 1587]
 gi|124113383|gb|EAY32203.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae 1587]
          Length = 244

 Score =  204 bits (519), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 103/232 (44%), Positives = 153/232 (65%), Gaps = 7/232 (3%)

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK--- 159
           +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V +G GYVPA    
Sbjct: 15  ITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVERGRGYVPASARI 74

Query: 160 HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  
Sbjct: 75  HTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRR 134

Query: 220 ASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIV 279
           A+ IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I 
Sbjct: 135 AATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIH 191

Query: 280 YMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 192 YIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 243


>gi|119668291|emb|CAK95501.1| RNA polymerase alpha subunit [Lactobacillus collinoides]
          Length = 209

 Score =  204 bits (519), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 104/207 (50%), Positives = 148/207 (71%), Gaps = 3/207 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN K I
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNTKKI 60

Query: 93  NLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +LK+ G  D  + + I  +GP  VTAGDI   +D+ VLNPD  I  +   A   M +T +
Sbjct: 61  SLKLEGPDDEIESMEIDVKGPAQVTAGDITADSDVTVLNPDLYIATVAEGATFHMRMTAN 120

Query: 151 KGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           KG GYV A  ++ + D PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TD 
Sbjct: 121 KGRGYVSADRNKAKEDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDS 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEE 236
           SIT  +S++LA++IL + L MF++  +
Sbjct: 181 SITPSESISLAAKILTEHLAMFVDLTD 207


>gi|190411123|gb|ACE78316.1| RpoA [Vibrio parahaemolyticus]
          Length = 243

 Score =  204 bits (519), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 106/246 (43%), Positives = 166/246 (67%), Gaps = 8/246 (3%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVT 105
           LRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T
Sbjct: 1   LRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFIT 60

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HH 161
           + K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H+
Sbjct: 61  LNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHN 120

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
             +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+
Sbjct: 121 EEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAA 180

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
            IL +QL  F++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+
Sbjct: 181 TILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYI 237

Query: 282 GDLIQR 287
           GDL+QR
Sbjct: 238 GDLVQR 243


>gi|329565841|gb|AEB92257.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
 gi|329565847|gb|AEB92260.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
 gi|329565849|gb|AEB92261.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
 gi|329565851|gb|AEB92262.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
 gi|329565859|gb|AEB92266.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
          Length = 250

 Score =  204 bits (519), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 110/261 (42%), Positives = 169/261 (64%), Gaps = 22/261 (8%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL+SSL GAA  +V+IDGVLHE S++ GV ED+ +IILN+K + +K+  D    
Sbjct: 1   GNSLRRVLLSSLPGAAPKSVKIDGVLHEFSTLPGVKEDVVEIILNLKEVAVKLHSDEPVV 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
             I   G G VTAG I+   DIE+LNPDH I  L  D  + ME+   KG GYVP+  ++ 
Sbjct: 61  GRIDVEGKGEVTAGHIKGSADIEILNPDHHIATLSDDGKLHMEIVFVKGKGYVPSDKNKE 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
            N PIG+I +D++++P+K+VSY V++ R G V DYDKL++ + T+G+IT ++++++AS +
Sbjct: 121 PNQPIGVIPVDSIFTPVKRVSYNVKNTRVGHVTDYDKLTLEVWTNGTITPKEAISMASDM 180

Query: 224 LQDQLGMFINF-----------EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
           L      FI+F           ++P+K+V++ +++            +EEL+LSVRS NC
Sbjct: 181 LIKYFQKFISFTGEYKSSDIFVDKPEKKVEKPLDM-----------TIEELDLSVRSYNC 229

Query: 273 LRGENIVYMGDLIQRTEADML 293
           L+   I  + +L Q+TE +M+
Sbjct: 230 LKRAGINTVQELTQKTEEEMM 250


>gi|332144692|dbj|BAK19506.1| RNA polymerase alpha subunit [Lactobacillus otakiensis]
          Length = 233

 Score =  204 bits (519), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 108/213 (50%), Positives = 147/213 (69%), Gaps = 4/213 (1%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K
Sbjct: 1   VVEPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVK 60

Query: 91  GINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
            I+LK+ G  D  + + I   GP  VTAGDIQ   D+ VLNPD  I  +   A   M LT
Sbjct: 61  KISLKLDGPEDEEENLEIDVIGPADVTAGDIQADGDVTVLNPDLHIATVAEGATFHMRLT 120

Query: 149 VSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            +KG GYV A     R+   PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ I 
Sbjct: 121 ANKGRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDIW 180

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           TDGSIT  ++V+LA++IL + L MF++  +  K
Sbjct: 181 TDGSITPSEAVSLAAKILTEHLEMFVDLTDEAK 213


>gi|312899071|ref|ZP_07758455.1| DNA-directed RNA polymerase, alpha subunit [Megasphaera
           micronuciformis F0359]
 gi|310619856|gb|EFQ03432.1| DNA-directed RNA polymerase, alpha subunit [Megasphaera
           micronuciformis F0359]
          Length = 334

 Score =  204 bits (519), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 113/308 (36%), Positives = 175/308 (56%), Gaps = 20/308 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + +PL RG+  TLGN+LRR+L+SSL G AIT+++IDG+LHE ++I GV ED+++IILN+
Sbjct: 23  FVCKPLDRGYGITLGNSLRRILLSSLEGVAITSIKIDGILHEFTTIPGVREDVSEIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFK--RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K + +K   +      I     G    TA D+   +DIE+LNP   I  LD DA +RM+ 
Sbjct: 83  KQVRMKFHKEDQMEADIIVDISGECDFTAADLNVNSDIEILNPTLHIATLDEDAHIRMQC 142

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            + +G GYVP+  ++ + D IG+I ID+++SPI +  Y V + R G  +DYD L+M + T
Sbjct: 143 HIERGKGYVPSTKNKKDTDVIGVIPIDSIFSPILRAKYEVGNVRVGNEMDYDSLTMEVLT 202

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVK------------------EDINVKS 249
           DGS+T ED++A ++ IL   L        P + ++                  E      
Sbjct: 203 DGSLTAEDAMAESASILSSYLEKIKQLAAPGRNLQQGKFTEDELGAGANGANAEGAGADG 262

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                   + ++ L+LSVR++NCL+  NI  + +LI  T++D+ ++ N G KS+ EI   
Sbjct: 263 TDMGEGGDESIDTLQLSVRASNCLKRANIYTIKELISHTKSDLGKIRNLGSKSVEEIIEK 322

Query: 310 LGTMGLFL 317
           L   G  L
Sbjct: 323 LSQFGYKL 330


>gi|71056826|emb|CAH58968.1| DNA-directed RNA polymerase alpha chain [Tetragenococcus
           solitarius]
          Length = 226

 Score =  204 bits (519), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 100/210 (47%), Positives = 145/210 (69%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNI
Sbjct: 5   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVAQIILNI 64

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+  +  K++ I   GP  +TAGDI   +D+E+LN D  IC +         L+V
Sbjct: 65  KGLALKLYSEEEKKLEIDITGPATITAGDIIVDSDVEILNKDMYICTVAEGTRFHARLSV 124

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GY  A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  DYDKL+M + TDG
Sbjct: 125 QPGRGYDQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDYDKLTMELWTDG 184

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   D+++L+++IL + L +F+N  +  K
Sbjct: 185 SIEPLDALSLSAKILTEHLEIFVNMTDEAK 214


>gi|161513422|emb|CAP16854.1| DNA-directed RNA polymerase subunit alpha [Pediococcus damnosus]
          Length = 222

 Score =  204 bits (518), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 100/206 (48%), Positives = 144/206 (69%), Gaps = 2/206 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+T++QIDGVLHE SSI+GV ED+T IILNIK ++LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSSIEGVVEDVTQIILNIKKVSLKIES 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A
Sbjct: 61  DDEKSLEIDVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAILTADTGRGYVSA 120

Query: 159 KHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   D  PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSIT  ++
Sbjct: 121 DENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSITPSEA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVK 242
            +L+++IL + L +F+N  +  K+ +
Sbjct: 181 TSLSAKILTEHLALFVNLTDEAKDAE 206


>gi|15605668|ref|NP_213043.1| DNA-directed RNA polymerase subunit alpha [Aquifex aeolicus VF5]
 gi|6226037|sp|O66483|RPOA_AQUAE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|2982817|gb|AAC06440.1| RNA polymerase alpha subunit [Aquifex aeolicus VF5]
          Length = 317

 Score =  204 bits (518), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 124/318 (38%), Positives = 187/318 (58%), Gaps = 12/318 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           E I P+ I +     EE+  T   ++ EPL RGF  T+GN+LRRVL+SS+ G AITAV+I
Sbjct: 4   EFIYPDKIFW-----EEKTDTYGRLVVEPLERGFGTTVGNSLRRVLLSSISGTAITAVKI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF-KRGPGVVTAGDIQTVND 124
            G+ HE S+I+GV ED  ++I N+K I   M GDS   +    K+G G V A DI+T  +
Sbjct: 59  YGIYHEFSAIEGVQEDAIELIANLKKIKFLMKGDSDVEILYLQKKGEGEVKASDIKTPPN 118

Query: 125 IEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           +E+LNPD  I  + D +  + +E+ V +G GYVP +      + +G I +DA +SP+KKV
Sbjct: 119 VEILNPDQYIATITDPNKELNIEIRVERGRGYVPVEEMEAIGE-VGWILVDADFSPVKKV 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
            + V++ R G+   Y++L++ I T+G  T +  +  A  IL+    +  N    K  V +
Sbjct: 178 GFRVDNVRVGKKSTYERLTLEIFTNGIKTPDQCMQEAIEILKKHYELLENIFTEKPTVPQ 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            + V  L    +L   +EEL++S R+ N L+   I  +GDL++ TE ++    N GRK+L
Sbjct: 238 KVAVDELAEKLSL--SIEELDISQRALNSLKRIGITTIGDLVRMTEDELKSTKNIGRKAL 295

Query: 304 VEIKGVLGTMGLFLGMNL 321
            EIK  L  +GL LGMN+
Sbjct: 296 AEIKEALHKLGLELGMNI 313


>gi|71056949|emb|CAH59035.1| DNA-directed RNA polymerase alpha chain [Enterococcus hirae]
 gi|72534401|emb|CAH59031.1| DNA-directed RNA polymerase alpha chain [Enterococcus villorum]
          Length = 219

 Score =  204 bits (518), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 100/203 (49%), Positives = 143/203 (70%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+ LKM
Sbjct: 1   RGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGLALKM 60

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
            G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV  G GYV
Sbjct: 61  YGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTVKPGRGYV 120

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
            A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI   ++
Sbjct: 121 QADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIEPLEA 180

Query: 217 VALASRILQDQLGMFINFEEPKK 239
           ++L+++I+ + L +F+N  +  K
Sbjct: 181 MSLSAKIMTEHLDIFVNLTDEAK 203


>gi|119662351|emb|CAJ33164.1| RNA polymerase alpha subunit [Lactobacillus ruminis]
          Length = 203

 Score =  204 bits (518), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 100/203 (49%), Positives = 146/203 (71%), Gaps = 2/203 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAAIT VQIDGVLHE S++KGV ED+T+IILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAITDVQIDGVLHEFSTVKGVLEDVTEIILNLKKVA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK++ +  + +     GP  VTAGDI T +D+E+LNPD  IC +   A     +T +KG 
Sbjct: 61  LKLNSEEPQSLEFDIVGPKEVTAGDISTNSDVEILNPDLYICTVADGASFHARMTANKGR 120

Query: 154 GYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GYV A  ++ + D  PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T+GSI
Sbjct: 121 GYVSANENKAKADDMPIGVLAIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINF 234
           T  ++++L+++IL + L +F+N 
Sbjct: 181 TPSEAISLSAKILTEHLALFVNL 203


>gi|332144694|dbj|BAK19507.1| RNA polymerase alpha subunit [Lactobacillus parafarraginis]
          Length = 236

 Score =  204 bits (518), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 108/213 (50%), Positives = 148/213 (69%), Gaps = 4/213 (1%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           I EPL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K
Sbjct: 1   IVEPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVK 60

Query: 91  GINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
            I+LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT
Sbjct: 61  KISLKLDGPEDEEENLEIDVIGPADVTAGDIQGDSDVTVLNPDLHIATVAEGATFHMRLT 120

Query: 149 VSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            +KG GYV A     R+   PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ + 
Sbjct: 121 ANKGRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDVW 180

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           TDGSIT  ++V+LA++IL + L MF++  +  K
Sbjct: 181 TDGSITPSEAVSLAAKILTEHLEMFVDLTDEAK 213


>gi|150036782|emb|CAM98034.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. dextranicum]
          Length = 248

 Score =  204 bits (518), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 105/247 (42%), Positives = 158/247 (63%), Gaps = 2/247 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T 
Sbjct: 61  KKVVLAIDSDDERSLEIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTA 120

Query: 150 SKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GY  A  ++   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T
Sbjct: 121 VKGRGYTSADENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +GSI   D+++L ++IL + LG+F++      E    +  + +  + +    +E+L+LSV
Sbjct: 181 NGSIKPSDALSLGAKILAEHLGLFMDISPVAAEASVMVEAEPVAASASDSAPIEDLDLSV 240

Query: 268 RSTNCLR 274
           RS NCL+
Sbjct: 241 RSYNCLK 247


>gi|329565845|gb|AEB92259.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
 gi|329565857|gb|AEB92265.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
          Length = 250

 Score =  204 bits (518), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 110/261 (42%), Positives = 168/261 (64%), Gaps = 22/261 (8%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL+SSL GAA  +V+IDGVLHE S++ GV ED+  IILN+K + +K+  D    
Sbjct: 1   GNSLRRVLLSSLPGAAPKSVKIDGVLHEFSTLPGVKEDVVKIILNLKEVAVKLHSDEPVV 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
             I   G G VTAG I+   DIE+LNPDH I  L  D  + ME+   KG GYVP+  ++ 
Sbjct: 61  GRIDVEGKGEVTAGHIKGSADIEILNPDHHIATLSDDGKLHMEIVFVKGKGYVPSNKNKE 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
            N PIG+I +D++++P+K+VSY V++ R G V DYDKL++ + T+G+IT ++++++AS +
Sbjct: 121 PNQPIGVIPVDSIFTPVKRVSYNVKNTRVGHVTDYDKLTLEVWTNGTITPKEAISMASDM 180

Query: 224 LQDQLGMFINF-----------EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
           L      FI+F           ++P+K+V++ +++            +EEL+LSVRS NC
Sbjct: 181 LIKYFQKFISFTGEYKSSDIFVDKPEKKVEKPLDM-----------TIEELDLSVRSYNC 229

Query: 273 LRGENIVYMGDLIQRTEADML 293
           L+   I  + +L Q+TE +M+
Sbjct: 230 LKRAGINTVQELTQKTEEEMM 250


>gi|119668289|emb|CAK95500.1| RNA polymerase alpha subunit [Lactobacillus buchneri]
          Length = 227

 Score =  204 bits (518), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 108/211 (51%), Positives = 147/211 (69%), Gaps = 4/211 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K I
Sbjct: 1   EPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKI 60

Query: 93  NLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT +
Sbjct: 61  SLKLDGPEDEEENLEIDVIGPADVTAGDIQADSDVTVLNPDLHIATVAEGATFHMRLTAN 120

Query: 151 KGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           KG GYV A     R+   PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ I TD
Sbjct: 121 KGRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDIWTD 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK 239
           GSIT  ++V+LA++IL + L MF++  +  K
Sbjct: 181 GSITPSEAVSLAAKILTEHLEMFVDLTDEAK 211


>gi|312880343|ref|ZP_07740143.1| DNA-directed RNA polymerase subunit alpha [Aminomonas paucivorans
           DSM 12260]
 gi|310783634|gb|EFQ24032.1| DNA-directed RNA polymerase subunit alpha [Aminomonas paucivorans
           DSM 12260]
          Length = 362

 Score =  204 bits (518), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 121/309 (39%), Positives = 178/309 (57%), Gaps = 20/309 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EPL RG+  TLGNALRRVL+SS+ GA+I+AV+I+GVLHE S++ GV ED+ ++++N+
Sbjct: 31  IVLEPLERGYGITLGNALRRVLLSSIPGASISAVRIEGVLHEFSTVPGVREDVIELLVNL 90

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L+      K + +   GP  VTA DIQ   D+E ++P+ VIC L+    + M+L V
Sbjct: 91  KHVPLRCYNAELKTLHLEVEGPKTVTAADIQPDADVEYVDPEAVICTLEAGHRISMDLYV 150

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY      R    P+  + IDA++SP K+V Y V+  R GQ  DYD+L + + T+G
Sbjct: 151 EQGIGYAAIDRPRPAYLPVDALLIDAVFSPAKRVKYEVQDVRMGQRTDYDRLVLEVWTNG 210

Query: 210 SITGEDSVALASRILQDQLGMFINF------------EEPKKEVKEDINVKSLP------ 251
            +T +++VA AS IL+       N             E+      E +  +  P      
Sbjct: 211 VVTPKEAVAKASAILEGYFRSLTNVLSSRPSQGGALPEDAISSEGEGVPAEGDPAEEPVR 270

Query: 252 -FNPALLKK-VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
            F  ALL + V +LELSVRS NCL    +  +GDL+ R   D+L++ N G+ SL EI+  
Sbjct: 271 FFENALLARPVRDLELSVRSENCLLRGGVHVIGDLVGRAREDLLKIRNLGKISLKEIEEK 330

Query: 310 LGTMGLFLG 318
           L   GL LG
Sbjct: 331 LEKFGLSLG 339


>gi|119662335|emb|CAJ33156.1| RNA polymerase alpha subunit [Lactobacillus paracasei subsp.
           paracasei]
          Length = 213

 Score =  204 bits (518), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 100/210 (47%), Positives = 148/210 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNIK +
Sbjct: 2   EPLERGYGTTLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNIKKL 61

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV KG
Sbjct: 62  ALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVKKG 121

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI+
Sbjct: 122 RGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSIS 181

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVK 242
             ++++LA++IL + L +F+N  +  K  +
Sbjct: 182 PREAISLAAKILTEHLDIFVNLTDEAKNAE 211


>gi|329565853|gb|AEB92263.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
 gi|329565855|gb|AEB92264.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
 gi|329565861|gb|AEB92267.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
          Length = 250

 Score =  203 bits (517), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 110/261 (42%), Positives = 168/261 (64%), Gaps = 22/261 (8%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL+SSL GAA  +V+IDGVLHE S++ GV ED+  IILN+K + +K+  D    
Sbjct: 1   GNSLRRVLLSSLPGAAPKSVKIDGVLHEFSTLPGVKEDVVKIILNLKEVAVKLHSDEPVV 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
             I   G G VTAG I+   DIE+LNPDH I  L  D  + ME+   KG GYVP+  ++ 
Sbjct: 61  GRIDVEGKGEVTAGHIKGSADIEILNPDHHIATLSDDGKLHMEIVFVKGKGYVPSDKNKE 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
            N PIG+I +D++++P+K+VSY V++ R G V DYDKL++ + T+G+IT ++++++AS +
Sbjct: 121 PNQPIGVIPVDSIFTPVKRVSYNVKNTRVGHVTDYDKLTLEVWTNGTITPKEAISMASDM 180

Query: 224 LQDQLGMFINF-----------EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
           L      FI+F           ++P+K+V++ +++            +EEL+LSVRS NC
Sbjct: 181 LIKYFQKFISFTGEYKSSDIFVDKPEKKVEKPLDM-----------TIEELDLSVRSYNC 229

Query: 273 LRGENIVYMGDLIQRTEADML 293
           L+   I  + +L Q+TE +M+
Sbjct: 230 LKRAGINTVQELTQKTEEEMM 250


>gi|307297367|ref|ZP_07577173.1| DNA-directed RNA polymerase, alpha subunit [Thermotogales bacterium
           mesG1.Ag.4.2]
 gi|306916627|gb|EFN47009.1| DNA-directed RNA polymerase, alpha subunit [Thermotogales bacterium
           mesG1.Ag.4.2]
          Length = 348

 Score =  203 bits (517), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 126/322 (39%), Positives = 186/322 (57%), Gaps = 27/322 (8%)

Query: 10  IKPNNIEYIVLGQEEENR--TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           I P N+  I   +E++N   T  I  P+ RG+A T+GN+LRRVL+SS+   AIT ++I G
Sbjct: 14  IMPKNLR-IEEEREDDNSYFTRFILSPMERGYATTIGNSLRRVLLSSIPSMAITRLKIPG 72

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
             HE   I GV ED+ +IILN K + LK  +      ++T+   GPGV+TAGDI+T   +
Sbjct: 73  KYHEYDVIDGVKEDILEIILNFKKVQLKPALEFSDAVKLTLETAGPGVITAGDIKTPTGV 132

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EV+NP   I  L+ D+V+ +EL    G G+VP      E+D + +I ID ++SP+ KV++
Sbjct: 133 EVVNPSQYIATLNTDSVIYIELFAEIGRGFVPVSEMEIEHD-VEMIYIDGIFSPVLKVNF 191

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN-FEEPKKEVK-- 242
             E+ R G+  DYDKL + + T  SIT  D++  A+ IL     +F N   +P + +   
Sbjct: 192 QTENVRVGKRTDYDKLILDVWTKKSITPSDALLRATDILIRHFEVFSNGLGKPGQGLTSS 251

Query: 243 ------------------EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDL 284
                             E   V+    N    KKVEEL+LSVRS NCL+ + I  +GDL
Sbjct: 252 ALKQEEEEIISEEAEVTVETPQVEEQDSNSLGAKKVEELDLSVRSLNCLKRDKINTIGDL 311

Query: 285 IQRTEADMLRMANFGRKSLVEI 306
           + ++EAD+LR+ NFG KS++E+
Sbjct: 312 LDKSEADLLRIRNFGEKSMLEV 333


>gi|325280941|ref|YP_004253483.1| DNA-directed RNA polymerase subunit alpha [Odoribacter splanchnicus
           DSM 20712]
 gi|324312750|gb|ADY33303.1| DNA-directed RNA polymerase subunit alpha [Odoribacter splanchnicus
           DSM 20712]
          Length = 330

 Score =  203 bits (517), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 113/298 (37%), Positives = 176/298 (59%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GN LRR+L+SSL G AIT ++I GV HE ++I GV ED+T+IILN+K + 
Sbjct: 28  PLEPGYGITIGNPLRRILLSSLEGFAITGIKIHGVEHEFATIPGVIEDVTEIILNLKQVR 87

Query: 94  LKMSGD--SHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K   +    +++T+   G     AGDI + +   EVLN + VIC++D     +ME+T+ 
Sbjct: 88  FKRKVEDVEDEKLTVLINGQEAFKAGDINKFLTGFEVLNTELVICHMDPSVNFQMEITIQ 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVP+  +       G I IDA+Y+PI+ V Y +E+ R     DY+KL   I+TDGS
Sbjct: 148 KGRGYVPSTENMPAEAEAGFIPIDAIYTPIRNVKYEIENYRVEGKTDYEKLLFEIETDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           I   D++  A++IL     +F    I+ E   K   E+ + + L     L  K+ +++LS
Sbjct: 208 IAPTDALKEAAKILIHHFMLFSDEKISLESEDKYGNEEFDEEVLHMRQLLKTKLVDMDLS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+   +  +G+L +  + D+L+  NFG+KSL E++ +L    L  GM++  +
Sbjct: 268 VRALNCLKAAEVETLGELCRFNKNDLLKFRNFGKKSLTELEALLENNNLEFGMDVTKY 325


>gi|257453242|ref|ZP_05618541.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp.
           3_1_5R]
 gi|317059776|ref|ZP_07924261.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp.
           3_1_5R]
 gi|313685452|gb|EFS22287.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp.
           3_1_5R]
          Length = 326

 Score =  203 bits (517), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 116/314 (36%), Positives = 184/314 (58%), Gaps = 24/314 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E E +   + EPL RG+ HTLGNALRRVL+SS+ GAAI  ++I+GVL E S + GV E 
Sbjct: 17  RESEFKGQFVVEPLYRGYGHTLGNALRRVLLSSIPGAAIKGIRIEGVLSEFSVMDGVKEA 76

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T+IILN+K I +K      +++T+  +GP VVTA DI     +E++NP+  IC +  D 
Sbjct: 77  VTEIILNVKEIVVKSETAGERKMTLSVKGPKVVTAADIIPDIGLEIINPEQEICTITTDR 136

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + +E  V  G G+V ++    +   +  I +DA+Y+PI+KVSY ++    G++ D+DKL
Sbjct: 137 ELDIEFLVDTGEGFVVSEEIERDGWAVDYIAVDAIYTPIRKVSYDIQDTMVGRMTDFDKL 196

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINF---------------EEPKKEVKEDIN 246
           +++++TDGSI   D+++ A  +L+  L  F+                 E     +++DIN
Sbjct: 197 TLSVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRVEVEEEVENQSSSIRDDIN 256

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           +           K+EEL+L+VRS NCL+   I  +G L + +  ++L++ N GRKSL EI
Sbjct: 257 LNI---------KIEELDLTVRSFNCLKKAGIEEVGQLSKLSMNELLKIKNLGRKSLDEI 307

Query: 307 KGVLGTMGLFLGMN 320
              +  +G  L  N
Sbjct: 308 LEKMKELGYDLAQN 321


>gi|119662849|emb|CAJ33217.1| RNA polymerase alpha subunit [Lactobacillus suebicus]
          Length = 219

 Score =  203 bits (516), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 101/205 (49%), Positives = 149/205 (72%), Gaps = 2/205 (0%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRR+L++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K I+LK+
Sbjct: 1   RGYGTTLGNSLRRILLASLPGAAITSIQIDGVLHEFSTVEGVTEDVTQIILNMKKISLKI 60

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             +  K + I  +GP  VTAGDI+   D+EVLNPD  I  +   A + +++T + G GYV
Sbjct: 61  DSEEDKALEIDVKGPAAVTAGDIEADGDVEVLNPDLHIATVADGAELHIQMTANTGRGYV 120

Query: 157 PAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A  ++   D  PIG++ ID++Y+PI++V+Y VE+AR GQ  DYDKL++ + TDGSIT  
Sbjct: 121 SADDNKARMDDLPIGVLPIDSIYTPIERVNYNVENARVGQRNDYDKLTLDVWTDGSITPS 180

Query: 215 DSVALASRILQDQLGMFINFEEPKK 239
           +S++LA++IL + L MF++  +  K
Sbjct: 181 ESISLAAKILTEHLSMFVDLTDTAK 205


>gi|212550426|ref|YP_002308743.1| DNA-directed RNA polymerase subunit alpha [Candidatus
           Azobacteroides pseudotrichonymphae genomovar. CFP2]
 gi|212548664|dbj|BAG83332.1| DNA-directed RNA polymerase alpha subunit [Candidatus
           Azobacteroides pseudotrichonymphae genomovar. CFP2]
          Length = 328

 Score =  203 bits (516), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 115/298 (38%), Positives = 186/298 (62%), Gaps = 7/298 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G+  T+GN+LRRVL+SSL G AIT+++I+GV +E + + GV ED+T+IIL +K + 
Sbjct: 28  PLESGYGITIGNSLRRVLLSSLEGYAITSIKIEGVSNEFAVVPGVVEDVTNIILKLKQVR 87

Query: 94  LK-MSGD-SHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            K ++ D  ++RV +         A DI + ++  EV+N D +I +LD  A + +ELT+ 
Sbjct: 88  FKRINKDFEYERVVLTISETDKFKADDISKRLSGFEVVNSDFIIAHLDKSANLNIELTIR 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVP++ +  ++D +  I ID++++PI  V Y VES R  Q  DY+KL++ I TDGS
Sbjct: 148 KGRGYVPSEENYRDSDDVNQIAIDSVFTPIVNVKYNVESFRVEQKTDYEKLTIEIMTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           +  + ++  AS IL   L +F    I  E+ + E  +D +   L     L  K+ ++ELS
Sbjct: 208 VCPKIALKSASDILIQHLELFSEGRIRLEKDEIETVKDFDEDVLRIRQLLKSKLSDMELS 267

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           VR+ NCL+ E I  + DL++  ++D+++  NFG+KSLVE+  +L  + L  GM++  +
Sbjct: 268 VRALNCLKAEAIETLEDLVKYQKSDLMKFRNFGKKSLVELDELLAKLNLTFGMDIEKY 325


>gi|332144696|dbj|BAK19508.1| RNA polymerase alpha subunit [Lactobacillus rapi]
          Length = 230

 Score =  203 bits (516), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 107/214 (50%), Positives = 149/214 (69%), Gaps = 4/214 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EPL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+
Sbjct: 1   VVVEPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNV 60

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K I+LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M L
Sbjct: 61  KKISLKLDGPEDEEENLEIDVIGPADVTAGDIQGDSDVTVLNPDLHIATVADGATFHMRL 120

Query: 148 TVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           T +KG GYV A     R+   PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ +
Sbjct: 121 TANKGRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDV 180

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
            TDGSIT  ++V+LA++IL + L MF++  +  K
Sbjct: 181 WTDGSITPSEAVSLAAKILTEHLEMFVDLTDEAK 214


>gi|15836158|ref|NP_300682.1| DNA-directed RNA polymerase subunit alpha [Chlamydophila pneumoniae
           J138]
 gi|12644496|sp|Q9Z7S8|RPOA_CHLPN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|8978998|dbj|BAA98833.1| RNA polymerase alpha [Chlamydophila pneumoniae J138]
          Length = 374

 Score =  203 bits (516), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 126/332 (37%), Positives = 186/332 (56%), Gaps = 22/332 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            IAEPL RG  HTLGNALRR L+  L   AI +  + GVLHE  +I+GV ED+T+IILN+
Sbjct: 35  FIAEPLERGMGHTLGNALRRALLIGLEAPAIISFAMTGVLHEYMAIEGVIEDVTNIILNL 94

Query: 90  KGINLK---MSGDSHKRVTIFKRGPGVVTAGDIQTVN--------------DIEVLNPDH 132
           KG  LK   M   S  R T   +    + A D+   N              D E +NPD 
Sbjct: 95  KGALLKKYPMQDSSLGRTTQVLKASISIDASDLAAANGQKEVTLQDLLQEGDFEAVNPDQ 154

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           VI  +     + + L ++ G GY P++    E+  +  I +DA +SP+  V+Y VE  R 
Sbjct: 155 VIFTVTQPIQLEVVLRIAFGRGYTPSERIVLEDKGVYEIVLDAAFSPVTLVNYFVEDTRV 214

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           GQ  D+D+L + ++TDG +T ++++A +++IL     +F N +E K   +E I+++    
Sbjct: 215 GQDTDFDRLVLIVETDGRVTPKEALAFSTQILTKHFSIFENMDEKKIVFEEAISIEKENK 274

Query: 253 NPALLK---KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           +  L K    + E+ELSVRSTNCL   NI  +G+L+   E  +L+  NFG+KSL EIK  
Sbjct: 275 DDILHKLILGINEIELSVRSTNCLSNANIETIGELVIMPEPRLLQFRNFGKKSLCEIKNK 334

Query: 310 LGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 335 LKEMKLELGMDLTQFGVGLDNVKEKMKWYAEK 366


>gi|15618536|ref|NP_224822.1| DNA-directed RNA polymerase subunit alpha [Chlamydophila pneumoniae
           CWL029]
 gi|33241983|ref|NP_876924.1| DNA-directed RNA polymerase subunit alpha [Chlamydophila pneumoniae
           TW-183]
 gi|4376924|gb|AAD18765.1| RNA Polymerase Alpha [Chlamydophila pneumoniae CWL029]
 gi|33236493|gb|AAP98581.1| DNA-directed RNA polymerase alpha chain [Chlamydophila pneumoniae
           TW-183]
          Length = 374

 Score =  203 bits (516), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 126/332 (37%), Positives = 186/332 (56%), Gaps = 22/332 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            IAEPL RG  HTLGNALRR L+  L   AI +  + GVLHE  +I+GV ED+T+IILN+
Sbjct: 35  FIAEPLERGMGHTLGNALRRALLIGLEAPAIISFAMTGVLHEYMAIEGVIEDVTNIILNL 94

Query: 90  KGINLK---MSGDSHKRVTIFKRGPGVVTAGDIQTVN--------------DIEVLNPDH 132
           KG  LK   M   S  R T   +    + A D+   N              D E +NPD 
Sbjct: 95  KGALLKKYPMQDSSLGRTTQVLKASISIDASDLAAANGQKEVTLQDLLQEGDFEAVNPDQ 154

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           VI  +     + + L ++ G GY P++    E+  +  I +DA +SP+  V+Y VE  R 
Sbjct: 155 VIFTVTQPIQLEVVLRIAFGRGYTPSERIVLEDKGVYEIVLDAAFSPVTLVNYFVEDTRV 214

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           GQ  D+D+L + ++TDG +T ++++A +++IL     +F N +E K   +E I+++    
Sbjct: 215 GQDTDFDRLVLIVETDGRVTPKEALAFSTQILTKHFSIFENMDEKKIVFEEAISIEKENK 274

Query: 253 NPALLK---KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           +  L K    + E+ELSVRSTNCL   NI  +G+L+   E  +L+  NFG+KSL EIK  
Sbjct: 275 DDILHKLILGINEIELSVRSTNCLSNANIETIGELVIMPEPRLLQFRNFGKKSLCEIKNK 334

Query: 310 LGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 335 LKEMKLELGMDLTQFGVGLDNVKEKMKWYAEK 366


>gi|189485112|ref|YP_001956053.1| DNA-directed RNA polymerase alpha chain [uncultured Termite group 1
           bacterium phylotype Rs-D17]
 gi|170287071|dbj|BAG13592.1| DNA-directed RNA polymerase alpha chain [uncultured Termite group 1
           bacterium phylotype Rs-D17]
          Length = 323

 Score =  202 bits (515), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 112/292 (38%), Positives = 177/292 (60%), Gaps = 4/292 (1%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
           A P  RG+ HT+GN+LRR+L+SSL GAAIT+V+I G  HE + +KGV ED+  I+LN+K 
Sbjct: 28  AGPFERGYGHTIGNSLRRILLSSLEGAAITSVKIAGAFHEFAVLKGVKEDVAQIVLNLKR 87

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           I +K+  +  +++ +  +  G VTA DI+    +E++NP+  I N+D    + MEL  S 
Sbjct: 88  IKVKLHSEGPEKLYLKVKKAGTVTAKDIEANASVEIMNPEQEIANIDNGTTLEMELEASL 147

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GYV A+  ++     G I +D+L+SPI KV+Y VE+ R  Q L+YDKL + I TDGS+
Sbjct: 148 GKGYVLAEEMKSNGYSSGTIILDSLFSPIIKVNYEVENTRVEQTLNYDKLIIEIWTDGSV 207

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTN 271
           + +D++  ++ IL+  L +F +     +EV  D   +    +  L K V  +++SV++  
Sbjct: 208 SPKDALMRSAEILRKILVIFTDNAFKTEEVSADKEEQ----DGILGKPVSIMDISVKTLK 263

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            L+   I  + DL++  E D+L   N  ++S  EIK  +  +GL LGM + D
Sbjct: 264 SLKSAGIETVEDLVKIKEEDLLNFNNLSKRSCEEIKNRVKELGLSLGMKIED 315


>gi|332181991|gb|AEE17679.1| DNA-directed RNA polymerase subunit alpha [Treponema brennaborense
           DSM 12168]
          Length = 350

 Score =  202 bits (515), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 130/335 (38%), Positives = 197/335 (58%), Gaps = 23/335 (6%)

Query: 1   MIQKNW-QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M +KN  +   KP  I +  L     N     A P   GF  T+GN LRRVL+SS++G A
Sbjct: 1   MARKNLLKGFKKPKGITFEQL-DSNPNYGKFTAYPFETGFGTTVGNTLRRVLLSSIQGYA 59

Query: 60  ITAVQI-----DGVLHEISS----IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK-R 109
           IT+V+I     D V H ISS    I  V ED  +++ ++K I L++ GD+ +   +F+ +
Sbjct: 60  ITSVRITSYDADNVPHVISSEFETIPNVVEDTLEVLNSLKQIRLRLPGDAEQETFLFEFK 119

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GPG +T+ D  +   +E+L+ D ++  +  +A +  E+ V  G GY PA+ +    + +G
Sbjct: 120 GPGTITSNDF-SREGLEILSKDMLVFTMMENAHLEFEVQVDLGRGYTPAEVNEHYIEIVG 178

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            I +DA+++PI KV Y +E  R GQ  DYDKL + I TDG+I+ ED++A A++I +D   
Sbjct: 179 TIPMDAIFTPIPKVKYAIEPCRVGQRNDYDKLVIEIWTDGTISPEDALAEAAKIAKDHFA 238

Query: 230 MFINFEEPK----KEVKE-DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDL 284
           +F+NF + +     E+ E D  ++ L   P     V+ELELSVRS+NCL+  NI  +G+L
Sbjct: 239 IFVNFNDSEIGHDGELDEGDERIRQLLNTP-----VDELELSVRSSNCLKNANIRTIGEL 293

Query: 285 IQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
            ++TE D+ +  NFG+KSL EIK  L    L LGM
Sbjct: 294 TKKTEDDIAKTRNFGKKSLTEIKEKLLEWNLNLGM 328


>gi|295111400|emb|CBL28150.1| DNA-directed RNA polymerase, alpha subunit, bacterial and
           chloroplast-type [Synergistetes bacterium SGP1]
          Length = 333

 Score =  202 bits (515), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 121/323 (37%), Positives = 191/323 (59%), Gaps = 19/323 (5%)

Query: 8   ELIKPNNIEYIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           E+++P      VL  EE   T   +  EPL RG+  TLGNALRRVL+SS+RGAAIT+V+I
Sbjct: 6   EILRP------VLKLEENTPTYGRLYLEPLERGYGMTLGNALRRVLLSSIRGAAITSVRI 59

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGVLHE S++ GV ED+ +I++N+K I ++      + V++     G+VTAGDI    +I
Sbjct: 60  DGVLHEFSTVPGVREDVMEILMNLKHIPVRSKSKEVRVVSLDVERAGLVTAGDIPENGEI 119

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E ++P+  IC ++  A + MEL + +G GY+ A+  R    P+  +  DA++SP+ +V+Y
Sbjct: 120 EFIDPNAKICTMEEGAHLSMELYIEQGTGYLSAERPRPAYLPVDALLTDAIFSPVLRVNY 179

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF---INFEEPKK--- 239
            VE+AR GQ  D+++L+M + T+G I  + +V  A++I++         +    P     
Sbjct: 180 GVEAARVGQRTDFERLAMDVWTNGIIAPDAAVGEAAQIIEKCFSYIVASVGQAGPDGVGG 239

Query: 240 -----EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
                ++  D  +        L + V ELELS+RS NCL    +  +GDL+Q++  D+L+
Sbjct: 240 GAYDIDLGADRRIGPAGNEELLARPVRELELSIRSENCLLRGGVQTIGDLLQKSREDLLK 299

Query: 295 MANFGRKSLVEIKGVLGTMGLFL 317
           + N G+ SL EI+  L + GL L
Sbjct: 300 IRNLGKISLTEIEEKLESAGLKL 322


>gi|291514968|emb|CBK64178.1| DNA-directed RNA polymerase subunit alpha [Alistipes shahii WAL
           8301]
          Length = 317

 Score =  202 bits (515), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 117/302 (38%), Positives = 185/302 (61%), Gaps = 15/302 (4%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AIT V++ GV HE ++I GV ED+ +IILN+K + 
Sbjct: 15  PLEPGFGMTVGNALRRILLSSLEGYAITTVKVAGVDHEFAAIPGVMEDMLNIILNLKQVR 74

Query: 94  LKMSGDSH--KRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
              + D+   ++V+I   G   +TAG I   ++  +VLNPD VIC+L     ++M LT+ 
Sbjct: 75  FIRTVDNQDAEKVSINVAGVTELTAGYISNYLSFFKVLNPDLVICHLAPGTKMQMTLTIG 134

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ +       G + ID++++PIK V Y++E+ R  Q  DY+KL++ I TDGS
Sbjct: 135 KGRGYVPAEENAPAESEFGTLPIDSIFTPIKNVKYSIENYRVEQKTDYEKLNLEITTDGS 194

Query: 211 ITGEDSVALASRILQDQLGMF------INFEEPK--KEVKEDINVKSLPFNPALLKKVEE 262
           I  ++++  A++IL     +F      +N E+    +E  ED+    L     L  K+ +
Sbjct: 195 IHPKEALKEAAKILIQHFMLFSDEKITVNMEDTNGAEEFDEDV----LHMRQLLKTKLSD 250

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
            +LSVR+ NCL+  ++  +GDL++    D+L+  NFG+KSL E+  +L ++ L  GM++ 
Sbjct: 251 QDLSVRALNCLKAADVDTVGDLVKLNRNDLLKFRNFGKKSLTELDELLTSLNLKFGMDVS 310

Query: 323 DW 324
            +
Sbjct: 311 IY 312


>gi|16752414|ref|NP_444673.1| DNA-directed RNA polymerase subunit alpha [Chlamydophila pneumoniae
           AR39]
 gi|7189055|gb|AAF38004.1| DNA-directed RNA polymerase, alpha subunit [Chlamydophila
           pneumoniae AR39]
          Length = 391

 Score =  202 bits (515), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 126/332 (37%), Positives = 186/332 (56%), Gaps = 22/332 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            IAEPL RG  HTLGNALRR L+  L   AI +  + GVLHE  +I+GV ED+T+IILN+
Sbjct: 52  FIAEPLERGMGHTLGNALRRALLIGLEAPAIISFAMTGVLHEYMAIEGVIEDVTNIILNL 111

Query: 90  KGINLK---MSGDSHKRVTIFKRGPGVVTAGDIQTVN--------------DIEVLNPDH 132
           KG  LK   M   S  R T   +    + A D+   N              D E +NPD 
Sbjct: 112 KGALLKKYPMQDSSLGRTTQVLKASISIDASDLAAANGQKEVTLQDLLQEGDFEAVNPDQ 171

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           VI  +     + + L ++ G GY P++    E+  +  I +DA +SP+  V+Y VE  R 
Sbjct: 172 VIFTVTQPIQLEVVLRIAFGRGYTPSERIVLEDKGVYEIVLDAAFSPVTLVNYFVEDTRV 231

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           GQ  D+D+L + ++TDG +T ++++A +++IL     +F N +E K   +E I+++    
Sbjct: 232 GQDTDFDRLVLIVETDGRVTPKEALAFSTQILTKHFSIFENMDEKKIVFEEAISIEKENK 291

Query: 253 NPALLK---KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           +  L K    + E+ELSVRSTNCL   NI  +G+L+   E  +L+  NFG+KSL EIK  
Sbjct: 292 DDILHKLILGINEIELSVRSTNCLSNANIETIGELVIMPEPRLLQFRNFGKKSLCEIKNK 351

Query: 310 LGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 352 LKEMKLELGMDLTQFGVGLDNVKEKMKWYAEK 383


>gi|269302410|gb|ACZ32510.1| DNA-directed RNA polymerase, alpha subunit [Chlamydophila
           pneumoniae LPCoLN]
          Length = 374

 Score =  202 bits (515), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 126/332 (37%), Positives = 186/332 (56%), Gaps = 22/332 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            IAEPL RG  HTLGNALRR L+  L   AI +  + GVLHE  +I+GV ED+T+IILN+
Sbjct: 35  FIAEPLERGMGHTLGNALRRALLIGLEAPAIISFAMTGVLHEYMAIEGVIEDVTNIILNL 94

Query: 90  KGINLK---MSGDSHKRVTIFKRGPGVVTAGDIQTVN--------------DIEVLNPDH 132
           KG  LK   M   S  R T   +    + A D+   N              D E +NPD 
Sbjct: 95  KGALLKKYPMQDSSLGRTTQVLKASISIDASDLAAANGQKEVTLQDLLQEGDFEAVNPDQ 154

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           VI  +     + + L ++ G GY P++    E+  +  I +DA +SP+  V+Y VE  R 
Sbjct: 155 VIFTVTQPIQLEVVLRIAFGRGYTPSERIVLEDKGVYEIILDAAFSPVTLVNYFVEDTRV 214

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           GQ  D+D+L + ++TDG +T ++++A +++IL     +F N +E K   +E I+++    
Sbjct: 215 GQDTDFDRLVLIVETDGRVTPKEALAFSTQILTKHFSIFENMDEKKIVFEEAISIEKENK 274

Query: 253 NPALLK---KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           +  L K    + E+ELSVRSTNCL   NI  +G+L+   E  +L+  NFG+KSL EIK  
Sbjct: 275 DDILHKLILGINEIELSVRSTNCLSNANIETIGELVIMPEPRLLQFRNFGKKSLCEIKNK 334

Query: 310 LGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 335 LKEMKLELGMDLTQFGVGLDNVKEKMKWYAEK 366


>gi|289803215|ref|ZP_06533844.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. AG3]
          Length = 222

 Score =  202 bits (515), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 103/222 (46%), Positives = 150/222 (67%), Gaps = 9/222 (4%)

Query: 113 VVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPI 168
           VVTA DI    D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PI
Sbjct: 2   VVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPI 61

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           G + +DA YSP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL
Sbjct: 62  GRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQL 121

Query: 229 GMFINFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
             F++  + ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QR
Sbjct: 122 EAFVDLRDVRQPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQR 177

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           TE ++L+  N G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 178 TEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASI 219


>gi|22257019|sp|Q8RE44|RPOA_FUSNN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 326

 Score =  202 bits (514), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 112/306 (36%), Positives = 185/306 (60%), Gaps = 7/306 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E   +   I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + GV E 
Sbjct: 17  KESNYKGQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDGVKEA 76

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T+IILN+K I +K      +R+++  +GP VV A DI     +E++NP+ VIC +  D 
Sbjct: 77  VTEIILNVKEIVVKAESSGERRMSLSIKGPKVVKAADIVADIGLEIVNPEQVICTVTTDR 136

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + +E  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D+DKL
Sbjct: 137 TLDIEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTDFDKL 196

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI-NVKSLPFNPALLK-- 258
           ++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI  +   P +  ++   
Sbjct: 197 TLNVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRDDIEEMIEEPMDIQVIDDK 256

Query: 259 ----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
               K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +  +G
Sbjct: 257 SHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKMKDLG 316

Query: 315 LFLGMN 320
             L  N
Sbjct: 317 YDLEKN 322


>gi|313677146|ref|YP_004055142.1| DNA-directed RNA polymerase subunit alpha [Marivirga tractuosa DSM
           4126]
 gi|312943844|gb|ADR23034.1| DNA-directed RNA polymerase subunit alpha [Marivirga tractuosa DSM
           4126]
          Length = 329

 Score =  202 bits (514), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 111/315 (35%), Positives = 189/315 (60%), Gaps = 6/315 (1%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           E + + + ++   L   +PL +G+  T+GNALRR+L+SSL G AIT ++I GVLHE S++
Sbjct: 10  EKVAMEKADDFHGLFTFKPLEKGYGVTVGNALRRILLSSLEGYAITGIKIPGVLHEFSAV 69

Query: 76  KGVHEDLTDIILNIKGINLK-MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHV 133
           +GV ED++++ILN+K +  K ++  +  ++ I  +      AGDI +     E+LNPD +
Sbjct: 70  EGVVEDVSELILNLKMVRFKKIAETADNKINISLKNTKEFKAGDINKFTTAFEILNPDLL 129

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           IC++D      +ELT+ KG GYV ++ +   +     I ID++++PIK V Y+VE+ R  
Sbjct: 130 ICHMDESINFEIELTIEKGRGYVSSEENTLVDQVADYIAIDSIFTPIKNVKYSVENTRVE 189

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKS 249
           Q  DY++L + I+TDGSI  E ++  A+ IL     +F +     +    +  E ++ + 
Sbjct: 190 QKTDYEQLVLDIETDGSIHPEVALKGAANILIKHFMLFSDQNMVLDAGGSDEPEAVDEEM 249

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           L     L   + +L+LSVR+ NCL+  ++  +GDL+    +DM++  NFG+KSL E++ +
Sbjct: 250 LHMRKLLKTALNDLDLSVRAYNCLKAADVKTLGDLVALEISDMMKFRNFGKKSLAELEQL 309

Query: 310 LGTMGLFLGMNLPDW 324
           +   GL  GM+L  +
Sbjct: 310 VADKGLTFGMDLSKY 324


>gi|71056937|emb|CAH59027.1| DNA-directed RNA polymerase alpha chain [Enterococcus malodoratus]
          Length = 221

 Score =  202 bits (514), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 99/201 (49%), Positives = 141/201 (70%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG+ LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNIKGLALKLFA 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G GYV A
Sbjct: 61  EEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTVKPGRGYVQA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDGSI  +++++
Sbjct: 121 DENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDGSIIAQEALS 180

Query: 219 LASRILQDQLGMFINFEEPKK 239
           LA++IL + L +F+N  +  K
Sbjct: 181 LAAKILTEHLDIFVNLTDEAK 201


>gi|19704618|ref|NP_604180.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium nucleatum
           subsp. nucleatum ATCC 25586]
 gi|19714918|gb|AAL95479.1| DNA-directed RNA polymerase alpha chain [Fusobacterium nucleatum
           subsp. nucleatum ATCC 25586]
          Length = 342

 Score =  202 bits (514), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 112/306 (36%), Positives = 185/306 (60%), Gaps = 7/306 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E   +   I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + GV E 
Sbjct: 33  KESNYKGQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDGVKEA 92

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T+IILN+K I +K      +R+++  +GP VV A DI     +E++NP+ VIC +  D 
Sbjct: 93  VTEIILNVKEIVVKAESSGERRMSLSIKGPKVVKAADIVADIGLEIVNPEQVICTVTTDR 152

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + +E  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D+DKL
Sbjct: 153 TLDIEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTDFDKL 212

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI-NVKSLPFNPALLK-- 258
           ++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI  +   P +  ++   
Sbjct: 213 TLNVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRDDIEEMIEEPMDIQVIDDK 272

Query: 259 ----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
               K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +  +G
Sbjct: 273 SHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKMKDLG 332

Query: 315 LFLGMN 320
             L  N
Sbjct: 333 YDLEKN 338


>gi|296329035|ref|ZP_06871541.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium nucleatum
           subsp. nucleatum ATCC 23726]
 gi|296153839|gb|EFG94651.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium nucleatum
           subsp. nucleatum ATCC 23726]
          Length = 342

 Score =  202 bits (514), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 112/306 (36%), Positives = 185/306 (60%), Gaps = 7/306 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E   +   I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + GV E 
Sbjct: 33  KESNYKGQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDGVKEA 92

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T+IILN+K I +K      +R+++  +GP VV A DI     +E++NP+ VIC +  D 
Sbjct: 93  VTEIILNVKEIVVKAESSGERRMSLSIKGPKVVKAADIVADIGLEIVNPEQVICTVTTDR 152

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + +E  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D+DKL
Sbjct: 153 ALDIEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTDFDKL 212

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI-NVKSLPFNPALLK-- 258
           ++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI  +   P +  ++   
Sbjct: 213 TLNVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRDDIEEMIEEPMDIQVIDDK 272

Query: 259 ----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
               K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +  +G
Sbjct: 273 SHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKMKDLG 332

Query: 315 LFLGMN 320
             L  N
Sbjct: 333 YDLEKN 338


>gi|153799480|gb|ABS50515.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
 gi|153799482|gb|ABS50516.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 240

 Score =  202 bits (513), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 102/221 (46%), Positives = 146/221 (66%), Gaps = 4/221 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLH
Sbjct: 3   KPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLH 58

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++VLNP
Sbjct: 59  EFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQVLNP 118

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES 
Sbjct: 119 DQYICTIAEGGHLHMELAVKNGRGYVTASDNKSDDMPIGVIPVDSLFSPIKKVNYQVEST 178

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F
Sbjct: 179 RVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVF 219


>gi|153799472|gb|ABS50511.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
 gi|153799474|gb|ABS50512.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
 gi|153799476|gb|ABS50513.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 240

 Score =  202 bits (513), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 102/221 (46%), Positives = 146/221 (66%), Gaps = 4/221 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLH
Sbjct: 3   KPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLH 58

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++VLNP
Sbjct: 59  EFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQVLNP 118

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES 
Sbjct: 119 DQYICTIAEGGHLHMELAVKNGRGYVTASDNKSDDMPIGVIPVDSLFSPIKKVNYQVEST 178

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F
Sbjct: 179 RVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVF 219


>gi|108792407|emb|CAJ33136.1| RNA polymerase alpha subunit [Lactobacillus acidipiscis]
          Length = 224

 Score =  202 bits (513), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 102/208 (49%), Positives = 148/208 (71%), Gaps = 2/208 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAAIT VQIDGVLHE SSI GV ED+T IILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAITDVQIDGVLHEFSSIDGVLEDVTTIILNLKKVA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK++ +  + + I   GP  VTAGDIQ  +++EVLNPD  IC +   A     +T +KG 
Sbjct: 61  LKLNSEDVQTLEIDVTGPMEVTAGDIQGSSEVEVLNPDLYICTVADGASFHARMTANKGR 120

Query: 154 GYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GYV A  +  +TE+ PIG++ ID++Y+PI++V+Y VE  R GQ  D+DKL++ + T+GSI
Sbjct: 121 GYVSANENKAKTEDMPIGVLAIDSIYTPIERVNYQVEKTRVGQKSDFDKLTLDVWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKK 239
           T  ++++L+++IL + L +F++  +  K
Sbjct: 181 TPSEAISLSAKILTEHLTLFVDLTDEAK 208


>gi|332144690|dbj|BAK19505.1| RNA polymerase alpha subunit [Lactobacillus kisonensis]
          Length = 232

 Score =  202 bits (513), Expect = 8e-50,   Method: Compositional matrix adjust.
 Identities = 107/211 (50%), Positives = 147/211 (69%), Gaps = 4/211 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K I
Sbjct: 2   EPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKI 61

Query: 93  NLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT +
Sbjct: 62  SLKLDGPEDEEENLEIDVIGPADVTAGDIQGDSDVTVLNPDLHIATVADGATFHMRLTAN 121

Query: 151 KGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           KG GYV A     R+   PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ + TD
Sbjct: 122 KGRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDVWTD 181

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK 239
           GSIT  ++V+LA++IL + L MF++  +  K
Sbjct: 182 GSITPSEAVSLAAKILTEHLEMFVDLTDEAK 212


>gi|153799478|gb|ABS50514.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 240

 Score =  202 bits (513), Expect = 8e-50,   Method: Compositional matrix adjust.
 Identities = 102/221 (46%), Positives = 146/221 (66%), Gaps = 4/221 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLH
Sbjct: 3   KPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLH 58

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++VLNP
Sbjct: 59  EFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQVLNP 118

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES 
Sbjct: 119 DQYICTIAEGGHLHMELAVKNGRGYVTASDNKSDDMPIGVIPVDSLFSPIKKVNYQVEST 178

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F
Sbjct: 179 RVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVF 219


>gi|153799484|gb|ABS50517.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 240

 Score =  202 bits (513), Expect = 8e-50,   Method: Compositional matrix adjust.
 Identities = 102/221 (46%), Positives = 146/221 (66%), Gaps = 4/221 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLH
Sbjct: 3   KPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLH 58

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++VLNP
Sbjct: 59  EFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQVLNP 118

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES 
Sbjct: 119 DQYICTIAEGGHLHMELAVKNGRGYVTASDNKSDDMPIGVIPVDSLFSPIKKVNYQVEST 178

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F
Sbjct: 179 RVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVF 219


>gi|153799470|gb|ABS50510.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 240

 Score =  202 bits (513), Expect = 9e-50,   Method: Compositional matrix adjust.
 Identities = 102/221 (46%), Positives = 146/221 (66%), Gaps = 4/221 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLH
Sbjct: 3   KPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLH 58

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++VLNP
Sbjct: 59  EFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQVLNP 118

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES 
Sbjct: 119 DQYICTIAEGGHLHMELAVKNGRGYVTASDNKSDDMPIGVIPVDSLFSPIKKVNYQVEST 178

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F
Sbjct: 179 RVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVF 219


>gi|161513442|emb|CAP16864.1| DNA-directed RNA polymerase subunit alpha [Pediococcus inopinatus]
          Length = 223

 Score =  201 bits (512), Expect = 9e-50,   Method: Compositional matrix adjust.
 Identities = 98/206 (47%), Positives = 144/206 (69%), Gaps = 2/206 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNIK ++LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNIKKVSLKIES 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A
Sbjct: 61  DDEKSLEIDVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAILTADTGRGYVSA 120

Query: 159 KHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   D  PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSI+  ++
Sbjct: 121 DENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSISPSEA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVK 242
            +L+++IL + L +F+N  +  K+ +
Sbjct: 181 TSLSAKILTEHLALFVNLTDEAKDAE 206


>gi|332144682|dbj|BAK19501.1| RNA polymerase alpha subunit [Lactobacillus buchneri]
          Length = 226

 Score =  201 bits (512), Expect = 9e-50,   Method: Compositional matrix adjust.
 Identities = 107/210 (50%), Positives = 146/210 (69%), Gaps = 4/210 (1%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K I+
Sbjct: 1   PLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKIS 60

Query: 94  LKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT +K
Sbjct: 61  LKLDGPEDEEENLEIDVIGPADVTAGDIQADSDVTVLNPDLHIATVAEGATFHMRLTANK 120

Query: 152 GHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           G GYV A     R+   PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ I TDG
Sbjct: 121 GRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SIT  ++V+LA++IL + L MF++  +  K
Sbjct: 181 SITPSEAVSLAAKILTEHLEMFVDLTDEAK 210


>gi|303231259|ref|ZP_07317997.1| DNA-directed RNA polymerase, alpha subunit [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302514166|gb|EFL56170.1| DNA-directed RNA polymerase, alpha subunit [Veillonella atypica
           ACS-049-V-Sch6]
          Length = 332

 Score =  201 bits (512), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 119/293 (40%), Positives = 184/293 (62%), Gaps = 17/293 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE S+I G+ ED+TDIILN+
Sbjct: 23  FVCEPLDRGYGITLGNSLRRILLSSLDGAAITSIKIDGVLHEFSTIPGIREDVTDIILNL 82

Query: 90  KGINLKMSGDSHKRVTI---FKRGPGVVTAGDI--QTVNDIEVLNPDHVICNLDVDAVVR 144
           K + +K+  D+   + +   F++  GV+TA D+  Q   ++EVLNP+ VI  +D  A + 
Sbjct: 83  KQLCIKLEEDAEWPLEVHFDFQKD-GVLTAADLAEQFPPEVEVLNPELVIATMDETAHLV 141

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           M++ + +G GYVP+  ++ + D IG I ID+++SPI +  Y V   R G  +D+DKL++ 
Sbjct: 142 MDVVIERGKGYVPSTKNKKDTDVIGCIPIDSIFSPILRAKYEVSDVRVGNEMDFDKLTLE 201

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK-EDINVKSLPFNPALLK----- 258
           + TDGSIT  D+VA ++ I+   LG F         V+ +D N++    +P         
Sbjct: 202 VWTDGSITAADAVAKSAAIMIGYLGNFTKLAHSTSVVELDDQNLEGDVVDPTPQDVQEDD 261

Query: 259 -----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
                 ++ELELSVR+ NCL+   I  + DL+ +T  D+ ++ N G+KS+ EI
Sbjct: 262 GPAKISIDELELSVRAYNCLKRAGINTIADLLDKTIDDLGKVRNLGKKSIDEI 314


>gi|161511719|emb|CAP16870.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           acidilactici]
          Length = 235

 Score =  201 bits (512), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 109/235 (46%), Positives = 151/235 (64%), Gaps = 2/235 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAITSVQIDNVLHEFSTIEGVVEDVTQIILNLKKVS 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK+  D  K + I   GP  VTAGDI    D+ VLNPD  IC +         LT   G 
Sbjct: 61  LKIESDDEKTLDINVVGPANVTAGDIMGDGDVTVLNPDSPICTVAEGTTFHAVLTADTGR 120

Query: 154 GYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A  +  R  + PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ I TDGSI
Sbjct: 121 GYTSADENKARKADMPIGVLPIDSIYTPIERVNYQVEKTRVGQRDDYDKLTLDIWTDGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T  ++ +L+++IL + L +F+N  +  KE +  +  +       L   +EEL+LS
Sbjct: 181 TPSEATSLSAKILTEHLAIFVNLNDQAKETEIMVEKEETHKEKMLEMTIEELDLS 235


>gi|303230143|ref|ZP_07316912.1| DNA-directed RNA polymerase, alpha subunit [Veillonella atypica
           ACS-134-V-Col7a]
 gi|302515204|gb|EFL57177.1| DNA-directed RNA polymerase, alpha subunit [Veillonella atypica
           ACS-134-V-Col7a]
          Length = 332

 Score =  201 bits (511), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 119/293 (40%), Positives = 184/293 (62%), Gaps = 17/293 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE S+I G+ ED+TDIILN+
Sbjct: 23  FVCEPLDRGYGITLGNSLRRILLSSLDGAAITSIKIDGVLHEFSTIPGIREDVTDIILNL 82

Query: 90  KGINLKMSGDSHKRVTI---FKRGPGVVTAGDI--QTVNDIEVLNPDHVICNLDVDAVVR 144
           K + +K+  D+   + +   F++  GV+TA D+  Q   ++EVLNP+ VI  +D  A + 
Sbjct: 83  KQLCIKLEEDAEWPLEVHFDFQKD-GVLTAADLAEQFPPEVEVLNPELVIATMDETAHLV 141

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           M++ + +G GYVP+  ++ + D IG I ID+++SPI +  Y V   R G  +D+DKL++ 
Sbjct: 142 MDVVIERGKGYVPSTKNKKDTDVIGCIPIDSIFSPILRAKYEVSDVRVGNEMDFDKLTLE 201

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK-EDINVKSLPFNPALLK----- 258
           + TDGSIT  D+VA ++ I+   LG F         V+ +D N++    +P         
Sbjct: 202 VWTDGSITAADAVAKSAAIMIGYLGNFTKLAHSTSVVELDDQNLEGDVVDPTPQDVQEDD 261

Query: 259 -----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
                 ++ELELSVR+ NCL+   I  + DL+ +T  D+ ++ N G+KS+ EI
Sbjct: 262 GPAKISIDELELSVRAYNCLKRAGINTIADLLDKTIDDLGKVRNLGKKSIDEI 314


>gi|207721872|ref|YP_002252310.1| dna-directed rna polymerase alpha chain (partial sequence n
           terminus) protein [Ralstonia solanacearum MolK2]
 gi|206587039|emb|CAQ17623.1| probable dna-directed rna polymerase alpha chain (partial sequence
           n terminus) protein [Ralstonia solanacearum MolK2]
          Length = 230

 Score =  201 bits (511), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 105/232 (45%), Positives = 152/232 (65%), Gaps = 6/232 (2%)

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           +++ K G GVVTA DI+  +D+E++NP HVI +L     + M++ V +G GYVP    + 
Sbjct: 1   MSLRKEGEGVVTAADIELPHDVEIINPGHVIASLSAGGKLDMQIKVEQGRGYVPGNVRKF 60

Query: 164 ENDP---IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
            ++    IG + +DA ++P+++VSY VESAR  Q  D DKL M I+T+G I+ E+++  +
Sbjct: 61  GDESSKVIGRVVLDASFAPVRRVSYAVESARVEQRTDLDKLVMNIETNGVISPEEAIRQS 120

Query: 221 SRILQDQLGMFINFEEPKKEVKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIV 279
           +RIL DQL +F   E    E   +      P  +P LL+ V++LEL+VRS NCL+ ENI 
Sbjct: 121 ARILVDQLSVFAALE--GTESAAEAAAARAPQIDPILLRPVDDLELTVRSANCLKAENIY 178

Query: 280 YMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           Y+GDLIQRTE ++L+  N GRKSL EIK VL + GL LGM L +WPP  +E+
Sbjct: 179 YIGDLIQRTENELLKTPNLGRKSLNEIKEVLASRGLTLGMKLENWPPAGLEK 230


>gi|295809866|emb|CBL85109.1| alpha subunit of RNA polymerase [Vibrio tapetis]
          Length = 247

 Score =  201 bits (511), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 105/248 (42%), Positives = 164/248 (66%), Gaps = 8/248 (3%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVT 115
           G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +K++ G     +T+ K G G V 
Sbjct: 3   GCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVKVAEGKDEVFITLNKSGSGPVV 62

Query: 116 AGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLI 171
           AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG +
Sbjct: 63  AGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASSRIHTEEDERPIGRL 122

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  ++ IL +QL  F
Sbjct: 123 LVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRSATILAEQLDAF 182

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           ++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE +
Sbjct: 183 VDLRDIRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVE 239

Query: 292 MLRMANFG 299
           +L+  N G
Sbjct: 240 LLKTPNLG 247


>gi|332144684|dbj|BAK19502.1| RNA polymerase alpha subunit [Lactobacillus diolivorans]
          Length = 216

 Score =  201 bits (511), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 107/210 (50%), Positives = 146/210 (69%), Gaps = 4/210 (1%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K I+
Sbjct: 1   PLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKIS 60

Query: 94  LKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT +K
Sbjct: 61  LKLDGPEDEEENLEIDVIGPADVTAGDIQGDSDVTVLNPDLHIATVAEGATFHMRLTANK 120

Query: 152 GHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           G GYV A     R+   PIG++ +D++Y+PI++V+Y VES R GQ  DYDKL++ + TDG
Sbjct: 121 GRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDYDKLTLDVWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SIT  ++V+LA++IL + L MF++  +  K
Sbjct: 181 SITPSEAVSLAAKILTEHLEMFVDLTDEAK 210


>gi|313158337|gb|EFR57739.1| DNA-directed RNA polymerase, alpha subunit [Alistipes sp. HGB5]
          Length = 330

 Score =  201 bits (511), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 117/302 (38%), Positives = 184/302 (60%), Gaps = 15/302 (4%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AIT V++ GV HE ++I GV ED+  IILN+K + 
Sbjct: 28  PLEPGFGMTVGNALRRILLSSLEGYAITTVKVAGVDHEFAAIPGVMEDMLKIILNLKQVR 87

Query: 94  LKMSGDSH--KRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
              + D+   ++V+I   G   +TAG I   ++  +VLNPD VIC+L     ++M LT+ 
Sbjct: 88  FIRTVDNQDAEKVSINVAGVTELTAGYISNYLSFFKVLNPDLVICHLAPGTKMQMTLTIG 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ +       G + ID++++PIK V Y++E+ R  Q  DY+KL++ I TDGS
Sbjct: 148 KGRGYVPAEENTPAECEFGTLPIDSIFTPIKNVKYSIENYRVEQKTDYEKLNLEITTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF------INFEEPK--KEVKEDINVKSLPFNPALLKKVEE 262
           I  ++++  A++IL     +F      +N E+    +E  ED+    L     L  K+ +
Sbjct: 208 IHPKEALKEAAKILIQHFMLFSDEKITVNMEDTNGAEEFDEDV----LHMRQLLKTKLSD 263

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
            +LSVR+ NCL+  ++  +GDL++    D+L+  NFG+KSL E+  +L ++ L  GM++ 
Sbjct: 264 QDLSVRALNCLKAADVDTVGDLVKLNRNDLLKFRNFGKKSLTELDELLTSLNLKFGMDVS 323

Query: 323 DW 324
            +
Sbjct: 324 IY 325


>gi|37523140|ref|NP_926517.1| DNA-directed RNA polymerase subunit alpha [Gloeobacter violaceus
           PCC 7421]
 gi|41688630|sp|Q7NFF5|RPOA_GLOVI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|35214143|dbj|BAC91512.1| RNA polymerase alpha subunit [Gloeobacter violaceus PCC 7421]
          Length = 314

 Score =  201 bits (511), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 114/297 (38%), Positives = 181/297 (60%), Gaps = 12/297 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG   TLGNALRRVL+S+L G A+TAV+I GV HE +++KG+ ED+ DI+LN+
Sbjct: 23  FVLEPLERGQGTTLGNALRRVLLSNLEGTAVTAVRITGVNHEFATMKGIREDVLDILLNM 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L+      +   +  +GP  VTA D++   +++V++P H I  L  D  + ME  +
Sbjct: 83  KELVLRSYTSDIQIGRLAVQGPKRVTAADLELPTEVQVVHPRHYIATLAEDGQLEMEFQI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY   +    +   I  ++IDA++ P++KV++TVES R    ++ D+L++ I T G
Sbjct: 143 ERGKGYRAIERGSEDGAAIDYLSIDAIFMPVRKVNWTVESERSAANVEQDRLTLEIWTSG 202

Query: 210 SITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDIN-VKSLPFNPALLKKVEELELS 266
           S++ +++++ A++IL DQL     I FE P +  +   N V  +P        +EEL+LS
Sbjct: 203 SLSPQEALSQAAKILVDQLRPLQEITFEPPAEPQRSAPNTVGQVP--------IEELQLS 254

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE-IKGVLGTMGLFLGMNLP 322
           VR+ NCL+   I  + DL++ TE D+L + NFG+KS  E I+ +   MGL L  + P
Sbjct: 255 VRAYNCLKRAQINTVADLLEYTEEDLLEIKNFGQKSAEEVIEALQDKMGLSLPKDKP 311


>gi|228470691|ref|ZP_04055542.1| DNA-directed RNA polymerase, alpha subunit [Porphyromonas uenonis
           60-3]
 gi|228307548|gb|EEK16544.1| DNA-directed RNA polymerase, alpha subunit [Porphyromonas uenonis
           60-3]
          Length = 317

 Score =  201 bits (511), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 114/299 (38%), Positives = 185/299 (61%), Gaps = 7/299 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           +PL  G+A T+GNALRR+L+SSL G AI +++I+GV HE ++I GV ED+T IILN+K I
Sbjct: 14  KPLEPGYAMTIGNALRRILLSSLEGYAIASIRIEGVEHEFATIPGVLEDVTHIILNLKQI 73

Query: 93  NLKMSGD--SHKRVTIFKRGPGVVTAGDIQTV-NDIEVLNPDHVICNLDVDAVVRMELTV 149
             + + +    + +T+   G     AGD+  V    +V NPD VICNL  DA   +E+ +
Sbjct: 74  RFRATVEDPQEETITLHVTGRNSFKAGDLNKVLTSYKVQNPDLVICNLAEDADFTIEIRI 133

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GYV ++ +R E+DP+  + ID +Y+PI+KV+ T E+ R  Q  DY+KL + I+TDG
Sbjct: 134 NKGRGYVVSEENRREDDPVNTLPIDGIYTPIRKVNQTTEAYRVDQRTDYEKLVLEIETDG 193

Query: 210 SITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
           +I   +++  A++IL     +F +     E P++E ++ ++ + +     L+  +   +L
Sbjct: 194 TIHPREALREAAKILISHFALFTDKEFEVELPEEEPEQLLDNQMMKVRSQLMTDLATTDL 253

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           SVR+ NCL+   I  + DL+ R   ++L++ NFG+KSLVE++  L    L   M+L  +
Sbjct: 254 SVRALNCLKAAGISTIADLLSRDREELLKIKNFGKKSLVELEQFLTDQKLDFDMDLSPY 312


>gi|328813949|gb|AEB52090.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 241

 Score =  201 bits (511), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 103/229 (44%), Positives = 155/229 (67%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           +LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNIK + LKM+ D  K + 
Sbjct: 1   SLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNTDEDKNIE 60

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
           I   GP  VTA DI    D+EVLNP+  IC +       + +TV KG GYV A  +++++
Sbjct: 61  IDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAADQNKSDD 120

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
            PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++IL 
Sbjct: 121 MPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKILT 180

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLR 274
           + L +F+N  +  K  +  +  +       L   +EEL+LSVRS NCL+
Sbjct: 181 EHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSVRSYNCLK 229


>gi|117575075|emb|CAJ84777.1| RNA polymerase alpha subunit [Lactobacillus amylotrophicus]
          Length = 225

 Score =  201 bits (511), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 97/200 (48%), Positives = 142/200 (71%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRVL++SL G+A++ VQIDGVLHE S+I GV ED+T IILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRVLLASLPGSAVSYVQIDGVLHEFSTIPGVLEDVTQIILNLKKLT 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK      K   I   GP  VTAGD++  +++E+LNP+  I  +   A +RM + V +G 
Sbjct: 61  LKSIAADEKLAEIDVEGPATVTAGDLKVDDEVEILNPNQYIATVAEGAHLRMTVAVKQGR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYVPA  +++++ PIG++ +D+L+SPI+KV+Y VE  R G+  DYDKL+M + TDGSIT 
Sbjct: 121 GYVPADQNKSDDMPIGVVPVDSLFSPIEKVNYQVEGTRVGRNNDYDKLTMEVWTDGSITP 180

Query: 214 EDSVALASRILQDQLGMFIN 233
            D+++  ++IL + L +F+N
Sbjct: 181 NDALSFGAKILTEHLNVFMN 200


>gi|329565863|gb|AEB92268.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
          Length = 250

 Score =  201 bits (511), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 109/261 (41%), Positives = 167/261 (63%), Gaps = 22/261 (8%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL+SSL GAA  +V+IDGVLHE S++ GV ED+  IILN+K + +K+  D    
Sbjct: 1   GNSLRRVLLSSLPGAAPKSVKIDGVLHEFSTLPGVKEDVVKIILNLKEVAVKLHSDEPVV 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
             I   G G VTAG I+   DIE+LNPDH I  L  D  + ME+   KG GYVP+  ++ 
Sbjct: 61  GRIDVEGKGEVTAGHIKGSADIEILNPDHHIATLSDDGKLHMEIVFVKGKGYVPSDKNKE 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
            N PIG+I +D++++P+K+VSY V++ R G V DYDKL++ + T+G+IT ++++++AS +
Sbjct: 121 PNQPIGVIPVDSIFTPVKRVSYNVKNTRVGHVTDYDKLTLEVWTNGTITPKEAISMASDM 180

Query: 224 LQDQLGMFINF-----------EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
           L      FI+F           ++P+K+V++ +++            +EEL+L VRS NC
Sbjct: 181 LIKYFQKFISFTGEYKSSDIFVDKPEKKVEKPLDM-----------TIEELDLFVRSYNC 229

Query: 273 LRGENIVYMGDLIQRTEADML 293
           L+   I  + +L Q+TE +M+
Sbjct: 230 LKRAGINTVQELTQKTEEEMM 250


>gi|161513426|emb|CAP16856.1| DNA-directed RNA polymerase subunit alpha [Pediococcus parvulus]
          Length = 223

 Score =  201 bits (511), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 97/206 (47%), Positives = 144/206 (69%), Gaps = 2/206 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNIK ++LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNIKKVSLKIES 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A
Sbjct: 61  DDEKSLEINVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAVLTADTGRGYVSA 120

Query: 159 KHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   D  PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSI+  ++
Sbjct: 121 DENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSISPSEA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVK 242
            +L+++IL + L +F+N  +  ++ +
Sbjct: 181 TSLSAKILTEHLALFVNLTDEAQDAE 206


>gi|329565843|gb|AEB92258.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
          Length = 250

 Score =  201 bits (510), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 110/261 (42%), Positives = 167/261 (63%), Gaps = 22/261 (8%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL+SSL GAA  +V+IDGVLHE S++ GV ED+ +IILN+K   +K+  D    
Sbjct: 1   GNSLRRVLLSSLPGAAPKSVKIDGVLHEFSTLPGVKEDVVEIILNLKEGAVKLHSDEPVV 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
             I   G G VTAG I+   DIE+LNPDH I  L  D    ME+   KG GYVP+  ++ 
Sbjct: 61  GRIDVEGKGEVTAGHIKGSADIEILNPDHHIATLSDDGKPHMEIVFVKGKGYVPSDKNKE 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
            N PIG+I +D++++P+K+VSY V++ R G V DYDKL++ + T+G+IT ++++++AS +
Sbjct: 121 PNQPIGVIPVDSIFTPVKRVSYNVKNTRVGHVTDYDKLTLEVWTNGTITPKEAISMASDM 180

Query: 224 LQDQLGMFINF-----------EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
           L      FI+F           ++P+K+V++ +++            +EEL+LSVRS NC
Sbjct: 181 LIKYFQKFISFTGEYKSSDIFVDKPEKKVEKPLDM-----------TIEELDLSVRSYNC 229

Query: 273 LRGENIVYMGDLIQRTEADML 293
           L+   I  + +L Q+TE +M+
Sbjct: 230 LKRAGINTVQELTQKTEEEMM 250


>gi|119662841|emb|CAJ33213.1| RNA polymerase alpha subunit [Lactobacillus fructivorans KCTC 3543]
          Length = 220

 Score =  201 bits (510), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 102/202 (50%), Positives = 148/202 (73%), Gaps = 4/202 (1%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRRVL++SL GAA+T++QIDGVLHE S++KGV ED+T IILN+K INLK++ D +
Sbjct: 3   TLGNSLRRVLLASLPGAAVTSIQIDGVLHEFSTVKGVVEDVTQIILNVKKINLKINSDDN 62

Query: 102 --KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             K ++I   GP  VTAGDI T +D+E+LNPD  I  +   A   M +T +KG GYV A+
Sbjct: 63  ETKSMSINVTGPADVTAGDIVTDSDVEILNPDLHIATVADGATFHMNMTANKGRGYVSAE 122

Query: 160 HHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
            ++ +ND  PIG++ +D++Y+PI++V+Y VE AR GQ  DYDKL++ + T+GSIT  D++
Sbjct: 123 ENKAKNDGMPIGVLPVDSIYTPIERVNYQVEDARVGQRDDYDKLTLDVWTNGSITPSDAI 182

Query: 218 ALASRILQDQLGMFINFEEPKK 239
           +LA++IL     +FI+  +  K
Sbjct: 183 SLAAKILNQHFQLFIDLTDRAK 204


>gi|71056933|emb|CAH59025.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 221

 Score =  200 bits (509), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 98/201 (48%), Positives = 143/201 (71%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+I GV ED+T IILNIKG+ LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIPGVREDVTQIILNIKGLALKLYA 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + I   GP  VTAGDI   +D+E+LN D VIC++   A     LTV  G GYV A
Sbjct: 61  EEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLVICSVAEGATFHARLTVKPGRGYVQA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI  +++++
Sbjct: 121 DENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIIPQEALS 180

Query: 219 LASRILQDQLGMFINFEEPKK 239
           LA++I+ + L +F+N  +  K
Sbjct: 181 LAAKIMTEHLDIFVNLTDEAK 201


>gi|209527118|ref|ZP_03275632.1| DNA-directed RNA polymerase, alpha subunit [Arthrospira maxima
           CS-328]
 gi|209492458|gb|EDZ92799.1| DNA-directed RNA polymerase, alpha subunit [Arthrospira maxima
           CS-328]
          Length = 314

 Score =  200 bits (509), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 116/291 (39%), Positives = 172/291 (59%), Gaps = 12/291 (4%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG   T+GNALRRVL+S+L G AITAV+I GV HE ++I+GV ED+ +I+LN+K   
Sbjct: 27  PLDRGQGITVGNALRRVLLSNLEGTAITAVRIAGVNHEFATIEGVREDVLEIMLNLKEAV 86

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK      +   +  +GP  VT G     +++EV+N +  I  L   A + ME  + KG 
Sbjct: 87  LKSHTYQKQIGRLLVQGPATVTVGHFDLPSEVEVVNKNQYIATLSPGATLEMECQIEKGT 146

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY     HR ++  +  + IDA++ P++KV+YTVE AR+G  L+ D+L++ I T GS+T 
Sbjct: 147 GYRAVDRHRDDSAALDFLQIDAIFMPVRKVNYTVEDARDGGSLEKDRLTLEIWTSGSLTP 206

Query: 214 EDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTN 271
           +++++ A+ IL D  G    IN E    + ++DI       +P     +EEL+LSVR+ N
Sbjct: 207 QEAISQAAAILVDLFGALKDINLESITSDQRDDI-------DPTSQIPIEELQLSVRAYN 259

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           CL+   I  + DL   TE D+L + NFG+KS  E+   L      LG+ LP
Sbjct: 260 CLKRAQINSVADLRDYTEEDLLEIKNFGQKSAEEVIEALQNR---LGITLP 307


>gi|298372561|ref|ZP_06982551.1| DNA-directed RNA polymerase, alpha subunit [Bacteroidetes oral
           taxon 274 str. F0058]
 gi|298275465|gb|EFI17016.1| DNA-directed RNA polymerase, alpha subunit [Bacteroidetes oral
           taxon 274 str. F0058]
          Length = 331

 Score =  200 bits (509), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 117/321 (36%), Positives = 191/321 (59%), Gaps = 10/321 (3%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +PN + Y+V   E + R      PL  G+  T+GNALRRVL+SSL G AIT+++I  V+H
Sbjct: 8   RPNQV-YMVEATEFKGRFEF--APLEPGYGITIGNALRRVLLSSLEGYAITSLKISEVVH 64

Query: 71  EISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEV 127
           E  +I  V +D+T+IILN+K +  K     ++ + ++I      V+ A D++  + + +V
Sbjct: 65  EFDTIPNVIDDVTNIILNLKQVRFKHIAGAETSESISITVSNKEVLKAKDLEEGMANFKV 124

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPDHVIC++D  A   MEL + KG GY+PA  ++  +  IG I IDA+++PI  V Y+V
Sbjct: 125 LNPDHVICSMDKSAEFTMELKIEKGRGYLPADENKNVSKEIGWIGIDAIFTPIVNVMYSV 184

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEVKE 243
           E  R  Q  DY+KL + I TDGS+  + ++  A++IL     +F    I  E    +  +
Sbjct: 185 EDERVEQKTDYNKLILEIQTDGSVHPKQALKEAAKILIQHFMLFTDEKITLEIEDIDDND 244

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           + +   L     L  ++ +L+LSVR+ NCL+  N+  +GDL +  + ++L+  NFG+KSL
Sbjct: 245 EFDEDFLKKRQLLKTQLTDLDLSVRALNCLKSANLETLGDLARIPKPELLKFRNFGKKSL 304

Query: 304 VEIKGVLGTMGLFLGMNLPDW 324
            E++  L ++ L  G+++  +
Sbjct: 305 TELEQKLESLNLHFGIDIAKY 325


>gi|269837094|ref|YP_003319322.1| DNA-directed RNA polymerase, alpha subunit [Sphaerobacter
           thermophilus DSM 20745]
 gi|269786357|gb|ACZ38500.1| DNA-directed RNA polymerase, alpha subunit [Sphaerobacter
           thermophilus DSM 20745]
          Length = 340

 Score =  200 bits (508), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 119/293 (40%), Positives = 181/293 (61%), Gaps = 12/293 (4%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL  G+  T+GNALRR+L+ SL G AI  V+I  V HE S+I+GV ED+T+I+LN+K +
Sbjct: 24  EPLEPGYGITIGNALRRILLRSLPGTAIVRVRIADVWHEFSTIEGVREDVTEIVLNLKRV 83

Query: 93  NLKMSGDSHK--RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV-DAVVRMELTV 149
            LK   +S +  R +++ +G GVV AGDI    D+EV+NP+HVI  LD  DA + M+L +
Sbjct: 84  RLKALTESFREGRASLYAQGEGVVRAGDIDWPGDVEVVNPEHVIATLDNDDARLEMDLVI 143

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           ++G GY PA+    E   IG I +DA+++PI+KV+Y VE  R GQ+ DYD+L + I TDG
Sbjct: 144 ARGRGYQPAETQ--EIYTIGEIPVDAIFTPIEKVNYVVEHTRVGQMTDYDRLIIEIITDG 201

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL--KKVEELELSV 267
           +I   D+++ A++IL D   +  +F     E +E+ +       P+++  + + EL LS 
Sbjct: 202 TIEPADALSEAAQILVDHARLIADFNREPSEPEEEEDK-----TPSIVDNRPLAELGLSP 256

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           R  N LR   I  +G ++   +  +L + NFG +SL E++  L   G  L M+
Sbjct: 257 RVLNALRSRQIERVGQVLSLPQEQLLSIRNFGPRSLQELRERLAEHGYTLAMD 309


>gi|71056900|emb|CAH59007.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 219

 Score =  200 bits (508), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 98/201 (48%), Positives = 143/201 (71%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+I GV ED+T IILNIKG+ LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIPGVREDVTQIILNIKGLALKLYA 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + I   GP  VTAGDI   +D+E+LN D VIC++   A     LTV  G GYV A
Sbjct: 61  EEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLVICSVAEGATFHARLTVKPGRGYVQA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI  +++++
Sbjct: 121 DENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIIPQEALS 180

Query: 219 LASRILQDQLGMFINFEEPKK 239
           LA++I+ + L +F+N  +  K
Sbjct: 181 LAAKIMTEHLDIFVNLTDEAK 201


>gi|225849517|ref|YP_002729682.1| DNA-directed RNA polymerase subunit alpha [Sulfurihydrogenibium
           azorense Az-Fu1]
 gi|225644691|gb|ACN99741.1| DNA-directed RNA polymerase, alpha subunit [Sulfurihydrogenibium
           azorense Az-Fu1]
          Length = 326

 Score =  200 bits (508), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 122/299 (40%), Positives = 177/299 (59%), Gaps = 6/299 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           EN   +  EPL RG+  TLGNALRRVL+SSL   AITAV+I GV HE +++KGV ED+++
Sbjct: 22  ENFGKLYVEPLERGYGITLGNALRRVLLSSLPSGAITAVKIVGVPHEFTTVKGVIEDVSE 81

Query: 85  IILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           IILN+K I LK+  +  +   I +  GPG V A DI+    IE++NPD  IC L  +  +
Sbjct: 82  IILNLKQIRLKIDENIERDFAILEVEGPGKVFAKDIKAPPGIEIVNPDEYICTLSENVKL 141

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
           +ME  + +G GY   +     N+ IG I ID  +SPIK+ ++ VE  R G   DYD+L +
Sbjct: 142 QMEFRIERGRGYKTVEELEDINE-IGWILIDTSFSPIKRCTFFVEPVRVGDKTDYDRLIL 200

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV-KEDINVKSLPFN---PALLKK 259
            I+TDG+IT ++++  ++ IL +   +       K +V K+ +  K+         L   
Sbjct: 201 EIETDGTITPDEALEKSANILIEHFTLLQKPTVRKAQVIKKTVAPKTEELKIEEDKLSLA 260

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           ++ELE+S R+ N LR   I  +GDL++ +E D+    + GRKSL EIK  L  MGL L 
Sbjct: 261 IDELEISSRAINTLRKLGINTIGDLVKLSEDDLKEAKSIGRKSLKEIKDALADMGLELA 319


>gi|161513436|emb|CAP16861.1| DNA-directed RNA polymerase subunit alpha [Pediococcus inopinatus]
          Length = 214

 Score =  200 bits (508), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 98/203 (48%), Positives = 143/203 (70%), Gaps = 2/203 (0%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNIK ++LK+  D  
Sbjct: 3   TLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNIKKVSLKIESDDE 62

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A  +
Sbjct: 63  KSLEIDVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAILTADTGRGYVSADEN 122

Query: 162 RTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           +   D  PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSI+  ++ +L
Sbjct: 123 KARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSISPSEATSL 182

Query: 220 ASRILQDQLGMFINFEEPKKEVK 242
           +++IL + L +F+N  +  K+ +
Sbjct: 183 SAKILTEHLALFVNLTDEAKDAE 205


>gi|71056866|emb|CAH58988.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           hermanniensis]
          Length = 214

 Score =  200 bits (508), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 98/201 (48%), Positives = 140/201 (69%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAAIT +QIDG LHE S+IKGV ED+  IILNIKG+ LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAITNIQIDGALHEFSTIKGVREDVVQIILNIKGLALKLFA 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G GYV A
Sbjct: 61  EEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTVKPGRGYVQA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDGSI  +++++
Sbjct: 121 DENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDGSIIAQEALS 180

Query: 219 LASRILQDQLGMFINFEEPKK 239
           LA++IL + L +F+N  +  K
Sbjct: 181 LAAKILTEHLDIFVNLTDEAK 201


>gi|167752412|ref|ZP_02424539.1| hypothetical protein ALIPUT_00656 [Alistipes putredinis DSM 17216]
 gi|167660653|gb|EDS04783.1| hypothetical protein ALIPUT_00656 [Alistipes putredinis DSM 17216]
          Length = 330

 Score =  200 bits (508), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 116/302 (38%), Positives = 184/302 (60%), Gaps = 15/302 (4%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNALRR+L+SSL G AIT V++ GV HE ++I GV E + DIILN+K + 
Sbjct: 28  PLEPGFGMTVGNALRRILLSSLEGYAITTVKVAGVDHEFAAIPGVMEGMIDIILNLKQVR 87

Query: 94  LKMSGDSH--KRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVS 150
              + D+   ++V++   G   +TAG I   ++  +VLNP+ VIC+L     +++ LT+ 
Sbjct: 88  FIRTVDNQDAEKVSVNVAGVTELTAGYISNYLSFFKVLNPELVICHLAPGTKMQLTLTIG 147

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVPA+ +   +   G + ID++++PIK V Y++E+ R  Q  DY+KL++ I TDGS
Sbjct: 148 KGRGYVPAEENTPADCEFGTLPIDSIFTPIKNVKYSIENYRVEQKTDYEKLNLEITTDGS 207

Query: 211 ITGEDSVALASRILQDQLGMF------INFEEPK--KEVKEDINVKSLPFNPALLKKVEE 262
           I   D++  A++IL     +F      +N E+    +E  EDI    L     L  K+ +
Sbjct: 208 IHPTDALKEAAKILIQHFMLFSDEKITVNMEDTNGAEEFDEDI----LHMRQLLKTKLSD 263

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
            +LSVR+ NCL+  ++  +GDL++    D+L+  NFG+KSL E+  +L ++ L  GM++ 
Sbjct: 264 QDLSVRALNCLKAADVDTVGDLVKLNRNDLLKFRNFGKKSLTELDELLASLNLKFGMDVS 323

Query: 323 DW 324
            +
Sbjct: 324 IY 325


>gi|296877834|ref|ZP_06901856.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           NAP07]
 gi|296431134|gb|EFH16959.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           NAP07]
          Length = 252

 Score =  200 bits (508), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 95/207 (45%), Positives = 146/207 (70%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  T+GNALRR+L+SSL G A+ A++IDGVLHE S+I GV ED+T+IIL +
Sbjct: 23  FVIEPLERGYGITIGNALRRILLSSLPGVAVNAIKIDGVLHEFSTIPGVKEDVTEIILTL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K ++  + G+  + + I  +GP  +T  DI    D+E+L+ D  I  LD +A + ME+ V
Sbjct: 83  KELSATIDGEGSRTLKIEAQGPCSITGADIICSPDVEILSKDLAIATLDDNAKLNMEIFV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYV A+ ++TEN PIG++ +D++Y+P++KVSY VE+ R GQ  DYDKL + + T+G
Sbjct: 143 DKGRGYVSAEENKTENVPIGVLPVDSIYTPVEKVSYHVENTRVGQKTDYDKLVLEVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEE 236
           SI  ++ ++LA+++L + L +FI+  E
Sbjct: 203 SINPQEGISLAAKVLVEHLNLFIDLTE 229


>gi|161511749|emb|CAP16885.1| DNA-directed RNA polymerase subunit alpha [Pediococcus parvulus]
          Length = 214

 Score =  200 bits (508), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 97/203 (47%), Positives = 143/203 (70%), Gaps = 2/203 (0%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNIK ++LK+  D  
Sbjct: 3   TLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNIKKVSLKIESDDE 62

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A  +
Sbjct: 63  KSLEINVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAVLTADTGRGYVSADEN 122

Query: 162 RTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           +   D  PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSI+  ++ +L
Sbjct: 123 KARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSISPSEATSL 182

Query: 220 ASRILQDQLGMFINFEEPKKEVK 242
           +++IL + L +F+N  +  ++ +
Sbjct: 183 SAKILTEHLALFVNLTDEAQDAE 205


>gi|328813985|gb|AEB52108.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 228

 Score =  200 bits (508), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 106/226 (46%), Positives = 153/226 (67%), Gaps = 2/226 (0%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK+  D  
Sbjct: 3   TLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTAIILNVKKIALKLESDET 62

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-- 159
           K + I  +GP  VTAGDI    D+EVLNPD  IC +   A   M +T + G GYV A+  
Sbjct: 63  KTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGAHFHMRMTANTGRGYVSAEDN 122

Query: 160 HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
            HR ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T+GSIT  ++++L
Sbjct: 123 KHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWTNGSITPSEAISL 182

Query: 220 ASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
           +++IL D L +F+N  +  K     +  +       L   +EEL+L
Sbjct: 183 SAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEMTIEELDL 228


>gi|119668353|emb|CAK95471.1| RNA polymerase alpha subunit [Lactobacillus plantarum]
          Length = 219

 Score =  200 bits (508), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 101/203 (49%), Positives = 145/203 (71%), Gaps = 2/203 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTAIILNVKKIALKLES 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A   M +T + G GYV A
Sbjct: 61  DETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGAHFHMRMTANTGRGYVSA 120

Query: 159 K--HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
           +   HR ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T+GSIT  ++
Sbjct: 121 EDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWTNGSITPSEA 180

Query: 217 VALASRILQDQLGMFINFEEPKK 239
           ++L+++IL D L +F+N  +  K
Sbjct: 181 ISLSAKILTDHLSIFVNLTDEAK 203


>gi|332144666|dbj|BAK19493.1| RNA polymerase alpha subunit [Lactobacillus sp. YIT 12364]
          Length = 239

 Score =  199 bits (507), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 110/239 (46%), Positives = 160/239 (66%), Gaps = 4/239 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR L+SSL GAAIT++QIDGVLHE S+IKGV ED+T IILN+K I
Sbjct: 1   EPLERGYGTTLGNSLRRTLLSSLPGAAITSIQIDGVLHEFSTIKGVVEDVTQIILNVKKI 60

Query: 93  NLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +LK+ G  +  + + I   GP  VTA DI   +D+ +LNPD  I  +   A   M LT +
Sbjct: 61  SLKLDGPDEEEENLEIDVIGPTEVTAADIVGGSDVTILNPDLHIATVADGASFHMNLTAN 120

Query: 151 KGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           KG GYV A  +  R+ + PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ + ++
Sbjct: 121 KGRGYVSAMENKKRSIDMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDVWSN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           GSIT  ++++LA++IL + L MF+N  +  K  +  +  +       L   +EEL+LSV
Sbjct: 181 GSITASEAISLAAKILTEHLEMFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSV 239


>gi|161513434|emb|CAP16860.1| DNA-directed RNA polymerase subunit alpha [Pediococcus cellicola]
          Length = 214

 Score =  199 bits (507), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 97/203 (47%), Positives = 143/203 (70%), Gaps = 2/203 (0%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNIK ++LK+  D  
Sbjct: 3   TLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNIKKVSLKIENDEE 62

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A  +
Sbjct: 63  KSLEINVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAVLTADTGRGYVSADEN 122

Query: 162 RTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           +   D  PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSI+  ++ +L
Sbjct: 123 KARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSISPSEATSL 182

Query: 220 ASRILQDQLGMFINFEEPKKEVK 242
           +++IL + L +F+N  +  + ++
Sbjct: 183 SAKILTEHLALFVNLTDEAQRLR 205


>gi|119662343|emb|CAJ33160.1| RNA polymerase alpha subunit [Lactobacillus plantarum]
          Length = 204

 Score =  199 bits (507), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 101/203 (49%), Positives = 145/203 (71%), Gaps = 2/203 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTAIILNVKKIALKLES 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A   M +T + G GYV A
Sbjct: 61  DETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGAHFHMRMTANTGRGYVSA 120

Query: 159 K--HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
           +   HR ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T+GSIT  ++
Sbjct: 121 EDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWTNGSITPSEA 180

Query: 217 VALASRILQDQLGMFINFEEPKK 239
           ++L+++IL D L +F+N  +  K
Sbjct: 181 ISLSAKILTDHLSIFVNLTDEAK 203


>gi|71056856|emb|CAH58983.1| DNA-directed RNA polymerase alpha chain [Enterococcus villorum]
          Length = 219

 Score =  199 bits (507), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 98/198 (49%), Positives = 140/198 (70%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+ LKM G   
Sbjct: 3   TLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGLALKMYGQEE 62

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV  G GYV A  +
Sbjct: 63  KTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTVKPGRGYVQADEN 122

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           + E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI   ++++L++
Sbjct: 123 KKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHCEDFDKLTMEIWTDGSIEPLEAMSLSA 182

Query: 222 RILQDQLGMFINFEEPKK 239
           +I+ + L +F+N  +  K
Sbjct: 183 KIMTEHLDIFVNLTDEAK 200


>gi|119662395|emb|CAJ33187.1| RNA polymerase alpha subunit [Lactobacillus aviarius subsp.
           aviarius]
          Length = 231

 Score =  199 bits (507), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 100/212 (47%), Positives = 146/212 (68%), Gaps = 2/212 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT VQIDGVLHE S+++GV ED+T IILN+
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAITDVQIDGVLHEFSTVEGVMEDVTTIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM  +  + + I   G   V AGDI    D+EVLNP+  IC +   A   + +T 
Sbjct: 61  KKVALKMDTEEPQILEIDVTGAKEVKAGDIHCGADVEVLNPELYICTVAEGASFHVRMTA 120

Query: 150 SKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +KG GYV A  ++ + D  PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T
Sbjct: 121 NKGRGYVSATENKAKADDMPIGVLAIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +GSIT  ++++L+++IL + L +F+N  +  K
Sbjct: 181 NGSITPSEAISLSAKILTEHLSIFVNLTDEAK 212


>gi|119662325|emb|CAJ33150.1| RNA polymerase alpha subunit [Lactobacillus intestinalis]
          Length = 211

 Score =  199 bits (506), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 96/202 (47%), Positives = 138/202 (68%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE +++ GV ED+T IILN+
Sbjct: 1   FVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFATVPGVREDVTKIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK   D  K + +   GP  VTA D++   D++VLNPD  IC +     + M++ V
Sbjct: 61  KKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMQIAV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYVPA  +++E+ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL++ I TDG
Sbjct: 121 KNGRGYVPASDNKSEDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTLEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMF 231
           SI   D+++ A++IL +   +F
Sbjct: 181 SIKPNDALSFAAKILVEHFKVF 202


>gi|119662313|emb|CAJ33144.1| RNA polymerase alpha subunit [Lactobacillus hilgardii]
          Length = 227

 Score =  199 bits (506), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 106/214 (49%), Positives = 148/214 (69%), Gaps = 4/214 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EPL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+
Sbjct: 1   VVVEPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNV 60

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K I+LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M L
Sbjct: 61  KKISLKLDGPEDEDENLEIDVIGPADVTAGDIQGDSDVTVLNPDLHIATVAEGATFHMRL 120

Query: 148 TVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           T ++G GYV A     R    PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ I
Sbjct: 121 TANRGRGYVSAVENKKRATEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDI 180

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
            T+GSIT  ++V+LA++IL + L MF++  +  K
Sbjct: 181 WTNGSITPSEAVSLAAKILTEHLEMFVDLTDEAK 214


>gi|119668359|emb|CAK95474.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
          Length = 221

 Score =  199 bits (506), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 99/211 (46%), Positives = 150/211 (71%), Gaps = 2/211 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRVL++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K ++
Sbjct: 1   PLERGYGTTLGNSLRRVLIASLPGAAITSMQIDGVLHEFSTVEGVTEDVTQIILNLKKVS 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK+  +  K + +  +GP  VTA DIQ  N++ +LNPD  I  +   A + ++LT  KG 
Sbjct: 61  LKLDSEDQKNLELDVKGPAEVTASDIQGDNEVTILNPDLHIATVADGAELHIKLTADKGR 120

Query: 154 GYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY+ A  ++   D   IG++ ID++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+
Sbjct: 121 GYLSANDNKARMDDLAIGVLPIDSIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSL 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           T  ++V+L ++IL + L MF++  E  +  +
Sbjct: 181 TPTEAVSLGAKILTEHLAMFVDLTETAQNAQ 211


>gi|119662353|emb|CAJ33165.1| RNA polymerase alpha subunit [Lactobacillus saerimneri]
          Length = 213

 Score =  199 bits (506), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 100/209 (47%), Positives = 143/209 (68%), Gaps = 2/209 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAAIT +QIDGVLHE S+++GV ED+T IILN+
Sbjct: 1   FVIEPLERGYGTTLGNSLRRVLLSSLPGAAITDIQIDGVLHEFSTVEGVLEDVTQIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L +  D    + I   GP  VTAGDIQ   D+E+ NPD  IC +   A   + +T 
Sbjct: 61  KKVALGIKSDDRVSLEIDVVGPMEVTAGDIQGSADVEIFNPDQYICTVADGASFHVRMTA 120

Query: 150 SKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           + G GYV AK ++   D  PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T
Sbjct: 121 NTGRGYVSAKENKEMADDMPIGVLPIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEE 236
           + SIT  ++V+L++++L + L +F+N  E
Sbjct: 181 NKSITPSEAVSLSAKVLTEHLSLFVNLTE 209


>gi|71056864|emb|CAH58987.1| DNA-directed RNA polymerase alpha chain [Enterococcus canis]
          Length = 217

 Score =  199 bits (506), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 96/201 (47%), Positives = 140/201 (69%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNIKG+ LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNIKGLALKLYA 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
              K + I   GP  VTAGDI   +D+E+LN D  +C +   A     LTV  G GYV A
Sbjct: 61  QEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLYLCTVSEGATFHARLTVKPGRGYVQA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++TE+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI  +++++
Sbjct: 121 DENKTEDMPIGVLPVDSIYTPVRRVNYQVENTRVGNRQDFDKLTMEIWTDGSIIPQEALS 180

Query: 219 LASRILQDQLGMFINFEEPKK 239
           L+++IL + L +F+N  +  K
Sbjct: 181 LSAKILTEHLDIFVNLTDEAK 201


>gi|119668369|emb|CAK95477.1| RNA polymerase alpha subunit [Lactobacillus ruminis]
          Length = 201

 Score =  199 bits (506), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 99/201 (49%), Positives = 144/201 (71%), Gaps = 2/201 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT VQIDGVLHE S++KGV ED+T+IILN+
Sbjct: 1   FVIEPLERGYGTTLGNSLRRILLSSLPGAAITDVQIDGVLHEFSTVKGVLEDVTEIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK++ +  + +     GP  VTAGDI T +D+E+LNPD  IC +   A     +T 
Sbjct: 61  KKVALKLNSEEPQSLEFDIVGPKEVTAGDISTNSDVEILNPDLYICTVADGASFHARMTA 120

Query: 150 SKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +KG GYV A  ++ + D  PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T
Sbjct: 121 NKGRGYVSANENKAKADDMPIGVLAIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQL 228
           +GSIT  ++++L+++IL + L
Sbjct: 181 NGSITPSEAISLSAKILTEHL 201


>gi|71056939|emb|CAH59028.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 220

 Score =  199 bits (506), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 98/198 (49%), Positives = 142/198 (71%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+I GV ED+T IILNIKG+ LK+  +  
Sbjct: 3   TLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIPGVREDVTQIILNIKGLALKLYAEEE 62

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I   GP  VTAGDI   +D+E+LN D VIC++   A     LTV  G GYV A  +
Sbjct: 63  KTLEIDITGPATVTAGDIIVDSDVEILNKDLVICSVAEGATFHARLTVKPGRGYVQADEN 122

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           + E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI  +++++LA+
Sbjct: 123 KKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIIPQEALSLAA 182

Query: 222 RILQDQLGMFINFEEPKK 239
           +I+ + L +F+N  +  K
Sbjct: 183 KIMTEHLDIFVNLTDEAK 200


>gi|161511773|emb|CAP16897.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 249

 Score =  199 bits (506), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 104/222 (46%), Positives = 147/222 (66%), Gaps = 2/222 (0%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E +N    + EPL RG+  TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+
Sbjct: 8   ENDNYGRFVIEPLERGYGTTLGNSLRRILLSSLPGAAITSVQIDSVLHEFSTIEGVVEDV 67

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  IC +     
Sbjct: 68  TQIILNLKKVSLKIESDEDKTLEINVAGPANVTAGDIMGDGDVVILNPELPICTVAEGTT 127

Query: 143 VRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
               LT   G GY  A  +  R  + PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDK
Sbjct: 128 FHAVLTADTGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDK 187

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           L++ I TDGSIT  ++ +L+++IL + L +F+N  +  KE +
Sbjct: 188 LTLDIWTDGSITPSEATSLSAKILTEHLAIFVNLNDQAKETE 229


>gi|328813973|gb|AEB52102.1| DNA-directed RNA polymerase alpha chain [Lactobacillus fermentum]
          Length = 243

 Score =  199 bits (505), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 106/243 (43%), Positives = 162/243 (66%), Gaps = 2/243 (0%)

Query: 48  RRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF 107
           RRV+++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K + LK+  +  K + I 
Sbjct: 1   RRVMLASLPGAAITSIQIDGVLHEFSTVQGVTEDVTQIILNLKQVALKIDSEDAKDLEID 60

Query: 108 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--EN 165
            +GP  VTA DIQ   D+ +LN D  I  +   A + +++T  KG GY  A  ++T  E 
Sbjct: 61  VKGPAEVTAADIQGDGDVTILNSDLHIATVSDGAELHVKMTADKGRGYSSADDNKTRMEG 120

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
             IG++ ID++Y+PI++V+YTVE+ R GQ  DYDKL++ + T+GS+T  ++++LA++IL 
Sbjct: 121 LAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYDKLTLDVWTNGSLTPTEAISLAAKILT 180

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLI 285
           + L MF+N  E  +  +  +  +       L K +EEL+LSVRS NCL+  +I  + DL 
Sbjct: 181 EHLTMFVNLTEEAQVTQVMVEREETHQEKVLDKTIEELDLSVRSYNCLKRADIQTVKDLT 240

Query: 286 QRT 288
           +RT
Sbjct: 241 ERT 243


>gi|71056862|emb|CAH58986.1| DNA-directed RNA polymerase alpha chain [Enterococcus malodoratus]
          Length = 205

 Score =  199 bits (505), Expect = 7e-49,   Method: Compositional matrix adjust.
 Identities = 98/197 (49%), Positives = 139/197 (70%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG+ LK+  +  K
Sbjct: 1   LGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNIKGLALKLFAEEEK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G GYV A  ++
Sbjct: 61  TLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTVKPGRGYVQADENK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDGSI  +++++LA++
Sbjct: 121 KEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDGSIIAQEALSLAAK 180

Query: 223 ILQDQLGMFINFEEPKK 239
           IL + L +F+N  +  K
Sbjct: 181 ILTEHLDIFVNLTDEAK 197


>gi|150187107|emb|CAK30172.1| RNA polymerase alpha subunit [Streptococcus downei MFe28]
          Length = 219

 Score =  199 bits (505), Expect = 7e-49,   Method: Compositional matrix adjust.
 Identities = 96/207 (46%), Positives = 145/207 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV+K 
Sbjct: 61  AVKSYVEDEKTIELDVTGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGHTLKATMTVAKN 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I 
Sbjct: 121 RGYVPAEGNKNDSAPVGTLAVDSIYTPVKKVNYQVEPARVGSNAGFDKLTIEIMTNGTII 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKK 239
            ED++ L++R+L + L +F +  E  K
Sbjct: 181 PEDALGLSARVLIEHLNLFTDLTEIAK 207


>gi|119672801|emb|CAK95516.1| RNA polymerase alpha subunit [Lactobacillus agilis]
          Length = 217

 Score =  199 bits (505), Expect = 7e-49,   Method: Compositional matrix adjust.
 Identities = 101/212 (47%), Positives = 147/212 (69%), Gaps = 2/212 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT VQIDGVLHE S+++GV ED+T IILN+
Sbjct: 1   FIIEPLERGYGTTLGNSLRRILLSSLPGAAITDVQIDGVLHEFSTVEGVLEDVTAIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  + + I   GP  VTAGDI   +D+E+LNPD  I  +   A   + +  
Sbjct: 61  KKVALKIDSEDAQALEINVVGPMDVTAGDINGSSDVEILNPDLHIATVAEGASFHVRMNA 120

Query: 150 SKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GYV A  ++ +ND  PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T
Sbjct: 121 DKGRGYVSASDNKAKNDEMPIGVLAIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +GSIT  ++++L+++IL + L +F++  E  K
Sbjct: 181 NGSITPSEAISLSAKILTEHLTLFVDLTEEAK 212


>gi|315186306|gb|EFU20067.1| DNA-directed RNA polymerase subunit alpha [Spirochaeta thermophila
           DSM 6578]
          Length = 363

 Score =  199 bits (505), Expect = 7e-49,   Method: Compositional matrix adjust.
 Identities = 119/301 (39%), Positives = 182/301 (60%), Gaps = 11/301 (3%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-----DGVLHEISS----IKGVHEDL 82
           A P  RG+  T+GN LRR+L+SS++G AI+AV+I      G  H +SS    I GV ED 
Sbjct: 32  AYPFERGYGVTIGNTLRRILLSSIQGYAISAVRITWYDDQGAAHVLSSEYEQIPGVVEDT 91

Query: 83  TDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
            +++ N+K + +++  +   K V +  +GP  VT  D + V+ +EV+N D  +  L  DA
Sbjct: 92  LELLANLKLLRVQLPDEMEQKTVMVEFKGPKEVTGADFE-VDQLEVMNKDFRVMTLMEDA 150

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              ME+ V  G GYVPA+  +   + +G I +DALYSP+++V + VE+ R G   DYDKL
Sbjct: 151 HFEMEMQVDLGRGYVPAEVQKNYIEVVGTIPLDALYSPVQRVRFNVENTRVGHRSDYDKL 210

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + + TDGSI+ ED++  A+++ ++   +FINF+E        ++ +       L   +E
Sbjct: 211 ILEVWTDGSISPEDALGEAAKLAKEHFTVFINFDEDAISHVRQLDHEEEQIRRLLETPIE 270

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           ELELSVRS+NCL+  NI  +GDL+ ++E ++ +  NFG+KSL+EIK  L    L LGM  
Sbjct: 271 ELELSVRSSNCLKNANIRTIGDLVSKSEEELSKTRNFGKKSLLEIKEKLKEWNLSLGMRD 330

Query: 322 P 322
           P
Sbjct: 331 P 331


>gi|119668321|emb|CAK95507.1| RNA polymerase alpha subunit [Lactobacillus gasseri]
          Length = 214

 Score =  198 bits (504), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 98/195 (50%), Positives = 139/195 (71%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G A++ +QIDGVLHE S+I GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTALSYIQIDGVLHEFSTIPGVREDVTKIILNLKKLELKSLS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K   I   GP +VTA D++  +DIEVLNPD  IC++     + M + +  G GYVPA
Sbjct: 61  DEEKIAEIDVTGPAIVTAADLKVDSDIEVLNPDQYICSIADGGHLHMNVAIKNGRGYVPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++T++ PIG+I +D+L+SPIKKV+Y VESAR G+  DYDKL++ I TDGSIT  D+++
Sbjct: 121 SENKTDDMPIGVIPVDSLFSPIKKVNYQVESARVGKRDDYDKLTLEIWTDGSITPNDALS 180

Query: 219 LASRILQDQLGMFIN 233
            A++IL +   +F++
Sbjct: 181 FAAKILVEHFKVFMS 195


>gi|71056858|emb|CAH58984.1| DNA-directed RNA polymerase alpha chain [Enterococcus villorum]
          Length = 208

 Score =  198 bits (504), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 98/198 (49%), Positives = 140/198 (70%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+ LKM G   
Sbjct: 3   TLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGLALKMYGQEE 62

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV  G GYV A  +
Sbjct: 63  KTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTVKPGRGYVQADEN 122

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           + E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI   ++++L++
Sbjct: 123 KKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHCEDFDKLTMEIWTDGSIEPLEAMSLSA 182

Query: 222 RILQDQLGMFINFEEPKK 239
           +I+ + L +F+N  +  K
Sbjct: 183 KIMTEHLDIFVNLTDEAK 200


>gi|161511727|emb|CAP16874.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 235

 Score =  198 bits (504), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 108/233 (46%), Positives = 152/233 (65%), Gaps = 2/233 (0%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++LK+  D  
Sbjct: 3   TLGNSLRRILLSSLPGAAITSVQIDSVLHEFSTIEGVVEDVTQIILNLKKVSLKIESDED 62

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I   GP  VTAGDI    D+ +LNP+  IC +         LT   G GY  A  +
Sbjct: 63  KTLEINVAGPANVTAGDIMGDGDVVILNPELPICTVAEGTTFHAVLTADTGRGYTSADEN 122

Query: 162 --RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
             R  + PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ I TDGSIT  ++ +L
Sbjct: 123 KARKVDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDIWTDGSITPSEATSL 182

Query: 220 ASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
           +++IL + L +F+N  +  KE +  +  +       L   +EEL+LSVRS NC
Sbjct: 183 SAKILTEHLAIFVNLNDQAKETEIMVEKEETHKEKMLEMTIEELDLSVRSYNC 235


>gi|119662317|emb|CAJ33146.1| RNA polymerase alpha subunit [Lactobacillus johnsonii]
          Length = 214

 Score =  198 bits (504), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 98/195 (50%), Positives = 139/195 (71%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G A++ +QIDGVLHE S+I GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTALSYIQIDGVLHEFSTIPGVREDVTKIILNLKKLELKSLS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K   I   GP +VTA D++  +DIEVLNPD  IC++     + M + +  G GYVPA
Sbjct: 61  DEEKIAEIDVTGPAIVTAADLKVDSDIEVLNPDQYICSIADGGHLHMNVAIKTGRGYVPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++T++ PIG+I +D+L+SPIKKV+Y VESAR G+  DYDKL++ I TDGSIT  D+++
Sbjct: 121 SENKTDDMPIGVIPVDSLFSPIKKVNYQVESARVGKRDDYDKLTLEIWTDGSITPNDALS 180

Query: 219 LASRILQDQLGMFIN 233
            A++IL +   +F++
Sbjct: 181 FAAKILVEHFKVFMS 195


>gi|161511765|emb|CAP16893.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           acidilactici]
          Length = 215

 Score =  198 bits (504), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 103/211 (48%), Positives = 141/211 (66%), Gaps = 2/211 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAITSVQIDNVLHEFSTIEGVVEDVTQIILNLKKVS 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK+  D  K + I   GP  VTAGDI    D+ VLNPD  IC +         LT   G 
Sbjct: 61  LKIESDDEKTLDINVVGPANVTAGDIMGDGDVTVLNPDSPICTVAEGTTFHAVLTADTGR 120

Query: 154 GYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A  +  R  + PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ I TDGSI
Sbjct: 121 GYTSADENKARKADMPIGVLPIDSIYTPIERVNYQVEKTRVGQRDDYDKLTLDIWTDGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           T  ++ +L+++IL + L +F+N  +  KE +
Sbjct: 181 TPSEATSLSAKILTEHLAIFVNLNDQAKETE 211


>gi|313892870|ref|ZP_07826447.1| DNA-directed RNA polymerase, alpha subunit [Veillonella sp. oral
           taxon 158 str. F0412]
 gi|313442223|gb|EFR60638.1| DNA-directed RNA polymerase, alpha subunit [Veillonella sp. oral
           taxon 158 str. F0412]
          Length = 334

 Score =  198 bits (504), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 122/298 (40%), Positives = 185/298 (62%), Gaps = 23/298 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE S+I G+ ED+TDIILN+
Sbjct: 23  FVCEPLDRGYGITLGNSLRRILLSSLDGAAITSIKIDGVLHEFSTIPGIREDVTDIILNL 82

Query: 90  KGINLKMSGDSHKRVTI---FKRGPGVVTAGDI--QTVNDIEVLNPDHVICNLDVDAVVR 144
           K + +K+  D+   + +   F++  GV+TA D+  Q   ++EVLNP+ VI  +D  A + 
Sbjct: 83  KQLCIKVEEDAQLPLEVHFDFQK-DGVLTAADLAEQFPPEVEVLNPELVIATMDETAHLV 141

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           M++ + +G GYVP+  ++ + D IG I ID+++SPI +  Y V   R G  +D+DKL++ 
Sbjct: 142 MDVVIERGKGYVPSTKNKKDTDVIGCIPIDSIFSPILRAKYEVSDVRVGNEMDFDKLTLE 201

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN----------VKSLPFNP 254
           + TDGSIT  D+VA ++ I+   LG F         V  D+N          V S    P
Sbjct: 202 VWTDGSITAADAVAKSAAIMIGYLGNFTKLAHSADVV--DVNTGEGGIVVDPVGSDNEEP 259

Query: 255 ALLK-----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           A+        ++ELELSVR+ NCL+   I  + DL+ +T  D+ ++ N G+KS+ EI+
Sbjct: 260 AVDDGPAKISIDELELSVRAYNCLKRAGINTIADLLDKTIDDLGKVRNLGKKSIDEIE 317


>gi|119668319|emb|CAK95460.1| RNA polymerase alpha subunit [Lactobacillus gasseri]
          Length = 198

 Score =  198 bits (503), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 98/195 (50%), Positives = 139/195 (71%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G A++ +QIDGVLHE S+I GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTALSYIQIDGVLHEFSTIPGVREDVTKIILNLKKLELKSLS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K   I   GP +VTA D++  +DIEVLNPD  IC++     + M + +  G GYVPA
Sbjct: 61  DEEKIAEIDVTGPAIVTAADLKVDSDIEVLNPDQYICSIADGGHLHMNVAIKNGRGYVPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++T++ PIG+I +D+L+SPIKKV+Y VESAR G+  DYDKL++ I TDGSIT  D+++
Sbjct: 121 SENKTDDMPIGVIPVDSLFSPIKKVNYQVESARVGKRDDYDKLTLEIWTDGSITPNDALS 180

Query: 219 LASRILQDQLGMFIN 233
            A++IL +   +F++
Sbjct: 181 FAAKILVEHFKVFMS 195


>gi|71056860|emb|CAH58985.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
          Length = 205

 Score =  198 bits (503), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 98/197 (49%), Positives = 139/197 (70%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG+ LK+  +  K
Sbjct: 1   LGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNIKGLALKLFAEEEK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G GYV A  ++
Sbjct: 61  TLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTVKPGRGYVQADENK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDGSI  +++++LA++
Sbjct: 121 KEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDGSIIAQEALSLAAK 180

Query: 223 ILQDQLGMFINFEEPKK 239
           IL + L +F+N  +  K
Sbjct: 181 ILTEHLDIFVNLTDEAK 197


>gi|332144688|dbj|BAK19504.1| RNA polymerase alpha subunit [Lactobacillus farraginis]
          Length = 218

 Score =  198 bits (503), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 105/211 (49%), Positives = 146/211 (69%), Gaps = 4/211 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K I
Sbjct: 1   EPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKI 60

Query: 93  NLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT +
Sbjct: 61  SLKLDGPEDEEENLEIDVIGPADVTAGDIQGDSDVTVLNPDLHIATVAEGATFHMRLTAN 120

Query: 151 KGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           +G GYV A     R    PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ + T+
Sbjct: 121 RGRGYVSAVENKKRATEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDVWTN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKK 239
           GSIT  ++V+LA++IL + L MF++  +  K
Sbjct: 181 GSITPSEAVSLAAKILTEHLEMFVDLTDEAK 211


>gi|72534420|emb|CAH59046.1| DNA-directed RNA polymerase alpha chain [Enterococcus canis]
          Length = 218

 Score =  198 bits (503), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 96/198 (48%), Positives = 139/198 (70%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNIKG+ LK+     
Sbjct: 1   TLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNIKGLALKLYAQEE 60

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I   GP  VTAGDI   +D+E+LN D  +C +   A     LTV  G GYV A  +
Sbjct: 61  KTLEIDITGPATVTAGDIIVDSDVEILNKDLYLCTVSEGATFHARLTVKPGRGYVQADEN 120

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           +TE+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI  +++++L++
Sbjct: 121 KTEDMPIGVLPVDSIYTPVRRVNYQVENTRVGNRQDFDKLTMEIWTDGSIIPQEALSLSA 180

Query: 222 RILQDQLGMFINFEEPKK 239
           +IL + L +F+N  +  K
Sbjct: 181 KILTEHLDIFVNLTDEAK 198


>gi|269784298|emb|CBH50794.1| alpha subunit of RNA polymerase [Vibrio sp. C 15.19]
          Length = 244

 Score =  198 bits (503), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 103/243 (42%), Positives = 162/243 (66%), Gaps = 8/243 (3%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVT 115
           G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V 
Sbjct: 3   GCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVV 62

Query: 116 AGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLI 171
           AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG +
Sbjct: 63  AGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRL 122

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F
Sbjct: 123 LVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAF 182

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           ++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE +
Sbjct: 183 VDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVE 239

Query: 292 MLR 294
           +L+
Sbjct: 240 LLK 242


>gi|238018650|ref|ZP_04599076.1| hypothetical protein VEIDISOL_00485 [Veillonella dispar ATCC 17748]
 gi|237865121|gb|EEP66411.1| hypothetical protein VEIDISOL_00485 [Veillonella dispar ATCC 17748]
          Length = 337

 Score =  198 bits (503), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 122/298 (40%), Positives = 185/298 (62%), Gaps = 23/298 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE S+I G+ ED+TDIILN+
Sbjct: 26  FVCEPLDRGYGITLGNSLRRILLSSLDGAAITSIKIDGVLHEFSTIPGIREDVTDIILNL 85

Query: 90  KGINLKMSGDSHKRVTI---FKRGPGVVTAGDI--QTVNDIEVLNPDHVICNLDVDAVVR 144
           K + +K+  D    + +   F++  GV+TA D+  Q   ++EVLNP+ VI  +D  A + 
Sbjct: 86  KQLCIKVEEDVQLPLEVHFDFQK-DGVLTAADLAEQFPPEVEVLNPELVIATMDETAHLV 144

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           M++ + +G GYVP+  ++ + D IG I ID+++SPI +  Y V   R G  +D+DKL++ 
Sbjct: 145 MDVVIERGKGYVPSTKNKKDTDVIGCIPIDSIFSPILRAKYEVSDVRVGNEMDFDKLTLE 204

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN----------VKSLPFNP 254
           + TDGSIT  D+VA ++ I+   LG F         V  D+N          V S    P
Sbjct: 205 VWTDGSITAADAVAKSAAIMIGYLGNFTKLAHSADVV--DVNTGEGGIVVDPVGSDNEEP 262

Query: 255 ALLK-----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           A+ +      ++ELELSVR+ NCL+   I  + DL+ +T  D+ ++ N G+KS+ EI+
Sbjct: 263 AVDEGPAKISIDELELSVRAYNCLKRAGINTIADLLDKTIDDLGKVRNLGKKSIDEIE 320


>gi|237739945|ref|ZP_04570426.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp.
           2_1_31]
 gi|229421962|gb|EEO37009.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp.
           2_1_31]
          Length = 342

 Score =  198 bits (503), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 112/306 (36%), Positives = 184/306 (60%), Gaps = 7/306 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E   +   + EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GV+ E + + GV E 
Sbjct: 33  KESNYKGQFVVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVMSEFTVMDGVKEA 92

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ VIC +  D 
Sbjct: 93  VTEIILNVKEIVVKAESSGERRMTLSVKGPKVVKAADIVADIGLEIVNPEQVICTVTTDR 152

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D+DKL
Sbjct: 153 TLDMEFLVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRITDFDKL 212

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFI-------NFEEPKKEVKEDINVKSLPFNP 254
           ++ ++TDGSI   D+++ A  +L+  L  F+       N  +  +E+ E+     +  + 
Sbjct: 213 TLNVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRDEIEEIIEEPIDIQVIDDK 272

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +  +G
Sbjct: 273 SHDMKIEELDLTVRSFNCLKKAGIEDVSQLASLSLNELLKIKNLGKKSLDEILEKMKDLG 332

Query: 315 LFLGMN 320
             L  N
Sbjct: 333 YDLEKN 338


>gi|269123125|ref|YP_003305702.1| DNA-directed RNA polymerase, alpha subunit [Streptobacillus
           moniliformis DSM 12112]
 gi|268314451|gb|ACZ00825.1| DNA-directed RNA polymerase, alpha subunit [Streptobacillus
           moniliformis DSM 12112]
          Length = 322

 Score =  198 bits (503), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 111/279 (39%), Positives = 171/279 (61%), Gaps = 5/279 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+ +T+GNALRRVL+SS+ G+AI  V+IDGVL+E S I+GV E +TDI+LNIK I
Sbjct: 28  EPLYRGYGNTIGNALRRVLLSSIPGSAIKGVRIDGVLNEFSMIEGVKEAVTDIVLNIKEI 87

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +++     KR+ +   GP V+TA DI     I ++NP+ VI  +     + ME  V  G
Sbjct: 88  VVELDEPVEKRMKLSVVGPKVITAADIVPEAGITIVNPEQVIATITTKKAIDMEFIVDSG 147

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            G+V +    T       + +DA+Y+PI+KVSY VE    G+V +YDKL++T+ TDGSI 
Sbjct: 148 EGFVVSDEINTSGWEADFLAVDAIYTPIRKVSYQVEDTMVGRVTNYDKLTLTVTTDGSID 207

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---PALLK--KVEELELSV 267
             D+++ A  ++      F N      + + +  ++    N   P+L++  ++EEL L++
Sbjct: 208 IHDALSYAVELINIHTKPFANIGTAMAKFRSEEELELEVSNDSYPSLVEDTRIEELGLTI 267

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           RS NCL+  +I  +G+LI+ T+ D+ ++ N G KS  EI
Sbjct: 268 RSYNCLKKVDINTVGELIRLTKEDLKKIKNLGNKSAKEI 306


>gi|294101657|ref|YP_003553515.1| DNA-directed RNA polymerase, alpha subunit [Aminobacterium
           colombiense DSM 12261]
 gi|293616637|gb|ADE56791.1| DNA-directed RNA polymerase, alpha subunit [Aminobacterium
           colombiense DSM 12261]
          Length = 339

 Score =  197 bits (502), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 122/304 (40%), Positives = 177/304 (58%), Gaps = 17/304 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +I EPL RG+  TLGNALRRVL+SS++GAAIT+V++DGVLHE S+I GV ED+ +++LN+
Sbjct: 24  VIVEPLERGYGVTLGNALRRVLLSSVKGAAITSVRVDGVLHEFSTIPGVREDVIELMLNL 83

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I +       K + +   GP  V A DIQ  ++IE ++PD  +C L+  A + M+L +
Sbjct: 84  KHIPVHSYSKDVKVLHLEAEGPKQVVAADIQPDSEIEFIDPDAPVCVLEDGAQLSMDLYI 143

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY      R    P   + IDA+YSP+ KV Y VE+AR GQ  DY++L + + T+G
Sbjct: 144 EQGVGYATIDRPRPAYLPADALLIDAIYSPVLKVHYDVEAARVGQRTDYERLVLDVTTNG 203

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA-------------- 255
            I  + +V  A++I++   G FI  +  K    E I+ +    +                
Sbjct: 204 VIAPDVAVGEAAKIIRSYFG-FIVEDVDKLHPLEGIDEEEAALSADEAAAEAAEAAKEED 262

Query: 256 --LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
             L + V ELELS+RS NCL    I  +GDL+ RT  D+L++ N G+ SL EI+  L   
Sbjct: 263 DLLSRPVRELELSIRSENCLLRGGIHTIGDLLTRTRDDLLKIRNLGKISLREIEERLEKQ 322

Query: 314 GLFL 317
           GL L
Sbjct: 323 GLRL 326


>gi|308125199|gb|ADO14948.1| DNA-directed RNA polymerase alpha chain [Enterococcus termitis]
          Length = 204

 Score =  197 bits (502), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 97/196 (49%), Positives = 141/196 (71%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+ LK+  +  K 
Sbjct: 1   GNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGLALKLYAEEEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I   GP  VTAGDI   +D+E+LN D VIC++   A     LTV  G GYV A  ++ 
Sbjct: 61  LEIDITGPATVTAGDIIVDSDVEILNKDLVICSVSEGATFHARLTVKPGRGYVQADENKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI  +++++LA++I
Sbjct: 121 EDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIIPQEALSLAAKI 180

Query: 224 LQDQLGMFINFEEPKK 239
           + + L +F+N  +  K
Sbjct: 181 MTEHLDIFVNLTDEAK 196


>gi|294782963|ref|ZP_06748289.1| DNA-directed RNA polymerase, alpha subunit [Fusobacterium sp.
           1_1_41FAA]
 gi|294481604|gb|EFG29379.1| DNA-directed RNA polymerase, alpha subunit [Fusobacterium sp.
           1_1_41FAA]
          Length = 342

 Score =  197 bits (502), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 112/306 (36%), Positives = 184/306 (60%), Gaps = 7/306 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E   +   + EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GV+ E + + GV E 
Sbjct: 33  KESNYKGQFVVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVMSEFTVMDGVKEA 92

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ VIC +  D 
Sbjct: 93  VTEIILNVKEIVVKAESSGERRMTLSVKGPKVVKAADIVADIGLEIVNPEQVICTVTTDR 152

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D+DKL
Sbjct: 153 TLDMEFLVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRITDFDKL 212

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFI-------NFEEPKKEVKEDINVKSLPFNP 254
           ++ ++TDGSI   D+++ A  +L+  L  F+       N  +  +E+ E+     +  + 
Sbjct: 213 TLNVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRDEIEEIIEEPIDIQVIDDK 272

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +  +G
Sbjct: 273 SHDMKIEELDLTVRSFNCLKKAGIEDVSQLASLSLNELLKIKNLGKKSLDEILEKMKDLG 332

Query: 315 LFLGMN 320
             L  N
Sbjct: 333 YDLEKN 338


>gi|221632951|ref|YP_002522174.1| DNA-directed RNA polymerase subunit alpha [Thermomicrobium roseum
           DSM 5159]
 gi|221156271|gb|ACM05398.1| DNA-directed RNA polymerase, alpha subunit [Thermomicrobium roseum
           DSM 5159]
          Length = 326

 Score =  197 bits (502), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 115/281 (40%), Positives = 170/281 (60%), Gaps = 9/281 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL  G+  TLGNALRR+L+ SL GAAIT ++I GV HE S+I+GV ED+T+I+LN+
Sbjct: 21  FVVEPLEPGYGTTLGNALRRILLRSLPGAAITRIRIAGVWHEFSTIEGVREDVTEIVLNL 80

Query: 90  KGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMEL 147
           KG+ L+   +  + R T+F +G GVV AGD+    ++EV+NPDHVI  LD D A + M+L
Sbjct: 81  KGVRLRAVTEFRETRATLFAQGEGVVRAGDVDWPAEVEVVNPDHVIATLDNDQARLEMDL 140

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            + +G GY+PA+    E   IG I IDA+++P  KV+Y VE  R G   DYD+L + I T
Sbjct: 141 WIGRGRGYLPAEAQ--EIRSIGEIPIDAIFTPTLKVNYVVEHTRVGGATDYDRLILEIVT 198

Query: 208 DGSITGEDSVALASRILQDQLGMFINFE-EPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           DG++    ++  A+RIL         FE E  +E  E+ +V  +       + + E+ LS
Sbjct: 199 DGTVEPAKALVEAARILVQHARWIAEFESEGAEEPVEEWSVAHVDDT----RLLSEIGLS 254

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            R  N LR   I  +G ++      +L + NFG ++L E++
Sbjct: 255 QRVLNALRARGIERVGQVLAMRPDQLLGIRNFGPRALQELR 295


>gi|291461038|ref|ZP_06026582.2| DNA-directed RNA polymerase, alpha subunit [Fusobacterium
           periodonticum ATCC 33693]
 gi|291379318|gb|EFE86836.1| DNA-directed RNA polymerase, alpha subunit [Fusobacterium
           periodonticum ATCC 33693]
          Length = 342

 Score =  197 bits (501), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 111/298 (37%), Positives = 181/298 (60%), Gaps = 7/298 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GV+ E + + GV E +T+IILN+
Sbjct: 41  FVVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVMSEFTVMDGVKEAVTEIILNV 100

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I +K      +R+T+  +GP VV A DI     +E++NP+ VIC +  D  + ME  V
Sbjct: 101 KEIVVKAESSGERRMTLSVKGPKVVKAADIVADIGLEIVNPEQVICTVTTDRTLDMEFLV 160

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D+DKL++ ++TDG
Sbjct: 161 DTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRITDFDKLTLNVETDG 220

Query: 210 SITGEDSVALASRILQDQLGMFI-------NFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           SI   D+++ A  +L+  L  F+       N  +  +E+ E+     +  + +   K+EE
Sbjct: 221 SIEIRDAISYAVELLRLHLDPFLEIGNKMENLRDEIEEIIEEPIDIQVIDDKSHDMKIEE 280

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           L+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +  +G  L  N
Sbjct: 281 LDLTVRSFNCLKKAGIEDVSQLASLSLNELLKIKNLGKKSLDEILEKMKDLGYDLEKN 338


>gi|291460345|ref|ZP_06599735.1| DNA-directed RNA polymerase, alpha subunit [Oribacterium sp. oral
           taxon 078 str. F0262]
 gi|291417100|gb|EFE90819.1| DNA-directed RNA polymerase, alpha subunit [Oribacterium sp. oral
           taxon 078 str. F0262]
          Length = 313

 Score =  197 bits (501), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 115/295 (38%), Positives = 182/295 (61%), Gaps = 22/295 (7%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A  LGN+LRR+L+SS+ GAAI+ V+++ V HE SSI GV ED+++II+N+K + 
Sbjct: 27  PLVKGEATVLGNSLRRILLSSMPGAAISEVKVESVYHEFSSIAGVKEDVSEIIMNLKKLA 86

Query: 94  LKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVVRMELTVS 150
           ++ +  S + V  +    G GV+ A DI+  ++IE++NP+ VI  L   DA + ME+ ++
Sbjct: 87  VRNTSSSDEAVMAYIDYAGEGVIRAADIRVSSEIEIVNPEQVIATLSGKDAKLYMEMKIT 146

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GY  A        PIG+I +DA+Y+P+ KV+ +V+     +     +L + + T+G+
Sbjct: 147 KGRGYDGANTRDHSELPIGVIAVDAVYTPVTKVNVSVKDLGRSE-----RLVLDVMTNGT 201

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA-------LLKKVEEL 263
           +  +D+V+LA++I+Q  L +FI+ +   KE         LP N A       + K ++EL
Sbjct: 202 LAPDDAVSLAAKIMQTHLQLFIDMDNTVKE-------PFLPGNTAVEDVQDEMNKSIDEL 254

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           ELSVRS NCL+   I  + DL ++T  D++++ N GRKSL EI   L +MGL L 
Sbjct: 255 ELSVRSYNCLKRAGINTVEDLCEKTMDDLMKVRNMGRKSLDEILNKLESMGLSLA 309


>gi|308125185|gb|ADO14941.1| DNA-directed RNA polymerase alpha chain [Enterococcus caccae]
 gi|308125191|gb|ADO14944.1| DNA-directed RNA polymerase alpha chain [Enterococcus sp.
           CCRI-16985]
 gi|308125197|gb|ADO14947.1| DNA-directed RNA polymerase alpha chain [Enterococcus silesiacus]
 gi|308125201|gb|ADO14949.1| DNA-directed RNA polymerase alpha chain [Enterococcus sp.
           CCRI-16620]
 gi|308125203|gb|ADO14950.1| DNA-directed RNA polymerase alpha chain [Enterococcus sp.
           CCRI-16986]
          Length = 204

 Score =  197 bits (501), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 96/196 (48%), Positives = 141/196 (71%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+ LK+  +  K 
Sbjct: 1   GNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGLALKLYAEEEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I   GP  VTAGDI   +D+E+LN D +IC++   A     LTV  G GYV A  ++ 
Sbjct: 61  LEIDITGPATVTAGDIIVDSDVEILNKDLIICSVSEGATFHARLTVKPGRGYVQADENKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI  +++++LA++I
Sbjct: 121 EDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIIPQEALSLAAKI 180

Query: 224 LQDQLGMFINFEEPKK 239
           + + L +F+N  +  K
Sbjct: 181 MTEHLDIFVNLTDEAK 196


>gi|108792411|emb|CAJ33183.1| RNA polymerase alpha subunit [Lactobacillus agilis]
          Length = 227

 Score =  197 bits (501), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 100/212 (47%), Positives = 147/212 (69%), Gaps = 2/212 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT VQIDGVLHE S+++GV ED+T IILN+
Sbjct: 1   FIIEPLERGYGTTLGNSLRRILLSSLPGAAITDVQIDGVLHEFSTVEGVLEDVTAIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  + + I   GP  VTAGDI   +D+E+LNPD  I  +   A   + +  
Sbjct: 61  KKVALKIDSEDAQALEINVVGPMDVTAGDINGSSDVEILNPDLHIATVAEGASFHVRMNA 120

Query: 150 SKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GYV A  ++ +ND  PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T
Sbjct: 121 DKGRGYVSASDNKAKNDEMPIGVLAIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +GSIT  ++++L+++IL + L +F++  +  K
Sbjct: 181 NGSITPSEAISLSAKILTEHLTLFVDLTDEAK 212


>gi|161511767|emb|CAP16894.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 219

 Score =  197 bits (500), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 102/215 (47%), Positives = 144/215 (66%), Gaps = 2/215 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+T IILN+
Sbjct: 1   FVIEPLERGYGTTLGNSLRRILLSSLPGAAITSVQIDSVLHEFSTIEGVVEDVTQIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  IC +         LT 
Sbjct: 61  KKVSLKIESDEDKTLEINVAGPANVTAGDIMGDGDVVILNPELPICTVAEGTTFHAVLTA 120

Query: 150 SKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             G GY  A  +  R  + PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ I T
Sbjct: 121 DTGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDIWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           DGSIT  ++ +L+++IL + L +F+N  +  KE +
Sbjct: 181 DGSITPSEATSLSAKILTEHLAIFVNLNDQAKETE 215


>gi|328813977|gb|AEB52104.1| DNA-directed RNA polymerase alpha chain [Lactobacillus helveticus]
          Length = 237

 Score =  197 bits (500), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 96/202 (47%), Positives = 136/202 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+
Sbjct: 5   FVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNL 64

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK   D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V
Sbjct: 65  KKLELKSFSDERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAV 124

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDG
Sbjct: 125 QNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDG 184

Query: 210 SITGEDSVALASRILQDQLGMF 231
           SI   D+++ A++IL +   +F
Sbjct: 185 SIKPNDALSFAAKILVEHFKVF 206


>gi|154424845|emb|CAL18525.1| RNA polymerase alpha subunit [Streptococcus pyogenes]
          Length = 219

 Score =  197 bits (500), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 96/210 (45%), Positives = 146/210 (69%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+
Sbjct: 1   FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNV 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     +R  +TV
Sbjct: 61  KGLAVKSYVEDEKIIELEVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLRATMTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 121 AKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           +I  ED++ L++R+L + L +F +  E  K
Sbjct: 181 TIIPEDALGLSARVLIEHLNLFTDLTEVAK 210


>gi|119672799|emb|CAK95483.1| RNA polymerase alpha subunit [Lactobacillus agilis]
          Length = 214

 Score =  197 bits (500), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 100/212 (47%), Positives = 147/212 (69%), Gaps = 2/212 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT VQIDGVLHE S+++GV ED+T IILN+
Sbjct: 1   FIIEPLERGYGTTLGNSLRRILLSSLPGAAITDVQIDGVLHEFSTVEGVLEDVTAIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  + + I   GP  VTAGDI   +D+E+LNPD  I  +   A   + +  
Sbjct: 61  KKVALKIDSEDAQALEINVVGPMDVTAGDINGSSDVEILNPDLHIATVAEGASFHVRMNA 120

Query: 150 SKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GYV A  ++ +ND  PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T
Sbjct: 121 DKGRGYVSASDNKAKNDEMPIGVLAIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +GSIT  ++++L+++IL + L +F++  +  K
Sbjct: 181 NGSITPSEAISLSAKILTEHLTLFVDLTDEAK 212


>gi|295809864|emb|CBL85108.1| alpha subunit of RNA polymerase [Vibrio tapetis]
          Length = 244

 Score =  197 bits (500), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 103/243 (42%), Positives = 162/243 (66%), Gaps = 8/243 (3%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVT 115
           G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +K++ G     +T+ K G G V 
Sbjct: 3   GCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVKVAEGKDEVFITLNKSGSGPVV 62

Query: 116 AGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLI 171
           AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG +
Sbjct: 63  AGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASSRIHTEEDERPIGRL 122

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  ++ IL +QL  F
Sbjct: 123 LVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRSATILAEQLDAF 182

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           ++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE +
Sbjct: 183 VDLRDIRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVE 239

Query: 292 MLR 294
           +L+
Sbjct: 240 LLK 242


>gi|119662289|emb|CAJ33131.1| RNA polymerase alpha subunit [Lactobacillus casei]
          Length = 211

 Score =  197 bits (500), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 96/202 (47%), Positives = 144/202 (71%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           G+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED+T IILNIK + LKM+
Sbjct: 1   GYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMN 60

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
            D  K + I   GP  VTA DI T  D+EVLNP+  IC +       + +TV KG GYV 
Sbjct: 61  TDEDKNIEIDVNGPAKVTAADIVTDPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVA 120

Query: 158 AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
           A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  +++
Sbjct: 121 ADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAI 180

Query: 218 ALASRILQDQLGMFINFEEPKK 239
           +LA++IL + L +F+N  +  K
Sbjct: 181 SLAAKILTEHLDIFVNLTDEAK 202


>gi|284053326|ref|ZP_06383536.1| DNA-directed RNA polymerase subunit alpha [Arthrospira platensis
           str. Paraca]
 gi|291567808|dbj|BAI90080.1| RNA polymerase alpha subunit [Arthrospira platensis NIES-39]
          Length = 314

 Score =  197 bits (500), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 114/291 (39%), Positives = 170/291 (58%), Gaps = 12/291 (4%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG   T+GNALRRVL+S+L G AITAV+I GV HE ++I G  ED+ +I+LN+K   
Sbjct: 27  PLDRGQGITVGNALRRVLLSNLEGTAITAVRIAGVNHEFATIDGAREDVLEIMLNLKEAV 86

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK      +   +  +GP  VT G     +++EV++ +  I  L   A + ME  + KG 
Sbjct: 87  LKSHTHQKQIGRLLVQGPATVTVGHFDLPSEVEVVDKNQYIATLSPGATLEMECQIEKGT 146

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY     HR ++  +  + IDA++ P++KV+YTVE AR+G  L+ D+L++ I T GS+T 
Sbjct: 147 GYRAVDRHRDDSAALDFLQIDAIFMPVRKVNYTVEDARDGGSLEKDRLTLEIWTSGSLTP 206

Query: 214 EDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTN 271
           +++++ A+ IL D  G    IN E    + ++DI       +P     +EEL+LSVR+ N
Sbjct: 207 QEAISQAAAILVDLFGALKDINLESITSDQRDDI-------DPTSQIPIEELQLSVRAYN 259

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           CL+   I  + DL   TE D+L + NFG+KS  E+   L      LG+ LP
Sbjct: 260 CLKRAQINSVADLRDYTEEDLLEIKNFGQKSAEEVIEALQNR---LGITLP 307


>gi|219849860|ref|YP_002464293.1| DNA-directed RNA polymerase subunit alpha [Chloroflexus aggregans
           DSM 9485]
 gi|219544119|gb|ACL25857.1| DNA-directed RNA polymerase, alpha subunit [Chloroflexus aggregans
           DSM 9485]
          Length = 318

 Score =  197 bits (500), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 107/277 (38%), Positives = 167/277 (60%), Gaps = 4/277 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL  G+ HTLGNALRRVL++++ G+AIT V++ GV  E   I GV ED+ ++ILN+KGI
Sbjct: 24  EPLDPGYGHTLGNALRRVLLTAIPGSAITHVRVTGVYQETDRIPGVTEDMVELILNLKGI 83

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSK 151
           +L+   +     TI K+GPGVVTA D+     + V++PDH IC L+ + A + +  T+ +
Sbjct: 84  HLRGHHEGTVTATIRKQGPGVVTAADLVLPEGLAVVDPDHYICTLEHEQAQIELTATIER 143

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GY+ A        P+G I IDA+++P+ +V+Y VE+ R GQ  D+D+L + + T+G++
Sbjct: 144 GRGYLSADQRGIL--PLGEIPIDAIFTPVPRVNYIVENTRIGQATDFDRLILEVWTNGTV 201

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL-KKVEELELSVRST 270
              D++  A+R+L        NF     E +       L   P++    +E LELS R+ 
Sbjct: 202 RPVDALDYAARVLVHYNTTIANFNRMAVEPEAQPETTGLEIPPSVYDTSIETLELSTRTY 261

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           NCL+   I  +G ++Q  E  +L + N G+KS+ EI+
Sbjct: 262 NCLKRAEITKIGQVLQMDEKALLSVRNLGQKSMEEIR 298


>gi|308125187|gb|ADO14942.1| DNA-directed RNA polymerase alpha chain [Enterococcus devriesei]
          Length = 204

 Score =  196 bits (499), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 97/196 (49%), Positives = 138/196 (70%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG+ LK+  +  K 
Sbjct: 1   GNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNIKGLALKLFAEEEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G GYV A  ++ 
Sbjct: 61  LEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTVKPGRGYVQADENKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDGSI  +++++LA++I
Sbjct: 121 EDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDGSIIAQEALSLAAKI 180

Query: 224 LQDQLGMFINFEEPKK 239
           L + L +F+N  +  K
Sbjct: 181 LTEHLDIFVNLTDEAK 196


>gi|119668355|emb|CAK95472.1| RNA polymerase alpha subunit [Lactobacillus plantarum]
          Length = 214

 Score =  196 bits (499), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 100/200 (50%), Positives = 143/200 (71%), Gaps = 2/200 (1%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK+  D  
Sbjct: 1   TLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTAIILNVKKIALKLESDET 60

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-- 159
           K + I  +GP  VTA DI    D+EVLNPD  IC +   A   M +T + G GYV A+  
Sbjct: 61  KTLEIDVKGPANVTASDIIGDADVEVLNPDLPICTVADGAHFHMRMTANTGRGYVSAEDN 120

Query: 160 HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
            HR ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T+GSIT  ++++L
Sbjct: 121 KHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWTNGSITPSEAISL 180

Query: 220 ASRILQDQLGMFINFEEPKK 239
           +++IL D L +F+N  +  K
Sbjct: 181 SAKILTDHLSIFVNLTDEAK 200


>gi|160947673|ref|ZP_02094840.1| hypothetical protein PEPMIC_01608 [Parvimonas micra ATCC 33270]
 gi|158446807|gb|EDP23802.1| hypothetical protein PEPMIC_01608 [Parvimonas micra ATCC 33270]
          Length = 313

 Score =  196 bits (499), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 113/292 (38%), Positives = 178/292 (60%), Gaps = 1/292 (0%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           E+N       PL RG+  TLGN++RRVL+ SL G+AI  V+IDGV HE ++IKG   D+ 
Sbjct: 17  EKNYGKFAIMPLDRGYGTTLGNSMRRVLLGSLPGSAIATVKIDGVGHEFTTIKGSIADVP 76

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           +I++NIKGI LK   D    + +  +GP VVTAGDI    ++E+ N DH I  L+ +  +
Sbjct: 77  EILINIKGIALKKFNDEPVILELNVKGPKVVTAGDISENQNVEIANKDHYITTLNEEGEI 136

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
           RM+L V  G GY  +  ++   D I  I +D+ +SP+KKV++ V + R GQ +D+DKL +
Sbjct: 137 RMDLLVLNGKGYRVSDLNKEYCD-INSIAVDSSFSPVKKVNFIVGNTRVGQSIDFDKLEI 195

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            + T+G+IT +++++  + I  D L +F +  +   +     + K L  N  L K VEEL
Sbjct: 196 EVWTNGTITPQEALSTGAGIFIDYLSLFRSLPDINLDNSSIKDGKILDANGVLSKSVEEL 255

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           +LS+RS NCL+  N+  + D+I +    + ++ NFG+KS+ E+   +  +GL
Sbjct: 256 DLSLRSFNCLKRANLDTVKDIISQDIEQLKKIKNFGKKSVEEVVDKIHELGL 307


>gi|119662297|emb|CAJ33135.1| RNA polymerase alpha subunit [Lactobacillus curvatus]
          Length = 223

 Score =  196 bits (499), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 94/206 (45%), Positives = 145/206 (70%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L++SL G A+T +QIDGVLHE S+I GV ED+T IILNIK + 
Sbjct: 1   PLERGYGTTLGNSLRRILLASLPGTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNIKKLA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK+  +  K + I  +GP  VTA DI + +D+EVLN D  IC +       + +TV KG 
Sbjct: 61  LKLHVEEDKTIEIDVKGPATVTAADIISDDDVEVLNTDQYICTVAEGGNFHVRMTVKKGR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYV A  +++++ PIG++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+ 
Sbjct: 121 GYVAADQNKSDDMPIGVLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISP 180

Query: 214 EDSVALASRILQDQLGMFINFEEPKK 239
            ++++LA++I+ + L +F++  +  K
Sbjct: 181 REAISLAAKIMTEHLAIFVDLTDEAK 206


>gi|308125189|gb|ADO14943.1| DNA-directed RNA polymerase alpha chain [Enterococcus pallens]
          Length = 204

 Score =  196 bits (499), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 97/196 (49%), Positives = 138/196 (70%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNIKG+ LK+  +  K 
Sbjct: 1   GNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVVQIILNIKGLALKLFTEEEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G GYV A  ++ 
Sbjct: 61  LEIDITGPATVTAGDIIVDSDVEILNKDLYICTVSEGATFHARLTVRPGRGYVQADENKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           E+ PIG++ +D++Y+P++KV+Y VE+ R G+  DYDKL+M I TDGSI  +++++LA++I
Sbjct: 121 EDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDYDKLTMEIWTDGSIIAQEALSLAAKI 180

Query: 224 LQDQLGMFINFEEPKK 239
           L + L +F+N  +  K
Sbjct: 181 LTEHLDIFVNLTDEAK 196


>gi|119668361|emb|CAK95513.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
          Length = 211

 Score =  196 bits (498), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 98/210 (46%), Positives = 149/210 (70%), Gaps = 2/210 (0%)

Query: 35  LPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL 94
           L RG+  TLGN+LRRVL++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K ++L
Sbjct: 1   LERGYGTTLGNSLRRVLIASLPGAAITSMQIDGVLHEFSTVEGVTEDVTQIILNLKKVSL 60

Query: 95  KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHG 154
           K+  +  K + +  +GP  VTA DIQ  N++ +LNPD  I  +   A + ++LT  KG G
Sbjct: 61  KLDSEDQKNLELDVKGPAEVTASDIQGDNEVTILNPDLHIATVADGAELHIKLTADKGRG 120

Query: 155 YVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           Y+ A  ++   D   IG++ ID++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T
Sbjct: 121 YLSANDNKARMDDLAIGVLPIDSIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLT 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVK 242
             ++V+L ++IL + L MF++  E  +  +
Sbjct: 181 PTEAVSLGAKILTEHLAMFVDLTETAQNAQ 210


>gi|86438814|emb|CAJ43372.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 226

 Score =  196 bits (498), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 96/202 (47%), Positives = 136/202 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+
Sbjct: 1   FVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK   D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V
Sbjct: 61  KKLELKSLSDERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDG
Sbjct: 121 QNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMF 231
           SI   D+++ A++IL +   +F
Sbjct: 181 SIKPNDALSFATKILVEHFKVF 202


>gi|86438804|emb|CAJ43367.1| RNA polymerase alpha subunit [Lactobacillus gallinarum]
 gi|119662307|emb|CAJ33141.1| RNA polymerase alpha subunit [Lactobacillus gallinarum]
          Length = 217

 Score =  196 bits (498), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 96/202 (47%), Positives = 136/202 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+
Sbjct: 1   FVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK   D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V
Sbjct: 61  KKLELKSLSDERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDG
Sbjct: 121 QNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMF 231
           SI   D+++ A++IL +   +F
Sbjct: 181 SIKPNDALSFAAKILVEHFKVF 202


>gi|282849891|ref|ZP_06259274.1| DNA-directed RNA polymerase, alpha subunit [Veillonella parvula
           ATCC 17745]
 gi|282580328|gb|EFB85728.1| DNA-directed RNA polymerase, alpha subunit [Veillonella parvula
           ATCC 17745]
          Length = 334

 Score =  196 bits (498), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 120/298 (40%), Positives = 185/298 (62%), Gaps = 23/298 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE S+I G+ ED+TDIILN+
Sbjct: 23  FVCEPLDRGYGITLGNSLRRILLSSLDGAAITSIKIDGVLHEFSTIPGIREDVTDIILNL 82

Query: 90  KGINLKMSGDSHKRVTI---FKRGPGVVTAGDI--QTVNDIEVLNPDHVICNLDVDAVVR 144
           K + +K+  ++   + +   F++  G++TA D+  Q   ++EVLNP+ VI  +D  A + 
Sbjct: 83  KQLCIKVEEEAQLPLEVHFDFQK-DGILTAADLAEQFPPEVEVLNPELVIATMDETAHLV 141

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           M++ + +G GYVP+  ++ + D IG I ID+++SPI +  Y V   R G  +D+DKL++ 
Sbjct: 142 MDVVIERGKGYVPSTKNKKDTDVIGCIPIDSIFSPILRAKYEVSDVRVGNEMDFDKLTLE 201

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN----------VKSLPFNP 254
           + TDGSIT  D+VA ++ I+   LG F         V  D+N          V S    P
Sbjct: 202 VWTDGSITAADAVAKSAAIMIGYLGNFTKLAHSADVV--DVNTGEGGIVIDPVGSDNEEP 259

Query: 255 ALLK-----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           A+        ++ELELSVR+ NCL+   I  + DL+ +T  D+ ++ N G+KS+ EI+
Sbjct: 260 AVDDGPAKISIDELELSVRAYNCLKRAGINTIADLLDKTIDDLGKVRNLGKKSIDEIE 317


>gi|224531785|ref|ZP_03672417.1| DNA-directed RNA polymerase, alpha subunit [Borrelia valaisiana
           VS116]
 gi|224511250|gb|EEF81656.1| DNA-directed RNA polymerase, alpha subunit [Borrelia valaisiana
           VS116]
          Length = 344

 Score =  196 bits (497), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 126/340 (37%), Positives = 195/340 (57%), Gaps = 29/340 (8%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++K  ++   P  IE++   Q++ +       P  RGF  T+GN LRRVL+SS+ G AIT
Sbjct: 3   VEKFLKDFTIPEKIEFLK-SQDDGSYGKFTIYPFERGFGVTIGNTLRRVLLSSIEGYAIT 61

Query: 62  AVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI-FK--- 108
           A+++           V  E   I GV ED  ++I NIK I+LK+ G+  +R TI F    
Sbjct: 62  AMRVQSNNKDSSSKIVSSEFDLIPGVSEDTLEVIANIKNIHLKL-GEGEQRKTISFSISG 120

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
           +   V+ A   +  + +EV N D VI NL  DA +  E  ++ G GYV ++ +    + +
Sbjct: 121 KDTSVLKASHFER-DGVEVFNKDLVIANLSHDANLDFEFQINYGRGYVSSEQNSKYLEEV 179

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
            +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L
Sbjct: 180 NVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREFL 239

Query: 229 GMFINFEEPKKEVKEDINV-----KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGD 283
              ++FE       +++N+     KS  +N  L   +E+L+LSVRS NCL  EN+  +G+
Sbjct: 240 FPLVDFE-------DNVNISFEKSKSESYN-LLDMSIEKLDLSVRSLNCLAKENVRTLGE 291

Query: 284 LIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           LI +   ++ +  NFG+KSL EI   LG+  LFLGM+  D
Sbjct: 292 LISKNAEELSKARNFGKKSLEEIIEKLGSYRLFLGMSKED 331


>gi|308125195|gb|ADO14946.1| DNA-directed RNA polymerase alpha chain [Enterococcus sanguinicola]
          Length = 204

 Score =  196 bits (497), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 97/196 (49%), Positives = 138/196 (70%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+ LKM G   K 
Sbjct: 1   GNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGLALKMYGQEEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV  G GYV A  ++ 
Sbjct: 61  LEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTVKPGRGYVQADENKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI   ++++L+++I
Sbjct: 121 EDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIEPLEAMSLSAKI 180

Query: 224 LQDQLGMFINFEEPKK 239
           + + L +F+N  +  K
Sbjct: 181 MTEHLDIFVNLTDEAK 196


>gi|150187102|emb|CAK30171.1| RNA polymerase alpha subunit [Streptococcus agalactiae]
          Length = 219

 Score =  196 bits (497), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 94/210 (44%), Positives = 146/210 (69%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+
Sbjct: 1   FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNV 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +   GP  +TAGDI T +DIE++NPDH +  +     ++  +TV
Sbjct: 61  KGLAVKSYVEDEKIIELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIAEGHSLKATMTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 121 AKNRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           +I  ED++ L++R+L + L +F +  E  K
Sbjct: 181 TIIPEDALGLSARVLIEHLNLFTDLTEVAK 210


>gi|294794575|ref|ZP_06759711.1| DNA-directed RNA polymerase, alpha subunit [Veillonella sp. 3_1_44]
 gi|294454905|gb|EFG23278.1| DNA-directed RNA polymerase, alpha subunit [Veillonella sp. 3_1_44]
          Length = 334

 Score =  196 bits (497), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 120/298 (40%), Positives = 184/298 (61%), Gaps = 23/298 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE S+I G+ ED+TDIILN+
Sbjct: 23  FVCEPLDRGYGITLGNSLRRILLSSLDGAAITSIKIDGVLHEFSTIPGIREDVTDIILNL 82

Query: 90  KGINLKMSGDSHKRVTI---FKRGPGVVTAGDI--QTVNDIEVLNPDHVICNLDVDAVVR 144
           K + +K+  ++   + +   F++  G++TA D+  Q   ++EVLNP+ VI  +D  A   
Sbjct: 83  KQLCIKVEEEAQLPLEVHFDFQK-DGILTAADLAEQFPPEVEVLNPELVIATMDETAHFV 141

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           M++ + +G GYVP+  ++ + D IG I ID+++SPI +  Y V   R G  +D+DKL++ 
Sbjct: 142 MDVVIERGKGYVPSTKNKKDTDVIGCIPIDSIFSPILRAKYEVSDVRVGNEMDFDKLTLE 201

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN----------VKSLPFNP 254
           + TDGSIT  D+VA ++ I+   LG F         V  D+N          V S    P
Sbjct: 202 VWTDGSITAADAVAKSAAIMIGYLGNFTKLAHSADVV--DVNTGEGGIVIDPVGSDNEEP 259

Query: 255 ALLK-----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           A+        ++ELELSVR+ NCL+   I  + DL+ +T  D+ ++ N G+KS+ EI+
Sbjct: 260 AVDDGPAKISIDELELSVRAYNCLKRAGINTIADLLDKTIDDLGKVRNLGKKSIDEIE 317


>gi|119662363|emb|CAJ33170.1| RNA polymerase alpha subunit [Lactobacillus spicheri]
          Length = 210

 Score =  195 bits (496), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 98/208 (47%), Positives = 145/208 (69%), Gaps = 4/208 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK++G
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNVKKIALKLNG 60

Query: 99  --DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             D  + + I  +GP  VTAGDI    D++VLNPD  I  +   A   M +T  KG GYV
Sbjct: 61  ADDQEETMEINVKGPAQVTAGDIVAGADVDVLNPDLYIATVADGATFHMRMTADKGRGYV 120

Query: 157 PAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A  ++  N   PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ + T+GSI   
Sbjct: 121 SADENKARNTEMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDVWTNGSINPS 180

Query: 215 DSVALASRILQDQLGMFINFEEPKKEVK 242
           ++++LA++IL + L MF++  +  K  +
Sbjct: 181 EAISLAAKILTEHLAMFVDLTDEAKNAE 208


>gi|239618237|ref|YP_002941559.1| DNA-directed RNA polymerase, alpha subunit [Kosmotoga olearia TBF
           19.5.1]
 gi|239507068|gb|ACR80555.1| DNA-directed RNA polymerase, alpha subunit [Kosmotoga olearia TBF
           19.5.1]
          Length = 346

 Score =  195 bits (496), Expect = 7e-48,   Method: Compositional matrix adjust.
 Identities = 119/305 (39%), Positives = 177/305 (58%), Gaps = 24/305 (7%)

Query: 22  QEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +EE+N      +  P+ RG+A T+GNALRRVL+SS+   AIT ++I G  HE  +I GV 
Sbjct: 24  REEQNSYYAKFVLSPMERGYAVTIGNALRRVLLSSIPSMAITRLKIPGKYHEYDTIDGVK 83

Query: 80  EDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           ED+ +IILN+K + LK  +      +++I K+GP ++TAGDI+    +EV+NP   I  L
Sbjct: 84  EDILEIILNLKKVQLKPALEFSDPVKLSIEKKGPAILTAGDIKAPTGVEVVNPSQYIATL 143

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + DA V MEL    G G+VP      E D + +I ID ++SP+ KV++  E+ R G+  D
Sbjct: 144 NEDAAVYMELFAEIGKGFVPVSEMELEQD-VEMIYIDGIFSPVLKVNFISENVRVGKKTD 202

Query: 198 YDKLSMTIDTDGSITGEDSVALASRIL--------------QDQLGMFIN-----FEEPK 238
           YDKL + + T  SI   +++  A+ IL               D  G+ +N       E  
Sbjct: 203 YDKLILEVWTKKSIKPTEALLKATDILIKHFEVTTSSLNQVLDNSGILVNSASIFEPEEP 262

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +  +E +       +  L +++EELELSVRS NCL+ + I  +GDLI RTEAD+L++ NF
Sbjct: 263 QPEEEPVEEPISEEDSVLSRRIEELELSVRSLNCLKRDKINTIGDLISRTEADLLKIRNF 322

Query: 299 GRKSL 303
           G KS+
Sbjct: 323 GDKSM 327


>gi|269798523|ref|YP_003312423.1| DNA-directed RNA polymerase, subunit alpha [Veillonella parvula DSM
           2008]
 gi|294792821|ref|ZP_06757968.1| DNA-directed RNA polymerase, alpha subunit [Veillonella sp. 6_1_27]
 gi|269095152|gb|ACZ25143.1| DNA-directed RNA polymerase, alpha subunit [Veillonella parvula DSM
           2008]
 gi|294456720|gb|EFG25083.1| DNA-directed RNA polymerase, alpha subunit [Veillonella sp. 6_1_27]
          Length = 334

 Score =  195 bits (496), Expect = 8e-48,   Method: Compositional matrix adjust.
 Identities = 120/298 (40%), Positives = 185/298 (62%), Gaps = 23/298 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE S+I G+ ED+TDIILN+
Sbjct: 23  FVCEPLDRGYGITLGNSLRRILLSSLDGAAITSIKIDGVLHEFSTIPGIREDVTDIILNL 82

Query: 90  KGINLKMSGDSHKRVTI---FKRGPGVVTAGDI--QTVNDIEVLNPDHVICNLDVDAVVR 144
           K + +K+  ++   + +   F++  G++TA D+  Q   ++EVLNP+ VI  +D  A + 
Sbjct: 83  KQLCIKVEEEAQLPLEVHFDFQK-DGILTATDLAEQFPPEVEVLNPELVIATMDETAHLV 141

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           M++ + +G GYVP+  ++ + D IG I ID+++SPI +  Y V   R G  +D+DKL++ 
Sbjct: 142 MDVVIERGKGYVPSTKNKKDTDVIGCIPIDSIFSPILRAKYEVSDVRVGNEMDFDKLTLE 201

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN----------VKSLPFNP 254
           + TDGSIT  D+VA ++ I+   LG F         V  D+N          V S    P
Sbjct: 202 VWTDGSITAADAVAKSAAIMIGYLGNFTKLAHSADVV--DVNTGEGGIVIDPVGSDNEEP 259

Query: 255 ALLK-----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           A+        ++ELELSVR+ NCL+   I  + DL+ +T  D+ ++ N G+KS+ EI+
Sbjct: 260 AVDDGPAKISIDELELSVRAYNCLKRAGINTIADLLDKTIDDLGKVRNLGKKSIDEIE 317


>gi|162955842|gb|ABY25296.1| RNA polymerase alpha subunit [Vibrio sp. MSSRF7]
          Length = 240

 Score =  195 bits (496), Expect = 8e-48,   Method: Compositional matrix adjust.
 Identities = 105/231 (45%), Positives = 158/231 (68%), Gaps = 8/231 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 12  EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 71

Query: 93  NLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS 150
            ++++ G     +T+ K G G V AGDI    D+E++NP+HVIC+L D +A V M + V 
Sbjct: 72  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLNDDNAEVAMRIKVQ 131

Query: 151 KGHGYVP--AKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVP  A+ H  E+D PIG + +DA YSP+ K++YTVE+AR  Q  D DKL + ++T
Sbjct: 132 RGRGYVPASARIHTDEDDRPIGRLLVDATYSPVDKIAYTVEAARVEQRTDLDKLVIDMET 191

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           +G+I  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+
Sbjct: 192 NGTIEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLR 239


>gi|150187156|emb|CAK30183.1| RNA polymerase alpha subunit [Streptococcus halichoeri]
          Length = 223

 Score =  195 bits (496), Expect = 8e-48,   Method: Compositional matrix adjust.
 Identities = 95/210 (45%), Positives = 146/210 (69%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+
Sbjct: 1   FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNV 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV
Sbjct: 61  KGLAVKSYVEDEKIIELDVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLKATMTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 121 AKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           +I  ED++ L++R+L + L +F +  E  K
Sbjct: 181 TIIPEDALGLSARVLIEHLNLFTDLTEVAK 210


>gi|289524824|emb|CBJ94468.1| alpha subunit of RNA polymerase [Vibrio sp. Cmf 6.5]
          Length = 241

 Score =  195 bits (495), Expect = 9e-48,   Method: Compositional matrix adjust.
 Identities = 103/242 (42%), Positives = 160/242 (66%), Gaps = 8/242 (3%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVT 115
           G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ + ++ G     +T+ K G G V 
Sbjct: 3   GCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVCVAEGKDEVFITLNKSGSGPVV 62

Query: 116 AGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLI 171
           AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG +
Sbjct: 63  AGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRL 122

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F
Sbjct: 123 LVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAF 182

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           ++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE +
Sbjct: 183 VDLRDVRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVE 239

Query: 292 ML 293
           +L
Sbjct: 240 LL 241


>gi|161511771|emb|CAP16896.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 229

 Score =  195 bits (495), Expect = 9e-48,   Method: Compositional matrix adjust.
 Identities = 101/211 (47%), Positives = 142/211 (67%), Gaps = 2/211 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAITSVQIDSVLHEFSTIEGVVEDVTQIILNLKKVS 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK+  D  K + I   GP  VTAGDI    D+ +LNP+  IC +         LT   G 
Sbjct: 61  LKIESDEDKTLEINVAGPANVTAGDIMGDGDVVILNPELPICTVAEGTTFHAVLTADTGR 120

Query: 154 GYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A  +  R  + PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ I TDGSI
Sbjct: 121 GYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDIWTDGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           T  ++ +L+++IL + L +F+N  +  KE +
Sbjct: 181 TPSEATSLSAKILTEHLAIFVNLNDQAKETE 211


>gi|161511747|emb|CAP16884.1| DNA-directed RNA polymerase subunit alpha [Pediococcus inopinatus]
          Length = 215

 Score =  195 bits (495), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 95/200 (47%), Positives = 140/200 (70%), Gaps = 2/200 (1%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNIK ++LK+  D  K +
Sbjct: 1   NSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNIKKVSLKIESDDEKSL 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A  ++  
Sbjct: 61  EIDVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAILTADTGRGYVSADENKAR 120

Query: 165 ND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            D  PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSI+  ++ +L+++
Sbjct: 121 KDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSISPSEATSLSAK 180

Query: 223 ILQDQLGMFINFEEPKKEVK 242
           IL + L +F+N  +  K+ +
Sbjct: 181 ILTEHLALFVNLTDEAKDAE 200


>gi|168805075|gb|ACA28616.1| DNA-directed RNA polymerase subunit alpha [Thiomonas perometabolis]
          Length = 228

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 100/228 (43%), Positives = 149/228 (65%), Gaps = 3/228 (1%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           G+ ED+  ++LN+KG+ LK+       +++ K G GVVTA DIQT +D+E++NPDHVI +
Sbjct: 1   GLQEDVIGVLLNLKGVVLKLHNRDEVTLSLRKEGEGVVTAADIQTPHDVEIINPDHVIAH 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSYTVESAREG 193
           L     + M++ V KG GYVP        +    IG I +DA +SP+++VSY VESAR  
Sbjct: 61  LSQGGKLDMQIKVEKGRGYVPGTLRNFGEEGGKSIGHIVLDASFSPVRRVSYAVESARVE 120

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL M I+T+G I+ E+++  ++RIL +QL +F + E  +     +    +  ++
Sbjct: 121 QRTDLDKLVMEIETNGVISAEEAIRSSARILVEQLSVFASLEGAEATEAAEAAAGAQTYD 180

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GRK
Sbjct: 181 PILLRPVDELELTVRSANCLKAENIYYIGDLIQRSETELLKTPNLGRK 228


>gi|168805065|gb|ACA28611.1| DNA-directed RNA polymerase subunit alpha [Thiomonas sp. CB1]
 gi|168805067|gb|ACA28612.1| DNA-directed RNA polymerase subunit alpha [Thiomonas sp. 3As]
 gi|168805069|gb|ACA28613.1| DNA-directed RNA polymerase subunit alpha [Thiomonas sp. CB3]
 gi|168805071|gb|ACA28614.1| DNA-directed RNA polymerase subunit alpha [Thiomonas sp. CB6]
 gi|168805073|gb|ACA28615.1| DNA-directed RNA polymerase subunit alpha [Thiomonas sp. CB2]
          Length = 228

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 100/228 (43%), Positives = 148/228 (64%), Gaps = 3/228 (1%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           G+ ED+  ++LN+KG+ LK+       +++ K G GVVTA DIQT +D+E++NPDHVI +
Sbjct: 1   GLQEDVIGVLLNLKGVVLKLHNRDEVTLSLRKEGEGVVTAADIQTPHDVEIINPDHVIAH 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSYTVESAREG 193
           L     + M++ V KG GYVP        +    IG I +DA +SP+++VSY VESAR  
Sbjct: 61  LSQGGKLDMQIKVEKGRGYVPGTLRNFGEEGGKSIGHIVLDASFSPVRRVSYAVESARVE 120

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL M I+T+G I+ E+++  ++RIL +QL +F + E  +     +       ++
Sbjct: 121 QRTDLDKLVMEIETNGVISAEEAIRSSARILVEQLSVFASLEGAETTEAAEAAAGGQTYD 180

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GRK
Sbjct: 181 PILLRPVDELELTVRSANCLKAENIYYIGDLIQRSETELLKTPNLGRK 228


>gi|197941213|gb|ACH78326.1| RNA polymerase [Streptococcus equi subsp. zooepidemicus]
          Length = 226

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 94/210 (44%), Positives = 146/210 (69%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+
Sbjct: 1   FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIRIDGVLHEFDTIPGVREDVMQIILNV 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV
Sbjct: 61  KGLAVKSYVEDEKIIELDVEGPAEVTAGDILTDSDIELVNPDHYLFTIADGYTLKASMTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 121 AKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           +I  ED++ L++R+L + L +F +  +  K
Sbjct: 181 TIIPEDALGLSARVLIEHLNLFTDLTDVAK 210


>gi|308125193|gb|ADO14945.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           saccharolyticus]
          Length = 204

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 96/196 (48%), Positives = 137/196 (69%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNIKG+ LKM G+  K 
Sbjct: 1   GNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNIKGLALKMYGEEEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I   GP  VTAGDI   +D+E+LN D  IC +         LTV  G GYV A  ++ 
Sbjct: 61  LEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGTTFHARLTVRPGRGYVQADENKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI   D+++LA++I
Sbjct: 121 EDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIEPLDAMSLAAKI 180

Query: 224 LQDQLGMFINFEEPKK 239
           + + L +F+N  +  K
Sbjct: 181 MTEHLDIFVNLTDEAK 196


>gi|329942432|ref|ZP_08291242.1| DNA-directed RNA polymerase, alpha subunit [Chlamydophila psittaci
           Cal10]
 gi|328815342|gb|EGF85330.1| DNA-directed RNA polymerase, alpha subunit [Chlamydophila psittaci
           Cal10]
          Length = 356

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 125/341 (36%), Positives = 185/341 (54%), Gaps = 22/341 (6%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
           G   + +   IAEPL RG  HTLGNALRR L+  L   AI +  + GVLHE  +I G+ E
Sbjct: 8   GGSVDKQASFIAEPLERGMGHTLGNALRRALLIGLEAPAIISFSMTGVLHEYMAINGIIE 67

Query: 81  DLTDIILNIKGINLK---MSGDSHKRVTIFKR--------------GPGVVTAGDIQTVN 123
           D+T+IILN+KG  LK        + R T   +              G   VT  D+    
Sbjct: 68  DVTNIILNLKGALLKKYPFQDSENGRCTQLLKSKVSIDASDLAACGGQKAVTLADLLQEG 127

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
             E +NPDHVI  +     + + L V+ G GY  ++    E+  +  I +DA +SP+  V
Sbjct: 128 GFESVNPDHVIFTVTQPMQLDITLRVAFGRGYTTSERIVLEDKGVNEIVLDAAFSPVVLV 187

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE  R GQ  D+D+L + ++TDG ++ ++++A +++IL     +F   +E K   +E
Sbjct: 188 NYFVEDTRVGQDTDFDRLILHVETDGRVSPKEALAFSTQILTKHFSIFEKMDEKKIVFEE 247

Query: 244 DINVKSLPFNPALLKKV---EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            I+++    +  L K V    E+ELSVRSTNCL   NI  +G+L+   E  +L+  NFG+
Sbjct: 248 AISIEKENKDDILHKLVLGINEIELSVRSTNCLSNANIETIGELVIMPEPRLLQFRNFGK 307

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           KSL EIK  L  M L LGM+L  +    ++++E  K Y DK
Sbjct: 308 KSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYADK 348


>gi|119668315|emb|CAK95458.1| RNA polymerase alpha subunit [Lactobacillus gallinarum]
          Length = 214

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 96/199 (48%), Positives = 135/199 (67%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K +
Sbjct: 2   EPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKL 61

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LK   D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V  G
Sbjct: 62  ELKSLSDERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNG 121

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI 
Sbjct: 122 RGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIK 181

Query: 213 GEDSVALASRILQDQLGMF 231
             D+++ A++IL +   +F
Sbjct: 182 PNDALSFAAKILVEHFKVF 200


>gi|195952671|ref|YP_002120961.1| DNA-directed RNA polymerase subunit alpha [Hydrogenobaculum sp.
           Y04AAS1]
 gi|229564248|sp|B4U772|RPOA_HYDS0 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|195932283|gb|ACG56983.1| DNA-directed RNA polymerase, alpha subunit [Hydrogenobaculum sp.
           Y04AAS1]
          Length = 319

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 113/320 (35%), Positives = 187/320 (58%), Gaps = 15/320 (4%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           +E I P  I +    ++++N    + EPL RG+  T+GNALRRVL+SS+ G+AITAV+I+
Sbjct: 2   KEFIFPMKIYW---EEKDKNYGRFVVEPLERGYGTTIGNALRRVLLSSIYGSAITAVKIE 58

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV HE S+I+GV ED+  II N+K +   +     + + + K  PGVV A DI+T  ++ 
Sbjct: 59  GVQHEFSTIEGVQEDVLQIIANLKNVRFDLKDSDLEILYLEKNAPGVVLASDIKTPPNVT 118

Query: 127 VLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           ++N D  I  ++  +  ++ME+ + +G GYV +       +  G + +DA +SPIK  ++
Sbjct: 119 IINKDAYIATINSANTTLKMEIRIERGKGYVMSDEMEQIGEA-GWVVLDADFSPIKVAAF 177

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN--FEEPK--KEV 241
            VE+ R G   DYDKL+  + T+G ++ + ++  A  ++   + M  N  +E P   + +
Sbjct: 178 RVEATRVGDRTDYDKLTFELTTNGVVSPDTAIQQAVELIVKHMNMLTNISYEVPTLPEPM 237

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
             D  ++ L F+      +EEL++S R+ N L+   +  +G+L+Q TE ++    N GRK
Sbjct: 238 PPDELMEKLTFS------IEELDISQRALNSLKRIGVTTIGELVQLTEDELKSSKNIGRK 291

Query: 302 SLVEIKGVLGTMGLFLGMNL 321
           +L EIK  L  MG  LGMN+
Sbjct: 292 ALTEIKEALKNMGFSLGMNI 311


>gi|313847669|emb|CBY16657.1| putative DNA-directed RNA polymerase alpha chain [Chlamydophila
           psittaci RD1]
 gi|325506783|gb|ADZ18421.1| DNA-directed RNA polymerase subunit alpha [Chlamydophila psittaci
           6BC]
 gi|328914306|gb|AEB55139.1| DNA-directed RNA polymerase, alpha subunit [Chlamydophila psittaci
           6BC]
          Length = 376

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 125/341 (36%), Positives = 185/341 (54%), Gaps = 22/341 (6%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
           G   + +   IAEPL RG  HTLGNALRR L+  L   AI +  + GVLHE  +I G+ E
Sbjct: 28  GGSVDKQASFIAEPLERGMGHTLGNALRRALLIGLEAPAIISFSMTGVLHEYMAINGIIE 87

Query: 81  DLTDIILNIKGINLK---MSGDSHKRVTIFKR--------------GPGVVTAGDIQTVN 123
           D+T+IILN+KG  LK        + R T   +              G   VT  D+    
Sbjct: 88  DVTNIILNLKGALLKKYPFQDSENGRCTQLLKSKVSIDASDLAACGGQKAVTLADLLQEG 147

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
             E +NPDHVI  +     + + L V+ G GY  ++    E+  +  I +DA +SP+  V
Sbjct: 148 GFESVNPDHVIFTVTQPMQLDITLRVAFGRGYTTSERIVLEDKGVNEIVLDAAFSPVVLV 207

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE  R GQ  D+D+L + ++TDG ++ ++++A +++IL     +F   +E K   +E
Sbjct: 208 NYFVEDTRVGQDTDFDRLILHVETDGRVSPKEALAFSTQILTKHFSIFEKMDEKKIVFEE 267

Query: 244 DINVKSLPFNPALLKKV---EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            I+++    +  L K V    E+ELSVRSTNCL   NI  +G+L+   E  +L+  NFG+
Sbjct: 268 AISIEKENKDDILHKLVLGINEIELSVRSTNCLSNANIETIGELVIMPEPRLLQFRNFGK 327

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           KSL EIK  L  M L LGM+L  +    ++++E  K Y DK
Sbjct: 328 KSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYADK 368


>gi|119662361|emb|CAJ33169.1| RNA polymerase alpha subunit [Lactobacillus zymae]
          Length = 202

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 98/199 (49%), Positives = 143/199 (71%), Gaps = 4/199 (2%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--D 99
           TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK++G  D
Sbjct: 2   TLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNVKKIALKLNGADD 61

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             + + I  +GP  VTAGDI    D++VLNPD  I  +   A   M +T  KG GYV A 
Sbjct: 62  QEETMEINVKGPAQVTAGDIVAGADVDVLNPDLYIATVADGATFHMRMTADKGRGYVSAD 121

Query: 160 HHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
            ++T N   PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ + T+GSI   +++
Sbjct: 122 ENKTRNTEMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDVWTNGSINPSEAI 181

Query: 218 ALASRILQDQLGMFINFEE 236
           +LA++IL + L MF++  +
Sbjct: 182 SLAAKILTEHLAMFVDLTD 200


>gi|158148899|dbj|BAF81984.1| RNA polymerase alpha subunit [Lactobacillus senmaizukei]
          Length = 199

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 98/197 (49%), Positives = 142/197 (72%), Gaps = 4/197 (2%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--D 99
           TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+K I LK++G  D
Sbjct: 3   TLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVTQIILNVKKIALKLNGSDD 62

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             + + I  +GP  VTAGDI T  D++VLNPD  I  +   A   M +T  KG GYV A 
Sbjct: 63  QEETMEINVKGPAQVTAGDIVTGADVDVLNPDLYIATVADGATFHMRMTADKGRGYVSAD 122

Query: 160 HHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
            ++  N   PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ + T+GSI   +++
Sbjct: 123 ENKARNTDMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDVWTNGSINPSEAI 182

Query: 218 ALASRILQDQLGMFINF 234
           ALA++IL + L MF++ 
Sbjct: 183 ALAAKILTEHLAMFVDL 199


>gi|220906743|ref|YP_002482054.1| DNA-directed RNA polymerase subunit alpha [Cyanothece sp. PCC 7425]
 gi|219863354|gb|ACL43693.1| DNA-directed RNA polymerase, alpha subunit [Cyanothece sp. PCC
           7425]
          Length = 314

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 111/297 (37%), Positives = 171/297 (57%), Gaps = 16/297 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG   T+GNALRRVL+S+L+G A+TAV+I GV HE ++I GV ED  DI+L +
Sbjct: 22  FVLEPLERGQGTTVGNALRRVLLSNLKGTAVTAVRIAGVNHEFATIPGVREDALDILLRM 81

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L+      +   +F +GP  VTA + +   D+EV+N DH I  L  DA + ME  +
Sbjct: 82  KELVLRSYSPDPQIGRLFIQGPATVTAINFEVSPDVEVINLDHYIATLSADATLEMEFKI 141

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY   +  + E+  +  + IDA++ P++KV+YTVE AR G +++ D+L + I T+G
Sbjct: 142 EQGKGYRAIERGKDESASLDFLQIDAIFMPVRKVNYTVEDARSGGLVEKDRLVLEIWTNG 201

Query: 210 SITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
           S+T ++++   + IL D             EP    +ED     +P        +E L L
Sbjct: 202 SLTPQEALNQGASILVDLFNPLKDVPFRSSEPSHSTEED-ETNQIP--------IESLNL 252

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           SVR+ NCL+   I  + DL++ ++ D+L + NFG KS  E   V+  +   LG+ LP
Sbjct: 253 SVRAYNCLKRAQINTVADLLEYSQEDLLEIKNFGAKSAEE---VIEALHKNLGITLP 306


>gi|119662817|emb|CAJ33200.1| RNA polymerase alpha subunit [Lactobacillus homohiochii]
          Length = 205

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 99/199 (49%), Positives = 145/199 (72%), Gaps = 4/199 (2%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--K 102
           N+LRRVL++SL GAA+T++QIDGVLHE S++KGV ED+T IILN+K INLK++ D +  K
Sbjct: 1   NSLRRVLLASLPGAAVTSIQIDGVLHEFSTVKGVVEDVTQIILNVKKINLKINSDDNETK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            ++I   GP  VTAGDI T +D+E+LNPD  I  +   A   M +T +KG GYV A+ ++
Sbjct: 61  SMSINVTGPADVTAGDIVTDSDVEILNPDLHIATVADGATFHMNMTANKGRGYVSAEENK 120

Query: 163 TEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
            +ND  PIG++ +D++Y+PI++V+Y VE AR GQ  DYDKL++ + T+GSIT  D+++LA
Sbjct: 121 AKNDGMPIGVLPVDSIYTPIERVNYQVEDARVGQRDDYDKLTLDVWTNGSITPSDAISLA 180

Query: 221 SRILQDQLGMFINFEEPKK 239
           ++IL     +FI+  +  K
Sbjct: 181 AKILNQHFQLFIDLTDRAK 199


>gi|161511709|emb|CAP16865.1| DNA-directed RNA polymerase subunit alpha [Pediococcus inopinatus]
          Length = 204

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 95/200 (47%), Positives = 140/200 (70%), Gaps = 2/200 (1%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNIK ++LK+  D  K +
Sbjct: 1   NSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNIKKVSLKIESDDEKSL 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A  ++  
Sbjct: 61  EIDVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAILTADTGRGYVSADENKAR 120

Query: 165 ND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            D  PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSI+  ++ +L+++
Sbjct: 121 KDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSISPSEATSLSAK 180

Query: 223 ILQDQLGMFINFEEPKKEVK 242
           IL + L +F+N  +  K+ +
Sbjct: 181 ILTEHLALFVNLTDEAKDAE 200


>gi|270307868|ref|YP_003329926.1| DNA-directed RNA polymerase alpha subunit/40 kD subunit
           [Dehalococcoides sp. VS]
 gi|270153760|gb|ACZ61598.1| DNA-directed RNA polymerase alpha subunit/40 kD subunit
           [Dehalococcoides sp. VS]
          Length = 330

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 111/289 (38%), Positives = 169/289 (58%), Gaps = 3/289 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL +GF  T+GN+LRR+L+S L G AIT V+IDG+ HE S++    ED  D +LN+
Sbjct: 21  FVVEPLEKGFGTTMGNSLRRILLSYLDGVAITRVRIDGIQHEFSALPKAKEDTLDFLLNL 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV-DAVVRMELT 148
           K I ++        + +   G  VVTA DI+  ND  V+NP+  +  LD  DAV+ +EL 
Sbjct: 81  KNIRVESLSGLEGILYLRASGSKVVTAADIEPSNDFAVVNPELYLLTLDSDDAVLNVELE 140

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V  G GY P +   TEN PIG I +DA+++PI+KV++T E    G+    ++L + + TD
Sbjct: 141 VELGRGYRPPES--TENTPIGTIPVDAIFTPIRKVNFTTEPMHVGRETSLERLVLEVWTD 198

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++    +V+ ++ IL  Q    ++  +   EV+    VK           +E+L+LSVR
Sbjct: 199 GTVEPATAVSRSADILVKQFAALVSHSKVVAEVEASEPVKYAIPEEKYNMPIEQLDLSVR 258

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + NCLR   I  +G++I R   ++L + NFG KSL E++  L T+GL L
Sbjct: 259 AVNCLRHAGITTVGEVINRGTKELLTLRNFGLKSLTELEDRLKTIGLSL 307


>gi|154424745|emb|CAL18475.1| RNA polymerase alpha subunit [Streptococcus salivarius]
          Length = 214

 Score =  194 bits (493), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 93/206 (45%), Positives = 144/206 (69%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILNIKG+ 
Sbjct: 1   PLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGLA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +K   +  K + +  +GP  VTAGDI T +DIE++NPDH +  +   A ++  +TV+   
Sbjct: 61  VKSYVEDEKTIELDVQGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGASLKATMTVATNR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  
Sbjct: 121 GYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIP 180

Query: 214 EDSVALASRILQDQLGMFINFEEPKK 239
           ED++ L++R+L + L +F +  +  K
Sbjct: 181 EDALGLSARVLIEHLNLFTDLTDVAK 206


>gi|71056854|emb|CAH58982.1| DNA-directed RNA polymerase alpha chain [Enterococcus asini]
          Length = 204

 Score =  194 bits (493), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 96/199 (48%), Positives = 140/199 (70%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAIT++QIDGVLHE S++KGV ED+  IILNIKG+ LKM     K 
Sbjct: 1   GNSLRRILLSSLPGAAITSIQIDGVLHEFSTVKGVREDVAQIILNIKGLALKMYTQEEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV  G GYV A  ++ 
Sbjct: 61  LEIDIAGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTVKPGRGYVQADENKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI   ++++LA++I
Sbjct: 121 EDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSILPLEAMSLAAKI 180

Query: 224 LQDQLGMFINFEEPKKEVK 242
           + + L +F+N  +  K V+
Sbjct: 181 MTEHLDIFVNLTDEAKNVE 199


>gi|154424747|emb|CAL18476.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
          Length = 216

 Score =  194 bits (493), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 94/206 (45%), Positives = 141/206 (68%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRRVL++SL GAA+T++ IDGVLHE  ++ GV ED+  IILNIKGI +K 
Sbjct: 2   RGYGTTLGNSLRRVLLASLPGAAVTSINIDGVLHEFDTVPGVREDVMQIILNIKGIAVKS 61

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             +  K + +   GP  VTAGDI T +DIE++NPDH +  +   + ++  +TV+ G GYV
Sbjct: 62  YVEDEKIIELDVEGPAEVTAGDILTDSDIEIVNPDHYLFTIGEGSSLKATMTVNSGRGYV 121

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
           PA  ++ +N P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED+
Sbjct: 122 PADENKKDNAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDA 181

Query: 217 VALASRILQDQLGMFINFEEPKKEVK 242
           + L++RIL + L +F N  E  K  +
Sbjct: 182 LGLSARILTEHLDLFTNLTEIAKSTE 207


>gi|320335496|ref|YP_004172207.1| DNA-directed RNA polymerase subunit alpha [Deinococcus maricopensis
           DSM 21211]
 gi|319756785|gb|ADV68542.1| DNA-directed RNA polymerase subunit alpha [Deinococcus maricopensis
           DSM 21211]
          Length = 321

 Score =  194 bits (492), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 118/300 (39%), Positives = 175/300 (58%), Gaps = 17/300 (5%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  T+GN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED+  +ILN+K +
Sbjct: 22  EPLKRGYGVTIGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVIQLILNLKEL 81

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K      K +T+  +G GVVTAG  +  +D E++NPD VI NL  D  + ME+ V +G
Sbjct: 82  VVKFHAPGPKTLTLRAQGQGVVTAGAFEVPSDAEIVNPDLVIANLAEDGKLVMEVRVEEG 141

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYVPA  H T+ D I  I +DA+YSP+++V+Y VE+ R GQ  D D+L + I TDGS  
Sbjct: 142 EGYVPADKHATK-DRINSIPVDAVYSPVRRVAYHVENTRVGQQTDLDRLIIRIWTDGSAD 200

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEV-----------KEDINVKSLPFNPALLKK-- 259
            + ++ +A   L+D+L +F N E  + E               +++   P+ PA L    
Sbjct: 201 PQSALDMAVDTLRDELSVFGNVETIQAETVVTPAAYDLPQPSALSINPQPY-PADLDSPK 259

Query: 260 --VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +E L L+ R  + L+ E I  +  L   ++ D+ ++   G +SL EIK  L   GL L
Sbjct: 260 VTLEGLGLTTRVLHSLKEEGIDSVDALCALSDRDLKKVPGIGERSLDEIKAQLAQFGLSL 319


>gi|119662319|emb|CAJ33147.1| RNA polymerase alpha subunit [Lactobacillus kalixensis]
          Length = 208

 Score =  194 bits (492), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 94/199 (47%), Positives = 137/199 (68%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K +
Sbjct: 1   EPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LK   D  K + +   GP  VTA D++  +D++VLNPD  IC++     + M++ V  G
Sbjct: 61  ELKSLSDEQKVIELDVEGPATVTADDLKVDSDVQVLNPDQYICSIAEGGHLHMQIAVKNG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  +++++ PIG+I +D+L+SPIKKV+Y VE+ R G+  D+DKL+  I TDGSI 
Sbjct: 121 RGYVAANDNKSDDMPIGVIPVDSLFSPIKKVNYQVEATRVGKRDDFDKLTFEIWTDGSIN 180

Query: 213 GEDSVALASRILQDQLGMF 231
             D+++ A++IL +   +F
Sbjct: 181 PNDALSFAAKILVEHFKVF 199


>gi|57234751|ref|YP_181246.1| DNA-directed RNA polymerase subunit alpha [Dehalococcoides
           ethenogenes 195]
 gi|90110837|sp|Q3Z953|RPOA_DEHE1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|57225199|gb|AAW40256.1| DNA-directed RNA polymerase, alpha subunit [Dehalococcoides
           ethenogenes 195]
          Length = 330

 Score =  194 bits (492), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 112/289 (38%), Positives = 169/289 (58%), Gaps = 3/289 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL +GF  T+GN+LRR+L+S L G AIT V+IDG+ HE S++    ED  D +LN+
Sbjct: 21  FVVEPLEKGFGTTMGNSLRRILLSYLDGVAITRVRIDGIQHEFSALPKAKEDTLDFLLNL 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV-DAVVRMELT 148
           K I ++        + +   G  VVTA DI+  ND EV+NP+  +  LD  DAV+ +EL 
Sbjct: 81  KNIRVESLSGLEGILYLKASGAKVVTAADIEPSNDFEVVNPELYLLTLDSDDAVLNVELE 140

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V  G GY   +   TEN PIG I +DA+++PI+KV++T E    G+    ++L + + TD
Sbjct: 141 VELGRGYRAPES--TENTPIGTIPVDAIFTPIRKVNFTTEPMHVGRETSLERLVLEVWTD 198

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G+I    +V+ ++ IL  Q    ++  +   EV+    VK           +E+L+LSVR
Sbjct: 199 GTIEPATAVSRSADILVKQFAALVSHNKVVAEVEASEPVKYAIPEEKYNMPIEQLDLSVR 258

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + NCLR   I  +G++I R   ++L + NFG KSL E++  L T+GL L
Sbjct: 259 AVNCLRHAGITTVGEVINRGTKELLTLRNFGLKSLTELEDRLKTIGLSL 307


>gi|297180261|gb|ADI16480.1| DNA-directed RNA polymerase, alpha subunit/40 kd subunit
           [uncultured bacterium HF4000_05M23]
          Length = 362

 Score =  194 bits (492), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 109/292 (37%), Positives = 177/292 (60%), Gaps = 9/292 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + + EE     +AEPL RG+  TLGN +RR L+++L G AIT V+IDG+ HE S++K 
Sbjct: 26  ITIQENEETYGRFVAEPLERGWGVTLGNPIRRSLLNALSGTAITWVRIDGIHHEYSTVKH 85

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           + E++ + +LN+KGI L+   D   R+ +   G G V AGDI    D E++NP+H +  L
Sbjct: 86  MREEVVEFLLNVKGIRLRSLADRPGRLRLEVDGEGEVRAGDIMATADFEIVNPEHHLATL 145

Query: 138 D-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           D   A + +E  V +G GY PA H   E  PIG++ +DA+++P++K ++ VE+ R GQ  
Sbjct: 146 DNGGARLSVEFNVEQGVGYEPANHE--EGLPIGVLPVDAIFTPVRKANFAVEATRVGQRS 203

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-FNPA 255
           D ++L + + TD +IT  D+V  A  +L ++  +F   ++P    ++D  V  +P   P 
Sbjct: 204 DLERLVVEVWTDRTITPLDAVRAAGNLLMERFFLFKRLDKP----QDDEEVLGVPGVLPE 259

Query: 256 LLKK-VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           +    VE L LS R+ NCL+   I  +G+++   + ++L++ NFG+KSL E+
Sbjct: 260 VFNTLVETLSLSARTLNCLKRAGINRVGEVLMMPKGELLKIRNFGQKSLDEL 311


>gi|5107487|pdb|1BDF|A Chain A, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit
           N-Terminal Domain
 gi|5107488|pdb|1BDF|B Chain B, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit
           N-Terminal Domain
 gi|5107489|pdb|1BDF|C Chain C, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit
           N-Terminal Domain
 gi|5107490|pdb|1BDF|D Chain D, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit
           N-Terminal Domain
          Length = 235

 Score =  194 bits (492), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 101/237 (42%), Positives = 153/237 (64%), Gaps = 7/237 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALR +L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRAILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++ 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDL 234


>gi|119668343|emb|CAK95510.1| RNA polymerase alpha subunit [Lactobacillus paracasei subsp.
           paracasei]
          Length = 214

 Score =  193 bits (491), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 95/201 (47%), Positives = 142/201 (70%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNIK + LKM+ 
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNT 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV KG GYV A
Sbjct: 61  DEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++
Sbjct: 121 DQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAIS 180

Query: 219 LASRILQDQLGMFINFEEPKK 239
           LA++IL + L +F+N  +  K
Sbjct: 181 LAAKILTEHLDIFVNLTDEAK 201


>gi|119668313|emb|CAK95457.1| RNA polymerase alpha subunit [Lactobacillus fructivorans KCTC 3543]
          Length = 192

 Score =  193 bits (491), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 98/192 (51%), Positives = 142/192 (73%), Gaps = 4/192 (2%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH-- 101
           GN+LRRVL++SL GAA+T++QIDGVLHE S++KGV ED+T IILN+K INLK++ D +  
Sbjct: 1   GNSLRRVLLASLPGAAVTSIQIDGVLHEFSTVKGVVEDVTQIILNVKKINLKINSDDNET 60

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K ++I   GP  VTAGDI T +D+E+LNPD  I  +   A   M +T +KG GYV A+ +
Sbjct: 61  KSMSINVTGPADVTAGDIVTDSDVEILNPDLHIATVADGATFHMNMTANKGRGYVSAEEN 120

Query: 162 RTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           + +ND  PIG++ +D++Y+PI++V+Y VE AR GQ  DYDKL++ + T+GSIT  D+++L
Sbjct: 121 KAKNDGMPIGVLPVDSIYTPIERVNYQVEDARVGQRDDYDKLTLDVWTNGSITPSDAISL 180

Query: 220 ASRILQDQLGMF 231
           A++IL     +F
Sbjct: 181 AAKILNQHFQLF 192


>gi|188996211|ref|YP_001930462.1| DNA-directed RNA polymerase, alpha subunit [Sulfurihydrogenibium
           sp. YO3AOP1]
 gi|188931278|gb|ACD65908.1| DNA-directed RNA polymerase, alpha subunit [Sulfurihydrogenibium
           sp. YO3AOP1]
          Length = 324

 Score =  193 bits (490), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 123/294 (41%), Positives = 172/294 (58%), Gaps = 6/294 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +  EPL RGF  T+GNALRRVL+SSL G AITAV+I GV HE ++IKGV ED+ +I+LN+
Sbjct: 26  LYVEPLERGFGITIGNALRRVLLSSLPGGAITAVKIMGVPHEFTTIKGVLEDVVEIVLNL 85

Query: 90  KGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           K I LK+  +  +   I +    G V A DI+    IE++ PD  IC +     ++ME  
Sbjct: 86  KQIRLKIDENIERDFAILEAENVGKVYAKDIKFPAGIELVTPDVHICTISEPTKLQMEFR 145

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V +G GY   +     ++ IG I ID  +SPI+KV++ VE  R G   DYDKL + I+TD
Sbjct: 146 VERGIGYKTVEELEPISE-IGWIIIDTAFSPIRKVAFNVEPTRVGDKTDYDKLILEIETD 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEV-KEDINVKSLPFN---PALLKKVEELE 264
           G+IT ++++  AS IL D   +       K +V K+ +  KS         L   ++ELE
Sbjct: 205 GTITPDEALTKASNILIDHFNILQKPTVKKVQVIKKTVAPKSEEIKIEEDKLSLSIDELE 264

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           +S R+ N LR   I  +GDL++ +E D+    + GRKSL EIK  L  MGL L 
Sbjct: 265 ISSRAINTLRKLGINTIGDLVRLSEEDLREAKSIGRKSLKEIKDALAEMGLELA 318


>gi|89898699|ref|YP_515809.1| DNA-directed RNA polymerase subunit alpha [Chlamydophila felis
           Fe/C-56]
 gi|119366672|sp|Q252X4|RPOA_CHLFF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|89332071|dbj|BAE81664.1| DNA-directed RNA polymerase alpha chain [Chlamydophila felis
           Fe/C-56]
          Length = 376

 Score =  193 bits (490), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 121/332 (36%), Positives = 184/332 (55%), Gaps = 22/332 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +AEPL RG  HTLGNALRR L+  L   AI +  + GVLHE  +I+G+ ED+T+I+LN+
Sbjct: 37  FVAEPLERGMGHTLGNALRRALLIGLEAPAIISFSMTGVLHEYMAIEGIIEDVTNIVLNL 96

Query: 90  KGINLK----MSGDSHKRVTIFKR-------------GPGVVTAGDIQTVNDIEVLNPDH 132
           KG  LK       +  +R  + K              G   VT  D+      E +NP+H
Sbjct: 97  KGALLKKYPFQDSEDGRRPQLLKSMISIDASDLAACGGQRAVTLADLLQEGGFEAVNPEH 156

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           VI  +     V + L V+ G GY  ++    E+  +  I +DA +SP+  V+Y VE  R 
Sbjct: 157 VIFTVTQPMQVEVALRVAFGRGYSTSERIILEDKGVNEIVLDAAFSPVVLVNYFVEDTRV 216

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           GQ  D+D+L + ++TDG ++ ++++A +++IL     +F   +E K   +E I+++    
Sbjct: 217 GQDTDFDRLILYVETDGRVSPKEALAFSTQILTKHFSIFEKMDEKKIVFEEAISIEKENK 276

Query: 253 NPALLKKV---EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           +  L K V    E+ELSVRSTNCL   NI  +G+L+   E  +L+  NFG+KSL EIK  
Sbjct: 277 DDILHKLVLGINEIELSVRSTNCLSNANIETIGELVIMPEPRLLQFRNFGKKSLCEIKNK 336

Query: 310 LGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 337 LKEMKLELGMDLSQFGVGLDNVKEKMKWYAEK 368


>gi|288818044|ref|YP_003432391.1| DNA-directed RNA polymerase alpha subunit [Hydrogenobacter
           thermophilus TK-6]
 gi|288787443|dbj|BAI69190.1| DNA-directed RNA polymerase alpha subunit [Hydrogenobacter
           thermophilus TK-6]
 gi|308751645|gb|ADO45128.1| DNA-directed RNA polymerase, alpha subunit [Hydrogenobacter
           thermophilus TK-6]
          Length = 316

 Score =  193 bits (490), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 119/320 (37%), Positives = 187/320 (58%), Gaps = 15/320 (4%)

Query: 7   QELIKPNNIEYIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           +E + P+ + +     EE  +T    + EPL RGF  TLGN+LRR L+SS++G AITAV+
Sbjct: 3   REFLFPSKVYW-----EERGKTYGRFVVEPLERGFGITLGNSLRRTLLSSIQGTAITAVK 57

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           I G+ HE S I+GV ED+ ++I N+K I   +     + + + K+G G VTA DI    +
Sbjct: 58  IYGIYHEFSPIEGVQEDVLEVIANLKKIRFNLKSSDVETLYLKKKGEGTVTAKDITCPPN 117

Query: 125 IEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           ++++NPD  I  + D +  + ME+ + +G GY+  +      + +G I +DA +SP+++V
Sbjct: 118 VDIINPDQKIATITDPNKELNMEIRIERGFGYMTTEEMEVIGE-VGWILVDADFSPVRQV 176

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEV 241
           S+ VE  R  +  DYD+L M I T+G+ T E+ V  A  IL         I++E P   V
Sbjct: 177 SFRVEKTRVEKRSDYDRLIMEIYTNGTKTPEEVVKEAISILVKYFSSLEHISYELPV--V 234

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +E + V    F   L   VEEL++S R+ N ++   I  +GDL++ +E D+    N GRK
Sbjct: 235 EEPVIVDE--FAEKLSLPVEELDVSQRALNSIKRMGINTIGDLVRLSEEDLKGTKNVGRK 292

Query: 302 SLVEIKGVLGTMGLFLGMNL 321
           ++ EIK  L  MGL+LGM++
Sbjct: 293 AINEIKEALKQMGLYLGMDI 312


>gi|282891929|ref|ZP_06300408.1| hypothetical protein pah_c200o089 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281498189|gb|EFB40529.1| hypothetical protein pah_c200o089 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 371

 Score =  192 bits (489), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 126/345 (36%), Positives = 195/345 (56%), Gaps = 42/345 (12%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            IAEP  +GF HT+GN+LRR+++SSL   AI +V+I+G+ HE  +I+G+ ED+T+IILN+
Sbjct: 28  FIAEPFEKGFGHTVGNSLRRMMLSSLEAPAIVSVRIEGISHEYMAIEGIVEDMTNIILNL 87

Query: 90  KGINLKM--------SGDSHKRVTIFK---------RGPGVVTAGDIQTVNDIEVLNPDH 132
           KG  ++         S D     +I +          G   VT GD+ T  + EV+NP  
Sbjct: 88  KGALIRKLPLDDAPNSRDDRIVTSILEITQDDLDKNHGKYHVTLGDVFTEGNYEVVNPQL 147

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAK----HHRTENDPIGLITIDALYSPIKKVSYTVE 188
            +  +      +++L V  G GYVP+     H +T ++    I IDA +SP++ V+Y VE
Sbjct: 148 HLFTVTQPMKRQVDLRVVIGRGYVPSDRLDVHGKTSDE----ILIDAAFSPVRLVNYAVE 203

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN-------FEEPKKEV 241
           + R GQ  D+D+L + I TDG +T  +++A A++I    + +F +       F+E +   
Sbjct: 204 NTRVGQDTDFDRLLLEITTDGRVTPAEALAFAAQIGVKHMSVFTHINPHLLLFDEGQS-- 261

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           ++D +  ++    AL  +++E+ELSVRSTNCL G NI  + +L+   E  ML   NFG+K
Sbjct: 262 RDDADQDAIMAKLAL--RIDEIELSVRSTNCLSGANIDTIAELVSIPERRMLEFRNFGKK 319

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP------PESIEELAKKYEDKC 340
           SL EIK  L  MGL LGM+L  +        E I +  K+ +DK 
Sbjct: 320 SLNEIKAKLTEMGLHLGMDLSKYGITADNVKEKIAQYHKEAKDKS 364


>gi|150186982|emb|CAK30141.1| RNA polymerase alpha subunit [Streptococcus suis]
          Length = 205

 Score =  192 bits (489), Expect = 5e-47,   Method: Compositional matrix adjust.
 Identities = 93/200 (46%), Positives = 142/200 (71%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRVL++SL GAA+T+++IDGVLHE  ++ GV ED+  IILNIKGI +K   +  K
Sbjct: 1   LGNSLRRVLLASLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
           ++ +   GP  VTAGDI T +DIE++NPDH +  +   A  +  LTV+ G GYVPA+ ++
Sbjct: 61  KIELDVVGPAEVTAGDILTDSDIEIVNPDHYLFTIADGATFKAVLTVNSGRGYVPAEDNK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I+T+G+I  ED++ L++R
Sbjct: 121 KDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTLEINTNGTIIPEDALGLSAR 180

Query: 223 ILQDQLGMFINFEEPKKEVK 242
           IL + LG+F +  E  K  +
Sbjct: 181 ILMEHLGLFTDLTEVAKSAE 200


>gi|46446067|ref|YP_007432.1| DNA-directed RNA polymerase subunit alpha [Candidatus
           Protochlamydia amoebophila UWE25]
 gi|81627550|sp|Q6ME42|RPOA_PARUW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|46399708|emb|CAF23157.1| putative DNA-directed RNA polymerase alpha chain [Candidatus
           Protochlamydia amoebophila UWE25]
          Length = 371

 Score =  192 bits (489), Expect = 5e-47,   Method: Compositional matrix adjust.
 Identities = 120/341 (35%), Positives = 186/341 (54%), Gaps = 22/341 (6%)

Query: 18  IVLGQE--EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           I + QE  E N    +AEP  RGF HT+GNALRR+++SSL   AI +V+++G+ HE  +I
Sbjct: 14  ITVDQESPESNFARYVAEPFERGFGHTIGNALRRMMLSSLEAPAIISVRVEGIPHEYMAI 73

Query: 76  KGVHEDLTDIILNIKGINL-KMSGDSHKRVTIF--------------KRGPGVVTAGDIQ 120
           +G+ ED+T+IILN KG  L K+  +   R T                 +G   VT  D+ 
Sbjct: 74  EGISEDMTNIILNFKGALLRKLPTEETPRDTRILTKVVEVTQDDLDRNQGQYCVTLQDVV 133

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              + E++NP+  +  +      +++L ++ G GYVP++ H   +     I +DA +SP+
Sbjct: 134 QEGNFEIVNPELHLFTVTKPMRRQVDLRIAFGRGYVPSERHVVRDKTSDEILVDAAFSPV 193

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           + ++Y +E+ R GQ  D+D+L M + TDG IT  ++++ A +I      +F  F      
Sbjct: 194 RLINYFIENTRVGQDTDFDRLIMEVTTDGRITPAEALSFAVQIGLKHFEVFNQFNNYALS 253

Query: 241 VKE---DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
             E   D N         L   ++E+ELSVRS NCL G NI  + +L+   E  ML   N
Sbjct: 254 FDEKDGDRNGDQDELMDKLSLGIDEIELSVRSANCLTGANIETLAELVCIPERRMLEFRN 313

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDW--PPESIEELAKKY 336
           FG+KSL EIK  L  M L LGM+L  +   P+++++  K+Y
Sbjct: 314 FGKKSLNEIKAKLHEMSLHLGMDLSRFGVSPDNVKDKIKQY 354


>gi|73748344|ref|YP_307583.1| DNA-directed RNA polymerase subunit alpha [Dehalococcoides sp.
           CBDB1]
 gi|147669124|ref|YP_001213942.1| DNA-directed RNA polymerase subunit alpha [Dehalococcoides sp.
           BAV1]
 gi|289432392|ref|YP_003462265.1| DNA-directed RNA polymerase subunit alpha [Dehalococcoides sp. GT]
 gi|90110838|sp|Q3ZZP6|RPOA_DEHSC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|73660060|emb|CAI82667.1| DNA-directed RNA polymerase, alpha subunit [Dehalococcoides sp.
           CBDB1]
 gi|146270072|gb|ABQ17064.1| DNA-directed RNA polymerase subunit alpha [Dehalococcoides sp.
           BAV1]
 gi|288946112|gb|ADC73809.1| DNA-directed RNA polymerase, alpha subunit [Dehalococcoides sp. GT]
          Length = 330

 Score =  192 bits (488), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 109/289 (37%), Positives = 168/289 (58%), Gaps = 3/289 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL +GF  T+GN+LRR+L+S L G AIT V+IDG+ HE  ++    ED  D +LN+
Sbjct: 21  FVVEPLEKGFGTTMGNSLRRILLSYLDGVAITRVRIDGIQHEFCALPKAKEDTLDFLLNL 80

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV-DAVVRMELT 148
           K I ++        + +   G  VVTA DI+  ND EV+NP+  +  LD  DAV+ +EL 
Sbjct: 81  KNIRVESLSGLEGILYLRASGSKVVTAADIEPSNDFEVVNPELYLLTLDSDDAVLNVELE 140

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V  G GY P +    EN PIG I +DA+++PI+KV++T E    G+    ++L + + TD
Sbjct: 141 VELGRGYRPPES--AENTPIGTIPVDAIFTPIRKVNFTTEPMHVGRETSLERLVLEVWTD 198

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++    +V+ ++ IL  Q    ++  +   E++    VK           +E+L+LSVR
Sbjct: 199 GTVEPATAVSRSADILVKQFASLVSHSKVVAEIEASEPVKYTIPEEKYNMPIEQLDLSVR 258

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + NCLR   I  +G++I R   ++L + NFG KSL E++  L T+GL L
Sbjct: 259 AVNCLRHAGITTVGEVINRGTKELLTLRNFGLKSLTELEDRLKTIGLSL 307


>gi|282857336|ref|ZP_06266573.1| DNA-directed RNA polymerase, alpha subunit [Pyramidobacter
           piscolens W5455]
 gi|282584836|gb|EFB90167.1| DNA-directed RNA polymerase, alpha subunit [Pyramidobacter
           piscolens W5455]
          Length = 338

 Score =  192 bits (488), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 106/305 (34%), Positives = 175/305 (57%), Gaps = 17/305 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++  PL RG+  T+GNALRRVL+SS++GAAI+AV+++G  HE ++I G+ ED+ +++LN+
Sbjct: 20  LVIGPLERGYGQTIGNALRRVLLSSIKGAAISAVRVEGAQHEFTTIPGMKEDVIELLLNL 79

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + ++     ++ + +   G   VTA D Q  +DIE ++PD  IC L     + +E+ +
Sbjct: 80  KHVPVRSHSAEYRTLKLDVEGGKKVTAADFQEDSDIEFIDPDAYICTLAEGHSLSLEVYI 139

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY      R    P+  + IDA+YSPI +V Y V++ R GQ  DY+K+ M + T+G
Sbjct: 140 EQGVGYATVDRPRPSYLPVDALMIDAIYSPILRVKYEVQNERVGQKTDYEKIVMNVTTNG 199

Query: 210 SITGEDSVALASRILQDQLGMFI-----------------NFEEPKKEVKEDINVKSLPF 252
            +  + +VA A+++L++   + I                 +  +P    +      + P 
Sbjct: 200 VVAPDIAVAEAAKLLREYFDIVIQELRKLHPAEPGLFDDESASQPSGNGQAGDGADNPPE 259

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           N  L K V ELELS+RS NCL    I  +GDL+ R++ D+L++ N G+ SL EI+  +  
Sbjct: 260 NALLNKPVRELELSIRSENCLLRGGIHTIGDLVSRSKDDLLKIRNLGKISLREIEEKMTK 319

Query: 313 MGLFL 317
            G+ L
Sbjct: 320 YGIVL 324


>gi|150187161|emb|CAK30184.1| RNA polymerase alpha subunit [Streptococcus equi subsp.
           ruminatorum]
          Length = 225

 Score =  192 bits (488), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 94/210 (44%), Positives = 145/210 (69%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG   TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+
Sbjct: 1   FVIEPLERGNGTTLGNSLRRVLLSSLPGAAVTSIRIDGVLHEFDTIPGVREDVMQIILNV 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV
Sbjct: 61  KGLAVKSYVEDEKIIELDVEGPAEVTAGDILTDSDIELVNPDHYLFTIADGYTLKASMTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 121 AKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           +I  ED++ L++R+L + L +F +  +  K
Sbjct: 181 TIIPEDALGLSARVLIEHLNLFTDLTDVAK 210


>gi|168805061|gb|ACA28609.1| DNA-directed RNA polymerase subunit alpha [Thiomonas sp. Ynys1]
          Length = 228

 Score =  192 bits (488), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 99/228 (43%), Positives = 150/228 (65%), Gaps = 3/228 (1%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           G+ ED+  ++LN+KG+ LK+       +++ K G GVVTA DIQT +D+E++NP+HVI +
Sbjct: 1   GLQEDVIGVLLNLKGVVLKLHNRDEVTLSLRKDGEGVVTAADIQTPHDVEIINPEHVIAH 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSYTVESAREG 193
           L     + M++ V KG GYVP       ++    IG I +DA +SP+++VSY VESAR  
Sbjct: 61  LSHGGKLDMQIKVEKGRGYVPGTLRNYGDEGGKSIGHIVLDASFSPVRRVSYAVESARVE 120

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL M I+T+G I+ E+++  ++RIL +QL +F + E  +     +    +  ++
Sbjct: 121 QRTDLDKLVMEIETNGVISAEEAIRSSARILVEQLSVFASLEGAETTETAEAAAGAQTYD 180

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GRK
Sbjct: 181 PILLRPVDELELTVRSANCLKAENIYYIGDLIQRSETELLKTPNLGRK 228


>gi|62184758|ref|YP_219543.1| DNA-directed RNA polymerase subunit alpha [Chlamydophila abortus
           S26/3]
 gi|81313062|sp|Q5L6Z9|RPOA_CHLAB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|62147825|emb|CAH63571.1| putative DNA-directed RNA polymerase alpha chain [Chlamydophila
           abortus S26/3]
          Length = 376

 Score =  192 bits (487), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 124/341 (36%), Positives = 185/341 (54%), Gaps = 22/341 (6%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
           G   + +   IAEPL RG  HTLGNALRR L+  L   AI +  + GVLHE  +I G+ E
Sbjct: 28  GGSVDKQASFIAEPLERGMGHTLGNALRRALLIGLEAPAIISFSMTGVLHEYMAINGIIE 87

Query: 81  DLTDIILNIKGINLK---MSGDSHKRVTIFKR--------------GPGVVTAGDIQTVN 123
           D+T+IILN+KG  LK        + R T   +              G   VT  D+    
Sbjct: 88  DVTNIILNLKGALLKKYPFQDSENGRCTQLLKSKVSIDASDLAACGGQKAVTLADLLQEG 147

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
             E +NPD+VI  +     + + L V+ G GY  ++    E+  +  I +DA +SP+  V
Sbjct: 148 GFESVNPDYVIFTVTQPMQLDITLRVAFGRGYTTSERIVLEDKGVNEIVLDAAFSPVVLV 207

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE  R GQ  D+D+L + ++TDG ++ ++++A +++IL     +F   +E K   +E
Sbjct: 208 NYFVEDTRVGQDTDFDRLILHVETDGRVSPKEALAFSTQILTKHFSIFEKMDEKKIVFEE 267

Query: 244 DINVKSLPFNPALLKKV---EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            I+++    +  L K V    E+ELSVRSTNCL   NI  +G+L+   E  +L+  NFG+
Sbjct: 268 AISLEKENKDDILHKLVLGINEIELSVRSTNCLSNANIETIGELVIMPEPRLLQFRNFGK 327

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           KSL EIK  L  M L LGM+L  +    ++++E  K Y DK
Sbjct: 328 KSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYADK 368


>gi|119668339|emb|CAK95509.1| RNA polymerase alpha subunit [Lactobacillus kefiri]
          Length = 218

 Score =  192 bits (487), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 103/205 (50%), Positives = 141/205 (68%), Gaps = 4/205 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K I+LK+ G
Sbjct: 1   YGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKISLKLDG 60

Query: 99  --DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             D  + + I   GP  VTAGDIQ   D+ VLNPD  I  +   A   M LT +KG GYV
Sbjct: 61  PEDEEENLEIDVIGPADVTAGDIQADGDVTVLNPDLHIATVAEGATFHMRLTANKGRGYV 120

Query: 157 PA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A     R+   PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ I TDGSIT  
Sbjct: 121 SAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDIWTDGSITPS 180

Query: 215 DSVALASRILQDQLGMFINFEEPKK 239
           ++V+LA++IL + L MF++  +  K
Sbjct: 181 EAVSLAAKILTEHLEMFVDLTDEAK 205


>gi|119672813|emb|CAK95487.1| RNA polymerase alpha subunit [Lactobacillus gasseri]
          Length = 195

 Score =  192 bits (487), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 94/190 (49%), Positives = 136/190 (71%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL++S+ G A++ +QIDGVLHE S++ GV ED+T IILN+K + LK   D  K 
Sbjct: 1   GNSLRRVLLTSIPGTALSYIQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLSDEEKI 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
             I   GP +VTA D++  +DIEVLNPD  IC++     + M + +  G GYVPA  ++T
Sbjct: 61  AEIDVTGPAIVTAADLKVDSDIEVLNPDQYICSIADGGHLHMNVAIKNGRGYVPASENKT 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           ++ PIG+I +D+L+SPIKKV+Y VESAR G+  DYDKL++ I TDGSIT  D+++ A++I
Sbjct: 121 DDMPIGVIPVDSLFSPIKKVNYQVESARVGKRDDYDKLTLEIWTDGSITPNDALSFAAKI 180

Query: 224 LQDQLGMFIN 233
           L +   +F++
Sbjct: 181 LVEHFKVFMS 190


>gi|330444134|ref|YP_004377120.1| DNA-directed RNA polymerase subunit alpha [Chlamydophila pecorum
           E58]
 gi|328807244|gb|AEB41417.1| DNA-directed RNA polymerase, alpha subunit [Chlamydophila pecorum
           E58]
          Length = 374

 Score =  192 bits (487), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 127/339 (37%), Positives = 185/339 (54%), Gaps = 36/339 (10%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +AEPL +G  HTLGNALRR L+  L   AI +  + GVLHE  +I+G+ ED+T+IILN+
Sbjct: 35  FVAEPLEKGMGHTLGNALRRALLIGLEAPAIISFSMTGVLHEYMAIEGIIEDVTNIILNL 94

Query: 90  KGINLK---MSGDSHKRVTIFKR--------------GPGVVTAGDIQTVNDIEVLNPDH 132
           K   LK   M G    R T   +              G   VT GD+      E +NP+ 
Sbjct: 95  KSALLKKHPMQGSEEGRSTQLLKSSISIDASDLAAVGGQKEVTLGDLLQEGGFEAVNPEQ 154

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           VI  +     + + L V+ G GY  ++    E+  +  I +DA +SP+  V+Y VE  R 
Sbjct: 155 VIFTVTQPMQLDITLRVAFGRGYTTSERIVLEDKGVNEIVLDAAFSPVCLVNYYVEDTRV 214

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF-------INFEEP---KKEVK 242
           GQ  D+D+L + ++TDG IT ++++A +++IL     +F       I FEE    +KE K
Sbjct: 215 GQDTDFDRLILQVETDGRITPKEALAFSTQILTKHFSIFEKMDEKRIVFEEAVSIEKENK 274

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           +DI  K       L+  + E+ELSVRSTNCL   NI  +G+L+   E  +L+  NFG+KS
Sbjct: 275 DDILHK-------LILGINEIELSVRSTNCLSNANIETIGELVIMPEPRLLQFRNFGKKS 327

Query: 303 LVEIKGVLGTMGLFLGMNLPDW--PPESIEELAKKYEDK 339
           L EIK  L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 328 LCEIKNKLKEMKLELGMDLSQFGIGLDNVKEKMKWYAEK 366


>gi|119668365|emb|CAK95514.1| RNA polymerase alpha subunit [Lactobacillus rhamnosus]
          Length = 205

 Score =  192 bits (487), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 94/198 (47%), Positives = 141/198 (71%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED+T IILNIK + LKM+ D  
Sbjct: 2   TLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNTDED 61

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV KG GYV A  +
Sbjct: 62  KNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAADQN 121

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           ++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA+
Sbjct: 122 KSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAA 181

Query: 222 RILQDQLGMFINFEEPKK 239
           +IL + L +F+N  +  K
Sbjct: 182 KILTEHLDIFVNLTDEAK 199


>gi|291460745|ref|ZP_06600135.1| DNA-directed RNA polymerase, alpha subunit [Oribacterium sp. oral
           taxon 078 str. F0262]
 gi|291416704|gb|EFE90423.1| DNA-directed RNA polymerase, alpha subunit [Oribacterium sp. oral
           taxon 078 str. F0262]
          Length = 320

 Score =  192 bits (487), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 114/318 (35%), Positives = 189/318 (59%), Gaps = 21/318 (6%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KPN    +V   E+E     + EPL RG+  TLGN+L+R+++S+L G+A++A +I+G   
Sbjct: 6   KPNI--RVVEISEDERFGRFVCEPLERGYGTTLGNSLKRIMLSALPGSALSAAKIEGADF 63

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQT-VNDIE- 126
           +  S+ GV E L+++I+N+K + ++   DS   KR+ +   G GVV A  IQ    D E 
Sbjct: 64  QSGSVPGVKESLSELIMNLKSLAIRDLSDSEDAKRLILTAEGSGVVRASSIQAETADTEF 123

Query: 127 -VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
            + N +  I  L  +  +R+EL +S+G GYV A+    E  P G+  +D+ Y+P+++V+ 
Sbjct: 124 VIANEEQSIATLTGEEALRIELLLSRGRGYVSAEEQ--EELPEGMFALDSSYTPVERVNM 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE------EPKK 239
           +VE+ R G + DYDKL++ + TDG++  +D+++L++R+L  +L +F++        E   
Sbjct: 182 SVENTRVGNMTDYDKLTVDVFTDGTLPPDDALSLSARLLSTELCLFVDLSANAAAAEVMV 241

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           E  +D   K+L  N      ++ELELSVRS NCL+   I  + +L  +T  DM+++ N G
Sbjct: 242 EKTDDEKGKALEMN------IDELELSVRSYNCLKRAGINTVQELCSKTPEDMMKVRNLG 295

Query: 300 RKSLVEIKGVLGTMGLFL 317
           RKSL E+   L  + L L
Sbjct: 296 RKSLEEVLAKLKELNLSL 313


>gi|237756134|ref|ZP_04584706.1| DNA-directed RNA polymerase, alpha subunit [Sulfurihydrogenibium
           yellowstonense SS-5]
 gi|237691698|gb|EEP60734.1| DNA-directed RNA polymerase, alpha subunit [Sulfurihydrogenibium
           yellowstonense SS-5]
          Length = 325

 Score =  192 bits (487), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 121/298 (40%), Positives = 175/298 (58%), Gaps = 14/298 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +  EPL RGF  T+GNALRRVL+SSL G AITAV+I GV HE ++IKGV ED+ +I+LN+
Sbjct: 26  LYVEPLERGFGITIGNALRRVLLSSLPGGAITAVKIMGVPHEFTTIKGVIEDVAEIVLNL 85

Query: 90  KGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           K I LK+  +  +   I +    G V A DI+    IE++ PD  IC +     ++ME  
Sbjct: 86  KQIRLKIDENIERDFAILEAENVGKVYAKDIKFPAGIELVTPDVHICTISEPTKLQMEFR 145

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V +G GY   +     ++ IG I ID  +SPIK+V++ VE  R G   DYDKL + I+TD
Sbjct: 146 VERGIGYKTVEELEPISE-IGWIIIDTAFSPIKRVAFNVEPTRVGDKTDYDKLILEIETD 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK--------KV 260
           G+IT ++++  AS IL D   +    ++P  + K  +  K++   P  +K         +
Sbjct: 205 GTITPDEALTKASNILIDHFNI---LQKPTVK-KVQVIKKTVAPKPEEIKIEEDKLSLSI 260

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           +ELE+S R+ N LR   I  +GDL++ +E D+    + GRKS+ EIK  L  MGL L 
Sbjct: 261 DELEISSRAINNLRKLGINTIGDLVRLSEEDLKEAKSIGRKSIKEIKDALAEMGLELA 318


>gi|119672805|emb|CAK95518.1| RNA polymerase alpha subunit [Lactobacillus vaccinostercus]
          Length = 197

 Score =  192 bits (487), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 96/192 (50%), Positives = 143/192 (74%), Gaps = 2/192 (1%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRR+L++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K I+LK+  +  K
Sbjct: 1   LGNSLRRILLASLPGAAITSIQIDGVLHEFSTVEGVTEDVTQIILNMKQISLKIDSEEDK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + I  +GP  VTAGDI+   D+EVLNP+  I  +   A + +++T + G GYV A  ++
Sbjct: 61  TLEIDVKGPAAVTAGDIEADGDVEVLNPELHIATVADGAELHIQMTANTGRGYVSADDNK 120

Query: 163 TEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
              D  PIG++ ID++Y+PI++V+YTVE+AR GQ  DYDKL++ + +DGSIT  +S++LA
Sbjct: 121 ARMDDLPIGVLPIDSIYTPIERVNYTVENARVGQRNDYDKLTLDVWSDGSITPSESISLA 180

Query: 221 SRILQDQLGMFI 232
           ++IL + L MF+
Sbjct: 181 AKILTEHLAMFV 192


>gi|117575079|emb|CAJ84779.1| RNA polymerase alpha subunit [Lactobacillus amylotrophicus]
          Length = 202

 Score =  191 bits (486), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 93/195 (47%), Positives = 138/195 (70%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL++SL G+A++ VQIDGVLHE S+I GV ED+T IILN+K + LK   
Sbjct: 1   YGTTLGNSLRRVLLASLPGSAVSYVQIDGVLHEFSTIPGVLEDVTQIILNLKKLTLKSIA 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
              K   I   GP  VTAGD++  +++E+LNP+  I  +   A +RM + V +G GYVPA
Sbjct: 61  ADEKLAEIDVEGPATVTAGDLKVDDEVEILNPNQYIATVAEGAHLRMTVAVKQGRGYVPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG++ +D+L+SPI+KV+Y VE  R G+  DYDKL+M + TDGSIT  D+++
Sbjct: 121 DQNKSDDMPIGVVPVDSLFSPIEKVNYQVEGTRVGRNNDYDKLTMEVWTDGSITPNDALS 180

Query: 219 LASRILQDQLGMFIN 233
             ++IL + L +F+N
Sbjct: 181 FGAKILTEHLNVFMN 195


>gi|119484809|ref|ZP_01619291.1| DNA-directed RNA polymerase alpha subunit [Lyngbya sp. PCC 8106]
 gi|119457627|gb|EAW38751.1| DNA-directed RNA polymerase alpha subunit [Lyngbya sp. PCC 8106]
          Length = 314

 Score =  191 bits (486), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 113/295 (38%), Positives = 172/295 (58%), Gaps = 12/295 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG   T+GNALRRVL+S+L G A+TAV+I GV HE ++I GV ED+ +I+LN+
Sbjct: 23  FVLEPLDRGQGTTVGNALRRVLLSNLEGTAVTAVRIAGVNHEFATIPGVREDVLEILLNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L    +  +   +  +GP  VTAG     +++EV++ +  I  L   + + ME  V
Sbjct: 83  KEIVLNSYSNQRQIGRLLVQGPATVTAGHFDLPSEVEVVDKNQYIATLSPGSTLEMEFQV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GY     +R E   +  + IDA++ P++KV+YTVE AR G  L+ D+L + I T+G
Sbjct: 143 EKGTGYRAIDRNRDEATAVDFLQIDAVFMPVRKVNYTVEDARVGGSLEKDRLILDIWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           S+T +++++ A+ IL D       I  E  K +  +D+       +P     +EEL+LSV
Sbjct: 203 SLTPQEALSQAATILVDLFVPLKDITLESIKTDQTDDV-------DPTSQIPIEELQLSV 255

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ NCL+   I  + DL   T+ D+L + NFG+KS  E   V+  +   LG+ LP
Sbjct: 256 RAYNCLKRAQINSVADLRDYTQEDLLEIKNFGQKSAEE---VIEALQKRLGITLP 307


>gi|33301631|sp|Q824N1|RPOA_CHLCV RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 376

 Score =  191 bits (486), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 120/332 (36%), Positives = 182/332 (54%), Gaps = 22/332 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +AEPL RG  HTLGNALRR L+  L   AI +  + GVLHE  +I+G+ ED+T+I+LN+
Sbjct: 37  FVAEPLERGMGHTLGNALRRALLIGLEAPAIISFSMTGVLHEYMAIEGIVEDVTNIVLNL 96

Query: 90  KGINLK---MSGDSHKRVTIFKR--------------GPGVVTAGDIQTVNDIEVLNPDH 132
           KG  LK          R T   +              G   +T  D+      E +NPDH
Sbjct: 97  KGALLKKYPFQDSEDGRCTQLLKSTISVDASDLAACGGQKSITLADLLQEGGFESVNPDH 156

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           VI  +     + + L V+ G GY  ++    E+  +  I +DA +SP+  V+Y VE  R 
Sbjct: 157 VIFTVTQPMQLEIALRVAFGRGYSTSERIVLEDKGVNEIVLDAAFSPVVLVNYFVEDTRV 216

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           GQ  D+D+L + ++TDG ++ ++++A +++IL     +F   +E K   +E I+++    
Sbjct: 217 GQDTDFDRLILHVETDGRVSPKEALAFSTQILTKHFSIFEKMDEKKIVFEEAISIEKENK 276

Query: 253 NPALLKKV---EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           +  L K V    E+ELSVRSTNCL   NI  +G+L+   E  +L+  NFG+KSL EIK  
Sbjct: 277 DDILHKLVLGINEIELSVRSTNCLSNANIETIGELVIMPEPRLLQFRNFGKKSLCEIKNK 336

Query: 310 LGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 337 LKEMKLELGMDLSQFGVGLDNVKEKMKSYAEK 368


>gi|311990563|gb|ADQ26408.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           helveticus]
          Length = 243

 Score =  191 bits (486), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 103/243 (42%), Positives = 151/243 (62%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   D  K + +
Sbjct: 1   LRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLSDERKVIEL 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
              GP  VTA D++   D++VLNPD  IC +     + ME+ V  G GYV A  +++++ 
Sbjct: 61  DVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNGRGYVAASDNKSDDM 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++ A++IL +
Sbjct: 121 PIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVE 180

Query: 227 QLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQ 286
              +F + +   K  +  +  +       L   +EEL+LSVRS NCL+   I  + +L  
Sbjct: 181 HFKVFESADADTKFSEVMVEKEDDKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELTD 240

Query: 287 RTE 289
            TE
Sbjct: 241 MTE 243


>gi|29839882|ref|NP_828988.1| DNA-directed RNA polymerase subunit alpha [Chlamydophila caviae
           GPIC]
 gi|29834229|gb|AAP04866.1| DNA-directed RNA polymerase, alpha subunit [Chlamydophila caviae
           GPIC]
          Length = 393

 Score =  191 bits (486), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 120/332 (36%), Positives = 182/332 (54%), Gaps = 22/332 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +AEPL RG  HTLGNALRR L+  L   AI +  + GVLHE  +I+G+ ED+T+I+LN+
Sbjct: 54  FVAEPLERGMGHTLGNALRRALLIGLEAPAIISFSMTGVLHEYMAIEGIVEDVTNIVLNL 113

Query: 90  KGINLK---MSGDSHKRVTIFKR--------------GPGVVTAGDIQTVNDIEVLNPDH 132
           KG  LK          R T   +              G   +T  D+      E +NPDH
Sbjct: 114 KGALLKKYPFQDSEDGRCTQLLKSTISVDASDLAACGGQKSITLADLLQEGGFESVNPDH 173

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           VI  +     + + L V+ G GY  ++    E+  +  I +DA +SP+  V+Y VE  R 
Sbjct: 174 VIFTVTQPMQLEIALRVAFGRGYSTSERIVLEDKGVNEIVLDAAFSPVVLVNYFVEDTRV 233

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           GQ  D+D+L + ++TDG ++ ++++A +++IL     +F   +E K   +E I+++    
Sbjct: 234 GQDTDFDRLILHVETDGRVSPKEALAFSTQILTKHFSIFEKMDEKKIVFEEAISIEKENK 293

Query: 253 NPALLKKV---EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           +  L K V    E+ELSVRSTNCL   NI  +G+L+   E  +L+  NFG+KSL EIK  
Sbjct: 294 DDILHKLVLGINEIELSVRSTNCLSNANIETIGELVIMPEPRLLQFRNFGKKSLCEIKNK 353

Query: 310 LGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 354 LKEMKLELGMDLSQFGVGLDNVKEKMKSYAEK 385


>gi|119662295|emb|CAJ33134.1| RNA polymerase alpha subunit [Lactobacillus crispatus]
          Length = 212

 Score =  191 bits (485), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 95/197 (48%), Positives = 133/197 (67%)

Query: 35  LPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL 94
           L RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + L
Sbjct: 1   LERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLEL 60

Query: 95  KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHG 154
           K   D  K + +   GP  VTA D++   D++VLNPD  IC +     + MEL V  G G
Sbjct: 61  KSLSDEQKVIELDIEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMELAVKNGRG 120

Query: 155 YVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
           YV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   
Sbjct: 121 YVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPN 180

Query: 215 DSVALASRILQDQLGMF 231
           D+++ A++IL +   +F
Sbjct: 181 DALSFAAKILVEHFKVF 197


>gi|119662847|emb|CAJ33216.1| RNA polymerase alpha subunit [Lactobacillus kunkeei]
          Length = 202

 Score =  191 bits (485), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 97/201 (48%), Positives = 141/201 (70%), Gaps = 4/201 (1%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS-- 100
           LGN+LRR+L+SSL GAA+T++QID VLHE S++ GV ED+T IILN+K I+LK+  +   
Sbjct: 1   LGNSLRRILLSSLPGAAVTSIQIDDVLHEFSTVPGVVEDVTQIILNVKKISLKLDAEDGE 60

Query: 101 HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
            K + I   GP  VTAGDIQ   D+ VLNPD  I  +   +   M +T +KG GYV A  
Sbjct: 61  DKEMEINVTGPAQVTAGDIQADGDVTVLNPDLHIATVAEGSTFHMRMTANKGRGYVSADE 120

Query: 161 HRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           ++  ND  PIG++ +D++Y+PI++V+Y VE+AR GQ  D+DKL++ + TDGSIT  ++++
Sbjct: 121 NKARNDGMPIGVLPVDSIYTPIERVNYQVENARVGQRSDFDKLTLDVWTDGSITPSEAIS 180

Query: 219 LASRILQDQLGMFINFEEPKK 239
           LA++IL D L MF++  +  K
Sbjct: 181 LAAKILNDHLAMFVDLTDEAK 201


>gi|224534741|ref|ZP_03675313.1| DNA-directed RNA polymerase, alpha subunit [Borrelia spielmanii
           A14S]
 gi|224513989|gb|EEF84311.1| DNA-directed RNA polymerase, alpha subunit [Borrelia spielmanii
           A14S]
          Length = 344

 Score =  191 bits (485), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 122/335 (36%), Positives = 190/335 (56%), Gaps = 19/335 (5%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++K  ++   P  IE++   Q++ +       P  RGF  T+GN LRRVL+SS+ G AIT
Sbjct: 3   VEKFLKDFTIPEKIEFLK-SQDDGSYGKFTIYPFERGFGVTIGNTLRRVLLSSIEGYAIT 61

Query: 62  AVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK---R 109
            +++           V  E   I GV ED  ++I NIK I+LK+     +++  F    +
Sbjct: 62  TMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLEVIANIKNIHLKLREGEQRKIISFSVSGK 121

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
              V+ A   + ++ +EV N D VI  L  DA +  E  ++ G GYV ++ +    + + 
Sbjct: 122 DTNVLKASHFE-MDGVEVFNKDLVIATLSHDANLDFEFQINYGRGYVSSEQNSKYLEEVN 180

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           +I +D+++SPI+KVSYTVE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L 
Sbjct: 181 VIALDSIFSPIEKVSYTVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAALIVREFLF 240

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKK-VEELELSVRSTNCLRGENIVYMGDLIQRT 288
             ++FE+    V   ++ KS   N  LL   +E+L+LSVRS NCL  EN+  +G+LI + 
Sbjct: 241 PLVDFEDS---VNTSVD-KSKSENSNLLDMGIEKLDLSVRSLNCLAKENVKTLGELISKN 296

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
             ++ +  NFG+KSL EI   LG+  LFLGM+  D
Sbjct: 297 ADELSKARNFGKKSLEEIIEKLGSYRLFLGMSKED 331


>gi|161511723|emb|CAP16872.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           acidilactici]
          Length = 229

 Score =  191 bits (485), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 105/227 (46%), Positives = 146/227 (64%), Gaps = 2/227 (0%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++LK+  D  
Sbjct: 3   TLGNSLRRILLSSLPGAAITSVQIDNVLHEFSTIEGVVEDVTQIILNLKKVSLKIESDDE 62

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I   GP  VTAGDI    D+ VLNPD  IC +         LT   G GY  A  +
Sbjct: 63  KTLDINVVGPANVTAGDIMGDGDVTVLNPDSPICTVAEGTTFHAVLTADTGRGYTSADEN 122

Query: 162 --RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
             R  + PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ I TDGSIT  ++ +L
Sbjct: 123 KARKADMPIGVLPIDSIYTPIERVNYQVEKTRVGQRDDYDKLTLDIWTDGSITPSEATSL 182

Query: 220 ASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           +++IL + L +F+N  +  KE +  +  +       L   +EEL+LS
Sbjct: 183 SAKILTEHLAIFVNLNDQAKETEIMVEKEETHKEKMLEMTIEELDLS 229


>gi|154249789|ref|YP_001410614.1| DNA-directed RNA polymerase subunit alpha [Fervidobacterium nodosum
           Rt17-B1]
 gi|171769360|sp|A7HM24|RPOA_FERNB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|154153725|gb|ABS60957.1| DNA-directed RNA polymerase, alpha subunit [Fervidobacterium
           nodosum Rt17-B1]
          Length = 328

 Score =  191 bits (484), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 118/286 (41%), Positives = 177/286 (61%), Gaps = 14/286 (4%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQI--DGVLHEISSIKGVHEDLTDIILNIKG 91
           PL +G+A T+GN LRRVL+SS+   AIT V+       HE  +I+G  ED+ DI+LN+K 
Sbjct: 29  PLEKGYAVTVGNTLRRVLLSSIPSFAITDVRFVKPEKYHEFDTIEGAKEDIMDILLNLKK 88

Query: 92  INLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           + L++    +S  ++TI K+GPGV+TAGDI+    + V+NP H +  L+ DA + +EL  
Sbjct: 89  VQLRVDTYVESPVKLTINKKGPGVLTAGDIECPAGVVVVNPGHYLATLNEDADLEIELYA 148

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           + G G+VPA   R E   IG I +D +YSP+ KV++ VE+ R  +  DY+KL + I T  
Sbjct: 149 TFGKGFVPAAD-RNERPEIGWIVLDGVYSPVIKVNWLVENVRVDKRTDYEKLILEIWTKK 207

Query: 210 SITGEDSVALASRILQDQLGMFI-----NFEE-PKKEVKEDINVKSLPFNP--ALLKKVE 261
           SI   +++  + +I+ D   MFI     + EE P   ++E   V     +P   + KKVE
Sbjct: 208 SIKPSEALKHSLKIILDHF-MFIEQSLSDVEELPIPIIQETAVVTEEIGSPEDVMSKKVE 266

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           ELELS RS NCL+ + I  +GDL+ RTE +++++ NFG KSL E++
Sbjct: 267 ELELSARSLNCLKRDKIETIGDLLSRTEEELMKIKNFGLKSLEEVR 312


>gi|288574689|ref|ZP_06393046.1| DNA-directed RNA polymerase, alpha subunit [Dethiosulfovibrio
           peptidovorans DSM 11002]
 gi|288570430|gb|EFC91987.1| DNA-directed RNA polymerase, alpha subunit [Dethiosulfovibrio
           peptidovorans DSM 11002]
          Length = 354

 Score =  191 bits (484), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 109/305 (35%), Positives = 179/305 (58%), Gaps = 17/305 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++  PL RGF  T+GNALRRVL+SS++GAAIT+V+IDGV+HE S+I GV ED+ +++LN+
Sbjct: 34  IVVGPLERGFGVTIGNALRRVLLSSIKGAAITSVRIDGVVHEFSTIPGVGEDVIELLLNL 93

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + ++      + + +   G   VTA D Q  ++IE ++P+  IC L   A + +E+ +
Sbjct: 94  KHVPIRSYSPEVRVLRLEAEGERRVTAADFQPDSEIEFVDPEAYICTLAEGARLSLEVYI 153

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY PA   +    P+  + IDA+++PI++V Y V++ R GQ  DY+++ M +DT+G
Sbjct: 154 EQGVGYAPADRPKPAYLPMDSLLIDAIFTPIQRVKYEVQAERVGQRTDYERIVMDVDTNG 213

Query: 210 SITGEDSVALASRILQDQLGMFI---------NFEEPKKEVKEDINVKSLPFNPA----- 255
            +  + +VA A+R+L+    + +            +P+    ++I+V             
Sbjct: 214 VVKPDLAVAEAARLLRKYFTIVVEEIQKLHPSEHTDPEIVESQEISVAEEETETEQESEE 273

Query: 256 ---LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
              L + V +LELS+RS NCL    I  +GDL+ R   D+L++ N G+ SL EI+  L  
Sbjct: 274 NTLLSRGVRDLELSIRSENCLLRGGIHTIGDLVSRGRDDLLKIRNLGKISLREIEEKLEN 333

Query: 313 MGLFL 317
           +G  L
Sbjct: 334 LGFSL 338


>gi|149192395|ref|ZP_01870596.1| DNA-directed RNA polymerase subunit alpha [Vibrio shilonii AK1]
 gi|148833786|gb|EDL50822.1| DNA-directed RNA polymerase subunit alpha [Vibrio shilonii AK1]
          Length = 238

 Score =  191 bits (484), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 101/240 (42%), Positives = 154/240 (64%), Gaps = 8/240 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E ++P  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLRPRLVDIEQISTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEISMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           Y P+ K++Y VE+AR  Q  D DKL + ++T G++  E++V  A+ IL +QL  F++  +
Sbjct: 178 YRPVDKIAYAVEAARVEQRTDLDKLVIDMETSGTLEPEEAVRRAATILAEQLDAFVDLRD 237


>gi|308125183|gb|ADO14940.1| DNA-directed RNA polymerase alpha chain [Enterococcus aquimarinus]
          Length = 204

 Score =  190 bits (483), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 94/199 (47%), Positives = 138/199 (69%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNIKG+ LKM G   K 
Sbjct: 1   GNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNIKGLALKMYGQEEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I   GP  VTAGDI   +D+E+LN +  IC +   A     LTV  G GYV A  ++ 
Sbjct: 61  LEIDITGPATVTAGDIIVDSDVEILNKEMYICTVSEGATFHARLTVRPGRGYVQADENKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           ++ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL++ I TDGSI   D+++LA++I
Sbjct: 121 DDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTIEIWTDGSIEPLDAMSLAAKI 180

Query: 224 LQDQLGMFINFEEPKKEVK 242
           + + L +F+N  +  K  +
Sbjct: 181 MTEHLDIFVNLTDEAKHAE 199


>gi|163848051|ref|YP_001636095.1| DNA-directed RNA polymerase subunit alpha [Chloroflexus aurantiacus
           J-10-fl]
 gi|222525940|ref|YP_002570411.1| DNA-directed RNA polymerase subunit alpha [Chloroflexus sp.
           Y-400-fl]
 gi|163669340|gb|ABY35706.1| DNA-directed RNA polymerase, alpha subunit [Chloroflexus
           aurantiacus J-10-fl]
 gi|222449819|gb|ACM54085.1| DNA-directed RNA polymerase, alpha subunit [Chloroflexus sp.
           Y-400-fl]
          Length = 335

 Score =  190 bits (483), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 117/311 (37%), Positives = 173/311 (55%), Gaps = 6/311 (1%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I L    EN       PL RG   +LGNALRRVL+SS+ GAA+T +++ GV+HE SSI G
Sbjct: 13  ITLVAAAENYGRFAIAPLQRGHGSSLGNALRRVLLSSIPGAAVTRIKVSGVIHEFSSIPG 72

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED T ++LNIKGI L+   D    + + K+GPG V A DI   + +E++NP H IC +
Sbjct: 73  VVEDGTQLVLNIKGIRLRSYSDRAVALQLIKQGPGPVFARDIDAPSTVEIVNPQHYICTI 132

Query: 138 DVD-AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           D +     M+LTV +G G   A        PIG I +DAL+SPI +V++ VE   +  + 
Sbjct: 133 DDEHTTFEMQLTVERGRGVQLAD--TVSGMPIGEIAVDALFSPIPRVNFLVEEMGDDPLT 190

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
            YD+L + I TDG+I   D+++ A++IL    G  +N  +P++          +P   A 
Sbjct: 191 GYDRLILEIWTDGTIKPGDALSHAAQILAQYFGRIVNLNQPEEPEPSAHLPPPIPEEIA- 249

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
            + ++EL LS R+ N LR   I  +G L++  +  ++ + N G K + EI   L  +G  
Sbjct: 250 SRTIDELGLSTRTYNSLRRAEIHTIGQLLRLDDRGLMSIRNLGAKGIEEIHQRLEALGYR 309

Query: 317 LGMN--LPDWP 325
            G +  LP  P
Sbjct: 310 SGSSSRLPAAP 320


>gi|119953291|ref|YP_945500.1| DNA-directed RNA polymerase subunit alpha [Borrelia turicatae
           91E135]
 gi|119862062|gb|AAX17830.1| DNA-directed RNA polymerase alpha chain [Borrelia turicatae 91E135]
          Length = 344

 Score =  190 bits (483), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 121/320 (37%), Positives = 187/320 (58%), Gaps = 16/320 (5%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID----G 67
           P+ IE+ V G+++ +    I  P  +GF  T+GN LRRVL+SS+ G AI+A++I     G
Sbjct: 14  PDRIEF-VRGEDDSSYGKFIMYPFEKGFGVTIGNTLRRVLLSSIEGYAISAMRIQSNQGG 72

Query: 68  VLHEISS----IKGVHEDLTDIILNIKGINLKMS---GDSHKRVTIFKRGPGVVTAGDIQ 120
            L  +SS    I GV ED  ++I NIK I+LK+      +   +++  +   V+ A  ++
Sbjct: 73  SLKIVSSEFDLIPGVVEDTLEVIANIKNIHLKLDEGVNSTTISLSVNGKDTNVLKAVHLE 132

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               +EV N D VI  L  +A +  E  ++ G GYV ++ +    + +  I +D+++SPI
Sbjct: 133 R-EGVEVFNKDLVIATLSSEANLDFEFQINYGRGYVSSEQNAKYLEEVNTIALDSIFSPI 191

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KV+Y+VE  R GQ  DYDKL M I T G I+ +D++  A+ I++D L   +NFE+   +
Sbjct: 192 EKVTYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVRDFLLPLVNFED---K 248

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V   +    L  +  L   +E+L LSVRS NCL  EN+  +G+LI ++  D+ +  NFG+
Sbjct: 249 VVHSVENSELRDSDILSINIEKLNLSVRSLNCLTKENVKTLGELISKSAEDLSKARNFGK 308

Query: 301 KSLVEIKGVLGTMGLFLGMN 320
           KSL EI   L T GLFLGM+
Sbjct: 309 KSLEEIIEKLNTYGLFLGMS 328


>gi|119668273|emb|CAK95495.1| RNA polymerase alpha subunit [Lactobacillus kefiri]
          Length = 203

 Score =  190 bits (483), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 102/202 (50%), Positives = 140/202 (69%), Gaps = 4/202 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K I+LK+ G
Sbjct: 1   YGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKISLKLDG 60

Query: 99  --DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             D  + + I   GP  VTAGDIQ   D+ VLNPD  I  +   A   M LT +KG GYV
Sbjct: 61  PEDEEENLEIDVIGPADVTAGDIQADGDVTVLNPDLHIATVAEGATFHMRLTANKGRGYV 120

Query: 157 PA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A     R+   PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ I TDGSIT  
Sbjct: 121 SAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDIWTDGSITPS 180

Query: 215 DSVALASRILQDQLGMFINFEE 236
           ++V+LA++IL + L MF++  +
Sbjct: 181 EAVSLAAKILTEHLEMFVDLTD 202


>gi|119668285|emb|CAK95451.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 217

 Score =  190 bits (483), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 94/195 (48%), Positives = 132/195 (67%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK 
Sbjct: 2   RGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKS 61

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             D  K + +   GP  VTA D++   D++VLNPD  IC +     + MEL V  G GYV
Sbjct: 62  LSDEQKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMELAVKNGRGYV 121

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
            A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+
Sbjct: 122 TASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDA 181

Query: 217 VALASRILQDQLGMF 231
           ++ A++IL +   +F
Sbjct: 182 LSFAAKILVEHFKVF 196


>gi|289523340|ref|ZP_06440194.1| DNA-directed RNA polymerase, alpha subunit [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
 gi|289503032|gb|EFD24196.1| DNA-directed RNA polymerase, alpha subunit [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
          Length = 340

 Score =  190 bits (483), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 113/291 (38%), Positives = 172/291 (59%), Gaps = 6/291 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGNA+RRVL+SS+ GAA++A++IDGVLHE S++ GV ED+ +IILNIK +
Sbjct: 19  EPLERGYGVTLGNAIRRVLLSSIPGAAVSAIRIDGVLHEFSTVPGVMEDVLEIILNIKKL 78

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +    D  + + +   GP VVT  DI   +++E  NP+  IC L+    + M+L V +G
Sbjct: 79  AVVSHSDDVRMLRLEAEGPKVVTVADIIPDSEVEFSNPEAYICTLEEGHKLEMDLYVERG 138

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GY+     R    PI ++ +DA++SP+ +V+Y V +AR GQ  DY+ L + + T+ ++ 
Sbjct: 139 VGYLTMDRPRPNYLPIDVLLVDAVFSPVLRVNYNVGAARVGQRTDYESLLIELWTNETVE 198

Query: 213 GEDSVALASRILQDQLGMFIN--FEEP----KKEVKEDINVKSLPFNPALLKKVEELELS 266
              +   A +IL    G   +   +EP      EV E +       +P L + + +LELS
Sbjct: 199 PAKAFLEAVKILNQYFGHIASLLLKEPVSPVAAEVPEAVVEAVAEEDPILSRPIRDLELS 258

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +RS NCL    +  +GDL+Q T  D+L++ N G+ SL EI+  L   GL L
Sbjct: 259 IRSENCLLRAGVRTIGDLVQYTRDDLLKIRNLGKISLKEIEEKLDIFGLSL 309


>gi|15835408|ref|NP_297167.1| DNA-directed RNA polymerase subunit alpha [Chlamydia muridarum
           Nigg]
 gi|7190822|gb|AAF39597.1| DNA-directed RNA polymerase, alpha subunit [Chlamydia muridarum
           Nigg]
          Length = 394

 Score =  190 bits (483), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 120/332 (36%), Positives = 182/332 (54%), Gaps = 22/332 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +A+PL +G  HTLG+ALRR L+  L   AI +  + GVLHE  +++G+ ED+T+I+LN+
Sbjct: 54  FVADPLEKGMGHTLGSALRRALLIGLEAPAIVSFSMTGVLHEYMAVEGIIEDVTNIVLNL 113

Query: 90  KGINLKM---------SGDSHKRVTI--------FKRGPGVVTAGDIQTVNDIEVLNPDH 132
           KG  LK                R TI           G   +T GD+      E +NP+H
Sbjct: 114 KGSLLKKYPLQDCEGGRASQKLRATISIDASDLAAAGGQKAITLGDLLQEGTFEAVNPEH 173

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           VI  +     + + L V+ G GY P++    E   +  I +DA +SP+  V+Y VE  R 
Sbjct: 174 VIFTVTRPMQLDVMLRVAFGRGYTPSERIVLEEREMNEIVLDAAFSPVVLVNYFVEDTRV 233

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           GQ  D+D+L + ++TDG +  +++VA A++IL     +F   +E +   +E I+V+    
Sbjct: 234 GQDTDFDRLILQVETDGRVAPKEAVAFATQILSKHFSVFEKMDEKRIVFEEAISVEKENK 293

Query: 253 NPALLKKV---EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           +  L K V    E+ELSVRSTNCL   NI  +G+L+   E  +L+  NFG+KSL EIK  
Sbjct: 294 DDILHKLVLGINEIELSVRSTNCLSNANIETIGELVIMPEPRLLQFRNFGKKSLCEIKNK 353

Query: 310 LGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 354 LKEMKLELGMDLSQFGVGLDNVKEKMKWYAEK 385


>gi|119668283|emb|CAK95498.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 220

 Score =  190 bits (482), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 94/195 (48%), Positives = 132/195 (67%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK 
Sbjct: 2   RGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKS 61

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             D  K + +   GP  VTA D++   D++VLNPD  IC +     + MEL V  G GYV
Sbjct: 62  LSDEQKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMELAVKNGRGYV 121

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
            A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+
Sbjct: 122 TASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDA 181

Query: 217 VALASRILQDQLGMF 231
           ++ A++IL +   +F
Sbjct: 182 LSFAAKILVEHFKVF 196


>gi|119662811|emb|CAJ33197.1| RNA polymerase alpha subunit [Lactobacillus psittaci]
          Length = 205

 Score =  190 bits (482), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 92/188 (48%), Positives = 133/188 (70%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL++S+ G A++ +QIDGVLHE S++ GV ED+T IILN+K + LK   D  K 
Sbjct: 1   GNSLRRVLLTSIPGTALSYIQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSVADEEKI 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + +   GP  VTAGD++  +D+ VLNPD  IC++     + M+L V  G GYV A  ++T
Sbjct: 61  IELDVEGPATVTAGDLKVDSDVTVLNPDQYICSIAEGGHLHMQLAVKTGRGYVSASENKT 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           E+ PIG+I +D+L+SPIKKV+Y VES R G+  DYDKL++ + TDGSIT  D+++ A++I
Sbjct: 121 EDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDYDKLTLEVWTDGSITPSDALSFAAKI 180

Query: 224 LQDQLGMF 231
           L +   +F
Sbjct: 181 LVEHFKVF 188


>gi|218961406|ref|YP_001741181.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           (Transcriptase alpha chain) (RNA polymerase alpha
           subunit) [Candidatus Cloacamonas acidaminovorans]
 gi|167730063|emb|CAO80975.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           (Transcriptase alpha chain) (RNA polymerase alpha
           subunit) [Candidatus Cloacamonas acidaminovorans]
          Length = 391

 Score =  190 bits (482), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 113/320 (35%), Positives = 182/320 (56%), Gaps = 20/320 (6%)

Query: 12  PNNIEYIVLGQEEENRTLMIAE--PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           PN ++Y    +   +RT    E  PL  G+  T+GN LRR+L+SS++GAA+  V+I+G+ 
Sbjct: 10  PNEVDY---DKASYSRTYGKFEIGPLEPGYGTTIGNTLRRILLSSIQGAAVRFVRIEGLH 66

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE   I G + D  D+IL +K + +  S      + +  +G GV+TA  IQ    ++++N
Sbjct: 67  HEFCPIPGTNSDYIDLILRLKQLVISSSSVEEVPLVLEHKGKGVITASMIQETAYVKIIN 126

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
            D  +  +  D   R+E+ V  G GYV A     E   +G I +D++YSP+ KV+++V  
Sbjct: 127 KDLYLLEVVDDIDFRLEMIVGIGRGYVSADRQNPEGKAVGFIPVDSIYSPVLKVNFSVSH 186

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EPKKEVKEDINVK 248
            R  + +++D+L M I T+G++    ++ LA++IL+D       FE EP+        ++
Sbjct: 187 QRVKERMNFDRLIMEIYTNGAVEPSIALFLAAKILKDMAAKISLFEIEPQ-------YIR 239

Query: 249 SLPFNPALLKK-------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            +  +P L +K       V+E+ELSVR+ NCL    I  +GDL+ +TEA+ML+  NFG+K
Sbjct: 240 DIELDPELEEKERILKTSVKEIELSVRAANCLAQAKIETIGDLVSKTEAEMLKFRNFGKK 299

Query: 302 SLVEIKGVLGTMGLFLGMNL 321
           SL EI   L    L LGM++
Sbjct: 300 SLEEIVQKLKKYDLHLGMDV 319


>gi|311990464|gb|ADQ26362.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 243

 Score =  190 bits (482), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 102/243 (41%), Positives = 151/243 (62%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           +LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   D  K + 
Sbjct: 1   SLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLSDERKVIE 60

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
           +   GP  VTA D++   D++VLNPD  IC +     + ME+ V  G GYV A  +++++
Sbjct: 61  LDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNGRGYVAASDNKSDD 120

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
            PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++ A++IL 
Sbjct: 121 MPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILV 180

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLI 285
           +   +F + +   K  +  +  +       L   +EEL+LSVRS NCL+   I  + +L 
Sbjct: 181 EHFKVFESADADTKFSEVMVEKEDDKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELT 240

Query: 286 QRT 288
             T
Sbjct: 241 DMT 243


>gi|119662845|emb|CAJ33215.1| RNA polymerase alpha subunit [Lactobacillus hamsteri]
          Length = 212

 Score =  190 bits (482), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 94/193 (48%), Positives = 132/193 (68%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + +   GP  VTA D++  +D+EVLNPD  IC +     + M++ V  G GYV A
Sbjct: 61  DEQKVIELDVEGPATVTADDLKVDSDVEVLNPDQYICTIAEGGHLHMQIAVKNGRGYVAA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++E+ PIG+I +D+L+SPIKKV+Y VESAR G+  D+DKL+  I TDGSI   D+++
Sbjct: 121 SDNKSEDMPIGVIPVDSLFSPIKKVNYQVESARVGKRDDFDKLTFEIWTDGSIKPNDALS 180

Query: 219 LASRILQDQLGMF 231
            AS+IL +   +F
Sbjct: 181 FASKILVEHFKVF 193


>gi|270285588|ref|ZP_06194982.1| DNA-directed RNA polymerase subunit alpha [Chlamydia muridarum
           Nigg]
 gi|270289598|ref|ZP_06195900.1| DNA-directed RNA polymerase subunit alpha [Chlamydia muridarum
           Weiss]
 gi|301336984|ref|ZP_07225186.1| DNA-directed RNA polymerase subunit alpha [Chlamydia muridarum
           MopnTet14]
 gi|12230602|sp|Q9PJN4|RPOA_CHLMU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 377

 Score =  190 bits (482), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 120/332 (36%), Positives = 182/332 (54%), Gaps = 22/332 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +A+PL +G  HTLG+ALRR L+  L   AI +  + GVLHE  +++G+ ED+T+I+LN+
Sbjct: 37  FVADPLEKGMGHTLGSALRRALLIGLEAPAIVSFSMTGVLHEYMAVEGIIEDVTNIVLNL 96

Query: 90  KGINLKM---------SGDSHKRVTI--------FKRGPGVVTAGDIQTVNDIEVLNPDH 132
           KG  LK                R TI           G   +T GD+      E +NP+H
Sbjct: 97  KGSLLKKYPLQDCEGGRASQKLRATISIDASDLAAAGGQKAITLGDLLQEGTFEAVNPEH 156

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           VI  +     + + L V+ G GY P++    E   +  I +DA +SP+  V+Y VE  R 
Sbjct: 157 VIFTVTRPMQLDVMLRVAFGRGYTPSERIVLEEREMNEIVLDAAFSPVVLVNYFVEDTRV 216

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           GQ  D+D+L + ++TDG +  +++VA A++IL     +F   +E +   +E I+V+    
Sbjct: 217 GQDTDFDRLILQVETDGRVAPKEAVAFATQILSKHFSVFEKMDEKRIVFEEAISVEKENK 276

Query: 253 NPALLKKV---EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           +  L K V    E+ELSVRSTNCL   NI  +G+L+   E  +L+  NFG+KSL EIK  
Sbjct: 277 DDILHKLVLGINEIELSVRSTNCLSNANIETIGELVIMPEPRLLQFRNFGKKSLCEIKNK 336

Query: 310 LGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 337 LKEMKLELGMDLSQFGVGLDNVKEKMKWYAEK 368


>gi|119668299|emb|CAK95504.1| RNA polymerase alpha subunit [Lactobacillus curvatus]
          Length = 212

 Score =  189 bits (481), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 91/202 (45%), Positives = 142/202 (70%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           G+  TLGN+LRR+L++SL G A+T +QIDGVLHE S+I GV ED+T IILNIK + LK+ 
Sbjct: 1   GYGTTLGNSLRRILLASLPGTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKLH 60

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
            +  K + I  +GP  VTA DI + +D+EVLN D  IC +       + +TV KG GYV 
Sbjct: 61  VEEDKTIEIDVKGPATVTAADIISDDDVEVLNTDQYICTVAEGGNFHVRMTVKKGRGYVA 120

Query: 158 AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
           A  +++++ PIG++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+  +++
Sbjct: 121 ADQNKSDDMPIGVLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAI 180

Query: 218 ALASRILQDQLGMFINFEEPKK 239
           +LA++I+ + L +F++  +  K
Sbjct: 181 SLAAKIMTEHLAIFVDLTDEAK 202


>gi|158334432|ref|YP_001515604.1| DNA-directed RNA polymerase subunit alpha [Acaryochloris marina
           MBIC11017]
 gi|158304673|gb|ABW26290.1| DNA-directed RNA polymerase, alpha subunit [Acaryochloris marina
           MBIC11017]
          Length = 313

 Score =  189 bits (481), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 107/295 (36%), Positives = 170/295 (57%), Gaps = 12/295 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG   T+GNALRRVL+++LRG A+TAV+I GV HE ++I GV ED+ DI+LN+
Sbjct: 23  FILEPLDRGQGTTVGNALRRVLLANLRGTAVTAVRIAGVNHEFATIPGVREDVLDILLNM 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L+   +  +   +F +GP  VT  D +   ++E++NP   +  L  DA + ME  +
Sbjct: 83  KQVVLRSHTNDPQIGRLFVQGPATVTTDDFELPTEVEIVNPTQYVATLSSDATLEMEFRI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY     +R E   +  + IDA+Y P+++V+Y VE AR G  L+ D+L + I T+G
Sbjct: 143 EQGKGYHAVGKNRDEAAALDFLEIDAIYMPVRRVNYEVEDARVGGALEKDRLILDIWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK--VEELELSV 267
           ++T ++S++ A+ IL D          P K+   ++             +  +E L LSV
Sbjct: 203 NLTPQESLSQAATILVDLFN-------PLKDATFNVVEDIELEEEDETNQIPIEGLNLSV 255

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ NCL+   I  + DL++ ++ D+L + NFG KS  E   V+  +   LG+ +P
Sbjct: 256 RAYNCLKRAQINSVADLLEYSQEDLLEIKNFGAKSADE---VIAALQDHLGITMP 307


>gi|203284412|ref|YP_002222152.1| DNA-directed RNA polymerase [Borrelia duttonii Ly]
 gi|201083855|gb|ACH93446.1| DNA-directed RNA polymerase [Borrelia duttonii Ly]
          Length = 343

 Score =  189 bits (481), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 119/320 (37%), Positives = 185/320 (57%), Gaps = 16/320 (5%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---- 67
           P+ IE+ V G+++ +    I  P  +GF  T+GN LRRVL+SS+ G AI+A++I      
Sbjct: 13  PDRIEF-VRGEDDGSYGKFIIYPFEKGFGVTIGNTLRRVLLSSIEGYAISAMRIQSNQEE 71

Query: 68  ----VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGP--GVVTAGDIQ 120
               V  E   I GV ED  ++I NIK ++LK+  G ++  + +   G    V+ AG ++
Sbjct: 72  SLKIVSSEFDLIPGVMEDTLEVIANIKNVHLKLDEGVTNTTINLSVNGKDNNVLKAGHLE 131

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               +EV N D VI  L  DA +  E  V+ G GYV ++ +    + +  I +D+++SPI
Sbjct: 132 R-EGVEVFNKDLVIATLSSDANLDFEFQVNYGRGYVSSEQNAKYLEEVNTIALDSIFSPI 190

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KV+Y+VE  R GQ  DYDKL M I T G I+ +D++  A+ ++++ L   +NFE+   +
Sbjct: 191 EKVTYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASVVREFLLPLVNFED---K 247

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V   ++      +  L   VE+L LSVRS NCL  EN+  +G+LI ++  ++ +  NFG+
Sbjct: 248 VIHSVDYAEFRDSDILSMNVEKLNLSVRSLNCLIKENVKTLGELISKSPVELSKARNFGK 307

Query: 301 KSLVEIKGVLGTMGLFLGMN 320
           KSL EI   L   GLFLGM+
Sbjct: 308 KSLEEIVEKLNAYGLFLGMS 327


>gi|237804858|ref|YP_002889012.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           B/TZ1A828/OT]
 gi|231273158|emb|CAX10071.1| DNA-directed RNA polymerase alpha chain [Chlamydia trachomatis
           B/TZ1A828/OT]
          Length = 377

 Score =  189 bits (480), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 128/354 (36%), Positives = 195/354 (55%), Gaps = 24/354 (6%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +K + +E  V G ++  R   +A+PL +G  HTLG+ALRR L+  L   AI +  + G
Sbjct: 17  ESVKMSPVEGAVGGIDKVAR--FVADPLEKGMGHTLGSALRRALLIGLEAPAIVSFSMTG 74

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKM-------SGDSHK--RVTI--------FKRG 110
           VLHE  +++G+ ED+T+I+LN+KG  LK         G   +  R TI           G
Sbjct: 75  VLHEYMAVEGIIEDVTNIVLNLKGSLLKKYPLQDCEGGRCSQKLRATISIDASDLAAAGG 134

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
              VT GD+      E +NP+HVI  +     + + L V+ G GY P++    E   +  
Sbjct: 135 QKEVTLGDLLQEGTFEAVNPEHVIFTVTRPMQLEVMLRVAFGRGYSPSERIVLEERGMNE 194

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +  +++VA A++IL     +
Sbjct: 195 IVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLVLQVETDGRVAPKEAVAFATQILSKHFSV 254

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLKKV---EELELSVRSTNCLRGENIVYMGDLIQR 287
           F   +E +   +E I+V+    +  L K V    E+ELSVRSTNCL   NI  +G+L+  
Sbjct: 255 FEKMDEKRIVFEEAISVEKENKDDILHKLVLGINEIELSVRSTNCLSNANIETIGELVIM 314

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
            E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 315 PEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYAEK 368


>gi|297748637|gb|ADI51183.1| DNA-directed RNA polymerase alpha chain [Chlamydia trachomatis
           D-EC]
 gi|297749517|gb|ADI52195.1| DNA-directed RNA polymerase alpha chain [Chlamydia trachomatis
           D-LC]
          Length = 394

 Score =  189 bits (480), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 128/354 (36%), Positives = 195/354 (55%), Gaps = 24/354 (6%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +K + +E  V G ++  R   +A+PL +G  HTLG+ALRR L+  L   AI +  + G
Sbjct: 34  ESVKMSPVEGAVGGIDKVAR--FVADPLEKGMGHTLGSALRRALLIGLEAPAIVSFSMTG 91

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKM-------SGDSHK--RVTI--------FKRG 110
           VLHE  +++G+ ED+T+I+LN+KG  LK         G   +  R TI           G
Sbjct: 92  VLHEYMAVEGIIEDVTNIVLNLKGSLLKKYPLQDCEGGRCSQKLRATISIDASDLAAAGG 151

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
              VT GD+      E +NP+HVI  +     + + L V+ G GY P++    E   +  
Sbjct: 152 QKEVTLGDLLQEGTFEAVNPEHVIFTVTRPMQLEVMLRVAFGRGYSPSERIVLEERGMNE 211

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +  +++VA A++IL     +
Sbjct: 212 IVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLVLQVETDGRVAPKEAVAFATQILSKHFSV 271

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLKKV---EELELSVRSTNCLRGENIVYMGDLIQR 287
           F   +E +   +E I+V+    +  L K V    E+ELSVRSTNCL   NI  +G+L+  
Sbjct: 272 FEKMDEKRIVFEEAISVEKENKDDILHKLVLGINEIELSVRSTNCLSNANIETIGELVIM 331

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
            E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 332 PEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYAEK 385


>gi|15605236|ref|NP_220022.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           D/UW-3/CX]
 gi|237802936|ref|YP_002888130.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           B/Jali20/OT]
 gi|255311325|ref|ZP_05353895.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           6276]
 gi|255317626|ref|ZP_05358872.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           6276s]
 gi|255348884|ref|ZP_05380891.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           70]
 gi|255503424|ref|ZP_05381814.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           70s]
 gi|255507102|ref|ZP_05382741.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           D(s)2923]
 gi|290463292|sp|P0CE08|RPOA_CHLTR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|3328944|gb|AAC68108.1| RNA Polymerase Alpha [Chlamydia trachomatis D/UW-3/CX]
 gi|231274170|emb|CAX10964.1| DNA-directed RNA polymerase alpha chain [Chlamydia trachomatis
           B/Jali20/OT]
 gi|289525552|emb|CBJ15030.1| DNA-directed RNA polymerase alpha chain [Chlamydia trachomatis
           Sweden2]
 gi|296435112|gb|ADH17290.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           E/150]
 gi|296436040|gb|ADH18214.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           G/9768]
 gi|296436968|gb|ADH19138.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           G/11222]
 gi|296437901|gb|ADH20062.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           G/11074]
 gi|296438832|gb|ADH20985.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           E/11023]
 gi|297140401|gb|ADH97159.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           G/9301]
          Length = 377

 Score =  189 bits (480), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 128/354 (36%), Positives = 195/354 (55%), Gaps = 24/354 (6%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +K + +E  V G ++  R   +A+PL +G  HTLG+ALRR L+  L   AI +  + G
Sbjct: 17  ESVKMSPVEGAVGGIDKVAR--FVADPLEKGMGHTLGSALRRALLIGLEAPAIVSFSMTG 74

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKM-------SGDSHK--RVTI--------FKRG 110
           VLHE  +++G+ ED+T+I+LN+KG  LK         G   +  R TI           G
Sbjct: 75  VLHEYMAVEGIIEDVTNIVLNLKGSLLKKYPLQDCEGGRCSQKLRATISIDASDLAAAGG 134

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
              VT GD+      E +NP+HVI  +     + + L V+ G GY P++    E   +  
Sbjct: 135 QKEVTLGDLLQEGTFEAVNPEHVIFTVTRPMQLEVMLRVAFGRGYSPSERIVLEERGMNE 194

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +  +++VA A++IL     +
Sbjct: 195 IVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLVLQVETDGRVAPKEAVAFATQILSKHFSV 254

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLKKV---EELELSVRSTNCLRGENIVYMGDLIQR 287
           F   +E +   +E I+V+    +  L K V    E+ELSVRSTNCL   NI  +G+L+  
Sbjct: 255 FEKMDEKRIVFEEAISVEKENKDDILHKLVLGINEIELSVRSTNCLSNANIETIGELVIM 314

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
            E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 315 PEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYAEK 368


>gi|119662375|emb|CAJ33176.1| RNA polymerase alpha subunit [Lactobacillus parabuchneri]
          Length = 201

 Score =  189 bits (480), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 100/200 (50%), Positives = 140/200 (70%), Gaps = 4/200 (2%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR L+SSL G+A+T++QID VLHE S+IKGV ED+T IILN+K I+LK+ G
Sbjct: 1   YGTTLGNSLRRTLLSSLPGSAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKISLKLDG 60

Query: 99  --DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT +KG GYV
Sbjct: 61  PEDEEENLEIDVIGPADVTAGDIQADSDVTVLNPDLHIATVAEGATFHMRLTANKGRGYV 120

Query: 157 PA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A     R+   PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ + TDGSIT  
Sbjct: 121 SAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDVWTDGSITPS 180

Query: 215 DSVALASRILQDQLGMFINF 234
           ++V+LA++IL + L MF++ 
Sbjct: 181 EAVSLAAKILTEHLEMFVDL 200


>gi|166154722|ref|YP_001654840.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           434/Bu]
 gi|166155597|ref|YP_001653852.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
 gi|301335996|ref|ZP_07224240.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           L2tet1]
 gi|238687389|sp|B0B881|RPOA_CHLT2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238687487|sp|B0BCE6|RPOA_CHLTB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|165930710|emb|CAP04207.1| DNA-directed RNA polymerase alpha chain [Chlamydia trachomatis
           434/Bu]
 gi|165931585|emb|CAP07161.1| DNA-directed RNA polymerase alpha chain [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
          Length = 377

 Score =  189 bits (480), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 128/354 (36%), Positives = 195/354 (55%), Gaps = 24/354 (6%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +K + +E  V G ++  R   +A+PL +G  HTLG+ALRR L+  L   AI +  + G
Sbjct: 17  ESVKMSPVEGAVGGIDKVAR--FVADPLEKGMGHTLGSALRRALLIGLEAPAIVSFSMTG 74

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKM-------SGDSHK--RVTI--------FKRG 110
           VLHE  +++G+ ED+T+I+LN+KG  LK         G   +  R TI           G
Sbjct: 75  VLHEYMAVEGIIEDVTNIVLNLKGSLLKKYPLQDCEGGRCSQKLRATISVDASDLAAAGG 134

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
              VT GD+      E +NP+HVI  +     + + L V+ G GY P++    E   +  
Sbjct: 135 QKEVTLGDLLQEGTFEAVNPEHVIFTVTRPMQLEVMLRVAFGRGYSPSERIVLEERGMNE 194

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +  +++VA A++IL     +
Sbjct: 195 IVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLVLQVETDGRVAPKEAVAFATQILSKHFSV 254

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLKKV---EELELSVRSTNCLRGENIVYMGDLIQR 287
           F   +E +   +E I+V+    +  L K V    E+ELSVRSTNCL   NI  +G+L+  
Sbjct: 255 FEKMDEKRIVFEEAISVEKENKDDILHKLVLGINEIELSVRSTNCLSNANIETIGELVIM 314

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
            E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 315 PEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYAEK 368


>gi|76789244|ref|YP_328330.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           A/HAR-13]
 gi|90110832|sp|Q3KLJ0|RPOA_CHLTA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|76167774|gb|AAX50782.1| DNA-directed RNA polymerase alpha chain [Chlamydia trachomatis
           A/HAR-13]
          Length = 377

 Score =  189 bits (479), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 127/354 (35%), Positives = 193/354 (54%), Gaps = 24/354 (6%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +K + +E  V G ++  R   +A+PL +G  HTLG+ALRR L+  L   AI +  + G
Sbjct: 17  ESVKMSPVEGAVGGIDKVAR--FVADPLEKGMGHTLGSALRRALLIGLEAPAIVSFSMTG 74

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKM---------SGDSHKRVTI--------FKRG 110
           VLHE  +++G+ ED+T+I+LN+KG  LK                R TI           G
Sbjct: 75  VLHEYMAVEGIIEDVTNIVLNLKGSLLKKYPLQDCEGGRCSQKLRATISIDASDLAAAGG 134

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
              VT GD+      E +NP+HVI  +     + + L V+ G GY P++    E   +  
Sbjct: 135 QKEVTLGDLLQEGTFEAVNPEHVIFTVTRPMQLEVMLRVAFGRGYSPSERIVLEERGMNE 194

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +  +++VA A++IL     +
Sbjct: 195 IVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLVLQVETDGRVAPKEAVAFATQILSKHFSV 254

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLKKV---EELELSVRSTNCLRGENIVYMGDLIQR 287
           F   +E +   +E I+V+    +  L K V    E+ELSVRSTNCL   NI  +G+L+  
Sbjct: 255 FEKMDEKRIVFEEAISVEKENKDDILHKLVLGINEIELSVRSTNCLSNANIETIGELVIM 314

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
            E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 315 PEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYAEK 368


>gi|203287946|ref|YP_002222961.1| DNA-directed RNA polymerase [Borrelia recurrentis A1]
 gi|201085166|gb|ACH94740.1| DNA-directed RNA polymerase [Borrelia recurrentis A1]
          Length = 343

 Score =  189 bits (479), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 118/320 (36%), Positives = 185/320 (57%), Gaps = 16/320 (5%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---- 67
           P+ IE+ V G+++ +    +  P  +GF  T+GN LRRVL+SS+ G AI+A++I      
Sbjct: 13  PDRIEF-VRGEDDGSYGKFVIYPFEKGFGVTIGNTLRRVLLSSIEGYAISAMRIQSNQEE 71

Query: 68  ----VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGP--GVVTAGDIQ 120
               V  E   I GV ED  ++I NIK ++LK+  G ++  + +   G    V+ AG ++
Sbjct: 72  SLKIVSSEFDLIPGVMEDTLEVIANIKNVHLKLDEGVTNTTINLSVNGKDNNVLKAGHLE 131

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               +EV N D VI  L  DA +  E  V+ G GYV ++ +    + +  I +D+++SPI
Sbjct: 132 R-EGVEVFNKDLVIATLSSDANLDFEFQVNYGRGYVSSEQNAKYLEEVNTIALDSIFSPI 190

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KV+Y+VE  R GQ  DYDKL M I T G I+ +D++  A+ ++++ L   +NFE+   +
Sbjct: 191 EKVTYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASVVREFLLPLVNFED---K 247

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V   ++      +  L   VE+L LSVRS NCL  EN+  +G+LI ++  ++ +  NFG+
Sbjct: 248 VIHSVDYAEFRDSDILSMNVEKLNLSVRSLNCLIKENVKTLGELISKSPVELSKARNFGK 307

Query: 301 KSLVEIKGVLGTMGLFLGMN 320
           KSL EI   L   GLFLGM+
Sbjct: 308 KSLEEIVEKLNAYGLFLGMS 327


>gi|119668341|emb|CAK95468.1| RNA polymerase alpha subunit [Lactobacillus paracasei subsp.
           paracasei]
          Length = 209

 Score =  189 bits (479), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 93/196 (47%), Positives = 139/196 (70%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNIK + LKM+ D  K 
Sbjct: 1   GNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNTDEDKN 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I   GP  VTA DI    D+EVLNP+  IC +       + +TV KG GYV A  +++
Sbjct: 61  IEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAADQNKS 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           ++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++I
Sbjct: 121 DDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKI 180

Query: 224 LQDQLGMFINFEEPKK 239
           L + L +F+N  +  K
Sbjct: 181 LTEHLDIFVNLTDEAK 196


>gi|150187048|emb|CAK30159.1| RNA polymerase alpha subunit [Streptococcus australis ATCC 700641]
          Length = 217

 Score =  189 bits (479), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 91/200 (45%), Positives = 137/200 (68%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRRVL++SL GAA+T++ I+GVLHE  ++ GV ED+  IILN+KGI +K 
Sbjct: 1   RGYGTTLGNSLRRVLLASLPGAAVTSINIEGVLHEFDTVPGVREDVMQIILNVKGIAVKS 60

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
                K + +   GP  VTAGDI T +DIE++NPDH +  +   +  +  LTV+ G GYV
Sbjct: 61  YVQDEKIIELDVEGPAEVTAGDILTDSDIEIVNPDHYLFTIGEGSSFKATLTVNSGRGYV 120

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
           PA  ++ ++ P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED+
Sbjct: 121 PADQNKKDDAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDA 180

Query: 217 VALASRILQDQLGMFINFEE 236
           + L++RIL + L +F N  E
Sbjct: 181 LGLSARILTEHLNLFTNLTE 200


>gi|328813999|gb|AEB52115.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 215

 Score =  189 bits (479), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 96/194 (49%), Positives = 138/194 (71%), Gaps = 2/194 (1%)

Query: 48  RRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF 107
           RR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK+  D  K + I 
Sbjct: 1   RRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTAIILNVKKIALKLESDETKTLEID 60

Query: 108 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK--HHRTEN 165
            +GP  VTAGDI    D+EVLNPD  IC +   A   M +T + G GYV A+   HR ++
Sbjct: 61  VKGPANVTAGDIIGDADVEVLNPDLPICTVADGAHFHMRMTANTGRGYVSAEDNKHREDD 120

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
            PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T+GSIT  ++++L+++IL 
Sbjct: 121 MPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWTNGSITPSEAISLSAKILT 180

Query: 226 DQLGMFINFEEPKK 239
           D L +F+N  +  K
Sbjct: 181 DHLSIFVNLTDEAK 194


>gi|161511721|emb|CAP16871.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           acidilactici]
          Length = 225

 Score =  189 bits (479), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 99/203 (48%), Positives = 136/203 (66%), Gaps = 2/203 (0%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++LK+  D  
Sbjct: 3   TLGNSLRRILLSSLPGAAITSVQIDNVLHEFSTIEGVVEDVTQIILNLKKVSLKIESDDE 62

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I   GP  VTAGDI    D+ VLNPD  IC +         LT   G GY  A  +
Sbjct: 63  KTLDINVVGPANVTAGDIMGDGDVTVLNPDSPICTVAEGTTFHAVLTADTGRGYTSADEN 122

Query: 162 --RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
             R  + PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ I TDGSIT  ++ +L
Sbjct: 123 KARKADMPIGVLPIDSIYTPIERVNYQVEKTRVGQRDDYDKLTLDIWTDGSITPSEATSL 182

Query: 220 ASRILQDQLGMFINFEEPKKEVK 242
           +++IL + L +F+N  +  KE +
Sbjct: 183 SAKILTEHLAIFVNLNDQAKETE 205


>gi|161511755|emb|CAP16888.1| DNA-directed RNA polymerase subunit alpha [Pediococcus damnosus]
          Length = 187

 Score =  188 bits (478), Expect = 8e-46,   Method: Compositional matrix adjust.
 Identities = 94/187 (50%), Positives = 132/187 (70%), Gaps = 2/187 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+T++QIDGVLHE SSI+GV ED+T IILNIK ++LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSSIEGVVEDVTQIILNIKKVSLKIES 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A
Sbjct: 61  DDEKSLEIDVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAILTADTGRGYVSA 120

Query: 159 KHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   D  PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSIT  ++
Sbjct: 121 DENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSITPSEA 180

Query: 217 VALASRI 223
            +L+++ 
Sbjct: 181 TSLSAKF 187


>gi|257456916|ref|ZP_05622097.1| DNA-directed RNA polymerase, alpha subunit [Treponema vincentii
           ATCC 35580]
 gi|257445625|gb|EEV20687.1| DNA-directed RNA polymerase, alpha subunit [Treponema vincentii
           ATCC 35580]
          Length = 351

 Score =  188 bits (478), Expect = 9e-46,   Method: Compositional matrix adjust.
 Identities = 112/300 (37%), Positives = 173/300 (57%), Gaps = 10/300 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-----DGVLHEISS----IKGVHE 80
             A P   GF  T+GN LRRVL+SS++G AI+AV+I     D V H ISS    I  V E
Sbjct: 30  FTASPFETGFGTTIGNCLRRVLLSSIQGYAISAVKITSYGADDVPHSISSEFEAIPNVTE 89

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           D  +++ N+K + L++  +  +   +F  +GP  V A D      +E+L+ D  I  L  
Sbjct: 90  DTMEVLNNLKQMRLRLPNEIEQDTFLFDFKGPRSVKAADFAKPGQLEILSGDLHIMELME 149

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           +A V +E+ V  G GYVPA+ +    + +G I++D ++SP++KVSY ++  R GQ  DYD
Sbjct: 150 NAHVELEVQVDFGRGYVPAETNEKYVEVVGTISLDTIFSPVRKVSYEIQPCRVGQRNDYD 209

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + I TDG+I  ED++A A++I ++   +F+NF E +    ++ +         L   
Sbjct: 210 KLVLEIWTDGTIRPEDALAEAAKIAKEHFTVFVNFNENELLSDDEADESDEMIKQLLDTP 269

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           + EL+LSVR++NCL+  N+  + DL   TE ++ +  N G+KSL EI+  L    L LGM
Sbjct: 270 ITELDLSVRASNCLKNANVSTIRDLTMMTEDEISKTRNVGKKSLQEIQEKLAERNLSLGM 329


>gi|163847950|ref|YP_001635994.1| DNA-directed RNA polymerase subunit alpha [Chloroflexus aurantiacus
           J-10-fl]
 gi|222525830|ref|YP_002570301.1| DNA-directed RNA polymerase subunit alpha [Chloroflexus sp.
           Y-400-fl]
 gi|163669239|gb|ABY35605.1| DNA-directed RNA polymerase, alpha subunit [Chloroflexus
           aurantiacus J-10-fl]
 gi|222449709|gb|ACM53975.1| DNA-directed RNA polymerase, alpha subunit [Chloroflexus sp.
           Y-400-fl]
          Length = 318

 Score =  188 bits (478), Expect = 9e-46,   Method: Compositional matrix adjust.
 Identities = 105/278 (37%), Positives = 164/278 (58%), Gaps = 6/278 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL  G+ HTLGNALRRVL++++ G+AIT V+I GV  E   I G+ ED+ ++ILN+KGI
Sbjct: 24  EPLDPGYGHTLGNALRRVLLTAIPGSAITHVRIAGVYQETDVIPGMTEDVVELILNLKGI 83

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSK 151
           +L+   +   + TI K+GP +VTA D+     + V++P H IC L+ D A + +  T+  
Sbjct: 84  HLRGRHEGTVQATIQKQGPAIVTAADLMLPEGLSVVDPTHYICTLEHDQARIEITATIEH 143

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GY+ A        P+G   IDA+++P+ +V+Y VE+ R GQ  DYD+L + + T+G+I
Sbjct: 144 GRGYLSADQRGIL--PLGEFPIDAIFTPVPRVNYVVENTRIGQATDYDRLILEVWTNGTI 201

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL--KKVEELELSVRS 269
             ++++  A+R+L        NF     E         L   PA +    +E L+LS R+
Sbjct: 202 RAQEALDYAARVLVHYYTTIANFNRLMVEPAAQPETNGLEI-PAHVYDTSIETLDLSTRT 260

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            NCL+   I  +G ++Q  E  +L + N G+KS+ EI+
Sbjct: 261 YNCLKRAEITKIGQVLQMDEKALLSVRNLGQKSMEEIR 298


>gi|289548514|ref|YP_003473502.1| DNA-directed RNA polymerase subunit alpha [Thermocrinis albus DSM
           14484]
 gi|289182131|gb|ADC89375.1| DNA-directed RNA polymerase, alpha subunit [Thermocrinis albus DSM
           14484]
          Length = 317

 Score =  188 bits (478), Expect = 9e-46,   Method: Compositional matrix adjust.
 Identities = 121/322 (37%), Positives = 187/322 (58%), Gaps = 18/322 (5%)

Query: 7   QELIKPNNIEYIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           +E + P+ + +     EE+ +T    + EPL RGF  T+GNALRR L+SS+ G AIT V+
Sbjct: 3   REFVYPSKVYW-----EEKTKTYGRFVVEPLERGFGITVGNALRRTLLSSIEGTAITGVK 57

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           + G  HE S+++GV ED+ +II N+K +  ++     + + + KRG G V A DI     
Sbjct: 58  VYGAYHEFSTVEGVLEDVLEIIANLKRVRFRLRESHVEILYLKKRGEGEVYARDIILPPS 117

Query: 125 IEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           ++++ PD  I  +   D  + +E+ V +G GYVP +   +  + +G I +DA +SP++ V
Sbjct: 118 VDLITPDVKIATITSPDTELHIEIRVERGFGYVPTEEMESFGE-VGWILVDADFSPVRHV 176

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV-- 241
           SY VE  R  +  DYD+L M I TDGS T E+ V  A +IL   L  F + E   +E+  
Sbjct: 177 SYRVEKTRVERRSDYDRLIMEIRTDGSKTPEEVVKEAVQIL---LRNFSSLENIAQEIPF 233

Query: 242 --KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
             +E + V  L    +L   +EEL++S RS N L+   I  +G+L++ TE D+    N G
Sbjct: 234 VAEEPVVVDELMEKLSL--PIEELDISQRSLNSLKRIGINTLGELVRLTEEDLKSTKNVG 291

Query: 300 RKSLVEIKGVLGTMGLFLGMNL 321
           RK++ EIK  L  MGL+LGM++
Sbjct: 292 RKAINEIKEALKQMGLYLGMDI 313


>gi|119668275|emb|CAK95496.1| RNA polymerase alpha subunit [Lactobacillus parabuchneri]
          Length = 216

 Score =  188 bits (478), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 100/201 (49%), Positives = 140/201 (69%), Gaps = 4/201 (1%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DS 100
           LGN+LRR L+SSL G+A+T++QID VLHE S+IKGV ED+T IILN+K I+LK+ G  D 
Sbjct: 1   LGNSLRRTLLSSLPGSAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKISLKLDGPEDE 60

Query: 101 HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA-- 158
            + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT +KG GYV A  
Sbjct: 61  EENLEIDVIGPADVTAGDIQADSDVTVLNPDLHIATVAEGATFHMRLTANKGRGYVSAVE 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
              R+   PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ + TDGSIT  ++V+
Sbjct: 121 NKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDVWTDGSITPSEAVS 180

Query: 219 LASRILQDQLGMFINFEEPKK 239
           LA++IL + L MF++  +  K
Sbjct: 181 LAAKILTEHLEMFVDLTDEAK 201


>gi|151416840|emb|CAO78491.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gelidum]
          Length = 233

 Score =  188 bits (478), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 99/233 (42%), Positives = 149/233 (63%), Gaps = 2/233 (0%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  
Sbjct: 1   TLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDEE 60

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           + + +  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  +
Sbjct: 61  RSLEVDIQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTITAFKGRGYSSADEN 120

Query: 162 RTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           +   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L
Sbjct: 121 KQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSL 180

Query: 220 ASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
            S+IL + L +F++      E    + V+ +  + +    +E+L+LSVRS NC
Sbjct: 181 GSKILAEHLNLFMDISPVAAEANVMVEVEPVAVSASDSAPIEDLDLSVRSYNC 233


>gi|319789266|ref|YP_004150899.1| DNA-directed RNA polymerase, alpha subunit [Thermovibrio
           ammonificans HB-1]
 gi|317113768|gb|ADU96258.1| DNA-directed RNA polymerase, alpha subunit [Thermovibrio
           ammonificans HB-1]
          Length = 316

 Score =  188 bits (478), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 121/327 (37%), Positives = 181/327 (55%), Gaps = 32/327 (9%)

Query: 8   ELIKPNNIEYIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           E I P    +     EE   T    + EPL +G+  T+GNALRRVL+SS+ GAA TAV+ 
Sbjct: 3   EFITPERFTW-----EEHTNTYGRFVVEPLEKGYGVTIGNALRRVLLSSIEGAAPTAVKF 57

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           +G  HE +++ GV EDLT+I+LNIK +   + G+    + + K+GPG V A D +  + +
Sbjct: 58  EGAYHEFTTLPGVVEDLTEIVLNIKKLRFVLHGEGPVFIELKKKGPGKVYAKDFELPSQL 117

Query: 126 EVLNPDHVICNLDVDAV-VRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKK 182
           E+L PD  I  LD ++  + + L V KG G+V ++  +   D   +G I +DA +SPIKK
Sbjct: 118 ELLTPDQEIATLDNESSEIEIHLRVDKGKGFVLSEDIQEIFDISTLGWIPLDADFSPIKK 177

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL---------GMFI- 232
           V++ VE  R G+  DY+KL+  I TDGSIT +D+V  AS IL D            +F  
Sbjct: 178 VTFKVEDTRVGRRTDYNKLTFEIWTDGSITPKDAVVRASNILIDHFSQIRDRLVEALFAV 237

Query: 233 -NFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
              +EPK+EV E +N           + +EE  LS R+   L+   I  + DL+     +
Sbjct: 238 EEAQEPKEEVSEVLN-----------QTLEEAGLSGRALKVLKEHGIETVKDLVALDRKE 286

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLG 318
           +  +   G+KS+ +I+  L  +GL LG
Sbjct: 287 LESLKGLGKKSIADIEAFLSQLGLELG 313


>gi|119662355|emb|CAJ33166.1| RNA polymerase alpha subunit [Lactobacillus salivarius]
          Length = 199

 Score =  188 bits (477), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 95/198 (47%), Positives = 140/198 (70%), Gaps = 2/198 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAAIT VQIDGVLHE S+I GV ED+T IILN+K + L M  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAITDVQIDGVLHEFSTIPGVLEDVTLIILNLKKVALSMES 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  + + I   GP  VTAGDIQ+ +D+EVLNP+  IC +   A + + +  +KG GYV A
Sbjct: 61  EDSQALEINVTGPMEVTAGDIQSNSDVEVLNPEQYICTVADGAELHVRMNANKGRGYVSA 120

Query: 159 KHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   D  PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T+GSIT  ++
Sbjct: 121 NDNKALADDMPIGVLPIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWTNGSITPSEA 180

Query: 217 VALASRILQDQLGMFINF 234
           ++L+++IL + L +F++ 
Sbjct: 181 ISLSAKILTEHLALFVDL 198


>gi|320160441|ref|YP_004173665.1| DNA-directed RNA polymerase alpha chain [Anaerolinea thermophila
           UNI-1]
 gi|319994294|dbj|BAJ63065.1| DNA-directed RNA polymerase alpha chain [Anaerolinea thermophila
           UNI-1]
          Length = 321

 Score =  188 bits (477), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 116/292 (39%), Positives = 180/292 (61%), Gaps = 10/292 (3%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E  N    I  PL  G+  TLGNALRRVL+SSL GAA+T+++I  VLHE S I GV ED+
Sbjct: 17  EARNYGKFIIGPLEGGYGVTLGNALRRVLLSSLEGAAVTSIRISDVLHEFSDIPGVREDV 76

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             ++LNIK + L +       + +  RG G VTA DIQ   ++E++NP+  +  +D D  
Sbjct: 77  IQVMLNIKQLRLILHDVETTHMHLEVRGEGTVTAADIQAPAEVEIVNPELELFTVD-DPN 135

Query: 143 VRMEL--TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
            R+E+  TVS+G GY PA   R+   PIG + +DA++SP+K+V+++V +AR GQ  +YD+
Sbjct: 136 TRLEIDFTVSRGRGYSPAS-ERSGRLPIGELPVDAIFSPVKRVNWSVTAARVGQSTNYDR 194

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLK 258
           L + I TDG+IT E++++ +++IL D L     ++ E     V++++    L  + A   
Sbjct: 195 LILEIWTDGTITPENALSTSAKILIDHLRYITGVSAESLAVTVEKEVAGGRLT-SEAAET 253

Query: 259 KVEELELSVRSTNCLRGENIVYMGD---LIQRTEADMLRMANFGRKSLVEIK 307
            +E L+LSVR  N L+   I  +GD   L+++ E  ++ + NFG KSL E++
Sbjct: 254 PIENLDLSVRVFNSLKRTGITTVGDVLELLEKGEDAVMSIRNFGEKSLDELR 305


>gi|150187071|emb|CAK30164.1| RNA polymerase alpha subunit [Streptococcus equi subsp. equi]
          Length = 215

 Score =  188 bits (477), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 91/203 (44%), Positives = 142/203 (69%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K 
Sbjct: 1   RGYGTTLGNSLRRVLLSSLPGAAVTSIRIDGVLHEFDTIPGVREDVMQIILNVKGLAVKS 60

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             +  K + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV+K  GYV
Sbjct: 61  YVEDEKIIELDVEGPAEVTAGDILTDSDIELVNPDHYLFTIADGYTLKASMTVAKKRGYV 120

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
           PA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED+
Sbjct: 121 PAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDA 180

Query: 217 VALASRILQDQLGMFINFEEPKK 239
           + L++R+L + L +F +  +  K
Sbjct: 181 LGLSARVLIEHLNLFTDLTDVAK 203


>gi|218282150|ref|ZP_03488449.1| hypothetical protein EUBIFOR_01031 [Eubacterium biforme DSM 3989]
 gi|218216860|gb|EEC90398.1| hypothetical protein EUBIFOR_01031 [Eubacterium biforme DSM 3989]
          Length = 318

 Score =  188 bits (477), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 114/298 (38%), Positives = 172/298 (57%), Gaps = 7/298 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL   +   LGNALRRVL+SS+ G AI +++IDGV HE + IKGV ED+  IILN+
Sbjct: 19  FLFEPLEYRYGTPLGNALRRVLLSSIPGGAIFSIRIDGVYHEFTGIKGVKEDVASIILNL 78

Query: 90  KGINLKMSGDSHKRVT--IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K + L +    ++  T  I + GP  V AGDI+    + VLN D  IC L     + MEL
Sbjct: 79  KQLILDIDIHDNEVYTLRIDQEGPKTVVAGDIECPTGVTVLNKDLPICTLSEGGSIHMEL 138

Query: 148 TVSKGHGYVPA----KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
               G G+V +    + ++ E  P+G+I  D+LYSP+K VSY     +      YD L +
Sbjct: 139 QARLGRGFVRSDVNKRMYQNEGQPLGIIYTDSLYSPVKNVSYVANPIKSEDGSMYDSLEL 198

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPK-KEVKEDINVKSLPFNPALLKKVEE 262
            I TD +I   +++A+A++IL+D L +  + +E   +  ++++ V   P      K +E+
Sbjct: 199 EITTDETIKPSEALAVAAKILRDHLSILASVDEASLEVKEQEVEVSEEPVVHTTHKMIED 258

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           LELSVRS NCL+   I  + +L Q+TE +M+ + N G+KSL E+K  +  +GL    N
Sbjct: 259 LELSVRSYNCLKRAGIATVDELTQKTEEEMIHVRNLGKKSLQEVKDKIKELGLSFRQN 316


>gi|257429027|ref|ZP_05605414.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus 68-397]
 gi|257279508|gb|EEV10095.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus 68-397]
          Length = 253

 Score =  188 bits (477), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 91/205 (44%), Positives = 143/205 (69%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+GVLHE S++  V ED++ II+NI
Sbjct: 23  FVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEGVLHEFSAVDNVVEDVSTIIMNI 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  R  G VTA DI   +D+E+LNP+  I  +     +++ L  
Sbjct: 83  KQLALKIYSEEDKTLEIDVRDEGEVTASDITHDSDVEILNPELKIATVSKGGHLKIRLVA 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTVE+ R GQ  D+DKL++ + T+G
Sbjct: 143 NKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTVENTRVGQSSDFDKLTLDVWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINF 234
           SIT ++SV+LA++I+ + L +F+  
Sbjct: 203 SITPQESVSLAAKIMTEHLNIFVGL 227


>gi|161511715|emb|CAP16868.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           acidilactici]
          Length = 225

 Score =  188 bits (477), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 103/225 (45%), Positives = 144/225 (64%), Gaps = 2/225 (0%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++LK+  D  K 
Sbjct: 1   GNSLRRILLSSLPGAAITSVQIDNVLHEFSTIEGVVEDVTQIILNLKKVSLKIESDDEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH-- 161
           + I   GP  VTAGDI    D+ VLNPD  IC +         LT   G GY  A  +  
Sbjct: 61  LDINVVGPANVTAGDIMGDGDVTVLNPDSPICTVAEGTTFHAVLTADTGRGYTSADENKA 120

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R  + PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ I TDGSIT  ++ +L++
Sbjct: 121 RKADMPIGVLPIDSIYTPIERVNYQVEKTRVGQRDDYDKLTLDIWTDGSITPSEATSLSA 180

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           +IL + L +F+N  +  KE +  +  +       L   +EEL+LS
Sbjct: 181 KILTEHLAIFVNLNDQAKETEIMVEKEETHKEKMLEMTIEELDLS 225


>gi|320451273|ref|YP_004203369.1| DNA-directed RNA polymerase subunit alpha [Thermus scotoductus
           SA-01]
 gi|320151442|gb|ADW22820.1| DNA-directed RNA polymerase, subunit alpha [Thermus scotoductus
           SA-01]
          Length = 313

 Score =  187 bits (476), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 114/290 (39%), Positives = 165/290 (56%), Gaps = 3/290 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED+ +IILN+
Sbjct: 23  FVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKR--GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K + ++      +  T+  +  GP VV AGD     D E+LNPD  I  LD    + ME+
Sbjct: 83  KELVVRFLDPKMQTTTLVLKAEGPKVVRAGDFVVPPDAEILNPDLTIATLDKGGKLYMEV 142

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            V +G GYVPA+ H  + D I  I +DA++SP+++V++ VE  R GQ  D DKL++ I T
Sbjct: 143 RVDRGVGYVPAERHGIK-DRINSIPVDAIFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWT 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           DGS+T  +++  A  IL++ L  F N +       E  +V+       L   +EEL LS 
Sbjct: 202 DGSVTPLEALNQAVEILKEHLSYFANPQATALPAPEPASVERAEGEEDLDLPLEELGLST 261

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           R  + L+ E I  +  L+     D+  +   G +SL EI+  L   G  L
Sbjct: 262 RVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIREALAKKGFAL 311


>gi|154424781|emb|CAL18493.1| RNA polymerase alpha subunit [Streptococcus dysgalactiae subsp.
           equisimilis]
          Length = 205

 Score =  187 bits (476), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 92/203 (45%), Positives = 142/203 (69%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K 
Sbjct: 2   RGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKS 61

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             +  K + +   GP  VTAGDI T +DIE++NPDH +  +     +R  +TV+K  GYV
Sbjct: 62  YVEDEKILELEVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLRATMTVAKKRGYV 121

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
           PA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED+
Sbjct: 122 PAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDA 181

Query: 217 VALASRILQDQLGMFINFEEPKK 239
           + L++R+L + L +F +  +  K
Sbjct: 182 LGLSARVLIEHLNLFTDLTDVAK 204


>gi|298253052|ref|ZP_06976844.1| DNA-directed RNA polymerase, alpha subunit [Gardnerella vaginalis
           5-1]
 gi|297532447|gb|EFH71333.1| DNA-directed RNA polymerase, alpha subunit [Gardnerella vaginalis
           5-1]
          Length = 290

 Score =  187 bits (476), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 110/273 (40%), Positives = 161/273 (58%), Gaps = 12/273 (4%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG 110
           ++SS+ GAA+T+V+I G LHE +++ GV ED+T+I+LNIKGI L    D    + + K G
Sbjct: 1   MLSSIPGAAVTSVRISGALHEFTTLPGVEEDVTEILLNIKGIVLTSEYDEPVVMYLRKNG 60

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
            G  TAGDI     + + NPD  I  L  D  + +E TV +G GYVPA+ ++ EN  IG 
Sbjct: 61  KGEATAGDITPPAGVTIANPDLHIATLAEDGELEIEFTVERGRGYVPAQMNKQENSEIGR 120

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           I +D++YSP+ KVSY VE+ R  Q  D+DKL + ++T  +IT  D+VA A   L +  G+
Sbjct: 121 IPVDSIYSPVLKVSYKVEATRVEQRTDFDKLILDVETKPAITPRDAVASAGSTLVELFGL 180

Query: 231 F--INFEEPKKEVKEDINVKSLP----FNPALLKKVEELELSVRSTNCLRGENIVYMGDL 284
              +N +       E + V   P     +  L   +E++  + RS NCL+ E I  +G+L
Sbjct: 181 CRELNVD------AEGVEVGPAPTHDEADSQLAIPIEDMNFTQRSYNCLKREGIHTVGEL 234

Query: 285 IQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +  TE D+L + NFG KS+ E+K  L  MGL L
Sbjct: 235 VVHTEQDLLDIRNFGMKSIDEVKEKLQAMGLSL 267


>gi|312148520|gb|ADQ31179.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           JD1]
          Length = 344

 Score =  187 bits (475), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 119/335 (35%), Positives = 186/335 (55%), Gaps = 17/335 (5%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +++K  ++   P  IE++   Q + +       P  RGF  T+GN LRRVL+SS+ G AI
Sbjct: 2   LVEKFLKDFTIPEKIEFLK-SQGDGSYGKFTIYPFERGFGITIGNTLRRVLLSSIEGYAI 60

Query: 61  TAVQI-----DGVLHEISS----IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK--- 108
           TA+++     D  L  +SS    I GV ED  ++I NIK I+LK+     K+   F    
Sbjct: 61  TAMRVQSNNKDASLKVVSSEFDLIPGVSEDTLEVIANIKNIHLKLGEGEQKKTISFSVSG 120

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
           +   V+ A   +  + +EV N D VI  L  D  + +E  ++ G GYV ++ +    + +
Sbjct: 121 KDTNVLKASHFER-DGVEVFNKDLVIATLSRDVNLDLEFQINYGRGYVSSEQNSKYLEEV 179

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
            +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L
Sbjct: 180 NVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREFL 239

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
              ++FE+    V           +  L   +E+L LSVRS NCL  EN+  +G+LI + 
Sbjct: 240 FPLVDFED---NVNTSFEKSKSESSNLLDMSIEKLNLSVRSLNCLAKENVRTLGELISKN 296

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
             ++ +  NFG+KSL EI   LG+  L+LGM+  D
Sbjct: 297 AEELSKARNFGKKSLEEIIEKLGSYRLYLGMSKED 331


>gi|161511729|emb|CAP16875.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 229

 Score =  187 bits (475), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 103/227 (45%), Positives = 147/227 (64%), Gaps = 2/227 (0%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++LK+  D  
Sbjct: 3   TLGNSLRRILLSSLPGAAITSVQIDSVLHEFSTIEGVVEDVTQIILNLKKVSLKIESDED 62

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I   GP  VTAGDI    D+ +LNP+  IC +         LT   G GY  A  +
Sbjct: 63  KTLEINVAGPANVTAGDIMGDGDVVILNPELPICTVAEGTTFHAVLTADTGRGYTSADEN 122

Query: 162 --RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
             R  + PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ I TDGSIT  ++ +L
Sbjct: 123 KARKVDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDIWTDGSITPSEATSL 182

Query: 220 ASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           +++IL + L +F+N  +  KE +  +  +       L   +EEL+LS
Sbjct: 183 SAKILTEHLAIFVNLNDQAKETEIMVEKEETHKEKMLEMTIEELDLS 229


>gi|219848267|ref|YP_002462700.1| DNA-directed RNA polymerase subunit alpha [Chloroflexus aggregans
           DSM 9485]
 gi|219542526|gb|ACL24264.1| DNA-directed RNA polymerase, alpha subunit [Chloroflexus aggregans
           DSM 9485]
          Length = 337

 Score =  187 bits (475), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 112/320 (35%), Positives = 180/320 (56%), Gaps = 8/320 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           EN       PL RG   +LGNALRRVL+SS+ GAA+T ++I GV+HE ++I GV ED T 
Sbjct: 20  ENYGRFAIAPLQRGHGTSLGNALRRVLLSSIPGAAVTRIKITGVIHEFTAIPGVVEDGTQ 79

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVV 143
           ++LN+KGI L+   D    + + K+GPG V AGDI   + +E++NP H +C +D +   +
Sbjct: 80  LVLNVKGIRLRSYSDRAVALQLVKQGPGPVFAGDIDAPSTVEIVNPQHYLCTIDDEHTTL 139

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            M+LTV +G G   A        PIG I +DAL+SPI +V++ VE      +  YD+L +
Sbjct: 140 EMQLTVERGRGVQLAD--TVSGMPIGEIAVDALFSPIPRVNFLVEEIGGDPLTGYDRLII 197

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            I TDG+I   D+++ A++IL       ++  +P++  ++      +P   A  + ++EL
Sbjct: 198 EIWTDGTIKPGDALSHAAQILTQYFSRIVSLNQPEESEQQPTLPPPIPDEIA-NRTIDEL 256

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM---- 319
            LS R+ N LR  +I  +G L++  +  ++ + N G K + EI   L  +G   G     
Sbjct: 257 GLSTRTYNSLRRADIQTIGQLLRLDDRGLMSIRNLGAKGIEEIHQRLAALGYRSGETTSG 316

Query: 320 NLPDWPPESIEELAKKYEDK 339
           +LPD   +++      Y ++
Sbjct: 317 HLPDTTNQNVPSTHDSYPEE 336


>gi|119366749|sp|Q110D1|RPOA_TRIEI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 314

 Score =  187 bits (475), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 110/297 (37%), Positives = 173/297 (58%), Gaps = 17/297 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG   T+GNALRRVL+S+L G AIT+V+I GV HE ++IKGV ED+ +I+LN+
Sbjct: 23  FIIEPLARGQGTTVGNALRRVLLSNLEGTAITSVRIAGVNHEFATIKGVREDVLEILLNM 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK   +  +   +   GP  VTA      +++EV++    I  L   +++ ME  +
Sbjct: 83  KEVVLKSYSEQPQIGRLRVEGPATVTADRFDVPSEVEVIDRSQYIATLSPGSILEMEFRI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GY      R +   +  + IDA++ P++KV+YT+E A  G  L+ D+L M I T+G
Sbjct: 143 EKGTGYKAVDRTRDDVATLDFLQIDAIFMPVRKVNYTIEDAHIGSSLEQDRLIMDIWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP----FNPALLKKVEELEL 265
           S T +D+++ A+       G+ ++  EP K++    N+  +P     +P     +EEL+L
Sbjct: 203 SYTPQDALSNAA-------GILMSLFEPLKDI---TNMADIPSGETTDPTSQIPIEELQL 252

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           SVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E   V+  +   LG+ LP
Sbjct: 253 SVRAYNCLKRAQINSVADLLDYSQEDLLEIKNFGQKSAEE---VIEALQKRLGITLP 306


>gi|86438812|emb|CAJ43371.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 213

 Score =  187 bits (475), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 93/197 (47%), Positives = 132/197 (67%)

Query: 35  LPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL 94
           L RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + L
Sbjct: 1   LERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLEL 60

Query: 95  KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHG 154
           K   D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V  G G
Sbjct: 61  KSLSDERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNGRG 120

Query: 155 YVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
           YV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   
Sbjct: 121 YVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPN 180

Query: 215 DSVALASRILQDQLGMF 231
           D+++ A++I  +   +F
Sbjct: 181 DALSFAAKISVEHFKVF 197


>gi|119668281|emb|CAK95497.1| RNA polymerase alpha subunit [Lactobacillus amylolyticus]
          Length = 217

 Score =  187 bits (474), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 92/193 (47%), Positives = 131/193 (67%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK + 
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSNS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + +   GP  VTA D++  +D+EVLNPD  IC +     + M++ V  G GYV A
Sbjct: 61  DEQKVIELDVEGPATVTADDLKVDSDVEVLNPDQYICTIAEGGHLHMQIAVKNGRGYVAA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++E+ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++
Sbjct: 121 SDNKSEDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSINPNDALS 180

Query: 219 LASRILQDQLGMF 231
            A+ IL +   +F
Sbjct: 181 FAANILVEHFKVF 193


>gi|119668297|emb|CAK95503.1| RNA polymerase alpha subunit [Lactobacillus curvatus]
          Length = 207

 Score =  187 bits (474), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 90/201 (44%), Positives = 141/201 (70%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L++SL G A+T +QIDGVLHE S+I GV ED+T IILNIK + LK+  
Sbjct: 1   YGTTLGNSLRRILLASLPGTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKLHV 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + I  +GP  VTA DI + +D+EVLN D  IC +       + +TV KG GYV A
Sbjct: 61  EEDKTIEIDVKGPATVTAADIISDDDVEVLNTDQYICTVAEGGNFHVRMTVKKGRGYVAA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++
Sbjct: 121 DQNKSDDMPIGVLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAIS 180

Query: 219 LASRILQDQLGMFINFEEPKK 239
           LA++I+ + L +F++  +  K
Sbjct: 181 LAAKIMTEHLAIFVDLTDEAK 201


>gi|113476555|ref|YP_722616.1| DNA-directed RNA polymerase subunit alpha [Trichodesmium erythraeum
           IMS101]
 gi|110167603|gb|ABG52143.1| DNA-directed RNA polymerase, alpha subunit [Trichodesmium
           erythraeum IMS101]
          Length = 321

 Score =  187 bits (474), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 110/297 (37%), Positives = 173/297 (58%), Gaps = 17/297 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG   T+GNALRRVL+S+L G AIT+V+I GV HE ++IKGV ED+ +I+LN+
Sbjct: 30  FIIEPLARGQGTTVGNALRRVLLSNLEGTAITSVRIAGVNHEFATIKGVREDVLEILLNM 89

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK   +  +   +   GP  VTA      +++EV++    I  L   +++ ME  +
Sbjct: 90  KEVVLKSYSEQPQIGRLRVEGPATVTADRFDVPSEVEVIDRSQYIATLSPGSILEMEFRI 149

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GY      R +   +  + IDA++ P++KV+YT+E A  G  L+ D+L M I T+G
Sbjct: 150 EKGTGYKAVDRTRDDVATLDFLQIDAIFMPVRKVNYTIEDAHIGSSLEQDRLIMDIWTNG 209

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP----FNPALLKKVEELEL 265
           S T +D+++ A+       G+ ++  EP K++    N+  +P     +P     +EEL+L
Sbjct: 210 SYTPQDALSNAA-------GILMSLFEPLKDI---TNMADIPSGETTDPTSQIPIEELQL 259

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           SVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E   V+  +   LG+ LP
Sbjct: 260 SVRAYNCLKRAQINSVADLLDYSQEDLLEIKNFGQKSAEE---VIEALQKRLGITLP 313


>gi|297623302|ref|YP_003704736.1| DNA-directed RNA polymerase subunit alpha [Truepera radiovictrix
           DSM 17093]
 gi|297164482|gb|ADI14193.1| DNA-directed RNA polymerase, alpha subunit [Truepera radiovictrix
           DSM 17093]
          Length = 310

 Score =  187 bits (474), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 113/292 (38%), Positives = 171/292 (58%), Gaps = 5/292 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPLPRG+  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED+  IILN+
Sbjct: 18  FIVEPLPRGYGVTLGNPLRRILLSSVAGTAVTSVYIEDVLHEFSTIPGVKEDVMQIILNL 77

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + +K+  D    +T+    PG VTA D +      ++NP+  +  L+    + ME+ V
Sbjct: 78  KELVVKLHDDEPVTLTLRAENPGRVTAADFEVPMGATLINPELYLATLNEGGKLVMEVRV 137

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYVPA+ H T+ D I  I +DA+++P+++V+Y VE  R GQ  D D+L + + TDG
Sbjct: 138 EPGIGYVPAEVHATK-DRINSIPVDAVFTPVRRVAYRVEDTRVGQKTDLDRLVLRVWTDG 196

Query: 210 SITGEDSVALASRILQDQLGMFIN--FEEPKKEVKEDINVKSLPFNPALLKKV--EELEL 265
           S++  +++  A  IL++QL +F     +EP   +         P + A   ++  E LEL
Sbjct: 197 SVSPREALDSAVEILRNQLSVFSGGVIDEPLPVMAIPPRSADEPLSRAEPARISLESLEL 256

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           S R  + L+ E I  +  L+  +E D+ ++   G KSL EIK  L   GL+L
Sbjct: 257 SSRVLHSLQEEGIDSVDALLALSERDLKKVGGVGDKSLEEIKERLQAQGLYL 308


>gi|119662383|emb|CAJ33180.1| RNA polymerase alpha subunit [Lactobacillus sakei subsp. carnosus]
          Length = 212

 Score =  187 bits (474), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 90/201 (44%), Positives = 141/201 (70%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L++SL G A+T +QIDGVLHE S+I GV ED+T IILNIK + LK+  
Sbjct: 1   YGTTLGNSLRRILLASLPGTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKLHV 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + I  +GP  VTA DI + +D+EVLN D  IC +       + +TV KG GYV A
Sbjct: 61  EEDKTIEIDVKGPATVTAADIISDDDVEVLNTDQYICTVAEGGNFHVRMTVKKGRGYVAA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++
Sbjct: 121 VQNKSDDMPIGVLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAIS 180

Query: 219 LASRILQDQLGMFINFEEPKK 239
           LA++I+ + L +F++  +  K
Sbjct: 181 LAAKIMTEHLAIFVDLTDEAK 201


>gi|119668335|emb|CAK95508.1| RNA polymerase alpha subunit [Lactobacillus johnsonii]
          Length = 185

 Score =  187 bits (474), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 93/185 (50%), Positives = 131/185 (70%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRRVL++S+ G A++ +QIDGVLHE S+I GV ED+T IILN+K + LK   D  K   I
Sbjct: 1   LRRVLLTSIPGTALSYIQIDGVLHEFSTIPGVREDVTKIILNLKKLELKSLSDEEKIAEI 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
              GP +VTA D++  +DIEVLNPD  IC++     + M + +  G GYVPA  ++T++ 
Sbjct: 61  DVTGPAIVTAADLKVDSDIEVLNPDQYICSIADGGHLHMNVAIKTGRGYVPASENKTDDM 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           PIG+I +D+L+SPIKKV+Y VESAR G+  DYDKL++ I TDGSIT  D+++ A++IL +
Sbjct: 121 PIGVIPVDSLFSPIKKVNYQVESARVGKRDDYDKLTLEIWTDGSITPNDALSFAAKILVE 180

Query: 227 QLGMF 231
              +F
Sbjct: 181 HFKVF 185


>gi|154424821|emb|CAL18513.1| RNA polymerase alpha subunit [Streptococcus mutans]
          Length = 200

 Score =  187 bits (474), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 92/198 (46%), Positives = 140/198 (70%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   +  
Sbjct: 1   TLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVEEE 60

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K V +   GP  +TAGDI T +DIE++NPDH +  +   A ++  +TV+   GYVPA+ +
Sbjct: 61  KIVELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIAEGANLKATMTVATNRGYVPAEKN 120

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           + ++ P+G + ID++Y+P+KKV+Y VE AR G   ++DKL++ I T+G+I  ED++ L++
Sbjct: 121 KRDDAPVGTLAIDSIYTPVKKVNYQVEPARVGSNDNFDKLTIEIMTNGTIIPEDALGLSA 180

Query: 222 RILQDQLGMFINFEEPKK 239
           R+L + L +F +  E  K
Sbjct: 181 RVLIEHLNLFTDLTEVAK 198


>gi|325294424|ref|YP_004280938.1| DNA-directed RNA polymerase subunit alpha [Desulfurobacterium
           thermolithotrophum DSM 11699]
 gi|325064872|gb|ADY72879.1| DNA-directed RNA polymerase subunit alpha [Desulfurobacterium
           thermolithotrophum DSM 11699]
          Length = 318

 Score =  186 bits (473), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 117/315 (37%), Positives = 179/315 (56%), Gaps = 7/315 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E I P   E  +  +  EN    + EPL +G+  T+GNALRRVL+SS+ GAA TAV+ +G
Sbjct: 3   EFITP---EKFLWEEHTENYGRFVVEPLEKGYGTTVGNALRRVLLSSIEGAAPTAVKFEG 59

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
             HE +++ GV ED+T+I+LN+K +   + G+    + + KRGPG V A D +  + +E+
Sbjct: 60  AYHEFTTLPGVVEDVTEIVLNLKQLRFILHGEGPVFIELKKRGPGKVYAKDFELPSQVEL 119

Query: 128 LNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVS 184
           L PD  I  LD  ++ + + L + KG G+V ++  +   D   IG I +DA +SPIKKV+
Sbjct: 120 LTPDQEIATLDNENSEIEIYLRIDKGKGFVLSEDIQEIFDISTIGWIPLDADFSPIKKVA 179

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN-FEEPKKEVKE 243
           + VE  R G+  DY++L+M I TDGSIT +D+V  A+ IL +   M  +   E      +
Sbjct: 180 FRVEDTRVGRRTDYNRLTMEIWTDGSITPKDAVVRAANILIEHFSMVRDKLVEAIFATAQ 239

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
              VK         + +EE  L  R+   L    I  +GDL++ T+ ++  M   G+KSL
Sbjct: 240 PEEVKKEEVPEIYNQTLEEAGLKGRALKILGENGITTVGDLVKLTKKELESMKGLGKKSL 299

Query: 304 VEIKGVLGTMGLFLG 318
            EI+  L ++G  LG
Sbjct: 300 AEIENFLASLGFELG 314


>gi|291296963|ref|YP_003508361.1| DNA-directed RNA polymerase subunit alpha [Meiothermus ruber DSM
           1279]
 gi|290471922|gb|ADD29341.1| DNA-directed RNA polymerase, alpha subunit [Meiothermus ruber DSM
           1279]
          Length = 321

 Score =  186 bits (473), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 115/299 (38%), Positives = 174/299 (58%), Gaps = 12/299 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED   +ILN+
Sbjct: 22  FVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDAIQLILNL 81

Query: 90  KGINLKMS--GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K + ++ +  G   K +T+   GP V+ A D++   D EV+NPD  I  L+    + ME+
Sbjct: 82  KELVVRFANPGTGPKTLTLRASGPKVIYARDLECPPDAEVVNPDQYIATLEEKGKLVMEI 141

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            V +G GYVPA+ H  + D I  I +DALYSP+++V+Y VE  R GQ  D DKL++ I T
Sbjct: 142 RVDEGVGYVPAEKHGIK-DRISSIPVDALYSPVRRVAYQVEDTRLGQRTDLDKLTLRIWT 200

Query: 208 DGSITGEDSVALASRILQDQLGMF----INFEEPKK-----EVKEDINVKSLPFNPALLK 258
           +G+++  D++  A  IL++QLG F    +   EPK               + P +P +  
Sbjct: 201 NGAVSPMDALQQAVAILREQLGYFDQSPVMRVEPKSTPAPAPAAPATTAPAAPASPGVGL 260

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            +++L L+ R  + L+ E I  +  L+  +E ++ R+   G +SL EIK  L   GL +
Sbjct: 261 TLDDLGLTTRVLHNLKEEGIESVESLLALSEKELRRVPGIGDRSLQEIKDCLAQHGLVM 319


>gi|154424851|emb|CAL18528.1| RNA polymerase alpha subunit [Streptococcus ratti]
          Length = 212

 Score =  186 bits (473), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 89/201 (44%), Positives = 140/201 (69%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ +K   
Sbjct: 1   YGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNLKGLAVKSYV 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + +   GP  +TAGDI T +DIE++NPDH +  +   A ++  LTV    GY+PA
Sbjct: 61  EEEKIIELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIAEGASLKATLTVGTNRGYIPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           + ++ ++ P+G + ID++Y+P+KKV+Y VE AR G   ++DKL++ I T+G+I  ED++ 
Sbjct: 121 EENKKDDAPVGTLAIDSIYTPVKKVNYQVEPARVGSNDNFDKLTIEIMTNGTIIPEDALG 180

Query: 219 LASRILQDQLGMFINFEEPKK 239
           L++R+L + L +F +  E  K
Sbjct: 181 LSARVLIEHLNLFTDLTEVAK 201


>gi|150036744|emb|CAM98026.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. mesenteroides]
          Length = 226

 Score =  186 bits (472), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 96/212 (45%), Positives = 139/212 (65%), Gaps = 2/212 (0%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           I EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K
Sbjct: 1   IVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            + L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  
Sbjct: 61  KVVLAIDSDDERSLEIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAV 120

Query: 151 KGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           KG GY  A  ++   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+
Sbjct: 121 KGRGYTSADENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           GSI   D+++L ++IL + LG+F++      E
Sbjct: 181 GSIKPSDALSLGAKILAEHLGLFMDISPVAAE 212


>gi|150036806|emb|CAM98276.1| DNA-directed RNA polymerase alpha chain [Fructobacillus
           pseudoficulneus]
          Length = 242

 Score =  186 bits (472), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 103/241 (42%), Positives = 149/241 (61%), Gaps = 2/241 (0%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL G A+  VQIDGV+HE S++ GV ED+T +ILN+K +
Sbjct: 2   EPLERGYGTTLGNSLRRVLLSSLPGVAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKV 61

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
                      + I  +GP  VTA D+    DIEVLNPD  I  L     + M +T  KG
Sbjct: 62  VFATDSAEEHALEIDVQGPKDVTAADLMGSADIEVLNPDLHIATLAAGKSLHMTVTAVKG 121

Query: 153 HGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            GY  A+ ++   D  PIG++T+D++Y+PI++V+Y VE+ R G   DYDKL+M + T+GS
Sbjct: 122 RGYSSAEENKQLRDEMPIGVLTVDSIYTPIERVNYHVENKRVGSRDDYDKLTMEVWTNGS 181

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I   D+++L S+IL + L +F +     ++ K  +  +      A    +E+L+LSVRS 
Sbjct: 182 IKPSDALSLGSKILTEHLNLFTDISPVAQDTKVMVESEPAANTAADAAPIEDLDLSVRSY 241

Query: 271 N 271
           N
Sbjct: 242 N 242


>gi|207721898|ref|YP_002252336.1| dna-directed rna polymerase alpha chain (partial sequence c
           terminus) protein [Ralstonia solanacearum MolK2]
 gi|206587066|emb|CAQ17650.1| probable dna-directed rna polymerase alpha chain (partial sequence
           c terminus) protein [Ralstonia solanacearum MolK2]
          Length = 215

 Score =  186 bits (472), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 94/206 (45%), Positives = 137/206 (66%), Gaps = 3/206 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EP  RG+ HTLGNALRRVL+SS+ G A T V I GV+HE S+I GV ED+ +++LN+KG+
Sbjct: 2   EPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGVVHEYSTIDGVQEDVVNLLLNLKGV 61

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
             K+       V++ K G GVVTA DI+  +D+E++NP HVI +L     + M++ V +G
Sbjct: 62  VFKLHNRDEVTVSLRKEGEGVVTAADIELPHDVEIINPGHVIASLSAGGKLDMQIKVEQG 121

Query: 153 HGYVPAKHHRTENDP---IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            GYVP    +  ++    IG + +DA ++P+++VSY VESAR  Q  D DKL M I+T+G
Sbjct: 122 RGYVPGNVRKFGDESSKVIGRVVLDASFAPVRRVSYAVESARVEQRTDLDKLVMNIETNG 181

Query: 210 SITGEDSVALASRILQDQLGMFINFE 235
            I+ E+++  ++RIL DQL +F   E
Sbjct: 182 VISPEEAIRQSARILVDQLSVFAALE 207


>gi|167626782|ref|YP_001677282.1| DNA-directed RNA polymerase subunit alpha [Francisella philomiragia
           subsp. philomiragia ATCC 25017]
 gi|167596783|gb|ABZ86781.1| DNA-directed RNA polymerase, alpha subunit [Francisella
           philomiragia subsp. philomiragia ATCC 25017]
          Length = 325

 Score =  186 bits (472), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 107/294 (36%), Positives = 175/294 (59%), Gaps = 9/294 (3%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P+ +G AH LGN++RR L+SSL GA+I  V IDGVLHE S+++ V ED+ +I+ N+K + 
Sbjct: 31  PVEKGMAHILGNSIRRFLLSSLSGASIIKVNIDGVLHEYSTLEDVKEDVVEIVSNLKKVA 90

Query: 94  LKMSGDSHK---RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +K+  +  K    +++ K G  VVTAGD +T   IE++N D  I  L  +    +  TVS
Sbjct: 91  IKLDKNVSKVELELSVTKSGVVVVTAGDFKTTQGIEIINKDQPIATLTNEREFSLTATVS 150

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            G          TE + +G I +D+ ++PIK+V++ +      + L+     + + T+G+
Sbjct: 151 VGRNVGILSALPTELEKVGDIAVDSDFNPIKRVAFEIFDNGTNETLE-----VFVKTNGT 205

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I    +V  A     +Q+ +F++   P      D  + S   +P LLK +++LEL+VRS+
Sbjct: 206 IEPLVAVTKALEYFCEQISVFVSLRVPSNGKTGDALLDS-NIDPILLKPIDDLELTVRSS 264

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L    L LG+ + ++
Sbjct: 265 NCLRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQILIDNNLSLGVQIDNF 318


>gi|225548741|ref|ZP_03769788.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           94a]
 gi|225370771|gb|EEH00207.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           94a]
          Length = 344

 Score =  186 bits (472), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 117/335 (34%), Positives = 183/335 (54%), Gaps = 17/335 (5%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +++K  ++   P  IE++   Q + +       P  RGF  T+GN LRRVL+SS+ G AI
Sbjct: 2   LVEKFLKDFTIPEKIEFLK-SQGDGSYGKFTIYPFERGFGITIGNTLRRVLLSSIEGYAI 60

Query: 61  TAVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK--- 108
           TA+++           V  E   I GV ED  ++I NIK I+LK+     K+   F    
Sbjct: 61  TAMRVQSNNKDASSKVVSSEFDLIPGVSEDTLEVIANIKNIHLKLGEGEQKKTISFSVSG 120

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
           +   V+ A   +  + +EV N D VI  L  D  + +E  ++ G GYV ++ +    + +
Sbjct: 121 KDTNVLKASHFER-DGVEVFNKDLVIATLSRDVNLDLEFQINYGRGYVSSEQNSKYLEEV 179

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
            +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L
Sbjct: 180 NVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREFL 239

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
              ++FE+    V           +  L   +E+L LSVRS NCL  EN+  +G+LI + 
Sbjct: 240 FPLVDFED---NVNTSFEKSKSESSNLLDMSIEKLNLSVRSLNCLAKENVRTLGELISKN 296

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
             ++ +  NFG+KSL EI   LG+  L+LGM+  D
Sbjct: 297 AEELSKARNFGKKSLEEIIEKLGSYRLYLGMSKED 331


>gi|149184060|ref|ZP_01862413.1| DNA-directed RNA polymerase subunit alpha [Bacillus sp. SG-1]
 gi|148848232|gb|EDL62529.1| DNA-directed RNA polymerase subunit alpha [Bacillus sp. SG-1]
          Length = 245

 Score =  186 bits (472), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 99/241 (41%), Positives = 152/241 (63%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+T II+NIK + LK+  D  K + I   G GVVTA DI   +D+EVLNP+  I  
Sbjct: 1   GVVEDVTTIIMNIKKLALKIYSDEEKTLEIDVNGEGVVTAADITHDSDVEVLNPELHIAT 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           L  ++  RM L   +G GY PA  ++ E+ PIG+I ID++Y+P+ +V+Y VE+ R GQ+ 
Sbjct: 61  LSANSNFRMRLAAQRGRGYTPADQNKREDLPIGVIPIDSIYTPVSRVNYQVENTRVGQLT 120

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           ++DKLS+ + TDGSI  +++++L ++IL + L +F+   +  +  +  +  +       L
Sbjct: 121 NFDKLSLDVWTDGSIGPKEAISLGAKILNEHLNIFVGLTDEAQNAEIMVEKEEDQKEKVL 180

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  +GL 
Sbjct: 181 EMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKVKLEDLGLG 240

Query: 317 L 317
           L
Sbjct: 241 L 241


>gi|119668301|emb|CAK95453.1| RNA polymerase alpha subunit [Lactobacillus curvatus]
          Length = 212

 Score =  186 bits (472), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 90/198 (45%), Positives = 140/198 (70%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L++SL G A+T +QIDGVLHE S+I GV ED+T IILNIK + LK+  +  
Sbjct: 3   TLGNSLRRILLASLPGTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKLHVEED 62

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I  +GP  VTA DI + +D+EVLN D  IC +       + +TV KG GYV A  +
Sbjct: 63  KTIEIDVKGPATVTAADIISDDDVEVLNTDQYICTVAEGGNFHVRMTVKKGRGYVAADQN 122

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           ++++ PIG++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA+
Sbjct: 123 KSDDMPIGVLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAA 182

Query: 222 RILQDQLGMFINFEEPKK 239
           +I+ + L +F++  +  K
Sbjct: 183 KIMTEHLAIFVDLTDEAK 200


>gi|119662321|emb|CAJ33148.1| RNA polymerase alpha subunit [Lactobacillus kefiranofaciens subsp.
           kefirgranum]
          Length = 215

 Score =  186 bits (471), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 92/193 (47%), Positives = 130/193 (67%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + +   GP  VTA D++   D++VLNPD  IC +     + MEL V  G GYV A
Sbjct: 61  DEQKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAKGGHLHMELAVKNGRGYVTA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++
Sbjct: 121 SDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALS 180

Query: 219 LASRILQDQLGMF 231
            A++IL +   +F
Sbjct: 181 FAAKILVEHFKVF 193


>gi|111115331|ref|YP_709949.1| DNA-directed RNA polymerase subunit alpha [Borrelia afzelii PKo]
 gi|119366667|sp|Q0SN05|RPOA_BORAP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|110890605|gb|ABH01773.1| DNA-directed RNA polymerase [Borrelia afzelii PKo]
          Length = 344

 Score =  186 bits (471), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 118/334 (35%), Positives = 186/334 (55%), Gaps = 17/334 (5%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +++  ++   P  IE++   Q++ +       P  RGF  T+GN LRRVL+SS+ G AIT
Sbjct: 3   MERFLKDFTIPEKIEFLK-SQDDGSYGKFTIYPFERGFGVTIGNTLRRVLLSSIEGYAIT 61

Query: 62  AVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGP 111
           A+++           V  E   I GV ED  ++I NIK I+LK+  G+  K ++    G 
Sbjct: 62  AMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLEVIANIKNIHLKLREGEQRKTISFSVSGK 121

Query: 112 --GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
              V+ A   +  + +EV N D VI  L  D  +  E  ++ G GYV ++ +    + + 
Sbjct: 122 DTNVLKASHFER-DGVEVFNKDLVIATLSHDVNLDFEFQINYGRGYVSSEQNSKYLEEVN 180

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L 
Sbjct: 181 VIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREFLF 240

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
             ++FE+    V    +      +  L   +E+L+LSVRS NCL  EN+  +G+LI +  
Sbjct: 241 PLVDFEDS---VSVSFDKSKSESSNLLDMSIEKLDLSVRSLNCLAKENVRTLGELISKNA 297

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            ++ +  NFG+KSL EI   LG+  LFLGM+  D
Sbjct: 298 EELSKARNFGKKSLEEIIEKLGSYQLFLGMSKED 331


>gi|51598757|ref|YP_072945.1| DNA-directed RNA polymerase subunit alpha [Borrelia garinii PBi]
 gi|61215870|sp|Q661B8|RPOA_BORGA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|51573328|gb|AAU07353.1| DNA-directed RNA polymerase [Borrelia garinii PBi]
          Length = 344

 Score =  186 bits (471), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 117/334 (35%), Positives = 184/334 (55%), Gaps = 17/334 (5%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++K  ++   P  IE++   Q++ +       P  RGF  T+GN LRRVL+SS+ G AIT
Sbjct: 3   VEKFLKDFTIPEKIEFLK-SQDDGSYGKFTIYPFERGFGVTIGNTLRRVLLSSIEGYAIT 61

Query: 62  AVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK---R 109
           A++I           V  E   I GV ED  ++I NIK I+LK+     +++  F    +
Sbjct: 62  AMRIQSNNKDSSSKVVSSEFDLIPGVSEDTLEVIANIKNIHLKLGEGEQRKIISFSVSGK 121

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
              V+ A   +  + +EV N D VI  L  D  + +E  ++ G GYV ++ +    + + 
Sbjct: 122 DTKVLKASHFER-DGVEVFNRDLVIATLSQDVNLDLEFQINYGRGYVSSEQNSKYLEEVN 180

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L 
Sbjct: 181 VIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIIREFLF 240

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
             I+FE+    +           +  L   +E+L+LSVRS NCL  EN+  +G+LI +  
Sbjct: 241 PLIDFED---NINTSFEKSKSESSNLLDMSIEKLDLSVRSLNCLAKENVRTLGELISKNA 297

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            ++ +  NFG+KSL EI   L +  LFLGM+  D
Sbjct: 298 EELSKARNFGKKSLEEIIEKLSSYQLFLGMSKED 331


>gi|216263341|ref|ZP_03435336.1| DNA-directed RNA polymerase, alpha subunit [Borrelia afzelii ACA-1]
 gi|215980185|gb|EEC21006.1| DNA-directed RNA polymerase, alpha subunit [Borrelia afzelii ACA-1]
          Length = 342

 Score =  186 bits (471), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 118/334 (35%), Positives = 186/334 (55%), Gaps = 17/334 (5%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +++  ++   P  IE++   Q++ +       P  RGF  T+GN LRRVL+SS+ G AIT
Sbjct: 1   MERFLKDFTIPEKIEFLK-SQDDGSYGKFTIYPFERGFGVTIGNTLRRVLLSSIEGYAIT 59

Query: 62  AVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGP 111
           A+++           V  E   I GV ED  ++I NIK I+LK+  G+  K ++    G 
Sbjct: 60  AMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLEVIANIKNIHLKLREGEQRKTISFSVSGK 119

Query: 112 --GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
              V+ A   +  + +EV N D VI  L  D  +  E  ++ G GYV ++ +    + + 
Sbjct: 120 DTNVLKASHFER-DGVEVFNKDLVIATLSHDVNLDFEFQINYGRGYVSSEQNSKYLEEVN 178

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L 
Sbjct: 179 VIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREFLF 238

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
             ++FE+    V    +      +  L   +E+L+LSVRS NCL  EN+  +G+LI +  
Sbjct: 239 PLVDFEDS---VSVSFDKSKSESSNLLDMSIEKLDLSVRSLNCLAKENVRTLGELISKNA 295

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            ++ +  NFG+KSL EI   LG+  LFLGM+  D
Sbjct: 296 EELSKARNFGKKSLEEIIEKLGSYQLFLGMSKED 329


>gi|168805063|gb|ACA28610.1| DNA-directed RNA polymerase subunit alpha [Thiomonas sp. WJ68]
          Length = 228

 Score =  186 bits (471), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 96/227 (42%), Positives = 147/227 (64%), Gaps = 3/227 (1%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           G  + +  ++LN+KG+ LK+       +++ K G GVVTA DIQT +D+E++NP+HVI +
Sbjct: 1   GKRQRVIGVLLNLKGVVLKLHNRDEVTLSLRKEGEGVVTAADIQTPHDVEIINPEHVIAH 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSYTVESAREG 193
           L     + M++ V KG GYVP       ++    IG I +DA +SP+++VSY VESAR  
Sbjct: 61  LSHGGKLDMQIKVEKGRGYVPGTLRNYGDEGGKSIGHIVLDASFSPVRRVSYAVESARVE 120

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL M I+T+G I+ E+++  ++RIL +QL +F + E  +     +    +  ++
Sbjct: 121 QRTDLDKLVMEIETNGVISAEEAIRSSARILVEQLSVFASLEGAETTEAAETAAGAQTYD 180

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GR
Sbjct: 181 PILLRPVDELELTVRSANCLKAENIYYIGDLIQRSETELLKTPNLGR 227


>gi|331703690|ref|YP_004400377.1| DNA directed RNA polymerase subunit alpha [Mycoplasma mycoides
           subsp. capri LC str. 95010]
 gi|256384042|gb|ACU78612.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma mycoides
           subsp. capri str. GM12]
 gi|256384874|gb|ACU79443.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma mycoides
           subsp. capri str. GM12]
 gi|296455853|gb|ADH22088.1| DNA-directed RNA polymerase, alpha subunit [synthetic Mycoplasma
           mycoides JCVI-syn1.0]
 gi|328802245|emb|CBW54399.1| DNA directed RNA polymerase alpha chain [Mycoplasma mycoides subsp.
           capri LC str. 95010]
          Length = 317

 Score =  186 bits (471), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 119/317 (37%), Positives = 186/317 (58%), Gaps = 12/317 (3%)

Query: 6   WQELIKPNNIEYIVLGQ-EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
            ++ ++P   E+I+L + +++N       PL RGF  TLGNA+RR L+++  GA++ A++
Sbjct: 1   MKQFVRP---EFILLKEGQDKNYGKFSVSPLERGFGITLGNAIRRTLLAATPGASVYAIK 57

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKM-----SGDSHKRVTIFKRGPGVVTAGDI 119
           I G  HE +SI G+ E++T IILNIK + LK+     S D   ++ I     G V AGD+
Sbjct: 58  IAGATHEFTSIPGIIENVTKIILNIKQLVLKIDTSIYSDDEVVQLRIRSDIQGPVYAGDL 117

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYS 178
                +E+LN D +I  +    V+ + L      GY   K ++ E N   G+ITID+ YS
Sbjct: 118 DIPAGVEILNKDLLIATISEGGVLDLVLYAKNSRGYKTFKDNKNEKNIEPGMITIDSNYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI KV+Y+V+SA+ G+ +D +KL + + TDGSIT  D++++ASRIL   L  FI+    +
Sbjct: 178 PIIKVAYSVDSAKIGRAIDLEKLELEVTTDGSITAIDAISIASRILVAHLEFFIDLNR-E 236

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
             V E I       +  L + VEEL+ + RS NCL+   I  + +L+ + E ++  + N 
Sbjct: 237 ISVLEVIGTNQTD-DKELDRTVEELDFTQRSLNCLKRAGINTLRELVSKNEDEIGSIRNL 295

Query: 299 GRKSLVEIKGVLGTMGL 315
           GRKSL EIK  + ++GL
Sbjct: 296 GRKSLKEIKDKVASLGL 312


>gi|119668325|emb|CAK95462.1| RNA polymerase alpha subunit [Lactobacillus hilgardii]
          Length = 200

 Score =  185 bits (470), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 100/200 (50%), Positives = 139/200 (69%), Gaps = 4/200 (2%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K I+LK+ G
Sbjct: 1   YGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKISLKLDG 60

Query: 99  --DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT ++G GYV
Sbjct: 61  PEDEDENLEIDVIGPADVTAGDIQGDSDVTVLNPDLHIATVAEGATFHMRLTANRGRGYV 120

Query: 157 PA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A     R    PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ I T+GSIT  
Sbjct: 121 SAVENKKRATEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDIWTNGSITPS 180

Query: 215 DSVALASRILQDQLGMFINF 234
           ++V+LA++IL + L MF++ 
Sbjct: 181 EAVSLAAKILTEHLEMFVDL 200


>gi|119662279|emb|CAJ33126.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 210

 Score =  185 bits (470), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 92/193 (47%), Positives = 130/193 (67%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + +   GP  VTA D++   D++VLNPD  IC +     + MEL V  G GYV A
Sbjct: 61  DEQKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMELAVKNGRGYVTA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++
Sbjct: 121 SDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALS 180

Query: 219 LASRILQDQLGMF 231
            A++IL +   +F
Sbjct: 181 FAAKILVEHFKVF 193


>gi|157363470|ref|YP_001470237.1| DNA-directed RNA polymerase subunit alpha [Thermotoga lettingae
           TMO]
 gi|172045986|sp|A8F4T9|RPOA_THELT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|157314074|gb|ABV33173.1| DNA-directed RNA polymerase, alpha subunit [Thermotoga lettingae
           TMO]
          Length = 332

 Score =  185 bits (470), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 123/332 (37%), Positives = 188/332 (56%), Gaps = 34/332 (10%)

Query: 15  IEYIV---LGQEEENR------TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           IEY++   L  EEE           +  P+ +G+  T+GNALRRVL+SS+   AI  ++ 
Sbjct: 2   IEYVIPKKLKIEEERSETEYYYARYVLSPMEKGYGTTIGNALRRVLLSSIPSVAIVGIRF 61

Query: 66  --DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV--TIFKRGPGVVTAGDIQT 121
                 HE  ++ GV ED+ +IILN+K I L+      +RV  T+ KRGPG +TA DI+ 
Sbjct: 62  IKPEKYHEFDTLPGVKEDILEIILNLKRIQLRADVPVRERVKMTVEKRGPGNLTAADIKV 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
               E+ NP   I  LD +A +  EL    G G+VPA+    ++  IG I ID ++SP+ 
Sbjct: 122 PAGFEIANPSLKIATLDEEADLFFELYAQAGKGFVPAQEM-DDHPEIGWIPIDGVFSPVM 180

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL---------GM-- 230
           KV++ VESAR  +  DYDK+ + I T  +I   +++  A  IL + L         GM  
Sbjct: 181 KVNFRVESARVEKRTDYDKMILEIWTKKTIFPNEALKRAVDILMNHLQIITDSLPEGMPP 240

Query: 231 ----FINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQ 286
               F+   + + +V++ ++ +   ++    KK++ELEL++RS NCLR + I  +GDL++
Sbjct: 241 LTTEFVPISQEEVKVEQTVSEEEAVYS----KKIDELELTIRSLNCLRRDKIETIGDLLK 296

Query: 287 RTEADMLRMANFGRKSLVEIK-GVLGTMGLFL 317
           RTE D+L++ NFG KSL E+K  +L   GL L
Sbjct: 297 RTEEDLLKIKNFGPKSLDEVKQKLLEKFGLSL 328


>gi|187918368|ref|YP_001883931.1| DNA-directed RNA polymerase subunit alpha [Borrelia hermsii DAH]
 gi|119861216|gb|AAX17011.1| DNA-directed RNA polymerase alpha chain [Borrelia hermsii DAH]
          Length = 344

 Score =  185 bits (470), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 119/320 (37%), Positives = 186/320 (58%), Gaps = 16/320 (5%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID----G 67
           P+ IE++  G+++ +    I  P  +GF  T+GN LRRVL+SS+ G AI+A++I     G
Sbjct: 14  PDRIEFL-RGEDDGSYGKFIIYPFEKGFGVTIGNTLRRVLLSSIEGYAISAMRIQSNQGG 72

Query: 68  VLHEISS----IKGVHEDLTDIILNIKGINLKMS---GDSHKRVTIFKRGPGVVTAGDIQ 120
            L  +SS    I GV ED  ++I NIK I+LK+      +   V++  +   V+ A  ++
Sbjct: 73  SLKIVSSEFDLIPGVVEDTLEVIANIKNIHLKLDEGVKSATISVSVNGKDTNVLKAVHLE 132

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               +EV N D VI  L  +A +  E  V  G GYV ++H+    + +  I +D+++SPI
Sbjct: 133 R-EGVEVCNKDLVIATLSSEANLDFEFQVDYGRGYVSSEHNAKYLEEVNTIALDSIFSPI 191

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KV+Y+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L   +NFE+   +
Sbjct: 192 EKVTYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREFLLPLVNFED---K 248

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V   ++      +  L   +E+L LSVRS NCL  EN+  +G+LI ++  ++ +  NFG+
Sbjct: 249 VVHSVDDSEFRDSDILNMNIEKLNLSVRSLNCLTKENVKTLGELISKSAEELSKARNFGK 308

Query: 301 KSLVEIKGVLGTMGLFLGMN 320
           KSL EI   L   GLFLGM+
Sbjct: 309 KSLEEIVEKLSVYGLFLGMS 328


>gi|119662367|emb|CAJ33172.1| RNA polymerase alpha subunit [Lactobacillus ultunensis]
          Length = 212

 Score =  185 bits (470), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 92/193 (47%), Positives = 130/193 (67%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + +   GP  VTA D++   D++VLNPD  IC +     + MEL V  G GYV A
Sbjct: 61  DEQKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMELAVKNGRGYVTA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++
Sbjct: 121 SDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALS 180

Query: 219 LASRILQDQLGMF 231
            A++IL +   +F
Sbjct: 181 FAAKILVEHFKVF 193


>gi|154424751|emb|CAL18478.1| RNA polymerase alpha subunit [Streptococcus salivarius]
          Length = 216

 Score =  185 bits (470), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 89/201 (44%), Positives = 140/201 (69%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILNIKG+ +K   
Sbjct: 1   YGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGLAVKSYV 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + +  +GP  VTAGDI T +DIE++NPDH +  +   A ++  +TV+   GYVPA
Sbjct: 61  EDEKTIELDVQGPAEVTAGDILTDSDIEIVNPDHYLFTIADGASLKATMTVATNRGYVPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ 
Sbjct: 121 DENKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALG 180

Query: 219 LASRILQDQLGMFINFEEPKK 239
           L++R+L + L +F +  +  K
Sbjct: 181 LSARVLIEHLNLFTDLTDVAK 201


>gi|150036812|emb|CAM98039.1| DNA-directed RNA polymerase alpha chain [Fructobacillus
           pseudoficulneus]
          Length = 240

 Score =  185 bits (470), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 102/240 (42%), Positives = 148/240 (61%), Gaps = 2/240 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRVL+SSL G A+  VQIDGV+HE S++ GV ED+T +ILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRVLLSSLPGVAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVV 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
                     + I  +GP  VTA D+    DIEVLNPD  I  L     + M +T  KG 
Sbjct: 61  FATDSAEEHALEIDVQGPKDVTAADLMGSADIEVLNPDLHIATLAAGKALHMTVTAVKGR 120

Query: 154 GYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A+ ++   D  PIG++T+D++Y+PI++V+Y VE+ R G   DYDKL+M + T+GSI
Sbjct: 121 GYSSAEENKQLRDEMPIGVLTVDSIYTPIERVNYHVENKRVGSRDDYDKLTMEVWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTN 271
              D+++L S+IL + L +F +     ++ K  +  +      A    +E+L+LSVRS N
Sbjct: 181 KPSDALSLGSKILTEHLNLFTDISPVAQDTKVMVESEPAANTAADAAPIEDLDLSVRSYN 240


>gi|83319728|ref|YP_424634.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma capricolum
           subsp. capricolum ATCC 27343]
 gi|119366699|sp|Q2SRH9|RPOA_MYCCT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|83283614|gb|ABC01546.1| DNA-directed RNA polymerase, alpha chain [Mycoplasma capricolum
           subsp. capricolum ATCC 27343]
          Length = 317

 Score =  185 bits (470), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 118/317 (37%), Positives = 188/317 (59%), Gaps = 12/317 (3%)

Query: 6   WQELIKPNNIEYIVLGQ-EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
            ++ ++P   E+I+L + +++N       PL RGF  TLGNA+RR L+++  GA++ A++
Sbjct: 1   MKQFVRP---EFILLKEGQDKNYGKFSVSPLERGFGITLGNAIRRTLLAATPGASVYAIK 57

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKM-----SGDSHKRVTIFKRGPGVVTAGDI 119
           I G  HE +SI G+ E++T IILNIK + L++     S D   ++ I     G V AGD+
Sbjct: 58  IAGATHEFTSIPGIIENVTKIILNIKQLVLRIDTSIYSDDEVVQLKIRSDIQGPVYAGDL 117

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYS 178
           +    +EVLN D +I  +    ++ + L      GY   K ++ E N   G+ITID+ YS
Sbjct: 118 ELPAGVEVLNQDLLIATISEGGILDLVLYAKNSRGYKTFKDNKNEKNIEPGMITIDSNYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI KV+Y+V+SA+ G+ +D +KL + + TDGSIT  D++++AS+IL   L  FI+    +
Sbjct: 178 PIIKVAYSVDSAKIGRAIDLEKLELEVTTDGSITAIDAISIASKILVAHLEFFIDLNR-E 236

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
             V E I V     +  L + VEEL+ + RS NCL+   I  + +L+ + E ++  + N 
Sbjct: 237 ISVLEVIGVNQTD-DKELDRTVEELDFTQRSLNCLKRAGINTLRELVTKNEDEIGSIRNL 295

Query: 299 GRKSLVEIKGVLGTMGL 315
           GRKSL EIK  + ++GL
Sbjct: 296 GRKSLKEIKDKVASLGL 312


>gi|216264217|ref|ZP_03436209.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           156a]
 gi|218249615|ref|YP_002375012.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           ZS7]
 gi|226320983|ref|ZP_03796528.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           29805]
 gi|226321812|ref|ZP_03797338.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           Bol26]
 gi|215980690|gb|EEC21497.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           156a]
 gi|218164803|gb|ACK74864.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           ZS7]
 gi|226233001|gb|EEH31754.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           Bol26]
 gi|226233584|gb|EEH32320.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           29805]
 gi|312149000|gb|ADQ29071.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           N40]
          Length = 344

 Score =  185 bits (469), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 118/335 (35%), Positives = 183/335 (54%), Gaps = 17/335 (5%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +++K  ++   P  IE++   Q + +       P  RGF  T+GN LRRVL+SS+ G AI
Sbjct: 2   LVEKFLKDFTIPEKIEFLK-SQGDGSYGKFTIYPFERGFGITIGNTLRRVLLSSIEGYAI 60

Query: 61  TAVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK--- 108
           TA+++           V  E   I GV ED  +II NIK I+LK+     K+   F    
Sbjct: 61  TAMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLEIIANIKNIHLKLGEGEQKKTISFSVSG 120

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
           +   V+ A   +  + +EV N D VI  L  D  + +E  ++ G GYV ++ +    + +
Sbjct: 121 KDTNVLKASHFER-DGVEVFNKDLVIATLSRDVNLDLEFQINYGRGYVSSEQNSKYLEEV 179

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
            +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L
Sbjct: 180 NVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREFL 239

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
              ++FE+    V           +  L   +E+L LSVRS NCL  EN+  +G+LI + 
Sbjct: 240 FPLVDFED---NVNTSFEKSKSESSNLLDMSIEKLNLSVRSLNCLAKENVRTLGELISKN 296

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
             ++ +  NFG+KSL EI   LG+  L+LGM+  D
Sbjct: 297 AEELSKARNFGKKSLEEIIEKLGSYRLYLGMSKED 331


>gi|4379135|emb|CAA83722.1| DNA-directed RNA Polymerase (alpha) [Mycoplasma capricolum subsp.
           capricolum ATCC 27343]
          Length = 317

 Score =  185 bits (469), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 118/317 (37%), Positives = 188/317 (59%), Gaps = 12/317 (3%)

Query: 6   WQELIKPNNIEYIVLGQ-EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
            ++ ++P   E+I+L + +++N       PL RGF  TLGNA+RR L+++  GA++ A++
Sbjct: 1   MKQFVRP---EFILLKEGQDKNYGKXXVSPLERGFGITLGNAIRRTLLAATPGASVYAIK 57

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKM-----SGDSHKRVTIFKRGPGVVTAGDI 119
           I G  HE +SI G+ E++T IILNIK + L++     S D   ++ I     G V AGD+
Sbjct: 58  IAGATHEFTSIPGIIENVTKIILNIKQLVLRIDTSIYSDDEVVQLKIRSDIQGPVYAGDL 117

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYS 178
           +    +EVLN D +I  +    ++ + L      GY   K ++ E N   G+ITID+ YS
Sbjct: 118 ELPAGVEVLNQDLLIATISEGGILDLVLYAKNSRGYKTFKDNKNEKNVEPGMITIDSNYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI KV+Y+V+SA+ G+ +D +KL + + TDGSIT  D++++AS+IL   L  FI+    +
Sbjct: 178 PIIKVAYSVDSAKIGRAIDLEKLELEVTTDGSITAIDAISIASKILVAHLEFFIDLNR-E 236

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
             V E I V     +  L + VEEL+ + RS NCL+   I  + +L+ + E ++  + N 
Sbjct: 237 ISVLEVIGVNQTD-DKELDRTVEELDFTQRSLNCLKRAGINTLRELVTKNEDEIGSIRNL 295

Query: 299 GRKSLVEIKGVLGTMGL 315
           GRKSL EIK  + ++GL
Sbjct: 296 GRKSLKEIKDKVASLGL 312


>gi|150036746|emb|CAM98260.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. mesenteroides]
          Length = 226

 Score =  185 bits (469), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 95/212 (44%), Positives = 138/212 (65%), Gaps = 2/212 (0%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K +
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKV 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG
Sbjct: 61  VLAIDSDDERSLEIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKG 120

Query: 153 HGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            GY  A  ++   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GS
Sbjct: 121 RGYTSADENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTNGS 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           I   D+++L ++IL + LG+F++      E  
Sbjct: 181 IKPSDALSLGAKILAEHLGLFMDISPVAAEAS 212


>gi|42561246|ref|NP_975697.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma mycoides
           subsp. mycoides SC str. PG1]
 gi|61215950|sp|Q6MSP9|RPOA_MYCMS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|42492744|emb|CAE77339.1| DNA-directed RNA polymerase alpha chain [Mycoplasma mycoides subsp.
           mycoides SC str. PG1]
 gi|301321162|gb|ADK69805.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma mycoides
           subsp. mycoides SC str. Gladysdale]
          Length = 317

 Score =  185 bits (469), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 118/317 (37%), Positives = 186/317 (58%), Gaps = 12/317 (3%)

Query: 6   WQELIKPNNIEYIVLGQ-EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
            ++ ++P   E+I+L + +++N       PL RGF  TLGNA+RR L+++  GA++ A++
Sbjct: 1   MKQFVRP---EFILLKEGQDKNYGKFSVSPLERGFGITLGNAIRRTLLAATPGASVYAIK 57

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKM-----SGDSHKRVTIFKRGPGVVTAGDI 119
           I G  HE +SI G+ E++T IILNIK + LK+     S D   ++ I     G + AGD+
Sbjct: 58  IAGATHEFTSIPGIIENVTKIILNIKQLVLKIDTSIYSDDEVVQLRIRSDIQGPIYAGDL 117

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYS 178
                +E+LN D +I  +    V+ + L      GY   K ++ E N   G+ITID+ YS
Sbjct: 118 DIPAGVEILNKDLLIATISEGGVLDLVLYAKNSRGYKTFKDNKNEKNIEPGMITIDSNYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI KV+Y+V+SA+ G+ +D +KL + + TDGSIT  D++++ASRIL   L  FI+    +
Sbjct: 178 PIIKVAYSVDSAKIGRAIDLEKLELEVTTDGSITAIDAISIASRILVAHLEFFIDLNR-E 236

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
             V E I       +  L + VEEL+ + RS NCL+   I  + +L+ + E ++  + N 
Sbjct: 237 ISVLEVIGTNQTD-DKELDRTVEELDFTQRSLNCLKRAGINTLRELVSKNEDEIGSIRNL 295

Query: 299 GRKSLVEIKGVLGTMGL 315
           GRKSL EIK  + ++GL
Sbjct: 296 GRKSLKEIKDKVASLGL 312


>gi|150036818|emb|CAM98041.1| DNA-directed RNA polymerase alpha chain [Leuconostoc fallax]
          Length = 222

 Score =  185 bits (469), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 95/218 (43%), Positives = 142/218 (65%), Gaps = 2/218 (0%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T +ILN+K +
Sbjct: 2   EPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKV 61

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            L +  D  K + I  +GP  VTA D+Q   DIEVLNP+  +  +     + M +T  KG
Sbjct: 62  VLAIDSDEEKSLEIDVQGPAEVTAADLQGSADIEVLNPELHLATVAAGKSLHMTVTAVKG 121

Query: 153 HGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            GY  A  ++   D  PIG++ +D++Y+PI++V+Y VE+ R GQ  DYDKL+  I T+GS
Sbjct: 122 RGYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGQRDDYDKLTFDIWTNGS 181

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           I   D+++L ++IL + L +F +      E +  ++V+
Sbjct: 182 IKPSDALSLGAKILSEHLNLFTDISSVAAETEVMVDVE 219


>gi|119668303|emb|CAK95505.1| RNA polymerase alpha subunit [Lactobacillus curvatus]
          Length = 217

 Score =  184 bits (468), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 89/197 (45%), Positives = 139/197 (70%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRR+L++SL G A+T +QIDGVLHE S+I GV ED+T IILNIK + LK+  +  K
Sbjct: 1   LGNSLRRILLASLPGTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKLHVEEDK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + I  +GP  VTA DI + +D+EVLN D  IC +       + +TV KG GYV A  ++
Sbjct: 61  TIEIDVKGPATVTAADIISDDDVEVLNTDQYICTVAEGGNFHVRMTVKKGRGYVAADQNK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
           +++ PIG++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++
Sbjct: 121 SDDMPIGVLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAK 180

Query: 223 ILQDQLGMFINFEEPKK 239
           I+ + L +F++  +  K
Sbjct: 181 IMTEHLAIFVDLTDEAK 197


>gi|150187035|emb|CAK30156.1| RNA polymerase alpha subunit [Streptococcus entericus]
          Length = 222

 Score =  184 bits (468), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 91/203 (44%), Positives = 140/203 (68%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ 
Sbjct: 1   PLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNLKGLA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +K   D  K + +   GP  VTAGDI T +DIE++N +H +  +   A  +  L V+   
Sbjct: 61  IKSHVDEEKTMELDIVGPAEVTAGDILTDSDIEIINTNHYLFTIAEGASFKAVLKVNTDR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYVPA++++  + P+G + IDA+Y+P+KKV+Y VE AR G    +DKL++ I+T+G+I  
Sbjct: 121 GYVPAENNKKGDAPVGTLAIDAIYTPVKKVNYQVEPARVGSNDGFDKLTIDIETNGTIIP 180

Query: 214 EDSVALASRILQDQLGMFINFEE 236
           ED++ L++ +L + L +F +  +
Sbjct: 181 EDALGLSANVLINHLNLFTDLTD 203


>gi|224532905|ref|ZP_03673517.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           WI91-23]
 gi|224512181|gb|EEF82570.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           WI91-23]
          Length = 344

 Score =  184 bits (467), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 121/336 (36%), Positives = 186/336 (55%), Gaps = 19/336 (5%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +++K  ++   P  IE++   Q + +       P  RGF  T+GN LRRVL+SS+ G AI
Sbjct: 2   LVEKFLKDFTIPEKIEFLK-SQGDGSYGKFTIYPFERGFGITIGNTLRRVLLSSIEGYAI 60

Query: 61  TAVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGP 111
           TA+++           V  E   I GV ED  +II NIK I+LK+ G+  +R TI     
Sbjct: 61  TAMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLEIIANIKNIHLKL-GEGEQRKTISFSVS 119

Query: 112 G----VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
           G    V+ A   +  + +EV N D VI  L  D  + +E  ++ G GYV ++ +    + 
Sbjct: 120 GKDTNVLKASHFER-DGVEVFNKDLVIATLSRDVNLDLEFQINYGRGYVSSEQNSKYLEE 178

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           + +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ 
Sbjct: 179 VNVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREF 238

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
           L   ++FE+    V           +  L   +E+L LSVRS NCL  EN+  +G+LI +
Sbjct: 239 LFPLVDFED---NVNTSFEKSKSESSNLLDMSIEKLNLSVRSLNCLAKENVRTLGELISK 295

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
              ++ +  NFG+KSL EI   LG+  L+LGM+  D
Sbjct: 296 NAEELSKARNFGKKSLEEIIEKLGSYRLYLGMSKED 331


>gi|119668293|emb|CAK95452.1| RNA polymerase alpha subunit [Lactobacillus collinoides]
          Length = 191

 Score =  184 bits (467), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 96/191 (50%), Positives = 137/191 (71%), Gaps = 3/191 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN K I+LK+ G
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNTKKISLKLEG 60

Query: 99  --DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             D  + + I  +GP  VTAGDI   +D+ VLNPD  I  +   A   M +T +KG GYV
Sbjct: 61  PDDEIESMEIDVKGPAQVTAGDITADSDVTVLNPDLYIATVAEGATFHMRMTANKGRGYV 120

Query: 157 PAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
            A  ++ + D PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TD SIT  +
Sbjct: 121 SADRNKAKEDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDSSITPSE 180

Query: 216 SVALASRILQD 226
           S++LA++IL +
Sbjct: 181 SISLAAKILTE 191


>gi|119668317|emb|CAK95459.1| RNA polymerase alpha subunit [Lactobacillus gallinarum]
          Length = 214

 Score =  184 bits (467), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 91/193 (47%), Positives = 130/193 (67%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V  G GYV A
Sbjct: 61  DERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNGRGYVAA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++
Sbjct: 121 SDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALS 180

Query: 219 LASRILQDQLGMF 231
            A++IL +   +F
Sbjct: 181 FAAKILVEHFKVF 193


>gi|195941639|ref|ZP_03087021.1| DNA-directed RNA polymerase subunit alpha [Borrelia burgdorferi
           80a]
 gi|221218042|ref|ZP_03589508.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           72a]
 gi|223889037|ref|ZP_03623628.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           64b]
 gi|224533576|ref|ZP_03674165.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           CA-11.2a]
 gi|225549661|ref|ZP_03770627.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           118a]
 gi|221191990|gb|EEE18211.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           72a]
 gi|223885853|gb|EEF56952.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           64b]
 gi|224513249|gb|EEF83611.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           CA-11.2a]
 gi|225369938|gb|EEG99385.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           118a]
          Length = 344

 Score =  184 bits (467), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 121/336 (36%), Positives = 186/336 (55%), Gaps = 19/336 (5%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +++K  ++   P  IE++   Q + +       P  RGF  T+GN LRRVL+SS+ G AI
Sbjct: 2   LVEKFLKDFTIPEKIEFLK-SQGDGSYGKFTIYPFERGFGITIGNTLRRVLLSSIEGYAI 60

Query: 61  TAVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGP 111
           TA+++           V  E   I GV ED  +II NIK I+LK+ G+  +R TI     
Sbjct: 61  TAMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLEIIANIKNIHLKL-GEGEQRKTISFSVS 119

Query: 112 G----VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
           G    V+ A   +  + +EV N D VI  L  D  + +E  ++ G GYV ++ +    + 
Sbjct: 120 GKDTNVLKASHFER-DGVEVFNKDLVIATLSHDVNLDLEFQINYGRGYVSSEQNSKYLEE 178

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           + +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ 
Sbjct: 179 VNVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREF 238

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
           L   ++FE+    V           +  L   +E+L LSVRS NCL  EN+  +G+LI +
Sbjct: 239 LFPLVDFED---NVNTSFEKSKSESSNLLDMSIEKLNLSVRSLNCLAKENVRTLGELISK 295

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
              ++ +  NFG+KSL EI   LG+  L+LGM+  D
Sbjct: 296 NAEELSKARNFGKKSLEEIIEKLGSYRLYLGMSKED 331


>gi|90567619|emb|CAJ31077.1| RNA polymerase alpha subunit [Lactobacillus helveticus R0052]
          Length = 197

 Score =  184 bits (467), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 91/193 (47%), Positives = 130/193 (67%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSFS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V  G GYV A
Sbjct: 61  DERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNGRGYVAA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++
Sbjct: 121 SDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALS 180

Query: 219 LASRILQDQLGMF 231
            A++IL +   +F
Sbjct: 181 FAAKILVEHFKVF 193


>gi|67923562|ref|ZP_00517035.1| DNA-directed RNA polymerase [Crocosphaera watsonii WH 8501]
 gi|67854588|gb|EAM49874.1| DNA-directed RNA polymerase [Crocosphaera watsonii WH 8501]
          Length = 314

 Score =  184 bits (467), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 108/293 (36%), Positives = 171/293 (58%), Gaps = 7/293 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG   T+GN+LRRVL+++L GAA+TA++I GV HE ++I GV ED+ +I+LN+
Sbjct: 23  FVLEPLERGQGTTVGNSLRRVLLANLEGAAVTAIRIGGVNHEFATIPGVREDVLEIMLNM 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK   +  +   +   G   VTAG  +  +++EV+NP   I  L   A + ME  +
Sbjct: 83  KEIVLKSYTEQPQIGRLVATGAAHVTAGQFELPSEVEVVNPTQPIATLTEGAKLEMEFRI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYVP +    E   +  + IDA++ P+ KV+Y+VES R  +    D+L + I T+G
Sbjct: 143 EKGVGYVPVERSSEEPAALDFLQIDAVFMPVTKVNYSVESIRGEEGEAKDRLMLEIWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           S   +++++ A+ IL D      +  + +  V+E  + +    NP     +EEL+LSVR+
Sbjct: 203 SFNPKEALSKAADILVDLFNPLKDLNQLETAVQEYPDEE----NPQSQIPIEELQLSVRA 258

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
            NCL+   I  + DL+  ++ D+L + NFG+KS  E   V+  +   LG+ LP
Sbjct: 259 YNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEE---VIEALQKRLGITLP 308


>gi|150036794|emb|CAM98273.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. mesenteroides]
          Length = 213

 Score =  184 bits (467), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 94/210 (44%), Positives = 138/210 (65%), Gaps = 2/210 (0%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K +
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKV 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG
Sbjct: 61  VLAIDSDDERSLEIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKG 120

Query: 153 HGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            GY  A  ++   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GS
Sbjct: 121 RGYTSADENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTNGS 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +   D+++L ++IL + LG+F++      E
Sbjct: 181 VKPSDALSLGAKILAEHLGLFMDISPVAAE 210


>gi|119662303|emb|CAJ33139.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           indicus]
          Length = 223

 Score =  184 bits (466), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 90/202 (44%), Positives = 131/202 (64%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN+LRRVL++S+ G  +  V+IDG+LHE +++ GV ED+T IILN+
Sbjct: 1   FVVEPLERGFGTTLGNSLRRVLLTSVPGTGLVKVKIDGILHEFTTVPGVKEDVTKIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L+   +  K + +   GP  VTA D++   D+EVLNPD  IC +     + M + V
Sbjct: 61  KKLELRAYTEEVKTIELDVEGPATVTAEDLKADADVEVLNPDQYICTIAQGGHLHMWIDV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYVPA  ++T    IG I +D+L+SPI+KV+Y VES R G+  D+DKL++ I T+G
Sbjct: 121 CNGRGYVPASENKTAEMSIGDIPVDSLFSPIEKVNYQVESTRVGKREDFDKLTLEIWTNG 180

Query: 210 SITGEDSVALASRILQDQLGMF 231
           SI   D++  A+R+L +    F
Sbjct: 181 SIAPNDALNFAARVLVEHFKAF 202


>gi|15594847|ref|NP_212636.1| DNA-directed RNA polymerase subunit alpha [Borrelia burgdorferi
           B31]
 gi|3914813|sp|O51455|RPOA_BORBU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|2688389|gb|AAC66840.1| DNA-directed RNA polymerase (rpoA) [Borrelia burgdorferi B31]
          Length = 345

 Score =  184 bits (466), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 121/336 (36%), Positives = 186/336 (55%), Gaps = 19/336 (5%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +++K  ++   P  IE++   Q + +       P  RGF  T+GN LRRVL+SS+ G AI
Sbjct: 3   LVEKFLKDFTIPEKIEFLK-SQGDGSYGKFTIYPFERGFGITIGNTLRRVLLSSIEGYAI 61

Query: 61  TAVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGP 111
           TA+++           V  E   I GV ED  +II NIK I+LK+ G+  +R TI     
Sbjct: 62  TAMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLEIIANIKNIHLKL-GEGEQRKTISFSVS 120

Query: 112 G----VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
           G    V+ A   +  + +EV N D VI  L  D  + +E  ++ G GYV ++ +    + 
Sbjct: 121 GKDTNVLKASHFER-DGVEVFNKDLVIATLSHDVNLDLEFQINYGRGYVSSEQNSKYLEE 179

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           + +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ 
Sbjct: 180 VNVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREF 239

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
           L   ++FE+    V           +  L   +E+L LSVRS NCL  EN+  +G+LI +
Sbjct: 240 LFPLVDFED---NVNTSFEKSKSESSNLLDMSIEKLNLSVRSLNCLAKENVRTLGELISK 296

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
              ++ +  NFG+KSL EI   LG+  L+LGM+  D
Sbjct: 297 NAEELSKARNFGKKSLEEIIEKLGSYRLYLGMSKED 332


>gi|151416838|emb|CAO78490.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gelidum]
          Length = 220

 Score =  184 bits (466), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 94/213 (44%), Positives = 138/213 (64%), Gaps = 2/213 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+
Sbjct: 1   FVIEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L +  D  + + +  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T 
Sbjct: 61  KKVVLAIDSDEERSLEVDIQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTITA 120

Query: 150 SKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GY  A  ++   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T
Sbjct: 121 FKGRGYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +GSI   D+++L S+IL + L +F++      E
Sbjct: 181 NGSIKPSDALSLGSKILAEHLNLFMDISPVAAE 213


>gi|94985940|ref|YP_605304.1| DNA-directed RNA polymerase subunit alpha [Deinococcus geothermalis
           DSM 11300]
 gi|119366678|sp|Q1IX99|RPOA_DEIGD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|94556221|gb|ABF46135.1| DNA-directed RNA polymerase subunit alpha [Deinococcus geothermalis
           DSM 11300]
          Length = 331

 Score =  184 bits (466), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 116/312 (37%), Positives = 172/312 (55%), Gaps = 25/312 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  T+GN +RR+LMSS+ G A+T+V I+ VLHE S+I GV ED+  IILN+
Sbjct: 19  FVLEPLTRGYGVTIGNPIRRILMSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVIRIILNL 78

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + +K      K +T+  +G GVV A   +  +D E++NPD  I  L  D  + ME+ V
Sbjct: 79  KELVVKFHAPGPKTLTLRAQGEGVVKASAFEVPSDAEIVNPDLTIATLAEDGKLVMEVRV 138

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYVPA  H T+ D I  I +DA++SP+++V+Y VE+ R GQ  D D+L + I TDG
Sbjct: 139 EEGEGYVPADKHATK-DRINSIPVDAVFSPVRRVAYHVENTRVGQQTDLDRLILRIWTDG 197

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS----------LPFNPAL--- 256
           S+  ++++  A  IL+D+L +F N E       E  +V +          LP  P L   
Sbjct: 198 SVGPQEALDRAVEILRDELTVFGNVETVSAAAPELPSVYTPAAPIVSGYDLPRQPELSIN 257

Query: 257 -----------LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                         +E L L+ R  + L+ E I  +  L   ++ D+ ++   G +SL E
Sbjct: 258 PQPYPADLDTPRVTLEGLGLTTRVLHSLKEEGIDSVDALCALSDRDLKKVPGIGERSLDE 317

Query: 306 IKGVLGTMGLFL 317
           IK  L   GL L
Sbjct: 318 IKQQLAQFGLAL 329


>gi|150036758|emb|CAM98029.1| DNA-directed RNA polymerase alpha chain [Leuconostoc lactis KCTC
           3528]
          Length = 228

 Score =  184 bits (466), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 94/213 (44%), Positives = 138/213 (64%), Gaps = 2/213 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T 
Sbjct: 61  KKVVLAIDSDDERSLEIDVQGPAEVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTA 120

Query: 150 SKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GY  A  ++   E  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T
Sbjct: 121 VKGRGYSSADENKQLREEMPIGVLAVDSIYTPIERVNYHVENTRVGARDDYDKLTFDIWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +GSI   D+++L ++IL + L +F++      E
Sbjct: 181 NGSIKPSDALSLGAKILAEHLNLFMDISPVAAE 213


>gi|154424803|emb|CAL18504.1| RNA polymerase alpha subunit [Streptococcus hyovaginalis]
          Length = 212

 Score =  184 bits (466), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 89/205 (43%), Positives = 141/205 (68%)

Query: 35  LPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL 94
           L RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ +
Sbjct: 1   LERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNVKGLAV 60

Query: 95  KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHG 154
           K   +  K + +  +GP  VTAGDI T +D+E++N DH +  +   A  +  +TV+   G
Sbjct: 61  KSYVEDEKIIELDVQGPAEVTAGDILTDSDVEIVNSDHYLFTIAEGASFKASMTVATNRG 120

Query: 155 YVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
           YV A+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  E
Sbjct: 121 YVAAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPE 180

Query: 215 DSVALASRILQDQLGMFINFEEPKK 239
           D++ L++R+L + L +F +  E  K
Sbjct: 181 DALGLSARVLIEHLNLFTDLTEVAK 205


>gi|150036790|emb|CAM98272.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 223

 Score =  183 bits (465), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 94/213 (44%), Positives = 139/213 (65%), Gaps = 2/213 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+
Sbjct: 2   VVIEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNL 61

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T 
Sbjct: 62  KKVVLAIDSDDERSLEIDVQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTA 121

Query: 150 SKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GY  A  ++   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T
Sbjct: 122 VKGRGYTSADENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGARDDYDKLTFDIWT 181

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +GSI   D+++L ++IL + L +F++      E
Sbjct: 182 NGSIKPSDALSLGAKILAEHLNLFMDISPVAAE 214


>gi|154424867|emb|CAL18536.1| RNA polymerase alpha subunit [Streptococcus uberis]
          Length = 210

 Score =  183 bits (465), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 90/201 (44%), Positives = 139/201 (69%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL+SSL GAA+T+++ DGVLHE  +I GV ED+  IILNIKG+ +K   
Sbjct: 1   YGTTLGNSLRRVLLSSLPGAAVTSIKFDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYV 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV+K  GYVPA
Sbjct: 61  EDEKMIELDVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLKATMTVAKKRGYVPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           + ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ 
Sbjct: 121 EGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALG 180

Query: 219 LASRILQDQLGMFINFEEPKK 239
           L++R+L + L +F +  E  K
Sbjct: 181 LSARVLIEHLNLFTDLTEVAK 201


>gi|119662323|emb|CAJ33149.1| RNA polymerase alpha subunit [Lactobacillus kimchii]
          Length = 213

 Score =  183 bits (465), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 86/201 (42%), Positives = 138/201 (68%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL++SL G A++ +QIDGVLHE S++ GV ED+T I+LN+K + LK   
Sbjct: 1   YGTTLGNSLRRVLLASLPGTAVSDIQIDGVLHEFSAVDGVIEDVTQIVLNVKKLKLKSYA 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D   +  I   GP  VTA DI+  +D+E+L+P+  IC +       M++TV  G GY PA
Sbjct: 61  DDSLKAEIDVVGPATVTANDIKADDDLEILDPEQFICTVAEGGHFHMQMTVINGRGYTPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           + ++T+  PIG++ +D++++P++KV+Y VE+ R G+  D+DKL++ I T+GSI   ++++
Sbjct: 121 EQNKTDETPIGVLPVDSIFTPVEKVNYQVENTRVGKRNDFDKLTIDIWTNGSIGPREAIS 180

Query: 219 LASRILQDQLGMFINFEEPKK 239
           L+++IL + L  F+N  E  K
Sbjct: 181 LSAKILTEHLTSFVNLTEEAK 201


>gi|154424871|emb|CAL18538.1| RNA polymerase alpha subunit [Streptococcus vestibularis]
          Length = 211

 Score =  183 bits (465), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 88/197 (44%), Positives = 138/197 (70%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILNIKG+ +K   +  K
Sbjct: 1   LGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGLAVKSYVEDEK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + +  +GP  VTAGDI T +DIE++NPDH +  +   A ++  +TV+   GYVPA  ++
Sbjct: 61  TIELDVQGPAEVTAGDILTDSDIEIVNPDHYLFTISEGASLKATMTVATNRGYVPADENK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R
Sbjct: 121 KDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSAR 180

Query: 223 ILQDQLGMFINFEEPKK 239
           +L + L +F +  +  K
Sbjct: 181 VLIEHLNLFTDLTDVAK 197


>gi|119662393|emb|CAJ33186.1| RNA polymerase alpha subunit [Lactobacillus plantarum]
          Length = 204

 Score =  183 bits (465), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 94/192 (48%), Positives = 136/192 (70%), Gaps = 2/192 (1%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           +L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK+  D  K + I  +
Sbjct: 1   ILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTAIILNVKKIALKLESDETKTLEIDVK 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK--HHRTENDP 167
           GP  VTAGDI    D+EVLNPD  IC +   A   M +T + G GYV A+   HR ++ P
Sbjct: 61  GPANVTAGDIIGDADVEVLNPDLPICTVADGAHFHMRMTANTGRGYVSAEDNKHREDDMP 120

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           IG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T+GSIT  ++++L+++IL D 
Sbjct: 121 IGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWTNGSITPSEAISLSAKILTDH 180

Query: 228 LGMFINFEEPKK 239
           L +F+N  +  K
Sbjct: 181 LSIFVNLTDEAK 192


>gi|119662347|emb|CAJ33162.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
          Length = 203

 Score =  183 bits (465), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 92/200 (46%), Positives = 142/200 (71%), Gaps = 2/200 (1%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K ++LK+  +  K +
Sbjct: 1   NSLRRVLIASLPGAAITSMQIDGVLHEFSTVEGVTEDVTQIILNLKKVSLKLDSEDQKNL 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +  +GP  VTA DIQ  N++ +LNPD  I  +   A + ++LT  KG GY+ A  ++  
Sbjct: 61  ELDVKGPAEVTASDIQGDNEVTILNPDLHIATVADGAELHIKLTADKGRGYLSANDNKAR 120

Query: 165 ND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            D   IG++ ID++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T  ++V+L ++
Sbjct: 121 MDDLAIGVLPIDSIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLTPTEAVSLGAK 180

Query: 223 ILQDQLGMFINFEEPKKEVK 242
           IL + L MF++  E  +  +
Sbjct: 181 ILTEHLAMFVDLTETAQNAQ 200


>gi|219685166|ref|ZP_03539986.1| DNA-directed RNA polymerase, alpha subunit [Borrelia garinii Far04]
 gi|219673262|gb|EED30281.1| DNA-directed RNA polymerase, alpha subunit [Borrelia garinii Far04]
          Length = 344

 Score =  183 bits (465), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 121/335 (36%), Positives = 185/335 (55%), Gaps = 19/335 (5%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++K  ++   P  IE++   Q + +       P  RGF  T+GN LRRVL+SS+ G AIT
Sbjct: 3   VEKFLKDFTIPEKIEFLK-SQGDGSYGKFTIYPFERGFGVTIGNTLRRVLLSSIEGYAIT 61

Query: 62  AVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
           A++I           V  E   I GV ED  ++I NIK I+LK+ G+  +R TI     G
Sbjct: 62  AMRIQSNNKDSSSKVVSSEFDLIPGVSEDTLEVIANIKNIHLKL-GEGEQRKTISFSVSG 120

Query: 113 ----VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
               V+ A   +  + +EV N D VI  L  D  + +E  ++ G GYV ++ +    + +
Sbjct: 121 KDTKVLKASHFER-DGVEVFNRDLVIATLSQDVNLDLEFQINYGRGYVSSEQNSKYLEEV 179

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
            +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L
Sbjct: 180 NVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIIREFL 239

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
              ++FE+    V           +  L   +E+L+LSVRS NCL  EN+  +G+LI + 
Sbjct: 240 YPLVDFED---NVNTSFEKSKSESSNLLDMSIEKLDLSVRSLNCLAKENVRTLGELISKN 296

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
             ++ +  NFG+KSL EI   L +  LFLGM+  D
Sbjct: 297 AEELSKARNFGKKSLEEIIEKLSSYQLFLGMSKED 331


>gi|219684168|ref|ZP_03539112.1| DNA-directed RNA polymerase, alpha subunit [Borrelia garinii PBr]
 gi|219672157|gb|EED29210.1| DNA-directed RNA polymerase, alpha subunit [Borrelia garinii PBr]
          Length = 344

 Score =  183 bits (465), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 121/335 (36%), Positives = 185/335 (55%), Gaps = 19/335 (5%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++K  ++   P  IE++   Q + +       P  RGF  T+GN LRRVL+SS+ G AIT
Sbjct: 3   VEKFLKDFTIPEKIEFLK-SQGDGSYGKFTIYPFERGFGVTIGNTLRRVLLSSIEGYAIT 61

Query: 62  AVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
           A++I           V  E   I GV ED  ++I NIK I+LK+ G+  +R TI     G
Sbjct: 62  AMRIQSNNKDSSSKVVSSEFDLIPGVSEDTLEVIANIKNIHLKL-GEGEQRKTISFSVSG 120

Query: 113 ----VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
               V+ A   +  + +EV N D VI  L  D  + +E  ++ G GYV ++ +    + +
Sbjct: 121 KDTKVLKASHFER-DGVEVFNRDLVIATLSQDVNLDLEFQINYGRGYVSSEQNSKYLEEV 179

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
            +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L
Sbjct: 180 NVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIIREFL 239

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
              ++FE+    V           +  L   +E+L+LSVRS NCL  EN+  +G+LI + 
Sbjct: 240 FPLVDFED---NVNTSFEKSKSESSNLLDMSIEKLDLSVRSLNCLAKENVRTLGELISKN 296

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
             ++ +  NFG+KSL EI   L +  LFLGM+  D
Sbjct: 297 AEELSKARNFGKKSLEEIIEKLSSYQLFLGMSKED 331


>gi|172038952|ref|YP_001805453.1| DNA-directed RNA polymerase subunit alpha [Cyanothece sp. ATCC
           51142]
 gi|171700406|gb|ACB53387.1| RNA polymerase alpha subunit [Cyanothece sp. ATCC 51142]
          Length = 314

 Score =  183 bits (465), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 109/293 (37%), Positives = 168/293 (57%), Gaps = 7/293 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG   T+GNALRRVL+++L G A+TA++I GV HE ++I GV ED+ +I+LN+
Sbjct: 23  FVLEPLERGQGTTVGNALRRVLLANLEGTAVTAIRIGGVNHEFATIPGVREDVLEIMLNM 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK   D  +   +   G   VTAG     +++EV+NP   I  L   A + ME  +
Sbjct: 83  KEIVLKSYTDQPQIGRLVATGAAHVTAGQFDLPSEVEVINPTQPIATLTEGAKLEMEFRI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYVP +    E   +  + IDA++ P+ KV+Y+VES R  +    D+L + I T+G
Sbjct: 143 EKGVGYVPVERSSDEPTALDFLQIDAVFMPVTKVNYSVESIRGEEGEAKDRLMLEIWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           S   +++++ A+ IL D      +  + +  V E  + +    NP     +EEL+LSVR+
Sbjct: 203 SFNPKEALSRAADILVDLFNPLKDLNQLETAVPEYPDEE----NPQSQIPIEELQLSVRA 258

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
            NCL+   I  + DL+  ++ D+L + NFG+KS  E   V+  +   LG+ LP
Sbjct: 259 YNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEE---VIEALQKRLGITLP 308


>gi|150036764|emb|CAM98032.1| DNA-directed RNA polymerase alpha chain [Leuconostoc lactis]
          Length = 227

 Score =  183 bits (465), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 94/213 (44%), Positives = 138/213 (64%), Gaps = 2/213 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T 
Sbjct: 61  KKVVLAIDSDDERSLEIDVQGPAEVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTA 120

Query: 150 SKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GY  A  ++   E  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T
Sbjct: 121 VKGRGYSSADENKQLREEMPIGVLAVDSIYTPIERVNYHVENTRVGARDDYDKLTFDIWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +GSI   D+++L ++IL + L +F++      E
Sbjct: 181 NGSIKPSDALSLGAKILAEHLNLFMDISPVAAE 213


>gi|317016851|gb|ADU85966.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 238

 Score =  183 bits (465), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 94/213 (44%), Positives = 138/213 (64%), Gaps = 2/213 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+
Sbjct: 7   FVIEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNL 66

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T 
Sbjct: 67  KKVVLAIDSDDERSLEIDVQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTA 126

Query: 150 SKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GY  A  ++   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T
Sbjct: 127 VKGRGYTSADENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGARDDYDKLTFDIWT 186

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +GSI   D+++L ++IL + L +F++      E
Sbjct: 187 NGSIKPSDALSLGAKILAEHLNLFMDISPVAAE 219


>gi|241667362|ref|ZP_04754940.1| DNA-directed RNA polymerase subunit alpha [Francisella philomiragia
           subsp. philomiragia ATCC 25015]
 gi|254875912|ref|ZP_05248622.1| DNA-directed RNA polymerase alpha subunit [Francisella philomiragia
           subsp. philomiragia ATCC 25015]
 gi|158523432|gb|ABW70830.1| DNA-directed RNA polymerase alpha subunit 1 [Francisella
           philomiragia subsp. philomiragia ATCC 25015]
 gi|254841933|gb|EET20347.1| DNA-directed RNA polymerase alpha subunit [Francisella philomiragia
           subsp. philomiragia ATCC 25015]
          Length = 323

 Score =  183 bits (465), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 106/292 (36%), Positives = 173/292 (59%), Gaps = 7/292 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P+ +G AH LGN++RR L+SSL GA+I  V IDGVLHE S+++ V ED+ +I+ N+K + 
Sbjct: 31  PVEKGMAHILGNSIRRFLLSSLSGASIIKVNIDGVLHEYSTLEDVKEDVVEIVSNLKKVA 90

Query: 94  LKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
           +K+  +  K  + +     GVVTAGD +T   IE++N D  I  L  +    +  TVS G
Sbjct: 91  IKLDKNVSKVELELSVTKSGVVTAGDFKTTQGIEIINKDQPIATLTNERKFSLTATVSVG 150

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
                     TE + +G I +D+ ++PIK+V++ +      + L+     + + T+G+I 
Sbjct: 151 RNVGILSALPTELEKVGDIAVDSDFNPIKRVAFEIFDNGTNETLE-----VFVKTNGTIE 205

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
              +V  A     +Q+ +F++   P      D  + S   +P LLK +++LEL+VRS+NC
Sbjct: 206 PLVAVTKALEYFCEQISVFVSLRVPSNGKTGDALLDS-NIDPILLKPIDDLELTVRSSNC 264

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           LR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L    L LG+ + ++
Sbjct: 265 LRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQILIDNNLSLGVQIDNF 316


>gi|313665551|ref|YP_004047422.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma leachii
           PG50]
 gi|312949424|gb|ADR24020.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma leachii
           PG50]
          Length = 317

 Score =  183 bits (465), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 117/317 (36%), Positives = 187/317 (58%), Gaps = 12/317 (3%)

Query: 6   WQELIKPNNIEYIVLGQ-EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
            ++ ++P   E+I+L + +++N       PL RGF  TLGNA+RR L+++  GA++ A++
Sbjct: 1   MKQFVRP---EFILLKEGQDKNYGKFSVSPLERGFGITLGNAIRRTLLAATPGASVYAIK 57

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKM-----SGDSHKRVTIFKRGPGVVTAGDI 119
           I G  HE +SI G+ E++T IILNIK + L++       D   ++ I     G V AGD+
Sbjct: 58  IAGATHEFTSIPGIIENVTKIILNIKQLVLRIDTSIYGDDEVVQLKIRSDIQGPVYAGDL 117

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYS 178
           +    +EVLN D +I  +    ++ + L      GY   K ++ E N   G+ITID+ YS
Sbjct: 118 ELPAGVEVLNQDLLIATISEGGILDLVLYAKNSRGYKTFKDNKNEKNIEPGMITIDSNYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI KV+Y+V+SA+ G+ +D +KL + + TDGSIT  D++++AS+IL   L  FI+    +
Sbjct: 178 PIIKVAYSVDSAKIGRAIDLEKLELEVTTDGSITAIDAISIASKILVAHLEFFIDLNR-E 236

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
             V E I V     +  L + VEEL+ + RS NCL+   I  + +L+ + E ++  + N 
Sbjct: 237 ISVLEVIGVNQTD-DKELDRTVEELDFTQRSLNCLKRAGINTLRELVTKNEDEIGSIRNL 295

Query: 299 GRKSLVEIKGVLGTMGL 315
           GRKSL EIK  + ++GL
Sbjct: 296 GRKSLKEIKDKVASLGL 312


>gi|119662371|emb|CAJ33174.1| RNA polymerase alpha subunit [Lactobacillus amylolyticus DSM 11664]
          Length = 208

 Score =  183 bits (464), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 90/189 (47%), Positives = 129/189 (68%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK + D  K
Sbjct: 1   LGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSNSDEQK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + +   GP  VTA D++  +D+EVLNPD  IC +     + M++ V  G GYV A  ++
Sbjct: 61  VIELDVEGPATVTADDLKVDSDVEVLNPDQYICTIAEGGHLHMQIAVKNGRGYVAASDNK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
           +E+ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++ A+ 
Sbjct: 121 SEDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSINPNDALSFAAN 180

Query: 223 ILQDQLGMF 231
           IL +   +F
Sbjct: 181 ILVEHFKVF 189


>gi|307128729|ref|YP_003880759.1| DNA-directed RNA polymerase subunit alpha [Candidatus Sulcia
           muelleri CARI]
 gi|306483191|gb|ADM90061.1| DNA-directed RNA polymerase subunit alpha [Candidatus Sulcia
           muelleri CARI]
          Length = 335

 Score =  183 bits (464), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 111/304 (36%), Positives = 178/304 (58%), Gaps = 18/304 (5%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL  G+  T+GN+LRRVL+SSL G AI++V+I+GV +E S+IKGV ED+T+IILN+K I
Sbjct: 27  EPLYPGWGLTIGNSLRRVLLSSLEGYAISSVKIEGVNNEYSTIKGVIEDMTEIILNLKKI 86

Query: 93  NLKMSGDSHKRVT-----IFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRME 146
             K   +     +     I       +TAGD+ + +N  E++NPD +I N +    + + 
Sbjct: 87  RFKKKIEDEDFESEEFHIIINNNKKEITAGDLGEFLNLFEIINPDLIILNKEKLISLNIT 146

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           L + +G GY+P++ ++   + IG I ID +++PIKKV Y +++    +   Y+ + + I 
Sbjct: 147 LVIKRGIGYLPSEKNKDMPNMIGTIPIDTIFTPIKKVKYKIDNCSINKNPFYESIILKIK 206

Query: 207 TDGSITGEDSVALASRILQDQLGMFIN------FEEPKKEVKEDINVKSLPFNPALLKKV 260
           TDGSI    ++  AS +L        N      +++PKK  K D N+  +     LLK  
Sbjct: 207 TDGSINPRKALTRASNLLIRHFQCLSNEKILLEYKKPKKRNKYDKNILKM---RNLLKSS 263

Query: 261 EELE---LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            E E   LSVR+ NCL+   I   GDL++  ++D+L++ NFGRKSL E+   +  + ++ 
Sbjct: 264 LEEEIDYLSVRTLNCLKSAKIFTWGDLVKSNKSDLLKLKNFGRKSLSELDKRMKKLNIYS 323

Query: 318 GMNL 321
           GM++
Sbjct: 324 GMDI 327


>gi|254373716|ref|ZP_04989199.1| DNA-directed RNA polymerase [Francisella novicida GA99-3548]
 gi|151571437|gb|EDN37091.1| DNA-directed RNA polymerase [Francisella novicida GA99-3548]
          Length = 323

 Score =  183 bits (464), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 106/292 (36%), Positives = 172/292 (58%), Gaps = 7/292 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P+ +G AH LGN++RRVL+SSL GA+I  V I  VLHE S+++ V ED+ +I+ N+K + 
Sbjct: 31  PVEKGMAHILGNSIRRVLLSSLSGASIIKVNISNVLHEYSTLEDVKEDVVEIVSNLKKVA 90

Query: 94  LKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
           +K+ +G     + +     GVV+AGD +T   +E++N D  I  L       +  TVS G
Sbjct: 91  IKLDTGIDRLDLELSVNKSGVVSAGDFKTTQGVEIINKDQPIATLTNQRAFSLTATVSVG 150

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
                     TE + +G I +DA ++PIK+V++ V         D + L + + T+G+I 
Sbjct: 151 RNVGILSAIPTELERVGDIAVDADFNPIKRVAFEVFDNG-----DSETLEVFVKTNGTIE 205

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
              +V  A     +Q+ +F++   P      D+ + S   +P LLK +++LEL+VRS+NC
Sbjct: 206 PLAAVTKALEYFCEQISVFVSLRVPSNGKTGDVLIDS-NIDPILLKPIDDLELTVRSSNC 264

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           LR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L    L LG+ + ++
Sbjct: 265 LRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQILIDNNLSLGVQIDNF 316


>gi|218294782|ref|ZP_03495636.1| DNA-directed RNA polymerase, alpha subunit [Thermus aquaticus
           Y51MC23]
 gi|218244690|gb|EED11214.1| DNA-directed RNA polymerase, alpha subunit [Thermus aquaticus
           Y51MC23]
          Length = 314

 Score =  183 bits (464), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 115/302 (38%), Positives = 169/302 (55%), Gaps = 26/302 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED+ +IILN+
Sbjct: 23  FVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKR--GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K + ++         T+  R  GP  V AGD     D+E++NPD  I  L+    + ME+
Sbjct: 83  KELVVRFLDPKMASTTLILRAEGPKEVRAGDFTPSADVEIMNPDLHIATLEEGGKLYMEV 142

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            V +G GYVPA+ H  + D I  I +DA++SP+++V++ VE  R GQ  D DKL++ I T
Sbjct: 143 RVDRGVGYVPAERHGIK-DRINAIPVDAIFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWT 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFE------------EPKKEVKEDINVKSLPFNPA 255
           DGS+T  +++  A  IL++ L  F N E            E ++  +ED++   LP    
Sbjct: 202 DGSVTPLEALNQAVAILKEHLNYFANPEASLLPTPEVSKGEKRESAEEDLD---LP---- 254

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
               +EEL LS R  + L+ E I  +  L+     D+  +   G +SL EI+  L   G 
Sbjct: 255 ----LEELGLSTRVLHSLKEEGIESVRALLALNLKDLRNIPGIGERSLEEIRQALAKKGF 310

Query: 316 FL 317
            L
Sbjct: 311 TL 312


>gi|150036766|emb|CAM98264.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides KCTC 3652]
          Length = 229

 Score =  182 bits (463), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 94/210 (44%), Positives = 137/210 (65%), Gaps = 2/210 (0%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K +
Sbjct: 2   EPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKV 61

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG
Sbjct: 62  VLAIDSDDERSLEIDVQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKG 121

Query: 153 HGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            GY  A  ++   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GS
Sbjct: 122 RGYTSADENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGARDDYDKLTFDIWTNGS 181

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKE 240
           I   D+++L ++IL + L +F++      E
Sbjct: 182 IKPSDALSLGAKILAEHLNLFMDISPVAAE 211


>gi|150187125|emb|CAK30176.1| RNA polymerase alpha subunit [Streptococcus intermedius]
          Length = 202

 Score =  182 bits (463), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 89/195 (45%), Positives = 135/195 (69%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL++SL GAA+T++ I+GVLHE  ++ GV ED+  IILNIKGI +K   +  K +
Sbjct: 1   NSLRRVLLASLPGAAVTSINIEGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEGEKTI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  VTAGDI T +DIE++NP+H +  +   A ++  +TV+ G GYVPA  ++ +
Sbjct: 61  ELDVEGPAEVTAGDILTDSDIEIVNPNHYLFTIGEGASLKAVMTVNTGRGYVPADENKKD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           + P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I TDG+I  ED++ L++RIL
Sbjct: 121 DAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDSFDKLTLEIMTDGTIIPEDALGLSARIL 180

Query: 225 QDQLGMFINFEEPKK 239
            + L +F N  E  K
Sbjct: 181 TEHLDLFTNLTEMAK 195


>gi|12230594|sp|Q9KWU8|RPOA_THEAQ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|21466003|pdb|1L9U|A Chain A, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 gi|21466004|pdb|1L9U|B Chain B, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 gi|21466009|pdb|1L9U|J Chain J, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 gi|21466010|pdb|1L9U|K Chain K, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 gi|21466016|pdb|1L9Z|A Chain A, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
           Promoter Dna Complex At 6.5 A Resolution
 gi|21466017|pdb|1L9Z|B Chain B, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
           Promoter Dna Complex At 6.5 A Resolution
 gi|62738680|pdb|1YNJ|A Chain A, Taq Rna Polymerase-Sorangicin Complex
 gi|62738681|pdb|1YNJ|B Chain B, Taq Rna Polymerase-Sorangicin Complex
 gi|62738686|pdb|1YNN|A Chain A, Taq Rna Polymerase-Rifampicin Complex
 gi|62738687|pdb|1YNN|B Chain B, Taq Rna Polymerase-Rifampicin Complex
 gi|109157854|pdb|2GHO|A Chain A, Recombinant Thermus Aquaticus Rna Polymerase For
           Structural Studies
 gi|109157855|pdb|2GHO|B Chain B, Recombinant Thermus Aquaticus Rna Polymerase For
           Structural Studies
 gi|7573271|emb|CAB65464.2| RNA polymerase, alpha subunit [Thermus aquaticus]
          Length = 314

 Score =  182 bits (463), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 115/293 (39%), Positives = 167/293 (56%), Gaps = 8/293 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED+ +IILN+
Sbjct: 23  FVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKR--GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K + ++         T+  R  GP  V AGD     D+E++NPD  I  L+    + ME+
Sbjct: 83  KELVVRFLDPKMASTTLILRAEGPKEVRAGDFTPSADVEIMNPDLHIATLEEGGKLYMEV 142

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            V +G GYVPA+ H  + D I  I +DA++SP+++V++ VE  R GQ  D DKL++ I T
Sbjct: 143 RVDRGVGYVPAERHGIK-DRINAIPVDAIFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWT 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEE---PKKEVKEDINVKSLPFNPALLKKVEELE 264
           DGS+T  +++  A  IL++ L  F N E    P  EV +    +S   +  L   +EEL 
Sbjct: 202 DGSVTPLEALNQAVAILKEHLNYFANPEASLLPTPEVSKGEKRESAEEDLDL--PLEELG 259

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS R  + L+ E I  +  L+     D+  +   G +SL EI+  L   G  L
Sbjct: 260 LSTRVLHSLKEEGIESVRALLALNLKDLRNIPGIGERSLEEIRQALAKKGFTL 312


>gi|154424859|emb|CAL18532.1| RNA polymerase alpha subunit [Streptococcus sobrinus]
          Length = 203

 Score =  182 bits (463), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 89/196 (45%), Positives = 137/196 (69%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   +  K 
Sbjct: 1   GNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVEDEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV+K  GYVPA+ ++ 
Sbjct: 61  IELDVTGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGHSLKATMTVAKNRGYVPAEGNKN 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+
Sbjct: 121 DSAPVGTLAVDSIYTPVKKVNYQVEPARVGSNAGFDKLTIEIMTNGTIIPEDALGLSARV 180

Query: 224 LQDQLGMFINFEEPKK 239
           L + L +F +  E  K
Sbjct: 181 LIEHLNLFTDLTEIAK 196


>gi|119668279|emb|CAK95450.1| RNA polymerase alpha subunit [Lactobacillus amylolyticus]
          Length = 213

 Score =  182 bits (463), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 90/189 (47%), Positives = 129/189 (68%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK + D  K
Sbjct: 1   LGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSNSDEQK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + +   GP  VTA D++  +D+EVLNPD  IC +     + M++ V  G GYV A  ++
Sbjct: 61  VIELDVEGPATVTADDLKVDSDVEVLNPDQYICTIAEGGHLHMQIAVKNGRGYVAASDNK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
           +E+ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++ A+ 
Sbjct: 121 SEDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSINPNDALSFAAN 180

Query: 223 ILQDQLGMF 231
           IL +   +F
Sbjct: 181 ILVEHFKVF 189


>gi|150036796|emb|CAM98274.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. mesenteroides]
          Length = 214

 Score =  182 bits (463), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 94/209 (44%), Positives = 137/209 (65%), Gaps = 2/209 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVV 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG 
Sbjct: 61  LAIDSDDERSLEIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGR 120

Query: 154 GYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A  ++   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI
Sbjct: 121 GYTSADENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKE 240
              D+++L ++IL + LG+F++      E
Sbjct: 181 KPSDALSLGAKILAEHLGLFMDISPVAAE 209


>gi|56707503|ref|YP_169399.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. tularensis SCHU S4]
 gi|89255695|ref|YP_513056.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica LVS]
 gi|110669974|ref|YP_666531.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. tularensis FSC198]
 gi|115314195|ref|YP_762918.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica OSU18]
 gi|134302561|ref|YP_001122531.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. tularensis WY96-3418]
 gi|156501643|ref|YP_001427708.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica FTNF002-00]
 gi|167010988|ref|ZP_02275919.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. holarctica FSC200]
 gi|187932118|ref|YP_001892103.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. mediasiatica FSC147]
 gi|224456566|ref|ZP_03665039.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. tularensis MA00-2987]
 gi|254370808|ref|ZP_04986813.1| hypothetical protein [Francisella tularensis subsp. tularensis
           FSC033]
 gi|254874323|ref|ZP_05247033.1| rpoA1, DNA-directed RNA polymerase, alpha subunit [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|290953188|ref|ZP_06557809.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica URFT1]
 gi|295313556|ref|ZP_06804145.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica URFT1]
 gi|81597921|sp|Q5NHU3|RPOA1_FRATT RecName: Full=DNA-directed RNA polymerase subunit alpha 1;
           Short=RNAP subunit alpha 1; AltName: Full=RNA polymerase
           subunit alpha 1; AltName: Full=Transcriptase subunit
           alpha 1
 gi|122325767|sp|Q0BNQ3|RPOA1_FRATO RecName: Full=DNA-directed RNA polymerase subunit alpha 1;
           Short=RNAP subunit alpha 1; AltName: Full=RNA polymerase
           subunit alpha 1; AltName: Full=Transcriptase subunit
           alpha 1
 gi|123094540|sp|Q2A5E5|RPOA1_FRATH RecName: Full=DNA-directed RNA polymerase subunit alpha 1;
           Short=RNAP subunit alpha 1; AltName: Full=RNA polymerase
           subunit alpha 1; AltName: Full=Transcriptase subunit
           alpha 1
 gi|123359594|sp|Q14J95|RPOA1_FRAT1 RecName: Full=DNA-directed RNA polymerase subunit alpha 1;
           Short=RNAP subunit alpha 1; AltName: Full=RNA polymerase
           subunit alpha 1; AltName: Full=Transcriptase subunit
           alpha 1
 gi|158513857|sp|A4IZQ9|RPOA1_FRATW RecName: Full=DNA-directed RNA polymerase subunit alpha 1;
           Short=RNAP subunit alpha 1; AltName: Full=RNA polymerase
           subunit alpha 1; AltName: Full=Transcriptase subunit
           alpha 1
 gi|171769926|sp|A7N9U9|RPOA1_FRATF RecName: Full=DNA-directed RNA polymerase subunit alpha 1;
           Short=RNAP subunit alpha 1; AltName: Full=RNA polymerase
           subunit alpha 1; AltName: Full=Transcriptase subunit
           alpha 1
 gi|56603995|emb|CAG44983.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. tularensis SCHU S4]
 gi|89143526|emb|CAJ78702.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. holarctica LVS]
 gi|110320307|emb|CAL08366.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. tularensis FSC198]
 gi|115129094|gb|ABI82281.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           holarctica OSU18]
 gi|134050338|gb|ABO47409.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. tularensis WY96-3418]
 gi|151569051|gb|EDN34705.1| hypothetical protein FTBG_00622 [Francisella tularensis subsp.
           tularensis FSC033]
 gi|156252246|gb|ABU60752.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. holarctica FTNF002-00]
 gi|187713027|gb|ACD31324.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. mediasiatica FSC147]
 gi|254840322|gb|EET18758.1| rpoA1, DNA-directed RNA polymerase, alpha subunit [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|282158647|gb|ADA78038.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. tularensis NE061598]
          Length = 323

 Score =  182 bits (463), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 106/292 (36%), Positives = 172/292 (58%), Gaps = 7/292 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P+ +G AH LGN++RRVL+SSL GA+I  V I  VLHE S+++ V ED+ +I+ N+K + 
Sbjct: 31  PVEKGMAHILGNSIRRVLLSSLSGASIIKVNIANVLHEYSTLEDVKEDVVEIVSNLKKVA 90

Query: 94  LKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
           +K+ +G     + +     GVV+AGD +T   +E++N D  I  L       +  TVS G
Sbjct: 91  IKLDTGIDRLDLELSVNKSGVVSAGDFKTTQGVEIINKDQPIATLTNQRAFSLTATVSVG 150

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
                     TE + +G I +DA ++PIK+V++ V         D + L + + T+G+I 
Sbjct: 151 RNVGILSAIPTELERVGDIAVDADFNPIKRVAFEVFDNG-----DSETLEVFVKTNGTIE 205

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
              +V  A     +Q+ +F++   P      D+ + S   +P LLK +++LEL+VRS+NC
Sbjct: 206 PLAAVTKALEYFCEQISVFVSLRVPSNGKTGDVLIDS-NIDPILLKPIDDLELTVRSSNC 264

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           LR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L    L LG+ + ++
Sbjct: 265 LRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQILIDNNLSLGVQIDNF 316


>gi|317447066|emb|CBX24362.1| DNA-directed RNA polymerase subunit alpha [Thiomonas perometabolis]
          Length = 201

 Score =  182 bits (462), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 94/198 (47%), Positives = 133/198 (67%), Gaps = 3/198 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EP  RG+ HTLGNALRRV++SSL G A T V I+GVLHE S + G+ ED+  ++LN+
Sbjct: 3   VVLEPFERGYGHTLGNALRRVMLSSLVGYAPTEVSINGVLHEYSVVDGLQEDVIGVLLNL 62

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+       +++ K G GVVTA DIQT +D+E++NPDHVI +L     + M++ V
Sbjct: 63  KGVVLKLHNRDEVTLSLRKEGEGVVTAADIQTPHDVEIINPDHVIAHLSQGGKLDMQIKV 122

Query: 150 SKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            KG GYVP        +    IG I +DA +SP+++VSY VESAR  Q  D DKL M I+
Sbjct: 123 EKGRGYVPGTLRNFGEEGGKSIGHIVLDASFSPVRRVSYAVESARVEQRTDLDKLVMEIE 182

Query: 207 TDGSITGEDSVALASRIL 224
           T+G I+ E+++  ++RIL
Sbjct: 183 TNGVISAEEAIRSSARIL 200


>gi|150187066|emb|CAK30163.1| RNA polymerase alpha subunit [Streptococcus dysgalactiae subsp.
           equisimilis]
          Length = 208

 Score =  182 bits (462), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 90/198 (45%), Positives = 139/198 (70%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  
Sbjct: 1   TLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDE 60

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + +   GP  VTAGDI T +DIE++NPDH +  +     +R  +TV+K  GYVPA+ +
Sbjct: 61  KILELEVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLRATMTVAKKRGYVPAEGN 120

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           + ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++
Sbjct: 121 KKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSA 180

Query: 222 RILQDQLGMFINFEEPKK 239
           R+L + L +F +  +  K
Sbjct: 181 RVLIEHLNLFTDLTDVAK 198


>gi|208780325|ref|ZP_03247666.1| DNA-directed RNA polymerase, alpha subunit [Francisella novicida
           FTG]
 gi|208743693|gb|EDZ89996.1| DNA-directed RNA polymerase, alpha subunit [Francisella novicida
           FTG]
          Length = 323

 Score =  182 bits (462), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 106/292 (36%), Positives = 172/292 (58%), Gaps = 7/292 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P+ +G AH LGN++RRVL+SSL GA+I  V I  VLHE S+++ V ED+ +I+ N+K + 
Sbjct: 31  PVEKGMAHILGNSIRRVLLSSLSGASIIKVNIANVLHEYSTLEDVKEDVVEIVSNLKKVA 90

Query: 94  LKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
           +K+ +G     + +     GVV+AGD +T   +E++N D  I  L       +  TVS G
Sbjct: 91  IKLDAGIDRLDLELSVNKSGVVSAGDFKTTQGVEIINKDQPIATLTNQRAFSLTATVSVG 150

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
                     TE + +G I +DA ++PIK+V++ V         D + L + + T+G+I 
Sbjct: 151 RNVGILSAIPTELERVGDIAVDADFNPIKRVAFEVFDNG-----DSETLEVFVKTNGTIE 205

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
              +V  A     +Q+ +F++   P      D+ + S   +P LLK +++LEL+VRS+NC
Sbjct: 206 PLAAVTKALEYFCEQISVFVSLRVPSNGKTGDVLIDS-NIDPILLKPIDDLELTVRSSNC 264

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           LR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L    L LG+ + ++
Sbjct: 265 LRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQILIDNNLSLGVQIDNF 316


>gi|154424847|emb|CAL18526.1| RNA polymerase alpha subunit [Streptococcus pyogenes]
          Length = 202

 Score =  182 bits (462), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 90/197 (45%), Positives = 138/197 (70%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K
Sbjct: 1   LGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + +   GP  VTAGDI T +DIE++NPDH +  +     +R  +TV+K  GYVPA+ ++
Sbjct: 61  IIELEVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLRATMTVAKKRGYVPAEGNK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R
Sbjct: 121 KDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSAR 180

Query: 223 ILQDQLGMFINFEEPKK 239
           +L + L +F +  E  K
Sbjct: 181 VLIEHLNLFTDLTEVAK 197


>gi|225552463|ref|ZP_03773403.1| DNA-directed RNA polymerase, alpha subunit [Borrelia sp. SV1]
 gi|225371461|gb|EEH00891.1| DNA-directed RNA polymerase, alpha subunit [Borrelia sp. SV1]
          Length = 344

 Score =  182 bits (462), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 112/302 (37%), Positives = 169/302 (55%), Gaps = 16/302 (5%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTD 84
           P  RGF  T+GN LRRVL+SS+ G AITA+++           V  E   I GV ED  +
Sbjct: 34  PFERGFGITIGNTLRRVLLSSIEGYAITAMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLE 93

Query: 85  IILNIKGINLKMSGDSHKRVTIFK---RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +I NIK I+LK+     K+   F    +   V+ A   +  + +EV N D VI  L  D 
Sbjct: 94  VIANIKNIHLKLGEGEQKKTISFSVSGKDTNVLKASHFER-DGVEVFNKDLVIATLSRDV 152

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + +E  ++ G GYV ++ +    + + +I +D+++SPI+KVSY+VE  R GQ  DYDKL
Sbjct: 153 NLDLEFQINYGRGYVSSEQNSKYLEEVNVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKL 212

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            M I T G I+ +D++  A+ I+++ L   ++FE+    V           +  L   +E
Sbjct: 213 VMEIWTTGVISAKDAIKKAASIVREFLFPLVDFED---NVNTSFEKSKSESSNLLDMSIE 269

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +L LSVRS NCL  EN+  +G+LI +   ++ +  NFG+KSL EI   LG+  L+LGM+ 
Sbjct: 270 KLNLSVRSLNCLAKENVRTLGELISKNAEELSKARNFGKKSLEEIIEKLGSYRLYLGMSK 329

Query: 322 PD 323
            D
Sbjct: 330 ED 331


>gi|328814011|gb|AEB52121.1| DNA-directed RNA polymerase alpha chain [Lactobacillus rhamnosus]
          Length = 218

 Score =  182 bits (462), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 93/216 (43%), Positives = 143/216 (66%)

Query: 59  AITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGD 118
           A++++QIDGVLHE S+I GV ED+T IILNIK + LKM+ D  K + I   GP  VTA D
Sbjct: 1   AVSSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNTDEDKNIEIDVNGPAKVTAAD 60

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           I    D+EVLNP+  IC +       + +TV KG GYV A  +++++ PIG++ ID++++
Sbjct: 61  IVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAADQNKSDDMPIGVLPIDSIFT 120

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++IL + L +F+N  +  
Sbjct: 121 PISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKILTEHLDIFVNLTDEA 180

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLR 274
           K  +  +  +       L   +EEL+LSVRS NCL+
Sbjct: 181 KNAEIMVEKEETHKEKMLEMTIEELDLSVRSYNCLK 216


>gi|150187061|emb|CAK30162.1| RNA polymerase alpha subunit [Streptococcus didelphis]
          Length = 209

 Score =  182 bits (462), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 90/197 (45%), Positives = 138/197 (70%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           +GN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K
Sbjct: 1   IGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNLKGLAVKSYVEDEK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + +   GP  VTAGDI T +DIE++NPDH +  +     +R  +TV+K  GYVPA+ ++
Sbjct: 61  MIELDVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLRATMTVAKKRGYVPAEGNK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            ++ P+G + ID++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R
Sbjct: 121 KDDAPVGTLAIDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSAR 180

Query: 223 ILQDQLGMFINFEEPKK 239
           +L + L +F +  E  K
Sbjct: 181 VLIEHLNLFTDLTEVAK 197


>gi|150036736|emb|CAM98023.1| DNA-directed RNA polymerase alpha chain [Leuconostoc citreum]
          Length = 223

 Score =  182 bits (462), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 94/209 (44%), Positives = 136/209 (65%), Gaps = 2/209 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVV 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG 
Sbjct: 61  LAIDSDDERSLEIDVQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGR 120

Query: 154 GYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A  ++   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI
Sbjct: 121 GYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKE 240
              D+++L S+IL + L +F++      E
Sbjct: 181 KPSDALSLGSKILAEHLNLFMDISPVAAE 209


>gi|150036820|emb|CAM98279.1| DNA-directed RNA polymerase alpha chain [Fructobacillus ficulneus]
          Length = 238

 Score =  182 bits (461), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 100/238 (42%), Positives = 143/238 (60%), Gaps = 2/238 (0%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL G A+  VQIDGV+HE S++ GV ED+T +I N+K +
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGVAVNTVQIDGVVHEXSTVDGVVEDVTQLIXNLKKV 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
                      + I  +GP  VTA D+    DIEVLNPD  I  L     + M +T  KG
Sbjct: 61  VFATDSAEEHALEIDVQGPKDVTAADLAGSADIEVLNPDLHIATLAAGKSLHMTVTAVKG 120

Query: 153 HGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            GY  A+ ++   D  PIG++T+D++Y+PI++V+Y VE+ R G   DYDKL+M + T+GS
Sbjct: 121 RGYSSAEENKQLRDEMPIGVLTVDSIYTPIERVNYHVENKRVGSRDDYDKLTMEVWTNGS 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           I   D+++L S+IL + L +F       +E K  +              +E+L+LSVR
Sbjct: 181 INPSDALSLGSKILTEHLNLFTXISPVAQETKVMVETXQAASTATDAAPIEDLDLSVR 238


>gi|620029|gb|AAA74989.1| RNA polymerase alpha-subunit [Chlamydia trachomatis]
          Length = 380

 Score =  182 bits (461), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 120/335 (35%), Positives = 182/335 (54%), Gaps = 25/335 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +A+PL +G  HTLG+ALRR L+  L   AI +  + GVLHE  +++G+ ED+T+++LN+
Sbjct: 37  FVADPLEKGMGHTLGSALRRALLIGLEAPAIVSFSMTGVLHEYMAVEGIIEDVTNMLLNL 96

Query: 90  KGINLKM---------SGDSHKRVTI--------FKRGPGVVTAGDIQTVNDIEVLNPDH 132
           KG  LK                R TI           G   VT GD+      E +NP+H
Sbjct: 97  KGSLLKKYPLQDCEGGRCSQKLRATISVDASDLAAAGGQKEVTLGDLLQEGTFEAVNPEH 156

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           VI  +     + + L V+ G GY P++    E   +  I +DA +SP+  V+Y VE  R 
Sbjct: 157 VIFTVTRPMQLEVMLRVAFGRGYSPSERIVLEERGMNEIVLDAAFSPVVLVNYFVEDTRV 216

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           GQ  D+D+L + ++TDG +  +++VA A++IL     +F   +E +   +E I+V+    
Sbjct: 217 GQDTDFDRLVLQVETDGRVAPKEAVAFATQILSKHFSVFEKMDEKRIVFEEAISVEKENK 276

Query: 253 NPALLKKV---EELELSV---RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           +  L K V    E+ELSV   RSTNCL   NI  +G+L+   E  +L+  NFG+KSL EI
Sbjct: 277 DDILHKLVLGINEIELSVRLIRSTNCLSNANIETIGELVIMPEPRLLQFRNFGKKSLCEI 336

Query: 307 KGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           K  L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 337 KNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYAEK 371


>gi|126658013|ref|ZP_01729165.1| DNA-directed RNA polymerase subunit alpha [Cyanothece sp. CCY0110]
 gi|126620651|gb|EAZ91368.1| DNA-directed RNA polymerase subunit alpha [Cyanothece sp. CCY0110]
          Length = 314

 Score =  182 bits (461), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 108/293 (36%), Positives = 168/293 (57%), Gaps = 7/293 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG   T+GNALRRVL+++L G A+TA++I GV HE ++I GV ED+ +I+LN+
Sbjct: 23  FVLEPLERGQGTTVGNALRRVLLANLEGTAVTAIRIGGVNHEFATIPGVREDVLEIMLNM 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK   +  +   +   G   VTAG     +++EV+NP   I  L   A + ME  +
Sbjct: 83  KEIVLKSYTEQPQIGRLVATGAAHVTAGQFDLPSEVEVINPTQPIATLTEGAKLEMEFRI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYVP +    E   +  + IDA++ P+ KV+Y+VES R  +    D+L + I T+G
Sbjct: 143 EKGVGYVPVERSSDEPTALDFLQIDAVFMPVTKVNYSVESIRGEEGEAKDRLMLEIWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           S   +++++ A+ IL D      +  + +  V E  + +    NP     +EEL+LSVR+
Sbjct: 203 SFNPKEALSRAADILVDLFNPLKDLNQLETAVPEYPDEE----NPQSQIPIEELQLSVRA 258

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
            NCL+   I  + DL+  ++ D+L + NFG+KS  E   V+  +   LG+ LP
Sbjct: 259 YNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEE---VIEALQKRLGITLP 308


>gi|15639205|ref|NP_218652.1| DNA-directed RNA polymerase subunit alpha [Treponema pallidum
           subsp. pallidum str. Nichols]
 gi|189025446|ref|YP_001933218.1| DNA-directed RNA polymerase subunit alpha [Treponema pallidum
           subsp. pallidum SS14]
 gi|6094122|sp|O83242|RPOA_TREPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|3322481|gb|AAC65201.1| DNA-directed RNA polymerase, alpha subunit (rpoA) [Treponema
           pallidum subsp. pallidum str. Nichols]
 gi|189018021|gb|ACD70639.1| DNA-directed RNA polymerase, alpha subunit [Treponema pallidum
           subsp. pallidum SS14]
 gi|291059617|gb|ADD72352.1| DNA-directed RNA polymerase, alpha subunit [Treponema pallidum
           subsp. pallidum str. Chicago]
          Length = 351

 Score =  182 bits (461), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 111/300 (37%), Positives = 169/300 (56%), Gaps = 10/300 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-----DGVLHEISS----IKGVHE 80
             A P   GF  T+GN LRRVL+SS++G A+T V+I     DGV H ISS    I  V E
Sbjct: 30  FTASPFETGFGTTVGNCLRRVLLSSIQGYAVTGVRITSFDADGVAHFISSEFEQIPHVRE 89

Query: 81  DLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           D  +I+ N K +   +  G      T   RG   +T  D      +EVL+ D +I  +  
Sbjct: 90  DTLEILNNFKRLRFLLPQGAESSTFTYEFRGAVSLTGKDFAKKFQLEVLSQDLLIMEMMD 149

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
            A V +EL V  G GYVPA+ H    D +G+I +DA++SP+ +V Y ++S R GQ  DYD
Sbjct: 150 GAHVEVELHVEFGRGYVPAESHDRYADLVGVIPVDAIFSPVLRVRYDIQSCRVGQRGDYD 209

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           +LS+ + TDG++  ED++A A++I+++   +F+NF+E   +++++           L  K
Sbjct: 210 QLSLEVWTDGTVRPEDAIAEAAKIIKEHFTVFVNFDETALDLEDEPEEDDPAVLELLNTK 269

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           + +++ SVR+ NCL    I  +G+L + +E  +    N G+KSL EI+G L    L LGM
Sbjct: 270 IADVDFSVRARNCLLTMGIKTLGELTRISEQTLANTRNVGKKSLSEIQGKLQEYNLRLGM 329


>gi|161511753|emb|CAP16887.1| DNA-directed RNA polymerase subunit alpha [Pediococcus damnosus]
          Length = 211

 Score =  181 bits (460), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 93/202 (46%), Positives = 136/202 (67%), Gaps = 3/202 (1%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+   V +  + GAA+T++QIDGVLHE SSI+GV ED+T IILNIK ++LK+  D  K
Sbjct: 2   LGNSCV-VFVVIITGAAVTSIQIDGVLHEFSSIEGVVEDVTQIILNIKKVSLKIESDDEK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A  ++
Sbjct: 61  SLEIDVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAILTADTGRGYVSADENK 120

Query: 163 TEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
              D  PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSIT  ++ +L+
Sbjct: 121 ARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSITPSEATSLS 180

Query: 221 SRILQDQLGMFINFEEPKKEVK 242
           ++IL + L +F+N  +  K+ +
Sbjct: 181 AKILTEHLALFVNLTDEAKDAE 202


>gi|154424753|emb|CAL18479.1| RNA polymerase alpha subunit [Streptococcus agalactiae]
          Length = 213

 Score =  181 bits (460), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 88/197 (44%), Positives = 138/197 (70%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K
Sbjct: 1   LGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + +   GP  +TAGDI T +DIE++NPDH +  +     ++  +TV+K  GYVPA+ ++
Sbjct: 61  IIELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIAEGHSLKATMTVAKNRGYVPAEGNK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R
Sbjct: 121 KDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSAR 180

Query: 223 ILQDQLGMFINFEEPKK 239
           +L + L +F +  E  K
Sbjct: 181 VLIEHLNLFTDLTEVAK 197


>gi|150187094|emb|CAK30169.1| RNA polymerase alpha subunit [Streptococcus constellatus subsp.
           constellatus]
 gi|154424831|emb|CAL18518.1| RNA polymerase alpha subunit [Streptococcus constellatus subsp.
           constellatus]
          Length = 202

 Score =  181 bits (460), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 88/195 (45%), Positives = 134/195 (68%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL++SL GAA+T++ I+GVLHE  ++ GV ED+  IILN+KGI +K   +  K +
Sbjct: 1   NSLRRVLLASLPGAAVTSINIEGVLHEFDTVPGVREDVMQIILNVKGIAVKSYVEDEKTI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  +TAGDI T +DIE++NPDH +  +   A ++  +TV+ G GYVPA  ++ +
Sbjct: 61  ELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIGEGASLKAIMTVNAGRGYVPADENKKD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           + P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I TDG+I  ED++ L++RIL
Sbjct: 121 DAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTLEIMTDGTIIPEDALGLSARIL 180

Query: 225 QDQLGMFINFEEPKK 239
              L +F N  E  K
Sbjct: 181 TQHLDLFTNLTEVAK 195


>gi|328675432|gb|AEB28107.1| DNA-directed RNA polymerase alpha subunit [Francisella cf. novicida
           3523]
          Length = 323

 Score =  181 bits (460), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 106/292 (36%), Positives = 171/292 (58%), Gaps = 7/292 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P+ +G AH LGN++RRVL+SSL GA+I  V I  VLHE S+++ V ED+ +I+ N+K + 
Sbjct: 31  PVEKGMAHILGNSIRRVLLSSLSGASIIKVNIANVLHEYSTLEDVKEDVVEIVSNLKKVA 90

Query: 94  LKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
           +K+  G     + +     GVV+AGD +T   +E++N D  I  L       +  TVS G
Sbjct: 91  IKLDKGIDRLDLELSVNKSGVVSAGDFKTTQGVEIINKDQPIATLTNQRAFNLTATVSIG 150

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
                     TE + +G I +DA ++PIK+V++ V         D + L + + T+G+I 
Sbjct: 151 RNVGILSAIPTELERVGDIAVDADFNPIKRVAFEVFDNG-----DSETLEVFVKTNGTIE 205

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
              +V  A     +Q+ +F++   P      D+ + S   +P LLK +++LEL+VRS+NC
Sbjct: 206 PLAAVTKALEYFCEQISVFVSLRVPSNGKTGDVLIDS-NIDPILLKPIDDLELTVRSSNC 264

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           LR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L    L LG+ + ++
Sbjct: 265 LRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQILIDNNLSLGVQIDNF 316


>gi|296126891|ref|YP_003634143.1| DNA-directed RNA polymerase, alpha subunit [Brachyspira murdochii
           DSM 12563]
 gi|296018707|gb|ADG71944.1| DNA-directed RNA polymerase, alpha subunit [Brachyspira murdochii
           DSM 12563]
          Length = 324

 Score =  181 bits (460), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 107/296 (36%), Positives = 173/296 (58%), Gaps = 9/296 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            IA+P  RG+A T+GNALRRVL+SS+ G AITA++IDGV +E  ++ G+ ED   +I+++
Sbjct: 30  FIAQPFERGYAVTVGNALRRVLLSSIPGYAITAIKIDGVSNEFENVPGMKEDTIVMIMHL 89

Query: 90  KGINLKMSGD-SHKRVTIFKRGPGVVTAGD-IQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K + + +      K + + K GP  +TAGD +   N+ +V NPD+ I  +       M++
Sbjct: 90  KNVVVSLPDRLETKTIHMKKEGPCTITAGDLVANDNEAQVHNPDYYIATIAEGYTFEMDI 149

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            +  G+ YVPA+ +    + +  I IDA+YSPI  V Y V+  R GQ +DY KL++ I+T
Sbjct: 150 QIEGGYSYVPAEMNIELVEDVNAIAIDAIYSPIVSVKYNVDPIRVGQRIDYGKLTLEIET 209

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL----LKKVEEL 263
            G+I  E +++ A++IL+D L  F++ EE      +D  ++  P +  L     K +EE+
Sbjct: 210 KGNIAPEKALSQAAKILRDNLKHFMDPEEAN---GDDEKIEETPKDSVLDSLKGKHIEEV 266

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           E SVR+ N L   ++  +  +  ++E+D+LR+       + EIK  L   G  LGM
Sbjct: 267 EFSVRTANFLMASDLKTLDKVAVKSESDLLRLIGANEMIIEEIKEKLAEYGAHLGM 322


>gi|86438810|emb|CAJ43370.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 208

 Score =  181 bits (460), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 90/193 (46%), Positives = 129/193 (66%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V  G GYV A
Sbjct: 61  DERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNGRGYVAA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++
Sbjct: 121 SDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALS 180

Query: 219 LASRILQDQLGMF 231
            A++I  +   +F
Sbjct: 181 FAAKISVEHFKVF 193


>gi|150036822|emb|CAM98042.1| DNA-directed RNA polymerase alpha chain [Leuconostoc fallax KCTC
           3537]
          Length = 204

 Score =  181 bits (460), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 92/203 (45%), Positives = 135/203 (66%), Gaps = 2/203 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T +ILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVV 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L +  D  K + I  +GP  VTA D+Q   DIEVLNP+  +  +     + M +T  KG 
Sbjct: 61  LAIDSDEEKSLEIDVQGPAEVTAADLQGSADIEVLNPELHLATVAAGKSLHMTVTAVKGR 120

Query: 154 GYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A  ++   D  PIG++ +D++Y+PI++V+Y VE+ R GQ  DYDKL+  I T+GSI
Sbjct: 121 GYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGQRDDYDKLTFDIWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINF 234
              D+++L ++IL + L +F + 
Sbjct: 181 KPSDALSLGAKILSEHLNLFTDI 203


>gi|297180267|gb|ADI16486.1| DNA-directed RNA polymerase, alpha subunit/40 kd subunit
           [uncultured bacterium HF4000_05M23]
          Length = 328

 Score =  181 bits (460), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 112/307 (36%), Positives = 175/307 (57%), Gaps = 12/307 (3%)

Query: 7   QELIKPNNIEY----IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           QEL+ P   E     I + + EE     +AEPL RG   TLGNALRR L++SL G AIT 
Sbjct: 6   QELLSPFTPEIPDLSIAIQENEEAYGRFVAEPLERGRGVTLGNALRRTLLNSLPGTAITW 65

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           V+IDG LHE S+I  + E++ + +L +KGI L+   D   R+ I   G G V AGDI   
Sbjct: 66  VRIDGALHEYSTIPHMPEEVVEFLLKVKGIRLRSLADRPGRLRIEVDGEGEVRAGDIMAT 125

Query: 123 NDIEVLNPDHVICNLDVDAVVRM--ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
            D E++NP+H +  LD  A+ R+  E  V +G GY PA     E  PIG++ +DA+++PI
Sbjct: 126 ADFEIVNPEHHLATLD-SAMARLSVEFNVEQGVGYQPAIQE--EGLPIGVLLVDAIFTPI 182

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +K +++VE+ R G   D ++L + + TD +I   +++  AS++L D    F    EP   
Sbjct: 183 RKSNFSVEATRAGHRSDLERLIVEVWTDRTIMPLEAMKSASKLLMDCFFPFTQVGEPVGG 242

Query: 241 VKEDINVKSLPFNPALLKK-VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
             +   +  +   P +    VE L LS R+ NCL+      +G+++   +++++++  FG
Sbjct: 243 EDDKPGIDGV--TPEVFNTLVETLALSARTHNCLKRAGFNRVGEILLLPKSELMKIRGFG 300

Query: 300 RKSLVEI 306
           +KSL E+
Sbjct: 301 QKSLDEL 307


>gi|119662301|emb|CAJ33138.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           delbrueckii]
          Length = 215

 Score =  181 bits (460), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 90/199 (45%), Positives = 132/199 (66%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF  TLGN+LRRVL++S+ G  +  V+IDG+LHE +++ GV ED+T IILN+K +
Sbjct: 1   EPLERGFGTTLGNSLRRVLLTSVPGTGLVKVKIDGILHEFTTVPGVKEDVTKIILNLKKL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            L+   +  K + +   GP  VTA D++   D+EVLNPD  IC +     + M + V  G
Sbjct: 61  VLRAYTEEVKTIELDVEGPATVTAEDLKADADVEVLNPDQYICTIAQGGHLHMWIDVCNG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYVPA  ++T+   IG I +D+L+SPI+KV+Y VES R G+  D+DKL++ I T+GSI 
Sbjct: 121 RGYVPASENKTDEMFIGDIPVDSLFSPIEKVNYQVESTRVGKREDFDKLTLEIWTNGSIA 180

Query: 213 GEDSVALASRILQDQLGMF 231
             D++  A+R+L +   +F
Sbjct: 181 PNDALNFAARVLVEHFKVF 199


>gi|119662329|emb|CAJ33152.1| RNA polymerase alpha subunit [Lactobacillus mindensis]
          Length = 197

 Score =  181 bits (459), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 85/195 (43%), Positives = 136/195 (69%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRRVL++SL G A++ +QIDGVLHE S+I GV ED+T I+LN+K + LK   +  
Sbjct: 1   TLGNSLRRVLLASLPGTAVSDIQIDGVLHEFSAIDGVIEDVTQIVLNVKKLKLKSYAEDS 60

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
            +  I   GP  VTA DI+  +D+EVL+P+  IC +       M++T+  G GY PA+ +
Sbjct: 61  LKAEIDVVGPATVTAKDIKADDDLEVLDPEQFICTVAEGGHFHMQMTIKNGRGYTPAEQN 120

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           +T+  PIG++ +D++++P++KV+Y VE+ R G+  D+DKL++ I T+GSI   ++++L++
Sbjct: 121 KTDETPIGVLPVDSIFTPVEKVNYQVENTRVGKRNDFDKLTIDIWTNGSIGPREAISLSA 180

Query: 222 RILQDQLGMFINFEE 236
           +IL + L  F+N  E
Sbjct: 181 KILTEHLNSFVNLTE 195


>gi|222099995|ref|YP_002534563.1| DNA-directed RNA polymerase subunit alpha [Thermotoga neapolitana
           DSM 4359]
 gi|221572385|gb|ACM23197.1| DNA-directed RNA polymerase subunit alpha [Thermotoga neapolitana
           DSM 4359]
          Length = 340

 Score =  181 bits (459), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 116/297 (39%), Positives = 171/297 (57%), Gaps = 21/297 (7%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQI--DGVLHEISSIKGVHEDLTDIILNIKG 91
           PL RG+A T+GNALRRVL+SS+   AI  V+       HE   I+GV ED+ DIILN+K 
Sbjct: 33  PLERGYAITIGNALRRVLLSSIPSLAIVGVRFIKPEKYHEYDYIEGVKEDILDIILNLKK 92

Query: 92  INLKMSGDSHKRVT--IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           +  +++     R+   + K+GPG + AGDI+T   IEV NPD  I  L+  A +  E+  
Sbjct: 93  VQFRVNVTVKDRIKMEVEKKGPGELVAGDIKTPAGIEVANPDLHIATLNSKADLFFEIYA 152

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G G+VP    R E   +G I ID ++SP+ KV++  E+ R G+  DYDKL + + T  
Sbjct: 153 EVGKGFVPV-SERDERPEVGWIPIDGVFSPVMKVNFLTENVRVGKRTDYDKLILEVWTKK 211

Query: 210 SITGEDSVALASRILQDQLGM-------------FINFEEPKKEV---KEDINVKSLPFN 253
           SI  E+++  A+ IL +   +             +I  EE ++E     E  + +S+   
Sbjct: 212 SIRPEEALRKAADILINHFRIVMEGLPEMKISEEYIITEEDEEEALTAVEGEDQESVENL 271

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
               KK++ELELSVRS NCL+   I  +GDL+ +TE ++L++ NFG+KSL E+K  L
Sbjct: 272 DVYSKKIDELELSVRSLNCLKRAKIETIGDLMSKTEDELLKIKNFGQKSLDEVKKKL 328


>gi|119672807|emb|CAK95484.1| RNA polymerase alpha subunit [Lactobacillus fermentum]
          Length = 196

 Score =  181 bits (459), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 92/196 (46%), Positives = 139/196 (70%), Gaps = 2/196 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRV+++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+
Sbjct: 1   FVVEPLERGYGTTLGNSLRRVMLASLPGAAITSIQIDGVLHEFSTVQGVTEDVTQIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  +GP  VTA DIQ   D+ +LN D  I  +   A + +++T 
Sbjct: 61  KQVALKIDSEDAKDLEIDVKGPAEVTAADIQGDGDVTILNSDLHIATVSDGAELHVKMTA 120

Query: 150 SKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GY  A  ++T  E   IG++ ID++Y+PI++V+YTVE+ R GQ  DYDKL++ + T
Sbjct: 121 DKGRGYSSADDNKTRMEGLAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRI 223
           +GS+T  ++++LA++I
Sbjct: 181 NGSLTPTEAISLAAKI 196


>gi|167957552|ref|ZP_02544626.1| DNA-directed RNA polymerase subunit alpha [candidate division TM7
           single-cell isolate TM7c]
          Length = 294

 Score =  181 bits (459), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 109/280 (38%), Positives = 164/280 (58%), Gaps = 21/280 (7%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL  G+ +TLGN+LRRVLMSS+ GAA+ + +I+G  HE +++ G+ ED+ DI LN+K +
Sbjct: 26  EPLRGGYGNTLGNSLRRVLMSSIHGAAVISFKIEGATHEFTTVPGIKEDVVDISLNLKSV 85

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
            +KM  D    + + K G G VTAGDIQ+  D+E++NP+ VIC + D  A   ++L +  
Sbjct: 86  KIKMHTDDPIELRLEKHGAGQVTAGDIQSHADVEIINPEQVICTVDDPSAKAVIDLVIDS 145

Query: 152 GHGYVP---AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GY+    +   R  +D I L   DA++SP+ +V Y VES R GQ  + +KL + IDTD
Sbjct: 146 GRGYLSIEDSSETRLHSDHIAL---DAVFSPVIRVRYKVESTRVGQETNLEKLIVVIDTD 202

Query: 209 GSITGEDSVALASRILQDQL----GMFINFEEPK--KEVKEDINVKSLPFNPALLKKVEE 262
           GSIT  D+   A+ IL +Q     G  +    P   +E +E+ N         L   +E+
Sbjct: 203 GSITPRDAFEEAAAILVNQYTALAGSTVVESAPALGQEREEESN--------ELNTSIED 254

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           L+L+ R+ N L   +I  + DL+  TE D+  +  FG K+
Sbjct: 255 LDLTARTANALINNDIRTVQDLVTLTEQDLRELKGFGSKA 294


>gi|320538142|ref|ZP_08038037.1| DNA-directed RNA polymerase, alpha subunit [Treponema phagedenis
           F0421]
 gi|320144959|gb|EFW36680.1| DNA-directed RNA polymerase, alpha subunit [Treponema phagedenis
           F0421]
          Length = 351

 Score =  181 bits (459), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 118/331 (35%), Positives = 185/331 (55%), Gaps = 12/331 (3%)

Query: 1   MIQKNW-QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M +KN  +   KP  +++ V    +E+    IA P   GF  T+GN LRRVL+SS++G A
Sbjct: 1   MARKNLLKGFKKPKGVDF-VAEVSDESHGKFIASPFETGFGTTIGNCLRRVLLSSIQGYA 59

Query: 60  ITAVQI-----DGVLHEISS----IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK-R 109
           IT+V+I     DGV H ISS    I  V ED  +I+ N+K I L +  +  +    F+ +
Sbjct: 60  ITSVRITTYDADGVGHSISSEFESIPHVREDTLEILNNLKQIRLLLPEEEEEGAFTFEFQ 119

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  +T  D++    +++L+ D  I  +   A V  E+ V  G GYVPA+ +    + +G
Sbjct: 120 GPCTITGADLEKEYQLQILSKDVHIMEMMEGAHVEFEVNVKFGRGYVPAETNEQYVEVVG 179

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            I +D+++SP+ KV Y ++  R GQ  DYDKL + I TDG++  ED++A A++I +D   
Sbjct: 180 TIPLDSIFSPVLKVRYEIQPCRVGQRNDYDKLVLEIWTDGTVRPEDALAEAAKIAKDHFS 239

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +F+NF+E     ++D +         L  K+ E++ SVR+ NCL    +  +G+L + +E
Sbjct: 240 IFVNFDESVLIGEDDADEDDAKIIDLLNTKISEVDFSVRARNCLANIGVKTLGELTKISE 299

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
             +    N G+KSL EI+G L    L LGM 
Sbjct: 300 QTLASTRNVGKKSLSEIQGKLQEYNLRLGMT 330


>gi|150036762|emb|CAM98031.1| DNA-directed RNA polymerase alpha chain [Leuconostoc carnosum]
          Length = 221

 Score =  181 bits (459), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 93/203 (45%), Positives = 135/203 (66%), Gaps = 2/203 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVV 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG 
Sbjct: 61  LAIDSDEERVLEIDVQGPSEVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGR 120

Query: 154 GYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A  ++   E  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI
Sbjct: 121 GYSSADENKQLREEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINF 234
              D+++L S+IL + L +F++ 
Sbjct: 181 KPSDALSLGSKILAEHLNLFMDI 203


>gi|86438806|emb|CAJ43368.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 192

 Score =  181 bits (458), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 90/190 (47%), Positives = 128/190 (67%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V  G GYV A
Sbjct: 61  DERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNGRGYVAA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++
Sbjct: 121 SDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALS 180

Query: 219 LASRILQDQL 228
            A++IL +  
Sbjct: 181 FATKILVEHF 190


>gi|317016853|gb|ADU85967.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 228

 Score =  181 bits (458), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 93/209 (44%), Positives = 136/209 (65%), Gaps = 2/209 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVV 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG 
Sbjct: 61  LAIDSDDERSLEIDVQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGR 120

Query: 154 GYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A  ++   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI
Sbjct: 121 GYTSADENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGARDDYDKLTFDIWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKE 240
              D+++L ++IL + L +F++      E
Sbjct: 181 KPSDALSLGAKILAEHLNLFMDISPVAAE 209


>gi|300867111|ref|ZP_07111777.1| DNA-directed RNA polymerase subunit alpha [Oscillatoria sp. PCC
           6506]
 gi|300334866|emb|CBN56943.1| DNA-directed RNA polymerase subunit alpha [Oscillatoria sp. PCC
           6506]
          Length = 320

 Score =  181 bits (458), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 106/295 (35%), Positives = 168/295 (56%), Gaps = 12/295 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG   T+GNALRRV++S+L G A+T+V+I GV HE ++I+GV ED+ +I+LN+
Sbjct: 30  FILEPLDRGQGTTVGNALRRVMLSNLEGTAVTSVRIAGVNHEFATIEGVREDVLEILLNM 89

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK      +   +   GP  VTA      ++++V++    I  L   + + ME  +
Sbjct: 90  KEVVLKSHSSQPQIGRLRVEGPATVTADRFDVPSEVDVIDRSQYIATLSPGSTLEMEFRI 149

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY      R +   +  + IDA++ P++KV+Y+VE AR G   + D+L M I T+G
Sbjct: 150 ERGVGYRAVDRSRDDGGALDFLAIDAIFMPVRKVNYSVEDARVGGSTEKDRLIMEIWTNG 209

Query: 210 SITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           S+T +++++ A+ IL D       I  E  + +V  D        +P     +EEL+LSV
Sbjct: 210 SLTPQEALSQAASILVDLFSPLKDITLESLRSDVGSDA-------DPTSQIPIEELQLSV 262

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ NCL+   I  + DL+  T+ D+L + NFG+KS  E   V+  +   LG+ LP
Sbjct: 263 RAYNCLKRAQINSVADLLDYTQEDLLEIKNFGQKSAEE---VIEALQKRLGITLP 314


>gi|42526303|ref|NP_971401.1| DNA-directed RNA polymerase subunit alpha [Treponema denticola ATCC
           35405]
 gi|61215985|sp|Q73PK8|RPOA_TREDE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|41816415|gb|AAS11282.1| DNA-directed RNA polymerase, alpha subunit [Treponema denticola
           ATCC 35405]
          Length = 351

 Score =  181 bits (458), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 118/332 (35%), Positives = 177/332 (53%), Gaps = 16/332 (4%)

Query: 1   MIQKNW-QELIKPNNIEYIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRG 57
           M +KN  +   KP  +E+    Q+E   +     A P   GF  T+GN LRR+L+SS++G
Sbjct: 1   MARKNLLKGFKKPKGLEF---AQQESTESYGKFTASPFETGFGTTIGNCLRRILLSSIQG 57

Query: 58  AAITAVQI-----DGVLHEISS----IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK 108
            AI+AV I     DGV H ISS    I  V ED  +I+  +K I L++S +S +    F+
Sbjct: 58  YAISAVLITSHDADGVPHTISSEFENIPNVSEDTLEILNKLKQIRLRLSDESEQGDFHFE 117

Query: 109 -RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
            +GP  +T+ D      +E+L     +  L   A V  ++ V  G GYVPA+ +    + 
Sbjct: 118 FKGPASITSKDFAVEGQLEILGEPFYVMELMKGANVSFDVQVDFGRGYVPAEVNEKYIEI 177

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           +G I +DA+Y P+ KVSY +E  R GQ  DYDKL + I TD ++  ED +  A++I +D 
Sbjct: 178 VGTIPMDAIYGPVLKVSYAIEPCRVGQRNDYDKLILEIWTDSTVRPEDVLGEAAKIAKDH 237

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
             +FINF E     +++ + +       L   +  L+ SVR+ NCL    I  +G+L Q+
Sbjct: 238 FSIFINFNENDYLGEDEDDNEEAVIKQLLATSINTLDFSVRAKNCLDSAGIKTLGELAQK 297

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +E ++  M N GR +L EI   L    L LGM
Sbjct: 298 SEDEIESMRNVGRMTLNEIHAKLAEYNLRLGM 329


>gi|254368646|ref|ZP_04984661.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           holarctica FSC022]
 gi|157121554|gb|EDO65739.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           holarctica FSC022]
          Length = 323

 Score =  181 bits (458), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 106/292 (36%), Positives = 171/292 (58%), Gaps = 7/292 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P+ +G AH LGN++RRVL+SSL GA+I  V I  VLHE S+++ V ED+ +I+ N+K + 
Sbjct: 31  PVEKGMAHILGNSIRRVLLSSLSGASIIKVNIANVLHEYSTLEDVKEDVVEIVSNLKKVA 90

Query: 94  LKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
           +K+ +G     + +     GVV AGD +T   +E++N D  I  L       +  TVS G
Sbjct: 91  IKLDTGIDRLDLELSVNKSGVVRAGDFKTTQGVEIINKDQPIATLTNQRAFSLTATVSVG 150

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
                     TE + +G I +DA ++PIK+V++ V         D + L + + T+G+I 
Sbjct: 151 RNVGILSAIPTELERVGDIAVDADFNPIKRVAFEVFDNG-----DSETLEVFVKTNGTIG 205

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
              +V  A     +Q+ +F++   P      D+ + S   +P LLK +++LEL+VRS+NC
Sbjct: 206 PLAAVTKALEYFCEQISVFVSLRVPSNGKTGDVLIDS-NIDPILLKPIDDLELTVRSSNC 264

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           LR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L    L LG+ + ++
Sbjct: 265 LRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQILIDNNLSLGVQIDNF 316


>gi|50364965|ref|YP_053390.1| DNA-directed RNA polymerase subunit alpha [Mesoplasma florum L1]
 gi|61215913|sp|Q6F1W7|RPOA_MESFL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|50363521|gb|AAT75506.1| DNA-directed RNA polymerase alpha chain [Mesoplasma florum L1]
          Length = 317

 Score =  181 bits (458), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 115/299 (38%), Positives = 165/299 (55%), Gaps = 16/299 (5%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
           A PL RGFA TLGNALRR L+SS  GA++ A++I G  HE +SI G+ E++T I+LN+K 
Sbjct: 25  AAPLERGFAVTLGNALRRTLLSSTPGASVFAIKIAGAQHEFTSISGIEENVTRIVLNVKK 84

Query: 92  INLKMSG-----DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           + L++       D    + +     G VTAG +     +EVLN D VI N+     + + 
Sbjct: 85  LILRIDSAIYNDDETVELKVGTSTIGPVTAGSLVLPAGVEVLNKDLVIANVAEGGNLDLV 144

Query: 147 LTVSKGHGYVPAKHHRTENDPI-GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           L      GY   K ++   D + G+ITID+ YSPI KV+Y       G+  D++KL + +
Sbjct: 145 LYAKNSRGYKTFKENKELKDVVPGMITIDSNYSPIIKVAYGSTPINLGKAQDFEKLILEV 204

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK----EDINVKSLPFNPALLKKVE 261
           +TDGSI   D+V+LAS+IL     +F    E  +EV     E +  K L       K VE
Sbjct: 205 ETDGSILASDAVSLASKILISHFDVFTTLAEEVEEVAIMGVETVEEKELD------KPVE 258

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           ELE + RS NCL+   I  + +L+ +TE ++  + N GRKSL EIK  +  + L    N
Sbjct: 259 ELEFTQRSLNCLKRAGISTLRELVSKTEDEIQDIRNLGRKSLKEIKDKVAALELTFKQN 317


>gi|15644221|ref|NP_229272.1| DNA-directed RNA polymerase subunit alpha [Thermotoga maritima
           MSB8]
 gi|7388097|sp|Q9X1I2|RPOA_THEMA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|4982038|gb|AAD36540.1|AE001798_5 DNA-directed RNA polymerase, alpha subunit [Thermotoga maritima
           MSB8]
          Length = 336

 Score =  181 bits (458), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 116/297 (39%), Positives = 170/297 (57%), Gaps = 28/297 (9%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQI--DGVLHEISSIKGVHEDLTDIILNIKG 91
           PL RG+A T+GNALRRVL+SS+   AI  V+       HE   I+GV ED+ DIILN+K 
Sbjct: 30  PLERGYAITIGNALRRVLLSSIPSLAIVGVRFIKPEKYHEYDYIEGVKEDILDIILNLKK 89

Query: 92  INLKM--SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           +  ++  +     ++ + K+GPG + AGDI+T   IEV+NPD  I  L+  A +  E+  
Sbjct: 90  VQFRINVTVKGTIKMEVEKKGPGELVAGDIKTPAGIEVVNPDLHIATLNSKADLFFEVYA 149

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G G+VP    R E   +G I ID ++SP+ KV++  E+ R G+  DYDKL + I T  
Sbjct: 150 EVGKGFVPV-SEREERPDVGWIPIDGVFSPVIKVNFLTENVRVGKRTDYDKLILEIWTKK 208

Query: 210 SITGEDSVALASRILQDQLGM--------------FINFEE-----PKKEVKEDINVKSL 250
           SI  E+++  A+ IL +   +               I  EE     P  E +E+    S 
Sbjct: 209 SIRPEEALRKAADILINHFKIVTEGLPELKISEEYIITSEEEEAEVPASEHEEEHRENSD 268

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            +N    +K++ELELSVRS NCL+   I  +GDL+ +TE ++L++ NFG+KSL E+K
Sbjct: 269 VYN----RKIDELELSVRSLNCLKRAKIETIGDLLSKTEEELLKIKNFGQKSLDEVK 321


>gi|150036814|emb|CAM98040.1| DNA-directed RNA polymerase alpha chain [Leuconostoc kimchii]
          Length = 226

 Score =  180 bits (457), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 92/211 (43%), Positives = 136/211 (64%), Gaps = 2/211 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVV 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L +  D  + + I  +GP  VTA D+Q   D+E+LNPD  +  +     + M +T  KG 
Sbjct: 61  LAIDSDDERSLEIDVQGPADVTAADLQAGADVEILNPDLHLATVAAGKSLHMTVTAVKGR 120

Query: 154 GYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A  ++   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI
Sbjct: 121 GYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVK 242
              D+++L S+IL + L +F++      E  
Sbjct: 181 KPSDALSLGSKILAEHLNLFMDISPVAAEAS 211


>gi|195973804|gb|ACG63467.1| DNA-directed RNA polymerase subunit alpha [Francisella noatunensis
           subsp. orientalis]
 gi|225624845|gb|ACN96557.1| RpoA [Francisella noatunensis subsp. orientalis]
          Length = 290

 Score =  180 bits (457), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 103/278 (37%), Positives = 166/278 (59%), Gaps = 7/278 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P+ +G AH LGN++RR L+SSL GA+I  V I GVLHE S+++ V ED+ +I+ N+K + 
Sbjct: 18  PVEKGMAHILGNSIRRFLLSSLSGASIIKVNISGVLHEYSTLEDVKEDVVEIVSNLKKVA 77

Query: 94  LKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
           +K+  +  K  + +     GVVTAGD +T   IE++N D  I  L  +    +  TVS G
Sbjct: 78  IKLDKNVSKVELELSVTKSGVVTAGDFKTTQGIEIINKDQPIATLTNEREFSLVATVSVG 137

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
                     TE + +G I +DA ++PIK+V++ +      + L+     + + T+G+I 
Sbjct: 138 RNVGILSALPTELEKVGDIAVDADFNPIKRVAFEIFDNGASETLE-----VFVKTNGTIE 192

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
              +V  A +   +Q+ +F++   P      D  + S   +P LLK +++LEL+VRS+NC
Sbjct: 193 SLAAVTKALKYFCEQISVFVSLRVPSNGKTGDALLDS-NIDPILLKPIDDLELTVRSSNC 251

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           LR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L
Sbjct: 252 LRAENIKYLGDLVQYSESQLIKIPNLGKKSLNEIKQIL 289


>gi|13096176|pdb|1HQM|A Chain A, Crystal Structure Of Thermus Aquaticus Core Rna
           Polymerase- Includes Complete Structure With Side-Chains
           (Except For Disordered Regions)-Further Refined From
           Original Deposition-Contains Additional Sequence
           Information
 gi|13096177|pdb|1HQM|B Chain B, Crystal Structure Of Thermus Aquaticus Core Rna
           Polymerase- Includes Complete Structure With Side-Chains
           (Except For Disordered Regions)-Further Refined From
           Original Deposition-Contains Additional Sequence
           Information
          Length = 313

 Score =  180 bits (457), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 116/293 (39%), Positives = 168/293 (57%), Gaps = 9/293 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED+ +IILN+
Sbjct: 23  FVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKR--GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K + ++   D   R T+  R  GP  V A D     D+E++NPD  I  L+    + ME+
Sbjct: 83  KELVVRFL-DPRWRTTLILRAEGPKEVRAVDFTPSADVEIMNPDLHIATLEEGGKLYMEV 141

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            V +G GYVPA+ H  + D I  I +DA++SP+++V++ VE  R GQ  D DKL++ I T
Sbjct: 142 RVDRGVGYVPAERHGIK-DRINAIPVDAIFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWT 200

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEE---PKKEVKEDINVKSLPFNPALLKKVEELE 264
           DGS+T  +++  A  IL++ L  F N E    P  EV +    +S   +  L   +EEL 
Sbjct: 201 DGSVTPLEALNQAVAILKEHLNYFANPEASLLPTPEVSKGEKRESAEEDLDL--PLEELG 258

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS R  + L+ E I  +  L+     D+  +   G +SL EI+  L   G  L
Sbjct: 259 LSTRVLHSLKEEGIESVRALLALNLKDLRNIPGIGERSLEEIRQALAKKGFTL 311


>gi|118496877|ref|YP_897927.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. novicida U112]
 gi|194324099|ref|ZP_03057873.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. novicida FTE]
 gi|254372234|ref|ZP_04987725.1| hypothetical protein FTCG_01300 [Francisella tularensis subsp.
           novicida GA99-3549]
 gi|158512418|sp|A0Q4K8|RPOA1_FRATN RecName: Full=DNA-directed RNA polymerase subunit alpha 1;
           Short=RNAP subunit alpha 1; AltName: Full=RNA polymerase
           subunit alpha 1; AltName: Full=Transcriptase subunit
           alpha 1
 gi|118422783|gb|ABK89173.1| DNA-directed RNA polymerase, alpha subunit [Francisella novicida
           U112]
 gi|151569963|gb|EDN35617.1| hypothetical protein FTCG_01300 [Francisella novicida GA99-3549]
 gi|194321546|gb|EDX19030.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. novicida FTE]
 gi|328676346|gb|AEB27216.1| DNA-directed RNA polymerase alpha subunit [Francisella cf. novicida
           Fx1]
          Length = 323

 Score =  180 bits (457), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 105/292 (35%), Positives = 171/292 (58%), Gaps = 7/292 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P+ +G AH LGN++RRVL+SSL GA+I  V I  VLHE S+++ V ED+ +I+ N+K + 
Sbjct: 31  PVEKGMAHILGNSIRRVLLSSLSGASIIKVNIANVLHEYSTLEDVKEDVVEIVSNLKKVA 90

Query: 94  LKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
           +K+ +      + +     GVV+AGD +T   +E++N D  I  L       +  TVS G
Sbjct: 91  IKLDTAIDRLDLELSVNKSGVVSAGDFKTTQGVEIINKDQPIATLTNQRAFSLTATVSVG 150

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
                     TE + +G I +DA ++PIK+V++ V         D + L + + T+G+I 
Sbjct: 151 RNVGILSAIPTELERVGDIAVDADFNPIKRVAFEVFDNG-----DSETLEVFVKTNGTIE 205

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
              +V  A     +Q+ +F++   P      D+ + S   +P LLK +++LEL+VRS+NC
Sbjct: 206 PLAAVTKALEYFCEQISVFVSLRVPSNGKTGDVLIDS-NIDPILLKPIDDLELTVRSSNC 264

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           LR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L    L LG+ + ++
Sbjct: 265 LRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQILIDNNLSLGVQIDNF 316


>gi|150187019|emb|CAK30152.1| RNA polymerase alpha subunit [Streptococcus sobrinus]
          Length = 202

 Score =  180 bits (457), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 88/195 (45%), Positives = 136/195 (69%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   +  K +
Sbjct: 1   NSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVEDEKTI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV+K  GYVPA+ ++ +
Sbjct: 61  ELDVTGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGHSLKATMTVAKNRGYVPAEGNKND 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           + P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L
Sbjct: 121 SAPVGTLAVDSIYTPVKKVNYQVEPARVGSNAGFDKLTIEIMTNGTIIPEDALGLSARVL 180

Query: 225 QDQLGMFINFEEPKK 239
            + L +F +  E  K
Sbjct: 181 IEHLNLFTDLTEIAK 195


>gi|160902228|ref|YP_001567809.1| DNA-directed RNA polymerase subunit alpha [Petrotoga mobilis SJ95]
 gi|160359872|gb|ABX31486.1| DNA-directed RNA polymerase, alpha subunit [Petrotoga mobilis SJ95]
          Length = 353

 Score =  180 bits (457), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 118/329 (35%), Positives = 187/329 (56%), Gaps = 29/329 (8%)

Query: 9   LIKPNNIEYIVLG-QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           LIKP     +    Q+E N +     PL +G+A TLGNALRRVL+SS+   AIT ++I G
Sbjct: 4   LIKPEKFRIVQKEEQDEYNYSKYELFPLEKGYAITLGNALRRVLLSSIPSLAITGLRIPG 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG-------DSHKRVTIFKRGPG--VVTAGD 118
            LHE  +++G+ ED+ +I LN+K + LK+         D    +++ K+     V+ +GD
Sbjct: 64  KLHEYDTVEGIKEDIIEITLNLKKVQLKVDDIEKINEIDYPILLSLRKKYKAGQVIKSGD 123

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           I+T  ++EV NPD VI +++ D  V  EL    G G++PA+    ++D I  I ID ++S
Sbjct: 124 IKTPAELEVANPDFVIAHVNKDMEVDFELYAQAGKGFIPAQELTFQSD-IEYIFIDGVFS 182

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ KV+Y  E+ R G+  DYDKL + I T  +IT  +++  A++IL +         E +
Sbjct: 183 PVLKVNYLTENIRVGRRTDYDKLILEIWTKKNITPTEALKEATKILMEHFDFISRLWERE 242

Query: 239 KEV-----------------KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
            +V                 +E+ N+  LP    +  +++ L+L+ R+ NCL+ E I  +
Sbjct: 243 GQVGAIEQTEVSVEKEEEEEEEEENIFGLP-KDLMETQLDSLDLTKRAKNCLKREKIDTI 301

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           G+L++R  AD+L++ NFGRKSL EIK  L
Sbjct: 302 GELLKRKPADLLKIKNFGRKSLDEIKNEL 330


>gi|119662837|emb|CAJ33211.1| RNA polymerase alpha subunit [Lactobacillus satsumensis]
          Length = 210

 Score =  180 bits (457), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 88/198 (44%), Positives = 139/198 (70%), Gaps = 2/198 (1%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAIT++QIDGVLHE S+IKGV ED+T IILN+K + L++  +  + 
Sbjct: 1   GNSLRRILLSSLPGAAITSIQIDGVLHEFSTIKGVLEDVTQIILNLKKVALRIDSEEDQT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I   GP  V AGDIQ  +D+EVLNPD  +C +   A   + +  + G GYV A  ++ 
Sbjct: 61  LEISVNGPLEVKAGDIQGSSDVEVLNPDLYLCTVAEGASFHVRMNANTGRGYVSADENKI 120

Query: 164 END--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           + D  PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T+G+++  ++++L++
Sbjct: 121 KADDMPIGVLPIDSIYTPIERVNYQVEKTRVGQRDDYDKLTLDVWTNGAVSPSEAISLSA 180

Query: 222 RILQDQLGMFINFEEPKK 239
           +IL + L +F++  +  K
Sbjct: 181 KILTEHLTLFVDLTDEAK 198


>gi|56751897|ref|YP_172598.1| DNA-directed RNA polymerase subunit alpha [Synechococcus elongatus
           PCC 6301]
 gi|81301018|ref|YP_401226.1| DNA-directed RNA polymerase subunit alpha [Synechococcus elongatus
           PCC 7942]
 gi|6226041|sp|O24710|RPOA_SYNP6 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366742|sp|Q31L30|RPOA_SYNE7 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|2446913|dbj|BAA22472.1| DNA-dircted RNA polymerase alpha chain [Synechococcus elongatus PCC
           6301]
 gi|56686856|dbj|BAD80078.1| RNA polymerase alpha subunit [Synechococcus elongatus PCC 6301]
 gi|81169899|gb|ABB58239.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus elongatus
           PCC 7942]
          Length = 309

 Score =  180 bits (456), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 104/286 (36%), Positives = 166/286 (58%), Gaps = 8/286 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG   T+GNALRRVL+S+L G A+TAV+I GV HE ++I GV ED+ DI+LN++ +
Sbjct: 25  EPLARGQGTTVGNALRRVLLSNLEGTAVTAVRIGGVNHEFATIPGVREDVLDILLNVREL 84

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +       +   +   GP  VTA D+    ++EV+NP+H I +L   A + MEL V  G
Sbjct: 85  VVHAHSPQPQIGRLRVVGPATVTAADVDFGPEVEVINPNHYIASLSEGATLEMELKVEWG 144

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GY        E   +  + +DA++ P+++V+Y+VE AR G+    D+L + + T+GS++
Sbjct: 145 TGYRAIDRSHDETTALDFLQLDAVFMPVRRVNYSVEDARVGESTAIDRLVLEVWTNGSLS 204

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF-NPALLKKVEELELSVRSTN 271
            +++++ A+  L   + +F    EP K V       + P   P     +E+L+LSVR+ N
Sbjct: 205 PQEALSQAASCL---VALF----EPLKNVSVGSTHTADPEPTPESQTPIEDLQLSVRAYN 257

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           CL+   +  + DL+  T  D+L + NFG+KS  E+   L  +G+ L
Sbjct: 258 CLKRAQVNSVADLLSYTYEDLLEIKNFGQKSAEEVVEALERIGIKL 303


>gi|153820464|ref|ZP_01973131.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae NCTC
           8457]
 gi|126508991|gb|EAZ71585.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae NCTC
           8457]
          Length = 215

 Score =  180 bits (456), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 95/218 (43%), Positives = 143/218 (65%), Gaps = 8/218 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E++NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIVNPEHVICHLTSDNAAIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
           +SP+ K++Y+VE+AR  Q  D DKL + ++T+G++  E
Sbjct: 178 FSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLEPE 215


>gi|16329917|ref|NP_440645.1| DNA-directed RNA polymerase subunit alpha [Synechocystis sp. PCC
           6803]
 gi|2500603|sp|P73297|RPOA_SYNY3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|1652403|dbj|BAA17325.1| RNA polymerase alpha subunit [Synechocystis sp. PCC 6803]
          Length = 314

 Score =  180 bits (456), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 112/293 (38%), Positives = 172/293 (58%), Gaps = 13/293 (4%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG   T+GNALRRVL+S+L GAA+TA++I GV HE ++I GV ED+ +I+LN+K +
Sbjct: 26  EPLDRGQGTTVGNALRRVLLSNLPGAAVTAIRIAGVNHEFATILGVREDVLEIMLNMKEL 85

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LK   D  +   +   GPG VTA   +  +++EV++P+  I  L   A + ME  V +G
Sbjct: 86  VLKSYTDQPQIGRLTAIGPGTVTAAQFEVPSEVEVIDPNQYIATLAEGAKLEMEFRVERG 145

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GY   +  + EN  +  + ID+++ P+ KV+YTVE  R   +   D+L + I T+GSI 
Sbjct: 146 VGYRVIERGKDENSSLDFLQIDSVFMPVTKVNYTVEDIRADGMSPKDRLILDIWTNGSIQ 205

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS---LPFNPALLKKVEELELSVRS 269
             ++++ AS I+ +   +FI    P K++ E     S      NP     +EEL+LSVR+
Sbjct: 206 PREALSEASDIIAN---LFI----PLKDLNELEAAHSDYQDEVNPESQIPIEELQLSVRA 258

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
            NCL+   I  + DL++ ++ D+L + NFG KS  E   V+  +   LG+ LP
Sbjct: 259 YNCLKRAQINSVADLLEYSQEDLLEIKNFGLKSAEE---VIEALQKRLGITLP 308


>gi|195973794|gb|ACG63462.1| DNA-directed RNA polymerase subunit alpha [Francisella philomiragia
           subsp. philomiragia ATCC 25015]
          Length = 290

 Score =  180 bits (456), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 103/278 (37%), Positives = 166/278 (59%), Gaps = 7/278 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P+ +G AH LGN++RR L+SSL GA+I  V IDGVLHE S+++ V ED+ +I+ N+K + 
Sbjct: 18  PVEKGMAHILGNSIRRFLLSSLSGASIIKVNIDGVLHEYSTLEDVKEDVVEIVSNLKKVA 77

Query: 94  LKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
           +K+  +  K  + +     GVVTAGD +T   IE++N D  I  L  +    +  TVS G
Sbjct: 78  IKLDKNVSKVELELSVTKSGVVTAGDFKTTQGIEIINKDQPIATLTNERKFSLTATVSVG 137

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
                     TE + +G I +D+ ++PIK+V++ +      + L+     + + T+G+I 
Sbjct: 138 RNVGILSALPTELEKVGDIAVDSDFNPIKRVAFEIFDNGTNETLE-----VFVKTNGTIE 192

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
              +V  A     +Q+ +F++   P      D  + S   +P LLK +++LEL+VRS+NC
Sbjct: 193 PLVAVTKALEYFCEQISVFVSLRVPSNGKTGDALLDS-NIDPILLKPIDDLELTVRSSNC 251

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           LR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L
Sbjct: 252 LRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQIL 289


>gi|325473246|gb|EGC76441.1| DNA-directed RNA polymerase subunit alpha [Treponema denticola
           F0402]
          Length = 351

 Score =  180 bits (456), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 118/332 (35%), Positives = 177/332 (53%), Gaps = 16/332 (4%)

Query: 1   MIQKNW-QELIKPNNIEYIVLGQEEENRTL--MIAEPLPRGFAHTLGNALRRVLMSSLRG 57
           M +KN  +   KP  +E+    Q+E   +     A P   GF  T+GN LRR+L+SS++G
Sbjct: 1   MARKNLLKGFKKPKGLEF---AQQESTESYGKFTASPFETGFGTTIGNCLRRILLSSIQG 57

Query: 58  AAITAVQI-----DGVLHEISS----IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK 108
            AI+AV I     DGV H ISS    I  V ED  +I+  +K I L++S +S +    F+
Sbjct: 58  YAISAVLITSHDADGVPHTISSEFENIPNVSEDTLEILNKLKQIRLRLSDESEQGDFHFE 117

Query: 109 -RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
            +GP  +T+ D      +E+L     +  L   A V  ++ V  G GYVPA+ +    + 
Sbjct: 118 FKGPASITSKDFAVEGQLEILGEPFHVMELMKGANVSFDVQVDFGRGYVPAEVNEKYIEI 177

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           +G I +DA+Y P+ KVSY +E  R GQ  DYDKL + I TD ++  ED +  A++I +D 
Sbjct: 178 VGTIPMDAIYGPVLKVSYAIEPCRVGQRNDYDKLILEIWTDSTVRPEDVLGEAAKIAKDH 237

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
             +FINF E     +++ + +       L   +  L+ SVR+ NCL    I  +G+L Q+
Sbjct: 238 FSIFINFNENDYLGEDEDDNEEAVIKQLLATSINTLDFSVRAKNCLDSAGIKTLGELAQK 297

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +E ++  M N GR +L EI   L    L LGM
Sbjct: 298 SEDEIESMRNVGRMTLNEIHAKLAEYNLRLGM 329


>gi|119668295|emb|CAK95502.1| RNA polymerase alpha subunit [Lactobacillus crispatus]
          Length = 203

 Score =  179 bits (455), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 89/188 (47%), Positives = 127/188 (67%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   D  K 
Sbjct: 1   GNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLSDEQKV 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + +   GP  VTA D++   D++VLNPD  IC +     + MEL V  G GYV A  +++
Sbjct: 61  IELDIEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMELAVKNGRGYVAASDNKS 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           ++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++ A++I
Sbjct: 121 DDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKI 180

Query: 224 LQDQLGMF 231
           L +   +F
Sbjct: 181 LVEHFKVF 188


>gi|195973796|gb|ACG63463.1| DNA-directed RNA polymerase subunit alpha [Francisella
           philomiragia]
 gi|195973798|gb|ACG63464.1| DNA-directed RNA polymerase subunit alpha [Francisella
           philomiragia]
 gi|195973800|gb|ACG63465.1| DNA-directed RNA polymerase subunit alpha [Francisella
           philomiragia]
          Length = 290

 Score =  179 bits (455), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 103/278 (37%), Positives = 166/278 (59%), Gaps = 7/278 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P+ +G AH LGN++RR L+SSL GA+I  V IDGVLHE S+++ V ED+ +I+ N+K + 
Sbjct: 18  PVEKGMAHILGNSIRRFLLSSLSGASIIKVNIDGVLHEYSTLEDVKEDVVEIVSNLKKVA 77

Query: 94  LKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
           +K+  +  K  + +     GVVTAGD +T   IE++N D  I  L  +    +  TVS G
Sbjct: 78  IKLDKNVSKVELELSVTKSGVVTAGDFKTTQGIEIINKDQPIATLTNEREFSLTATVSVG 137

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
                     TE + +G I +D+ ++PIK+V++ +      + L+     + + T+G+I 
Sbjct: 138 RNVGILSALPTELEKVGDIAVDSDFNPIKRVAFEIFDNGTNETLE-----VFVKTNGTIE 192

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
              +V  A     +Q+ +F++   P      D  + S   +P LLK +++LEL+VRS+NC
Sbjct: 193 PLVAVTKALEYFCEQISVFVSLRVPSNGKTGDALLDS-NIDPILLKPIDDLELTVRSSNC 251

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           LR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L
Sbjct: 252 LRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQIL 289


>gi|119662815|emb|CAJ33199.1| RNA polymerase alpha subunit [Lactobacillus kefiranofaciens subsp.
           kefiranofaciens]
          Length = 203

 Score =  179 bits (455), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 89/188 (47%), Positives = 127/188 (67%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   D  K 
Sbjct: 1   GNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLSDEQKV 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + +   GP  VTA D++   D++VLNPD  IC +     + MEL V  G GYV A  +++
Sbjct: 61  IELDVEGPATVTADDLKVDADVQVLNPDQYICTIAKGGHLHMELAVKNGRGYVTASDNKS 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           ++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++ A++I
Sbjct: 121 DDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKI 180

Query: 224 LQDQLGMF 231
           L +   +F
Sbjct: 181 LVEHFKVF 188


>gi|119668373|emb|CAK95478.1| RNA polymerase alpha subunit [Lactobacillus sakei subsp. carnosus]
          Length = 203

 Score =  179 bits (455), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 87/195 (44%), Positives = 137/195 (70%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRR+L++SL G A+T +QIDGVLHE S+I GV ED+T IILNIK + LK+  +  K +
Sbjct: 1   NSLRRILLASLPGTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKLHVEEDKTI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            I  +GP  VTA DI + +D+EVLN D  IC +       + +TV KG GYV A  ++++
Sbjct: 61  EIDVKGPATVTAADIISDDDVEVLNTDQYICTVAEGGNFHVRMTVKKGRGYVAAVQNKSD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           + PIG++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++I+
Sbjct: 121 DMPIGVLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKIM 180

Query: 225 QDQLGMFINFEEPKK 239
            + L +F++  +  K
Sbjct: 181 TEHLAIFVDLTDEAK 195


>gi|119662369|emb|CAJ33173.1| RNA polymerase alpha subunit [Lactobacillus versmoldensis]
          Length = 215

 Score =  179 bits (455), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 85/202 (42%), Positives = 139/202 (68%), Gaps = 1/202 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL++SL G A++ +QIDGVLHE  +I GV ED+T I+LNIK ++LK   
Sbjct: 1   YGTTLGNSLRRVLLASLPGTAVSDIQIDGVLHEFFAIDGVIEDVTQIVLNIKKLSLKSYA 60

Query: 99  DSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
           +    +  I   GP  +TA DIQ  +D+E+L+P+  IC +       M++T++ G GY P
Sbjct: 61  EEGSLKAEIDISGPATITAKDIQADDDLEILDPEQYICTVAEGGHFHMQMTITNGRGYTP 120

Query: 158 AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
           A+ ++T+  PIG++ +D++++P++KV+Y VE+ R G+  D+DKL++ I T+GSI   +++
Sbjct: 121 AEQNKTDETPIGVLPVDSIFTPVEKVNYQVENTRVGKRNDFDKLTIDIWTNGSIGPREAI 180

Query: 218 ALASRILQDQLGMFINFEEPKK 239
           +L+++IL + L  F+N  E  K
Sbjct: 181 SLSAKILTEHLTSFVNLTEEAK 202


>gi|119668337|emb|CAK95467.1| RNA polymerase alpha subunit [Lactobacillus johnsonii]
          Length = 187

 Score =  179 bits (455), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 89/183 (48%), Positives = 129/183 (70%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG 110
           L++S+ G A++ +QIDGVLHE S+I GV ED+T IILN+K + LK   D  K   I   G
Sbjct: 1   LLTSIPGTALSYIQIDGVLHEFSTIPGVREDVTKIILNLKKLELKSLSDEEKIAEIDVTG 60

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
           P +VTA D++  +DIEVLNPD  IC++     + M + +  G GYVPA  ++T++ PIG+
Sbjct: 61  PAIVTAADLKVDSDIEVLNPDQYICSIADGGHLHMNVAIKTGRGYVPASENKTDDMPIGV 120

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           I +D+L+SPIKKV+Y VESAR G+  DYDKL++ I TDGSIT  D+++ A++IL +   +
Sbjct: 121 IPVDSLFSPIKKVNYQVESARVGKRDDYDKLTLEIWTDGSITPNDALSFAAKILVEHFKV 180

Query: 231 FIN 233
           F++
Sbjct: 181 FMS 183


>gi|119668345|emb|CAK95469.1| RNA polymerase alpha subunit [Lactobacillus paracasei subsp.
           paracasei]
          Length = 186

 Score =  179 bits (454), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 89/186 (47%), Positives = 133/186 (71%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNIK + LKM+ D  K + I
Sbjct: 1   LRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNTDEDKNIEI 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
              GP  VTA DI    D+EVLNP+  IC +       + +TV KG GYV A  +++++ 
Sbjct: 61  DVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAADQNKSDDM 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++IL +
Sbjct: 121 PIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKILTE 180

Query: 227 QLGMFI 232
            L +F+
Sbjct: 181 HLDIFV 186


>gi|85057775|ref|YP_456691.1| DNA-directed RNA polymerase subunit alpha [Aster yellows
           witches'-broom phytoplasma AYWB]
 gi|119366664|sp|Q2NIY1|RPOA_AYWBP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|84789880|gb|ABC65612.1| DNA-directed RNA polymerase alpha chain [Aster yellows
           witches'-broom phytoplasma AYWB]
          Length = 330

 Score =  179 bits (454), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 106/303 (34%), Positives = 175/303 (57%), Gaps = 8/303 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           +PL RG+  T+GNALRRVL+SSL GAAI  V+I GV  E ++I GV+ED+  IILN+K I
Sbjct: 27  KPLERGYGITVGNALRRVLLSSLPGAAIVNVKIQGVEQEFTTIPGVYEDVMTIILNLKKI 86

Query: 93  NLKM---SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
              +   S D  +++ +  +GP  +TA   +    ++++NPDH I  L  D    M +T+
Sbjct: 87  VFAVDDESDDFEEKLELIAKGPQRLTAASFELPAGVKIINPDHYITTLSDDVCFHMTVTI 146

Query: 150 SKGHGYVPAKHHRTE-NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
            KG GYV AK ++    + +G+I ID+L++P+  VSY VE     ++ + D+L++ I T+
Sbjct: 147 KKGIGYVGAKENKVHIENQVGVIAIDSLFTPVVNVSYQVEK----KLGNKDELTIEITTN 202

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  ++++A A+ IL D   + +   +    V+     K    N  L  ++E+L+LSVR
Sbjct: 203 GALLAKEALATAASILVDHFNVLVELSQKPAHVEFVSESKKEAHNYVLDLEIEQLDLSVR 262

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPES 328
             N L+   I  +  L++ +E +++++ + GRKS  E+K      GL     L +    S
Sbjct: 263 LFNSLKRAGIDTVASLVKLSEKEVVKLKSLGRKSFQELKDKFLEYGLEFNDYLKEALHHS 322

Query: 329 IEE 331
           +EE
Sbjct: 323 VEE 325


>gi|14278481|pdb|1I6V|A Chain A, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
 gi|14278482|pdb|1I6V|B Chain B, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
          Length = 314

 Score =  179 bits (454), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 114/302 (37%), Positives = 168/302 (55%), Gaps = 26/302 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED+ +IILN+
Sbjct: 23  FVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKR--GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K + ++         T+  R  GP  V A D     D+E++NPD  I  L+    + ME+
Sbjct: 83  KELVVRFLDPKMASTTLILRAEGPKEVRAVDFTPSADVEIMNPDLHIATLEEGGKLYMEV 142

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            V +G GYVPA+ H  + D I  I +DA++SP+++V++ VE  R GQ  D DKL++ I T
Sbjct: 143 RVDRGVGYVPAERHGIK-DRINAIPVDAIFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWT 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFE------------EPKKEVKEDINVKSLPFNPA 255
           DGS+T  +++  A  IL++ L  F N E            E ++  +ED++   LP    
Sbjct: 202 DGSVTPLEALNQAVAILKEHLNYFANPEASSLPTPEVSKGEKRESAEEDLD---LP---- 254

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
               +EEL LS R  + L+ E I  +  L+     D+  +   G +SL EI+  L   G 
Sbjct: 255 ----LEELGLSTRVLHSLKEEGIESVRALLALNLKDLRNIPGIGERSLEEIRQALAKKGF 310

Query: 316 FL 317
            L
Sbjct: 311 TL 312


>gi|218440647|ref|YP_002378976.1| DNA-directed RNA polymerase subunit alpha [Cyanothece sp. PCC 7424]
 gi|218173375|gb|ACK72108.1| DNA-directed RNA polymerase, alpha subunit [Cyanothece sp. PCC
           7424]
          Length = 314

 Score =  179 bits (454), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 105/297 (35%), Positives = 171/297 (57%), Gaps = 15/297 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG   T+GNALRRVL+S+L GAA+TA++I GV HE ++I GV ED+ ++ILN+
Sbjct: 23  FILEPLDRGQGTTVGNALRRVLLSNLEGAAVTALRIAGVNHEFATISGVREDVMELILNM 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK      +   +   GP  VTA      ++IEV++P   +  L   + + ME  V
Sbjct: 83  KEITLKSYTSQPQIGRLVATGPATVTAAQFDVPSEIEVVDPSQYVATLSDGSKLEMEFRV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GY   +  + +   +  + ID+++ P+ KV+Y+VE  R       D+L++ I T+G
Sbjct: 143 EKGKGYRAIERGKDDTTSLDFLQIDSVFMPVTKVNYSVEDVRVDGTGSKDRLTLEIWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEE---PKKEVKEDINVKS-LPFNPALLKKVEELEL 265
           SI  +++++ A+ I+ D      +  E    + + ++++N +S +P        +EEL+L
Sbjct: 203 SINPKEALSEAAAIIVDLFSPLKDLNELEATQSDYQDEVNPESQIP--------IEELQL 254

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           SVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E   V+  +   LG+ LP
Sbjct: 255 SVRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEE---VIEALQKRLGITLP 308


>gi|148270450|ref|YP_001244910.1| DNA-directed RNA polymerase subunit alpha [Thermotoga petrophila
           RKU-1]
 gi|170289155|ref|YP_001739393.1| DNA-directed RNA polymerase, alpha subunit [Thermotoga sp. RQ2]
 gi|172047882|sp|A5IMB1|RPOA_THEP1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|147735994|gb|ABQ47334.1| DNA-directed RNA polymerase, alpha subunit [Thermotoga petrophila
           RKU-1]
 gi|170176658|gb|ACB09710.1| DNA-directed RNA polymerase, alpha subunit [Thermotoga sp. RQ2]
          Length = 336

 Score =  179 bits (453), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 116/297 (39%), Positives = 172/297 (57%), Gaps = 28/297 (9%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQI--DGVLHEISSIKGVHEDLTDIILNIKG 91
           PL RG+A T+GNALRRVL+SS+   AI  V+       HE   I+GV ED+ DIILN+K 
Sbjct: 30  PLERGYAITIGNALRRVLLSSIPSLAIVGVRFIKPEKYHEYDYIEGVKEDILDIILNLKK 89

Query: 92  INLKM--SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           +  ++  +     ++ + K+GPG + AGDI+T   IEV NPD  I  L+  A +  E+  
Sbjct: 90  VQFRVNVTVKGTIKMEVEKKGPGELVAGDIKTPAGIEVANPDLHIATLNSKADLFFEVYA 149

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G G+VP    R E   +G I ID ++SP+ KV++  E+ R G+  DYDKL + I T  
Sbjct: 150 EVGKGFVPV-SEREERPDVGWIPIDGVFSPVIKVNFLTENVRVGKRTDYDKLILEIWTKK 208

Query: 210 SITGEDSVALASRILQDQLGM--------------FINFEEPKKEV----KEDINVKSLP 251
           SI  E+++  A+ IL +   +               I  EE + E+     E+ N ++L 
Sbjct: 209 SIRPEEALRKAADILINHFKIVTEGLPELKISEEYIITSEEEEAEIPAVDHEEENRENLD 268

Query: 252 -FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            +N    +K++ELELSVRS NCL+   I  +GDL+ +TE ++L++ NFG+KSL E+K
Sbjct: 269 VYN----RKIDELELSVRSLNCLKRAKIETIGDLLSKTEEELLKIKNFGQKSLDEVK 321


>gi|154424857|emb|CAL18531.1| RNA polymerase alpha subunit [Streptococcus sanguinis]
          Length = 194

 Score =  179 bits (453), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 87/192 (45%), Positives = 131/192 (68%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL++SL GAA+T++ I+GVLHE  +I GV ED+  IILN+KGI +K      K +
Sbjct: 1   NSLRRVLLASLPGAAVTSINIEGVLHEFDTISGVREDVMQIILNVKGIAVKSYVQDEKII 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  VTAGDI T +DIE++NPDH +  +   A  +  +TV+ G GYVPA  ++ +
Sbjct: 61  ELDVEGPAEVTAGDILTDSDIEIINPDHYLFTIGEGASFKATMTVNSGRGYVPADENKKD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           + P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL
Sbjct: 121 DAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARIL 180

Query: 225 QDQLGMFINFEE 236
            + L +F N  E
Sbjct: 181 TEHLNLFTNLTE 192


>gi|311990468|gb|ADQ26364.1| RNA polymerase alpha subunit [Lactobacillus fermentum]
          Length = 220

 Score =  179 bits (453), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 91/198 (45%), Positives = 139/198 (70%), Gaps = 2/198 (1%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRV+++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K + LK+  +  K 
Sbjct: 1   GNSLRRVMLASLPGAAITSIQIDGVLHEFSTVQGVTEDVTQIILNLKQVALKIDSEDAKD 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I  +GP  VTA DIQ   D+ +LN D  I  +   A + +++T  KG GY  A  ++T
Sbjct: 61  LEIDVKGPAEVTAADIQGDGDVTILNSDLHIATVSDGAELHVKMTADKGRGYSSADDNKT 120

Query: 164 --ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
             E   IG++ ID++Y+PI++V+YTVE+ R GQ  DYDKL++ + T+GS+T  ++++LA+
Sbjct: 121 RMEGLAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYDKLTLDVWTNGSLTPTEAISLAA 180

Query: 222 RILQDQLGMFINFEEPKK 239
           +IL + L MF+N  E  +
Sbjct: 181 KILTEHLTMFVNLTEEAQ 198


>gi|119662357|emb|CAJ33167.1| RNA polymerase alpha subunit [Lactobacillus salivarius]
          Length = 194

 Score =  179 bits (453), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 91/192 (47%), Positives = 135/192 (70%), Gaps = 2/192 (1%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRR+L+SSL GAAIT VQIDGVLHE S+I GV ED+T IILN+K + L M  +  + + I
Sbjct: 1   LRRILLSSLPGAAITDVQIDGVLHEFSTIPGVLEDVTLIILNLKKVALSMESEDSQALEI 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
              GP  VTAGDIQ+ +D+EVLNP+  IC +   A + + +  +KG GYV A  ++   D
Sbjct: 61  NVTGPMEVTAGDIQSNSDVEVLNPEQYICTVADGAELHVRMNANKGRGYVSANDNKALAD 120

Query: 167 --PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
             PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T+GSIT  ++++L+++IL
Sbjct: 121 DMPIGVLPIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWTNGSITPSEAISLSAKIL 180

Query: 225 QDQLGMFINFEE 236
            + L +F++  +
Sbjct: 181 TEHLALFVDLTD 192


>gi|150186952|emb|CAK30135.1| RNA polymerase alpha subunit [Streptococcus equi subsp.
           zooepidemicus]
          Length = 205

 Score =  179 bits (453), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 87/196 (44%), Positives = 137/196 (69%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K 
Sbjct: 1   GNSLRRVLLSSLPGAAVTSIRIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKI 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV+K  GYVPA+ ++ 
Sbjct: 61  IELDVEGPAEVTAGDILTDSDIELVNPDHYLFTIADGYTLKASMTVAKKRGYVPAEGNKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+
Sbjct: 121 DDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARV 180

Query: 224 LQDQLGMFINFEEPKK 239
           L + L +F +  +  K
Sbjct: 181 LIEHLNLFTDLTDVAK 196


>gi|119668349|emb|CAK95511.1| RNA polymerase alpha subunit [Lactobacillus paraplantarum]
          Length = 177

 Score =  179 bits (453), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 93/176 (52%), Positives = 127/176 (72%), Gaps = 2/176 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTAIILNVKKIALKLES 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A   M +T + G GYV A
Sbjct: 61  DETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGAHFHMRMTANTGRGYVSA 120

Query: 159 K--HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           +   HR ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T+GSIT
Sbjct: 121 EDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWTNGSIT 176


>gi|119668309|emb|CAK95455.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           delbrueckii]
          Length = 200

 Score =  179 bits (453), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 89/198 (44%), Positives = 130/198 (65%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RGF  TLGN+LRRVL++S+ G  +  V+IDG+LHE +++ GV ED+T IILN+K
Sbjct: 1   VVEPLERGFGTTLGNSLRRVLLTSVPGTGLVKVKIDGILHEFTTVPGVKEDVTKIILNLK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            + L+   +  K + +   GP  VTA D++   D+EVLNPD  IC +     + M + V 
Sbjct: 61  KLVLRAYTEEVKTIELDVEGPATVTAEDLKADADVEVLNPDQYICTIAQGGHLHMWIDVC 120

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            G GYVPA  ++T    IG I +D+L+SPI+KV+Y VES R G+  D+DKL++ I T+GS
Sbjct: 121 NGRGYVPASENKTAEMFIGDIPVDSLFSPIEKVNYQVESTRVGKREDFDKLTLEIWTNGS 180

Query: 211 ITGEDSVALASRILQDQL 228
           I   D++  A+R+L +  
Sbjct: 181 IAPNDALNFAARVLVEHF 198


>gi|281412757|ref|YP_003346836.1| DNA-directed RNA polymerase, alpha subunit [Thermotoga naphthophila
           RKU-10]
 gi|281373860|gb|ADA67422.1| DNA-directed RNA polymerase, alpha subunit [Thermotoga naphthophila
           RKU-10]
          Length = 336

 Score =  178 bits (452), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 116/297 (39%), Positives = 172/297 (57%), Gaps = 28/297 (9%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQI--DGVLHEISSIKGVHEDLTDIILNIKG 91
           PL RG+A T+GNALRRVL+SS+   AI  V+       HE   I+GV ED+ DIILN+K 
Sbjct: 30  PLERGYAITIGNALRRVLLSSIPSLAIIGVRFIKPEKYHEYDYIEGVKEDILDIILNLKK 89

Query: 92  INLKM--SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           +  ++  +     ++ + K+GPG + AGDI+T   IEV NPD  I  L+  A +  E+  
Sbjct: 90  VQFRVNVTVKGTIKMEVEKKGPGELVAGDIKTPAGIEVANPDLHIATLNSKADLFFEVYA 149

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G G+VP    R E   +G I ID ++SP+ KV++  E+ R G+  DYDKL + I T  
Sbjct: 150 EVGKGFVPV-SEREERPDVGWIPIDGVFSPVIKVNFLTENVRVGKRTDYDKLILEIWTKK 208

Query: 210 SITGEDSVALASRILQDQLGM--------------FINFEEPKKEV----KEDINVKSLP 251
           SI  E+++  A+ IL +   +               I  EE + E+     E+ N ++L 
Sbjct: 209 SIRPEEALRKAADILINHFKIVTEGLPELKISEEYIITSEEEEAEIPAVDHEEENRENLD 268

Query: 252 -FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            +N    +K++ELELSVRS NCL+   I  +GDL+ +TE ++L++ NFG+KSL E+K
Sbjct: 269 VYN----RKIDELELSVRSLNCLKRAKIETIGDLLSKTEEELLKIKNFGQKSLDEVK 321


>gi|226356865|ref|YP_002786605.1| DNA-directed RNA polymerase subunit alpha [Deinococcus deserti
           VCD115]
 gi|226318855|gb|ACO46851.1| putative DNA-directed RNA polymerase alpha chain (DNA-dependent RNA
           polymerase) [Deinococcus deserti VCD115]
          Length = 333

 Score =  178 bits (452), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 115/314 (36%), Positives = 172/314 (54%), Gaps = 27/314 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  T+GN +RR+LMSS+ G A+T+V I+ VLHE S+I GV ED+  +ILN+
Sbjct: 19  FVLEPLTRGYGVTIGNPIRRILMSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVIQLILNL 78

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + ++      K +T+  +G GVV A   +  +D E++NPD  I  L  D  + ME+ V
Sbjct: 79  KELVVRFHTSGPKTLTLRAQGEGVVKASAFEVPSDAEIVNPDLTIATLAEDGKLVMEVRV 138

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYVPA  H T+ D I  I +DA++SP+++V+Y VE+ R GQ  D D+L + + TDG
Sbjct: 139 EEGEGYVPADKHATK-DRINSIPVDAVFSPVRRVAYHVENTRVGQQTDLDRLILRVWTDG 197

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI-----------NVKSLPFN----- 253
           S   +D++  +  IL+D+L +F N E     V +             NV  LP       
Sbjct: 198 STGPQDALDKSVEILRDELTVFGNVEALPALVSDVAPVYTPTPVPAHNVYDLPPTSGSVN 257

Query: 254 ------PALLKK----VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                 PA L      +E L L+ R  + L+ E I  +  L   ++ D+ ++   G +SL
Sbjct: 258 LNPGDYPAELDSPRVTLEGLGLTTRVLHSLKEEGIDSVDALCALSDRDLKKVPGIGERSL 317

Query: 304 VEIKGVLGTMGLFL 317
            EIK  L   GL L
Sbjct: 318 DEIKQQLAQFGLAL 331


>gi|150186939|emb|CAK30132.1| RNA polymerase alpha subunit [Streptococcus equinus]
          Length = 185

 Score =  178 bits (452), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 87/185 (47%), Positives = 132/185 (71%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   
Sbjct: 1   YGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYV 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + +   GP  VTAGDI T +D+E++NPDH +  +     ++  +TV+K  GYVPA
Sbjct: 61  DDEKIIELDVEGPAEVTAGDILTDSDVEIVNPDHYLFTIAEGHSLKATMTVAKKRGYVPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           + ++ E+ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ 
Sbjct: 121 EGNKKEDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALG 180

Query: 219 LASRI 223
           L++R+
Sbjct: 181 LSARV 185


>gi|150187122|emb|CAK30175.1| RNA polymerase alpha subunit [Streptococcus lutetiensis]
          Length = 201

 Score =  178 bits (452), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 88/194 (45%), Positives = 135/194 (69%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           +LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + 
Sbjct: 1   SLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIE 60

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
           +   GP  VTAGDI T +D+E++NPDH +  +     ++  +TV+K  GYVPA+ ++ E+
Sbjct: 61  LDVEGPAEVTAGDILTDSDVEIVNPDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKED 120

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
            P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L 
Sbjct: 121 APVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLI 180

Query: 226 DQLGMFINFEEPKK 239
           + L +F +  E  K
Sbjct: 181 EHLNLFTDLTEVAK 194


>gi|225621052|ref|YP_002722310.1| DNA-directed RNA polymerase subunit alpha [Brachyspira
           hyodysenteriae WA1]
 gi|225215872|gb|ACN84606.1| DNA-directed RNA polymerase alpha subunit [Brachyspira
           hyodysenteriae WA1]
          Length = 324

 Score =  178 bits (452), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 112/299 (37%), Positives = 175/299 (58%), Gaps = 15/299 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            IA+P  RG+A T+GNALRRVL+SS+ G AIT ++IDGV +E  ++ G+ ED   +I+++
Sbjct: 30  FIAQPFERGYAVTVGNALRRVLLSSIPGYAITTIKIDGVSNEFENVPGMKEDTIVMIMHL 89

Query: 90  KGINLKMSGDSH---KRVTIFKRGPGVVTAGDIQTVNDIE--VLNPDHVICNLDVDAVVR 144
           K  N+ +S  SH   K + + K GP V+TAGD+   +D E  V NPD+ I  +       
Sbjct: 90  K--NVVVSLPSHMDTKTIHMKKEGPCVITAGDL-VADDTEAQVHNPDYYIATIAEGYTFE 146

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           M++ +  G+ YVPA+ +    + I  I IDA+YSPI  V Y V+  R GQ +DY KL++ 
Sbjct: 147 MDIQIEGGYSYVPAEMNIELLEDINAIAIDAIYSPIVSVKYNVDPIRVGQRIDYGKLTLE 206

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL----LKKV 260
           I+T G+I  + +++ A++IL+D L  F++ EE      +D  ++  P +  L     K +
Sbjct: 207 IETKGNIAPDKALSQAAKILRDNLKHFMDPEEAN---GDDEKIEETPKDSVLDSLKGKHI 263

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           EE+E SVR+ N L   ++  +  +  +T+AD+LR+       + EIK  L      LGM
Sbjct: 264 EEVEFSVRTANFLMASDLKTLDKVAVKTDADLLRLIGANEMIIEEIKEKLAEYNAHLGM 322


>gi|150036754|emb|CAM98262.1| DNA-directed RNA polymerase alpha chain [Fructobacillus durionis]
          Length = 220

 Score =  178 bits (452), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 95/211 (45%), Positives = 133/211 (63%), Gaps = 2/211 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRVL+SSL G AI  VQIDGV+HE S++ GV ED+T +ILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRVLLSSLPGVAINTVQIDGVVHEFSTVDGVAEDVTQLILNLKKVV 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
                     + I  +GP  VTA D     DIEVLNPD  I  L     + M +TV KG 
Sbjct: 61  FATDSAEEHTLEIDVQGPKDVTAADFVGSADIEVLNPDLHIATLAAGKSLHMTVTVVKGR 120

Query: 154 GYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A+ ++   D  PIG++T+D++Y+PI++V+Y VE  R G   D+DKL+M + T+GSI
Sbjct: 121 GYASAEENKQLRDEMPIGVLTVDSIYTPIERVNYHVEQKRVGSRDDFDKLTMEVWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVK 242
              D+++L S+IL + L +F +     +E K
Sbjct: 181 KPSDALSLGSKILTEHLNLFTDISPVAQETK 211


>gi|195973806|gb|ACG63468.1| DNA-directed RNA polymerase subunit alpha [Francisella noatunensis]
 gi|198417145|gb|ACH87846.1| RpoA [Francisella noatunensis subsp. noatunensis]
          Length = 290

 Score =  178 bits (451), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 102/278 (36%), Positives = 165/278 (59%), Gaps = 7/278 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P+ +G AH LGN++RR L+SSL GA+I  V I G+LHE S+++ V ED+ +I+ N+K + 
Sbjct: 18  PVEKGMAHILGNSIRRFLLSSLSGASIIKVNISGILHEYSTLEDVKEDVVEIVSNLKKVA 77

Query: 94  LKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
           +K+  +  K  + +     GVVTAGD +T   IE++N D  I  L  +    +  TVS G
Sbjct: 78  IKLDKNVSKVELELSVTKSGVVTAGDFKTTQGIEIINKDQPIATLTNEREFSLVATVSVG 137

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
                     TE + +G I +DA ++PIK+V++ +      + L+     + + T+G+I 
Sbjct: 138 RNVGILSALPTELEKVGDIAVDADFNPIKRVAFEIFDNGASETLE-----VFVKTNGTIE 192

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
              +V  A     +Q+ +F++   P      D  + S   +P LLK +++LEL+VRS+NC
Sbjct: 193 PLAAVTKALEYFCEQISVFVSLRVPSNGKTGDALLDS-NIDPILLKPIDDLELTVRSSNC 251

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           LR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L
Sbjct: 252 LRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQIL 289


>gi|195973802|gb|ACG63466.1| DNA-directed RNA polymerase subunit alpha [Francisella
           philomiragia]
          Length = 290

 Score =  178 bits (451), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 102/278 (36%), Positives = 165/278 (59%), Gaps = 7/278 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P+ +G AH LGN++RR L+SSL GA+I  V IDGVLHE S+++ V ED+ +I+ N+K + 
Sbjct: 18  PVEKGMAHILGNSIRRFLLSSLSGASIIKVNIDGVLHEYSTLEDVKEDVVEIVSNLKKVA 77

Query: 94  LKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
           +K+  +  K  + +     G VTAGD +T   IE++N D  I  L  +    +  TVS G
Sbjct: 78  IKLDKNVSKVELELSVTKSGAVTAGDFKTTQGIEIINKDQPIATLTNEREFSLTATVSVG 137

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
                     TE + +G I +D+ ++PIK+V++ +      + L+     + + T+G+I 
Sbjct: 138 RNVGILSALPTELEKVGDIAVDSDFNPIKRVAFEIFDNGTNETLE-----VFVKTNGTIE 192

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
              +V  A     +Q+ +F++   P      D  + S   +P LLK +++LEL+VRS+NC
Sbjct: 193 PLVAVTKALEYFCEQISVFVSLRVPSNGKTGDALLDS-NIDPILLKPIDDLELTVRSSNC 251

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           LR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L
Sbjct: 252 LRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQIL 289


>gi|119662315|emb|CAJ33145.1| RNA polymerase alpha subunit [Lactobacillus iners DSM 13335]
          Length = 209

 Score =  178 bits (451), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 91/191 (47%), Positives = 137/191 (71%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRVL++S+ G A++ + IDGVLHE S+I GV ED+T IILN+K + LK+  D  K
Sbjct: 1   LGNSLRRVLLTSISGTALSYIMIDGVLHEFSTIPGVREDVTKIILNLKKLELKLLVDEEK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            V I   GP VVTA D++   D+E+LNPD  IC +     + M + +  G GY+PA  ++
Sbjct: 61  MVEIDVEGPAVVTAADLKVDADVEILNPDQYICTIAEGGHLHMSIAIKNGRGYIPASENK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
           +++ PIG+I +D+L+SPIKKV+Y VE+AR G+  DYDKL++ + TDGSIT  D+++ A++
Sbjct: 121 SDDMPIGVIPVDSLFSPIKKVNYQVENARVGKRDDYDKLTLELWTDGSITPNDALSFAAK 180

Query: 223 ILQDQLGMFIN 233
           IL++   +F++
Sbjct: 181 ILEEHFKVFMS 191


>gi|150187043|emb|CAK30158.1| RNA polymerase alpha subunit [Streptococcus anginosus]
          Length = 203

 Score =  178 bits (451), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 86/192 (44%), Positives = 132/192 (68%)

Query: 48  RRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF 107
           RRVL++SL GAA+T++ I+GVLHE  ++ GV ED+  IILN+KGI +K   +  K + + 
Sbjct: 1   RRVLLASLPGAAVTSINIEGVLHEFDTVPGVREDVMQIILNVKGIAVKSYVEDEKTIELD 60

Query: 108 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
             GP  +TAGDI T +DIE++NPDH +  +   A ++  +TV+ G GYVPA  ++ ++ P
Sbjct: 61  VEGPAEITAGDILTDSDIEIVNPDHYLFTIGEGASLKAIMTVNTGRGYVPADENKKDDAP 120

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           +G + +D++Y+P+KKV+Y VE AR G    +DKL++ I TDG+I  ED++ L++RIL + 
Sbjct: 121 VGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTLEIMTDGTIIPEDALGLSARILTEH 180

Query: 228 LGMFINFEEPKK 239
           L +F N  E  K
Sbjct: 181 LDLFTNLTEVAK 192


>gi|154424861|emb|CAL18533.1| RNA polymerase alpha subunit [Streptococcus suis]
          Length = 203

 Score =  178 bits (451), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 90/201 (44%), Positives = 139/201 (69%), Gaps = 2/201 (0%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG 110
           L++SL GAA+T+++IDGVLHE  ++ GV ED+  IILNIKGI +K   +  K++ +   G
Sbjct: 1   LLASLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKKIELDVVG 60

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
           P  VTAGDI T +DIE++NPDH +  +   A  +  LTV+ G GYVPA+ ++ ++ P+G 
Sbjct: 61  PAEVTAGDILTDSDIEIVNPDHYLFTIADGATFKAVLTVNSGRGYVPAEGNKKDDAPVGT 120

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           + +D++Y+P+KKV+Y VE AR G    +DKL++ I+T+G+I  ED++ L++RIL + LG+
Sbjct: 121 LAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTLEINTNGTIIPEDALGLSARILMEHLGL 180

Query: 231 FINFEEPKK--EVKEDINVKS 249
           F +  E  K  EV ++  V S
Sbjct: 181 FTDLTEVAKSAEVMKEAEVAS 201


>gi|161511717|emb|CAP16869.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           dextrinicus]
          Length = 205

 Score =  178 bits (451), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 87/186 (46%), Positives = 131/186 (70%)

Query: 54  SLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGV 113
           SL G+A++++QIDGVLHE S+I GV ED+T IILNIK I +K   +  K + I   GP  
Sbjct: 1   SLPGSAVSSIQIDGVLHEFSTIDGVMEDVTQIILNIKKIAIKNHSEEQKVIEIDVDGPAT 60

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITI 173
           VTA DI+  +DIEVLNP+  IC++     V M++TVS G GYVPA  ++  + PIG+I +
Sbjct: 61  VTAADIKADDDIEVLNPEQYICSIAEGGHVHMQMTVSNGRGYVPADQNKNGDMPIGVIAV 120

Query: 174 DALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           D++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++IL D L +FI+
Sbjct: 121 DSIFTPINRVNYQVESTRVGKRNDFDKLTLDVWTNGSISPREAISLAAKILSDHLNIFID 180

Query: 234 FEEPKK 239
             +  K
Sbjct: 181 LSDEAK 186


>gi|150187166|emb|CAK30185.1| RNA polymerase alpha subunit [Streptococcus marimammalium]
          Length = 210

 Score =  177 bits (450), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 89/191 (46%), Positives = 132/191 (69%)

Query: 49  RVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK 108
           RVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   +  K + +  
Sbjct: 1   RVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSHVEDEKTIELDV 60

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
           +GP  VTAGDI T +DIE++NPDH +  +   A  R  LTV+   GYVPA+ ++ EN P+
Sbjct: 61  QGPMEVTAGDILTDSDIEIVNPDHYLFTILEGASFRATLTVATKRGYVPAEENKKENAPV 120

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L
Sbjct: 121 GTLAVDSIYTPVKKVNYQVEPARVGSNDAFDKLTIEIMTNGTIIPEDALGLSARVLIEHL 180

Query: 229 GMFINFEEPKK 239
            +F +  E  K
Sbjct: 181 NLFTDLTEIAK 191


>gi|118475267|ref|YP_891269.1| DNA-directed RNA polymerase subunit alpha [Campylobacter fetus
           subsp. fetus 82-40]
 gi|158512499|sp|A0RM36|RPOA_CAMFF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|118414493|gb|ABK82913.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter fetus
           subsp. fetus 82-40]
          Length = 332

 Score =  177 bits (450), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 112/316 (35%), Positives = 177/316 (56%), Gaps = 19/316 (6%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  IE + +    EN   +IA P   G+A TL + LRR+L +S  G A TAV+IDGV HE
Sbjct: 11  PTEIEVVNVS---ENVAKIIAYPFETGYAVTLAHPLRRLLYTSTVGFAPTAVKIDGVAHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDI-EVLN 129
             S++G+ ED+T  I+N+K +  K+  DS + V  +  +GP  +T  D+   NDI E++N
Sbjct: 68  FDSMRGMLEDVTLFIINLKNLRFKLKNDSKREVIEYSFKGPKEITGIDLN--NDIVEIVN 125

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  +  ++ DA ++  L V KG GYVP++  R   D    I +DA ++P+KK  Y +E+
Sbjct: 126 PDSYLATINEDAELKFSLIVEKGIGYVPSEEIRDYIDS-EYIALDAFFTPVKKAVYEIEN 184

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV-- 247
                  DY+K+ +T+ TDG ++  ++   +   +  Q+ +F N       +  D+N+  
Sbjct: 185 VLVEDNPDYEKIVLTVTTDGQVSPIEAFKHSIEAMYKQMSIFNNV------LNIDVNMAL 238

Query: 248 ---KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              ++   +  LL+ VE L LS RS NCL   +I Y+G+L    E+++  + N G+KSL 
Sbjct: 239 TSSQNSNEHSKLLESVENLNLSARSFNCLDKADIRYIGELALMEESELKDLKNLGKKSLD 298

Query: 305 EIKGVLGTMGLFLGMN 320
           EIK V+  +G   G N
Sbjct: 299 EIKAVMAEIGYPFGEN 314


>gi|307154818|ref|YP_003890202.1| DNA-directed RNA polymerase subunit alpha [Cyanothece sp. PCC 7822]
 gi|306985046|gb|ADN16927.1| DNA-directed RNA polymerase, alpha subunit [Cyanothece sp. PCC
           7822]
          Length = 314

 Score =  177 bits (450), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 104/296 (35%), Positives = 171/296 (57%), Gaps = 13/296 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG   T+GNALRRVL+S+L GAA+TA++I GV HE ++I GV ED+ ++ILN+
Sbjct: 23  FILEPLDRGQGTTVGNALRRVLLSNLEGAAVTALRIAGVNHEFATISGVREDVMELILNM 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK      +   +   GP  VTAG     +++E+++P   +  L   + + ME  +
Sbjct: 83  KEITLKSYTSQPQIGRLVATGPATVTAGQFDLPSEVEIVDPSQYVATLAEGSKLEMEFRI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GY   +  + ++  +  + ID+++ P+ KV+Y+VE  R       D+L++ I T+G
Sbjct: 143 EKGKGYRAIERGKDDSTSLDFLQIDSVFMPVTKVNYSVEDVRVDGTSSKDRLTIEIWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKE-DINVKSLP--FNPALLKKVEELELS 266
           S+  +++++ A+ I+ D   +F     P +++ E +      P   NP     +EEL+LS
Sbjct: 203 SVNPKEALSEAAAIIVD---LF----SPLRDLNELEATQSDYPDEVNPESQIPIEELQLS 255

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           VR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E   V+  +   LG+ LP
Sbjct: 256 VRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEE---VIEALQKRLGITLP 308


>gi|315451275|gb|ADU24722.1| RNA polymerase alpha subunit [Lactobacillus sp. YM 0181]
 gi|315451277|gb|ADU24723.1| RNA polymerase alpha subunit [Lactobacillus sp. YM 0188]
          Length = 213

 Score =  177 bits (450), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 82/196 (41%), Positives = 135/196 (68%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL++SL G A++ +QIDGVLHE S+I GV ED+T I+LN+K + LK   +   +
Sbjct: 1   GNSLRRVLLASLPGTAVSDIQIDGVLHEFSAIDGVIEDVTQIVLNVKKLKLKSYAEDSLK 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
             +   GP  VTA DI+  +D+E+L+P+  IC +       M++T+  G GY PA+ ++T
Sbjct: 61  AEVDIVGPATVTAKDIKADDDLEILDPEQFICTVAEGGHFHMQMTIKNGRGYTPAEQNKT 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           +  PIG++ +D++++P++KV+Y VE+ R G+  D+DKL++ I T+GSI   ++++L+++I
Sbjct: 121 DETPIGVLPVDSIFTPVEKVNYQVENTRVGKRNDFDKLTIDIWTNGSIGPREAISLSAKI 180

Query: 224 LQDQLGMFINFEEPKK 239
           L + L  F+N  E  K
Sbjct: 181 LTEHLNSFVNLTEEAK 196


>gi|170077662|ref|YP_001734300.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp. PCC
           7002]
 gi|169885331|gb|ACA99044.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus sp. PCC
           7002]
          Length = 313

 Score =  177 bits (450), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 109/297 (36%), Positives = 170/297 (57%), Gaps = 14/297 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG   TLGN+LRR+L+S+L G A+TA++I GV HE ++I GV ED  +IILN+
Sbjct: 23  FVFEPLERGQGTTLGNSLRRILLSNLEGTAVTALRIGGVNHEFATIPGVREDALEIILNM 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK      +   +   GPG VTA      +++EV++P   I  L   A + ME  +
Sbjct: 83  KEIILKSYTHQPQIGRLTATGPGQVTAAQFDLPSEVEVVDPTQYIATLADGAKLEMEFRI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR-EGQVLDYDKLSMTIDTD 208
            KG  Y   + +R E   +  + IDA++ P+ KV+Y+V+S   EG  +  D+L++ I T+
Sbjct: 143 EKGKSYRAVQRNRDEATALDFLQIDAVFMPVTKVNYSVDSIHSEGDAV-RDRLTLEIWTN 201

Query: 209 GSITGEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           GSI  E++++ A+ I  +       +  E  + E++ED        +P     +EEL+LS
Sbjct: 202 GSIKPEEALSQAAAIAVELFNPLKDLTLEAIQDELQED-------EDPTSQIPIEELQLS 254

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           VR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L T    LG+ LP+
Sbjct: 255 VRAYNCLKRAQINSVADLLDYSQEDLLEIKNFGQKSAEEVIDALKTR---LGITLPE 308


>gi|150186968|emb|CAK30138.1| RNA polymerase alpha subunit [Streptococcus mutans]
          Length = 192

 Score =  177 bits (450), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 87/190 (45%), Positives = 134/190 (70%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   +  K V +
Sbjct: 1   LRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVEEEKIVEL 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
              GP  +TAGDI T +DIE++NPDH +  +   A ++  +TV+   GYVPA+ ++ ++ 
Sbjct: 61  DVEGPAEITAGDILTDSDIEIVNPDHYLFTIAEGANLKATMTVATNRGYVPAEKNKRDDA 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           P+G + ID++Y+P+KKV+Y VE AR G   ++DKL++ I T+G+I  ED++ L++R+L +
Sbjct: 121 PVGTLAIDSIYTPVKKVNYQVEPARVGSNDNFDKLTIEIMTNGTIIPEDALGLSARVLIE 180

Query: 227 QLGMFINFEE 236
            L +F +  E
Sbjct: 181 HLNLFTDLTE 190


>gi|158563962|sp|Q6YQZ5|RPOA_ONYPE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 330

 Score =  177 bits (449), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 113/333 (33%), Positives = 185/333 (55%), Gaps = 11/333 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           + IKP  +E I    E       I +PL RG+  T+GNALRRVL+SSL G AI  V+I G
Sbjct: 5   KFIKPFFVEEI---DENPISGKFIIKPLERGYGITVGNALRRVLLSSLPGTAIVNVKIQG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKM---SGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           V  E ++I GV+ED+  IILN+K I   +   S D  +++ +  +GP  +TA   +    
Sbjct: 62  VEQEFTTIPGVYEDVMTIILNLKKIVFAVDDESDDFEEKLELIAKGPQRLTASSFELPAG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKV 183
           ++++NPDH I  L  D    M +T+ KG GYV AK ++   +  +G+I ID+L++P+  V
Sbjct: 122 VKIINPDHYITTLSDDVCFHMTVTLKKGIGYVGAKDNKVHGENQVGVIAIDSLFTPVVNV 181

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VE     ++ + D+L++ I T+G++  ++++A A+ IL D   + +   +    V+ 
Sbjct: 182 SYQVEK----KLGNKDELTIEITTNGALLAKEALATAASILVDHFNVLVELSQKPAHVEF 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               K    N  L  ++E+L+LSVR  N L+   I  +  L++ +E +++++ + GRKS 
Sbjct: 238 VSESKKEAHNSVLDLEIEQLDLSVRLFNSLKRAGIDTVAALVKLSEKEVVKLKSLGRKSF 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKY 336
            E+K      GL     L +    S+EE   K+
Sbjct: 298 QELKDKFLEYGLEFNDYLKEVLHHSVEEDKDKH 330


>gi|150036808|emb|CAM98277.1| DNA-directed RNA polymerase alpha chain [Fructobacillus
           pseudoficulneus]
          Length = 235

 Score =  177 bits (448), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 98/235 (41%), Positives = 144/235 (61%), Gaps = 2/235 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRVL+SSL G A+  VQIDGV+HE S++ GV ED+T +ILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRVLLSSLPGVAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVV 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
                     + I  +GP  VTA D+    DIEVLNPD  I  L     + M +T  KG 
Sbjct: 61  FATDSAEEHALEIDVQGPKDVTAADLMGSADIEVLNPDLHIATLAAGKSLHMTVTAVKGR 120

Query: 154 GYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A+ ++   D  PIG++T+D++Y+PI++V+Y VE+ R G   DYDKL+M + T+GSI
Sbjct: 121 GYSSAEENKQLRDEMPIGVLTVDSIYTPIERVNYHVENKRVGSRDDYDKLTMEVWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
              D+++L S+IL + L +F +     ++ K  +  +      A    +E+L+LS
Sbjct: 181 KPSDALSLGSKILTEHLNLFTDISPVAQDTKVMVESEPAANTAADAAPIEDLDLS 235


>gi|75906938|ref|YP_321234.1| DNA-directed RNA polymerase subunit alpha [Anabaena variabilis ATCC
           29413]
 gi|119366663|sp|Q3MF97|RPOA_ANAVT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|75700663|gb|ABA20339.1| DNA-directed RNA polymerase subunit alpha [Anabaena variabilis ATCC
           29413]
          Length = 315

 Score =  177 bits (448), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 102/302 (33%), Positives = 169/302 (55%), Gaps = 11/302 (3%)

Query: 24  EENR---TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
           EE+R   +  I EPL RG   T+GNALRRVL+S+L G A+TAV+I GV HE +++ GV E
Sbjct: 14  EESRNHYSKFILEPLERGQGTTVGNALRRVLLSNLEGTAVTAVRIAGVSHEFATVPGVRE 73

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+ +II+ +K + LK      +   +   GP  +TA      +++EV++P   +  +   
Sbjct: 74  DVLEIIMRMKEVILKSYSSQAQIGRLLVNGPTTITASHFDLPSEVEVIDPTQYVATIAEG 133

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             + ME  + +G GY   +  R E   +  + ID+++ P++KV+Y+VE  R    +  D+
Sbjct: 134 GKLEMEFRIERGKGYRTVERGREEATSLDFLQIDSIFMPVRKVNYSVEEVRADGSIPKDR 193

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + + T+GSI+ +++++ A+ IL D      +      +   DI     P +P     +
Sbjct: 194 LLLEVWTNGSISPQEALSSAAGILVDLFNPLKDISLEPTDTNSDI-----PDDPTAQIPI 248

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           EEL+LSVR+ NCL+   +  + DL+  T+ D+L + NFG+KS  E   V+  +   LG+ 
Sbjct: 249 EELQLSVRAYNCLKRAQVNSVADLLDYTQEDLLEIKNFGQKSAEE---VVEALQRRLGIT 305

Query: 321 LP 322
           LP
Sbjct: 306 LP 307


>gi|17231683|ref|NP_488231.1| DNA-directed RNA polymerase subunit alpha [Nostoc sp. PCC 7120]
 gi|20139485|sp|Q8YPK3|RPOA_ANASP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|17133326|dbj|BAB75890.1| RNA polymerase alpha subunit [Nostoc sp. PCC 7120]
          Length = 315

 Score =  177 bits (448), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 102/302 (33%), Positives = 169/302 (55%), Gaps = 11/302 (3%)

Query: 24  EENR---TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
           EE+R   +  I EPL RG   T+GNALRRVL+S+L G A+TAV+I GV HE +++ GV E
Sbjct: 14  EESRNHYSKFILEPLERGQGTTVGNALRRVLLSNLEGTAVTAVRIAGVSHEFATVPGVRE 73

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+ +II+ +K + LK      +   +   GP  +TA      +++EV++P   +  +   
Sbjct: 74  DVLEIIMRMKEVILKSYSSQAQIGRLLVNGPTTITASHFDLPSEVEVIDPTQYVATIAEG 133

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             + ME  + +G GY   +  R E   +  + ID+++ P++KV+Y+VE  R    +  D+
Sbjct: 134 GKLEMEFRIERGKGYRTVERGREEATSLDFLQIDSIFMPVRKVNYSVEEVRADGSIPKDR 193

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + + T+GSI+ +++++ A+ IL D      +      +   DI     P +P     +
Sbjct: 194 LLLEVWTNGSISPQEALSSAAGILVDLFNPLKDISLEPTDTNSDI-----PDDPTAQIPI 248

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           EEL+LSVR+ NCL+   +  + DL+  T+ D+L + NFG+KS  E   V+  +   LG+ 
Sbjct: 249 EELQLSVRAYNCLKRAQVNSVADLLDYTQEDLLEIKNFGQKSAEE---VVEALQRRLGIT 305

Query: 321 LP 322
           LP
Sbjct: 306 LP 307


>gi|195973808|gb|ACG63469.1| DNA-directed RNA polymerase subunit alpha [Francisella noatunensis]
          Length = 290

 Score =  177 bits (448), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 102/278 (36%), Positives = 165/278 (59%), Gaps = 7/278 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P+ +G AH LGN++RR L+SSL GA+I  V I GVLHE S+++ V ED+ +I+ N+K + 
Sbjct: 18  PVEKGMAHILGNSIRRFLLSSLSGASIIKVNISGVLHEYSTLEDVKEDVVEIVSNLKKVA 77

Query: 94  LKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
           +K+  +  K  + +     GVVTAGD +T   IE++N D  I  L  +    +  TVS G
Sbjct: 78  IKLDKNVSKVELELSVTKSGVVTAGDFKTTQGIEIINKDQPIATLTNEREFSLVATVSVG 137

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
                      E + +G I +DA ++PIK+V++ +      + L+     + + T+G+I 
Sbjct: 138 RNVGILSALPIELEKVGDIAVDADFNPIKRVAFEIFDNGASETLE-----VFVKTNGTIE 192

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
              +V  A     +Q+ +F++ + P      D  + S   +P LLK +++LEL+VRS+NC
Sbjct: 193 PLAAVTKALEYFCEQISVFVSLKVPSNGKTGDALLDS-NIDPILLKPIDDLELTVRSSNC 251

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           LR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L
Sbjct: 252 LRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQIL 289


>gi|328951208|ref|YP_004368543.1| DNA-directed RNA polymerase subunit alpha [Marinithermus
           hydrothermalis DSM 14884]
 gi|328451532|gb|AEB12433.1| DNA-directed RNA polymerase subunit alpha [Marinithermus
           hydrothermalis DSM 14884]
          Length = 317

 Score =  177 bits (448), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 115/303 (37%), Positives = 168/303 (55%), Gaps = 12/303 (3%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           E N    + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+  LHE S++ GV ED+ 
Sbjct: 16  EGNYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDALHEFSTLPGVKEDVV 75

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            IILN+K + +K      K +T+   GP  + A D++   D E++NPD  I  L     +
Sbjct: 76  QIILNLKELVVKFHAPGSKILTLRAEGPRTIYARDLECPPDAEIINPDLYIATLGEGGKL 135

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            ME+ V +G GYVPA+ H  + D I  I +DALYSP+++V+Y VE  R GQ  D DKL +
Sbjct: 136 VMEVRVDEGVGYVPAEKHGIK-DRINSIPVDALYSPVRRVAYHVEDTRLGQRTDLDKLIL 194

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMF---------INFEEPKKEVKEDINVKSLPFNP 254
            I TDGS++  D++  A  IL++ LG F                    E +  +     P
Sbjct: 195 RIWTDGSVSPLDALQSAVGILREHLGFFDQAAVVAEAEAEPVEAAPEVEAVGAEEAAERP 254

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           AL   +++L LS R  + L+ E I  + +L+  TE ++ ++   G +S+ EIK  L   G
Sbjct: 255 AL--TLDDLGLSTRVLHNLKEEGIDSIENLLALTERELKKVPGIGERSVEEIKERLAEHG 312

Query: 315 LFL 317
           L L
Sbjct: 313 LSL 315


>gi|72534426|emb|CAH59048.1| DNA-directed RNA polymerase alpha chain [Enterococcus sp. LMG
           22681]
          Length = 213

 Score =  177 bits (448), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 88/185 (47%), Positives = 126/185 (68%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           L GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG+ LK+ G+  K + I   GP  V
Sbjct: 9   LPGAAITNIQIDGVLHEFSTIKGVREDVAQIILNIKGLALKLYGEDEKTLEIDITGPATV 68

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITID 174
           TAGDI   +D+E+LN D  IC +   A     LTV  G GYV A  ++ ++ PIG++ +D
Sbjct: 69  TAGDIIVDSDVEILNKDMYICTVSEGATFHARLTVKPGRGYVQADENKKDDMPIGVLPVD 128

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           ++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI   D+++LA++I+ + L +F+N 
Sbjct: 129 SIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIEPLDAMSLAAKIMTEHLDIFVNL 188

Query: 235 EEPKK 239
            +  K
Sbjct: 189 TDEAK 193


>gi|150186989|emb|CAK30143.1| RNA polymerase alpha subunit [Streptococcus gordonii]
          Length = 202

 Score =  176 bits (447), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 87/195 (44%), Positives = 132/195 (67%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL++SL GAA+T++ I+GVLHE  +I GV ED+  IILNIKGI +K      K +
Sbjct: 1   NSLRRVLLASLPGAAVTSINIEGVLHEFDTIPGVREDVMQIILNIKGIAVKSYVQDEKMI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  +TAGDI T +DIE++NPDH +  +   A  +  +TV+ G GYVPA  ++ +
Sbjct: 61  ELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIGEGARFKAVMTVNSGRGYVPADQNKRD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           + P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL
Sbjct: 121 DAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEIMTNGTIIPEDALGLSARIL 180

Query: 225 QDQLGMFINFEEPKK 239
            + L +F +  E  K
Sbjct: 181 TEHLDLFTDLTEVAK 195


>gi|254424496|ref|ZP_05038214.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus sp. PCC
           7335]
 gi|196191985|gb|EDX86949.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus sp. PCC
           7335]
          Length = 315

 Score =  176 bits (447), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 109/314 (34%), Positives = 178/314 (56%), Gaps = 9/314 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           N +E I+   + +    +I EPL R    T+GNALRRVL+S+L G A+T+V+I G  HE 
Sbjct: 7   NCVESIIEDDQSQFSRFVI-EPLGRSQGTTVGNALRRVLLSNLEGTAVTSVRIAGASHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           S+I GV ED+ DI+LN+K   LK      +   +  +GP  VTA +    +++E+++ D 
Sbjct: 66  STIPGVREDVLDILLNMKETVLKSYSAQPQIGRLVVQGPAKVTAANFDLPSEVELISTDR 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I ++     + ME  + +G GY      R E   +  + IDA++ P++KV+Y+VE+  +
Sbjct: 126 YIASVAAGHKLEMEFRIERGKGYKAIDRSREETGGVEFMQIDAVFMPVRKVNYSVENFID 185

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            +    D+L M I T+GS+T + +++ A+ +L D   MF   ++   E K D + K    
Sbjct: 186 PEGFPKDRLVMEIWTNGSLTAQQAMSEAAALLVD---MFNPLKDVTLEPKRDEDTKEE-- 240

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P     +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E   V+  
Sbjct: 241 DPTYQIPIEELQLSVRAYNCLKRAQINAVSDLLDYSQEDLLEIKNFGQKSAEE---VVEA 297

Query: 313 MGLFLGMNLPDWPP 326
           + + LG+ LP   P
Sbjct: 298 LQIHLGIMLPLEKP 311


>gi|119662285|emb|CAJ33129.1| RNA polymerase alpha subunit [Lactobacillus brevis]
          Length = 190

 Score =  176 bits (446), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 88/189 (46%), Positives = 133/189 (70%), Gaps = 4/189 (2%)

Query: 52  MSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKR 109
           +SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+K I LK++G  D  + + I  +
Sbjct: 1   LSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVTQIILNVKKIALKLNGSDDQEETMEINVK 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--P 167
           GP  +TAGDI    D+++LNPD  I  +   A   M +T  KG GYV A  ++T N   P
Sbjct: 61  GPAQITAGDIVAGADVDILNPDLYIATVADGATFHMRMTADKGRGYVSADENKTRNTDMP 120

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           IG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ + T+GSI   +++ALA++IL + 
Sbjct: 121 IGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDVWTNGSINPSEAIALAAKILTEH 180

Query: 228 LGMFINFEE 236
           L MF++  +
Sbjct: 181 LAMFVDLTD 189


>gi|186684486|ref|YP_001867682.1| DNA-directed RNA polymerase subunit alpha [Nostoc punctiforme PCC
           73102]
 gi|186466938|gb|ACC82739.1| DNA-directed RNA polymerase, alpha subunit RpoA [Nostoc punctiforme
           PCC 73102]
          Length = 315

 Score =  176 bits (446), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 101/302 (33%), Positives = 171/302 (56%), Gaps = 11/302 (3%)

Query: 24  EENR---TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
           EE+R   +  + EPL RG   T+GNALRRVL+S+L G A+TAV+I GV HE +++ GV E
Sbjct: 14  EESRNHYSKFVLEPLERGQGTTVGNALRRVLLSNLEGTAVTAVRIAGVSHEFATVPGVRE 73

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+ +I++ +K + LK      +   +   GP  +TA      +++EV++P   +  +   
Sbjct: 74  DVLEILMRMKEVILKNYSSQPQIGRLLVSGPTTITAAHFDLPSEVEVIDPTQYVATIAEG 133

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             + ME  + KG GY   +  R E   +  + ID+++ P++KV+Y+VE +R   ++  D+
Sbjct: 134 GKLEMEFRIEKGKGYRTVERGREEATSLDFLQIDSIFMPVRKVNYSVEESRGEGLIPKDR 193

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + + T+GSI+ +++++ A+ IL D      +      +   DI     P +P     +
Sbjct: 194 LLLEVWTNGSISPQEALSSAAGILVDLFNPLKDISLEPTDTGSDI-----PDDPTAQIPI 248

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           EEL+LSVR+ NCL+   +  + DL+  T+ D+L + NFG+KS  E   V+  +   LG+ 
Sbjct: 249 EELQLSVRAYNCLKRAQVNSVADLLDYTQEDLLEIKNFGQKSAEE---VVEALQRRLGIT 305

Query: 321 LP 322
           LP
Sbjct: 306 LP 307


>gi|150036810|emb|CAM98038.1| DNA-directed RNA polymerase alpha chain [Fructobacillus
           pseudoficulneus]
          Length = 235

 Score =  176 bits (446), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 98/235 (41%), Positives = 144/235 (61%), Gaps = 2/235 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL+SSL G A+  VQIDGV+HE S++ GV ED+T +ILN+K +      
Sbjct: 1   YGTTLGNSLRRVLLSSLPGVAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVVFATDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
                + I  +GP  VTA D+    DIEVLNPD  I  L     + M +T  KG GY  A
Sbjct: 61  AEEHALEIDVQGPKDVTAADLMGSADIEVLNPDLHIATLAAGKALHMTVTAVKGRGYSSA 120

Query: 159 KHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
           + ++   D  PIG++T+D++Y+PI++V+Y VE+ R G   DYDKL+M + T+GSI   D+
Sbjct: 121 EENKQLRDEMPIGVLTVDSIYTPIERVNYHVENKRVGSRDDYDKLTMEVWTNGSIKPSDA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTN 271
           ++L S+IL + L +F +     ++ K  +  +      A    +E+L+LSVRS N
Sbjct: 181 LSLGSKILTEHLNLFTDISPVAQDTKVMVESEPAANTAADAAPIEDLDLSVRSYN 235


>gi|254412021|ref|ZP_05025796.1| DNA-directed RNA polymerase, alpha subunit [Microcoleus
           chthonoplastes PCC 7420]
 gi|196180987|gb|EDX75976.1| DNA-directed RNA polymerase, alpha subunit [Microcoleus
           chthonoplastes PCC 7420]
          Length = 315

 Score =  176 bits (446), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 106/298 (35%), Positives = 168/298 (56%), Gaps = 18/298 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG   T+GNALRRVL+S+L G AITAV+I GV HE ++I G+ ED+ +I+LN+
Sbjct: 23  FVLEPLDRGQGTTVGNALRRVLLSNLEGTAITAVRIAGVNHEFATIAGIREDVLEILLNM 82

Query: 90  KGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K + LK    G    RV I   GP  V +      +D+E ++P   I  L   A + ME 
Sbjct: 83  KEVVLKSYTPGPHIGRVMI--TGPSTVRSAQFDLPSDVEFVDPGQYIATLADGAKLEMEF 140

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            + +G GY   +  R E   +  + +DA++ P+ KV+Y+VE  R    L+ D+L + + T
Sbjct: 141 RIERGKGYRSVERGRDETSSVDFLQLDAVFMPVTKVNYSVEDTRVDGSLEKDRLILDVWT 200

Query: 208 DGSITGEDSVALASRILQDQLGMFINFE---EPKKEVKEDINVKSLPFNPALLKKVEELE 264
           +GS++ +++++ A+ IL D      + E   EP    +++     +P        +EEL+
Sbjct: 201 NGSVSPQEALSQAANILVDLFNPLKDIELKPEPVGRPEDEDPTSQIP--------IEELQ 252

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E   V+  +   LG+ LP
Sbjct: 253 LSVRAYNCLKRAQINSVADLLDYSQEDLLEIKNFGQKSAEE---VIDALQKRLGITLP 307


>gi|119662283|emb|CAJ33128.1| RNA polymerase alpha subunit [Lactobacillus antri]
          Length = 203

 Score =  176 bits (446), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 90/193 (46%), Positives = 137/193 (70%), Gaps = 2/193 (1%)

Query: 52  MSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGP 111
           ++SL GAAIT +QIDGVLHE S++KGV ED+T IILN+K ++LK++ +  K + +  +GP
Sbjct: 1   IASLPGAAITTMQIDGVLHEFSTVKGVTEDVTQIILNLKKVSLKINSEDQKDLELDVKGP 60

Query: 112 GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIG 169
             VTAGDIQ  +++ VLNPD  I  +   A + +++T  KG GY+ A  +  R E+  IG
Sbjct: 61  AEVTAGDIQGDSEVSVLNPDLHIATVADGAELHIKMTADKGRGYLSANDNKARMEDLAIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           ++ ID++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGSIT  ++V+L ++IL + L 
Sbjct: 121 VLPIDSIYTPIERVNYTVENARVGQRSDYDKLTLDVWTDGSITPTEAVSLGAKILTEHLA 180

Query: 230 MFINFEEPKKEVK 242
           MF+N  E  +  +
Sbjct: 181 MFVNLTETAQNAQ 193


>gi|150036778|emb|CAM98268.1| DNA-directed RNA polymerase alpha chain [Fructobacillus fructosus
           KCTC 3544]
          Length = 206

 Score =  176 bits (445), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 93/206 (45%), Positives = 132/206 (64%), Gaps = 2/206 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRRVL+SSL G AI  VQIDGV+HE S++ GV ED+T +ILN+
Sbjct: 1   FIVEPLERGYGTTLGNSLRRVLLSSLPGVAINTVQIDGVVHEFSTVDGVVEDVTQLILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K +           + +   GP  VTA D+    D+EVLNPD  I  L     + M +TV
Sbjct: 61  KKVVFATDSAEEHSLELDVTGPRDVTAADLVGSADVEVLNPDLHIATLAAGKSLHMTVTV 120

Query: 150 SKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GY  A+ ++   D  PIG++T+D++Y+PI++V+Y VE  R G   D+DKL+M + T
Sbjct: 121 VKGRGYASAEENKQLRDEMPIGVLTVDSIYTPIERVNYHVEQKRVGARDDFDKLTMEVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFIN 233
           +GSI   D+++L S+IL + L +F +
Sbjct: 181 NGSIKPSDALSLGSKILTEHLNLFTD 206


>gi|34849417|gb|AAP58916.1| DNA-directed RNA polymerase alpha subunit [Spiroplasma kunkelii
           CR2-3x]
          Length = 317

 Score =  176 bits (445), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 108/316 (34%), Positives = 177/316 (56%), Gaps = 10/316 (3%)

Query: 6   WQELIKPNNIEYIVLGQEEENRT-LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
            ++ I+P   E+ +  +++ N     + EPL RGF  TLGNA+RR L+S+  GAA+ AV+
Sbjct: 1   MKQFIRP---EFKLQAEDKANNYGKFLVEPLERGFGVTLGNAIRRTLLSATPGAAVFAVR 57

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-----SHKRVTIFKRGPGVVTAGDI 119
           I G  HE ++I GV E +T IILNIK + LK++ D         + +F    G + A D+
Sbjct: 58  IKGSSHEFTAIPGVVEHVTKIILNIKNLVLKINQDIIPDGESVILKVFSSKEGEIYARDL 117

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
                +EV+N D ++  +     + +EL      GY     ++ E     LI ID+ Y P
Sbjct: 118 VVPTGVEVINGDLLLATIAKGGELDLELHARNSRGYKSFTDNKKEKKYADLIVIDSNYCP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I++V+Y VE  + G+  D +KL + I TD SIT  ++VA+A++++ + L  F+N  E  K
Sbjct: 178 IQRVAYNVEPTKVGKNADLEKLELEIQTDSSITPVNAVAMAAKVITEHLEFFVNLNEAIK 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
              + I+ ++      L + ++ELE + RS NCL+   I  + DL+ ++E ++  + N G
Sbjct: 238 -ATQIISSEAEAEEDELDRSIDELEFTQRSQNCLKRAKIDTLRDLVSKSEDEIQEIRNLG 296

Query: 300 RKSLVEIKGVLGTMGL 315
           +KSL EIK  +  +GL
Sbjct: 297 KKSLTEIKDKVAQLGL 312


>gi|119662835|emb|CAJ33210.1| RNA polymerase alpha subunit [Lactobacillus rossiae]
          Length = 173

 Score =  176 bits (445), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 87/173 (50%), Positives = 124/173 (71%), Gaps = 2/173 (1%)

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           QIDGVLHE S+++GV ED+T IILN+K ++LKM+ D  K + I  +GP  VTAGDIQT  
Sbjct: 1   QIDGVLHEFSTVEGVVEDVTQIILNMKKVSLKMATDEEKGMDIDVKGPATVTAGDIQTDA 60

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIK 181
           D+EV+NPD  IC +   A   M LT +KG GYV A  ++   D  PIG++ ID++Y+PI+
Sbjct: 61  DVEVMNPDLYICTVADGATFHMHLTANKGRGYVSADENKARQDDMPIGVLPIDSIYTPIE 120

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           +V+Y VE+ R GQ  DYDKL++ + TDGSIT  ++++LA++IL + L MF++ 
Sbjct: 121 RVNYQVENTRVGQRDDYDKLTLDVWTDGSITPSEAISLAAKILTEHLAMFVDL 173


>gi|154424797|emb|CAL18501.1| RNA polymerase alpha subunit [Streptococcus gordonii]
          Length = 194

 Score =  176 bits (445), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 86/192 (44%), Positives = 131/192 (68%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL++SL GAA+T++ I+GVLHE  +I GV ED+  IILNIKGI +K      K +
Sbjct: 1   NSLRRVLLASLPGAAVTSINIEGVLHEFDTIPGVREDVMQIILNIKGIAVKSYVQDEKMI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  +TAGDI T +DIE++NPDH +  +   A  +  +TV+ G GYVPA  ++ +
Sbjct: 61  ELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIGEGARFKAVMTVNSGRGYVPADQNKRD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           + P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL
Sbjct: 121 DAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEIMTNGTIIPEDALGLSARIL 180

Query: 225 QDQLGMFINFEE 236
            + L +F +  E
Sbjct: 181 TEHLDLFTDLTE 192


>gi|150187089|emb|CAK30168.1| RNA polymerase alpha subunit [Streptococcus alactolyticus]
          Length = 202

 Score =  176 bits (445), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 87/195 (44%), Positives = 135/195 (69%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K +
Sbjct: 1   NSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKII 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  VTAGDI T +D+E++N DH +  +     ++  +TV+K  GYVPA+ ++ +
Sbjct: 61  ELDVEGPAEVTAGDILTDSDVEIVNSDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           + P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L
Sbjct: 121 DAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVL 180

Query: 225 QDQLGMFINFEEPKK 239
            + L +F +  E  K
Sbjct: 181 IEHLNLFTDLTEVAK 195


>gi|119662825|emb|CAJ33205.1| RNA polymerase alpha subunit [Lactobacillus fermentum]
          Length = 190

 Score =  175 bits (444), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 90/190 (47%), Positives = 135/190 (71%), Gaps = 2/190 (1%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRV+++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRVMLASLPGAAITSIQIDGVLHEFSTVQGVTEDVTQIILNLKQVA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK+  +  K + I  +GP  VTA DIQ   D+ +LN D  I  +   A + +++T  KG 
Sbjct: 61  LKIDSEDAKDLEIDVKGPAEVTAADIQGDGDVTILNSDLHIATVSDGAELHVKMTADKGR 120

Query: 154 GYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A  ++T  E   IG++ ID++Y+PI++V+YTVE+ R GQ  DYDKL++ + T+GS+
Sbjct: 121 GYSSADDNKTRMEGLAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYDKLTLDVWTNGSL 180

Query: 212 TGEDSVALAS 221
           T  ++++LA+
Sbjct: 181 TPTEAISLAA 190


>gi|229021749|ref|ZP_04178329.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH1272]
 gi|228739536|gb|EEL89952.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH1272]
          Length = 233

 Score =  175 bits (444), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 91/229 (39%), Positives = 144/229 (62%)

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           +K + LK+  +  K + I  +G G+VTA DI   +D+E+LNPD  I  L  +A  RM LT
Sbjct: 1   MKKLALKIYSEEEKTLEIDVQGEGIVTAADITHDSDVEILNPDLHIATLAKNAHFRMRLT 60

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
             +G GY PA  +++E+ PIG+I ID++Y+P+ +V+Y VE  R GQV +YDKL++ + TD
Sbjct: 61  AKRGRGYTPADANKSEDQPIGVIPIDSIYTPVSRVTYQVEKTRVGQVANYDKLTLDVWTD 120

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           GSI  +++++L ++IL + L +F+   +  +  +  +  +       L   +EEL+LSVR
Sbjct: 121 GSIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEKEEDQKEKVLEMTIEELDLSVR 180

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           S NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 181 SYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKHKLEELGLGL 229


>gi|284929584|ref|YP_003422106.1| DNA-directed RNA polymerase subunit alpha [cyanobacterium UCYN-A]
 gi|284810028|gb|ADB95725.1| DNA-directed RNA polymerase subunit alpha [cyanobacterium UCYN-A]
          Length = 314

 Score =  175 bits (444), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 102/280 (36%), Positives = 162/280 (57%), Gaps = 10/280 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG   T+GNALRRVL+++L G A+TA++I GV HE ++I GV ED+ +IILN+
Sbjct: 23  FVLEPLERGQGITVGNALRRVLLANLEGTAVTAIRIGGVNHEFATIPGVREDVLEIILNM 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK   D  +   +   G   VTA      +++E++NP   I  L   A + ME  +
Sbjct: 83  KEIVLKSHTDQIQIGRLVAVGAAHVTAAQFDLPSEVEIINPTQPIATLTDGAKLEMEFRI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYVP +  + +   +  + IDA++ P+ KV+Y+VE+ R  +    D L + I T+G
Sbjct: 143 EKGMGYVPVERGKEKQGALDFLQIDAVFMPVTKVNYSVENIRGERNEVKDSLMLEIWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKE-DINVKSLP--FNPALLKKVEELELS 266
           S+  +++++ A+ +L       +N   P K + + +  V   P   NP     +EEL+LS
Sbjct: 203 SVNPKEALSQATEVL-------VNLFSPLKNINQIETVVPEYPDEENPQSQIPIEELQLS 255

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           VR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+
Sbjct: 256 VRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEEV 295


>gi|150187139|emb|CAK30179.1| RNA polymerase alpha subunit [Streptococcus peroris ATCC 700780]
          Length = 181

 Score =  175 bits (444), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 87/181 (48%), Positives = 126/181 (69%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL++SL GAA+T++ IDGVLHE  +I GV ED+  IILNIKGI +K      K 
Sbjct: 1   GNSLRRVLLASLPGAAVTSIDIDGVLHEFDTIPGVREDVMQIILNIKGIAVKSYVKDEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + +   GP  VTAGDI T +DIE++NPDH +  +   A  +  +TV+ G GYVPA  ++ 
Sbjct: 61  IELDVEGPAEVTAGDILTDSDIEIVNPDHYLFTIGEGASFKATMTVNTGRGYVPADENKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           +N P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RI
Sbjct: 121 DNAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARI 180

Query: 224 L 224
           L
Sbjct: 181 L 181


>gi|315451273|gb|ADU24721.1| RNA polymerase alpha subunit [Lactobacillus sp. YM 0097]
          Length = 212

 Score =  175 bits (444), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 81/195 (41%), Positives = 134/195 (68%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL++SL G A++ +QIDGVLHE S+I GV ED+T I+LN+K + LK   +   + 
Sbjct: 1   NSLRRVLLASLPGTAVSDIQIDGVLHEFSAIDGVIEDVTQIVLNVKKLKLKSYAEDSLKA 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  VTA DI+  +D+E+L+P+  IC +       M++T+  G GY PA+ ++T+
Sbjct: 61  EVDIVGPATVTAKDIKADDDLEILDPEQFICTVAEGGHFHMQMTIKNGRGYTPAEQNKTD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
             PIG++ +D++++P++KV+Y VE+ R G+  D+DKL++ I T+GSI   ++++L+++IL
Sbjct: 121 ETPIGVLPVDSIFTPVEKVNYQVENTRVGKRNDFDKLTIDIWTNGSIGPREAISLSAKIL 180

Query: 225 QDQLGMFINFEEPKK 239
            + L  F+N  E  K
Sbjct: 181 TEHLNSFVNLTEEAK 195


>gi|15807122|ref|NP_295851.1| DNA-directed RNA polymerase subunit alpha [Deinococcus radiodurans
           R1]
 gi|12230608|sp|Q9RSJ6|RPOA_DEIRA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|6459926|gb|AAF11678.1|AE002047_11 DNA-directed RNA polymerase, alpha subunit [Deinococcus radiodurans
           R1]
          Length = 341

 Score =  175 bits (444), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 111/324 (34%), Positives = 173/324 (53%), Gaps = 39/324 (12%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  T+GN +RR+LMSS+ G A+T+V I+ VLHE S+I GV ED+  +ILN+
Sbjct: 19  FVLEPLARGYGVTIGNPIRRILMSSIPGTAVTSVYIEDVLHEFSTIPGVREDVIRLILNL 78

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + +K      K +T+  +G G V A   +   D E++NPD VI NL  D  + ME+ V
Sbjct: 79  KELVVKFHAPGPKTLTLRAQGEGEVRASAFEVPTDAEIVNPDLVIANLAEDGKLVMEVRV 138

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYV A  H T+ D I  I +DA++SP+++V+Y VE+ R GQ  D D+L + + TDG
Sbjct: 139 EEGEGYVSADKHATK-DRINSIPVDAMFSPVRRVAYHVENTRVGQQTDLDRLILRVWTDG 197

Query: 210 SITGEDSVALASRILQDQLGMFIN-------------------------------FEEPK 238
           S   ++++  A  IL+D+L +F N                               ++ P+
Sbjct: 198 SAGPQEALDKAVEILRDELSVFGNVEPMPALESSYAAATPAAVYDPATATLPASVYDSPR 257

Query: 239 KEVKEDINVKSLPF-----NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           +     +++   PF      P +   +E L L+ R  + L+ E I  +  L   ++ D+ 
Sbjct: 258 QPDLGSLSINPQPFPTDQDTPRV--TLEGLGLTTRVLHSLKEEGIDSVDALCALSDRDLK 315

Query: 294 RMANFGRKSLVEIKGVLGTMGLFL 317
           ++   G +SL EIK  L   GL L
Sbjct: 316 KVPGIGERSLDEIKQQLAQFGLAL 339


>gi|213612397|ref|ZP_03370223.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E98-2068]
          Length = 195

 Score =  175 bits (444), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 87/191 (45%), Positives = 129/191 (67%), Gaps = 8/191 (4%)

Query: 143 VRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M + V +G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q  D D
Sbjct: 6   ISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLD 65

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLK 258
           KL + ++T+G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F+P LL+
Sbjct: 66  KLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEE----KPEFDPILLR 121

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 122 PVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 181

Query: 319 MNLPDWPPESI 329
           M L +WPP SI
Sbjct: 182 MRLENWPPASI 192


>gi|325282668|ref|YP_004255209.1| DNA-directed RNA polymerase subunit alpha [Deinococcus
           proteolyticus MRP]
 gi|324314477|gb|ADY25592.1| DNA-directed RNA polymerase subunit alpha [Deinococcus
           proteolyticus MRP]
          Length = 328

 Score =  175 bits (443), Expect = 9e-42,   Method: Compositional matrix adjust.
 Identities = 113/315 (35%), Positives = 174/315 (55%), Gaps = 22/315 (6%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           E N    + EPL RG+  T+GN +RR+LMSS++G A+T+V I+ VLHE S+I GV ED+ 
Sbjct: 13  EGNYGEFVLEPLKRGYGVTIGNPIRRILMSSIQGTAVTSVYIEDVLHEFSTIPGVKEDVI 72

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            +ILN+K + +K      K +T+  +G GV+ A D +  +D E++NPD  I NL     +
Sbjct: 73  RLILNLKELVVKFHAPGPKTLTLRAQGQGVIRASDFEVPSDAEIVNPDLEIANLADGGQL 132

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            ME+ V +G GYVPA  H T+ D I  I +DA+++P+++V+Y VE+ R G+  D DKL +
Sbjct: 133 VMEVRVEEGEGYVPADKHATK-DRINSIPVDAMFNPVRRVAYHVENTRVGRQTDLDKLIL 191

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEE-------------PKKEVKEDINVKSL 250
            I TDGS + +D +  A  IL+++L +F + EE               + V+ +  V   
Sbjct: 192 RIWTDGSASPQDVLDQAIDILREELLVFGSVEELEDSESSALDYTISAETVQPEAEVAPE 251

Query: 251 PFNPALLK--------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              PA            +E L L+ R  + L+ E I  +  L   ++ D+ ++   G +S
Sbjct: 252 SAAPAEESVSSGEPSVSLEGLGLTTRVLHSLKEEGIDNVDALCALSDRDLKKVPGIGERS 311

Query: 303 LVEIKGVLGTMGLFL 317
           L EIK  L   G  L
Sbjct: 312 LDEIKQQLAQFGKAL 326


>gi|119662821|emb|CAJ33203.1| RNA polymerase alpha subunit [Lactobacillus parakefiri]
          Length = 203

 Score =  175 bits (443), Expect = 9e-42,   Method: Compositional matrix adjust.
 Identities = 95/192 (49%), Positives = 132/192 (68%), Gaps = 4/192 (2%)

Query: 52  MSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKR 109
           +SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K I+LK+ G  D  + + I   
Sbjct: 1   LSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKISLKLDGPEDEEENLEIDVI 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDP 167
           GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT +KG GYV A     R+   P
Sbjct: 61  GPADVTAGDIQADSDVTVLNPDLHIATVAEGATFHMRLTANKGRGYVSAVENKKRSSEMP 120

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           IG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ I TDGSIT  ++V+LA++IL + 
Sbjct: 121 IGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDIWTDGSITPSEAVSLAAKILTEH 180

Query: 228 LGMFINFEEPKK 239
           L MF++  +  K
Sbjct: 181 LEMFVDLTDEAK 192


>gi|150186942|emb|CAK30133.1| RNA polymerase alpha subunit [Streptococcus canis]
          Length = 204

 Score =  175 bits (443), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 86/194 (44%), Positives = 135/194 (69%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           +LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + 
Sbjct: 1   SLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKIIE 60

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
           +   GP  VTAGDI T +DIE++NPDH +  +     +R  +TV+K  GYVPA+ ++ ++
Sbjct: 61  LEVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLRATMTVAKKRGYVPAEGNKKDD 120

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
            P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L 
Sbjct: 121 APVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLI 180

Query: 226 DQLGMFINFEEPKK 239
           + L +F +  +  K
Sbjct: 181 EHLNLFTDLTDVAK 194


>gi|297567256|ref|YP_003686228.1| DNA-directed RNA polymerase subunit alpha [Meiothermus silvanus DSM
           9946]
 gi|296851705|gb|ADH64720.1| DNA-directed RNA polymerase, alpha subunit [Meiothermus silvanus
           DSM 9946]
          Length = 319

 Score =  174 bits (442), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 110/295 (37%), Positives = 168/295 (56%), Gaps = 10/295 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN +RR+L+SS+ G A+T+V I+ VLHE S+I GV ED+  +ILN+
Sbjct: 22  FVLEPLERGFGVTLGNPIRRILLSSIPGTAVTSVYIEDVLHEFSTINGVKEDVVQLILNL 81

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + +K      K +T+  +GP  V A D++   D EV+NPD  +  L   A + ME+ V
Sbjct: 82  KELVVKFHTPGSKTLTLRAQGPRSVYARDLEVPADAEVVNPDLYLATLGEGARLVMEVRV 141

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GYVPA+ H  + D I  I +DAL+SP+++V++ VE  R GQ  D DKL++ I TDG
Sbjct: 142 DEGVGYVPAEKHGIK-DRISSIPVDALFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDG 200

Query: 210 SITGEDSVALASRILQDQLGMF-----INFEEPKKEVKEDINVKSLPFNPALLK----KV 260
           S++  + +  +  IL++QL  F     I  E+ K          S     A        +
Sbjct: 201 SVSPMEVLQRSVAILREQLSFFDQSPVIRVEKEKPAPVAAAPAPSPATPAAAAVSTGLTL 260

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           ++L L+ R  + L+ E I  +  L+  +E ++ ++   G +SL EIK +L   GL
Sbjct: 261 DDLGLTTRVLHNLKEEGIESVESLLALSERELKKVPGIGERSLQEIKDILAQHGL 315


>gi|150187039|emb|CAK30157.1| RNA polymerase alpha subunit [Streptococcus agalactiae ATCC 13813]
          Length = 188

 Score =  174 bits (442), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 84/187 (44%), Positives = 133/187 (71%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K +
Sbjct: 1   NSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKII 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  +TAGDI T +DIE++NPDH +  +     ++  +TV+K  GYVPA+ ++ +
Sbjct: 61  ELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIAEGHSLKATMTVAKNRGYVPAEGNKKD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           + P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L
Sbjct: 121 DAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVL 180

Query: 225 QDQLGMF 231
            + L +F
Sbjct: 181 IEHLNLF 187


>gi|217077310|ref|YP_002335028.1| DNA-directed RNA polymerase subunit alpha [Thermosipho africanus
           TCF52B]
 gi|217037165|gb|ACJ75687.1| DNA-directed RNA polymerase, alpha subunit [Thermosipho africanus
           TCF52B]
          Length = 330

 Score =  174 bits (442), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 111/305 (36%), Positives = 174/305 (57%), Gaps = 21/305 (6%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI--DGVLHEISSIKGVHEDLTDIILN 88
           +  PL +G+A T+GN LRRVL+SS+   AIT V+       HE  +I+GV ED+ +I+LN
Sbjct: 26  VLSPLEKGYATTIGNTLRRVLLSSIPSLAITDVKFVRPEKYHEFDTIEGVKEDILEILLN 85

Query: 89  IKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           +K + L M    +    +TI  +G G + AGDI     + V NP+  I  L+ DA + ++
Sbjct: 86  LKKVQLSMEDYVEDPVELTIQHKGAGEIKAGDIIVPAGVSVTNPNLHIATLNEDADLEIK 145

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           L  + G G+VPA   R E   IG I +D +Y+P+ KV++  E+ R G+  DYDKL + I 
Sbjct: 146 LYATIGKGFVPAAE-RNEKPDIGWIVLDGVYNPVLKVNWIAENVRVGKKTDYDKLVLEIW 204

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV------------KSLPFNP 254
           T  +I   D++  A +I+ D    F   EE   E  E+ ++            + +  N 
Sbjct: 205 TKKNIKPSDALKKAVKIINDH---FRIIEESFGEFDEENDIAEVSEVSTVEEEEVVDEND 261

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK-GVLGTM 313
            L +K++EL+LS+R+ NCL+ + I  +GDL+ R E ++L++ NFG+KSL E+K  ++   
Sbjct: 262 ILSRKIDELDLSMRALNCLKRDKIETIGDLLSRGEEELLKIKNFGQKSLDEVKEKLMEKF 321

Query: 314 GLFLG 318
           GL  G
Sbjct: 322 GLSFG 326


>gi|150187098|emb|CAK30170.1| RNA polymerase alpha subunit [Streptococcus criceti]
          Length = 181

 Score =  174 bits (442), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 83/181 (45%), Positives = 132/181 (72%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K
Sbjct: 1   LGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + +  +GP  VTAGD+ T +DIE++NPDH +  +     ++  +TV+K  GYVPA+ ++
Sbjct: 61  TIELDVQGPAEVTAGDVLTDSDIEIINPDHYLFTIAEGHSLKATMTVAKNRGYVPAEGNK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
           +++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R
Sbjct: 121 SDSAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSAR 180

Query: 223 I 223
           +
Sbjct: 181 V 181


>gi|150036760|emb|CAM98030.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 223

 Score =  174 bits (442), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 90/205 (43%), Positives = 133/205 (64%), Gaps = 2/205 (0%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           G+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L + 
Sbjct: 1   GYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAID 60

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
            D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  
Sbjct: 61  SDDERSLEIDVQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTS 120

Query: 158 AKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
           A  ++   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D
Sbjct: 121 ADENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGARDDYDKLTFDIWTNGSIKPSD 180

Query: 216 SVALASRILQDQLGMFINFEEPKKE 240
           +++L ++IL + L +F++      E
Sbjct: 181 ALSLGAKILAEHLNLFMDISPVAAE 205


>gi|254431538|ref|ZP_05045241.1| DNA-directed RNA polymerase, alpha subunit [Cyanobium sp. PCC 7001]
 gi|197625991|gb|EDY38550.1| DNA-directed RNA polymerase, alpha subunit [Cyanobium sp. PCC 7001]
          Length = 312

 Score =  174 bits (442), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 111/309 (35%), Positives = 171/309 (55%), Gaps = 14/309 (4%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ V     +    +I  PL RG A TLGNALRRVL+  L G+AITAV+I GV HE 
Sbjct: 7   DRIEHHVAEDRAQTGVFLIG-PLDRGQATTLGNALRRVLIGGLEGSAITAVRISGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           +++ GV ED+ DI+LN K + +       +   +   GP  VTA D+Q  + ++V++PD 
Sbjct: 66  ATVPGVREDVLDILLNCKQVAVSSRSRELEIGRLVVNGPATVTAADLQFSSQVQVIDPDR 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           +I  +     + ME+ V +G GY P   H  +   I L+ IDA++ P+K+V+YTV+    
Sbjct: 126 LIATVAEGFGLEMEVHVERGVGYRPVDRHSEDTSAIDLLQIDAVFKPVKRVNYTVDETAV 185

Query: 193 GQVLDY-DKLSMTIDTDGSITGEDSVALASR---ILQDQLGMFINFEEPKKEVKEDINVK 248
           G+     ++L + I+T+GSIT +D++A A+     L   L      EEP +E +     +
Sbjct: 186 GEGGSARERLRLEIETNGSITPDDAMAQAANQLIALFQPLATLSVVEEPGQEPEPSAEAQ 245

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
            +P         EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+  
Sbjct: 246 -IPL--------EELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIE 296

Query: 309 VLGTMGLFL 317
            L  +G+ L
Sbjct: 297 ALERIGITL 305


>gi|72534423|emb|CAH59047.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 190

 Score =  174 bits (441), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 87/182 (47%), Positives = 125/182 (68%)

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
           AAIT +QIDGVLHE S+IKGV ED+T IILNIKG+ LKM G   K + I   GP  VTAG
Sbjct: 1   AAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGLALKMYGQEEKTLEIDITGPATVTAG 60

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI   +D+E+LN D  IC++   A     LTV  G GYV A  ++ E+ PIG++ +D++Y
Sbjct: 61  DIIVDSDVEILNKDMYICSVSEGATFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIY 120

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           +P+++V+Y VE+ R G   D+DKL+M I TDGSI   ++++L+++I+ + L +F+N  + 
Sbjct: 121 TPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDE 180

Query: 238 KK 239
            K
Sbjct: 181 AK 182


>gi|298491422|ref|YP_003721599.1| DNA-directed RNA polymerase subunit alpha ['Nostoc azollae' 0708]
 gi|298233340|gb|ADI64476.1| DNA-directed RNA polymerase, alpha subunit ['Nostoc azollae' 0708]
          Length = 314

 Score =  174 bits (441), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 104/302 (34%), Positives = 171/302 (56%), Gaps = 12/302 (3%)

Query: 24  EENRT---LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
           EE+R+     + EPL RG   T+GNALRRVL+S+L G A+TAV+IDGV HE +++ GV E
Sbjct: 14  EESRSHYSKFVLEPLERGQGITVGNALRRVLLSNLEGTAVTAVRIDGVSHEFATVPGVRE 73

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+ +I++ +K + LK      +   +   GP  VTA      +++EV++P   +  +   
Sbjct: 74  DVLEILMRMKEVILKNYSSQPQIGRLLVNGPVTVTAAHFDLPSEVEVIDPTQYVATIADG 133

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             + ME  + +G GY   +  R E   +  + ID+++ P++KV+Y+VE AR    L  D+
Sbjct: 134 GKLEMEFRIERGKGYRTVERGREEATSLDFLQIDSVFMPVRKVNYSVEEARGDGSLK-DR 192

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + + T+GSI+ +++++ A+ IL D      +      +   DI     P +P     +
Sbjct: 193 LLLEVWTNGSISPQEALSSAAGILVDLFNPLKDISLEPTDTGSDI-----PDDPTAQIPI 247

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           EEL+LSVR+ NCL+   +  + DL+  T+ D+L + NFG+KS  E   V+  +   LG+ 
Sbjct: 248 EELQLSVRAYNCLKRAQVNSVADLLDYTQEDLLEIKNFGQKSAEE---VVEALQRRLGIT 304

Query: 321 LP 322
           LP
Sbjct: 305 LP 306


>gi|110004254|emb|CAK98592.1| probable dna-directed rna polymerase alpha chain protein
           [Spiroplasma citri]
          Length = 317

 Score =  174 bits (440), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 107/316 (33%), Positives = 176/316 (55%), Gaps = 10/316 (3%)

Query: 6   WQELIKPNNIEYIVLGQEEENRT-LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
            ++ I+P   E+ +  +++ N     + EPL RGF  TLGNA+RR L+S+  GAA+ AV+
Sbjct: 1   MKQFIRP---EFKLQAEDKANNYGKFLVEPLERGFGVTLGNAIRRTLLSATPGAAVFAVR 57

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-----SHKRVTIFKRGPGVVTAGDI 119
           I G  HE ++I GV E +T IILNIK + LK++ D         + +     G + A D+
Sbjct: 58  IKGASHEFTAIPGVVEHVTKIILNIKNLVLKINQDIIPDGESVILKVVSSKEGEIYARDL 117

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
                +EV+N D ++  +     + +EL      GY     ++ E     LI ID+ Y P
Sbjct: 118 VVPTGVEVINGDLLLATIAKGGELDLELYARNSRGYKSFTDNKKEKKYADLIVIDSNYCP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I++V+Y VE  + G+  D +KL + I TD SIT  ++VA+A++++ + L  F+N  E  K
Sbjct: 178 IQRVAYNVEPTKVGKNADLEKLELEIQTDSSITPVNAVAMAAKVITEHLEFFVNLNEAIK 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
              + I+ ++      L + ++ELE + RS NCL+   I  + DL+ ++E ++  + N G
Sbjct: 238 -ATQIISSEAEAEEDELERSIDELEFTQRSQNCLKRAKIDTLRDLVSKSEDEIQEIRNLG 296

Query: 300 RKSLVEIKGVLGTMGL 315
           +KSL EIK  +  +GL
Sbjct: 297 KKSLTEIKDKVAQLGL 312


>gi|257459220|ref|ZP_05624339.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter gracilis
           RM3268]
 gi|257443605|gb|EEV18729.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter gracilis
           RM3268]
          Length = 332

 Score =  174 bits (440), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 105/301 (34%), Positives = 166/301 (55%), Gaps = 15/301 (4%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           EN   +IA P   G+A TL + LRR+L +S  G A TAV+I+GV HE  S++G+ ED+  
Sbjct: 12  ENVAKIIAYPFETGYAVTLAHPLRRLLYTSTVGFAPTAVKIEGVSHEFDSMRGMLEDMAA 71

Query: 85  IILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            I+N+KG+  K+ GDS + V  +  +GP  +   D+   + +E++NP   +  ++ DA +
Sbjct: 72  FIINLKGLRFKIKGDSLREVVEYSFKGPKEIYGSDLNN-DAVEIVNPSAYLATINEDADL 130

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
           +  L + KG GYVP++  R EN     I +DA ++P+ K  Y +E+       DY+K+  
Sbjct: 131 KFTLIIEKGIGYVPSEEIR-ENLDADFIALDAFFTPVTKAVYDIENVFVEDNPDYEKVVF 189

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMF---INFEEPKKEVKEDINVKSLPFN---PALL 257
           TI TDG I+  D+   A   +  QL +F   +N          D   +++P N     L 
Sbjct: 190 TITTDGQISAIDAFKNALEAMYQQLAVFKGIVNISAA------DTFGRAIPANSEFAKLF 243

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + V  L LS RS NCL   +I ++G+L    E+++  + N G+KSL EIK V+  +G  +
Sbjct: 244 ESVSNLSLSARSFNCLDRADIRFIGELAIMEESELKDLKNLGKKSLEEIKAVMEEIGYPI 303

Query: 318 G 318
           G
Sbjct: 304 G 304


>gi|119668347|emb|CAK95470.1| RNA polymerase alpha subunit [Lactobacillus paracasei subsp.
           paracasei]
          Length = 180

 Score =  174 bits (440), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 87/180 (48%), Positives = 129/180 (71%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNIK + LKM+ D  K + I
Sbjct: 1   LRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNTDEDKNIEI 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
              GP  VTA DI    D+EVLNP+  IC +       + +TV KG GYV A  +++++ 
Sbjct: 61  DVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAADQNKSDDM 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++IL +
Sbjct: 121 PIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKILTE 180


>gi|154424839|emb|CAL18522.1| RNA polymerase alpha subunit [Streptococcus pluranimalium]
          Length = 203

 Score =  174 bits (440), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 85/196 (43%), Positives = 135/196 (68%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ +K   +  K 
Sbjct: 1   GNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNVKGLAVKSYVEDEKI 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + +  +GP  VTAGDI T +DIE++N DH +  +   A  +  +TV+   GYV A+ ++ 
Sbjct: 61  IELDVQGPAEVTAGDILTDSDIEIVNSDHYLFTIAEGASFKASMTVATNRGYVAAEGNKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+
Sbjct: 121 DDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTVEIMTNGTIIPEDALGLSARV 180

Query: 224 LQDQLGMFINFEEPKK 239
           L + L +F +  E  K
Sbjct: 181 LIEHLNLFTDLTEVAK 196


>gi|260655357|ref|ZP_05860845.1| DNA-directed RNA polymerase, alpha subunit [Jonquetella anthropi
           E3_33 E1]
 gi|260629805|gb|EEX47999.1| DNA-directed RNA polymerase, alpha subunit [Jonquetella anthropi
           E3_33 E1]
          Length = 338

 Score =  173 bits (439), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 102/314 (32%), Positives = 172/314 (54%), Gaps = 23/314 (7%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
            +  +I  PL RG+  T+GNALRRVL+SS++GA +TAV+++G LHE +++ GV ED+ ++
Sbjct: 13  TKARLIIGPLERGYGVTIGNALRRVLLSSIKGAGVTAVRVEGALHEFTTLPGVREDIIEL 72

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
            LN+K I ++      + + +   GP  VT  DIQ  ++IE ++P+  IC L     + M
Sbjct: 73  QLNLKHIPVRSHSVEVRVLRLEATGPKKVTVADIQPDSEIEFIDPNFYICTLAEGHSISM 132

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           EL + +G GY  A   R +  P+  + +D  ++PI +V Y V++ R G   DY+K+ M I
Sbjct: 133 ELYIEQGVGYATADRPRPDYLPVDALMVDPNFAPISRVKYDVQAERVGHKTDYEKVVMDI 192

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF------------- 252
            ++G I  + +VA A+++L++   + +  +E  K       + + P              
Sbjct: 193 YSNGVIAPDMAVAEAAKLLREYFSIVV--KEILKRYPASAEMAASPVEMEQEQPSLGQAI 250

Query: 253 --------NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
                   N  L   V +LELS+RS NCL    I  +G+L+ R++ ++L++ N G+ SL 
Sbjct: 251 VHSDDGAENSLLGHGVRDLELSIRSENCLLRGGIHTIGELVSRSKEELLKIRNLGKISLR 310

Query: 305 EIKGVLGTMGLFLG 318
           EI+  +    L L 
Sbjct: 311 EIEEKMAKYNLSLA 324


>gi|89256013|ref|YP_513375.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica LVS]
 gi|115314492|ref|YP_763215.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica OSU18]
 gi|167010243|ref|ZP_02275174.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica FSC200]
 gi|254367357|ref|ZP_04983383.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. holarctica 257]
 gi|122325482|sp|Q0BMV6|RPOA2_FRATO RecName: Full=DNA-directed RNA polymerase subunit alpha 2;
           Short=RNAP subunit alpha 2; AltName: Full=RNA polymerase
           subunit alpha 2; AltName: Full=Transcriptase subunit
           alpha 2
 gi|122501012|sp|Q2A4H7|RPOA2_FRATH RecName: Full=DNA-directed RNA polymerase subunit alpha 2;
           Short=RNAP subunit alpha 2; AltName: Full=RNA polymerase
           subunit alpha 2; AltName: Full=Transcriptase subunit
           alpha 2
 gi|89143844|emb|CAJ79056.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. holarctica LVS]
 gi|115129391|gb|ABI82578.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           holarctica OSU18]
 gi|134253173|gb|EBA52267.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. holarctica 257]
          Length = 317

 Score =  173 bits (439), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 108/327 (33%), Positives = 184/327 (56%), Gaps = 20/327 (6%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI- 65
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I 
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKIN 60

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVND 124
           DG +  +  +    E + DIILN+K +++ ++ D       F+  G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLSVTLAEDVETGTITFELSGSEEEIFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG G+ PA+    +N   G   +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQ----DNFKDGEFLLDATFSPVVFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK----E 240
           + ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K    E
Sbjct: 177 FEIKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGIFVE 236

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             +DIN       P LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+
Sbjct: 237 DPKDIN-------PILLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGK 289

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           KSL EIK  L  +GL LG  + +WP +
Sbjct: 290 KSLTEIKDKLSELGLSLGTLIENWPQD 316


>gi|150036834|emb|CAM98282.1| DNA-directed RNA polymerase alpha chain [Leuconostoc fallax]
          Length = 228

 Score =  173 bits (439), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 93/226 (41%), Positives = 143/226 (63%), Gaps = 2/226 (0%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T +ILN+K + L +  D  
Sbjct: 3   TLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVVLAIDSDEE 62

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I  +GP  VTA D+Q   DIEVLNP+  +  +     + M +T  KG GY  A  +
Sbjct: 63  KSLEIDVQGPAEVTAADLQGSADIEVLNPELHLATVAAGKSLHMTVTAVKGRGYSSADEN 122

Query: 162 RTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           +   D  PIG++ +D++Y+PI++V+Y VE+ R GQ  DYDKL+  I T+GSI   D+++L
Sbjct: 123 KQLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGQRDDYDKLTFDIWTNGSIKPSDALSL 182

Query: 220 ASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            ++IL + L +F +      E +  ++V+    +      +E+L+L
Sbjct: 183 GAKILSEHLNLFTDISSVAAETEVMVDVEQTVSSVQDSAPIEDLDL 228


>gi|150036798|emb|CAM98035.1| DNA-directed RNA polymerase alpha chain [Leuconostoc fallax]
          Length = 208

 Score =  173 bits (439), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 89/206 (43%), Positives = 133/206 (64%), Gaps = 2/206 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T +ILN+K + L +  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVVLAIDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + I  +GP  VTA D+Q   DIEVLNP+  +  +     + M +T  KG GY  A
Sbjct: 61  DEEKSLEIDVQGPAEVTAADLQGSADIEVLNPELHLATVAAGKSLHMTVTAVKGRGYSSA 120

Query: 159 KHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   D  PIG++ +D++Y+PI++V+Y VE+ R GQ  DYDKL+  I T+GSI   D+
Sbjct: 121 DENKQLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGQRDDYDKLTFDIWTNGSIKPSDA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVK 242
           ++L ++IL + L +F +      E +
Sbjct: 181 LSLGAKILSEHLNLFTDISSVAAETE 206


>gi|71056848|emb|CAH58979.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           haemoperoxidus]
          Length = 199

 Score =  173 bits (439), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 84/180 (46%), Positives = 126/180 (70%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           IT +QIDGVLHE S+IKGV ED+T IILNIKG+ LK+  +  K + I   GP  VTAGDI
Sbjct: 1   ITNIQIDGVLHEFSTIKGVREDVTQIILNIKGLALKLYAEEEKTLEIDITGPATVTAGDI 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
              +D+E+LN D +IC++   A     LTV  G GYV A  ++ E+ PIG++ +D++Y+P
Sbjct: 61  IVDSDVEILNKDLIICSVSEGATFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTP 120

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +++V+Y VE+ R G+  D+DKL+M I TDGSI  +++++LA++I+ + L +F+N  +  K
Sbjct: 121 VRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIIPQEALSLAAKIMTEHLDIFVNLTDEAK 180


>gi|208779606|ref|ZP_03246951.1| DNA-directed RNA polymerase, alpha subunit [Francisella novicida
           FTG]
 gi|208744567|gb|EDZ90866.1| DNA-directed RNA polymerase, alpha subunit [Francisella novicida
           FTG]
          Length = 318

 Score =  173 bits (438), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 106/321 (33%), Positives = 182/321 (56%), Gaps = 11/321 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI- 65
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I 
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKIN 60

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVND 124
           DG +  +  +    E + DIILN+K + + ++ G     +T    G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLPVTLAEGVETGTITFELSGSEEEIFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG G+ PA+ +  E    G   +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQDNFKE----GEFLLDATFSPVVFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +  +
Sbjct: 177 FEIKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGIFVE 236

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              K +  NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL 
Sbjct: 237 DPTKDI--NPILLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLT 294

Query: 305 EIKGVLGTMGLFLGMNLPDWP 325
           EIK  L  +GL LG  + +WP
Sbjct: 295 EIKDKLSELGLSLGTLIENWP 315


>gi|154424761|emb|CAL18483.1| RNA polymerase alpha subunit [Streptococcus equinus]
          Length = 183

 Score =  173 bits (438), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 85/180 (47%), Positives = 129/180 (71%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K +
Sbjct: 1   NSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKII 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  VTAGDI T +D+E++NPDH +  +     ++  +TV+K  GYVPA+ ++ E
Sbjct: 61  ELDVEGPAEVTAGDILTDSDVEIVNPDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKE 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           + P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L
Sbjct: 121 DAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVL 180


>gi|154424829|emb|CAL18517.1| RNA polymerase alpha subunit [Streptococcus alactolyticus]
          Length = 200

 Score =  173 bits (438), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 86/193 (44%), Positives = 133/193 (68%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +
Sbjct: 1   LRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIEL 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
              GP  VTAGDI T +D+E++N DH +  +     ++  +TV+K  GYVPA+ ++ ++ 
Sbjct: 61  DVEGPAEVTAGDILTDSDVEIVNSDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKDDA 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L +
Sbjct: 121 PVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIE 180

Query: 227 QLGMFINFEEPKK 239
            L +F +  E  K
Sbjct: 181 HLNLFTDLTEVAK 193


>gi|150036838|emb|CAM98284.1| DNA-directed RNA polymerase alpha chain [Leuconostoc lactis]
          Length = 228

 Score =  173 bits (438), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 92/226 (40%), Positives = 142/226 (62%), Gaps = 2/226 (0%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  
Sbjct: 3   TLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDE 62

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  +
Sbjct: 63  RSLEIDVQGPAEVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSADEN 122

Query: 162 RT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           +   E  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L
Sbjct: 123 KQLREEMPIGVLAVDSIYTPIERVNYHVENTRVGARDDYDKLTFDIWTNGSIKPSDALSL 182

Query: 220 ASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            ++IL + L +F++      E    +  + +  + +    +E+L+L
Sbjct: 183 GAKILAEHLNLFMDISPVAAEANVMVEAEPVAVSASDSAPIEDLDL 228


>gi|255027946|ref|ZP_05299932.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL J2-003]
          Length = 219

 Score =  173 bits (438), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 89/219 (40%), Positives = 139/219 (63%)

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + I  +GPGVVTA DI   +D+E+LNPD  I  L  +A   + L  ++G GY PA
Sbjct: 1   DEEKTLEIDMQGPGVVTAADINYDSDVEILNPDLHIATLSDNAKFHVRLNATRGRGYTPA 60

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++ EN PIG++ +D+++SP+ +V+Y VE+ R GQ  +YDKL+  + TDGSI+ E++V+
Sbjct: 61  DQNKRENMPIGVLPVDSIFSPVIRVNYQVENTRVGQSTNYDKLTFDVLTDGSISPEEAVS 120

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENI 278
           L ++IL + L +F+N  +  ++ +  I  +       L   +EEL+LSVRS NCL+   I
Sbjct: 121 LGAKILSEHLSIFVNLTDEAQKAEIMIEKEESHKEKVLEMTIEELDLSVRSYNCLKRAGI 180

Query: 279 VYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             + +L  ++E DM+++ N GRKSL E+K  L  +GL L
Sbjct: 181 NTVQELADKSEDDMMKVRNLGRKSLEEVKVKLADLGLSL 219


>gi|150036816|emb|CAM98278.1| DNA-directed RNA polymerase alpha chain [Leuconostoc fallax]
          Length = 220

 Score =  172 bits (437), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 90/209 (43%), Positives = 136/209 (65%), Gaps = 2/209 (0%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T +ILN+K + L +  D  
Sbjct: 3   TLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVVLAIDSDEE 62

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I  +GP  VTA D+Q   DIEVLNP+  +  +     + M +T  KG GY  A  +
Sbjct: 63  KSLEIDVQGPAEVTAADLQGSADIEVLNPELHLATVAAGKSLHMTVTAVKGRGYSSADEN 122

Query: 162 RTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           +   D  PIG++ +D++Y+PI++V+Y VE+ R GQ  DYDKL+  I T+GSI   D+++L
Sbjct: 123 KQLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGQRDDYDKLTFDIWTNGSIKPSDALSL 182

Query: 220 ASRILQDQLGMFINFEEPKKEVKEDINVK 248
            ++IL + L +F +      E +  ++V+
Sbjct: 183 GAKILSEHLNLFTDISSVAAETEVMVDVE 211


>gi|150036774|emb|CAN89786.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gasicomitatum]
          Length = 219

 Score =  172 bits (437), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 89/204 (43%), Positives = 132/204 (64%), Gaps = 2/204 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  + + +  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A
Sbjct: 61  DEERSLEVDIQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTITAFKGRGYSSA 120

Query: 159 KHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+
Sbjct: 121 DENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDA 180

Query: 217 VALASRILQDQLGMFINFEEPKKE 240
           ++L S+IL + L +F++      E
Sbjct: 181 LSLGSKILAEHLNLFMDISPVAAE 204


>gi|154424833|emb|CAL18519.1| RNA polymerase alpha subunit [Streptococcus parauberis]
          Length = 194

 Score =  172 bits (437), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 84/192 (43%), Positives = 133/192 (69%)

Query: 48  RRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF 107
           RRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + + 
Sbjct: 1   RRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKMIELD 60

Query: 108 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
             GP  VTAGDI T +DIE++NPDH +  +     ++  +TV+K  GY+PA+ ++ ++ P
Sbjct: 61  VEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLKATMTVAKKRGYIPAEGNKQDDAP 120

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           +G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + 
Sbjct: 121 VGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEH 180

Query: 228 LGMFINFEEPKK 239
           L +F +  E  K
Sbjct: 181 LNLFTDLTEVAK 192


>gi|119672815|emb|CAK95519.1| RNA polymerase alpha subunit [Lactobacillus gasseri]
          Length = 165

 Score =  172 bits (437), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 87/165 (52%), Positives = 118/165 (71%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRRVL++S+ G A++ +QIDGVLHE S+I GV ED+T IILN+K + LK   D  K   I
Sbjct: 1   LRRVLLTSIPGTALSYIQIDGVLHEFSTIPGVREDVTKIILNLKKLELKSLSDEEKIAEI 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
              GP +VTA D++  +DIEVLNPD  IC++     + M + +  G GYVPA  ++T++ 
Sbjct: 61  DVTGPAIVTAADLKVDSDIEVLNPDQYICSIADGGHLHMNVAIKNGRGYVPASENKTDDM 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           PIG+I +D+L+SPIKKV+Y VESAR G+  DYDKL++ I TDGSI
Sbjct: 121 PIGVIPVDSLFSPIKKVNYQVESARVGKRDDYDKLTLEIWTDGSI 165


>gi|150186960|emb|CAK30137.1| RNA polymerase alpha subunit [Streptococcus infantis ATCC 700779]
          Length = 173

 Score =  172 bits (437), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 84/172 (48%), Positives = 118/172 (68%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRVL++SL GAA+T++ IDGVLHE  +I GV ED+  IILNIKGI 
Sbjct: 1   PLERGYGTTLGNSLRRVLLASLPGAAVTSIDIDGVLHEFDTIPGVREDVMQIILNIKGIA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +K      K + +   GP  VTAGDI T +DIE++NPDH +  +   A  +  +TV+ G 
Sbjct: 61  VKSYVKDEKTIELDVEGPAEVTAGDILTDSDIEIVNPDHYLFTIGEGASFKATMTVNTGR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           GYVPA  ++ +N P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ I
Sbjct: 121 GYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEI 172


>gi|150036740|emb|CAM98259.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. dextranicum]
          Length = 195

 Score =  172 bits (436), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 89/195 (45%), Positives = 130/195 (66%), Gaps = 2/195 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A
Sbjct: 61  DDERSLEIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSA 120

Query: 159 KHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+
Sbjct: 121 DENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTNGSIKPSDA 180

Query: 217 VALASRILQDQLGMF 231
           ++L ++IL + LG+F
Sbjct: 181 LSLGAKILAEHLGLF 195


>gi|154424855|emb|CAL18530.1| RNA polymerase alpha subunit [Streptococcus sanguinis]
          Length = 198

 Score =  172 bits (436), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 84/188 (44%), Positives = 127/188 (67%)

Query: 49  RVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK 108
           RVL++SL GAA+T++ I+GVLHE  +I GV ED+  IILN+KGI +K      K + +  
Sbjct: 1   RVLLASLPGAAVTSINIEGVLHEFDTISGVREDVMQIILNVKGIAVKSYVQDEKIIELDV 60

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
            GP  VTAGDI T +DIE++NPDH +  +   A  +  +TV+ G GYVPA  ++ ++ P+
Sbjct: 61  EGPAEVTAGDILTDSDIEIINPDHYLFTIGEGASFKATMTVNSGRGYVPADENKKDDAPV 120

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           G + +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L
Sbjct: 121 GTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHL 180

Query: 229 GMFINFEE 236
            +F N  E
Sbjct: 181 NLFTNLTE 188


>gi|261886106|ref|ZP_06010145.1| DNA-directed RNA polymerase subunit alpha [Campylobacter fetus
           subsp. venerealis str. Azul-94]
          Length = 326

 Score =  172 bits (436), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 107/303 (35%), Positives = 171/303 (56%), Gaps = 16/303 (5%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           EN   +IA P    +A TL + LRR+L +S  G A TAV+IDGV HE  S++G+ ED+T 
Sbjct: 15  ENVAKIIAYPFETVYAVTLAHPLRRLLYTSTVGFAPTAVKIDGVAHEFDSMRGMLEDVTL 74

Query: 85  IILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDI-EVLNPDHVICNLDVDAV 142
            I+N+K +  K+  DS + V  +  +GP  +T  D+   NDI E++NPD  +  ++ DA 
Sbjct: 75  FIINLKNLRFKLKNDSKREVIEYSFKGPKEITGIDLN--NDIVEIVNPDSYLATINEDAE 132

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           ++  L V KG GYVP++  R   D    I +DA ++P+KK  Y +E+       DY+K+ 
Sbjct: 133 LKFSLIVEKGIGYVPSEEIRDYIDS-EYIALDAFFTPVKKAVYEIENVLVEDNPDYEKIV 191

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV-----KSLPFNPALL 257
           +++ TDG ++  ++   +   +  Q+ +F N       +  D+N+     ++   +  LL
Sbjct: 192 LSVSTDGQVSPIEAFKHSIEAMYKQMSIFNNV------LNIDVNMALTSSQNSNEHSKLL 245

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + VE L LS RS NCL   +I Y+G+L    E+++  + N G+KSL EIK V+  +G   
Sbjct: 246 ESVENLNLSARSFNCLDKADIRYIGELALMEESELKDLKNLGKKSLDEIKAVMAEIGYPF 305

Query: 318 GMN 320
           G N
Sbjct: 306 GEN 308


>gi|332178481|gb|AEE14170.1| DNA-directed RNA polymerase subunit alpha [Thermodesulfobium
           narugense DSM 14796]
          Length = 341

 Score =  172 bits (436), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 106/304 (34%), Positives = 178/304 (58%), Gaps = 18/304 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPLP G+  T+GNALRRVL++S+ G+A+ AV++D   HE  ++ G+ ED+ +  LN+
Sbjct: 27  FVLEPLPPGYGATIGNALRRVLLTSIPGSAVIAVRVDDAPHEYMTLPGMVEDILEFHLNL 86

Query: 90  KGINLKMSGD----SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           K + + +S D      +++ +  +GP +V A DIQ   +++++N D  +  L+ +  +R 
Sbjct: 87  KKLVVVVSPDISEEETRKLILDVKGPKIVKASDIQPNAEVQIINKDLYLATLEENGELRA 146

Query: 146 ELTVSKGHGYVPAKHHRTENDPI--GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
           E+TV KG GY+  +  +     +  G I +DA + PI +V+Y+VES R GQ  D+DKL  
Sbjct: 147 EITVKKGKGYISIEKMKENTRWLSPGSIPLDANFLPITRVNYSVESTRVGQETDWDKLIF 206

Query: 204 TIDTDGSITGEDSVALAS-------RILQDQLGMFINFEEP---KKEVKEDINVKSLPFN 253
            I T+G+I   +++ +A+       RI   + G F++ E+P    KE K+D  ++S    
Sbjct: 207 EIWTNGAIEPVNALRIAAEDLISHFRIFA-EYGTFLDSEKPVSDYKETKKDSYLRSQA-K 264

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
             L + +EE+ L  R  N L+   I  +GDLI +T  D+L + +FG+KSL E++ +L   
Sbjct: 265 MDLEQSIEEIGLQTRIANVLKRSGISTLGDLISKTREDILNVPSFGKKSLDELEEILHAK 324

Query: 314 GLFL 317
           G  L
Sbjct: 325 GYRL 328


>gi|156502016|ref|YP_001428081.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica FTNF002-00]
 gi|290954162|ref|ZP_06558783.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica URFT1]
 gi|295312432|ref|ZP_06803209.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica URFT1]
 gi|171769927|sp|A7NAX2|RPOA2_FRATF RecName: Full=DNA-directed RNA polymerase subunit alpha 2;
           Short=RNAP subunit alpha 2; AltName: Full=RNA polymerase
           subunit alpha 2; AltName: Full=Transcriptase subunit
           alpha 2
 gi|156252619|gb|ABU61125.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. holarctica FTNF002-00]
          Length = 317

 Score =  172 bits (436), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 106/327 (32%), Positives = 185/327 (56%), Gaps = 20/327 (6%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI- 65
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I 
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKIN 60

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVND 124
           DG +  +  +    E + DIILN+K +++ ++ D       F+  G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLSVTLAEDVETGTITFELSGSEEEIFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG G+ PA+ +  + + +    +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQDNFKDCEFL----LDATFSPVVFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK----E 240
           + ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K    E
Sbjct: 177 FEIKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGIFVE 236

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             +DIN       P LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+
Sbjct: 237 DPKDIN-------PILLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGK 289

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           KSL EIK  L  +GL LG  + +WP +
Sbjct: 290 KSLTEIKDKLSELGLSLGTLIENWPQD 316


>gi|167627502|ref|YP_001678002.1| DNA-directed RNA polymerase subunit alpha [Francisella philomiragia
           subsp. philomiragia ATCC 25017]
 gi|241668071|ref|ZP_04755649.1| DNA-directed RNA polymerase subunit alpha [Francisella philomiragia
           subsp. philomiragia ATCC 25015]
 gi|254876606|ref|ZP_05249316.1| DNA-directed RNA polymerase alpha subunit [Francisella philomiragia
           subsp. philomiragia ATCC 25015]
 gi|158523436|gb|ABW70833.1| DNA-directed RNA polymerase alpha subunit 2 [Francisella
           philomiragia subsp. philomiragia ATCC 25015]
 gi|167597503|gb|ABZ87501.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Francisella philomiragia subsp. philomiragia ATCC
           25017]
 gi|254842627|gb|EET21041.1| DNA-directed RNA polymerase alpha subunit [Francisella philomiragia
           subsp. philomiragia ATCC 25015]
          Length = 318

 Score =  172 bits (436), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 105/321 (32%), Positives = 182/321 (56%), Gaps = 11/321 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI- 65
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+V+I 
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGYALKQTMLYSIHGACVTSVKIN 60

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVND 124
           DG +  +  +    E + DIILN+K + + ++      V  F+  G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLPVTLAEGVDTGVITFELSGSEEEVFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG GY  A+ +    + +    +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGIGYRQAQENFKNEEFL----LDAAFSPVSFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y ++ AR G+  D DKL + I T+G+++ E+++ +A+  +Q+QL   ++ EE  K +  +
Sbjct: 177 YEIKDARVGRRTDLDKLELNIKTNGNVSCEEALRIAATKIQNQLRNIVDVEEINKGIFVE 236

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              K +  NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL 
Sbjct: 237 DPTKDI--NPLLLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLT 294

Query: 305 EIKGVLGTMGLFLGMNLPDWP 325
           EIK  L  +GL LG  + +WP
Sbjct: 295 EIKDKLSELGLSLGTMIDNWP 315


>gi|86438816|emb|CAJ43373.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 203

 Score =  172 bits (436), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 85/184 (46%), Positives = 123/184 (66%)

Query: 48  RRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF 107
           RRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   D  K + + 
Sbjct: 1   RRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSFSDERKVIELD 60

Query: 108 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
             GP  VTA D++   D++VLNPD  IC +     + ME+ V  G GYV A  +++++ P
Sbjct: 61  VEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNGRGYVAASDNKSDDMP 120

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           IG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++ A++IL + 
Sbjct: 121 IGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEH 180

Query: 228 LGMF 231
             +F
Sbjct: 181 FKVF 184


>gi|218282068|ref|ZP_03488367.1| hypothetical protein EUBIFOR_00938 [Eubacterium biforme DSM 3989]
 gi|218216942|gb|EEC90480.1| hypothetical protein EUBIFOR_00938 [Eubacterium biforme DSM 3989]
          Length = 321

 Score =  172 bits (435), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 103/304 (33%), Positives = 170/304 (55%), Gaps = 16/304 (5%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           EE N    I EPL RGF  T+GN + R L++S+ G  I   ++ G   + + + G+ ED+
Sbjct: 21  EENNTGSYIFEPLERGFGITIGNTICRTLLTSVPGTRIVGFKVSGFDGKATMVDGILEDI 80

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             I LN+K + L   G+  + + I K+GP  + A DI     +EV++P+ VIC L+  A 
Sbjct: 81  YRISLNLKAVQLYNDGEGFQTLHISKKGPATIQAADIICPEAVEVVDPEQVICTLEKGAS 140

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIG--LITIDALYSPIKKVSYTVESAREGQVLDYDK 200
           + ME+    G GY  +  ++   D  G  ++ +DA ++PI+K  Y  E AR G    YDK
Sbjct: 141 LEMEIYAVTGTGYKSSIENKVSYD-FGEDVVVLDATFTPIRKADYLSEPARVGLDKKYDK 199

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL--LK 258
           + + ++TDG+IT   ++ +A+++  + L   +   +   E++E   V+     P +  +K
Sbjct: 200 VHINVETDGTITPLQAITMAAKVCMENLDEVLTVSDL--ELEESFMVQ----KPQVEDVK 253

Query: 259 KV-----EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           KV     E+L+LSVRS NCL+   I  + +L Q+TE +M+ + N G+KSL E+K  +  +
Sbjct: 254 KVNTMMIEDLDLSVRSYNCLKRAGIQTVDELTQKTEDEMMHVKNLGKKSLKEVKDKMYQL 313

Query: 314 GLFL 317
           GLF 
Sbjct: 314 GLFF 317


>gi|118497985|ref|YP_899035.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. novicida U112]
 gi|134301520|ref|YP_001121488.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. tularensis WY96-3418]
 gi|194323208|ref|ZP_03056992.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. novicida FTE]
 gi|254374799|ref|ZP_04990280.1| DNA-directed RNA polymerase [Francisella novicida GA99-3548]
 gi|158512424|sp|A0Q7R6|RPOA2_FRATN RecName: Full=DNA-directed RNA polymerase subunit alpha 2;
           Short=RNAP subunit alpha 2; AltName: Full=RNA polymerase
           subunit alpha 2; AltName: Full=Transcriptase subunit
           alpha 2
 gi|158513850|sp|A4IWR6|RPOA2_FRATW RecName: Full=DNA-directed RNA polymerase subunit alpha 2;
           Short=RNAP subunit alpha 2; AltName: Full=RNA polymerase
           subunit alpha 2; AltName: Full=Transcriptase subunit
           alpha 2
 gi|118423891|gb|ABK90281.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Francisella novicida U112]
 gi|134049297|gb|ABO46368.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. tularensis WY96-3418]
 gi|151572518|gb|EDN38172.1| DNA-directed RNA polymerase [Francisella novicida GA99-3548]
 gi|194322572|gb|EDX20052.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. novicida FTE]
          Length = 318

 Score =  172 bits (435), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 106/321 (33%), Positives = 182/321 (56%), Gaps = 11/321 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI- 65
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I 
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKIN 60

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVND 124
           DG +  +  +    E + DIILN+K + + ++ G     +T    G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLPVTLAEGVETGTITFELSGSEEEIFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG G+ PA+    +N   G   +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQ----DNFKDGEFLLDATFSPVVFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +  +
Sbjct: 177 FEIKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGIFVE 236

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              K +  NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL 
Sbjct: 237 DPTKDI--NPILLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLT 294

Query: 305 EIKGVLGTMGLFLGMNLPDWP 325
           EIK  L  +GL LG  + +WP
Sbjct: 295 EIKDKLSELGLSLGTLIENWP 315


>gi|119668307|emb|CAK95506.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           delbrueckii]
          Length = 209

 Score =  172 bits (435), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 86/194 (44%), Positives = 126/194 (64%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           GF  TLGN+LRRVL++S+ G  +  V+IDG+LHE +++ GV ED+T IILN+K + L+  
Sbjct: 1   GFGTTLGNSLRRVLLTSVPGTGLVKVKIDGILHEFTTVPGVKEDVTKIILNLKKLVLRAY 60

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
            +  K + +   GP  VTA D++   D+EVLNPD  IC +     + M + V  G GYVP
Sbjct: 61  TEEVKTIELNVEGPATVTAEDLKADADVEVLNPDQYICTIAQGGHLHMWIDVCNGRGYVP 120

Query: 158 AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
           A  ++T    IG I +D+L+SPI+KV+Y VES R G+  D+DKL++ I T+GSI   D++
Sbjct: 121 ASENKTAEMFIGDIPVDSLFSPIEKVNYQVESTRVGKREDFDKLTLEIWTNGSIAPNDAL 180

Query: 218 ALASRILQDQLGMF 231
             A+R+L +    F
Sbjct: 181 NFAARVLVEHFKAF 194


>gi|90567617|emb|CAJ31076.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
 gi|119662365|emb|CAJ33171.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 193

 Score =  172 bits (435), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 85/184 (46%), Positives = 123/184 (66%)

Query: 48  RRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF 107
           RRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   D  K + + 
Sbjct: 1   RRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSFSDERKVIELD 60

Query: 108 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
             GP  VTA D++   D++VLNPD  IC +     + ME+ V  G GYV A  +++++ P
Sbjct: 61  VEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNGRGYVAASDNKSDDMP 120

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           IG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++ A++IL + 
Sbjct: 121 IGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEH 180

Query: 228 LGMF 231
             +F
Sbjct: 181 FKVF 184


>gi|254368844|ref|ZP_04984857.1| hypothetical protein FTAG_00654 [Francisella tularensis subsp.
           holarctica FSC022]
 gi|157121765|gb|EDO65935.1| hypothetical protein FTAG_00654 [Francisella tularensis subsp.
           holarctica FSC022]
          Length = 317

 Score =  172 bits (435), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 108/325 (33%), Positives = 182/325 (56%), Gaps = 20/325 (6%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI- 65
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I 
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKIN 60

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVND 124
           DG +  +  +    E + DIILN+K + + ++ D       F+  G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLPVTLAEDVEMGTITFELSGSEEEIFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG G+ PA+    +N   G   +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQ----DNFKDGEFLLDATFSPVVFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK----E 240
           + ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K    E
Sbjct: 177 FEIKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGIFVE 236

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             +DIN       P LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+
Sbjct: 237 DPKDIN-------PILLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGK 289

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL EIK  L  +GL LG  + +WP
Sbjct: 290 KSLTEIKDKLSELGLSLGTLIENWP 314


>gi|150036772|emb|CAN89785.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gasicomitatum
           LMG 18811]
          Length = 203

 Score =  172 bits (435), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 88/198 (44%), Positives = 131/198 (66%), Gaps = 2/198 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  + + +  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A
Sbjct: 61  DEERSLEVDIQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTITAFKGRGYSSA 120

Query: 159 KHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+
Sbjct: 121 DENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDA 180

Query: 217 VALASRILQDQLGMFINF 234
           ++L S+IL + L +F++ 
Sbjct: 181 LSLGSKILAEHLNLFMDI 198


>gi|254373336|ref|ZP_04988824.1| DNA-directed RNA polymerase [Francisella tularensis subsp. novicida
           GA99-3549]
 gi|151571062|gb|EDN36716.1| DNA-directed RNA polymerase [Francisella novicida GA99-3549]
          Length = 318

 Score =  172 bits (435), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 106/321 (33%), Positives = 182/321 (56%), Gaps = 11/321 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI- 65
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I 
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKIN 60

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVND 124
           DG +  +  +    E + DIILN+K + + ++ G     +T    G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLPVTLAEGVETGTITFELSGSEEEIFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG G+ PA+    +N   G   +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQ----DNFKNGEFLLDATFSPVVFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +  +
Sbjct: 177 FEIKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGIFVE 236

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              K +  NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL 
Sbjct: 237 DPTKDI--NPILLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLT 294

Query: 305 EIKGVLGTMGLFLGMNLPDWP 325
           EIK  L  +GL LG  + +WP
Sbjct: 295 EIKDKLSELGLSLGTLIENWP 315


>gi|150036784|emb|CAM98269.1| DNA-directed RNA polymerase alpha chain [Leuconostoc lactis]
          Length = 211

 Score =  171 bits (434), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 89/204 (43%), Positives = 132/204 (64%), Gaps = 2/204 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A
Sbjct: 61  DDERSLEIDVQGPAEVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSA 120

Query: 159 KHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   E  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+
Sbjct: 121 DENKQLREEMPIGVLAVDSIYTPIERVNYHVENTRVGARDDYDKLTFDIWTNGSIKPSDA 180

Query: 217 VALASRILQDQLGMFINFEEPKKE 240
           ++L ++IL + L +F++      E
Sbjct: 181 LSLGAKILAEHLNLFMDISPVAAE 204


>gi|119668327|emb|CAK95463.1| RNA polymerase alpha subunit [Lactobacillus hilgardii]
          Length = 198

 Score =  171 bits (434), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 94/193 (48%), Positives = 132/193 (68%), Gaps = 4/193 (2%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFK 108
           L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K I+LK+ G  D  + + I  
Sbjct: 1   LLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKISLKLDGPEDEDENLEIDV 60

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTEND 166
            GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT ++G GYV A     R    
Sbjct: 61  IGPADVTAGDIQDDSDVTVLNPDLHIATVAEGATFHMRLTANRGRGYVSAVENKKRATEM 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ I T+GSIT  ++V+LA++IL +
Sbjct: 121 PIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDIWTNGSITPSEAVSLAAKILTE 180

Query: 227 QLGMFINFEEPKK 239
            L MF++  +  K
Sbjct: 181 HLEMFVDLTDEAK 193


>gi|194246759|ref|YP_002004398.1| DNA-directed RNA polymerase, alpha chain [Candidatus Phytoplasma
           mali]
 gi|193807116|emb|CAP18554.1| DNA-directed RNA polymerase, alpha chain [Candidatus Phytoplasma
           mali]
          Length = 331

 Score =  171 bits (434), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 106/292 (36%), Positives = 167/292 (57%), Gaps = 11/292 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I + L   +  T+GN LRRVL+SSL GA I  V+I GV HE S+I GV+ED+  I+LN+
Sbjct: 25  FIIQNLEPSYGVTIGNPLRRVLLSSLPGAGIVYVEIKGVDHEFSTIPGVYEDVMSIVLNL 84

Query: 90  KGINLKMSG---DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRM 145
           K + + +     D  + + +F  G   VTA   + V  I+++NP+  I NL   +A ++M
Sbjct: 85  KQVVISVDSIDDDFEQEMELFVTGKQKVTASCFEQVEGIKIINPEQEIANLVSENASLKM 144

Query: 146 ELTVSKGHGYVPAKHHRT-ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
            + + +G GYV A+ ++       GLI+ID LY+P+ KVSY +E     ++ D ++L++ 
Sbjct: 145 TVLIKRGIGYVSAEENKIYTKKKKGLISIDTLYTPVSKVSYDIEK----KLGDKEELAIE 200

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN-VKSLPFNPALLKKVEEL 263
           I T+ S T +D++  AS+IL D      N  E K ++       K LP N +L  ++++L
Sbjct: 201 ITTNKSTTAKDALTTASKILFDHFSFLANLNEKKDQISFIYKPKKELP-NKSLELRIDQL 259

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           ELSVR  NCL+   I  + DL+   E ++ ++ + GRKS  E+K      GL
Sbjct: 260 ELSVRLFNCLKKSGIEKVSDLVLLKEEEVFKLKSLGRKSFNELKEKFKQHGL 311


>gi|119662299|emb|CAJ33137.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           bulgaricus]
          Length = 214

 Score =  171 bits (434), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 85/193 (44%), Positives = 125/193 (64%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  V+IDG+LHE +++ GV ED+T IILN+K + L+   
Sbjct: 1   FGTTLGNSLRRVLLTSVPGTGLVKVKIDGILHEFTTVPGVKEDVTKIILNLKKLELRAYT 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + +   GP  VTA D++   D+EVLNPD  IC +     + M + V  G GYVPA
Sbjct: 61  EEVKTIELDVEGPATVTAEDLKADADVEVLNPDQYICTIAQGGHLHMWIDVCNGRGYVPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++T    IG I +D+L+SPI+KV+Y VES R G+  D+DKL++ I T+GSI   D++ 
Sbjct: 121 SENKTAEMSIGDIPVDSLFSPIEKVNYQVESTRVGKREDFDKLTLEIWTNGSIAPNDALN 180

Query: 219 LASRILQDQLGMF 231
            A+R+L +    F
Sbjct: 181 FAARVLVEHFKAF 193


>gi|119662373|emb|CAJ33175.1| RNA polymerase alpha subunit [Lactobacillus panis]
          Length = 190

 Score =  171 bits (434), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 87/190 (45%), Positives = 134/190 (70%), Gaps = 2/190 (1%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           L GAAIT +QIDGVLHE S++KGV ED+T IILN+K ++LK++ +  K + +  +GP  V
Sbjct: 1   LPGAAITTMQIDGVLHEFSTVKGVTEDVTQIILNLKKVSLKLNSEDQKNLELDVKGPAEV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLIT 172
           TA DIQ  +++ +LNPD  I  +   A + +++T  KG GY+ A  +  R E+ PIG++ 
Sbjct: 61  TASDIQGDSEVTILNPDLHIATVADGAELHIKMTADKGRGYLSANDNKARMEDLPIGVLP 120

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           ID++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T  ++V+L ++IL + L MF+
Sbjct: 121 IDSIYTPIERVNYTVENARVGQRSDYDKLTLDVWTDGSLTPIEAVSLGAKILTEHLDMFV 180

Query: 233 NFEEPKKEVK 242
           N  E  +  +
Sbjct: 181 NLTETAQNAQ 190


>gi|150036756|emb|CAM98263.1| DNA-directed RNA polymerase alpha chain [Leuconostoc inhae KCTC
           3774]
          Length = 214

 Score =  171 bits (434), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 89/201 (44%), Positives = 131/201 (65%), Gaps = 2/201 (0%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  
Sbjct: 3   TLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDEE 62

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           + + +  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  +
Sbjct: 63  RSLEVDIQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTITAVKGRGYSSADEN 122

Query: 162 RTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           +   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L
Sbjct: 123 KQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSL 182

Query: 220 ASRILQDQLGMFINFEEPKKE 240
            S+IL + L +F++      E
Sbjct: 183 GSKILAEHLNLFMDISPVAAE 203


>gi|150036830|emb|CAM98044.1| DNA-directed RNA polymerase alpha chain [Leuconostoc kimchii]
          Length = 216

 Score =  171 bits (434), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 88/204 (43%), Positives = 132/204 (64%), Gaps = 2/204 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  + + I  +GP  VTA D+Q   D+E+LNPD  +  +     + M +T  KG GY  A
Sbjct: 61  DDERSLEIDVQGPADVTAADLQAGADVEILNPDLHLATVAAGKSLHMTVTAVKGRGYSSA 120

Query: 159 KHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+
Sbjct: 121 DENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDA 180

Query: 217 VALASRILQDQLGMFINFEEPKKE 240
           ++L S+IL + L +F++      E
Sbjct: 181 LSLGSKILAEHLNLFMDISPVAAE 204


>gi|56708484|ref|YP_170380.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. tularensis SCHU S4]
 gi|110670955|ref|YP_667512.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. tularensis FSC198]
 gi|224457644|ref|ZP_03666117.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. tularensis MA00-2987]
 gi|254371109|ref|ZP_04987111.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           tularensis FSC033]
 gi|254875331|ref|ZP_05248041.1| rpoA2, DNA-directed RNA polymerase, alpha subunit [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|81597191|sp|Q5NF12|RPOA2_FRATT RecName: Full=DNA-directed RNA polymerase subunit alpha 2;
           Short=RNAP subunit alpha 2; AltName: Full=RNA polymerase
           subunit alpha 2; AltName: Full=Transcriptase subunit
           alpha 2
 gi|122970868|sp|Q14GG5|RPOA2_FRAT1 RecName: Full=DNA-directed RNA polymerase subunit alpha 2;
           Short=RNAP subunit alpha 2; AltName: Full=RNA polymerase
           subunit alpha 2; AltName: Full=Transcriptase subunit
           alpha 2
 gi|54113777|gb|AAV29522.1| NT02FT1997 [synthetic construct]
 gi|56604976|emb|CAG46075.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. tularensis SCHU S4]
 gi|110321288|emb|CAL09458.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. tularensis FSC198]
 gi|151569349|gb|EDN35003.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           tularensis FSC033]
 gi|254841330|gb|EET19766.1| rpoA2, DNA-directed RNA polymerase, alpha subunit [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|282159688|gb|ADA79079.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. tularensis NE061598]
          Length = 318

 Score =  171 bits (434), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 106/321 (33%), Positives = 182/321 (56%), Gaps = 11/321 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI- 65
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I 
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKIN 60

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVND 124
           DG +  +  +    E + DIILN+K + + ++ G     +T    G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLPVTLAEGVETGTITFELSGSEEEIFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG G+ PA+    +N   G   +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQ----DNFKDGEFLLDATFSPVVFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +  +
Sbjct: 177 FEIKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNILDIEEINKGIFVE 236

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              K +  NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL 
Sbjct: 237 DPTKDI--NPILLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLT 294

Query: 305 EIKGVLGTMGLFLGMNLPDWP 325
           EIK  L  +GL LG  + +WP
Sbjct: 295 EIKDKLSELGLSLGTLIENWP 315


>gi|119668331|emb|CAK95465.1| RNA polymerase alpha subunit [Lactobacillus iners]
          Length = 201

 Score =  171 bits (433), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 88/187 (47%), Positives = 133/187 (71%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRRVL++S+ G A++ + IDGVLHE S+I GV ED+T IILN+K + LK+  D  K V I
Sbjct: 1   LRRVLLTSISGTALSYIMIDGVLHEFSTIPGVREDVTKIILNLKKLELKLLVDEEKMVEI 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
              GP VVTA D++   D+E+LNPD  IC +     + M + +  G GY+PA  +++++ 
Sbjct: 61  DVEGPAVVTAADLKVDADVEILNPDQYICTIAEGGHLHMSIAIKNGRGYIPASENKSDDM 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           PIG+I +D+L+SPIKKV+Y VE+AR G+  DYDKL++ + TDGSIT  D+++ A++IL++
Sbjct: 121 PIGVIPVDSLFSPIKKVNYQVENARVGKRDDYDKLTLELWTDGSITPNDALSFAAKILEE 180

Query: 227 QLGMFIN 233
              +F++
Sbjct: 181 HFKVFMS 187


>gi|150036786|emb|CAM98270.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 221

 Score =  171 bits (433), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 89/201 (44%), Positives = 131/201 (65%), Gaps = 2/201 (0%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  
Sbjct: 3   TLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDE 62

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  +
Sbjct: 63  RSLEIDVQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSADEN 122

Query: 162 RTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           +   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L
Sbjct: 123 KKLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGARDDYDKLTFDIWTNGSIKPSDALSL 182

Query: 220 ASRILQDQLGMFINFEEPKKE 240
            ++IL + L +F++      E
Sbjct: 183 GAKILAEHLNLFMDISPVAAE 203


>gi|154149371|ref|YP_001405812.1| DNA-directed RNA polymerase subunit alpha [Campylobacter hominis
           ATCC BAA-381]
 gi|166229267|sp|A7HZX1|RPOA_CAMHC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|153805380|gb|ABS52387.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter hominis
           ATCC BAA-381]
          Length = 338

 Score =  171 bits (432), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 112/327 (34%), Positives = 181/327 (55%), Gaps = 24/327 (7%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           EN   +IA P   G+A TL + LRR+L +S  G A TAV+IDGV HE  S++G+ ED+  
Sbjct: 21  ENVAKIIAYPFETGYAVTLAHPLRRLLYTSTVGYAPTAVKIDGVSHEFDSMRGMLEDVAI 80

Query: 85  IILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDI-EVLNPDHVICNLDVDAV 142
            I+N+KGI  K+ GDS + V  +   GP  +T  D+   NDI E++NPD  +  ++ DA 
Sbjct: 81  FIINLKGIRFKIKGDSKREVIEYNFTGPKEITGKDLN--NDIVEIVNPDAYLATINEDAD 138

Query: 143 VRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
           ++  + + KG GYVP++  R    +D I L   DA ++P+ +  Y +E+       DY+K
Sbjct: 139 LKFSVVIEKGIGYVPSESIRDYVSSDYIAL---DAFFTPVIRAIYDIENVFVEDNPDYEK 195

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMF---INFEEPKKEVKEDINVKSLPF--NPA 255
           +  TI TDG ++  D+   A   +  Q+ +F   ++ +  K   K+      +P   +  
Sbjct: 196 IIFTITTDGQVSAVDAFKNALEAMYQQMSVFKGIVDIDTGKSFTKQ------IPSGEHSK 249

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           L + +E L LS RS NCL   +I ++G+++   E+++  + N G+KSL EIK V+  +G 
Sbjct: 250 LFESIENLNLSARSFNCLEKADIKFVGEIVIMDESELKGIKNLGKKSLEEIKSVMEEIGY 309

Query: 316 FLG----MNLPDWPPESIEELAKKYED 338
            +G     +  +   + I EL KK +D
Sbjct: 310 PIGNEEIKDKKEVLSKKIAELKKKAKD 336


>gi|223038488|ref|ZP_03608782.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter rectus
           RM3267]
 gi|222880345|gb|EEF15432.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter rectus
           RM3267]
          Length = 328

 Score =  171 bits (432), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 106/319 (33%), Positives = 177/319 (55%), Gaps = 16/319 (5%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           EN   + A P   G+A TL + LRR+L SS  G A T V+I+GV HE  S++G+ ED+  
Sbjct: 12  ENVARITAYPFETGYAVTLAHPLRRLLYSSTVGFAATGVKIEGVSHEFDSMRGMLEDVAQ 71

Query: 85  IILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            I+N+K I  K+  +S + V  +  +GP  + AGD+++ + ++++NPD  +  ++ DA +
Sbjct: 72  FIINLKNIRFKLKNESEREVVEYSFKGPKEIKAGDLKS-DVVDIVNPDAYLATINEDAEL 130

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
           +  + + KG GYVP++  R + +  G I +DA ++P+KK  Y + +       DY+K+  
Sbjct: 131 KFSVIIQKGIGYVPSEEIRGDTEE-GYIALDAFFTPVKKAVYELVNVLVEDNPDYEKIIF 189

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMF---INFEEPKKEVKEDINVKSLPFNPA-LLKK 259
           T+ TDG +   ++   A   +  Q+ +F   +N      ++   +N ++     A LL+ 
Sbjct: 190 TVTTDGQVGAIEAFKHAIEAMYQQMSVFKGVLNI-----DISAGLNAQTSGSEHAKLLQS 244

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           VEEL LS RS NCL    I ++G+L    E ++  + N G+KSL EIK V+  +G  +G 
Sbjct: 245 VEELNLSARSFNCLDKAEIRFIGELALMDENELKELKNLGKKSLEEIKAVMQEIGYPVGG 304

Query: 320 NLPDWPPESIEELAKKYED 338
           +L        E+L KK  D
Sbjct: 305 DLGGGK----EQLKKKIAD 319


>gi|119662333|emb|CAJ33155.1| RNA polymerase alpha subunit [Lactobacillus oris]
          Length = 200

 Score =  171 bits (432), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 87/190 (45%), Positives = 134/190 (70%), Gaps = 2/190 (1%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           L G+AIT +QIDGVLHE S++KGV ED+T IILN+K ++LK++ +  K + +  +GP  V
Sbjct: 1   LPGSAITTMQIDGVLHEFSTVKGVTEDVTQIILNLKKVSLKINSEDQKDLELDVKGPAKV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLIT 172
           TAGDIQ  +++ VLNPD  I  +   A + +++T  KG GY+ A  +  R E+  IG++ 
Sbjct: 61  TAGDIQGDSEVSVLNPDLHIATVADGAELHIKMTADKGRGYLSANDNKARMEDLAIGVLP 120

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           ID++Y+PI++V+YTVE+AR GQ  D+DKL++ + TDGSIT  ++V+L ++IL + L MF+
Sbjct: 121 IDSIYTPIERVNYTVENARVGQRSDFDKLTLDVWTDGSITPTEAVSLGAKILTEHLAMFV 180

Query: 233 NFEEPKKEVK 242
           N  E  +  +
Sbjct: 181 NLTETAQNAQ 190


>gi|150036844|emb|CAM98287.1| DNA-directed RNA polymerase alpha chain [Leuconostoc holzapfelii]
          Length = 199

 Score =  171 bits (432), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 89/195 (45%), Positives = 130/195 (66%), Gaps = 2/195 (1%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  
Sbjct: 3   TLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDE 62

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  +
Sbjct: 63  RSLEIDVQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSADEN 122

Query: 162 RT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           +   E  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L
Sbjct: 123 KQLREEMPIGVLAVDSIYTPIERVNYHVENTRVGARDDYDKLTFDIWTNGSIKPSDALSL 182

Query: 220 ASRILQDQLGMFINF 234
            S+IL + L +F++ 
Sbjct: 183 GSKILAEHLNLFMDI 197


>gi|119672791|emb|CAK95479.1| RNA polymerase alpha subunit [Lactobacillus sakei subsp. sakei]
          Length = 176

 Score =  171 bits (432), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 85/175 (48%), Positives = 124/175 (70%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           G+  TLGN+LRR+L++SL G A+T +QIDGVLHE S+I GV ED+T IILNIK + LK+ 
Sbjct: 1   GYGTTLGNSLRRILLASLPGTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKLH 60

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
            +  K + I  +GP  VTA DI + +D+EVLN D  IC +       + +TV KG GYV 
Sbjct: 61  VEEDKTIEIDVKGPATVTAADIISDDDVEVLNTDQYICTVAEGGNFHVRMTVKKGRGYVA 120

Query: 158 AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           A  +++++ PIG++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+
Sbjct: 121 AVQNKSDDMPIGVLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSIS 175


>gi|150036802|emb|CAM98037.1| DNA-directed RNA polymerase alpha chain [Fructobacillus
           pseudoficulneus]
          Length = 231

 Score =  170 bits (431), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 95/231 (41%), Positives = 141/231 (61%), Gaps = 2/231 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL+SSL G A+  VQIDGV+HE S++ GV ED+T +ILN+K +      
Sbjct: 1   YGTTLGNSLRRVLLSSLPGVAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVVFATDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
                + I  +GP  VTA D+    DIEVLNPD  I  L     + M +T  KG GY  A
Sbjct: 61  AEEHALEIDVQGPKDVTAADLMGSADIEVLNPDLHIATLAAGKALHMTVTAVKGRGYSSA 120

Query: 159 KHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
           + ++   D  PIG++T+D++Y+PI++V+Y VE+ R G   DYDKL+M + T+GSI   D+
Sbjct: 121 EENKQLRDEMPIGVLTVDSIYTPIERVNYHVENKRVGSRDDYDKLTMEVWTNGSIKPSDA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           ++L S+IL + L +F +     ++ K  +  +      A    +E+L+LSV
Sbjct: 181 LSLGSKILTEHLNLFTDISPVAQDTKVMVESEPAANTAADAAPIEDLDLSV 231


>gi|305432400|ref|ZP_07401562.1| DNA-directed RNA polymerase subunit alpha [Campylobacter coli JV20]
 gi|304444439|gb|EFM37090.1| DNA-directed RNA polymerase subunit alpha [Campylobacter coli JV20]
          Length = 337

 Score =  170 bits (431), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 98/289 (33%), Positives = 160/289 (55%), Gaps = 5/289 (1%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
           A P   G+  TL + LRR+L +S  G A TA+ IDGV HE  S++G+ ED+   I+N+K 
Sbjct: 28  AWPFEIGYGITLAHPLRRLLYTSTIGYAPTAIHIDGVAHEFDSMRGMLEDVALFIINLKK 87

Query: 92  INLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +  K+  DS+K +  F  +GP  +   D+   + +EV+N D  +  ++ DA ++  L + 
Sbjct: 88  LQFKLKSDSNKEIVEFSFKGPKEIYGKDLNN-DQVEVVNTDAYLATINEDAELKFTLIIE 146

Query: 151 KGHGYVPAKH-HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           KG GYVP++      NDP   I +DA ++P+++ +Y +E        DY+K+ +T+ TDG
Sbjct: 147 KGIGYVPSEEIKELLNDP-KFIALDAFFTPVREATYDIEKVLFEDNPDYEKVVLTVTTDG 205

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
            IT  ++   A   +  QL +F      +  +K       L  N  LL+ + +L LS RS
Sbjct: 206 QITPNEAFQNALEAMYKQLSVFDKITNVRSIIKSQATSNELE-NTKLLQNITDLNLSARS 264

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            NCL    IVY+G+L   +  ++  + N G+KSL EIK ++ ++G  +G
Sbjct: 265 YNCLEKAGIVYIGELALMSVNELAGLKNLGKKSLDEIKSIMESIGFPVG 313


>gi|296044726|gb|ADG85772.1| RpoA [Vibrio sp. WH134]
          Length = 200

 Score =  170 bits (431), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 87/199 (43%), Positives = 136/199 (68%), Gaps = 5/199 (2%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKR 103
           NALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     
Sbjct: 1   NALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVF 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK--- 159
           +T+ K G G V AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    
Sbjct: 61  ITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARI 120

Query: 160 HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  
Sbjct: 121 HTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRR 180

Query: 220 ASRILQDQLGMFINFEEPK 238
           A+ IL +QL  F++  + +
Sbjct: 181 AATILAEQLDAFVDLRDVR 199


>gi|119511155|ref|ZP_01630272.1| DNA-directed RNA polymerase alpha subunit [Nodularia spumigena
           CCY9414]
 gi|119464143|gb|EAW45063.1| DNA-directed RNA polymerase alpha subunit [Nodularia spumigena
           CCY9414]
          Length = 315

 Score =  170 bits (431), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 101/303 (33%), Positives = 170/303 (56%), Gaps = 13/303 (4%)

Query: 24  EENRT---LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
           EE+R+     + EPL RG   T+GNALRRVL+S+L G A+TAV+I GV HE +++ GV E
Sbjct: 14  EESRSHYSKFVLEPLERGQGTTVGNALRRVLLSNLEGTAVTAVRIAGVSHEFATVPGVRE 73

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+ +I++ +K + L+      +   +   GP  VT       +++EV++    +  L   
Sbjct: 74  DVLEILMKMKEVILRSYSSQPQIGRLLVNGPATVTVAHFDLPSEVEVIDQTQYVATLAEG 133

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             + ME  + KG GY   +  R E   +  + ID+++ P++KV+Y+VE AR    +  D+
Sbjct: 134 GKLEMEFRIEKGKGYRTVERGREEATSLDFLQIDSVFMPVRKVNYSVEEARGESSIPKDR 193

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EPKKEVKEDINVKSLPFNPALLKK 259
           L + + T+GSI+ +++++ A+ IL +      +   EP +   E      +P +P     
Sbjct: 194 LLLEVWTNGSISPQEALSSAAGILVELFNPLKDISLEPTETGAE------VPDDPTAQIP 247

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +EEL+LSVR+ NCL+   +  + DL+  T+ D+L + NFG+KS  E   V+  +   LG+
Sbjct: 248 IEELQLSVRAYNCLKRAQVNSVADLLDFTQEDLLEIKNFGQKSAEE---VVEALQRRLGI 304

Query: 320 NLP 322
            LP
Sbjct: 305 TLP 307


>gi|187932094|ref|YP_001892079.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. mediasiatica FSC147]
 gi|187713003|gb|ACD31300.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Francisella tularensis subsp. mediasiatica FSC147]
          Length = 318

 Score =  170 bits (431), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 105/321 (32%), Positives = 181/321 (56%), Gaps = 11/321 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI- 65
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I 
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKIN 60

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVND 124
           DG +  +  +    E + DIILN+K + + ++ G     +T    G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLPVTLTEGVETGTITFELSGSEEEIFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG G+ PA+    +N   G   +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQ----DNFKDGEFLLDATFSPVVFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +  +
Sbjct: 177 FEIKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGIFVE 236

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              K +  NP LLK  EEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL 
Sbjct: 237 DPTKDI--NPILLKHAEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLT 294

Query: 305 EIKGVLGTMGLFLGMNLPDWP 325
           EIK  L  +GL LG  + +WP
Sbjct: 295 EIKDKLSELGLSLGTLIENWP 315


>gi|119662851|emb|CAJ33218.1| RNA polymerase alpha subunit [Lactobacillus fuchuensis]
          Length = 202

 Score =  170 bits (431), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 82/190 (43%), Positives = 131/190 (68%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           +L++SL G A+T +QIDGVLHE S+I GV ED+T IILN+K + LK+  +  K + I  +
Sbjct: 1   ILLASLPGTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNVKKLALKLHVEEDKTIEIDVK 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  VTA DI   +D+EVLN D  IC +       + +TV KG GYV A  +++++ PIG
Sbjct: 61  GPATVTAADIVADDDVEVLNTDQYICTVAEGGNFHVRMTVKKGRGYVAADQNKSDDMPIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           ++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++I+ + L 
Sbjct: 121 VLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKIMTEHLA 180

Query: 230 MFINFEEPKK 239
           +F++  +  K
Sbjct: 181 IFVDLTDEAK 190


>gi|119662377|emb|CAJ33177.1| RNA polymerase alpha subunit [Lactobacillus paraplantarum]
          Length = 176

 Score =  170 bits (431), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 89/176 (50%), Positives = 127/176 (72%), Gaps = 2/176 (1%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG 110
           L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK+  D  K + I  +G
Sbjct: 1   LLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTAIILNVKKIALKLESDETKTLEIDVKG 60

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK--HHRTENDPI 168
           P  VTAGDI    D+EVLNPD  IC +   A   M +T + G GYV A+   HR ++ PI
Sbjct: 61  PANVTAGDIIGDADVEVLNPDLPICTVADGAHFHMRMTANTGRGYVSAEDNKHREDDMPI 120

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           G++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T+GSIT  ++++L+++IL
Sbjct: 121 GVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWTNGSITPSEAISLSAKIL 176


>gi|119668371|emb|CAK95515.1| RNA polymerase alpha subunit [Lactobacillus sakei subsp. carnosus]
          Length = 196

 Score =  170 bits (431), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 83/190 (43%), Positives = 132/190 (69%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           +L++SL G A+T +QIDGVLHE S+I GV ED+T IILNIK + LK+  +  K + I  +
Sbjct: 1   ILLASLPGTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKLHVEEDKTIEIDVK 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  VTA DI + +D+EVLN D  IC +       + +TV KG GYV A  +++++ PIG
Sbjct: 61  GPATVTAADIISDDDVEVLNTDQYICTVAEGGNFHVRMTVKKGRGYVAAVQNKSDDMPIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           ++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++I+ + L 
Sbjct: 121 VLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKIMTEHLA 180

Query: 230 MFINFEEPKK 239
           +F++  +  K
Sbjct: 181 IFVDLTDEAK 190


>gi|282898333|ref|ZP_06306324.1| DNA-directed RNA polymerase, alpha subunit [Raphidiopsis brookii
           D9]
 gi|281196864|gb|EFA71769.1| DNA-directed RNA polymerase, alpha subunit [Raphidiopsis brookii
           D9]
          Length = 314

 Score =  170 bits (431), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 100/296 (33%), Positives = 168/296 (56%), Gaps = 15/296 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG   T+GNALRRVL+S+L G A+TAV+I GV HE +++ GV ED+ +II+ +
Sbjct: 23  FVLEPLERGQGTTVGNALRRVLLSNLEGTAVTAVRIAGVTHEFATVPGVREDVMEIIMRM 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK      +   +   GP  VTA       ++EV++P   +  L     + ME  +
Sbjct: 83  KEVILKSYSHQPQIGRLLVTGPTTVTAAHFDLPGEVEVIDPTQYVATLAEGGKLEMEFRI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY   +  R E   +  + ID+++ P++KV+Y+VE +R    L  D+L + + T+G
Sbjct: 143 ERGKGYRTVEKGREEATSLDFLQIDSVFMPVRKVNYSVEESRGDGSLK-DRLLLEVWTNG 201

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVK---EDINVKSLPFNPALLKKVEELELS 266
           SI+ +++++ ++ IL       +    P K++     D+ +  +P +P     +EEL+LS
Sbjct: 202 SISPQEALSSSAAIL-------VELFNPLKDISLEPTDMGL-DMPDDPTAQIPIEELQLS 253

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           VR+ NCL+   +  + DL+  T+ D+L + NFG+KS  E   V+  +   LG+ LP
Sbjct: 254 VRAYNCLKRAQVNSVADLLDYTQEDLLEIKNFGQKSAEE---VVEALQRRLGITLP 306


>gi|282899976|ref|ZP_06307937.1| DNA-directed RNA polymerase, alpha subunit [Cylindrospermopsis
           raciborskii CS-505]
 gi|281195246|gb|EFA70182.1| DNA-directed RNA polymerase, alpha subunit [Cylindrospermopsis
           raciborskii CS-505]
          Length = 314

 Score =  170 bits (430), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 100/296 (33%), Positives = 168/296 (56%), Gaps = 15/296 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG   T+GNALRRVL+S+L G A+TAV+I GV HE +++ GV ED+ +II+ +
Sbjct: 23  FVLEPLERGQGTTVGNALRRVLLSNLEGTAVTAVRIAGVTHEFATVPGVREDVMEIIMRM 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK      +   +   GP  VTA       ++EV++P   +  L     + ME  +
Sbjct: 83  KEVILKSYSHQPQIGRLLVTGPTTVTAAHFDLPGEVEVIDPTQYVATLAEGGKLEMEFRI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +G GY   +  R E   +  + ID+++ P++KV+Y+VE +R    L  D+L + + T+G
Sbjct: 143 ERGKGYRTVEKGREEATSLDFLQIDSVFMPVRKVNYSVEESRGDGSLK-DRLLLEVWTNG 201

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVK---EDINVKSLPFNPALLKKVEELELS 266
           SI+ +++++ ++ IL       +    P K++     D+ +  +P +P     +EEL+LS
Sbjct: 202 SISPQEALSSSAAIL-------VELFNPLKDISLEPTDMGL-DMPDDPTAQIPIEELQLS 253

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           VR+ NCL+   +  + DL+  T+ D+L + NFG+KS  E   V+  +   LG+ LP
Sbjct: 254 VRAYNCLKRAQVNSVADLLDYTQEDLLEIKNFGQKSAEE---VVEALQRRLGITLP 306


>gi|119668333|emb|CAK95466.1| RNA polymerase alpha subunit [Lactobacillus intestinalis]
          Length = 191

 Score =  170 bits (430), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 83/182 (45%), Positives = 123/182 (67%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           VL++S+ G  +  VQIDGVLHE +++ GV ED+T IILN+K + LK   D  K + +   
Sbjct: 1   VLLTSIPGTGLVYVQIDGVLHEFATVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVE 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  VTA D++   D++VLNPD  IC +     + M++ V  G GYVPA  +++E+ PIG
Sbjct: 61  GPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMQIAVKNGRGYVPASDNKSEDMPIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           +I +D+L+SPIKKV+Y VES R G+  D+DKL++ I TDGSI   D+++ A++IL +   
Sbjct: 121 VIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTLEIWTDGSIKPNDALSFAAKILVEHFK 180

Query: 230 MF 231
           +F
Sbjct: 181 VF 182


>gi|119662833|emb|CAJ33209.1| RNA polymerase alpha subunit [Lactobacillus ingluviei]
          Length = 180

 Score =  170 bits (430), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 86/180 (47%), Positives = 125/180 (69%), Gaps = 1/180 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRV+++SL GAAIT++ IDGVLHE S+++GV ED+T I+LN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRVMLASLPGAAITSIDIDGVLHEFSTVEGVTEDVTQIVLNLKKVA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK+  +  K + +  +GP  VTA DIQ   D+ +LNPD  I  +   A + M +T   G 
Sbjct: 61  LKIESEDAKNLELDVKGPAEVTAADIQADGDVTILNPDLHIATVADGAELHMRMTADTGR 120

Query: 154 GYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           GY  A  ++   D  IG++ ID++Y+PI++V+YTVE+ R GQ  DYDKL++ + TDGS+T
Sbjct: 121 GYNSADVNKARMDLAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYDKLTLDVWTDGSLT 180


>gi|57504893|ref|ZP_00370868.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter coli
           RM2228]
 gi|57019321|gb|EAL56023.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter coli
           RM2228]
          Length = 337

 Score =  170 bits (430), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 98/289 (33%), Positives = 160/289 (55%), Gaps = 5/289 (1%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
           A P   G+  TL + LRR+L +S  G A TA+ IDGV HE  S++G+ ED+   I+N+K 
Sbjct: 28  AWPFEIGYGITLAHPLRRLLYTSTIGYAPTAIHIDGVAHEFDSMRGMLEDVALFIINLKK 87

Query: 92  INLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +  K+  DS+K +  F  +GP  +   D+   + +EV+N D  +  ++ DA ++  L + 
Sbjct: 88  LRFKLKSDSNKEIVEFSFKGPKEIYGKDLNN-DQVEVVNTDAYLATINEDAELKFTLIIE 146

Query: 151 KGHGYVPAKH-HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           KG GYVP++      NDP   I +DA ++P+++ +Y +E        DY+K+ +T+ TDG
Sbjct: 147 KGIGYVPSEEIKELLNDP-KFIALDAFFTPVREATYDIEKVLFEDNPDYEKVVLTVTTDG 205

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
            IT  ++   A   +  QL +F      +  +K       L  N  LL+ + +L LS RS
Sbjct: 206 QITPNEAFQNALEAMYKQLSVFDKITNVRSIIKSQATSNELE-NTKLLQNITDLNLSARS 264

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            NCL    IVY+G+L   +  ++  + N G+KSL EIK ++ ++G  +G
Sbjct: 265 YNCLEKAGIVYIGELALMSVNELAGLKNLGKKSLDEIKSIMESIGFPVG 313


>gi|150187144|emb|CAK30180.1| RNA polymerase alpha subunit [Streptococcus phocae]
          Length = 204

 Score =  170 bits (430), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 83/190 (43%), Positives = 131/190 (68%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           VL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   
Sbjct: 1   VLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKTIELEVE 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  VTAGDI T +DIE++NPDH +  +     +R  +TV+K  GYVPA+ ++ ++ P+G
Sbjct: 61  GPATVTAGDILTDSDIELVNPDHYLFTIAEGHSLRATMTVAKKRGYVPAEGNKKDDAPVG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L 
Sbjct: 121 TLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTVEIMTNGTIIPEDALGLSARVLIEHLN 180

Query: 230 MFINFEEPKK 239
           +F +  +  K
Sbjct: 181 LFTDLTDVAK 190


>gi|154424827|emb|CAL18516.1| RNA polymerase alpha subunit [Streptococcus parasanguinis]
          Length = 194

 Score =  170 bits (430), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 83/187 (44%), Positives = 127/187 (67%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           VL++SL GAA+T++ I+GVLHE  ++ GV ED+  IILN+KGI +K      K + +   
Sbjct: 1   VLLASLPGAAVTSINIEGVLHEFDTVPGVREDVMQIILNVKGIAVKSYVQDEKIIELDVE 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  VTAGDI T +DIE++NPDH +  +   A ++  LTV+ G GYVPA  ++ ++ P+G
Sbjct: 61  GPAEVTAGDILTDSDIEIVNPDHYLFTIGEGASLKATLTVNSGRGYVPADQNKKDDAPVG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L 
Sbjct: 121 TLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLN 180

Query: 230 MFINFEE 236
           +F N  E
Sbjct: 181 LFTNLTE 187


>gi|151416836|emb|CAO78489.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gelidum]
          Length = 193

 Score =  170 bits (430), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 88/192 (45%), Positives = 128/192 (66%), Gaps = 2/192 (1%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  
Sbjct: 2   TLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLXIDSDEE 61

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           + + +  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  +
Sbjct: 62  RSLEVDIQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTITAFKGRGYSSADEN 121

Query: 162 RTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           +   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L
Sbjct: 122 KQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSL 181

Query: 220 ASRILQDQLGMF 231
            S+IL + L +F
Sbjct: 182 GSKILAEHLNLF 193


>gi|86149413|ref|ZP_01067644.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni CF93-6]
 gi|88596039|ref|ZP_01099276.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni 84-25]
 gi|218563184|ref|YP_002344964.1| DNA-directed RNA polymerase subunit alpha [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|12230603|sp|Q9PM80|RPOA_CAMJE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|85840195|gb|EAQ57453.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni CF93-6]
 gi|88190880|gb|EAQ94852.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni 84-25]
 gi|112360891|emb|CAL35692.1| DNA-directed RNA polymerase alpha chain [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|284926790|gb|ADC29142.1| DNA-directed RNA polymerase alpha chain [Campylobacter jejuni
           subsp. jejuni IA3902]
 gi|315927659|gb|EFV06990.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni DFVF1099]
 gi|315929466|gb|EFV08663.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni 305]
          Length = 337

 Score =  170 bits (430), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 98/289 (33%), Positives = 162/289 (56%), Gaps = 5/289 (1%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
           A P   G+  TL + LRR+L +S  G A TA+ IDGV HE  S++G+ ED+   I+N+K 
Sbjct: 28  AWPFEIGYGITLAHPLRRLLYTSTIGYAPTAIHIDGVAHEFDSMRGMLEDVALFIINLKK 87

Query: 92  INLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +  K+ GDS+K +  F  +G   +   D+   + +EV+N D  +  ++ DA ++  L V 
Sbjct: 88  LRFKIKGDSNKEIVEFSFKGSKEIYGKDLNN-DQVEVVNKDAYLATINEDAELKFTLIVE 146

Query: 151 KGHGYVPAKHHRTE-NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           KG GYVP++  +   NDP   I +DA ++P+++ +Y +E        DY+K+ +T+ TDG
Sbjct: 147 KGIGYVPSEEIKELINDP-KFIALDAFFTPVREATYDIEKVLFEDNPDYEKVVLTVTTDG 205

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
            IT  ++   A   +  QL +F      +  +K       L  N  LL+ + +L LS RS
Sbjct: 206 QITPNEAFQNALEAMYKQLSVFDKITNVRSVIKNQATSNELE-NTKLLQNITDLNLSARS 264

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            NCL    +VY+G+L   + +++  + N G+KSL EIK ++ ++G  +G
Sbjct: 265 YNCLEKAGVVYIGELALMSVSELAGLKNLGKKSLDEIKNIMESIGFPVG 313


>gi|149179437|ref|ZP_01857991.1| DNA-directed RNA polymerase subunit alpha [Planctomyces maris DSM
           8797]
 gi|148841748|gb|EDL56157.1| DNA-directed RNA polymerase subunit alpha [Planctomyces maris DSM
           8797]
          Length = 208

 Score =  169 bits (429), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 85/200 (42%), Positives = 129/200 (64%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
           + +AEP  RGF  T+ N+LRR+L+SSL G+++T V+I GV HE ++I GV ED+T+I LN
Sbjct: 7   MFVAEPFERGFGATIANSLRRILLSSLEGSSVTRVKIQGVQHEFTTIPGVVEDITEICLN 66

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           +K + +K S  + K + I K   GVVT  D+ T + +EV+N D VI  +  D  + MELT
Sbjct: 67  LKSLIVKNSSSTSKTLRIEKHERGVVTGADVITDDQVEVINKDLVIATMTDDVPLNMELT 126

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           +  G GY PA  H   +  +G+I +DA +SP+ +V Y +E  R GQ  +YDKL + I T+
Sbjct: 127 IENGRGYSPASEHAQHDSEVGVIPLDATFSPVVRVRYKIEDTRVGQRTNYDKLILEIWTN 186

Query: 209 GSITGEDSVALASRILQDQL 228
           G++  + ++  AS+IL+  L
Sbjct: 187 GTVKPDMALVEASKILRKHL 206


>gi|119662305|emb|CAJ33140.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           lactis]
          Length = 214

 Score =  169 bits (429), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 85/193 (44%), Positives = 125/193 (64%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  V+IDG+LHE +++ GV ED+T IILN+K + L+   
Sbjct: 1   FGTTLGNSLRRVLLTSVPGTGLVKVKIDGILHEFTTVPGVKEDVTKIILNLKKLVLRAYT 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + +   GP  VTA D++   D+EVLNPD  IC +     + M + V  G GYVPA
Sbjct: 61  EEVKTIELDVEGPATVTAEDLKADADVEVLNPDQYICTIAQGGHLHMWIDVCNGRGYVPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++T    IG I +D+L+SPI+KV+Y VES R G+  D+DKL++ I T+GSI   D++ 
Sbjct: 121 SENKTAEMFIGDIPVDSLFSPIEKVNYQVESTRVGKREDFDKLTLEIWTNGSIAPNDALN 180

Query: 219 LASRILQDQLGMF 231
            A+R+L +    F
Sbjct: 181 FAARVLVEHFKAF 193


>gi|332184519|gb|AEE26773.1| DNA-directed RNA polymerase alpha subunit [Francisella cf. novicida
           3523]
          Length = 318

 Score =  169 bits (429), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 104/321 (32%), Positives = 181/321 (56%), Gaps = 11/321 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI- 65
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I 
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKIN 60

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVND 124
           DG +  +  +    E + DIILN+K + + ++      +  F+  G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLPVTLAEGVETGIITFELSGSEEEIFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG G+ PA+    +N   G   +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQ----DNFKDGEFLLDATFSPVVFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +  +
Sbjct: 177 FEIKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGIFVE 236

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              K +  NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL 
Sbjct: 237 DPTKDI--NPILLKHVEELNLTARSSNCLKAVNIKLIGELVQKTENELLKAPNFGKKSLT 294

Query: 305 EIKGVLGTMGLFLGMNLPDWP 325
           EIK  L  + L LG  + +WP
Sbjct: 295 EIKDKLSELSLSLGTIIENWP 315


>gi|161511725|emb|CAP16873.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           acidilactici]
          Length = 199

 Score =  169 bits (429), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 90/189 (47%), Positives = 125/189 (66%), Gaps = 2/189 (1%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           +L+SSL GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++LK+  D  K + I   
Sbjct: 9   ILLSSLPGAAITSVQIDNVLHEFSTIEGVVEDVTQIILNLKKVSLKIESDDEKTLDINVV 68

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDP 167
           GP  VTAGDI    D+ VLNPD  IC +         LT   G GY  A  +  R  + P
Sbjct: 69  GPANVTAGDIMGDGDVTVLNPDSPICTVAEGTTFHAVLTADTGRGYTSADENKARKADMP 128

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           IG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ I TDGSIT  ++ +L+++IL + 
Sbjct: 129 IGVLPIDSIYTPIERVNYQVEKTRVGQRDDYDKLTLDIWTDGSITPSEATSLSAKILTEH 188

Query: 228 LGMFINFEE 236
           L +F+N  +
Sbjct: 189 LAIFVNLND 197


>gi|150036728|emb|CAM98255.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 194

 Score =  169 bits (428), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 88/194 (45%), Positives = 129/194 (66%), Gaps = 2/194 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A
Sbjct: 61  DDERSLEIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSA 120

Query: 159 KHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+
Sbjct: 121 DENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTNGSIKPSDA 180

Query: 217 VALASRILQDQLGM 230
           ++L ++IL + LG+
Sbjct: 181 LSLGAKILAEHLGL 194


>gi|159027085|emb|CAO89270.1| rpoA [Microcystis aeruginosa PCC 7806]
          Length = 313

 Score =  169 bits (428), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 99/296 (33%), Positives = 164/296 (55%), Gaps = 13/296 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG   T+GNALRR+L+S+L GAA+TA++I GV HE ++++GV ED+ +++LN+
Sbjct: 23  FVLEPLERGQGTTVGNALRRILISNLEGAAVTALRIAGVNHEFATVEGVREDVMELMLNM 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK   +  +   +   GP  V A      +++E+++ +  +  L   A + ME  V
Sbjct: 83  KEITLKSYTNQTQIGRLVATGPATVVAAQFDLPSEVEIVDRNQYVATLAEGAKLEMEFRV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GY      + E   +  + ID+++ P+ KV+Y+VE  R       D+L + I T+G
Sbjct: 143 EKGKGYRAIDRSKEEATSLDFLQIDSIFMPVTKVNYSVEDIRSESGQARDRLLLEIWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALLKKVEELELS 266
           SI  +++++ A+        M +N   P K+   ++   N      N      +EEL+LS
Sbjct: 203 SINPKEALSQAA-------DMLVNLFNPLKDLNALESSGNFDDQEINQENQIPIEELQLS 255

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           VR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E   V+  +   LG+ LP
Sbjct: 256 VRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEE---VIEALQKRLGITLP 308


>gi|313680487|ref|YP_004058226.1| DNA-directed RNA polymerase subunit alpha [Oceanithermus profundus
           DSM 14977]
 gi|313153202|gb|ADR37053.1| DNA-directed RNA polymerase subunit alpha [Oceanithermus profundus
           DSM 14977]
          Length = 322

 Score =  169 bits (428), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 115/305 (37%), Positives = 166/305 (54%), Gaps = 12/305 (3%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           E N    + EPL RGF  TLGN LRR+LMSS+ G A+T+V I+  LHE +++ G+ ED+ 
Sbjct: 17  EGNYGEFVLEPLERGFGVTLGNPLRRILMSSIPGTAVTSVYIEDALHEFATLPGIKEDVV 76

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            I+LN+K + +K      K + +   GP  V A D+   +  E++NPD  I  L   A +
Sbjct: 77  QIVLNLKELIVKFHEPGSKTLLLRVEGPREVYARDLVVPSSAELVNPDLYIATLGEGAKL 136

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            ME+ V +G GYV A+ H  + D I  I +DAL+SPIK+V++ VE  R GQ  D DKL +
Sbjct: 137 VMEVRVDEGVGYVAAEKHGIK-DRINSIPVDALFSPIKRVAFHVEDTRLGQRTDLDKLIL 195

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK----- 258
            I TDGS+T + ++A A  IL+ QLG F           E     +    PA  +     
Sbjct: 196 RIWTDGSVTPDAALAQAVEILRGQLGYFDQLAPQAAPEPEAAEAPAPEAAPAEPEEAAAE 255

Query: 259 ------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                  +E+L LS R  + LR E I  + +L   TE ++ ++   G +S+ EIK  L  
Sbjct: 256 PGREGIALEDLGLSTRVLHNLREEGIDSVANLTALTERELKKVPGIGERSVEEIKERLAA 315

Query: 313 MGLFL 317
           +GL L
Sbjct: 316 LGLAL 320


>gi|222823139|ref|YP_002574712.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter lari
           RM2100]
 gi|222538360|gb|ACM63461.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter lari
           RM2100]
          Length = 337

 Score =  169 bits (428), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 104/303 (34%), Positives = 164/303 (54%), Gaps = 7/303 (2%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
           A P   G+A TL + LRR+L SS  G A T V+I GV HE  S++G+ ED+   I+N+K 
Sbjct: 28  AWPFEIGYAITLAHPLRRLLYSSTVGFAPTGVKIKGVAHEFDSMRGMLEDVALFIINLKK 87

Query: 92  INLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVND-IEVLNPDHVICNLDVDAVVRMELTV 149
           +  K+  DS K +  F  +GP  +   D+   ND +EV+N D  +  ++ DA +   L +
Sbjct: 88  LRFKLKTDSEKEIVTFSFKGPKEICGKDLD--NDVVEVVNADSYLATINEDADLEFTLII 145

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYVP++  +   DP   I +DA ++P+K   Y +E        DY+K+  TI TDG
Sbjct: 146 EKGIGYVPSEEVQNFLDP-EFIALDAFFTPVKHAVYDIEKVLFEDNPDYEKVVFTITTDG 204

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
            I+  D+   A   +  QL +F      +  V+       +  +  LL+ + EL L  RS
Sbjct: 205 QISPSDAFKNALEAMYKQLSVFDKITNAQSVVRSQTQNNEVE-HVKLLQNITELNLGARS 263

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN-LPDWPPES 328
            NCL   N+VY+G+L     +++  + N G+KSL EIK V+ ++G  +G + L D   E+
Sbjct: 264 FNCLEKANVVYIGELALMNASELADLKNLGKKSLDEIKSVMESIGFPIGNSKLSDSAKET 323

Query: 329 IEE 331
           +++
Sbjct: 324 LKK 326


>gi|119662391|emb|CAJ33185.1| RNA polymerase alpha subunit [Lactobacillus amylophilus]
          Length = 174

 Score =  169 bits (427), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 82/174 (47%), Positives = 123/174 (70%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           +LRRVL++SL G+A++ +QIDGVLHE S+I GV ED+T IILN+K + LK      K   
Sbjct: 1   SLRRVLLASLPGSAVSYLQIDGVLHEFSTIPGVLEDVTQIILNLKKLTLKSIAADEKLAE 60

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
           I   GP  VTAGD++  +++++LNPD  I  +   A +RM + + +G GYVPA  +++++
Sbjct: 61  IDVEGPATVTAGDLKVDDEVQILNPDQYIATVAEGAHLRMTVAIKQGRGYVPADQNKSDD 120

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
            PIG++ +D+L+SPI+KV+Y VE  R G+  DYDKL+M + TDGSIT  D+++ 
Sbjct: 121 MPIGVVPVDSLFSPIEKVNYQVEGTRVGRNNDYDKLTMEVWTDGSITPNDALSF 174


>gi|166367995|ref|YP_001660268.1| DNA-directed RNA polymerase subunit alpha [Microcystis aeruginosa
           NIES-843]
 gi|166090368|dbj|BAG05076.1| RNA polymerase alpha subunit [Microcystis aeruginosa NIES-843]
          Length = 313

 Score =  169 bits (427), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 99/296 (33%), Positives = 164/296 (55%), Gaps = 13/296 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG   T+GNALRR+L+S+L GAA+TA++I GV HE ++++GV ED+ +++LN+
Sbjct: 23  FVLEPLERGQGTTVGNALRRILISNLEGAAVTALRIAGVNHEFATVQGVREDVMELMLNM 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK   +  +   +   GP  V A      +++E+++ +  +  L   A + ME  V
Sbjct: 83  KEIILKSYTNQTQIGRLVATGPATVVAAQFDLPSEVEIVDRNQYVATLAEGAKLEMEFRV 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GY      + E   +  + ID+++ P+ KV+Y+VE  R       D+L + I T+G
Sbjct: 143 EKGKGYRAIDRSKDEATSLDFLQIDSIFMPVTKVNYSVEDIRSESGQARDRLLLEIWTNG 202

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALLKKVEELELS 266
           SI  +++++ A+        M +N   P K+   ++   N      N      +EEL+LS
Sbjct: 203 SINPKEALSQAA-------DMLVNLFNPLKDLNALESSSNFDDQEINQENQIPIEELQLS 255

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           VR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E   V+  +   LG+ LP
Sbjct: 256 VRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEE---VIEALQKRLGITLP 308


>gi|154424837|emb|CAL18521.1| RNA polymerase alpha subunit [Streptococcus pluranimalium]
          Length = 204

 Score =  169 bits (427), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 83/193 (43%), Positives = 132/193 (68%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ +K   +  K + +
Sbjct: 1   LRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNVKGLAVKSYVEDEKIIEL 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
             +GP  VTAGDI T +DIE++N DH +  +   A  +  +TV+   GYV A+ ++ ++ 
Sbjct: 61  DVQGPAEVTAGDILTDSDIEIVNSDHYLFTIAEGASFKASMTVATNRGYVAAEGNKKDDA 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L +
Sbjct: 121 PVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTVEIMTNGTIIPEDALGLSARVLIE 180

Query: 227 QLGMFINFEEPKK 239
            L +F +  E  K
Sbjct: 181 HLNLFTDLTEVAK 193


>gi|121489391|emb|CAJ44676.1| RNA polymerase alpha subunit [Carnobacterium maltaromaticum]
 gi|145586275|emb|CAM91232.1| RNA polymerase alpha-subunit [Carnobacterium maltaromaticum]
          Length = 199

 Score =  169 bits (427), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 81/183 (44%), Positives = 127/183 (69%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T +QIDGVLHE S+I GV ED+T IILNIK + LK+     K + I  +GP VVTA DI
Sbjct: 1   VTTIQIDGVLHEFSTIDGVVEDVTSIILNIKKLALKLYSGEDKTIEIDVKGPAVVTAADI 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
              +D+E+LNPD  IC +   A   + LT  +G GY  A+H++ ++ PIG++ +D++Y+P
Sbjct: 61  TYDSDVEILNPDLYICTVAEGARFHVRLTAKQGRGYARAEHNKHDDMPIGVLPVDSIYTP 120

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           + +V+Y VE+ R GQ  ++DKL++ +  DGSI+ ED+V+LA++IL + L +F+N  +  +
Sbjct: 121 VSRVNYQVENTRVGQKDNFDKLTLDVWADGSISPEDAVSLAAKILTEHLDIFVNLSDEAR 180

Query: 240 EVK 242
           +V+
Sbjct: 181 KVE 183


>gi|270265493|emb|CBI68383.1| RNA polymerase alpha-subunit [Vibrio tapetis]
          Length = 200

 Score =  168 bits (426), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 87/203 (42%), Positives = 132/203 (65%), Gaps = 7/203 (3%)

Query: 114 VTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIG 169
           V AGDI    D+E+ NP+HVIC+L D +A + M + V +G GYVPA    H   +  PIG
Sbjct: 1   VVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASSRIHTEEDERPIG 60

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  ++ IL +QL 
Sbjct: 61  RLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRSATILAEQLD 120

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
            F++  + +   +     +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 121 AFVDLRDIRVPEE---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 177

Query: 290 ADMLRMANFGRKSLVEIKGVLGT 312
            ++L+  N G KSL EIK VL +
Sbjct: 178 VELLKTPNLGNKSLTEIKDVLAS 200


>gi|119662831|emb|CAJ33208.1| RNA polymerase alpha subunit [Lactobacillus mucosae]
          Length = 180

 Score =  168 bits (426), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 87/173 (50%), Positives = 124/173 (71%), Gaps = 2/173 (1%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRRV+M+SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K ++LK+  +  
Sbjct: 3   TLGNSLRRVMMASLPGAAITSIQIDGVLHEFSTVQGVTEDVTQIILNLKKVSLKIESEDA 62

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + +  +GP  VTAGDIQ   D+ +LNPD  I  +   A + + +T  KG GYVPA  +
Sbjct: 63  KDLELDVKGPAEVTAGDIQGDGDVTILNPDLHIATVADGAELHIMMTADKGRGYVPADQN 122

Query: 162 --RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
             R     IG + ID++Y+PI++V+YTVE+ R GQ  D+DKL++ + TDGS+T
Sbjct: 123 KLRLSGLEIGTLPIDSIYTPIERVNYTVENTRVGQSNDFDKLTLDVWTDGSLT 175


>gi|150036804|emb|CAM98275.1| DNA-directed RNA polymerase alpha chain [Fructobacillus
           pseudoficulneus]
          Length = 230

 Score =  168 bits (426), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 94/230 (40%), Positives = 140/230 (60%), Gaps = 2/230 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL+SSL G A+  VQIDGV+HE S++ GV ED+T +ILN+K +      
Sbjct: 1   YGTTLGNSLRRVLLSSLPGVAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVVFATDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
                + I  +GP  VTA D+    DIEVLNPD  I  L     + M +T  KG GY  A
Sbjct: 61  AEEHALEIDVQGPKDVTAADLMGSADIEVLNPDLHIATLAAGKSLHMTVTAVKGRGYSSA 120

Query: 159 KHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
           + ++   D  PIG++T+D++Y+PI++V+Y VE+ R G   DYDKL+M + T+GSI   D+
Sbjct: 121 EENKQLRDEMPIGVLTVDSIYTPIERVNYHVENKRVGSRDDYDKLTMEVWTNGSIKPSDA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           ++L S+IL + L +F +     ++ K  +  +      A    +E+L+LS
Sbjct: 181 LSLGSKILTEHLNLFTDISPVAQDTKVMVESEPAANTAADAAPIEDLDLS 230


>gi|71056955|emb|CAH59038.1| DNA-directed RNA polymerase alpha chain [Enterococcus avium]
          Length = 177

 Score =  168 bits (426), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 83/176 (47%), Positives = 121/176 (68%)

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T +QIDGVLHE S+IKGV ED+  IILNIKG+ LK+  +  K + I   GP  VTAGDI 
Sbjct: 1   TNIQIDGVLHEFSTIKGVREDVVQIILNIKGLALKLFAEEEKTLEIDITGPATVTAGDII 60

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             +D+E+LN D  IC +   A     LTV  G GYV A  ++ E+ PIG++ +D++Y+P+
Sbjct: 61  VDSDVEILNKDMYICTVAEGATFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPV 120

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +KV+Y VE+ R G+  D+DKL+M I TDGSI  +++++LA++IL + L +F+N  +
Sbjct: 121 RKVNYQVENTRVGRRDDFDKLTMEIWTDGSIIAQEALSLAAKILTEHLDIFVNLTD 176


>gi|283953793|ref|ZP_06371324.1| DNA-directed RNA polymerase alpha chain [Campylobacter jejuni
           subsp. jejuni 414]
 gi|283794834|gb|EFC33572.1| DNA-directed RNA polymerase alpha chain [Campylobacter jejuni
           subsp. jejuni 414]
          Length = 337

 Score =  168 bits (426), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 96/289 (33%), Positives = 160/289 (55%), Gaps = 5/289 (1%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
           A P   G+  TL + LRR+L +S  G A TA+ IDGV HE  S++G+ ED+   I+N+K 
Sbjct: 28  AWPFEIGYGITLAHPLRRLLYTSTIGYAPTAIHIDGVAHEFDSMRGMLEDVALFIINLKK 87

Query: 92  INLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +  K+ GDS+K +  F  +G   +   D+   + +EV+N D  +  ++ D  ++  L + 
Sbjct: 88  LRFKIKGDSNKEIVEFNFKGSKEIYGKDLNN-DQVEVVNKDAYLATINEDTELKFTLIIE 146

Query: 151 KGHGYVPAKH-HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           KG GYVP++      NDP   I +DA ++P+++ +Y +E        DY+K+ +T+ TDG
Sbjct: 147 KGIGYVPSEEIKELLNDP-KFIALDAFFTPVREATYDIEKVLFEDNPDYEKVVLTVTTDG 205

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
            IT  ++   A   +  QL +F      +  +K       L  N  LL+ + +L LS RS
Sbjct: 206 QITPNEAFQNALEAMYKQLSVFDKITNVRSAIKNQATSNELE-NTKLLQNITDLNLSARS 264

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            NCL    +VY+G+L   + +++  + N G+KSL EIK ++ ++G  +G
Sbjct: 265 YNCLEKAGVVYIGELALMSVSELAGLKNLGKKSLDEIKNIMESIGFPVG 313


>gi|150187022|emb|CAK30153.1| RNA polymerase alpha subunit [Streptococcus thoraltensis]
          Length = 184

 Score =  168 bits (425), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 82/184 (44%), Positives = 129/184 (70%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ +K   
Sbjct: 1   YGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNVKGLAVKSYV 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + +  +GP  VTAGDI T +DIE++N DH +  +   A  +  +TV+   GYV A
Sbjct: 61  EDEKIIELDVQGPAEVTAGDILTDSDIEIVNSDHYLFTIAEGASFKASMTVATNRGYVAA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           + ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ 
Sbjct: 121 EGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALG 180

Query: 219 LASR 222
           L++R
Sbjct: 181 LSAR 184


>gi|46199602|ref|YP_005269.1| DNA-directed RNA polymerase subunit alpha [Thermus thermophilus
           HB27]
 gi|55981633|ref|YP_144930.1| DNA-directed RNA polymerase subunit alpha [Thermus thermophilus
           HB8]
 gi|7388103|sp|Q9Z9H6|RPOA_THETH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61215969|sp|Q72I32|RPOA_THET2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|66773873|sp|Q5SHR6|RPOA_THET8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|7434691|pir||JE0397 DNA-directed RNA polymerase (EC 2.7.7.6) alpha chain - Thermus
           aquaticus (strain HB8)
 gi|21730337|pdb|1IW7|A Chain A, Crystal Structure Of The Rna Polymerase Holoenzyme From
           Thermus Thermophilus At 2.6a Resolution
 gi|21730338|pdb|1IW7|B Chain B, Crystal Structure Of The Rna Polymerase Holoenzyme From
           Thermus Thermophilus At 2.6a Resolution
 gi|21730343|pdb|1IW7|K Chain K, Crystal Structure Of The Rna Polymerase Holoenzyme From
           Thermus Thermophilus At 2.6a Resolution
 gi|21730344|pdb|1IW7|L Chain L, Crystal Structure Of The Rna Polymerase Holoenzyme From
           Thermus Thermophilus At 2.6a Resolution
 gi|49259055|pdb|1SMY|A Chain A, Structural Basis For Transcription Regulation By Alarmone
           Ppgpp
 gi|49259056|pdb|1SMY|B Chain B, Structural Basis For Transcription Regulation By Alarmone
           Ppgpp
 gi|49259061|pdb|1SMY|K Chain K, Structural Basis For Transcription Regulation By Alarmone
           Ppgpp
 gi|49259062|pdb|1SMY|L Chain L, Structural Basis For Transcription Regulation By Alarmone
           Ppgpp
 gi|78101157|pdb|1ZYR|A Chain A, Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Streptolydigin
 gi|78101158|pdb|1ZYR|B Chain B, Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Streptolydigin
 gi|78101163|pdb|1ZYR|K Chain K, Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Streptolydigin
 gi|78101164|pdb|1ZYR|L Chain L, Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Streptolydigin
 gi|78101219|pdb|2A68|A Chain A, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifabutin
 gi|78101220|pdb|2A68|B Chain B, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifabutin
 gi|78101225|pdb|2A68|K Chain K, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifabutin
 gi|78101226|pdb|2A68|L Chain L, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifabutin
 gi|78101231|pdb|2A69|A Chain A, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifapentin
 gi|78101232|pdb|2A69|B Chain B, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifapentin
 gi|78101237|pdb|2A69|K Chain K, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifapentin
 gi|78101238|pdb|2A69|L Chain L, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifapentin
 gi|78101243|pdb|2A6E|A Chain A, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme
 gi|78101244|pdb|2A6E|B Chain B, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme
 gi|78101249|pdb|2A6E|K Chain K, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme
 gi|78101250|pdb|2A6E|L Chain L, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme
 gi|78101255|pdb|2A6H|A Chain A, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Sterptolydigin
 gi|78101256|pdb|2A6H|B Chain B, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Sterptolydigin
 gi|78101261|pdb|2A6H|K Chain K, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Sterptolydigin
 gi|78101262|pdb|2A6H|L Chain L, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Sterptolydigin
 gi|78101757|pdb|2CW0|A Chain A, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme At 3.3 Angstroms Resolution
 gi|78101758|pdb|2CW0|B Chain B, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme At 3.3 Angstroms Resolution
 gi|78101763|pdb|2CW0|K Chain K, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme At 3.3 Angstroms Resolution
 gi|78101764|pdb|2CW0|L Chain L, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme At 3.3 Angstroms Resolution
 gi|83754372|pdb|2BE5|A Chain A, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Inhibitor Tagetitoxin
 gi|83754373|pdb|2BE5|B Chain B, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Inhibitor Tagetitoxin
 gi|83754378|pdb|2BE5|K Chain K, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Inhibitor Tagetitoxin
 gi|83754379|pdb|2BE5|L Chain L, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Inhibitor Tagetitoxin
 gi|151567769|pdb|2O5I|A Chain A, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Elongation Complex
 gi|151567770|pdb|2O5I|B Chain B, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Elongation Complex
 gi|151567774|pdb|2O5I|K Chain K, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Elongation Complex
 gi|151567775|pdb|2O5I|L Chain L, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Elongation Complex
 gi|151567785|pdb|2O5J|A Chain A, Crystal Structure Of The T. Thermophilus Rnap Polymerase
           Elongation Complex With The Ntp Substrate Analog
 gi|151567786|pdb|2O5J|B Chain B, Crystal Structure Of The T. Thermophilus Rnap Polymerase
           Elongation Complex With The Ntp Substrate Analog
 gi|151567790|pdb|2O5J|K Chain K, Crystal Structure Of The T. Thermophilus Rnap Polymerase
           Elongation Complex With The Ntp Substrate Analog
 gi|151567791|pdb|2O5J|L Chain L, Crystal Structure Of The T. Thermophilus Rnap Polymerase
           Elongation Complex With The Ntp Substrate Analog
 gi|152149351|pdb|2PPB|A Chain A, Crystal Structure Of The T. Thermophilus Rnap Polymerase
           Elongation Complex With The Ntp Substrate Analog And
           Antibiotic Streptolydigin
 gi|152149352|pdb|2PPB|B Chain B, Crystal Structure Of The T. Thermophilus Rnap Polymerase
           Elongation Complex With The Ntp Substrate Analog And
           Antibiotic Streptolydigin
 gi|152149356|pdb|2PPB|K Chain K, Crystal Structure Of The T. Thermophilus Rnap Polymerase
           Elongation Complex With The Ntp Substrate Analog And
           Antibiotic Streptolydigin
 gi|152149357|pdb|2PPB|L Chain L, Crystal Structure Of The T. Thermophilus Rnap Polymerase
           Elongation Complex With The Ntp Substrate Analog And
           Antibiotic Streptolydigin
 gi|209447473|pdb|3DXJ|A Chain A, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Myxopyronin
 gi|209447474|pdb|3DXJ|B Chain B, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Myxopyronin
 gi|209447479|pdb|3DXJ|K Chain K, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Myxopyronin
 gi|209447480|pdb|3DXJ|L Chain L, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Myxopyronin
 gi|210061064|pdb|3EQL|A Chain A, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Myxopyronin
 gi|210061065|pdb|3EQL|B Chain B, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Myxopyronin
 gi|210061070|pdb|3EQL|K Chain K, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Myxopyronin
 gi|210061071|pdb|3EQL|L Chain L, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Myxopyronin
 gi|313754163|pdb|3AOH|A Chain A, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
 gi|313754164|pdb|3AOH|B Chain B, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
 gi|313754168|pdb|3AOH|F Chain F, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
 gi|313754169|pdb|3AOH|G Chain G, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
 gi|313754173|pdb|3AOH|K Chain K, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
 gi|313754174|pdb|3AOH|L Chain L, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
 gi|313754183|pdb|3AOI|A Chain A, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
 gi|313754184|pdb|3AOI|B Chain B, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
 gi|313754188|pdb|3AOI|F Chain F, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
 gi|313754189|pdb|3AOI|G Chain G, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
 gi|313754193|pdb|3AOI|K Chain K, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
 gi|313754194|pdb|3AOI|L Chain L, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
 gi|4519423|dbj|BAA75549.1| RNA polymerase alpha subunit [Thermus thermophilus]
 gi|46197228|gb|AAS81642.1| DNA-directed RNA polymerase alpha chain [Thermus thermophilus HB27]
 gi|55773046|dbj|BAD71487.1| DNA-directed RNA polymerase alpha chain [Thermus thermophilus HB8]
          Length = 315

 Score =  168 bits (425), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 91/206 (44%), Positives = 133/206 (64%), Gaps = 3/206 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED+ +IILN+
Sbjct: 23  FVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKR--GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K + ++    S + VT+  +  GP  V A D   V D+E++NPD  I  L+    + ME+
Sbjct: 83  KELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIMNPDLHIATLEEGGRLNMEV 142

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            V +G GYVPA+ H  + D I  I +DA++SP+++V++ VE  R GQ  D DKL++ I T
Sbjct: 143 RVDRGVGYVPAEKHGIK-DRINAIPVDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWT 201

Query: 208 DGSITGEDSVALASRILQDQLGMFIN 233
           DGS+T  +++  A  IL++ L  F N
Sbjct: 202 DGSVTPLEALNQAVEILREHLTYFSN 227


>gi|57238608|ref|YP_179739.1| DNA-directed RNA polymerase subunit alpha [Campylobacter jejuni
           RM1221]
 gi|86152271|ref|ZP_01070482.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni 260.94]
 gi|86152503|ref|ZP_01070708.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni HB93-13]
 gi|121612721|ref|YP_001001238.1| DNA-directed RNA polymerase subunit alpha [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|157415815|ref|YP_001483071.1| DNA-directed RNA polymerase subunit alpha [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|167006131|ref|ZP_02271889.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|205355609|ref|ZP_03222379.1| DNA-directed RNA polymerase alpha chain [Campylobacter jejuni
           subsp. jejuni CG8421]
 gi|315125003|ref|YP_004067007.1| DNA-directed RNA polymerase alpha subunit [Campylobacter jejuni
           subsp. jejuni ICDCCJ07001]
 gi|73621841|sp|Q5HSJ6|RPOA_CAMJR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158513890|sp|A1W1J7|RPOA_CAMJJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172047194|sp|A8FNQ7|RPOA_CAMJ8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|57167412|gb|AAW36191.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           RM1221]
 gi|85840760|gb|EAQ58011.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni 260.94]
 gi|85843388|gb|EAQ60598.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni HB93-13]
 gi|87249974|gb|EAQ72933.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|157386779|gb|ABV53094.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|205346386|gb|EDZ33019.1| DNA-directed RNA polymerase alpha chain [Campylobacter jejuni
           subsp. jejuni CG8421]
 gi|307748452|gb|ADN91722.1| DNA-directed RNA polymerase subunit alpha [Campylobacter jejuni
           subsp. jejuni M1]
 gi|315018725|gb|ADT66818.1| DNA-directed RNA polymerase alpha subunit [Campylobacter jejuni
           subsp. jejuni ICDCCJ07001]
 gi|315059046|gb|ADT73375.1| DNA-directed RNA polymerase alpha subunit [Campylobacter jejuni
           subsp. jejuni S3]
 gi|315931274|gb|EFV10244.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni 327]
          Length = 337

 Score =  168 bits (425), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 97/289 (33%), Positives = 162/289 (56%), Gaps = 5/289 (1%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
           A P   G+  TL + LRR+L +S  G A TA+ IDGV HE  S++G+ ED+   I+N+K 
Sbjct: 28  AWPFEIGYGITLAHPLRRLLYTSTIGYAPTAIHIDGVAHEFDSMRGMLEDVALFIINLKK 87

Query: 92  INLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +  K+ G+S+K +  F  +G   +   D+   + +EV+N D  +  ++ DA ++  L V 
Sbjct: 88  LRFKIKGESNKEIVEFSFKGSKEIYGKDLNN-DQVEVVNKDAYLATINEDAELKFTLIVE 146

Query: 151 KGHGYVPAKHHRTE-NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           KG GYVP++  +   NDP   I +DA ++P+++ +Y +E        DY+K+ +T+ TDG
Sbjct: 147 KGIGYVPSEEIKELINDP-KFIALDAFFTPVREATYDIEKVLFEDNPDYEKVVLTVTTDG 205

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
            IT  ++   A   +  QL +F      +  +K       L  N  LL+ + +L LS RS
Sbjct: 206 QITPNEAFQNALEAMYKQLSVFDKITNVRSVIKNQATSNELE-NTKLLQNITDLNLSARS 264

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            NCL    +VY+G+L   + +++  + N G+KSL EIK ++ ++G  +G
Sbjct: 265 YNCLEKAGVVYIGELALMSVSELAGLKNLGKKSLDEIKNIMESIGFPVG 313


>gi|23012374|ref|ZP_00052476.1| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Magnetospirillum magnetotacticum MS-1]
          Length = 146

 Score =  168 bits (425), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 84/147 (57%), Positives = 111/147 (75%), Gaps = 1/147 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN + ++  G + +    ++AEPL RGF  TLGN+LRRVL+SSL+GAA+
Sbjct: 1   MIQKNWQELIKPNKL-HVEPGADAQRSATVVAEPLERGFGMTLGNSLRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGVLHE SSI GV ED+TDIILNIK + L+M G+  KR+ +   GPG VTAG I+
Sbjct: 60  TAIQIDGVLHEFSSIPGVREDVTDIILNIKTLGLRMHGEGPKRMHLRAVGPGEVTAGLIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMEL 147
             +DIE+++P+ V+C LD  A + +E 
Sbjct: 120 VGHDIEIMDPELVLCTLDEGAKLNIEF 146


>gi|119662341|emb|CAJ33159.1| RNA polymerase alpha subunit [Lactobacillus parabuchneri]
          Length = 200

 Score =  168 bits (425), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 90/187 (48%), Positives = 128/187 (68%), Gaps = 4/187 (2%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVV 114
           G+A+T++QID VLHE S+IKGV ED+T IILN+K I+LK+ G  D  + + I   GP  V
Sbjct: 1   GSAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKISLKLDGPEDEEENLEIDVIGPADV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLIT 172
           TAGDIQ  +D+ VLNPD  I  +   A   M LT +KG GYV A     R+   PIG++ 
Sbjct: 61  TAGDIQADSDVTVLNPDLHIATVAEGATFHMRLTANKGRGYVSAVENKKRSSEMPIGVLP 120

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           +D++Y+PI++V+Y VES R GQ  D+DKL++ + TDGSIT  ++V+LA++IL + L MF+
Sbjct: 121 VDSIYTPIERVNYQVESTRVGQRDDFDKLTLDVWTDGSITPSEAVSLAAKILTEHLEMFV 180

Query: 233 NFEEPKK 239
           +  +  K
Sbjct: 181 DLTDEAK 187


>gi|283956979|ref|ZP_06374451.1| DNA-directed RNA polymerase alpha chain [Campylobacter jejuni
           subsp. jejuni 1336]
 gi|283791480|gb|EFC30277.1| DNA-directed RNA polymerase alpha chain [Campylobacter jejuni
           subsp. jejuni 1336]
          Length = 337

 Score =  168 bits (425), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 97/289 (33%), Positives = 162/289 (56%), Gaps = 5/289 (1%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
           A P   G+  TL + LRR+L +S  G A TA+ IDGV HE  S++G+ ED+   I+N+K 
Sbjct: 28  AWPFEIGYGITLAHPLRRLLYTSTIGYAPTAIHIDGVAHEFDSMRGMLEDVALFIINLKK 87

Query: 92  INLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +  K+ G+S+K +  F  +G   +   D+   + +EV+N D  +  ++ DA ++  L V 
Sbjct: 88  LRFKIKGESNKEIVEFSFKGSKEIYGKDLNN-DQVEVVNKDTYLATINEDAELKFTLIVE 146

Query: 151 KGHGYVPAKHHRTE-NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           KG GYVP++  +   NDP   I +DA ++P+++ +Y +E        DY+K+ +T+ TDG
Sbjct: 147 KGIGYVPSEEIKELINDP-KFIALDAFFTPVREATYDIEKVLFEDNPDYEKVVLTVTTDG 205

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
            IT  ++   A   +  QL +F      +  +K       L  N  LL+ + +L LS RS
Sbjct: 206 QITPNEAFQNALEAMYKQLSVFDKITNVRSVIKNQATSNELE-NTKLLQNITDLNLSARS 264

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            NCL    +VY+G+L   + +++  + N G+KSL EIK ++ ++G  +G
Sbjct: 265 YNCLEKAGVVYIGELALMSVSELAGLKNLGKKSLDEIKNIMESIGFPVG 313


>gi|148925739|ref|ZP_01809427.1| DNA-directed RNA polymerase alpha chain [Campylobacter jejuni
           subsp. jejuni CG8486]
 gi|145845749|gb|EDK22840.1| DNA-directed RNA polymerase alpha chain [Campylobacter jejuni
           subsp. jejuni CG8486]
          Length = 342

 Score =  168 bits (425), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 97/289 (33%), Positives = 162/289 (56%), Gaps = 5/289 (1%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
           A P   G+  TL + LRR+L +S  G A TA+ IDGV HE  S++G+ ED+   I+N+K 
Sbjct: 28  AWPFEIGYGITLAHPLRRLLYTSTIGYAPTAIHIDGVAHEFDSMRGMLEDVALFIINLKK 87

Query: 92  INLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +  K+ G+S+K +  F  +G   +   D+   + +EV+N D  +  ++ DA ++  L V 
Sbjct: 88  LRFKIKGESNKEIVEFSFKGSKEIYGKDLNN-DQVEVVNKDAYLATINEDAELKFTLIVE 146

Query: 151 KGHGYVPAKHHRTE-NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           KG GYVP++  +   NDP   I +DA ++P+++ +Y +E        DY+K+ +T+ TDG
Sbjct: 147 KGIGYVPSEEIKELINDP-KFIALDAFFTPVREATYDIEKVLFEDNPDYEKVVLTVTTDG 205

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
            IT  ++   A   +  QL +F      +  +K       L  N  LL+ + +L LS RS
Sbjct: 206 QITPNEAFQNALEAMYKQLSVFDKITNVRSVIKNQATSNELE-NTKLLQNITDLNLSARS 264

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            NCL    +VY+G+L   + +++  + N G+KSL EIK ++ ++G  +G
Sbjct: 265 YNCLEKAGVVYIGELALMSVSELAGLKNLGKKSLDEIKNIMESIGFPVG 313


>gi|218245116|ref|YP_002370487.1| DNA-directed RNA polymerase subunit alpha [Cyanothece sp. PCC 8801]
 gi|257058141|ref|YP_003136029.1| DNA-directed RNA polymerase subunit alpha [Cyanothece sp. PCC 8802]
 gi|218165594|gb|ACK64331.1| DNA-directed RNA polymerase, alpha subunit [Cyanothece sp. PCC
           8801]
 gi|256588307|gb|ACU99193.1| DNA-directed RNA polymerase, alpha subunit [Cyanothece sp. PCC
           8802]
          Length = 316

 Score =  168 bits (425), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 102/303 (33%), Positives = 170/303 (56%), Gaps = 15/303 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG   T+GNALRRVL+++L+GAA+TA++I GV HE ++I GV ED+ +I+LN+
Sbjct: 25  FVLEPLARGQGTTVGNALRRVLLANLQGAAVTAIRIAGVNHEFATIPGVREDVLEIMLNM 84

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK   D  +   +     G VTA + +  +++EV++P   +  L   + + ME  +
Sbjct: 85  KEIVLKSYSDQAQIGRLVATSAGTVTAANFELPSEVEVVDPTQYVATLTEGSKLEMEFRI 144

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GY   +  + +   +  + IDA++ P+ KV+Y VE  R       D+L + I T+G
Sbjct: 145 ETGTGYKGVERGKDDGTSLDFLEIDAVFMPVTKVNYIVEDIRGEHGEAQDRLILEIWTNG 204

Query: 210 SITGEDSVALASRILQDQLGMFIN---FEEPKKEVKEDINVKS-LPFNPALLKKVEELEL 265
           S   +++++ A+ I+ D      +    E    + ++D N +S +P        +EEL+L
Sbjct: 205 SFNPKEALSEAAEIVVDLFSPLKDLNQLETTTPDYQDDENPQSQIP--------IEELQL 256

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           SVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E   V+  +   LG+ LP   
Sbjct: 257 SVRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEE---VIEALQKRLGITLPQEK 313

Query: 326 PES 328
            +S
Sbjct: 314 AKS 316


>gi|150036748|emb|CAM98027.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 210

 Score =  167 bits (424), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 87/199 (43%), Positives = 129/199 (64%), Gaps = 2/199 (1%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + 
Sbjct: 1   GNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERS 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++ 
Sbjct: 61  LEIDVQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSADENKK 120

Query: 164 END--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
             D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L +
Sbjct: 121 LRDEMPIGVLAVDSIYTPIERVNYQVENTRVGARDDYDKLTFDIWTNGSIKPSDALSLGA 180

Query: 222 RILQDQLGMFINFEEPKKE 240
           +IL + L +F++      E
Sbjct: 181 KILAEHLNLFMDISPVAAE 199


>gi|268680561|ref|YP_003304992.1| DNA-directed RNA polymerase, subunit alpha [Sulfurospirillum
           deleyianum DSM 6946]
 gi|268618592|gb|ACZ12957.1| DNA-directed RNA polymerase, alpha subunit [Sulfurospirillum
           deleyianum DSM 6946]
          Length = 337

 Score =  167 bits (424), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 112/320 (35%), Positives = 173/320 (54%), Gaps = 19/320 (5%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           N+  + A P   GFA TL + LRR+L+ S  G+A TAV+I+GV HE  S++G+ ED+   
Sbjct: 22  NKVQISAYPFESGFAVTLAHPLRRLLLGSTIGSAPTAVKIEGVTHEFDSMRGMLEDVALF 81

Query: 86  ILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           I+N+K I  K+ GD  +  V     GP  +   D+   + IE++ PD  +  ++ DA   
Sbjct: 82  IINLKNIRFKIKGDEKRVEVNYSFSGPKEIKGSDLAN-SHIEIVTPDTYLATINEDAEFN 140

Query: 145 MELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
             L + KG GYVP+++ R    +D I L   DA ++P+K+  Y +E+       +Y+K+ 
Sbjct: 141 FSLIIEKGIGYVPSENIRDLLTDDYIAL---DAFFTPVKRAVYDIENVLVEDNPNYEKIV 197

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEE----PKKEVKEDINVKSLPFNPALLK 258
            TI+TDG ++  ++   A   +  Q+ +F    +    PK E   D NV+       LL+
Sbjct: 198 FTIETDGLVSPIEAFKNALEAMYAQMSVFNGILDIAVAPKNETSHD-NVEL----GKLLQ 252

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            VEEL LS RS NCL    + Y+G+L   +E ++  + N G+KSL EI+ V+   G  +G
Sbjct: 253 SVEELNLSARSFNCLDRAEVKYIGELALMSETELKDLKNLGKKSLEEIRQVMEESGYPVG 312

Query: 319 MNLPDWPPESIEELAKKYED 338
            N  D   E+   L KK ED
Sbjct: 313 YNFSD---ETASLLKKKIED 329


>gi|150036828|emb|CAM98281.1| DNA-directed RNA polymerase alpha chain [Leuconostoc lactis]
          Length = 208

 Score =  167 bits (424), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 86/193 (44%), Positives = 128/193 (66%), Gaps = 2/193 (1%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + 
Sbjct: 1   GNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERS 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++ 
Sbjct: 61  LEIDVQGPAEVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSADENKQ 120

Query: 164 --ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
             E  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L +
Sbjct: 121 LREEMPIGVLAVDSIYTPIERVNYHVENTRVGARDDYDKLTFDIWTNGSIKPSDALSLGA 180

Query: 222 RILQDQLGMFINF 234
           +IL + L +F++ 
Sbjct: 181 KILAEHLNLFMDI 193


>gi|150036768|emb|CAM98265.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. cremoris]
          Length = 212

 Score =  167 bits (424), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 86/192 (44%), Positives = 128/192 (66%), Gaps = 2/192 (1%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + +
Sbjct: 1   NSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIESDDERSL 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++  
Sbjct: 61  EIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSADENKKL 120

Query: 165 ND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L ++
Sbjct: 121 RDEMPIGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTNGSIKPSDALSLGAK 180

Query: 223 ILQDQLGMFINF 234
           IL + LG+F++ 
Sbjct: 181 ILAEHLGLFMDI 192


>gi|150036776|emb|CAM98267.1| DNA-directed RNA polymerase alpha chain [Weissella viridescens]
          Length = 175

 Score =  167 bits (423), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 85/172 (49%), Positives = 119/172 (69%), Gaps = 2/172 (1%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRVL+SSL GAAI +VQIDGVLHE S+++GV ED+T IILN+K +++++  D  K
Sbjct: 4   LGNSLRRVLLSSLPGAAINSVQIDGVLHEFSTVEGVVEDVTQIILNLKKVSMRIDSDDEK 63

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + +   GP  VTAGD     D+EVLN D  I  +   A + M +T  +G GYV    ++
Sbjct: 64  TLEVNVNGPATVTAGDFVGDADVEVLNKDQYIATVAAGATLHMTVTAVRGRGYVSGDQNK 123

Query: 163 T--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
              E+ PIG++ ID++++PI++V+Y VE  R GQ  DYDKL+M I TDGS+T
Sbjct: 124 ELHEDTPIGVLAIDSIFTPIERVNYQVEETRVGQRNDYDKLTMDIWTDGSLT 175


>gi|150020873|ref|YP_001306227.1| DNA-directed RNA polymerase subunit alpha [Thermosipho
           melanesiensis BI429]
 gi|172048670|sp|A6LLP1|RPOA_THEM4 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|149793394|gb|ABR30842.1| DNA-directed RNA polymerase, alpha subunit [Thermosipho
           melanesiensis BI429]
          Length = 328

 Score =  167 bits (423), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 110/305 (36%), Positives = 177/305 (58%), Gaps = 21/305 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI--DGVLHEISSIKGVHEDLTDIIL 87
            +  PL +G+A T+GN LRRVL+SS+   AIT V+       HE  +I+GV ED+ +I+L
Sbjct: 25  FVLSPLEKGYATTIGNTLRRVLLSSIPSLAITDVKFVRPEKYHEFDTIEGVKEDIIEILL 84

Query: 88  NIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           N+K + LKM    ++   +TI  +G G + AGDI     + V NP+  I  L+ DA + +
Sbjct: 85  NLKKVQLKMESYVNTPVELTIQHKGEGEIKAGDIVVPAGVTVTNPNLHIATLNEDADIEI 144

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           ++  + G G+VPA   R E   IG I +D +Y+PI KV++ +E+ R G+  DYDKL + +
Sbjct: 145 KMYATVGKGFVPAAE-RNERPDIGWIVLDGVYNPILKVNWKIENVRVGKKTDYDKLILEV 203

Query: 206 DTDGSITGEDSVALASRILQDQLGMF-----------INFEEPKKEVKEDINVKSLPFNP 254
            T  +I   +++  A +I+ D   +            I  E  K E+ E+     +  N 
Sbjct: 204 WTKKNIKPVEALKQAVKIINDHFKLIEESFGDMEDAGIVIETTKAEIVEE----KIDENE 259

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK-GVLGTM 313
            L KK++EL+LS+R+ NCL+ + I  +GDL++R E ++L++ NFG+KSL E+K  ++   
Sbjct: 260 ILNKKIDELDLSMRALNCLKRDKIETIGDLLERGEEELLKIKNFGQKSLDEVKEKLMEKF 319

Query: 314 GLFLG 318
           G+  G
Sbjct: 320 GISFG 324


>gi|31544832|ref|NP_853410.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma gallisepticum
           str. R(low)]
 gi|31541678|gb|AAP56978.1| DNA-directed RNA polymerase subunit alpha (RpoA) [Mycoplasma
           gallisepticum str. R(low)]
 gi|284930906|gb|ADC30845.1| DNA-directed RNA polymerase subunit alpha (RpoA) [Mycoplasma
           gallisepticum str. R(high)]
 gi|284931662|gb|ADC31600.1| DNA-directed RNA polymerase subunit alpha (RpoA) [Mycoplasma
           gallisepticum str. F]
          Length = 340

 Score =  167 bits (423), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 107/304 (35%), Positives = 174/304 (57%), Gaps = 17/304 (5%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           ++N    I +PL +GF  TLGNALRRV++S L G+++ A++I G+ HE   I GV ED+T
Sbjct: 32  DKNYGKYIVKPLEKGFGITLGNALRRVMLSHLPGSSVFALKIKGISHEFGFIPGVKEDVT 91

Query: 84  DIILNIKGINLKMSG-------------DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
            IILNIK + + +S              +    +TI     G++ AGDI+     EV N 
Sbjct: 92  QIILNIKNLVVWISDNMITDETLSETPIEKWPVMTIRANKAGIIKAGDIECPLGFEVFNK 151

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  IC L  DA V +++  ++G G+  A  +R+E   + +I ID+ ++PI KV Y VE  
Sbjct: 152 DLEICTLSEDAEVAIDIYATRGRGFKTAAENRSEIGSLSIIPIDSNFNPIIKVGYHVE-- 209

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
            E   +  DKL + + T+G I   D++A+AS+IL D L   I+  +   ++ + +N K++
Sbjct: 210 EETSDVITDKLIIEVGTNGLIKSGDAIAIASKILSDHLKPLIDINKSLHDI-QVLNEKNV 268

Query: 251 -PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              N  L   +E+L+L+VRS NCL+   I  + +L+ R+++++  + N G+KS+ EI   
Sbjct: 269 EEKNKKLSIPIEQLDLTVRSYNCLKRHGIQTVEELVTRSKSEIENIRNLGKKSVREINKK 328

Query: 310 LGTM 313
           L  +
Sbjct: 329 LSEL 332


>gi|315639079|ref|ZP_07894247.1| DNA-directed RNA polymerase subunit alpha [Campylobacter
           upsaliensis JV21]
 gi|315480855|gb|EFU71491.1| DNA-directed RNA polymerase subunit alpha [Campylobacter
           upsaliensis JV21]
          Length = 337

 Score =  167 bits (423), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 102/311 (32%), Positives = 168/311 (54%), Gaps = 7/311 (2%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
           A P   G+  TL + LRR+L +S  G A TA+ I+GV HE  S++G+ ED+   I+N+K 
Sbjct: 28  AWPFEIGYGITLAHPLRRLLYTSTVGYAPTAIYIEGVAHEFDSMRGMLEDVALFIINLKK 87

Query: 92  INLKMSGDSHKR-VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +  K+  DS+K  V  + +GP  +   D+   + + V+N D  +  ++ DA ++  L + 
Sbjct: 88  LRFKLKSDSNKEIVEFYFKGPKEIHGRDLDN-DQVSVVNEDAYLATINEDAELKFTLIIE 146

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVP++  +   D    I +DA ++PI++ +Y +E        DY+K+ +TI TDG 
Sbjct: 147 KGIGYVPSEEIKELLDDNKFIALDAFFTPIREATYDIEKVLFEDNPDYEKVVLTITTDGQ 206

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           IT  ++   A   +  QL +F      +  +K   +   L  N  LL+ + +L LS RS 
Sbjct: 207 ITPNEAFQNALEAMYKQLSVFDKITNVRSMIKTQASHNELE-NTKLLQNITDLNLSARSY 265

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL----PDWPP 326
           NCL    +VY+G+L   +  ++  + N G+KSL EIK V+ ++G  +G +      D   
Sbjct: 266 NCLEKAGVVYIGELALMSVNELAGLKNLGKKSLDEIKSVMESIGFAVGTSKLSDNKDLLK 325

Query: 327 ESIEELAKKYE 337
           + IEEL  + E
Sbjct: 326 KKIEELKAQNE 336


>gi|119668367|emb|CAK95476.1| RNA polymerase alpha subunit [Lactobacillus rhamnosus]
          Length = 198

 Score =  167 bits (422), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 82/182 (45%), Positives = 126/182 (69%)

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
           AA++++QIDGVLHE S+I GV ED+T IILNIK + LKM+ D  K + I   GP  VTA 
Sbjct: 1   AAVSSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNTDEDKNIEIDVNGPAKVTAA 60

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI    D+EVLNP+  IC +       + +TV KG GYV A  +++++ PIG++ ID+++
Sbjct: 61  DIVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAADQNKSDDMPIGVLPIDSIF 120

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           +PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++IL + L +F+N  + 
Sbjct: 121 TPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKILTEHLDIFVNLTDE 180

Query: 238 KK 239
            K
Sbjct: 181 AK 182


>gi|255321746|ref|ZP_05362901.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter showae
           RM3277]
 gi|255301226|gb|EET80488.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter showae
           RM3277]
          Length = 328

 Score =  167 bits (422), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 107/319 (33%), Positives = 176/319 (55%), Gaps = 16/319 (5%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           EN   + A P   G+A TL + LRR+L SS  G A T V+I+GV HE  S++G+ ED+  
Sbjct: 12  ENVARITAYPFETGYAVTLAHPLRRLLYSSTVGFAATGVKIEGVSHEFDSMRGMLEDVAQ 71

Query: 85  IILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            I+N+K I  K+  +S + V  +  +GP  + AGD+++ + ++++N D  +  ++ DA +
Sbjct: 72  FIINLKNIRFKLKNESEREVVEYSFKGPKEIKAGDLKS-DVVDIVNLDAYLATINEDAEL 130

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
           +  + + KG GYVP++  R +N   G I +DA ++P+KK  Y + +       DY+K+  
Sbjct: 131 KFSVIIQKGIGYVPSEEIR-DNTEEGYIALDAFFTPVKKAVYELVNVLVEDNPDYEKIIF 189

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMF---INFEEPKKEVKEDINVKSLPFNPA-LLKK 259
           T+ TDG +   ++   A   +  Q+ +F   +N      +V   +N ++     A LL+ 
Sbjct: 190 TVTTDGQVGAIEAFKHAIEAMYQQMSVFKGVLNI-----DVSAGLNAQTSGSEHAKLLQS 244

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           VEEL LS RS NCL    I ++G+L    E ++  + N G+KSL EIK V+  +G  +G 
Sbjct: 245 VEELNLSARSFNCLDKAEIRFIGELALMDENELKELKNLGKKSLDEIKAVMQEIGYPVGG 304

Query: 320 NLPDWPPESIEELAKKYED 338
           +L        E+L KK  D
Sbjct: 305 DLGGGK----EQLKKKIAD 319


>gi|12230607|sp|Q9RDV6|RPOA_MYCGA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|16924180|gb|AAF19039.2| DNA-directed RNA polymerase alpha chain [Mycoplasma gallisepticum]
          Length = 325

 Score =  167 bits (422), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 107/304 (35%), Positives = 174/304 (57%), Gaps = 17/304 (5%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           ++N    I +PL +GF  TLGNALRRV++S L G+++ A++I G+ HE   I GV ED+T
Sbjct: 17  DKNYGKYIVKPLEKGFGITLGNALRRVMLSHLPGSSVFALKIKGISHEFGFIPGVKEDVT 76

Query: 84  DIILNIKGINLKMSG-------------DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
            IILNIK + + +S              +    +TI     G++ AGDI+     EV N 
Sbjct: 77  QIILNIKNLVVWISDNMITDETLSETPIEKWPVMTIRANKAGIIKAGDIECPLGFEVFNK 136

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  IC L  DA V +++  ++G G+  A  +R+E   + +I ID+ ++PI KV Y VE  
Sbjct: 137 DLEICTLSEDAEVAIDIYATRGRGFKTAAENRSEIGSLSIIPIDSNFNPIIKVGYHVE-- 194

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
            E   +  DKL + + T+G I   D++A+AS+IL D L   I+  +   ++ + +N K++
Sbjct: 195 EETSDVITDKLIIEVGTNGLIKSGDAIAIASKILSDHLKPLIDINKSLHDI-QVLNEKNV 253

Query: 251 -PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              N  L   +E+L+L+VRS NCL+   I  + +L+ R+++++  + N G+KS+ EI   
Sbjct: 254 EEKNKKLSIPIEQLDLTVRSYNCLKRHGIQTVEELVTRSKSEIENIRNLGKKSVREINKK 313

Query: 310 LGTM 313
           L  +
Sbjct: 314 LSEL 317


>gi|11467399|ref|NP_043256.1| RNA polymerase alpha subunit [Cyanophora paradoxa]
 gi|1350840|sp|P48118|RPOA_CYAPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1016200|gb|AAA81287.1| alpha subunit of RNA polymerase [Cyanophora paradoxa]
          Length = 315

 Score =  167 bits (422), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 106/299 (35%), Positives = 174/299 (58%), Gaps = 21/299 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL  G   T+GN+LRRVL+S + G+AITAV+I GV HE  SI GV ED+ +++LN+
Sbjct: 23  FIVEPLEPGQGITIGNSLRRVLLSDIEGSAITAVRIAGVNHEFCSIPGVKEDVLELLLNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK   +  +   +  +G   VT  + +  +++E+++    +  +  +A++ ME  +
Sbjct: 83  KNIVLKSYTNEPQIGRLKIQGACKVTTANFELPSEVEIIHGTQYVATVAENAILEMEFKI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA--REGQVLDYDKLSMTIDT 207
            KG GY      +TEN  I  + IDA++ P++KV+Y VE    R  ++   ++L + I  
Sbjct: 143 EKGRGYKIIDKKQTENS-IDFLPIDAIFMPVRKVNYMVEEIFLRNSEI--KERLILEIWR 199

Query: 208 DGSITGEDSVALASRILQDQLGMF--INFE--EPKKEVKEDINVKSLPFNPALLKKVEEL 263
           +GS+T +DS++ A+ +L +    F  INFE  +   E  ED  +  +P        +EEL
Sbjct: 200 NGSVTPQDSISQAAEVLLNLFNPFKKINFENTDDSTEQTED-KISQIP--------IEEL 250

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           +LSVR+ NCL+   I  +GDL+  ++ ++L + NFG+KS    K V+  +   LG++LP
Sbjct: 251 QLSVRAYNCLKRAQIHSIGDLLNVSQEELLEIRNFGQKSA---KEVIDALQKRLGISLP 306


>gi|730608|sp|Q01569|RPOA_PYRSA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|938275|emb|CAA46702.1| DNA-directed RNA polymerase alpha subunit [Pyrenomonas salina]
          Length = 314

 Score =  166 bits (421), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 106/297 (35%), Positives = 171/297 (57%), Gaps = 23/297 (7%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL +G   TLGNALRR L++ L G AI AV+I GV HE S+I G+ ED+ +I+LN+K +
Sbjct: 26  EPLNQGQGTTLGNALRRTLLADLEGTAIVAVRIAGVSHEFSTIPGIREDVLEILLNLKEV 85

Query: 93  NLK----MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
            LK     SG    RV    +GP +VT   ++  ++IE+++P+  I  +  + ++ ME  
Sbjct: 86  VLKSQIGTSGVGRLRV----QGPAIVTTNHLELPSEIELIDPNQYIATICGNNILEMEFR 141

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           +  G GY   +    E+  I  + +DA++ P+KKV+Y  +  R    L  ++L++ + T+
Sbjct: 142 IETGKGYNLVERDSDESS-IDFLQVDAIFMPVKKVNYLSKDIRSENNLIQEQLTLEVWTN 200

Query: 209 GSITGEDSVALASRILQDQLGMF--INFEEPKKE-VKEDINVKSLPFNPALLKKVEELEL 265
           GSI  +D+V+ A +IL + L     INF+    E + ED  +  +         +EEL+L
Sbjct: 201 GSIDPQDAVSQAGKILTELLFPLKEINFKPDDSESIIEDSKINQI--------LIEELQL 252

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           SVR+ NCL+   I  + DL+  ++ D++ + NFG+KS  E   V+  +   LG+NLP
Sbjct: 253 SVRAYNCLKRAQIHSVADLLDYSQEDLIEIKNFGQKSAEE---VIDALQKRLGINLP 306


>gi|300088169|ref|YP_003758691.1| DNA-directed RNA polymerase subunit alpha [Dehalogenimonas
           lykanthroporepellens BL-DC-9]
 gi|299527902|gb|ADJ26370.1| DNA-directed RNA polymerase, alpha subunit [Dehalogenimonas
           lykanthroporepellens BL-DC-9]
          Length = 333

 Score =  166 bits (421), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 108/288 (37%), Positives = 173/288 (60%), Gaps = 11/288 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL +GF  TLGNALRRVL+SSL GAA+  V+I+GV HE S + G  ED  D +LN+K +
Sbjct: 24  EPLEKGFGTTLGNALRRVLLSSLSGAAVAQVRIEGVQHEFSPLPGAKEDTMDFLLNLKNL 83

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSK 151
           +LK       R+ +  +GP  VTA DI+  ++ E+ NPD  +  L D ++ + +E+ V  
Sbjct: 84  HLKPLFGRPGRLILDVKGPREVTAADIEASSEYEIANPDLYLVTLDDAESHLYVEMEVEV 143

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G G+V A     +N  IG I  DA+++P++KV+Y +E    GQ + Y++L + I TDG++
Sbjct: 144 GRGFVEAT--SADNVAIGTIPQDAIFNPVEKVNYEIEPVHMGQEMSYERLHLRIWTDGTL 201

Query: 212 TGEDSVALASRILQDQLGMF--INFEEP--KKEVKEDINVKSLPFNPALLKKVEELELSV 267
              D++A ++ IL +    F  I    P  +++ +E +++    +N      +E+L+LSV
Sbjct: 202 APTDALAQSAAILVNHFQPFTAIGGSLPIIQEKKQEKLSIPDEKYN----MPIEQLDLSV 257

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           RS NCLR   +  +G+L+ +   +++ + NFG KSL E++  L   GL
Sbjct: 258 RSLNCLRHAGLNTVGELLSKGVDELMSLRNFGLKSLNELEERLQANGL 305


>gi|119662397|emb|CAJ33188.1| RNA polymerase alpha subunit [Lactobacillus vaccinostercus]
          Length = 174

 Score =  166 bits (421), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 85/174 (48%), Positives = 128/174 (73%), Gaps = 2/174 (1%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG 110
           L++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K I+LK+  +  K + I  +G
Sbjct: 1   LLASLPGAAITSIQIDGVLHEFSTVEGVTEDVTQIILNMKQISLKIDSEEDKTLEIDVKG 60

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PI 168
           P  VTAGDI+   D+EVLNP+  I  +   A + +++T + G GYV A  ++   D  PI
Sbjct: 61  PAAVTAGDIEADGDVEVLNPELHIATVADGAELHIQMTANTGRGYVSADDNKARMDDLPI 120

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
           G++ ID++Y+PI++V+YTVE+AR GQ  DYDKL++ + +DGSIT  +S++LA++
Sbjct: 121 GVLPIDSIYTPIERVNYTVENARVGQRNDYDKLTLDVWSDGSITPSESISLAAK 174


>gi|153951055|ref|YP_001398875.1| DNA-directed RNA polymerase subunit alpha [Campylobacter jejuni
           subsp. doylei 269.97]
 gi|171769458|sp|A7H5U5|RPOA_CAMJD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|152938501|gb|ABS43242.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. doylei 269.97]
          Length = 337

 Score =  166 bits (420), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 96/289 (33%), Positives = 159/289 (55%), Gaps = 5/289 (1%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
           A P   G+  TL + LRR+L +S  G A TA+ IDGV HE  S++G+ ED+   I+N+K 
Sbjct: 28  AWPFEIGYGITLAHPLRRLLYTSTVGYAPTAIHIDGVAHEFDSMRGMLEDVALFIINLKK 87

Query: 92  INLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +  K+  DS+K +  F  +G   +   D+   + +EV+N D  +  ++ DA +   L V 
Sbjct: 88  LRFKIKSDSNKEIVEFSFKGSKEIYGKDLNN-DQVEVVNKDAYLATINEDAELEFTLIVE 146

Query: 151 KGHGYVPAKHHRTE-NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           KG GY+P++  +   NDP   I +DA ++P+++ +Y +E        DY+K+ +T+ TDG
Sbjct: 147 KGIGYIPSEEIKEFLNDP-KFIALDAFFTPVREATYDIEKVLFEDNPDYEKVVLTVTTDG 205

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
            IT  ++   A   +  QL +F      +  +K       L  N  LL+ + +L LS RS
Sbjct: 206 QITPNEAFQNALEAMYKQLSVFDKITNVRSVIKNQATSNELE-NTKLLQNITDLNLSARS 264

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            NCL    +VY+G+L   + +++  + N G+KSL EIK ++  +G  +G
Sbjct: 265 YNCLEKAGVVYIGELALMSVSELAGLKNLGKKSLDEIKNIMENIGFPVG 313


>gi|119672793|emb|CAK95480.1| RNA polymerase alpha subunit [Lactobacillus salivarius]
          Length = 199

 Score =  166 bits (420), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 85/185 (45%), Positives = 127/185 (68%), Gaps = 2/185 (1%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAAIT VQIDGVLHE S+I GV ED+T IILN+K + L M  +  + + I   GP  VTA
Sbjct: 2   GAAITDVQIDGVLHEFSTIPGVLEDVTLIILNLKKVALSMESEDSQALEINVTGPMEVTA 61

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITID 174
           GDIQ+ +D+EVLNP+  IC +   A + + +  +KG GYV A  ++   D  PIG++ ID
Sbjct: 62  GDIQSNSDVEVLNPEQYICTVADGAELHVRMNANKGRGYVSANDNKALADDMPIGVLPID 121

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           ++Y+PI++V+Y VE  R GQ  DYDKL++ + T+GSIT  ++++L+++IL + L +F++ 
Sbjct: 122 SIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWTNGSITPSEAISLSAKILTEHLALFVDL 181

Query: 235 EEPKK 239
            +  K
Sbjct: 182 TDEAK 186


>gi|119672795|emb|CAK95481.1| RNA polymerase alpha subunit [Lactobacillus saerimneri]
          Length = 170

 Score =  166 bits (419), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 85/170 (50%), Positives = 116/170 (68%), Gaps = 2/170 (1%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           G+  TLGN+LRRVL+SSL GAAIT +QIDGVLHE S+++GV ED+T IILN+K + L + 
Sbjct: 1   GYGTTLGNSLRRVLLSSLPGAAITDIQIDGVLHEFSTVEGVLEDVTQIILNLKKVALGIK 60

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
            D    + I   GP  VTAGDIQ   D+E+ NPD  IC +   A   + +T + G GYV 
Sbjct: 61  SDDRVSLEIDVVGPMEVTAGDIQGSADVEIFNPDQYICTVADGASFHVRMTANTGRGYVS 120

Query: 158 AKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           AK ++   D  PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ +
Sbjct: 121 AKENKEMADDMPIGVLPIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDV 170


>gi|150036770|emb|CAM98266.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gasicomitatum]
          Length = 210

 Score =  166 bits (419), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 86/198 (43%), Positives = 128/198 (64%), Gaps = 2/198 (1%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + +
Sbjct: 1   NSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDEERSL 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++  
Sbjct: 61  EVDIQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTITAFKGRGYSSADENKQL 120

Query: 165 ND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L S+
Sbjct: 121 RDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSLGSK 180

Query: 223 ILQDQLGMFINFEEPKKE 240
           IL + L +F++      E
Sbjct: 181 ILAEHLNLFMDISPVAAE 198


>gi|256370803|ref|YP_003108628.1| DNA-directed RNA polymerase subunit alpha [Candidatus Sulcia
           muelleri SMDSEM]
 gi|256009595|gb|ACU52955.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Sulcia
           muelleri SMDSEM]
          Length = 349

 Score =  166 bits (419), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 106/313 (33%), Positives = 171/313 (54%), Gaps = 24/313 (7%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL  G+  T+GN LRRVL+SSL G AI++V+I+GV HE ++IKGV ED+T+I+LN+K I
Sbjct: 27  EPLYPGWGVTIGNTLRRVLLSSLEGYAISSVKIEGVDHEFATIKGVKEDMTEILLNLKKI 86

Query: 93  NLKMSGDSHKRVT---------------IFKRGPGVVTAGDI-QTVNDIEVLNPDHVICN 136
             K   +  +                  I K     +TAGD+ + ++  E++NPD +I N
Sbjct: 87  RFKKKMEMEEEEEEEEEEEEEEGEKFNIIIKNEKEEITAGDLGEYIHLFEIINPDLIILN 146

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
                 + + + + KG GYVP++ +    +  G I++D++++PIKKV YT+E+    +  
Sbjct: 147 KKKFIYLNITIVIKKGIGYVPSEENEKHINTNGTISMDSIFTPIKKVKYTIENCSVSKNS 206

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN-----FEEPKKEVKEDINVKSLP 251
            Y++L   I TDG+I  +D++  AS ++   L +  N         K + K+  N   L 
Sbjct: 207 TYERLFFEIKTDGTINPKDALIKASNLVIRHLKLLSNKKISLNYNKKYKKKKQTNENYLK 266

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L   +E   LSVR+ NCL+   I   GDLI+    +   +   G+KSL E+  ++ 
Sbjct: 267 LRNILNSSLERKNLSVRTLNCLKKAKIFTWGDLIKSNPTNFKYL---GKKSLEELDLIMK 323

Query: 312 TMGLFLGMNLPDW 324
            + ++ GMNL D+
Sbjct: 324 KLTIYYGMNLEDY 336


>gi|119662823|emb|CAJ33204.1| RNA polymerase alpha subunit [Lactobacillus coleohominis DSM 14060]
          Length = 173

 Score =  166 bits (419), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 82/173 (47%), Positives = 123/173 (71%), Gaps = 1/173 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRV+++SL GAAIT++ IDGVLHE S+++GV ED+T IILN+K ++
Sbjct: 1   PLERGYGTTLGNSLRRVMLASLPGAAITSINIDGVLHEFSTVEGVTEDVTQIILNLKKVS 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L++  +  K + +  +GP  VTAGDIQ   D+ VLNPD  I  +   A + +++T  KG 
Sbjct: 61  LRIDSEDQKNLELNVKGPAEVTAGDIQGDGDVTVLNPDLHIATVADGAELHIQMTADKGR 120

Query: 154 GYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           GY  A  ++   D  IG++ ID++Y+PI++V+YTVE+ R GQ  DY+KL++ +
Sbjct: 121 GYSSADDNKARMDLAIGVLPIDSIYTPIERVNYTVENTRVGQNNDYNKLTLDV 173


>gi|57242509|ref|ZP_00370447.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter
           upsaliensis RM3195]
 gi|57016794|gb|EAL53577.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter
           upsaliensis RM3195]
          Length = 337

 Score =  166 bits (419), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 101/306 (33%), Positives = 166/306 (54%), Gaps = 7/306 (2%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
           A P   G+  TL + LRR+L +S  G A TA+ I+GV HE  S++G+ ED+   I+N+K 
Sbjct: 28  AWPFEIGYGITLAHPLRRLLYTSTVGYAPTAIYIEGVAHEFDSMRGMLEDVALFIINLKK 87

Query: 92  INLKMSGDSHKR-VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +  K+  DS+K  V  + +GP  +   D+   + + V+N D  +  ++ DA ++  L + 
Sbjct: 88  LRFKLKSDSNKEIVEFYFKGPKEIHGRDLDN-DQVSVVNEDAYLATINEDAELKFTLIIE 146

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYVP++  +   D    I +DA ++PI++ +Y +E        DY+K+ +TI TDG 
Sbjct: 147 KGIGYVPSEEIKELLDDNKFIALDAFFTPIREATYDIEKVLFEDNPDYEKVVLTITTDGQ 206

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           IT  ++   A   +  QL +F      +  +K   +   L  N  LL+ + +L LS RS 
Sbjct: 207 ITPNEAFQNALGAMYKQLSVFDKITNVRSMIKTQASHNELE-NTKLLQNITDLNLSARSY 265

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL----PDWPP 326
           NCL    +VY+G+L   +  ++  + N G+KSL EIK V+ ++G  +G +      D   
Sbjct: 266 NCLEKAGVVYIGELALMSVNELAGLKNLGKKSLDEIKSVMESIGFAVGTSKLSDNKDLLK 325

Query: 327 ESIEEL 332
           + IEEL
Sbjct: 326 KKIEEL 331


>gi|161511713|emb|CAP16867.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 207

 Score =  166 bits (419), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 85/191 (44%), Positives = 128/191 (67%), Gaps = 2/191 (1%)

Query: 54  SLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGV 113
           SL GAA+T+VQIDGVLHE S+I+GV ED+T IILN+K ++LK+  D  K + I   GP  
Sbjct: 1   SLPGAALTSVQIDGVLHEFSTIEGVVEDVTQIILNLKKVSLKVESDEEKSLEINVMGPAN 60

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLI 171
           VTAGDI    D+ +LNP+  IC +         LT  KG GY  A  +  R  + PIG++
Sbjct: 61  VTAGDIVGDGDVTILNPELPICTVAEGTTFHAVLTAEKGRGYTSADENKARKVDMPIGVL 120

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGS+   ++++L+++IL + L +F
Sbjct: 121 PIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSLAASEAISLSAKILTEHLTIF 180

Query: 232 INFEEPKKEVK 242
           +N ++  K+ +
Sbjct: 181 VNLDDQAKDTE 191


>gi|150186978|emb|CAK30140.1| RNA polymerase alpha subunit [Streptococcus sanguinis SK1]
          Length = 194

 Score =  166 bits (419), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 81/184 (44%), Positives = 123/184 (66%)

Query: 53  SSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
           +SL GAA+T++ I+GVLHE  +I GV ED+  IILN+KGI +K      K + +   GP 
Sbjct: 1   ASLPGAAVTSINIEGVLHEFDTISGVREDVMQIILNVKGIAVKSYVQDEKIIELDVEGPA 60

Query: 113 VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT 172
            VTAGDI T +DIE++NPDH +  +   A  +  +TV+ G GYVPA  ++ ++ P+G + 
Sbjct: 61  EVTAGDILTDSDIEIINPDHYLFTIGEGASFKATMTVNSGRGYVPADENKKDDAPVGTLA 120

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F 
Sbjct: 121 VDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLFT 180

Query: 233 NFEE 236
           N  E
Sbjct: 181 NLTE 184


>gi|150187001|emb|CAK30147.1| RNA polymerase alpha subunit [Streptococcus ovis]
          Length = 202

 Score =  165 bits (418), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 81/183 (44%), Positives = 124/183 (67%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAA+T+++IDGVLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  VTA
Sbjct: 2   GAAVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKTIELDVVGPAEVTA 61

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
           GDI T +DIE++NPDH +  +   A  +  LTV+ G GYVPA+ ++ +  P+G + +D++
Sbjct: 62  GDILTDSDIEIVNPDHYLFTISEGATFKATLTVNTGRGYVPAEGNKKDEAPVGTLAVDSI 121

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + LG+F +  +
Sbjct: 122 YTPVVKVNYQVEPARVGSNDGFDKLTLEIMTNGTIIPEDALGLSARILMEHLGLFTDLTD 181

Query: 237 PKK 239
             K
Sbjct: 182 VAK 184


>gi|90567615|emb|CAJ31075.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
 gi|119662311|emb|CAJ33143.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 197

 Score =  165 bits (418), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 82/181 (45%), Positives = 120/181 (66%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG 110
           L++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   D  K + +   G
Sbjct: 1   LLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLSDERKVIELDVEG 60

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
           P  VTA D++   D++VLNPD  IC +     + ME+ V  G GYV A  +++++ PIG+
Sbjct: 61  PATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNGRGYVAASDNKSDDMPIGV 120

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++ A++IL +   +
Sbjct: 121 IPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFATKILVEHFKV 180

Query: 231 F 231
           F
Sbjct: 181 F 181


>gi|150036788|emb|CAM98271.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 205

 Score =  165 bits (418), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 86/198 (43%), Positives = 128/198 (64%), Gaps = 2/198 (1%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + +
Sbjct: 1   NSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSL 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++  
Sbjct: 61  EIDVQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSADENKKL 120

Query: 165 ND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L ++
Sbjct: 121 RDEMPIGVLAVDSIYTPIERVNYQVENTRVGARDDYDKLTFDIWTNGSIKPSDALSLGAK 180

Query: 223 ILQDQLGMFINFEEPKKE 240
           IL + L +F++      E
Sbjct: 181 ILAEHLNLFMDISPVAAE 198


>gi|71842332|ref|YP_277420.1| RNA polymerase alpha subunit [Emiliania huxleyi]
 gi|90110842|sp|Q4G347|RPOA_EMIHU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|60101575|gb|AAX13919.1| RNA polymerase alpha subunit [Emiliania huxleyi]
          Length = 309

 Score =  165 bits (417), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 100/286 (34%), Positives = 165/286 (57%), Gaps = 9/286 (3%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           EN      EPL +G   T+GNALRR L+S++ G AI   +I GV HE S I GV ED  +
Sbjct: 16  ENVAKFCIEPLSKGQGITIGNALRRTLLSNIPGTAIVGTRISGVDHEFSVIPGVKEDALE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           I+LN+K +  K + +      +  +GP +VTAGDI    D+E+++P   I  +   + + 
Sbjct: 76  ILLNLKQLVFKGNLNEPIITRLNIQGPCIVTAGDIDIPTDLELIDPQQYIATITDFSHLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           ME  + +G  YV ++   + N+P G + +DA+++PIKKV++ VE++   + L+ ++L + 
Sbjct: 136 MEFILEQGESYVLSEKTAS-NNPRGFLAVDAVFTPIKKVNFFVETSSSKERLEKERLIIE 194

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKKV 260
           I+T+GSI   +++ LA+  L     +     +  E P  EV+  + V        L   +
Sbjct: 195 IETNGSILPLEALNLAAERLSSLFKLVNSADLTAEFP-TEVENIVQVSQTDVTGVL---I 250

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           EELELSVR+ NCL+   I  +G+L++ ++ ++L   NFG+KS  E+
Sbjct: 251 EELELSVRAYNCLKRAQIHTLGELLKYSKENLLEFKNFGQKSANEV 296


>gi|154424755|emb|CAL18480.1| RNA polymerase alpha subunit [Streptococcus alactolyticus]
          Length = 196

 Score =  165 bits (417), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 82/189 (43%), Positives = 129/189 (68%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG 110
           L+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   G
Sbjct: 1   LLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEG 60

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
           P  VTAGDI T +D+E++N DH +  +     ++  +TV+K  GYVPA+ ++ ++ P+G 
Sbjct: 61  PAEVTAGDILTDSDVEIVNSDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKDDAPVGT 120

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +
Sbjct: 121 LAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNL 180

Query: 231 FINFEEPKK 239
           F +  E  K
Sbjct: 181 FTDLTEVAK 189


>gi|119668323|emb|CAK95461.1| RNA polymerase alpha subunit [Lactobacillus gasseri]
          Length = 166

 Score =  164 bits (416), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 84/166 (50%), Positives = 116/166 (69%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           VL++S+ G A++ +QIDGVLHE S++ GV ED+T IILN+K + LK   D  K   I   
Sbjct: 1   VLLTSIPGTALSYIQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLSDEEKIAEIDVT 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP +VTA D++  +DIEVLN D  IC++     + M + +  G GYVPA  ++T++ PIG
Sbjct: 61  GPAIVTAADLKVDSDIEVLNTDQYICSIADGGHLHMNVAIKNGRGYVPASENKTDDMPIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
           +I +D+L+SPIKKV+Y VESAR G+  DYDKL++ I TDGSIT  D
Sbjct: 121 VIPVDSLFSPIKKVNYQVESARVGKRDDYDKLTLEIWTDGSITPND 166


>gi|260434747|ref|ZP_05788717.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus sp. WH
           8109]
 gi|260412621|gb|EEX05917.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus sp. WH
           8109]
          Length = 312

 Score =  164 bits (416), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 110/313 (35%), Positives = 171/313 (54%), Gaps = 26/313 (8%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ V     ++   +I  PL RG A TLGNALRRVLM  L G+A+TA++I GV HE 
Sbjct: 7   DRIEHQVAEDRAQSGVFLIG-PLERGQATTLGNALRRVLMGGLEGSAVTAIRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           +++ GV ED+ DI+LN K I++       +   +   GP  V AGD+Q  + ++V++ D 
Sbjct: 66  ATVPGVREDVLDILLNCKEISVNSRSAELQIGRLVVAGPAEVKAGDLQFSSQVQVVDADR 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE---- 188
            I  +     + +E+ V +G GY P   H  E   I L+ IDA++ P+ +V++T++    
Sbjct: 126 SIATVADGHSLELEVHVERGVGYRPVDRHNEETSAIDLLQIDAVFMPVTRVNFTIDETAV 185

Query: 189 ----SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK-- 242
               SARE       +L M I TDGSIT +D++A ++  L       I   +P   V   
Sbjct: 186 AEGGSARE-------RLRMEIVTDGSITPDDALAQSANQL-------IELFQPLATVTLV 231

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           E++  +  P   A +  +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS
Sbjct: 232 EEVPAEPEPSAEAQI-PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKS 290

Query: 303 LVEIKGVLGTMGL 315
             E+   L  +G+
Sbjct: 291 ADEVIEALERIGI 303


>gi|51209922|ref|YP_063586.1| RNA polymerase alpha subunit [Gracilaria tenuistipitata var. liui]
 gi|68053119|sp|Q6B8X4|RPOA_GRATL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|50657676|gb|AAT79661.1| RNA polymerase alpha subunit [Gracilaria tenuistipitata var. liui]
          Length = 314

 Score =  164 bits (416), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 100/298 (33%), Positives = 167/298 (56%), Gaps = 19/298 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL +G   TLGN+LRR ++S L+GAAI AV+I G+ HE S+I GV ED+ +I+LN+
Sbjct: 23  FILEPLNKGQGITLGNSLRRTILSDLQGAAIVAVRIAGINHEFSTITGVREDVLEILLNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK   D+ +   I  +GP ++T G  +   +I +++P   I  +  + +  ME  +
Sbjct: 83  KKVVLKSHSDTPQIGRIRLQGPAIITTGLFEVPPEILIIDPQQYIATICNNTIFEMEFRI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GY    +   +   I  + IDA++ P+ K +YTVE  +   +L  +KL + + T+G
Sbjct: 143 EKGSGY-KLVNKGFDKKSIDFLQIDAVFMPVTKFNYTVEEKKISPILIQEKLFLEVWTNG 201

Query: 210 SITGEDSVALASRILQDQLG-----MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           S++ +++++  +++L           F N      E +E+IN         +L  +EEL+
Sbjct: 202 SLSPQEAISEGAQVLHSLFYPLTNLNFQNANNTDNEYEEEIN--------QVL--IEELQ 251

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           LSVR+ NCL+   I  + DL+  ++ ++L + NFG+KS  E+   L      LG+ LP
Sbjct: 252 LSVRAYNCLKRAQINSISDLLDYSQDELLEIKNFGQKSAEEVIEALQNK---LGIRLP 306


>gi|150036792|emb|CAN89787.1| DNA-directed RNA polymerase alpha chain [Leuconostoc lactis]
          Length = 198

 Score =  164 bits (416), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 86/194 (44%), Positives = 126/194 (64%), Gaps = 2/194 (1%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  +
Sbjct: 1   LGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDER 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++
Sbjct: 61  SLEIDVQGPAEVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSADENK 120

Query: 163 T--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
              E  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L 
Sbjct: 121 QLREEMPIGVLAVDSIYTPIERVNYHVENTRVGARDDYDKLTFDIWTNGSIKPSDALSLG 180

Query: 221 SRILQDQLGMFINF 234
           ++IL + L     +
Sbjct: 181 AKILAEHLNFVYGY 194


>gi|161511731|emb|CAP16876.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 199

 Score =  164 bits (416), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 88/191 (46%), Positives = 125/191 (65%), Gaps = 2/191 (1%)

Query: 54  SLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGV 113
           SL GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++LK+  D  K + I   GP  
Sbjct: 1   SLPGAAITSVQIDSVLHEFSTIEGVVEDVTQIILNLKKVSLKIESDEDKTLEINVAGPAN 60

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLI 171
           VTAGDI    D+ +LNP+  IC +         LT   G GY  A  +  R  + PIG++
Sbjct: 61  VTAGDIMGDGDVVILNPELPICTVAEGTTFHAVLTADTGRGYTSADENKARKVDMPIGVL 120

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            ID++Y+PI++V+Y VE+ R GQ  DYDKL++ I TDGSIT  ++ +L+++IL + L +F
Sbjct: 121 PIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDIWTDGSITPSEATSLSAKILTEHLAIF 180

Query: 232 INFEEPKKEVK 242
           +N  +  KE +
Sbjct: 181 VNLNDQAKETE 191


>gi|150036836|emb|CAM98283.1| DNA-directed RNA polymerase alpha chain [Leuconostoc fallax]
          Length = 215

 Score =  164 bits (415), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 86/204 (42%), Positives = 131/204 (64%), Gaps = 2/204 (0%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T +ILN+K + L +  D  K + I
Sbjct: 1   LRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVVLAIDSDEEKSLEI 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
             +GP  VTA D+Q   DIEVLNP+  +  +     + M +T  KG GY  A  ++   D
Sbjct: 61  DVQGPAEVTAADLQGSADIEVLNPELHLATVAAGKSLHMTVTAVKGRGYSSADENKQLRD 120

Query: 167 --PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
             PIG++ +D++Y+PI++V+Y VE+ R GQ  DYDKL+  I T+GSI   D+++L ++IL
Sbjct: 121 EMPIGVLAVDSIYTPIERVNYQVENTRVGQRDDYDKLTFDIWTNGSIKPSDALSLGAKIL 180

Query: 225 QDQLGMFINFEEPKKEVKEDINVK 248
            + L +F +      E +  ++V+
Sbjct: 181 SEHLNLFTDISSVAAETEVMVDVE 204


>gi|150036722|emb|CAM98252.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. dextranicum]
          Length = 189

 Score =  164 bits (415), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 86/188 (45%), Positives = 125/188 (66%), Gaps = 2/188 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A
Sbjct: 61  DDERSLEIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSA 120

Query: 159 KHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+
Sbjct: 121 DENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTNGSIKPSDA 180

Query: 217 VALASRIL 224
           ++L ++IL
Sbjct: 181 LSLGAKIL 188


>gi|119662381|emb|CAJ33179.1| RNA polymerase alpha subunit [Lactobacillus sakei subsp. sakei]
          Length = 184

 Score =  164 bits (415), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 80/183 (43%), Positives = 127/183 (69%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           G A+T +QIDGVLHE S+I GV ED+T IILNIK + LK+  +  K + I  +GP  VTA
Sbjct: 2   GTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKLHVEEDKTIEIDVKGPATVTA 61

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
            DI + +D+EVLN D  IC +       +++TV KG GYV A  +++++ PIG++ ID++
Sbjct: 62  ADIISDDDVEVLNTDQYICTVAEGGNFHVQMTVKKGRGYVAAVQNKSDDMPIGVLPIDSI 121

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++I+ + L +F++  +
Sbjct: 122 YTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKIMTEHLAIFVDLTD 181

Query: 237 PKK 239
             K
Sbjct: 182 EAK 184


>gi|321310954|ref|YP_004193283.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma haemofelis
           str. Langford 1]
 gi|319802798|emb|CBY93444.1| DNA-directed RNA polymerase alpha subunit [Mycoplasma haemofelis
           str. Langford 1]
          Length = 326

 Score =  164 bits (414), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 111/317 (35%), Positives = 174/317 (54%), Gaps = 18/317 (5%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
           NI++ +L   +   +++I+ PL +GF  T+GNALRRVL+ S+ GAA+ A++IDGV HE  
Sbjct: 8   NIDFKLLESSQYMASVVIS-PLKQGFGTTIGNALRRVLLGSIPGAAVFAIKIDGVDHEFM 66

Query: 74  SIKGVHEDLTDIILNIKGINLKM-------------SGDSHKRVTIFKRGPGVVTAGDIQ 120
           + +GV ED+T+IILN+K + + +             S      + I K   GVV A DI+
Sbjct: 67  APEGVLEDVTNIILNVKKLVISIDEKVVDVQSLEEKSISEWPTMKIKKNKAGVVYANDIE 126

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               ++V+N D  IC L  D    MEL  +   GY     +R   D + +I+ID+L+SPI
Sbjct: 127 CPPGMKVINKDLKICELSKDVEFGMELYATLDRGYRSFSENRERLDTLKIISIDSLFSPI 186

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF--EEPK 238
            KV + V   +  +    DKL +T+ T+GS+   D+++LA+  L   L     F  E  K
Sbjct: 187 VKVEWKVVEEKTTKQGTTDKLHLTLVTNGSVKAADALSLAAHTLISLLEPISAFNPETSK 246

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +++  +  V +     A+   ++ELEL++RS NCL+   I  + +L + T A+   + N 
Sbjct: 247 RKLIGEAEVATKKV--AMATPIDELELTMRSFNCLKQNGINTITELAEMTRAEAENIKNL 304

Query: 299 GRKSLVEIKGVLGTMGL 315
           G+KSL EI   L   GL
Sbjct: 305 GKKSLNEIIAKLAEKGL 321


>gi|11467449|ref|NP_043595.1| RNA polymerase alpha subunit [Odontella sinensis]
 gi|1350842|sp|P49465|RPOA_ODOSI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1185144|emb|CAA91627.1| RNA polymerase alpha-chain [Odontella sinensis]
          Length = 312

 Score =  164 bits (414), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 96/277 (34%), Positives = 156/277 (56%), Gaps = 1/277 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + + L  G   T+GN  RRVL+S L G AIT V+I GV  E S+I G+ ED+ +I+LN+
Sbjct: 23  FVIKSLHPGQGITIGNLFRRVLLSDLGGTAITGVRIAGVRDEFSTIPGIREDILEILLNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KGI LK   +  K   +  +GP VVTA  IQ  +++E++NP+H I  +    V+ +E  +
Sbjct: 83  KGIVLKSKTNDLKFGRLKIKGPAVVTANCIQLPSEVEIVNPNHYIATITTSNVLEIEFKI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GY  A     +      + IDA++ P++KV + +E+  +      ++L + I T+G
Sbjct: 143 ESGTGYKLAGQTFCKKSQ-DYLQIDAIFMPVQKVDFKIENIYDNSNDLTERLFLDIWTNG 201

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           S++ E++V+ ASR +       +  + P++  + +    S P NP     +EEL LSVR+
Sbjct: 202 SMSPEEAVSSASRFIISFFSSLLENKLPQETKESENKTLSAPKNPHTNIAIEELHLSVRA 261

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            NCL+   I  +GDL++ +   +  + NFGRKS  E+
Sbjct: 262 YNCLKRAQINTIGDLLKYSPEKLQELKNFGRKSADEV 298


>gi|22297649|ref|NP_680896.1| DNA-directed RNA polymerase subunit alpha [Thermosynechococcus
           elongatus BP-1]
 gi|34222870|sp|Q8DML0|RPOA_THEEB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|22293826|dbj|BAC07658.1| RNA polymerase alpha subunit [Thermosynechococcus elongatus BP-1]
          Length = 321

 Score =  164 bits (414), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 104/297 (35%), Positives = 167/297 (56%), Gaps = 16/297 (5%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G   T+GNALRRVL+S+L G+A+TAV+I GV HE S+I GV ED+ DI+L +K + 
Sbjct: 26  PLAPGQGITVGNALRRVLLSNLPGSAVTAVRIAGVNHEFSTIPGVREDVMDILLQMKQLV 85

Query: 94  LKMSGDSHKRVTIFKRGPG----VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           ++      +   +F + P      VTAG +Q  +++EV+NP+H I  L   A + ME  +
Sbjct: 86  IRSHTSEPQMGRLFAQAPENEPLTVTAGMVQLGSEVEVVNPNHYIATLMPGATLEMEFKI 145

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR----EGQVLDYDKLSMTI 205
            K  GY   +  R +   +  + +DA++ P+++V+YTV+S R    EG     D L + I
Sbjct: 146 EKDRGYRSVERVRDDRLALDYLQLDAVFMPVRRVNYTVDSVRSAGAEGDRQLQDYLKLEI 205

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+GS+T +D++  A+ IL D   +F   +E      E            +   +E+L L
Sbjct: 206 WTNGSLTPQDALNQAATILVD---LFSPLKEVPLHTSEATATDDHDETGQI--PIEQLNL 260

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           SVR+ NCL+   +  + DL++ ++ ++L + NFG+KS  E   V+  +   LG+ LP
Sbjct: 261 SVRAYNCLKRAQVNTVADLLEYSQEELLEIKNFGQKSAEE---VIEALQKHLGITLP 314


>gi|283794918|ref|YP_003359271.1| RNA polymerase alpha subunit [Cryptomonas paramecium]
 gi|253981890|gb|ACT46807.1| RNA polymerase alpha subunit [Cryptomonas paramecium]
          Length = 310

 Score =  164 bits (414), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 103/294 (35%), Positives = 166/294 (56%), Gaps = 17/294 (5%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           +PL  G   T+GNALRRVL+S L G AIT+ ++ G +HE S I G  ED+ +I+LN+K I
Sbjct: 26  QPLKLGQGLTIGNALRRVLLSDLEGIAITSARVSGSVHEFSEIPGTREDVLEILLNLKKI 85

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LK S        +  +GP +VTA D +  + ++ ++P   I  +    V+ +E+++S G
Sbjct: 86  VLKGSSKDAGIARLKVQGPCIVTASDFELPSFVKAVDPSQYIATICDSNVLEIEVSISAG 145

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GY        ++    L  +DA++ P+ KV+YT+E       +  +KL++ I T+GS+T
Sbjct: 146 RGYKLVNRQSLDSGKDSL-ELDAVFMPVNKVNYTIEEINTDFPIAEEKLTLEIWTNGSLT 204

Query: 213 GEDSVALASRILQDQLG----MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
            E+S+  A+ +L D L     + +  EE     KE   VK+LP        +E+L+LSVR
Sbjct: 205 PEESLMQAATVLTDILAPIQRIHLTDEEDFPADKEP-EVKNLP--------IEDLKLSVR 255

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           + NCL+  NI Y  DL+ R++ ++L + NFG+K   E+   L  +   +G+ LP
Sbjct: 256 AYNCLKQINIDYTEDLLTRSQEELLEIKNFGKKCCEEVTQALKNI---VGLTLP 306


>gi|150186935|emb|CAK30131.1| RNA polymerase alpha subunit [Streptococcus macedonicus]
          Length = 203

 Score =  164 bits (414), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 82/187 (43%), Positives = 127/187 (67%)

Query: 53  SSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
           SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP 
Sbjct: 1   SSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPA 60

Query: 113 VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT 172
            VTAGDI T +D+E++NPDH +  +     ++  +TV+K  GYV A+ ++ E+ P+G + 
Sbjct: 61  EVTAGDILTDSDVEIVNPDHYLFTIAEGHSLKATMTVAKERGYVSAEGNKKEDAPVGTLA 120

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F 
Sbjct: 121 VDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFT 180

Query: 233 NFEEPKK 239
           +  E  K
Sbjct: 181 DLTEVAK 187


>gi|150036716|emb|CAM98021.1| DNA-directed RNA polymerase alpha chain [Fructobacillus durionis]
          Length = 197

 Score =  164 bits (414), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 88/194 (45%), Positives = 124/194 (63%), Gaps = 2/194 (1%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRVL+SSL G AI  VQIDGV+HE S++ GV ED+T +ILN+K +          
Sbjct: 1   LGNSLRRVLLSSLPGVAINTVQIDGVVHEFSTVDGVAEDVTQLILNLKKVVFATDSAEEH 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + I  +GP  VTA D     DIEVLNPD  I  L     + M +TV KG GY  A+ ++
Sbjct: 61  TLEIDVQGPKDVTAADFVGSADIEVLNPDLHIATLAAGKSLHMTVTVVKGRGYASAEENK 120

Query: 163 TEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
              D  PIG++T+D++Y+PI++V+Y VE  R G   D+DKL+M + T+GSI   D+++L 
Sbjct: 121 QLRDEMPIGVLTVDSIYTPIERVNYHVEQKRVGSRDDFDKLTMEVWTNGSIKPSDALSLG 180

Query: 221 SRILQDQLGMFINF 234
           S+IL + L +F + 
Sbjct: 181 SKILTEHLNLFTDI 194


>gi|76665073|emb|CAJ17984.1| DNA-directed RNA polymerase alpha subunit [Candidatus Phytoplasma
           solani]
          Length = 318

 Score =  164 bits (414), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 104/307 (33%), Positives = 174/307 (56%), Gaps = 10/307 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I +PL RG+  T+GNALRR+L+SSL GAAI  V+I+GV  E ++I GV+ED+  IILN+
Sbjct: 15  FIIQPLERGYGVTIGNALRRILLSSLPGAAIVNVKIEGVEQEFTTIPGVYEDVMTIILNL 74

Query: 90  KGINLKM---SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           K I  K+   S D  +++ I   GP  VTA   +    + ++NP H I  +  +    M 
Sbjct: 75  KKIVFKVDDESDDFEEQLEINLTGPKKVTAACFELPAGVTIINPKHHITTISDNINFHMT 134

Query: 147 LTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVL-DYDKLSMT 204
           +T+ KG GYV AK ++  ++  IG+I ID+L++P+  V+Y V     G+ L + D+L++ 
Sbjct: 135 VTIKKGIGYVGAKDNKIHSENQIGVIAIDSLFTPVLDVAYQV-----GKKLGNKDELTIQ 189

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           I T+G+   ++++  A++IL +   + +   +    ++     K    N  L  ++E+L+
Sbjct: 190 ITTNGAAVAKEALVTAAKILVEHFNVIVELSQKVANIEFIPETKEEAHNYVLDLEIEQLD 249

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           LSVR  N L+   I  +  L++ +E +++++ + GRKS  E+K      GL     L + 
Sbjct: 250 LSVRLFNSLKRAGINTVAALVKLSEKEVVKLKSLGRKSFQELKDKFVEYGLEFNDYLKEA 309

Query: 325 PPESIEE 331
              S EE
Sbjct: 310 LHHSTEE 316


>gi|148243238|ref|YP_001228395.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp.
           RCC307]
 gi|172047891|sp|A5GVY3|RPOA_SYNR3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|147851548|emb|CAK29042.1| DNA-directed RNA polymerase alpha chain [Synechococcus sp. RCC307]
          Length = 312

 Score =  163 bits (413), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 107/309 (34%), Positives = 169/309 (54%), Gaps = 14/309 (4%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + ++Y +   + ++   +I  PL RG A TLG ALRRVLMS L G A+TAV+I GV HE 
Sbjct: 7   DRVDYQIADDQSQSGVFVIG-PLDRGQATTLGTALRRVLMSGLEGTAVTAVRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           +++ GV ED+ DI+LN K + L       +   +   GP  VTAGD+Q  + + V+N D 
Sbjct: 66  ATVPGVREDVLDILLNCKELVLSSRSRDTEIGRLVVNGPASVTAGDLQFSSQVSVVNADC 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P +    +   + L+ IDA++ P+++V++TV+    
Sbjct: 126 PIATVADGHALELEVHVERGVGYRPVERTSEDAAALDLLQIDAVFMPVRRVNFTVDETAV 185

Query: 193 GQVLDY-DKLSMTIDTDGSITGEDSVALASR---ILQDQLGMFINFEEPKKEVKEDINVK 248
           G+     ++L + I+T+GSIT +D++A A+     L   L      EEP +E  E     
Sbjct: 186 GEGGSARERLRLEINTNGSITPDDALAYAANQLIALFQPLATVTLAEEPGQE-PEPSAES 244

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
            +P         EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+  
Sbjct: 245 QIPL--------EELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGAKSADEVIE 296

Query: 309 VLGTMGLFL 317
            L  +G+ L
Sbjct: 297 ALERIGISL 305


>gi|77409855|ref|ZP_00786488.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae COH1]
 gi|77171535|gb|EAO74771.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae COH1]
          Length = 212

 Score =  163 bits (413), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 83/208 (39%), Positives = 135/208 (64%)

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  +TAGDI T +DIE++NPDH +  +     ++  +TV+K  GYVPA+ ++ ++ P+G
Sbjct: 1   GPAEITAGDILTDSDIEIVNPDHYLFTIAEGHSLKATMTVAKNRGYVPAEGNKKDDAPVG 60

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L 
Sbjct: 61  TLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLN 120

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +F +  E  K  +     + +     L + +EEL+LSVRS NCL+   I  + DL ++TE
Sbjct: 121 LFTDLTEVAKATEVMKETEKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVXDLTEKTE 180

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            +M+++ N GRKSL E+K  L  +GL L
Sbjct: 181 PEMMKVRNLGRKSLEEVKIKLADLGLGL 208


>gi|300870622|ref|YP_003785493.1| DNA directed RNA polymerase subunit alpha [Brachyspira pilosicoli
           95/1000]
 gi|300688321|gb|ADK30992.1| DNA directed RNA polymerase alpha subunit [Brachyspira pilosicoli
           95/1000]
          Length = 325

 Score =  163 bits (413), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 104/301 (34%), Positives = 170/301 (56%), Gaps = 10/301 (3%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           N    +A+P  RG+A T+GNALRRVL+SS+ G AITA++IDGV +E  ++ G+ ED   +
Sbjct: 26  NYGKFVAQPFERGYATTIGNALRRVLLSSIPGYAITAIKIDGVTNEFENVPGMKEDTIVM 85

Query: 86  ILNIKGINLKMSGD-SHKRVTIFKRGPGVVT-AGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           I+++K + + +  +   K + I K GP  VT A       D+ V NP+H I  +      
Sbjct: 86  IMHLKNVVVALPENVDAKTIHIKKEGPCTVTAADFASADADVSVFNPEHHIATIAEGYTF 145

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD-YDKLS 202
            M++ +  G+ YVPA+ +    + +  I IDA+YSPI  V + V+  R GQ ++ Y KL+
Sbjct: 146 EMDVQIESGYNYVPAEVNMELLEDVNAIAIDAIYSPIVSVKFAVDDVRVGQRINYYGKLT 205

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL----LK 258
           + I+T G+I  E +++ A+++L+D L  F+    P++   +D  ++  P +  L     K
Sbjct: 206 LEIETKGNIAPEKALSWAAKLLRDNLTPFM---LPEEANGDDEKIEETPKDSVLDSLKDK 262

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            VEE+E SVR+ N L   ++  +  +  +T+AD+LR+       + EIK  L      LG
Sbjct: 263 HVEEVEFSVRTANFLISSDLKTLDKVALKTDADLLRLIGANEMIIEEIKEKLAEYNAHLG 322

Query: 319 M 319
           M
Sbjct: 323 M 323


>gi|124112107|ref|YP_001019081.1| alpha subunit of RNA polymerase [Chlorokybus atmophyticus]
 gi|158512761|sp|A2CI44|RPOA_CHLAT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|124012216|gb|ABM87965.1| alpha subunit of RNA polymerase [Chlorokybus atmophyticus]
          Length = 318

 Score =  163 bits (412), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 104/297 (35%), Positives = 161/297 (54%), Gaps = 23/297 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +  PL  G   T+GN  RRVL+  L GA IT+VQI GV HE S+I GV E + DI+LN+
Sbjct: 28  FVIAPLEIGQGITVGNVFRRVLLGDLEGACITSVQIPGVNHEFSTIHGVREAVLDILLNL 87

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK      +R  +  +GP  V A D+Q  + IE+++PD  I  +     + ME TV
Sbjct: 88  KEIVLKTQSQETQRGHLSVQGPSTVLARDLQLPSSIELVDPDQYIATISGRVSLNMEFTV 147

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GY    + + +   + ++ IDA++ P+ KV+YTVE    G     +++ + + T+G
Sbjct: 148 EVGKGYQLPDYEKKKTFQVDVLPIDAVFMPVTKVNYTVEENYGGD-RSQERVIIEVWTNG 206

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK--------VE 261
           SI    ++ L+       +   IN   P +      NV+S+   P + +K        VE
Sbjct: 207 SINSRQAIDLS-------VNKIINLFSPLQ------NVRSIEHEPLVKEKDSKMTEVLVE 253

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE-IKGVLGTMGLFL 317
           EL+LSVR+ NCL+   I  + DL+  ++ D+L + NFGR+S  E I+G+   +G+ L
Sbjct: 254 ELDLSVRAYNCLKRAQIHTVSDLLSYSQEDLLEIKNFGRRSAEEVIEGLQKRLGIHL 310


>gi|88807908|ref|ZP_01123419.1| DNA-directed RNA polymerase alpha subunit [Synechococcus sp. WH
           7805]
 gi|88787947|gb|EAR19103.1| DNA-directed RNA polymerase alpha subunit [Synechococcus sp. WH
           7805]
          Length = 312

 Score =  163 bits (412), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 107/313 (34%), Positives = 169/313 (53%), Gaps = 26/313 (8%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ +     +    +I  PL RG A TLGN+LRRVLM +L G A+TAV+I GV HE 
Sbjct: 7   DRIEHQIADDRSQTGVFLIG-PLERGQATTLGNSLRRVLMGNLEGTAVTAVRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K I +       +   +   GP  V A D+Q  + ++V++ + 
Sbjct: 66  ATIPGVREDVLDILLNCKQITVNSRTSELEIGRLVVAGPATVKARDLQFSSQVQVIDGER 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE---- 188
           VI  +     + +E+ V +G GY P   H  +   I L+ IDA++ P+ +V++T++    
Sbjct: 126 VIATVGESYSLELEVHVERGIGYRPVDRHNEDTSAIDLLQIDAVFMPVHRVNFTIDETAV 185

Query: 189 ----SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK-- 242
               SARE       +L M + TDGSIT +D++A A+          I   +P   V   
Sbjct: 186 AEGGSARE-------RLRMEVVTDGSITPDDAIAQAA-------NQLIELFQPLATVTMV 231

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           E+++ +  P   A +  +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS
Sbjct: 232 EEVSAEPEPTAEAQI-PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKS 290

Query: 303 LVEIKGVLGTMGL 315
             E+   L  +G+
Sbjct: 291 ADEVIEALERIGI 303


>gi|119668357|emb|CAK95473.1| RNA polymerase alpha subunit [Lactobacillus pontis]
          Length = 179

 Score =  163 bits (412), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 85/177 (48%), Positives = 128/177 (72%), Gaps = 2/177 (1%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           G+  TLG++LR VL++SL GAAIT++QIDGVLHE S+ +GV ED+T IILN+K ++LK++
Sbjct: 1   GYGTTLGDSLRGVLLASLPGAAITSMQIDGVLHEFSTDEGVTEDVTQIILNLKKVSLKIN 60

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
            +  K + +  +GP  VTA DIQ   ++ +LNPD  I  +   A + +++T  KG GY+ 
Sbjct: 61  SEDQKDLELDVKGPAEVTAADIQGDGEVTILNPDLHIATVADGAELHIKMTADKGRGYLS 120

Query: 158 AKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           A  +  R E+  IG++ ID++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T
Sbjct: 121 ANDNKARMEDLAIGVLPIDSIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLT 177


>gi|87124986|ref|ZP_01080833.1| Bacterial RNA polymerase, alpha chain [Synechococcus sp. RS9917]
 gi|86167306|gb|EAQ68566.1| Bacterial RNA polymerase, alpha chain [Synechococcus sp. RS9917]
          Length = 312

 Score =  163 bits (412), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 103/293 (35%), Positives = 162/293 (55%), Gaps = 27/293 (9%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG A TLGNALRRVLM  L G+A+TAV+I GV HE +++ GV ED+ DI+LN K ++
Sbjct: 27  PLERGQATTLGNALRRVLMGGLEGSAVTAVRIAGVNHEYATVPGVREDVLDILLNCKQLS 86

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +       +   +   GP  V A D+Q  + ++V++P+  I  +     + +E+ V +G 
Sbjct: 87  VNSRTSELEIGRLVVAGPAEVKARDLQFSSQVQVVDPERPIATVSDGHSLELEVHVERGI 146

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE--------SAREGQVLDYDKLSMTI 205
           GY P   H  +   I L+ IDA++ P+++V+++++        SARE       +L M +
Sbjct: 147 GYRPVDRHNEDTSAIDLLQIDAVFMPVQRVNFSIDETAVAEGGSARE-------RLRMEV 199

Query: 206 DTDGSITGEDSVALASRILQD---QLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
            TDGSIT +D++A A+ +L +    L      EEP  E +     + +P         EE
Sbjct: 200 VTDGSITPDDAIAQAANLLIELFQPLATVTMVEEPGLEPEPSAEAQ-IPL--------EE 250

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           L LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L  +G+
Sbjct: 251 LNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALERIGI 303


>gi|150186985|emb|CAK30142.1| RNA polymerase alpha subunit [Streptococcus gallolyticus subsp.
           gallolyticus]
          Length = 204

 Score =  163 bits (412), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 80/183 (43%), Positives = 125/183 (68%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTA
Sbjct: 2   GAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTA 61

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
           GDI T +D+E++NPDH +  +     ++  +TV+K  GYVPA+ ++ E+ P+G + +D++
Sbjct: 62  GDILTDSDVEIVNPDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKEDAPVGTLAVDSI 121

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E
Sbjct: 122 YTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTE 181

Query: 237 PKK 239
             K
Sbjct: 182 VAK 184


>gi|197294604|ref|YP_001799145.1| DNA-directed RNA polymerase subunit alpha [Candidatus Phytoplasma
           australiense]
 gi|171853931|emb|CAM11894.1| DNA-directed RNA polymerase alpha subunit [Candidatus Phytoplasma
           australiense]
          Length = 330

 Score =  163 bits (412), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 98/290 (33%), Positives = 167/290 (57%), Gaps = 8/290 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A ++GN+LRR L+SSL G AI  V I+GV HE ++I GV+ED+  IILN+
Sbjct: 24  FIFYPLVKGHATSIGNSLRRTLLSSLPGTAIVNVSIEGVEHEFTTISGVYEDVMTIILNL 83

Query: 90  KGINLKM---SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           K I  K+   S D  +++ I   GP  +TA        ++++NP+  I  +  D    M 
Sbjct: 84  KKIIFKVDDESNDFEEKLKISLSGPQKITAASFGLPEGVKIINPEAPIATISSDINFNMT 143

Query: 147 LTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
            T+ KG GYV AK ++  ++  +G+I ID+L++P+  V+Y VE     ++ + ++L+M I
Sbjct: 144 ATIKKGIGYVSAKDNKVHSENQLGVIPIDSLFTPVVNVAYQVEK----KIGNKEELTMEI 199

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  ++++A A++IL +   +     +    V+     K    N  L  ++E+L+L
Sbjct: 200 TTNGALLAKEALATAAKILVEHFNVVSELSQQTPNVEFVSERKPEAHNYFLDLEIEQLDL 259

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           SVR  N L+   I  + DL++ +E +++++ + GRKS  E+K      GL
Sbjct: 260 SVRLFNSLKRAGINTVADLVKLSEREVVKLKSLGRKSFQELKDKFVEYGL 309


>gi|11465443|ref|NP_045166.1| RNA polymerase alpha subunit [Cyanidium caldarium]
 gi|12230610|sp|Q9TLV2|RPOA_CYACA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|6466346|gb|AAF12928.1|AF022186_50 unknown [Cyanidium caldarium]
          Length = 310

 Score =  162 bits (411), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 107/298 (35%), Positives = 174/298 (58%), Gaps = 12/298 (4%)

Query: 15  IEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS 74
           +E +V+   E     MI EPL  G A T+GNALRRVL+S + G  I +V+I G+ HE S+
Sbjct: 13  LESMVINSREIYGKFMI-EPLSYGQAITVGNALRRVLLSDVPGVTIVSVRIAGINHEFST 71

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           +KGV ED+ +I+LN+K I LK +   ++   +  +GP +VT+G I+   DI V++P   I
Sbjct: 72  VKGVKEDVLEILLNLKNIVLKGNVLKNQIGRLKVQGPAIVTSGQIEFPLDITVVDPCQYI 131

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
             +  +  + MEL V K  GY   +   ++  P+  + ID+++ P+KKV+Y VE   + +
Sbjct: 132 ATISGNDYLEMELKVEKSSGYKLVETF-SKKSPLDFLPIDSIFMPVKKVNYYVEEILDSK 190

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
           V  Y+KL + + T+GS++ + S+  AS    D L    N   P + +       S+    
Sbjct: 191 V-AYEKLILELWTNGSLSPQQSINYAS----DNLVKLFN---PLRVLDFSKESSSVYEQN 242

Query: 255 ALLKK--VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           +L+K+  +EEL LSVR+ NCL+   +  +GDL++ +  D+L + NFG+KS+ E+   L
Sbjct: 243 SLIKQKLIEELCLSVRAYNCLKRVQVDSIGDLLEYSIGDLLEIKNFGQKSVEEVSKAL 300


>gi|34558004|ref|NP_907819.1| DNA-directed RNA polymerase subunit alpha [Wolinella succinogenes
           DSM 1740]
 gi|41688621|sp|Q7M8F7|RPOA_WOLSU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|34483722|emb|CAE10719.1| RNA POLYMERASE ALPHA SUBUNIT [Wolinella succinogenes]
          Length = 331

 Score =  162 bits (410), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 106/303 (34%), Positives = 171/303 (56%), Gaps = 10/303 (3%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +N+  + A P   G+A TL + LRR+L+ S  G A TA++I+G  HE  S++G+ ED+  
Sbjct: 21  KNKIKISAYPFESGYAITLAHPLRRLLLGSSVGFAPTALKIEGAAHEFDSVRGIMEDVAL 80

Query: 85  IILNIKGINLKMSGDSHKRVTI---FKRGPGVVTAGDIQTVND-IEVLNPDHVICNLDVD 140
            I+N+K I  KM GD+ +RVT+   FK GP  +   D+  VND ++V+ P+  +  ++ D
Sbjct: 81  FIVNLKSIRFKMRGDA-ERVTLDYSFK-GPATIKGSDL--VNDYVDVVTPNQHLATINED 136

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
           A +   L V KG GYVP++  R    P G I +DA ++P+KK +Y +E+        Y+K
Sbjct: 137 ATLTFSLIVQKGIGYVPSEETRNLI-PEGYIPLDAYFTPVKKATYEIENVLVEDNPTYEK 195

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           + + I+TDG I    +   A  ++Q Q+ +F N E      +   + +  P    LL+K+
Sbjct: 196 IVLEIETDGLIEPIAAFKDALGVMQKQMSVF-NSEWSVSSAESTSSDEEDPELKPLLQKI 254

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           E L LS RS NCL    + ++G+L+   E ++  + N G+KS  EIK  L  +G  +G +
Sbjct: 255 EALNLSARSFNCLDRAGMKFVGELVLLGENELKEVKNLGKKSFDEIKDKLEEIGYPVGSD 314

Query: 321 LPD 323
           L +
Sbjct: 315 LAE 317


>gi|154424865|emb|CAL18535.1| RNA polymerase alpha subunit [Streptococcus thoraltensis]
          Length = 203

 Score =  162 bits (410), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 80/190 (42%), Positives = 129/190 (67%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           VL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ +K   +  K + +  +
Sbjct: 1   VLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNVKGLAVKSYVEDEKIIELDVQ 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  VTAGDI T +DIE++N DH +  +   A  +  +TV+   GYV A+ ++ ++ P+G
Sbjct: 61  GPAEVTAGDILTDSDIEIVNSDHYLFTIAEGASFKASMTVATNRGYVAAEGNKKDDAPVG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L 
Sbjct: 121 TLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLN 180

Query: 230 MFINFEEPKK 239
           +F +  E  K
Sbjct: 181 LFTDLTEVAK 190


>gi|154424863|emb|CAL18534.1| RNA polymerase alpha subunit [Streptococcus thoraltensis]
          Length = 200

 Score =  162 bits (410), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 80/190 (42%), Positives = 129/190 (67%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           VL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ +K   +  K + +  +
Sbjct: 1   VLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNVKGLAVKSYVEDEKIIELDVQ 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  VTAGDI T +DIE++N DH +  +   A  +  +TV+   GYV A+ ++ ++ P+G
Sbjct: 61  GPAEVTAGDILTDSDIEIVNSDHYLFTIAEGASFKASMTVATNRGYVAAEGNKKDDAPVG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L 
Sbjct: 121 TLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLN 180

Query: 230 MFINFEEPKK 239
           +F +  E  K
Sbjct: 181 LFTDLTEVAK 190


>gi|150036708|emb|CAM98019.1| DNA-directed RNA polymerase alpha chain [Leuconostoc carnosum]
          Length = 199

 Score =  162 bits (410), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 86/196 (43%), Positives = 126/196 (64%), Gaps = 2/196 (1%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + + I
Sbjct: 1   LRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDEERVLEI 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--E 164
             +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++   E
Sbjct: 61  DVQGPSEVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSADENKQLRE 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
             PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L S+IL
Sbjct: 121 EMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSLGSKIL 180

Query: 225 QDQLGMFINFEEPKKE 240
            + L +F++      E
Sbjct: 181 AEHLNLFMDISPVAAE 196


>gi|227871774|ref|ZP_03990179.1| DNA-directed RNA polymerase [Oribacterium sinus F0268]
 gi|227842375|gb|EEJ52600.1| DNA-directed RNA polymerase [Oribacterium sinus F0268]
          Length = 314

 Score =  162 bits (410), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 103/323 (31%), Positives = 181/323 (56%), Gaps = 19/323 (5%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE + +  E++     + EPL RG+  TLGN+LRR+++SSL GAAI+A++I+ 
Sbjct: 3   DFTKPN-IEILEI-SEDKRFGRFVCEPLERGYGSTLGNSLRRMMLSSLPGAAISAIKIEN 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIE 126
           +  +   + G+ E   +++ N+K I + +  +     V++   G   + A D    ++++
Sbjct: 61  LSGD--KVSGIQESFPELLTNLKSIAVILPEEVESLEVSVDLSGKSEILAEDFIGESELK 118

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           + NP   I  ++  A   + L +S+G GY   K       P     IDALY+P+++V+ +
Sbjct: 119 LSNPTEHIATVEAGAQGSISLFISRGQGYSGEKAEGRVEAPKEYQDIDALYTPVERVNMS 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK---- 242
           +E+ R G + DYD+L++ + T+GS++ ED+++ A+++L   L +F+   E     +    
Sbjct: 179 IENTRVGNMTDYDRLTLDVYTNGSMSPEDAISKAAQMLFQHLDLFVALSEEVAATELMVD 238

Query: 243 --EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ED   K +  N      ++ELELSVRS NCL+   I  + +L  +T  DM+++ N GR
Sbjct: 239 KPEDEKGKVMEMN------IDELELSVRSYNCLKRAGINTVSELTSKTPEDMMKVRNLGR 292

Query: 301 KSLVEIKGVLGTMGLFLGMNLPD 323
           KSL E+   L    L LG++ P+
Sbjct: 293 KSLEEVLAKL--RDLNLGLSFPE 313


>gi|78211905|ref|YP_380684.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp.
           CC9605]
 gi|119366745|sp|Q3AMQ3|RPOA_SYNSC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|78196364|gb|ABB34129.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus sp.
           CC9605]
          Length = 312

 Score =  162 bits (410), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 109/313 (34%), Positives = 170/313 (54%), Gaps = 26/313 (8%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ V     ++   +I  PL RG A TLGNALRRVLM  L G+A+TA++I GV HE 
Sbjct: 7   DRIEHQVADDRAQSGVFLIG-PLERGQATTLGNALRRVLMGGLEGSAVTAIRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           +++ GV ED+ DI+LN K + +       +   +   GP  V AGD+Q  + ++V++ D 
Sbjct: 66  ATVPGVREDVLDILLNCKELTVNSRSAELEIGRLVVAGPAEVKAGDLQFSSQVQVVDTDR 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE---- 188
            I  +     + +EL V +G GY P   H  E   I L+ IDA++ P+ +V++T++    
Sbjct: 126 PIATVADGHSLELELHVERGVGYRPVDRHNEETSAIDLLQIDAVFMPVTRVNFTIDETAV 185

Query: 189 ----SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK-- 242
               SARE       +L M I TDGSIT ++++A ++  L       I   +P   V   
Sbjct: 186 AEGGSARE-------RLRMEIVTDGSITPDEALAQSANQL-------IELFQPLATVTLV 231

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           E++  +  P   A +  +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS
Sbjct: 232 EEVPAEPEPSAEAQI-PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKS 290

Query: 303 LVEIKGVLGTMGL 315
             E+   L  +G+
Sbjct: 291 ADEVIEALERIGI 303


>gi|194477035|ref|YP_002049214.1| DNA-directed RNA polymerase alpha subunit [Paulinella
           chromatophora]
 gi|171192042|gb|ACB43004.1| DNA-directed RNA polymerase alpha subunit [Paulinella
           chromatophora]
          Length = 308

 Score =  162 bits (409), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 105/287 (36%), Positives = 155/287 (54%), Gaps = 11/287 (3%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG A TLGN+LRRVLM SL G+AITAV+I GV HE ++I GV ED+ DI+LN K ++
Sbjct: 27  PLDRGHAITLGNSLRRVLMGSLEGSAITAVRIAGVSHEYATIPGVREDVLDILLNCKQVS 86

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +       +   +   GP  VTA D Q  + ++V+     I  +     + ME+ V +G 
Sbjct: 87  ISSRNQELEIGRLVVSGPANVTAADFQFSSQVQVVYGSSPIVTIAEGHSIEMEVHVERGV 146

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY-DKLSMTIDTDGSIT 212
           GY P   H  +   I L+ IDA++ P+++V+YT++    G+     ++L + I+T+GSIT
Sbjct: 147 GYRPVNRHNEDTSAIDLLQIDAVFMPVRRVNYTIDETAVGEGGSARERLRLEIETNGSIT 206

Query: 213 GEDSVALASRILQDQLGMFINFE--EPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
            ED++A A+  L        N    E      E      +P         EEL LSVR+ 
Sbjct: 207 PEDAMAEAANQLISMFQPLANLTMVEEPIPEPEPPTEAQIPL--------EELNLSVRAY 258

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           NCL+   +  + DL+  +  D+L + NFG KS  E+   L  +GL L
Sbjct: 259 NCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALERIGLSL 305


>gi|119662827|emb|CAJ33206.1| RNA polymerase alpha subunit [Lactobacillus gastricus]
          Length = 172

 Score =  162 bits (409), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 82/172 (47%), Positives = 122/172 (70%), Gaps = 2/172 (1%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRV+++SL GAAIT++QIDGVLHE S++ GV ED+T IILN+K + L++ GD  K
Sbjct: 1   LGNSLRRVMLASLPGAAITSIQIDGVLHEFSTVDGVTEDVTQIILNLKKVALRIDGDDAK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + +  +GP  VTA DIQ   D+ +LNPD  +  +   A + +++T  KG GY  A  ++
Sbjct: 61  DLEVDVKGPTEVTAADIQGYGDVSILNPDLHLATVADGAELHIKMTADKGRGYSSADDNK 120

Query: 163 TEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           +  D   IG++ ID++Y+PI +V+YTVE+ R GQ  DYDKL++ + T+GS+T
Sbjct: 121 SNMDMSAIGVLPIDSIYTPIDRVNYTVENTRVGQSNDYDKLTLDVWTNGSLT 172


>gi|150187178|emb|CAK30188.1| RNA polymerase alpha subunit [Streptococcus acidominimus]
          Length = 174

 Score =  162 bits (409), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 78/173 (45%), Positives = 121/173 (69%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAA+T+++IDGVLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  +TA
Sbjct: 2   GAAVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKTIELDVTGPAEITA 61

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
           GDI T +DIE++NPDH +  +   A  +  +TV+ G GYVPA+ ++ ++ P+G + +D++
Sbjct: 62  GDILTDSDIEIVNPDHYLFTISEGATFKAMMTVNTGRGYVPAEGNKKDDAPVGTLAVDSI 121

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + LG
Sbjct: 122 YTPVKKVNYQVEPARVGSNDGFDKLTLEIMTNGTIIPEDALGLSARILMEHLG 174


>gi|26554440|ref|NP_758374.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma penetrans
           HF-2]
 gi|38372493|sp|Q8EUD7|RPOA_MYCPE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|26454450|dbj|BAC44778.1| RNA polymerase subunit alpha [Mycoplasma penetrans HF-2]
          Length = 331

 Score =  162 bits (409), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 99/296 (33%), Positives = 169/296 (57%), Gaps = 21/296 (7%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
           + + +PL RGF HTLGN+LRRVL+S++ G ++ A++I  V HE  SIKGV EDLT IILN
Sbjct: 23  VFVFKPLERGFGHTLGNSLRRVLLSNIIGHSLFAIKIPNVSHEFQSIKGVKEDLTQIILN 82

Query: 89  IKGINLKMS----GDSHKRVTIFKRGP---------GVVTAGDIQTVNDIEVLNPDHVIC 135
           +K + +K+     G+  ++ T  ++ P         GV+ A DI+T    E++N D  I 
Sbjct: 83  LKRLVVKIDQEIFGEEEQKETSLEKWPTLKIDFSKGGVLKASDIETPVGFEIINKDMYIA 142

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
            ++     +MEL V  G G+     ++   + I +I +D+ +SP+ KV Y V   +  + 
Sbjct: 143 TIESGVKFKMELFVKTGRGFTTFSENKELINAINVIAVDSNFSPVLKVGYKVSDIKTTKN 202

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLG-----MFINFEEPKKEVKEDINVKSL 250
              D L + + T+G+++  ++VA++++IL +        +F N+ + +  + E+  V S 
Sbjct: 203 EINDVLELEVATNGAVSAAEAVAMSAKILLEHYKPIVTELFDNYNDLRI-INEEATVSSS 261

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
             + A+   ++ELELSVRS NCL+   I  +  L  +T+ ++ ++ N G+KS  EI
Sbjct: 262 KSSLAI--SIDELELSVRSYNCLKRAGIHTITQLTDKTKGEIEKIRNLGKKSFKEI 315


>gi|145586271|emb|CAM91230.1| RNA polymerase alpha-subunit [Lactobacillus plantarum subsp.
           argentoratensis]
          Length = 176

 Score =  162 bits (409), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 84/176 (47%), Positives = 121/176 (68%), Gaps = 2/176 (1%)

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGVLHE S+I+GV ED+T IILN+K I LK+  D  K + I  +GP  VTAGDI    D+
Sbjct: 1   DGVLHEFSTIEGVTEDVTAIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADV 60

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK--HHRTENDPIGLITIDALYSPIKKV 183
           EVLNPD  IC +   A   M +T + G GYV A+   HR ++ PIG++ +D+LYSPI++V
Sbjct: 61  EVLNPDLPICTVADGAHFHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +Y VE+ R GQ  D+DKL++ + T+GSIT  ++++L+++IL D L +F+N  +  K
Sbjct: 121 NYQVENTRVGQRDDFDKLTLDVWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAK 176


>gi|90994483|ref|YP_536973.1| RNA polymerase alpha subunit [Porphyra yezoensis]
 gi|109900623|sp|Q1XDJ5|RPOA_PORYE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|90819047|dbj|BAE92416.1| DNA directed RNA polymerase alpha subunit [Porphyra yezoensis]
 gi|116266126|gb|ABJ91301.1| DNA-directed RNA polymerase alpha subunit [Porphyra yezoensis]
          Length = 311

 Score =  162 bits (409), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 101/296 (34%), Positives = 164/296 (55%), Gaps = 15/296 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL +G   TLGNALRR ++S L G AI AV+I GV HE S+I GV ED+ +I+LN+
Sbjct: 23  FVIEPLNQGQGITLGNALRRSILSDLEGTAIVAVRIAGVNHEFSTIPGVREDVLEILLNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K +  K      +   I  +GP +VTAG  +  +DIEV++P   I  +  + +  ME  +
Sbjct: 83  KEVVFKSYNKESQIGRIRVQGPAIVTAGLFELSSDIEVVDPRQYIATICNNTIFEMEFKI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            K  GY  A+    E   +  + +D+++ P+ KV+Y VE  R G     D+L + I T+G
Sbjct: 143 EKNCGYRLAEKAVDEL-SVDFLQVDSVFMPVNKVNYKVEEVRIGSNSIKDRLIIQIWTNG 201

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALLKKVEELELS 266
           SI+ +++++  + +L +      N +    +    KED  +  +         +EEL+LS
Sbjct: 202 SISPQEAISQGATVLTNLFCSLRNLDFKSADNYRSKEDKKISQVL--------IEELQLS 253

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           VR+ NCL+   I  + DL+  ++ ++L + NFG+KS  E   V+  +   LG++LP
Sbjct: 254 VRAYNCLKRAQIHSIADLLDYSQEELLEIKNFGQKSAEE---VIYALQKKLGISLP 306


>gi|150187007|emb|CAK30149.1| RNA polymerase alpha subunit [Streptococcus pluranimalium]
          Length = 200

 Score =  162 bits (409), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 79/189 (41%), Positives = 128/189 (67%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG 110
           L+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ +K   +  K + +  +G
Sbjct: 1   LLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNVKGLAVKSYVEDEKTIELDVQG 60

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
           P  VTAGDI T +DIE++N DH +  +   A  +  +TV+   GYV A+ ++ ++ P+G 
Sbjct: 61  PAEVTAGDILTDSDIEIVNSDHYLFTIAEGASFKASMTVATNRGYVAAEGNKKDDAPVGT 120

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +
Sbjct: 121 LAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTVEIMTNGTIIPEDALGLSARVLIEHLNL 180

Query: 231 FINFEEPKK 239
           F +  E  K
Sbjct: 181 FTDLTEVAK 189


>gi|116075744|ref|ZP_01473003.1| DNA-directed RNA polymerase alpha subunit [Synechococcus sp.
           RS9916]
 gi|116067059|gb|EAU72814.1| DNA-directed RNA polymerase alpha subunit [Synechococcus sp.
           RS9916]
          Length = 312

 Score =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 106/314 (33%), Positives = 169/314 (53%), Gaps = 28/314 (8%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ +     +    +I  PL RG A TLGN+LRRVLM  L G+A+TAV+I GV HE 
Sbjct: 7   DRIEHQIADDRAQTGVFLIG-PLERGQATTLGNSLRRVLMGGLEGSAVTAVRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           +++ GV ED+ DI+LN K +++       +   +   GP  V A D+Q  + ++V++P+ 
Sbjct: 66  ATVPGVREDVLDILLNCKQLSVNSRSSELEIGRLVVAGPSEVKARDLQFSSQVQVVDPER 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE---- 188
            I  +     + +EL V +G GY P   H  + + I L+ IDA++ P+ +V+++++    
Sbjct: 126 TIATVSDGHSLELELHVERGIGYRPVDRHSEDTNAIDLLQIDAVFMPVHRVNFSIDETAV 185

Query: 189 ----SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD---QLGMFINFEEPKKEV 241
               SARE       +L M + TDGSIT +D++A A+  L +    L      EEP  E 
Sbjct: 186 AEGGSARE-------RLRMEVVTDGSITPDDAIAEAANQLIELFQPLATVTMVEEPGLEP 238

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +     + +P         EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG K
Sbjct: 239 EPSAEAQ-IPL--------EELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSK 289

Query: 302 SLVEIKGVLGTMGL 315
           S  E+   L  +G+
Sbjct: 290 SADEVIEALERIGI 303


>gi|161511775|emb|CAP16898.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 193

 Score =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 86/188 (45%), Positives = 123/188 (65%), Gaps = 2/188 (1%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++LK+  D  K + I   GP  VTA
Sbjct: 2   GAAITSVQIDSVLHEFSTIEGVVEDVTQIILNLKKVSLKIESDEDKTLEINVAGPANVTA 61

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITID 174
           GDI    D+ +LNP+  IC +         LT   G GY  A  +  R  + PIG++ ID
Sbjct: 62  GDIMGDGDVVILNPELPICTVAEGTTFHAVLTADTGRGYTSADENKARKVDMPIGVLPID 121

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           ++Y+PI++V+Y VE+ R GQ  DYDKL++ I TDGSIT  ++ +L+++IL + L +F+N 
Sbjct: 122 SIYTPIERVNYQVENTRVGQRDDYDKLTLDIWTDGSITPSEATSLSAKILTEHLAIFVNL 181

Query: 235 EEPKKEVK 242
            +  KE +
Sbjct: 182 NDQAKETE 189


>gi|154424813|emb|CAL18509.1| RNA polymerase alpha subunit [Streptococcus intermedius]
          Length = 177

 Score =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 78/177 (44%), Positives = 121/177 (68%)

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
           AA+T++ I+GVLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  VTAG
Sbjct: 1   AAVTSINIEGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEGEKTIELDVEGPAEVTAG 60

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI T +DIE++NP+H +  +   A ++  +TV+ G GYVPA  ++ ++ P+G + +D++Y
Sbjct: 61  DILTDSDIEIVNPNHYLFTIGEGASLKAVMTVNTGRGYVPADENKKDDAPVGTLAVDSIY 120

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           +P+KKV+Y VE AR G    +DKL++ I TDG+I  ED++ L++RIL + L +F N 
Sbjct: 121 TPVKKVNYQVEPARVGSNDSFDKLTLEIMTDGTIIPEDALGLSARILTEHLDLFTNL 177


>gi|150187174|emb|CAK30187.1| RNA polymerase alpha subunit [Streptococcus devriesei]
          Length = 161

 Score =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 76/160 (47%), Positives = 113/160 (70%)

Query: 35  LPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL 94
           L RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ +
Sbjct: 1   LERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNLKGLAV 60

Query: 95  KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHG 154
           K   +  K + +   GP  +TAGDI T +DIE++NPDH +  +   A ++  LTV    G
Sbjct: 61  KSYVEEEKIIELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIAEGASLKATLTVDTNRG 120

Query: 155 YVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
           Y+PA+ ++ ++ P+G + ID++Y+P+KKV+Y VE AR G 
Sbjct: 121 YIPAEENKKDDAPVGTLAIDSIYTPVKKVNYQVEPARVGS 160


>gi|150036842|emb|CAM98286.1| DNA-directed RNA polymerase alpha chain [Leuconostoc carnosum]
          Length = 179

 Score =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 84/179 (46%), Positives = 119/179 (66%), Gaps = 2/179 (1%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVV 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L +  D  + + I  +GP  VTA D+Q   D++VLNPD  I  +     + M +T  KG 
Sbjct: 61  LAIDSDEERVLEIDVQGPSEVTAADLQAGADVKVLNPDLHIATVAAGKSLHMTVTAVKGR 120

Query: 154 GYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           GY  A  ++   E  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GS
Sbjct: 121 GYSSADENKQLREEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGS 179


>gi|159904196|ref|YP_001551540.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. MIT 9211]
 gi|159889372|gb|ABX09586.1| Bacterial RNA polymerase, alpha chain [Prochlorococcus marinus str.
           MIT 9211]
          Length = 312

 Score =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 107/290 (36%), Positives = 162/290 (55%), Gaps = 11/290 (3%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
           L +  PL RG A TLGN+LRRVLM  L G+A+TAV+I GV HE ++I GV ED+ DI+LN
Sbjct: 22  LFLIGPLERGQATTLGNSLRRVLMGGLEGSAVTAVRISGVNHEYATIPGVREDVLDILLN 81

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
            K +++       +   +   GP  V A D+Q  + ++V++ D  I  +     + +EL 
Sbjct: 82  CKQLSVNSRSPELEIGRLVVNGPAEVKARDVQFSSQVQVVDGDRPIATVHSGHSLELELH 141

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV-ESAREGQVLDYDKLSMTIDT 207
           V +G GY P   H  E   I L+ IDA++ PIKKV++ + E+A        ++L M I T
Sbjct: 142 VERGVGYRPVDRHNEETTSIDLLHIDAVFMPIKKVNFNIDETAVAEGGSTRERLKMEIVT 201

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVK--EDINVKSLPFNPALLKKVEELEL 265
           DGS++ +D++A A+  L       I   +P   V   E+I  +  P   A +  +EEL L
Sbjct: 202 DGSMSPDDALAEAANQL-------IELFQPLATVTMVEEIPQEPEPSAEAQI-PLEELNL 253

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           SVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L  +G+
Sbjct: 254 SVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALERIGI 303


>gi|154424731|emb|CAL18468.1| RNA polymerase alpha subunit [Streptococcus thermophilus]
          Length = 179

 Score =  161 bits (407), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 78/178 (43%), Positives = 123/178 (69%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAA+T+++IDGVLHE  ++ GV ED+  IILNIKG+ +K   +  K + +  +GP  VTA
Sbjct: 1   GAAVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGLAVKSYVEDEKTIELDVQGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
           GDI T +DIE++NPDH +  +   A  +  +TVS   GYVPA+ ++ ++ P+G + +D++
Sbjct: 61  GDILTDSDIEIVNPDHYLFTIAEGASFQATMTVSTNRGYVPAEENKKDDAPVGTLAVDSI 120

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F + 
Sbjct: 121 YTPVKKVNYQVEPARVGSNDGFDKLTIEIVTNGTIIPEDALGLSARILIEHLNLFTDL 178


>gi|150036732|emb|CAM98257.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. mesenteroides]
          Length = 186

 Score =  161 bits (407), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 84/186 (45%), Positives = 123/186 (66%), Gaps = 2/186 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A
Sbjct: 61  DDERSLEIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSA 120

Query: 159 KHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+
Sbjct: 121 DENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTNGSIKPSDA 180

Query: 217 VALASR 222
           ++L ++
Sbjct: 181 LSLGAK 186


>gi|87300890|ref|ZP_01083732.1| DNA-directed RNA polymerase alpha subunit [Synechococcus sp. WH
           5701]
 gi|87284761|gb|EAQ76713.1| DNA-directed RNA polymerase alpha subunit [Synechococcus sp. WH
           5701]
          Length = 312

 Score =  161 bits (407), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 107/288 (37%), Positives = 160/288 (55%), Gaps = 13/288 (4%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG A TLGNALRRVLM  + G+AITAV+I GV HE ++I GV ED+ DI+LN K + 
Sbjct: 27  PLDRGQAITLGNALRRVLMGGMEGSAITAVRIAGVNHEYATIPGVREDVLDILLNCKEVV 86

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +       +   +   GP  VTA D+Q  + ++V++ D  I  +     + +E+ V KG 
Sbjct: 87  VNSRNRDLEIGRLIVNGPASVTAADLQFSSQVQVIDFDRPIATVAEGHSLELEVHVEKGV 146

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY-DKLSMTIDTDGSIT 212
           GY P   H  +   I L+ IDA++ P+++V+YTV+    G+     ++L + I T GSIT
Sbjct: 147 GYRPVDRHHEDTSAIDLLQIDAVFMPVRRVNYTVDETAVGEGGSARERLRLEIVTSGSIT 206

Query: 213 GEDSVALAS-RILQ--DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
            +D++A A+ +++Q    L      EEP  E  E      +P         EEL LSVR+
Sbjct: 207 PDDAMAQAANQLIQLFQPLASLTMVEEPGLE-PEPSAESQIPL--------EELNLSVRA 257

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   +  + DL+  +  D+L + NFG KS  E+   L  +G+ L
Sbjct: 258 YNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALERIGISL 305


>gi|148238747|ref|YP_001224134.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp. WH
           7803]
 gi|158513313|sp|A5GIS2|RPOA_SYNPW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|147847286|emb|CAK22837.1| DNA-directed RNA polymerase alpha chain [Synechococcus sp. WH 7803]
          Length = 312

 Score =  161 bits (407), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 107/313 (34%), Positives = 169/313 (53%), Gaps = 26/313 (8%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ +     +    +I  PL RG A TLGN+LRRVLM +L G A+TAV+I GV HE 
Sbjct: 7   DRIEHQIADDRSQTGVFLIG-PLERGQATTLGNSLRRVLMGNLEGTAVTAVRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K I +       +   +   GP  V A D+Q  + ++V++ + 
Sbjct: 66  ATIPGVREDVLDILLNCKQITVNSRTSELEIGRLVVAGPATVKARDLQFSSQVQVVDGER 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE---- 188
            I  +     + +E+ V +G GY P   H  +   I L+ IDA++ P+ +V++T++    
Sbjct: 126 AIATVGEGYSLELEVHVERGIGYRPVDRHNEDTSAIDLLQIDAVFMPVHRVNFTIDETAV 185

Query: 189 ----SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK-- 242
               SARE       +L M + TDGSIT +D++A A+  L       I   +P   V   
Sbjct: 186 AEGGSARE-------RLRMEVVTDGSITPDDAIAQAANQL-------IELFQPLATVTMV 231

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           E+++ +  P   A +  +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS
Sbjct: 232 EEVSAEPEPTAEAQI-PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKS 290

Query: 303 LVEIKGVLGTMGL 315
             E+   L  +G+
Sbjct: 291 ADEVIEALERIGI 303


>gi|150187056|emb|CAK30161.1| RNA polymerase alpha subunit [Streptococcus cristatus ATCC 51100]
          Length = 172

 Score =  161 bits (407), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 79/172 (45%), Positives = 118/172 (68%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL++SL GAA+T++ I+GVLHE  +I GV ED+  IILNIKGI +K      K +
Sbjct: 1   NSLRRVLLASLPGAAVTSINIEGVLHEFDTISGVREDVMQIILNIKGIAVKSYVQDEKMI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  VTAGDI T +DIE++NPDH +  +   A  + ++ V+ G GYVPA  ++ +
Sbjct: 61  ELDVEGPAEVTAGDILTDSDIEIVNPDHYLFTISEGARFKAKMAVNSGRGYVPADENKKD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
           + P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED+
Sbjct: 121 DAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDA 172


>gi|149072030|ref|YP_001293601.1| RNA polymerase alpha subunit [Rhodomonas salina]
 gi|172048721|sp|A6MW22|RPOA_RHDSA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134302981|gb|ABO70785.1| RNA polymerase alpha subunit [Rhodomonas salina]
          Length = 314

 Score =  161 bits (407), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 103/292 (35%), Positives = 167/292 (57%), Gaps = 13/292 (4%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL +G   TLGNALRR L+S L G AI AV+I GV HE S+I G+ ED+ +I+LN+K +
Sbjct: 26  EPLEQGQGVTLGNALRRTLLSDLEGTAIVAVRIAGVSHEFSTIPGIREDVLEILLNLKEV 85

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LK    +     +  +GP +VT  +++  +++E+++P+  I  +  + ++ ME  +  G
Sbjct: 86  VLKSQTKNPSVGRLRVQGPAIVTTSNLELPSEVELIDPNQYIATICGNNILEMEFRIETG 145

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GY   +    E   I  + +DA++ P+KKV+Y  +  R    L  ++L + + T+GSI 
Sbjct: 146 KGYHLIERSIDETS-IDFLQVDAIFMPVKKVNYLTKDIRSNDNLLQEQLLLEVWTNGSID 204

Query: 213 GEDSVALASRILQDQLGMF--INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
            +D+V+   +IL + L     INF    K  +ED   +    N  L   +EEL+LSVR+ 
Sbjct: 205 PQDAVSQGGKILTELLHPLKEINF----KSDEEDTVAEDSKINQIL---IEELQLSVRAY 257

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           NCL+   I  + DL+  ++ D++ + NFG+KS  E   V+  +   LG+NLP
Sbjct: 258 NCLKRAQIHSVADLLDYSQEDLIEIKNFGQKSAEE---VIDALQKRLGINLP 306


>gi|47679549|gb|AAT36718.1| RNA polymerase alpha subunit [Chaetoceros gracilis]
          Length = 300

 Score =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 98/268 (36%), Positives = 155/268 (57%), Gaps = 7/268 (2%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-- 99
           T+GN LRRVL+S L G  ITAV+I GV  E S I G+ ED+ +I+LN+KG+ +K +    
Sbjct: 37  TIGNLLRRVLLSDLEGTTITAVRIAGVQDEFSIIPGIREDILEILLNLKGVVVKSATPDI 96

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
           S  R+ I  +GP VVTA  IQ   +IE++NP+H I  +    V+ +E    +G GY  A 
Sbjct: 97  SFGRLKI--KGPAVVTADSIQLPPNIEIINPNHYIATISTSNVLEIEFKFERGTGYKLAG 154

Query: 160 HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
               +      + IDA++ PI+KV + +E+  +      ++L + I T+GSI+ +D+++ 
Sbjct: 155 QTFCDKSE-DFLQIDAIFMPIQKVDFKIENVYDNSNSITERLFLDIWTNGSISPDDAISY 213

Query: 220 ASRILQDQLGMFI-NFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENI 278
           AS+ + +     + N      E+ ED N  +   NP +   +EEL+LSVR+ NCL+   I
Sbjct: 214 ASKFIIEFFNSLLENKITQNLEIIEDTNSLT-QLNPHINIAIEELQLSVRAYNCLKRAQI 272

Query: 279 VYMGDLIQRTEADMLRMANFGRKSLVEI 306
             +GDL++ +   +  + NFGRKS  E+
Sbjct: 273 NTIGDLLEYSPEKLQELKNFGRKSADEV 300


>gi|154424853|emb|CAL18529.1| RNA polymerase alpha subunit [Streptococcus salivarius]
          Length = 199

 Score =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 77/183 (42%), Positives = 125/183 (68%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAA+T+++IDGVLHE  ++ GV ED+  IILNIKG+ +K   +  K + +  +GP  VTA
Sbjct: 1   GAAVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGLAVKSYVEDEKTIELDVQGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
           GDI T +DIE++NPDH +  +   A ++  +TV+   GYVPA  ++ ++ P+G + +D++
Sbjct: 61  GDILTDSDIEIVNPDHYLFTIADGASLKATMTVATNRGYVPADENKKDDAPVGTLAVDSI 120

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  +
Sbjct: 121 YTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTD 180

Query: 237 PKK 239
             K
Sbjct: 181 VAK 183


>gi|47679551|gb|AAT36719.1| RNA polymerase alpha subunit [Thalassiosira sp. Cleve BA153110]
          Length = 300

 Score =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 98/280 (35%), Positives = 153/280 (54%), Gaps = 7/280 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + + L  G   T+GN LRRVL+  L+G AIT V+I GV  E S I GV ED+ +I+LN+
Sbjct: 25  FLIDSLSSGQGITIGNLLRRVLLGDLKGTAITGVRIAGVKDEFSLIPGVREDILEILLNL 84

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KGI LK    + +   +   GP V+TA  IQ   D+E++NP+H I  L    ++ +E  +
Sbjct: 85  KGIVLKSKNSTRQFARLRLHGPAVITASSIQLPPDVEIINPNHYIATLSSSHILEIEFKI 144

Query: 150 SKGHGYVPAKHHRTENDPIG-LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
             GH Y  A  + T +D +   I  DA++ P +K  + VE+  +      +++ + + T+
Sbjct: 145 ESGHDYRLA--NETFSDKLSNFIETDAIFMPDQKDDFKVENVYDNSNNVKERVFLDVWTN 202

Query: 209 GSITGEDSVALASRILQDQLGMFI--NFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           GSI+ E ++  AS ++ D           + K+ +KE    K  P +P     +EEL+LS
Sbjct: 203 GSISPEQAIFSASNLIIDLFKSITEHKINQEKESIKEKTQTK--PVDPYTHIAIEELQLS 260

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           VR  NCL+   I  +GDL+  +   +L + NFGRKS  E+
Sbjct: 261 VRPYNCLKRAQINTIGDLLDYSPEKLLELKNFGRKSADEV 300


>gi|150187076|emb|CAK30165.1| RNA polymerase alpha subunit [Streptococcus ferus]
          Length = 191

 Score =  160 bits (405), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 78/179 (43%), Positives = 122/179 (68%)

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI 
Sbjct: 1   TSIKIDGVLHEFDTIPGVREDVMQIILNLKGLAVKSYVEDEKTMELDVEGPAEVTAGDIL 60

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIE++NPDH +  +   A ++  LTV+   GYVPA+ ++ ++ P+G + ID++Y+P+
Sbjct: 61  TDSDIEIVNPDHYLFTIADGASMKATLTVATNRGYVPAEENKNDSAPVGTLAIDSIYTPV 120

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           KKV+Y VE AR G   +YDKL++ I T+G+I  ED++ L++R+L + L +F +  E  K
Sbjct: 121 KKVNYQVEPARVGSKDNYDKLTIEIMTNGTIIPEDALGLSARVLMEHLNLFTDLTEVAK 179


>gi|33866622|ref|NP_898181.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp. WH
           8102]
 gi|41688634|sp|Q7U4H7|RPOA_SYNPX RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|33633400|emb|CAE08605.1| RNA polymerase alpha subunit [Synechococcus sp. WH 8102]
          Length = 312

 Score =  160 bits (405), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 108/307 (35%), Positives = 170/307 (55%), Gaps = 28/307 (9%)

Query: 22  QEEENRT---LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
           Q EE+R+   + +  PL RG A TLGNALRRVLM  L G+A+TA++I GV HE +++ GV
Sbjct: 12  QVEEDRSQSGVFLIGPLERGQATTLGNALRRVLMGGLEGSAVTAIRIAGVNHEYATVPGV 71

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+ DI+LN K +++       +   +   GP  VTA D+Q  + +EV++ +  I  + 
Sbjct: 72  REDVLDILLNCKELSVNSRSPELEIGRLVVAGPAEVTAKDLQFSSQVEVVDGNRSIATVA 131

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE--------SA 190
               + +E+ V +G GY P   H  +   I L+ IDA++ P+ +V++T++        SA
Sbjct: 132 DGYSLELEVHVERGVGYRPVDRHSEDTSAIDLLQIDAVFMPVIRVNFTIDETAVAEGGSA 191

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK--EDINVK 248
           RE       +L M I TDGSIT +D++A ++  L       I   +P   V   E+  ++
Sbjct: 192 RE-------RLRMEIVTDGSITPDDALAQSANYL-------IELFQPLATVTLVEEPGIE 237

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
             P   A +  +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+  
Sbjct: 238 PEPSAEAQI-PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIE 296

Query: 309 VLGTMGL 315
            L  +G+
Sbjct: 297 ALERIGI 303


>gi|318042541|ref|ZP_07974497.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp.
           CB0101]
          Length = 312

 Score =  160 bits (404), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 102/288 (35%), Positives = 159/288 (55%), Gaps = 13/288 (4%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG A TLGN+LRRVLM +L G+AITAV+I GV HE +++ GV ED+ DI+LN K I 
Sbjct: 27  PLERGQAITLGNSLRRVLMGALEGSAITAVRIAGVNHEYATVPGVREDVLDILLNCKDIA 86

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +       +   +   GP  VTA D+Q  + + V++ D  I  +     + +E+ V +G 
Sbjct: 87  VSSRTRELEIGRLVANGPCTVTASDLQFSSQVSVIDGDRPIATVADGYSLELEVHVERGV 146

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY-DKLSMTIDTDGSIT 212
           GY P      +   I L+ IDA++ P+++V+Y+V+    G+     ++L + I+TDGS+T
Sbjct: 147 GYRPVDRRSEDTSAIDLLQIDAVFMPVRRVNYSVDETAVGEGGSARERLRLEIETDGSVT 206

Query: 213 GEDSVALASR---ILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
            +D++A A+     L   L      +EP  E +     + +P         EEL LSVR+
Sbjct: 207 PDDAMAQAANQLIALFQPLASLTMVDEPGLEPEPSAEAQ-IPL--------EELNLSVRA 257

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            NCL+   +  + DL+  +  D+L + NFG KS  E+   L  +G+ L
Sbjct: 258 YNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALERIGISL 305


>gi|330850862|ref|YP_004376612.1| DNA-directed RNA polymerase alpha chain [Fistulifera sp. JPCC
           DA0580]
 gi|328835682|dbj|BAK18978.1| DNA-directed RNA polymerase alpha chain [Fistulifera sp. JPCC
           DA0580]
          Length = 311

 Score =  160 bits (404), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 97/289 (33%), Positives = 161/289 (55%), Gaps = 2/289 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +   L  G   T+GN LRRVL+  L G AI+AV+I G+ HE S+I GV ED+ +I+LN+
Sbjct: 23  FVINALRAGQGITIGNQLRRVLLGDLGGMAISAVRIAGITHEFSTIPGVREDILEILLNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KGI LK   +  +   +  +GP VVTA  IQ  +++E++NP+H I  +    ++ +E   
Sbjct: 83  KGIVLKSEINDIQFGRLKVQGPAVVTADLIQLPSNLEIINPNHYIATISTSNILEIEFKF 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GY  A    T+ D    + +D ++ PI+KV + +E+  +      ++L + I T+G
Sbjct: 143 EYGTGYKLATQTFTD-DSENYLQLDTVFMPIQKVDFKIENVYDSANNITERLLLDIWTNG 201

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI+  +++  A++++ D   + IN +      + +   +S    P     +EEL+LSVR+
Sbjct: 202 SISPNEALESAAQVIVDLFTLLINNKNMVNTNQLESKPESSSIEPYTNIAIEELQLSVRA 261

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL-GTMGLFL 317
            NCL+   I  +GDL+Q +   +  + NFGRKS  E+   L   +G+ L
Sbjct: 262 YNCLKKAQINTVGDLLQYSPEKLQELKNFGRKSADEVFSTLKNKLGIIL 310


>gi|119662281|emb|CAJ33127.1| RNA polymerase alpha subunit [Lactobacillus animalis KCTC 3501]
          Length = 167

 Score =  159 bits (403), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 83/167 (49%), Positives = 116/167 (69%), Gaps = 2/167 (1%)

Query: 53  SSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
           SSL GAAIT VQIDGVLHE S++KGV ED+T IILN+K + LK+  +  + +     GP 
Sbjct: 1   SSLPGAAITDVQIDGVLHEFSTVKGVLEDVTAIILNLKKVALKLDSEDSQTLEFDVVGPK 60

Query: 113 VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGL 170
            VTAGDIQ  +D+E+LNPD  IC +   AV    +T +KG GYV A  +  + E+ PIG+
Sbjct: 61  EVTAGDIQGSSDVEILNPDQYICTVADGAVFHARMTANKGRGYVSATENKAKAEDMPIGV 120

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
           + ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T+GSIT  +++
Sbjct: 121 LPIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWTNGSITPSEAI 167


>gi|11465759|ref|NP_053903.1| RNA polymerase alpha subunit [Porphyra purpurea]
 gi|1710668|sp|P51293|RPOA_PORPU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1276759|gb|AAC08179.1| DNA directed RNA polymerase alpha subunit [Porphyra purpurea]
          Length = 311

 Score =  159 bits (403), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 100/296 (33%), Positives = 164/296 (55%), Gaps = 15/296 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + E L +G   TLGNALRR ++S L G AI AV+I GV HE S+I GV ED+ +I+LN+
Sbjct: 23  FVIEALNQGQGITLGNALRRSILSDLEGTAIVAVRIAGVNHEFSTIPGVREDVLEILLNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K +  K +    +   I  +GP +VTAG  +  +DIEV++P   I  +  + +  ME  +
Sbjct: 83  KEVVFKSNNQESQIGRIKVQGPAIVTAGLFELSSDIEVVDPRQYIATICNNTIFEMEFKI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            K  GY  A+    E   +  + +D+++ P+ KV+Y VE  R G     D+L + I T+G
Sbjct: 143 EKSCGYRLAEKAVDEL-SLDFLQVDSVFMPVNKVNYKVEEVRVGTNSIKDRLILQIWTNG 201

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEV---KEDINVKSLPFNPALLKKVEELELS 266
           SI+ +++++  + +L +      N +    +    KED  +  +         +EEL+LS
Sbjct: 202 SISPQEAISQGATVLTNLFCSLRNLDFKSVDTYRNKEDKKISQVL--------IEELQLS 253

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           VR+ NCL+   I  + DL+  ++ ++L + NFG+KS  E   V+  +   LG++LP
Sbjct: 254 VRAYNCLKRAQIHSIADLLDYSQEELLEIKNFGQKSAEE---VIYALQKTLGISLP 306


>gi|150036800|emb|CAM98036.1| DNA-directed RNA polymerase alpha chain [Leuconostoc fallax]
          Length = 196

 Score =  159 bits (403), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 83/194 (42%), Positives = 124/194 (63%), Gaps = 2/194 (1%)

Query: 49  RVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK 108
           R+L+SSL GAA+  VQIDGV+HE S++ GV ED+T +ILN+K + L +  D  K + I  
Sbjct: 2   RILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVVLAIDSDEEKSLEIDV 61

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND-- 166
           +GP  VTA D+Q   DIEVLNP+  +  +     + M +T  KG GY  A  ++   D  
Sbjct: 62  QGPAEVTAADLQGSADIEVLNPELHLATVAAGKSLHMTVTAVKGRGYSSADENKQLRDEM 121

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           PIG++ +D++Y+PI++V+Y VE+ R GQ  DYDKL+  I T+GSI   D+++L ++IL +
Sbjct: 122 PIGVLAVDSIYTPIERVNYQVENTRVGQRDDYDKLTFDIWTNGSIKPSDALSLGAKILSE 181

Query: 227 QLGMFINFEEPKKE 240
            L +F +      E
Sbjct: 182 HLNLFTDISSVAAE 195


>gi|119662389|emb|CAJ33184.1| RNA polymerase alpha subunit [Lactobacillus alimentarius]
          Length = 165

 Score =  159 bits (403), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 74/162 (45%), Positives = 112/162 (69%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG  + LGN+LRRVL++SL G A++ +QIDGVLHE S+I GV ED+T I+LN+K +
Sbjct: 1   EPLERGLWYNLGNSLRRVLLASLPGTAVSDIQIDGVLHEFSAIDGVIEDVTQIVLNVKKL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LK   D   +  I   GP  VTA DI+  +D+E+L+P+  IC +       M++TV  G
Sbjct: 61  KLKSYADDSLKAEIDVVGPATVTAKDIKADDDLEILDPEQFICTVAEGGHFHMQMTVING 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
            GY PA+ ++T+  PIG++ +D++++P++KV+Y VE+ R G+
Sbjct: 121 RGYTPAEQNKTDETPIGVLPVDSIFTPVEKVNYQVENTRVGK 162


>gi|150186992|emb|CAK30144.1| RNA polymerase alpha subunit [Streptococcus minor]
          Length = 189

 Score =  159 bits (403), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 77/181 (42%), Positives = 123/181 (67%)

Query: 59  AITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGD 118
           A+T+++IDGVLHE  ++ GV ED+  IILNIKGI +K   +  K++ +   GP  +TAGD
Sbjct: 1   AVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKKIELDVVGPAEITAGD 60

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           I T +DIE++NPDH +  +   A  +  LTV++G GYVPA+ ++ +  P+G + +D++Y+
Sbjct: 61  ILTDSDIEIVNPDHYLFTIGEGASFKAILTVNRGRGYVPAEGNKKDEAPVGTLAVDSIYT 120

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ KV+Y VE AR G    +DKL++ I T+G+   ED++ L++RIL + LG+F +  +  
Sbjct: 121 PVVKVNYQVEPARVGSNDGFDKLTLEIMTNGTTNPEDALGLSARILMEHLGLFTDLTDVA 180

Query: 239 K 239
           K
Sbjct: 181 K 181


>gi|154424721|emb|CAL18463.1| RNA polymerase alpha subunit [Streptococcus thermophilus]
          Length = 169

 Score =  159 bits (402), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 78/169 (46%), Positives = 119/169 (70%)

Query: 49  RVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK 108
           RVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILNIKG+ +K   +  K + +  
Sbjct: 1   RVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGLAVKSYVEDEKTIELDV 60

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
           +GP  VTAGDI T +DIE++NPDH +  +   A  +  +TVS   GYVPA+ ++ ++ P+
Sbjct: 61  QGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGASFQATMTVSTNRGYVPAEENKKDDAPV 120

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
           G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++
Sbjct: 121 GTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIVTNGTIIPEDAL 169


>gi|150187112|emb|CAK30173.1| RNA polymerase alpha subunit [Streptococcus equinus]
          Length = 191

 Score =  159 bits (402), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 79/183 (43%), Positives = 124/183 (67%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTA
Sbjct: 2   GAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTA 61

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
           GDI T +D+E++N DH +  +     ++  +TV+K  GYVPA+ ++ E+ P+G + +D++
Sbjct: 62  GDILTDSDVEIVNTDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKEDAPVGTLAVDSI 121

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E
Sbjct: 122 YTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTE 181

Query: 237 PKK 239
             K
Sbjct: 182 VAK 184


>gi|119662803|emb|CAJ33193.1| RNA polymerase alpha subunit [Lactobacillus mali]
          Length = 196

 Score =  159 bits (402), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 80/183 (43%), Positives = 126/183 (68%), Gaps = 2/183 (1%)

Query: 59  AITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGD 118
           AIT +QIDGVLHE S+IKGV ED+T IILN+K + L++  + ++ + I   GP  VTAGD
Sbjct: 1   AITDIQIDGVLHEFSTIKGVLEDVTQIILNLKKVALRIDSEENQTLEINVAGPVEVTAGD 60

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDAL 176
           IQ  +D+EVLN D  IC +   A   + +T + G GYV A  ++   D  PIG++ ID++
Sbjct: 61  IQGSSDVEVLNSDLYICTVAEGASFHVRMTANTGRGYVSADDNKARADDMPIGVLPIDSI 120

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           Y+PI++V+Y VE AR GQ  D+DKL++ + T+G++T  ++++L+++IL + L +F++  +
Sbjct: 121 YTPIERVNYQVEKARVGQKDDFDKLTLDVWTNGAVTPSEAISLSAKILTEHLTLFVDLTD 180

Query: 237 PKK 239
             K
Sbjct: 181 EAK 183


>gi|119672797|emb|CAK95482.1| RNA polymerase alpha subunit [Lactobacillus animalis]
          Length = 190

 Score =  159 bits (402), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 79/177 (44%), Positives = 121/177 (68%), Gaps = 2/177 (1%)

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           IDGVLHE S++KGV ED+T IILN+K + LK+  +  + +     GP  VTAGDIQ  +D
Sbjct: 1   IDGVLHEFSTVKGVLEDVTAIILNLKKVALKLDSEDSQTLEFDVVGPKEVTAGDIQGSSD 60

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKK 182
           +E+LNPD  IC +   AV    +T +KG GYV A  +  + E+ PIG++ ID++Y+PI++
Sbjct: 61  VEILNPDQYICTVADGAVFHARMTANKGRGYVSATENKAKAEDMPIGVLPIDSIYTPIER 120

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           V+Y VE  R GQ  DYDKL++ + T+GSIT  ++++L+++IL + L +F++  +  K
Sbjct: 121 VNYQVEKTRVGQKNDYDKLTLDVWTNGSITPSEAISLSAKILTEHLTLFVDLTDEAK 177


>gi|154424727|emb|CAL18466.1| RNA polymerase alpha subunit [Streptococcus gallolyticus]
          Length = 184

 Score =  159 bits (402), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 79/183 (43%), Positives = 124/183 (67%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTA
Sbjct: 2   GAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTA 61

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
           GDI T +D+E++NPDH +  +     ++  +TV+K  GYV A+ ++ E+ P+G + +D++
Sbjct: 62  GDILTDSDVEIVNPDHYLFTIAEGHSLKATMTVAKERGYVSAEGNKKEDAPVGTLAVDSI 121

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E
Sbjct: 122 YTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTE 181

Query: 237 PKK 239
             K
Sbjct: 182 VAK 184


>gi|313683415|ref|YP_004061153.1| DNA-directed RNA polymerase subunit alpha [Sulfuricurvum kujiense
           DSM 16994]
 gi|313156275|gb|ADR34953.1| DNA-directed RNA polymerase subunit alpha [Sulfuricurvum kujiense
           DSM 16994]
          Length = 330

 Score =  159 bits (402), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 96/312 (30%), Positives = 170/312 (54%), Gaps = 14/312 (4%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
            V+ Q   N   +IA P   GFA +L + +RR L+SS  G A   ++I+G  HE  S++G
Sbjct: 14  FVVEQISANEANIIAYPFETGFAVSLAHPIRRFLLSSSVGFAPIGIKIEGAKHEFDSVRG 73

Query: 78  VHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           + ED++D I+N+KGI  K+ +G   K +T    GP  +   D+   +D+EV+ P+  +  
Sbjct: 74  MLEDISDFIINLKGIRFKLKNGLKEKEITYSFAGPCEIHGSDLDN-DDVEVVTPNAFLAT 132

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPI--GLITIDALYSPIKKVSYTVESAREGQ 194
           L+ DA +   + + +G GY P++  R   D +  G I +DA ++P+++ +Y +E+     
Sbjct: 133 LNEDATLNFSVKIHQGIGYAPSEDVR---DILGDGYIALDAYFTPVRRATYAIENVLVED 189

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF---INFEEPKKEVKEDINVKSLP 251
             +++K+ + I TDG I+  D+   A  ++  Q+ +F   ++ + P    + D +    P
Sbjct: 190 NPNFEKVVINIATDGQISPVDAFKNALEVMYAQMAVFNSEVSIKAPAAAERGDEH----P 245

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  ++E+L LS RS NCL   NI Y+G+++  ++ D+  + N G+KS  EI   + 
Sbjct: 246 ELKRLGARIEDLGLSARSFNCLDRSNIKYIGEIVMMSQNDLKEVKNLGKKSFEEILEKIT 305

Query: 312 TMGLFLGMNLPD 323
             G  +G +L D
Sbjct: 306 EYGYTVGQDLAD 317


>gi|119663530|emb|CAK22336.1| RNA polymerase alpha subunit [Lactobacillus kitasatonis]
          Length = 171

 Score =  159 bits (401), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 81/171 (47%), Positives = 114/171 (66%)

Query: 48  RRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF 107
           RRVL++S+ G  +  VQIDGVL E S++ GV ED+T IILN+K + LK   D  K + + 
Sbjct: 1   RRVLLTSIPGTGLVYVQIDGVLPEFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELD 60

Query: 108 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
             GP  VTA D++   D++VLNPD  IC +     + MEL V  G GYV A  +++++ P
Sbjct: 61  VEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMELAVKNGRGYVTASDNKSDDMP 120

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           IG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++
Sbjct: 121 IGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALS 171


>gi|154173639|ref|YP_001409131.1| DNA-directed RNA polymerase subunit alpha [Campylobacter curvus
           525.92]
 gi|171769258|sp|A7H0Y9|RPOA_CAMC5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|112802250|gb|EAT99594.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter curvus
           525.92]
          Length = 338

 Score =  159 bits (401), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 109/318 (34%), Positives = 168/318 (52%), Gaps = 19/318 (5%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           EN   + A P   G+A TL + LRR+L +S  G A   V+I GV HE  S++G+ ED+  
Sbjct: 21  ENVAKITAYPFETGYAVTLAHPLRRLLYTSTVGFAPIGVKIKGVSHEFDSMRGMLEDVAF 80

Query: 85  IILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVND-IEVLNPDHVICNLDVDAV 142
            I+N+K I  K+  DS + V  +  +GP  +T  D+   ND +E++NPD  +  ++ DA 
Sbjct: 81  FIINLKKIRFKLKNDSEREVVEYSFKGPKEITGADLN--NDVVEIVNPDAYLATINEDAE 138

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           +   + + KG GYVP++  R E +    I +DA ++P+KK  Y +E+       DY+K+ 
Sbjct: 139 LNFSVIIQKGIGYVPSEEIREEIE-DDYIALDAFFTPVKKAVYELENVLVEDDPDYEKIV 197

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN-----PALL 257
            TI TDG +   ++       +  Q+ +F      K  +  D+N   +  +       LL
Sbjct: 198 FTITTDGQVGPIEAFKHCLEAMYQQMSVF------KGVLDIDVNAPMMSSSVGGEHAKLL 251

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             VEEL LS RS NCL    I Y+G+L    E ++  + N G+KSL EIK V+  +G  +
Sbjct: 252 SSVEELNLSARSFNCLDKAEIRYIGELALMDENELKDLKNLGKKSLEEIKAVMEEIGYPV 311

Query: 318 GMNLPDWPPESIEELAKK 335
           G    D   +S E+L KK
Sbjct: 312 G---SDVLKDSKEQLRKK 326


>gi|154424757|emb|CAL18481.1| RNA polymerase alpha subunit [Streptococcus anginosus]
          Length = 184

 Score =  159 bits (401), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 77/179 (43%), Positives = 120/179 (67%)

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T++ I+GVLHE  ++ GV ED+  IILN+KGI +K   +  K + +   GP  +TAGDI 
Sbjct: 1   TSINIEGVLHEFDTVPGVREDVMQIILNVKGIAVKSYVEDEKTIELDVEGPAEITAGDIL 60

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIE++NPDH +  +   A ++  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+
Sbjct: 61  TDSDIEIVNPDHYLFTIGEGASLKAIMTVNTGRGYVPADENKKDDAPVGTLAVDSIYTPV 120

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           KKV+Y VE AR G    +DKL++ I TDG+I  ED++ L++RIL + L +F N  E  K
Sbjct: 121 KKVNYQVEPARVGSNDGFDKLTLEIMTDGTIIPEDALGLSARILTEHLDLFTNLTEVAK 179


>gi|319955882|ref|YP_004167145.1| DNA-directed RNA polymerase subunit alpha [Nitratifractor
           salsuginis DSM 16511]
 gi|319418286|gb|ADV45396.1| DNA-directed RNA polymerase subunit alpha [Nitratifractor
           salsuginis DSM 16511]
          Length = 332

 Score =  159 bits (401), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 100/297 (33%), Positives = 161/297 (54%), Gaps = 14/297 (4%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           + R  +IA P   G+A TL + LRR+L+ S  G A  +V+I+G  HE  SI+G+HED+  
Sbjct: 21  DTRAQVIAYPFESGYAVTLAHPLRRLLLGSSIGYAPISVKIEGAAHEFDSIRGMHEDIAV 80

Query: 85  IILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            I+++K I  K+     + V  +  +GP  V AGD+   + +EV+NPD  +  L+ D  +
Sbjct: 81  FIIHLKNIRFKIKEGLDRAVVSYSFKGPREVVAGDLNN-DQVEVVNPDQPLATLNEDGEL 139

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
              L ++KG GYVP++  + E D    I +DA ++P++K +Y +E+       DY+K+  
Sbjct: 140 TFTLEIAKGIGYVPSEDLQEEVDG-DAIALDAFFTPVRKANYAIENVLVEDNPDYEKIVF 198

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMF-----INFEEPKKEVKEDINVKSLPFNPALLK 258
            I+TDG I+   + A A   +  Q+ +F     ++ E       E+  +K  PF    L 
Sbjct: 199 EIETDGQISPVAAFANALETMHKQMSVFGEVMNLDLERSSGNSAENSELK--PF----LV 252

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
            V+ L L  RS N L    I Y+G+L+  +E ++  + N G+KSL EI+ VL   G 
Sbjct: 253 PVDALGLGARSFNSLDRAGIKYLGELVLMSENELKEIKNLGKKSLDEIQEVLAEHGF 309


>gi|33241138|ref|NP_876080.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           subsp. marinus str. CCMP1375]
 gi|41688642|sp|Q7V9Y5|RPOA_PROMA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|33238668|gb|AAQ00733.1| DNA-directed RNA polymerase alpha subunit/40 kD subunit
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
          Length = 312

 Score =  158 bits (400), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 103/285 (36%), Positives = 157/285 (55%), Gaps = 11/285 (3%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG A TLGN+LRRVLM  L G+A+TAV+I GV HE +++ GV ED+ DI+LN K + 
Sbjct: 27  PLERGQATTLGNSLRRVLMGGLEGSAVTAVRISGVNHEYATVPGVREDVLDILLNCKELT 86

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +       +   +   GP  V A D+Q  + +++++ D  I  +     + +EL V +G 
Sbjct: 87  VNSRSQELEIGRLVVTGPAEVKARDLQFSSQVQIVDVDRPIATVHSGHSLELELHVERGV 146

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV-ESAREGQVLDYDKLSMTIDTDGSIT 212
           GY P          I L+ IDA++ P+KKV++T+ E+A        ++L M I TDGSIT
Sbjct: 147 GYRPVDRRNEATTAIDLLQIDAVFMPVKKVNFTIDETAVSEGGSTRERLRMEIVTDGSIT 206

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVK--EDINVKSLPFNPALLKKVEELELSVRST 270
            +D+VA A+          I   +P   V   E++  +  P   A +  +EEL LSVR+ 
Sbjct: 207 PDDAVAEAA-------NQLIELFQPLATVTMVEEVPQEPEPTAEAQI-PLEELNLSVRAY 258

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           NCL+   +  + DL+  +  D+L + NFG KS  E+   L  +G+
Sbjct: 259 NCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALERIGI 303


>gi|161511711|emb|CAP16866.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 209

 Score =  158 bits (400), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 89/209 (42%), Positives = 130/209 (62%), Gaps = 2/209 (0%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           IT+VQID VLHE S+I+GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI
Sbjct: 1   ITSVQIDSVLHEFSTIEGVVEDVTQIILNLKKVSLKIESDEDKTLEINVAGPANVTAGDI 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALY 177
               D+ +LNP+  IC +         LT   G GY  A  +  R  + PIG++ ID++Y
Sbjct: 61  MGDGDVVILNPELPICTVAEGTTFHAVLTADTGRGYTSADENKARKVDMPIGVLPIDSIY 120

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           +PI++V+Y VE+ R GQ  DYDKL++ I TDGSIT  ++ +L+++IL + L +F+N  + 
Sbjct: 121 TPIERVNYQVENTRVGQRDDYDKLTLDIWTDGSITPSEATSLSAKILTEHLAIFVNLNDQ 180

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELS 266
            KE +  +  +       L   +EEL+LS
Sbjct: 181 AKETEIMVEKEETHKEKMLEMTIEELDLS 209


>gi|113955543|ref|YP_729644.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp.
           CC9311]
 gi|119366743|sp|Q0ID28|RPOA_SYNS3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|113882894|gb|ABI47852.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus sp.
           CC9311]
          Length = 312

 Score =  158 bits (400), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 106/314 (33%), Positives = 167/314 (53%), Gaps = 28/314 (8%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ +     +    +I  PL RG A TLGN+LRR+LM +L G A+TAV+I GV HE 
Sbjct: 7   DRIEHQITDDRSQTGVFLIG-PLERGQATTLGNSLRRMLMGNLAGTAVTAVRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K + +    D  +   +   GP VV A D+Q  + ++V++ + 
Sbjct: 66  ATIPGVREDVLDILLNCKQLTVTSRTDELEIGRLIVSGPAVVKAKDLQFSSQVQVVDGER 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE---- 188
            I  +     + +E+ V +G GY P   H  +   I L+ IDA++ P+ +V++T +    
Sbjct: 126 PIATVSEGHSLELEVHVERGVGYRPVDRHNEDTSAIDLLQIDAVFMPVHRVNFTTDETAV 185

Query: 189 ----SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD---QLGMFINFEEPKKEV 241
               SARE       +L M + TDGS+T +D++A A+  L +    L      EEP  E 
Sbjct: 186 AEGGSARE-------RLRMEVVTDGSMTPDDAIAQAANQLIELFQPLATVTMVEEPGIEP 238

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +     + +P         EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG K
Sbjct: 239 EPSAEAQ-IPL--------EELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSK 289

Query: 302 SLVEIKGVLGTMGL 315
           S  E+   L  +G+
Sbjct: 290 SADEVIEALERIGI 303


>gi|150187135|emb|CAK30178.1| RNA polymerase alpha subunit [Streptococcus oralis ATCC 35037]
          Length = 177

 Score =  158 bits (400), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 76/176 (43%), Positives = 119/176 (67%)

Query: 59  AITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGD 118
           A+T++ IDGVLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  +TAGD
Sbjct: 1   AVTSINIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEITAGD 60

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           I T +DIE++NPDH +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+
Sbjct: 61  ILTDSDIEIVNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYT 120

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N 
Sbjct: 121 PVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNL 176


>gi|78185545|ref|YP_377979.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp.
           CC9902]
 gi|119366744|sp|Q3AW70|RPOA_SYNS9 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|78169839|gb|ABB26936.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus sp.
           CC9902]
          Length = 312

 Score =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 103/292 (35%), Positives = 163/292 (55%), Gaps = 25/292 (8%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG A TLGNALRRVLM  L G+A+TA++I GV HE +++ GV ED+ DI+LN K ++
Sbjct: 27  PLERGQATTLGNALRRVLMGGLEGSAVTAIRIAGVNHEYATVPGVREDVLDILLNCKELS 86

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +       +   +   GP  V A D+Q  + ++V++ +  I  +     + +E+ V +G 
Sbjct: 87  VNSRSAELEIGRLVVAGPAEVKASDLQFSSQVQVIDGNRTIATVADGHSLELEVHVERGI 146

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE--------SAREGQVLDYDKLSMTI 205
           GY P   H  +   I L+ IDA++ P+K+V++ ++        SARE       +L + I
Sbjct: 147 GYRPVDRHNEDTSAIDLLQIDAVFMPVKRVNFNIDETAVAEGGSARE-------RLRIEI 199

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK--EDINVKSLPFNPALLKKVEEL 263
            TDGSIT +D++A  +  L   L +F    +P   V   E++ V+  P   A +  +EEL
Sbjct: 200 STDGSITPDDALAQTANQL---LELF----QPLATVTLVEEVGVEPEPSAEAQI-PLEEL 251

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
            LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L  +G+
Sbjct: 252 NLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALERIGI 303


>gi|119662807|emb|CAJ33195.1| RNA polymerase alpha subunit [Lactobacillus pantheris]
          Length = 165

 Score =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 83/165 (50%), Positives = 119/165 (72%), Gaps = 1/165 (0%)

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           HE S+I GV ED+T IILNIK + LK+ G+   K+ TI   GP VVTA DI+T  D+EVL
Sbjct: 1   HEFSTIDGVLEDVTQIILNIKKLALKVEGEEEDKKATILVEGPAVVTAADIKTDADVEVL 60

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NPD  IC +     + ME+T+  G GYVPA  +++++ PIG+I +D++++PI KV+YTVE
Sbjct: 61  NPDQYICTIAEGGRLEMEMTIKTGRGYVPADQNKSDDQPIGVIAVDSIFTPISKVNYTVE 120

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           SAR G+  D+DKL++ + T+GSIT   ++ALA++IL D L +F+N
Sbjct: 121 SARVGRRSDFDKLTLDVWTNGSITPSAAIALAAKILTDHLAIFVN 165


>gi|152989998|ref|YP_001355720.1| DNA-directed RNA polymerase subunit alpha [Nitratiruptor sp.
           SB155-2]
 gi|172048727|sp|A6Q1K4|RPOA_NITSB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|151421859|dbj|BAF69363.1| DNA-directed RNA polymerase, alpha subunit [Nitratiruptor sp.
           SB155-2]
          Length = 328

 Score =  157 bits (398), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 100/309 (32%), Positives = 169/309 (54%), Gaps = 12/309 (3%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           +EN   +   P   G+A ++ + LRR+L+SS  G A   ++I+GV HE  S++G+ ED+ 
Sbjct: 20  KENAIRLHVYPYESGYAISVAHPLRRLLLSSTAGYAPIGLKIEGVQHEFDSVRGMLEDVA 79

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKR--GPGVVTAGDIQTVND-IEVLNPDHVICNLDVD 140
             I+N+K +  K+     + VT+     GP  +   D +  ND +EV+ PD  +  L+ D
Sbjct: 80  AFIINLKNVRFKLRDSEQENVTLEYEFSGPKELFGKDFE--NDLVEVVTPDAFLATLNED 137

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
           A ++M + V KG GYVP++  R +  P G I +DA ++P+KK  Y +E        +Y+K
Sbjct: 138 AELKMSIIVQKGIGYVPSEMIR-DLLPQGYIPLDAFFTPVKKAVYEIEKVLVEDNPNYEK 196

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           +   I+TDG +    ++ +A  ++Q Q+ +F N  E  + V ++I    + + P     +
Sbjct: 197 IVFDIETDGQVDPVSALKMAMNVMQSQMEIFTNDIEVTETVGQNIENSEIFYQP-----L 251

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           + L+LS RS NCL    I Y+G+L+  +   +  + N G+KSL EI+  L  + + LG  
Sbjct: 252 DILDLSARSYNCLDKAGIKYVGELLLMSNEALKSIKNLGKKSLDEIQEKLSELNIDLG-K 310

Query: 321 LPDWPPESI 329
           L D   E+I
Sbjct: 311 LSDQEKETI 319


>gi|154424795|emb|CAL18500.1| RNA polymerase alpha subunit [Streptococcus gordonii]
          Length = 183

 Score =  157 bits (398), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 78/182 (42%), Positives = 120/182 (65%)

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
           AA+T++ I+GVLHE  +I GV ED+  IILNIKGI +K      K + +   GP  +TAG
Sbjct: 1   AAVTSINIEGVLHEFDTIPGVREDVMQIILNIKGIAVKSYVQDEKMIELDVEGPAEITAG 60

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI T +DIE++NPDH +  +   A  +  +TV+ G GYVPA  ++ ++ P+G + +D++Y
Sbjct: 61  DILTDSDIEIVNPDHYLFTIGEGARFKAVMTVNSGRGYVPADQNKRDDAPVGTLAVDSIY 120

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           +P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F +  E 
Sbjct: 121 TPVTKVNYQVEPARVGSNDGFDKLTLEIMTNGTIIPEDALGLSARILTEHLDLFTDLTEV 180

Query: 238 KK 239
            K
Sbjct: 181 AK 182


>gi|154424785|emb|CAL18495.1| RNA polymerase alpha subunit [Streptococcus ferus]
          Length = 175

 Score =  157 bits (398), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 76/174 (43%), Positives = 120/174 (68%)

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI 
Sbjct: 1   TSIKIDGVLHEFDTIPGVREDVMQIILNLKGLAVKSYVEDEKTMELDVEGPAEVTAGDIL 60

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIE++NPDH +  +   A ++  LTV+   GYVPA+ ++ ++ P+G + ID++Y+P+
Sbjct: 61  TDSDIEIVNPDHYLFTIADGASMKATLTVATNRGYVPAEENKNDSAPVGTLAIDSIYTPV 120

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           KKV+Y VE AR G   +YDKL++ I T+G+I  ED++ L++R+L + L +F + 
Sbjct: 121 KKVNYQVEPARVGSKDNYDKLTIEIMTNGTIIPEDALGLSARVLMEHLNLFTDL 174


>gi|150036726|emb|CAM98254.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. dextranicum]
          Length = 189

 Score =  157 bits (397), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 82/187 (43%), Positives = 123/187 (65%), Gaps = 2/187 (1%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           +L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + + I  +
Sbjct: 1   ILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDIQ 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--P 167
           GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++   D  P
Sbjct: 61  GPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSADENKKLRDEMP 120

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           IG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L ++IL + 
Sbjct: 121 IGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTNGSIKPSDALSLGAKILAEH 180

Query: 228 LGMFINF 234
           LG+F++ 
Sbjct: 181 LGLFMDI 187


>gi|116072177|ref|ZP_01469445.1| DNA-directed RNA polymerase alpha subunit [Synechococcus sp. BL107]
 gi|116065800|gb|EAU71558.1| DNA-directed RNA polymerase alpha subunit [Synechococcus sp. BL107]
          Length = 312

 Score =  157 bits (396), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 103/292 (35%), Positives = 163/292 (55%), Gaps = 25/292 (8%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG A TLGNALRRVLM  L G+A+TA++I GV HE +++ GV ED+ DI+LN K ++
Sbjct: 27  PLERGQATTLGNALRRVLMGGLEGSAVTAIRIAGVNHEYATVPGVREDVLDILLNCKELS 86

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +       +   +   GP  V A D+Q  + ++V++ +  I  +     + +E+ V +G 
Sbjct: 87  VNSRSAELEIGRLVVAGPAEVKASDLQFSSQVQVIDGNRTIATVADGHSLELEVHVERGI 146

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE--------SAREGQVLDYDKLSMTI 205
           GY P   H  +   I L+ IDA++ P+K+V++ ++        SARE       +L + I
Sbjct: 147 GYRPVDRHNEDTSAIDLLQIDAVFMPVKRVNFNIDETAVAEGGSARE-------RLRIEI 199

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK--EDINVKSLPFNPALLKKVEEL 263
            TDGSIT +D++A  +  L   L +F    +P   V   E++ V+  P   A +  +EEL
Sbjct: 200 CTDGSITPDDALAQTANQL---LELF----QPLATVTLVEEVGVEPEPSAEAQI-PLEEL 251

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
            LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L  +G+
Sbjct: 252 NLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALERIGI 303


>gi|154424835|emb|CAL18520.1| RNA polymerase alpha subunit [Streptococcus phocae]
          Length = 153

 Score =  157 bits (396), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 74/153 (48%), Positives = 110/153 (71%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   
Sbjct: 1   YGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYV 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + +   GP  VTAGDI T +DIE++NPDH +  +     +R  +TV+K  GYVPA
Sbjct: 61  EDEKTIELEVEGPATVTAGDILTDSDIELVNPDHYLFTIAEGHSLRATMTVAKKRGYVPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
           + ++ ++ P+G + +D++Y+P+KKV+Y VE AR
Sbjct: 121 EGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPAR 153


>gi|154424787|emb|CAL18496.1| RNA polymerase alpha subunit [Streptococcus ferus]
          Length = 177

 Score =  156 bits (395), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 77/176 (43%), Positives = 119/176 (67%)

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI T +
Sbjct: 1   KIDGVLHEFDTIPGVREDVMQIILNLKGLAVKSYVEDEKTMELDVEGPAEVTAGDILTDS 60

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIE++NPDH +  +   A ++  LTV+   GYVPA+ ++ ++ P+G + ID++Y+P+KKV
Sbjct: 61  DIEIVNPDHYLFTIADGASMKATLTVATNRGYVPAEENKNDSAPVGTLAIDSIYTPVKKV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +Y VE AR G   +YDKL++ I T+G+I  ED++ L++R+L + L +F +  E  K
Sbjct: 121 NYQVEPARVGSKDNYDKLTIEIMTNGTIIPEDALGLSARVLMEHLNLFTDLTEVAK 176


>gi|119663532|emb|CAK22337.1| RNA polymerase alpha subunit [Lactobacillus sharpeae]
          Length = 164

 Score =  156 bits (394), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 75/160 (46%), Positives = 110/160 (68%)

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+T IILNIK + LKM GD  K   I   GP  VTA DI+T  D++VLNP+  IC +  
Sbjct: 1   EDVTQIILNIKKLALKMHGDGEKTAEINIEGPATVTAADIKTDADVDVLNPEQYICTVAE 60

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
            A + M +TV  G GYVPA  ++T++ PIG+I +D++++PI +V+Y VESAR G+  D+D
Sbjct: 61  GAELHMRMTVKSGRGYVPAVQNKTDDMPIGVIAVDSIFTPISRVNYQVESARVGRRSDFD 120

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           KL++ + T+GSI   +++ALA++IL D L +F+N  +  K
Sbjct: 121 KLTLDVWTNGSINPREAIALAAKILTDHLAIFVNLTDDAK 160


>gi|150187117|emb|CAK30174.1| RNA polymerase alpha subunit [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 187

 Score =  156 bits (394), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 77/180 (42%), Positives = 122/180 (67%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI
Sbjct: 1   VTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDI 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
            T +D+E++NPDH +  +     ++  +TV+K  GYVPA+ ++ E+ P+G + +D++Y+P
Sbjct: 61  LTDSDVEIVNPDHYLFTIAEGHSLKAIMTVAKKRGYVPAEGNKKEDAPVGTLAVDSIYTP 120

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K
Sbjct: 121 VKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAK 180


>gi|118411080|ref|YP_874475.1| DNA-directed RNA polymerase alpha chain [Phaeodactylum tricornutum]
 gi|125987637|sp|A0T0K0|RPOA_PHATC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|116739827|gb|ABK20698.1| DNA-directed RNA polymerase alpha chain [Phaeodactylum tricornutum]
          Length = 311

 Score =  155 bits (393), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 94/281 (33%), Positives = 159/281 (56%), Gaps = 10/281 (3%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI----NLKMS 97
           T+GN LRRVL+  L G AI+AV+I G+ HE S+I GV ED+ +I+LN+KGI     ++ +
Sbjct: 35  TIGNQLRRVLLGDLGGVAISAVRIAGITHEFSTIPGVREDILEILLNLKGIICTSQIQDT 94

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
              H +V    +GP VVTA  IQ    +E++NP+H I  +    ++ +E     G GY  
Sbjct: 95  QFGHLKV----QGPSVVTADLIQLPPGVEIINPNHYIATISTSNILEIEFKFEYGSGYHL 150

Query: 158 AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
           A  +  E D    + +D ++ P++KV + +E+  +      ++L + I T+GSI+  D++
Sbjct: 151 ASQNFVEEDE-NYLQLDTIFMPVQKVDFKIENIYDATNNISERLFLDIWTNGSISPNDAL 209

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGEN 277
             A++++ D   + IN +      + ++  +++   P     +EEL+LSVR+ NCL+   
Sbjct: 210 ESAAQVIIDLFTLLINNKNINNNNRLELKPETISIEPYTNIAIEELQLSVRAYNCLKKAQ 269

Query: 278 IVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL-GTMGLFL 317
           I  +GDL+Q +   +  + NFGRKS  E+   L   +G+ L
Sbjct: 270 INTVGDLLQYSPEKLQELKNFGRKSADEVFSTLKNKLGIIL 310


>gi|317968839|ref|ZP_07970229.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp.
           CB0205]
          Length = 312

 Score =  155 bits (392), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 101/293 (34%), Positives = 159/293 (54%), Gaps = 23/293 (7%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG A TLGN+LRR+LM +L G+AITAV+I GV HE +++ GV ED+ DI+LN K + 
Sbjct: 27  PLERGQATTLGNSLRRMLMGALEGSAITAVRIAGVNHEYATVPGVREDVLDILLNCKDVA 86

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +       +   +   GP  VTAGD+Q  + + V++P   I  +     + +E+ V +G 
Sbjct: 87  VNSRTRELEIGRLVVNGPATVTAGDLQFSSQVSVIDPARPIATVAEGHSLELEVHVERGV 146

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE--------SAREGQVLDYDKLSMTI 205
           GY P      +   + L+ IDA++ P+++ +YT++        SARE       +L + I
Sbjct: 147 GYRPVDRRVEDTSAVDLLQIDAVFMPVQRANYTIDETAVGEGGSARE-------RLRLEI 199

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK-KVEELE 264
            TDGS+T +D++A A+  L       I   +P   +  +      P   A  +  +EEL 
Sbjct: 200 QTDGSLTPDDAMAQAANQL-------ITLIQPMATLTMEEEQGQEPEPSAEAQIPLEELN 252

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L  +G+ L
Sbjct: 253 LSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALERIGISL 305


>gi|150186996|emb|CAK30145.1| RNA polymerase alpha subunit [Streptococcus mitis]
          Length = 160

 Score =  155 bits (392), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 75/158 (47%), Positives = 110/158 (69%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRRVL++SL GAA+T++ IDGVLHE  ++ GV ED+  IILNIKGI +K   +  
Sbjct: 3   TLGNSLRRVLLASLPGAAVTSINIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDE 62

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + +   GP  VTAGDI T +DIE++NPDH +  +   + ++  +TV+ G GYVPA  +
Sbjct: 63  KIIELDVEGPAEVTAGDILTDSDIEIVNPDHYLFTIGEGSSLKATMTVNSGRGYVPADEN 122

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + +N P+G + +D++Y+P+ KV+Y VE AR G    +D
Sbjct: 123 KKDNAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDGFD 160


>gi|47679557|gb|AAT36722.1| RNA polymerase alpha subunit [Navicula salinicola]
          Length = 298

 Score =  155 bits (392), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 91/269 (33%), Positives = 150/269 (55%), Gaps = 1/269 (0%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           G   T+GN LRRVL+  L G AI+AV+I GV HE S+I GV ED+ +I+LN+KGI L   
Sbjct: 31  GQGITIGNQLRRVLLGDLGGVAISAVRIAGVSHEFSTIPGVREDILEILLNLKGIVLTSK 90

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
               +   +  +GP VVTA  IQ   ++E++NP+  I  +    ++ +E     G GY  
Sbjct: 91  TQETQFGRLKIQGPCVVTADLIQLPPNLEIVNPNQYIATITTSNIIEIEFKFEYGIGYKF 150

Query: 158 AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
           A    ++ +    + +D ++ P+ KV + +E+  +      ++L + I T+GSI   D++
Sbjct: 151 ASQTFSD-EADNFLQLDTVFMPVPKVDFKIENVYDTANNITERLFIDIWTNGSIPPNDAL 209

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGEN 277
             A++I+ D   + IN ++  +  +     +S+   P     +EEL+LSVR+ NCL+   
Sbjct: 210 ESAAQIIIDLFTLLINNKDTNESSQLKTKARSISMEPYTNIAIEELQLSVRAYNCLKKAQ 269

Query: 278 IVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           I  +GDL+Q +   +  + NFGRKS  E+
Sbjct: 270 INTVGDLLQYSPEKLQELKNFGRKSADEV 298


>gi|150036710|emb|CAM98249.1| DNA-directed RNA polymerase alpha chain [Leuconostoc carnosum]
          Length = 189

 Score =  155 bits (392), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 82/187 (43%), Positives = 122/187 (65%), Gaps = 2/187 (1%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           +L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + + I  +
Sbjct: 1   ILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDEERVLEIDVQ 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDP 167
           GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++   E  P
Sbjct: 61  GPSEVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSADENKQLREEMP 120

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           IG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L S+IL + 
Sbjct: 121 IGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSLGSKILAEH 180

Query: 228 LGMFINF 234
           L +F++ 
Sbjct: 181 LNLFMDI 187


>gi|150187170|emb|CAK30186.1| RNA polymerase alpha subunit [Streptococcus iniae]
          Length = 183

 Score =  155 bits (392), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 75/181 (41%), Positives = 123/181 (67%)

Query: 59  AITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGD 118
           A+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGD
Sbjct: 1   AVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKMIELDVEGPAEVTAGD 60

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           I T +DIE++NPDH +  +     ++  +TV+K  GY+PA+ ++ ++ P+G + +D++Y+
Sbjct: 61  ILTDSDIELVNPDHYLFTIAEGHSLKATMTVAKKRGYIPAEGNKKDDAPVGTLAVDSIYT 120

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  
Sbjct: 121 PVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVA 180

Query: 239 K 239
           K
Sbjct: 181 K 181


>gi|150186909|emb|CAK30125.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
          Length = 171

 Score =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 76/171 (44%), Positives = 117/171 (68%)

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
           AA+T++ IDGVLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  VTAG
Sbjct: 1   AAVTSINIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEVTAG 60

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI T +DIE++NPDH +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y
Sbjct: 61  DILTDSDIEIVNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIY 120

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           +P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L
Sbjct: 121 TPVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHL 171


>gi|118411212|ref|YP_874606.1| DNA-directed RNA polymerase alpha chain [Thalassiosira pseudonana]
 gi|125987639|sp|A0T0Z4|RPOA_THAPS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|116739959|gb|ABK20829.1| DNA-directed RNA polymerase alpha chain [Thalassiosira pseudonana]
          Length = 313

 Score =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 98/286 (34%), Positives = 157/286 (54%), Gaps = 11/286 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + + L  G   T+GN LRRVL+  L+G AIT V+I GV  E S I GV ED+ +I+LN+
Sbjct: 25  FLIDSLSSGQGITIGNLLRRVLLGDLQGTAITGVRIAGVKDEFSLIPGVREDILEILLNL 84

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KGI LK    + +   +  +GP V+TA  IQ   +IE++NP+H I  +    ++ +E  +
Sbjct: 85  KGIVLKSKTPNRQFGRLRLQGPAVITASSIQLPPEIEIINPNHYIATISSSHILEIEFKI 144

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G  Y  A    ++      I  DA++ P++KV + VE+  +      ++L + I T+G
Sbjct: 145 ESGSKYRLANELFSDKFE-DFIETDAIFMPVQKVDFKVENVYDNSNNIKERLLIDIWTNG 203

Query: 210 SITGEDSVALASRILQDQLGMFINFEEP-----KKEVKEDINVKSLPFNPALLKKVEELE 264
           SI+ E ++   S ++   + +F +  E      K+ +KE  ++K  P +P     +EEL+
Sbjct: 204 SISPEQAIFSGSNLI---INLFKSIGEQKINKEKENIKEKNHIK--PIDPYTHIAIEELQ 258

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           LSVR  NCL+   I  +GDL+  +   +L + NFGRKS  E+   L
Sbjct: 259 LSVRPYNCLKRAQINTIGDLLDYSPEKLLELKNFGRKSADEVFATL 304


>gi|150036824|emb|CAM98043.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gasicomitatum]
          Length = 179

 Score =  154 bits (390), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 81/179 (45%), Positives = 118/179 (65%), Gaps = 2/179 (1%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + +
Sbjct: 1   NSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDEERSL 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++  
Sbjct: 61  EVDIQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTITAFKGRGYSSADENKQL 120

Query: 165 ND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
            D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L S
Sbjct: 121 RDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSLGS 179


>gi|154424773|emb|CAL18489.1| RNA polymerase alpha subunit [Streptococcus cristatus]
          Length = 182

 Score =  154 bits (390), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 75/177 (42%), Positives = 117/177 (66%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T++ I+GVLHE  +I GV ED+  IILNIKGI +K      K + +   GP  VTAGDI
Sbjct: 1   VTSINIEGVLHEFDTISGVREDVMQIILNIKGIAVKSYVQDEKMIELDVEGPAEVTAGDI 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
            T +DIE++NPDH +  +   A  + ++ V+ G GYVPA  ++ ++ P+G + +D++Y+P
Sbjct: 61  LTDSDIEIVNPDHYLFTISEGARFKAKMAVNSGRGYVPADENKKDDAPVGTLAVDSIYTP 120

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           + KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F +  E
Sbjct: 121 VTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLFTDLTE 177


>gi|154424809|emb|CAL18507.1| RNA polymerase alpha subunit [Streptococcus iniae]
          Length = 174

 Score =  154 bits (390), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 74/174 (42%), Positives = 121/174 (69%)

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
           AA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAG
Sbjct: 1   AAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKMIELDVEGPAEVTAG 60

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI T +DIE++NPDH +  +     ++  +TV+K  GY+PA+ ++ ++ P+G + +D++Y
Sbjct: 61  DILTDSDIELVNPDHYLFTIAEGHSLKATMTVAKKRGYIPAEGNKKDDAPVGTLAVDSIY 120

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           +P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F
Sbjct: 121 TPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLF 174


>gi|154424743|emb|CAL18474.1| RNA polymerase alpha subunit [Streptococcus salivarius]
          Length = 201

 Score =  154 bits (389), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 74/179 (41%), Positives = 121/179 (67%)

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+++IDGVLHE  ++ GV ED+  IILNIKG+ +K   +  K + +  +GP  VTAGDI 
Sbjct: 1   TSIKIDGVLHEFDTVPGVREDVMQIILNIKGLAVKSYVEDEKTIELDVQGPAEVTAGDIL 60

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIE++NPDH +  +   A ++  +TV+   GYVPA  ++ ++ P+G + +D++Y+P+
Sbjct: 61  TDSDIEIVNPDHYLFTIAEGASLKATMTVATNRGYVPADENKKDDAPVGTLAVDSIYTPV 120

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  +  K
Sbjct: 121 KKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTDVAK 179


>gi|299830620|ref|YP_003735068.1| DNA-directed RNA polymerase alpha subunit [Durinskia baltica]
 gi|297384984|gb|ADI40283.1| DNA-directed RNA polymerase alpha subunit [Durinskia baltica]
          Length = 311

 Score =  154 bits (388), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 94/267 (35%), Positives = 150/267 (56%), Gaps = 5/267 (1%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           T+GN LRRVL++ L G AI+AV+I G+ HE S+I GV ED+ +I+LN+K I LK    + 
Sbjct: 35  TIGNQLRRVLLNDLGGVAISAVRIAGISHEFSTIPGVREDILEILLNLKEIVLKSKTQTP 94

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           +   +  +GP VVTA  IQ  + IE++N    I  +    +V +E     G GY  A   
Sbjct: 95  QFGRLKIQGPAVVTADLIQLPSTIEIVNSHQYIMTISTSNIVEIEFKFEYGTGYKLASQS 154

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
             E +    + +DA++ PI+KV + +E+  + +    ++L + I T+GSI+  +++ +A+
Sbjct: 155 FLEENE-NYLQLDAIFMPIQKVDFKIENVYDNRNSLTERLLLDIWTNGSISPNEAIKMAA 213

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVK--SLPFNPALLKKVEELELSVRSTNCLRGENIV 279
            I  D     +  E      +E++  K  SL   P     +EEL+LSVR+ NCL+   I 
Sbjct: 214 EITIDLFTALL--ENKATNSQEEVKSKTSSLSIEPYTNIAIEELQLSVRAYNCLKKAQIN 271

Query: 280 YMGDLIQRTEADMLRMANFGRKSLVEI 306
            +GDL+Q +   +  + NFGRKS  E+
Sbjct: 272 TVGDLLQYSPEKLQELKNFGRKSADEV 298


>gi|47679553|gb|AAT36720.1| RNA polymerase alpha subunit [Thalassionema frauenfeldii]
          Length = 298

 Score =  153 bits (387), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 90/277 (32%), Positives = 154/277 (55%), Gaps = 1/277 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + + L  G   T+GN LRRVL+  + G AI+AV+I G+ HE ++I GV ED+ +I+LN+
Sbjct: 23  FLIDKLKLGQGITIGNQLRRVLLGEIGGTAISAVRIVGIRHEFATIPGVREDILEILLNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KGI +K      K   +  +GP V+TA  I   + I+++NP+H I  +     + +E  +
Sbjct: 83  KGIVIKSDTTEIKFGRLKVQGPLVLTADSIDLPSGIKIVNPNHYIATISTSINLELEFKI 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GY  A     + +    + ID+++ P++KV++ +E+  +      ++L + I T+G
Sbjct: 143 EHGIGYKLASQLFNDENK-NFLQIDSIFMPVQKVNFKIENLYDADNSISERLILEIWTNG 201

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI   +++  A +I+ +     +  +  K+  K+  N + L   P     +EEL+LSVRS
Sbjct: 202 SIEPIEALKKACKIIINCFNSLLKTQNTKETTKKTSNNRKLTIEPYTNIAIEELQLSVRS 261

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            NCL+   I  +GDL+Q +   +  + NFGRKS  E+
Sbjct: 262 YNCLKKAKINTVGDLLQYSPDQLQELKNFGRKSADEV 298


>gi|33862091|ref|NP_893652.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           subsp. pastoris str. CCMP1986]
 gi|41688638|sp|Q7UZW6|RPOA_PROMP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|33634309|emb|CAE19994.1| Bacterial RNA polymerase, alpha chain [Prochlorococcus marinus
           subsp. pastoris str. CCMP1986]
          Length = 312

 Score =  153 bits (387), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 102/305 (33%), Positives = 166/305 (54%), Gaps = 10/305 (3%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + I++ +     +  T +I  PL RG A TLGN+LRRVLM  L G+A+TAV+I G+ HE 
Sbjct: 7   DRIDHQISDDRSQTGTFLIG-PLERGQATTLGNSLRRVLMGGLEGSAVTAVRISGINHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K +++  S    +   +   GP  V A DIQ  + +E+++ + 
Sbjct: 66  ATIPGVREDVLDILLNCKQLSINSSNPETEIGRLVVNGPMEVKANDIQFSSQVEIVDGEK 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV-ESAR 191
            I  +     + +E+ V +G GY P      E   I L+ IDA++ P+K+V++T+ E+A 
Sbjct: 126 PIATIQEGHNLELEIHVERGVGYRPVDRRNQETTAIDLLQIDAVFMPVKRVNFTIDETAV 185

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L+M + TDGS + +D++A A+  L       I   +P   V     +   P
Sbjct: 186 AEGATGRERLTMEVVTDGSTSPDDAIAEAANQL-------IELFQPLATVTMVEEIPEEP 238

Query: 252 FNPALLK-KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +  +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L
Sbjct: 239 EPSPEAQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEAL 298

Query: 311 GTMGL 315
             +G+
Sbjct: 299 ERIGI 303


>gi|33864022|ref|NP_895582.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. MIT 9313]
 gi|41688640|sp|Q7V523|RPOA_PROMM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|33635606|emb|CAE21930.1| Bacterial RNA polymerase, alpha chain [Prochlorococcus marinus str.
           MIT 9313]
          Length = 312

 Score =  153 bits (387), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 106/307 (34%), Positives = 165/307 (53%), Gaps = 14/307 (4%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ V     +    +I  PL RG A TLGN+LRRVLM  L G+AITAV+I GV HE 
Sbjct: 7   DRIEHQVADDRAQTGVFLIG-PLERGQATTLGNSLRRVLMGGLEGSAITAVRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K +++       +   +   GP  V A D+Q  + ++V++ D 
Sbjct: 66  ATIPGVREDVLDILLNCKQLSVNSRTSELEIGRLVVTGPAQVKAKDLQFSSQVQVVDGDR 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV-ESAR 191
            I  +     + +E+ V +G GY P   H  +   I L+ IDA++ P+++V++T+ E+A 
Sbjct: 126 QIATVHEGHSLELEVHVERGIGYRPVDRHNEDVSAIDLLQIDAVFMPVRRVNFTIDETAV 185

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD---QLGMFINFEEPKKEVKEDINVK 248
                  ++L + I TDGS T +D++A ++  L +    L      EEP  E  E     
Sbjct: 186 AEGGSTRERLRIEIVTDGSTTPDDALAESANQLIELFQPLATVTMVEEPGLE-PEPSAES 244

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
            +P         EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+  
Sbjct: 245 QIPL--------EELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIE 296

Query: 309 VLGTMGL 315
            L  +G+
Sbjct: 297 ALERIGI 303


>gi|154424771|emb|CAL18488.1| RNA polymerase alpha subunit [Streptococcus cristatus]
          Length = 181

 Score =  153 bits (387), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 75/176 (42%), Positives = 116/176 (65%)

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T++ I+GVLHE  +I GV ED+  IILNIKGI +K      K + +   GP  VTAGDI 
Sbjct: 1   TSINIEGVLHEFDTISGVREDVMQIILNIKGIAVKSYVQDEKMIELDVEGPAEVTAGDIL 60

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIE++NPDH +  +   A  + ++ V+ G GYVPA  ++ ++ P+G + +D++Y+P+
Sbjct: 61  TDSDIEIVNPDHYLFTISEGARFKAKMAVNSGRGYVPADENKKDDAPVGTLAVDSIYTPV 120

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
            KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F +  E
Sbjct: 121 TKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLFTDLTE 176


>gi|150186920|emb|CAK30128.1| RNA polymerase alpha subunit [Streptococcus pasteurianus]
          Length = 177

 Score =  153 bits (387), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 75/176 (42%), Positives = 118/176 (67%)

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI T +
Sbjct: 1   KIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDS 60

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           D+E++NPDH +  +     ++  +T++K  GYVPA+ ++ E+ P+G + +D++Y+P+KKV
Sbjct: 61  DVEIVNPDHYLFTIAEGHSLKATMTIAKNRGYVPAEGNKKEDAPVGTLAVDSIYTPVKKV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K
Sbjct: 121 NYQVEPARVGSNDGFDKLTLEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAK 176


>gi|124024019|ref|YP_001018326.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. MIT 9303]
 gi|156637356|sp|A2CC51|RPOA_PROM3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|123964305|gb|ABM79061.1| Bacterial RNA polymerase, alpha chain [Prochlorococcus marinus str.
           MIT 9303]
          Length = 312

 Score =  153 bits (387), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 106/307 (34%), Positives = 165/307 (53%), Gaps = 14/307 (4%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ V     +    +I  PL RG A TLGN+LRRVLM  L G+AITAV+I GV HE 
Sbjct: 7   DRIEHQVADDRAQTGVFLIG-PLERGQATTLGNSLRRVLMGGLEGSAITAVRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K +++       +   +   GP  V A D+Q  + ++V++ D 
Sbjct: 66  ATIPGVREDVLDILLNCKQLSVNSRTSELEIGRLVVTGPAQVKAKDLQFSSQVQVVDGDR 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV-ESAR 191
            I  +     + +E+ V +G GY P   H  +   I L+ IDA++ P+++V++T+ E+A 
Sbjct: 126 QIATVHEGHSLELEVHVERGIGYRPVDRHNEDISAIDLLQIDAVFMPVRRVNFTIDETAV 185

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD---QLGMFINFEEPKKEVKEDINVK 248
                  ++L + I TDGS T +D++A ++  L +    L      EEP  E  E     
Sbjct: 186 AEGGSTRERLRIEIVTDGSTTPDDALAESANQLIELFQPLATVTMVEEPGLE-PEPSAES 244

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
            +P         EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+  
Sbjct: 245 QIPL--------EELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIE 296

Query: 309 VLGTMGL 315
            L  +G+
Sbjct: 297 ALERIGI 303


>gi|154424805|emb|CAL18505.1| RNA polymerase alpha subunit [Streptococcus hyovaginalis]
          Length = 183

 Score =  153 bits (387), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 74/183 (40%), Positives = 123/183 (67%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ +K   +  K + +  +GP  VTA
Sbjct: 1   GAAVTSIKIDGVLHEFDTVPGVREDVMQIILNVKGLAVKSYVEDEKIIELDVQGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
           GDI T +D+E++N DH +  +   A  +  +TV+   GYV A+ ++ ++ P+G + +D++
Sbjct: 61  GDILTDSDVEIVNSDHYLFTIAEGASFKASMTVATNRGYVAAEGNKKDDAPVGTLAVDSI 120

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E
Sbjct: 121 YTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTE 180

Query: 237 PKK 239
             K
Sbjct: 181 VAK 183


>gi|224417911|ref|ZP_03655917.1| DNA-directed RNA polymerase subunit alpha [Helicobacter canadensis
           MIT 98-5491]
 gi|253827250|ref|ZP_04870135.1| DNA-directed RNA polymerase alpha subunit [Helicobacter canadensis
           MIT 98-5491]
 gi|313141452|ref|ZP_07803645.1| DNA-directed RNA polymerase subunit alpha [Helicobacter canadensis
           MIT 98-5491]
 gi|253510656|gb|EES89315.1| DNA-directed RNA polymerase alpha subunit [Helicobacter canadensis
           MIT 98-5491]
 gi|313130483|gb|EFR48100.1| DNA-directed RNA polymerase subunit alpha [Helicobacter canadensis
           MIT 98-5491]
          Length = 329

 Score =  153 bits (386), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 96/294 (32%), Positives = 152/294 (51%), Gaps = 12/294 (4%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           N+  + A P   G+A TL + LRR+L+ S  G A  A+ I GV HE  S++GV ED++  
Sbjct: 22  NKVQITAYPFENGYAITLAHPLRRLLLGSSVGFAPVALHIAGVAHEFDSVRGVTEDVSQF 81

Query: 86  ILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVND-IEVLNPDHVICNLDVDAVV 143
           I+N+K I  K+  DS    V     GP V+T  D+   ND +EV+ PD  +  ++ DA +
Sbjct: 82  IVNLKTIRFKIKDDSDSVSVDYTFNGPKVITGADLS--NDLVEVVTPDVHLATINKDATL 139

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
              + + KG GYVP++  R  N P G + +DA ++P+   +Y  E+       +Y+K+  
Sbjct: 140 SFSIVIYKGIGYVPSEEIRA-NVPEGFMPLDAYFTPVTSATYATENMLLEDDPNYEKVIF 198

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMF---INFEEPKKEVKEDINVKSLPFNPALLKKV 260
            I TDG +    +   A  ++  Q+ +F   +N E P+  + E+      P    L + +
Sbjct: 199 EIQTDGQVDPLTAFKNALSVMHKQMSIFNSELNIEIPEVAISEE----ERPELKVLSQTI 254

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           + L  S R  NCL    I Y+G+L+   E  +  + N G+KSL EI   L  +G
Sbjct: 255 DSLNFSARCFNCLDRSGIKYLGELVLLNEEQIKNIKNLGKKSLDEITAKLDELG 308


>gi|119668329|emb|CAK95464.1| RNA polymerase alpha subunit [Lactobacillus iners]
          Length = 188

 Score =  153 bits (386), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 80/169 (47%), Positives = 119/169 (70%)

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           IDGVLHE S+I GV ED+T IILN+K + LK+  D  K V I   GP VVTA D++   D
Sbjct: 2   IDGVLHEFSTIPGVREDVTKIILNLKKLELKLLVDEEKMVEIDVEGPAVVTAADLKVDAD 61

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           +E+LNPD  IC +     + M + +  G GY+PA  +++++ PIG+I +D+L+SPIKKV+
Sbjct: 62  VEILNPDQYICTIAEGGHLHMSIAIKNGRGYIPASENKSDDMPIGVIPVDSLFSPIKKVN 121

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           Y VE+AR G+  DYDKL++ + TDGSIT  D+++ A++IL++   +F++
Sbjct: 122 YQVENARVGKRDDYDKLTLELWTDGSITPNDALSFAAKILEEHFKVFMS 170


>gi|119473466|ref|ZP_01614972.1| DNA-directed RNA polymerase subunit alpha [Alteromonadales
           bacterium TW-7]
 gi|119444456|gb|EAW25790.1| DNA-directed RNA polymerase subunit alpha [Alteromonadales
           bacterium TW-7]
          Length = 173

 Score =  153 bits (386), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 74/165 (44%), Positives = 114/165 (69%), Gaps = 3/165 (1%)

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           PIG + +DA +SP+++++Y+VESAR  Q  D DKL + ++T+G++  E+++  AS IL +
Sbjct: 12  PIGRLLLDASFSPVERIAYSVESARVEQRTDLDKLIIDMETNGTLDREEAIRRASTILAE 71

Query: 227 QLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQ 286
           QL  F++    +   + +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+Q
Sbjct: 72  QLDAFVDL---RDVTEPEEKEEKPEFDPILLRPVDDLELTVRSANCLKAEQIQYIGDLVQ 128

Query: 287 RTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           RTE ++L+  N G+KSL EIK VL + GL LGM L +WPP S+ E
Sbjct: 129 RTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASLAE 173


>gi|154424765|emb|CAL18485.1| RNA polymerase alpha subunit [Streptococcus canis]
          Length = 188

 Score =  153 bits (386), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 75/179 (41%), Positives = 121/179 (67%)

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI 
Sbjct: 1   TSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKIIELEVEGPAEVTAGDIL 60

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIE++NPDH +  +     +R  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+
Sbjct: 61  TDSDIELVNPDHYLFTIAEGHSLRATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPV 120

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  +  K
Sbjct: 121 KKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTDVAK 179


>gi|269929659|gb|ACZ53725.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929703|gb|ACZ53747.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
          Length = 166

 Score =  153 bits (386), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 79/166 (47%), Positives = 118/166 (71%), Gaps = 2/166 (1%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAAIT++QIDGVLHE S++KGV ED+T IILN+K ++LK+  +  K + +  +GP  VTA
Sbjct: 1   GAAITSMQIDGVLHEFSTVKGVTEDVTQIILNLKKVSLKLDSEDQKNLELDVKGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITID 174
            DIQ  N++ +LNPD  I  +   A + ++LT  KG GY+ A  ++   D   IG++ ID
Sbjct: 61  SDIQGDNEVTILNPDLHIATVADGAELHIKLTADKGRGYLSANDNKARMDDLAIGVLPID 120

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           ++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T  ++V+L 
Sbjct: 121 SIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLTPTEAVSLG 166


>gi|150036714|emb|CAM98250.1| DNA-directed RNA polymerase alpha chain [Leuconostoc citreum]
          Length = 186

 Score =  152 bits (385), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 81/184 (44%), Positives = 119/184 (64%), Gaps = 2/184 (1%)

Query: 53  SSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
           SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + + I  +GP 
Sbjct: 1   SSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDVQGPA 60

Query: 113 VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGL 170
            VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++   D  PIG+
Sbjct: 61  DVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSADENKQLRDEMPIGV 120

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           + +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L S+IL + L +
Sbjct: 121 LAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSLGSKILAEHLNL 180

Query: 231 FINF 234
           F++ 
Sbjct: 181 FMDI 184


>gi|123969275|ref|YP_001010133.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. AS9601]
 gi|123199385|gb|ABM71026.1| Bacterial RNA polymerase, alpha chain [Prochlorococcus marinus str.
           AS9601]
          Length = 340

 Score =  152 bits (385), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 102/305 (33%), Positives = 165/305 (54%), Gaps = 10/305 (3%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + I++ +     +  T +I  PL RG A TLGN+LRRVLM  L G+A+TAV+I G+ HE 
Sbjct: 35  DRIDHQIADDRSQTGTFLIG-PLERGQATTLGNSLRRVLMGGLEGSAVTAVRIAGINHEY 93

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K +++  S    +   +   GP  V A DIQ  + +E+++ + 
Sbjct: 94  ATIPGVREDVLDILLNCKQLSINSSNPELEIGRLVASGPMEVKANDIQFSSQVEIVDGEK 153

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV-ESAR 191
            I  +     + +E+ V +G GY P      E   I L+ IDA++ P+K+V++T+ E+A 
Sbjct: 154 PIATIQEGHNLELEIHVERGVGYRPVDRKSEETTAIDLLQIDAVFMPVKRVNFTIDETAV 213

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L M + TDGS + +D++A A+  L       I   +P   V     +   P
Sbjct: 214 AEGATGRERLKMEVVTDGSTSPDDAIAEAANQL-------IELFQPLATVTMVEEIPEEP 266

Query: 252 FNPALLK-KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +  +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L
Sbjct: 267 EPSPEAQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEAL 326

Query: 311 GTMGL 315
             +G+
Sbjct: 327 ERIGI 331


>gi|154424823|emb|CAL18514.1| RNA polymerase alpha subunit [Streptococcus mutans]
          Length = 176

 Score =  152 bits (385), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 76/175 (43%), Positives = 118/175 (67%)

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           IDGVLHE  +I GV ED+  IILNIKG+ +K   +  K V +   GP  +TAGDI T +D
Sbjct: 1   IDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVEEEKIVELDVEGPAEITAGDILTDSD 60

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           IE++NPDH +  +   A ++  +TV+   GYVPA+ ++ ++ P+G + ID++Y+P+KKV+
Sbjct: 61  IEIVNPDHYLFTIAEGANLKATMTVATNRGYVPAEKNKRDDAPVGTLAIDSIYTPVKKVN 120

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           Y VE AR G   ++DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K
Sbjct: 121 YQVEPARVGSNDNFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAK 175


>gi|154424783|emb|CAL18494.1| RNA polymerase alpha subunit [Streptococcus equi subsp. equi]
          Length = 171

 Score =  152 bits (385), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 74/168 (44%), Positives = 118/168 (70%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTA
Sbjct: 2   GAAVTSIRIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKIIELDVEGPAEVTA 61

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
           GDI T +DIE++NPDH +  +     ++  +TV+K  GYVPA+ ++ ++ P+G + +D++
Sbjct: 62  GDILTDSDIELVNPDHYLFTIADGYTLKASMTVAKKRGYVPAEGNKKDDAPVGTLAVDSI 121

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L
Sbjct: 122 YTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVL 169


>gi|156637358|sp|A2BTB5|RPOA_PROMS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 312

 Score =  152 bits (385), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 102/305 (33%), Positives = 165/305 (54%), Gaps = 10/305 (3%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + I++ +     +  T +I  PL RG A TLGN+LRRVLM  L G+A+TAV+I G+ HE 
Sbjct: 7   DRIDHQIADDRSQTGTFLIG-PLERGQATTLGNSLRRVLMGGLEGSAVTAVRIAGINHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K +++  S    +   +   GP  V A DIQ  + +E+++ + 
Sbjct: 66  ATIPGVREDVLDILLNCKQLSINSSNPELEIGRLVASGPMEVKANDIQFSSQVEIVDGEK 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV-ESAR 191
            I  +     + +E+ V +G GY P      E   I L+ IDA++ P+K+V++T+ E+A 
Sbjct: 126 PIATIQEGHNLELEIHVERGVGYRPVDRKSEETTAIDLLQIDAVFMPVKRVNFTIDETAV 185

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L M + TDGS + +D++A A+  L       I   +P   V     +   P
Sbjct: 186 AEGATGRERLKMEVVTDGSTSPDDAIAEAANQL-------IELFQPLATVTMVEEIPEEP 238

Query: 252 FNPALLK-KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +  +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L
Sbjct: 239 EPSPEAQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEAL 298

Query: 311 GTMGL 315
             +G+
Sbjct: 299 ERIGI 303


>gi|30468203|ref|NP_849090.1| RNA polymerase alpha subunit [Cyanidioschyzon merolae strain 10D]
 gi|41688691|sp|Q85FU3|RPOA_CYAME RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|30409303|dbj|BAC76252.1| DNA-directed RNA polymerase alpha chain [Cyanidioschyzon merolae
           strain 10D]
          Length = 316

 Score =  152 bits (384), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 97/286 (33%), Positives = 160/286 (55%), Gaps = 16/286 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I +PL    A T+GN+LRRVL+S L   +ITAV+I G  HE++++KGV ED+  I+LN+
Sbjct: 29  FILQPLSYTQALTMGNSLRRVLLSELESISITAVRIAGASHELATLKGVREDVLQIMLNL 88

Query: 90  KGINLKMSGDSHKRVTIFK---RGPGVVTAGDIQTV--NDIEVLNPDHVICNLDVDAVVR 144
           K I  +  G   K+ TI +   +GP +VTA   Q+   +   +++    I  +D   ++ 
Sbjct: 89  KQIVWR--GQLKKQPTITRLKVQGPAIVTAAAFQSEANSSANIIDTCQYIATIDTQDILE 146

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           ME  + +  GY  AK     ++ I  + ID ++ P+K+V++ V+ A   +VL    L + 
Sbjct: 147 MECQLEQSSGYRLAK----PSEMIDWLPIDGVFMPVKRVNFWVDKALVDKVLVDKALHLE 202

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           I T+GSI+ ++++  A+RIL          E      K +  +  L     +L  +EEL+
Sbjct: 203 IWTNGSISPQEALHQAARILTHWFNPLQTLEWKTSHTKNEQTMAQL---SNML--IEELD 257

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           LSVR+ NCL+   I  + DL+Q T+ ++L + NFG+KS+ E+   L
Sbjct: 258 LSVRAYNCLKRAQIHSVADLMQYTQEELLALKNFGQKSVEEVNKAL 303


>gi|269929683|gb|ACZ53737.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
          Length = 166

 Score =  152 bits (383), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 78/166 (46%), Positives = 119/166 (71%), Gaps = 2/166 (1%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAAIT++QIDGVLHE S+++GV ED+T IILN+K ++LK+  ++ K + +  +GP  VTA
Sbjct: 1   GAAITSMQIDGVLHEFSTVEGVTEDVTQIILNLKKVSLKLDSENQKNLELDVKGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITID 174
            DIQ  N++ +LNPD  I  +   A + ++LT  KG GY+ A  ++   D   IG++ ID
Sbjct: 61  SDIQGDNEVTILNPDLHIATVADGAELHIKLTADKGRGYLSANDNKARMDDLAIGVLPID 120

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           ++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T  ++V+L 
Sbjct: 121 SIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLTPTEAVSLG 166


>gi|254527170|ref|ZP_05139222.1| DNA-directed RNA polymerase, alpha subunit [Prochlorococcus marinus
           str. MIT 9202]
 gi|221538594|gb|EEE41047.1| DNA-directed RNA polymerase, alpha subunit [Prochlorococcus marinus
           str. MIT 9202]
          Length = 311

 Score =  152 bits (383), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 102/305 (33%), Positives = 165/305 (54%), Gaps = 10/305 (3%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + I++ +     +  T +I  PL RG A TLGN+LRRVLM  L G+A+TAV+I G+ HE 
Sbjct: 6   DRIDHQIADDRSQTGTFLIG-PLERGQATTLGNSLRRVLMGGLEGSAVTAVRIAGINHEY 64

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K +++  S    +   +   GP  V A DIQ  + +E+++ + 
Sbjct: 65  ATIPGVREDVLDILLNCKQLSINSSSPDLEIGRLVASGPMEVKANDIQFSSQVEIVDGEK 124

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV-ESAR 191
            I  +     + +E+ V +G GY P      E   I L+ IDA++ P+K+V++T+ E+A 
Sbjct: 125 PIATIQEGHNLELEIHVERGVGYRPVDRKSEETTAIDLLQIDAVFMPVKRVNFTIDETAV 184

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L M + TDGS + +D++A A+  L       I   +P   V     +   P
Sbjct: 185 AEGGTGRERLKMEVVTDGSTSPDDAIAEAANQL-------IELFQPLATVTMVEEIPEEP 237

Query: 252 FNPALLK-KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +  +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L
Sbjct: 238 EPSPEAQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIDAL 297

Query: 311 GTMGL 315
             +G+
Sbjct: 298 ERIGI 302


>gi|47679555|gb|AAT36721.1| RNA polymerase alpha subunit [Cylindrotheca fusiformis]
          Length = 291

 Score =  152 bits (383), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 95/274 (34%), Positives = 161/274 (58%), Gaps = 4/274 (1%)

Query: 35  LPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL 94
           L  G   T+GN LRRVL++ L G AI+A +I GV HE S+I GV ED+ +I+LN+KGI L
Sbjct: 20  LKPGQGITIGNQLRRVLLNDLGGVAISAARIAGVSHEFSTIPGVREDILEILLNLKGIVL 79

Query: 95  KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHG 154
           K    + +   +  +GP VVTA  IQ  +D+E++NP+H +  +    V+ +E     G G
Sbjct: 80  KSKTQTAQFGRLKIQGPTVVTADLIQLPSDLEIVNPNHYLMTISTSNVLEIEFKFEYGTG 139

Query: 155 Y-VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           Y + ++    E+D    + +D ++ P++KV++ +E+  +      +++ + I T+GSI+ 
Sbjct: 140 YKLTSQAFLDESD--NYLQLDTIFMPVQKVNFKIENVYDNNNNITEQVFLDIWTNGSISP 197

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVK-EDINVKSLPFNPALLKKVEELELSVRSTNC 272
            +++  A++I  D   + +  +E K++ K E   V S+   P     +EEL+LSVR+ NC
Sbjct: 198 NEALKSAAQITIDLFELLLKNKETKEKNKLEATKVPSISIEPYTNIAIEELQLSVRAYNC 257

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           L+   I  +GDL++ +   +  + NFGRKS  E+
Sbjct: 258 LKKAQINTVGDLLKYSPEKLQELKNFGRKSADEV 291


>gi|154424779|emb|CAL18492.1| RNA polymerase alpha subunit [Streptococcus dysgalactiae subsp.
           equisimilis]
          Length = 179

 Score =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 74/177 (41%), Positives = 121/177 (68%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI
Sbjct: 1   VTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKILELEVEGPAEVTAGDI 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
            T +DIE++NPDH +  +     +R  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P
Sbjct: 61  LTDSDIELVNPDHYLFTIAEGHSLRATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTP 120

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  +
Sbjct: 121 VKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLKLFTDLTD 177


>gi|108792431|emb|CAJ44678.1| RNA polymerase alpha subunit [Lactobacillus acidipiscis]
          Length = 196

 Score =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 77/174 (44%), Positives = 119/174 (68%), Gaps = 2/174 (1%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE SSI GV ED+T IILN+K + LK++ +  + + I   GP  VTAGDIQ  +++EV
Sbjct: 1   VLHEFSSIDGVLEDVTTIILNLKKVALKLNSEDVQTLEIDVTGPMEVTAGDIQGSSEVEV 60

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSY 185
           LNPD  IC +   A     +T +KG GYV A  +  +TE+ PIG++ ID++Y+PI++V+Y
Sbjct: 61  LNPDLYICTVADGASFHARMTANKGRGYVSANENKAKTEDMPIGVLAIDSIYTPIERVNY 120

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
            VE  R GQ  D+DKL++ + T+GSIT  ++++L+++IL + L +F++  +  K
Sbjct: 121 QVEKTRVGQKSDFDKLTLDVWTNGSITPSEAISLSAKILTEHLTLFVDLTDEAK 174


>gi|108792433|emb|CAJ44679.1| RNA polymerase alpha subunit [Lactobacillus acidipiscis]
          Length = 194

 Score =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 77/174 (44%), Positives = 119/174 (68%), Gaps = 2/174 (1%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE SSI GV ED+T IILN+K + LK++ +  + + I   GP  VTAGDIQ  +++EV
Sbjct: 1   VLHEFSSIDGVLEDVTTIILNLKKVALKLNSEDVQTLEIDVTGPMEVTAGDIQGSSEVEV 60

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSY 185
           LNPD  IC +   A     +T +KG GYV A  +  +TE+ PIG++ ID++Y+PI++V+Y
Sbjct: 61  LNPDLYICTVADGASFHARMTANKGRGYVSANENKAKTEDMPIGVLAIDSIYTPIERVNY 120

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
            VE  R GQ  D+DKL++ + T+GSIT  ++++L+++IL + L +F++  +  K
Sbjct: 121 QVEKTRVGQKSDFDKLTLDVWTNGSITPSEAISLSAKILTEHLTLFVDLTDEAK 174


>gi|150036724|emb|CAM98253.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. mesenteroides]
          Length = 181

 Score =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 81/181 (44%), Positives = 118/181 (65%), Gaps = 2/181 (1%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG 110
           L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + + I  +G
Sbjct: 1   LLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDIQG 60

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PI 168
           P  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++   D  PI
Sbjct: 61  PADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSADENKKLRDEMPI 120

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           G++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L ++IL + L
Sbjct: 121 GVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTNGSIKPSDALSLGAKILAEHL 180

Query: 229 G 229
           G
Sbjct: 181 G 181


>gi|150187014|emb|CAK30151.1| RNA polymerase alpha subunit [Streptococcus sinensis]
          Length = 171

 Score =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 73/171 (42%), Positives = 114/171 (66%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T++ I+GVLHE  +I GV ED+  IILNIKGI +K      K + +   GP  VTAGDI
Sbjct: 1   VTSINIEGVLHEFDTISGVREDVMQIILNIKGIAVKSYVQDEKMIELDVEGPAAVTAGDI 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
            T +DIE++NPDH +  +   A  + ++ V+ G GYVPA  ++ ++ P+G + +D++Y+P
Sbjct: 61  LTDSDIEIINPDHYLFTISEGASFKAKMAVNSGRGYVPADENKKDDAPVGTLAVDSIYTP 120

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           + KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L +
Sbjct: 121 VTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNL 171


>gi|119662327|emb|CAJ33151.1| RNA polymerase alpha subunit [Lactobacillus lindneri]
          Length = 191

 Score =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 80/173 (46%), Positives = 116/173 (67%), Gaps = 4/173 (2%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE S++KGV ED+T IILN+K I LK+  D +    ++I   GP  VTAGDI T +D 
Sbjct: 1   VLHEFSTVKGVTEDVTKIILNLKKIKLKIESDDNDLHTMSINVTGPADVTAGDIVTDSDT 60

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKV 183
            +LNPD  I  +   A + M +T +KG GYV A+ ++  ND  PIG++ +D++Y+PI++V
Sbjct: 61  TILNPDLHIATVAEGATLHMTMTANKGRGYVSAEENKARNDDMPIGVLPVDSIYTPIERV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +Y VE  R GQ  D+DKL++ + TDGSIT  DS++LA++IL   L MF+   +
Sbjct: 121 NYQVEDTRVGQRDDFDKLTLDVWTDGSITPSDSISLAAKILSQHLDMFVGLTD 173


>gi|254458753|ref|ZP_05072177.1| DNA-directed RNA polymerase, alpha subunit [Campylobacterales
           bacterium GD 1]
 gi|207084519|gb|EDZ61807.1| DNA-directed RNA polymerase, alpha subunit [Campylobacterales
           bacterium GD 1]
          Length = 332

 Score =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 96/322 (29%), Positives = 174/322 (54%), Gaps = 17/322 (5%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           Q  EN   ++A P   G+A +L + LRR L+SS  G A  A++I+G  HE  S++G+ ED
Sbjct: 18  QISENEANIMAYPFETGYAISLAHPLRRFLLSSSVGYAPIAIKIEGAKHEFDSVRGMLED 77

Query: 82  LTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           ++D ILN+K I  K+  + S  +++    GP  +   D+ + +++EV+ PD  +  L+ D
Sbjct: 78  ISDFILNLKEIRFKLKDEASEAKISYSFAGPCTIKGADLNS-DEVEVVTPDAPLATLNED 136

Query: 141 AVVRMELTVSKGHGYVPAK--HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
           + +   + +++G GYVP++  H   E+   G I +DA ++P++  +Y +E+       ++
Sbjct: 137 STLNFVIKIAQGIGYVPSEDTHDELED---GYIALDAYFTPVRSATYKIENVLVEDNPNF 193

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           +++ + I TDG I+  D+   +  ++  QL +F      +  +K    ++ +  NP L K
Sbjct: 194 ERVILNIRTDGQISPLDAFKNSLEVMYAQLAVF----NSEISIKAATTMERVEENPDLKK 249

Query: 259 ---KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
               ++ L LS RS NCL   +I  +G++   ++ D+  + N G+KS  EI   L   G 
Sbjct: 250 LVTHIDSLGLSARSFNCLDRSSIKLVGEIALMSQNDLKNVKNLGKKSYDEIVDKLLEFGF 309

Query: 316 FLGMNLPDWPPESIEELAKKYE 337
            +G +L D   + +  L KK E
Sbjct: 310 AVGADLAD---DVVSALKKKIE 328


>gi|157414140|ref|YP_001485006.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. MIT 9215]
 gi|172047296|sp|A8G739|RPOA_PROM2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|157388715|gb|ABV51420.1| DNA-directed RNA polymerase, alpha subunit [Prochlorococcus marinus
           str. MIT 9215]
          Length = 312

 Score =  151 bits (381), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 102/305 (33%), Positives = 165/305 (54%), Gaps = 10/305 (3%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + I++ +     +  T +I  PL RG A TLGN+LRRVLM  L G+A+TAV+I G+ HE 
Sbjct: 7   DRIDHQIADDRSQTGTFLIG-PLERGQATTLGNSLRRVLMGGLEGSAVTAVRIAGINHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K +++  S    +   +   GP  V A DIQ  + +E+++ + 
Sbjct: 66  ATIPGVREDVLDILLNCKQLSINSSSPDLEIGRLVASGPMDVKANDIQFSSQVEIVDGEK 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV-ESAR 191
            I  +     + +E+ V +G GY P      E   I L+ IDA++ P+K+V++T+ E+A 
Sbjct: 126 PIATIQEGHNLELEIHVERGVGYRPVDRKSEETTAIDLLQIDAVFMPVKRVNFTIDETAV 185

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L M + TDGS + +D++A A+  L       I   +P   V     +   P
Sbjct: 186 AEGGTGRERLKMEVVTDGSTSPDDAIAEAANQL-------IELFQPLATVTMVEEIPEEP 238

Query: 252 FNPALLK-KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +  +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L
Sbjct: 239 EPSPEAQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIDAL 298

Query: 311 GTMGL 315
             +G+
Sbjct: 299 ERIGI 303


>gi|269929661|gb|ACZ53726.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929663|gb|ACZ53727.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929665|gb|ACZ53728.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929667|gb|ACZ53729.1| RNA polymerase alpha subunit [Lactobacillus reuteri ATCC 53608]
 gi|269929669|gb|ACZ53730.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929671|gb|ACZ53731.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929673|gb|ACZ53732.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929675|gb|ACZ53733.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929677|gb|ACZ53734.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929679|gb|ACZ53735.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929681|gb|ACZ53736.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929685|gb|ACZ53738.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929687|gb|ACZ53739.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929689|gb|ACZ53740.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929691|gb|ACZ53741.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929693|gb|ACZ53742.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929695|gb|ACZ53743.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929697|gb|ACZ53744.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929699|gb|ACZ53745.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929701|gb|ACZ53746.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929705|gb|ACZ53748.1| RNA polymerase alpha subunit [Lactobacillus reuteri ATCC 53608]
 gi|269929707|gb|ACZ53749.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929709|gb|ACZ53750.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929711|gb|ACZ53751.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929713|gb|ACZ53752.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929715|gb|ACZ53753.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929717|gb|ACZ53754.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929719|gb|ACZ53755.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929721|gb|ACZ53756.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929723|gb|ACZ53757.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929725|gb|ACZ53758.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929727|gb|ACZ53759.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929729|gb|ACZ53760.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929731|gb|ACZ53761.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929733|gb|ACZ53762.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929735|gb|ACZ53763.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929737|gb|ACZ53764.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929739|gb|ACZ53765.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929741|gb|ACZ53766.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929743|gb|ACZ53767.1| RNA polymerase alpha subunit [Lactobacillus reuteri DSM 20016]
 gi|269929745|gb|ACZ53768.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929747|gb|ACZ53769.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929749|gb|ACZ53770.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929751|gb|ACZ53771.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929753|gb|ACZ53772.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929755|gb|ACZ53773.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929757|gb|ACZ53774.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929759|gb|ACZ53775.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929761|gb|ACZ53776.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929763|gb|ACZ53777.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929765|gb|ACZ53778.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929767|gb|ACZ53779.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929769|gb|ACZ53780.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929771|gb|ACZ53781.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929773|gb|ACZ53782.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929775|gb|ACZ53783.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929777|gb|ACZ53784.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929779|gb|ACZ53785.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929781|gb|ACZ53786.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929783|gb|ACZ53787.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929785|gb|ACZ53788.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929787|gb|ACZ53789.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929789|gb|ACZ53790.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929791|gb|ACZ53791.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929793|gb|ACZ53792.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929795|gb|ACZ53793.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929797|gb|ACZ53794.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929799|gb|ACZ53795.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929801|gb|ACZ53796.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929803|gb|ACZ53797.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929805|gb|ACZ53798.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929807|gb|ACZ53799.1| RNA polymerase alpha subunit [Lactobacillus reuteri lpuph]
 gi|269929809|gb|ACZ53800.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929811|gb|ACZ53801.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929813|gb|ACZ53802.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929815|gb|ACZ53803.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929817|gb|ACZ53804.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929819|gb|ACZ53805.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929821|gb|ACZ53806.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929823|gb|ACZ53807.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929825|gb|ACZ53808.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929827|gb|ACZ53809.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929831|gb|ACZ53811.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929833|gb|ACZ53812.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929835|gb|ACZ53813.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929837|gb|ACZ53814.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929839|gb|ACZ53815.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929841|gb|ACZ53816.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929843|gb|ACZ53817.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929845|gb|ACZ53818.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929847|gb|ACZ53819.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929849|gb|ACZ53820.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929851|gb|ACZ53821.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929853|gb|ACZ53822.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929855|gb|ACZ53823.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929857|gb|ACZ53824.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929859|gb|ACZ53825.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929861|gb|ACZ53826.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929863|gb|ACZ53827.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929865|gb|ACZ53828.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929867|gb|ACZ53829.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929869|gb|ACZ53830.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929871|gb|ACZ53831.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929873|gb|ACZ53832.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929875|gb|ACZ53833.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929877|gb|ACZ53834.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929879|gb|ACZ53835.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929881|gb|ACZ53836.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929883|gb|ACZ53837.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929885|gb|ACZ53838.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929887|gb|ACZ53839.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929889|gb|ACZ53840.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
          Length = 166

 Score =  151 bits (381), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 78/166 (46%), Positives = 118/166 (71%), Gaps = 2/166 (1%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAAIT++QIDGVLHE S+++GV ED+T IILN+K ++LK+  +  K + +  +GP  VTA
Sbjct: 1   GAAITSMQIDGVLHEFSTVEGVTEDVTQIILNLKKVSLKLDSEDQKNLELDVKGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITID 174
            DIQ  N++ +LNPD  I  +   A + ++LT  KG GY+ A  ++   D   IG++ ID
Sbjct: 61  SDIQGDNEVTILNPDLHIATVADGAELHIKLTADKGRGYLSANDNKARMDDLAIGVLPID 120

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           ++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T  ++V+L 
Sbjct: 121 SIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLTPTEAVSLG 166


>gi|151416842|emb|CAO78492.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gelidum]
          Length = 164

 Score =  151 bits (381), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 76/164 (46%), Positives = 109/164 (66%), Gaps = 2/164 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K +
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKV 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            L +  D  + + +  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG
Sbjct: 61  VLAIDSDEERSLEVDIQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTITAFKG 120

Query: 153 HGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQ 194
            GY  A  ++   D  PIG++ +D++Y+PI++V+Y VE+ R G 
Sbjct: 121 RGYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGS 164


>gi|154424811|emb|CAL18508.1| RNA polymerase alpha subunit [Streptococcus intermedius]
          Length = 168

 Score =  151 bits (381), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 74/167 (44%), Positives = 114/167 (68%)

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           I+GVLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  VTAGDI T +D
Sbjct: 1   IEGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEGEKTIELDVEGPAEVTAGDILTDSD 60

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           IE++NP+H +  +   A ++  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+KKV+
Sbjct: 61  IEIVNPNHYLFTIGEGASLKAVMTVNTGRGYVPADENKKDDAPVGTLAVDSIYTPVKKVN 120

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           Y VE AR G    +DKL++ I TDG+I  ED++ L++RIL + L +F
Sbjct: 121 YQVEPARVGSNDSFDKLTLEIMTDGTIIPEDALGLSARILTEHLDLF 167


>gi|300379501|gb|ADK08381.1| DNA-directed RNA polymerase alpha subunit [Lactobacillus reuteri]
          Length = 166

 Score =  151 bits (381), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 78/166 (46%), Positives = 118/166 (71%), Gaps = 2/166 (1%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAA+T++QIDGVLHE S++KGV ED+T IILN+K ++LK+  +  K + +  +GP  VTA
Sbjct: 1   GAAVTSMQIDGVLHEFSTVKGVTEDVTQIILNLKKVSLKIDSEDQKDLELDVKGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITID 174
            DIQ  N++ +LNPD  I  +   A + ++LT  KG GY+ A  ++   D   IG++ ID
Sbjct: 61  SDIQGDNEVTILNPDLHIATVADGAELHIKLTADKGRGYLSANDNKARMDDLAIGVLPID 120

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           ++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T  ++V+L 
Sbjct: 121 SIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLTPTEAVSLG 166


>gi|315320586|ref|YP_004072643.1| DNA-directed RNA polymerase subunit alpha [Thalassiosira oceanica
           CCMP1005]
 gi|283569059|gb|ADB27596.1| DNA-directed RNA polymerase subunit alpha [Thalassiosira oceanica
           CCMP1005]
          Length = 332

 Score =  151 bits (381), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 98/286 (34%), Positives = 154/286 (53%), Gaps = 9/286 (3%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + + L  G   T GN LRRVL+  L G AIT V+I GV  E S I GV ED+ +I+LN+
Sbjct: 42  FLIDSLNSGQGITNGNLLRRVLLGDLEGIAITGVRIAGVKDEFSLIPGVREDILEILLNL 101

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK +  + +   +  +GP V+TA  IQ   +IE +NP+H I  +    +V +E  +
Sbjct: 102 KGVILKSNIVTRQFGRLRIQGPAVITASSIQLPPEIETINPNHYIATISTSDIVEIEFKI 161

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G  Y  A    ++      I  DA++ P++KV + VE+  +      ++L + + T+G
Sbjct: 162 ESGRQYRLANELFSDKFE-DFIETDAIFMPVQKVDFKVENVYDNSNNIKERLFLDVWTNG 220

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPK-KEVKEDINV----KSLPFNPALLKKVEELE 264
           SI  +D++  AS  +   +  F +  E K K   E  N+    +  P +P +   +EEL+
Sbjct: 221 SIAPQDAIISASNSI---IAFFQSISEQKVKNALEKENIIEKNQVKPIDPYIHIAIEELQ 277

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           LSVR  NCL+   I  +GDL++ +   +L + NFGRKS  E+   L
Sbjct: 278 LSVRPYNCLKRARINTIGDLLEYSPEKLLELKNFGRKSADEVFATL 323


>gi|150186998|emb|CAK30146.1| RNA polymerase alpha subunit [Streptococcus orisratti]
          Length = 199

 Score =  151 bits (381), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 73/181 (40%), Positives = 122/181 (67%)

Query: 59  AITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGD 118
           A+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   +  K + +   GP  +TAGD
Sbjct: 1   AVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVEDEKIIELDVEGPAEITAGD 60

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           I T +DIE++NP+H +  +     ++  +TV+   GYVPA+ ++ ++ P+G + +D++Y+
Sbjct: 61  ILTDSDIEIVNPNHYLFTIAEGHSLKATMTVNTNRGYVPAEGNKKDDAPVGTLAVDSIYT 120

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  +  
Sbjct: 121 PVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDAIGLSARVLIEHLNLFTDLTDVA 180

Query: 239 K 239
           K
Sbjct: 181 K 181


>gi|269929829|gb|ACZ53810.1| RNA polymerase alpha subunit [Lactobacillus reuteri mlc3]
          Length = 166

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 78/166 (46%), Positives = 118/166 (71%), Gaps = 2/166 (1%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAAIT++QIDGVLHE S+++GV ED+T IILN+K ++LK+  +  K + +  +GP  VTA
Sbjct: 1   GAAITSMQIDGVLHEFSTVEGVTEDVTQIILNLKKVSLKLDSEDQKNLELDVKGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITID 174
            DIQ  N++ +LNPD  I  +   A + ++LT  KG GY+ A  ++   D   IG++ ID
Sbjct: 61  SDIQGDNEVTILNPDLHITTVADGAELHIKLTADKGRGYLSANDNKARMDDLAIGVLPID 120

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           ++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T  ++V+L 
Sbjct: 121 SIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLTPTEAVSLG 166


>gi|154424791|emb|CAL18498.1| RNA polymerase alpha subunit [Streptococcus gallolyticus subsp.
           gallolyticus]
          Length = 172

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 74/171 (43%), Positives = 116/171 (67%)

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI T +
Sbjct: 1   KIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDS 60

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           D+E++NPDH +  +     ++  +TV+K  GYVPA+ ++ E+ P+G + +D++Y+P+KKV
Sbjct: 61  DVEIVNPDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKEDAPVGTLAVDSIYTPVKKV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           +Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F + 
Sbjct: 121 NYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDL 171


>gi|108792429|emb|CAJ44677.1| RNA polymerase alpha subunit [Lactobacillus acidipiscis]
          Length = 187

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 77/174 (44%), Positives = 119/174 (68%), Gaps = 2/174 (1%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE SSI GV ED+T IILN+K + LK++ +  + + I   GP  VTAGDIQ  +++EV
Sbjct: 1   VLHEFSSIDGVLEDVTTIILNLKKVALKLNSEDVQTLEIDVTGPMEVTAGDIQGSSEVEV 60

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSY 185
           LNPD  IC +   A     +T +KG GYV A  +  +TE+ PIG++ ID++Y+PI++V+Y
Sbjct: 61  LNPDLYICTVADGASFHARMTANKGRGYVSANENKAKTEDMPIGVLAIDSIYTPIERVNY 120

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
            VE  R GQ  D+DKL++ + T+GSIT  ++++L+++IL + L +F++  +  K
Sbjct: 121 QVEKTRVGQKSDFDKLTLDVWTNGSITPSEAISLSAKILTEHLTLFVDLTDEAK 174


>gi|154424735|emb|CAL18470.1| RNA polymerase alpha subunit [Streptococcus pasteurianus]
          Length = 168

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 73/168 (43%), Positives = 115/168 (68%)

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI T +
Sbjct: 1   KIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDS 60

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           D+E++NPDH +  +     ++  +T++K  GYVPA+ ++ E+ P+G + +D++Y+P+KKV
Sbjct: 61  DVEIVNPDHYLFTIAEGHSLKATMTIAKNRGYVPAEGNKKEDAPVGTLAVDSIYTPVKKV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           +Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F
Sbjct: 121 NYQVEPARVGSNDGFDKLTLEIMTNGTIIPEDALGLSARVLIEHLNLF 168


>gi|150186912|emb|CAK30126.1| RNA polymerase alpha subunit [Streptococcus lutetiensis]
 gi|154424793|emb|CAL18499.1| RNA polymerase alpha subunit [Streptococcus gallolyticus subsp.
           gallolyticus]
          Length = 171

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 74/171 (43%), Positives = 116/171 (67%)

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI T +
Sbjct: 1   KIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDS 60

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           D+E++NPDH +  +     ++  +TV+K  GYVPA+ ++ E+ P+G + +D++Y+P+KKV
Sbjct: 61  DVEIVNPDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKEDAPVGTLAVDSIYTPVKKV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           +Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F + 
Sbjct: 121 NYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDL 171


>gi|123966950|ref|YP_001012031.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. MIT 9515]
 gi|156637357|sp|A2BYR3|RPOA_PROM5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|123201316|gb|ABM72924.1| Bacterial RNA polymerase, alpha chain [Prochlorococcus marinus str.
           MIT 9515]
          Length = 312

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 101/305 (33%), Positives = 165/305 (54%), Gaps = 10/305 (3%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + I++       +  T +I  PL RG A TLGN+LRRVLM  L G+A+TAV+I G+ HE 
Sbjct: 7   DRIDHQTANDRSQTGTFLIG-PLERGQATTLGNSLRRVLMGGLEGSAVTAVRIAGINHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K +++  S    +   +   GP  V A DIQ  + +E+++ D 
Sbjct: 66  ATIPGVREDVLDILLNCKQLSINSSNPELEIGRLVVSGPMEVKANDIQFSSQVEIVDGDK 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV-ESAR 191
            I  +     + +E+ V +G GY P      E   + L+ IDA++ P+K+V++++ E+A 
Sbjct: 126 PIATIQEGHNLELEIHVERGVGYRPVDRRNQETTSVDLLQIDAVFMPVKRVNFSIDETAV 185

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L+M + TDGS + +D++A A+  L       I   +P   V     +   P
Sbjct: 186 AEGGTGRERLTMEVVTDGSTSPDDAIAEAANQL-------IELFQPLATVTMVEEIPEEP 238

Query: 252 FNPALLK-KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +  +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L
Sbjct: 239 EPSPEAQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEAL 298

Query: 311 GTMGL 315
             +G+
Sbjct: 299 ERIGI 303


>gi|108773284|ref|YP_635780.1| RNA polymerase alpha subunit [Chara vulgaris]
 gi|122237365|sp|Q1ACG7|RPOA_CHAVU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|77157940|gb|ABA61981.1| alpha subunit of RNA polymerase [Chara vulgaris]
          Length = 358

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 98/297 (32%), Positives = 160/297 (53%), Gaps = 23/297 (7%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A+TLG  LRR L+S L G  IT+V+ID + HE  ++ GV E + DI+LN+K I 
Sbjct: 33  PLKKGQANTLGITLRRTLLSDLDGICITSVKIDNIKHEYCTLTGVRESIQDILLNLKEIV 92

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
            K   D  ++  IF +GP  +TA DIQ    IE+L+ + +I +L      ++ELT+ K  
Sbjct: 93  FKGVCDKTQKGFIFVKGPKKITASDIQIEPCIEILDSNQIIAHLTEPIDFKVELTIEKSM 152

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           G+      +   D     +IDA++ PI+ V+Y++    +      + L + I T+GSIT 
Sbjct: 153 GFRLQNATQISKDS---FSIDAIFMPIRNVNYSIHPVEKAGDWKSELLILEIWTNGSITP 209

Query: 214 EDSVALASRIL-------------QDQLGMFINFEEPKKEVKEDIN----VKSLPFNPAL 256
           +++   AS  +             Q Q     NFEE ++ + ++I+     K      +L
Sbjct: 210 KEAFHQASEKIMNIFLSLSNSSDNQIQEKSTKNFEEKEEFIFQNIDGFKQDKETKVQESL 269

Query: 257 -LKKVE--ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             KK+   +LELS R+ NCL+ E I  + DL+  ++ D+L++ NFG++S  ++   L
Sbjct: 270 GWKKISINQLELSARAYNCLKNEKISTLFDLLNYSQEDLLKIKNFGKRSFEQVVNAL 326


>gi|171920602|ref|ZP_02931853.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 13 str. ATCC 33698]
 gi|185179070|ref|ZP_02964804.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 5 str. ATCC 27817]
 gi|188024263|ref|ZP_02996959.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 7 str. ATCC 27819]
 gi|188518671|ref|ZP_03004106.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 11 str. ATCC 33695]
 gi|188524445|ref|ZP_03004458.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 12 str. ATCC 33696]
 gi|195867590|ref|ZP_03079592.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 9 str. ATCC 33175]
 gi|198273610|ref|ZP_03206145.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 4 str. ATCC 27816]
 gi|209554135|ref|YP_002284656.1| DNA-directed RNA polymerase subunit alpha [Ureaplasma urealyticum
           serovar 10 str. ATCC 33699]
 gi|225551180|ref|ZP_03772126.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 8 str. ATCC 27618]
 gi|171903312|gb|EDT49601.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 13 str. ATCC 33698]
 gi|184209067|gb|EDU06110.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 5 str. ATCC 27817]
 gi|188018926|gb|EDU56966.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 7 str. ATCC 27819]
 gi|188997781|gb|EDU66878.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 11 str. ATCC 33695]
 gi|195659713|gb|EDX53093.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 12 str. ATCC 33696]
 gi|195660647|gb|EDX53902.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 9 str. ATCC 33175]
 gi|198249638|gb|EDY74419.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 4 str. ATCC 27816]
 gi|209541636|gb|ACI59865.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 10 str. ATCC 33699]
 gi|225378995|gb|EEH01360.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 8 str. ATCC 27618]
          Length = 327

 Score =  150 bits (379), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 96/307 (31%), Positives = 164/307 (53%), Gaps = 27/307 (8%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +  E++NRT++   PL  GF  TLGNALRR+ +SS+ GA++ AV+  G  HE    +GV 
Sbjct: 14  INSEDKNRTVVKIAPLEIGFGDTLGNALRRICLSSIPGASMFAVKFGGYSHEFQPYEGVK 73

Query: 80  EDLTDIILNIKGINLKMSG-------------DSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           ED+T IILN+K + +K+               D   ++ I  +GPGV+TA DI      E
Sbjct: 74  EDITHIILNLKNLAIKIDELIYSEDYFNNLLIDKWPKMKINFKGPGVITAKDIVCPVGFE 133

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           ++N D  I  +     V +E+    G G V    ++     + +I  D+ YSP+   +Y 
Sbjct: 134 IVNQDLYIAEVTKPIDVEIEIFAKTGRGRVDFNTNKDFVSTLHIIATDSNYSPVLHYAYN 193

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE  ++ +    + L++ I T+G+I+G +++A+A++I+Q  L       EP   + + IN
Sbjct: 194 VEMIKDSKSSMSEILTIDIATNGTISGSEAIAIAAKIMQAHL-------EPIMNIDKTIN 246

Query: 247 VKSLPFNPALLKK-------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
              +       +K       +++L+L+VR+ N L+   I    +LI+ T++ + ++ N G
Sbjct: 247 EMIIMREREEEEKRQNASISIDDLDLTVRAYNALKQSGINTTAELIELTKSQLEKIKNLG 306

Query: 300 RKSLVEI 306
           RKS+ EI
Sbjct: 307 RKSVTEI 313


>gi|154424789|emb|CAL18497.1| RNA polymerase alpha subunit [Streptococcus gallolyticus subsp.
           gallolyticus]
          Length = 169

 Score =  150 bits (379), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 74/168 (44%), Positives = 115/168 (68%)

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI T +
Sbjct: 1   KIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDS 60

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           D+E++NPDH +  +     ++  +TV+K  GYVPA+ ++ E+ P+G + +D++Y+P+KKV
Sbjct: 61  DVEIVNPDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKEDAPVGTLAVDSIYTPVKKV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           +Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F
Sbjct: 121 NYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLF 168


>gi|119672811|emb|CAK95486.1| RNA polymerase alpha subunit [Lactobacillus farciminis]
          Length = 172

 Score =  150 bits (379), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 69/171 (40%), Positives = 116/171 (67%)

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           QIDGVLHE S+I GV ED+T I+LN+K + LK   +   +  +   GP  VTA DI+  +
Sbjct: 1   QIDGVLHEFSAIDGVIEDVTQIVLNVKKLKLKSYAEDSLKAEVDIVGPATVTAKDIKADD 60

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           D+E+L+P+  IC +       M++T+  G GY PA+ ++T+  PIG++ +D++++P++KV
Sbjct: 61  DLEILDPEQFICTVAEGGHFHMQMTIKNGRGYTPAEQNKTDETPIGVLPVDSIFTPVEKV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           +Y VE+ R G+  D+DKL++ I T+GSI   ++++L+++IL + L  F+N 
Sbjct: 121 NYQVENTRVGKRNDFDKLTIDIWTNGSIGPREAISLSAKILTEHLNSFVNL 171


>gi|154424759|emb|CAL18482.1| RNA polymerase alpha subunit [Streptococcus anginosus]
          Length = 184

 Score =  150 bits (378), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 73/171 (42%), Positives = 113/171 (66%)

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE  ++ GV ED+  IILN+KGI +K   +  K + +   GP  +TAGDI T +DIE++
Sbjct: 1   LHEFDTVPGVREDVMQIILNVKGIAVKSYVEDEKTIELDVEGPAEITAGDILTDSDIEIV 60

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NPDH +  +   A ++  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y VE
Sbjct: 61  NPDHYLFTIGEGASLKAIMTVNTGRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQVE 120

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
            AR G    +DKL++ I TDG+I  ED++ L++RIL + L +F N  E  K
Sbjct: 121 PARVGSNDGFDKLTLEIMTDGTIIPEDALGLSARILTEHLDLFTNLTEVAK 171


>gi|11467738|ref|NP_050790.1| RNA polymerase alpha subunit [Guillardia theta]
 gi|3914811|sp|O46914|RPOA_GUITH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|3603063|gb|AAC35724.1| RNA polymerase a subunit [Guillardia theta]
          Length = 318

 Score =  150 bits (378), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 102/299 (34%), Positives = 175/299 (58%), Gaps = 19/299 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + +PL  G   TLGNALRR L+S L G AITAV+I GV HE S+I G+ ED+ +I+LN+
Sbjct: 23  FVIDPLKPGQGTTLGNALRRTLLSELEGLAITAVRIAGVSHEFSTINGIREDVLEILLNL 82

Query: 90  KGINL--KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K I    ++   +  R+T+  +GP +VTA   +   +I++++P+  I  +  +  + ME 
Sbjct: 83  KEIVFSGQLQESTIGRLTV--QGPAIVTARSFELPPEIKLIDPEQYIATICGNNTLEMEF 140

Query: 148 TVSKGHGY-VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR-EGQVLDYDKLSMTI 205
            +  G GY +  K + TE+     + +D+++ P+KKV++ +E  R E  +L+ ++L + I
Sbjct: 141 KIEVGSGYKIVEKDNSTEH--FEFLQVDSVFMPVKKVNFRIEETRGENNILN-EQLILDI 197

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+GSI+ +++++ A+  L   + +F   +    E + D           +L  +EEL+L
Sbjct: 198 WTNGSISAKEAISNAADNL---INLFSPLKTIDGESETDYETNETSHINQIL--IEELQL 252

Query: 266 SVRSTNCL-RG-ENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           SVR+ NCL RG  +I  + DL+  ++ D++ + NFG+KS  E   V+  +   LG+NLP
Sbjct: 253 SVRAYNCLKRGCAHIHSVADLLDYSQEDLIEIKNFGQKSAEE---VIDALQKRLGINLP 308


>gi|13357817|ref|NP_078091.1| DNA-directed RNA polymerase subunit alpha [Ureaplasma parvum
           serovar 3 str. ATCC 700970]
 gi|170762312|ref|YP_001752340.1| DNA-directed RNA polymerase subunit alpha [Ureaplasma parvum
           serovar 3 str. ATCC 27815]
 gi|171920389|ref|ZP_02931716.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma parvum
           serovar 1 str. ATCC 27813]
 gi|183508783|ref|ZP_02958249.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma parvum
           serovar 14 str. ATCC 33697]
 gi|186701955|ref|ZP_02971592.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma parvum
           serovar 6 str. ATCC 27818]
 gi|225550927|ref|ZP_03771876.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 2 str. ATCC 27814]
 gi|12230604|sp|Q9PQN4|RPOA_UREPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|11261081|pir||B82918 DNA-directed RNA polymerase alpha chain UU257 [imported] -
           Ureaplasma urealyticum
 gi|6899227|gb|AAF30666.1|AE002122_35 DNA-directed RNA polymerase alpha chain [Ureaplasma parvum serovar
           3 str. ATCC 700970]
 gi|168827889|gb|ACA33151.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma parvum
           serovar 3 str. ATCC 27815]
 gi|171902824|gb|EDT49113.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma parvum
           serovar 1 str. ATCC 27813]
 gi|182675728|gb|EDT87633.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma parvum
           serovar 14 str. ATCC 33697]
 gi|186700710|gb|EDU18992.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma parvum
           serovar 6 str. ATCC 27818]
 gi|225380081|gb|EEH02443.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 2 str. ATCC 27814]
          Length = 327

 Score =  150 bits (378), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 96/307 (31%), Positives = 164/307 (53%), Gaps = 27/307 (8%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +  E++NRT++   PL  GF  TLGNALRR+ +SS+ GA++ AV+  G  HE    +GV 
Sbjct: 14  INSEDKNRTVVKIAPLEIGFGDTLGNALRRICLSSIPGASMFAVKFGGYSHEFQPYEGVK 73

Query: 80  EDLTDIILNIKGINLKMSG-------------DSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           ED+T IILN+K + +K+               D   ++ I  +GPGV+TA DI      E
Sbjct: 74  EDITHIILNLKNLAIKIDELIYSEDYFNNLLIDKWPKMKINFKGPGVITAKDIVCPVGFE 133

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           ++N D  I  +     V +E+    G G V    ++     + +I  D+ YSP+   +Y 
Sbjct: 134 IVNQDLYIAEVTKPIDVEIEIFAKTGRGRVDFNTNKDFVSTLHIIATDSNYSPVLHYAYN 193

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE  ++ +    + L++ I T+G+I+G +++A+A++I+Q  L       EP   + + IN
Sbjct: 194 VEMIKDSKSSMSEILTIDIATNGTISGSEAIAIAAKIMQAHL-------EPIVNIDKTIN 246

Query: 247 VKSLPFNPALLKK-------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
              +       +K       +++L+L+VR+ N L+   I    +LI+ T++ + ++ N G
Sbjct: 247 EMIIMREREEEEKRQNASISIDDLDLTVRAYNALKQSGINTTAELIELTKSQLEKIKNLG 306

Query: 300 RKSLVEI 306
           RKS+ EI
Sbjct: 307 RKSVTEI 313


>gi|154424723|emb|CAL18464.1| RNA polymerase alpha subunit [Streptococcus gallolyticus]
          Length = 175

 Score =  150 bits (378), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 74/174 (42%), Positives = 118/174 (67%)

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI 
Sbjct: 1   TSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDIL 60

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +D+E++NPDH +  +     ++  +TV+K  GYV A+ ++ E+ P+G + +D++Y+P+
Sbjct: 61  TDSDVEIVNPDHYLFTIAEGHSLKATMTVAKERGYVSAEGNKKEDAPVGTLAVDSIYTPV 120

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F + 
Sbjct: 121 KKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDL 174


>gi|242309345|ref|ZP_04808500.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pullorum
           MIT 98-5489]
 gi|239523916|gb|EEQ63782.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pullorum
           MIT 98-5489]
          Length = 329

 Score =  150 bits (378), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 96/317 (30%), Positives = 164/317 (51%), Gaps = 13/317 (4%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           N+  + A P   G+A TL + LRR+L+ S  G A  A++I GV HE  S++GV ED++  
Sbjct: 22  NKVQITAYPFENGYAITLAHPLRRLLLGSSVGFAPIALRISGVAHEFDSVRGVVEDVSQF 81

Query: 86  ILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           I+N+K I  ++  +S      +K  G  V+T  D+     +EV+ PD  +  ++ DA + 
Sbjct: 82  IVNLKAIRFRIKDNSDNVSVDYKFNGSKVITGADLSN-ELVEVVTPDIHLATINEDATLA 140

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
             + + KG GYVP++  R  + P G + +DA ++P+   +YT E+       +Y+K+   
Sbjct: 141 FSIIIYKGIGYVPSEEIRA-SVPEGFMPLDAYFTPVTSATYTTENMLLEDDPNYEKIIFD 199

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF---INFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           I TDG +    +   A  ++  Q+ +F   +N E P+  V E+      P    L + ++
Sbjct: 200 IQTDGQVDPLTAFKNALSVMHKQMSIFNSELNIEMPETTVSEE----ERPELKVLSQTID 255

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
            L  S R  NCL    I Y+G+L+   E  +  + N G+KSL EI   L  +G  +   +
Sbjct: 256 SLNFSARCFNCLDRSGIRYLGELVLLNEDQIKNIKNLGKKSLDEITAKLDELGYPVNREI 315

Query: 322 PDWPPESIEELAKKYED 338
           P+   + ++ L KK+ +
Sbjct: 316 PE---DLLQILKKKFSN 329


>gi|154424807|emb|CAL18506.1| RNA polymerase alpha subunit [Streptococcus lutetiensis]
          Length = 167

 Score =  149 bits (377), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 73/165 (44%), Positives = 115/165 (69%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI
Sbjct: 1   VTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDI 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
            T +D+E++NPDH +  +     ++  +TV+K  GYVPA+ ++ E+ P+G + +D++Y+P
Sbjct: 61  LTDSDVEIVNPDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKEDAPVGTLAVDSIYTP 120

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           +KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L
Sbjct: 121 VKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVL 165


>gi|126697065|ref|YP_001091951.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. MIT 9301]
 gi|156637354|sp|A3PF25|RPOA_PROM0 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|126544108|gb|ABO18350.1| Bacterial RNA polymerase, alpha chain [Prochlorococcus marinus str.
           MIT 9301]
          Length = 312

 Score =  149 bits (377), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 101/303 (33%), Positives = 164/303 (54%), Gaps = 10/303 (3%)

Query: 15  IEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS 74
           I++ +     +  T +I  PL RG A TLGN+LRRVLM  L G+A+TAV+I G+ HE ++
Sbjct: 9   IDHQIADDRSQTGTFLIG-PLERGQATTLGNSLRRVLMGGLEGSAVTAVRIAGINHEYAT 67

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           I GV ED+ DI+LN K +++  +    +   +   GP  V A DIQ  + +E+++ +  I
Sbjct: 68  IPGVREDVLDILLNCKQLSINSTNPELEIGRLVASGPMEVKANDIQFSSQVEIVDGEKPI 127

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV-ESAREG 193
             +     + +E+ V +G GY P      E   I L+ IDA++ P+K+V++T+ E+A   
Sbjct: 128 ATIQEGHNLELEIHVERGVGYRPVDRKSEETTAIDLLQIDAVFMPVKRVNFTIDETAVAE 187

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
                ++L M + TDGS + +D++A A+  L       I   +P   V     +   P  
Sbjct: 188 GGTGRERLKMEVVTDGSTSPDDAIAEAANQL-------IELFQPLATVTMVEEIPEEPEP 240

Query: 254 PALLK-KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
               +  +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L  
Sbjct: 241 SPEAQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALER 300

Query: 313 MGL 315
           +G+
Sbjct: 301 IGI 303


>gi|72382944|ref|YP_292299.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. NATL2A]
 gi|124026686|ref|YP_001015801.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. NATL1A]
 gi|90110857|sp|Q46IT2|RPOA_PROMT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|156637355|sp|A2C4X7|RPOA_PROM1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|72002794|gb|AAZ58596.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. NATL2A]
 gi|123961754|gb|ABM76537.1| Bacterial RNA polymerase, alpha chain [Prochlorococcus marinus str.
           NATL1A]
          Length = 312

 Score =  149 bits (377), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 103/284 (36%), Positives = 155/284 (54%), Gaps = 9/284 (3%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG A TLGN+LRRVLM  L G+A+TAV+I GV HE ++I GV ED+ DI+LN K I+
Sbjct: 27  PLERGQATTLGNSLRRVLMGGLEGSAVTAVRIAGVNHEYATIPGVREDVLDILLNCKQIS 86

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +       +   +   GP  V A DIQ  + +EV++ D  I  +     + +E+ V +G 
Sbjct: 87  VDSRSQELEIGRLVVTGPADVKAKDIQFSSQVEVVDGDRPIATVQEGHNLELEIHVERGV 146

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV-ESAREGQVLDYDKLSMTIDTDGSIT 212
           GY P      E   I L+ IDA++ PI +V++T+ E+A        ++L M + TDGS +
Sbjct: 147 GYRPVDRKNEETSAIDLLQIDAVFMPINRVNFTIDETAVAEGGSTRERLKMELVTDGSTS 206

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK-KVEELELSVRSTN 271
            +D++A A+  L       I   +P   V     +   P   A  +  +EEL LSVR+ N
Sbjct: 207 PDDALAEAANQL-------IELFQPLATVSMVEEIPEEPEPAAEAQIPLEELNLSVRAYN 259

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           CL+   +  + DL+  +  D+L + NFG KS  E+   L  +G+
Sbjct: 260 CLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALERIGI 303


>gi|13507930|ref|NP_109879.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma pneumoniae
           M129]
 gi|2500601|sp|Q50295|RPOA_MYCPN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|1215697|gb|AAC43690.1| RpoA [Mycoplasma pneumoniae]
 gi|1674345|gb|AAB96288.1| RNA polymerase alpha core subunit [Mycoplasma pneumoniae M129]
          Length = 327

 Score =  149 bits (377), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 93/303 (30%), Positives = 162/303 (53%), Gaps = 25/303 (8%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNA+RRVL+S + GA++ A+ I G   E ++++G+ ED+T+++LN K + 
Sbjct: 29  PLESGFVITIGNAMRRVLLSCIPGASVFALSISGAKQEFAAVEGMKEDVTEVVLNFKQLV 88

Query: 94  LKMSG-------------DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           +K+S              +    +T+     G V A D++     EV+N D  + +L  D
Sbjct: 89  VKISDLLFEDGEMVEPPLERWPLLTVTAEKAGPVYAKDLECPAGFEVVNKDLYLFSLQTD 148

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             V + + V +G G+V    +R   + +G+I  D+ +SP+    Y V+  +  +    D 
Sbjct: 149 KKVTVNVYVKQGRGFVTFLENREMINSLGIIATDSNFSPVLHCGYEVQELKTSKQKITDH 208

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK------EVKEDINVKSLPFNP 254
           L+  I T+G+I+  D+ A+A++IL + L   +N  E  K      E  E+  V+S     
Sbjct: 209 LTFKIATNGAISAVDAFAMAAKILIEHLNPIVNVNESIKALNIIQEKAEERRVRSFA--- 265

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
              K++EEL+ +VR+ NCL+   I  + +L+ ++ AD+  + N G+KS  EI   +  +G
Sbjct: 266 ---KQIEELDFTVRTFNCLKRSGIHTLQELLSKSLADIREIRNLGKKSEREIIKKVHELG 322

Query: 315 LFL 317
           L L
Sbjct: 323 LKL 325


>gi|301633194|gb|ADK86748.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma pneumoniae
           FH]
          Length = 327

 Score =  149 bits (377), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 93/303 (30%), Positives = 162/303 (53%), Gaps = 25/303 (8%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNA+RRVL+S + GA++ A+ I G   E ++++G+ ED+T+++LN K + 
Sbjct: 29  PLESGFGITIGNAMRRVLLSCIPGASVFALSISGAKQEFAAVEGMKEDVTEVVLNFKQLV 88

Query: 94  LKMSG-------------DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           +K+S              +    +T+     G V A D++     EV+N D  + +L  D
Sbjct: 89  VKISDLLFEDGEMVEPPLERWPLLTVTAEKAGPVYAKDLECPAGFEVVNKDLYLFSLQTD 148

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             V + + V +G G+V    +R   + +G+I  D+ +SP+    Y V+  +  +    D 
Sbjct: 149 KKVTVNVYVKQGRGFVTFLENREMINSLGIIATDSNFSPVLHCGYEVQELKTSKQKITDH 208

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK------EVKEDINVKSLPFNP 254
           L+  I T+G+I+  D+ A+A++IL + L   +N  E  K      E  E+  V+S     
Sbjct: 209 LTFKIATNGAISAVDAFAMAAKILIEHLNPIVNVNESIKALNIIQEKAEERRVRSFA--- 265

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
              K++EEL+ +VR+ NCL+   I  + +L+ ++ AD+  + N G+KS  EI   +  +G
Sbjct: 266 ---KQIEELDFTVRTFNCLKRSGIHTLQELLSKSLADIREIRNLGKKSEREIIKKVHELG 322

Query: 315 LFL 317
           L L
Sbjct: 323 LKL 325


>gi|78780012|ref|YP_398124.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. MIT 9312]
 gi|119366708|sp|Q318K7|RPOA_PROM9 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|78713511|gb|ABB50688.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. MIT 9312]
          Length = 311

 Score =  149 bits (377), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 101/303 (33%), Positives = 164/303 (54%), Gaps = 10/303 (3%)

Query: 15  IEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS 74
           I++ +     +  T +I  PL RG A TLGN+LRRVLM  L G+A+TAV+I G+ HE ++
Sbjct: 8   IDHQIADDRSQTGTFLIG-PLERGQATTLGNSLRRVLMGGLEGSAVTAVRIAGINHEYAT 66

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           I GV ED+ DI+LN K +++  S    +   +   GP  V A DIQ  + +E+++ +  I
Sbjct: 67  IPGVREDVLDILLNCKQLSINSSNPELEIGRLVASGPLDVKANDIQFSSQVEIVDGEKPI 126

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV-ESAREG 193
             +     + +E+ V +G GY P      E   I L+ IDA++ P+K+V++++ E+A   
Sbjct: 127 ATIQEGHNLELEIHVERGVGYRPVDRKNQETTAIDLLQIDAVFMPVKRVNFSIDETAVAE 186

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
                ++L M + TDGS + +D++A A+  L       I   +P   V     +   P  
Sbjct: 187 GGTGRERLKMEVVTDGSTSPDDAIAEAANQL-------IELFQPLATVTMVEEIPEEPEP 239

Query: 254 PALLK-KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
               +  +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L  
Sbjct: 240 SPEAQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALER 299

Query: 313 MGL 315
           +G+
Sbjct: 300 IGI 302


>gi|154424775|emb|CAL18490.1| RNA polymerase alpha subunit [Streptococcus dysgalactiae subsp.
           dysgalactiae]
          Length = 169

 Score =  149 bits (376), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 73/169 (43%), Positives = 116/169 (68%)

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           ++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI T 
Sbjct: 1   IKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKIIELEVEGPAEVTAGDILTD 60

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           +DIE++NPDH +  +     +R  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KK
Sbjct: 61  SDIELVNPDHYLFTIAEGHSLRATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKK 120

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           V+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F
Sbjct: 121 VNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLF 169


>gi|150187152|emb|CAK30182.1| RNA polymerase alpha subunit [Streptococcus vestibularis ATCC
           49124]
          Length = 190

 Score =  149 bits (376), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 72/174 (41%), Positives = 116/174 (66%)

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGVLHE  ++ GV ED+  IILNIKG+ +K   +  K + +  +GP  VTAGDI T +DI
Sbjct: 1   DGVLHEFDTVPGVREDVMQIILNIKGLAVKSYVEDEKTIELDVQGPAEVTAGDILTDSDI 60

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++NPDH +  +   A ++  +TV+   GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y
Sbjct: 61  EIVNPDHYLFTISEGASLKATMTVATNRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNY 120

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
            VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  +  K
Sbjct: 121 QVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTDVAK 174


>gi|150036832|emb|CAO03476.1| DNA-directed RNA polymerase alpha chain [Leuconostoc carnosum]
          Length = 174

 Score =  149 bits (376), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 79/168 (47%), Positives = 111/168 (66%), Gaps = 2/168 (1%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  
Sbjct: 3   TLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDEE 62

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  +
Sbjct: 63  RVLEIDVQGPSEVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSADEN 122

Query: 162 RT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +   E  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T
Sbjct: 123 KQLREEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWT 170


>gi|157165509|ref|YP_001467695.1| DNA-directed RNA polymerase subunit alpha [Campylobacter concisus
           13826]
 gi|171855074|sp|A7ZFY7|RPOA_CAMC1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|112800819|gb|EAT98163.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter concisus
           13826]
          Length = 338

 Score =  149 bits (375), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 104/313 (33%), Positives = 166/313 (53%), Gaps = 9/313 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           EN   + A P   G+A TL + LRR+L +S  G A   V+I GV HE  S++G+ ED+  
Sbjct: 21  ENVANITAYPFEAGYAVTLAHPLRRLLYTSTVGFAPIGVKIKGVSHEFDSMRGMLEDVAF 80

Query: 85  IILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVND-IEVLNPDHVICNLDVDAV 142
            I+N+K I  K+   S + V  +  +GP  +T  D+   ND +E++NPD  +  ++ DA 
Sbjct: 81  FIINLKKIRFKLKSGSEREVIEYSFKGPKEITGADLN--NDLVEIVNPDAYLATINEDAE 138

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           +   + + KG GYVP++  R E +    I +DA ++P+KK  Y +++       DY+K+ 
Sbjct: 139 LNFSVIIQKGIGYVPSEEIREEIE-DEYIALDAFFTPVKKAVYEIQNVLVEDDPDYEKIV 197

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
            TI TDG +   ++       +  Q+ +F    +         +  S  F+  LL  VE+
Sbjct: 198 FTITTDGQVGPVEAFKNCLEAMYQQMSVFKGILDIDVSAPVASSSASGEFS-KLLSSVED 256

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           L LS RS NCL    I ++G+L    E ++  + N G+KSL EIK V+  +G  +G+   
Sbjct: 257 LNLSARSFNCLDKAEIRFIGELALMDENELKELKNLGKKSLEEIKAVMEEIGYPVGV--- 313

Query: 323 DWPPESIEELAKK 335
           D   +S E+L KK
Sbjct: 314 DVLKDSKEQLRKK 326


>gi|47679559|gb|AAT36723.1| RNA polymerase alpha subunit [Phaeodactylum sp. Bohlin BA153065]
          Length = 298

 Score =  149 bits (375), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 90/269 (33%), Positives = 151/269 (56%), Gaps = 9/269 (3%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI----NLKMS 97
           T+GN LRRVL+  L G AI+AV+I G+ HE S+I GV ED+ +I+LN+KGI     ++ +
Sbjct: 35  TIGNQLRRVLLGDLGGVAISAVRIAGITHEFSTIPGVREDILEILLNLKGIICTSQIQDT 94

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
              H +V    +GP VVTA  IQ   ++E++NP+H I  +    ++ +E     G GY  
Sbjct: 95  QFGHLKV----QGPSVVTADLIQLPPEVEIINPNHYIATITTSNILEIEFKFVYGGGYHL 150

Query: 158 AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
           A       D    + +D ++ P++KV + +E+  +      ++L + I T+GSI+  D++
Sbjct: 151 ASQKFCREDE-NYLQLDTIFMPVQKVDFKIENIYDATNNISERLFLDIWTNGSISPNDAL 209

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGEN 277
             A++++ D   + IN        +    ++++   P     +EEL+LSVR+ NCL+   
Sbjct: 210 ESAAQVIIDLFTLLINNTNINNNNRLVKAIRAISIEPYTNIAIEELQLSVRAYNCLKKAQ 269

Query: 278 IVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           I  +GDL+Q +   +  + NFGRKS  E+
Sbjct: 270 INTVGDLLQYSPEKLQELKNFGRKSADEV 298


>gi|289524820|emb|CBJ94466.1| alpha subunit of RNA polymerase [Vibrio sp. C15.18]
          Length = 173

 Score =  149 bits (375), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 75/176 (42%), Positives = 114/176 (64%), Gaps = 6/176 (3%)

Query: 145 MELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           M + V +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL
Sbjct: 1   MRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKL 60

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + ++T+G++  E+++  A+ IL +QL  F++  + +   +     +   F+P LL+ V+
Sbjct: 61  VIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEE---KEEKPEFDPILLRPVD 117

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 118 DLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 173


>gi|242624287|ref|YP_003002205.1| DNA-directed RNA polymerase alpha chain [Aureoumbra lagunensis]
 gi|239997395|gb|ACS36917.1| DNA-directed RNA polymerase alpha chain [Aureoumbra lagunensis]
          Length = 303

 Score =  149 bits (375), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 97/267 (36%), Positives = 149/267 (55%), Gaps = 13/267 (4%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           T+GNALRRVL++ L G AITAV+I GV HE  +I GV ED+ +I+LN+K I    +    
Sbjct: 35  TIGNALRRVLLTDLMGTAITAVRIYGVNHEYGTIPGVREDVLEILLNLKQIKFHGTCSDP 94

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY--VPAK 159
             +T+   GP ++TA DI   +++ V+N    I  +     +++EL +  G GY  V  +
Sbjct: 95  VLITLEIEGPYLLTAVDITVPSNLNVINTKQYIATISEQTKLKLELQIESGCGYRLVTDE 154

Query: 160 HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
            HR   D    + IDA+++P+K VSY V           + L + I TDGS+  +D++  
Sbjct: 155 LHR---DSGTFLNIDAIFTPVKNVSYKVLDLYRFDEKLLEDLVLEITTDGSLNPKDALIQ 211

Query: 220 ASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIV 279
           A+ ILQ+  G  +   EPK  +K+   + S          +EEL+LSVR+ NCL+  NI 
Sbjct: 212 AANILQNMFGS-LTVGEPKA-LKQTTTISSRQI------LIEELQLSVRAYNCLKRANIR 263

Query: 280 YMGDLIQRTEADMLRMANFGRKSLVEI 306
            + DL Q +  ++  + NFG+KS  E+
Sbjct: 264 TIDDLTQYSIKELKELKNFGQKSANEV 290


>gi|162751059|gb|ABY19884.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  149 bits (375), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 72/146 (49%), Positives = 105/146 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R E+TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAEMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPADENKVDGAPIGTIAVDSIYT 146


>gi|150187052|emb|CAK30160.1| RNA polymerase alpha subunit [Streptococcus constellatus subsp.
           pharyngis]
          Length = 150

 Score =  148 bits (374), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 69/150 (46%), Positives = 106/150 (70%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL++SL GAA+T++ I+GVLHE  ++ GV ED+  IILN+KGI +K   +  K +
Sbjct: 1   NSLRRVLLASLPGAAVTSINIEGVLHEFDTVPGVREDVMQIILNVKGIAVKSYVEDEKTI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  +TAGDI T +DIE++NPDH +  +   A ++  +TV+ G GYVPA  ++ +
Sbjct: 61  ELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIGEGASLKAIMTVNAGRGYVPADENKKD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQ 194
           + P+G + +D++Y+P+KKV+Y VE AR G 
Sbjct: 121 DSPVGTLAVDSIYTPVKKVNYQVEPARVGS 150


>gi|154424799|emb|CAL18502.1| RNA polymerase alpha subunit [Streptococcus hyointestinalis]
          Length = 167

 Score =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 72/165 (43%), Positives = 115/165 (69%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI
Sbjct: 1   VTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKMIELDVEGPAEVTAGDI 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
            T +DIE++NPDH +  +     ++  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P
Sbjct: 61  LTDSDIEIVNPDHYLFTIAEGHSLKATMTVAKNRGYVPAEGNKKDDAPVGTLAVDSIYTP 120

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           +KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL
Sbjct: 121 VKKVNYQVEPARVGSNDGFDKLTVEIMTNGTIIPEDALGLSARIL 165


>gi|150187130|emb|CAK30177.1| RNA polymerase alpha subunit [Streptococcus macacae NCTC 11558]
          Length = 178

 Score =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 73/176 (41%), Positives = 115/176 (65%)

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +IDGVLHE  +I GV ED+  IILNIKG+ +K   +  K + +   GP  +TAGDI T +
Sbjct: 1   KIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVEEEKIIELDVEGPAEITAGDILTDS 60

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIE++N DH +  +   A ++  +TV    GY+PA+ ++ +  P+G + ID++Y+P+KKV
Sbjct: 61  DIEIVNSDHYLFTIAEGASLKATMTVETNRGYIPAEENKKDGAPVGTLAIDSIYTPVKKV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K
Sbjct: 121 NYQVEPARVGSKDSFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAK 176


>gi|254779835|ref|YP_003057941.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori B38]
 gi|254001747|emb|CAX29978.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           (Transcriptase alpha chain) (RNA polymerase alpha
           subunit) [Helicobacter pylori B38]
          Length = 344

 Score =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 105/328 (32%), Positives = 174/328 (53%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ + + IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GPMELRARDLNS-DHIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKKV Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKKVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELSSEQRESLKKRLEKLEDK 340


>gi|119662331|emb|CAJ33154.1| RNA polymerase alpha subunit [Lactobacillus nagelii]
          Length = 175

 Score =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 74/171 (43%), Positives = 119/171 (69%), Gaps = 2/171 (1%)

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGVLHE S+IKGV ED+T IILN+K + LK+  +  + + I   GP  VTA DIQ  +++
Sbjct: 1   DGVLHEFSTIKGVREDVTQIILNLKKVALKIDSEEDQALEIDVTGPLDVTASDIQGSSEV 60

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKV 183
           EVLN D  +C++   A + + +  +KG GYV A  ++T+ D  PIG++ ID++Y+PI++V
Sbjct: 61  EVLNKDLYLCSVAEGASLHVRMNANKGRGYVSADENKTKADDMPIGVLPIDSIYTPIERV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           +Y VE  R GQ  DYDKL++ + T+GSI+  ++++L+++IL + L +F++ 
Sbjct: 121 NYQVEKTRVGQKNDYDKLTLDVWTNGSISPSEAISLSAKILTEHLTLFVDL 171


>gi|308183403|ref|YP_003927530.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           PeCan4]
 gi|308065588|gb|ADO07480.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           PeCan4]
          Length = 344

 Score =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 105/328 (32%), Positives = 173/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKESNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GPMELRARDLNS-EQIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKKV Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKKVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|299830399|ref|YP_003734614.1| RNA polymerase alpha subunit [Kryptoperidinium foliaceum]
 gi|297385101|gb|ADI40399.1| RNA polymerase alpha subunit [Kryptoperidinium foliaceum]
          Length = 311

 Score =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 92/289 (31%), Positives = 156/289 (53%), Gaps = 2/289 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + + L  G   T+GN LRRVL++ L G AI+AV+I GV HE S+I GV ED+ +I+LN+
Sbjct: 23  FLIQTLRPGQGITIGNQLRRVLLNDLGGVAISAVRIAGVSHEFSTIPGVREDILEILLNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+    + +   +  +GP VVTA  IQ  + +E++NP+  I  +    ++ +E   
Sbjct: 83  KEIVLRSKTQTPQFGRLKIQGPAVVTADLIQLPSTVEIVNPNQYIMTISTSNILEIEFKF 142

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GY  A     E +    + +DA++ PI+KV + +E+  +      ++L + I T+G
Sbjct: 143 DYGTGYRLASQTFLEENE-NYLQLDAIFMPIQKVDFKIENVYDKANNITERLFLDIWTNG 201

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI+  +++  A++I  D     +  ++     +      ++   P     +EEL+LSVR+
Sbjct: 202 SISPTEAMKSAAQITIDVFTSLLENKDTNSSNEVPSKTSAISLEPYTNIAIEELQLSVRA 261

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL-GTMGLFL 317
            NCL+   I  +GDL+  +   +  + NFGRKS  E+   L   +G+ L
Sbjct: 262 YNCLKKAQINTVGDLLHYSPEKLQELKNFGRKSADEVFSTLKNKLGIIL 310


>gi|317009976|gb|ADU80556.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           India7]
          Length = 344

 Score =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 105/328 (32%), Positives = 173/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKESNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GPMELRARDLNS-EHIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKKV Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKKVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSTKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|11466357|ref|NP_038360.1| RNA polymerase alpha subunit [Mesostigma viride]
 gi|12230597|sp|Q9MUV0|RPOA_MESVI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|7259500|gb|AAF43801.1|AF166114_13 alpha subunit of RNA polymerase [Mesostigma viride]
          Length = 316

 Score =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 99/298 (33%), Positives = 161/298 (54%), Gaps = 9/298 (3%)

Query: 12  PNNIEYIVLGQEEENRTL---MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           P+ I Y +  + E  R L    + EPL  G   T+GN LRR+L+  + GAAIT+V+I G 
Sbjct: 8   PSTI-YCIESKIESPRNLYGRFLIEPLAIGQGITVGNTLRRILLGDIEGAAITSVKIPGA 66

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            +E S + G+ E + +I+LN+K I  +      ++  +  +GP VV A ++Q    IEV+
Sbjct: 67  NNEFSILPGIRESVLEILLNLKEIVFRTKSLDVQKGYLSIQGPCVVKAANLQLPTSIEVV 126

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L  +A + ME  ++ G GY  A +   +N  I  + +DA++ PI KV+Y VE
Sbjct: 127 DGGQYIATLSGNANLDMEFVINTGKGYQMADYAIKKNSYISSLPVDAIFMPIHKVNYMVE 186

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
                + L  +++ + I T+GSI+  D++ +  + + D      +        K D + +
Sbjct: 187 QDHTSKFLT-ERVILEIWTNGSISPRDALDIGIKKVIDLFNPLHHCSSEYSTNKNDFSTE 245

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           S   N  L   VEELELSVR+ NCL+   I  + DL+  ++ D+L + NFGR+S  E+
Sbjct: 246 S-KINDIL---VEELELSVRAYNCLKRAQIHTISDLLAYSQEDLLEIKNFGRRSAEEV 299


>gi|210135452|ref|YP_002301891.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori P12]
 gi|210133420|gb|ACJ08411.1| DNA-directed RNA polymerase alpha subunit [Helicobacter pylori P12]
          Length = 344

 Score =  147 bits (371), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 105/328 (32%), Positives = 173/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKESNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPIGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GPMELRARDLNS-EQIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKKV Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKKVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYTQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|15645906|ref|NP_208085.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           26695]
 gi|2500600|sp|P56001|RPOA_HELPY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|2314459|gb|AAD08336.1| DNA-directed RNA polymerase, alpha subunit (rpoA) [Helicobacter
           pylori 26695]
          Length = 344

 Score =  147 bits (371), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 105/328 (32%), Positives = 173/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GPMELRARDLNS-EQIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKKV Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKKVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|154424825|emb|CAL18515.1| RNA polymerase alpha subunit [Streptococcus parasanguinis]
          Length = 167

 Score =  147 bits (371), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 72/166 (43%), Positives = 111/166 (66%)

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           +GVLHE  ++ GV ED+  IILN+KGI +K      K + +   GP  VTAGDI T +DI
Sbjct: 1   EGVLHEFDTVPGVREDVMQIILNVKGIAVKSYVQDEKIIELDVEGPAEVTAGDILTDSDI 60

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++NPDH +  +   A ++  LTV+ G GYVPA  ++ ++ P+G + +D++Y+P+ KV+Y
Sbjct: 61  EIVNPDHYLFTIGEGASLKATLTVNSGRGYVPADQNKKDDAPVGTLAVDSIYTPVTKVNY 120

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F
Sbjct: 121 QVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLF 166


>gi|149195168|ref|ZP_01872259.1| DNA-directed RNA polymerase subunit alpha [Caminibacter
           mediatlanticus TB-2]
 gi|149134720|gb|EDM23205.1| DNA-directed RNA polymerase subunit alpha [Caminibacter
           mediatlanticus TB-2]
          Length = 333

 Score =  147 bits (371), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 104/318 (32%), Positives = 167/318 (52%), Gaps = 11/318 (3%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +E N+  +   P   GF  ++ + +RR L+++  G A   ++I+GV HE  S+KG+ ED
Sbjct: 17  NKEGNKASIEVYPFEAGFGVSVAHPIRRTLIAATTGFAPVGLKIEGVKHEFDSLKGMLED 76

Query: 82  LTDIILNIKGINLKMSGDSHKRVTI--FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           +   I+N+K I  K+   S   V +  F  GP  +   D+    +I+V+ PD  I  L+ 
Sbjct: 77  VASFIINLKNIRFKIKNSSKDEVVVEYFFTGPKEIKGADLIN-EEIDVVTPDEYIATLNE 135

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           +  +++ L + KG G+V  ++ R +  P G I +DA +SPIKK  Y +E+       +Y+
Sbjct: 136 EGELKLTLLIKKGMGFVAVENFR-DTLPEGFIGLDAYFSPIKKAVYNIENVLVEDDPNYE 194

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP--FNPALL 257
           K+   ++TDG I   D+   A     +Q G+F   +E K E K+  NV+ LP  +N  L 
Sbjct: 195 KVIFEVETDGQIDPIDAFKNAVNNYLNQFGVFS--KEFKLETKKVENVE-LPDEYN-ILF 250

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           K +EEL L  RS N L    I ++G+L+   +  +  + N G KSL EI   L  +G  +
Sbjct: 251 KPIEELNLRSRSFNALDRAGIKFIGELVLMGKEKISNIKNLGTKSLEEIFEKLEEIGFSI 310

Query: 318 GMNLP-DWPPESIEELAK 334
              LP D+     E+LAK
Sbjct: 311 NKTLPLDFKKAIEEKLAK 328


>gi|255023418|ref|ZP_05295404.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL J1-208]
          Length = 195

 Score =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 75/191 (39%), Positives = 121/191 (63%)

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +LNPD  I  L  +A   + L  ++G GY PA  ++ EN PIG++ +D+++SP+ +V+Y 
Sbjct: 1   MLNPDLHIATLSDNAKFHVRLNATRGRGYTPADQNKRENMPIGVLPVDSIFSPVIRVNYQ 60

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+ R GQ  +YDKL+  + TDGSI+ E++V+L ++IL + L +F+N  +  ++ +  I 
Sbjct: 61  VENTRVGQSTNYDKLTFDVLTDGSISPEEAVSLGAKILSEHLSIFVNLTDEAQKAEIMIE 120

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L   +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N GRKSL E+
Sbjct: 121 KEESHKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELADKSEDDMMKVRNLGRKSLEEV 180

Query: 307 KGVLGTMGLFL 317
           K  L  +GL L
Sbjct: 181 KVKLADLGLSL 191


>gi|308185045|ref|YP_003929178.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           SJM180]
 gi|308060965|gb|ADO02861.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           SJM180]
          Length = 344

 Score =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 105/328 (32%), Positives = 173/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GPMELRARDLSS-EHIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKKV Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKKVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELSHEQRESLKKRLEKLEDK 340


>gi|317013080|gb|ADU83688.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           Lithuania75]
          Length = 344

 Score =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 105/328 (32%), Positives = 173/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GPMELRARDLNS-EHIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKKV Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKKVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|162751159|gb|ABY19934.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
          Length = 146

 Score =  146 bits (369), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 72/146 (49%), Positives = 104/146 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R E+TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAEMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D+ Y+
Sbjct: 121 YGYVPADENKVDGAPIGTIAVDSNYT 146


>gi|307720213|ref|YP_003891353.1| DNA-directed RNA polymerase subunit alpha [Sulfurimonas
           autotrophica DSM 16294]
 gi|306978306|gb|ADN08341.1| DNA-directed RNA polymerase subunit alpha [Sulfurimonas
           autotrophica DSM 16294]
          Length = 333

 Score =  146 bits (369), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 94/322 (29%), Positives = 171/322 (53%), Gaps = 16/322 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           Q  +N   ++A P   G+A +L + LRR L+SS  G A  A++I+G  HE  S++G+ ED
Sbjct: 18  QISDNEANIMAYPFEVGYAISLAHPLRRFLLSSSVGYAPIAIKIEGAKHEFDSVRGMLED 77

Query: 82  LTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           ++D ILN+K I  K++ D +   +     GP  +   D+   +++EV+ PD  +  L+ D
Sbjct: 78  ISDFILNLKEIRFKLNNDATQAEINYSFAGPCTIKGADLSN-DEVEVVTPDAPLATLNED 136

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
           + +   L +++G GYV ++    E      I +DA ++P++  +Y +++       ++++
Sbjct: 137 STLNFTLKIAQGIGYVASEDTAVEVADDDYIALDAYFTPVRSATYKIDNVLVEDNPNFER 196

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMF---INFEEPK--KEVKEDINVKSLPFNPA 255
           + M I TDG I+  D+   +  ++  QL +F   I+ + P   + V+E  ++K L  N  
Sbjct: 197 VIMNIKTDGQISPIDAFRNSLEVMYAQLAVFNSEISIKAPATIERVEESPDLKKLTTN-- 254

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
               ++ L LS RS NCL   +I  +G+++  +  D+  + N G+KS  EI   +   G 
Sbjct: 255 ----IDSLGLSARSFNCLDRSSIKLIGEIVLMSTNDLKNVKNLGKKSYDEIVEKIQEFGF 310

Query: 316 FLGMNLPDWPPESIEELAKKYE 337
            +G +L D   + +  L KK E
Sbjct: 311 EVGADLAD---DVVTALKKKIE 329


>gi|119668305|emb|CAK95454.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           bulgaricus]
          Length = 173

 Score =  146 bits (368), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 73/169 (43%), Positives = 108/169 (63%)

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           V+IDG+LHE +++ GV ED+T IILN+K + L+   +  K + +   GP  VTA D++  
Sbjct: 2   VKIDGILHEFTTVPGVKEDVTKIILNLKKLELRAYTEEVKTIELDVEGPATVTAEDLKAD 61

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
            D+EVLNPD  IC +     + M + V  G GYVPA  ++T    IG I +D+L+SPI+K
Sbjct: 62  ADVEVLNPDQYICTIAQGGHLHMWIDVCNGRGYVPASENKTAEMSIGDIPVDSLFSPIEK 121

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           V+Y VES R G+  D+DKL++ I T+GSI   D++  A+R+L +    F
Sbjct: 122 VNYQVESTRVGKREDFDKLTLEIWTNGSIAPNDALNFAARVLVEHFKAF 170


>gi|308062578|gb|ADO04466.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           Cuz20]
          Length = 344

 Score =  146 bits (368), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 105/328 (32%), Positives = 173/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRIKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVNYSFK-GPMELRARDLNS-EHIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKKV Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKKVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|162751067|gb|ABY19888.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  146 bits (368), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 71/146 (48%), Positives = 104/146 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSIRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPADENKVDGAPIGTIAVDSIYT 146


>gi|307637964|gb|ADN80414.1| DNA-directed RNA polymerase alpha subunit [Helicobacter pylori 908]
 gi|325996569|gb|ADZ51974.1| DNA-directed RNA polymerase alpha subunit [Helicobacter pylori
           2018]
 gi|325998159|gb|ADZ50367.1| DNA-directed RNA polymerase alpha subunit [Helicobacter pylori
           2017]
          Length = 344

 Score =  145 bits (367), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 104/328 (31%), Positives = 172/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GPMEIRARDLNS-EQIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIK V Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKNVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|39938713|ref|NP_950479.1| DNA-directed RNA polymerase alpha subunit [Onion yellows
           phytoplasma OY-M]
 gi|39721822|dbj|BAD04312.1| DNA-directed RNA polymerase alpha subunit [Onion yellows
           phytoplasma OY-M]
          Length = 247

 Score =  145 bits (367), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 86/239 (35%), Positives = 139/239 (58%), Gaps = 11/239 (4%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           + IKP  +E I    E       I +PL RG+  T+GNALRRVL+SSL G AI  V+I G
Sbjct: 5   KFIKPFFVEEI---DENPISGKFIIKPLERGYGITVGNALRRVLLSSLPGTAIVNVKIQG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKM---SGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           V  E ++I GV+ED+  IILN+K I   +   S D  +++ +  +GP  +TA   +    
Sbjct: 62  VEQEFTTIPGVYEDVMTIILNLKKIVFAVDDESDDFEEKLELIAKGPQRLTASSFELPAG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKV 183
           ++++NPDH I  L  D    M +T+ KG GYV AK ++   +  +G+I ID+L++P+  V
Sbjct: 122 VKIINPDHYITTLSDDVCFHMTVTLKKGIGYVGAKDNKVHGENQVGVIAIDSLFTPVVNV 181

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           SY VE     ++ + D+L++ I T+G++  ++++A A+ IL D   + +   +    V+
Sbjct: 182 SYQVEK----KLGNKDELTIEITTNGALLAKEALATAASILVDHFNVLVELSQKPAHVE 236


>gi|154424869|emb|CAL18537.1| RNA polymerase alpha subunit [Streptococcus uberis]
          Length = 170

 Score =  145 bits (367), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 72/170 (42%), Positives = 114/170 (67%)

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE  +I GV ED+  IILNIKG+ +K   +  K + +   GP  VTAGDI T +DIE
Sbjct: 1   GVLHEFDTIPGVREDVMQIILNIKGLAVKSYVEDEKMIELDVEGPAEVTAGDILTDSDIE 60

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           ++NPDH +  +     ++  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y 
Sbjct: 61  LVNPDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQ 120

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E
Sbjct: 121 VEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTE 170


>gi|162751008|gb|ABY19859.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751010|gb|ABY19860.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751012|gb|ABY19861.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751014|gb|ABY19862.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751016|gb|ABY19863.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751018|gb|ABY19864.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751020|gb|ABY19865.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751028|gb|ABY19869.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751030|gb|ABY19870.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis bv. diacetylactis]
 gi|162751034|gb|ABY19872.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis bv. diacetylactis]
 gi|162751036|gb|ABY19873.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751039|gb|ABY19874.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751041|gb|ABY19875.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751043|gb|ABY19876.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751045|gb|ABY19877.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751047|gb|ABY19878.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751049|gb|ABY19879.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751053|gb|ABY19881.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751055|gb|ABY19882.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751057|gb|ABY19883.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751061|gb|ABY19885.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751063|gb|ABY19886.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751065|gb|ABY19887.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751069|gb|ABY19889.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751071|gb|ABY19890.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751073|gb|ABY19891.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751075|gb|ABY19892.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751077|gb|ABY19893.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751079|gb|ABY19894.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751081|gb|ABY19895.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751083|gb|ABY19896.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751085|gb|ABY19897.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751087|gb|ABY19898.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751089|gb|ABY19899.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751091|gb|ABY19900.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751093|gb|ABY19901.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751095|gb|ABY19902.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751097|gb|ABY19903.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751099|gb|ABY19904.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751101|gb|ABY19905.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751103|gb|ABY19906.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751105|gb|ABY19907.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751107|gb|ABY19908.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751109|gb|ABY19909.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751113|gb|ABY19911.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751115|gb|ABY19912.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751117|gb|ABY19913.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751119|gb|ABY19914.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751123|gb|ABY19916.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751125|gb|ABY19917.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751127|gb|ABY19918.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751129|gb|ABY19919.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751131|gb|ABY19920.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751137|gb|ABY19923.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|162751139|gb|ABY19924.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|162751141|gb|ABY19925.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|162751143|gb|ABY19926.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751145|gb|ABY19927.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751149|gb|ABY19929.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751153|gb|ABY19931.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|162751157|gb|ABY19933.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|162751161|gb|ABY19935.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|162751163|gb|ABY19936.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|162751165|gb|ABY19937.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751169|gb|ABY19939.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751173|gb|ABY19941.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|162751175|gb|ABY19942.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis bv. diacetylactis]
 gi|162751177|gb|ABY19943.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis bv. diacetylactis]
 gi|164458717|gb|ABY57708.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  145 bits (366), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 71/146 (48%), Positives = 104/146 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPADENKVDGAPIGTIAVDSIYT 146


>gi|162751151|gb|ABY19930.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  145 bits (366), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 71/146 (48%), Positives = 104/146 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQILLGVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPADENKVDGAPIGTIAVDSIYT 146


>gi|119662359|emb|CAJ33168.1| RNA polymerase alpha subunit [Lactobacillus sanfranciscensis]
          Length = 186

 Score =  145 bits (366), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 85/186 (45%), Positives = 130/186 (69%), Gaps = 4/186 (2%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIF 107
           +L++SL GAA+T+VQIDGVLHE S++KGV ED+T IILN+K + LK+  + +    ++I 
Sbjct: 1   ILLASLPGAAVTSVQIDGVLHEFSTVKGVTEDVTKIILNLKKLKLKIDSEDNDIHTLSIN 60

Query: 108 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND- 166
             GP  VTA DI T ++  +LNPD  I  +   A + M +T +KG G+V A+ ++  ND 
Sbjct: 61  VTGPADVTAADITTDSETTILNPDLHIATVAEGATLHMTMTANKGRGFVSAEENKARNDD 120

Query: 167 -PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
            PIG++ ID++Y+PI++V+Y VE  R GQ  D+DKL++ + T+GSI+  D+++LA++IL 
Sbjct: 121 MPIGVLPIDSIYTPIERVNYQVEDTRVGQRDDFDKLTLDVWTNGSISPSDAISLAAKILS 180

Query: 226 DQLGMF 231
             L MF
Sbjct: 181 QHLDMF 186


>gi|15612278|ref|NP_223931.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori J99]
 gi|7388104|sp|Q9ZJT5|RPOA_HELPJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|4155841|gb|AAD06815.1| RNA POLYMERASE ALPHA SUBUNIT [Helicobacter pylori J99]
          Length = 344

 Score =  145 bits (366), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 104/328 (31%), Positives = 173/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ + + IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GPMELRARDLNS-DHIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIK V Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKNVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|162751024|gb|ABY19867.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751133|gb|ABY19921.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751181|gb|ABY19945.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis bv. diacetylactis]
          Length = 146

 Score =  145 bits (365), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 71/146 (48%), Positives = 104/146 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPADKNKVDGAPIGTIAVDSIYT 146


>gi|12045030|ref|NP_072840.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma genitalium
           G37]
 gi|255660326|ref|ZP_05405735.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma genitalium
           G37]
 gi|1350841|sp|P47423|RPOA_MYCGE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|3844773|gb|AAC71396.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma genitalium
           G37]
 gi|166078895|gb|ABY79513.1| DNA-directed RNA polymerase, alpha subunit [synthetic Mycoplasma
           genitalium JCVI-1.0]
          Length = 328

 Score =  145 bits (365), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 94/301 (31%), Positives = 159/301 (52%), Gaps = 25/301 (8%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  GF  T+GNA+RRVL+S + GA++ A+ I GV  E S+++GV ED+T+++LN K + 
Sbjct: 30  PLESGFGITIGNAMRRVLLSCIPGASVFAIAISGVKQEFSNVEGVLEDVTEMVLNFKQLV 89

Query: 94  LKMSG----DSHKRVTIFKRGP---------GVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           +++S     D        +R P         G V A D++     EV+N D  + +L  D
Sbjct: 90  VRISDLLFEDGEMIEPPLERWPVLKVTAEKKGAVYAKDLECPAGFEVINKDLYLFSLQKD 149

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             + + + V +G G+     +R   + +G+I  DA +SP+    Y V+  +  +    D 
Sbjct: 150 MKLTVSVYVKQGRGFTSFLENRELINSLGIIATDANFSPVLHCGYEVQEVKTSKQKLTDH 209

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK------EVKEDINVKSLPFNP 254
           L+  I T+G+I   D+ A+A++IL + L   ++  E  K      E  E+  VKS     
Sbjct: 210 LTFKIATNGAIKAVDAFAMAAKILIEHLNPIVSVNESIKNLTIIQEKAEERKVKSFA--- 266

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
              K++EEL+ +VR+ NCL+   I  + +L+ ++  D+  + N G+KS  EI   +  +G
Sbjct: 267 ---KQIEELDFTVRTFNCLKRSGIHTLQELLSKSLTDIREIRNLGKKSEREIIKKVQELG 323

Query: 315 L 315
           L
Sbjct: 324 L 324


>gi|297380475|gb|ADI35362.1| DNA-directed RNA polymerase, alpha subunit [Helicobacter pylori
           v225d]
          Length = 344

 Score =  145 bits (365), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 105/328 (32%), Positives = 173/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRIKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GPMELRARDLSS-EYIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKKV Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKKVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLNAKIENMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELNPEQRESLKKRLEKLEDK 340


>gi|237752997|ref|ZP_04583477.1| RNA polymerase alpha subunit [Helicobacter winghamensis ATCC
           BAA-430]
 gi|229375264|gb|EEO25355.1| RNA polymerase alpha subunit [Helicobacter winghamensis ATCC
           BAA-430]
          Length = 329

 Score =  145 bits (365), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 99/312 (31%), Positives = 164/312 (52%), Gaps = 15/312 (4%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  IE   +G    N+  + A P   G+A TL + LRR+L+ S  G A  A++I+GV HE
Sbjct: 11  PTKIEVKEVGA---NKIEITAYPFEAGYAITLAHPLRRLLLGSSVGFAPVALRIEGVAHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR-GPGVVTAGDIQTVND-IEVLN 129
             S++GV ED++  I+N+K I  K+  DS      +K  GP V+T  D++  ND ++++ 
Sbjct: 68  FDSVRGVVEDVSHFIVNLKTIRFKVKDDSESVSIDYKFIGPKVITGEDLK--NDLVDIVT 125

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  +  ++ DA++   + V KG GYVP++  R      G + +DA ++P+  V+Y  E+
Sbjct: 126 PNIHLATINEDAILNFSIIVRKGIGYVPSEDIRNLISE-GYMPLDAYFTPVTSVTYDTEN 184

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF---INFEEPKKEVKEDIN 246
                  +Y+K+   I TDG I    +   A  ++  Q+ +F   +N E P+  + E+  
Sbjct: 185 VLVEDDPNYEKVVFNIQTDGQIEPLTAFKNALSVMHKQMAIFNSELNIEVPEVSLGEE-- 242

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
               P    L + ++ L  S R  NCL    I Y+G+L+  +E  +  + N G+KSL EI
Sbjct: 243 --DSPEIRVLSQSIDSLNFSARCFNCLDRSGIKYLGELVLLSEDQIKNIKNLGKKSLDEI 300

Query: 307 KGVLGTMGLFLG 318
              L  +G  +G
Sbjct: 301 TVKLEELGYPIG 312


>gi|162751111|gb|ABY19910.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  144 bits (364), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 71/146 (48%), Positives = 104/146 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPADENKVDGWPIGTIAVDSIYT 146


>gi|162751167|gb|ABY19938.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
          Length = 146

 Score =  144 bits (364), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 70/146 (47%), Positives = 104/146 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN++RRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSMRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPADENKVDGAPIGTIAVDSIYT 146


>gi|317014684|gb|ADU82120.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           Gambia94/24]
          Length = 344

 Score =  144 bits (364), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 104/328 (31%), Positives = 172/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GPMELRARDLNS-EHIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIK V Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKNVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|217033612|ref|ZP_03439040.1| hypothetical protein HP9810_899g48 [Helicobacter pylori 98-10]
 gi|216943958|gb|EEC23392.1| hypothetical protein HP9810_899g48 [Helicobacter pylori 98-10]
          Length = 344

 Score =  144 bits (363), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 104/328 (31%), Positives = 172/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALIGQDSSLENQSVVVDYSFK-GPMELKARDLSS-EHIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIK V Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKNVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMGKQLGVF--GERPITNTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELSSEQRESLKKRLEKLEDK 340


>gi|315587182|gb|ADU41563.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori 35A]
          Length = 344

 Score =  144 bits (363), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 104/328 (31%), Positives = 172/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GPMELRARDLNS-EHIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIK V Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKNVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELNPEQRESLKKRLEKLEDK 340


>gi|330850661|ref|YP_004376542.1| RNA polymerase alpha subunit [Ptilidium pulcherrimum]
 gi|302024790|gb|ADK89636.1| RNA polymerase alpha subunit [Ptilidium pulcherrimum]
          Length = 336

 Score =  144 bits (363), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 92/292 (31%), Positives = 158/292 (54%), Gaps = 25/292 (8%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P  +G A+T+G A+RR L++ + GA+IT V+I  V HE S+I G+ E + DI++N+K I 
Sbjct: 36  PFRKGQANTIGIAMRRALLNEIEGASITYVEIKKVKHEYSTITGIQESIHDILINLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
            K      ++  I   GP  +TA DI+  + I +++    I  L     + +EL + K H
Sbjct: 96  SKSDSYEPQKAYISIYGPKKITARDIKGTSSIRIIDNTQYIATLTEAISLDIELNIEKDH 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY      +  +   G+ TIDA++ PI+ V+Y+V S   G+    + L + I TDGS+T 
Sbjct: 156 GYRIENLQKYRD---GIFTIDAVFMPIRNVNYSVHSFESGEKTK-EILFLEIWTDGSLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEV------KEDINVKSLPFNPALLKK-------- 259
           ++++  ASR L D     +N E  +KE+      K ++++   PF    L          
Sbjct: 212 KEALYEASRSLIDLFIPLMNSE--RKEINSGMKKKNELDIPCFPFRFISLDMEEMTKDIA 269

Query: 260 -----VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
                +++LEL  R+ NCL+  N+  + D +  +E D++++ NFG+KS+ ++
Sbjct: 270 FKHIFIDQLELPARAYNCLKRVNVHTIADSLNYSEDDLVKIKNFGKKSIEQV 321


>gi|317178416|dbj|BAJ56204.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori F30]
          Length = 344

 Score =  144 bits (363), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 104/328 (31%), Positives = 172/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GPMELRARDLSS-EHIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIK V Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKNVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMGKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKSVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELNPEQRESLKKRLEKLEDK 340


>gi|119668311|emb|CAK95456.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           lactis]
          Length = 191

 Score =  144 bits (363), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 72/169 (42%), Positives = 108/169 (63%)

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           V+IDG+LHE +++ GV ED+T IILN+K + L+   +  K + +   GP  VTA D++  
Sbjct: 6   VKIDGILHEFTTVPGVKEDVTKIILNLKKLVLRAYTEEVKTIELDVEGPATVTAEDLKAD 65

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
            D+EVLNPD  IC +     + M + V  G GYVPA  +++    IG I +D+L+SPI+K
Sbjct: 66  ADVEVLNPDQYICTIAQGGHLHMWIDVCNGRGYVPASENKSAEMSIGDIPVDSLFSPIEK 125

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           V+Y VES R G+  D+DKL++ I T+GSI   D++  A+R+L +    F
Sbjct: 126 VNYQVESTRVGKREDFDKLTLEIWTNGSIAPNDALNFAARVLVEHFKAF 174


>gi|150036742|emb|CAM98025.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. dextranicum]
          Length = 178

 Score =  144 bits (363), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 75/177 (42%), Positives = 114/177 (64%), Gaps = 2/177 (1%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+
Sbjct: 1   VNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDIQGPADVTAADL 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALY 177
           Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++   D  PIG++ +D++Y
Sbjct: 61  QGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSADENKKLRDEMPIGVLAVDSIY 120

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           +PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L ++IL + LG+F++ 
Sbjct: 121 TPIERVNYQVENTRIGARDDYDKLTFDIWTNGSIKPSDALSLGAKILAEHLGLFMDI 177


>gi|317182539|dbj|BAJ60323.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori F57]
          Length = 344

 Score =  144 bits (362), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 104/328 (31%), Positives = 172/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GPMELRARDLNS-EHIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIK V Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKNVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELSPDQRESLKKRLEKLEDK 340


>gi|162751135|gb|ABY19922.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  144 bits (362), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 70/146 (47%), Positives = 104/146 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +G+VPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGFVPADENKVDGAPIGTIAVDSIYT 146


>gi|11466735|ref|NP_039331.1| RNA polymerase alpha subunit [Marchantia polymorpha]
 gi|133401|sp|P06270|RPOA_MARPO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|11706|emb|CAA28117.1| rpoA [Marchantia polymorpha]
          Length = 340

 Score =  144 bits (362), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 95/306 (31%), Positives = 162/306 (52%), Gaps = 24/306 (7%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P  +G A+T+G A+RR L++ + GA+IT  +I  V HE S+I G+ E + DI++N+K I 
Sbjct: 36  PFRKGQANTVGIAMRRALLNEIEGASITYAKIKKVKHEYSTIIGLQESIHDILINLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK      ++  I   GP  +TA DI+  + I+++     I  L+ D ++ +EL + K  
Sbjct: 96  LKSESFEPQKAYISVLGPKKITAQDIKGPSCIKIMIIAQYIATLNKDILLEIELNIEKDR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY      + +    GL  +DA++ PI+  +Y+V S    + +  + L + I TDGS+T 
Sbjct: 156 GYRIENLQKYQE---GLFPVDAVFMPIRNANYSVHSFESEKKIK-EILFLEIWTDGSLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKK----EVKEDINVKSLPFNPALLK----------- 258
           ++++  ASR L D     IN E+ +K    E   + N+   PF    L            
Sbjct: 212 KEALYEASRNLIDLFIPLINSEKKEKNFGIEKTNESNMSYFPFQSVSLDIEKMTKDVAFK 271

Query: 259 --KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +++LEL  R+ NCL+  N+  + DL+  +E D++++ NFG+KS   ++ VL  +   
Sbjct: 272 HIFIDQLELPARAYNCLKKVNVHTIADLLHYSEDDLIKIKNFGKKS---VEQVLEALKKR 328

Query: 317 LGMNLP 322
             + LP
Sbjct: 329 FSIQLP 334


>gi|162751006|gb|ABY19858.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  144 bits (362), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 71/146 (48%), Positives = 103/146 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R   TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVKTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPADENKVDGAPIGTIAVDSIYT 146


>gi|317181015|dbj|BAJ58801.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori F32]
          Length = 344

 Score =  143 bits (361), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 103/328 (31%), Positives = 173/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GPMELRARDLNS-EHIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ +A +   L + KG GYVP+++ R E  P G + +D  ++PIKKV Y +E+  
Sbjct: 136 MPLATINENAQLNFSLIICKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKKVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     E++++  +K EDK
Sbjct: 313 DLGYPVGTELNPEQRENLKKRLEKLEDK 340


>gi|150036720|emb|CAM98251.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. cremoris]
          Length = 176

 Score =  143 bits (361), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 75/174 (43%), Positives = 113/174 (64%), Gaps = 2/174 (1%)

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+Q  
Sbjct: 3   VQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIESDDERSLEIDIQGPADVTAADLQGG 62

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPI 180
            D+EVLNPD  I  +     + M +T  KG GY  A  ++   D  PIG++ +D++Y+PI
Sbjct: 63  ADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSADENKKLRDEMPIGVLAVDSIYTPI 122

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           ++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L ++IL + LG+F++ 
Sbjct: 123 ERVNYQVENTRIGARDDYDKLTFDIWTNGSIKPSDALSLGAKILAEHLGLFMDI 176


>gi|317011493|gb|ADU85240.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           SouthAfrica7]
          Length = 344

 Score =  143 bits (361), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 104/328 (31%), Positives = 172/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPIGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GPMELRARDLNS-EQIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP++  R E  P G + +D  ++PIK V Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSEITR-ELMPEGYMPLDGSFTPIKNVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E+P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GEKPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLS 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|217032047|ref|ZP_03437547.1| hypothetical protein HPB128_16g7 [Helicobacter pylori B128]
 gi|298735682|ref|YP_003728207.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori B8]
 gi|216946195|gb|EEC24803.1| hypothetical protein HPB128_16g7 [Helicobacter pylori B128]
 gi|298354871|emb|CBI65743.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori B8]
          Length = 344

 Score =  143 bits (361), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 104/328 (31%), Positives = 172/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPIGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GPMELRARDLNS-EQIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E    G + +D  ++PIKKV Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMSEGYMPLDGSFTPIKKVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELSHEQRESLKKRLEKLEDK 340


>gi|162751026|gb|ABY19868.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  143 bits (361), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 70/146 (47%), Positives = 103/146 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           + YVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YAYVPADENKVDGAPIGTIAVDSIYT 146


>gi|119662853|emb|CAJ33219.1| RNA polymerase alpha subunit [Lactobacillus farciminis KCTC 3681]
          Length = 164

 Score =  143 bits (361), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 66/162 (40%), Positives = 112/162 (69%)

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           +QIDGVLHE S+I GV ED+T I+LN+K + LK   +   +  +   GP  VTA DI+  
Sbjct: 2   IQIDGVLHEFSAIDGVIEDVTQIVLNVKKLKLKSYAEDSLKAEVDIVGPATVTAKDIKAD 61

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           +D+E+L+P+  IC +       M++T+  G GY PA+ ++T+  PIG++ +D++++P++K
Sbjct: 62  DDLEILDPEQFICTVAEGGHFHMQMTIKNGRGYTPAEQNKTDETPIGVLPVDSIFTPVEK 121

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           V+Y VE+ R G+  D+DKL++ I T+GSI   ++++L+++IL
Sbjct: 122 VNYQVENTRVGKRNDFDKLTIDIWTNGSIGPREAISLSAKIL 163


>gi|261838612|gb|ACX98378.1| alpha subunit of the DNA-dependent RNA polymerase core enzyme
           [Helicobacter pylori 51]
          Length = 344

 Score =  143 bits (360), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 103/328 (31%), Positives = 172/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALIGQDSSLENQSVVVDYSFK-GPMEIRARDLSS-EHIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG G+VP+++ R E  P G + +D  ++PIK V Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGHVPSENTR-ELMPEGYMPLDGSFTPIKNVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|150036712|emb|CAM98020.1| DNA-directed RNA polymerase alpha chain [Leuconostoc citreum]
          Length = 181

 Score =  143 bits (360), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 75/177 (42%), Positives = 113/177 (63%), Gaps = 2/177 (1%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+
Sbjct: 1   VNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDVQGPADVTAADL 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALY 177
           Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++   D  PIG++ +D++Y
Sbjct: 61  QAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSADENKQLRDEMPIGVLAVDSIY 120

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           +PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L S+IL + L +F++ 
Sbjct: 121 TPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSLGSKILAEHLNLFMDI 177


>gi|109946783|ref|YP_664011.1| DNA-directed RNA polymerase subunit alpha [Helicobacter acinonychis
           str. Sheeba]
 gi|123173594|sp|Q17ZB4|RPOA_HELAH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|109714004|emb|CAJ99012.1| DNA-directed RNA polymerase alpha chain [Helicobacter acinonychis
           str. Sheeba]
          Length = 344

 Score =  143 bits (360), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 104/328 (31%), Positives = 173/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRIKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSPLENQSVVVDYSFK-GPMELRARDLNS-EHIEIINPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
            ++  ++ DA +   L + KG GYVP++  R E  P G + +D  ++PIK V Y +E+  
Sbjct: 136 MLLATINEDAQLNFSLIIYKGMGYVPSEITR-ELMPEGYMPLDGSFTPIKNVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E+P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GEKPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELSLEQRESLKKRLEKLEDK 340


>gi|162751121|gb|ABY19915.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  142 bits (359), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 70/146 (47%), Positives = 103/146 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++ I+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIHIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPADENKVDGAPIGTIAVDSIYT 146


>gi|119668351|emb|CAK95512.1| RNA polymerase alpha subunit [Lactobacillus pentosus]
          Length = 160

 Score =  142 bits (359), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 75/160 (46%), Positives = 110/160 (68%), Gaps = 2/160 (1%)

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S+++GV ED+T IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EVLNP
Sbjct: 1   EFSTVEGVTEDVTAIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEVLNP 60

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAK--HHRTENDPIGLITIDALYSPIKKVSYTVE 188
           D  IC +   A   M +T + G GYV A+   HR ++ PIG++ +D+LYSPI++V+Y VE
Sbjct: 61  DLPICTVADGAHFHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVE 120

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           + R GQ  D+DKL++ + T+GSIT  ++++L+++IL D L
Sbjct: 121 TTRVGQRDDFDKLTLDVWTNGSITPSEAISLSAKILTDHL 160


>gi|162751032|gb|ABY19871.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis bv. diacetylactis]
 gi|162751147|gb|ABY19928.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751179|gb|ABY19944.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis bv. diacetylactis]
          Length = 146

 Score =  142 bits (359), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 70/146 (47%), Positives = 103/146 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVP   ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPDDENKVDGAPIGTIAVDSIYT 146


>gi|161511745|emb|CAP16883.1| DNA-directed RNA polymerase subunit alpha [Pediococcus inopinatus]
          Length = 141

 Score =  142 bits (359), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 71/141 (50%), Positives = 99/141 (70%), Gaps = 2/141 (1%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           +LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNIK ++LK+  D  K + 
Sbjct: 1   SLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNIKKVSLKIESDDEKSLE 60

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
           I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A  ++   
Sbjct: 61  IDVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAILTADTGRGYVSADENKARK 120

Query: 166 D--PIGLITIDALYSPIKKVS 184
           D  PIG++ ID++Y+PI++V+
Sbjct: 121 DDMPIGVLPIDSIYTPIERVN 141


>gi|317178032|dbj|BAJ55821.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori F16]
          Length = 344

 Score =  142 bits (359), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 103/328 (31%), Positives = 172/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GPMELRARDLNS-EHIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIK V Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKNVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEITEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     E++++  +K EDK
Sbjct: 313 DLGYPVGTELNPEQRENLKKRLEKLEDK 340


>gi|108563663|ref|YP_627979.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           HPAG1]
 gi|119366688|sp|Q1CRW7|RPOA_HELPH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|107837436|gb|ABF85305.1| DNA-directed RNA polymerase, alpha subunit [Helicobacter pylori
           HPAG1]
          Length = 344

 Score =  142 bits (359), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 104/328 (31%), Positives = 172/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPIGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK G   + A D+ + + IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GSMELRARDLNS-DHIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP++  R E  P G + +D  ++PIKKV Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSETTR-ELMPEGYMPLDGSFTPIKKVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|119029438|gb|ABL59935.1| DNA-directed RNA polymerase alpha subunit [uncultured bacterium]
          Length = 219

 Score =  142 bits (358), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 82/207 (39%), Positives = 126/207 (60%), Gaps = 17/207 (8%)

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF-KRGPGVVTAGDIQT 121
           ++IDGVLH+ S++ G+ ED+ +++LN+K +   ++ D +     F K  PG V A D   
Sbjct: 19  IKIDGVLHDYSALDGLQEDVVEVLLNLKELAFNIASDENTVAINFEKSSPGPVLASDFAD 78

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSP 179
            ++IEV NP+ VICN+    V++MELT  +G GY  A +   + +   IG++ +DA YSP
Sbjct: 79  QSNIEVFNPNLVICNV-TSGVLKMELTAQRGRGYELAVNRDVDRNEKSIGVLQLDASYSP 137

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE---- 235
           +KKVSY VE AR G   D DKL + ++T+G+I+ ED++ ++S ILQ QL  F+N +    
Sbjct: 138 VKKVSYNVEVARFGGRADLDKLVIDLETNGAISPEDAIRISSTILQQQLLAFVNLDSKLL 197

Query: 236 -EPKKEVKEDINVKSLPFNPALLKKVE 261
            EP K+ +E        F+P L  K E
Sbjct: 198 KEPTKKEEE--------FDPILCDKGE 216


>gi|162751171|gb|ABY19940.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  142 bits (357), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 69/146 (47%), Positives = 104/146 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +G+VPA  ++ +  PIG I ++++Y+
Sbjct: 121 YGFVPADENKVDGAPIGTIAVNSIYT 146


>gi|162751022|gb|ABY19866.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  142 bits (357), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 70/146 (47%), Positives = 103/146 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           + YVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YRYVPADENKVDGAPIGTIAVDSIYT 146


>gi|154424767|emb|CAL18486.1| RNA polymerase alpha subunit [Streptococcus constellatus subsp.
           constellatus]
          Length = 171

 Score =  142 bits (357), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 70/163 (42%), Positives = 107/163 (65%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+  IILN+KGI +K   +  K + +   GP  +TAGDI T +DIE++NPDH +  
Sbjct: 2   GVREDVMQIILNVKGIAVKSYVEDEKTIELDVEGPAEITAGDILTDSDIEIVNPDHYLFT 61

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +   A ++  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y VE AR G   
Sbjct: 62  IGEGASLKAIMTVNAGRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSND 121

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
            +DKL++ I TDG+I  ED++ L++RIL   L +F N  E  K
Sbjct: 122 GFDKLTLEIMTDGTIIPEDALGLSARILTQHLDLFTNLTEVAK 164


>gi|162751051|gb|ABY19880.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  142 bits (357), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 70/146 (47%), Positives = 103/146 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +   +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMLAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPADENKFDGAPIGTIAVDSIYT 146


>gi|162751155|gb|ABY19932.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
          Length = 146

 Score =  142 bits (357), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 69/146 (47%), Positives = 103/146 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++  DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVTKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +G+VPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGFVPADENKVDGAPIGTIAVDSIYT 146


>gi|152993919|ref|YP_001359640.1| DNA-directed RNA polymerase subunit alpha [Sulfurovum sp. NBC37-1]
 gi|172048748|sp|A6QCS4|RPOA_SULNB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|151425780|dbj|BAF73283.1| DNA-directed RNA polymerase, alpha subunit [Sulfurovum sp. NBC37-1]
          Length = 333

 Score =  141 bits (356), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 98/299 (32%), Positives = 159/299 (53%), Gaps = 19/299 (6%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           NR  ++A P   G+A TL + LRR+++ S  G A  +V+I+G  HE  +I+G+HED+   
Sbjct: 22  NRAEIVAYPFESGYAVTLAHPLRRLILGSSIGYAPISVKIEGAAHEFDNIRGMHEDVAVF 81

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGV--VTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           I+N+K I  K+  D   RV +     G   VTA D+   + IEV+N D  +  L+ DA +
Sbjct: 82  IINLKNIRFKIK-DGSDRVELKYSFSGYKEVTAQDLNN-DQIEVVNGDLPLATLNEDAEL 139

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
              + ++KG GYVP++  R E  P   I +DA ++P++K +Y +E        +++K++ 
Sbjct: 140 NFTMVIAKGIGYVPSEDLRDEVAPDS-IALDAFFTPVRKANYKIEPVLVEDNPNFEKITF 198

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMF-------INFEEPKKEVKEDINVKSLPFNPAL 256
            I+TD  I   ++   A  ++  QL +F       I+   PK+   +D  +K  PF    
Sbjct: 199 DIETDAQIGPVEAFTNALEVMNKQLSVFNGVLDVDISTTLPKR-TNDDNELK--PF---- 251

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           L  V+ L LS RS N L    I ++G+L+  +E ++  + N G+KSL E    L   G 
Sbjct: 252 LAAVDALGLSARSFNSLDRAGIKFLGELVLMSENEIKNIKNLGKKSLDETNECLVEHGF 310


>gi|153831468|ref|ZP_01984135.1| DNA-directed RNA polymerase alpha chain [Vibrio cholerae 623-39]
 gi|148873049|gb|EDL71184.1| DNA-directed RNA polymerase alpha chain [Vibrio cholerae 623-39]
          Length = 174

 Score =  141 bits (356), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 77/177 (43%), Positives = 113/177 (63%), Gaps = 8/177 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ ++++ G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITI 173
              D+E++NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +
Sbjct: 118 HDGDVEIVNPEHVICHLTSDNAAIAMRIKVERGRGYVPASARIHTEEDERPIGRLLV 174


>gi|119662379|emb|CAJ33178.1| RNA polymerase alpha subunit [Lactobacillus pentosus]
          Length = 158

 Score =  141 bits (355), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 73/157 (46%), Positives = 107/157 (68%), Gaps = 2/157 (1%)

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+T IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EVLNPD  IC +  
Sbjct: 2   EDVTAIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVAD 61

Query: 140 DAVVRMELTVSKGHGYVPAK--HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
            A   M +T + G GYV A+   HR ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D
Sbjct: 62  GAHFHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVETTRVGQRDD 121

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           +DKL++ + T+GSIT  ++++L+++IL D L +F+N 
Sbjct: 122 FDKLTLDVWTNGSITPSEAISLSAKILTDHLSIFVNL 158


>gi|208435191|ref|YP_002266857.1| DNA-directed RNA polymerase, alpha subunit [Helicobacter pylori
           G27]
 gi|208433120|gb|ACI27991.1| DNA-directed RNA polymerase, alpha subunit [Helicobacter pylori
           G27]
          Length = 336

 Score =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 104/327 (31%), Positives = 170/327 (51%), Gaps = 18/327 (5%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GPMELRARDLNS-EHIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKKV Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKKVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYED 338
            +G  +G  L     E  E L K+ E+
Sbjct: 313 DLGYPVGTELSH---EQRESLKKRLEN 336


>gi|188528081|ref|YP_001910768.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           Shi470]
 gi|188144321|gb|ACD48738.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           Shi470]
          Length = 344

 Score =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 103/328 (31%), Positives = 172/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++N +
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GPMELRARDLSS-EHIEIVNLE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKKV Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKKVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     E++++  +K EDK
Sbjct: 313 DLGYPVGTELSPEQRENLKKRLEKLEDK 340


>gi|308064070|gb|ADO05957.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           Sat464]
          Length = 344

 Score =  140 bits (354), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 103/328 (31%), Positives = 172/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++N +
Sbjct: 78  VSLFIMNLKNIRFIAKVLVGQDSSLENQSVVVDYSFK-GPMELRARDLSS-EHIEIVNLE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKKV Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKKVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     E++++  +K EDK
Sbjct: 313 DLGYPVGTELSPEQRENLKKRLEKLEDK 340


>gi|154424819|emb|CAL18512.1| RNA polymerase alpha subunit [Streptococcus mitis]
          Length = 171

 Score =  140 bits (354), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 70/166 (42%), Positives = 108/166 (65%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+  IILNIKGI +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  
Sbjct: 2   GVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEVTAGDILTDSDIEIVNPDHYLFT 61

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y VE AR G   
Sbjct: 62  IGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQVEPARVGSND 121

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
            +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  K  +
Sbjct: 122 GFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSTE 167


>gi|224373703|ref|YP_002608075.1| DNA-directed RNA polymerase subunit alpha [Nautilia profundicola
           AmH]
 gi|223588998|gb|ACM92734.1| DNA-directed RNA polymerase, alpha subunit [Nautilia profundicola
           AmH]
          Length = 330

 Score =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 97/316 (30%), Positives = 164/316 (51%), Gaps = 10/316 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E++ P+++ +    +EE N+  +   P   GF  ++ + +RR L++S  G A  A++I+G
Sbjct: 7   EVLIPSDVSF----KEEGNKATIEVYPFEAGFGVSVAHPIRRTLIASTPGFAPIALKIEG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND-IE 126
           V HE  S+KG+ ED+   I+N+K I  K+       V     GP  +   D+   ND ++
Sbjct: 63  VKHEFDSLKGMLEDVASFIINLKNIRFKIKEGDEAVVDYVFVGPKEIKGSDL--ANDLVD 120

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           ++ P+  I  L+ +A +++ L + KG G+V  ++ R E  P G I +DA +SPIKKV Y 
Sbjct: 121 IVTPNEYIATLNEEAELKLTLIIRKGMGFVAVENFRDE-IPEGFIGLDAYFSPIKKVVYN 179

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           +E+       +++K+   ++TDG I+  D+   A     +Q  +F   +E K E K   +
Sbjct: 180 IENILVEDDPNFEKVIFEVETDGQISPIDAFKNAVNNYLNQFSVFS--KEFKLEQKTSQS 237

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           V+       L + +E L L  RS N L    I ++G+L+   +  +  + N G KSL EI
Sbjct: 238 VELDEVYNVLFEPIENLNLRSRSFNALDRAGIRFVGELVLMGKEKISNIKNLGTKSLEEI 297

Query: 307 KGVLGTMGLFLGMNLP 322
              L  +G  L   LP
Sbjct: 298 FDKLEEIGFPLNKTLP 313


>gi|150036780|emb|CAM98033.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. cremoris]
          Length = 153

 Score =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 71/153 (46%), Positives = 100/153 (65%), Gaps = 2/153 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T 
Sbjct: 61  KKVVLAIESDDERSLEIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTA 120

Query: 150 SKGHGYVPAKHHRTEND--PIGLITIDALYSPI 180
            KG GY  A  ++   D  PIG++ +D++Y+PI
Sbjct: 121 VKGRGYTSADENKKLRDEMPIGVLAVDSIYTPI 153


>gi|119663528|emb|CAK22335.1| RNA polymerase alpha subunit [Lactobacillus malefermentans]
          Length = 175

 Score =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 74/167 (44%), Positives = 110/167 (65%), Gaps = 4/167 (2%)

Query: 77  GVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           G+ ED+T IILN+K I+LK+ G  D  + + +  +GP  VTAGDI   +D+ VLNPD  I
Sbjct: 1   GIVEDVTQIILNVKKISLKLEGADDEVETLEVNVKGPAQVTAGDITADSDVTVLNPDLYI 60

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESARE 192
             +   A   M +T +KG GYV A  +  R E+ PIG++ ID++Y+PI++V+Y VE+ R 
Sbjct: 61  ATVAEGATFHMRMTANKGRGYVSADQNKVRDEDMPIGVLPIDSIYTPIERVNYQVENTRV 120

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           G   DYDKL++ + TDGSI   +S++LA++IL + L MF+N  +  K
Sbjct: 121 GHKSDYDKLTLDVWTDGSINPSESISLAAKILMEHLDMFVNLTDEAK 167


>gi|261840008|gb|ACX99773.1| DNA-directed RNA polymerase alpha subunit [Helicobacter pylori 52]
          Length = 344

 Score =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 103/328 (31%), Positives = 171/328 (52%), Gaps = 15/328 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18  EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRGVTED 77

Query: 82  LTDIILNIKGINL-------KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPD 131
           ++  I+N+K I         + S   ++ V +   FK GP  + A D+ +   IE++NP+
Sbjct: 78  VSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFK-GPMELRARDLNS-EHIEIVNPE 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   L + KG GYVP+++ R E    G + +D  ++PIK V Y +E+  
Sbjct: 136 MPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMHEGYMPLDGSFTPIKNVVYEIENVL 194

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +     
Sbjct: 195 VEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTEYSGDYAQRD 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 253 DAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLN 312

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +G  +G  L     ES+++  +K EDK
Sbjct: 313 DLGYPVGTELNPEQRESLKKRLEKLEDK 340


>gi|32266902|ref|NP_860934.1| DNA-directed RNA polymerase subunit alpha [Helicobacter hepaticus
           ATCC 51449]
 gi|41688644|sp|Q7VGB9|RPOA_HELHP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|32262954|gb|AAP78000.1| DNA-dependent RNA polymerase [Helicobacter hepaticus ATCC 51449]
          Length = 334

 Score =  140 bits (352), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 97/312 (31%), Positives = 159/312 (50%), Gaps = 29/312 (9%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           NR  + A P   G+A TL + +RR+L+SS  G A TA++I GV HE  SI+G+ ED++  
Sbjct: 22  NRIRISAYPFESGYAITLAHPIRRLLLSSSVGYAPTALRIQGVTHEFDSIRGIVEDVSHF 81

Query: 86  ILNIKGINLKMSGDSHKRVTIFK--RGPGVVTAGDIQTVND-IEVLNPDHVICNLDVDAV 142
           I N+K I   +       V +    +GP V++A ++  VND + ++NP+  +  ++ +A 
Sbjct: 82  ITNLKNIRFLIKDTESDNVQLHYEFKGPMVLSANEL--VNDMVGIVNPEAYLATINENAS 139

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           +   L V KG GYVP++  R +      I +DA ++P+KK  Y +E+       +Y+K+ 
Sbjct: 140 LSFSLIVQKGIGYVPSESIRGKISE-DYIPLDAYFTPVKKAVYEIENVLVEDNPNYEKIV 198

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF-----------INFEEPKKEVKEDINVKSLP 251
             I+TDG I    +   A  I+  Q+ +F            N  E   E+K         
Sbjct: 199 FDIETDGQIEPITAFKEAIAIMHKQMSIFGVDLSTASSGTRNISEDSGELK--------- 249

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L+ K++ L LS R  NCL    + Y+G+L+  +E ++  + N G+KS  EI   L 
Sbjct: 250 ---TLMIKIDTLNLSARCFNCLDRSGLKYVGELVIMSENELKNIKNMGKKSYDEIADKLE 306

Query: 312 TMGLFLGMNLPD 323
            +G  +G  + D
Sbjct: 307 ELGYPVGGEIAD 318


>gi|42906|emb|CAA23646.1| unnamed protein product [Escherichia coli]
          Length = 159

 Score =  139 bits (351), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 73/158 (46%), Positives = 104/158 (65%), Gaps = 4/158 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA 158
             D+E++ P HVIC+L D +A + M + V +G GYVPA
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPA 155


>gi|119662839|emb|CAJ33212.1| RNA polymerase alpha subunit [Lactobacillus acidophilus]
          Length = 151

 Score =  139 bits (351), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 70/151 (46%), Positives = 99/151 (65%)

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++VLN
Sbjct: 1   HEFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQVLN 60

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES
Sbjct: 61  PDQYICTIAEGGHLHMELAVKNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVES 120

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
            R G+  D+DKL+  I TDGSI   D+++ A
Sbjct: 121 TRVGKRDDFDKLTFEIWTDGSIKPNDALSFA 151


>gi|154424841|emb|CAL18523.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
          Length = 150

 Score =  139 bits (350), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 67/149 (44%), Positives = 101/149 (67%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAA+T++ IDGVLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  VTA
Sbjct: 1   GAAVTSINIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
           GDI T +DIE++NPDH +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++
Sbjct: 61  GDILTDSDIEIVNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSI 120

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           Y+P+ KV+Y VE AR G    +DKL++ I
Sbjct: 121 YTPVTKVNYQVEPARVGSNDGFDKLTLEI 149


>gi|154424815|emb|CAL18510.1| RNA polymerase alpha subunit [Streptococcus minor]
          Length = 174

 Score =  139 bits (349), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 68/165 (41%), Positives = 109/165 (66%)

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           + GV ED+  IILNIKGI +K   +  K++ +   GP  +TAGDI T +DIE++NPDH +
Sbjct: 1   VPGVREDVMQIILNIKGIAVKSYVEDEKKIELDVVGPAEITAGDILTDSDIEIVNPDHYL 60

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
             +   A  +  LTV++G GYVPA+ ++ +  P+G + +D++Y+P+ KV+Y VE AR G 
Sbjct: 61  FTIGEGASFKAILTVNRGRGYVPAEGNKKDEAPVGTLAVDSIYTPVVKVNYQVEPARVGS 120

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
              +DKL++ I T+G+   ED++ L++RIL + LG+F +  +  K
Sbjct: 121 NDGFDKLTLEIMTNGTTNPEDALGLSARILMEHLGLFTDLTDVAK 165


>gi|161511737|emb|CAP16879.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 171

 Score =  139 bits (349), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 72/171 (42%), Positives = 111/171 (64%), Gaps = 2/171 (1%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +
Sbjct: 1   VLHEFSTIEGVVEDVTQIILNLKKVSLKVESDEEKSLEINVMGPANVTAGDIVGDGDVTI 60

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSY 185
           LNP+  IC +         LT  KG GY  A  +  R  + PIG++ ID++Y+PI++V+Y
Sbjct: 61  LNPELPICTVAEGTTFHAVLTAEKGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNY 120

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
            VE+ R GQ  DYDKL++ + TD S+   ++++L+++IL + L +F+N ++
Sbjct: 121 QVENTRVGQRDDYDKLTLDVWTDVSLAASEAISLSAKILTEHLTIFVNLDD 171


>gi|163804149|ref|ZP_02197920.1| DNA-directed RNA polymerase subunit alpha [Vibrio sp. AND4]
 gi|159172035|gb|EDP57006.1| DNA-directed RNA polymerase subunit alpha [Vibrio sp. AND4]
          Length = 174

 Score =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 73/159 (45%), Positives = 107/159 (67%), Gaps = 5/159 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQINSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG++++++ G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLSVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA 158
              D+E+ NP+HVIC+L D +A + M + V +G GYVPA
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPA 156


>gi|150186916|emb|CAK30127.1| RNA polymerase alpha subunit [Streptococcus oligofermentans]
          Length = 170

 Score =  138 bits (347), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 68/163 (41%), Positives = 106/163 (65%)

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           +I GV ED+  IILNIKGI +K      K + +   GP  VTAGDI T +DIE++NPDH 
Sbjct: 3   TISGVREDVMQIILNIKGIAVKSYVQDEKMIELDVEGPAEVTAGDILTDSDIEIVNPDHY 62

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           +  +   A  + ++ V+ G GYVPA  ++ ++ P+G + +D++Y+P+ KV+Y VE AR G
Sbjct: 63  LFTISEGARFKAKMAVNSGRGYVPADENKKDDAPVGTLAVDSIYTPVTKVNYQVEPARVG 122

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
               +DKL++ I T+G+I  ED++ L++RIL + L +F +  E
Sbjct: 123 SNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLFTDLTE 165


>gi|154424737|emb|CAL18471.1| RNA polymerase alpha subunit [Streptococcus oligofermentans]
          Length = 168

 Score =  138 bits (347), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 68/163 (41%), Positives = 106/163 (65%)

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           +I GV ED+  IILNIKGI +K      K + +   GP  VTAGDI T +DIE++NPDH 
Sbjct: 3   TISGVREDVMQIILNIKGIAVKSYVQDEKMIELDVEGPAEVTAGDILTDSDIEIVNPDHY 62

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           +  +   A  + ++ V+ G GYVPA  ++ ++ P+G + +D++Y+P+ KV+Y VE AR G
Sbjct: 63  LFTISEGARFKAKMAVNSGRGYVPADENKKDDAPVGTLAVDSIYTPVTKVNYQVEPARVG 122

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
               +DKL++ I T+G+I  ED++ L++RIL + L +F +  E
Sbjct: 123 SNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLFTDLTE 165


>gi|242620061|ref|YP_003002065.1| DNA-directed RNA polymerase alpha chain [Aureococcus
           anophagefferens]
 gi|239997306|gb|ACS36829.1| DNA-directed RNA polymerase alpha chain [Aureococcus
           anophagefferens]
          Length = 305

 Score =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 96/301 (31%), Positives = 164/301 (54%), Gaps = 43/301 (14%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E+ +R L+  + L +G   T+GN LRRVL++ L G AITAV+I+G+ +E ++I GV ED+
Sbjct: 18  EQSSRFLL--KELTQGQGLTIGNTLRRVLLTELEGTAITAVRINGINNEFATIPGVREDV 75

Query: 83  TDIILNIKGINLKMSG------DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
            +I+LN+K I  K +G       +H  V    +GP +VTA +I   + + +LN +H I  
Sbjct: 76  LEILLNLKQI--KFTGLVTEPFFTHVSV----QGPQLVTAANISLPDGLSLLNSNHYIAA 129

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREG 193
           +       +EL +  G GY    +   E + I     +++D++++P+K V+Y ++ + + 
Sbjct: 130 VAEQTNFEIELKIESGTGY----NFTDEENRICSGDFLSLDSIFTPVKNVNYQIKDSYKI 185

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
                + L + I T+GSIT  D++  A+ +LQ   G  +              +  L  N
Sbjct: 186 DEKITEILDLEIITNGSITPNDALNKAALVLQTLFGSLV--------------IDELQTN 231

Query: 254 PALLKK--------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           P L ++        +EEL+LSVR+ NCL+  NI  + DL+Q +  ++  + NFG+KS  E
Sbjct: 232 PVLPEQTETELDILIEELQLSVRAYNCLKRVNIKTIADLVQYSVKELKDIKNFGQKSANE 291

Query: 306 I 306
           +
Sbjct: 292 V 292


>gi|119672803|emb|CAK95517.1| RNA polymerase alpha subunit [Lactobacillus alimentarius]
          Length = 149

 Score =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 64/146 (43%), Positives = 100/146 (68%)

Query: 49  RVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK 108
           RVL++SL G A++ +QIDGVLHE S+I GV ED+T I+LN+K + LK   D   +  I  
Sbjct: 1   RVLLASLPGTAVSDIQIDGVLHEFSAIDGVIEDVTQIVLNVKKLKLKSYADDSLKAEIDV 60

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
            GP  VTA DI+  +D+E+L+P+  IC +       M++TV  G GY PA+ ++T+  PI
Sbjct: 61  VGPATVTAKDIKADDDLEILDPEQFICTVAEGGHFHMQMTVINGRGYTPAEQNKTDETPI 120

Query: 169 GLITIDALYSPIKKVSYTVESAREGQ 194
           G++ +D++++P++KV+Y VE+ R G+
Sbjct: 121 GVLPVDSIFTPVEKVNYQVENTRVGK 146


>gi|150187149|emb|CAK30181.1| RNA polymerase alpha subunit [Streptococcus ratti]
          Length = 178

 Score =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 66/166 (39%), Positives = 110/166 (66%)

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           ++ GV ED+  IILN+KG+ +K   +  K + +   GP  +TAGDI T +DIE++NPDH 
Sbjct: 3   TVPGVREDVMQIILNLKGLAVKSYVEEEKIIELDVEGPAEITAGDILTDSDIEIVNPDHY 62

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           +  +   A ++  LTV    GY+PA+ ++ ++ P+G + ID++Y+P+KKV+Y VE AR G
Sbjct: 63  LFTIAEGASLKATLTVGTNRGYIPAEENKKDDAPVGTLAIDSIYTPVKKVNYQVEPARVG 122

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
              ++DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K
Sbjct: 123 SNDNFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAK 168


>gi|296272962|ref|YP_003655593.1| DNA-directed RNA polymerase subunit alpha [Arcobacter nitrofigilis
           DSM 7299]
 gi|296097136|gb|ADG93086.1| DNA-directed RNA polymerase, alpha subunit [Arcobacter nitrofigilis
           DSM 7299]
          Length = 332

 Score =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 90/307 (29%), Positives = 161/307 (52%), Gaps = 18/307 (5%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E    + A P   GFA TL + LRR+L+SS  G +  AV+I+G  HE  S++G+ ED+  
Sbjct: 21  ETEAKISAYPFESGFAITLAHPLRRLLLSSSVGYSPIAVKIEGASHEFDSLRGMLEDIAI 80

Query: 85  IILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            I+N+K I  K+  D ++  V     GP  +   D+   +D+E+++P+  +  ++ D  +
Sbjct: 81  FIINLKNIKFKILSDENQVEVEYSFNGPKEIKGSDLVN-SDVEIVSPEAHLATINADCNL 139

Query: 144 RMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + + KG GY+P++  R    +D    I +DA ++P+KKV Y +E        +++K 
Sbjct: 140 TFSVIIQKGIGYMPSEDIRDMVSSD---YIPLDAFFTPVKKVVYDIEKMLVEDNPNFEKA 196

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMF---INFEE--PKKEVKEDINVKSLPFNPAL 256
             T+ T+G IT  ++   A  ++  Q+ +F    +  E       +E + +K       L
Sbjct: 197 VFTVQTNGQITPINAFKEAVSVMYSQMSVFNKVFDLSEVTVSDSTEEPVELKD------L 250

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
           + K+++L LS RS N L    + Y+G+L+  +E ++  + N G+KS  EI   L ++G  
Sbjct: 251 IVKIDDLNLSARSFNSLDRAGLKYLGELVLMSEVEVKNIKNLGKKSYDEIADKLASLGFP 310

Query: 317 LGMNLPD 323
           +   LP+
Sbjct: 311 VENTLPE 317


>gi|117575081|emb|CAJ84780.1| RNA polymerase alpha subunit [Lactobacillus amylophilus]
          Length = 159

 Score =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 67/159 (42%), Positives = 106/159 (66%)

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            S+I GV ED+T IILN+K + LK      K   I   GP  VTAGD++  +++++LNPD
Sbjct: 1   FSTIPGVLEDVTQIILNLKKLTLKSIAADEKLAEIDVEGPATVTAGDLKVDDEVQILNPD 60

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             I  +   A ++M + + +G GYVPA  +++++ PIG++ +D+L+SPI+KV+Y VE  R
Sbjct: 61  QYIATVAEGAHLQMTVAIKQGRGYVPADQNKSDDMPIGVVPVDSLFSPIEKVNYQVEGTR 120

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
            G+  DYDKL+M + TDGSIT  D+++  ++IL + L +
Sbjct: 121 VGRNNDYDKLTMEVWTDGSITPNDALSFGAKILTEHLNV 159


>gi|119663524|emb|CAK22333.1| RNA polymerase alpha subunit [Lactobacillus graminis]
          Length = 160

 Score =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 67/160 (41%), Positives = 109/160 (68%)

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           I GV ED+T IILNIK + LK+  +  K + I  +GP  VTA DI + +D+EVLN D  I
Sbjct: 1   IDGVLEDVTQIILNIKKLALKLHVEEDKTIEIDVKGPATVTAADIISDDDVEVLNTDQYI 60

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
           C +       + +TV KG GYV A  +++++ PIG++ ID++Y+PI +V+Y VES R G+
Sbjct: 61  CTVAEGGNFHVRMTVKKGRGYVAADQNKSDDMPIGVLPIDSIYTPISRVNYQVESTRVGR 120

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
             D+DKL++ + T+GSI+  ++++LA++I+ + L +F++ 
Sbjct: 121 RNDFDKLTLDVWTNGSISPREAISLAAKIMTEHLAIFVDL 160


>gi|293977954|ref|YP_003543384.1| DNA-directed RNA polymerase subunit alpha/40 kD subunit [Candidatus
           Sulcia muelleri DMIN]
 gi|292667885|gb|ADE35520.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Candidatus Sulcia muelleri DMIN]
          Length = 239

 Score =  137 bits (345), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 85/218 (38%), Positives = 130/218 (59%), Gaps = 7/218 (3%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
           L   EPL  G+  T+GN LRRVL+SSL G AI++V+I+GV HE S+IKGV ED+T+IILN
Sbjct: 23  LFKIEPLFPGWGVTIGNTLRRVLLSSLEGYAISSVKIEGVNHEFSTIKGVIEDMTEIILN 82

Query: 89  IKGINLKMSGDSHKRVT-----IFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAV 142
           +K +  K +       +     I       +TAGD+ + +N  ++LNPD +I N      
Sbjct: 83  LKKVRFKKNKKKENFESEVFNMIISNDKEEITAGDLGKYINKFDILNPDLIILNKQKLIS 142

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + + + + KG GYVP++ ++      G I +D++++PIK V Y +++    +  +Y+ L 
Sbjct: 143 LDISIVIKKGIGYVPSEENKENLIVSGSIPMDSIFTPIKNVKYKIDNCSINKNSNYESLL 202

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           + I TDGSI   D++  AS IL   L MFI +E  KK+
Sbjct: 203 LEIKTDGSINPRDALTNASNILIQHLKMFI-YETRKKK 239


>gi|78776528|ref|YP_392843.1| DNA-directed RNA polymerase subunit alpha [Sulfurimonas
           denitrificans DSM 1251]
 gi|119366748|sp|Q30TS3|RPOA_SULDN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|78497068|gb|ABB43608.1| DNA-directed RNA polymerase, alpha subunit [Sulfurimonas
           denitrificans DSM 1251]
          Length = 330

 Score =  137 bits (345), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 93/320 (29%), Positives = 165/320 (51%), Gaps = 13/320 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           Q  EN   ++A P   GFA +L + LRR L+SS  G A  A++I+G  HE  S++G+ ED
Sbjct: 18  QISENEANIMAYPFETGFAISLAHPLRRFLLSSSVGYAPIAIKIEGAKHEFDSVRGMLED 77

Query: 82  LTDIILNIKGINLK-MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           ++D ILN+K    K + G +   +     GP  +   ++   +++E++ P+  +  L+ D
Sbjct: 78  ISDFILNLKETRFKLLGGATEAEINYNFTGPCDIKGSNLSN-SEVEIVTPNTHLATLNED 136

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
           + +   + +++G GYV ++    E    G I +DA ++P++  +Y +E+       ++++
Sbjct: 137 STLNFSIRIAQGIGYVASEDTYDELQD-GYIALDAYFTPVRSATYKIENVLVEDNPNFER 195

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK-- 258
           + + I TDG IT  D+   +  ++  QL +F      +  VK    ++    +P L K  
Sbjct: 196 VILNIKTDGQITPLDAFRNSLEVMYAQLAVF----NSEISVKAPATIERAEESPDLKKLT 251

Query: 259 -KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             ++ L LS RS NCL   NI  +G++   +  D+  + N G+KS  EI   L   G  +
Sbjct: 252 AHIDSLGLSARSFNCLDRSNIKLIGEIALMSTNDLKNVKNLGKKSYDEIVEKLQEFGYEV 311

Query: 318 GMNLPDWPPESIEELAKKYE 337
           G +L D   + +  L KK E
Sbjct: 312 GGDLAD---DVVSALKKKIE 328


>gi|161833842|ref|YP_001598038.1| DNA-directed RNA polymerase subunit alpha [Candidatus Sulcia
           muelleri GWSS]
 gi|152206332|gb|ABS30642.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Sulcia
           muelleri GWSS]
          Length = 239

 Score =  137 bits (345), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 85/218 (38%), Positives = 130/218 (59%), Gaps = 7/218 (3%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
           L   EPL  G+  T+GN LRRVL+SSL G AI++V+I+GV HE S+IKGV ED+T+IILN
Sbjct: 23  LFKIEPLFPGWGVTIGNTLRRVLLSSLEGYAISSVKIEGVNHEFSTIKGVIEDMTEIILN 82

Query: 89  IKGINLKMSGDSHKRVT-----IFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLDVDAV 142
           +K +  K +       +     I       +TAGD+ + +N  ++LNPD +I N      
Sbjct: 83  LKKVRFKKNKKKENFESEVFNMIISNDKEEITAGDLGKYINKFDILNPDLIILNKQKLIS 142

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + + + + KG GYVP++ ++      G I +D++++PIK V Y +++    +  +Y+ L 
Sbjct: 143 LDISIVIKKGIGYVPSEENKENLIGSGSIPMDSIFTPIKNVKYKIDNCSINKNSNYESLL 202

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           + I TDGSI   D++  AS IL   L MFI +E  KK+
Sbjct: 203 LEIKTDGSINPRDALTNASNILIQHLKMFI-YETRKKK 239


>gi|117575083|emb|CAJ84781.1| RNA polymerase alpha subunit [Lactobacillus amylophilus]
          Length = 171

 Score =  137 bits (345), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 65/154 (42%), Positives = 104/154 (67%)

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+T IILN+K + LK      K   I   GP  VTAGD++  +++++LNPD  I  +  
Sbjct: 1   EDVTQIILNLKKLTLKSIAADEKLAEIDVEGPATVTAGDLKVDDEVQILNPDQYIATVAE 60

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
            A ++M + + +G GYVPA  +++++ PIG++ +D+L+SPI+KV+Y VE  R G+  DYD
Sbjct: 61  GAHLQMTVAIKQGRGYVPADQNKSDDMPIGVVPVDSLFSPIEKVNYQVEGTRVGRNNDYD 120

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           KL+M + TDGSIT  D+++  ++IL + L +F+N
Sbjct: 121 KLTMEVWTDGSITPNDALSFGAKILTEHLNVFMN 154


>gi|154424725|emb|CAL18465.1| RNA polymerase alpha subunit [Streptococcus gallolyticus]
          Length = 158

 Score =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 69/158 (43%), Positives = 107/158 (67%)

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           ++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI T 
Sbjct: 1   IKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDILTD 60

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           +D+E++NPDH +  +     ++  +TV+K  GYV A+ ++ E+ P+G + +D++Y+P+KK
Sbjct: 61  SDVEIVNPDHYLFTIAEGHSLKATMTVAKERGYVSAEGNKKEDAPVGTLAVDSIYTPVKK 120

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           V+Y VE AR G    +DKL++ I T+G+I  ED++ L+
Sbjct: 121 VNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLS 158


>gi|290790733|gb|ADD62991.1| RNA polymerase alpha subunit [Oryza australiensis]
          Length = 337

 Score =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 99/309 (32%), Positives = 160/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL      R+EL +
Sbjct: 92  KEIVLRSNLYGVRNASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPTDFRIELRI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY       T++   G   IDA+  P++ V+Y++ S   G    Y+ L + I T+G
Sbjct: 152 KRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFSCGNGNA-KYEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKRLTNLKKNKKRI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    + + K +  T+
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---RMQDGKQIWDTL 324

Query: 314 GLFLGMNLP 322
              L M+LP
Sbjct: 325 EKHLPMDLP 333


>gi|150187010|emb|CAK30150.1| RNA polymerase alpha subunit [Streptococcus pyogenes]
          Length = 184

 Score =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 68/166 (40%), Positives = 110/166 (66%)

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH 
Sbjct: 1   TIPGVREDVMQIILNVKGLAVKSYVEDEKIIELEVEGPAEVTAGDILTDSDIELVNPDHY 60

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           +  +     +R  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G
Sbjct: 61  LFTIAEGHSLRATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVG 120

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
               +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K
Sbjct: 121 SNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAK 166


>gi|84874036|gb|ABC68041.1| RNA polymerase subunit [Oryza officinalis]
 gi|84874042|gb|ABC68044.1| RNA polymerase subunit [Oryza australiensis]
          Length = 317

 Score =  136 bits (343), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 99/309 (32%), Positives = 160/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 12  FILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGIEESVQEILLNL 71

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL      R+EL +
Sbjct: 72  KEIVLRSNLYGVRNASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPTDFRIELRI 131

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY       T++   G   IDA+  P++ V+Y++ S   G    Y+ L + I T+G
Sbjct: 132 KRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFSCGNGNA-KYEILFLEIWTNG 187

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 188 SLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKRLTNLKKNKKRI 247

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    + + K +  T+
Sbjct: 248 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---RMQDGKQIWDTL 304

Query: 314 GLFLGMNLP 322
              L M+LP
Sbjct: 305 EKHLPMDLP 313


>gi|84874038|gb|ABC68042.1| RNA polymerase subunit [Oryza rhizomatis]
          Length = 317

 Score =  136 bits (343), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 99/309 (32%), Positives = 160/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 12  FILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGIEESVQEILLNL 71

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL      R+EL +
Sbjct: 72  KEIVLRSNLYGVRNASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPTDFRIELRI 131

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY       T++   G   IDA+  P++ V+Y++ S   G    Y+ L + I T+G
Sbjct: 132 KRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFSCGNGNA-KYEILFLEIWTNG 187

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 188 SLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENQNRFTSPLLSFQKRLTNLKKNKKRI 247

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    + + K +  T+
Sbjct: 248 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---RMQDGKQIWDTL 304

Query: 314 GLFLGMNLP 322
              L M+LP
Sbjct: 305 EKHLPMDLP 313


>gi|119668277|emb|CAK95449.1| RNA polymerase alpha subunit [Lactobacillus acidophilus]
          Length = 150

 Score =  136 bits (343), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 69/150 (46%), Positives = 98/150 (65%)

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++VLNP
Sbjct: 1   EFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQVLNP 60

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES 
Sbjct: 61  DQYICTIAEGGHLHMELAVKNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVEST 120

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           R G+  D+DKL+  I TDGSI   D+++ A
Sbjct: 121 RVGKRDDFDKLTFEIWTDGSIKPNDALSFA 150


>gi|84874040|gb|ABC68043.1| RNA polymerase subunit [Oryza punctata]
          Length = 317

 Score =  136 bits (343), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 99/309 (32%), Positives = 160/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 12  FILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGIEESVQEILLNL 71

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL      R+EL +
Sbjct: 72  KEIVLRSNLYGVRNASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPEDFRIELRI 131

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY       T++   G   IDA+  P++ V+Y++ S   G    Y+ L + I T+G
Sbjct: 132 KRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFSCGNGNA-KYEILFLEIWTNG 187

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 188 SLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKRLTNLKKNKKRI 247

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    + + K +  T+
Sbjct: 248 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---RMQDGKQIWDTL 304

Query: 314 GLFLGMNLP 322
              L M+LP
Sbjct: 305 EKHLPMDLP 313


>gi|154424843|emb|CAL18524.1| RNA polymerase alpha subunit [Streptococcus porcinus]
          Length = 148

 Score =  136 bits (342), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 66/148 (44%), Positives = 102/148 (68%)

Query: 52  MSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGP 111
           +SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP
Sbjct: 1   LSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKMIELDVEGP 60

Query: 112 GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI 171
             VTAGDI T +DIE++NPDH +  +     ++  +TV+K  GYVPA+ ++ ++ P+G +
Sbjct: 61  AEVTAGDILTDSDIELVNPDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKDDAPVGTL 120

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYD 199
            +D++Y+P+KKV+Y VE AR G    +D
Sbjct: 121 AVDSIYTPVKKVNYQVEPARVGSNDGFD 148


>gi|11466821|ref|NP_039417.1| RNA polymerase alpha subunit [Oryza sativa Japonica Group]
 gi|50234003|ref|YP_052781.1| RNA polymerase alpha subunit [Oryza nivara]
 gi|109156616|ref|YP_654235.1| RNA polymerase alpha subunit [Oryza sativa Indica Group]
 gi|68053137|sp|Q6ENE2|RPOA_ORYNI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|148839633|sp|P0C498|RPOA_ORYSA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|148839634|sp|P0C499|RPOA_ORYSI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|148839635|sp|P0C500|RPOA_ORYSJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|12018|emb|CAA33979.1| RNA polymerase alpha subunit [Oryza sativa Japonica Group]
 gi|40253573|dbj|BAD05519.1| RNA polymerase alpha chain [Oryza sativa Japonica Group]
 gi|42795508|gb|AAS46075.1| RNA polymerase alpha chain [Oryza sativa Indica Group]
 gi|42795575|gb|AAS46141.1| RNA polymerase alpha chain [Oryza sativa Japonica Group]
 gi|42795639|gb|AAS46204.1| RNA polymerase alpha chain [Oryza sativa Japonica Group]
 gi|49615027|dbj|BAD26810.1| RNA polymerase alpha chain [Oryza nivara]
 gi|290790595|gb|ADD62855.1| RNA polymerase alpha subunit [Oryza sativa Japonica Group]
 gi|290790664|gb|ADD62923.1| RNA polymerase alpha subunit [Oryza meridionalis]
 gi|226639|prf||1603356BN RNA polymerase alpha
          Length = 337

 Score =  135 bits (341), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 98/309 (31%), Positives = 160/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL      R+EL +
Sbjct: 92  KEIVLRSNLYGVRTASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPTDFRIELRI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY       T++   G   IDA+  P++ V+Y++ +   G    Y+ L + I T+G
Sbjct: 152 KRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFACGNGNA-KYEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKRLTNLKKNKKRI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    + + K +  T+
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---RMQDGKQIWDTL 324

Query: 314 GLFLGMNLP 322
              L M+LP
Sbjct: 325 EKHLPMDLP 333


>gi|20160832|dbj|BAB89772.1| Chloroplast RNA polymerase alpha chain [Oryza sativa Japonica
           Group]
          Length = 337

 Score =  135 bits (341), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 98/309 (31%), Positives = 160/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL      R+EL +
Sbjct: 92  KEIVLRSNLYGVRTASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPTDFRIELRI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY       T++   G   IDA+  P++ V+Y++ +   G    Y+ L + I T+G
Sbjct: 152 KRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFACGNGNA-KYEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKRLTNLKKNKKRI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    + + K +  T+
Sbjct: 268 PLSCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---RMQDGKQIWDTL 324

Query: 314 GLFLGMNLP 322
              L M+LP
Sbjct: 325 EKHLPMDLP 333


>gi|84874024|gb|ABC68035.1| RNA polymerase subunit [Oryza sativa]
 gi|84874026|gb|ABC68036.1| RNA polymerase subunit [Oryza sativa]
 gi|84874030|gb|ABC68038.1| RNA polymerase subunit [Oryza nivara]
 gi|84874034|gb|ABC68040.1| RNA polymerase subunit [Oryza sp. IRGC 81916]
          Length = 317

 Score =  135 bits (340), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 98/309 (31%), Positives = 160/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 12  FILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGIEESVQEILLNL 71

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL      R+EL +
Sbjct: 72  KEIVLRSNLYGVRTASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPTDFRIELRI 131

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY       T++   G   IDA+  P++ V+Y++ +   G    Y+ L + I T+G
Sbjct: 132 KRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFACGNGNA-KYEILFLEIWTNG 187

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 188 SLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKRLTNLKKNKKRI 247

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    + + K +  T+
Sbjct: 248 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---RMQDGKQIWDTL 304

Query: 314 GLFLGMNLP 322
              L M+LP
Sbjct: 305 EKHLPMDLP 313


>gi|119662801|emb|CAJ33192.1| RNA polymerase alpha subunit [Lactobacillus kefiri]
          Length = 153

 Score =  135 bits (340), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 77/151 (50%), Positives = 100/151 (66%), Gaps = 4/151 (2%)

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVN 123
           D VLHE S+IKGV ED+T IILN+K I+LK+ G  D  + + I   GP  VTAGDIQ   
Sbjct: 1   DDVLHEFSTIKGVVEDVTQIILNVKKISLKLDGPEDEEENLEIDVIGPADVTAGDIQADG 60

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIK 181
           D+ VLNPD  I  +   A   M LT +KG GYV A     R+   PIG++ +D++Y+PI+
Sbjct: 61  DVTVLNPDLHIATVAEGATFHMRLTANKGRGYVSAVENKKRSSEMPIGVLPVDSIYTPIE 120

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           +V+Y VES R GQ  D+DKL++ I TDGSIT
Sbjct: 121 RVNYQVESTRVGQRDDFDKLTLDIWTDGSIT 151


>gi|84874044|gb|ABC68045.1| RNA polymerase subunit [Oryza granulata]
          Length = 317

 Score =  135 bits (340), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 98/309 (31%), Positives = 160/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 12  FILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGIEESVQEILLNL 71

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL      R+EL +
Sbjct: 72  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDMAQPIANLTEPMDFRIELRI 131

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY        ++   G   IDA+  P++ V+Y++ S   G    Y+ L + I T+G
Sbjct: 132 KRDRGYHTEVRKNAQD---GSYPIDAVSMPVRNVNYSIFSCGNGNA-KYEILFLEIWTNG 187

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 188 SLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKRLTNLKKNKKRI 247

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    + + K +  T+
Sbjct: 248 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---RMQDGKQIWDTL 304

Query: 314 GLFLGMNLP 322
             +L M+LP
Sbjct: 305 EKYLPMDLP 313


>gi|154424777|emb|CAL18491.1| RNA polymerase alpha subunit [Streptococcus dysgalactiae subsp.
           dysgalactiae]
          Length = 185

 Score =  135 bits (340), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 67/166 (40%), Positives = 110/166 (66%)

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH 
Sbjct: 3   TIPGVREDVMQIILNVKGLAVKSYVEDEKIIELEVEGPAEVTAGDILTDSDIELVNPDHY 62

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           +  +     +R  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G
Sbjct: 63  LFTIAEGHSLRATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVG 122

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
               +DKL++ I T+G+I  ED++ L++R+L + L +F +  +  K
Sbjct: 123 SNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTDVAK 168


>gi|47679547|gb|AAT36717.1| RNA polymerase alpha subunit [Corethron hystrix]
          Length = 301

 Score =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 92/279 (32%), Positives = 151/279 (54%), Gaps = 19/279 (6%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           G   T+G  LRR L+S L   AIT V+I GV +E S I+GV ED+ +++LN++ I +K +
Sbjct: 32  GQGITIGTVLRRFLLSELNATAITGVRIAGVNNEFSIIEGVREDVLELLLNLRPIVIKNN 91

Query: 98  GDSHK----RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
            D+ +    R+ +  +GP V+TA  IQ   ++E+LNP+  I  +    ++ ME     G 
Sbjct: 92  SDNSEMKFGRLKV--QGPAVITANAIQLPTELEILNPNQYIATISRSMILEMEFKFESGI 149

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY      + E+     + IDA++ P++KV + VE+  +      + L + I T+GSI+ 
Sbjct: 150 GYRLVNQTKMESSS-DFLEIDAVFMPVQKVDFKVENIYDKNKHISENLIIDIWTNGSISP 208

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK------VEELELSV 267
           E ++  +S  + +     I   + KKE+ E      LP N  +  +      +EEL+LSV
Sbjct: 209 ETALYESSNNIIELFNSLIE-NKFKKEILE-----PLPENTRINSENHTNISIEELQLSV 262

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           RS NCL+   I  + DL++ +   +  + NFGRKS  E+
Sbjct: 263 RSYNCLKRAQINSISDLLKYSPEKLQEIKNFGRKSADEV 301


>gi|237751462|ref|ZP_04581942.1| DNA-directed RNA polymerase subunit alpha [Helicobacter bilis ATCC
           43879]
 gi|229372828|gb|EEO23219.1| DNA-directed RNA polymerase subunit alpha [Helicobacter bilis ATCC
           43879]
          Length = 337

 Score =  134 bits (338), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 90/315 (28%), Positives = 162/315 (51%), Gaps = 35/315 (11%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           N   + A P    +A T+ + +RR+L+SS  G A   ++I+GV HE  +++GV ED+   
Sbjct: 22  NHIRLHAYPFEPHYAVTIAHPVRRLLLSSSVGYAPIGIKIEGVRHEFDTVRGVAEDVAPF 81

Query: 86  ILNIKGINLKMSGD--SHKRVTIFKRGPGVVT-AGDIQTVNDIEVLNPDHVICNLDVDAV 142
           I+NIK +  K++ D   H++  +     G +   G+  +  +I VL+ D  + N++ DA 
Sbjct: 82  IVNIKNLKFKVNEDMQQHEKFELHYEFNGPMELRGEHLSNENITVLSTDSHLANINSDAK 141

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIG--LITIDALYSPIKKVSYTVESAREGQVLDYDK 200
           ++  + + KG G+V ++  R E   IG   I +DA ++P+K+  Y +E+       +++K
Sbjct: 142 LKFSILIHKGLGFVASETIREE---IGSEYIPLDADFTPVKRAVYDIENVLHESNPNFEK 198

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMF-------------INFEEPKKEVKEDINV 247
           +   ++T+G I   ++   A  I+  Q+ +F             +N + P+ +V      
Sbjct: 199 IVFEVETNGQIEPMEAFKEAVAIMHSQMSVFGAELSDVPTSNGRLNDDSPELKV------ 252

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                   LL  VE L L  R +NCL+  NI Y+G+L+   E+D+  + N G++S  EI 
Sbjct: 253 --------LLSSVEILNLEHRPSNCLQKSNIKYIGELVLMNESDLKNIKNLGKRSFDEIT 304

Query: 308 GVLGTMGLFLGMNLP 322
             L  +G  +G +LP
Sbjct: 305 AKLNEVGYAVGADLP 319


>gi|161511741|emb|CAP16881.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 179

 Score =  134 bits (338), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 69/171 (40%), Positives = 110/171 (64%), Gaps = 2/171 (1%)

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           +I+GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  
Sbjct: 1   TIEGVVEDVTQIILNLKKVSLKVESDEEKSLEINVMGPANVTAGDIVGDGDVTILNPELP 60

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAR 191
           IC +         LT  KG GY  A  +  R  + PIG++ ID++Y+PI++V+Y VE+ R
Sbjct: 61  ICTVAEGTTFHAVLTAEKGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTR 120

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
            GQ  DYDKL++ + TDGS+   ++++L+++IL + L +F+N ++  K+ +
Sbjct: 121 VGQRDDYDKLTLDVWTDGSLAASEAISLSAKILTEHLTIFVNLDDQAKDTE 171


>gi|119662401|emb|CAJ33190.1| RNA polymerase alpha subunit [Lactobacillus frumenti]
          Length = 162

 Score =  134 bits (338), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 71/162 (43%), Positives = 110/162 (67%), Gaps = 2/162 (1%)

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            S++KGV ED+T IILN+K ++LK+  +  K + I  +GP  VTA DIQ   ++ VLNPD
Sbjct: 1   FSTVKGVTEDVTQIILNLKKVSLKIDSEEPKDLEIDVKGPAEVTASDIQGDGEVMVLNPD 60

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVES 189
             I  +   A + +++T  KG GY+ A  ++   D   IG++ ID++Y+PI++V+YTVE+
Sbjct: 61  LYIATVADGAELHIKMTADKGRGYLSANDNKARMDDLAIGVLPIDSIYTPIERVNYTVEN 120

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           AR GQ  DYDKL++ + TDGS+T  ++V+L ++IL + L MF
Sbjct: 121 ARVGQRNDYDKLTLDVWTDGSLTPTEAVSLGAKILTEHLKMF 162


>gi|32487326|emb|CAE05901.1| OSJNBa0061C08.8 [Oryza sativa Japonica Group]
 gi|57834095|emb|CAE04760.3| OSJNBa0079C19.1 [Oryza sativa Japonica Group]
          Length = 446

 Score =  134 bits (338), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 98/309 (31%), Positives = 160/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 141 FILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGIEESVQEILLNL 200

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL      R+EL +
Sbjct: 201 KEIVLRSNLYGVRTASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPTDFRIELRI 260

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY       T++   G   IDA+  P++ V+Y++ +   G    Y+ L + I T+G
Sbjct: 261 KRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFACGNGNA-KYEILFLEIWTNG 316

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 317 SLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKRLTNLKKNKKRI 376

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    + + K +  T+
Sbjct: 377 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---RMQDGKQIWDTL 433

Query: 314 GLFLGMNLP 322
              L M+LP
Sbjct: 434 EKHLPMDLP 442


>gi|154424763|emb|CAL18484.1| RNA polymerase alpha subunit [Streptococcus canis]
          Length = 173

 Score =  134 bits (338), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 67/165 (40%), Positives = 109/165 (66%)

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +
Sbjct: 1   IPGVREDVMQIILNVKGLAVKSYVEDEKIIELEVEGPAEVTAGDILTDSDIELVNPDHYL 60

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
             +     +R  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G 
Sbjct: 61  FTIAEGHSLRATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGS 120

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
              +DKL++ I T+G+I  ED++ L++R+L + L +F +  +  K
Sbjct: 121 NDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTDVAK 165


>gi|18767372|gb|AAL79338.1|AC099402_2 Putative RNA polymerase alpha subunit [Oryza sativa]
 gi|21327372|gb|AAM48277.1|AC122148_30 Putative RNA polymerase alpha subunit [Oryza sativa Japonica Group]
 gi|110288947|gb|ABB47310.2| DNA-directed RNA polymerase alpha chain, putative, expressed [Oryza
           sativa Japonica Group]
          Length = 446

 Score =  134 bits (338), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 98/309 (31%), Positives = 160/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 141 FILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGIEESVQEILLNL 200

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL      R+EL +
Sbjct: 201 KEIVLRSNLYGVRTASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPTDFRIELRI 260

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY       T++   G   IDA+  P++ V+Y++ +   G    Y+ L + I T+G
Sbjct: 261 KRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFACGNGNA-RYEILFLEIWTNG 316

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 317 SLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKRLTNLKKNKKRI 376

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    + + K +  T+
Sbjct: 377 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---RMQDGKQIWDTL 433

Query: 314 GLFLGMNLP 322
              L M+LP
Sbjct: 434 EKHLPMDLP 442


>gi|7388083|sp|O98462|RPOA_SPIMX RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|4007878|gb|AAC95318.1| RNA polymerase alpha subunit [Spirogyra maxima]
          Length = 344

 Score =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 95/322 (29%), Positives = 162/322 (50%), Gaps = 42/322 (13%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
           L IA PL  G A TLG A+RR L+ S++G AI A +I G  HE S+++G+ E + DI+LN
Sbjct: 33  LFIASPLLAGQATTLGVAIRRTLLESIQGTAIVAAKIYGAAHEYSTLEGIQESIHDILLN 92

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           +K + +K      ++  I   GP  VTA DI+   +I + NP H I  +      ++EL 
Sbjct: 93  LKQVIIKNKICEFQKCLISIIGPKKVTAADIELSQNITISNPYHHIATITKPIRFQVELI 152

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           ++KG GY+    +  ++   G   +DAL++P++ V++++ +  E Q    + L + I T+
Sbjct: 153 INKGRGYLIQDGNDVQD---GYFPVDALFNPVRNVNFSIHNLAEQQ----EALILEIWTN 205

Query: 209 GSITGEDSVALASRILQDQLGMFI-----------------------------NFEEPKK 239
           G+IT  D++   S   ++ + +F+                              FE    
Sbjct: 206 GAITPLDALRQGS---ENLIHLFLPPFGLEDDTYMTSLGSQDYNIHIKNSLKEKFELHSI 262

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           E  ED ++    F       +E LELS R   CL+  NI  + DL++ ++ D+L+++N G
Sbjct: 263 ERIEDSHLIKDQFLEYSKTPIELLELSTRPFKCLKNANIYTINDLLKLSQQDLLKISNMG 322

Query: 300 RKSLVEIKGVLGTMGLFLGMNL 321
             S   +K ++  +    G+NL
Sbjct: 323 PSS---VKQIVEALDKRFGINL 341


>gi|77406098|ref|ZP_00783172.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae H36B]
 gi|77175279|gb|EAO78074.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae H36B]
          Length = 179

 Score =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 68/175 (38%), Positives = 114/175 (65%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           ++  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL+
Sbjct: 1   MKATMTVAKNRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLT 60

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + I T+G+I  ED++ L++R+L + L +F +  E  K  +     + +     L + +EE
Sbjct: 61  IEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKETEKVNDEKVLDRTIEE 120

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K  L  +GL L
Sbjct: 121 LDLSVRSYNCLKRAGINTIFDLTEKTEPEMMKVRNLGRKSLEEVKIKLADLGLGL 175


>gi|307702711|ref|ZP_07639663.1| putative DNA-directed RNA polymerase, alpha subunit [Streptococcus
           oralis ATCC 35037]
 gi|307623827|gb|EFO02812.1| putative DNA-directed RNA polymerase, alpha subunit [Streptococcus
           oralis ATCC 35037]
          Length = 163

 Score =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 70/155 (45%), Positives = 100/155 (64%), Gaps = 4/155 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
           +NPDH +  +   + ++  +TV+ G GYVPA  ++
Sbjct: 119 VNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENK 153


>gi|154424801|emb|CAL18503.1| RNA polymerase alpha subunit [Streptococcus hyointestinalis]
          Length = 162

 Score =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 66/161 (40%), Positives = 107/161 (66%)

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E  +I GV ED+  IIL +KG+ +K   +  K + +   GP  VTAGDI T +DIE++NP
Sbjct: 1   EFDTIPGVREDVMQIILKVKGLAVKSYVEDEKMIELDVEGPAEVTAGDILTDSDIEIVNP 60

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           DH +  +     ++  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE A
Sbjct: 61  DHYLFTIAEGHSLKATMTVAKNRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPA 120

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           R G    +DKL++ I T+G+I  ED++ L++RIL + L +F
Sbjct: 121 RVGSNDGFDKLTVEIMTNGTIIPEDALGLSARILIEHLNLF 161


>gi|165932201|emb|CAP66258.1| RNA polymerase alpha subunit [Lactobacillus oligofermentans]
          Length = 151

 Score =  134 bits (336), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 70/151 (46%), Positives = 103/151 (68%), Gaps = 2/151 (1%)

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE SS++GV ED+T IILNIK I LK+  +  K + I  +GP VVTAGDIQ   D+ +LN
Sbjct: 1   HEFSSVEGVTEDVTQIILNIKKIALKIDSEDDKTLEIDVKGPAVVTAGDIQADGDVTILN 60

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTV 187
           PD  +  +     + M++T + G GYV A  +  R E+ PIG++ ID++Y+PI++V+Y V
Sbjct: 61  PDLQLATVADGVELHMQMTANTGRGYVSADDNKSRMEDLPIGVLPIDSIYTPIERVNYNV 120

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           E AR GQ  DYDKL++ + +DGSIT  ++++
Sbjct: 121 EDARVGQRNDYDKLTLDVWSDGSITPSEAIS 151


>gi|84874032|gb|ABC68039.1| RNA polymerase subunit [Oryza glumipatula]
          Length = 317

 Score =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 98/309 (31%), Positives = 159/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 12  FILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGIEESVQEILLNL 71

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL      R+EL +
Sbjct: 72  KEIVLRSNLYGVRTASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPTDFRIELRI 131

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY       T++   G   IDA+  P++ V+Y++ +   G    Y+ L + I T+G
Sbjct: 132 KRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFACGNGNA-KYEILFLEIWTNG 187

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T  +++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 188 SLTPMEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKRLTNLKKNKKRI 247

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    + + K +  T+
Sbjct: 248 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---RMQDGKQIWDTL 304

Query: 314 GLFLGMNLP 322
              L M+LP
Sbjct: 305 EKHLPMDLP 313


>gi|254553679|gb|ACT67298.1| RNA polymerase alpha subunit [Joinvillea plicata]
          Length = 339

 Score =  133 bits (335), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 98/312 (31%), Positives = 166/312 (53%), Gaps = 29/312 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLIKGQADTIGIAMRRALLGEIEGTCITRAKSGKVPHEYSTIVGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +    +  +I  +GP  +TA DI +   +E+++    I NL   +D  + +++
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIISPPSVEIVDTTQHIANLTEPIDLCIELQI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA-REGQVLDYDKLSMTID 206
              +G+   P K     N   G   IDA+  P++ V+Y++ S   E +   Y+ L + I 
Sbjct: 152 KRDRGYHTEPRK-----NSQDGSYPIDAVSMPVRNVNYSIYSCGNENE--KYEILFLEIW 204

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK-- 259
           T+GS+T ++++  ASR L D    F++ EE     +E+ N  +LP   F   L  LKK  
Sbjct: 205 TNGSLTPKEALYEASRNLIDLFIPFLHAEEEDTNFEENKNRFTLPLLTFQKRLTNLKKNK 264

Query: 260 ---------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                    +++LEL  R+ NCL+  NI  + DL+ ++E D++++ NF    + + K +L
Sbjct: 265 KGIPLNCIFIDQLELPSRTYNCLKRSNIHTLLDLLSKSEEDLMKIENF---RMEDGKQIL 321

Query: 311 GTMGLFLGMNLP 322
            T+   L M+LP
Sbjct: 322 DTLQKHLSMDLP 333


>gi|291277242|ref|YP_003517014.1| DNA-directed RNA polymerase subunit alpha [Helicobacter mustelae
           12198]
 gi|290964436|emb|CBG40286.1| DNA-directed RNA polymerase alpha chain [Helicobacter mustelae
           12198]
          Length = 336

 Score =  133 bits (334), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 93/312 (29%), Positives = 167/312 (53%), Gaps = 30/312 (9%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           N+  ++A P   G+A TL + LRR+L+SS  G A  A++I+GV HE  SI+G+ ED++  
Sbjct: 22  NKVRVMAYPFESGYAVTLAHPLRRLLLSSSVGLAPIALKIEGVAHEFDSIRGIVEDVSPF 81

Query: 86  ILNIKGINL--KMSG---DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           I+N+K I    K  G   +    +    +GP V++ G +   + I+++N +  +  ++ D
Sbjct: 82  IVNLKNIRFLGKEGGFLEEEKVELHYSFQGPMVLSGGHLAN-DQIDIVNKEAPLATINED 140

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLIT-----IDALYSPIKKVSYTVESAREGQV 195
           AV+   + V KG GYVP++  R      GLI+     +DA ++P++K  Y +E+      
Sbjct: 141 AVLNFSIIVQKGIGYVPSEDIR------GLISEDYIPLDAYFTPVRKAVYEIENVLVEDN 194

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF------INFEEPKKEVKEDINVKS 249
             Y+K+   ++TDG +   ++   A  I+  Q+ +F      I+  + K+ ++++ + K 
Sbjct: 195 PTYEKIIFDVETDGQVDPYEAFKQAIAIMYSQMSIFNADISSISTTQ-KQAIEDNFDFKD 253

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 LL K++ L L+ R  NCL    I Y+G+L+  +E+++  + N G+ S  EI   
Sbjct: 254 ------LLMKIDSLNLNARCFNCLDRIGIRYVGELVLMSESEIKGVKNLGKTSYNEIVEK 307

Query: 310 LGTMGLFLGMNL 321
           L  +G  +G  L
Sbjct: 308 LQEIGYPIGTEL 319


>gi|84874028|gb|ABC68037.1| RNA polymerase subunit [Oryza sativa]
          Length = 317

 Score =  133 bits (334), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 97/309 (31%), Positives = 159/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 12  FILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGIEESVQEILLNL 71

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 72  KEIVLRSNLYGVRTASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPTDFHIELRI 131

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY       T++   G   IDA+  P++ V+Y++ +   G    Y+ L + I T+G
Sbjct: 132 KRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFACGNGNA-KYEILFLEIWTNG 187

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 188 SLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKRLTNLKKNKKRI 247

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    + + K +  T+
Sbjct: 248 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---RMQDGKQIWDTL 304

Query: 314 GLFLGMNLP 322
              L M+LP
Sbjct: 305 EKHLPMDLP 313


>gi|157737266|ref|YP_001489949.1| DNA-directed RNA polymerase subunit alpha [Arcobacter butzleri
           RM4018]
 gi|315636983|ref|ZP_07892207.1| DNA-directed RNA polymerase subunit alpha [Arcobacter butzleri
           JV22]
 gi|172045649|sp|A8ETK6|RPOA_ARCB4 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|157699120|gb|ABV67280.1| DNA-directed RNA polymerase, alpha chain [Arcobacter butzleri
           RM4018]
 gi|315478813|gb|EFU69522.1| DNA-directed RNA polymerase subunit alpha [Arcobacter butzleri
           JV22]
          Length = 332

 Score =  132 bits (333), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 88/302 (29%), Positives = 160/302 (52%), Gaps = 8/302 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +N   + A P   GFA TL + LRR+L+SS  G A  AV+I+G  HE  S++G+ ED+  
Sbjct: 21  DNEAKISAYPFEDGFAITLAHPLRRLLLSSSVGCAPIAVKIEGASHEFDSLRGMLEDVAI 80

Query: 85  IILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            ++N+K I  K++GD  + V  +   GP  +   D+   ++++V++ D  +  ++ D  +
Sbjct: 81  FVINLKNIKFKINGDKEQVVVEYSFNGPRDIKGEDLIN-SEVDVVSKDAHLATINSDCNL 139

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIG--LITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + + KG GY+P++  R   D +G   I IDA ++P+KKV Y +E        +Y+K 
Sbjct: 140 TFSVILQKGIGYMPSEDIR---DIVGADYIPIDAFFTPVKKVVYDIEKMLVEDNPNYEKA 196

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
              + T+G I+   +   A  ++  Q+ +F    +  +    D   + +     L+ +++
Sbjct: 197 VFRVQTNGQISPVTAFKEAVSVMYSQMSVFNKVFDLSEVAVSDSGEEPVELK-ELVIRID 255

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +L LS RS N L    + Y+G+L+  +E ++  + N G+KS  EI   L ++G  +   L
Sbjct: 256 DLNLSARSFNSLDRAGLKYLGELVLMSEVEVKNIKNLGKKSYDEIAEKLESLGYPVENTL 315

Query: 322 PD 323
           P+
Sbjct: 316 PE 317


>gi|150036738|emb|CAM98024.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. dextranicum]
          Length = 171

 Score =  132 bits (333), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 69/169 (40%), Positives = 108/169 (63%), Gaps = 2/169 (1%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE S++ GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+Q   D+EV
Sbjct: 1   VVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDIQGPADVTAADLQGGADVEV 60

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSY 185
           LNPD  I  +     + M ++  KG GY  A  ++   D  PIG++ +D++Y+PI++V+Y
Sbjct: 61  LNPDLHIATVAAGKSLHMTVSAVKGRGYTSADENKKLRDEMPIGVLAVDSIYTPIERVNY 120

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
            VE+ R G   DYDKL+  I T+GSI   D+++L ++IL + LG+F++ 
Sbjct: 121 QVENTRIGARDDYDKLTFDIWTNGSIKPSDALSLGAKILAEHLGLFMDI 169


>gi|150036718|emb|CAM98022.1| DNA-directed RNA polymerase alpha chain [Fructobacillus durionis]
          Length = 178

 Score =  132 bits (332), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 72/178 (40%), Positives = 107/178 (60%), Gaps = 2/178 (1%)

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S++ GV ED+T +ILN+K +           + I  +GP  VTA D     DIE
Sbjct: 1   GVVHEFSTVDGVAEDVTQLILNLKKVVFATDSAEEHTLEIDVQGPKDVTAADFVGSADIE 60

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVS 184
           VLNPD  I  L     + M +TV KG GY  A+ ++   D  PIG++T+D++Y+PI++V+
Sbjct: 61  VLNPDLHIATLAAGKSLHMTVTVVKGRGYASAEENKQLRDEMPIGVLTVDSIYTPIERVN 120

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           Y VE  R G   D+DKL+M + T+GSI   D+++L S+IL + L +F +     +E K
Sbjct: 121 YHVEQKRVGSRDDFDKLTMEVWTNGSIKPSDALSLGSKILTEHLNLFTDISPVAQETK 178


>gi|150187031|emb|CAK30155.1| RNA polymerase alpha subunit [Streptococcus urinalis 2285-97]
          Length = 169

 Score =  132 bits (332), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 65/160 (40%), Positives = 106/160 (66%)

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+  IILN+KG+ +K   D  K V +   GP  +TAGDI T +DIE++NPDH +  +  
Sbjct: 1   EDVMQIILNVKGLAVKSYVDDEKVVELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIAE 60

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              ++  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +D
Sbjct: 61  GHSLKATMTVAKDRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFD 120

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           KL++ I T+G+I  ED++ L++R+L + L +F +  E  K
Sbjct: 121 KLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAK 160


>gi|154424741|emb|CAL18473.1| RNA polymerase alpha subunit [Streptococcus thermophilus]
          Length = 155

 Score =  132 bits (331), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 64/151 (42%), Positives = 103/151 (68%)

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           ++ GV ED+  IILNIKG+ +K   +  K + +  +GP  VTAGDI T +DIE++NPDH 
Sbjct: 3   TVPGVREDVMQIILNIKGLAVKSYVEDEKTIELDVQGPAEVTAGDILTDSDIEIVNPDHY 62

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           +  +   A  +  +TVS   GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G
Sbjct: 63  LFTIAEGASFQATMTVSTNRGYVPAEENKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVG 122

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
               +DKL++ I T+G+I  ED++ L++R+L
Sbjct: 123 SNDGFDKLTIEIVTNGTIIPEDALGLSARVL 153


>gi|119662843|emb|CAJ33214.1| RNA polymerase alpha subunit [Lactobacillus bifermentans]
          Length = 142

 Score =  132 bits (331), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 68/140 (48%), Positives = 95/140 (67%)

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            S+I GV ED+T IILNIK + LK+  D  K V I  +GP  VTAGDI+  +D+EVLNPD
Sbjct: 1   FSTIDGVTEDVTQIILNIKKLALKLESDDDKTVEIDVQGPATVTAGDIEADSDVEVLNPD 60

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             IC +         +TV KG GYV A+ ++ ++ PIG++ ID++Y+PI +V+Y VES R
Sbjct: 61  LYICTVAEGGHFHARMTVRKGRGYVAAEGNKVDDMPIGVLPIDSIYTPISRVNYQVESTR 120

Query: 192 EGQVLDYDKLSMTIDTDGSI 211
            GQ  D+DKL++ + T+GSI
Sbjct: 121 VGQRNDFDKLTLDVWTNGSI 140


>gi|60117163|ref|YP_209497.1| RNA polymerase alpha subunit [Huperzia lucidula]
 gi|68053058|sp|Q5SD25|RPOA_HUPLU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|50659971|gb|AAT80693.1| RNA polymerase alpha subunit [Huperzia lucidula]
          Length = 336

 Score =  132 bits (331), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 93/308 (30%), Positives = 162/308 (52%), Gaps = 23/308 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL  G A+T+G  +RR L+  ++G  IT  + + + HE S++ G+ E + DI++N 
Sbjct: 35  FILSPLKVGQANTIGLVMRRALLGEIKGTCITCAKFENITHEYSTMDGIQESVHDILINS 94

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK      ++  I   GP  VTA DI+    +EV++P   I  +     + +EL +
Sbjct: 95  KEIVLKSKSSEAQKAFISIVGPRRVTAQDIELPTSVEVIDPMQHIATITKKVKLNIELKI 154

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES-AREGQVLDYDKLSMTIDTD 208
            K  GY   +         G  T+DA+++PI+ V+Y++       + +  + L   I ++
Sbjct: 155 EKDSGY---RRQNIVEYKDGNFTVDAVFTPIRSVNYSIHCFESHDKSIMKEMLLYEIWSN 211

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVK-EDINVKSLPFNPA-------LLKKV 260
           GSIT E+++  ASR   +    F+  E+ K++ K EDI+ +S   +P+       + KKV
Sbjct: 212 GSITPEEAIYEASRSSINLFLPFLQAEKEKEDFKGEDIH-ESNALHPSVSIVVDQMAKKV 270

Query: 261 -------EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                  E+LELS ++ N L+  N+  + DL+  ++ D+++M NFG+KS   ++ +L  +
Sbjct: 271 TFQHIFIEQLELSPKAYNFLKKINVHTISDLLDYSQDDLMKMKNFGKKS---VEQILEAL 327

Query: 314 GLFLGMNL 321
               GM L
Sbjct: 328 QKRFGMRL 335


>gi|168042925|ref|XP_001773937.1| DNA-directed RNA polymerase alpha chain [Physcomitrella patens
           subsp. patens]
 gi|41688609|sp|P60315|RPOA_PHYPA RecName: Full=DNA-directed RNA polymerase subunit alpha,
           chloroplastic; AltName: Full=Plastid-encoded RNA
           polymerase subunit alpha; Short=PEP; Short=RNA
           polymerase subunit alpha; Flags: Precursor
 gi|34494700|dbj|BAC85012.1| DNA-dircted RNA polymerase alpha chain [Physcomitrella patens]
 gi|34494702|dbj|BAC85013.1| RNA polymerase alpha subunit [Physcomitrella patens]
 gi|162674781|gb|EDQ61285.1| DNA-directed RNA polymerase alpha chain [Physcomitrella patens
           subsp. patens]
          Length = 450

 Score =  131 bits (330), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 96/341 (28%), Positives = 168/341 (49%), Gaps = 26/341 (7%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++ N Q  ++   +E  V G+        ++ P   G A+T+G ++++ L+  + GAA++
Sbjct: 117 LKSNAQSALQWKCVETQVEGERLHYGRFAVS-PFRSGQANTVGVSMQKALLGEVEGAAVS 175

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
                 V  E +++KGV E   DI++N+K + ++   D  ++  I   GPG VTAGDI  
Sbjct: 176 CATFKNVKSEYAAMKGVEETPMDILVNLKELVIRSDSDEPQKAIISAIGPGPVTAGDIVL 235

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              +EV +P   I  L  +  + +EL V KG GY    H ++ +   G   ID+++ P++
Sbjct: 236 PPSLEVTDPTQHIAYLTKEVSLDIELDVEKGCGYRMGDHTKSGD---GRFYIDSVFMPVR 292

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP-KKE 240
             +Y+V S      +  + L + I T+GSIT E+++  A+R L D   +F+ F  P KKE
Sbjct: 293 NANYSVHSYESEPDVTQEILFLEIWTNGSITPEEALHEAARCLID---LFLPFLHPKKKE 349

Query: 241 VKEDINVKSLPFNPALLKK---------------VEELELSVRSTNCLRGENIVYMGDLI 285
           V          F  +                   V++L +  ++ N L+  NI  + DL+
Sbjct: 350 VTNSATKMHKSFTMSQFNSSAEMSAKEVDLRHVYVDQLRIPSKAYNSLKRANINTVSDLL 409

Query: 286 QRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
             T+ D+L + NFGRKS   +  +L  +     ++LP+  P
Sbjct: 410 DYTQDDLLSIPNFGRKS---VDDILEALQAQFSIDLPENNP 447


>gi|154424733|emb|CAL18469.1| RNA polymerase alpha subunit [Streptococcus pasteurianus]
          Length = 173

 Score =  131 bits (330), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 64/159 (40%), Positives = 105/159 (66%)

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+  IILNIKG+ +K   D  K + +   GP  VTAGDI T +D+E++NPDH +  +   
Sbjct: 1   DVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDSDVEIVNPDHYLFTIAEG 60

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             ++  +T++K  GYVPA+ ++ E+ P+G + +D++Y+P+KKV+Y VE AR G    +DK
Sbjct: 61  HSLKATMTIAKNRGYVPAEGNKKEDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDK 120

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           L++ I T+G+I  ED++ L++R+L + L +F +  E  K
Sbjct: 121 LTLEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAK 159


>gi|161511733|emb|CAP16877.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 180

 Score =  131 bits (329), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 68/171 (39%), Positives = 109/171 (63%), Gaps = 2/171 (1%)

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           +I+GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  
Sbjct: 1   TIEGVVEDVTQIILNLKKVSLKVESDEEKSLEINVMGPANVTAGDIVGDGDVTILNPELP 60

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAR 191
           IC +         LT  KG GY  A  +  R  + PIG++ ID++Y+PI++V+Y VE+ R
Sbjct: 61  ICTVAEGTTFHAVLTAEKGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTR 120

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
            GQ  DYDKL++ + TD S+   ++++L+++IL + L +F+N ++  K+ +
Sbjct: 121 VGQRDDYDKLTLDVWTDXSLAASEAISLSAKILTEHLTIFVNLDDQVKDTE 171


>gi|119662345|emb|CAJ33161.1| RNA polymerase alpha subunit [Lactobacillus pontis]
          Length = 160

 Score =  130 bits (327), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 67/160 (41%), Positives = 110/160 (68%), Gaps = 2/160 (1%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+T IILN+K ++LK++ +  K + +  +GP  VTA DIQ   ++ +LNPD  I  
Sbjct: 1   GVTEDVTQIILNLKKVSLKINSEDQKDLELDVKGPAEVTAADIQGDGEVTILNPDLHIAT 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
           +   A + +++T  KG GY+ A  +  R E+  IG++ ID++Y+PI++V+YTVE+AR GQ
Sbjct: 61  VADGAELHIKMTADKGRGYLSANDNKARMEDLAIGVLPIDSIYTPIERVNYTVENARVGQ 120

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
             DYDKL++ + TDGS+T  ++V+L ++IL + L +F++ 
Sbjct: 121 RNDYDKLTLDVWTDGSLTPTEAVSLGAKILTEHLAIFVDL 160


>gi|154424849|emb|CAL18527.1| RNA polymerase alpha subunit [Streptococcus ratti]
          Length = 170

 Score =  130 bits (327), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 63/159 (39%), Positives = 105/159 (66%)

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+  IILN+KG+ +K   +  K + +   GP  +TAGDI T +DIE++NPDH +  +   
Sbjct: 1   DVMQIILNLKGLAVKSYVEEEKIIELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIAEG 60

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
           A ++  LTV    GY+PA+ ++ ++ P+G + ID++Y+P+KKV+Y VE AR G   ++DK
Sbjct: 61  ASLKATLTVGTNRGYIPAEENKKDDAPVGTLAIDSIYTPVKKVNYQVEPARVGSNDNFDK 120

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           L++ I T+G+I  ED++ L++R+L + L +F +  E  K
Sbjct: 121 LTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLPEVAK 159


>gi|169142819|ref|YP_001687243.1| RNA polymerase alpha subunit [Aneura mirabilis]
 gi|153973845|gb|ABS54505.1| RNA polymerase alpha subunit [Aneura mirabilis]
          Length = 342

 Score =  130 bits (327), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 96/314 (30%), Positives = 164/314 (52%), Gaps = 40/314 (12%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P  +G A+T+G A+RR L++ + GA+IT+  I G+ HE S+I G+ E + DI++N+K I 
Sbjct: 37  PFRKGQANTVGIAMRRALLNEIEGASITSATIRGIKHEYSAINGIRESIHDILINLKEII 96

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      ++  I   GP  VTA DIQ  + I V++    +  +     + +EL + K  
Sbjct: 97  LRSDSPEPQKAYICVSGPSEVTARDIQGSSLIHVIDNTQYVATITGKISLDIELDIEKDR 156

Query: 154 GYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVES--AREGQVLDYDKLSMTIDTD 208
           GY      R EN      G   IDA++ PI+  +Y+V S  +RE      + L + I T+
Sbjct: 157 GY------RMENSRKYREGFFPIDAVFMPIRNANYSVHSFGSREKT---KEILLLEIWTN 207

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEP---------KKEVKEDINVKSLPFNPALLKK 259
           GS+T E ++  ASR L D   +FI    P         K++ + D++  ++ F    +++
Sbjct: 208 GSLTPEKALYEASRNLID---LFIPSMNPGGEEKNSGTKEKPESDLSHSTVQFLSTDMEQ 264

Query: 260 -----------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                      +++LEL  R+ NCL+  N+  + DL+   E D++++ NFG++S+ ++  
Sbjct: 265 MTRDVAPKHIFIDQLELPARAYNCLKRVNVHTVADLLDYGENDLMKIKNFGKESIKQVSE 324

Query: 309 VLGTMGLFLGMNLP 322
            L    L   +NLP
Sbjct: 325 ALKKRFL---VNLP 335


>gi|295311758|ref|YP_003587497.1| RNA polymerase a-subunit [Oncidium Gower Ramsey]
 gi|254833135|gb|ACT83138.1| RNA polymerase a-subunit [Oncidium Gower Ramsey]
          Length = 339

 Score =  130 bits (327), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 95/310 (30%), Positives = 163/310 (52%), Gaps = 25/310 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +  PL +G A T+G A+RR L+  + G  IT    + VLHE S I G+ E + DI++N+
Sbjct: 32  FVLSPLMKGQADTIGIAMRRALLGRIEGTCITRATSENVLHEYSMIAGIEESVHDILINL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK +    +  +I  RGP  +TA DI +   +++++    I NL     + +EL +
Sbjct: 92  KEIVLKSNLYGVRDASICVRGPKYITAQDIISPPSVKIVDTTQHIANLTEPIDLCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPI-GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
            +G GY    H ++ N+   G   ID +  P++  ++++ S   G     + L + I T+
Sbjct: 152 KRGRGY----HMKSTNESHDGSYPIDIVSMPVRNANHSIHSYGNGNE-KQEILFLEIWTN 206

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK---- 259
           GS+T ++++  ASR L D L  F++ EE    ++E+    +LP   F      LKK    
Sbjct: 207 GSLTPKEALYEASRNLIDLLIPFLHAEEEDMNLEENEKRWNLPLFSFQDRFTNLKKNKKG 266

Query: 260 -------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                  +++ ELS R+ NCL+  NI  + DL+  ++ D+++M  F    + ++K +LGT
Sbjct: 267 IPLTCIFIDQSELSSRTYNCLKRSNIHTLLDLLNHSQEDLMKMEYF---RIEDVKQILGT 323

Query: 313 MGLFLGMNLP 322
           +     +NLP
Sbjct: 324 LQKHFAINLP 333


>gi|290489666|gb|ADD31217.1| RNA polymerase alpha subunit protein [Meliosma aff. cuneifolia
           Moore 333]
          Length = 337

 Score =  130 bits (327), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 89/309 (28%), Positives = 166/309 (53%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FIMSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSETIPHEYSTIVGIEESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  RGPG VTA DI + + +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTRDASICVRGPGYVTAQDIISPSSVEIVDTTQHIASLTEPINLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            + HGY   +    +N   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNHGY---RMKTPKNSQDGSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF-----NPALLKK----- 259
           S+T ++++  ASR L D    F++ EE    ++++ N  ++PF       A L+K     
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHTEEEDIIIEDNQNRFTVPFFTFHDRLAKLRKNKKEI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++ EL  R+ NCL+  NI  + DL+ +++ D++R+ +F    + ++K +LG +
Sbjct: 268 ALKFIFIDQSELPPRTYNCLKRSNIHTLLDLLNKSQEDLMRIEHF---RIEDVKHILGIL 324

Query: 314 GLFLGMNLP 322
                +NLP
Sbjct: 325 QKHFEINLP 333


>gi|150186957|emb|CAK30136.1| RNA polymerase alpha subunit [Streptococcus hyointestinalis]
          Length = 171

 Score =  130 bits (327), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 64/159 (40%), Positives = 105/159 (66%)

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+  IILN+KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +   
Sbjct: 1   DVMQIILNVKGLAVKSYVEDEKMIELDVEGPAEVTAGDILTDSDIEIVNPDHYLFTIAEG 60

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             ++  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DK
Sbjct: 61  HSLKATMTVAKNRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDK 120

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           L++ I T+G+I  ED++ L++RIL + L +F +  E  K
Sbjct: 121 LTVEIMTNGTIIPEDALGLSARILIEHLNLFTDLTEVAK 159


>gi|69215828|gb|AAZ03870.1| RNA polymerase alpha chain [Yucca schidigera]
          Length = 337

 Score =  130 bits (326), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 97/309 (31%), Positives = 162/309 (52%), Gaps = 25/309 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + V HE S+I G+ E + +I +N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKVPHEYSTIVGIEESVHEIFINL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L + G   +  +I  RGP  VTA DI +   +E+++    I NL     +R+EL +
Sbjct: 92  KEIVLNLYGV--RDASICVRGPRYVTAQDIISPPSVEIVDTTQHIANLTEPIDLRIELQI 149

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   + + T N   G   IDA+  P++  ++++ S   G     + L + I T+G
Sbjct: 150 KRDRGY---RINPTNNSQDGSYPIDAVSMPVRNANHSIHSYGNGNE-KQEILFLEIWTNG 205

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  +LP   F   L  LKK     
Sbjct: 206 SLTPKEALYEASRNLIDLFIPFLHAEEGDIHFEENKNRFTLPLFTFQNRLTNLKKNKKGI 265

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R+ NCL+  NI  + DL+  ++ D++R+  F  +   ++K +L T+
Sbjct: 266 PLKCIFIDQLELPPRTYNCLKRSNIHTLLDLLSNSQEDLMRIEYFRTE---DVKQILDTL 322

Query: 314 GLFLGMNLP 322
                +NLP
Sbjct: 323 QKHFAINLP 331


>gi|119662293|emb|CAJ33133.1| RNA polymerase alpha subunit [Lactobacillus coryniformis subsp.
           torquens KCTC 3535]
          Length = 161

 Score =  130 bits (326), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 62/152 (40%), Positives = 100/152 (65%)

Query: 88  NIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           NIK + LK+  D  K + I  +GP  VTAGDI+   D+E+LNPD  IC +       + +
Sbjct: 1   NIKKLALKLDSDDDKTLEIDVKGPATVTAGDIEADGDVEILNPDLYICTVAEGGRFHIRM 60

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           T  KG GYV A  ++ ++ PIG++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T
Sbjct: 61  TAHKGRGYVAADGNKVDDMPIGVLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWT 120

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +GSI+  ++++LA++IL + L +F+N  +  K
Sbjct: 121 NGSISPREAISLAAKILTEHLDIFVNLTDEAK 152


>gi|228016583|gb|ACP51413.1| RNA polymerase alpha subunit [Abies firma]
          Length = 336

 Score =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 91/306 (29%), Positives = 153/306 (50%), Gaps = 24/306 (7%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V++D + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLCKGRADTIGIAMRRALLGEVEGTCITHVKLDNIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITFDIRLRIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIR-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPK----KEVKEDINVKSLPFNPALLKK---------- 259
            +++  ASR L D L  F++ EE         K   N+   P +                
Sbjct: 212 REALYEASRNLIDLLIPFLHGEEQNIDGMNNRKGSSNMPPFPLSHVFTDTGETKEKIAFQ 271

Query: 260 ---VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +++LEL  R+ NCLR  NI  + DL+  +  D++R+ +FG++S   I+ VL  +   
Sbjct: 272 HIFIDQLELPPRTYNCLRRANIHTLLDLLNYSREDLMRIEHFGKES---IEQVLEVLRKR 328

Query: 317 LGMNLP 322
             +NLP
Sbjct: 329 FAINLP 334


>gi|291533601|emb|CBL06714.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Megamonas
           hypermegale ART12/1]
          Length = 179

 Score =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 68/142 (47%), Positives = 95/142 (66%), Gaps = 1/142 (0%)

Query: 24  EENRT-LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E+NR    + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE S+I GV +D+
Sbjct: 16  EDNRYGKFVCEPLERGYGTTLGNSLRRILLSSLEGAAITSIKIDGVLHEFSTIPGVRDDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T+IILN+K + LKM  +    + I   G   VTA DI   +DIE+LN D  I  +D    
Sbjct: 76  TNIILNLKELCLKMHDEEPHTIRIDVTGEKEVTAADIIVDSDIEILNKDLHIATVDETGS 135

Query: 143 VRMELTVSKGHGYVPAKHHRTE 164
           ++ME+ V +G GY PA  ++ +
Sbjct: 136 LKMEMVVERGRGYTPADKNKNQ 157


>gi|119663526|emb|CAK22334.1| RNA polymerase alpha subunit [Lactobacillus paracollinoides]
          Length = 154

 Score =  129 bits (325), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 71/154 (46%), Positives = 103/154 (66%), Gaps = 3/154 (1%)

Query: 77  GVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           GV ED+T IILN K I+LK+ G  D  + + I  +GP  VTAGDI   +D+ VLNPD  I
Sbjct: 1   GVVEDVTQIILNTKKISLKLEGPDDEIESMEIDVKGPAQVTAGDITADSDVTVLNPDLYI 60

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREG 193
             +   A   M +T +KG GYV A  ++ + D PIG++ ID++Y+PI++V+Y VE+ R G
Sbjct: 61  ATVAEGATFHMRMTANKGRGYVSADRNKAKEDMPIGVLPIDSIYTPIERVNYQVENTRVG 120

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           Q  DYDKL++ + TD SIT  +S++LA++IL + 
Sbjct: 121 QRDDYDKLTLDVWTDNSITPSESISLAAKILTEH 154


>gi|58758766|gb|AAW81772.1| RNA polymerase alpha subunit [Buxbaumia aphylla]
          Length = 340

 Score =  129 bits (323), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 90/305 (29%), Positives = 160/305 (52%), Gaps = 23/305 (7%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P   G A+T+G A+RR L+  ++G +IT  + + V HE S+I G+ E + DI +N K I 
Sbjct: 36  PFRCGQANTVGIAMRRALLGEVKGTSITCAKFEKVTHEYSTIAGIQESVHDISINSKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+ +    ++  I   GP  +TA DI     +++++    I  L     + +EL + K +
Sbjct: 96  LESNSSETQKAFISILGPKKITAQDIILPPSVKIIDGKQYIATLTKAIQLDIELEIEKDY 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY     +++ N       IDA++ PI+  +Y+V S  E +    + L + I T+GSIT 
Sbjct: 156 GYRIQNSNKSTNSH---FFIDAIFMPIRNANYSVHSF-ENENKTQEMLFIEIWTNGSITP 211

Query: 214 EDSVALASRILQDQLGMFINFE--EPKKEVKEDINVKSL-------PFNPALLKKV---- 260
           +D++  ASR L D    F++ E  E   E++ +  + ++       P    + K+V    
Sbjct: 212 KDALYEASRSLIDLFIPFLHAERREIINELENEYKLSNISYFSSFSPLADKITKEVSFKH 271

Query: 261 ---EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
              ++LEL  R+ NCL+  N+  + DL+  ++ D++++ NFG+KS   ++ VL  +    
Sbjct: 272 IFIDQLELPARAYNCLKRVNVNTLADLLNYSQEDLMKIKNFGKKS---VEQVLEALQKQF 328

Query: 318 GMNLP 322
            +NLP
Sbjct: 329 SINLP 333


>gi|309322375|ref|YP_003934455.1| RNA polymerase alpha chain [Cathaya argyrophylla]
 gi|307683301|dbj|BAJ19608.1| RNA polymerase alpha chain [Cathaya argyrophylla]
          Length = 335

 Score =  129 bits (323), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 85/297 (28%), Positives = 153/297 (51%), Gaps = 20/297 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +  PL +G A T+G A+RR L+  ++G  IT V+++ + HE S+I G+ E + DI++N+
Sbjct: 32  FVLSPLRKGRADTIGIAMRRALLGEVKGTCITHVKLENIKHEYSAIIGIEESVHDILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+      +  +I+  GP  VTA DI     +++++    I  L       + L +
Sbjct: 92  KEIVLRSDSYGIQEASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITFDIRLRI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            K  GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G
Sbjct: 152 EKNRGYLI---HSPTNYGDGIFPIDAVFMPVRDANYSIHSYGSGNEIR-EVLFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALLKK------- 259
            +T  +++  ASR L +    F++ EE   +    ++  N+ S P +  L          
Sbjct: 208 GLTPREALYEASRNLINFFIPFLHGEEQNIDGMNSRKGSNIPSFPLSHVLTNTGETKEIF 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++LEL  R  NCLR  NI  + DL+  ++ D++R+  FG+KS+ ++  +L
Sbjct: 268 EFQHIFIDQLELPSRIYNCLRRANIYTLLDLLNYSQEDLMRIEQFGKKSVEQVLEIL 324


>gi|325989737|ref|YP_004249436.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma suis KI3806]
 gi|323574822|emb|CBZ40482.1| DNA-directed RNA polymerase subunit alpha (RNAP subunit alpha)
           [Mycoplasma suis]
          Length = 337

 Score =  129 bits (323), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 92/318 (28%), Positives = 161/318 (50%), Gaps = 37/318 (11%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E    ++  PL RG  +T+GN LRR+L+SS+   A+ A+++ G+ HE S IKGV ED+T 
Sbjct: 18  ETSASVVFYPLERGLGNTIGNTLRRLLLSSIPSPAVFAIRVAGLPHEFSPIKGVAEDVTQ 77

Query: 85  IILNIKGINL----KMSGDSHKR---------VTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
           +I+ IK + L    K++   H +         + I K   GVV A DI+    +EV+NP+
Sbjct: 78  LIIAIKKLVLKVDEKIADFEHLKDLPIEKWPFLKIRKSKVGVVQAKDIECFAGVEVVNPE 137

Query: 132 HVICNLDVDAV-VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
             +C +  +   + ++L      G+  +  +R     + LI ID  +SP+  V + V   
Sbjct: 138 LKLCEITEEGTSLEIDLYCMVDRGHRSSNENRERLSTLSLIPIDTTFSPVLLVDWKVSEE 197

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV--------- 241
           +  +    D+L + + T+GSI   D+V  A++IL   + MF    E   E+         
Sbjct: 198 KTTKYGISDRLRLNVSTNGSIKALDAVWYAAKIL---ISMFTKIAEHDVELFKLDSYAKK 254

Query: 242 -----KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
                KE+++  S+  +P     +E+LEL+ R+ N L+   I  + +L+  +  ++    
Sbjct: 255 VDRKEKEEVH-SSISSSP-----IEDLELTQRTFNILKNSGINTISELVAYSFDELAEFR 308

Query: 297 NFGRKSLVEIKGVLGTMG 314
           N G+K+L+E++  L   G
Sbjct: 309 NLGKKALLEVQAKLEERG 326


>gi|118430333|ref|YP_874768.1| RNA polymerase alpha subunit [Agrostis stolonifera]
 gi|125987636|sp|A1EA40|RPOA_AGRST RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|118201242|gb|ABK79611.1| RNA polymerase alpha subunit [Agrostis stolonifera]
          Length = 339

 Score =  129 bits (323), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 96/308 (31%), Positives = 160/308 (51%), Gaps = 23/308 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    + + K +  T+
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIESF---RMEDRKQIWDTL 324

Query: 314 GLFLGMNL 321
             +L M+L
Sbjct: 325 EKYLPMDL 332


>gi|325973301|ref|YP_004250365.1| DNA-directed RNA polymerase, subunit alpha [Mycoplasma suis str.
           Illinois]
 gi|323651903|gb|ADX97985.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma suis str.
           Illinois]
          Length = 340

 Score =  128 bits (322), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 92/318 (28%), Positives = 161/318 (50%), Gaps = 37/318 (11%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E    ++  PL RG  +T+GN LRR+L+SS+   A+ A+++ G+ HE S IKGV ED+T 
Sbjct: 21  ETSASVVFYPLERGLGNTIGNTLRRLLLSSIPSPAVFAIRVAGLPHEFSPIKGVAEDVTQ 80

Query: 85  IILNIKGINL----KMSGDSHKR---------VTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
           +I+ IK + L    K++   H +         + I K   GVV A DI+    +EV+NP+
Sbjct: 81  LIIAIKKLVLKVDEKIADFEHLKDLPIEKWPFLKIRKSKVGVVQAKDIECFAGVEVVNPE 140

Query: 132 HVICNLDVDAV-VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
             +C +  +   + ++L      G+  +  +R     + LI ID  +SP+  V + V   
Sbjct: 141 LKLCEITEEGTSLEIDLYCMVDRGHRSSNENRERLSTLSLIPIDTTFSPVLLVDWKVSEE 200

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV--------- 241
           +  +    D+L + + T+GSI   D+V  A++IL   + MF    E   E+         
Sbjct: 201 KTTKYGISDRLRLNVSTNGSIKALDAVWYAAKIL---ISMFTKIAEHDVELFKLDSYAKK 257

Query: 242 -----KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
                KE+++  S+  +P     +E+LEL+ R+ N L+   I  + +L+  +  ++    
Sbjct: 258 VDRKEKEEVH-SSISSSP-----IEDLELTQRTFNILKNSGINTISELVAYSFDELAEFR 311

Query: 297 NFGRKSLVEIKGVLGTMG 314
           N G+K+L+E++  L   G
Sbjct: 312 NLGKKALLEVQAKLEERG 329


>gi|313678392|ref|YP_004056132.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma bovis PG45]
 gi|312950669|gb|ADR25264.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma bovis PG45]
          Length = 336

 Score =  128 bits (322), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 97/313 (30%), Positives = 161/313 (51%), Gaps = 24/313 (7%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           N      +PL RGF +T+  ALRRVL+S++   A+ A++I GV HE  +I G+ ED+T I
Sbjct: 22  NEVTFSLKPLERGFGNTVAVALRRVLLSNVTSLALFAIKISGVSHEFQTIPGIVEDVTAI 81

Query: 86  ILNIKGINLKMSGDSHK-----RVTIFKRGPGVVTAGDIQTVN-DIEVLNPDHVICNLDV 139
           I+N++ +  K + +  K     + TI    PG+VT+  I+  N  +E++N    I N+  
Sbjct: 82  IMNLRKVKFKYNPEFVKDGEIIKATIKAEQPGIVTSKSIEITNPSVEIINKSQEIANIQK 141

Query: 140 DAVVRMELTVSKGHGYVPAKHHRT--ENDPI-----------GL-ITIDALYSPIKKVSY 185
            ++V +EL +  G G++  + ++   +ND +           GL I +D+ +SP++K SY
Sbjct: 142 GSLV-IELFLRPGRGFISNESNKKFIQNDSLFASKIESNIKKGLFIAVDSNFSPVEKCSY 200

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TV           ++L  TI TDG+I  + ++  A +IL        + +  K +V E+ 
Sbjct: 201 TVRELNTSSNKIEEELLFTIKTDGTIDAKSAINQACKILVAHFMAVGDVDSMKLDVFEEE 260

Query: 246 NVKS-LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
            VK+  P    +   + +L LSVRS N L+        ++   T  ++ +  N GRKSL 
Sbjct: 261 KVKNDEPIENDV--DINQLGLSVRSLNALKRIGKTKASEVAAMTWEELEQTKNLGRKSLD 318

Query: 305 EIKGVLGTMGLFL 317
           EI+  L   G  L
Sbjct: 319 EIQECLKVNGFTL 331


>gi|148377782|ref|YP_001256658.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma agalactiae
           PG2]
 gi|148291828|emb|CAL59218.1| DNA directed RNA polymerase alpha chain (RNAPalpha subunit)
           (Transcriptase alpha chain) (RNApolymerase alpha
           subunit) [Mycoplasma agalactiae PG2]
          Length = 336

 Score =  128 bits (322), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 100/325 (30%), Positives = 164/325 (50%), Gaps = 46/325 (14%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           N      +PL RGFA+T+  ALRRVL+S++   A+ A++I GV HE  +I G+ ED+T I
Sbjct: 22  NEVTFSLKPLERGFANTVAVALRRVLLSNITSLALFAIKISGVSHEFQTIPGIVEDVTAI 81

Query: 86  ILNIKGINLKMSGDSHK-----RVTIFKRGPGVVTAGDIQTVN-DIEVLNPDHVICNLDV 139
           I+N++ +  K + +  K     + TI    PGVVT+  I+  N  +E++N    I N+  
Sbjct: 82  IMNLRKVKFKYNPEFVKDGEIIKATIKAEQPGVVTSKSIEISNPSVEIINKSQEIANIQK 141

Query: 140 DAVVRMELTVSKGHGYVPAKHHRT--ENDPI-----------GL-ITIDALYSPIKKVSY 185
            A+V +EL +  G G++  + ++   +ND +           GL I +D+ +SP++K SY
Sbjct: 142 GALV-IELFLRPGRGFISNESNKKFIQNDSLFASKIESNIKKGLFIAVDSNFSPVEKCSY 200

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL-------GMFIN-FEEP 237
           TV+          ++L  TI TDG++  + ++  A +IL            M I+ FEE 
Sbjct: 201 TVKELNTSSNKIEEELLFTIKTDGTVDAKSAINQACKILVAHFMTVGDVDAMKIDVFEEE 260

Query: 238 K----KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           K    + ++ D+++              +L LSVRS N L+        ++   T  ++ 
Sbjct: 261 KINNDEPIENDVDIN-------------QLGLSVRSLNALKRIGKTKASEVAAMTWEELE 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLG 318
           +  N GRKSL EI+  L   G  L 
Sbjct: 308 QTKNLGRKSLDEIQECLKLNGFTLN 332


>gi|323149114|ref|YP_004222678.1| RNA polymerase alpha subunit [Anthriscus cerefolium]
 gi|289645607|gb|ADD13670.1| RNA polymerase alpha subunit [Anthriscus cerefolium]
          Length = 338

 Score =  128 bits (322), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 93/312 (29%), Positives = 161/312 (51%), Gaps = 25/312 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + D + HE S++ G+ E + DI++N+
Sbjct: 32  FIMSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFDKIPHEYSTLMGIQESVHDILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGPG VTA DI     +EV++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTCDASICVRGPGYVTAQDIILPPYVEVVDNTQHIASLTEPIELCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK---LSMTID 206
            +  GY+    +    D  G   IDA++ P++  ++++ S   G     DK   L + I 
Sbjct: 152 ERNRGYLIKTPNNNSQD--GSYPIDAVFMPVRNANHSIHSYGNGN----DKQEILFLEIW 205

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLKK---- 259
           T+GS+T ++++  ASR L D    F++ EE    + ++ ++  LP   F+  L KK    
Sbjct: 206 TNGSLTPKEALHEASRNLIDLFITFLHTEEENLHLADNQHMVPLPPFTFHDKLRKKQKKI 265

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++ EL  R  NCL+  NI  + DL+  ++ D++++  F  K   ++K +LG +
Sbjct: 266 ALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQKDLMKIDRFRIK---DVKHILGIL 322

Query: 314 GLFLGMNLPDWP 325
              L ++LP  P
Sbjct: 323 EKHLSIDLPKKP 334


>gi|118614523|ref|YP_899439.1| RNA polymerase alpha subunit [Sorghum bicolor]
 gi|125987638|sp|A1E9V6|RPOA_SORBI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|118201157|gb|ABK79527.1| RNA polymerase alpha subunit [Sorghum bicolor]
          Length = 339

 Score =  128 bits (321), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 94/312 (30%), Positives = 159/312 (50%), Gaps = 29/312 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGNVPHEYSTIVGIEESIQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLREPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY       +++   G   IDA++ P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYHTELRKNSQD---GSYPIDAVFMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFIN-------FEEPKKEVKEDI------------NVKSL 250
           S+T ++++  ASR L D    FI+       FEE K  +   +            N K +
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFIHTEEEGTSFEESKNRLTPPLLTFQKRFTNLKKNKKGI 267

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           P N      +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    + + K + 
Sbjct: 268 PLNCIF---IDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRINSF---RMEDGKLIW 321

Query: 311 GTMGLFLGMNLP 322
            T+   L ++LP
Sbjct: 322 DTLEKHLPIDLP 333


>gi|260677450|ref|YP_003208218.1| RNA polymerase alpha subunit [Coix lacryma-jobi]
 gi|209361388|gb|ACI43303.1| RNA polymerase alpha subunit [Coix lacryma-jobi]
          Length = 339

 Score =  128 bits (321), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 95/309 (30%), Positives = 160/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGNVPHEYSTIVGIEESIQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTTQPIANLREPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY       +++   G   IDA++ P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYHTELRKNSQD---GSYPIDAVFMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    FI+ EE     +E+ N  + P   F      LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFIHTEEEGTSFEENKNRLTPPLLTFQKRFTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    + + K +  T+
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRSNIHTLLDLLSKTEEDLMRINSF---RMEDGKLIWDTL 324

Query: 314 GLFLGMNLP 322
              L ++LP
Sbjct: 325 EKHLPIDLP 333


>gi|150187084|emb|CAK30167.1| RNA polymerase alpha subunit [Streptococcus hyovaginalis]
          Length = 165

 Score =  128 bits (321), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 63/163 (38%), Positives = 106/163 (65%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+  IILN+KG+ +K   +  K + +  +GP  VTAGDI T +D+E++N DH +  
Sbjct: 1   GVREDVMQIILNVKGLAVKSYVEDEKIIELDVQGPAEVTAGDILTDSDVEIVNSDHYLFT 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +   A  +  +TV+   GYV A+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G   
Sbjct: 61  IAEGASFKASMTVATNRGYVAAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSND 120

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
            +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K
Sbjct: 121 GFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAK 163


>gi|307683477|dbj|BAJ19717.1| RNA polymerase alpha chain [Pseudotsuga sinensis var. wilsoniana]
          Length = 335

 Score =  128 bits (321), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 88/293 (30%), Positives = 149/293 (50%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RRVL+  + G  IT VQ D + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRVLLGEVEGTCITHVQFDNIKHEYSAIIGIEESVHDILVNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLRIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYI---MHSPNNYKDGIFPIDAVFMPVRDANYSIHSYGSGNEIR-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALLKK----------- 259
            +++  ASR L D    F++ EE   +    ++  N+   P +  L              
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNNRKGSNMPPFPLSHVLTDTRETIEKIAFQY 271

Query: 260 --VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  R  NCLR  NI  + DL+  +  D++R+ N G++S+ ++  VL
Sbjct: 272 IFIDQLELPPRIYNCLRRANIHTLLDLLNYSREDLMRIENLGKESVEQVLEVL 324


>gi|22711961|ref|NP_683832.1| RNA polymerase alpha subunit [Chaetosphaeridium globosum]
 gi|25009134|sp|Q8M9V7|RPOA_CHAGL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|22416965|gb|AAM96565.1| alpha subunit of RNA polymerase [Chaetosphaeridium globosum]
          Length = 334

 Score =  128 bits (321), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 89/295 (30%), Positives = 156/295 (52%), Gaps = 30/295 (10%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A+T+G ALRR L+S + G  IT+V+I   +HE SS+ GV E + DI++N+
Sbjct: 32  FIISPLWKGQANTIGLALRRTLLSEVEGTCITSVKIKNAIHEYSSLSGVQESVHDILINL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L  S        +   GP  V A D+   + I+++NPD  I  ++      +++ +
Sbjct: 92  KKIILSSSFSGIFEGFLSVVGPKTVLASDLNLPSFIKIVNPDQYIATVNKPINFNLQIYI 151

Query: 150 SKGHGYVPAKHHRTENDPI----GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
            KG GY       +  +PI    G   +D ++ PI+ V+Y++ S  + +    + L + +
Sbjct: 152 QKGKGY-------SLKNPISIKQGFFLVDPVFIPIRSVNYSIHSFEDEKATK-EFLIVEV 203

Query: 206 DTDGSITGEDSVALASRILQDQLGMFIN--FEEPKKEV-KEDINVKSLPF---------- 252
            T+GSI  ++++  AS  L +     ++  +++ K ++ KED   K L F          
Sbjct: 204 WTNGSIEPKEAIKEASYNLVNLFTPLVSQEYQQLKNQLFKEDEKNKELNFIETNSNAISD 263

Query: 253 ---NPALLKKV--EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +  L  ++  ++LELS R+ N L+  NI  + DL++ +  D+L++ NFG+KS
Sbjct: 264 NENSYNLYNQIFLDQLELSSRAYNSLKKNNINTISDLLKYSYEDLLKIKNFGKKS 318


>gi|48478801|ref|YP_024408.1| RNA polymerase alpha subunit [Saccharum hybrid cultivar SP-80-3280]
 gi|50812559|ref|YP_054661.1| RNA polymerase alpha subunit [Saccharum officinarum]
 gi|68053147|sp|Q6ENT2|RPOA_SACOF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|75261480|sp|Q6L370|RPOA_SACHY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|48478703|gb|AAT44723.1| RNA polymerase alpha chain [Saccharum hybrid cultivar SP80-3280]
 gi|49659543|dbj|BAD27324.1| RNA polymerase alpha subunit [Saccharum hybrid cultivar NCo 310]
          Length = 339

 Score =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 95/309 (30%), Positives = 160/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFWNVPHEYSTIVGIEESIQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTTQPIANLREPVDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY       +++   G   IDA++ P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYHTELRKNSQD---GSYPIDAVFMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    FI+ EE     +E+ N  + P   F      LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFIHTEEEGTSFEENKNRLTPPLLTFQKRFTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    + + K +  T+
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRINSF---RMEDGKLIWDTL 324

Query: 314 GLFLGMNLP 322
              L ++LP
Sbjct: 325 EKHLPIDLP 333


>gi|291320469|ref|YP_003515733.1| DNA directed RNA polymerase subunit alpha (RNAPsubunit alpha)
           (Transcriptase subunit alpha) (RNApolymerase subunit
           alpha) [Mycoplasma agalactiae]
 gi|290752804|emb|CBH40779.1| DNA directed RNA polymerase alpha chain (RNAPalpha subunit)
           (Transcriptase alpha chain) (RNApolymerase alpha
           subunit) [Mycoplasma agalactiae]
          Length = 336

 Score =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 97/314 (30%), Positives = 162/314 (51%), Gaps = 24/314 (7%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           N      +PL RGFA+T+  ALRRVL+S++   A+ A++I GV HE  +I G+ ED+T I
Sbjct: 22  NEVTFSLKPLERGFANTVAVALRRVLLSNITSLALFAIKISGVSHEFQTIPGIVEDVTAI 81

Query: 86  ILNIKGINLKMSGDSHK-----RVTIFKRGPGVVTAGDIQTVN-DIEVLNPDHVICNLDV 139
           I+N++ +  K + +  K     + TI    PGVVT+  I+  N  +E++N    I N+  
Sbjct: 82  IMNLRKVKFKYNPEFVKDGEIIKATIKAEQPGVVTSKSIEISNPSVEIINKSQEIANIQK 141

Query: 140 DAVVRMELTVSKGHGYVPAKHHR--TENDPI-----------GL-ITIDALYSPIKKVSY 185
            A+V +EL +  G G++  + ++   +ND +           GL I +D+ +SP++K SY
Sbjct: 142 GALV-IELFLRPGRGFISNESNKRFIQNDSLFASKIESNIKKGLFIAVDSNFSPVEKCSY 200

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TV+          ++L  TI TDG++  + ++  A +IL        + +  K +V E+ 
Sbjct: 201 TVKELNTSSNKIEEELLFTIKTDGTVDAKSAINQACKILVAHFMTVGDVDTMKIDVFEEE 260

Query: 246 NVKS-LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
            + +  P    +   + +L LSVRS N L+        ++   T  ++ +  N GRKSL 
Sbjct: 261 RINNDEPIENDV--DINQLGLSVRSLNALKRIGKTKASEVAAMTWEELEQTKNLGRKSLD 318

Query: 305 EIKGVLGTMGLFLG 318
           EI+  L   G  L 
Sbjct: 319 EIQECLKLNGFTLN 332


>gi|154424729|emb|CAL18467.1| RNA polymerase alpha subunit [Streptococcus gallolyticus]
          Length = 167

 Score =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 64/159 (40%), Positives = 104/159 (65%)

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+  IILNIKG+ +K   D  K + +   GP  VTAGDI T +D+E++NPDH +  +   
Sbjct: 1   DVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDSDVEIVNPDHYLFTIAEG 60

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             ++  +TV+K  GYV A+ ++ E+ P+G + +D++Y+P+KKV+Y VE AR G    +DK
Sbjct: 61  HSLKATMTVAKERGYVSAEGNKKEDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDK 120

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           L++ I T+G+I  ED++ L++R+L + L +F +  E  K
Sbjct: 121 LTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAK 159


>gi|150036752|emb|CAM98261.1| DNA-directed RNA polymerase alpha chain [Leuconostoc lactis]
          Length = 187

 Score =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 67/166 (40%), Positives = 104/166 (62%), Gaps = 2/166 (1%)

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+Q   D+EVLNP
Sbjct: 1   EFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDVQGPAEVTAADLQAGADVEVLNP 60

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVE 188
           D  I  +     + M +T  KG GY  A  ++   E  PIG++ +D++Y+PI++V+Y VE
Sbjct: 61  DLHIATVAAGKSLHMTVTAVKGRGYSSADENKQLREEMPIGVLAVDSIYTPIERVNYHVE 120

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           + R G   DYDKL+  I T+GSI   D+++L ++IL + L +F++ 
Sbjct: 121 NTRVGARDDYDKLTFDIWTNGSIKPSDALSLGAKILAEHLNLFMDI 166


>gi|22657270|gb|AAM97438.1| RNA polymerase alpha subunit [Elymus canadensis]
 gi|22657294|gb|AAM97450.1| RNA polymerase alpha subunit [Elymus virginicus]
 gi|22657296|gb|AAM97451.1| RNA polymerase alpha subunit [Elymus virginicus]
 gi|22657298|gb|AAM97452.1| RNA polymerase alpha subunit [Elymus virginicus]
          Length = 339

 Score =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 90/285 (31%), Positives = 149/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF--------NPALLKK-- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P         NP   KK  
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNPKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF 312


>gi|150186949|emb|CAK30134.1| RNA polymerase alpha subunit [Streptococcus dysgalactiae subsp.
           dysgalactiae]
          Length = 161

 Score =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 63/159 (39%), Positives = 105/159 (66%)

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+  IILN+KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +   
Sbjct: 1   DVMQIILNVKGLAVKSYVEDEKIIELEVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEG 60

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             +R  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DK
Sbjct: 61  HSLRATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDK 120

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           L++ I T+G+I  ED++ L++R+L + L +F +  +  K
Sbjct: 121 LTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTDVAK 159


>gi|41688710|sp|Q8MAJ0|RPOA_AEGUN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|22657234|gb|AAM97420.1| RNA polymerase alpha subunit [Aegilops uniaristata]
          Length = 339

 Score =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 92/285 (32%), Positives = 151/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + GA IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGACITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF 312


>gi|290489654|gb|ADD31211.1| RNA polymerase alpha subunit protein [Antirrhinum majus]
          Length = 336

 Score =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 90/308 (29%), Positives = 163/308 (52%), Gaps = 22/308 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT V+ + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRVKSENIPHEYSTITGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGPG VTA DI     +E+++    I +L       + L +
Sbjct: 92  KEIVLRTNLYGTCDASICARGPGYVTAQDIILPPYVEIVDNTQHIASLTEPINFCIGLEI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY+    H  ++   G  +IDA++ P++ V++++ S   G     + L + I T+G
Sbjct: 152 ERNRGYLIKMPHNFQD---GSYSIDAVFMPVRNVNHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEE---PKKEVKEDINVKSLPFNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE   P  + +  I +    F+  L  L+K     
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHKEEENLPLDDNQHTIPLSPFSFHDKLDKLRKNKKIA 267

Query: 260 -----VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +++ ELS R+ NCL+  NI  + DL+  ++ D++++ +F    L ++K +LG + 
Sbjct: 268 LKSIFIDQSELSPRAYNCLKRSNIYTLFDLLNNSQEDLMKIEHF---RLKDVKEILGILE 324

Query: 315 LFLGMNLP 322
               ++LP
Sbjct: 325 KHFAIDLP 332


>gi|311990456|gb|ADQ26358.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii]
          Length = 185

 Score =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 65/155 (41%), Positives = 96/155 (61%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+T IILN+K + L+   +  K + +   GP  VTA D++   D+EVLNPD  IC 
Sbjct: 2   GVKEDVTKIILNLKKLVLRAYTEEVKTIELDVEGPATVTAEDLKADADVEVLNPDQYICT 61

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +     + M + V  G GYVPA  +++    IG I +D+L+SPI+KV+Y VES R G+  
Sbjct: 62  IAQGGHLHMWIDVCNGRGYVPASENKSAEMSIGDIPVDSLFSPIEKVNYQVESTRVGKRE 121

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           D+DKL++ I T+GSI   D++  A+R+L +    F
Sbjct: 122 DFDKLTLEIWTNGSIAPNDALNFAARVLVEHFKAF 156


>gi|119662809|emb|CAJ33196.1| RNA polymerase alpha subunit [Lactobacillus perolens]
          Length = 138

 Score =  127 bits (319), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 61/135 (45%), Positives = 94/135 (69%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+T IILNIK + LK++ D  K V I   GP  VTA +I T +D+E+LNP+  IC 
Sbjct: 1   GVLEDVTQIILNIKKLALKLNTDQEKTVEIDAEGPATVTAANIITDDDVEILNPEQYICT 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +     + M +TV  G GYVPA  +++++ PIG++ +D++++PI++V+Y VES R G+  
Sbjct: 61  IANGGHLHMRMTVKTGRGYVPADQNKSDDMPIGVLPVDSIFTPIERVNYQVESTRVGKRN 120

Query: 197 DYDKLSMTIDTDGSI 211
           D+DKL++ + T+GSI
Sbjct: 121 DFDKLTLAVWTNGSI 135


>gi|187233921|gb|ACD01207.1| RNA polymerase alpha subunit [Phyllostachys propinqua]
          Length = 339

 Score =  127 bits (318), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 95/309 (30%), Positives = 160/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY       +++   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYHTELRKNSQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLLTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    + + K +  T+
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---RMEDGKQIWDTL 324

Query: 314 GLFLGMNLP 322
              L ++LP
Sbjct: 325 EKHLPIDLP 333


>gi|124302938|ref|YP_001023733.1| RNA polymerase alpha subunit [Angiopteris evecta]
 gi|158512827|sp|A2T365|RPOA_ANGEV RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|110628336|gb|ABG79632.1| RNA polymerase alpha subunit [Angiopteris evecta]
          Length = 341

 Score =  127 bits (318), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 90/308 (29%), Positives = 156/308 (50%), Gaps = 28/308 (9%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P  +G A+T+G A+RR L+  + G AIT  +   V+HE S+I G+ E + DI++N K I 
Sbjct: 36  PFRKGQANTVGIAIRRSLLGEIEGTAITYAKSKNVIHEYSTIIGIEESINDILINFKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      ++  I   GP  +TA DI     ++ ++    I  +  D  + +E+ + K  
Sbjct: 96  LRSDSYETQKAYISITGPKDITAEDILLPPSVQAIDDSQHIATITKDITLDIEIEIQKDR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY   +   ++    G   IDA++ PI+K +Y+V S    +    + L + I TDGS+T 
Sbjct: 156 GY---RIQDSKESQAGEFFIDAVFMPIRKANYSVHSFGNNKKFQ-EILFIEIWTDGSLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK-------------- 259
           ++++  ASR L D    F++ EE  +E+  D + KS      LL                
Sbjct: 212 KEALYEASRNLIDLFLPFLHTEE--EEIISDRDEKSESNGNILLSNSISTDIDRMAKEVA 269

Query: 260 -----VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +++LEL  R+ NCL+  ++  + DL++ ++ D+ ++ NFG+KS   +  VL  + 
Sbjct: 270 FKHIFIDQLELPARAYNCLKKVDVHTISDLLKYSQDDLRKIKNFGKKS---VDQVLEALQ 326

Query: 315 LFLGMNLP 322
               +NLP
Sbjct: 327 ERFAINLP 334


>gi|313183899|ref|YP_004021753.1| RNA polymerase alpha subunit [Equisetum arvense]
 gi|281371619|gb|ADA63552.1| RNA polymerase alpha subunit [Equisetum arvense]
          Length = 337

 Score =  127 bits (318), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 87/287 (30%), Positives = 151/287 (52%), Gaps = 19/287 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P  +G A+T+G A+RR L+  + G +IT+ +  G  HE S++ G+ E + DI++N+K I 
Sbjct: 36  PFQKGQANTVGIAIRRALLGEVGGTSITSAKFQGAAHEYSTMAGIQESIHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+ +    ++  I   GP  + AGDIQ  + +++++P   I  +     + +EL + K  
Sbjct: 96  LENNSYEVQKGFIQVIGPKKILAGDIQVCSSVKIIDPSQYIATITKSISLNIELKIEKDR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY        EN+      IDA++ PI+  +Y+V S ++ + L Y+ L + I T+GS+T 
Sbjct: 156 GYRIKNTDLKENE----FPIDAIFMPIRNANYSVHSFQKNKQL-YEILFLEIWTNGSLTP 210

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEV----KEDINVKSLPFNPALLKKVEE------- 262
           E +++ A+R L D +   I+  +   E       DIN  S+     L K  +E       
Sbjct: 211 EKAISEATRNLIDLVVPLIHIGDKLTENPINGTSDINFPSVSGTNDLNKIAQEVAFKNIF 270

Query: 263 ---LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
              LEL  R+ N L+  N+  + DL+  TE D+  + + G+KS+ +I
Sbjct: 271 IDQLELPARAYNGLKKVNVHTVSDLLMYTETDLRNIRSLGKKSVEQI 317


>gi|156618855|ref|YP_001430136.1| RNA polymerase alpha subunit [Cuscuta reflexa]
 gi|166209247|sp|Q8SKY1|RPOA_CUSRE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|156556040|emb|CAM98423.1| RNA polymerase alpha chain [Cuscuta reflexa]
 gi|165910451|gb|ABY73980.1| RNA polymerase alpha subunit [Cuscuta reflexa]
          Length = 335

 Score =  127 bits (318), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 92/312 (29%), Positives = 161/312 (51%), Gaps = 31/312 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L++ + G  IT V+     HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLTKGQADTIGIAMRRALLAEIEGTRITRVKFANTSHEYSTIAGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  +GPG VTA DI     +E+++    I  L       + L +
Sbjct: 92  KEIVLRSNLYGTCDASISIKGPGYVTAEDIILPPHVEIVDSTQHIAWLTEPINFFIGLKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES-AREGQVLDYDKLSMTIDTD 208
            + HGY    H   E+   G   IDAL+ P++  ++++ S   E Q +    L + I T+
Sbjct: 152 ERNHGYFIKTHANFED---GSYPIDALFMPVRNANHSINSYGNEKQEI----LFLEIWTN 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP-------ALLKK-- 259
           GS+T ++++  ASR L D    F++ EE    + ED +  ++P +P       A L+K  
Sbjct: 205 GSLTPKEALHEASRNLIDLFIPFLHMEEENLHL-EDAD-HTIPLSPFTVYDKVAKLRKNK 262

Query: 260 ---------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                    +++LE   +  NCL+  NI  + DL+  ++ D++++ +F    L ++K +L
Sbjct: 263 KKLSLESIFIDQLEFPPKIYNCLKKSNIFTLLDLLNNSQEDLIKIEHF---HLEDVKQIL 319

Query: 311 GTMGLFLGMNLP 322
           G +G    ++LP
Sbjct: 320 GILGKHFALDLP 331


>gi|228017404|gb|ACP52221.1| RNA polymerase alpha subunit [Larix occidentalis]
          Length = 335

 Score =  127 bits (318), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 86/293 (29%), Positives = 152/293 (51%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLRIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIR-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALLKK----------- 259
            +++  ASR L D L  F++ EE   +    ++  N+   P +  L              
Sbjct: 212 REALYEASRNLIDLLIPFLHGEEQNIDGMNNRKGSNMPPFPLSHVLTDTRETKEKIAFKH 271

Query: 260 --VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  R+ NCLR  NI  + DL+  +  D++R+ +FG++S+ ++  VL
Sbjct: 272 IFIDQLELPPRTYNCLRRANIHTLLDLLNYSREDLMRIEHFGKESVEQVLEVL 324


>gi|289065121|ref|YP_003434007.1| RNA polymerase alpha subunit [Typha latifolia]
 gi|69215826|gb|AAZ03869.1| RNA polymerase alpha chain [Typha latifolia]
 gi|281371804|gb|ADA63731.1| RNA polymerase alpha subunit [Typha latifolia]
          Length = 339

 Score =  127 bits (318), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 94/309 (30%), Positives = 158/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSERVPHEYSTIIGIEESVHEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  RGP  VTA DI     +E+++P   I NL     + +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVRGPRYVTAQDIILPPSVEIVDPTQHIANLTEPIDLYIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +   T N   G   IDA+  P++  ++++ S   G     + L + I T+G
Sbjct: 152 KRDRGY---RMEPTNNSQDGSYPIDAVSMPVRNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF-----NPALLKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  +LPF         LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFIPFLHAEEEDINFEENKNRFTLPFLTFQDRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R+ NCL+  NI  + DL+   + D++R+       + ++K +L T+
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRSNIHTLLDLLSNGQEDLMRIEYL---RMEDVKQILDTL 324

Query: 314 GLFLGMNLP 322
                ++LP
Sbjct: 325 QKNFAIDLP 333


>gi|193216735|ref|YP_001999977.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma arthritidis
           158L3-1]
 gi|193002058|gb|ACF07273.1| DNA-directed RNA polymerase alpha subunit [Mycoplasma arthritidis
           158L3-1]
          Length = 350

 Score =  126 bits (317), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 86/304 (28%), Positives = 151/304 (49%), Gaps = 34/304 (11%)

Query: 28  TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIIL 87
           T  + EPL RG+A+TLG  LRR L+SS+   A  A++I+ V HE  ++ GV ED+  +I 
Sbjct: 22  TTFVIEPLMRGYANTLGTVLRRTLLSSITSVAPFAIKINNVQHEFETLPGVKEDVVTLIA 81

Query: 88  NIKGINLK-----MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           NI+ I           ++  R++      G +TA DI   + +E++N D  IC+L     
Sbjct: 82  NIRKIRFTYKPELFEKENLARISFKATHDGDITASDINEPSGLEIVNKDQHICSLQKGTT 141

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIG-----------LITIDALYSPIKKVSYTVESAR 191
           +  +L +  G GY+  + ++T     G            + ID+ +SP+K  +   E   
Sbjct: 142 LEFDLFLRVGRGYIDFEENKTIIQEYGPKLESKIKKGQFLAIDSDFSPVKNCAIHFEELN 201

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ---------DQLGMFINFEEPKKEVK 242
                  ++L +++ TDG++  + ++  A+ I+          D LG  IN  E  ++ K
Sbjct: 202 TSAKNVEERLKISVQTDGTLDAKSAMQQAATIIVAHFQIIGNIDALGT-INLFEEARDKK 260

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           E     +LP        +E+L L++RS N LR  N   + +L++ +E ++  + N G+KS
Sbjct: 261 EKTTKLNLP--------IEKLNLTIRSLNALRRANYNTIDELLKLSEDELSNIKNLGKKS 312

Query: 303 LVEI 306
           + +I
Sbjct: 313 VQDI 316


>gi|150036826|emb|CAM98280.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gasicomitatum]
          Length = 186

 Score =  126 bits (317), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 66/165 (40%), Positives = 103/165 (62%), Gaps = 2/165 (1%)

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            S++ GV ED+T IILN+K + L +  D  + + +  +GP  VTA D+Q   D+EVLNPD
Sbjct: 1   FSTVDGVVEDVTQIILNLKKVVLAIDSDEERSLEVDIQGPADVTAADLQAGADVEVLNPD 60

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVES 189
             I  +     + M +T  KG GY  A  ++   D  PIG++ +D++Y+PI++V+Y VE+
Sbjct: 61  LHIATVAAGKSLHMTITAFKGRGYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYHVEN 120

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
            R G   DYDKL+  I T+GSI   D+++L S+IL + L +F++ 
Sbjct: 121 TRVGSRDDYDKLTFDIWTNGSIKPSDALSLGSKILAEHLNLFMDI 165


>gi|78103281|ref|YP_358613.1| RNA polymerase alpha subunit [Phalaenopsis aphrodite subsp.
           formosana]
 gi|90110856|sp|Q3BAK5|RPOA_PHAAO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|58802811|gb|AAW82531.1| RNA polymerase alpha chain [Phalaenopsis aphrodite subsp.
           formosana]
          Length = 337

 Score =  126 bits (316), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 91/308 (29%), Positives = 158/308 (51%), Gaps = 23/308 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +  PL +G A T+G A+RR L+  + G  IT    + VLHE S+I G+ E + +I+LN+
Sbjct: 32  FVLSPLMKGQADTIGIAIRRALLGEIEGTCITRATSENVLHEYSTIAGIEESVHEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  RGP  +TA DI +   +E+++    I NL     + +EL +
Sbjct: 92  KDIVLRSNLYGVRNASICVRGPKYITAQDIISPPSVEIVDTTQHIANLTEPINLCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +   T +   G   ID +  P++  ++++ S   G     + L + I T+G
Sbjct: 152 KRDRGY---RMKSTNDSHDGSYPIDIVSMPVRNANHSIHSYGNGNE-KQEILFIEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL-PFN--------------- 253
           S+T ++++  ASR L D L  F++ EE     KE+ N  +L PF+               
Sbjct: 208 SLTPKEALYEASRNLIDLLIPFLHAEEEDMNFKENENRWNLPPFSFQDKFTNFKKNKKGI 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P     +++ ELS R+ NCL+  NI  + DL+  ++ D+++M  F  +   ++K +L T+
Sbjct: 268 PLTCIFIDQSELSSRTYNCLKRSNIHTLLDLLSHSQEDLMKMEYFRTE---DVKQILSTV 324

Query: 314 GLFLGMNL 321
                +NL
Sbjct: 325 QKHFAINL 332


>gi|73747870|gb|AAZ82836.1| RNA polymerase subunit a [Elymus mutabilis]
          Length = 339

 Score =  126 bits (316), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 91/285 (31%), Positives = 151/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICIKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G +  ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNG-IEKHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF 312


>gi|284110424|ref|ZP_06386522.1| DNA-directed RNA polymerase subunit alpha [Candidatus Poribacteria
           sp. WGA-A3]
 gi|283829770|gb|EFC34077.1| DNA-directed RNA polymerase subunit alpha [Candidatus Poribacteria
           sp. WGA-A3]
          Length = 155

 Score =  125 bits (315), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 69/143 (48%), Positives = 98/143 (68%), Gaps = 3/143 (2%)

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PIK+V++ VE+AR G+V DYDKL++ + TDGS+T  ++V+ ++ IL++ L + I  EE  
Sbjct: 1   PIKRVNFHVENARVGRVTDYDKLNLEVWTDGSVTPLEAVSSSASILREHLAICIPSEE-M 59

Query: 239 KEVKEDINVK--SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           KEV+ D   +      N  L + V ELELSVR+ NCL+  NI  + DL+Q+TE +ML+  
Sbjct: 60  KEVEHDSAYEETQAELNKHLARSVNELELSVRAANCLKNANIKTIEDLVQKTEIEMLKTK 119

Query: 297 NFGRKSLVEIKGVLGTMGLFLGM 319
           NFG+KSL EIK VL  MGL LG+
Sbjct: 120 NFGKKSLNEIKEVLAEMGLSLGL 142


>gi|7388080|sp|P93993|RPOA_AUSVE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1769912|emb|CAB01381.1| alpha subunit of RNA polymerase [Australopyrum velutinum]
          Length = 339

 Score =  125 bits (315), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 91/285 (31%), Positives = 150/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVXMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF 312


>gi|32171671|sp|Q8MAI6|RPOA_LOPEL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|22657342|gb|AAM97474.1| RNA polymerase alpha subunit [Lophopyrum elongatum]
          Length = 339

 Score =  125 bits (315), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 89/287 (31%), Positives = 148/287 (51%), Gaps = 24/287 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK---------- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P  P   KK          
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPP--PFTFKKRLTNLKKNKK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                   +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F
Sbjct: 266 GIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF 312


>gi|222084117|ref|YP_002519569.1| RNA polymerase alpha chain [Keteleeria davidiana]
 gi|220983669|dbj|BAH11435.1| RNA polymerase alpha chain [Keteleeria davidiana]
          Length = 336

 Score =  125 bits (315), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 87/294 (29%), Positives = 147/294 (50%), Gaps = 21/294 (7%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V ++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVTLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITFDIRLRIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIR-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPK----KEVKEDINVKSLPFNPALLKK---------- 259
            +++  ASR L D    F++ EE         K   N+   P    L             
Sbjct: 212 REALYEASRNLIDFFIPFLHGEEQNIDGINNRKGSSNMPPFPLLHVLTDTGETKEKIAFQ 271

Query: 260 ---VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
              +++LEL  R+ NCLR  NI  + DL+  +  D++RM +FG++S+ ++  VL
Sbjct: 272 HIFIDQLELPPRTYNCLRRANIHTLLDLLNYSREDLMRMEHFGKESVEQVLEVL 325


>gi|300431268|gb|ADK12599.1| RNA polymerase alpha subunit [Poa holciformis]
          Length = 341

 Score =  125 bits (315), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 92/287 (32%), Positives = 149/287 (51%), Gaps = 22/287 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIGGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     IE+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSIEIVDTSQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL----LKK--- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L    LKK   
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLLTFQKRLTNLNLKKNKK 267

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                   +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 GIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 314


>gi|154424769|emb|CAL18487.1| RNA polymerase alpha subunit [Streptococcus criceti]
          Length = 168

 Score =  125 bits (315), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 59/153 (38%), Positives = 103/153 (67%)

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+KG+ +K   +  K + +  +GP  VTAGD+ T +DIE++NPDH +  +     ++  
Sbjct: 1   LNVKGLAVKSYVEDEKTIELDVQGPAEVTAGDVLTDSDIEIINPDHYLFTIAEGHSLKAT 60

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           +TV+K  GYVPA+ +++++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I 
Sbjct: 61  MTVAKNRGYVPAEGNKSDSAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIM 120

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           T+G+I  ED++ L++R+L + L +F +  E  K
Sbjct: 121 TNGTIIPEDALGLSARVLIEHLNLFTDLTEIAK 153


>gi|309322294|ref|YP_003934145.1| RNA polymerase alpha chain [Cedrus deodara]
 gi|228017091|gb|ACP51913.1| RNA polymerase alpha subunit [Cedrus deodara]
 gi|307683220|dbj|BAJ19528.1| RNA polymerase alpha chain [Cedrus deodara]
          Length = 335

 Score =  125 bits (315), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 85/293 (29%), Positives = 152/293 (51%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     +++++    I  L       ++L + K  
Sbjct: 96  LRSDSYGVREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIKLRIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIR-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALLKK----------- 259
            +++  ASR L D    F++ EE   +    ++  N+   P +  L              
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNNRKGSNMPPFPLSHVLTDTGETKEKIAFQH 271

Query: 260 --VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  R+ NCLR  NI  + DL+  +  D++R+ +FG++S+ ++  VL
Sbjct: 272 IFIDQLELPPRTYNCLRRANIHTLLDLLNYSREDLMRIEHFGKESVEQVLEVL 324


>gi|22657314|gb|AAM97460.1| RNA polymerase alpha subunit [Heteranthelium piliferum]
          Length = 339

 Score =  125 bits (315), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 91/285 (31%), Positives = 150/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFWSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPKYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELIKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF 312


>gi|68053189|sp|Q7H6G1|RPOA_PSEPI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|68053190|sp|Q7H6I5|RPOA_ELYCA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1769861|emb|CAB01378.1| alpha subunit of RNA polymerase [Australopyrum retrofractum]
 gi|1770228|emb|CAB01300.1| alpha subunit of RNA polymerase [Dasypyrum villosum]
 gi|1770247|emb|CAB01316.1| alpha subunit of RNA polymerase [Eremopyrum triticeum]
 gi|1770348|emb|CAB01321.1| alpha subunit of RNA polymerase [Henrardia persica]
 gi|1771184|emb|CAB01306.1| alpha subunit of RNA polymerase [Lophopyrum elongatum]
 gi|1771497|emb|CAB01309.1| alpha subunit of RNA polymerase [Pseudoroegneria spicata]
 gi|1771501|emb|CAB01324.1| alpha subunit of RNA polymerase [Peridictyon sanctum]
 gi|22657242|gb|AAM97424.1| RNA polymerase alpha subunit [Australopyrum retrofractum]
 gi|22657244|gb|AAM97425.1| RNA polymerase alpha subunit [Australopyrum velutinum]
 gi|22657264|gb|AAM97435.1| RNA polymerase alpha subunit [Dasypyrum villosum]
 gi|22657268|gb|AAM97437.1| RNA polymerase alpha subunit [Elymus canadensis]
 gi|22657272|gb|AAM97439.1| RNA polymerase alpha subunit [Elymus canadensis]
 gi|22657274|gb|AAM97440.1| RNA polymerase alpha subunit [Elymus ciliaris]
 gi|22657276|gb|AAM97441.1| RNA polymerase alpha subunit [Elymus elymoides]
 gi|22657278|gb|AAM97442.1| RNA polymerase alpha subunit [Elymus glaucus]
 gi|22657280|gb|AAM97443.1| RNA polymerase alpha subunit [Elymus glaucus]
 gi|22657282|gb|AAM97444.1| RNA polymerase alpha subunit [Elymus glaucus]
 gi|22657286|gb|AAM97446.1| RNA polymerase alpha subunit [Elymus lanceolatus]
 gi|22657288|gb|AAM97447.1| RNA polymerase alpha subunit [Elymus lanceolatus]
 gi|22657290|gb|AAM97448.1| RNA polymerase alpha subunit [Elymus trachycaulus]
 gi|22657292|gb|AAM97449.1| RNA polymerase alpha subunit [Elymus trachycaulus]
 gi|22657300|gb|AAM97453.1| RNA polymerase alpha subunit [Elymus wawawaiensis]
 gi|22657302|gb|AAM97454.1| RNA polymerase alpha subunit [Elymus wawawaiensis]
 gi|22657304|gb|AAM97455.1| RNA polymerase alpha subunit [Eremopyrum bonaepartis]
 gi|22657306|gb|AAM97456.1| RNA polymerase alpha subunit [Eremopyrum bonaepartis]
 gi|22657310|gb|AAM97458.1| RNA polymerase alpha subunit [Eremopyrum orientale]
 gi|22657312|gb|AAM97459.1| RNA polymerase alpha subunit [Henrardia persica]
 gi|22657316|gb|AAM97461.1| RNA polymerase alpha subunit [Peridictyon sanctum]
 gi|22657318|gb|AAM97462.1| RNA polymerase alpha subunit [Pseudoroegneria strigosa]
 gi|22657320|gb|AAM97463.1| RNA polymerase alpha subunit [Pseudoroegneria strigosa]
 gi|22657322|gb|AAM97464.1| RNA polymerase alpha subunit [Pseudoroegneria tauri subsp.
           libanotica]
 gi|22657324|gb|AAM97465.1| RNA polymerase alpha subunit [Pseudoroegneria spicata]
 gi|22657326|gb|AAM97466.1| RNA polymerase alpha subunit [Pseudoroegneria spicata]
 gi|22657328|gb|AAM97467.1| RNA polymerase alpha subunit [Pseudoroegneria spicata]
 gi|22657330|gb|AAM97468.1| RNA polymerase alpha subunit [Pseudoroegneria spicata]
 gi|34329585|gb|AAQ63942.1| RNA polymerase alpha subunit [Elymus repens]
 gi|34329587|gb|AAQ63943.1| RNA polymerase alpha subunit [Elymus repens]
 gi|34329589|gb|AAQ63944.1| RNA polymerase alpha subunit [Elymus repens]
 gi|34329591|gb|AAQ63945.1| RNA polymerase alpha subunit [Elymus repens]
 gi|34329593|gb|AAQ63946.1| RNA polymerase alpha subunit [Elymus repens]
 gi|34329595|gb|AAQ63947.1| RNA polymerase alpha subunit [Elymus repens]
 gi|73747864|gb|AAZ82833.1| RNA polymerase subunit a [Elymus abolinii]
 gi|73747866|gb|AAZ82834.1| RNA polymerase subunit a [Elymus caucasicus]
 gi|317017396|gb|ADU86100.1| RNA polymerase alpha subunit [Elymus caucasicus]
 gi|317017398|gb|ADU86101.1| RNA polymerase alpha subunit [Elymus canadensis]
 gi|317017400|gb|ADU86102.1| RNA polymerase alpha subunit [Elymus semicostatus]
 gi|317017402|gb|ADU86103.1| RNA polymerase alpha subunit [Elymus sibiricus]
          Length = 339

 Score =  125 bits (315), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 91/285 (31%), Positives = 150/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF 312


>gi|7388089|sp|P92389|RPOA_HETPI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1770352|emb|CAB01327.1| alpha subunit of RNA polymerase [Heteranthelium piliferum]
          Length = 339

 Score =  125 bits (315), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 91/285 (31%), Positives = 150/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFWSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPKYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELIKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F
Sbjct: 268 PLNCIFIDQLELTSRTXNCLKRANIHTLLDLLSKTEEDLLRIDSF 312


>gi|3122776|sp|P92439|RPOA_THIBE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1771793|emb|CAB01384.1| alpha subunit of RNA polymerase [Thinopyrum bessarabicum]
 gi|22657340|gb|AAM97473.1| RNA polymerase alpha subunit [Thinopyrum bessarabicum]
 gi|22657344|gb|AAM97475.1| RNA polymerase alpha subunit [Thinopyrum scirpeum]
          Length = 339

 Score =  125 bits (315), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 91/285 (31%), Positives = 150/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPPFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF 312


>gi|14017603|ref|NP_114289.1| RNA polymerase alpha subunit [Triticum aestivum]
 gi|17380278|sp|P12073|RPOA_WHEAT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|68053005|sp|P92892|RPOA_AEGSP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|68053170|sp|Q6YLW2|RPOA_SECCE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|68053185|sp|Q7GED0|RPOA_TAECM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|68053186|sp|Q7GED9|RPOA_AEGCM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1769857|emb|CAB01345.1| alpha subunit of RNA polymerase [Amblyopyrum muticum]
 gi|1770118|emb|CAB01303.1| alpha subunit of RNA polymerase [Aegilops comosa]
 gi|1770176|emb|CAB01348.1| alpha subunit of RNA polymerase [Triticum monococcum]
 gi|1771730|emb|CAB01375.1| alpha subunit of RNA polymerase [Aegilops speltoides]
 gi|1771811|emb|CAB01357.1| alpha subunit of RNA polymerase [Taeniatherum caput-medusae]
 gi|13928236|dbj|BAB47065.1| RNA polymerase alpha subunit [Triticum aestivum]
 gi|22657228|gb|AAM97417.1| RNA polymerase alpha subunit [Aegilops markgrafii]
 gi|22657230|gb|AAM97418.1| RNA polymerase alpha subunit [Aegilops speltoides]
 gi|22657332|gb|AAM97469.1| RNA polymerase alpha subunit [Secale montanum]
 gi|22657334|gb|AAM97470.1| RNA polymerase alpha subunit [Secale cereale]
 gi|22657336|gb|AAM97471.1| RNA polymerase alpha subunit [Secale montanum]
 gi|22657338|gb|AAM97472.1| RNA polymerase alpha subunit [Taeniatherum caput-medusae]
          Length = 339

 Score =  125 bits (315), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 91/285 (31%), Positives = 150/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF 312


>gi|154424817|emb|CAL18511.1| RNA polymerase alpha subunit [Streptococcus minor]
          Length = 167

 Score =  125 bits (315), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 61/155 (39%), Positives = 101/155 (65%)

Query: 88  NIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           NIKGI +K   +  K++ +   GP  +TAGDI T +DIE++NPDH +  +   A  +  L
Sbjct: 1   NIKGIAVKSYVEDEKKIELDVVGPAEITAGDILTDSDIEIVNPDHYLFTIGEGASFKAIL 60

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           TV++G GYVPA+ ++ +  P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ I T
Sbjct: 61  TVNRGRGYVPAEGNKKDEAPVGTLAVDSIYTPVVKVNYQVEPARVGSNDGFDKLTLEIMT 120

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           +G+   ED++ L++RIL + LG+F +  +  K  +
Sbjct: 121 NGTTNPEDALGLSARILMEHLGLFTDLTDVAKSAE 155


>gi|22657232|gb|AAM97419.1| RNA polymerase alpha subunit [Aegilops tauschii]
          Length = 339

 Score =  125 bits (314), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 91/285 (31%), Positives = 150/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F
Sbjct: 268 PLNSIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF 312


>gi|2500618|sp|P92429|RPOA_AEGTA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1771509|emb|CAB01351.1| alpha subunit of RNA polymerase [Aegilops tauschii]
          Length = 339

 Score =  125 bits (314), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 91/285 (31%), Positives = 150/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F
Sbjct: 268 PLNSIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF 312


>gi|73747868|gb|AAZ82835.1| RNA polymerase subunit a [Elymus dentatus]
          Length = 339

 Score =  125 bits (314), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 91/285 (31%), Positives = 150/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICIKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF 312


>gi|7388095|sp|P93974|RPOA_EREDI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1770241|emb|CAB01312.1| alpha subunit of RNA polymerase [Eremopyrum distans]
 gi|22657308|gb|AAM97457.1| RNA polymerase alpha subunit [Eremopyrum orientale]
          Length = 339

 Score =  125 bits (314), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 91/285 (31%), Positives = 150/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFKKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF 312


>gi|161511739|emb|CAP16880.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 166

 Score =  125 bits (314), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 64/162 (39%), Positives = 102/162 (62%), Gaps = 2/162 (1%)

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  IC +     
Sbjct: 1   TQIILNLKKVSLKVESDEEKSLEINVMGPANVTAGDIVGDGDVTILNPELPICTVAEGTT 60

Query: 143 VRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
               LT  KG GY  A  +  R  + PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDK
Sbjct: 61  FHAVLTAEKGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDK 120

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           L++ + TDGS+   ++++L+++IL + L +F+N ++  K+ +
Sbjct: 121 LTLDVWTDGSLAASEAISLSAKILTEHLTIFVNLDDQAKDTE 162


>gi|300431284|gb|ADK12607.1| RNA polymerase alpha subunit [Nassella arcuata]
          Length = 339

 Score =  125 bits (314), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 86/285 (30%), Positives = 146/285 (51%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I+ +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPMDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------------- 253
           S+T ++++  ASR L D    F++ EE     +E+ N  + P                  
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKKLTNLKKNKKGI 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|58491826|gb|AAW78552.1| RNA polymerase alpha subunit [Sphagnum fimbriatum]
          Length = 338

 Score =  125 bits (314), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 98/310 (31%), Positives = 164/310 (52%), Gaps = 36/310 (11%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P   G A+T+G A+RR L+  + G  IT  + + V HE S+I G+ E + DI++N+K I 
Sbjct: 37  PFRSGQANTVGIAVRRALLGGVEGTCITRAKSEKVTHEYSTILGIQESVRDILINLKEIV 96

Query: 94  LKMSGDSHKR----VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           LK   +S +     ++IF  GP  VTA DI     +EV++    I  L     + +EL +
Sbjct: 97  LKSKSNSCETQKAFLSIF--GPKEVTARDIIFPPSVEVIDTTQYIATLTKAIHLDIELKI 154

Query: 150 SKGHGYVPAKHHRTENDPI----GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
            K  GY      RT+ D I    G  ++DA+++PI+  +Y+V S  E +    + L + I
Sbjct: 155 EKDCGY------RTQ-DSIKSADGYFSVDAVFTPIRNANYSVHSF-ENKNETQEILFIEI 206

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN------VKSLPFNPALLKK 259
            T+GS+T ++++  ASR L D    F++ E  K+EV  D N        S P    + K+
Sbjct: 207 WTNGSVTPKEALYEASRSLIDLFIPFLHAE--KEEVMHDKNESNTLHFSSSPSENKMEKE 264

Query: 260 -------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                  +++LEL  R+ NCL+  ++  + DL+  ++ D++++ NFG+KS   ++ VL  
Sbjct: 265 MTFKHIFIDQLELPARAYNCLKRVDVHTISDLLSYSQDDLMKIKNFGKKS---VEQVLEA 321

Query: 313 MGLFLGMNLP 322
           +     + LP
Sbjct: 322 LQKRFSIKLP 331


>gi|7388079|sp|P92209|RPOA_AGRCR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1769834|emb|CAB01390.1| alpha subunit of RNA polymerase [Agropyron cristatum]
 gi|22657236|gb|AAM97421.1| RNA polymerase alpha subunit [Agropyron cristatum]
 gi|22657238|gb|AAM97422.1| RNA polymerase alpha subunit [Agropyron cristatum]
 gi|22657240|gb|AAM97423.1| RNA polymerase alpha subunit [Agropyron mongolicum]
          Length = 339

 Score =  125 bits (314), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 91/285 (31%), Positives = 150/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDRAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF 312


>gi|300431329|gb|ADK12627.1| RNA polymerase alpha subunit [Achnatherum diegoense]
          Length = 339

 Score =  125 bits (314), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 86/285 (30%), Positives = 146/285 (51%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I+ +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 QRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------------- 253
           S+T ++++  ASR L D    F++ EE     +E+ N  + P                  
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKKLTNLKKNKKGI 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|7388090|sp|P93956|RPOA_FESSE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1770282|emb|CAB01778.1| alpha subunit of RNA polymerase [Festucopsis serpentini]
 gi|22657262|gb|AAM97434.1| RNA polymerase alpha subunit [Dasypyrum villosum]
          Length = 339

 Score =  125 bits (314), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 91/285 (31%), Positives = 150/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFWSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF 312


>gi|300431309|gb|ADK12619.1| RNA polymerase alpha subunit [Achnatherum psilantherum]
          Length = 339

 Score =  125 bits (314), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 86/285 (30%), Positives = 146/285 (51%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I+ +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVDTGQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------------- 253
           S+T ++++  ASR L D    F++ EE     +E+ N  + P                  
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKKLTNLKKNKKGI 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|224437309|ref|ZP_03658281.1| DNA-directed RNA polymerase subunit alpha [Helicobacter cinaedi
           CCUG 18818]
 gi|313143764|ref|ZP_07805957.1| DNA-directed RNA polymerase subunit alpha [Helicobacter cinaedi
           CCUG 18818]
 gi|313128795|gb|EFR46412.1| DNA-directed RNA polymerase subunit alpha [Helicobacter cinaedi
           CCUG 18818]
          Length = 334

 Score =  125 bits (314), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 93/300 (31%), Positives = 160/300 (53%), Gaps = 15/300 (5%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           NR  + A P   G+A TL + LRR+L+ S  G A TA++I GV HE  SI+G+ ED++  
Sbjct: 22  NRIKISAYPFESGYAITLAHPLRRLLLLSSVGYAPTALKIQGVTHEFDSIRGIVEDVSHF 81

Query: 86  ILNIKGINLKMSGDSHKRVTIFK--RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           I N+K I   +  ++   V +    +GP V++A ++     ++V+NP+  +  ++ +A +
Sbjct: 82  ISNLKNIRFLIKDETLDSVQVHYEFKGPMVLSANELAN-ESVDVVNPEAYLATINENASI 140

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
              L V KG GYVP++  R +      I +DA ++P+KK  Y +E+       +Y+K+  
Sbjct: 141 SFSLIVQKGIGYVPSESIRGKIAE-DYIPLDAYFTPVKKAIYEIENVLVEDNPNYEKIIF 199

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMF-INFEEP---KKEVKEDI-NVKSLPFNPALLK 258
            I+TDG I    +   A  ++  Q+ +F ++        K + ED   +K+      L+ 
Sbjct: 200 DIETDGQIEPLTAFKEAISVMHKQMSIFGVDLSATPNGSKSIAEDSGELKT------LMI 253

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           K++ L LS R  NCL    + Y+G+L+  +E ++  + N G+KS  EI   L  +G  +G
Sbjct: 254 KIDTLNLSARCFNCLDRSGLKYVGELVIMSENELKNIKNMGKKSYDEITEKLEELGYPVG 313


>gi|300431276|gb|ADK12603.1| RNA polymerase alpha subunit [Nassella pampagrandensis]
 gi|300431282|gb|ADK12606.1| RNA polymerase alpha subunit [Nassella melanosperma]
 gi|300431318|gb|ADK12622.1| RNA polymerase alpha subunit [Amelichloa brachychaeta]
 gi|300431325|gb|ADK12625.1| RNA polymerase alpha subunit [Austrostipa nodosa]
          Length = 339

 Score =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 86/285 (30%), Positives = 146/285 (51%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I+ +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------------- 253
           S+T ++++  ASR L D    F++ EE     +E+ N  + P                  
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKKLTNLKKNKKGI 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|12661177|gb|AAK01152.2|AF311314_2 RPoA [Marsilea quadrifolia]
          Length = 347

 Score =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 81/297 (27%), Positives = 154/297 (51%), Gaps = 22/297 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +  P  +G A+T+G A+RR L+  + GA+IT+ + +GV HE S++ G+ E + DI++N+
Sbjct: 38  FVISPFKKGQANTVGIAMRRALLGEVGGASITSARFEGVAHEYSTVAGIQETIHDILVNL 97

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+   D +++  +   GP  VTAGDI     ++V++    I  +     V +EL +
Sbjct: 98  KEIVLRSDSDGNQKAILSVTGPKRVTAGDISLPPSVKVIDDSQYIVTITQPISVNIELNI 157

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
               GY     +   +   G   +DA++ P++ V+Y+V     G+ +  + L + + T+G
Sbjct: 158 ECDCGYRIESLNEYRD---GEFPVDAVFMPVRNVNYSVHPFGSGKEM-REILFIEVWTNG 213

Query: 210 SITGEDSVALASRILQDQLGMFI--------NFEEPKKEVK--------EDINVKSLPFN 253
           S+T  ++++ AS+   D L  F+        +FE  +            +D++     F 
Sbjct: 214 SLTPTEAISKASKSSIDLLSPFLHTKHEDIPDFESNRDSSSLMKFSSRVDDVDKSEGDFF 273

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++LEL  R+ NCL+   I  + DL+  +  D+L++ +FG+KS+ ++   L
Sbjct: 274 KNTF--IDQLELPARAFNCLKRAEIHTISDLLSYSRDDLLKLKSFGKKSVDQVSRAL 328


>gi|125987861|sp|Q9BBN0|RPOA_MARQU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
          Length = 341

 Score =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 81/297 (27%), Positives = 154/297 (51%), Gaps = 22/297 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +  P  +G A+T+G A+RR L+  + GA+IT+ + +GV HE S++ G+ E + DI++N+
Sbjct: 32  FVISPFKKGQANTVGIAMRRALLGEVGGASITSARFEGVAHEYSTVAGIQETIHDILVNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+   D +++  +   GP  VTAGDI     ++V++    I  +     V +EL +
Sbjct: 92  KEIVLRSDSDGNQKAILSVTGPKRVTAGDISLPPSVKVIDDSQYIVTITQPISVNIELNI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
               GY     +   +   G   +DA++ P++ V+Y+V     G+ +  + L + + T+G
Sbjct: 152 ECDCGYRIESLNEYRD---GEFPVDAVFMPVRNVNYSVHPFGSGKEM-REILFIEVWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFI--------NFEEPKKEVK--------EDINVKSLPFN 253
           S+T  ++++ AS+   D L  F+        +FE  +            +D++     F 
Sbjct: 208 SLTPTEAISKASKSSIDLLSPFLHTKHEDIPDFESNRDSSSLMKFSSRVDDVDKSEGDFF 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++LEL  R+ NCL+   I  + DL+  +  D+L++ +FG+KS+ ++   L
Sbjct: 268 KNTF--IDQLELPARAFNCLKRAEIHTISDLLSYSRDDLLKLKSFGKKSVDQVSRAL 322


>gi|307683665|dbj|BAJ19811.1| RNA polymerase alpha chain [Picea morrisonicola]
          Length = 336

 Score =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 87/294 (29%), Positives = 153/294 (52%), Gaps = 21/294 (7%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RRVL+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRVLLGEVEGTCITHVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I   GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIRGASICIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGNGNEIR-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALL-------KK---- 259
            ++++ ASRIL +    F++ EE   +    ++  N+   P +  L        KK    
Sbjct: 212 REALSEASRILIELFIPFLHGEEQNIDGMNNRKGSNMPPFPLSHVLTDTGETKEKKIAFQ 271

Query: 260 ---VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
              +++LEL  R  NCLR  NI  + DL+  +  D++R+  FG++S+ ++  +L
Sbjct: 272 HIFIDQLELPPRVYNCLRRANIHTLSDLLNYSREDLMRIERFGKESVEQVFEIL 325


>gi|326392491|ref|ZP_08213872.1| RNA polymerase insert [Thermoanaerobacter ethanolicus JW 200]
 gi|325991466|gb|EGD50077.1| RNA polymerase insert [Thermoanaerobacter ethanolicus JW 200]
          Length = 136

 Score =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 67/126 (53%), Positives = 85/126 (67%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA  +V+IDGVLHE S++ GV ED+ +IILN+K +
Sbjct: 2   EPLERGYGITLGNSLRRVLLSSLPGAAPKSVKIDGVLHEFSTLPGVKEDVVEIILNLKEV 61

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K+  D      I   G G VTAG I+   DIE+LNPDH I  L  D  + ME+   KG
Sbjct: 62  AVKLHSDEPVVGRIDVEGKGEVTAGHIKGSADIEILNPDHHIATLSDDGKLHMEIVFVKG 121

Query: 153 HGYVPA 158
            GYVP+
Sbjct: 122 KGYVPS 127


>gi|51859695|gb|AAU11127.1| RNA polymerase alpha subunit [Psathyrostachys caduca]
          Length = 339

 Score =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 90/285 (31%), Positives = 150/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|7388093|sp|P93964|RPOA_SECST RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1771726|emb|CAB01374.1| alpha subunit of RNA polymerase [Secale strictum]
          Length = 339

 Score =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 91/285 (31%), Positives = 149/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLXEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+  F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDXF 312


>gi|68053188|sp|Q7H6F6|RPOA_PSAJU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1770335|emb|CAB01363.1| alpha subunit of RNA polymerase [Hordeum murinum subsp. glaucum]
 gi|1771433|emb|CAB01336.1| alpha subunit of RNA polymerase [Psathyrostachys fragilis]
 gi|22657248|gb|AAM97427.1| RNA polymerase alpha subunit [Hordeum brevisubulatum]
 gi|22657256|gb|AAM97431.1| RNA polymerase alpha subunit [Hordeum murinum]
 gi|22657258|gb|AAM97432.1| RNA polymerase alpha subunit [Hordeum murinum]
 gi|22657346|gb|AAM97476.1| RNA polymerase alpha subunit [Psathyrostachys fragilis]
 gi|22657348|gb|AAM97477.1| RNA polymerase alpha subunit [Psathyrostachys juncea]
 gi|51859675|gb|AAU11117.1| RNA polymerase alpha subunit [Psathyrostachys juncea]
 gi|51859677|gb|AAU11118.1| RNA polymerase alpha subunit [Psathyrostachys lanuginosa]
 gi|51859685|gb|AAU11122.1| RNA polymerase alpha subunit [Psathyrostachys fragilis subsp.
           villosus]
 gi|51859687|gb|AAU11123.1| RNA polymerase alpha subunit [Psathyrostachys fragilis subsp.
           villosus]
 gi|51859689|gb|AAU11124.1| RNA polymerase alpha subunit [Psathyrostachys huashanica]
 gi|51859693|gb|AAU11126.1| RNA polymerase alpha subunit [Psathyrostachys rupestris subsp.
           rupestris]
 gi|193885480|gb|ACF28432.1| RNA polymerase alpha subunit [Leymus angustus]
 gi|193885484|gb|ACF28435.1| RNA polymerase alpha subunit [Leymus chinensis]
 gi|193885488|gb|ACF28438.1| RNA polymerase alpha subunit [Leymus paboanus]
 gi|193885492|gb|ACF28441.1| RNA polymerase alpha subunit [Leymus racemosus]
 gi|193885496|gb|ACF28444.1| RNA polymerase alpha subunit [Leymus karelinii]
 gi|193885500|gb|ACF28447.1| RNA polymerase alpha subunit [Leymus sabulosus]
 gi|193885504|gb|ACF28450.1| RNA polymerase alpha subunit [Leymus mollis]
 gi|193885508|gb|ACF28453.1| RNA polymerase alpha subunit [Leymus secalinus]
 gi|307696913|gb|ADN85913.1| RNA polymerase alpha subunit [Leymus erianthus]
 gi|307696921|gb|ADN85919.1| RNA polymerase alpha subunit [Leymus arenarius]
 gi|307696925|gb|ADN85922.1| RNA polymerase alpha subunit [Leymus salinus]
 gi|307696929|gb|ADN85925.1| RNA polymerase alpha subunit [Leymus cinereus]
 gi|307696933|gb|ADN85928.1| RNA polymerase alpha subunit [Leymus pseudoracemosus]
 gi|307696937|gb|ADN85931.1| RNA polymerase alpha subunit [Leymus akmolinensis]
 gi|307696941|gb|ADN85934.1| RNA polymerase alpha subunit [Leymus karelinii]
 gi|307696945|gb|ADN85937.1| RNA polymerase alpha subunit [Leymus paboanus]
 gi|307696949|gb|ADN85940.1| RNA polymerase alpha subunit [Leymus angustus]
          Length = 339

 Score =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 90/285 (31%), Positives = 150/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|307697293|gb|ADN86101.1| RNA polymerase alpha subunit [Chasmanthium latifolium]
          Length = 339

 Score =  124 bits (312), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 95/313 (30%), Positives = 159/313 (50%), Gaps = 31/313 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGNVPHEYSTIVGIEESIQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLREPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY       +++   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYHTELRKNSQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL---------LKK- 259
           S+T ++++  ASR L D    F++ EE     +E+ N     F P L         LKK 
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGSSFEENKNR----FTPPLLTFQKRFTNLKKN 263

Query: 260 ----------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    + + K +
Sbjct: 264 KKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---RMEDGKLI 320

Query: 310 LGTMGLFLGMNLP 322
             T+   L ++LP
Sbjct: 321 WDTLEKHLPIDLP 333


>gi|300431307|gb|ADK12618.1| RNA polymerase alpha subunit [Achnatherum chingii]
          Length = 339

 Score =  124 bits (312), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 87/285 (30%), Positives = 144/285 (50%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y++ S   G    ++ L + I T G
Sbjct: 152 KRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTTG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------------- 253
           S+T ++++  ASR L D    F++ EE     +E+ N  + P                  
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKKLTNLKKNKKGI 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ NF
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDNF 312


>gi|51859683|gb|AAU11121.1| RNA polymerase alpha subunit [Psathyrostachys fragilis subsp.
           secaliformis]
          Length = 339

 Score =  124 bits (312), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 90/285 (31%), Positives = 150/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIXIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|307696909|gb|ADN85910.1| RNA polymerase alpha subunit [Leymus innovatus]
 gi|307696917|gb|ADN85916.1| RNA polymerase alpha subunit [Leymus triticoides]
          Length = 339

 Score =  124 bits (312), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 90/285 (31%), Positives = 150/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|83858541|ref|ZP_00952063.1| DNA-directed RNA polymerase alpha subunit [Oceanicaulis alexandrii
           HTCC2633]
 gi|83853364|gb|EAP91216.1| DNA-directed RNA polymerase alpha subunit [Oceanicaulis alexandrii
           HTCC2633]
          Length = 81

 Score =  124 bits (312), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 57/80 (71%), Positives = 70/80 (87%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           ++ELELSVRS NCL+ +NIVY+GDLIQ++EA+MLR  NFGRKSL EIK VL  MGL LGM
Sbjct: 1   MDELELSVRSANCLKNDNIVYIGDLIQKSEAEMLRTPNFGRKSLNEIKEVLAQMGLHLGM 60

Query: 320 NLPDWPPESIEELAKKYEDK 339
           + P+WPPE+IE+LAKKYED+
Sbjct: 61  DAPNWPPENIEDLAKKYEDQ 80


>gi|7388091|sp|P93960|RPOA_PSARU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1771473|emb|CAB01342.1| alpha subunit of RNA polymerase [Psathyrostachys rupestris]
          Length = 339

 Score =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 90/285 (31%), Positives = 150/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGXVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTXQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNYIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|322378754|ref|ZP_08053183.1| DNA-directed RNA polymerase subunit alpha [Helicobacter suis HS1]
 gi|322380603|ref|ZP_08054755.1| DNA-directed RNA polymerase subunit alpha [Helicobacter suis HS5]
 gi|321146925|gb|EFX41673.1| DNA-directed RNA polymerase subunit alpha [Helicobacter suis HS5]
 gi|321148784|gb|EFX43255.1| DNA-directed RNA polymerase subunit alpha [Helicobacter suis HS1]
          Length = 337

 Score =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 88/295 (29%), Positives = 155/295 (52%), Gaps = 19/295 (6%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM- 96
           G+A TL + LRR+L+ S  G A  A++I+GV HE  S++G+ ED+   I N+K I L   
Sbjct: 35  GYAITLAHPLRRLLLQSSVGFAPIAIKIEGVAHEFDSVRGMAEDVALFIANLKNIRLVAK 94

Query: 97  ---SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
              + +    V     GP  ++  D+ T  ++EV++ +  +  ++ D  +   L + KG 
Sbjct: 95  NLENAEDQLVVHYSFNGPAKLSGKDLAT-EEVEVVDTETYLATINEDGQLGFSLIIQKGM 153

Query: 154 GYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GYVP++  R    +D    I +DA ++PIKK  Y +E+       +++K+   I++DG +
Sbjct: 154 GYVPSESIRGFISSD---YIPLDACFTPIKKAIYHIENILVDGNPNFEKVIFEIESDGQV 210

Query: 212 TGEDSVALASRILQDQLGMF-INFEEPKK--EVKEDINVKSLPFNPALLKKVEELELSVR 268
             + +   A + +  Q+ +F  N  + K    ++ ++ +K       L+KKVE+L+LS R
Sbjct: 211 DPKQAFQEAIKTMHAQMHIFSTNLSDSKNAYHLENNLEIKE------LIKKVEDLDLSAR 264

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
             NCL    I Y+G+L+     ++  + N G+KS  EI   L  +   +G  LP+
Sbjct: 265 CLNCLDKVGIKYIGELVLMDVYELKGIKNLGKKSYDEIAEKLEQLKYPVGQELPE 319


>gi|117575077|emb|CAJ84778.1| RNA polymerase alpha subunit [Lactobacillus amylophilus]
          Length = 138

 Score =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 61/136 (44%), Positives = 92/136 (67%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+T IILN+K + LK      K   I   GP  VTAGD++  +++++LNPD  I  
Sbjct: 2   GVLEDVTQIILNLKKLTLKSIAADEKLAEIDVEGPATVTAGDLKVDDEVQILNPDQYIAT 61

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +   A ++M + + +G GYVPA  +++++ PIG++ +D+L+SPI+KV+Y VE  R G+  
Sbjct: 62  VAEGAHLQMTVAIKQGRGYVPADQNKSDDMPIGVVPVDSLFSPIEKVNYQVEGTRVGRNN 121

Query: 197 DYDKLSMTIDTDGSIT 212
           DYDKL+M + TDGSIT
Sbjct: 122 DYDKLTMEVWTDGSIT 137


>gi|300431297|gb|ADK12613.1| RNA polymerase alpha subunit [Anatherostipa brevis]
 gi|300431301|gb|ADK12615.1| RNA polymerase alpha subunit [Aciachne pulvinata]
 gi|300431327|gb|ADK12626.1| RNA polymerase alpha subunit [Lorenzochloa erectifolia]
          Length = 339

 Score =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 86/285 (30%), Positives = 145/285 (50%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDITLPPSVEIVDTAQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------------- 253
           S+T ++++  ASR L D    F++ EE     +E+ N  + P                  
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKKLTNLKKNKKGI 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|189162303|ref|YP_001936549.1| RNA polymerase alpha subunit [Fagopyrum esculentum subsp.
           ancestrale]
 gi|166065389|gb|ABY79764.1| RNA polymerase alpha subunit [Fagopyrum esculentum subsp.
           ancestrale]
          Length = 337

 Score =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 91/309 (29%), Positives = 164/309 (53%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGPG VTA DI +   +E+++    I NL     +R+EL +
Sbjct: 92  KEIVLRSTFYGTCDASICVRGPGGVTAQDIISPPYVEIVDTTQHIANLTEPIDLRIELQL 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +     N   G   ID ++ P++ V++++ S   G     + L + I T+G
Sbjct: 152 ERNRGY---RIKTPNNFQDGSYPIDVVFMPVRNVNHSIHSYSNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F+  E+    ++++ +  +LP   F+  L  L+K     
Sbjct: 208 SLTPKEALYEASRNLIDLFIPFLYAEKENFHLEDNQDRVTLPLFLFHDRLIELRKNKKKI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F   S+ ++K +L T+
Sbjct: 268 ALKSIFIDQLELPPRIYNCLKNSNIHTLLDLLTNSQDDIMKIEHF---SIEDVKQILDTL 324

Query: 314 GLFLGMNLP 322
                +NLP
Sbjct: 325 EKHFAINLP 333


>gi|7388094|sp|P93968|RPOA_FESFE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1770264|emb|CAB01387.1| alpha subunit of RNA polymerase [Festucopsis festucoides]
          Length = 339

 Score =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 90/285 (31%), Positives = 150/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ ++Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNLNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF 312


>gi|41688709|sp|Q8MAI9|RPOA_ELYCL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|22657266|gb|AAM97436.1| RNA polymerase alpha subunit [Leymus californicus]
          Length = 339

 Score =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 90/285 (31%), Positives = 150/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFWSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|2500619|sp|P92418|RPOA_PSAFR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1771429|emb|CAB01333.1| alpha subunit of RNA polymerase [Psathyrostachys fragilis]
          Length = 339

 Score =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 90/285 (31%), Positives = 150/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGXVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|41688708|sp|Q8MAI8|RPOA_ELYHY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|22657284|gb|AAM97445.1| RNA polymerase alpha subunit [Elymus hystrix]
          Length = 339

 Score =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 91/285 (31%), Positives = 149/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA   P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAESMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF 312


>gi|58758781|gb|AAW81783.1| RNA polymerase alpha subunit [Polytrichastrum pallidisetum]
          Length = 338

 Score =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 95/308 (30%), Positives = 159/308 (51%), Gaps = 31/308 (10%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P   G A+T+G A+RR L+  + G  IT      V HE S+I G+ E + DI++N+K I 
Sbjct: 36  PFRCGQANTVGIAMRRALLGEIEGTCITCAIFKKVTHEYSTIVGIQESVHDILINLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK +    ++  I   GP  +TA DI     +++++    I  +     + +EL + K  
Sbjct: 96  LKSNSSETQKAFISILGPKKITAQDIILPPSVKIIDTTQYIATITKPIHLDIELEIEKDC 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY      ++ +   G   IDA++ PI+  +Y+V S      +  + L + I T+GSIT 
Sbjct: 156 GYRIQDSVKSID---GYFPIDAIFMPIRNANYSVHSFENNNKIQ-EILFIEIWTNGSITP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDIN-VKSLP--------FNPA---LLKK-- 259
           ++++  ASR L D   +FI F  P+K  KE I+ +K  P        F+P    L K+  
Sbjct: 212 KEALYEASRSLID---LFIPFLHPEK--KETIDRLKYTPNDISDFSSFSPVTGKLTKEIT 266

Query: 260 -----VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +++LEL  R+ NCL+  N   + DL+  ++ D++++ NFG+KS   ++ VL  + 
Sbjct: 267 FKHIFIDQLELPARAYNCLKRVNGHTISDLLNYSQDDLMKIKNFGKKS---VEQVLEALE 323

Query: 315 LFLGMNLP 322
               +NLP
Sbjct: 324 KQFSINLP 331


>gi|54020095|ref|YP_115726.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma hyopneumoniae
           232]
 gi|71893520|ref|YP_278966.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma hyopneumoniae
           J]
 gi|81603664|sp|Q601I9|RPOA_MYCH2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|90110849|sp|Q4AAG6|RPOA_MYCHJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|53987268|gb|AAV27469.1| DNA-directed RNA polymerase alpha chain [Mycoplasma hyopneumoniae
           232]
 gi|71851647|gb|AAZ44255.1| DNA-directed RNA polymerase alpha subunit [Mycoplasma hyopneumoniae
           J]
 gi|312601096|gb|ADQ90351.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma hyopneumoniae
           168]
          Length = 332

 Score =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 86/303 (28%), Positives = 153/303 (50%), Gaps = 19/303 (6%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           Q  E  T    +PL RG  +TLGNALRR ++SS+   A+  V+I+G+ HE + +  V ED
Sbjct: 16  QVNEFETSFEIKPLERGLGNTLGNALRRTVLSSIPSCAVFGVKIEGIKHEFTVLDDVIED 75

Query: 82  LTDIILNIKGINLK-----MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           +  I+ N+K +         S +S    +   +  G + A DI++ + ++++NPD  I +
Sbjct: 76  VVTILNNLKRVRFFYNPSVFSQNSIHVASFLGQKAGQIYARDIESHSGLKIVNPDLYIAD 135

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGL---------ITIDALYSPIKKVSYT 186
           +     ++ EL ++ G G+V  + ++   N+ I L         + +D+ +SP+   +Y 
Sbjct: 136 VSKVGALKFELFITNGKGFVDFETNKKYVNEVISLLESQIEGSVLAVDSDFSPVLNANYQ 195

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE--- 243
                    +  +KL+ +I TDGSI  +D+++  ++IL   L +  + E   K   +   
Sbjct: 196 AVEINSASPIIEEKLNFSIKTDGSIFAKDALSQGAKILIAHLNLLADVENLNKFSADFFG 255

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           D  +K  P        ++ L+LSVRS N LR      + D+ + ++ D   + N GRKS+
Sbjct: 256 DQEIKEEPIRR-FSNSIDALDLSVRSLNALRRAQYYKISDIEKLSQDDFENIKNLGRKSV 314

Query: 304 VEI 306
            EI
Sbjct: 315 QEI 317


>gi|119663522|emb|CAK22332.1| RNA polymerase alpha subunit [Lactobacillus acetotolerans]
          Length = 140

 Score =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 62/140 (44%), Positives = 92/140 (65%)

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+  +ILN+K + LK   D  K + +   GP  VTA D++   D+EVLNPD  IC + 
Sbjct: 1   REDVAKMILNLKKLELKCLSDDQKIIELDVEGPATVTADDLKADADVEVLNPDQYICTIA 60

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + M++ V KG GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+
Sbjct: 61  EGGHLHMQIAVRKGRGYVTASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDF 120

Query: 199 DKLSMTIDTDGSITGEDSVA 218
           DKL++ I TDGSI   D+++
Sbjct: 121 DKLTLEIWTDGSIKPNDALS 140


>gi|237688485|ref|YP_002905104.1| RNA polymerase alpha subunit [Picea sitchensis]
 gi|226875313|gb|ACO89052.1| RNA polymerase alpha subunit [Picea sitchensis]
          Length = 336

 Score =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 86/294 (29%), Positives = 152/294 (51%), Gaps = 21/294 (7%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RRVL+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRVLLGEVEGTCITHVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I   GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIRGASICIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIR-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALL-------KK---- 259
            ++++ ASRIL +    F++ EE   +    ++  N+   P +  L        KK    
Sbjct: 212 REALSEASRILIELFIPFLHGEEQNIDGMNNRKGSNMPPFPLSHVLTDTGETKEKKIAFQ 271

Query: 260 ---VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
              +++LE   R  NCLR  NI  + DL+  +  D++R+  FG++S+ ++  +L
Sbjct: 272 HIFIDQLEFPPRVYNCLRRANIHTLSDLLNYSREDLMRIERFGKESVEQVFEIL 325


>gi|300431322|gb|ADK12624.1| RNA polymerase alpha subunit [Amelichloa brevipes]
          Length = 339

 Score =  124 bits (310), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 86/285 (30%), Positives = 146/285 (51%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL     + +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDLCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------------- 253
           S+T ++++  ASR L D    F++ EE     +E+ N  + P                  
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKKLTNLKKNKKGI 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|118430418|ref|YP_874684.1| RNA polymerase alpha subunit [Hordeum vulgare subsp. vulgare]
 gi|68053191|sp|Q7H6J0|RPOA_HORMA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|68053192|sp|Q7H6J1|RPOA_HORJU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|68053193|sp|Q7H6J2|RPOA_HORBU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|126302597|sp|P92392|RPOA_HORVU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1770313|emb|CAB01360.1| alpha subunit of RNA polymerase [Hordeum brachyantherum subsp.
           californicum]
 gi|1770331|emb|CAB01774.1| alpha subunit of RNA polymerase [Hordeum erectifolium]
 gi|1770339|emb|CAB01366.1| alpha subunit of RNA polymerase [Hordeum marinum subsp.
           gussoneanum]
 gi|22657246|gb|AAM97426.1| RNA polymerase alpha subunit [Hordeum brachyantherum]
 gi|22657250|gb|AAM97428.1| RNA polymerase alpha subunit [Hordeum bulbosum]
 gi|22657252|gb|AAM97429.1| RNA polymerase alpha subunit [Hordeum jubatum]
 gi|22657254|gb|AAM97430.1| RNA polymerase alpha subunit [Hordeum marinum]
 gi|22657260|gb|AAM97433.1| RNA polymerase alpha subunit [Hordeum pusillum]
 gi|118201072|gb|ABK79443.1| RNA polymerase alpha subunit [Hordeum vulgare subsp. vulgare]
 gi|317017394|gb|ADU86099.1| RNA polymerase alpha subunit [Elymus enysii]
 gi|317017404|gb|ADU86104.1| RNA polymerase alpha subunit [Stenostachys gracilis]
          Length = 339

 Score =  124 bits (310), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 90/285 (31%), Positives = 149/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E ++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVETVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|159106895|ref|YP_001531313.1| RNA polymerase alpha subunit [Lolium perenne]
 gi|172048163|sp|A8Y9B8|RPOA_LOLPR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|158934429|emb|CAO86007.1| RNA polymerase alpha subunit [Lolium perenne]
          Length = 341

 Score =  124 bits (310), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 90/287 (31%), Positives = 148/287 (51%), Gaps = 22/287 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  I   +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCIARAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTSQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL----LKK--- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L    LKK   
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLNLKKNKK 267

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                   +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 GIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 314


>gi|300431303|gb|ADK12616.1| RNA polymerase alpha subunit [Aciachne flagellifera]
          Length = 339

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 86/285 (30%), Positives = 145/285 (50%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------------- 253
           S+T ++++  ASR L D    F++ EE     +E+ N  + P                  
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKKLTNLKKNKKGI 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|300431320|gb|ADK12623.1| RNA polymerase alpha subunit [Amelichloa caudata]
          Length = 339

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 86/285 (30%), Positives = 145/285 (50%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I+ +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------------- 253
           S T ++++  ASR L D    F++ EE     +E+ N  + P                  
Sbjct: 208 SSTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKKLTNLKKNKKGI 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|51859679|gb|AAU11119.1| RNA polymerase alpha subunit [Psathyrostachys lanuginosa]
          Length = 339

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 90/285 (31%), Positives = 150/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGXVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDMAQPIANLTEPIDFCIDLRI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|254751247|ref|ZP_05203285.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           Vollum]
          Length = 136

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 68/134 (50%), Positives = 94/134 (70%), Gaps = 2/134 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L ++ +    +I EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDG
Sbjct: 3   EIEKPK-IETVELNEDAKYGKFVI-EPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K + LK+  +  K + I  +G G+VTA DI   +D+E+
Sbjct: 61  VLHEFSTVEGVVEDVTTIILNLKKLALKIYSEEEKTLEIDVQGEGIVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDA 141
           LNPD  I  L  DA
Sbjct: 121 LNPDLHIATLAKDA 134


>gi|58758770|gb|AAW81775.1| RNA polymerase alpha subunit [Oedipodium griffithianum]
          Length = 340

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 94/307 (30%), Positives = 158/307 (51%), Gaps = 27/307 (8%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P   G A+T+G A+RR L+  + G  IT  +   V HE S+I G+ E + DI++N+K I 
Sbjct: 36  PFRCGQANTVGIAMRRALLGEVEGTCITCAKFKKVTHEYSTIAGIQESVHDILINLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+ +    ++  I   GP  VTA DI     +++++    I  L     + +EL + K  
Sbjct: 96  LRSNSYETQKAFISILGPKKVTAQDIILPPSVKIIDTTQYIATLTKTIHLDIELEIEKDC 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY      ++ +   G   IDA++ PI+  +Y+V S  E +    + L + I T+GSIT 
Sbjct: 156 GYRIQDSIKSTD---GHFPIDAIFMPIRNANYSVHSF-EHENKTQEILFIEIWTNGSITP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEV------KEDINVKSL-----PFNPALLKKV-- 260
           ++++  ASR L D    F++ E  KKE+      K + N  S      P    + K+V  
Sbjct: 212 KEALYEASRSLIDLFIPFLHAE--KKEIINGLENKYESNNMSYFSSFSPLADRITKEVTF 269

Query: 261 -----EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
                ++LEL  R+ NCL+  N+  + DL+  ++ D++++ NFG+KS   ++ VL  +  
Sbjct: 270 KHIFIDQLELPARAYNCLKRVNVHTISDLLNYSQDDLMKIKNFGKKS---VEQVLEALQK 326

Query: 316 FLGMNLP 322
              +NLP
Sbjct: 327 QFSINLP 333


>gi|161511735|emb|CAP16878.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 161

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 66/161 (40%), Positives = 102/161 (63%), Gaps = 2/161 (1%)

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           S+I+GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+ 
Sbjct: 1   STIEGVVEDVTQIILNLKKVSLKVESDEEKSLEINVMGPANVTAGDIVGDGDVTILNPEL 60

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESA 190
            IC +         LT  KG GY  A  +  R  + PIG++ ID++Y+PI++V+Y VE+ 
Sbjct: 61  PICTVAEGTTFHAVLTAEKGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENT 120

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           R GQ  DYDKL++ + TD S+   ++++ +++IL + L +F
Sbjct: 121 RVGQRDDYDKLTLDVWTDVSLAASEAISPSAKILTEHLTIF 161


>gi|150186925|emb|CAK30129.1| RNA polymerase alpha subunit [Streptococcus thermophilus]
          Length = 145

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 60/145 (41%), Positives = 98/145 (67%)

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           ILNIKG+ +K   +  K + +  +GP  VTAGDI T +DIE++NPDH +  +   A  + 
Sbjct: 1   ILNIKGLAVKSYVEDEKTIELDVQGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGASFQA 60

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
            +TVS   GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I
Sbjct: 61  TMTVSTNRGYVPAEENKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEI 120

Query: 206 DTDGSITGEDSVALASRILQDQLGM 230
            T+G+I  ED++ L++R+L + L +
Sbjct: 121 VTNGTIIPEDALGLSARVLIEHLNL 145


>gi|300431288|gb|ADK12609.1| RNA polymerase alpha subunit [Jarava leptostachya]
          Length = 339

 Score =  123 bits (309), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 85/285 (29%), Positives = 146/285 (51%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I+ +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------------- 253
           S+T ++++  ASR L D    F++ EE     +++ N  + P                  
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGASFEKNKNRFTPPLFTFQKKLTNLKKNKKGI 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|72080507|ref|YP_287565.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma hyopneumoniae
           7448]
 gi|90110848|sp|Q4A8J7|RPOA_MYCH7 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|71913631|gb|AAZ53542.1| DNA-directed RNA polymerase alpha subunit [Mycoplasma hyopneumoniae
           7448]
          Length = 332

 Score =  123 bits (309), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 83/303 (27%), Positives = 152/303 (50%), Gaps = 19/303 (6%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           Q  E  T    +PL RG  +TLGNALRR ++SS+   A+  V+I+G+ HE + +  V ED
Sbjct: 16  QVNEFETSFEIKPLERGLGNTLGNALRRTVLSSIPSCAVFGVKIEGIKHEFTVLDDVIED 75

Query: 82  LTDIILNIKGINLK-----MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           +  I+ N+K +         S +S    +   +  G + A DI++ + ++++NPD  I +
Sbjct: 76  VVTILNNLKRVRFFYNPSVFSQNSIHVASFLGQKAGQIYARDIESHSGLKIVNPDLYIAD 135

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPI----------GLITIDALYSPIKKVSYT 186
           +     ++ EL ++ G G+V  + ++   + +           ++ +D+ +SP+   +Y 
Sbjct: 136 VSKVGALKFELFITNGKGFVDFETNKKYVNEVISRLESQIEGSVLAVDSDFSPVLNANYQ 195

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE--- 243
                    +  +KL+ +I TDGSI  +D+++  ++IL   L +  + E   K   +   
Sbjct: 196 AVEINSASPIIEEKLNFSIKTDGSIFAKDALSQGAKILIAHLNLLADVENLNKFSADFFG 255

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           D  +K  P        ++ L+LSVRS N LR      + D+ + ++ D   + N GRKS+
Sbjct: 256 DQEIKEEPIR-RFSNSIDALDLSVRSLNALRRAQYYKISDIEKLSQDDFENIKNLGRKSV 314

Query: 304 VEI 306
            EI
Sbjct: 315 QEI 317


>gi|1771084|emb|CAB01369.1| alpha subunit of RNA polymerase [Hordeum vulgare subsp. spontaneum]
          Length = 339

 Score =  123 bits (309), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 90/285 (31%), Positives = 148/285 (51%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E ++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVETVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+  F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDXF 312


>gi|114329779|ref|YP_740597.1| RNA polymerase alpha subunit [Platanus occidentalis]
 gi|122166006|sp|Q09G14|RPOA_PLAOC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|114054417|gb|ABI49811.1| RNA polymerase alpha subunit [Platanus occidentalis]
          Length = 337

 Score =  123 bits (309), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 87/309 (28%), Positives = 160/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLIKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTIVGIEESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  RGPG VTA DI +   +E ++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGTRNASICIRGPGYVTAQDIISPPSVETVDNTQHIANLTEPIDFCIELEI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +     N   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGY---RMKTPNNSQDGSYPIDAVFMPVRNANHSIHSYANGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF-----NPALLKK----- 259
           S+T ++++  ASR L D    F++ +E    ++++ N  +LPF       A ++K     
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHAQEENILLEDNQNGVTLPFFTFHDRLAKIRKNEKEI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++ EL  R+ NCL+  NI  + DL   ++ D++++ +F    + ++K +LG +
Sbjct: 268 ALKYIFIDQSELPPRTYNCLKRSNIHTLLDLFNNSQEDLMKIEDF---RIEDVKQILGIL 324

Query: 314 GLFLGMNLP 322
                ++LP
Sbjct: 325 QKHFTVDLP 333


>gi|157325562|ref|YP_001468340.1| RNA polymerase alpha subunit [Ipomoea purpurea]
 gi|171769953|sp|A7Y3I1|RPOA_IPOPU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|157056790|gb|ABV02380.1| RNA polymerase alpha subunit [Ipomoea purpurea]
          Length = 337

 Score =  123 bits (308), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 86/311 (27%), Positives = 160/311 (51%), Gaps = 27/311 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT V+ +   HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRVKSEKAPHEYSTIAGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  +GPG VTA DI     +E+++    I  L       + L +
Sbjct: 92  KEIVLRSNLYGTCDASICVKGPGCVTAEDIILPPSVEIVDNTQHIAWLTEPIDFCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY+   HH  E+   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGYILKTHHNFED---GSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP-------ALLKK--- 259
           S+T ++++  ASR L D    F++ EE    +++     ++P +P       A L+K   
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHMEEENLHLED--GEHTIPLSPLSFHDKVAKLRKNKK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +++LE   +  NCL+  NI  + DL+ +++ D++++ +F    + ++K +LG
Sbjct: 266 KLALKSIFIDQLEFPPKIYNCLKKSNISTLLDLLNKSQEDLMKIEHF---HIEDVKQILG 322

Query: 312 TMGLFLGMNLP 322
            +     ++LP
Sbjct: 323 ILEKHFAIDLP 333


>gi|300431335|gb|ADK12628.1| RNA polymerase alpha subunit [Achnatherum eminens]
          Length = 339

 Score =  123 bits (308), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 85/285 (29%), Positives = 145/285 (50%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I+ +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------------- 253
            +T ++++  ASR L D    F++ EE     +E+ N  + P                  
Sbjct: 208 RLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKKLTNLKKNKKGI 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|149390385|ref|YP_001294384.1| RNA polymerase alpha subunit [Dioscorea elephantipes]
 gi|172048699|sp|A6MMN9|RPOA_DIOEL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|148668077|gb|ABR01461.1| RNA polymerase alpha subunit [Dioscorea elephantipes]
          Length = 337

 Score =  123 bits (308), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 90/311 (28%), Positives = 161/311 (51%), Gaps = 27/311 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ++RR L+  + G  IT  + + V HE S++ G+ E + +I+ N+
Sbjct: 32  FILSPLMKGQADTIGISMRRALLGEIEGTCITRAKSEKVPHEYSTVVGIEESVHEILFNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +    +  +I  RGP  VTA DI +   +E+++    I NL   +D  + +E+
Sbjct: 92  KEIVLRSNLYEIRDASICVRGPRYVTAQDIISPPYVEIVDTTQYIANLTEPIDLCIELEI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
              +G+   P       N   G   IDA++ P++  ++++ S   G     + L + I T
Sbjct: 152 KRDRGYRMKPIT-----NSQDGSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK--- 259
           +GS+T ++++  ASR L D    F++ EE     +E+ N  +LP   F   L  LKK   
Sbjct: 206 NGSLTPKEALYEASRNLIDLFVPFLHAEEEDINFEENKNKFTLPPLTFQDRLSNLKKNKK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +++LEL  R+ NCL+  NI  + DL+ + + ++++M  F    + ++K +L 
Sbjct: 266 GIPLKYIFIDQLELPSRTYNCLKRSNIHTLLDLLSKGQENLIKMEYF---HIEDVKQILD 322

Query: 312 TMGLFLGMNLP 322
           T+     ++LP
Sbjct: 323 TLQKHFAVDLP 333


>gi|11467223|ref|NP_043055.1| RNA polymerase alpha subunit [Zea mays]
 gi|1173146|sp|P09562|RPOA_MAIZE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|902253|emb|CAA60317.1| RNA polymerase alpha subunit [Zea mays]
          Length = 339

 Score =  123 bits (308), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 92/309 (29%), Positives = 159/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGNVPHEYSTIVGIEESIQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTTQPIANLREPVDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +   Y       +++   G   IDA++ P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRAYHTELRKNSQD---GSYPIDAVFMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F      LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHTEEEGTSFEENKNRLTPPLLTFQKRFTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R+ NCL+  NI  + DL+ +TE D++++ +F    + + K +  T+
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMQINSF---RMEDGKLIWDTL 324

Query: 314 GLFLGMNLP 322
              L ++LP
Sbjct: 325 EKHLPIDLP 333


>gi|295065759|ref|YP_003587699.1| RNA polymerase alpha subunit [Anomochloa marantoidea]
 gi|251765283|gb|ACT15437.1| RNA polymerase alpha subunit [Anomochloa marantoidea]
          Length = 339

 Score =  123 bits (308), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 96/313 (30%), Positives = 162/313 (51%), Gaps = 31/313 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  + + V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLIKGQADTVGIALRRALLGEIEGTCITRAKSENVPHEYSTIVGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI +   +E+++    I  L       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIISPPSVEIVDTAQHIATLTEPIDFCIELQI 151

Query: 150 SKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            +  GY     K+ + E+ P     IDA+  P++ V+Y++ S   G     + L + I T
Sbjct: 152 KRDRGYYTELRKNSQDESYP-----IDAVSMPVQNVNYSIFSCGNGNE-KQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK-------- 259
           +GS+T ++++  ASR L D    F++ EE     +E+ N  + P  P  L+K        
Sbjct: 206 NGSLTPKEALYEASRNLIDLFIPFLHAEEESTNFEENKNRFTQP--PLTLQKKLTNLKKN 263

Query: 260 ----------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                     +++L+L  R+ NCL+  NI  + DL+ +TE D+LR+ NF    + + K +
Sbjct: 264 KKGVPLNSIFIDQLKLPSRTYNCLKRANIHTLLDLLSKTEEDLLRIDNF---RMEDGKQI 320

Query: 310 LGTMGLFLGMNLP 322
           L T+   L ++LP
Sbjct: 321 LDTLEKDLPIDLP 333


>gi|156598227|gb|ABU85377.1| RNA polymerase alpha subunit [Elaeis oleifera]
          Length = 339

 Score =  123 bits (308), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 93/308 (30%), Positives = 158/308 (51%), Gaps = 23/308 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKVAHEYSTIVGIEESVHEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGP  VTA DI +   +E+++    I NL     + +EL +
Sbjct: 92  KEIILRSNLYGVIDASICVRGPRYVTAQDIISPPYVEIVDTTQHIANLTEPIDLCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +     N   G   IDA+  P++  ++++ S   G     + L + I T+G
Sbjct: 152 KRDRGY---RMKSANNSQDGSYPIDAVSMPVRNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N   LP   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFIPFLHAEEEDINFEENKNRFPLPLFTFQNRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++ EL  R+ NCL+G NI  + DL+  ++ D++R+  F    + ++K +L T+
Sbjct: 268 PLKCIFIDQSELPSRTYNCLKGSNIHTLSDLLSNSQEDLMRIKFF---RIEDVKQILDTL 324

Query: 314 GLFLGMNL 321
             +  ++L
Sbjct: 325 QKYFAIDL 332


>gi|300431299|gb|ADK12614.1| RNA polymerase alpha subunit [Hesperostipa comata]
          Length = 339

 Score =  123 bits (308), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 87/285 (30%), Positives = 146/285 (51%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FN------------- 253
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F              
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPRFTFQKKLTNLKKNKKGI 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|292559539|ref|YP_003540963.1| DNA-directed RNA polymerase alpha chain [Phoenix dactylifera]
 gi|290790947|gb|ADD63202.1| DNA-directed RNA polymerase alpha chain [Phoenix dactylifera]
 gi|294620609|gb|ADF28178.1| DNA-directed RNA polymerase alpha chain [Phoenix dactylifera]
          Length = 337

 Score =  123 bits (308), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 93/308 (30%), Positives = 158/308 (51%), Gaps = 23/308 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKVAHEYSTIVGIEESVHEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGP  VTA DI +   +E+++    I NL     + +EL +
Sbjct: 92  KEIILRSNLYGVIDASICVRGPRYVTAKDIISPPYVEIVDTTQHIANLTEPIDLCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +     N   G   IDA+  P++  ++++ S   G     + L + I T+G
Sbjct: 152 KRDRGY---RMKSANNSQDGSYPIDAVSMPVRNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N   LP   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFIPFLHAEEEDINFEENKNRFPLPLFTFQDRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++ EL  R+ NCL+G NI  + DL+  ++ D++R+  F    + ++K +L T+
Sbjct: 268 PLKCIFIDQSELPSRTYNCLKGSNIHTLSDLLNNSQEDLMRIEFF---RIEDVKQILDTL 324

Query: 314 GLFLGMNL 321
             +  ++L
Sbjct: 325 QKYFAIDL 332


>gi|313199607|ref|YP_004021222.1| RNA polymerase alpha subunit [Isoetes flaccida]
 gi|291575336|gb|ADE18049.1| RNA polymerase alpha subunit [Isoetes flaccida]
          Length = 341

 Score =  122 bits (307), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 87/323 (26%), Positives = 164/323 (50%), Gaps = 33/323 (10%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E  + +  I  PL  G A+TLG A+RR  +  L G  IT+ + + ++HE S++ G+ E +
Sbjct: 26  ERLHHSRFIISPLGIGQANTLGIAMRRASLGELEGTCITSAKFEKIIHEYSTVVGIQESV 85

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
            D ++N+K I L+ +    ++  I   GPG +TA DI     IE+++P   I  L     
Sbjct: 86  HDTLINLKEIVLRSNSSEIQKAYISIIGPGEITAQDIILPPSIEIIDPAQHIATLTKKIH 145

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES--AREGQVLDYDK 200
           + +EL + +  GY      ++++   G   ++A++ PI+ V+Y++    + + +++  + 
Sbjct: 146 LNIELRIERDRGYRRQNIVKSQD---GNFPLNAVFMPIRNVNYSIHCFESHDKKIMK-EM 201

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE---------------------PKK 239
           L + I T+GSIT  +++  ASR L +    F++ E                      P  
Sbjct: 202 LLLEIWTNGSITPREAIYEASRSLINLFIPFLHAENGEKIYGMGNINESNALSCSVLPPM 261

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            ++ D   K + F       +++LEL  R+ NCL+  N+  + DL+  ++ D++++ NFG
Sbjct: 262 SIQVDQMAKEVTFRHIF---IDQLELPPRAYNCLKRINVHTISDLLDYSQDDLMKIKNFG 318

Query: 300 RKSLVEIKGVLGTMGLFLGMNLP 322
            KS   ++ VL  +    G++LP
Sbjct: 319 IKS---VEQVLEALWKRFGISLP 338


>gi|7388087|sp|P92220|RPOA_BROIN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1769950|emb|CAB01354.1| alpha subunit of RNA polymerase [Bromus inermis]
          Length = 339

 Score =  122 bits (307), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 89/285 (31%), Positives = 149/285 (52%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  I   +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCIARAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFKKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|300431293|gb|ADK12611.1| RNA polymerase alpha subunit [Piptatherum miliaceum]
          Length = 339

 Score =  122 bits (307), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 86/285 (30%), Positives = 145/285 (50%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S++ G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTLAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASISVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPVDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------------- 253
           S+T ++++  ASR L D    F++ EE     +E+ N  + P                  
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKKLTNLKKNKKGI 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|300431291|gb|ADK12610.1| RNA polymerase alpha subunit [Jarava plumosula]
          Length = 339

 Score =  122 bits (307), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 85/285 (29%), Positives = 145/285 (50%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I+ +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------------- 253
           S+T ++++  AS  L D    F++ EE     +E+ N  + P                  
Sbjct: 208 SLTPKEALYEASHNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKKLTNLKKNKKGI 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|228017032|gb|ACP51855.1| RNA polymerase alpha subunit [Pinus canariensis]
          Length = 335

 Score =  122 bits (307), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 85/293 (29%), Positives = 151/293 (51%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
            +      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  FRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H   N   G+  IDA++ P++ V+Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSPNNYQDGIFPIDAVFMPVRDVNYSIHSYGSGNEIR-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPAL-------------L 257
            +++  ASR L D    F++ EE   +    K+  N+   P +  L             L
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTDTGETKEKIAFQL 271

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  ++ N LR  NI  + DL+  +  D++R+ +FG++S+ ++  VL
Sbjct: 272 IFIDQLELPPKTYNSLRRANIHTLSDLLNYSREDLMRIEHFGKESVEQVLEVL 324


>gi|300431295|gb|ADK12612.1| RNA polymerase alpha subunit [Aciachne acicularis]
          Length = 339

 Score =  122 bits (307), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 86/285 (30%), Positives = 144/285 (50%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDITLPPSVEIVDTAQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------------- 253
           S+T ++++  ASR L D    F++ EE     +E+ N  + P                  
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKKLTNLKKNKKGI 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  R+ NCL+  NI  + DL+ +TE D+ R+ +F
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLRRIDSF 312


>gi|253729586|ref|YP_003029770.1| RpoA [Bambusa oldhamii]
 gi|255961413|ref|YP_003097606.1| RNA polymerase a-subunit [Dendrocalamus latiflorus]
 gi|246367096|gb|ACS94707.1| RpoA [Bambusa oldhamii]
 gi|255040290|gb|ACT99950.1| RNA polymerase a-subunit [Dendrocalamus latiflorus]
          Length = 339

 Score =  122 bits (307), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 93/313 (29%), Positives = 155/313 (49%), Gaps = 31/313 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDMAQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY        +N   G   IDA+  P++ V+Y++     G    ++ L + I T+G
Sbjct: 152 KRDRGY---HTELRKNSQDGSYPIDAVSMPVRNVNYSIFYCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK----------- 258
           S+T ++++  ASR L D    F++ EE     +E+ N     F P LL            
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNR----FTPPLLTFQKKLTNLKKN 263

Query: 259 ---------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    + + K +
Sbjct: 264 KKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---RMEDGKQI 320

Query: 310 LGTMGLFLGMNLP 322
             T+   L ++LP
Sbjct: 321 WDTLEKHLPIDLP 333


>gi|19702212|emb|CAD28795.1| RNA polymerase alpha subunit [Cuscuta reflexa]
          Length = 335

 Score =  122 bits (306), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 91/312 (29%), Positives = 159/312 (50%), Gaps = 31/312 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L++ + G  IT V+     HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLTKGQADTIGIAMRRALLAEIEGTRITRVKFANTSHEYSTIAGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  +GPG VTA DI     +E+++    I  L       + L +
Sbjct: 92  KEIVLRSNLYGTCDASISIKGPGYVTAEDIILPPHVEIVDSTQHIAWLTEPINFFIGLKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES-AREGQVLDYDKLSMTIDTD 208
            + HGY    H   E+   G   IDAL  P++  ++++ S   E Q +    L + I T+
Sbjct: 152 ERNHGYFIKTHANFED---GSYPIDALLMPVRNANHSINSYGNEKQEI----LFLEIWTN 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP-------ALLKK-- 259
           GS+T ++++  ASR L D    F++ EE    + ED +  ++P +P       A L+K  
Sbjct: 205 GSLTPKEALHEASRNLIDLFIPFLHMEEENLHL-EDAD-HTIPLSPFTVYDKVAKLRKNK 262

Query: 260 ---------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                    +++LE   +  NCL+  NI  + DL+  ++ D++++ +F    L ++K +L
Sbjct: 263 KKLSLESIFIDQLEFPPKIYNCLKKSNIFTLLDLLNNSQEDLIKIEHF---HLEDVKQIL 319

Query: 311 GTMGLFLGMNLP 322
           G +G    ++ P
Sbjct: 320 GILGKHFALDSP 331


>gi|307683571|dbj|BAJ19764.1| RNA polymerase alpha chain [Larix decidua]
          Length = 335

 Score =  122 bits (306), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 85/293 (29%), Positives = 150/293 (51%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLRIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H   N   G+  IDA++ P+   +Y++ S      +  + L + I T+G +T 
Sbjct: 156 GYII---HSPNNYQDGIFPIDAVFMPVPDANYSIHSYGSRNEIR-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALLKK----------- 259
            +++  ASR L D L  F++ EE   +    ++  N+   P +  L              
Sbjct: 212 REALYEASRNLIDLLIPFLHGEEQNIDGMNNRKGSNMPPFPLSHVLTDTRETKEKIAFQH 271

Query: 260 --VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  R+ NCLR  NI  + DL+  +  D++R+ +FG++S+ ++  VL
Sbjct: 272 IFIDQLELPPRTYNCLRRANIHTLLDLLNYSREDLMRIEHFGKESVEQVLEVL 324


>gi|110227111|ref|YP_665590.1| RNA polymerase alpha subunit [Populus alba]
 gi|122243407|sp|Q14FC5|RPOA_POPAL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|109945549|dbj|BAE97237.1| RNA polymerase alpha chain [Populus alba]
          Length = 339

 Score =  122 bits (306), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 89/311 (28%), Positives = 164/311 (52%), Gaps = 25/311 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  +   + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSKKIPHEFSTITGIQESIHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +       +I  +GPG VTA DI     +E+++    I +L   +D  + +E+
Sbjct: 92  KEIVLRSNLYGTHNASICVKGPGCVTAQDIILPPSVEIIDNTQHIASLREPIDLHIGLEI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+   P K     N   G  +IDA++ P++  +++V S   G     + L + I T
Sbjct: 152 ERNRGYCMKPPK-----NFQDGSYSIDAVFMPVRNANHSVHSYGNGNE-KQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP-----ALLKK--- 259
           +GS+T ++++  ASR L D    F++ EE    ++++ +  +LP        A L+K   
Sbjct: 206 NGSLTPKEALHEASRNLIDLFIPFLHAEEESFHLEKNQHKITLPLFAFHDRLAKLRKNQK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +++LEL+ +  NCL+  NI  + DL++ ++ D++++ +F  + +  I G+L 
Sbjct: 266 EIALKSIFIDQLELAPKIYNCLKRSNIHTLWDLLKNSQEDLMKIEHFRIEDVKHIFGILK 325

Query: 312 TMGLFLGMNLP 322
               F  +NLP
Sbjct: 326 IEKHF-TINLP 335


>gi|108802673|ref|YP_636331.1| RNA polymerase alpha subunit [Eucalyptus globulus subsp. globulus]
 gi|309322478|ref|YP_003933992.1| RNA polymerase alpha subunit [Eucalyptus grandis]
 gi|90110843|sp|Q49KW6|RPOA_EUCGG RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|60460839|gb|AAX21059.1| RNA polymerase alpha subunit [Eucalyptus globulus subsp. globulus]
 gi|308223312|gb|ADO23620.1| RNA polymerase alpha subunit [Eucalyptus grandis]
          Length = 337

 Score =  122 bits (306), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 86/301 (28%), Positives = 158/301 (52%), Gaps = 25/301 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFEKIPHEYSTIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GPG VTA DI     +E+++    I NL     + + L +
Sbjct: 92  KEIVLRSNLYGTRNASICVKGPGCVTAQDIILPTSVEIVDNTQYIANLTEPINLCIGLQI 151

Query: 150 SKGHGYVPAKHHRT-ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
            +  GY    H +T +N   G   IDA++ P++  ++++ S   G     + L + I T+
Sbjct: 152 ERNRGY----HIKTPKNFQDGSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWTN 206

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF-----NPALLKK---- 259
           GS+T ++++  ASR L D    F++ EE    ++ +    +LPF       A L+K    
Sbjct: 207 GSLTPKEALHEASRNLIDLFIPFLHAEEENLHLENNQYKVTLPFFTFHDRLAKLRKTKKE 266

Query: 260 -------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                  +++ EL  R+ NCL+  NI  + DL+ +++ D+++M  F    + ++K +L +
Sbjct: 267 IALKSIFIDQFELPPRTYNCLKRYNIHTLFDLLNKSQEDLMKMEYF---RIEDVKQILDS 323

Query: 313 M 313
           +
Sbjct: 324 L 324


>gi|262286211|gb|ACY41679.1| RNA polymerase alpha subunit [Streptococcus intermedius]
          Length = 140

 Score =  122 bits (306), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 60/140 (42%), Positives = 94/140 (67%)

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+  IILN+KGI +K   +  K + +   GP  +TAGDI T +DIE++NPDH +  +
Sbjct: 1   VREDVMQIILNVKGIAVKSYVEDEKTIELDVEGPAEITAGDILTDSDIEIVNPDHYLFTI 60

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
              A ++  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    
Sbjct: 61  GEGASLKAIMTVNAGRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDG 120

Query: 198 YDKLSMTIDTDGSITGEDSV 217
           +DKL++ I TDG+I  ED++
Sbjct: 121 FDKLTLEIMTDGTIIPEDAL 140


>gi|156598421|gb|ABU85470.1| RNA polymerase alpha subunit [Musa acuminata]
          Length = 339

 Score =  122 bits (305), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 92/311 (29%), Positives = 160/311 (51%), Gaps = 27/311 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +  PL +G A T+G A+RR L+  + G  IT    + V HE S+I G+ E + +I+LN+
Sbjct: 32  FVLSPLMKGQADTIGIAMRRALLGEIEGTCITRANSEKVPHEYSTIIGIEESVHEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +    +  +I  RGP  VTA DI +   +E+++    I NL   +D  + +++
Sbjct: 92  KEIVLRSNIYGVRDASICARGPKYVTAQDIISPPSVEIVDTTQHIANLTEPIDLCIGLQI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
              +G+   P     T N   G   IDA+  P++  ++++ S   G     + L + I T
Sbjct: 152 RRDRGYRTKP-----TTNSQNGSYPIDAVSMPVRNANHSIHSYGNGNE-KQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK--- 259
           +GS+T ++++  ASR L D    F++ EE     KE+ N  +LP   F   L  LKK   
Sbjct: 206 NGSLTPKEALYEASRNLIDLFIPFLHAEEEDINFKENKNRFTLPIFTFQDRLTNLKKNKK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +++ EL  R+ NCL+  NI  + DL+ +++ D++R+  F    + ++K +  
Sbjct: 266 EIPLKCIFIDQSELPSRTYNCLKRSNIHTLLDLLNKSQEDLMRIEYF---RIEDVKEISD 322

Query: 312 TMGLFLGMNLP 322
           T+     ++LP
Sbjct: 323 TLQKHFAIDLP 333


>gi|262286213|gb|ACY41680.1| RNA polymerase alpha subunit [Streptococcus anginosus SK52]
          Length = 140

 Score =  122 bits (305), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 60/140 (42%), Positives = 94/140 (67%)

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+  IILN+KGI +K   +  K + +   GP  +TAGDI T +DIE++NPDH +  +
Sbjct: 1   VREDVMQIILNVKGIAVKSYVEDEKTIELDVEGPAEITAGDILTDSDIEIVNPDHYLFTI 60

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
              A ++  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    
Sbjct: 61  GEGASLKAIMTVNTGRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDG 120

Query: 198 YDKLSMTIDTDGSITGEDSV 217
           +DKL++ I TDG+I  ED++
Sbjct: 121 FDKLTLEIMTDGTIIPEDAL 140


>gi|229915452|gb|ACQ90797.1| alpha subunit of RNA polymerase [Oocystis solitaria]
          Length = 356

 Score =  122 bits (305), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 92/339 (27%), Positives = 165/339 (48%), Gaps = 45/339 (13%)

Query: 24  EENRTL---MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
           EEN+      I  P   G   TL N+LRR L+S + G AI A++I+G LHE S++ GV E
Sbjct: 20  EENKNFYGRFILGPFEVGQGLTLANSLRRTLLSEISGLAIVAMEIEGALHEYSNLPGVQE 79

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKR--GPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            + DI+LN+K I L    +  + V  F +  GPG+VTA D++  + I+ ++P   I  L 
Sbjct: 80  SILDILLNLKQIVLVSRFEMDQPVFGFLKVQGPGIVTASDLKLPSSIQCVDPHQYIATLS 139

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTE--------------------------NDPIGLIT 172
            +  + ++  V +   Y+  K+   +                          N    +++
Sbjct: 140 YNGFLSIKFFVCQKKNYIFLKNASLKKKKIYKLKKNKIQSPILEKKKSNFLINKTSNVVS 199

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDK----LSMTIDTDGSITGEDSVALASRILQDQL 228
           ID  +  + KV+Y +E+     +  ++K    + + I T+GS+    ++  A++ + +  
Sbjct: 200 IDPNFFSVNKVNYLIETC---SLFLFEKPKEQIFLEIWTNGSLHPRQAINEAAKRIVNIF 256

Query: 229 GMF--INFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLI 285
             F    F +P + +  +  ++K   F       +  L+LS+RS  CL+  NI  + +L+
Sbjct: 257 SPFQETRFYKPGRLKSSKLFSLKRENFKKFTSLDIANLDLSLRSYTCLKRANIHTIDNLL 316

Query: 286 QRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           Q +  ++L + NFG +SL E+  +L  +GL    NL D+
Sbjct: 317 QYSSEELLLLKNFGTRSLEEVLNILQQIGL----NLRDF 351


>gi|18860343|ref|NP_569660.1| RNA polymerase alpha subunit [Psilotum nudum]
 gi|22654078|sp|Q8WHZ1|RPOA_PSINU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|18389496|dbj|BAB84248.1| RNA polymerase alpha subunit [Psilotum nudum]
          Length = 340

 Score =  122 bits (305), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 81/289 (28%), Positives = 152/289 (52%), Gaps = 20/289 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P  +G A T+G A+RR L+  + G +IT  +   V+HE S++ G+ E + DI++N+K I 
Sbjct: 36  PFRKGQASTVGVAMRRALLGEVEGTSITYAKFKNVVHEYSTLVGIKESIHDILINLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      ++ +I   GP  VTAGDI     +++++    I  +     + +EL + +  
Sbjct: 96  LQSDSYETQKASISILGPRDVTAGDILLPTSVKIIDASQHIATITTAIPLDVELRIERDC 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY       +++   G   IDAL++PI+  +Y++ S      +  + L + + T+GS+T 
Sbjct: 156 GYRTLNLKESQS---GEFFIDALFTPIRNANYSIHSFESNNKVR-EILFLEVWTNGSLTP 211

Query: 214 EDSVALASRILQDQLGMFINF---EEPKKEVKEDINVKSLPFNP-----------ALLKK 259
             +++ ASR L D   +F+N    E  K+    ++N+K+ P                 K+
Sbjct: 212 GAALSEASRDLIDLFIIFLNMEKEESIKEIENNELNIKNFPSTSISVDIDRMAKEVAFKQ 271

Query: 260 --VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
             +++LEL  R+ NCL+   +  + DL++ T+ D+ ++ NFG KS+ ++
Sbjct: 272 IFIDQLELPARAYNCLKKMQVHTVSDLLKYTQYDLKKVKNFGNKSVEQV 320


>gi|300431278|gb|ADK12604.1| RNA polymerase alpha subunit [Piptochaetium montevidense]
          Length = 339

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 85/285 (29%), Positives = 145/285 (50%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDRAQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------------- 253
           S+T ++++  ASR L D    F++ EE     +E+ N  + P                  
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKKLTNLKKNKKGI 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  R+ NCL+  NI  + DL+ +TE D++++ +F
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMKIDSF 312


>gi|12372|emb|CAA33618.1| unnamed protein product [Triticum aestivum]
          Length = 339

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 89/285 (31%), Positives = 148/285 (51%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G     + L +   ++G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KLEILFLEYGSNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF 312


>gi|290489684|gb|ADD31226.1| RNA polymerase alpha subunit protein [Euonymus americanus]
          Length = 338

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 87/298 (29%), Positives = 160/298 (53%), Gaps = 22/298 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G +IT  + + + HE S++ G+ E + ++++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTSITRAKSEKIPHEYSTVVGIQETVHELLMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GPG VTA D+     +E+++    I  L       +EL +
Sbjct: 92  KEIVLRGNLYGIQNGSICIKGPGYVTAQDLVLPPSVEIVDNTQHIAILTEPIYFCIELQI 151

Query: 150 SKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
            +  GY    H +T N+   G   IDA++ P++  +Y+++S R G   + + L + I T+
Sbjct: 152 ERHRGY----HIKTPNNFQEGSFPIDAVFMPVRNTNYSIQSYRNGSEKE-EILFLEIWTN 206

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK---- 259
           GS+T ++++  ASR L D    F++ EE    ++ D    +LP   F+  L  LKK    
Sbjct: 207 GSLTPKEALHEASRNLIDLFIPFLHAEEENLHLENDWYKVTLPLFTFHDRLTKLKKNQKE 266

Query: 260 -------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                  +++LEL+ R+ NCL+  NI  + DL+ ++   +++M +F  + +  I  +L
Sbjct: 267 MALKYIFIDQLELTSRTYNCLKRSNIHTLFDLLNKSHEYLMKMEHFHIEDVKHILNIL 324


>gi|290489662|gb|ADD31215.1| RNA polymerase alpha subunit protein [Ilex cornuta]
          Length = 337

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 87/309 (28%), Positives = 161/309 (52%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFEKIPHEYSTIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGPG VT  DI     +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTCDASICVRGPGYVTTQDIILPPYVEIVDNTQHIASLTEPIDLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY+    +  ++   G   IDA++ P++  ++++ S R G     + L + I T+G
Sbjct: 152 ERNRGYLIKTPNNFQD---GSYPIDAVFMPVRNANHSIHSYRNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL-PFNP----ALLKK----- 259
           S+T ++++  ASR L D    F++ EE    ++++ +   L PFN     A L+K     
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHMEEENLHLEDNQHTIPLPPFNFHDKLAKLRKNKKKI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R  NCL+  NI  + DL+   + D++++ +F    + ++K +LG +
Sbjct: 268 ALKSIFIDQLELPPRIYNCLKRSNIYTLLDLLNNVQEDLMKIEHF---RIEDVKQILGVL 324

Query: 314 GLFLGMNLP 322
                ++LP
Sbjct: 325 EKHFAIDLP 333


>gi|290489658|gb|ADD31213.1| RNA polymerase alpha subunit protein [Dillenia indica]
          Length = 353

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 87/309 (28%), Positives = 160/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+++G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTMRGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  RGPG VTA DI     +E+++    I +L     + +EL +
Sbjct: 92  KEIVLRSNLYGTRNASICARGPGYVTAQDIILPPSVEIIDNTQHIASLTEPINLYIELQI 151

Query: 150 SKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
            +  GY    H +T N+       IDA++ P++  ++++ S   G     + L + I T+
Sbjct: 152 ERNRGY----HIKTPNNFQDESYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWTN 206

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLK------- 258
           GS+T ++++  ASR   D    FI+ E+    + ++ +  + P   F+  L K       
Sbjct: 207 GSLTPKEALHEASRNFIDLFIPFIHVEKENLYLGDNQDKDTFPLFTFHDELAKLRKNKKE 266

Query: 259 ------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL-G 311
                  +++LEL  R  NCL+  NI  + DL+  ++ D++++  F R+ + +I G+L  
Sbjct: 267 IALKYLFIDQLELPPRIYNCLKRSNIHTLLDLLNNSQEDLMKIEYFRREDVKQIFGILEK 326

Query: 312 TMGLFLGMN 320
            +  FL  N
Sbjct: 327 HLNFFLTKN 335


>gi|134093233|ref|YP_001109534.1| RNA polymerase alpha subunit [Populus trichocarpa]
 gi|158513819|sp|A4GYU3|RPOA_POPTR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|133712095|gb|ABO36738.1| RNA polymerase alpha subunit [Populus trichocarpa]
          Length = 339

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 89/311 (28%), Positives = 164/311 (52%), Gaps = 25/311 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  +   + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSKKIPHEFSTITGIQESIHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +       +I  +GPG VTA DI     +E+++    I +L   +D  + +E+
Sbjct: 92  KEIVLRSNLYGTHDASICVKGPGCVTAQDIILPPSVEIIDNTQHIASLREPIDLHIGLEI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+   P K     N   G  +IDA++ P++  +++V S   G     + L + I T
Sbjct: 152 ERNRGYCMKPPK-----NFQDGSYSIDAVFMPVRNANHSVHSYGNGNE-KQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP-----ALLKK--- 259
           +GS+T ++++  ASR L D    F++ EE    ++++ +  +LP        A L+K   
Sbjct: 206 NGSLTPKEALHEASRNLIDLFIPFLHAEEENFHLEKNQHKITLPLFAFHDRLAKLRKNQK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +++LEL+ +  NCL+  NI  + DL++ ++ D++++ +F  + +  I G+L 
Sbjct: 266 EIALKSIFIDQLELAPKIYNCLKRSNIHTLWDLLKNSQEDLMKIEHFRIEDVKHIFGILK 325

Query: 312 TMGLFLGMNLP 322
               F  +NLP
Sbjct: 326 IEKHF-TINLP 335


>gi|290489694|gb|ADD31231.1| RNA polymerase alpha subunit protein [Oxalis latifolia]
          Length = 339

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 86/310 (27%), Positives = 163/310 (52%), Gaps = 25/310 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S++ G+ E + +I++N+
Sbjct: 34  FILSPLMKGQADTIGIAIRRALLGEIEGTCITRAKSEKIPHEYSTLAGIQESIHEILMNL 93

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       ++  +GPG VTA DI     +E+++    I +L     + + L +
Sbjct: 94  KEIVLRSNLYGTHDASLCVKGPGYVTAQDIILPPSVEIIDNTQHIASLTEPIELCIGLQI 153

Query: 150 SKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
            +  GY    H +T N+   G   IDA++ P++  ++++ S R G     + L + I T+
Sbjct: 154 ERNRGY----HKKTPNNFQDGSYPIDAVFMPVRNANHSIHSYRNGNE-KQEMLFLEIWTN 208

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF-----NPALLKK---- 259
           GS+T ++++  ASR L D    F++ EE    ++ + +  +LP        A L+K    
Sbjct: 209 GSLTPKEALHEASRNLIDLFIPFLHAEEENSHLETNQHKVTLPLFTFHDRLAKLRKIKKK 268

Query: 260 -------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                  +++LEL+ R  NCL+  NI  + DL+  ++ D++ + +F    + ++K ++G 
Sbjct: 269 ISLKYIFIDQLELTPRIYNCLKRSNIHTLLDLLNNSQEDLMNIEHF---HIEDVKHIMGV 325

Query: 313 MGLFLGMNLP 322
           +   L ++LP
Sbjct: 326 LENNLAIDLP 335


>gi|119662399|emb|CAJ33189.1| RNA polymerase alpha subunit [Lactobacillus equi]
          Length = 170

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 64/159 (40%), Positives = 103/159 (64%), Gaps = 2/159 (1%)

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           ILN+K + LKM  +  + + I   GP  VTAGDI+  +D+EVLN D  I  +     + +
Sbjct: 1   ILNLKKVALKMDSEESQTLEIDVVGPLEVTAGDIKGPSDVEVLNDDLYIATVAEGHSLHV 60

Query: 146 ELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +T  KG GYV A  ++ +ND  PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++
Sbjct: 61  RMTADKGRGYVSANENKAKNDDMPIGVLAIDSIYTPIERVNYQVEKTRVGQKNDYDKLTL 120

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
            + T+GSIT  ++++L+++IL + L +F +  +  K V+
Sbjct: 121 DVWTNGSITPSEAISLSAKILTEHLTLFGDLTDEAKNVE 159


>gi|290489670|gb|ADD31219.1| RNA polymerase alpha subunit protein [Nerium oleander]
          Length = 337

 Score =  121 bits (303), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 90/311 (28%), Positives = 159/311 (51%), Gaps = 27/311 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT V+ D V HE S+IKG+ E + +I++N+
Sbjct: 32  FILSPLLKGQADTIGIAMRRALLGEIEGTCITRVKFDKVPHEYSTIKGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGPG VTA DI     +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTCDASICVRGPGYVTAQDIVLPPYVEIVDNTQHIASLMEPINLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY+       +N   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGYLIQT---PQNFQDGSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL----------KK 259
           S+T ++++  ASR L D    F++ EE    ++   N  ++P  P +           KK
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHMEEENSHLEN--NQHAVPLFPFIFHDKLTKLIKNKK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F    + ++K +L 
Sbjct: 266 EIALKSIFIDQLELPPRIYNCLKRSNIYTLLDLLNNSQEDLMKIEHF---RIEDVKQILV 322

Query: 312 TMGLFLGMNLP 322
            +   L + LP
Sbjct: 323 ILEKHLAIFLP 333


>gi|161511751|emb|CAP16886.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           dextrinicus]
          Length = 138

 Score =  121 bits (303), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 56/129 (43%), Positives = 90/129 (69%)

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITI 173
           VTA DI+  +DIEVLNP+  IC++     V M++TVS G GYVPA  ++  + PIG+I +
Sbjct: 1   VTAADIKADDDIEVLNPEQYICSIAEGGHVHMQMTVSNGRGYVPADQNKNGDMPIGVIAV 60

Query: 174 DALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           D++++PI +V+Y VES R G+  D+DKL++ + T+GSI+   +++LA++IL D L +FI+
Sbjct: 61  DSIFTPINRVNYQVESTRVGKRNDFDKLTLDVWTNGSISPRXAISLAAKILSDHLNIFID 120

Query: 234 FEEPKKEVK 242
             +  K  +
Sbjct: 121 LSDEAKNTE 129


>gi|7388092|sp|P93962|RPOA_PSAST RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1771505|emb|CAB01339.1| alpha subunit of RNA polymerase [Psathyrostachys stoloniformis]
          Length = 339

 Score =  121 bits (303), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 86/287 (29%), Positives = 153/287 (53%), Gaps = 24/287 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +     HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSXPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL   +D  + +++
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTXQPIANLTEPIDFCIDLQI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
              +G+     K+++  + PI  +++     P++ V+Y++ S   G    ++ L + I T
Sbjct: 152 KRDRGYQTELRKNYQDGSYPIXXVSM-----PVRNVNYSIFSCGNGNE-KHEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK--- 259
           +GS+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK   
Sbjct: 206 NGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                   +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 266 GIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|228016968|gb|ACP51792.1| RNA polymerase alpha subunit [Pinus banksiana]
          Length = 335

 Score =  121 bits (303), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 86/293 (29%), Positives = 150/293 (51%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIR-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPAL-------------L 257
            +++  ASR L D    F++ EE   +    K+  N+   P +  L             L
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHLLTDTGETKEKIAFQL 271

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  +  N LR  NI  + DL+  +  D++R+ NFG++S+ ++  VL
Sbjct: 272 IFIDQLELPPKIYNSLRRANIHTLLDLLNYSREDLMRIKNFGKESVEQVLEVL 324


>gi|58758777|gb|AAW81780.1| RNA polymerase alpha subunit [Dendroligotrichum dendroides]
          Length = 340

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 89/306 (29%), Positives = 155/306 (50%), Gaps = 23/306 (7%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P   G A+T+G A+RR L+  + G  IT  +   V HE S+I G+ E   DI++N+K I 
Sbjct: 36  PFRCGQANTVGIAMRRALLGEIEGTCITCARSKKVTHEYSTIVGIQESAHDILINLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK +    ++  +   GP  +TA DI     +++++    I  +     + +EL + K  
Sbjct: 96  LKSNSYETQKAFLSILGPKKITAQDIILPPSVKIIDTTQYIATITKPIHLDIELEIDKDC 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY      ++ +   G  +IDA++ PI+  +Y+V S      +  + L + I T+GSIT 
Sbjct: 156 GYRIXDSVKSID---GYFSIDAIFMPIRNANYSVHSFENNNKIQ-EILFIEIWTNGSITP 211

Query: 214 EDSVALASRILQDQLGMFINFEEP------KKEVKEDINVKSLPFNP---ALLKK----- 259
           ++++  ASR L D    F++ E+       K E K +       F+P    L K+     
Sbjct: 212 KEALYEASRSLIDLFIPFLHTEKKETINGLKTEYKSNDMSDFSSFSPLADKLTKEIKFKH 271

Query: 260 --VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +++LEL  R+ NCL+  N+  + DL+   + D +++ NFG+KS   ++ VL  +    
Sbjct: 272 IFIDQLELPARAYNCLKRVNVHPISDLLNYXQDDFMKIKNFGKKS---VEQVLEALQKQF 328

Query: 318 GMNLPD 323
            +NLP+
Sbjct: 329 SINLPE 334


>gi|290489688|gb|ADD31228.1| RNA polymerase alpha subunit protein [Gunnera manicata]
          Length = 330

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 87/297 (29%), Positives = 158/297 (53%), Gaps = 20/297 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FIMSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK +    +  +I  RGPG VTA DI +   +E+++    I +L     + ++L +
Sbjct: 92  KEIILKSNIYGTRDASICVRGPGYVTAQDIISPPSVEIVDNTQHIASLTEPIDLCIQLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            K  GY   K   T  D  G   IDA++ P++  ++++ S   G+    + L + I T+G
Sbjct: 152 EKNRGY-RIKTPNTYQD--GSYPIDAVFMPVRNANHSIHSYGNGKE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF-----NPALLKK----- 259
           S+T ++++  ASR L D    F++ EE    ++++    +LPF       A L+K     
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHAEEENLHLEDNQYKVTLPFFTFHDRLAKLRKNKKEI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++ EL  R+ NCL+  NI  + DL+  ++ D++++ +F  + + +I  +L
Sbjct: 268 ALKSIFIDQSELPSRTYNCLKSSNIHTLLDLLNNSQEDLMKIKHFSIEDVKQILDIL 324


>gi|300431270|gb|ADK12600.1| RNA polymerase alpha subunit [Piptochaetium medium]
          Length = 339

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 85/285 (29%), Positives = 145/285 (50%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDRAQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------------- 253
           S+T ++++  ASR L D    F++ EE     +E+ N  + P                  
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTCFEENKNRFTPPLFTFQKKLTNLKKNKKGI 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  R+ NCL+  NI  + DL+ +TE D++++ +F
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMKIDSF 312


>gi|326200311|gb|ADZ52350.1| RNA polymerase alpha subunit [Asclepias syriaca]
          Length = 340

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 90/309 (29%), Positives = 157/309 (50%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +  A T+G A+RR L+  + G  IT V+ D + HE S+IKG+ E + +I++N+
Sbjct: 32  FILSPLLKSQADTIGIAMRRALLGEIEGTCITHVKFDKIPHEYSTIKGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +        I  RGP  VTA DI     +E+++    I NL     + + L +
Sbjct: 92  KEIVLRSNLYEPCDAYICVRGPRSVTAQDIVLPPYVEIVDNTQHIANLTEPINLCIVLKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY+       +N P G   IDA++ P++  +++V S   G     + L + I T+G
Sbjct: 152 ERNRGYLIQT---PQNVPDGSYPIDAVFMPVRNANHSVHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN-VKSLPFN-----PALLKK---- 259
           S+T ++++  ASR L D    F++ EE    ++ + + V   PF        L+K     
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHMEEENSHLENNQHRVPLFPFTFHDKLTKLIKNKKEI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F    + ++K +L  +
Sbjct: 268 ALKSIFIDQLELPPRIYNCLKRSNIYTLLDLLNNSQEDLMKIEHF---RIEDVKQILVVL 324

Query: 314 GLFLGMNLP 322
              L + LP
Sbjct: 325 EKHLAIFLP 333


>gi|194132131|gb|ACF33385.1| RNA polymerase alpha subunit [Gonystylus bancanus]
          Length = 329

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 84/300 (28%), Positives = 156/300 (52%), Gaps = 26/300 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S I G+ E + +I++N+
Sbjct: 34  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSIIAGIQESVHEILMNL 93

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +    +   I  +GPG VTA DI     +E+++    I +L   +D  + +++
Sbjct: 94  KEIVLRSNLYGTRNAFICAKGPGYVTAQDIILPPSVEIVDNTQHIASLTEPIDLCIGLQI 153

Query: 148 TVSKGHGY-VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
             ++G+G   P   H       G   ID ++ P++ V++++ S   G     + L + I 
Sbjct: 154 ERNRGYGIKTPNNFHD------GSYPIDVVFMPVRNVNHSIHSYGNGNE-KQEILFLEIW 206

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA----------- 255
           T+GS+T ++++  ASR L D    F++ EE    ++   +  +LPF P            
Sbjct: 207 TNGSLTPKEALHEASRNLIDLFIPFLHAEEENSHLENSQHKVTLPFFPFHDKLTKLRKKK 266

Query: 256 ---LLKK--VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
               LK   +++ EL  R  NCL+  NI  + DL+ +++ D++++ +F R+ + +I G++
Sbjct: 267 KEIALKYFFIDQSELPPRIYNCLKTSNIHTLFDLLNKSQEDLMKIEHFHREDVKQILGII 326


>gi|150036840|emb|CAM98285.1| DNA-directed RNA polymerase alpha chain [Leuconostoc argentinum
           KCTC 3773]
          Length = 190

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 63/157 (40%), Positives = 98/157 (62%), Gaps = 2/157 (1%)

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+T IILN+K + L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +  
Sbjct: 7   EDVTQIILNLKKVVLAIDSDDERSLEIDVQGPAEVTAADLQAGADVEVLNPDLHIATVAA 66

Query: 140 DAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
              + M +T  KG GY  A  ++   E  PIG++ +D++Y+PI++V+Y VE+ R G   D
Sbjct: 67  GKSLHMTVTAVKGRGYSSADENKQLREEMPIGVLAVDSIYTPIERVNYHVENTRVGARDD 126

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           YDKL+  I T+GSI   D+++L ++IL + L +F++ 
Sbjct: 127 YDKLTFDIWTNGSIKPSDALSLGAKILAEHLNLFMDI 163


>gi|49574614|ref|NP_848091.2| RNA polymerase alpha subunit [Adiantum capillus-veneris]
 gi|60393869|sp|Q85FJ1|RPOA_ADICA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|48476025|gb|AAP29422.2| RNA polymerase alpha chain [Adiantum capillus-veneris]
          Length = 345

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 91/317 (28%), Positives = 151/317 (47%), Gaps = 35/317 (11%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +  P  RG A T+G A+RR L+  + G +IT  +  GV+HE S+I G+ E + D+++N+
Sbjct: 32  FLVSPFKRGQASTVGIAMRRALLQEIEGTSITCARFCGVVHEYSTITGLQETIHDVLVNL 91

Query: 90  KGINLKMSGDSHKRVT---IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           K I L+  GDS + +    +   GP  VTAGD+     +E ++    I  +     + +E
Sbjct: 92  KEIVLR--GDSKEDIQEAFLSVTGPKEVTAGDLSLPPGVEAIDNSQYIATITQPISLTIE 149

Query: 147 LTVSKGHGYVPAKHHRTEN---DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
           L + K  GY      R EN      G   IDA++ P++ V+Y++     G+    + L +
Sbjct: 150 LEIEKDCGY------RIENLAKSGKGQFPIDAVFMPVRNVNYSIHLFGSGRATQ-EILFI 202

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN-----VKSLPFNPAL-- 256
            I T+GS+T  +++  AS  L D L  F+        + E+        KS    P    
Sbjct: 203 EIWTNGSLTPHEALRKASEKLMDLLTTFLYVRGGDVSLFENGEDSLDLTKSPSLQPQFGD 262

Query: 257 ----------LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
                      + +++LEL  R+ NCL+   I  + DL+  +  D+ ++ NFGRKS+ ++
Sbjct: 263 TNNLEERVLENRFIDQLELPARAFNCLKRAEIYTIADLLNYSREDLSKLKNFGRKSVDQV 322

Query: 307 KGVLGTMGLFLGMNLPD 323
              L          LPD
Sbjct: 323 SEALWDR---FAKELPD 336


>gi|150187079|emb|CAK30166.1| RNA polymerase alpha subunit [Streptococcus parasanguinis ATCC
           15912]
          Length = 150

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 56/128 (43%), Positives = 87/128 (67%)

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
            GP  VTAGDI T +DIE++NPDH +  +   A ++  LTV+ G GYVPA  ++ ++ P+
Sbjct: 9   EGPAEVTAGDILTDSDIEIVNPDHYLFTIGEGASLKATLTVNSGRGYVPADQNKKDDAPV 68

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           G + +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L
Sbjct: 69  GTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHL 128

Query: 229 GMFINFEE 236
            +F N  E
Sbjct: 129 NLFTNLTE 136


>gi|228016469|gb|ACP51301.1| RNA polymerase alpha subunit [Pinus torreyana subsp. insularis]
 gi|228016530|gb|ACP51361.1| RNA polymerase alpha subunit [Pinus torreyana subsp. torreyana]
          Length = 335

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 85/293 (29%), Positives = 151/293 (51%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIR-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPAL-------------L 257
            +++  ASR L D    F++ EE   +    K+  N+   P +  L             L
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHLLTDTGETKEKIAFQL 271

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  ++ N LR  NI  + DL+  +  D++R+ +FG++S+ ++  VL
Sbjct: 272 IFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMRIEHFGKESVEQVLEVL 324


>gi|300431280|gb|ADK12605.1| RNA polymerase alpha subunit [Piptochaetium napostaense]
          Length = 339

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 84/285 (29%), Positives = 145/285 (50%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDRAQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------------- 253
           S+T ++++  ASR L D    F++ EE     +E+ N  + P                  
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKKLTNLKKNKKGI 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  ++ NCL+  NI  + DL+ +TE D++++ +F
Sbjct: 268 PLNCIFIDQLELPSKTYNCLKRANIHTLLDLLSKTEEDLMKIDSF 312


>gi|51859681|gb|AAU11120.1| RNA polymerase alpha subunit [Psathyrostachys lanuginosa]
          Length = 339

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 89/285 (31%), Positives = 148/285 (51%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTXQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+   ++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMXVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLLTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 + +LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 268 PLNCIFIXQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|161511743|emb|CAP16882.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 158

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 62/154 (40%), Positives = 96/154 (62%), Gaps = 2/154 (1%)

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  IC +     
Sbjct: 1   TQIILNLKKVSLKVESDEEKSLEINVMGPANVTAGDIVGDGDVTILNPELPICTVAEGTT 60

Query: 143 VRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
               LT  KG GY  A  +  R  + PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDK
Sbjct: 61  FHAVLTAEKGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDK 120

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           L++ + TDGS+   ++++L+++IL + L +F+  
Sbjct: 121 LTLDVWTDGSLAASEAISLSAKILTEHLXIFVTL 154


>gi|159161282|ref|YP_001542560.1| RNA polymerase alpha subunit [Cuscuta exaltata]
 gi|172048134|sp|A8W3F3|RPOA_CUSEX RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|158938707|gb|ABW83724.1| RNA polymerase alpha subunit [Cuscuta exaltata]
          Length = 335

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 91/312 (29%), Positives = 161/312 (51%), Gaps = 31/312 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L++ + G  IT V+     HE S+I G+ E + +I +N+
Sbjct: 32  FILSPLRKGQADTIGIAMRRALLAEIEGTRITRVKFAKASHEYSTIAGIQESVHEIFMNL 91

Query: 90  KGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K I L+  + G     ++I  +GPG VTA DI     +E+++    I  L     + + L
Sbjct: 92  KEIVLRSNLYGTCDASISI--KGPGHVTAKDIILPPHVEIVDSTQHIAWLTEPIDLCIGL 149

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES-AREGQVLDYDKLSMTID 206
            + +  GY    H   E+   G   IDA++ P++  ++++ S   E Q +    L + I 
Sbjct: 150 KIERNRGYFIKTHPNFED---GSYPIDAVFMPVRNANHSIHSYGNEKQEI----LFLEIW 202

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL-PFN----PALLKK-- 259
           T+GS+T ++++  ASR L D    F++ EE    +++  +  SL PF      A L+K  
Sbjct: 203 TNGSLTPKEALHEASRNLIDLFIPFLHMEEENLHLEDADHTISLSPFTVYDKVAKLRKNK 262

Query: 260 ---------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                    +++LE   +  NCL+  NI  + DL+  ++ D++++ +F    L ++K +L
Sbjct: 263 KKRSLESIFIDQLEFPPKIYNCLKKSNIFTLLDLLNNSQEDLIKIEHF---RLEDVKQIL 319

Query: 311 GTMGLFLGMNLP 322
           G +G    ++LP
Sbjct: 320 GILGKHFALDLP 331


>gi|228015949|gb|ACP50789.1| RNA polymerase alpha subunit [Pinus ponderosa]
 gi|228016842|gb|ACP51668.1| RNA polymerase alpha subunit [Pinus attenuata]
          Length = 335

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 85/293 (29%), Positives = 151/293 (51%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIR-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPAL-------------L 257
            +++  ASR L D    F++ EE   +    K+  N+   P +  L             L
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHLLTDTGETKEKIAFQL 271

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  ++ N LR  NI  + DL+  +  D++R+ +FG++S+ ++  VL
Sbjct: 272 IFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMRIEHFGKESVEQVLEVL 324


>gi|159161193|ref|YP_001542479.1| RNA polymerase alpha subunit [Ceratophyllum demersum]
 gi|172048124|sp|A8SED5|RPOA_CERDE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|148508476|gb|ABQ81483.1| RNA polymerase alpha subunit [Ceratophyllum demersum]
 gi|227481150|emb|CAP62529.1| RNA polymerase alpha subunit [Ceratophyllum demersum]
          Length = 337

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 87/311 (27%), Positives = 165/311 (53%), Gaps = 27/311 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ++RR L+  + G  IT  + D V HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGISMRRALLGEIEGTCITRAKFDKVTHEYSTIVGIEESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +       +I  RGP  VTA DI +   +E+++    I NL   +D  + +++
Sbjct: 92  KEIVLRSNLYGTLDASICVRGPRSVTAQDIISPPSVEIVDTTQHIANLTEPIDLCIGLQI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
              +G+      +++  + P     ID ++ P++  ++++ S   G     + L + I T
Sbjct: 152 ERDRGYRLKTPNNYQDGSYP-----IDTVFMPVRNANHSIHSYGNG-TEKQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK--- 259
           +GS+T ++++  ASR L +    F++ EE +  +++  N+ ++P   F+  L  LKK   
Sbjct: 206 NGSLTPKEALYEASRNLINLFIPFLHAEEQEILLEDSENISTVPLFTFHNELANLKKNKK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +++LEL  R+ NCL+  NI  + DL+  ++ D++R+ +F    + ++K +L 
Sbjct: 266 GIALKCIFIDQLELPSRTYNCLKRSNIHTLFDLLSNSKEDLMRIEHF---RVEDVKQILD 322

Query: 312 TMGLFLGMNLP 322
            +     MNLP
Sbjct: 323 ILQKNFAMNLP 333


>gi|290489702|gb|ADD31235.1| RNA polymerase alpha subunit protein [Trochodendron aralioides]
          Length = 337

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 88/310 (28%), Positives = 158/310 (50%), Gaps = 25/310 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTIVGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGPG VTA DI +   +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTLDASICVRGPGYVTAQDIISPPSVEIVDATQHIASLTEPIDLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +     N   G   IDA++ P++  S+++ S   G     + L + I T+G
Sbjct: 152 ERNRGY---RMKTPNNSQDGSYPIDAVFMPVRNASHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL------ 263
           S+T ++++  ASR L D    F++ EE   +++++ N  SLPF  A   ++  L      
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHAEEESIKLEDNQNGISLPFF-AFHDRLANLKKKKKE 266

Query: 264 -----------ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                      EL  R+ NCL+  NI  + DL+  ++ D++++ +F    + ++K +L  
Sbjct: 267 IAFKCIFIDQSELPPRTYNCLKRSNIYTLLDLLNNSQEDLMKIDHF---HIEDVKQILDI 323

Query: 313 MGLFLGMNLP 322
           +     ++LP
Sbjct: 324 LQKHFSIDLP 333


>gi|225544155|ref|YP_002720144.1| rpoA [Jatropha curcas]
 gi|224979596|gb|ACN72723.1| rpoA [Jatropha curcas]
          Length = 339

 Score =  120 bits (300), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 87/311 (27%), Positives = 163/311 (52%), Gaps = 25/311 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEFSTIAGIQESIHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL--DVDAVVRMEL 147
           K + LK +       +I+ +GPG VTA DI     +E+++    I +L   +D  + +++
Sbjct: 92  KNVVLKSNLYGTCDASIYVKGPGYVTAQDIILPPFVEIIDNTQHIASLTESIDLCIGLQI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+   P     T N   G   IDA++ P++  +++V S   G     + L + I T
Sbjct: 152 ERNRGYRIKP-----TNNFQDGSYPIDAVFMPVRNANHSVHSYGNGNE-KQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLK------ 258
           +GS+T ++++  ASR L D    F++ EE    ++ + +  +LP   F+  L K      
Sbjct: 206 NGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLEINQHKVTLPLFTFHGRLTKLRKNQK 265

Query: 259 -------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +++ EL+ ++ NCL+  NI  + DL+ +++ D++++ NF    +  I G+L 
Sbjct: 266 EIALKYIFIDQSELTPKTYNCLKRSNIHTLSDLLNKSQEDLMKIENFRIDDVKHILGILE 325

Query: 312 TMGLFLGMNLP 322
               F  ++LP
Sbjct: 326 IEKHF-AIDLP 335


>gi|304373166|ref|YP_003856375.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma hyorhinis
           HUB-1]
 gi|304309357|gb|ADM21837.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma hyorhinis
           HUB-1]
 gi|330723976|gb|AEC46346.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma hyorhinis
           MCLD]
          Length = 333

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 90/301 (29%), Positives = 156/301 (51%), Gaps = 36/301 (11%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           +PL RGFA+TLGN+LRR ++SS+   A+  V+I+GV HE S I  V ED+  I+ N+K +
Sbjct: 27  QPLERGFANTLGNSLRRTILSSVPSVAVFGVKIEGVEHEFSVIDKVREDVVTILNNLKKL 86

Query: 93  NLKMSGD----SHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
                 +    +  +V  F  R  G +T  DI   + +E++N D V+ N      ++ E+
Sbjct: 87  RFSFKKEVFLQNEIQVASFDGRKVGKITGADILVNSALEIVNKDQVVANTSEVGALKFEM 146

Query: 148 TVSKGHGYVPAKHHRTENDPIG-----------LITIDALYSPIKKVSYTVESAREGQVL 196
            ++ G G+V  + ++ +   +G           +I +D+ +S ++ V ++         +
Sbjct: 147 FLTYGRGFVDFETNKRKIQELGPALESKLGYGQIIAVDSDFSAVENVKFSSTELNSSNPI 206

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN-----------FEEPKKEVKEDI 245
             +KL+ ++ TDG+I  +D++A A++IL   L +  +           FEE K+  KE+ 
Sbjct: 207 VEEKLTFSVKTDGTILAKDALAEAAKILIAHLKLVSDTANLDAEVDSFFEEVKQ--KEEA 264

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             K    N A L     L+L+VRS N LR      + DL++ T  ++  + N G+KS+ E
Sbjct: 265 PKK----NSADLTT---LDLTVRSLNALRRAQYYKISDLLELTLEELENIKNLGKKSVEE 317

Query: 306 I 306
           I
Sbjct: 318 I 318


>gi|7388088|sp|P92225|RPOA_CRIDE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1770151|emb|CAB01330.1| alpha subunit of RNA polymerase [Crithopsis delileana]
          Length = 339

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 88/285 (30%), Positives = 147/285 (51%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL+ R+ NC +      + DL+ +TE D+LR+ +F
Sbjct: 268 PLNCIFIDQLELTSRTYNCXKRXXXXTLLDLLSKTEEDLLRIDSF 312


>gi|165910449|gb|ABY73979.1| RNA polymerase alpha subunit [Cuscuta lupuliformis]
          Length = 335

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 91/312 (29%), Positives = 161/312 (51%), Gaps = 31/312 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L++ + G  IT V+     HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIALRRALLAEIEGTRITRVKFANASHEYSTIAGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  +GPG VTA DI     +EV++    I  L     + + L +
Sbjct: 92  KEIVLRSNLYGTCDASISIKGPGYVTAEDIILPPHVEVVDSTQHIAWLMEPIDLCIGLKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES-AREGQVLDYDKLSMTIDTD 208
            +  GY    H   E+   G   IDA++ P++  ++++ S   E Q +    L + I T+
Sbjct: 152 ERNRGYFLKTHANFED---GSYPIDAVFMPVQNANHSIHSYGNEKQEI----LFLEIWTN 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP-------ALLKK-- 259
           GS+T ++++  ASR L D    F++ E+    + ED + +++P +P       A L+K  
Sbjct: 205 GSLTPKEALHEASRNLIDLFIPFLHIEKENLHL-EDAD-RTIPLSPFTVYDKVAKLRKNK 262

Query: 260 ---------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                    +++LE      NCL+  NI  + DL+  ++ D++++ +F    L ++K +L
Sbjct: 263 KKLALESLFIDQLEFPPNIYNCLKKSNIFTLLDLLNNSQEDLMKIEHF---RLEDVKQIL 319

Query: 311 GTMGLFLGMNLP 322
           G +G    ++LP
Sbjct: 320 GILGKHFALDLP 331


>gi|262286159|gb|ACY41653.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
 gi|262286161|gb|ACY41654.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
 gi|262286163|gb|ACY41655.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
 gi|262286167|gb|ACY41657.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
 gi|262286169|gb|ACY41658.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
 gi|262286171|gb|ACY41659.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
 gi|262286173|gb|ACY41660.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
 gi|262286175|gb|ACY41661.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
 gi|262286197|gb|ACY41672.1| RNA polymerase alpha subunit [Streptococcus mitis]
 gi|262286199|gb|ACY41673.1| RNA polymerase alpha subunit [Streptococcus mitis]
 gi|262286201|gb|ACY41674.1| RNA polymerase alpha subunit [Streptococcus mitis]
 gi|262286203|gb|ACY41675.1| RNA polymerase alpha subunit [Streptococcus mitis]
 gi|262286205|gb|ACY41676.1| RNA polymerase alpha subunit [Streptococcus mitis]
 gi|262286207|gb|ACY41677.1| RNA polymerase alpha subunit [Streptococcus mitis]
 gi|262286209|gb|ACY41678.1| RNA polymerase alpha subunit [Streptococcus mitis]
          Length = 140

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 60/140 (42%), Positives = 93/140 (66%)

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+  IILNIKGI +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +
Sbjct: 1   VREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEVTAGDILTDSDIEIVNPDHYLFTI 60

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
              + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y VE AR G    
Sbjct: 61  GEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDG 120

Query: 198 YDKLSMTIDTDGSITGEDSV 217
           +DKL++ I T+G+I  ED++
Sbjct: 121 FDKLTLEILTNGTIIPEDAL 140


>gi|7524684|ref|NP_042438.1| RNA polymerase alpha subunit [Pinus thunbergii]
 gi|1173147|sp|P41629|RPOA_PINTH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1262678|dbj|BAA04395.1| RNA polymerase alpha subunit [Pinus thunbergii]
 gi|228016402|gb|ACP51235.1| RNA polymerase alpha subunit [Pinus thunbergii]
          Length = 335

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 84/293 (28%), Positives = 150/293 (51%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLHKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
            +      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  FRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIR-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPAL-------------L 257
            +++  ASR L D    F++ EE   +    K+  N+   P +  L             L
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTDTGETKEKIAFQL 271

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  ++ N LR  NI  + DL+  +  D++R+ +FG++S+ ++  VL
Sbjct: 272 IFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMRIEHFGKESVEQVLEVL 324


>gi|315453710|ref|YP_004073980.1| DNA-directed RNA polymerase alpha chain [Helicobacter felis ATCC
           49179]
 gi|315132762|emb|CBY83390.1| DNA-directed RNA polymerase alpha chain [Helicobacter felis ATCC
           49179]
          Length = 336

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 86/287 (29%), Positives = 147/287 (51%), Gaps = 13/287 (4%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL--- 94
           G+A TL + LRR L+ S  G A   ++++GV HE  S++G+ ED+   I N+K I L   
Sbjct: 34  GYAITLAHPLRRFLLLSSVGYAPIGIKVEGVNHEFDSLRGISEDMALFIANLKNIRLVGK 93

Query: 95  KMSGDSHKRVTIFK--RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +    + +V +    +GP  ++  D++   +I V+N D  +  ++ DA +   L V KG
Sbjct: 94  HLDSAQNDQVVVHYTFKGPAKLSGKDLEN-EEISVVNHDAYLATINEDAHLEFSLIVQKG 152

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYVP++  R        I +DA ++PIKKV Y +E+       +++KL   I++DG + 
Sbjct: 153 MGYVPSESIRGYISS-DYIPLDAYFTPIKKVVYNIENMLVDGNPNFEKLIFEIESDGQVD 211

Query: 213 GEDSVALASRILQDQLGMF-INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTN 271
            + +   A R +  Q+ +F  N  + K     +  ++       LL ++E L LS R  N
Sbjct: 212 PQRAFQEAIRTMNAQMHIFNTNIADYKGNAHLEEGLER-----DLLMEIEGLNLSARCFN 266

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           CL    + Y+G+L+     ++  + N G+KS  EI   L  +G  +G
Sbjct: 267 CLDKIGLKYVGELVLMDAYELKNIKNLGKKSYDEIAEKLEGLGYPVG 313


>gi|54144446|dbj|BAD60947.1| DNA-dependent RNA polymerase alpha subunit [Sphagnum girgensohnii]
          Length = 341

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 93/311 (29%), Positives = 158/311 (50%), Gaps = 35/311 (11%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P   G A+T+G A+RR L+  + G  IT  + + V HE S+I G+ E + DI++N+K I 
Sbjct: 37  PFRSGQANTVGIAVRRALLGGVEGTCITRAKSEKVTHEYSTILGIQESVRDILINLKEIV 96

Query: 94  LKMSGDSHKRVTIFKR--GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           LK   +S +    F    GP  VTA DI     +EV++    I  L     + +EL + K
Sbjct: 97  LKSKSNSCETQKAFLSIFGPKEVTARDIVFPPSVEVIDTTQYIATLTKAIHLDIELKIEK 156

Query: 152 GHGYVPAKHHRTEN---DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
             GY      RT++      G  ++DA+++PI+  +Y+V S  E +    + L + I T+
Sbjct: 157 DCGY------RTQDSIKSADGYFSVDAVFTPIRNANYSVHSF-ENKNETQEILFIEIWTN 209

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEV-------KEDINVKSLPFNPALLKK-- 259
           GS+T ++++  ASR L D   +FI F   +KE        K + N      +P+  K   
Sbjct: 210 GSVTPKEALYEASRSLID---LFIPFLHAEKEEVMHGLGNKNESNTLHFSSSPSENKMEK 266

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +++LEL  R+ NC +  ++  + DL+  ++ D++++ NFG+KS   ++ VL 
Sbjct: 267 EMTFKHIFIDQLELPARAYNCPKRVDVHTISDLLSYSQDDLMKIKNFGKKS---VEQVLE 323

Query: 312 TMGLFLGMNLP 322
            +     + LP
Sbjct: 324 ALQKRFSIKLP 334


>gi|228016017|gb|ACP50856.1| RNA polymerase alpha subunit [Pinus resinosa]
          Length = 335

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 84/293 (28%), Positives = 150/293 (51%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
            +      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  FRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIR-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPAL-------------L 257
            +++  ASR L D    F++ EE   +    K+  N+   P +  L             L
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTDTGETKEKIAFQL 271

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  ++ N LR  NI  + DL+  +  D++R+ +FG++S+ ++  VL
Sbjct: 272 IFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMRIEHFGKESVEQVLEVL 324


>gi|28202204|ref|NP_777445.1| RNA polymerase alpha subunit [Anthoceros formosae]
 gi|41688674|sp|Q85A01|RPOA_ANTFO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|27807906|dbj|BAC55381.1| RNA polymerase alpha subunit [Anthoceros formosae]
 gi|27808054|dbj|BAC55478.1| RNA polymerase alpha subunit [Anthoceros formosae]
          Length = 340

 Score =  119 bits (299), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 92/311 (29%), Positives = 161/311 (51%), Gaps = 36/311 (11%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G A+T+G A+RR L+  + G  IT V+ + V HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRPGQANTVGIAIRRALLGEIEGTCITYVKFEKVTHEYSTIMGIQESVHDILINLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK +    +  +I   GP  VTA DI   + +EV++    I  +       ++L + K  
Sbjct: 96  LKSNSYKTQEASISILGPKRVTAEDIVLPSSVEVIDATQHIATITKAVYFNIKLGIRKDR 155

Query: 154 GYVPAKHHRTENDPI----GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           GY      R EN P+    G   ++A ++PI+  +Y+V S  E +    + L + + T+G
Sbjct: 156 GY------RIEN-PVKYEDGNFAVNAAFTPIRNANYSVHSF-ENEKEKQEILFIEVWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEV-------KEDINVKSLPF---NPALLKK 259
           S+T ++++  AS   Q  + +FI     KKE        K++ NV    F   N   ++K
Sbjct: 208 SLTPKEALREAS---QSLINLFIPLLHEKKERENRKLENKDEYNVLRSCFSLTNIGEVRK 264

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +++LEL  R+ N L+  ++  + DL+  ++ D++++ NFG+KS   I+ V+ 
Sbjct: 265 EISFKHIFIDQLELPARAYNGLKKVDVHTISDLLNYSQEDLMKIKNFGKKS---IQQVVE 321

Query: 312 TMGLFLGMNLP 322
            +     ++LP
Sbjct: 322 ALQKHFAIHLP 332


>gi|300431314|gb|ADK12620.1| RNA polymerase alpha subunit [Pappostipa vaginata]
          Length = 319

 Score =  119 bits (299), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 85/285 (29%), Positives = 143/285 (50%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A  +G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 12  FILSPLRKGQADPVGIALRRALLXEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 71

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+ +    I NL     + +EL +
Sbjct: 72  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIXDTAQPIANLTEPIDLCIELQI 131

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y++ S   G     + L + I T+G
Sbjct: 132 KRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KPEILFLEIWTNG 187

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------------- 253
           S+T ++++  ASR L D    F++ EE     +E+ N  + P                  
Sbjct: 188 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKKLTNLKKNKKGI 247

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 248 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 292


>gi|150251505|ref|YP_001312238.1| RNA polymerase alpha chain [Cycas taitungensis]
 gi|172048628|sp|A6H5L3|RPOA_CYCTA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|149941555|dbj|BAF64979.1| RNA polymerase alpha chain [Cycas taitungensis]
 gi|156598071|gb|ABU85301.1| RNA polymerase alpha subunit [Cycas micronesica]
          Length = 340

 Score =  119 bits (299), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 86/293 (29%), Positives = 151/293 (51%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT  +++ V HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGQASTIGIAMRRALLGEIEGTCITHAKLEKVTHEYSAIIGIEESVHDILINLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I   GP  VTA DI     + +++    I +L       + L + K  
Sbjct: 96  LRSDPYGTREASICIVGPRNVTAQDIILPPSVRIIDATQHIASLTKSITFDIRLWIEKDR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY   +    +N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+GS+  
Sbjct: 156 GY---RIQSPKNYQDGIFPIDAVFMPVRNANYSIHSYGNGNDIQ-EILFLEIWTNGSLAP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-FN----PALLKKVEE------ 262
            +++  ASR L D    F+  EE   +  ++ N  ++P F+     A ++++EE      
Sbjct: 212 REALYRASRNLIDLFIPFLRAEEQNIDGMDNQNGSNMPSFSFSNISADMERMEEEVAFKH 271

Query: 263 -----LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 EL  R  NCL   NI  + DL+  ++ D++R+ +FG+KS+ ++  VL
Sbjct: 272 IFIDQSELPPRVYNCLGRVNIHTLSDLLNYSQEDLMRIGHFGKKSVEQVSEVL 324


>gi|262286165|gb|ACY41656.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
 gi|262286177|gb|ACY41662.1| RNA polymerase alpha subunit [Streptococcus oralis]
 gi|262286179|gb|ACY41663.1| RNA polymerase alpha subunit [Streptococcus oralis]
 gi|262286181|gb|ACY41664.1| RNA polymerase alpha subunit [Streptococcus oralis]
 gi|262286183|gb|ACY41665.1| RNA polymerase alpha subunit [Streptococcus oralis]
 gi|262286185|gb|ACY41666.1| RNA polymerase alpha subunit [Streptococcus oralis]
 gi|262286187|gb|ACY41667.1| RNA polymerase alpha subunit [Streptococcus oralis]
 gi|262286189|gb|ACY41668.1| RNA polymerase alpha subunit [Streptococcus oralis]
 gi|262286191|gb|ACY41669.1| RNA polymerase alpha subunit [Streptococcus oralis]
 gi|262286193|gb|ACY41670.1| RNA polymerase alpha subunit [Streptococcus oralis]
 gi|262286195|gb|ACY41671.1| RNA polymerase alpha subunit [Streptococcus oralis]
          Length = 140

 Score =  119 bits (298), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 59/140 (42%), Positives = 93/140 (66%)

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+  IILNIKGI +K   +  K + +   GP  +TAGDI T +DIE++NPDH +  +
Sbjct: 1   VREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEITAGDILTDSDIEIVNPDHYLFTI 60

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
              + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y VE AR G    
Sbjct: 61  GEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDG 120

Query: 198 YDKLSMTIDTDGSITGEDSV 217
           +DKL++ I T+G+I  ED++
Sbjct: 121 FDKLTLEILTNGTIIPEDAL 140


>gi|290489668|gb|ADD31218.1| RNA polymerase alpha subunit protein [Nelumbo nucifera]
          Length = 339

 Score =  119 bits (298), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 85/311 (27%), Positives = 160/311 (51%), Gaps = 25/311 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTIVGIEESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +   I  RGPG VTA DI +   +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTRDAFICVRGPGYVTAQDIISPPSVEIVDTTQHIASLTEPIDLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +     N   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGY---RMKTPNNSQDGSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF-----NPALLKK----- 259
           S+T ++++  ASR L D    F++ +E   +++++ N  +LPF         L+K     
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLDAQEEDIQLEDNQNKVTLPFFTFHDRLTKLRKNKKEK 267

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +++ EL  R+ NCL+  NI  + DL+  ++ D+++M +F    + ++K +L 
Sbjct: 268 EIALKCIFIDQSELPPRTYNCLKRSNIHTLLDLLNNSQEDLMKMFHF---QIEDVKQILD 324

Query: 312 TMGLFLGMNLP 322
            +     ++LP
Sbjct: 325 ILQKHFAIDLP 335


>gi|228017724|gb|ACP52536.1| RNA polymerase alpha subunit [Pinus pinaster]
          Length = 335

 Score =  119 bits (298), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 84/293 (28%), Positives = 149/293 (50%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
            +      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  FRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIR-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPAL-------------L 257
            +++  ASR L D    F++ EE   +    K+  N+   P +  L             L
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTDTGETKEKIAFQL 271

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  ++ N LR  NI  + DL+  +  D++R+  FG++S+ ++  VL
Sbjct: 272 IFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMRIERFGKESVEQVLEVL 324


>gi|47459096|ref|YP_015958.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma mobile 163K]
 gi|61215933|sp|Q6KI29|RPOA_MYCMO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|47458425|gb|AAT27747.1| DNA-directed RNA polymerase alpha chain [Mycoplasma mobile 163K]
          Length = 333

 Score =  119 bits (298), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 97/316 (30%), Positives = 155/316 (49%), Gaps = 35/316 (11%)

Query: 28  TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIIL 87
           T  I +PL +G A TLG A+RRVL+SS+   A  AV+I GV HE  +I  V ED+  I+L
Sbjct: 22  TSFIVQPLEKGLATTLGTAIRRVLLSSISSVAPFAVKIKGVEHEFMAINKVTEDVPQILL 81

Query: 88  NIKGINLKMSGDSHKRVTIFKRG-PGVVTAGDIQTVNDI-----EVLNPDHVICNLDVDA 141
            ++ I +  + +  +   I+K        AGDI   + I     E++NP  +I       
Sbjct: 82  RLRDIKIAYNPEIFEDGKIYKLSLKSNKEAGDIYAKDFILPIGAEIVNPGLLIATTAAAN 141

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIG-----------LITIDALYSPIKKVSYTVESA 190
           V+ +++ V  G GYV  + ++   D I             I +D+ +SPI+KVS++    
Sbjct: 142 VLEIDVFVRAGRGYVDFEENKKYIDEIKTNLTSSISNGQYIAVDSNFSPIEKVSFSSSEL 201

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF--IN-------FEEPKKEV 241
               V+  +KL M I T G+I  ++++A A++IL   L +   +N       FEE   E 
Sbjct: 202 NTSSVIVQEKLEMEIVTKGTIDAKNAIAQAAKILVAHLNIIGDVNSLNIKDIFEEGNTE- 260

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           KE    +++         ++ L+LS+RS N L+  N   +  L   +  D+  + N G K
Sbjct: 261 KEHSKTQNIL--------IQSLDLSIRSFNALKRANYTTVQQLEALSLDDLKNIKNLGEK 312

Query: 302 SLVEIKGVLGTMGLFL 317
           S+ EI   L    +FL
Sbjct: 313 SINEIVEKLEKYNVFL 328


>gi|284103857|ref|ZP_06386117.1| DNA-directed RNA polymerase subunit alpha [Candidatus Poribacteria
           sp. WGA-A3]
 gi|283830235|gb|EFC34482.1| DNA-directed RNA polymerase subunit alpha [Candidatus Poribacteria
           sp. WGA-A3]
          Length = 137

 Score =  119 bits (298), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 59/109 (54%), Positives = 76/109 (69%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
             AEP  RGF  T+GN+LRRVL+SSL GAA+T+V+I+G  HE S++ GV ED+T IILNI
Sbjct: 28  FTAEPFERGFGTTVGNSLRRVLLSSLTGAAVTSVKIEGAFHEFSTLPGVTEDVTIIILNI 87

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
           K + LK+  D  K + + K+GPG V A DIQ   DI +LNP+  I  LD
Sbjct: 88  KNLRLKLHTDKSKAMQLKKKGPGKVRAADIQHDADITILNPELHIATLD 136


>gi|114107164|ref|YP_740149.1| RNA polymerase alpha subunit [Daucus carota]
 gi|122239960|sp|Q0G9T0|RPOA_DAUCA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|113200939|gb|ABI32455.1| RNA polymerase alpha subunit [Daucus carota]
          Length = 353

 Score =  119 bits (298), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 94/329 (28%), Positives = 166/329 (50%), Gaps = 28/329 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ++RR L+  + G  IT  + + + HE S++ G+ E + DI++N+
Sbjct: 32  FILSPLMKGQADTIGISMRRALLGEIEGTCITRAKSEKIPHEYSTLVGIQESVHDILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGPG VTA DI     +EV++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTCDASICVRGPGYVTAQDIILPPYVEVVDNTQHIASLTEPIELCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK---LSMTID 206
            +  GY+    +    D  G   IDA++ P++  ++++ S   G     DK   L + I 
Sbjct: 152 ERNRGYLIKTPNNNSKD--GSYPIDAVFMPVRNANHSIHSYGNGN----DKQEILFLEIW 205

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK-- 259
           T+GS+T ++++  ASR L D    F++ EE    +  + ++  LP   F+  L  L+K  
Sbjct: 206 TNGSLTPKEALHEASRNLIDLFIPFLHTEEENLHLANNQHMVPLPPFTFHDKLDKLRKNK 265

Query: 260 ---------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                    +++ EL  R  NCL+  NI  + DL+  ++ D++++ +F  K   ++K +L
Sbjct: 266 KKRALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDLMKIEHFRIK---DVKQIL 322

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           G +     +NL   P    E LA+  + K
Sbjct: 323 GILEKNFSINLGKKPKMGFESLAQLIDSK 351


>gi|57115498|gb|AAW33058.1| RNA polymerase alpha subunit [Plantago rugelii]
          Length = 308

 Score =  119 bits (298), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 85/298 (28%), Positives = 154/298 (51%), Gaps = 24/298 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +  PL +G A T+G A+RR L+  ++G  IT V+ + V HE S+I G+ E + +I++N+
Sbjct: 17  FVLSPLMKGQADTIGIAMRRALLGEIQGTCITRVKSENVPHEYSTIAGIQESVPEILMNL 76

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGPG VTA DI     +E+ +    I  L       + L +
Sbjct: 77  KEIVLRSNLYGTCGASICARGPGYVTAQDIILPPCVEIGDNTQHIARLTEPISFCIGLEI 136

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES-AREGQVLDYDKLSMTIDTD 208
            +  GY+    H  ++       IDA++ P++ V++++ S   E Q +    L + I T+
Sbjct: 137 ERSRGYLIKSPHIFQDRS---YPIDAVFMPVRNVNHSIHSYGNEKQEI----LFLEIWTN 189

Query: 209 GSITGEDSVALASRILQDQLGMFINFEE---PKKEVKEDINVKSLPFNPAL--LKK---- 259
           GS+T ++++  ASR L D    F++ EE   P +  ++ ++     F+  L   +K    
Sbjct: 190 GSLTPKEALHEASRNLIDLFIPFLHKEEENLPLENNQDTVSFSPFSFHEKLDQFRKNKKK 249

Query: 260 -------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                  +++ ELS R  NCL+  NI  + D + +++ D+++M +F  + L +  G+L
Sbjct: 250 KALQSIFIDQFELSPRVYNCLKKSNIYTLFDFLTKSQEDLMKMEHFRLEDLKQTLGIL 307


>gi|290489680|gb|ADD31224.1| RNA polymerase alpha subunit protein [Bulnesia arborea]
          Length = 352

 Score =  119 bits (297), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 86/301 (28%), Positives = 159/301 (52%), Gaps = 28/301 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +  PL +G A T+G A+RRVL+  + G +IT+ + + + HE SSI GV E + +I++N+
Sbjct: 32  FLLSPLKKGQADTIGIAMRRVLLGEIEGTSITSAKSENIPHEYSSIVGVEESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+         +I  +GPG VTA DI   + +E+++    I NL   +D  +R+++
Sbjct: 92  KEIVLRSHLYGICDASICVKGPGCVTAQDIILPSYVEIVDNTQHIANLTEPIDFCIRLQI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+        +      G+  IDA++ P++  ++++ S   G     + L + I T
Sbjct: 152 ERNRGYRIKTPNQFQE-----GIYPIDAVFMPVRNANHSIHSYGNGSETQ-EILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-------FNPALLKK- 259
           +GS+T ++++  ASR L D    F++ EE    ++ + N  +LP       FN   +KK 
Sbjct: 206 NGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLENNQNKYTLPLFSFHDQFNQ--IKKN 263

Query: 260 ----------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                     +++LEL+ +  NCL+  NI  + DL+   + D++R+ +F  + +  I  +
Sbjct: 264 QKEIEFKSIFIDQLELTPKIYNCLKRSNIHTLFDLLNNRKEDLMRIEHFRIEDINHIFHI 323

Query: 310 L 310
           L
Sbjct: 324 L 324


>gi|91209019|ref|YP_538881.1| RNA polymerase alpha subunit [Solanum bulbocastanum]
 gi|108773161|ref|YP_635671.1| RNA polymerase alpha subunit [Solanum tuberosum]
 gi|90110868|sp|Q2VEE8|RPOA_SOLTU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|109900624|sp|Q2MIF6|RPOA_SOLBU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|82754657|gb|ABB90071.1| RNA polymerase alpha chain [Solanum tuberosum]
 gi|84371926|gb|ABC56244.1| RNA polymerase alpha subunit [Solanum bulbocastanum]
 gi|88656835|gb|ABD47088.1| RNA polymerase alpha subunit [Solanum tuberosum]
          Length = 337

 Score =  119 bits (297), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 85/299 (28%), Positives = 156/299 (52%), Gaps = 24/299 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT V+ + V HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRVKSEKVPHEYSTITGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  +GPG VTA DI     +E+++    I +L       + L +
Sbjct: 92  KEIVLRSNLYGTSDASICVKGPGYVTAQDIILPPYVEIVDNTQHIASLTEPIDFCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY+    H  ++   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGYLIKTPHNFQD---GSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFIEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP--------ALLKK-- 259
           S+T ++++  ASR L D    F++ EE    +++  N  ++P +P         L+K   
Sbjct: 208 SLTPKEALHDASRNLIDLFIPFLHMEEDNLYLQD--NQHTVPLSPFTFHDKLAKLIKNKK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                   +++ ELS R  NCL+  NI  + DL+  ++ D++++ +F  + + +I G+L
Sbjct: 266 KIALKSIFIDQSELSSRIYNCLKMSNIYTLLDLLNNSQEDLMKIEHFRSEDIKQILGIL 324


>gi|237688548|ref|YP_002905166.1| RNA polymerase alpha subunit [Pinus contorta]
 gi|226875376|gb|ACO89114.1| RNA polymerase alpha subunit [Pinus contorta]
          Length = 335

 Score =  119 bits (297), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 85/293 (29%), Positives = 150/293 (51%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIR-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPAL-------------L 257
            +++  ASR L D    F++ EE   +    K+  N+   P +  L             L
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHLLTDTGETKEKIAFQL 271

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  +  N LR  NI  + DL+  +  D++R+ +FG++S+ ++  VL
Sbjct: 272 IFIDQLELPPKIYNSLRRANIHTLLDLLNYSREDLMRIKHFGKESVEQVLEVL 324


>gi|228016715|gb|ACP51543.1| RNA polymerase alpha subunit [Pinus aristata]
          Length = 335

 Score =  119 bits (297), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 83/293 (28%), Positives = 150/293 (51%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H + N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIQ-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALLKK----------- 259
            +++  ASR L D    F++ EE   +    K+  N+   P +  L              
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNKKKGSNMLPFPLSHVLTDTGETKEKIAFQH 271

Query: 260 --VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  ++ N LR  NI  + DL+  +  D++R+ + G++S+ ++  VL
Sbjct: 272 IFIDQLELPPQTYNSLRRANIHTLLDLLNYSREDLMRIEHLGKESVEQVLEVL 324


>gi|50346815|ref|YP_053186.1| RNA polymerase alpha subunit [Nymphaea alba]
 gi|68053159|sp|Q6EW20|RPOA_NYMAL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|50250360|emb|CAF28626.1| RNA polymerase alpha subunit [Nymphaea alba]
          Length = 341

 Score =  119 bits (297), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 86/297 (28%), Positives = 158/297 (53%), Gaps = 21/297 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +  PL +G A T+G A+RR L+  L G  IT  + D V HE S++ G+ E + +I++N+
Sbjct: 32  FVLSPLMKGQADTIGIAMRRALLGELEGTCITRAKSDKVPHEYSTVVGIEESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K +  +         +I  RGP  VTA DI +   +E+++    I  L     + +EL +
Sbjct: 92  KKMVFRSDLYGTLDASICVRGPRHVTAQDIISPPSVEIVDTTQHIAVLTEPVDLCIELKI 151

Query: 150 SKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
            +G GY      RT+N+   G   IDA+  P++  ++++ S   G     + L + I T+
Sbjct: 152 ERGRGYCT----RTQNNYQDGSYPIDAVSMPVRNANHSIHSYGNGNE-KQEILFLEIWTN 206

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEP--KKEVKEDINVKSLPF-----------NPA 255
           GS+T ++++  ASR L D    F++ EE    + +++++   S+PF              
Sbjct: 207 GSLTPKEALYEASRNLIDLFIPFLHAEEQDINRNMEDNLKRASVPFFAFDDGLDNIKREI 266

Query: 256 LLKK--VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           +LK+  +++LEL  R+ NCL+  NI  + DL+ +++ D++R+ +F  + + +I  +L
Sbjct: 267 ILKRIFIDQLELPPRTYNCLKRSNIHTLLDLLSKSQEDLMRIEHFRVEDVKQIFDIL 323


>gi|324986527|ref|YP_004276397.1| RNA polymerase alpha subunit [Pinus nelsonii]
 gi|323522715|gb|ADX94963.1| RNA polymerase alpha subunit [Pinus nelsonii]
          Length = 335

 Score =  119 bits (297), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 83/293 (28%), Positives = 150/293 (51%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIKESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H + N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHSYGNGNEIQ-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALLKK----------- 259
            +++  ASR L D    F++ EE   +    K+  N+   P +  L              
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNKKKGSNMLPFPLSHVLTDTGETKEKIAFQH 271

Query: 260 --VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  ++ N LR  NI  + DL+  +  D++R+ + G++S+ ++  VL
Sbjct: 272 IFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMRIEHLGKESVEQVLEVL 324


>gi|324986455|ref|YP_004276326.1| RNA polymerase alpha subunit [Pinus monophylla]
 gi|228016086|gb|ACP50924.1| RNA polymerase alpha subunit [Pinus rzedowskii]
 gi|323522550|gb|ADX94892.1| RNA polymerase alpha subunit [Pinus monophylla]
          Length = 335

 Score =  119 bits (297), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 83/293 (28%), Positives = 150/293 (51%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H + N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIQ-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALLKK----------- 259
            +++  ASR L D    F++ EE   +    K+  N+   P +  L              
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNKKKGSNMLPFPLSHVLTDTGETKEKIAFQH 271

Query: 260 --VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  ++ N LR  NI  + DL+  +  D++R+ + G++S+ ++  VL
Sbjct: 272 IFIDQLELPPQTYNSLRRANIHTLLDLLNYSREDLMRIEHLGKESVEQVLEVL 324


>gi|167391838|ref|YP_001671715.1| RNA polymerase alpha subunit [Carica papaya]
 gi|166344165|gb|ABY86815.1| RNA polymerase alpha chain [Carica papaya]
          Length = 327

 Score =  119 bits (297), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 84/297 (28%), Positives = 157/297 (52%), Gaps = 20/297 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +   I  +GPG VTA DI     +E+++    I +L     +R+ L +
Sbjct: 92  KEIVLRSNLYGTRDAFICVKGPGYVTAQDIVLPPSVEIVDNTQHIASLTEPIDLRIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGYGIKTPNNFQD---GSYPIDAVFMPVQNANHSIHSYGTGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP-----ALLKK----- 259
           S+T ++++  ASR L +    F++ EE K  ++ + +  +LPF P     A L+K     
Sbjct: 208 SLTPKEALHEASRNLINLFIPFLHAEEEKFYLENNQHKVTLPFFPFHDRLAKLRKKKTEI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F  + + +I  +L
Sbjct: 268 AFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLMKIEHFRTEDVKQILSIL 324


>gi|290489698|gb|ADD31233.1| RNA polymerase alpha subunit protein [Quercus nigra]
          Length = 331

 Score =  119 bits (297), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 86/297 (28%), Positives = 152/297 (51%), Gaps = 20/297 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAVRRALLGEIEGTCITRAKSEKIPHEYSTIIGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  +GP  VTA DI     +++++    I NL     + +EL +
Sbjct: 92  KEIVLRSNLYGISGASICVKGPRYVTAQDIILPPSVQIVDNTQHIANLTEPINLYIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +   T N   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERDRGY---RIKTTNNSQDGSYPIDAVFMPVRNANHSIHSYVNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF-----NPALLKK----- 259
           S+T ++++  ASR L +    F++ EE K  ++ +    +LPF       A L K     
Sbjct: 208 SLTPKEALHEASRNLIELFIPFLHAEEEKLHLENNQQKVTLPFFTCHDRLAKLNKNSTEI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++ EL  R  NCL+G NI  + DL+  ++ D ++M +F R+ +  I  +L
Sbjct: 268 ALKSIFIDQSELPPRIYNCLKGSNIHTLLDLLNNSQTDFMKMKHFRREDIKHILDIL 324


>gi|313184025|ref|YP_004021182.1| RNA polymerase alpha subunit [Castanea mollissima]
 gi|309321552|gb|ADO65092.1| RNA polymerase alpha subunit [Castanea mollissima]
          Length = 331

 Score =  119 bits (297), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 86/297 (28%), Positives = 152/297 (51%), Gaps = 20/297 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAVRRALLGEIEGTCITRAKSEKIPHEYSTIIGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  +GP  VTA DI     +++++    I NL     + +EL +
Sbjct: 92  KEIVLRSNLYGISGASICVKGPRYVTAQDIILPPSVQIVDNTQHIANLTEPINLYIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +   T N   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERDRGY---RIKTTNNSQDGSYPIDAVFMPVRNANHSIHSYVNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF-----NPALLKK----- 259
           S+T ++++  ASR L +    F++ EE K  ++ +    +LPF       A L K     
Sbjct: 208 SLTPKEALHEASRNLIELFIPFLHAEEEKLHLENNQQKVTLPFFTCHDRLAKLNKNSTEI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++ EL  R  NCL+G NI  + DL+  ++ D ++M +F R+ +  I  +L
Sbjct: 268 TLKSIFIDQSELPPRIYNCLKGSNIHTLLDLLNNSQTDFMKMKHFRREDIKHILDIL 324


>gi|290489682|gb|ADD31225.1| RNA polymerase alpha subunit protein [Cornus florida]
          Length = 337

 Score =  119 bits (297), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 84/299 (28%), Positives = 159/299 (53%), Gaps = 24/299 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIQHEYSTIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +       +I  +GPG VTA DI +   +E+++    I +L   +D  + +++
Sbjct: 92  KEIVLRSTLYGTCDASICVKGPGYVTAQDIISPPYVEIVDNTQYIASLTEPIDLCIGLQI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+   P  + +  N P     IDA++ P++  ++++ S   G     + L + I T
Sbjct: 152 ERNRGYRIKPPNNFQDGNYP-----IDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLK------ 258
           +GS+T ++++  ASR L D    F++ EE    ++++ +  +LP   F+  L K      
Sbjct: 206 NGSLTPKEALHEASRNLIDLFIPFLHTEEENLHLEDNQHKVTLPTFTFHDKLAKLRKNKK 265

Query: 259 -------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                   +++ ELS R  NCL+  NI  + DL+  ++ D+++M +F  + + EI  +L
Sbjct: 266 KIAFKYIFIDQSELSPRIYNCLKRSNIYTLLDLLNNSQEDLMKMKDFRIEDVKEILDIL 324


>gi|296936704|gb|ADH94376.1| RNA polymerase alpha subunit [Syzygium cumini]
          Length = 337

 Score =  119 bits (297), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 84/301 (27%), Positives = 158/301 (52%), Gaps = 25/301 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFEKIPHEYSTIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GPG VTA DI     +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTRNASICVKGPGCVTAQDIILPTSVEIVDNTQYIASLTEPINLCIGLQI 151

Query: 150 SKGHGYVPAKHHRT-ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
            +  GY    H +T +N   G   IDA++ P++  ++++ S   G     + L + I T+
Sbjct: 152 ERNRGY----HIKTPKNFQDGSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWTN 206

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLK------- 258
           GS+T ++++  ASR L D    F++ EE    ++ +    +LP   F+  L+K       
Sbjct: 207 GSLTPKEALHEASRNLIDLFIPFLHAEEENLHLENNQYKVTLPLFTFHDRLVKLRKTKKE 266

Query: 259 ------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                  +++ EL  R+ NCL+  NI  + DL+ +++ D+++M  F    + ++K +L +
Sbjct: 267 IALKSIFIDQFELPPRTYNCLKRYNIHTLFDLLNKSQEDLMKMEYF---RIEDVKQILNS 323

Query: 313 M 313
           +
Sbjct: 324 L 324


>gi|75755691|ref|YP_319795.1| RNA polymerase alpha subunit [Acorus calamus]
 gi|161622341|ref|YP_001586213.1| RNA polymerase alpha subunit [Acorus americanus]
 gi|90101572|sp|Q3V502|RPOA_ACOCL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|69215818|gb|AAZ03865.1| RNA polymerase alpha chain [Acorus americanus]
 gi|74381741|emb|CAI53826.1| RNA polymerase alpha subunit [Acorus calamus]
 gi|160369884|gb|ABX38775.1| RNA polymerase alpha subunit [Acorus americanus]
          Length = 337

 Score =  119 bits (297), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 90/309 (29%), Positives = 160/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + V HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLLKGQADTIGIAMRRALLGEIEGTCITRAKSEKVPHEYSTIAGIEESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  RGP  VTA DI +   +EV++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTRDASICVRGPRCVTAQDIISPPSVEVVDTTQHIASLTEPIDLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +   T+N   G   IDA+  P++  ++++ S   G     + L + I T+G
Sbjct: 152 QRDRGY---RMKTTKNSQDGSYPIDAVSMPVRNANHSIHSYGNGNQ-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  ++P   F   L  LKK     
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHAEEEDINFEENQNRFTVPPFTFPDRLANLKKNKKEI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++ EL  R+ NCL+  NI  + DL+  ++ D++++  F    + ++K +L T+
Sbjct: 268 ALKCIFIDQSELPPRTYNCLKRSNIHTLLDLLSNSQEDLMKIEYF---RIEDVKQILDTL 324

Query: 314 GLFLGMNLP 322
                ++LP
Sbjct: 325 QKHFAIDLP 333


>gi|228017468|gb|ACP52284.1| RNA polymerase alpha subunit [Pinus merkusii]
          Length = 335

 Score =  119 bits (297), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 84/293 (28%), Positives = 149/293 (50%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
            +      +  +I+  GP  VTA DI     ++ ++    I  L       + L + K  
Sbjct: 96  FRSDSYGIREASIYIVGPRNVTAQDIILPPSVKTIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIR-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPAL-------------L 257
            +++  ASR L D    F++ EE   +    K+  N+   P +  L             L
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTDTGETKEKIAFQL 271

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  ++ N LR  NI  + DL+  +  D++R+ +FG++S+ ++  VL
Sbjct: 272 IFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMRIEHFGKESVEQVLEVL 324


>gi|149390571|ref|YP_001294216.1| RNA polymerase alpha subunit [Buxus microphylla]
 gi|172048681|sp|A6MM68|RPOA_BUXMI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|146762316|gb|ABQ45280.1| RNA polymerase alpha subunit [Buxus microphylla]
          Length = 337

 Score =  119 bits (297), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/311 (27%), Positives = 163/311 (52%), Gaps = 27/311 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITCAKSEKIPHEYSNIVGIEESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +    +  +I  RGP  VTA DI +   +E+++    I +L   +D  + +++
Sbjct: 92  KEIVLRSNLYGTRDASICVRGPRHVTAQDIISPPSVEIIDTTQHIASLTEPIDLCIGLQI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+     K     N   G   IDA++ P++  ++++ S   G     + L + I T
Sbjct: 152 ERNRGYNMKTPK-----NSQDGRYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLKK----- 259
           +GS+T ++++  ASR L D    F++  E    +K++ N  +LP   F+  L K+     
Sbjct: 206 NGSLTPKEALHEASRNLIDLFIPFLHANEENFILKDNQNKVALPLFTFHDRLAKQRKNKK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +++ EL  R+ NCL+  NI  + DL+  ++ D++++ +F    + ++K +LG
Sbjct: 266 EISFQCIFIDQSELPPRTYNCLKRSNIHTLLDLLNNSQEDLMKIEHF---RIEDVKQILG 322

Query: 312 TMGLFLGMNLP 322
            +     ++LP
Sbjct: 323 ILQKHFAIDLP 333


>gi|116617139|ref|YP_817514.1| RNA polymerase alpha subunit [Coffea arabica]
 gi|122153651|sp|A0A367|RPOA_COFAR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|116242195|gb|ABJ89710.1| RNA polymerase alpha subunit [Coffea arabica]
          Length = 335

 Score =  119 bits (297), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 87/301 (28%), Positives = 154/301 (51%), Gaps = 28/301 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT V+ + V HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRVKSEKVAHEYSTIAGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL--DVDAVVRMEL 147
           K I  + +       +I  RGPG VTA DI     +E+++    I  L   ++  +R+E 
Sbjct: 92  KEIVFRSNLYGTCDASICVRGPGYVTAQDIVLPPYVEIVDNTQHIARLMEPINLCIRLE- 150

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            + +  GY+       +N   G   IDA++ PI+  +Y++ S   G     + L + I T
Sbjct: 151 -IERNRGYLIKT---PQNFQDGSYPIDAVFMPIRNANYSIHSYGNGNE-KQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL-------LKK- 259
           +GS+T ++++  ASR L D    F++ EE    ++   N  ++P  P         L+K 
Sbjct: 206 NGSLTPKEALHQASRNLIDLFIPFLHMEEQNSHLEN--NQHTVPLAPFFFHDKLDKLRKN 263

Query: 260 ----------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                     +++ EL  R  NCL+  NI  + DL+  ++ +++++ +F  + + EI G+
Sbjct: 264 KKEIALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQENLMKIEHFHIEDVKEILGI 323

Query: 310 L 310
           L
Sbjct: 324 L 324


>gi|68053044|sp|Q5QA74|RPOA_ACOGR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|56122468|gb|AAV74359.1| RpoA [Acorus gramineus]
          Length = 337

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 90/309 (29%), Positives = 160/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + V HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLLKGQADTIGIAMRRALLGEIEGTCITRAKSEKVPHEYSTIAGIEESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  RGP  VTA DI +   +EV++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTRDASICVRGPRCVTAQDIISPPSVEVVDTTQHIASLTEPIDLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +   T+N   G   IDA+  P++  ++++ S   G     + L + I T+G
Sbjct: 152 QRDRGY---RMKTTKNSQDGSYPIDAVSMPVRNANHSIHSYGNGNQ-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  ++P   F   L  LKK     
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHAEEEDINFEENQNRFTVPPFTFPDRLANLKKNKKEI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++ EL  R+ NCL+  NI  + DL+  ++ D++++  F    + ++K +L T+
Sbjct: 268 ALKCIFIDQSELPPRTYNCLKRSNIHTLLDLLSNSQEDLMKIEYF---RIEDVKQILDTL 324

Query: 314 GLFLGMNLP 322
                ++LP
Sbjct: 325 RKHFAIDLP 333


>gi|118572712|sp|Q60F88|RPOA_TAKLE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|99653933|dbj|BAD60944.2| DNA-dependent RNA polymerase alpha subunit [Takakia lepidozioides]
          Length = 341

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 89/313 (28%), Positives = 149/313 (47%), Gaps = 38/313 (12%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P   G A T+G A+RR L+  + G  IT  +   V HE S+I G+ E + D+++N+  I 
Sbjct: 36  PFRSGQASTVGIAMRRALLGEVEGTCITCAEFKRVTHEYSTILGIQESVHDVLINLGEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      ++  I   GP  VTA DI     +++++    I  +     + +EL + K  
Sbjct: 96  LRSDSYETQKAFISILGPKKVTAQDIILPPSVKIIDTTQYIATVTKAIHLDIELKIEKDF 155

Query: 154 GYVPAKHHRTENDPI----GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           GY      R E DPI    G   +DA++ PI+ V+Y+V S   G     + L + I T+G
Sbjct: 156 GY------RIE-DPIKSADGNFPVDAVFMPIRNVNYSVHSFENGNETQ-EILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFIN--------------------FEEPKKEVKEDINVKS 249
           S+T ++++  ASR L +    F++                    F  P      D   K 
Sbjct: 208 SVTPKEALYEASRSLINLFIPFLHAEKKEFIYGLKNTYESNMSYFSSPSLSADIDEMTKG 267

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           + F       +++LEL  R+ NCL+  N   + DL+  ++ D++++ NFG+KS   ++ V
Sbjct: 268 VTFKHIF---IDQLELPARAYNCLKRVNAHTISDLLNYSQDDLMKIKNFGKKS---VEQV 321

Query: 310 LGTMGLFLGMNLP 322
           L  +     +NLP
Sbjct: 322 LEALQKRFSINLP 334


>gi|156597913|gb|ABU85224.1| RNA polymerase alpha subunit [Anethum graveolens]
          Length = 338

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 89/310 (28%), Positives = 160/310 (51%), Gaps = 22/310 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  +   + HE S++ G+ E + DI++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSKKIPHEYSTLVGIQESVHDILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGPG VTA DI     +EV++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTCDASICVRGPGYVTAQDIILPPYVEVVDNTQHIASLTEPIELHIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK-LSMTIDTD 208
            +  GY+    +    D  G   IDA++ PI+  ++++ S   G   D  + L + I T+
Sbjct: 152 ERSRGYLIKTPNNNFQD--GSYPIDAVFMPIRNANHSIHSYGNGNGNDKQEILFLEIWTN 209

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK---- 259
           GS+T ++++  ASR L D    F++ EE    + ++ ++  LP   F+  L  L+K    
Sbjct: 210 GSLTPKEALHEASRNLIDLFIPFLHTEEENLHLADNQHMVPLPPFTFHDNLDKLRKNKKK 269

Query: 260 -------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                  +++ EL  R  NCL+  NI  + DL+  ++ D++++ +F    + ++K +LG 
Sbjct: 270 IALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDLMKIEHF---RINDVKQILGI 326

Query: 313 MGLFLGMNLP 322
           +     ++LP
Sbjct: 327 LEKHFSIDLP 336


>gi|51859691|gb|AAU11125.1| RNA polymerase alpha subunit [Psathyrostachys caduca]
          Length = 339

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 88/278 (31%), Positives = 144/278 (51%), Gaps = 20/278 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       ++L +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDXAQPIANLTEPIDFCIDLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK----- 259
           S+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  LKK     
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLKKNKKGI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
                 +++LEL+ R+ NCL+  NI  + DL+ +TE D
Sbjct: 268 PLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEED 305


>gi|115605053|ref|YP_784505.1| RNA polymerase alpha subunit [Piper cenocladum]
 gi|122164330|sp|Q06GM8|RPOA_PIPCE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|112253782|gb|ABI14503.1| RNA polymerase alpha subunit [Piper cenocladum]
          Length = 339

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 89/313 (28%), Positives = 158/313 (50%), Gaps = 29/313 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A  +G A+RR L+  + G  IT V+ + V HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADMIGIAMRRALLGEIEGTCITRVKSEKVPHEFSTIVGIEESVHEIVMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGP  VTA DI     +E+++    I NL     + ++L +
Sbjct: 92  KEIVLRSNLYGTLDASICIRGPRYVTAQDIILPPSVEIVDATQHIANLTERVDLCIKLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     H   ND  G   IDA++ P++  +++V S   G     + L + I T+G
Sbjct: 152 ERDRGYSMKTPH---NDEDGSYPIDAIFMPVRNANHSVHSYGNGNE-KQEILFIEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---------FNPALLKK- 259
           S+T ++++  ASR L D    F++ EE  +E+  + N   +P         F    ++K 
Sbjct: 208 SLTPKEALYEASRNLIDLFIPFLHAEE--REIHLEDNANGVPLALFTFHDEFAITNIRKN 265

Query: 260 ----------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                     +++ EL  ++ NCL+  NI  + DL+  ++ D+L++ +F    + ++K +
Sbjct: 266 KKKMALKSIFIDQSELPSKTYNCLKKSNIHTLLDLLNNSQEDLLKIEHF---CMEDVKRI 322

Query: 310 LGTMGLFLGMNLP 322
           L  +    G +LP
Sbjct: 323 LDILQKHFGFDLP 335


>gi|150186930|emb|CAK30130.1| RNA polymerase alpha subunit [Streptococcus salivarius]
          Length = 141

 Score =  118 bits (295), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 58/141 (41%), Positives = 95/141 (67%)

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+  IILNIKG+ +K   +  K + +  +GP  VTAGDI T +DIE++NPDH +  +   
Sbjct: 1   DVMQIILNIKGLAVKSYVEDEKTIELDVQGPAEVTAGDILTDSDIEIVNPDHYLFTIADG 60

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
           A ++  +TV+   GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DK
Sbjct: 61  ASLKATMTVATNRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDK 120

Query: 201 LSMTIDTDGSITGEDSVALAS 221
           L++ I T+G+I  ED++ L++
Sbjct: 121 LTIEIMTNGTIIPEDALGLSA 141


>gi|228016331|gb|ACP51165.1| RNA polymerase alpha subunit [Pinus taeda]
          Length = 335

 Score =  118 bits (295), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 85/293 (29%), Positives = 149/293 (50%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKXIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+         +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIXEASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIR-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPAL-------------L 257
            +++  ASR L D    F++ EE   +    K+  N+   P +  L             L
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHLLTDTGETKEKIAFQL 271

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  +  N LR  NI  + DL+  +  D++R+ +FG++S+ ++  VL
Sbjct: 272 IFIDQLELPPKIYNSLRRANIHTLLDLLNYSREDLMRIEHFGKESVEQVLEVL 324


>gi|300431305|gb|ADK12617.1| RNA polymerase alpha subunit [Achnatherum inebrians]
          Length = 330

 Score =  118 bits (295), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 83/285 (29%), Positives = 142/285 (49%), Gaps = 29/285 (10%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   + HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSLPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I+ +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y            ++ L + I T+G
Sbjct: 152 KRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYR----------KHEILFLEIWTNG 198

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------------- 253
           S+T ++++  ASR L D    F++ EE     +E+ N  + P                  
Sbjct: 199 SLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKKLTNLKKNKKGI 258

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 259 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 303


>gi|165910447|gb|ABY73978.1| RNA polymerase alpha subunit [Cuscuta japonica]
          Length = 332

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 88/309 (28%), Positives = 159/309 (51%), Gaps = 28/309 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L++ + G  IT V+     HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIALRRALLAEIEGTRITRVKFANASHEYSTIAGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  +GPG VTA DI     +E+++    I  L     + + L +
Sbjct: 92  KEIVLRSNLYGTCDASISFKGPGYVTAEDIILPPHVEIVDSTQHIAWLTEPIDLCIGLKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES-AREGQVLDYDKLSMTIDTD 208
            +  GY    H   E+   G   IDA++ P++  ++++ S   E Q    + L + I T+
Sbjct: 152 ERNRGYFIKTHANFED---GSYPIDAVFMPVQNANHSIHSYGNEKQ----EILFLEIWTN 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL-------KK-- 259
           GS+T ++++  ASR L D    F++ E+    + ED +  ++P +P  +       KK  
Sbjct: 205 GSLTPKEALHEASRNLIDLFIPFLHMEKENLPL-EDAD-HTIPLSPFTVYYKVAKNKKKL 262

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LE   +  NCL+  NI  + DL+  ++ D++++ +F    L ++K +L  +
Sbjct: 263 SLESLFIDQLEFPPKIYNCLKKSNIFTLLDLLNNSQEDLIKIEHF---RLEDVKQILAIL 319

Query: 314 GLFLGMNLP 322
           G    ++LP
Sbjct: 320 GKHFALDLP 328


>gi|194033178|ref|YP_002000517.1| RNA polymerase alpha subunit [Brachypodium distachyon]
 gi|193075586|gb|ACF08669.1| RNA polymerase alpha subunit [Brachypodium distachyon]
          Length = 338

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 85/287 (29%), Positives = 151/287 (52%), Gaps = 24/287 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLIKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILVNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +    +  +I  +GP  +TA DI     +EV++    I NL   +D  +++++
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRCITAQDIILPPSVEVVDTAQPIANLTEPIDFCIQLQI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
              +G+     K+++  + P     IDA+  P++ V+Y++ S   G    ++ L + I T
Sbjct: 152 KRDRGYQTELRKNYQDGSYP-----IDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLKK----- 259
           +GS+T ++++  ASR L D    F++ EE     +E+ N  + P   F   L  +     
Sbjct: 206 NGSLTPKEALYEASRNLIDLFLPFLHAEEEGTGFEENKNRFTPPLFTFQKRLTNRKKNKK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                   +++LEL  R+ N L+  NI  + DL+ +TE D++R+ +F
Sbjct: 266 GIPLNFIFIDQLELPSRTYNYLKRANIHTLLDLLSKTEEDLMRIDSF 312


>gi|28261749|ref|NP_783263.1| RNA polymerase alpha subunit [Atropa belladonna]
 gi|41688712|sp|Q8S8V9|RPOA_ATRBE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|20068363|emb|CAC88076.1| RNA polymerase alpha subunit [Atropa belladonna]
          Length = 337

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 84/299 (28%), Positives = 154/299 (51%), Gaps = 24/299 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT V+ + V HE S+I G+ E + +II+N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRVKFEKVPHEYSTITGIQESVHEIIMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       ++  +GPG VTA DI     +E+++    I +L       + L +
Sbjct: 92  KEIVLRSNLYGTSEASVCVKGPGYVTAQDIILPPYVEIVDNTQHIASLTEPIDFCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY+       +N   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGYLIKT---PQNFQDGSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP--------ALLKK-- 259
           S+T ++++  ASR L D    F++ EE    +++  N  ++P +P         L+K   
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHMEEDNLYLQD--NQHTVPLSPFTFHDKLAKLIKNNK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                   +++ EL  R  NCL+  NI  + DL+  ++ D++++ +F  + + +I G+L
Sbjct: 266 KIALKSIFIDQSELPSRIYNCLKMSNIYTLLDLLNNSQEDLMKIEHFRSEDIKQILGIL 324


>gi|121720645|ref|YP_001001566.1| RNA polymerase alpha subunit [Nuphar advena]
 gi|69215822|gb|AAZ03867.1| RNA polymerase alpha chain [Nuphar advena]
 gi|84682236|gb|ABC60490.1| RNA polymerase alpha subunit [Nuphar advena]
          Length = 336

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 85/295 (28%), Positives = 155/295 (52%), Gaps = 19/295 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +  PL +G A T+G A+RR L+  L G  IT  + D V HE S+I G+ E + +I++N+
Sbjct: 32  FVLSPLMKGQADTIGIAMRRALLGELEGTCITRAKSDKVPHEYSTIVGIEESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I  +         +I  RGP  VTA DI +   +E+++    I  L     + +EL +
Sbjct: 92  KKIVFRSDLYGTLDASICVRGPRHVTAQDIISPPSVEIVDTTQHIAILTEPVDLCIELKI 151

Query: 150 SKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
            +G GY      RT N+   G   IDA+  P++  ++++ S   G     + L + I T+
Sbjct: 152 ERGRGYC----MRTPNNYQDGSYPIDAVSMPVRNANHSIHSYGNGNE-KQEILFLEIWTN 206

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF-----------NPALL 257
           GS+T ++++  ASR L D    F++ EE    +++++   ++PF              +L
Sbjct: 207 GSLTPKEALYEASRNLIDLFIPFLHAEEQDINIEDNLKRATVPFFTFHDGLDNMKREIIL 266

Query: 258 KK--VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           K+  +++ EL  R+ NCL+  NI  + +L+ +++ D++R+ +F  + + +I  +L
Sbjct: 267 KRIFIDQSELPPRTYNCLKKSNIHTLLNLLSKSQEDLMRIEHFRVEDVKQIFDIL 321


>gi|237688617|ref|YP_002905234.1| RNA polymerase alpha subunit [Pinus gerardiana]
 gi|226876077|gb|ACO89333.1| RNA polymerase alpha subunit [Pinus gerardiana]
          Length = 335

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 83/293 (28%), Positives = 150/293 (51%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H + N   G+  IDA++ P++ V+Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSSNNYQDGIFPIDAVFMPVRDVNYSIHSYGSGNEIQ-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALLKK----------- 259
            +++  ASR L D    F++ EE   +    K+  N+   P +  L              
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTDTGETKEKIAFQH 271

Query: 260 --VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  ++ N LR  NI  + DL+  +  D++R+ +  ++S+ ++  VL
Sbjct: 272 IFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMRIEHLEKESVEQVLEVL 324


>gi|183217772|ref|YP_001837392.1| RNA polymerase alpha subunit [Guizotia abyssinica]
 gi|179366287|gb|ACB86558.1| RNA polymerase alpha subunit [Guizotia abyssinica]
          Length = 335

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 86/297 (28%), Positives = 155/297 (52%), Gaps = 22/297 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + D + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSDKISHEYSTIMGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGPG VTA DI     +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTYEASICVRGPGYVTAQDIILPPYVEIVDNTQHIASLTEPIELVIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            K  GY+  K   T  D  G   ID ++ P++  ++++ S   G   + + L + I T+G
Sbjct: 152 EKNRGYL-IKAPNTFQD--GSYPIDPVFMPVRNANHSIHSYENG---NKEILFLEIWTNG 205

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLK-------- 258
           S+T ++++  ASR L D L  F++ +E    ++++ ++  LP   F   L K        
Sbjct: 206 SLTPKEALHEASRNLIDLLIPFLHTKEENLNLEDNQHIVPLPPFTFYDKLAKLTKNKKKM 265

Query: 259 -----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++ EL  R  NCL+  NI  + DL+  ++ D++++ +F  + + +I G+L
Sbjct: 266 ALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDLMKIEHFRIEDVKQILGIL 322


>gi|90110835|sp|Q49CA2|RPOA_CUSJA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|66876488|gb|AAY58033.1| RpoA [Cuscuta japonica]
          Length = 332

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 88/309 (28%), Positives = 159/309 (51%), Gaps = 28/309 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L++ + G  IT V+     HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIALRRALLAEIEGTRITRVKFANASHEYSTIAGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  +GPG VTA DI     +E+++    I  L     + + L +
Sbjct: 92  KEIVLRSNLYGTCDASISFKGPGYVTAEDIILPPHVEIVDSTQHIAWLTEPIDLCIGLKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES-AREGQVLDYDKLSMTIDTD 208
            +  GY    H   E+   G   IDA++ P++  ++++ S   E Q +    L + I T+
Sbjct: 152 ERNRGYFIKTHANFED---GSYPIDAVFMPVQNANHSIHSYGNEKQEI----LFLEIWTN 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL-------KK-- 259
           GS+T ++++  ASR L D    F++ E+    + ED +  ++P +P  +       KK  
Sbjct: 205 GSLTPKEALHEASRNLIDLFIPFLHMEKENLPL-EDAD-HTIPLSPFTVYYKVAKNKKKL 262

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LE   +  NCL+  NI  + DL+  ++ D++++ +F    L ++K +L  +
Sbjct: 263 SLESLFIDQLEFPPKIYNCLKKSNIFTLLDLLNNSQEDLIKIEHF---RLEDVKQILAIL 319

Query: 314 GLFLGMNLP 322
           G    ++LP
Sbjct: 320 GKHFALDLP 328


>gi|81301600|ref|YP_398896.1| RNA polymerase alpha subunit [Nicotiana tomentosiformis]
 gi|90110851|sp|Q33C00|RPOA_NICTO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|80750959|dbj|BAE48035.1| RNA polymerase alpha subunit [Nicotiana tomentosiformis]
          Length = 337

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 84/299 (28%), Positives = 155/299 (51%), Gaps = 24/299 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT V+ + V HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRVKSEKVPHEYSTIMGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  +GPG VTA DI     +E+++    I +L       + L +
Sbjct: 92  KEIVLRSNLYGTSDASICVKGPGYVTAQDIILPPYVEIVDNTQHIASLTETIDFCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY+    H  ++   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 KRNRGYLIKTPHNFQD---GSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP--------ALLKK-- 259
           S+T ++++  ASR L D    F++ EE    +++  N  ++P +P         L+K   
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHIEEDNLYLQD--NQHTVPLSPFTFHDKLAKLIKNKK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                   +++ EL  R  NCL+  NI  + DL+  ++ D++++ +F  + + +I G+L
Sbjct: 266 KIALKSIFIDQSELPSRIYNCLKMSNIYTLLDLLNNSQEDLMKIEHFRSEDVKQILGIL 324


>gi|150036750|emb|CAM98028.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gelidum KCTC
           3527]
          Length = 153

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 63/153 (41%), Positives = 96/153 (62%), Gaps = 2/153 (1%)

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           ++ GV ED+T IILN+K + L +  D  + + +  +GP  VTA D+Q   D+EVLNPD  
Sbjct: 1   TVDGVVEDVTQIILNLKKVVLAIDSDEERSLEVDIQGPADVTAADLQAGADVEVLNPDLH 60

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAR 191
           I  +     + M +T  KG GY  A  ++   D  PIG++ +D++Y+PI++V+Y VE+ R
Sbjct: 61  IATVAAGKSLHMTITAFKGRGYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTR 120

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
            G   DYDKL+  I T+GSI   D+++L S+IL
Sbjct: 121 VGSRDDYDKLTFDIWTNGSIKPSDALSLGSKIL 153


>gi|290489678|gb|ADD31223.1| RNA polymerase alpha subunit protein [Berberidopsis corallina]
          Length = 337

 Score =  117 bits (293), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 85/309 (27%), Positives = 159/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGPG VTA DI +   +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTCDASICVRGPGYVTAQDIISPPSVEIVDNTQHIASLTEPIDLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +     N   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGY---RIKTLNNFQDGSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLK-------- 258
           S+T ++++  ASR L D    F++ EE    ++++ +  + P   F+  L K        
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHAEEENLHLEDNQHKATFPLFTFHDRLAKLRKNKKEI 267

Query: 259 -----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F    + ++K +LG +
Sbjct: 268 ALKYIFIDQLELPPRIYNCLKRSNIHTLSDLLNNSQEDLMKIEHF---RIEDVKQILGIL 324

Query: 314 GLFLGMNLP 322
                ++LP
Sbjct: 325 EKHFTIDLP 333


>gi|68124013|emb|CAJ01914.1| DNA-directed RNA polymerase alpha chain [Chrysanthemum x
           morifolium]
          Length = 335

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 86/297 (28%), Positives = 154/297 (51%), Gaps = 22/297 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFEKISHEYSTIMGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGPG VTA DI     +E+++    I  L     + + L +
Sbjct: 92  KEIVLRSNLYGTCEASICVRGPGYVTAQDIILPPYVEIVDNTQHIATLTEPIELVIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            K  GY+  K   T  D  G   ID ++ P++  ++++ S   G   + + L + I T+G
Sbjct: 152 EKNRGYL-IKAPNTFQD--GSYPIDPVFMPVRNANHSIHSYENG---NKEILFLEIWTNG 205

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLK-------- 258
           S+T ++++  ASR L D L  F++ +E    ++++ ++  LP   F   L K        
Sbjct: 206 SLTPKEALHEASRNLIDLLIPFLHTKEENLNLEDNQHMIPLPPFTFYDKLAKLTKNKKKM 265

Query: 259 -----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++ EL  R  NCL+  NI  + DL+  ++ D+++M +F  + + +I G+L
Sbjct: 266 ALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQDDLMKMEHFHIEDVKQILGIL 322


>gi|114330001|ref|YP_740682.1| RNA polymerase alpha subunit [Nandina domestica]
 gi|122165930|sp|Q09FS9|RPOA_NANDO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|114054503|gb|ABI49896.1| RNA polymerase alpha subunit [Nandina domestica]
          Length = 338

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 87/308 (28%), Positives = 162/308 (52%), Gaps = 22/308 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FVLSPLMKGQADTIGIAMRRALLGEIEGTCITHAKSEKIPHEYSTIVGIEESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  +GP  +TA DI +   +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTCDASICVKGPINITAKDIISPPSVEIVDTTQHIASLTEPFDLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     ++ +N   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGYRMKTPNKAQN---GSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP-----ALLKKVEEL- 263
           S+T ++++  ASR L D    F++ EE    ++++ N  +LPF       A LKK  E+ 
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHAEEQDIILEDNQNRVTLPFFTFHDGLAKLKKKNEIA 267

Query: 264 ---------ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                    EL  R+ NCL+  NI  + DL+ +++ D+L++ +F    + ++K VLG + 
Sbjct: 268 LKFIFIDQSELPSRTYNCLKKSNINTLLDLLNKSQEDLLKIEHF---RIEDVKRVLGILQ 324

Query: 315 LFLGMNLP 322
               ++LP
Sbjct: 325 KRFVIDLP 332


>gi|229577786|ref|YP_002836122.1| RNA polymerase alpha subunit [Megaleranthis saniculifolia]
 gi|226933914|gb|ACO92047.1| RNA polymerase alpha subunit [Megaleranthis saniculifolia]
          Length = 328

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 83/301 (27%), Positives = 157/301 (52%), Gaps = 20/301 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTIVGIEESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GPG VTA DI +   +E+++    I +L     + +EL +
Sbjct: 92  KEIVLRSNLYGTRDASICVKGPGYVTAQDIISPPSVEIVDITQHIASLTEPIDLCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +     N       IDA++ P++  ++++ S   G     + L + I TDG
Sbjct: 152 ERNRGY---RMKTPNNAQERSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWTDG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP------ALLKKVEEL 263
           S+T ++++  ASR L D    F++ EE   +++++ +  +LPF         + K  +E+
Sbjct: 208 SLTPKEALYEASRNLIDLFIPFLHAEEQDTKLEDNQSRVTLPFFTFHDGLDKVRKNKKEI 267

Query: 264 ELSV----------RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           EL            R+ NCL+  NI  + DL+ +++ D+++M +F  + +  I G++  +
Sbjct: 268 ELKCIFIDQSELPSRTYNCLKRFNIHTLLDLLNKSQEDLMKMEHFRIEDVRRILGIIKNI 327

Query: 314 G 314
            
Sbjct: 328 S 328


>gi|300431272|gb|ADK12601.1| RNA polymerase alpha subunit [Piptochaetium lasianthum]
          Length = 339

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 83/285 (29%), Positives = 142/285 (49%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDRAQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y       G    ++ L + + T+G
Sbjct: 152 KRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYXXXXXGNGNE-KHEILFLELWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------------- 253
           S+T ++++  ASR L D    F++ EE     +E+ N  + P                  
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKKLTNLKKNKKGI 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  R+ NCL+  NI  + DL+ +TE D++++ +F
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMKIDSF 312


>gi|150186973|emb|CAK30139.1| RNA polymerase alpha subunit [Streptococcus porcinus]
          Length = 161

 Score =  117 bits (292), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 57/149 (38%), Positives = 97/149 (65%)

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           G+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV+
Sbjct: 1   GLAVKSYVEDEKMIELDVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLKATMTVA 60

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+
Sbjct: 61  KKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGT 120

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKK 239
           I  ED++ L++R+L + L +F +  E  K
Sbjct: 121 IIPEDALGLSARVLIEHLNLFTDLTEVAK 149


>gi|91984023|ref|YP_567109.1| RNA polymerase alpha subunit [Vitis vinifera]
 gi|122230333|sp|Q0ZIY7|RPOA_VITVI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|91701681|gb|ABE47565.1| RNA polymerase alpha subunit [Vitis vinifera]
          Length = 331

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 83/299 (27%), Positives = 157/299 (52%), Gaps = 24/299 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLIKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL--DVDAVVRMEL 147
           K I L+ +    +   I  RGPG VTA DI +   +E+++    I  L   +D  + +++
Sbjct: 92  KEIVLRSNLYGTRGAFICARGPGYVTAQDIISPPSVEIVDNTQHIARLMEPIDLCIGLQI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+        R  N   G   IDA++ P++  ++++ S   G     + L + I T
Sbjct: 152 ERNRGYSI-----KRPNNFQDGSYPIDAVFMPVRNANHSIHSYGNGNERQ-EILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLK------ 258
           +GS+T ++++  ASR L D    F++ EE    ++ + +  +LP   F+  L K      
Sbjct: 206 NGSLTPKEALHEASRNLIDLFIPFLHAEEETLHLEYNQHKSTLPPLTFHDRLAKLRKNKK 265

Query: 259 -------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                   +++LEL  R  NCL+  NI  + DL+ +++ D++++ +F  + + ++ G+L
Sbjct: 266 EIELKYIFIDQLELPPRIYNCLKRSNIHTLLDLLNKSQKDLMKIEDFRIEDVKQLLGIL 324


>gi|81176283|ref|YP_398360.1| RNA polymerase alpha subunit [Lactuca sativa]
 gi|90110846|sp|Q332U5|RPOA_LACSA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|78675201|dbj|BAE47627.1| RNA polymerase alpha chain [Lactuca sativa]
          Length = 335

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 87/297 (29%), Positives = 154/297 (51%), Gaps = 22/297 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKISHEYSTIMGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGPG VTA DI     +E+L+    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTCEASICVRGPGYVTAQDIILPPYVEILDNTQHIASLTEPIELVIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            K  GY+  K   T  D  G   ID ++ P++  ++++ S   G   + + L + I T+G
Sbjct: 152 EKNRGYL-IKAPNTFQD--GSYPIDPVFMPVRNANHSIHSYENG---NKEILFLEIWTNG 205

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLK-------- 258
           S+T ++++  ASR L D L  F++ +E    ++ + ++  LP   F   L K        
Sbjct: 206 SLTPKEALYEASRNLIDLLIPFLHTKEENLNLEGNQHMVPLPPFTFYDKLAKLTKNKKKM 265

Query: 259 -----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++ EL  R  NCL+  NI  + DL+  ++ D+++M +F  + + +I G+L
Sbjct: 266 ALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDLMKMEHFRIEDVKQILGIL 322


>gi|89280667|ref|YP_514884.1| RNA polymerase alpha subunit [Solanum lycopersicum]
 gi|109900622|sp|Q2MI69|RPOA_SOLLC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|84372014|gb|ABC56331.1| RNA polymerase alpha subunit [Solanum lycopersicum]
 gi|89241703|emb|CAJ32426.1| RNA polymerase alpha chain [Solanum lycopersicum]
          Length = 337

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 84/299 (28%), Positives = 155/299 (51%), Gaps = 24/299 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT V+ + V HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRVKSEKVPHEYSTITGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  +GPG VTA DI     +E+++    I +L       + L +
Sbjct: 92  KEIVLRSNLYGTSEASICVKGPGYVTAQDIILPPYVEIVDNTQHIASLTEPIDFCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY+    H  ++   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGYLIKTPHNFQD---GSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFIEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP--------ALLKK-- 259
           S+T ++++  ASR L D    F++ EE    +++  N  ++P +P         L+K   
Sbjct: 208 SLTPKEALHDASRNLIDLFIPFLHMEEDNLYLQD--NQHTVPLSPFTFHDKLAKLIKNKK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                   +++ ELS R  NCL+  NI  + DL+  ++ D++++ +F  + + +I  +L
Sbjct: 266 KIALKSIFIDQSELSSRIYNCLKMSNIYTLLDLLNNSQEDLMKIEHFRSEDIKQILDIL 324


>gi|88657014|gb|ABD47264.1| RNA polymerase alpha subunit [Lactuca sativa]
          Length = 337

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 87/297 (29%), Positives = 154/297 (51%), Gaps = 22/297 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 34  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKISHEYSTIMGIQESVHEILMNL 93

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGPG VTA DI     +E+L+    I +L     + + L +
Sbjct: 94  KEIVLRSNLYGTCEASICVRGPGYVTAQDIILPPYVEILDNTQHIASLTEPIELVIGLQI 153

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            K  GY+  K   T  D  G   ID ++ P++  ++++ S   G   + + L + I T+G
Sbjct: 154 EKNRGYL-IKAPNTFQD--GSYPIDPVFMPVRNANHSIHSYENG---NKEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLK-------- 258
           S+T ++++  ASR L D L  F++ +E    ++ + ++  LP   F   L K        
Sbjct: 208 SLTPKEALYEASRNLIDLLIPFLHTKEENLNLEGNQHMVPLPPFTFYDKLAKLTKNKKKM 267

Query: 259 -----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++ EL  R  NCL+  NI  + DL+  ++ D+++M +F  + + +I G+L
Sbjct: 268 ALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDLMKMEHFRIEDVKQILGIL 324


>gi|326909424|ref|YP_004327694.1| RNA polymerase alpha subunit [Hevea brasiliensis]
 gi|308523538|gb|ADO33588.1| RNA polymerase alpha subunit [Hevea brasiliensis]
          Length = 341

 Score =  116 bits (291), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 84/311 (27%), Positives = 165/311 (53%), Gaps = 23/311 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEFSTIAGIQESIHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +       +I   GPG VTA DI     +E+++    I +L   +D  + +++
Sbjct: 92  KEIVLRSNLYGTCNASICVEGPGYVTAQDIILPPFVEIIDNTQHIASLTEAIDLCIGLQI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+   P  + + ++   G  +IDA++ P++  +++V S   G     + L + I T
Sbjct: 152 ERNRGYRINPTNNFQVQD---GSYSIDAVFMPVRNANHSVHSYGNGNE-KQEILFLEIWT 207

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLK------ 258
           +GS+T ++++  ASR L D    F++ EE    ++++ +  +LP   F+  L K      
Sbjct: 208 NGSLTPKEALHEASRNLIDFFIPFLHAEEENLHLEKNQHKVTLPLFTFHDRLTKLRKNKK 267

Query: 259 -------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +++ EL+ +  NCL+  NI  + DL+++++ D++++ +F    +  I G+L 
Sbjct: 268 EIALKYIFIDQSELTPKIYNCLKRSNIHTLSDLLKKSQEDLMKIEHFRIDDVKHILGILE 327

Query: 312 TMGLFLGMNLP 322
               F  ++LP
Sbjct: 328 IEKHF-AIDLP 337


>gi|237688685|ref|YP_002905301.1| RNA polymerase alpha subunit [Pinus krempfii]
 gi|226951142|gb|ACO94205.1| RNA polymerase alpha subunit [Pinus krempfii]
          Length = 335

 Score =  116 bits (291), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 82/293 (27%), Positives = 149/293 (50%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIREASIYIVGPKNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H + N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIQ-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALLKK----------- 259
            +++  ASR L D    F++ EE   +    K+  N+   P +  L              
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTDTGETKEKIAFQH 271

Query: 260 --VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  ++ N LR  NI  + DL+  +  D++R+ +  ++S+ ++  VL
Sbjct: 272 IFIDQLELPSKTYNSLRRANIHTLLDLLNYSREDLMRIEHLEKESVEQVLEVL 324


>gi|52220841|ref|YP_086997.1| RNA polymerase alpha subunit [Panax ginseng]
 gi|68053096|sp|Q68RX5|RPOA_PANGI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|51235344|gb|AAT98540.1| RNA polymerase alpha subunit [Panax ginseng]
          Length = 353

 Score =  116 bits (290), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 88/321 (27%), Positives = 161/321 (50%), Gaps = 22/321 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S++ G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTLVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK +       +I  RGPG VTA DI +   +E+++    I +L     + + L +
Sbjct: 92  KEIILKSNLYGTCDASICIRGPGYVTAQDIISPPYVEIVDNTQHIASLAEPIDLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY+    +    D  G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGYLIKTPNNNFQD--GSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWTNG 208

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLK-------- 258
           S+T ++++  ASR L D    F++ EE    + ++ +   LP   F+  L K        
Sbjct: 209 SLTPKEALHQASRNLIDLFIPFLHTEEENLHLADNQHTVPLPPFTFHEKLTKLRKNKKKI 268

Query: 259 -----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++ EL  R  NCL   NI  + DL+  ++ D++++ +F    + ++K +LG +
Sbjct: 269 ALKSIFIDQSELPPRIYNCLIRSNIYTLLDLLNNSQEDLMKIEHF---RIEDVKAILGIL 325

Query: 314 GLFLGMNLPDWPPESIEELAK 334
                ++LP       E LA+
Sbjct: 326 EKHFAIDLPKKLKIGFESLAQ 346


>gi|197294143|ref|YP_002149764.1| RNA polymerase alpha subunit [Cicer arietinum]
 gi|197089831|gb|ACH41101.1| RNA polymerase alpha subunit [Cicer arietinum]
          Length = 333

 Score =  116 bits (290), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 80/287 (27%), Positives = 152/287 (52%), Gaps = 22/287 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR+L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRILLGEIEGTCITRAKSEKIPHEYSTIVGIQESIHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GPG VTA DI     +E+++    I NL     + MEL +
Sbjct: 92  KEIVLRSNLYGTRDASICFKGPGSVTAQDIILPPSVEIVDNTQHIANLTEPINLCMELKL 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  +++     TIDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGYRIKTLNNIQDES---YTIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLKK------- 259
           S+T ++++  ASR L D    F++ EE K  ++ +    +LP   F+   +K        
Sbjct: 208 SLTPKEALFEASRNLIDLFIPFLHAEEDKLNLENNQQKVTLPLFTFHDRFVKDKLRKNKK 267

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                   +++LEL  R  NCL+  NI  + +L+ +++ +++++ +F
Sbjct: 268 EIALKSIFIDQLELPPRIYNCLKKSNIHTLLELLNKSQEELMKIEHF 314


>gi|119662339|emb|CAJ33158.1| RNA polymerase alpha subunit [Lactobacillus paralimentarius]
          Length = 134

 Score =  116 bits (290), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 51/130 (39%), Positives = 89/130 (68%)

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  VTA DI+  +D+E+L+P+  IC +       M++TV  G GY PA+ ++T+  PIG
Sbjct: 3   GPATVTANDIKADDDLEILDPEQFICTVAEGGHFHMQMTVINGRGYTPAEQNKTDETPIG 62

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           ++ +D++++P++KV+Y VE+ R G+  D+DKL++ I T+GSI   ++++L+++IL + L 
Sbjct: 63  VLPVDSIFTPVEKVNYQVENTRVGKRNDFDKLTIDIWTNGSIGPREAISLSAKILTEHLT 122

Query: 230 MFINFEEPKK 239
            F+N  E  K
Sbjct: 123 SFVNLTEEAK 132


>gi|290489686|gb|ADD31227.1| RNA polymerase alpha subunit protein [Ficus sp. Moore 315]
          Length = 323

 Score =  116 bits (290), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 86/297 (28%), Positives = 156/297 (52%), Gaps = 23/297 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL RG A T+G A+RR L+  + G  IT V+ + + HE S+I G+ E + +I++N+
Sbjct: 32  FILAPLMRGQADTIGIAMRRALLGEIEGTCITRVKFEKLPHEYSTIIGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  VTA DI     +E+++    I NL     + +EL +
Sbjct: 92  KEIVLRSNLYGTRDASICVKGPRYVTAQDIILPPSVEIVDNTQHIANLTEPITLCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  +N   G   IDA++ P++  ++++ S   G   + + L + I T+G
Sbjct: 152 KRDRGYRIKTPNNFQN---GSYPIDAVFMPVRNANHSIHSYVNGNE-NQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-FN-------PALLKK-- 259
           S+T ++++  ASR L D   +FI F   ++ ++ + +  +LP FN       P   KK  
Sbjct: 208 SLTPKEALHEASRNLID---LFIPFFHAEEHLENNQHKGTLPLFNFHGRLAKPRKTKKEK 264

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++ EL+ R  NCL+  NI    DL+  ++ +++++ +F  + +  I  VL
Sbjct: 265 ALKYIYIDQSELTPRVYNCLKRSNINTFLDLLNNSQEELMKIKDFTIEDVKHILDVL 321


>gi|150186905|emb|CAK30124.1| RNA polymerase alpha subunit [Streptococcus gallinaceus]
          Length = 138

 Score =  116 bits (290), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 56/138 (40%), Positives = 92/138 (66%)

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILNIKGI +K   +  K + +   GP  +TAGDI T +DIE++NPDH +  +   A  +
Sbjct: 1   IILNIKGIAVKSYVEDEKTIELDVVGPAEITAGDILTDSDIEIVNPDHYLFTIAAGATFK 60

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
             +TV+ G GY+PA+ ++ ++ P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ 
Sbjct: 61  AVMTVNTGRGYIPAEGNKKDDAPVGTLAVDSIYTPVVKVNYQVEPARVGSNDGFDKLTLE 120

Query: 205 IDTDGSITGEDSVALASR 222
           I T+G+   ED++ L++R
Sbjct: 121 IMTNGTTIPEDALGLSAR 138


>gi|11465990|ref|NP_054532.1| RNA polymerase alpha subunit [Nicotiana tabacum]
 gi|78102570|ref|YP_358710.1| RNA polymerase alpha subunit [Nicotiana sylvestris]
 gi|133409|sp|P06269|RPOA_TOBAC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|90110850|sp|Q3C1M3|RPOA_NICSY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|11860|emb|CAA77376.1| RNA polymerase alpha subunit [Nicotiana tabacum]
 gi|10442805|gb|AAG15578.1| RNA polymerase alpha subunit [synthetic construct]
 gi|77799597|dbj|BAE46686.1| RNA polymerase alpha subunit [Nicotiana sylvestris]
 gi|225228|prf||1211235BK RNA polymerase alpha
          Length = 337

 Score =  116 bits (290), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 84/299 (28%), Positives = 154/299 (51%), Gaps = 24/299 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT V+ + V HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRVKSEKVPHEYSTITGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  +GPG VTA DI     +E+++    I +L       + L +
Sbjct: 92  KEIILRSNLYGTSDASICVKGPGSVTAQDIILPPYVEIVDNTQHIASLTEPIDFCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY+    H  ++   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGYLIKTPHNFQD---GSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP--------ALLKK-- 259
           S+T ++++  ASR L D    F++ EE    +++  N  ++P +P         L+K   
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHMEEDNLYLQD--NQHTVPLSPFTFHDKLAKLIKNKK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                   +++ EL  R  NCL+  NI  + DL+  ++ D++++ +F  + +  I G+L
Sbjct: 266 KIALKSIFIDQSELPSRIYNCLKMSNIYTLLDLLNNSQEDLMKIEHFRSEDVKRILGIL 324


>gi|170784739|ref|YP_001718655.1| RNA polymerase alpha subunit [Trachelium caeruleum]
 gi|156598871|gb|ABU85688.1| RNA polymerase alpha subunit [Trachelium caeruleum]
 gi|157267487|gb|ABV26480.1| RNA polymerase alpha subunit [Trachelium caeruleum]
          Length = 337

 Score =  116 bits (290), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 85/309 (27%), Positives = 162/309 (52%), Gaps = 25/309 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A  +G A+RR L+  L G  IT  + + + HE S++ G+ E + +I++N+
Sbjct: 32  FILSPLLKGQADIIGIAMRRALLGELEGTCITRAKSEKLPHEYSTLVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +        I  +GPG VTA DI +   +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTCDAAICVKGPGYVTAQDIISPPYVEIIDNTQHIASLTEPIELCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY+  K  +   D  G   IDA++ P++ V++++ S   G    ++ L + I T+G
Sbjct: 152 ERNRGYL-IKTAKNFQD--GSYPIDAVFMPVRNVNHSIYSYGTGND-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK---------- 259
           S+T ++++  A+R L D    F++ EE   ++++  N   LPF P++L +          
Sbjct: 208 SLTPKEALHEAARNLIDLFIPFLHTEEENLDLED--NQHMLPFRPSILPEKFVKIKNKKI 265

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++ EL  R  NCL+  NI  + DL+  ++ D++++ +F    + ++K +L  +
Sbjct: 266 SLKSIFIDQSELPPRVYNCLKRSNIYTLLDLLNNSQEDLMKIEHF---RVEDLKRILDIL 322

Query: 314 GLFLGMNLP 322
               G++LP
Sbjct: 323 EKNFGIDLP 331


>gi|154795220|ref|YP_588149.2| RNA polymerase alpha subunit [Helianthus annuus]
 gi|158518528|sp|Q1KXS7|RPOA_HELAN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
          Length = 335

 Score =  116 bits (290), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 85/297 (28%), Positives = 155/297 (52%), Gaps = 22/297 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE ++I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKISHEYATIMGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGPG VTA DI     +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTCEASICVRGPGYVTAQDIILPPYVEIVDNTQHIASLTEPIELVIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            K  GY+  K   T  D  G   ID ++ P++  ++++ S   G   + + L + I T+G
Sbjct: 152 EKNRGYL-IKAPNTFQD--GSYPIDPVFMPVRNANHSIHSYENG---NKEILFLEIWTNG 205

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLK-------- 258
           S+T ++++  ASR L D L  F++ +E    ++++ ++  LP   F   L K        
Sbjct: 206 SLTPKEALHEASRNLIDLLIPFLHTKEENLSLEDNQHIVPLPPFTFYDKLAKLTKNKKKM 265

Query: 259 -----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++ EL  R  NCL+  NI  + DL+  ++ D+++M +F  + + +I G+L
Sbjct: 266 ALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDLMKMEHFRIEDVKQILGIL 322


>gi|323148937|ref|YP_004222491.1| RNA polymerase alpha subunit [Smilax china]
 gi|308742628|gb|ADO33479.1| RNA polymerase alpha subunit [Smilax china]
          Length = 339

 Score =  116 bits (290), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 91/311 (29%), Positives = 159/311 (51%), Gaps = 27/311 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + V HE  +I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKVPHEYFTIVGIKESVHEILINL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +    +   I  RGP  VTA DI +   +E+++    I  L   +D  + +++
Sbjct: 92  KEIVLRSTLYGVRDAAICVRGPRYVTAQDIISPPSVEIVDTTQHIATLTEPIDLCIGLQI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
              +G+   P     T N   G   IDA+  P++  ++++ S   G     + L + I T
Sbjct: 152 KRDRGYRMKP-----TNNSKDGSYPIDAVSMPVRNANHSIHSYGNGNE-KQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP--------FNPALLKK 259
           +GS+T ++++  ASR L D    F++ EE     KE+ N  +LP         N    KK
Sbjct: 206 NGSLTPKEALYEASRNLIDLFIPFLHAEEEGINFKENENRFTLPPFTLQDRLINLKKTKK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +++LEL  R+ NCL+  NI  + DL+  ++ D++R+ ++ R  + ++K +L 
Sbjct: 266 CIPLKCIFIDQLELPPRTYNCLKRSNIHTLLDLLSNSQEDLMRI-DYLR--IEDVKQILD 322

Query: 312 TMGLFLGMNLP 322
           T+   L  +LP
Sbjct: 323 TLQKHLASDLP 333


>gi|88656926|gb|ABD47177.1| RNA polymerase alpha subunit [Helianthus annuus]
          Length = 337

 Score =  115 bits (289), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 85/297 (28%), Positives = 155/297 (52%), Gaps = 22/297 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE ++I G+ E + +I++N+
Sbjct: 34  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKISHEYATIMGIQESVHEILMNL 93

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGPG VTA DI     +E+++    I +L     + + L +
Sbjct: 94  KEIVLRSNLYGTCEASICVRGPGYVTAQDIILPPYVEIVDNTQHIASLTEPIELVIGLQI 153

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            K  GY+  K   T  D  G   ID ++ P++  ++++ S   G   + + L + I T+G
Sbjct: 154 EKNRGYL-IKAPNTFQD--GSYPIDPVFMPVRNANHSIHSYENG---NKEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLK-------- 258
           S+T ++++  ASR L D L  F++ +E    ++++ ++  LP   F   L K        
Sbjct: 208 SLTPKEALHEASRNLIDLLIPFLHTKEENLSLEDNQHIVPLPPFTFYDKLAKLTKNKKKM 267

Query: 259 -----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++ EL  R  NCL+  NI  + DL+  ++ D+++M +F  + + +I G+L
Sbjct: 268 ALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDLMKMEHFRIEDVKQILGIL 324


>gi|34500945|ref|NP_904130.1| RNA polymerase alpha subunit [Amborella trichopoda]
 gi|41688608|sp|P60314|RPOA_AMBTC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|34481660|emb|CAD45138.1| RNA polymerase alpha subunit [Amborella trichopoda]
          Length = 334

 Score =  115 bits (289), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 88/313 (28%), Positives = 158/313 (50%), Gaps = 33/313 (10%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +  PL +G A T+G A+RR L+  + G  IT  + + V HE S+I G+ E + +I++N+
Sbjct: 32  FVLSPLMKGQADTIGTAMRRSLLGEIEGTCITCAKSERVPHEYSTIVGIEESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I ++      +   I  RGP  VTA DI +   +++++    I ++       + L +
Sbjct: 92  KEIIVRSDLYGTRDAFICVRGPKYVTAQDIISPPSVKIVDTTQHIASITEPINFCIGLEI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE---SAREGQVLDYDKLSMTID 206
            +  GY      RT N       IDA+  P++  +Y+++   +  E Q +    L + I 
Sbjct: 152 ERNRGY----RTRTTNQDASY-PIDAVSMPVRNANYSIQCYGNENEKQEI----LFLEIW 202

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA----------- 255
           T+GS+T ++++  ASR L D    F++ EE    + +D N+ + PF P            
Sbjct: 203 TNGSLTPKEALYEASRNLIDLFIPFLHAEERDLHLDDDQNIFTAPFFPFHEGLAYIGIGE 262

Query: 256 -----LLKK--VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                 LK+  +++LELS R+ NCL+  NI  + DL+ +++ D+ ++ +F    + ++K 
Sbjct: 263 SKKRIALKRIFIDQLELSPRTYNCLKRSNIHTLLDLLSKSQEDLRKIQHF---RVEDVKR 319

Query: 309 VLGTMGLFLGMNL 321
           VL  +     MNL
Sbjct: 320 VLDILKKRFAMNL 332


>gi|228016207|gb|ACP51043.1| RNA polymerase alpha subunit [Pinus squamata]
          Length = 335

 Score =  115 bits (289), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 82/293 (27%), Positives = 149/293 (50%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H + N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIQ-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALLKK----------- 259
            +++  ASR L D    F++ EE   +    K+  N+   P +  L              
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTDTRETKEKIAFQH 271

Query: 260 --VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  ++ N LR  NI  + DL+  +  D++R+ +  ++S+ ++  VL
Sbjct: 272 IFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMRIEHLEKESVEQVLEVL 324


>gi|91208933|ref|YP_538968.1| RNA polymerase alpha subunit [Gossypium hirsutum]
 gi|325210961|ref|YP_004286036.1| RNA polymerase alpha subunit [Gossypium thurberi]
 gi|109900621|sp|Q2L938|RPOA_GOSHI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|85687447|gb|ABC73659.1| RNA polymerase alpha subunit [Gossypium hirsutum]
 gi|290775823|gb|ADD62319.1| RNA polymerase alpha subunit [Gossypium thurberi]
          Length = 329

 Score =  115 bits (289), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 85/302 (28%), Positives = 157/302 (51%), Gaps = 30/302 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  L G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 34  FILSPLMKGQADTIGIAMRRALLGELEGTCITRAKSEKIPHEYSTIVGIQESVHEILMNL 93

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +    +   I  +GPG VTA DI     +E+++    + +L   +D  + +++
Sbjct: 94  KEIVLRGNLYGTRNAFICAKGPGYVTAQDIILPPSVEIVDNTQHVASLTEPIDLCIGLQI 153

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA---REGQVLDYDKLSMT 204
             ++G+G    K+    + P     IDA++ P++  ++++       E Q +    L + 
Sbjct: 154 ERNRGYGIKTPKNFHDGSYP-----IDAVFMPVRNANHSIHCYGNDNEKQEI----LFLE 204

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP------ALLK 258
           I T+GS+T ++++  ASR L D    F++ EE    ++ + +  +LPF P       L K
Sbjct: 205 IWTNGSLTPKEALHEASRNLIDLFIPFLHTEEENLHLENNQHDVTLPFFPFHDRLVKLTK 264

Query: 259 KVEEL----------ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
           K +E+          EL  R  NCL+  NI  + DL+  +  D++++ +F  + + +I G
Sbjct: 265 KKKEIALKYIFIDQSELPPRIYNCLKKSNIHTLLDLLNNSREDLMKIEHFRIEDVKQILG 324

Query: 309 VL 310
           +L
Sbjct: 325 IL 326


>gi|294155443|ref|YP_003559827.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma crocodyli
           MP145]
 gi|291600072|gb|ADE19568.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma crocodyli
           MP145]
          Length = 333

 Score =  115 bits (289), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 88/292 (30%), Positives = 147/292 (50%), Gaps = 19/292 (6%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           +PL RGFA TLG ALRRVL+S++   A   V+I+GV HE   I GV ED+  +I+N++ +
Sbjct: 27  QPLERGFATTLGVALRRVLLSNITSLAPFCVRIEGVTHEFQGITGVIEDVPSLIMNLRKV 86

Query: 93  NLK-----MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV--DAVVRM 145
                   +  D   +V +     G + +  ++ V+++ V   DH I   DV  +  +R+
Sbjct: 87  RFSYDPELVKDDEIIKVELKADQIGEINSRYLEVVDNLNVEVIDHNIHIADVALENSLRL 146

Query: 146 ELTVSKGHGYVPAKHHR-----------TENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
           EL +  G G+V ++ ++           T+      I +D+ +SP++KV+Y V       
Sbjct: 147 ELYLRPGRGFVSSEENKALVSKLETQLETKIKKGKFIAVDSNFSPVEKVNYVVSELNSSS 206

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
           V   +KL   + TDG++  +D++  A+ IL     +  N +E K  + E    K L    
Sbjct: 207 VKIEEKLEFNVITDGTVKPKDAIKQAAEILISHFKVIGNVDEIKDSIFETSEDKVLDVQE 266

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
             +  + +L LSVRS N LR        ++ + T  ++ +  N G+KSL EI
Sbjct: 267 QDI-DINQLGLSVRSLNALRRIGKTKASEVAKMTYDELEQTKNLGKKSLDEI 317


>gi|290489656|gb|ADD31212.1| RNA polymerase alpha subunit protein [Aucuba japonica]
          Length = 349

 Score =  115 bits (289), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 83/299 (27%), Positives = 155/299 (51%), Gaps = 24/299 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +  A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKSQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTIVGIQESIHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGPG +TA DI     +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTCDTSICVRGPGYITAQDIILPPYVEIVDKTQHIASLTEPIDLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY+    +  ++   G   IDA++ P++ V+Y++ S   G     + L + I T+G
Sbjct: 152 ERNRGYLIKTPNNFQD---GSYPIDAVFMPVRNVNYSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP-------ALLKK--- 259
           S+T ++++  ASR L D    F++ EE    +++  N  ++P +P       A L+K   
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHMEEENLHLED--NQHTVPLSPFTFHDKLAKLRKNKN 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                   +++ EL  R  NCL+  NI  + DL+  ++ D++++  F  + + +I G+L
Sbjct: 266 KIALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDLMKIEQFRIQDVKQILGIL 324


>gi|32480874|ref|NP_862785.1| RNA polymerase alpha subunit [Calycanthus floridus var. glaucus]
 gi|41688654|sp|Q7YJU6|RPOA_CALFG RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|32399410|emb|CAD28752.1| RNA polymerase alpha subunit [Calycanthus floridus var. glaucus]
          Length = 340

 Score =  115 bits (289), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 87/311 (27%), Positives = 156/311 (50%), Gaps = 25/311 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +  PL +G A T+G A+R+ L+  + G  IT  + + V HE S+I G+ E + +I++N+
Sbjct: 32  FVLSPLMKGQADTIGIAMRKALLGEIEGTCITRAKSEKVPHEYSTIVGIEESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK +    +  +I  RGP  VTA DI +   +E+++    I +L     + +EL +
Sbjct: 92  KEIVLKSNLYGTRDASICVRGPKYVTAQDIISPPSVEIVDTTQHIASLTEPINLCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +     N   G   IDA+  P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERDRGY---RMKAPNNYQDGSYPIDAVSMPVRNANHSIHSYGSGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL----------KK 259
           S+T ++++  ASR L D    F++ EE    +  + N      +P  L          KK
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHAEEQDIHLNLEDNQNRFTVSPFTLHDRLGNIRKNKK 267

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +++ EL  R+ NCL+  NI  + DL+  ++ D++R+ +F    + +IK +L 
Sbjct: 268 EIALKCIFIDQSELPTRTYNCLKRSNIHTLLDLLNNSQEDLMRIEHF---RIEDIKQILD 324

Query: 312 TMGLFLGMNLP 322
            +    G++LP
Sbjct: 325 ILQKHFGIDLP 335


>gi|153012181|ref|YP_001381697.1| RNA polymerase alpha subunit [Medicago truncatula]
          Length = 333

 Score =  115 bits (289), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 87/299 (29%), Positives = 157/299 (52%), Gaps = 22/299 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR+L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLRKGQADTIGIAMRRILLGEIEGTCITRAKSEKIPHEYSTIVGIQESIHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK +    +  +I  +GPG VTA DI     +E+++    I NL     + +EL +
Sbjct: 92  KEIVLKSNLYGTRDASICFKGPGYVTAQDIILPPSVEIVDNTQHIANLTEPINLCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +     N   G  TIDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERKRGY---RIKTLNNIQDGSYTIDAVFMPVRNANHSIHSYVNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLKK------- 259
           S+T ++++  ASR L D    F++ EE     + + +  +LP   F+  LLK        
Sbjct: 208 SLTPKEALYEASRNLIDLFIPFLHAEEENLNFENNQHKVTLPLFTFHDRLLKDKLRKNKK 267

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                   +++LELS R  NCL+  NI  + +L+ +++ D++++ +F  + +  I  +L
Sbjct: 268 EIALKSIFIDQLELSPRIYNCLKKSNIHTLLELLNKSQEDLMKIEHFRVEDVKNILNIL 326


>gi|119662387|emb|CAJ33182.1| RNA polymerase alpha subunit [Lactobacillus acidifarinae]
          Length = 132

 Score =  115 bits (288), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 61/131 (46%), Positives = 87/131 (66%), Gaps = 4/131 (3%)

Query: 85  IILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILN+K I LK++G  D  + + I  +GP  VTAGDI    D++VLNPD  I  +   A 
Sbjct: 2   IILNVKKIALKLNGADDQEETMEINVKGPAQVTAGDIVAGADVDVLNPDLYIATVADGAT 61

Query: 143 VRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             M +T  KG GYV A  ++T N   PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDK
Sbjct: 62  FHMRMTADKGRGYVSADENKTRNTEMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDK 121

Query: 201 LSMTIDTDGSI 211
           L++ + T+GSI
Sbjct: 122 LTLDVWTNGSI 132


>gi|154424739|emb|CAL18472.1| RNA polymerase alpha subunit [Streptococcus oligofermentans]
          Length = 136

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 57/136 (41%), Positives = 89/136 (65%)

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILNIKGI +K      K + +   GP  VTAGDI T +DIE++NPDH +  +   A  +
Sbjct: 1   IILNIKGIAVKSYVQDEKMIELDVEGPAEVTAGDILTDSDIEIVNPDHYLFTISEGARFK 60

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
            ++ V+ G GYVPA  ++ ++ P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ 
Sbjct: 61  AKMAVNSGRGYVPADENKKDDAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLE 120

Query: 205 IDTDGSITGEDSVALA 220
           I T+G+I  ED++ L+
Sbjct: 121 ILTNGTIIPEDALGLS 136


>gi|228017530|gb|ACP52345.1| RNA polymerase alpha subunit [Pinus monticola]
          Length = 335

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 81/293 (27%), Positives = 149/293 (50%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITFDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H + N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIQ-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALLKK----------- 259
            +++  ASR L D    F++ EE   +    K+  N+   P +  L              
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTDTGETKEKIAFKH 271

Query: 260 --VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  ++ N LR  NI  + DL+  +  D++++ +  ++S+ ++  VL
Sbjct: 272 IFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMKIEHLEKESVEQVLEVL 324


>gi|290489660|gb|ADD31214.1| RNA polymerase alpha subunit protein [Ehretia acuminata]
          Length = 339

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 83/301 (27%), Positives = 155/301 (51%), Gaps = 26/301 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG--VLHEISSIKGVHEDLTDIIL 87
            I  PL +G A T+G A+RR L+  + G +IT V+ +   V HE S+I G+ E + +I++
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTSITRVKSESEKVPHEYSTISGIQESVHEILM 91

Query: 88  NIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           N+K I L+ +       +I  RGPG VTA DI     +E+++    I +L     + + L
Sbjct: 92  NLKEIVLRSNLYGTCDASICVRGPGYVTAQDIILPPYVEIVDNTQHIASLTEPIDLCIGL 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            + +  GY+    H  ++   G   IDA++ P++  ++++ S   G     + L + I T
Sbjct: 152 QIERNRGYLIKTPHNFQD---GSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWT 207

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK-------- 259
           +GS+T ++++  ASR L D    F++ EE    +++  N  ++P +P +           
Sbjct: 208 NGSLTPKEALHEASRNLIDLFIPFLHMEEENVHLED--NQHTVPLSPFIFHDKLAKLRKK 265

Query: 260 ----------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                     +++ EL  R  NCL+  NI  + DL+  ++ D++++ +F  + + +I G+
Sbjct: 266 KKKIALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDLMKIEHFRIEDVKQILGI 325

Query: 310 L 310
           L
Sbjct: 326 L 326


>gi|69215824|gb|AAZ03868.1| RNA polymerase alpha chain [Ranunculus macranthus]
          Length = 339

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 86/312 (27%), Positives = 167/312 (53%), Gaps = 27/312 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTIVGIEESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +    +  +I  +GPG VTA DI +   +E+++    I +L   VD  + +++
Sbjct: 92  KEIVLRSNLYGTRDASICVKGPGYVTAQDIISPPSVEIVDTTQHIASLTEPVDFCIGLQI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+     +     N   G   IDA++ P++  ++++ S   G   + + L + I T
Sbjct: 152 ESNRGY-----RMKTPNNAQKGSYPIDAVFMPVRNANHSIHSYGNGNE-NQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI-NVKSLPFNPA-----LLKK-- 259
           +GS+T ++++  ASR L D    F++ EE  + +K++  N  +LPF         LKK  
Sbjct: 206 NGSLTPKEALYEASRNLIDLFIPFLHAEEQDQNLKDNQKNGVTLPFFTFHDGFDKLKKNK 265

Query: 260 ---------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                    +++ EL  R+ NCL+  NI  + DL+ +++ D++++ +F  + + +I  ++
Sbjct: 266 KEIELKCIFIDQSELPSRTYNCLKRANIHTLLDLLNKSQEDLMKIEHFRIEDVKQILDII 325

Query: 311 GTMGLFLGMNLP 322
                F+ ++LP
Sbjct: 326 QKH--FVVIDLP 335


>gi|283794999|ref|YP_003359390.1| RNA polymerase alpha subunit [Olea europaea]
 gi|330850774|ref|YP_004376452.1| RNA polymerase alpha subunit [Olea europaea subsp. europaea]
 gi|281428718|gb|ADA69957.1| RNA polymerase alpha subunit [Olea europaea]
 gi|291059284|gb|ADD72120.1| RNA polymerase alpha subunit [Olea europaea]
 gi|328795464|emb|CBR30346.1| RNA polymerase alpha subunit [Olea europaea subsp. europaea]
          Length = 337

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/309 (28%), Positives = 158/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT V+ + V HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRVKSENVPHEYSTIAGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGPG VTA DI     +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTCDASICVRGPGYVTAQDIILPPYVEIVDNTQHIASLTEPIDLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY+    H  ++   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 KRNRGYLIKMPHNFQD---GSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEE---PKKEVKEDINVKSLPFNPAL--LKK----- 259
           S+T ++++  A R L D    F++ EE   P ++ +  + +  L F+  L  L+K     
Sbjct: 208 SLTPKEALHEACRNLIDLFIPFLHKEEENLPLEDNQHTVPLSPLTFHDKLDKLRKNKKKI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++ E S R  NCL+  NI  + DL+  +  D++++ +     L +IK +L  +
Sbjct: 268 ALKSIFIDQSEFSPRVYNCLKRSNIYTLLDLLNNSPEDLMKIEHL---RLEDIKQILVIL 324

Query: 314 GLFLGMNLP 322
                ++LP
Sbjct: 325 EKHFAIDLP 333


>gi|290489672|gb|ADD31220.1| RNA polymerase alpha subunit protein [Phoradendron serotinum]
          Length = 326

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 82/297 (27%), Positives = 161/297 (54%), Gaps = 25/297 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + D + HE S+I+G+ E + DI++N+
Sbjct: 32  FILSPLIKGQADTIGIAMRRALLGEIEGTCITRAKSDQIPHEYSTIRGIQESVHDILINL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL--DVDAVVRMEL 147
           K I L+ +       +I+ +GP  +TA DI     +E+++   +I +L   +D  + +++
Sbjct: 92  KEIVLRSNLYGTCNASIYIKGPRYITAQDIILPPYVEIIDHTQIIASLTEQIDFGIGLQI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+  +  K     N   G  +I+A++ P++  ++++ +  E      + L + I T
Sbjct: 152 EKNRGYRIITPK-----NLQEGNFSIEAIFMPVRNANHSIHNYNE----KLEILFLEIWT 202

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL-PFNPAL--LKK----- 259
           +GS+T ++++  A+R L D    F++ ++ K  V+++ +  SL  F+  L  L+K     
Sbjct: 203 NGSLTPKEALHEAARNLIDLFIPFLHVKKEKLHVEDNQHKLSLFTFHDRLQKLRKTKEKI 262

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++ ELS R  NCL+  NI  + DL+ +   D++++ +F  + L  I G+L
Sbjct: 263 ALKSIFIDQSELSPRIYNCLKSSNIQNILDLLNKNREDLMKIEHFRIEDLKHIWGIL 319


>gi|139387483|ref|YP_001122838.1| RNA polymerase alpha subunit [Phaseolus vulgaris]
 gi|158513617|sp|A4GGD7|RPOA_PHAVU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|112031005|gb|ABH88117.1| RNA polymerase alpha subunit [Phaseolus vulgaris]
 gi|158187119|gb|ABW22752.1| RNA polymerase alpha subunit [Phaseolus vulgaris]
          Length = 333

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 82/287 (28%), Positives = 151/287 (52%), Gaps = 22/287 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR+L+  + G  IT V+ + + HE S+I G+ E + +I +N+
Sbjct: 32  FILSPLMKGQADTIGIAIRRILLGEIEGTCITCVKSEKIPHEYSTIIGIEESVHEIFMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK +    +  +I  +GPG +TA DI     +E+++    I N+     + +EL +
Sbjct: 92  KEIVLKSNMYGIQDASISFKGPGYITAQDIILPPSVEIVDNRQHIANVTEPVHLCIELKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA + P++ V+Y++ S   G     + L + I T+G
Sbjct: 152 ERNRGY---RIKTLKNFQDGSYDIDARFMPVRNVNYSIHSYVNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLKK------- 259
           S+T ++++  AS+ L +    F++ EE    ++++ +  +LP   F+  L+K        
Sbjct: 208 SLTPKEALYEASQNLIELFIPFLHAEEDNFHLEKNQHKVTLPLFTFHDILVKDKLRKNQK 267

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                   +++LEL  R  NCL+  NI  + +L+  ++ D+L+  +F
Sbjct: 268 EIALKSIFIDQLELPPRIYNCLKRSNIHTLLELLSNSQEDLLKFEHF 314


>gi|119672817|emb|CAK95488.1| RNA polymerase alpha subunit [Lactobacillus johnsonii]
          Length = 115

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 55/103 (53%), Positives = 76/103 (73%)

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP +VTA D++  +DIEVLNPD  IC++     + M + +  G GYVPA  ++T++ PIG
Sbjct: 11  GPAIVTAADLKVDSDIEVLNPDQYICSIADGGHLHMNVAIKTGRGYVPASENKTDDMPIG 70

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           +I +D+L+SPIKKV+Y VESAR G+  DYDKL++ I TDGSIT
Sbjct: 71  VIPVDSLFSPIKKVNYQVESARVGKRDDYDKLTLEIWTDGSIT 113


>gi|122894022|ref|YP_001004218.1| RNA polymerase alpha subunit [Ranunculus macranthus]
 gi|158514028|sp|A1XGS0|RPOA_RANMC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|85540836|gb|ABC70788.1| RNA polymerase alpha subunit [Ranunculus macranthus]
          Length = 346

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 86/312 (27%), Positives = 167/312 (53%), Gaps = 27/312 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTIVGIEESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +    +  +I  +GPG VTA DI +   +E+++    I +L   VD  + +++
Sbjct: 92  KEIVLRSNLYGTRDASICVKGPGYVTAQDIISPPSVEIVDTTQHIASLTEPVDFCIGLQI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+     +     N   G   IDA++ P++  ++++ S   G   + + L + I T
Sbjct: 152 ESNRGY-----RMKTPNNAQKGSYPIDAVFMPVRNANHSIHSYGNGNE-NQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI-NVKSLPFNPA-----LLKK-- 259
           +GS+T ++++  ASR L D    F++ EE  + +K++  N  +LPF         LKK  
Sbjct: 206 NGSLTPKEALYEASRNLIDLFIPFLHAEEQDQNLKDNQKNGVTLPFFTFHDGFDKLKKNK 265

Query: 260 ---------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                    +++ EL  R+ NCL+  NI  + DL+ +++ D++++ +F  + + +I  ++
Sbjct: 266 KEIELKCIFIDQSELPSRTYNCLKRANIHTLLDLLNKSQEDLMKIEHFRIEDVKQILDII 325

Query: 311 GTMGLFLGMNLP 322
                F+ ++LP
Sbjct: 326 QKH--FVVIDLP 335


>gi|269115047|ref|YP_003302810.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma hominis]
 gi|268322672|emb|CAX37407.1| DNA-directed RNA polymerase alpha chain [Mycoplasma hominis ATCC
           23114]
          Length = 344

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 75/304 (24%), Positives = 152/304 (50%), Gaps = 34/304 (11%)

Query: 28  TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIIL 87
           T  + EPL RG+ +T+G  +RR L+SS+   A  A++I  V HE ++I+G+ ED   ++ 
Sbjct: 22  TTFVIEPLMRGYGNTIGTVIRRTLLSSITSVAPFAIKISHVEHEFTAIEGLREDAITLVA 81

Query: 88  NIKGINLK-----MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           NI+ I           D+  +++      G V A DI+T+  ++++N D  I  +  +  
Sbjct: 82  NIRKIRFAYDPELFEKDNLAKISFKSTKEGEVHASDIETIPGLDIVNKDQYIATISKNGS 141

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIG-----------LITIDALYSPIKKVSYTVESAR 191
           +  EL +  G GYV  + ++      G            + +D+ +SPIKKV+   E   
Sbjct: 142 LEFELYLRTGRGYVSFEDNKKTILEYGPKLESKIKNGQFLAMDSDFSPIKKVAILFEELN 201

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ---------DQLGMFINFEEPKKEVK 242
               +  ++L + ++TDG++  ++ +  A++I+          D LG    F++ K++ +
Sbjct: 202 STSNIIEERLKIKVETDGTVEAKNVMEEAAKIIVAHFQIIGNIDALGTIDLFDDQKEKHE 261

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           +          P +   +++L L++RS N LR      + ++++ ++ ++  + N G+KS
Sbjct: 262 K---------TPKVSVSIDKLNLTIRSLNALRRAGFNNVDEIMKLSDEELSNIKNLGKKS 312

Query: 303 LVEI 306
           + +I
Sbjct: 313 VQDI 316


>gi|228016646|gb|ACP51475.1| RNA polymerase alpha subunit [Pinus albicaulis]
          Length = 335

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 81/293 (27%), Positives = 149/293 (50%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H + N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIQ-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALLKK----------- 259
            +++  ASR L D    F++ EE   +    K+  N+   P +  L              
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNKKKGSNMLPFPLSHVLTDTGETKEKIAFKH 271

Query: 260 --VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  ++ N LR  NI  + DL+  +  D++++ +  ++S+ ++  VL
Sbjct: 272 IFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMKIEHLEKESVEQVLEVL 324


>gi|228016268|gb|ACP51103.1| RNA polymerase alpha subunit [Pinus strobus]
 gi|228016903|gb|ACP51728.1| RNA polymerase alpha subunit [Pinus ayacahuite]
 gi|228017272|gb|ACP52091.1| RNA polymerase alpha subunit [Pinus flexilis]
 gi|228017337|gb|ACP52155.1| RNA polymerase alpha subunit [Pinus lambertiana]
          Length = 335

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 81/293 (27%), Positives = 149/293 (50%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H + N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIQ-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALLKK----------- 259
            +++  ASR L D    F++ EE   +    K+  N+   P +  L              
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTDTGETKEKIAFQH 271

Query: 260 --VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  ++ N LR  NI  + DL+  +  D++++ +  ++S+ ++  VL
Sbjct: 272 IFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMKIEHLEKESVEQVLEVL 324


>gi|119662799|emb|CAJ33191.1| RNA polymerase alpha subunit [Lactobacillus jensenii]
          Length = 117

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 55/117 (47%), Positives = 79/117 (67%)

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE S++ GV ED+T I+LN+K + LK   D  K V +   GP  VTAGD++  +++ 
Sbjct: 1   GVLHEFSTVPGVREDVTKIVLNLKKLELKSIADEEKIVELDVEGPATVTAGDLKVDSEVT 60

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           VLNPD  IC +     + M++ V  G GYVPA  ++T++ PIG+I +D+L+SPIKKV
Sbjct: 61  VLNPDQYICTVAEGGHLHMQIAVKNGRGYVPASENKTDDMPIGVIPVDSLFSPIKKV 117


>gi|228017657|gb|ACP52470.1| RNA polymerase alpha subunit [Pinus peuce]
          Length = 335

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 81/293 (27%), Positives = 149/293 (50%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H + N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIQ-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALLKK----------- 259
            +++  ASR L D    F++ EE   +    K+  N+   P +  L              
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTDTGETKEKIAFQH 271

Query: 260 --VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  ++ N LR  NI  + DL+  +  D++++ +  ++S+ ++  VL
Sbjct: 272 IFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMKIEHLEKESVEQVLEVL 324


>gi|114804296|ref|YP_762293.1| RNA polymerase alpha subunit [Morus indica]
 gi|122166773|sp|Q09WY5|RPOA_MORIN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|78100348|gb|ABB20989.1| RNA polymerase alpha subunit [Morus indica]
          Length = 323

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 84/293 (28%), Positives = 154/293 (52%), Gaps = 23/293 (7%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+K I 
Sbjct: 36  PLMRGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTIVGIQESVHEILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+ +    +  +I  +GPG VTA DI     +E+++    I NL     + +EL + +  
Sbjct: 96  LRSNLYGTRDASICVKGPGYVTAQDIILPPSVEIVDNTQHIANLTEPITLCIELQIERNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY     +  +N   G   IDA++ P++  ++++ S   G   + + L + I T+GS+T 
Sbjct: 156 GYRIKTPNNFQN---GSYPIDAVFMPVRNANHSIHSYVNGNE-NQEILFLEIWTNGSLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-FN-------PALLKK------ 259
           ++++  ASR L D   +FI F   ++ ++ + +  +LP FN       P   KK      
Sbjct: 212 KEALHEASRNLID---LFIPFFHAEEHLENNQHKGTLPLFNFHGRLAKPRKTKKEIALKY 268

Query: 260 --VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++ EL  R  NCL+  NI    +L+  ++ +++++ +F  + +  I  VL
Sbjct: 269 IYIDQSELPPRVYNCLKRSNINTFLELLNNSQEELMKIQDFRIEDVKHILDVL 321


>gi|91214173|ref|YP_538797.1| RNA polymerase alpha subunit [Glycine max]
 gi|90110869|sp|Q2PMQ3|RPOA_SOYBN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|83595774|gb|ABC25155.1| RNA polymerase alpha subunit [Glycine max]
          Length = 333

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 85/287 (29%), Positives = 152/287 (52%), Gaps = 22/287 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RRVL+  + G  IT V+ + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRVLLGEIEGTCITRVKSEKIPHEYSTIIGIEESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GPG VTA DI     +E+++    I N+     + +EL +
Sbjct: 92  KEIVLRSNLYGTRDASICFKGPGYVTAQDIILPPSVEIVDNTQHIANVTEPVNLCIELKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA + P++ V++++ S   G     + L + I T+G
Sbjct: 152 ERNRGY---RIKTLKNFQDGSYPIDATFMPVRNVNHSIHSYVNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL---------- 256
           S+T ++++  ASR L D    F++ EE    ++ + +  +LP   F+  L          
Sbjct: 208 SLTPKEALYEASRNLIDLFIPFLHAEEDNFNLENNQHKVTLPLFTFHDILAKEKLRKKKK 267

Query: 257 ---LKK--VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              LK   +++LEL  R  NCL+  NI  + +L+  ++ D+L++ +F
Sbjct: 268 EIALKSIFIDQLELPPRIYNCLKRSNIHTLLELLNNSQEDLLKIEHF 314


>gi|29565639|ref|NP_817218.1| RNA polymerase alpha subunit [Pinus koraiensis]
 gi|324986384|ref|YP_004276256.1| RNA polymerase alpha subunit [Pinus lambertiana]
 gi|41688693|sp|Q85X01|RPOA_PINKO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|29469738|gb|AAO74066.1| RNA polymerase alpha subunit [Pinus koraiensis]
 gi|228016141|gb|ACP50978.1| RNA polymerase alpha subunit [Pinus sibirica]
 gi|228016779|gb|ACP51606.1| RNA polymerase alpha subunit [Pinus armandii]
 gi|228017149|gb|ACP51970.1| RNA polymerase alpha subunit [Pinus cembra]
 gi|228017593|gb|ACP52407.1| RNA polymerase alpha subunit [Pinus parviflora var. pentaphylla]
 gi|323514233|gb|ADX89780.1| RNA polymerase alpha subunit [Pinus lambertiana]
          Length = 335

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 81/293 (27%), Positives = 149/293 (50%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I 
Sbjct: 36  PLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     +++++    I  L       + L + K  
Sbjct: 96  LRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY+    H + N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T 
Sbjct: 156 GYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIQ-EVLFLEIWTNGGLTP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALLKK----------- 259
            +++  ASR L D    F++ EE   +    K+  N+   P +  L              
Sbjct: 212 REALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTDTGETKEKIAFKH 271

Query: 260 --VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +++LEL  ++ N LR  NI  + DL+  +  D++++ +  ++S+ ++  VL
Sbjct: 272 IFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMKIEHLEKESVEQVLEVL 324


>gi|300431286|gb|ADK12608.1| RNA polymerase alpha subunit [Nassella novarae]
          Length = 339

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 85/285 (29%), Positives = 145/285 (50%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I+ +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVDTAQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------------- 253
           S+T ++++  ASR L D    F++ EE     +E+ N  + P                  
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLHAEEEGXXFEENKNRFTPPLFTFQKKLTNLKKNKKGI 267

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P     +++LEL  R+ NCL+  NI  + DL+ +TE D++ + +F
Sbjct: 268 PLNCIFIDQLELPSRTYNCLKRANIHTILDLLSKTEEDLMXIDSF 312


>gi|21039418|gb|AAM33638.1| RpoA [Pseudomonas putida]
          Length = 127

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 61/131 (46%), Positives = 87/131 (66%), Gaps = 9/131 (6%)

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE---EPKKEVKEDINVKSL 250
           Q  D DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   EP    +ED      
Sbjct: 3   QRTDLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDSEPVVVEQED------ 56

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G+KSL EIK VL
Sbjct: 57  EIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNLGKKSLTEIKDVL 116

Query: 311 GTMGLFLGMNL 321
            + GL LGM L
Sbjct: 117 ASRGLSLGMRL 127


>gi|303308474|gb|ADM14340.1| RNA polymerase alpha subunit [Punica granatum]
          Length = 337

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 86/304 (28%), Positives = 158/304 (51%), Gaps = 22/304 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFEKIPHEYSTIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  +GPG VTA DI     +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTCNASICVKGPGCVTAQDIILPPSVEIIDNTQHIASLMEPINLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
            +  GY    H +T N+   G   IDA++ P++  ++++ S   G     + L + I T+
Sbjct: 152 ERNRGY----HIKTPNNFQDGSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWTN 206

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLK------- 258
           GS+T ++++  ASR L D L  F++ EE    ++ +    +LP   F+  L K       
Sbjct: 207 GSLTPKEALHEASRNLIDLLIPFLHAEEENLHLENNQYKVTLPLFTFHDRLTKLRKTKKG 266

Query: 259 ------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                  +++LEL  R  N L+  NI  + DL+ +++ D++++ +F R+ + +I  +L  
Sbjct: 267 IALKYIFIDQLELPPRIYNFLKKSNIHTLLDLLNKSQEDLMKIKHFRREDVKQILDILEI 326

Query: 313 MGLF 316
             +F
Sbjct: 327 EKVF 330


>gi|313183854|ref|YP_004021697.1| RNA polymerase alpha subunit [Prunus persica]
 gi|309321466|gb|ADO65007.1| RNA polymerase alpha subunit [Prunus persica]
          Length = 326

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 83/297 (27%), Positives = 154/297 (51%), Gaps = 20/297 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILAPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTIIGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GPG VTA DI     +E+++    I NL     + +EL +
Sbjct: 92  KEIVLRSNLYGTRNASICIKGPGYVTAQDIILPPSVEIVDNTQHIANLTEPINLCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +     N   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGY---RIKTPNNFQDGSYPIDAVFMPVRNANHSIHSYVNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLKK------- 259
           S+T ++++  ASR L D    F++ EE   +++ + +  +LP   F+  L K+       
Sbjct: 208 SLTPKEALHDASRNLIDLFIPFLHAEEENLQLENNQHKVTLPLFTFHGRLAKQRKNKKEI 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++ EL  R  NCL+  NI  + DL+  ++ D++++ +F  + +  I  +L
Sbjct: 268 ALQYIFIDQSELFPRVYNCLKRSNIHTLLDLLNNSQEDLMKIKHFRIEDVKHILNIL 324


>gi|325126897|ref|YP_004286134.1| RNA polymerase alpha subunit [Fragaria vesca subsp. vesca]
 gi|324022809|gb|ADY15383.1| RNA polymerase alpha subunit [Fragaria vesca subsp. vesca]
          Length = 331

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 83/297 (27%), Positives = 150/297 (50%), Gaps = 20/297 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+  G+ E + +I++N+
Sbjct: 32  FILAPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTFVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GPG VTA DI     IE+++    I NL     + +EL +
Sbjct: 92  KEIVLRSNLYGTRNASICVKGPGYVTAQDIILPPSIEIVDNTQHIANLTEPINLCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +     N   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGY---RIKTPNNFQEGSYPIDAVFMPVRNANHSIHSYVNGNE-KQEILFIEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF--------NPALLKK-- 259
           S+T ++++  ASR L D    F++ EE     + + +  +LP         NP  +KK  
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHAEEENLHFENNQHKVTLPLFTFHGKLANPKKIKKEN 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++ EL  R  NCL+  NI  + DL+  ++ D++++ +   + +  I  +L
Sbjct: 268 TLKYIFIDQSELPPRVYNCLKRSNIHTLLDLLNNSQEDLMKIKHLRIEDVKHILNIL 324


>gi|293363953|ref|ZP_06610689.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma alligatoris
           A21JP2]
 gi|292552443|gb|EFF41217.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma alligatoris
           A21JP2]
          Length = 334

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 84/295 (28%), Positives = 151/295 (51%), Gaps = 19/295 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I +PL RGF  TLG ALRRVL+S++   A   V+I+GV HE   I+GV ED+  +I+N+
Sbjct: 25  FIIQPLERGFGTTLGVALRRVLLSNITSLAPFCVRIEGVTHEFRGIEGVVEDVPSLIMNL 84

Query: 90  KGINLK-----MSGDSHKRVTIFKRGPGVVTAGDIQTVN--DIEVLNPDHVICNLDVDAV 142
           + +        +  D   RV +     G + +  ++ V+  ++EV++ +  I  +  +  
Sbjct: 85  RKVRFSYDPELVKDDDIIRVELKADQVGEINSRYLEVVDNLNVEVIDHNVHIAEVSQENA 144

Query: 143 VRMELTVSKGHGYVPAKHHR-----------TENDPIGLITIDALYSPIKKVSYTVESAR 191
           +R+EL +  G G+V ++ ++           T+      I +D+ +SP++KV+Y V    
Sbjct: 145 LRLELYLRPGRGFVSSEENKALVSKLEAQLETKIKKGKFIAVDSNFSPVEKVNYVVSELN 204

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
              +   +KL   + TDG++  +D++  A+ IL        N +E + ++ E  + K + 
Sbjct: 205 SSSIKIEEKLEFNVYTDGTVKPKDAIKQAADILIAHFKEIGNVDEIRNDIFETADDK-IT 263

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            N      + +L LSVRS N LR      + D+ + +  ++ +  N G+KSL EI
Sbjct: 264 DNQETDIDITQLGLSVRSLNALRRIGRTKVSDISKMSYEELEQTKNLGKKSLDEI 318


>gi|154483160|ref|ZP_02025608.1| hypothetical protein EUBVEN_00861 [Eubacterium ventriosum ATCC
           27560]
 gi|149735968|gb|EDM51854.1| hypothetical protein EUBVEN_00861 [Eubacterium ventriosum ATCC
           27560]
          Length = 161

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 59/153 (38%), Positives = 102/153 (66%), Gaps = 8/153 (5%)

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           G+I +D++Y+P+++V+ +V++ R GQV D+DKL++ + T+G++  +++V+LAS++L + L
Sbjct: 7   GVIAVDSIYTPVERVNMSVQNTRVGQVTDFDKLTLDVYTNGTLDTDEAVSLASKVLCEHL 66

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLK----KVEELELSVRSTNCLRGENIVYMGDL 284
            +FI+  E  K    DI V + P +  + K     ++ELELSVRS NCL+   I  + +L
Sbjct: 67  KLFIDLSETSK----DIEVIAEPVDDEIDKVLEMNIDELELSVRSYNCLKRAGINTVEEL 122

Query: 285 IQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + +T  DM+++ N GRKSL E+   L  +GL L
Sbjct: 123 VNKTSEDMMKVRNLGRKSLEEVLAKLKELGLGL 155


>gi|289066858|ref|YP_003434376.1| RNA polymerase alpha subunit [Vigna radiata]
 gi|259020045|gb|ACV90243.1| RNA polymerase alpha subunit [Vigna radiata]
          Length = 333

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 81/287 (28%), Positives = 150/287 (52%), Gaps = 22/287 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR+L+  + G  IT V+ + + HE S+I G+ E + +I +N+
Sbjct: 32  FILSPLMKGQADTIGIAIRRILLGEIEGTCITRVKSEKIPHEYSTIIGIEESVHEIFMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK +    +  +I  +GPG +TA DI     +E+++    I N+       +EL +
Sbjct: 92  KEIVLKSNMYGTQDASISFKGPGYITAQDIILPPSVEIVDNRQHIANVTEPVNFCIELKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY        +++      IDA + P++ V+Y++ S   G     + L + I T+G
Sbjct: 152 ERNRGYRIKTLKNFQDESYD---IDARFMPVRNVNYSIHSYVNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLKK------- 259
           S+T ++++  AS+ L D    F++ EE    ++++ +  +LP   F+  L+K        
Sbjct: 208 SLTPKEALYEASQNLIDLFIPFLHAEEENFNLEKNKDKVTLPLFTFHDILVKDKLRKNKK 267

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                   +++LEL  R  NCL+  NI  + +L+  ++ D+L++ +F
Sbjct: 268 EIALKSIFIDQLELPPRIYNCLKRSNIHTLLELLNNSQEDLLKIEHF 314


>gi|99024202|dbj|BAE94567.1| plastid DNA-dependent RNA polymerase subunit alpha [Takakia
           lepidozioides]
          Length = 341

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 87/313 (27%), Positives = 147/313 (46%), Gaps = 38/313 (12%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P   G A T+G A+RR L+  + G  IT  +   V HE S+I G+ E + D+++N+  I 
Sbjct: 36  PFRSGQASTVGIAMRRALLGEVEGTCITCAEFKRVTHEYSTILGIQESVHDVLINLGEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      ++  I   GP  VTA DI     +++++    I  +     + +EL + K  
Sbjct: 96  LRSDSYETQKAFISILGPKKVTAQDIILPPSVKIIDTTQYIATVXKAIHLDIELKIEKDF 155

Query: 154 GYVPAKHHRTENDPI----GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           GY      R E DPI    G   +DA++ PI+ V+Y+V S   G     + L + I T+G
Sbjct: 156 GY------RIE-DPIKSADGNFPVDAVFMPIRNVNYSVHSFENGNETQ-EILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFIN--------------------FEEPKKEVKEDINVKS 249
           S+T ++++  ASR L +    F++                    F  P      D   K 
Sbjct: 208 SVTPKEALYEASRSLINLFIPFLHAEKKEFIYGLKNTYESNMSYFSSPSLSADIDEMTKG 267

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           + F       +++LEL  R+ NC +  N   + DL+  ++ D++++ NFG+KS   ++ V
Sbjct: 268 VTFKHIF---IDQLELPARAYNCXKRVNXHTISDLLNYSQDDLMKIKNFGKKS---VEQV 321

Query: 310 LGTMGLFLGMNLP 322
           L  +     +N P
Sbjct: 322 LEALQKRFSINXP 334


>gi|169794105|ref|YP_001718469.1| RNA polymerase alpha subunit [Manihot esculenta]
 gi|157695917|gb|ABV66186.1| RNA polymerase alpha subunit [Manihot esculenta]
          Length = 343

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 82/301 (27%), Positives = 161/301 (53%), Gaps = 24/301 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEFSTIAGIQESIHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +       +I  +GPG VTA DI     +E+++    I +L   +D  + +++
Sbjct: 92  KEIVLRSNLYGTCDASICVKGPGYVTAQDIILPPFVEIIDNTQHIASLTKAIDLCIGLQI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+   P  + + ++   G  +IDA++ P++  +++V S   G     + L + I T
Sbjct: 152 ERNRGYRIKPTNNFQVQD---GSYSIDAVFMPVRNANHSVHSYGNGNE-KQEILFLEIWT 207

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPK--KEVKEDINVKSLP---FNPALLK---- 258
           +GS+T ++++  ASR L D    F++ EE     E++++ +  +LP   F+  L K    
Sbjct: 208 NGSLTPKEALHEASRNLIDFFIPFLHAEEENLHLEIEKNQHKVTLPLFCFHDKLTKLRKN 267

Query: 259 ---------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                     +++ EL+ +  NCL+  NI  + DL+ +++ D++++ +F    +  I G+
Sbjct: 268 KKEIVLKYIFIDQSELTPKIYNCLKRSNIHTLSDLLNKSQEDLMKIEHFRIDDVKHILGI 327

Query: 310 L 310
           L
Sbjct: 328 L 328


>gi|150187003|emb|CAK30148.1| RNA polymerase alpha subunit [Streptococcus parauberis]
          Length = 161

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 54/141 (38%), Positives = 93/141 (65%)

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV+K  GY+PA
Sbjct: 4   EDEKMIELDVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLKATMTVAKKRGYIPA 63

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           + ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ 
Sbjct: 64  EGNKQDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALG 123

Query: 219 LASRILQDQLGMFINFEEPKK 239
           L++R+L + L +F +  E  K
Sbjct: 124 LSARVLIEHLNLFTDLTEVAK 144


>gi|156598719|gb|ABU85614.1| RNA polymerase alpha subunit [Scaevola aemula]
          Length = 332

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 87/311 (27%), Positives = 165/311 (53%), Gaps = 26/311 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L++ + G AIT  + + V HE S+I+G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIALRRALLAEIEGTAITRAKFEKVPHEYSTIRGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +       +I  +GPG VTA DI +   +E+++    I +L   ++ ++R+++
Sbjct: 92  KEIVLRSNLYGTCEASICVKGPGYVTAQDIISPPYVEIVDNTQHIASLTEPIELIIRLQI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++   ++  K   T  D  G   I A+  P++ ++Y++ S+  G+    + L + I T
Sbjct: 152 EKNR---FIQLKERNTFQD--GSYAIGAVLMPVRHMNYSIHSSGNGK---QEILFLEIWT 203

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED-INVKSLPFNPALLKKVEELELS 266
           +GS+T ++++  A R L D    F++ EE   E  +D I   S  F   L K  +  +++
Sbjct: 204 NGSLTPKEALHEACRNLIDLFIPFLHKEEGNLENNQDRIPFPSFTFYDKLSKLKKNKKMA 263

Query: 267 VRST------------NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           ++S             NCL+  NI  + DL+  ++ D+++ A+     + ++K +LG + 
Sbjct: 264 LKSIFIDQSELPPSIYNCLKRSNIYTLFDLLNNSQEDLMKKAHL---HIEDVKRILGLLE 320

Query: 315 LFLGMNLPDWP 325
               ++LP  P
Sbjct: 321 KNCVIDLPKNP 331


>gi|149390299|ref|YP_001294130.1| RNA polymerase alpha subunit [Chloranthus spicatus]
 gi|172048690|sp|A6MMF4|RPOA_CHLSC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|146744219|gb|ABQ43291.1| RNA polymerase alpha subunit [Chloranthus spicatus]
          Length = 334

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 84/299 (28%), Positives = 155/299 (51%), Gaps = 22/299 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +  PL +G A T+G A+RR L+  + G  IT  ++D V HE S+I G+ E + +I +N+
Sbjct: 32  FMLSPLMKGQADTIGIAMRRALLGEIEGTCITRAKLDKVPHEYSTIVGIEESIHEIFMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  RGP  VTA DI +   +E+++    I +L     + +EL +
Sbjct: 92  KEIVLRSNLYGTRNASICVRGPRYVTAQDIISPPSVEIVDTTQHIASLTEPIDLCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     ++ +N   G   IDA+  P++  ++++ S   G     + L + I T+G
Sbjct: 152 QRDRGYRMKTPNKYQN---GSYPIDAVSMPVRNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF--------NPALLKK-- 259
           S+T ++++  ASR L D    F++ EE    ++++ N  ++PF        N  + KK  
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHAEEEGIRLEDNPNRFNIPFFTFHDGLANTNIRKKKK 267

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                   +++ EL  R+ N L+  NI  + DL+  ++ D L++ +F  + + +I  +L
Sbjct: 268 GIALKCIFIDQSELPPRTYNYLKRSNINTLLDLLSNSQEDFLKIEHFRIEDVKQILDIL 326


>gi|12467|emb|CAA30670.1| RNA polymerase alpha-subunit (AA 1-341) [Zea mays]
          Length = 341

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 93/311 (29%), Positives = 156/311 (50%), Gaps = 25/311 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGNVPHEYSTIVGIEESIQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+ +    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIDDTTQPIANLREPVDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +   Y       +++   G   IDA++ P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRAYHTELRKNSQD---GSYPIDAVFMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SIT-GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK---- 259
            +T  E  +  ASR L D    F++ EE     +E+ N  + P   F      LKK    
Sbjct: 208 KLTPKEGGIYEASRNLIDLFLPFLHTEEEGTSFEENKNRLTPPLLTFQKRFTNLKKNKKG 267

Query: 260 -------VEELELSVRSTNCLRGENI-VYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                  +++LEL  R+ NCL+  NI   + DL+ +TE D++++ +FG   + + K +  
Sbjct: 268 IPLNCIFIDQLELPSRTYNCLKRANIPSALLDLLVKTEEDLIKINSFG---MEDGKLIWD 324

Query: 312 TMGLFLGMNLP 322
           T+   L ++LP
Sbjct: 325 TLEKHLPIDLP 335


>gi|149390473|ref|YP_001294302.1| RNA polymerase alpha subunit [Illicium oligandrum]
 gi|172048708|sp|A6MMX6|RPOA_ILLOL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|147917426|gb|ABQ52550.1| RNA polymerase alpha subunit [Illicium oligandrum]
          Length = 331

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 85/297 (28%), Positives = 153/297 (51%), Gaps = 20/297 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +  PL +G A T+G A+RR L+  + G  IT  + + V HE S+I G+ E + +I++N+
Sbjct: 32  FVLSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKVPHEYSTIVGIEESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I  +      +  +I  RGP  VTA DI +   +++++    I +L     + +EL +
Sbjct: 92  KEIVFRSHLYGTRGASICVRGPRYVTAQDIISPPSVKIVDTTQYIASLTEPIDLCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +     N   G   IDA+  P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERDRGY---RIKTPNNYQDGSYPIDAVSMPVRNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL---------- 256
           S T ++++  ASR L D    F++ EE    V+++ N  + P   F+  L          
Sbjct: 208 SFTPKEALYEASRNLIDLFLPFLHAEEQDINVEDNQNRATAPLFTFHDGLTNIGKRKKGI 267

Query: 257 -LKKV--EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
            LK+V  ++ EL  R+ NCL+  NI  + DL+  ++ D++R+ +F  + + +I G+L
Sbjct: 268 ALKRVFIDQSELPTRTYNCLKRSNIHTLLDLLSNSQEDLMRIEHFRIEDVKQILGIL 324


>gi|108796837|ref|YP_636429.1| alpha subunit of RNA polymerase [Staurastrum punctulatum]
 gi|122245550|sp|Q32RU7|RPOA_STAPU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|61393605|gb|AAX45746.1| alpha subunit of RNA polymerase [Staurastrum punctulatum]
          Length = 383

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 101/357 (28%), Positives = 173/357 (48%), Gaps = 73/357 (20%)

Query: 22  QEEENRTLMIAE----PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           Q + NR L  +     PL    A T+G A+RR L+S + G +I +  I G +HE S++ G
Sbjct: 20  QPDHNRRLHYSRFALSPLLVDQAMTIGVAIRRALLSEVEGISIISANIVGAVHEYSTLDG 79

Query: 78  VHEDLTDIILNIKGINLK-MSGDS-----HK--RVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           V E + +I+LN+K I +K   G S     HK  R +IF +GPGVVTA  I+  + I  ++
Sbjct: 80  VRESVDEILLNLKQIVIKGAKGASITPLDHKEYRASIFAQGPGVVTAEHIKFPSSILAVD 139

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L  +  + +EL + +G   +  +  RT+ +  G   IDA ++P++K ++++ S
Sbjct: 140 PDQSIATLLNETQLCIELFIRQG---IAKQLTRTKKNHQGFF-IDANFTPVQKANFSIHS 195

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD----------------------- 226
             + + L    L + I T+ ++T  +++  A   L +                       
Sbjct: 196 VGDPKGLQ-QLLLLEIWTNKTLTPAEALYQAHASLLNLFHQISPPLLHKELSPSKNILNQ 254

Query: 227 ----------QLGMFINFEEPK-----------KEVKEDINVKSLP---------FNPAL 256
                       G  ++ E  +           KE++  + +KS            N ++
Sbjct: 255 NSDSNSLGGSSFGRVVSLETRRDSTQTNNSSIPKEIQPSVRLKSYTDTNLSIDKQMNDSV 314

Query: 257 LKK---VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
            K+   ++ELELS R +NCL+  NI  + DL+  T+ D+L++ NFGRKS+ ++  VL
Sbjct: 315 NKENLSIDELELSPRISNCLKKANINTIADLLNYTQEDLLKIKNFGRKSVEQVSLVL 371


>gi|172072879|ref|YP_001806640.1| RNA polymerase alpha subunit [Cryptomeria japonica]
 gi|171854898|dbj|BAG16638.1| RNA polymerase alpha subunit [Cryptomeria japonica]
 gi|239794267|dbj|BAH73264.1| RNA polymerase alpha subunit [Cryptomeria japonica]
 gi|239794349|dbj|BAH73345.1| RNA polymerase alpha subunit [Cryptomeria japonica]
          Length = 342

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 83/298 (27%), Positives = 150/298 (50%), Gaps = 32/298 (10%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A+T+G+A+RRVL+  + G  IT  +   + +E S I G+ E + +I++N+K I 
Sbjct: 36  PLRKGQANTIGSAIRRVLLGEVEGTCITRAKFHNISNEYSVIIGIEESIHEILMNLKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I   GP  VTA DI     + +++    I N++    + + L + KG 
Sbjct: 96  LRSDAYGIREGSIHVVGPKKVTAQDIMLPPSVRIIDTTQHIANINKSITLDISLQIEKGR 155

Query: 154 GYV---PAKHHRTEN----DPIGLITIDALYSPIKKVSYTVE---SAREGQVLDYDKLSM 203
           GY+   P  ++  +     D   +  IDA ++P++ V+Y++    S  E Q +    L +
Sbjct: 156 GYIIQNPNNYNPKDEIFAIDAAFVFPIDAAFAPVQNVNYSIHSYWSENETQEI----LFL 211

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL------- 256
            I T+G +  ++++  ASR L D    F+ F   K+E  +  N  S    P+L       
Sbjct: 212 EIWTNGGLAPKEALYEASRNLID---FFLPFLNAKEENSDGTNSLSDDITPSLPILHIST 268

Query: 257 -LKK-------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
             K+       +++L  S R  NCL+  NI  + DL+  +  D++++ + G +S+ EI
Sbjct: 269 DTKRIAFDQMYIDQLNFSTRVYNCLKKANINTVSDLLNYSREDLMKIKHLGEQSVKEI 326


>gi|303308472|gb|ADM14339.1| RNA polymerase alpha subunit [Punica granatum]
          Length = 337

 Score =  113 bits (283), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 86/304 (28%), Positives = 157/304 (51%), Gaps = 22/304 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFEKIPHEYSTIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+         +I  +GPG VTA DI     +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSYLYGTCNASICVKGPGCVTAQDIILPPSVEIIDNTQHIASLMEPINLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
            +  GY    H +T N+   G   IDA++ P++  ++++ S   G     + L + I T+
Sbjct: 152 ERNRGY----HIKTPNNFQDGSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWTN 206

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLK------- 258
           GS+T ++++  ASR L D L  F++ EE    ++ +    +LP   F+  L K       
Sbjct: 207 GSLTPKEALHEASRNLIDLLIPFLHAEEENLHLENNQYKVTLPLFTFHDRLTKLRKTKKE 266

Query: 259 ------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                  +++LEL  R  N L+  NI  + DL+ +++ D++++ +F R+ + +I  +L  
Sbjct: 267 IALKYIFIDQLELPPRIYNFLKKSNIHTLLDLLNKSQEDLMKIKHFRREDVEQILDILEI 326

Query: 313 MGLF 316
             +F
Sbjct: 327 EKVF 330


>gi|119662291|emb|CAJ33132.1| RNA polymerase alpha subunit [Lactobacillus collinoides]
          Length = 135

 Score =  113 bits (283), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 62/134 (46%), Positives = 88/134 (65%), Gaps = 3/134 (2%)

Query: 80  EDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           ED+T IILN K I+LK+ G  D  + + I  +GP  VTAGDI   +D+ VLNPD  I  +
Sbjct: 2   EDVTQIILNTKKISLKLEGPDDEIESMEIDVKGPAQVTAGDITADSDVTVLNPDLYIATV 61

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVL 196
              A   M +T +KG GYV A  ++ + D PIG++ ID++Y+PI++V+Y VE+ R GQ  
Sbjct: 62  AEGATFHMRMTANKGRGYVSADRNKAKEDMPIGVLPIDSIYTPIERVNYQVENTRVGQRD 121

Query: 197 DYDKLSMTIDTDGS 210
           DYDKL++ + TD S
Sbjct: 122 DYDKLTLDVWTDSS 135


>gi|306486177|gb|ADM92734.1| RNA polymerase alpha subunit protein [Davidia involucrata]
          Length = 328

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 82/297 (27%), Positives = 152/297 (51%), Gaps = 20/297 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G  E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFERIPHEYSTIVGTQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  +GPG VTA DI +   +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTCDASICVKGPGYVTAQDIISPPYVEIVDSTQYIASLTEPIDLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +     N   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGY---RIKMPNNFQDGSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLK-------- 258
           S+T ++++  ASR L D    F++ EE    ++++ +  +LP   F+  L K        
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHTEEENLHLEDNQHKVTLPLFTFHEKLAKLRKNKKKI 267

Query: 259 -----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++ EL  R  NCL+  NI  + D +  ++ D++++ +F  + + EI G+L
Sbjct: 268 ALKYIFIDQSELPTRIYNCLKRSNIYTLLDFLNNSQEDLMKIEHFRIEDVKEILGIL 324


>gi|295136921|ref|YP_003587754.1| RNA polymerase alpha subunit [Lathyrus sativus]
 gi|293338643|gb|ADE43615.1| RNA polymerase alpha subunit [Lathyrus sativus]
          Length = 335

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 86/316 (27%), Positives = 155/316 (49%), Gaps = 40/316 (12%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR+L+  + G  IT  + + + HE S++ G+ E + +I++N+
Sbjct: 32  FILSPLLKGQADTIGIAMRRILLGEIDGTCITRAKSEKIPHEYSTVVGIQESIHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GPG VTA DI     +EV++    I NL     + +EL +
Sbjct: 92  KEIVLRSNLYGTREASISFKGPGYVTAQDIILPPSVEVIDKTQHIANLTEPINLCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +     N   G  TIDA++ P++  +Y++ S   G     D L + I T+G
Sbjct: 152 ERKRGY---RIKTLNNIQDGSYTIDAVFMPVRNANYSIHSYVNGNE-KQDILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFIN---------------------FEEPKKEVKE----- 243
           S T ++++  ASR L D    F++                     F +  + VK+     
Sbjct: 208 SFTPKEALYEASRNLIDLFIPFLHAEEENFNLENNQHKMTWPLFTFHDHDRFVKDKLTNT 267

Query: 244 --DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
             +I +KS+         +++LEL  R  NCL+  NI  + + + +++ D++++ +F  +
Sbjct: 268 QKEITLKSI--------FIDQLELPPRIYNCLKKSNIHTVFEFLNKSQEDLMKIEHFRVE 319

Query: 302 SLVEIKGVLGTMGLFL 317
            L  I  +L     F+
Sbjct: 320 DLKNILNILKIENHFV 335


>gi|29427831|sp|Q8MC99|RPOA_PHAAN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|22725692|gb|AAN04898.1| RNA polymerase alpha subunit [Vigna angularis]
          Length = 333

 Score =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 82/287 (28%), Positives = 150/287 (52%), Gaps = 22/287 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR+L+  + G  IT V+ + + HE S+I G+ E + +I +N+
Sbjct: 32  FILSPLMKGQADTIGIAIRRILLGEIEGTCITRVKSEKIPHEYSTIIGIEESVHEIFMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK +    +  +I  +GPG +TA DI     +E+++    I N+     + +EL +
Sbjct: 92  KEIVLKSNMYGTQDASISFKGPGYITAQDIILPPSVEIVDNRQHIANVTEPVNLCIELKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA + P++ V+Y++ S   G     + L + I T+G
Sbjct: 152 ERNRGY---RIKTLKNFQDGSYDIDARFMPVRNVNYSIHSYVNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLKK------- 259
           S+T ++++  AS+ L D    F++ EE    +++  +  +LP   F+  L+K        
Sbjct: 208 SLTPKEALYEASQNLIDLFIPFLHAEEENFNLEKKKHKVTLPLFTFHDILVKDKLRKNKK 267

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                   +++LEL  R  NCL+  NI  + +L+  ++  +L++ +F
Sbjct: 268 EIALKSIFIDQLELPPRIYNCLKRSNIHTLLELLNNSQEXLLKIEHF 314


>gi|308190154|ref|YP_003923085.1| DNA-directed RNA polymerase alpha chain [Mycoplasma fermentans JER]
 gi|319777458|ref|YP_004137109.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma fermentans
           M64]
 gi|307624896|gb|ADN69201.1| DNA-directed RNA polymerase alpha chain [Mycoplasma fermentans JER]
 gi|318038533|gb|ADV34732.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma fermentans
           M64]
          Length = 337

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 94/339 (27%), Positives = 163/339 (48%), Gaps = 30/339 (8%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M +  +Q++ K NN           N T    +PL RG   TLG ALRR+L+S++   A+
Sbjct: 4   MTKLEYQKVTKLNN--------STSNVTAFTLQPLERGMGQTLGVALRRILLSNITSLAL 55

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-----RVTIFKRGPGVVT 115
            A++I+ V HE   + G  ED+  II+N++ +  + + +  K     +VT+    PG VT
Sbjct: 56  FAIKIEDVNHEFQVVDGCVEDVATIIMNLRKVKFQYNPEFVKDDEIIKVTLKADQPGEVT 115

Query: 116 AGDIQTVN-DIEVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHRT--ENDPIG- 169
           +  ++  N  IE+LN    I +L  +    + +EL +  G G++  + ++    N  I  
Sbjct: 116 SRLLEVNNSSIEILNKSLEIAHLSANGKHKLNIELYLRPGRGFISNEENKKLLNNSSITT 175

Query: 170 ----------LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
                      I  D+ +SPI+KV+YTVE          ++L+ +  TDG++  + ++  
Sbjct: 176 RMESKIKNGIFIATDSNFSPIEKVNYTVEELNSSSNKIEERLTFSFQTDGTVDPKSALQQ 235

Query: 220 ASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIV 279
           A  IL     +  N +E K  V  + + ++   N   +  +  L LSVRS N L+     
Sbjct: 236 ACEILVGHFKLIGNVDEMKVNVFAEESEQTQETNDNDV-DINSLNLSVRSLNALKRIGKT 294

Query: 280 YMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +  + + +  ++ ++ N GRKSL EI+  L   G  L 
Sbjct: 295 KISQVAEMSLEELEQVKNLGRKSLDEIQQRLKEYGYELS 333


>gi|238810271|dbj|BAH70061.1| hypothetical protein [Mycoplasma fermentans PG18]
          Length = 339

 Score =  112 bits (280), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 94/339 (27%), Positives = 163/339 (48%), Gaps = 30/339 (8%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M +  +Q++ K NN           N T    +PL RG   TLG ALRR+L+S++   A+
Sbjct: 6   MTKLEYQKVTKLNN--------STSNVTAFTLQPLERGMGQTLGVALRRILLSNITSLAL 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-----RVTIFKRGPGVVT 115
            A++I+ V HE   + G  ED+  II+N++ +  + + +  K     +VT+    PG VT
Sbjct: 58  FAIKIEDVNHEFQVVDGCVEDVATIIMNLRKVKFQYNPEFVKDDEIIKVTLKADQPGEVT 117

Query: 116 AGDIQTVN-DIEVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHRT--ENDPIG- 169
           +  ++  N  IE+LN    I +L  +    + +EL +  G G++  + ++    N  I  
Sbjct: 118 SRLLEVNNSSIEILNKSLEIAHLSANGKHKLNIELYLRPGRGFISNEENKKLLNNSSITT 177

Query: 170 ----------LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
                      I  D+ +SPI+KV+YTVE          ++L+ +  TDG++  + ++  
Sbjct: 178 RMESKIKNGIFIATDSNFSPIEKVNYTVEELNSSSNKIEERLTFSFQTDGTVDPKSALQQ 237

Query: 220 ASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIV 279
           A  IL     +  N +E K  V  + + ++   N   +  +  L LSVRS N L+     
Sbjct: 238 ACEILVGHFKLIGNVDEMKVNVFAEESEQTQETNDNDV-DINSLNLSVRSLNALKRIGKT 296

Query: 280 YMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +  + + +  ++ ++ N GRKSL EI+  L   G  L 
Sbjct: 297 KISQVAEMSLEELEQVKNLGRKSLDEIQQRLKEYGYELS 335


>gi|21039420|gb|AAM33639.1| RpoA [Escherichia coli]
          Length = 127

 Score =  112 bits (280), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 59/129 (45%), Positives = 89/129 (68%), Gaps = 5/129 (3%)

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPF 252
           Q  + DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++ EVKE+       F
Sbjct: 3   QRTNLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEE----KPEF 58

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 59  DPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 118

Query: 313 MGLFLGMNL 321
            GL LGM L
Sbjct: 119 RGLSLGMRL 127


>gi|290489696|gb|ADD31232.1| RNA polymerase alpha subunit protein [Plumbago auriculata]
          Length = 333

 Score =  112 bits (280), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 84/300 (28%), Positives = 159/300 (53%), Gaps = 26/300 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S++ G+ E + +I++N+
Sbjct: 32  FILFPLRKGQADTIGIAMRRALLGEIEGTCITRAKSEKIAHEYSTLVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +    +  +I  RGP  +TA DI     +E+++    I  L   +D  + ++L
Sbjct: 92  KEIVLRSNLYGTRDASICVRGPRCITAHDIILPPGVEIIDNTQHIATLTEPIDLCIGLQL 151

Query: 148 TVSKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
             ++G+        +T+N+   G   IDA++ P++ V++++ S   G     + L + I 
Sbjct: 152 ERNRGYRI------QTQNNFQDGSYPIDAVFMPVRNVNHSIHSYGNGNE-KQEILFLEIW 204

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK-- 259
           T+GS+T ++++  ASR L D    F++ EE     + + +  +LP   F+  L  L+K  
Sbjct: 205 TNGSLTPKEALYEASRNLIDLFIPFLHAEEENLHFEANQHKVTLPPFTFHDKLNELRKDK 264

Query: 260 ---------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                    +++LE   R  NCL+  NI  + DL+ +++ D++++ +F  + L +I G L
Sbjct: 265 KKIALKSIFIDQLEFPPRIYNCLKNSNIHTLLDLLNKSQEDLMQIEDFRIEDLKQIWGTL 324


>gi|165910441|gb|ABY73975.1| RNA polymerase alpha subunit [Cuscuta nitida]
          Length = 339

 Score =  112 bits (280), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 82/314 (26%), Positives = 154/314 (49%), Gaps = 36/314 (11%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+  A+RR L+S + G  IT V      HE S I G+ E + DI++N+
Sbjct: 32  FILSPLMKGQADTIAIAMRRALLSEIEGTCITRVTFQNASHEYSIIAGIQESVHDILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK +       +++ +GP  VTA DI     +E+++    I +L     + + L +
Sbjct: 92  KEIVLKSNLYGTCDASLYIKGPRYVTAQDIILPPHVEIVDSTQHIASLTEPINLCIGLKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY+   H   +N+   L   DA++ P+  V++++ S    +    + L + I T+G
Sbjct: 152 ERNRGYLIKAHPPFQNETYSL---DAVFMPVLNVNHSIYSYGNEKK---EILFLEIWTNG 205

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK----SLPFNPALLKK------ 259
           S+T ++++  A++ L D    F+  EE      E++N++     +PF+P           
Sbjct: 206 SLTPKEALHEAAQNLMDLFIPFLQMEE------ENLNLEDAEHQIPFSPFTFYDKVSKLI 259

Query: 260 -----------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                      +++L    +  NCL   NI  + DL+ +++ D+L++ +F    + ++K 
Sbjct: 260 KKKKRSLKSIFIDQLAFPPKIYNCLTKSNIFTLLDLLNKSQEDLLKIEHF---HIEDVKQ 316

Query: 309 VLGTMGLFLGMNLP 322
           +LG +     ++LP
Sbjct: 317 ILGILEKNFALDLP 330


>gi|158512705|sp|A0ZZ67|RPOA_GOSBA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
          Length = 330

 Score =  112 bits (280), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 85/306 (27%), Positives = 158/306 (51%), Gaps = 37/306 (12%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  L G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 34  FILSPLMKGQADTIGIAMRRALLGELEGTCITRAKSEKIPHEYSTIVGIQESVHEILMNL 93

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +    +   I  +GPG VTA DI     +E+++    + +L   +D  + +++
Sbjct: 94  KEIVLRGNLYGTRNAFICAKGPGYVTAQDIILPPSVEIVDNTQHVASLTEPIDLCIGLQI 153

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA---REGQVLDYDKLSMT 204
             ++G+G    K+    + P     IDA++ P++  ++++       E Q +    L + 
Sbjct: 154 ERNRGYGIKTPKNFHDGSYP-----IDAVFMPVRNANHSIHCYGNDNEKQEI----LFLE 204

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE------VKEDINVK-SLPFNPALL 257
           I T+GS+T ++++  ASR L D   +FI+F   K+E       + D+ +    PF+  L+
Sbjct: 205 IWTNGSLTPKEALHEASRNLID---LFIHFLHAKEENLHLENNQHDVTLHFFFPFHYRLV 261

Query: 258 K-------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           K              +++ EL  R  NCL+  NI  + DL+  +  D+++M +F  + + 
Sbjct: 262 KLTKKKKEIALKYIFIDQSELPPRIYNCLKKSNIHTLLDLLNNSREDLMKMEHFRIEDVK 321

Query: 305 EIKGVL 310
           +I G+L
Sbjct: 322 QILGIL 327


>gi|108792413|emb|CAJ33201.1| RNA polymerase alpha subunit [Lactobacillus acidipiscis]
          Length = 133

 Score =  112 bits (280), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 53/126 (42%), Positives = 87/126 (69%), Gaps = 2/126 (1%)

Query: 116 AGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITI 173
           AGDIQ  +++EVLNPD  IC +   A     +T +KG GYV A  ++  TE+ PIG++ I
Sbjct: 1   AGDIQGSSEVEVLNPDLYICTVADGASFHARMTANKGRGYVSANENKAKTEDMPIGVLAI 60

Query: 174 DALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           D++Y+PI++V+Y VE  R GQ  D+DKL++ + T+GSIT  ++++L+++IL + L +F++
Sbjct: 61  DSIYTPIERVNYQVEKTRVGQKSDFDKLTLDVWTNGSITPSEAISLSAKILTEHLTLFVD 120

Query: 234 FEEPKK 239
             +  K
Sbjct: 121 LTDEAK 126


>gi|12265|emb|CAA27214.1| unnamed protein product [Spinacia oleracea]
          Length = 335

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 87/302 (28%), Positives = 163/302 (53%), Gaps = 28/302 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTILGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +       +I  RGP  VTA DI     +E+++    I +L   +D  + ++L
Sbjct: 92  KEIVLRSNLYGACEASICVRGPRGVTAQDIILPPYVEIVDNTQHIASLTEPIDLCIGLQL 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+ ++ A ++  +    G   IDAL+ P++ V++++ S   G     + L + I T
Sbjct: 152 ERNRGY-HIKAPNNFQD----GSFPIDALFMPVRNVNHSIHSYGNGNE-KQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF-----NPALLKK--- 259
           +GS+T ++++  ASR L D L  F++ EE    ++++ +  SLP        A ++K   
Sbjct: 206 NGSLTPKEALYEASRNLIDLLIPFLHAEE-NVNLEDNQHKVSLPLFTFHNRLAEIRKNKK 264

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +++LEL  R  NCL+  NI  + DL+  ++ D+++M +F    + ++K + G
Sbjct: 265 KIALKFIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLIKMKHF---RIEDVKQIFG 321

Query: 312 TM 313
           T+
Sbjct: 322 TL 323


>gi|113170453|ref|YP_717245.1| RpoA [Ostreococcus tauri]
 gi|122241423|sp|Q0P3L0|RPOA_OSTTA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|112806860|emb|CAL36367.1| RpoA [Ostreococcus tauri]
          Length = 356

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 91/333 (27%), Positives = 162/333 (48%), Gaps = 61/333 (18%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P+  G   T+GN LRR+L++ L G  +   +I+GV  E S++ G+ E + +I LN++ + 
Sbjct: 29  PVNPGQGLTIGNTLRRILLNDLPGIGVIGAEINGVQSEFSTLPGIRESVIEIFLNLRELI 88

Query: 94  LKMSGDSHKRVTIFK--------------RGPGVVTAGDIQTVNDIEVLNPDHVICN-LD 138
              +    ++V   K                P VVTA D+  + + E ++P+  I   L 
Sbjct: 89  FTPTATCAQKVKQTKPFVYAKLNSELKIDNFPYVVTAKDLH-IPEYEFVDPNQQIATILS 147

Query: 139 VDAVVRMELT--VSKGHGY--------VPA--------KHHRTENDPIGL-ITIDALYSP 179
             A    +LT  + +G GY        VP         +   T+ +   +   IDA++ P
Sbjct: 148 PTAAENFKLTLLIGQGRGYQSWKKLPGVPQLMDQRFFEQFDSTQTNSKSVTFPIDAIFMP 207

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI-----------LQDQL 228
           I++V++TV+       +D + +   + T+GSI   D+V  A+++           LQDQ 
Sbjct: 208 IRQVNFTVQE----HSVDGEYIYFEVWTNGSINPFDAVKSAAKVGMKLMTACLTTLQDQQ 263

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKK------VEELELSVRSTNCLRGENIVYMG 282
              +  +E K  + E  N   + +N    +       +E+LELS+R+ NCL+  NI+ + 
Sbjct: 264 ---VYLDESK--LPETPNFVQVNYNKMESESNFDQIFIEQLELSLRAYNCLKRANILTLA 318

Query: 283 DLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           DL Q++  D++++ NFG+KS  E++  L T G+
Sbjct: 319 DLSQQSFRDLMKLRNFGQKSADEVRAALSTYGI 351


>gi|313622252|gb|EFR92762.1| DNA-directed RNA polymerase subunit alpha [Listeria innocua FSL
           J1-023]
          Length = 129

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 53/120 (44%), Positives = 82/120 (68%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I  +GPGVVTA DI   +D+E+LNPD  I  L  +A   + L  ++G GY PA  +
Sbjct: 2   KTLEIDMQGPGVVTAADINYDSDVEILNPDLHIATLSDNAKFHVRLNATRGRGYTPADQN 61

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           + EN PIG++ +D+++SP+ +V+Y VE+ R GQ  +YDKL+  + TDGSI+ E++V+L +
Sbjct: 62  KRENMPIGVLPVDSIFSPVIRVNYQVENTRVGQSTNYDKLTFDVLTDGSISPEEAVSLGA 121


>gi|11497558|ref|NP_054966.1| RNA polymerase alpha subunit [Spinacia oleracea]
 gi|12644101|sp|P06505|RPOA_SPIOL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|7636139|emb|CAB88759.1| RNA polymerase alpha subunit [Spinacia oleracea]
          Length = 335

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 87/302 (28%), Positives = 163/302 (53%), Gaps = 28/302 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTILGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +       +I  RGP  VTA DI     +E+++    I +L   +D  + ++L
Sbjct: 92  KEIVLRSNLYGTCEASICVRGPRGVTAQDIILPPYVEIVDNTQHIASLTEPIDLCIGLQL 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+ ++ A ++  +    G   IDAL+ P++ V++++ S   G     + L + I T
Sbjct: 152 ERNRGY-HIKAPNNFQD----GSFPIDALFMPVRNVNHSIHSYGNGNE-KQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF-----NPALLKK--- 259
           +GS+T ++++  ASR L D L  F++ EE    ++++ +  SLP        A ++K   
Sbjct: 206 NGSLTPKEALYEASRNLIDLLIPFLHAEE-NVNLEDNQHKVSLPLFTFHNRLAEIRKNKK 264

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +++LEL  R  NCL+  NI  + DL+  ++ D+++M +F    + ++K + G
Sbjct: 265 KIALKFIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLIKMKHF---RIEDVKQIFG 321

Query: 312 TM 313
           T+
Sbjct: 322 TL 323


>gi|197131690|gb|ACH47363.1| RNA polymerase alpha subunit [Geranium carolinianum]
          Length = 329

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 78/292 (26%), Positives = 152/292 (52%), Gaps = 18/292 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A  +G A+RR L+  + G  IT  + + + HE ++I G+ E + +I++N+
Sbjct: 32  FILSPLKKGQADIIGIAMRRALLGEIEGTCITHAKFEKIPHEYTTIVGIQESIYEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL-NPDHVICNLD-VDAVVRMEL 147
           K I L+ + D  +  +I  RGP  VTA DI   N   ++ N  H++   + +D  + +++
Sbjct: 92  KEIVLRSNLDGTRDASICVRGPRDVTAQDIILPNSAAIVDNTQHIVTLTEPIDFCIGLQI 151

Query: 148 TVSKGHGY---VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
             ++G+     +P   H     P     IDA++ P+K V++++ S   G    ++ L + 
Sbjct: 152 DRNRGYSRKIPMPTNFHDDRGYP-----IDAVFLPVKNVNHSIHSYENGS---HEMLFLE 203

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--VKSLPFNPALLKKV-- 260
           I T+GS+T ++++  ASR L +    F++ EE     + + N     LP +   LK +  
Sbjct: 204 IWTNGSLTPKEALREASRKLINLFIPFLHAEEENFHFENNQNEHTDELPIDLCELKDIYI 263

Query: 261 -EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            + +EL  R  NCL+   I  + DL+ +    ++++ +F ++ + ++  +L 
Sbjct: 264 DQLVELPARFYNCLKRSGIHTVMDLLNKNTDGLMKITHFRQEDVEKVMNILN 315


>gi|12644248|sp|P38018|RPOA_MYCSP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|7330636|gb|AAA61685.2| RNA polymerase alpha subunit [Chlamydia muridarum]
          Length = 353

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 73/295 (24%), Positives = 145/295 (49%), Gaps = 16/295 (5%)

Query: 28  TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIIL 87
           T  + EPL RG+A+T+G  LRR L+SS+   A  A++I+ V HE  +I G+ ED   ++ 
Sbjct: 22  TTFVIEPLARGYANTMGTVLRRTLLSSITSVAPFAIKINNVEHEFQTISGLKEDAITLVR 81

Query: 88  NIKGINLKMSGDSHKRVTIFK-----RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           NI+ I    + +  ++  + K        G + A DI  V+ +E++N D  I N+     
Sbjct: 82  NIRNIRFVYNEEIFEKENLAKISFKTNKEGEIFASDIPEVSGLEIVNKDQYIANIAKGGS 141

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIG-----------LITIDALYSPIKKVSYTVESAR 191
           +  +L + KG G++  + ++      G            + +D+ +SP+KK + + E   
Sbjct: 142 LEFDLFLRKGRGFIDFEENKNVISQYGSRLESSIKNGQFLAMDSDFSPVKKCAISFEELN 201

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
               L  ++L + I+TD +++ ++++  A++I+     +  N    +     + N +   
Sbjct: 202 SSSKLIEERLKIKIETDCTVSAKEAIEQAAKIIVAHFQIIGNINALETIELFEENKEKKE 261

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
                   + +L LSVRS N LR      + +++  ++ ++  + N G+KS+ +I
Sbjct: 262 REIKSTTPITKLGLSVRSENALRRAKYNTVEEVLGLSDEELSNIKNLGKKSIQDI 316


>gi|625804|pir||E49923 DNA-directed RNA polymerase (EC 2.7.7.6) alpha chain - Chlamydia
           trachomatis
          Length = 353

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 73/295 (24%), Positives = 145/295 (49%), Gaps = 16/295 (5%)

Query: 28  TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIIL 87
           T  + EPL RG+A+T+G  LRR L+SS+   A  A++I+ V HE  +I G+ ED   ++ 
Sbjct: 22  TTFVIEPLARGYANTMGTVLRRTLLSSITSVAPFAIKINNVEHEFETISGLKEDAITLVR 81

Query: 88  NIKGINLKMSGDSHKRVTIFK-----RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           NI+ I    + +  ++  + K        G + A DI  V+ +E++N D  I N+     
Sbjct: 82  NIRNIRFVYNEEIFEKENLAKISFKTNKEGEIFASDIPEVSGLEIVNKDQYIANIAKGGS 141

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIG-----------LITIDALYSPIKKVSYTVESAR 191
           +  +L + KG G++  + ++      G            + +D+ +SP+KK + + E   
Sbjct: 142 LEFDLFLRKGRGFIDFEENKNVISQYGSRLESSIKNGQFLAMDSDFSPVKKCAISFEELN 201

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
               L  ++L + I+TD +++ ++++  A++I+     +  N    +     + N +   
Sbjct: 202 SSSKLIEERLKIKIETDCTVSAKEAIEQAAKIIVAHFQIIGNINALETIELFEENKEKKE 261

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
                   + +L LSVRS N LR      + +++  ++ ++  + N G+KS+ +I
Sbjct: 262 REIKSTTPITKLGLSVRSENALRRAKYNTVEEVLGLSDEELSNIKNLGKKSIQDI 316


>gi|290489676|gb|ADD31222.1| RNA polymerase alpha subunit protein [Ximenia americana]
          Length = 337

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 87/310 (28%), Positives = 158/310 (50%), Gaps = 25/310 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RRVL+  + G  IT  + + V HE S+  G+ E + +I++N+
Sbjct: 32  FILSPLMKGRADTIGIAMRRVLLGEIEGTCITRAKSEQVPHEYSTAIGIQESIHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGP  +TA DI +   +E+++    I +L       +EL +
Sbjct: 92  KEIVLRSNLYGTCNASICVRGPRYITAQDIISPPSVEIVDNTQYIASLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
            +  GY    H +  N+   G   IDA++ P++  ++++ S   G     + L + I T+
Sbjct: 152 ERNRGY----HIKMPNNFQDGSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWTN 206

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-FNP----ALLKK---- 259
           GS+T + ++  AS+ L D    F++ EE    ++++ +   LP F P    A L+K    
Sbjct: 207 GSLTPKKALYEASQNLIDLFIPFLHAEEENLHLEDNQHKVILPLFTPHDRLAKLRKNKEK 266

Query: 260 -------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                  +++ EL  R  NCL+  NI  + DL   ++ D++++ +F    + + K +LG 
Sbjct: 267 IALKSIFIDQSELPSRIYNCLKRSNIHTLLDLFNNSQKDLMKIEHF---RVEDGKQILGI 323

Query: 313 MGLFLGMNLP 322
           +     ++LP
Sbjct: 324 LEKHFAVDLP 333


>gi|219674007|ref|YP_002456491.1| RNA polymerase alpha subunit [Trifolium subterraneum]
 gi|193788976|gb|ACF20572.1| RNA polymerase alpha subunit [Trifolium subterraneum]
          Length = 337

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 84/309 (27%), Positives = 159/309 (51%), Gaps = 33/309 (10%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G  +RR+L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGITMRRILLGEIEGTCITRAKSEKIPHEYSTIVGIQESIHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GPG VTA DI     +E+++    I NL     + +EL +
Sbjct: 92  KQIVLRSNLYGTRDASICFKGPGYVTARDIILPPSVEIVDNTQHIANLTEPINLCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDA--LYSPIKKVSYTVES---AREGQVLDYDKLSMT 204
            +  GY   +    +N   G  TID   ++ P+   +Y++ S   A E Q +    L + 
Sbjct: 152 ERARGY---RKKTIDNIQDGSYTIDVDPVFMPVIHANYSIHSYLNANEKQEI----LFLE 204

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLKK-- 259
           I T+GS+T ++++  A+R L D    F++ EE     + + +  +LP   F+  L+K   
Sbjct: 205 IWTNGSLTPKEALYEAARNLIDLFIPFLHAEEENFHFENNQHKVTLPLFAFHDRLVKDKL 264

Query: 260 -------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
                        +++LEL  R  NCL+  +I  +  L+ +++ D++++ +F   S+ ++
Sbjct: 265 RKNKKQIELKSVFIDQLELPPRIYNCLKKSDIHTLYQLLNKSQEDLMKIEDF---SVEDV 321

Query: 307 KGVLGTMGL 315
           K +L  + +
Sbjct: 322 KNILNILQI 330


>gi|639724|gb|AAA61684.1| RNA polymerase alpha subunit [Chlamydia muridarum]
          Length = 322

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 72/295 (24%), Positives = 144/295 (48%), Gaps = 16/295 (5%)

Query: 28  TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIIL 87
           T  + EPL RG+A+T+G  LRR L+SS+   A  A++I+ V HE  +I G+ ED   ++ 
Sbjct: 22  TTFVIEPLARGYANTMGTVLRRTLLSSITSVAPFAIKINNVEHEFQTISGLKEDAITLVR 81

Query: 88  NIKGINLK-----MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           NI+ I           ++  +++      G + A DI  V+ +E++N D  I N+     
Sbjct: 82  NIRNIRFVYNEEIFEKENLAKISFKTNKEGEIFASDIPEVSGLEIVNKDQYIANIAKGGS 141

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIG-----------LITIDALYSPIKKVSYTVESAR 191
           +  +L + KG G++  + ++      G            + +D+ +SP+KK + + E   
Sbjct: 142 LEFDLFLRKGRGFIDFEENKNVISQYGSRLESSIKNGQFLAMDSDFSPVKKCAISFEELN 201

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
               L  ++L + I+TD +++ ++++  A++I+     +  N    +     + N +   
Sbjct: 202 SSSKLIEERLKIKIETDCTVSAKEAIEQAAKIIVAHFQIIGNINALETIELFEENKEKKE 261

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
                   + +L LSVRS N LR      + +++  ++ ++  + N G+KS+ +I
Sbjct: 262 REIKSTTPITKLGLSVRSENALRRAKYNTVEEVLGLSDEELSNIKNLGKKSIQDI 316


>gi|317046205|ref|YP_004072494.1| RNA polymerase alpha subunit [Corynocarpus laevigata]
 gi|309252922|gb|ADO60342.1| RNA polymerase alpha subunit [Corynocarpus laevigata]
          Length = 331

 Score =  110 bits (276), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 81/285 (28%), Positives = 145/285 (50%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+R+ L+  + G  IT  + + + HE S+I G+ E + +I +N+
Sbjct: 32  FILSPLMKGQADTIGIAMRKALLGEIEGTCITRAKSEKIPHEYSTIVGIQESVHEIFMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GPG VTA DI     +E+++    I NL     + +EL +
Sbjct: 92  KEIVLRSNLYGTRDASICVKGPGYVTAQDIILPPSVEIVDNTQHIANLTEPINLCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +     N   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGY---RIKTPNNFQDGSYPIDAVFMPVRNANHSIHSYVNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLK-------- 258
           S+T ++++  ASR L D    F++ EE    +K + +  +LP   F+  L K        
Sbjct: 208 SLTPKEALYEASRNLIDFFIPFLHAEEENFHLKNNQHKVTLPLFTFHDRLAKLRKNKKEI 267

Query: 259 -----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++ EL  R  NCL+  NI  + DL+  +  D++++ +F
Sbjct: 268 ALKYIFIDQSELPPRIYNCLKRSNIHTLLDLLNNSPDDLMKIKHF 312


>gi|290489690|gb|ADD31229.1| RNA polymerase alpha subunit protein [Heuchera sanguinea]
          Length = 337

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 83/309 (26%), Positives = 158/309 (51%), Gaps = 23/309 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L+ +    +  +I   GPG VTA DI +   +E+++    I +L     + + L +
Sbjct: 92  KEVVLRSNLYGTRNASICVSGPGYVTAQDIISPPSVEIVDNTQHIASLTEPIDLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            K  GY   +     N   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 EKNRGY---RIKTPNNFQDGSYPIDAVFMPVRNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLK-------- 258
           S+T ++++  ASR L D    F++ EE    ++++ +  +LP   F+  L K        
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHAEEENLHLEDNQHKVTLPLFTFHDRLAKLRKNKKEI 267

Query: 259 -----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++ EL  R   CL+  NI  + DL+  ++ D++++ +F    + ++K +LG +
Sbjct: 268 ALKYIFIDQSELPPRIYTCLKRSNIHTLLDLLNNSQEDLMKIEHF---RIEDVKEILGFL 324

Query: 314 GLFLGMNLP 322
                ++LP
Sbjct: 325 EKHFEIDLP 333


>gi|290489700|gb|ADD31234.1| RNA polymerase alpha subunit protein [Staphylea colchica]
          Length = 342

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 86/315 (27%), Positives = 159/315 (50%), Gaps = 30/315 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GPG VTA DI     +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTRDASICIKGPGYVTAQDIILPPSVEIVDNTQHIASLTEPMDLCIGLQI 151

Query: 150 SKGHGY---VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            +  GY    P   H  +    G   IDA++ P++ V+Y++ S   G     + L + I 
Sbjct: 152 ERNRGYSIKTPNNFHFQD----GSYPIDAVFMPVRNVNYSIHSYGNGNE-KQEILFLEIW 206

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF-------------- 252
           T+GS+T ++++  ASR L D    F++ EE    ++ + +  +LP               
Sbjct: 207 TNGSLTPKEALHEASRNLIDLFIPFLHAEEDNGHLENNHHKLTLPLFTFHDRLAKLRKKK 266

Query: 253 ---NPALLKK--VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                 +LK   +++ ELS R  NCL+  NI  + DL+  ++ D+L++ +     + ++K
Sbjct: 267 KEQKEIVLKYIFIDQSELSPRIYNCLKRSNIHTLLDLLNNSQEDLLKIEDL---RIEDVK 323

Query: 308 GVLGTMGLFLGMNLP 322
            +L  + +   ++LP
Sbjct: 324 QILDILEIENTIDLP 338


>gi|169142742|ref|YP_001687169.1| RNA polymerase alpha subunit [Oenothera argillicola]
 gi|169143063|ref|YP_001687483.1| RNA polymerase alpha subunit [Oenothera parviflora]
 gi|159792980|gb|ABW98736.1| RNA polymerase alpha subunit [Oenothera argillicola]
 gi|159895589|gb|ABX10153.1| RNA polymerase alpha subunit [Oenothera parviflora]
          Length = 366

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 82/298 (27%), Positives = 152/298 (51%), Gaps = 22/298 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFEKIPHEYSTIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  +GPG VTA DI     +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTCNASICVKGPGCVTAQDILLPPSVEIIDNTQHIASLMEPIHLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
            +  GY    H ++ N+   G   IDA++ P++  ++++ S    Q    + L + I T+
Sbjct: 152 ERNRGY----HIKSPNNFQDGSYPIDAVFMPVRNANHSIHSY-GNQNEKQEILFLEIWTN 206

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEV---KEDINVKSLPFNPALLK------- 258
           GS+T ++++  ASR L D    F++ EE    +   K ++      F+  L K       
Sbjct: 207 GSLTPKEALHEASRNLIDLFLPFLHAEEENLHLGNNKYNVTFPLFTFHKKLAKLRKPKNE 266

Query: 259 ------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                  +++LEL  R  N L+G  I  + DL+ +++ D+++M +F  + + +I  +L
Sbjct: 267 IALKSIFIDQLELPPRIYNSLKGSKIHTLSDLLNKSQEDLMKMKHFRIEDVKQILDIL 324


>gi|313199734|ref|YP_004021348.1| RNA polymerase alpha subunit [Theobroma cacao]
 gi|309321298|gb|ADO64841.1| RNA polymerase alpha subunit [Theobroma cacao]
 gi|328924811|gb|ADO64922.2| RNA polymerase alpha subunit [Theobroma cacao]
          Length = 327

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 83/303 (27%), Positives = 152/303 (50%), Gaps = 32/303 (10%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +   I  +GPG VTA DI     +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTRNAFICAKGPGYVTAQDIILPPSVEIVDNTQHIASLTEPIDLCIGLQI 151

Query: 150 SKGHGY---VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA---REGQVLDYDKLSM 203
            +  GY    P   H       G   +DA++ P++  ++++       E Q +    L +
Sbjct: 152 ERNRGYRIKTPNNFHD------GSYPLDAVFMPVRNANHSIHCYGNDNEKQEI----LFL 201

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA-------- 255
            I T+GS+T ++++  ASR L D    F++ EE    ++ + +  +LPF P         
Sbjct: 202 EIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLENNQHNVTLPFFPFHDRLAKLR 261

Query: 256 ------LLKK--VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                  LK   +++ EL  R  NCL+  NI  + DL+  ++ D++++ +F  + + +I 
Sbjct: 262 KKKKEIALKYIFIDQSELPPRIYNCLKKSNIHTLLDLLNNSQEDLMKIEHFRIEDVKQIL 321

Query: 308 GVL 310
           G+L
Sbjct: 322 GIL 324


>gi|164597832|ref|NP_084725.2| RNA polymerase alpha subunit [Oenothera elata subsp. hookeri]
 gi|169142892|ref|YP_001687315.1| RNA polymerase alpha subunit [Oenothera glazioviana]
 gi|169142977|ref|YP_001687399.1| RNA polymerase alpha subunit [Oenothera biennis]
 gi|172045760|sp|Q9MTJ3|RPOA_OENEH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|159793150|gb|ABW98904.1| RNA polymerase alpha subunit [Oenothera biennis]
 gi|159895504|gb|ABX10069.1| RNA polymerase alpha subunit [Oenothera glazioviana]
 gi|162423699|emb|CAB67191.2| RNA polymerase alpha subunit [Oenothera elata subsp. hookeri]
          Length = 366

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 82/298 (27%), Positives = 152/298 (51%), Gaps = 22/298 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFEKIPHEYSTIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  +GPG VTA DI     +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTCNASICVKGPGCVTAQDILLPPSVEIIDNTQHIASLMEPIHLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
            +  GY    H ++ N+   G   IDA++ P++  ++++ S    Q    + L + I T+
Sbjct: 152 ERNRGY----HIKSPNNFQDGSYPIDAVFMPVRNANHSIHSY-GNQNEKQEILFLEIWTN 206

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEV---KEDINVKSLPFNPALLK------- 258
           GS+T ++++  ASR L D    F++ EE    +   K ++      F+  L K       
Sbjct: 207 GSLTPKEALHEASRNLIDLFLPFLHAEEENLHLGKNKYNVTFPLFTFHKKLAKLRKPKNE 266

Query: 259 ------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                  +++LEL  R  N L+G  I  + DL+ +++ D+++M +F  + + +I  +L
Sbjct: 267 IALKSIFIDQLELPPRIYNSLKGSKIHTLSDLLNKSQEDLMKMKHFRIEDVKQILDIL 324


>gi|161511777|emb|CAP16899.1| DNA-directed RNA polymerase subunit alpha [Pediococcus stilesii]
          Length = 141

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 62/138 (44%), Positives = 85/138 (61%), Gaps = 2/138 (1%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  IC 
Sbjct: 1   GVVEDVTQIILNLKKVSLKIESDDEKTLDINVVGPANVTAGDIMGDGDVTILNPEAPICT 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
           +         LT   G GY  A  +  R  + PI ++ ID++Y+PI++V+Y VE+ R GQ
Sbjct: 61  VAEGTTFHAVLTADTGRGYTSADENKARKVDMPISVLPIDSIYTPIERVNYQVENTRVGQ 120

Query: 195 VLDYDKLSMTIDTDGSIT 212
             DYDKL++ I TDGSIT
Sbjct: 121 RDDYDKLTLDIWTDGSIT 138


>gi|197131698|gb|ACH47367.1| RNA polymerase alpha subunit [Sarcocaulon vanderietiae]
          Length = 333

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 78/291 (26%), Positives = 151/291 (51%), Gaps = 12/291 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A  +G A+RR L+  + G  IT  +   + HE +++ G+ E + +I++N+
Sbjct: 32  FILSPLKKGQADIIGIAMRRALLVEIEGTCITHAKFAKIPHEYTTMAGIKESIYEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  RGP  VTA DI       +++    I  L       +EL +
Sbjct: 92  KEIVLRSNLYGTRDASICVRGPRDVTAQDIILPPSTAIVDNTQHIVTLTEPIDFCVELKI 151

Query: 150 SKGHGY---VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            +G GY   +P   +   +D    I IDA++ P++ V++++ S + G     + L + I 
Sbjct: 152 ERGRGYSIKIPMPTNPFHHDSGYPIPIDAVFMPVRNVNHSIYSYKRGS---REILFLEIW 208

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKK---EVKEDINVKSLPFNPALLKKV--- 260
           T+GS+T ++++  ASR L +    F++ EE      E  ++ + + LP +   LK++   
Sbjct: 209 TNGSLTPKEALREASRKLINLFIPFLHAEEENFYLLENNQNQHTEELPIDSCGLKEIYID 268

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
           + +EL  R  NCL+   I  + DL+ ++  D++++ +F ++ +  +  +L 
Sbjct: 269 QLVELPPRFYNCLKRSGIHTVMDLLDKSRDDLMKITHFRQEDVERVMNILN 319


>gi|139387284|ref|YP_001123405.1| RNA polymerase alpha subunit [Capsella bursa-pastoris]
 gi|158513962|sp|A4QKM4|RPOA_CAPBU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134286605|dbj|BAF50229.1| RNA polymerase alpha subunit [Capsella bursa-pastoris]
          Length = 327

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 80/297 (26%), Positives = 152/297 (51%), Gaps = 20/297 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + H+ S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENIPHDYSNIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
             I L+ +    +   I  +GPG +TA DI     +E+++    I  L     + +EL +
Sbjct: 92  NEIVLRSNLYGTRNALICVQGPGYITARDIILPPSVEIIDNTQHIATLTEPIDLCIELKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  E+       IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGYSLKMSNNFEDRS---YPIDAVFMPVQNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA------LLKK---- 259
           S+T ++++  ASR L +    F++ EE    ++ + +  +LPF P       L KK    
Sbjct: 208 SLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQVTLPFFPFHNRLVNLRKKTKEL 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F  + + +I  +L
Sbjct: 268 AFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLIKIEHFHVEDVKKILDIL 324


>gi|308746019|ref|YP_003934590.1| RNA polymerase alpha subunit [Cheilanthes lindheimeri]
 gi|302375452|gb|ADL29826.1| RNA polymerase alpha subunit [Cheilanthes lindheimeri]
          Length = 342

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 90/330 (27%), Positives = 155/330 (46%), Gaps = 41/330 (12%)

Query: 10  IKPNNIEYIVLGQEEENRTL----MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           I    I++  L  + E++ L     +  P  RG A T+G A+RR L   + G +IT  + 
Sbjct: 8   ISTQRIQWKCLESKTESKRLHYGRFVVSPFKRGQASTVGIAMRRALSQEVGGTSITRAKF 67

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR--GPGVVTAGDIQTVN 123
            GV+HE S+I G+ E + D+++N+K I LK   DS+     F    GP  VTAGD     
Sbjct: 68  HGVVHEYSTITGIQETIHDVLVNLKEIVLK--SDSNDIWEAFPSVMGPKEVTAGDTSLPP 125

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPI 180
            ++ ++    I  +       +EL + +  GY      R EN      G  +IDA++ P+
Sbjct: 126 RVKAIDNSQYIATITQPISSNIELKIERDCGY------RIENSNECRDGQFSIDAVFMPV 179

Query: 181 KKVSYTVE---SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF------ 231
           + V+Y++    + R  Q + +    + I T+GS T  ++++ AS+ L D    F      
Sbjct: 180 RNVNYSIHLFGNGRATQEISF----IEIWTNGSPTPHEALSEASKKLIDLSTPFSGVKCR 235

Query: 232 -INFEEPKKEVKEDINVKSLPFNPALLKKVE----------ELELSVRSTNCLRGENIVY 280
            ++F E  ++  +      L        K+E          +LEL  R+ NCL+   I  
Sbjct: 236 DVSFLEDHEDSSDSTRSPFLQLQFGNACKLEGKLFENMFIDQLELPARAFNCLKRAEIHT 295

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           + D +  +  D+ ++ NFG+KS+ ++   L
Sbjct: 296 IADSLNYSREDLSKIRNFGQKSVDQVSKAL 325


>gi|139389450|ref|YP_001123147.1| RNA polymerase alpha subunit [Olimarabidopsis pumila]
 gi|158513629|sp|A4QJW3|RPOA_OLIPU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134286344|dbj|BAF49971.1| RNA polymerase alpha subunit [Olimarabidopsis pumila]
          Length = 327

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 80/297 (26%), Positives = 152/297 (51%), Gaps = 20/297 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + H+ S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENIPHDYSNIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
             I L+ +    +   I  +GPG +TA DI     +E+++    I  L     + +EL +
Sbjct: 92  NEIVLRSNLYGTRNALICVQGPGYITARDIILPPSVEIIDNTQHIATLTEPIDLCIELKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  E+       IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGYSLKMSNNFEDRS---YPIDAVFMPVQNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA------LLKK---- 259
           S+T ++++  ASR L +    F++ EE    ++ + +  +LPF P       L KK    
Sbjct: 208 SLTPKEALHEASRNLINLFIPFLHVEEETVYLENNQHQVTLPFFPFHNRLVNLRKKKKEL 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F  + + +I  +L
Sbjct: 268 AFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLIKIEHFHIEDVKKILDIL 324


>gi|168026922|ref|XP_001765980.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162682886|gb|EDQ69301.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 438

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 83/294 (28%), Positives = 149/294 (50%), Gaps = 28/294 (9%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQID--GVLHEISSIKGVHEDLTDIILNIKG 91
           P  +G A T+GNALRR L+  ++GAAIT       G++HE  ++ G+ E + DI+LN++ 
Sbjct: 135 PFRQGQAITVGNALRRALLGEVQGAAITCATFKDMGIVHEYQAVDGIQETVQDILLNVRD 194

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           + +  +    ++  I   GP  V AGDI     + V +P   I  +       +E+ V K
Sbjct: 195 VAIGSNTHEPQKAFISVMGPRQVIAGDILCPPSLVVPDPSQNIALVTAAIPFNVEIEVEK 254

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
             GY      ++ N   G   ID+++ P+ + +Y+V S  E + +  + L + I T+GSI
Sbjct: 255 DVGYRIVDPGKSTN---GRFYIDSVFMPVVQANYSVHSF-EVEDVTREILFLEIYTNGSI 310

Query: 212 TGEDSVALASR--------ILQDQLGMFINFEEPKKEVKE-----------DINVKSLPF 252
           + E+++  A+R        +L+ ++    N  E +   +            D   K + +
Sbjct: 311 SPEEALIEAARSLIDLLLPLLESEVIEVTNTTEKENGSRNISMLSSFLSSSDQITKEVTY 370

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
                  +++L+L  R+ NCL+  NI  + DL+  T+ D++R+ NFG+KS+ E+
Sbjct: 371 KHVF---IDQLKLPARAYNCLKRANIHTVSDLLDYTQDDLMRIKNFGKKSVEEV 421


>gi|297837931|ref|XP_002886847.1| RNA polymerase alpha subunit [Arabidopsis lyrata subsp. lyrata]
 gi|297841001|ref|XP_002888382.1| RNA polymerase alpha subunit [Arabidopsis lyrata subsp. lyrata]
 gi|297332688|gb|EFH63106.1| RNA polymerase alpha subunit [Arabidopsis lyrata subsp. lyrata]
 gi|297334223|gb|EFH64641.1| RNA polymerase alpha subunit [Arabidopsis lyrata subsp. lyrata]
          Length = 327

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 80/297 (26%), Positives = 152/297 (51%), Gaps = 20/297 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + H+ S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENIPHDYSNIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
             I L+ +    +   I  +GPG +TA DI     +E+++    I  L     + +EL +
Sbjct: 92  NEIVLRSNLYGTRNALICVQGPGYITARDIILPPSVEIIDNTQHIATLTETIDLCIELKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  E+       IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGYSLKMSNNFEDRS---YPIDAVFMPVENANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA------LLKK---- 259
           S+T ++++  ASR L +    F++ EE    ++ + +  +LPF P       L KK    
Sbjct: 208 SLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQVTLPFFPFHNRLVNLRKKTKEL 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F  + + +I  +L
Sbjct: 268 AFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLIKIEHFHVEDVKKILDIL 324


>gi|162964321|dbj|BAF95589.1| DNA-directed RNA polymerase alpha chain [Physcomitrella patens]
 gi|162964323|dbj|BAF95590.1| DNA-directed RNA polymerase alpha chain [Physcomitrella patens]
          Length = 525

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 87/310 (28%), Positives = 155/310 (50%), Gaps = 31/310 (10%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQID--GVLHEISSIKGVHEDLTDIILNIKG 91
           P  +G A T+GNALRR L+  ++GAAIT       G++HE  ++ G+ E + DI+LN++ 
Sbjct: 222 PFRQGQAITVGNALRRALLGEVQGAAITCATFKDMGIVHEYQAVDGIQETVQDILLNVRD 281

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           + +  +    ++  I   GP  V AGDI     + V +P   I  +       +E+ V K
Sbjct: 282 VAIGSNTHEPQKAFISVMGPRQVIAGDILCPPSLVVPDPSQNIALVTAAIPFNVEIEVEK 341

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
             GY      ++ N   G   ID+++ P+ + +Y+V S  E + +  + L + I T+GSI
Sbjct: 342 DVGYRIVDPGKSTN---GRFYIDSVFMPVVQANYSVHSF-EVEDVTREILFLEIYTNGSI 397

Query: 212 TGEDSVALASR--------ILQDQLGMFINFEEPKKEVKE-----------DINVKSLPF 252
           + E+++  A+R        +L+ ++    N  E +   +            D   K + +
Sbjct: 398 SPEEALIEAARSLIDLLLPLLESEVIEVTNTTEKENGSRNISMLSSFLSSSDQITKEVTY 457

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                  +++L+L  R+ NCL+  NI  + DL+  T+ D++R+ NFG+KS+ E   VL  
Sbjct: 458 KHVF---IDQLKLPARAYNCLKRANIHTVSDLLDYTQDDLMRIKNFGKKSVEE---VLEA 511

Query: 313 MGLFLGMNLP 322
           +     ++LP
Sbjct: 512 LRAQFNISLP 521


>gi|7525065|ref|NP_051090.1| RNA polymerase alpha subunit [Arabidopsis thaliana]
 gi|6685903|sp|P56762|RPOA_ARATH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|5881726|dbj|BAA84417.1| RNA polymerase alpha subunit [Arabidopsis thaliana]
          Length = 329

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 80/299 (26%), Positives = 152/299 (50%), Gaps = 22/299 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + H+ S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENIPHDYSNIAGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
             I L+ +    +   I  +GPG +TA DI     +E+++    I  L     + +EL +
Sbjct: 92  NEIVLRSNLYGTRNALICVQGPGYITARDIILPPAVEIIDNTQHIATLTEPIDLCIELKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  E+       IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGYSLKMSNNFEDRS---YPIDAVFMPVENANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA------LLKK---- 259
           S+T ++++  ASR L +    F++ EE    ++ + +  +LPF P       L KK    
Sbjct: 208 SLTPKEALHQASRNLINLFIPFLHVEEETFYLENNQHQVTLPFFPFHNRLVNLRKKKKTK 267

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                   +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F  + + +I  +L
Sbjct: 268 ELAFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLIKIEHFHVEDVKKILDIL 326


>gi|301353363|ref|YP_003795612.1| RNA polymerase alpha subunit [Pteridium aquilinum subsp. aquilinum]
 gi|301016281|gb|ADK47568.1| RNA polymerase alpha subunit [Pteridium aquilinum subsp. aquilinum]
          Length = 347

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 80/310 (25%), Positives = 148/310 (47%), Gaps = 22/310 (7%)

Query: 15  IEYIVLGQEEENRTL----MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           I++  +  + E++ L     +  P  RG   T+G A+RR  +  + G +IT  +  GV+H
Sbjct: 13  IQWKCVESKTESKRLHYGRFVVSPFKRGQVSTVGIAMRRASLEEVEGTSITCARFHGVVH 72

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S+I G+ E + D+++N+K I  K   +  +       GP  VTAGD      ++ ++ 
Sbjct: 73  EYSTITGIQETIRDVLVNLKEIAPKSDSNDIQEAVSSVTGPKKVTAGDTLLPPSVKAIDD 132

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
              +  +     V +E  + K  GY     H       G   +DA+  P++ V+Y+V   
Sbjct: 133 SQYVVTITQPISVNIESKIEKDCGYRIENSHGYGG---GEFPVDAVSMPVRNVNYSVHLF 189

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EPKKEVKEDINVKS 249
             G+ +  + L + I T+GS+T ++++  AS+ L D L  F++ + E      ++ +  +
Sbjct: 190 GSGKAM-RETLFIEIWTNGSLTPDEAICEASKKLIDLLTPFLHVKCEDVPHSGDNQDFSA 248

Query: 250 LPFNPALLKKVEE-------------LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
              +P+    V E             LEL  R+ NCL+   I  + DL+  +  D  R+ 
Sbjct: 249 STGSPSHFDDVSELEGKISKNTFIDQLELPARAFNCLKRAEIHTISDLLNYSREDSSRIK 308

Query: 297 NFGRKSLVEI 306
           +FG+KS+ ++
Sbjct: 309 SFGQKSVDQV 318


>gi|254755535|ref|ZP_05207569.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           Vollum]
          Length = 150

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 56/145 (38%), Positives = 92/145 (63%)

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           ID++Y+P+ +V+Y VE  R GQV +YDKL++ + TDGSI  +++++L ++IL + L +F+
Sbjct: 2   IDSIYTPVSRVTYQVEKTRVGQVANYDKLTLDVWTDGSIGPKEAISLGAKILTEHLNIFV 61

Query: 233 NFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
              +  +  +  +  +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM
Sbjct: 62  GLTDEAQNAEIMVEKEEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDM 121

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFL 317
           +++ N GRKSL E+K  L  +GL L
Sbjct: 122 MKVRNLGRKSLEEVKHKLEELGLGL 146


>gi|150036846|emb|CAM98288.1| DNA-directed RNA polymerase alpha chain [Fructobacillus
           pseudoficulneus]
          Length = 169

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 62/161 (38%), Positives = 96/161 (59%), Gaps = 2/161 (1%)

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND-- 166
           +GP  VTA D+    DIEVLNPD  I  L     + M +T  KG GY  A+ ++   D  
Sbjct: 9   QGPKDVTAADLMGSADIEVLNPDLHIATLAAGKALHMTVTAVKGRGYSSAEENKQLRDEM 68

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           PIG++T+D++Y+PI++V+Y VE+ R G   DYDKL+M + T+GSI   D+++L S+IL +
Sbjct: 69  PIGVLTVDSIYTPIERVNYHVENKRVGSRDDYDKLTMEVWTNGSIKPSDALSLGSKILTE 128

Query: 227 QLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
            L +F +     ++ K  +  +      A    +E+L+LSV
Sbjct: 129 HLNLFTDISPVAQDTKVMVESEPAANTAADAAPIEDLDLSV 169


>gi|150036734|emb|CAM98258.1| DNA-directed RNA polymerase alpha chain [Leuconostoc citreum]
          Length = 145

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 60/145 (41%), Positives = 89/145 (61%), Gaps = 2/145 (1%)

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           + GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I
Sbjct: 1   VDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDVQGPADVTAADLQAGADVEVLNPDLHI 60

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESARE 192
             +     + M +T  KG GY  A  ++   D  PIG++ +D++Y+PI++V+Y VE+ R 
Sbjct: 61  ATVAAGKSLHMTVTAVKGRGYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRV 120

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSV 217
           G   DYDKL+  I T+GSI   D++
Sbjct: 121 GSRDDYDKLTFDIWTNGSIKPSDAL 145


>gi|300431316|gb|ADK12621.1| RNA polymerase alpha subunit [Lorenzochloa erectifolia]
          Length = 339

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 84/288 (29%), Positives = 138/288 (47%), Gaps = 26/288 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+ E + +I+LN+
Sbjct: 32  FILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGIEESVQEILLNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL       +EL +
Sbjct: 92  KEIVLRSNLYGVRDASICVKGPRYITAQDITLPPSVEIVDTAQPIANLTEPIDFCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  ++   G   IDA+  P++ V+Y++ S   G    ++ L + I T+G
Sbjct: 152 KRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFI--------------NFEEP-----KKEVKEDINVKSL 250
           S+T ++++  ASR L D    F+               F  P     KK      N K +
Sbjct: 208 SLTPKEALYEASRNLIDLFLPFLXXXXXXXXXXXNKNRFTPPLFTFQKKLTNLXKNKKGI 267

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           P          +LEL  R+ NCL+   I  + DL+ +TE  ++ + +F
Sbjct: 268 PXXCIF---XXQLELPSRTYNCLKRAXIHTLLDLLSKTEEXLMXIDSF 312


>gi|154424749|emb|CAL18477.1| RNA polymerase alpha subunit [Streptococcus pyogenes]
          Length = 128

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 54/127 (42%), Positives = 86/127 (67%)

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     +R
Sbjct: 2   IILNVKGLAVKSYVEDEKIIELEVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLR 61

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
             +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ 
Sbjct: 62  ATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIE 121

Query: 205 IDTDGSI 211
           I T+G+I
Sbjct: 122 IMTNGTI 128


>gi|69215820|gb|AAZ03866.1| RNA polymerase alpha chain [Ginkgo biloba]
          Length = 337

 Score =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 84/293 (28%), Positives = 142/293 (48%), Gaps = 20/293 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL +G A+T+G A+RR L+  + G  IT  + + + HE S+I G+ E + DI +N++GI 
Sbjct: 36  PLQKGQANTIGIAMRRALLGEVEGTCITHAKFENMTHEYSAIMGIEESVHDISINLRGIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      +  +I+  GP  VTA DI     + +++    I +L       +   + K  
Sbjct: 96  LQSDPYGIREASIYSVGPRDVTAQDIILPPSVRIIDTTQHIASLKESITSDIRSQIGKDR 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY   +     N   G+ + DA+  P++  +Y++ S   G  +  + L   I T+GS+  
Sbjct: 156 GY---RIQSPNNSRDGIFSTDAVSMPVRNANYSIHSYGNGNEMQ-EILFSEIWTNGSLAP 211

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKED---INVKSLPFN--PALLKKVEE------ 262
            +++  ASR L D    F+  EE   +  ++    N+   PF+      +K+EE      
Sbjct: 212 GEALYEASRNLIDLFIPFMRAEEQNIDGIDNWNGYNMSLFPFSHISTDTEKMEEEIAFKH 271

Query: 263 -----LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 EL  R  NCL+  NI  + DL+  +  D  R+ NFG +S+ +I  VL
Sbjct: 272 IFIDQSELPPRVYNCLKRVNIHTLSDLLNYSRDDPTRIENFGNQSVEQILEVL 324


>gi|139389833|ref|YP_001123494.1| RNA polymerase alpha subunit [Crucihimalaya wallichii]
 gi|158513969|sp|A4QKW3|RPOA_CRUWA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134286695|dbj|BAF50318.1| RNA polymerase alpha subunit [Crucihimalaya wallichii]
          Length = 327

 Score =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 79/299 (26%), Positives = 156/299 (52%), Gaps = 24/299 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT V+ + + H+ S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEMEGTCITRVKSENIPHDYSNIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
             I L+ +    +   I  +GPG +TA DI     +E+++    I  L   +D  + +++
Sbjct: 92  NEIVLRSNLYGTRNALICVQGPGYITARDIILPPSVEIVDNTQHIATLTEPIDLCIGLKI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+    + +    + P     IDA++ P++  ++++ S   G     + L + I T
Sbjct: 152 ERNRGYSLKISNNLEDRSYP-----IDAVFMPVQNANHSIHSYGNGNE-KQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA------LLKK-- 259
           +GS+T ++++  ASR L +    F++ EE    ++ + +  +LPF P       L KK  
Sbjct: 206 NGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQVTLPFFPFHNRFFNLRKKKK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                   +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F  + + +I  +L
Sbjct: 266 ELAFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLIKIEHFHVEDVKKILDIL 324


>gi|295137036|ref|YP_003587583.1| RNA polymerase alpha subunit [Pisum sativum]
 gi|133405|sp|P13911|RPOA_PEA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|12180|emb|CAA33668.1| RNA polymerase alpha subunit (AA 1-334) [Pisum sativum]
 gi|293338608|gb|ADE43581.1| RNA polymerase alpha subunit [Pisum sativum]
          Length = 334

 Score =  108 bits (271), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 84/311 (27%), Positives = 155/311 (49%), Gaps = 31/311 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G  +RR+L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGITMRRILLGEIEGTCITRAKSEKIPHEYSTIVGIQESIHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GPG VTA DI  +  +EV++    I NL     + +EL +
Sbjct: 92  KEIVLRSNLYGTREASICFKGPGYVTAQDI-ILPSVEVIDNTQHIANLTEPINLCIELQI 150

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +     N   G  TIDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 151 ERKRGY---RIKTLNNIQDGSYTIDAVFMPVRNANHSIHSYVNGNQ-KQEILFLEIWTNG 206

Query: 210 SITGEDSVALASRILQDQLGMFIN---------------------FEEPKKEVKEDI--N 246
           S+T ++++  ASR L D    F++                     F +  + VK+ +  N
Sbjct: 207 SLTPKEALYEASRNLIDLFIPFLHAEEENLNFENNQHKMTLPLFTFHDHDRFVKDKLRKN 266

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            K +         +++LEL  R  NCL+  NI  + +L+ +++ D++++ +F  + L  I
Sbjct: 267 QKEITLKSIF---IDQLELPPRIYNCLKKSNIHTVLELLNKSQEDLMKIEHFRVEDLKFI 323

Query: 307 KGVLGTMGLFL 317
             +L     F+
Sbjct: 324 LNILQIENHFV 334


>gi|119662829|emb|CAJ33207.1| RNA polymerase alpha subunit [Lactobacillus ingluviei]
          Length = 132

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 55/127 (43%), Positives = 83/127 (65%), Gaps = 1/127 (0%)

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND-P 167
           +GP  VTA DIQ   D+ +LNPD  I  +   A + M +T   G GY  A  ++   D  
Sbjct: 3   KGPAEVTAADIQADGDVTILNPDLHIATVADGAELHMRMTADTGRGYNSADVNKARMDLA 62

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           IG++ ID++Y+PI++V+YTVE+ R GQ  DYDKL++ + TDGS+T  ++++LA++IL   
Sbjct: 63  IGVLPIDSIYTPIERVNYTVENTRVGQSNDYDKLTLDVWTDGSLTPTEAISLAAKILTSH 122

Query: 228 LGMFINF 234
           L MF+N 
Sbjct: 123 LTMFVNL 129


>gi|61676006|gb|AAX51668.1| DNA dependent RNA polymerase alpha subunit [Waddlia chondrophila
           WSU 86-1044]
          Length = 174

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 66/174 (37%), Positives = 98/174 (56%), Gaps = 17/174 (9%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM- 96
           G  HTLGN+LRR++++SL   AI  V+I+GV HE  +I  + ED+T+IILNIKG  L+  
Sbjct: 1   GMGHTLGNSLRRLMLTSLEAPAIIGVRIEGVAHEYMAIDSIVEDMTNIILNIKGAKLRKL 60

Query: 97  ----SGDSHKRVTIFK------------RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
               + ++  R  + K            +G   V  GDI      EV+NP+H +  + V 
Sbjct: 61  PMEDTPNARNRGLLTKVLEITQEDIDNGKGQYEVRLGDIVEGGIFEVVNPNHHVFTVTVP 120

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
              +++L VS G GYVP++ H   +     I IDA ++P+K V+Y VE+ R GQ
Sbjct: 121 MQKQVDLRVSFGRGYVPSERHVVNDKSTDEILIDAAFTPVKLVNYHVENTRVGQ 174


>gi|139390184|ref|YP_001123757.1| RNA polymerase alpha subunit [Lobularia maritima]
 gi|158513990|sp|A4QLM6|RPOA_LOBMA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134286961|dbj|BAF50581.1| RNA polymerase alpha subunit [Lobularia maritima]
          Length = 327

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 79/297 (26%), Positives = 151/297 (50%), Gaps = 20/297 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + H+ S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENIPHDYSNIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
             I L+ +    +   I  +GPG +TA DI     +E+++    I  L     + +EL +
Sbjct: 92  NEIVLRSNLYGTRNALICVQGPGYITAQDIILPPSVEIIDNTQHIATLTEPIDLCIELKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  E+       IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGYSLKMSNNFEDRS---YPIDAVFMPVQNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA------LLKK---- 259
           S+T ++++  ASR L +    F++ EE    ++ + +  +LP  P       L KK    
Sbjct: 208 SLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQVTLPLFPFHNRLVNLRKKKKEL 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F  + + +I  +L
Sbjct: 268 AFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLIKIEHFHMEDVKKILDIL 324


>gi|189095413|ref|YP_001936426.1| DNA-directed RNA polymerase alpha subunit [Heterosigma akashiwo]
 gi|157694756|gb|ABV66032.1| DNA-directed RNA polymerase alpha subunit [Heterosigma akashiwo]
 gi|157777987|gb|ABV70173.1| DNA-directed RNA polymerase alpha subunit [Heterosigma akashiwo]
          Length = 402

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 65/200 (32%), Positives = 112/200 (56%), Gaps = 11/200 (5%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           G   T+G+ALRRVL++ L G AI  ++I  +  E SS+ GV ED+ +IILN+K I ++  
Sbjct: 29  GQGTTVGSALRRVLLTDLPGLAIVGLRIANINTEFSSLPGVREDILEIILNVKDIVIEGE 88

Query: 98  GDSHKRVTIFK---RGPGVVTAGDIQTVND--IEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +S K   + +   +GPGVVTA  I+   D  I+++NP   I  ++V++ + ME  V  G
Sbjct: 89  FNSSKPWVLGRLKLKGPGVVTAALIEFEEDANIQIINPSQYIATIEVNSSIEMEFLVQTG 148

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR------EGQVLDYDKLSMTID 206
             Y   +   +       + IDA++ P+ KV++ V S +         + D + L++ I 
Sbjct: 149 KNYRLVESENSITYSTDFLQIDAIFMPVTKVAFEVTSTKTNALENNSSIQDNENLTLEIW 208

Query: 207 TDGSITGEDSVALASRILQD 226
           T+GSI+   ++  ++ IL++
Sbjct: 209 TNGSISPIKALVFSASILEN 228



 Score = 43.5 bits (101), Expect = 0.047,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 34/54 (62%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           +EEL LSVR+ N L+  NI  + DL+Q +  D+  + NFG+KSL E+   L  +
Sbjct: 343 IEELILSVRAYNGLKRANIHSVSDLVQYSIKDLKDIKNFGKKSLDEVVASLKNL 396


>gi|114329687|ref|YP_740508.1| RNA polymerase alpha subunit [Citrus sinensis]
 gi|122166151|sp|Q09ME5|RPOA_CITSI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|113952653|gb|ABI49051.1| RNA polymerase alpha subunit [Citrus sinensis]
          Length = 328

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 84/297 (28%), Positives = 150/297 (50%), Gaps = 19/297 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RRVL+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRVLLGEIEGTCITRAKSEKIPHEYSTIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +        I  +GPG VTA DI     +E+++    I +L     + + L +
Sbjct: 92  KDIVLRSNLYGTCDALICVKGPGYVTAQDILLPPSVEIVDNTQHIASLTEPIDLSIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   K   T  D      IDA++ P++  +++++S   G     + L + I T+G
Sbjct: 152 ERSRGY-NIKTPNTFQDG-NCYPIDAVFMPVRNANHSIQSYGNGNE-KQEILFLEIWTNG 208

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN------PALLKKVEEL 263
           S+T ++++  ASR L D    F+  E+    ++ +    +LPF         L KK +E+
Sbjct: 209 SLTPKEALHEASRSLIDLFIPFLQAEDENLPLENNQYKVTLPFFTFHDRLAKLTKKKKEI 268

Query: 264 ----------ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                     E+S R  NCL+  NI  + DL+   + D++++ +F  + + +I  +L
Sbjct: 269 ALKSIFIDQSEMSPRIYNCLKKSNIHTLFDLLNTRQEDLMKIEHFRIEDVKQIMSIL 325


>gi|165910443|gb|ABY73976.1| RNA polymerase alpha subunit [Cuscuta epilinum]
          Length = 330

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 86/309 (27%), Positives = 150/309 (48%), Gaps = 27/309 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT V+ +   HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLIKGQADTIGIAMRRALLGEIEGTCITRVKSEKASHEYSTIGGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  +GP  VTA DI     +++++    I  L       + L +
Sbjct: 92  KEIVLRSNLYGTCDASICIKGPRHVTAQDIILPPHVQIVDNTQHIAWLTEPIDFFIGLKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES-AREGQVLDYDKLSMTIDTD 208
            +  GY        ++   G+  IDAL+ P++  ++++ S   E Q    + L + I T+
Sbjct: 152 ERNRGYFNKVDLHFDD---GIYPIDALFMPVQNANHSIHSYGNEKQ----EILFLEIWTN 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPK---KEVKEDINVKSLPFNPALLKK------ 259
           GS+T ++++  A+RIL D    F + EE      + +  I + SL F   + K       
Sbjct: 205 GSLTPKEALHEAARILIDFFIPFFHMEEENLYLADAEHTIPLSSLIFYNKVTKLIKKKKK 264

Query: 260 -------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                  +++LE   +  NCL   NI  + DL    E D+L++ +F    L +IK +LG 
Sbjct: 265 LSLKLIFIDQLEFPPKIYNCLTKSNIFTLFDLFNHKEEDLLKIEHF---QLEDIKKILGI 321

Query: 313 MGLFLGMNL 321
           +  +  + L
Sbjct: 322 LAKYFALYL 330


>gi|242910197|ref|YP_002970676.1| RNA polymerase a-subunit [Alsophila spinulosa]
 gi|218454866|gb|ACK77203.1| RNA polymerase a-subunit [Alsophila spinulosa]
          Length = 338

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 80/298 (26%), Positives = 150/298 (50%), Gaps = 26/298 (8%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           +  P  RG  +T+G A+RR L+  + GA+IT  + +GV+HE S+I G+ E + DI +N+K
Sbjct: 33  VISPFKRGQVNTVGIAMRRALLEEVGGASITCAKFEGVIHEYSTITGIQETIHDISVNLK 92

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
               +   +  K   +   GP  VTAGD      +++++    I  +     V +E  + 
Sbjct: 93  ETVPRSDSNDSKEAFLSVTGPKRVTAGDTSLPPSVKIIDDSQYIVTITQPISVNIESRIE 152

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE---SAREGQVLDYDKLSMTIDT 207
           K  GY   + +   +   G   +DA+  P++ V+Y+V    S RE + + +    + I T
Sbjct: 153 KDCGYRIEEFNGYRD---GEFPVDAVPMPVRNVNYSVHPFGSGREMREISF----IEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEE---PKKEVKEDINVKSLPFNPALL------- 257
           +GS T  +++  AS+ L D L  F++ +    P  E ++D +  ++  +  L+       
Sbjct: 206 NGSPTPNEALCEASKNLIDLLIPFLHMKHEDVPHFEDEQDSSDLTI-LSSQLIGVGESEG 264

Query: 258 -----KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                  +++LE   R+ NCL+   I  + DL+  +  D+L++ +FG+KS+ ++   L
Sbjct: 265 EVLRNTFIDQLESPARAFNCLKRAEIHTITDLLNHSREDLLKIKSFGKKSVDQVSRAL 322


>gi|289571691|ref|ZP_06451918.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis T17]
 gi|289545445|gb|EFD49093.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis T17]
          Length = 130

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 55/108 (50%), Positives = 80/108 (74%), Gaps = 4/108 (3%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T+
Sbjct: 16  DNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNP 130
           IILN+K  +L +S +  + VT++  K+GPG VTAGDI     + V NP
Sbjct: 76  IILNLK--SLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNP 121


>gi|115604965|ref|YP_784418.1| RNA polymerase alpha subunit [Drimys granadensis]
 gi|122164409|sp|Q06GW5|RPOA_DRIGR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|112032693|gb|ABH88328.1| RNA polymerase alpha subunit [Drimys granadensis]
          Length = 339

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 84/309 (27%), Positives = 156/309 (50%), Gaps = 21/309 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A  +G A+RR L+  + G  IT  + D + HE S+I G+ E +  I++N+
Sbjct: 32  FILSPLMKGQADMIGIAMRRALLGEIEGTCITRAKSDKIPHEYSTIVGIEESVHQILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +IF RGP  VTA DI +   +++++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTCDASIFVRGPRCVTAQDIISPPSVKMVDTTQHIASLTEPIDLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   K    + D    I I+A+  P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERDRGYR-MKTPNNDQDGSYPIPIEAVSMPVRNANHSIHSYGNGNE-KQEILFLEIWTNG 209

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF-----NPALLKK----- 259
           S+T ++++  AS  L D    F++ EE    +++ +N  +LPF       A L+K     
Sbjct: 210 SLTPKEALHEASHNLIDLFIPFLHGEEEDINLEDSLNRGTLPFFTFQDKLANLRKNKKAI 269

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +++ EL  R+ NCL+  NI  + DL+  ++ D++R+ +     + ++K +L  +
Sbjct: 270 ALECIFIDQSELPPRTYNCLKRSNIHTLLDLLSNSQEDLMRIEHL---RIEDVKRILDIL 326

Query: 314 GLFLGMNLP 322
                ++LP
Sbjct: 327 QKHFTIDLP 335


>gi|262400792|gb|ACY66281.1| RNA polymerase alpha subunit [Brassica napus]
          Length = 327

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 80/297 (26%), Positives = 150/297 (50%), Gaps = 20/297 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + H+ S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENIPHDYSNIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
             I LK +    +   I  +GPG +TA DI     +E+++    I  L     + + L +
Sbjct: 92  NEIVLKSNLYGTRNALICVQGPGYITARDIVLPPSVEIVDNTQHIATLTEPINLCIGLKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  E+       IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGYSLKMSNNFEDRS---YPIDAVFMPVQNANHSIHSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA------LLKK---- 259
           S+T ++++  ASR L +    F++ EE    ++ + +  +LP  P       L KK    
Sbjct: 208 SLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQVTLPLFPFHNRLVNLRKKKKEL 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++LEL  R  NCL+  NI  + DL+  ++ D+++M +F  + + +I  +L
Sbjct: 268 AFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLIKMEHFHIEDVKKILDIL 324


>gi|309322228|ref|YP_003934306.1| RNA polymerase alpha subunit [Monsonia speciosa]
 gi|197131696|gb|ACH47366.1| RNA polymerase alpha subunit [Monsonia speciosa]
 gi|300069321|gb|ADJ66441.1| RNA polymerase alpha subunit [Monsonia speciosa]
          Length = 331

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 81/293 (27%), Positives = 150/293 (51%), Gaps = 17/293 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A  +G A+RR L+  + G  IT  +   + HE ++I G+ E + +I++N+
Sbjct: 32  FILSPLKKGQADIIGIAMRRALLGEIEGTCITHAKFAKIPHEYTTIAGIKESIYEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  RGP  VTA DI       +++    I  L       + L +
Sbjct: 92  KEIVLRSNLYGTRDASICVRGPRDVTAQDIILPPSTAIVDNTQHIFTLTEPIDFCVGLKI 151

Query: 150 SKGHGY---VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            +G GY   +P       +D      IDA++ P++ V++++ S   G    ++ L + I 
Sbjct: 152 ERGRGYSIKIPMPTDLFHHD--SAYPIDAVFMPVRNVNHSIHSYERGS---HEMLFLEIW 206

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKK---EVKEDINVKSLPFNPALLKKV--- 260
           T+GS+T ++++  ASR L + L  F++ EE      E  ++ + + LP +   LK +   
Sbjct: 207 TNGSLTPKEALREASRKLINLLMPFLHAEEENFYLVENNQNQDTEELPIDLCGLKDIYID 266

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           + +EL  R  NCL+   I  + DL+ +   D+++M +F ++   +I+GV+  +
Sbjct: 267 QLVELPPRFYNCLKRSGIHTVMDLLDKNRDDLMKMTHFRQE---DIEGVMNIL 316


>gi|323148861|ref|YP_004221953.1| RNA polymerase alpha subunit [Erodium carvifolium]
 gi|316926325|gb|ADU58178.1| RNA polymerase alpha subunit [Erodium carvifolium]
          Length = 324

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 79/288 (27%), Positives = 152/288 (52%), Gaps = 12/288 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A  +G A+RR L+  L G  IT  +   + HE ++I G+ E + +I++N+
Sbjct: 32  FILSPLKKGQADIIGIAMRRALLGELEGTCITHAKFGKIPHEYTTIVGIQESVYEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL-NPDHVICNLD-VDAVVRMEL 147
           K I L+ +    +  +I  RGP  VTA DI     + ++ N  H++   + +D  V +++
Sbjct: 92  KEIVLRSNLYGTRGASICVRGPRDVTAQDIVLPPSVAIVDNTQHIVTLTEPIDFCVGLQI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+         + ND  G   IDA++ P+K V++++ S   G    ++ L + I T
Sbjct: 152 ERNRGYSIKIPTATNSHND--GGYPIDAVFMPVKNVNHSIHSYENG---SHEMLFLEIWT 206

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--VKSLPFNPALLKKV---EE 262
           +GS+T ++++  ASR L +    F+N EE    ++ + N   + L  +   LK +   + 
Sbjct: 207 NGSLTPKEALREASRKLINLFIPFLNAEEENSHLENNQNEHTEELSRDFCGLKDIYIDQL 266

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           +EL  R  N L+G  I  + DL+ +   D++++ +F ++ + ++  +L
Sbjct: 267 VELPPRLYNSLKGSGIHTVMDLLDKNPDDLMKITHFRQEDVEKVMNIL 314


>gi|66876504|gb|AAY58043.1| RpoA [Cuscuta europaea]
          Length = 329

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 83/307 (27%), Positives = 148/307 (48%), Gaps = 27/307 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT V+ +   HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLIKGQADTIGIAMRRALLGEIEGTCITRVKSEKASHEYSTIGGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  +GP  VTA DI     +++++    I  L       + L +
Sbjct: 92  KEIVLRSNLYESCDASICIKGPRHVTAQDIILPPHVQIVDNTQHIAWLTEPIDFFIGLKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES-AREGQVLDYDKLSMTIDTD 208
            +  GY        ++   G   IDAL+ P++  ++++ S   E Q    + L + I T+
Sbjct: 152 ERNRGYFNKVDLHFDD---GSYPIDALFMPVQNANHSIHSYGNEKQ----EILFLEIWTN 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPK---KEVKEDINVKSLPFNPALLKK------ 259
           GS+T ++++  ++RIL D    F   EE      + K  I +  L F   +         
Sbjct: 205 GSLTPKEALHESARILIDFFIPFFQMEEENLYLADAKHTIXLPPLIFYNKVTTLIKKKKK 264

Query: 260 -------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                  +++LE   +  NCL+  NI  + DL  + + D+L++ +F    L +IK +LG 
Sbjct: 265 LSLKLIFIDQLEFPPKIYNCLKKSNIFTLFDLFNQKQEDLLKIEHF---QLEDIKHILGI 321

Query: 313 MGLFLGM 319
           +G +  +
Sbjct: 322 LGKYFAL 328


>gi|165910445|gb|ABY73977.1| RNA polymerase alpha subunit [Cuscuta europaea]
          Length = 329

 Score =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 83/307 (27%), Positives = 148/307 (48%), Gaps = 27/307 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT V+ +   HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLIKGQADTIGIAMRRALLGEIEGTCITRVKSEKASHEYSTIGGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  +GP  VTA DI     +++++    I  L       + L +
Sbjct: 92  KEIVLRSNLYESCDASICIKGPRHVTAQDIILPPHVQIVDNTQHIAWLTEPIDFFIGLKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES-AREGQVLDYDKLSMTIDTD 208
            +  GY        ++   G   IDAL+ P++  ++++ S   E Q    + L + I T+
Sbjct: 152 ERNRGYFNKVDLHFDD---GSYPIDALFMPVQNANHSIHSYGNEKQ----EILFLEIWTN 204

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPK---KEVKEDINVKSLPFNPALLKK------ 259
           GS+T ++++  ++RIL D    F   EE      + K  I +  L F   +         
Sbjct: 205 GSLTPKEALHESARILIDFFIPFFQMEEENLYLADAKHTIPLPPLIFYNKVTTLIKKKKK 264

Query: 260 -------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                  +++LE   +  NCL+  NI  + DL  + + D+L++ +F    L +IK +LG 
Sbjct: 265 LSLKLIFIDQLEFPPKIYNCLKKSNIFTLFDLFNQKQEDLLKIEHF---QLEDIKHILGI 321

Query: 313 MGLFLGM 319
           +G +  +
Sbjct: 322 LGKYFAL 328


>gi|197131686|gb|ACH47361.1| RNA polymerase alpha subunit [Erodium chrysanthum]
          Length = 329

 Score =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 81/292 (27%), Positives = 144/292 (49%), Gaps = 18/292 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A  +G A+RR L+  + G  IT  Q + + HE ++  G+ E + +I++N+
Sbjct: 32  FILSPLKKGQADIIGIAMRRALLGEIEGTCITHAQFEKIPHEYTTRVGIQESVYEIVMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ S    +  +I  RGP  VTA DI     + +++    I  L       + L +
Sbjct: 92  KEIVLRSSLYGTRDASICVRGPRDVTAQDIILPPSVSIVDNTQHIVTLTEPIEFCVALQI 151

Query: 150 SKGHGY-----VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
            +  GY      P   H     P     IDA++ P+K V++++ S   G    ++ L   
Sbjct: 152 ERNRGYSLRIPTPNNSHDERGYP-----IDAVFMPVKNVNHSIHSYENG---SHEMLFFE 203

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--VKSLPFNPALLKKV-- 260
           I T+GS+T ++++  ASR L +    F++ EE K   + + N     L  +   LK++  
Sbjct: 204 IWTNGSLTPKEALREASRKLINLFIPFLHAEEEKPHFENNQNEPRDELLVDLCELKEIYI 263

Query: 261 -EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            + +ELS R  N L+G  I  + DL+ +   D+L++ +F ++ +  +  +L 
Sbjct: 264 DQLVELSPRLYNILKGSGIHTVMDLLDKNPDDLLKLRHFRQEDVERVMNILN 315


>gi|218755235|ref|ZP_03534031.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis GM 1503]
          Length = 118

 Score =  106 bits (264), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 52/97 (53%), Positives = 76/97 (78%), Gaps = 4/97 (4%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T+
Sbjct: 16  DNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTE 75

Query: 85  IILNIKGINLKMSGDSHKRVTIF--KRGPGVVTAGDI 119
           IILN+K  +L +S +  + VT++  K+GPG VTAGDI
Sbjct: 76  IILNLK--SLVVSSEEDEPVTMYLRKQGPGEVTAGDI 110


>gi|269991336|emb|CAX12520.1| DNA-directed RNA polymerase alpha chain [Fucus vesiculosus]
          Length = 368

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 84/343 (24%), Positives = 163/343 (47%), Gaps = 62/343 (18%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +   L +   +T+GN LRR L+S+L G  I  V+  G+ +E + ++GV EDL +IILN+
Sbjct: 24  FVFTALEKSQGNTIGNVLRRTLLSNLYGFRIVGVRFAGINNEFALLEGVREDLFEIILNL 83

Query: 90  KGINL----KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           K I +    ++    + R+ ++  GP V+TAG ++  N++++LNP++ +  +  ++++ +
Sbjct: 84  KEIIILNSNRIDQTCYGRLKVY--GPAVITAGSLELPNNVKILNPNNHLLTISDESLIEI 141

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS-YTVESAREGQVLDYDKLSMT 204
           E+ +  G  Y+ AK  + E   +  I ID+ ++P+ KV+ Y +   ++G+ ++ ++L + 
Sbjct: 142 EVKIEAGKSYILAKDQKLEG-ALDFIPIDSNFAPVLKVNWYIISLPQDGESIN-EELHLE 199

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFE------EPKKEVKEDINVKSLPF------ 252
           I T+G++    ++  A  ++   L      E        K+E+ +  ++KSL +      
Sbjct: 200 IYTNGTLLPHQALLQARTMIGYMLSPISTIEFSCLDTYEKEEIHDTNHIKSLTYITDPIS 259

Query: 253 ---------------------------------NPALLKKVEELE--------LSVRSTN 271
                                               L+K + +LE        LS R  N
Sbjct: 260 RDQNKTVLRSNLIKNKSKFEKINLDKINQVSIDEQKLIKNIVDLEYESLKNLGLSNRIIN 319

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
            L   NI ++ DLI    + ++ +   G KS+ EIK  L    
Sbjct: 320 ALNKVNINFISDLIHYPSSSLINIVGLGPKSVEEIKNKLNQFS 362


>gi|240047283|ref|YP_002960671.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma conjunctivae
           HRC/581]
 gi|239984855|emb|CAT04845.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma conjunctivae]
          Length = 332

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 84/304 (27%), Positives = 155/304 (50%), Gaps = 21/304 (6%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           +PL RG  +T+GNALRR ++SS+  A++ A++I  + HE S +  V ED+  I+ N+K I
Sbjct: 27  KPLERGLGNTIGNALRRTILSSVSSASVFAIKIANIDHEFSVLDNVVEDVVSILNNLKKI 86

Query: 93  NLK-----MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
             +        D  ++V+      G + A DI     +E++N D  I ++     ++ E+
Sbjct: 87  RFRYHEELFDNDQIQKVSFSGDKAGNIYAKDIDNTGGLEIVNQDQYIASVGKVGALKFEM 146

Query: 148 TVSKGHGYVPAKHHRT---------ENDPIG-LITIDALYSPIKKVSYTVESAREGQVLD 197
            +  G G+   + ++          ++D +G +I +D+ +SP+ KV Y          + 
Sbjct: 147 FIIGGKGFTDFETNKKRVSDLAGKLQSDLLGTIIAVDSDFSPVVKVHYEANELNSSNPIV 206

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
            ++L + + TDG+I  +D++A A++IL   L +  N E    ++ ++   +S  ++    
Sbjct: 207 EERLVLNLKTDGTIFAKDALAEAAKILIAHLQLVSNTENL-DQIADNFFEES-RYHEEQP 264

Query: 258 KK----VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           KK    +  L+LSVRS N LR      + D+   T+ ++  + N G+KS+ EI   L   
Sbjct: 265 KKNLIDLSALDLSVRSLNALRRAQYYKVSDIQDLTQEELENIKNLGKKSVQEILDKLKEQ 324

Query: 314 GLFL 317
           G+ L
Sbjct: 325 GIEL 328


>gi|139388942|ref|YP_001123669.1| RNA polymerase alpha subunit [Lepidium virginicum]
 gi|158513983|sp|A4QLD8|RPOA_LEPVR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134286872|dbj|BAF50493.1| RNA polymerase alpha subunit [Lepidium virginicum]
          Length = 327

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 77/299 (25%), Positives = 156/299 (52%), Gaps = 24/299 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + H+ S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENIPHDYSNIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL-NPDHVICNLD-VDAVVRMEL 147
             I L+ +    +   I  +GPG +TA DI     +E++ N  H+   ++ +D  + +++
Sbjct: 92  NEIVLRSNLYGTRNALICVQGPGYITAQDIILPPSVEIIDNTQHIATLMEPIDLCIGLKI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+    + +    + P     IDA++ P++  ++++ S   G     + L + I T
Sbjct: 152 ERNRGYSLKMSNNFEDRSYP-----IDAVFMPVQNANHSIHSYGNGNE-KQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA------LLKK-- 259
           +GS+T ++++  ASR L +    F++ EE    ++ + +  +LP  P       L KK  
Sbjct: 206 NGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQVTLPLFPFHNRLVNLRKKKK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                   +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F  + + +I  +L
Sbjct: 266 ELAFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLIKIEHFHIEDVKKILDIL 324


>gi|309322147|ref|YP_003934062.1| RNA polymerase alpha subunit [Geranium palmatum]
 gi|197131694|gb|ACH47365.1| RNA polymerase alpha subunit [Geranium palmatum]
 gi|300069240|gb|ADJ66361.1| RNA polymerase alpha subunit [Geranium palmatum]
          Length = 329

 Score =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 79/297 (26%), Positives = 154/297 (51%), Gaps = 13/297 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A  +G A+RR L+  + G  IT  + D + HE +++ G+ E + +I++N+
Sbjct: 32  FILSPLKKGQADIIGIAMRRALLGEIEGTCITHAKFDKIPHEYTTLVGIQESIYEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL-NPDHVICNLD-VDAVVRMEL 147
           K I L+      +  +I  RGP  VTA DI       ++ N  H++   + +D  V +++
Sbjct: 92  KEIVLRSHLYGTRDASICVRGPRDVTAQDIILPTSATIVDNTQHIVTITEPIDFCVGLQI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+ ++        +D  G   ID+++ P+K V++++ S   G    +  L + I T
Sbjct: 152 ERNRGY-FIQIPMLTNLHDDRGY-PIDSVFMPVKNVNHSIHSYENGI---HAMLFLEIWT 206

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--VKSLPFNPALLKKV---EE 262
           +GS+T ++++  ASR L +    F++ EE     + + N     LP +   LK +   + 
Sbjct: 207 NGSLTPKEALREASRKLSNLFIPFLHAEEQNFHFENNQNEHTDELPIDFCALKDIYIDQL 266

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL-GTMGLFLG 318
           +EL  R  NCL+   I  + DL+ +   D++++ +F ++ + ++  +L  T+  FL 
Sbjct: 267 VELPARFYNCLKISGIHTVMDLLNKNTEDLMKITHFRQQDIEKVMHILNNTISQFLS 323


>gi|290489692|gb|ADD31230.1| RNA polymerase alpha subunit protein [Liquidambar styraciflua]
          Length = 338

 Score =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 82/315 (26%), Positives = 162/315 (51%), Gaps = 34/315 (10%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K + L+ +    +  +I  RGPG VTA DI +   +E+++    I +L   +D  + +++
Sbjct: 92  KEVVLRSNLYGTRDASICVRGPGYVTAQDIISPPSVEIVDNTQHIASLTEPIDLCIGLKM 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES---AREGQVLDYDKLSMT 204
             ++G+      + +  + P     IDA++ P++  ++++ S     E Q +    L + 
Sbjct: 152 ERNRGYRIKTPNNFQDRSYP-----IDAVFMPVRNANHSIHSYGNENEKQEI----LFLE 202

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPALLKK-- 259
           I T+GS+T ++++  ASR L D    F++ EE    ++++ +   LP   F+  L K   
Sbjct: 203 IWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLEDNQHKTILPLFTFHDRLAKLKE 262

Query: 260 ------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                       +++ EL  R   CL+  NI  + DL+   + D++++ +F    + ++K
Sbjct: 263 KTKKKKALKSIFIDQSELPPRIYTCLKRSNIHTLLDLLNNNQEDLMKIEHF---RIEDVK 319

Query: 308 GVLGTMGLFLGMNLP 322
            +LG +     ++LP
Sbjct: 320 KILGILEKHFAIDLP 334


>gi|139389128|ref|YP_001123846.1| RNA polymerase alpha subunit [Nasturtium officinale]
 gi|158513997|sp|A4QLW5|RPOA_NASOF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134287051|dbj|BAF50670.1| RNA polymerase alpha subunit [Nasturtium officinale]
          Length = 327

 Score =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 77/299 (25%), Positives = 154/299 (51%), Gaps = 24/299 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + H+ S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENIPHDYSNIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
             I L+ +    +   I  +GPG +TA DI     +E+++    I  L   +D  + +++
Sbjct: 92  NEIVLRSNLYGTRNALICVQGPGYITARDIILPPSVEIIDNTQHIATLTEPIDLCIGLKI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+    + +    + P     IDA++ P++  ++++ S   G     + L + I T
Sbjct: 152 ERNRGYSLKMSNNFEDRSYP-----IDAVFMPVQNANHSIHSYGNGNE-KQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA------LLKK-- 259
           +GS+T ++++  ASR L +    F++ EE    ++ + +  +LP  P       L KK  
Sbjct: 206 NGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQVTLPLFPFHNRLVNLRKKKK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                   +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F  + + +I  +L
Sbjct: 266 ELAFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLIKIEHFHIEDVKKILDIL 324


>gi|114107078|ref|YP_740234.1| RNA polymerase alpha subunit [Liriodendron tulipifera]
 gi|122239940|sp|Q0G9I7|RPOA_LIRTU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|113201026|gb|ABI32541.1| RNA polymerase alpha subunit [Liriodendron tulipifera]
          Length = 337

 Score =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 86/312 (27%), Positives = 160/312 (51%), Gaps = 29/312 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT V+ + V +E  +I G+ E + +I++N+
Sbjct: 32  FILAPLMKGQADTIGIAMRRALLGEIEGTCITRVKSEKVPNEYYTIVGIEESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+      +  +I  RGP  VTA DI     +E+++    I +L     + +EL +
Sbjct: 92  KEIVLRSHLYGTRDASICVRGPRYVTAQDIIPPPSVEIVDTTQHIASLTEPIDLCIELQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA---REGQVLDYDKLSMTID 206
            +  GY   +     N   G   IDA+  P++  ++++ S     E Q +    L + I 
Sbjct: 152 ERDRGY---RMKTPNNYQDGSYPIDAVSMPVRNANHSIHSYGNRNEKQEI----LFLEIW 204

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPAL--LKK-- 259
           T+GS+T ++++  ASR L D    F++ EE    ++++ N  ++P   F+  L  ++K  
Sbjct: 205 TNGSLTPKEALHEASRNLIDLFIPFLHAEEQDIVLEDNPNRFTVPLFTFHDRLANIRKNK 264

Query: 260 ---------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                    +++ EL  R+ NCL+  NI  + DL+  ++ D++R+ +F    + ++K +L
Sbjct: 265 KGIALKCIFIDQSELPPRTYNCLKRSNIHTLLDLLSNSQEDLMRIEHF---RIEDVKQIL 321

Query: 311 GTMGLFLGMNLP 322
             +     ++LP
Sbjct: 322 DILQKHFTIDLP 333


>gi|108796735|ref|YP_636498.1| alpha subunit of RNA polymerase [Zygnema circumcarinatum]
 gi|122226721|sp|Q32RM8|RPOA_ZYGCR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|61393719|gb|AAX45861.1| alpha subunit of RNA polymerase [Zygnema circumcarinatum]
          Length = 356

 Score =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 80/315 (25%), Positives = 150/315 (47%), Gaps = 46/315 (14%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G A T+G A+RR L+  +    IT+  + G  HE S++KG+ E + DI+LN+K I 
Sbjct: 33  PLFPGQAITIGTAIRRALLGEVHSTCITSAYVVGASHEYSTLKGIRESIHDILLNLKDIV 92

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
            K      +   +   GPG+VTA  I+    ++V++    I  L++   + + +T+    
Sbjct: 93  FKSDTLERQEGILLFNGPGIVTAQHIKLPPVVQVVDNTQYIARLEMPTSIEIHITLENTK 152

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
                    T     G   +DA   P++ ++Y++ S  EG  +  + L + + T+GS+T 
Sbjct: 153 TCTSLNTMPTTK---GRFILDAALKPVRNMNYSIHSLGEGD-MRQEMLVLEVWTNGSLTP 208

Query: 214 EDSVALASRILQDQLGMFINFE---EPKKEV----------KEDINVKSL---------- 250
           ++ ++ AS+ L D L   +  E   + K+ +           E++N+  +          
Sbjct: 209 QEVISQASQNLNDLLKPLLKVERYFQAKQNIHKKRMFTPTQSENLNMDQIEMIGGNKLID 268

Query: 251 -PFNPA--------------LLK----KVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
            P  PA              L+      +++L++SVR++NCL+   I  +  L+  T+ D
Sbjct: 269 QPLLPADSHLNSSLSLNIDNLVHLEGISIDDLQISVRASNCLKKVGIYTIRQLLSYTQQD 328

Query: 292 MLRMANFGRKSLVEI 306
           + ++ N G+KS+ +I
Sbjct: 329 LFQIKNLGKKSVEQI 343


>gi|139388126|ref|YP_001123318.1| RNA polymerase alpha subunit [Barbarea verna]
 gi|158513955|sp|A4QKD7|RPOA_BARVE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134286517|dbj|BAF50142.1| RNA polymerase alpha subunit [Barbarea verna]
          Length = 327

 Score =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 77/299 (25%), Positives = 154/299 (51%), Gaps = 24/299 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + H+ S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENIPHDYSNIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
             I L+ +    +   I  +GPG +TA DI     +E+++    I  L   +D  + +++
Sbjct: 92  NEIVLRSNLYGTRNALICVQGPGYITARDIILPPSVEIIDNTQHIATLTEPIDLCIGLKI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+    + +    + P     IDA++ P++  ++++ S   G     + L + I T
Sbjct: 152 ERNRGYSLKMSNNFEDRSYP-----IDAVFMPVQNANHSIHSYGNGNE-KQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA------LLKK-- 259
           +GS+T ++++  ASR L +    F++ EE    ++ + +  +LP  P       L KK  
Sbjct: 206 NGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQVTLPLFPFHNRLVNLRKKKK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                   +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F  + + +I  +L
Sbjct: 266 EQGFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLIKIEHFHIEDVKKILDIL 324


>gi|158564066|sp|Q06RA0|RPOA_JASNU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
          Length = 355

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 76/291 (26%), Positives = 144/291 (49%), Gaps = 29/291 (9%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+   +RR L+  + G  IT V+   V HE S+I G+ E + +I++N 
Sbjct: 32  FILSPLRKGQADTIAIGIRRALLGEIEGTCITRVKSKNVPHEYSTIAGIQESVHEILMNF 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGPG VTA DI     +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTCDASICVRGPGYVTAQDIILPPYVEIVDNTQHIASLTEPIDLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY+    H +++   G   IDA++ P++  ++++ S   G    ++ L + I T+G
Sbjct: 152 ERNRGYLMKMPHNSQD---GSYPIDAVFMPVRNANHSIHSYGSGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK---------- 259
           S+T ++++  A R L D    F++ EE    +++  N  ++P +P               
Sbjct: 208 SLTPKEALHEACRNLIDLFIPFLHKEEETSPLED--NHHTVPLSPLTFHDKADKLRKRKK 265

Query: 260 ------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                       +++ EL  +  NCL+G N+  + DL+ +++ D+++M + 
Sbjct: 266 EIKKKIALKSIFIDQSELP-KVYNCLKGSNLYTLLDLLNKSQEDLMKMEHL 315


>gi|228017206|gb|ACP52026.1| RNA polymerase alpha subunit [Pinus leiophylla var. chihuahuana]
          Length = 335

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 78/285 (27%), Positives = 141/285 (49%), Gaps = 20/285 (7%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           T+G A+RR L+  + G  IT V+++ + HE S+I G+ E + DI++N+K I L+      
Sbjct: 44  TIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEESVHDILMNLKEIVLRSDSYGI 103

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           +  +I+  GP  VTA DI     +++++    I  L       + L + K  GY+    H
Sbjct: 104 REASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSITSDIRLQIEKNRGYII---H 160

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
              N   G+  IDA++ P++  +Y++ S   G  +  + L + I T+G +T  +++  AS
Sbjct: 161 SPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEIR-EVLFLEIWTNGGLTPREALYEAS 219

Query: 222 RILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPAL-------------LKKVEELEL 265
           R L D    F++ EE   +    K+  N+   P +  L             L  +++L  
Sbjct: 220 RNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHLLTDTGETKEKIAFQLIFIDQLXX 279

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                  LR  NI  + DL+  +  D++R+ +FG++S+ ++  VL
Sbjct: 280 XXXXXXXLRRANIHTLLDLLNYSREDLMRIEHFGKESVEQVLEVL 324


>gi|207092984|ref|ZP_03240771.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 235

 Score =  104 bits (260), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 73/231 (31%), Positives = 123/231 (53%), Gaps = 4/231 (1%)

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
           +GP  + A D+ + + IE++NP+  +  ++ DA +   L + KG GYVP+++ R E  P 
Sbjct: 5   KGPMELRARDLNSEH-IEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPE 62

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           G + +D  ++PIKKV Y +E+       +Y+K+   I+TDG I    +   A +++  QL
Sbjct: 63  GYMPLDGSFTPIKKVVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQL 122

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
           G+F   E P   ++   +         L  K+E + LS R  NCL    I Y+G+L+  +
Sbjct: 123 GVF--GERPIANMEYSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMS 180

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           E ++  + N G+KS  EI   L  +G  +G  L     ES+++  +K EDK
Sbjct: 181 EEELKGVKNMGKKSYDEIAEKLNDLGYPVGTELSLEQRESLKKRLEKLEDK 231


>gi|213612396|ref|ZP_03370222.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E98-2068]
          Length = 117

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 55/118 (46%), Positives = 78/118 (66%), Gaps = 3/118 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADI 115


>gi|139389982|ref|YP_001123582.1| RNA polymerase alpha subunit [Draba nemorosa]
 gi|158513976|sp|A4QL51|RPOA_DRANE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134286784|dbj|BAF50406.1| RNA polymerase alpha subunit [Draba nemorosa]
          Length = 327

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 76/299 (25%), Positives = 154/299 (51%), Gaps = 24/299 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + H+ S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENIPHDYSNIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL--DVDAVVRMEL 147
             I L+ +    +   I  +GPG +TA DI     +E+++    I  +   +D  + +++
Sbjct: 92  NEIVLRSNLYGTRNALICVQGPGYITARDIILPPSVEIVDNTQHIATVTESIDLCIGLKI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+    + +    + P     IDA++ P++  ++++ S   G     + L + I T
Sbjct: 152 ERNRGYSLKMSNNFEDRSYP-----IDAVFMPVQNANHSIHSYGNGNG-KQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA------LLKK-- 259
           +GS+T ++++  ASR L +    F++ EE    ++ + +  +LP  P       L KK  
Sbjct: 206 NGSLTPKEALHEASRNLINLFIPFLHVEEETFHLENNQHQVTLPLFPFHNRLVNLRKKKK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                   +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F  + + +I  +L
Sbjct: 266 ELAFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLIKIEHFHIEDVKKILDIL 324


>gi|68164836|ref|YP_247632.1| RNA polymerase alpha subunit [Cucumis sativus]
 gi|75317292|sp|Q4VZK3|RPOA_CUCSA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|67511431|emb|CAJ00791.1| RNA polymerase alpha chain [Cucumis sativus]
 gi|74027132|gb|AAZ94682.1| RNA polymerase alpha subunit [Cucumis sativus]
 gi|115432835|gb|ABI97448.1| RNA polymerase alpha subunit [Cucumis sativus]
 gi|115498335|gb|ABI98777.1| RNA polymerase alpha subunit [Cucumis sativus]
          Length = 333

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 80/288 (27%), Positives = 147/288 (51%), Gaps = 24/288 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G   T+G A+R+ L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQGDTIGIAMRKALLGEIEGTCITRAKSEKIPHEYSTIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GPG VTA DI     +E+++    I NL     + +EL +
Sbjct: 92  KEIVLRSNLYGTRDASICVKGPGCVTAQDIILPPSVEIVDNTQHIANLMEPINLCIELKI 151

Query: 150 SKGHGYVPAKHHRTEND-PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
            +  GY    H +T N+       +DA++ P++ V++++ S   G     + L + I T+
Sbjct: 152 ERNRGY----HIQTPNNFQDASYPMDAIFMPVRNVNHSIHSYVNGNE-KQEILFLEIWTN 206

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPK-----KEVKEDINVKSLPFNPALLKK---- 259
           GS+T ++++  ASR L D    F++ EE K     K  K+ + +    F+  L K     
Sbjct: 207 GSLTPKEALHEASRNLIDLFIPFLHAEEEKENFHLKNNKKKVTLPLFTFHEKLAKLRKKK 266

Query: 260 ---------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                    +++ EL  R  NCL+  NI  + DL+  +  +++++ +F
Sbjct: 267 KEIALKYIFIDQSELPPRIYNCLKRCNIHTLFDLLNNSPDELMKIKHF 314


>gi|116335037|ref|YP_802532.1| RNA polymerase alpha subunit [Candidatus Carsonella ruddii PV]
 gi|123126152|sp|Q05FK5|RPOA_CARRP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116235318|dbj|BAF35166.1| RNA polymerase alpha subunit [Candidatus Carsonella ruddii PV]
          Length = 322

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 83/294 (28%), Positives = 146/294 (49%), Gaps = 8/294 (2%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
           R+++  E     F  +LGN ++RV+  +     I  ++I  +  E   + G+ E+   I+
Sbjct: 22  RSIIRIETFNNSFCDSLGNFIKRVIFLTTNSYKIIYLKIYKIKSEFYDLPGIIENTQTIL 81

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR-- 144
            N+  I +K++ D+   + I K+GP ++TA DI +  +I + NP+ +I N+  + V    
Sbjct: 82  KNLDNIIIKINNDNVANLIIKKKGPCIITAKDIFSDKNITIFNPNKIIANVSNNIVFYCI 141

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           M+   S    Y   +  + +     +I ++   SPI  ++Y +      + L   KL   
Sbjct: 142 MKCVNSLFKNYTD-EFFQFKIFKENIIFLNNFKSPIISLNYYINKKIFNKKLK--KLFFD 198

Query: 205 IDTDGSITGEDSVALASRILQ---DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           I+T+GSI   D        ++   D +  FI F++ KK   E  N  +L  N   L  + 
Sbjct: 199 IETNGSIKPVDCFKNCIFYIKKYFDLIFSFIGFKKYKKINVEKKNNLNLKINSVYLNSIN 258

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
            L+LS+RS NCL+  NI  +GDLI+ ++ +++ + N G+KS  EI   L   GL
Sbjct: 259 NLKLSIRSLNCLKNNNIFLIGDLIKISKNNLINIPNLGKKSYNEILNSLKNFGL 312


>gi|254701950|ref|ZP_05163778.1| DNA-directed RNA polymerase subunit alpha [Brucella suis bv. 5
          str. 513]
          Length = 70

 Score =  103 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 50/71 (70%), Positives = 57/71 (80%), Gaps = 2/71 (2%)

Query: 1  MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
          MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1  MIQKNWQELIKPNKVDFITHGSR--THATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61 TAVQIDGVLHE 71
          TAVQIDGVLHE
Sbjct: 59 TAVQIDGVLHE 69


>gi|115350008|ref|YP_764409.1| alpha subunit of RNA polymerase [Stigeoclonium helveticum]
 gi|122165139|sp|Q06SF7|RPOA_STIHE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|98990222|gb|ABF60189.1| alpha subunit of RNA polymerase [Stigeoclonium helveticum]
          Length = 517

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 56/126 (44%), Positives = 80/126 (63%), Gaps = 4/126 (3%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL  G   TL NALRR L+S L G AIT V+I+GV HE S++ GV E + DI+LN+K I 
Sbjct: 42  PLEVGQGITLANALRRALLSELNGLAITTVEIEGVSHEYSTLMGVRESVLDILLNLKQIV 101

Query: 94  LKMSGDSHKRVT---IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           LK S  S KR     I+ +GPGV+ AGDI   + I+ ++P+  I  L  D +++M++ + 
Sbjct: 102 LK-SKKSVKRAQTAYIYCQGPGVIRAGDIILPSSIQCVDPEQYIATLSSDGILKMKVIIR 160

Query: 151 KGHGYV 156
           +G  Y+
Sbjct: 161 QGKNYL 166


>gi|13518470|ref|NP_084829.1| RNA polymerase alpha subunit [Lotus japonicus]
 gi|22654080|sp|Q9BBQ4|RPOA_LOTJA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|13359011|dbj|BAB33228.1| RNA polymerase alpha subunit [Lotus japonicus]
          Length = 333

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 78/299 (26%), Positives = 152/299 (50%), Gaps = 22/299 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR+L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRILLGEMEGTCITRAKSEKISHEYSTIVGIQEPVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK +    +  +I  +GPG VTA +I     + +++    I N+     + + L +
Sbjct: 92  KEIVLKSNLYGIRDASICFKGPGYVTAQNIILPPSVVIVDNTQHIANVTEPIQLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   + +  +N   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERDRGY---RINTLKNFQDGSYNIDAIFMPVRNANHSIHSYVNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA-------------- 255
           S+T ++++  ASR L D    F++ EE K   + + +  +LP                  
Sbjct: 208 SLTPKEALYEASRNLIDLFIPFLHAEEEKLNFENNEHKVTLPLFTCHDLLAKTKLKKKKK 267

Query: 256 --LLKK--VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
               K   +++LEL  +  NCL+  NI  + +L+ +++ D++++ +F  + +  I  +L
Sbjct: 268 EIAFKSIFIDQLELPPKIYNCLKKSNIHTLLELLTKSKEDLMKIEHFRVEDVKHILDIL 326


>gi|154483161|ref|ZP_02025609.1| hypothetical protein EUBVEN_00862 [Eubacterium ventriosum ATCC
           27560]
 gi|149735969|gb|EDM51855.1| hypothetical protein EUBVEN_00862 [Eubacterium ventriosum ATCC
           27560]
          Length = 127

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 57/122 (46%), Positives = 84/122 (68%), Gaps = 4/122 (3%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFK 108
           ++SSL G+A++ ++IDGVLHE SS+ GV ED+T+I+LNIK + +K   + D  K   I  
Sbjct: 1   MLSSLPGSAVSQIKIDGVLHEFSSVPGVKEDVTEIVLNIKQLEIKNNSTTDEPKVAHIDV 60

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMELTVSKGHGYVPAKHHRTEND 166
            G  VVTA DIQ  +DIE+LNPD VI  L+   D+ + MEL ++KG GYV ++ ++ ++ 
Sbjct: 61  TGDCVVTAADIQVDSDIEILNPDLVIATLNGGADSKLSMELIITKGRGYVSSEKNKNDSL 120

Query: 167 PI 168
           PI
Sbjct: 121 PI 122


>gi|139389674|ref|YP_001123231.1| RNA polymerase alpha subunit [Arabis hirsuta]
 gi|158513635|sp|A4QK50|RPOA_ARAHI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134286429|dbj|BAF50055.1| RNA polymerase alpha subunit [Arabis hirsuta]
          Length = 337

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 77/299 (25%), Positives = 152/299 (50%), Gaps = 24/299 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + H+ S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENIPHDYSNIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL--DVDAVVRMEL 147
             I L+ +    +   I  +GPG +TA DI     +E+++    I  L   +D  + +++
Sbjct: 92  NEIVLRSNLYGARNAIICVQGPGYITARDIILPPSVEIIDNTQHIATLTESIDLCIGLKI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+           + P     IDA++ P++  ++++ S   G     + L + I T
Sbjct: 152 ERNRGYSLKILNTFEDRSYP-----IDAVFMPVQNANHSIHSYGNGNG-KQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA------LLKK-- 259
           +GS+T ++++  ASR L +    F++ EE    ++ + +  +LP  P       L KK  
Sbjct: 206 NGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHHVTLPLFPFHNRLVNLRKKKK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                   +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F  + + +I  +L
Sbjct: 266 ELAFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLIKIEHFHIEDVKKILDIL 324


>gi|119662855|emb|CAJ33220.1| RNA polymerase alpha subunit [Lactobacillus vaginalis]
          Length = 120

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 50/118 (42%), Positives = 77/118 (65%)

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D +IC++   A     LTV
Sbjct: 3   KGLALKLYAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLIICSVSEGATFHARLTV 62

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I T
Sbjct: 63  KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWT 120


>gi|253795635|ref|YP_003038731.1| putative DNA-directed RNA polymerase, alpha subunit [Candidatus
           Hodgkinia cicadicola Dsem]
 gi|253739943|gb|ACT34278.1| putative DNA-directed RNA polymerase, alpha subunit [Candidatus
           Hodgkinia cicadicola Dsem]
          Length = 228

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 62/189 (32%), Positives = 99/189 (52%), Gaps = 6/189 (3%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
           AHTL  ALRR LM+ + G A+  + +DG  H ++  +GV ED+  +  N   I  +    
Sbjct: 25  AHTLAVALRRTLMARVEGWAVVGLCVDGAAHALARAEGVIEDVLGVAANAARIVFEGECG 84

Query: 100 SHKRV-TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           S + V  + +   GVVTAG +     + V+N +  +C++    V R E  V++G GY+ A
Sbjct: 85  SRRVVKAVVRASAGVVTAGQLVLPEGLRVVNTNERVCSVGAGCVFRAEFVVARGVGYMRA 144

Query: 159 KHHRTENDPI--GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
              R     +  G   +DA +SP+K+VSY V SA + +    D+  + I+T+G + G  +
Sbjct: 145 AQARARWSRVLAGYTVVDAHFSPVKRVSYKVSSAEDDR--SCDRAQLVIETNG-VDGAHA 201

Query: 217 VALASRILQ 225
           V  A R L 
Sbjct: 202 VVDACRELS 210


>gi|139389296|ref|YP_001123062.1| RNA polymerase alpha subunit [Aethionema grandiflorum]
 gi|158513623|sp|A4QJN1|RPOA_AETGR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134286258|dbj|BAF49886.1| RNA polymerase alpha subunit [Aethionema grandiflorum]
          Length = 333

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 76/297 (25%), Positives = 150/297 (50%), Gaps = 20/297 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + H+ S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEMEGTCITRAKSENIPHDYSNIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           + I L+ +        I  +GPG +TA DI     +E+++    I  L     + + L +
Sbjct: 92  QEIVLRSNLYGTCNALICVQGPGYITARDIILPPSVEIMDNTQHIATLTEPIDLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  E+   G   IDAL+ P++  ++++ S   G   + + L + I T+G
Sbjct: 152 ERNRGYSLKMPNPFED---GSYPIDALFMPVQNANHSIHSYGTGNE-NQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK---------- 259
           ++T ++++  ASR L +    F++ EE    ++ + +  +LP  P   +           
Sbjct: 208 NLTPKEALHEASRNLINLFIPFLHVEEETFYLENNEDKVTLPLFPFHNRLVKLRKKKKEL 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F  + + +I  +L
Sbjct: 268 VFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLIKIEHFHIEDVKKILDIL 324


>gi|139390380|ref|YP_001122978.1| RNA polymerase alpha subunit [Aethionema cordifolium]
 gi|158513605|sp|A4QJE7|RPOA_AETCO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134286173|dbj|BAF49802.1| RNA polymerase alpha subunit [Aethionema cordifolium]
          Length = 333

 Score =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 75/299 (25%), Positives = 151/299 (50%), Gaps = 24/299 (8%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + H+ S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEMEGTCITRAKSENIPHDYSNIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           + I L+ +        I  +GPG +TA DI     +E+++    I  L   +D  + +++
Sbjct: 92  QEIVLRSNLYGTCNALICVQGPGSITARDIILPPSVEIIDNTQHIATLTEPIDLCIGLQI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             ++G+      H    + P     IDAL+ P++  ++++ S   G     + L + I T
Sbjct: 152 ERNRGYSLKMPNHFEDGSYP-----IDALFMPVQNANHSIHSYGTGNE-KQEILFLEIWT 205

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK-------- 259
           +G++T ++++  ASR L +    F++ EE    ++ + +  +LP  P   +         
Sbjct: 206 NGNLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHKVTLPLFPFHNRLVKLRKKKK 265

Query: 260 --------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                   +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F  + + +I  +L
Sbjct: 266 ELVFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLIKIEHFHIEDVKKILEIL 324


>gi|228311784|pdb|2JZB|A Chain A, Solution Structure Of The Complex Between E.Coli Nusa-Ar2
           And Rnap-Actd
          Length = 99

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 46/78 (58%), Positives = 60/78 (76%)

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
           F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL 
Sbjct: 19  FDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLA 78

Query: 312 TMGLFLGMNLPDWPPESI 329
           + GL LGM L +WPP SI
Sbjct: 79  SRGLSLGMRLENWPPASI 96


>gi|56554702|pdb|1XS9|D Chain D, A Model Of The Ternary Complex Formed Between Mara, The
           Alpha-Ctd Of Rna Polymerase And Dna
          Length = 84

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 46/80 (57%), Positives = 61/80 (76%)

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
           F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL 
Sbjct: 4   FDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLA 63

Query: 312 TMGLFLGMNLPDWPPESIEE 331
           + GL LGM L +WPP SI +
Sbjct: 64  SRGLSLGMRLENWPPASIAD 83


>gi|24158833|pdb|1LB2|B Chain B, Structure Of The E. Coli Alpha C-Terminal Domain Of Rna
           Polymerase In Complex With Cap And Dna
 gi|24158834|pdb|1LB2|E Chain E, Structure Of The E. Coli Alpha C-Terminal Domain Of Rna
           Polymerase In Complex With Cap And Dna
          Length = 84

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 46/78 (58%), Positives = 60/78 (76%)

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
           F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL 
Sbjct: 4   FDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLA 63

Query: 312 TMGLFLGMNLPDWPPESI 329
           + GL LGM L +WPP SI
Sbjct: 64  SRGLSLGMRLENWPPASI 81


>gi|255645616|gb|ACU23302.1| unknown [Glycine max]
          Length = 269

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 68/223 (30%), Positives = 122/223 (54%), Gaps = 4/223 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RRVL+  + G  IT V+++ + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRVLLGEIEGTCITRVKLEKIPHEYSTIIGIEESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GPG VTA DI     +E+++    I N+     + +EL +
Sbjct: 92  KEIVLRSNLYGTRDASICFKGPGYVTAQDIILPPSVEIVDNTQHIANVTEPVNLCIELKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +    +N   G   IDA + P++ V++++ S   G     + L + I T+G
Sbjct: 152 ERNRGY---RIKTLKNFQDGSYPIDATFMPVRNVNHSIHSYVNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           S+T ++++  ASR L D    F++ EE    ++ + +  +LP 
Sbjct: 208 SLTPKEALYEASRNLIDLFIPFLHAEEDNFNLENNQHKVTLPL 250


>gi|157830665|pdb|1COO|A Chain A, The Cooh-Terminal Domain Of Rna Polymerase Alpha Subunit
          Length = 98

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 46/80 (57%), Positives = 61/80 (76%)

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
           F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL 
Sbjct: 18  FDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLA 77

Query: 312 TMGLFLGMNLPDWPPESIEE 331
           + GL LGM L +WPP SI +
Sbjct: 78  SRGLSLGMRLENWPPASIAD 97


>gi|226968665|ref|YP_002808625.1| RNA polymerase alpha chain [Micromonas sp. RCC299]
 gi|226431143|gb|ACO55549.1| RNA polymerase alpha chain [Micromonas sp. RCC299]
          Length = 352

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 88/327 (26%), Positives = 149/327 (45%), Gaps = 50/327 (15%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++  PL  G   TLGN  RR+L++ L G AITA +++    E  ++ G+ E + +I LN+
Sbjct: 29  LVLGPLAPGQGVTLGNTFRRLLLNDLPGVAITAAKLNETRTEFMTLPGIRESVVEIFLNL 88

Query: 90  KGINLKMSGD----SHKRVTIFKR----------GPGVVTAGDIQTVNDIEVLNPDHVIC 135
           + I    +          +TI  R           P V+ AGD+Q    I  ++P   I 
Sbjct: 89  RDIVFFNTFPDVLAPQGTITISPRPQTDESKSFHTPRVICAGDMQLPEGITCVDPTQPIA 148

Query: 136 NL-DVDAVVRMELTVSKGHGY----VPAKHHRTENDPIGLI--------------TIDAL 176
            L + D    +   + +  GY     P + + T   P   I               ID  
Sbjct: 149 TLMNGDTAFNLTFILEQSTGYRVWKKPTQSYGTGFYPSPQIESVQIEQVKSGVFQPIDGN 208

Query: 177 YSPIKKVSYTV-ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           + P+K V++ V E    G+ + ++     I T+GSI   ++   A  IL +        +
Sbjct: 209 FMPVKNVNFAVHEVQPHGEYIHFE-----ITTNGSIHPHNAFKHAGAILTEITRA--TLQ 261

Query: 236 EPKKEVKEDINVKSLPFNPALLKK-------VEELELSVRSTNCLRGENIVYMGDLIQRT 288
           +P+  V   I+  S P + A+ +K       +E+LELS+R+ NCL+   I+ + DL + +
Sbjct: 262 DPRPVV--GIDEASTPVDTAVAQKAYFENIAIEQLELSLRAYNCLKRAQILTLADLSRES 319

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGL 315
            + +L + NFG+KS  E+   L T G+
Sbjct: 320 YSSLLALRNFGQKSAEEVAKALETYGI 346


>gi|197131692|gb|ACH47364.1| RNA polymerase alpha subunit [Geranium macrorrhizum]
          Length = 329

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 81/298 (27%), Positives = 153/298 (51%), Gaps = 15/298 (5%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A  +G A+RR L+  + G  IT  + D + HE +++ G+ E + +I++N+
Sbjct: 32  FILSPLKKGQADMIGIAMRRALLGEIEGTCITHAKFDKIPHEYTTLVGIQESIYEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDI--QTVNDIEVLNPDHVICNLD-VDAVVRME 146
           K I L+      +  +I  RGP  VT+ DI   T   I V N  H++   + +D  V ++
Sbjct: 92  KEIVLRSHLYGTRDASICVRGPRDVTSQDIILPTFATI-VDNTQHIVTLTEPIDFCVGLQ 150

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           +  ++G+ ++        +D  G   IDA++ P+K V++++ S   G    +  L + I 
Sbjct: 151 IERNRGY-FIQIPMLSNLHDDRGY-PIDAVFMPVKNVNHSIHSYENGI---HAMLFLEIW 205

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--VKSLPFNPALLKKV---E 261
           T+GS+T ++++  ASR L +    F++ EE     + + N     L  +   LK +   +
Sbjct: 206 TNGSLTPKEALRGASRKLINLFIPFLHAEEQNCHFENNQNEHTDELSIDFCALKDIYIDQ 265

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL-GTMGLFLG 318
            +EL  R   CL+G  I  + DL+ +   D++++  F ++ + ++  +L  T+  FL 
Sbjct: 266 LVELPARFYKCLKGSGIDTVMDLLNKNTDDLIKITQFCQQDVEKVMNILNNTISQFLS 323


>gi|7388101|sp|Q9XQN8|RPOA_SINAL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|5541932|emb|CAB51131.1| putative RNA polymerase alpha subunit (PEP) [Sinapis alba]
          Length = 327

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 76/285 (26%), Positives = 143/285 (50%), Gaps = 20/285 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+ R L+  + G  IT  + + + H+ S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMARALLGEIEGTCITRAKSENIPHDYSNIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
             I LK +    +   I  +GPG +TA DI     +E+++    I  L     + + L +
Sbjct: 92  NEIVLKSNLYGTRNPFICVQGPGYITARDIILPPSVEIVDNTQHIATLTEPINLCIGLKI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY     +  E+       IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 ERNRGYSLKMSNNFEDRS---YPIDAVFMPVQNANHSIHSYGNGNE-KQEILFIEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPK---KEVKEDINVKSLPFNPALL----KK--- 259
           S+T ++++  ASR L +    F++ EE     +  +  + +   PF+  L+    KK   
Sbjct: 208 SLTPKEALYEASRNLINLFIPFLHVEEETFYLENNQHQVTLPVFPFHNKLVNLRQKKKEL 267

Query: 260 ------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                 +++LEL  R  NCL+  NI  + DL+  ++ D+++M +F
Sbjct: 268 AFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLIKMEHF 312


>gi|224178085|ref|YP_002600906.1| alpha subunit of RNA polymerase [Pyramimonas parkeae]
 gi|215882752|gb|ACJ71125.1| alpha subunit of RNA polymerase [Pyramimonas parkeae]
          Length = 351

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 82/314 (26%), Positives = 151/314 (48%), Gaps = 43/314 (13%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTD 84
           P   G   T+ N LRR L++++ G  IT+V+ +           +HE S+I G+ E + +
Sbjct: 54  PFSHGQGLTIANGLRRTLLNNIIGFGITSVKFEPKWVDISKEVFIHEYSTIPGIWESIFE 113

Query: 85  IILNIKGINLKMSGDSH-----KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH-VICNLD 138
           II N+K I ++           + + I +  PGV+ A  I+    +++LN +  ++  + 
Sbjct: 114 IIENLKKIKIRRENSPFEPFEKQVIRITQDKPGVLRADSIKLPPFLKILNQNQPIVSMMS 173

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + ++ + +T+    G     +H   N     I +  +  PIK V+Y +++         
Sbjct: 174 SNLILDIIITIEAQTG-----NHLCNNQ---FIHVSEVCLPIKWVNYVIKTDPLLGSKSP 225

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L   I TDG+IT +++++ A+ I  D    F          ++++ VKS+       +
Sbjct: 226 ESLFFEISTDGTITPQEALSKAADICIDLYSCF-------STAQKELEVKSIVKEKVTEE 278

Query: 259 ----------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                      +E L LSVR+ NCL+  NI  + DL+ ++++D+L M NFG+KS  E+  
Sbjct: 279 VKEEIITNKVTIENLGLSVRAYNCLKRANIYTVTDLLTKSKSDLLAMKNFGKKSADEVYE 338

Query: 309 VLGTMGLFLGMNLP 322
            L      LG++LP
Sbjct: 339 ALQNR---LGIDLP 349


>gi|218176272|ref|YP_002364529.1| RNA polymerase alpha subunit [Festuca arundinacea]
 gi|215882356|gb|ACJ70786.1| RNA polymerase alpha subunit [Festuca arundinacea]
          Length = 346

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 86/298 (28%), Positives = 144/298 (48%), Gaps = 39/298 (13%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI--TAVQIDGVLHEISSIKGV 78
           GQ E  R L +     RGF            +  + G  +  T  +   V HE S+I G+
Sbjct: 41  GQAEHRRVLALG----RGFN-----------LEKIEGNNVLATRAKFGSVPHEYSTIAGI 85

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 86  EESVQEILLNLKEIVLRSNLYGVRDASISVKGPRYITAQDIILPPSVEIVDTSQPIANLT 145

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY   +    +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 146 EPIDFCIELQIKRDRGY---QTELRKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 201

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP---FNPA 255
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P   F   
Sbjct: 202 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 261

Query: 256 L----LKK-----------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           L    LKK           +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F
Sbjct: 262 LTNLNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF 319


>gi|75764945|ref|ZP_00744283.1| DNA-directed RNA polymerase alpha chain [Bacillus thuringiensis
           serovar israelensis ATCC 35646]
 gi|74487569|gb|EAO51447.1| DNA-directed RNA polymerase alpha chain [Bacillus thuringiensis
           serovar israelensis ATCC 35646]
          Length = 119

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 47/85 (55%), Positives = 65/85 (76%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDGVLHE S+++GV ED+T IILN+
Sbjct: 23  FVIEPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDGVLHEFSTVEGVVEDVTTIILNL 82

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVV 114
           K + LK+  +  K + I  +G G+V
Sbjct: 83  KKLALKIYSEEEKTLEIDVQGEGIV 107


>gi|56807381|ref|ZP_00365362.1| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Streptococcus pyogenes M49 591]
          Length = 145

 Score =  100 bits (248), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 55/141 (39%), Positives = 89/141 (63%)

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +F  
Sbjct: 1   YTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDFFF 60

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
             K  +     + +     L + +EEL+LSVRS NCL+   I  + DL +++E +M+++ 
Sbjct: 61  VAKATEVMKETEKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKSEPEMMKVR 120

Query: 297 NFGRKSLVEIKGVLGTMGLFL 317
           N GR+SL E+K  L  +GL L
Sbjct: 121 NLGRRSLEEVKVKLADLGLGL 141


>gi|290489674|gb|ADD31221.1| RNA polymerase alpha subunit protein [Rhododendron simsii]
          Length = 262

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 72/221 (32%), Positives = 114/221 (51%), Gaps = 5/221 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV--LHEISSIKGVHEDLTDIILNIKG 91
           PL RG A TLG A+RR L+  + G  IT  +   V   HE SSI+G+ E + +I++N+K 
Sbjct: 36  PLRRGEAETLGIAMRRALLGEIEGTCITRAKFGRVRVTHEYSSIEGIQESVNEILMNLKE 95

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           I LK +        I+ +GP  VTA DI     +E+++    I +L     + M+L + K
Sbjct: 96  IILKSNLYGPCSGLIWVQGPRDVTARDIMVAPYVEIIDNTQHIASLTKRIDLYMKLEIQK 155

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
             GY       T  D  G    DA++ P++  +Y + S  + +V   + L   I T+GS+
Sbjct: 156 NRGYQIKSPKNTLQD--GSYPTDAVFMPVRNANYNIYSYLD-RVAREEILFFEIWTNGSL 212

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           T ++++  ASR L D    F+N EE    + E+ +  +LP 
Sbjct: 213 TPKEALHEASRKLVDLFSPFLNTEEENVHLDENQHKINLPL 253


>gi|309322061|ref|YP_003933879.1| RNA polymerase alpha subunit [Erodium texanum]
 gi|197131688|gb|ACH47362.1| RNA polymerase alpha subunit [Erodium texanum]
 gi|300069154|gb|ADJ66276.1| RNA polymerase alpha subunit [Erodium texanum]
          Length = 328

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 74/291 (25%), Positives = 150/291 (51%), Gaps = 18/291 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A  +G A+RR L+  + G  IT  + + + HE +++ G+ E + +I++N+
Sbjct: 32  FILSPLKKGQADIIGIAMRRALLGEIEGTCITYAKFEKIPHEYTTLVGIQESVYEIVMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL-NPDHVICNLD-VDAVVRMEL 147
           K I L+ +    +  +I  RGP  VTA DI     + ++ N  H++   + +D  V +++
Sbjct: 92  KEIVLRSNLYGTRDASICVRGPRDVTAQDIILPPSVAIVDNTQHIVTLTEPIDFCVGLQI 151

Query: 148 TVSKGHGY---VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
             ++G+     +P   H     P     IDA++ P+K V++++ +   G    ++ L   
Sbjct: 152 ERNRGYSMKIPMPTNSHDDRGYP-----IDAVFMPVKNVNHSIHAYENG---SHEMLFFE 203

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--VKSLPFNPALLKKV-- 260
           I T+GS+T ++++  ASR L +    F++ EE    ++ + N   + L  +   LK +  
Sbjct: 204 IWTNGSLTPKEALREASRKLINLFIPFLHAEEENSHLENNQNQHTEELSIDLCGLKDIYI 263

Query: 261 -EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
            + +EL  R  N L+G  I  + DL+ +    ++++ +F  + + ++  +L
Sbjct: 264 DQLVELPPRLYNSLKGSGIHTVMDLMDKNTDALMKIPHFRHEDVEKVMNIL 314


>gi|13560647|gb|AAK30140.1|AF346704_1 DNA-directed RNA polymerase [Fucus vesiculosus]
          Length = 226

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 55/187 (29%), Positives = 114/187 (60%), Gaps = 9/187 (4%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +   L +   +T+GN LRR L+S+L G  I  V+  G+ +E + ++GV EDL +IILN+
Sbjct: 24  FVFTALKKSQGNTIGNVLRRTLLSNLYGFRIVGVRFAGINNEFALLEGVREDLFEIILNL 83

Query: 90  KGINL----KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           K I +    ++    + R+ ++  GP V+TAG ++  N++++LNP++ +  +  ++++ +
Sbjct: 84  KEIIILNSNRIDQTCYGRLKVY--GPAVITAGSLELPNNVKILNPNNHLLTISDESLIEI 141

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS-YTVESAREGQVLDYDKLSMT 204
           E+ +  G  Y+ AK  + E   +  I ID+ ++P+ KV+ Y +   ++G+ ++ ++L + 
Sbjct: 142 EVKIEAGKSYILAKDQKLEG-ALDFIPIDSNFAPVLKVNWYIISLPQDGESIN-EELHLE 199

Query: 205 IDTDGSI 211
           I T+G++
Sbjct: 200 IYTNGTL 206


>gi|58761465|gb|AAW82426.1| RNA polymerase alpha subunit [Takakia lepidozioides]
          Length = 382

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 84/310 (27%), Positives = 146/310 (47%), Gaps = 32/310 (10%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P   G A T+G A+RR  +  + G  IT  +   V HE S+I G+ E + D+ +N   I 
Sbjct: 36  PFRSGQASTVGIAMRRASLGEVEGTCITCAESKRVTHEYSTILGIQESVHDVSINSGEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L+      ++  I   GP  VTA DI +   +++++       +       +EL + K  
Sbjct: 96  LRSDSYETQKAFISILGPKKVTAQDIISPPSVKIIDTTQYTATVTKAIHSDIELKIEKDF 155

Query: 154 GYVPAKHHRTENDPI----GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           GY      R E DPI    G    DA++ PI+  +Y+V S   G     + L + I T+G
Sbjct: 156 GY------RIE-DPIKSADGNSPADAVFMPIRNANYSVHSFENGNETQ-EILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEP------KKEVKEDINVKSLPFNPALLKK---- 259
           S+T ++++  ASR L +    F++ E+       K   + +++  S P   A + +    
Sbjct: 208 SVTPKEALYEASRSLINLFIPFLHAEKKEFIYGLKNTYESNMSYFSSPSLSADIDEMTKG 267

Query: 260 -------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                  +++LEL  R+ NC +  N   + D +  ++ D++++ NFG+KS   ++ VL  
Sbjct: 268 VTFKHIFIDQLELPARAYNCPKRVNAHTISDPLNYSQDDLMKIKNFGKKS---VEQVLEA 324

Query: 313 MGLFLGMNLP 322
                 +NLP
Sbjct: 325 SQKRFSINLP 334


>gi|167010108|ref|ZP_02275039.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica FSC200]
          Length = 224

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 121/224 (54%), Gaps = 9/224 (4%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI- 65
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I 
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKIN 60

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK-RGPGVVTAGDIQTVND 124
           DG +  +  +    E + DIILN+K +++ ++ D       F+  G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLSVTLAEDVETGTITFELSGSEEEIFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG G+ PA+    +N   G   +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQ----DNFKDGEFLLDATFSPVVFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           + ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL
Sbjct: 177 FEIKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQL 220


>gi|150036730|emb|CAM98256.1| DNA-directed RNA polymerase alpha chain [Leuconostoc citreum]
          Length = 133

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 54/133 (40%), Positives = 80/133 (60%), Gaps = 2/133 (1%)

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           ILN+K + L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M
Sbjct: 1   ILNLKKVVLAIDSDDERSLEIDVQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHM 60

Query: 146 ELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +T  KG GY  A  ++   D  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+ 
Sbjct: 61  TVTAVKGRGYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTF 120

Query: 204 TIDTDGSITGEDS 216
            I T+GSI   D+
Sbjct: 121 DIWTNGSIKPSDA 133


>gi|215400751|ref|YP_002327512.1| RNA polyperase alpha-chain [Vaucheria litorea]
 gi|194441201|gb|ACF70929.1| RNA polyperase alpha-chain [Vaucheria litorea]
          Length = 230

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 66/220 (30%), Positives = 117/220 (53%), Gaps = 14/220 (6%)

Query: 14  NIEYI-VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           N+E+I +L   +EN    I +PL  G   ++GN  RR+L++ +    IT V+  G+ +E 
Sbjct: 4   NLEFINLLEVPDENFGKYIIKPLNLGMGVSIGNLFRRILLTQMPRTNITGVRFAGITNEF 63

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV--NDIEVLNP 130
           S+IKGV ED+ +I+LN+K I  K   +    V I   GP V+T+  +Q+   ++I ++NP
Sbjct: 64  STIKGVREDVLEILLNLKQIIFKGFKEEKTYVRIKITGPTVITSSCLQSALPDEITLVNP 123

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI----GLITIDALYSPIKKVSYT 186
              I  +  D+ +  EL +         K +   N  I      + +D + SPI+++ + 
Sbjct: 124 SQYIATITNDSTLEFELKIESEK-----KSNLANNQAIFESSDFLEVDKITSPIRQILFD 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           V    E +    ++L + I TDGSIT  D++  + +++Q+
Sbjct: 179 VYKKSETET--QEELVLQIWTDGSITPIDALITSVKLVQN 216


>gi|119672809|emb|CAK95485.1| RNA polymerase alpha subunit [Lactobacillus mucosae]
          Length = 121

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 49/115 (42%), Positives = 76/115 (66%), Gaps = 2/115 (1%)

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSPIK 181
           D+ +LNPD  I  +   A + + +T  KG GYVPA  +  R     IG + ID++Y+PI+
Sbjct: 5   DVTILNPDLHIATVADGAELHIMMTADKGRGYVPADQNKLRLSGLEIGTLPIDSIYTPIE 64

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +V+YTVE+ R GQ  D+DKL++ + TDGS+T   +++LA++IL + L MF+N  E
Sbjct: 65  RVNYTVENTRVGQSNDFDKLTLDVWTDGSLTPTAAISLAAKILTEHLEMFVNLTE 119


>gi|206896507|ref|YP_002247307.1| RNA-polymerase DNA-directed [Coprothermobacter proteolyticus DSM
           5265]
 gi|206739124|gb|ACI18202.1| RNA-polymerase DNA-directed [Coprothermobacter proteolyticus DSM
           5265]
          Length = 319

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 59/195 (30%), Positives = 99/195 (50%), Gaps = 1/195 (0%)

Query: 35  LPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL 94
           LP G   TLGNALRRVL+  + G  +   +++G+ HE    +GV ED   I LN+K +  
Sbjct: 32  LPEGEGITLGNALRRVLLGQIGGTGVLGFRLEGLDHEFMVPEGVVEDGLTIGLNLKKVLF 91

Query: 95  KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHG 154
           K  GD  K + I  +GP  + A DI    D+EV N D  I  +  D  + ME+ ++ G G
Sbjct: 92  KYYGDGVKVLYIKAKGPAEIKAADIVPDADVEVFNLDQTILTVSTDREIYMEIYLTNGVG 151

Query: 155 YVPAK-HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           Y   + + +    P   I +D  +SP+++  Y V  A   +   ++ L + + T+ ++  
Sbjct: 152 YRTVEDNKKLYQFPFRTIYLDTSFSPVRRAEYHVTPAIVDEPGTFESLELIVYTNLAVDP 211

Query: 214 EDSVALASRILQDQL 228
            + +  A+  L ++ 
Sbjct: 212 VEVIRQAANFLSEEF 226


>gi|119662813|emb|CAJ33198.1| RNA polymerase alpha subunit [Lactobacillus vaccinostercus]
          Length = 114

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 50/114 (43%), Positives = 76/114 (66%), Gaps = 2/114 (1%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K I+LK+  +  K + I  +GP  VTAGDI+   D+EV
Sbjct: 1   VLHEFSTVEGVTEDVTQIILNMKQISLKIDSEEDKTLEIDVKGPAAVTAGDIEADGDVEV 60

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSP 179
           LNP+  I  +   A + +++T + G GYV A  ++   D  PIG++ ID++Y+P
Sbjct: 61  LNPELHIATVADGAELHIQMTANTGRGYVSADDNKARMDDLPIGVLPIDSIYTP 114


>gi|222084158|ref|YP_002519753.1| RNA polymerase alpha chain [Gnetum parvifolium]
 gi|149941454|dbj|BAF64894.1| RNA polymerase alpha subunit [Brassica napus]
 gi|220983495|dbj|BAH11263.1| RNA polymerase alpha chain [Gnetum parvifolium]
          Length = 326

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 78/296 (26%), Positives = 145/296 (48%), Gaps = 14/296 (4%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQID-GVLHEISSIKGVHEDLTDIILNIKGI 92
           PL +G A+T+  A+RR L+  + G +IT  +I+   +H+ S++ G+ E + DI+LN+K I
Sbjct: 36  PLLKGQANTIAIAIRRTLLGEVEGTSITYAKIEKTTVHDYSTMSGIKESVHDILLNLKEI 95

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LK       + +I   GP  VTA DI   + I++++    I +L       + LT+ + 
Sbjct: 96  VLKSELYGIHKASICTVGPRNVTAQDIILPSSIKIIDGTQHIASLTKSVPFNVMLTIERN 155

Query: 153 HGY-VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
            GY +P++  R   +  GL  IDA   P++ V++++ S +    +  + L   I T+G +
Sbjct: 156 QGYAIPSQSSRRHKN--GLFPIDAPCMPVRNVNFSIHSYKSENDIR-EMLIFEIWTNGGL 212

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP----FNPALLKKV--EELEL 265
           T  ++   A   L D +   ++ EE     K+   +  L        AL + +   +LEL
Sbjct: 213 TPREAFYEACWKLIDLIVPLLHMEEDMNGAKDFFALPILTRMDKLGKALFQHLFMNQLEL 272

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           S ++++C +   I  + D +  +  +     +  +KS   IK ++       G+NL
Sbjct: 273 SSKNSSCFQQTFIYRLSDFLNYSRQNSKTFEDLDKKS---IKKIMEFFQKRFGINL 325


>gi|2951864|gb|AAC05400.1| RNA polymerase alpha subunit [Buchnera aphidicola]
 gi|448401|prf||1917188B RNA polymerase:SUBUNIT=alpha
          Length = 113

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 52/115 (45%), Positives = 75/115 (65%), Gaps = 3/115 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +    +KP  +E   + Q     T +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQNSIIGFLKPRLVE---IEQITATHTKVTLEPLERGFGHTLGNALRRILLSSMPGYAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
            V+IDGVLHE S+ +GV ED+ +I+LN+K + +K+ G     +++ K G G VTA
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKELAVKVHGKDEVFMSLNKSGIGSVTA 112


>gi|119662287|emb|CAJ33130.1| RNA polymerase alpha subunit [Lactobacillus buchneri]
          Length = 125

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 49/112 (43%), Positives = 73/112 (65%), Gaps = 2/112 (1%)

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTV 187
           PD  I  +   A   M LT +KG GYV A     R+   PIG++ +D++Y+PI++V+Y V
Sbjct: 1   PDLHIATVAEGATFHMRLTANKGRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERVNYQV 60

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           ES R GQ  D+DKL++ I TDGSIT  ++V+LA++IL + L MF++  +  K
Sbjct: 61  ESTRVGQRDDFDKLTLDIWTDGSITPSEAVSLAAKILTEHLEMFVDLTDEAK 112


>gi|161784224|ref|YP_001595540.1| RNA polymerase alpha subunit [Lemna minor]
 gi|88696802|gb|ABD48527.1| RNA polymerase alpha subunit [Lemna minor]
          Length = 284

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 64/223 (28%), Positives = 117/223 (52%), Gaps = 4/223 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            +  PL +G A T+G A+RR L+  + G  IT  + + V HE S+I G+ E + +I++N+
Sbjct: 32  FVLSPLMKGQADTIGIAMRRALLEEMEGTCITRAKSEKVPHEYSTIVGIEESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +    +  +I  +GP  +TA DI     +E+++    I  L     + + L +
Sbjct: 92  KEIVLRSNLYGTREASICVKGPKTITAEDIILPASVEIVDTTQHIATLTEPLDLYIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY   +   T N   G   IDA++ P++  ++++ S   G     + L + I T+G
Sbjct: 152 QRDRGY---RMRPTNNSQDGSYPIDAVFMPVRNANHSIYSYGNGNE-KQEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           S+T ++++  ASR L D    F++ EE    ++E+ +  +LP 
Sbjct: 208 SLTPKEALHEASRNLIDLFIPFLHAEEKDINLEENKSRFTLPL 250


>gi|153820406|ref|ZP_01973073.1| DNA-directed RNA polymerase alpha chain [Vibrio cholerae NCTC 8457]
 gi|126509049|gb|EAZ71643.1| DNA-directed RNA polymerase alpha chain [Vibrio cholerae NCTC 8457]
          Length = 75

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 43/74 (58%), Positives = 56/74 (75%)

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 1   RPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 60

Query: 318 GMNLPDWPPESIEE 331
           GM L +WPP SI E
Sbjct: 61  GMRLENWPPASIAE 74


>gi|115391932|ref|YP_778521.1| RNA polymerase alpha subunit [Jasminum nudiflorum]
 gi|110456253|gb|ABG74658.1| RNA polymerase alpha subunit [Jasminum nudiflorum]
          Length = 270

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 118/225 (52%), Gaps = 6/225 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+   +RR L+  + G  IT V+   V HE S+I G+ E + +I++N 
Sbjct: 32  FILSPLRKGQADTIAIGIRRALLGEIEGTCITRVKSKNVPHEYSTIAGIQESVHEILMNF 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I L+ +       +I  RGPG VTA DI     +E+++    I +L     + + L +
Sbjct: 92  KEIVLRSNLYGTCDASICVRGPGYVTAQDIILPPYVEIVDNTQHIASLTEPIDLCIGLQI 151

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            +  GY+    H +++   G   IDA++ P++  ++++ S   G    ++ L + I T+G
Sbjct: 152 ERNRGYLMKMPHNSQD---GSYPIDAVFMPVRNANHSIHSYGSGNE-KHEILFLEIWTNG 207

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
           S+T ++++  A R L D    F++ EE    +++  N  ++P +P
Sbjct: 208 SLTPKEALHEACRNLIDLFIPFLHKEEETSPLED--NHHTVPLSP 250


>gi|269101036|ref|YP_003289184.1| DNA-directed RNA polymerase subunit alpha [Ectocarpus siliculosus]
 gi|266631544|emb|CAV31215.1| DNA-directed RNA polymerase subunit alpha [Ectocarpus siliculosus]
 gi|270118674|emb|CAT18735.1| DNA-directed RNA polymerase subunit alpha [Ectocarpus siliculosus]
          Length = 361

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 70/202 (34%), Positives = 111/202 (54%), Gaps = 10/202 (4%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLH-EISSIKGVHEDLTDIILNIKGINLK---MS 97
           T+GN LRRVL+S+L G  IT V++  V H E + + GV ED  ++ILN+K I LK     
Sbjct: 36  TIGNMLRRVLLSNLYGLKITGVRLPDVTHNEFNLLDGVREDFLEVILNLKEIILKDENKY 95

Query: 98  GDS-HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
           G S H  + I  +GP VVTAG I+    I+VLNP++ +  +  D+ V + L +  G  YV
Sbjct: 96  GQSYHGLLKI--QGPAVVTAGSIKFSKGIKVLNPNNYLLTISDDSFVEIHLKLEHGKAYV 153

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD-KLSMTIDTDGSITGED 215
            AK  + E      + ID+ ++P+ KV+  V++  +  + + D +L + I T+GS+    
Sbjct: 154 LAKDQKLEGSTY-FLPIDSNFAPVLKVNSYVKTLPQ-HIENTDVELHLEIFTNGSLLPHQ 211

Query: 216 SVALASRILQDQLGMFINFEEP 237
           ++  A  ++   L      E P
Sbjct: 212 ALLQAKNMIGYMLSTVNKMEFP 233


>gi|15829032|ref|NP_326392.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma pulmonis UAB
           CTIP]
 gi|20139643|sp|Q98Q08|RPOA_MYCPU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|14089976|emb|CAC13734.1| DNA-DIRECTED RNA POLYMERASE ALPHA CHAIN (TRANSCRIPTASE ALPHA CHAIN)
           (RNA POLYMERASE ALPHA SUBUNIT)rpo [Mycoplasma pulmonis]
          Length = 333

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 84/302 (27%), Positives = 149/302 (49%), Gaps = 39/302 (12%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF  T+G ALRR L+SS+      A++I  V  E  +I  + ED+  I+LN+K I
Sbjct: 27  EPLERGFGSTIGTALRRTLLSSITSVVPFAIKIKDVDQEFDTISDIVEDVQMIMLNVKNI 86

Query: 93  NLKMSGDSHKRVTIFKRGPGV-------VTAGDIQTVN--DIEVLNPDHVICNLDVDAVV 143
           +L    +  +   I++   GV       +T+ D++     +IE++N D  I   +     
Sbjct: 87  HLVYDENIFEDNKIYR---GVIETKNEKITSSDLKFPENPEIEIVNKDLEIATNNGQKPF 143

Query: 144 RMELTVSKGHGYVPAKHHRT--------ENDPI---GLITIDALYSPIKKVSYTVESARE 192
            ME+    G GY+  + ++          N  I     + ID+ +SP++KV   V+    
Sbjct: 144 VMEVYFHVGRGYISFEDNKKLIEEKVALLNSTIKRGKFLAIDSDFSPVEKVKVKVQEINS 203

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF--------INFEEPKKEVKED 244
             +   ++L + I T G+I  ++ ++ A++IL   L +         ++  E KK+ K +
Sbjct: 204 SSLNIEEELEIEIKTKGTIDTKNILSQAAQILIAHLQVIGDVKNLDAVDVFEQKKQEKVE 263

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
            ++ S+         +  L+LSVRS N L+ +    + D++  TE D++ + N G+KS+ 
Sbjct: 264 PSIHSVD--------ITSLDLSVRSINALKRQGYTKLADILTLTEDDLVAVKNLGKKSVE 315

Query: 305 EI 306
           EI
Sbjct: 316 EI 317


>gi|300193165|pdb|3K4G|A Chain A, Crystal Structure Of E. Coli Rna Polymerase Alpha Subunit
           C-Terminal Domain
 gi|300193166|pdb|3K4G|B Chain B, Crystal Structure Of E. Coli Rna Polymerase Alpha Subunit
           C-Terminal Domain
 gi|300193167|pdb|3K4G|C Chain C, Crystal Structure Of E. Coli Rna Polymerase Alpha Subunit
           C-Terminal Domain
 gi|300193168|pdb|3K4G|D Chain D, Crystal Structure Of E. Coli Rna Polymerase Alpha Subunit
           C-Terminal Domain
 gi|300193169|pdb|3K4G|E Chain E, Crystal Structure Of E. Coli Rna Polymerase Alpha Subunit
           C-Terminal Domain
 gi|300193170|pdb|3K4G|F Chain F, Crystal Structure Of E. Coli Rna Polymerase Alpha Subunit
           C-Terminal Domain
 gi|300193171|pdb|3K4G|G Chain G, Crystal Structure Of E. Coli Rna Polymerase Alpha Subunit
           C-Terminal Domain
 gi|300193172|pdb|3K4G|H Chain H, Crystal Structure Of E. Coli Rna Polymerase Alpha Subunit
           C-Terminal Domain
          Length = 86

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 44/78 (56%), Positives = 55/78 (70%)

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
           F+P LL+ V++LEL+VRS NCL  E I Y+GDL+QRTE ++L   N G  SL EI  VL 
Sbjct: 6   FDPILLRPVDDLELTVRSANCLXAEAIHYIGDLVQRTEVELLXTPNLGXXSLTEIXDVLA 65

Query: 312 TMGLFLGMNLPDWPPESI 329
           + GL LGM L +WPP SI
Sbjct: 66  SRGLSLGMRLENWPPASI 83


>gi|119368531|ref|YP_913219.1| RNA polymerase alpha subunit [Gossypium barbadense]
 gi|119224893|dbj|BAF41279.1| RNA polymerase alpha subunit [Gossypium barbadense]
          Length = 270

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 64/216 (29%), Positives = 117/216 (54%), Gaps = 17/216 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  L G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 34  FILSPLMKGQADTIGIAMRRALLGELEGTCITRAKSEKIPHEYSTIVGIQESVHEILMNL 93

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           K I L+ +    +   I  +GPG VTA DI     +E+++    + +L   +D  + +++
Sbjct: 94  KEIVLRGNLYGTRNAFICAKGPGYVTAQDIILPPSVEIVDNTQHVASLTEPIDLCIGLQI 153

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA---REGQVLDYDKLSMT 204
             ++G+G    K+    + P     IDA++ P++  ++++       E Q +    L + 
Sbjct: 154 ERNRGYGIKTPKNFHDGSYP-----IDAVFMPVRNANHSIHCYGNDNEKQEI----LFLE 204

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           I T+GS+T ++++  ASR L D   +FI+F   K+E
Sbjct: 205 IWTNGSLTPKEALHEASRNLID---LFIHFLHAKEE 237


>gi|11466523|ref|NP_044772.1| RNA polymerase subunit alpha [Reclinomonas americana]
 gi|7388081|sp|O21260|RPOA_RECAM RecName: Full=DNA-directed RNA polymerase subunit alpha,
           mitochondrial; Short=RNA polymerase subunit alpha;
           AltName: Full=Transcriptase alpha chain
 gi|2258353|gb|AAD11887.1| RNA polymerase subunit alpha [Reclinomonas americana]
          Length = 222

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 59/213 (27%), Positives = 111/213 (52%), Gaps = 12/213 (5%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV--LHEISSIKGVH 79
           + + N   ++  PL + F+ +  N LR+++     G +I  ++I+G+  LH  S I GV 
Sbjct: 16  KHDFNSIQVLIGPLEKNFSGSFANLLRKIIFRYTSGVSIIGLKINGIDSLHSYSLIPGVK 75

Query: 80  EDLTDIILNIKGINLKMSGDSHKRV--TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           ED+ +++ N+K + +++    +K +  TI K+GP ++ + DI   ++I++LN D  IC L
Sbjct: 76  EDVLNVLNNLKHLLIQIDDYDYKPILLTIQKKGPYIIKSKDIICPSNIKILNDDLYICTL 135

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + D+ + + L    G GYV + +         ++  D  + PIK VSY V S        
Sbjct: 136 ENDSQIDLTLIGDIGCGYVLSTYFGNRK---SIVYSDTNFCPIKHVSYYVRSYTT----- 187

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           Y++L   I T+G+      +  A   L+D++ +
Sbjct: 188 YEELIFYIKTNGTCNPLFVMKNAFSFLKDKINI 220


>gi|290489664|gb|ADD31216.1| RNA polymerase alpha subunit protein [Lonicera japonica]
          Length = 264

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 66/230 (28%), Positives = 124/230 (53%), Gaps = 16/230 (6%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+ E + +I++N+
Sbjct: 32  FILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTIVGIQESVHEILMNL 91

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL-NPDHVICNLD-VDAVVRMEL 147
           K I L+ +       +I  RGPG VTA DI +   +E++ N  H++   + +D  + +++
Sbjct: 92  KEIVLRSNLYGTCDASICVRGPGNVTAQDIISPPYVEIIDNTQHIVSLTEPIDFCIGLQI 151

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES---AREGQVLDYDKLSMT 204
             ++G+      H +  + P     IDA++ P++  ++++ S     E Q +    L + 
Sbjct: 152 ERNRGYLIKTPNHFQDGSYP-----IDAVFMPVRNANHSIHSYGNENEKQEI----LFLE 202

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
           I T+GS+T ++++  ASR L D    F++ EE    +++  N  ++P  P
Sbjct: 203 IWTNGSLTPKEALHEASRNLIDLFIPFLHTEEENLHLED--NQHTVPLTP 250


>gi|226968553|ref|YP_002808506.1| RNA polymerase alpha chain [Micromonas pusilla CCMP1545]
 gi|226348848|gb|ACO50751.1| RNA polymerase alpha chain [Micromonas pusilla CCMP1545]
          Length = 358

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 84/332 (25%), Positives = 145/332 (43%), Gaps = 54/332 (16%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++  P+  G   TLGN  RR+L++ L G AITA +++    E  ++ G+ E + +I LN+
Sbjct: 29  LVLGPVAPGQGVTLGNTFRRLLLNDLPGVAITAAKLNDARTEFVTLPGIRESVVEIFLNL 88

Query: 90  KGI--------------NLKMSGDSHKRVTIFKRG------PGVVTAGDIQTVNDIEVLN 129
           + I               + +    H+  T    G      P V+ AGD+Q    +  ++
Sbjct: 89  RDIVFFNTFPDVLAPQGTITIDPSVHEGPTDAGEGFELSTSPRVICAGDMQLPEGVYCVD 148

Query: 130 PDHVICNLDVDAVVRMEL----------------TVSKGHGYVPAKH---HRTENDPIGL 170
           P   I  L ++A     L                T   G G+ P +     + E    GL
Sbjct: 149 PTQPIATL-MNAHTPFHLSFILEQATGYRVWKKPTQPYGRGFYPPRQTAAPQMEQVKSGL 207

Query: 171 I-TIDALYSPIKKVSYTV-ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
              ID  + P++ V++ V +    G+ + ++     I T+GSI    +   A  IL +  
Sbjct: 208 FQPIDGNFMPVRTVNFKVHDGPPHGEYIHFE-----ITTNGSIHPHAAFKHAGAILTEIT 262

Query: 229 GMFINFEEPKK-----EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGD 283
                 +EP+      EV +  +V +          +E+LELS+R+ NCL+   I+ + D
Sbjct: 263 RA--TLQEPRPLVGMDEVSQPADVPNNQMAYFETIAIEQLELSLRAYNCLKRAQILTLAD 320

Query: 284 LIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           L + +   +L + NFG+KS  E+   L T G+
Sbjct: 321 LSRESYQSLLALRNFGQKSAEEVAKALETYGI 352


>gi|254798672|ref|YP_003058319.1| alpha subunit of RNA polymerase [Parachlorella kessleri]
 gi|229915620|gb|ACQ90963.1| alpha subunit of RNA polymerase [Parachlorella kessleri]
          Length = 275

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 75/249 (30%), Positives = 112/249 (44%), Gaps = 52/249 (20%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG A T+ NALRR L+  L    +T V IDGV+HE SSI GV E + DI+LN+K +   +
Sbjct: 33  RGQALTVANALRRTLLGELPYLIVTKVHIDGVVHEFSSIPGVQESVLDILLNLKRLTFTI 92

Query: 97  SGDSHKRVTIFK------------RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD---- 140
              S+K+  IF             RGP  VTA D++    +  + P+H I  L  +    
Sbjct: 93  ---SNKKFNIFSNSWLKTKVFLKIRGPAKVTAADLKLPPHLACVWPNHYIATLSSNAELA 149

Query: 141 -----AVVRMELTVSKGHGYVPAKHH---RTENDPI--------------------GLIT 172
                AVV  +  +S     V +K+    +  ND                       + +
Sbjct: 150 CVLELAVVHPKQKISIAKNEVGSKNKIFGKVTNDVFEKGKGTESKKILTDSIEKNKKIFS 209

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           +D  YSPI+KV+Y +      +  +Y  L + I TDGSI  + ++  A + L     +F 
Sbjct: 210 LDTNYSPIRKVNYVIYELDSKKNSEY--LVLEIVTDGSIEPKQALRFAFKQLTK---LFY 264

Query: 233 NFEEPKKEV 241
            F +  K V
Sbjct: 265 EFTQISKNV 273


>gi|55274199|gb|AAV48981.1| DNA-directed RNA polymerase [Leuconostoc pseudomesenteroides]
          Length = 101

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 49/101 (48%), Positives = 65/101 (64%), Gaps = 8/101 (7%)

Query: 8   ELIKPN--NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           E  KPN  NIE      E+      + EPL RG+  TLGN+LRR+L+SSL GAA+  VQI
Sbjct: 3   EFEKPNIHNIE------EDARYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           DGV+HE S++ GV ED+T IILN+K + L +  D  + + I
Sbjct: 57  DGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEI 97


>gi|108773381|ref|YP_635843.1| alpha subunit of RNA polymerase [Oltmannsiellopsis viridis]
 gi|122238319|sp|Q20F02|RPOA_OLTVI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|82541963|gb|ABB82004.1| alpha subunit of RNA polymerase [Oltmannsiellopsis viridis]
          Length = 508

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 49/127 (38%), Positives = 71/127 (55%), Gaps = 6/127 (4%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P   G   T+GNA RR L+S L G  IT ++IDGV HE S++ GV E + DI+LN+K   
Sbjct: 27  PFDLGQGLTVGNAFRRTLLSELSGVGITLIEIDGVCHEYSTLPGVRESVLDILLNLK--Q 84

Query: 94  LKMSGDSHKRVT----IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           L ++ D+   V     +   GPGVVTA D++    +  ++PD  I  L  DA +  +  V
Sbjct: 85  LVLTSDTTFTVPQVGYLNFTGPGVVTAKDLKLPVSVYCVDPDQPIATLSADATLNFKFLV 144

Query: 150 SKGHGYV 156
            +G  Y+
Sbjct: 145 CQGKNYI 151


>gi|304323004|ref|YP_003795543.1| alpha subunit of RNA polymerase [Floydiella terrestris]
 gi|270048203|gb|ACZ58498.1| alpha subunit of RNA polymerase [Floydiella terrestris]
          Length = 316

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 52/145 (35%), Positives = 79/145 (54%), Gaps = 5/145 (3%)

Query: 17  YIVLGQEEENRTL---MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
           Y++  ++E N+T        P   G + T+ NALRR L+S + G  +T+V+I+GV HE S
Sbjct: 25  YLIKEEKENNQTFYGRFYIGPFEIGQSLTMANALRRSLLSEVPGLGLTSVEIEGVAHEYS 84

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR--GPGVVTAGDIQTVNDIEVLNPD 131
           +I GV E + DI+LNIK I  K +    K    + R  GP  + A D+     I+ +NPD
Sbjct: 85  TIPGVQETVFDILLNIKNIVFKSTTYLKKAEIGYCRASGPKTLRAKDLLLPAHIQCVNPD 144

Query: 132 HVICNLDVDAVVRMELTVSKGHGYV 156
             I  L  D  + M+L + +G  Y+
Sbjct: 145 QYIATLKSDGTLNMKLKIRQGTHYL 169


>gi|307069669|ref|YP_003878146.1| putative DNA-directed RNA polymerase subunit alpha [Candidatus
           Zinderia insecticola CARI]
 gi|306482929|gb|ADM89800.1| putative DNA-directed RNA polymerase, alpha subunit [Candidatus
           Zinderia insecticola CARI]
          Length = 224

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 53/193 (27%), Positives = 103/193 (53%), Gaps = 15/193 (7%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           N +L   + L  G A+ + N ++++ ++ ++G  +  +    + +EIS IKG+ ED+ DI
Sbjct: 14  NYSLFYLKNLKNGIANIIANFIKKISLNQIKGFCVYKIIFKNIKNEISYIKGIKEDIIDI 73

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGP--GVVTAGDIQTVN-DIEVLNPDHVICNLDVDAV 142
           +LNIK +  K+  +   + T F +    G + A +I+T+N +I++LNP H+I N  +   
Sbjct: 74  VLNIKNVIFKIKNN---KTTFFLKNYFLGPIYAYNIKTLNKNIKILNPSHLIANAIIKTK 130

Query: 143 VRMELTVSKGHGYV------PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           + + + V KG GY+        K++  E   I +I +D  Y+P+    +  +  ++    
Sbjct: 131 LNILIKVKKGKGYINNNEKKKFKYYNKEKKKI-VIYLDTNYTPV--KKFFFKIKKKIIKK 187

Query: 197 DYDKLSMTIDTDG 209
            Y+ L + I T+G
Sbjct: 188 KYEDLKIYIKTNG 200


>gi|152218428|gb|ABS31648.1| RpoA [Francisella noatunensis subsp. noatunensis]
 gi|152218430|gb|ABS31649.1| RpoA [Francisella noatunensis subsp. noatunensis]
 gi|152218432|gb|ABS31650.1| RpoA [Francisella noatunensis subsp. noatunensis]
 gi|152218434|gb|ABS31651.1| RpoA [Francisella noatunensis subsp. noatunensis]
 gi|152218436|gb|ABS31652.1| RpoA [Francisella noatunensis subsp. noatunensis]
 gi|152218438|gb|ABS31653.1| RpoA [Francisella noatunensis subsp. noatunensis]
 gi|152218440|gb|ABS31654.1| RpoA [Francisella noatunensis subsp. noatunensis]
          Length = 167

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 54/170 (31%), Positives = 93/170 (54%), Gaps = 6/170 (3%)

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           IE++N D  I  L  +    +  TVS G          TE + +G I +DA ++PIK+V+
Sbjct: 4   IEIINKDQPIATLTNEREFSLVATVSVGRNVGILSALPTELEKVGDIAVDADFNPIKRVA 63

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + +      + L+     + + T+G+I    +V  A     +Q+ +F++   P      D
Sbjct: 64  FEIFDNGASETLE-----VFVKTNGTIEPLAAVTKALEYFCEQISVFVSLRVPSNGKTGD 118

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
             + S   +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ +++
Sbjct: 119 ALLDS-NIDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMK 167


>gi|218672329|ref|ZP_03521998.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli GR56]
          Length = 57

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 40/56 (71%), Positives = 48/56 (85%)

Query: 284 LIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           LIQ+TEA+MLR  NFGRKSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 1   LIQKTEAEMLRTPNFGRKSLNEIKEVLASMGLHLGMEVPAWPPENIEDLAKRYEDQ 56


>gi|324533916|gb|ADY49343.1| DNA-directed RNA polymerase subunit alpha [Ascaris suum]
          Length = 179

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 52/178 (29%), Positives = 100/178 (56%), Gaps = 5/178 (2%)

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MELT   G GY  A  +R +     +I +D++Y+P+K  SY VE  R G + +YD+L + 
Sbjct: 1   MELTARTGIGYKLADENRGKEKKANVIYVDSIYTPVKVFSYRVEDTRVGDITNYDRLLID 60

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE----VKEDINVKSLPFNPALLKK- 259
           I+T+G+I+ E++++ ++ I+++ + +  N EE   +    ++  + V +   N    +  
Sbjct: 61  IETNGTISPEEALSYSAHIMKEHMMLVENIEEAINQSQVFIESKVEVDTQIVNETDNQNA 120

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +E L++S R+ N L+   I  + DL  +T+ ++  + N G K++ EI+  L  +G  L
Sbjct: 121 IETLDISNRAYNGLKKAGIDTIEDLCNKTKKEIAAVDNIGAKTVDEIQKQLQELGYVL 178


>gi|85717255|ref|ZP_01048210.1| DNA-directed RNA polymerase alpha subunit [Nitrobacter sp. Nb-311A]
 gi|85695896|gb|EAQ33799.1| DNA-directed RNA polymerase alpha subunit [Nitrobacter sp. Nb-311A]
          Length = 317

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 37/80 (46%), Positives = 63/80 (78%)

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           L + ++ELELSVR++ CL+ +++  +GD  + +EA++LR+ NFGRKSL E+K +LG +GL
Sbjct: 157 LYRSIDELELSVRTSLCLKNDDVRLVGDFARNSEAELLRIPNFGRKSLNELKEILGQVGL 216

Query: 316 FLGMNLPDWPPESIEELAKK 335
            LG+ LP+WPP +++ L+++
Sbjct: 217 QLGLALPEWPPPNVDFLSQQ 236



 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 39/70 (55%), Positives = 55/70 (78%)

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           LL++V++LELSVRS NCL+ + I ++G+L+Q++E +MLR  NFGR+SL EIK +L   GL
Sbjct: 240 LLERVDDLELSVRSANCLKKDGINHVGELVQKSEDEMLRTPNFGRRSLNEIKDLLAASGL 299

Query: 316 FLGMNLPDWP 325
            LGM+L  WP
Sbjct: 300 HLGMDLSGWP 309


>gi|152218442|gb|ABS31655.1| RpoA [Francisella philomiragia]
 gi|152218444|gb|ABS31656.1| RpoA [Francisella philomiragia]
 gi|152218446|gb|ABS31657.1| RpoA [Francisella philomiragia]
          Length = 167

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 53/170 (31%), Positives = 93/170 (54%), Gaps = 6/170 (3%)

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           IE++N D  I  L  +    +  TVS G          TE + +G I +D+ ++PIK+V+
Sbjct: 4   IEIINKDQPIATLTNEREFSLTATVSVGRNVGILSALPTELEKVGDIAVDSDFNPIKRVA 63

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + +      + L+     + + T+G+I    +V  A     +Q+ +F++   P      D
Sbjct: 64  FEIFDNGTNETLE-----VFVKTNGTIEPLVAVTKALEYFCEQISVFVSLRVPSNGKTGD 118

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
             + S   +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ +++
Sbjct: 119 ALLDS-NIDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMK 167


>gi|152218448|gb|ABS31658.1| RpoA [Francisella philomiragia subsp. philomiragia ATCC 25015]
          Length = 167

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 53/170 (31%), Positives = 93/170 (54%), Gaps = 6/170 (3%)

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           IE++N D  I  L  +    +  TVS G          TE + +G I +D+ ++PIK+V+
Sbjct: 4   IEIINKDQPIATLTNERKFSLTATVSVGRNVGILSALPTELEKVGDIAVDSDFNPIKRVA 63

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + +      + L+     + + T+G+I    +V  A     +Q+ +F++   P      D
Sbjct: 64  FEIFDNGTNETLE-----VFVKTNGTIEPLVAVTKALEYFCEQISVFVSLRVPSNGKTGD 118

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
             + S   +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ +++
Sbjct: 119 ALLDS-NIDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMK 167


>gi|166714636|gb|ABY88043.1| RpoA [Stenotrophomonas koreensis]
          Length = 122

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 47/122 (38%), Positives = 71/122 (58%), Gaps = 6/122 (4%)

Query: 145 MELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           M L V +G GY PA   R    E   IG + +DA +SP+++V+Y VE+AR  Q  D DKL
Sbjct: 4   MRLKVERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLDKL 63

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + IDT+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ ++
Sbjct: 64  VLDIDTNGTIDAEEAVRTAADILTDQLSVFGDFTHRDRGAAKPTNNG---VDPVLLRPID 120

Query: 262 EL 263
           +L
Sbjct: 121 DL 122


>gi|166714644|gb|ABY88047.1| RpoA [Stenotrophomonas sp. LMG 10857]
          Length = 122

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 46/125 (36%), Positives = 73/125 (58%), Gaps = 6/125 (4%)

Query: 142 VVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M L + +G GY PA   R    E   IG + +DA +SP+++V+Y+VE+AR  Q  D 
Sbjct: 1   AINMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYSVEAARVEQRTDL 60

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL M I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+
Sbjct: 61  DKLVMDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNG---VDPVLLR 117

Query: 259 KVEEL 263
            +++L
Sbjct: 118 PIDDL 122


>gi|119662819|emb|CAJ33202.1| RNA polymerase alpha subunit [Lactobacillus diolivorans]
          Length = 98

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 50/95 (52%), Positives = 61/95 (64%), Gaps = 2/95 (2%)

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVN 123
           D VLHE S+IKGV ED+T IILN+K I+LK+ G  D  + + I   GP  VTAGDIQ  +
Sbjct: 1   DDVLHEFSTIKGVVEDVTQIILNVKKISLKLDGPEDEEENLEIDVIGPADVTAGDIQGDS 60

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D+ VLNPD  I  +   A   M LT +KG GYV A
Sbjct: 61  DVTVLNPDLHIATVAEGATFHMRLTANKGRGYVSA 95


>gi|48374282|gb|AAT41971.1| putative RNA polymerase alpha subunit [Fremyella diplosiphon Fd33]
          Length = 155

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 50/155 (32%), Positives = 88/155 (56%), Gaps = 8/155 (5%)

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           +  + ID+++ P++KV+Y+VE AR    +  D+L + + T+GSI+ +++++ A+ IL D 
Sbjct: 1   MDFLQIDSVFMPVRKVNYSVEEARGDGSITKDRLLLEVWTNGSISPQEALSSAAGILVDL 60

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
                +      +   DI     P +P     +EEL+LSVR+ NCL+   +  + DL+  
Sbjct: 61  FNPLKDISLEPTDTGSDI-----PDDPTAQIPIEELQLSVRAYNCLKRAQVNSVADLLDY 115

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           T+ D+L + NFG+KS  E   V+  +   LG+ LP
Sbjct: 116 TQEDLLEIKNFGQKSAEE---VVEALQRRLGITLP 147


>gi|166714668|gb|ABY88059.1| RpoA [Stenotrophomonas sp. LMG 10888]
 gi|166714670|gb|ABY88060.1| RpoA [Stenotrophomonas sp. LMG 10883]
 gi|166714688|gb|ABY88069.1| RpoA [Stenotrophomonas sp. LMG 10882]
          Length = 122

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 46/125 (36%), Positives = 73/125 (58%), Gaps = 6/125 (4%)

Query: 142 VVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M L V +G GY PA   R    E+  IG + +DA +SP+++V+Y VE+AR  Q  D 
Sbjct: 1   AINMRLKVERGFGYQPAAARRRPDEESRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDL 60

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+
Sbjct: 61  DKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNG---VDPVLLR 117

Query: 259 KVEEL 263
            +++L
Sbjct: 118 PIDDL 122


>gi|11467766|ref|NP_050817.1| RNA polymerase alpha chain [Nephroselmis olivacea]
 gi|24638188|sp|Q9TL28|RPOA_NEPOL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|5880695|gb|AAD54788.1|AF137379_11 alpha subunit of RNA polymerase [Nephroselmis olivacea]
          Length = 495

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 50/144 (34%), Positives = 74/144 (51%), Gaps = 10/144 (6%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PLP G   TLGNALRR+L+  L G A T+  + G  HE  ++ G+ E + +I+LNIK + 
Sbjct: 25  PLPAGQGITLGNALRRILLGDLVGFAATSANLAGASHEFDTLPGIRESVLEILLNIKQLV 84

Query: 94  LKMSGDSHK-------RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
            K      K       R ++   GP  VTA D+   + ++V++P   I  L   A +  E
Sbjct: 85  FKQISSRPKDTNRFAMRASLNLTGPATVTAKDLVLPSWMKVVDPSQYIATLASGASLEFE 144

Query: 147 LTVSKGHGYVPAKHHRTENDPIGL 170
           + +S+G GY   +  RT   P G 
Sbjct: 145 IQLSQGSGY---RLRRTSLVPPGF 165



 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 50/153 (32%), Positives = 78/153 (50%), Gaps = 28/153 (18%)

Query: 173 IDALYSPIKKVSYTVESA------REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           IDA++ P+ +V+Y VE        RE  V+D       I T+GS++   ++  A+ IL  
Sbjct: 240 IDAVFFPVTRVNYRVEEEVINGRRREELVID-------IWTNGSLSPRKALDQAAVIL-- 290

Query: 227 QLGMFINFE-------EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIV 279
            + M  + +       EP+K+       K +   P     +E L+LSVRS NCL+  NI 
Sbjct: 291 -IRMLASLQAPPPLLIEPEKKPTTKTIAKEIALTP-----IESLDLSVRSFNCLKRANIT 344

Query: 280 YMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
            +G LI  T  ++L++ NFG KS  E+  VL +
Sbjct: 345 NVGKLIAYTRQELLQLKNFGTKSASEVVDVLNS 377


>gi|229915533|gb|ACQ90877.1| alpha subunit of RNA polymerase [Pedinomonas minor]
          Length = 365

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 78/340 (22%), Positives = 150/340 (44%), Gaps = 62/340 (18%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P   G A T+ N+LRR L+S  +G  + AV+IDG +HE S ++G+ E + DI+LN++ ++
Sbjct: 28  PFQAGQALTVANSLRRTLLSDQQGVFLAAVEIDGAIHEYSRLEGLKESILDILLNLRQVS 87

Query: 94  LKMSGDSHKRVTIFK-----------RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           + ++ D+ K  + F            +GP  V A D++    IE  NP+  I  L  +  
Sbjct: 88  VLLTDDTSKTASEFANQETFVGYFDLQGPMEVKAKDLKFPKQIECGNPNQHIATLTRNCT 147

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI------------------GLITIDALYSPIKKVS 184
            +    +    G      +++  DP+                    + ++ + + I++V+
Sbjct: 148 FQGRFLILTNPGLT--FKNQSIGDPLLFTKQVAKLEIGNRLLEKNWLYVNPITNAIRRVN 205

Query: 185 YTVESAREGQVLDYDK-LSMTIDTDGSITGEDSV--ALASRILQDQLGMFIN-------- 233
           Y VE  + G V +  + + + + T+G+I  + ++  A             +N        
Sbjct: 206 YVVE--QFGDVWEQKEVVVLEVWTNGTIHPKQAIHSACTKLSTLFSSLSSVNTTAFKFPA 263

Query: 234 ----FEEPKKEVKEDINVKSLPF-------NPALLK-------KVEELELSVRSTNCLRG 275
               F++ K +   D N+   P        +PA  K        +  L+LS+++   L+ 
Sbjct: 264 SVARFKKVKTDSGADGNLTVKPMTEFSGQESPAGDKLTILFDLDIANLQLSLKTYLVLKN 323

Query: 276 ENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
             I  +G+L+Q  ++D+ R+ N     + EI+  L   GL
Sbjct: 324 AKIQNIGNLLQYNKSDLTRLLNLANSQIEEIETALNVFGL 363


>gi|166714634|gb|ABY88042.1| RpoA [Stenotrophomonas nitritireducens]
          Length = 122

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 46/125 (36%), Positives = 72/125 (57%), Gaps = 6/125 (4%)

Query: 142 VVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M L V +G GY PA   R    E   IG + +DA +SP+++V+Y VE+AR  Q  D 
Sbjct: 1   AINMRLKVERGFGYQPAASRRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDL 60

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+
Sbjct: 61  DKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNG---VDPVLLR 117

Query: 259 KVEEL 263
            +++L
Sbjct: 118 PIDDL 122


>gi|166714650|gb|ABY88050.1| RpoA [Stenotrophomonas sp. LMG 10890]
          Length = 122

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 46/125 (36%), Positives = 72/125 (57%), Gaps = 6/125 (4%)

Query: 142 VVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            V M L + +G GY PA   R    E   IG + +DA +SP+++V+Y VE+AR  Q  D 
Sbjct: 1   AVNMRLKIDRGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDL 60

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+
Sbjct: 61  DKLVIDIETNGTIDAEEAVQTAADILSDQLSVFGDFTHRDRGAAKPANNG---VDPVLLR 117

Query: 259 KVEEL 263
            +++L
Sbjct: 118 PIDDL 122


>gi|166714654|gb|ABY88052.1| RpoA [Stenotrophomonas sp. LMG 1108]
 gi|166714658|gb|ABY88054.1| RpoA [Stenotrophomonas sp. LMG 6608]
 gi|166714672|gb|ABY88061.1| RpoA [Stenotrophomonas sp. ICB91]
 gi|166714674|gb|ABY88062.1| RpoA [Stenotrophomonas sp. ICB194]
 gi|166714676|gb|ABY88063.1| RpoA [Stenotrophomonas pavanii]
 gi|166714686|gb|ABY88068.1| RpoA [Stenotrophomonas sp. LMG 10879]
 gi|166714690|gb|ABY88070.1| RpoA [Stenotrophomonas sp. LMG 10989]
 gi|166714694|gb|ABY88072.1| RpoA [Stenotrophomonas sp. LMG 11087]
          Length = 122

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 46/125 (36%), Positives = 72/125 (57%), Gaps = 6/125 (4%)

Query: 142 VVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            V M L + +G GY PA   R    E   IG + +DA +SP+++V+Y VE+AR  Q  D 
Sbjct: 1   AVNMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDL 60

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+
Sbjct: 61  DKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNG---VDPVLLR 117

Query: 259 KVEEL 263
            +++L
Sbjct: 118 PIDDL 122


>gi|166714628|gb|ABY88039.1| RpoA [Stenotrophomonas maltophilia]
          Length = 122

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 44/125 (35%), Positives = 74/125 (59%), Gaps = 6/125 (4%)

Query: 142 VVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M + + +G+GY PA   R+   E   IG + +DA +SP+++V+Y VE+AR  Q  D 
Sbjct: 1   AINMAVKIERGYGYQPAAARRSPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDL 60

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+
Sbjct: 61  DKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFNHRDRGAAKPANNG---VDPVLLR 117

Query: 259 KVEEL 263
            +++L
Sbjct: 118 PIDDL 122


>gi|166714682|gb|ABY88066.1| RpoA [Stenotrophomonas sp. LMG 981]
          Length = 122

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 45/124 (36%), Positives = 73/124 (58%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R    E   IG + +DA +SP+++V+Y+VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYSVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ 
Sbjct: 62  KLVIEIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNG---VDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|166714632|gb|ABY88041.1| RpoA [Stenotrophomonas acidaminiphila]
          Length = 119

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 46/122 (37%), Positives = 71/122 (58%), Gaps = 6/122 (4%)

Query: 145 MELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           M L V +G GY PA   R    E   IG + +DA +SP+++V+Y VE+AR  Q  D DKL
Sbjct: 1   MRLKVERGFGYQPAASRRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLDKL 60

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ ++
Sbjct: 61  VIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNG---VDPVLLRPID 117

Query: 262 EL 263
           +L
Sbjct: 118 DL 119


>gi|166714656|gb|ABY88053.1| RpoA [Stenotrophomonas sp. LMG 11114]
          Length = 122

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 45/125 (36%), Positives = 71/125 (56%), Gaps = 6/125 (4%)

Query: 142 VVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M L + +G GY PA   R    E   IG + +DA +SP+++V+Y VE+AR  Q  D 
Sbjct: 1   AINMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDL 60

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + I+T+G+I  ED+V   + IL DQL +F +F    +   +  N      +P LL+
Sbjct: 61  DKLVIDIETNGTIDAEDAVRTGADILSDQLSVFGDFTHRDRGAAKPANNG---VDPVLLR 117

Query: 259 KVEEL 263
            +++L
Sbjct: 118 PIDDL 122


>gi|166714720|gb|ABY88085.1| RpoA [Stenotrophomonas sp. ICB141]
 gi|166714722|gb|ABY88086.1| RpoA [Stenotrophomonas sp. ICB129]
 gi|166714724|gb|ABY88087.1| RpoA [Stenotrophomonas sp. ICB133]
          Length = 122

 Score = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 45/125 (36%), Positives = 72/125 (57%), Gaps = 6/125 (4%)

Query: 142 VVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M L + +G GY PA   R    E   IG + +DA +SP+++V+Y VE+AR  Q  D 
Sbjct: 1   AINMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDL 60

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+
Sbjct: 61  DKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRARGAAKPANNG---VDPVLLR 117

Query: 259 KVEEL 263
            +++L
Sbjct: 118 PIDDL 122


>gi|166714684|gb|ABY88067.1| RpoA [Stenotrophomonas sp. LMG 10874]
 gi|166714696|gb|ABY88073.1| RpoA [Stenotrophomonas sp. LMG 11111]
 gi|166714698|gb|ABY88074.1| RpoA [Stenotrophomonas sp. ICB130]
 gi|166714700|gb|ABY88075.1| RpoA [Stenotrophomonas sp. ICB134]
 gi|166714702|gb|ABY88076.1| RpoA [Stenotrophomonas sp. ICB209]
          Length = 122

 Score = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 45/125 (36%), Positives = 72/125 (57%), Gaps = 6/125 (4%)

Query: 142 VVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M L + +G GY PA   R    E   IG + +DA +SP+++V+Y VE+AR  Q  D 
Sbjct: 1   AINMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDL 60

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+
Sbjct: 61  DKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNG---VDPVLLR 117

Query: 259 KVEEL 263
            +++L
Sbjct: 118 PIDDL 122


>gi|166714646|gb|ABY88048.1| RpoA [Stenotrophomonas sp. LMG 10881]
          Length = 122

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 46/124 (37%), Positives = 71/124 (57%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L V +G GY PA   R    E   IG + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKVERGFGYQPAASRRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + I+T+G+I  E++V  A  IL DQL +F +F    +   +  N      +P LL+ 
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAGDILSDQLSVFGDFTHRDRGAAKPANNG---VDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|213517416|gb|ACJ50122.1| RNA polymerase alpha subunit [Chlamydomonas reinhardtii]
          Length = 737

 Score = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 43/139 (30%), Positives = 76/139 (54%), Gaps = 11/139 (7%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P     + TL N LRR L+S L G AIT+++I+GVLH+ S++ G+ E + D+I N++ I 
Sbjct: 42  PFDESLSQTLANDLRRTLLSELTGLAITSIEIEGVLHKFSTLTGMKEPVLDLICNLQNIV 101

Query: 94  LK----MSGDSHKRVT-------IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           L+     S + + R T       +   GP V+ A D++    ++ ++P+  I  L  D  
Sbjct: 102 LRKETISSTNMNYRATKKTYIGFLSVNGPRVIKAADLKLPAGLQCVDPNQYIATLAEDGF 161

Query: 143 VRMELTVSKGHGYVPAKHH 161
           + M+  +++G  Y+  K +
Sbjct: 162 LNMKFNINEGKNYIKQKPY 180



 Score = 41.2 bits (95), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 20/55 (36%), Positives = 34/55 (61%)

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L++S+RS   L+   I  + DLI+ ++ D+  + N G+KS+ EI+  L  +GL L
Sbjct: 680 LKISLRSYTALKKAGITTLKDLIKYSKKDLFAIKNLGQKSVFEIEQNLALLGLTL 734


>gi|62361814|gb|AAX81443.1| RNA polymerase alpha subunit [Simkania negevensis]
          Length = 159

 Score = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 53/157 (33%), Positives = 84/157 (53%), Gaps = 17/157 (10%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLK---------------MSGD 99
           L   AI +++I+G  HE ++I+GV ED+T IILN+KG  L+               +S D
Sbjct: 1   LEAPAIISIKIEGAPHEYTAIEGVIEDMTHIILNLKGTLLRKIPLVENKDTRAPTIISQD 60

Query: 100 SHKRVTIFKRGPG--VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
                 +   G G  VV    I   ++ E++NPDH I  +      R++L ++ G GYVP
Sbjct: 61  LDVTQDMLDTGGGQFVVKFKHIMGESNFEMINPDHHIFTITKPMRKRIDLKIAIGRGYVP 120

Query: 158 AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
           ++ H   +  +  I ID+ +SP++ V+Y VE+ R GQ
Sbjct: 121 SERHELPDKVVDEIVIDSAFSPVRLVNYFVENTRVGQ 157


>gi|41179033|ref|NP_958389.1| RNA polymerase alpha subunit [Chlamydomonas reinhardtii]
 gi|32699675|sp|Q8HUH2|RPOA_CHLRE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|23307781|gb|AAN17816.1| RNA polymerase alpha subunit [Chlamydomonas reinhardtii]
 gi|28269756|tpg|DAA00934.1| TPA_inf: RNA polymerase alpha subunit [Chlamydomonas reinhardtii]
          Length = 550

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 43/139 (30%), Positives = 76/139 (54%), Gaps = 11/139 (7%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P     + TL N LRR L+S L G AIT+++I+GVLH+ S++ G+ E + D+I N++ I 
Sbjct: 42  PFDESLSQTLANDLRRTLLSELTGLAITSIEIEGVLHKFSTLTGMKEPVLDLICNLQNIV 101

Query: 94  LK----MSGDSHKRVT-------IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           L+     S + + R T       +   GP V+ A D++    ++ ++P+  I  L  D  
Sbjct: 102 LRKETISSTNMNYRATKKTYIGFLSVNGPRVIKAADLKLPAGLQCVDPNQYIATLAEDGF 161

Query: 143 VRMELTVSKGHGYVPAKHH 161
           + M+  +++G  Y+  K +
Sbjct: 162 LNMKFNINEGKNYIKQKPY 180


>gi|166714642|gb|ABY88046.1| RpoA [Stenotrophomonas sp. LMG 10992]
          Length = 122

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 44/125 (35%), Positives = 73/125 (58%), Gaps = 6/125 (4%)

Query: 142 VVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M + + +G GY PA   R+   E   IG + +DA +SP+++V+Y VE+AR  Q  D 
Sbjct: 1   AINMAVKIERGFGYQPAAARRSPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDL 60

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+
Sbjct: 61  DKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFNHRDRGAAKPANNG---VDPVLLR 117

Query: 259 KVEEL 263
            +++L
Sbjct: 118 PIDDL 122


>gi|150187027|emb|CAK30154.1| RNA polymerase alpha subunit [Streptococcus uberis]
          Length = 101

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 41/101 (40%), Positives = 65/101 (64%)

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           +I GV ED+  IILNIKG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH 
Sbjct: 1   TIPGVREDVMQIILNIKGLAVKSYVEDEKMIELDVEGPAEVTAGDILTDSDIELVNPDHY 60

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITID 174
           +  +     ++  +TV+K  GYVPA+ ++ ++ P+G + +D
Sbjct: 61  LFTIAEGHSLKATMTVAKKRGYVPAEGNKKDDAPVGTLAVD 101


>gi|166714638|gb|ABY88044.1| RpoA [Pseudoxanthomonas dokdonensis]
          Length = 122

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 46/124 (37%), Positives = 73/124 (58%), Gaps = 10/124 (8%)

Query: 145 MELTVSKGHGYVPA---KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           M L + +G GY PA   +H   E   IG + +DA +SP+++V+Y VE+AR  Q  D DKL
Sbjct: 4   MRLKIERGFGYQPAAARRHPDDETRTIGRLVLDASFSPVRRVAYAVEAARVEQRTDLDKL 63

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP--FNPALLKK 259
            + I+T+G+I  E++V  A+ IL DQL +F +F   ++        K  P   +P LL+ 
Sbjct: 64  VLDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRQRG-----EAKPSPTGVDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|166714704|gb|ABY88077.1| RpoA [Stenotrophomonas sp. ICB220]
          Length = 122

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 46/123 (37%), Positives = 73/123 (59%), Gaps = 8/123 (6%)

Query: 145 MELTVSKGHGYVPA---KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           M L + +G GY PA   +H   E   IG + +DA +SP+++V+Y VE+AR  Q  D DKL
Sbjct: 4   MRLKIERGFGYQPAAARRHPDDETRTIGRLVLDASFSPVRRVAYAVEAARVEQRTDLDKL 63

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDINVKSLPFNPALLKKV 260
            + I+T+G+I  E++V  A+ IL DQL +F +F   ++ E K          +P LL+ +
Sbjct: 64  VLDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRQRGEAKP----SKTGVDPVLLRPI 119

Query: 261 EEL 263
           ++L
Sbjct: 120 DDL 122


>gi|166714678|gb|ABY88064.1| RpoA [Stenotrophomonas sp. ICB128]
          Length = 122

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 44/125 (35%), Positives = 72/125 (57%), Gaps = 6/125 (4%)

Query: 142 VVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            ++M L + +G GY P    R    E   IG + +DA +SP+++V+Y VE+AR  Q  D 
Sbjct: 1   AIKMRLKIERGFGYQPGAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDL 60

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+
Sbjct: 61  DKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNG---VDPVLLR 117

Query: 259 KVEEL 263
            +++L
Sbjct: 118 PIDDL 122


>gi|156619301|gb|ABU88330.1| RNA polymerase alpha subunit [Chlamydomonas moewusii]
          Length = 633

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 45/127 (35%), Positives = 73/127 (57%), Gaps = 2/127 (1%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P     + T+ N LRR L+S + G AI +V+I+G  HE SS+ GVHE + DI+LN+K I 
Sbjct: 27  PFEPSQSLTIANTLRRTLLSEIYGLAIVSVEIEGASHEYSSLPGVHESVLDILLNLKEIV 86

Query: 94  LKMS-GDSHKRVTIFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           LK S  +   ++   + RGPGVVT   ++    I+ ++PD  I  L  +  + ++  V  
Sbjct: 87  LKKSIKNFTPQIGYLRARGPGVVTGSHLRLPPFIQCVDPDQYIATLSHNGFLNIKFVVQY 146

Query: 152 GHGYVPA 158
           G+ ++ +
Sbjct: 147 GNKWLAS 153


>gi|208751315|gb|ACI31270.1| RNA polymerase alpha subunit [Volvox carteri]
 gi|261888190|gb|ACY06045.1| alpha subunit of RNA polymerase [Volvox carteri f. nagariensis]
          Length = 768

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 41/139 (29%), Positives = 76/139 (54%), Gaps = 11/139 (7%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P     + T+ N +RR L+S L   AIT+++I+G+LH+ SS+ G+ E + D+I N++ I 
Sbjct: 42  PFDDSLSQTIANDIRRTLLSELTSLAITSIEIEGILHKYSSLPGMKETVLDLICNLQSIV 101

Query: 94  LKMSGDSHKRVTIFK-----------RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           LK    S   +T+              GP V+ A D++  + ++ ++P+  I  L  D +
Sbjct: 102 LKKQEISFTNITLRSTKKTYRGFLNVSGPRVIKAMDLKLPSGLQCVDPNQYIATLAEDGL 161

Query: 143 VRMELTVSKGHGYVPAKHH 161
           + M+L +++G  ++  K H
Sbjct: 162 LNMKLNINEGKNFIKQKPH 180



 Score = 42.0 bits (97), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 20/55 (36%), Positives = 37/55 (67%)

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L++S+R+   L+   I+ + DL++ ++ D+L++ N G+KSLV I+  L  +GL L
Sbjct: 710 LKISLRAYTALKKAGILTINDLVKCSKNDLLKINNLGKKSLVLIETSLSYLGLTL 764


>gi|166714706|gb|ABY88078.1| RpoA [Stenotrophomonas sp. LMG 11108]
          Length = 122

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 47/125 (37%), Positives = 71/125 (56%), Gaps = 6/125 (4%)

Query: 142 VVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M L   +G GY PA   R    E   IG + +DA +SP+++V+Y+VE+AR  Q  D 
Sbjct: 1   AINMRLKSERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYSVEAARVEQRTDL 60

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL M I+T+G+I  +++V  A  IL DQL  F +F  P +     I   +   +P LL+
Sbjct: 61  DKLVMDIETNGTIDAQEAVRTAPDILNDQLSAFGDF--PHRHRGAPIPANNG-MDPVLLR 117

Query: 259 KVEEL 263
            +E+L
Sbjct: 118 PIEDL 122


>gi|108773091|ref|YP_636000.1| alpha subunit of RNA polymerase [Scenedesmus obliquus]
 gi|115311625|sp|P19587|RPOA_SCEOB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|88696657|gb|ABD48283.1| alpha subunit of RNA polymerase [Scenedesmus obliquus]
          Length = 478

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 44/119 (36%), Positives = 70/119 (58%), Gaps = 2/119 (1%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P     + T+ NALRR L++ L   AIT ++I+GV HE S++ GV E + D++LN KGI 
Sbjct: 31  PFKNSQSLTVANALRRTLLAELSNIAITHLEIEGVTHEYSTLVGVRESVLDLLLNFKGIA 90

Query: 94  LKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           LK +    K +  +   RGPGVV A D++    I+ ++PD  I  L+ +  + ++  +S
Sbjct: 91  LKNTSPVTKPLFGYLQVRGPGVVRASDLKFPPMIQCVDPDQYIATLNENGKLILKFRIS 149


>gi|260780686|ref|YP_003227042.1| RNA polymerase alpha subunit [Bryopsis hypnoides]
 gi|260176764|gb|ACX33773.1| RNA polymerase alpha subunit [Bryopsis hypnoides]
          Length = 363

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 69/279 (24%), Positives = 133/279 (47%), Gaps = 34/279 (12%)

Query: 35  LPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL 94
            P+    T+ NALRR L++     +IT V I+ + HE S++KG+ E + DI++N+K I +
Sbjct: 43  FPKNQGLTIANALRRTLLTESTECSITGVLIEDIKHEYSNLKGIKETVFDILMNLKKI-I 101

Query: 95  KMSGDSHKRVTI---FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
             SG S  +  +    ++GP V+ A +++  + +  +NPD  I  L+ ++ + M + + +
Sbjct: 102 FFSGQSFFKTQVSFLSEKGPIVLKAKNLKLPSFLFCINPDQYITTLETNSKINMTIFIDQ 161

Query: 152 G---------HGY----------VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
                     H Y             K + T+N     + +D  + PI  ++Y ++  +E
Sbjct: 162 STPKNFSYFTHCYYSNFSNNFFPFKLKKNFTQNQQSNFLFLDTQFCPISNLNYKIK-KKE 220

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK--EDINVKSL 250
            Q    + L   I T+GS+     +  A + L   L  F +    K E +  E+  ++ +
Sbjct: 221 SQK---EILFFEIWTNGSVHPNFILKKAIKNLLLNLIPFHSLRNSKIEFEDYENKKIQKI 277

Query: 251 PFNPALLKKVEELEL-----SVRSTNCLRGENIVYMGDL 284
                 ++K+ +L+L     S+ +   L+  NI+ +GDL
Sbjct: 278 VSQKKFIQKLIKLDLTNFPISLETYQSLKKLNILTIGDL 316


>gi|183397277|gb|ACC62185.1| RpoA1 [Francisella sp. PQ1104]
 gi|183397283|gb|ACC62188.1| RpoA1 [Francisella sp. PQ1105]
          Length = 154

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 48/145 (33%), Positives = 82/145 (56%), Gaps = 6/145 (4%)

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           TVS G          TE + +G I +DA ++PIK+V++ +      + L+     + + T
Sbjct: 16  TVSVGRNVGILSALPTELEKVGDIAVDADFNPIKRVAFEIFDNGASETLE-----VFVKT 70

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G+I    +V  A +   +Q+ +F++   P      D  + S   +P LLK +++LEL+V
Sbjct: 71  NGTIESLAAVTKALKYFCEQISVFVSLRVPSNGKTGDALLDS-NIDPILLKPIDDLELTV 129

Query: 268 RSTNCLRGENIVYMGDLIQRTEADM 292
           RS+NCLR ENI Y+GDL+Q +E+ +
Sbjct: 130 RSSNCLRAENIKYLGDLVQYSESQL 154


>gi|166714648|gb|ABY88049.1| RpoA [Stenotrophomonas sp. LMG 10887]
          Length = 122

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 44/125 (35%), Positives = 71/125 (56%), Gaps = 6/125 (4%)

Query: 142 VVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M L + +G GY P    R    E   IG + +DA +SP+++V+Y VE+AR  Q  D 
Sbjct: 1   AINMRLKIERGFGYQPVAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDL 60

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+
Sbjct: 61  DKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNG---VDPVLLR 117

Query: 259 KVEEL 263
            +++L
Sbjct: 118 PIDDL 122


>gi|71894584|ref|YP_278692.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma synoviae 53]
 gi|123747931|sp|Q4A5J0|RPOA_MYCS5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|71851372|gb|AAZ43981.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma synoviae 53]
          Length = 333

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 79/312 (25%), Positives = 140/312 (44%), Gaps = 45/312 (14%)

Query: 35  LPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL 94
           L RGF +TL  ALRR+L+S++ G A   V+I+GV HE ++++ V ED+  I+ N+K + L
Sbjct: 31  LERGFGNTLAVALRRILLSNITGIAPFCVRIEGVEHEFTALEKVSEDIVTILSNLKKVVL 90

Query: 95  KMSGDSHKRVTIFKRGPGV-----VTAGDIQTVN--DIEVLNPDHVICNLDVDAVVRMEL 147
               D  K   I K          +T+  +   N   +EV N D  I  L    V+++E+
Sbjct: 91  NYDEDYVKDNQIIKLSLNANEDNRITSNHLTVTNAPRVEVQNKDVEIATLSKPGVLKLEM 150

Query: 148 TVSKGHGYVPAKHHR-------------TENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
            +  G GYV  + ++             +       I +D+++SP+  V++ V       
Sbjct: 151 FLRAGRGYVDFEDNKKFIEEKEKELKELSSLSKGAFIAMDSVFSPVVNVAWKVTELNTAS 210

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRIL------------QDQLGMFINFEEPKKEVK 242
           +   ++L + ++T   +T E ++ LA +IL             D   +F + ++  ++ +
Sbjct: 211 LKIEEQLELELETKLGVTPESAIKLACKILVAHFQTIGDLTDLDSDEIFQSEKQSLEKEE 270

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           +D+ ++              L LS+RS N L    I  + +L       +  + N G KS
Sbjct: 271 DDMEIRL-------------LNLSMRSQNALAKSGIKTLNELASYPIEKLKEIKNLGEKS 317

Query: 303 LVEIKGVLGTMG 314
             EI   L   G
Sbjct: 318 REEIIRKLNEYG 329


>gi|166714630|gb|ABY88040.1| RpoA [Stenotrophomonas maltophilia]
          Length = 107

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 40/95 (42%), Positives = 61/95 (64%), Gaps = 3/95 (3%)

Query: 143 VRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G+GY PA   R    E   IG + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGYGYQPAAARRCPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           KL + I+T+G+I  E++V  A+ IL DQL +F +F
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDF 96


>gi|166714664|gb|ABY88057.1| RpoA [Stenotrophomonas sp. LMG 10853]
          Length = 122

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 44/125 (35%), Positives = 71/125 (56%), Gaps = 6/125 (4%)

Query: 142 VVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M L + +G GY PA   R    E   IG + +DA +SP+++V+Y VE+AR  Q  D 
Sbjct: 1   AINMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDL 60

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + I+T+G+I  E++V  A+ I  DQL +F +F    +   +  N      +P LL+
Sbjct: 61  DKLVIDIETNGTIDAEEAVRTAADIPSDQLSVFGDFTHRDRGAAKPANNG---VDPVLLR 117

Query: 259 KVEEL 263
            +++L
Sbjct: 118 PIDDL 122


>gi|166714692|gb|ABY88071.1| RpoA [Stenotrophomonas sp. LMG 11000]
          Length = 122

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 44/125 (35%), Positives = 71/125 (56%), Gaps = 6/125 (4%)

Query: 142 VVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M L + +G  Y PA   R    E   IG + +DA +SP+++V+Y VE+AR  Q  D 
Sbjct: 1   AINMRLKIERGFAYQPAALRRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDL 60

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+
Sbjct: 61  DKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNG---VDPVLLR 117

Query: 259 KVEEL 263
            +++L
Sbjct: 118 PIDDL 122


>gi|166714680|gb|ABY88065.1| RpoA [Stenotrophomonas sp. ICB207]
          Length = 122

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 40/93 (43%), Positives = 59/93 (63%), Gaps = 3/93 (3%)

Query: 145 MELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           M L + +G GY PA   R    E   IG + +DA +SP+++V+Y VE+AR  Q  D DKL
Sbjct: 4   MRLKIERGFGYQPAAARRRPDEETRTIGRLVLDASFSPVRRVAYAVEAARVEQRTDLDKL 63

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
            + I+T+G+I  E++V  A+ IL DQL +F +F
Sbjct: 64  VIDIETNGTIDAEEAVRTAADILSDQLSVFGDF 96


>gi|194033308|ref|YP_002000450.1| alpha subunit of RNA polymerase [Oedogonium cardiacum]
 gi|156619050|gb|ABU88203.1| RNA polymerase alpha subunit [Oedogonium cardiacum]
 gi|186968925|gb|ACC97248.1| alpha subunit of RNA polymerase [Oedogonium cardiacum]
          Length = 442

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 57/211 (27%), Positives = 97/211 (45%), Gaps = 47/211 (22%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P   G   T+ NALRR L+S L   A+T++QI  V+H+  +I+G+ E + D++LN+K I 
Sbjct: 116 PFFIGQGLTIANALRRTLLSELSSLAVTSIQIQDVVHQYQTIQGLQESVFDLLLNMKDIV 175

Query: 94  LKMSGD------SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           LK           + +V    +GP ++ A D+     I+ ++P+  I  L  D ++ M+ 
Sbjct: 176 LKSKTTIPVPQIGYLQV----QGPCIIKAKDLLLPPFIQCVDPEQYIATLSEDGILNMKF 231

Query: 148 TVSKG--------------------HGYVPAK----HHRTENDPIGLIT-------IDAL 176
            + +G                    H Y        H     + + L+        IDA 
Sbjct: 232 VIRQGKHSLTHVTPGYDSFTQKYDQHSYNSTCDTNVHSNKNRNSLSLLNTYSKHLIIDAS 291

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           ++P+ KV+Y +E      VLD+D+L    D+
Sbjct: 292 FNPVIKVNYIIE------VLDFDQLFFEKDS 316


>gi|183397279|gb|ACC62186.1| RpoA1 [Francisella noatunensis]
          Length = 154

 Score = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 48/145 (33%), Positives = 81/145 (55%), Gaps = 6/145 (4%)

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           TVS G          TE + +G I +DA ++PIK+V++ +      + L+     + + T
Sbjct: 16  TVSVGRNVGILSALPTELEKVGDIAVDADFNPIKRVAFEIFDNGASETLE-----VFVKT 70

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G+I    +V  A     +Q+ +F++   P      D  + S   +P LLK +++LEL+V
Sbjct: 71  NGTIEPLAAVTKALEYFCEQISVFVSLRVPSNGKTGDALLDS-NIDPILLKPIDDLELTV 129

Query: 268 RSTNCLRGENIVYMGDLIQRTEADM 292
           RS+NCLR ENI Y+GDL+Q +E+ +
Sbjct: 130 RSSNCLRAENIKYLGDLVQYSESQL 154


>gi|94502224|ref|ZP_01308710.1| DNA-directed RNA polymerase alpha chain [Candidatus Sulcia
          muelleri str. Hc (Homalodisca coagulata)]
 gi|94451195|gb|EAT14134.1| DNA-directed RNA polymerase alpha chain [Candidatus Sulcia
          muelleri str. Hc (Homalodisca coagulata)]
          Length = 92

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 39/67 (58%), Positives = 51/67 (76%)

Query: 29 LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
          L   EPL  G+  T+GN LRRVL+SSL G AI++V+I+GV HE S+IKGV ED+T+IILN
Sbjct: 23 LFKIEPLFPGWGVTIGNTLRRVLLSSLEGYAISSVKIEGVNHEFSTIKGVIEDMTEIILN 82

Query: 89 IKGINLK 95
          +K +  K
Sbjct: 83 LKKVRFK 89


>gi|58758774|gb|AAW81778.1| RNA polymerase alpha subunit [Andreaea rupestris]
          Length = 195

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 47/156 (30%), Positives = 80/156 (51%), Gaps = 3/156 (1%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P   G A+T+G A+RR L+  + G  IT  +   V HE S+I G+ E + DI++N K I 
Sbjct: 36  PFRCGQANTVGIAMRRALLGEIEGTCITCAKFKKVTHEYSTILGIQESVHDILINSKEIV 95

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK +    ++  I   GP  +TA DI     +++++    I  L     + +E  + K  
Sbjct: 96  LKSNSYETQKAFISILGPKKITAQDIILPPSVKIIDTTQYIATLTKAIHLDIESEIEKDC 155

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           GY      ++ +   GL  +DA++ PI+  +Y++ S
Sbjct: 156 GYRIQDSKKSTD---GLFFVDAVFMPIRNANYSIHS 188


>gi|166714708|gb|ABY88079.1| RpoA [Stenotrophomonas sp. LMG 10878]
          Length = 116

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 43/118 (36%), Positives = 69/118 (58%), Gaps = 6/118 (5%)

Query: 149 VSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           + +G GY PA   R    E   IG + +DA +SP+++V+Y VE+AR  Q  D DKL + I
Sbjct: 2   IERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLDKLVIDI 61

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
           +T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ +++L
Sbjct: 62  ETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNG---VDPVLLRPIDDL 116


>gi|183397281|gb|ACC62187.1| RpoA1 [Francisella noatunensis]
          Length = 154

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 50/147 (34%), Positives = 82/147 (55%), Gaps = 10/147 (6%)

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV--ESAREGQVLDYDKLSMTI 205
           TVS G           E + +G I +DA ++PIK+V++ +   SA E        L + +
Sbjct: 16  TVSVGRNVGILSALPIELEKVGDIAVDADFNPIKRVAFEIFDNSASE-------TLEVFV 68

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G+I    +V  A     +Q+ +F++ + P      D  + S   +P LLK +++LEL
Sbjct: 69  KTNGTIEPLAAVTKALEYFCEQISVFVSLKVPSNGKTGDALLDS-NIDPILLKPIDDLEL 127

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADM 292
           +VRS+NCLR ENI Y+GDL+Q +E+ +
Sbjct: 128 TVRSSNCLRAENIKYLGDLVQYSESQL 154


>gi|169835538|ref|ZP_02868726.1| hypothetical protein cdivTM_00193 [candidate division TM7
           single-cell isolate TM7a]
          Length = 96

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 36/78 (46%), Positives = 54/78 (69%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL  G+ +TLGN+LRRVLMSS+ GAA+ + +I+G  HE +++ G+ ED+ DI LN+K +
Sbjct: 19  EPLRGGYGNTLGNSLRRVLMSSIHGAAVISFKIEGATHEFTTVPGIKEDVVDISLNLKSV 78

Query: 93  NLKMSGDSHKRVTIFKRG 110
            +KM  D    + + K G
Sbjct: 79  KIKMHTDDPIELRLEKHG 96


>gi|166714666|gb|ABY88058.1| RpoA [Stenotrophomonas sp. LMG 10991]
          Length = 122

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 44/125 (35%), Positives = 70/125 (56%), Gaps = 6/125 (4%)

Query: 142 VVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M L + +G GY PA   R    E   IG   +DA +SP+++V+Y VE+A   Q  D 
Sbjct: 1   AINMRLKIERGFGYQPAAARRRPDEETRAIGRRVLDASFSPVRRVAYAVEAALVEQRTDL 60

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+
Sbjct: 61  DKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNG---VDPVLLR 117

Query: 259 KVEEL 263
            +++L
Sbjct: 118 PIDDL 122


>gi|307702712|ref|ZP_07639664.1| DNA-directed RNA polymerase alpha chain domain protein
           [Streptococcus oralis ATCC 35037]
 gi|307623828|gb|EFO02813.1| DNA-directed RNA polymerase alpha chain domain protein
           [Streptococcus oralis ATCC 35037]
          Length = 115

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 47/113 (41%), Positives = 74/113 (65%), Gaps = 4/113 (3%)

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKK--EVKEDINVKSLPFNPALLKKVEELE 264
           T+G+I  ED++ L++RIL + L +F N  E  K  EV ++ + +S   +  L + +EEL+
Sbjct: 2   TNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSTEVMKEADTES--DDRILDRTIEELD 59

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E+K  L  +GL L
Sbjct: 60  LSVRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEEVKLKLIDLGLGL 112


>gi|166714660|gb|ABY88055.1| RpoA [Stenotrophomonas sp. LMG 957]
          Length = 97

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 40/95 (42%), Positives = 59/95 (62%), Gaps = 3/95 (3%)

Query: 143 VRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R    E   IG + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFGYQPAAWRRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           KL + I+T+G+I  E++V  A  IL DQL +F +F
Sbjct: 62  KLVIDIETNGTIDAEEAVRTADDILSDQLSVFGDF 96


>gi|183397285|gb|ACC62189.1| RpoA1 [Francisella philomiragia]
          Length = 154

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 47/145 (32%), Positives = 81/145 (55%), Gaps = 6/145 (4%)

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           TVS G          TE + +G I +D+ ++PIK+V++ +      + L+     + + T
Sbjct: 16  TVSVGRNVGILSALPTELEKVGDIAVDSDFNPIKRVAFEIFDNGTNETLE-----VFVKT 70

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G+I    +V  A     +Q+ +F++   P      D  + S   +P LLK +++LEL+V
Sbjct: 71  NGTIEPLVAVTKALEYFCEQISVFVSLRVPSNGKTGDALLDS-NIDPILLKPIDDLELTV 129

Query: 268 RSTNCLRGENIVYMGDLIQRTEADM 292
           RS+NCLR ENI Y+GDL+Q +E+ +
Sbjct: 130 RSSNCLRAENIKYLGDLVQYSESQL 154


>gi|323149183|ref|YP_004222012.1| alpha subunit of RNA polymerase [Coccomyxa sp. C-169]
 gi|317467239|gb|ADV29860.1| alpha subunit of RNA polymerase [Coccomyxa sp. C-169]
          Length = 624

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 48/135 (35%), Positives = 71/135 (52%), Gaps = 10/135 (7%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P   G   T+  ALRR L+S L+G AI+AV+I G  H+ SSI GV E   DI+LN+K I 
Sbjct: 27  PFKVGQGTTVATALRRTLLSELQGIAISAVEIKGATHQYSSIAGVRESTLDIVLNLKQIV 86

Query: 94  LKMSGDSHKRVT----IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           L  +GD    +     +  +GP    A D++  N I  ++ D  I ++  +  + M+  +
Sbjct: 87  L--TGDVRNGLPAVGYLAVQGPKAARARDLKLPNGIRCVDGDQYIASVSANGSLTMKFVI 144

Query: 150 SKGHGYV----PAKH 160
           S G  YV    P+ H
Sbjct: 145 SAGKNYVSPHSPSAH 159


>gi|166714652|gb|ABY88051.1| RpoA [Stenotrophomonas sp. LMG 11004]
          Length = 98

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 39/95 (41%), Positives = 59/95 (62%), Gaps = 3/95 (3%)

Query: 143 VRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA        E   IG + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFGYQPAAARCRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           KL + I+T+G+I  E++V  A+ IL DQL +F +F
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDF 96


>gi|108796892|ref|YP_636190.1| alpha subunit of RNA polymerase [Pseudendoclonium akinetum]
 gi|122245934|sp|Q3ZJ77|RPOA_PSEAK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|56159590|gb|AAV80614.1| alpha subunit of RNA polymerase [Pseudendoclonium akinetum]
          Length = 577

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 55/183 (30%), Positives = 97/183 (53%), Gaps = 33/183 (18%)

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL--- 224
           IG   IDA++ PI +V+Y +ES  + ++   D++ + + T+GSI    ++  A++ L   
Sbjct: 394 IGYFPIDAIFMPINRVNYLIESTEDIKLKIKDRVILEVWTNGSIHPRHAIHKAAKALIQL 453

Query: 225 -----QDQLGMFI-----NFEEPKKEVKEDIN-------VKSLP---FNPALLKK----- 259
                Q +  +F+     +FEE + ++K+ I+       +K+ P    NP L K+     
Sbjct: 454 FLPLQQIRTNLFLISDNSHFEEGQDKIKKRIDNFKKEALLKANPQIQANPQLKKRNFDHR 513

Query: 260 -----VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +  LEL+ R  +CL+  NI  + DLI  ++ D+L + NFGR+SL+E++  L  M 
Sbjct: 514 LLELDIANLELTARPYSCLKLANINTIEDLISYSQEDLLSIKNFGRRSLIEVQKALQLMK 573

Query: 315 LFL 317
           L L
Sbjct: 574 LTL 576



 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 43/125 (34%), Positives = 64/125 (51%), Gaps = 2/125 (1%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P   G A T+ NALRR L+S L G +IT V++ G  +E   I GV E + DI+LN+K I 
Sbjct: 63  PFAPGQALTVANALRRSLLSQLPGTSITLVEVRGASNEYEIITGVRESILDILLNLKQIV 122

Query: 94  LKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           L    +       F    GPGV+ A D++  + I  ++P+  I  L     + M+  +  
Sbjct: 123 LTSDFEIFSPQIGFLSVEGPGVIRANDLKLPSFIYAVDPNQYIATLSNSGRLNMKFLICC 182

Query: 152 GHGYV 156
           G  Y+
Sbjct: 183 GKNYI 187


>gi|119662805|emb|CAJ33194.1| RNA polymerase alpha subunit [Lactobacillus manihotivorans]
          Length = 89

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 36/87 (41%), Positives = 55/87 (63%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K V I   GP  VTA DI + +D+EVLNP+  IC +       + +TV  G GYV A  +
Sbjct: 3   KTVEIDVAGPATVTAADIVSDSDVEVLNPEQYICTVAEGGRFHVRMTVKTGRGYVAADQN 62

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVE 188
           + ++ PIG++ ID++++PI +V+Y VE
Sbjct: 63  KVDDMPIGVLPIDSIFTPISRVNYQVE 89


>gi|331268154|ref|YP_004347803.1| alpha subunit of RNA polymerase [Chlorella variabilis]
 gi|325296331|gb|ADZ05051.1| alpha subunit of RNA polymerase [Chlorella variabilis]
          Length = 239

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 59/213 (27%), Positives = 103/213 (48%), Gaps = 16/213 (7%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           +G A T  NALRR L+S + G  +T + ++G  HE + + GV E + DIILN+K +    
Sbjct: 33  QGQALTFANALRRTLLSEIPGIIMTDILVEGASHEFAILPGVEETVLDIILNLKKLVFAP 92

Query: 97  SGDSHKRVTIFKR-------GPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMEL 147
           S      +  F+        GP  ++  D++    ++ + P   I  +    +  +R  L
Sbjct: 93  STSKLINLENFQATGFLKSCGPRKLSGADVKLPLTLKCVEPKAHIATITNGAEFALRFNL 152

Query: 148 TVSKGHGYVPAK-HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            +      V  K ++  EN    L+ +D +  PI+KV+Y +++    Q L+Y  + + + 
Sbjct: 153 ELRNPQQSVTNKIYYPVENKTRKLV-LDNVPMPIQKVNYVIKALNGKQGLEY--IVLEVW 209

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           TDGS+  ++SV  A   L++    F  F E  K
Sbjct: 210 TDGSVLPQESVQFA---LKNLTNFFFQFAEMSK 239


>gi|255961329|ref|YP_003097511.1| RNA polymerase alpha chain [Selaginella moellendorffii]
 gi|302824557|ref|XP_002993921.1| hypothetical protein SELMODRAFT_137778 [Selaginella moellendorffii]
 gi|254941501|gb|ACT89016.1| RNA polymerase alpha chain [Selaginella moellendorffii]
 gi|296399215|gb|ADH10390.1| RNA polymerase alpha subunit [Selaginella moellendorffii]
 gi|300138288|gb|EFJ05062.1| hypothetical protein SELMODRAFT_137778 [Selaginella moellendorffii]
          Length = 247

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 67/223 (30%), Positives = 103/223 (46%), Gaps = 16/223 (7%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV--QIDGVLHEISSIKGVHEDLTDIIL 87
            I  P   G A+TLG A+RR L+  L GA IT      + + HE ++I GV E + DI++
Sbjct: 30  FIISPPKIGQANTLGIAMRRALLGELEGACITPAGSPPERINHEYTAIAGVRESVHDILM 89

Query: 88  NIKGINLK---MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           N+K I LK    S      + I   GP  VTA DI     +  ++P   I  +       
Sbjct: 90  NLKEIVLKTNPFSAAQEAHIPIV--GPRKVTAQDIVLPPSVGTMDPTQHIATITRKIHSS 147

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES-AREGQVLDYDKLSM 203
           + L V +G G+   K +  E    G +  DA++ PI+  +Y++      G  +  + L +
Sbjct: 148 IGLRVERGCGF--RKRNMIEYQ-KGSLPPDAVFMPIRHANYSIHRLGSHGGGIMKEMLLL 204

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
              TDGS T  +++  ASR L +    F     P   + E I+
Sbjct: 205 EARTDGSPTPREAIYEASRNLANLFSPF-----PHNNIHEHID 242


>gi|289804411|ref|ZP_06535040.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
          subsp. enterica serovar Typhi str. AG3]
          Length = 74

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 38/77 (49%), Positives = 51/77 (66%), Gaps = 3/77 (3%)

Query: 2  IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
          +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1  MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62 AVQIDGVLHEISSIKGV 78
           V+IDGVLHE S+ +GV
Sbjct: 58 EVEIDGVLHEYSTKEGV 74


>gi|246880788|gb|ACS95100.1| alpha subunit of RNA polymerase [Dunaliella salina]
          Length = 547

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 48/147 (32%), Positives = 75/147 (51%), Gaps = 25/147 (17%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM- 96
           G + T+ NALRR L+S   G AI +V+ID V HE S++ GV + + DI+LN K I LK  
Sbjct: 24  GQSITVANALRRSLLSDCTGLAIISVKIDAVQHEYSTLPGVRDSVLDILLNFKEIVLKKV 83

Query: 97  -------SGDSHKRV---------TIFK--------RGPGVVTAGDIQTVNDIEVLNPDH 132
                  +G  +K +         T FK        +GPG++ A D++    I+ ++P+ 
Sbjct: 84  KNPFGGPNGYKNKGLSSVYDKVGSTFFKPVVGYLKVKGPGIIRAKDLRLPPFIQCVDPNQ 143

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAK 159
            I  L  D V+ ++  + +G  Y   K
Sbjct: 144 YIATLAEDGVLNVKFVIMEGKSYYVQK 170


>gi|119662857|emb|CAJ33221.1| RNA polymerase alpha subunit [Lactobacillus coryniformis subsp.
           coryniformis KCTC 3167]
          Length = 98

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 36/98 (36%), Positives = 65/98 (66%)

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           ++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++IL + L 
Sbjct: 1   VLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKILTEHLD 60

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +F+N  +  K  +  +  +  P    L   +EEL+LSV
Sbjct: 61  IFVNLTDEAKNAEIMVEKEETPKEKMLEMTIEELDLSV 98


>gi|81301|pir||S05342 DNA-directed RNA polymerase (EC 2.7.7.6) alpha chain - green alga
           KS3/2 chloroplast (fragment)
          Length = 129

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 40/99 (40%), Positives = 60/99 (60%), Gaps = 2/99 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P     + T+ NALRR L++ L   AIT ++I+GV HE S++ GV E + D++LN KGI 
Sbjct: 31  PFKNSQSLTVANALRRTLLAELSNIAITHLEIEGVTHEYSTLVGVRESVLDLLLNFKGIA 90

Query: 94  LKMSGDSHKRVTIF--KRGPGVVTAGDIQTVNDIEVLNP 130
           LK +    K +  +   RGPGVV A D++    I+ ++P
Sbjct: 91  LKNTSPVTKPLFGYLQVRGPGVVRASDLKFPPMIQCVDP 129


>gi|187763133|ref|YP_001876608.1| RNA polymerase alpha subunit [Welwitschia mirabilis]
 gi|163311663|gb|ABY26821.1| RNA polymerase alpha subunit [Welwitschia mirabilis]
 gi|220983428|dbj|BAH11197.1| RNA polymerase alpha chain [Welwitschia mirabilis]
          Length = 340

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 77/306 (25%), Positives = 135/306 (44%), Gaps = 24/306 (7%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQI--DGVLHEISS--IKGVHEDLTDIILNI 89
           PL RG   T+G+ALRR L+  + G  +T V+     V H  SS  I G+ E + DII+N+
Sbjct: 36  PLLRGQGGTIGSALRRTLLRDVEGTNVTHVKFFNKRVKHLFSSSTILGIEESVHDIIMNL 95

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           + I  +       +  I+  GP  VTA DI     I++++    I ++     + + L +
Sbjct: 96  REIVFRCELHGIHKAYIYTVGPKNVTAQDIILPPFIQIVDGTQHIASITKPIHLHVTLKI 155

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR-EGQVLDYDKLSMTIDTD 208
            K  G      H         I  +  Y P++ V+Y V   + E  +  YD L   + T+
Sbjct: 156 EKNWGETTESIHPITKYFTRYIPTEIFYMPVRSVTYNVYFYKDEYDIHIYDILIFELWTN 215

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKE---VKEDINVKSLPFNPALLKK------ 259
           G +T ++++  A   L D +   ++      E   VKE I    LP    + +       
Sbjct: 216 GELTPKEALYEACWRLIDLIIPLLDVPLLHVEGSGVKESI---PLPIVSNMNRTQEDLFV 272

Query: 260 ----VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
               +++L L  + +  LR  +I  + D +  ++ D L+   + +K  +E    L  +  
Sbjct: 273 QHLFIDQLGLPSKISKSLRESHIYRVSDFMNYSQQD-LKNLEYSKKESIE--QTLEILHK 329

Query: 316 FLGMNL 321
           + G+NL
Sbjct: 330 YFGINL 335


>gi|77406111|ref|ZP_00783185.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae H36B]
 gi|77175292|gb|EAO78087.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae H36B]
          Length = 110

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 43/90 (47%), Positives = 61/90 (67%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E ++    + EPL RG+  TLGN+LRR L+SSL GAA+T+++IDGVLHE  +I GV ED+
Sbjct: 14  ENKDYGRFVIEPLERGYGTTLGNSLRRXLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDV 73

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
             IILN+KG+ +K   +  K + +   GP 
Sbjct: 74  MQIILNVKGLAVKSYVEDEKIIELDVEGPA 103


>gi|222139917|ref|YP_002519985.1| RNA polymerase alpha chain [Ephedra equisetina]
 gi|220983586|dbj|BAH11353.1| RNA polymerase alpha chain [Ephedra equisetina]
          Length = 258

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 58/218 (26%), Positives = 105/218 (48%), Gaps = 5/218 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQID-GVLHEISSIKGVHEDLTDIILNIKGI 92
           PL +G A+TL  A+R+ L+  ++G  IT  +    +LHE SSI G+ E + DI++N+K I
Sbjct: 36  PLFKGQANTLAIAIRKTLLQEVKGTYITYARFQKNILHEYSSIIGIKESVHDILMNLKQI 95

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            L+         +I   GP  VTA DI   + I++++    I +L       + L + K 
Sbjct: 96  VLRSELYGIHEASICTVGPKNVTAQDIILPSSIQIIDDTQHIASLTKRIPFNVTLKIEKK 155

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
             Y      + ++       ID +  P++ V++++ S +    +  + L   I T+G +T
Sbjct: 156 KRYTIENMKQPKD---IFFPIDGVSLPVQNVNFSIHSYKSSDNIQ-EMLIFEIWTNGGLT 211

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
             +++  A   L D +   +  E+  K  ++  N  SL
Sbjct: 212 PRETIYEACWSLLDLIIPLLCVEQNIKNSQKKPNPLSL 249


>gi|207109275|ref|ZP_03243437.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           HPKX_438_CA4C1]
          Length = 176

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 51/165 (30%), Positives = 84/165 (50%), Gaps = 3/165 (1%)

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
           P+++ R E  P G + +D  ++PIKKV Y +E+       +Y+K+   I+TDG I    +
Sbjct: 1   PSENTR-ELMPEGYMPLDGSFTPIKKVVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKA 59

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGE 276
              A +++  QLG+F   E P   ++   +         L  K+E + LS R  NCL   
Sbjct: 60  FLSAVKVMSKQLGVF--GERPIANMEYSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKI 117

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
            I Y+G+L+  +E ++  + N G+KS  EI   L  +G  +G  L
Sbjct: 118 GIKYVGELVLMSEEELKGVKNMGKKSYDEIAEKLNDLGYPVGTEL 162


>gi|153805627|ref|YP_001382211.1| alpha subunit of RNA polymerase [Leptosira terrestris]
 gi|134270158|gb|ABO69347.1| alpha subunit of RNA polymerase [Leptosira terrestris]
          Length = 537

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 38/124 (30%), Positives = 66/124 (53%), Gaps = 2/124 (1%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P   G   T+ N LRR L+S L G AITAV+I    HE  ++ G+ E + DIILN+K + 
Sbjct: 33  PFAHGQGITVANMLRRTLLSELSGLAITAVEIKEASHEYMTLPGISESVQDIILNLKQLI 92

Query: 94  LKMSGDSHKRVTIFK--RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
            + + D  +    F   +GP ++ A   +  + I+ ++P+  I  L  +  + +++ + +
Sbjct: 93  FRSNFDLKQPEFGFLSIQGPAIIKASHFRLPSFIKCVDPNQYIATLAFNGQLNLKVQICQ 152

Query: 152 GHGY 155
           G  Y
Sbjct: 153 GKNY 156


>gi|222446775|gb|ACM51431.1| RNA polymerase alpha subunit [Caulerpa filiformis]
          Length = 301

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 51/194 (26%), Positives = 90/194 (46%), Gaps = 20/194 (10%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           T  N+LRR L+          +QI GV HE SS+ GV E + DII N++ +  ++S   H
Sbjct: 32  TFANSLRRTLLEDNSRYIFDTIQISGVEHEYSSLIGVRESVIDIIFNLQKLIFEVSDKVH 91

Query: 102 --------KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS--- 150
                   +   +   GPG++ A  I    D   + PD  I  L+VD  +  +L  S   
Sbjct: 92  LVGKDPKPQIAFLNFTGPGILRAQHIHLPKDFHFVYPDQYIATLEVDGKLNFKLFFSPKI 151

Query: 151 --KGHGYVPAKHHRTENDPIGL-----ITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
             K +  + +K       P  +     + +D+ +  I++V+YT++S  +    ++  +  
Sbjct: 152 FQKKYKSLHSKSGSGRQMPPSVLLENYLFLDSDFCSIERVNYTIQSGNQNPKEEF--ILF 209

Query: 204 TIDTDGSITGEDSV 217
            I T+GSI  + ++
Sbjct: 210 EIWTNGSIHPQKAI 223


>gi|7524918|ref|NP_045920.1| RNA polymerase alpha chain [Chlorella vulgaris]
 gi|3024560|sp|P56298|RPOA_CHLVU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|2224512|dbj|BAA57996.1| RNA polymerase alpha subunit [Chlorella vulgaris]
          Length = 278

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 103/242 (42%), Gaps = 47/242 (19%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG A T GN++RR L+S + G  +T V+I G  HE + +  V E + +I+LN+K      
Sbjct: 33  RGQALTFGNSIRRALLSEMPGFLMTDVRIQGATHEFAVLPDVEETVLEILLNLKKTVFVP 92

Query: 97  SGDSHKRVTIFK-------RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
               +++   F+        GPG V A DI+    ++ ++P+  I  L   A + +   +
Sbjct: 93  RIPKNQKFETFQGFGFLKNNGPGKVRAADIRLPETVQCVSPEVHIATLTSGAELSLRFNL 152

Query: 150 S--------KGHGYVPAK---HHRTENDPIGLIT-------------------------- 172
                    K  G   +K     +TE+  +   T                          
Sbjct: 153 QFRNFSQLEKREGTFKSKTVAQAKTEDGNVQDTTNELPTLEKNSLFFQQLQNKRNSKDQL 212

Query: 173 -IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +D +  P++KV+Y ++S       +Y  + + I TDGS+  ++SV  A R L D    F
Sbjct: 213 FLDTVPMPVQKVNYVIKSLNAKNGSEY--IILEIWTDGSLYPQESVEFALRNLTDLFFQF 270

Query: 232 IN 233
            N
Sbjct: 271 AN 272


>gi|70945266|ref|XP_742471.1| DNA-directed RNA polymerase alpha chain [Plasmodium chabaudi
           chabaudi]
 gi|56521474|emb|CAH79423.1| DNA-directed RNA polymerase alpha chain, putative [Plasmodium
           chabaudi chabaudi]
          Length = 529

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 54/179 (30%), Positives = 90/179 (50%), Gaps = 13/179 (7%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM---SGDSH 101
           NA RRV +  L+G   TA++I G+ HE   I GV E+  D+  N++ I  K    + D +
Sbjct: 255 NAFRRVAIKHLKGGRATALRIPGMKHEYYCIVGVRENFFDLSQNLRQITFKNVPENADMN 314

Query: 102 KRVT-IFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV-PA 158
             +T  F+ +GP +V AG +Q   +IE++N +  IC +   + + M++ +     YV P 
Sbjct: 315 NYITGKFRIKGPMIVVAGHMQLPKNIEIINKNQYICYVAAGSYLEMDVKIESIEEYVMPE 374

Query: 159 KHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDY--DKLSMTIDTDGSIT 212
              ++ N  I     I   +  +P++   +T    R G  LD   +   + + TDGSIT
Sbjct: 375 YGSQSRNRDICKDNFIHFCSSCTPVEHFGFT--GQRRGINLDVLGEINIVEMHTDGSIT 431


>gi|213420797|ref|ZP_03353863.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E01-6750]
          Length = 56

 Score = 68.9 bits (167), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 31/54 (57%), Positives = 40/54 (74%)

Query: 278 IVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 2   IHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 55


>gi|124512894|ref|XP_001349803.1| DNA-directed RNA polymerase alpha chain, putative [Plasmodium
           falciparum 3D7]
 gi|23615220|emb|CAD52210.1| DNA-directed RNA polymerase alpha chain, putative [Plasmodium
           falciparum 3D7]
          Length = 619

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 50/181 (27%), Positives = 89/181 (49%), Gaps = 17/181 (9%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLK-----MSGD 99
           NA RRV +  L+G  +TA++I  + HE   I GV E+  D+  N++ I  K     +  D
Sbjct: 267 NAFRRVAIKHLKGGRVTALRIPNMKHEFYCIVGVRENFFDLAQNLRQITFKNVPEDVDMD 326

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV-PA 158
           ++       +GP +V AG +Q   ++E++N +  IC++   + + M++ +     YV P 
Sbjct: 327 NYMIGKFRIKGPMIVVAGHMQLPKNVEIVNRNQYICSVAAGSYLSMDVKIESIEEYVMPE 386

Query: 159 KHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYDKLS----MTIDTDGSI 211
              ++ N  I     I   +  +P++   +T    R G  ++ D L     + + TDGSI
Sbjct: 387 YGSQSRNRDICKDNFIHFSSSCTPVEHFVFT--GQRRG--INLDTLGEINIVEMHTDGSI 442

Query: 212 T 212
           T
Sbjct: 443 T 443


>gi|221060799|ref|XP_002261969.1| dna-directed rna polymerase alpha chain [Plasmodium knowlesi strain
           H]
 gi|193811119|emb|CAQ41847.1| dna-directed rna polymerase alpha chain,putative [Plasmodium
           knowlesi strain H]
          Length = 674

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 51/181 (28%), Positives = 87/181 (48%), Gaps = 17/181 (9%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLK-----MSGD 99
           NA RRV M  L+G  +TA++I  + HE   I GV E+  D+  N++ I  K     +  D
Sbjct: 322 NAFRRVAMKHLKGGRVTALRIPNMKHEFYCIVGVRENFFDLAQNLRQITFKNVPENIDMD 381

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV-PA 158
           ++       +GP +V AG +Q    IE++N +  IC++   + + M++ +     YV P 
Sbjct: 382 NYITGKFRIKGPMIVVAGHMQLPKGIEIVNKNQYICSVSAGSYLEMDVKIESIEEYVMPE 441

Query: 159 KHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYDKLS----MTIDTDGSI 211
              ++ N  I     I   +  +P++   +     R G  ++ D L     + + TDGSI
Sbjct: 442 YGSQSRNRDICKDNFIHFSSSCTPVEYFGFM--GQRRG--INLDTLGEINIVEMHTDGSI 497

Query: 212 T 212
           T
Sbjct: 498 T 498


>gi|213585431|ref|ZP_03367257.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E98-0664]
          Length = 54

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/52 (57%), Positives = 39/52 (75%)

Query: 280 YMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 2   YIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 53


>gi|218755234|ref|ZP_03534030.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis GM 1503]
          Length = 153

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 43/134 (32%), Positives = 75/134 (55%), Gaps = 16/134 (11%)

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNPA 255
           +++T  SI+  D++A A + L +  G+   +N E       P     + I   +LP    
Sbjct: 1   SVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALP---- 56

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
               +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL
Sbjct: 57  ----IDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGL 112

Query: 316 FLGMNLPDWPPESI 329
            L  + P + P  +
Sbjct: 113 SLKDSPPSFDPSEV 126


>gi|83314615|ref|XP_730437.1| DNA-directed RNA polymerase subunit alpha [Plasmodium yoelii yoelii
           str. 17XNL]
 gi|23490159|gb|EAA22002.1| DNA-directed RNA polymerase alpha chain [Plasmodium yoelii yoelii]
          Length = 656

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 54/179 (30%), Positives = 90/179 (50%), Gaps = 13/179 (7%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLK-MSGDSHKR 103
           NA RRV +  L+G  +TA++I G+ HE   I GV E+  D+  N++ I  K +  D+   
Sbjct: 304 NAFRRVAIKHLKGGRVTALRIPGMKHEYYCIVGVRENFFDLSQNLRQITFKNVPEDADMN 363

Query: 104 VTI---FK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV-PA 158
             I   F+ +GP +V AG +Q   +IE++N +  IC +   + + M++ +     YV P 
Sbjct: 364 NYIIGKFRIKGPMIVVAGHMQLPKNIEIINKNQYICYVAAGSYLEMDVKIESIEEYVMPE 423

Query: 159 KHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDY--DKLSMTIDTDGSIT 212
              ++ N  I     I   +  +P++   +T    R G  LD   +   + + TDGSIT
Sbjct: 424 YGSQSRNRDICKDNFIHFCSSCTPVEYFGFT--GQRRGINLDILGEINIVEMHTDGSIT 480


>gi|166714710|gb|ABY88080.1| RpoA [Stenotrophomonas sp. LMG 10851]
 gi|166714712|gb|ABY88081.1| RpoA [Stenotrophomonas sp. LMG 10877]
          Length = 93

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 36/96 (37%), Positives = 60/96 (62%), Gaps = 3/96 (3%)

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           IG + +DA +SP+++V+Y VE+AR  Q  D DKL + I+T+G+I  E++V  A+ IL DQ
Sbjct: 1   IGRLVLDASFSPVRRVAYAVEAARVEQRTDLDKLVIDIETNGTIDAEEAVRTAADILSDQ 60

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
           L +F +F    +   +  N      +P LL+ +++L
Sbjct: 61  LSVFGDFTHRDRGAAKPANNG---VDPVLLRPIDDL 93


>gi|289445057|ref|ZP_06434801.1| LOW QUALITY PROTEIN: probable DNA-directed RNA polymerase rpoa
           [Mycobacterium tuberculosis T46]
 gi|289417976|gb|EFD15216.1| LOW QUALITY PROTEIN: probable DNA-directed RNA polymerase rpoa
           [Mycobacterium tuberculosis T46]
          Length = 173

 Score = 67.0 bits (162), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 43/135 (31%), Positives = 75/135 (55%), Gaps = 16/135 (11%)

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNP 254
           + ++T  SI+  D++A A + L +  G+   +N E       P     + I   +LP   
Sbjct: 20  LDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALP--- 76

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +G
Sbjct: 77  -----IDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLG 131

Query: 315 LFLGMNLPDWPPESI 329
           L L  + P + P  +
Sbjct: 132 LSLKDSPPSFDPSEV 146


>gi|313616947|gb|EFR89580.1| DNA-directed RNA polymerase subunit alpha [Listeria innocua FSL
           S4-378]
 gi|313622258|gb|EFR92767.1| DNA-directed RNA polymerase subunit alpha [Listeria innocua FSL
           J1-023]
          Length = 107

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 37/103 (35%), Positives = 62/103 (60%)

Query: 215 DSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLR 274
           ++V+L ++IL + L +F+N  +  ++ +  I  +       L   +EEL+LSVRS NCL+
Sbjct: 1   EAVSLGAKILSEHLSIFVNLTDEAQKAEIMIEKEESHKEKVLEMTIEELDLSVRSYNCLK 60

Query: 275 GENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
              I  + +L  ++E DM+++ N GRKSL E+K  L  +GL L
Sbjct: 61  RAGINTVQELADKSEDDMMKVRNLGRKSLEEVKVKLADLGLSL 103


>gi|156102625|ref|XP_001617005.1| hypothetical protein [Plasmodium vivax SaI-1]
 gi|148805879|gb|EDL47278.1| hypothetical protein, conserved [Plasmodium vivax]
          Length = 668

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 52/181 (28%), Positives = 88/181 (48%), Gaps = 17/181 (9%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLK---MSGDSH 101
           NA RRV +  L+G  +TA++I  + HE   I GV E+  D+  N++ I  K      D  
Sbjct: 316 NAFRRVAIKHLKGGRVTALRIPNMKHEFYCIVGVRENFFDLAQNLRHITFKNVPEEADID 375

Query: 102 KRVT-IFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV-PA 158
             +T  F+ +GP +V AG +Q    IE++N +  IC++   + + M++ +     YV P 
Sbjct: 376 NYITGKFRIKGPMIVVAGHMQLPKGIEIVNKNQYICSVSAGSYLEMDVKIESIEEYVMPE 435

Query: 159 KHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYDKLS----MTIDTDGSI 211
              ++ N  I     I   +  +P++   +     R G  ++ D L     + + TDGSI
Sbjct: 436 YGSQSRNRDICKDNFIHFSSSCTPVEYFGFM--GQRRG--INLDTLGEINIVEMHTDGSI 491

Query: 212 T 212
           T
Sbjct: 492 T 492


>gi|260202639|ref|ZP_05770130.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis T46]
 gi|289763639|ref|ZP_06523017.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis GM 1503]
 gi|289711145|gb|EFD75161.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis GM 1503]
          Length = 152

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 43/133 (32%), Positives = 74/133 (55%), Gaps = 16/133 (12%)

Query: 205 IDTDGSITGEDSVALASRILQDQLGMF--INFEE------PKKEVKEDINVKSLPFNPAL 256
           ++T  SI+  D++A A + L +  G+   +N E       P     + I   +LP     
Sbjct: 1   METKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALP----- 55

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL 
Sbjct: 56  ---IDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLS 112

Query: 317 LGMNLPDWPPESI 329
           L  + P + P  +
Sbjct: 113 LKDSPPSFDPSEV 125


>gi|68076655|ref|XP_680247.1| DNA-directed RNA polymerase alpha chain [Plasmodium berghei strain
           ANKA]
 gi|56501153|emb|CAH98242.1| DNA-directed RNA polymerase alpha chain, putative [Plasmodium
           berghei]
          Length = 573

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 53/179 (29%), Positives = 90/179 (50%), Gaps = 14/179 (7%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLK---MSGDSH 101
           NA RRV +  L+G  +TA++I G+ HE   I GV E+  D+  N++ I  K    + D +
Sbjct: 222 NAFRRVAIKHLKGGRVTALRIPGMKHEYYCIVGVRENFFDLSQNLRQITFKNVPENADMN 281

Query: 102 KRVT-IFK-RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV-PA 158
             +   F+ +GP +V AG +Q   +IE++N +  IC +   + + M++ +     YV P 
Sbjct: 282 NYIIGKFRIKGPMIVVAGHMQLPKNIEIINKNQYICYVAAGSYLEMDVKIESIEEYVMPE 341

Query: 159 KHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDY--DKLSMTIDTDGSIT 212
              ++ N  I     I   +  +P++   +T    R G  LD   +   + + TDGSIT
Sbjct: 342 YGSQSRNRDICKDNFIFCSSC-TPVEYFGFT--GQRRGINLDILGEINIVEMHTDGSIT 397


>gi|143452|gb|AAA22708.1| RNA polymerase alpha subunit [Bacillus subtilis]
          Length = 65

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 28/43 (65%), Positives = 36/43 (83%)

Query: 30 MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE 
Sbjct: 23 FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEF 65


>gi|225466312|ref|XP_002271159.1| PREDICTED: similar to Os04g0237300, partial [Vitis vinifera]
          Length = 274

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 39/130 (30%), Positives = 71/130 (54%), Gaps = 4/130 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTL----MIAEPLPRGFAHTLGNALRRVLMSSLRG 57
           I+++ +  +    +++  +    +N+ L     I  PL +G A T+G A+RR L+  + G
Sbjct: 145 IRRSEKVTVSTRTLQWKCVESRVDNKRLCYGRFILSPLIKGQADTIGIAMRRALLGEIEG 204

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
             IT  + + + HE S+I G+ E + +I++N+K I L+ +    +   I  RGPG VTA 
Sbjct: 205 TCITRAKSEKIPHEYSTIVGIQESVHEILMNLKEIVLRSNLYGTRGAFICARGPGYVTAQ 264

Query: 118 DIQTVNDIEV 127
           DI +   +E+
Sbjct: 265 DIISPPSVEI 274


>gi|58618634|gb|AAW80815.1| RNA polymerase alpha subunit [Polytrichadelphus purpureus]
          Length = 165

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 47/162 (29%), Positives = 83/162 (51%), Gaps = 20/162 (12%)

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           + PI+  +Y+V S      +  + L + I T+GSIT ++++  ASR L D    F++ E+
Sbjct: 1   FMPIRNANYSVHSFENNNKIQ-EILFIEIWTNGSITPKEALYEASRSLXDLFIPFLHTEK 59

Query: 237 P------KKEVKEDINVKSLPFNPALLKK----------VEELELSVRSTNCLRGENIVY 280
                  K E K +       F+P   K           +++LELS R+ NCL+  N+  
Sbjct: 60  KETIDGLKTEYKSNDMSDFSSFSPLANKSTKEITFKHIFIDQLELSARAYNCLKRVNVHT 119

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           + DL+  ++ D++++ NFG+KS   ++ VL  +     +NLP
Sbjct: 120 ISDLLNYSQDDLMKIKNFGKKS---VEQVLEALXKXFSINLP 158


>gi|302858180|ref|XP_002960035.1| hypothetical protein VOLCADRAFT_72193 [Volvox carteri f.
           nagariensis]
 gi|300253491|gb|EFJ38900.1| hypothetical protein VOLCADRAFT_72193 [Volvox carteri f.
           nagariensis]
          Length = 136

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 33/108 (30%), Positives = 59/108 (54%), Gaps = 11/108 (10%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P     + T+ N +RR L+S L   AIT+++I+G+LH+ SS+ G+ E + D+I N++ I 
Sbjct: 29  PFDDSLSQTIANDIRRTLLSELTSLAITSIEIEGILHKYSSLPGMKETVLDLICNLQSIV 88

Query: 94  LKMSGDSHKRVTIFK-----------RGPGVVTAGDIQTVNDIEVLNP 130
           LK    S   +T+              GP V+ A D++  + ++ ++P
Sbjct: 89  LKKQEISFTNITLRSTKKTYRGFLNVSGPRVIKAMDLKLPSGLQCVDP 136


>gi|166714662|gb|ABY88056.1| RpoA [Stenotrophomonas sp. LMG 978]
          Length = 81

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 31/78 (39%), Positives = 48/78 (61%), Gaps = 3/78 (3%)

Query: 143 VRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R    E   IG + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSV 217
           KL + I+ +G+I  E++V
Sbjct: 62  KLVIDIENNGTIDAEEAV 79


>gi|296120871|ref|YP_003628649.1| RNA polymerase subunit alpha domain protein [Planctomyces
           limnophilus DSM 3776]
 gi|296013211|gb|ADG66450.1| RNA polymerase alpha subunit domain protein [Planctomyces
           limnophilus DSM 3776]
          Length = 451

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 31/66 (46%), Positives = 44/66 (66%)

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           L + V + ELSVRS NCL   +I  +GDL + +E+D+L+  NFG  SLVEI+ ++   GL
Sbjct: 289 LSRPVTDFELSVRSRNCLASMDIHTLGDLTRVSESDLLQGKNFGETSLVEIRDLMQQHGL 348

Query: 316 FLGMNL 321
            +G NL
Sbjct: 349 KVGQNL 354



 Score = 42.0 bits (97), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 36/61 (59%), Gaps = 1/61 (1%)

Query: 251 PFNPALLKK-VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           P   ALL + V +L LSVR+  C+    I  +G+L+Q++  ++L   NFG  SL EI+  
Sbjct: 381 PQEQALLSRPVSDLNLSVRARKCMARLQIGTLGELVQKSADELLATKNFGVTSLNEIRAQ 440

Query: 310 L 310
           L
Sbjct: 441 L 441


>gi|156089709|ref|XP_001612261.1| hypothetical protein [Babesia bovis T2Bo]
 gi|154799515|gb|EDO08693.1| hypothetical protein BBOV_III011410 [Babesia bovis]
          Length = 610

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 55/196 (28%), Positives = 90/196 (45%), Gaps = 26/196 (13%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI---NLKMSGD 99
           L N+LRRV    L    ITA++I G+ +E  SI G+ ED  D+  N+  +   N+ M+  
Sbjct: 237 LLNSLRRVAKRHLGAGRITALRIPGMKNEFYSIVGLREDFFDLSRNLTKVIFRNVPMTAT 296

Query: 100 SHKRV--TIFKRGPGVVTAGDI---QTVND--------------IEVLNPDHVICNLDVD 140
            H+ +   +  +GP +  AG I   QT                 IE++N +  IC L  D
Sbjct: 297 FHRPLIGRLRLKGPIIAVAGHIELDQTFQKEGVGSSSGSKDDRRIEIVNKNQYICALSRD 356

Query: 141 AVVRMELTVSKGHGYV-PAKHHRTEN---DPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           A + ME+ +     YV P K   + N    P G I   +  +PI+  ++  +     +  
Sbjct: 357 AYLDMEVKIEYIANYVMPEKGPESLNRDITPDGFIHFSSSCTPIEVFAFDGDRRGIDEES 416

Query: 197 DYDKLSMTIDTDGSIT 212
             + +++ + TDGS T
Sbjct: 417 TSEIVTLELHTDGSTT 432


>gi|84999732|ref|XP_954587.1| DNA-directed RNA polymerase alpha chain [Theileria annulata]
 gi|65305585|emb|CAI73910.1| DNA-directed RNA polymerase alpha chain, putative [Theileria
           annulata]
          Length = 680

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 35/123 (28%), Positives = 66/123 (53%), Gaps = 2/123 (1%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P P     T+G+ L+ +  S   G A+ AV+I   +++ +++ GV +DL +I LN K + 
Sbjct: 269 PYPVTMGWTIGSLLKVMTQSRCPGHAVVAVKIHN-MNKDTTVDGVADDLLNIALNFKMVA 327

Query: 94  LK-MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
           L+ +      RV    +GP +V AG ++    +++ NP+  I  L+  A + +E+ +  G
Sbjct: 328 LQTLEPGKEARVRTKIKGPAMVCAGALEWPPFVKICNPESYITKLEEGAELDLEIKIEWG 387

Query: 153 HGY 155
            G+
Sbjct: 388 RGF 390


>gi|149173495|ref|ZP_01852125.1| probable DNA-directed RNA polymerase alpha chain [Planctomyces
           maris DSM 8797]
 gi|148847677|gb|EDL62010.1| probable DNA-directed RNA polymerase alpha chain [Planctomyces
           maris DSM 8797]
          Length = 415

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 30/64 (46%), Positives = 42/64 (65%)

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + V + ELSVRS NCL   +I  +GDL + +E D+L   NFG+ SL EI+ +L + GL +
Sbjct: 265 RPVTDFELSVRSRNCLHAMDIHTLGDLTRVSENDLLAGKNFGQTSLDEIREMLSSFGLHI 324

Query: 318 GMNL 321
           G NL
Sbjct: 325 GQNL 328



 Score = 45.4 bits (106), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 28/68 (41%), Positives = 39/68 (57%)

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           L  NPA  K + +L LSVRS  C+    I  +G+L++R+  ++L   NFG  SL EI+  
Sbjct: 345 LADNPATEKPISDLGLSVRSRKCMSRLGIGTIGELLRRSPDELLASRNFGVTSLNEIREK 404

Query: 310 LGTMGLFL 317
           L  M L L
Sbjct: 405 LTEMNLKL 412


>gi|156083567|ref|XP_001609267.1| DNA-directed RNA polymerase, alpha subunit [Babesia bovis T2Bo]
 gi|154796518|gb|EDO05699.1| DNA-directed RNA polymerase, alpha subunit, putative [Babesia
           bovis]
          Length = 676

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 64/122 (52%), Gaps = 2/122 (1%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           P P     TLG+ L+ + +S   G  + AV++   ++E ++I GV +DL +I LN+  + 
Sbjct: 264 PYPITMGWTLGSLLKVLALSRSPGHGVVAVKVHN-MNEDTTIDGVTDDLMNIALNLNEVA 322

Query: 94  LK-MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
           L+ +      RV    +GP  V AG I+  + +++  PD  I N++    + +E+ +  G
Sbjct: 323 LETLEPGGEARVRTVIKGPAQVCAGSIEWPSFVKIATPDAYITNVEEGGTLDIEIKIEWG 382

Query: 153 HG 154
            G
Sbjct: 383 RG 384


>gi|94502342|ref|ZP_01308812.1| DNA-directed RNA polymerase alpha chain [Candidatus Sulcia muelleri
           str. Hc (Homalodisca coagulata)]
 gi|94451097|gb|EAT14052.1| DNA-directed RNA polymerase alpha chain [Candidatus Sulcia muelleri
           str. Hc (Homalodisca coagulata)]
          Length = 87

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 32/87 (36%), Positives = 52/87 (59%), Gaps = 1/87 (1%)

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYVP++ ++      G I +D++++PIK V Y +++    +  +Y+ L + I TDGSI  
Sbjct: 2   GYVPSEENKENLIGSGSIPMDSIFTPIKNVKYKIDNCSINKNSNYESLLLEIKTDGSINP 61

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE 240
            D++  AS IL   L MFI +E  KK+
Sbjct: 62  RDALTNASNILIQHLKMFI-YETRKKK 87


>gi|300431274|gb|ADK12602.1| RNA polymerase alpha subunit [Pappostipa vaginata]
          Length = 167

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 41/141 (29%), Positives = 73/141 (51%), Gaps = 17/141 (12%)

Query: 174 DALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           DA+  P++ V+Y++ S   G    ++ L + I T+GS+T ++++  ASR L D    F++
Sbjct: 1   DAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLH 59

Query: 234 FEEPKKEVKEDINVKSLPFN----------------PALLKKVEELELSVRSTNCLRGEN 277
            EE     +E+ N  + P                  P     +++LEL  R+ NCL+  N
Sbjct: 60  AEEEGTSFEENKNRFTPPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRAN 119

Query: 278 IVYMGDLIQRTEADMLRMANF 298
           I  + DL+ +TE D++R+ +F
Sbjct: 120 IHTLLDLLSKTEEDLMRIDSF 140


>gi|237749604|ref|ZP_04580084.1| RpoA [Helicobacter bilis ATCC 43879]
 gi|229374800|gb|EEO25191.1| RpoA [Helicobacter bilis ATCC 43879]
          Length = 88

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 29/58 (50%), Positives = 40/58 (68%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 27  IEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGL 84


>gi|258597949|ref|XP_001348869.2| DNA-directed RNA polymerase, alpha subunit, putative [Plasmodium
           falciparum 3D7]
 gi|255528941|gb|AAN37308.2| DNA-directed RNA polymerase, alpha subunit, putative [Plasmodium
           falciparum 3D7]
          Length = 861

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 36/125 (28%), Positives = 70/125 (56%), Gaps = 6/125 (4%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL     HT G+ ++ V  + + G AI  +++   ++E + I  V EDL +I LNI  + 
Sbjct: 486 PLNITDGHTFGSLIKYVCQTQIYGYAIVGIKVHN-MNEDTKINNVQEDLLEIALNISDVC 544

Query: 94  L---KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +   +++ +S+ R+ IFK GP ++ AG I   + ++++N +H IC +  D  + + + + 
Sbjct: 545 IYSKEINLESNIRL-IFK-GPLMLVAGMIPLPSHLKIINKEHYICTIKEDGFIDISIKIE 602

Query: 151 KGHGY 155
            G G+
Sbjct: 603 YGKGH 607


>gi|87307747|ref|ZP_01089890.1| probable DNA-directed RNA polymerase alpha chain [Blastopirellula
           marina DSM 3645]
 gi|87289361|gb|EAQ81252.1| probable DNA-directed RNA polymerase alpha chain [Blastopirellula
           marina DSM 3645]
          Length = 455

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 46/118 (38%), Positives = 62/118 (52%), Gaps = 13/118 (11%)

Query: 220 ASRILQDQLG---MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGE 276
           AS  L+D      MF + EE +K+      V S+P        V + ELSVRS NCL+  
Sbjct: 273 ASMFLKDAQASSDMFYD-EEAQKKRDRIAQVLSIP--------VTDFELSVRSRNCLQKM 323

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD-WPPESIEELA 333
            I  +GDL + +E ++L   NFG  SLVEI+ +L + GL LG    D   PE   E+A
Sbjct: 324 GIQTLGDLSRCSEQELLSSKNFGETSLVEIREMLNSKGLELGQFSSDKGQPEPTIEVA 381



 Score = 42.4 bits (98), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 31/86 (36%), Positives = 45/86 (52%), Gaps = 2/86 (2%)

Query: 234 FEEPKKEVKEDINVKSL-PFNPALLKK-VEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           F   K + +  I V  L P   ALL + + EL LSVR+  C+    I  +G+L++RT  +
Sbjct: 367 FSSDKGQPEPTIEVAGLSPDEQALLDRPISELNLSVRARKCMVRLGISTIGELVRRTGDE 426

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFL 317
           +L   NFG  SL E++  L    L L
Sbjct: 427 LLECKNFGVTSLNEVREKLTASNLKL 452


>gi|224983719|pdb|3GFK|B Chain B, Crystal Structure Of Bacillus Subtilis SpxRNA POLYMERASE
           Alpha Subunit C-Terminal Domain Complex
          Length = 79

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 29/58 (50%), Positives = 40/58 (68%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 18  IEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGL 75


>gi|168704678|ref|ZP_02736955.1| probable DNA-directed RNA polymerase alpha chain [Gemmata
           obscuriglobus UQM 2246]
          Length = 458

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 29/62 (46%), Positives = 40/62 (64%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           + + ELSVRS NCL+  NI  +GDL + TE  +L   NFG  SL EI+ ++ T GL +G 
Sbjct: 309 ITDFELSVRSRNCLKRMNIRTLGDLTRVTEPQLLASKNFGETSLDEIRAIMVTKGLRIGQ 368

Query: 320 NL 321
           +L
Sbjct: 369 SL 370



 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 26/62 (41%), Positives = 37/62 (59%)

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           L K V +L LSVR+  C+   NI  +G+L+QRT  ++L   NFG+ SL E++  L    L
Sbjct: 394 LGKPVSDLNLSVRARKCMNRLNIGTLGELVQRTADELLEAKNFGQTSLTEVRERLQQFNL 453

Query: 316 FL 317
            L
Sbjct: 454 KL 455


>gi|82407558|pdb|1Z3E|B Chain B, Crystal Structure Of Spx In Complex With The C-Terminal
           Domain Of The Rna Polymerase Alpha Subunit
          Length = 73

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 29/58 (50%), Positives = 40/58 (68%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 11  IEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGL 68


>gi|285803273|pdb|3IHQ|B Chain B, Crystal Structure Of Reduced C10s Spx In Complex With The
           Alpha C-Terminal Domain Of Rna Polymeras
          Length = 75

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 29/58 (50%), Positives = 40/58 (68%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 13  IEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEELGLGL 70


>gi|75764303|ref|ZP_00743839.1| DNA-directed RNA polymerase alpha chain [Bacillus thuringiensis
           serovar israelensis ATCC 35646]
 gi|74488206|gb|EAO51886.1| DNA-directed RNA polymerase alpha chain [Bacillus thuringiensis
           serovar israelensis ATCC 35646]
          Length = 78

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 29/58 (50%), Positives = 40/58 (68%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  +GL L
Sbjct: 17  IEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKHKLEELGLGL 74


>gi|221058981|ref|XP_002260136.1| DNA-directed RNA polymerase, alpha subunit,truncated [Plasmodium
           knowlesi strain H]
 gi|193810209|emb|CAQ41403.1| DNA-directed RNA polymerase, alpha subunit,truncated, putative
           [Plasmodium knowlesi strain H]
          Length = 805

 Score = 57.0 bits (136), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 36/123 (29%), Positives = 63/123 (51%), Gaps = 14/123 (11%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI-------KGI 92
            HT G  L+ V  + + G AI A+++   ++E + I  V EDL +I LN+       K I
Sbjct: 427 GHTFGTLLKYVCQTQVYGYAIVAIKVHN-MNEDTRIDNVQEDLLEIALNLSDVCIYSKEI 485

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
           N++ +      V +  +GP +V AG I   + ++V+N +  IC L  D  + + + +  G
Sbjct: 486 NIETN------VRLIFKGPLMVVAGMIPLPSHLQVVNKEQYICTLKEDGYLDISIKIEYG 539

Query: 153 HGY 155
            G+
Sbjct: 540 KGH 542


>gi|85000353|ref|XP_954895.1| DNA-directed RNA polymerase D subunit [Theileria annulata strain
           Ankara]
 gi|65303041|emb|CAI75419.1| DNA-directed RNA polymerase D subunit, putative [Theileria
           annulata]
          Length = 587

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 54/223 (24%), Positives = 95/223 (42%), Gaps = 54/223 (24%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI---NLKMSGD 99
           L N+LRRV    L    ITA++I G+ +E  S+ G+ ED  +++ N++G+   N+  +  
Sbjct: 181 LLNSLRRVAKRHLGSGRITALRIPGMENEFYSVVGLREDFFELVRNLRGVIFKNVPKTAT 240

Query: 100 SHKRV--TIFKRGPGVVTAGDIQ---------------------------------TVND 124
            H+ V  T+  +GP +  AG ++                                  +ND
Sbjct: 241 FHRPVIATLRLKGPIIAVAGHLKFDNKRSTKTASDIDNKTENKNDNTDTKADNEEGVIND 300

Query: 125 ----------IEVLNPDHVICNLDVDAVVRMELTVSKGHGYV-----PAKHHRTENDPIG 169
                     IEV+N +H IC+L     + M++ +     YV     P   +R +  P G
Sbjct: 301 YVYDKKYTGEIEVINKNHYICSLSQGCYLTMDVKIEYISNYVIPEFGPESLNR-DITPDG 359

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            I   +  +P++   +T E     +    + +S+ + TDGS T
Sbjct: 360 FIHFCSSCNPVEIFGFTGERRGLDEQSTSEIVSLELHTDGSAT 402


>gi|315283810|ref|ZP_07871881.1| DNA-directed RNA polymerase subunit alpha [Listeria marthii FSL
           S4-120]
 gi|313612547|gb|EFR86618.1| DNA-directed RNA polymerase subunit alpha [Listeria marthii FSL
           S4-120]
          Length = 86

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 28/58 (48%), Positives = 40/58 (68%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N GRKSL E+K  L  +GL L
Sbjct: 25  IEELDLSVRSYNCLKRAGINTVQELADKSEDDMMKVRNLGRKSLEEVKVKLADLGLSL 82


>gi|207092544|ref|ZP_03240331.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
          HPKX_438_AG0C1]
          Length = 126

 Score = 56.2 bits (134), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 28/73 (38%), Positives = 45/73 (61%)

Query: 22 QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
          ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18 EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPIGLKIEGVHHEFDSLRGVTED 77

Query: 82 LTDIILNIKGINL 94
          ++  I+N+K I  
Sbjct: 78 VSLFIMNLKNIRF 90


>gi|86148803|ref|ZP_01067070.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. MED222]
 gi|85833393|gb|EAQ51584.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. MED222]
          Length = 82

 Score = 55.8 bits (133), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 29/65 (44%), Positives = 41/65 (63%), Gaps = 3/65 (4%)

Query: 2  IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
          +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1  MQGSVTEFLKPRLVDIEQINTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62 AVQID 66
           V+I+
Sbjct: 58 EVEIE 62


>gi|291533600|emb|CBL06713.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Megamonas
           hypermegale ART12/1]
          Length = 85

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/48 (52%), Positives = 37/48 (77%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +E+L+LSVRS NCL+   I  + DL+Q++E DM+++ N GRKSL E+K
Sbjct: 31  IEDLDLSVRSYNCLKRAEINTVADLMQKSEDDMIKVRNLGRKSLEEVK 78


>gi|320103200|ref|YP_004178791.1| RNA polymerase subunit alpha domain-containing protein [Isosphaera
           pallida ATCC 43644]
 gi|319750482|gb|ADV62242.1| RNA polymerase alpha subunit domain protein [Isosphaera pallida
           ATCC 43644]
          Length = 448

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 29/60 (48%), Positives = 37/60 (61%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           V + ELSVRS NCL+   I  +GDL + TE+ +L   NFG  SL EIK ++    L LGM
Sbjct: 296 VTDFELSVRSRNCLKKMGIRTLGDLTRITESQLLSSKNFGETSLTEIKAMMEAKSLRLGM 355



 Score = 43.1 bits (100), Expect = 0.064,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 33/58 (56%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + EL LSVR+  C+    I  +G+LI  T+  +L   NFG  SL E++  L  +GL L
Sbjct: 388 ITELNLSVRARKCMNKLGITTVGELIAHTQDQLLECKNFGVTSLNEVRDKLSELGLKL 445


>gi|207108315|ref|ZP_03242477.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
          HPKX_438_CA4C1]
          Length = 130

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 28/73 (38%), Positives = 45/73 (61%)

Query: 22 QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
          ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++GV ED
Sbjct: 18 EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPIGLKIEGVHHEFDSLRGVTED 77

Query: 82 LTDIILNIKGINL 94
          ++  I+N+K I  
Sbjct: 78 VSLFIMNLKNIRF 90


>gi|32471678|ref|NP_864671.1| DNA-directed RNA polymerase alpha chain [Rhodopirellula baltica SH
           1]
 gi|32397049|emb|CAD72353.1| probable DNA-directed RNA polymerase alpha chain [Rhodopirellula
           baltica SH 1]
 gi|327539093|gb|EGF25725.1| RNA polymerase alpha subunit domain protein [Rhodopirellula baltica
           WH47]
          Length = 500

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 29/59 (49%), Positives = 37/59 (62%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           V   ELSVRS NCL+   I  +GDL + +E ++L   NFG  SLVEI+ +L   GL LG
Sbjct: 352 VANFELSVRSRNCLQKMGIETIGDLTRHSEQELLSSKNFGETSLVEIREMLSQKGLSLG 410



 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 28/66 (42%), Positives = 41/66 (62%), Gaps = 1/66 (1%)

Query: 251 PFNPALLKK-VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           P   ALL++ + +L LSVR+  C+    I  +G+LI++T  DML   NFG  SL E++  
Sbjct: 430 PDEQALLERPIADLNLSVRARKCMTRLQINSIGELIRKTGDDMLECKNFGVTSLNEVREK 489

Query: 310 LGTMGL 315
           LG +GL
Sbjct: 490 LGDLGL 495


>gi|156099322|ref|XP_001615663.1| DNA-directed RNA polymerase, alpha subunit [Plasmodium vivax SaI-1]
 gi|148804537|gb|EDL45936.1| DNA-directed RNA polymerase, alpha subunit, putative [Plasmodium
           vivax]
          Length = 843

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 37/119 (31%), Positives = 67/119 (56%), Gaps = 6/119 (5%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL---KM 96
            HT G  L+ V  + L G AI A++I   ++E + I  V EDL +I LN+  + +   ++
Sbjct: 450 GHTFGTLLKYVCQTQLYGYAIVAIKIHN-MNEDTRIDNVQEDLLEIALNLSDVCIYSKEV 508

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY 155
           + +++ R+ IFK GP ++ AG I   + ++V+N +  IC L  D  + + + +  G G+
Sbjct: 509 NIETNIRL-IFK-GPLMLVAGMIPLPSHLQVVNKEQYICTLKEDGHLDISIKIEYGKGH 565


>gi|283781750|ref|YP_003372505.1| RNA polymerase subunit alpha [Pirellula staleyi DSM 6068]
 gi|283440203|gb|ADB18645.1| RNA polymerase alpha subunit domain protein [Pirellula staleyi DSM
           6068]
          Length = 440

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/59 (47%), Positives = 39/59 (66%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           V + ELSVRS NCL+   +  +GDL + +E ++L   NFG  SLVEI+ +L + GL LG
Sbjct: 292 VTDFELSVRSRNCLQKMGVRTLGDLTRTSEQELLASKNFGETSLVEIRDMLHSKGLELG 350



 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 33/94 (35%), Positives = 55/94 (58%), Gaps = 7/94 (7%)

Query: 227 QLGMFINFEEPKKEVKEDI-NVKSL-PFNPALLKK-VEELELSVRSTNCLRGENIVYMGD 283
           +LG F      +K V E + ++ S+ P   ALL++ + EL LSVR+  C+    +  +G+
Sbjct: 348 ELGQFA----AEKAVAEPVLDLASMSPDEQALLERPISELNLSVRARKCMARLGLTLIGE 403

Query: 284 LIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+++T  D+L   NFG  SL E++  L T+G+ L
Sbjct: 404 LVRKTGDDLLECKNFGVTSLNEVREKLTTLGIKL 437


>gi|20451756|emb|CAD30546.1| DNA-directed RNA polymerase alpha subunit [Listonella
          anguillarum]
          Length = 61

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/64 (45%), Positives = 39/64 (60%), Gaps = 3/64 (4%)

Query: 2  IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
          +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1  MQGSVTEFLKPRLVDIEQISTTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62 AVQI 65
           V I
Sbjct: 58 EVVI 61


>gi|255018323|ref|ZP_05290449.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL F2-515]
          Length = 62

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/58 (48%), Positives = 40/58 (68%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N GRKSL E+K  L  +GL L
Sbjct: 1   MEELDLSVRSYNCLKRAGINTVQELADKSEDDMMKVRNLGRKSLEEVKVKLADLGLSL 58


>gi|91203075|emb|CAJ72714.1| hypothetical protein kustd1969 [Candidatus Kuenenia
           stuttgartiensis]
          Length = 380

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 29/61 (47%), Positives = 37/61 (60%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           + + ELSVRS NCL   NI  + DL + +E D+L   NFG  SL EIK +L   GL LG 
Sbjct: 298 ISDFELSVRSRNCLEKMNIHTLRDLTRISEPDLLTFKNFGETSLNEIKAILIQKGLQLGQ 357

Query: 320 N 320
           +
Sbjct: 358 S 358


>gi|326392492|ref|ZP_08213873.1| RNA polymerase dimerization [Thermoanaerobacter ethanolicus JW 200]
 gi|325991467|gb|EGD50078.1| RNA polymerase dimerization [Thermoanaerobacter ethanolicus JW 200]
          Length = 85

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 28/79 (35%), Positives = 49/79 (62%), Gaps = 11/79 (13%)

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF- 234
           L+   K+VSY VE+ R G V DYDKL++ + T+G+IT ++++++AS +L      FI+F 
Sbjct: 3   LFYTSKRVSYNVENTRVGHVTDYDKLTLEVWTNGTITPKEAISMASDMLIKYFQKFISFT 62

Query: 235 ----------EEPKKEVKE 243
                     ++P+K+ +E
Sbjct: 63  GEYKSSDIFVDKPEKKSRE 81


>gi|325106907|ref|YP_004267975.1| RNA polymerase subunit alpha domain protein [Planctomyces
           brasiliensis DSM 5305]
 gi|324967175|gb|ADY57953.1| RNA polymerase alpha subunit domain protein [Planctomyces
           brasiliensis DSM 5305]
          Length = 436

 Score = 53.5 bits (127), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 36/100 (36%), Positives = 50/100 (50%), Gaps = 9/100 (9%)

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           MF + EE  +  K+   + S+P +        + ELS RS NCL    I  + DL + +E
Sbjct: 268 MFYD-EEAARRDKQLEQILSIPMS--------DFELSARSRNCLERAGIDRLEDLTKMSE 318

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
             +L   NFG  SL EIK +L   GL LG N+    PE +
Sbjct: 319 EQLLAGKNFGETSLKEIKAILEMHGLKLGQNVHKKQPEPL 358



 Score = 42.0 bits (97), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 35/58 (60%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           V +LELSVR+  CL    I  +G+L+ R+  ++L + NFG  SL EI+  LG   + L
Sbjct: 376 VSDLELSVRARKCLARLGINTVGELVSRSADELLSVRNFGVTSLNEIREKLGEKNIRL 433


>gi|85713167|ref|ZP_01044199.1| DNA-directed RNA polymerase alpha subunit [Idiomarina baltica
          OS145]
 gi|85693037|gb|EAQ31003.1| DNA-directed RNA polymerase alpha subunit [Idiomarina baltica
          OS145]
          Length = 70

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 28/65 (43%), Positives = 40/65 (61%), Gaps = 3/65 (4%)

Query: 2  IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
          +Q +  E +KP  ++   +       TL   EPL RGF +TL NALRR+L+SS+ G A+T
Sbjct: 1  MQGSVTEFLKPRLVDIEQISTTHAKVTL---EPLERGFGYTLRNALRRILLSSMPGCAVT 57

Query: 62 AVQID 66
           V+ID
Sbjct: 58 EVEID 62


>gi|87309222|ref|ZP_01091359.1| probable DNA-directed RNA polymerase alpha chain [Blastopirellula
           marina DSM 3645]
 gi|87288213|gb|EAQ80110.1| probable DNA-directed RNA polymerase alpha chain [Blastopirellula
           marina DSM 3645]
          Length = 93

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 30/77 (38%), Positives = 45/77 (58%), Gaps = 10/77 (12%)

Query: 250 LPFNPA------LLKKVE----ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           +P N A      L+ K+E    E+ L+VR+TNCL    I  + DL+  T AD+L ++NFG
Sbjct: 4   IPLNAAAQESESLMSKLEMSTAEIGLTVRTTNCLEERGIFTVRDLLNCTRADLLSISNFG 63

Query: 300 RKSLVEIKGVLGTMGLF 316
            K+L E+   L ++G F
Sbjct: 64  EKTLDEVYSSLESIGFF 80


>gi|166714640|gb|ABY88045.1| RpoA [Stenotrophomonas rhizophila]
          Length = 79

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 30/82 (36%), Positives = 49/82 (59%), Gaps = 3/82 (3%)

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +V+Y VE+AR  Q  D DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +  
Sbjct: 1   RVAYAVEAARVEQRTDLDKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGA 60

Query: 242 KEDINVKSLPFNPALLKKVEEL 263
            +  N      +P LL+ +++L
Sbjct: 61  AKPANNG---VDPVLLRPIDDL 79


>gi|260903552|ref|ZP_05911947.1| DNA-directed RNA polymerase, alpha subunit [Vibrio
          parahaemolyticus AQ4037]
 gi|308109055|gb|EFO46595.1| DNA-directed RNA polymerase, alpha subunit [Vibrio
          parahaemolyticus AQ4037]
          Length = 58

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 27/60 (45%), Positives = 37/60 (61%), Gaps = 3/60 (5%)

Query: 2  IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
          +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1  MQGSVTEFLKPRLVDIEQISSTHAKVTL---EPLERGFGHTLGNALRRILLSSMPGCAVT 57


>gi|82540505|ref|XP_724565.1| DNA-directed RNA polymerase [Plasmodium yoelii yoelii str. 17XNL]
 gi|23479250|gb|EAA16130.1| DNA-directed RNA polymerase [Plasmodium yoelii yoelii]
          Length = 803

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 34/125 (27%), Positives = 69/125 (55%), Gaps = 6/125 (4%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL     HT G+ ++ V  S + G AI  ++I   ++E + I+   EDL +I LN+  + 
Sbjct: 419 PLNITDGHTFGSLIKYVCQSQIYGYAIVGIKIHN-MNEDTKIENTQEDLLEIALNLSDVC 477

Query: 94  L---KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +   +++ +++ R+ IFK GP ++ AG I   + ++V+N +  IC +  +  + + + + 
Sbjct: 478 IYSKEINIETNIRL-IFK-GPLMLVAGMIPLPSHLKVVNKEQYICTIKENGYIDISIKIE 535

Query: 151 KGHGY 155
            G G+
Sbjct: 536 YGKGH 540


>gi|68075539|ref|XP_679688.1| DNA-directed RNA polymerase, alpha subunit, truncated, [Plasmodium
           berghei strain ANKA]
 gi|56500488|emb|CAH98184.1| DNA-directed RNA polymerase, alpha subunit, truncated, putative
           [Plasmodium berghei]
          Length = 727

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 34/125 (27%), Positives = 69/125 (55%), Gaps = 6/125 (4%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL     HT G+ ++ V  S + G AI  ++I   ++E + I+   EDL +I LN+  + 
Sbjct: 343 PLNITDGHTFGSLIKYVCQSQIYGYAIVGIKIHN-MNEDTKIENTQEDLLEIALNLSDVC 401

Query: 94  L---KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +   +++ +++ R+ IFK GP ++ AG I   + ++V+N +  IC +  +  + + + + 
Sbjct: 402 IYSKEINIETNIRL-IFK-GPLMLVAGMIPLPSHLKVVNKEQYICTIKENGYIDISIKIE 459

Query: 151 KGHGY 155
            G G+
Sbjct: 460 YGKGH 464


>gi|239933877|ref|ZP_04690830.1| DNA-directed RNA polymerase subunit alpha [Streptomyces ghanaensis
           ATCC 14672]
          Length = 88

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/63 (38%), Positives = 41/63 (65%)

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL + ++T  ++   D++A A + L + 
Sbjct: 10  IGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVEL 69

Query: 228 LGM 230
            G+
Sbjct: 70  FGL 72


>gi|218508353|ref|ZP_03506231.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli Brasil
          5]
          Length = 37

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 22/40 (55%), Positives = 26/40 (65%), Gaps = 3/40 (7%)

Query: 1  MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFA 40
          MIQKNWQELIKPN +E+         R  ++AEPL RGF 
Sbjct: 1  MIQKNWQELIKPNKVEF---SSSSRTRATLVAEPLERGFG 37


>gi|67968322|dbj|BAE00222.1| RNA polymerase alpha chain like [Selaginella uncinata]
          Length = 245

 Score = 49.7 bits (117), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 55/202 (27%), Positives = 84/202 (41%), Gaps = 11/202 (5%)

Query: 34  PLPR-GFAHTLGNALRRVLMSSLRGAAIT-AVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
           P P+ G A TLG A+RR       GA  T A   + + HE  +I GV E + +  +N+K 
Sbjct: 33  PPPKIGQASTLGIAMRRAPPGESEGACTTPAGSPERINHEYPAIAGVRESVHETSMNLKE 92

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           I L     + +   I   GPG V A D    + I ++ P      +           V  
Sbjct: 93  IALTAHPSAAQEAHIPIVGPGKVAARDTVPPSSIGIIYPAQHAATVTRKIRSSTGSRVEG 152

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE--SAREGQVLDYDKLSMTIDTDG 209
           G GY   + +  E    G    DA+  PI+  +Y++    +  G ++  +       TDG
Sbjct: 153 GCGY--RRRNMVEYQ-KGSPPPDAVSMPIRNANYSIHRLESHSGGIMK-EMPPPEARTDG 208

Query: 210 SITGEDSVALASRILQDQLGMF 231
           S T  ++   ASR   D   +F
Sbjct: 209 SPTPGEATYEASR---DSANLF 227


>gi|237835983|ref|XP_002367289.1| DNA-directed RNA polymerase alpha chain, putative [Toxoplasma
           gondii ME49]
 gi|211964953|gb|EEB00149.1| DNA-directed RNA polymerase alpha chain, putative [Toxoplasma
           gondii ME49]
 gi|221506032|gb|EEE31667.1| DNA-directed RNA polymerase alpha chain, putative [Toxoplasma
           gondii VEG]
          Length = 836

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 22/44 (50%), Positives = 29/44 (65%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
           NALRR  +S L   AI+AV+I+G  HE  S+ G+ ED+ D I N
Sbjct: 74  NALRRTSLSRLESLAISAVKIEGAKHEFYSLPGIREDIVDDIFN 117


>gi|221484912|gb|EEE23202.1| DNA-directed RNA polymerase alpha chain, putative [Toxoplasma
           gondii GT1]
          Length = 837

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 22/44 (50%), Positives = 29/44 (65%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
           NALRR  +S L   AI+AV+I+G  HE  S+ G+ ED+ D I N
Sbjct: 74  NALRRTSLSRLESLAISAVKIEGAKHEFYSLPGIREDIVDDIFN 117


>gi|255027531|ref|ZP_05299517.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
          FSL J2-003]
          Length = 55

 Score = 48.5 bits (114), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 20/33 (60%), Positives = 27/33 (81%)

Query: 30 MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           + EPL RG+  TLGN+LRR+L+SSL GAA+T+
Sbjct: 23 FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTS 55


>gi|237830453|ref|XP_002364524.1| RNA polymerase Rpb3/Rpb11 dimerization domain-containing protein
           [Toxoplasma gondii ME49]
 gi|211962188|gb|EEA97383.1| RNA polymerase Rpb3/Rpb11 dimerization domain-containing protein
           [Toxoplasma gondii ME49]
          Length = 623

 Score = 48.5 bits (114), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 46/205 (22%), Positives = 86/205 (41%), Gaps = 33/205 (16%)

Query: 72  ISSIKGVHEDLTDIILNIKGINLK-MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           ++ +  V EDL +I LN+KG+  + +       V +   GP ++ AG I   + + V NP
Sbjct: 225 VTQLPNVREDLLEIALNLKGVAFETLRPRESACVRVKAVGPQLLVAGMIDWPSFVRVGNP 284

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTEN---------------DPIGLIT 172
           +H I  ++   V+ +E+ +  G G   A  H   R E                D  G   
Sbjct: 285 EHFIAKVEEGGVLDLEMKLEWGRGAWLADLHGLYREEEGVDTRCYKRRRIWEVDHRGFYP 344

Query: 173 IDALYSPIKKVSYTVESA--------REGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
              ++     +   V           R+      ++L + I TD S + ++ +A A   L
Sbjct: 345 TSCIFGACTMMRLAVHKLMGTRFCQDRQASTNPTEQLVLEIWTDASKSPKEVLAFA---L 401

Query: 225 QDQLGMFINFEEPKKEVKEDINVKS 249
           QD L   ++    ++++ ED++ K+
Sbjct: 402 QDMLAWLVDL---RRQLVEDVDWKT 423


>gi|4140424|gb|AAD04047.1| DNA-directed RNA polymerase [Chlamydia trachomatis]
          Length = 62

 Score = 47.8 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 22/49 (44%), Positives = 30/49 (61%)

Query: 31 IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
          +A+PL +G  HTLG+ALRR L+  L   AI +  + GVL  I   +G H
Sbjct: 14 VADPLEKGMGHTLGSALRRALLIGLEAPAIVSFSMTGVLQRIYGGRGDH 62


>gi|71904766|gb|AAZ52664.1| DNA-dependent RNA polymerase alpha chain [Mycoplasma hominis ATCC
           23114]
          Length = 180

 Score = 47.4 bits (111), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 32/146 (21%), Positives = 76/146 (52%), Gaps = 18/146 (12%)

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ---- 225
            + +D+ +SPIKKV+   E       +  ++L + ++TDG++  ++ +  A++I+     
Sbjct: 16  FLAMDSDFSPIKKVAILFEELNSTSNIIEERLKIKVETDGTVEAKNVMEEAAKIIVAHFQ 75

Query: 226 -----DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVY 280
                D LG    F++ K++ ++          P +   +++L L++RS N LR      
Sbjct: 76  IIGNIDALGTIDLFDDQKEKHEK---------TPKVSVSIDKLNLTIRSLNALRRAGFNN 126

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEI 306
           + ++++ ++ ++  + N G+KS+ +I
Sbjct: 127 VDEIMKLSDEELSNIKNLGKKSVQDI 152


>gi|166714718|gb|ABY88084.1| RpoA [Stenotrophomonas sp. LMG 11002]
          Length = 65

 Score = 47.0 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 28/63 (44%), Positives = 44/63 (69%)

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           G + +DA +SP+++V+Y VE+A   Q  D DKL + I+T+G+I  E++V  A+ IL DQL
Sbjct: 1   GRLVLDASFSPVRRVAYAVEAAAVEQRTDLDKLVIDIETNGTIDAEEAVRTAADILSDQL 60

Query: 229 GMF 231
            +F
Sbjct: 61  SVF 63


>gi|325120592|emb|CBZ56146.1| putative DNA-directed RNA polymerase alpha chain [Neospora caninum
           Liverpool]
          Length = 941

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 20/44 (45%), Positives = 28/44 (63%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
           NALRR  +S +   A+ AV+I+G  HE  S+ G+ ED+ D I N
Sbjct: 183 NALRRTSLSRIESLAVAAVKIEGAKHEFYSLPGIREDIVDDIFN 226


>gi|221487600|gb|EEE25832.1| hypothetical protein TGGT1_089410 [Toxoplasma gondii GT1]
          Length = 1082

 Score = 46.6 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 47/205 (22%), Positives = 87/205 (42%), Gaps = 33/205 (16%)

Query: 72  ISSIKGVHEDLTDIILNIKGINLK-MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           ++ +  V EDL +I LN+KG+  + +       V +   GP ++ AG I   + + V NP
Sbjct: 684 VTQLPNVREDLLEIALNLKGVAFETLRPRESACVRVKAVGPQLLVAGMIDWPSFVRVGNP 743

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTEN---------------DPIGLIT 172
           +H I  ++   V+ +E+ +  G G   A  H   R E                D  G   
Sbjct: 744 EHFIAKVEEGGVLDLEMKLEWGRGAWLADLHGLYREEEGVDTRCYKRRRIWEVDHRGFYP 803

Query: 173 IDALYSPIKKVSYTVESA--------REGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
              ++     +   V           R+      ++L + I TD S + ++ +A A   L
Sbjct: 804 TSCIFGACTMMRLAVHKLMGTRFCQDRQASTNPTEQLVLEIWTDASKSPKEVLAFA---L 860

Query: 225 QDQLGMFINFEEPKKEVKEDINVKS 249
           QD L  F++    ++++ ED++ K+
Sbjct: 861 QDMLAWFVDL---RRQLVEDVDWKT 882


>gi|32474617|ref|NP_867611.1| DNA-directed RNA polymerase alpha chain [Rhodopirellula baltica SH
           1]
 gi|32445156|emb|CAD75158.1| probable DNA-directed RNA polymerase alpha chain [Rhodopirellula
           baltica SH 1]
 gi|327540701|gb|EGF27273.1| DNA-directed RNA polymerase, alpha subunit [Rhodopirellula baltica
           WH47]
          Length = 92

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 36/57 (63%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
           + E+ L+VR+TNCL    I+ + DL+  T   +L+++NFG K+L E+   L  +G +
Sbjct: 25  IAEMGLTVRTTNCLEETGILTVRDLLNATPRRLLKISNFGEKTLEEVYDALEQLGFY 81


>gi|68000767|ref|XP_669714.1| hypothetical protein [Plasmodium berghei strain ANKA]
 gi|56484216|emb|CAI01628.1| hypothetical protein PB300311.00.0 [Plasmodium berghei]
          Length = 212

 Score = 45.4 bits (106), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 32/117 (27%), Positives = 65/117 (55%), Gaps = 6/117 (5%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL     HT G+ ++ V  S + G AI  ++I   ++E + I+   EDL +I LN+  + 
Sbjct: 99  PLNITDGHTFGSLIKYVCQSQIYGYAIVGIKIHN-MNEDTKIENTQEDLLEIALNLSDVC 157

Query: 94  L---KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           +   +++ +++ R+ IFK GP ++ AG I   + ++V+N +  IC +  +  + + +
Sbjct: 158 IYSKEINIETNIRL-IFK-GPLMLVAGMIPLPSHLKVVNKEQYICTIKENGYIDISI 212


>gi|310658943|ref|YP_003936664.1| RNA polymerase subunit alpha domain-containing protein [Clostridium
           sticklandii DSM 519]
 gi|308825721|emb|CBH21759.1| RNA polymerase, alpha subunit domain protein [Clostridium
           sticklandii]
          Length = 911

 Score = 44.7 bits (104), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 20/49 (40%), Positives = 34/49 (69%)

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           ++E+L LSVR+ NCL+ + I Y   L+ +   +++ + N G+KSLVEI+
Sbjct: 97  EIEKLCLSVRAYNCLKSDGIEYYSQLVDKLVEELITIPNMGQKSLVEIE 145


>gi|84687559|ref|ZP_01015435.1| RNA polymerase sigma factor [Maritimibacter alkaliphilus HTCC2654]
 gi|84664468|gb|EAQ10956.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2654]
          Length = 562

 Score = 44.7 bits (104), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 28/52 (53%)

Query: 276 ENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           E IV +G  +Q T  D+LR    G+KS  E +  L  +GL LGM L  W  E
Sbjct: 4   EGIVLVGSFVQLTAGDILRKQGLGKKSYREARATLEALGLSLGMELCGWDEE 55


>gi|118595065|ref|ZP_01552412.1| hypothetical protein MB2181_05315 [Methylophilales bacterium
           HTCC2181]
 gi|118440843|gb|EAV47470.1| hypothetical protein MB2181_05315 [Methylophilales bacterium
           HTCC2181]
          Length = 808

 Score = 44.7 bits (104), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 19/41 (46%), Positives = 30/41 (73%)

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           L+L +RSTNCLR   I  + DL++ ++ ++LR+ N GR+SL
Sbjct: 147 LDLDIRSTNCLRSRGIDKIEDLLKLSDTELLRIDNLGRRSL 187


>gi|110004169|emb|CAK98507.1| hypothetical protein with alpha rna polymerase domain pd001179
           [Spiroplasma citri]
          Length = 111

 Score = 44.7 bits (104), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 25/92 (27%), Positives = 48/92 (52%), Gaps = 13/92 (14%)

Query: 224 LQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGD 283
           +Q+Q+ +++  +E ++             N  L   +++LE++ R+  CL    I  + D
Sbjct: 29  IQEQITIWLEMDETER-------------NQLLNHSIDDLEITQRTQICLEKAKIYRLSD 75

Query: 284 LIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           L+ +TE ++  + N G KSL EIK  +  +GL
Sbjct: 76  LVSKTENEIKNIKNLGEKSLTEIKEKMHELGL 107


>gi|150389913|ref|YP_001319962.1| RNA polymerase subunit alpha [Alkaliphilus metalliredigens QYMF]
 gi|149949775|gb|ABR48303.1| RNA polymerase, alpha subunit domain protein [Alkaliphilus
           metalliredigens QYMF]
          Length = 912

 Score = 44.3 bits (103), Expect = 0.027,   Method: Compositional matrix adjust.
 Identities = 19/54 (35%), Positives = 35/54 (64%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           +E L LSVR+ NCL+  ++ Y   LI   + +++ + N GRK+L+E++ +  T+
Sbjct: 98  IENLNLSVRAFNCLKSTSVDYYSQLIDVLDEELIAIPNMGRKTLLELEHIKKTV 151


>gi|221507397|gb|EEE33001.1| RNA polymerase Rpb3/Rpb11 dimerisation domain-containing protein,
           putative [Toxoplasma gondii VEG]
          Length = 1084

 Score = 44.3 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 46/205 (22%), Positives = 86/205 (41%), Gaps = 33/205 (16%)

Query: 72  ISSIKGVHEDLTDIILNIKGINLK-MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           ++ +  V EDL +I LN+KG+  + +       V +   GP ++ AG I   + + V NP
Sbjct: 686 VTQLPNVREDLLEIALNLKGVAFETLRPRESACVRVKAVGPQLLVAGMIDWPSFVRVGNP 745

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTEN---------------DPIGLIT 172
           +H I  ++   V+ +E+ +  G G   A  H   R E                D  G   
Sbjct: 746 EHFIAKVEEGGVLDLEMKLEWGRGAWLADLHGLYREEEGVDTRCYKRRRIWEVDHRGFYP 805

Query: 173 IDALYSPIKKVSYTVESA--------REGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
              ++     +   V           R+      ++L + I TD S + ++ +A A   L
Sbjct: 806 TSCIFGACTMMRLAVHKLMGTRFCQDRQASTNPTEQLVLEIWTDASKSPKEVLAFA---L 862

Query: 225 QDQLGMFINFEEPKKEVKEDINVKS 249
           QD L   ++    ++++ ED++ K+
Sbjct: 863 QDMLAWLVDL---RRQLVEDVDWKT 884


>gi|115443569|ref|YP_778588.1| RNA polymerase alpha subunit [Bigelowiella natans]
 gi|122221272|sp|Q06J39|RPOA_BIGNA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|110810214|gb|ABG91420.1| RNA polymerase alpha subunit [Bigelowiella natans]
          Length = 358

 Score = 43.9 bits (102), Expect = 0.035,   Method: Compositional matrix adjust.
 Identities = 72/332 (21%), Positives = 131/332 (39%), Gaps = 55/332 (16%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED------LTDIIL 87
           P  +  A    N LRRVL+S      ITAV I G  HE S + GV E           ++
Sbjct: 27  PFLKNQAFLYSNVLRRVLLSDSSNIVITAVNIVGAKHEYSLLPGVRESSLDLLLNLKELV 86

Query: 88  NIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA--VVRM 145
            +K I  K +      +     GP ++   DI   N I  ++    I  +  +   +++M
Sbjct: 87  FVKDIYTKFNKSYFAYLK--SNGPKIIRCSDIILPNTIYAVDSTQYIATISNNKSLILKM 144

Query: 146 ELTVSKGHGYVPAKHHR------------TENDPIGLITIDALYSPIKKVSYTVESAREG 193
           +LT +  + +    ++              E     LI ID  +S + KV+ ++ S    
Sbjct: 145 KLTANLLNNFYSNLNYELNSLLSYYTNDILEKTNFSLI-IDPNFSCVNKVNSSLISLDNL 203

Query: 194 QVLDYDKLSMTIDTDGS----ITGEDSV-ALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +  + D +S+ + T+ S    I  ++S+ ++ +  L      FI+ +    +   + ++ 
Sbjct: 204 ENYN-DSISLEVWTNSSYSPRIIIQNSIKSMVNLFLSIYDTSFIDIKLENSDNFLENHLV 262

Query: 249 SLPFNPALLKK--------------------------VEELELSVRSTNCLRGENIVYMG 282
           SL       KK                          ++EL+LS+ S   L+  NI+ + 
Sbjct: 263 SLSNRATFFKKSFFNICTEFNTVKYKTSFDKNLTLISIDELDLSIYSKFLLKRHNILTLY 322

Query: 283 DLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           DL +  +  + R  N   K+L  I+  +   G
Sbjct: 323 DLFKIDKRVLERFYNISYKTLQSIERKMVKYG 354


>gi|296329094|ref|ZP_06871599.1| hypothetical protein HMPREF0397_1792 [Fusobacterium nucleatum
           subsp. nucleatum ATCC 23726]
 gi|296153813|gb|EFG94626.1| hypothetical protein HMPREF0397_1792 [Fusobacterium nucleatum
           subsp. nucleatum ATCC 23726]
          Length = 979

 Score = 43.5 bits (101), Expect = 0.043,   Method: Compositional matrix adjust.
 Identities = 20/64 (31%), Positives = 37/64 (57%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           ++ L LSVR+ NCL+  NI Y   LI +TE +++ + + G  +L E++ +   +  + G 
Sbjct: 164 IDFLGLSVRAKNCLKSANIEYYSQLISKTEEELMTIKHMGVTTLKELQRLKFLIFFYFGF 223

Query: 320 NLPD 323
            + D
Sbjct: 224 PVVD 227


>gi|325119669|emb|CBZ55222.1| putative RNA polymerase Rpb3/Rpb11 dimerisation domain-containing
           protein [Neospora caninum Liverpool]
          Length = 980

 Score = 43.1 bits (100), Expect = 0.059,   Method: Compositional matrix adjust.
 Identities = 24/86 (27%), Positives = 44/86 (51%), Gaps = 5/86 (5%)

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHK---RVTIFKRGPGVVTAGDIQTVNDIEVL 128
           ++ +  V ED+ +I LN+KG+  +          RV +   GP ++ AG I   + + V 
Sbjct: 552 VTKLPSVREDILEIALNLKGVAFETLAPRESACIRVKVV--GPQLLVAGMIGWPSFVRVA 609

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHG 154
           NP+H I  ++   V+ +E+ +  G G
Sbjct: 610 NPEHFIAKVEEGGVLDLEIKLEWGRG 635


>gi|169836384|ref|ZP_02869572.1| DNA-directed RNA polymerase alpha chain [candidate division TM7
           single-cell isolate TM7a]
          Length = 74

 Score = 42.4 bits (98), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 3/71 (4%)

Query: 117 GDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHHRTENDPI--GLITI 173
           GDIQ+  D+E++NP+ VIC + D  A   ++L +  G GY+  +        I   +I +
Sbjct: 1   GDIQSHADVEIINPEQVICTVDDPSAKAVIDLVIDSGRGYLSIEDSSETRLTISRSIIAL 60

Query: 174 DALYSPIKKVS 184
           DA  SP+ +V+
Sbjct: 61  DASISPVIRVT 71


>gi|108773408|ref|YP_635927.1| PEP RNA polymerase alpha subunit [Helicosporidium sp. ex Simulium
           jonesii]
 gi|122197336|sp|Q2EEW7|RPOA_HELSJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|87242983|gb|ABD33975.1| RNA polymerase alpha chain [Helicosporidium sp. ex Simulium jonesi]
          Length = 246

 Score = 42.0 bits (97), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 38/78 (48%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PLP G A +LG  +R VL+      A+  ++ +   +   +  G  E +  II  I GI+
Sbjct: 25  PLPEGIAQSLGFNIRSVLLKEFPYFAVKNIRFNPENNNYKTHIGTKESIETIINTILGID 84

Query: 94  LKMSGDSHKRVTIFKRGP 111
              S D +K + ++K  P
Sbjct: 85  FNYSFDFYKAMGLYKSKP 102


>gi|24638176|sp|Q8SL86|RPOA_EUGVI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|19168446|gb|AAL83368.1| RNA polymerase alpha subunit [Euglena viridis]
          Length = 214

 Score = 42.0 bits (97), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 39/182 (21%), Positives = 80/182 (43%), Gaps = 41/182 (22%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVL-------------HEISSIKGVHEDLTDIILNI 89
             N LRR+L+    G  +  ++I G +             +E S  + ++E +  + LNI
Sbjct: 35  FANQLRRILLGKSEG--LRFLKISGFIANKNSKFSVYQKINEFSEFEEINESVFQLFLNI 92

Query: 90  KGINLKM-SGDSHKRV--TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           K I+L   S D++KR   T+    P   +  DI    +I+++  +  I +L     ++M+
Sbjct: 93  KNIDLYYRSCDANKRFFGTLEAYYPKTYSQDDIILSKNIKLIKKNQHIFSLS-SLKLKMK 151

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
             +    G                  I + ++P+K+V+Y +E  +    L + ++ + ++
Sbjct: 152 FILEAKKG------------------IGSFFTPVKRVNYIIEENK----LSFSRVVLELE 189

Query: 207 TD 208
           TD
Sbjct: 190 TD 191


>gi|301500977|ref|YP_003795442.1| RNA polymerase alpha subunit [Alveolata sp. CCMP3155]
 gi|300069523|gb|ADJ66630.1| RNA polymerase alpha subunit [Chromerida sp. RM11]
          Length = 233

 Score = 41.6 bits (96), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 32/125 (25%), Positives = 55/125 (44%), Gaps = 3/125 (2%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGV--LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           NA+RR L+S      +  V+I+     +      G  +   D+I  ++ +++++   S  
Sbjct: 36  NAVRRTLLSFSTQLKLVGVKINSSRNTYPWCMFSGCRDSYLDLISRLQRLSVRIRETSLC 95

Query: 103 RVTIFKR-GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
            V   K  GP VV AG + T   +E+L P+  + +L     + MEL  S     VP  + 
Sbjct: 96  YVLQLKSSGPLVVVAGHMITPPTLEILTPNKYLTSLAAKCALDMELIFSSYVLAVPVSYW 155

Query: 162 RTEND 166
               D
Sbjct: 156 EKTTD 160


>gi|213580698|ref|ZP_03362524.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
          subsp. enterica serovar Typhi str. E98-0664]
          Length = 46

 Score = 39.7 bits (91), Expect = 0.62,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 28/49 (57%), Gaps = 3/49 (6%)

Query: 2  IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRV 50
          +Q +  E +KP  ++   +       TL   EPL RGF HTLGNALRR+
Sbjct: 1  MQGSVTEFLKPRLVDIEQVSSTHAKVTL---EPLERGFGHTLGNALRRI 46


>gi|126348269|emb|CAJ89990.1| putative oxidoreductase [Streptomyces ambofaciens ATCC 23877]
          Length = 310

 Score = 39.7 bits (91), Expect = 0.65,   Method: Compositional matrix adjust.
 Identities = 32/109 (29%), Positives = 46/109 (42%), Gaps = 9/109 (8%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  + ++VL   + NRT    E         LG AL   L S   G  +  ++I    H 
Sbjct: 137 PVKLSHVVLNSPDLNRTREWYE-------RHLGFALSDTLSSPHMGEVMHFMRISSQHHS 189

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR--GPGVVTAGD 118
           ++  KG H  L  +   ++GI+  M G        FK+  GPG   AGD
Sbjct: 190 MALAKGPHTSLHHVSFEMRGIDEYMRGSGRVIRAGFKKVWGPGRHMAGD 238


>gi|301060344|ref|ZP_07201207.1| bacterial RNA polymerase, alpha chain C-terminal domain protein
           [delta proteobacterium NaphS2]
 gi|300445540|gb|EFK09442.1| bacterial RNA polymerase, alpha chain C-terminal domain protein
           [delta proteobacterium NaphS2]
          Length = 772

 Score = 39.3 bits (90), Expect = 0.81,   Method: Compositional matrix adjust.
 Identities = 22/56 (39%), Positives = 37/56 (66%), Gaps = 1/56 (1%)

Query: 259 KVEELELSVRSTNCLRGE-NIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           K+E++ LS R+ + L  +  +  +GD++  T  D+L + NFGRKSL EIK V+ ++
Sbjct: 142 KLEDIRLSHRTFHTLLNQGQMETIGDVMLTTCTDLLSLKNFGRKSLNEIKEVIRSL 197


>gi|313906563|ref|ZP_07839891.1| RNA polymerase alpha subunit domain protein [Eubacterium
           cellulosolvens 6]
 gi|313468593|gb|EFR63967.1| RNA polymerase alpha subunit domain protein [Eubacterium
           cellulosolvens 6]
          Length = 976

 Score = 39.3 bits (90), Expect = 0.97,   Method: Compositional matrix adjust.
 Identities = 20/42 (47%), Positives = 28/42 (66%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           LS RSTN L  E I  +GD++  TE  +L++ N G+KS+ EI
Sbjct: 13  LSARSTNALHREEIHTVGDMLGFTEESLLQVKNLGKKSVEEI 54


>gi|315651633|ref|ZP_07904644.1| conserved hypothetical protein [Eubacterium saburreum DSM 3986]
 gi|315486087|gb|EFU76458.1| conserved hypothetical protein [Eubacterium saburreum DSM 3986]
          Length = 596

 Score = 38.9 bits (89), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 17/51 (33%), Positives = 34/51 (66%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           ++ LEL VRS N L+  NI+ +  L++ ++ ++L++ N G++ + EI+  L
Sbjct: 227 IDNLELGVRSYNVLKRANIISIKKLLKMSDDELLKIRNLGKRQVAEIRTQL 277


>gi|295091278|emb|CBK77385.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Clostridium cf. saccharolyticum K10]
          Length = 1539

 Score = 38.5 bits (88), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 38/74 (51%), Gaps = 9/74 (12%)

Query: 234 FEEPKKEVKEDI-NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           FEE  K +KE + NV+  P        +E L L  R+TN LR   I  +G LIQ ++ D+
Sbjct: 85  FEERAKRIKEILPNVQDAP--------IESLGLGTRATNALRRGGIHTVGALIQMSQKDI 136

Query: 293 LRMANFGRKSLVEI 306
             + N G  S  EI
Sbjct: 137 FELRNVGVLSREEI 150


>gi|224179501|ref|YP_002601032.1| alpha subunit of RNA polymerase [Monomastix sp. OKE-1]
 gi|217314544|gb|ACK36887.1| alpha subunit of RNA polymerase [Monomastix sp. OKE-1]
          Length = 324

 Score = 38.5 bits (88), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 64/270 (23%), Positives = 105/270 (38%), Gaps = 79/270 (29%)

Query: 35  LPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDI 85
           L +G   T+ NALRRVL+  + G  IT V+ +           LHE S+I G+ E + ++
Sbjct: 50  LKKGQGITVANALRRVLLYDIMGLGITKVKFNSKNNENLSSQKLHEFSTISGIRESILEL 109

Query: 86  ILNIKGI---------NLKMSGDS-------HKRVTI------------------FK--- 108
           ++N++ +         N K+SGDS       H+ + I                  FK   
Sbjct: 110 LMNLRLLVWTTSPLDSNQKVSGDSSSDPLLVHEELDISSSPSLTSYLGQFSLPEYFKSKD 169

Query: 109 ----------------RGPGVVTAGDI--QTVNDIEVLNPDHVICNL--------DVDAV 142
                           RG  +++A     Q  N  +++NP+  +  +         +   
Sbjct: 170 WLSEKNKNNQSSVFVLRGKHLISADQRTNQNPNFAQLINPEQYLATILPIQKTATGLSKF 229

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG--QVLDYDK 200
              E+    G G +        N+   L+     + P+KKV+YTVE  +      L    
Sbjct: 230 PEFEIEYKIGKGNLFENLDLQSNNEEFLLNSGPFF-PVKKVNYTVEDIKNSTNNFLWERG 288

Query: 201 LS----MTIDTDGSITGEDSVALASRILQD 226
            S      I TDGS+  E +++ A  IL D
Sbjct: 289 FSECVFFEIWTDGSLHPEKALSQAFDILLD 318


>gi|221194869|ref|ZP_03567926.1| DNA-directed RNA polymerase, beta' subunit [Atopobium rimae ATCC
            49626]
 gi|221185773|gb|EEE18163.1| DNA-directed RNA polymerase, beta' subunit [Atopobium rimae ATCC
            49626]
          Length = 1480

 Score = 38.1 bits (87), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 28/89 (31%), Positives = 45/89 (50%), Gaps = 1/89 (1%)

Query: 246  NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            N ++L    A L   ++L +S R TN      I  +GDLI +TE D+LR+   G K++ E
Sbjct: 1321 NGRTLSSEDAKLYLFDDLGVSQRWTNKFSEVGIETVGDLIGKTEEDLLRIDGIGSKAIEE 1380

Query: 306  IKGVLGTMGLFLGMNLPDWPPESIEELAK 334
            ++  L    L   +  PD      E+L++
Sbjct: 1381 LRQGLDARNLLYILE-PDEDEADAEDLSQ 1408


>gi|166714716|gb|ABY88083.1| RpoA [Stenotrophomonas sp. LMG 980]
          Length = 66

 Score = 38.1 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 22/67 (32%), Positives = 38/67 (56%), Gaps = 3/67 (4%)

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           D DKL + I+T+G+I  E++V  A+ I  DQL +F +F    +   +  N      +P L
Sbjct: 3   DLDKLVIDIETNGTIDAEEAVRTAADITSDQLSVFGDFTHRDRGAAKPANNG---VDPVL 59

Query: 257 LKKVEEL 263
           L+ +++L
Sbjct: 60  LRPIDDL 66


>gi|251788175|ref|YP_003002896.1| threonine synthase [Dickeya zeae Ech1591]
 gi|247536796|gb|ACT05417.1| threonine synthase [Dickeya zeae Ech1591]
          Length = 429

 Score = 37.7 bits (86), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 29/95 (30%), Positives = 47/95 (49%), Gaps = 8/95 (8%)

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDG-SITGEDSVALASRILQDQL-----GMFIN 233
            ++ ++ ++    G V D    +  ++ D    T E   A+A R+L+DQL     G+F+ 
Sbjct: 316 FRRKNWQLKELAFGAVSDETTKTTMLELDALGYTSEPHAAIAYRLLRDQLQPGEYGLFLG 375

Query: 234 FEEPKK--EVKEDINVKSLPFNPALLKKVEELELS 266
              P K  E  E I  K+LP  PAL ++ E+  LS
Sbjct: 376 TAHPAKFKESVEAILGKTLPLPPALAERAEQALLS 410


>gi|166714714|gb|ABY88082.1| RpoA [Stenotrophomonas sp. LMG 10996]
          Length = 67

 Score = 37.4 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 22/67 (32%), Positives = 38/67 (56%), Gaps = 3/67 (4%)

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           D DKL + I+T+G+I  E++V  A+ I  DQL +F +F    +   +  N      +P L
Sbjct: 4   DLDKLVIDIETNGTIDAEEAVRTAADIPSDQLSVFGDFTHRDRGAAKPANNG---VDPVL 60

Query: 257 LKKVEEL 263
           L+ +++L
Sbjct: 61  LRPIDDL 67


>gi|157962130|ref|YP_001502164.1| sigma-70 region 4 domain-containing protein [Shewanella pealeana
           ATCC 700345]
 gi|157847130|gb|ABV87629.1| sigma-70 region 4 domain protein [Shewanella pealeana ATCC 700345]
          Length = 930

 Score = 37.4 bits (85), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 31/61 (50%), Gaps = 1/61 (1%)

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           LPF+  L K +EEL L VR  N         + DL   T+  ML   NFGRKS  ++  +
Sbjct: 276 LPFS-LLEKPLEELNLPVRLFNVFNVNGFTSLNDLKDITDKTMLSWPNFGRKSARDLYSL 334

Query: 310 L 310
           L
Sbjct: 335 L 335


>gi|170694673|ref|ZP_02885824.1| RNA polymerase alpha subunit domain protein [Burkholderia graminis
           C4D1M]
 gi|170140304|gb|EDT08481.1| RNA polymerase alpha subunit domain protein [Burkholderia graminis
           C4D1M]
          Length = 77

 Score = 37.4 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 21/52 (40%), Positives = 30/52 (57%)

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           L+L+ R TN L    I  +GDL   + +D+L+M  FG KSL E++  L   G
Sbjct: 17  LDLNFRVTNRLASAGIFRVGDLCVCSASDLLKMPGFGVKSLQEVERSLQRAG 68


>gi|68062152|ref|XP_673079.1| hypothetical protein [Plasmodium berghei strain ANKA]
 gi|56490663|emb|CAI02138.1| hypothetical protein PB300573.00.0 [Plasmodium berghei]
          Length = 299

 Score = 37.4 bits (85), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 30/110 (27%), Positives = 53/110 (48%), Gaps = 8/110 (7%)

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV-PAKHHRTENDP 167
           +GP +V AG +Q   +IE++N +  IC +   + + M++ +     YV P    ++ N  
Sbjct: 16  KGPMIVVAGHMQLPKNIEIINKNQYICYVAAGSYLEMDVKIESIEEYVMPEYGSQSRNRD 75

Query: 168 I---GLITIDALYSPIKKVSYTVESAREGQVLDY--DKLSMTIDTDGSIT 212
           I     I   +  +P++   +T    R G  LD   +   + + TDGSIT
Sbjct: 76  ICKDNFIHFCSSCTPVEYFGFT--GQRRGINLDILGEINIVEMHTDGSIT 123


>gi|302336390|ref|YP_003801597.1| DNA-directed RNA polymerase subunit beta' [Olsenella uli DSM 7084]
 gi|301320230|gb|ADK68717.1| DNA-directed RNA polymerase subunit beta' [Olsenella uli DSM 7084]
          Length = 1476

 Score = 37.0 bits (84), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 22/62 (35%), Positives = 35/62 (56%)

Query: 246  NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            N ++L    A L   ++L +S R TN      I  +GDLI +TE D+LR+   G K++ E
Sbjct: 1320 NGRTLSSEDAKLYLFDDLGVSQRWTNKFSEVGIETVGDLIGKTEDDLLRIDGIGAKAIEE 1379

Query: 306  IK 307
            ++
Sbjct: 1380 LR 1381


>gi|257784971|ref|YP_003180188.1| DNA-directed RNA polymerase, beta' subunit [Atopobium parvulum DSM
            20469]
 gi|257473478|gb|ACV51597.1| DNA-directed RNA polymerase, beta' subunit [Atopobium parvulum DSM
            20469]
          Length = 1475

 Score = 37.0 bits (84), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 22/62 (35%), Positives = 35/62 (56%)

Query: 246  NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            N ++L    A L   ++L +S R TN      I  +GDLI +TE D+LR+   G K++ E
Sbjct: 1319 NGRTLSSEDAKLYLFDDLGVSQRWTNKFSEVGIETVGDLIGKTEEDLLRIDGIGAKAIEE 1378

Query: 306  IK 307
            ++
Sbjct: 1379 LR 1380


>gi|289809444|ref|ZP_06540073.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. AG3]
          Length = 45

 Score = 36.6 bits (83), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 18/44 (40%), Positives = 30/44 (68%)

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA
Sbjct: 1   STKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTA 44


>gi|14591566|ref|NP_143648.1| TRK system potassium uptake protein [Pyrococcus horikoshii OT3]
 gi|3258249|dbj|BAA30932.1| 496aa long hypothetical TRK system potassium uptake protein
           [Pyrococcus horikoshii OT3]
          Length = 496

 Score = 36.6 bits (83), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 27/96 (28%), Positives = 43/96 (44%), Gaps = 4/96 (4%)

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           + FE  K  +++ I    LP    + +KV E E S      + G  + Y   L+  T   
Sbjct: 370 LTFESLKWTIQQAI----LPKGAVIRRKVGEYEFSEDEIQEVLGFTMTYFAFLLFGTMYM 425

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           MLR+      +L E    +G +GL +G+  P  PP+
Sbjct: 426 MLRIGARFADALFESASAIGNVGLSVGITSPLLPPD 461


>gi|260840788|ref|XP_002613804.1| hypothetical protein BRAFLDRAFT_124174 [Branchiostoma floridae]
 gi|229299194|gb|EEN69813.1| hypothetical protein BRAFLDRAFT_124174 [Branchiostoma floridae]
          Length = 601

 Score = 36.2 bits (82), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 30/113 (26%), Positives = 53/113 (46%), Gaps = 26/113 (23%)

Query: 195 VLDYDKLSMTID-----TDGSITGEDSVALASRILQDQLG------------MFINFEEP 237
           + D+DK+S T+        G  T   +  +A+R ++ +LG            +F     P
Sbjct: 243 IADWDKVSATVAGLTLLAVGVYTARGATGVAARYIEARLGKPALVRETSRISVFEGIRHP 302

Query: 238 KKEVK------EDINVKSLPFNPALLKKVEELELSVRSTNCLRG--ENIVYMG 282
            K VK      ED  ++ + FNP+L  +V ++ ++ R+T   RG   NI++ G
Sbjct: 303 VKTVKRLMTKPEDA-LEGILFNPSLESRVRDIAIATRNTKANRGVYRNILFHG 354


>gi|332158054|ref|YP_004423333.1| TRK system potassium uptake protein [Pyrococcus sp. NA2]
 gi|331033517|gb|AEC51329.1| TRK system potassium uptake protein [Pyrococcus sp. NA2]
          Length = 493

 Score = 36.2 bits (82), Expect = 6.9,   Method: Compositional matrix adjust.
 Identities = 27/96 (28%), Positives = 42/96 (43%), Gaps = 4/96 (4%)

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           + FE  K  +++ I    LP    + +KV E E S      + G  + Y   L   T   
Sbjct: 366 LTFESLKWTIQQAI----LPKGAIIRRKVGEYEFSEDEIQEVLGFTMTYFAFLFLGTMYM 421

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           MLR+      +L E    +G +GL +G+  P  PP+
Sbjct: 422 MLRLGARFADALFESASAIGNVGLSVGITSPLLPPD 457


>gi|308233483|ref|ZP_07664220.1| DNA-directed RNA polymerase subunit beta' [Atopobium vaginae DSM
            15829]
 gi|328943547|ref|ZP_08241012.1| DNA-directed RNA polymerase subunit beta' [Atopobium vaginae DSM
            15829]
 gi|327491516|gb|EGF23290.1| DNA-directed RNA polymerase subunit beta' [Atopobium vaginae DSM
            15829]
          Length = 1485

 Score = 36.2 bits (82), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 28/89 (31%), Positives = 45/89 (50%), Gaps = 1/89 (1%)

Query: 246  NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            N +SL    A L   ++L +S R TN      I  +GDLI +TE ++LR+   G K++ E
Sbjct: 1322 NGRSLSTEDAKLYLFDDLGVSQRWTNKFSEVGIETVGDLIGKTEDELLRIDGIGAKAIEE 1381

Query: 306  IKGVLGTMGLFLGMNLPDWPPESIEELAK 334
            ++  L    L   +  PD      E+L++
Sbjct: 1382 LREGLEARNLLYILE-PDEDEADSEDLSQ 1409


>gi|327312665|ref|YP_004328102.1| hypothetical protein HMPREF9137_0370 [Prevotella denticola F0289]
 gi|326944759|gb|AEA20644.1| hypothetical protein HMPREF9137_0370 [Prevotella denticola F0289]
          Length = 488

 Score = 35.8 bits (81), Expect = 8.8,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 36/61 (59%), Gaps = 1/61 (1%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEA-DMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           V+ L LSVR+ N L    I   G++ +   A  +L++ N GRK++ +I+  +G  GL LG
Sbjct: 406 VQNLNLSVRAINVLNVIGISTFGEIPKIDAAVTLLKVRNSGRKTVHDIEVFIGKFGLQLG 465

Query: 319 M 319
           M
Sbjct: 466 M 466


>gi|315607208|ref|ZP_07882212.1| DNA-directed RNA polymerase subunit alpha [Prevotella buccae ATCC
           33574]
 gi|315251262|gb|EFU31247.1| DNA-directed RNA polymerase subunit alpha [Prevotella buccae ATCC
           33574]
          Length = 488

 Score = 35.8 bits (81), Expect = 9.2,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 36/61 (59%), Gaps = 1/61 (1%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEA-DMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           V+ L LSVR+ N L    I   G++ +   A  +L++ N GRK++ +I+  +G  GL LG
Sbjct: 406 VQNLNLSVRAINVLNVIGISTFGEIPKIDAAVTLLKVRNSGRKTVHDIEVFIGKFGLQLG 465

Query: 319 M 319
           M
Sbjct: 466 M 466


>gi|320161915|ref|YP_004175140.1| 50S ribosomal protein L31 [Anaerolinea thermophila UNI-1]
 gi|319995769|dbj|BAJ64540.1| 50S ribosomal protein L31 [Anaerolinea thermophila UNI-1]
          Length = 158

 Score = 35.8 bits (81), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 29/104 (27%), Positives = 48/104 (46%), Gaps = 19/104 (18%)

Query: 233 NFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGD---LIQRTE 289
           +F E KK  +E           +L + +  L L  R T  L    I  +G    L+++ E
Sbjct: 70  SFAEQKKAREEA--------RTSLERPIASLNLGTRPTEALAKAGITTVGQVIALLEQGE 121

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELA 333
           A +L +  FGRK+L+++K  L  +G  L        P + +E+A
Sbjct: 122 AALLNVEGFGRKALIDLKKTLRGLGYQL--------PAAADEIA 157


Searching..................................................done


Results from round 2




>gi|62290120|ref|YP_221913.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 1
           str. 9-941]
 gi|82700043|ref|YP_414617.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis
           biovar Abortus 2308]
 gi|189024358|ref|YP_001935126.1| RNA polymerase, alpha chain, bacterial and organelle [Brucella
           abortus S19]
 gi|225627680|ref|ZP_03785717.1| DNA-directed RNA polymerase, alpha subunit [Brucella ceti str.
           Cudo]
 gi|237815628|ref|ZP_04594625.1| DNA-directed RNA polymerase, alpha subunit [Brucella abortus str.
           2308 A]
 gi|254689429|ref|ZP_05152683.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 6
           str. 870]
 gi|254693914|ref|ZP_05155742.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 3
           str. Tulya]
 gi|254697564|ref|ZP_05159392.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 2
           str. 86/8/59]
 gi|254710280|ref|ZP_05172091.1| DNA-directed RNA polymerase subunit alpha [Brucella pinnipedialis
           B2/94]
 gi|254714277|ref|ZP_05176088.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti M644/93/1]
 gi|254717714|ref|ZP_05179525.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti M13/05/1]
 gi|254730458|ref|ZP_05189036.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 4
           str. 292]
 gi|256031774|ref|ZP_05445388.1| DNA-directed RNA polymerase subunit alpha [Brucella pinnipedialis
           M292/94/1]
 gi|256159944|ref|ZP_05457662.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti M490/95/1]
 gi|256255175|ref|ZP_05460711.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti B1/94]
 gi|256257675|ref|ZP_05463211.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 9
           str. C68]
 gi|256369633|ref|YP_003107143.1| DNA-directed RNA polymerase alpha subunit [Brucella microti CCM
           4915]
 gi|260168908|ref|ZP_05755719.1| DNA-directed RNA polymerase subunit alpha [Brucella sp. F5/99]
 gi|260546668|ref|ZP_05822407.1| RNA polymerase [Brucella abortus NCTC 8038]
 gi|260754952|ref|ZP_05867300.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 6
           str. 870]
 gi|260758168|ref|ZP_05870516.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 4
           str. 292]
 gi|260761994|ref|ZP_05874337.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 2
           str. 86/8/59]
 gi|260883961|ref|ZP_05895575.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 9
           str. C68]
 gi|261214205|ref|ZP_05928486.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 3
           str. Tulya]
 gi|261219556|ref|ZP_05933837.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti M13/05/1]
 gi|261222371|ref|ZP_05936652.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti B1/94]
 gi|261317842|ref|ZP_05957039.1| DNA-directed RNA polymerase subunit alpha [Brucella pinnipedialis
           B2/94]
 gi|261322051|ref|ZP_05961248.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti M644/93/1]
 gi|261758400|ref|ZP_06002109.1| RNA polymerase [Brucella sp. F5/99]
 gi|265988872|ref|ZP_06101429.1| DNA-directed RNA polymerase subunit alpha [Brucella pinnipedialis
           M292/94/1]
 gi|265998336|ref|ZP_06110893.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti M490/95/1]
 gi|297248515|ref|ZP_06932233.1| DNA-directed RNA polymerase, alpha subunit [Brucella abortus bv. 5
           str. B3196]
 gi|306840325|ref|ZP_07473097.1| DNA-directed RNA polymerase, alpha subunit [Brucella sp. BO2]
 gi|306844112|ref|ZP_07476706.1| DNA-directed RNA polymerase, alpha subunit [Brucella sp. BO1]
 gi|75496695|sp|Q57CT2|RPOA_BRUAB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366668|sp|Q2YRU0|RPOA_BRUA2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238689381|sp|B2S655|RPOA_BRUA1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|62196252|gb|AAX74552.1| RpoA, DNA-directed RNA polymerase, alpha subunit [Brucella abortus
           bv. 1 str. 9-941]
 gi|82616144|emb|CAJ11187.1| RNA polymerase, alpha chain, bacterial and organelle [Brucella
           melitensis biovar Abortus 2308]
 gi|189019930|gb|ACD72652.1| RNA polymerase, alpha chain, bacterial and organelle [Brucella
           abortus S19]
 gi|225617685|gb|EEH14730.1| DNA-directed RNA polymerase, alpha subunit [Brucella ceti str.
           Cudo]
 gi|237788926|gb|EEP63137.1| DNA-directed RNA polymerase, alpha subunit [Brucella abortus str.
           2308 A]
 gi|255999795|gb|ACU48194.1| DNA-directed RNA polymerase alpha subunit [Brucella microti CCM
           4915]
 gi|260095718|gb|EEW79595.1| RNA polymerase [Brucella abortus NCTC 8038]
 gi|260668486|gb|EEX55426.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 4
           str. 292]
 gi|260672426|gb|EEX59247.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 2
           str. 86/8/59]
 gi|260675060|gb|EEX61881.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 6
           str. 870]
 gi|260873489|gb|EEX80558.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 9
           str. C68]
 gi|260915812|gb|EEX82673.1| DNA-directed RNA polymerase subunit alpha [Brucella abortus bv. 3
           str. Tulya]
 gi|260920955|gb|EEX87608.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti B1/94]
 gi|260924645|gb|EEX91213.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti M13/05/1]
 gi|261294741|gb|EEX98237.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti M644/93/1]
 gi|261297065|gb|EEY00562.1| DNA-directed RNA polymerase subunit alpha [Brucella pinnipedialis
           B2/94]
 gi|261738384|gb|EEY26380.1| RNA polymerase [Brucella sp. F5/99]
 gi|262552804|gb|EEZ08794.1| DNA-directed RNA polymerase subunit alpha [Brucella ceti M490/95/1]
 gi|264661069|gb|EEZ31330.1| DNA-directed RNA polymerase subunit alpha [Brucella pinnipedialis
           M292/94/1]
 gi|297175684|gb|EFH35031.1| DNA-directed RNA polymerase, alpha subunit [Brucella abortus bv. 5
           str. B3196]
 gi|306275555|gb|EFM57287.1| DNA-directed RNA polymerase, alpha subunit [Brucella sp. BO1]
 gi|306289724|gb|EFM60913.1| DNA-directed RNA polymerase, alpha subunit [Brucella sp. BO2]
          Length = 337

 Score =  423 bits (1088), Expect = e-116,   Method: Composition-based stats.
 Identities = 228/339 (67%), Positives = 279/339 (82%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFITHGSRTH--ATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K GPGVVTAGDIQ
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKEGPGVVTAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 119 TVGDVEILNPEHVICTLDEGAEIRMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY +E+ REGQVLDYDKL++ I+T+GS+TGED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKIENTREGQVLDYDKLTLNIETNGSVTGEDAVAYAARILQDQLSIFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 APQEQ-VAELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 298 KSLNEIKEVLASMGLHLGMEIPAWPPENIEDLAKRYEDQ 336


>gi|256061289|ref|ZP_05451439.1| DNA-directed RNA polymerase subunit alpha [Brucella neotomae 5K33]
 gi|261325296|ref|ZP_05964493.1| DNA-directed RNA polymerase subunit alpha [Brucella neotomae 5K33]
 gi|261301276|gb|EEY04773.1| DNA-directed RNA polymerase subunit alpha [Brucella neotomae 5K33]
          Length = 337

 Score =  423 bits (1088), Expect = e-116,   Method: Composition-based stats.
 Identities = 228/339 (67%), Positives = 279/339 (82%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFITHGSRTH--ATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K GPGVVTAGDIQ
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIVIRMEGEGPKRMVVRKEGPGVVTAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 119 TVGDVEILNPEHVICTLDEGAEIRMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY +E+ REGQVLDYDKL++ I+T+GS+TGED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKIENTREGQVLDYDKLTLNIETNGSVTGEDAVAYAARILQDQLSIFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 APQEQ-VAELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 298 KSLNEIKEVLASMGLHLGMEIPAWPPENIEDLAKRYEDQ 336


>gi|254719267|ref|ZP_05181078.1| DNA-directed RNA polymerase subunit alpha [Brucella sp. 83/13]
 gi|265984266|ref|ZP_06097001.1| DNA-directed RNA polymerase subunit alpha [Brucella sp. 83/13]
 gi|306838018|ref|ZP_07470876.1| DNA-directed RNA polymerase, alpha subunit [Brucella sp. NF 2653]
 gi|264662858|gb|EEZ33119.1| DNA-directed RNA polymerase subunit alpha [Brucella sp. 83/13]
 gi|306406942|gb|EFM63163.1| DNA-directed RNA polymerase, alpha subunit [Brucella sp. NF 2653]
          Length = 337

 Score =  423 bits (1088), Expect = e-116,   Method: Composition-based stats.
 Identities = 227/339 (66%), Positives = 278/339 (82%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFITHGSRTH--ATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K GPGVVT GDIQ
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKEGPGVVTTGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 119 TVGDVEILNPEHVICTLDEGAEIRMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY +E+ REGQVLDYDKL++ I+T+GS+TGED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKIENTREGQVLDYDKLTLNIETNGSVTGEDAVAYAARILQDQLSIFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 APQEQ-VAELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 298 KSLNEIKEVLASMGLHLGMEIPAWPPENIEDLAKRYEDQ 336


>gi|17987064|ref|NP_539698.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           1 str. 16M]
 gi|225852705|ref|YP_002732938.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis ATCC
           23457]
 gi|256044859|ref|ZP_05447763.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           1 str. Rev.1]
 gi|256113763|ref|ZP_05454567.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           3 str. Ether]
 gi|256263804|ref|ZP_05466336.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           2 str. 63/9]
 gi|260565539|ref|ZP_05836023.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           1 str. 16M]
 gi|265991286|ref|ZP_06103843.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           1 str. Rev.1]
 gi|265995123|ref|ZP_06107680.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           3 str. Ether]
 gi|20139479|sp|Q8YHL6|RPOA_BRUME RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|254765245|sp|C0RJH6|RPOA_BRUMB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|17982721|gb|AAL51962.1| DNA-directed RNA polymerase alpha chain [Brucella melitensis bv. 1
           str. 16M]
 gi|225641070|gb|ACO00984.1| DNA-directed RNA polymerase, alpha subunit [Brucella melitensis
           ATCC 23457]
 gi|260151607|gb|EEW86701.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           1 str. 16M]
 gi|262766236|gb|EEZ12025.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           3 str. Ether]
 gi|263002070|gb|EEZ14645.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           1 str. Rev.1]
 gi|263093932|gb|EEZ17866.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis bv.
           2 str. 63/9]
 gi|326409230|gb|ADZ66295.1| DNA-directed RNA polymerase subunit alpha [Brucella melitensis M28]
 gi|326538938|gb|ADZ87153.1| DNA-directed RNA polymerase, alpha subunit [Brucella melitensis
           M5-90]
          Length = 337

 Score =  423 bits (1087), Expect = e-116,   Method: Composition-based stats.
 Identities = 228/339 (67%), Positives = 279/339 (82%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFITHGSRTH--ATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K GPGVVTAGDIQ
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVHKEGPGVVTAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 119 TVGDVEILNPEHVICTLDEGAEIRMEFTVNTGKGYVPADCNRAEDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY +E+ REGQVLDYDKL++ I+T+GS+TGED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKIENTREGQVLDYDKLTLNIETNGSVTGEDAVAYAARILQDQLSIFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 APQEQ-VAELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 298 KSLNEIKEVLASMGLHLGMEIPAWPPENIEDLAKRYEDQ 336


>gi|23502086|ref|NP_698213.1| DNA-directed RNA polymerase subunit alpha [Brucella suis 1330]
 gi|163843474|ref|YP_001627878.1| DNA-directed RNA polymerase subunit alpha [Brucella suis ATCC
           23445]
 gi|254704494|ref|ZP_05166322.1| DNA-directed RNA polymerase subunit alpha [Brucella suis bv. 3 str.
           686]
 gi|260566262|ref|ZP_05836732.1| DNA-directed RNA polymerase subunit alpha [Brucella suis bv. 4 str.
           40]
 gi|261755176|ref|ZP_05998885.1| DNA-directed RNA polymerase subunit alpha [Brucella suis bv. 3 str.
           686]
 gi|38258599|sp|Q8G094|RPOA_BRUSU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|189043832|sp|B0CH07|RPOA_BRUSI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|23348045|gb|AAN30128.1| DNA-directed RNA polymerase, alpha subunit [Brucella suis 1330]
 gi|163674197|gb|ABY38308.1| DNA-directed RNA polymerase, alpha subunit [Brucella suis ATCC
           23445]
 gi|260155780|gb|EEW90860.1| DNA-directed RNA polymerase subunit alpha [Brucella suis bv. 4 str.
           40]
 gi|261744929|gb|EEY32855.1| DNA-directed RNA polymerase subunit alpha [Brucella suis bv. 3 str.
           686]
          Length = 337

 Score =  422 bits (1086), Expect = e-116,   Method: Composition-based stats.
 Identities = 228/339 (67%), Positives = 279/339 (82%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFITHGSRTH--ATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K GPGVVTAGDIQ
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKEGPGVVTAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 119 TVGDVEILNPEHVICTLDEGAEIRMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY +E+ REGQVLDYDKL++ I+T+GS+TGED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKIENTREGQVLDYDKLTLNIETNGSVTGEDAVAYAARILQDQLSIFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 APQEQ-VAELAFNPALLKKVDELELSVRSANCLKTDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 298 KSLNEIKEVLASMGLHLGMEIPAWPPENIEDLAKRYEDQ 336


>gi|148560545|ref|YP_001259129.1| DNA-directed RNA polymerase subunit alpha [Brucella ovis ATCC
           25840]
 gi|166229260|sp|A5VQY2|RPOA_BRUO2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|148371802|gb|ABQ61781.1| DNA-directed RNA polymerase, alpha subunit [Brucella ovis ATCC
           25840]
          Length = 337

 Score =  422 bits (1086), Expect = e-116,   Method: Composition-based stats.
 Identities = 226/339 (66%), Positives = 277/339 (81%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFITHGSRAH--ATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K GPGVVTAGDIQ
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKEGPGVVTAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+H IC LD  A + ME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 119 TVGDVEILNPEHAICTLDEGAEICMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY +E+ REGQVLDYDKL++ I+T+GS+TGED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKIENTREGQVLDYDKLTLNIETNGSVTGEDAVAYAARILQDQLSIFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 APQEQ-VAELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 298 KSLNEIKEVLASMGLHLGMEIPAWPPENIEDLAKRYEDQ 336


>gi|294852544|ref|ZP_06793217.1| DNA-directed RNA polymerase [Brucella sp. NVSL 07-0026]
 gi|294821133|gb|EFG38132.1| DNA-directed RNA polymerase [Brucella sp. NVSL 07-0026]
          Length = 337

 Score =  422 bits (1085), Expect = e-116,   Method: Composition-based stats.
 Identities = 227/339 (66%), Positives = 278/339 (82%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFITHGSRTH--ATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K GPGVVTAGDIQ
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKEGPGVVTAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 119 TVGDVEILNPEHVICTLDEGAEIRMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY +E+ REGQVLDYDKL++ I+T+GS+TGED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKIENTREGQVLDYDKLTLNIETNGSVTGEDAVAYAARILQDQLSIFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++  V  L FN ALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 APQEQ-VAELAFNAALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 298 KSLNEIKEVLASMGLHLGMEIPAWPPENIEDLAKRYEDQ 336


>gi|161619164|ref|YP_001593051.1| DNA-directed RNA polymerase subunit alpha [Brucella canis ATCC
           23365]
 gi|189043831|sp|A9M5M5|RPOA_BRUC2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|161335975|gb|ABX62280.1| DNA-directed RNA polymerase, alpha subunit [Brucella canis ATCC
           23365]
          Length = 337

 Score =  422 bits (1085), Expect = e-116,   Method: Composition-based stats.
 Identities = 227/339 (66%), Positives = 278/339 (82%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFITHGSRTH--ATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K GPGVVTAGDIQ
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKEGPGVVTAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 119 TVGDVEILNPEHVICTLDEGAEIRMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY +E+ REGQVLDYDKL++ I+T+GS+TGED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKIENTREGQVLDYDKLTLNIETNGSVTGEDAVAYAARILQDQLSIFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++  V  L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 APQEQ-VAELAFNPVLLKKVDELELSVRSANCLKTDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 298 KSLNEIKEVLASMGLHLGMEIPAWPPENIEDLAKRYEDQ 336


>gi|153009310|ref|YP_001370525.1| DNA-directed RNA polymerase subunit alpha [Ochrobactrum anthropi
           ATCC 49188]
 gi|239832098|ref|ZP_04680427.1| DNA-directed RNA polymerase, alpha subunit [Ochrobactrum
           intermedium LMG 3301]
 gi|166229274|sp|A6X0E2|RPOA_OCHA4 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|151561198|gb|ABS14696.1| DNA-directed RNA polymerase, alpha subunit [Ochrobactrum anthropi
           ATCC 49188]
 gi|239824365|gb|EEQ95933.1| DNA-directed RNA polymerase, alpha subunit [Ochrobactrum
           intermedium LMG 3301]
          Length = 337

 Score =  422 bits (1085), Expect = e-116,   Method: Composition-based stats.
 Identities = 226/339 (66%), Positives = 279/339 (82%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFITNGSRTH--ATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGVLHE SSI GV ED+TDI+LN+K I ++M G+  KR+ + K GPGVVTAGDIQ
Sbjct: 59  TAIQIDGVLHEFSSIPGVREDVTDIVLNVKEIAIRMEGEGPKRMVVRKEGPGVVTAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNPDHVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 119 TVGDVEILNPDHVICTLDEGAEIRMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY +E+ REGQVLDYDKL++ I+T+GS++GED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKIENTREGQVLDYDKLTLNIETNGSVSGEDAVAYAARILQDQLAIFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 APQEQ-VAELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 298 KSLNEIKEVLASMGLHLGMEIPSWPPENIEDLAKRYEDQ 336


>gi|254780237|ref|YP_003064650.1| DNA-directed RNA polymerase subunit alpha [Candidatus Liberibacter
           asiaticus str. psy62]
 gi|254039914|gb|ACT56710.1| DNA-directed RNA polymerase subunit alpha [Candidatus Liberibacter
           asiaticus str. psy62]
          Length = 340

 Score =  422 bits (1084), Expect = e-116,   Method: Composition-based stats.
 Identities = 340/340 (100%), Positives = 340/340 (100%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI
Sbjct: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ
Sbjct: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI
Sbjct: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE
Sbjct: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR
Sbjct: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
           KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC
Sbjct: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340


>gi|254706610|ref|ZP_05168438.1| DNA-directed RNA polymerase subunit alpha [Brucella pinnipedialis
           M163/99/10]
 gi|261314070|ref|ZP_05953267.1| DNA-directed RNA polymerase subunit alpha [Brucella pinnipedialis
           M163/99/10]
 gi|261303096|gb|EEY06593.1| DNA-directed RNA polymerase subunit alpha [Brucella pinnipedialis
           M163/99/10]
          Length = 337

 Score =  420 bits (1081), Expect = e-115,   Method: Composition-based stats.
 Identities = 227/339 (66%), Positives = 278/339 (82%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFITHGSRTH--ATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K GPGVVTAGDIQ
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKEGPGVVTAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 119 TVGDVEILNPEHVICTLDEGAEIRMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY +E+ REGQVLDYDKL++ I+T+GS+TGED+VA A+RILQDQL +F+NFEE +KE
Sbjct: 179 RKVSYKIENTREGQVLDYDKLTLNIETNGSVTGEDAVAYAARILQDQLSIFVNFEELQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 APQEQ-VAELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 298 KSLNEIKEVLASMGLHLGMEIPAWPPENIEDLAKRYEDQ 336


>gi|110634006|ref|YP_674214.1| DNA-directed RNA polymerase subunit alpha [Mesorhizobium sp. BNC1]
 gi|119366696|sp|Q11HS6|RPOA_MESSB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|110284990|gb|ABG63049.1| DNA-directed RNA polymerase subunit alpha [Chelativorans sp. BNC1]
          Length = 336

 Score =  418 bits (1076), Expect = e-115,   Method: Composition-based stats.
 Identities = 237/339 (69%), Positives = 284/339 (83%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP+ IE+   G+ + N   ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPSKIEFTSKGRTQTN---LVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M GD  KR+ + K+GPG VTAGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIAGVREDVTDIVLNIKEIAIRMEGDGPKRMVLRKQGPGAVTAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDVEILNPEHVICTLDQGAEIRMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQVLDYDKL+MTI+TDGS+TGED+VA A+RILQDQLG+F+NFEEP+KE
Sbjct: 178 KKVSYKVENTREGQVLDYDKLTMTIETDGSVTGEDAVAFAARILQDQLGLFVNFEEPQKE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V  +  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 238 VPAEQ-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +PDWPP++IEELAK+YED+
Sbjct: 297 KSLNEIKEVLASMGLHLGMEVPDWPPDNIEELAKRYEDQ 335


>gi|15965133|ref|NP_385486.1| DNA-directed RNA polymerase subunit alpha [Sinorhizobium meliloti
           1021]
 gi|150396231|ref|YP_001326698.1| DNA-directed RNA polymerase subunit alpha [Sinorhizobium medicae
           WSM419]
 gi|307314383|ref|ZP_07593989.1| DNA-directed RNA polymerase, alpha subunit [Sinorhizobium meliloti
           BL225C]
 gi|307322095|ref|ZP_07601471.1| DNA-directed RNA polymerase, alpha subunit [Sinorhizobium meliloti
           AK83]
 gi|20139518|sp|Q925Z2|RPOA_RHIME RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|166229280|sp|A6U883|RPOA_SINMW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|15074313|emb|CAC45959.1| DNA-directed RNA polymerase, alpha subunit [Sinorhizobium meliloti
           1021]
 gi|16588802|gb|AAL26901.1| RNA polymerase alpha-subunit [Sinorhizobium meliloti]
 gi|150027746|gb|ABR59863.1| DNA-directed RNA polymerase, alpha subunit [Sinorhizobium medicae
           WSM419]
 gi|306892277|gb|EFN23087.1| DNA-directed RNA polymerase, alpha subunit [Sinorhizobium meliloti
           AK83]
 gi|306899081|gb|EFN29723.1| DNA-directed RNA polymerase, alpha subunit [Sinorhizobium meliloti
           BL225C]
          Length = 336

 Score =  418 bits (1076), Expect = e-115,   Method: Composition-based stats.
 Identities = 234/339 (69%), Positives = 284/339 (83%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+   G+    +  ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVEFASSGR---TKATLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I +KM GD  KR+ + K+GPGVVTAGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIKMDGDDAKRMVVRKQGPGVVTAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA  +R+E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDIEILNPNHVICTLDEGAEIRMEFTVNNGKGYVPADRNRSEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQVLDYDKL+M+I+TDGS+TGED++A A+RILQDQL +F+NF+EP+KE
Sbjct: 178 KKVSYKVENTREGQVLDYDKLTMSIETDGSVTGEDAIAFAARILQDQLSVFVNFDEPQKE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 238 TEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 297 KSLNEIKEVLASMGLHLGMEVPSWPPENIEDLAKRYEDQ 335


>gi|227821779|ref|YP_002825749.1| DNA-directed RNA polymerase subunit alpha [Sinorhizobium fredii
           NGR234]
 gi|254765259|sp|C3MB03|RPOA_RHISN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|227340778|gb|ACP24996.1| DNA-directed RNA polymerase alpha chain [Sinorhizobium fredii
           NGR234]
          Length = 336

 Score =  418 bits (1075), Expect = e-115,   Method: Composition-based stats.
 Identities = 233/339 (68%), Positives = 285/339 (84%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++   G+    +  ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFTSSGR---TKATLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I +KM GD  KR+ + K+GPGVVTAGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIKMDGDDSKRMVVRKQGPGVVTAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +R+E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDIEILNPNHVICTLDEGAEIRMEFTVNNGKGYVPAERNRSEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQVLDYDKL+M+I+TDGS+TGED++A A+RILQDQL +F+NF+EP+KE
Sbjct: 178 KKVSYKVENTREGQVLDYDKLTMSIETDGSVTGEDAIAFAARILQDQLSVFVNFDEPQKE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 238 AEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 297 KSLNEIKEVLASMGLHLGMEVPSWPPENIEDLAKRYEDQ 335


>gi|254418751|ref|ZP_05032475.1| DNA-directed RNA polymerase, alpha subunit [Brevundimonas sp. BAL3]
 gi|196184928|gb|EDX79904.1| DNA-directed RNA polymerase, alpha subunit [Brevundimonas sp. BAL3]
          Length = 339

 Score =  418 bits (1074), Expect = e-115,   Method: Composition-based stats.
 Identities = 212/339 (62%), Positives = 269/339 (79%), Gaps = 1/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI++NWQELI+P   + I +G + + +  ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIERNWQELIRPEKPQ-IEIGSDAQRKARLVAEPLERGFGVTLGNALRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGV+HE SS++GV ED+ DI+LNIK + L+M  +  KR+T+   GPG VTAG I 
Sbjct: 60  TAIQIDGVVHEFSSLEGVREDVVDIVLNIKQLALRMHAEGPKRMTLRATGPGAVTAGQID 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DIEVLNPDHVIC LD  A VRMELTV  G GYV A+ +R E+ PIGLI +DALYSP+
Sbjct: 120 VSADIEVLNPDHVICTLDDGASVRMELTVQNGKGYVAAELNRPEDAPIGLIAVDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V+Y VE  R+GQ LDYDKL + ++T+G++T  D+VA A+RILQDQL +FI FEEPKK 
Sbjct: 180 KRVAYRVEPTRQGQSLDYDKLLLEVETNGAVTPVDAVAYAARILQDQLQIFITFEEPKKA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V++      LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE +MLR  NFGR
Sbjct: 240 VEQSDGKPDLPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEGEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL TMGL LGM++P+WPPE+IE+LAKK++D+
Sbjct: 300 KSLNEIKEVLATMGLSLGMDVPNWPPENIEDLAKKFDDQ 338


>gi|329889151|ref|ZP_08267494.1| DNA-directed RNA polymerase, alpha subunit [Brevundimonas diminuta
           ATCC 11568]
 gi|328844452|gb|EGF94016.1| DNA-directed RNA polymerase, alpha subunit [Brevundimonas diminuta
           ATCC 11568]
          Length = 339

 Score =  417 bits (1072), Expect = e-114,   Method: Composition-based stats.
 Identities = 206/339 (60%), Positives = 266/339 (78%), Gaps = 1/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI++NWQELI+P   +    G + +++  +IAEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIERNWQELIRPEKPQVEG-GSDPQHKARLIAEPLERGFGVTLGNALRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGV+HE SS++GV ED+ DI+LNIK + L+M  +  KR+T+   GPG VTA  I 
Sbjct: 60  TAIQIDGVVHEFSSLEGVREDVVDIVLNIKQLALRMHAEGPKRMTLRATGPGPVTAAQID 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DIEVLNPDHVIC LD  A VRMELTV  G GYV A+ +R E+ PIGLI +DALYSP+
Sbjct: 120 LPADIEVLNPDHVICTLDDGASVRMELTVQNGKGYVAAELNRPEDAPIGLIAVDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V+Y VE  R+GQ LDYDKL + ++T+G+++  D+VA A+RILQDQL +FI F+EP K 
Sbjct: 180 KRVAYRVEPTRQGQSLDYDKLILEVETNGAVSPVDAVAYAARILQDQLQIFITFDEPTKA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V++      LPFNP+LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE +MLR  NFGR
Sbjct: 240 VEQSDGKPELPFNPSLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEGEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM++P+WPPE+IE+LAKK++D+
Sbjct: 300 KSLNEIKEVLASMGLSLGMDVPNWPPENIEDLAKKFDDQ 338


>gi|315122794|ref|YP_004063283.1| DNA-directed RNA polymerase subunit alpha [Candidatus Liberibacter
           solanacearum CLso-ZC1]
 gi|313496196|gb|ADR52795.1| DNA-directed RNA polymerase subunit alpha [Candidatus Liberibacter
           solanacearum CLso-ZC1]
          Length = 340

 Score =  417 bits (1072), Expect = e-114,   Method: Composition-based stats.
 Identities = 299/340 (87%), Positives = 321/340 (94%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPNNIE+ VLG EEENRT+++AEP PRGFAHTLGNALRRVL+SSLRGAAI
Sbjct: 1   MIQKNWQELIKPNNIEFTVLGHEEENRTMVVAEPFPRGFAHTLGNALRRVLLSSLRGAAI 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHEISSIKGV ED+TDIILNIKGINLKMS DS KRVTI+KRGPGVVTAGDIQ
Sbjct: 61  TAVQIDGVLHEISSIKGVREDITDIILNIKGINLKMSSDSSKRVTIYKRGPGVVTAGDIQ 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TVNDIE+LNPDHVICNLDVDAVVRMELTVSKG GYVPAKHHRTENDPIGLITIDALYSPI
Sbjct: 121 TVNDIEILNPDHVICNLDVDAVVRMELTVSKGQGYVPAKHHRTENDPIGLITIDALYSPI 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VESAREGQ+LDYDKL+M IDTDGSI GED+VA ASRILQDQL +FINF+EP KE
Sbjct: 181 KKVSYKVESAREGQILDYDKLNMIIDTDGSIGGEDAVAFASRILQDQLNVFINFDEPTKE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            KED++V  LPFNPALLKKVEELELSVRS NCLRG+NI+Y+GDLIQ+TEA+MLR ANFGR
Sbjct: 241 EKEDMDVDRLPFNPALLKKVEELELSVRSANCLRGDNIIYIGDLIQKTEAEMLRTANFGR 300

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
           KSL+EIKGVL TMGLFLGMNLPDWPPESIE+LAKKYEDKC
Sbjct: 301 KSLLEIKGVLATMGLFLGMNLPDWPPESIEDLAKKYEDKC 340


>gi|86357329|ref|YP_469221.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli CFN 42]
 gi|116251564|ref|YP_767402.1| DNA-directed RNA polymerase subunit alpha [Rhizobium leguminosarum
           bv. viciae 3841]
 gi|190891379|ref|YP_001977921.1| DNA-directed RNA polymerase protein, alpha subunit [Rhizobium etli
           CIAT 652]
 gi|209548959|ref|YP_002280876.1| DNA-directed RNA polymerase subunit alpha [Rhizobium leguminosarum
           bv. trifolii WSM2304]
 gi|218516292|ref|ZP_03513132.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli 8C-3]
 gi|241204189|ref|YP_002975285.1| DNA-directed RNA polymerase subunit alpha [Rhizobium leguminosarum
           bv. trifolii WSM1325]
 gi|119366712|sp|Q2K9J2|RPOA_RHIEC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366713|sp|Q1MIB7|RPOA_RHIL3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238057757|sp|B5ZZ57|RPOA_RHILW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238692528|sp|B3PWU5|RPOA_RHIE6 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|86281431|gb|ABC90494.1| DNA-directed RNA polymerase alpha chain protein [Rhizobium etli CFN
           42]
 gi|115256212|emb|CAK07293.1| putative DNA-directed RNA polymerase alpha chain [Rhizobium
           leguminosarum bv. viciae 3841]
 gi|190696658|gb|ACE90743.1| DNA-directed RNA polymerase protein, alpha subunit [Rhizobium etli
           CIAT 652]
 gi|209534715|gb|ACI54650.1| DNA-directed RNA polymerase, alpha subunit [Rhizobium leguminosarum
           bv. trifolii WSM2304]
 gi|240858079|gb|ACS55746.1| DNA-directed RNA polymerase, alpha subunit [Rhizobium leguminosarum
           bv. trifolii WSM1325]
 gi|327189694|gb|EGE56841.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli CNPAF512]
          Length = 336

 Score =  417 bits (1071), Expect = e-114,   Method: Composition-based stats.
 Identities = 238/339 (70%), Positives = 283/339 (83%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+         R  ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVEF---SSSSRTRATLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I +KM GD  KR+ + K+GPGVVTAGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIKMDGDDAKRMVVRKQGPGVVTAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDIEILNPEHVICTLDEGAEIRMEFTVNNGKGYVPAERNRAEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQVLDYDKL+MTI+TDGSITGED+VA A+RILQDQLG+F+NF+EP+KE
Sbjct: 178 KKVSYKVENTREGQVLDYDKLNMTIETDGSITGEDAVAFAARILQDQLGVFVNFDEPQKE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 238 TEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 297 KSLNEIKEVLASMGLHLGMEVPAWPPENIEDLAKRYEDQ 335


>gi|222148390|ref|YP_002549347.1| DNA-directed RNA polymerase subunit alpha [Agrobacterium vitis S4]
 gi|254765240|sp|B9JVR1|RPOA_AGRVS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|221735378|gb|ACM36341.1| DNA-directed RNA polymerase alpha subunit [Agrobacterium vitis S4]
          Length = 336

 Score =  417 bits (1071), Expect = e-114,   Method: Composition-based stats.
 Identities = 234/339 (69%), Positives = 282/339 (83%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+   G+    +  ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVEFSSSGR---TKATLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I +KM GD  KR+ + K+GPGVVTAGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIKMDGDDAKRMVVRKQGPGVVTAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIE+LNP HVIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDIEILNPHHVICTLDEGAEIRMEFTVNNGKGYVPADRNRAEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQVLDYDKL+MTI+TDGS++GED+VA A+RILQDQL +F+NF+EP++E
Sbjct: 178 KKVSYKVENTREGQVLDYDKLTMTIETDGSVSGEDAVAFAARILQDQLSVFVNFDEPQRE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 238 AEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 297 KSLNEIKEVLASMGLHLGMEVPAWPPENIEDLAKRYEDQ 335


>gi|15889218|ref|NP_354899.1| DNA-directed RNA polymerase subunit alpha [Agrobacterium
           tumefaciens str. C58]
 gi|325293312|ref|YP_004279176.1| DNA-directed RNA polymerase subunit alpha [Agrobacterium sp. H13-3]
 gi|61234197|sp|P0A4E3|RPOA_AGRT5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61234204|sp|P0A4E4|RPOA_RHIRD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|5712306|gb|AAD47422.1|AF111855_1 RNA polymerase alpha subunit [Agrobacterium tumefaciens]
 gi|15157043|gb|AAK87684.1| DNA-directed RNA polymerase alpha subunit [Agrobacterium
           tumefaciens str. C58]
 gi|325061165|gb|ADY64856.1| DNA-directed RNA polymerase subunit alpha [Agrobacterium sp. H13-3]
          Length = 336

 Score =  416 bits (1070), Expect = e-114,   Method: Composition-based stats.
 Identities = 234/339 (69%), Positives = 282/339 (83%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+         +  ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVEFT---SSSRTKATLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I +KM GD  KR+ + K+GPG VTAGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIKMDGDDSKRMVVRKQGPGSVTAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIE+LNPDHVIC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDIEILNPDHVICTLDEGAEIRMEFTVNNGKGYVPAERNRAEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQVLDYDKL MTI+T+GS++GED+VA A+RILQDQLG+F+NF+EP+KE
Sbjct: 178 KKVSYKVENTREGQVLDYDKLIMTIETNGSVSGEDAVAFAARILQDQLGVFVNFDEPQKE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E+ +V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 238 AEEE-SVTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 297 KSLNEIKEVLASMGLHLGMEVPAWPPENIEDLAKRYEDQ 335


>gi|163851599|ref|YP_001639642.1| DNA-directed RNA polymerase subunit alpha [Methylobacterium
           extorquens PA1]
 gi|163663204|gb|ABY30571.1| DNA-directed RNA polymerase, alpha subunit [Methylobacterium
           extorquens PA1]
          Length = 365

 Score =  416 bits (1070), Expect = e-114,   Method: Composition-based stats.
 Identities = 212/338 (62%), Positives = 271/338 (80%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN ++ +  G + +    ++AEPL RGF  TLGN+LRRVL+SSL+GAA+
Sbjct: 28  VIQKNWQELIKPNKLQ-VTAGDDPKRVATVVAEPLERGFGTTLGNSLRRVLLSSLQGAAV 86

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQIDGVLHE SSI GV ED+TDI+LNIK I ++   D  KR+T+ K GPG+VTAGDI 
Sbjct: 87  TSVQIDGVLHEFSSIPGVREDVTDIVLNIKTIAIRSQTDQPKRMTLRKTGPGLVTAGDIG 146

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
            V DI++LNPD VIC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +DALYSP+
Sbjct: 147 AVGDIQILNPDLVICTLDDGAEIRMEFTVATGKGYVPAERNRPEDAPIGLIPVDALYSPV 206

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY VE+ REGQ LD DKL+MT++T+G+++ ED++A A+RI+QDQL +F+NFEEP+KE
Sbjct: 207 TKVSYRVETTREGQDLDKDKLTMTLETNGAVSPEDALAYAARIIQDQLQVFVNFEEPRKE 266

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +       LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++E +MLR  NFGR
Sbjct: 267 -EAAPLAPQLPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSEGEMLRTPNFGR 325

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++P WPPE+IE+LAK++E+
Sbjct: 326 KSLNEIKEVLAGMGLHLGMDVPGWPPENIEDLAKRFEE 363


>gi|222085699|ref|YP_002544229.1| DNA-directed RNA polymerase, alpha subunit [Agrobacterium
           radiobacter K84]
 gi|254765239|sp|B9JDV2|RPOA_AGRRK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|221723147|gb|ACM26303.1| DNA-directed RNA polymerase, alpha subunit [Agrobacterium
           radiobacter K84]
          Length = 336

 Score =  416 bits (1070), Expect = e-114,   Method: Composition-based stats.
 Identities = 238/339 (70%), Positives = 285/339 (84%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+   G+    +  ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVEFTSSGR---TKATLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I +KM GD  KR+ + K+GPGVVTAGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIKMDGDDAKRMVVRKQGPGVVTAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDIEILNPEHVICTLDEGAEIRMEFTVNNGKGYVPAERNRAEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQVLDYDKLSM+I+TDGSITGED+VA A+RILQDQLG+F+NF+EP+KE
Sbjct: 178 KKVSYKVENTREGQVLDYDKLSMSIETDGSITGEDAVAFAARILQDQLGVFVNFDEPQKE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 238 AEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 297 KSLNEIKEVLASMGLHLGMEVPAWPPENIEDLAKRYEDQ 335


>gi|295688930|ref|YP_003592623.1| DNA-directed RNA polymerase subunit alpha [Caulobacter segnis ATCC
           21756]
 gi|295430833|gb|ADG10005.1| DNA-directed RNA polymerase, alpha subunit [Caulobacter segnis ATCC
           21756]
          Length = 338

 Score =  416 bits (1070), Expect = e-114,   Method: Composition-based stats.
 Identities = 207/339 (61%), Positives = 267/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI++NW ELI+P   +    G +   +  ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIERNWNELIRPEKPQIET-GADASRKARIVAEPLERGFGVTLGNALRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGV+HE SS++GV ED+ DI+LNIK + ++M  +  KR+T+   GPG VTAG I+
Sbjct: 60  TAIQIDGVVHEFSSLEGVREDVVDIVLNIKQLAVRMHAEGPKRMTLRATGPGPVTAGQIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T  DIE+LNPDHV+C LD  A VRME TV+ G GYVPA  +R E+ PIGLI +DALYSP+
Sbjct: 120 TPADIEILNPDHVLCTLDDGASVRMEFTVNTGKGYVPADRNRPEDAPIGLIAVDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V+Y VE  R+GQ LDYDKL + ++T+G++T  D+VA A+RILQDQL +FI FEEPK +
Sbjct: 180 KRVAYRVEPTRQGQSLDYDKLILEVETNGAVTPVDAVAYAARILQDQLQIFITFEEPKAK 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++ +   LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SADE-SKPELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++P+WPPE+IE+LAKK+ED+
Sbjct: 299 KSLNEIKEVLAGMGLHLGMDVPNWPPENIEDLAKKFEDQ 337


>gi|167645602|ref|YP_001683265.1| DNA-directed RNA polymerase subunit alpha [Caulobacter sp. K31]
 gi|189043833|sp|B0T2E6|RPOA_CAUSK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|167348032|gb|ABZ70767.1| DNA-directed RNA polymerase, alpha subunit [Caulobacter sp. K31]
          Length = 338

 Score =  416 bits (1070), Expect = e-114,   Method: Composition-based stats.
 Identities = 208/339 (61%), Positives = 268/339 (79%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI++NW ELI+P   +    G +   +  ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIERNWNELIRPEKPQIET-GADATRKARIVAEPLERGFGVTLGNALRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGV+HE SS++GV ED+ DI+LNIK + ++M  +  KR+T+   GPGVVTAG I+
Sbjct: 60  TAIQIDGVVHEFSSLEGVREDVVDIVLNIKQLAVRMHAEGPKRMTLRATGPGVVTAGQIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIE+LNPDHV+C LD  A VRME TV+ G GYVPA  +R E+ PIGLI +DALYSP+
Sbjct: 120 TPSDIEILNPDHVLCTLDDGASVRMEFTVNTGKGYVPADKNRPEDAPIGLIAVDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V+Y VE  R+GQ LDYDKL + ++T+G++T  D+VA A+RILQDQL +FI FEEPK +
Sbjct: 180 KRVAYRVEPTRQGQSLDYDKLILEVETNGAVTPVDAVAYAARILQDQLQIFITFEEPKAK 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++     LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 TADEA-KPELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++P+WPPE+IE+LAKK+ED+
Sbjct: 299 KSLNEIKEVLAGMGLHLGMDVPNWPPENIEDLAKKFEDQ 337


>gi|319783344|ref|YP_004142820.1| DNA-directed RNA polymerase subunit alpha [Mesorhizobium ciceri
           biovar biserrulae WSM1271]
 gi|317169232|gb|ADV12770.1| DNA-directed RNA polymerase, alpha subunit [Mesorhizobium ciceri
           biovar biserrulae WSM1271]
          Length = 336

 Score =  416 bits (1069), Expect = e-114,   Method: Composition-based stats.
 Identities = 237/339 (69%), Positives = 281/339 (82%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN IE+     +++  T ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKIEF---SSKKKTLTTLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M GD  KR+ + K+GPG V AGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIAGVREDVTDIVLNIKEIAIRMEGDGPKRMVVRKQGPGAVLAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNPDHVIC LD  A +RME TV  G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDVEILNPDHVICTLDEGAEIRMEFTVDTGKGYVPADRNRAEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQVLDYDKL+MTI+TDGSITGED+VA A+RILQDQLG+F+NF+EP+KE
Sbjct: 178 KKVSYKVENTREGQVLDYDKLTMTIETDGSITGEDAVAFAARILQDQLGLFVNFDEPQKE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V  +  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 238 VAAEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +PDWPPE+IE+LAK+YED+
Sbjct: 297 KSLNEIKEVLAAMGLHLGMEVPDWPPENIEDLAKRYEDQ 335


>gi|328543382|ref|YP_004303491.1| DNA-directed RNA polymerase subunit alpha [Polymorphum gilvum
           SL003B-26A1]
 gi|326413127|gb|ADZ70190.1| DNA-directed RNA polymerase subunit alpha [Polymorphum gilvum
           SL003B-26A1]
          Length = 353

 Score =  416 bits (1069), Expect = e-114,   Method: Composition-based stats.
 Identities = 221/337 (65%), Positives = 277/337 (82%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELIKP  ++    G++      ++AEPL RG+  TLGNALRR+L+SSL+GAA+T
Sbjct: 16  IQKNWQELIKPTKLDVK-PGEDPRFVATVVAEPLERGYGLTLGNALRRILLSSLQGAAVT 74

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           AVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K+GPG+VTAGDIQT
Sbjct: 75  AVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKQGPGLVTAGDIQT 134

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V D+EVLNP+ V+C LD  A +RME TV+ G GYVP+  +R E+ PIGLI +D+LYSP+K
Sbjct: 135 VGDVEVLNPELVLCTLDEGAEIRMEFTVNTGKGYVPSDRNRPEDAPIGLIPVDSLYSPVK 194

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQVLDYDKL++T++TDGS+  +D+VA A+RILQDQL +F+NFEEPK+EV
Sbjct: 195 KVSYKVEATREGQVLDYDKLTLTVETDGSVKPDDAVAYAARILQDQLSIFVNFEEPKREV 254

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ED +V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGRK
Sbjct: 255 AED-HVPELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRK 313

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM++ +WPPE+IE+LAK+YED
Sbjct: 314 SLNEIKEVLAQMGLHLGMDVANWPPENIEDLAKRYED 350


>gi|16125521|ref|NP_420085.1| DNA-directed RNA polymerase subunit alpha [Caulobacter crescentus
           CB15]
 gi|221234267|ref|YP_002516703.1| DNA-directed RNA polymerase subunit alpha [Caulobacter crescentus
           NA1000]
 gi|20139678|sp|Q9A8S9|RPOA_CAUCR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|254765246|sp|B8H4F8|RPOA_CAUCN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|13422605|gb|AAK23253.1| DNA-directed RNA polymerase, alpha subunit [Caulobacter crescentus
           CB15]
 gi|220963439|gb|ACL94795.1| DNA-directed RNA polymerase alpha chain [Caulobacter crescentus
           NA1000]
          Length = 338

 Score =  416 bits (1069), Expect = e-114,   Method: Composition-based stats.
 Identities = 207/339 (61%), Positives = 267/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI++NW ELI+P   +    G +   +  ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIERNWNELIRPEKPQIET-GADATRKARIVAEPLERGFGVTLGNALRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGV+HE SS++GV ED+ DI+LNIK + ++M  +  KR+T+   GPG VTAG I+
Sbjct: 60  TAIQIDGVVHEFSSLEGVREDVVDIVLNIKQLAVRMHAEGPKRMTLRATGPGPVTAGQIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T  DIE+LNPDHV+C LD  A VRME TV+ G GYVPA  +R E+ PIGLI +DALYSP+
Sbjct: 120 TPADIEILNPDHVLCTLDDGASVRMEFTVNNGKGYVPADRNRPEDAPIGLIAVDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V+Y VE  R+GQ LDYDKL + ++T+G++T  D+VA A+RILQDQL +FI FEEPK +
Sbjct: 180 KRVAYRVEPTRQGQSLDYDKLILEVETNGAVTPVDAVAYAARILQDQLQIFITFEEPKAK 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++ +   LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SADE-SKPELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++P+WPPE+IE+LAKK+ED+
Sbjct: 299 KSLNEIKEVLAGMGLHLGMDVPNWPPENIEDLAKKFEDQ 337


>gi|302382643|ref|YP_003818466.1| DNA-directed RNA polymerase subunit alpha [Brevundimonas
           subvibrioides ATCC 15264]
 gi|302193271|gb|ADL00843.1| DNA-directed RNA polymerase, alpha subunit [Brevundimonas
           subvibrioides ATCC 15264]
          Length = 339

 Score =  415 bits (1068), Expect = e-114,   Method: Composition-based stats.
 Identities = 208/339 (61%), Positives = 271/339 (79%), Gaps = 1/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI++NWQELI+P   + I LG + + +  ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIERNWQELIRPEKPQ-IELGSDAQRKARLVAEPLERGFGVTLGNALRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGV+HE SS++GV ED+ DI+LNIK + L+M  +  KR+T+   GPG VTAG I+
Sbjct: 60  TAIQIDGVVHEFSSLEGVREDVVDIVLNIKQLALRMHAEGPKRMTLRATGPGPVTAGQIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             +DIEVLNP+HVIC LD  A +RMELTV  G GYV ++ +R E+ PIGLI +DALYSP+
Sbjct: 120 VPSDIEVLNPNHVICTLDDGASIRMELTVQNGKGYVASEFNRPEDAPIGLIAVDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V+Y VE  R+GQ LDYDKL + ++T+G+++  D+VA ASRILQDQL +FI F+EPKK 
Sbjct: 180 KRVAYRVEPTRQGQSLDYDKLVLEVETNGAVSPVDAVAYASRILQDQLQIFITFDEPKKA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V++      LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE +MLR  NFGR
Sbjct: 240 VEQVDGKPDLPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEGEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM++P+WPPE+IE+LAKK++D+
Sbjct: 300 KSLNEIKEVLTSMGLSLGMDVPNWPPENIEDLAKKFDDQ 338


>gi|13470575|ref|NP_102144.1| DNA-directed RNA polymerase subunit alpha [Mesorhizobium loti
           MAFF303099]
 gi|260468530|ref|ZP_05813697.1| DNA-directed RNA polymerase, alpha subunit [Mesorhizobium
           opportunistum WSM2075]
 gi|20139638|sp|Q98N33|RPOA_RHILO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|14021317|dbj|BAB47930.1| DNA-directed RNA polymerase alpha subunit [Mesorhizobium loti
           MAFF303099]
 gi|259028686|gb|EEW29995.1| DNA-directed RNA polymerase, alpha subunit [Mesorhizobium
           opportunistum WSM2075]
          Length = 336

 Score =  415 bits (1066), Expect = e-114,   Method: Composition-based stats.
 Identities = 236/339 (69%), Positives = 282/339 (83%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN IE+     +++  T ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKIEF---SSKKKTLTTLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I ++M GD  KR+ + K+GPG V AGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIAGVREDVTDIVLNIKEIAIRMEGDGPKRMVVRKQGPGAVLAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNPDHVIC LD  A +RME TV  G GYVPA+ +R E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDVEILNPDHVICTLDEGAEIRMEFTVDTGKGYVPAERNRAEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQVLDYDKL+MTI+TDGSI+GED+VA A+RILQDQLG+F+NF+EP+KE
Sbjct: 178 KKVSYKVENTREGQVLDYDKLTMTIETDGSISGEDAVAFAARILQDQLGLFVNFDEPQKE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V  +  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 238 VAAEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +PDWPPE+IE+LAK+YED+
Sbjct: 297 KSLNEIKEVLAAMGLHLGMEVPDWPPENIEDLAKRYEDQ 335


>gi|323136111|ref|ZP_08071194.1| DNA-directed RNA polymerase, alpha subunit [Methylocystis sp. ATCC
           49242]
 gi|322399202|gb|EFY01721.1| DNA-directed RNA polymerase, alpha subunit [Methylocystis sp. ATCC
           49242]
          Length = 339

 Score =  414 bits (1064), Expect = e-113,   Method: Composition-based stats.
 Identities = 215/337 (63%), Positives = 270/337 (80%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELIKPN +E +  G +       +AEPL RGF  TLGNALRR+L+SSL+GAAIT
Sbjct: 3   IQKNWQELIKPNKLE-VTAGDDPRRVATAVAEPLERGFGVTLGNALRRILLSSLQGAAIT 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           ++ IDGVLHE SSI GV ED+TDI+LNIK I +K  G+  KR+T+ K GPG VTAGDIQ 
Sbjct: 62  SIHIDGVLHEFSSIPGVREDVTDIVLNIKDIAIKYQGEGVKRLTLKKTGPGAVTAGDIQA 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
             D++VLNPD VIC LD  A +R+E TVS G GYVPA  +R E+ PIGLI +D+LYSP+K
Sbjct: 122 TGDVQVLNPDLVICTLDEGAEIRIEFTVSTGKGYVPADRNRAEDAPIGLIPVDSLYSPVK 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQVLDYDKL++TI+T+G+IT ED++A ++RILQDQL +F+NFEEP++E 
Sbjct: 182 KVSYRVENTREGQVLDYDKLTLTIETNGAITPEDALAFSARILQDQLNVFVNFEEPRRE- 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +   ++  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++EA+MLR  NFGRK
Sbjct: 241 EAAPSIPQLAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I++LAK++E+
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDDLAKRFEE 337


>gi|115525561|ref|YP_782472.1| DNA-directed RNA polymerase subunit alpha [Rhodopseudomonas
           palustris BisA53]
 gi|122295431|sp|Q07KP2|RPOA_RHOP5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|115519508|gb|ABJ07492.1| DNA-directed RNA polymerase, alpha subunit [Rhodopseudomonas
           palustris BisA53]
          Length = 339

 Score =  414 bits (1064), Expect = e-113,   Method: Composition-based stats.
 Identities = 216/337 (64%), Positives = 273/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +  G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQ-VTPGSDSGRFATLVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I++KM G+  KR+ + K+GPG VTAGDIQT
Sbjct: 62  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDISIKMQGEGPKRMVVKKQGPGTVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V DI VLNPD  IC LD  A +RME TV+ G GYV A+ +R E+ PIGLI +D+L+SP++
Sbjct: 122 VGDIVVLNPDLQICTLDDGAEIRMEFTVNTGKGYVAAERNRPEDAPIGLIPVDSLFSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+MTI+T+G+IT +D+VA A+RILQDQL +F+NFEEP+KEV
Sbjct: 182 KVSYKVENTREGQILDYDKLTMTIETNGAITPDDAVAYAARILQDQLNVFVNFEEPRKEV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 242 TQEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 337


>gi|170738679|ref|YP_001767334.1| DNA-directed RNA polymerase subunit alpha [Methylobacterium sp.
           4-46]
 gi|226699356|sp|B0UHU5|RPOA_METS4 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|168192953|gb|ACA14900.1| DNA-directed RNA polymerase, alpha subunit [Methylobacterium sp.
           4-46]
          Length = 339

 Score =  413 bits (1063), Expect = e-113,   Method: Composition-based stats.
 Identities = 212/338 (62%), Positives = 273/338 (80%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN +E +  G + +    ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 2   VIQKNWQELIKPNKLEVV-PGHDPKRVATVVAEPLERGFGTTLGNALRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V IDGVLHE SSI GV ED+TDI+LNIK I ++ + D+ KR+T+ K GPG+VTAGDI 
Sbjct: 61  TSVHIDGVLHEFSSIPGVREDVTDIVLNIKTIAIRSNSDAPKRMTLRKTGPGLVTAGDIS 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T+ DI++LNPD V+C LD  A +RME TV+ G GYVPA  +R E+ PIGLI +DAL+SP+
Sbjct: 121 TIGDIQILNPDLVLCTLDEGAEIRMEFTVATGKGYVPADRNRPEDAPIGLIPVDALFSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY +E+ REGQ LD DKL+MT++T+G+++ ED++A A+RI+QDQL +F+NFEEP+KE
Sbjct: 181 TKVSYRIENTREGQDLDKDKLTMTVETNGAVSPEDALAYAARIIQDQLQIFVNFEEPRKE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +       LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 241 -EAAPLAPQLPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++P WPPE+IE+LAK++E+
Sbjct: 300 KSLNEIKEVLAAMGLHLGMDVPGWPPENIEDLAKRFEE 337


>gi|27380487|ref|NP_772016.1| DNA-directed RNA polymerase subunit alpha [Bradyrhizobium japonicum
           USDA 110]
 gi|41688696|sp|Q89JA7|RPOA_BRAJA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|27353651|dbj|BAC50641.1| DNA-directed RNA polymerase alpha subunit [Bradyrhizobium japonicum
           USDA 110]
          Length = 343

 Score =  413 bits (1063), Expect = e-113,   Method: Composition-based stats.
 Identities = 217/337 (64%), Positives = 275/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +  G +      ++AEPL RGF  TLGNALRR+L+SSL+GAA+ 
Sbjct: 7   IQKNWQELIRPNKLQ-VTPGSDPARFATIVAEPLERGFGQTLGNALRRILLSSLQGAAVQ 65

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I++KM G+  KR+ + K+GPGVVTAGDIQT
Sbjct: 66  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDISIKMQGEGPKRMVVKKQGPGVVTAGDIQT 125

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V D+ VLNPD  IC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +D+LYSP++
Sbjct: 126 VGDVVVLNPDLQICTLDEGAEIRMEFTVATGKGYVPAERNRPEDAPIGLIPVDSLYSPVR 185

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+MTI+T+G+I+ +DSVA A+RILQDQL +F+NFEEP+KEV
Sbjct: 186 KVSYKVENTREGQILDYDKLTMTIETNGAISPDDSVAYAARILQDQLNVFVNFEEPRKEV 245

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 246 AQEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 304

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 305 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 341


>gi|304321464|ref|YP_003855107.1| DNA-directed RNA polymerase subunit alpha [Parvularcula bermudensis
           HTCC2503]
 gi|303300366|gb|ADM09965.1| DNA-directed RNA polymerase alpha subunit [Parvularcula bermudensis
           HTCC2503]
          Length = 338

 Score =  413 bits (1062), Expect = e-113,   Method: Composition-based stats.
 Identities = 206/339 (60%), Positives = 275/339 (81%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M++KNWQELIKP  +E +    + + +  ++A+PL RGF  TLGN+LRR+LMSSL+GAA+
Sbjct: 1   MLEKNWQELIKPQKLEVVS-SYDPQRKATIVAQPLERGFGLTLGNSLRRILMSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGV+HE SSI GV ED+T I+LNIK + L+M  D  +R+T+ K+GPG+VTAGDIQ
Sbjct: 60  TAIQIDGVVHEFSSIPGVREDVTIIVLNIKQLALRMHVDGPRRLTLKKQGPGIVTAGDIQ 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DIE+L+ DHVIC LD  A +RME+TV  G GYVPA  +R E+ PIGLI +D+LYSP+
Sbjct: 120 ETADIEILDKDHVICTLDEGADLRMEITVQTGKGYVPADRNRPEDAPIGLIPVDSLYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY+VE+ REGQVLDYDKL + ++T+G++T ED+ A A+RILQDQL +F+NF+EPK++
Sbjct: 180 RRVSYSVENTREGQVLDYDKLILEVETNGAVTPEDAAAFAARILQDQLQIFVNFDEPKRD 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +   + + L FN ALL+KV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 DQGGAD-EELLFNAALLRKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL T+GL LGM++PDWPP++IEELA+K+ED+
Sbjct: 299 KSLNEIKEVLATLGLHLGMDVPDWPPDNIEELARKFEDQ 337


>gi|316933551|ref|YP_004108533.1| DNA-directed RNA polymerase subunit alpha [Rhodopseudomonas
           palustris DX-1]
 gi|315601265|gb|ADU43800.1| DNA-directed RNA polymerase, alpha subunit [Rhodopseudomonas
           palustris DX-1]
          Length = 339

 Score =  413 bits (1062), Expect = e-113,   Method: Composition-based stats.
 Identities = 219/337 (64%), Positives = 273/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +  G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQ-VTAGSDATRFATLVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I+LKM G+  KR+ I K GPGVVTAGDIQT
Sbjct: 62  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDISLKMQGEGPKRMVIKKSGPGVVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V DI VLNPD  +C LD  A +RME TV+ G GYV A+ +R E+ PIGLI +D+LYSP++
Sbjct: 122 VGDIVVLNPDLQLCTLDDGAEIRMEFTVNTGKGYVAAERNRPEDAPIGLIPVDSLYSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+MT++T+G+IT ED+VA A+RILQDQL +F+NFEEP+KEV
Sbjct: 182 KVSYKVENTREGQILDYDKLTMTVETNGAITPEDAVAYAARILQDQLNVFVNFEEPRKEV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 242 TQEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 337


>gi|254501022|ref|ZP_05113173.1| DNA-directed RNA polymerase, alpha subunit [Labrenzia alexandrii
           DFL-11]
 gi|222437093|gb|EEE43772.1| DNA-directed RNA polymerase, alpha subunit [Labrenzia alexandrii
           DFL-11]
          Length = 340

 Score =  413 bits (1061), Expect = e-113,   Method: Composition-based stats.
 Identities = 221/337 (65%), Positives = 273/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELIKP  +E I  G +      ++AEPL RG+  TLGNALRR+L+SSL+GAA+T
Sbjct: 3   IQKNWQELIKPTKLE-IKPGDDPRFLATVVAEPLERGYGLTLGNALRRILLSSLQGAAVT 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           AVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K+GPGVVTAGDIQT
Sbjct: 62  AVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKQGPGVVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V D+EVLNPD V+C LD  A +RME TV+ G GY  +  +R E+ PIGLI +D+LYSP+K
Sbjct: 122 VGDVEVLNPDLVLCTLDEGAEIRMEFTVNTGKGYHSSDRNRPEDAPIGLIPVDSLYSPVK 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQVLDYDKL++T++TDGS+  +D+VA A+RILQDQL +F+NFEEP++EV
Sbjct: 182 KVSYKVENTREGQVLDYDKLTLTVETDGSVKPDDAVAFAARILQDQLSIFVNFEEPQREV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ED  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGRK
Sbjct: 242 AEDT-VPELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM + +WPPE+I++LAK+YED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVANWPPENIDDLAKRYED 337


>gi|209884837|ref|YP_002288694.1| DNA-directed RNA polymerase, alpha subunit [Oligotropha
           carboxidovorans OM5]
 gi|229564255|sp|B6JEY9|RPOA_OLICO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|209873033|gb|ACI92829.1| DNA-directed RNA polymerase, alpha subunit [Oligotropha
           carboxidovorans OM5]
          Length = 339

 Score =  412 bits (1060), Expect = e-113,   Method: Composition-based stats.
 Identities = 213/337 (63%), Positives = 272/337 (80%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +  G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQ-VTPGSDPSRFATLVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I++KM G+  KR+ I K+GPGVVTAGDIQT
Sbjct: 62  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDISIKMQGEGPKRMVIKKQGPGVVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V D+ VLNP+  +C LD  A +RME TV  G GYV A  +R E+ PIGLI +D+L+SP++
Sbjct: 122 VGDVVVLNPELQLCTLDDGAEIRMEFTVDTGKGYVAADRNRPEDAPIGLIPVDSLFSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL++TI+T+G+IT ED++A ++RILQDQL +F+NFEEP+KEV
Sbjct: 182 KVSYKVENTREGQILDYDKLTLTIETNGAITPEDALAYSARILQDQLNVFVNFEEPRKEV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 242 VQEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 337


>gi|23010819|ref|ZP_00051380.1| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Magnetospirillum magnetotacticum MS-1]
          Length = 339

 Score =  412 bits (1060), Expect = e-113,   Method: Composition-based stats.
 Identities = 212/338 (62%), Positives = 271/338 (80%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN ++ +  G + +    ++AEPL RGF  TLGN+LRRVL+SSL+GAA+
Sbjct: 2   VIQKNWQELIKPNKLQ-VTAGDDPKRVATVVAEPLERGFGTTLGNSLRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQIDGVLHE SSI GV ED+TDI+LNIK I ++   D  KR+T+ K GPG+VTAGDI 
Sbjct: 61  TSVQIDGVLHEFSSIPGVREDVTDIVLNIKTIAIRSQTDQPKRLTLRKTGPGLVTAGDIG 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
            V DI++LNPD VIC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +DALYSP+
Sbjct: 121 AVGDIQILNPDLVICTLDDGAEIRMEFTVATGKGYVPAERNRPEDAPIGLIPVDALYSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY VE+ REGQ LD DKL+MT++T+G+++ ED++A A+RI+QDQL +F+NFEEP+KE
Sbjct: 181 TKVSYRVETTREGQDLDKDKLTMTVETNGAVSPEDALAYAARIIQDQLQVFVNFEEPRKE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +       LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++E +MLR  NFGR
Sbjct: 241 -EAAPLAPQLPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSEGEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++P WPPE+IE+LAK++E+
Sbjct: 300 KSLNEIKEVLAGMGLHLGMDVPGWPPENIEDLAKRFEE 337


>gi|188581391|ref|YP_001924836.1| DNA-directed RNA polymerase subunit alpha [Methylobacterium populi
           BJ001]
 gi|226699354|sp|B1Z768|RPOA_METPB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|179344889|gb|ACB80301.1| DNA-directed RNA polymerase, alpha subunit [Methylobacterium populi
           BJ001]
          Length = 339

 Score =  412 bits (1060), Expect = e-113,   Method: Composition-based stats.
 Identities = 211/338 (62%), Positives = 270/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN ++ +  G + +    ++AEPL RGF  TLGN+LRRVL+SSL+GAA+
Sbjct: 2   VIQKNWQELIKPNKLQ-VSAGDDPKRVATVVAEPLERGFGTTLGNSLRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQIDGVLHE SSI GV ED+TDI+LNIK I ++   D  KR+T+ K GPG+VTAGDI 
Sbjct: 61  TSVQIDGVLHEFSSIPGVREDVTDIVLNIKTIAIRSQTDQPKRMTLRKTGPGLVTAGDIG 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
            V DI++LNPD VIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +DAL+SP+
Sbjct: 121 AVGDIQILNPDLVICTLDDGAEIRMEFTVATGKGYVPADRNRPEDAPIGLIPVDALFSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY VE+ REGQ LD DKL+MT++T+G+++ ED++A A+RI+QDQL +F+NFEEP+KE
Sbjct: 181 TKVSYRVETTREGQDLDKDKLTMTVETNGAVSPEDALAYAARIIQDQLQVFVNFEEPRKE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +       LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++E +MLR  NFGR
Sbjct: 241 -EAAPLAPQLPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSEGEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++P WPPE+IE+LAK++E+
Sbjct: 300 KSLNEIKEVLAGMGLHLGMDVPGWPPENIEDLAKRFEE 337


>gi|90424913|ref|YP_533283.1| DNA-directed RNA polymerase subunit alpha [Rhodopseudomonas
           palustris BisB18]
 gi|119366716|sp|Q211H2|RPOA_RHOPB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|90106927|gb|ABD88964.1| DNA-directed RNA polymerase, alpha subunit [Rhodopseudomonas
           palustris BisB18]
          Length = 339

 Score =  412 bits (1060), Expect = e-113,   Method: Composition-based stats.
 Identities = 214/337 (63%), Positives = 272/337 (80%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN +  +  G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKL-VVTPGSDPTRFATLVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I++KM G+  KR+ + K+GPG VTAGDIQT
Sbjct: 62  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDISIKMQGEGPKRMVVKKQGPGTVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V D+ VLNPD  IC LD  A +RME TV+ G GYV A+ +R E+ PIGLI +D+L+SP++
Sbjct: 122 VGDVVVLNPDLQICTLDEGAEIRMEFTVAGGKGYVAAERNRPEDAPIGLIPVDSLFSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+MTI+T+G+I+ +D+VA A+RILQDQL +F+NFEEP+KEV
Sbjct: 182 KVSYKVENTREGQILDYDKLTMTIETNGAISPDDAVAYAARILQDQLNVFVNFEEPRKEV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 242 TQEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 337


>gi|91977628|ref|YP_570287.1| DNA-directed RNA polymerase subunit alpha [Rhodopseudomonas
           palustris BisB5]
 gi|119366717|sp|Q134V3|RPOA_RHOPS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|91684084|gb|ABE40386.1| DNA-directed RNA polymerase, alpha subunit [Rhodopseudomonas
           palustris BisB5]
          Length = 339

 Score =  412 bits (1060), Expect = e-113,   Method: Composition-based stats.
 Identities = 218/337 (64%), Positives = 275/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +  G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQ-VSPGSDATRFATLVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +VQIDGVLHE SSI GV ED+TDI+LNIK I+LKM G+  KR+ + K+GPGVVTAGDIQT
Sbjct: 62  SVQIDGVLHEFSSIAGVREDVTDIVLNIKDISLKMQGEGPKRMVVKKQGPGVVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V DI VLNPD  IC LD  A +RME TV+ G GYV A+ +R E+ PIGLI +D+LYSP++
Sbjct: 122 VGDIVVLNPDLQICTLDEGAEIRMEFTVNTGKGYVAAERNRPEDAPIGLIPVDSLYSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+MT++T+G++T +D+VA A+RILQDQL +F+NFEEP+KEV
Sbjct: 182 KVSYKVENTREGQILDYDKLTMTVETNGALTPDDAVAFAARILQDQLNVFVNFEEPRKEV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 242 TQEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 337


>gi|298291462|ref|YP_003693401.1| DNA-directed RNA polymerase, subunit alpha [Starkeya novella DSM
           506]
 gi|296927973|gb|ADH88782.1| DNA-directed RNA polymerase, alpha subunit [Starkeya novella DSM
           506]
          Length = 338

 Score =  412 bits (1059), Expect = e-113,   Method: Composition-based stats.
 Identities = 219/338 (64%), Positives = 278/338 (82%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP  +E + +G + +    ++AEPL RGF  TLGNALRR+L+SSL+GAA+
Sbjct: 1   MIQKNWQELIKPEKLE-VAVGSDPKRLATVVAEPLERGFGQTLGNALRRILLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V IDGVLHE SSI GV ED+TDI+LNIK I +KM+GD  KR+ + K+GPG+VTAGDIQ
Sbjct: 60  TSVHIDGVLHEFSSIPGVREDVTDIVLNIKDIAIKMAGDGPKRMVVKKQGPGIVTAGDIQ 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D++VLNP+ V+C LD  A +RME TV  G GYV  + +R E+ PIGLI +D+LYSP+
Sbjct: 120 TVGDVQVLNPELVLCTLDDGAEIRMEFTVDTGKGYVAGERNRPEDAPIGLIPVDSLYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQ+LDYDKL+MTI+T+GS++ ED++A A+RILQDQL +F+NFEEPK+E
Sbjct: 180 KKVSYKVENTREGQILDYDKLTMTIETNGSVSPEDALAFAARILQDQLEIFVNFEEPKRE 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +    ++ LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 TESPA-MQELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK++ED
Sbjct: 299 KSLNEIKEVLASMGLHLGMEVPGWPPENIEDLAKRFED 336


>gi|86749439|ref|YP_485935.1| DNA-directed RNA polymerase subunit alpha [Rhodopseudomonas
           palustris HaA2]
 gi|119366715|sp|Q2IXN6|RPOA_RHOP2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|86572467|gb|ABD07024.1| DNA-directed RNA polymerase, alpha subunit [Rhodopseudomonas
           palustris HaA2]
          Length = 339

 Score =  412 bits (1059), Expect = e-113,   Method: Composition-based stats.
 Identities = 217/337 (64%), Positives = 274/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +  G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQ-VTAGSDATRFATLVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I+LKM G+  KR+ + K+GPGVVTAGDIQT
Sbjct: 62  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDISLKMQGEGPKRMVVKKQGPGVVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V DI VLNPD  IC LD  A +RME TV+ G GYV A+ +R E+ PIGLI +D+LYSP++
Sbjct: 122 VGDIVVLNPDLQICTLDEGAEIRMEFTVNTGKGYVAAERNRPEDAPIGLIPVDSLYSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+MT++T+G++T +D+VA A+RILQDQL +F+NFEEP+KEV
Sbjct: 182 KVSYKVENTREGQILDYDKLTMTVETNGALTPDDAVAFAARILQDQLNVFVNFEEPRKEV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 242 TQEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 337


>gi|299135233|ref|ZP_07028424.1| DNA-directed RNA polymerase, alpha subunit [Afipia sp. 1NLS2]
 gi|298590210|gb|EFI50414.1| DNA-directed RNA polymerase, alpha subunit [Afipia sp. 1NLS2]
          Length = 339

 Score =  412 bits (1059), Expect = e-113,   Method: Composition-based stats.
 Identities = 211/337 (62%), Positives = 273/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +  G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQ-VTPGADATRFATVVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I++KM G+  KR+ I K+GPGVVTAGDIQT
Sbjct: 62  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDISVKMQGEGPKRMVIKKQGPGVVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V D+ VLNP+  +C LD  A +RME T++ G GYV A  +R E+ PIGLI +D+L+SP++
Sbjct: 122 VGDVVVLNPELQLCTLDDGAEIRMEFTINTGKGYVAADRNRPEDAPIGLIPVDSLFSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL++TI+T+G+I+ ED++A ++RILQDQL +F+NFEEP+KEV
Sbjct: 182 KVSYKVENTREGQILDYDKLTLTIETNGAISPEDALAYSARILQDQLNVFVNFEEPRKEV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 242 VQEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 337


>gi|146340081|ref|YP_001205129.1| DNA-directed RNA polymerase subunit alpha [Bradyrhizobium sp.
           ORS278]
 gi|148256368|ref|YP_001240953.1| DNA-directed RNA polymerase subunit alpha [Bradyrhizobium sp.
           BTAi1]
 gi|158513287|sp|A5ELK3|RPOA_BRASB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158514218|sp|A4YSL6|RPOA_BRASO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|146192887|emb|CAL76892.1| DNA-directed RNA polymerase alpha chain [Bradyrhizobium sp. ORS278]
 gi|146408541|gb|ABQ37047.1| DNA-directed RNA polymerase subunit alpha [Bradyrhizobium sp.
           BTAi1]
          Length = 343

 Score =  412 bits (1058), Expect = e-113,   Method: Composition-based stats.
 Identities = 216/337 (64%), Positives = 274/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +  G +      ++AEPL RGF  TLGNALRR+L+SSL+GAA+ 
Sbjct: 7   IQKNWQELIRPNKLQ-VTPGSDATRFATVVAEPLERGFGQTLGNALRRILLSSLQGAAVQ 65

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I++KM G+  KR+ + K+GPG VTAGDIQT
Sbjct: 66  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDISIKMQGEGPKRMVVKKQGPGAVTAGDIQT 125

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V DI VLNPD  +C LD  A +RME TV+ G GYVPA+ +R E+ PIGLI ID+L+SP++
Sbjct: 126 VGDIVVLNPDLQLCTLDEGAEIRMEFTVATGKGYVPAERNRPEDAPIGLIPIDSLFSPVR 185

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+MTI+T+G+I+ ED+VA A+RILQDQL +F+NFEEP+KEV
Sbjct: 186 KVSYKVENTREGQILDYDKLTMTIETNGAISPEDAVAYAARILQDQLNVFVNFEEPRKEV 245

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 246 AQEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 304

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 305 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 341


>gi|171769752|sp|A7HWT5|RPOA_PARL1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 338

 Score =  412 bits (1058), Expect = e-113,   Method: Composition-based stats.
 Identities = 218/339 (64%), Positives = 273/339 (80%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNW+ELIKPN +E I  G + +    ++AEPL RGF  TLGNALRRVLMSSL+GAA+
Sbjct: 1   MIQKNWEELIKPNKLE-INPGHDAQRFATVVAEPLERGFGLTLGNALRRVLMSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDIILNIK + L++  +  KR+++ K+GPGVVTAGDI 
Sbjct: 60  TAVQIDGVLHEFSSIAGVREDVTDIILNIKQLALRLHAEGPKRMSLSKKGPGVVTAGDIT 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DIEVLNPD V+C LD  A +RME TV+ G GYV +  +R E+ PIGL+ +D+LYSP+
Sbjct: 120 AGADIEVLNPDLVLCTLDEGAEIRMEFTVALGKGYVASDRNRPEDAPIGLMPVDSLYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VSY VE+ REGQVLDYDKL++ I+T+G+IT +D+VA A+RILQDQL  F+NFEEP+++
Sbjct: 180 KRVSYKVENTREGQVLDYDKLTLQIETNGAITPDDAVAYAARILQDQLQTFVNFEEPEQK 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E+ +   L FN ALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE++MLR  NFGR
Sbjct: 240 HVEE-SRPELEFNAALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P+WPPE+IEELAK+YED+
Sbjct: 299 KSLNEIKEVLAQMGLHLGMEVPNWPPENIEELAKRYEDQ 337


>gi|307946311|ref|ZP_07661646.1| DNA-directed RNA polymerase, alpha subunit [Roseibium sp.
           TrichSKD4]
 gi|307769975|gb|EFO29201.1| DNA-directed RNA polymerase, alpha subunit [Roseibium sp.
           TrichSKD4]
          Length = 340

 Score =  412 bits (1058), Expect = e-113,   Method: Composition-based stats.
 Identities = 220/337 (65%), Positives = 273/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELIKP  +E    G +      ++AEPL RG+  TLGNALRR+L+SSL+GAA+T
Sbjct: 3   IQKNWQELIKPTKLEVK-PGDDPRFLATVVAEPLERGYGLTLGNALRRILLSSLQGAAVT 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           AVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K+GPGVVTAGDIQT
Sbjct: 62  AVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKQGPGVVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V D+EVLNP+ V+C LD  A +RME TV+ G GYV +  +R E+ PIGLI +D+LYSP+K
Sbjct: 122 VGDVEVLNPELVLCTLDEGAEIRMEFTVNTGKGYVASDRNRPEDAPIGLIPVDSLYSPVK 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQVLDYDKL++T++TDGS+  +D+VA A+RILQDQL +F+NFEEP++EV
Sbjct: 182 KVSYKVENTREGQVLDYDKLTLTVETDGSVKPDDAVAFAARILQDQLSIFVNFEEPQREV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ED  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGRK
Sbjct: 242 AEDT-VPELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM + +WPPE+I++LAK+YED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVANWPPENIDDLAKRYED 337


>gi|220921923|ref|YP_002497224.1| DNA-directed RNA polymerase subunit alpha [Methylobacterium
           nodulans ORS 2060]
 gi|254765257|sp|B8IT35|RPOA_METNO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|219946529|gb|ACL56921.1| DNA-directed RNA polymerase, alpha subunit [Methylobacterium
           nodulans ORS 2060]
          Length = 339

 Score =  412 bits (1058), Expect = e-113,   Method: Composition-based stats.
 Identities = 213/338 (63%), Positives = 273/338 (80%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN +E +  G + +    ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 2   VIQKNWQELIKPNKLE-VAPGHDPKRIATVVAEPLERGFGTTLGNALRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V IDGVLHE SSI GV ED+TDI+LNIK I ++ S D+ KR+T+ K GPG+VTAGDI 
Sbjct: 61  TSVHIDGVLHEFSSIPGVREDVTDIVLNIKTIAIRSSSDTPKRMTLRKTGPGLVTAGDIS 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T+ DI++LNPD V+C LD  A +RME TV+ G GYVPA  +R E+ PIGLI +DAL+SP+
Sbjct: 121 TIGDIQILNPDLVLCTLDEGAEIRMEFTVATGKGYVPADRNRPEDAPIGLIPVDALFSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY +E+ REGQ LD DKL+MT++T+G+++ ED++A A+RI+QDQL +F+NFEEP+KE
Sbjct: 181 TKVSYRIENTREGQDLDKDKLTMTVETNGAVSPEDALAYAARIIQDQLQIFVNFEEPRKE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +       LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 241 -EAAPLAPQLPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++P WPPE+IE+LAK++E+
Sbjct: 300 KSLNEIKEVLAAMGLHLGMDVPGWPPENIEDLAKRFEE 337


>gi|304391480|ref|ZP_07373422.1| DNA-directed RNA polymerase, alpha subunit [Ahrensia sp. R2A130]
 gi|303295709|gb|EFL90067.1| DNA-directed RNA polymerase, alpha subunit [Ahrensia sp. R2A130]
          Length = 335

 Score =  412 bits (1058), Expect = e-113,   Method: Composition-based stats.
 Identities = 221/339 (65%), Positives = 271/339 (79%), Gaps = 5/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI +NWQELIKP  ++          +  ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIHRNWQELIKPTKLDV----SSNGTKGTLVAEPLERGFGLTLGNALRRVLLSSLQGAAV 56

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDIILNIK + ++M G+  KR+ + K G GVVTAGDIQ
Sbjct: 57  TAVQIDGVLHEFSSIPGVREDVTDIILNIKELAIRMEGEGPKRMVVRKEGAGVVTAGDIQ 116

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HV+C LD DA +RME TV  G GYV A  +R E+ PIGLI +DAL+SP+
Sbjct: 117 TVGDLEILNPEHVLCTLDEDAEIRMEFTVDTGKGYVAADRNRPEDAPIGLIPVDALFSPV 176

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY  E+ REGQVLDYDKL+MTI+TDGS+T ED+VA  +RILQDQL +F+NFEEP+KE
Sbjct: 177 RKVSYKTENTREGQVLDYDKLTMTIETDGSVTPEDAVAYGARILQDQLSIFVNFEEPQKE 236

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V ++  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE +MLR  NFGR
Sbjct: 237 VVQEQ-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEGEMLRTPNFGR 295

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL TMGL LGM +P WPPE+I++LAK+YED+
Sbjct: 296 KSLNEIKEVLATMGLHLGMEIPAWPPENIDDLAKRYEDQ 334


>gi|170748609|ref|YP_001754869.1| DNA-directed RNA polymerase subunit alpha [Methylobacterium
           radiotolerans JCM 2831]
 gi|226699355|sp|B1LWP9|RPOA_METRJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|170655131|gb|ACB24186.1| DNA-directed RNA polymerase, alpha subunit [Methylobacterium
           radiotolerans JCM 2831]
          Length = 339

 Score =  412 bits (1058), Expect = e-113,   Method: Composition-based stats.
 Identities = 211/338 (62%), Positives = 273/338 (80%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN ++ +  G + +    ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 2   VIQKNWQELIKPNKLQ-VTTGDDPKRVATVVAEPLERGFGTTLGNALRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQIDGVLHE SSI GV ED+TDI+LNIK I ++   D+ KR+T+ K GPG+VTAGDI 
Sbjct: 61  TSVQIDGVLHEFSSIPGVREDVTDIVLNIKTIAIRSQTDAPKRMTLRKTGPGLVTAGDIG 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DI++LNPD VIC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +D+L+SP+
Sbjct: 121 TVGDIQILNPDLVICTLDDGAEIRMEFTVATGKGYVPAERNRPEDAPIGLIPVDSLFSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY VE+ REGQ LD DKL+MT++T+G+++ ED++A A+RI+QDQL +F+NFE+P+KE
Sbjct: 181 TKVSYRVETTREGQDLDKDKLTMTVETNGAVSPEDALAYAARIIQDQLQVFVNFEDPRKE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +       LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++E +MLR  NFGR
Sbjct: 241 -EAAPLAPQLPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSEGEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++P WPPE+IE+LAK++E+
Sbjct: 300 KSLNEIKEVLAGMGLHLGMDIPGWPPENIEDLAKRFEE 337


>gi|163760824|ref|ZP_02167903.1| putative DNA-directed RNA polymerase alpha chain [Hoeflea
           phototrophica DFL-43]
 gi|162281868|gb|EDQ32160.1| putative DNA-directed RNA polymerase alpha chain [Hoeflea
           phototrophica DFL-43]
          Length = 336

 Score =  412 bits (1058), Expect = e-113,   Method: Composition-based stats.
 Identities = 227/339 (66%), Positives = 280/339 (82%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP+ +E+     +   +  ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPSKVEF---STQSRTKASVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDIILNIK I ++M GD  KR+ + K+GPGVVTAGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIPGVREDVTDIILNIKEIAIRMEGDEAKRMVVRKQGPGVVTAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIE+LNP+H +C LD  A +RME TV+ G GYV A  +R E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDIEILNPEHALCTLDEGAEIRMEFTVNNGKGYVAADRNRAEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KK SY VE+ REGQVLDYDKL+++++TDGS++GED+VA A+RILQDQLG+F+NF+EP+KE
Sbjct: 178 KKCSYKVENTREGQVLDYDKLTLSLETDGSVSGEDAVAYAARILQDQLGVFVNFDEPQKE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V E+  V  L FNP+LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 238 VHEET-VAELAFNPSLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 297 KSLNEIKEVLASMGLHLGMEVPSWPPENIEDLAKRYEDQ 335


>gi|75675580|ref|YP_318001.1| DNA-directed RNA polymerase subunit alpha [Nitrobacter winogradskyi
           Nb-255]
 gi|90110853|sp|Q3SSU2|RPOA_NITWN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|74420450|gb|ABA04649.1| DNA-directed RNA polymerase subunit alpha [Nitrobacter winogradskyi
           Nb-255]
          Length = 339

 Score =  412 bits (1058), Expect = e-113,   Method: Composition-based stats.
 Identities = 215/337 (63%), Positives = 270/337 (80%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +  G +      +IAEPL RGF  TLGNALRR+L+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQVV-PGSDPSRFATLIAEPLERGFGQTLGNALRRILLSSLQGAAVQ 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K+GPG VTAGDIQT
Sbjct: 62  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDIAIRMQGEGPKRMVVKKQGPGTVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V D+ VLNPD  IC LD  A +RME TV+ G GYV A+ +R E+ PIGLI +D+LYSP++
Sbjct: 122 VGDVVVLNPDLQICTLDDGAEIRMEFTVASGKGYVAAERNRPEDAPIGLIPVDSLYSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+MTI+T+G +T ED+VA A+RILQDQL +F+NFEEP+KEV
Sbjct: 182 KVSYKVENTREGQILDYDKLTMTIETNGGVTPEDAVAFAARILQDQLNVFVNFEEPRKEV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
             +I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 242 TTEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 337


>gi|296445047|ref|ZP_06887008.1| DNA-directed RNA polymerase, alpha subunit [Methylosinus
           trichosporium OB3b]
 gi|296257468|gb|EFH04534.1| DNA-directed RNA polymerase, alpha subunit [Methylosinus
           trichosporium OB3b]
          Length = 339

 Score =  411 bits (1056), Expect = e-113,   Method: Composition-based stats.
 Identities = 212/337 (62%), Positives = 270/337 (80%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELIKP+ +E +  G +     + +AEPL RGF  TLGNALRR+L+SSL+G+AIT
Sbjct: 3   IQKNWQELIKPSKLE-VTAGDDPRRVAVAVAEPLERGFGVTLGNALRRILLSSLQGSAIT 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           ++ IDGVLHE SSI GV ED+TDI+LNIK I +K   +  KR+T+ K GPG VTAGDIQT
Sbjct: 62  SIHIDGVLHEFSSIPGVREDVTDIVLNIKDIAIKNHAEGVKRMTLKKTGPGPVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
             D+++LNPD VIC LD  A +R+E TV+ G GYVPA  +R E+ PIGLI ID+LYSP+K
Sbjct: 122 PGDVQILNPDLVICTLDEGAEIRVEFTVATGKGYVPADRNRAEDAPIGLIPIDSLYSPVK 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ R GQVLDYDKL++TI+T+G+I+ EDS+A A+RILQDQL +F+NFEEP++E 
Sbjct: 182 KVSYRVENTRAGQVLDYDKLTLTIETNGAISPEDSLAYAARILQDQLSVFVNFEEPRRE- 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +   ++  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++EA+MLR  NFGRK
Sbjct: 241 ETAPSIPQLAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I++LAK++E+
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDDLAKRFEE 337


>gi|118591156|ref|ZP_01548555.1| DNA-directed RNA polymerase subunit alpha [Stappia aggregata IAM
           12614]
 gi|118436232|gb|EAV42874.1| DNA-directed RNA polymerase subunit alpha [Stappia aggregata IAM
           12614]
          Length = 340

 Score =  411 bits (1056), Expect = e-113,   Method: Composition-based stats.
 Identities = 221/337 (65%), Positives = 275/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELIKP  +E I  G++      ++AEPL RG+  TLGNALRR+L+SSL+GAA+T
Sbjct: 3   IQKNWQELIKPTKLE-IKPGEDPRFLATVVAEPLERGYGLTLGNALRRILLSSLQGAAVT 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           AVQIDGVLHE SSI GV ED+TDI+LNIK I ++M G+  KR+ + K+GPGVVTAGDIQT
Sbjct: 62  AVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKQGPGVVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V D+EVLNP+ V+C LD  A +RME TV+ G GY  +  +R E+ PIGLI +D+LYSP+K
Sbjct: 122 VGDVEVLNPELVLCTLDEGAEIRMEFTVNTGKGYHSSDRNRPEDAPIGLIPVDSLYSPVK 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQVLDYDKL++T++TDGS+  ED+VA A+RILQDQL +F+NFEEP++EV
Sbjct: 182 KVSYKVENTREGQVLDYDKLTLTVETDGSVKPEDAVAFAARILQDQLSIFVNFEEPQREV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ED +V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGRK
Sbjct: 242 AED-SVPELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM + +WPPE+I++LAK+YED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVANWPPENIDDLAKRYED 337


>gi|240138767|ref|YP_002963239.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           (Transcriptase alpha chain) (RNA polymerase alpha
           subunit) [Methylobacterium extorquens AM1]
 gi|254561367|ref|YP_003068462.1| DNA-directed RNA polymerase alpha chain [Methylobacterium
           extorquens DM4]
 gi|240008736|gb|ACS39962.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           (Transcriptase alpha chain) (RNA polymerase alpha
           subunit) [Methylobacterium extorquens AM1]
 gi|254268645|emb|CAX24604.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           (Transcriptase alpha chain) (RNA polymerase alpha
           subunit) [Methylobacterium extorquens DM4]
          Length = 339

 Score =  411 bits (1056), Expect = e-113,   Method: Composition-based stats.
 Identities = 212/338 (62%), Positives = 271/338 (80%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN ++ +  G + +    ++AEPL RGF  TLGN+LRRVL+SSL+GAA+
Sbjct: 2   VIQKNWQELIKPNKLQ-VTAGDDPKRVATVVAEPLERGFGTTLGNSLRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQIDGVLHE SSI GV ED+TDI+LNIK I ++   D  KR+T+ K GPG+VTAGDI 
Sbjct: 61  TSVQIDGVLHEFSSIPGVREDVTDIVLNIKTIAIRSQTDQPKRMTLRKTGPGLVTAGDIG 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
            V DI++LNPD VIC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +DALYSP+
Sbjct: 121 AVGDIQILNPDLVICTLDDGAEIRMEFTVATGKGYVPAERNRPEDAPIGLIPVDALYSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY VE+ REGQ LD DKL+MT++T+G+++ ED++A A+RI+QDQL +F+NFEEP+KE
Sbjct: 181 TKVSYRVETTREGQDLDKDKLTMTLETNGAVSPEDALAYAARIIQDQLQVFVNFEEPRKE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +       LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++E +MLR  NFGR
Sbjct: 241 -EAAPLAPQLPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSEGEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++P WPPE+IE+LAK++E+
Sbjct: 300 KSLNEIKEVLAGMGLHLGMDVPGWPPENIEDLAKRFEE 337


>gi|197104720|ref|YP_002130097.1| DNA-directed RNA polymerase alpha subunit [Phenylobacterium
           zucineum HLK1]
 gi|238690127|sp|B4R8P1|RPOA_PHEZH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|196478140|gb|ACG77668.1| DNA-directed RNA polymerase alpha subunit [Phenylobacterium
           zucineum HLK1]
          Length = 338

 Score =  411 bits (1056), Expect = e-113,   Method: Composition-based stats.
 Identities = 206/339 (60%), Positives = 265/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI++NW ELI+P   +    G +   +  ++AEPL RGF  TLGN+LRRVL+SSL+GAA+
Sbjct: 1   MIERNWNELIRPEKPQIET-GADASRKARLVAEPLERGFGVTLGNSLRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGV+HE SS++GV ED+ DI+LNIK + L+M  +  KR+T+   GPG VTA  I+
Sbjct: 60  TAVQIDGVVHEFSSLEGVREDVVDIVLNIKQLALRMHAEGPKRMTLRATGPGAVTASQIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DIE+LN DHV+C LD  A VRME TV  G GYVPA+ +R E+ PIGLI +D+L+SP+
Sbjct: 120 APADIEILNGDHVLCTLDDGASVRMEFTVQTGKGYVPAEMNRPEDAPIGLIAVDSLFSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V+Y VE  R+GQ LDYDKL M ++T+G+++  D+VA A+RILQDQL +FI FEEPKK+
Sbjct: 180 KRVAYRVEPTRQGQSLDYDKLIMEVETNGAVSPVDAVAYAARILQDQLQIFITFEEPKKK 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V+ +     LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 VEGEA-KPELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++P+WPPE+IEELAKK+ED+
Sbjct: 299 KSLNEIKEVLAGMGLHLGMDVPNWPPENIEELAKKFEDQ 337


>gi|39936289|ref|NP_948565.1| DNA-directed RNA polymerase subunit alpha [Rhodopseudomonas
           palustris CGA009]
 gi|192292012|ref|YP_001992617.1| DNA-directed RNA polymerase subunit alpha [Rhodopseudomonas
           palustris TIE-1]
 gi|61215951|sp|Q6N4V7|RPOA_RHOPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|229564256|sp|B3QBV5|RPOA_RHOPT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|39650144|emb|CAE28667.1| DNA-directed RNA polymerase alpha subunit [Rhodopseudomonas
           palustris CGA009]
 gi|192285761|gb|ACF02142.1| DNA-directed RNA polymerase, alpha subunit [Rhodopseudomonas
           palustris TIE-1]
          Length = 339

 Score =  410 bits (1055), Expect = e-112,   Method: Composition-based stats.
 Identities = 216/337 (64%), Positives = 273/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +  G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQ-VTPGSDATRFATLVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I+LKM G+  KR+ + K+GPG VTAGDIQT
Sbjct: 62  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDISLKMQGEGPKRMVVKKQGPGAVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V DI VLNPD  +C LD  A +RME TV+ G GYV A+ +R E+ PIGLI +D+LYSP++
Sbjct: 122 VGDIVVLNPDLQLCTLDDGAEIRMEFTVNTGKGYVAAERNRPEDAPIGLIPVDSLYSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+MT++T+G+I+ ED+VA A+RILQDQL +F+NFEEP+KEV
Sbjct: 182 KVSYKVENTREGQILDYDKLTMTVETNGAISPEDAVAFAARILQDQLNVFVNFEEPRKEV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 242 TQEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 337


>gi|218530408|ref|YP_002421224.1| DNA-directed RNA polymerase subunit alpha [Methylobacterium
           chloromethanicum CM4]
 gi|254765256|sp|B7L0S5|RPOA_METC4 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|218522711|gb|ACK83296.1| DNA-directed RNA polymerase, alpha subunit [Methylobacterium
           chloromethanicum CM4]
          Length = 339

 Score =  410 bits (1055), Expect = e-112,   Method: Composition-based stats.
 Identities = 211/338 (62%), Positives = 271/338 (80%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN ++ +  G + +    ++AEPL RGF  TLGN+LRRVL+SSL+GAA+
Sbjct: 2   VIQKNWQELIKPNKLQ-VTAGDDPKRVATVVAEPLERGFGTTLGNSLRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQIDGVLHE SSI GV ED+TDI+LNIK I ++   D  KR+T+ K GPG+VTAGDI 
Sbjct: 61  TSVQIDGVLHEFSSIPGVREDVTDIVLNIKTIAIRSQTDQPKRMTLRKTGPGLVTAGDIG 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
            V DI++LNPD VIC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +DALYSP+
Sbjct: 121 AVGDIQILNPDLVICTLDDGAEIRMEFTVATGKGYVPAERNRPEDAPIGLIPVDALYSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY VE+ REGQ LD DKL++T++T+G+++ ED++A A+RI+QDQL +F+NFEEP+KE
Sbjct: 181 TKVSYRVETTREGQDLDKDKLTITLETNGAVSPEDALAYAARIIQDQLQVFVNFEEPRKE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +       LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++E +MLR  NFGR
Sbjct: 241 -EAAPLAPQLPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSEGEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++P WPPE+IE+LAK++E+
Sbjct: 300 KSLNEIKEVLAGMGLHLGMDVPGWPPENIEDLAKRFEE 337


>gi|85715106|ref|ZP_01046090.1| DNA-directed RNA polymerase alpha subunit [Nitrobacter sp. Nb-311A]
 gi|85698021|gb|EAQ35894.1| DNA-directed RNA polymerase alpha subunit [Nitrobacter sp. Nb-311A]
          Length = 343

 Score =  410 bits (1055), Expect = e-112,   Method: Composition-based stats.
 Identities = 215/337 (63%), Positives = 270/337 (80%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++ +  G +      ++AEPL RGF  TLGNALRR+L+SSL+GAA+ 
Sbjct: 7   IQKNWQELIRPNKLQVV-PGSDPSRFATLVAEPLERGFGQTLGNALRRILLSSLQGAAVQ 65

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I +KM G+  KR+ + K+GPG VTAGDIQT
Sbjct: 66  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDIAIKMQGEGPKRMVVKKQGPGSVTAGDIQT 125

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V DI VLNPD  IC LD  A +RME TV+ G GY+ A+ +R E+ PIGLI +D+LYSP++
Sbjct: 126 VGDIVVLNPDLQICTLDDGAEIRMEFTVAAGKGYIAAERNRPEDAPIGLIPVDSLYSPVR 185

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+MTI+T+G +T ED+VA A+RILQDQL +F+NFEEP+KEV
Sbjct: 186 KVSYKVENTREGQILDYDKLTMTIETNGGVTPEDAVAFAARILQDQLNVFVNFEEPRKEV 245

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
             +I +  L FNPA LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 246 ATEI-IPDLAFNPAFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 304

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 305 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 341


>gi|315497997|ref|YP_004086801.1| DNA-directed RNA polymerase, alpha subunit [Asticcacaulis
           excentricus CB 48]
 gi|315416009|gb|ADU12650.1| DNA-directed RNA polymerase, alpha subunit [Asticcacaulis
           excentricus CB 48]
          Length = 338

 Score =  410 bits (1054), Expect = e-112,   Method: Composition-based stats.
 Identities = 210/339 (61%), Positives = 264/339 (77%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI++NWQ+LI+P   + I  GQ+ + +  ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIERNWQQLIRPEKPQ-IESGQDSQRKMRLVAEPLERGFGVTLGNALRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGV+HE SSI+GV ED+ DIILNIK + L+M  +  KR+ +     G VTAG I 
Sbjct: 60  TAVQIDGVVHEFSSIEGVREDVVDIILNIKQLALRMHAEGPKRMVLRASSAGPVTAGMID 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             +DIEVLNPDHVIC LD  A VRME TV  G GYVPA   R E+ PIGLI +DALYSP+
Sbjct: 120 VPSDIEVLNPDHVICTLDEGASVRMEFTVQTGKGYVPADRLRPEDAPIGLIAVDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKV+Y VE  R+GQ LDYDKL + ++T+ ++T  D+VA A+RILQDQL +FI FEEPK  
Sbjct: 180 KKVAYRVEPTRQGQSLDYDKLVLDVETNAAVTPVDAVAYAARILQDQLQIFITFEEPKPA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           + E+     LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE++MLR  NFGR
Sbjct: 240 IVEE-GKPELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM++P+WPPE++E+LAKK+ED+
Sbjct: 299 KSLNEIKEVLQSMGLSLGMDVPNWPPENVEDLAKKFEDQ 337


>gi|154253201|ref|YP_001414025.1| DNA-directed RNA polymerase subunit alpha [Parvibaculum
           lavamentivorans DS-1]
 gi|154157151|gb|ABS64368.1| DNA-directed RNA polymerase, alpha subunit [Parvibaculum
           lavamentivorans DS-1]
          Length = 357

 Score =  410 bits (1054), Expect = e-112,   Method: Composition-based stats.
 Identities = 217/339 (64%), Positives = 273/339 (80%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNW+ELIKPN +E I  G + +    ++AEPL RGF  TLGNALRRVLMSSL+GAA+
Sbjct: 20  LIQKNWEELIKPNKLE-INPGHDAQRFATVVAEPLERGFGLTLGNALRRVLMSSLQGAAV 78

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDIILNIK + L++  +  KR+++ K+GPGVVTAGDI 
Sbjct: 79  TAVQIDGVLHEFSSIAGVREDVTDIILNIKQLALRLHAEGPKRMSLSKKGPGVVTAGDIT 138

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DIEVLNPD V+C LD  A +RME TV+ G GYV +  +R E+ PIGL+ +D+LYSP+
Sbjct: 139 AGADIEVLNPDLVLCTLDEGAEIRMEFTVALGKGYVASDRNRPEDAPIGLMPVDSLYSPV 198

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VSY VE+ REGQVLDYDKL++ I+T+G+IT +D+VA A+RILQDQL  F+NFEEP+++
Sbjct: 199 KRVSYKVENTREGQVLDYDKLTLQIETNGAITPDDAVAYAARILQDQLQTFVNFEEPEQK 258

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E+ +   L FN ALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE++MLR  NFGR
Sbjct: 259 HVEE-SRPELEFNAALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 317

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P+WPPE+IEELAK+YED+
Sbjct: 318 KSLNEIKEVLAQMGLHLGMEVPNWPPENIEELAKRYEDQ 356


>gi|92117122|ref|YP_576851.1| DNA-directed RNA polymerase subunit alpha [Nitrobacter hamburgensis
           X14]
 gi|119366703|sp|Q1QN06|RPOA_NITHX RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|91800016|gb|ABE62391.1| DNA-directed RNA polymerase subunit alpha [Nitrobacter hamburgensis
           X14]
          Length = 339

 Score =  409 bits (1052), Expect = e-112,   Method: Composition-based stats.
 Identities = 216/337 (64%), Positives = 270/337 (80%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN + ++V G +      +IAEPL RGF  TLGNALRR+L+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKL-HVVPGSDPSRFATLIAEPLERGFGQTLGNALRRILLSSLQGAAVQ 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V IDGVLHE SSI GV ED+TDI+LNIK I++KM G+  KR+ + K+GPG VTAGDIQT
Sbjct: 62  SVHIDGVLHEFSSIAGVREDVTDIVLNIKDISIKMQGEGPKRMVVKKQGPGTVTAGDIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V DI VLNPD  IC LD  A +RME TV+ G GYV A+ +R E+ PIGLI +D+LYSP++
Sbjct: 122 VGDIVVLNPDLPICTLDDGAEIRMEFTVASGKGYVAAERNRPEDAPIGLIPVDSLYSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQ+LDYDKL+M I+T+G +T ED+VA A+RILQDQL +F+NFEEP+KEV
Sbjct: 182 KVSYKVENTREGQILDYDKLTMMIETNGGVTPEDAVAFAARILQDQLNVFVNFEEPRKEV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
             +I +  L FNP  LKKV+ELELSVRS NCL+ +NIVY+GDL+Q++EA+MLR  NFGRK
Sbjct: 242 ATEI-IPDLAFNPGFLKKVDELELSVRSANCLKNDNIVYIGDLVQKSEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM +P WPPE+I+ELAK++ED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVPGWPPENIDELAKRFED 337


>gi|83949763|ref|ZP_00958496.1| DNA-directed RNA polymerase alpha subunit [Roseovarius nubinhibens
           ISM]
 gi|83837662|gb|EAP76958.1| DNA-directed RNA polymerase alpha subunit [Roseovarius nubinhibens
           ISM]
          Length = 338

 Score =  407 bits (1047), Expect = e-112,   Method: Composition-based stats.
 Identities = 208/338 (61%), Positives = 265/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   +  ++AEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLDVK-PGNDPLRQATVVAEPLERGFGLTLGNALRRVLLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG+ L+M  +  KR++I  +GPGVVTA DI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKGVALRMDVEGPKRLSISAKGPGVVTAADIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + +ELTV+ G GYV A  ++ E+ PIG+I +DA+YSP+
Sbjct: 120 ETAGIEVLNRDHVICHLDEGADLYVELTVNTGKGYVAADKNKPEDAPIGMIPVDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY V+  REGQVLDYDKL+M I+TDGSIT +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 RRVSYDVQPTREGQVLDYDKLTMKIETDGSITPDDAVAFAARILQDQLSIFVNFDEPEAA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 GRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|182679004|ref|YP_001833150.1| DNA-directed RNA polymerase subunit alpha [Beijerinckia indica
           subsp. indica ATCC 9039]
 gi|226699352|sp|B2IF96|RPOA_BEII9 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|182634887|gb|ACB95661.1| DNA-directed RNA polymerase, alpha subunit [Beijerinckia indica
           subsp. indica ATCC 9039]
          Length = 338

 Score =  407 bits (1047), Expect = e-112,   Method: Composition-based stats.
 Identities = 212/338 (62%), Positives = 270/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP+ ++ +  G + +    +IAEPL RGF  TLGNALRR+L+SSL+GAAI
Sbjct: 1   MIQKNWQELIKPSKLD-VTPGDDSKRFATIIAEPLERGFGLTLGNALRRILLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V IDGVLHE SSI GV ED+TDIILNIK I +KM G+  KR+ + K+GPG V AGDI 
Sbjct: 60  TSVHIDGVLHEFSSIPGVREDVTDIILNIKDIAIKMQGEGPKRMVLKKQGPGKVLAGDIG 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
            V D+++LNP+ VIC LD  A +RME TV+ G GYV A  +R E+ PIGLI +D+LYSP+
Sbjct: 120 AVGDVQILNPNLVICTLDEGAEIRMEFTVNTGKGYVAADRNRAEDAPIGLIPVDSLYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQ+LDYDKL++ I+T+GS+T ED+VA ++RILQDQL +F+NFEEP++E
Sbjct: 180 KKVSYKVENTREGQILDYDKLTLQIETNGSLTPEDAVAFSARILQDQLNVFVNFEEPRRE 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +   ++  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 -EATPSIPELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM +  WPP++I+ELAK++E+
Sbjct: 299 KSLNEIKEVLAQMGLHLGMEVTGWPPDNIDELAKRFEE 336


>gi|260432472|ref|ZP_05786443.1| DNA-directed RNA polymerase, alpha subunit [Silicibacter
           lacuscaerulensis ITI-1157]
 gi|260416300|gb|EEX09559.1| DNA-directed RNA polymerase, alpha subunit [Silicibacter
           lacuscaerulensis ITI-1157]
          Length = 372

 Score =  407 bits (1047), Expect = e-111,   Method: Composition-based stats.
 Identities = 213/338 (63%), Positives = 265/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   +  ++AEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 35  MIHKNWAELIKPTQLDGK-PGNDPARQATIVAEPLERGFGLTLGNALRRVLMSSLQGAAI 93

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+K + L+M  +  KR++I  +GP VVTAGDI 
Sbjct: 94  TSVQIDNVLHEFSSVAGVREDVTDIILNLKQVALRMEVEGPKRLSINAKGPAVVTAGDIS 153

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + MELTV+ G GYV A+ ++ E+ PIGLI IDA+YSP+
Sbjct: 154 ESAGIEVLNRDHVICHLDDGAELFMELTVNTGKGYVSAEKNKPEDAPIGLIPIDAIYSPV 213

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKV+Y V+  REGQVLDYDKL+M I+TDGSIT ED++A A+RILQDQL +F+NF+EP+  
Sbjct: 214 KKVAYDVQPTREGQVLDYDKLTMKIETDGSITPEDALAFAARILQDQLSIFVNFDEPESA 273

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 274 GRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 332

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 333 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 370


>gi|154248691|ref|YP_001419649.1| DNA-directed RNA polymerase subunit alpha [Xanthobacter
           autotrophicus Py2]
 gi|254765264|sp|A7IPP6|RPOA_XANP2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|154162776|gb|ABS69992.1| DNA-directed RNA polymerase, alpha subunit [Xanthobacter
           autotrophicus Py2]
          Length = 338

 Score =  407 bits (1047), Expect = e-111,   Method: Composition-based stats.
 Identities = 211/338 (62%), Positives = 270/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP  ++ +  G + +    +IAEPL RGF  TLGNALRR+L+SSL+GAA+
Sbjct: 1   MIQKNWQELIKPEKLQ-VNPGHDPKRFATVIAEPLERGFGMTLGNALRRILLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T++ IDGVLHE SSI GV ED+TDIILN+K + ++M GD  KR+   K GPGV+ AGDIQ
Sbjct: 60  TSIHIDGVLHEFSSIPGVREDVTDIILNVKDVAIRMQGDGPKRMVAKKTGPGVLLAGDIQ 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+ +LNP+  IC LD  A +R+E TV  G GYV A  +R E+ PIGLI ID+LYSP+
Sbjct: 120 TVGDVAILNPNLPICTLDEGAELRIEFTVDTGKGYVAADRNRPEDAPIGLIPIDSLYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQ+LDYDKL++ I+T+GSIT ED++A A+RILQDQL +F+NFEEPK+E
Sbjct: 180 RKVSYKVENTREGQILDYDKLTLQIETNGSITAEDALAYAARILQDQLEIFVNFEEPKRE 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E   +++LPF+PALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++E +MLR  NFGR
Sbjct: 240 -SETTAIQTLPFSPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSETEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL ++GL LGM +P WPPE+IEELAK++E+
Sbjct: 299 KSLNEIKEVLASLGLHLGMEVPGWPPENIEELAKRFEE 336


>gi|83312207|ref|YP_422471.1| DNA-directed RNA polymerase subunit alpha [Magnetospirillum
           magneticum AMB-1]
 gi|119366694|sp|Q2W2L3|RPOA_MAGSA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|82947048|dbj|BAE51912.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Magnetospirillum magneticum AMB-1]
          Length = 338

 Score =  407 bits (1046), Expect = e-111,   Method: Composition-based stats.
 Identities = 207/338 (61%), Positives = 267/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN + ++  G + +   +++AEPL RGF  TLGN+LRRVL+SSL+GAA+
Sbjct: 1   MIQKNWQELIKPNKL-HVEPGADPQRTAIVVAEPLERGFGMTLGNSLRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGVLHE SSI GV ED+TDIILNIK + L+M G+  KR+ +   GPG VTAG I+
Sbjct: 60  TAIQIDGVLHEFSSIPGVREDVTDIILNIKTLGLRMHGEGPKRMHLRAVGPGEVTAGLIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             +DIE+++P+ V+C LD  A + +E TV  G GYVPA  +R E+ PIGLI IDA++SP+
Sbjct: 120 VGHDIEIMDPELVLCTLDEGAKLNIEFTVETGKGYVPASQNRPEDSPIGLIPIDAIFSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KV+Y VE+ R GQV DYDKLSMT++T+G++T +D+VALA+RILQDQL +FINFEEP   
Sbjct: 180 RKVAYKVENTRVGQVTDYDKLSMTVETNGAVTPDDAVALAARILQDQLQLFINFEEPTAV 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V+E+     LPFN  LL+KV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+MLR  NFGR
Sbjct: 240 VEEE-KKDELPFNKNLLRKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM + +WPPE+IEELAKK E+
Sbjct: 299 KSLNEIKEVLAQMGLHLGMEIANWPPENIEELAKKLEE 336


>gi|114767226|ref|ZP_01446091.1| DNA-directed RNA polymerase alpha subunit [Pelagibaca bermudensis
           HTCC2601]
 gi|114540636|gb|EAU43707.1| DNA-directed RNA polymerase alpha subunit [Roseovarius sp.
           HTCC2601]
          Length = 338

 Score =  407 bits (1046), Expect = e-111,   Method: Composition-based stats.
 Identities = 209/339 (61%), Positives = 266/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E +  G +      ++AEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLE-VRPGADPSRVATVVAEPLERGFGLTLGNALRRVLLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG++L+M  +  KR++I   GPG VTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKGVSLRMEVEGPKRLSINATGPGAVTAGDIA 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + +ELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ETAGIEVLNKDHVICHLDDGADLYVELTVNTGKGYVSADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V+Y V+  REGQVLDYDKL+M ++TDGS+T ED++A A+RILQDQL +F+NF+EP+  
Sbjct: 180 KRVAYEVQPTREGQVLDYDKLTMKVETDGSVTPEDAIAFAARILQDQLSIFVNFDEPEAA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 GRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM++ DWPP++IE+LAKK ED+
Sbjct: 299 KSLNEIKEVLSSMGLHLGMDVEDWPPDNIEDLAKKLEDQ 337


>gi|119383536|ref|YP_914592.1| DNA-directed RNA polymerase subunit alpha [Paracoccus denitrificans
           PD1222]
 gi|158512588|sp|A1B052|RPOA_PARDP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119373303|gb|ABL68896.1| DNA-directed RNA polymerase subunit alpha [Paracoccus denitrificans
           PD1222]
          Length = 338

 Score =  407 bits (1046), Expect = e-111,   Method: Composition-based stats.
 Identities = 209/339 (61%), Positives = 262/339 (77%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E I  G +      ++AEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLE-IKPGADSSRVATVVAEPLERGFGLTLGNALRRVLLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG+ LKM  D+ KR+T+  +GPG V AGDIQ
Sbjct: 60  TSVQIDNVLHEFSSVPGVREDVTDIVLNLKGVTLKMDVDAPKRLTLSAKGPGEVKAGDIQ 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               I +LN DHVIC+LD  A + MEL V+ G GYV A  +R E+ PIGLI IDA++SP+
Sbjct: 120 ESAGITILNRDHVICHLDEGAELHMELAVANGKGYVAADKNRPEDAPIGLIPIDAIFSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VSY V   REGQVLDYDKL+M ++TDGS+T ED+VA A+RI+QDQL +F+NF+EP+  
Sbjct: 180 KRVSYEVTPTREGQVLDYDKLTMKVETDGSLTPEDAVAYAARIIQDQLSVFVNFDEPETA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            + D     L F+P LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 TRSDAE-DGLEFDPRLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPPE+IE+LAK+++D+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVVDWPPENIEDLAKRFDDQ 337


>gi|158424154|ref|YP_001525446.1| DNA-directed RNA polymerase subunit alpha [Azorhizobium caulinodans
           ORS 571]
 gi|172047974|sp|A8IAN5|RPOA_AZOC5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158331043|dbj|BAF88528.1| DNA-directed RNA polymerase alpha subunit [Azorhizobium caulinodans
           ORS 571]
          Length = 341

 Score =  406 bits (1044), Expect = e-111,   Method: Composition-based stats.
 Identities = 218/338 (64%), Positives = 272/338 (80%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKP  ++ +  G + +    ++AEPL RGF  TLGN+LRR+L+SSL+GAA+
Sbjct: 4   VIQKNWQELIKPEKLQ-VTAGADPKRLATVVAEPLERGFGMTLGNSLRRILLSSLQGAAV 62

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V IDGVLHE SSI GV ED+TDIILNIK I +KM GD  KR+   K GPGV+ AGDIQ
Sbjct: 63  TSVHIDGVLHEFSSIPGVREDVTDIILNIKDIAIKMQGDGPKRLVAKKNGPGVLVAGDIQ 122

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DI++LNP  V+C LD  A +RME TV  G GYVPA+ +R E+ PIGLI ID+LYSP+
Sbjct: 123 TVGDIQILNPHLVLCTLDEGAELRMEFTVDTGKGYVPAERNRPEDAPIGLIPIDSLYSPV 182

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQ+LDYDKL+M I+TDGS++ ED++A A+RILQDQL +F+NFEEPK+E
Sbjct: 183 RKVSYKVENTREGQILDYDKLTMQIETDGSVSAEDALAYAARILQDQLEIFVNFEEPKRE 242

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E   ++ LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++E +MLR  NFGR
Sbjct: 243 -SETAAIQELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSETEMLRTPNFGR 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL +MGL LGM +P WPPE+IEELAK++ED
Sbjct: 302 KSLNEIKEVLASMGLHLGMEVPGWPPENIEELAKRFED 339


>gi|288958717|ref|YP_003449058.1| DNA-directed RNA polymerase subunit alpha [Azospirillum sp. B510]
 gi|288911025|dbj|BAI72514.1| DNA-directed RNA polymerase subunit alpha [Azospirillum sp. B510]
          Length = 338

 Score =  405 bits (1042), Expect = e-111,   Method: Composition-based stats.
 Identities = 208/338 (61%), Positives = 267/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M+QKNWQELIKP+ +E I  G + +    ++AEPL RGF  TLGNALRR+L+SSL+GAA+
Sbjct: 1   MLQKNWQELIKPSKLE-IQPGDDADRFATVVAEPLERGFGLTLGNALRRILLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T++ IDGVLHE SSI GV ED+TDI+LNIK + L+M GD  KR+ +   GPG V AG I+
Sbjct: 60  TSIHIDGVLHEFSSIPGVREDVTDIVLNIKTMGLRMGGDGPKRMRLRAEGPGEVKAGMIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T  DI+V++P+ VIC LD  A + MELTV  G GYVPA  +R E+ PIGLI IDAL+SP+
Sbjct: 120 TGPDIQVMDPELVICTLDNGARLNMELTVETGKGYVPASQNRPEDAPIGLIPIDALFSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY V++AR GQV DYD+LSMT++T+GS+  +D+VALA+RI+QDQL +FINFEEP   
Sbjct: 180 RKVSYKVDNARVGQVTDYDRLSMTVETNGSVKPDDAVALAARIMQDQLQLFINFEEPTHA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V E+ + + +PFN  LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q+TEA+MLR  NFGR
Sbjct: 240 VSEEKH-EEVPFNKNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM +P+WPPE+IEELAK+ E+
Sbjct: 299 KSLNEIKEVLSQMGLHLGMEIPNWPPENIEELAKRLEE 336


>gi|330993873|ref|ZP_08317805.1| DNA-directed RNA polymerase subunit alpha [Gluconacetobacter sp.
           SXCC-1]
 gi|329759141|gb|EGG75653.1| DNA-directed RNA polymerase subunit alpha [Gluconacetobacter sp.
           SXCC-1]
          Length = 339

 Score =  405 bits (1041), Expect = e-111,   Method: Composition-based stats.
 Identities = 203/338 (60%), Positives = 258/338 (76%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++QKNWQ LIKP  +E    G E      ++AEPL RGF  TLGNA+RRVL+SSL+GAA+
Sbjct: 2   VLQKNWQSLIKPEKLEVE-PGAEPSRIATVVAEPLERGFGMTLGNAIRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGVLHE SS+ GV ED+TDI+LNIK + L+M G+  KR+ +   GPG V AG IQ
Sbjct: 61  TAIQIDGVLHEFSSVAGVREDVTDIVLNIKQLALRMHGEGPKRMVLTATGPGEVRAGQIQ 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIEV+NPD VIC LD      ME TV+ G GYVPA  +R E+ PIGLI +DA+YSP+
Sbjct: 121 TGHDIEVMNPDLVICTLDEGVKFGMEFTVNMGKGYVPAAANRPEDAPIGLIPVDAIYSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY VE  R GQV DYD+L +T++T+G++T ED+VALA+RILQDQL +FINF+EP+  
Sbjct: 181 RRVSYKVEQTRVGQVTDYDRLLLTVETNGAVTPEDAVALAARILQDQLQLFINFDEPRTV 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E+     LPFN  LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q+TE +MLR  NFGR
Sbjct: 241 RTEEP-QDDLPFNRNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKTEQEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGMN+P WPPE+IE+LAK+ ++
Sbjct: 300 KSLNEIKEVLTAMGLSLGMNVPAWPPENIEDLAKRLDE 337


>gi|162149150|ref|YP_001603611.1| DNA-directed RNA polymerase subunit alpha [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|209545106|ref|YP_002277335.1| DNA-directed RNA polymerase subunit alpha [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|189043839|sp|A9H3I9|RPOA_GLUDA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|161787727|emb|CAP57323.1| DNA-directed RNA polymerase alpha chain [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|209532783|gb|ACI52720.1| DNA-directed RNA polymerase, alpha subunit [Gluconacetobacter
           diazotrophicus PAl 5]
          Length = 339

 Score =  405 bits (1041), Expect = e-111,   Method: Composition-based stats.
 Identities = 202/338 (59%), Positives = 259/338 (76%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++QKNWQ LIKP  +E    G E      ++AEPL RGF  TLGNA+RRVL+SSL+GAA+
Sbjct: 2   VLQKNWQSLIKPEKLEVE-PGGEPLRTATVVAEPLERGFGMTLGNAIRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGVLHE SS+ GV ED+TDI+LN+K + L+M G+  KR+ +   GPG V AG IQ
Sbjct: 61  TAIQIDGVLHEFSSVAGVREDVTDIVLNVKQLALRMHGEGPKRMVLTATGPGEVRAGQIQ 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIEV+NPD VIC LD      ME TV+ G GYVPA  +R E+ PIGLI +DA+YSP+
Sbjct: 121 TGHDIEVMNPDLVICTLDEGVKFGMEFTVNLGKGYVPAAANRPEDAPIGLIPVDAIYSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY VE  R GQV DYD+L +T++T+G++T ED+VALA+RILQDQL +FINF+EP+  
Sbjct: 181 RRVSYKVEPTRVGQVTDYDRLLLTVETNGAVTPEDAVALAARILQDQLQLFINFDEPRPV 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E+     LPFN  LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q+TE +MLR  NFGR
Sbjct: 241 RTEEP-QDDLPFNRNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKTEQEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL +MGL LGMN+P WPPE+IE+LAK+ ++
Sbjct: 300 KSLNEIKEVLTSMGLSLGMNVPAWPPENIEDLAKRLDE 337


>gi|296534011|ref|ZP_06896527.1| DNA-directed RNA polymerase subunit alpha [Roseomonas cervicalis
           ATCC 49957]
 gi|296265677|gb|EFH11786.1| DNA-directed RNA polymerase subunit alpha [Roseomonas cervicalis
           ATCC 49957]
          Length = 338

 Score =  405 bits (1040), Expect = e-111,   Method: Composition-based stats.
 Identities = 195/338 (57%), Positives = 259/338 (76%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M+++NW+ LI+P  ++    G +     +++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MLERNWRSLIRPEKLDVE-PGADPSRVAVVVAEPLERGFGMTLGNALRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA++IDG LHE SS++GV ED+TDI+LNIK + ++M  +  KR+ +   GPG VTAG IQ
Sbjct: 60  TAIRIDGALHEFSSLQGVREDVTDIVLNIKRLAIRMQSEGPKRLQLTATGPGEVTAGQIQ 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T  DIE+ NP+ VIC LD  A + MELTV  G GYVPA  +R E+ PIGLI +DA+YSP+
Sbjct: 120 TTGDIEIANPELVICTLDDGAKLSMELTVDVGKGYVPASENRPEDAPIGLIPVDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++V+Y V+  R GQ  DYDKL +T++TDG++  ED+VALA+RILQDQL +FINF+EP++ 
Sbjct: 180 RRVAYQVQPTRVGQRTDYDKLVLTVETDGTVAPEDAVALAARILQDQLQLFINFDEPRER 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E++    LPFN  LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q+TE +MLR  NFGR
Sbjct: 240 KVEEV-QDDLPFNRNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKTEQEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL +MGL LGM +P WPPE+IE+LAKK E+
Sbjct: 299 KSLNEIKEVLASMGLSLGMTVPGWPPENIEDLAKKIEE 336


>gi|329850231|ref|ZP_08265076.1| DNA-directed RNA polymerase, alpha subunit [Asticcacaulis
           biprosthecum C19]
 gi|328840546|gb|EGF90117.1| DNA-directed RNA polymerase, alpha subunit [Asticcacaulis
           biprosthecum C19]
          Length = 338

 Score =  405 bits (1040), Expect = e-111,   Method: Composition-based stats.
 Identities = 206/339 (60%), Positives = 258/339 (76%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI++NWQ+LI+P   +    G +   +  ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIERNWQQLIRPEKPQVEA-GTDASRKMRLVAEPLERGFGVTLGNALRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQIDGV+HE SSI+GV ED+ DIILNIK + L+M  +  KR+ +   G G VTAG I 
Sbjct: 60  TSVQIDGVVHEFSSIEGVREDVVDIILNIKQLALRMHAEGPKRMVLRASGAGPVTAGQID 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DIEVLNPDHVIC LD  A VRME TV  G GYV A   R E+ PIGLI +DALYSP+
Sbjct: 120 VPADIEVLNPDHVICTLDEGASVRMEFTVQNGKGYVAADRLRPEDAPIGLIAVDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKV+Y VE  R+GQ LDYDKL + ++T+ ++T  D+VA A+RILQDQL +FI FEEPK  
Sbjct: 180 KKVAYRVEPTRQGQSLDYDKLILDVETNAAVTPVDAVAFAARILQDQLQIFITFEEPKAP 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V E+     LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLI +TE++MLR  NFGR
Sbjct: 240 VVEE-GKPELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLILKTESEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +M L LGM++P+WPPE++E+LAKK+ED+
Sbjct: 299 KSLNEIKEVLASMNLSLGMDIPNWPPENVEDLAKKFEDQ 337


>gi|254470353|ref|ZP_05083757.1| DNA-directed RNA polymerase, alpha subunit [Pseudovibrio sp. JE062]
 gi|211960664|gb|EEA95860.1| DNA-directed RNA polymerase, alpha subunit [Pseudovibrio sp. JE062]
          Length = 340

 Score =  405 bits (1040), Expect = e-111,   Method: Composition-based stats.
 Identities = 225/337 (66%), Positives = 275/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELIKP  ++ I  G +   +  +IAEPL RG+  TLGNALRRVL+SSL+GAA+T
Sbjct: 3   IQKNWQELIKPTKLD-IRAGDDARFKASVIAEPLERGYGLTLGNALRRVLLSSLQGAAVT 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           AVQIDGVLHE SSI GV ED+TDIILNIK + L+M G+  KR+ + K+GPG V AGDI+T
Sbjct: 62  AVQIDGVLHEFSSIPGVREDVTDIILNIKEVALRMEGEGPKRMVLRKQGPGAVYAGDIET 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           V DIEVLNP  ++CNLD  A VR+E TV+ G GYVPA  +R E+ PIGLI +D+LYSP+K
Sbjct: 122 VGDIEVLNPGLLLCNLDEGAEVRIEFTVNTGKGYVPAAANRPEDAPIGLIPVDSLYSPVK 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY VE+ REGQVLDYDKL++T++TDGS+  ED+VA A+RILQDQL +F+NFEEP++EV
Sbjct: 182 KVSYKVENTREGQVLDYDKLTLTVETDGSVIPEDAVAFAARILQDQLSIFVNFEEPQREV 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +ED  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGRK
Sbjct: 242 QEDT-VAELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM + +WPPE+I+ELAK+YED
Sbjct: 301 SLNEIKEVLAQMGLHLGMEVANWPPENIDELAKRYED 337


>gi|146278544|ref|YP_001168703.1| DNA-directed RNA polymerase subunit alpha [Rhodobacter sphaeroides
           ATCC 17025]
 gi|166229275|sp|A4WVI4|RPOA_RHOS5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|145556785|gb|ABP71398.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacter sphaeroides
           ATCC 17025]
          Length = 338

 Score =  405 bits (1040), Expect = e-111,   Method: Composition-based stats.
 Identities = 216/339 (63%), Positives = 265/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +  +  G +      +IAEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQL-VVKPGADPARVATVIAEPLERGFGLTLGNALRRVLLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG+++KM  +  KR++I  +GPGVVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKGVSIKMDVEGPKRLSISAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             N IE+LN DHVIC+LD  A V MELTV+ G GYV A  +R E+ PIGLI IDA+YSP+
Sbjct: 120 ESNGIEILNKDHVICHLDEGADVFMELTVNTGKGYVAADKNRPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V   REGQVLDYDKL+M ++TDG +T ED+VA A+RILQDQL +F+NFEEP+  
Sbjct: 180 KKVSYEVTPTREGQVLDYDKLTMRVETDGGLTPEDAVAYAARILQDQLSIFVNFEEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            + D+    L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 TRHDVE-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPPE+IE+LAK++ED+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPENIEDLAKRFEDQ 337


>gi|114570321|ref|YP_757001.1| DNA-directed RNA polymerase subunit alpha [Maricaulis maris MCS10]
 gi|119366695|sp|Q0ANS4|RPOA_MARMM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|114340783|gb|ABI66063.1| DNA-directed RNA polymerase subunit alpha [Maricaulis maris MCS10]
          Length = 339

 Score =  405 bits (1040), Expect = e-111,   Method: Composition-based stats.
 Identities = 208/338 (61%), Positives = 264/338 (78%), Gaps = 1/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI+KNWQELI+P   E I  G +   +  ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIEKNWQELIRPMKPE-IEPGHDPARQAKIVAEPLERGFGMTLGNALRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T V IDGV+HE SSI GV ED+TDI+LNIK I L+M G+  KRV + K GPG+VTAGDI+
Sbjct: 60  TNVHIDGVVHEFSSIDGVREDVTDIVLNIKQIALRMHGEGPKRVVLKKSGPGIVTAGDIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              D+E++N D  +C LD  A +RME T++ G GYVP++ +R E+ PIGLI +DALYSP+
Sbjct: 120 ETADVEIVNKDLALCTLDEGAEIRMEFTINTGKGYVPSERNRPEDAPIGLIGVDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VSY VE+ REGQVLDYDKL++ ++TDG++T EDSVA A+RILQDQ  +FINFEE  + 
Sbjct: 180 KRVSYKVENTREGQVLDYDKLTLEVETDGTVTPEDSVAFAARILQDQFQIFINFEEAVEA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
              + +   L FNPALL+KV+ELELSVRS NCL+ +NIVY+GDLIQ++EA+MLR  NFGR
Sbjct: 240 RPAEDDKPELDFNPALLRKVDELELSVRSANCLKNDNIVYIGDLIQKSEAEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM  P+WPPE+IE+LAK++ED
Sbjct: 300 KSLNEIKEVLAQMGLHLGMEAPNWPPENIEDLAKRFED 337


>gi|296116709|ref|ZP_06835319.1| DNA-directed RNA polymerase subunit alpha [Gluconacetobacter
           hansenii ATCC 23769]
 gi|295976921|gb|EFG83689.1| DNA-directed RNA polymerase subunit alpha [Gluconacetobacter
           hansenii ATCC 23769]
          Length = 339

 Score =  404 bits (1038), Expect = e-110,   Method: Composition-based stats.
 Identities = 205/338 (60%), Positives = 258/338 (76%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++QKNWQ LIKP  +E    G E      ++AEPL RGF  TLGNA+RRVL+SSL+GAA+
Sbjct: 2   VLQKNWQSLIKPEKLEVE-PGAEPSRTATVVAEPLERGFGMTLGNAIRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGVLHE SS+ GV ED+TDI+LNIK + L+M G+  KR+ +   GPG V AG IQ
Sbjct: 61  TAIQIDGVLHEFSSVAGVREDVTDIVLNIKQLALRMHGEGPKRMVLTATGPGEVRAGQIQ 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIEV+NPD VIC LD      ME TV+ G GYVPA  +R E+ PIGLI IDA+YSP+
Sbjct: 121 TGHDIEVMNPDLVICTLDEGVKFGMEFTVNMGKGYVPAAANRPEDAPIGLIPIDAIYSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY VE  R GQV DYD+L +T++T+G++T EDSVALA+RILQDQL +FINF+EP+  
Sbjct: 181 RRVSYKVEQTRVGQVTDYDRLLLTVETNGAVTPEDSVALAARILQDQLQLFINFDEPRAV 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E+     LPFN  LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q+TE +MLR  NFGR
Sbjct: 241 RTEEP-QDDLPFNRNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKTEQEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGMN+P WPPE+IE+LAK+ ++
Sbjct: 300 KSLNEIKEVLTAMGLSLGMNVPAWPPENIEDLAKRLDE 337


>gi|260427855|ref|ZP_05781834.1| DNA-directed RNA polymerase, alpha subunit [Citreicella sp. SE45]
 gi|260422347|gb|EEX15598.1| DNA-directed RNA polymerase, alpha subunit [Citreicella sp. SE45]
          Length = 338

 Score =  403 bits (1037), Expect = e-110,   Method: Composition-based stats.
 Identities = 209/339 (61%), Positives = 268/339 (79%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E +  G +      ++AEPL RGF  T+GNALRR+L+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLE-VRPGADPSRVATVVAEPLERGFGLTMGNALRRILLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG++L+M  +  KR++I  +GPGVVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKGVSLRMEVEGPKRLSINAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + +ELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ETAGIEVLNKDHVICHLDDGADLYVELTVNTGKGYVSADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VSY V+  REGQVLDYDKL+M ++TDGS+T +D++A A+RILQDQL +F+NFEEP+  
Sbjct: 180 KRVSYEVQPTREGQVLDYDKLTMKVETDGSVTPDDAIAFAARILQDQLSIFVNFEEPEAA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 GRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM++ DWPP++IE+LAKK ED+
Sbjct: 299 KSLNEIKEVLSSMGLHLGMDVEDWPPDNIEDLAKKLEDQ 337


>gi|209964064|ref|YP_002296979.1| DNA-directed RNA polymerase subunit alpha [Rhodospirillum centenum
           SW]
 gi|259494170|sp|B6IRT0|RPOA_RHOCS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|209957530|gb|ACI98166.1| DNA-directed RNA polymerase, alpha subunit [Rhodospirillum centenum
           SW]
          Length = 338

 Score =  403 bits (1037), Expect = e-110,   Method: Composition-based stats.
 Identities = 200/338 (59%), Positives = 259/338 (76%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQ L KP+ ++ I  G + +    ++A PL RGF  TLGNA+RRVL+SSL+GAA+
Sbjct: 1   MIQKNWQTLEKPSKLD-ITPGSDPKREATIVAGPLERGFGLTLGNAIRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T++ IDGVLHE SSI GV ED+TDI+LNIK + LKM  +  +R+ +   GP  VTAG I+
Sbjct: 60  TSIHIDGVLHEFSSIPGVREDVTDIVLNIKAMALKMGAEGPRRMRLRAEGPCEVTAGMIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T  DIEVL+P HVIC LD  A + MELTV+ G GYVPA  +R E+ PIGLI +DA++SP+
Sbjct: 120 TGADIEVLDPGHVICTLDSGARLNMELTVAMGKGYVPASQNRPEDAPIGLIPVDAIFSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KV+Y VE+ R GQ  DYDKL + ++T+G+++ ED+VA+A+RILQDQL MFINFEEP+  
Sbjct: 180 RKVAYKVENTRVGQTTDYDKLLLNVETNGAVSPEDAVAIAARILQDQLQMFINFEEPQAA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V E      +PFN  LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q+TEA+MLR  NFGR
Sbjct: 240 VAE-TKADEIPFNKNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM +P+WPPE+IE+LAK+ E+
Sbjct: 299 KSLNEIKEVLAQMGLHLGMEIPNWPPENIEDLAKRLEE 336


>gi|114798821|ref|YP_761505.1| DNA-directed RNA polymerase subunit alpha [Hyphomonas neptunium
           ATCC 15444]
 gi|119366689|sp|Q0BYD8|RPOA_HYPNA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|114738995|gb|ABI77120.1| DNA-directed RNA polymerase, alpha subunit [Hyphomonas neptunium
           ATCC 15444]
          Length = 342

 Score =  403 bits (1037), Expect = e-110,   Method: Composition-based stats.
 Identities = 200/335 (59%), Positives = 252/335 (75%), Gaps = 1/335 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW+ LI+PN    +  G + + +  ++ EPL RG+  TLGNALRRVL+SSL+GAAI  V
Sbjct: 7   RNWKVLIRPNRP-VVQAGYDAKRKAKLVVEPLERGYGTTLGNALRRVLLSSLQGAAIIGV 65

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           QIDGV+HE S+I GV ED+T I+LN+K + + M  D+ KR+ +  +GPG V AG I+T  
Sbjct: 66  QIDGVVHEFSAIPGVREDVTTIVLNLKQVAIFMESDTPKRMVLRAKGPGEVKAGQIETPG 125

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           D+++LNPD VIC LD  + VRME TV+ G GYV A+ HR E+ PIG I IDA+YSP+++V
Sbjct: 126 DVKILNPDLVICTLDGGSEVRMEFTVATGKGYVAAEAHRPEDAPIGYIPIDAIYSPVRRV 185

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
            Y VE  REG VLDYDKL++ I+TDGS++ EDSVA A+RILQDQL +FINFEEP  E   
Sbjct: 186 GYQVEDTREGTVLDYDKLTLDIETDGSLSPEDSVAYAARILQDQLQLFINFEEPTLETGG 245

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++EA+MLR  NFGRKSL
Sbjct: 246 AADETDLGFNPVLLKKVDELELSVRSANCLKNDNIVYIGDLIQKSEAEMLRTPNFGRKSL 305

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
            EIK VL  MGL LGM +PDWPPE IE LAKKY+D
Sbjct: 306 NEIKEVLAGMGLHLGMEVPDWPPEDIEGLAKKYDD 340


>gi|77462283|ref|YP_351787.1| DNA-directed RNA polymerase subunit alpha [Rhodobacter sphaeroides
           2.4.1]
 gi|126461159|ref|YP_001042273.1| DNA-directed RNA polymerase subunit alpha [Rhodobacter sphaeroides
           ATCC 17029]
 gi|221638137|ref|YP_002524399.1| DNA-directed RNA polymerase subunit alpha [Rhodobacter sphaeroides
           KD131]
 gi|90110864|sp|Q3J5P8|RPOA_RHOS4 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158513430|sp|A3PGN5|RPOA_RHOS1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|254765260|sp|B9KLB5|RPOA_RHOSK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|77386701|gb|ABA77886.1| RNA polymerase, alpha chain [Rhodobacter sphaeroides 2.4.1]
 gi|126102823|gb|ABN75501.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacter sphaeroides
           ATCC 17029]
 gi|221158918|gb|ACL99897.1| DNA-directed RNA polymerase subunit alpha [Rhodobacter sphaeroides
           KD131]
          Length = 338

 Score =  403 bits (1036), Expect = e-110,   Method: Composition-based stats.
 Identities = 216/339 (63%), Positives = 265/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +  +  G +      +IAEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQL-VVKPGADPARVATVIAEPLERGFGLTLGNALRRVLLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG+++KM  +  KR++I  +GPGVVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKGVSIKMEVEGPKRLSISAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             N IE+LN DHVIC+LD  A V MELTV+ G GYV A  +R E+ PIGLI IDA+YSP+
Sbjct: 120 ESNGIEILNKDHVICHLDEGADVFMELTVNTGKGYVAADKNRPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V   REGQVLDYDKL+M I+TDG +T +D+VA A+RILQDQL +F+NFEEP+  
Sbjct: 180 KKVSYEVTPTREGQVLDYDKLTMRIETDGGLTPDDAVAYAARILQDQLSIFVNFEEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            + D+    L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 TRHDVE-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPPE+IE+LAK++ED+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPENIEDLAKRFEDQ 337


>gi|144900908|emb|CAM77772.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           [Magnetospirillum gryphiswaldense MSR-1]
          Length = 338

 Score =  403 bits (1036), Expect = e-110,   Method: Composition-based stats.
 Identities = 204/338 (60%), Positives = 264/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP+ ++    G +      +IAEPL RGF  TLGN+LRR+L+SSL+GAA+
Sbjct: 1   MIQKNWQELIKPSKLQVE-PGADAARVATVIAEPLERGFGMTLGNSLRRILLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QI+GVLHE SS+ GV ED+TDIILNIK + L+M G+  KR+ +   GPG V AG I+
Sbjct: 60  TAIQIEGVLHEFSSVPGVREDVTDIILNIKNLGLRMHGEGPKRMQLRASGPGEVKAGMIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             +DIE+++PD V+C LD  A + +E TV  G GYVPA  +RTE+ PIGLI IDA++SP+
Sbjct: 120 AGHDIEIMDPDLVLCTLDQGAKLNIEFTVETGKGYVPASQNRTEDSPIGLIPIDAIFSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKV+Y VE+ R GQV DYDKLSM ++T+G++T +D+VALA+RILQDQL +FINF+EP   
Sbjct: 180 KKVAYKVENTRVGQVTDYDKLSMVLETNGAVTPDDAVALAARILQDQLQLFINFDEPTHV 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V+E+     LPFN  LL+KV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+MLR  NFGR
Sbjct: 240 VEEE-KKDELPFNKNLLRKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM +P+WPPE+IE+LAKK E+
Sbjct: 299 KSLNEIKEVLSHMGLHLGMEIPNWPPENIEDLAKKLEE 336


>gi|149202868|ref|ZP_01879839.1| DNA-directed RNA polymerase subunit alpha [Roseovarius sp. TM1035]
 gi|149143414|gb|EDM31450.1| DNA-directed RNA polymerase subunit alpha [Roseovarius sp. TM1035]
          Length = 338

 Score =  403 bits (1036), Expect = e-110,   Method: Composition-based stats.
 Identities = 213/338 (63%), Positives = 267/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E    G +   + ++IAEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLEVK-PGNDPLRQAVLIAEPLERGFGLTLGNALRRVLLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID VLHE SS+ GV ED+TDI+LN+KG+ ++M  +  KR+++  +GPGVVTAGDI 
Sbjct: 60  TAVQIDNVLHEFSSVAGVREDVTDIVLNLKGVAIRMEVEGPKRLSVNAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD  A + MELTV++G GYV A  ++ E+ PIGLI IDA+YSPI
Sbjct: 120 DSAGIEILNKDHVICHLDEGADLFMELTVNQGKGYVSADKNKPEDAPIGLIPIDAIYSPI 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            +VSY V+  REGQVLDYDKL+M I+TDGSIT +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 SRVSYEVQPTREGQVLDYDKLTMKIETDGSITPDDAVAYAARILQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SRQD-DDDGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|240850811|ref|YP_002972211.1| DNA-directed RNA polymerase subunit alpha [Bartonella grahamii
           as4aup]
 gi|240267934|gb|ACS51522.1| DNA-directed RNA polymerase subunit alpha [Bartonella grahamii
           as4aup]
          Length = 337

 Score =  403 bits (1035), Expect = e-110,   Method: Composition-based stats.
 Identities = 228/339 (67%), Positives = 274/339 (80%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E      +  N   +IAEPL RGF  TLGNALRRVL+SSLRGAAI
Sbjct: 1   MIQKNWQELIKPNKVESCA--HDNPNVISVIAEPLERGFGLTLGNALRRVLLSSLRGAAI 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDIILNIK I L+M  +  KRV ++K GPGVV AGDI 
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIILNIKEIALRMEEEGPKRVVVYKEGPGVVKAGDIS 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNPDHVIC LD DA +RME  V+ G GYVP+  +  ++  IGLI ID+LYSPI
Sbjct: 119 TVGDMEILNPDHVICTLDEDAEIRMEFIVNTGKGYVPSDRNCVDDARIGLIPIDSLYSPI 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQVLDYDKL++TI+T+G++ GED+VA A+RILQDQL +FINFEEP+KE
Sbjct: 179 RKVSYKVENTREGQVLDYDKLTLTIETNGAVNGEDAVAFAARILQDQLSLFINFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E+ + + L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE++MLR  NFGR
Sbjct: 239 PVEEADSE-LSFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPPE+I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEIPAWPPENIDDLAKRYEDQ 336


>gi|256636186|dbj|BAI02155.1| DNA-directed RNA polymerase alpha subunit (variant) [Acetobacter
           pasteurianus IFO 3283-03]
 gi|256645350|dbj|BAI11298.1| DNA-directed RNA polymerase alpha subunit (variant) [Acetobacter
           pasteurianus IFO 3283-26]
          Length = 339

 Score =  403 bits (1035), Expect = e-110,   Method: Composition-based stats.
 Identities = 202/338 (59%), Positives = 257/338 (76%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++QKNWQ LIKP  +E    G E      ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 2   VLQKNWQSLIKPEKLEVES-GVEPARIATVVAEPLERGFGMTLGNALRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SS+ GV ED+TDI+LNIK + L+M G+  KR+ +   GPG V A  IQ
Sbjct: 61  TAVQIDGVLHEFSSVAGVREDVTDIVLNIKQLALRMHGEGPKRMMLTATGPGEVRARQIQ 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIE++NPD VIC LD    + ME  V+ G GYVPA  +R E+ PIGLI +DA+YSP+
Sbjct: 121 TGHDIEIMNPDLVICTLDDGVKLGMEFIVNMGKGYVPAAANRPEDAPIGLIPVDAIYSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VSY VE  R GQV DYDKL +T++T+G++T ED+VALA+RILQDQL +FINF+EP+  
Sbjct: 181 KRVSYKVEPTRVGQVTDYDKLLLTVETNGAVTPEDAVALAARILQDQLQLFINFDEPRPV 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E+      PFN  LL+KV+ELELSVRS NCL+ +NI+Y+GDL+Q++E +MLR  NFGR
Sbjct: 241 QAEEPE-DDQPFNRNLLRKVDELELSVRSANCLKNDNIIYIGDLVQKSEQEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL +MGL LGMN+P WPPE+IEELAK+ ++
Sbjct: 300 KSLNEIKEVLTSMGLSLGMNVPAWPPENIEELAKRLDE 337


>gi|254510629|ref|ZP_05122696.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacteraceae
           bacterium KLH11]
 gi|221534340|gb|EEE37328.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacteraceae
           bacterium KLH11]
          Length = 348

 Score =  403 bits (1035), Expect = e-110,   Method: Composition-based stats.
 Identities = 214/338 (63%), Positives = 267/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   +  ++AEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 11  MIHKNWAELIKPTQLDGK-PGNDPARQATLVAEPLERGFGLTLGNALRRVLMSSLQGAAI 69

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KG++L+M  +  KR++I  +GP VVTAGDI 
Sbjct: 70  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGVSLRMEVEGPKRLSINAKGPAVVTAGDIS 129

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + MELTV+ G GYV A+ ++ E+ PIGLI IDA+YSP+
Sbjct: 130 ESAGIEVLNRDHVICHLDDGADLFMELTVNTGKGYVSAEKNKPEDAPIGLIPIDAIYSPV 189

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKV+Y V+  REGQVLDYDKL++ IDTDGSIT ED++A A+RILQDQL +F+NF+EP+  
Sbjct: 190 KKVAYDVQPTREGQVLDYDKLTLKIDTDGSITPEDALAFAARILQDQLSIFVNFDEPESA 249

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 250 GRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 308

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 309 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 346


>gi|148260915|ref|YP_001235042.1| DNA-directed RNA polymerase subunit alpha [Acidiphilium cryptum
           JF-5]
 gi|172047769|sp|A5FZU1|RPOA_ACICJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|146402596|gb|ABQ31123.1| DNA-directed RNA polymerase subunit alpha [Acidiphilium cryptum
           JF-5]
          Length = 345

 Score =  403 bits (1035), Expect = e-110,   Method: Composition-based stats.
 Identities = 205/337 (60%), Positives = 259/337 (76%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q+NWQ L KP  ++ I  G ++     +IAEPL RGF  TLGNALRRVL+SSL GAA+T
Sbjct: 9   LQRNWQSLRKPEKLD-IEPGADDTRVATIIAEPLERGFGLTLGNALRRVLLSSLHGAAVT 67

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+IDGVLHE SSI GV ED+TDI+LNIK I ++M GD  KR+T+   GP  VTAG IQT
Sbjct: 68  SVRIDGVLHEFSSIAGVREDVTDIVLNIKQIAVRMHGDGPKRMTVSATGPCEVTAGMIQT 127

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +DIEV+NP+ VIC LD  A + ME TV  G GYVPA  +R E+ PIGLI +D++YSP++
Sbjct: 128 GHDIEVMNPELVICTLDDGATLGMEFTVESGRGYVPAAANRPEDAPIGLIPVDSIYSPVR 187

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +VSY VE  R GQV DYD+L + I+T+G++T ED+VALA+RILQDQLGMFINFEEP++  
Sbjct: 188 RVSYRVEPTRVGQVTDYDRLILNIETNGAVTPEDAVALAARILQDQLGMFINFEEPQRLR 247

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+     LPFNP LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q++E +MLR  NFGRK
Sbjct: 248 AEEP-RPELPFNPNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKSEQEMLRTPNFGRK 306

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM + DWPPE+IEEL K+ ++
Sbjct: 307 SLNEIKEVLSAMGLGLGMVVQDWPPENIEELVKRSDN 343


>gi|126728199|ref|ZP_01744015.1| DNA-directed RNA polymerase subunit alpha [Sagittula stellata E-37]
 gi|126711164|gb|EBA10214.1| DNA-directed RNA polymerase subunit alpha [Sagittula stellata E-37]
          Length = 338

 Score =  403 bits (1035), Expect = e-110,   Method: Composition-based stats.
 Identities = 211/338 (62%), Positives = 262/338 (77%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E I  G +   +   +AEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLE-IKPGADPSKQATCVAEPLERGFGLTLGNALRRVLLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+K + LKM  +  KR+++  +GPGVV AGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKQVALKMEVEGPKRLSVSAKGPGVVKAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC++D  A V ME TV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ESAGIEILNRDHVICHVDEGAEVYMEFTVNTGKGYVSADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKV+Y V+  REGQVLDYDKL+M ++TDGS+T ED++A A+RILQDQL +F+NFEEP+  
Sbjct: 180 KKVAYDVQPTREGQVLDYDKLTMKVETDGSVTPEDAIAYAARILQDQLSIFVNFEEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 TRQD-DDDGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKLED 336


>gi|149915869|ref|ZP_01904393.1| DNA-directed RNA polymerase subunit alpha [Roseobacter sp. AzwK-3b]
 gi|149810192|gb|EDM70038.1| DNA-directed RNA polymerase subunit alpha [Roseobacter sp. AzwK-3b]
          Length = 338

 Score =  402 bits (1034), Expect = e-110,   Method: Composition-based stats.
 Identities = 212/339 (62%), Positives = 267/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   +  +IAEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLDVK-PGNDPMRQATVIAEPLERGFGLTLGNALRRVLLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG++L+M  +  KR++I  +GP +VTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKGVSLRMEVEGPKRLSISAKGPAIVTAGDIT 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 DSAGIEVLNKDHVICHLDDGADLFMELTVNTGKGYVAADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL++ ++TDGSIT +D+VA A+RILQDQL +F+NFEEP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTLKLETDGSITPDDAVAYAARILQDQLSIFVNFEEPEAA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E  + + L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 GRESED-EGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFEDQ 337


>gi|254488277|ref|ZP_05101482.1| DNA-directed RNA polymerase, alpha subunit [Roseobacter sp. GAI101]
 gi|214045146|gb|EEB85784.1| DNA-directed RNA polymerase, alpha subunit [Roseobacter sp. GAI101]
          Length = 338

 Score =  402 bits (1034), Expect = e-110,   Method: Composition-based stats.
 Identities = 215/338 (63%), Positives = 268/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   +  ++AEPL RGF  T+GNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPQQLDVK-PGNDPARQATVVAEPLERGFGLTMGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KG++L+M  +  KR++I  +GPGVVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGVSLRMEVEGPKRLSISAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD  A V MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ESAGIEILNRDHVICHLDDGADVYMELTVNTGKGYVAADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGSIT +D+VA A+RILQDQLG+F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSITPDDAVAFAARILQDQLGIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SRQD-DDDGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|89053108|ref|YP_508559.1| DNA-directed RNA polymerase subunit alpha [Jannaschia sp. CCS1]
 gi|119366690|sp|Q28US8|RPOA_JANSC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|88862657|gb|ABD53534.1| DNA-directed RNA polymerase subunit alpha [Jannaschia sp. CCS1]
          Length = 338

 Score =  402 bits (1034), Expect = e-110,   Method: Composition-based stats.
 Identities = 211/338 (62%), Positives = 267/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNWQELIKP  +  +  G +   +  ++AEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWQELIKPTQL-VVQPGTDPARKATVVAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQIDGVLHE SS+ GV ED+TDI+LN+KG+ ++M  +  KRV+I  +GP VVTAGDI 
Sbjct: 60  TSVQIDGVLHEFSSVAGVREDVTDIVLNLKGVAIRMDAEGPKRVSISAKGPRVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               I+VLN DHVIC+LD  A + +ELTV+ G GYV A  +R E+ PIGL+ IDA+YSP+
Sbjct: 120 ESAGIDVLNKDHVICHLDDGADLYIELTVNTGKGYVAADKNRPEDAPIGLMPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL++ ++TDGS++ +D+VA A+RI+QDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTLKLETDGSLSPDDAVAYAARIIQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 TRQD-DEDDLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IEELAKKYED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDIVDWPPDNIEELAKKYED 336


>gi|258542051|ref|YP_003187484.1| DNA-directed RNA polymerase subunit alpha [Acetobacter pasteurianus
           IFO 3283-01]
 gi|329114194|ref|ZP_08242956.1| DNA-directed RNA polymerase subunit alpha [Acetobacter pomorum
           DM001]
 gi|256633129|dbj|BAH99104.1| DNA-directed RNA polymerase alpha subunit [Acetobacter pasteurianus
           IFO 3283-01]
 gi|256639241|dbj|BAI05203.1| DNA-directed RNA polymerase alpha subunit [Acetobacter pasteurianus
           IFO 3283-07]
 gi|256642295|dbj|BAI08250.1| DNA-directed RNA polymerase alpha subunit [Acetobacter pasteurianus
           IFO 3283-22]
 gi|256648405|dbj|BAI14346.1| DNA-directed RNA polymerase alpha subunit [Acetobacter pasteurianus
           IFO 3283-32]
 gi|256651458|dbj|BAI17392.1| DNA-directed RNA polymerase alpha subunit [Acetobacter pasteurianus
           IFO 3283-01-42C]
 gi|256654449|dbj|BAI20376.1| DNA-directed RNA polymerase alpha subunit [Acetobacter pasteurianus
           IFO 3283-12]
 gi|326696270|gb|EGE47949.1| DNA-directed RNA polymerase subunit alpha [Acetobacter pomorum
           DM001]
          Length = 339

 Score =  402 bits (1034), Expect = e-110,   Method: Composition-based stats.
 Identities = 203/338 (60%), Positives = 258/338 (76%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++QKNWQ LIKP  +E    G E      ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 2   VLQKNWQSLIKPEKLEVES-GVEPARIATVVAEPLERGFGMTLGNALRRVLLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SS+ GV ED+TDI+LNIK + L+M G+  KR+ +   GPG V A  IQ
Sbjct: 61  TAVQIDGVLHEFSSVAGVREDVTDIVLNIKQLALRMHGEGPKRMMLTATGPGEVRARQIQ 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIE++NPD VIC LD    + ME  V+ G GYVPA  +R E+ PIGLI +DA+YSP+
Sbjct: 121 TGHDIEIMNPDLVICTLDDGVKLGMEFIVNMGKGYVPAAANRPEDAPIGLIPVDAIYSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VSY VE  R GQV DYDKL +T++T+G++T ED+VALA+RILQDQL +FINF+EP+  
Sbjct: 181 KRVSYKVEPTRVGQVTDYDKLLLTVETNGAVTPEDAVALAARILQDQLQLFINFDEPRPV 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E+     LPFN  LL+KV+ELELSVRS NCL+ +NI+Y+GDL+Q++E +MLR  NFGR
Sbjct: 241 QAEEPE-DDLPFNRNLLRKVDELELSVRSANCLKNDNIIYIGDLVQKSEQEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL +MGL LGMN+P WPPE+IEELAK+ ++
Sbjct: 300 KSLNEIKEVLTSMGLSLGMNVPAWPPENIEELAKRLDE 337


>gi|89070528|ref|ZP_01157817.1| DNA-directed RNA polymerase alpha subunit [Oceanicola granulosus
           HTCC2516]
 gi|89043835|gb|EAR50033.1| DNA-directed RNA polymerase alpha subunit [Oceanicola granulosus
           HTCC2516]
          Length = 338

 Score =  402 bits (1033), Expect = e-110,   Method: Composition-based stats.
 Identities = 209/339 (61%), Positives = 264/339 (77%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E    G +   +  +IAEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLEVK-PGNDPMRQATVIAEPLERGFGLTLGNALRRVLLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID VLHE SS+ GV ED+TDI+LN+KG+ ++M  +  KR+T+  +GPGVVTAGDI 
Sbjct: 60  TAVQIDNVLHEFSSVSGVREDVTDIVLNLKGVAIRMEVEGPKRLTVNAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD  A + MELTV+ G GYV A  ++ E+ PIG++ IDA+YSP+
Sbjct: 120 ESAGIEILNKDHVICHLDEGADLYMELTVNTGKGYVSADKNKPEDAPIGMMAIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGS++ +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSLSPDDAVAYAARILQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 TS-TSDDDGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFEDQ 337


>gi|326404313|ref|YP_004284395.1| DNA-directed RNA polymerase subunit alpha [Acidiphilium multivorum
           AIU301]
 gi|325051175|dbj|BAJ81513.1| DNA-directed RNA polymerase subunit alpha [Acidiphilium multivorum
           AIU301]
          Length = 339

 Score =  402 bits (1033), Expect = e-110,   Method: Composition-based stats.
 Identities = 204/337 (60%), Positives = 259/337 (76%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q+NWQ L KP  ++ I  G ++     +IAEPL RGF  TLGNALRRVL+SSL GAA+T
Sbjct: 3   LQRNWQSLRKPEKLD-IEPGADDTRVATIIAEPLERGFGLTLGNALRRVLLSSLHGAAVT 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+IDGVLHE SSI GV ED+TDI+LNIK I ++M GD  KR+T+   GP  VTAG IQT
Sbjct: 62  SVRIDGVLHEFSSIAGVREDVTDIVLNIKQIAVRMHGDGPKRMTVSATGPCEVTAGMIQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +DIEV+NP+ VIC LD  A + ME TV  G GY+PA  +R E+ PIGLI +D++YSP++
Sbjct: 122 GHDIEVMNPELVICTLDDGATLGMEFTVESGRGYLPAAANRPEDAPIGLIPVDSIYSPVR 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +VSY VE  R GQV DYD+L + I+T+G++T ED+VALA+RILQDQLGMFINFEEP++  
Sbjct: 182 RVSYRVEPTRVGQVTDYDRLILNIETNGAVTPEDAVALAARILQDQLGMFINFEEPQRLR 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+     LPFNP LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q++E +MLR  NFGRK
Sbjct: 242 AEEP-RPELPFNPNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKSEQEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM + DWPPE+IEEL K+ ++
Sbjct: 301 SLNEIKEVLSAMGLGLGMVVQDWPPENIEELVKRSDN 337


>gi|85706695|ref|ZP_01037787.1| DNA-directed RNA polymerase alpha subunit [Roseovarius sp. 217]
 gi|85668753|gb|EAQ23622.1| DNA-directed RNA polymerase alpha subunit [Roseovarius sp. 217]
          Length = 338

 Score =  402 bits (1033), Expect = e-110,   Method: Composition-based stats.
 Identities = 213/338 (63%), Positives = 267/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   + ++IAEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLDVK-PGNDPLRQAVLIAEPLERGFGLTLGNALRRVLLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID VLHE SS+ GV ED+TDI+LN+KG+ ++M  +  KR+++  +GPGVVTAGDI 
Sbjct: 60  TAVQIDNVLHEFSSVAGVREDVTDIVLNLKGVAIRMEVEGPKRLSVNAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD  A + MELTV++G GYV A  ++ E+ PIGLI IDA+YSPI
Sbjct: 120 DSAGIEILNKDHVICHLDEGADLFMELTVNQGKGYVSADKNKPEDAPIGLIPIDAIYSPI 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY V+  REGQVLDYDKL+M I+TDGSIT +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 SKVSYEVQPTREGQVLDYDKLTMKIETDGSITPDDAVAYAARILQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SRQD-DDDGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|58038831|ref|YP_190795.1| DNA-directed RNA polymerase subunit alpha [Gluconobacter oxydans
           621H]
 gi|81557187|sp|Q5FU07|RPOA_GLUOX RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|58001245|gb|AAW60139.1| DNA-directed RNA polymerase alpha chain [Gluconobacter oxydans
           621H]
          Length = 339

 Score =  402 bits (1033), Expect = e-110,   Method: Composition-based stats.
 Identities = 197/338 (58%), Positives = 258/338 (76%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++QKNWQ LIKP  +E    G        ++AEPL RGF  TLGNALRR+L+SSL+GAA+
Sbjct: 2   VLQKNWQSLIKPEKLEVE-PGPVASRIATVVAEPLERGFGMTLGNALRRILLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGVLHE S++ GV ED+TDI+LN+K + L+M G+  KR+ +   GPG VTAG IQ
Sbjct: 61  TAIQIDGVLHEFSAVPGVREDVTDIVLNVKQLALRMHGEGPKRMILTATGPGEVTAGQIQ 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             +DIE++NPD VIC LD    + ME TV+ G GYV A  +R E+ PIGLI IDA+YSP+
Sbjct: 121 AGHDIEIMNPDLVICTLDDGVKLGMEFTVNMGKGYVAAAANRPEDAPIGLIPIDAIYSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY +E  R GQV DYDKL +T++T+G++T EDS+ALA+RILQDQL +FINF+EP+  
Sbjct: 181 RRVSYKIEQTRVGQVTDYDKLLLTVETNGAVTPEDSLALAARILQDQLQLFINFDEPR-P 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V+ +     LPFN  LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q++E +MLR  NFGR
Sbjct: 240 VQHEEPQDDLPFNRNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKSEQEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++P WPPE+IE+LAK+ ++
Sbjct: 300 KSLNEIKEVLTGMGLSLGMSVPAWPPENIEDLAKRLDE 337


>gi|310816986|ref|YP_003964950.1| DNA-directed RNA polymerase alpha subunit [Ketogulonicigenium
           vulgare Y25]
 gi|308755721|gb|ADO43650.1| DNA-directed RNA polymerase alpha subunit [Ketogulonicigenium
           vulgare Y25]
          Length = 338

 Score =  402 bits (1033), Expect = e-110,   Method: Composition-based stats.
 Identities = 210/339 (61%), Positives = 265/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI +NW ELIKP  ++ +  G +   +  ++AEPL RGF  TLGNALRR+L+SSL+GAAI
Sbjct: 1   MIHRNWSELIKPTQLD-VRPGADAARQATIVAEPLERGFGLTLGNALRRILLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID VLHE SSI GV ED+TDI+LN+KG+ ++M  +  +RV+I  +GP VVTAGDI 
Sbjct: 60  TAVQIDNVLHEFSSITGVREDVTDIVLNLKGVAIRMDVEGPRRVSIQVKGPAVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             N IE+LN DHVIC+LD  A + MELTV+ G GYV A  ++ E+ PIGLI IDALYSP+
Sbjct: 120 ESNGIEILNKDHVICHLDDGASLYMELTVNTGKGYVAADRNKPEDAPIGLIAIDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYD+L+M I+T+G ++ ED+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDRLTMKIETNGGLSPEDAVAYAARILQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           +    +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 LGGAAD-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ +WPPE+IEELAKKYED+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEEWPPENIEELAKKYEDQ 337


>gi|319408741|emb|CBI82398.1| DNA-directed RNA polymerase alpha subunit [Bartonella
           schoenbuchensis R1]
          Length = 337

 Score =  402 bits (1032), Expect = e-110,   Method: Composition-based stats.
 Identities = 222/339 (65%), Positives = 271/339 (79%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+   G    N   ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVEFHADGNS--NVVSVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDIILNIK I ++M  +  K V I K GPGVV AGDI+
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIILNIKEIAIRMEEEGPKHVIICKEGPGVVRAGDIR 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME  V+ G GYVP+  +  ++  IGLI ID+LYSP+
Sbjct: 119 TVGDMEILNPEHVICTLDEGAEIRMEFIVNTGKGYVPSDRNCVDDAVIGLIPIDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQVLDYDKL++TI+T+G++ GED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKVENTREGQVLDYDKLTLTIETNGAVNGEDAVAFAARILQDQLSVFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           + E+     L FN ALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 LVEEP-ASELSFNLALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPPE+I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEIPAWPPENIDDLAKRYEDQ 336


>gi|300022565|ref|YP_003755176.1| DNA-directed RNA polymerase, subunit alpha [Hyphomicrobium
           denitrificans ATCC 51888]
 gi|299524386|gb|ADJ22855.1| DNA-directed RNA polymerase, alpha subunit [Hyphomicrobium
           denitrificans ATCC 51888]
          Length = 340

 Score =  402 bits (1032), Expect = e-110,   Method: Composition-based stats.
 Identities = 213/339 (62%), Positives = 269/339 (79%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++QKNWQ+LIKP+ +E    G++      ++AEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 3   VLQKNWQDLIKPSKLEIQT-GRDRSRIATVVAEPLERGFGMTLGNALRRVLLSSLQGAAI 61

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
             VQIDGVLHE SS+ GV ED+T+IILNIK I L++  +  KR+ + K G G VTAGDI+
Sbjct: 62  KTVQIDGVLHEFSSVPGVREDVTNIILNIKEIALRIHSEGVKRMVLKKEGAGPVTAGDIE 121

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             +++EVLNPDHVIC+LD  A +RME T   G GYV +  +R E+ PIGLI +D+LYSP+
Sbjct: 122 ASSEVEVLNPDHVICHLDQGASIRMEFTADMGKGYVASDRNRPEDAPIGLIPVDSLYSPV 181

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQ+LDYDKL+M ++TDGS+  ED+VALA+RILQDQL +FINFEEPKK 
Sbjct: 182 KKVSYKVENTREGQILDYDKLTMVVETDGSVRPEDAVALAARILQDQLAVFINFEEPKK- 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E+     L FN ALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 241 AQEEQRHPELAFNAALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 300

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL TMGL LGM +P+WPP++I+ELAK++ED+
Sbjct: 301 KSLNEIKEVLATMGLHLGMEVPNWPPDNIDELAKRFEDQ 339


>gi|217979117|ref|YP_002363264.1| DNA-directed RNA polymerase subunit alpha [Methylocella silvestris
           BL2]
 gi|254765258|sp|B8EIT5|RPOA_METSB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|217504493|gb|ACK51902.1| DNA-directed RNA polymerase, alpha subunit [Methylocella silvestris
           BL2]
          Length = 338

 Score =  402 bits (1032), Expect = e-110,   Method: Composition-based stats.
 Identities = 209/338 (61%), Positives = 263/338 (77%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQEL KPN +E I  G + +    ++A PL  GF  TLGN+LRR+L+SSL+GAAI
Sbjct: 1   MIQKNWQELTKPNKLEVIS-GDDPKRFATIVAGPLELGFGLTLGNSLRRILLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V IDGVLHE SSI GV ED+TDI+LNIK I +KM GD  KR+ + K+GPG VTAGDIQ
Sbjct: 60  TSVHIDGVLHEFSSIPGVREDVTDIVLNIKDIAIKMPGDGPKRLVLKKQGPGKVTAGDIQ 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T  DI +LNP  VIC LD  A +RME TV  G GYV A  +R E+ PIGLI ID+LYSP+
Sbjct: 120 TSGDISILNPGLVICTLDEGAEIRMEFTVHTGKGYVAADRNRAEDAPIGLIPIDSLYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQ LD DKL++ ++T+G++T ED+VA A+RILQDQL +F+NFEEP++ 
Sbjct: 180 KKVSYRVENTREGQNLDLDKLTLQVETNGALTPEDAVAFAARILQDQLNVFVNFEEPRR- 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V+   ++  L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++E +MLR  NFGR
Sbjct: 239 VEATPSIPELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSEGEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM +  WPP++I++LAK++E+
Sbjct: 299 KSLNEIKEVLAQMGLHLGMEVNGWPPDNIDDLAKRFEE 336


>gi|126736630|ref|ZP_01752370.1| DNA-directed RNA polymerase alpha subunit [Roseobacter sp. CCS2]
 gi|126713943|gb|EBA10814.1| DNA-directed RNA polymerase alpha subunit [Roseobacter sp. CCS2]
          Length = 338

 Score =  402 bits (1032), Expect = e-110,   Method: Composition-based stats.
 Identities = 208/339 (61%), Positives = 265/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E    G +   +  +IAEPL RGF  TLGNALRR+LMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLEVK-PGNDPARQATVIAEPLERGFGLTLGNALRRILMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID VLHE SS+ GV ED+TDI+LN+KG+ ++M  +  KR+++  +GPGVVTA DI 
Sbjct: 60  TAVQIDNVLHEFSSVSGVREDVTDIVLNLKGVAIRMEVEGPKRLSVQAKGPGVVTAADIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + MELTV+ G GYV A  ++ E+ PIG++++DA+YSP+
Sbjct: 120 ETAGIEVLNKDHVICHLDDGADLYMELTVNTGKGYVSADKNKPEDAPIGMMSVDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGS+T +D+VA A+RILQDQL +F+NF+EP + 
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSLTPDDAVAYAARILQDQLSIFVNFDEP-ES 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +   +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 AQAGQDDDGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFEDQ 337


>gi|126737032|ref|ZP_01752767.1| DNA-directed RNA polymerase subunit alpha [Roseobacter sp.
           SK209-2-6]
 gi|126721617|gb|EBA18320.1| DNA-directed RNA polymerase subunit alpha [Roseobacter sp.
           SK209-2-6]
          Length = 338

 Score =  401 bits (1031), Expect = e-110,   Method: Composition-based stats.
 Identities = 215/338 (63%), Positives = 266/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E    G +   +  +IAEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLEAK-PGNDPARQATIIAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KG++L+M  +  KR++I  +GP VVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGVSLRMEVEGPKRLSINAKGPAVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ESAGIEVLNRDHVICHLDDGADLFMELTVNTGKGYVSADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL++ I+TDGS+T +D++A A+RILQDQL +F+NFEEP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTLKIETDGSVTPDDALAYAARILQDQLSIFVNFEEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 NRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|114327242|ref|YP_744399.1| DNA-directed RNA polymerase subunit alpha [Granulibacter
           bethesdensis CGDNIH1]
 gi|119366685|sp|Q0BUM6|RPOA_GRABC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|114315416|gb|ABI61476.1| DNA-directed RNA polymerase alpha chain [Granulibacter bethesdensis
           CGDNIH1]
          Length = 339

 Score =  401 bits (1031), Expect = e-110,   Method: Composition-based stats.
 Identities = 203/338 (60%), Positives = 260/338 (76%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQ+NWQ LIKP  ++    G E      ++AEPL RGF  TLGNA+RR+L+SSL+GAA+
Sbjct: 2   VIQRNWQSLIKPEKLDVE-PGNEPSRIATIVAEPLERGFGMTLGNAIRRILLSSLQGAAV 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SS+ GV ED+TDI+LNIK + L+M G+  KR+ +   GPG VTAG IQ
Sbjct: 61  TAVQIDGVLHEFSSVAGVREDVTDIVLNIKQLALRMHGEGPKRMMLTATGPGEVTAGQIQ 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             +DIE++NPD V+C LD    + ME TV+ G GYVPA  +R E+ PIGLI IDA+YSP+
Sbjct: 121 AGHDIEIMNPDLVLCTLDDGVKLGMEFTVNLGKGYVPASQNRQEDSPIGLIPIDAIYSPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY VE  R GQV DYDKL +T++T+G++T EDSVALA+RILQDQL +FINFEEP ++
Sbjct: 181 RRVSYKVEPTRVGQVTDYDKLLLTVETNGAVTPEDSVALAARILQDQLQLFINFEEP-QQ 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V+ D     LPFN  LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q++E +MLR  NFGR
Sbjct: 240 VRHDEPQDDLPFNRNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKSEQEMLRTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++  WPPE+IE+LAK+ E+
Sbjct: 300 KSLNEIKEVLANMGLSLGMSVSGWPPENIEDLAKRLEE 337


>gi|84499816|ref|ZP_00998104.1| DNA-directed RNA polymerase alpha subunit [Oceanicola batsensis
           HTCC2597]
 gi|84392960|gb|EAQ05171.1| DNA-directed RNA polymerase alpha subunit [Oceanicola batsensis
           HTCC2597]
          Length = 338

 Score =  401 bits (1031), Expect = e-110,   Method: Composition-based stats.
 Identities = 212/339 (62%), Positives = 268/339 (79%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   +  ++AEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLDVK-PGFDPSRQATVVAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SSI GV ED+TD++LN+KG++L+M  +  KR++I  +GPGVVTA +I 
Sbjct: 60  TSVQIDNVLHEFSSIAGVREDVTDVVLNLKGVSLRMDVEGPKRLSINAKGPGVVTAAEIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN +HVIC+LD  A + MELTV+ G GYVPA  ++ E+ PIGLI IDA+YSPI
Sbjct: 120 ESAGIEVLNKNHVICHLDEGASLFMELTVNTGKGYVPADRNKPEDAPIGLIPIDAIYSPI 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGS+T +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSVTPDDAVAYAARILQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 GRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFEDQ 337


>gi|254463868|ref|ZP_05077279.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacterales
           bacterium Y4I]
 gi|206684776|gb|EDZ45258.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacterales
           bacterium Y4I]
          Length = 338

 Score =  401 bits (1031), Expect = e-110,   Method: Composition-based stats.
 Identities = 215/338 (63%), Positives = 266/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E    G +   +  ++AEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPAQLEVK-PGNDPARQATVVAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+K ++L+M  +  KR++I  +GP VVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKQVSLRMEVEGPKRLSINAKGPAVVTAGDIA 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ETAGIEVLNRDHVICHLDDGADLFMELTVNTGKGYVSADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGSIT +D+VA A+RILQDQLG+F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSITPDDAVAFAARILQDQLGIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 GRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|49474380|ref|YP_032422.1| DNA-directed RNA polymerase subunit alpha [Bartonella quintana str.
           Toulouse]
 gi|61215920|sp|Q6FZE6|RPOA_BARQU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|49239884|emb|CAF26282.1| DNA-directed RNA polymerase alpha chain [Bartonella quintana str.
           Toulouse]
          Length = 337

 Score =  401 bits (1030), Expect = e-110,   Method: Composition-based stats.
 Identities = 221/339 (65%), Positives = 274/339 (80%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+     +  N + +I EPL RGF  TLGNALRRVL+SSLRGAAI
Sbjct: 1   MIQKNWQELIKPNKVEFCT--HDNPNISSVIVEPLERGFGLTLGNALRRVLLSSLRGAAI 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDIILNIK I L+M  +  KRV + K GPGVV AGDI 
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIILNIKEIALRMQEEGPKRVVVCKEGPGVVRAGDIN 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME  V+ G GY+P+  +  ++  IGLI +D+LYSPI
Sbjct: 119 TVGDMEILNPEHVICTLDEGAEIRMEFIVNTGKGYIPSDRNCVDDGRIGLIPVDSLYSPI 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQVLDYDKL++TI+T+G++ GED+VA A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKVENTREGQVLDYDKLTLTIETNGAVNGEDAVAFAARILQDQLSLFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           + ++ + + L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE++MLR  NFGR
Sbjct: 239 IVDESDSE-LTFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPPE+I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEIPTWPPENIDDLAKRYEDQ 336


>gi|56695425|ref|YP_165773.1| DNA-directed RNA polymerase subunit alpha [Ruegeria pomeroyi DSS-3]
 gi|62287367|sp|Q5LW32|RPOA_SILPO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|56677162|gb|AAV93828.1| DNA-directed RNA polymerase, alpha subunit [Ruegeria pomeroyi
           DSS-3]
          Length = 338

 Score =  401 bits (1030), Expect = e-110,   Method: Composition-based stats.
 Identities = 213/338 (63%), Positives = 265/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E    G +   +  +IAEPL RGF  TLGNALRR+LMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLEVK-PGNDPARQATVIAEPLERGFGLTLGNALRRILMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           ++VQID VLHE SS+ GV ED+TDIILN+K ++L+M  +  KR+++  +GP VVTAGDI 
Sbjct: 60  SSVQIDNVLHEFSSVAGVREDVTDIILNLKQVSLRMDVEGPKRLSVNAKGPAVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + MELTV+ G GYV A  +R E+ PIGLI IDA+YSP+
Sbjct: 120 ESAGIEVLNRDHVICHLDDGADLFMELTVNTGKGYVSADKNRPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKV+Y V+  REGQVLDYDKL+M I+TDGSIT +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 KKVAYDVQPTREGQVLDYDKLTMKIETDGSITPDDAVAFAARILQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 GRQD-DDDGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|159042865|ref|YP_001531659.1| DNA-directed RNA polymerase subunit alpha [Dinoroseobacter shibae
           DFL 12]
 gi|157910625|gb|ABV92058.1| DNA-directed RNA polymerase, alpha subunit [Dinoroseobacter shibae
           DFL 12]
          Length = 343

 Score =  400 bits (1029), Expect = e-109,   Method: Composition-based stats.
 Identities = 212/339 (62%), Positives = 262/339 (77%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNWQELIKP  +E    G E   +  ++AEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 6   MIHKNWQELIKPTQLEVK-PGNEPARQATVVAEPLERGFGLTLGNALRRVLMSSLQGAAI 64

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+K + ++M  +  KRV+I  +GP VVTAGDI 
Sbjct: 65  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKQVAIRMEVEGPKRVSISAKGPRVVTAGDIS 124

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A + MEL V+ G GYV A  +R E+ PIGLI IDA++SP+
Sbjct: 125 ESAGIEVLNRDHVICHLDEGADLFMELIVNTGKGYVSADKNRPEDAPIGLIPIDAIFSPV 184

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL++ ++TDGS+T +D+VA A+RILQDQL +F+NF+EP + 
Sbjct: 185 KKVSYDVQPTREGQVLDYDKLTLKLETDGSVTPDDAVAYAARILQDQLSVFVNFDEP-EA 243

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +       L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 244 ARSQSEEDDLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 303

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPPE+IE+LAKK+ED+
Sbjct: 304 KSLNEIKEVLSGMGLHLGMDILDWPPENIEDLAKKFEDQ 342


>gi|163733783|ref|ZP_02141225.1| DNA-directed RNA polymerase subunit alpha [Roseobacter litoralis
           Och 149]
 gi|161392894|gb|EDQ17221.1| DNA-directed RNA polymerase subunit alpha [Roseobacter litoralis
           Och 149]
          Length = 338

 Score =  400 bits (1029), Expect = e-109,   Method: Composition-based stats.
 Identities = 214/338 (63%), Positives = 268/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   +  + AEPL RGF  T+GNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPQQLDVK-PGNDPARQATVTAEPLERGFGLTMGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KG++++M  +  KR++I  +GPGVVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGVSIRMEVEGPKRLSISAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD  A V MELTV++G GYV A+ ++ E+ PIGLI IDA+YSP+
Sbjct: 120 DSAGIEILNRDHVICHLDDGADVYMELTVNQGKGYVSAEKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGS+T +D+VA A+RILQDQLG+F+NFEEP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSLTPDDAVAFAARILQDQLGIFVNFEEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            + D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SRADED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|254477240|ref|ZP_05090626.1| DNA-directed RNA polymerase, alpha subunit [Ruegeria sp. R11]
 gi|214031483|gb|EEB72318.1| DNA-directed RNA polymerase, alpha subunit [Ruegeria sp. R11]
          Length = 338

 Score =  400 bits (1029), Expect = e-109,   Method: Composition-based stats.
 Identities = 214/338 (63%), Positives = 266/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   +  ++AEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLDVK-PGNDPARQATVVAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KG++L+M  +  KR++I  +GP VVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGVSLRMEVEGPKRLSINAKGPAVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN +HVIC+LD  A + MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ESAGIEVLNREHVICHLDDGADLFMELTVNTGKGYVSADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGSIT ED+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSITPEDAVAFAARILQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 GRQD-DDDGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|254460512|ref|ZP_05073928.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacterales
           bacterium HTCC2083]
 gi|206677101|gb|EDZ41588.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacteraceae
           bacterium HTCC2083]
          Length = 342

 Score =  400 bits (1029), Expect = e-109,   Method: Composition-based stats.
 Identities = 212/338 (62%), Positives = 267/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   +  ++AEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 5   MIHKNWAELIKPTQLDVK-PGNDAGRQATVVAEPLERGFGLTLGNALRRVLMSSLQGAAI 63

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG++L+M  +  KR++I  +GPG+VTAGDI 
Sbjct: 64  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKGVSLRMEVEGPKRLSINAKGPGIVTAGDIS 123

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN +HVIC+LD  A V MELTV+ G GYV A+ ++ E+ PIGLI IDA+YSP+
Sbjct: 124 DSAGIEVLNREHVICHLDDGADVYMELTVNTGKGYVAAEKNKPEDAPIGLIPIDAIYSPV 183

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGS+T +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 184 KKVSYDVQPTREGQVLDYDKLTMKVETDGSLTPDDAVAYAARILQDQLSIFVNFDEPESA 243

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             +D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 244 SAKDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 302

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 303 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 340


>gi|260577155|ref|ZP_05845132.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacter sp. SW2]
 gi|259020629|gb|EEW23948.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacter sp. SW2]
          Length = 338

 Score =  400 bits (1028), Expect = e-109,   Method: Composition-based stats.
 Identities = 218/339 (64%), Positives = 269/339 (79%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +  +  G +      +IAEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQL-VVKPGPDASRTATVIAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG++LKM  +  KR++I  +GPGVVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKGVSLKMEVEGPKRLSISAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             N IEVLN DHVIC+LD  A V MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ESNGIEVLNKDHVICHLDDGADVFMELTVNTGKGYVAADKNKPEDAPIGLIAIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M I+TDGS+T +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 KKVSYEVQPTREGQVLDYDKLTMKIETDGSLTPDDAVAYAARILQDQLSVFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           ++ D++   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 LRHDVD-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPPE+IE+LAK++ED+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPENIEDLAKRFEDQ 337


>gi|163745568|ref|ZP_02152928.1| DNA-directed RNA polymerase subunit alpha [Oceanibulbus indolifex
           HEL-45]
 gi|161382386|gb|EDQ06795.1| DNA-directed RNA polymerase subunit alpha [Oceanibulbus indolifex
           HEL-45]
          Length = 338

 Score =  400 bits (1028), Expect = e-109,   Method: Composition-based stats.
 Identities = 216/338 (63%), Positives = 268/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   +  ++AEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPQQLDVK-PGNDPARQATVMAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KG++L+M  +  KR++I  +GPGVVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGVSLRMEVEGPKRLSISAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN +HVIC+LD  A V MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ESAGIEILNREHVICHLDDGADVYMELTVNTGKGYVSADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGSIT +D+VA A+RILQDQLG+F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSITPDDAVAFAARILQDQLGIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SRQD-DDDGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPPE+IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPENIEDLAKKFED 336


>gi|119366721|sp|Q16AB8|RPOA_ROSDO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 338

 Score =  400 bits (1028), Expect = e-109,   Method: Composition-based stats.
 Identities = 213/338 (63%), Positives = 268/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   +  + AEPL RGF  T+GNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPQQLDVK-PGNDPARQATVTAEPLERGFGLTMGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KG++++M  +  KR++I  +GPGVVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGVSIRMEVEGPKRLSISAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD  A V MELTV++G GYV A+ ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ESAGIEILNRDHVICHLDDGADVYMELTVNQGKGYVSAEKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGS+T +D+VA A+RILQDQLG+F+NFEEP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSLTPDDAVAFAARILQDQLGIFVNFEEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            + D +   L FNP LLKKV++LELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SRADED-DGLEFNPLLLKKVDDLELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|163796895|ref|ZP_02190852.1| lipoyltransferase [alpha proteobacterium BAL199]
 gi|159177884|gb|EDP62433.1| lipoyltransferase [alpha proteobacterium BAL199]
          Length = 338

 Score =  400 bits (1027), Expect = e-109,   Method: Composition-based stats.
 Identities = 206/338 (60%), Positives = 264/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQ LIKP+ ++ I  G + +    ++AEPL RGF  TLGNALRR+L+SSL+GAAI
Sbjct: 1   MIQKNWQALIKPSKLD-IQAGYDPKRTATVVAEPLERGFGLTLGNALRRILLSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           +A+QIDGVLHE SS+ GV ED+TDI+LNIK + ++M G+  K++ +   GPG VTAG I+
Sbjct: 60  SAIQIDGVLHEFSSVPGVREDVTDIVLNIKSVAIRMHGEGPKKMRLKAEGPGEVTAGMIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIE++NP HVIC LD DA + MELTV  G GYV A  +R E+ PIGLI +D++YSP+
Sbjct: 120 TVGDIEIMNPKHVICTLDRDATLSMELTVETGKGYVAASANRPEDAPIGLIPVDSIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY VE+ R GQV DYDKLSMT++TDGS+T ED+VA A+RILQDQL +F+NFEEP   
Sbjct: 180 RQVSYKVENTRVGQVTDYDKLSMTLETDGSMTPEDAVAYAARILQDQLQLFVNFEEPTHR 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            + +     LPFN  LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q+TE +MLR  NFGR
Sbjct: 240 AEAE-EAHDLPFNKNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKTEPEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL +MGL LGM + +WPPE+IEELAK+ E+
Sbjct: 299 KSLNEIKEVLASMGLSLGMEITNWPPENIEELAKRLEE 336


>gi|110678754|ref|YP_681761.1| DNA-directed RNA polymerase subunit alpha [Roseobacter
           denitrificans OCh 114]
 gi|109454870|gb|ABG31075.1| DNA-directed RNA polymerase, alpha subunit [Roseobacter
           denitrificans OCh 114]
          Length = 342

 Score =  400 bits (1027), Expect = e-109,   Method: Composition-based stats.
 Identities = 213/338 (63%), Positives = 268/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   +  + AEPL RGF  T+GNALRRVLMSSL+GAAI
Sbjct: 5   MIHKNWAELIKPQQLDVK-PGNDPARQATVTAEPLERGFGLTMGNALRRVLMSSLQGAAI 63

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KG++++M  +  KR++I  +GPGVVTAGDI 
Sbjct: 64  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGVSIRMEVEGPKRLSISAKGPGVVTAGDIS 123

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD  A V MELTV++G GYV A+ ++ E+ PIGLI IDA+YSP+
Sbjct: 124 ESAGIEILNRDHVICHLDDGADVYMELTVNQGKGYVSAEKNKPEDAPIGLIPIDAIYSPV 183

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGS+T +D+VA A+RILQDQLG+F+NFEEP+  
Sbjct: 184 KKVSYDVQPTREGQVLDYDKLTMKVETDGSLTPDDAVAFAARILQDQLGIFVNFEEPESA 243

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            + D +   L FNP LLKKV++LELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 244 SRADED-DGLEFNPLLLKKVDDLELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 302

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 303 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 340


>gi|83593996|ref|YP_427748.1| DNA-directed RNA polymerase subunit alpha [Rhodospirillum rubrum
           ATCC 11170]
 gi|119366718|sp|Q2RQY4|RPOA_RHORT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|83576910|gb|ABC23461.1| DNA-directed RNA polymerase, alpha subunit [Rhodospirillum rubrum
           ATCC 11170]
          Length = 340

 Score =  399 bits (1026), Expect = e-109,   Method: Composition-based stats.
 Identities = 206/338 (60%), Positives = 262/338 (77%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN +   ++G   +    ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 3   VIQKNWQELIKPNKLMIELVGG-SKKVATVVAEPLERGFGLTLGNALRRVLLSSLQGAAV 61

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QI+GVLHE SSI GV ED+TD+ILNIKG+ L M  +  +R+T+   GPG VTA  I+
Sbjct: 62  TAIQIEGVLHEFSSIPGVREDVTDVILNIKGLALLMHSEGPRRMTLKASGPGEVTAAQIE 121

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             +DIE++NPD VIC+LD  A + ME TV  G GYVP+  +R E+ PIG I ID+++SP+
Sbjct: 122 MGSDIEIMNPDLVICHLDEGATLSMEFTVGMGKGYVPSTQNRPEDAPIGYIPIDSIFSPV 181

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY VE++R GQV DYDKLSM ++TDGS+  ED+VALA+RILQDQL +FINFEEP + 
Sbjct: 182 TKVSYRVENSRVGQVTDYDKLSMVVETDGSVGPEDAVALAARILQDQLQLFINFEEP-QA 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V E+     LPFN  LL+KV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+MLR  NFGR
Sbjct: 241 VSEEKKDDELPFNKNLLRKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEMLRTPNFGR 300

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM + +WPPE+IE+LAKK E+
Sbjct: 301 KSLNEIKEVLAQMGLHLGMEISNWPPENIEDLAKKLEE 338


>gi|86135793|ref|ZP_01054372.1| DNA-directed RNA polymerase alpha subunit [Roseobacter sp. MED193]
 gi|85826667|gb|EAQ46863.1| DNA-directed RNA polymerase alpha subunit [Roseobacter sp. MED193]
          Length = 338

 Score =  399 bits (1026), Expect = e-109,   Method: Composition-based stats.
 Identities = 214/338 (63%), Positives = 266/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E    G +   +  +IAEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLEAK-PGNDPARQATIIAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KG++L+M  +  KR++I  +GP VVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGVSLRMEVEGPKRLSINAKGPAVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN +HVIC+LD  A + MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ESAGIEVLNREHVICHLDDGADLFMELTVNTGKGYVSADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL++ I+TDGS+T +D++A A+RILQDQL +F+NFEEP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTLKIETDGSVTPDDALAYAARILQDQLSIFVNFEEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 NRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|83854948|ref|ZP_00948478.1| DNA-directed RNA polymerase alpha subunit [Sulfitobacter sp.
           NAS-14.1]
 gi|83941471|ref|ZP_00953933.1| DNA-directed RNA polymerase alpha subunit [Sulfitobacter sp. EE-36]
 gi|83842791|gb|EAP81958.1| DNA-directed RNA polymerase alpha subunit [Sulfitobacter sp.
           NAS-14.1]
 gi|83847291|gb|EAP85166.1| DNA-directed RNA polymerase alpha subunit [Sulfitobacter sp. EE-36]
          Length = 338

 Score =  399 bits (1026), Expect = e-109,   Method: Composition-based stats.
 Identities = 214/338 (63%), Positives = 269/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   +  +IAEPL RGF  T+GNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPQQLDVK-PGNDPARQATVIAEPLERGFGLTMGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG++L+M  +  KR++I  +GPGVVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKGVSLRMEVEGPKRLSISAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD +A V MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ESAGIEILNRDHVICHLDDNADVYMELTVNTGKGYVAADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGSI+ +D+VA A+RILQDQLG+F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSISPDDAVAFAARILQDQLGIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SRQD-DDDGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|163868626|ref|YP_001609835.1| DNA-directed RNA polymerase subunit alpha [Bartonella tribocorum
           CIP 105476]
 gi|189043830|sp|A9IVZ5|RPOA_BART1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|161018282|emb|CAK01840.1| DNA-directed RNA polymerase alpha subunit [Bartonella tribocorum
           CIP 105476]
          Length = 337

 Score =  399 bits (1025), Expect = e-109,   Method: Composition-based stats.
 Identities = 227/339 (66%), Positives = 274/339 (80%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E      +  N   +IAEPL RGF  TLGNALRRVL+SSLRGAAI
Sbjct: 1   MIQKNWQELIKPNKVESFT--HDNSNIISVIAEPLERGFGLTLGNALRRVLLSSLRGAAI 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDIILNIK I L+M  +  KR+ ++K GPGVV AGDI 
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIILNIKEIALRMEEEGPKRLVVYKEGPGVVRAGDIN 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNPDHVIC LD DA +RME  V+ G GYVP+  +  ++  IGLI ID+LYSPI
Sbjct: 119 TVGDMEILNPDHVICTLDEDAEIRMEFIVNTGKGYVPSDRNCVDDGRIGLIPIDSLYSPI 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQVLDYDKL++TI+T+G++ GED+VA A+RILQDQL +FINFEEP+KE
Sbjct: 179 RKVSYKVENTREGQVLDYDKLTLTIETNGAVNGEDAVAFAARILQDQLSLFINFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E+ + + L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE++MLR  NFGR
Sbjct: 239 PVEEADSE-LSFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPPE+I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEIPAWPPENIDDLAKRYEDQ 336


>gi|259416700|ref|ZP_05740620.1| DNA-directed RNA polymerase, alpha subunit [Silicibacter sp.
           TrichCH4B]
 gi|259348139|gb|EEW59916.1| DNA-directed RNA polymerase, alpha subunit [Silicibacter sp.
           TrichCH4B]
          Length = 338

 Score =  399 bits (1025), Expect = e-109,   Method: Composition-based stats.
 Identities = 213/338 (63%), Positives = 265/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E    G +   +  ++AEPL RGF  TLGNALRR+LMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLEVK-PGNDPARQATLVAEPLERGFGLTLGNALRRILMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+K ++L+M  +  KR++I  +GP VVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKQVSLRMEVEGPKRLSINAKGPAVVTAGDIA 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN +HVIC+LD  A + MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ETAGIEVLNREHVICHLDDGADLFMELTVNTGKGYVSADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL++ +DTDGSIT ED++A A+RILQDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTLKVDTDGSITPEDALAFAARILQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 GRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IEELAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEELAKKFED 336


>gi|312115711|ref|YP_004013307.1| DNA-directed RNA polymerase, subunit alpha [Rhodomicrobium
           vannielii ATCC 17100]
 gi|311220840|gb|ADP72208.1| DNA-directed RNA polymerase, alpha subunit [Rhodomicrobium
           vannielii ATCC 17100]
          Length = 346

 Score =  398 bits (1024), Expect = e-109,   Method: Composition-based stats.
 Identities = 204/338 (60%), Positives = 266/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++ KNWQ+LIKP  I  +  G   +    ++AEPL RGF  TLGNALRRVL+SSL+G A+
Sbjct: 9   VLNKNWQDLIKPGKINVV-PGANPKYVASIVAEPLERGFGLTLGNALRRVLLSSLQGGAV 67

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T + IDGVLHE SSI GV ED+TDI+LN+K + L++  +  KR+ + K GPGV  A DI+
Sbjct: 68  TTIHIDGVLHEFSSIPGVREDVTDIVLNVKEVALRIHSEGVKRMVLRKEGPGVARARDIE 127

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              D+E+LNPDHV+C LD  A VRMELT + G GYVPA+ +R ++ PIGLI +D+LYSP+
Sbjct: 128 AGPDVEILNPDHVLCTLDEGATVRMELTAAIGKGYVPAERNRPDDAPIGLIPVDSLYSPV 187

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY + + REGQ+LDYDKL++ ++T+G+++ ED+VALA+RI+QDQL +F+NFEEP+KE
Sbjct: 188 KKVSYRIANTREGQILDYDKLTLDVETNGAVSPEDAVALAARIIQDQLSIFVNFEEPRKE 247

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V E+  +  L FN ALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 248 VAEE-RIPQLEFNAALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 306

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM +P+WPPE+IEELAK++ED
Sbjct: 307 KSLNEIKEVLAGMGLHLGMEVPNWPPENIEELAKRFED 344


>gi|163739473|ref|ZP_02146883.1| DNA-directed RNA polymerase subunit alpha [Phaeobacter
           gallaeciensis BS107]
 gi|163740266|ref|ZP_02147660.1| DNA-directed RNA polymerase subunit alpha [Phaeobacter
           gallaeciensis 2.10]
 gi|161386124|gb|EDQ10499.1| DNA-directed RNA polymerase subunit alpha [Phaeobacter
           gallaeciensis 2.10]
 gi|161387226|gb|EDQ11585.1| DNA-directed RNA polymerase subunit alpha [Phaeobacter
           gallaeciensis BS107]
          Length = 338

 Score =  398 bits (1024), Expect = e-109,   Method: Composition-based stats.
 Identities = 213/338 (63%), Positives = 266/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   +  ++AEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLDVK-PGNDPARQATVVAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KG++L+M  +  KR++I  +GP VVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGVSLRMEVEGPKRLSINAKGPAVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN +HVIC+LD  A + MELTV+ G GYV A  ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ESAGIEVLNREHVICHLDDGADLFMELTVNTGKGYVSADKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M I+TDGSIT +D+VA A+RI+QDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKIETDGSITPDDAVAYAARIVQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 NRQD-DDDGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 336


>gi|84515660|ref|ZP_01003021.1| DNA-directed RNA polymerase alpha subunit [Loktanella vestfoldensis
           SKA53]
 gi|84510102|gb|EAQ06558.1| DNA-directed RNA polymerase alpha subunit [Loktanella vestfoldensis
           SKA53]
          Length = 338

 Score =  398 bits (1024), Expect = e-109,   Method: Composition-based stats.
 Identities = 206/339 (60%), Positives = 263/339 (77%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   +  M+AEPL RGF  TLGNALRR+LMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPMQLDVK-PGNDPMRQATMVAEPLERGFGLTLGNALRRILMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID VLHE SS+ GV ED+TDI+LN+KG+ ++M  +  KR+++  +GPGVVTA DI 
Sbjct: 60  TAVQIDNVLHEFSSVPGVREDVTDIVLNLKGVAIRMEVEGPKRLSVQAKGPGVVTAADIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD  A + MELTV+ G GYV A  ++ E+ PIG+I IDA++SP+
Sbjct: 120 ETAGIEILNKDHVICHLDDGADLYMELTVNTGKGYVAADKNKPEDAPIGMIVIDAIFSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGS++ +D+VA A+RILQDQL +F+NF+EP + 
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTMKVETDGSLSPDDAVAYAARILQDQLSIFVNFDEP-ES 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 ASAGSDDDGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFEDQ 337


>gi|84685391|ref|ZP_01013289.1| DNA-directed RNA polymerase alpha subunit [Maritimibacter
           alkaliphilus HTCC2654]
 gi|84666548|gb|EAQ13020.1| DNA-directed RNA polymerase alpha subunit [Rhodobacterales
           bacterium HTCC2654]
          Length = 338

 Score =  398 bits (1024), Expect = e-109,   Method: Composition-based stats.
 Identities = 209/339 (61%), Positives = 267/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   +  +IAEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLDVK-PGNDPSRQATVIAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+KG++++M  +  KR++I  +GP VVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKGVSIRMEVEGPKRLSISAKGPMVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD  A + MELTV+ G GYV A  ++ E+ PIGLI +DA+YSP+
Sbjct: 120 ESAGIEILNKDHVICHLDDGADLFMELTVNTGKGYVSADKNKPEDAPIGLIPVDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL++ ++TDGSIT +D+VA A+RI+QDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTLKVETDGSITPDDAVAFAARIIQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SRQD-DDDGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ +WPPE+IE+LAKK+ED+
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEEWPPENIEDLAKKFEDQ 337


>gi|49475770|ref|YP_033811.1| DNA-directed RNA polymerase subunit alpha [Bartonella henselae str.
           Houston-1]
 gi|51704335|sp|Q9FDC7|RPOA_BARHE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|49238577|emb|CAF27818.1| DNA-directed RNA polymerase alpha chain [Bartonella henselae str.
           Houston-1]
          Length = 337

 Score =  398 bits (1023), Expect = e-109,   Method: Composition-based stats.
 Identities = 221/339 (65%), Positives = 273/339 (80%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+     +  N + +I EPL RGF  TLGNALRRVL+SSLRGAAI
Sbjct: 1   MIQKNWQELIKPNKVEFSK--HDNPNISSVIVEPLERGFGLTLGNALRRVLLSSLRGAAI 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDIILNIK I L+M  +  KR+ + K GPGV+ AGDI 
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIILNIKEIALRMREEGPKRIVVCKEGPGVLRAGDIS 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNPDHVIC LD DA +RME  V+ G GYVP+  +  ++  IGLI +D+LYSPI
Sbjct: 119 TVGDMEILNPDHVICTLDEDAEIRMEFIVNTGKGYVPSDRNCIDDARIGLIPVDSLYSPI 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQVLDYDKL++T++T+G++ GED++A A+RILQDQL +FINF+EP+K 
Sbjct: 179 RKVSYKVENTREGQVLDYDKLTLTVETNGAVNGEDALAFAARILQDQLALFINFKEPEKP 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E+ N + L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE++MLR  NFGR
Sbjct: 239 TVEESNSE-LAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPPE+I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEVPTWPPENIDDLAKRYEDQ 336


>gi|99080120|ref|YP_612274.1| DNA-directed RNA polymerase subunit alpha [Ruegeria sp. TM1040]
 gi|119366729|sp|Q1GK04|RPOA_SILST RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|99036400|gb|ABF63012.1| DNA-directed RNA polymerase alpha subunit [Ruegeria sp. TM1040]
          Length = 338

 Score =  398 bits (1023), Expect = e-109,   Method: Composition-based stats.
 Identities = 213/338 (63%), Positives = 266/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E    G +   +  ++AEPL RGF  TLGNALRR+LMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLEVK-PGNDPARQATLVAEPLERGFGLTLGNALRRILMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+K ++L+M  +  KR++I  +GP VVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKQVSLRMEVEGPKRLSINAKGPAVVTAGDIA 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN +HVIC+LD  A + MELTV+ G GYV A+ ++ E+ PIGLI IDA+YSP+
Sbjct: 120 ETAGIEVLNREHVICHLDDGADLFMELTVNTGKGYVSAEKNKPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL++ +DTDGSIT ED++A A+RILQDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTLKVDTDGSITPEDALAFAARILQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 GRQDED-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IEELAKK+ED
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEELAKKFED 336


>gi|294675883|ref|YP_003576498.1| DNA-directed RNA polymerase subunit alpha [Rhodobacter capsulatus
           SB 1003]
 gi|294474703|gb|ADE84091.1| DNA-directed RNA polymerase, alpha subunit [Rhodobacter capsulatus
           SB 1003]
          Length = 338

 Score =  398 bits (1023), Expect = e-109,   Method: Composition-based stats.
 Identities = 221/339 (65%), Positives = 266/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E I  G + + +  +IAEPL RGF  TLGNALRRVLMSSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLE-IKAGNDPQRQATVIAEPLERGFGLTLGNALRRVLMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDIILN+KGI+LKM  +  KR++I  +GP VVT  DI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIILNLKGISLKMDVEGPKRLSISAKGPRVVTGADIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DHVIC+LD  A V MELTV+ G GYV A  +R E+ PIGLI IDA+YSP+
Sbjct: 120 ESMGIEVLNKDHVICHLDDGADVFMELTVNTGKGYVAADKNRPEDAPIGLIPIDAIYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKV+Y V+  REGQVLDYDKL+M I+TDGS+T ED+VA A+RILQDQL +F+NFEEP+  
Sbjct: 180 KKVAYDVQPTREGQVLDYDKLTMKIETDGSLTPEDAVAYAARILQDQLSIFVNFEEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            K D +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SKTDAD-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM + DWPPE+IE+LAK++ED+
Sbjct: 299 KSLNEIKEVLSSMGLHLGMEVEDWPPENIEDLAKRFEDQ 337


>gi|254294416|ref|YP_003060439.1| DNA-directed RNA polymerase subunit alpha [Hirschia baltica ATCC
           49814]
 gi|254042947|gb|ACT59742.1| DNA-directed RNA polymerase, alpha subunit [Hirschia baltica ATCC
           49814]
          Length = 341

 Score =  398 bits (1022), Expect = e-109,   Method: Composition-based stats.
 Identities = 200/335 (59%), Positives = 260/335 (77%), Gaps = 2/335 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNW+ELI+P+    +    +   +  +I EPL RGF  TLG++LRR+L+SSL+GAAIT V
Sbjct: 9   KNWKELIRPSRP-VVEHDFDAGRKASLIVEPLERGFGTTLGSSLRRILLSSLQGAAITGV 67

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           QIDGV+HE SSI GV ED+TDI+LN+K + + M  ++ KR+T+   GPGVVTAG I+   
Sbjct: 68  QIDGVVHEFSSIPGVREDVTDIVLNLKRVAISMVSETSKRMTLSASGPGVVTAGQIELPG 127

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           D+E+LNPDHVIC LD  A +RME TV+ G GYVPA  +R ++ P+G I +DA++SP+++V
Sbjct: 128 DMEILNPDHVICTLDDGANIRMEFTVASGKGYVPADRNRPDDAPLGFIPVDAIFSPVERV 187

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
            + V+  REGQVLDYDKL++T++TDGS+T ED+VA A+RILQDQL + INF+EP  E + 
Sbjct: 188 GFKVDDTREGQVLDYDKLTLTVETDGSVTPEDAVAYAARILQDQLQLLINFDEPVVEQEA 247

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +     L FNP LLKKV+ELELSVRS NCLR +NIVY+GDLIQ++EA+MLR  NFGRKSL
Sbjct: 248 EQE-PDLGFNPVLLKKVDELELSVRSANCLRNDNIVYIGDLIQKSEAEMLRTPNFGRKSL 306

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
            EIK VL TMGL LGM++P WPPE+IE+LAKKYED
Sbjct: 307 NEIKEVLATMGLHLGMDVPSWPPENIEDLAKKYED 341


>gi|319407401|emb|CBI81052.1| DNA-directed RNA polymerase alpha subunit [Bartonella sp. 1-1C]
          Length = 337

 Score =  397 bits (1021), Expect = e-109,   Method: Composition-based stats.
 Identities = 217/339 (64%), Positives = 277/339 (81%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP+ +E+      + N   ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPSKVEF--HAHNDPNIVSVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID +LHE SSI GV ED+TDIILNIK I ++M  +  KRV + K GPGVV AGDIQ
Sbjct: 59  TAVQIDSILHEFSSIPGVREDVTDIILNIKEIAIRMEEEGPKRVILCKEGPGVVKAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+ +LNP+HVIC LD DA VRMEL ++ G GYVP++ +  ++ PIGLI +D+LYSP+
Sbjct: 119 TVGDMAILNPEHVICTLDEDAEVRMELIINTGKGYVPSERNCIDDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY VE+ REGQ+LDYDKL++TI+T+G++ GED++A A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RRVSYKVENTREGQILDYDKLTLTIETNGAVNGEDAIAFAARILQDQLLVFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           + E+ + + L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 LVEEPDSE-LSFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPP++I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEIPAWPPDNIDDLAKRYEDQ 336


>gi|319404401|emb|CBI78004.1| DNA-directed RNA polymerase alpha subunit [Bartonella rochalimae
           ATCC BAA-1498]
          Length = 337

 Score =  397 bits (1021), Expect = e-108,   Method: Composition-based stats.
 Identities = 219/339 (64%), Positives = 277/339 (81%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP+ +E+      + N   ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPSKVEF--HAHNDPNIVSVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID +LHE SSI GV ED+TDIILNIK I ++M  +  KRV + K GPGVV AGDIQ
Sbjct: 59  TAVQIDSILHEFSSIPGVREDVTDIILNIKEIAIRMEEEGPKRVILCKEGPGVVKAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+ +LNP+HVIC LD DA VRMEL V+ G GYVP++ +  ++ PIGLI +D+LYSP+
Sbjct: 119 TVGDMAILNPEHVICTLDEDAEVRMELIVNTGKGYVPSERNCIDDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQ+LDYDKL++TI+T+G++ GED++A A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKVENTREGQILDYDKLTLTIETNGAVNGEDAIAFAARILQDQLLVFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           + E+ + + L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 LVEEPDSE-LSFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPP++I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEIPAWPPDNIDDLAKRYEDQ 336


>gi|319405874|emb|CBI79506.1| DNA-directed RNA polymerase alpha subunit [Bartonella sp. AR 15-3]
          Length = 337

 Score =  397 bits (1019), Expect = e-108,   Method: Composition-based stats.
 Identities = 220/339 (64%), Positives = 276/339 (81%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+      + N   ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVEF--HAHNDPNIVSVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID +LHE SSI GV ED+TDIILNIK I ++M  +  KRV + K GPGVV AGDIQ
Sbjct: 59  TAVQIDSILHEFSSIPGVREDVTDIILNIKEIAIRMEEEGPKRVILCKEGPGVVKAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T+ D+ +LNP+HVIC LD D  VRMEL V+ G GYVPA+ + T + PIGLI +D+LYSP+
Sbjct: 119 TIGDMAILNPEHVICTLDEDVEVRMELIVNTGKGYVPAERNCTNDTPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQ+LDYDKL++T++T+G++ GED++A A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKVENTREGQILDYDKLTLTVETNGAVNGEDAIAFAARILQDQLLVFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           + E+ + + L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 LIEEPDPE-LSFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPPE+I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEIPAWPPENIDDLAKRYEDQ 336


>gi|319899075|ref|YP_004159168.1| DNA-directed RNA polymerase alpha subunit [Bartonella clarridgeiae
           73]
 gi|319403039|emb|CBI76594.1| DNA-directed RNA polymerase alpha subunit [Bartonella clarridgeiae
           73]
          Length = 337

 Score =  396 bits (1018), Expect = e-108,   Method: Composition-based stats.
 Identities = 219/339 (64%), Positives = 275/339 (81%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP+ +E+      + N   ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPSKVEFHT--HNDPNIVSVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID +LHE SSI GV ED+TDIILNIK I ++M  +  KR+ + K GPGVV AGDIQ
Sbjct: 59  TAVQIDSILHEFSSIPGVREDVTDIILNIKEIAIRMEEEGPKRIILCKEGPGVVKAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+ +LNP+HVIC LD DA VRMEL V+ G GYVP++ +  ++ PIGLI +D+LYSP+
Sbjct: 119 TVGDMAILNPEHVICTLDEDAEVRMELIVNTGKGYVPSERNCVDDAPIGLIPVDSLYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQ+LDYDKL++TI+T+G++ GED++A A+RILQDQL +F+NFEEP+KE
Sbjct: 179 RKVSYKVENTREGQILDYDKLTLTIETNGAVNGEDAIAFAARILQDQLLVFVNFEEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           + E+     L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 LIEEP-ASELTFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPPE+I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEIPAWPPENIDDLAKRYEDQ 336


>gi|126724892|ref|ZP_01740735.1| DNA-directed RNA polymerase subunit alpha [Rhodobacterales
           bacterium HTCC2150]
 gi|126706056|gb|EBA05146.1| DNA-directed RNA polymerase subunit alpha [Rhodobacterales
           bacterium HTCC2150]
          Length = 338

 Score =  395 bits (1015), Expect = e-108,   Method: Composition-based stats.
 Identities = 209/338 (61%), Positives = 265/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNWQELIKPN ++    G +   +  +IAEPL RGF  T+GNALRR+LMSSL+GAAI
Sbjct: 1   MIHKNWQELIKPNQLKVQ-PGNDPSRQATVIAEPLERGFGLTMGNALRRILMSSLQGAAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TDI+LN+K + ++M  +  KR++I  +GPGVVTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDIVLNLKSVAIRMEVEGPKRLSIAAKGPGVVTAGDIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHVIC+LD  A V MELTV+ G GYV A+ ++ E+ PIGLI IDA++SP+
Sbjct: 120 DSAGIEILNKDHVICHLDDGADVFMELTVNTGKGYVSAEKNKPEDAPIGLIPIDAIFSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL++ ++TDGS+T +D+VA A+RILQDQL +F+NF+EP+  
Sbjct: 180 KKVSYDVQPTREGQVLDYDKLTLKLETDGSLTPDDAVAFAARILQDQLSIFVNFDEPESA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            + D     L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 SRAD-EEDELEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK +D
Sbjct: 299 KSLNEIKEVLSGMGLHLGMDIVDWPPDNIEDLAKKLDD 336


>gi|255264362|ref|ZP_05343704.1| DNA-directed RNA polymerase, alpha subunit [Thalassiobium sp.
           R2A62]
 gi|255106697|gb|EET49371.1| DNA-directed RNA polymerase, alpha subunit [Thalassiobium sp.
           R2A62]
          Length = 342

 Score =  395 bits (1015), Expect = e-108,   Method: Composition-based stats.
 Identities = 207/339 (61%), Positives = 265/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   +  ++AEPL RGF  T+GNALRRVLMSSL+GAAI
Sbjct: 5   MIHKNWAELIKPTQLDVK-PGNDPSRQATVVAEPLERGFGLTMGNALRRVLMSSLQGAAI 63

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID VLHE SS+ G+ ED+TDI+LN+KG+ ++M  +  KR++I  +GPGVVTAGDI 
Sbjct: 64  TAVQIDNVLHEFSSVSGLREDVTDIVLNLKGVAIRMEVEGPKRLSIQAKGPGVVTAGDIS 123

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN +HVIC+LD  A + MELTV+ G GYV A+ ++ E+ PIG+++IDA+YSP+
Sbjct: 124 ESAGIEILNKEHVICHLDDGADLFMELTVNTGKGYVSAEKNKPEDAPIGMMSIDAIYSPV 183

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGSIT +D+VA A+RILQDQL +F+NF+EP + 
Sbjct: 184 KKVSYDVQPTREGQVLDYDKLTMKVETDGSITPDDAVAFAARILQDQLSIFVNFDEP-ES 242

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                    L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 243 ASTAQEDDGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 302

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED+
Sbjct: 303 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFEDQ 341


>gi|90417743|ref|ZP_01225655.1| DNA-directed RNA polymerase, alpha subunit [Aurantimonas
           manganoxydans SI85-9A1]
 gi|90337415|gb|EAS51066.1| DNA-directed RNA polymerase, alpha subunit [Aurantimonas
           manganoxydans SI85-9A1]
          Length = 342

 Score =  394 bits (1013), Expect = e-108,   Method: Composition-based stats.
 Identities = 216/343 (62%), Positives = 269/343 (78%), Gaps = 6/343 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI  NWQ+L KPN + +   G     +  + AEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIASNWQDLTKPNQVVFKNGGSRS--KASLTAEPLERGFGLTLGNALRRVLLSSLQGAAI 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGVLHE SSI GV ED+TDI+LN+K IN+ M G+  KR+ + K+GPG+V AGDIQ
Sbjct: 59  TAIQIDGVLHEFSSIPGVREDVTDIVLNVKEINIGMQGEGPKRMVVRKQGPGIVRAGDIQ 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIEVLNP+H IC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+L+SP+
Sbjct: 119 TVGDIEVLNPEHEICTLDEGAEIRMEFTVNTGKGYVPADQNRAEDAPIGLIPVDSLFSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQ L+ DKL+M I+TDGSI+GED+VA A+RILQDQL +F+NFEEP+++
Sbjct: 179 KKVSYKVEATREGQDLNKDKLTMQIETDGSISGEDAVAYAARILQDQLSVFVNFEEPQRD 238

Query: 241 VKEDINVKSLP----FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +     +       FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  
Sbjct: 239 QRAPAGAEEQMAELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTP 298

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           NFGRKSL EIK VL +MGL LGM + DWPPE+I++LAK+YED+
Sbjct: 299 NFGRKSLNEIKEVLASMGLHLGMEVSDWPPENIDDLAKRYEDQ 341


>gi|254437251|ref|ZP_05050745.1| DNA-directed RNA polymerase, alpha subunit [Octadecabacter
           antarcticus 307]
 gi|198252697|gb|EDY77011.1| DNA-directed RNA polymerase, alpha subunit [Octadecabacter
           antarcticus 307]
          Length = 342

 Score =  394 bits (1013), Expect = e-108,   Method: Composition-based stats.
 Identities = 208/338 (61%), Positives = 264/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   +  +IAEPL RGF  TLGNALRR+LMSSL+GAAI
Sbjct: 5   MIHKNWAELIKPTQLDVQ-PGNDPSRQATVIAEPLERGFGLTLGNALRRILMSSLQGAAI 63

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID VLHE SSI GV ED+TD++LN+KG+ ++M  +  KR+ +  +GPGVVTAGDI 
Sbjct: 64  TAVQIDNVLHEFSSISGVREDVTDVVLNLKGVAIRMEVEGPKRLQVQAKGPGVVTAGDIS 123

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+LN DHV+C+LD  A + MELTV+ G+GYV A  ++ E+ PIG++ IDA+YSP+
Sbjct: 124 ESAGIEILNKDHVLCHLDEGAELYMELTVNTGNGYVAADKNKPEDAPIGMMAIDAIYSPV 183

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY V+  REGQVLDYDKL+M ++TDGSIT +D+VA A+RILQDQL +F+NF+EP + 
Sbjct: 184 KKVSYDVQPTREGQVLDYDKLTMKVETDGSITPDDAVAFAARILQDQLSIFVNFDEP-ES 242

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +   +   L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 243 AQTASDDDGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 302

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM++ DWPP++IE+LAKK+ED
Sbjct: 303 KSLNEIKEVLSGMGLHLGMDVEDWPPDNIEDLAKKFED 340


>gi|108758094|ref|YP_631525.1| DNA-directed RNA polymerase subunit alpha [Myxococcus xanthus DK
           1622]
 gi|119366701|sp|Q1D748|RPOA_MYXXD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|108461974|gb|ABF87159.1| DNA-directed RNA polymerase, alpha subunit [Myxococcus xanthus DK
           1622]
          Length = 340

 Score =  393 bits (1010), Expect = e-107,   Method: Composition-based stats.
 Identities = 164/327 (50%), Positives = 224/327 (68%), Gaps = 1/327 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
            + KNW++LIKP  +E              +AEPL RGF  TLGN+LRRVL+SSL+GAAI
Sbjct: 5   FVAKNWRDLIKPRRMEVDQ-DSATPTYGKFVAEPLERGFGTTLGNSLRRVLLSSLQGAAI 63

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T V+I+GV HE ++I  V ED+TD++LN+K + L+M  +  K + I   GP  V AGDI 
Sbjct: 64  TTVKIEGVDHEFTTIPEVSEDVTDVVLNLKEVLLRMHTNETKTLRIEAEGPKEVKAGDII 123

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T  D E+LNP H IC +     +RMELT  +G GY PA  ++    PIG I ID+L+SPI
Sbjct: 124 TDPDTEILNPGHHICTISEGGKLRMELTCRRGRGYTPANVNKVAGSPIGTIPIDSLFSPI 183

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KV+Y V +AR GQV D+DKLS+ + TDGS++ +D+VA A++I+++QL +F+NF+E ++ 
Sbjct: 184 RKVNYQVTNARVGQVTDFDKLSLEVWTDGSVSPQDAVAYAAKIIKEQLTVFVNFDETEEP 243

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V  +   +    N  L + V+ELELSVRS NCL+  NI  +GDL+QRTEA+ML+  NFGR
Sbjct: 244 VVAEAPKEEAKLNENLFRSVDELELSVRSANCLQQANIKSIGDLVQRTEAEMLKTKNFGR 303

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           KSL EIK +L  MGL LGM L +WPP+
Sbjct: 304 KSLKEIKEILAEMGLSLGMKLENWPPK 330


>gi|9837272|gb|AAG00506.1|AF285111_1 RNA polymerase alpha subunit [Bartonella henselae]
          Length = 337

 Score =  392 bits (1008), Expect = e-107,   Method: Composition-based stats.
 Identities = 219/339 (64%), Positives = 271/339 (79%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELI PN +E+     +  N + +I EPL RGF  TLGNALRRVL+S LRGAAI
Sbjct: 1   MIQKNWQELINPNKVEFSK--HDNPNISSVIVEPLERGFGLTLGNALRRVLLSYLRGAAI 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDIILNIK I L+M  +  KR+ + K GPGV+ AGDI 
Sbjct: 59  TAVQIDGVLHEFSSIPGVREDVTDIILNIKEIALRMREEGPKRIVVCKEGPGVLRAGDIS 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNPDHVIC LD DA +RME  V+ G GYVP+  +  ++  IGLI +D+LYSPI
Sbjct: 119 TVGDMEILNPDHVICTLDEDAEIRMEFIVNTGKGYVPSDRNCIDDARIGLIPVDSLYSPI 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KVSY VE+ REGQVLDYDKL++T++T+G++ GED++A A+RILQDQL +FINF+EP+K 
Sbjct: 179 RKVSYKVENTREGQVLDYDKLTLTVETNGAVNGEDALAFAARILQDQLALFINFKEPEKP 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E+ N + L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE++MLR  NFGR
Sbjct: 239 TVEESNSE-LAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPPE+I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEVPTWPPENIDDLAKRYEDQ 336


>gi|87200540|ref|YP_497797.1| DNA-directed RNA polymerase subunit alpha [Novosphingobium
           aromaticivorans DSM 12444]
 gi|119366705|sp|Q2G5B0|RPOA_NOVAD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|87136221|gb|ABD26963.1| DNA-directed RNA polymerase subunit alpha [Novosphingobium
           aromaticivorans DSM 12444]
          Length = 353

 Score =  392 bits (1008), Expect = e-107,   Method: Composition-based stats.
 Identities = 198/346 (57%), Positives = 254/346 (73%), Gaps = 11/346 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPNN+E I  G + + R   +AEPL RGF  TLGNALRRVL+SSL+GAA+T++
Sbjct: 6   KNWQELKKPNNLE-IKPGNDSKRRATFVAEPLERGFGLTLGNALRRVLLSSLQGAAVTSI 64

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LN+K I LKM G+  KR+ +   GPG V AGDI    
Sbjct: 65  KIENVLHEFSSLAGVREDVTDIVLNVKQIALKMQGEGPKRLQLSATGPGEVKAGDIAVTG 124

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+N D VIC+LD  A   MELTV  G GYVPA  +R  + PIGLI +D+LYSP+++V
Sbjct: 125 DIEVMNKDLVICHLDEGATFNMELTVDTGKGYVPAVSNRPVDAPIGLIPVDSLYSPVRQV 184

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK---- 239
           SY VE+AR GQ LDYDKL++T++TDG++T ED+VA A+RILQDQL +F++F++       
Sbjct: 185 SYKVENARIGQELDYDKLNLTVETDGTVTPEDAVAYAARILQDQLALFVHFDDQVPVGHV 244

Query: 240 ------EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                          +   N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+ML
Sbjct: 245 PMVAGVPAHAPEESDANQLNRYLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEML 304

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           R  NFGRKSL EIK VL +MGL LGM++P WPPE+IEE+AKK E +
Sbjct: 305 RTPNFGRKSLNEIKEVLSSMGLRLGMDIPGWPPENIEEMAKKLEQE 350


>gi|121601834|ref|YP_989021.1| DNA-directed RNA polymerase subunit alpha [Bartonella bacilliformis
           KC583]
 gi|158513082|sp|A1USR8|RPOA_BARBK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|120614011|gb|ABM44612.1| DNA-directed RNA polymerase, alpha subunit [Bartonella
           bacilliformis KC583]
          Length = 337

 Score =  392 bits (1006), Expect = e-107,   Method: Composition-based stats.
 Identities = 216/339 (63%), Positives = 269/339 (79%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN IE+        N   ++AEPL RGF  TLGNALRR+L+SSLRGAAI
Sbjct: 1   MIQKNWQELIKPNKIEFHAHSNP--NVLSVVAEPLERGFGLTLGNALRRILLSSLRGAAI 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQ++GVLHE SSI GV ED+ DIILNIK I ++M  +  KR+ + K GPG+V AGDI+
Sbjct: 59  TAVQVEGVLHEFSSIPGVREDVADIILNIKEIAIRMEEEGPKRIVVCKEGPGIVKAGDIR 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV D+E+LNP+HVIC LD  A +RME  V+ G GYVP+  +  ++ PIGLI ID+LYSPI
Sbjct: 119 TVGDMEILNPEHVICTLDEGAEIRMEFIVNTGKGYVPSDRNCFDDAPIGLIPIDSLYSPI 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY VE+ REGQVLDYDKL++TI+T+G++ G+D+VA A+RILQDQL +F+NF+EP+KE
Sbjct: 179 NKVSYKVENTREGQVLDYDKLTLTIETNGAVNGKDAVAFAARILQDQLSVFVNFKEPQKE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           + E+     L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE++MLR  NFGR
Sbjct: 239 LVEEQ-TSELSFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +  WPPE+I++LAK YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEISAWPPENIDDLAKHYEDQ 336


>gi|326387079|ref|ZP_08208689.1| DNA-directed RNA polymerase subunit alpha [Novosphingobium
           nitrogenifigens DSM 19370]
 gi|326208260|gb|EGD59067.1| DNA-directed RNA polymerase subunit alpha [Novosphingobium
           nitrogenifigens DSM 19370]
          Length = 353

 Score =  391 bits (1005), Expect = e-107,   Method: Composition-based stats.
 Identities = 196/346 (56%), Positives = 252/346 (72%), Gaps = 11/346 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN++E    G + + R   IAEPL RGF  TLGNALRRVL+SSL+GAA+T++
Sbjct: 6   KNWQELKKPNSLEVK-PGNDPQRRATFIAEPLERGFGLTLGNALRRVLLSSLQGAAVTSI 64

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LN+K I LKM G+  KR+ +   GPG V AGDI    
Sbjct: 65  RIENVLHEFSSLAGVREDVTDIVLNVKQIALKMQGEGPKRLQLSATGPGEVRAGDIAVTG 124

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+N D VIC+LD  A   MELT   G GYVPA  +R  + PIGLI ID+LYSP+++V
Sbjct: 125 DIEVMNKDLVICHLDEGATFNMELTADTGKGYVPAVSNRPIDAPIGLIPIDSLYSPVRQV 184

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE--- 240
           SY V++AR GQ LDYDKL++T++TDG++T ED+VA A+RILQDQL +F++F++       
Sbjct: 185 SYKVDNARIGQELDYDKLNLTVETDGTVTPEDAVAYAARILQDQLSLFVHFDDQLPTGHV 244

Query: 241 -------VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                          +   N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+ML
Sbjct: 245 AVVSGLATHAPEESDANQLNRYLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEML 304

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           R  NFGRKSL EIK VL +MGL LGM++P WPPE+IEE+AKK E +
Sbjct: 305 RTPNFGRKSLNEIKEVLSSMGLRLGMDIPGWPPENIEEMAKKLEQE 350


>gi|114771243|ref|ZP_01448663.1| DNA-directed RNA polymerase alpha subunit [alpha proteobacterium
           HTCC2255]
 gi|114548168|gb|EAU51055.1| DNA-directed RNA polymerase alpha subunit [alpha proteobacterium
           HTCC2255]
          Length = 338

 Score =  391 bits (1005), Expect = e-107,   Method: Composition-based stats.
 Identities = 214/339 (63%), Positives = 261/339 (76%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNWQELIKP  +E I  G +      +IAEPL RGF  TLGNALRRVL+SSL+G+AI
Sbjct: 1   MIHKNWQELIKPTQLE-IKPGADPLRMATVIAEPLERGFGLTLGNALRRVLLSSLQGSAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+VQID VLHE SS+ GV ED+TD++LN+KG+ + M  +  KRV+I  +GP +VTAGDI 
Sbjct: 60  TSVQIDNVLHEFSSVAGVREDVTDMVLNLKGVAIAMEVEGPKRVSISAKGPTIVTAGDIA 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IEVLN DH+IC+LD  A + MELTV  G GYV A  +R E+ PIGLI IDALYSP+
Sbjct: 120 ETAGIEVLNKDHIICHLDDGASLFMELTVDTGKGYVAADQNRPEDAPIGLIPIDALYSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KVSY V+  REGQVLDYD+L+M I+TDGS++ ED+VA A+RILQDQL  F+NF EP+  
Sbjct: 180 LKVSYDVQPTREGQVLDYDQLTMKIETDGSVSAEDAVAFAARILQDQLATFVNFNEPEAA 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++D     L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 QRQD-EEDDLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPPE+IEELAKK+ED+
Sbjct: 299 KSLNEIKEVLTVMGLHLGMDIVDWPPENIEELAKKFEDQ 337


>gi|296282607|ref|ZP_06860605.1| DNA-directed RNA polymerase subunit alpha [Citromicrobium
           bathyomarinum JL354]
          Length = 352

 Score =  390 bits (1001), Expect = e-106,   Method: Composition-based stats.
 Identities = 199/344 (57%), Positives = 254/344 (73%), Gaps = 8/344 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KP ++E    G +++ +   +AEPL RGF  TLGNALRRVL+SSL+GAAIT++
Sbjct: 6   KNWQELKKPTSLELKDTGADKKRKATFVAEPLERGFGLTLGNALRRVLLSSLQGAAITSI 65

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LN+K I LKM G+  KR+ +   GPG V AGDI    
Sbjct: 66  KIENVLHEFSSLAGVREDVTDIVLNVKQIALKMEGEGPKRLQLSATGPGAVKAGDIAVSG 125

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIE+LN D VIC LD  A + MELT   G GYVPA  +R  + PIGLI +D+LYSPIK+V
Sbjct: 126 DIEILNKDLVICQLDEGATLNMELTADTGKGYVPAVQNRPADAPIGLIPVDSLYSPIKQV 185

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE--- 240
           SY VE+AR GQ LDYDKL++TI+TDG++T ED+VA A+RILQDQL +F++FE+   +   
Sbjct: 186 SYKVENARVGQELDYDKLNLTIETDGTVTPEDAVAYAARILQDQLTLFVHFEDGIPQPSS 245

Query: 241 -----VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
                  E     +   N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+MLR 
Sbjct: 246 PMIGMAAEPQESDANQLNRYLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEMLRT 305

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            NFGRKSL EIK VL +MGL LGM++P WPPE+IEE+AKK E +
Sbjct: 306 PNFGRKSLNEIKEVLSSMGLRLGMDIPGWPPENIEEMAKKLEQE 349


>gi|332186889|ref|ZP_08388631.1| DNA-directed RNA polymerase, alpha subunit [Sphingomonas sp. S17]
 gi|332013222|gb|EGI55285.1| DNA-directed RNA polymerase, alpha subunit [Sphingomonas sp. S17]
          Length = 354

 Score =  388 bits (996), Expect = e-106,   Method: Composition-based stats.
 Identities = 187/348 (53%), Positives = 248/348 (71%), Gaps = 14/348 (4%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN +E    G + + +   +AEPL RGF  TLGNALRRVL+SSL+GAA+T++
Sbjct: 6   KNWQELKKPNALEKK--GGDGKRKATFVAEPLERGFGLTLGNALRRVLLSSLQGAAVTSI 63

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LN+K + ++M G+  KR+ +   GP  V AGDI    
Sbjct: 64  KIENVLHEFSSLAGVREDVTDIVLNVKQLAIRMQGEGPKRLQLSATGPTTVKAGDIAVSG 123

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+N D VIC+LD  A + MELT   G GYVPA  +R  + PIGLI +DALYSP+++V
Sbjct: 124 DIEVMNKDLVICHLDEGATLNMELTADIGKGYVPAASNRPADAPIGLIPVDALYSPVRQV 183

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK----- 238
           SY V+  R GQ LDYDKL+++++TDG++T ED+VA A+RILQDQL +F++F++       
Sbjct: 184 SYKVDPTRVGQDLDYDKLTLSVETDGTVTPEDAVAYAARILQDQLALFVHFDDSALTRAA 243

Query: 239 -------KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
                       +    +   N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+ +TEA+
Sbjct: 244 PVGQAAIPAAGGEPQSDAQQINRYLLKKVDELELSVRSANCLKNDNIIYIGDLVGKTEAE 303

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           MLR  NFGRKSL EIK VL +MGL LGM +P WPPE+IEE+AKK E +
Sbjct: 304 MLRTPNFGRKSLNEIKEVLSSMGLRLGMEIPGWPPENIEEMAKKLEQE 351


>gi|114704508|ref|ZP_01437416.1| DNA-directed RNA polymerase alpha subunit [Fulvimarina pelagi
           HTCC2506]
 gi|114539293|gb|EAU42413.1| DNA-directed RNA polymerase alpha subunit [Fulvimarina pelagi
           HTCC2506]
          Length = 350

 Score =  387 bits (995), Expect = e-105,   Method: Composition-based stats.
 Identities = 219/352 (62%), Positives = 271/352 (76%), Gaps = 16/352 (4%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI  NWQ+L KPN + +   G+    +  + AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIASNWQDLSKPNQVVFKGSGR---TKASLTAEPLERGFGLTLGNALRRVLLSSLQGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK IN+ M G+  KR+ + K+GPGVV AGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEINIGMQGEGPKRMVVRKQGPGVVRAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIEVLNPDH IC LD  A +RME TV+ G GY+PA  +R E+ PIGLI IDAL+SP+
Sbjct: 118 TVGDIEVLNPDHEICTLDEGAEIRMEFTVNTGKGYIPADQNRAEDAPIGLIPIDALFSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VE+ REGQ L+ DKL+M I+TDGSI+GED+VA A+RI+QDQL +F+NFEEP+++
Sbjct: 178 KKVSYKVENTREGQDLNKDKLTMQIETDGSISGEDAVAYAARIIQDQLSVFVNFEEPQRD 237

Query: 241 -------------VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
                           +  ++ L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+
Sbjct: 238 QRGMAIGAGVGGGAAAEEPMQELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQK 297

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           TEA+MLR  NFGRKSL EIK VL +MGL LGM +  WPPE+I++LAK+YED+
Sbjct: 298 TEAEMLRTPNFGRKSLNEIKEVLASMGLHLGMEVQAWPPENIDDLAKRYEDQ 349


>gi|149184338|ref|ZP_01862656.1| DNA-directed RNA polymerase subunit alpha [Erythrobacter sp. SD-21]
 gi|148831658|gb|EDL50091.1| DNA-directed RNA polymerase subunit alpha [Erythrobacter sp. SD-21]
          Length = 351

 Score =  385 bits (990), Expect = e-105,   Method: Composition-based stats.
 Identities = 198/344 (57%), Positives = 254/344 (73%), Gaps = 9/344 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN ++ I  G ++  +   +AEPL RGF  TLGNALRRVL+SSL+GAAIT++
Sbjct: 6   KNWQELKKPNTLD-IKDGGDKGRKATFVAEPLERGFGLTLGNALRRVLLSSLQGAAITSI 64

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LN+K I LKM G+  KR+ +   GPG V AGDI    
Sbjct: 65  KIENVLHEFSSLAGVREDVTDIVLNVKQIALKMEGEGLKRLQLSATGPGEVKAGDIAVTG 124

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+N D VIC+LD  A + MELT   G GY PA  +R  + PIGLI +D+LYSP+++V
Sbjct: 125 DIEVMNKDLVICHLDEGATLNMELTADSGKGYRPAVMNRPVDAPIGLIPVDSLYSPVRQV 184

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK---- 239
           SY VE+AR GQ LDYDKLS+TI+TDG++T ED+VA A+RILQDQL +F++FE+       
Sbjct: 185 SYKVENARVGQELDYDKLSLTIETDGTVTPEDAVAYAARILQDQLTLFVHFEDGIPQPSS 244

Query: 240 ----EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
               +  E     +   N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+MLR 
Sbjct: 245 AMIGQAAEPQESDTNQLNRYLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEMLRT 304

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            NFGRKSL EIK VL +MGL LGM++P WPPE+IEE+AKK E +
Sbjct: 305 PNFGRKSLNEIKEVLSSMGLRLGMDIPGWPPENIEEMAKKLEQE 348


>gi|239787588|emb|CAX84056.1| DNA-directed RNA polymerase subunit alpha [uncultured bacterium]
          Length = 339

 Score =  385 bits (989), Expect = e-105,   Method: Composition-based stats.
 Identities = 173/339 (51%), Positives = 244/339 (71%), Gaps = 3/339 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +NW ELIKP  +E +  G + + +  ++AEPL RGF  TLGNALRRVL+SSL+GAA++
Sbjct: 1   MYRNWTELIKPRKVELVGEG-DSQYKATLVAEPLERGFGTTLGNALRRVLLSSLQGAAVS 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           AV+I+GVLHE SSI GV ED+TDIILN+KG+ ++M     + +T+     GVVTAGDI  
Sbjct: 60  AVRIEGVLHEFSSIPGVLEDVTDIILNLKGVAIRMRSGVTRTMTLVADKEGVVTAGDIDC 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN-DPIGLITIDALYSPI 180
            +DIE+LNP H I  L+    + M +TV+ G GYV A     +    IG I +D  Y+P+
Sbjct: 120 GHDIEILNPGHHIATLNKSGKLNMTMTVTTGKGYVRATTGADDQPTNIGDIPLDCSYNPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VSY V +AR GQ  DYD+L + I+T+G ++ ED++ALA++ILQDQL +FINF++    
Sbjct: 180 KRVSYKVSNARVGQQTDYDRLVLDIETNGVVSPEDALALAAKILQDQLSLFINFDDIPIH 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
              D N  +  +NP L +KV+ELELSVRS NCL+ ++IVY+GDL+Q+TE++ML+  NFGR
Sbjct: 240 EGRDDNA-TPKWNPNLFRKVDELELSVRSANCLKNDDIVYIGDLVQKTESEMLKTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  M L LGM+L  WPPE++E+LA++++++
Sbjct: 299 KSLNEIKEVLEEMDLSLGMHLDGWPPENLEDLARQFDEE 337


>gi|294010565|ref|YP_003544025.1| DNA-directed RNA polymerase alpha subunit [Sphingobium japonicum
           UT26S]
 gi|292673895|dbj|BAI95413.1| DNA-directed RNA polymerase alpha subunit [Sphingobium japonicum
           UT26S]
          Length = 354

 Score =  385 bits (988), Expect = e-105,   Method: Composition-based stats.
 Identities = 197/347 (56%), Positives = 254/347 (73%), Gaps = 12/347 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN++E  V G     +   +AEPL RGF  TLGNALRRVL+SSL+GAA+T++
Sbjct: 6   KNWQELKKPNSLEIKVAGDGR-RKATFVAEPLERGFGLTLGNALRRVLLSSLQGAAVTSI 64

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LNIK + L+M GD  +R+ +   GP  V AGDI TV 
Sbjct: 65  KIENVLHEFSSLAGVREDVTDIVLNIKQVALRMEGDGPRRLQLSATGPAEVRAGDITTVG 124

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+NPD VIC+LD  A + MELT   G GYVPA  +R  + PIGLI IDALYSP+++V
Sbjct: 125 DIEVMNPDLVICHLDQGATLNMELTADVGKGYVPAVANRPADAPIGLIPIDALYSPVRQV 184

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP------ 237
           +Y V++ R GQ LDYDKLS+T++TDG++T ED+VA A+RILQDQL +F++FE+       
Sbjct: 185 AYKVDNTRVGQELDYDKLSLTVETDGTVTPEDAVAYAARILQDQLQLFVHFEDALPAAAP 244

Query: 238 -----KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                      +    +   N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+M
Sbjct: 245 AAGAAAGGSASEGESDANQINRYLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEM 304

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           LR  NFGRKSL EIK VL +MGL LGM++P WPPE+IEE+AKK E +
Sbjct: 305 LRTPNFGRKSLNEIKEVLSSMGLRLGMDIPGWPPENIEEMAKKLEQE 351


>gi|307294931|ref|ZP_07574773.1| DNA-directed RNA polymerase, alpha subunit [Sphingobium
           chlorophenolicum L-1]
 gi|306879405|gb|EFN10623.1| DNA-directed RNA polymerase, alpha subunit [Sphingobium
           chlorophenolicum L-1]
          Length = 354

 Score =  384 bits (987), Expect = e-104,   Method: Composition-based stats.
 Identities = 197/347 (56%), Positives = 254/347 (73%), Gaps = 12/347 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN++E  V G     +   +AEPL RGF  TLGNALRRVL+SSL+GAA+T++
Sbjct: 6   KNWQELKKPNSLEIKVSGDGR-RKATFVAEPLERGFGLTLGNALRRVLLSSLQGAAVTSI 64

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LNIK + L+M GD  +R+ +   GP  V AGDI TV 
Sbjct: 65  KIENVLHEFSSLAGVREDVTDIVLNIKQVALRMEGDGPRRLQLSATGPAEVRAGDITTVG 124

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+NPD VIC+LD  A + MELT   G GYVPA  +R  + PIGLI IDALYSP+++V
Sbjct: 125 DIEVMNPDLVICHLDQGATLNMELTADVGKGYVPAVANRPADAPIGLIPIDALYSPVRQV 184

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP------ 237
           +Y V++ R GQ LDYDKLS+T++TDG++T ED+VA A+RILQDQL +F++FE+       
Sbjct: 185 AYKVDNTRVGQELDYDKLSLTVETDGTVTPEDAVAYAARILQDQLQLFVHFEDALPAAAP 244

Query: 238 -----KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                      +    +   N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+M
Sbjct: 245 AAGAAAGGSASEGESDANQINRYLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEM 304

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           LR  NFGRKSL EIK VL +MGL LGM++P WPPE+IEE+AKK E +
Sbjct: 305 LRTPNFGRKSLNEIKEVLSSMGLRLGMDIPGWPPENIEEMAKKLEQE 351


>gi|115376084|ref|ZP_01463329.1| DNA-directed RNA polymerase, alpha subunit [Stigmatella aurantiaca
           DW4/3-1]
 gi|310821022|ref|YP_003953380.1| DNA-directed RNA polymerase subunit alpha [Stigmatella aurantiaca
           DW4/3-1]
 gi|115366899|gb|EAU65889.1| DNA-directed RNA polymerase, alpha subunit [Stigmatella aurantiaca
           DW4/3-1]
 gi|309394094|gb|ADO71553.1| DNA-directed RNA polymerase subunit alpha [Stigmatella aurantiaca
           DW4/3-1]
          Length = 343

 Score =  383 bits (985), Expect = e-104,   Method: Composition-based stats.
 Identities = 159/324 (49%), Positives = 222/324 (68%), Gaps = 1/324 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
            I KNW++LIKP  +E              +AEPL RGF  TLGN+LRRVL+SSL+G+AI
Sbjct: 5   FIAKNWRDLIKPRRLEVDQ-DSLSTTYGKFVAEPLERGFGTTLGNSLRRVLLSSLQGSAI 63

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V+I+ V HE +++  V ED+TDI+LN+K + L+M  +  K + I   GP  + AGDI 
Sbjct: 64  TSVKIENVDHEFTTLPEVAEDVTDIVLNLKEVLLRMHTNETKTLRIEAEGPKEIKAGDII 123

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              D+E+LNP H IC +     VRMEL+  +G GYVPA  ++    P+G I ID+L++PI
Sbjct: 124 ADQDVEILNPGHHICTVSEGGKVRMELSCRRGRGYVPASVNKVAGAPLGTIPIDSLFAPI 183

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KV+Y V +AR GQV DYDKL++ + TDGS+T +D+VA A++I+++QL +F+NF+E ++ 
Sbjct: 184 RKVNYQVTNARVGQVTDYDKLTLEVWTDGSVTPQDAVAYAAKIIKEQLTVFVNFDETEEP 243

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V  +   +    N  L + V+ELELSVRS NCL+  NI  +GDL+QRTEA+ML+  NFGR
Sbjct: 244 VVAEAPKEEAKLNENLFRSVDELELSVRSANCLQQANIKSIGDLVQRTEAEMLKTKNFGR 303

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDW 324
           KSL EIK +L  MGL LGM L +W
Sbjct: 304 KSLKEIKEILAEMGLSLGMKLENW 327


>gi|85709029|ref|ZP_01040095.1| DNA-directed RNA polymerase alpha subunit [Erythrobacter sp. NAP1]
 gi|85690563|gb|EAQ30566.1| DNA-directed RNA polymerase alpha subunit [Erythrobacter sp. NAP1]
          Length = 351

 Score =  383 bits (985), Expect = e-104,   Method: Composition-based stats.
 Identities = 198/344 (57%), Positives = 256/344 (74%), Gaps = 9/344 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN +E I  G +++ +T  +AEPL RGF  TLGNALRRVL+SSL+GAAIT++
Sbjct: 6   KNWQELKKPNALE-IKEGGDKQRKTTFVAEPLERGFGLTLGNALRRVLLSSLQGAAITSI 64

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LN+K I LKM G+  KR+ +   GP  VTAGDI    
Sbjct: 65  KIENVLHEFSSLAGVREDVTDIVLNVKQIALKMEGEGPKRLQLSMTGPAEVTAGDIAVTG 124

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+N D V+C+LD  A + MELT   G GY PA  +R  + PIGLI +D+LYSP+++V
Sbjct: 125 DIEVMNKDLVLCHLDEGATLNMELTADVGKGYSPAVQNRPADAPIGLIPVDSLYSPVRQV 184

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VE+AR GQ LDYDKLS+TI+TDG++T ED+VA A+RILQDQL +F++FE+   + + 
Sbjct: 185 SYKVENARVGQELDYDKLSLTIETDGTVTPEDAVAYAARILQDQLTLFVHFEDGIPQPQS 244

Query: 244 --------DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
                        +   N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+MLR 
Sbjct: 245 AMIGQAATPQEDDANQLNRYLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEMLRT 304

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            NFGRKSL EIK VL +MGL LGM++P WPPE+IEE+AKK E +
Sbjct: 305 PNFGRKSLNEIKEVLSSMGLRLGMDIPGWPPENIEEMAKKLEQE 348


>gi|153004800|ref|YP_001379125.1| DNA-directed RNA polymerase subunit alpha [Anaeromyxobacter sp.
           Fw109-5]
 gi|171769306|sp|A7HBP5|RPOA_ANADF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|152028373|gb|ABS26141.1| DNA-directed RNA polymerase, alpha subunit [Anaeromyxobacter sp.
           Fw109-5]
          Length = 339

 Score =  383 bits (984), Expect = e-104,   Method: Composition-based stats.
 Identities = 165/332 (49%), Positives = 224/332 (67%), Gaps = 1/332 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNW++LIKP  +  +            +AEPL RGF  TLGN+LRRVL+SSL+GAAIT+V
Sbjct: 8   KNWRDLIKPRGL-VVDQESLSNTYGKFVAEPLERGFGITLGNSLRRVLLSSLQGAAITSV 66

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+GV HE  +I  V ED+TDIILN+K + L++  +  K + I   GP  + AGDI    
Sbjct: 67  KIEGVEHEFMTIPEVAEDVTDIILNLKEVLLQIHTNEVKTLRIEADGPREIKAGDIIADG 126

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            +E+LNP H I  +     VRME+T  +G GYVPA  ++    PIG I IDAL+SPI+KV
Sbjct: 127 QVEILNPGHHILTISEGGRVRMEMTARRGRGYVPADKNKVPGQPIGTIPIDALFSPIRKV 186

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y V +AR GQ  DYDKLS+ + TDGS+   D+VA A++I+++QL +FINF+E ++  +E
Sbjct: 187 NYQVTNARVGQQTDYDKLSLEVWTDGSVAPNDAVAYAAKIVKEQLSIFINFDEAEEPAEE 246

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
              V+    N  L + V+ELELSVRS NCL+  NI  +GDL+Q+TEA+ML+  NFGRKSL
Sbjct: 247 VKPVEEQKLNENLFRSVDELELSVRSANCLQNANIKTIGDLVQKTEAEMLKTKNFGRKSL 306

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
            EIK +L  MGL LGM L +WPP++  + A K
Sbjct: 307 KEIKEILAEMGLSLGMKLENWPPKAAPQGAPK 338


>gi|149922187|ref|ZP_01910625.1| DNA-directed RNA polymerase subunit alpha [Plesiocystis pacifica
           SIR-1]
 gi|149816927|gb|EDM76412.1| DNA-directed RNA polymerase subunit alpha [Plesiocystis pacifica
           SIR-1]
          Length = 337

 Score =  383 bits (984), Expect = e-104,   Method: Composition-based stats.
 Identities = 156/331 (47%), Positives = 219/331 (66%), Gaps = 4/331 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           I +NW++LI+P  ++        ++      EPL RG+  T+GN+LRRVL+SSL+GAA+T
Sbjct: 7   IARNWRDLIRPKKLDVDN-DSLTDSYGKFTCEPLERGYGITIGNSLRRVLLSSLQGAAVT 65

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+G LHE +SI  V ED+TDIILNIK + L M   + + + I K G G VTA DIQ 
Sbjct: 66  TVRIEGALHEFTSIPAVVEDVTDIILNIKALRLSMDDATPRTLLISKTGEGPVTAADIQA 125

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            + + VL+P   I  L     ++ME+T + G GY  A  ++TE  PIG+I ID+L+SPI+
Sbjct: 126 PSGVHVLDPSQHIATLSKGGRLQMEMTCAMGRGYATADQNKTEGMPIGVIPIDSLFSPIR 185

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KV+Y V +AR G   DYD+L + + TDGS+  +D++A A++I+++QL +FIN EE  +E 
Sbjct: 186 KVNYRVTNARVGHRTDYDRLILQVWTDGSVKPDDALAYAAKIVKEQLSIFINHEEI-EET 244

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +     +    N  L + V+ELELSVRS NCL+  NI Y+GDL+QRTEA+ML+  NFGRK
Sbjct: 245 QAPSQSEQDKLNDVLWRSVDELELSVRSANCLQNANIHYIGDLVQRTEAEMLKTKNFGRK 304

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW--PPESIE 330
           SL EIK +L  MGL LGM +  W  PP + E
Sbjct: 305 SLKEIKEILAQMGLSLGMKIEGWQGPPPNRE 335


>gi|148554247|ref|YP_001261829.1| DNA-directed RNA polymerase subunit alpha [Sphingomonas wittichii
           RW1]
 gi|166229281|sp|A5V5X5|RPOA_SPHWW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|148499437|gb|ABQ67691.1| DNA-directed RNA polymerase, alpha subunit [Sphingomonas wittichii
           RW1]
          Length = 353

 Score =  383 bits (983), Expect = e-104,   Method: Composition-based stats.
 Identities = 189/348 (54%), Positives = 249/348 (71%), Gaps = 13/348 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN +E    G + + +   +AEPL RGF  TLGN+LRRVL+SSL+GAA+T++
Sbjct: 6   KNWQELKKPNGLEKKS-GGDGKRKATFVAEPLERGFGLTLGNSLRRVLLSSLQGAAVTSI 64

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LN+K I LKM GD  +R+ +   GP  VTAG I    
Sbjct: 65  KIENVLHEFSSLAGVREDVTDIVLNVKQIALKMQGDGPRRLQLSATGPAEVTAGMIAASG 124

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+N D VIC+LD  A + MELT   G GYV A  +R  + PIGLI +DALYSP+++V
Sbjct: 125 DIEVMNTDLVICHLDDGATLNMELTADVGKGYVTAAANRPVDAPIGLIPVDALYSPVRQV 184

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE------- 236
           +Y VE+ R GQ LDYDKL++TI+TDG++T ED++A ++RILQDQL +F++F++       
Sbjct: 185 AYKVENTRVGQELDYDKLTLTIETDGTVTPEDALAYSARILQDQLQLFVHFDDGMAISAP 244

Query: 237 -----PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
                       +    +   N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+
Sbjct: 245 AAGAGAAGGAAGEPEGDANQLNRYLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAE 304

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           MLR  NFGRKSL EIK VL +MGL LGM +P WPPE+IEE+AKK E +
Sbjct: 305 MLRTPNFGRKSLNEIKEVLASMGLRLGMEIPGWPPENIEEMAKKLEQE 352


>gi|94496225|ref|ZP_01302803.1| DNA-directed RNA polymerase, alpha subunit [Sphingomonas sp. SKA58]
 gi|94424404|gb|EAT09427.1| DNA-directed RNA polymerase, alpha subunit [Sphingomonas sp. SKA58]
          Length = 350

 Score =  382 bits (982), Expect = e-104,   Method: Composition-based stats.
 Identities = 196/347 (56%), Positives = 254/347 (73%), Gaps = 12/347 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN++E    G   + +   +AEPL RGF  TLGNALRRVL+SSL+GAA+T++
Sbjct: 2   KNWQELKKPNSLEIKASGDG-KRKATFVAEPLERGFGLTLGNALRRVLLSSLQGAAVTSI 60

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LNIK + LKM G+  KR+ +   GP VV AGDI  V 
Sbjct: 61  KIENVLHEFSSLTGVREDVTDIVLNIKQVALKMEGEGPKRLQLSATGPAVVKAGDISVVG 120

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+NPD VIC+LD  A + MELT   G GYVPA  +R  + PIGLI +DALYSP+++V
Sbjct: 121 DIEVMNPDLVICHLDQGATLNMELTADVGKGYVPAVANRPADAPIGLIPVDALYSPVRQV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE------- 236
           +Y V++ R GQ LDYDKLS+T++TDG++T ED+VA A+RILQDQL +F++FE+       
Sbjct: 181 AYKVDNTRVGQELDYDKLSLTLETDGTVTPEDAVAYAARILQDQLQLFVHFEDALPAAAP 240

Query: 237 ----PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                      +    +   N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+M
Sbjct: 241 ATGHAAGAAASEGESDANQINRYLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEM 300

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           LR  NFGRKSL EIK VL +MGL LGM++P WPPE+IEE+AKK E +
Sbjct: 301 LRTPNFGRKSLNEIKEVLSSMGLRLGMDIPGWPPENIEEMAKKLEQE 347


>gi|103486058|ref|YP_615619.1| DNA-directed RNA polymerase subunit alpha [Sphingopyxis alaskensis
           RB2256]
 gi|119366731|sp|Q1GVN6|RPOA_SPHAL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|98976135|gb|ABF52286.1| DNA-directed RNA polymerase, alpha subunit [Sphingopyxis alaskensis
           RB2256]
          Length = 352

 Score =  382 bits (980), Expect = e-104,   Method: Composition-based stats.
 Identities = 192/345 (55%), Positives = 252/345 (73%), Gaps = 10/345 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NWQEL KP+N+E    G + + +   +AEPL RGF  TLGNALRRVL+SSL+GAAIT++
Sbjct: 6   RNWQELKKPSNLEIKT-GGDGKRKATFVAEPLERGFGLTLGNALRRVLLSSLQGAAITSI 64

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LN+K I LKM G+  KR+ +   GP  V AGDI    
Sbjct: 65  KIENVLHEFSSLAGVREDVTDIVLNVKQIALKMEGEGPKRLQLSATGPATVKAGDIMVSG 124

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DI+V+NP+HVIC+LD  A + MEL    G GYVPA  +R  + PIGLI +D+LYSP+++V
Sbjct: 125 DIKVMNPNHVICHLDEGATLNMELVADTGKGYVPATANRPADAPIGLIPVDSLYSPVRQV 184

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP------ 237
           +Y V++AR GQ LDYDKL++T++TDG++T ED+VA A+RILQDQL +F++FEE       
Sbjct: 185 AYKVDNARIGQELDYDKLNLTVETDGTVTPEDAVAYAARILQDQLQVFVHFEEAMSDSGL 244

Query: 238 ---KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
                             N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+MLR
Sbjct: 245 IGMAAPSAASDESDVNQLNRFLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEMLR 304

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             NFGRKSL EIK VL +MGL LGM++P WPPE+IEE+AKK E +
Sbjct: 305 TPNFGRKSLNEIKEVLSSMGLRLGMDIPGWPPENIEEMAKKLEQE 349


>gi|117924180|ref|YP_864797.1| DNA-directed RNA polymerase subunit alpha [Magnetococcus sp. MC-1]
 gi|158512333|sp|A0L5Z8|RPOA_MAGSM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|117607936|gb|ABK43391.1| DNA-directed RNA polymerase subunit alpha [Magnetococcus sp. MC-1]
          Length = 340

 Score =  381 bits (979), Expect = e-104,   Method: Composition-based stats.
 Identities = 179/340 (52%), Positives = 243/340 (71%), Gaps = 4/340 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +NW ELIKP+ IE      E + +  ++AEPL RGF  TLGNALRRVL+SSL+GAA++
Sbjct: 1   MYRNWTELIKPHTIELGGDETEIQRKATLVAEPLERGFGTTLGNALRRVLLSSLQGAAVS 60

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GVLHE SS+ GV ED+TDIILNIKG+ L+M     K + +     G VTAG I+ 
Sbjct: 61  TVRIEGVLHEFSSVPGVIEDVTDIILNIKGLALRMESTGIKNIYLRVDKEGPVTAGMIEC 120

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP-IGLITIDALYSPI 180
              IE+LNPDH I  L+    + + +TV+ G GYV A+ +R +    IG I IDA Y+P+
Sbjct: 121 ETGIEILNPDHHIATLNKSGTLDITMTVTTGKGYVRAQLNREDESYAIGDIPIDASYNPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE-PKK 239
           KKV+Y VE+AR GQ  DYDKL M I+T+G +T ED++ALA++ILQDQL  FINF++ P  
Sbjct: 181 KKVAYRVENARVGQQTDYDKLIMDIETNGVVTPEDALALAAKILQDQLNPFINFDDVPTA 240

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
              E  +     +NP L +KV+ELELSVRS NCL+ ++IVY+GDL+Q++E++ML+  NFG
Sbjct: 241 HDHEMEDRPQ--WNPNLFRKVDELELSVRSANCLKNDDIVYIGDLVQKSESEMLKTPNFG 298

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           RKSL EIK VL  MGL LGM L  WPPE+I++L+K++E++
Sbjct: 299 RKSLNEIKEVLDEMGLSLGMTLDTWPPENIDDLSKQFEEE 338


>gi|56551437|ref|YP_162276.1| DNA-directed RNA polymerase subunit alpha [Zymomonas mobilis subsp.
           mobilis ZM4]
 gi|241761084|ref|ZP_04759173.1| DNA-directed RNA polymerase, alpha subunit [Zymomonas mobilis
           subsp. mobilis ATCC 10988]
 gi|260752950|ref|YP_003225843.1| DNA-directed RNA polymerase subunit alpha [Zymomonas mobilis subsp.
           mobilis NCIMB 11163]
 gi|61215794|sp|Q5NQ40|RPOA_ZYMMO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|56543011|gb|AAV89165.1| DNA-directed RNA polymerase, alpha subunit [Zymomonas mobilis
           subsp. mobilis ZM4]
 gi|241374703|gb|EER64164.1| DNA-directed RNA polymerase, alpha subunit [Zymomonas mobilis
           subsp. mobilis ATCC 10988]
 gi|258552313|gb|ACV75259.1| DNA-directed RNA polymerase, alpha subunit [Zymomonas mobilis
           subsp. mobilis NCIMB 11163]
          Length = 353

 Score =  380 bits (975), Expect = e-103,   Method: Composition-based stats.
 Identities = 197/348 (56%), Positives = 252/348 (72%), Gaps = 13/348 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN +E    G   + +   +AEPL RGF  TLGNALRRVL+SSL+GAAITA+
Sbjct: 6   KNWQELKKPNALEKKASGNG-KCKATFVAEPLERGFGLTLGNALRRVLLSSLQGAAITAI 64

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LNIK + +KM GD  +R+ I + GPGVVTAGDI    
Sbjct: 65  KIENVLHEFSSLNGVREDVTDIVLNIKQVAIKMQGDGSRRLHISRTGPGVVTAGDIAVSG 124

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+NP+ VIC+LD  AV   ELTV  G GYV A  +R  + PIGLI +DALYSP+++V
Sbjct: 125 DIEVMNPELVICHLDQGAVFNAELTVDTGKGYVAAVANRPADAPIGLIPVDALYSPVRQV 184

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE------- 236
           +Y VE+AR GQ LDYDKL +TI+TDG+I+ ED++A ++RILQDQL +F++F++       
Sbjct: 185 AYKVENARVGQELDYDKLLLTIETDGTISPEDAIAYSARILQDQLQLFVHFDDGLAPPTS 244

Query: 237 -----PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
                       +    +   N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+
Sbjct: 245 AIGQSSLPSSSSEAENSANQLNRNLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAE 304

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           MLR  NFGRKSL EIK VL  MGL LGM +P WPPE+IEE+AKK E +
Sbjct: 305 MLRTPNFGRKSLNEIKEVLSGMGLRLGMEIPGWPPENIEEMAKKLEQE 352


>gi|116749017|ref|YP_845704.1| DNA-directed RNA polymerase subunit alpha [Syntrophobacter
           fumaroxidans MPOB]
 gi|158512349|sp|A0LIL7|RPOA_SYNFM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116698081|gb|ABK17269.1| DNA-directed RNA polymerase, alpha subunit [Syntrophobacter
           fumaroxidans MPOB]
          Length = 335

 Score =  379 bits (974), Expect = e-103,   Method: Composition-based stats.
 Identities = 181/337 (53%), Positives = 239/337 (70%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q+NW+ELIKP  +E    G           EPL RGF  TLGNALRRVL+SSL+GAAIT
Sbjct: 1   MQRNWRELIKPKRLEVETKGLPN-TYGKFECEPLERGFGITLGNALRRVLLSSLQGAAIT 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V++DGVLHE S+I GV ED+TD+ILN+K +  KM  D  + V I K G G V AGDIQ 
Sbjct: 60  SVKVDGVLHEFSTIPGVLEDVTDVILNLKEVRFKMHSDGPRLVVIEKDGEGEVAAGDIQG 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              +EVLNP+  IC L+ DA +RMELTV +G GY+PA  +  EN PIG I IDA++SPI+
Sbjct: 120 GPHVEVLNPEQHICTLEKDARLRMELTVKQGKGYLPADRNIEENQPIGTIPIDAIFSPIR 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSYTV  AR  Q+ DYDKL+M I +DGS+  +D++A +++IL+DQL +FINFEE  +  
Sbjct: 180 KVSYTVTQARVAQITDYDKLTMEIWSDGSVKPDDALAYSAKILKDQLTIFINFEEEMETT 239

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +E++  + + FN  L + V+ELELSVRS NCL+  +I Y+G+L+Q+TEA+ML+  NFGRK
Sbjct: 240 EEEVRAEPV-FNDHLFRSVDELELSVRSANCLKNADIRYIGELVQKTEAEMLKTKNFGRK 298

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP-PESIEELAKKYE 337
           SL EIK +L  MGL LGM L ++P  + IE   K+ E
Sbjct: 299 SLNEIKEILTEMGLSLGMKLENFPSRDDIENRRKEQE 335


>gi|294085982|ref|YP_003552742.1| DNA-directed RNA polymerase subunit alpha [Candidatus
           Puniceispirillum marinum IMCC1322]
 gi|292665557|gb|ADE40658.1| DNA-directed RNA polymerase, alpha subunit [Candidatus
           Puniceispirillum marinum IMCC1322]
          Length = 338

 Score =  379 bits (973), Expect = e-103,   Method: Composition-based stats.
 Identities = 186/338 (55%), Positives = 257/338 (76%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI+KNW +L KP+ +E I + +   ++ ++   P  RGF  T+GNALRRVL+SSL+G+AI
Sbjct: 1   MIEKNWLDLKKPDELE-IKVSEYNPSQAVVAVGPFERGFGVTIGNALRRVLLSSLQGSAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQI GV+HE SSI GV ED+TD++LN+KG+ ++   +  KR+ +   GP  VTAG I 
Sbjct: 60  TAVQIQGVVHEFSSIPGVREDVTDLVLNLKGVAVRKDEEGSKRLRLSAEGPLAVTAGMIS 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               +E++NPDHV+C+LD  A + MELTV+ G GYVPA  +R+E+ PIGLI IDA++SP+
Sbjct: 120 ESAGVEIMNPDHVLCHLDKGASLAMELTVASGKGYVPAVANRSEDSPIGLIPIDAIFSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            +V+Y VE+AR GQ+ DYDKL +T++TDGS+T ED+VA A+RILQ+QL  FINFEEPK  
Sbjct: 180 LQVAYKVENARVGQITDYDKLLLTLETDGSVTPEDAVAYAARILQEQLQTFINFEEPKSN 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +++ +   LPF+  LL+KV+ELELSVRS NCL+ +NIVY+GDL+ +TE +MLR  NFGR
Sbjct: 240 TQDE-DPDPLPFSRNLLRKVDELELSVRSANCLKNDNIVYIGDLVLKTEHEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  M L LGM++ +WPPE++EELA++ ++
Sbjct: 299 KSLNEIKEVLKGMELELGMDIANWPPENVEELARRLDE 336


>gi|85374439|ref|YP_458501.1| DNA-directed RNA polymerase subunit alpha [Erythrobacter litoralis
           HTCC2594]
 gi|123099515|sp|Q2N9D7|RPOA_ERYLH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|84787522|gb|ABC63704.1| DNA-directed RNA polymerase alpha subunit [Erythrobacter litoralis
           HTCC2594]
          Length = 351

 Score =  379 bits (973), Expect = e-103,   Method: Composition-based stats.
 Identities = 194/344 (56%), Positives = 250/344 (72%), Gaps = 9/344 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KP  ++      ++  +   IAEPL RG+  TLGNALRRVL++SL+GAAIT++
Sbjct: 6   KNWQELKKPTQLDVKE-SSDKARKATFIAEPLERGYGLTLGNALRRVLLASLQGAAITSI 64

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+ VLHE SS+ GV ED+TDI+LN+K I LKM G+  KR+ +   GP  V AGDI    
Sbjct: 65  KIENVLHEFSSLAGVREDVTDIVLNVKQIALKMEGEGPKRLQLSATGPAEVKAGDIAVSG 124

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIEV+N D VIC+LD  A + MELT   G GYVPA  +R  + PIGLI +D+LYSPI++V
Sbjct: 125 DIEVMNKDLVICHLDEGATLNMELTADIGSGYVPAVQNRPADAPIGLIPVDSLYSPIRQV 184

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE--- 240
           SY VE AR GQ LD+DKLS+TI+TDG++T ED+VA A+RILQDQL +F++FE+   +   
Sbjct: 185 SYKVEKARVGQELDFDKLSLTIETDGTVTPEDAVAYAARILQDQLTLFVHFEDGIPQPQS 244

Query: 241 -----VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
                  E     +   N  LLKKV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+MLR 
Sbjct: 245 AMIGVAAEPQQDDANQLNRYLLKKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEMLRT 304

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            NFGRKSL EIK VL +MGL LGM++P WPPE+IEE+AKK E +
Sbjct: 305 PNFGRKSLNEIKEVLSSMGLRLGMDIPGWPPENIEEMAKKLEQE 348


>gi|39997923|ref|NP_953874.1| DNA-directed RNA polymerase subunit alpha [Geobacter sulfurreducens
           PCA]
 gi|61215992|sp|Q749B3|RPOA_GEOSL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|39984868|gb|AAR36224.1| DNA-directed RNA polymerase, alpha subunit [Geobacter
           sulfurreducens PCA]
 gi|298506861|gb|ADI85584.1| DNA-directed RNA polymerase, alpha subunit [Geobacter
           sulfurreducens KN400]
          Length = 340

 Score =  378 bits (970), Expect = e-103,   Method: Composition-based stats.
 Identities = 169/340 (49%), Positives = 231/340 (67%), Gaps = 3/340 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +NW++LI P  ++               AEP  RGF  TLGN+LRRVL+SSL+GA IT
Sbjct: 1   MYRNWRDLISPKKLQVES-ETLTNKYGKFYAEPFERGFGTTLGNSLRRVLLSSLQGAGIT 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+I GVLHE SSI GV ED+T+IILN+KG++LKM G   K V I  +G G++TAGDI T
Sbjct: 60  SVRIKGVLHEFSSIPGVTEDVTNIILNLKGVSLKMYGTEPKTVRIIHKGDGIITAGDIIT 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              +E+LNP+H I     DA + ME+ V  G GYVPA  +R E  P+G I IDAL+SPI+
Sbjct: 120 DPQVEILNPEHHIATCSKDANLEMEMVVKVGKGYVPADRNRDEKAPVGTIPIDALFSPIR 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KV++TV +AR GQ+ DYDKL++ + T+GS+  ED+VA A++IL++QL +FINF+E  +  
Sbjct: 180 KVNFTVSNARVGQMTDYDKLTLEVWTNGSVIPEDAVAFAAKILKEQLSIFINFDEEAEPS 239

Query: 242 -KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            + ++     P N  L + V+ELELSVRS NCL+   I  +G+L+ RTEA+ML+  NFGR
Sbjct: 240 GEAEVGEGESPINENLYRSVDELELSVRSANCLKNAGIKLIGELVSRTEAEMLKTQNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP-PESIEELAKKYEDK 339
           KSL EIK +L  MGL LGM L  +P PE +  L  + +D+
Sbjct: 300 KSLNEIKDILAEMGLTLGMKLEGFPDPEVMRRLRGERKDE 339


>gi|162456219|ref|YP_001618586.1| DNA-directed RNA polymerase, alpha subunit [Sorangium cellulosum
           'So ce 56']
 gi|229564257|sp|A9FGB8|RPOA_SORC5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|161166801|emb|CAN98106.1| DNA-directed RNA polymerase, alpha subunit [Sorangium cellulosum
           'So ce 56']
          Length = 346

 Score =  374 bits (961), Expect = e-101,   Method: Composition-based stats.
 Identities = 166/337 (49%), Positives = 229/337 (67%), Gaps = 1/337 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI +NW++LI+P  I  I      +       EPL RGF  T+GN+LRRVL+SSL+GAA 
Sbjct: 10  MIARNWRDLIRPKGI-SIDAESGTQFYAKFTCEPLERGFGITIGNSLRRVLLSSLQGAAA 68

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA++I+G LHE +++  V ED++DIILN+K +  K +      V I + GPG V A DIQ
Sbjct: 69  TAIRIEGALHEFTTVPDVVEDVSDIILNVKEVVFKAATPKTYSVRIDREGPGPVYARDIQ 128

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
            V  + VLNPDH+I  LD    + MELTV+ G GYVPA+ ++T   PIG I IDAL+SPI
Sbjct: 129 LVEGLSVLNPDHLIAVLDKKGPLSMELTVNVGRGYVPAERNKTPTMPIGTIPIDALFSPI 188

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KV+YTV++AR GQV DYDKL++ + T+GS++  D+VA A++IL++QL +++NFEE ++ 
Sbjct: 189 RKVNYTVQNARVGQVTDYDKLTLEVWTNGSVSPADAVAFAAKILKEQLSIWVNFEESEET 248

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             + +     P N  L + VEELELSVRS NCL+  NI  +G+L+QRTE DML+  NFGR
Sbjct: 249 SYQAVMSDDEPLNENLFRSVEELELSVRSANCLQNANITLIGELVQRTEQDMLKTKNFGR 308

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
           KSL EIK +L  MGL LGM + +WP       A++ +
Sbjct: 309 KSLKEIKEILANMGLSLGMKIDNWPQLLERWKAQQAQ 345


>gi|254449927|ref|ZP_05063364.1| DNA-directed RNA polymerase, alpha subunit [Octadecabacter
           antarcticus 238]
 gi|198264333|gb|EDY88603.1| DNA-directed RNA polymerase, alpha subunit [Octadecabacter
           antarcticus 238]
          Length = 322

 Score =  371 bits (954), Expect = e-101,   Method: Composition-based stats.
 Identities = 197/321 (61%), Positives = 253/321 (78%), Gaps = 1/321 (0%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +  G +   +  ++AEPL RGF  TLGNALRR+LMSSL+GAAITAVQID VLHE SSI G
Sbjct: 1   MKPGNDPSRQATVVAEPLERGFGLTLGNALRRILMSSLQGAAITAVQIDNVLHEFSSISG 60

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+TD++LN+KG+ ++M  +  KR+ +  +GPGVVTAGDI     IE+LN DHV+C+L
Sbjct: 61  VREDVTDVVLNLKGVAIRMEVEGPKRLQVQAKGPGVVTAGDISESAGIEILNKDHVLCHL 120

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           D  A + MELTV+ G GYV A+ ++ E+ PIG++ IDA+YSP+KKVSY V+  REGQVLD
Sbjct: 121 DEGAELYMELTVNTGKGYVAAEKNKPEDAPIGMMAIDAIYSPVKKVSYDVQPTREGQVLD 180

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           YDKL+M ++TDGSIT +D+VA A+RILQDQL +F+NF+EP+     + +   L FNP LL
Sbjct: 181 YDKLTMKVETDGSITPDDAVAFAARILQDQLSIFVNFDEPESAQAAN-DDDGLEFNPLLL 239

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           KKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGRKSL EIK VL  MGL L
Sbjct: 240 KKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRKSLNEIKEVLSGMGLHL 299

Query: 318 GMNLPDWPPESIEELAKKYED 338
           GM++ DWPP++IE+LAKK+ED
Sbjct: 300 GMDVEDWPPDNIEDLAKKFED 320


>gi|199598858|ref|ZP_03212269.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus rhamnosus
           HN001]
 gi|229552733|ref|ZP_04441458.1| DNA-directed RNA polymerase [Lactobacillus rhamnosus LMS2-1]
 gi|258509456|ref|YP_003172207.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus rhamnosus
           GG]
 gi|258540654|ref|YP_003175153.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus rhamnosus
           Lc 705]
 gi|199590270|gb|EDY98365.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus rhamnosus
           HN001]
 gi|229313939|gb|EEN79912.1| DNA-directed RNA polymerase [Lactobacillus rhamnosus LMS2-1]
 gi|257149383|emb|CAR88356.1| DNA-directed RNA polymerase, subunit alpha [Lactobacillus rhamnosus
           GG]
 gi|257152330|emb|CAR91302.1| DNA-directed RNA polymerase, subunit alpha [Lactobacillus rhamnosus
           Lc 705]
 gi|259650735|dbj|BAI42897.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus rhamnosus
           GG]
          Length = 312

 Score =  370 bits (951), Expect = e-100,   Method: Composition-based stats.
 Identities = 137/310 (44%), Positives = 200/310 (64%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E  N    + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDG
Sbjct: 3   EFEKPN----ITKVDESTNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILNIK + LKM+ D  K + I   GP  VTA DI    D+EV
Sbjct: 59  VLHEFSTIDGVLEDVTQIILNIKKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  IC +       + +TV KG GYV A  +++++ PIG++ ID++++PI +V+Y V
Sbjct: 119 LNPEQYICTVADGGHFHVRMTVKKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL++ + T+GSI+  ++++LA++IL + L +F+N  +  K  +  +  
Sbjct: 179 ESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TEADM+++ N GRKSL E+K
Sbjct: 239 EETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTNKTEADMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLADLGLGL 308


>gi|295401893|ref|ZP_06811856.1| DNA-directed RNA polymerase, alpha subunit [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312109288|ref|YP_003987604.1| DNA-directed RNA polymerase, subunit alpha [Geobacillus sp.
           Y4.1MC1]
 gi|294976023|gb|EFG51638.1| DNA-directed RNA polymerase, alpha subunit [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311214389|gb|ADP72993.1| DNA-directed RNA polymerase, alpha subunit [Geobacillus sp.
           Y4.1MC1]
          Length = 314

 Score =  370 bits (950), Expect = e-100,   Method: Composition-based stats.
 Identities = 142/313 (45%), Positives = 207/313 (66%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDG
Sbjct: 3   EIEKPR-IETVEIS-EDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILNIK + LK+  D  K + I  +G GVVTA DI   +D+E+
Sbjct: 61  VLHEFSTIDGVVEDVTAIILNIKKLALKIYSDEEKTLEIDAQGEGVVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L     +RM +T  +G GYVPA+ ++ E+ PIG+I ID++Y+P+ +V+Y V
Sbjct: 121 LNPDLHIATLAEGGRLRMRMTAKRGRGYVPAEANKREDQPIGVIPIDSIYTPVSRVAYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV DYDKL++ + TDGSI  ++++AL ++IL + L +F++  +  +  +  +  
Sbjct: 181 ENTRVGQVTDYDKLTIDVWTDGSIGPKEAIALGAKILTEHLNIFVSLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L Q+TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTQKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 AKLAELGLSLRKD 313


>gi|2896137|gb|AAC03116.1| DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa]
          Length = 358

 Score =  370 bits (949), Expect = e-100,   Method: Composition-based stats.
 Identities = 152/338 (44%), Positives = 228/338 (67%), Gaps = 9/338 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+ Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQSSVNEFLTPRHIDVQVVSQ---TRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLAKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++N DHVI NL  +  + M+L V++G GY PA   +++ D    IG + +DA +S
Sbjct: 118 DHDVEIINGDHVIANLADNGALNMKLKVARGRGYEPADARQSDEDESRSIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRVSYVVENARVEQRTNLDKLVLDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V E+   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPVVEEQEDE---IDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKY 336
           G+KSL EIK VL + GL LGM L +WPP S+ E  + +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLTERRQGH 332


>gi|95930496|ref|ZP_01313232.1| DNA-directed RNA polymerase, alpha subunit [Desulfuromonas
           acetoxidans DSM 684]
 gi|95133536|gb|EAT15199.1| DNA-directed RNA polymerase, alpha subunit [Desulfuromonas
           acetoxidans DSM 684]
          Length = 338

 Score =  370 bits (949), Expect = e-100,   Method: Composition-based stats.
 Identities = 165/338 (48%), Positives = 233/338 (68%), Gaps = 2/338 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW++LIKP  ++         N     AEP  RGF  T+GN+LRR+L+SSL+GAAIT
Sbjct: 1   MYKNWRDLIKPKRLQVDSRS-LTANYGKFFAEPFERGFGTTIGNSLRRILLSSLQGAAIT 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+I GVLHE S++ GV ED+TDIILN+K + L++ G   + + I K+G GV+TAGDI T
Sbjct: 60  SVRIKGVLHEFSTVPGVTEDVTDIILNLKSVLLRLEGQESRNIRIVKKGAGVITAGDIVT 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +++E+LNPD  I     +A V +++ VS G GYV A+ +R +  P+G I ID+++SPIK
Sbjct: 120 DSNVEILNPDLYIATCTKEADVEIDMVVSMGKGYVTAERNRDDKAPVGTIPIDSIFSPIK 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KV+Y V +AR GQ+ DYDKL++ + TD S+  ED+VA +++IL++ L MFINF+E +   
Sbjct: 180 KVNYAVTNARVGQITDYDKLTLEVWTDASVKPEDAVAYSAKILKEHLQMFINFDEEQIPE 239

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +E    +    N  L + VEELELSVRS NCL+   I  +GDL+Q+TEA+ML+  NFGRK
Sbjct: 240 EEPEEEEVQKINENLYRSVEELELSVRSANCLKNARISLIGDLVQKTEAEMLKTQNFGRK 299

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP-PESIEELAKKYED 338
           SL EIK +L  MGL LGM L ++P PE ++ L K  E+
Sbjct: 300 SLNEIKDILAEMGLTLGMKLENFPDPEYLKVLQKSREE 337


>gi|116495921|ref|YP_807655.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus casei ATCC
           334]
 gi|191639403|ref|YP_001988569.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus casei
           BL23]
 gi|227533985|ref|ZP_03964034.1| DNA-directed RNA polymerase [Lactobacillus paracasei subsp.
           paracasei ATCC 25302]
 gi|239630326|ref|ZP_04673357.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus paracasei
           subsp. paracasei 8700:2]
 gi|301067478|ref|YP_003789501.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus casei str.
           Zhang]
 gi|122262679|sp|Q035A9|RPOA_LACC3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238693011|sp|B3WAJ2|RPOA_LACCB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116106071|gb|ABJ71213.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus casei ATCC
           334]
 gi|190713705|emb|CAQ67711.1| DNA-directed RNA polymerase subunit alpha (RNAP subunit alpha)
           (Transcriptase subunit alpha) (RNA polymerase subunit
           alpha) [Lactobacillus casei BL23]
 gi|227188362|gb|EEI68429.1| DNA-directed RNA polymerase [Lactobacillus paracasei subsp.
           paracasei ATCC 25302]
 gi|239527938|gb|EEQ66939.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus paracasei
           subsp. paracasei 8700:2]
 gi|300439885|gb|ADK19651.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Lactobacillus casei str. Zhang]
 gi|327383491|gb|AEA54967.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus casei
           LC2W]
 gi|327386684|gb|AEA58158.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus casei
           BD-II]
          Length = 312

 Score =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 138/310 (44%), Positives = 200/310 (64%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E  N    + EPL RG+  TLGN+LRR+L+SSL GAAI+++QIDG
Sbjct: 3   EFEKPN----ITKVDESTNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAISSIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILNIK + LKM+ D  K + I   GP  VTA DI    D+EV
Sbjct: 59  VLHEFSTIDGVLEDVTQIILNIKKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  IC +       + +TV KG GYV A  +++++ PIG++ ID++++PI +V+Y V
Sbjct: 119 LNPEQYICTVADGGHFHVRMTVKKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL++ + T+GSI+  ++++LA++IL + L +F+N  +  K  +  +  
Sbjct: 179 ESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TEADM+++ N GRKSL E+K
Sbjct: 239 EETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTNKTEADMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLADLGLGL 308


>gi|239825720|ref|YP_002948344.1| DNA-directed RNA polymerase subunit alpha [Geobacillus sp. WCH70]
 gi|239806013|gb|ACS23078.1| DNA-directed RNA polymerase, alpha subunit [Geobacillus sp. WCH70]
          Length = 314

 Score =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 143/313 (45%), Positives = 207/313 (66%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDG
Sbjct: 3   EIEKPR-IETVEIS-EDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILNIK + LK+  D  K + I  +G GVVTA DI   +D+E+
Sbjct: 61  VLHEFSTIDGVVEDVTAIILNIKKLALKIYSDEEKTLEIDAQGEGVVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L     +RM +T  +G GYVPA+ ++ E+ PIG+I ID++Y+P+ +VSY V
Sbjct: 121 LNPDLHIATLAEGGRLRMRMTAKRGRGYVPAEANKREDQPIGVIPIDSIYTPVSRVSYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV DYDKL++ + TDGSI  ++++AL ++IL + L +F++  +  +  +  +  
Sbjct: 181 ENTRVGQVTDYDKLTIDVWTDGSIGPKEAIALGAKILTEHLNIFVSLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L Q+TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTQKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 AKLAELGLSLRKD 313


>gi|138893810|ref|YP_001124263.1| DNA-directed RNA polymerase subunit alpha [Geobacillus
           thermodenitrificans NG80-2]
 gi|196250997|ref|ZP_03149679.1| DNA-directed RNA polymerase, alpha subunit [Geobacillus sp.
           G11MC16]
 gi|158513827|sp|A4IJL4|RPOA_GEOTN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|134265323|gb|ABO65518.1| DNA-directed RNA polymerase alpha chain [Geobacillus
           thermodenitrificans NG80-2]
 gi|196209469|gb|EDY04246.1| DNA-directed RNA polymerase, alpha subunit [Geobacillus sp.
           G11MC16]
          Length = 314

 Score =  369 bits (947), Expect = e-100,   Method: Composition-based stats.
 Identities = 142/313 (45%), Positives = 207/313 (66%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDG
Sbjct: 3   EIEKP-KIETVELS-EDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IILN+K + LK+  D  K + I  +G GVVTA DI   +D+E+
Sbjct: 61  VLHEFSTIEGVVEDVTAIILNVKKLALKIYSDEEKTLEIDVQGEGVVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L     +RM +T  +G GYVPA+ ++ E+ PIG+I ID++Y+P+ +VSY V
Sbjct: 121 LNPDLHIATLAEGGRLRMRMTARRGRGYVPAEANKREDQPIGVIPIDSIYTPVSRVSYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV DYDKL++ + TDGSI  +++++L ++IL + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQVTDYDKLTIDVWTDGSIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L Q+TE DM+++ N GRKSL E+K
Sbjct: 241 EDDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTQKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 AKLAELGLSLRKD 313


>gi|262277117|ref|ZP_06054910.1| DNA-directed RNA polymerase, alpha subunit [alpha proteobacterium
           HIMB114]
 gi|262224220|gb|EEY74679.1| DNA-directed RNA polymerase, alpha subunit [alpha proteobacterium
           HIMB114]
          Length = 338

 Score =  369 bits (947), Expect = e-100,   Method: Composition-based stats.
 Identities = 185/339 (54%), Positives = 258/339 (76%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI+KNW+EL+KP+ ++      ++++   +  EPL +GFA TLGNALRR+L+SS++G A+
Sbjct: 1   MIEKNWKELVKPSKLDVQT--NDDKSYAKITIEPLEKGFALTLGNALRRILLSSIQGTAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGV+HE SSI GV ED+TDI+LNIK ++LK+     K++ +  +GPG + A D++
Sbjct: 59  TAIQIDGVVHEFSSINGVREDVTDIVLNIKALSLKLKNPGPKKLVLDAQGPGEIKAKDLK 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DIE+LNP+ VICNLD +  + MELTV+ G GYV A+ +R ++ P+GLI +D++YSP+
Sbjct: 119 ESADIEILNPEQVICNLDDNTKIYMELTVNTGKGYVSAEKNREKDSPLGLIPVDSVYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VSY V   REG  +DYDKL+M ++T+GS+  ED VA A+RILQDQLGMFINFEEPK+ 
Sbjct: 179 KRVSYNVSETREGLSIDYDKLTMEVETNGSVEAEDCVAYAARILQDQLGMFINFEEPKEA 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V +        FN  LL++V+ELELSVRS NCL+ +NI+Y+GDL+Q+TE +MLR  NFGR
Sbjct: 239 VAQ-QTKSEPEFNKNLLRRVDELELSVRSMNCLKNDNIIYIGDLVQKTEGEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  M L+LG+ +P+WPPE+I EL+KK E++
Sbjct: 298 KSLNEIKEVLSGMSLYLGIEIPNWPPENIAELSKKLEEE 336


>gi|330814176|ref|YP_004358415.1| DNA-directed RNA polymerase alpha subunit [Candidatus Pelagibacter
           sp. IMCC9063]
 gi|327487271|gb|AEA81676.1| DNA-directed RNA polymerase alpha subunit [Candidatus Pelagibacter
           sp. IMCC9063]
          Length = 338

 Score =  368 bits (946), Expect = e-100,   Method: Composition-based stats.
 Identities = 188/339 (55%), Positives = 257/339 (75%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW+ELIKP+ I+      E++    ++ EPL RGFA TLGNALRRVL+SS++G A+
Sbjct: 1   MIDKNWKELIKPSKIDIQA--SEDKKFAKIVVEPLERGFALTLGNALRRVLLSSIQGTAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGVLHE SSI GV ED+TDI+LNIK ++LK++ +  K++ +  +GPG +TA  I 
Sbjct: 59  TAIQIDGVLHEFSSINGVREDVTDIVLNIKSLSLKLNTNGPKKLILDAKGPGEITAKMIN 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DIE+LNPD VICNLD ++ V ME  V+ G GYV A  +R ++ P+GLI ID++YSP+
Sbjct: 119 PNPDIEILNPDQVICNLDENSKVYMEFVVNTGKGYVSADKNREKDSPLGLIPIDSVYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VSY V + REG  +DYDKL+M I+T+GS+  +D +A A+RILQDQL +F+NF+EPK+ 
Sbjct: 179 KRVSYNVSNTREGLSIDYDKLTMEIETNGSVASDDCLAFAARILQDQLSLFVNFDEPKEV 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V +    +   FN  LL++V+ELELSVRS NCL+ +NI+Y+GDL+Q+TE +MLR  NFGR
Sbjct: 239 VVQPTQSEP-EFNKNLLRRVDELELSVRSMNCLKNDNIIYIGDLVQKTEGEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK V+  M L+LG+ +P+WPPE+I EL+KK ED+
Sbjct: 298 KSLNEIKEVISGMSLYLGIEIPNWPPENISELSKKLEDE 336


>gi|56418668|ref|YP_145986.1| DNA-directed RNA polymerase subunit alpha [Geobacillus kaustophilus
           HTA426]
 gi|261417634|ref|YP_003251316.1| DNA-directed RNA polymerase subunit alpha [Geobacillus sp.
           Y412MC61]
 gi|297528509|ref|YP_003669784.1| DNA-directed RNA polymerase subunit alpha [Geobacillus sp. C56-T3]
 gi|319765292|ref|YP_004130793.1| DNA-directed RNA polymerase, subunit alpha [Geobacillus sp.
           Y412MC52]
 gi|61215780|sp|Q5L3R2|RPOA_GEOKA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|56378510|dbj|BAD74418.1| DNA-directed RNA polymerase alpha subunit [Geobacillus kaustophilus
           HTA426]
 gi|261374091|gb|ACX76834.1| DNA-directed RNA polymerase, alpha subunit [Geobacillus sp.
           Y412MC61]
 gi|297251761|gb|ADI25207.1| DNA-directed RNA polymerase, alpha subunit [Geobacillus sp. C56-T3]
 gi|317110158|gb|ADU92650.1| DNA-directed RNA polymerase, alpha subunit [Geobacillus sp.
           Y412MC52]
          Length = 314

 Score =  368 bits (946), Expect = e-100,   Method: Composition-based stats.
 Identities = 143/313 (45%), Positives = 206/313 (65%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDG
Sbjct: 3   EIEKP-KIETVELS-EDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILNIK + LK+  D  K + I  +G GVVTA DI   +D+E+
Sbjct: 61  VLHEFSTIDGVVEDVTAIILNIKKLALKIYSDEEKTLEIDVQGEGVVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L     +RM +T  +G GYVPA+ ++ E+ PIG+I ID++Y+P+ +VSY V
Sbjct: 121 LNPDLHIATLAEGGRLRMRMTAKRGRGYVPAEANKREDQPIGVIPIDSIYTPVSRVSYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV DYDKL++ + TDGSI  +++++L ++IL + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQVTDYDKLTIDVWTDGSIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L Q+TE DM+++ N GRKSL E+K
Sbjct: 241 EDDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTQKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 AKLAELGLSLRKD 313


>gi|77918342|ref|YP_356157.1| DNA-directed RNA polymerase subunit alpha [Pelobacter carbinolicus
           DSM 2380]
 gi|90110854|sp|Q3A6M0|RPOA_PELCD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|77544425|gb|ABA87987.1| DNA-directed RNA polymerase subunit alpha [Pelobacter carbinolicus
           DSM 2380]
          Length = 338

 Score =  368 bits (946), Expect = e-100,   Method: Composition-based stats.
 Identities = 173/338 (51%), Positives = 240/338 (71%), Gaps = 2/338 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW+ELIKP  ++        +     +AEP  RGF  TLGN+LRRVL+SSL+GAAIT
Sbjct: 1   MYKNWRELIKPKRLQVDA-DSLSDTYGKFMAEPFERGFGTTLGNSLRRVLLSSLQGAAIT 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+I GVLHE S+I GV ED+TDIILN+KG+ LK+ G   + + I K+G GV+TA DI T
Sbjct: 60  SVRIKGVLHEFSNIPGVTEDVTDIILNLKGVLLKLHGSDSRNIRIVKKGAGVITAADIIT 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            + ++VLNPDH I     DA + +++ V+ G GYVPA+ +R +  P+G I ID+L+SP+K
Sbjct: 120 DSHVDVLNPDHHILTCGKDADIELDMVVAMGKGYVPAERNRDDKAPVGTIPIDSLFSPVK 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KV++TV +AR GQ+ DYDKL + + TDGS+  +D VA A++IL++QL +FINF+E  + V
Sbjct: 180 KVNFTVTNARVGQITDYDKLILEVLTDGSVRPDDGVAYAAKILKEQLQIFINFDEETETV 239

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + +S   N  L + VEELELSVRS NCL+  NI  +GDL+QR+EA+ML+  NFGRK
Sbjct: 240 VEEESEESRKINENLYRSVEELELSVRSANCLKNANIHLIGDLVQRSEAEMLKTQNFGRK 299

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP-PESIEELAKKYED 338
           SL EIK +L  MGL LGM L ++P PE ++ + +  ED
Sbjct: 300 SLNEIKDILAEMGLSLGMMLENFPDPEYLKMIQEGKED 337


>gi|313903124|ref|ZP_07836518.1| DNA-directed RNA polymerase subunit alpha [Thermaerobacter
           subterraneus DSM 13965]
 gi|313466626|gb|EFR62146.1| DNA-directed RNA polymerase subunit alpha [Thermaerobacter
           subterraneus DSM 13965]
          Length = 315

 Score =  368 bits (946), Expect = e-100,   Method: Composition-based stats.
 Identities = 128/314 (40%), Positives = 204/314 (64%), Gaps = 2/314 (0%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E+ KP  I+ + L  ++      + EPL RG+  TLGNALRRVL+SSL GAA+T+V+I
Sbjct: 1   MSEMEKPT-IQTVELS-DDGTYGRFVVEPLERGYGITLGNALRRVLLSSLPGAAVTSVRI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           +GVLHE S++ GV ED T+IILN+K + +KM  D  + + I  +G G V A DI T  D+
Sbjct: 59  EGVLHEFSTLPGVVEDTTEIILNLKELAIKMYTDEPQVLRIEAQGEGEVRAADIITPPDV 118

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++N DH+I  L+ D  + ME+TV +G GYVPA  ++  +  IG+I +D++++PI+KV++
Sbjct: 119 EIVNGDHLIATLEPDGRLFMEMTVQRGRGYVPADRNKDPDRSIGVIPVDSIFTPIRKVNF 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R G+V DYD+L++ + T+G+I  +++ + A++IL D L +F+   +  +     +
Sbjct: 179 QVENTRVGKVTDYDRLTLEVWTNGTIAPDEAASQAAQILTDHLALFLTLTDQARGTGTAV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   ++EL+LSVRS NCL+   I  +G+L+++T  DM+R+ N G+KSL E
Sbjct: 239 EKEDDARAKLLEMSIDELDLSVRSYNCLKRAGINTIGELVEKTPEDMMRVRNLGKKSLEE 298

Query: 306 IKGVLGTMGLFLGM 319
           ++  L  +GL L  
Sbjct: 299 VEEKLAALGLSLKQ 312


>gi|304405589|ref|ZP_07387248.1| DNA-directed RNA polymerase, alpha subunit [Paenibacillus
           curdlanolyticus YK9]
 gi|304345628|gb|EFM11463.1| DNA-directed RNA polymerase, alpha subunit [Paenibacillus
           curdlanolyticus YK9]
          Length = 314

 Score =  368 bits (946), Expect = e-100,   Method: Composition-based stats.
 Identities = 141/313 (45%), Positives = 209/313 (66%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  +       + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDG
Sbjct: 3   EIEKP-KIETVEL-TDNGTYGRFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T+IILN+KG++LK+  D  K + I   G G VTAGDI+  +D+E+
Sbjct: 61  VLHEFSTVPGVIEDVTEIILNLKGLSLKIHSDEEKVLEIDAEGEGNVTAGDIRADSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L   A + M +  ++G GYVPA  ++ E+ PIG+I +D++Y+PI +V+Y+V
Sbjct: 121 LNPDLHIATLASGARLHMRVFANRGRGYVPADRNKKEDQPIGVIPVDSIYTPITRVNYSV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV +YDKL++ + TDGSI  E++V+L ++IL + L +F+   +  K+ +  +  
Sbjct: 181 ENTRVGQVTNYDKLTLEVWTDGSIRPEEAVSLGAKILTEHLDLFVGLTDEAKDAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +LI +TE DM+++ N GRKSL E++
Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELITKTEEDMMKVRNLGRKSLEEVQ 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L M 
Sbjct: 301 EKLEELGLGLRME 313


>gi|49087442|gb|AAT51459.1| PA4238 [synthetic construct]
          Length = 334

 Score =  368 bits (945), Expect = e-100,   Method: Composition-based stats.
 Identities = 152/336 (45%), Positives = 228/336 (67%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+ Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQSSVNEFLTPRHIDVQVVSQ---TRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLAKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++N DHVI NL  +  + M+L V++G GY PA   +++ D    IG + +DA +S
Sbjct: 118 DHDVEIINGDHVIANLADNGALNMKLKVARGRGYEPADARQSDEDESRSIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRVSYVVENARVEQRTNLDKLVLDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V E+   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPVVEEQEDE---IDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>gi|328953130|ref|YP_004370464.1| DNA-directed RNA polymerase subunit alpha [Desulfobacca acetoxidans
           DSM 11109]
 gi|328453454|gb|AEB09283.1| DNA-directed RNA polymerase subunit alpha [Desulfobacca acetoxidans
           DSM 11109]
          Length = 336

 Score =  368 bits (944), Expect = e-100,   Method: Composition-based stats.
 Identities = 162/325 (49%), Positives = 217/325 (66%), Gaps = 1/325 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW +LI+P  +E I              EPL RGF  TLGNALRRVL+SSLRG AIT
Sbjct: 1   MHKNWTDLIRPKKLE-IDPDTHNRFYGKFTCEPLERGFGATLGNALRRVLLSSLRGTAIT 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+I G+ HE S I GV ED+T++ILN+K +  KM     K + +  R  G VTAG  +T
Sbjct: 60  SVKIKGIHHEFSPIPGVIEDVTEVILNLKAVRFKMHSQEEKVIYLEAREEGEVTAGAFKT 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              IE+LNPD  I  L  D  + +E TV  G GY PA+ ++ E   IG I +DA++SPI+
Sbjct: 120 DGTIEILNPDSHIATLARDGELFIEATVKSGKGYRPAEENKQEGQSIGTIPVDAIFSPIR 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KV++ V  AR GQ  DYDKL++ + TDGS++ ED+VALA++IL++QL +FINFEEP +E 
Sbjct: 180 KVNHIVTQARVGQQTDYDKLTLEVWTDGSVSPEDAVALAAKILKEQLTIFINFEEPCEET 239

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +E    +    N  L + V ELELSVRS NCL+  NI ++G+L+Q++EA+ML+  NFGRK
Sbjct: 240 EEKPATEISRLNENLFRPVNELELSVRSANCLKNANIRFIGELVQKSEAEMLKTKNFGRK 299

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPP 326
           SL EIK +L  MGL LGM L ++PP
Sbjct: 300 SLNEIKEILSEMGLNLGMKLENFPP 324


>gi|15599434|ref|NP_252928.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas aeruginosa
           PAO1]
 gi|107103754|ref|ZP_01367672.1| hypothetical protein PaerPA_01004825 [Pseudomonas aeruginosa PACS2]
 gi|116054394|ref|YP_788881.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|152984557|ref|YP_001346248.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas aeruginosa
           PA7]
 gi|218889433|ref|YP_002438297.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas aeruginosa
           LESB58]
 gi|254237102|ref|ZP_04930425.1| DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa
           C3719]
 gi|254242909|ref|ZP_04936231.1| DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa
           2192]
 gi|296387205|ref|ZP_06876704.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas aeruginosa
           PAb1]
 gi|313111392|ref|ZP_07797197.1| DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa
           39016]
 gi|12230944|sp|O52760|RPOA_PSEAE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|122261422|sp|Q02T55|RPOA_PSEAB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|171460895|sp|A6UZL3|RPOA_PSEA7 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|9950455|gb|AAG07626.1|AE004841_4 DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa
           PAO1]
 gi|115589615|gb|ABJ15630.1| DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|126169033|gb|EAZ54544.1| DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa
           C3719]
 gi|126196287|gb|EAZ60350.1| DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa
           2192]
 gi|150959715|gb|ABR81740.1| DNA-directed RNA polymerase, alpha subunit [Pseudomonas aeruginosa
           PA7]
 gi|218769656|emb|CAW25416.1| DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa
           LESB58]
 gi|310883699|gb|EFQ42293.1| DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa
           39016]
          Length = 333

 Score =  367 bits (943), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 152/336 (45%), Positives = 228/336 (67%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+ Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQSSVNEFLTPRHIDVQVVSQ---TRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLAKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++N DHVI NL  +  + M+L V++G GY PA   +++ D    IG + +DA +S
Sbjct: 118 DHDVEIINGDHVIANLADNGALNMKLKVARGRGYEPADARQSDEDESRSIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRVSYVVENARVEQRTNLDKLVLDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V E+   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPVVEEQEDE---IDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>gi|262197162|ref|YP_003268371.1| DNA-directed RNA polymerase, subunit alpha [Haliangium ochraceum
           DSM 14365]
 gi|262080509|gb|ACY16478.1| DNA-directed RNA polymerase, alpha subunit [Haliangium ochraceum
           DSM 14365]
          Length = 344

 Score =  366 bits (941), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 164/325 (50%), Positives = 225/325 (69%), Gaps = 4/325 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
            + KNW++LI+P  +E     Q+ +N      EPL RGF  TLGN+LRRVL+SSL+GAA 
Sbjct: 17  FMAKNWRDLIRPRMLET---EQKTDNYGKFSCEPLERGFGTTLGNSLRRVLLSSLQGAAF 73

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T V+I+  LHE SS+ GV ED+TDIILN+K   LK+  D    V + K G G  TAGDI 
Sbjct: 74  THVKIEHALHEFSSLPGVVEDVTDIILNLKETMLKVEEDRVYTVRLEKEGEGPFTAGDIS 133

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV  + +LNPDHVI +L  D  + MEL +  G GYV A+ H T +  +G + IDALYSPI
Sbjct: 134 TVTGVNILNPDHVIGHLARDGKISMELIIGTGRGYVSAERHTT-SPGVGYVPIDALYSPI 192

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +K ++TV +AR GQ  DYDKL++ + T+G +T +D+VA A++IL++QL +FINFEE  + 
Sbjct: 193 RKANFTVTNARVGQQTDYDKLTLEVWTNGGVTPDDAVAFAAKILKEQLNIFINFEEQAEP 252

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V++ ++ +    N  L + V+ELELSVRS NCL+  NI Y+G+L+Q++E++ML+  NFGR
Sbjct: 253 VEQHVDEEQEKLNENLWRTVDELELSVRSANCLQNANIKYIGELVQKSESEMLKTKNFGR 312

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL EIK +L  MGL LGM L +WP
Sbjct: 313 KSLKEIKEILAEMGLSLGMKLDNWP 337


>gi|146308898|ref|YP_001189363.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas mendocina
           ymp]
 gi|330505182|ref|YP_004382051.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas mendocina
           NK-01]
 gi|172046039|sp|A4XZ65|RPOA_PSEMY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|145577099|gb|ABP86631.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas mendocina
           ymp]
 gi|328919468|gb|AEB60299.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas mendocina
           NK-01]
          Length = 333

 Score =  366 bits (941), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 150/336 (44%), Positives = 227/336 (67%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+   +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQEVS---PTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+GPGVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLAKKGPGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++N DHVI NL  +  + M+LTV++G GY PA   +++ D    IG + +DA +S
Sbjct: 118 DHDVEIVNGDHVIANLAANGSLNMKLTVARGRGYEPADARQSDEDESRSIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++V+Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRVAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V  +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPVVVEQEDE---IDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>gi|51894182|ref|YP_076873.1| DNA-directed RNA polymerase subunit alpha [Symbiobacterium
           thermophilum IAM 14863]
 gi|61215885|sp|Q67JX1|RPOA_SYMTH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|51857871|dbj|BAD42029.1| RNA polymerase alpha subunit [Symbiobacterium thermophilum IAM
           14863]
          Length = 315

 Score =  366 bits (940), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 137/309 (44%), Positives = 208/309 (67%), Gaps = 2/309 (0%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           + KP  IE +VL  E+ +    + EPL RG+  TLGN+LRR+L+SSL GAA+T+V+IDGV
Sbjct: 4   MEKP-KIETVVL-AEDNSYGKFVVEPLERGYGITLGNSLRRILLSSLPGAAVTSVKIDGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S++ GV ED+TDIILN+K ++L+M  D  K + +   G G VTAGDI T  D+E+L
Sbjct: 62  LHEFSTLPGVVEDVTDIILNLKQLSLRMHSDEPKVLRLHAEGEGEVTAGDIHTDADVEIL 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NPD  I  LD    +  E+TVSKG GYVPA  ++T + PIG+I +D+++SPI++V+YT+E
Sbjct: 122 NPDLHIATLDKGGRLIAEITVSKGRGYVPADQNKTPDMPIGVIPVDSIFSPIRRVNYTIE 181

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
             R G   +YDKL++ + T+G+I  +++ + A++IL++ L +FI+  E   E++     +
Sbjct: 182 HTRVGNKTNYDKLTLEVWTNGAIRPDEACSWAAKILKEHLELFISLTEDADEIEVMQEKE 241

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
               N  +   +EEL+LSVRS NCL+   I  + +L+ +T+ +M+++ N G+KSL E+K 
Sbjct: 242 DDERNKLMEMTIEELDLSVRSYNCLKRAGINTIAELVSKTDEEMMKVRNLGKKSLEEVKT 301

Query: 309 VLGTMGLFL 317
            L   GL L
Sbjct: 302 KLAAFGLSL 310


>gi|86158342|ref|YP_465127.1| DNA-directed RNA polymerase subunit alpha [Anaeromyxobacter
           dehalogenans 2CP-C]
 gi|119366661|sp|Q2IJ57|RPOA_ANADE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|85774853|gb|ABC81690.1| DNA-directed RNA polymerase subunit alpha [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 339

 Score =  366 bits (940), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 163/332 (49%), Positives = 225/332 (67%), Gaps = 1/332 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNW++LIKP  +  +            +AEPL RGF  TLGN+LRRVL+SSL+GAAIT+V
Sbjct: 8   KNWRDLIKPRGL-VVDQDSLSNTYGKFVAEPLERGFGITLGNSLRRVLLSSLQGAAITSV 66

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +++GV HE  +I  V ED+TDIILN+K + L++  +  K + I   GP  + AGD+ T  
Sbjct: 67  KVEGVEHEFMTIPEVAEDVTDIILNLKEVLLQIHTNDVKTIRIEADGPKEIKAGDLITDA 126

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            +EVLNP H I  +     VR E+T  +G GYVPA+ ++    PIG I IDAL+SPI+KV
Sbjct: 127 QVEVLNPGHHILTISEGGRVRAEMTARRGRGYVPAERNKVPGSPIGTIPIDALFSPIRKV 186

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y V +AR GQ  DYDKL++ + TDGS+   D+VA A++I+++QL +FINF+E ++  +E
Sbjct: 187 NYQVTNARVGQQTDYDKLTLEVWTDGSVAPADAVAFAAKIVKEQLSIFINFDEAEEPAEE 246

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
              V+    N  L + V+ELELSVRS NCL+  NI  +GDL+Q+TEA+ML+  NFGRKSL
Sbjct: 247 IKPVEEQKLNENLFRSVDELELSVRSANCLQNANIKTIGDLVQKTEAEMLKTKNFGRKSL 306

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
            EIK +L  MGL LGM L +WPP++  + A K
Sbjct: 307 KEIKEILAEMGLSLGMKLENWPPKAAPQGAPK 338


>gi|226309835|ref|YP_002769729.1| DNA-directed RNA polymerase subunit alpha [Brevibacillus brevis
           NBRC 100599]
 gi|254765244|sp|C0ZIK7|RPOA_BREBN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|226092783|dbj|BAH41225.1| DNA-directed RNA polymerase alpha chain [Brevibacillus brevis NBRC
           100599]
          Length = 314

 Score =  366 bits (939), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 136/313 (43%), Positives = 209/313 (66%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  ++ +    + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDG
Sbjct: 3   EIEKP-KIEVVEVS-DDNSYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVRTVQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T+IILNIKG+ LK+  D  K + I   G GVV AGDI+  +D+EV
Sbjct: 61  VLHEFSTVEGVVEDVTEIILNIKGLALKIHSDEEKVIEIDAEGEGVVKAGDIRADSDVEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L     + + +T  +G GYV +  +++E+ PIG+I ID++Y+PIK+V+Y V
Sbjct: 121 LNPDLHIATLANGGRLHIRMTAGRGRGYVQSDGNKSEDLPIGVIPIDSIYTPIKRVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ +YDKL++ + T+GSI+ E++V+L ++I+ + L +F+   +  K+ +  +  
Sbjct: 181 ENTRVGQMTNYDKLTLEVWTNGSISPEEAVSLGAKIMTEHLNLFVGLTDEAKDAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L Q+TE DM+++ N GRKSL E++
Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTQKTEEDMMKVRNLGRKSLEEVQ 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 EKLAELGLSLRSD 313


>gi|197122366|ref|YP_002134317.1| DNA-directed RNA polymerase subunit alpha [Anaeromyxobacter sp. K]
 gi|220917148|ref|YP_002492452.1| DNA-directed RNA polymerase, alpha subunit [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|238689847|sp|B4UBC6|RPOA_ANASK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|254765241|sp|B8J887|RPOA_ANAD2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|196172215|gb|ACG73188.1| DNA-directed RNA polymerase, alpha subunit [Anaeromyxobacter sp. K]
 gi|219955002|gb|ACL65386.1| DNA-directed RNA polymerase, alpha subunit [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 340

 Score =  366 bits (939), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 161/324 (49%), Positives = 221/324 (68%), Gaps = 1/324 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNW++LIKP  +  +            +AEPL RGF  TLGN+LRRVL+SSL+GAAIT+V
Sbjct: 8   KNWRDLIKPRGL-VVDQDSLSNTYGKFVAEPLERGFGITLGNSLRRVLLSSLQGAAITSV 66

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +++GV HE  +I  V ED+TDIILN+K + L++  +  K + I   GP  + AGD+ T  
Sbjct: 67  KVEGVEHEFMTIPEVAEDVTDIILNLKEVLLQIHTNDVKTIRIEADGPKEIKAGDLITDA 126

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            +EVLNP H I  +     VR E+T  +G GYVPA+ ++    PIG I IDAL+SPI+KV
Sbjct: 127 QVEVLNPGHHILTISEGGRVRAEMTARRGRGYVPAERNKIPGSPIGTIPIDALFSPIRKV 186

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y V +AR GQ  DYDKL++ + TDGS+   D+VA A++I+++QL +FINF+E ++  +E
Sbjct: 187 NYQVTNARVGQQTDYDKLTLEVWTDGSVAPADAVAFAAKIVKEQLSIFINFDEAEEPAEE 246

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
              V+    N  L + V+ELELSVRS NCL+  NI  +GDL+Q+TEA+ML+  NFGRKSL
Sbjct: 247 IKPVEEQKLNENLFRSVDELELSVRSANCLQNANIKTIGDLVQKTEAEMLKTKNFGRKSL 306

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPE 327
            EIK +L  MGL LGM L +WPP+
Sbjct: 307 KEIKEILAEMGLSLGMKLENWPPK 330


>gi|251799614|ref|YP_003014345.1| DNA-directed RNA polymerase subunit alpha [Paenibacillus sp. JDR-2]
 gi|247547240|gb|ACT04259.1| DNA-directed RNA polymerase, alpha subunit [Paenibacillus sp.
           JDR-2]
          Length = 314

 Score =  365 bits (938), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 138/313 (44%), Positives = 210/313 (67%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDG
Sbjct: 3   EIEKP-KIETVDLN-EDGTYGRFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T+IILN+KG++LK+  D  K + I   G G+VTAGDI+  +D+E+
Sbjct: 61  VLHEFSTVPGVIEDVTEIILNLKGLSLKIHSDEEKVLEIDAEGEGIVTAGDIRADSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L   A + + +  ++G GYV A  ++ ++ PIG+I +D++Y+PI +V+Y+V
Sbjct: 121 LNPDLHIATLASGARLHLRIFANRGRGYVQADRNKRDDQPIGVIPVDSIYTPITRVNYSV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV +YDKL++ + TDGSI  E++V+L ++IL + L +F+   +  K+ +  +  
Sbjct: 181 ENTRVGQVTNYDKLTLEVWTDGSIRPEEAVSLGAKILTEHLDLFVGLTDEAKDAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +LI ++E DM+++ N GRKSL E++
Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELITKSEEDMMKVRNLGRKSLEEVQ 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L M 
Sbjct: 301 EKLEELGLGLRME 313


>gi|222056679|ref|YP_002539041.1| DNA-directed RNA polymerase, alpha subunit [Geobacter sp. FRC-32]
 gi|221565968|gb|ACM21940.1| DNA-directed RNA polymerase, alpha subunit [Geobacter sp. FRC-32]
          Length = 340

 Score =  365 bits (938), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 169/340 (49%), Positives = 231/340 (67%), Gaps = 3/340 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW++LIKP  ++               AEP  RGF  TLGN+LRRVL+SSL+GAAIT
Sbjct: 1   MYKNWRDLIKPKKLQVET-ESLTNTYGKFYAEPFERGFGTTLGNSLRRVLLSSLQGAAIT 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+  GVLHE S+I GV ED TDIILN+KG+  KM G   + V I ++G G+V AGDI T
Sbjct: 60  SVKAKGVLHEFSAIPGVTEDATDIILNLKGVRFKMHGHEPRVVRIAQKGEGIVRAGDIIT 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
             +IEVLNP+H I     DA + ME+ V  G GYVPA  +R E  P+G I ID+++SP+ 
Sbjct: 120 DPNIEVLNPNHHIATCSKDANLEMEMVVKLGKGYVPADRNRDEKAPVGTIPIDSIFSPLT 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KV++TV +AR GQ+ DYDKL++ + TDGS+  +D+VA AS+IL+DQL +FINF+E  + V
Sbjct: 180 KVNFTVTNARVGQITDYDKLTIEVWTDGSVKPQDAVAYASKILKDQLTIFINFDEEVEPV 239

Query: 242 KEDINVKSLPF-NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           +E   ++     N  L + V+ELELSVRS NCL+   I  +G+L+ R+EA+ML+  NFGR
Sbjct: 240 EEAEPMEERERLNENLYRSVDELELSVRSANCLKNAGIKLIGELVSRSEAEMLKTQNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP-PESIEELAKKYEDK 339
           KSL EIK +L  MGL LGM L ++P PE +  L  + +++
Sbjct: 300 KSLNEIKDILVDMGLTLGMKLDNFPDPEIMRRLRGEQKEE 339


>gi|317123070|ref|YP_004103073.1| DNA-directed RNA polymerase subunit alpha [Thermaerobacter
           marianensis DSM 12885]
 gi|315593050|gb|ADU52346.1| DNA-directed RNA polymerase subunit alpha [Thermaerobacter
           marianensis DSM 12885]
          Length = 315

 Score =  365 bits (936), Expect = 8e-99,   Method: Composition-based stats.
 Identities = 129/314 (41%), Positives = 202/314 (64%), Gaps = 2/314 (0%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E+ KP  IE + +  E+      + EPL RG+  TLGNALRRVL+SSL GAA+T+V+I
Sbjct: 1   MNEMEKPT-IETVEIS-EDGTYGRFVVEPLERGYGITLGNALRRVLLSSLPGAAVTSVRI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           +GVLHE S+I GV ED T+IILN+K + +KM  D  + + +  +G G V A DI    ++
Sbjct: 59  EGVLHEFSTIPGVVEDTTEIILNLKELAIKMHTDEPQILRVEAQGEGEVRAADIIAPPEV 118

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++N DH+I  L+ D  + ME+TV +G GYVPA  ++  +  IGLI +D++++PI+KV++
Sbjct: 119 EIVNGDHLIATLEHDGRLFMEMTVQRGRGYVPADRNKGPDRSIGLIPVDSIFTPIRKVNF 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R G+V DYD+L++ I T+G++  +++ + A+RIL D L +F+   +  +      
Sbjct: 179 QVENTRVGKVTDYDRLTLEIWTNGTVAPDEAASQAARILTDHLALFLTLTDQTRGAGTAA 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   ++EL+LSVRS NCL+   I  +G+L+++T  DM+R+ N G+KSL E
Sbjct: 239 EKEDDARAKLLEMSIDELDLSVRSYNCLKRAGINTIGELVEKTPEDMMRVRNLGKKSLEE 298

Query: 306 IKGVLGTMGLFLGM 319
           ++  L  +GL L  
Sbjct: 299 VEEKLAALGLSLKQ 312


>gi|152998246|ref|YP_001343081.1| DNA-directed RNA polymerase subunit alpha [Marinomonas sp. MWYL1]
 gi|150839170|gb|ABR73146.1| DNA-directed RNA polymerase, alpha subunit [Marinomonas sp. MWYL1]
          Length = 334

 Score =  365 bits (936), Expect = 8e-99,   Method: Composition-based stats.
 Identities = 157/336 (46%), Positives = 229/336 (68%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  EL+ P NIE   LG     R  +  +PL RGF HTLGNALRR+L+SS+ G AI 
Sbjct: 1   MQRSVSELLTPRNIEVQELGN---CRAKVTLQPLERGFGHTLGNALRRILLSSMPGCAIV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ +I+LN+KG+ + + G     +T+ K+GPG+VTAGDIQ 
Sbjct: 58  EVEIDGVLHEYSAIEGVKEDVIEILLNLKGVAIALHGQDEATLTLSKKGPGIVTAGDIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
           V D E+ NPDH+I +LD  A + M++ V++G GY PA        E  PIG + +DA +S
Sbjct: 118 VADAEIANPDHIIAHLDDTAELTMQIKVARGRGYEPADARVAGDDETRPIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++V+Y+V++AR  Q  D DKL + I+++G+I  E+++  A+ ILQ Q+ +F+  E   
Sbjct: 178 PVRRVAYSVDNARVEQRTDLDKLVLDIESNGTIDPEEAIRRAATILQQQIAVFVALE--- 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E +  +  +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 235 SESEAPVVEEEDEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL   GL LGM L +WPP S+++ +K
Sbjct: 295 GKKSLTEIKDVLAQRGLSLGMRLENWPPASLKDDSK 330


>gi|299138174|ref|ZP_07031354.1| DNA-directed RNA polymerase, alpha subunit [Acidobacterium sp.
           MP5ACTX8]
 gi|298600104|gb|EFI56262.1| DNA-directed RNA polymerase, alpha subunit [Acidobacterium sp.
           MP5ACTX8]
          Length = 359

 Score =  364 bits (935), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 145/318 (45%), Positives = 206/318 (64%), Gaps = 1/318 (0%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           W+   KP  +                A+P  RGF  T+GNALRR L+SS+ GAA+TAV+I
Sbjct: 3   WRGFQKPKRLAVDQ-ETLTPTFGKFSAQPFERGFGTTIGNALRRTLLSSIEGAAVTAVKI 61

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           +GVLHE  SI GV ED TDIILN+K I  K++GD  K + +     GVVT+G I+  +D+
Sbjct: 62  EGVLHEFQSIAGVVEDATDIILNLKQIPFKLNGDGPKTLYLRADAAGVVTSGSIEADSDV 121

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E+L+P   IC +     + ME+ + +G GYV A  +   +  IG I +D+++SP++KV+Y
Sbjct: 122 EILDPSVYICTISEGGRIDMEMRLKRGRGYVSADKNFDSDLGIGFIPVDSVHSPVRKVNY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+AR GQ+ DYDKL++ I T+G+I   D++ L++++L+D + +FINFEE  +      
Sbjct: 182 LVEAARLGQITDYDKLTLEIWTNGTILPADALGLSAKLLKDHMTIFINFEEEMEAGASGD 241

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           +   L  N  L + VEELELSVRS NCL+  NI  +G+LIQ+TEA+ML+  NFGRKSL E
Sbjct: 242 HDGPLLRNENLNRSVEELELSVRSYNCLKNANIATIGELIQKTEAEMLKTKNFGRKSLNE 301

Query: 306 IKGVLGTMGLFLGMNLPD 323
           IK +L  MGL LGM + +
Sbjct: 302 IKEILAQMGLSLGMKIDE 319


>gi|189424437|ref|YP_001951614.1| DNA-directed RNA polymerase subunit alpha [Geobacter lovleyi SZ]
 gi|189420696|gb|ACD95094.1| DNA-directed RNA polymerase, alpha subunit [Geobacter lovleyi SZ]
          Length = 340

 Score =  364 bits (935), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 157/340 (46%), Positives = 227/340 (66%), Gaps = 3/340 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW++LIKP  ++ I            +AEP  RGF  TLGN+LRRVL+SSL+GAAIT
Sbjct: 1   MYKNWRDLIKPKQLQ-IEKETLTTTYGKFVAEPFERGFGTTLGNSLRRVLLSSLQGAAIT 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+I GV HE SSI GV ED+TDIILN+K + L+  G     + I  +G G++ A DI  
Sbjct: 60  SVRIKGVQHEFSSIPGVTEDVTDIILNLKSVRLRFHGADQATIRIIHKGDGIIKAADIMV 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +++E++NP+  I     DAV+ ME+TV  G GYV A  +R E  P+G I IDA++SPI 
Sbjct: 120 PHNVEIMNPEMHIATCGKDAVLEMEMTVKIGKGYVSADRNRDEKAPVGTIPIDAIFSPII 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KV++ V +AR GQ+ DYDKL++ + TDGS+  +D++A A++I+++Q+ +FINF+E  + +
Sbjct: 180 KVNFVVSNARVGQMTDYDKLTLEVWTDGSVKPDDAIAYAAKIVKEQMSIFINFDEESEPL 239

Query: 242 -KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +++        N  L + VEELELSVRS NCL+   I  +G+L+ +TEA+ML+  NFGR
Sbjct: 240 FQDEAAEDDSKINENLYRTVEELELSVRSANCLKNAGIKLIGELVSKTEAEMLKTQNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP-PESIEELAKKYEDK 339
           KSL EIK +L  MGL  GM L  +P PE ++ L  + +D+
Sbjct: 300 KSLNEIKDILNEMGLTFGMKLDSFPDPEVVKRLRGEQKDE 339


>gi|78221873|ref|YP_383620.1| DNA-directed RNA polymerase subunit alpha [Geobacter
           metallireducens GS-15]
 gi|119366684|sp|Q39XX9|RPOA_GEOMG RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|78193128|gb|ABB30895.1| DNA-directed RNA polymerase subunit alpha [Geobacter
           metallireducens GS-15]
          Length = 340

 Score =  364 bits (934), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 165/340 (48%), Positives = 232/340 (68%), Gaps = 3/340 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +NW++LI P  ++               AEP  RGF  TLGN+LRRVL+SSL+GAAI+
Sbjct: 1   MYRNWRDLISPKKLQVES-ESLTNTYGKFFAEPFERGFGTTLGNSLRRVLLSSLQGAAIS 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+I GVLHE SSI GV ED+T+IILN+KG++LKM G+  + V I  +G G+V AGDI T
Sbjct: 60  SVKIKGVLHEFSSIPGVTEDVTNIILNLKGVSLKMHGNEARTVRIIHKGDGIVKAGDIVT 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
             ++E+LNPDH I     DA + ME+ V  G GYVP+  +R E  P+G + IDA++SPIK
Sbjct: 120 DANVEILNPDHHIATCSKDANLEMEMVVKLGKGYVPSDRNRDEKAPVGTMPIDAIFSPIK 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KV++TV +AR GQ+ DYDKL++ + T+GS+  ED+VA A++IL++QL +FINF+E  +  
Sbjct: 180 KVNFTVSNARVGQMTDYDKLTLEVWTNGSVVPEDAVAFAAKILKEQLSIFINFDEEAEPA 239

Query: 242 KEDINVKSLPF-NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           +E    +     N  L + V+ELELSVRS NCL+   I  +G+L+ R+EA+ML+  NFGR
Sbjct: 240 EEAETEEERERVNENLYRSVDELELSVRSANCLKNAGIKMIGELVSRSEAEMLKTQNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP-PESIEELAKKYEDK 339
           KSL EIK +L  MGL LGM L  +P PE +  +  + +D+
Sbjct: 300 KSLNEIKDILADMGLTLGMKLDGFPDPEVMRRIRGERKDE 339


>gi|26987220|ref|NP_742645.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas putida
           KT2440]
 gi|104779780|ref|YP_606278.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas entomophila
           L48]
 gi|148545764|ref|YP_001265866.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas putida F1]
 gi|167031524|ref|YP_001666755.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas putida GB-1]
 gi|170723881|ref|YP_001751569.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas putida W619]
 gi|325272033|ref|ZP_08138476.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas sp. TJI-51]
 gi|37999653|sp|Q88QL1|RPOA_PSEPK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|123079274|sp|Q1IFU1|RPOA_PSEE4 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172048432|sp|A5VXS2|RPOA_PSEP1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|24981859|gb|AAN66109.1|AE016239_4 DNA-directed RNA polymerase, alpha subunit [Pseudomonas putida
           KT2440]
 gi|95108767|emb|CAK13461.1| RNA polymerase, alpha subunit [Pseudomonas entomophila L48]
 gi|148509822|gb|ABQ76682.1| DNA-directed RNA polymerase, alpha subunit [Pseudomonas putida F1]
 gi|166858012|gb|ABY96419.1| DNA-directed RNA polymerase, alpha subunit [Pseudomonas putida
           GB-1]
 gi|169761884|gb|ACA75200.1| DNA-directed RNA polymerase, alpha subunit [Pseudomonas putida
           W619]
 gi|313496844|gb|ADR58210.1| RpoA [Pseudomonas putida BIRD-1]
 gi|324102837|gb|EGC00241.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas sp. TJI-51]
          Length = 333

 Score =  364 bits (934), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 151/336 (44%), Positives = 228/336 (67%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVVS---PTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  +  + M+LTV++G GY PA   +T+ D    IG + +DA +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGALNMKLTVARGRGYEPADSRQTDEDESRSIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V  +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPVVVEQEDE---IDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>gi|288554753|ref|YP_003426688.1| DNA-directed RNA polymerase subunit alpha [Bacillus pseudofirmus
           OF4]
 gi|288545913|gb|ADC49796.1| DNA-directed RNA polymerase subunit alpha [Bacillus pseudofirmus
           OF4]
          Length = 314

 Score =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 138/310 (44%), Positives = 205/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KPN IE + +  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQID 
Sbjct: 3   EIEKPN-IETVEVS-EDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDS 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IILN+K + LK+  D  K + +  +G GVVTAGD+   +DIEV
Sbjct: 61  VLHEFSTIEGVVEDVTTIILNLKKLALKIYSDEEKTLEVDVQGEGVVTAGDLTHDSDIEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L   A   M LT  +G GY  A+ ++ ++ PIG++ ID++Y+P+ +V+Y V
Sbjct: 121 LNPDLHIATLAKGAHFHMRLTAKRGRGYALAEGNKNDDQPIGVLPIDSIYTPVSRVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV +YDKL++ + TDGSI  E++V+L ++IL + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQVTNYDKLTLDVWTDGSIRPEEAVSLGAKILTEHLNIFVGLTDQAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L Q++E DM+++ N GRKSL E++
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTQKSEEDMMKVRNLGRKSLEEVQ 300

Query: 308 GVLGTMGLFL 317
             LG +GL L
Sbjct: 301 EKLGELGLGL 310


>gi|146281195|ref|YP_001171348.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas stutzeri
           A1501]
 gi|158514171|sp|A4VHQ5|RPOA_PSEU5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|145569400|gb|ABP78506.1| DNA-directed RNA polymerase alpha chain [Pseudomonas stutzeri
           A1501]
 gi|327479348|gb|AEA82658.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas stutzeri DSM
           4166]
          Length = 333

 Score =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 147/336 (43%), Positives = 225/336 (66%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQSSVNEFLTPRHIDVQVVS---PTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KGI +K+ G     +++ K+G G VTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGIAIKLHGRDEVTLSLVKKGAGAVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++N DH+I NL  +  + M+L V++G GY PA   +++ D    IG + +DA +S
Sbjct: 118 DHDVEIVNGDHLIANLAANGSLNMKLKVARGRGYEPADARQSDEDESRSIGRLQLDATFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++V+Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRVAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V  +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPVVVEQEDE---IDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>gi|37999710|sp|Q8L2F8|RPOA_PSEPU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|21039415|gb|AAM33636.1|AF506984_1 RpoA [Pseudomonas putida]
          Length = 333

 Score =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 148/336 (44%), Positives = 227/336 (67%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQSSVNEFLTPRHIDVQVVS---PTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  +  + M+L V++G GY PA   +++ D    IG + +D+ +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGALNMKLVVARGRGYEPADSRQSDEDESRSIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V  +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPVVVEQEDE---IDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>gi|294497011|ref|YP_003560711.1| DNA-directed RNA polymerase subunit alpha [Bacillus megaterium QM
           B1551]
 gi|295702376|ref|YP_003595451.1| DNA-directed RNA polymerase subunit alpha [Bacillus megaterium DSM
           319]
 gi|294346948|gb|ADE67277.1| DNA-directed RNA polymerase, alpha subunit [Bacillus megaterium QM
           B1551]
 gi|294800035|gb|ADF37101.1| DNA-directed RNA polymerase, alpha subunit [Bacillus megaterium DSM
           319]
          Length = 314

 Score =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 142/313 (45%), Positives = 207/313 (66%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  + +     + EPL RG+  TLGN+LRR+L+SSL GAA+T++QI+G
Sbjct: 3   EIEKP-KIETVEISDDRK-YGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T+IILN+K + LK+  D  K + I  +GPG VTA DIQ  +DIEV
Sbjct: 61  VLHEFSTVPGVVEDVTNIILNVKKLALKIYSDEEKTLEIDVKGPGTVTAADIQADSDIEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L+ DA  RM LT   G GY PA  ++ E+ PIG++ ID++Y+P+ +VSY V
Sbjct: 121 LNPDLHIATLESDAHFRMRLTARTGRGYNPADANKREDQPIGVLPIDSIYTPVTRVSYYV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ +YDKL++ + TDGSI  E +VAL ++IL + L +F+N  +  ++ +  +  
Sbjct: 181 ENTRVGQMTNYDKLTLDVWTDGSIEPEKAVALGAKILTEHLNIFVNLTDEAQKAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 AKLEELGLGLRKD 313


>gi|212637981|ref|YP_002314501.1| DNA-directed RNA polymerase subunit alpha [Anoxybacillus
           flavithermus WK1]
 gi|212559461|gb|ACJ32516.1| DNA-directed RNA polymerase alpha subunit [Anoxybacillus
           flavithermus WK1]
          Length = 314

 Score =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 142/313 (45%), Positives = 206/313 (65%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDG
Sbjct: 3   EIEKP-KIETVEIS-EDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILNIK + LK+  D  K + I  +G GVVTA DI   +D+E+
Sbjct: 61  VLHEFSTIDGVVEDVTTIILNIKKLALKIYSDEEKTLEIDVQGEGVVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  D  +RM +T  +G GY PA  ++ E+ PIG+I ID++Y+P+ +VSY V
Sbjct: 121 LNPDLQIATLAKDGRLRMRMTAKRGRGYTPADANKREDQPIGVIPIDSIYTPVSRVSYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ +YDKL++ + TDGSI  +++++L ++IL + L +F+N  +  +  +  I  
Sbjct: 181 ENTRVGQMTNYDKLTIDVWTDGSIGPKEAISLGAKILTEHLNIFVNLTDEAQHAEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L Q+TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELAQKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 AKLEELGLSLRKD 313


>gi|224827042|ref|ZP_03700139.1| DNA-directed RNA polymerase, alpha subunit [Lutiella nitroferrum
           2002]
 gi|224600708|gb|EEG06894.1| DNA-directed RNA polymerase, alpha subunit [Lutiella nitroferrum
           2002]
          Length = 327

 Score =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 156/332 (46%), Positives = 219/332 (65%), Gaps = 8/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+   +         +  EP  RG+AHTLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSASEFLKPRLIDVQPVS---ATHARVSMEPFERGYAHTLGNALRRILLSSMPGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE S++ GV ED+ DI+LN+KG+ LK+ G     +T+ K G G V AGDI+ 
Sbjct: 58  EVTIAGVLHEYSALDGVREDVVDILLNLKGVVLKLHGRDSVVLTLKKEGEGAVLAGDIEL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP--AKHHRTENDPIGLITIDALYSP 179
            +D+EV+NPDHVIC+L     + +E+ V KG GY P   + ++ +N  IG I +DA +SP
Sbjct: 118 PHDVEVINPDHVICHLAAGGKIDLEVKVEKGRGYQPVSVRVNQDDNRAIGTIQLDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +++VS+ VESAR  Q  D D+L + I+T+G I  E +V  A+RIL DQL +F + +    
Sbjct: 178 VRRVSFGVESARVEQRTDLDRLVLDIETNGVIEPEQAVRNAARILMDQLSIFADLQGTAV 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
              E++  K+ P +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G
Sbjct: 238 ---EEVVEKAPPIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTETELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           RKSL EIK VL + GL LGM L +WPP  +E+
Sbjct: 295 RKSLNEIKEVLASKGLTLGMKLENWPPAGLEK 326


>gi|311029077|ref|ZP_07707167.1| DNA-directed RNA polymerase subunit alpha [Bacillus sp. m3-13]
          Length = 314

 Score =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 137/313 (43%), Positives = 204/313 (65%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  ++ N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETVEIS-DDANYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T +ILN+K + LK+  D  K + I  +G G VTA DI   +D+EV
Sbjct: 61  VLHEFSTIEGVVEDVTTVILNVKKLALKIYSDDEKTLEIDVQGEGAVTAADITHDSDVEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  DA +R+  T  +G GYV A  ++ E+ PIG+I ID++++P+ +VSY V
Sbjct: 121 LNPDLHIATLAKDAHLRIRFTAKRGRGYVTADGNKREDQPIGVIPIDSIFTPVSRVSYYV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV +YDKL++ + TDGS   +++VAL ++IL + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQVSNYDKLTLDVWTDGSNGPQEAVALGAKILTEHLNIFVGLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 HKLEELGLGLRKD 313


>gi|148263165|ref|YP_001229871.1| DNA-directed RNA polymerase subunit alpha [Geobacter uraniireducens
           Rf4]
 gi|146396665|gb|ABQ25298.1| DNA-directed RNA polymerase subunit alpha [Geobacter uraniireducens
           Rf4]
          Length = 340

 Score =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 167/340 (49%), Positives = 228/340 (67%), Gaps = 3/340 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +NW++LIKP  ++               AEP  RGF  TLGN+LRRVL+SSL+GAAIT
Sbjct: 1   MYRNWRDLIKPKKLQVET-ESLTNTYGKFYAEPFERGFGTTLGNSLRRVLLSSLQGAAIT 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+  GVLHE S+I GV ED TDIILN+KG+  KM G   + V I ++G G+V AGDI T
Sbjct: 60  SVKAKGVLHEFSAIPGVTEDATDIILNLKGVRFKMHGHESRVVRIVQKGEGLVKAGDIIT 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
             ++EVLNP+H I     DA + ME+ V  G GYVPA  +R E  P+G I ID+++SP+ 
Sbjct: 120 DPNVEVLNPNHHIATCSKDANLEMEMVVKMGKGYVPADRNRDEKAPVGTIPIDSIFSPLT 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EPKKE 240
           KV++TV +AR GQ+ DYDKL + I TDGS+  +D++A AS+IL+DQL +FINF+ E +  
Sbjct: 180 KVNFTVSNARVGQITDYDKLIIEIWTDGSVKPQDALAYASKILKDQLTIFINFDEEVEPV 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            + +   +   FN  L + V+ELELSVRS NCL+   I  +G+L+ RTEA+ML+  NFGR
Sbjct: 240 EEVEPEEERERFNENLYRSVDELELSVRSANCLKNAGIKLIGELVSRTEAEMLKTQNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP-PESIEELAKKYEDK 339
           KSL EIK +L  MGL LGM L ++P PE +  L  +  ++
Sbjct: 300 KSLNEIKDILVDMGLTLGMRLDNFPDPEIMRRLRGEQNEE 339


>gi|218289978|ref|ZP_03494155.1| DNA-directed RNA polymerase, alpha subunit [Alicyclobacillus
           acidocaldarius LAA1]
 gi|258512642|ref|YP_003186076.1| DNA-directed RNA polymerase, alpha subunit [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|218239963|gb|EED07150.1| DNA-directed RNA polymerase, alpha subunit [Alicyclobacillus
           acidocaldarius LAA1]
 gi|257479368|gb|ACV59687.1| DNA-directed RNA polymerase, alpha subunit [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 312

 Score =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 130/313 (41%), Positives = 206/313 (65%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP     I + ++  +    + EPL RG+  TLGN+LRR+L+SS+ GAA+ +V+I+G
Sbjct: 3   EIEKPR----IEIVEQTGDYGKFVCEPLERGYGTTLGNSLRRILLSSIPGAAVRSVKIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T+IILN+K ++LK+  D  K + I   GPGVVTAGDI+  +D+++
Sbjct: 59  VLHEFSTIPGVVEDVTEIILNLKRLSLKIHSDEEKTLIIDAVGPGVVTAGDIRADSDVDI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPD  I  L   A + ME+   +G GYVPA  ++ E   IGLI ID+LYSPI +V+++V
Sbjct: 119 MNPDLHIATLTEGARIYMEMRAGRGRGYVPAHRNKPEEQEIGLIPIDSLYSPISRVNFSV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ DYDKL++ + TDGS+  +++V++ ++IL + L +F+   +  ++    +  
Sbjct: 179 ENTRVGQITDYDKLTLEVWTDGSVAPDEAVSIGAKILTEHLMLFVGLTDRARDTDLMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           ++   +  L   +EEL+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E+ 
Sbjct: 239 ENAHNDKILDMPIEELDLSVRSYNCLKRAGINTVAELCAKSEEEMMKVRNLGRKSLEEVV 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 EKLHALGLSLRKD 311


>gi|89093590|ref|ZP_01166538.1| DNA-directed RNA polymerase, alpha subunit [Oceanospirillum sp.
           MED92]
 gi|89082280|gb|EAR61504.1| DNA-directed RNA polymerase, alpha subunit [Oceanospirillum sp.
           MED92]
          Length = 334

 Score =  363 bits (932), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 154/336 (45%), Positives = 225/336 (66%), Gaps = 8/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  E + P +I+   + +    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQRSVNEFLSPRHIDVQEISK---TRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ +I+LN+KGI + +  +    +T+ K   G VTAGDIQ 
Sbjct: 58  EVEIDGVLHEYSTIEGVQEDVIEILLNLKGIAVLLHNNDEAVLTLSKSEAGPVTAGDIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
             D+E+ NPDHVI +L+  A + M+LT+ +G GYVPA        E   IG + +DA +S
Sbjct: 118 NQDVEIANPDHVIAHLNEGASLNMQLTIGRGRGYVPADLRVSDEEETRAIGRLQLDATFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY VESAR  Q  D DKL + I+++G+I  E+++  A+ ILQ QL +F++ E+  
Sbjct: 178 PVRRVSYVVESARVEQRTDLDKLVIDIESNGTIDPEEAIRRAATILQQQLIVFVDLEDGA 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            + K++     +  +P LL+ V++LEL+VRS NCL+ E I Y+GDLIQRTE ++L+  N 
Sbjct: 238 DQAKDEPEEPEI--DPILLRPVDDLELTVRSANCLKAEQIYYIGDLIQRTEVELLKTPNL 295

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S++   K
Sbjct: 296 GKKSLTEIKDVLASKGLSLGMRLENWPPASLKNDDK 331


>gi|330891907|gb|EGH24568.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           mori str. 301020]
          Length = 333

 Score =  363 bits (932), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 149/336 (44%), Positives = 228/336 (67%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVVS---PTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +I GVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIGGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  + V+ M+LTV++G GY PA   +++ D    IG + +D+ +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGVLNMKLTVARGRGYEPADSRQSDEDESRSIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V  +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPVVIEQEDE---IDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>gi|320322297|gb|EFW78391.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           glycinea str. B076]
 gi|320331955|gb|EFW87891.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           glycinea str. race 4]
          Length = 333

 Score =  363 bits (932), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 150/336 (44%), Positives = 229/336 (68%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVVS---PTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  + V+ M+LTV++G GY PA   +++ D    IG + +D+ +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGVLNMKLTVARGRGYEPADSRQSDEDESRSIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDMETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V  +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPVVIEQEDE---IDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>gi|325560586|gb|ADZ31263.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus sp.
           SL1108]
          Length = 298

 Score =  363 bits (932), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 129/297 (43%), Positives = 195/297 (65%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I    E  N    + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGV+HE S+I G
Sbjct: 2   ITKVDEGTNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVVHEFSTIDG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+T IILN+K + LK+ GD  K V I  +GP  VTA DI   +D+EVLNP+  IC +
Sbjct: 62  VLEDVTQIILNVKELALKIEGDEDKTVEIDVQGPATVTAADIVADSDVEVLNPEQYICTV 121

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
                  + +T+ KG GYV A  ++ ++ PIG++ ID++++PI +V+Y VES R G+  D
Sbjct: 122 AEGGHFHVRMTIKKGRGYVAADQNKVDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRND 181

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL++ + T+GSI+  ++++LA++IL + L +F+N  +  K  +  +  +       L 
Sbjct: 182 FDKLTLDVWTNGSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLE 241

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
             +EEL+LSVRS NCL+   I  + +L  +TEADM+++ N GRKSL E+K  L  +G
Sbjct: 242 MTIEELDLSVRSYNCLKRAGINTVQELTNKTEADMMKVRNLGRKSLEEVKNKLSDLG 298


>gi|226939212|ref|YP_002794283.1| DNA-directed RNA polymerase subunit alpha [Laribacter hongkongensis
           HLHK9]
 gi|254765253|sp|C1DAU3|RPOA_LARHH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|226714136|gb|ACO73274.1| RpoA [Laribacter hongkongensis HLHK9]
          Length = 327

 Score =  363 bits (931), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 155/332 (46%), Positives = 217/332 (65%), Gaps = 8/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+   +      +  +  EP  RG+A+TLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSASEFLKPRLIDVQPVS---ATQARVAMEPFERGYAYTLGNALRRILLSSMPGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE S++ GV ED+ DI+LN+KG+  K+ G     +T+ K G G V A DI  
Sbjct: 58  EVSIAGVLHEYSALDGVREDVVDILLNLKGVVFKLHGRDSVLLTLKKEGEGAVRASDIDL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSP 179
            +D+EV+NPDHVIC+L     + ME+ V KG GY PA     + +N  IG I +DA +SP
Sbjct: 118 PHDVEVVNPDHVICHLAAGGKIDMEIKVEKGRGYQPAPARVKQDDNRQIGTILLDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +++VS++VESAR  Q  D D+L M I+T+G I  E++V  A+RIL DQL +F + +    
Sbjct: 178 LRRVSFSVESARVEQRTDLDRLVMDIETNGVIEPEEAVRSAARILIDQLSIFADLQGTTV 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           EV   +  ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G
Sbjct: 238 EV---VEERAPQVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTETELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           RKSL EIK VL + GL LGM L +WPP  +E+
Sbjct: 295 RKSLNEIKEVLASKGLTLGMKLENWPPAGLEK 326


>gi|77461276|ref|YP_350783.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas fluorescens
           Pf0-1]
 gi|330812051|ref|YP_004356513.1| DNA-directed RNA polymerase alpha chain [Pseudomonas brassicacearum
           subsp. brassicacearum NFM421]
 gi|90110861|sp|Q3K612|RPOA_PSEPF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|77385279|gb|ABA76792.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas fluorescens
           Pf0-1]
 gi|327380159|gb|AEA71509.1| DNA-directed RNA polymerase alpha chain [Pseudomonas brassicacearum
           subsp. brassicacearum NFM421]
          Length = 333

 Score =  363 bits (931), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 149/336 (44%), Positives = 228/336 (67%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVVS---PTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  +  + M+LTV++G GY PA   +++ D    IG + +D+ +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGALNMKLTVARGRGYEPADSRQSDEDESRSIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V  +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPVVVEQEDE---IDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>gi|226942803|ref|YP_002797876.1| DNA-directed RNA polymerase subunit alpha [Azotobacter vinelandii
           DJ]
 gi|226717730|gb|ACO76901.1| DNA-directed RNA polymerase, alpha subunit [Azotobacter vinelandii
           DJ]
          Length = 333

 Score =  363 bits (931), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 145/336 (43%), Positives = 222/336 (66%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+   +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQSSVNEFLTPRHIDVQAVS---PTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +++ K+G G VTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLSLSKKGSGAVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++N  HVI NL  +  + M+L V++G GY PA   +++ D    IG + +DA +S
Sbjct: 118 DHDVEIVNGGHVIANLADNGALNMKLKVARGRGYEPADARQSDEDESRSIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++V+Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRVAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDT 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
             V  +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 APVVVEQEDE---IDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>gi|28867879|ref|NP_790498.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           tomato str. DC3000]
 gi|66047751|ref|YP_237592.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           syringae B728a]
 gi|71737175|ref|YP_276681.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|213969239|ref|ZP_03397377.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           tomato T1]
 gi|237797457|ref|ZP_04585918.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           oryzae str. 1_6]
 gi|257483210|ref|ZP_05637251.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           tabaci ATCC 11528]
 gi|289623824|ref|ZP_06456778.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           aesculi str. NCPPB3681]
 gi|289648917|ref|ZP_06480260.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           aesculi str. 2250]
 gi|289675513|ref|ZP_06496403.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           syringae FF5]
 gi|298489071|ref|ZP_07007093.1| DNA-directed RNA polymerase alpha subunit [Pseudomonas savastanoi
           pv. savastanoi NCPPB 3335]
 gi|301381746|ref|ZP_07230164.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           tomato Max13]
 gi|302061054|ref|ZP_07252595.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           tomato K40]
 gi|302130805|ref|ZP_07256795.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           tomato NCPPB 1108]
 gi|302189302|ref|ZP_07265975.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           syringae 642]
 gi|37999595|sp|Q889U6|RPOA_PSESM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|75500423|sp|Q4ZMR8|RPOA_PSEU2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|90110858|sp|Q48D61|RPOA_PSE14 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|28851115|gb|AAO54193.1| DNA-directed RNA polymerase, alpha subunit [Pseudomonas syringae
           pv. tomato str. DC3000]
 gi|63258458|gb|AAY39554.1| DNA-directed RNA polymerase [Pseudomonas syringae pv. syringae
           B728a]
 gi|71557728|gb|AAZ36939.1| DNA-directed RNA polymerase, alpha subunit [Pseudomonas syringae
           pv. phaseolicola 1448A]
 gi|213925917|gb|EEB59474.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           tomato T1]
 gi|298156383|gb|EFH97481.1| DNA-directed RNA polymerase alpha subunit [Pseudomonas savastanoi
           pv. savastanoi NCPPB 3335]
 gi|330869406|gb|EGH04115.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           aesculi str. 0893_23]
 gi|330879417|gb|EGH13566.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
 gi|330899711|gb|EGH31130.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           japonica str. M301072PT]
 gi|330940915|gb|EGH43866.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           pisi str. 1704B]
 gi|330953172|gb|EGH53432.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae Cit
           7]
 gi|330966886|gb|EGH67146.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           actinidiae str. M302091]
 gi|330988257|gb|EGH86360.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           lachrymans str. M301315]
 gi|331012438|gb|EGH92494.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           tabaci ATCC 11528]
 gi|331020307|gb|EGI00364.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           oryzae str. 1_6]
          Length = 333

 Score =  363 bits (931), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 150/336 (44%), Positives = 229/336 (68%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVVS---PTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  + V+ M+LTV++G GY PA   +++ D    IG + +D+ +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGVLNMKLTVARGRGYEPADSRQSDEDESRSIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V  +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPVVIEQEDE---IDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>gi|229592878|ref|YP_002874997.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas fluorescens
           SBW25]
 gi|312963345|ref|ZP_07777828.1| DNA-directed RNA polymerase, alpha subunit [Pseudomonas fluorescens
           WH6]
 gi|229364744|emb|CAY52723.1| DNA-directed RNA polymerase alpha chain [Pseudomonas fluorescens
           SBW25]
 gi|311282425|gb|EFQ61023.1| DNA-directed RNA polymerase, alpha subunit [Pseudomonas fluorescens
           WH6]
 gi|330962500|gb|EGH62760.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 333

 Score =  363 bits (931), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 149/336 (44%), Positives = 228/336 (67%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVVS---PTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  +  + M+LTV++G GY PA   +++ D    IG + +D+ +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGALNMKLTVARGRGYEPADSRQSDEDESRSIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V  +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPVVIEQEDE---IDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>gi|120553677|ref|YP_958028.1| DNA-directed RNA polymerase subunit alpha [Marinobacter aquaeolei
           VT8]
 gi|158513044|sp|A1TYM2|RPOA_MARAV RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|120323526|gb|ABM17841.1| DNA-directed RNA polymerase subunit alpha [Marinobacter aquaeolei
           VT8]
          Length = 334

 Score =  362 bits (930), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 156/331 (47%), Positives = 225/331 (67%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  EL+ P  I+     +    R  +  EPL RGF HTLG+ALRR+L+SS+ G A+T
Sbjct: 1   MQRSVHELLTPRTIDVK---ESSATRAKVTLEPLERGFGHTLGSALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             QIDGVLHE S+I+GV ED+ +I+LN+KG+ +KM+G     +T+ K+GPGVVTAGDI+ 
Sbjct: 58  EAQIDGVLHEYSAIEGVQEDVIEILLNLKGVAVKMNGRDDAELTLSKKGPGVVTAGDIKL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
            +D+E+ NP+HVIC+L  +  V M L V++G GY PA        E   IG + +DA +S
Sbjct: 118 DHDVEIANPEHVICHLSENGEVNMRLRVARGRGYEPADQRGLDEDETRAIGRLQLDATFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++V+Y VESAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++F+  K
Sbjct: 178 PVRRVAYAVESARVEQRTDLDKLVIDLETNGTIDPEEAIRRAATILQQQLAVFVDFDHEK 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +        +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPE---RVEEEEEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASL 325


>gi|152973983|ref|YP_001373500.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus subsp.
           cytotoxis NVH 391-98]
 gi|171769269|sp|A7GK47|RPOA_BACCN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|152022735|gb|ABS20505.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cytotoxicus
           NVH 391-98]
          Length = 314

 Score =  362 bits (930), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 138/313 (44%), Positives = 205/313 (65%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDG
Sbjct: 3   EIEKP-KIETVELN-EDAKYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K + LK+  D  K + I  +G G+VTA DI   +D+E+
Sbjct: 61  VLHEFSTVEGVVEDVTTIILNLKKLALKIYSDEEKTLEIDVQGEGIVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  DA  R+ LT  +G GY PA  +++E+ PIG+I ID++Y+P+ +V+Y V
Sbjct: 121 LNPDLYIATLAKDAHFRVRLTAKRGRGYTPADANKSEDQPIGVIPIDSIYTPVSRVTYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R GQV +YDKL++ + TDGSI  +++++L ++IL + L +F+   +  +  +  +  
Sbjct: 181 EKTRVGQVANYDKLTLDVWTDGSIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 HKLEELGLGLRKD 313


>gi|330879400|gb|EGH13549.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           glycinea str. race 4]
          Length = 333

 Score =  362 bits (929), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 149/336 (44%), Positives = 228/336 (67%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVVS---PTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GV TA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVGTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  + V+ M+LTV++G GY PA   +++ D    IG + +D+ +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGVLNMKLTVARGRGYEPADSRQSDEDESRSIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDMETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V  +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPVVIEQEDE---IDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>gi|330430070|gb|AEC21404.1| DNA-directed RNA polymerase alpha chain [Pusillimonas sp. T7-7]
          Length = 329

 Score =  362 bits (929), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 150/327 (45%), Positives = 213/327 (65%), Gaps = 6/327 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           Q  +KP +IE   +G+   N   ++ EP  RG+ HTLGNALRR+L+SS+ G A T VQ+ 
Sbjct: 4   QGFLKPRSIEVEPVGK---NHARVVMEPFERGYGHTLGNALRRILLSSMTGYAPTEVQMT 60

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S++ GV ED+ DI+LN+KG+  K+       + + K+G GVV A DI+  +D+E
Sbjct: 61  GVVHEYSTVAGVREDVVDILLNLKGVVFKLHNREEVTLVLRKQGAGVVLASDIELPHDVE 120

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKV 183
           ++NPDHVI NL     + M++ V +G GYVP       +D    IG I +DA YSP+++V
Sbjct: 121 IINPDHVIANLTDAGKLEMQIKVEQGRGYVPGNVRALSDDRTHTIGRIVLDASYSPVRRV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VESAR  Q  D DKL + I+T+G ++ E++V  ++RIL DQ+ +F   E      ++
Sbjct: 181 SYAVESARVEQRTDLDKLVLDIETNGVVSPEEAVRQSARILMDQISVFAALEGAGDSYED 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             +  +   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 241 APSRAAQQIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 300

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIE 330
            EIK VL   GL LGM L +WPP  +E
Sbjct: 301 NEIKEVLAARGLTLGMKLENWPPLGLE 327


>gi|322381101|ref|ZP_08055104.1| DNA-directed RNA polymerase subunit alpha-like protein
           [Paenibacillus larvae subsp. larvae B-3650]
 gi|321154677|gb|EFX46948.1| DNA-directed RNA polymerase subunit alpha-like protein
           [Paenibacillus larvae subsp. larvae B-3650]
          Length = 314

 Score =  362 bits (929), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 140/310 (45%), Positives = 209/310 (67%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  E+ +    + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDG
Sbjct: 3   EIEKP-KIETVSVN-EDGSYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T+IILN+KG++LK+  D  K + I   G G V AGDI+  +D+E+
Sbjct: 61  VLHEFSTIPGVIEDVTEIILNLKGLSLKIHSDEEKILEIDVEGEGRVVAGDIRADSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  DA + M +   +G GYV A  +++E+ PIG+I +D++Y+PI +V+Y+V
Sbjct: 121 LNPDLHIATLSSDARLHMRIHAGRGRGYVQADKNKSEDQPIGVIPVDSIYTPITRVNYSV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV +YDKL++ + TDGSI  E++V+L ++IL + L +F+   +  K+ +  +  
Sbjct: 181 ENTRVGQVTNYDKLTLEVWTDGSIRPEEAVSLGAKILTEHLMLFVGLTDEAKDAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +LI +TE DM+++ N GRKSL E++
Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELITKTEEDMMKVRNLGRKSLEEVQ 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 EKLEELGLGL 310


>gi|70732859|ref|YP_262626.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas fluorescens
           Pf-5]
 gi|90110859|sp|Q4K557|RPOA_PSEF5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|68347158|gb|AAY94764.1| DNA-directed RNA polymerase, alpha subunit [Pseudomonas fluorescens
           Pf-5]
          Length = 333

 Score =  361 bits (928), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 148/336 (44%), Positives = 227/336 (67%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVVS---PTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  +  + M+L V++G GY PA   +++ D    IG + +D+ +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGALNMKLVVARGRGYEPADSRQSDEDESRSIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V  +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPVVVEQEDE---IDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>gi|297717806|gb|ADI50046.1| DNA-directed RNA polymerase alpha subunit [Candidatus Odyssella
           thessalonicensis L13]
          Length = 338

 Score =  361 bits (928), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 188/338 (55%), Positives = 250/338 (73%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++Q NW+ LIKPN ++ +  G  +     +I EPL RG+  TLGNALRR+L+SSL+GAA 
Sbjct: 1   VLQNNWEALIKPNKLD-VRYGTPDLRHADIIVEPLERGYGLTLGNALRRILLSSLQGAAF 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V+I+GVLHE S+I GV ED+TDIILN+K + ++   +  KRV +   G G V A  I+
Sbjct: 60  TSVKIEGVLHEFSTIPGVMEDVTDIILNLKTVGVRSQVEGVKRVKLVASGKGPVYARQIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+L+ D +IC+LD  A + ME+TV  G GY+PA     E+ PIGLI IDA++SP+
Sbjct: 120 CPAGIEILDEDIIICHLDEGAKLSMEMTVESGKGYIPANSTSHEDKPIGLIPIDAIFSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VSY +E  R GQ  D+DKL M+I TDGS+  +D+VALA+RI+QDQL  FINF+EPK  
Sbjct: 180 KRVSYKIEQTRVGQRTDFDKLIMSISTDGSLKPDDAVALAARIMQDQLYSFINFDEPKTI 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            K++  ++ LPFNP LL+KV+ELELSVRS NCL+ ENI+Y+GDL+Q++E +MLR  NFGR
Sbjct: 240 DKKESKIE-LPFNPNLLRKVDELELSVRSANCLKNENIIYIGDLVQKSEHEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EI+ VL TMGL LGM +P+WPPE+IEEL KK ED
Sbjct: 299 KSLNEIREVLETMGLTLGMIIPNWPPENIEELTKKLED 336


>gi|326203867|ref|ZP_08193729.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           papyrosolvens DSM 2782]
 gi|325985965|gb|EGD46799.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           papyrosolvens DSM 2782]
          Length = 315

 Score =  361 bits (928), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 139/311 (44%), Positives = 204/311 (65%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE  V   ++      I EPL RG+  TLGN+LRR+L+SSL GAA+ +++IDG
Sbjct: 3   EIEKPR-IE-CVSNSDDNTYGKFIVEPLERGYGITLGNSLRRILLSSLPGAAVNSIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T+IILNIK ++L + G+  K + I   G G +TAGDI T  D+E+
Sbjct: 61  VLHEFSTVPGVVEDVTEIILNIKSLSLLIHGEGSKVIYIDANGEGPITAGDIITDQDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L+ D    ME+ +SKG GYV A  ++    PIG++ +D++Y+P+KKV+YTV
Sbjct: 121 LNPDLHIATLNGDHRFYMEMVISKGRGYVSADKNKQAGQPIGVVPVDSIYTPVKKVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ DYDKL++ + TDGSI  +++++L ++IL + L +F++  +  K  +  +  
Sbjct: 181 ENTRVGQITDYDKLTLEVWTDGSINPDEAISLGAKILSEHLNLFVDLSDQAKHTEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + DL  RTE DM+++ N GRKSL E+ 
Sbjct: 241 EETKKEKVLEMTIEELDLSVRSYNCLKRAGINTVEDLTNRTEEDMMKVRNLGRKSLEEVL 300

Query: 308 GVLGTMGLFLG 318
             L  +GLFL 
Sbjct: 301 QKLQALGLFLA 311


>gi|157828836|ref|YP_001495078.1| DNA-directed RNA polymerase subunit alpha [Rickettsia rickettsii
           str. 'Sheila Smith']
 gi|165933563|ref|YP_001650352.1| DNA-directed RNA polymerase subunit alpha [Rickettsia rickettsii
           str. Iowa]
 gi|166229279|sp|A8GT45|RPOA_RICRS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|189043844|sp|B0BUN6|RPOA_RICRO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|157801317|gb|ABV76570.1| DNA-directed RNA polymerase subunit alpha [Rickettsia rickettsii
           str. 'Sheila Smith']
 gi|165908650|gb|ABY72946.1| DNA-directed RNA polymerase alpha chain [Rickettsia rickettsii str.
           Iowa]
          Length = 340

 Score =  361 bits (928), Expect = 7e-98,   Method: Composition-based stats.
 Identities = 183/337 (54%), Positives = 251/337 (74%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y     E  N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNKVAYENF-PETNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE SSI GV ED++++ILNIKGI +KM     + + +   GP VVTAG I+T
Sbjct: 63  SIKIPAIEHEFSSIPGVKEDVSEVILNIKGIEVKMHVAEKRIMKLKATGPCVVTAGMIET 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNPDHVIC+L  D  + MELT   G GYV + ++  +N PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPDHVICDLAKDKQLEMELTCKVGKGYVLSTNNYEDNLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
            V+Y VE+ R GQV DYDKL M ++T+G++  E +V LA+RILQ+QL +FI+FEE +++ 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGAVLPEMAVGLAARILQEQLQLFISFEEQEEDK 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +  +   +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTEADMLR  NFGRK
Sbjct: 243 Q--VKTDALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTEADMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+++EL+K+YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENMQELSKRYED 337


>gi|163938145|ref|YP_001643029.1| DNA-directed RNA polymerase subunit alpha [Bacillus
           weihenstephanensis KBAB4]
 gi|229131145|ref|ZP_04260057.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           BDRD-ST196]
 gi|163860342|gb|ABY41401.1| DNA-directed RNA polymerase, alpha subunit [Bacillus
           weihenstephanensis KBAB4]
 gi|228652358|gb|EEL08283.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           BDRD-ST196]
          Length = 314

 Score =  361 bits (927), Expect = 7e-98,   Method: Composition-based stats.
 Identities = 137/313 (43%), Positives = 205/313 (65%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDG
Sbjct: 3   EIEKP-KIETVELN-EDAKYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T +ILN+K + LK+  D  K + I  +G G+VTA DI   +D+E+
Sbjct: 61  VLHEFSTVEGVVEDVTTMILNLKKLALKIYSDEEKTLEIDVQGEGIVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  +A  RM LT  +G GY PA  +++E+ PIG+I ID++Y+P+ +V+Y V
Sbjct: 121 LNPDLHIATLAKNAHFRMRLTAKRGRGYTPADANKSEDQPIGVIPIDSIYTPVSRVTYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R GQV +YDKL++ + TDGSI  +++++L ++IL + L +F+   +  +  +  +  
Sbjct: 181 EKTRVGQVANYDKLTLDVWTDGSIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 HKLEELGLGLRKD 313


>gi|229015538|ref|ZP_04172535.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH1273]
 gi|229027985|ref|ZP_04184138.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH1271]
 gi|229170988|ref|ZP_04298589.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus MM3]
 gi|228612528|gb|EEK69749.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus MM3]
 gi|228733373|gb|EEL84202.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH1271]
 gi|228745761|gb|EEL95766.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH1273]
          Length = 314

 Score =  361 bits (927), Expect = 7e-98,   Method: Composition-based stats.
 Identities = 137/313 (43%), Positives = 205/313 (65%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDG
Sbjct: 3   EIEKP-KIETVELN-EDAKYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K + LK+  +  K + I  +G G+VTA DI   +D+E+
Sbjct: 61  VLHEFSTVEGVVEDVTTIILNLKKLALKIYSEEEKTLEIDVQGEGIVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  +A  RM LT  +G GY PA  +++E+ PIG+I ID++Y+P+ +V+Y V
Sbjct: 121 LNPDLHIATLAKNAHFRMRLTAKRGRGYTPADANKSEDQPIGVIPIDSIYTPVSRVTYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R GQV +YDKL++ + TDGSI  +++++L ++IL + L +F+   +  +  +  +  
Sbjct: 181 EKTRVGQVANYDKLTLDVWTDGSIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 HKLEELGLGLRKD 313


>gi|28377858|ref|NP_784750.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus plantarum
           WCFS1]
 gi|254556043|ref|YP_003062460.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus plantarum
           JDM1]
 gi|300767846|ref|ZP_07077756.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus plantarum
           subsp. plantarum ATCC 14917]
 gi|308180036|ref|YP_003924164.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus plantarum
           subsp. plantarum ST-III]
 gi|38258532|sp|Q88XW0|RPOA_LACPL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|28270691|emb|CAD63597.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus plantarum
           WCFS1]
 gi|254044970|gb|ACT61763.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus plantarum
           JDM1]
 gi|300494831|gb|EFK29989.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus plantarum
           subsp. plantarum ATCC 14917]
 gi|308045527|gb|ADN98070.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus plantarum
           subsp. plantarum ST-III]
          Length = 314

 Score =  361 bits (927), Expect = 8e-98,   Method: Composition-based stats.
 Identities = 142/312 (45%), Positives = 203/312 (65%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E +N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EFEKPN----IHKIDENDNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EV
Sbjct: 59  VLHEFSTIEGVTEDVTAIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSY 185
           LNPD  IC +   A   M +T + G GYV A+ ++   ++ PIG++ +D+LYSPI++V+Y
Sbjct: 119 LNPDLPICTVADGAHFHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R GQ  D+DKL++ + T+GSIT  ++++L+++IL D L +F+N  +  K     +
Sbjct: 179 QVENTRVGQRDDFDKLTLDVWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   +EEL+LSVRS NCL+   I  + +L  +TEADM+++ N GRKSL E
Sbjct: 239 EKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTNKTEADMMKVRNLGRKSLEE 298

Query: 306 IKGVLGTMGLFL 317
           +K  L  +GL L
Sbjct: 299 VKAKLADLGLSL 310


>gi|192362391|ref|YP_001981233.1| DNA-directed RNA polymerase subunit alpha [Cellvibrio japonicus
           Ueda107]
 gi|238692458|sp|B3PK62|RPOA_CELJU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|190688556|gb|ACE86234.1| DNA-directed RNA polymerase, alpha subunit [Cellvibrio japonicus
           Ueda107]
          Length = 328

 Score =  361 bits (927), Expect = 8e-98,   Method: Composition-based stats.
 Identities = 155/332 (46%), Positives = 226/332 (68%), Gaps = 9/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    E + P +I+   + +    R  ++ EPL RGF HTLGNALRR+L+SS+ G AI 
Sbjct: 1   MQTAVNEFLTPRHID---VSEITPTRARVVLEPLERGFGHTLGNALRRILLSSMAGCAIV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ + M G     +T+ K+GPGVVTAGDIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVREDVIEILLNLKGVAVVMHGKDSTVLTLSKKGPGVVTAGDIQV 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYS 178
            +D+E+ NPDHVI N+  +  ++M LT+++G GY PA   R ++D     G + +DA +S
Sbjct: 118 DHDVEIKNPDHVIANITGNTELKMRLTIARGRGYQPADSRRRDDDESRAIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+K+++Y+VESAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++ E  K
Sbjct: 178 PVKRLAYSVESARVEQRTDLDKLVLDLETNGTIDPEEAIRRAATILQQQLAVFVDLEGEK 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +        K    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 QSA---PEQKEEAIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           G+KSL EIK VL + GL LGM L +WPP S++
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLK 326


>gi|56961959|ref|YP_173681.1| DNA-directed RNA polymerase subunit alpha [Bacillus clausii
           KSM-K16]
 gi|61215810|sp|Q5WLN5|RPOA_BACSK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|56908193|dbj|BAD62720.1| DNA-directed RNA polymerase alpha subunit [Bacillus clausii
           KSM-K16]
          Length = 314

 Score =  361 bits (927), Expect = 8e-98,   Method: Composition-based stats.
 Identities = 138/310 (44%), Positives = 203/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KPN IE + +  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDG
Sbjct: 3   EIEKPN-IETVEVS-EDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IILN+K + LK+  D  K + I  +G G VTAGD+   +D+EV
Sbjct: 61  VLHEFSTIEGVVEDVTTIILNLKKLALKIYSDEEKTLEIDVQGEGNVTAGDLTHDSDVEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L   A  RM L   +G GYV A+ ++ ++ PIG++ ID++Y+P+ +V+Y V
Sbjct: 121 LNPDLHIATLTKGASFRMRLQAKRGRGYVLAEGNKNDDQPIGVLPIDSIYTPVARVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV +YDKL++ + TDGS   E++V+L  +IL + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQVTNYDKLTLDVWTDGSTRPEEAVSLGVKILTEHLNIFVGLTDQAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E++
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTHKTEEDMMKVRNLGRKSLEEVQ 300

Query: 308 GVLGTMGLFL 317
             LG +GL L
Sbjct: 301 EKLGELGLGL 310


>gi|220928236|ref|YP_002505145.1| DNA-directed RNA polymerase subunit alpha [Clostridium
           cellulolyticum H10]
 gi|254765248|sp|B8I808|RPOA_CLOCE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|219998564|gb|ACL75165.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           cellulolyticum H10]
          Length = 315

 Score =  361 bits (927), Expect = 8e-98,   Method: Composition-based stats.
 Identities = 139/311 (44%), Positives = 204/311 (65%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE  V   ++      I EPL RG+  TLGN+LRR+L+SSL G+A+ +++IDG
Sbjct: 3   EIEKPR-IE-CVSNSDDNTYGKFIVEPLERGYGITLGNSLRRILLSSLPGSAVNSIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T+IILNIK ++L + G+  K + I   G G +TAGDI T  D+E+
Sbjct: 61  VLHEFSTVPGVVEDVTEIILNIKSLSLLVHGEGSKVIYIDANGEGPITAGDIITDQDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L+ D    ME+ +SKG GYV A  ++    PIG+I +D++Y+P+KKV+YTV
Sbjct: 121 LNPDLHIATLNGDHRFYMEMVISKGRGYVSADKNKQAGQPIGVIPVDSIYTPVKKVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ DYDKL++ + TDGSI  +++++L ++IL + L +F++  +  K  +  +  
Sbjct: 181 ENTRVGQITDYDKLTLEVWTDGSINPDEAISLGAKILSEHLNLFVDLSDQAKHTEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + DL  RTE DM+++ N GRKSL E+ 
Sbjct: 241 EETKKEKVLEMTIEELDLSVRSYNCLKRAGINTVEDLTNRTEEDMMKVRNLGRKSLEEVL 300

Query: 308 GVLGTMGLFLG 318
             L  +GLFL 
Sbjct: 301 QKLQALGLFLA 311


>gi|228989345|ref|ZP_04149336.1| DNA-directed RNA polymerase subunit alpha [Bacillus pseudomycoides
           DSM 12442]
 gi|228995528|ref|ZP_04155196.1| DNA-directed RNA polymerase subunit alpha [Bacillus mycoides
           Rock3-17]
 gi|229003153|ref|ZP_04160999.1| DNA-directed RNA polymerase subunit alpha [Bacillus mycoides
           Rock1-4]
 gi|229083457|ref|ZP_04215805.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock3-44]
 gi|228699890|gb|EEL52527.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock3-44]
 gi|228758116|gb|EEM07315.1| DNA-directed RNA polymerase subunit alpha [Bacillus mycoides
           Rock1-4]
 gi|228764257|gb|EEM13136.1| DNA-directed RNA polymerase subunit alpha [Bacillus mycoides
           Rock3-17]
 gi|228770423|gb|EEM18996.1| DNA-directed RNA polymerase subunit alpha [Bacillus pseudomycoides
           DSM 12442]
          Length = 314

 Score =  361 bits (927), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 137/313 (43%), Positives = 205/313 (65%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDG
Sbjct: 3   EIEKP-KIETVELN-EDAKYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K + LK+  +  K + I  +G G+VTA DI   +D+E+
Sbjct: 61  VLHEFSTVEGVVEDVTTIILNLKKLALKIYSEEEKTLEIDVQGEGIVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  DA  R+ LT  +G GY PA  +++E+ PIG+I ID++Y+P+ +V+Y V
Sbjct: 121 LNPDLYIATLAKDAHFRVRLTAKRGRGYTPADANKSEDQPIGVIPIDSIYTPVSRVTYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R GQV +YDKL++ + TDGSI  +++++L ++IL + L +F+   +  +  +  +  
Sbjct: 181 EKTRVGQVANYDKLTLDVWTDGSIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 HKLEELGLGLRKD 313


>gi|157804011|ref|YP_001492560.1| DNA-directed RNA polymerase subunit alpha [Rickettsia canadensis
           str. McKiel]
 gi|166229278|sp|A8EZJ2|RPOA_RICCK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|157785274|gb|ABV73775.1| DNA-directed RNA polymerase subunit alpha [Rickettsia canadensis
           str. McKiel]
          Length = 340

 Score =  361 bits (927), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 183/337 (54%), Positives = 251/337 (74%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y  +  E  N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNALIKPNKVAYENVS-ETNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE S+I GV ED++++ILNIKGI +KM     + + +   GP VVTAG I+T
Sbjct: 63  SIKIPAIEHEFSAIPGVKEDVSEMILNIKGIEVKMYVAEKRIIKLKAIGPCVVTAGMIET 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNPDHVICNL  +  + MELT   G GYV + +   +N PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPDHVICNLAKNKQLEMELTCKVGKGYVLSTNSYADNLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
            V+Y VE+ R GQV DYDKL M ++T+G +  E +V LA+RILQ+QL +FI+FEE +++ 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDLLPEMAVGLAARILQEQLQLFISFEEQEEDK 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +  +   +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTEADMLR  NFGRK
Sbjct: 243 Q--VKTDALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTEADMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L  + L  GM++PDWPPE+I+EL+K+YED
Sbjct: 301 SLNEIKEILAKLNLRFGMDVPDWPPENIQELSKRYED 337


>gi|257054498|ref|YP_003132330.1| DNA-directed RNA polymerase subunit alpha [Saccharomonospora
           viridis DSM 43017]
 gi|256584370|gb|ACU95503.1| DNA-directed RNA polymerase subunit alpha [Saccharomonospora
           viridis DSM 43017]
          Length = 358

 Score =  361 bits (927), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 125/307 (40%), Positives = 187/307 (60%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
                E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S++ GV 
Sbjct: 11  EETVNETRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFSTVPGVK 70

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+T+IILN+K + +    D    + + K+GPG VTA DI   + + V NPD  I +L+ 
Sbjct: 71  EDVTEIILNLKELVVSSEEDEPVTMYLRKQGPGEVTAADIVPPSGVTVHNPDLHIASLNG 130

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              + +EL V +G GYVPA  ++     IG I ID++YSP+ KV+Y VE+ R  Q  D+D
Sbjct: 131 KGKLEIELVVERGRGYVPALQNKQAGAEIGRIPIDSIYSPVLKVTYKVEATRVEQRTDFD 190

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + ++T  SIT  D+VA A + L +  G+        + ++   + +      A    
Sbjct: 191 KLVLDVETKPSITPRDAVASAGKTLVELFGLARELNVDAEGIEIGPSPQEADTIAAYAMP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  +GL L  
Sbjct: 251 IEDLDLTVRSYNCLKREGIHTVGELVSRSEADLLDIRNFGAKSIDEVKMKLAGLGLTLKD 310

Query: 320 NLPDWPP 326
           + P + P
Sbjct: 311 SPPGFDP 317


>gi|319948695|ref|ZP_08022816.1| DNA-directed RNA polymerase subunit alpha [Dietzia cinnamea P4]
 gi|319437597|gb|EFV92596.1| DNA-directed RNA polymerase subunit alpha [Dietzia cinnamea P4]
          Length = 344

 Score =  361 bits (927), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 126/319 (39%), Positives = 197/319 (61%), Gaps = 4/319 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V     ENR+  + EPL  GF +T+GN+LRR L+SS+ GAA+T+++I+GVLH
Sbjct: 6   RPTLTEEVV----SENRSRFVLEPLEPGFGYTIGNSLRRTLLSSIPGAAVTSIRIEGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TDIILN+KG+ +    D    + + K+GPG VTAGDI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDIILNLKGLVVSSVEDEPVTMYLKKQGPGAVTAGDIVPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLHIATLNEKGRLEIELVVERGRGYVPAGLNKDAGHEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  S+T  D++A A + L +  G+     E  + ++   +    
Sbjct: 182 RVHQRTDFDRLVLDVETKNSMTARDALASAGKTLVELFGLARELNEEAEGIEIGPSPAEA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
               A    +++L+LSVRS NCL+ E +  +G+L+ R+E+D+L + NFG+KS+ E+K  L
Sbjct: 242 DHIAAYGMPIDDLDLSVRSYNCLKREGVHTVGELVARSESDLLDIRNFGQKSIDEVKVKL 301

Query: 311 GTMGLFLGMNLPDWPPESI 329
             +GL L    P + P S+
Sbjct: 302 VELGLSLKDAPPGFDPASV 320


>gi|330969796|gb|EGH69862.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           aceris str. M302273PT]
          Length = 333

 Score =  361 bits (927), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 150/336 (44%), Positives = 229/336 (68%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVVS---PTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  + V+ M+LTV++G GY PA   +++ D    IG + +D+ +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGVLNMKLTVARGRGYEPADSRQSDEDESRSIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V  +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPVVIEQEDE---IDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLVSRGLSLGMRLDNWPPASLKKDDK 330


>gi|331699145|ref|YP_004335384.1| DNA-directed RNA polymerase subunit alpha [Pseudonocardia
           dioxanivorans CB1190]
 gi|326953834|gb|AEA27531.1| DNA-directed RNA polymerase subunit alpha [Pseudonocardia
           dioxanivorans CB1190]
          Length = 347

 Score =  361 bits (926), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 125/309 (40%), Positives = 187/309 (60%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                 E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV
Sbjct: 10  TEDSVTETRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+TDIILN+K + +    D    + + K+GPG VTAGDI     + V NPD  I  L+
Sbjct: 70  KEDVTDIILNLKELVVSSEEDEPVTMYLRKQGPGPVTAGDIVPPAGVTVHNPDLHIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+
Sbjct: 130 DKGRLEVELVVERGRGYVPAMQNKATGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  SIT  D++A A + L +  G+        + ++   + +      A   
Sbjct: 190 DKLVLDVETKPSITPRDALASAGKTLVELFGLARELNVDAEGIEIGPSPQEADTIAAFAM 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +EEL+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  +GL L 
Sbjct: 250 PIEELDLTVRSYNCLKREGIHTVGELVGRSEADLLDIRNFGAKSIDEVKMKLVGLGLALK 309

Query: 319 MNLPDWPPE 327
            + P + P 
Sbjct: 310 DSPPGFDPS 318


>gi|295694866|ref|YP_003588104.1| DNA-directed RNA polymerase, alpha subunit [Bacillus tusciae DSM
           2912]
 gi|295410468|gb|ADG04960.1| DNA-directed RNA polymerase, alpha subunit [Bacillus tusciae DSM
           2912]
          Length = 314

 Score =  361 bits (926), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 130/310 (41%), Positives = 196/310 (63%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  +E + +  E       + EPL RG+  TLGNALRR+L+SSL GAA T+V+IDG
Sbjct: 3   EMEKPR-LETVEIN-ESGTYGKFVIEPLERGYGTTLGNALRRILLSSLPGAACTSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED T+IILN+K + L++  D  K + I   G G + AGDIQ  +D+++
Sbjct: 61  VLHEFSTIPGVVEDTTEIILNLKHLALRIHSDEEKTLIIDAEGEGEIKAGDIQADSDVDI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  L   A +  E+  ++G GYVPA  ++ E  PIG+I +D++++PI +V+Y++
Sbjct: 121 LNPELHIATLAEGARLYAEIKAARGRGYVPADRNKNEEQPIGVIPMDSIFTPISRVNYSI 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV DYDKL+  + TDGSI  +++V+  +RIL + L +F+   +  +     +  
Sbjct: 181 ENTRVGQVTDYDKLTFEVWTDGSIRPDEAVSYGARILTEHLTLFLGLTDQPRAGDVLVER 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                   L   +EEL+LSVRS NCL+   I  + +L  +TE +M+++ N GRKSL E++
Sbjct: 241 DEQRREKVLDMTIEELDLSVRSYNCLKRAGINTVAELCSKTEEEMMKVRNLGRKSLEEVQ 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 EKLAELGLAL 310


>gi|254455604|ref|ZP_05069033.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Pelagibacter
           sp. HTCC7211]
 gi|207082606|gb|EDZ60032.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Pelagibacter
           sp. HTCC7211]
          Length = 342

 Score =  361 bits (926), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 180/335 (53%), Positives = 258/335 (77%), Gaps = 3/335 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNW+ LIKP+ ++  +   ++     +IAEPL +G+  TLGN+LRR+L+SS+RGAA+T++
Sbjct: 9   KNWKSLIKPSKLDVQI--SDDLTHAKIIAEPLEKGYGLTLGNSLRRILLSSIRGAAVTSI 66

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           QIDGVLHE +SIKGV ED+TDI+LN+K + LK + +  K++ +  +GPG + A DI  V 
Sbjct: 67  QIDGVLHEFTSIKGVREDVTDIVLNVKSLALKSNSEGTKKLVLDAKGPGEIKASDIAPVA 126

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           D+E+LNPD VICNLD +    ME+ V+ G GYVPA  ++ E  P+GLI ID+LYSP+KKV
Sbjct: 127 DVEILNPDLVICNLDENTNFHMEMNVNTGKGYVPADLNKPEEPPLGLIAIDSLYSPVKKV 186

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY++ +AREG+ LDYDKL+M ++T+G+I+ ED+VA ++RI QDQL MF+NF+EP +   +
Sbjct: 187 SYSISTAREGKALDYDKLTMEVETNGAISAEDAVAYSARIFQDQLKMFVNFDEPVEAPVK 246

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +++ +   FN  LL+KV+ELELSVRS NCL+ +NI+Y+GDL+Q++E +MLR  NFGRKSL
Sbjct: 247 EVSTEP-EFNKNLLRKVDELELSVRSMNCLKNDNIIYIGDLVQKSEGEMLRTPNFGRKSL 305

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
            EIK VL  M L+LGM +P+WPP++I E++KK E+
Sbjct: 306 NEIKEVLTGMSLYLGMEIPNWPPDNIAEMSKKLEE 340


>gi|30018406|ref|NP_830037.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus ATCC
           14579]
 gi|30260328|ref|NP_842705.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           Ames]
 gi|42779218|ref|NP_976465.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus ATCC
           10987]
 gi|47525393|ref|YP_016742.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           'Ames Ancestor']
 gi|47570249|ref|ZP_00240900.1| DNA-directed RNA polymerase alpha chain [Bacillus cereus G9241]
 gi|49183171|ref|YP_026423.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           Sterne]
 gi|49481737|ref|YP_034488.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar konkukian str. 97-27]
 gi|52145083|ref|YP_081747.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus E33L]
 gi|65317583|ref|ZP_00390542.1| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Bacillus anthracis str. A2012]
 gi|118475905|ref|YP_893056.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           str. Al Hakam]
 gi|167642075|ref|ZP_02400299.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           A0193]
 gi|170689688|ref|ZP_02880866.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           A0465]
 gi|177656195|ref|ZP_02937176.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           A0174]
 gi|190567453|ref|ZP_03020367.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis
           Tsiankovskii-I]
 gi|196041162|ref|ZP_03108458.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus
           NVH0597-99]
 gi|206972214|ref|ZP_03233161.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus AH1134]
 gi|217957712|ref|YP_002336256.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH187]
 gi|218232273|ref|YP_002364986.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus B4264]
 gi|218895272|ref|YP_002443683.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus G9842]
 gi|218901342|ref|YP_002449176.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus AH820]
 gi|222093907|ref|YP_002527957.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus Q1]
 gi|225862189|ref|YP_002747567.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus
           03BB102]
 gi|227812810|ref|YP_002812819.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           CDC 684]
 gi|228898890|ref|ZP_04063172.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           IBL 4222]
 gi|228905934|ref|ZP_04069831.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           IBL 200]
 gi|228912876|ref|ZP_04076523.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar pulsiensis BGSC 4CC1]
 gi|228919087|ref|ZP_04082466.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar huazhongensis BGSC 4BD1]
 gi|228925390|ref|ZP_04088486.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar pondicheriensis BGSC 4BA1]
 gi|228931639|ref|ZP_04094545.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar andalousiensis BGSC 4AW1]
 gi|228937440|ref|ZP_04100086.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar berliner ATCC 10792]
 gi|228943942|ref|ZP_04106327.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar monterrey BGSC 4AJ1]
 gi|228950685|ref|ZP_04112819.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar kurstaki str. T03a001]
 gi|228956578|ref|ZP_04118374.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar pakistani str. T13001]
 gi|228963237|ref|ZP_04124406.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar sotto str. T04001]
 gi|228970326|ref|ZP_04130985.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar thuringiensis str. T01001]
 gi|228976896|ref|ZP_04137308.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           Bt407]
 gi|228983392|ref|ZP_04143605.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar tochigiensis BGSC 4Y1]
 gi|229041042|ref|ZP_04189805.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH676]
 gi|229067902|ref|ZP_04201219.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus F65185]
 gi|229074198|ref|ZP_04207244.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock4-18]
 gi|229089268|ref|ZP_04220549.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock3-42]
 gi|229094859|ref|ZP_04225864.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock3-29]
 gi|229100936|ref|ZP_04231740.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock3-28]
 gi|229107823|ref|ZP_04237459.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock1-15]
 gi|229113813|ref|ZP_04243248.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus Rock1-3]
 gi|229119799|ref|ZP_04249060.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus 95/8201]
 gi|229125654|ref|ZP_04254686.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           BDRD-Cer4]
 gi|229136983|ref|ZP_04265610.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           BDRD-ST26]
 gi|229142943|ref|ZP_04271384.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           BDRD-ST24]
 gi|229148546|ref|ZP_04276802.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus m1550]
 gi|229153915|ref|ZP_04282045.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus ATCC
           4342]
 gi|229159310|ref|ZP_04287334.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus R309803]
 gi|229176737|ref|ZP_04304141.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus 172560W]
 gi|229182531|ref|ZP_04309782.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus BGSC
           6E1]
 gi|229188422|ref|ZP_04315470.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus ATCC
           10876]
 gi|229194527|ref|ZP_04321330.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus m1293]
 gi|229602997|ref|YP_002864788.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           A0248]
 gi|254686636|ref|ZP_05150495.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           CNEVA-9066]
 gi|254726284|ref|ZP_05188066.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           A1055]
 gi|254735289|ref|ZP_05192997.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           Western North America USA6153]
 gi|254739481|ref|ZP_05197179.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           Kruger B]
 gi|254756844|ref|ZP_05208872.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           Australia 94]
 gi|296500970|ref|YP_003662670.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           BMB171]
 gi|300119550|ref|ZP_07057094.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus SJ1]
 gi|301051874|ref|YP_003790085.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis CI]
 gi|33301600|sp|Q81J18|RPOA_BACCR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|33301605|sp|Q81VQ4|RPOA_BACAN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61215852|sp|Q63H64|RPOA_BACCZ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61215930|sp|Q6HPN2|RPOA_BACHK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61215979|sp|Q73F69|RPOA_BACC1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158512483|sp|A0R8K6|RPOA_BACAH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|29893946|gb|AAP07238.1| DNA-directed RNA polymerase alpha chain [Bacillus cereus ATCC
           14579]
 gi|30253649|gb|AAP24191.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           Ames]
 gi|42735133|gb|AAS39073.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus ATCC
           10987]
 gi|47500541|gb|AAT29217.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           'Ames Ancestor']
 gi|47553073|gb|EAL11473.1| DNA-directed RNA polymerase alpha chain [Bacillus cereus G9241]
 gi|49177098|gb|AAT52474.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           Sterne]
 gi|49333293|gb|AAT63939.1| DNA-directed RNA polymerase [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|51978552|gb|AAU20102.1| DNA-directed RNA polymerase [Bacillus cereus E33L]
 gi|118415130|gb|ABK83549.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           str. Al Hakam]
 gi|167509962|gb|EDR85384.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           A0193]
 gi|170666359|gb|EDT17144.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           A0465]
 gi|172079843|gb|EDT64957.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           A0174]
 gi|190561580|gb|EDV15551.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis
           Tsiankovskii-I]
 gi|196028097|gb|EDX66708.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus
           NVH0597-99]
 gi|206732788|gb|EDZ49963.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus AH1134]
 gi|217066667|gb|ACJ80917.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus AH187]
 gi|218160230|gb|ACK60222.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus B4264]
 gi|218539881|gb|ACK92279.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus AH820]
 gi|218541781|gb|ACK94175.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus G9842]
 gi|221237955|gb|ACM10665.1| DNA-directed RNA polymerase [Bacillus cereus Q1]
 gi|225788641|gb|ACO28858.1| DNA-directed RNA polymerase, alpha subunit [Bacillus cereus
           03BB102]
 gi|227006086|gb|ACP15829.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           CDC 684]
 gi|228588993|gb|EEK47008.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus m1293]
 gi|228595096|gb|EEK52867.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus ATCC
           10876]
 gi|228600986|gb|EEK58555.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus BGSC
           6E1]
 gi|228606780|gb|EEK64197.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus 172560W]
 gi|228624202|gb|EEK81004.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus R309803]
 gi|228629596|gb|EEK86293.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus ATCC
           4342]
 gi|228634962|gb|EEK91535.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus m1550]
 gi|228640564|gb|EEK96953.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           BDRD-ST24]
 gi|228646521|gb|EEL02728.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           BDRD-ST26]
 gi|228657846|gb|EEL13652.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           BDRD-Cer4]
 gi|228663700|gb|EEL19279.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus 95/8201]
 gi|228669684|gb|EEL25091.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus Rock1-3]
 gi|228675672|gb|EEL30880.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock1-15]
 gi|228682515|gb|EEL36588.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock3-28]
 gi|228688602|gb|EEL42475.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock3-29]
 gi|228694107|gb|EEL47789.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock3-42]
 gi|228708968|gb|EEL61095.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus
           Rock4-18]
 gi|228715261|gb|EEL67120.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus F65185]
 gi|228727339|gb|EEL78533.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH676]
 gi|228776382|gb|EEM24735.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar tochigiensis BGSC 4Y1]
 gi|228782866|gb|EEM31032.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           Bt407]
 gi|228789435|gb|EEM37355.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar thuringiensis str. T01001]
 gi|228796495|gb|EEM43934.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar sotto str. T04001]
 gi|228803143|gb|EEM49965.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar pakistani str. T13001]
 gi|228809036|gb|EEM55521.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar kurstaki str. T03a001]
 gi|228815775|gb|EEM62011.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar monterrey BGSC 4AJ1]
 gi|228822273|gb|EEM68255.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar berliner ATCC 10792]
 gi|228828067|gb|EEM73795.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar andalousiensis BGSC 4AW1]
 gi|228834312|gb|EEM79853.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar pondicheriensis BGSC 4BA1]
 gi|228840612|gb|EEM85874.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar huazhongensis BGSC 4BD1]
 gi|228846812|gb|EEM91817.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar pulsiensis BGSC 4CC1]
 gi|228853749|gb|EEM98509.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           IBL 200]
 gi|228860790|gb|EEN05168.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           IBL 4222]
 gi|229267405|gb|ACQ49042.1| DNA-directed RNA polymerase, alpha subunit [Bacillus anthracis str.
           A0248]
 gi|296322022|gb|ADH04950.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           BMB171]
 gi|298723022|gb|EFI63920.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus SJ1]
 gi|300374043|gb|ADK02947.1| DNA-directed RNA polymerase alpha subunit [Bacillus cereus biovar
           anthracis str. CI]
 gi|324324128|gb|ADY19388.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar finitimus YBT-020]
 gi|326937932|gb|AEA13828.1| DNA-directed RNA polymerase subunit alpha [Bacillus thuringiensis
           serovar chinensis CT-43]
          Length = 314

 Score =  361 bits (926), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 137/313 (43%), Positives = 205/313 (65%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDG
Sbjct: 3   EIEKP-KIETVELN-EDAKYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K + LK+  +  K + I  +G G+VTA DI   +D+E+
Sbjct: 61  VLHEFSTVEGVVEDVTTIILNLKKLALKIYSEEEKTLEIDVQGEGIVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  DA  R+ LT  +G GY PA  +++E+ PIG+I ID++Y+P+ +V+Y V
Sbjct: 121 LNPDLHIATLAKDAHFRVRLTAKRGRGYTPADANKSEDQPIGVIPIDSIYTPVSRVTYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R GQV +YDKL++ + TDGSI  +++++L ++IL + L +F+   +  +  +  +  
Sbjct: 181 EKTRVGQVANYDKLTLDVWTDGSIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 HKLEELGLGLRKD 313


>gi|81429352|ref|YP_396353.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus sakei
           subsp. sakei 23K]
 gi|90110847|sp|Q38UT7|RPOA_LACSS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|78610995|emb|CAI56047.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus sakei
           subsp. sakei 23K]
          Length = 312

 Score =  361 bits (926), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 132/310 (42%), Positives = 199/310 (64%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E  N    + EPL RG+  TLGN+LRR+L++SL G A+T +QIDG
Sbjct: 3   EFEKPN----ITKVDESTNYGKFVVEPLERGYGTTLGNSLRRILLASLPGTAVTDIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILNIK + LK+  +  K + I  +GP  VTA DI + +D+EV
Sbjct: 59  VLHEFSTIDGVLEDVTQIILNIKKLALKLHVEEDKTIEIDVKGPATVTAADIISDDDVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D  IC +       + +TV KG GYV A  +++++ PIG++ ID++Y+PI +V+Y V
Sbjct: 119 LNTDQYICTVAEGGNFHVRMTVKKGRGYVAAVQNKSDDMPIGVLPIDSIYTPISRVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL++ + T+GSI+  ++++LA++I+ + L +F++  +  K  +  +  
Sbjct: 179 ESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKIMTEHLAIFVDLTDEAKNAEIMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+++ N GRKSL E+K
Sbjct: 239 EETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTDKSEADMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLFDLGLGL 308


>gi|284992846|ref|YP_003411400.1| DNA-directed RNA polymerase subunit alpha [Geodermatophilus
           obscurus DSM 43160]
 gi|284066091|gb|ADB77029.1| DNA-directed RNA polymerase, alpha subunit [Geodermatophilus
           obscurus DSM 43160]
          Length = 358

 Score =  360 bits (925), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 121/322 (37%), Positives = 189/322 (58%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                 E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++I+G LHE +++ GV
Sbjct: 10  TEETISEQRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIEGTLHEFTTVPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+IILN+KG+ +    D    + + K+GPG VTA DI     +EV NP+  I  L+
Sbjct: 70  KEDVTEIILNLKGLVVSSDSDEPVTMYLRKQGPGEVTAADIAPPAGVEVHNPELHIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+
Sbjct: 130 GKGRLEIELVVERGRGYVPAPQNKQPGQEIGRIPVDSIYSPVLKVTYAVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           D+L + ++T  SI   D++A A   L +  G+        + ++   +            
Sbjct: 190 DRLVVDVETKPSIAPRDAIASAGSTLVELFGLLRELNIDAEGIEVGPSPAEAADIANFSM 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+++L+VRS NCL+ E +  +G+L+ R+EAD+L + NFG KS+ E+K  L  MGL L 
Sbjct: 250 PIEDMDLTVRSYNCLKREGVHTVGELVTRSEADLLDIRNFGAKSIDEVKMKLAAMGLALK 309

Query: 319 MNLPDWPPESIEELAKKYEDKC 340
            + P + P S+E   + YE   
Sbjct: 310 DSPPGFIPTSVESYDEGYETDA 331


>gi|52078637|ref|YP_077428.1| DNA-directed RNA polymerase subunit alpha [Bacillus licheniformis
           ATCC 14580]
 gi|52783999|ref|YP_089828.1| DNA-directed RNA polymerase subunit alpha [Bacillus licheniformis
           ATCC 14580]
 gi|319649088|ref|ZP_08003296.1| DNA-directed RNA polymerase subunit alpha [Bacillus sp. BT1B_CT2]
 gi|81667225|sp|Q65P79|RPOA_BACLD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|52001848|gb|AAU21790.1| RNA polymerase (alpha subunit) [Bacillus licheniformis ATCC 14580]
 gi|52346501|gb|AAU39135.1| RpoA [Bacillus licheniformis ATCC 14580]
 gi|317388788|gb|EFV69607.1| DNA-directed RNA polymerase subunit alpha [Bacillus sp. BT1B_CT2]
          Length = 314

 Score =  360 bits (925), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 135/313 (43%), Positives = 204/313 (65%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  ++      + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETVEIS-DDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IILNIK + LK+  +  K + I  +G GVVTA DI   +D+E+
Sbjct: 61  VLHEFSTIEGVVEDVTTIILNIKKLALKIYSEEEKTLEIDVQGEGVVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  +A  R+ LT  +G GY PA  ++ ++ PIG+I ID++++P+ +VSY V
Sbjct: 121 LNPDLHIATLGQNASFRVRLTAQRGRGYTPADANKRDDQPIGVIPIDSIFTPVSRVSYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ +YDKL++ + TDGS   ++++AL S+IL + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQITNYDKLTLDVWTDGSTGPKEAIALGSKILTEHLNIFVGLTDEAQHAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 AKLEELGLGLRKD 313


>gi|296268581|ref|YP_003651213.1| DNA-directed RNA polymerase subunit alpha [Thermobispora bispora
           DSM 43833]
 gi|296091368|gb|ADG87320.1| DNA-directed RNA polymerase, alpha subunit [Thermobispora bispora
           DSM 43833]
          Length = 340

 Score =  360 bits (925), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 127/321 (39%), Positives = 190/321 (59%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                 E R+  I EPL  GF +T+GN+LRR L+SS+ GAA+T+++I+GVLHE S++ GV
Sbjct: 10  QEEPLSEYRSRFILEPLEPGFGYTIGNSLRRTLLSSIPGAAVTSIRIEGVLHEFSTVPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+TDIILN+K + +    D    + + K+GPG VTA DI     +EV NP+  I  L+
Sbjct: 70  KEDVTDIILNLKQLVVSSEHDEPVVMYLRKQGPGEVTAADIAPPAGVEVHNPELHIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
             A + MELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+ R  Q  D+
Sbjct: 130 GKAKLEMELTVERGRGYVSAAQNKQPGQEIGRIPIDSIYSPVLKVTYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           D+L + ++T  SI   D+VA A + L +  G+        + ++   +         L  
Sbjct: 190 DRLILDVETKPSIKPRDAVASAGKTLVELFGLARELNVEAEGIEIGPSPTDAALAADLAL 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +EEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  MGL L 
Sbjct: 250 PIEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLDIRNFGAKSIEEVKQKLAEMGLTLK 309

Query: 319 MNLPDWPPESIEELAKKYEDK 339
            + P + P ++     + +D+
Sbjct: 310 DSPPGFDPATVAGGGGRLDDE 330


>gi|34499615|ref|NP_903830.1| DNA-directed RNA polymerase subunit alpha [Chromobacterium
           violaceum ATCC 12472]
 gi|41688632|sp|Q7NQH7|RPOA_CHRVO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|34105466|gb|AAQ61821.1| DNA-directed RNA polymerase (alpha subunit) [Chromobacterium
           violaceum ATCC 12472]
          Length = 327

 Score =  360 bits (925), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 154/332 (46%), Positives = 217/332 (65%), Gaps = 8/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+   +         +  EP  RG+AHTLGN+LRR+L+SS+ G A T
Sbjct: 1   MQNSASEFLKPRLIDVQPVS---ATHARVSMEPFERGYAHTLGNSLRRILLSSMPGYAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE S++ GV ED+ DI+LN+KG+ LK+ G     +T+ K G G V A DI+ 
Sbjct: 58  EVTIAGVLHEYSALDGVREDVVDILLNLKGVVLKLHGRDSVVLTLKKEGEGAVLASDIEL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP--AKHHRTENDPIGLITIDALYSP 179
            +D+EV+NP+HVIC++     + ME+ V KG GY P  A+    +N  IG I +DA +SP
Sbjct: 118 PHDVEVINPEHVICHISSGGKIDMEVKVEKGRGYQPVSARTSHDDNRSIGTIQLDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +++VS+ VESAR  Q  D D+L + I+T+G I  E +V  A+RIL DQL +F + +    
Sbjct: 178 VRRVSFAVESARVEQRTDLDRLVLDIETNGVIEPEQAVRNAARILMDQLSIFADLQGTAV 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
              E++  K+ P +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G
Sbjct: 238 ---EEVVEKAPPIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTETELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           RKSL EIK VL + GL LGM L +WPP  +E+
Sbjct: 295 RKSLNEIKEVLASKGLTLGMKLENWPPAGLEK 326


>gi|15612725|ref|NP_241028.1| DNA-directed RNA polymerase subunit alpha [Bacillus halodurans
           C-125]
 gi|6094120|sp|O50634|RPOA_BACHD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|2760185|dbj|BAA24194.1| RNA polymerase alpha subunit [Bacillus halodurans]
 gi|4512431|dbj|BAA75298.1| rpoA homologue (identity of 85% to B. subtilis ) [Bacillus
           halodurans]
 gi|10172774|dbj|BAB03881.1| DNA-directed RNA polymerase alpha subunit [Bacillus halodurans
           C-125]
          Length = 314

 Score =  360 bits (925), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 140/310 (45%), Positives = 208/310 (67%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I +  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDG
Sbjct: 3   EIEKP-VIETIEIS-EDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T I+LN+K + LK+  D  K + I  +G GVVTAGD+   +D++V
Sbjct: 61  VLHEFSTIEGVVEDVTTIVLNLKQLALKIYSDEDKTLEIDTQGEGVVTAGDLTHDSDVDV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L   A +RM +T  +G GYVPA+ ++++   IG+I ID++Y+P+ +V+Y V
Sbjct: 121 LNPDLHIATLTTGAHLRMRITAKRGRGYVPAEGNKSDELAIGVIPIDSIYTPVSRVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV +YDKL++ + TDGSI  E++V+L ++IL + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQVTNYDKLTLDVWTDGSIRPEEAVSLGAKILTEHLNIFVGLTDQAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L Q+TE DM+++ N GRKSL E++
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTQKTEEDMMKVRNLGRKSLEEVQ 300

Query: 308 GVLGTMGLFL 317
             LG +GL L
Sbjct: 301 EKLGELGLGL 310


>gi|229009646|ref|ZP_04166872.1| DNA-directed RNA polymerase subunit alpha [Bacillus mycoides DSM
           2048]
 gi|229053983|ref|ZP_04195417.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH603]
 gi|229165125|ref|ZP_04292920.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH621]
 gi|228618388|gb|EEK75418.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH621]
 gi|228721401|gb|EEL72922.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH603]
 gi|228751668|gb|EEM01468.1| DNA-directed RNA polymerase subunit alpha [Bacillus mycoides DSM
           2048]
          Length = 314

 Score =  360 bits (925), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 136/313 (43%), Positives = 205/313 (65%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDG
Sbjct: 3   EIEKP-KIETVELN-EDAKYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T +ILN+K + LK+  +  K + I  +G G+VTA DI   +D+E+
Sbjct: 61  VLHEFSTVEGVVEDVTTMILNLKKLALKIYSEEEKTLEIDVQGEGIVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  +A  RM LT  +G GY PA  +++E+ PIG+I ID++Y+P+ +V+Y V
Sbjct: 121 LNPDLHIATLAKNAHFRMRLTAKRGRGYTPADANKSEDQPIGVIPIDSIYTPVSRVTYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R GQV +YDKL++ + TDGSI  +++++L ++IL + L +F+   +  +  +  +  
Sbjct: 181 EKTRVGQVANYDKLTLDVWTDGSIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 HKLEELGLGLRKD 313


>gi|229542177|ref|ZP_04431237.1| DNA-directed RNA polymerase, alpha subunit [Bacillus coagulans
           36D1]
 gi|229326597|gb|EEN92272.1| DNA-directed RNA polymerase, alpha subunit [Bacillus coagulans
           36D1]
          Length = 314

 Score =  360 bits (924), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 133/313 (42%), Positives = 207/313 (66%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  ++      + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETVEVS-DDATYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE S+++GV ED+T IILN+K + LK+  D  K + I  +G G VTA DI   +D+E+
Sbjct: 61  VMHEFSTVEGVVEDVTSIILNLKKLALKIYSDEEKTLEIDVQGEGAVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  +  +  +RM +T ++G GYVPA  ++ E+ PIG+I ID++Y+P+++V+Y V
Sbjct: 121 LNPDLYIATVAENGHLRMRMTANQGRGYVPADQNKREDHPIGVIPIDSIYTPVQRVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ +YDKLS+ + TDGSI  ++++AL ++IL + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQISNYDKLSLDVTTDGSIGPKEAIALGAKILTEHLNIFVGLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 AKLEDLGLGLRKD 313


>gi|205372042|ref|ZP_03224859.1| DNA-directed RNA polymerase subunit alpha [Bacillus coahuilensis
           m4-4]
          Length = 314

 Score =  360 bits (924), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 136/313 (43%), Positives = 205/313 (65%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  ++      + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETVEVS-DDATYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T +ILNIK + LK+  D  K + I  +G GVVTA DI   +D+E+
Sbjct: 61  VLHEFSTIEGVVEDVTSMILNIKKLALKIYSDEEKTLEIDIKGNGVVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  D+ +RM L   +G GY PA  ++ E+ PIG+I ID++Y+P+ +V+Y V
Sbjct: 121 LNPDLHIATLSGDSHLRMRLNAQRGRGYTPADQNKREDLPIGVIPIDSIYTPVSRVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ +YDKLS+ + TDGSI  +++++L ++IL + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQLTNYDKLSLDVWTDGSIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 AKLDELGLGLRKD 313


>gi|261409493|ref|YP_003245734.1| DNA-directed RNA polymerase subunit alpha [Paenibacillus sp.
           Y412MC10]
 gi|315649671|ref|ZP_07902755.1| DNA-directed RNA polymerase subunit alpha [Paenibacillus vortex
           V453]
 gi|329922053|ref|ZP_08277846.1| DNA-directed RNA polymerase, alpha subunit [Paenibacillus sp. HGF5]
 gi|261285956|gb|ACX67927.1| DNA-directed RNA polymerase, alpha subunit [Paenibacillus sp.
           Y412MC10]
 gi|315274859|gb|EFU38235.1| DNA-directed RNA polymerase subunit alpha [Paenibacillus vortex
           V453]
 gi|328942436|gb|EGG38700.1| DNA-directed RNA polymerase, alpha subunit [Paenibacillus sp. HGF5]
          Length = 314

 Score =  360 bits (924), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 139/310 (44%), Positives = 205/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  EE      + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETVDVN-EEGTYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T++ILN+K ++LK+  D  K   I   G GVVTAGDI+  +D+E+
Sbjct: 61  VLHEFSTIPGVMEDVTEVILNLKALSLKIHSDEEKVFEIDAEGEGVVTAGDIRADSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L   A + M +  S+G GYV A  ++ ++ PIG+I +D++Y+PI +V+Y V
Sbjct: 121 LNPDLHIATLGPGARLHMRIFASRGRGYVQADRNKRDDQPIGVIPVDSIYTPISRVNYGV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV +YDKL++ I TDGSI  E++V+L ++IL + L +F+   +  K+ +  +  
Sbjct: 181 ENTRVGQVTNYDKLTLEIWTDGSIRPEEAVSLGAKILTEHLFLFVGLTDEAKDAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E++
Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTTKTEEDMMKVRNLGRKSLEEVQ 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 EKLEELGLGL 310


>gi|16077211|ref|NP_388024.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|221307956|ref|ZP_03589803.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|221312277|ref|ZP_03594082.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis subsp.
           subtilis str. NCIB 3610]
 gi|221317211|ref|ZP_03598505.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis subsp.
           subtilis str. JH642]
 gi|221321474|ref|ZP_03602768.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis subsp.
           subtilis str. SMY]
 gi|296333140|ref|ZP_06875594.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305672843|ref|YP_003864514.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|321313815|ref|YP_004206102.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis BSn5]
 gi|133395|sp|P20429|RPOA_BACSU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|142463|gb|AAA22217.1| RNA polymerase alpha-core-subunit [Bacillus subtilis]
 gi|1044991|gb|AAB06826.1| RNA polymerase alpha-core-subunit [Bacillus subtilis]
 gi|2632410|emb|CAB11919.1| RNA polymerase (alpha subunit) [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|116733896|gb|ABK20007.1| DNA-directed RNA polymerase alpha subunit [synthetic construct]
 gi|291482515|dbj|BAI83590.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis subsp.
           natto BEST195]
 gi|296149756|gb|EFG90651.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305411086|gb|ADM36204.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|320020089|gb|ADV95075.1| DNA-directed RNA polymerase subunit alpha [Bacillus subtilis BSn5]
          Length = 314

 Score =  360 bits (924), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 136/313 (43%), Positives = 203/313 (64%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  + +     + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETVEISDDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IIL+IK + LK+  D  K + I  +G G VTA DI   +D+E+
Sbjct: 61  VLHEFSTIEGVVEDVTTIILHIKKLALKIYSDEEKTLEIDVQGEGTVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  +A  R+ LT  +G GY PA  ++ ++ PIG+I ID++Y+P+ +VSY V
Sbjct: 121 LNPDLHIATLGENASFRVRLTAQRGRGYTPADANKRDDQPIGVIPIDSIYTPVSRVSYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV +YDKL++ + TDGS   ++++AL S+IL + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQVANYDKLTLDVWTDGSTGPKEAIALGSKILTEHLNIFVGLTDEAQHAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 AKLEELGLGLRKD 313


>gi|307543850|ref|YP_003896329.1| DNA-directed RNA polymerase subunit alpha [Halomonas elongata DSM
           2581]
 gi|307215874|emb|CBV41144.1| DNA-directed RNA polymerase subunit alpha [Halomonas elongata DSM
           2581]
          Length = 332

 Score =  360 bits (924), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 141/335 (42%), Positives = 223/335 (66%), Gaps = 9/335 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  E ++P +I+   +         ++ EP  RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQRSVTEFLRPRDIKVEEISAH---HAKIVLEPFERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +I GV HE S+I+G+ ED+ +I+LN+K + +KM       +++ K+GP VVTAGDI  
Sbjct: 58  EAEIAGVDHEYSAIEGIQEDVIEILLNLKDVAIKMHSRDEAVLSLNKQGPAVVTAGDIAL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYS 178
            +D+EV+NP+HVI +++  A ++M+L +++G GY PA      +D     G + +DA +S
Sbjct: 118 DHDVEVVNPEHVIAHVNEGAELKMQLKIARGRGYEPADVRGDADDESRAIGRLQLDATFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY+VE+AR  Q  D DKL + ++TDG++  E+++  ++ ILQ+QL  F++ E  K
Sbjct: 178 PVRRVSYSVEAARVEQRTDLDKLIIDLETDGTLDPEEAIRRSATILQEQLAAFVDLEADK 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           ++    +  +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EQE---VEEEEDHIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELA 333
           G+KSL EIK VL   GL LGM L +WPP S+++  
Sbjct: 295 GKKSLNEIKDVLAARGLSLGMRLENWPPASLKDDK 329


>gi|253577207|ref|ZP_04854527.1| DNA-directed RNA polymerase, alpha subunit [Paenibacillus sp. oral
           taxon 786 str. D14]
 gi|251843451|gb|EES71479.1| DNA-directed RNA polymerase, alpha subunit [Paenibacillus sp. oral
           taxon 786 str. D14]
          Length = 314

 Score =  360 bits (923), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 134/310 (43%), Positives = 205/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  +E      + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDG
Sbjct: 3   EIEKP-KIETVEVN-DEGTYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE +++ GV ED+T+IILN+K ++LK+  D  K + I   G GVVTAGDI+  +D+E+
Sbjct: 61  VLHEFATVPGVMEDVTEIILNLKALSLKIHSDEEKILEIDAEGEGVVTAGDIRADSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D  I  L+  + + M +   +G GYV A  ++ ++ PIG+I +D++Y+PI +V+Y V
Sbjct: 121 LNTDLHIATLEPGSRLHMRIYAGRGRGYVQADRNKRDDQPIGVIPVDSIYTPITRVNYVV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV +YDKL++ + TDGSI  E++V+L ++IL + L +F+   +  K+ +  +  
Sbjct: 181 ENTRVGQVTNYDKLTLEVWTDGSIRPEEAVSLGAKILTEHLFLFVGLTDEAKDAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E++
Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTTKTEEDMMKVRNLGRKSLEEVQ 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 EKLQELGLGL 310


>gi|34581393|ref|ZP_00142873.1| DNA-directed RNA polymerase alpha chain [Rickettsia sibirica 246]
 gi|28262778|gb|EAA26282.1| DNA-directed RNA polymerase alpha chain [Rickettsia sibirica 246]
          Length = 340

 Score =  360 bits (923), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 183/337 (54%), Positives = 250/337 (74%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y  +  E  N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNKVAYENV-PETNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE SSI GV ED++++ILNIKGI +KM     + + +   GP VVTAG I+T
Sbjct: 63  SIKIPAIEHEFSSIPGVKEDVSEVILNIKGIEVKMYVAEKRIMKLKATGPCVVTAGMIET 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNPDHVIC+L  D  + MELT   G GYV + +   +N PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPDHVICDLAKDKQLEMELTCKVGKGYVLSTNSYEDNLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
            V+Y VE+ R GQV DYDKL M ++T+G +  E +V LA+RILQ+QL +FI+FEE +++ 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDVLPEMAVGLAARILQEQLQLFISFEEQEEDK 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +  +   +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFGRK
Sbjct: 243 Q--VKTDALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>gi|320108368|ref|YP_004183958.1| DNA-directed RNA polymerase subunit alpha [Terriglobus saanensis
           SP1PR4]
 gi|319926889|gb|ADV83964.1| DNA-directed RNA polymerase, alpha subunit [Terriglobus saanensis
           SP1PR4]
          Length = 366

 Score =  360 bits (923), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 141/318 (44%), Positives = 207/318 (65%), Gaps = 1/318 (0%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           W+   KP  +  +      E      A+P  RGF  T+GN LRR L+SS+ GAA+TAV++
Sbjct: 3   WRGFQKPKRL-AVEGETLTEKYGKFSAQPFERGFGTTIGNGLRRTLLSSIEGAAVTAVRL 61

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           +GVLHE  SI GV ED TDIILN+K I  K++G+  K + +    PGVVT+G I+   D+
Sbjct: 62  EGVLHEFQSITGVVEDATDIILNLKQIPFKLNGEGPKALYLRVDQPGVVTSGMIEADGDV 121

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E+L+ D  I  +     + ME+ + +G GYV A  +   +  IG I +D+++SP++KV+Y
Sbjct: 122 EILDKDVYIATVSEGGKMDMEMRLKRGRGYVSADKNFDPDLGIGFIPVDSVHSPVRKVNY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TV++AR GQ+ DYDKL++ I T+G++   D++ L++++L+D + +FINFEE  +   +  
Sbjct: 182 TVDAARLGQITDYDKLTIEIWTNGTVLPADALGLSAKLLKDHMTIFINFEEEMEAGLDGS 241

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           +      N  L + VEELELSVRS NCL+  NI  +G+LIQ+TEA+ML+  NFGRKSL E
Sbjct: 242 HDGPAMRNDNLNRSVEELELSVRSYNCLKNANIATIGELIQKTEAEMLKTKNFGRKSLNE 301

Query: 306 IKGVLGTMGLFLGMNLPD 323
           IK +L  MGL LGM + +
Sbjct: 302 IKEILAQMGLSLGMKIDE 319


>gi|331018185|gb|EGH98241.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           lachrymans str. M302278PT]
          Length = 333

 Score =  360 bits (923), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 149/336 (44%), Positives = 227/336 (67%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVVS---PTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ +K+ G     +T+ K+G GVVTA DIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVQEDVIEILLNLKGLAIKLHGRDEVTLTLSKKGSGVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL  + V+ M+LTV++G GY PA   +++ D    IG + +D+ +S
Sbjct: 118 DHDVEIVNPDHVIANLASNGVLNMKLTVARGRGYEPADSRQSDEDESRSIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   
Sbjct: 178 PVRRIAYVVENARVEQRTNLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V  +   +    +P LL+ V +LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPVVIEQEDE---IDPILLRPVYDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL +  L LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRSLSLGMRLDNWPPASLKKDDK 330


>gi|332107893|gb|EGJ09117.1| DNA-directed RNA polymerase subunit alpha [Rubrivivax
           benzoatilyticus JA2]
          Length = 328

 Score =  360 bits (923), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 153/326 (46%), Positives = 212/326 (65%), Gaps = 6/326 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG     R   + EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKAIHVEPLG---GYRAKAVLEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+I GV ED+  I+LN+KG+  ++       + + K G G VTA DIQT +D+E++
Sbjct: 62  LHEYSAIDGVQEDVVHIMLNLKGVVFRLHNRDEVTLVLRKEGEGAVTAADIQTPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSY 185
           NPDHVI +L     + M++ V KG GYVP    R  ++     G I +DA +SP+K+VSY
Sbjct: 122 NPDHVIAHLSQGGKLDMQIKVEKGRGYVPGNLRRYGDEATKAIGRIVLDASFSPVKRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+AR  Q  D DKL M I+T+G+IT E+++  +++IL +QL +F   E    ++ E  
Sbjct: 182 AVENARVEQRTDLDKLVMEIETNGAITPEEAIRQSAKILVEQLAVFAQLEGQVSDIFEPQ 241

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 242 PQRTPNFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTETELLKTPNLGRKSLNE 301

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LG  L +WPP+ +++
Sbjct: 302 IKEVLASRGLTLGARLENWPPQGLDK 327


>gi|94968283|ref|YP_590331.1| DNA-directed RNA polymerase subunit alpha [Candidatus Koribacter
           versatilis Ellin345]
 gi|119366658|sp|Q1IS93|RPOA_ACIBL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|94550333|gb|ABF40257.1| DNA-directed RNA polymerase subunit alpha [Candidatus Koribacter
           versatilis Ellin345]
          Length = 368

 Score =  360 bits (923), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 148/318 (46%), Positives = 212/318 (66%), Gaps = 2/318 (0%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           W+   KP  + +       +      A+P  RGF  T+GNALRRVL+SS+ GAAITAV+I
Sbjct: 3   WKGFQKPKRLAFDS-ESLTDKYGHFWAQPFERGFGTTIGNALRRVLLSSIEGAAITAVKI 61

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           +GVLHE  SI GV ED TDIILN+K I  +++GD+ K + +    PG+VT+G I+T  D+
Sbjct: 62  EGVLHEFQSIPGVVEDATDIILNLKQIPFRLNGDAPKAIYLRAEQPGIVTSGMIETDADV 121

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E+L+ D  I  +     + ME+ + KG GYV A  +  E+  +G I ID+++SP++K +Y
Sbjct: 122 EILDKDVYIATISEGGKLDMEMRLKKGRGYVSADKNFDEDLGLGFIPIDSVHSPVRKCNY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           +VE+AR GQ+ DYDKLS+ + T+GS+   D++ LA+++L+D + +FINFEE   E     
Sbjct: 182 SVEAARLGQITDYDKLSIELWTNGSVNPADALGLAAKLLKDHMNIFINFEEE-IEASHAE 240

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           + K    N  L + VEELELSVRS NCL+  NI  +G+L+Q+TEA+ML+  NFGRKSL E
Sbjct: 241 DRKPEIRNENLNRSVEELELSVRSYNCLKNANIQTIGELVQKTEAEMLKTKNFGRKSLNE 300

Query: 306 IKGVLGTMGLFLGMNLPD 323
           IK +L +MGL LGM + +
Sbjct: 301 IKEILASMGLSLGMKIDE 318


>gi|15604481|ref|NP_220999.1| DNA-directed RNA polymerase subunit alpha [Rickettsia prowazekii
           str. Madrid E]
 gi|6226040|sp|Q9ZCS9|RPOA_RICPR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|3861175|emb|CAA15075.1| DNA-DIRECTED RNA POLYMERASE ALPHA CHAIN (rpoA) [Rickettsia
           prowazekii]
 gi|292572263|gb|ADE30178.1| DNA-directed RNA polymerase alpha chain [Rickettsia prowazekii
           Rp22]
          Length = 340

 Score =  359 bits (922), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 185/337 (54%), Positives = 247/337 (73%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y     E  N+  +I EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNRVTYENF-PETNNKAKIIVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE SSI GV ED++++ILNIKGI +KM     + + +   GP VVTAG I T
Sbjct: 63  SIKIPAIEHEFSSIPGVQEDVSEVILNIKGIEVKMHVSEKRIIKLKAMGPCVVTAGMIDT 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNPDHVICNL  +  + MELT   G GYV + +   +N PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPDHVICNLAKNKQLEMELTCKVGKGYVLSTNSYEDNLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
            V+Y VE+ R GQV DYDKL M ++T+G +  E +V LA+RILQ+QL +FI FEE +++ 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDVLPEMAVGLAARILQEQLQLFIAFEEQEEDK 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +  +   SLPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFGRK
Sbjct: 243 Q--VKTDSLPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>gi|221064829|ref|ZP_03540934.1| DNA-directed RNA polymerase, alpha subunit [Comamonas testosteroni
           KF-1]
 gi|264680560|ref|YP_003280470.1| DNA-directed RNA polymerase, subunit alpha [Comamonas testosteroni
           CNB-2]
 gi|299532876|ref|ZP_07046263.1| DNA-directed RNA polymerase subunit alpha [Comamonas testosteroni
           S44]
 gi|220709852|gb|EED65220.1| DNA-directed RNA polymerase, alpha subunit [Comamonas testosteroni
           KF-1]
 gi|262211076|gb|ACY35174.1| DNA-directed RNA polymerase, alpha subunit [Comamonas testosteroni
           CNB-2]
 gi|298719100|gb|EFI60070.1| DNA-directed RNA polymerase subunit alpha [Comamonas testosteroni
           S44]
          Length = 332

 Score =  359 bits (922), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 163/337 (48%), Positives = 218/337 (64%), Gaps = 13/337 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N   L+KP  I    LG    NR  ++ EP  RG+ HTLGNALRRVL+SS+ G A T
Sbjct: 1   MQTN---LLKPKTINVEQLG---HNRAKVVLEPFERGYGHTLGNALRRVLLSSMVGYAAT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE SSI GV ED+T+I+LN+KG+  K+       +++ K G GVVTA DIQT
Sbjct: 55  EVTIAGVLHEYSSIDGVQEDVTNILLNLKGVVFKLHNRDEVTLSLRKDGEGVVTARDIQT 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYS 178
            +D+E++NPDHVI +L     + M++ V KG GYVP    R  ++     G I +DA +S
Sbjct: 115 PHDVEIVNPDHVIAHLSQGGKLDMQIKVEKGRGYVPGNVRRYGDESTKSIGRIVLDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+K+VSY VESAR  Q  D DKL + I+T+G+IT ED+V  +++IL +QL +F   +   
Sbjct: 175 PVKRVSYAVESARVEQRTDLDKLVLEIETNGAITAEDAVRASAKILVEQLAVFAQLDGGD 234

Query: 239 KEVKEDINVK----SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
                D        +  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+
Sbjct: 235 IASVFDAPAGGRGAATSFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLK 294

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
             N GRKSL EIK VL + GL LGM L +WPP  +E+
Sbjct: 295 TPNLGRKSLNEIKEVLASRGLTLGMKLENWPPAGLEK 331


>gi|15892905|ref|NP_360619.1| DNA-directed RNA polymerase subunit alpha [Rickettsia conorii str.
           Malish 7]
 gi|20139543|sp|Q92GZ0|RPOA_RICCN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|15620096|gb|AAL03520.1| DNA-directed RNA polymerase alpha chain [Rickettsia conorii str.
           Malish 7]
          Length = 340

 Score =  359 bits (922), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 183/337 (54%), Positives = 249/337 (73%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y     E  N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNKVAYENF-PETNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE SSI GV ED++++ILNIKGI +KM     + + +   GP VVTAG I+T
Sbjct: 63  SIKIPAIEHEFSSIPGVKEDVSEVILNIKGIEVKMHVAEKRIMKLKATGPCVVTAGMIET 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNPDHVIC+L  D  + MELT   G GYV + +   +N PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPDHVICDLAKDKQLEMELTCKVGKGYVLSTNSYEDNLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
            V+Y VE+ R GQV DYDKL M ++T+G +  E +V LA+RILQ+QL +FI+FEE +++ 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDVLPEMAVGLAARILQEQLQLFISFEEQEEDK 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +  +   +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFGRK
Sbjct: 243 Q--VKTDTLPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>gi|319654896|ref|ZP_08008971.1| DNA-directed RNA polymerase subunit alpha [Bacillus sp. 2_A_57_CT2]
 gi|317393459|gb|EFV74222.1| DNA-directed RNA polymerase subunit alpha [Bacillus sp. 2_A_57_CT2]
          Length = 314

 Score =  359 bits (921), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 137/313 (43%), Positives = 203/313 (64%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  ++      + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETVEIS-DDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IILNIK + LK+  D  K + I  +G GVV A D+   +D+E+
Sbjct: 61  VLHEFSTIEGVVEDVTSIILNIKKLALKIYSDEEKTLEIDVQGEGVVKAADVTHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  +A +RM LT  +G GY PA  ++ E+ PIG+I ID++Y+P+ ++SY V
Sbjct: 121 LNPDLHIATLGSNAHLRMRLTARRGRGYTPADQNKREDQPIGVIPIDSIYTPVSRISYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ +YDKL+  + TDGS   +D+VAL ++IL + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQMTNYDKLTFDVWTDGSTGPQDAVALGAKILTEHLNIFVGLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 HKLEDLGLGLRKD 313


>gi|332040527|gb|EGI76903.1| DNA-directed RNA polymerase subunit alpha [Hylemonella gracilis
           ATCC 19624]
          Length = 328

 Score =  359 bits (921), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 160/328 (48%), Positives = 215/328 (65%), Gaps = 6/328 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP  I    LG    NR  +  EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPKTINVEQLG---PNRAKVALEPFERGYGHTLGNALRRVLLSSMPGYAATEVTIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE SSI GV ED+ +I+LN+KG+  K+       +++ K G GVVTAGDIQT +D+E
Sbjct: 60  GVLHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGVVTAGDIQTPHDVE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKV 183
           ++NP+HVI  L     + M++ V KG GYVP    R  ++     G I +DA YSP+K+V
Sbjct: 120 IINPEHVIATLSAGGKLDMQIKVEKGRGYVPGTMRRHTDEQSKSIGRIVLDASYSPVKRV 179

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VESAR  Q  D DKL + I+T+G+IT ED+V  +++IL +QL +F   +  +K    
Sbjct: 180 SYAVESARVEQRTDLDKLVIEIETNGTITAEDAVRASAKILVEQLAVFAQLDGSEKIFDT 239

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                +  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GRKSL
Sbjct: 240 PSQRSAGQFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRSENELLKTPNLGRKSL 299

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP ++E+
Sbjct: 300 NEIKEVLASRGLTLGMKLENWPPAALEK 327


>gi|126666788|ref|ZP_01737765.1| DNA-directed RNA polymerase subunit alpha [Marinobacter sp. ELB17]
 gi|126628833|gb|EAZ99453.1| DNA-directed RNA polymerase subunit alpha [Marinobacter sp. ELB17]
          Length = 334

 Score =  359 bits (921), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 154/331 (46%), Positives = 225/331 (67%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  EL+ P  I+    G     R  +  EPL RGF HTLG+ALRR+L+SS+ G A+T
Sbjct: 1   MQRSVHELLTPRTIDVKESGS---TRAKVTLEPLERGFGHTLGSALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             QIDGVLHE S+I+GV ED+ +I+LN+KG+ +KM G     + + K+GPGVVTAGDI+ 
Sbjct: 58  EAQIDGVLHEYSAIEGVQEDVIEILLNLKGVAVKMHGRDDAELMLSKKGPGVVTAGDIKL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
            +D+E+ NP+HVIC+L  +  V M L++++G GY PA        E   IG + +DA +S
Sbjct: 118 DHDVEIANPEHVICHLSENGEVNMRLSIARGRGYEPADQRGLDEDETRAIGRLQLDATFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++V+Y+VESAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++F+  K
Sbjct: 178 PVRRVAYSVESARVEQRTDLDKLVIDLETNGTIDPEEAIRRAATILQQQLAVFVDFDHEK 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +        +    +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPE---RVEEEEEIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASL 325


>gi|324999252|ref|ZP_08120364.1| DNA-directed RNA polymerase subunit alpha [Pseudonocardia sp. P1]
          Length = 350

 Score =  358 bits (920), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 126/317 (39%), Positives = 194/317 (61%), Gaps = 4/317 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V     E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPSLTEDVV----TETRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TDIILN+K + +    D    + + K+GPG VTAGDI     + V NP
Sbjct: 62  EFTTVPGVKEDVTDIILNLKELVVSSEEDEPVTMYLRKQGPGAVTAGDIVPPAGVTVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I +L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLHIASLNDKGRLEVELVVERGRGYVPAMQNKATGAEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + +++  SIT  D++A + + L +  G+        + ++   + +  
Sbjct: 182 RVEQRTDFDKLVLDVESKPSITPRDALASSGKTLVELFGLARELNVDAEGIEIGPSPQEA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
               A    +EEL+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 DTIAAFAMPIEELDLTVRSYNCLKREGIHTVGELVGRSEADLLDIRNFGAKSIDEVKMKL 301

Query: 311 GTMGLFLGMNLPDWPPE 327
             +GL L  + P + P 
Sbjct: 302 VGLGLALKDSPPGFDPS 318


>gi|254785104|ref|YP_003072532.1| DNA-directed RNA polymerase subunit alpha [Teredinibacter turnerae
           T7901]
 gi|237684107|gb|ACR11371.1| DNA-directed RNA polymerase, alpha subunit [Teredinibacter turnerae
           T7901]
          Length = 329

 Score =  358 bits (920), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 148/332 (44%), Positives = 221/332 (66%), Gaps = 9/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    E + P +I+   L      R  ++ EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQSAVNEFLTPRHIDVTEL---APTRAKVVLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I GV HE S+I+GV ED+ +I+LNIK + + M G     +++ K+GPGVVT  DIQ 
Sbjct: 58  EVEIAGVQHEYSAIEGVREDVIEILLNIKNLAVVMHGKDTTTLSLVKQGPGVVTGADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYS 178
            +D+E+ NP+ VI N+  D  + M+LT+++G GY P    +++ D     G + +DA +S
Sbjct: 118 DHDVEIANPELVIANITGDVTLDMKLTIARGRGYQPVDARQSDEDETRAIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++YTVESAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++ E  K
Sbjct: 178 PVRRLAYTVESARVEQRTDLDKLVLDLETNGTIDPEEAIRRAATILQQQLAVFVDLEGEK 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              + +   K    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 ---EVEPEQKEDQIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           G+KSL EIK +L + GL LGM L +WPP S++
Sbjct: 295 GKKSLTEIKDILASRGLSLGMRLENWPPASLK 326


>gi|317126889|ref|YP_004093171.1| DNA-directed RNA polymerase, subunit alpha [Bacillus
           cellulosilyticus DSM 2522]
 gi|315471837|gb|ADU28440.1| DNA-directed RNA polymerase, alpha subunit [Bacillus
           cellulosilyticus DSM 2522]
          Length = 314

 Score =  358 bits (920), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 132/310 (42%), Positives = 202/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  E+ +    + EPL RG+  TLGN+LRR+L+SSL G+A+T+VQ DG
Sbjct: 3   EIEKP-KIEAVEVS-EDGSYGKFVVEPLERGYGTTLGNSLRRILLSSLPGSAVTSVQFDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IILN+K + LK+  D  K + I   G GVVTA D    +D+EV
Sbjct: 61  VLHEFSTIEGVVEDITSIILNLKKLALKIYSDEEKTLEIEATGEGVVTAADFMHDSDVEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L   A   M++  ++G GYVPA+ +++E  PIG+I +D++Y+P+ +V+Y V
Sbjct: 121 LNPDLHIATLSKGAQFHMKVAANRGRGYVPAEGNKSEELPIGVIPVDSIYTPVARVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ +YDKL++ + TDGS   E++V+L ++IL + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQITNYDKLTLDVWTDGSTRPEEAVSLGAKILTEHLNIFVGLTDQAQHAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N GRKSL E++
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTHKSEEDMMKVRNLGRKSLEEVQ 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 EKLAELGLGL 310


>gi|158518607|sp|Q6MJ36|RPOA_BDEBA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 343

 Score =  358 bits (920), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 160/326 (49%), Positives = 218/326 (66%), Gaps = 2/326 (0%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
            K W+E+IKP   E       ++     I  PL RGF  TLGN+LRR+L+SS+ G+AITA
Sbjct: 6   YKFWREMIKPKGFEVDRDSLRDD-YAKFIIRPLERGFGVTLGNSLRRILLSSMMGSAITA 64

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           V+ +GVLHE ++I  V ED+TDIILN+K +  K        + I K+GPG VTA DIQT 
Sbjct: 65  VKFEGVLHEFTTIPDVLEDVTDIILNLKEVRFKQYTADSLTLKISKKGPGKVTAADIQTT 124

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IEVLNPD  I  L  +A    E+ VS G GYVP + +R  + P+G I +DALYSPI+K
Sbjct: 125 DKIEVLNPDLPIATLGANANFNAEIVVSFGRGYVPVE-NRETDLPVGFIGVDALYSPIRK 183

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+Y V +AR GQ  DYD L++ + TDGS+  E++VAL+S+I+++QL +F+ F+E  +  +
Sbjct: 184 VNYNVSNARVGQRTDYDALTLEVWTDGSLKPEEAVALSSKIMKEQLQIFLTFDETMEPAE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           E   + S   N  L + V++LELSVRS NCL+  NI Y+G+L+ R+EA+ML+  NFGRKS
Sbjct: 244 EARELGSPTLNENLFRSVDDLELSVRSANCLKNANIRYIGELVVRSEAEMLKTKNFGRKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPES 328
           L EIK +LG MGL LGM +  WPP  
Sbjct: 304 LNEIKEILGEMGLGLGMKIEGWPPAG 329


>gi|89100320|ref|ZP_01173185.1| DNA-directed RNA polymerase alpha subunit [Bacillus sp. NRRL
           B-14911]
 gi|89084941|gb|EAR64077.1| DNA-directed RNA polymerase alpha subunit [Bacillus sp. NRRL
           B-14911]
          Length = 314

 Score =  358 bits (920), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 135/313 (43%), Positives = 202/313 (64%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  ++      + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETVEIS-DDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T +ILNIK + LK+  D  K + I  +G G VTA D+   +D+E+
Sbjct: 61  VLHEFSTIEGVVEDVTSVILNIKKLALKIYSDDEKTLEIDIQGEGAVTAADVTHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  +  +RM LT  +G GY PA  ++ E+ PIG+I ID++Y+P+ ++SY V
Sbjct: 121 LNPDLHIATLGSNGHLRMRLTAKRGRGYTPADQNKREDQPIGVIPIDSIYTPVSRISYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ +YDKL+  + TDGS   +D+VAL ++IL + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQMTNYDKLTFDVWTDGSTGPQDAVALGAKILTEHLNIFVGLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 HKLEELGLGLRKD 313


>gi|71083781|ref|YP_266501.1| DNA-directed RNA polymerase subunit alpha [Candidatus Pelagibacter
           ubique HTCC1062]
 gi|91763183|ref|ZP_01265147.1| DNA-directed RNA polymerase alpha subunit [Candidatus Pelagibacter
           ubique HTCC1002]
 gi|90110855|sp|Q4FLP1|RPOA_PELUB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|71062894|gb|AAZ21897.1| DNA-directed RNA polymerase [Candidatus Pelagibacter ubique
           HTCC1062]
 gi|91717596|gb|EAS84247.1| DNA-directed RNA polymerase alpha subunit [Candidatus Pelagibacter
           ubique HTCC1002]
          Length = 342

 Score =  358 bits (920), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 184/336 (54%), Positives = 259/336 (77%), Gaps = 3/336 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNW+ LIKP  ++  +   ++++   +IAEPL +G+  TLGN+LRR+L+SS+RGAA+T++
Sbjct: 9   KNWKALIKPAQLDVKI--SDDKSHAKIIAEPLEKGYGLTLGNSLRRILLSSIRGAAVTSI 66

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           QIDGVLHE +SIKGV ED+TDI+LN+K + LK S ++ K++ +  +GPG + A DI  V 
Sbjct: 67  QIDGVLHEFTSIKGVREDVTDIVLNVKSLALKSSSETTKKLILDAKGPGEIKASDIAPVA 126

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIE+LNPD VICNLD +    ME+ V  G GYVPA  ++ E  P+GLI ID+LYSP+KKV
Sbjct: 127 DIEILNPDLVICNLDENTHFHMEMNVGTGKGYVPAVMNKPEEPPLGLIAIDSLYSPVKKV 186

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY++ +AREG+ LDYDKL M ++T+GSI+ ED+VA ++RI QDQL MF+NF+EP +   +
Sbjct: 187 SYSISTAREGKALDYDKLIMEVETNGSISAEDAVAYSARIFQDQLNMFVNFDEPVEVPVK 246

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +++ +   FN  LL+KV+ELELSVRS NCL+ +NI+Y+GDL+Q++E +MLR  NFGRKSL
Sbjct: 247 EVSSEP-EFNKNLLRKVDELELSVRSMNCLKNDNIIYIGDLVQKSEGEMLRTPNFGRKSL 305

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            EIK VL  M L+LGM +P+WPPE+I E++KK E++
Sbjct: 306 NEIKEVLTGMSLYLGMEIPNWPPENIAEMSKKLEEQ 341


>gi|157964782|ref|YP_001499606.1| DNA-directed RNA polymerase subunit alpha [Rickettsia massiliae
           MTU5]
 gi|166991522|sp|A8F2C3|RPOA_RICM5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|157844558|gb|ABV85059.1| DNA-directed RNA polymerase alpha chain [Rickettsia massiliae MTU5]
          Length = 340

 Score =  358 bits (920), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 182/337 (54%), Positives = 247/337 (73%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y     E  N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNALIKPNKVAYENF-PETNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE SSI GV ED++++ILNIKGI +KM     + + +   GP VVTAG I T
Sbjct: 63  SIKIPAIEHEFSSIPGVKEDVSEVILNIKGIEVKMHVAEKRIMKLKVTGPCVVTAGMIDT 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNPDHVIC+L  D  + M LT   G GYV + +   +N PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPDHVICDLAKDKQLEMALTCKVGKGYVLSTNSYEDNLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
            V+Y VE+ R GQV DYDKL M ++T+G +  E +V LA+RILQ+QL +FI+FEE +++ 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDLLPEMAVGLAARILQEQLQLFISFEEQEEDK 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +  +   +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFGRK
Sbjct: 243 Q--VKTDALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>gi|218779736|ref|YP_002431054.1| DNA-directed RNA polymerase subunit alpha [Desulfatibacillum
           alkenivorans AK-01]
 gi|218761120|gb|ACL03586.1| DNA-directed RNA polymerase, alpha subunit [Desulfatibacillum
           alkenivorans AK-01]
          Length = 343

 Score =  358 bits (920), Expect = 6e-97,   Method: Composition-based stats.
 Identities = 154/341 (45%), Positives = 225/341 (65%), Gaps = 7/341 (2%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++  NW+ELIKP  ++     +        I EPL RGF  TLGNALRR+++SSL GAAI
Sbjct: 6   LMYMNWRELIKPQRVQV----ESSPTHGKFITEPLERGFGLTLGNALRRIILSSLHGAAI 61

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
            +V+ D V+HE S+I GV ED++++ILN+K + L M+      + + K+GPGVVTAGD+ 
Sbjct: 62  VSVKFDNVMHEFSAIPGVLEDVSELILNLKEVRLTMTETGPCPLNLEKQGPGVVTAGDLI 121

Query: 121 TVND-IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
           + N  ++VLNPD  I  +  D+V RME+    G GY  A+ ++ E+DP+G I ID+++SP
Sbjct: 122 SPNGKVQVLNPDLYIATISDDSVFRMEMQCQVGKGYAMAEANKNEDDPVGTIPIDSVFSP 181

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--EP 237
           I++V+Y V +AR GQ  DYDKL++ + TDGS+T ED+VA A++IL++Q+ +FINF+    
Sbjct: 182 IRRVNYVVGNARVGQRTDYDKLTLEVWTDGSLTPEDAVAYAAKILKEQISIFINFDEEME 241

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            ++  E     +  FN  L + V+ELELSVRS NCL+  +I  + +L+++TE++ML+  N
Sbjct: 242 PEQEVEAEETDAPEFNENLYRSVDELELSVRSANCLKNASIHKIFELVRKTESEMLKTKN 301

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           FGRKSL EIK VL  MGL  GM L  + P    +     ED
Sbjct: 302 FGRKSLNEIKEVLSEMGLSFGMKLEGFQPPEESDEEGDTED 342


>gi|154684661|ref|YP_001419822.1| DNA-directed RNA polymerase subunit alpha [Bacillus
           amyloliquefaciens FZB42]
 gi|308172034|ref|YP_003918739.1| RNA polymerase subunit alpha [Bacillus amyloliquefaciens DSM 7]
 gi|171854997|sp|A7Z0R5|RPOA_BACA2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|52313146|emb|CAH55603.1| DNA-directed RNA polymerase alpha chain [Bacillus amyloliquefaciens
           FZB42]
 gi|154350512|gb|ABS72591.1| RpoA [Bacillus amyloliquefaciens FZB42]
 gi|307604898|emb|CBI41269.1| RNA polymerase (alpha subunit) [Bacillus amyloliquefaciens DSM 7]
 gi|328551844|gb|AEB22336.1| DNA-directed RNA polymerase subunit alpha [Bacillus
           amyloliquefaciens TA208]
 gi|328910100|gb|AEB61696.1| DNA-directed RNA polymerase subunit alpha [Bacillus
           amyloliquefaciens LL3]
          Length = 314

 Score =  358 bits (920), Expect = 6e-97,   Method: Composition-based stats.
 Identities = 134/313 (42%), Positives = 203/313 (64%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  + +     + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETVEISDDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IIL+IK + LK+  D  K + I  +G G VTA DI   +D+E+
Sbjct: 61  VLHEFSTIEGVVEDVTTIILHIKKLALKIYSDEEKTLEIDVQGEGTVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  +A  R+ LT  +G GY PA  ++ ++ PIG+I ID++++P+ ++SY V
Sbjct: 121 LNPDLHIATLGENASFRVRLTAQRGRGYTPADSNKRDDQPIGVIPIDSIFTPVSRLSYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV +YDKL++ + TDGS   ++++AL S+IL + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQVANYDKLTLDVWTDGSTGPKEAIALGSKILTEHLNIFVGLTDEAQHAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 AKLEELGLGLRKD 313


>gi|308070947|ref|YP_003872552.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           [Paenibacillus polymyxa E681]
 gi|305860226|gb|ADM72014.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           [Paenibacillus polymyxa E681]
          Length = 314

 Score =  358 bits (919), Expect = 7e-97,   Method: Composition-based stats.
 Identities = 131/310 (42%), Positives = 205/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  ++      + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDG
Sbjct: 3   EIEKP-KIETVDVN-DDGTYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE +++ GV ED+T+IILN+K ++LK+  D  K + I   G GVVTAGDI+  +D+E+
Sbjct: 61  VLHEFATVPGVKEDVTEIILNLKALSLKIHSDEEKVLEIDAEGEGVVTAGDIRADSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L   + + M +  ++G GYV    ++ ++ PIG+I +D++Y+PI +V+Y V
Sbjct: 121 LNPDLHIATLGPGSRLHMRIFANRGRGYVKQDRNKRDDQPIGVIPVDSIYTPIARVNYGV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV +YDKL++ + TDGSI  E++V+L ++IL + + +F+   +  K+ +  +  
Sbjct: 181 ENTRVGQVTNYDKLTLEVWTDGSIRPEEAVSLGAKILTEHVMLFVGLTDEAKDAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N GRKSL E++
Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTTKSEEDMMKVRNLGRKSLEEVQ 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 EKLEELGLGL 310


>gi|225873050|ref|YP_002754509.1| DNA-directed RNA polymerase, alpha subunit [Acidobacterium
           capsulatum ATCC 51196]
 gi|225794173|gb|ACO34263.1| DNA-directed RNA polymerase, alpha subunit [Acidobacterium
           capsulatum ATCC 51196]
          Length = 363

 Score =  358 bits (919), Expect = 8e-97,   Method: Composition-based stats.
 Identities = 142/318 (44%), Positives = 206/318 (64%), Gaps = 1/318 (0%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           W+   KP  +  +      E      A+P  RGF  T+GNALRR L+SS+ GAA+TAV+I
Sbjct: 3   WRGFQKPKRL-VVDPETLTEKFGKFSAQPFERGFGTTIGNALRRTLLSSIEGAAVTAVKI 61

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           +GVLHE  SI GV ED TDIILN+K +  K++GD  K + +    PGVVT+G I+   D+
Sbjct: 62  EGVLHEFQSIPGVVEDATDIILNLKQVPFKLNGDGPKALYVRADQPGVVTSGMIEADADV 121

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E+L+ D  I  +     + ME+ + +G G+V A  +   +  IG I +D+++SP++KV+Y
Sbjct: 122 EILDKDIYIATVSEGGKLEMEMRLKRGRGFVSADKNHDNDLGIGFIPVDSVHSPVRKVNY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+AR GQ+ DYDKL++ + T+G++   D+V LA+++L+D + +FINFEE  +      
Sbjct: 182 FVEAARLGQITDYDKLTLEVMTNGTVLPADAVGLAAKLLKDHMSIFINFEEEIEAESHSE 241

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +    N  L + VEELELSVRS NCL+  NI  +G+L+Q+TEA+ML+  NFGRKSL E
Sbjct: 242 EGRVQLRNENLNRSVEELELSVRSYNCLKNANIQTIGELVQKTEAEMLKTKNFGRKSLNE 301

Query: 306 IKGVLGTMGLFLGMNLPD 323
           IK +L  MGL LGM + +
Sbjct: 302 IKEILAQMGLSLGMKIDE 319


>gi|134103231|ref|YP_001108892.1| DNA-directed RNA polymerase subunit alpha [Saccharopolyspora
           erythraea NRRL 2338]
 gi|291007977|ref|ZP_06565950.1| DNA-directed RNA polymerase subunit alpha [Saccharopolyspora
           erythraea NRRL 2338]
 gi|158513554|sp|A4FPJ2|RPOA_SACEN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|133915854|emb|CAM05967.1| DNA-directed RNA polymerase, alpha subunit [Saccharopolyspora
           erythraea NRRL 2338]
          Length = 359

 Score =  358 bits (919), Expect = 8e-97,   Method: Composition-based stats.
 Identities = 125/308 (40%), Positives = 185/308 (60%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
                E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV 
Sbjct: 11  EEAVAETRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSLRIDGVLHEFTTIPGVK 70

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+TD+ILN+K + +    D    + + K+GPG VTA DI     + V NPD  I  L+ 
Sbjct: 71  EDVTDVILNLKELVVSSEEDEPVTMYLRKQGPGEVTAADIVPPAGVTVHNPDLHIATLNG 130

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D
Sbjct: 131 KGKLEIELVVERGRGYVPAVQNKQTGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFD 190

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + ++T  SIT  D+VA A R L +  G+        + ++   +        A    
Sbjct: 191 KLILDVETKPSITPRDAVASAGRTLVELFGLARELNVDAEGIEIGPSPAEADTIAAYAMP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  +GL L  
Sbjct: 251 IEDLDLTVRSYNCLKREGIHTVGELVSRSEADLLDIRNFGAKSIDEVKLKLVGLGLSLKD 310

Query: 320 NLPDWPPE 327
           + P + P 
Sbjct: 311 SPPGFDPS 318


>gi|51473815|ref|YP_067572.1| DNA-directed RNA polymerase subunit alpha [Rickettsia typhi str.
           Wilmington]
 gi|61215890|sp|Q68WA2|RPOA_RICTY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|51460127|gb|AAU04090.1| RNA nucleotidyltransferase (DNA-directed) [Rickettsia typhi str.
           Wilmington]
          Length = 340

 Score =  358 bits (919), Expect = 8e-97,   Method: Composition-based stats.
 Identities = 183/337 (54%), Positives = 247/337 (73%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y     E  N+  +I EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNRVTYENF-PETNNKAKIIVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE SSI GV ED++++ILNIKGI +KM     + + +   GP VVTAG I T
Sbjct: 63  SIKIPAIEHEFSSIPGVQEDVSEVILNIKGIEVKMHVSEKRIMKLKATGPCVVTAGMIDT 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNP+HVICNL  +  + MELT   G GYV + +   +N PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPNHVICNLAKNKQLEMELTCKVGKGYVLSTNSYEDNLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
            V+Y VE+ R GQV DYDKL + ++T+G +  E +V LA+RILQ+QL +FI FEE +++ 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIIFVETNGDVLPEMAVGLAARILQEQLQLFIAFEEQEEDK 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +  +   SLPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFGRK
Sbjct: 243 Q--VKTDSLPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>gi|90020631|ref|YP_526458.1| DNA-directed RNA polymerase subunit alpha [Saccharophagus degradans
           2-40]
 gi|119366723|sp|Q21M33|RPOA_SACD2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|89950231|gb|ABD80246.1| DNA-directed RNA polymerase, alpha subunit [Saccharophagus
           degradans 2-40]
          Length = 329

 Score =  358 bits (919), Expect = 8e-97,   Method: Composition-based stats.
 Identities = 153/332 (46%), Positives = 222/332 (66%), Gaps = 9/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    E + P +I+   LG     R  ++ EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQSAVNEFLTPRHIDVTELG---PTRAKVVLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGV HE S+I+GV ED+ +I+LN+K + + M G     +++ K+GPG VTAGDIQ 
Sbjct: 58  EVEIDGVQHEYSAIEGVQEDVIEILLNLKNVAVVMHGKDQAVLSLSKQGPGAVTAGDIQV 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYS 178
            +DIE+ NP+ VI N+  D  + M LTVS+G GY P     T+ D     G + +DA +S
Sbjct: 118 DHDIEIKNPELVIANITSDTSLSMRLTVSRGRGYQPVDARATDEDETRAIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y+VESAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++ E  K
Sbjct: 178 PVRRLAYSVESARVEQRTDLDKLVLDLETNGTIDPEEAIRRAATILQQQLAVFVDLEGEK 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              + +   K    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 ---EAEPEQKEDQIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           G+KSL EIK +L + GL LGM L +WPP S++
Sbjct: 295 GKKSLTEIKDILASRGLSLGMRLENWPPASLK 326


>gi|310644172|ref|YP_003948931.1| DNA-directed RNA polymerase subunit alpha [Paenibacillus polymyxa
           SC2]
 gi|309249123|gb|ADO58690.1| DNA-directed RNA polymerase subunit alpha [Paenibacillus polymyxa
           SC2]
          Length = 314

 Score =  358 bits (918), Expect = 8e-97,   Method: Composition-based stats.
 Identities = 130/310 (41%), Positives = 205/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  ++      + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDG
Sbjct: 3   EIEKP-KIETVDVN-DDGTYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE +++ GV ED+T+IILN+K ++LK+  D  K + I   G GVVTAGDI+  +D+E+
Sbjct: 61  VLHEFATVPGVKEDVTEIILNLKALSLKIHSDEEKVLEIDAEGEGVVTAGDIRADSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L   + + M +  ++G GYV    ++ ++ PIG+I +D++Y+PI +V+Y V
Sbjct: 121 LNPDLHIATLGPGSRLHMRIFANRGRGYVKQDRNKRDDQPIGVIPVDSIYTPIARVNYGV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV +YDKL++ + TDG+I  E++V+L ++IL + + +F+   +  K+ +  +  
Sbjct: 181 ENTRVGQVTNYDKLTLEVWTDGTIRPEEAVSLGAKILTEHVMLFVGLTDEAKDAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N GRKSL E++
Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTTKSEEDMMKVRNLGRKSLEEVQ 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 EKLEELGLGL 310


>gi|254776830|ref|ZP_05218346.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium avium
           subsp. avium ATCC 25291]
          Length = 347

 Score =  358 bits (918), Expect = 8e-97,   Method: Composition-based stats.
 Identities = 119/306 (38%), Positives = 188/306 (61%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
            +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T
Sbjct: 15  TDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVT 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            IILN+K + +    D    + + K+GPG VTAGDI     + V NP+  I  L+    +
Sbjct: 75  AIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPELHIATLNDKGKL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL +
Sbjct: 135 EVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLIL 194

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T  SIT  D++A A + L +  G+        + ++   +        +    +++L
Sbjct: 195 DVETKSSITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPPEADHIASFALPIDDL 254

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  + P 
Sbjct: 255 DLTVRSYNCLKREGVHTVGELVSRTESDLLDIRNFGQKSIDEVKVKLHQLGLSLKDSPPS 314

Query: 324 WPPESI 329
           + P  +
Sbjct: 315 FDPSQV 320


>gi|163859245|ref|YP_001633543.1| DNA-directed RNA polymerase subunit alpha [Bordetella petrii DSM
           12804]
 gi|229564247|sp|A9IHR6|RPOA_BORPD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|163262973|emb|CAP45276.1| DNA-directed RNA polymerase alpha chain [Bordetella petrii]
          Length = 328

 Score =  358 bits (918), Expect = 9e-97,   Method: Composition-based stats.
 Identities = 151/330 (45%), Positives = 209/330 (63%), Gaps = 7/330 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            + Q  +KP +IE   +G        ++ EP  RG+ HTLGNALRR+L+SS+ G A T V
Sbjct: 1   MSTQGFLKPRSIEVEPVGTH---HAKIVMEPFERGYGHTLGNALRRILLSSMTGYAPTEV 57

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           Q+ GV+HE S+I GV ED+ DI+LN+KG+  K+       + + K G G V A DI+  +
Sbjct: 58  QMTGVVHEYSTIPGVREDVVDILLNLKGVVFKLHNRDEVTLVLRKNGAGTVVASDIELPH 117

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPI 180
           D+E++NPDH+ICNL     V M++ V KG GYVP        D    IG I +DA +SP+
Sbjct: 118 DVEIINPDHLICNLTEAGKVEMQIKVEKGRGYVPGNVRALSEDRTHTIGRIVLDASFSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY VESAR  Q  D DKL + I+T+G I+ E++V  ++RIL DQ+ +F   E     
Sbjct: 178 RRVSYAVESARVEQRTDLDKLVLDIETNGVISPEEAVRQSARILMDQISVFAALEGAGDS 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +  +   +   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GR
Sbjct: 238 YEAPV-RGTPQIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           KSL EIK VL   GL LGM L +WPP  +E
Sbjct: 297 KSLNEIKEVLAARGLTLGMKLENWPPLGLE 326


>gi|120402447|ref|YP_952276.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           vanbaalenii PYR-1]
 gi|158513011|sp|A1T520|RPOA_MYCVP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119955265|gb|ABM12270.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           vanbaalenii PYR-1]
          Length = 350

 Score =  358 bits (918), Expect = 9e-97,   Method: Composition-based stats.
 Identities = 122/305 (40%), Positives = 188/305 (61%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ENR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+TD
Sbjct: 16  ENRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+KG+ +    D    + + K+GPG VTAGDI     + V NPD  I  L+    + 
Sbjct: 76  IILNLKGLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPDMHIATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL + 
Sbjct: 136 VELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLILD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           ++T  SIT  D++A A + L +  G+        + ++   +             +++L+
Sbjct: 196 VETKNSITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADQAAHFALPIDDLD 255

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  +   +
Sbjct: 256 LTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPASF 315

Query: 325 PPESI 329
            P  +
Sbjct: 316 DPSEV 320


>gi|312140889|ref|YP_004008225.1| DNA-directed RNA polymerase alpha subunit rpoa [Rhodococcus equi
           103S]
 gi|325675473|ref|ZP_08155157.1| DNA-directed RNA polymerase subunit alpha [Rhodococcus equi ATCC
           33707]
 gi|311890228|emb|CBH49546.1| DNA-directed RNA polymerase alpha subunit RpoA [Rhodococcus equi
           103S]
 gi|325553444|gb|EGD23122.1| DNA-directed RNA polymerase subunit alpha [Rhodococcus equi ATCC
           33707]
          Length = 354

 Score =  358 bits (918), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 125/319 (39%), Positives = 197/319 (61%), Gaps = 4/319 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E ++     ENR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLTEEVI----AENRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TDIILN+KG+ +    D    + + K+GPGVVTAGDI     + V NP
Sbjct: 62  EFTTVPGVKEDVTDIILNLKGLVVSSEEDEPVTMYVRKQGPGVVTAGDIVPPAGVTVNNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLHIATLNDKGKLEIELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  SIT  D++A A + L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDRLILDVETKNSITARDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
               +    +E+L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L
Sbjct: 242 DHIASFGLPIEDLDLTVRSYNCLKREGVHTVGELVGRTESDLLDIRNFGQKSIDEVKVKL 301

Query: 311 GTMGLFLGMNLPDWPPESI 329
            ++GL L  +   + P ++
Sbjct: 302 HSLGLALKDSPASFDPTTV 320


>gi|118469556|ref|YP_885906.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium smegmatis
           str. MC2 155]
 gi|158512464|sp|A0QSL8|RPOA_MYCS2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|118170843|gb|ABK71739.1| DNA-directed RNA polymerase, alpha subunit [Mycobacterium smegmatis
           str. MC2 155]
          Length = 350

 Score =  358 bits (918), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 122/310 (39%), Positives = 189/310 (60%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
                ENR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV 
Sbjct: 11  EETVAENRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVK 70

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+TDIILN+KG+ +    D    + + K+GPGVVTAGDI     + V NPD  I  L+ 
Sbjct: 71  EDVTDIILNLKGLVVSSDDDEPVTMYLRKQGPGVVTAGDIVPPAGVTVHNPDMHIATLND 130

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D
Sbjct: 131 KGKLEVELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFD 190

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + ++T  SI+  D++A A   L +  G+        + ++   +        +    
Sbjct: 191 KLIIDVETKNSISPRDALASAGGTLVELFGLARELNADSEHIEIGPSPAEADHIASFALP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  
Sbjct: 251 IDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKD 310

Query: 320 NLPDWPPESI 329
           +   + P  +
Sbjct: 311 SPATFDPSEV 320


>gi|311070791|ref|YP_003975714.1| DNA-directed RNA polymerase subunit alpha [Bacillus atrophaeus
           1942]
 gi|310871308|gb|ADP34783.1| DNA-directed RNA polymerase subunit alpha [Bacillus atrophaeus
           1942]
          Length = 314

 Score =  358 bits (918), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 135/313 (43%), Positives = 203/313 (64%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  + +     + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETVEISDDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IIL+IK + LK+  D  K + I  +G G VTA DI   +DIE+
Sbjct: 61  VLHEFSTIEGVVEDVTTIILHIKKLALKIYSDEEKTLEIDVQGEGTVTAADITHDSDIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  +A  R+ LT  +G GY PA  ++ ++ PIG+I ID++++P+ ++SY V
Sbjct: 121 LNPDLHIATLGENASFRVRLTAQRGRGYTPADSNKRDDQPIGVIPIDSIFTPVSRLSYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV +YDKL++ + TDGS   ++++AL S+IL + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQVANYDKLTLDVWTDGSTGPKEAIALGSKILTEHLNIFVGLTDEAQHAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 AKLEELGLGLRKD 313


>gi|303240944|ref|ZP_07327455.1| DNA-directed RNA polymerase, alpha subunit [Acetivibrio
           cellulolyticus CD2]
 gi|302591530|gb|EFL61267.1| DNA-directed RNA polymerase, alpha subunit [Acetivibrio
           cellulolyticus CD2]
          Length = 315

 Score =  358 bits (918), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 139/311 (44%), Positives = 204/311 (65%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE  V+  E+      + EPL RG+  TLGN+LRR+L+SSL G A+T+++IDG
Sbjct: 3   EIEKP-KIE-CVISSEDNTYGKFVVEPLERGYGITLGNSLRRILLSSLPGIAVTSIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T+IILN+KG+ L + GD  K V I   G G VTA DI+   D+E+
Sbjct: 61  VLHEFSTVPGVVEDVTEIILNVKGLALNLHGDGPKVVYIDADGEGEVTAADIKADADVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+H I  L  D  + MEL++ KG GYV A+ ++    PIG+I +D++Y+P+ KV+YTV
Sbjct: 121 LNPEHKIATLSGDHKLYMELSLDKGRGYVSAEKNKHPGQPIGVIPVDSIYTPVSKVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV DYDKL++ + T+GSI  +++++L ++I+ + L +FI+  +  K  +  +  
Sbjct: 181 ENTRVGQVTDYDKLTLEVWTNGSIKPDEAISLGAKIMSEHLNLFIDLSDNAKNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + DL  RTE DM+++ N GRKSL E+ 
Sbjct: 241 EETKKEKVLEMTIEELDLSVRSYNCLKRAGINTVEDLTNRTEEDMMKVRNLGRKSLEEVF 300

Query: 308 GVLGTMGLFLG 318
             L  +GL L 
Sbjct: 301 NKLKALGLALA 311


>gi|226305370|ref|YP_002765328.1| DNA-directed RNA polymerase alpha chain [Rhodococcus erythropolis
           PR4]
 gi|229489661|ref|ZP_04383524.1| DNA-directed RNA polymerase, alpha subunit [Rhodococcus
           erythropolis SK121]
 gi|226184485|dbj|BAH32589.1| DNA-directed RNA polymerase alpha chain [Rhodococcus erythropolis
           PR4]
 gi|229323758|gb|EEN89516.1| DNA-directed RNA polymerase, alpha subunit [Rhodococcus
           erythropolis SK121]
          Length = 353

 Score =  358 bits (918), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 123/319 (38%), Positives = 196/319 (61%), Gaps = 4/319 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E ++     +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLTEEVI----ADNRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TDIILN+KG+ +    D    + + K+GPG VTAGDI     + V NP
Sbjct: 62  EFTTVPGVKEDVTDIILNLKGLVVNSEEDEPVTMYVRKQGPGAVTAGDIVPPAGVTVNNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLHIATLNDKGKLEIELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  SIT  D++A A + L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDRLVLDVETKNSITARDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
               +    +E+L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L
Sbjct: 242 DHIASFGLPIEDLDLTVRSYNCLKREGVHTVGELVGRTESDLLDIRNFGQKSIDEVKVKL 301

Query: 311 GTMGLFLGMNLPDWPPESI 329
            ++GL L  +   + P ++
Sbjct: 302 HSLGLSLKDSPASFDPTTV 320


>gi|256380567|ref|YP_003104227.1| DNA-directed RNA polymerase subunit alpha [Actinosynnema mirum DSM
           43827]
 gi|255924870|gb|ACU40381.1| DNA-directed RNA polymerase, alpha subunit [Actinosynnema mirum DSM
           43827]
          Length = 350

 Score =  358 bits (918), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 123/308 (39%), Positives = 186/308 (60%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
                E R+  + EPL  GF +TLGN++RR L+SS+ GAA+T+++IDGVLHE +++ GV 
Sbjct: 11  EEAVSETRSRFVIEPLEPGFGYTLGNSIRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVK 70

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+TDIILN+K + +    D    + + K+GPG VTAGDI     + V NPD  I  L+ 
Sbjct: 71  EDVTDIILNLKELVVSSEEDEPVTMYLRKQGPGAVTAGDIVPPAGVTVHNPDLHIATLNG 130

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D
Sbjct: 131 KGKLEIELVVERGRGYVPAVQNKQAGAEIGRIPVDSIYSPVMKVTYKVEATRVEQRTDFD 190

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + +++  SIT  D+VA A + L +  G+        + ++   +        A    
Sbjct: 191 KLILDVESKPSITPRDAVASAGKTLVELFGLARELNVDAEGIEIGPSPAEADTIAAFAMP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  +GL L  
Sbjct: 251 IEDLDLTVRSYNCLKREGIHTVGELVSRSEADLLDIRNFGAKSIDEVKMKLVGLGLALKD 310

Query: 320 NLPDWPPE 327
           + P + P 
Sbjct: 311 SPPGFDPS 318


>gi|145225546|ref|YP_001136224.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium gilvum
           PYR-GCK]
 gi|315445898|ref|YP_004078777.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium sp. Spyr1]
 gi|145218032|gb|ABP47436.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium gilvum
           PYR-GCK]
 gi|315264201|gb|ADU00943.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium sp. Spyr1]
          Length = 354

 Score =  357 bits (917), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 124/319 (38%), Positives = 193/319 (60%), Gaps = 4/319 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V     ENR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLSEEVV----AENRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TDIILN+KG+ +    D    + + K+GPG VTAGDI     + V NP
Sbjct: 62  EFTTVPGVKEDVTDIILNLKGLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DMHIATLNDKGKLEVELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  SI+  D++A A + L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDKLILDVETKNSISPRDALASAGKTLVELFGLARELNIEAEGIEIGPSPAEA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                    +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L
Sbjct: 242 DQAAHFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKL 301

Query: 311 GTMGLFLGMNLPDWPPESI 329
             +GL L  +   + P  +
Sbjct: 302 HQLGLSLKDSPASFDPSEV 320


>gi|326793583|ref|YP_004311403.1| DNA-directed RNA polymerase subunit alpha [Marinomonas mediterranea
           MMB-1]
 gi|326544347|gb|ADZ89567.1| DNA-directed RNA polymerase subunit alpha [Marinomonas mediterranea
           MMB-1]
          Length = 334

 Score =  357 bits (917), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 156/336 (46%), Positives = 228/336 (67%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  EL+ P NIE   +      R  +  +PL RGF HTLGNALRR+L+SS+ G AI 
Sbjct: 1   MQRSVSELLTPRNIEVQEISS---TRAKVTLQPLERGFGHTLGNALRRILLSSMPGCAIV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ +I+LN+KG+ + + G     +T+ K+GPGVVTAGDIQ 
Sbjct: 58  EVEIDGVLHEYSAIEGVKEDVIEILLNLKGVAIALHGQDEATLTLSKKGPGVVTAGDIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
           V D E+ NPDHVI +LD  A + M++ V++G GY PA        E  PIG + +DA +S
Sbjct: 118 VTDSEISNPDHVIAHLDDTAELNMQIKVARGRGYEPADARVASDDETRPIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++V+Y+V++AR  Q  D DKL + I+++G+I  E+++  A+ ILQ Q+ +F+     +
Sbjct: 178 PVRRVAYSVDNARVEQRTDLDKLVLDIESNGTIDPEEAIRRAATILQQQIAVFVAL---E 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E +  +  +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 235 SESEAVVEEEEDEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL   GL LGM L +WPP S+++ +K
Sbjct: 295 GKKSLTEIKDVLAQRGLSLGMRLENWPPASLKDDSK 330


>gi|157826039|ref|YP_001493759.1| DNA-directed RNA polymerase subunit alpha [Rickettsia akari str.
           Hartford]
 gi|166229276|sp|A8GPC6|RPOA_RICAH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|157799997|gb|ABV75251.1| DNA-directed RNA polymerase subunit alpha [Rickettsia akari str.
           Hartford]
          Length = 340

 Score =  357 bits (917), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 179/337 (53%), Positives = 248/337 (73%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y    +   N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNRVAYENFPEIN-NKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE SSI GV ED++++ILNIKG+ LKM     + + +   GP VVTAG I+T
Sbjct: 63  SIKIPAIEHEFSSIPGVKEDVSEVILNIKGVELKMHVAEKRIMKLKATGPCVVTAGMIET 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNPDH+ICNL  +  + M LT   G GYV + +   ++ PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPDHIICNLAKNKQLEMALTCKVGKGYVLSTNSYEDDLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
            V+Y VE+ R GQV DYDKL M ++T+G +  E +V LA+RILQ+QL +FI+FEE +++ 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGGLLPEMAVGLAARILQEQLQLFISFEEHEEDK 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +  +   +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFGRK
Sbjct: 243 Q--VKTDTLPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>gi|41410331|ref|NP_963167.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium avium
           subsp. paratuberculosis K-10]
 gi|118463576|ref|YP_883533.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium avium 104]
 gi|61215987|sp|Q73S43|RPOA_MYCPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158512444|sp|A0QKU5|RPOA_MYCA1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|41399165|gb|AAS06783.1| RpoA [Mycobacterium avium subsp. paratuberculosis K-10]
 gi|118164863|gb|ABK65760.1| DNA-directed RNA polymerase, alpha subunit [Mycobacterium avium
           104]
          Length = 347

 Score =  357 bits (917), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 119/306 (38%), Positives = 188/306 (61%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
            +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T
Sbjct: 15  TDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVT 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            IILN+K + +    D    + + K+GPG VTAGDI     + V NP+  I  L+    +
Sbjct: 75  AIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPELHIATLNDKGKL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL +
Sbjct: 135 EVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLIL 194

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T  SIT  D++A A + L +  G+        + ++   +        +    +++L
Sbjct: 195 DVETKSSITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALPIDDL 254

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  + P 
Sbjct: 255 DLTVRSYNCLKREGVHTVGELVSRTESDLLDIRNFGQKSIDEVKVKLHQLGLSLKDSPPS 314

Query: 324 WPPESI 329
           + P  +
Sbjct: 315 FDPSQV 320


>gi|239948295|ref|ZP_04700048.1| DNA-directed RNA polymerase, alpha subunit [Rickettsia endosymbiont
           of Ixodes scapularis]
 gi|239922571|gb|EER22595.1| DNA-directed RNA polymerase, alpha subunit [Rickettsia endosymbiont
           of Ixodes scapularis]
          Length = 340

 Score =  357 bits (917), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 181/337 (53%), Positives = 248/337 (73%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y     E  N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNKVAYENF-PETNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE S I GV ED++++ILNIKGI +KM     + + +   GP VVTAG I+T
Sbjct: 63  SIKIPAIEHEFSFIPGVKEDVSEVILNIKGIEVKMHVAEKRIMKLKATGPCVVTAGMIET 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNPDHVICN+  +  + MELT   G GYV + +   +N PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPDHVICNIAKNKQLEMELTCKVGKGYVLSTNSYEDNLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
            V+Y VE+ R GQV DYDKL M ++T+G +  E +V LA+RILQ+QL +FI+FEE +++ 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDLLPEMAVGLAARILQEQLRLFISFEEQEEDK 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +  +   +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFGRK
Sbjct: 243 Q--VKTDALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>gi|157690927|ref|YP_001485389.1| DNA-directed RNA polymerase subunit alpha [Bacillus pumilus
           SAFR-032]
 gi|194017476|ref|ZP_03056087.1| DNA-directed RNA polymerase, alpha subunit [Bacillus pumilus ATCC
           7061]
 gi|172045997|sp|A8F9B2|RPOA_BACP2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|157679685|gb|ABV60829.1| DNA-directed RNA polymerase subunit alpha [Bacillus pumilus
           SAFR-032]
 gi|194010748|gb|EDW20319.1| DNA-directed RNA polymerase, alpha subunit [Bacillus pumilus ATCC
           7061]
          Length = 314

 Score =  357 bits (917), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 134/313 (42%), Positives = 202/313 (64%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  ++      + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETVEIS-DDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IILNIK + LK+  +  K + I  +  G VTA DI   +DIE+
Sbjct: 61  VLHEFSTIEGVVEDVTTIILNIKKLALKIYSEEEKTLEIDVQDEGTVTAADITHDSDIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  +A  R+ LT  +G GY PA  ++ ++ PIG+I ID++Y+P+ +V+Y V
Sbjct: 121 LNPDLHIATLGKNASFRVRLTAQRGRGYNPADANKRDDQPIGVIPIDSIYTPVSRVTYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ +YDKL++ + TDGS   ++++AL S+IL + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQITNYDKLTLDVWTDGSTGPKEAIALGSKILTEHLNIFVGLTDEAQHAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 AKLEELGLGLRKD 313


>gi|171060593|ref|YP_001792942.1| DNA-directed RNA polymerase subunit alpha [Leptothrix cholodnii
           SP-6]
 gi|238689121|sp|B1Y7M9|RPOA_LEPCP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|170778038|gb|ACB36177.1| DNA-directed RNA polymerase, alpha subunit [Leptothrix cholodnii
           SP-6]
          Length = 328

 Score =  357 bits (917), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 156/333 (46%), Positives = 215/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N   L+KP  I    LG     R  +  EP  RGF HTLGNALRRVL+SS+ G A T
Sbjct: 1   MQTN---LLKPKAINVDPLGGH---RAKVTLEPFERGFGHTLGNALRRVLLSSMVGYAPT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE S++ GV ED+  I+LN+KG+  ++       + + K G G V A DIQT
Sbjct: 55  EVTIAGVLHEYSTVDGVQEDVVHIMLNLKGVVFRLHNRDEVTLVLRKEGEGPVKASDIQT 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYS 178
            +D+E++NPDHVI +L     + M++ V KG GYVP    R  ++P    G I +DA +S
Sbjct: 115 PHDVEIINPDHVIAHLAQGGKLDMQIKVEKGRGYVPGSMRRYADEPTKSIGRIVLDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+K+VSYTVESAR  Q  D DKL M I+T+G+I+ E+++  +++IL +QL +F   E   
Sbjct: 175 PLKRVSYTVESARVEQRTDLDKLVMEIETNGAISPEEAIRASAKILVEQLAVFAQLEGSD 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
             + E    ++  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 235 LAIFEAPAPRAQHFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTETELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL + GL LG  L +WPP+ +++
Sbjct: 295 GRKSLNEIKEVLASRGLTLGARLENWPPQGLDK 327


>gi|187476574|ref|YP_784598.1| DNA-directed RNA polymerase subunit alpha [Bordetella avium 197N]
 gi|119366666|sp|Q2L238|RPOA_BORA1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|115421160|emb|CAJ47644.1| DNA-directed RNA polymerase alpha chain [Bordetella avium 197N]
          Length = 328

 Score =  357 bits (917), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 150/330 (45%), Positives = 210/330 (63%), Gaps = 7/330 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            + Q  +KP +IE   +G    N   ++ EP  RG+ HTLGNALRR+L+SS+ G A T V
Sbjct: 1   MSTQGFLKPRSIEVEPVG---PNHAKIVMEPFERGYGHTLGNALRRILLSSMTGYAPTEV 57

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           Q+ GV+HE S+I GV ED+ DI+LN+KG+  K+       + + K G G+V A DI+  +
Sbjct: 58  QMTGVVHEYSTIPGVREDVVDILLNLKGVVFKLHNRDEVTLILRKNGSGLVLASDIELPH 117

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPI 180
           D+E++NP+H ICNL     + M++ V KG GYVP        D    IG I +DA +SP+
Sbjct: 118 DVEIVNPEHPICNLTDAGKLEMQIKVEKGRGYVPGNVRALSEDRTHTIGRIILDASFSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY VESAR  Q  D DKL + I+T+G I+ E++V  ++RIL DQ+ +F   E     
Sbjct: 178 RRVSYAVESARVEQRTDLDKLVLDIETNGVISPEEAVRQSARILMDQISVFAALEGAGDS 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +  +   +   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GR
Sbjct: 238 YEAPV-RGTPQIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           KSL EIK VL   GL LGM L +WPP  +E
Sbjct: 297 KSLNEIKEVLAARGLTLGMKLENWPPLGLE 326


>gi|238650948|ref|YP_002916804.1| DNA-directed RNA polymerase subunit alpha [Rickettsia peacockii
           str. Rustic]
 gi|259494172|sp|C4K2F5|RPOA_RICPU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238625046|gb|ACR47752.1| DNA-directed RNA polymerase subunit alpha [Rickettsia peacockii
           str. Rustic]
          Length = 340

 Score =  357 bits (916), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 182/337 (54%), Positives = 247/337 (73%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y     E  N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNKVAYENF-PETNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE SSI GV ED++++ILNIKGI +KM     + + +   GP VV AG I+T
Sbjct: 63  SIKIPAIEHEFSSIPGVKEDVSEVILNIKGIEVKMHVAEKRIMKLKATGPCVVKAGMIET 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNPDHVIC+L  D  + MELT   G GYV + +   +N PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPDHVICDLAKDKQLEMELTCKVGKGYVLSTNSYEDNLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
            V+Y VE+ R GQV DYDKL M ++T+G +  E +V LA+RILQ+QL +FI+FEE +++ 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDVLPEMAVGLAARILQEQLQLFISFEEQEEDK 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +  +   +LPF P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFGRK
Sbjct: 243 Q--VKTDALPFAPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>gi|78044042|ref|YP_361090.1| DNA-directed RNA polymerase subunit alpha [Carboxydothermus
           hydrogenoformans Z-2901]
 gi|90110830|sp|Q3A9U4|RPOA_CARHZ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|77996157|gb|ABB15056.1| DNA-directed RNA polymerase, alpha subunit [Carboxydothermus
           hydrogenoformans Z-2901]
          Length = 313

 Score =  357 bits (916), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 134/310 (43%), Positives = 207/310 (66%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP     I   +  +     + EPL RG+  TLGN++RR+L+SSL GAA+T+++I+G
Sbjct: 3   EIEKPK----IETEELNDRYGRFVIEPLERGYGITLGNSMRRILLSSLPGAAVTSIKIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T+IILNIK + LK+ GD  + + I   G GV+TA DI    ++E+
Sbjct: 59  VLHEFSTVPGVVEDVTEIILNIKNLTLKLHGDEEQVLRIEAEGEGVITAKDIIAPPEVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD VI ++     + ME+TV++G GYVPA+ ++     IG+I +D+++SP+ KV++ V
Sbjct: 119 LNPDLVIAHIAEGGRLFMEMTVARGRGYVPAERNKKGEHVIGVIPVDSIFSPVLKVNFQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ DYDKL++ + TDGSI  +++V+LA+RI+ + L +F+N  E    V+  +  
Sbjct: 179 ENTRVGQITDYDKLTLEVWTDGSIRPDEAVSLAARIMVEHLQLFVNLNERATGVEIMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +           +E+L+LSVRS NCL+   I  +G+LIQ+TEADM+++ N G+KSL E+ 
Sbjct: 239 EEDAKEKLAEMPIEDLDLSVRSYNCLKRAGINTVGELIQKTEADMMKVRNLGKKSLEEVI 298

Query: 308 GVLGTMGLFL 317
             L +MGL L
Sbjct: 299 SKLNSMGLSL 308


>gi|88799194|ref|ZP_01114774.1| DNA-directed RNA polymerase alpha subunit [Reinekea sp. MED297]
 gi|88778177|gb|EAR09372.1| DNA-directed RNA polymerase alpha subunit [Reinekea sp. MED297]
          Length = 333

 Score =  357 bits (916), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 154/336 (45%), Positives = 225/336 (66%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  + + P +I+   +     NR  +  EPL RGF HTLGNALRR+L+SS+ GAAIT
Sbjct: 1   MQRSANDFLTPRHIDVQEVN---ANRAKITLEPLERGFGHTLGNALRRILLSSMPGAAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ +I+LN+K + +K+       +T+ K G G +TAGDIQ 
Sbjct: 58  EVEIDGVLHEYSTIEGVQEDVQEILLNLKDVAVKLHEREECTLTLRKSGAGTLTAGDIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            + +EV NPDHVI +L   A V M L V+ G GYVPA+   +E D   PIG + +DA +S
Sbjct: 118 DHGVEVANPDHVIAHLGSSADVNMTLKVALGRGYVPAEARSSEEDESKPIGRLQLDATFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +V+Y+VE+AR  Q  D DKL + ++T+G++  E+++  ++ ILQ Q+  F++ +   
Sbjct: 178 PVVRVAYSVENARVEQRTDLDKLVIELETNGTLDPEEAIRRSATILQQQVAAFVDLDHQA 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V+E    +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EAVQE---KEEDKIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L  WPP S++   K
Sbjct: 295 GKKSLTEIKDVLASKGLSLGMVLEAWPPASLKNDDK 330


>gi|300782639|ref|YP_003762930.1| DNA-directed RNA polymerase subunit alpha [Amycolatopsis
           mediterranei U32]
 gi|299792153|gb|ADJ42528.1| DNA-directed RNA polymerase subunit alpha [Amycolatopsis
           mediterranei U32]
          Length = 356

 Score =  357 bits (916), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 124/307 (40%), Positives = 186/307 (60%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
                E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV 
Sbjct: 11  EETVNETRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVK 70

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+TDIILN+K + +    D    + + K+GPG VTA DI     + V NPD  I +L+ 
Sbjct: 71  EDVTDIILNLKELVVSSEEDEPVTMYLRKQGPGEVTAADIVPPAGVTVHNPDLHIASLNG 130

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D
Sbjct: 131 KGKLEIELVVERGRGYVPALQNKQAGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFD 190

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + ++T  SIT  D+VA A + L +  G+        + ++   + +      A    
Sbjct: 191 KLILDVETKPSITPRDAVASAGKTLVELFGLARELNVDAEGIEIGPSPQEADTIAAYAMP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  +GL L  
Sbjct: 251 IEDLDLTVRSYNCLKREGIHTVGELVSRSEADLLDIRNFGAKSIDEVKLKLVGLGLALKD 310

Query: 320 NLPDWPP 326
           + P + P
Sbjct: 311 SPPGFDP 317


>gi|111023125|ref|YP_706097.1| DNA-directed RNA polymerase subunit alpha [Rhodococcus jostii RHA1]
 gi|226365624|ref|YP_002783407.1| DNA-directed RNA polymerase subunit alpha [Rhodococcus opacus B4]
 gi|119366719|sp|Q0S3E7|RPOA_RHOSR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|110822655|gb|ABG97939.1| DNA-directed RNA polymerase alpha subunit [Rhodococcus jostii RHA1]
 gi|226244114|dbj|BAH54462.1| DNA-directed RNA polymerase alpha subunit [Rhodococcus opacus B4]
          Length = 353

 Score =  357 bits (916), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 123/319 (38%), Positives = 196/319 (61%), Gaps = 4/319 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E ++     +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLTEEVI----ADNRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TDIILN+KG+ +    D    + + K+GPG VTAGDI     + V NP
Sbjct: 62  EFTTVPGVKEDVTDIILNLKGLVVSSEEDEPVTMYVRKQGPGAVTAGDIVPPAGVTVNNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLHIATLNDKGKLEIELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  SIT  D++A A + L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDRLVLDVETKNSITARDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
               +    +E+L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L
Sbjct: 242 DHIASFGLPIEDLDLTVRSYNCLKREGVHTVGELVGRTESDLLDIRNFGQKSIDEVKVKL 301

Query: 311 GTMGLFLGMNLPDWPPESI 329
            ++GL L  +   + P ++
Sbjct: 302 HSLGLALKDSPASFDPTTV 320


>gi|126654446|ref|ZP_01726183.1| DNA-directed RNA polymerase subunit alpha [Bacillus sp. B14905]
 gi|169830005|ref|YP_001700163.1| DNA-directed RNA polymerase subunit alpha [Lysinibacillus
           sphaericus C3-41]
 gi|299541958|ref|ZP_07052281.1| DNA-directed RNA polymerase subunit alpha [Lysinibacillus
           fusiformis ZC1]
 gi|126589096|gb|EAZ83300.1| DNA-directed RNA polymerase subunit alpha [Bacillus sp. B14905]
 gi|168994493|gb|ACA42033.1| DNA-directed RNA polymerase alpha chain [Lysinibacillus sphaericus
           C3-41]
 gi|298725696|gb|EFI66337.1| DNA-directed RNA polymerase subunit alpha [Lysinibacillus
           fusiformis ZC1]
          Length = 314

 Score =  357 bits (916), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 129/310 (41%), Positives = 202/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + + ++ +     + EPL RG+ +TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETVEISEDSK-YGKFVVEPLERGYGNTLGNSLRRILLSSLPGAAVTSIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+  IILN+K + LK+  D  K + I  +G G VTA DI   +D+E+
Sbjct: 61  VLHEFSTVEGVVEDVASIILNVKKLALKIYSDEEKVIEIDVKGDGTVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  +  +  +RM +   +G GY PA  ++ E+ PIG+I ID++Y+P+ +V++ V
Sbjct: 121 LNPDLYIATIAKNGHLRMRMYAQRGRGYTPADQNKREDLPIGVIPIDSIYTPVSRVNFQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  DYDKLS+ + TDGSI  +++++L ++IL + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQSSDYDKLSLDVWTDGSIGPKEAISLGAKILTEHLNIFVGMTDEAQTAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVLELANKSEDDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 AKLEELGLGL 310


>gi|33594507|ref|NP_882151.1| DNA-directed RNA polymerase subunit alpha [Bordetella pertussis
           Tohama I]
 gi|33594778|ref|NP_882421.1| DNA-directed RNA polymerase subunit alpha [Bordetella parapertussis
           12822]
 gi|33599050|ref|NP_886610.1| DNA-directed RNA polymerase subunit alpha [Bordetella
           bronchiseptica RB50]
 gi|61234210|sp|P0A4E5|RPOA_BORPE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61234215|sp|P0A4E6|RPOA_BORBR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61234219|sp|P0A4E7|RPOA_BORPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|406284|emb|CAA81390.1| RNA polymerase alpha subunit [Bordetella pertussis Tohama I]
 gi|33564583|emb|CAE43899.1| DNA-directed RNA polymerase alpha chain [Bordetella pertussis
           Tohama I]
 gi|33564854|emb|CAE39798.1| DNA-directed RNA polymerase alpha chain [Bordetella parapertussis]
 gi|33575096|emb|CAE30559.1| DNA-directed RNA polymerase alpha chain [Bordetella bronchiseptica
           RB50]
          Length = 328

 Score =  357 bits (916), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 151/330 (45%), Positives = 209/330 (63%), Gaps = 7/330 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            + Q  +KP +IE   +G        ++ EP  RG+ HTLGNALRR+L+SS+ G A T V
Sbjct: 1   MSTQGFLKPRSIEVEPVGAH---HAKIVMEPFERGYGHTLGNALRRILLSSMTGYAPTEV 57

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           Q+ GV+HE S+I GV ED+ DI+LN+KG+  K+       + + K G G V A DI+  +
Sbjct: 58  QMTGVVHEYSTIAGVREDVVDILLNLKGVVFKLHNRDEVTLVLRKNGAGAVVASDIELPH 117

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPI 180
           D+E++NPDH+ICNL     + M++ V KG GYVP        D    IG I +DA +SP+
Sbjct: 118 DVEIINPDHLICNLTDAGKIEMQVKVEKGRGYVPGNVRALSEDRTHTIGRIVLDASFSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY VESAR  Q  D DKL + I+T+G I+ E++V  A+RIL DQ+ +F   E     
Sbjct: 178 RRVSYAVESARVEQRTDLDKLVLDIETNGVISPEEAVRQAARILMDQISVFAALEGAGDA 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +  +   +   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GR
Sbjct: 238 YEPPV-RGTPQIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           KSL EIK VL   GL LGM L +WPP  +E
Sbjct: 297 KSLNEIKEVLAARGLTLGMKLENWPPLGLE 326


>gi|67458694|ref|YP_246318.1| DNA-directed RNA polymerase subunit alpha [Rickettsia felis
           URRWXCal2]
 gi|75536844|sp|Q4UMQ5|RPOA_RICFE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|67004227|gb|AAY61153.1| DNA-directed RNA polymerase alpha chain [Rickettsia felis
           URRWXCal2]
          Length = 340

 Score =  356 bits (915), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 181/337 (53%), Positives = 248/337 (73%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y     E  N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNKVAYENF-PETNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE SSI GV ED++++ILNIKGI +KM     + + +   GP V+TAG I+T
Sbjct: 63  SIKIPAIEHEFSSIPGVKEDVSEVILNIKGIEVKMHVAEKRIMKLKATGPCVITAGMIET 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNPDHVICNL  +  + MELT   G GYV + +   +N PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPDHVICNLAKNKQLEMELTCKVGKGYVLSTNSYEDNLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
            V+Y VE+ R GQV DYDKL M ++T+G +  E +V LA+RILQ+QL +FI+FEE +++ 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDLLPEMAVGLAARILQEQLQLFISFEEQEEDK 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +  +   +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFGRK
Sbjct: 243 Q--VKTDALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+I+EL+ +YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENIQELSNRYED 337


>gi|119478107|ref|ZP_01618186.1| DNA-directed RNA polymerase alpha subunit [marine gamma
           proteobacterium HTCC2143]
 gi|119448813|gb|EAW30056.1| DNA-directed RNA polymerase alpha subunit [marine gamma
           proteobacterium HTCC2143]
          Length = 334

 Score =  356 bits (915), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 151/336 (44%), Positives = 222/336 (66%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    E + P  I+   +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQSAVNEFLTPRVIDVDEVSS---TRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V IDGVLHE S+I+GV ED+ +I+LN+KG+++ M G     +T+ K G G VTAGDIQ 
Sbjct: 58  EVAIDGVLHEYSAIEGVQEDVIEILLNLKGVSILMHGKDEAVLTLSKSGAGPVTAGDIQV 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +DIE+ NPDH+I  L+    + M LT+ +G GYVPA   +++++    IG + +DA +S
Sbjct: 118 DHDIEISNPDHLIATLNEAGSLNMTLTIGRGRGYVPADARQSDDEETRSIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +V+Y VESAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++    +
Sbjct: 178 PVHRVAYVVESARVEQRTDLDKLVLDLETNGTIDPEEAIRRAATILQQQLSVFVDL---E 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E + +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N 
Sbjct: 235 SEKEAEPEEEEDEVDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LG+ L +WPP S++   K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGLRLDNWPPASLKNDDK 330


>gi|254366058|ref|ZP_04982103.1| DNA-directed RNA polymerase (alpha chain) rpoA [Mycobacterium
           tuberculosis str. Haarlem]
 gi|134151571|gb|EBA43616.1| DNA-directed RNA polymerase (alpha chain) rpoA [Mycobacterium
           tuberculosis str. Haarlem]
          Length = 348

 Score =  356 bits (915), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 118/307 (38%), Positives = 187/307 (60%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
             E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+
Sbjct: 15  SPETRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDV 74

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T+IILN+K + +    D    + + K+GPG VTAGDI     + V NP   I  L+    
Sbjct: 75  TEIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIATLNDKGK 134

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL 
Sbjct: 135 LEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLI 194

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + ++T  SI+  D++A A + L +  G+        + ++   +        +    +++
Sbjct: 195 LDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALPIDD 254

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  + P
Sbjct: 255 LDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPP 314

Query: 323 DWPPESI 329
            + P  +
Sbjct: 315 SFDPSEV 321


>gi|322436518|ref|YP_004218730.1| DNA-directed RNA polymerase, alpha subunit [Acidobacterium sp.
           MP5ACTX9]
 gi|321164245|gb|ADW69950.1| DNA-directed RNA polymerase, alpha subunit [Acidobacterium sp.
           MP5ACTX9]
          Length = 367

 Score =  356 bits (915), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 141/318 (44%), Positives = 207/318 (65%), Gaps = 1/318 (0%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           W+   KP  +                A+P  RGF  T+GNALRR L+SS+ GAA+TAV+I
Sbjct: 3   WRGFQKPKRLAVDN-ETITPKYGKFSAQPFERGFGTTIGNALRRTLLSSIEGAAVTAVRI 61

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           +GVLHE  SI GV ED TDIILN+K I  K++GD  K + +     GV+T+G I+   D+
Sbjct: 62  EGVLHEFQSITGVVEDATDIILNLKQIPFKLAGDGPKALYLRSDAAGVITSGMIEADADV 121

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E+L+P+  IC +     + ME+ + +G GY+ A  +   +  +G I +D+++SP++KV+Y
Sbjct: 122 EILDPNVYICTISEGGKIDMEMRLKRGRGYISADKNFDGDLGLGFIPVDSVHSPVRKVNY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+AR GQ+ DYDKLS+ I T+G++   D++ L++++L+D + +FINFEE  +   ++ 
Sbjct: 182 VVEAARLGQITDYDKLSIEIWTNGTVLPADALGLSAKLLKDHMTIFINFEEEMEAGHDNG 241

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           +      N  L + VEELELSVRS NCL+  NI  +G+LIQ+TEA+ML+  NFGRKSL E
Sbjct: 242 HDGPAMRNENLNRSVEELELSVRSYNCLKNANIATIGELIQKTEAEMLKTKNFGRKSLNE 301

Query: 306 IKGVLGTMGLFLGMNLPD 323
           IK +L  MGL LGM + +
Sbjct: 302 IKEILAQMGLSLGMKIDE 319


>gi|327438303|dbj|BAK14668.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Solibacillus silvestris StLB046]
          Length = 314

 Score =  356 bits (915), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 130/310 (41%), Positives = 200/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  E+      + EPL RG+ +TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETVEIS-EDAKYGKFVVEPLERGYGNTLGNSLRRILLSSLPGAAVTSIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+  IILN+K + LK+  D  K + I  +G G VTA DI   +D+E+
Sbjct: 61  VLHEFSTVEGVVEDVASIILNVKKLALKIYSDEEKVIEIDVKGDGTVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  +  +  +RM +   +G GY PA  ++ E+ PIG+I ID++Y+P+ +V++ V
Sbjct: 121 LNPDLYIATIAKNGHLRMRMYAQRGRGYTPADQNKREDLPIGVIPIDSIYTPVSRVNFQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  DYDKLS+ + TDGSI  +++++L ++IL + L +F+      +  +  +  
Sbjct: 181 ENTRVGQNSDYDKLSLDVWTDGSIGPKEAISLGAKILTEHLNIFVGMTNEAQTAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVLELANKSEDDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 HKLEELGLGL 310


>gi|229586985|ref|YP_002845486.1| DNA-directed RNA polymerase subunit alpha [Rickettsia africae
           ESF-5]
 gi|259494171|sp|C3PP83|RPOA_RICAE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|228022035|gb|ACP53743.1| DNA-directed RNA polymerase alpha chain [Rickettsia africae ESF-5]
          Length = 340

 Score =  356 bits (915), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 182/337 (54%), Positives = 248/337 (73%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y     E  N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNKVAYENF-PETNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I  + HE SSI GV ED++++ILNIKGI +KM     + + +   GP VVTAG I+T
Sbjct: 63  SIKIPAIEHEFSSIPGVKEDVSEVILNIKGIEVKMHVAEKRIMKLKATGPCVVTAGMIET 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E+LNPDHVIC+L  D  + MELT   G GYV + +   +N PIG I IDAL++P+K
Sbjct: 123 GHDVEILNPDHVICDLAKDKQLEMELTCKVGKGYVLSTNSYEDNLPIGEIAIDALFNPVK 182

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
            V+Y VE+ R GQV DYDKL M ++T+G +  E +V LA+RILQ+QL +FI+FEE +++ 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDVLPEMAVGLAARILQEQLQLFISFEEQEEDK 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +  +   +L F+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFGRK
Sbjct: 243 Q--VKTDALLFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>gi|87122790|ref|ZP_01078663.1| DNA-directed RNA polymerase alpha subunit [Marinomonas sp. MED121]
 gi|86161955|gb|EAQ63247.1| DNA-directed RNA polymerase alpha subunit [Marinomonas sp. MED121]
          Length = 334

 Score =  356 bits (915), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 158/336 (47%), Positives = 231/336 (68%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  EL+ P NIE    G+    R+ +  +PL RGF HTLGNALRR+L+SS+ G AI 
Sbjct: 1   MQRSVSELLTPRNIEVQEAGK---TRSKVTLQPLERGFGHTLGNALRRILLSSMPGCAIV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ +I+LN+KG+ + + G     +T+ K+GPGVVTAGDIQ 
Sbjct: 58  EVEIDGVLHEYSAIEGVKEDVIEILLNLKGVAIALHGQDEATLTLSKKGPGVVTAGDIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
           V D E+ NPDHVI +LD  A + M++ V++G GY PA        E  PIG + +DA +S
Sbjct: 118 VADAEISNPDHVIAHLDDTAELNMQIKVARGCGYEPADARIASDDETRPIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY+V++AR  Q  D DKL + I+++G+I  E+++  A+ ILQ Q+ +F+     +
Sbjct: 178 PVRRVSYSVDNARVEQRTDLDKLVIDIESNGTIDPEEAIRRAATILQQQIAVFVAL---E 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E ++ +  +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 235 SESEQVVEEEEDEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL   GL LGM L +WPP S+++ +K
Sbjct: 295 GKKSLTEIKDVLAQRGLSLGMRLENWPPASLKDDSK 330


>gi|326905303|gb|EGE52236.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis W-148]
          Length = 348

 Score =  356 bits (914), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 118/308 (38%), Positives = 187/308 (60%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
               NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED
Sbjct: 14  SSPNNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKED 73

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T+IILN+K + +    D    + + K+GPG VTAGDI     + V NP   I  L+   
Sbjct: 74  VTEIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIATLNDKG 133

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL
Sbjct: 134 KLEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKL 193

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + ++T  SI+  D++A A + L +  G+        + ++   +        +    ++
Sbjct: 194 ILDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALPID 253

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  + 
Sbjct: 254 DLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSP 313

Query: 322 PDWPPESI 329
           P + P  +
Sbjct: 314 PSFDPSEV 321


>gi|296168685|ref|ZP_06850434.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           parascrofulaceum ATCC BAA-614]
 gi|295896594|gb|EFG76235.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           parascrofulaceum ATCC BAA-614]
          Length = 347

 Score =  356 bits (914), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 120/306 (39%), Positives = 189/306 (61%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
            +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T
Sbjct: 15  TDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVAGVKEDVT 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            IILN+KG+ +    D    + + K+GPG VTAGDI     + V NP+  I  L+    +
Sbjct: 75  AIILNLKGLVVSSEEDEPVTMYLRKQGPGAVTAGDIVPPAGVTVHNPEMHIATLNDKGKL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL +
Sbjct: 135 EVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLIL 194

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T  SIT  D++A A + L +  G+        + ++   +        +    +++L
Sbjct: 195 DVETKSSITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALPIDDL 254

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  + P 
Sbjct: 255 DLTVRSYNCLKREGVHTVGELVSRTESDLLDIRNFGQKSIDEVKVKLHQLGLSLKDSPPS 314

Query: 324 WPPESI 329
           + P  +
Sbjct: 315 FDPSQV 320


>gi|160896495|ref|YP_001562077.1| DNA-directed RNA polymerase subunit alpha [Delftia acidovorans
           SPH-1]
 gi|238687179|sp|A9BRX5|RPOA_DELAS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|160362079|gb|ABX33692.1| DNA-directed RNA polymerase, alpha subunit [Delftia acidovorans
           SPH-1]
          Length = 332

 Score =  356 bits (914), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 163/337 (48%), Positives = 217/337 (64%), Gaps = 13/337 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N   L+KP  I    LG    NR  ++ EP  RG+ HTLGNALRRVL+SS+ G A T
Sbjct: 1   MQTN---LLKPKTINVEQLG---HNRAKVVLEPFERGYGHTLGNALRRVLLSSMVGYAAT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE SSI GV ED+ +I+LN+KG+  K+       +++ K G GVVTA DIQT
Sbjct: 55  EVTIAGVLHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGVVTARDIQT 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYS 178
            +D+E++NPDHVI NL     + M++ V KG GYVP    R  ++     G I +DA +S
Sbjct: 115 PHDVEIINPDHVIANLSQGGKLDMQIKVEKGRGYVPGNVRRYGDESTKSIGRIVLDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+K+VSY VESAR  Q  D DKL + I+T+G+IT ED+V  +++IL +QL +F   +   
Sbjct: 175 PVKRVSYAVESARVEQRTDLDKLVVEIETNGAITAEDAVRASAKILVEQLAVFAQLDGGD 234

Query: 239 KEVKEDINVK----SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
                D        +  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+
Sbjct: 235 IASVFDAPAGGRGAATAFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLK 294

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
             N GRKSL EIK VL + GL LGM L +WPP  +E+
Sbjct: 295 TPNLGRKSLNEIKEVLASRGLTLGMKLENWPPAGLEK 331


>gi|20808632|ref|NP_623803.1| DNA-directed RNA polymerase subunit alpha [Thermoanaerobacter
           tengcongensis MB4]
 gi|22257018|sp|Q8R7Y2|RPOA_THETN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|20517265|gb|AAM25407.1| DNA-directed RNA polymerase alpha subunit/40 kD subunit
           [Thermoanaerobacter tengcongensis MB4]
          Length = 315

 Score =  356 bits (914), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 135/311 (43%), Positives = 199/311 (63%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+I+P  IE IV   E+      + EPL RG+  TLGN+LRRVL+SS+ GAA  +V+IDG
Sbjct: 3   EIIEP-KIE-IVEQSEDGRYGKFVVEPLERGYGITLGNSLRRVLLSSIPGAAPKSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+ +IILN+K + +K+  D      I   G G VTAG I+   ++E+
Sbjct: 61  VLHEFSTLPGVKEDVVEIILNLKEVAVKLHSDEPVIGRIDVEGKGEVTAGHIKGGPELEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPDH I  L  D  + ME+   KG GYVPA+ ++  N PIG+I +D++++PI+KV+YTV
Sbjct: 121 LNPDHHIATLSDDGKIHMEIVFVKGKGYVPAEKNKEPNQPIGVIPVDSIFTPIRKVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G V DYDKL++ + T+G+IT +++V++A+ +L      FI+F    K     +  
Sbjct: 181 ENTRVGHVTDYDKLTLEVWTNGTITPKEAVSMAADMLIKYFQKFISFTGEYKSPDVFVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L Q+TE +M+++ N G+KSL E+K
Sbjct: 241 QEKKVEKPLDMTIEELDLSVRSYNCLKRAGINTVQELTQKTEEEMMKIRNLGKKSLEEVK 300

Query: 308 GVLGTMGLFLG 318
             L  +GL L 
Sbjct: 301 QKLAALGLSLK 311


>gi|172056167|ref|YP_001812627.1| DNA-directed RNA polymerase subunit alpha [Exiguobacterium
           sibiricum 255-15]
 gi|171988688|gb|ACB59610.1| DNA-directed RNA polymerase, alpha subunit [Exiguobacterium
           sibiricum 255-15]
          Length = 314

 Score =  356 bits (913), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 133/310 (42%), Positives = 199/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  +       + EPL RGF  TLGN+LRR+L+SSL GAA+TAVQIDG
Sbjct: 3   EIEKP-KIETVELS-DNATFGKFVVEPLERGFGTTLGNSLRRILLSSLPGAAVTAVQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILN+K + LK+  +  K + I  +G GVVTA +I   +D+E+
Sbjct: 61  VLHEFSTIDGVVEDVTQIILNLKKLALKVYSEEEKTLEIDIQGAGVVTAANITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  L   A + M LT  +G GYV A+ ++ ++ PIG+I ID++Y+PI++V+Y V
Sbjct: 121 LNPELHIATLAEGASLHMRLTARRGRGYVQAEDNKRDDMPIGVIPIDSIYTPIQRVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R GQ   +DKL++ + TDGSI  E++V+L ++I+ + L +F+   +     +  +  
Sbjct: 181 EKTRVGQDASFDKLTLDVWTDGSIRPEEAVSLGAKIMTEHLNIFVGLTDEALHAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E++
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKSEDEMMKVRNLGRKSLEEVQ 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 AKLDELGLGL 310


>gi|92112579|ref|YP_572507.1| DNA-directed RNA polymerase subunit alpha [Chromohalobacter
           salexigens DSM 3043]
 gi|119366673|sp|Q1R0F0|RPOA_CHRSD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|91795669|gb|ABE57808.1| DNA-directed RNA polymerase subunit alpha [Chromohalobacter
           salexigens DSM 3043]
          Length = 333

 Score =  356 bits (913), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 147/336 (43%), Positives = 226/336 (67%), Gaps = 10/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  E ++P +I+   +     N   ++ EP  RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQRSVTEFLRPRDIKVEEIN---ANHAKIVLEPFERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQ 120
             +I+GVLHE S+I+GV ED+ +I+LN+K + +KM G+     + + K+GP VVTAGDI 
Sbjct: 58  EAEIEGVLHEYSAIEGVQEDVIEILLNLKDVAVKMHGNRDEVVLALSKQGPSVVTAGDIA 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALY 177
             +D+E++NPDHVI +L+    ++M+L V +G GY PA    +E D     G + +DA +
Sbjct: 118 VDHDVEIVNPDHVIAHLNDSGELKMQLKVVRGRGYEPADTRASEEDESRAIGRLQLDATF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++VSY+VE+AR  Q  D DKL + ++TDG++  E+++  ++ ILQ+QL  F++ E  
Sbjct: 178 SPVRRVSYSVEAARVEQRTDLDKLIIDLETDGTLDPEEAIRRSATILQEQLAAFVDLEAD 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           K++    +  +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N
Sbjct: 238 KEQE---VEEEEDQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELA 333
            G+KSL EIK VL   GL LGM L +WPP S+++  
Sbjct: 295 LGKKSLNEIKDVLAARGLSLGMRLENWPPASLKDDK 330


>gi|261400077|ref|ZP_05986202.1| DNA-directed RNA polymerase, alpha subunit [Neisseria lactamica
           ATCC 23970]
 gi|313667466|ref|YP_004047750.1| DNA-directed RNA polymerase alpha chain [Neisseria lactamica
           ST-640]
 gi|269210302|gb|EEZ76757.1| DNA-directed RNA polymerase, alpha subunit [Neisseria lactamica
           ATCC 23970]
 gi|309379134|emb|CBX22265.1| DNA-directed RNA polymerase, alpha subunit [Neisseria lactamica
           Y92-1009]
 gi|313004928|emb|CBN86354.1| DNA-directed RNA polymerase alpha chain [Neisseria lactamica
           020-06]
          Length = 328

 Score =  355 bits (912), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 160/333 (48%), Positives = 216/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+          R  +  +P  RGF HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSTAEFLKPRQIDVNTFS---ATRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE S++ GV ED+ DI+LNIKGI  K+ G S  ++ + K G GVV+AGDI+ 
Sbjct: 58  EVAIAGVLHEYSTVDGVQEDVVDILLNIKGIVFKLHGRSQVQLVLKKTGSGVVSAGDIEL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
            +D+E+LNPDHVIC+L  +  + ME+ V +G GY         R EN  IG I +DA +S
Sbjct: 118 PHDVEILNPDHVICHLADNGQIEMEIKVEQGRGYQSVSGRQAVRDENRQIGAIQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI +VS+ VE AR  Q  D DKL + I+TDGSI  E++V  A+RIL DQ+ +F N    +
Sbjct: 178 PISRVSFEVEPARVEQRTDLDKLVLDIETDGSIDPEEAVRSAARILIDQMSIFANL---Q 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
               E++  K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N 
Sbjct: 235 GTPVEEVEEKAPPIDPVLLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 295 GRKSLNEIKEVLASKGLTLGSKLEAWPPAGLEK 327


>gi|78357274|ref|YP_388723.1| DNA-directed RNA polymerase subunit alpha [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
 gi|90110839|sp|Q30Z68|RPOA_DESDG RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|78219679|gb|ABB39028.1| DNA-directed RNA polymerase subunit alpha [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
          Length = 348

 Score =  355 bits (912), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 148/337 (43%), Positives = 217/337 (64%), Gaps = 1/337 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW EL+KP+ I        +      + EPL RG+  T+GNA+RRVL++SL+GAA  AV
Sbjct: 13  RNWSELVKPDQI-SRASESADTMYGKFVCEPLERGYGTTIGNAMRRVLLASLQGAAFVAV 71

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I GV HE ++I GV ED+TDI+LN+K + L M  +  + + +     G V AGDI+   
Sbjct: 72  KISGVQHEFTTIPGVLEDVTDIVLNLKQVRLAMDTEEPQHLELHVNKSGEVKAGDIKCNQ 131

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            + VLN D  +  L  D  +  EL V  G GYVPA  H   +D IGLI +DA +SP++KV
Sbjct: 132 HVMVLNADQHLMTLTEDVELTFELEVRMGKGYVPADMHEGLSDEIGLIALDASFSPVRKV 191

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +YTVE AR GQ+ +YDKL + + TDGSI+ ED++A +++I++DQ+ +FINF+E   E + 
Sbjct: 192 AYTVEQARVGQMTNYDKLILEVWTDGSISPEDAIAYSAKIIKDQISVFINFDERISEQEN 251

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +    +   N  L K ++ELELSVR+TNCL+  NI  +G+L+Q++E +ML+  NFGRKSL
Sbjct: 252 EGRSSASDVNENLFKGIDELELSVRATNCLKSANISLVGELVQKSEGEMLKTKNFGRKSL 311

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
            EI+ VLG M L  GM +  +  +  E L +K +++ 
Sbjct: 312 DEIRRVLGEMSLDFGMKVDGFEKKYQEWLKRKQQNEA 348


>gi|315640136|ref|ZP_07895258.1| DNA-directed RNA polymerase subunit alpha [Enterococcus italicus
           DSM 15952]
 gi|315484113|gb|EFU74587.1| DNA-directed RNA polymerase subunit alpha [Enterococcus italicus
           DSM 15952]
          Length = 312

 Score =  355 bits (912), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 138/313 (44%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDG
Sbjct: 3   EFEKPR----IAKIDEEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+IKGV ED+  IILNIKG+ LK+ G+  K + I   GP  VTAGDI   +D+E+
Sbjct: 59  VLHEFSTIKGVREDVAQIILNIKGLALKLYGEDEKTLEIDITGPATVTAGDIIVDSDVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D  IC +   A     LTV  G GYV A  ++ ++ PIG++ +D++Y+P+++V+Y V
Sbjct: 119 LNKDMYICTVSEGATFHARLTVKPGRGYVQADENKKDDMPIGVLPVDSIYTPVRRVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G   D+DKL+M I TDGSI   D+++LA++I+ + L +F+N  +  K  +  +  
Sbjct: 179 ENTRVGHRDDFDKLTMEIWTDGSIEPLDAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E+K
Sbjct: 239 EETQKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTNKSEPEMIKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 AKLHDLGLGLRKD 311


>gi|169630849|ref|YP_001704498.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium abscessus
           ATCC 19977]
 gi|169242816|emb|CAM63844.1| DNA-directed RNA polymerase alpha chain RpoA [Mycobacterium
           abscessus]
          Length = 350

 Score =  355 bits (912), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 121/305 (39%), Positives = 188/305 (61%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ENR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+TD
Sbjct: 16  ENRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTD 75

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+K + +    D    + + K+GPG VTAGDI     + V NPD  I  L+    + 
Sbjct: 76  IILNLKSLVVSSEEDEPVTMYLRKQGPGAVTAGDIVPPAGVTVHNPDMHIATLNDKGKLE 135

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL + 
Sbjct: 136 IELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYNVEATRVEQRTDFDKLVLD 195

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           ++T  SI+  D++A A + L +  G+        + ++   +        +    +E+L+
Sbjct: 196 VETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALPIEDLD 255

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  +   +
Sbjct: 256 LTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPTSF 315

Query: 325 PPESI 329
            P  +
Sbjct: 316 DPSEV 320


>gi|83591247|ref|YP_431256.1| DNA-directed RNA polymerase subunit alpha [Moorella thermoacetica
           ATCC 39073]
 gi|119366698|sp|Q2RFS6|RPOA_MOOTA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|83574161|gb|ABC20713.1| DNA-directed RNA polymerase subunit alpha [Moorella thermoacetica
           ATCC 39073]
          Length = 313

 Score =  355 bits (912), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 138/310 (44%), Positives = 203/310 (65%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP     I     ++     + EPL RG+  TLGN+LRR+L+SSL GAA+T+V+I+G
Sbjct: 3   EIEKPK----IECQHLDDKYGRFVVEPLERGYGITLGNSLRRMLLSSLPGAAVTSVKIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED TDIILNIK + LK+  D  + + I     GVVTAGDI T  D+E+
Sbjct: 59  VLHEFSTIPGVVEDTTDIILNIKSLALKLHSDEPRVIRIEADDEGVVTAGDIITGADVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+ VI  ++    + ME+TV KG GYV A  ++ E+ PIG+I +D+L+SPI KV+YTV
Sbjct: 119 LNPEQVIATVEKGGRLYMEMTVEKGRGYVSADKNKKEDQPIGIIPVDSLFSPIHKVNYTV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ DYDKL++ + TDGSI  +++V+ A++IL + + +F+   E   +    +  
Sbjct: 179 ENTRVGQITDYDKLTLEVWTDGSIAPDEAVSSAAKILIEHMRLFLGLTERVSDEVTMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    +  +   +EEL+LSVRS NCL+   I  + +L+QR+E DM+++ N G+KSL E+ 
Sbjct: 239 EEETRDRLMDMSIEELDLSVRSYNCLKRAGINTVAELLQRSEEDMMKVRNLGKKSLEEVT 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 QKLSELGLSL 308


>gi|220935467|ref|YP_002514366.1| DNA-directed RNA polymerase subunit alpha [Thioalkalivibrio sp.
           HL-EbGR7]
 gi|254765261|sp|B8GV33|RPOA_THISH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|219996777|gb|ACL73379.1| DNA-directed RNA polymerase subunit alpha [Thioalkalivibrio sp.
           HL-EbGR7]
          Length = 334

 Score =  355 bits (912), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 155/337 (45%), Positives = 228/337 (67%), Gaps = 9/337 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    EL+KP +IE   +    + +  ++ EPL RGF HTLGNALRR+L+SS+ GAA+ 
Sbjct: 1   MQTKVNELLKPRHIEVTSVS---DRQAKVVLEPLERGFGHTLGNALRRILLSSIPGAAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +I+GVLHE +SI+GV ED+ DI+LN+KGI L+M       +T+ K+GPGVVTAGDI  
Sbjct: 58  EAEIEGVLHEYTSIEGVQEDVVDILLNLKGIALRMHNRDEATLTLKKKGPGVVTAGDITL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYS 178
            +D+E++NP+HVI +L  +  + M L + +G GY P    R   +E+ PIG + +DA +S
Sbjct: 118 DHDVEIVNPEHVIAHLTKNGELSMSLKLGRGRGYQPVTARRSSESEDRPIGRLMLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI++V+Y VESAR  Q  D D+L + ++T+G++  +D++  A+ ILQ QL  F+  +  +
Sbjct: 178 PIRRVAYKVESARVEQRTDMDRLVIELETNGTVEADDAIRQAAGILQSQLAAFVELQGDE 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
             V E    K +  +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 STVTES---KQMEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
           G+KSL EIK VL + GL +GM L +WPP  +++  KK
Sbjct: 295 GKKSLTEIKDVLASHGLSMGMRLENWPPPGLKDQDKK 331


>gi|269128485|ref|YP_003301855.1| DNA-directed RNA polymerase subunit alpha [Thermomonospora curvata
           DSM 43183]
 gi|268313443|gb|ACY99817.1| DNA-directed RNA polymerase, alpha subunit [Thermomonospora curvata
           DSM 43183]
          Length = 337

 Score =  355 bits (912), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 127/308 (41%), Positives = 185/308 (60%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
              Q +E R+  I EPL  GF +T+GN+LRR L+SS+ GAA+T+++I+GVLHE S+I GV
Sbjct: 10  TEEQIDEYRSRFIIEPLEPGFGYTIGNSLRRTLLSSIPGAAVTSIRIEGVLHEFSTIPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+TDIILN+K + +    D    + + K+GPG VTA DI     +EV NPD  I  L+
Sbjct: 70  KEDVTDIILNLKELVVSSEHDEPVVMYLRKQGPGQVTAADIAPPAGVEVHNPDLHIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
             A + MELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+ R  Q  D+
Sbjct: 130 SKAKLEMELTVERGRGYVSAAQNKQPGQEIGRIPIDSIYSPVLKVTYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           D+L + ++T  ++   D+VA A + L +  G+        + +    +         L  
Sbjct: 190 DRLILDVETKPAMLPRDAVASAGKTLVELFGLARELNVEAEGIDMGPSPTDAALAADLAL 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +EEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  MGL L 
Sbjct: 250 PIEELNLTVRSYNCLKREGIHTVGELVARSEQDLLDIRNFGAKSIEEVKQKLADMGLSLK 309

Query: 319 MNLPDWPP 326
            + P + P
Sbjct: 310 DSPPGFDP 317


>gi|323703520|ref|ZP_08115166.1| DNA-directed RNA polymerase, alpha subunit [Desulfotomaculum
           nigrificans DSM 574]
 gi|323531511|gb|EGB21404.1| DNA-directed RNA polymerase, alpha subunit [Desulfotomaculum
           nigrificans DSM 574]
          Length = 315

 Score =  355 bits (912), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 136/313 (43%), Positives = 204/313 (65%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE IV   E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+V+I+G
Sbjct: 3   EIEKP-KIE-IVEQSEDNTYGKFVVEPLERGYGITLGNSLRRILLSSLPGAAVTSVKIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+TDIILN+K + LK+  D  K + I     G VTAGDI    D+E+
Sbjct: 61  VLHEFSTVPGVREDVTDIILNLKNLCLKIHSDEEKVLRIEADTEGPVTAGDIIHDADVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  +  LD    + ME+T +KG GYV A+ ++     IG+I +D++Y+P++KV+Y V
Sbjct: 121 LNPDLHLATLDAGGRLYMEITANKGRGYVSAEKNKKGEHIIGVIPVDSIYTPVRKVNYNV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ DYDKL++ + T+GSI  +++ +L+++IL + L +FI   E   +V+  +  
Sbjct: 181 ENTRVGQITDYDKLTLEVWTNGSIRPDEATSLSAKILSEHLRLFIGLTETVNDVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    +  +   +EEL+LSVRS NCL+   I  + +LIQR E DM+++ N G+KSL E+ 
Sbjct: 241 EEEQKDKIMEMTIEELDLSVRSYNCLKRAGINTVEELIQRNEEDMMKVRNLGKKSLEEVM 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 NKLAELGLSLRKD 313


>gi|54022804|ref|YP_117046.1| DNA-directed RNA polymerase subunit alpha [Nocardia farcinica IFM
           10152]
 gi|61215826|sp|Q5Z1K9|RPOA_NOCFA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|54014312|dbj|BAD55682.1| putative RNA polymerase alpha subunit [Nocardia farcinica IFM
           10152]
          Length = 352

 Score =  355 bits (912), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 124/319 (38%), Positives = 194/319 (60%), Gaps = 4/319 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E ++     ENR+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLTEEVI----AENRSKFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TDIILN+KG+ +    D    + + K+GPG VTAGDI     + V NP
Sbjct: 62  EFTTVPGVKEDVTDIILNLKGLVVSSEEDEPVTMYVRKQGPGTVTAGDIVPPAGVVVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DMHIATLNDKGKLEIELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  SI+  D++A A + L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDRLILDVETKNSISARDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
               +    +E+L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L
Sbjct: 242 DHIASFGLPIEDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKVKL 301

Query: 311 GTMGLFLGMNLPDWPPESI 329
             +GL L  +   + P S+
Sbjct: 302 HALGLSLKDSPASFDPSSV 320


>gi|302344329|ref|YP_003808858.1| DNA-directed RNA polymerase, subunit alpha [Desulfarculus baarsii
           DSM 2075]
 gi|301640942|gb|ADK86264.1| DNA-directed RNA polymerase, alpha subunit [Desulfarculus baarsii
           DSM 2075]
          Length = 334

 Score =  355 bits (911), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 164/324 (50%), Positives = 226/324 (69%), Gaps = 2/324 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +++NW+ELIKP+ ++ I              EPL RGF HT+GNALRR+L+SSL+GAA+T
Sbjct: 1   MERNWRELIKPSRLQ-IDEEIHTSRYGKFSCEPLERGFGHTIGNALRRILISSLQGAAVT 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            ++++GVLHE S+I GV ED+TDIILN+KGI L+  G     +TI  +G GVV AGDI+T
Sbjct: 60  NLRMEGVLHEFSTIPGVLEDVTDIILNLKGIQLRYLGFDSTTMTISAQGEGVVKAGDIKT 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
             D+E+LNP+H I  L  +  +  ELTV  G GYV A+ +++  DPIG I ID+ +SPI 
Sbjct: 120 PPDVEILNPEHHIATLSPEGRLEAELTVRTGKGYVTAERNKSPEDPIGYIAIDSAFSPIT 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KVSY V  AR GQ+ DYDKL++ + T+G++  ED+VA A++IL++QL +FINF E  +  
Sbjct: 180 KVSYVVTQARVGQITDYDKLTLEVHTNGAVRPEDAVAYAAKILKEQLQIFINFPEEPEPT 239

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+   +    N  L + V+ELELSVRS NCL+  +I Y+G+L+QR+EA+ML+  NFGRK
Sbjct: 240 HEEEREEPR-LNENLFRTVDELELSVRSANCLKNADIKYIGELVQRSEAEMLKTKNFGRK 298

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL EIK +L  MGL LGM L  +P
Sbjct: 299 SLNEIKEMLTDMGLSLGMKLDGFP 322


>gi|120609326|ref|YP_969004.1| DNA-directed RNA polymerase subunit alpha [Acidovorax citrulli
           AAC00-1]
 gi|326315415|ref|YP_004233087.1| DNA-directed RNA polymerase subunit alpha [Acidovorax avenae subsp.
           avenae ATCC 19860]
 gi|158513025|sp|A1TJU2|RPOA_ACIAC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|120587790|gb|ABM31230.1| DNA-directed RNA polymerase subunit alpha [Acidovorax citrulli
           AAC00-1]
 gi|323372251|gb|ADX44520.1| DNA-directed RNA polymerase subunit alpha [Acidovorax avenae subsp.
           avenae ATCC 19860]
          Length = 330

 Score =  355 bits (911), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 163/335 (48%), Positives = 217/335 (64%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N   L+KP  I    LG    NR  +  EP  RG+ HTLGNA+RRVL+SS+ G A T
Sbjct: 1   MQTN---LLKPKTINVEQLG---HNRAKVALEPFERGYGHTLGNAIRRVLLSSMVGYAAT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE SSI GV ED+ +I+LN+KG+  K+       +++ K G GVVTA DIQT
Sbjct: 55  EVTIAGVLHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGVVTARDIQT 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYS 178
            +D+E++NPDHVI +L     + M++ V KG GYVP    R  ++     G I +DA +S
Sbjct: 115 PHDVEIVNPDHVIAHLSQGGKLDMQIKVEKGRGYVPGNLRRYADESTKSIGRIVLDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--E 236
           P+K+VSYTVESAR  Q  D DKL + I+T+G+IT ED+V  +++IL +QL +F   E  E
Sbjct: 175 PVKRVSYTVESARVEQRTDLDKLVVEIETNGAITAEDAVRASAKILVEQLAVFAQLEGGE 234

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
                       S  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  
Sbjct: 235 LAAFDTPAGPRGSATFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N GRKSL EIK VL + GL LGM L +WPP  +++
Sbjct: 295 NLGRKSLNEIKEVLASRGLTLGMKLENWPPAGLDK 329


>gi|307266986|ref|ZP_07548502.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           wiegelii Rt8.B1]
 gi|326390633|ref|ZP_08212188.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           ethanolicus JW 200]
 gi|306917971|gb|EFN48229.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           wiegelii Rt8.B1]
 gi|325993311|gb|EGD51748.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 315

 Score =  355 bits (911), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 136/311 (43%), Positives = 197/311 (63%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+I+P  IE IV   E+      + EPL RG+  TLGN+LRRVL+SSL GAA  +V+IDG
Sbjct: 3   EMIEP-KIE-IVEQSEDGTYGKFVVEPLERGYGITLGNSLRRVLLSSLPGAAPKSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+ +IILN+K + +K+  D      I   G G VTAG I+   DIE+
Sbjct: 61  VLHEFSTLPGVKEDVVEIILNLKEVAVKLHSDEPVVGRIDVEGKGEVTAGHIKGSADIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPDH I  L  D  + ME+   KG GYVP+  ++  N PIG+I +D++++P+K+VSY V
Sbjct: 121 LNPDHHIATLSDDGKLHMEIVFVKGKGYVPSDKNKEPNQPIGVIPVDSIFTPVKRVSYNV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G V DYDKL++ + T+G+IT ++++++AS +L      FI+F    K     ++ 
Sbjct: 181 ENTRVGHVTDYDKLTLEVWTNGTITPKEAISMASDMLIKYFQKFISFTGEYKSSDIFVDK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                   L   +EEL+LSVRS NCL+   I  + +L Q+TE +M+++ N G+KSL E+K
Sbjct: 241 PEKKVEKPLDMTIEELDLSVRSYNCLKRAGINTVQELTQKTEEEMMKVRNLGKKSLEEVK 300

Query: 308 GVLGTMGLFLG 318
             L  +GL L 
Sbjct: 301 QKLEALGLSLK 311


>gi|212704609|ref|ZP_03312737.1| hypothetical protein DESPIG_02671 [Desulfovibrio piger ATCC 29098]
 gi|212672008|gb|EEB32491.1| hypothetical protein DESPIG_02671 [Desulfovibrio piger ATCC 29098]
          Length = 347

 Score =  355 bits (911), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 150/335 (44%), Positives = 214/335 (63%), Gaps = 1/335 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW EL+KP+ I               + EPL RG+  T+GNA+RRVL++SL+GAA  +V
Sbjct: 13  RNWNELVKPDQI-LRDEDTASSTHGKFVCEPLERGYGTTIGNAMRRVLLASLQGAAFVSV 71

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I GV HE ++I GV ED+TD++LNIK + L+M  D  +R+T+     G VTA  IQ   
Sbjct: 72  KITGVQHEFTTIHGVLEDVTDVVLNIKQVRLRMDTDEPQRLTLRVDSKGPVTAAQIQANQ 131

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            + VLNP+  I  L  D V+ ME  V  G GYVPA  H    D IGLI +D+ +SP++KV
Sbjct: 132 HVTVLNPEQHIATLTEDVVLEMEFEVRMGKGYVPADMHEGLADEIGLIKLDSSFSPVRKV 191

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE AR GQ+ +YD+L + + TDGS+T ED++A +++I++DQ+ +FINF+E       
Sbjct: 192 AYAVEQARVGQMTNYDRLILEVWTDGSLTPEDAIAYSAKIIKDQISVFINFDERVSGDMR 251

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             +  S   N  L K +++LELSVR+TNCLR  NI  +G+L+QR+EA+ML+  NFGRKSL
Sbjct: 252 HGSSDSGETNEHLFKSIDDLELSVRATNCLRSANIALVGELVQRSEAEMLKTKNFGRKSL 311

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
            EIK VL  MGL  GM +  +  +  +   K+  +
Sbjct: 312 DEIKEVLHDMGLDFGMKVDGFEKKYQDWKRKQQNE 346


>gi|254819221|ref|ZP_05224222.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           intracellulare ATCC 13950]
          Length = 347

 Score =  355 bits (911), Expect = 6e-96,   Method: Composition-based stats.
 Identities = 118/306 (38%), Positives = 186/306 (60%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
            +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T
Sbjct: 15  TDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVT 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            IILN+K + +    D    + + K+GPG VTAGDI     + V NPD  I  L+    +
Sbjct: 75  AIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPDLHIATLNDKGKL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL +
Sbjct: 135 EVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLIL 194

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T  SI   D++A A + L +  G+        + ++   +        +    +++L
Sbjct: 195 DVETKSSINPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALPIDDL 254

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  +   
Sbjct: 255 DLTVRSYNCLKREGVHTVGELVSRTESDLLDIRNFGQKSIDEVKVKLHQLGLSLKDSPAS 314

Query: 324 WPPESI 329
           + P  +
Sbjct: 315 FDPSQV 320


>gi|240167783|ref|ZP_04746442.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium kansasii
           ATCC 12478]
          Length = 347

 Score =  355 bits (911), Expect = 6e-96,   Method: Composition-based stats.
 Identities = 121/306 (39%), Positives = 187/306 (61%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
            +NR+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T
Sbjct: 15  TDNRSQFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVT 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           DIILN+K + +    D    + + K+GPG VTAGDI     + V NP   I  L+    +
Sbjct: 75  DIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIATLNDKGKL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL +
Sbjct: 135 EVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLIL 194

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T  SIT  D++A A + L +  G+        + ++   +        +    +++L
Sbjct: 195 DVETKSSITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALPIDDL 254

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  + P 
Sbjct: 255 DLTVRSYNCLKREGVHTVGELVSRTESDLLDIRNFGQKSIDEVKVKLHQLGLSLKDSPPT 314

Query: 324 WPPESI 329
           + P  +
Sbjct: 315 FDPSEV 320


>gi|293602598|ref|ZP_06685041.1| DNA-directed RNA polymerase subunit alpha [Achromobacter piechaudii
           ATCC 43553]
 gi|311109576|ref|YP_003982429.1| DNA-directed RNA polymerase subunit alpha [Achromobacter
           xylosoxidans A8]
 gi|292818970|gb|EFF78008.1| DNA-directed RNA polymerase subunit alpha [Achromobacter piechaudii
           ATCC 43553]
 gi|310764265|gb|ADP19714.1| DNA-directed RNA polymerase, alpha subunit [Achromobacter
           xylosoxidans A8]
 gi|317401574|gb|EFV82203.1| DNA-directed RNA polymerase subunit alpha [Achromobacter
           xylosoxidans C54]
          Length = 328

 Score =  355 bits (911), Expect = 6e-96,   Method: Composition-based stats.
 Identities = 149/330 (45%), Positives = 207/330 (62%), Gaps = 7/330 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            + Q  +KP +IE   +G        ++ EP  RG+ HTLGNALRR+L+SS+ G A T V
Sbjct: 1   MSTQGFLKPRSIEVEPVGTH---HAKIVMEPFERGYGHTLGNALRRILLSSMTGYAPTEV 57

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           Q+ GV+HE S+I GV ED+ DI+LN+KG+  K+       + + K G G V A DI+  +
Sbjct: 58  QMTGVVHEYSTIPGVREDVVDILLNLKGVVFKLHNRDEVTLVLRKTGAGTVLASDIELPH 117

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPI 180
           D+E++NP H ICNL     + M++ V KG GYVP        D    IG I +DA +SP+
Sbjct: 118 DVEIINPGHAICNLTDAGKLEMQIKVEKGRGYVPGNVRALSEDRTHTIGRIVLDASFSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY VESAR  Q  D DKL + I+T+G I+ E++V  ++RIL DQ+ +F   E     
Sbjct: 178 RRVSYAVESARVEQRTDLDKLVLDIETNGVISPEEAVRQSARILMDQISVFAALEGAGDS 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +  +   +   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GR
Sbjct: 238 YEAPV-RGTPQIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           KSL EIK VL   GL LGM L +WPP  +E
Sbjct: 297 KSLNEIKEVLAARGLTLGMKLENWPPLGLE 326


>gi|91205853|ref|YP_538208.1| DNA-directed RNA polymerase subunit alpha [Rickettsia bellii
           RML369-C]
 gi|119366720|sp|Q1RHP5|RPOA_RICBR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|91069397|gb|ABE05119.1| DNA-directed RNA polymerase alpha chain [Rickettsia bellii
           RML369-C]
          Length = 341

 Score =  355 bits (911), Expect = 7e-96,   Method: Composition-based stats.
 Identities = 181/338 (53%), Positives = 248/338 (73%), Gaps = 4/338 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIK + + Y     E  N++ +I EPL RGF  TLGNA+RRVL+SSL+GAA+T
Sbjct: 4   LSKNWNALIKTDKVSYESF-PETNNKSKIIVEPLERGFGLTLGNAMRRVLLSSLQGAAVT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I G+ HE SSI GV ED+++IILN+KGI +KM     + + +   GPG +TAG I+ 
Sbjct: 63  SIKIPGIEHEFSSIPGVKEDISEIILNVKGIEIKMHVAEKRVIRLKATGPGAITAGMIEA 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPI 180
            +D+E+LNPDHVICNL  +    MELT   G GY  + ++  +N+ PIG I IDAL++P+
Sbjct: 123 GHDVEILNPDHVICNLAKNKQFEMELTCKVGKGYTLSTNNNEDNNLPIGEIAIDALFNPV 182

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K V+Y VE+ R GQV DYDKL M ++T+G I  E +V LA+RILQ+QL +FI+FEE +++
Sbjct: 183 KSVTYKVENTRIGQVTDYDKLIMFVETNGDILPEMAVGLAARILQEQLQLFISFEEQEED 242

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +  +   +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTEADMLR  NFGR
Sbjct: 243 KQ--VKTDALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTEADMLRTPNFGR 300

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK +L    L  GM++PDWPPE+I EL+K+YED
Sbjct: 301 KSLNEIKEILAKFSLRFGMDVPDWPPENIHELSKRYED 338


>gi|221126761|ref|XP_002164946.1| PREDICTED: similar to alpha subunit of RNA polymerase [Hydra
           magnipapillata]
 gi|260222202|emb|CBA31529.1| DNA-directed RNA polymerase subunit alpha [Curvibacter putative
           symbiont of Hydra magnipapillata]
          Length = 329

 Score =  355 bits (910), Expect = 7e-96,   Method: Composition-based stats.
 Identities = 162/334 (48%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N   L+KP +I    LG    NR  +  EP  RG+ HTLGNALRRVL+SS+ G A T
Sbjct: 1   MQNN---LLKPKSISVEQLG---PNRAKVALEPFERGYGHTLGNALRRVLLSSMPGFAAT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE SSI GV ED+ +I+LN+KG+  K+       +++ K   GVVTA DIQT
Sbjct: 55  EVTIAGVLHEYSSIDGVQEDVVNILLNLKGVVFKLHNREEVTLSLRKDTEGVVTAADIQT 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYS 178
            +D+E++NP+HVI NL     + M++ V KG GYVP    R  ++P    G I +DA +S
Sbjct: 115 PHDVEIINPEHVIANLSHGGKLDMQIKVEKGRGYVPGSMRRYADEPNKSIGRIVLDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSYTVESAR  Q  D DKL + I+T+G++T ED+V  +++IL +QL +F   E  +
Sbjct: 175 PVRRVSYTVESARVEQRTDLDKLVVEIETNGAVTAEDAVRASAKILVEQLAVFAQLEGSE 234

Query: 239 KEV-KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +         +  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N
Sbjct: 235 LDAFTAPAPRGNTQFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            GRKSL EIK VL + GL LGM L  WPP S+E+
Sbjct: 295 LGRKSLNEIKEVLASRGLTLGMKLESWPPASLEK 328


>gi|289555728|ref|ZP_06444938.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis KZN 605]
 gi|289440360|gb|EFD22853.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis KZN 605]
          Length = 346

 Score =  355 bits (910), Expect = 7e-96,   Method: Composition-based stats.
 Identities = 118/306 (38%), Positives = 188/306 (61%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
            +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T
Sbjct: 14  TDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVT 73

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           +IILN+K + +    D    + + K+GPG VTAGDI     + V NP   I  L+    +
Sbjct: 74  EIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIATLNDKGKL 133

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL +
Sbjct: 134 EVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLIL 193

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T  SI+  D++A A + L +  G+        + ++   +        +    +++L
Sbjct: 194 DVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALPIDDL 253

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  + P 
Sbjct: 254 DLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPPS 313

Query: 324 WPPESI 329
           + P  +
Sbjct: 314 FDPSEV 319


>gi|113869405|ref|YP_727894.1| DNA-directed RNA polymerase subunit alpha [Ralstonia eutropha H16]
 gi|194290997|ref|YP_002006904.1| DNA-directed RNA polymerase subunit alpha [Cupriavidus taiwanensis
           LMG 19424]
 gi|123328832|sp|Q0K645|RPOA_RALEH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238692784|sp|B3R7E3|RPOA_CUPTR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|57506670|dbj|BAD86667.1| RNA polymerase alpha subunit [Cupriavidus necator]
 gi|113528181|emb|CAJ94526.1| DNA-directed RNA polymerase alpha subunit [Ralstonia eutropha H16]
 gi|193224832|emb|CAQ70843.1| RNA polymerase, alpha subunit; RNA polymerase alpha chain family
           [Cupriavidus taiwanensis LMG 19424]
          Length = 326

 Score =  355 bits (910), Expect = 7e-96,   Method: Composition-based stats.
 Identities = 151/326 (46%), Positives = 213/326 (65%), Gaps = 7/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG        ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVEPLGDH---HAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S+I GV ED+ +++LN+KG+  K+       V++ K G GVVTA DI+  +D+E++
Sbjct: 62  VHEYSTIDGVQEDVVNLLLNLKGVVFKLHNRDEVTVSLRKDGEGVVTAADIELPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKVSY 185
           NP+HVI +L     + M++ V +G GYVP    +  ++    IG I +DA +SP+++VSY
Sbjct: 122 NPNHVIAHLSAGGKLDMQIKVEQGRGYVPGNVRKFGDESGKVIGRIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+TDG I+ E+++  ++RIL DQL +F   E   +   E  
Sbjct: 182 AVESARVEQRTDLDKLVMNIETDGVISPEEAIRQSARILVDQLSVFAALEG-TESAAEAA 240

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           + ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 241 SSRTPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 300

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +E+
Sbjct: 301 IKEVLASRGLTLGMKLENWPPAGLEK 326


>gi|118579145|ref|YP_900395.1| DNA-directed RNA polymerase subunit alpha [Pelobacter propionicus
           DSM 2379]
 gi|158512561|sp|A1ALW7|RPOA_PELPD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|118501855|gb|ABK98337.1| DNA-directed RNA polymerase subunit alpha [Pelobacter propionicus
           DSM 2379]
          Length = 340

 Score =  355 bits (910), Expect = 7e-96,   Method: Composition-based stats.
 Identities = 154/340 (45%), Positives = 228/340 (67%), Gaps = 3/340 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW++LI+P  +++       +      AEP  RGFA TLGN+LRR+L+SSL+G+AIT
Sbjct: 1   MYKNWRDLIRPKQLQFEK-ESLSDTYGKFFAEPFERGFATTLGNSLRRILLSSLQGSAIT 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+I GVLHE S+I+GV ED+TDIILN+KG+ LK+       + +   G GVV AGD   
Sbjct: 60  SVRIKGVLHEFSAIQGVTEDVTDIILNLKGVRLKLHSVVQATIRVVHTGEGVVKAGDFVV 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +++E++NP+H I     DA   M++TV  G GYV A  +R E  P+G I ID+++SPIK
Sbjct: 120 GHNVEIMNPEHHIATCGKDAHFEMDMTVKMGKGYVSADKNRDEKAPVGTIPIDSIFSPIK 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KV++T+ +AR GQ+ DYDKL++ I TDGS+  +D++A +++I+++QL +FINF+E  +  
Sbjct: 180 KVNFTISNARVGQMTDYDKLTLEIWTDGSVKPDDALAYSAKIMKEQLSIFINFDEEAEPQ 239

Query: 242 KEDINVKSLPF-NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             + +   +   N  L + VEELELSVRS NCL+   I  +G+L+ +TEA+ML+  NFGR
Sbjct: 240 APEESQDEIDKINENLYRTVEELELSVRSANCLKNAGIKLIGELVSKTEAEMLKTQNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP-PESIEELAKKYEDK 339
           KSL EIK +L  MGL  GM L  +P P+ +  L  +  ++
Sbjct: 300 KSLNEIKDILSDMGLTFGMKLDSFPEPDMLRRLRGEQNEE 339


>gi|15610593|ref|NP_217974.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis H37Rv]
 gi|15843052|ref|NP_338089.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis CDC1551]
 gi|31794633|ref|NP_857126.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium bovis
           AF2122/97]
 gi|121639377|ref|YP_979601.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium bovis BCG
           str. Pasteur 1173P2]
 gi|148663322|ref|YP_001284845.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis H37Ra]
 gi|148824667|ref|YP_001289421.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis F11]
 gi|215405496|ref|ZP_03417677.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis 02_1987]
 gi|215413370|ref|ZP_03422055.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis 94_M4241A]
 gi|215428964|ref|ZP_03426883.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis T92]
 gi|215432428|ref|ZP_03430347.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis EAS054]
 gi|215447794|ref|ZP_03434546.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis T85]
 gi|224991873|ref|YP_002646562.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium bovis BCG
           str. Tokyo 172]
 gi|253800502|ref|YP_003033503.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis KZN 1435]
 gi|254234049|ref|ZP_04927374.1| DNA-directed RNA polymerase (alpha chain) rpoA [Mycobacterium
           tuberculosis C]
 gi|260188512|ref|ZP_05765986.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis CPHL_A]
 gi|289449161|ref|ZP_06438905.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis CPHL_A]
 gi|289747290|ref|ZP_06506668.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis 02_1987]
 gi|289752181|ref|ZP_06511559.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis T92]
 gi|289755590|ref|ZP_06514968.1| RNA polymerase subunit alpha [Mycobacterium tuberculosis EAS054]
 gi|289759620|ref|ZP_06518998.1| RNA polymerase subunit alpha [Mycobacterium tuberculosis T85]
 gi|294993005|ref|ZP_06798696.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis 210]
 gi|297636116|ref|ZP_06953896.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis KZN 4207]
 gi|297733116|ref|ZP_06962234.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis KZN R506]
 gi|298526941|ref|ZP_07014350.1| DNA-directed RNA polymerase (alpha chain) rpoA [Mycobacterium
           tuberculosis 94_M4241A]
 gi|306777804|ref|ZP_07416141.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu001]
 gi|306782523|ref|ZP_07420860.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu002]
 gi|306786342|ref|ZP_07424664.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu003]
 gi|306790711|ref|ZP_07429033.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu004]
 gi|306795239|ref|ZP_07433541.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu005]
 gi|306799429|ref|ZP_07437731.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu006]
 gi|306805275|ref|ZP_07441943.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu008]
 gi|306809461|ref|ZP_07446129.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu007]
 gi|306969569|ref|ZP_07482230.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu009]
 gi|306973923|ref|ZP_07486584.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu010]
 gi|307081632|ref|ZP_07490802.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu011]
 gi|307086238|ref|ZP_07495351.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu012]
 gi|313660447|ref|ZP_07817327.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis KZN V2475]
 gi|54039274|sp|P66702|RPOA_MYCBO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|54042185|sp|P66701|RPOA_MYCTU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158512956|sp|A1KPE3|RPOA_MYCBP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172047915|sp|A5U8D3|RPOA_MYCTA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|2104380|emb|CAB08723.1| PROBABLE DNA-DIRECTED RNA POLYMERASE (ALPHA CHAIN) RPOA
           (TRANSCRIPTASE ALPHA CHAIN) (RNA POLYMERASE ALPHA
           SUBUNIT) (DNA-DIRECTED RNA NUCLEOTIDYLTRANSFERASE)
           [Mycobacterium tuberculosis H37Rv]
 gi|13883396|gb|AAK47903.1| DNA-directed RNA polymerase, alpha subunit [Mycobacterium
           tuberculosis CDC1551]
 gi|31620230|emb|CAD95673.1| PROBABLE DNA-DIRECTED RNA POLYMERASE (ALPHA CHAIN) RPOA
           (TRANSCRIPTASE ALPHA CHAIN) (RNA POLYMERASE ALPHA
           SUBUNIT) (DNA-DIRECTED RNA NUCLEOTIDYLTRANSFERASE)
           [Mycobacterium bovis AF2122/97]
 gi|121495025|emb|CAL73511.1| Probable DNA-directed RNA polymerase (alpha chain) rpoA
           [Mycobacterium bovis BCG str. Pasteur 1173P2]
 gi|124599578|gb|EAY58682.1| DNA-directed RNA polymerase (alpha chain) rpoA [Mycobacterium
           tuberculosis C]
 gi|148507474|gb|ABQ75283.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis H37Ra]
 gi|148723194|gb|ABR07819.1| DNA-directed RNA polymerase alpha subunit rpoA [Mycobacterium
           tuberculosis F11]
 gi|224774988|dbj|BAH27794.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium bovis BCG
           str. Tokyo 172]
 gi|253322005|gb|ACT26608.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis KZN 1435]
 gi|289422119|gb|EFD19320.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis CPHL_A]
 gi|289687818|gb|EFD55306.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis 02_1987]
 gi|289692768|gb|EFD60197.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis T92]
 gi|289696177|gb|EFD63606.1| RNA polymerase subunit alpha [Mycobacterium tuberculosis EAS054]
 gi|289715184|gb|EFD79196.1| RNA polymerase subunit alpha [Mycobacterium tuberculosis T85]
 gi|298496735|gb|EFI32029.1| DNA-directed RNA polymerase (alpha chain) rpoA [Mycobacterium
           tuberculosis 94_M4241A]
 gi|308213889|gb|EFO73288.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu001]
 gi|308324840|gb|EFP13691.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu002]
 gi|308329094|gb|EFP17945.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu003]
 gi|308332902|gb|EFP21753.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu004]
 gi|308336562|gb|EFP25413.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu005]
 gi|308340437|gb|EFP29288.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu006]
 gi|308344301|gb|EFP33152.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu007]
 gi|308348192|gb|EFP37043.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu008]
 gi|308352916|gb|EFP41767.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu009]
 gi|308356759|gb|EFP45610.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu010]
 gi|308360704|gb|EFP49555.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu011]
 gi|308364319|gb|EFP53170.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis SUMu012]
 gi|323717941|gb|EGB27130.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis CDC1551A]
 gi|328460233|gb|AEB05656.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis KZN 4207]
          Length = 347

 Score =  355 bits (910), Expect = 7e-96,   Method: Composition-based stats.
 Identities = 118/306 (38%), Positives = 188/306 (61%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
            +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T
Sbjct: 15  TDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVT 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           +IILN+K + +    D    + + K+GPG VTAGDI     + V NP   I  L+    +
Sbjct: 75  EIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIATLNDKGKL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL +
Sbjct: 135 EVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLIL 194

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T  SI+  D++A A + L +  G+        + ++   +        +    +++L
Sbjct: 195 DVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALPIDDL 254

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  + P 
Sbjct: 255 DLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPPS 314

Query: 324 WPPESI 329
           + P  +
Sbjct: 315 FDPSEV 320


>gi|262203540|ref|YP_003274748.1| DNA-directed RNA polymerase subunit alpha [Gordonia bronchialis DSM
           43247]
 gi|262086887|gb|ACY22855.1| DNA-directed RNA polymerase, alpha subunit [Gordonia bronchialis
           DSM 43247]
          Length = 350

 Score =  355 bits (910), Expect = 8e-96,   Method: Composition-based stats.
 Identities = 123/319 (38%), Positives = 192/319 (60%), Gaps = 4/319 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E I+     +NR+  + EPL  GF +TLGN+LRR L+SS+ GAAIT+++IDGVLH
Sbjct: 6   RPTLTEEIL----ADNRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAITSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TDIILN+KG+ +    D    + + K+GPG VT  DI     + V NP
Sbjct: 62  EFTTVPGVKEDVTDIILNLKGLVVSSEEDEPVTMYVRKQGPGTVTGADIVPPAGVTVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLHIATLNDKGKLEIELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  SI+  D++A A + L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDRLVLDVETKNSISARDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
               +    +E+LEL+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L
Sbjct: 242 DHIASFSLPIEDLELTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKVKL 301

Query: 311 GTMGLFLGMNLPDWPPESI 329
             +GL L  +   + P  +
Sbjct: 302 HALGLSLKDSPASFDPSQV 320


>gi|283853179|ref|ZP_06370432.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio sp.
           FW1012B]
 gi|283571437|gb|EFC19444.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio sp.
           FW1012B]
          Length = 347

 Score =  355 bits (910), Expect = 8e-96,   Method: Composition-based stats.
 Identities = 155/337 (45%), Positives = 224/337 (66%), Gaps = 2/337 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW EL+KP  +E        +     + EPL RGF  TLGNALRRVL+SSL+GAAI A 
Sbjct: 13  RNWTELVKPEKLEKDP--GATDTFGRFVCEPLERGFGTTLGNALRRVLLSSLQGAAIVAA 70

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+GV HE S+I GV ED+T+IILN+K + L M+ +  +R+T+F    G V A  IQ   
Sbjct: 71  RIEGVQHEFSTIPGVIEDVTEIILNLKQVRLAMTTEDPQRLTLFANQKGEVLASAIQGNQ 130

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           ++ VL+ D +I  L  D   R++L V  G GYVPA  H   +  IGLI +D+ +SP+KKV
Sbjct: 131 NVTVLSDDVLIATLSEDRDFRIDLEVRMGKGYVPADMHEGLDSEIGLILLDSSFSPVKKV 190

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +YT+E AR GQ+ +YDKL + + TDGSI+ +D+++ +++IL+DQL +FINF+E + E  +
Sbjct: 191 AYTIEQARVGQMTNYDKLVLEVGTDGSISPDDAISYSAKILKDQLTVFINFDEKESEADK 250

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                 +  NP+L K ++ELELSVR+TNCL+  NI  +G+L+Q+TE +ML+  NFG+KSL
Sbjct: 251 ARRRDDIELNPSLFKSIDELELSVRATNCLKSANIQTVGELMQKTENEMLKTKNFGKKSL 310

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
            EI+ VL  MGL  GM + ++  +  E L +K  D+ 
Sbjct: 311 EEIRRVLEDMGLEFGMRIENFEQKYQEWLKRKQVDET 347


>gi|90962380|ref|YP_536296.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus salivarius
           UCC118]
 gi|227891570|ref|ZP_04009375.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus salivarius
           ATCC 11741]
 gi|119366692|sp|Q1WSB6|RPOA_LACS1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|90821574|gb|ABE00213.1| DNA-directed RNA polymerase alpha chain [Lactobacillus salivarius
           UCC118]
 gi|227866717|gb|EEJ74138.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus salivarius
           ATCC 11741]
 gi|300215021|gb|ADJ79437.1| DNA-directed RNA polymerase subunit alpha (RNAP subunit alpha)
           (Transcriptase subunit alpha) (RNA polymerase subunit
           alpha) [Lactobacillus salivarius CECT 5713]
          Length = 314

 Score =  355 bits (910), Expect = 8e-96,   Method: Composition-based stats.
 Identities = 136/312 (43%), Positives = 202/312 (64%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I   +E+ N    + EPL RG+  TLGN+LRR+L+SSL GAAIT VQIDG
Sbjct: 3   EFEKPK----IHKIEEDNNYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAITDVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILN+K + L M  +  + + I   GP  VTAGDIQ+ +D+EV
Sbjct: 59  VLHEFSTIPGVLEDVTLIILNLKKVALSMESEDSQALEINVTGPMEVTAGDIQSNSDVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
           LNP+  IC +   A + + +  +KG GYV A  ++   ++ PIG++ ID++Y+PI++V+Y
Sbjct: 119 LNPEQYICTVADGAELHVRMNANKGRGYVSANDNKALADDMPIGVLPIDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE  R GQ  DYDKL++ + T+GSIT  ++++L+++IL + L +F++  +  K  +  +
Sbjct: 179 QVEKTRVGQKNDYDKLTLDVWTNGSITPSEAISLSAKILTEHLALFVDLTDEAKNAEIMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+++ N GRKSL E
Sbjct: 239 EKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTNKSEADMMKVRNLGRKSLDE 298

Query: 306 IKGVLGTMGLFL 317
           +K  L  +GL L
Sbjct: 299 VKAKLADLGLSL 310


>gi|157826787|ref|YP_001495851.1| DNA-directed RNA polymerase subunit alpha [Rickettsia bellii OSU
           85-389]
 gi|166229277|sp|A8GVD7|RPOA_RICB8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|157802091|gb|ABV78814.1| DNA-directed RNA polymerase subunit alpha [Rickettsia bellii OSU
           85-389]
          Length = 341

 Score =  355 bits (910), Expect = 8e-96,   Method: Composition-based stats.
 Identities = 181/338 (53%), Positives = 248/338 (73%), Gaps = 4/338 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIK + + Y     E  N++ +I EPL RGF  TLGNA+RRVL+SSL+GAA+T
Sbjct: 4   LSKNWNALIKTDKVSYESF-HETNNKSKIIVEPLERGFGLTLGNAMRRVLLSSLQGAAVT 62

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I G+ HE SSI GV ED+++IILN+KGI +KM     + + +   GPG +TAG I+ 
Sbjct: 63  SIKIPGIEHEFSSIPGVKEDISEIILNVKGIEIKMHVAEKRVIRLKATGPGAITAGMIEA 122

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPI 180
            +D+E+LNPDHVICNL  +    MELT   G GY  + ++  +N+ PIG I IDAL++P+
Sbjct: 123 GHDVEILNPDHVICNLAKNKQFEMELTCKVGKGYTLSTNNNEDNNLPIGEIAIDALFNPV 182

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K V+Y VE+ R GQV DYDKL M ++T+G I  E +V LA+RILQ+QL +FI+FEE +++
Sbjct: 183 KSVTYKVENTRIGQVTDYDKLIMFVETNGDILPEMAVGLAARILQEQLQLFISFEEQEED 242

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +  +   +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTEADMLR  NFGR
Sbjct: 243 KQ--VKTDALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTEADMLRTPNFGR 300

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK +L    L  GM++PDWPPE+I EL+K+YED
Sbjct: 301 KSLNEIKEILAKFSLRFGMDVPDWPPENIHELSKRYED 338


>gi|108798085|ref|YP_638282.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium sp. MCS]
 gi|119867181|ref|YP_937133.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium sp. KMS]
 gi|126433745|ref|YP_001069436.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium sp. JLS]
 gi|119366700|sp|Q1BD08|RPOA_MYCSS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158513059|sp|A1UBY5|RPOA_MYCSK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158513450|sp|A3PVL8|RPOA_MYCSJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|108768504|gb|ABG07226.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium sp. MCS]
 gi|119693270|gb|ABL90343.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium sp. KMS]
 gi|126233545|gb|ABN96945.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium sp. JLS]
          Length = 350

 Score =  355 bits (910), Expect = 8e-96,   Method: Composition-based stats.
 Identities = 119/310 (38%), Positives = 188/310 (60%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
                +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV 
Sbjct: 11  EETVADNRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVK 70

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+TDIILN+K + +    D    + + K+GPG VTAGDI     + V NP+  I  L+ 
Sbjct: 71  EDVTDIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPEMHIATLND 130

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D
Sbjct: 131 KGKLEVELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFD 190

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + ++T  SIT  D++A A + L +  G+        + ++   +        +    
Sbjct: 191 KLILDVETKNSITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  
Sbjct: 251 IDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKD 310

Query: 320 NLPDWPPESI 329
           +   + P  +
Sbjct: 311 SPATFDPSEV 320


>gi|256005300|ref|ZP_05430266.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           thermocellum DSM 2360]
 gi|281419375|ref|ZP_06250390.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           thermocellum JW20]
 gi|255990736|gb|EEU00852.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           thermocellum DSM 2360]
 gi|281406995|gb|EFB37258.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           thermocellum JW20]
 gi|316939529|gb|ADU73563.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           thermocellum DSM 1313]
          Length = 315

 Score =  355 bits (910), Expect = 8e-96,   Method: Composition-based stats.
 Identities = 138/311 (44%), Positives = 203/311 (65%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE  V+  E+      + EPL RG+  TLGN+LRR+L+SSL G A+T+++IDG
Sbjct: 3   EIEKP-KIE-CVVCSEDNRYGKFVVEPLERGYGITLGNSLRRILLSSLPGVAVTSIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T+IILNIK ++L   G+  K + I   G G V A DI+   D+E+
Sbjct: 61  VLHEFSTIPGVIEDVTEIILNIKELSLNFHGEGPKVIYIDAEGEGEVKAKDIKADADVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+H I  L  D  + ME+T+ KG GYV A+ ++    PIG+I +D++++P+ KV+YTV
Sbjct: 121 LNPEHKIATLSGDHRLYMEMTIDKGRGYVSAEKNKHPGQPIGVIPVDSIFTPVHKVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV DYDKL++ + T+GSI  +++++L ++IL + L +FI+  +  K  +  +  
Sbjct: 181 ENTRVGQVTDYDKLTLEVWTNGSIKPDEAISLGAKILSEHLNLFIDLSDNAKNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + DLI RTE DM+++ N GRKSL E+ 
Sbjct: 241 EETKKEKVLEMTIEELDLSVRSYNCLKRAGINTVEDLISRTEEDMMKVRNLGRKSLEEVV 300

Query: 308 GVLGTMGLFLG 318
             L  +GL L 
Sbjct: 301 NKLKALGLSLA 311


>gi|322418391|ref|YP_004197614.1| DNA-directed RNA polymerase subunit alpha [Geobacter sp. M18]
 gi|320124778|gb|ADW12338.1| DNA-directed RNA polymerase, alpha subunit [Geobacter sp. M18]
          Length = 339

 Score =  354 bits (909), Expect = 9e-96,   Method: Composition-based stats.
 Identities = 162/340 (47%), Positives = 227/340 (66%), Gaps = 3/340 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +NW++LI+P  ++               AEP  RGF  TLG  LRRVL+SSL+GAAI 
Sbjct: 1   MYRNWRDLIRPKKLQVET-ESLTNTYGKFYAEPFERGFGTTLGTGLRRVLISSLQGAAIV 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+  GVLHE S++ GV ED+TDIILN+KG+ LK+ G+  + + I ++G GVV A DI T
Sbjct: 60  SVKAKGVLHEFSAVPGVTEDMTDIILNLKGVRLKVHGNESRMIRIVQKGEGVVKAKDIVT 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            N++E+LNP+H I     DA + M+L V  G GYVPA  +R E  P+G I IDA++SP+ 
Sbjct: 120 DNNVEILNPEHHIATCSKDANLEMDLMVKVGKGYVPADRNRDEKAPVGTIPIDAIFSPVH 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KV++TV +AR GQ+ DYDKL++ + TDGS+  +D+VA AS+IL+DQL +FINF+E  +  
Sbjct: 180 KVNFTVTNARVGQITDYDKLTIEVWTDGSVKPQDAVAYASKILKDQLSIFINFDEDVEPQ 239

Query: 242 KEDINVKSLPFNPALLK-KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           +E    +        L   V+ELELSVRS NCL+   I  +G+L+ RTEA+ML+  NFGR
Sbjct: 240 EEAEPEEERERFNENLYRSVDELELSVRSANCLKNAGIKLIGELVSRTEAEMLKTQNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP-PESIEELAKKYEDK 339
           KSL EIK +L  MGL LGM L ++P PE +  L  + +++
Sbjct: 300 KSLNEIKDILVDMGLTLGMKLENFPDPEIMRRLRGEQKEE 339


>gi|239905884|ref|YP_002952623.1| DNA-directed RNA polymerase alpha subunit [Desulfovibrio magneticus
           RS-1]
 gi|259494168|sp|C4XLK3|RPOA_DESMR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|239795748|dbj|BAH74737.1| DNA-directed RNA polymerase alpha subunit [Desulfovibrio magneticus
           RS-1]
          Length = 347

 Score =  354 bits (909), Expect = 9e-96,   Method: Composition-based stats.
 Identities = 156/337 (46%), Positives = 224/337 (66%), Gaps = 2/337 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW EL+KP  ++        E     + EPL RGF  TLGNALRRVL+SSL+GAAI A 
Sbjct: 13  RNWTELVKPEVLDKDP--SSTETFGRFVCEPLERGFGTTLGNALRRVLLSSLQGAAIVAA 70

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+GV HE S+I GV ED+T+IILN+K + L M+ D  +R+T+  +  G V A  IQ  +
Sbjct: 71  RIEGVQHEFSTIPGVIEDVTEIILNLKQVRLAMATDEPQRLTLLAKEKGEVRASAIQGNH 130

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           ++ VL+ D +I  L  D   R++L V  G GYVPA  H      IGLI +DA +SP+KKV
Sbjct: 131 NVSVLSEDVLIATLSEDRDFRIDLEVRMGKGYVPADMHEGLESEIGLILLDASFSPVKKV 190

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +YT+E AR GQ+ +YDKL + + TDGSI  ED+++ +++IL+DQL +FINF+E + E ++
Sbjct: 191 AYTIEQARVGQMTNYDKLVLEVTTDGSIAPEDAISYSAKILKDQLTVFINFDEKESEAEK 250

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +     +  NP+L K ++ELELSVR+TNCL+  NI  +G+L+Q+TE +ML+  NFG+KS 
Sbjct: 251 NRRRDDIELNPSLFKSIDELELSVRATNCLKSANIQTVGELMQKTEHEMLKTKNFGKKSF 310

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
            EI+ VL  MGL  GM + ++  +  E L +K  D+ 
Sbjct: 311 EEIRRVLEDMGLEFGMRIENFDQKYQEWLKRKQTDEA 347


>gi|121592838|ref|YP_984734.1| DNA-directed RNA polymerase subunit alpha [Acidovorax sp. JS42]
 gi|222109618|ref|YP_002551882.1| DNA-directed RNA polymerase subunit alpha [Acidovorax ebreus TPSY]
 gi|158513895|sp|A1W333|RPOA_ACISJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|254765252|sp|B9MBW2|RPOA_ACIET RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|120604918|gb|ABM40658.1| DNA-directed RNA polymerase subunit alpha [Acidovorax sp. JS42]
 gi|221729062|gb|ACM31882.1| DNA-directed RNA polymerase, alpha subunit [Acidovorax ebreus TPSY]
          Length = 330

 Score =  354 bits (909), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 162/335 (48%), Positives = 218/335 (65%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N   L+KP  I    LG    NR  +  EP  RG+ HTLGNA+RRVL+SS+ G A T
Sbjct: 1   MQTN---LLKPKAINVEQLG---PNRAKVALEPFERGYGHTLGNAIRRVLLSSMVGYAAT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE SSI GV ED+ +I+LN+KG+  K+       +++ K G GVVTA DIQT
Sbjct: 55  EVTIAGVLHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGVVTARDIQT 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NP+HVI  L     + M++ V KG GYVP    R  ++    IG I +DA +S
Sbjct: 115 PHDVEIVNPEHVIATLSAGGKLDMQIKVEKGRGYVPGNLRRYADEATKSIGRIVLDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--E 236
           P+K+VSYTVESAR  Q  D DKL + I+T+G+IT ED+V  +++IL +QL +F   E  E
Sbjct: 175 PVKRVSYTVESARVEQRTDLDKLVVEIETNGAITAEDAVRASAKILVEQLAVFAQLEGGE 234

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
                    +  +  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  
Sbjct: 235 LAAFDAPASSRGAATFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N GRKSL EIK VL + GL LGM L +WPP  +++
Sbjct: 295 NLGRKSLNEIKEVLASRGLTLGMKLENWPPAGLDK 329


>gi|153952889|ref|YP_001393654.1| DNA-directed RNA polymerase subunit alpha [Clostridium kluyveri DSM
           555]
 gi|219853554|ref|YP_002470676.1| hypothetical protein CKR_0211 [Clostridium kluyveri NBRC 12016]
 gi|189043836|sp|A5N4S5|RPOA_CLOK5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|254765249|sp|B9DYD7|RPOA_CLOK1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|146345770|gb|EDK32306.1| RpoA [Clostridium kluyveri DSM 555]
 gi|219567278|dbj|BAH05262.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 315

 Score =  354 bits (909), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 135/313 (43%), Positives = 209/313 (66%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE +    E+ N    + EPL RG+  TLGNALRR+L+SSL G A + V+IDG
Sbjct: 3   EIEKP-KIECVETS-EDGNYGKFVVEPLERGYGTTLGNALRRILLSSLPGVAASHVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED++++ILNIK + LKM+GD  K + I  +GPG V AGDI+T  D+E+
Sbjct: 61  VLHEFSTVRGVKEDVSELILNIKELALKMNGDGTKTIYIDAQGPGEVVAGDIKTDGDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N +  I  LD ++ + ME+TV+ G GYV  + ++ E+ PIG I +D++Y+PIK+V++ V
Sbjct: 121 INGELHIATLDENSRLYMEITVNGGRGYVSQRRNKFEDMPIGTIPVDSIYTPIKRVNFNV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ DYDKLS+ + T+G+I  +++V+L+++IL +   +F+   +    V+  +  
Sbjct: 181 ENTRVGQITDYDKLSLEVWTNGTILPDEAVSLSAKILIEHFKLFMTLTDHANNVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L +RT  DM+++ N G+KSL E++
Sbjct: 241 EEDKKEKVLEMAIEELDLSVRSYNCLKRAGINTVQELTERTMDDMMKVRNLGKKSLEEVE 300

Query: 308 GVLGTMGLFLGMN 320
             L T+GL L  N
Sbjct: 301 QKLDTLGLSLKQN 313


>gi|300362364|ref|ZP_07058540.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus gasseri
           JV-V03]
 gi|300353355|gb|EFJ69227.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus gasseri
           JV-V03]
          Length = 312

 Score =  354 bits (909), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 141/313 (45%), Positives = 201/313 (64%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +EE     + EPL RGF  TLGN+LRRVL++S+ G A++ +QIDG
Sbjct: 3   EFEKPN----ITVVDQEEAYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTALSYIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILN+K + LK   D  K   I   GP +VTA D++  +DIEV
Sbjct: 59  VLHEFSTIPGVREDVTKIILNLKKLELKSLSDEEKIAEIDVTGPAIVTAADLKVDSDIEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC++     + M + +  G GYVPA  ++T++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICSIADGGHLHMNVAIKNGRGYVPASENKTDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ESAR G+  DYDKL++ I TDGSIT  D+++ A++IL +   +F++ +   +     +  
Sbjct: 179 ESARVGKRDDYDKLTLEIWTDGSITPNDALSFAAKILVEHFKVFMSTDMDAQFDDVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+R+ N GRKSL E+K
Sbjct: 239 EDDKNEKKLEMTIEELDLSVRSYNCLKRAGINTVQELTDKSEADMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 NKLAELGLSLRQD 311


>gi|301300224|ref|ZP_07206436.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus
           salivarius ACS-116-V-Col5a]
 gi|300852165|gb|EFK79837.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus
           salivarius ACS-116-V-Col5a]
          Length = 314

 Score =  354 bits (909), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 135/312 (43%), Positives = 202/312 (64%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I   +E+ N    + EPL RG+  TLGN+LRR+L+SSL GAAIT VQIDG
Sbjct: 3   EFEKPK----IHKIEEDNNYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAITDVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILN+K + L +  +  + + I   GP  VTAGDIQ+ +D+EV
Sbjct: 59  VLHEFSTIPGVLEDVTLIILNLKKVALSIESEDSQALEINVTGPMEVTAGDIQSNSDVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
           LNP+  IC +   A + + +  +KG GYV A  ++   ++ PIG++ ID++Y+PI++V+Y
Sbjct: 119 LNPEQYICTVADGAELHVRMNANKGRGYVSANDNKALADDMPIGVLPIDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE  R GQ  DYDKL++ + T+GSIT  ++++L+++IL + L +F++  +  K  +  +
Sbjct: 179 QVEKTRVGQKNDYDKLTLDVWTNGSITPSEAISLSAKILTEHLALFVDLTDEAKNAEIMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+++ N GRKSL E
Sbjct: 239 EKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTNKSEADMMKVRNLGRKSLDE 298

Query: 306 IKGVLGTMGLFL 317
           +K  L  +GL L
Sbjct: 299 VKAKLADLGLSL 310


>gi|329893624|ref|ZP_08269758.1| DNA-directed RNA polymerase alpha subunit [gamma proteobacterium
           IMCC3088]
 gi|328923551|gb|EGG30863.1| DNA-directed RNA polymerase alpha subunit [gamma proteobacterium
           IMCC3088]
          Length = 334

 Score =  354 bits (909), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 156/336 (46%), Positives = 224/336 (66%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    E + P     I + ++   R L+  EPL RGF HTLGNALRR+L+SS+ G AIT
Sbjct: 1   MQSAVNEFLTPR---VITVDEKSNTRALVTLEPLERGFGHTLGNALRRILLSSMPGCAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            VQIDGVLHE S+I+GV ED+ +I+LN+K + + ++G     +T+ K+ PG VTAGDI  
Sbjct: 58  EVQIDGVLHEYSTIEGVQEDVIEILLNLKDVAVVLNGKDEAELTLSKKEPGPVTAGDITL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYS 178
            +D+E+ NPDHVICN+   + V ++L VS+G GY PA     E D     G + +DA +S
Sbjct: 118 DHDVEICNPDHVICNVTGGSGVNLKLVVSRGRGYSPADSRGNEEDETRAIGRLQLDATFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI++V+Y VESAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++ E   
Sbjct: 178 PIRRVAYVVESARVEQRTDLDKLVLDLETNGTIDPEEAIRRAATILQQQLAVFVDLE--- 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E + +  V+    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N 
Sbjct: 235 SEGEAEAVVEEDEVDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S++   +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKNDDR 330


>gi|296141062|ref|YP_003648305.1| DNA-directed RNA polymerase subunit alpha [Tsukamurella
           paurometabola DSM 20162]
 gi|296029196|gb|ADG79966.1| DNA-directed RNA polymerase, alpha subunit [Tsukamurella
           paurometabola DSM 20162]
          Length = 352

 Score =  354 bits (908), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 122/320 (38%), Positives = 194/320 (60%), Gaps = 4/320 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E ++     + R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLSEEVI----SDARSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TDIILN+KG+ +    D    + + K+GPG VTAGDI     + V NP
Sbjct: 62  EFTTVPGVKEDVTDIILNLKGLVVSSEDDEPVTMYVRKQGPGAVTAGDIVPPASVTVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLHIATLNDKGKLEIELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  S+T  D++A A + L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDRLILDVETKNSMTARDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
               A    +E+L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L
Sbjct: 242 DHIAAFSLPIEDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKVKL 301

Query: 311 GTMGLFLGMNLPDWPPESIE 330
             +GL L  +   + P  ++
Sbjct: 302 HALGLALKDSPASFDPSQVD 321


>gi|257876158|ref|ZP_05655811.1| DNA directed RNA polymerase [Enterococcus casseliflavus EC20]
 gi|257810324|gb|EEV39144.1| DNA directed RNA polymerase [Enterococcus casseliflavus EC20]
          Length = 312

 Score =  354 bits (908), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 137/313 (43%), Positives = 200/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E+++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDG
Sbjct: 3   EFEKPR----IAKIDEDKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++KGV ED+  IILNIKG+ LKM GD  K + I   GP  VTAGDI   +D+E+
Sbjct: 59  VLHEFSTVKGVREDVAQIILNIKGLALKMYGDEEKTLEIDISGPATVTAGDIIVDSDVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D  IC +   A     LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y V
Sbjct: 119 LNKDMYICTVSEGATFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G+  D+DKL+M I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  
Sbjct: 179 ENTRVGRRDDFDKLTMEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E+K
Sbjct: 239 EETQKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTNKSEPEMIKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLHDLGLGLRKD 311


>gi|149926592|ref|ZP_01914852.1| DNA-directed RNA polymerase subunit alpha [Limnobacter sp. MED105]
 gi|149824521|gb|EDM83737.1| DNA-directed RNA polymerase subunit alpha [Limnobacter sp. MED105]
          Length = 326

 Score =  354 bits (908), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 152/327 (46%), Positives = 216/327 (66%), Gaps = 9/327 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
            L+KP  +E   +     N   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I G
Sbjct: 5   SLLKPRIVEVETV---APNSAKVVMEPFERGYGHTLGNALRRVLLSSMIGYAPTEVSIAG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE S++ GV ED+ D++LN+KGI  K+       VT+ +   GVVTAGDI+  +D+E+
Sbjct: 62  VVHEYSTLDGVQEDVVDLLLNLKGIVFKLESRDVVTVTLKREVEGVVTAGDIELPHDVEI 121

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVS 184
           +NPDHVI +L     + M++ V KG GYVP    R  ++P    G I +DA +SP+K+VS
Sbjct: 122 INPDHVIAHLSQGGKLDMQIKVEKGRGYVPGSVRRFPDEPSKAIGRIVLDASFSPVKRVS 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VESAR  Q  D D+L M+I+T+G ++ E+S+ LA+RIL +QL +F   E      + +
Sbjct: 182 YAVESARVEQRTDLDRLVMSIETNGVLSPEESIRLAARILVEQLSVFAALEN---TAEPE 238

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           ++ ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL 
Sbjct: 239 VSQRAPQVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLN 298

Query: 305 EIKGVLGTMGLFLGMNLPDWPPESIEE 331
           EIK VL   GL LGM L +WPP  +++
Sbjct: 299 EIKEVLAARGLTLGMKLENWPPAGLDK 325


>gi|116334243|ref|YP_795770.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus brevis
           ATCC 367]
 gi|122269075|sp|Q03PY3|RPOA_LACBA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116099590|gb|ABJ64739.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Lactobacillus brevis ATCC 367]
          Length = 316

 Score =  354 bits (908), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 140/314 (44%), Positives = 203/314 (64%), Gaps = 8/314 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E  N    I EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EFEKPN----IHKIDESNNYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE S+++GV ED+T IILN+K I LK++G  D  + + I  +GP  +TAGDI    D+
Sbjct: 59  VLHEFSTVEGVVEDVTQIILNVKKIALKLNGSDDQEETMEINVKGPAQITAGDIVAGADV 118

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKV 183
           ++LNPD  I  +   A   M +T  KG GYV A  ++T   + PIG++ +D++Y+PI++V
Sbjct: 119 DILNPDLYIATVADGATFHMRMTADKGRGYVSADENKTRNTDMPIGVLAVDSIYTPIERV 178

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR GQ  DYDKL++ + T+GSI   +++ALA++IL + L MF++  +  K  + 
Sbjct: 179 NYQVENARVGQRADYDKLTLDVWTNGSINPSEAIALAAKILTEHLAMFVDLTDEAKNAEI 238

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  +       L   +EEL+LSVRS NCL+   I  + +L  +TEADM+++ N GRKSL
Sbjct: 239 MVEKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELNNKTEADMMKVRNLGRKSL 298

Query: 304 VEIKGVLGTMGLFL 317
            E+K  L  +GL L
Sbjct: 299 EEVKAKLADLGLSL 312


>gi|227520018|ref|ZP_03950067.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           TX0104]
 gi|227555879|ref|ZP_03985926.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           HH22]
 gi|229546938|ref|ZP_04435663.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           TX1322]
 gi|229550527|ref|ZP_04439252.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           ATCC 29200]
 gi|255971735|ref|ZP_05422321.1| DNA-directed RNA polymerase [Enterococcus faecalis T1]
 gi|255974735|ref|ZP_05425321.1| DNA-directed RNA polymerase [Enterococcus faecalis T2]
 gi|256762030|ref|ZP_05502610.1| DNA-directed RNA polymerase [Enterococcus faecalis T3]
 gi|256855189|ref|ZP_05560550.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           T8]
 gi|256956836|ref|ZP_05561007.1| DNA-directed RNA polymerase [Enterococcus faecalis DS5]
 gi|256960643|ref|ZP_05564814.1| DNA-directed RNA polymerase [Enterococcus faecalis Merz96]
 gi|256964158|ref|ZP_05568329.1| DNA-directed RNA polymerase [Enterococcus faecalis HIP11704]
 gi|257078506|ref|ZP_05572867.1| DNA-directed RNA polymerase [Enterococcus faecalis JH1]
 gi|257081523|ref|ZP_05575884.1| DNA-directed RNA polymerase [Enterococcus faecalis E1Sol]
 gi|257084171|ref|ZP_05578532.1| DNA-directed RNA polymerase [Enterococcus faecalis Fly1]
 gi|257087998|ref|ZP_05582359.1| DNA-directed RNA polymerase [Enterococcus faecalis D6]
 gi|257088675|ref|ZP_05583036.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           CH188]
 gi|257417601|ref|ZP_05594595.1| DNA-directed RNA polymerase [Enterococcus faecalis AR01/DG]
 gi|257418673|ref|ZP_05595667.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           T11]
 gi|257421525|ref|ZP_05598515.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           X98]
 gi|293382732|ref|ZP_06628657.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           R712]
 gi|293388085|ref|ZP_06632613.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           S613]
 gi|294781077|ref|ZP_06746428.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           PC1.1]
 gi|300861766|ref|ZP_07107846.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TUSoD Ef11]
 gi|307269113|ref|ZP_07550474.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX4248]
 gi|307274197|ref|ZP_07555405.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0855]
 gi|307276422|ref|ZP_07557545.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX2134]
 gi|307278632|ref|ZP_07559702.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0860]
 gi|307286988|ref|ZP_07567063.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0109]
 gi|307291671|ref|ZP_07571546.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0411]
 gi|312901096|ref|ZP_07760384.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0470]
 gi|312904658|ref|ZP_07763813.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0635]
 gi|312908627|ref|ZP_07767569.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           DAPTO 512]
 gi|312909225|ref|ZP_07768082.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           DAPTO 516]
 gi|312952633|ref|ZP_07771497.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0102]
 gi|227072566|gb|EEI10529.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           TX0104]
 gi|227175046|gb|EEI56018.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           HH22]
 gi|229304246|gb|EEN70242.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           ATCC 29200]
 gi|229307866|gb|EEN73853.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           TX1322]
 gi|255962753|gb|EET95229.1| DNA-directed RNA polymerase [Enterococcus faecalis T1]
 gi|255967607|gb|EET98229.1| DNA-directed RNA polymerase [Enterococcus faecalis T2]
 gi|256683281|gb|EEU22976.1| DNA-directed RNA polymerase [Enterococcus faecalis T3]
 gi|256709702|gb|EEU24749.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           T8]
 gi|256947332|gb|EEU63964.1| DNA-directed RNA polymerase [Enterococcus faecalis DS5]
 gi|256951139|gb|EEU67771.1| DNA-directed RNA polymerase [Enterococcus faecalis Merz96]
 gi|256954654|gb|EEU71286.1| DNA-directed RNA polymerase [Enterococcus faecalis HIP11704]
 gi|256986536|gb|EEU73838.1| DNA-directed RNA polymerase [Enterococcus faecalis JH1]
 gi|256989553|gb|EEU76855.1| DNA-directed RNA polymerase [Enterococcus faecalis E1Sol]
 gi|256992201|gb|EEU79503.1| DNA-directed RNA polymerase [Enterococcus faecalis Fly1]
 gi|256996028|gb|EEU83330.1| DNA-directed RNA polymerase [Enterococcus faecalis D6]
 gi|256997487|gb|EEU84007.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           CH188]
 gi|257159429|gb|EEU89389.1| DNA-directed RNA polymerase [Enterococcus faecalis ARO1/DG]
 gi|257160501|gb|EEU90461.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           T11]
 gi|257163349|gb|EEU93309.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           X98]
 gi|291079892|gb|EFE17256.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           R712]
 gi|291082536|gb|EFE19499.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           S613]
 gi|294451880|gb|EFG20331.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           PC1.1]
 gi|295112524|emb|CBL31161.1| DNA-directed RNA polymerase subunit alpha [Enterococcus sp. 7L76]
 gi|300848291|gb|EFK76048.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TUSoD Ef11]
 gi|306497290|gb|EFM66832.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0411]
 gi|306501934|gb|EFM71223.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0109]
 gi|306504692|gb|EFM73892.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0860]
 gi|306506902|gb|EFM76049.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX2134]
 gi|306509159|gb|EFM78221.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0855]
 gi|306514593|gb|EFM83147.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX4248]
 gi|310625414|gb|EFQ08697.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           DAPTO 512]
 gi|310629421|gb|EFQ12704.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0102]
 gi|310632010|gb|EFQ15293.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0635]
 gi|311290467|gb|EFQ69023.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           DAPTO 516]
 gi|311291768|gb|EFQ70324.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0470]
 gi|315026809|gb|EFT38741.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX2137]
 gi|315028850|gb|EFT40782.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX4000]
 gi|315031165|gb|EFT43097.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0017]
 gi|315035989|gb|EFT47921.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0027]
 gi|315145362|gb|EFT89378.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX2141]
 gi|315147145|gb|EFT91161.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX4244]
 gi|315151097|gb|EFT95113.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0012]
 gi|315153583|gb|EFT97599.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0031]
 gi|315156237|gb|EFU00254.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0043]
 gi|315158618|gb|EFU02635.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0312]
 gi|315160753|gb|EFU04770.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0645]
 gi|315165876|gb|EFU09893.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX1302]
 gi|315168126|gb|EFU12143.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX1341]
 gi|315171434|gb|EFU15451.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX1342]
 gi|315172668|gb|EFU16685.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX1346]
 gi|315573540|gb|EFU85731.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0309B]
 gi|315579352|gb|EFU91543.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0630]
 gi|315582112|gb|EFU94303.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX0309A]
 gi|323479448|gb|ADX78887.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           62]
 gi|327534030|gb|AEA92864.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           OG1RF]
 gi|329577723|gb|EGG59149.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           TX1467]
          Length = 312

 Score =  354 bits (908), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 138/313 (44%), Positives = 202/313 (64%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP  IE I    E  +    + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDG
Sbjct: 3   EFEKPR-IEKI---DENRDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILNIKG+ LK+  +  K + I   GP  VTAGDI   +D+E+
Sbjct: 59  VLHEFSTIPGVREDVTQIILNIKGLALKLYAEEEKTLEIDITGPATVTAGDIIVDSDVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D VIC++   A     LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y V
Sbjct: 119 LNKDLVICSVAEGATFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G+  D+DKL+M I TDGSI  +++++LA++I+ + L +F+N  +  K  +  +  
Sbjct: 179 ENTRVGRRDDFDKLTMEIWTDGSIIPQEALSLAAKIMTEHLDIFVNLTDEAKNAEIMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E+K
Sbjct: 239 EETQKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTNKSEPEMIKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 LKLHDLGLGLRKD 311


>gi|116628988|ref|YP_814160.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus gasseri
           ATCC 33323]
 gi|238853457|ref|ZP_04643835.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus gasseri
           202-4]
 gi|282852675|ref|ZP_06262017.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus gasseri
           224-1]
 gi|311111214|ref|ZP_07712611.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus gasseri
           MV-22]
 gi|122274014|sp|Q046A0|RPOA_LACGA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116094570|gb|ABJ59722.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus gasseri
           ATCC 33323]
 gi|238833897|gb|EEQ26156.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus gasseri
           202-4]
 gi|282556417|gb|EFB62037.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus gasseri
           224-1]
 gi|311066368|gb|EFQ46708.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus gasseri
           MV-22]
          Length = 312

 Score =  354 bits (908), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 140/313 (44%), Positives = 201/313 (64%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +EE     + EPL RGF  TLGN+LRRVL++S+ G A++ +QIDG
Sbjct: 3   EFEKPN----ITVVDQEEAYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTALSYIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK   D  K   I   GP +VTA D++  +DIEV
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSLSDEEKIAEIDVTGPAIVTAADLKVDSDIEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC++     + M + +  G GYVPA  ++T++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICSIADGGHLHMNVAIKNGRGYVPASENKTDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ESAR G+  DYDKL++ I TDGSIT  D+++ A++IL +   +F++ +   +     +  
Sbjct: 179 ESARVGKRDDYDKLTLEIWTDGSITPNDALSFAAKILVEHFKVFMSTDMDAQFDDVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+R+ N GRKSL E+K
Sbjct: 239 EDDKNEKKLEMTIEELDLSVRSYNCLKRAGINTVQELTDKSEADMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 NKLAELGLSLRQD 311


>gi|241763535|ref|ZP_04761587.1| DNA-directed RNA polymerase, alpha subunit [Acidovorax delafieldii
           2AN]
 gi|241367266|gb|EER61606.1| DNA-directed RNA polymerase, alpha subunit [Acidovorax delafieldii
           2AN]
          Length = 330

 Score =  354 bits (908), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 163/335 (48%), Positives = 217/335 (64%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N   L+KP  I    LG    NR  +  EP  RG+ HTLGNA+RRVL+SS+ G A T
Sbjct: 1   MQTN---LLKPKAINVEQLG---HNRAKVALEPFERGYGHTLGNAIRRVLLSSMVGYAAT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE SSI GV ED+ +I+LN+KG+  K+       +++ K G GVVTA DIQT
Sbjct: 55  EVTIAGVLHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGVVTARDIQT 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYS 178
            +D+E++NPDHVI NL     + M++ V KG GYVP    R  ++     G I +DA +S
Sbjct: 115 PHDVEIVNPDHVIANLSAGGKLDMQIKVEKGRGYVPGNLRRYADESTKSIGRIVLDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--E 236
           P+K+VSYTVESAR  Q  D DKL + I+T+G+IT ED+V  +++IL +QL +F   E  E
Sbjct: 175 PVKRVSYTVESARVEQRTDLDKLVVEIETNGAITAEDAVRASAKILVEQLAVFAQLEGGE 234

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
                       +  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  
Sbjct: 235 LAAFDAPAGPRGNATFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N GRKSL EIK VL + GL LGM L +WPP  +++
Sbjct: 295 NLGRKSLNEIKEVLASRGLTLGMKLENWPPAGLDK 329


>gi|312127254|ref|YP_003992128.1| DNA-directed RNA polymerase subunit alpha [Caldicellulosiruptor
           hydrothermalis 108]
 gi|312793911|ref|YP_004026834.1| DNA-directed RNA polymerase subunit alpha [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312877393|ref|ZP_07737358.1| DNA-directed RNA polymerase, alpha subunit [Caldicellulosiruptor
           lactoaceticus 6A]
 gi|311777273|gb|ADQ06759.1| DNA-directed RNA polymerase, alpha subunit [Caldicellulosiruptor
           hydrothermalis 108]
 gi|311795867|gb|EFR12231.1| DNA-directed RNA polymerase, alpha subunit [Caldicellulosiruptor
           lactoaceticus 6A]
 gi|312181051|gb|ADQ41221.1| DNA-directed RNA polymerase, alpha subunit [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 324

 Score =  354 bits (908), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 140/324 (43%), Positives = 205/324 (63%), Gaps = 4/324 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP           +      + EPL RG+  T+GNALRR L+SSL GAA+TAV+IDG
Sbjct: 3   EFQKPTI--RCEELSPDNKYGRYVIEPLERGYGITVGNALRRTLLSSLPGAAVTAVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+ +IILN+KG+ +KMS    K + I  +G   V A DI+   DIE+
Sbjct: 61  VLHEFSTIPGVLEDVPEIILNLKGLAIKMSSPGPKVMYIEAQGECEVKAKDIKADADIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
            NPDH I  L+ DA + ME+TV++G GYVPA+ ++  N PIG+I +D++Y+P+ KV+Y V
Sbjct: 121 CNPDHHIATLNSDARLFMEITVNQGKGYVPAERNKQPNQPIGVIPVDSIYTPVVKVNYKV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV DYDKL+M I T+G+I  ++++ +A++IL +   +F +      +++  +  
Sbjct: 181 ENTRVGQVTDYDKLTMEIWTNGTIRPDEALTVAAKILIEHFNLFTDLSNIPTKIETVVKQ 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    N  L   +EELELSVRS NCL+   I  + DL+ +TE +M+++ N G+KSL E+ 
Sbjct: 241 EPPKRNKLLDMTIEELELSVRSYNCLKRAGINTVEDLVNKTEEEMMKVRNLGKKSLEEVI 300

Query: 308 GVLGTMGLFLGMNLPDWPPESIEE 331
             L ++GL L     D  P+  EE
Sbjct: 301 QKLHSLGLSLKK--SDSTPKEEEE 322


>gi|42518455|ref|NP_964385.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus johnsonii
           NCC 533]
 gi|227888827|ref|ZP_04006632.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus johnsonii
           ATCC 33200]
 gi|61215995|sp|Q74L64|RPOA_LACJO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|41582740|gb|AAS08351.1| DNA-directed RNA polymerase alpha chain [Lactobacillus johnsonii
           NCC 533]
 gi|227850664|gb|EEJ60750.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus johnsonii
           ATCC 33200]
 gi|329666718|gb|AEB92666.1| DNA-directed RNA polymerase alpha chain [Lactobacillus johnsonii
           DPC 6026]
          Length = 312

 Score =  354 bits (908), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 141/313 (45%), Positives = 201/313 (64%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +EE     + EPL RGF  TLGN+LRRVL++S+ G A++ +QIDG
Sbjct: 3   EFEKPN----ITVVDQEEAYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTALSYIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILN+K + LK   D  K   I   GP +VTA D++  +DIEV
Sbjct: 59  VLHEFSTIPGVREDVTKIILNLKKLELKSLSDEEKIAEIDVTGPAIVTAADLKVDSDIEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC++     + M + +  G GYVPA  ++T++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICSIADGGHLHMNVAIKTGRGYVPASENKTDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ESAR G+  DYDKL++ I TDGSIT  D+++ A++IL +   +F++ +   +     +  
Sbjct: 179 ESARVGKRDDYDKLTLEIWTDGSITPNDALSFAAKILVEHFKVFMSTDMDAQFDDVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+R+ N GRKSL E+K
Sbjct: 239 EDDKNEKKLEMTIEELDLSVRSYNCLKRAGINTVQELTDKSEADMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 NKLADLGLSLRQD 311


>gi|167036829|ref|YP_001664407.1| DNA-directed RNA polymerase subunit alpha [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|167039548|ref|YP_001662533.1| DNA-directed RNA polymerase subunit alpha [Thermoanaerobacter sp.
           X514]
 gi|256752660|ref|ZP_05493512.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300915201|ref|ZP_07132516.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter sp.
           X561]
 gi|307725125|ref|YP_003904876.1| DNA-directed RNA polymerase subunit alpha [Thermoanaerobacter sp.
           X513]
 gi|320115251|ref|YP_004185410.1| DNA-directed RNA polymerase subunit alpha [Thermoanaerobacter
           brockii subsp. finnii Ako-1]
 gi|238687620|sp|B0K5S1|RPOA_THEPX RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238687717|sp|B0KCM8|RPOA_THEP3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|166853788|gb|ABY92197.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter sp.
           X514]
 gi|166855663|gb|ABY94071.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|256748480|gb|EEU61532.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300888925|gb|EFK84072.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter sp.
           X561]
 gi|307582186|gb|ADN55585.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter sp.
           X513]
 gi|319928342|gb|ADV79027.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           brockii subsp. finnii Ako-1]
          Length = 315

 Score =  354 bits (908), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 134/311 (43%), Positives = 197/311 (63%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+I+P  IE I+   E+      + EPL RG+  TLGN+LRRVL+SSL GAA  +V+IDG
Sbjct: 3   EMIEP-KIE-IIEQSEDGTYGKFVVEPLERGYGITLGNSLRRVLLSSLPGAAPKSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+ +IILN+K + +K+  D      I   G G VTAG I+   DIE+
Sbjct: 61  VLHEFSTLPGVKEDVVEIILNLKEVAVKLHSDEPVVGRIDVEGRGEVTAGHIKGSADIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPDH I  L  D  + ME+   KG GYVP+  ++  N PIG+I +D++++P+K+VSY V
Sbjct: 121 LNPDHHIATLSDDGKLHMEIVFVKGKGYVPSDKNKEPNQPIGVIPVDSIFTPVKRVSYNV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G V DYDKL++ + T+G++T ++++++AS +L      FI+F    K     ++ 
Sbjct: 181 ENTRVGHVTDYDKLTLEVWTNGAVTPKEAISMASDMLIKYFQKFISFTGEYKSSDIFVDK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                   L   +EEL+LSVRS NCL+   I  + +L Q+TE +M+++ N G+KSL E+K
Sbjct: 241 PEKKVEKPLDMTIEELDLSVRSYNCLKRAGINTVQELTQKTEEEMMKVRNLGKKSLEEVK 300

Query: 308 GVLGTMGLFLG 318
             L  +GL L 
Sbjct: 301 QKLEALGLSLK 311


>gi|220903960|ref|YP_002479272.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
 gi|254765250|sp|B8IYL7|RPOA_DESDA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|219868259|gb|ACL48594.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
          Length = 347

 Score =  353 bits (907), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 157/335 (46%), Positives = 220/335 (65%), Gaps = 1/335 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW EL+KP+ I               + EPL RG+  T+GNA+RRVL++SL+GAA  +V
Sbjct: 13  RNWSELVKPDQI-LREEETASGTHGKFVCEPLERGYGTTIGNAMRRVLLASLQGAAFVSV 71

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I GV HE ++I GV ED+TD+ILNIK + L+M  +  +R+T+     G VTA DI    
Sbjct: 72  KIIGVQHEFTTIHGVLEDITDVILNIKQVRLRMDTEEPQRLTLRVERKGPVTAADIVANQ 131

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            +EVLNPD  I  L  D V+ MEL V  G GYVPA  H    D IGLI +D+ +SP++KV
Sbjct: 132 HVEVLNPDLHIATLTEDVVLEMELEVRMGKGYVPADMHEGLADEIGLIKLDSSFSPVRKV 191

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +YTVE AR GQ+ +YD+L + + TDGS+T ED++A +++I++DQ+ +FINF+E       
Sbjct: 192 AYTVEQARVGQMTNYDRLLLEVWTDGSLTPEDAIAYSAKIIKDQISVFINFDERVSGDMR 251

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           + + +S   N  L K +++LELSVR+TNCLR  NI  +G+L+QRTEA+ML+  NFGRKSL
Sbjct: 252 NGSGESGEVNEHLFKSIDDLELSVRATNCLRSANIGLVGELVQRTEAEMLKTKNFGRKSL 311

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
            EIKGVL  MGL  GM +  +  +  E   K+  +
Sbjct: 312 DEIKGVLLGMGLDFGMKVDSFDKKYQEWKRKQQNE 346


>gi|210623215|ref|ZP_03293654.1| hypothetical protein CLOHIR_01604 [Clostridium hiranonis DSM 13275]
 gi|210153752|gb|EEA84758.1| hypothetical protein CLOHIR_01604 [Clostridium hiranonis DSM 13275]
          Length = 315

 Score =  353 bits (907), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 129/313 (41%), Positives = 203/313 (64%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  ++ I L  E+      + EPL RG+  T+GNALRR+L+SSL G A+ AV+I+G
Sbjct: 3   EIEKP-KVDIIELS-EDFRYGKFVVEPLERGYGITIGNALRRILLSSLPGVAVNAVKIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T+IIL +K ++  + G+ ++ + I  +GP  VT  DI    D+E+
Sbjct: 61  VLHEFSTIPGVKEDVTEIILTLKELSATIDGEGNRTLKIEAQGPCTVTGADIICPPDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N D  I  LD  + + M++ V KG GYVPA+ ++TEN PIG++ +D++Y+P++KV+Y V
Sbjct: 121 INKDLKIATLDEGSKLNMDIHVDKGRGYVPAEENKTENMPIGVLPVDSIYTPVEKVNYHV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  DYDKL++ + T+GSI  ++ ++LA+++L + L +FI+  E    V+  +  
Sbjct: 181 ENTRVGQKSDYDKLTLEVWTNGSINPQEGISLAAKVLVEHLKLFIDLTEHVSNVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N G+KSL E+ 
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVEELANKSEDDMMKVRNLGKKSLEEVI 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  N
Sbjct: 301 QKLDELGLGLKPN 313


>gi|227530231|ref|ZP_03960280.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus vaginalis
           ATCC 49540]
 gi|227349906|gb|EEJ40197.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus vaginalis
           ATCC 49540]
          Length = 314

 Score =  353 bits (907), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 138/315 (43%), Positives = 207/315 (65%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E ++    + EPL RG+  TLGN+LRRVL++SL GAAIT++QIDG
Sbjct: 3   EFEKPN----IHKVEETDSYGKFVVEPLERGYGTTLGNSLRRVLLASLPGAAITSIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K ++LK+  +  K + I  +GP  VTAGDIQ   ++EV
Sbjct: 59  VLHEFSTVEGVTEDVTQIILNLKKVSLKLDSEEQKDLEIDVKGPAEVTAGDIQGDGEVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
           LNPD  I  +   A + +++T  KG GY+ A  ++   ++  IG++ ID++Y+PI++V+Y
Sbjct: 119 LNPDLYIATVADGAELHIKMTADKGRGYLSANDNKARMDDLAIGVLPIDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVE+AR GQ  DYDKL++ + TDGS+T  ++V+L ++IL + L MF+N  E  +  +  +
Sbjct: 179 TVENARVGQRNDYDKLTLDVWTDGSLTPTEAVSLGAKILTEHLAMFVNLTEEAQNAQVMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   +EEL+LSVRS NCL+   I  + +L  RTEADM+++ N G+KSL E
Sbjct: 239 EKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVKELTDRTEADMMKVRNLGQKSLEE 298

Query: 306 IKGVLGTMGLFLGMN 320
           IK  L  +G+    +
Sbjct: 299 IKLKLNDLGVSFRQD 313


>gi|119773379|ref|YP_926119.1| DNA-directed RNA polymerase subunit alpha [Shewanella amazonensis
           SB2B]
 gi|158513008|sp|A1S243|RPOA_SHEAM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119765879|gb|ABL98449.1| DNA-directed RNA polymerase [Shewanella amazonensis SB2B]
          Length = 329

 Score =  353 bits (907), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 144/333 (43%), Positives = 214/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVILEGKDEAMLTLSKSGAGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
             D+ + NPDHVIC+L  +  + M + V +G GYVPA     +  ++ PIG + +DA +S
Sbjct: 118 DGDVTIANPDHVICHLTGNHDISMRIRVERGRGYVPASARAQNEDDDRPIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   +  
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFVELRDVS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 VP---EQKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>gi|56477619|ref|YP_159208.1| DNA-directed RNA polymerase subunit alpha [Aromatoleum aromaticum
           EbN1]
 gi|81598738|sp|Q5P307|RPOA_AZOSE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|56313662|emb|CAI08307.1| DNA-directed RNA polymerase (alpha subunit) [Aromatoleum aromaticum
           EbN1]
          Length = 326

 Score =  353 bits (907), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 151/333 (45%), Positives = 217/333 (65%), Gaps = 10/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N   L+KP  I+   +   +     +  EP  RGF HTLGNALRR+L+SSL G A T
Sbjct: 1   MQSN--SLLKPRIIDVQSVSPVQ---ARVTMEPFERGFGHTLGNALRRILLSSLPGYAPT 55

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I+GVLHE S++ GV ED+ D++LN+KG+ LK+   S   + + K G GVVTA DI+ 
Sbjct: 56  EVSIEGVLHEYSTLDGVREDIVDLLLNLKGVVLKLHSRSEATLRLAKSGDGVVTARDIEV 115

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSP 179
            +D+E++NPDHVI +L     + M++ V +G GYVP        +   IG + +DA +SP
Sbjct: 116 GHDVEIINPDHVIAHLAPGGKLDMQIKVEEGRGYVPGNVRPAAGDTKTIGRVVLDASFSP 175

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +++VSY VESAR  Q  D D+L + I+T+G++  E+++  A+R+L DQL +F + E    
Sbjct: 176 VRRVSYLVESARVEQRTDLDRLVIDIETNGAVDPEEAIRYAARVLMDQLSVFADLEGTAP 235

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            V++     +   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G
Sbjct: 236 VVEQSA---AQTIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTETELLKTPNLG 292

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEEL 332
           RKSL EIK VL + GL LGM L +WPP  +E+L
Sbjct: 293 RKSLNEIKEVLASRGLTLGMKLENWPPAGLEKL 325


>gi|134096296|ref|YP_001101371.1| DNA-directed RNA polymerase subunit alpha [Herminiimonas
           arsenicoxydans]
 gi|158513574|sp|A4G9R3|RPOA_HERAR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|133740199|emb|CAL63250.1| RNA polymerase, alpha subunit [Herminiimonas arsenicoxydans]
          Length = 325

 Score =  353 bits (907), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 155/333 (46%), Positives = 214/333 (64%), Gaps = 11/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +   L+KP  IE  VLG        ++ EP  RG+ HTLGNALRRVL+SS+ G A T
Sbjct: 1   MQNS---LLKPRIIEVEVLG---AGHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GV+HE SS+ GV ED+ D++LN+KG+  K+       +T+ K G G V A DI+ 
Sbjct: 55  EVTIAGVVHEYSSLDGVQEDVVDLLLNLKGVVFKLHNRDDVTLTLKKEGEGAVLASDIEL 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYS 178
            +D+E++NPDHVI +L     + M++ V KG GYVP    R     N  IG I +DA +S
Sbjct: 115 PHDVELVNPDHVIAHLTAGGKLDMQIKVEKGRGYVPGNVRRLSEDTNKTIGRIILDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY VESAR  Q  D DKL + I+T+G IT E+++  ++R+L DQL +F   E   
Sbjct: 175 PVRRVSYAVESARVEQRTDLDKLVINIETNGVITPEEAIRQSARVLVDQLNVFAALE--G 232

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E   D   ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N 
Sbjct: 233 TEAPADAPSRAPAVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRSENELLKTPNL 292

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL + GL LGM L +WPP  +E+
Sbjct: 293 GRKSLNEIKEVLASRGLTLGMKLENWPPAGLEK 325


>gi|254283060|ref|ZP_04958028.1| DNA-directed RNA polymerase, alpha subunit [gamma proteobacterium
           NOR51-B]
 gi|219679263|gb|EED35612.1| DNA-directed RNA polymerase, alpha subunit [gamma proteobacterium
           NOR51-B]
          Length = 334

 Score =  353 bits (907), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 153/336 (45%), Positives = 219/336 (65%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P     I + ++   R  +  EPL RGF HTLGNALRR+L+SS+ G AIT
Sbjct: 1   MQSSVNEFLTPR---VIKVDEKSTTRAQVTLEPLERGFGHTLGNALRRILLSSMPGCAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ +I+LN+KG+ L M+G     +++  +GP  VTAGDIQ 
Sbjct: 58  EVEIDGVLHEYSAIEGVQEDVIEILLNLKGVALTMAGKDEAELSLVAKGPCTVTAGDIQV 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+EV NPDHVIC L  D  + + L   +G GY PA       D    IG + +DA +S
Sbjct: 118 DHDVEVSNPDHVICTLTSDQELAVRLVAQRGRGYSPADSREDPEDETRSIGRLHLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI+++SY VESAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++ E   
Sbjct: 178 PIRRISYVVESARVEQRTDLDKLVIDLETNGTIDPEEAIRRAATILQQQLSVFVDLESEA 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +    +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N 
Sbjct: 238 QTTATEQEDE---VDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S++   +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLKNDER 330


>gi|146297257|ref|YP_001181028.1| DNA-directed RNA polymerase, alpha subunit [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|166229266|sp|A4XLQ2|RPOA_CALS8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|145410833|gb|ABP67837.1| DNA-directed RNA polymerase subunit alpha [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 324

 Score =  353 bits (907), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 142/324 (43%), Positives = 210/324 (64%), Gaps = 4/324 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  I    L Q ++     + EPL RG+  T+GNALRR L+SSL GAA+TAV+IDG
Sbjct: 3   EIQKPT-IRCEELSQ-DQKYGRYVIEPLERGYGITIGNALRRTLLSSLPGAAVTAVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+ +IILN+KG+ +KMS    K + I  +G   V A DI+   DIE+
Sbjct: 61  VLHEFSTIPGVLEDVPEIILNLKGLAIKMSSPGPKVMYIEAQGECEVKAKDIKADADIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
            NP+H I  L+ DA + ME+TV++G GYVPA+ ++  N PIG+I +D++Y+P+ KV+Y V
Sbjct: 121 CNPEHHIATLNEDARLFMEITVNQGKGYVPAERNKQSNQPIGVIPVDSIYTPVTKVNYKV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV DYDKL+M I T+G+I  ++++ +A++IL +   +F +      +++  +  
Sbjct: 181 ENTRVGQVTDYDKLTMEIWTNGTIRPDEALTVAAKILIEHFNLFTDLSNIPTKIETVVKQ 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    N  L   +EELELSVRS NCL+   I  + DL+ +TE +M+++ N G+KSL E+ 
Sbjct: 241 EPPKRNKLLDMTIEELELSVRSYNCLKRAGINTVEDLVNKTEEEMMKVRNLGKKSLEEVI 300

Query: 308 GVLGTMGLFLGMNLPDWPPESIEE 331
             L ++GL L     D  P+  EE
Sbjct: 301 QKLHSLGLSLKK--SDSTPKGEEE 322


>gi|303247018|ref|ZP_07333294.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio
           fructosovorans JJ]
 gi|302491725|gb|EFL51608.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio
           fructosovorans JJ]
          Length = 347

 Score =  353 bits (907), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 156/337 (46%), Positives = 224/337 (66%), Gaps = 2/337 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW EL+KP  +E        +     + EPL RGF  TLGNALRRVL+SSL+GAAI A 
Sbjct: 13  RNWTELVKPETLERD--SASTDTHGRFVCEPLERGFGTTLGNALRRVLLSSLQGAAIVAA 70

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+GV HE S+I GV ED+T++ILN+K + L M+ +  +R+T+F    G V A  IQ   
Sbjct: 71  RIEGVQHEFSTIPGVIEDVTEVILNLKQVRLAMATEDPQRLTLFANKKGEVLASAIQGNQ 130

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           ++ VL+ D +I  L  D   R+EL V  G GYV A  H   +  IGLI +D+ +SP+KKV
Sbjct: 131 NVTVLSEDVLIATLSEDRDFRIELEVRMGKGYVTADMHEGLDSEIGLILLDSSFSPVKKV 190

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +YT+E AR GQ+ +YDKL + +DTDGSI+ ED+++ +++IL+DQL +FINF+E + E  +
Sbjct: 191 AYTIEQARVGQMTNYDKLVLEVDTDGSISPEDAISYSAKILKDQLTVFINFDEKESEADK 250

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                 +  NP+L K ++ELELSVR+TNCL+  NI  +G+L+Q+TE +ML+  NFG+KSL
Sbjct: 251 ARRRDDIELNPSLFKSIDELELSVRATNCLKSANIQTVGELMQKTENEMLKTKNFGKKSL 310

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
            EI+ VL  MGL  GM + ++  +  E L +K  D+ 
Sbjct: 311 EEIRRVLEDMGLEFGMRIENFEQKYQEWLKRKQVDET 347


>gi|254516935|ref|ZP_05128993.1| DNA-directed RNA polymerase, alpha subunit [gamma proteobacterium
           NOR5-3]
 gi|219674440|gb|EED30808.1| DNA-directed RNA polymerase, alpha subunit [gamma proteobacterium
           NOR5-3]
          Length = 334

 Score =  353 bits (907), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 158/336 (47%), Positives = 224/336 (66%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q + +EL+ P  I    + ++ + R  +  EPL RGF HTLGNALRR+L+SS+ G AIT
Sbjct: 1   MQSSVKELLTPRKIN---VAEKSKTRAQVTLEPLERGFGHTLGNALRRILLSSMPGCAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ +I+LN+KG+ L M+G     + + K G G VTA DIQT
Sbjct: 58  EVEIDGVLHEYSAIEGVQEDVIEILLNLKGVALIMNGKDEAELVLSKEGEGPVTAADIQT 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
            +DIE+ NPDH+IC L+  + V M+LTV++G GY PA        E   IG + +DA +S
Sbjct: 118 DHDIEICNPDHLICTLNSKSAVHMKLTVARGRGYSPADARENPEEETRSIGRLQLDATFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +VSY VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL DQL +F++ +   
Sbjct: 178 PVLRVSYVVEAARVEQRTDLDKLVLDLETNGTIDPEEAIRRAATILNDQLRVFVDLQSET 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V  D   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N 
Sbjct: 238 QAVTSDAEDE---VDPVLLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L  WPP S+    K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLESWPPASLRNDEK 330


>gi|312622073|ref|YP_004023686.1| DNA-directed RNA polymerase subunit alpha [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312202540|gb|ADQ45867.1| DNA-directed RNA polymerase, alpha subunit [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 324

 Score =  353 bits (906), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 141/324 (43%), Positives = 205/324 (63%), Gaps = 4/324 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP           +      + EPL RG+  T+GNALRR L+SSL GAA+TAV+IDG
Sbjct: 3   EFQKPTI--RCEELSPDNKYGRYVIEPLERGYGITVGNALRRTLLSSLPGAAVTAVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+ +IILN+KG+ +KMS    K + I  +G   V A DI+   DIE+
Sbjct: 61  VLHEFSTIPGVLEDVPEIILNLKGLAIKMSSPGPKVMYIEAQGECEVKAKDIKADADIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
            NPDH I  L+ DA + ME+TVS+G GYVPA+ ++  N PIG+I +D++Y+P+ KV+Y V
Sbjct: 121 CNPDHHIATLNSDARLFMEITVSQGKGYVPAERNKQPNQPIGVIPVDSIYTPVVKVNYKV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV DYDKL+M I T+G+I  ++++ +A++IL +   +F +      +++  +  
Sbjct: 181 ENTRVGQVTDYDKLTMEIWTNGTIRPDEALTVAAKILIEHFNLFTDLSNIPTKIETVVKQ 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    N  L   +EELELSVRS NCL+   I  + DL+ +TE +M+++ N G+KSL E+ 
Sbjct: 241 EPPKRNKLLDMTIEELELSVRSYNCLKRAGINTVEDLVNKTEEEMMKVRNLGKKSLEEVI 300

Query: 308 GVLGTMGLFLGMNLPDWPPESIEE 331
             L ++GL L     D  P+  EE
Sbjct: 301 QKLHSLGLSLKK--SDSTPKEEEE 322


>gi|152980446|ref|YP_001355075.1| DNA-directed RNA polymerase subunit alpha [Janthinobacterium sp.
           Marseille]
 gi|166229272|sp|A6T3H8|RPOA_JANMA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|151280523|gb|ABR88933.1| DNA-directed RNA polymerase subunit alpha [Janthinobacterium sp.
           Marseille]
          Length = 325

 Score =  353 bits (906), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 154/333 (46%), Positives = 214/333 (64%), Gaps = 11/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +   L+KP  IE  VLG        ++ EP  RG+ HTLGNALRRVL+SS+ G A T
Sbjct: 1   MQNS---LLKPRIIEVEVLG---AGHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GV+HE SS+ GV ED+ D++LN+KG+  K+       +T+ K G G V A DI+ 
Sbjct: 55  EVTIAGVVHEYSSLDGVQEDVVDLLLNLKGVVFKLHNRDDVTLTLKKDGEGAVLASDIEL 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYS 178
            +D+E++NPDHVI +L     + M++ V KG GYVP    R     N  IG I +DA +S
Sbjct: 115 PHDVELVNPDHVIAHLTAGGKLDMQIKVEKGRGYVPGNVRRLSEDTNKTIGRIILDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY VESAR  Q  D DKL + I+T+G I+ E+++  ++R+L DQL +F   E   
Sbjct: 175 PVRRVSYAVESARVEQRTDLDKLVINIETNGVISPEEAIRQSARVLVDQLNVFAALE--G 232

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E   D   ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N 
Sbjct: 233 TEAPADAPSRAPAVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRSENELLKTPNL 292

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL + GL LGM L +WPP  +E+
Sbjct: 293 GRKSLNEIKEVLASRGLTLGMKLENWPPAGLEK 325


>gi|114561361|ref|YP_748874.1| DNA-directed RNA polymerase subunit alpha [Shewanella frigidimarina
           NCIMB 400]
 gi|119366726|sp|Q089M9|RPOA_SHEFN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|114332654|gb|ABI70036.1| DNA-directed RNA polymerase, alpha subunit [Shewanella
           frigidimarina NCIMB 400]
          Length = 329

 Score =  353 bits (906), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 144/333 (43%), Positives = 216/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVNSTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVTIEGKDEALLTLSKSGTGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  + M + V +G GYVPA        ++ PIG + +DA +S
Sbjct: 118 DGDVTIVNPDHVICHLTGNNDISMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   +  
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFVELRDV- 236

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              ++ +  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 237 --TEQAVVEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>gi|307694123|ref|ZP_07636360.1| DNA-directed RNA polymerase subunit alpha [Ruminococcaceae
           bacterium D16]
          Length = 316

 Score =  353 bits (906), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 132/313 (42%), Positives = 194/313 (61%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP      V    + +    + EPL RG+  TLGN+LRR+L+SSL G A+T+++I G
Sbjct: 3   EIEKPRI--DCVENPGDASYGKYVVEPLERGYGTTLGNSLRRILLSSLPGTAVTSIKIAG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE S+I G+ ED+T+I+LNIK I  K+  + +K V I   G   VTAGDI+   D+E+
Sbjct: 61  VQHEFSTIPGIKEDVTEIVLNIKSIIAKLHCEENKTVHIEASGECEVTAGDIKCDADVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  L  DA + MELT+S G GYVPA  ++     IGLI +D++Y+P++KV+YTV
Sbjct: 121 LNPELHIATLGPDATLSMELTLSHGRGYVPADRNKPAQTIIGLIPVDSIYTPVRKVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G   DYDKL++ + TDG+I   D+V+L +RIL D   +F +  E        +  
Sbjct: 181 ENTRVGDATDYDKLTLEVWTDGTIDARDAVSLGARILCDHFALFTDLSETMGSRSTVVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                +  +   +++++LSVRS NCL+  NI  + DLI +TE +M+++ N GRKSL E+ 
Sbjct: 241 AETQRDKVMEMTIDDMDLSVRSYNCLKRANINTVEDLISKTEEEMMKVRNLGRKSLEEVI 300

Query: 308 GVLGTMGLFLGMN 320
             L  MGL L  +
Sbjct: 301 NKLAMMGLSLASD 313


>gi|16801816|ref|NP_472084.1| DNA-directed RNA polymerase subunit alpha [Listeria innocua
           Clip11262]
 gi|16804644|ref|NP_466129.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           EGD-e]
 gi|46908778|ref|YP_015167.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           str. 4b F2365]
 gi|47093972|ref|ZP_00231706.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           str. 4b H7858]
 gi|47097177|ref|ZP_00234742.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           str. 1/2a F6854]
 gi|116873972|ref|YP_850753.1| DNA-directed RNA polymerase subunit alpha [Listeria welshimeri
           serovar 6b str. SLCC5334]
 gi|217966195|ref|YP_002351873.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           HCC23]
 gi|224499278|ref|ZP_03667627.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           Finland 1988]
 gi|224503600|ref|ZP_03671907.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL R2-561]
 gi|226225152|ref|YP_002759259.1| RNA polymerase (alpha subunit) [Listeria monocytogenes Clip81459]
 gi|254825033|ref|ZP_05230034.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL J1-194]
 gi|254829055|ref|ZP_05233742.1| rpoA [Listeria monocytogenes FSL N3-165]
 gi|254830963|ref|ZP_05235618.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           10403S]
 gi|254854189|ref|ZP_05243537.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL R2-503]
 gi|254899943|ref|ZP_05259867.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           J0161]
 gi|254912851|ref|ZP_05262863.1| rpoA [Listeria monocytogenes J2818]
 gi|254931124|ref|ZP_05264483.1| rpoA [Listeria monocytogenes HPB2262]
 gi|254937231|ref|ZP_05268928.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           F6900]
 gi|254992726|ref|ZP_05274916.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL J2-064]
 gi|255520569|ref|ZP_05387806.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL J1-175]
 gi|284800508|ref|YP_003412373.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           08-5578]
 gi|284993694|ref|YP_003415462.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           08-5923]
 gi|290891791|ref|ZP_06554788.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL J2-071]
 gi|300763643|ref|ZP_07073641.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           FSL N1-017]
 gi|54039273|sp|P66700|RPOA_LISIN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|54042184|sp|P66699|RPOA_LISMO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61215961|sp|Q71WH2|RPOA_LISMF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|123461447|sp|A0ALU2|RPOA_LISW6 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|254765254|sp|B8DB34|RPOA_LISMH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|259494169|sp|C1KZF5|RPOA_LISMC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|16412094|emb|CAD00684.1| rpoA [Listeria monocytogenes EGD-e]
 gi|16415291|emb|CAC97981.1| rpoA [Listeria innocua Clip11262]
 gi|46882051|gb|AAT05344.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           serotype 4b str. F2365]
 gi|47014436|gb|EAL05404.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           str. 1/2a F6854]
 gi|47017633|gb|EAL08432.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           str. 4b H7858]
 gi|116742850|emb|CAK21974.1| DNA-directed RNA polymerase, alpha subunit [Listeria welshimeri
           serovar 6b str. SLCC5334]
 gi|217335465|gb|ACK41259.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           HCC23]
 gi|225877614|emb|CAS06328.1| Putative RNA polymerase (alpha subunit) [Listeria monocytogenes
           serotype 4b str. CLIP 80459]
 gi|258601464|gb|EEW14789.1| rpoA [Listeria monocytogenes FSL N3-165]
 gi|258607581|gb|EEW20189.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL R2-503]
 gi|258609836|gb|EEW22444.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           F6900]
 gi|284056070|gb|ADB67011.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           08-5578]
 gi|284059161|gb|ADB70100.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           08-5923]
 gi|290558385|gb|EFD91902.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL J2-071]
 gi|293582672|gb|EFF94704.1| rpoA [Listeria monocytogenes HPB2262]
 gi|293590849|gb|EFF99183.1| rpoA [Listeria monocytogenes J2818]
 gi|293594275|gb|EFG02036.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL J1-194]
 gi|300515920|gb|EFK42969.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           FSL N1-017]
 gi|307572195|emb|CAR85374.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           L99]
 gi|328468090|gb|EGF39096.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           1816]
 gi|328469778|gb|EGF40695.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           220]
          Length = 314

 Score =  353 bits (906), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 136/310 (43%), Positives = 203/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I +  ++      + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETIEIS-DDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
            LHE S I+GV ED+T +ILNIK + LK+  D  K + I  +GPGVVTA DI   +D+E+
Sbjct: 61  ALHEFSVIEGVVEDVTTMILNIKKLALKIYSDEEKTLEIDMQGPGVVTAADINYDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  +A   + L  ++G GY PA  ++ EN PIG++ +D+++SP+ +V+Y V
Sbjct: 121 LNPDLHIATLSDNAKFHVRLNATRGRGYTPADQNKRENMPIGVLPVDSIFSPVIRVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  +YDKL+  + TDGSI+ E++V+L ++IL + L +F+N  +  ++ +  I  
Sbjct: 181 ENTRVGQSTNYDKLTFDVLTDGSISPEEAVSLGAKILSEHLSIFVNLTDEAQKAEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N GRKSL E+K
Sbjct: 241 EESHKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELADKSEDDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 VKLADLGLSL 310


>gi|302524022|ref|ZP_07276364.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. AA4]
 gi|302432917|gb|EFL04733.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. AA4]
          Length = 357

 Score =  353 bits (906), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 124/308 (40%), Positives = 186/308 (60%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
                E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV 
Sbjct: 11  EETVNETRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVK 70

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+TDIILN+K + +    D    + + K+GPG VTA DI     + V NPD  I +L+ 
Sbjct: 71  EDVTDIILNLKELVVSSEEDEPVTMYLRKQGPGEVTAADIVPPAGVTVHNPDLHIASLNG 130

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D
Sbjct: 131 KGKLEIELVVERGRGYVPALQNKQAGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFD 190

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + ++T  SIT  D+VA A + L +  G+        + ++   + +      A    
Sbjct: 191 KLILDVETKPSITARDAVASAGKTLVELFGLARELNVDAEGIEIGPSPQEADTIAAYAMP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  +GL L  
Sbjct: 251 IEDLDLTVRSYNCLKREGIHTVGELVSRSEADLLDIRNFGAKSIDEVKLKLVGLGLALKD 310

Query: 320 NLPDWPPE 327
           + P + P 
Sbjct: 311 SPPGFDPS 318


>gi|119899680|ref|YP_934893.1| DNA-directed RNA polymerase subunit alpha [Azoarcus sp. BH72]
 gi|158512916|sp|A1KB01|RPOA_AZOSB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119672093|emb|CAL96007.1| DNA-directed RNA polymerase [Azoarcus sp. BH72]
          Length = 326

 Score =  353 bits (906), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 156/333 (46%), Positives = 221/333 (66%), Gaps = 10/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N   L+KP  I+   +   +     +  EP  RGF HTLGNALRR+L+SSL G A T
Sbjct: 1   MQSNA--LLKPRIIDVQSISPVQ---ARVTMEPFERGFGHTLGNALRRILLSSLPGHAPT 55

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I+GVLHE S++ G+ ED+ D++LN+KG+ LK+   S   +T+ K G GVVTA DI+ 
Sbjct: 56  EVSIEGVLHEYSTLDGMREDIVDLLLNLKGVVLKLHNRSEAMLTLSKSGEGVVTARDIEG 115

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP--AKHHRTENDPIGLITIDALYSP 179
            +D+E++NPDHVI +L     + M++ V +G GYVP  A+    EN  IG I +DA +SP
Sbjct: 116 GHDVEIINPDHVIAHLAPGGKLEMQIKVEQGRGYVPGNARPVSAENKTIGRIVLDASFSP 175

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +++VSY VESAR  Q  D D+L + I+T+G++  E+++  A+R+L DQL +F + E    
Sbjct: 176 VRRVSYLVESARVEQRTDLDRLVIDIETNGAVDPEEAIRYAARVLMDQLSVFADLEGTPV 235

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            V   +  K+   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G
Sbjct: 236 AV---VPEKTPSIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTETELLKTPNLG 292

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEEL 332
           RKSL EIK VL + GL LGM L +WPP  +E+L
Sbjct: 293 RKSLNEIKEVLASRGLTLGMKLENWPPAGLEKL 325


>gi|158317764|ref|YP_001510272.1| DNA-directed RNA polymerase subunit alpha [Frankia sp. EAN1pec]
 gi|158113169|gb|ABW15366.1| DNA-directed RNA polymerase, alpha subunit [Frankia sp. EAN1pec]
          Length = 375

 Score =  353 bits (906), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 124/307 (40%), Positives = 186/307 (60%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
                E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVLHE S++ GV 
Sbjct: 37  EDPISEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVLHEFSTVPGVK 96

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+TD+ILN+K + +    D    + + K+GPG VTA DI     +EV NPD  +  L+ 
Sbjct: 97  EDVTDLILNLKELVVSSDNDEPTVMYLRKQGPGEVTAADIAPPAGVEVHNPDLHLATLND 156

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              + +ELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+ R  Q  D+D
Sbjct: 157 KGKLEIELTVERGRGYVSAAQNKQPGQEIGRIPIDSIYSPVLKVTYKVEATRVEQRTDFD 216

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           +L + ++T  SI+  D++A A + L    G+        + V    +         L   
Sbjct: 217 RLIVDVETKQSISPRDAMASAGKTLVGLFGLAQELNAEAEGVDIGPSAADAALAADLALP 276

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +EE++L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  LG MGL L  
Sbjct: 277 IEEMDLTVRSYNCLKREGIHTIGELVSRSEADLLDIRNFGQKSIDEVKTKLGAMGLQLKD 336

Query: 320 NLPDWPP 326
           + P + P
Sbjct: 337 SPPGFDP 343


>gi|289579114|ref|YP_003477741.1| DNA-directed RNA polymerase subunit alpha [Thermoanaerobacter
           italicus Ab9]
 gi|297545301|ref|YP_003677603.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           mathranii subsp. mathranii str. A3]
 gi|289528827|gb|ADD03179.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           italicus Ab9]
 gi|296843076|gb|ADH61592.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacter
           mathranii subsp. mathranii str. A3]
          Length = 315

 Score =  353 bits (906), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 138/311 (44%), Positives = 197/311 (63%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+I+P  IE IV   E+      + EPL RG+  TLGN+LRRVL+SSL GAA  +V+IDG
Sbjct: 3   EIIEP-KIE-IVEQAEDGTYGKFVVEPLERGYGITLGNSLRRVLLSSLPGAAPKSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+ +IILN+K I +K+  D      I   G G VTAG I+   DIE+
Sbjct: 61  VLHEFSTLPGVKEDVVEIILNLKEIAVKLHSDEPVVGRIDVEGKGEVTAGHIKGSADIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPDH I  L  D  + ME+   KG GYVP+  ++  N PIG+I +D++++P+KKVSY V
Sbjct: 121 LNPDHHIATLSDDGKLHMEIVFVKGKGYVPSDKNKEPNQPIGVIPVDSIFTPVKKVSYNV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G V DYDKL++ + T+G+IT ++++++AS +L      FI+F    K     ++ 
Sbjct: 181 ENTRVGNVTDYDKLTLEVWTNGTITPKEAISMASDMLIRYFQKFISFSGEYKSSDIFVDK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                   L   +EEL+LSVRS NCL+   I  + +L Q+TE +M+++ N G+KSL E+K
Sbjct: 241 PDKKIEKPLDMTIEELDLSVRSYNCLKRAGINTVQELTQKTEEEMMKVRNLGKKSLEEVK 300

Query: 308 GVLGTMGLFLG 318
             L  +GL L 
Sbjct: 301 QKLQALGLSLK 311


>gi|147676684|ref|YP_001210899.1| DNA-directed RNA polymerase subunit alpha [Pelotomaculum
           thermopropionicum SI]
 gi|146272781|dbj|BAF58530.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 315

 Score =  353 bits (906), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 137/313 (43%), Positives = 208/313 (66%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  ++      + EPL RG+  TLGN+LRR+L+SSL GAA+T+V+IDG
Sbjct: 3   EIEKP-KIEIVEMS-DDNTYGKFVVEPLERGYGITLGNSLRRILLSSLPGAAVTSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+TDIILN+K + LK+ GD  K + +     GVV A DI    D+E+
Sbjct: 61  VLHEFSTIPGVVEDVTDIILNLKNLCLKIYGDEEKVLRVEASTEGVVKAKDIIHDADVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPD  I  L  +A + ME+TV+KG GYV A+ ++  +  IG+I +D++++P++KV+YTV
Sbjct: 121 MNPDLTIATLAENARLYMEITVAKGRGYVSAERNKKGDHIIGVIPVDSVFTPVRKVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ DYDKL++ + TDGSI  +++ +L+++IL + L +FI   E   +V+  +  
Sbjct: 181 ENTRVGQITDYDKLTLEVWTDGSIRPDEATSLSAKILSEHLRLFIGLTETVSDVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    +  L   +EEL+LSVRS NCL+   I  + +LIQR E DM+++ N G+KSL E+ 
Sbjct: 241 EEEHKDRVLEMTIEELDLSVRSYNCLKRAGINTVEELIQRNEEDMMKVRNLGKKSLEEVI 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 NKLHELGLSLRKD 313


>gi|118616625|ref|YP_904957.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium ulcerans
           Agy99]
 gi|183981110|ref|YP_001849401.1| DNA-directed RNA polymerase (alpha chain), RpoA [Mycobacterium
           marinum M]
 gi|158512379|sp|A0PMB7|RPOA_MYCUA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|118568735|gb|ABL03486.1| DNA-directed RNA polymerase (alpha chain), RpoA [Mycobacterium
           ulcerans Agy99]
 gi|183174436|gb|ACC39546.1| DNA-directed RNA polymerase (alpha chain), RpoA [Mycobacterium
           marinum M]
          Length = 347

 Score =  353 bits (906), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 119/306 (38%), Positives = 189/306 (61%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
            ++R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T
Sbjct: 15  TDSRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVT 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           DIILN+K + +    D    + + K+GPG VTAGDI     + V NP+  I  L+    +
Sbjct: 75  DIILNLKALVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPNMRIATLNDKGKL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL +
Sbjct: 135 EVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLIL 194

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T  SIT  D++A A + L +  G+        + ++   +        +    +++L
Sbjct: 195 DVETKNSITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALPIDDL 254

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  + P 
Sbjct: 255 DLTVRSYNCLKREGVHTVGELVSRTESDLLDIRNFGQKSIDEVKVKLHQLGLSLKDSPPS 314

Query: 324 WPPESI 329
           + P  +
Sbjct: 315 FDPSEV 320


>gi|299820982|ref|ZP_07052871.1| DNA-directed RNA polymerase subunit alpha [Listeria grayi DSM
           20601]
 gi|299818003|gb|EFI85238.1| DNA-directed RNA polymerase subunit alpha [Listeria grayi DSM
           20601]
          Length = 314

 Score =  353 bits (906), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 138/310 (44%), Positives = 203/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I +  ++      + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETIEIS-DDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
            LHE S I GV ED+T +ILNIK + LK+  D  K + I  +GPGVVTAGDI   +D+E+
Sbjct: 61  ALHEFSVIDGVVEDVTTMILNIKKLALKIYSDDEKTLEIDVQGPGVVTAGDINYDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  +A   + L  ++G GY PA  ++ EN PIG++ +D+++SP+ +V+Y V
Sbjct: 121 LNPDLHIATLSDNAKFHVRLNATRGRGYTPADLNKHENMPIGVLPVDSIFSPVIRVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  +YDKLS  + TDGSI+ E++V+L ++IL + L +F+N  +  ++ +  I  
Sbjct: 181 ENTRVGQSTNYDKLSFDVLTDGSISPEEAVSLGAKILSEHLSIFVNLTDEAQKAEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N GRKSL E+K
Sbjct: 241 EESHKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELADKSEDDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 VKLADLGLSL 310


>gi|229821593|ref|YP_002883119.1| DNA-directed RNA polymerase, alpha subunit [Beutenbergia cavernae
           DSM 12333]
 gi|259494164|sp|C5C0G1|RPOA_BEUC1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|229567506|gb|ACQ81357.1| DNA-directed RNA polymerase, alpha subunit [Beutenbergia cavernae
           DSM 12333]
          Length = 338

 Score =  353 bits (906), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 128/334 (38%), Positives = 201/334 (60%), Gaps = 9/334 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V     +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLTEEVV----ADNRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+T+IILNIK I +    D    + + K+GPGVVTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTEIILNIKNIVVSSENDEPVVMYLRKQGPGVVTAADITPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  ++    + +ELTV +G GYV A+ ++  +  IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLHIATVNGKGKLEVELTVERGRGYVSAQQNKAYDTEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + +++  +I+  D+VA A + L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDKLIVDVESKPAISPRDAVASAGKTLVELFGLARELNTAAEGIEIGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +E+L+L++RS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEDLDLTIRSYNCLKREGIHQVGELVARSEADLLDIRNFGAKSITEVKEKL 301

Query: 311 GTMGLFLGMNLPDWPPESIE-----ELAKKYEDK 339
             +GL L  +  D+ P  +      +L   Y D+
Sbjct: 302 AALGLSLKDSPADFDPSLVTDAYDGDLDADYADE 335


>gi|125975413|ref|YP_001039323.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           thermocellum ATCC 27405]
 gi|158513382|sp|A3DJK1|RPOA_CLOTH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|125715638|gb|ABN54130.1| DNA-directed RNA polymerase subunit alpha [Clostridium thermocellum
           ATCC 27405]
          Length = 315

 Score =  353 bits (906), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 137/311 (44%), Positives = 203/311 (65%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE  V+  E+      + EPL RG+  TLGN+LRR+L+SSL G A+T+++IDG
Sbjct: 3   EIEKP-KIE-CVVCSEDNRYGKFVVEPLERGYGITLGNSLRRILLSSLPGVAVTSIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           +LHE S+I GV ED+T+IILNIK ++L   G+  K + I   G G V A DI+   D+E+
Sbjct: 61  ILHEFSTIPGVIEDVTEIILNIKELSLNFHGEGPKVIYIDAEGEGEVKAKDIKADADVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+H I  L  D  + ME+T+ KG GYV A+ ++    PIG+I +D++++P+ KV+YTV
Sbjct: 121 LNPEHKIATLSGDHRLYMEMTIDKGRGYVSAEKNKHPGQPIGVIPVDSIFTPVHKVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV DYDKL++ + T+GSI  +++++L ++IL + L +FI+  +  K  +  +  
Sbjct: 181 ENTRVGQVTDYDKLTLEVWTNGSIKPDEAISLGAKILSEHLNLFIDLSDNAKNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + DLI RTE DM+++ N GRKSL E+ 
Sbjct: 241 EETKKEKVLEMTIEELDLSVRSYNCLKRAGINTVEDLISRTEEDMMKVRNLGRKSLEEVV 300

Query: 308 GVLGTMGLFLG 318
             L  +GL L 
Sbjct: 301 NKLKALGLSLA 311


>gi|197117350|ref|YP_002137777.1| DNA-directed RNA polymerase subunit alpha [Geobacter bemidjiensis
           Bem]
 gi|197086710|gb|ACH37981.1| DNA-directed RNA polymerase, alpha subunit [Geobacter bemidjiensis
           Bem]
          Length = 339

 Score =  353 bits (906), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 161/340 (47%), Positives = 227/340 (66%), Gaps = 3/340 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +NW++LI+P  ++               AEP  RGF  TLG  LRRVL+SSL+GAAI 
Sbjct: 1   MYRNWRDLIRPKKLQVET-ESLTNTYGKFFAEPFERGFGTTLGTGLRRVLISSLQGAAIV 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+  GVLHE S++ GV ED+TDIILN+KG+ LK+ G+  + + I ++G GVV A DI T
Sbjct: 60  SVKAKGVLHEFSAVPGVTEDMTDIILNLKGVRLKVHGNESRMIRIVQKGEGVVKAKDIIT 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            N++E+LNP+H I     DA + M+L V  G GYVPA  +R E  P+G I IDA++SP+ 
Sbjct: 120 DNNVEILNPEHHIATCSKDANLEMDLMVKVGKGYVPADRNRDEKAPVGTIPIDAIFSPVH 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KV++TV +AR GQ+ DYDKL++ + TDGS+  +D+VA AS+IL+DQL +FINF+E  +  
Sbjct: 180 KVNFTVTNARVGQITDYDKLTIEVWTDGSVKPQDAVAYASKILKDQLSIFINFDEDVEPQ 239

Query: 242 KEDINVKSLPFNPALLK-KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           +E    +        L   V+ELELSVRS NCL+   I  +G+L+ R+EA+ML+  NFGR
Sbjct: 240 EEAEPEEERERFNENLYRSVDELELSVRSANCLKNAGIKLIGELVSRSEAEMLKTQNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP-PESIEELAKKYEDK 339
           KSL EIK +L  MGL LGM L ++P PE +  L  + +++
Sbjct: 300 KSLNEIKDILVDMGLTLGMKLDNFPDPEIMRRLRGEQKEE 339


>gi|300857219|ref|YP_003782203.1| DNA-directed RNA polymerase subunit alpha [Clostridium ljungdahlii
           DSM 13528]
 gi|300437334|gb|ADK17101.1| DNA-directed RNA polymerase alpha chain [Clostridium ljungdahlii
           DSM 13528]
          Length = 315

 Score =  353 bits (905), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 133/313 (42%), Positives = 205/313 (65%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE +    E+ N    + EPL RG+  TLGNALRR+L+SSL G A   ++IDG
Sbjct: 3   EIEKP-KIECVETS-EDGNYGKFVVEPLERGYGITLGNALRRILLSSLPGVAANHIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+ ++ILNIK + LKM+G+  K + I  +GPG V AGDI+T  D+E+
Sbjct: 61  VLHEFSTIRGVKEDVAELILNIKELALKMNGEGPKTIYIDAQGPGEVVAGDIKTDGDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N D  I  LD D  + ME+ V+ G GYV  + +++E+ PIG I +D++Y+PIK+V++ V
Sbjct: 121 INKDLHIATLDDDGKLYMEIAVNGGRGYVSQRKNKSEDMPIGTIPVDSIYTPIKRVNFAV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ DYDKLS+ + T+G+I  +++V+L+++IL +   +F+   +    V+  +  
Sbjct: 181 ENTRVGQITDYDKLSLEVWTNGTILPDEAVSLSAKILIEHFKLFMTLTDHANNVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L +RT  DM+++ N G+KSL E++
Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTERTMDDMMKVRNLGKKSLEEVE 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 QKLDALGLSLKQS 313


>gi|312135468|ref|YP_004002806.1| DNA-directed RNA polymerase subunit alpha [Caldicellulosiruptor
           owensensis OL]
 gi|311775519|gb|ADQ05006.1| DNA-directed RNA polymerase, alpha subunit [Caldicellulosiruptor
           owensensis OL]
          Length = 324

 Score =  353 bits (905), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 140/324 (43%), Positives = 205/324 (63%), Gaps = 4/324 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP           +      + EPL RG+  T+GNALRR L+SSL GAA+TAV+IDG
Sbjct: 3   EFQKPAI--RCEELSPDNKYGRYVIEPLERGYGITVGNALRRTLLSSLPGAAVTAVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+ +IILN+KG+ +KMS    K + I  +G   V A DI+   DIE+
Sbjct: 61  VLHEFSTIPGVLEDVPEIILNLKGLAIKMSSPGPKIMYIEAQGECEVKAKDIKADADIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
            NPDH I  L+ DA + ME+TV++G GYVPA+ ++  N PIG+I +D++Y+P+ KV+Y V
Sbjct: 121 CNPDHHIATLNQDARLFMEITVNQGKGYVPAERNKQPNQPIGVIPVDSIYTPVVKVNYKV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV DYDKL+M I T+G+I  ++++ +A++IL +   +F +      +++  +  
Sbjct: 181 ENTRVGQVTDYDKLTMEIWTNGTIRPDEALTVAAKILIEHFSLFTDLSNIPTKIETVVKQ 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    N  L   +EELELSVRS NCL+   I  + DL+ +TE +M+++ N G+KSL E+ 
Sbjct: 241 EPPKRNKLLDMTIEELELSVRSYNCLKRAGINTVEDLVNKTEEEMMKVRNLGKKSLEEVI 300

Query: 308 GVLGTMGLFLGMNLPDWPPESIEE 331
             L ++GL L     D  P+  EE
Sbjct: 301 QKLHSLGLSLKK--SDSTPKEEEE 322


>gi|257866554|ref|ZP_05646207.1| DNA directed RNA polymerase [Enterococcus casseliflavus EC30]
 gi|257872930|ref|ZP_05652583.1| DNA directed RNA polymerase [Enterococcus casseliflavus EC10]
 gi|257800512|gb|EEV29540.1| DNA directed RNA polymerase [Enterococcus casseliflavus EC30]
 gi|257807094|gb|EEV35916.1| DNA directed RNA polymerase [Enterococcus casseliflavus EC10]
          Length = 312

 Score =  353 bits (905), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 136/313 (43%), Positives = 200/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E+++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDG
Sbjct: 3   EFEKPR----IAKIDEDKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++KGV ED+  IILNIKG+ LKM G+  K + I   GP  VTAGDI   +D+E+
Sbjct: 59  VLHEFSTVKGVREDVAQIILNIKGLALKMYGNEEKTLEIDISGPATVTAGDIIVDSDVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D  IC +   A     LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y V
Sbjct: 119 LNKDMYICTVSEGATFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G+  D+DKL+M I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  
Sbjct: 179 ENTRVGRRDDFDKLTMEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E+K
Sbjct: 239 EETQKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTNKSEPEMIKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLHDLGLGLRKD 311


>gi|89902964|ref|YP_525435.1| DNA-directed RNA polymerase subunit alpha [Rhodoferax ferrireducens
           T118]
 gi|119366714|sp|Q21QP9|RPOA_RHOFD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|89347701|gb|ABD71904.1| DNA-directed RNA polymerase, alpha subunit [Rhodoferax
           ferrireducens T118]
          Length = 329

 Score =  353 bits (905), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 160/334 (47%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +   L+KP  I    +G    NR  +  EP  RG+ HTLGNALRRVL++S+ G A T
Sbjct: 1   MQNS---LLKPKAINVEQMG---GNRAKVALEPFERGYGHTLGNALRRVLLASMPGYAAT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE SSI GV ED+ +I+LN+KG+  K+       +++ K G G+VTA DIQT
Sbjct: 55  EVTIAGVLHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGLVTASDIQT 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYS 178
            +D+E++NPDHVI +L     + M++ V KG GYVP    R  ++P    G I +DA +S
Sbjct: 115 PHDVEIINPDHVIAHLSQGGKLDMQIKVEKGRGYVPGTMRRHGDEPTKSIGRIILDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+K+VSYTVESAR  Q  D DKL + I+T+G+I+ ED+V  +++IL +QL +F   E  +
Sbjct: 175 PVKRVSYTVESARVEQRTDLDKLVVDIETNGAISAEDAVRASAKILVEQLAVFAQLEGSE 234

Query: 239 KEVKEDINV-KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
               +  +   S  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N
Sbjct: 235 LAAFDTPSPRGSTQFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            GRKSL EIK VL + GL LGM L  WPP ++E+
Sbjct: 295 LGRKSLNEIKEVLASRGLTLGMKLESWPPAALEK 328


>gi|289435872|ref|YP_003465744.1| DNA-directed RNA polymerase subunit alpha [Listeria seeligeri
           serovar 1/2b str. SLCC3954]
 gi|315304917|ref|ZP_07875021.1| DNA-directed RNA polymerase, alpha subunit [Listeria ivanovii FSL
           F6-596]
 gi|289172116|emb|CBH28662.1| DNA-directed RNA polymerase subunit alpha [Listeria seeligeri
           serovar 1/2b str. SLCC3954]
 gi|313626708|gb|EFR95737.1| DNA-directed RNA polymerase, alpha subunit [Listeria ivanovii FSL
           F6-596]
 gi|313631790|gb|EFR98970.1| DNA-directed RNA polymerase, alpha subunit [Listeria seeligeri FSL
           N1-067]
 gi|313636142|gb|EFS02005.1| DNA-directed RNA polymerase, alpha subunit [Listeria seeligeri FSL
           S4-171]
          Length = 314

 Score =  352 bits (904), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 136/310 (43%), Positives = 204/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I +  ++      + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETIEIS-DDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
            LHE S I+GV ED+T +ILNIK + LK+  D  K + I  +GPGVVTA DI   +D+E+
Sbjct: 61  ALHEFSVIEGVVEDVTTMILNIKKLALKIYSDEEKTLEIDMQGPGVVTAADINYDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  +A   + L  ++G GY PA  ++ EN PIG++ +D+++SP+ +V+Y V
Sbjct: 121 LNPDLHIATLSDNAKFHVRLNATRGRGYTPADQNKRENMPIGVLPVDSIFSPVIRVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ +YDKL+  + TDGSI+ E++V+L ++IL + L +F+N  +  ++ +  I  
Sbjct: 181 ENTRVGQLTNYDKLTFDVLTDGSISPEEAVSLGAKILSEHLSIFVNLTDEAQKAEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N GRKSL E+K
Sbjct: 241 EESHKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELADKSEDDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 VKLADLGLSL 310


>gi|15896355|ref|NP_349704.1| DNA-directed RNA polymerase subunit alpha [Clostridium
           acetobutylicum ATCC 824]
 gi|20139603|sp|Q97EK6|RPOA_CLOAB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|15026170|gb|AAK81044.1|AE007807_2 DNA-dependent RNA polymerase alpha subunit [Clostridium
           acetobutylicum ATCC 824]
 gi|325510511|gb|ADZ22147.1| DNA-directed RNA polymerase subunit alpha [Clostridium
           acetobutylicum EA 2018]
          Length = 315

 Score =  352 bits (904), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 133/313 (42%), Positives = 203/313 (64%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE  V   E+ +    + EPL RG+  TLGN+LRR+L+SSL G A  +V+I+G
Sbjct: 3   EIEKP-KIE-CVESTEDGSYGRFVVEPLERGYGITLGNSLRRILLSSLPGVAANSVRIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++KGV ED+T++ILNIK + LKM G+  K + I   GPG VT  DI+T   +EV
Sbjct: 61  VLHEFSTVKGVKEDVTELILNIKALCLKMEGEDSKVIYIDAHGPGEVTGADIRTDGSVEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N D  I  LD D  + ME+ V++G GYV    ++ ++ PIG I +D++YSPIK+V++TV
Sbjct: 121 INKDLHIATLDEDGKLYMEIEVNRGRGYVTQNKNKRDDMPIGTIAVDSIYSPIKRVNFTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R  Q+ DYDKL++ +  +G+I  E++++LA++IL +   +F+   +   +V+  +  
Sbjct: 181 ENTRVAQITDYDKLTIEVWGNGTIRPEEAISLAAKILIEHFKLFMTLTDHADDVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L QR+  DM+++ N GRKSL E++
Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTQRSMEDMMKVRNLGRKSLEEVE 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L +N
Sbjct: 301 QKLKALGLSLKLN 313


>gi|29374877|ref|NP_814030.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecalis
           V583]
 gi|41688668|sp|Q839D9|RPOA_ENTFA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|29342335|gb|AAO80101.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecalis
           V583]
          Length = 312

 Score =  352 bits (904), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 138/313 (44%), Positives = 201/313 (64%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP  IE I    E  +    + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDG
Sbjct: 3   EFEKPR-IEKI---DENRDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILNIKG+ LK+  +  K + I   GP  VTAGDI   +D+E+
Sbjct: 59  VLHEFSTIPGVREDVTQIILNIKGLALKLYAEEEKTLEIDITGPATVTAGDIIVDSDVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D VIC++   A     LTV  G GYV A  ++ E+ PIG++ +D++Y+P+ +V+Y V
Sbjct: 119 LNKDLVICSVAEGATFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVLRVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G+  D+DKL+M I TDGSI  +++++LA++I+ + L +F+N  +  K  +  +  
Sbjct: 179 ENTRVGRRDDFDKLTMEIWTDGSIIPQEALSLAAKIMTEHLDIFVNLTDEAKNAEIMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E+K
Sbjct: 239 EETQKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTNKSEPEMIKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 LKLHDLGLGLRKD 311


>gi|329907624|ref|ZP_08274694.1| DNA-directed RNA polymerase alpha subunit [Oxalobacteraceae
           bacterium IMCC9480]
 gi|327546929|gb|EGF31838.1| DNA-directed RNA polymerase alpha subunit [Oxalobacteraceae
           bacterium IMCC9480]
          Length = 325

 Score =  352 bits (904), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 152/333 (45%), Positives = 213/333 (63%), Gaps = 11/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +   L+KP  IE   LG        ++ EP  RG+ HTLGNALRRVL+SS+ G A T
Sbjct: 1   MQNS---LLKPRIIEVETLG---AGHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GV+HE SS+ GV ED+ D++LN+KG+  K+       +T+ K G G V A DI  
Sbjct: 55  EVTIAGVVHEYSSLDGVQEDVVDMLLNLKGVVFKLHNRDEVTLTLKKDGEGAVLASDIDL 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYS 178
            +D+E++NPDHVI +L     + M++ V KG GYVP    R     N  IG I +DA +S
Sbjct: 115 PHDVELINPDHVIAHLTAGGKLDMQIKVEKGRGYVPGNVRRLAEDANKTIGRIILDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY+VESAR  Q  D DKL + I+T+G I+ E+++  ++R+L DQL +F   E  +
Sbjct: 175 PVRRVSYSVESARVEQRTDLDKLVINIETNGVISPEEAIRQSARVLVDQLNVFAALEGTE 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              +      S+  +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N 
Sbjct: 235 AAAEAPSRAPSV--DPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRSENELLKTPNL 292

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL + GL LGM L +WPP  +E+
Sbjct: 293 GRKSLNEIKEVLASRGLTLGMKLENWPPAGLEK 325


>gi|302871526|ref|YP_003840162.1| DNA-directed RNA polymerase, alpha subunit [Caldicellulosiruptor
           obsidiansis OB47]
 gi|302574385|gb|ADL42176.1| DNA-directed RNA polymerase, alpha subunit [Caldicellulosiruptor
           obsidiansis OB47]
          Length = 324

 Score =  352 bits (904), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 139/324 (42%), Positives = 205/324 (63%), Gaps = 4/324 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP           +      + EPL RG+  T+GNALRR L+SSL GAA+TAV+IDG
Sbjct: 3   EFQKPTI--RCEELSPDNKYGRYVIEPLERGYGITVGNALRRTLLSSLPGAAVTAVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+ +IILN+KG+ +KMS    K + I  +G   V A DI+   DIE+
Sbjct: 61  VLHEFSTIPGVLEDVPEIILNLKGLAIKMSSPGPKIMYIEAQGECEVKAKDIKADADIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
            NPDH I  L+ DA + ME+TV++G GY+PA+ ++  N PIG+I +D++Y+P+ KV+Y V
Sbjct: 121 CNPDHHIATLNQDARLFMEITVNQGKGYIPAERNKQPNQPIGVIPVDSIYTPVVKVNYKV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV DYDKL+M I T+G+I  ++++ +A++IL +   +F +      +++  +  
Sbjct: 181 ENTRVGQVTDYDKLTMEIWTNGTIRPDEALTIAAKILIEHFNLFTDLSNIPTKIETVVKQ 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    N  L   +EELELSVRS NCL+   I  + DL+ +TE +M+++ N G+KSL E+ 
Sbjct: 241 EPPKRNKLLDMTIEELELSVRSYNCLKRAGINTVEDLVNKTEEEMMKVRNLGKKSLEEVI 300

Query: 308 GVLGTMGLFLGMNLPDWPPESIEE 331
             L ++GL L     D  P+  EE
Sbjct: 301 QKLHSLGLSLKK--SDSTPKEEEE 322


>gi|240948150|ref|ZP_04752553.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus minor
           NM305]
 gi|240297503|gb|EER48010.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus minor
           NM305]
          Length = 329

 Score =  352 bits (904), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 151/334 (45%), Positives = 224/334 (67%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ +    + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVN---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G VTAGDI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQSKDDVVLTLNKSGIGPVTAGDITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++NPDHVIC+L D +A + M + V +G GYVPA    H + ++ PIG + +DA +
Sbjct: 118 DGDVEIVNPDHVICHLTDKNASINMRIRVQRGRGYVPASARVHTQDDDRPIGRLLVDARF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++ V   +  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQPV---VKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|323706479|ref|ZP_08118040.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacterium
           xylanolyticum LX-11]
 gi|323534199|gb|EGB23989.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacterium
           xylanolyticum LX-11]
          Length = 316

 Score =  352 bits (904), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 136/310 (43%), Positives = 208/310 (67%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE IV    ++     + EPL RG+  TLGN+LRR+L+SSL GAA   ++IDG
Sbjct: 4   EIEKP-KIE-IVEQSNDDTYAKFVIEPLERGYGITLGNSLRRMLLSSLPGAAAKTIKIDG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T+IILN+K + +K+  D  K V I   G G VTAGDI +  D+E+
Sbjct: 62  VLHEFSTVPGVKEDVTEIILNLKELAVKLYTDEPKIVRIEAEGKGEVTAGDIISDGDVEI 121

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPD  I  L  +  + ME+ + KG GYVP+  ++  N PIG+I +D++++P+KKVSY+V
Sbjct: 122 MNPDLHIATLSDNGKLNMEIELVKGKGYVPSDKNKEPNQPIGIIPVDSIFTPVKKVSYSV 181

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV DYDKL+M + T+G+I+ +++++LA++IL D   +F +F +   +++  +  
Sbjct: 182 ENTRVGQVTDYDKLTMEVWTNGTISPKEAISLAAKILIDHFNLFTSFADNYNDMEVLVEK 241

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                +  L   +EEL+LSVRS NCL+   I  + DL+Q+TE +M+++ N G+KSLVE++
Sbjct: 242 SEKKTDKPLDMTIEELDLSVRSYNCLKRAGINTVQDLVQKTEEEMMKVRNLGKKSLVEVE 301

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 302 QKLKALGLSL 311


>gi|319764614|ref|YP_004128551.1| DNA-directed RNA polymerase, alpha subunit [Alicycliphilus
           denitrificans BC]
 gi|330826871|ref|YP_004390174.1| DNA-directed RNA polymerase subunit alpha [Alicycliphilus
           denitrificans K601]
 gi|317119175|gb|ADV01664.1| DNA-directed RNA polymerase, alpha subunit [Alicycliphilus
           denitrificans BC]
 gi|329312243|gb|AEB86658.1| DNA-directed RNA polymerase, alpha subunit [Alicycliphilus
           denitrificans K601]
          Length = 331

 Score =  352 bits (904), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 158/336 (47%), Positives = 218/336 (64%), Gaps = 12/336 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N   L+KP  I    LG    NR  +  EP  RG+ HTLGNA+RRVL+SS+ G A T
Sbjct: 1   MQTN---LLKPKAINVEQLG---HNRAKVELEPFERGYGHTLGNAIRRVLLSSMVGYAAT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE SSI GV ED+ +I+LN+KG+  K+       +++ K G GVVTA DIQT
Sbjct: 55  EVTIAGVLHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGVVTARDIQT 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYS 178
            +D+E++NPDHVI  L     + M++ V KG GYVP    R  ++     G I +DA +S
Sbjct: 115 PHDVEIVNPDHVIATLSAGGKLDMQIKVEKGRGYVPGNLRRFADESTKSIGRIVLDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+K+VSYTVESAR  Q  D DKL + I+T+G+I+ E++V  +++IL +QL +F   +  +
Sbjct: 175 PVKRVSYTVESARVEQRTDLDKLVLEIETNGAISAEEAVRASAKILVEQLAVFAQLDGGE 234

Query: 239 KEVKEDINVKSLP---FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
               +    ++     F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+ 
Sbjct: 235 IFESQATGARAASGATFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKT 294

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N GRKSL EIK VL + GL LGM L +WPP  +++
Sbjct: 295 PNLGRKSLNEIKEVLASRGLTLGMKLENWPPAGLDK 330


>gi|325567351|ref|ZP_08144018.1| DNA-directed RNA polymerase subunit alpha [Enterococcus
           casseliflavus ATCC 12755]
 gi|325158784|gb|EGC70930.1| DNA-directed RNA polymerase subunit alpha [Enterococcus
           casseliflavus ATCC 12755]
          Length = 312

 Score =  352 bits (904), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 136/313 (43%), Positives = 200/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E+++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDG
Sbjct: 3   EFEKPR----IAKIDEDKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VL+E S++KGV ED+  IILNIKG+ LKM GD  K + I   GP  VTAGDI   +D+E+
Sbjct: 59  VLYEFSTVKGVREDVAQIILNIKGLALKMYGDEEKTLEIDISGPATVTAGDIIVDSDVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D  IC +   A     LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y V
Sbjct: 119 LNKDMYICTVSEGATFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G+  D+DKL+M I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  
Sbjct: 179 ENTRVGRRDDFDKLTMEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E+K
Sbjct: 239 EETQKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTNKSEPEMIKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLHDLGLGLRKD 311


>gi|222529702|ref|YP_002573584.1| DNA-directed RNA polymerase subunit alpha [Caldicellulosiruptor
           bescii DSM 6725]
 gi|254765242|sp|B9MKF3|RPOA_ANATD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|222456549|gb|ACM60811.1| DNA-directed RNA polymerase, alpha subunit [Caldicellulosiruptor
           bescii DSM 6725]
          Length = 324

 Score =  352 bits (904), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 139/324 (42%), Positives = 204/324 (62%), Gaps = 4/324 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP           +      + EPL RG+  T+GNALRR L+SSL GAA+TAV+IDG
Sbjct: 3   EFQKPTI--RCEELSPDNKYGRYVIEPLERGYGITVGNALRRTLLSSLPGAAVTAVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+ +IILN+KG+ +KMS    K + I  +G   V A DI+   DIE+
Sbjct: 61  VLHEFSTIPGVLEDVPEIILNLKGLAIKMSSPGPKVMYIEAQGECEVKAKDIKADADIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
            NPDH I  L+ DA + ME+TV++G GYV A+ ++  N PIG+I +D++Y+P+ KV+Y V
Sbjct: 121 CNPDHHIATLNQDARLFMEITVNQGKGYVLAERNKQPNQPIGVIPVDSIYTPVVKVNYKV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV DYDKL+M I T+G+I  ++++ +A++IL +   +F +      +++  +  
Sbjct: 181 ENTRVGQVTDYDKLTMEIWTNGTIRPDEALTVAAKILIEHFNLFTDLSNIPTKIETVVKQ 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    N  L   +EELELSVRS NCL+   I  + DL+ +TE +M+++ N G+KSL E+ 
Sbjct: 241 EPPKRNKLLDMTIEELELSVRSYNCLKRAGINTVEDLVNKTEEEMMKVRNLGKKSLEEVI 300

Query: 308 GVLGTMGLFLGMNLPDWPPESIEE 331
             L ++GL L     D  P+  EE
Sbjct: 301 QKLHSLGLSLKK--SDSTPKEEEE 322


>gi|313606573|gb|EFR83374.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           FSL F2-208]
          Length = 314

 Score =  352 bits (904), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 135/310 (43%), Positives = 203/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I +  ++      + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETIEIS-DDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
            LHE S I+GV ED+T +ILNIK + LK+  D  K + I  +GPG+VTA DI   +D+E+
Sbjct: 61  ALHEFSVIEGVVEDVTTMILNIKKLALKIYSDEEKTLEIDMQGPGIVTAADINYDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  +A   + L  ++G GY PA  ++ EN PIG++ +D+++SP+ +V+Y V
Sbjct: 121 LNPDLHIATLSDNAKFHVRLNATRGRGYTPADQNKRENMPIGVLPVDSIFSPVIRVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  +YDKL+  + TDGSI+ E++V+L ++IL + L +F+N  +  ++ +  I  
Sbjct: 181 ENTRVGQSTNYDKLTFDVLTDGSISPEEAVSLGAKILSEHLSIFVNLTDEAQKAEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N GRKSL E+K
Sbjct: 241 EESHKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELADKSEDDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 VKLADLGLSL 310


>gi|91774660|ref|YP_544416.1| DNA-directed RNA polymerase subunit alpha [Methylobacillus
           flagellatus KT]
 gi|119366697|sp|Q1H4L2|RPOA_METFK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|91708647|gb|ABE48575.1| DNA-directed RNA polymerase subunit alpha [Methylobacillus
           flagellatus KT]
          Length = 328

 Score =  352 bits (903), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 157/334 (47%), Positives = 217/334 (64%), Gaps = 9/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++  V+      R  +  EP+ RGF +TLGNALRRVL+SS+ G AIT
Sbjct: 1   MQNSPTEYLKPRVVDVDVISPV---RARVTLEPMERGFGYTLGNALRRVLLSSIPGFAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGV+HE S++ GV ED+ DI+LN+KG+ LK++  +   +T+ K   GVVTAGD  T
Sbjct: 58  EVKIDGVVHEYSTLDGVQEDVVDILLNLKGVALKLNSKNEATLTLNKSTEGVVTAGDFDT 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYS 178
            +D E+ NPDHVI +L     + +E+ V  G GY P    R    E+  +G I +DA +S
Sbjct: 118 GHDAEIANPDHVIAHLTKGGKLNLEVKVEMGRGYQPVPQRRKTEDEDRVLGFIQVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI KVSY VESAR  Q  D DKL M ++T+G I  E ++  A+RIL  QL +F + E   
Sbjct: 178 PISKVSYQVESARVEQRTDLDKLIMDVETNGIIEPEQAIRDAARILMGQLSVFADLEGAP 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            EV+     ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 SEVEV---KQAPQVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKAPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEEL 332
           GRKSL EIK VL + GL LGM L +WPP  +E++
Sbjct: 295 GRKSLNEIKDVLASKGLTLGMKLENWPPAGLEKV 328


>gi|59802135|ref|YP_208847.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae FA
           1090]
 gi|194099939|ref|YP_002003077.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           NCCP11945]
 gi|239997951|ref|ZP_04717875.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           35/02]
 gi|240015071|ref|ZP_04721984.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           DGI18]
 gi|240017520|ref|ZP_04724060.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           FA6140]
 gi|240081663|ref|ZP_04726206.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           FA19]
 gi|240113941|ref|ZP_04728431.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           MS11]
 gi|240116675|ref|ZP_04730737.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           PID18]
 gi|240118897|ref|ZP_04732959.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           PID1]
 gi|240122143|ref|ZP_04735105.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           PID24-1]
 gi|240124435|ref|ZP_04737391.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           PID332]
 gi|240124696|ref|ZP_04737582.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           SK-92-679]
 gi|240129111|ref|ZP_04741772.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           SK-93-1035]
 gi|254494696|ref|ZP_05107867.1| DNA-directed RNA polymerase subunit alpha chain [Neisseria
           gonorrhoeae 1291]
 gi|260439566|ref|ZP_05793382.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           DGI2]
 gi|268593801|ref|ZP_06127968.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           35/02]
 gi|268597760|ref|ZP_06131927.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           FA19]
 gi|268600005|ref|ZP_06134172.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           MS11]
 gi|268602342|ref|ZP_06136509.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           PID18]
 gi|268604606|ref|ZP_06138773.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           PID1]
 gi|268683063|ref|ZP_06149925.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           PID332]
 gi|268683270|ref|ZP_06150132.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           SK-92-679]
 gi|268687493|ref|ZP_06154355.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           SK-93-1035]
 gi|291042802|ref|ZP_06568543.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           DGI2]
 gi|293398177|ref|ZP_06642382.1| DNA-directed RNA polymerase, alpha subunit [Neisseria gonorrhoeae
           F62]
 gi|75432361|sp|Q5F5V2|RPOA_NEIG1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|59719030|gb|AAW90435.1| putative DNA-directed RNA polymerase alpha chain [Neisseria
           gonorrhoeae FA 1090]
 gi|193935229|gb|ACF31053.1| DNA-directed RNA polymerase alpha subunit [Neisseria gonorrhoeae
           NCCP11945]
 gi|226513736|gb|EEH63081.1| DNA-directed RNA polymerase subunit alpha chain [Neisseria
           gonorrhoeae 1291]
 gi|268547190|gb|EEZ42608.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           35/02]
 gi|268551548|gb|EEZ46567.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           FA19]
 gi|268584136|gb|EEZ48812.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           MS11]
 gi|268586473|gb|EEZ51149.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           PID18]
 gi|268588737|gb|EEZ53413.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           PID1]
 gi|268623347|gb|EEZ55747.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           PID332]
 gi|268623554|gb|EEZ55954.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           SK-92-679]
 gi|268627777|gb|EEZ60177.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           SK-93-1035]
 gi|291013236|gb|EFE05202.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           DGI2]
 gi|291611440|gb|EFF40510.1| DNA-directed RNA polymerase, alpha subunit [Neisseria gonorrhoeae
           F62]
 gi|317165391|gb|ADV08932.1| DNA-directed RNA polymerase subunit alpha [Neisseria gonorrhoeae
           TCDC-NG08107]
          Length = 328

 Score =  352 bits (903), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 159/333 (47%), Positives = 214/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+          R  +  +P  RGF HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSTTEFLKPRQIDVNTFS---ATRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE S++ GV ED+ DI+LNIKGI  K+ G S  ++ + K G GVV+AGDI+ 
Sbjct: 58  EVAIAGVLHEYSTVGGVQEDVVDILLNIKGIVFKLHGRSQVQLVLKKSGSGVVSAGDIEL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
            +D+E+LNP HVIC+L  +  + ME+ V +G GY         R EN  IG I +DA +S
Sbjct: 118 PHDVEILNPGHVICHLADNGQIEMEIKVEQGRGYQSVSGRQVVRDENRQIGAIQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI +VS+ VE AR  Q  D DKL + I+TDGSI  E++V  A+RIL DQ+ +F +    +
Sbjct: 178 PISRVSFEVEPARVEQRTDLDKLVLDIETDGSIDPEEAVRSAARILIDQMSIFADL---Q 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
               E++  KS P +P LL  V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N 
Sbjct: 235 GTPVEEVEEKSPPIDPVLLHPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 295 GRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 327


>gi|149675708|dbj|BAF64734.1| DNA-directed RNA polymerase alpha subunit [Shewanella
           livingstonensis]
          Length = 329

 Score =  352 bits (903), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 143/333 (42%), Positives = 216/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVNSTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVTIEGKDEALLTLSKSGTGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  + M + V +G GYVPA        ++ PIG + +DA +S
Sbjct: 118 DGDVTIVNPDHVICHLTGNNDISMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   +  
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFVELRDV- 236

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              ++ +  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 237 --TEQAVVEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL +IK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTDIKDVLASRGLSLGMRLENWPPASLAD 327


>gi|253701895|ref|YP_003023084.1| DNA-directed RNA polymerase subunit alpha [Geobacter sp. M21]
 gi|251776745|gb|ACT19326.1| DNA-directed RNA polymerase, alpha subunit [Geobacter sp. M21]
          Length = 339

 Score =  352 bits (903), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 161/340 (47%), Positives = 227/340 (66%), Gaps = 3/340 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +NW++LI+P  ++               AEP  RGF  TLG  LRRVL+SSL+GAAI 
Sbjct: 1   MYRNWRDLIRPKKLQVET-ESLTNTYGKFFAEPFERGFGTTLGTGLRRVLISSLQGAAIV 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+  GVLHE S++ GV ED+TDIILN+KG+ LK+ G+  + + I ++G GVV A DI T
Sbjct: 60  SVKAKGVLHEFSAVPGVTEDMTDIILNLKGVRLKVHGNESRMIRIVQKGEGVVKAKDIIT 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            N++E+LNP+H I     DA + M+L V  G GYVPA  +R E  P+G I IDA++SP+ 
Sbjct: 120 DNNVEILNPEHHIATCSKDANLEMDLMVKVGKGYVPADRNRDEKAPVGTIPIDAIFSPVH 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KV++TV +AR GQ+ DYDKL++ + TDGS+  +D+VA AS+IL+DQL +FINF+E  +  
Sbjct: 180 KVNFTVTNARVGQITDYDKLTIELWTDGSVKPQDAVAYASKILKDQLSIFINFDEDVEPQ 239

Query: 242 KEDINVKSLPFNPALLK-KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           +E    +        L   V+ELELSVRS NCL+   I  +G+L+ R+EA+ML+  NFGR
Sbjct: 240 EEAEPEEERERFNENLYRSVDELELSVRSANCLKNAGIKLIGELVSRSEAEMLKTQNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP-PESIEELAKKYEDK 339
           KSL EIK +L  MGL LGM L ++P PE +  L  + +++
Sbjct: 300 KSLNEIKDILVDMGLTLGMKLENFPDPEIMRRLRGEQKEE 339


>gi|257870543|ref|ZP_05650196.1| DNA directed RNA polymerase [Enterococcus gallinarum EG2]
 gi|257804707|gb|EEV33529.1| DNA directed RNA polymerase [Enterococcus gallinarum EG2]
          Length = 312

 Score =  352 bits (903), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 140/313 (44%), Positives = 201/313 (64%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDG
Sbjct: 3   EFEKPR----IAKIDEEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++KGV ED+  IILNIKG+ LKM GD  K + I   GP  VTAGDI   +D+E+
Sbjct: 59  VLHEFSTVKGVREDVAQIILNIKGLALKMYGDEEKTLEIDITGPATVTAGDIIVDSDVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D  ICN+   A     LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y V
Sbjct: 119 LNKDMYICNVSEGASFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G+  D+DKL+M I TDGSI   ++++LA++I+ + L +F+N  +  K  +  +  
Sbjct: 179 ENTRVGRRDDFDKLTMEIWTDGSIEPLEAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E+K
Sbjct: 239 EETQKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTNKSEPEMIKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLHDLGLGLRKD 311


>gi|268318877|ref|YP_003292533.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus johnsonii
           FI9785]
 gi|262397252|emb|CAX66266.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus johnsonii
           FI9785]
          Length = 312

 Score =  352 bits (903), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 140/313 (44%), Positives = 201/313 (64%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +EE     + EPL RGF  TLGN+LRRVL++S+ G A++ +QIDG
Sbjct: 3   EFEKPN----ITVVDQEEAYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTALSYIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK   D  K   I   GP +VTA D++  +DIEV
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSLSDEEKIAEIDVTGPAIVTAADLKVDSDIEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC++     + M + +  G GYVPA  ++T++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICSIADGGHLHMNVAIKTGRGYVPASENKTDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ESAR G+  DYDKL++ I TDGSIT  D+++ A++IL +   +F++ +   +     +  
Sbjct: 179 ESARVGKRDDYDKLTLEIWTDGSITPNDALSFAAKILVEHFKVFMSTDMDAQFDDVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+R+ N GRKSL E+K
Sbjct: 239 EDDKNEKKLEMTIEELDLSVRSYNCLKRAGINTVQELTDKSEADMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 NKLTDLGLSLRQD 311


>gi|167626015|ref|YP_001676309.1| DNA-directed RNA polymerase subunit alpha [Shewanella halifaxensis
           HAW-EB4]
 gi|167356037|gb|ABZ78650.1| DNA-directed RNA polymerase, alpha subunit [Shewanella halifaxensis
           HAW-EB4]
          Length = 329

 Score =  352 bits (903), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 144/333 (43%), Positives = 215/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVNPTRARVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVVIEGKDEAMLTLSKSGAGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  V M + V +G GYVPA        ++ PIG + +D+ +S
Sbjct: 118 DGDVTIMNPDHVICHLTGNNDVSMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   +  
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFVELRDVT 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +    +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 ETAPVE---EKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>gi|260206828|ref|ZP_05774319.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis K85]
 gi|289576193|ref|ZP_06456420.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis K85]
 gi|289540624|gb|EFD45202.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis K85]
          Length = 347

 Score =  352 bits (903), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 118/306 (38%), Positives = 188/306 (61%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
            +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T
Sbjct: 15  TDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVT 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           +IILN+K + +    D    + + K+GPG VTAGDI     + V NP   I  L+    +
Sbjct: 75  EIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIATLNDKGKL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL +
Sbjct: 135 EVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLIL 194

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T  SI+  D++A A + L +  G+        + ++   +        +    +++L
Sbjct: 195 DVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALPIDDL 254

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  + P 
Sbjct: 255 DLTVRSYNCLKREGVHIVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPPS 314

Query: 324 WPPESI 329
           + P  +
Sbjct: 315 FDPSEV 320


>gi|116624174|ref|YP_826330.1| DNA-directed RNA polymerase subunit alpha [Candidatus Solibacter
           usitatus Ellin6076]
 gi|122253110|sp|Q01WC0|RPOA_SOLUE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116227336|gb|ABJ86045.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Solibacter
           usitatus Ellin6076]
          Length = 347

 Score =  352 bits (903), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 142/316 (44%), Positives = 205/316 (64%), Gaps = 1/316 (0%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           ++   KP  +         E   +  A+P  RGF  T+GN+LRRVL+SS+ GAAITAV+I
Sbjct: 2   FKGFQKPKRL-VANTETLTERYGMFTAQPFQRGFGTTIGNSLRRVLLSSIEGAAITAVRI 60

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           +GV HE S I GV ED TDIILN+K I  K+S D  K V +     G V +G I+T  D+
Sbjct: 61  EGVEHEFSPIPGVVEDATDIILNLKQIPFKISSDGIKTVRLSVDSHGDVRSGQIETDADV 120

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVL+ D  +  +     + +E+ +  G GYV A  +  E+  +G I ID+++SP++KV++
Sbjct: 121 EVLDRDVHVATVSEGGKLNIEMRLKSGRGYVSADKNFDEDLALGYIPIDSVHSPVRKVNF 180

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+AR GQ+ DYDKL++ + T+G+++ +DS+  A+++L+D + +FINFEE  ++ +E  
Sbjct: 181 AVEAARLGQMTDYDKLTLEVWTNGAVSPQDSIGYAAKLLKDHMTIFINFEEVPEQTEEIS 240

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                  N  L + VEELELSVRS NCL+  NI  +G+L+Q+TEA+MLR  NFGRKSL E
Sbjct: 241 ERGMDKMNEVLNRSVEELELSVRSYNCLKNANIQSIGELVQKTEAEMLRTKNFGRKSLNE 300

Query: 306 IKGVLGTMGLFLGMNL 321
           IK +L  MGL LGM +
Sbjct: 301 IKEILANMGLSLGMRI 316


>gi|317485796|ref|ZP_07944660.1| DNA-directed RNA polymerase [Bilophila wadsworthia 3_1_6]
 gi|316922902|gb|EFV44124.1| DNA-directed RNA polymerase [Bilophila wadsworthia 3_1_6]
          Length = 347

 Score =  352 bits (903), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 154/335 (45%), Positives = 215/335 (64%), Gaps = 1/335 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW +L++P  I        +        EPL RG+  T+GNALRRVL+SSL+GAA  AV
Sbjct: 13  RNWAKLVRPEQI-VCDSDPNDTMYGKFTYEPLERGYGVTIGNALRRVLLSSLQGAAFVAV 71

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I GV HE ++I GV ED+TD+ILNIK + L M+ D  + +T+     G VTA DI T  
Sbjct: 72  KISGVQHEFTTIPGVLEDITDVILNIKQVRLGMTTDEPQHLTLSVSKKGPVTAADIMTNA 131

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           ++EVLNP+  I  L  D  + ME  V  G GYVPA  H    D IGLI +DA +SP++KV
Sbjct: 132 NVEVLNPELHIATLTEDMELSMEFEVRMGKGYVPADMHEGLPDTIGLIKLDASFSPVRKV 191

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +YTVE AR GQ+ +YDKL + + TDGS+  ED++A +++I++DQ+ +FI+F+E       
Sbjct: 192 AYTVEQARVGQMTNYDKLILEVWTDGSVLPEDAIAYSAKIIKDQISVFISFDERISGESG 251

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                S   N  L K ++ELELSVR+TNCLR  NI  +G+L+QR EA+ML+  NFG+KSL
Sbjct: 252 GEGGGSADINDNLFKGIDELELSVRATNCLRSANIATVGELVQRPEAEMLKTKNFGKKSL 311

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
            EIK VL +MGL  GM + ++  +  E   K++ +
Sbjct: 312 DEIKAVLESMGLDFGMKIDNFEKKYQEWKRKQHHE 346


>gi|237653970|ref|YP_002890284.1| DNA-directed RNA polymerase subunit alpha [Thauera sp. MZ1T]
 gi|237625217|gb|ACR01907.1| DNA-directed RNA polymerase, alpha subunit [Thauera sp. MZ1T]
          Length = 326

 Score =  352 bits (903), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 153/333 (45%), Positives = 216/333 (64%), Gaps = 10/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N   L+KP  I+       +     +  EP  RGF HTLGNALRR+L+SSL G A T
Sbjct: 1   MQSNA--LLKPRIIDVQSTSPVQ---ARVTMEPFERGFGHTLGNALRRILLSSLPGHAPT 55

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I+GVLHE S++ GV ED+ D++LN+KG+  K++G S   V + K G GVVTA DI+ 
Sbjct: 56  EVTIEGVLHEYSTLDGVREDIVDLLLNLKGVVFKLNGRSEVTVRLAKAGEGVVTAADIEV 115

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSP 179
            +D+E++NPDHVI +L     + M++ V +G GYVP        E+  IG + +DA + P
Sbjct: 116 GHDVEIINPDHVIAHLAPGGKLDMQIKVEEGRGYVPGNSRPENAESKSIGRVVLDASFGP 175

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +++VSY VESAR  Q  D D+L + I+T+G++  E+++  A+R+L DQL +F + E    
Sbjct: 176 VRRVSYLVESARVEQRTDLDRLIIDIETNGAVDPEEAIRYAARVLMDQLSVFADLEGTAP 235

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           E    +   S   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G
Sbjct: 236 ER---VEAASPTIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTETELLKTPNLG 292

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEEL 332
           RKSL EIK VL + GL LGM L +WPP  +E+L
Sbjct: 293 RKSLNEIKEVLASRGLTLGMKLENWPPAGLEKL 325


>gi|212634854|ref|YP_002311379.1| DNA-directed RNA polymerase subunit alpha [Shewanella piezotolerans
           WP3]
 gi|212556338|gb|ACJ28792.1| DNA-directed RNA polymerase [Shewanella piezotolerans WP3]
          Length = 329

 Score =  352 bits (903), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 145/333 (43%), Positives = 215/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVNPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVVIEGKDEAMLTLSKSGAGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
             D+ V+NPDHVIC+L  +  V M + V +G GYVPA        ++ PIG + +D+ +S
Sbjct: 118 DGDVTVMNPDHVICHLTGNNEVSMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   +  
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFVELRDVT 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +    +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 EAAPVE---EKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>gi|326383232|ref|ZP_08204920.1| DNA-directed RNA polymerase subunit alpha [Gordonia neofelifaecis
           NRRL B-59395]
 gi|326197982|gb|EGD55168.1| DNA-directed RNA polymerase subunit alpha [Gordonia neofelifaecis
           NRRL B-59395]
          Length = 350

 Score =  352 bits (903), Expect = 6e-95,   Method: Composition-based stats.
 Identities = 122/319 (38%), Positives = 193/319 (60%), Gaps = 4/319 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E ++     ENR+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLSEEVI----AENRSKFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+T+IILN+KG+ +    D    + + K+GPG VT  DI     + V NP
Sbjct: 62  EFTTVPGVKEDVTNIILNLKGLVVSSEEDEPVTMYVRKQGPGAVTGADIVPPAGVTVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLHIATLNDKGKLEIELVVERGRGYVPAVQNKATGAEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  S+T  D++A A + L +  G+        + ++   + +  
Sbjct: 182 RVEQRTDFDRLVLDVETKNSMTARDALASAGKTLVELFGLARELNVEAEGIEIGPSPQEA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
               A    +E+LEL+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L
Sbjct: 242 DHIAAFSLPIEDLELTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKVKL 301

Query: 311 GTMGLFLGMNLPDWPPESI 329
            ++GL L  +   + P  +
Sbjct: 302 HSLGLALKDSPASFDPSQV 320


>gi|304315969|ref|YP_003851114.1| DNA-directed RNA polymerase, subunit alpha [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302777471|gb|ADL68030.1| DNA-directed RNA polymerase, alpha subunit [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 316

 Score =  351 bits (902), Expect = 6e-95,   Method: Composition-based stats.
 Identities = 137/310 (44%), Positives = 207/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE IV    ++     + EPL RG+  TLGN+LRR+L+SSL GAA   ++IDG
Sbjct: 4   EIEKP-KIE-IVEQSNDDTYAKFVIEPLERGYGITLGNSLRRMLLSSLPGAAAKTIKIDG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T+IILN+K + +K+  D  K V I   G G VTAGDI +  D+E+
Sbjct: 62  VLHEFSTVPGVKEDVTEIILNLKELAVKLYTDEPKIVRIEAEGKGEVTAGDIISDGDVEI 121

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPD  I  L  +  + ME+ + KG GYVP+  ++  N PIG+I +D++++P+KKVSY V
Sbjct: 122 MNPDLHIATLSDNGKLNMEIELVKGKGYVPSDKNKEPNQPIGIIPVDSIFTPVKKVSYNV 181

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV DYDKL+M + T+G+I+ +++++LA++IL D   +F +F E   +++  +  
Sbjct: 182 ENTRVGQVTDYDKLTMEVWTNGTISPKEAISLAAKILIDHFNLFTSFAENYNDMEVLVEK 241

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                +  L   +EEL+LSVRS NCL+   I  + DL+Q+TE +M+++ N G+KSLVE++
Sbjct: 242 SEKKTDKPLDMTIEELDLSVRSYNCLKRAGINTVQDLVQKTEEEMMKVRNLGKKSLVEVE 301

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 302 QKLKALGLSL 311


>gi|15676095|ref|NP_273226.1| DNA-directed RNA polymerase subunit alpha [Neisseria meningitidis
           MC58]
 gi|121634042|ref|YP_974287.1| DNA-directed RNA polymerase subunit alpha [Neisseria meningitidis
           FAM18]
 gi|161871037|ref|YP_001600069.1| DNA-directed RNA polymerase subunit alpha [Neisseria meningitidis
           053442]
 gi|218767142|ref|YP_002341654.1| DNA-directed RNA polymerase subunit alpha [Neisseria meningitidis
           Z2491]
 gi|254805788|ref|YP_003084009.1| DNA-directed RNA polymerase alpha chain [Neisseria meningitidis
           alpha14]
 gi|304388968|ref|ZP_07371015.1| DNA-directed RNA polymerase subunit alpha [Neisseria meningitidis
           ATCC 13091]
 gi|54039275|sp|P66704|RPOA_NEIMB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|54042186|sp|P66703|RPOA_NEIMA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158513130|sp|A1KRJ9|RPOA_NEIMF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|7225386|gb|AAF40625.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           MC58]
 gi|120865748|emb|CAM09477.1| DNA-directed RNA polymerase alpha chain [Neisseria meningitidis
           FAM18]
 gi|121051150|emb|CAM07421.1| DNA-directed RNA polymerase alpha chain [Neisseria meningitidis
           Z2491]
 gi|161596590|gb|ABX74250.1| DNA-directed RNA polymerase alpha chain [Neisseria meningitidis
           053442]
 gi|254669330|emb|CBA08369.1| DNA-directed RNA polymerase alpha chain [Neisseria meningitidis
           alpha14]
 gi|254670763|emb|CBA07039.1| DNA-directed RNA polymerase alpha chain [Neisseria meningitidis
           alpha153]
 gi|254672693|emb|CBA06591.1| DNA-directed RNA polymerase alpha chain [Neisseria meningitidis
           alpha275]
 gi|261391704|emb|CAX49153.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit;
           transcriptase alpha chain; RNA polymerase alpha subunit)
           [Neisseria meningitidis 8013]
 gi|304337102|gb|EFM03289.1| DNA-directed RNA polymerase subunit alpha [Neisseria meningitidis
           ATCC 13091]
 gi|308388384|gb|ADO30704.1| DNA-directed RNA polymerase alpha chain [Neisseria meningitidis
           alpha710]
 gi|316985690|gb|EFV64636.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           H44/76]
 gi|319411348|emb|CBY91759.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit;
           transcriptase alpha chain; RNA polymerase alpha subunit)
           [Neisseria meningitidis WUE 2594]
 gi|325129087|gb|EGC51936.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           N1568]
 gi|325131058|gb|EGC53782.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           OX99.30304]
 gi|325133080|gb|EGC55752.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           M6190]
 gi|325135174|gb|EGC57800.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           M13399]
 gi|325137226|gb|EGC59821.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           M0579]
 gi|325139058|gb|EGC61604.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           ES14902]
 gi|325141181|gb|EGC63681.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           CU385]
 gi|325143258|gb|EGC65597.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           961-5945]
 gi|325145365|gb|EGC67642.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           M01-240013]
 gi|325197455|gb|ADY92911.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           G2136]
 gi|325199381|gb|ADY94836.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           H44/76]
 gi|325202997|gb|ADY98451.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           M01-240149]
 gi|325203288|gb|ADY98741.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           M01-240355]
 gi|325205261|gb|ADZ00714.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           M04-240196]
 gi|325207205|gb|ADZ02657.1| DNA-directed RNA polymerase, alpha subunit [Neisseria meningitidis
           NZ-05/33]
          Length = 328

 Score =  351 bits (902), Expect = 7e-95,   Method: Composition-based stats.
 Identities = 157/333 (47%), Positives = 215/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+          R  +  +P  RGF HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSTTEFLKPRQIDVNTFS---ATRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE S++ G+ ED+ DI+LNIKGI  K+ G S  ++ + K G GVV+AGDI+ 
Sbjct: 58  EVAIAGVLHEYSTVDGIQEDVVDILLNIKGIVFKLHGRSQVQLVLKKSGSGVVSAGDIEL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
            +D+E+LNP HVIC+L  +  + ME+ V +G GY         R EN  IG I +DA +S
Sbjct: 118 PHDVEILNPGHVICHLADNGQIEMEIKVEQGRGYQSVSGRQVVRDENRQIGAIQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI +VS+ VE AR  Q  D DKL + I+TDGSI  E++V  A+RIL DQ+ +F +    +
Sbjct: 178 PISRVSFEVEPARVEQRTDLDKLVLDIETDGSIDPEEAVRSAARILIDQMSIFADL---Q 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
               E++  K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N 
Sbjct: 235 GTPVEEVEEKAPPIDPVLLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 295 GRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 327


>gi|124268601|ref|YP_001022605.1| DNA-directed RNA polymerase subunit alpha [Methylibium
           petroleiphilum PM1]
 gi|158512865|sp|A2SLD1|RPOA_METPP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|124261376|gb|ABM96370.1| DNA-directed RNA polymerase [Methylibium petroleiphilum PM1]
          Length = 333

 Score =  351 bits (902), Expect = 7e-95,   Method: Composition-based stats.
 Identities = 155/335 (46%), Positives = 218/335 (65%), Gaps = 8/335 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEE-ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +Q N   L+KP  I    L   +  +R  +  EP  RG+ HTLGNALRRVL+SS+ G A 
Sbjct: 1   MQTN---LLKPKAINVEPLSAAKGAHRAKVTLEPFERGYGHTLGNALRRVLLSSMVGYAP 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T V I GVLHE S+I GV ED+  ++LN+KG+  ++       + + K G G V AGDIQ
Sbjct: 58  TEVTIAGVLHEYSAIDGVQEDVVHVMLNLKGVVFRLHNRDEVTLVLRKEGEGPVKAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALY 177
           T +D+E++NPDHVI +L     + M++ V KG GYVP    R  ++P    G I +DA +
Sbjct: 118 TPHDVEIINPDHVITHLSQGGKLDMQIKVEKGRGYVPGTMRRFGDEPTKSIGRIVLDASF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++VSYTVESAR  Q  D DKL M I+T+G+IT E+++  +++IL +QL +F   E  
Sbjct: 178 SPVRRVSYTVESARVEQRTDLDKLVMEIETNGAITPEEAIRASAKILVEQLAVFAQLEGQ 237

Query: 238 KKEVKEDINVK-SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
             ++ +    + S  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  
Sbjct: 238 INDIFDAQPAQRSTQFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTETELLKTP 297

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N GRKSL EIK VL + GL LG  L +WPP+ +++
Sbjct: 298 NLGRKSLNEIKEVLASRGLTLGGRLENWPPQGLDK 332


>gi|157960038|ref|YP_001500072.1| DNA-directed RNA polymerase subunit alpha [Shewanella pealeana ATCC
           700345]
 gi|157845038|gb|ABV85537.1| DNA-directed RNA polymerase, alpha subunit [Shewanella pealeana
           ATCC 700345]
          Length = 329

 Score =  351 bits (901), Expect = 7e-95,   Method: Composition-based stats.
 Identities = 144/333 (43%), Positives = 215/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVNPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVVIEGKDEAMLTLSKSGAGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  V M + V +G GYVPA        ++ PIG + +D+ +S
Sbjct: 118 DGDVTIMNPDHVICHLTGNNEVSMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   +  
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFVELRDVT 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +    +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 ETAPVE---EKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>gi|188584865|ref|YP_001916410.1| DNA-directed RNA polymerase, alpha subunit [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|229564254|sp|B2A4Q0|RPOA_NATTJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|179349552|gb|ACB83822.1| DNA-directed RNA polymerase, alpha subunit [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 315

 Score =  351 bits (901), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 132/313 (42%), Positives = 207/313 (66%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE   + +E       + EPL RG+  TLGN+LRR+L+SSL GAA+T+V+IDG
Sbjct: 3   EIEKP-QIECHEMNEES-TYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE SSI GV ED T+I+LN+K + LK+  D ++ +T+ K G G VTAGDIQ  +D++V
Sbjct: 61  VLHEFSSIPGVVEDTTEIVLNLKRLALKIHSDENQVLTLEKEGKGPVTAGDIQAGSDVDV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NP+  I  L  D  + ME+T   G GYV A+ ++    PIGLI +D++++P+ K ++ V
Sbjct: 121 INPELHIATLSEDTRLYMEITAKNGRGYVRAERNKEPEQPIGLIPVDSVFTPVTKANFYV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           +  R GQV DYD+L++ + TDGS+  +++V+++++I+Q+ L +FIN  E   +++  +  
Sbjct: 181 DDTRVGQVTDYDRLTLEVWTDGSLKPDEAVSMSAKIMQEHLDLFINLTEKATDMEVMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       +   ++EL+LSVRS NCL+   I  +G+L Q+T  DM+++ N G+KSL E+K
Sbjct: 241 EEDNKEKIMELSIDELDLSVRSYNCLKRAGINTIGELTQKTPEDMMKVRNLGKKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 NKLTELGLSLKDS 313


>gi|161523455|ref|YP_001578467.1| DNA-directed RNA polymerase subunit alpha [Burkholderia multivorans
           ATCC 17616]
 gi|189351772|ref|YP_001947400.1| DNA-directed RNA polymerase subunit alpha [Burkholderia multivorans
           ATCC 17616]
 gi|221201591|ref|ZP_03574629.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           multivorans CGD2M]
 gi|221207334|ref|ZP_03580344.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           multivorans CGD2]
 gi|221213472|ref|ZP_03586447.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           multivorans CGD1]
 gi|238687015|sp|A9ADL9|RPOA_BURM1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|160340884|gb|ABX13970.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           multivorans ATCC 17616]
 gi|189335794|dbj|BAG44864.1| DNA-directed RNA polymerase subunit alpha [Burkholderia multivorans
           ATCC 17616]
 gi|221166924|gb|EED99395.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           multivorans CGD1]
 gi|221172922|gb|EEE05359.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           multivorans CGD2]
 gi|221178407|gb|EEE10816.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           multivorans CGD2M]
          Length = 325

 Score =  351 bits (901), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 157/328 (47%), Positives = 212/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP  I    LG   EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPKIIAVESLG---ENHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVVTAGDI+  +D E
Sbjct: 60  GVVHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVTAGDIELAHDCE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKV 183
           V+NPDHVI +L     + +++ V KG GYVP    R   D    IG I +DA +SP+++V
Sbjct: 120 VINPDHVIAHLSKGGKLDVQIKVEKGRGYVPGNVRRYGEDTAKIIGRIVLDASFSPVRRV 179

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VESAR  Q  D DKL M I+T G IT E+++  ++RIL DQL +F   E    E   
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETTGVITPEEAIRQSARILVDQLSVFAALE--GTETAA 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 238 EAPSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|295425627|ref|ZP_06818314.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           amylolyticus DSM 11664]
 gi|295064643|gb|EFG55564.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           amylolyticus DSM 11664]
          Length = 312

 Score =  351 bits (901), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 135/310 (43%), Positives = 196/310 (63%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDG
Sbjct: 3   EFEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK + D  K + +   GP  VTA D++  +D+EV
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSNSDEQKVIELDVEGPATVTADDLKVDSDVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + M++ V  G GYV A  +++E+ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMQIAVKNGRGYVAASDNKSEDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL+  I TDGSI   D+++ A+ IL +   +F + +   K  +  +  
Sbjct: 179 ESTRVGKRDDFDKLTFEIWTDGSINPNDALSFAANILVEHFKVFESADADNKFSEVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+R+ N GRKSL E+K
Sbjct: 239 EDNKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELTDKSEADMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLADLGLSL 308


>gi|251793851|ref|YP_003008583.1| DNA-directed RNA polymerase subunit alpha [Aggregatibacter
           aphrophilus NJ8700]
 gi|247535250|gb|ACS98496.1| DNA-directed RNA polymerase, alpha subunit [Aggregatibacter
           aphrophilus NJ8700]
          Length = 329

 Score =  351 bits (901), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 150/334 (44%), Positives = 224/334 (67%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    +  ++ EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTQAKVVLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVLLTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++NP+HVIC+L D +A + M + V +G GYVPA     ++ E+ PIG + +DA Y
Sbjct: 118 DGDVEIVNPEHVICHLTDENASINMRIRVQRGRGYVPASARAQNQDEDRPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  ED++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLVIELETNGTIDPEDAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    +I  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EIKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|256618354|ref|ZP_05475200.1| DNA-directed RNA polymerase [Enterococcus faecalis ATCC 4200]
 gi|256597881|gb|EEU17057.1| DNA-directed RNA polymerase [Enterococcus faecalis ATCC 4200]
          Length = 312

 Score =  351 bits (901), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 138/313 (44%), Positives = 202/313 (64%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP  IE I    E  +    + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDG
Sbjct: 3   EFEKPR-IEKI---DENRDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILNIKG+ LK+  +  K + I   GP  VTAGDI   +D+E+
Sbjct: 59  VLHEFSTIPGVREDVTQIILNIKGLALKLYAEEEKTLEIDITGPATVTAGDIIVDSDVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D VIC++   A     LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y V
Sbjct: 119 LNKDLVICSVAEGATFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G+  D+DKL+M I TDGSI  +++++LA++I+ + L +F+N  +  K  +  +  
Sbjct: 179 ENTRVGRRDDFDKLTMEIWTDGSIIPQEALSLAAKIMTEHLDIFVNLTDEAKNAEIMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E+K
Sbjct: 239 EETQKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTNKSEPEMIKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 LNLHDLGLGLRKD 311


>gi|223042028|ref|ZP_03612209.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus minor
           202]
 gi|198246530|gb|ACH82222.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus minor
           202]
          Length = 329

 Score =  351 bits (901), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 223/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ +    + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVN---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G VTAGDI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQSKDDVVLTLNKSGIGPVTAGDITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALY 177
             D+E++NPDHVIC+L D +A + M + V +G GYVPA      + ++ PIG + +DA +
Sbjct: 118 DGDVEIVNPDHVICHLTDKNASINMRIRVQRGRGYVPASARIHAQDDDRPIGRLLVDARF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|74316448|ref|YP_314188.1| DNA-directed RNA polymerase subunit alpha [Thiobacillus
           denitrificans ATCC 25259]
 gi|90110875|sp|Q3SLM4|RPOA_THIDA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|74055943|gb|AAZ96383.1| DNA-directed RNA polymerase, alpha subunit [Thiobacillus
           denitrificans ATCC 25259]
          Length = 326

 Score =  351 bits (901), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 155/331 (46%), Positives = 216/331 (65%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  +E   + +       +I EP  RG+ HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQ-SATEFLKPRIVE---VDRASPLHAKVIMEPFERGYGHTLGNALRRILLSSMVGYAPT 56

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GV+HE S+I+GV ED+ DI+LN+KGI  KM G +   + + K G GVVTAGDI+ 
Sbjct: 57  EVAISGVVHEYSTIEGVQEDVVDILLNLKGIAFKMHGKAEAILKVSKSGEGVVTAGDIEV 116

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSP 179
            +DIEVLNPDHVI +L     + ME+ +  G GY PA   +   E   +G I +DA +SP
Sbjct: 117 GHDIEVLNPDHVIAHLTKGGKLDMEIKIEAGRGYQPATARKVSEETRAVGSILVDASFSP 176

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +++V+Y VESAR  Q  D D+L + I+T+G +  E++V  A+RIL  QL +F + E    
Sbjct: 177 VRRVAYAVESARVEQRTDLDRLVIDIETNGVVEPEEAVRTAARILVSQLSVFADLEGTPA 236

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           E +   + +S   +P LL+ V++LEL+VRS NCL+ ENI ++GDLIQR+E ++LR  N G
Sbjct: 237 ESE---SPRSPQVDPLLLRPVDDLELTVRSANCLKAENIYFIGDLIQRSETELLRTPNLG 293

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           RKSL EIK VL + GL LGM L +WPP  +E
Sbjct: 294 RKSLNEIKDVLASKGLSLGMKLENWPPAGLE 324


>gi|256830513|ref|YP_003159241.1| DNA-directed RNA polymerase, alpha subunit [Desulfomicrobium
           baculatum DSM 4028]
 gi|256579689|gb|ACU90825.1| DNA-directed RNA polymerase, alpha subunit [Desulfomicrobium
           baculatum DSM 4028]
          Length = 348

 Score =  351 bits (901), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 143/337 (42%), Positives = 218/337 (64%), Gaps = 2/337 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW EL++P  +E     +  +     + EPL RGF  T+GNALRRVL+SSL+GAA  +V
Sbjct: 14  RNWAELVRPEQLEKDP--KCNDMYGRFVCEPLERGFGTTIGNALRRVLLSSLQGAAPVSV 71

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
            I G+ HE ++I GV ED+TDI+LN+K + + M+    +RV +     G VTA  I    
Sbjct: 72  NIQGIQHEFTTIPGVTEDITDIVLNLKQLRVAMNTPEPQRVQLIANAKGEVTASAIVENQ 131

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            I++LNP+  I  L  D  + M L    G GYVPA+ H   ++ IG+IT+D+ +SPI+KV
Sbjct: 132 HIKILNPELHIATLSEDIDLVMNLEFRMGKGYVPAEMHEDLDNEIGVITLDSSFSPIRKV 191

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE AR GQ+ +YDKL + + TDGSIT +D++A +++IL++QL +FINF+E   ++++
Sbjct: 192 AYAVEQARVGQMTNYDKLIIEVWTDGSITPDDALAFSAKILKEQLTVFINFDEGSADIEK 251

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             +      N  L K +E+LEL VR++NCL+   I  +G+L+Q+TEAD+L+  NFGRKSL
Sbjct: 252 AKSKPQDKINENLFKNIEDLELPVRASNCLKSAGIHIVGELVQKTEADLLKTKNFGRKSL 311

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
            +I+ VL +MGL  G+ + ++     + L +  ED+ 
Sbjct: 312 EDIRRVLESMGLDFGIRVDNFDELYQDWLKRNEEDEA 348


>gi|241759603|ref|ZP_04757704.1| DNA-directed RNA polymerase, alpha subunit [Neisseria flavescens
           SK114]
 gi|261380584|ref|ZP_05985157.1| DNA-directed RNA polymerase, alpha subunit [Neisseria subflava
           NJ9703]
 gi|241319975|gb|EER56356.1| DNA-directed RNA polymerase, alpha subunit [Neisseria flavescens
           SK114]
 gi|284796552|gb|EFC51899.1| DNA-directed RNA polymerase, alpha subunit [Neisseria subflava
           NJ9703]
          Length = 328

 Score =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 156/333 (46%), Positives = 215/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+   L      R  +  +P  RGF HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSTTEFLKPRQIDVDTLSS---TRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE S+I GV ED+ D++LNIKGI  K+ G +  ++T+ K G G V AGDI  
Sbjct: 58  EVVISGVLHEYSTIDGVQEDVVDVLLNIKGIVFKLHGRNQVQLTLKKTGAGAVVAGDIDL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
            +D+E++NP+HVIC+L  +  + ME+ V +G GY         R EN  IG I +DA +S
Sbjct: 118 PHDVEIINPEHVICHLADNGQIDMEIKVEQGRGYQSVSGRRVLRDENKQIGAIQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI +VS+ VE AR  Q  D DKL + I+T+GSI  E++V  A+RIL DQ+ +F +    +
Sbjct: 178 PISRVSFEVEPARVEQRTDLDKLVLDIETNGSIDPEEAVRSAARILIDQMSIFADL---Q 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
               E++  K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N 
Sbjct: 235 GTPVEEVEEKAPPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 295 GRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 327


>gi|229917331|ref|YP_002885977.1| DNA-directed RNA polymerase subunit alpha [Exiguobacterium sp.
           AT1b]
 gi|229468760|gb|ACQ70532.1| DNA-directed RNA polymerase, alpha subunit [Exiguobacterium sp.
           AT1b]
          Length = 314

 Score =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 131/310 (42%), Positives = 198/310 (63%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+TAVQIDG
Sbjct: 3   EIEKP-KIETVEIS-EDATFGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTAVQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T I+LN+K + LK+  +  K + I     G VTA DI   +D+E+
Sbjct: 61  VLHEFSTIDGVVEDVTQIVLNLKKLALKVYSEEEKTLEINVSSAGAVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  L  +A +RM LT  +G GYV A+ ++ ++ PIG+I ID++Y+PI++V+Y V
Sbjct: 121 LNPELHIATLADNATLRMRLTARRGRGYVQAEDNKRDDMPIGVIPIDSIYTPIQRVNYEV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           +  R GQ   +DKL + + TDGSI  E++V+L ++IL + L +F+   +     +  +  
Sbjct: 181 DKTRVGQDASFDKLLLDVWTDGSIRPEEAVSLGAKILTEHLNIFVGLTDEALNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E++
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKSEEEMMKVRNLGRKSLEEVQ 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 HKLDELGLGL 310


>gi|298370566|ref|ZP_06981881.1| DNA-directed RNA polymerase, alpha subunit [Neisseria sp. oral
           taxon 014 str. F0314]
 gi|298281176|gb|EFI22666.1| DNA-directed RNA polymerase, alpha subunit [Neisseria sp. oral
           taxon 014 str. F0314]
          Length = 328

 Score =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 158/333 (47%), Positives = 216/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+   L      R  +  +P  RGF HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSTTEFLKPRQIDVDTLST---TRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE S++ GV ED+ DI+LNIKGI  K+ G S  ++T+ K G G V AGDI+ 
Sbjct: 58  EVAIAGVLHEYSTVDGVQEDVVDILLNIKGIVFKLYGRSQVQLTLKKSGTGTVVAGDIEL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
            +D+E++NP+HVIC+L  +  + ME+ V +G GY         R EN  IG I +DA +S
Sbjct: 118 PHDVEIINPEHVICHLSDNGQIEMEIKVEQGRGYQSVSGRRVFRDENKQIGAIQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI +VS+ VE AR  Q  D DKL + I+TDGS+  E++V  A+RIL DQ+ +F +    +
Sbjct: 178 PISRVSFEVEPARVEQRTDLDKLVLDIETDGSLDPEEAVRSAARILIDQMSIFADL---Q 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
               E+I  K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N 
Sbjct: 235 GTPVEEIEEKAPPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 295 GRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 327


>gi|225076420|ref|ZP_03719619.1| hypothetical protein NEIFLAOT_01465 [Neisseria flavescens
           NRL30031/H210]
 gi|224952268|gb|EEG33477.1| hypothetical protein NEIFLAOT_01465 [Neisseria flavescens
           NRL30031/H210]
          Length = 328

 Score =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 155/333 (46%), Positives = 215/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+   L      R  +  +P  RGF HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSTTEFLKPRQIDVDTLSS---TRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE S+I GV ED+ D++LNIKGI  K+ G +  ++T+ K G G V AGDI  
Sbjct: 58  EVVISGVLHEYSTIDGVQEDVVDVLLNIKGIVFKLHGRNQVQLTLKKTGAGAVVAGDIDL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
            +D+E++NP+HVIC+L  +  + ME+ V +G GY         R +N  IG I +DA +S
Sbjct: 118 PHDVEIINPEHVICHLSDNGQIDMEIKVEQGRGYQSVSGRRVLRDDNKQIGAIQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI +VS+ VE AR  Q  D DKL + I+T+GSI  E++V  A+RIL DQ+ +F +    +
Sbjct: 178 PISRVSFEVEPARVEQRTDLDKLVLDIETNGSIDPEEAVRSAARILIDQMSIFADL---Q 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
               E++  K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N 
Sbjct: 235 GTPVEEVEEKAPPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 295 GRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 327


>gi|323340399|ref|ZP_08080656.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus ruminis
           ATCC 25644]
 gi|323092175|gb|EFZ34790.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus ruminis
           ATCC 25644]
          Length = 314

 Score =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 136/312 (43%), Positives = 202/312 (64%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I   +E  N    + EPL RG+  TLGN+LRR+L+SSL GAAIT VQIDG
Sbjct: 3   EFEKPK----IHKIEESNNHGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAITDVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++KGV ED+T+IILN+K + LK++ +  + +     GP  VTAGDI T +D+E+
Sbjct: 59  VLHEFSTVKGVLEDVTEIILNLKKVALKLNSEEPQSLEFDIVGPKEVTAGDISTNSDVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
           LNPD  IC +   A     +T +KG GYV A  ++   ++ PIG++ ID++Y+PI++V+Y
Sbjct: 119 LNPDLYICTVADGASFHARMTANKGRGYVSANENKAKADDMPIGVLAIDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE  R GQ  DYDKL++ + T+GSIT  ++++L+++IL + L +F+N  +  K  +  +
Sbjct: 179 QVEKTRVGQKNDYDKLTLDVWTNGSITPSEAISLSAKILTEHLALFVNLTDEAKNAEIMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   +EEL+LSVRS NCL+  +I  +  L  ++E+DM+++ N GRKSL E
Sbjct: 239 EKEETHKEKMLEMTIEELDLSVRSYNCLKRASINTVQALTNKSESDMMKVRNLGRKSLEE 298

Query: 306 IKGVLGTMGLFL 317
           +K  L  +GL L
Sbjct: 299 VKAKLADLGLSL 310


>gi|312795804|ref|YP_004028726.1| DNA-directed RNA polymerase alpha chain [Burkholderia rhizoxinica
           HKI 454]
 gi|312167579|emb|CBW74582.1| DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) [Burkholderia
           rhizoxinica HKI 454]
          Length = 325

 Score =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 152/328 (46%), Positives = 213/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP  I    LG   +N   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPKIIAVDSLG---DNHAKVVMEPFERGYGHTLGNALRRVLLSSMIGYAPTEVTIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVV AGDI+  +D E
Sbjct: 60  GVVHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVIAGDIEVPHDCE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKV 183
           V+NP+HVI +L     + +++ V KG GYVP    R  ++    IG I +DA +SP+++V
Sbjct: 120 VINPEHVIAHLSKGGKLDVQIKVEKGRGYVPGNVRRYGDESAKVIGRIVLDASFSPVRRV 179

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL DQL +F   E    E   
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALE--GTETTA 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 238 EAPSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|154498913|ref|ZP_02037291.1| hypothetical protein BACCAP_02905 [Bacteroides capillosus ATCC
           29799]
 gi|150271753|gb|EDM98979.1| hypothetical protein BACCAP_02905 [Bacteroides capillosus ATCC
           29799]
          Length = 315

 Score =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 137/313 (43%), Positives = 195/313 (62%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE  V    + +    + EPL RG+  TLGN+LRR+L+SSL G A+T+++I G
Sbjct: 3   EIEKPR-IE-CVENPGDGSYGKYVVEPLERGYGTTLGNSLRRILLSSLPGTAVTSIKIAG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE  SI GV ED+T+I+LN+K I  K+  +  K V I   G   VTAGDI+   ++EV
Sbjct: 61  VQHEFCSIPGVKEDVTEIVLNVKSIIAKLHCEGVKTVYIEASGECEVTAGDIKADGEVEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  DA + MELT+S G GYVPA  ++   + IG+I +D++Y+P++KV+YTV
Sbjct: 121 LNPDLHIATLGPDASLNMELTLSHGRGYVPADRNKPAQNIIGVIPVDSVYTPVRKVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R G   D+DKL++ + T+G+IT  D+V+L +RIL D   +F +  E        +  
Sbjct: 181 EPTRVGDQTDFDKLTLEVWTNGTITARDAVSLGARILCDHFVLFTDLSETMGNKSTVVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                +  L   +EEL+LSVRS NCL+  NI  + DLI +TE +M+++ N GRKSL E+ 
Sbjct: 241 AEAQRDKVLEMTIEELDLSVRSFNCLKRANINTVEDLISKTEDEMMKVRNLGRKSLEEVV 300

Query: 308 GVLGTMGLFLGMN 320
             L  MGL L  +
Sbjct: 301 NKLAMMGLSLASD 313


>gi|69247195|ref|ZP_00604257.1| DNA-directed RNA polymerase [Enterococcus faecium DO]
 gi|227550745|ref|ZP_03980794.1| DNA-directed RNA polymerase [Enterococcus faecium TX1330]
 gi|257878750|ref|ZP_05658403.1| DNA directed RNA polymerase [Enterococcus faecium 1,230,933]
 gi|257881392|ref|ZP_05661045.1| DNA directed RNA polymerase [Enterococcus faecium 1,231,502]
 gi|257885659|ref|ZP_05665312.1| DNA directed RNA polymerase [Enterococcus faecium 1,231,501]
 gi|257887996|ref|ZP_05667649.1| DNA directed RNA polymerase [Enterococcus faecium 1,141,733]
 gi|257890609|ref|ZP_05670262.1| DNA directed RNA polymerase [Enterococcus faecium 1,231,410]
 gi|257893200|ref|ZP_05672853.1| DNA directed RNA polymerase [Enterococcus faecium 1,231,408]
 gi|257896385|ref|ZP_05676038.1| DNA directed RNA polymerase [Enterococcus faecium Com12]
 gi|257899360|ref|ZP_05679013.1| DNA directed RNA polymerase [Enterococcus faecium Com15]
 gi|258615185|ref|ZP_05712955.1| DNA-directed RNA polymerase subunit alpha [Enterococcus faecium DO]
 gi|260558313|ref|ZP_05830509.1| DNA directed RNA polymerase [Enterococcus faecium C68]
 gi|261207018|ref|ZP_05921707.1| DNA directed RNA polymerase [Enterococcus faecium TC 6]
 gi|289565347|ref|ZP_06445797.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           D344SRF]
 gi|293379471|ref|ZP_06625615.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           PC4.1]
 gi|293553904|ref|ZP_06674510.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E1039]
 gi|293562972|ref|ZP_06677439.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E1162]
 gi|293567906|ref|ZP_06679247.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E1071]
 gi|293570709|ref|ZP_06681759.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E980]
 gi|294615368|ref|ZP_06695241.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E1636]
 gi|294618294|ref|ZP_06697875.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E1679]
 gi|294621104|ref|ZP_06700295.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           U0317]
 gi|314937634|ref|ZP_07844960.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0133a04]
 gi|314942867|ref|ZP_07849680.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0133C]
 gi|314947997|ref|ZP_07851401.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0082]
 gi|314950914|ref|ZP_07853983.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0133A]
 gi|314991438|ref|ZP_07856915.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0133B]
 gi|314995041|ref|ZP_07860161.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0133a01]
 gi|68194960|gb|EAN09428.1| DNA-directed RNA polymerase [Enterococcus faecium DO]
 gi|227180206|gb|EEI61178.1| DNA-directed RNA polymerase [Enterococcus faecium TX1330]
 gi|257812978|gb|EEV41736.1| DNA directed RNA polymerase [Enterococcus faecium 1,230,933]
 gi|257817050|gb|EEV44378.1| DNA directed RNA polymerase [Enterococcus faecium 1,231,502]
 gi|257821515|gb|EEV48645.1| DNA directed RNA polymerase [Enterococcus faecium 1,231,501]
 gi|257824050|gb|EEV50982.1| DNA directed RNA polymerase [Enterococcus faecium 1,141,733]
 gi|257826969|gb|EEV53595.1| DNA directed RNA polymerase [Enterococcus faecium 1,231,410]
 gi|257829579|gb|EEV56186.1| DNA directed RNA polymerase [Enterococcus faecium 1,231,408]
 gi|257832950|gb|EEV59371.1| DNA directed RNA polymerase [Enterococcus faecium Com12]
 gi|257837272|gb|EEV62346.1| DNA directed RNA polymerase [Enterococcus faecium Com15]
 gi|260075487|gb|EEW63793.1| DNA directed RNA polymerase [Enterococcus faecium C68]
 gi|260078646|gb|EEW66348.1| DNA directed RNA polymerase [Enterococcus faecium TC 6]
 gi|289162837|gb|EFD10687.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           D344SRF]
 gi|291589491|gb|EFF21298.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E1071]
 gi|291591742|gb|EFF23378.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E1636]
 gi|291595388|gb|EFF26700.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E1679]
 gi|291599340|gb|EFF30366.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           U0317]
 gi|291601956|gb|EFF32202.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E1039]
 gi|291605098|gb|EFF34565.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E1162]
 gi|291609181|gb|EFF38453.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           E980]
 gi|292641994|gb|EFF60160.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           PC4.1]
 gi|313590767|gb|EFR69612.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0133a01]
 gi|313593918|gb|EFR72763.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0133B]
 gi|313596923|gb|EFR75768.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0133A]
 gi|313598339|gb|EFR77184.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0133C]
 gi|313643011|gb|EFS07591.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0133a04]
 gi|313645595|gb|EFS10175.1| DNA-directed RNA polymerase, alpha subunit [Enterococcus faecium
           TX0082]
          Length = 312

 Score =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 139/310 (44%), Positives = 199/310 (64%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDG
Sbjct: 3   EFEKPR----IAKIDEEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+IKGV ED+T IILNIKG+ LKM G   K + I   GP  VTAGDI   +D+E+
Sbjct: 59  VLHEFSTIKGVREDVTQIILNIKGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D  IC++   A     LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y V
Sbjct: 119 LNKDMYICSVSEGATFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G   D+DKL+M I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  
Sbjct: 179 ENTRVGHREDFDKLTMEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E+K
Sbjct: 239 EETQKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTNKSEPEMIKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 AKLHDLGLGL 308


>gi|301628933|ref|XP_002943603.1| PREDICTED: DNA-directed RNA polymerase subunit alpha-like [Xenopus
           (Silurana) tropicalis]
          Length = 332

 Score =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 163/337 (48%), Positives = 220/337 (65%), Gaps = 13/337 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N   L+KP  I+   LG    NR  +  EP  RG+ HTLGNALRRVL+SS+ G A T
Sbjct: 1   MQTN---LLKPKTIQVEQLG---HNRAKVELEPFERGYGHTLGNALRRVLLSSMVGYAAT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE SSI GV ED+ +I+LN+KG+  K+       +++ K G GVVTA DIQT
Sbjct: 55  EVTIVGVLHEYSSIDGVQEDVVNILLNLKGVVFKLYNRDEVTLSLRKDGEGVVTARDIQT 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYS 178
            +D+E++NPDHVI +L   A + M++ V KG GYVP    R  ++P    G I +DA +S
Sbjct: 115 PHDVEIINPDHVIAHLSQGAKLDMQIKVEKGRGYVPGNVRRYGDEPTKTIGRIVLDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+K+VSYTVESAR  Q  D DKL + I+T+G+IT E++V  +++IL +QL +F   E   
Sbjct: 175 PVKRVSYTVESARVEQRTDLDKLVVEIETNGAITAEEAVRASAKILVEQLAVFAQLEGGD 234

Query: 239 KE----VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
            +            +  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+
Sbjct: 235 IDGMLIGSGASRSSATTFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLK 294

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
             N GRKSL EIK VL + GL LGM L +WPP  +++
Sbjct: 295 TPNLGRKSLNEIKEVLASRGLTLGMKLENWPPAGLDK 331


>gi|121603260|ref|YP_980589.1| DNA-directed RNA polymerase subunit alpha [Polaromonas
           naphthalenivorans CJ2]
 gi|158513921|sp|A1VJ40|RPOA_POLNA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|120592229|gb|ABM35668.1| DNA-directed RNA polymerase subunit alpha [Polaromonas
           naphthalenivorans CJ2]
          Length = 330

 Score =  350 bits (899), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 161/335 (48%), Positives = 216/335 (64%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N   L+KP  I    LG    NR  +  EP  RG+ HTLGNALRRVL+SS+ G A T
Sbjct: 1   MQTN---LLKPKTINVEQLG---ANRAKVTLEPFERGYGHTLGNALRRVLLSSMVGHAAT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE SSI GV ED+ +I+LN+KG+  K+       +++ K G G +TA DIQT
Sbjct: 55  EVTIAGVLHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGPITAADIQT 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYS 178
            +D+E++NPDHVI NL     + M++ V  G GYVP    R  ++     G I +DA +S
Sbjct: 115 PHDVEIVNPDHVIMNLSHGGKIDMQIKVENGRGYVPGNVRRYGDESPKSIGRIVLDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--E 236
           P+K+VSYTVESAR  Q  D DKL + I+T+G++T ED+V  +++IL +QL +F   E  E
Sbjct: 175 PVKRVSYTVESARVEQRTDLDKLVLEIETNGAVTAEDAVRASAKILVEQLAVFAQLEGNE 234

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
               + +     S  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  
Sbjct: 235 LGAIINDPAPRSSQQFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N GRKSL EIK VL + GL LGM L  WPP  +++
Sbjct: 295 NLGRKSLNEIKEVLASRGLTLGMRLESWPPAGLDK 329


>gi|15828059|ref|NP_302322.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium leprae TN]
 gi|221230536|ref|YP_002503952.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium leprae
           Br4923]
 gi|7388099|sp|Q9X798|RPOA_MYCLE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|4539112|emb|CAB39833.1| putative DNA-directed RNA polymerase alpha chain [Mycobacterium
           leprae]
 gi|13093612|emb|CAC30912.1| [alpha] subunit of RNA polymerase [Mycobacterium leprae]
 gi|219933643|emb|CAR72054.1| [alpha] subunit of RNA polymerase [Mycobacterium leprae Br4923]
          Length = 347

 Score =  350 bits (899), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 118/306 (38%), Positives = 187/306 (61%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
            +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T
Sbjct: 15  TDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVT 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           +IILN+KG+ +    D    + + K+GPG VTAGDI     + + NP   I  L+    +
Sbjct: 75  EIILNLKGLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTLHNPGMRIATLNDKGKI 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
             EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++ R  Q  D+DKL +
Sbjct: 135 EAELVVERGRGYVPAVQNRALGAEIGRIPVDSIYSPVLKVTYKVDATRVEQRTDFDKLIL 194

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T  SIT  D++A A + L +  G+        + ++   +        +    +++L
Sbjct: 195 DVETKSSITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALPIDDL 254

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  +   
Sbjct: 255 DLTVRSYNCLKREGVHTVGELVSRTESDLLDIRNFGQKSIDEVKVKLHQLGLSLKDSPDS 314

Query: 324 WPPESI 329
           + P  +
Sbjct: 315 FDPSEV 320


>gi|319639574|ref|ZP_07994321.1| DNA-directed RNA polymerase subunit alpha [Neisseria mucosa C102]
 gi|317399145|gb|EFV79819.1| DNA-directed RNA polymerase subunit alpha [Neisseria mucosa C102]
          Length = 328

 Score =  350 bits (899), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 156/333 (46%), Positives = 215/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+   L      R  +  +P  RGF HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSTTEFLKPRQIDVDTLSS---TRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE S+I GV ED+ D++LNIKGI  K+ G +  ++T+ K G G V AGDI  
Sbjct: 58  EVVISGVLHEYSTIDGVQEDVVDVLLNIKGIVFKLHGRNQVQLTLKKAGAGAVVAGDIDL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
            +D+E++NP+HVIC+L  +  + ME+ V +G GY         R EN  IG I +DA +S
Sbjct: 118 PHDVEIINPEHVICHLSDNGQIDMEIKVEQGRGYQSVSGRRVLRDENKQIGAIQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI +VS+ VE AR  Q  D DKL + I+T+GSI  E++V  A+RIL DQ+ +F +    +
Sbjct: 178 PISRVSFEVEPARVEQRTDLDKLVLDIETNGSIDPEEAVRSAARILIDQMSIFADL---Q 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
               E++  K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N 
Sbjct: 235 GTPVEEVEEKAPPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 295 GRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 327


>gi|221133740|ref|ZP_03560045.1| DNA-directed RNA polymerase subunit alpha [Glaciecola sp. HTCC2999]
          Length = 326

 Score =  350 bits (899), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 146/331 (44%), Positives = 223/331 (67%), Gaps = 9/331 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            +  E +KP  ++   +      R  ++ EPL RGF HTLGNALRR+L+SS+ G A+T V
Sbjct: 2   GSVTEFLKPRLVDIENVS---PTRAKVVLEPLERGFGHTLGNALRRILLSSMPGVAVTEV 58

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G +   +T+ K G G V AGDIQ   
Sbjct: 59  EIDGVLHEYSTKEGVQEDVIEILLNLKGLAVRLEGKTEATLTLVKSGAGAVVAGDIQHDG 118

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPI 180
           D+E++NP+HVIC L  +A V M + V  G GYVPA   R+   ++ PIG + +DA +SP+
Sbjct: 119 DVEIINPEHVICTLTGEAEVSMRIKVETGRGYVPASVRRSSEEDDRPIGRLLVDASFSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++++Y+VESAR  Q  D DKL + ++T+G++  E+++  ++ IL +QL  F++  +  + 
Sbjct: 179 ERIAYSVESARVEQRTDLDKLIIDMETNGTLDPEEAIRRSATILAEQLDAFVDLRDVSQP 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
              +   +   F+P LL+ V++LEL+VRS NCL+ E + Y+GDL+QRTE ++L+  N G+
Sbjct: 239 ---EAKEEKPEFDPILLRPVDDLELTVRSANCLKAEAVQYIGDLVQRTEVELLKTPNLGK 295

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           KSL EIK VL + GL LGM L +WPPESI +
Sbjct: 296 KSLTEIKDVLASRGLSLGMRLENWPPESIAD 326


>gi|53720795|ref|YP_109781.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei K96243]
 gi|53723828|ref|YP_104140.1| DNA-directed RNA polymerase subunit alpha [Burkholderia mallei ATCC
           23344]
 gi|76808919|ref|YP_335114.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei 1710b]
 gi|121599305|ref|YP_994430.1| DNA-directed RNA polymerase subunit alpha [Burkholderia mallei
           SAVP1]
 gi|124385479|ref|YP_001027921.1| DNA-directed RNA polymerase subunit alpha [Burkholderia mallei NCTC
           10229]
 gi|126440174|ref|YP_001060724.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei 668]
 gi|126450024|ref|YP_001083016.1| DNA-directed RNA polymerase subunit alpha [Burkholderia mallei NCTC
           10247]
 gi|126453965|ref|YP_001068008.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei 1106a]
 gi|134283239|ref|ZP_01769940.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 305]
 gi|167001673|ref|ZP_02267465.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           PRL-20]
 gi|167721551|ref|ZP_02404787.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei DM98]
 gi|167740525|ref|ZP_02413299.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei 14]
 gi|167817730|ref|ZP_02449410.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei 91]
 gi|167826127|ref|ZP_02457598.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei 9]
 gi|167847639|ref|ZP_02473147.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei B7210]
 gi|167896211|ref|ZP_02483613.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei 7894]
 gi|167904593|ref|ZP_02491798.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei NCTC 13177]
 gi|167912858|ref|ZP_02499949.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei 112]
 gi|167920817|ref|ZP_02507908.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           pseudomallei BCC215]
 gi|217424731|ref|ZP_03456228.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 576]
 gi|226198177|ref|ZP_03793748.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei Pakistan 9]
 gi|237814119|ref|YP_002898570.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei MSHR346]
 gi|238562959|ref|ZP_00439640.2| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei GB8
           horse 4]
 gi|242316674|ref|ZP_04815690.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 1106b]
 gi|254174996|ref|ZP_04881657.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           ATCC 10399]
 gi|254180365|ref|ZP_04886963.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 1655]
 gi|254190328|ref|ZP_04896836.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei Pasteur 52237]
 gi|254198455|ref|ZP_04904876.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei S13]
 gi|254201213|ref|ZP_04907577.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           FMH]
 gi|254206554|ref|ZP_04912905.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           JHU]
 gi|254260470|ref|ZP_04951524.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 1710a]
 gi|254300602|ref|ZP_04968047.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 406e]
 gi|254357093|ref|ZP_04973367.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           2002721280]
 gi|61215842|sp|Q62GN1|RPOA_BURMA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61215856|sp|Q63Q37|RPOA_BURPS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|90101574|sp|Q3JMT9|RPOA_BURP1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158513536|sp|A3P087|RPOA_BURP0 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|166229261|sp|A3MRY0|RPOA_BURM7 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|166229262|sp|A2S7K2|RPOA_BURM9 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|166229263|sp|A1V877|RPOA_BURMS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|166229264|sp|A3NEF3|RPOA_BURP6 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|52211209|emb|CAH37198.1| DNA-directed RNA polymerase alpha chain [Burkholderia pseudomallei
           K96243]
 gi|52427251|gb|AAU47844.1| dna-directed rna polymerase alpha chain [Burkholderia mallei ATCC
           23344]
 gi|76578372|gb|ABA47847.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 1710b]
 gi|121228115|gb|ABM50633.1| DNA-directed rna polymerase, alpha subunit [Burkholderia mallei
           SAVP1]
 gi|124293499|gb|ABN02768.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           NCTC 10229]
 gi|126219667|gb|ABN83173.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 668]
 gi|126227607|gb|ABN91147.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 1106a]
 gi|126242894|gb|ABO05987.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           NCTC 10247]
 gi|134245434|gb|EBA45527.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 305]
 gi|147747107|gb|EDK54183.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           FMH]
 gi|147752096|gb|EDK59162.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           JHU]
 gi|148026157|gb|EDK84242.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           2002721280]
 gi|157810631|gb|EDO87801.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 406e]
 gi|157938004|gb|EDO93674.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei Pasteur 52237]
 gi|160696041|gb|EDP86011.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           ATCC 10399]
 gi|169655195|gb|EDS87888.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei S13]
 gi|184210904|gb|EDU07947.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 1655]
 gi|217392187|gb|EEC32212.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 576]
 gi|225929697|gb|EEH25713.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei Pakistan 9]
 gi|237503877|gb|ACQ96195.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei MSHR346]
 gi|238521642|gb|EEP85092.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei GB8
           horse 4]
 gi|242139913|gb|EES26315.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 1106b]
 gi|243062570|gb|EES44756.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia mallei
           PRL-20]
 gi|254219159|gb|EET08543.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           pseudomallei 1710a]
          Length = 325

 Score =  350 bits (899), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 156/328 (47%), Positives = 214/328 (65%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP  I    LG   EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPKIIAVESLG---ENHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVVTAGDI+  +D E
Sbjct: 60  GVVHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVTAGDIELAHDCE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKV 183
           V+NP+HVI +L     + +++ V KG GYVP    R  ++    IG I +DA +SP+++V
Sbjct: 120 VINPNHVIAHLSKGGKLDVQIKVEKGRGYVPGNVRRYGDETAKIIGRIVLDASFSPVRRV 179

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SYTVESAR  Q  D DKL M I+T G IT E+++  ++RIL DQL +F   E    E   
Sbjct: 180 SYTVESARVEQRTDLDKLVMNIETSGVITPEEAIRQSARILVDQLSVFAALE--GTETAA 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 238 EAPSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|83648827|ref|YP_437262.1| DNA-directed RNA polymerase subunit alpha [Hahella chejuensis KCTC
           2396]
 gi|119366687|sp|Q2S937|RPOA_HAHCH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|83636870|gb|ABC32837.1| DNA-directed RNA polymerase, alpha subunit [Hahella chejuensis KCTC
           2396]
          Length = 334

 Score =  350 bits (899), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 147/331 (44%), Positives = 219/331 (66%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  E + P  IE   + Q       +  EPL RGF HTLG+ALRR+L+SS+ G A+ 
Sbjct: 1   MQRSLNEFLTPRTIE---VNQINATHAKVTLEPLERGFGHTLGSALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+++GV ED+ +I+LN+K + +KM       +++ K+G G V A DIQ 
Sbjct: 58  EVEIDGVLHEYSTVEGVQEDVIEILLNLKNLAIKMHNRDEATLSLNKKGAGPVLASDIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYS 178
            +D+E+ NPD VICNL+ +  V+M+L V++G GY PA    + +D     G + +D+ +S
Sbjct: 118 DHDVEIANPDMVICNLNSNGDVKMKLKVARGRGYEPADQRNSADDETRAIGRLQLDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +V+Y VESAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++F++  
Sbjct: 178 PVLRVAYNVESARVEQRTDLDKLVIDLETNGTIDPEEAIRRAATILQQQLAVFVDFDQQN 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +        +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EPE---KVEEQEEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASI 325


>gi|319778699|ref|YP_004129612.1| DNA-directed RNA polymerase alpha subunit [Taylorella equigenitalis
           MCE9]
 gi|317108723|gb|ADU91469.1| DNA-directed RNA polymerase alpha subunit [Taylorella equigenitalis
           MCE9]
          Length = 327

 Score =  350 bits (899), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 151/325 (46%), Positives = 209/325 (64%), Gaps = 7/325 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  I   V+    E    ++ EP  RGF HTLGNALRR+L+SS+ G A T VQI GV
Sbjct: 5   FLKPRTI---VVNPITEFHAKVVMEPFERGFGHTLGNALRRILLSSMTGYAATEVQIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE +SI+GV ED+ DI+LN+KG+  K+ G     +T+ K  PG + A DI+  +D+E++
Sbjct: 62  VHEYASIQGVQEDVVDILLNLKGVVFKLHGREEVTLTLSKSEPGEIRASDIELPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSY 185
           NP+HVI NL     + M + V +G GYVP          +  IG I +DA YSPI++VSY
Sbjct: 122 NPNHVIANLQEGGRLDMHIKVEQGRGYVPGNVRALREDRHHSIGRIILDASYSPIRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+AR GQ  D DKL + I+T+G +T ED+V  A+RIL DQ+ +F + E     + E  
Sbjct: 182 EVENARVGQRTDQDKLILDIETNGVLTPEDAVRQAARILMDQISVFASLEG-SPNMYEAP 240

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
              +   +P LL+ V++LEL+VRS NCL+ EN+ Y+GDLIQ+TE ++L+  N GRKSL E
Sbjct: 241 ARGTPQIDPVLLRSVDDLELTVRSANCLKAENVFYIGDLIQKTENELLKTPNLGRKSLNE 300

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIE 330
           IK VL   GL LGM L +WPP  ++
Sbjct: 301 IKDVLTARGLSLGMKLENWPPIGLD 325


>gi|296131864|ref|YP_003639111.1| DNA-directed RNA polymerase, alpha subunit [Thermincola sp. JR]
 gi|296030442|gb|ADG81210.1| DNA-directed RNA polymerase, alpha subunit [Thermincola potens JR]
          Length = 315

 Score =  350 bits (899), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 140/311 (45%), Positives = 209/311 (67%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+V+IDG
Sbjct: 3   EIEKP-KIECVELS-EDNTYGKFVVEPLERGYGITLGNSLRRILLSSLPGAAVTSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV+ED+TDIILN+K + LKM  D  K + I   GPG V AG+I T  D+E+
Sbjct: 61  VLHEFSTVPGVYEDVTDIILNLKELCLKMYTDEEKVLRIESEGPGEVKAGNIITDADVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  L  DA + ME+ V+KG GYVPA+ ++ ++  IG+I +D+ +SP+++V+Y +
Sbjct: 121 LNPELHIATLSDDARLVMEINVAKGRGYVPAERNKKDDHVIGIIPVDSAFSPVRRVNYYI 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R GQ+ DYDKL++ + T+GSI  +++ +L+++IL + L +FI   E  K+V+  +  
Sbjct: 181 EDTRVGQITDYDKLTLEVWTNGSIRPDEATSLSAKILSEHLRLFIGLTENIKDVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    +  L   +EEL+LSVRS NCL+   I  + +L QRTE DM+++ N G+KSL E+ 
Sbjct: 241 EEEEKDKILEMTIEELDLSVRSYNCLKRAGINTVEELTQRTEEDMIKVRNLGKKSLEEVI 300

Query: 308 GVLGTMGLFLG 318
             L  +GL L 
Sbjct: 301 NKLAELGLSLK 311


>gi|312199992|ref|YP_004020053.1| DNA-directed RNA polymerase, subunit alpha [Frankia sp. EuI1c]
 gi|311231328|gb|ADP84183.1| DNA-directed RNA polymerase, alpha subunit [Frankia sp. EuI1c]
          Length = 350

 Score =  350 bits (898), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 123/307 (40%), Positives = 187/307 (60%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
                E R+  + EPL  GF +TLGN+LRR L+SS+ GA++T+++IDGVLHE S++ GV 
Sbjct: 11  EEPIAEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIRIDGVLHEFSTVPGVK 70

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+TD+ILN+K + +    D    + + K+GPG VTA DI     +EV NP+  +  ++ 
Sbjct: 71  EDVTDVILNLKELVVSSDNDEPTVMYLRKQGPGEVTAADIAPPAGVEVHNPELHLATIND 130

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              + +ELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+ R  Q  D+D
Sbjct: 131 KGKLEIELTVERGRGYVSAAQNKQPGQEIGRIPIDSIYSPVLKVTYKVEATRVEQRTDFD 190

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + ++T  SI+  D++A A + L    G+        + V    + +       L   
Sbjct: 191 KLIVDVETKPSISPRDAMASAGKTLVGLFGLAQELNAEAEGVDIGPSAQDAQLAADLALP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +EE++L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  LG MGL L  
Sbjct: 251 IEEMDLTVRSYNCLKREGIHTIGELVSRSEADLLDIRNFGQKSIDEVKTKLGAMGLQLKD 310

Query: 320 NLPDWPP 326
           + P + P
Sbjct: 311 SPPGFDP 317


>gi|325577151|ref|ZP_08147635.1| DNA-directed RNA polymerase subunit alpha [Haemophilus
           parainfluenzae ATCC 33392]
 gi|301155355|emb|CBW14821.1| RNA polymerase, alpha subunit [Haemophilus parainfluenzae T3T1]
 gi|325160733|gb|EGC72854.1| DNA-directed RNA polymerase subunit alpha [Haemophilus
           parainfluenzae ATCC 33392]
          Length = 329

 Score =  350 bits (898), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 150/334 (44%), Positives = 222/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVILTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALY 177
             D+E++NP HVIC+L D +A + M + V +G GYVPA    H + E+ PIG + +DA Y
Sbjct: 118 DGDVEIVNPSHVICHLTDENASINMRIRVQRGRGYVPASARTHSQNEDRPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|256821687|ref|YP_003145650.1| DNA-directed RNA polymerase subunit alpha [Kangiella koreensis DSM
           16069]
 gi|256795226|gb|ACV25882.1| DNA-directed RNA polymerase, alpha subunit [Kangiella koreensis DSM
           16069]
          Length = 326

 Score =  350 bits (898), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 146/329 (44%), Positives = 218/329 (66%), Gaps = 9/329 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            +  E + P  I+   +   E  +  ++ EP  RGF HTLGN+LRR+L+SS+ GAA+T V
Sbjct: 1   MSATEFLTPRQIK---VESSEGTKARVVLEPFERGFGHTLGNSLRRILLSSMPGAAVTEV 57

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +IDGVLHE S+I+GV ED+ DI+LN+KG+ +++       +T+ K+G GVVTA DI+ V+
Sbjct: 58  EIDGVLHEYSAIEGVQEDVIDILLNLKGLAVRLEDKEVATLTLQKKGEGVVTAADIEEVS 117

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPI 180
             EV+N DH I  L+    + M + +  G GY  +   +    E+  IG++ +DA +SP+
Sbjct: 118 GTEVVNKDHYIATLNKGGALNMRIKIRLGRGYEASNTRKQPEGEDKAIGVLQVDASFSPM 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSYTVESAR  Q  D DKL + ++T+G+I  E+++  ++ ILQ+QL  F++ ++ K+ 
Sbjct: 178 KKVSYTVESARVEQRTDLDKLVLDLETNGTIDPEEAIRRSATILQEQLAAFVDLKDEKQA 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
              +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G+
Sbjct: 238 ---EPEKEEPEIDPILLRPVDDLELTVRSANCLKTENIHYIGDLVQRTEVELLKTPNLGK 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           KSL EIK VL + GL LGM L +WPP SI
Sbjct: 295 KSLTEIKDVLASRGLSLGMRLENWPPSSI 323


>gi|163840858|ref|YP_001625263.1| DNA-directed RNA polymerase subunit alpha [Renibacterium
           salmoninarum ATCC 33209]
 gi|189043843|sp|A9WSR1|RPOA_RENSM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|162954334|gb|ABY23849.1| DNA-directed RNA polymerase alpha chain [Renibacterium salmoninarum
           ATCC 33209]
          Length = 336

 Score =  350 bits (898), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 122/328 (37%), Positives = 194/328 (59%), Gaps = 4/328 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V     +NR+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLSEEVV----SDNRSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+T+IILNIK +++    D      + K+GPGVVTA DI     +E  NP
Sbjct: 62  EFTTVPGVKEDVTEIILNIKNLSVSSEHDEPVVAYLRKQGPGVVTAADIAPPAGVEFHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+      +ELT+ +G GYV A  +++ +  IG I +D++YSP+ KV++ VE+ 
Sbjct: 122 DLHIATLNSKGKFELELTIERGRGYVSAAQNKSGDAEIGRIPVDSIYSPVLKVTFRVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  +I   D+VA A   L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDRLIVDVETKQAIAPRDAVASAGTTLVELFGLARELNTAAEGIEIGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                +   +E+L+L+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L
Sbjct: 242 ALAADMALPIEDLDLTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKYED 338
             +GL L  + P +   +      + +D
Sbjct: 302 VELGLSLKDSPPGFDLAARAAAIDESDD 329


>gi|126697669|ref|YP_001086566.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           630]
 gi|254973760|ref|ZP_05270232.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           QCD-66c26]
 gi|255091150|ref|ZP_05320628.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           CIP 107932]
 gi|255099261|ref|ZP_05328238.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           QCD-63q42]
 gi|255305044|ref|ZP_05349216.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           ATCC 43255]
 gi|255312804|ref|ZP_05354387.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           QCD-76w55]
 gi|255515563|ref|ZP_05383239.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           QCD-97b34]
 gi|255648658|ref|ZP_05395560.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           QCD-37x79]
 gi|260681875|ref|YP_003213160.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           CD196]
 gi|260685473|ref|YP_003216606.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           R20291]
 gi|306518780|ref|ZP_07405127.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           QCD-32g58]
 gi|119366674|sp|Q18CI5|RPOA_CLOD6 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|115249106|emb|CAJ66917.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile]
 gi|260208038|emb|CBA60238.1| DNA-directed RNA polymerase alpha chain [Clostridium difficile
           CD196]
 gi|260211489|emb|CBE01629.1| DNA-directed RNA polymerase alpha chain [Clostridium difficile
           R20291]
          Length = 315

 Score =  350 bits (898), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 128/311 (41%), Positives = 200/311 (64%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  ++ + L  E+      + EPL RG+  T+GNALRR+L+SSL G A+ A++IDG
Sbjct: 3   EIEKP-KVDIVELS-EDYRYGKFVIEPLERGYGITIGNALRRILLSSLPGVAVNAIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T+IIL +K ++  + G+  + + I  +GP  +T  DI    D+E+
Sbjct: 61  VLHEFSTIPGVKEDVTEIILTLKELSATIDGEGSRTLKIEAQGPCSITGADIICPPDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           L+ D  I  LD +A + ME+ V KG GYV A+ ++TEN PIG++ +D++Y+P++KVSY V
Sbjct: 121 LSKDLAIATLDDNAKLNMEIFVDKGRGYVSAEENKTENVPIGVLPVDSIYTPVEKVSYHV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  DYDKL + + T+GSI  ++ ++LA+++L + L +FI+  E    V+  +  
Sbjct: 181 ENTRVGQKTDYDKLVLEVWTNGSINPQEGISLAAKVLVEHLNLFIDLTEHVSSVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N G+KSL E+ 
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVEELANKSEDDMMKVRNLGKKSLEEVI 300

Query: 308 GVLGTMGLFLG 318
             L  +GL L 
Sbjct: 301 QKLEELGLGLK 311


>gi|290477168|ref|YP_003470083.1| RNA polymerase subunit alpha [Xenorhabdus bovienii SS-2004]
 gi|289176516|emb|CBJ83325.1| RNA polymerase, alpha subunit [Xenorhabdus bovienii SS-2004]
          Length = 329

 Score =  350 bits (898), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVQGKDEVILTLNKSGIGPVTAADIIH 117

Query: 122 VNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L    A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDGSASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|326692212|ref|ZP_08229217.1| DNA-directed RNA polymerase subunit alpha [Leuconostoc argentinum
           KCTC 3773]
          Length = 314

 Score =  350 bits (898), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 130/312 (41%), Positives = 191/312 (61%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E+      + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDG
Sbjct: 3   EFEKPN----IHNIEEDARYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE S++ GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+Q   D+EV
Sbjct: 59  VVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDVQGPAEVTAADLQAGADVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
           LNPD  I  +     + M +T  KG GY  A  ++   E  PIG++ +D++Y+PI++V+Y
Sbjct: 119 LNPDLHIATVAAGKSLHMTVTAVKGRGYSSADENKQLREEMPIGVLAVDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R G   DYDKL+  I T+GSI   D+++L ++IL + L +F++      E    +
Sbjct: 179 HVENTRVGARDDYDKLTFDIWTNGSIKPSDALSLGAKILAEHLNLFMDISPVAAEANVMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             + +  + +    +E+L+LSVRS NCL+   I  + +L  RTEADM+++ N GRKSL E
Sbjct: 239 EAEPVAVSASDSAPIEDLDLSVRSYNCLKRAGINTIVELTDRTEADMMKVRNLGRKSLDE 298

Query: 306 IKGVLGTMGLFL 317
           I+  L  MGL  
Sbjct: 299 IQEKLTEMGLGF 310


>gi|257069480|ref|YP_003155735.1| DNA-directed RNA polymerase subunit alpha [Brachybacterium faecium
           DSM 4810]
 gi|256560298|gb|ACU86145.1| DNA-directed RNA polymerase subunit alpha [Brachybacterium faecium
           DSM 4810]
          Length = 331

 Score =  350 bits (898), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 119/329 (36%), Positives = 193/329 (58%), Gaps = 4/329 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V     ENR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLTEEVV----SENRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T++ILNIK + +    D    + + +   G VTA DI     +E+ NP
Sbjct: 62  EFSTVPGVKEDITEVILNIKNLVVSSENDEPVVMYLRREEAGRVTAADITPPAGVEIHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+    + +EL V +G GYV A  ++  +  IG + +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLHIATLNEKGRLEIELIVERGRGYVSAAQNKGVDGEIGRVPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  +I+  D+VA A + L +  G+     +  + ++   +    
Sbjct: 182 RVEQRTDFDKLIVDVETKPAISPRDAVASAGKTLVELFGLAHELNQEAEGIEIGPSPTDQ 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   + +L L+VRS NCL  E +  +G+L  R+EAD+L + NFG+KS+ E+K  L
Sbjct: 242 ALAADLALPINDLNLTVRSYNCLMREGVHTVGELTARSEADLLDIRNFGQKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             +GL L  +   + P +++  +  + D+
Sbjct: 302 ADLGLSLKDSPAGFDPSALDSYSDDFGDQ 330


>gi|121534660|ref|ZP_01666481.1| DNA-directed RNA polymerase, alpha subunit [Thermosinus
           carboxydivorans Nor1]
 gi|121306680|gb|EAX47601.1| DNA-directed RNA polymerase, alpha subunit [Thermosinus
           carboxydivorans Nor1]
          Length = 319

 Score =  350 bits (898), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 139/315 (44%), Positives = 198/315 (62%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  E+     ++ EPL RGF  TLGN+LRRVL+SSL GAA+T+V+IDG
Sbjct: 3   EIEKP-KIEIVEIS-EDNRYGKIVWEPLERGFGITLGNSLRRVLLSSLPGAAVTSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+TDIILN+K + LKM  D  K + I  +G   V AGDI T  D+E+
Sbjct: 61  VLHEFSTIPGVREDVTDIILNLKELCLKMHSDEPKVLRIEAQGERDVKAGDIITDADVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  LD    ++ME+TV +G GYVPA  ++  +  IG+I +D+++SP+ +V+YTV
Sbjct: 121 LNPELHIATLDASGSLKMEITVERGRGYVPADKNKKPDHVIGVIPVDSIFSPVLRVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED--- 244
              R G V DYDKL++ + TDGS+  E++V+ A+ IL   L +F N      E +     
Sbjct: 181 TDTRVGNVTDYDKLTLEVWTDGSMRPEEAVSKAAGILVAHLKLFQNITGTPAEDEAGDGP 240

Query: 245 -INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                       +   +E+L+LSVRS NCL+   I  + +L Q+TE +M+++ N GRKSL
Sbjct: 241 FAETPEETGPKTMEMTIEDLDLSVRSYNCLKRAGINTVAELTQKTEEEMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFLG 318
            E+K  L  +GL L 
Sbjct: 301 EEVKKKLEELGLSLA 315


>gi|83720584|ref|YP_443546.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           thailandensis E264]
 gi|167564390|ref|ZP_02357306.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           oklahomensis EO147]
 gi|167571537|ref|ZP_02364411.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           oklahomensis C6786]
 gi|167582597|ref|ZP_02375471.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           thailandensis TXDOH]
 gi|167620711|ref|ZP_02389342.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           thailandensis Bt4]
 gi|167838186|ref|ZP_02465045.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           thailandensis MSMB43]
 gi|257137668|ref|ZP_05585930.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           thailandensis E264]
 gi|119366670|sp|Q2SU53|RPOA_BURTA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|83654409|gb|ABC38472.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           thailandensis E264]
          Length = 325

 Score =  350 bits (898), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 155/328 (47%), Positives = 213/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP  I    LG   EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPKIIAVESLG---ENHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVVTAGDI+  +D E
Sbjct: 60  GVVHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVTAGDIELAHDCE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKV 183
           V+NP+HVI +L     + +++ V KG GYVP    R  ++    IG I +DA +SP+++V
Sbjct: 120 VINPNHVIAHLSKGGKLDVQIKVEKGRGYVPGNVRRYGDETAKIIGRIVLDASFSPVRRV 179

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VESAR  Q  D DKL M I+T G IT E+++  ++RIL DQL +F   E    E   
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETSGVITPEEAIRQSARILVDQLSVFAALE--GTETAA 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 238 EAPSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|88704351|ref|ZP_01102065.1| DNA-directed RNA polymerase alpha chain [Congregibacter litoralis
           KT71]
 gi|88701402|gb|EAQ98507.1| DNA-directed RNA polymerase alpha chain [Congregibacter litoralis
           KT71]
          Length = 334

 Score =  350 bits (898), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 155/336 (46%), Positives = 224/336 (66%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q + ++L+ P  I    + ++ + R  +  EPL RGF HTLGNALRR+L+SS+ G AIT
Sbjct: 1   MQSSVKDLLTPRKIN---VAEKSKTRAQVTLEPLERGFGHTLGNALRRILLSSMPGCAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ +I+LN+KG+ L M+G     + + K G G VTA DIQT
Sbjct: 58  EVEIDGVLHEYSAIEGVQEDVIEILLNLKGVALIMNGKDEAELVLSKEGEGPVTAADIQT 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
            +DIE+ NP+H+IC L+  + V M+LT+++G GY PA        E   IG + +DA +S
Sbjct: 118 DHDIEICNPEHLICTLNSKSAVHMKLTIARGRGYSPADARENPEEETRSIGRLQLDATFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +VSY VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL DQL +F++ +   
Sbjct: 178 PVMRVSYVVEAARVEQRTDLDKLVLDLETNGTIDPEEAIRRAATILNDQLRVFVDLQSET 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V  D   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N 
Sbjct: 238 QAVTSDAEDE---VDPVLLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L  WPP S+    K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLESWPPASLRNDEK 330


>gi|261346910|ref|ZP_05974554.1| DNA-directed RNA polymerase, alpha subunit [Providencia rustigianii
           DSM 4541]
 gi|282564976|gb|EFB70511.1| DNA-directed RNA polymerase, alpha subunit [Providencia rustigianii
           DSM 4541]
          Length = 329

 Score =  350 bits (898), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVQGKDEVILTLNKSGIGPVTAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A V M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASVNMRIKVQRGRGYVPASARVHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|258406159|ref|YP_003198901.1| DNA-directed RNA polymerase subunit alpha [Desulfohalobium
           retbaense DSM 5692]
 gi|257798386|gb|ACV69323.1| DNA-directed RNA polymerase, alpha subunit [Desulfohalobium
           retbaense DSM 5692]
          Length = 347

 Score =  350 bits (897), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 151/337 (44%), Positives = 214/337 (63%), Gaps = 2/337 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW  L+ P  +E        EN      EPL RGF  TLGNALRRVL+SSL+GAAI AV
Sbjct: 13  RNWSTLVHPETLERD--EDSTENYGKFSCEPLERGFGTTLGNALRRVLLSSLQGAAIVAV 70

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I G+ HE ++I GV ED+TDI+LN+K + L+M+ D  +R+ +     G VTA   QT  
Sbjct: 71  RIKGIQHEFTTIPGVMEDITDIVLNLKQLRLRMNTDEPQRIELNVNTKGAVTASAFQTTQ 130

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           ++E+LNPD  I  L  D    +E  V  G GYVPA+ H    + IGLI++DA +SPI+KV
Sbjct: 131 NLEILNPDLHIATLSEDIEFGIEAEVRMGKGYVPAEMHEGLEEEIGLISMDASFSPIRKV 190

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE AR GQ+ +YDKL M + TDGS+  ED+VA +++IL++QL +FINF E    V E
Sbjct: 191 AYRVEQARVGQMTNYDKLVMEVWTDGSVLPEDAVAYSAKILKEQLAVFINFNEDSANVCE 250

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                +   N  L K +++LEL VR++NCL+  NI  +G+L+Q+TE +ML+  NFGRKSL
Sbjct: 251 SKGAGTESLNSNLFKHIDDLELPVRASNCLKSANINLVGELVQKTEGEMLKTKNFGRKSL 310

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
            +I+ V+  +GL  GM L  +  +  +   +  +D+ 
Sbjct: 311 EDIRKVIHELGLDFGMKLDGFEEQYKKWRERNQQDEA 347


>gi|23097600|ref|NP_691066.1| DNA-directed RNA polymerase subunit alpha [Oceanobacillus iheyensis
           HTE831]
 gi|33301658|sp|Q8ETV9|RPOA_OCEIH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|22775823|dbj|BAC12101.1| DNA-directed RNA polymerase alpha subunit [Oceanobacillus iheyensis
           HTE831]
          Length = 314

 Score =  350 bits (897), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 129/313 (41%), Positives = 200/313 (63%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  E       + EPL RG+  TLGN+LRR+L+SSL GAA+T VQIDG
Sbjct: 3   EIEKP-KIETVEIS-ENATFGKFVVEPLERGYGATLGNSLRRILLSSLPGAAVTTVQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
            LHE S++ GV ED+T IILN+K + LK+  +  K + I  +G G VTA D+   +D+EV
Sbjct: 61  ALHEFSTVDGVVEDVTTIILNLKKLALKIYSEEPKTLEIDVQGEGAVTAADLTYDSDVEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPD  I  L+    + M+L   +G GY PA+ ++ ++ PIG+I ID++++P+ +V+Y V
Sbjct: 121 MNPDLHIATLNSKGNLHMKLIAERGRGYRPAEENKNDDQPIGVIPIDSIFTPVSRVTYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV +YDKL+M + TDGSI  E++V+L ++I+ + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQVANYDKLTMDVSTDGSIRPEEAVSLGAKIITEHLNIFVGLTDEAQNAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       +   +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVMEMTIEELDLSVRSYNCLKRAGINTVQELANKSEEDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 VKLEDLGLGLRDD 313


>gi|241895163|ref|ZP_04782459.1| DNA-directed RNA polymerase alpha chain [Weissella
           paramesenteroides ATCC 33313]
 gi|241871469|gb|EER75220.1| DNA-directed RNA polymerase alpha chain [Weissella
           paramesenteroides ATCC 33313]
          Length = 331

 Score =  350 bits (897), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 133/316 (42%), Positives = 197/316 (62%), Gaps = 6/316 (1%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            +  E   P     I+L +E+ N    + EPL RG+  TLGN+LRRVL+SSL GAAI +V
Sbjct: 16  NSMLEFENPK----IMLVEEDSNYGKFVVEPLERGYGTTLGNSLRRVLLSSLPGAAINSV 71

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           QIDGVLHE S+++GV ED+T IILN+K +++++  D  K + +   GP  VTAGDI   +
Sbjct: 72  QIDGVLHEFSTVEGVVEDVTQIILNLKKVSMRIDSDDEKTLEVNVTGPADVTAGDIAGDS 131

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIK 181
           D+E+LN D  I  +   A + M LT  +G GYV    ++   +  PIG++ ID++++PI+
Sbjct: 132 DVEILNGDLHIATVAAGATLHMTLTAVRGRGYVSGDQNKELHDEMPIGVLAIDSIFTPIE 191

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +V+Y VE+ R GQ  D+DKL++ + TDGS+T  ++V+LA+RI+ D L  FI+  E     
Sbjct: 192 RVNYQVENTRVGQRDDFDKLTLDVWTDGSLTATEAVSLAARIMSDHLNAFIDMSERAITA 251

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +   + +  P        +EEL+LSVRS NCL+   I  + +L +RTE  M+ + N GRK
Sbjct: 252 QVMADKEEEPTTKHADTPIEELDLSVRSYNCLKRAGINSVQELTERTETQMMSVRNLGRK 311

Query: 302 SLVEIKGVLGTMGLFL 317
           SL EI+  L  +GL  
Sbjct: 312 SLDEIQDKLKLLGLGF 327


>gi|78064950|ref|YP_367719.1| DNA-directed RNA polymerase subunit alpha [Burkholderia sp. 383]
 gi|107024277|ref|YP_622604.1| DNA-directed RNA polymerase subunit alpha [Burkholderia cenocepacia
           AU 1054]
 gi|115350348|ref|YP_772187.1| DNA-directed RNA polymerase subunit alpha [Burkholderia ambifaria
           AMMD]
 gi|116688398|ref|YP_834021.1| DNA-directed RNA polymerase subunit alpha [Burkholderia cenocepacia
           HI2424]
 gi|134294469|ref|YP_001118204.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           vietnamiensis G4]
 gi|170700720|ref|ZP_02891715.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia ambifaria
           IOP40-10]
 gi|170731708|ref|YP_001763655.1| DNA-directed RNA polymerase subunit alpha [Burkholderia cenocepacia
           MC0-3]
 gi|171318374|ref|ZP_02907532.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia ambifaria
           MEX-5]
 gi|172059367|ref|YP_001807019.1| DNA-directed RNA polymerase subunit alpha [Burkholderia ambifaria
           MC40-6]
 gi|206558667|ref|YP_002229427.1| DNA-directed RNA polymerase subunit alpha [Burkholderia cenocepacia
           J2315]
 gi|254246577|ref|ZP_04939898.1| DNA-directed RNA polymerase [Burkholderia cenocepacia PC184]
 gi|90101525|sp|Q39KE1|RPOA_BURS3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366669|sp|Q1BRX4|RPOA_BURCA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|122324240|sp|Q0BJ20|RPOA_BURCM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158512278|sp|A0K3Q1|RPOA_BURCH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|166229265|sp|A4JAR6|RPOA_BURVG RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238688546|sp|B1JU48|RPOA_BURCC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238689152|sp|B1YRQ5|RPOA_BURA4 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238693061|sp|B4E5E6|RPOA_BURCJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|77965695|gb|ABB07075.1| DNA-directed RNA polymerase subunit alpha [Burkholderia sp. 383]
 gi|105894466|gb|ABF77631.1| DNA-directed RNA polymerase subunit alpha [Burkholderia cenocepacia
           AU 1054]
 gi|115280336|gb|ABI85853.1| DNA-directed RNA polymerase subunit alpha [Burkholderia ambifaria
           AMMD]
 gi|116646487|gb|ABK07128.1| DNA-directed RNA polymerase subunit alpha [Burkholderia cenocepacia
           HI2424]
 gi|124871353|gb|EAY63069.1| DNA-directed RNA polymerase [Burkholderia cenocepacia PC184]
 gi|134137626|gb|ABO53369.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           vietnamiensis G4]
 gi|169814950|gb|ACA89533.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           cenocepacia MC0-3]
 gi|170134390|gb|EDT02723.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia ambifaria
           IOP40-10]
 gi|171096452|gb|EDT41351.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia ambifaria
           MEX-5]
 gi|171991884|gb|ACB62803.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia ambifaria
           MC40-6]
 gi|198034704|emb|CAR50571.1| DNA-directed RNA polymerase alpha chain [Burkholderia cenocepacia
           J2315]
          Length = 325

 Score =  350 bits (897), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 155/328 (47%), Positives = 212/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP  I    LG   EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPKIIAVESLG---ENHARVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVVTAGDI+  +D E
Sbjct: 60  GVVHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVTAGDIELAHDCE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKV 183
           V+NP+HVI +L     + +++ + KG GYVP    R   D    IG I +DA +SP+++V
Sbjct: 120 VINPNHVIAHLSKGGKLDVQIKIEKGRGYVPGNVRRYGEDTAKIIGRIVLDASFSPVRRV 179

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VESAR  Q  D DKL M I+T G IT E+++  ++RIL DQL +F   E    E   
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETSGVITPEEAIRQSARILVDQLSVFAALE--GTETAA 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 238 EAPSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|121609260|ref|YP_997067.1| DNA-directed RNA polymerase subunit alpha [Verminephrobacter
           eiseniae EF01-2]
 gi|158514002|sp|A1WK92|RPOA_VEREI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|121553900|gb|ABM58049.1| DNA-directed RNA polymerase, alpha subunit [Verminephrobacter
           eiseniae EF01-2]
          Length = 330

 Score =  350 bits (897), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 159/335 (47%), Positives = 217/335 (64%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N   L+KP  I    LG    +   +  EP  RG+ HTLGNA+RRVL+SS+ G A T
Sbjct: 1   MQTN---LLKPKAINVEQLG---HHHAKVALEPFERGYGHTLGNAIRRVLLSSMVGYAAT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE SSI GV ED+ +I+LN+KG+  K+       +++ K G G+VTA DIQT
Sbjct: 55  EVTIAGVLHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGMVTARDIQT 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +D+E++NPDHVI NL     + M++ V KG GY+P    R  ++    IG I +DA +S
Sbjct: 115 PHDVEIVNPDHVIANLSQGGKLDMQIKVEKGRGYMPGNLRRYADEVTKSIGRIVLDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--E 236
           P+++VSYTVESAR  Q  D DKL + I+T+G+IT ED+V  +++IL +QL +F   E  E
Sbjct: 175 PVRRVSYTVESARVEQRTDLDKLVVEIETNGAITAEDAVRASAKILVEQLAVFAQLEGGE 234

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
                       +  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  
Sbjct: 235 LAAFDAPTGPRGNASFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N GRKSL EIK VL + GL LGM L +WPP  +++
Sbjct: 295 NLGRKSLNEIKEVLASRGLTLGMKLENWPPAGLDK 329


>gi|117927543|ref|YP_872094.1| DNA-directed RNA polymerase subunit alpha [Acidothermus
           cellulolyticus 11B]
 gi|158512363|sp|A0LRP8|RPOA_ACIC1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|117648006|gb|ABK52108.1| DNA-directed RNA polymerase subunit alpha [Acidothermus
           cellulolyticus 11B]
          Length = 341

 Score =  350 bits (897), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 121/309 (39%), Positives = 184/309 (59%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I      + R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S++ G
Sbjct: 9   ITEEPVHDTRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSLRIDGVLHEFSTVPG 68

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
             ED+T++ILNIK + +    D  + + + K+GP  VTA DI     +EV NPD  I  L
Sbjct: 69  AKEDVTEMILNIKELVVSSEHDDPQVIYLRKQGPCEVTAADIVAPAGVEVHNPDLHIATL 128

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           +    + +E+ V +G GYVPA  ++     IG I ID++YSP+ KV+Y VE+ R  Q  D
Sbjct: 129 NDKGKLEIEMVVERGRGYVPAAQNKLPGHEIGRIPIDSIYSPVLKVTYKVEATRVEQRTD 188

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +D+L M ++T  S+   D++A A + L +  G+        + +    +         L 
Sbjct: 189 FDRLIMDVETKPSMRPRDAMASAGKTLVELFGLVRELNVDAEGIDIGPSPSDAALAADLA 248

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +E+L L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  L  MGL L
Sbjct: 249 LPIEDLNLTVRSYNCLKREGIHTVGELVARSEADLLDIRNFGQKSIEEVKTKLAEMGLSL 308

Query: 318 GMNLPDWPP 326
             + P + P
Sbjct: 309 KDSPPGFDP 317


>gi|296137039|ref|YP_003644281.1| DNA-directed RNA polymerase, alpha subunit [Thiomonas intermedia
           K12]
 gi|295797161|gb|ADG31951.1| DNA-directed RNA polymerase, alpha subunit [Thiomonas intermedia
           K12]
          Length = 328

 Score =  350 bits (897), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 151/326 (46%), Positives = 215/326 (65%), Gaps = 6/326 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L++P +I+   LG    NR+ ++ EP  RG+ HTLGNALRRV++SSL G A T V I+GV
Sbjct: 5   LLRPKSIQVESLG---HNRSKVVLEPFERGYGHTLGNALRRVMLSSLVGYAPTEVSINGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S + G+ ED+  ++LN+KG+ LK+       +++ K G GVVTA DIQT +D+E++
Sbjct: 62  LHEYSVVDGLQEDVIGVLLNLKGVVLKLHNRDEVTLSLRKEGEGVVTAADIQTPHDVEIV 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSY 185
           NPDHVI +L     + M++ V KG GYVP        +    IG I +DA +SP+++VSY
Sbjct: 122 NPDHVIAHLSQGGKLDMQIKVEKGRGYVPGTLRNFGEEGGKSIGHIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL +QL +F + E  +     + 
Sbjct: 182 AVESARVEQRTDLDKLVMEIETNGVISAEEAIRSSARILVEQLSVFASLEGAETTEAAEA 241

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                 ++P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GRKSL E
Sbjct: 242 AAGGQTYDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRSETELLKTPNLGRKSLNE 301

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL   GL LGM L +WPP  +++
Sbjct: 302 IKEVLAARGLTLGMKLDNWPPSGLDK 327


>gi|304310040|ref|YP_003809638.1| DNA-directed RNA polymerase alpha subunit [gamma proteobacterium
           HdN1]
 gi|301795773|emb|CBL43972.1| DNA-directed RNA polymerase alpha subunit [gamma proteobacterium
           HdN1]
          Length = 334

 Score =  350 bits (897), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 141/335 (42%), Positives = 218/335 (65%), Gaps = 8/335 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  E + P +I    +      +  +  EPL RGF HTLGNALRR+L+SS+ GAAI 
Sbjct: 1   MQRSVSEFLTPKSIAVQQV---TATQAKVTLEPLERGFGHTLGNALRRILLSSMPGAAIV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ D++LN+K + +KM       ++I K GPG+VTAGDI+ 
Sbjct: 58  EVEIDGVLHEYSTIEGVQEDVLDVLLNLKNVAVKMQDRDEAFLSISKEGPGLVTAGDIKC 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI--GLITIDALYSP 179
              ++++N  H+I NL     + M + V +G GY PA+     ++    G + +DA +SP
Sbjct: 118 DASVDIVNKAHIIANLSAGTKLNMRVKVVRGRGYCPAEAQLEADESKTIGRLMLDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +++V+Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++ E+   
Sbjct: 178 VRRVAYVVENARVEQRTDLDKLVIDLETNGTIDPEEAIRRAATILQQQLSIFVDLEKESL 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
               +   +    +P LL+ V++LEL+VRS NCL+ EN+ Y+GDL+QRTE ++L+  N G
Sbjct: 238 PEPVEEREE---IDPILLRPVDDLELTVRSANCLKAENVYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           +KSL EIK VL + GL LGM L +WPP S+++  +
Sbjct: 295 KKSLTEIKDVLASKGLSLGMRLENWPPASLKDDDR 329


>gi|42524352|ref|NP_969732.1| DNA-directed RNA polymerase subunit alpha [Bdellovibrio
           bacteriovorus HD100]
 gi|39576561|emb|CAE80725.1| DNA-directed RNA polymerase, alpha subunit [Bdellovibrio
           bacteriovorus HD100]
          Length = 332

 Score =  350 bits (897), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 157/320 (49%), Positives = 214/320 (66%), Gaps = 2/320 (0%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           +IKP   E       ++     I  PL RGF  TLGN+LRR+L+SS+ G+AITAV+ +GV
Sbjct: 1   MIKPKGFEVDRDSLRDD-YAKFIIRPLERGFGVTLGNSLRRILLSSMMGSAITAVKFEGV 59

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE ++I  V ED+TDIILN+K +  K        + I K+GPG VTA DIQT + IEVL
Sbjct: 60  LHEFTTIPDVLEDVTDIILNLKEVRFKQYTADSLTLKISKKGPGKVTAADIQTTDKIEVL 119

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NPD  I  L  +A    E+ VS G GYVP + +R  + P+G I +DALYSPI+KV+Y V 
Sbjct: 120 NPDLPIATLGANANFNAEIVVSFGRGYVPVE-NRETDLPVGFIGVDALYSPIRKVNYNVS 178

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +AR GQ  DYD L++ + TDGS+  E++VAL+S+I+++QL +F+ F+E  +  +E   + 
Sbjct: 179 NARVGQRTDYDALTLEVWTDGSLKPEEAVALSSKIMKEQLQIFLTFDETMEPAEEARELG 238

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
           S   N  L + V++LELSVRS NCL+  NI Y+G+L+ R+EA+ML+  NFGRKSL EIK 
Sbjct: 239 SPTLNENLFRSVDDLELSVRSANCLKNANIRYIGELVVRSEAEMLKTKNFGRKSLNEIKE 298

Query: 309 VLGTMGLFLGMNLPDWPPES 328
           +LG MGL LGM +  WPP  
Sbjct: 299 ILGEMGLGLGMKIEGWPPAG 318


>gi|256852062|ref|ZP_05557449.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           27-2-CHN]
 gi|260661369|ref|ZP_05862282.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           115-3-CHN]
 gi|282932823|ref|ZP_06338223.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           208-1]
 gi|297205063|ref|ZP_06922459.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus jensenii
           JV-V16]
 gi|256615474|gb|EEU20664.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           27-2-CHN]
 gi|260547824|gb|EEX23801.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           115-3-CHN]
 gi|281303052|gb|EFA95254.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           208-1]
 gi|297149641|gb|EFH29938.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus jensenii
           JV-V16]
          Length = 313

 Score =  350 bits (897), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 136/311 (43%), Positives = 197/311 (63%), Gaps = 5/311 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +E+     + EPL RGF  TLGN+LRRVL++S+ G A++ +QIDG
Sbjct: 3   EFEKPN----ITVVDQEDAYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTALSYIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T I+LN+K + LK   D  K V +   GP  VTAGD++  +++ V
Sbjct: 59  VLHEFSTIPGVREDVTKIVLNLKKLELKSVADEEKIVELDVEGPATVTAGDLKVDSEVTV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + M++ V  G GYVPA  ++T++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTVAEGGHLHMQIAVKNGRGYVPASENKTDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDIN 246
           ES R G+  DYDKL++ + TDGSIT  D+++ AS+IL +   +F   +       +  + 
Sbjct: 179 ESTRVGKRDDYDKLTLEVWTDGSITPSDALSFASKILIEHFKVFKFSDAQTDFGGEVMVE 238

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L   +EEL+LSVRS NCL+   I  + +L  ++E+DM+R+ N GRKSL E+
Sbjct: 239 KEDDKKERQLEMTIEELDLSVRSYNCLKRAGINTLQELTDKSESDMMRVRNLGRKSLEEV 298

Query: 307 KGVLGTMGLFL 317
           K  L  +GL L
Sbjct: 299 KNKLADLGLSL 309


>gi|88861469|ref|ZP_01136095.1| DNA-directed RNA polymerase alpha chain [Pseudoalteromonas tunicata
           D2]
 gi|88816517|gb|EAR26346.1| DNA-directed RNA polymerase alpha chain [Pseudoalteromonas tunicata
           D2]
          Length = 328

 Score =  349 bits (896), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 225/334 (67%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  +E   +      R+ ++ EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVEIDAVS---PTRSKVVLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DIQ 
Sbjct: 58  EVEIDGVLHEYSAKEGVQEDIIEILLNLKGLAVTLEGKDEVFLTLTKSGVGPVTAADIQH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALY 177
             D+ + NPDHVIC+L   ++ + M + V +G GYVPA +  + +D   PIG + +DA +
Sbjct: 118 DGDVTICNPDHVICHLTTANSSISMRIRVERGRGYVPASNRLSSDDDERPIGRLLLDASF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y+VESAR  Q  D DKL + ++T+G++  E+++  AS IL +QL  F++  + 
Sbjct: 178 SPVERIAYSVESARVEQRTDLDKLIIDMETNGTLDPEEAIRRASTILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            + V ++   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 TEPVAKE---EKPEFDPILLRPVDDLELTVRSANCLKAEQIQYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP S+ E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASLAE 328


>gi|297537556|ref|YP_003673325.1| DNA-directed RNA polymerase subunit alpha [Methylotenera sp. 301]
 gi|297256903|gb|ADI28748.1| DNA-directed RNA polymerase, alpha subunit [Methylotenera sp. 301]
          Length = 328

 Score =  349 bits (896), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 158/333 (47%), Positives = 217/333 (65%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++  VL      R  +  EP+ RGF +TLGNALRRVL+SS+ G AIT
Sbjct: 1   MQNSPTEYLKPRVVDVEVLSPL---RARVTLEPMERGFGYTLGNALRRVLLSSIPGFAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGV+HE S++ GV ED+ DI+LN+KG+ LK++  S   + + K   GVVTAGD +T
Sbjct: 58  EVKIDGVVHEYSTLDGVQEDVVDILLNLKGVALKLNTKSETILVLNKSVEGVVTAGDFET 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYS 178
            +D E++NPDHVI +L     + +E+ V+ G GY P    +    E+  +G I +DA +S
Sbjct: 118 GHDAEIVNPDHVIAHLTKGGKLNLEVKVAMGRGYQPVPARQKANEEDRVLGFIMVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI KVSY VESAR  Q  D DKL M ++T+G I  E ++  A+RIL  QL +F + E   
Sbjct: 178 PINKVSYQVESARVEQRTDLDKLVMDVETNGVIEPEQAIRDAARILMGQLSVFADLEGAP 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            EV+      +   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 SEVEV---KSAPQVDPILLRPVDDLELTVRSANCLKAENIFYIGDLIQRTENELLKAPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL T GL LGM L +WPP  +E+
Sbjct: 295 GRKSLNEIKDVLATRGLTLGMKLENWPPVGLEK 327


>gi|330831946|ref|YP_004400771.1| DNA-directed RNA polymerase subunit alpha [Streptococcus suis ST3]
 gi|329306169|gb|AEB80585.1| DNA-directed RNA polymerase subunit alpha [Streptococcus suis ST3]
          Length = 312

 Score =  349 bits (896), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 134/313 (42%), Positives = 203/313 (64%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T+++IDG
Sbjct: 3   EFEKPT----ITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K   +  K++ +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKKIELDVVGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A  +  LTV+ G GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIADGATFKAVLTVNSGRGYVPAEDNKKDDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I+T+G+I  ED++ L++RIL + LG+F +  E  K  +     
Sbjct: 179 EPARVGSNDGFDKLTLEINTNGTIVPEDALGLSARILMEHLGLFTDLTEVAKSAEVMKEA 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    +  L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 EVASDDRMLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKKD 311


>gi|220913400|ref|YP_002488709.1| DNA-directed RNA polymerase subunit alpha [Arthrobacter
           chlorophenolicus A6]
 gi|325964132|ref|YP_004242038.1| DNA-directed RNA polymerase, subunit alpha [Arthrobacter
           phenanthrenivorans Sphe3]
 gi|254765243|sp|B8HCX4|RPOA_ARTCA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|219860278|gb|ACL40620.1| DNA-directed RNA polymerase, alpha subunit [Arthrobacter
           chlorophenolicus A6]
 gi|323470219|gb|ADX73904.1| DNA-directed RNA polymerase, alpha subunit [Arthrobacter
           phenanthrenivorans Sphe3]
          Length = 336

 Score =  349 bits (896), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 123/315 (39%), Positives = 190/315 (60%), Gaps = 4/315 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V     ENR+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLSEEVV----SENRSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+T+IILNIK +++    D      + K+GPGVVTA DI     +E  NP
Sbjct: 62  EFTTVPGVKEDVTEIILNIKSLSVSSEHDEPVVAYLRKQGPGVVTAADIAPPAGVEFHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+      +ELT+ +G GYV A  +++ +  IG I +D++YSP+ KV++ VE+ 
Sbjct: 122 DLHIATLNSKGKFELELTIERGRGYVSAAQNKSGDAEIGRIPVDSIYSPVLKVTFRVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  +I   D+VA A   L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAIAPRDAVASAGTTLVELFGLARELNTAAEGIEIGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                +   +E+L+L+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L
Sbjct: 242 ALAADMALPIEDLDLTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWP 325
             +GL L  + P + 
Sbjct: 302 VELGLSLKDSPPGFD 316


>gi|183600727|ref|ZP_02962220.1| hypothetical protein PROSTU_04323 [Providencia stuartii ATCC 25827]
 gi|188019707|gb|EDU57747.1| hypothetical protein PROSTU_04323 [Providencia stuartii ATCC 25827]
          Length = 329

 Score =  349 bits (896), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 148/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVQGKDEVILTLNKSGIGPVTAADIVH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D  A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDESASINMRIKVQRGRGYVPASARVHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|91786411|ref|YP_547363.1| DNA-directed RNA polymerase subunit alpha [Polaromonas sp. JS666]
 gi|119366707|sp|Q12G77|RPOA_POLSJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|91695636|gb|ABE42465.1| DNA-directed RNA polymerase subunit alpha [Polaromonas sp. JS666]
          Length = 329

 Score =  349 bits (896), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 160/334 (47%), Positives = 214/334 (64%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N   L+KP  I    LG    NR  +  EP  RG+ HTLGNALRRVL+SS+ G A T
Sbjct: 1   MQTN---LLKPKTINVEQLG---ANRAKVTLEPFERGYGHTLGNALRRVLLSSMVGHAAT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE SSI GV ED+ +I+LN+KG+  K+       +++ K G G VTA DIQT
Sbjct: 55  EVTIAGVLHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGPVTAADIQT 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYS 178
            +D+E++NP+HVI NL     + M++ V  G GYVP    R  ++     G I +DA +S
Sbjct: 115 PHDVEIINPEHVIVNLSHGGKIDMQIKVENGRGYVPGTMRRYGDESPKSIGRIVLDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EP 237
           P+K+VSYTVESAR  Q  D DKL + I+T+G++T ED+V  +++IL +QL +F   E   
Sbjct: 175 PVKRVSYTVESARVEQRTDLDKLVLEIETNGAVTAEDAVRASAKILVEQLAVFAQLEGNE 234

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
                  +   S  F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N
Sbjct: 235 LAAFDAPVQRSSQQFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            GRKSL EIK VL + GL LGM L  WPP  +++
Sbjct: 295 LGRKSLNEIKEVLASRGLTLGMRLESWPPAGLDK 328


>gi|212709004|ref|ZP_03317132.1| hypothetical protein PROVALCAL_00036 [Providencia alcalifaciens DSM
           30120]
 gi|212688370|gb|EEB47898.1| hypothetical protein PROVALCAL_00036 [Providencia alcalifaciens DSM
           30120]
          Length = 329

 Score =  349 bits (896), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 148/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVQGKDEVILTLNKSGIGPVTAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D  A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDESASINMRIKVQRGRGYVPASARVHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|300309482|ref|YP_003773574.1| DNA-directed RNA polymerase subunit alpha [Herbaspirillum
           seropedicae SmR1]
 gi|124483590|emb|CAM32668.1| probable DNA-directed RNA polymerase (alpha chain) protein
           [Herbaspirillum seropedicae]
 gi|300072267|gb|ADJ61666.1| DNA-directed RNA polymerase alpha chain protein [Herbaspirillum
           seropedicae SmR1]
          Length = 325

 Score =  349 bits (896), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 154/333 (46%), Positives = 211/333 (63%), Gaps = 11/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +   L+KP  IE   L         ++ EP  RG+ HTLGNALRRVL+S++ G A T
Sbjct: 1   MQNS---LLKPRIIEVETL---APGHAKVVMEPFERGYGHTLGNALRRVLLSTMSGYAPT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GV+HE SS+ GV ED+ DI+LN+KG+  K+       +T+ K G G V A DI  
Sbjct: 55  EVTIAGVVHEYSSLDGVQEDVVDILLNLKGVVFKLHNRDEVTLTLKKEGEGAVLASDIDL 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYS 178
            +D+E++NPDHVI NL     + M++ V KG GYVP    R     N  IG I +DA +S
Sbjct: 115 PHDVELINPDHVIANLTGGGKLDMQIKVEKGRGYVPGNVRRLSEDTNKTIGRIILDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY VESAR  Q  D DKL M I+T+G IT E+++  ++R+L DQL +F   E   
Sbjct: 175 PVRRVSYAVESARVEQRTDLDKLVMNIETNGVITPEEAIRQSARVLVDQLNVFAALE--G 232

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E   +   ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N 
Sbjct: 233 TEATAEAPSRAPQVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRSENELLKTPNL 292

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL + GL LGM L +WPP  +E+
Sbjct: 293 GRKSLNEIKEVLASRGLTLGMKLENWPPAGLEK 325


>gi|186477561|ref|YP_001859031.1| DNA-directed RNA polymerase subunit alpha [Burkholderia phymatum
           STM815]
 gi|209521360|ref|ZP_03270073.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia sp. H160]
 gi|238691303|sp|B2JI39|RPOA_BURP8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|184194020|gb|ACC71985.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia phymatum
           STM815]
 gi|209498180|gb|EDZ98322.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia sp. H160]
          Length = 325

 Score =  349 bits (896), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 154/328 (46%), Positives = 213/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP  I    LG   E+   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPKIIAVESLG---ESHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVVTAGDI+  +D E
Sbjct: 60  GVVHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVTAGDIELAHDCE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKV 183
           V+NPDHVI +L     + +++ V KG GYVP    R   +    IG I +DA +SP+++V
Sbjct: 120 VINPDHVIAHLSKGGKLDVQIKVEKGRGYVPGNVRRYGEESAKIIGRIVLDASFSPVRRV 179

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL DQL +F   E    E   
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALE--GTEAAA 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 238 EAPSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|254253494|ref|ZP_04946812.1| DNA-directed RNA polymerase [Burkholderia dolosa AUO158]
 gi|124896103|gb|EAY69983.1| DNA-directed RNA polymerase [Burkholderia dolosa AUO158]
 gi|325529704|gb|EGD06567.1| DNA-directed RNA polymerase subunit alpha [Burkholderia sp. TJI49]
          Length = 325

 Score =  349 bits (896), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 155/328 (47%), Positives = 212/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP  I    LG   EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPKIIAVESLG---ENHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVVTAGDI+  +D E
Sbjct: 60  GVVHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVTAGDIELAHDCE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKV 183
           V+NP+HVI +L     + +++ + KG GYVP    R   D    IG I +DA +SP+++V
Sbjct: 120 VINPNHVIAHLSKGGKLDVQIKIEKGRGYVPGNVRRYGEDTAKIIGRIVLDASFSPVRRV 179

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VESAR  Q  D DKL M I+T G IT E+++  ++RIL DQL +F   E    E   
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETSGVITPEEAIRQSARILVDQLSVFAALE--GTETAA 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 238 EAPSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|260907114|ref|ZP_05915436.1| DNA-directed RNA polymerase subunit alpha [Brevibacterium linens
           BL2]
          Length = 332

 Score =  349 bits (896), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 122/329 (37%), Positives = 195/329 (59%), Gaps = 4/329 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V     ENR+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLTEEVV----SENRSRFAIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T+ ILN+K + +    D      + K+GPG VTA D+     +E+ NP
Sbjct: 62  EFSTVPGVKEDVTEFILNLKSLVVSSEFDEPVVAYLRKQGPGTVTAADVSAPAGVEIHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+ +  + MELT+ +G GYV +  ++  +  IG + +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLHIATLNGEGRLDMELTIERGRGYVSSAQNKNADAEIGRVPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + I+T  S+T  D++A A + L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDRLVLDIETKPSMTPRDAIASAGKTLVELFGLARELNVEAEGIEIGPSPVDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +E+L+L+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L
Sbjct: 242 ALAADLALAIEDLDLTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGSKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             +GL L  +   +    ++E     ED+
Sbjct: 302 NELGLSLKDSPAGFEAGLVDEDQSYVEDE 330


>gi|315037556|ref|YP_004031124.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus amylovorus
           GRL 1112]
 gi|325956029|ref|YP_004286639.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           acidophilus 30SC]
 gi|312275689|gb|ADQ58329.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus amylovorus
           GRL 1112]
 gi|325332594|gb|ADZ06502.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           acidophilus 30SC]
 gi|327182852|gb|AEA31299.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus amylovorus
           GRL 1118]
          Length = 312

 Score =  349 bits (896), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 134/310 (43%), Positives = 195/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDG
Sbjct: 3   EFEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++V
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMELAVKNGRGYVTASDNKSDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   +  +  +  
Sbjct: 179 ESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADANTQFSEVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE+DM+R+ N GRKSL E+K
Sbjct: 239 EDDKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELTDKTESDMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLADLGLSL 308


>gi|53803448|ref|YP_114763.1| DNA-directed RNA polymerase subunit alpha [Methylococcus capsulatus
           str. Bath]
 gi|61215838|sp|Q605D7|RPOA_METCA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|53757209|gb|AAU91500.1| DNA-directed RNA polymerase, alpha subunit [Methylococcus
           capsulatus str. Bath]
          Length = 328

 Score =  349 bits (895), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 153/334 (45%), Positives = 220/334 (65%), Gaps = 7/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +  ELIKP  +E +  G        ++ EPL RGF HTLGNALRRVL+S++ GAA+T
Sbjct: 1   MHNSLAELIKPRTVEVVPHGSHS---ARVVIEPLERGFGHTLGNALRRVLLSAIPGAAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V IDGVLHE S+I+GV ED+ D++LN+K + ++++G     + + K GPG V AGDI+ 
Sbjct: 58  DVVIDGVLHEYSTIEGVQEDVIDVLLNLKNLAIRLNGPHDVYLNVDKHGPGPVLAGDIEA 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSPI 180
            +D+EVLNP+ +I +++ +  +RM L V KG GY P  +   E +  IG + +DA +SPI
Sbjct: 118 SHDVEVLNPELLIAHINGNGRLRMTLHVQKGRGYQPVANRAIEGDSAIGTLHLDASFSPI 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VESAR  Q  D D+L + + T+G++  E++V  A+ IL   L + ++ +     
Sbjct: 178 KKVSYVVESARVEQRTDLDRLVIELQTNGTVQPEEAVKHAANILNQHLAILVDLKGEDLP 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           +          F+P LL  V++LEL+VRS NCL+ ENI Y+GDLIQR+EAD+L+  N G+
Sbjct: 238 L---FGEDGPQFDPLLLHPVDDLELTVRSANCLKAENIFYIGDLIQRSEADLLKTPNLGK 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           KSL EIK VL T GL LGM L +WPPE +++L +
Sbjct: 295 KSLTEIKDVLATKGLSLGMRLENWPPEGLKKLNQ 328


>gi|303328068|ref|ZP_07358507.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio sp.
           3_1_syn3]
 gi|302861894|gb|EFL84829.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio sp.
           3_1_syn3]
          Length = 347

 Score =  349 bits (895), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 150/335 (44%), Positives = 215/335 (64%), Gaps = 1/335 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW EL+KP+ I               I EPL RG+  T+GNA+RRVL++SL+GAA  +V
Sbjct: 13  RNWSELVKPDQI-LREEETASGTHGKFICEPLERGYGTTIGNAMRRVLLASLQGAAFVSV 71

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I GV HE ++I GV ED+TD+ILN+K + L++  D  +R+ +     G VTA  IQT  
Sbjct: 72  KITGVQHEFTTIHGVLEDVTDVILNLKQVRLRLDTDEPQRLILRVDRKGPVTAAQIQTNQ 131

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            +EVLNP+  I  L  D V+ MEL    G GYVPA  H   ++ IGLI +D+ +SP++KV
Sbjct: 132 HVEVLNPELHIATLTEDVVLEMELEARMGKGYVPADMHEGLSEEIGLIKLDSSFSPVRKV 191

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +YTVE AR GQ+ +YD+L + + TDGS+T ED++A +++I++DQ+ +FINF+E       
Sbjct: 192 AYTVEQARVGQMTNYDRLLLEVWTDGSLTPEDAIAYSAKIIKDQISVFINFDERVSGDMR 251

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             +      N  L K +++LELSVR+TNCLR  NI  +G+L+QR+E +ML+  NFGRKSL
Sbjct: 252 LGSSDGGEVNEHLFKSIDDLELSVRATNCLRSANIALVGELVQRSEGEMLKTKNFGRKSL 311

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
            EIK VL  MGL  GM +  +  +  E   K+  +
Sbjct: 312 DEIKSVLLDMGLDFGMKVDGFDKKYQEWKRKQQNE 346


>gi|315633479|ref|ZP_07888769.1| DNA-directed RNA polymerase subunit alpha [Aggregatibacter segnis
           ATCC 33393]
 gi|315477521|gb|EFU68263.1| DNA-directed RNA polymerase subunit alpha [Aggregatibacter segnis
           ATCC 33393]
          Length = 329

 Score =  349 bits (895), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 150/334 (44%), Positives = 224/334 (67%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    +  +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTQAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A +I  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDIIEVLLNLKGLAVKVQNKDDVLLTLSKSGIGPVVAANITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALY 177
             D+E++NP+HVIC+L D +A + M + V +G GYVPA     ++ E+ PIG + +DA Y
Sbjct: 118 DGDVEIVNPEHVICHLTDENASINMRIRVQRGRGYVPASARTQNQDEDRPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPI +++Y VE+AR  Q  D DKL + ++T+G+I  ED++  A+ IL +QL  F++  + 
Sbjct: 178 SPIDRIAYNVEAARVEQRTDLDKLVIELETNGTIDPEDAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|146317755|ref|YP_001197467.1| DNA-directed RNA polymerase subunit alpha [Streptococcus suis
           05ZYH33]
 gi|146319946|ref|YP_001199657.1| DNA-directed RNA polymerase subunit alpha [Streptococcus suis
           98HAH33]
 gi|253751015|ref|YP_003024156.1| DNA-directed RNA polymerase alpha chain [Streptococcus suis SC84]
 gi|253752915|ref|YP_003026055.1| DNA-directed RNA polymerase alpha chain [Streptococcus suis P1/7]
 gi|253754740|ref|YP_003027880.1| DNA-directed RNA polymerase alpha chain [Streptococcus suis BM407]
 gi|158514125|sp|A4VSH8|RPOA_STRSY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158514142|sp|A4VYR8|RPOA_STRS2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|145688561|gb|ABP89067.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Streptococcus suis 05ZYH33]
 gi|145690752|gb|ABP91257.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Streptococcus suis 98HAH33]
 gi|251815304|emb|CAZ50872.1| DNA-directed RNA polymerase alpha chain [Streptococcus suis SC84]
 gi|251817204|emb|CAZ54927.1| DNA-directed RNA polymerase alpha chain [Streptococcus suis BM407]
 gi|251819160|emb|CAR44293.1| DNA-directed RNA polymerase alpha chain [Streptococcus suis P1/7]
 gi|292557557|gb|ADE30558.1| DNA-directed RNA polymerase alpha subunit [Streptococcus suis GZ1]
 gi|319757266|gb|ADV69208.1| DNA-directed RNA polymerase subunit alpha [Streptococcus suis JS14]
          Length = 312

 Score =  349 bits (895), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 134/313 (42%), Positives = 203/313 (64%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T+++IDG
Sbjct: 3   EFEKPT----ITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K   +  K++ +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKKIELDVVGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A  +  LTV+ G GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIADGATFKAVLTVNSGRGYVPAEDNKKDDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I+T+G+I  ED++ L++RIL + LG+F +  E  K  +     
Sbjct: 179 EPARVGSNDGFDKLTLEINTNGTIIPEDALGLSARILMEHLGLFTDLTEVAKSAEVMKEA 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    +  L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 EVASDDRMLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKKD 311


>gi|110812362|gb|ABG91718.1| DNA-directed RNA polymerase, alpha subunit [Shewanella putrefaciens
           200]
          Length = 336

 Score =  349 bits (895), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 143/333 (42%), Positives = 214/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 8   MQGSVTEFLKPRLVD---IEQVNSTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 64

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G V A DI  
Sbjct: 65  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVTIEGKDEAMLTLSKSGAGPVIAADITH 124

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  + M + V +G GYVPA        ++ PIG + +DA +S
Sbjct: 125 DGDVTIVNPDHVICHLTGNNDISMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDASFS 184

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   +  
Sbjct: 185 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFVELRDVT 244

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +     +  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 245 EPE---LKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 301

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 302 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 334


>gi|288919690|ref|ZP_06414017.1| DNA-directed RNA polymerase, alpha subunit [Frankia sp. EUN1f]
 gi|288348879|gb|EFC83129.1| DNA-directed RNA polymerase, alpha subunit [Frankia sp. EUN1f]
          Length = 349

 Score =  349 bits (895), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 125/316 (39%), Positives = 190/316 (60%), Gaps = 4/316 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P  +E        E R+  + EPL  GF +TLGN+LRR L+SS+ GA++T++++DGVLH
Sbjct: 6   RPTLVE----DPITEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIRVDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+TD+ILN+K + +    D    + + K+GPG VTA DI     +EV NP
Sbjct: 62  EFSTVPGVKEDVTDLILNLKELVVSSDNDEPTVMYLRKQGPGDVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  +  L+    + +ELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+ 
Sbjct: 122 DLHLATLNDKGKLEIELTVERGRGYVSAAQNKQPGQEIGRIPIDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  SI+  D++A A + L    G+        + V    +    
Sbjct: 182 RVEQRTDFDRLIVDVETKQSISPRDAMASAGKTLVGLFGLAQELNAEAEGVDIGPSAADA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EE++L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  L
Sbjct: 242 ALAADLALPIEEMDLTVRSYNCLKREGIHTIGELVSRSEADLLDIRNFGQKSIDEVKTKL 301

Query: 311 GTMGLFLGMNLPDWPP 326
           G MGL L  + P + P
Sbjct: 302 GAMGLQLKDSPPGFDP 317


>gi|227894546|ref|ZP_04012351.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus ultunensis
           DSM 16047]
 gi|227863705|gb|EEJ71126.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus ultunensis
           DSM 16047]
          Length = 312

 Score =  349 bits (895), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 135/310 (43%), Positives = 195/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDG
Sbjct: 3   EFEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++V
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMELAVKNGRGYVTASDNKSDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   K  +  +  
Sbjct: 179 ESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADANTKFSEVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE+DM+R+ N GRKSL E+K
Sbjct: 239 EDDKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELTDKTESDMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLADLGLSL 308


>gi|260914656|ref|ZP_05921122.1| DNA-directed RNA polymerase subunit alpha [Pasteurella dagmatis
           ATCC 43325]
 gi|260631255|gb|EEX49440.1| DNA-directed RNA polymerase subunit alpha [Pasteurella dagmatis
           ATCC 43325]
          Length = 329

 Score =  349 bits (895), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVFLTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALY 177
             D+E++NP+HVIC+L D +A + M + V +G GYVPA      + E  PIG + +DA Y
Sbjct: 118 DGDVEIVNPEHVICHLTDENASINMRIRVQRGRGYVPASARVHAQDEERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|156932260|ref|YP_001436176.1| DNA-directed RNA polymerase subunit alpha [Cronobacter sakazakii
           ATCC BAA-894]
 gi|260599615|ref|YP_003212186.1| DNA-directed RNA polymerase subunit alpha [Cronobacter turicensis
           z3032]
 gi|171769808|sp|A7MPF8|RPOA_ENTS8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|156530514|gb|ABU75340.1| hypothetical protein ESA_00031 [Cronobacter sakazakii ATCC BAA-894]
 gi|260218792|emb|CBA34140.1| DNA-directed RNA polymerase subunit alpha [Cronobacter turicensis
           z3032]
          Length = 329

 Score =  349 bits (895), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVVLTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|238928128|ref|ZP_04659888.1| DNA-directed RNA polymerase [Selenomonas flueggei ATCC 43531]
 gi|238884088|gb|EEQ47726.1| DNA-directed RNA polymerase [Selenomonas flueggei ATCC 43531]
          Length = 319

 Score =  349 bits (895), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 130/319 (40%), Positives = 198/319 (62%), Gaps = 6/319 (1%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             ++ KP  IE   +  E+      I EPL  G+  T GN+LRR+L+SSL GAA+T++QI
Sbjct: 1   MTDIEKP-KIEIAEIS-EDGRYGRFICEPLEPGYGTTFGNSLRRMLLSSLDGAAVTSIQI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGVLHE S+I GV +D+T I+L +K + ++M     + + I   G   VTA DI+  +DI
Sbjct: 59  DGVLHEFSTIPGVRDDVTSIVLALKQLCIRMQDSEPRTIRIDAAGACEVTAADIECGSDI 118

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E+LNPD  I  L     +++++TV +G GYVPA  ++  +D IG+I ID+++SP+++V+Y
Sbjct: 119 EILNPDLHIATLGDTGKLKIDMTVERGRGYVPADRNKKPDDVIGVIPIDSIFSPVQRVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVE  R G V DYD+L + + T+GSI  E++V+ A+ IL   L +F N +    E +E++
Sbjct: 179 TVEDTRVGNVTDYDRLILDVWTNGSIRPEEAVSKAAAILVMHLRLFQNMDGSAAEEEEEV 238

Query: 246 ----NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
                 +       L   +++L+LSVRS NCL+   I  + DL Q+TE DM+++ N GRK
Sbjct: 239 PNFPPEEVDDSAKVLEMTIDDLDLSVRSFNCLKRAGINTVADLAQKTEDDMMKVRNLGRK 298

Query: 302 SLVEIKGVLGTMGLFLGMN 320
           SL E+K  L  +GL L  +
Sbjct: 299 SLDEVKKKLEELGLSLRQD 317


>gi|294341216|emb|CAZ89617.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           (Transcriptase alpha chain) (RNA polymerase alpha
           subunit) [Thiomonas sp. 3As]
          Length = 328

 Score =  349 bits (895), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 151/326 (46%), Positives = 215/326 (65%), Gaps = 6/326 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L++P +I+   LG    NR+ ++ EP  RG+ HTLGNALRRV++SSL G A T V I+GV
Sbjct: 5   LLRPKSIQVESLG---HNRSKVVLEPFERGYGHTLGNALRRVMLSSLVGYAPTEVSINGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S + G+ ED+  ++LN+KG+ LK+       +++ K G GVVTA DIQT +D+E++
Sbjct: 62  LHEYSVVDGLQEDVIGVLLNLKGVVLKLHNRDEVTLSLRKEGEGVVTAADIQTPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSY 185
           NPDHVI +L     + M++ V KG GYVP        +    IG I +DA +SP+++VSY
Sbjct: 122 NPDHVIAHLSQGGKLDMQIKVEKGRGYVPGTLRNFGEEGGKSIGHIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL +QL +F + E  +     + 
Sbjct: 182 AVESARVEQRTDLDKLVMEIETNGVISAEEAIRSSARILVEQLSVFASLEGAETTEAAEA 241

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                 ++P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GRKSL E
Sbjct: 242 AAGGQTYDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRSETELLKTPNLGRKSLNE 301

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL   GL LGM L +WPP  +++
Sbjct: 302 IKEVLAARGLTLGMKLDNWPPSGLDK 327


>gi|302388740|ref|YP_003824561.1| DNA-directed RNA polymerase subunit alpha [Thermosediminibacter
           oceani DSM 16646]
 gi|302199368|gb|ADL06938.1| DNA-directed RNA polymerase subunit alpha [Thermosediminibacter
           oceani DSM 16646]
          Length = 316

 Score =  349 bits (895), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 137/313 (43%), Positives = 200/313 (63%), Gaps = 2/313 (0%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E+ KP  IE + +  E+     ++ EPL RG+  TLGN+LRRVL+SSL GAAIT+V+I
Sbjct: 1   MTEIEKPR-IELVEIS-EDNTYGKIVIEPLERGYGTTLGNSLRRVLLSSLPGAAITSVKI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGV HE S+I GV ED  +II+NIKG+ +KM  D  K + I  +G G VTA DI    D+
Sbjct: 59  DGVQHEFSTIPGVLEDTVEIIMNIKGLAIKMHSDEPKLLRIEAQGEGEVTAKDIICDADV 118

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++N DH I  LD D  +  ELT+ KG GYV A+ ++    PIG+I ID++++P+ K +Y
Sbjct: 119 EIINKDHHIATLDKDGRLFAELTLEKGKGYVTAEKNKKPGQPIGIIPIDSIFTPVIKANY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVE  R GQV DYDKL++ + T+G+I  +++V+ A++IL D   +F       K+V+  +
Sbjct: 179 TVEHTRVGQVTDYDKLTLEVWTNGTIKPDEAVSAAAKILIDYFNLFTGLTTAVKKVEAPV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   +EEL+LSVRS NCL+   I  +G+LIQ+T  +M+++ N G+KSL E
Sbjct: 239 EKEKDERERILEMPIEELDLSVRSYNCLKRAGINTIGELIQKTPEEMMKVRNLGKKSLEE 298

Query: 306 IKGVLGTMGLFLG 318
           ++  L  + L L 
Sbjct: 299 VEEKLAALNLSLK 311


>gi|238025958|ref|YP_002910189.1| DNA-directed RNA polymerase subunit alpha [Burkholderia glumae
           BGR1]
 gi|237875152|gb|ACR27485.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia glumae
           BGR1]
          Length = 325

 Score =  349 bits (895), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 154/328 (46%), Positives = 212/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP  I    LG   EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPKIIAVESLG---ENHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S++ GV ED+ +++LN+KG+  K+       VT+ K G G+VTAGDI+  +D E
Sbjct: 60  GVVHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGIVTAGDIELAHDCE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKV 183
           V+NPDHVI +L     + +++ + KG GYVP    R   +    IG I +DA +SP+++V
Sbjct: 120 VINPDHVIAHLTKGGKLDVQIKIEKGRGYVPGNVRRYGEETAKIIGRIVLDASFSPVRRV 179

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VESAR  Q  D DKL M I+T G IT E+++  ++RIL DQL +F   E    E   
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETSGVITPEEAIRQSARILVDQLSVFAALE--GTETAA 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 238 EAPSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|268593566|ref|ZP_06127787.1| DNA-directed RNA polymerase, alpha subunit [Providencia rettgeri
           DSM 1131]
 gi|291310843|gb|EFE51296.1| DNA-directed RNA polymerase, alpha subunit [Providencia rettgeri
           DSM 1131]
          Length = 329

 Score =  348 bits (894), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVQGKDEVILTLNKSGIGPVTAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P H+IC+L D  A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHIICHLTDESASINMRIKVQRGRGYVPASARVHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|259502556|ref|ZP_05745458.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus antri DSM
           16041]
 gi|259169508|gb|EEW54003.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus antri DSM
           16041]
          Length = 314

 Score =  348 bits (894), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 138/315 (43%), Positives = 206/315 (65%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E +N    + EPL RG+  TLGN+LRRVL++SL GAAIT +QIDG
Sbjct: 3   EFEKPN----IHKVEETDNYGKFVVEPLERGYGTTLGNSLRRVLIASLPGAAITTMQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++KGV ED+T IILN+K ++LK++ +  K + +  +GP  VTAGDIQ  +++ V
Sbjct: 59  VLHEFSTVKGVTEDVTQIILNLKKVSLKINSEDQKDLELDVKGPAEVTAGDIQGDSEVSV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
           LNPD  I  +   A + +++T  KG GY+ A  ++   E+  IG++ ID++Y+PI++V+Y
Sbjct: 119 LNPDLHIATVADGAELHIKMTADKGRGYLSANDNKARMEDLAIGVLPIDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVE+AR GQ  DYDKL++ + TDGSIT  ++V+L ++IL + L MF+N  E  +  +  +
Sbjct: 179 TVENARVGQRSDYDKLTLDVWTDGSITPTEAVSLGAKILTEHLAMFVNLTETAQNAQVMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   +EEL+LSVRS NCL+   I  + +L  RT +DM+++ N G+KSL E
Sbjct: 239 EKEETHKEKTLEMTIEELDLSVRSYNCLKRAGINTVKELTDRTVSDMMKVRNLGQKSLEE 298

Query: 306 IKGVLGTMGLFLGMN 320
           IK  L  +G+    +
Sbjct: 299 IKLKLNDLGVSFRQD 313


>gi|116671486|ref|YP_832419.1| DNA-directed RNA polymerase subunit alpha [Arthrobacter sp. FB24]
 gi|158512270|sp|A0JZ49|RPOA_ARTS2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116611595|gb|ABK04319.1| DNA-directed RNA polymerase subunit alpha [Arthrobacter sp. FB24]
          Length = 336

 Score =  348 bits (894), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 123/315 (39%), Positives = 190/315 (60%), Gaps = 4/315 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V     ENR+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLSEEVV----SENRSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+T+IILNIK +++    D      + K+GPGVVTA DI     +E  NP
Sbjct: 62  EFTTVPGVKEDVTEIILNIKNLSVSSEHDEPVVAYLRKQGPGVVTAADIAPPAGVEFHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+      +ELT+ +G GYV A  +++ +  IG I +D++YSP+ KV++ VE+ 
Sbjct: 122 DLHIATLNSKGKFELELTIERGRGYVSAAQNKSGDSEIGRIPVDSIYSPVLKVTFRVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  +I   D+VA A   L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAIAPRDAVASAGTTLVELFGLARELNTAAEGIEIGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                +   +E+L+L+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L
Sbjct: 242 ALAADMALPIEDLDLTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWP 325
             +GL L  + P + 
Sbjct: 302 VELGLSLKDSPPGFD 316


>gi|46579740|ref|YP_010548.1| DNA-directed RNA polymerase subunit alpha [Desulfovibrio vulgaris
           str. Hildenborough]
 gi|120602783|ref|YP_967183.1| DNA-directed RNA polymerase subunit alpha [Desulfovibrio vulgaris
           DP4]
 gi|61215968|sp|Q72CF4|RPOA_DESVH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158513912|sp|A1VE90|RPOA_DESVV RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|46449155|gb|AAS95807.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio vulgaris
           str. Hildenborough]
 gi|120563012|gb|ABM28756.1| DNA-directed RNA polymerase subunit alpha [Desulfovibrio vulgaris
           DP4]
 gi|311233531|gb|ADP86385.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio vulgaris
           RCH1]
          Length = 347

 Score =  348 bits (894), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 149/335 (44%), Positives = 217/335 (64%), Gaps = 1/335 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW EL+KP  I       +       + EPL RG+A T+GNA+RRVL+SSL+GAA  AV
Sbjct: 13  RNWSELVKPEQISRDGEVSDT-MYGKFVCEPLERGYATTIGNAMRRVLLSSLQGAAFVAV 71

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I GV HE ++I GV ED+TD++LN+K + L M  +  + + +     G +TAGD++T  
Sbjct: 72  KISGVQHEFTTIPGVLEDVTDVVLNLKQVRLAMDTEEPQYLELKVDKRGAITAGDVRTNQ 131

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            + VLNPD  I  L  D  +  EL V  G GYVPA  H   ++ IGLI +DA +SP++KV
Sbjct: 132 HVMVLNPDQHIATLTEDIELTFELEVRMGKGYVPADMHEGLSEEIGLIKLDASFSPVRKV 191

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +YTVE AR GQ+ +YDKL + + TDGS++ ED++A +++I++DQ+ +FINF+E       
Sbjct: 192 AYTVEQARVGQMTNYDKLILEVWTDGSVSPEDAIAYSAKIIKDQISVFINFDERISGENS 251

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           + +  S  FN  L K ++ELELSVR+TNCL+  NI  +G+L+Q++E +ML+  NFGRKSL
Sbjct: 252 NGSADSGEFNEHLFKSIDELELSVRATNCLKSANIALVGELVQKSENEMLKTKNFGRKSL 311

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
            EI+ VLG MGL  G  +  +  +  E   K+  +
Sbjct: 312 DEIRRVLGDMGLDFGTKVDGFEKKYQEWKRKQQHE 346


>gi|120597014|ref|YP_961588.1| DNA-directed RNA polymerase subunit alpha [Shewanella sp. W3-18-1]
 gi|146294816|ref|YP_001185240.1| DNA-directed RNA polymerase subunit alpha [Shewanella putrefaciens
           CN-32]
 gi|158512973|sp|A1RED9|RPOA_SHESW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172046873|sp|A4YBV8|RPOA_SHEPC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|120557107|gb|ABM23034.1| DNA-directed RNA polymerase, alpha subunit [Shewanella sp. W3-18-1]
 gi|145566506|gb|ABP77441.1| DNA-directed RNA polymerase, alpha subunit [Shewanella putrefaciens
           CN-32]
 gi|319424605|gb|ADV52679.1| DNA-directed RNA polymerase, alpha subunit [Shewanella putrefaciens
           200]
          Length = 329

 Score =  348 bits (894), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 143/333 (42%), Positives = 214/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVNSTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVTIEGKDEAMLTLSKSGAGPVIAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  + M + V +G GYVPA        ++ PIG + +DA +S
Sbjct: 118 DGDVTIVNPDHVICHLTGNNDISMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   +  
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFVELRDVT 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +     +  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 EPE---LKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>gi|24371854|ref|NP_715896.1| DNA-directed RNA polymerase subunit alpha [Shewanella oneidensis
           MR-1]
 gi|113968569|ref|YP_732362.1| DNA-directed RNA polymerase subunit alpha [Shewanella sp. MR-4]
 gi|114045732|ref|YP_736282.1| DNA-directed RNA polymerase subunit alpha [Shewanella sp. MR-7]
 gi|117918682|ref|YP_867874.1| DNA-directed RNA polymerase subunit alpha [Shewanella sp. ANA-3]
 gi|41688704|sp|Q8EK47|RPOA_SHEON RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366727|sp|Q0HNR2|RPOA_SHESM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366728|sp|Q0I080|RPOA_SHESR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158512311|sp|A0KRP9|RPOA_SHESA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|24345671|gb|AAN53341.1|AE015474_4 DNA-directed RNA polymerase, alpha subunit [Shewanella oneidensis
           MR-1]
 gi|113883253|gb|ABI37305.1| DNA-directed RNA polymerase, alpha subunit [Shewanella sp. MR-4]
 gi|113887174|gb|ABI41225.1| DNA-directed RNA polymerase, alpha subunit [Shewanella sp. MR-7]
 gi|117611014|gb|ABK46468.1| DNA-directed RNA polymerase, alpha subunit [Shewanella sp. ANA-3]
          Length = 329

 Score =  348 bits (894), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 143/333 (42%), Positives = 214/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVNSTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVTIEGKDEAMLTLSKSGAGPVIAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  + M + V +G GYVPA        ++ PIG + +DA +S
Sbjct: 118 DGDVTIVNPDHVICHLTGNNDISMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   +  
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFVELRDVT 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +     +  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 EPE---MKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>gi|183601970|ref|ZP_02963339.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium animalis
           subsp. lactis HN019]
 gi|219682882|ref|YP_002469265.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium animalis
           subsp. lactis AD011]
 gi|241190459|ref|YP_002967853.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium animalis
           subsp. lactis Bl-04]
 gi|241195865|ref|YP_002969420.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium animalis
           subsp. lactis DSM 10140]
 gi|183218855|gb|EDT89497.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium animalis
           subsp. lactis HN019]
 gi|219620532|gb|ACL28689.1| DNA-directed RNA polymerase, alpha subunit [Bifidobacterium
           animalis subsp. lactis AD011]
 gi|240248851|gb|ACS45791.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium animalis
           subsp. lactis Bl-04]
 gi|240250419|gb|ACS47358.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium animalis
           subsp. lactis DSM 10140]
 gi|289178183|gb|ADC85429.1| DNA-directed RNA polymerase alpha chain [Bifidobacterium animalis
           subsp. lactis BB-12]
 gi|295793446|gb|ADG32981.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium animalis
           subsp. lactis V9]
          Length = 331

 Score =  348 bits (894), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 121/312 (38%), Positives = 183/312 (58%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                   R+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ G+
Sbjct: 10  TEESLNPQRSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTTLPGI 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+I+LNIKGI L    D    + + K G G  TAGDI     + + NPD  I  L 
Sbjct: 70  EEDVTEILLNIKGIVLTSEYDEPVVMYLRKAGSGEATAGDITPPAGVTIANPDLHIATLA 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  + +E TV +G GYVPA+ ++ + D IG I +D++YSP+ KVSY VE+ R  Q  D+
Sbjct: 130 EDGELEIEFTVERGRGYVPAQMNKQDGDEIGRIPVDSIYSPVLKVSYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  +I+  D+VA A   L +  G+        + V+      +   +P +  
Sbjct: 190 DKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNTQAEGVEIGPAPVAEQADPGMSV 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L ++GL L 
Sbjct: 250 PIEDLNLTQRSYNCLKREGIHTVGELVNHTEQDLLDIRNFGMKSIDEVKEKLQSLGLSLK 309

Query: 319 MNLPDWPPESIE 330
            +   +   ++E
Sbjct: 310 SSPLGFDTNNLE 321


>gi|22127885|ref|NP_671308.1| DNA-directed RNA polymerase subunit alpha [Yersinia pestis KIM 10]
 gi|45440092|ref|NP_991631.1| DNA-directed RNA polymerase subunit alpha [Yersinia pestis biovar
           Microtus str. 91001]
 gi|51597963|ref|YP_072154.1| DNA-directed RNA polymerase subunit alpha [Yersinia
           pseudotuberculosis IP 32953]
 gi|108809230|ref|YP_653146.1| DNA-directed RNA polymerase subunit alpha [Yersinia pestis Antiqua]
 gi|108813995|ref|YP_649762.1| DNA-directed RNA polymerase subunit alpha [Yersinia pestis
           Nepal516]
 gi|145597475|ref|YP_001161550.1| DNA-directed RNA polymerase subunit alpha [Yersinia pestis
           Pestoides F]
 gi|150260718|ref|ZP_01917446.1| DNA-directed RNA polymerase alpha chain [Yersinia pestis CA88-4125]
 gi|153948087|ref|YP_001402838.1| DNA-directed RNA polymerase subunit alpha [Yersinia
           pseudotuberculosis IP 31758]
 gi|162420536|ref|YP_001605197.1| DNA-directed RNA polymerase subunit alpha [Yersinia pestis Angola]
 gi|165927880|ref|ZP_02223712.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Orientalis str. F1991016]
 gi|165936419|ref|ZP_02224987.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Orientalis str. IP275]
 gi|166010435|ref|ZP_02231333.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Antiqua str. E1979001]
 gi|166213170|ref|ZP_02239205.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Antiqua str. B42003004]
 gi|167398622|ref|ZP_02304146.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Antiqua str. UG05-0454]
 gi|167419336|ref|ZP_02311089.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Orientalis str. MG05-1020]
 gi|167425603|ref|ZP_02317356.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Mediaevalis str. K1973002]
 gi|170022569|ref|YP_001719074.1| DNA-directed RNA polymerase subunit alpha [Yersinia
           pseudotuberculosis YPIII]
 gi|186897159|ref|YP_001874271.1| DNA-directed RNA polymerase subunit alpha [Yersinia
           pseudotuberculosis PB1/+]
 gi|218927440|ref|YP_002345315.1| DNA-directed RNA polymerase subunit alpha [Yersinia pestis CO92]
 gi|229836284|ref|ZP_04456451.1| RNA polymerase, alpha subunit [Yersinia pestis Pestoides A]
 gi|229840092|ref|ZP_04460251.1| RNA polymerase, alpha subunit [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229842174|ref|ZP_04462329.1| RNA polymerase, alpha subunit [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229904526|ref|ZP_04519637.1| RNA polymerase, alpha subunit [Yersinia pestis Nepal516]
 gi|270488256|ref|ZP_06205330.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis KIM
           D27]
 gi|294502309|ref|YP_003566371.1| DNA-directed RNA polymerase alpha subunit [Yersinia pestis Z176003]
 gi|311277750|ref|YP_003939981.1| DNA-directed RNA polymerase, alpha subunit [Enterobacter cloacae
           SCF1]
 gi|20139507|sp|Q8ZJ87|RPOA_YERPE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61215876|sp|Q664U6|RPOA_YERPS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366751|sp|Q1C2X1|RPOA_YERPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366752|sp|Q1CCW8|RPOA_YERPN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158514063|sp|A4TH15|RPOA_YERPP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|171769159|sp|A7FNL0|RPOA_YERP3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|21961021|gb|AAM87559.1|AE014003_17 RNA polymerase, alpha subunit [Yersinia pestis KIM 10]
 gi|45434947|gb|AAS60508.1| DNA-directed RNA polymerase alpha chain [Yersinia pestis biovar
           Microtus str. 91001]
 gi|51591245|emb|CAH22911.1| DNA-directed RNA polymerase alpha chain [Yersinia
           pseudotuberculosis IP 32953]
 gi|108777643|gb|ABG20162.1| DNA-directed RNA polymerase alpha chain [Yersinia pestis Nepal516]
 gi|108781143|gb|ABG15201.1| DNA-directed RNA polymerase alpha chain [Yersinia pestis Antiqua]
 gi|115346051|emb|CAL18917.1| DNA-directed RNA polymerase alpha chain [Yersinia pestis CO92]
 gi|145209171|gb|ABP38578.1| DNA-directed RNA polymerase alpha chain [Yersinia pestis Pestoides
           F]
 gi|149290126|gb|EDM40203.1| DNA-directed RNA polymerase alpha chain [Yersinia pestis CA88-4125]
 gi|152959582|gb|ABS47043.1| DNA-directed RNA polymerase, alpha subunit [Yersinia
           pseudotuberculosis IP 31758]
 gi|162353351|gb|ABX87299.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis Angola]
 gi|165915535|gb|EDR34144.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Orientalis str. IP275]
 gi|165920156|gb|EDR37457.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Orientalis str. F1991016]
 gi|165990525|gb|EDR42826.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Antiqua str. E1979001]
 gi|166205468|gb|EDR49948.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Antiqua str. B42003004]
 gi|166963330|gb|EDR59351.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Orientalis str. MG05-1020]
 gi|167051126|gb|EDR62534.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Antiqua str. UG05-0454]
 gi|167055293|gb|EDR65087.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis biovar
           Mediaevalis str. K1973002]
 gi|169749103|gb|ACA66621.1| DNA-directed RNA polymerase, alpha subunit [Yersinia
           pseudotuberculosis YPIII]
 gi|186700185|gb|ACC90814.1| DNA-directed RNA polymerase, alpha subunit [Yersinia
           pseudotuberculosis PB1/+]
 gi|229678644|gb|EEO74749.1| RNA polymerase, alpha subunit [Yersinia pestis Nepal516]
 gi|229690484|gb|EEO82538.1| RNA polymerase, alpha subunit [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229696458|gb|EEO86505.1| RNA polymerase, alpha subunit [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229706352|gb|EEO92359.1| RNA polymerase, alpha subunit [Yersinia pestis Pestoides A]
 gi|262360389|gb|ACY57110.1| DNA-directed RNA polymerase alpha subunit [Yersinia pestis D106004]
 gi|262364339|gb|ACY60896.1| DNA-directed RNA polymerase alpha subunit [Yersinia pestis D182038]
 gi|270336760|gb|EFA47537.1| DNA-directed RNA polymerase, alpha subunit [Yersinia pestis KIM
           D27]
 gi|294352768|gb|ADE63109.1| DNA-directed RNA polymerase alpha subunit [Yersinia pestis Z176003]
 gi|308746945|gb|ADO46697.1| DNA-directed RNA polymerase, alpha subunit [Enterobacter cloacae
           SCF1]
 gi|320013367|gb|ADV96938.1| RNA polymerase, alpha subunit [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 329

 Score =  348 bits (894), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASINMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|297564065|ref|YP_003683038.1| DNA-directed RNA polymerase, alpha subunit [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296848514|gb|ADH70532.1| DNA-directed RNA polymerase, alpha subunit [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 340

 Score =  348 bits (894), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 122/321 (38%), Positives = 188/321 (58%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                 + R+  + EPL  GF +T+GN+LRR L+SS+ GAA+T+++I+GV HE +++ GV
Sbjct: 10  TEEASSDLRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGAAVTSIRIEGVEHEFTTVPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T++ILN+KG+ +    D    + + K+GPGVVTA DI     +EV NPD  I  L+
Sbjct: 70  KEDVTEMILNLKGLVVSSEHDEPVLMYLRKQGPGVVTAADIAPPAGVEVHNPDLHIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + MELTV +G GYV A  ++     IG I ID++YSP+ +V+Y VE+ R  Q  D+
Sbjct: 130 GKGKLEMELTVERGRGYVSATQNKQAGQEIGRIPIDSIYSPVLRVTYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           D+L + I+T  +I   D+VA A + L +  G+        + +    +         L  
Sbjct: 190 DRLIVDIETKPAIRPRDAVASAGKTLVELFGLARELNVDAEGIDMGPSPTDAALAADLAL 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  MGL L 
Sbjct: 250 PIEDLNLTVRSYNCLKREGIHSVGELVARSEQDLLDIRNFGAKSIDEVKQKLVDMGLSLK 309

Query: 319 MNLPDWPPESIEELAKKYEDK 339
            + P + P S  +     +D+
Sbjct: 310 DSPPGFDPSSAADSYSSEDDE 330


>gi|62181920|ref|YP_218337.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Choleraesuis str. SC-B67]
 gi|75480371|sp|Q57J56|RPOA_SALCH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|62129553|gb|AAX67256.1| DNA-directed RNA polymerase alpha chain [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|322716406|gb|EFZ07977.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Choleraesuis str. A50]
          Length = 329

 Score =  348 bits (894), Expect = 6e-94,   Method: Composition-based stats.
 Identities = 148/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L DWPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLEDWPPASIAD 328


>gi|251787996|ref|YP_003002717.1| DNA-directed RNA polymerase subunit alpha [Dickeya zeae Ech1591]
 gi|271502221|ref|YP_003335247.1| DNA-directed RNA polymerase subunit alpha [Dickeya dadantii Ech586]
 gi|307132814|ref|YP_003884830.1| DNA-directed RNA polymerase subunit alpha [Dickeya dadantii 3937]
 gi|247536617|gb|ACT05238.1| DNA-directed RNA polymerase, alpha subunit [Dickeya zeae Ech1591]
 gi|270345776|gb|ACZ78541.1| DNA-directed RNA polymerase, alpha subunit [Dickeya dadantii
           Ech586]
 gi|306530343|gb|ADN00274.1| DNA-directed RNA polymerase alpha subunit [Dickeya dadantii 3937]
          Length = 329

 Score =  348 bits (894), Expect = 6e-94,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASINMRIKVQRGRGYVPASARIHTEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|295677906|ref|YP_003606430.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia sp.
           CCGE1002]
 gi|295437749|gb|ADG16919.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia sp.
           CCGE1002]
          Length = 325

 Score =  348 bits (894), Expect = 6e-94,   Method: Composition-based stats.
 Identities = 153/328 (46%), Positives = 212/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP  I    LG   E+   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPKIIAVESLG---ESHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVVTAGDI+  +D E
Sbjct: 60  GVVHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVTAGDIELAHDCE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKV 183
           V+NPDHVI +L     + +++ V KG GYVP    R   +     G I +DA +SP+++V
Sbjct: 120 VINPDHVIAHLSKGGKLDVQIKVEKGRGYVPGNVRRYGEESSKIIGRIVLDASFSPVRRV 179

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL DQL +F   E    E   
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALE--GTEAAA 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 238 ETPSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|255526607|ref|ZP_05393514.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           carboxidivorans P7]
 gi|296187296|ref|ZP_06855692.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           carboxidivorans P7]
 gi|255509715|gb|EET86048.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           carboxidivorans P7]
 gi|296048167|gb|EFG87605.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           carboxidivorans P7]
          Length = 315

 Score =  348 bits (894), Expect = 6e-94,   Method: Composition-based stats.
 Identities = 132/313 (42%), Positives = 205/313 (65%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  E+ +    + EPL RG+  TLGNALRR+L+SSL G A   ++IDG
Sbjct: 3   EIEKP-KIECVEVN-EDGSYGKFVVEPLERGYGITLGNALRRILLSSLPGVAANHIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+ +++LNIK + LKM+G+  K + I  +GPG V AGDI+T  DIE+
Sbjct: 61  VLHEFSTVRGVKEDVAELVLNIKCLALKMNGEGPKTIYIDAQGPGEVVAGDIKTDGDIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N D  I  LD D  + ME+ V+ G GYV    +++E+ PIG I ID++Y+PIK+V++ V
Sbjct: 121 INKDLHIATLDDDGKLYMEIQVNTGRGYVSQTKNKSEDMPIGTIAIDSIYTPIKRVNFVV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ DYDKLS+ + T+G+I  E++++L+++IL +   +F+   +    V+  +  
Sbjct: 181 ENTRVGQITDYDKLSLEVWTNGTIMPEEAISLSAKILIEHFKLFMTLTDHANNVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L +RT  DM+++ N G+KSL E++
Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTERTMDDMMKVRNLGKKSLEEVE 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 301 QKLEALGLSLKQS 313


>gi|119502948|ref|ZP_01625033.1| DNA-directed RNA polymerase subunit alpha [marine gamma
           proteobacterium HTCC2080]
 gi|119461294|gb|EAW42384.1| DNA-directed RNA polymerase subunit alpha [marine gamma
           proteobacterium HTCC2080]
          Length = 334

 Score =  348 bits (894), Expect = 6e-94,   Method: Composition-based stats.
 Identities = 147/336 (43%), Positives = 219/336 (65%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  N  E + P     I + ++   R  +  EPL RGF HTLGNALRR+L+SS+ G AIT
Sbjct: 1   MSTNVNEFLTPR---VIKVDEKSPTRAQVTLEPLERGFGHTLGNALRRILLSSMPGCAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGV HE S+++G  ED+ +I+LN+KG+ L M+G     +++  +GP  VTA +IQT
Sbjct: 58  EVEIDGVQHEYSAVEGAQEDVIEILLNLKGVALSMTGKDEAELSLVAKGPCTVTAAEIQT 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
            +D+++ NPDHVIC+L  D  + M + V +G GY PA        E   IG + +DA +S
Sbjct: 118 DHDVQIGNPDHVICHLTADQELVMRVVVERGRGYSPADSRINPEEETRSIGKLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY V+SAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++ E   
Sbjct: 178 PVRRVSYVVDSARVEQRTDLDKLIIDLETNGTIDPEEAIRRAATILQQQLLVFVDLESEA 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +   ++ + +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N 
Sbjct: 238 QATAQEADDE---VDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+    +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLRNDER 330


>gi|119961601|ref|YP_948627.1| DNA-directed RNA polymerase subunit alpha [Arthrobacter aurescens
           TC1]
 gi|158512966|sp|A1R8R5|RPOA_ARTAT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119948460|gb|ABM07371.1| DNA-directed RNA polymerase, alpha subunit [Arthrobacter aurescens
           TC1]
          Length = 336

 Score =  348 bits (894), Expect = 6e-94,   Method: Composition-based stats.
 Identities = 123/315 (39%), Positives = 190/315 (60%), Gaps = 4/315 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V     ENR+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLSEEVV----SENRSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+T+IILNIK +++    D      + K+GPGVVTA DI     +E  NP
Sbjct: 62  EFTTVPGVKEDVTEIILNIKNLSVSSEHDEPVVAYLRKQGPGVVTAADIAPPAGVEFHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+      +ELT+ +G GYV A  +++ +  IG I +D++YSP+ KV++ VE+ 
Sbjct: 122 DLHIATLNSKGKFELELTIERGRGYVSAAQNKSGDSEIGRIPVDSIYSPVMKVTFRVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  +I   D+VA A   L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAIAPRDAVASAGTTLVELFGLARELNTAAEGIEIGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                +   +E+L+L+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L
Sbjct: 242 ALAADMALPIEDLDLTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWP 325
             +GL L  + P + 
Sbjct: 302 VELGLSLKDSPPGFD 316


>gi|224283735|ref|ZP_03647057.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium bifidum
           NCIMB 41171]
 gi|310287998|ref|YP_003939257.1| rpoA DNA-directed RNA polymerase alpha chain [Bifidobacterium
           bifidum S17]
 gi|311064871|ref|YP_003971597.1| DNA-directed RNA polymerase subunit alpha RpoA [Bifidobacterium
           bifidum PRL2010]
 gi|313140891|ref|ZP_07803084.1| DNA-directed RNA polymerase [Bifidobacterium bifidum NCIMB 41171]
 gi|309251935|gb|ADO53683.1| rpoA DNA-directed RNA polymerase alpha chain [Bifidobacterium
           bifidum S17]
 gi|310867191|gb|ADP36560.1| RpoA DNA-directed RNA polymerase alpha chain [Bifidobacterium
           bifidum PRL2010]
 gi|313133401|gb|EFR51018.1| DNA-directed RNA polymerase [Bifidobacterium bifidum NCIMB 41171]
          Length = 331

 Score =  348 bits (894), Expect = 6e-94,   Method: Composition-based stats.
 Identities = 124/312 (39%), Positives = 184/312 (58%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                   R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ GV
Sbjct: 10  TEESINPQRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTTLPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+I+LNIKGI L    D    + + K G G VTAGDI     + + NPD  I  L 
Sbjct: 70  VEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGNGEVTAGDITPPAGVTIANPDQHIATLA 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  + +E TV +G GYVPA+ ++ + D IG I +D++YSP+ KVSY VE+ R  Q  D+
Sbjct: 130 DDGELEIEFTVERGRGYVPAQMNKQDTDEIGRIPVDSIYSPVLKVSYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  +I+  D+VA A   L +  G+        + V+      +   NP +  
Sbjct: 190 DKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNVQAEGVEVGPAPVAEETNPEMAV 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L +MGL L 
Sbjct: 250 PIEDLNLTQRSYNCLKREGIHTIGELVAHTEQDLLDIRNFGMKSIDEVKDKLQSMGLSLK 309

Query: 319 MNLPDWPPESIE 330
            +   +   ++E
Sbjct: 310 SSPLGFDTNNLE 321


>gi|127511117|ref|YP_001092314.1| DNA-directed RNA polymerase subunit alpha [Shewanella loihica PV-4]
 gi|158513465|sp|A3Q9A7|RPOA_SHELP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|126636412|gb|ABO22055.1| DNA-directed RNA polymerase, alpha subunit [Shewanella loihica
           PV-4]
          Length = 329

 Score =  348 bits (894), Expect = 6e-94,   Method: Composition-based stats.
 Identities = 143/333 (42%), Positives = 214/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVNPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVVIEGKDEAMLTLSKSGAGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  + M + V +G GYVPA        ++ PIG + +D+ +S
Sbjct: 118 DGDVTIMNPDHVICHLTGNNDISMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   +  
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFVELRDVT 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +        +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 EPE---QKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>gi|91791564|ref|YP_561215.1| DNA-directed RNA polymerase subunit alpha [Shewanella denitrificans
           OS217]
 gi|119366725|sp|Q12ST4|RPOA_SHEDO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|91713566|gb|ABE53492.1| DNA-directed RNA polymerase, alpha subunit [Shewanella
           denitrificans OS217]
          Length = 329

 Score =  348 bits (894), Expect = 6e-94,   Method: Composition-based stats.
 Identities = 144/331 (43%), Positives = 213/331 (64%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVNPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVTIEGKDEAMLTLSKSGTGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  + M + V +G GYVPA        ++ PIG + +DA +S
Sbjct: 118 DGDVTIMNPDHVICHLTGNNDISMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   +  
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFVELRDVT 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +        +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 EPE---QKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASL 325


>gi|15603255|ref|NP_246329.1| DNA-directed RNA polymerase subunit alpha [Pasteurella multocida
           subsp. multocida str. Pm70]
 gi|13431846|sp|P57941|RPOA_PASMU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|12721765|gb|AAK03474.1| RpoA [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 329

 Score =  348 bits (893), Expect = 6e-94,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVFLTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALY 177
             D+E++NP+HVIC+L D  A + M + V +G GYVPA      + E  PIG + +DA Y
Sbjct: 118 DGDVEIVNPEHVICHLTDESASINMRIRVQRGRGYVPASARVHAQDEERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|258651412|ref|YP_003200568.1| DNA-directed RNA polymerase subunit alpha [Nakamurella multipartita
           DSM 44233]
 gi|258554637|gb|ACV77579.1| DNA-directed RNA polymerase, alpha subunit [Nakamurella
           multipartita DSM 44233]
          Length = 360

 Score =  348 bits (893), Expect = 6e-94,   Method: Composition-based stats.
 Identities = 119/309 (38%), Positives = 183/309 (59%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                 +NR+  I EPL  GF +TLGN+LRR L+SS+ GA++T++++DGVLHE +++ GV
Sbjct: 10  TEEPVADNRSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIRVDGVLHEFTTVPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T++ILN+K + +    D    + + K+GPG VTA DI     + V N D  +  L 
Sbjct: 70  KEDITELILNLKELVVSSEDDEPVTMYLRKQGPGDVTAADIAPPAGVTVHNSDLKLATLT 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+
Sbjct: 130 KKGKLEIELVVERGRGYVPASPNKVVGAEIGRIPVDSIYSPVLKVTYRVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  SIT  D++A A   L +  G+        + ++   +        A   
Sbjct: 190 DKLVLDVETKPSITPRDALASAGTTLVELFGLARELNVDAEGIEIGPSPAEADHIAAFGL 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +EE++L+VRS NCL+ E I  +G+L+ RTEAD+L + NFG+KS+ E+K  L  MGL L 
Sbjct: 250 PIEEMDLTVRSYNCLKREGIHTVGELVSRTEADLLDIRNFGQKSIDEVKIKLAGMGLALK 309

Query: 319 MNLPDWPPE 327
            +   + P 
Sbjct: 310 DSPAGFDPA 318


>gi|238797219|ref|ZP_04640720.1| DNA-directed RNA polymerase subunit alpha [Yersinia mollaretii ATCC
           43969]
 gi|238718856|gb|EEQ10671.1| DNA-directed RNA polymerase subunit alpha [Yersinia mollaretii ATCC
           43969]
          Length = 329

 Score =  348 bits (893), Expect = 6e-94,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRVKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|242237884|ref|YP_002986065.1| DNA-directed RNA polymerase subunit alpha [Dickeya dadantii Ech703]
 gi|242129941|gb|ACS84243.1| DNA-directed RNA polymerase, alpha subunit [Dickeya dadantii
           Ech703]
          Length = 329

 Score =  348 bits (893), Expect = 6e-94,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASINMRIKVQRGRGYVPASARIHTEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|238754197|ref|ZP_04615555.1| DNA-directed RNA polymerase subunit alpha [Yersinia ruckeri ATCC
           29473]
 gi|238758785|ref|ZP_04619959.1| DNA-directed RNA polymerase subunit alpha [Yersinia aldovae ATCC
           35236]
 gi|238783188|ref|ZP_04627214.1| DNA-directed RNA polymerase subunit alpha [Yersinia bercovieri ATCC
           43970]
 gi|238792960|ref|ZP_04636590.1| DNA-directed RNA polymerase subunit alpha [Yersinia intermedia ATCC
           29909]
 gi|238703082|gb|EEP95625.1| DNA-directed RNA polymerase subunit alpha [Yersinia aldovae ATCC
           35236]
 gi|238707693|gb|EEQ00053.1| DNA-directed RNA polymerase subunit alpha [Yersinia ruckeri ATCC
           29473]
 gi|238715984|gb|EEQ07970.1| DNA-directed RNA polymerase subunit alpha [Yersinia bercovieri ATCC
           43970]
 gi|238727814|gb|EEQ19338.1| DNA-directed RNA polymerase subunit alpha [Yersinia intermedia ATCC
           29909]
          Length = 329

 Score =  348 bits (893), Expect = 7e-94,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|28212154|ref|NP_783098.1| DNA-directed RNA polymerase subunit alpha [Clostridium tetani E88]
 gi|41688695|sp|Q890R0|RPOA_CLOTE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|28204598|gb|AAO37035.1| DNA-directed RNA polymerase alpha chain [Clostridium tetani E88]
          Length = 315

 Score =  348 bits (893), Expect = 7e-94,   Method: Composition-based stats.
 Identities = 134/313 (42%), Positives = 207/313 (66%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I +  E  +    + EPL RG+  TLGNALRR+L+SSL G A+ +++I+ 
Sbjct: 3   EIEKP-KIECIEM-TENGSYGKFVVEPLERGYGITLGNALRRILLSSLPGVAVNSIKIEN 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++KGV ED+T+IILNIK + LKM+G+  K + I  +GPGVVTA DI+T +D+E+
Sbjct: 61  VLHEFSTVKGVKEDVTEIILNIKLLALKMTGEGPKTIYIDAKGPGVVTAADIKTDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N D  I  LD D  + +E+TV +G GYV    ++ E  PIG I ID++Y+P+K+V++TV
Sbjct: 121 INKDLHIATLDDDGKLYIEMTVDRGRGYVSQNRNKVEGMPIGTIPIDSIYTPVKRVNFTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
            + R GQ+ DYDKL++ I T+G+I  +D+++L+++IL +   +F+   +   +V+  +  
Sbjct: 181 ANTRVGQITDYDKLTLEIWTNGTIMPDDAISLSAKILIEHFKLFMTLTDHADDVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L +RT  DM+++ N GRKSL E++
Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTERTVEDMMKVRNLGRKSLEEVE 300

Query: 308 GVLGTMGLFLGMN 320
             L  + L L  +
Sbjct: 301 QKLEALELGLKQS 313


>gi|320540586|ref|ZP_08040236.1| RNA polymerase, alpha subunit [Serratia symbiotica str. Tucson]
 gi|320029517|gb|EFW11546.1| RNA polymerase, alpha subunit [Serratia symbiotica str. Tucson]
          Length = 329

 Score =  348 bits (893), Expect = 7e-94,   Method: Composition-based stats.
 Identities = 145/334 (43%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++   HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA +
Sbjct: 118 DGDVEIVKSQHVICHLTDENAAISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLIIEMETNGAIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL  V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLCPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|94987424|ref|YP_595357.1| DNA-directed RNA polymerase subunit alpha [Lawsonia intracellularis
           PHE/MN1-00]
 gi|119366693|sp|Q1MPP1|RPOA_LAWIP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|94731673|emb|CAJ55036.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Lawsonia
           intracellularis PHE/MN1-00]
          Length = 347

 Score =  348 bits (893), Expect = 7e-94,   Method: Composition-based stats.
 Identities = 150/335 (44%), Positives = 218/335 (65%), Gaps = 1/335 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW +L++P  +    +            EPL RG+  T+GNALRRVL+SSL+GAA  +V
Sbjct: 13  RNWAKLVRPEAV-INNMESNTTTYGRFEYEPLERGYGITIGNALRRVLLSSLQGAAFVSV 71

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I GV HE ++I G+ ED+TDIILN+K + L M  D  + +++F    G+VTA DIQT  
Sbjct: 72  KILGVQHEFTTIPGILEDVTDIILNLKQVRLAMDTDEPQHLSLFVSKKGIVTAADIQTNQ 131

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            +EVLNP+  I  L  D  +RME  V  G GYVPA+ H   ++ IGLI +D+ +SPI+ V
Sbjct: 132 HVEVLNPEQHIATLTEDIELRMEFEVRMGKGYVPAEMHEDLHEEIGLIKLDSSFSPIRNV 191

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE AR GQ+ +YDKL + + TDGS++ ED++A +++I++DQ+ +FINF+E       
Sbjct: 192 TYVVEQARVGQMTNYDKLVLEVWTDGSVSPEDAIAYSAKIIKDQISVFINFDERISGSGG 251

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +    S   N  L K ++ELELSVR+TNCLR  NI  +G+L+Q+ EADML+  NFG+KSL
Sbjct: 252 NEGSGSSDLNDNLFKGIDELELSVRATNCLRSANISTVGELVQKAEADMLKTKNFGKKSL 311

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
            EIK +L +MGL  GM +  +  +  E   K++ +
Sbjct: 312 DEIKALLTSMGLDFGMKIDGFEKKYQEWKRKQHHE 346


>gi|322515610|ref|ZP_08068589.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus ureae
           ATCC 25976]
 gi|322118320|gb|EFX90595.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus ureae
           ATCC 25976]
          Length = 329

 Score =  348 bits (893), Expect = 7e-94,   Method: Composition-based stats.
 Identities = 150/334 (44%), Positives = 224/334 (67%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ +    + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVN---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +G+ ED+ +++LN+KG+ +K+S      +T+ K G G VTA DI  
Sbjct: 58  EVKIDGVLHEYSSKEGIQEDILEVLLNLKGLAVKVSNKDDIILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++NPDHVIC+L D +A + M + V +G GYVPA    H + E+ PIG + +DA +
Sbjct: 118 DGDVEIVNPDHVICHLTDKNASINMCIRVQRGRGYVPASARVHSQDEDRPIGRLLVDARF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|167587746|ref|ZP_02380134.1| DNA-directed RNA polymerase subunit alpha [Burkholderia ubonensis
           Bu]
          Length = 325

 Score =  348 bits (893), Expect = 7e-94,   Method: Composition-based stats.
 Identities = 154/328 (46%), Positives = 211/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP  I    LG   EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPKIIAVESLG---ENHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVVTA DI+  +D E
Sbjct: 60  GVVHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVTAADIELAHDCE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKV 183
           V+NP+HVI +L     + +++ + KG GYVP    R   D    IG I +DA +SP+++V
Sbjct: 120 VINPNHVIAHLSKGGKLDVQIKIEKGRGYVPGNVRRYGEDTAKIIGRIVLDASFSPVRRV 179

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VESAR  Q  D DKL M I+T G IT E+++  ++RIL DQL +F   E    E   
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETSGVITPEEAIRQSARILVDQLSVFAALE--GTETAA 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 238 EAPSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|163790168|ref|ZP_02184602.1| DNA-directed RNA polymerase subunit alpha [Carnobacterium sp. AT7]
 gi|328958703|ref|YP_004376089.1| DNA-directed RNA polymerase subunit alpha [Carnobacterium sp. 17-4]
 gi|159874659|gb|EDP68729.1| DNA-directed RNA polymerase subunit alpha [Carnobacterium sp. AT7]
 gi|328675027|gb|AEB31073.1| DNA-directed RNA polymerase subunit alpha [Carnobacterium sp. 17-4]
          Length = 314

 Score =  348 bits (893), Expect = 7e-94,   Method: Composition-based stats.
 Identities = 133/313 (42%), Positives = 202/313 (64%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I +  + +     + EPL RG+  TLGN+LRR+L+SSL GAA+T +QIDG
Sbjct: 3   EIEKPR-IETIEISDDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTTIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILNIK + LK+     K + I  +GP VVTA DI   +D+E+
Sbjct: 61  VLHEFSTVDGVVEDVTSIILNIKKLALKLYSGEDKTIEIDVKGPAVVTAADIIYDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +   A   + +T   G GYV A+H++ ++ PIG++ ID++Y+P+ +V+Y V
Sbjct: 121 LNPDLYICTVAEGARFHVRMTAKSGRGYVRAEHNKQDDMPIGVLPIDSIYTPVSRVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ    DKL++ +  DGSI+ E++V+LA++IL + L +F+N  +  ++ +  +  
Sbjct: 181 ENTRVGQKNISDKLTLDVWADGSISPEEAVSLAAKILTEHLNVFVNLTDEARKAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TEA+M+++ N GRKSL E+K
Sbjct: 241 EETHKEKMLEMTIEELDLSVRSYNCLKRAGINSVQELTDKTEAEMIKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  + L L  +
Sbjct: 301 FKLAELDLNLRQD 313


>gi|169830464|ref|YP_001716446.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Desulforudis
           audaxviator MP104C]
 gi|238688212|sp|B1I1B3|RPOA_DESAP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|169637308|gb|ACA58814.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Desulforudis
           audaxviator MP104C]
          Length = 315

 Score =  348 bits (893), Expect = 7e-94,   Method: Composition-based stats.
 Identities = 139/310 (44%), Positives = 206/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +   E      + +PL RG+  TLGN+LRRVL++SL GAA+TAV+IDG
Sbjct: 3   EIEKP-KIECVEMD-PEGTYGKFVVDPLERGYGITLGNSLRRVLLASLPGAAVTAVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE SSI GV ED+T++ILN+K + LK+ G+  + + I   G G +TAGDI T  D+E+
Sbjct: 61  VLHEFSSIPGVREDVTELILNLKSLRLKLYGEEDRLMRIEAEGEGRITAGDIITSPDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L+ DA + MELTV +G GYVPA+ ++  N  IG+I +D++++P+ KV++TV
Sbjct: 121 LNPDLHIATLEPDARLYMELTVGRGRGYVPAEKNKRGNHVIGVIPVDSIFTPVTKVNFTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           +  R G   D+DKL+M + TDGS+  +++++LA+RI  + L +F+   E    V+  +  
Sbjct: 181 DKTRVGHDTDFDKLTMEVWTDGSLRPDEALSLAARITTEHLRLFVGLTESVNNVEIMVTK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    N  L   +EEL+LSVRS NCL+   I  + +LIQR E +M+++ N G+KSL E+ 
Sbjct: 241 EEEKKNKLLEMPIEELDLSVRSYNCLKRAGINTVEELIQRNEEEMMKVRNLGKKSLEEVV 300

Query: 308 GVLGTMGLFL 317
             LG +GL L
Sbjct: 301 RKLGELGLDL 310


>gi|126176330|ref|YP_001052479.1| DNA-directed RNA polymerase subunit alpha [Shewanella baltica
           OS155]
 gi|152998774|ref|YP_001364455.1| DNA-directed RNA polymerase subunit alpha [Shewanella baltica
           OS185]
 gi|160873350|ref|YP_001552666.1| DNA-directed RNA polymerase subunit alpha [Shewanella baltica
           OS195]
 gi|217975176|ref|YP_002359927.1| DNA-directed RNA polymerase subunit alpha [Shewanella baltica
           OS223]
 gi|304412789|ref|ZP_07394391.1| DNA-directed RNA polymerase, alpha subunit [Shewanella baltica
           OS183]
 gi|307307453|ref|ZP_07587188.1| DNA-directed RNA polymerase, alpha subunit [Shewanella baltica
           BA175]
 gi|171704509|sp|A6WHV3|RPOA_SHEB8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|171769979|sp|A3DA47|RPOA_SHEB5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|125999535|gb|ABN63610.1| DNA-directed RNA polymerase, alpha subunit [Shewanella baltica
           OS155]
 gi|151363392|gb|ABS06392.1| DNA-directed RNA polymerase, alpha subunit [Shewanella baltica
           OS185]
 gi|160858872|gb|ABX47406.1| DNA-directed RNA polymerase, alpha subunit [Shewanella baltica
           OS195]
 gi|217500311|gb|ACK48504.1| DNA-directed RNA polymerase, alpha subunit [Shewanella baltica
           OS223]
 gi|304348869|gb|EFM13285.1| DNA-directed RNA polymerase, alpha subunit [Shewanella baltica
           OS183]
 gi|306910241|gb|EFN40674.1| DNA-directed RNA polymerase, alpha subunit [Shewanella baltica
           BA175]
 gi|315265578|gb|ADT92431.1| DNA-directed RNA polymerase, alpha subunit [Shewanella baltica
           OS678]
          Length = 329

 Score =  348 bits (893), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 142/333 (42%), Positives = 214/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVNSTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVTIEGKDEAMLTLSKSGAGPVIAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
             D+ ++NPDH+IC+L  +  + M + V +G GYVPA        ++ PIG + +DA +S
Sbjct: 118 DGDVTIVNPDHIICHLTGNNDISMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   +  
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFVELRDVT 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +     +  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 EPE---LKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>gi|94312222|ref|YP_585432.1| DNA-directed RNA polymerase subunit alpha [Cupriavidus
           metallidurans CH34]
 gi|119366711|sp|Q1LI63|RPOA_RALME RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|93356074|gb|ABF10163.1| RNA polymerase, alpha subunit [Cupriavidus metallidurans CH34]
          Length = 326

 Score =  348 bits (893), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 150/326 (46%), Positives = 211/326 (64%), Gaps = 7/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG        ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVEPLGDH---HAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S+I GV ED+ +++LN+KG+  K+       V++ K G GVVTA DI+  +D+E++
Sbjct: 62  VHEYSTIDGVQEDVVNLLLNLKGVVFKLHNRDEVTVSLRKDGEGVVTAADIELPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSY 185
           NP HVI +L     + M++ V +G GYVP    +  ++     G I +DA +SP+++VSY
Sbjct: 122 NPGHVIAHLSAGGKLDMQIKVEQGRGYVPGNVRKFGDEASKVIGRIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+TDG I+ E+++  ++RIL DQL +F   E   +   E  
Sbjct: 182 AVESARVEQRTDLDKLVMNIETDGVISPEEAIRQSARILVDQLSVFAALEG-TESAAEAA 240

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           + ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 241 SSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 300

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +E+
Sbjct: 301 IKEVLASRGLTLGMKLENWPPAGLEK 326


>gi|253995744|ref|YP_003047808.1| DNA-directed RNA polymerase subunit alpha [Methylotenera mobilis
           JLW8]
 gi|253982423|gb|ACT47281.1| DNA-directed RNA polymerase, alpha subunit [Methylotenera mobilis
           JLW8]
          Length = 328

 Score =  348 bits (893), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 156/333 (46%), Positives = 215/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++  VL      R  +  EP+ RGF +TLGNALRRVL+SS+ G AIT
Sbjct: 1   MQNSPTEYLKPRVVDVEVLSPL---RARVTLEPMERGFGYTLGNALRRVLLSSIPGFAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGV+HE S++ GV ED+ DI+LN+KG+ LK++  S   + + K   GVVTA D +T
Sbjct: 58  EVKIDGVVHEYSTLDGVQEDVVDILLNLKGVALKLNSKSETILKLNKSVEGVVTAADFET 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYS 178
            +D E++NPDHVI +L     + +E+ V  G GY P    +    E+  +G I +DA +S
Sbjct: 118 GHDAEIVNPDHVIAHLTKGGKLNLEVKVEIGRGYQPVPVRQKSNDEDRVLGFIMVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI KVSY V+SAR  Q  D DKL M ++T+G I  E ++  A+RIL  QL +F + E   
Sbjct: 178 PINKVSYYVDSARVEQRTDLDKLVMDVETNGVIEPEQAIRDAARILMGQLSVFADLEGAP 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            EV+      +   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 SEVEV---KSAPQVDPVLLRPVDDLELTVRSANCLKAENIFYIGDLIQRTENELLKAPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL T GL LGM L +WPP  +E+
Sbjct: 295 GRKSLNEIKDVLATRGLTLGMKLENWPPVGLEK 327


>gi|146313360|ref|YP_001178434.1| DNA-directed RNA polymerase subunit alpha [Enterobacter sp. 638]
 gi|152972203|ref|YP_001337349.1| DNA-directed RNA polymerase subunit alpha [Klebsiella pneumoniae
           subsp. pneumoniae MGH 78578]
 gi|157372752|ref|YP_001480741.1| DNA-directed RNA polymerase subunit alpha [Serratia proteamaculans
           568]
 gi|206579035|ref|YP_002236303.1| DNA-directed RNA polymerase, alpha subunit [Klebsiella pneumoniae
           342]
 gi|238896792|ref|YP_002921537.1| DNA-directed RNA polymerase subunit alpha [Klebsiella pneumoniae
           NTUH-K2044]
 gi|259909975|ref|YP_002650331.1| DNA-directed RNA polymerase subunit alpha [Erwinia pyrifoliae
           Ep1/96]
 gi|261342765|ref|ZP_05970623.1| DNA-directed RNA polymerase, alpha subunit [Enterobacter
           cancerogenus ATCC 35316]
 gi|262045154|ref|ZP_06018181.1| DNA-directed RNA polymerase subunit alpha [Klebsiella pneumoniae
           subsp. rhinoscleromatis ATCC 13884]
 gi|270264348|ref|ZP_06192614.1| DNA-directed RNA polymerase subunit alpha [Serratia odorifera
           4Rx13]
 gi|288933291|ref|YP_003437350.1| DNA-directed RNA polymerase, subunit alpha [Klebsiella variicola
           At-22]
 gi|290512093|ref|ZP_06551461.1| DNA-directed RNA polymerase, alpha subunit [Klebsiella sp. 1_1_55]
 gi|292489824|ref|YP_003532714.1| DNA-directed RNA polymerase subunit alpha [Erwinia amylovora
           CFBP1430]
 gi|292900866|ref|YP_003540235.1| DNA-directed RNA polymerase subunit alpha [Erwinia amylovora ATCC
           49946]
 gi|296105003|ref|YP_003615149.1| DNA-directed RNA polymerase subunit alpha [Enterobacter cloacae
           subsp. cloacae ATCC 13047]
 gi|322831097|ref|YP_004211124.1| DNA-directed RNA polymerase, subunit alpha [Rahnella sp. Y9602]
 gi|330002270|ref|ZP_08304264.1| DNA-directed RNA polymerase, alpha subunit [Klebsiella sp. MS 92-3]
 gi|172046001|sp|A4WFA3|RPOA_ENT38 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172047787|sp|A8GKH3|RPOA_SERP5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172052443|sp|A6TEU8|RPOA_KLEP7 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|145320236|gb|ABP62383.1| DNA-directed RNA polymerase subunit alpha [Enterobacter sp. 638]
 gi|150957052|gb|ABR79082.1| DNA-directed RNA polymerase alpha subunit [Klebsiella pneumoniae
           subsp. pneumoniae MGH 78578]
 gi|157324516|gb|ABV43613.1| DNA-directed RNA polymerase, alpha subunit [Serratia proteamaculans
           568]
 gi|190341369|gb|ACE74761.1| RpoA [Enterobacter sp. 638]
 gi|206568093|gb|ACI09869.1| DNA-directed RNA polymerase, alpha subunit [Klebsiella pneumoniae
           342]
 gi|224965597|emb|CAX57129.1| DNA-directed RNA polymerase subunit alpha [Erwinia pyrifoliae
           Ep1/96]
 gi|238549119|dbj|BAH65470.1| DNA-directed RNA polymerase alpha subunit [Klebsiella pneumoniae
           subsp. pneumoniae NTUH-K2044]
 gi|259037474|gb|EEW38718.1| DNA-directed RNA polymerase subunit alpha [Klebsiella pneumoniae
           subsp. rhinoscleromatis ATCC 13884]
 gi|270041484|gb|EFA14582.1| DNA-directed RNA polymerase subunit alpha [Serratia odorifera
           4Rx13]
 gi|283480074|emb|CAY75990.1| DNA-directed RNA polymerase alpha chain [Erwinia pyrifoliae DSM
           12163]
 gi|288314944|gb|EFC53882.1| DNA-directed RNA polymerase, alpha subunit [Enterobacter
           cancerogenus ATCC 35316]
 gi|288888020|gb|ADC56338.1| DNA-directed RNA polymerase, alpha subunit [Klebsiella variicola
           At-22]
 gi|289775883|gb|EFD83883.1| DNA-directed RNA polymerase, alpha subunit [Klebsiella sp. 1_1_55]
 gi|291200714|emb|CBJ47847.1| DNA-directed RNA polymerase alpha chain [Erwinia amylovora ATCC
           49946]
 gi|291555261|emb|CBA23539.1| DNA-directed RNA polymerase alpha chain [Erwinia amylovora
           CFBP1430]
 gi|295059462|gb|ADF64200.1| DNA-directed RNA polymerase subunit alpha [Enterobacter cloacae
           subsp. cloacae ATCC 13047]
 gi|295096939|emb|CBK86029.1| DNA-directed RNA polymerase subunit alpha [Enterobacter cloacae
           subsp. cloacae NCTC 9394]
 gi|310765573|gb|ADP10523.1| DNA-directed RNA polymerase subunit alpha [Erwinia sp. Ejp617]
 gi|312174006|emb|CBX82259.1| DNA-directed RNA polymerase alpha chain [Erwinia amylovora ATCC
           BAA-2158]
 gi|321166298|gb|ADW71997.1| DNA-directed RNA polymerase, alpha subunit [Rahnella sp. Y9602]
 gi|328537343|gb|EGF63593.1| DNA-directed RNA polymerase, alpha subunit [Klebsiella sp. MS 92-3]
          Length = 329

 Score =  348 bits (893), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENAAISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|260579894|ref|ZP_05847724.1| DNA-directed RNA polymerase, alpha subunit [Haemophilus influenzae
           RdAW]
 gi|260093178|gb|EEW77111.1| DNA-directed RNA polymerase, alpha subunit [Haemophilus influenzae
           RdAW]
          Length = 328

 Score =  348 bits (893), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 151/333 (45%), Positives = 223/333 (66%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVILTLNKSGIGPVVAADITY 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYS 178
             D+E++NPDHVIC+L D +A + M + V +G GYVPA  + H  E  PIG + +DA YS
Sbjct: 118 DGDVEIVNPDHVICHLTDENASISMRIRVQRGRGYVPASSRTHTQEERPIGRLLVDACYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +
Sbjct: 178 PVERIAYNVEAARVEQRTDLDKLVIELETNGALEPEEAIRRAATILAEQLDAFVDLRDVR 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +    +I  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 QP---EIKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 327


>gi|254449307|ref|ZP_05062752.1| DNA-directed RNA polymerase, alpha subunit [gamma proteobacterium
           HTCC5015]
 gi|198261066|gb|EDY85366.1| DNA-directed RNA polymerase, alpha subunit [gamma proteobacterium
           HTCC5015]
          Length = 330

 Score =  348 bits (893), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 155/335 (46%), Positives = 224/335 (66%), Gaps = 9/335 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  N  E +KP  ++   L    + R  ++ EPL RGF HTLGNALRR+L+SS+ GAA+T
Sbjct: 1   MSGNVNEFLKPRLVDVQQLS---DTRAKVVLEPLERGFGHTLGNALRRILLSSMPGAAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            VQIDGVLHE ++I+GV ED+ +I+LN+K + + ++  +   +++ K+G G V AGDIQ 
Sbjct: 58  EVQIDGVLHEYTTIEGVQEDVLEILLNLKNLAIVLNAKNEAVLSLSKKGKGPVKAGDIQA 117

Query: 122 VNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYS 178
            +D+E++NPD VI NL  D + + M L V KG GY PA   R   E   +G + +DA YS
Sbjct: 118 DHDVEIVNPDFVIANLTQDSSELSMTLKVKKGRGYEPASQRREEAETAAVGTLQLDASYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +V+YTV+SAR  Q  D DKL + ++T+G+I  E+S+  A+ ILQ+Q+ +F++ +   
Sbjct: 178 PVYRVAYTVDSARVEQRTDLDKLIIDLETNGTIDPEESIRRAATILQEQISVFVDLQAED 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              +ED    +   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 VSEEED---DASDIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELA 333
           G+KSL EIK VL   GL LGM L +WPP SI + A
Sbjct: 295 GKKSLTEIKDVLAQHGLSLGMRLENWPPASIAKEA 329


>gi|123444073|ref|YP_001008043.1| DNA-directed RNA polymerase subunit alpha [Yersinia enterocolitica
           subsp. enterocolitica 8081]
 gi|238752666|ref|ZP_04614137.1| DNA-directed RNA polymerase subunit alpha [Yersinia rohdei ATCC
           43380]
 gi|238788887|ref|ZP_04632677.1| DNA-directed RNA polymerase subunit alpha [Yersinia frederiksenii
           ATCC 33641]
 gi|332163236|ref|YP_004299813.1| DNA-directed RNA polymerase subunit alpha [Yersinia enterocolitica
           subsp. palearctica 105.5R(r)]
 gi|158512898|sp|A1JS01|RPOA_YERE8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|122091034|emb|CAL13917.1| DNA-directed RNA polymerase alpha chain [Yersinia enterocolitica
           subsp. enterocolitica 8081]
 gi|238709093|gb|EEQ01340.1| DNA-directed RNA polymerase subunit alpha [Yersinia rohdei ATCC
           43380]
 gi|238722914|gb|EEQ14564.1| DNA-directed RNA polymerase subunit alpha [Yersinia frederiksenii
           ATCC 33641]
 gi|318607720|emb|CBY29218.1| DNA-directed RNA polymerase alpha subunit [Yersinia enterocolitica
           subsp. palearctica Y11]
 gi|325667466|gb|ADZ44110.1| DNA-directed RNA polymerase subunit alpha [Yersinia enterocolitica
           subsp. palearctica 105.5R(r)]
 gi|330861829|emb|CBX72000.1| DNA-directed RNA polymerase subunit alpha [Yersinia enterocolitica
           W22703]
          Length = 330

 Score =  348 bits (893), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|68249398|ref|YP_248510.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           86-028NP]
 gi|145628303|ref|ZP_01784104.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           22.1-21]
 gi|145638396|ref|ZP_01794006.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           PittII]
 gi|148827991|ref|YP_001292744.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           PittGG]
 gi|81336175|sp|Q4QM97|RPOA_HAEI8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172048058|sp|A5UHV5|RPOA_HAEIG RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|68057597|gb|AAX87850.1| DNA-directed RNA polymerase alpha chain [Haemophilus influenzae
           86-028NP]
 gi|144980078|gb|EDJ89737.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           22.1-21]
 gi|145272725|gb|EDK12632.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           PittII]
 gi|148719233|gb|ABR00361.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           PittGG]
 gi|301169521|emb|CBW29122.1| RNA polymerase, alpha subunit [Haemophilus influenzae 10810]
 gi|309751536|gb|ADO81520.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           R2866]
          Length = 328

 Score =  348 bits (893), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 151/333 (45%), Positives = 223/333 (66%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVILTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYS 178
             D+E++NPDHVIC+L D +A + M + V +G GYVPA  + H  E  PIG + +DA YS
Sbjct: 118 DGDVEIVNPDHVICHLTDENASISMRIRVQRGRGYVPASSRTHTQEERPIGRLLVDACYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +
Sbjct: 178 PVERIAYNVEAARVEQRTDLDKLVIELETNGALEPEEAIRRAATILAEQLDAFVDLRDVR 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +    +I  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 QP---EIKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 327


>gi|15803822|ref|NP_289856.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O157:H7
           EDL933]
 gi|15833414|ref|NP_312187.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O157:H7
           str. Sakai]
 gi|16131174|ref|NP_417754.1| RNA polymerase, alpha subunit [Escherichia coli str. K-12 substr.
           MG1655]
 gi|16762868|ref|NP_458485.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. CT18]
 gi|16766704|ref|NP_462319.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhimurium str. LT2]
 gi|24114573|ref|NP_709083.1| DNA-directed RNA polymerase subunit alpha [Shigella flexneri 2a
           str. 301]
 gi|26249880|ref|NP_755920.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli CFT073]
 gi|29144355|ref|NP_807697.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. Ty2]
 gi|30065404|ref|NP_839575.1| DNA-directed RNA polymerase subunit alpha [Shigella flexneri 2a
           str. 2457T]
 gi|56415334|ref|YP_152409.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Paratyphi A str. ATCC 9150]
 gi|74313814|ref|YP_312233.1| DNA-directed RNA polymerase subunit alpha [Shigella sonnei Ss046]
 gi|82545658|ref|YP_409605.1| DNA-directed RNA polymerase subunit alpha [Shigella boydii Sb227]
 gi|89110715|ref|AP_004495.1| RNA polymerase, alpha subunit [Escherichia coli str. K-12 substr.
           W3110]
 gi|91212722|ref|YP_542708.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli UTI89]
 gi|110643534|ref|YP_671264.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli 536]
 gi|110807143|ref|YP_690663.1| DNA-directed RNA polymerase subunit alpha [Shigella flexneri 5 str.
           8401]
 gi|117625577|ref|YP_858900.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli APEC
           O1]
 gi|157148870|ref|YP_001456189.1| DNA-directed RNA polymerase subunit alpha [Citrobacter koseri ATCC
           BAA-895]
 gi|157157450|ref|YP_001464763.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli
           E24377A]
 gi|157162769|ref|YP_001460087.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli HS]
 gi|161506032|ref|YP_001573144.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|161616440|ref|YP_001590405.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Paratyphi B str. SPB7]
 gi|168264704|ref|ZP_02686677.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Hadar str. RI_05P066]
 gi|168468028|ref|ZP_02701865.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Newport str. SL317]
 gi|168752256|ref|ZP_02777278.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4113]
 gi|168758523|ref|ZP_02783530.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4401]
 gi|168764978|ref|ZP_02789985.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4501]
 gi|168769157|ref|ZP_02794164.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4486]
 gi|168777847|ref|ZP_02802854.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4196]
 gi|168786185|ref|ZP_02811192.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC869]
 gi|168802724|ref|ZP_02827731.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC508]
 gi|170018469|ref|YP_001723423.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli ATCC
           8739]
 gi|170082815|ref|YP_001732135.1| RNA polymerase, alpha subunit [Escherichia coli str. K-12 substr.
           DH10B]
 gi|170683426|ref|YP_001745557.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli
           SMS-3-5]
 gi|187731728|ref|YP_001881980.1| DNA-directed RNA polymerase subunit alpha [Shigella boydii CDC
           3083-94]
 gi|188495000|ref|ZP_03002270.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli 53638]
 gi|191169307|ref|ZP_03031056.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli B7A]
 gi|193066493|ref|ZP_03047537.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli E22]
 gi|193071560|ref|ZP_03052469.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           E110019]
 gi|194430287|ref|ZP_03062782.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli B171]
 gi|194440020|ref|ZP_03072078.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli 101-1]
 gi|194442652|ref|YP_002042666.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Newport str. SL254]
 gi|194447380|ref|YP_002047439.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Heidelberg str. SL476]
 gi|194469288|ref|ZP_03075272.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Kentucky str. CVM29188]
 gi|194735121|ref|YP_002116358.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Schwarzengrund str. CVM19633]
 gi|195939843|ref|ZP_03085225.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O157:H7
           str. EC4024]
 gi|197248562|ref|YP_002148335.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Agona str. SL483]
 gi|197262940|ref|ZP_03163014.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Saintpaul str. SARA23]
 gi|197364264|ref|YP_002143901.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Paratyphi A str. AKU_12601]
 gi|198244932|ref|YP_002217378.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Dublin str. CT_02021853]
 gi|200387689|ref|ZP_03214301.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Virchow str. SL491]
 gi|204931405|ref|ZP_03222074.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Javiana str. GA_MM04042433]
 gi|205354957|ref|YP_002228758.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Gallinarum str. 287/91]
 gi|207858657|ref|YP_002245308.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Enteritidis str. P125109]
 gi|208806531|ref|ZP_03248868.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4206]
 gi|208813497|ref|ZP_03254826.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4045]
 gi|208818909|ref|ZP_03259229.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4042]
 gi|209396788|ref|YP_002272751.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4115]
 gi|209920761|ref|YP_002294845.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli SE11]
 gi|213027592|ref|ZP_03342039.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. 404ty]
 gi|213052883|ref|ZP_03345761.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E00-7866]
 gi|213425776|ref|ZP_03358526.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E02-1180]
 gi|213647329|ref|ZP_03377382.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. J185]
 gi|213859911|ref|ZP_03385615.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. M223]
 gi|215488595|ref|YP_002331026.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O127:H6
           str. E2348/69]
 gi|217324841|ref|ZP_03440925.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. TW14588]
 gi|218550571|ref|YP_002384362.1| DNA-directed RNA polymerase subunit alpha [Escherichia fergusonii
           ATCC 35469]
 gi|218555853|ref|YP_002388766.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli IAI1]
 gi|218560357|ref|YP_002393270.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli S88]
 gi|218691582|ref|YP_002399794.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli ED1a]
 gi|218696988|ref|YP_002404655.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli 55989]
 gi|218702058|ref|YP_002409687.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli IAI39]
 gi|218706903|ref|YP_002414422.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli UMN026]
 gi|237703025|ref|ZP_04533506.1| RNA polymerase [Escherichia sp. 3_2_53FAA]
 gi|238902386|ref|YP_002928182.1| RNA polymerase, alpha subunit [Escherichia coli BW2952]
 gi|238913870|ref|ZP_04657707.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Tennessee str. CDC07-0191]
 gi|253771881|ref|YP_003034712.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254038456|ref|ZP_04872512.1| DNA-directed RNA polymerase [Escherichia sp. 1_1_43]
 gi|254163223|ref|YP_003046331.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli B str.
           REL606]
 gi|254795232|ref|YP_003080069.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O157:H7
           str. TW14359]
 gi|256020654|ref|ZP_05434519.1| DNA-directed RNA polymerase subunit alpha [Shigella sp. D9]
 gi|256025977|ref|ZP_05439842.1| DNA-directed RNA polymerase subunit alpha [Escherichia sp. 4_1_40B]
 gi|260846093|ref|YP_003223871.1| RNA polymerase, alpha subunit [Escherichia coli O103:H2 str. 12009]
 gi|260857416|ref|YP_003231307.1| RNA polymerase, alpha subunit [Escherichia coli O26:H11 str. 11368]
 gi|260870038|ref|YP_003236440.1| RNA polymerase, alpha subunit [Escherichia coli O111:H- str. 11128]
 gi|261224600|ref|ZP_05938881.1| RNA polymerase, alpha subunit [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261254506|ref|ZP_05947039.1| RNA polymerase, alpha subunit [Escherichia coli O157:H7 str.
           FRIK966]
 gi|283788069|ref|YP_003367934.1| DNA-directed RNA polymerase alpha chain [Citrobacter rodentium
           ICC168]
 gi|289824200|ref|ZP_06543795.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E98-3139]
 gi|291284653|ref|YP_003501471.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O55:H7
           str. CB9615]
 gi|293406892|ref|ZP_06650816.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli
           FVEC1412]
 gi|293412714|ref|ZP_06655382.1| DNA-directed RNA polymerase [Escherichia coli B354]
 gi|293416714|ref|ZP_06659351.1| DNA-directed RNA polymerase [Escherichia coli B185]
 gi|293453614|ref|ZP_06664033.1| DNA-directed RNA polymerase [Escherichia coli B088]
 gi|297517819|ref|ZP_06936205.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli OP50]
 gi|298382633|ref|ZP_06992228.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli
           FVEC1302]
 gi|300815494|ref|ZP_07095719.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           107-1]
 gi|300822901|ref|ZP_07103037.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           119-7]
 gi|300896644|ref|ZP_07115160.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           198-1]
 gi|300903544|ref|ZP_07121466.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           84-1]
 gi|300918270|ref|ZP_07134874.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           115-1]
 gi|300921895|ref|ZP_07138051.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           182-1]
 gi|300932189|ref|ZP_07147468.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           187-1]
 gi|300935294|ref|ZP_07150304.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           21-1]
 gi|300946518|ref|ZP_07160783.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           116-1]
 gi|300954830|ref|ZP_07167256.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           175-1]
 gi|300973975|ref|ZP_07172382.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           200-1]
 gi|300979868|ref|ZP_07174744.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           45-1]
 gi|301018839|ref|ZP_07183083.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           69-1]
 gi|301021165|ref|ZP_07185203.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           196-1]
 gi|301046067|ref|ZP_07193245.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           185-1]
 gi|301305505|ref|ZP_07211597.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           124-1]
 gi|301325137|ref|ZP_07218671.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           78-1]
 gi|301643884|ref|ZP_07243915.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           146-1]
 gi|306816362|ref|ZP_07450500.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli NC101]
 gi|307139978|ref|ZP_07499334.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli H736]
 gi|307315126|ref|ZP_07594709.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli W]
 gi|309794571|ref|ZP_07688993.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           145-7]
 gi|312972444|ref|ZP_07786618.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           1827-70]
 gi|331643991|ref|ZP_08345120.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli H736]
 gi|331649092|ref|ZP_08350178.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli M605]
 gi|331659585|ref|ZP_08360523.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli TA206]
 gi|331664908|ref|ZP_08365809.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli TA143]
 gi|331670124|ref|ZP_08370963.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli TA271]
 gi|331674801|ref|ZP_08375558.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli TA280]
 gi|331679364|ref|ZP_08380034.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli H591]
 gi|331684937|ref|ZP_08385523.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli H299]
 gi|62287386|sp|Q5PK10|RPOA_SALPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|62288914|sp|P0A7Z4|RPOA_ECOLI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|62288915|sp|P0A7Z5|RPOA_ECOL6 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|62288916|sp|P0A7Z6|RPOA_ECO57 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|62288917|sp|P0A7Z7|RPOA_SALTY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|62288918|sp|P0A7Z8|RPOA_SALTI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|62288919|sp|P0A7Z9|RPOA_SHIFL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|90110865|sp|Q31VY1|RPOA_SHIBS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|90110867|sp|Q3YWW4|RPOA_SHISS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366680|sp|Q0TCG6|RPOA_ECOL5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366681|sp|Q1R637|RPOA_ECOUT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|123342435|sp|Q0T007|RPOA_SHIF8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158512617|sp|A1AGI6|RPOA_ECOK1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|171855221|sp|A7ZSI4|RPOA_ECO24 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172044360|sp|A8A5A0|RPOA_ECOHS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172045613|sp|A8AQJ0|RPOA_CITK8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|25288369|pir||AB1009 DNA-directed RNA polymerase (EC 2.7.7.6) alpha chain [imported] -
           Salmonella enterica subsp. enterica serovar Typhi
           (strain CT18)
 gi|266618715|pdb|3IYD|A Chain A, Three-Dimensional Em Structure Of An Intact Activator-
           Dependent Transcription Initiation Complex
 gi|266618716|pdb|3IYD|B Chain B, Three-Dimensional Em Structure Of An Intact Activator-
           Dependent Transcription Initiation Complex
 gi|307776495|pdb|3LU0|A Chain A, Molecular Model Of Escherichia Coli Core Rna Polymerase
 gi|307776496|pdb|3LU0|B Chain B, Molecular Model Of Escherichia Coli Core Rna Polymerase
 gi|12517924|gb|AAG58416.1|AE005556_9 RNA polymerase, alpha subunit [Escherichia coli O157:H7 str.
           EDL933]
 gi|26110308|gb|AAN82494.1|AE016767_254 DNA-directed RNA polymerase alpha chain [Escherichia coli CFT073]
 gi|42807|emb|CAA25337.1| unnamed protein product [Escherichia coli]
 gi|147715|gb|AAA24577.1| RNA polymerase alpha subunit [Escherichia coli]
 gi|154353|gb|AAA27214.1| RNA polymerase alpha-subunit [Salmonella enterica subsp. enterica
           serovar Typhimurium]
 gi|606229|gb|AAA58092.1| CG Site No. 234 [Escherichia coli str. K-12 substr. MG1655]
 gi|1789690|gb|AAC76320.1| RNA polymerase, alpha subunit [Escherichia coli str. K-12 substr.
           MG1655]
 gi|13363633|dbj|BAB37583.1| RNA polymerase, alpha subunit [Escherichia coli O157:H7 str. Sakai]
 gi|16421971|gb|AAL22278.1| RNA polymerase, alpha subunit [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|16505175|emb|CAD09171.1| DNA-directed RNA polymerase alpha chain [Salmonella enterica subsp.
           enterica serovar Typhi]
 gi|22774035|gb|AAN07185.1| RNA polymerase alpha subunit [Cloning vector pIA423]
 gi|24053769|gb|AAN44790.1| RNA polymerase, alpha subunit [Shigella flexneri 2a str. 301]
 gi|29139993|gb|AAO71557.1| DNA-directed RNA polymerase alpha chain [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|30043666|gb|AAP19386.1| RNA polymerase, alpha subunit [Shigella flexneri 2a str. 2457T]
 gi|56129591|gb|AAV79097.1| DNA-directed RNA polymerase alpha chain [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|73857291|gb|AAZ89998.1| RNA polymerase, alpha subunit [Shigella sonnei Ss046]
 gi|81247069|gb|ABB67777.1| RNA polymerase alpha subunit [Shigella boydii Sb227]
 gi|85676746|dbj|BAE77996.1| RNA polymerase, alpha subunit [Escherichia coli str. K12 substr.
           W3110]
 gi|91074296|gb|ABE09177.1| RNA polymerase, alpha subunit [Escherichia coli UTI89]
 gi|110345126|gb|ABG71363.1| DNA-directed RNA polymerase alpha chain [Escherichia coli 536]
 gi|110616691|gb|ABF05358.1| RNA polymerase, alpha subunit [Shigella flexneri 5 str. 8401]
 gi|115514701|gb|ABJ02776.1| RNA polymerase, alpha subunit [Escherichia coli APEC O1]
 gi|157068449|gb|ABV07704.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli HS]
 gi|157079480|gb|ABV19188.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           E24377A]
 gi|157086075|gb|ABV15753.1| hypothetical protein CKO_04708 [Citrobacter koseri ATCC BAA-895]
 gi|160867379|gb|ABX24002.1| hypothetical protein SARI_04213 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
 gi|161365804|gb|ABX69572.1| hypothetical protein SPAB_04255 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|169753397|gb|ACA76096.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli ATCC
           8739]
 gi|169890650|gb|ACB04357.1| RNA polymerase, alpha subunit [Escherichia coli str. K-12 substr.
           DH10B]
 gi|170521144|gb|ACB19322.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           SMS-3-5]
 gi|187428720|gb|ACD07994.1| DNA-directed RNA polymerase, alpha subunit [Shigella boydii CDC
           3083-94]
 gi|187766995|gb|EDU30839.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4196]
 gi|188013845|gb|EDU51967.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4113]
 gi|188490199|gb|EDU65302.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli 53638]
 gi|189354678|gb|EDU73097.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4401]
 gi|189361767|gb|EDU80186.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4486]
 gi|189365126|gb|EDU83542.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4501]
 gi|189374058|gb|EDU92474.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC869]
 gi|189375355|gb|EDU93771.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC508]
 gi|190900662|gb|EDV60462.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli B7A]
 gi|192925874|gb|EDV80524.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli E22]
 gi|192955148|gb|EDV85642.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           E110019]
 gi|194401315|gb|ACF61537.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Newport str. SL254]
 gi|194405684|gb|ACF65903.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Heidelberg str. SL476]
 gi|194411676|gb|EDX28003.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli B171]
 gi|194421072|gb|EDX37101.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli 101-1]
 gi|194455652|gb|EDX44491.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Kentucky str. CVM29188]
 gi|194710623|gb|ACF89844.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Schwarzengrund str. CVM19633]
 gi|195628904|gb|EDX48314.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Newport str. SL317]
 gi|197095741|emb|CAR61311.1| DNA-directed RNA polymerase alpha chain [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|197212265|gb|ACH49662.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Agona str. SL483]
 gi|197241195|gb|EDY23815.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Saintpaul str. SARA23]
 gi|197939448|gb|ACH76781.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Dublin str. CT_02021853]
 gi|199604787|gb|EDZ03332.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Virchow str. SL491]
 gi|204319833|gb|EDZ05043.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Javiana str. GA_MM04042433]
 gi|205274738|emb|CAR39794.1| DNA-directed RNA polymerase alpha chain [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205346884|gb|EDZ33515.1| DNA-directed RNA polymerase, alpha subunit [Salmonella enterica
           subsp. enterica serovar Hadar str. RI_05P066]
 gi|206710460|emb|CAR34818.1| DNA-directed RNA polymerase alpha chain [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|208726332|gb|EDZ75933.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4206]
 gi|208734774|gb|EDZ83461.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4045]
 gi|208739032|gb|EDZ86714.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4042]
 gi|209158188|gb|ACI35621.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. EC4115]
 gi|209757288|gb|ACI76956.1| RNA polymerase, alpha subunit [Escherichia coli]
 gi|209757290|gb|ACI76957.1| RNA polymerase, alpha subunit [Escherichia coli]
 gi|209757292|gb|ACI76958.1| RNA polymerase, alpha subunit [Escherichia coli]
 gi|209757294|gb|ACI76959.1| RNA polymerase, alpha subunit [Escherichia coli]
 gi|209757296|gb|ACI76960.1| RNA polymerase, alpha subunit [Escherichia coli]
 gi|209914020|dbj|BAG79094.1| RNA polymerase alpha subunit [Escherichia coli SE11]
 gi|215266667|emb|CAS11106.1| RNA polymerase, alpha subunit [Escherichia coli O127:H6 str.
           E2348/69]
 gi|217321062|gb|EEC29486.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           O157:H7 str. TW14588]
 gi|218353720|emb|CAU99996.1| RNA polymerase, alpha subunit [Escherichia coli 55989]
 gi|218358112|emb|CAQ90759.1| RNA polymerase, alpha subunit [Escherichia fergusonii ATCC 35469]
 gi|218362621|emb|CAR00247.1| RNA polymerase, alpha subunit [Escherichia coli IAI1]
 gi|218367126|emb|CAR04900.1| RNA polymerase, alpha subunit [Escherichia coli S88]
 gi|218372044|emb|CAR19904.1| RNA polymerase, alpha subunit [Escherichia coli IAI39]
 gi|218429146|emb|CAR10098.2| RNA polymerase, alpha subunit [Escherichia coli ED1a]
 gi|218434000|emb|CAR14917.1| RNA polymerase, alpha subunit [Escherichia coli UMN026]
 gi|222035004|emb|CAP77747.1| DNA-directed RNA polymerase alpha chain [Escherichia coli LF82]
 gi|226838962|gb|EEH70985.1| DNA-directed RNA polymerase [Escherichia sp. 1_1_43]
 gi|226902289|gb|EEH88548.1| RNA polymerase [Escherichia sp. 3_2_53FAA]
 gi|238863493|gb|ACR65491.1| RNA polymerase, alpha subunit [Escherichia coli BW2952]
 gi|242378822|emb|CAQ33614.1| RNA polymerase, alpha subunit, subunit of RNA polymerase, core
           enzyme, RNA polymerase sigma 70, RNA polymerase sigma
           54, RNA polymerase sigma 32, RNA polymerase sigma 38,
           RNA polymerase sigma 28, RNA polymerase sigma 19 and RNA
           polymerase sigma 24 [Escherichia coli BL21(DE3)]
 gi|253322925|gb|ACT27527.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253975124|gb|ACT40795.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli B str.
           REL606]
 gi|253979280|gb|ACT44950.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli
           BL21(DE3)]
 gi|254594632|gb|ACT73993.1| RNA polymerase, alpha subunit [Escherichia coli O157:H7 str.
           TW14359]
 gi|257756065|dbj|BAI27567.1| RNA polymerase, alpha subunit [Escherichia coli O26:H11 str. 11368]
 gi|257761240|dbj|BAI32737.1| RNA polymerase, alpha subunit [Escherichia coli O103:H2 str. 12009]
 gi|257766394|dbj|BAI37889.1| RNA polymerase, alpha subunit [Escherichia coli O111:H- str. 11128]
 gi|260447686|gb|ACX38108.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli DH1]
 gi|261248572|emb|CBG26410.1| DNA-directed RNA polymerase alpha chain [Salmonella enterica subsp.
           enterica serovar Typhimurium str. D23580]
 gi|267995624|gb|ACY90509.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhimurium str. 14028S]
 gi|281180330|dbj|BAI56660.1| RNA polymerase alpha subunit [Escherichia coli SE15]
 gi|281602660|gb|ADA75644.1| DNA-directed RNA polymerase subunit alpha [Shigella flexneri
           2002017]
 gi|282951523|emb|CBG91222.1| DNA-directed RNA polymerase alpha chain [Citrobacter rodentium
           ICC168]
 gi|284923301|emb|CBG36395.1| DNA-directed RNA polymerase alpha chain [Escherichia coli 042]
 gi|290764526|gb|ADD58487.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O55:H7
           str. CB9615]
 gi|291321740|gb|EFE61171.1| DNA-directed RNA polymerase [Escherichia coli B088]
 gi|291425703|gb|EFE98737.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli
           FVEC1412]
 gi|291431290|gb|EFF04275.1| DNA-directed RNA polymerase [Escherichia coli B185]
 gi|291468361|gb|EFF10854.1| DNA-directed RNA polymerase [Escherichia coli B354]
 gi|294490097|gb|ADE88853.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           IHE3034]
 gi|298276469|gb|EFI17987.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli
           FVEC1302]
 gi|299881641|gb|EFI89852.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           196-1]
 gi|300301893|gb|EFJ58278.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           185-1]
 gi|300308985|gb|EFJ63505.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           200-1]
 gi|300318230|gb|EFJ68014.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           175-1]
 gi|300359475|gb|EFJ75345.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           198-1]
 gi|300399549|gb|EFJ83087.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           69-1]
 gi|300404417|gb|EFJ87955.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           84-1]
 gi|300409379|gb|EFJ92917.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           45-1]
 gi|300414531|gb|EFJ97841.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           115-1]
 gi|300421743|gb|EFK05054.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           182-1]
 gi|300453764|gb|EFK17384.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           116-1]
 gi|300459450|gb|EFK22943.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           21-1]
 gi|300460013|gb|EFK23506.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           187-1]
 gi|300524667|gb|EFK45736.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           119-7]
 gi|300532386|gb|EFK53448.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           107-1]
 gi|300839200|gb|EFK66960.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           124-1]
 gi|300848016|gb|EFK75776.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           78-1]
 gi|301077787|gb|EFK92593.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           146-1]
 gi|301159958|emb|CBW19477.1| DNA-directed RNA polymerase alpha chain [Salmonella enterica subsp.
           enterica serovar Typhimurium str. SL1344]
 gi|305850758|gb|EFM51215.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli NC101]
 gi|306905475|gb|EFN36010.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli W]
 gi|307555383|gb|ADN48158.1| DNA-directed RNA polymerase alpha chain [Escherichia coli ABU
           83972]
 gi|307628330|gb|ADN72634.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli UM146]
 gi|308121621|gb|EFO58883.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           145-7]
 gi|309703707|emb|CBJ03048.1| DNA-directed RNA polymerase alpha chain [Escherichia coli ETEC
           H10407]
 gi|310334821|gb|EFQ01026.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           1827-70]
 gi|312914438|dbj|BAJ38412.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhimurium str. T000240]
 gi|312947846|gb|ADR28673.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O83:H1
           str. NRG 857C]
 gi|313647395|gb|EFS11847.1| DNA-directed RNA polymerase, alpha subunit [Shigella flexneri 2a
           str. 2457T]
 gi|315062587|gb|ADT76914.1| RNA polymerase, alpha subunit [Escherichia coli W]
 gi|315137870|dbj|BAJ45029.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli DH1]
 gi|315255879|gb|EFU35847.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           85-1]
 gi|315284629|gb|EFU44074.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           110-3]
 gi|315292387|gb|EFU51739.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           153-1]
 gi|315298594|gb|EFU57849.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           16-3]
 gi|315617097|gb|EFU97707.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli 3431]
 gi|320087860|emb|CBY97623.1| DNA-directed RNA polymerase alpha chain [Salmonella enterica subsp.
           enterica serovar Weltevreden str. 2007-60-3289-1]
 gi|320173939|gb|EFW49115.1| DNA-directed RNA polymerase alpha subunit [Shigella dysenteriae CDC
           74-1112]
 gi|320182707|gb|EFW57593.1| DNA-directed RNA polymerase alpha subunit [Shigella boydii ATCC
           9905]
 gi|320187016|gb|EFW61728.1| DNA-directed RNA polymerase alpha subunit [Shigella flexneri CDC
           796-83]
 gi|320191671|gb|EFW66321.1| DNA-directed RNA polymerase alpha subunit [Escherichia coli O157:H7
           str. EC1212]
 gi|320195387|gb|EFW70014.1| DNA-directed RNA polymerase alpha subunit [Escherichia coli
           WV_060327]
 gi|320199482|gb|EFW74072.1| DNA-directed RNA polymerase alpha subunit [Escherichia coli
           EC4100B]
 gi|320639600|gb|EFX09194.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O157:H7
           str. G5101]
 gi|320645098|gb|EFX14114.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O157:H-
           str. 493-89]
 gi|320650409|gb|EFX18875.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O157:H-
           str. H 2687]
 gi|320655934|gb|EFX23854.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O55:H7
           str. 3256-97 TW 07815]
 gi|320661386|gb|EFX28801.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O55:H7
           str. USDA 5905]
 gi|320666408|gb|EFX33391.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli O157:H7
           str. LSU-61]
 gi|321226466|gb|EFX51516.1| DNA-directed RNA polymerase alpha subunit [Salmonella enterica
           subsp. enterica serovar Typhimurium str. TN061786]
 gi|322615044|gb|EFY11968.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 315996572]
 gi|322617331|gb|EFY14232.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 495297-1]
 gi|322625553|gb|EFY22378.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 495297-3]
 gi|322626395|gb|EFY23204.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 495297-4]
 gi|322632093|gb|EFY28846.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 515920-1]
 gi|322635028|gb|EFY31751.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 515920-2]
 gi|322643271|gb|EFY39838.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 531954]
 gi|322646645|gb|EFY43152.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str.
           NC_MB110209-0054]
 gi|322649991|gb|EFY46410.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. OH_2009072675]
 gi|322652708|gb|EFY49048.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str.
           CASC_09SCPH15965]
 gi|322665523|gb|EFY61710.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 81038-01]
 gi|322670417|gb|EFY66556.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. MD_MDA09249507]
 gi|322670490|gb|EFY66624.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 414877]
 gi|322675066|gb|EFY71149.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 366867]
 gi|322681603|gb|EFY77632.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 413180]
 gi|322685947|gb|EFY81936.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 446600]
 gi|323131773|gb|ADX19203.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhimurium str. 4/74]
 gi|323154133|gb|EFZ40336.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           EPECa14]
 gi|323162974|gb|EFZ48809.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           E128010]
 gi|323164859|gb|EFZ50650.1| DNA-directed RNA polymerase, alpha subunit [Shigella sonnei 53G]
 gi|323173931|gb|EFZ59559.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli LT-68]
 gi|323179169|gb|EFZ64743.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli 1180]
 gi|323182773|gb|EFZ68174.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli 1357]
 gi|323189100|gb|EFZ74384.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           RN587/1]
 gi|323195817|gb|EFZ80990.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 609458-1]
 gi|323196427|gb|EFZ81578.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 556150-1]
 gi|323202334|gb|EFZ87379.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 609460]
 gi|323207317|gb|EFZ92267.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 507440-20]
 gi|323211247|gb|EFZ96092.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 556152]
 gi|323216044|gb|EGA00775.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. MB101509-0077]
 gi|323223465|gb|EGA07793.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. MB102109-0047]
 gi|323226805|gb|EGA10995.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. MB110209-0055]
 gi|323231833|gb|EGA15943.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. MB111609-0052]
 gi|323233214|gb|EGA17309.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 2009083312]
 gi|323237281|gb|EGA21346.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 2009085258]
 gi|323245516|gb|EGA29515.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 315731156]
 gi|323249022|gb|EGA32944.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. IA_2009159199]
 gi|323250645|gb|EGA34526.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. IA_2010008282]
 gi|323256874|gb|EGA40588.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. IA_2010008283]
 gi|323263023|gb|EGA46570.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. IA_2010008284]
 gi|323266023|gb|EGA49518.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. IA_2010008285]
 gi|323272780|gb|EGA56183.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. IA_2010008287]
 gi|323376826|gb|ADX49094.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli KO11]
 gi|323934506|gb|EGB30914.1| DNA-directed RNA polymerase [Escherichia coli E1520]
 gi|323939283|gb|EGB35495.1| DNA-directed RNA polymerase [Escherichia coli E482]
 gi|323944284|gb|EGB40360.1| DNA-directed RNA polymerase [Escherichia coli H120]
 gi|323950209|gb|EGB46091.1| DNA-directed RNA polymerase [Escherichia coli H252]
 gi|323954582|gb|EGB50365.1| DNA-directed RNA polymerase [Escherichia coli H263]
 gi|323959554|gb|EGB55207.1| DNA-directed RNA polymerase [Escherichia coli H489]
 gi|323966257|gb|EGB61692.1| DNA-directed RNA polymerase [Escherichia coli M863]
 gi|323970099|gb|EGB65373.1| DNA-directed RNA polymerase [Escherichia coli TA007]
 gi|323974752|gb|EGB69865.1| DNA-directed RNA polymerase [Escherichia coli TW10509]
 gi|324009030|gb|EGB78249.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           57-2]
 gi|324014912|gb|EGB84131.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           60-1]
 gi|324017886|gb|EGB87105.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli MS
           117-3]
 gi|324111974|gb|EGC05953.1| DNA-directed RNA polymerase [Escherichia fergusonii B253]
 gi|324116315|gb|EGC10235.1| DNA-directed RNA polymerase [Escherichia coli E1167]
 gi|325498864|gb|EGC96723.1| DNA-directed RNA polymerase subunit alpha [Escherichia fergusonii
           ECD227]
 gi|326342543|gb|EGD66317.1| DNA-directed RNA polymerase alpha subunit [Escherichia coli O157:H7
           str. 1044]
 gi|326344530|gb|EGD68279.1| DNA-directed RNA polymerase alpha subunit [Escherichia coli O157:H7
           str. 1125]
 gi|326625159|gb|EGE31504.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Dublin str. 3246]
 gi|326630106|gb|EGE36449.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Gallinarum str. 9]
 gi|330909339|gb|EGH37853.1| DNA-directed RNA polymerase alpha subunit [Escherichia coli AA86]
 gi|331036285|gb|EGI08511.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli H736]
 gi|331041590|gb|EGI13734.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli M605]
 gi|331052800|gb|EGI24833.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli TA206]
 gi|331057418|gb|EGI29404.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli TA143]
 gi|331062186|gb|EGI34106.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli TA271]
 gi|331067710|gb|EGI39108.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli TA280]
 gi|331072536|gb|EGI43861.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli H591]
 gi|331077308|gb|EGI48520.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli H299]
 gi|332085444|gb|EGI90610.1| DNA-directed RNA polymerase, alpha subunit [Shigella boydii
           5216-82]
 gi|332104202|gb|EGJ07548.1| RNA polymerase alpha subunit [Shigella sp. D9]
          Length = 329

 Score =  348 bits (893), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|114319644|ref|YP_741327.1| DNA-directed RNA polymerase subunit alpha [Alkalilimnicola
           ehrlichii MLHE-1]
 gi|119366660|sp|Q0ABF0|RPOA_ALHEH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|114226038|gb|ABI55837.1| DNA-directed RNA polymerase subunit alpha [Alkalilimnicola
           ehrlichii MLHE-1]
          Length = 331

 Score =  348 bits (893), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 146/331 (44%), Positives = 220/331 (66%), Gaps = 6/331 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q  +++ +KP  ++    G   E R  ++ EPL RGF HTLGNALRRVL+SS+ G+A+ 
Sbjct: 1   MQGTFRDFLKPRTVDIQEQG---ERRAKIVLEPLERGFGHTLGNALRRVLLSSMPGSAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +I+GV HE SS++GV ED+ DI+LN+K + ++M       +T+  +GPG VTAGDIQT
Sbjct: 58  QAEIEGVEHEYSSMEGVQEDVVDILLNLKSLAVRMHDRDEAELTVSVQGPGPVTAGDIQT 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR-TENDPIGLITIDALYSPI 180
            +D+EV NP+ +IC L        +L V++G GY  A      E+  IG + +DA YSP+
Sbjct: 118 AHDVEVKNPELLICTLTKAVAFNAKLMVARGRGYEAATQRDGDEDRVIGRLQLDASYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V+YTVESAR  Q  + DKL + ++T+G +  E++V  A+ +L+DQL +F++ E  + E
Sbjct: 178 KRVAYTVESARVEQRTNLDKLVLDVETNGVLEPEEAVRFAAGLLRDQLSVFVDLEGGEFE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +++     +  +P LL+ ++ELEL+VRS NCL+ E+I Y+GDL+QRTE ++L+  N G+
Sbjct: 238 AEQEEQEPDV--DPILLRPIDELELTVRSANCLKAESIHYVGDLVQRTEVELLKTPNLGK 295

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           KSL EIK  L + GL LGM L +WPP  + E
Sbjct: 296 KSLTEIKETLASHGLSLGMRLENWPPAGLGE 326


>gi|300718680|ref|YP_003743483.1| DNA-directed RNA polymerase subunit alpha [Erwinia billingiae
           Eb661]
 gi|299064516|emb|CAX61636.1| DNA-directed RNA polymerase subunit alpha [Erwinia billingiae
           Eb661]
          Length = 329

 Score =  348 bits (892), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+EV+ P HVIC+L D +A + M + + +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEVVKPQHVICHLTDENAAISMRIKIQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|71905987|ref|YP_283574.1| DNA-directed RNA polymerase subunit alpha [Dechloromonas aromatica
           RCB]
 gi|90110836|sp|Q47J77|RPOA_DECAR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|71845608|gb|AAZ45104.1| DNA-directed RNA polymerase subunit alpha [Dechloromonas aromatica
           RCB]
          Length = 324

 Score =  348 bits (892), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 147/331 (44%), Positives = 211/331 (63%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +   L+KP  I+   +   +     ++ EP  RG+ HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQSS--GLLKPRIIDVQSVSPVQ---AKVVMEPFERGYGHTLGNALRRILLSSMVGYAPT 55

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V IDGVLHE S++ GV ED+ DI+LN+KG+  K+       + + K G G V AGDI+ 
Sbjct: 56  EVGIDGVLHEYSTVDGVQEDVVDILLNLKGVVFKLHNRDVVNLKLVKEGEGAVRAGDIEL 115

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-HHRTENDPIGLITIDALYSPI 180
            +D+E++NP+HVI +L     + ME+ V KG GYVP    +  +   IG + +DA +SPI
Sbjct: 116 PHDVEIINPEHVIAHLSPGGKLAMEIKVEKGRGYVPGNVRNLGDAKTIGKLVLDASFSPI 175

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++V+Y VESAR  Q  D DKL + I+T+G +  E+++  A+R+L +QL +F + E     
Sbjct: 176 RRVAYAVESARVEQRTDLDKLIVDIETNGVVEPEEAIRYAARVLMEQLSVFADLEGTAPV 235

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +     K    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GR
Sbjct: 236 AE---ASKPAQVDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGR 292

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           KSL EIK VL   GL LGM L +WPP  +E+
Sbjct: 293 KSLNEIKEVLAARGLTLGMKLENWPPAGLEK 323


>gi|82778591|ref|YP_404940.1| DNA-directed RNA polymerase subunit alpha [Shigella dysenteriae
           Sd197]
 gi|90110866|sp|Q32B56|RPOA_SHIDS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|81242739|gb|ABB63449.1| RNA polymerase, alpha subunit [Shigella dysenteriae Sd197]
          Length = 329

 Score =  348 bits (892), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVRRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|291619150|ref|YP_003521892.1| RpoA [Pantoea ananatis LMG 20103]
 gi|317049815|ref|YP_004117463.1| DNA-directed RNA polymerase subunit alpha [Pantoea sp. At-9b]
 gi|291154180|gb|ADD78764.1| RpoA [Pantoea ananatis LMG 20103]
 gi|316951432|gb|ADU70907.1| DNA-directed RNA polymerase, alpha subunit [Pantoea sp. At-9b]
 gi|327395479|dbj|BAK12901.1| DNA-directed RNA polymerase alpha chain RpoA [Pantoea ananatis
           AJ13355]
          Length = 329

 Score =  348 bits (892), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|225175646|ref|ZP_03729640.1| DNA-directed RNA polymerase, alpha subunit [Dethiobacter
           alkaliphilus AHT 1]
 gi|225168975|gb|EEG77775.1| DNA-directed RNA polymerase, alpha subunit [Dethiobacter
           alkaliphilus AHT 1]
          Length = 314

 Score =  348 bits (892), Expect = 8e-94,   Method: Composition-based stats.
 Identities = 136/313 (43%), Positives = 200/313 (63%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE +    E+      + EPL RG+  TLGNALRR+L+SSL GAA+T V+I+ 
Sbjct: 3   EIEKPR-IERVD-SNEDNTHGTFVIEPLERGYGITLGNALRRILLSSLPGAAVTNVKIEN 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED T+IILN+K + +K+  D  + + +   G GVVTAGDI+   D+EV
Sbjct: 61  VLHEFSTIPGVLEDTTEIILNLKQLAMKIHSDEPQTLVVVAAGQGVVTAGDIKLPADVEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L+    + MELT   G GYVPA+ ++    PIG+I +D+L++PI++V+Y V
Sbjct: 121 LNPDMHIATLEEGGRLYMELTAVNGRGYVPAERNKEPGQPIGVIAVDSLFAPIQRVNYKV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  DYDKL+M + TDGSI  +++++L ++IL   LG+F+N  E   EV+     
Sbjct: 181 ENTRVGQHTDYDKLTMDVWTDGSIRPDEAISLGAKILSKHLGLFVNLTEKVDEVEILDEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                   +   +EEL+LSVRS NCL+   I  + +L+ ++E +M+++ N G+KSL E++
Sbjct: 241 DEDDKTKVMEMTIEELDLSVRSYNCLKRAGINTVQELVNKSEDEMMKVRNLGKKSLEEVQ 300

Query: 308 GVLGTMGLFLGMN 320
             L  + L L  N
Sbjct: 301 HKLEELQLNLRDN 313


>gi|164686554|ref|ZP_02210582.1| hypothetical protein CLOBAR_00121 [Clostridium bartlettii DSM
           16795]
 gi|164604423|gb|EDQ97888.1| hypothetical protein CLOBAR_00121 [Clostridium bartlettii DSM
           16795]
          Length = 315

 Score =  348 bits (892), Expect = 9e-94,   Method: Composition-based stats.
 Identities = 126/311 (40%), Positives = 202/311 (64%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  ++ + L  E+      + EPL RG+  T+GNALRR+L+SSL G A+ +++IDG
Sbjct: 3   EIEKP-KVDIVELS-EDYRYGKFVVEPLERGYGITIGNALRRILLSSLPGVAVNSIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T+IIL++K ++  + G+  + + I  +GP  +   DI    D+E+
Sbjct: 61  VLHEFSTIPGVKEDVTEIILSLKELSATIDGEGSRTLKIEAQGPCSIKGSDIICPPDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           L+ D  I  LD +A + ME+ V KG GYVPA+ ++T+N PIG++ +D++Y+P++KVSY V
Sbjct: 121 LSKDLHIATLDDNAKLNMEIYVDKGRGYVPAEENKTDNMPIGVLPVDSIYTPVEKVSYHV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  DYDKL++ + T+GSI  ++ ++LA+++L + L +FI+  E    V+  +  
Sbjct: 181 ENTRVGQKSDYDKLTLEVMTNGSINPQEGISLAAKVLVEHLNLFIDLTEHVSNVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N G+KSL E+ 
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVEELANKSEDDMMKVRNLGKKSLEEVI 300

Query: 308 GVLGTMGLFLG 318
             L  +GL L 
Sbjct: 301 QKLEELGLGLK 311


>gi|170769532|ref|ZP_02903985.1| DNA-directed RNA polymerase, alpha subunit [Escherichia albertii
           TW07627]
 gi|170121589|gb|EDS90520.1| DNA-directed RNA polymerase, alpha subunit [Escherichia albertii
           TW07627]
          Length = 329

 Score =  348 bits (892), Expect = 9e-94,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASSRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|271962664|ref|YP_003336860.1| RNA polymerase subunit alpha [Streptosporangium roseum DSM 43021]
 gi|270505839|gb|ACZ84117.1| RNA polymerase, alpha chain, N terminal domain protein
           [Streptosporangium roseum DSM 43021]
          Length = 344

 Score =  348 bits (892), Expect = 9e-94,   Method: Composition-based stats.
 Identities = 129/330 (39%), Positives = 192/330 (58%), Gaps = 6/330 (1%)

Query: 2   IQKNWQELI--KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           +Q     LI  +P  +E       EE R+  I EPL  GF +T+GN+LRR L+SS+ GAA
Sbjct: 1   MQGETHMLIAQRPTLLE----ESLEETRSKFIIEPLEPGFGYTIGNSLRRTLLSSIPGAA 56

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T+++I+GVLHE S++ GV ED+TDIILN+K + +    D    + + K+GPG VTA DI
Sbjct: 57  VTSIRIEGVLHEFSTVPGVKEDVTDIILNLKELVVSSEHDEPVVMYLRKQGPGEVTAADI 116

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
                +EV NP+  I  L+  A + MELTV +G GYV A  ++     IG I ID++YSP
Sbjct: 117 APPAGVEVHNPELRIATLNGKAKLEMELTVERGRGYVSAAQNKQPGQEIGRIPIDSIYSP 176

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           + KV+Y VE+ R  Q  D+D+L + ++T   +   D+VA A + L +  G+        +
Sbjct: 177 VLKVTYKVEATRVEQRTDFDRLILDVETKPCMKPRDAVASAGKTLVELFGLARELNVEAE 236

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            +    +         L   +EEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG
Sbjct: 237 GIDIGPSPTDAALAADLALPIEELNLTVRSYNCLKREGIHTVGELVARSEQDLLDIRNFG 296

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            KS+ E+K  L  M L L  + P + P ++
Sbjct: 297 AKSIEEVKQKLHEMTLALKDSPPGFDPSAV 326


>gi|237728630|ref|ZP_04559111.1| RNA polymerase [Citrobacter sp. 30_2]
 gi|283835712|ref|ZP_06355453.1| hypothetical protein CIT292_10105 [Citrobacter youngae ATCC 29220]
 gi|226909252|gb|EEH95170.1| RNA polymerase [Citrobacter sp. 30_2]
 gi|291068392|gb|EFE06501.1| DNA-directed RNA polymerase, alpha subunit [Citrobacter youngae
           ATCC 29220]
          Length = 329

 Score =  348 bits (892), Expect = 9e-94,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDDVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|91785439|ref|YP_560645.1| DNA-directed RNA polymerase subunit alpha [Burkholderia xenovorans
           LB400]
 gi|170695707|ref|ZP_02886849.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia graminis
           C4D1M]
 gi|187925590|ref|YP_001897232.1| DNA-directed RNA polymerase subunit alpha [Burkholderia
           phytofirmans PsJN]
 gi|296163295|ref|ZP_06846056.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia sp. Ch1-1]
 gi|323527576|ref|YP_004229729.1| DNA-directed RNA polymerase subunit alpha [Burkholderia sp.
           CCGE1001]
 gi|119366671|sp|Q13TJ6|RPOA_BURXL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238689619|sp|B2T725|RPOA_BURPP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|91689393|gb|ABE32593.1| DNA-directed RNA polymerase subunit alpha [Burkholderia xenovorans
           LB400]
 gi|170139312|gb|EDT07498.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia graminis
           C4D1M]
 gi|187716784|gb|ACD18008.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia
           phytofirmans PsJN]
 gi|295886434|gb|EFG66291.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia sp. Ch1-1]
 gi|323384578|gb|ADX56669.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia sp.
           CCGE1001]
          Length = 325

 Score =  348 bits (892), Expect = 9e-94,   Method: Composition-based stats.
 Identities = 154/328 (46%), Positives = 213/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP  I    LG   E+   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPKIIAVESLG---ESHAKVVMEPFERGYGHTLGNALRRVLLSSMIGYAPTEVTIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVVTAGDI+  +D E
Sbjct: 60  GVVHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVTAGDIELAHDCE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKV 183
           V+NPDHVI +L     + +++ V KG GYVP    R   +    IG I +DA +SP+++V
Sbjct: 120 VINPDHVIAHLSKGGKLDVQIKVEKGRGYVPGNVRRYGEESAKIIGRIVLDASFSPVRRV 179

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL DQL +F   E    E   
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALE--GTEATA 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 238 EAPSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|330815274|ref|YP_004358979.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia gladioli
           BSR3]
 gi|327367667|gb|AEA59023.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia gladioli
           BSR3]
          Length = 325

 Score =  348 bits (892), Expect = 9e-94,   Method: Composition-based stats.
 Identities = 154/328 (46%), Positives = 212/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP  I    LG   EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPKIIAVESLG---ENHAKVVMEPFERGYGHTLGNALRRVLLSSMIGYAPTEVTIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S++ GV ED+ +++LN+KG+  K+       VT+ K G G+VTAGDI+  +D E
Sbjct: 60  GVVHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGIVTAGDIELAHDCE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKV 183
           V+NPDHVI +L     + +++ + KG GYVP    R   +    IG I +DA +SP+++V
Sbjct: 120 VINPDHVIAHLTKGGKLDVQIKIEKGRGYVPGNVRRYGEESAKIIGRIVLDASFSPVRRV 179

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VESAR  Q  D DKL M I+T G IT E+++  ++RIL DQL +F   E    E   
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETSGVITPEEAIRQSARILVDQLSVFAALE--GTETAA 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 238 EAPSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|330722390|gb|EGH00238.1| DNA-directed RNA polymerase alpha subunit [gamma proteobacterium
           IMCC2047]
          Length = 335

 Score =  348 bits (892), Expect = 9e-94,   Method: Composition-based stats.
 Identities = 151/335 (45%), Positives = 211/335 (62%), Gaps = 8/335 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +   E + P +I+   +G    N   ++ EP  RGF HTLGN+LRR+L+SS+ GAAI 
Sbjct: 1   MSRPVTEFLTPKHIQVEEVGV---NHAKVVLEPFERGFGHTLGNSLRRILLSSMPGAAIV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V IDGV HE S+I+GV ED+ DI+LN+KG+ + M+G     +T+ K   G V AGDIQ 
Sbjct: 58  EVSIDGVQHEYSAIEGVQEDVIDILLNLKGVAVAMNGRDEATLTLNKTEAGPVLAGDIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSP 179
            +DIE+ NP+HVI NL+    + M + VS G GY  A+      E   IG + +DA YSP
Sbjct: 118 DHDIEIANPEHVIANLNAKGKLNMSIKVSSGRGYESAESRDLDGETRSIGTLQLDATYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           + +V+Y VESAR  Q  D DKL + I+++G+I  E+ +  A+ ILQ QL  F++ E  K+
Sbjct: 178 VTRVAYVVESARVEQRTDLDKLVLDIESNGTIDPEECIRRAATILQQQLTAFVDLEADKE 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
                        +P LL+ V++LEL+VRS NCL+ EN+ Y+GDLIQRTE D+L+  N G
Sbjct: 238 PE---QQEDEDEVDPILLRPVDDLELTVRSANCLKAENLYYIGDLIQRTEVDLLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           +KSL EIK VL + GL LGM L  WPP S++   +
Sbjct: 295 KKSLTEIKDVLASKGLSLGMRLEKWPPASLKNDDR 329


>gi|27262232|gb|AAN87397.1| DNA-directed RNA polymerase alpha chain [Heliobacillus mobilis]
          Length = 315

 Score =  348 bits (892), Expect = 9e-94,   Method: Composition-based stats.
 Identities = 135/310 (43%), Positives = 199/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE +    E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+V+I+G
Sbjct: 3   EIEKP-KIECVDRS-EDATYGKFVVEPLERGYGVTLGNSLRRILLSSLPGAAVTSVKIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED TDIILN+K +++KM  D  + + +   G GVVT  DI    D+E+
Sbjct: 61  VLHEFSTIPGVVEDTTDIILNLKLLSIKMYTDEPRIIRVEAEGEGVVTGKDIICDADVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  LD    + MELTV K  GY+ A  H+     IG+I +DA +SP++KV+Y V
Sbjct: 121 LNPDQPIATLDKGGRLFMELTVEKDRGYMTATKHKKSEHVIGVIPVDANFSPVRKVNYRV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R GQ+ +YD+L + + ++GS+T E++++L+++I+ D L +F+   E  + V+  +  
Sbjct: 181 EDTRVGQITNYDRLILEVWSNGSLTPEEAISLSAKIMNDHLKLFVGLTESTENVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +  P +  L   +EEL+LSVRS NCL+   I  + DL  +TE DM+++ N GRKSL E+ 
Sbjct: 241 EERPQDKVLDMTIEELDLSVRSYNCLKRAGINSVRDLTLKTEEDMIKVRNLGRKSLEEVD 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 AKLNALGLSL 310


>gi|157377426|ref|YP_001476026.1| DNA-directed RNA polymerase subunit alpha [Shewanella sediminis
           HAW-EB3]
 gi|157319800|gb|ABV38898.1| DNA-directed RNA polymerase, alpha subunit [Shewanella sediminis
           HAW-EB3]
          Length = 329

 Score =  348 bits (892), Expect = 9e-94,   Method: Composition-based stats.
 Identities = 143/333 (42%), Positives = 214/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E ++P  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLRPRLVD---IEQVNPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVVIEGKDEAMLTLSKSGAGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  V M + V +G GYVPA        ++ PIG + +D+ +S
Sbjct: 118 DGDVTIMNPDHVICHLTGNNDVSMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   +  
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFVELRDVT 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +        +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 EPE---QKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>gi|304399265|ref|ZP_07381131.1| DNA-directed RNA polymerase, alpha subunit [Pantoea sp. aB]
 gi|308188331|ref|YP_003932462.1| DNA-directed RNA polymerase alpha chain [Pantoea vagans C9-1]
 gi|304353191|gb|EFM17572.1| DNA-directed RNA polymerase, alpha subunit [Pantoea sp. aB]
 gi|308058841|gb|ADO11013.1| DNA-directed RNA polymerase alpha chain [Pantoea vagans C9-1]
          Length = 329

 Score =  348 bits (892), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENAAISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|165977221|ref|YP_001652814.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 3 str. JL03]
 gi|190151139|ref|YP_001969664.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|303250037|ref|ZP_07336239.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|303253211|ref|ZP_07339360.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|165877322|gb|ABY70370.1| RNA polymerase alpha subunit [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|189916270|gb|ACE62522.1| DNA-directed RNA polymerase alpha chain [Actinobacillus
           pleuropneumoniae serovar 7 str. AP76]
 gi|302647893|gb|EFL78100.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 2 str. 4226]
 gi|302651100|gb|EFL81254.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
          Length = 329

 Score =  348 bits (892), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 152/334 (45%), Positives = 224/334 (67%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ +    + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVN---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+SG     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVSGKDDIILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++NP HVIC+L D DA + M + V +G GYVPA    H + E+ PIG + +DA +
Sbjct: 118 DGDVEIVNPHHVICHLTDKDASISMRIRVQRGRGYVPASARVHSQDEDRPIGRLLVDARF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|255654191|ref|ZP_05399600.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           QCD-23m63]
 gi|296449770|ref|ZP_06891539.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           NAP08]
 gi|296261368|gb|EFH08194.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           NAP08]
          Length = 315

 Score =  348 bits (892), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 128/311 (41%), Positives = 200/311 (64%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  ++ + L  E+      + EPL RG+  T+GNALRR+L+SSL G A+ A++IDG
Sbjct: 3   EIEKP-KVDIVELS-EDYRYGKFVIEPLERGYGITIGNALRRILLSSLPGVAVNAIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T+IIL +K ++  + G+  + + I  +GP  +T  DI    D+E+
Sbjct: 61  VLHEFSTIPGVKEDVTEIILTLKELSATIDGEGSRTLKIEAQGPCSITGADIICSPDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           L+ D  I  LD +A + ME+ V KG GYV A+ ++TEN PIG++ +D++Y+P++KVSY V
Sbjct: 121 LSKDLAIATLDDNAKLNMEIFVDKGRGYVSAEENKTENVPIGVLPVDSIYTPVEKVSYHV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  DYDKL + + T+GSI  ++ ++LA+++L + L +FI+  E    V+  +  
Sbjct: 181 ENTRVGQKTDYDKLVLEVWTNGSINPQEGISLAAKVLVEHLNLFIDLTEHVSSVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N G+KSL E+ 
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVEELANKSEDDMMKVRNLGKKSLEEVI 300

Query: 308 GVLGTMGLFLG 318
             L  +GL L 
Sbjct: 301 QKLEELGLGLK 311


>gi|197287093|ref|YP_002152965.1| DNA-directed RNA polymerase subunit alpha [Proteus mirabilis
           HI4320]
 gi|227354911|ref|ZP_03839325.1| DNA-directed RNA polymerase alpha chain [Proteus mirabilis ATCC
           29906]
 gi|194684580|emb|CAR46430.1| DNA-directed RNA polymerase alpha chain [Proteus mirabilis HI4320]
 gi|227164993|gb|EEI49832.1| DNA-directed RNA polymerase alpha chain [Proteus mirabilis ATCC
           29906]
          Length = 329

 Score =  348 bits (892), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVHGKDEVILTLSKSGIGPVIAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASINMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++YTVE+AR  Q  D DKL + ++T+G+I  E+S+  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYTVEAARVEQRTDLDKLVIEMETNGTIDPEESIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|84494744|ref|ZP_00993863.1| DNA-directed RNA polymerase alpha subunit [Janibacter sp. HTCC2649]
 gi|84384237|gb|EAQ00117.1| DNA-directed RNA polymerase alpha subunit [Janibacter sp. HTCC2649]
          Length = 346

 Score =  348 bits (892), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 123/320 (38%), Positives = 191/320 (59%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            +      E+R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S+I 
Sbjct: 8   ILTEDVVSEHRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFSTIP 67

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+T+IILNIKG+ +    D    + + K+G G VTA DI     +EV+NPD  I  
Sbjct: 68  GVKEDVTEIILNIKGLVVSSEHDEPVVMYLRKQGSGAVTAADIAPPAGVEVINPDLHIAT 127

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           L+    + MELTV +G GYV A+ +++ +  IG I +D++YSP+  V+Y VE  R  Q  
Sbjct: 128 LNDKGSIEMELTVERGRGYVSAQQNKSGDQEIGRIPVDSIYSPVLNVTYKVELTRVEQRT 187

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           D++ L + ++T  ++T  D++A A + L +  G+        + +    +         L
Sbjct: 188 DFNSLVLDVETKQAVTPRDALASAGKTLVELFGLARELNVEAEGIDMGPSPTDAALAADL 247

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  L  MGL 
Sbjct: 248 ALPIEDLDLTVRSYNCLKREGIHTVGELVGRSEADLLDIRNFGQKSIDEVKAKLHGMGLA 307

Query: 317 LGMNLPDWPPESIEELAKKY 336
           L  +   + P  I     ++
Sbjct: 308 LKDSPAGFDPSQIASYDDEF 327


>gi|253682321|ref|ZP_04863118.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum D
           str. 1873]
 gi|253562033|gb|EES91485.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum D
           str. 1873]
          Length = 315

 Score =  348 bits (892), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 130/311 (41%), Positives = 202/311 (64%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE  V   E+      + EPL RG+  TLGN+LRR+L+SSL G A  +++IDG
Sbjct: 3   EIEKP-KIE-CVEASEDGTYGKFVIEPLERGYGITLGNSLRRILLSSLPGVAANSIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T++ILNIKG+ LKM+G+    + I  +GPG VTA DI +  +IEV
Sbjct: 61  VLHEFSTVTGVKEDVTELILNIKGLALKMNGEGPSTIYIEAQGPGEVTAADIISDGNIEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N D  I  LD D  + ME+ + +G GYV    ++ ++ PIG I +D++Y+P+K+V++TV
Sbjct: 121 MNKDMHIATLDDDGKLYMEINIDRGRGYVTQNKNKKDDLPIGTIPVDSIYTPVKRVNFTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ DYDKLS+ + T+G+I  E++++L+++IL +   +F+   +    V+  +  
Sbjct: 181 ENTRVGQITDYDKLSIEVWTNGTIQPEEAISLSAKILIEHFKLFMTLTDHADNVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L +RT  DM+++ N G+KSL E++
Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTERTIDDMMKVRNLGKKSLEEVQ 300

Query: 308 GVLGTMGLFLG 318
             L  +GL L 
Sbjct: 301 EKLAALGLGLK 311


>gi|161506898|ref|YP_001576852.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus helveticus
           DPC 4571]
 gi|172048388|sp|A8YXN0|RPOA_LACH4 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|160347887|gb|ABX26561.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus
           helveticus DPC 4571]
          Length = 312

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 134/310 (43%), Positives = 194/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDG
Sbjct: 3   EFEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++V
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSLSDERKVIELDVEGPATVTADDLKVDADVQV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + ME+ V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMEIAVQNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   K  +  +  
Sbjct: 179 ESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADADTKFSEVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L   TE+DM+R+ N GRKSL E+K
Sbjct: 239 EDDKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELTDMTESDMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLTDLGLSL 308


>gi|254362772|ref|ZP_04978854.1| DNA-directed RNA polymerase subunit alpha [Mannheimia haemolytica
           PHL213]
 gi|261492717|ref|ZP_05989265.1| DNA-directed RNA polymerase subunit alpha [Mannheimia haemolytica
           serotype A2 str. BOVINE]
 gi|261495668|ref|ZP_05992114.1| DNA-directed RNA polymerase subunit alpha [Mannheimia haemolytica
           serotype A2 str. OVINE]
 gi|153094401|gb|EDN75250.1| DNA-directed RNA polymerase subunit alpha [Mannheimia haemolytica
           PHL213]
 gi|261308775|gb|EEY10032.1| DNA-directed RNA polymerase subunit alpha [Mannheimia haemolytica
           serotype A2 str. OVINE]
 gi|261311570|gb|EEY12725.1| DNA-directed RNA polymerase subunit alpha [Mannheimia haemolytica
           serotype A2 str. BOVINE]
          Length = 329

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 148/334 (44%), Positives = 223/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ +    + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVN---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDIILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++NPDHVIC+L D +A + M + V +G GYVPA    H + ++ PIG + +DA +
Sbjct: 118 DGDVEIVNPDHVICHLTDKNASINMRIRVQRGRGYVPASARLHTQNDDRPIGRLLVDARF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|37528519|ref|NP_931864.1| DNA-directed RNA polymerase subunit alpha [Photorhabdus luminescens
           subsp. laumondii TTO1]
 gi|253991664|ref|YP_003043020.1| DNA-directed RNA polymerase subunit alpha [Photorhabdus asymbiotica
           subsp. asymbiotica ATCC 43949]
 gi|41688627|sp|Q7MYH5|RPOA_PHOLL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|36787957|emb|CAE17074.1| RNA polymerase alpha subunit [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|253783114|emb|CAQ86279.1| DNA-directed RNA polymerase alpha chain [Photorhabdus asymbiotica]
          Length = 329

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADIIH 117

Query: 122 VNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L  + A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDETASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|194435073|ref|ZP_03067311.1| DNA-directed RNA polymerase, alpha subunit [Shigella dysenteriae
           1012]
 gi|194416680|gb|EDX32811.1| DNA-directed RNA polymerase, alpha subunit [Shigella dysenteriae
           1012]
          Length = 329

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVI 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|331654888|ref|ZP_08355887.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli M718]
 gi|331046903|gb|EGI18981.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli M718]
          Length = 329

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDAYY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|184155965|ref|YP_001844305.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus fermentum
           IFO 3956]
 gi|227515513|ref|ZP_03945562.1| DNA-directed RNA polymerase [Lactobacillus fermentum ATCC 14931]
 gi|260662778|ref|ZP_05863672.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus fermentum
           28-3-CHN]
 gi|183227309|dbj|BAG27825.1| DNA-directed RNA polymerase alpha subunit [Lactobacillus fermentum
           IFO 3956]
 gi|227086126|gb|EEI21438.1| DNA-directed RNA polymerase [Lactobacillus fermentum ATCC 14931]
 gi|260552859|gb|EEX25858.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus fermentum
           28-3-CHN]
 gi|299783528|gb|ADJ41526.1| DNA-directed RNA polymerase alpha subunit [Lactobacillus fermentum
           CECT 5716]
          Length = 314

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 137/312 (43%), Positives = 203/312 (65%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E +N    + EPL RG+  TLGN+LRRV+++SL GAAIT++QIDG
Sbjct: 3   EFEKPN----IHKVEETDNYGKFVVEPLERGYGTTLGNSLRRVMLASLPGAAITSIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K + LK+  +  K + I  +GP  VTA DIQ   D+ +
Sbjct: 59  VLHEFSTVQGVTEDVTQIILNLKQVALKIDSEDAKDLEIDVKGPAEVTAADIQGDGDVTI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
           LN D  I  +   A + +++T  KG GY  A  ++T  E   IG++ ID++Y+PI++V+Y
Sbjct: 119 LNSDLHIATVSDGAELHVKMTADKGRGYSSADDNKTRMEGLAIGVLPIDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVE+ R GQ  DYDKL++ + T+GS+T  ++++LA++IL + L MF+N  E  +  +  +
Sbjct: 179 TVENTRVGQSNDYDKLTLDVWTNGSLTPTEAISLAAKILTEHLTMFVNLTEEAQVTQVMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L K +EEL+LSVRS NCL+  +I  + DL +RTEADM+++ N G KSL E
Sbjct: 239 EREETHQEKVLDKTIEELDLSVRSYNCLKRADIQTVKDLTERTEADMMKVRNLGTKSLDE 298

Query: 306 IKGVLGTMGLFL 317
           IK  L  +G+  
Sbjct: 299 IKLKLAELGVGF 310


>gi|223933080|ref|ZP_03625073.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus suis
           89/1591]
 gi|223898267|gb|EEF64635.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus suis
           89/1591]
          Length = 312

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 134/313 (42%), Positives = 203/313 (64%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T+++IDG
Sbjct: 3   EFEKPT----ITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K   +  K++ +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKKIELDVVGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A  +  LTV+ G GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIADGATFKAVLTVNSGRGYVPAEDNKKDDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I+T+G+I  ED++ L++RIL + LG+F +  E  K  +     
Sbjct: 179 EPARVGSNDGFDKLTLEINTNGTIVPEDTLGLSARILMEHLGLFTDLTEVAKSAEVMKEA 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    +  L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 EVASDDRMLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKKD 311


>gi|73542838|ref|YP_297358.1| DNA-directed RNA polymerase subunit alpha [Ralstonia eutropha
           JMP134]
 gi|90110863|sp|Q46WG9|RPOA_RALEJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|72120251|gb|AAZ62514.1| DNA-directed RNA polymerase, alpha subunit [Ralstonia eutropha
           JMP134]
          Length = 326

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 148/326 (45%), Positives = 212/326 (65%), Gaps = 7/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG        ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVEPLGDH---HAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S+I GV ED+ +++LN+KG+  K+       V++ K G G+VTA DI+  +D+E++
Sbjct: 62  VHEYSTIDGVQEDVVNLLLNLKGVVFKLHNRDEVTVSLRKDGEGIVTAADIELPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSY 185
           NP+HVI +L     + M++ V +G GYVP    +  ++     G I +DA +SP+++VSY
Sbjct: 122 NPNHVIAHLSAGGKLDMQIKVEQGRGYVPGNVRKFGDESSKVIGRIVLDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+TDG I+ E+++  ++RIL DQL +F   E   +   E  
Sbjct: 182 AVESARVEQRTDLDKLVMNIETDGVISPEEAIRQSARILVDQLSVFAALEG-TESAAEAA 240

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           + ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 241 SSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 300

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +++
Sbjct: 301 IKEVLASRGLTLGMKLENWPPAGLDK 326


>gi|293380402|ref|ZP_06626473.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus crispatus
           214-1]
 gi|290923085|gb|EFE00017.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus crispatus
           214-1]
          Length = 312

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 134/310 (43%), Positives = 195/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDG
Sbjct: 3   EFEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++V
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDIEGPATVTADDLKVDADVQV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPI+KV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMELAVKNGRGYVAASDNKSDDMPIGVIPVDSLFSPIRKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   K  +  +  
Sbjct: 179 ESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADANAKFSEVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE+DM+R+ N GRKSL E+K
Sbjct: 239 EDDKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELTDKTESDMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLTDLGLSL 308


>gi|85858173|ref|YP_460375.1| DNA-directed RNA polymerase subunit alpha [Syntrophus
           aciditrophicus SB]
 gi|119366739|sp|Q2LQC9|RPOA_SYNAS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|85721264|gb|ABC76207.1| DNA-directed RNA polymerase alpha chain [Syntrophus aciditrophicus
           SB]
          Length = 345

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 165/345 (47%), Positives = 223/345 (64%), Gaps = 9/345 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +NW  LI+P  IE I            + +PL RGF  TLGNALRRVL+SS++GAAI 
Sbjct: 1   MVRNWCSLIRPRRIE-IDESTHTRFYGEFVCQPLERGFGITLGNALRRVLLSSIQGAAIV 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+ID VLHE S++ GV ED+TDIILN+KG+ LK+  D  + + I  +  GV+TA DI T
Sbjct: 60  SVKIDNVLHEFSTVPGVKEDITDIILNLKGVRLKLLSDGPRVIRIDTKKEGVITAADIIT 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              +EVLN DH I +L  D   RME+ V+ G GYV AK  +  + P G I IDALYSPIK
Sbjct: 120 DGTVEVLNEDHYIASLSGDMPFRMEMVVNSGRGYVQAKKEKDVDQPEGTINIDALYSPIK 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF------E 235
           KV+YTV  AR GQ+ DYDKLS+ + TDG++  ED+VA A++IL+ QL +F+        E
Sbjct: 180 KVNYTVTHARVGQIADYDKLSLEVWTDGNVLPEDAVAFAAKILKKQLQVFVGLHTVIGTE 239

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           E ++E + +   +    N  LL+ VE+LELSVRS NCL+   I  +G+L+Q++EA+ML+ 
Sbjct: 240 EVEEEEEGEAVSEKENLNDILLRHVEDLELSVRSANCLKNAGINLIGELVQKSEAEMLKT 299

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLP--DWPPESIEELAKKYED 338
            NFGRKSL EIK +L   GL  GM L    W  +  EE+ +  E+
Sbjct: 300 KNFGRKSLSEIKEILAEYGLTFGMKLEFTPWNKDVREEMGEIQEE 344


>gi|260581619|ref|ZP_05849416.1| DNA-directed RNA polymerase, alpha subunit [Haemophilus influenzae
           NT127]
 gi|260095212|gb|EEW79103.1| DNA-directed RNA polymerase, alpha subunit [Haemophilus influenzae
           NT127]
          Length = 328

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 151/333 (45%), Positives = 223/333 (66%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVILTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYS 178
             D+E++NPDHVIC+L D +A + M + V +G GYVPA  + H  E  PIG + +DA YS
Sbjct: 118 DGDVEIVNPDHVICHLTDENASISMRIRVQRGRGYVPASSRTHTQEERPIGRLLVDACYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +
Sbjct: 178 PVERITYNVEAARVEQRTDLDKLVIELETNGALEPEEAIRRAATILAEQLDAFVDLRDVR 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +    +I  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 QP---EIKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 327


>gi|238855094|ref|ZP_04645422.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           269-3]
 gi|260664879|ref|ZP_05865730.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           SJ-7A-US]
 gi|282931913|ref|ZP_06337385.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           208-1]
 gi|313472571|ref|ZP_07813060.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           1153]
 gi|238832338|gb|EEQ24647.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           269-3]
 gi|239530011|gb|EEQ69012.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           1153]
 gi|260561362|gb|EEX27335.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           SJ-7A-US]
 gi|281303965|gb|EFA96095.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus jensenii
           208-1]
          Length = 313

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 135/311 (43%), Positives = 197/311 (63%), Gaps = 5/311 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +E+     + EPL RGF  TLGN+LRRVL++S+ G A++ +QIDG
Sbjct: 3   EFEKPN----ITVVDQEDAYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTALSYIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T I+LN+K + LK   D  K V +   GP  VTAGD++  +++ V
Sbjct: 59  VLHEFSTVPGVREDVTKIVLNLKKLELKSIADEEKIVELDVEGPATVTAGDLKVDSEVTV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + M++ V  G GYVPA  ++T++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTVAEGGHLHMQIAVKNGRGYVPASENKTDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK-EVKEDIN 246
           ES R G+  DYDKL++ + TDGSIT  D+++ AS+IL +   +F   +       +  + 
Sbjct: 179 ESTRVGKKDDYDKLTLEVWTDGSITPSDALSFASKILIEHFKVFKFSDAQTDFGGEVMVE 238

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L   +EEL+LSVRS NCL+   I  + +L  ++E+DM+R+ N GRKSL E+
Sbjct: 239 KEDDKKERQLEMTIEELDLSVRSYNCLKRAGINTLQELTDKSESDMMRVRNLGRKSLEEV 298

Query: 307 KGVLGTMGLFL 317
           K  L  +GL L
Sbjct: 299 KNKLADLGLSL 309


>gi|239818003|ref|YP_002946913.1| DNA-directed RNA polymerase subunit alpha [Variovorax paradoxus
           S110]
 gi|319796380|ref|YP_004158020.1| DNA-directed RNA polymerase, alpha subunit [Variovorax paradoxus
           EPS]
 gi|259494174|sp|C5CQ75|RPOA_VARPS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|239804580|gb|ACS21647.1| DNA-directed RNA polymerase, alpha subunit [Variovorax paradoxus
           S110]
 gi|315598843|gb|ADU39909.1| DNA-directed RNA polymerase, alpha subunit [Variovorax paradoxus
           EPS]
          Length = 329

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 157/327 (48%), Positives = 214/327 (65%), Gaps = 7/327 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I+   L     N+  +  EP  RG+ HTLGNALRRVL+SS+ G + T V I GV
Sbjct: 5   LLKPKTIQVEQL---AANKAKVTLEPFERGYGHTLGNALRRVLLSSMVGYSATEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE SSI GV ED+ +I+LN+KG+  K+       +++ K G G V A DIQT +D+E++
Sbjct: 62  LHEYSSIDGVQEDVVNILLNLKGVVFKLHNRDEVTLSLRKDGEGPVLASDIQTPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSY 185
           NPDHVI +L     + M++ V KG GYVP    R  ++P    G I +DA +SP+K+VSY
Sbjct: 122 NPDHVIAHLSQGGKLDMQIKVEKGRGYVPGTMRRYADEPTKSIGRIVLDASFSPVKRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVESAR  Q  D DKL + I+T+G+IT ED+V  +++IL +QL +F   E  +    +  
Sbjct: 182 TVESARVEQRTDLDKLLVEIETNGAITAEDAVRASAKILVEQLAVFAQLEGGELAAFDAP 241

Query: 246 NVKS-LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
             +S   F+P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL 
Sbjct: 242 APRSAQQFDPILLRPVDELELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLN 301

Query: 305 EIKGVLGTMGLFLGMNLPDWPPESIEE 331
           EIK VL + GL LGM L  WPP  +++
Sbjct: 302 EIKEVLASRGLTLGMKLESWPPAGLDK 328


>gi|118443967|ref|YP_877227.1| DNA-directed RNA polymerase subunit alpha [Clostridium novyi NT]
 gi|168187785|ref|ZP_02622420.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum C
           str. Eklund]
 gi|158512402|sp|A0PXX5|RPOA_CLONN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|118134423|gb|ABK61467.1| DNA-directed RNA polymerase, alpha subunit [Clostridium novyi NT]
 gi|169294320|gb|EDS76453.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum C
           str. Eklund]
          Length = 315

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 130/311 (41%), Positives = 201/311 (64%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE  V   E+      + EPL RG+  TLGN+LRR+L+SSL G A  +++IDG
Sbjct: 3   EIEKP-KIE-CVEASEDGTYGKFVIEPLERGYGITLGNSLRRILLSSLPGGAANSIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T++ILNIKG+ LKM+G+    + I  +GPG VTA DI +  ++E+
Sbjct: 61  VLHEFSTVTGVKEDVTELILNIKGLALKMNGEGPSTIYIDAQGPGEVTAADIISDGNVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N D  I  LD D  + ME+ V  G GYV    ++ E+ PIG I +D++Y+P+K+V++TV
Sbjct: 121 MNKDMHIATLDDDGKLYMEINVDNGRGYVTQNKNKKEDLPIGTIPVDSIYTPVKRVNFTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ DYDKLS+ + T+G+I  E++++L+++IL +   +F+   +    V+  +  
Sbjct: 181 ENTRVGQITDYDKLSIEVWTNGTIQPEEAISLSAKILIEHFKLFMTLTDHADNVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L +RT  DM+++ N G+KSL E++
Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTERTIDDMMKVRNLGKKSLEEVQ 300

Query: 308 GVLGTMGLFLG 318
             L  +GL L 
Sbjct: 301 EKLAALGLGLK 311


>gi|237747390|ref|ZP_04577870.1| RNA polymerase [Oxalobacter formigenes HOxBLS]
 gi|229378741|gb|EEO28832.1| RNA polymerase [Oxalobacter formigenes HOxBLS]
          Length = 325

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 156/333 (46%), Positives = 215/333 (64%), Gaps = 11/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N    +KP  I    LG     R+++  EP  RG+ HTLGNALRRVL+SS+ G A T
Sbjct: 1   MQNN---FLKPRIINVESLG---GGRSIVEMEPFERGYGHTLGNALRRVLLSSMTGYAPT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GV+HE S++ GV ED+ D++LN+KG+  K+       +T+ K GPG+VTA DI+ 
Sbjct: 55  EVTIAGVVHEYSTLDGVQEDVVDLLLNLKGVVFKLHNRDVITLTLKKSGPGIVTAADIEL 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYS 178
            +D+E++NPDHVI NL  +  + M++ V KG GYVP    R     N  IG I +DA +S
Sbjct: 115 PHDVEIINPDHVIANLADNGKLDMQIKVEKGRGYVPGNVRRLSEDANKTIGRIILDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY VESAR  Q  D DKL + I+T+G IT E+++  ++RIL DQL +F   E   
Sbjct: 175 PVRRVSYAVESARVEQRTDLDKLIINIETNGVITAEEAIRQSARILVDQLSVFAALE--G 232

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E   +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N 
Sbjct: 233 TETTSEALTQVPAVDPILLRPVDDLELTVRSANCLKAENINYIGDLIQRSENELLKTPNL 292

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL + GL LGM L +WPP   E+
Sbjct: 293 GRKSLNEIKEVLASRGLTLGMRLDNWPPAGFEK 325


>gi|300721391|ref|YP_003710662.1| RNA polymerase subunit alpha [Xenorhabdus nematophila ATCC 19061]
 gi|297627879|emb|CBJ88425.1| RNA polymerase, alpha subunit [Xenorhabdus nematophila ATCC 19061]
          Length = 329

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 148/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVQGKDEVILTVNKSGIGPVTAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D  A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDESASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|170728984|ref|YP_001763010.1| DNA-directed RNA polymerase subunit alpha [Shewanella woodyi ATCC
           51908]
 gi|169814331|gb|ACA88915.1| DNA-directed RNA polymerase, alpha subunit [Shewanella woodyi ATCC
           51908]
          Length = 329

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 143/333 (42%), Positives = 214/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E ++P  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLRPRLVD---IEQVNPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDVLEILLNLKGLAVVVEGKDEAMLTLSKSGAGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
             D+ ++NPDHVIC+L  +  V M + V +G GYVPA        +  PIG + +D+ +S
Sbjct: 118 DGDVTIMNPDHVICHLTGNNDVSMRIRVERGRGYVPASARAQTEDDERPIGRLLVDSSFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G+I  E+++  ++ IL +QL  F+   +  
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTIDPEEAIRRSATILAEQLDAFVELRDVT 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +     +  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 EPE---LKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>gi|304385388|ref|ZP_07367733.1| DNA-directed RNA polymerase subunit alpha [Pediococcus acidilactici
           DSM 20284]
 gi|304328595|gb|EFL95816.1| DNA-directed RNA polymerase subunit alpha [Pediococcus acidilactici
           DSM 20284]
          Length = 314

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 140/312 (44%), Positives = 193/312 (61%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E +N    + EPL RG+  TLGN+LRR+L+SSL GAAIT+VQID 
Sbjct: 3   EFEKPK----IHKIDENDNYGRFVIEPLERGYGTTLGNSLRRILLSSLPGAAITSVQIDN 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ V
Sbjct: 59  VLHEFSTIEGVVEDVTQIILNLKKVSLKIESDDEKTLDINVVGPANVTAGDIMGDGDVTV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSY 185
           LNPD  IC +         LT   G GY  A  ++    + PIG++ ID++Y+PI++V+Y
Sbjct: 119 LNPDSPICTVAEGTTFHAVLTADTGRGYTSADENKARKADMPIGVLPIDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE  R GQ  DYDKL++ I TDGSIT  ++ +L+++IL + L +F+N  +  KE +  +
Sbjct: 179 QVEKTRVGQRDDYDKLTLDIWTDGSITPSEATSLSAKILTEHLAIFVNLNDQAKETEIMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   +EEL+LSVRS NCL+   I  + +L  RTEA M+++ N GRKSLVE
Sbjct: 239 EKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINSVQELTDRTEAQMMKVRNLGRKSLVE 298

Query: 306 IKGVLGTMGLFL 317
           I+  L  +GL  
Sbjct: 299 IQEKLNALGLSF 310


>gi|269955462|ref|YP_003325251.1| DNA-directed RNA polymerase subunit alpha [Xylanimonas
           cellulosilytica DSM 15894]
 gi|269304143|gb|ACZ29693.1| DNA-directed RNA polymerase, alpha subunit [Xylanimonas
           cellulosilytica DSM 15894]
          Length = 334

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 126/317 (39%), Positives = 191/317 (60%), Gaps = 4/317 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E ++     ENRT    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLTEEVI----SENRTRFAIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+T+IILNIK + +    D    + + K+G G VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTEIILNIKNLVVSSENDEPVVMYLRKQGAGAVTAADIVPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+    + +ELTV +G GYV A  +++ +  IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLHIATLNDKGKLEIELTVERGRGYVSAAQNKSLDAEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  +IT  D++A A + L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDKLIVDVETKPAITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPTDS 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EEL L++RS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEELNLTIRSYNCLKREGIHQVGELVARSEADLLDIRNFGAKSINEVKEKL 301

Query: 311 GTMGLFLGMNLPDWPPE 327
             +GL L  +  D+ P 
Sbjct: 302 AELGLALKDSPLDFDPS 318


>gi|167855325|ref|ZP_02478093.1| DNA-directed RNA polymerase alpha chain [Haemophilus parasuis
           29755]
 gi|219871571|ref|YP_002475946.1| DNA-directed RNA polymerase subunit alpha [Haemophilus parasuis
           SH0165]
 gi|167853583|gb|EDS24829.1| DNA-directed RNA polymerase alpha chain [Haemophilus parasuis
           29755]
 gi|219691775|gb|ACL32998.1| DNA-directed RNA polymerase subunit alpha [Haemophilus parasuis
           SH0165]
          Length = 329

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 223/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ +    + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVN---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDIILTLTKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++NPDHVICNL D +A + M + V +G GYVPA    H + ++ PIG + +DA +
Sbjct: 118 DGDVEIVNPDHVICNLTDKNASISMRIRVQRGRGYVPASARVHTQDDDRPIGRLLVDARF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|331268442|ref|YP_004394934.1| DNA-directed RNA polymerase subunit alpha [Clostridium botulinum
           BKT015925]
 gi|329124992|gb|AEB74937.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           BKT015925]
          Length = 315

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 131/311 (42%), Positives = 202/311 (64%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE  V   E+      + EPL RG+  TLGN+LRR+L+SSL G A  +++IDG
Sbjct: 3   EIEKP-KIE-CVEASEDGTYGKFVIEPLERGYGITLGNSLRRILLSSLPGVAANSIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T++ILNIKG+ LKM+G+    + I  +GPG VTA DI +  +IEV
Sbjct: 61  VLHEFSTVTGVKEDVTELILNIKGLALKMNGEGPSTIYIEAQGPGEVTAADIISDGNIEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N D  I  LD D  + ME+ + +G GYV    ++ E+ PIG I +D++Y+P+K+V++TV
Sbjct: 121 MNKDMHIATLDDDGKLYMEINIDRGRGYVTQNKNKKEDLPIGTIPVDSIYTPVKRVNFTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ DYDKLS+ + T+G+I  E++++L+++IL +   +F+   +    V+  +  
Sbjct: 181 ENTRVGQITDYDKLSIEVWTNGTIQPEEAISLSAKILIEHFKLFMTLTDHADNVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L +RT  DM+++ N G+KSL E++
Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTERTIDDMMKVRNLGKKSLEEVQ 300

Query: 308 GVLGTMGLFLG 318
             L  +GL L 
Sbjct: 301 EKLAALGLGLK 311


>gi|170017919|ref|YP_001728838.1| DNA-directed RNA polymerase alpha chain [Leuconostoc citreum KM20]
 gi|169804776|gb|ACA83394.1| DNA-directed RNA polymerase alpha chain [Leuconostoc citreum KM20]
          Length = 314

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 130/312 (41%), Positives = 192/312 (61%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E+ +    + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDG
Sbjct: 3   EFEKPN----IHNIEEDAHYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE S++ GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+Q   D+EV
Sbjct: 59  VVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDVQGPADVTAADLQAGADVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
           LNPD  I  +     + M +T  KG GY  A  ++   +  PIG++ +D++Y+PI++V+Y
Sbjct: 119 LNPDLHIATVAAGKSLHMTVTAVKGRGYSSADENKQLRDEMPIGVLAVDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R G   DYDKL+  I T+GSI   D+++L S+IL + L +F++      E    +
Sbjct: 179 HVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSLGSKILAEHLNLFMDISPVAAEANVMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             + +  + +    +E+L+LSVRS NCL+   I  + +L  RTEADM+++ N GRKSL E
Sbjct: 239 EAEPVAASASDSAPIEDLDLSVRSYNCLKRAGINTIVELTDRTEADMMKVRNLGRKSLDE 298

Query: 306 IKGVLGTMGLFL 317
           I+  L  MGL  
Sbjct: 299 IQEKLTEMGLGF 310


>gi|323490649|ref|ZP_08095854.1| DNA-directed RNA polymerase subunit alpha [Planococcus donghaensis
           MPA1U2]
 gi|323395741|gb|EGA88582.1| DNA-directed RNA polymerase subunit alpha [Planococcus donghaensis
           MPA1U2]
          Length = 314

 Score =  347 bits (890), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 127/310 (40%), Positives = 198/310 (63%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +    +     + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETVEIDNNAKF-GKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+  IILNIK + LK+  D  K + I  +G G VTA DI   +D+E+
Sbjct: 61  VLHEFSTVEGVEEDVATIILNIKKLALKIYSDEEKVIEIDVKGDGTVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  +  +  +RM +  ++G GY  A  ++ E+ PIG+I ID++Y+P+ +V++ V
Sbjct: 121 LNPDLYIATIAKNGHLRMRMYANRGRGYARADQNKREDLPIGVIPIDSIYTPVSRVNFQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+  +DKLS+ + TDGSI  ++++AL ++I  + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQLAHFDKLSLDVWTDGSIGPKEAIALGAKIFTEHLNIFVGLTDEAQTAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVHELASKSEDDMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 VKLEDLGLGL 310


>gi|86739323|ref|YP_479723.1| DNA-directed RNA polymerase subunit alpha [Frankia sp. CcI3]
 gi|119366683|sp|Q2JFE8|RPOA_FRASC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|86566185|gb|ABD09994.1| DNA-directed RNA polymerase subunit alpha [Frankia sp. CcI3]
          Length = 349

 Score =  347 bits (890), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 126/316 (39%), Positives = 190/316 (60%), Gaps = 4/316 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P  IE        E R+  + EPL  GF +TLGN+LRR L+SS+ GA++T+++IDGVLH
Sbjct: 6   RPTLIE----DPISEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+TD+ILN+K + +    D    + + K+GPG VTA DI     +EV NP
Sbjct: 62  EFSTVPGVKEDVTDLILNLKELVVSSDNDEPTVMYLRKQGPGEVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           +  +  L+    + +ELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+ 
Sbjct: 122 ELRLATLNDKGKLEIELTVERGRGYVSAAQNKQAGQEIGRIPIDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  SI+  D++A A + L    G+        + V    +    
Sbjct: 182 RVEQRTDFDRLIVDVETKPSISPRDAMASAGKTLVGLFGLAQELNAEAEGVDIGPSAADA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EE++L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  L
Sbjct: 242 ALAADLALPIEEMDLTVRSYNCLKREGIHTIGELVSRSEADLLDIRNFGQKSIDEVKTKL 301

Query: 311 GTMGLFLGMNLPDWPP 326
           G MGL L  + P + P
Sbjct: 302 GAMGLQLKDSPPGFDP 317


>gi|16272744|ref|NP_438962.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           Rd KW20]
 gi|1173145|sp|P43737|RPOA_HAEIN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|1573813|gb|AAC22461.1| DNA-directed RNA polymerase, alpha chain (rpoA) [Haemophilus
           influenzae Rd KW20]
          Length = 328

 Score =  347 bits (890), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 151/333 (45%), Positives = 222/333 (66%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVILTLNKSGIGPVVAADITY 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYS 178
             D+E++NPDHVIC+L D +A + M + V +G GYVPA  + H  E  PIG + +DA YS
Sbjct: 118 DGDVEIVNPDHVICHLTDENASISMRIRVQRGRGYVPASSRTHTQEERPIGRLLVDACYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +
Sbjct: 178 PVERIAYNVEAARVEQRTDLDKLVIELETNGALEPEEAIRRAATILAEQLDAFVDLRDVR 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +    +I  +   F P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 QP---EIKEEKPEFXPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 327


>gi|58336655|ref|YP_193240.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           acidophilus NCFM]
 gi|227903213|ref|ZP_04021018.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           acidophilus ATCC 4796]
 gi|75433035|sp|Q5FM65|RPOA_LACAC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|58253972|gb|AAV42209.1| RNA-polymerase DNA-directed [Lactobacillus acidophilus NCFM]
 gi|227869018|gb|EEJ76439.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           acidophilus ATCC 4796]
          Length = 312

 Score =  347 bits (890), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 135/310 (43%), Positives = 195/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDG
Sbjct: 3   EFEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++V
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMELAVKNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   K  +  +  
Sbjct: 179 ESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADANTKFSEVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE+DM+R+ N GRKSL E+K
Sbjct: 239 EDDKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELTDKTESDMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLTDLGLSL 308


>gi|50122926|ref|YP_052093.1| DNA-directed RNA polymerase subunit alpha [Pectobacterium
           atrosepticum SCRI1043]
 gi|227115247|ref|ZP_03828903.1| DNA-directed RNA polymerase subunit alpha [Pectobacterium
           carotovorum subsp. brasiliensis PBR1692]
 gi|227328924|ref|ZP_03832948.1| DNA-directed RNA polymerase subunit alpha [Pectobacterium
           carotovorum subsp. carotovorum WPP14]
 gi|253690158|ref|YP_003019348.1| DNA-directed RNA polymerase, alpha subunit [Pectobacterium
           carotovorum subsp. carotovorum PC1]
 gi|261823207|ref|YP_003261313.1| DNA-directed RNA polymerase subunit alpha [Pectobacterium wasabiae
           WPP163]
 gi|61215910|sp|Q6CZZ5|RPOA_ERWCT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|49613452|emb|CAG76903.1| DNA-directed RNA polymerase alpha chain [Pectobacterium
           atrosepticum SCRI1043]
 gi|251756736|gb|ACT14812.1| DNA-directed RNA polymerase, alpha subunit [Pectobacterium
           carotovorum subsp. carotovorum PC1]
 gi|261607220|gb|ACX89706.1| DNA-directed RNA polymerase, alpha subunit [Pectobacterium wasabiae
           WPP163]
          Length = 329

 Score =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P H+IC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHLICHLTDENASISMRIKVQRGRGYVPASARIHTEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|239996312|ref|ZP_04716836.1| DNA-directed RNA polymerase subunit alpha [Alteromonas macleodii
           ATCC 27126]
 gi|332142181|ref|YP_004427919.1| DNA-directed RNA polymerase subunit alpha [Alteromonas macleodii
           str. 'Deep ecotype']
 gi|327552203|gb|AEA98921.1| DNA-directed RNA polymerase subunit alpha [Alteromonas macleodii
           str. 'Deep ecotype']
          Length = 328

 Score =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 150/331 (45%), Positives = 220/331 (66%), Gaps = 9/331 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            +  E +KP  +E   +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+T V
Sbjct: 2   GSVTEFLKPRLVEIENVS---PTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEV 58

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G +   +T+ K G G V AGDIQ   
Sbjct: 59  EIDGVLHEYSTKEGVQEDVIEILLNLKGLAVRLEGKTEATLTLVKSGAGPVVAGDIQHDG 118

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPI 180
           D+E+ NPDHVIC L  +A + M + V  G GYVPA   R+   ++ PIG + +DA YSP+
Sbjct: 119 DVEITNPDHVICTLTGEAEISMRIKVEMGRGYVPASTRRSSEEDDRPIGRLLVDASYSPV 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++++Y+VESAR  Q  D DKL + ++T+G++  E+++  ++ IL +QL  F++  +  + 
Sbjct: 179 ERIAYSVESARVEQRTDLDKLIIDMETNGTLDPEEAIRRSATILAEQLDAFVDLRDVSEP 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+
Sbjct: 239 E---AKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIQYIGDLVQRTEVELLKTPNLGK 295

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           KSL EIK VL + GL LGM L +WPPESI E
Sbjct: 296 KSLTEIKDVLASRGLSLGMRLENWPPESIAE 326


>gi|297569395|ref|YP_003690739.1| DNA-directed RNA polymerase, alpha subunit [Desulfurivibrio
           alkaliphilus AHT2]
 gi|296925310|gb|ADH86120.1| DNA-directed RNA polymerase, alpha subunit [Desulfurivibrio
           alkaliphilus AHT2]
          Length = 341

 Score =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 154/324 (47%), Positives = 216/324 (66%), Gaps = 3/324 (0%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
            +NW +LI P  +E         +    I +PL RGFA T+GN+LRR+L+SS+RGAAIT+
Sbjct: 9   YRNWHDLIFPEKLEVDQ-DTHTASFGKFICQPLERGFATTIGNSLRRILLSSIRGAAITS 67

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           V+I+GVLHE+S+I G+ ED T+IILN+K + L++     K V I K+  GVVTAGDI   
Sbjct: 68  VKIEGVLHELSTIPGIKEDATEIILNLKEVRLRLHSGEAKTVRIEKKKKGVVTAGDIIGD 127

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
             +EV+NP+  IC +  D     EL V  G GYVPA+ ++ E+ PIG+I +D++++PI+ 
Sbjct: 128 PQVEVMNPEQHICTITGDGKFDAELEVDWGKGYVPAERNKREDQPIGVIPLDSVFTPIRN 187

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK--KE 240
           V      AR GQ  DYDKL++ I TDGSI  ED++A A++IL++Q+ +FINF+E      
Sbjct: 188 VRVITSQARVGQQTDYDKLTLEITTDGSILPEDALAYAAKILKEQMQVFINFDESAVVPV 247

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            KE  + +    N  L + VE+LELSVRS NCLR   I ++G+L+Q+TEA+ML+  NFGR
Sbjct: 248 KKEKESGEQPQLNENLYRSVEDLELSVRSANCLRNAEIRHIGELVQKTEAEMLKTKNFGR 307

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDW 324
           KSL EIK +L  M L+LGM +  W
Sbjct: 308 KSLNEIKQLLSEMDLYLGMKIDGW 331


>gi|229818214|ref|ZP_04448496.1| hypothetical protein BIFANG_03512 [Bifidobacterium angulatum DSM
           20098]
 gi|229784465|gb|EEP20579.1| hypothetical protein BIFANG_03512 [Bifidobacterium angulatum DSM
           20098]
          Length = 332

 Score =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 125/313 (39%), Positives = 182/313 (58%), Gaps = 1/313 (0%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                   R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ GV
Sbjct: 10  TEESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTTLPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+I+LNIKGI L    D    + + K G G  TAGDI     + + NPD  I  L 
Sbjct: 70  QEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGVTIANPDKHIATLA 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  + +E TV +G GYVPA  ++ + D IG I +D++YSP+ KVSY VE+ R  Q  D+
Sbjct: 130 EDGELEIEFTVERGRGYVPASMNKQDADEIGRIPVDSIYSPVLKVSYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  +I+  D+VA A   L +  G+        + V+          NP    
Sbjct: 190 DKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNVQAEGVEVGSAPVVEEANPEHAV 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L ++GL L 
Sbjct: 250 PIEDLNLTQRSYNCLKREGIHTIGELVSHTEQDLLDIRNFGMKSIDEVKEKLQSLGLSLK 309

Query: 319 MN-LPDWPPESIE 330
            + L D+ P ++E
Sbjct: 310 ASPLGDFDPNNLE 322


>gi|17547712|ref|NP_521114.1| DNA-directed RNA polymerase subunit alpha [Ralstonia solanacearum
           GMI1000]
 gi|20139458|sp|Q8XV38|RPOA_RALSO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|17430017|emb|CAD16702.1| probable dna-directed rna polymerase alpha chain (rnap
           alphasubunit) (transcriptase alpha chain) (rna
           polymerase alpha subunit) protein [Ralstonia
           solanacearum GMI1000]
 gi|299065441|emb|CBJ36610.1| RNA polymerase, alpha subunit; RNA polymerase alpha chain family
           [Ralstonia solanacearum CMR15]
          Length = 326

 Score =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 148/326 (45%), Positives = 210/326 (64%), Gaps = 7/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG        ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVEPLGDH---HAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S+I GV ED+ +++LN+KG+  K+       V++ K G GVVTA DI+  +D+E++
Sbjct: 62  VHEYSTIDGVQEDVVNLLLNLKGVVFKLHNRDEVTVSLRKEGEGVVTAADIELPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSY 185
           NP HVI +L     + M++ V +G GYVP    +  ++     G I +DA ++P+++VSY
Sbjct: 122 NPGHVIASLSAGGKLDMQIKVEQGRGYVPGNVRKFGDESSKVIGRIVLDASFAPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL DQL +F   E   +   E  
Sbjct: 182 AVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALEG-TESAAEAA 240

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 241 AARAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 300

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +E+
Sbjct: 301 IKEVLASRGLTLGMKLENWPPAGLEK 326


>gi|270291108|ref|ZP_06197331.1| DNA-directed RNA polymerase, alpha subunit [Pediococcus
           acidilactici 7_4]
 gi|270280504|gb|EFA26339.1| DNA-directed RNA polymerase, alpha subunit [Pediococcus
           acidilactici 7_4]
          Length = 314

 Score =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 140/312 (44%), Positives = 194/312 (62%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E +N    + EPL RG+  TLGN+LRR+L+SSL GAAIT+VQID 
Sbjct: 3   EFEKPK----IHKIDENDNYGRFVIEPLERGYGTTLGNSLRRILLSSLPGAAITSVQIDN 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ V
Sbjct: 59  VLHEFSTIEGVVEDVTQIILNLKKVSLKIESDDEKTLDINVVGPANVTAGDIMGDGDVTV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSY 185
           LNPD  IC +         LT   G GY  A  ++    + PIG++ ID++Y+PI++V+Y
Sbjct: 119 LNPDSPICTVAEGTTFHAVLTADTGRGYTSADENKARKADMPIGVLPIDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE  R GQ  DYDKL++ I TDGSIT  ++ +L+++IL + L +F+N  +  KE +  +
Sbjct: 179 QVEKTRVGQRDDYDKLTLDIWTDGSITPSEATSLSAKILTEHLAIFVNLNDQAKETEIMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   +EEL+LSVRS NCL+   I  + +L  RTEA M+++ N GRKSLVE
Sbjct: 239 EKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINSVQELTDRTEAQMMKVRNLGRKSLVE 298

Query: 306 IKGVLGTMGLFL 317
           I+  L ++GL  
Sbjct: 299 IQEKLNSLGLSF 310


>gi|227879268|ref|ZP_03997138.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus crispatus
           JV-V01]
 gi|256844455|ref|ZP_05549941.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus crispatus
           125-2-CHN]
 gi|256849157|ref|ZP_05554590.1| RNA-polymerase DNA-directed [Lactobacillus crispatus MV-1A-US]
 gi|262047173|ref|ZP_06020131.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus crispatus
           MV-3A-US]
 gi|295692185|ref|YP_003600795.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus crispatus
           ST1]
 gi|227861162|gb|EEJ68811.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus crispatus
           JV-V01]
 gi|256613533|gb|EEU18736.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus crispatus
           125-2-CHN]
 gi|256713933|gb|EEU28921.1| RNA-polymerase DNA-directed [Lactobacillus crispatus MV-1A-US]
 gi|260572418|gb|EEX28980.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus crispatus
           MV-3A-US]
 gi|295030291|emb|CBL49770.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus crispatus
           ST1]
          Length = 312

 Score =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 135/310 (43%), Positives = 195/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDG
Sbjct: 3   EFEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++V
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDIEGPATVTADDLKVDADVQV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMELAVKNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   K  +  +  
Sbjct: 179 ESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADANAKFSEVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  +TE+DM+R+ N GRKSL E+K
Sbjct: 239 EDDKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELTDKTESDMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLTDLGLSL 308


>gi|253998041|ref|YP_003050104.1| DNA-directed RNA polymerase subunit alpha [Methylovorus sp. SIP3-4]
 gi|313200106|ref|YP_004038764.1| DNA-directed RNA polymerase subunit alpha [Methylovorus sp. MP688]
 gi|253984720|gb|ACT49577.1| DNA-directed RNA polymerase, alpha subunit [Methylovorus sp.
           SIP3-4]
 gi|312439422|gb|ADQ83528.1| DNA-directed RNA polymerase, alpha subunit [Methylovorus sp. MP688]
          Length = 327

 Score =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 156/332 (46%), Positives = 215/332 (64%), Gaps = 8/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++  V+      R  +  EP+ RGF +TLGNALRRVL+SS+ G AIT
Sbjct: 1   MQNSPTEYLKPRVVDVEVISPV---RARVTLEPMERGFGYTLGNALRRVLLSSIPGFAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGV+HE S++ GV ED+ DI+LN+KG+ LK++  S   +T+ K   GVVTAGD  T
Sbjct: 58  EVKIDGVVHEYSTLDGVQEDVVDILLNLKGVALKLNSKSETTLTLKKSVEGVVTAGDFDT 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY--VPAKHHRTENDPIGLITIDALYSP 179
            +D E+ NP HVI +L     + +E+ V  G GY  VPA+    E+  +G I +DA +SP
Sbjct: 118 GHDAEIANPGHVIAHLTKGGKIDLEVKVEMGRGYQPVPARQKTDEDRVLGFIMVDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I KVSY VESAR  Q  D DKL M ++T+G +  E ++  A+RIL  QL +F + E    
Sbjct: 178 INKVSYHVESARVEQRTDLDKLIMDVETNGVVEPEQAIRDAARILMGQLSVFADLEGAPT 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           EV+      +   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQR E ++L+  N G
Sbjct: 238 EVEV---KHTPQVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRGENELLKAPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           RKSL EIK VL + GL LGM L +WPP  +E+
Sbjct: 295 RKSLNEIKDVLASKGLTLGMKLENWPPVGLEK 326


>gi|52426078|ref|YP_089215.1| DNA-directed RNA polymerase subunit alpha [Mannheimia
           succiniciproducens MBEL55E]
 gi|61215866|sp|Q65QY0|RPOA_MANSM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|52308130|gb|AAU38630.1| RpoA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 329

 Score =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 222/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVD---IEQVSPTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVFLTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALY 177
             D+E++NP+HVIC+L D +A + M + V +G GYVPA      + E  PIG + +DA Y
Sbjct: 118 DGDVEIVNPEHVICHLTDENASINMRIRVQRGRGYVPASARVHAQDEERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLVIELETNGAIDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|119947101|ref|YP_944781.1| DNA-directed RNA polymerase subunit alpha [Psychromonas ingrahamii
           37]
 gi|158513126|sp|A1T0B7|RPOA2_PSYIN RecName: Full=DNA-directed RNA polymerase subunit alpha 2;
           Short=RNAP subunit alpha 2; AltName: Full=RNA polymerase
           subunit alpha 2; AltName: Full=Transcriptase subunit
           alpha 2
 gi|119865705|gb|ABM05182.1| DNA-directed RNA polymerase, alpha subunit [Psychromonas ingrahamii
           37]
          Length = 328

 Score =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 148/333 (44%), Positives = 223/333 (66%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KPN +    + Q    R  +   PL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVIEFLKPNLV---GIEQINATRAKVTLGPLERGFGHTLGNALRRILLSSMPGTAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGV HE S+ +GV ED+ +I+LN+KG+ +K+ G  +  V++ K G G VTAGDI  
Sbjct: 58  EVEIDGVQHEYSTKEGVQEDILEILLNLKGLAVKLEGKDNVLVSLTKSGAGPVTAGDITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
            +D+E++NP+HVIC+L  +A + M + +  G GYVPA        +  PIG + +DA +S
Sbjct: 118 GSDVEIVNPEHVICHLTGNAEISMRIKIESGRGYVPASSRIHTEEDERPIGRLLVDATFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y+VESAR  Q  D DKL + ++TDG++  E+++  A+ IL +QL  F++  +  
Sbjct: 178 PVERIAYSVESARVEQRTDLDKLVIDMETDGTLDPEEAIRRAATILAEQLDAFVDLRKVS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V ++   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 EPVAKE---EKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ E
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLSE 327


>gi|42799|emb|CAA26395.1| unnamed protein product [Escherichia coli]
          Length = 329

 Score =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETTGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|158319572|ref|YP_001512079.1| DNA-directed RNA polymerase, alpha subunit [Alkaliphilus oremlandii
           OhILAs]
 gi|172048250|sp|A8MLG9|RPOA_ALKOO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158139771|gb|ABW18083.1| DNA-directed RNA polymerase, alpha subunit [Alkaliphilus oremlandii
           OhILAs]
          Length = 317

 Score =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 141/310 (45%), Positives = 213/310 (68%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  +E + +   E        EPL RG+  TLGN+LRR+++SSL GAA+T+V+IDG
Sbjct: 5   EMEKP-KVEVVEIN-AENTYGKFTVEPLERGYGTTLGNSLRRIMLSSLPGAAVTSVKIDG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+ +II+N+KG++++M G+  K V I  +G GV+TAGDI    D+E+
Sbjct: 63  VLHEFSTIPGVKEDVAEIIINLKGLSIRMHGNEPKTVRIEAKGEGVITAGDIIADADVEI 122

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           L+PD  I  LD DAV+ MELT++KG GYVPA++++T   PIG++ ID++++P+ KVSY V
Sbjct: 123 LSPDTHIATLDTDAVLNMELTIAKGRGYVPAENNKTPGMPIGVLPIDSIFTPVTKVSYHV 182

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQV DYDKL + + TDGSI  +++++LA++I+ + L +FI   +   +V+  +  
Sbjct: 183 ENTRVGQVTDYDKLVIEVFTDGSIVPDEAISLAAKIMNEHLNLFITLTDHVNDVEIMVQK 242

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L Q++E DM+++ N GRKSL E++
Sbjct: 243 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVDELAQKSEEDMMKVRNLGRKSLEEVQ 302

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 303 KKLEELGLGL 312


>gi|323465848|gb|ADX69535.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus helveticus
           H10]
          Length = 312

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 134/310 (43%), Positives = 194/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDG
Sbjct: 3   EFEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++V
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSLSDERKVIELDFEGPATVTADDLKVDADVQV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + ME+ V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMEIAVQNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   K  +  +  
Sbjct: 179 ESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADADTKFSEVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L   TE+DM+R+ N GRKSL E+K
Sbjct: 239 EDDKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELTDMTESDMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLTDLGLSL 308


>gi|226329506|ref|ZP_03805024.1| hypothetical protein PROPEN_03415 [Proteus penneri ATCC 35198]
 gi|225202692|gb|EEG85046.1| hypothetical protein PROPEN_03415 [Proteus penneri ATCC 35198]
          Length = 329

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 148/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVHGKDEVILTLSKSGIGPVIAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASINMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+S+  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEESIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|72163017|ref|YP_290674.1| DNA-directed RNA polymerase subunit alpha [Thermobifida fusca YX]
 gi|90110874|sp|Q47LM1|RPOA_THEFY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|71916749|gb|AAZ56651.1| DNA-directed RNA polymerase, alpha subunit [Thermobifida fusca YX]
          Length = 338

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 120/308 (38%), Positives = 180/308 (58%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                 E R+  I EPL  GF +T+GN+LRR L+SS+ GAA+T+++I+GV HE +++ GV
Sbjct: 10  TEEPISEFRSKFILEPLEPGFGYTIGNSLRRTLLSSIPGAAVTSIRIEGVEHEFTTVPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+IILN+KG+ +    D    + + K+GPGVVTA DI     +EV NP+  I  L+
Sbjct: 70  KEDVTEIILNLKGLVVSSEHDEPVLMYLRKQGPGVVTAADIAPPAGVEVHNPEMHIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + ME+TV +G GYV A  ++     IG I ID++YSP+ +V+Y VE+ R  Q  D+
Sbjct: 130 SKGKLEMEMTVERGRGYVSAAQNKQPGQEIGRIPIDSIYSPVMRVTYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           D+L + + T  +I   D+VA A + L +  G+        + +    +         L  
Sbjct: 190 DRLILDVWTKPAIRPRDAVASAGKTLVELFGLARELNVDAEGIDMGPSPTDAALAADLAL 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L L+VRS NCL+ E I  +G+L+ RTE D+L + NFG KS+ E+K  L  MGL L 
Sbjct: 250 PIEDLNLTVRSYNCLKREGIHTVGELVARTEQDLLDIRNFGAKSIEEVKQKLSDMGLALK 309

Query: 319 MNLPDWPP 326
                + P
Sbjct: 310 DAQGGFDP 317


>gi|134298121|ref|YP_001111617.1| DNA-directed RNA polymerase subunit alpha [Desulfotomaculum
           reducens MI-1]
 gi|172044239|sp|A4J139|RPOA_DESRM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|134050821|gb|ABO48792.1| DNA-directed RNA polymerase subunit alpha [Desulfotomaculum
           reducens MI-1]
          Length = 315

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 133/310 (42%), Positives = 204/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE IV   E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+V+I+G
Sbjct: 3   EIEKP-KIE-IVEQSEDNTYGKFVVEPLERGYGITLGNSLRRILLSSLPGAAVTSVKIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE +++ GV ED+TDIILN+K + LK+  D  K + +  +  G VTAGDI    D+E+
Sbjct: 61  VLHEFATVPGVQEDVTDIILNLKNLCLKIHSDEEKVLRVEAQTEGPVTAGDIIHDADVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  +  LD    + ME++V+KG GY  A+ ++     IG+I ID++Y+P+++V+Y V
Sbjct: 121 LNPDLHLATLDTGGRLFMEISVNKGRGYSSAEKNKKGEHIIGVIPIDSIYTPVRRVNYNV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ DYDKL++ + T+GSI  +++ +L+++IL + L +FI   E   +V+  +  
Sbjct: 181 ENTRVGQITDYDKLTLEVWTNGSIRPDEATSLSAKILSEHLRLFIGLTETVNDVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    +  L   +EEL++SVRS NCL+   I  + +LIQR E DM+++ N G+KSL E+ 
Sbjct: 241 EEEQKDKILEMTIEELDMSVRSYNCLKRAGINTVEELIQRNEEDMMKVRNLGKKSLEEVI 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 NKLHELGLSL 310


>gi|329298509|ref|ZP_08255845.1| DNA-directed RNA polymerase subunit alpha [Plautia stali symbiont]
          Length = 329

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ L++ G     +T+ + G G VTAGDI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLALRVQGKDEVILTLNQSGIGPVTAGDITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  AS IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRASTILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|238763709|ref|ZP_04624668.1| DNA-directed RNA polymerase subunit alpha [Yersinia kristensenii
           ATCC 33638]
 gi|238698011|gb|EEP90769.1| DNA-directed RNA polymerase subunit alpha [Yersinia kristensenii
           ATCC 33638]
          Length = 330

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFVPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|315222793|ref|ZP_07864679.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus anginosus
           F0211]
 gi|315188096|gb|EFU21825.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus anginosus
           F0211]
          Length = 312

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 133/313 (42%), Positives = 201/313 (64%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E +N  + + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKNYGIFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILN+KGI +K   +  K + +   GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNVKGIAVKSYVEDEKTIELDVEGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A ++  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIGEGASLKAIMTVNTGRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I TDG+I  ED++ L++RIL + L +F N  E  K        
Sbjct: 179 EPARVGSNDGFDKLTLEIMTDGTIIPEDALGLSARILTEHLDLFTNLTEVAKSTDVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +  +  L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 EKVSDDRVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKND 311


>gi|188535253|ref|YP_001909050.1| DNA-directed RNA polymerase subunit alpha [Erwinia tasmaniensis
           Et1/99]
 gi|188030295|emb|CAO98184.1| DNA-directed RNA polymerase alpha chain [Erwinia tasmaniensis
           Et1/99]
          Length = 329

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P H IC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHAICHLTDENAAISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|56460991|ref|YP_156272.1| DNA-directed RNA polymerase subunit alpha [Idiomarina loihiensis
           L2TR]
 gi|61215803|sp|Q5QXV8|RPOA_IDILO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|56180001|gb|AAV82723.1| DNA-directed RNA polymerase alpha subunit [Idiomarina loihiensis
           L2TR]
          Length = 329

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 142/333 (42%), Positives = 219/333 (65%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF +TLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISPTHAKVTLEPLERGFGYTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ + + G     +T+ K G G VTAGD   
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDVIEVLLNLKGLAVSVEGKDEATLTLNKSGAGPVTAGDFTH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
             D+E++NP+HVIC+L  D  + M + V +G GYVPA   ++ +D   PIG + +DA +S
Sbjct: 118 DGDVEIVNPEHVICHLTGDYELVMRVKVERGRGYVPAASRQSADDDERPIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F+   +  
Sbjct: 178 PVERIAYSVDAARVEQRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLDAFVELRDIS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +        +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 EPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIQYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLID 327


>gi|145632161|ref|ZP_01787896.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           3655]
 gi|145634786|ref|ZP_01790494.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           PittAA]
 gi|145636639|ref|ZP_01792306.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           PittHH]
 gi|145640901|ref|ZP_01796483.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           R3021]
 gi|229844670|ref|ZP_04464809.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           6P18H1]
 gi|229845853|ref|ZP_04465965.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           7P49H1]
 gi|144987068|gb|EDJ93598.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           3655]
 gi|145267952|gb|EDK07948.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           PittAA]
 gi|145270165|gb|EDK10101.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           PittHH]
 gi|145274415|gb|EDK14279.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           22.4-21]
 gi|229810857|gb|EEP46574.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           7P49H1]
 gi|229812384|gb|EEP48074.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           6P18H1]
 gi|309973706|gb|ADO96907.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           R2846]
          Length = 328

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 150/333 (45%), Positives = 223/333 (66%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVILTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYS 178
             ++E++NPDHVIC+L D +A + M + V +G GYVPA  + H  E  PIG + +DA YS
Sbjct: 118 DGNVEIVNPDHVICHLTDENASISMRIRVQRGRGYVPASSRTHTQEERPIGRLLVDACYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +
Sbjct: 178 PVERIAYNVEAARVEQRTDLDKLVIELETNGALEPEEAIRRAATILAEQLDAFVDLRDVR 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +    +I  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 QP---EIKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 327


>gi|109897339|ref|YP_660594.1| DNA-directed RNA polymerase subunit alpha [Pseudoalteromonas
           atlantica T6c]
 gi|119366709|sp|Q15X48|RPOA_PSEA6 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|109699620|gb|ABG39540.1| DNA-directed RNA polymerase subunit alpha [Pseudoalteromonas
           atlantica T6c]
          Length = 329

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 150/333 (45%), Positives = 219/333 (65%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +  E +KP  +E   +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MSGSVTEFLKPRLVE---IDNVSPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G +   +T+ K G G V AGDIQ 
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDVIEILLNLKGLAVRLEGKTEATLTLVKSGAGPVLAGDIQH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYS 178
             D+E++NP HV+C L  +A + M + V  G GYVPA   R+   ++ PIG + +DA +S
Sbjct: 118 DGDVEIVNPSHVLCTLTGEAELSMRIKVEMGRGYVPASTRRSSEEDDRPIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ ++SY VESAR  Q  D DKL + ++T+G+I  E+++  ++ IL +QL  F+   +  
Sbjct: 178 PVSRISYNVESARVEQRTDLDKLIIDMETNGTIDPEEAIRRSATILAEQLDAFVELRDMS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V      +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 EPV---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIQYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPPESI E
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPESIAE 327


>gi|291457229|ref|ZP_06596619.1| DNA-directed RNA polymerase, alpha subunit [Bifidobacterium breve
           DSM 20213]
 gi|291381064|gb|EFE88582.1| DNA-directed RNA polymerase, alpha subunit [Bifidobacterium breve
           DSM 20213]
          Length = 331

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 121/312 (38%), Positives = 183/312 (58%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                   R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ GV
Sbjct: 10  TEESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTTLPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+I+LNIKGI L    D    + + K G G  TAGDI   + + + NP+  I  L 
Sbjct: 70  QEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPSGVTIANPEQHIATLA 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  + +E TV +G GYVPA+ ++ + D IG I +D++YSP+ KVSY VE+ R  Q  D+
Sbjct: 130 EDGELEIEFTVERGRGYVPAQMNKQDTDEIGRIPVDSIYSPVLKVSYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  +I+  D+VA A   L +  G+        + V+      +   NP +  
Sbjct: 190 DKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNAQAEGVEVGPAPVAEETNPEMAV 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L L+ RS NCL+ E +  +G+L+  TE D+L + NFG KS+ E+K  L T+GL L 
Sbjct: 250 PIEDLNLTQRSYNCLKREGVHTIGELVSHTEQDLLDIRNFGMKSIDEVKEKLQTLGLSLK 309

Query: 319 MNLPDWPPESIE 330
            +   +   ++E
Sbjct: 310 SSPMAFDTNNLE 321


>gi|322659535|gb|EFY55779.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 19N]
          Length = 329

 Score =  346 bits (888), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICRLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|330432099|gb|AEC17158.1| DNA-directed RNA polymerase subunit alpha [Gallibacterium anatis
           UMN179]
          Length = 327

 Score =  346 bits (888), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 146/332 (43%), Positives = 220/332 (66%), Gaps = 8/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVD---IEQISPTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVFLTLTKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHH-RTENDPIGLITIDALYSP 179
             D+E++NPDH+IC+L D +A + M + V +G GY+PA      E  PIG + +DA YSP
Sbjct: 118 DGDVEIVNPDHIICHLTDENASINMRIRVQRGRGYIPASSRTHDEERPIGRLLVDACYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           + +++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++
Sbjct: 178 VDRIAYNVEAARVEQRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRQ 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
               ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G
Sbjct: 238 P---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 KKSLTEIKDVLASRGLSLGMRLENWPPASIAE 326


>gi|329122808|ref|ZP_08251380.1| DNA-directed RNA polymerase subunit alpha [Haemophilus aegyptius
           ATCC 11116]
 gi|327472072|gb|EGF17510.1| DNA-directed RNA polymerase subunit alpha [Haemophilus aegyptius
           ATCC 11116]
          Length = 328

 Score =  346 bits (888), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 150/333 (45%), Positives = 222/333 (66%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS  GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKGGVQEDILEVLLNLKGLAVKVQNKDDVILTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYS 178
             ++E++NPDHVIC+L D +A + M + V +G GYVPA  + H  E  PIG + +DA YS
Sbjct: 118 DGNVEIVNPDHVICHLTDENASISMRIRVQRGRGYVPASSRTHTQEERPIGRLLVDACYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +
Sbjct: 178 PVERIAYNVEAARVEQRTDLDKLVIELETNGALEPEEAIRRAATILAEQLDAFVDLRDVR 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +    +I  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 QP---EIKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 327


>gi|302519632|ref|ZP_07271974.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. SPB78]
 gi|318058101|ref|ZP_07976824.1| DNA-directed RNA polymerase subunit alpha [Streptomyces sp.
           SA3_actG]
 gi|318076046|ref|ZP_07983378.1| DNA-directed RNA polymerase subunit alpha [Streptomyces sp.
           SA3_actF]
 gi|302428527|gb|EFL00343.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. SPB78]
          Length = 340

 Score =  346 bits (888), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 130/321 (40%), Positives = 195/321 (60%), Gaps = 4/321 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPGVVTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGVVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNAKGKLEMELTVERGRGYVSAVQNKQAGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNVDAEGIDMGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPPESIEE 331
             MGL L  + P + P S  +
Sbjct: 302 AGMGLALKDSPPGFDPTSAAD 322


>gi|218885213|ref|YP_002434534.1| DNA-directed RNA polymerase subunit alpha [Desulfovibrio vulgaris
           str. 'Miyazaki F']
 gi|226699353|sp|B8DNK9|RPOA_DESVM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|218756167|gb|ACL07066.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio vulgaris
           str. 'Miyazaki F']
          Length = 347

 Score =  346 bits (888), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 147/335 (43%), Positives = 211/335 (62%), Gaps = 1/335 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW EL+KP  I        +      + EPL RG+  T+GNALRRVL+SSL+GAA  +V
Sbjct: 13  RNWSELVKPEQITRDS-DPADAMYGKFVCEPLERGYGTTIGNALRRVLLSSLQGAAFVSV 71

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           ++ GV HE ++I GV ED+TDI+LN+K + L M  D  + + +     G V AGDI+T  
Sbjct: 72  KVSGVQHEFTTIPGVLEDVTDIVLNLKQVRLAMDTDEPQFLELSVNKKGAVKAGDIKTNQ 131

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            + VLNPD  I  L  D  +  E  V  G GYVPA  H   ++ IGLI +D+ ++P++KV
Sbjct: 132 HVMVLNPDLHIATLTEDLELTFEFEVRMGKGYVPADMHEGLSEEIGLIKLDSSFAPVRKV 191

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +YTVE AR GQ+ +YDKL + + TDGS+T ED++A +++I++DQ+ +FINF+E       
Sbjct: 192 AYTVEQARVGQMTNYDKLIIEVWTDGSVTPEDAIAYSAKIIKDQISVFINFDERISGESS 251

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             +  S   N  L K ++ELELSVR+TNCL+  NI  +G+L+Q++E +ML+  NFGRKSL
Sbjct: 252 GNSSGSSDVNENLFKGIDELELSVRATNCLKSANITLVGELVQKSENEMLKTKNFGRKSL 311

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
            EIK VL  M L  GM +  +  +  E   K+  +
Sbjct: 312 DEIKRVLCDMSLDFGMKVDGFEKKYQEWKRKQQNE 346


>gi|317153932|ref|YP_004121980.1| DNA-directed RNA polymerase subunit alpha [Desulfovibrio
           aespoeensis Aspo-2]
 gi|316944183|gb|ADU63234.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio
           aespoeensis Aspo-2]
          Length = 346

 Score =  346 bits (888), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 153/337 (45%), Positives = 224/337 (66%), Gaps = 3/337 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW EL+KP  +  +  G+        I EPL RG+A T+GNA+RRVL+SS++G AI A 
Sbjct: 13  RNWSELVKPEKL--MRDGKSNIRYGKFICEPLERGYATTIGNAMRRVLLSSMQGCAIVAA 70

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
            I+GV HE +++ GV ED+T+++LN+K + + M+ D  +R+ +     G V AG IQ   
Sbjct: 71  SIEGVQHEFTTLPGVLEDMTEVVLNLKQVRIAMTTDEPQRLVLEADKKGQVIAGMIQENQ 130

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           ++ +LN D +I  L  D  ++MEL V  G GYVPA  H    + IG + +DA YSP+KKV
Sbjct: 131 NVRILNTDQLIATLTEDRPLKMELEVRMGKGYVPADMHEGLTEEIGAVILDASYSPVKKV 190

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+VE AR GQ+ +YDKL + + TDGS+T ED+ A +++IL+DQL +FINF+E   E  E
Sbjct: 191 AYSVEQARVGQMTNYDKLILEVWTDGSVTPEDACAYSAKILKDQLSVFINFDELSSETME 250

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +++  S+  NP L K ++ELELSVR+TNCL+  NI  +G+L+QRTE  ML+  NFGRKSL
Sbjct: 251 EVD-SSIDLNPNLFKSIDELELSVRATNCLKAANIQLVGELVQRTEQAMLKTKNFGRKSL 309

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
            EI+ VL +M L  GM + D+  +  E L +K +++ 
Sbjct: 310 DEIRRVLDSMSLKFGMGVEDFDKKYQEWLKRKEKNEA 346


>gi|89893245|ref|YP_516732.1| DNA-directed RNA polymerase subunit alpha [Desulfitobacterium
           hafniense Y51]
 gi|219666518|ref|YP_002456953.1| DNA-directed RNA polymerase subunit alpha [Desulfitobacterium
           hafniense DCB-2]
 gi|119366679|sp|Q250K4|RPOA_DESHY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|254765251|sp|B8G1Z4|RPOA_DESHD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|89332693|dbj|BAE82288.1| hypothetical protein [Desulfitobacterium hafniense Y51]
 gi|219536778|gb|ACL18517.1| DNA-directed RNA polymerase, alpha subunit [Desulfitobacterium
           hafniense DCB-2]
          Length = 315

 Score =  346 bits (888), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 137/310 (44%), Positives = 201/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE  V   ++ +    + EPL RG+  TLGN+LRR+L+SSL G A+T+V+I+G
Sbjct: 3   EIEKP-KIE-CVERTDDNSYAKFVVEPLERGYGITLGNSLRRILLSSLPGTAVTSVKIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+TDIILN+K + LK   D  K + +   G GV+ AGDI T  DIE+
Sbjct: 61  VLHEFSTVPGVLEDVTDIILNLKSLALKGHTDEPKVLRLEAEGEGVIKAGDIITDADIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  LD D  + ME+T  +G GYV A  ++  +  IG+I ID++++PI KV+YTV
Sbjct: 121 LNPDLKIATLDKDGRLFMEMTAERGRGYVSADKNKKPDQAIGIIPIDSIFAPIYKVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R G V DYDKL++ + ++GSIT E++ +LA++IL + L +FI   +    V+  +  
Sbjct: 181 EDTRVGMVTDYDKLTLEVWSNGSITPEEATSLAAKILSEHLRLFIGLTDKLNNVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    +  L   +E+L+LSVRS NCL+   I  + +L Q+TE DM+++ N GRKSL E++
Sbjct: 241 EEEAKDKILEMTIEDLDLSVRSYNCLKRAGINSVEELTQKTEEDMIKVRNLGRKSLEEVE 300

Query: 308 GVLGTMGLFL 317
             L  +GL  
Sbjct: 301 SKLKELGLGF 310


>gi|317125840|ref|YP_004099952.1| DNA-directed RNA polymerase subunit alpha [Intrasporangium calvum
           DSM 43043]
 gi|315589928|gb|ADU49225.1| DNA-directed RNA polymerase subunit alpha [Intrasporangium calvum
           DSM 43043]
          Length = 341

 Score =  346 bits (888), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 128/323 (39%), Positives = 196/323 (60%), Gaps = 3/323 (0%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            +      +NR+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ 
Sbjct: 8   VLSEEVVADNRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVP 67

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+T++ILNIKG+ +    D    + + K+GPGVVTAGDI     +EV NPD  I  
Sbjct: 68  GVKEDVTEMILNIKGLVVSSEHDEPVVMYLRKQGPGVVTAGDITPPAGVEVHNPDLAIAT 127

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           L+    + MELTV +G GYV A+ +++ +  IG I +D++YSP+  V+Y VE+ R  Q  
Sbjct: 128 LNDKGKLEMELTVERGRGYVSAQQNKSGDQEIGRIPVDSIYSPVLAVTYKVEATRVEQRT 187

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           D+DKL + ++T  S+T  D++A + + L +  G+        + +    +         L
Sbjct: 188 DFDKLIVDVETKNSMTPRDAMASSGKTLVELFGLARELNVEAEGIDMGPSPTDAALAADL 247

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  MGL 
Sbjct: 248 ALPIEDLDLTVRSYNCLKREGIHTVGELVGRSEADLLDIRNFGAKSIDEVKAKLVGMGLA 307

Query: 317 LGMNLPDWPPESIEELAKKYEDK 339
           L  + P + P +   L   Y D+
Sbjct: 308 LKDSPPGFDPSA---LVDNYGDE 327


>gi|213964907|ref|ZP_03393106.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           amycolatum SK46]
 gi|213952443|gb|EEB63826.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           amycolatum SK46]
          Length = 341

 Score =  346 bits (888), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 126/322 (39%), Positives = 191/322 (59%), Gaps = 2/322 (0%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                + +R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV
Sbjct: 10  TEDYIDSSRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTIPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED++DIILNIKG+ L    D    V + + G G VTA DI+    +E+ NPDH I  L+
Sbjct: 70  KEDVSDIILNIKGLVLSSEFDEPATVYLRREGAGAVTAADIECPAGVEIHNPDHHIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +E+ V +G GYVPA  +      IG I +D +YSP+ KVSY VE+ R  Q  D+
Sbjct: 130 ESGRLEIEMIVERGRGYVPATPNSGGE--IGRIPMDQIYSPVLKVSYKVEATRVEQRTDF 187

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  SIT  D++A A + L +  G+     E  + ++   + +      A   
Sbjct: 188 DKLIIDVETKNSITARDAMASAGKTLVELFGLARELNEAAEGIEIGPSPREAEDVAAYQT 247

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L+ S+RS NCL+ E I  +G+L  RTE+D+L + NFG KS+ E+K  L  +GL L 
Sbjct: 248 PIEDLDFSMRSYNCLKREEIHTVGELAARTESDLLDIRNFGDKSINEVKEKLAELGLALK 307

Query: 319 MNLPDWPPESIEELAKKYEDKC 340
            +  ++ P ++ +L     D  
Sbjct: 308 DSPNNFDPAAVADLDAASGDDA 329


>gi|187930338|ref|YP_001900825.1| DNA-directed RNA polymerase subunit alpha [Ralstonia pickettii 12J]
 gi|241664506|ref|YP_002982866.1| DNA-directed RNA polymerase subunit alpha [Ralstonia pickettii 12D]
 gi|309782860|ref|ZP_07677580.1| DNA-directed RNA polymerase, alpha subunit [Ralstonia sp.
           5_7_47FAA]
 gi|238691836|sp|B2UEJ3|RPOA_RALPJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|187727228|gb|ACD28393.1| DNA-directed RNA polymerase, alpha subunit [Ralstonia pickettii
           12J]
 gi|240866533|gb|ACS64194.1| DNA-directed RNA polymerase, alpha subunit [Ralstonia pickettii
           12D]
 gi|308918284|gb|EFP63961.1| DNA-directed RNA polymerase, alpha subunit [Ralstonia sp.
           5_7_47FAA]
          Length = 326

 Score =  346 bits (888), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 149/326 (45%), Positives = 210/326 (64%), Gaps = 7/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG        ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVEPLGDH---HAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S+I GV ED+ +++LN+KG+  K+       V++ K G GVVTA DI+  +D+E++
Sbjct: 62  VHEYSTIDGVQEDVVNLLLNLKGVVFKLHNRDEVTVSLRKEGEGVVTAADIELPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSY 185
           NP HVI NL     + ++L V +G GYVP    +  ++     G I +DA ++P+++VSY
Sbjct: 122 NPGHVIANLSAGGKLDLQLKVEQGRGYVPGNVRKFGDESSKVIGRIVLDASFAPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL DQL +F   E   +   E  
Sbjct: 182 AVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALEG-TESAAEAA 240

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 241 AARAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 300

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +E+
Sbjct: 301 IKEVLASRGLTLGMKLENWPPAGLEK 326


>gi|319944770|ref|ZP_08019034.1| DNA-directed RNA polymerase subunit alpha [Lautropia mirabilis ATCC
           51599]
 gi|319742019|gb|EFV94442.1| DNA-directed RNA polymerase subunit alpha [Lautropia mirabilis ATCC
           51599]
          Length = 359

 Score =  346 bits (888), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 146/354 (41%), Positives = 207/354 (58%), Gaps = 34/354 (9%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           ++KP  +E   +         ++ EP  RG+ HTLGNALRRVL+SS+ G A T VQI GV
Sbjct: 5   MLKPRLVEVQEISGPSH--ARVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVQIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S++ G+ ED+ D++LN+KG+  K+ G S   +T+ K  PG V A DI+  +D+E++
Sbjct: 63  VHEYSTVDGLREDVVDLLLNLKGVVFKLRGRSEVFLTLRKEVPGPVKASDIELPHDVEII 122

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI-GLITIDALYSPIKKVSYTV 187
           NPDHVI  L     + M++ V +G GYVP       +    G I +DA +SP+++VSY V
Sbjct: 123 NPDHVIATLTEGGKLDMQIKVEQGRGYVPGNMRNLGDSKTIGRIVLDASFSPVRRVSYAV 182

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ESAR  Q  D D+L + I+T+G+I  E++V  ++ IL DQL +F + E     V    + 
Sbjct: 183 ESARVEQRTDLDRLLIDIETNGAIAPEEAVRKSAAILVDQLQVFASIEGNDPAVPIGGSQ 242

Query: 248 KSL-------------------------------PFNPALLKKVEELELSVRSTNCLRGE 276
             +                                 +P LL+ V++LEL+VRS NCL+ E
Sbjct: 243 TPMGATIGGHVSSVPSGVEGLGAGGAAGFGASTGTIDPILLRPVDDLELTVRSANCLKAE 302

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           NI Y+GDLIQRTE ++L+  N GRKSL EIK VL + GL LGM L DWPP  +E
Sbjct: 303 NIYYIGDLIQRTENELLKTPNLGRKSLNEIKEVLASRGLTLGMRLDDWPPAGLE 356


>gi|145630549|ref|ZP_01786329.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           R3021]
 gi|144983939|gb|EDJ91381.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           R3021]
          Length = 328

 Score =  346 bits (887), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 151/333 (45%), Positives = 222/333 (66%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVILTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYS 178
             D+E++NPDHVIC+L D +A + M + V +G GYVPA  + H  E  PIG + +DA YS
Sbjct: 118 DGDVEIVNPDHVICHLTDENASISMRIRVQRGRGYVPASSRTHTQEERPIGRLLVDACYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  D DKL + ++T+G +  E+++  A+ IL +QL  F++  + +
Sbjct: 178 PVERIAYNVEAARVEQRTDLDKLVIELETNGELEPEEAIRRAATILAEQLDAFVDLRDVR 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +    +I  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 QP---EIKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 327


>gi|319775263|ref|YP_004137751.1| RNA polymerase subunit alpha [Haemophilus influenzae F3047]
 gi|319897703|ref|YP_004135900.1| RNA polymerase, alpha subunit [Haemophilus influenzae F3031]
 gi|317433209|emb|CBY81584.1| RNA polymerase, alpha subunit [Haemophilus influenzae F3031]
 gi|317449854|emb|CBY86065.1| RNA polymerase, alpha subunit [Haemophilus influenzae F3047]
          Length = 328

 Score =  346 bits (887), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 150/333 (45%), Positives = 222/333 (66%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVILTLNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYS 178
             ++E++NPDHVIC+L D +A + M + V +G GYVPA  + H  E  PIG + +DA YS
Sbjct: 118 DGNVEIVNPDHVICHLTDENASISMRIRVQRGRGYVPASSRTHTQEERPIGRLLVDACYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL  QL  F++  + +
Sbjct: 178 PVERIAYNVEAARVEQRTDLDKLVIELETNGALEPEEAIRRAATILAGQLDAFVDLRDVR 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +    +I  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 QP---EIKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 327


>gi|260102381|ref|ZP_05752618.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus helveticus
           DSM 20075]
 gi|260083825|gb|EEW67945.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus helveticus
           DSM 20075]
 gi|328463390|gb|EGF35063.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus helveticus
           MTCC 5463]
          Length = 312

 Score =  346 bits (887), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 134/310 (43%), Positives = 194/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDG
Sbjct: 3   EFEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++V
Sbjct: 59  VLHEFSTVPGVREDVTKIILNLKKLELKSLSDERKVIELDVEGPATVTADDLKVDADVQV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + ME+ V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMEIAVQNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   K  +  +  
Sbjct: 179 ESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFATKILVEHFKVFESADADTKFSEVMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L   TE+DM+R+ N GRKSL E+K
Sbjct: 239 EDDKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELTDMTESDMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLTDLGLSL 308


>gi|119366682|sp|Q2GH33|RPOA_EHRCR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 372

 Score =  346 bits (887), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 171/342 (50%), Positives = 239/342 (69%), Gaps = 5/342 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +W +L KP++I+ +  G    N+  +I EPL  GFA TLGNALRRV+MSSLRG A+ 
Sbjct: 32  MSDHWSKLTKPSSIKVVPSG-ASPNKADLIIEPLESGFALTLGNALRRVMMSSLRGFAVY 90

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+ VLHE +SI GV ED+TDI+LNI  + +K+SG + K +++  +GP  V +G I  
Sbjct: 91  GVEIENVLHEFTSISGVREDVTDILLNISMMRVKLSGMNSKVLSLKVKGPCEVRSGMIPD 150

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH----HRTENDPIGLITIDALY 177
            +D  +LN D +IC LD      +++ V+ G GYVPA      ++  + PI  I  +ALY
Sbjct: 151 TDDCIILNKDLLICTLDQGVDFNIKMYVNAGKGYVPAVKRKSVNKLGDIPINFIATNALY 210

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPIKK S+ VES+R GQ  DYD+L M+++TDGSI  +++VALA+RILQDQ   FINF+E 
Sbjct: 211 SPIKKASFKVESSRIGQFTDYDRLIMSVETDGSILPDEAVALAARILQDQFQPFINFDET 270

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +  K+     +LP++  LL+KV+ELELSVRS NCL+ +NI Y+GDL+Q+TE+DMLR  N
Sbjct: 271 DEPHKKVDAKDTLPYDSNLLRKVDELELSVRSYNCLKNDNITYIGDLVQKTESDMLRTPN 330

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           FGRKSL EI  +L +M L LGM + +WPPESIE L+K+Y ++
Sbjct: 331 FGRKSLNEINELLASMNLHLGMKIANWPPESIESLSKQYSEE 372


>gi|152978166|ref|YP_001343795.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           succinogenes 130Z]
 gi|171704199|sp|A6VLL3|RPOA_ACTSZ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|150839889|gb|ABR73860.1| DNA-directed RNA polymerase, alpha subunit [Actinobacillus
           succinogenes 130Z]
          Length = 329

 Score =  346 bits (887), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 224/334 (67%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V AGDI  
Sbjct: 58  EVEIEGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVFLTLNKSGIGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++NP+HVIC+L D +A + M + V +G GYVPA    H + E  PIG + +DA Y
Sbjct: 118 DGDVEIVNPEHVICHLTDENASISMRIRVQRGRGYVPASARAHSQDEERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLVIELETNGTLDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLDNWPPASIAE 328


>gi|308048016|ref|YP_003911582.1| DNA-directed RNA polymerase subunit alpha [Ferrimonas balearica DSM
           9799]
 gi|307630206|gb|ADN74508.1| DNA-directed RNA polymerase subunit alpha [Ferrimonas balearica DSM
           9799]
          Length = 330

 Score =  346 bits (887), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 145/334 (43%), Positives = 215/334 (64%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IDQVSPYRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDVLEILLNLKGLAVKLEGKDEAILTLSKSGAGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALY 177
             D+E++NP+H+IC L   DA + M + V  G GY+PA        +  PIG + +DA +
Sbjct: 118 DGDVEIVNPEHLICTLTGADAEISMRIKVELGRGYIPASARAQVEEDERPIGRLLVDASF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + + TDG++  E+++  ++ IL +QL  F++  + 
Sbjct: 178 SPVVRIAYNVEAARVEQRTDLDKLIIDMHTDGTLDPEEAIRRSATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +        +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 SEPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 328


>gi|294790438|ref|ZP_06755596.1| DNA-directed RNA polymerase, alpha subunit [Scardovia inopinata
           F0304]
 gi|294458335|gb|EFG26688.1| DNA-directed RNA polymerase, alpha subunit [Scardovia inopinata
           F0304]
          Length = 331

 Score =  346 bits (887), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 122/302 (40%), Positives = 181/302 (59%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
              Q    R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ GV
Sbjct: 10  TEEQVTPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTTLPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+I+LNIK + L    D    + + K G G  TA DI     + + NPD  I  L 
Sbjct: 70  KEDVTEILLNIKELVLTSEYDEPVVMYLRKSGEGEATAADITPPAGVVIANPDLHIATLA 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  + +E TV +G GYVPA+ ++ E D IG I +D++YSP+ KVSY VE+ R  Q  D+
Sbjct: 130 EDGELEIEFTVERGRGYVPAQMNKQEGDEIGRIPVDSIYSPVVKVSYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  +IT  D+VA A   L +  G+F       + V+      +   +P +  
Sbjct: 190 DKLIVDVETKPAITPRDAVASAGSTLVELFGLFHELNNQAEGVEVGPAPVTEEVDPQMEI 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L L+ RS NCL+ E I  +G+L++R+E D+L + NFG+KS+ E+K  L +MGL L 
Sbjct: 250 PIEDLNLTQRSYNCLKREGIHTIGELVKRSEQDLLDIRNFGQKSIDEVKDKLASMGLSLK 309

Query: 319 MN 320
            +
Sbjct: 310 QS 311


>gi|307731229|ref|YP_003908453.1| DNA-directed RNA polymerase subunit alpha [Burkholderia sp.
           CCGE1003]
 gi|307585764|gb|ADN59162.1| DNA-directed RNA polymerase, alpha subunit [Burkholderia sp.
           CCGE1003]
          Length = 325

 Score =  346 bits (887), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 153/328 (46%), Positives = 213/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP  I    LG   E+   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPKIIAVESLG---ESHAKVVMEPFERGYGHTLGNALRRVLLSSMIGYAPTEVTIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S++ GV ED+ +++LN+KG+  K+       VT+ K G GVVTAG+I+  +D E
Sbjct: 60  GVVHEYSTLDGVQEDVVNLLLNLKGVVFKLHNRDEVTVTLRKEGEGVVTAGEIELAHDCE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP---IGLITIDALYSPIKKV 183
           V+NPDHVI +L     + +++ V KG GYVP    R   +    IG I +DA +SP+++V
Sbjct: 120 VINPDHVIAHLSKGGKLDVQIKVEKGRGYVPGNVRRYGEESAKIIGRIVLDASFSPVRRV 179

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL DQL +F   E    E   
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALE--GTEATA 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 238 EAPSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>gi|212716586|ref|ZP_03324714.1| hypothetical protein BIFCAT_01515 [Bifidobacterium catenulatum DSM
           16992]
 gi|225351019|ref|ZP_03742042.1| hypothetical protein BIFPSEUDO_02601 [Bifidobacterium
           pseudocatenulatum DSM 20438]
 gi|212660290|gb|EEB20865.1| hypothetical protein BIFCAT_01515 [Bifidobacterium catenulatum DSM
           16992]
 gi|225158475|gb|EEG71717.1| hypothetical protein BIFPSEUDO_02601 [Bifidobacterium
           pseudocatenulatum DSM 20438]
          Length = 332

 Score =  346 bits (887), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 123/313 (39%), Positives = 184/313 (58%), Gaps = 1/313 (0%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                   R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I GV HE +++ GV
Sbjct: 10  TEESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGVPHEFTTLPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+I+LNIKGI L    D    + + K G G  TAGDI     + + NPD  I  L 
Sbjct: 70  EEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGVTIANPDMHIATLA 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  + +E TV +G GYVPA+ ++ +N  IG I +D++YSP+ KVSY VE+ R  Q  D+
Sbjct: 130 EDGELEIEFTVERGRGYVPAQMNKQDNAEIGRIPVDSIYSPVLKVSYRVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  +I+  D+VA A   L +  G+        + V+      +   NP +  
Sbjct: 190 DKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNTQAEGVEVGPAPVAEETNPEMAV 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L ++GL L 
Sbjct: 250 PIEDLNLTQRSYNCLKREGIHTIGELVAHTEQDLLDIRNFGMKSIDEVKEKLQSLGLALK 309

Query: 319 MN-LPDWPPESIE 330
            + L ++   ++E
Sbjct: 310 ASPLGNFDTNNLE 322


>gi|261854974|ref|YP_003262257.1| DNA-directed RNA polymerase, subunit alpha [Halothiobacillus
           neapolitanus c2]
 gi|261835443|gb|ACX95210.1| DNA-directed RNA polymerase, alpha subunit [Halothiobacillus
           neapolitanus c2]
          Length = 331

 Score =  346 bits (887), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 149/335 (44%), Positives = 222/335 (66%), Gaps = 7/335 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    EL+KP  ++  VL   +  R  ++ EPL RGF +TLGNALRR+L+SS+ G A+T
Sbjct: 1   MQLGSTELLKPRLVDVQVL---DATRARVVLEPLERGFGYTLGNALRRILLSSIPGVAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +I+GV+HE ++I+GVHED+ +I+LN+KG+++ + G     ++I K G G +TA DI+ 
Sbjct: 58  EAEIEGVVHEYTTIEGVHEDVLEILLNLKGLSVMLHGRDEAMLSIKKTGAGAITAADIKA 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSPI 180
            + +E++NP+H I  L+    + M   V++G GYVPA   R E    IG + +DA +SP+
Sbjct: 118 DHAVEIINPEHHIATLNDQGSLVMTFKVTRGKGYVPASARREEAGGQIGRLLVDASFSPL 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY+VE AR  Q  D D L + I+T+GSI+ ED++  A+ IL DQL +F++    K E
Sbjct: 178 RRVSYSVERARVEQRTDLDSLVLDIETNGSISAEDAIRQAAGILVDQLSVFVDL---KAE 234

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E +  ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G+
Sbjct: 235 KVEPVVEQAPAVDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEIELLKTPNLGK 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
           KSL EIK VL   GL LG  L +WPP  +  LA+ 
Sbjct: 295 KSLTEIKDVLAKQGLSLGQRLENWPPAELLNLAES 329


>gi|51245004|ref|YP_064888.1| DNA-directed RNA polymerase subunit alpha [Desulfotalea
           psychrophila LSv54]
 gi|61215903|sp|Q6AP43|RPOA_DESPS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|50876041|emb|CAG35881.1| probable DNA-directed RNA polymerase, alpha subunit [Desulfotalea
           psychrophila LSv54]
          Length = 343

 Score =  346 bits (887), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 156/328 (47%), Positives = 224/328 (68%), Gaps = 2/328 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +NW ELI+P  +E        E     I +PL RGFA T+GN+LRR+L+SS++GAAIT
Sbjct: 11  VYRNWHELIRPEKVEIDQ-SNHSETYGKFICQPLERGFATTIGNSLRRILLSSIQGAAIT 69

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+G LHE++S+K V ED+++IILN+K + LK++ +  + V I K+GPG V AGDI  
Sbjct: 70  TVKIEGALHELTSMKDVKEDVSEIILNLKQVRLKLNCEESQTVRIEKQGPGPVVAGDIIP 129

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              +E++N DH++CNL  D     ELTV  G GY PA++   ++  +G I IDA+++P+K
Sbjct: 130 SAFVEIMNEDHILCNLTSDMTFCAELTVEWGKGYQPAENQEKDDLTVGQIPIDAIFTPVK 189

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           K+ Y V SAR GQ  DYDKL+  I+TDGS+  ED++A +++IL++QL +FINF+E   E 
Sbjct: 190 KIQYVVSSARVGQQTDYDKLTYEIETDGSVRPEDALAYSAKILKEQLDIFINFDETAVEP 249

Query: 242 K-EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           + + +  +    NP L K VE+LELSVRS NCL+  +I ++GDL+QRT+ +ML+  NFGR
Sbjct: 250 EKKAVETEEKQENPYLDKPVEDLELSVRSANCLKNADINFIGDLVQRTDQEMLKTKNFGR 309

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPES 328
           KSL EIK +L  M L LG+ L  W   S
Sbjct: 310 KSLNEIKTLLQDMDLTLGVKLEGWNAPS 337


>gi|332175074|gb|AEE24328.1| DNA-directed RNA polymerase, alpha subunit [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 329

 Score =  346 bits (887), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 151/333 (45%), Positives = 219/333 (65%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +  E +KP  +E   +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MSGSVTEFLKPRLVE---IDNVSPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G +   +T+ K G G V AGDIQ 
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDVIEILLNLKGLAVRLEGKTEATLTLVKSGAGPVLAGDIQH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYS 178
             D+E++NP HV+C L  +A + M + V  G GYVPA   R+   ++ PIG + +DA +S
Sbjct: 118 DGDVEIVNPSHVLCTLTGEAELSMRIKVEMGRGYVPASTRRSSEEDDRPIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI ++SY VESAR  Q  D DKL + ++T+G+I  E+++  ++ IL +QL  F+   +  
Sbjct: 178 PISRISYNVESARVEQRTDLDKLIIDMETNGTIDPEEAIRRSATILAEQLDAFVELRDMS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + V      +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 EPV---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIQYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPPESI E
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPESIAE 327


>gi|256847789|ref|ZP_05553234.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus
           coleohominis 101-4-CHN]
 gi|256715478|gb|EEU30454.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus
           coleohominis 101-4-CHN]
          Length = 313

 Score =  346 bits (887), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 136/311 (43%), Positives = 205/311 (65%), Gaps = 5/311 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E +N    + EPL RG+  TLGN+LRRV+++SL GAAIT++ IDG
Sbjct: 3   EFEKPN----IHKVEETDNYGKFVVEPLERGYGTTLGNSLRRVMLASLPGAAITSINIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K ++L++  +  K + +  +GP  VTAGDIQ   D+ V
Sbjct: 59  VLHEFSTVEGVTEDVTQIILNLKKVSLRIDSEDQKNLELDVKGPAEVTAGDIQGDGDVTV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSPIKKVSYT 186
           LNPD  I  +   A + +++T  KGHGY  A  ++T  +  IG++ ID++Y+PI++V+YT
Sbjct: 119 LNPDLHIATVADGAELHIQMTADKGHGYSSADDNKTRMDLAIGVLPIDSIYTPIERVNYT 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+ R GQ  DYDKL++ + T+GS+T  ++V+LA++IL   L MF+N  E  +  +  + 
Sbjct: 179 VENTRVGQNNDYDKLTLDVWTNGSLTPTEAVSLAAKILTSHLAMFVNLTEEAQSAQVMVE 238

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L K +EE +LSVRS NCL+  +I  + DL ++TEADM+++ N G+KSL EI
Sbjct: 239 REESHQEKVLDKTIEEFDLSVRSYNCLKRADIQTVKDLTEKTEADMMKVRNLGQKSLDEI 298

Query: 307 KGVLGTMGLFL 317
           K  L  +G+  
Sbjct: 299 KIKLNELGVGF 309


>gi|312870507|ref|ZP_07730626.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus oris
           PB013-T2-3]
 gi|311093969|gb|EFQ52294.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus oris
           PB013-T2-3]
          Length = 314

 Score =  346 bits (887), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 136/315 (43%), Positives = 206/315 (65%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E +N    + EPL RG+  TLGN+LRRVL++SL G+AIT +QIDG
Sbjct: 3   EFEKPN----IHKVEETDNYGKFVVEPLERGYGTTLGNSLRRVLIASLPGSAITTMQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++KGV ED+T IILN+K ++LK++ +  K + +  +GP  VTAGDIQ  +++ V
Sbjct: 59  VLHEFSTVKGVTEDVTQIILNLKKVSLKINSEDQKDLELDVKGPAKVTAGDIQGDSEVSV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
           LNPD  I  +   A + +++T  KG GY+ A  ++   E+  IG++ ID++Y+PI++V+Y
Sbjct: 119 LNPDLHIATVADGAELHIKMTADKGRGYLSANDNKARMEDLAIGVLPIDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVE+AR GQ  D+DKL++ + TDGSIT  ++V+L ++IL + L MF+N  E  +  +  +
Sbjct: 179 TVENARVGQRSDFDKLTLDVWTDGSITPTEAVSLGAKILTEHLAMFVNLTETAQNAQVMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   +EEL+LSVRS NCL+   I  + +L  RT +DM+++ N G+KSL E
Sbjct: 239 EKEETHKEKTLEMTIEELDLSVRSYNCLKRAGINTVKELTDRTVSDMMKVRNLGQKSLEE 298

Query: 306 IKGVLGTMGLFLGMN 320
           IK  L  +G+    +
Sbjct: 299 IKLKLNDLGVSFRQD 313


>gi|171741248|ref|ZP_02917055.1| hypothetical protein BIFDEN_00323 [Bifidobacterium dentium ATCC
           27678]
 gi|283455392|ref|YP_003359956.1| polA DNA-directed RNA polymerase subunit alpha [Bifidobacterium
           dentium Bd1]
 gi|306823542|ref|ZP_07456917.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium dentium
           ATCC 27679]
 gi|309802902|ref|ZP_07697003.1| DNA-directed RNA polymerase, alpha subunit [Bifidobacterium dentium
           JCVIHMP022]
 gi|171276862|gb|EDT44523.1| hypothetical protein BIFDEN_00323 [Bifidobacterium dentium ATCC
           27678]
 gi|283102026|gb|ADB09132.1| polA DNA-directed RNA polymerase alpha chain [Bifidobacterium
           dentium Bd1]
 gi|304553249|gb|EFM41161.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium dentium
           ATCC 27679]
 gi|308220369|gb|EFO76680.1| DNA-directed RNA polymerase, alpha subunit [Bifidobacterium dentium
           JCVIHMP022]
          Length = 331

 Score =  346 bits (887), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 122/312 (39%), Positives = 182/312 (58%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                   R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I GV HE +++ GV
Sbjct: 10  TEESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGVPHEFTTLPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+I+LNIKGI L    D    + + K G G  TAGDI     + + NPD  I +L 
Sbjct: 70  EEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGVTIANPDMHIASLA 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  + +E TV +G GYVPA+ ++ +N  IG I +D++YSP+ KVSY VE+ R  Q  D+
Sbjct: 130 DDGELEIEFTVERGRGYVPAQMNKQDNAEIGRIPVDSIYSPVLKVSYRVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  +I+  D+VA A   L +  G+        + V+      +   NP +  
Sbjct: 190 DKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNTQAEGVEVGPAPVAEETNPEMAV 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L  +GL L 
Sbjct: 250 PIEDLNLTQRSYNCLKREGIHTIGELVAHTEQDLLDIRNFGMKSIDEVKEKLQALGLALK 309

Query: 319 MNLPDWPPESIE 330
            +   +   ++E
Sbjct: 310 ASPLGFDANNLE 321


>gi|83748175|ref|ZP_00945202.1| DNA-directed RNA polymerase alpha chain [Ralstonia solanacearum
           UW551]
 gi|300702806|ref|YP_003744407.1| RNA polymerase subunit alpha; RNA polymerase alpha chain family
           [Ralstonia solanacearum CFBP2957]
 gi|83725143|gb|EAP72294.1| DNA-directed RNA polymerase alpha chain [Ralstonia solanacearum
           UW551]
 gi|299070468|emb|CBJ41763.1| RNA polymerase, alpha subunit; RNA polymerase alpha chain family
           [Ralstonia solanacearum CFBP2957]
          Length = 326

 Score =  346 bits (887), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 147/326 (45%), Positives = 210/326 (64%), Gaps = 7/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG        ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVEPLGDH---HAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S+I GV ED+ +++LN+KG+  K+       V++ K G GVVTA DI+  +D+E++
Sbjct: 62  VHEYSTIDGVQEDVVNLLLNLKGVVFKLHNRDEVTVSLRKEGEGVVTAADIELPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSY 185
           NP HVI +L     + M++ V +G GYVP    +  ++     G + +DA ++P+++VSY
Sbjct: 122 NPGHVIASLSAGGKLDMQIKVEQGRGYVPGNVRKFGDESSKVIGRVVLDASFAPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL DQL +F   E   +   E  
Sbjct: 182 AVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALEG-TESAAEAA 240

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 241 AARAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 300

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +E+
Sbjct: 301 IKEVLASRGLTLGMKLENWPPAGLEK 326


>gi|317494317|ref|ZP_07952731.1| DNA-directed RNA polymerase [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316917567|gb|EFV38912.1| DNA-directed RNA polymerase [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 329

 Score =  346 bits (887), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 148/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   L         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQLSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + + +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKIQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+S+  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEESIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|113460233|ref|YP_718291.1| DNA-directed RNA polymerase subunit alpha [Haemophilus somnus
           129PT]
 gi|170718274|ref|YP_001785292.1| DNA-directed RNA polymerase subunit alpha [Haemophilus somnus 2336]
 gi|119366686|sp|Q0I137|RPOA_HAES1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|112822276|gb|ABI24365.1| DNA-directed RNA polymerase subunit alpha [Haemophilus somnus
           129PT]
 gi|168826403|gb|ACA31774.1| DNA-directed RNA polymerase, alpha subunit [Haemophilus somnus
           2336]
          Length = 329

 Score =  346 bits (887), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 150/334 (44%), Positives = 222/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGYAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+    +  +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDIIEVLLNLKGLAVKVQNKDNVFLTLSKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++NPDHVIC+L D +A + M + V +G GYVPA    H   E  PIG + +DA Y
Sbjct: 118 DGDVEIVNPDHVICHLTDENASINMRIRVQRGRGYVPASSRVHSLDEERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y V++AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVQAARVEQRTDLDKLVIELETNGTIEPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLVSRGLSLGMRLENWPPASIAE 328


>gi|85060231|ref|YP_455933.1| DNA-directed RNA polymerase subunit alpha [Sodalis glossinidius
           str. 'morsitans']
 gi|119366730|sp|Q2NQP7|RPOA_SODGM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|84780751|dbj|BAE75528.1| RNA polymerase alpha chain [Sodalis glossinidius str. 'morsitans']
          Length = 329

 Score =  345 bits (886), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVQGKDDVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HV+C+L D +A + M + V +G GYVPA    H      PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVLCHLTDENAAISMRIKVQRGRGYVPASARIHSEEYERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|116617354|ref|YP_817725.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Leuconostoc mesenteroides subsp. mesenteroides ATCC
           8293]
 gi|122272445|sp|Q03ZM0|RPOA_LEUMM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116096201|gb|ABJ61352.1| DNA-directed RNA polymerase subunit alpha [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
          Length = 314

 Score =  345 bits (886), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 129/312 (41%), Positives = 191/312 (61%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E+      + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDG
Sbjct: 3   EFEKPN----IHNIEEDARYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE S++ GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+Q   D+EV
Sbjct: 59  VVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDIQGPADVTAADLQGGADVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
           LNPD  I  +     + M +T  KG GY  A  ++   +  PIG++ +D++Y+PI++V+Y
Sbjct: 119 LNPDLHIATVAAGKSLHMTVTAVKGRGYTSADENKKLRDEMPIGVLAVDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R G   DYDKL+  I T+GSI   D+++L ++IL + LG+F++      E    +
Sbjct: 179 QVENTRIGARDDYDKLTFDIWTNGSIKPSDALSLGAKILAEHLGLFMDISPVAAEASVMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             + +  + +    +E+L+LSVRS NCL+   I  + +L  RTEADM+++ N GRKSL E
Sbjct: 239 EAEPVAASASDSAPIEDLDLSVRSYNCLKRAGINTIVELTDRTEADMMKVRNLGRKSLDE 298

Query: 306 IKGVLGTMGLFL 317
           I+  L  M L  
Sbjct: 299 IQEKLTDMNLGF 310


>gi|296111454|ref|YP_003621836.1| DNA-directed RNA polymerase alpha subunit [Leuconostoc kimchii
           IMSNU 11154]
 gi|295832986|gb|ADG40867.1| DNA-directed RNA polymerase alpha subunit [Leuconostoc kimchii
           IMSNU 11154]
          Length = 314

 Score =  345 bits (886), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 128/312 (41%), Positives = 192/312 (61%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E++     + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDG
Sbjct: 3   EFEKPN----IHNIEEDDRYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE S++ GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+Q   D+E+
Sbjct: 59  VVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDVQGPADVTAADLQAGADVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
           LNPD  +  +     + M +T  KG GY  A  ++   +  PIG++ +D++Y+PI++V+Y
Sbjct: 119 LNPDLHLATVAAGKSLHMTVTAVKGRGYSSADENKQLRDEMPIGVLAVDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R G   DYDKL+  I T+GSI   D+++L S+IL + L +F++      E    +
Sbjct: 179 HVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSLGSKILAEHLNLFMDISPVAAEASVMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             + +  N +    +E+L+LSVRS NCL+   I  + +L  RTEADM+++ N GRKSL E
Sbjct: 239 EAEPVATNASDSAPIEDLDLSVRSYNCLKRAGINTIVELTDRTEADMMKVRNLGRKSLDE 298

Query: 306 IKGVLGTMGLFL 317
           I+  L  MG+  
Sbjct: 299 IQEKLTEMGIGF 310


>gi|238921419|ref|YP_002934934.1| DNA-directed RNA polymerase subunit alpha [Edwardsiella ictaluri
           93-146]
 gi|269140549|ref|YP_003297250.1| DNA-directed RNA polymerase subunit alpha [Edwardsiella tarda
           EIB202]
 gi|294638029|ref|ZP_06716289.1| DNA-directed RNA polymerase, alpha subunit [Edwardsiella tarda ATCC
           23685]
 gi|238870988|gb|ACR70699.1| DNA-directed RNA polymerase subunit alpha, putative [Edwardsiella
           ictaluri 93-146]
 gi|267986210|gb|ACY86039.1| DNA-directed RNA polymerase subunit alpha [Edwardsiella tarda
           EIB202]
 gi|291088821|gb|EFE21382.1| DNA-directed RNA polymerase, alpha subunit [Edwardsiella tarda ATCC
           23685]
 gi|304560334|gb|ADM42998.1| DNA-directed RNA polymerase alpha subunit [Edwardsiella tarda
           FL6-60]
          Length = 329

 Score =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   L         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQLSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPHHVICHLTDENASINMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+S+  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEESIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|158512702|sp|A1A095|RPOA_BIFAA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 332

 Score =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 123/313 (39%), Positives = 184/313 (58%), Gaps = 1/313 (0%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                   R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I GV HE +++ GV
Sbjct: 10  TEESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGVPHEFTTLPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+I+LNIKGI L    D    + + K G G  TAGDI     + + NPD  I  L 
Sbjct: 70  EEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGVTIANPDMHIATLA 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  + +E TV +G GYVPA+ ++ +N  IG I +D++YSP+ KVSY VE+ R  Q  D+
Sbjct: 130 EDGELEIEFTVERGRGYVPAQMNKQDNAEIGRIPVDSIYSPVLKVSYRVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  +I+  D+VA A   L +  G+        + V+      +   NP +  
Sbjct: 190 DKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNTQAEGVEVGPAPVAEETNPEMNI 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L ++GL L 
Sbjct: 250 PIEDLNLTQRSYNCLKREGIHTIGELVAHTEQDLLDIRNFGMKSIDEVKEKLQSLGLALK 309

Query: 319 MN-LPDWPPESIE 330
            + L ++   ++E
Sbjct: 310 ASPLGNFDANNLE 322


>gi|306832573|ref|ZP_07465713.1| DNA-directed RNA polymerase subunit alpha [Streptococcus bovis ATCC
           700338]
 gi|304425331|gb|EFM28457.1| DNA-directed RNA polymerase subunit alpha [Streptococcus bovis ATCC
           700338]
          Length = 312

 Score =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 131/313 (41%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EFEKP----IITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI T +D+E+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDSDVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +     ++  +T++K  GYVPA+ ++ E+ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIAEGHSLKATMTIAKNRGYVPAEGNKKEDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K        
Sbjct: 179 EPARVGSNDGFDKLTLEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKNTDVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +     L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 EKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKND 311


>gi|149912289|ref|ZP_01900860.1| DNA-directed RNA polymerase alpha subunit [Moritella sp. PE36]
 gi|149804634|gb|EDM64693.1| DNA-directed RNA polymerase alpha subunit [Moritella sp. PE36]
          Length = 328

 Score =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 149/333 (44%), Positives = 218/333 (65%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E ++P  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLRPRLVD---IEQISSTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDVLEILLNLKGLAIKLEGKDEALLTLTKSGTGPVLAGDITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
             D+E++NP+HVICNL   A + M + V+KG GYVPA        E  PIG + +DA +S
Sbjct: 118 DGDVEIINPEHVICNLTGQADISMRIRVAKGRGYVPASTRIQSDDEERPIGRLLVDAAFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  + DKL + ++TDG++  E+++  A+ IL +QL  F++  +  
Sbjct: 178 PVSRIAYNVEAARVEQRTNLDKLVIDMETDGTLDPEEAIRRAATILAEQLDAFVDLRDVT 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +        +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 EPE---QKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 327


>gi|301057476|ref|ZP_07198572.1| DNA-directed RNA polymerase, alpha subunit [delta proteobacterium
           NaphS2]
 gi|300448404|gb|EFK12073.1| DNA-directed RNA polymerase, alpha subunit [delta proteobacterium
           NaphS2]
          Length = 388

 Score =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 160/335 (47%), Positives = 220/335 (65%), Gaps = 1/335 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW+ELIKP  IE              + EPL RGF  T+GNALRR+L+SSL+GAAI +V
Sbjct: 7   RNWRELIKPKRIEIDQ-ETNTSTYGKFVCEPLERGFGITIGNALRRILLSSLQGAAIVSV 65

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           + + V+HE SS+ GV ED+TDIILN+K I LK        + + + G G+VTAGDI+T  
Sbjct: 66  KFEDVVHEFSSMPGVLEDVTDIILNLKEIKLKTLDVEEAVIKVNREGEGIVTAGDIETDG 125

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            +EVL P   I  L+ +  + ME+ V  G GYVPA+  + EN PIG+I IDA +S +KKV
Sbjct: 126 SVEVLEPVQHIATLNKEGKLNMEMVVKMGKGYVPAERLKEENTPIGVIAIDATFSCVKKV 185

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y V ++R GQV DYDKL++ + TDGS+  ED+VA A++IL++Q+  FINFEE  + V+E
Sbjct: 186 NYVVTNSRVGQVTDYDKLTLEVWTDGSVFPEDAVAFAAKILKEQMNPFINFEEEIEPVEE 245

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +    N  L + V +LELSVRS NCL+   I  +G+L+Q+T+A+ML+  NFGRKSL
Sbjct: 246 EEVREDQEVNENLFRPVSDLELSVRSANCLQNAKINLIGELVQKTDAEMLKTKNFGRKSL 305

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
            EIK +L  MGL LGM L  +PP    +   +  D
Sbjct: 306 NEIKAILSDMGLSLGMKLDFFPPSQESDDEGEKTD 340


>gi|254468410|ref|ZP_05081816.1| DNA-directed RNA polymerase, alpha subunit [beta proteobacterium
           KB13]
 gi|207087220|gb|EDZ64503.1| DNA-directed RNA polymerase, alpha subunit [beta proteobacterium
           KB13]
          Length = 327

 Score =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 149/331 (45%), Positives = 213/331 (64%), Gaps = 8/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  +E  ++     NR  ++ EP+ RGF  TLGNALRRVL+SS+ G AIT
Sbjct: 1   MQNSPTEYLKPRIVEVDLIN---PNRAKVVLEPMERGFGFTLGNALRRVLLSSIPGFAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGV+HE S+I GV ED+ DI+LN+K + LK+   +   + + K   G VTA D + 
Sbjct: 58  EVKIDGVVHEYSTIDGVQEDVVDILLNLKKVALKIHDGAEATINLKKDSEGEVTAADFEL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYSP 179
            +++E++N D VI N++    + +E  V  G GY P     ++ +++ IG + IDA +SP
Sbjct: 118 PHNVEIVNKDLVIANVNKGGNLNIEAKVEMGRGYQPVPQRVNKDQDNVIGHLMIDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I KVSY VESAR  Q  D DKL M ++T+G +  E ++  A+RIL  QL +F N E    
Sbjct: 178 IFKVSYVVESARVEQRTDLDKLIMDVETNGVVDAEQAIRDAARILMGQLSVFANLESELT 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           EV+     ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQR E D+L+  N G
Sbjct: 238 EVEV---QQAPQIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRHENDLLKAPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           RKSL EIK +L T GL LGM + +WPP+ +E
Sbjct: 295 RKSLNEIKDILATKGLSLGMKVDNWPPQGVE 325


>gi|121997624|ref|YP_001002411.1| DNA-directed RNA polymerase subunit alpha [Halorhodospira halophila
           SL1]
 gi|158514009|sp|A1WV97|RPOA_HALHL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|121589029|gb|ABM61609.1| DNA-directed RNA polymerase subunit alpha [Halorhodospira halophila
           SL1]
          Length = 332

 Score =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 138/334 (41%), Positives = 221/334 (66%), Gaps = 6/334 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++   ++ +KP ++E   L    +NR  ++ EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MKGYLKDFLKPRSVEIEPLS---DNRAKVVLEPLERGFGHTLGNALRRLLLSSMPGTAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GV HE ++++G+HED  DI+LN+K + ++++      +++ K+GPG VTA DI T
Sbjct: 58  EVEIEGVQHEYTAVEGIHEDTVDILLNLKDLAVRLNERDSVTLSVEKQGPGSVTAADIAT 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN-DPIGLITIDALYSPI 180
            +D+E+ NPD  I  +  +   +  L + +G GY+P      E+   IG + +DA +SP+
Sbjct: 118 DHDVEIQNPDLHIATITHEQPFKASLKIERGRGYLPVTAREEEDTRTIGHLALDASFSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VSY VESAR  Q  D DKL + ++T+G +T E++V  A+ +L+DQL +F++ E    E
Sbjct: 178 RRVSYAVESARVEQRTDLDKLVLDVETNGVVTPEEAVKFAASLLRDQLSVFVDLEGGLLE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++     +  +P LL+ +++LEL+VRS NCL+ E+I ++GDL+QRTE ++L+  N G+
Sbjct: 238 GGDEQEEPEI--DPVLLRPIDDLELTVRSANCLKAESIHFVGDLVQRTEVELLKTPNLGK 295

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           KSL EIK  L   GL LGM L +WPP S+ + A+
Sbjct: 296 KSLNEIKDTLAEHGLSLGMQLDNWPPPSLGDRAR 329


>gi|23466156|ref|NP_696759.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium longum
           NCC2705]
 gi|46190439|ref|ZP_00121528.2| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Bifidobacterium longum DJO10A]
 gi|189440595|ref|YP_001955676.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium longum
           DJO10A]
 gi|213693062|ref|YP_002323648.1| DNA-directed RNA polymerase, alpha subunit [Bifidobacterium longum
           subsp. infantis ATCC 15697]
 gi|227546502|ref|ZP_03976551.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium longum
           subsp. infantis ATCC 55813]
 gi|239621036|ref|ZP_04664067.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium longum
           subsp. infantis CCUG 52486]
 gi|296454844|ref|YP_003661988.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium longum
           subsp. longum JDM301]
 gi|312133900|ref|YP_004001239.1| rpoa [Bifidobacterium longum subsp. longum BBMN68]
 gi|317483424|ref|ZP_07942414.1| DNA-directed RNA polymerase [Bifidobacterium sp. 12_1_47BFAA]
 gi|322689903|ref|YP_004209637.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium longum
           subsp. infantis 157F]
 gi|322691844|ref|YP_004221414.1| DNA-directed RNA polymerase alpha subunit [Bifidobacterium longum
           subsp. longum JCM 1217]
 gi|41688707|sp|Q8G3Z3|RPOA_BIFLO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|23326893|gb|AAN25395.1| DNA-directed RNA polymerase alpha chain [Bifidobacterium longum
           NCC2705]
 gi|189429030|gb|ACD99178.1| DNA-directed RNA polymerase alpha subunit [Bifidobacterium longum
           DJO10A]
 gi|213524523|gb|ACJ53270.1| DNA-directed RNA polymerase, alpha subunit [Bifidobacterium longum
           subsp. infantis ATCC 15697]
 gi|227213051|gb|EEI80930.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium longum
           subsp. infantis ATCC 55813]
 gi|239516137|gb|EEQ56004.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium longum
           subsp. infantis CCUG 52486]
 gi|296184276|gb|ADH01158.1| DNA-directed RNA polymerase, alpha subunit [Bifidobacterium longum
           subsp. longum JDM301]
 gi|311773194|gb|ADQ02682.1| RpoA [Bifidobacterium longum subsp. longum BBMN68]
 gi|316915110|gb|EFV36542.1| DNA-directed RNA polymerase [Bifidobacterium sp. 12_1_47BFAA]
 gi|320456700|dbj|BAJ67322.1| DNA-directed RNA polymerase alpha subunit [Bifidobacterium longum
           subsp. longum JCM 1217]
 gi|320459240|dbj|BAJ69861.1| DNA-directed RNA polymerase alpha subunit [Bifidobacterium longum
           subsp. infantis ATCC 15697]
 gi|320461239|dbj|BAJ71859.1| DNA-directed RNA polymerase alpha subunit [Bifidobacterium longum
           subsp. infantis 157F]
          Length = 331

 Score =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 122/312 (39%), Positives = 182/312 (58%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                   R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ GV
Sbjct: 10  TEESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTTLPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+I+LNIKGI L    D    + + K G G   AGDI     + + NP+  I  L 
Sbjct: 70  QEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGKGEAVAGDITPPAGVTIANPEQHIATLA 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  + +E TV +G GYVPA+ ++ +ND IG I +D++YSP+ KVSY VE+ R  Q  D+
Sbjct: 130 DDGELEIEFTVERGRGYVPAQMNKQDNDEIGRIPVDSIYSPVLKVSYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  +I+  D+VA A   L +  G+        + V+      +   NP +  
Sbjct: 190 DKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNAQAEGVEVGPAPVAEETNPEMAV 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L T+GL L 
Sbjct: 250 PIEDLNLTQRSYNCLKREGIHTIGELVSHTEQDLLDIRNFGMKSIDEVKEKLQTLGLSLK 309

Query: 319 MNLPDWPPESIE 330
            +   +   ++E
Sbjct: 310 SSPMAFDTNNLE 321


>gi|312866534|ref|ZP_07726751.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus downei
           F0415]
 gi|311097965|gb|EFQ56192.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus downei
           F0415]
          Length = 312

 Score =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 131/313 (41%), Positives = 202/313 (64%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EFEKPT----ITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILNIKG+ +K   +  K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNIKGLAVKSYVEDEKTIELDVTGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +     ++  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIAEGHTLKATMTVAKNRGYVPAEGNKNDSAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K  +     
Sbjct: 179 EPARVGSNAGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEIAKTTEVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +S+  +  L + +EE++LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 ESVSNDQVLDRTIEEIDLSVRSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLAELGLGLKND 311


>gi|148826553|ref|YP_001291306.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           PittEE]
 gi|172048050|sp|A5UDS2|RPOA_HAEIE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|148716713|gb|ABQ98923.1| DNA-directed RNA polymerase subunit alpha [Haemophilus influenzae
           PittEE]
          Length = 328

 Score =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 149/333 (44%), Positives = 222/333 (66%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       + + K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVILILNKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYS 178
             ++E++NPDHVIC+L D +A + M + V +G GYVPA  + H  E  PIG + +DA YS
Sbjct: 118 DGNVEIVNPDHVICHLTDENASISMRIRVQRGRGYVPASSRTHTQEERPIGRLLVDACYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +
Sbjct: 178 PVERIAYNVEAARVEQRTDLDKLVIELETNGALEPEEAIRRAATILAEQLDAFVDLRDVR 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +    +I  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 QP---EIKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 327


>gi|90414981|ref|ZP_01222943.1| DNA-directed RNA polymerase alpha subunit [Photobacterium profundum
           3TCK]
 gi|90323920|gb|EAS40520.1| DNA-directed RNA polymerase alpha subunit [Photobacterium profundum
           3TCK]
          Length = 329

 Score =  345 bits (885), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 148/334 (44%), Positives = 216/334 (64%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVILTLNKSGAGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIANPEHVICHLTDDHAEISMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|258591343|emb|CBE67642.1| DNA-directed RNA polymerase alpha chain [NC10 bacterium 'Dutch
           sediment']
          Length = 342

 Score =  345 bits (885), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 150/325 (46%), Positives = 209/325 (64%), Gaps = 2/325 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQK ++ + KP  +E   L           AEP  RGF  T+GNALRR L+S++ GAA+
Sbjct: 1   MIQK-FKGIQKPKRLE-CELESLTSTYGKFFAEPFERGFGLTIGNALRRTLLSAIEGAAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAV+I G LHE S+I GV ED+TDIILN+KG+ L++  D  K + +     G V A  I 
Sbjct: 59  TAVRITGALHEFSTIPGVKEDVTDIILNLKGLRLRLHVDHPKTLYLKAFSEGEVRAEHIV 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           +  D+EVLNPD  I  L+ D  + +EL V  G GYVPA+ ++ E  P+ +I ID+++SPI
Sbjct: 119 SDPDVEVLNPDLRIATLEQDGKLELELEVRLGRGYVPAERNKREGQPVDVIAIDSIFSPI 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KV++ VE  R GQV DY+KL++ + TDGS+   D++A A++IL+D L +F NFEE  + 
Sbjct: 179 RKVNFRVEDTRVGQVTDYNKLTLEVWTDGSVLPRDAIAYAAKILKDHLSIFTNFEEEPEG 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
               ++         L + V+ELELSVRS NCL+  +I Y+ +L+ R+EA+ML+  NFGR
Sbjct: 239 EGVVVDEARKQLLDNLNRSVDELELSVRSANCLKHSDIRYIYELVVRSEAEMLKTKNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL EIK +L  MGL LGM L   P
Sbjct: 299 KSLNEIKEILTGMGLTLGMKLEGLP 323


>gi|50955540|ref|YP_062828.1| DNA-directed RNA polymerase subunit alpha [Leifsonia xyli subsp.
           xyli str. CTCB07]
 gi|50952022|gb|AAT89723.1| DNA-directed RNA polymerase, alpha subunit [Leifsonia xyli subsp.
           xyli str. CTCB07]
          Length = 359

 Score =  345 bits (885), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 120/307 (39%), Positives = 184/307 (59%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                 E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S++ GV
Sbjct: 37  TEENISEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFSTVPGV 96

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+IILNIKG+ +    D      + K G G VTA DI     +E+ NP+ VI  L+
Sbjct: 97  KEDVTEIILNIKGLVVSSEHDEPITAYLRKTGAGQVTAADISAPAGVEIHNPELVIATLN 156

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
             A   +ELT+ +G GYV A+ +R E    G I ID++YSP+ KV+Y VE+ R G+  D+
Sbjct: 157 DKAKFEVELTIERGRGYVSAQQNRNEYSEAGQIPIDSIYSPVLKVTYRVEATRAGERTDF 216

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           D+L + ++T  +I+  D++A A R L +  G+        + ++          +  L  
Sbjct: 217 DRLVVDVETKPAISPRDAIASAGRTLVELFGLARELNSAAEGIEIGPAPVDQVLSSELSM 276

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L+LSVRS NCL+ E I  + +L+  +E  ++ + NFG+KS+ E+K  L  MGL L 
Sbjct: 277 PIEDLDLSVRSYNCLKREGINTVSELVSLSETQLMNIRNFGQKSVDEVKDKLTEMGLSLK 336

Query: 319 MNLPDWP 325
            ++P + 
Sbjct: 337 DSVPGFD 343


>gi|119025365|ref|YP_909210.1| DNA-directed RNA polymerase subunit alpha [Bifidobacterium
           adolescentis ATCC 15703]
 gi|118764949|dbj|BAF39128.1| DNA-directed RNA polymerase alpha chain [Bifidobacterium
           adolescentis ATCC 15703]
          Length = 344

 Score =  345 bits (885), Expect = 6e-93,   Method: Composition-based stats.
 Identities = 123/313 (39%), Positives = 184/313 (58%), Gaps = 1/313 (0%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                   R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I GV HE +++ GV
Sbjct: 22  TEESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGVPHEFTTLPGV 81

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+I+LNIKGI L    D    + + K G G  TAGDI     + + NPD  I  L 
Sbjct: 82  EEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGVTIANPDMHIATLA 141

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  + +E TV +G GYVPA+ ++ +N  IG I +D++YSP+ KVSY VE+ R  Q  D+
Sbjct: 142 EDGELEIEFTVERGRGYVPAQMNKQDNAEIGRIPVDSIYSPVLKVSYRVEATRVEQRTDF 201

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  +I+  D+VA A   L +  G+        + V+      +   NP +  
Sbjct: 202 DKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNTQAEGVEVGPAPVAEETNPEMNI 261

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L ++GL L 
Sbjct: 262 PIEDLNLTQRSYNCLKREGIHTIGELVAHTEQDLLDIRNFGMKSIDEVKEKLQSLGLALK 321

Query: 319 MN-LPDWPPESIE 330
            + L ++   ++E
Sbjct: 322 ASPLGNFDANNLE 334


>gi|89076299|ref|ZP_01162640.1| DNA-directed RNA polymerase alpha subunit [Photobacterium sp.
           SKA34]
 gi|89048003|gb|EAR53592.1| DNA-directed RNA polymerase alpha subunit [Photobacterium sp.
           SKA34]
          Length = 329

 Score =  345 bits (885), Expect = 6e-93,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 217/334 (64%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVILTLNKSGAGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E+ NP+HVIC++  D A + M + V +G GYVPA    H   +  PIG + +DA+Y
Sbjct: 118 DGDVEIANPEHVICHITDDNAELSMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAIY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|307823466|ref|ZP_07653695.1| DNA-directed RNA polymerase, alpha subunit [Methylobacter
           tundripaludum SV96]
 gi|307735451|gb|EFO06299.1| DNA-directed RNA polymerase, alpha subunit [Methylobacter
           tundripaludum SV96]
          Length = 337

 Score =  345 bits (885), Expect = 6e-93,   Method: Composition-based stats.
 Identities = 145/333 (43%), Positives = 221/333 (66%), Gaps = 6/333 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +   L+KP  +E +    +  N + ++ EPL RGF H++GNALRRVL+S++ G A+T
Sbjct: 1   MQNSISGLLKPRLVEVV---SKTPNHSKIVIEPLERGFGHSIGNALRRVLLSTIPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GVLHE ++I+GV ED+ DI+LN+K + + +       +T+ K G G VTA DI  
Sbjct: 58  DVEIEGVLHEYTTIEGVQEDVIDILLNLKKLAVVLHSKDEVELTLSKHGAGCVTAADIIL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYS 178
            +D+E++NPD VI NL    V+ M++ V +G GY P    +  ++     G + +DA YS
Sbjct: 118 PHDVEIINPDLVIANLTQVGVLNMKIRVRRGRGYEPVSVRKLNSEHSLVVGALQLDASYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI KV+Y VES R  Q  + DKL + ++T+G++  E+++ LA+ IL DQL +F++FE+  
Sbjct: 178 PIVKVAYQVESTRVEQRTNLDKLVIELETNGTVDPEETIKLAATILHDQLSVFVDFEKVN 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            ++ E+       F+P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 DQLAEEEVEVEEIFDPVLLRPVDDLELTVRSANCLKAENIFYIGDLIQRTEVELLKTPNL 297

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK +L   GL LGM L +WPPE++ +
Sbjct: 298 GKKSLTEIKDILALKGLSLGMRLENWPPENLAD 330


>gi|90581703|ref|ZP_01237491.1| DNA-directed RNA polymerase alpha subunit [Vibrio angustum S14]
 gi|330447012|ref|ZP_08310662.1| DNA-directed RNA polymerase, alpha subunit [Photobacterium
           leiognathi subsp. mandapamensis svers.1.1.]
 gi|90437118|gb|EAS62321.1| DNA-directed RNA polymerase alpha subunit [Vibrio angustum S14]
 gi|328491203|dbj|GAA05159.1| DNA-directed RNA polymerase, alpha subunit [Photobacterium
           leiognathi subsp. mandapamensis svers.1.1.]
          Length = 329

 Score =  345 bits (885), Expect = 6e-93,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 216/334 (64%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVILTLNKSGAGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E+ NP+HVIC++  D A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIANPEHVICHITDDNAELSMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|297582477|ref|YP_003698257.1| DNA-directed RNA polymerase subunit alpha [Bacillus
           selenitireducens MLS10]
 gi|297140934|gb|ADH97691.1| DNA-directed RNA polymerase, alpha subunit [Bacillus
           selenitireducens MLS10]
          Length = 314

 Score =  345 bits (885), Expect = 6e-93,   Method: Composition-based stats.
 Identities = 127/310 (40%), Positives = 204/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L++SL G+A+T+VQ + 
Sbjct: 3   EIEKP-KIEAVELS-EDGTYGKFVVEPLERGYGTTLGNSLRRILLNSLPGSAVTSVQFNN 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IILN+K ++LK+  +  K + I  +G GV+TA D+   +D+EV
Sbjct: 61  VLHEFSTIEGVVEDVTTIILNLKKLSLKIFSEEEKTLEIEAQGEGVITARDLTHDSDVEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L   A V+M++T  +G GYVPA+ + T++ PIG+I +D++++P+ +V+Y V
Sbjct: 121 LNPDLHIATLSKGAQVQMKVTAKRGRGYVPAEGNNTDDLPIGVIPVDSIFTPVSRVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ ++DKL++ + TDGSI  E++ +L ++IL + L +F+   +  +  +  +  
Sbjct: 181 ENTRVGQITNFDKLTLDVWTDGSIRPEEATSLGAKILNEHLNIFVGLTDQAQHAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N GRKSL E++
Sbjct: 241 EEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTHKSEEDMMKVRNLGRKSLEEVQ 300

Query: 308 GVLGTMGLFL 317
             L  + L L
Sbjct: 301 EKLHELSLGL 310


>gi|294789219|ref|ZP_06754458.1| DNA-directed RNA polymerase, alpha subunit [Simonsiella muelleri
           ATCC 29453]
 gi|294482960|gb|EFG30648.1| DNA-directed RNA polymerase, alpha subunit [Simonsiella muelleri
           ATCC 29453]
          Length = 327

 Score =  345 bits (885), Expect = 7e-93,   Method: Composition-based stats.
 Identities = 154/332 (46%), Positives = 216/332 (65%), Gaps = 8/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+   L      R  +  +P  RGF HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSTTEFLKPRQIDVDTLS---ATRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I  VLHE S++ GV ED+ DI+LNIKGI  K+   +   V++ K G GVV AGDI+ 
Sbjct: 58  EVSIANVLHEYSTLDGVQEDVVDILLNIKGIVFKLHNRTEVTVSLKKSGAGVVRAGDIEL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSP 179
            +D+E++NPDHV+C+L  +  + ME+ V +G GY      R   E + IG I +DA +SP
Sbjct: 118 SHDVEIINPDHVLCHLAENGNIEMEIKVEQGRGYQSVSGRRQGKEQNKIGAIQLDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I +VS+ VE+AR  Q  D D L + I+T+G+I  E++V  A+RIL DQ+ +F + +    
Sbjct: 178 ISRVSFDVEAARVEQRTDLDSLILDIETNGAIDPEEAVRAAARILIDQMSIFADLQGTPV 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           EV+E+   K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N G
Sbjct: 238 EVEEE---KAPPIDPVLLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           RKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 295 RKSLNEIKEVLASKGLTLGSKLEAWPPAGLEK 326


>gi|254483442|ref|ZP_05096671.1| DNA-directed RNA polymerase, alpha subunit [marine gamma
           proteobacterium HTCC2148]
 gi|214036316|gb|EEB76994.1| DNA-directed RNA polymerase, alpha subunit [marine gamma
           proteobacterium HTCC2148]
          Length = 334

 Score =  345 bits (884), Expect = 7e-93,   Method: Composition-based stats.
 Identities = 155/336 (46%), Positives = 224/336 (66%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    E + P     I + ++   R  +  EPL RGF HTLGNALRR+L+SS+ G AIT
Sbjct: 1   MQSAVNEFLTPR---VINVDEKNSTRAQVTLEPLERGFGHTLGNALRRILLSSMPGCAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ +I+LN+KG+ L M+G     +T+ K+G G VTA DIQ 
Sbjct: 58  EVEIDGVLHEYSAIEGVQEDVIEILLNLKGVALVMNGKEEAELTLSKKGSGAVTAADIQV 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
            +DIE+ NPDHVIC+L+  + + M+LTV++G GY PA        E   IG + +DA ++
Sbjct: 118 DHDIEIRNPDHVICHLNGASEINMKLTVARGRGYSPADSRENPEEETRSIGRLQLDATFA 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +VSY VESAR  Q  D DKL + ++T+G+I  E+++  A+ ILQ QL +F++    +
Sbjct: 178 PVHRVSYVVESARVEQRTDLDKLVLDLETNGTIDPEEAIRRAATILQQQLAVFVDL---E 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E + +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N 
Sbjct: 235 SESESESVEEEDEVDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S++   +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKNDDR 330


>gi|148544670|ref|YP_001272040.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus reuteri
           DSM 20016]
 gi|184154023|ref|YP_001842364.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus reuteri
           JCM 1112]
 gi|194466927|ref|ZP_03072914.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus reuteri
           100-23]
 gi|227363793|ref|ZP_03847900.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus reuteri
           MM2-3]
 gi|227543597|ref|ZP_03973646.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus reuteri
           CF48-3A]
 gi|300909374|ref|ZP_07126835.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus reuteri
           SD2112]
 gi|325683004|ref|ZP_08162520.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus reuteri
           MM4-1A]
 gi|166991521|sp|A5VLH9|RPOA_LACRD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|229564249|sp|B2G8V2|RPOA_LACRJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|148531704|gb|ABQ83703.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus reuteri
           DSM 20016]
 gi|183225367|dbj|BAG25884.1| DNA-directed RNA polymerase alpha subunit [Lactobacillus reuteri
           JCM 1112]
 gi|194453963|gb|EDX42860.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus reuteri
           100-23]
 gi|227071150|gb|EEI09466.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus reuteri
           MM2-3]
 gi|227186437|gb|EEI66508.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus reuteri
           CF48-3A]
 gi|300893239|gb|EFK86598.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus reuteri
           SD2112]
 gi|324977354|gb|EGC14305.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus reuteri
           MM4-1A]
          Length = 314

 Score =  345 bits (884), Expect = 7e-93,   Method: Composition-based stats.
 Identities = 134/315 (42%), Positives = 205/315 (65%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E +N    + EPL RG+  TLGN+LRRVL++SL GAAIT++QIDG
Sbjct: 3   EFEKPN----IHKVEETDNYGKFVVEPLERGYGTTLGNSLRRVLIASLPGAAITSMQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K ++LK+  +  K + +  +GP  VTA DIQ  N++ +
Sbjct: 59  VLHEFSTVEGVTEDVTQIILNLKKVSLKLDSEDQKNLELDVKGPAEVTASDIQGDNEVTI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
           LNPD  I  +   A + ++LT  KG GY+ A  ++   ++  IG++ ID++Y+PI++V+Y
Sbjct: 119 LNPDLHIATVADGAELHIKLTADKGRGYLSANDNKARMDDLAIGVLPIDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVE+AR GQ  DYDKL++ + TDGS+T  ++V+L ++IL + L MF++  E  +  +  +
Sbjct: 179 TVENARVGQRNDYDKLTLDVWTDGSLTPTEAVSLGAKILTEHLAMFVDLTETAQNAQVMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   +EEL+LSVRS NCL+   I  + +L  RT +DM+++ N G+KSL E
Sbjct: 239 EKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVKELTDRTVSDMMKVRNLGQKSLEE 298

Query: 306 IKGVLGTMGLFLGMN 320
           IK  L  +G+    +
Sbjct: 299 IKLKLNDLGVSFRQD 313


>gi|311896536|dbj|BAJ28944.1| putative DNA-directed RNA polymerase subunit alpha [Kitasatospora
           setae KM-6054]
          Length = 340

 Score =  345 bits (884), Expect = 7e-93,   Method: Composition-based stats.
 Identities = 127/316 (40%), Positives = 193/316 (61%), Gaps = 4/316 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPGVVTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGVVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           + V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 ELVLATLNGKGKLEMELTVERGRGYVSAVQNKASGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKPAMRPRDAMASAGKTLVELFGLARELNVDAEGIDMGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEELELTVRSYNCLKREGIHTVGELVARSEADLLDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPP 326
             MGL L  + P + P
Sbjct: 302 AGMGLALKDSPPGFDP 317


>gi|302876505|ref|YP_003845138.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           cellulovorans 743B]
 gi|307687177|ref|ZP_07629623.1| DNA-directed RNA polymerase subunit alpha [Clostridium
           cellulovorans 743B]
 gi|302579362|gb|ADL53374.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           cellulovorans 743B]
          Length = 315

 Score =  345 bits (884), Expect = 7e-93,   Method: Composition-based stats.
 Identities = 132/313 (42%), Positives = 206/313 (65%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE  V   E+ +    + EPL RG+  TLGN+LRR+L+SSL G A  +++IDG
Sbjct: 3   EIEKP-KIE-CVESTEDGSYGKFVIEPLERGYGITLGNSLRRILLSSLPGVAANSIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++KGV ED+T++ILN+K + LKM+G+  K + I  +GP VVTA DI T + +EV
Sbjct: 61  VLHEFSTVKGVKEDVTELILNVKPLALKMNGEGPKTIYIDAQGPAVVTAADIITDDSVEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           ++ D  I  LD D  ++ME+ V+ G GYV    ++ ++ PIG I ID++Y+PI +V++TV
Sbjct: 121 ISKDLHIATLDEDGRLQMEIEVNSGRGYVTQNKNKRDDMPIGTIAIDSIYTPITRVNFTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ DYDKL++ + T+G+I  E++++L+S+IL + L +F+   +    V+  +  
Sbjct: 181 ENTRVGQITDYDKLTLEVWTNGTIRPEEAISLSSKILIEHLKLFMTLTDNADNVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L +R+  DM+++ N G+KSL E+ 
Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELTERSMDDMMKVRNLGKKSLEEVD 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L +N
Sbjct: 301 QKLTALGLGLKLN 313


>gi|295838431|ref|ZP_06825364.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. SPB74]
 gi|197695771|gb|EDY42704.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. SPB74]
          Length = 340

 Score =  345 bits (884), Expect = 7e-93,   Method: Composition-based stats.
 Identities = 129/321 (40%), Positives = 195/321 (60%), Gaps = 4/321 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPGVVTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGVVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + +ELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNAKGKLELELTVERGRGYVSAVQNKQAGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNVDAEGIDMGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPPESIEE 331
             MGL L  + P + P S  +
Sbjct: 302 AGMGLALKDSPPGFDPTSAAD 322


>gi|311111944|ref|YP_003983166.1| DNA-directed RNA polymerase subunit alpha [Rothia dentocariosa ATCC
           17931]
 gi|310943438|gb|ADP39732.1| DNA-directed RNA polymerase subunit alpha [Rothia dentocariosa ATCC
           17931]
          Length = 330

 Score =  345 bits (884), Expect = 7e-93,   Method: Composition-based stats.
 Identities = 121/329 (36%), Positives = 194/329 (58%), Gaps = 9/329 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V      NR+    EPL  GF +T+GN+LRR L+SS+ GAA+T+V+IDGVLH
Sbjct: 6   RPTLTEEVV----APNRSRFTIEPLEPGFGYTMGNSLRRTLLSSIPGAAVTSVRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T+IILN+K +++    D      + K+G G +TA DI+    +E+ NP
Sbjct: 62  EFSTVPGVTEDVTEIILNVKKLSISSENDEPVVAYLRKQGEGELTAADIEVPAGVEIHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           +  I  L+  A    EL + +G GYV A  ++T +  IG I +D++YSP+ KV+++V + 
Sbjct: 122 ELHIATLNAKANFNAELIIERGRGYVSAAQNKTGDAEIGRIPVDSIYSPVLKVTFSVNAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D L++ ++T  +I   D+VA A   L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDSLTLDVETKEAIAPRDAVASAGSTLVELFGLARELNVAAEGIEVGPSPADE 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +E+L +SVRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L
Sbjct: 242 SMAADLALPIEDLNMSVRSYNCLKREGIHTVGELVTRSEADLMDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             +GL L  + P + P     +A+ Y+D+
Sbjct: 302 HELGLALKDSPPGFEP-----VARAYDDE 325


>gi|73667205|ref|YP_303221.1| DNA-directed RNA polymerase subunit alpha [Ehrlichia canis str.
           Jake]
 gi|90110840|sp|Q3YRN2|RPOA_EHRCJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|72394346|gb|AAZ68623.1| DNA-directed RNA polymerase subunit alpha [Ehrlichia canis str.
           Jake]
          Length = 372

 Score =  345 bits (884), Expect = 8e-93,   Method: Composition-based stats.
 Identities = 171/342 (50%), Positives = 240/342 (70%), Gaps = 5/342 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +W +L KP++I+    G    N+  +I EPL  GFA TLGNALRRV+MSSLRG A+ 
Sbjct: 32  MSDHWSKLTKPSSIKVESNG-ASPNKADLIVEPLESGFALTLGNALRRVMMSSLRGFAVY 90

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+ VLHE +SI GV ED+TDI+LNI  + +K+SG S+K +++  +GP  V +G I  
Sbjct: 91  GVEIENVLHEFTSISGVREDVTDILLNISMMRVKLSGLSNKVLSLRVKGPCEVRSGMIPD 150

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT----ENDPIGLITIDALY 177
            +D  +LN D +IC LD D    +++ V+ G GYVPA   ++     + P+  I  +ALY
Sbjct: 151 TDDCIILNKDLLICTLDQDVDFNIKMYVNSGKGYVPAVKRKSVSKLSDVPVNFIATNALY 210

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPIKK S+ VES+R GQ  DYD+L ++++TDGSI  +++VALA+RILQDQ   FINF+E 
Sbjct: 211 SPIKKASFKVESSRIGQFTDYDRLVLSVETDGSILPDEAVALAARILQDQFQPFINFDET 270

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +  K+     +LP++  LL+KV+ELELSVRS NCL+ +NI Y+GDL+Q+TE+DMLR  N
Sbjct: 271 DEPHKKIDTKDALPYDSNLLRKVDELELSVRSYNCLKNDNITYIGDLVQKTESDMLRTPN 330

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           FGRKSL EI  +L +M L LGM + +WPPESIE L+K+Y ++
Sbjct: 331 FGRKSLNEINELLASMNLHLGMKIANWPPESIESLSKQYSEE 372


>gi|308178106|ref|YP_003917512.1| DNA-directed RNA polymerase subunit alpha [Arthrobacter
           arilaitensis Re117]
 gi|307745569|emb|CBT76541.1| DNA-directed RNA polymerase alpha chain [Arthrobacter arilaitensis
           Re117]
          Length = 333

 Score =  345 bits (884), Expect = 8e-93,   Method: Composition-based stats.
 Identities = 122/315 (38%), Positives = 193/315 (61%), Gaps = 4/315 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V     ENR+  + EPL  GF +TLGN+LRR L+SS+ GA++T+++IDGVLH
Sbjct: 6   RPTLTEEVV----AENRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+T+++LNIK +++    D      + K+GPG+VTA DI     +E  NP
Sbjct: 62  EFTTVAGVKEDVTELVLNIKNLSVSSEHDEPVVAYLRKQGPGIVTAADITPPAGVEFHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+ +    MELT+ +G GYV A  +++ +  IG I +D++YSP+ KV++ VE+ 
Sbjct: 122 DLHIATLNANGKFDMELTIERGRGYVSAAQNKSADGEIGRIPVDSIYSPVLKVTFRVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  SIT  D+VA A   L +  G+F       + ++   +    
Sbjct: 182 RVEQRTDFDRLIVDVETKESITPRDAVASAGTTLVELFGLFRELNTQAEGIEIGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                +   +E+LEL+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L
Sbjct: 242 AMAADMALPIEDLELTVRSYNCLKREGIHSVGELVTRSEADLMDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWP 325
             +GL L  + P + 
Sbjct: 302 VELGLALKDSPPGFD 316


>gi|126209248|ref|YP_001054473.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae L20]
 gi|158513517|sp|A3N382|RPOA_ACTP2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|126098040|gb|ABN74868.1| DNA-directed RNA polymerase alpha chain [Actinobacillus
           pleuropneumoniae serovar 5b str. L20]
          Length = 329

 Score =  345 bits (884), Expect = 8e-93,   Method: Composition-based stats.
 Identities = 152/334 (45%), Positives = 223/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ +    + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVN---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+SG     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVSGKDDIILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++NP HVIC+L D DA + M + V +G GYVPA    H + E+ PIG + +DA +
Sbjct: 118 DGDVEIVNPHHVICHLTDKDASISMRIRVQRGRGYVPASARVHSQDEDRPIGRLLVDARF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VESAR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVESARVEQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+ DL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSHNCLKAETIHYICDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|57239313|ref|YP_180449.1| DNA-directed RNA polymerase subunit alpha [Ehrlichia ruminantium
           str. Welgevonden]
 gi|57161392|emb|CAH58316.1| DNA-directed RNA polymerase alpha chain [Ehrlichia ruminantium str.
           Welgevonden]
          Length = 358

 Score =  345 bits (884), Expect = 8e-93,   Method: Composition-based stats.
 Identities = 171/344 (49%), Positives = 237/344 (68%), Gaps = 7/344 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +W +L KP++I+ +  G    N+  +I EPL  GFA TLGNALRRV+MSSLRG A+ 
Sbjct: 16  MSDHWNKLTKPSSIKVVNHGNA-LNKADLIIEPLESGFALTLGNALRRVMMSSLRGFAVY 74

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+ VLHE +SI GV ED+TDI+LNI  I LK+SG  +K +++  +GP  V +G I  
Sbjct: 75  GVEIENVLHEFTSISGVREDVTDILLNISMIRLKLSGMDNKVLSLKVKGPCEVRSGMIAD 134

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT------ENDPIGLITIDA 175
             D  +LN D +IC LD D    +++ V+ G GYVPA   ++       + P+  I  +A
Sbjct: 135 TPDCTILNKDLLICTLDQDVDFNIKMYVNSGKGYVPAVKRKSINKFGLNDVPVNFIATNA 194

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           LYSPIKK S+ VES+R GQ  DYD+L M+++TD SI  +++VALA+RILQDQ   FINF+
Sbjct: 195 LYSPIKKASFRVESSRIGQFTDYDRLIMSVETDHSILPDEAVALAARILQDQFQQFINFD 254

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           E  +  ++      LP++  LL+KV+ELELSVRS NCL+ +NI Y+GDL+Q+TE+DMLR 
Sbjct: 255 ETDEPHQKVDTKDVLPYDSNLLRKVDELELSVRSYNCLKNDNITYIGDLVQKTESDMLRT 314

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            NFGRKSL EI  +L +M L LGM + +WPPESIE L+K+Y ++
Sbjct: 315 PNFGRKSLNEINELLASMNLHLGMKIANWPPESIESLSKQYSEE 358


>gi|154486773|ref|ZP_02028180.1| hypothetical protein BIFADO_00598 [Bifidobacterium adolescentis
           L2-32]
 gi|154084636|gb|EDN83681.1| hypothetical protein BIFADO_00598 [Bifidobacterium adolescentis
           L2-32]
          Length = 332

 Score =  345 bits (884), Expect = 8e-93,   Method: Composition-based stats.
 Identities = 123/313 (39%), Positives = 184/313 (58%), Gaps = 1/313 (0%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                   R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I GV HE +++ GV
Sbjct: 10  TEESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGVPHEFTTLPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+I+LNIKGI L    D    + + K G G  TAGDI     + + NPD  I  L 
Sbjct: 70  EEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGVTIANPDMHIATLA 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  + +E TV +G GYVPA+ ++ +N  IG I +D++YSP+ KVSY VE+ R  Q  D+
Sbjct: 130 EDGELEIEFTVERGRGYVPAQMNKQDNAEIGRIPVDSIYSPVLKVSYRVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  +I+  D+VA A   L +  G+        + V+      +   NP +  
Sbjct: 190 DKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNTQAEGVEVGPAPVAEETNPEMNI 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L ++GL L 
Sbjct: 250 PIEDLNLTQRSYNCLKREGIHTIGELVAHTEQDLLDIRNFGMKSIDEVKEKLQSLGLALK 309

Query: 319 MN-LPDWPPESIE 330
            + L ++   ++E
Sbjct: 310 ASPLGNFDTNNLE 322


>gi|300690186|ref|YP_003751181.1| RNA polymerase, alpha subunit; RNA polymerase alpha chain family
           [Ralstonia solanacearum PSI07]
 gi|299077246|emb|CBJ49872.1| RNA polymerase, alpha subunit; RNA polymerase alpha chain family
           [Ralstonia solanacearum PSI07]
          Length = 326

 Score =  345 bits (884), Expect = 9e-93,   Method: Composition-based stats.
 Identities = 148/326 (45%), Positives = 210/326 (64%), Gaps = 7/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    LG        ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKIIAVEPLGDH---HAKVVMEPFERGYGHTLGNALRRVLLSSMVGYASTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S+I GV ED+ +++LN+KG+  K+       V++ K G GVVTA DI+  +D+E++
Sbjct: 62  VHEYSTIDGVQEDVVNLLLNLKGVVFKLHNRDEVTVSLRKEGEGVVTAADIELPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSY 185
           NP HVI +L     + M++ V +G GYVP    +  ++     G I +DA ++P+++VSY
Sbjct: 122 NPGHVIASLSAGGKLDMQIKVEQGRGYVPGNVRKFGDESSKVIGRIVLDASFAPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL M I+T+G I+ E+++  ++RIL DQL +F   E   +   E  
Sbjct: 182 AVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALEG-TESAAEAA 240

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 241 AARAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 300

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +E+
Sbjct: 301 IKEVLASRGLTLGMKLENWPPAGLEK 326


>gi|58617333|ref|YP_196532.1| DNA-directed RNA polymerase subunit alpha [Ehrlichia ruminantium
           str. Gardel]
 gi|75432689|sp|Q5FFS1|RPOA_EHRRG RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|58416945|emb|CAI28058.1| DNA-directed RNA polymerase alpha chain [Ehrlichia ruminantium str.
           Gardel]
          Length = 374

 Score =  345 bits (884), Expect = 9e-93,   Method: Composition-based stats.
 Identities = 172/344 (50%), Positives = 237/344 (68%), Gaps = 7/344 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +W +L KP++I+ +  G    N+  +I EPL  GFA TLGNALRRV+MSSLRG A+ 
Sbjct: 32  MSDHWNKLTKPSSIKVVNHGNA-LNKADLIIEPLESGFALTLGNALRRVMMSSLRGFAVY 90

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+ VLHE +SI GV ED+TDI+LNI  I LK+SG  +K +++  +GP  V +G I  
Sbjct: 91  GVEIENVLHEFTSISGVREDVTDILLNISMIRLKLSGMDNKVLSLKVKGPCEVRSGMIAD 150

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND------PIGLITIDA 175
             D  +LN D +IC LD D    +++ V+ G GYVPA   ++ N       P+  I  +A
Sbjct: 151 TPDCTILNKDLLICTLDQDVDFNIKMYVNSGKGYVPAVKRKSINKFGLSDVPVNFIATNA 210

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           LYSPIKK S+ VES+R GQ  DYD+L M+++TD SI  +++VALA+RILQDQ   FINF+
Sbjct: 211 LYSPIKKASFRVESSRIGQFTDYDRLIMSVETDHSILPDEAVALAARILQDQFQQFINFD 270

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           E  +  ++      LP++  LL+KV+ELELSVRS NCL+ +NI Y+GDL+Q+TE+DMLR 
Sbjct: 271 ETDEPHQKVDTKDVLPYDSNLLRKVDELELSVRSYNCLKNDNITYIGDLVQKTESDMLRT 330

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            NFGRKSL EI  +L +M L LGM + +WPPESIE L+K+Y ++
Sbjct: 331 PNFGRKSLNEINELLASMNLHLGMKIANWPPESIESLSKQYSEE 374


>gi|55821879|ref|YP_140321.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           thermophilus LMG 18311]
 gi|55823795|ref|YP_142236.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           thermophilus CNRZ1066]
 gi|116628572|ref|YP_821191.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           thermophilus LMD-9]
 gi|81558875|sp|Q5LXT7|RPOA_STRT1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|81560062|sp|Q5M2D9|RPOA_STRT2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|122266834|sp|Q03IH7|RPOA_STRTD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|55737864|gb|AAV61506.1| DNA-directed RNA polymerase alpha subunit [Streptococcus
           thermophilus LMG 18311]
 gi|55739780|gb|AAV63421.1| DNA-directed RNA polymerase alpha subunit [Streptococcus
           thermophilus CNRZ1066]
 gi|116101849|gb|ABJ66995.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Streptococcus thermophilus LMD-9]
 gi|312279233|gb|ADQ63890.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           thermophilus ND03]
          Length = 312

 Score =  345 bits (884), Expect = 9e-93,   Method: Composition-based stats.
 Identities = 131/313 (41%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EFEKP----IITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKG+ +K   +  K + +  +GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGLAVKSYVEDEKTIELDVQGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A  +  +TVS   GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIAEGASFQATMTVSTNRGYVPAEENKKDDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F +  +  K        
Sbjct: 179 EPARVGSNDGFDKLTIEIVTNGTIIPEDALGLSARILIEHLNLFTDLTDVAKATDVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +     L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 EKVNDEKLLDRTIEELDLSVRSYNCLKRAGINTVHDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKND 311


>gi|311693295|gb|ADP96168.1| DNA-directed RNA polymerase subunit alpha [marine bacterium HP15]
          Length = 319

 Score =  345 bits (884), Expect = 9e-93,   Method: Composition-based stats.
 Identities = 151/311 (48%), Positives = 215/311 (69%), Gaps = 6/311 (1%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +    R  +  EPL RGF HTLG+ALRR+L+SS+ G A+T  QIDGVLHE S+I+GV ED
Sbjct: 3   ESSATRAKVTLEPLERGFGHTLGSALRRILLSSMPGCAVTEAQIDGVLHEYSAIEGVQED 62

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + +I+LN+KG+ +KM+G     +T+ K+GPGVVTAGDI+  +D+E+ NP+HVIC+L  + 
Sbjct: 63  VIEILLNLKGVAVKMNGRDDAELTLSKKGPGVVTAGDIKLDHDVEIANPEHVICHLSENG 122

Query: 142 VVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            V M L V++G GY PA        E   IG + +DA +SP+++V+Y VESAR  Q  D 
Sbjct: 123 EVNMRLRVARGRGYEPADQRGLDEDETRAIGRLQLDATFSPVRRVAYAVESARVEQRTDL 182

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T+G+I  E+++  A+ ILQ QL +F++F+  K+        +    +P LL+
Sbjct: 183 DKLVIDLETNGTIDPEEAIRRAATILQQQLAVFVDFDHEKEPE---RVEEEEEIDPILLR 239

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 240 PVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 299

Query: 319 MNLPDWPPESI 329
           M L +WPP S+
Sbjct: 300 MRLDNWPPASL 310


>gi|269104037|ref|ZP_06156734.1| DNA-directed RNA polymerase alpha subunit [Photobacterium damselae
           subsp. damselae CIP 102761]
 gi|268163935|gb|EEZ42431.1| DNA-directed RNA polymerase alpha subunit [Photobacterium damselae
           subsp. damselae CIP 102761]
          Length = 329

 Score =  345 bits (884), Expect = 9e-93,   Method: Composition-based stats.
 Identities = 148/334 (44%), Positives = 217/334 (64%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVNSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVILTLNKSGAGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E+ NP+HVIC++  D A + M + V +G GYVPA    H   +  PIG + +DA +
Sbjct: 118 DGDVEIANPEHVICHITDDNAELSMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ ++SY VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRISYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|284006138|emb|CBA71380.1| DNA-directed RNA polymerase alpha chain [Arsenophonus nasoniae]
          Length = 329

 Score =  345 bits (884), Expect = 9e-93,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVHGKDEVILTLNKSGIGPVTAADITP 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
            +DIE++ P HVIC+L D  A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 NDDIEIVKPQHVICHLTDESAAINMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+ R  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEATRVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
               K ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 A---KVEVKDEKPEFDPILLRAVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|58579279|ref|YP_197491.1| DNA-directed RNA polymerase subunit alpha [Ehrlichia ruminantium
           str. Welgevonden]
 gi|90110841|sp|Q5HAU5|RPOA_EHRRW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|58417905|emb|CAI27109.1| DNA-directed RNA polymerase alpha chain [Ehrlichia ruminantium str.
           Welgevonden]
          Length = 374

 Score =  344 bits (883), Expect = 9e-93,   Method: Composition-based stats.
 Identities = 171/344 (49%), Positives = 237/344 (68%), Gaps = 7/344 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +W +L KP++I+ +  G    N+  +I EPL  GFA TLGNALRRV+MSSLRG A+ 
Sbjct: 32  MSDHWNKLTKPSSIKVVNHGNA-LNKADLIIEPLESGFALTLGNALRRVMMSSLRGFAVY 90

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+ VLHE +SI GV ED+TDI+LNI  I LK+SG  +K +++  +GP  V +G I  
Sbjct: 91  GVEIENVLHEFTSISGVREDVTDILLNISMIRLKLSGMDNKVLSLKVKGPCEVRSGMIAD 150

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT------ENDPIGLITIDA 175
             D  +LN D +IC LD D    +++ V+ G GYVPA   ++       + P+  I  +A
Sbjct: 151 TPDCTILNKDLLICTLDQDVDFNIKMYVNSGKGYVPAVKRKSINKFGLNDVPVNFIATNA 210

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           LYSPIKK S+ VES+R GQ  DYD+L M+++TD SI  +++VALA+RILQDQ   FINF+
Sbjct: 211 LYSPIKKASFRVESSRIGQFTDYDRLIMSVETDHSILPDEAVALAARILQDQFQQFINFD 270

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           E  +  ++      LP++  LL+KV+ELELSVRS NCL+ +NI Y+GDL+Q+TE+DMLR 
Sbjct: 271 ETDEPHQKVDTKDVLPYDSNLLRKVDELELSVRSYNCLKNDNITYIGDLVQKTESDMLRT 330

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            NFGRKSL EI  +L +M L LGM + +WPPESIE L+K+Y ++
Sbjct: 331 PNFGRKSLNEINELLASMNLHLGMKIANWPPESIESLSKQYSEE 374


>gi|289209304|ref|YP_003461370.1| DNA-directed RNA polymerase, subunit alpha [Thioalkalivibrio sp.
           K90mix]
 gi|288944935|gb|ADC72634.1| DNA-directed RNA polymerase, alpha subunit [Thioalkalivibrio sp.
           K90mix]
          Length = 328

 Score =  344 bits (883), Expect = 9e-93,   Method: Composition-based stats.
 Identities = 155/333 (46%), Positives = 217/333 (65%), Gaps = 11/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N  EL+K   IE   +  E  N+  +  EPL RGF HTLGNALRRVL+SS+ GAAI 
Sbjct: 1   MQSN--ELVKKQQIE---VEAENRNQAKVALEPLERGFGHTLGNALRRVLLSSIPGAAIV 55

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +I+GVLHE ++I+GV ED+ DI+LN+KG+ L+M       +++ K+GP VVTAGDI  
Sbjct: 56  EARIEGVLHEYTAIEGVQEDVVDILLNLKGVALRMHSREESTLSLKKKGPCVVTAGDITV 115

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYS 178
            +D+EV+NP+HVI  +  +  + M LT   G GY P    R    +   IG + +DA +S
Sbjct: 116 DHDVEVVNPEHVIATITKNVEIDMTLTARAGRGYEPVSTRRQAEGDETGIGRLLLDASFS 175

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI++V+Y VESAR  Q  D D+L + ++T+G+I  +D+V  A+ ILQ QL  F++ +E  
Sbjct: 176 PIRRVAYRVESARLAQRTDMDRLVLELETNGAIAPDDAVRQAATILQGQLAPFVDLQEET 235

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            EV       +   +P LL+ V+ELEL+VRS NCL+ EN+ Y+GDL+QRTE ++LR  N 
Sbjct: 236 GEV---PGTTAGAIDPILLRPVDELELTVRSANCLKAENLYYIGDLVQRTEVELLRAPNL 292

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK  L T GL LGM L +WPP  + +
Sbjct: 293 GKKSLTEIKDTLATHGLSLGMRLENWPPPGLRD 325


>gi|82701925|ref|YP_411491.1| DNA-directed RNA polymerase subunit alpha [Nitrosospira multiformis
           ATCC 25196]
 gi|119366704|sp|Q2YAX2|RPOA_NITMU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|82409990|gb|ABB74099.1| DNA-directed RNA polymerase subunit alpha [Nitrosospira multiformis
           ATCC 25196]
          Length = 334

 Score =  344 bits (883), Expect = 9e-93,   Method: Composition-based stats.
 Identities = 149/335 (44%), Positives = 216/335 (64%), Gaps = 10/335 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N    + P  I+   +         +  EP  RG+ HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQSNT--FLTPRIIDVQNISPL---HARITMEPFERGYGHTLGNALRRILLSSMPGFAPT 55

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            VQI GV+HE S++ GV ED+ DI+LN+KGI LK+   +   +T+ K+G G VTAGDI+ 
Sbjct: 56  EVQISGVVHEYSALDGVQEDVVDILLNLKGIVLKLHNRTEALLTLSKKGEGTVTAGDIEG 115

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSP 179
            +D+E++NPDHV+ +L     + M++ V  G GYVP    +   E+  IG I +DA +SP
Sbjct: 116 GHDVEIINPDHVVAHLTSGGKLDMQIKVEMGRGYVPGTVRQLAHESRAIGSILLDASFSP 175

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +++VSY VESAR  Q  D DKL M I+T+G +  E+++  A+++L +QL +F + +    
Sbjct: 176 VRRVSYAVESARVEQRTDLDKLVMDIETNGVVDPEEAIRYAAKVLVEQLSVFADLKGTPL 235

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            V++    K    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G
Sbjct: 236 PVEQP---KLPQIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTETELLKTPNLG 292

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           RKSL EIK VL + GL LGM L  WPP ++++  K
Sbjct: 293 RKSLNEIKEVLASRGLTLGMKLESWPPSNLDKGKK 327


>gi|42810|emb|CAA37839.1| unnamed protein product [Escherichia coli]
          Length = 329

 Score =  344 bits (883), Expect = 9e-93,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+A   Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAACVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|111220574|ref|YP_711368.1| DNA-directed RNA polymerase subunit alpha [Frankia alni ACN14a]
 gi|122954575|sp|Q0RRP3|RPOA_FRAAA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|111148106|emb|CAJ59774.1| RNA polymerase, alpha subunit [Frankia alni ACN14a]
          Length = 349

 Score =  344 bits (883), Expect = 9e-93,   Method: Composition-based stats.
 Identities = 124/316 (39%), Positives = 190/316 (60%), Gaps = 4/316 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P  +E        E R+  + EPL  GF +TLGN+LRR L+SS+ GA++T+++IDGVLH
Sbjct: 6   RPTLVE----DPISEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+TD+ILN+K + +    D    + + K+GPG VTA DI     +EV +P
Sbjct: 62  EFSTVPGVKEDVTDLILNLKELVVSSDNDEPTVMYLRKQGPGEVTAADIAPPAGVEVHSP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           +  +  L+    + +ELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+ 
Sbjct: 122 ELRLATLNDKGKLEIELTVERGRGYVSAAQNKQAGQEIGRIPIDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  SI+  D++A A + L    G+        + V    +    
Sbjct: 182 RVEQRTDFDRLIVDVETKPSISPRDAMASAGKTLVGLFGLAQELNAEAEGVDIGPSAADA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EE++L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  L
Sbjct: 242 ALAADLALPIEEMDLTVRSYNCLKREGIHTIGELVSRSEADLLDIRNFGQKSIDEVKTKL 301

Query: 311 GTMGLFLGMNLPDWPP 326
           G MGL L  + P + P
Sbjct: 302 GAMGLQLKDSPPGFDP 317


>gi|225024813|ref|ZP_03714005.1| hypothetical protein EIKCOROL_01700 [Eikenella corrodens ATCC
           23834]
 gi|224942416|gb|EEG23625.1| hypothetical protein EIKCOROL_01700 [Eikenella corrodens ATCC
           23834]
          Length = 325

 Score =  344 bits (883), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 148/330 (44%), Positives = 213/330 (64%), Gaps = 6/330 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+   L      R  +  EP  RGF +TLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSTYEFLKPRQIDVDALS---ATRAKVFMEPFERGFGYTLGNALRRILLSSMNGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V IDG LHE S++ GV ED+ DI+LNIKG+  K+ G    +V++ K G GVVTA D++ 
Sbjct: 58  EVVIDGALHEYSTLDGVQEDVVDILLNIKGVVFKLQGRDSVQVSLNKSGSGVVTAADLEL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+EV+NP+HVIC L  +  + + +TV KG GY        ++  IG I +DA +SP+ 
Sbjct: 118 PHDVEVINPEHVICRLSDNGKIELTITVEKGRGYQTVSSRNDDHKQIGAIHLDANFSPVH 177

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +VS+ V++AR  Q  D D L + I+T+G+I  E++V  A+RIL DQ+ +F + E      
Sbjct: 178 RVSFEVQAARVEQRTDLDCLVLDIETNGAIDPEEAVRRAARILIDQMSVFADLEG---TP 234

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+   ++ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N GRK
Sbjct: 235 VEESKEEAPPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPNLGRK 294

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           SL EIK VL + GL LG  L  WPP  +++
Sbjct: 295 SLNEIKEVLASKGLTLGSKLDVWPPVGLDK 324


>gi|297625818|ref|YP_003687581.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           (Transcriptase alpha chain) (RNA polymerase subunit
           alpha) [Propionibacterium freudenreichii subsp.
           shermanii CIRM-BIA1]
 gi|296921583|emb|CBL56137.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           (Transcriptase alpha chain) (RNA polymerase subunit
           alpha) [Propionibacterium freudenreichii subsp.
           shermanii CIRM-BIA1]
          Length = 339

 Score =  344 bits (883), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 128/329 (38%), Positives = 191/329 (58%), Gaps = 7/329 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V     + R+  + EPL  GF +TLGN+LRR L+SS+ GA+IT+++I+G  H
Sbjct: 6   RPTLSEEVV----NDFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASITSIKIEGNQH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T+IILN+KG+ L    D    + + K G G VTA DI     +E+ NP
Sbjct: 62  EFSTLPGVVEDVTEIILNLKGLVLSSEEDEPVAMYLRKSGAGEVTAADIAVPTGVEIYNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L  D  + MEL V +G GYV +  +   +  IG I +D+LYSP+  VSY VE+ 
Sbjct: 122 DLHIATLADDGSIEMELVVERGRGYVSSTLNNNPDAEIGRIAVDSLYSPVLTVSYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R     D+D+L + ++T  SI   D+VA A + L +  G+F       + V+   +    
Sbjct: 182 RVETRTDFDRLIVDVETKPSIRPHDAVASAGKTLVELFGLFRELNVEAEGVEMGPSPVDE 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                +   VE+L LSVRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L
Sbjct: 242 QLAADMALPVEDLNLSVRSYNCLKREGIHTVGELVSRSEQDLLDIRNFGSKSIDEVKEKL 301

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           G +GL L  + P + P +    A ++ED+
Sbjct: 302 GDLGLTLKDSTPGFDPLAA---ADRFEDE 327


>gi|184200289|ref|YP_001854496.1| DNA-directed RNA polymerase subunit alpha [Kocuria rhizophila
           DC2201]
 gi|183580519|dbj|BAG28990.1| DNA-directed RNA polymerase alpha subunit [Kocuria rhizophila
           DC2201]
          Length = 339

 Score =  344 bits (883), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 123/321 (38%), Positives = 194/321 (60%), Gaps = 3/321 (0%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                 ENR+  + EPL  GF +TLGN+LRR L+SS+ GA++T+++IDGVLHE S+++GV
Sbjct: 10  TEEAVAENRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIRIDGVLHEFSTVEGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T++ILNIK ++L    D      + K+GPG VTA DI     +EV NP+  I  L+
Sbjct: 70  KEDVTELILNIKKLSLSSEEDEPVTAWLRKQGPGEVTAADISAPAGVEVHNPELHIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +ELT+ +G GYV A  +++ +  +G I +D++YSP+ KV++ VE+ R  Q  D+
Sbjct: 130 SKGQLEIELTIERGRGYVSASQNKSGDAEVGRIPVDSIYSPVLKVTFRVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  +I+  D+VA A   L +  G+        + ++   +         +  
Sbjct: 190 DKLILDVETKEAISPRDAVASAGTTLVELFGLARELNSSAEGIEIGPSPTDAAAAADMAL 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+LELSVRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  LG +GL L 
Sbjct: 250 PIEDLELSVRSYNCLKREGIHSVGELVGRSEADLMDIRNFGAKSIDEVKDKLGELGLALK 309

Query: 319 MNLPDWPPESIEELAKKYEDK 339
            + P +    +   A   ED+
Sbjct: 310 DSPPGYD---LAAHAASLEDE 327


>gi|317131398|ref|YP_004090712.1| DNA-directed RNA polymerase, alpha subunit [Ethanoligenens
           harbinense YUAN-3]
 gi|315469377|gb|ADU25981.1| DNA-directed RNA polymerase, alpha subunit [Ethanoligenens
           harbinense YUAN-3]
          Length = 316

 Score =  344 bits (883), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 134/314 (42%), Positives = 200/314 (63%), Gaps = 3/314 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE   L   + +    + EPL RG+  TLGN+LRRVL+SSL G A+T V+IDG
Sbjct: 3   EIEKPR-IETAEL-TSDGSYGRFVVEPLERGYGTTLGNSLRRVLLSSLPGVAVTQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE S++ GV ED+T+IILNIKG+  K+  D  K V I   G   VTAGDI+T +++E+
Sbjct: 61  VQHEFSTVPGVKEDVTEIILNIKGLTAKLHSDGPKVVYIDAEGECKVTAGDIKTDSEVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP-IGLITIDALYSPIKKVSYT 186
           L+P+  I  L   A + ME+T+ KG GYV A+ ++    P IG+I +D++Y+P+ KV+Y 
Sbjct: 121 LDPNMHIATLAAGAKLYMEITLDKGRGYVAAERNKQNLQPAIGVIPVDSIYTPVLKVNYA 180

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+ R GQ+ DYDKL++ + TD +I+ +++V++ ++IL + LG+F+      +  +  + 
Sbjct: 181 VENTRVGQITDYDKLTLEVWTDATISAKEAVSIGAKILNEHLGLFVALCAETQSTEIMVE 240

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
                    L   +EEL+LSVRS NCL+   I  + DLI RTE DM+++ N GRKSL E+
Sbjct: 241 KDDKSKEKVLEMTIEELDLSVRSFNCLKRAGINTVEDLINRTEDDMMKVRNLGRKSLEEV 300

Query: 307 KGVLGTMGLFLGMN 320
              L ++G  L  +
Sbjct: 301 ISKLNSLGFSLKRD 314


>gi|88658298|ref|YP_507250.1| DNA-directed RNA polymerase subunit alpha [Ehrlichia chaffeensis
           str. Arkansas]
 gi|88599755|gb|ABD45224.1| DNA-directed RNA polymerase, alpha subunit [Ehrlichia chaffeensis
           str. Arkansas]
          Length = 341

 Score =  344 bits (883), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 171/342 (50%), Positives = 239/342 (69%), Gaps = 5/342 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +W +L KP++I+ +  G    N+  +I EPL  GFA TLGNALRRV+MSSLRG A+ 
Sbjct: 1   MSDHWSKLTKPSSIKVVPSG-ASPNKADLIIEPLESGFALTLGNALRRVMMSSLRGFAVY 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+ VLHE +SI GV ED+TDI+LNI  + +K+SG + K +++  +GP  V +G I  
Sbjct: 60  GVEIENVLHEFTSISGVREDVTDILLNISMMRVKLSGMNSKVLSLKVKGPCEVRSGMIPD 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH----HRTENDPIGLITIDALY 177
            +D  +LN D +IC LD      +++ V+ G GYVPA      ++  + PI  I  +ALY
Sbjct: 120 TDDCIILNKDLLICTLDQGVDFNIKMYVNAGKGYVPAVKRKSVNKLGDIPINFIATNALY 179

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPIKK S+ VES+R GQ  DYD+L M+++TDGSI  +++VALA+RILQDQ   FINF+E 
Sbjct: 180 SPIKKASFKVESSRIGQFTDYDRLIMSVETDGSILPDEAVALAARILQDQFQPFINFDET 239

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +  K+     +LP++  LL+KV+ELELSVRS NCL+ +NI Y+GDL+Q+TE+DMLR  N
Sbjct: 240 DEPHKKVDAKDTLPYDSNLLRKVDELELSVRSYNCLKNDNITYIGDLVQKTESDMLRTPN 299

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           FGRKSL EI  +L +M L LGM + +WPPESIE L+K+Y ++
Sbjct: 300 FGRKSLNEINELLASMNLHLGMKIANWPPESIESLSKQYSEE 341


>gi|237806900|ref|YP_002891340.1| DNA-directed RNA polymerase subunit alpha [Tolumonas auensis DSM
           9187]
 gi|259494173|sp|C4L7V5|RPOA_TOLAT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|237499161|gb|ACQ91754.1| DNA-directed RNA polymerase, alpha subunit [Tolumonas auensis DSM
           9187]
          Length = 329

 Score =  344 bits (883), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +  + +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MLGSVTDFLKPRLVD---IEQLSPTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVA 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KGI +K+ G     +++ K G G VTAGDI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGIAVKLEGKDEVILSLTKSGAGPVTAGDIIH 117

Query: 122 VNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
            +D+ ++NP+HVIC+L   +A + M L V +G GYVPA    H   E+ PIG + +DA +
Sbjct: 118 GDDVVIVNPEHVICHLTGANAEISMRLRVQRGRGYVPASARLHTDDEDRPIGRLLLDAAF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVVRIAYNVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
               K++       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 SVPEKKE---DKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 328


>gi|319940035|ref|ZP_08014389.1| DNA-directed RNA polymerase subunit alpha [Streptococcus anginosus
           1_2_62CV]
 gi|319810749|gb|EFW07076.1| DNA-directed RNA polymerase subunit alpha [Streptococcus anginosus
           1_2_62CV]
          Length = 312

 Score =  344 bits (883), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 132/313 (42%), Positives = 201/313 (64%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++  + + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKDYGIFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILN+KGI +K   +  K + +   GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNVKGIAVKSYVEDEKTIELDVEGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A ++  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIGEGASLKAIMTVNTGRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I TDG+I  ED++ L++RIL + L +F N  E  K        
Sbjct: 179 EPARVGSNDGFDKLTLEIMTDGTIIPEDALGLSARILTEHLDLFTNLTEVAKSTDVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +  +  L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 EKVSDDRVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKND 311


>gi|24380343|ref|NP_722298.1| DNA-directed RNA polymerase subunit alpha [Streptococcus mutans
           UA159]
 gi|290581264|ref|YP_003485656.1| DNA-directed RNA polymerase subunit alpha [Streptococcus mutans
           NN2025]
 gi|41688701|sp|Q8DS36|RPOA_STRMU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|24378361|gb|AAN59604.1|AE015023_5 DNA-directed RNA polymerase, alpha subunit [Streptococcus mutans
           UA159]
 gi|254998163|dbj|BAH88764.1| DNA-directed RNA polymerase alpha subunit [Streptococcus mutans
           NN2025]
          Length = 312

 Score =  344 bits (883), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 131/313 (41%), Positives = 201/313 (64%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EFEKP----IITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILNIKG+ +K   +  K V +   GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNIKGLAVKSYVEEEKIVELDVEGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A ++  +TV+   GYVPA+ ++ ++ P+G + ID++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIAEGANLKATMTVATNRGYVPAEKNKRDDAPVGTLAIDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G   ++DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K        
Sbjct: 179 EPARVGSNDNFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKATDVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +     L + +EEL+LSVRS NCL+   I  + DL +++E++M+++ N GRKSL E+K
Sbjct: 239 EQVSDEKVLDRTIEELDLSVRSYNCLKRAGINTVYDLTEKSESEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKND 311


>gi|261867279|ref|YP_003255201.1| DNA-directed RNA polymerase subunit alpha [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261412611|gb|ACX81982.1| DNA-directed RNA polymerase, alpha subunit [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 329

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 151/334 (45%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    E +KP  ++   + Q    +  +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGAVTEFLKPRLVD---IEQISSTQAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVLLTLSKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+EV+NP+HVIC+L D +A + M + V +G GYVPA      + E  PIG + +DA Y
Sbjct: 118 DGDVEVINPEHVICHLTDENASISMRIRVRRGRGYVPASVRAQIQDEERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPI++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPIERIAYNVEAARVEQRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL  V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLLPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|33152929|ref|NP_874282.1| DNA-directed RNA polymerase subunit alpha [Haemophilus ducreyi
           35000HP]
 gi|41688646|sp|Q7VKF8|RPOA_HAEDU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|33149154|gb|AAP96671.1| RNA polymerase alpha subunit [Haemophilus ducreyi 35000HP]
          Length = 329

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 151/334 (45%), Positives = 224/334 (67%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ +    + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQGSVIEFLKPHLVN---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVA 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+SG +   +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVSGKNDVTLTLNKSGIGPVLAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++NP+HVIC+L D DA + M + V +G GYVPA    H + E+ PIG + +DA +
Sbjct: 118 DGDVEIINPNHVICHLTDKDASINMRIYVQRGRGYVPASARVHSQDEDRPIGRLLVDARF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYNVEAARVEQRTDLDKLIIDMETNGTIDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    +I  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EIKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|330718947|ref|ZP_08313547.1| DNA-directed RNA polymerase subunit alpha [Leuconostoc fallax KCTC
           3537]
          Length = 314

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 129/312 (41%), Positives = 192/312 (61%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E+      + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDG
Sbjct: 3   EFEKPN----IHNIEEDARYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE S++ GV ED+T +ILN+K + L +  D  K + I  +GP  VTA D+Q   DIEV
Sbjct: 59  VVHEFSTVDGVVEDVTQLILNLKKVVLAIDSDEEKSLEIDVQGPAEVTAADLQGSADIEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
           LNP+  +  +     + M +T  KG GY  A  ++   +  PIG++ +D++Y+PI++V+Y
Sbjct: 119 LNPELHLATVAAGKSLHMTVTAVKGRGYSSADENKQLRDEMPIGVLAVDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R GQ  DYDKL+  I T+GSI   D+++L ++IL + L +F +      E +  +
Sbjct: 179 QVENTRVGQRDDYDKLTFDIWTNGSIKPSDALSLGAKILSEHLNLFTDISSVAAETEVMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           +V+    +      +E+L+LSVRS NCL+   I  + +L  R+EADM+++ N GRKSL E
Sbjct: 239 DVEQTVSSVQDSAPIEDLDLSVRSYNCLKRAGINTISELTDRSEADMMKVRNLGRKSLDE 298

Query: 306 IKGVLGTMGLFL 317
           I+  L  MGL  
Sbjct: 299 IQEKLIEMGLGF 310


>gi|227431316|ref|ZP_03913369.1| DNA-directed RNA polymerase, alpha subunit [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
 gi|227352909|gb|EEJ43082.1| DNA-directed RNA polymerase, alpha subunit [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
          Length = 314

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 129/312 (41%), Positives = 191/312 (61%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E+      + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDG
Sbjct: 3   EFEKPN----IHNIEEDARYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE S++ GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+Q   D+EV
Sbjct: 59  VVHEFSTVDGVVEDVTQIILNLKKVVLAIESDDERSLEIDIQGPADVTAADLQGGADVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
           LNPD  I  +     + M +T  KG GY  A  ++   +  PIG++ +D++Y+PI++V+Y
Sbjct: 119 LNPDLHIATVAAGKSLHMTVTAVKGRGYTSADENKKLRDEMPIGVLAVDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R G   DYDKL+  I T+GSI   D+++L ++IL + LG+F++      E    +
Sbjct: 179 QVENTRIGARDDYDKLTFDIWTNGSIKPSDALSLGAKILAEHLGLFMDISPVAAEASVMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             + +  + +    +E+L+LSVRS NCL+   I  + +L  RTEADM+++ N GRKSL E
Sbjct: 239 EAEPVAASESDSAPIEDLDLSVRSYNCLKRAGINTILELTDRTEADMMKVRNLGRKSLDE 298

Query: 306 IKGVLGTMGLFL 317
           I+  L  M L  
Sbjct: 299 IQEKLTDMNLGF 310


>gi|262283556|ref|ZP_06061321.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sp.
           2_1_36FAA]
 gi|262260613|gb|EEY79314.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sp.
           2_1_36FAA]
          Length = 312

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 132/313 (42%), Positives = 196/313 (62%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILNIKGI +K      K + +   GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNIKGIAVKSYVQDEKMIELDVEGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A  +  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGARFKAVMTVNSGRGYVPADQNKRDDAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F +  E  K       V
Sbjct: 179 EPARVGSNDGFDKLTLEIMTNGTIIPEDALGLSARILTEHLDLFTDLTEVAKATDVMKEV 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                +  L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 DKSSDDHVLERTIEELDLSVRSYNCLKRAGINTVYDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLTDLGLGLKND 311


>gi|227509956|ref|ZP_03940005.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus brevis
           subsp. gravesensis ATCC 27305]
 gi|227190562|gb|EEI70629.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus brevis
           subsp. gravesensis ATCC 27305]
          Length = 319

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 143/314 (45%), Positives = 204/314 (64%), Gaps = 8/314 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E +N   ++ EPL RG+  TLGN+LRR L+SSL GAA+T++QID 
Sbjct: 6   EFEKPN----IHKIEETKNFGEVVVEPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDD 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE S+IKGV ED+T IILN+K I+LK+ G  D  + + I   GP  VTAGDIQ  +D+
Sbjct: 62  VLHEFSTIKGVVEDVTQIILNVKKISLKLDGPEDEEENLEIDVIGPADVTAGDIQGDSDV 121

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKV 183
            VLNPD  I  +   A   M LT ++G GYV A  ++      PIG++ +D++Y+PI++V
Sbjct: 122 TVLNPDLHIATVAEGATFHMRLTANRGRGYVSAVENKKRATEMPIGVLPVDSIYTPIERV 181

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VES R GQ  D+DKL++ I T+GSIT  ++V+LA++IL + L MF++  +  K  + 
Sbjct: 182 NYQVESTRVGQRDDFDKLTLDIWTNGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEI 241

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  +       L   +EEL+LSVRS NCL+   I  + +L ++TEADM+++ N GRKSL
Sbjct: 242 MVEKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTEKTEADMMKVRNLGRKSL 301

Query: 304 VEIKGVLGTMGLFL 317
            E+K  L  +GL L
Sbjct: 302 EEVKEKLAALGLSL 315


>gi|163752127|ref|ZP_02159332.1| DNA-directed RNA polymerase alpha subunit [Shewanella benthica
           KT99]
 gi|161327962|gb|EDP99137.1| DNA-directed RNA polymerase alpha subunit [Shewanella benthica
           KT99]
          Length = 329

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 142/331 (42%), Positives = 213/331 (64%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E ++P  +    + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLRPRLVN---IEQVNPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVVIEGKDEAMLTLSKSGAGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
             D+ ++NP+H+IC+L  +  + M + V +G GYVPA        ++ PIG + +DA +S
Sbjct: 118 DGDVTIMNPEHIICHLTGNNEISMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++YTVE+AR  Q  D DKL + + T+G++  E+++  A+ IL +QL  F+   +  
Sbjct: 178 PVARIAYTVEAARVEQRTDLDKLVIDMTTNGTLDPEEAIRRAATILAEQLDAFVELRDVT 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +        +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 EPE---QKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASL 325


>gi|300742030|ref|ZP_07072051.1| DNA-directed RNA polymerase, alpha subunit [Rothia dentocariosa
           M567]
 gi|300381215|gb|EFJ77777.1| DNA-directed RNA polymerase, alpha subunit [Rothia dentocariosa
           M567]
          Length = 330

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 121/329 (36%), Positives = 194/329 (58%), Gaps = 9/329 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V      NR+    EPL  GF +T+GN+LRR L+SS+ GAA+T+V+IDGVLH
Sbjct: 6   RPTLTEEVV----APNRSRFTIEPLEPGFGYTMGNSLRRTLLSSIPGAAVTSVRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T+IILN+K +++    D      + K+G G +TA DI+    +E+ NP
Sbjct: 62  EFSTVPGVTEDVTEIILNVKKLSISSENDEPVVAYLRKQGEGELTAADIEVPAGVEIHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           +  I  L+  A    EL + +G GYV A  ++T +  IG I +D++YSP+ KV+++V + 
Sbjct: 122 ELHIATLNAKANFNAELIIERGRGYVSAAQNKTGDAEIGRIPVDSIYSPVLKVTFSVNAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D L++ ++T  +I   D+VA A   L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDSLTLDVETKEAIAPRDAVASAGSTLVELFGLARELNVAAEGIEVGPSPADE 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +E+L +SVRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L
Sbjct: 242 SMAADLALPIEDLSMSVRSYNCLKREGIHTVGELVTRSEADLMDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             +GL L  + P + P     +A+ Y+D+
Sbjct: 302 HELGLALKDSPPGFEP-----VARAYDDE 325


>gi|227512889|ref|ZP_03942938.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus buchneri
           ATCC 11577]
 gi|227523017|ref|ZP_03953066.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus hilgardii
           ATCC 8290]
 gi|227083889|gb|EEI19201.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus buchneri
           ATCC 11577]
 gi|227089835|gb|EEI25147.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus hilgardii
           ATCC 8290]
          Length = 319

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 143/314 (45%), Positives = 204/314 (64%), Gaps = 8/314 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E +N   ++ EPL RG+  TLGN+LRR L+SSL GAA+T++QID 
Sbjct: 6   EFEKPN----IHKIEETKNFGEVVVEPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDD 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE S+IKGV ED+T IILN+K I+LK+ G  D  + + I   GP  VTAGDIQ  +D+
Sbjct: 62  VLHEFSTIKGVVEDVTQIILNVKKISLKLDGPEDEDENLEIDVIGPADVTAGDIQGDSDV 121

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKV 183
            VLNPD  I  +   A   M LT ++G GYV A  ++      PIG++ +D++Y+PI++V
Sbjct: 122 TVLNPDLHIATVAEGATFHMRLTANRGRGYVSAVENKKRATEMPIGVLPVDSIYTPIERV 181

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VES R GQ  D+DKL++ I T+GSIT  ++V+LA++IL + L MF++  +  K  + 
Sbjct: 182 NYQVESTRVGQRDDFDKLTLDIWTNGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEI 241

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  +       L   +EEL+LSVRS NCL+   I  + +L ++TEADM+++ N GRKSL
Sbjct: 242 MVEKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTEKTEADMMKVRNLGRKSL 301

Query: 304 VEIKGVLGTMGLFL 317
            E+K  L  +GL L
Sbjct: 302 EEVKEKLAALGLSL 315


>gi|289641138|ref|ZP_06473306.1| DNA-directed RNA polymerase, alpha subunit [Frankia symbiont of
           Datisca glomerata]
 gi|289509079|gb|EFD30010.1| DNA-directed RNA polymerase, alpha subunit [Frankia symbiont of
           Datisca glomerata]
          Length = 350

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 124/316 (39%), Positives = 188/316 (59%), Gaps = 4/316 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P  IE        E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLIE----ESISEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+TD+ILN+K + +    D    + + K+GPGVVTA DI     +EV + 
Sbjct: 62  EFSTVPGVKEDVTDLILNLKELVVSSENDEPTVMYLRKQGPGVVTAADIAPPAGVEVHSL 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  +  L+    + +ELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLALATLNDKGKLEIELTVERGRGYVSAAQNKQPGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  SI+  D++A A + L    G+        + V    +    
Sbjct: 182 RVEQRTDFDRLIVDVETKQSISPRDAMASAGKTLVGLFGLAQELNAEAEGVDIGPSAADA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EE++L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  L
Sbjct: 242 ALAADLALPIEEMDLTVRSYNCLKREGIHTIGELVSRSEADLLDIRNFGQKSIDEVKTKL 301

Query: 311 GTMGLFLGMNLPDWPP 326
             M L L  + P + P
Sbjct: 302 AAMALQLKDSPPGFDP 317


>gi|228478065|ref|ZP_04062676.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           salivarius SK126]
 gi|228250245|gb|EEK09498.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           salivarius SK126]
          Length = 312

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 129/313 (41%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EFEKP----IITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKG+ +K   +  K + +  +GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGLAVKSYVEDEKTIELDVQGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A ++  +TV+   GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIADGASLKATMTVATNRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  +  K        
Sbjct: 179 EPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTDVAKATDVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +     L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 EKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVHDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKND 311


>gi|54307566|ref|YP_128586.1| DNA-directed RNA polymerase subunit alpha [Photobacterium profundum
           SS9]
 gi|61215937|sp|Q6LV91|RPOA_PHOPR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|46911986|emb|CAG18784.1| putative DNA-directed RNA polymerase, alpha subunit [Photobacterium
           profundum SS9]
          Length = 329

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 218/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GVHED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI  
Sbjct: 58  EVEIDGVLHEYSTKEGVHEDILEILLNLKGLAIKVEGKDEVILTLNKSGAGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIANPEHVICHLTDDHAEISMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ +++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDRIAYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|182418825|ref|ZP_02950090.1| DNA-directed RNA polymerase, alpha subunit [Clostridium butyricum
           5521]
 gi|237666885|ref|ZP_04526870.1| DNA-directed RNA polymerase, alpha subunit [Clostridium butyricum
           E4 str. BoNT E BL5262]
 gi|182377322|gb|EDT74883.1| DNA-directed RNA polymerase, alpha subunit [Clostridium butyricum
           5521]
 gi|237658084|gb|EEP55639.1| DNA-directed RNA polymerase, alpha subunit [Clostridium butyricum
           E4 str. BoNT E BL5262]
          Length = 315

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 129/313 (41%), Positives = 207/313 (66%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  I   +   E+      + EPL RG+  TLGNALRR+L+SSL G A T+V+IDG
Sbjct: 3   EIEKP--IIECIESNEDGTYGKYVVEPLERGYGITLGNALRRILLSSLPGVAPTSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T++ILNIK + LKM+G+  K + I  +GPG VT  DI+T  D+EV
Sbjct: 61  VLHEFSTVQGVKEDVTELILNIKSLALKMNGEGPKVIYIDAKGPGEVTGADIKTDGDVEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N D  I  LD D  + MELTV+ G GYV    +++++ PI  I +D++Y+P+K+V++TV
Sbjct: 121 VNKDLHIATLDSDGRLYMELTVNNGRGYVTQNKNKSDDLPISSIAVDSIYTPVKRVNFTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ++ R GQ+ DYDKL++ I T+G+I  +++++L+++IL +   +F++  +   +++  +  
Sbjct: 181 DNTRVGQITDYDKLTLEIWTNGTIRIDEAISLSAKILIEHFKLFMSLTDNTNDIEVMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   VEEL+LSVRS NCL+   I  + +L  ++  DM+++ N G+KSL E++
Sbjct: 241 EEDKKEKVLEMTVEELDLSVRSYNCLKRAGINTVQELATKSMDDMMKVRNLGKKSLEEVE 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L ++
Sbjct: 301 RKLKELGLCLKLS 313


>gi|288904299|ref|YP_003429520.1| RNA polymerase (alpha subunit) [Streptococcus gallolyticus UCN34]
 gi|306830328|ref|ZP_07463499.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325977278|ref|YP_004286994.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
 gi|288731024|emb|CBI12568.1| RNA polymerase (alpha subunit) [Streptococcus gallolyticus UCN34]
 gi|304427575|gb|EFM30676.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325177206|emb|CBZ47250.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
          Length = 312

 Score =  344 bits (882), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 132/313 (42%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EFEKP----IITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI T +D+E+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDSDVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +     ++  +TV+K  GYVPA+ ++ E+ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKEDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K        
Sbjct: 179 EPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKNTDVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +     L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 EKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKND 311


>gi|61215897|sp|Q6AD21|RPOA_LEIXX RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 332

 Score =  343 bits (881), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 120/307 (39%), Positives = 184/307 (59%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                 E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S++ GV
Sbjct: 10  TEENISEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFSTVPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+IILNIKG+ +    D      + K G G VTA DI     +E+ NP+ VI  L+
Sbjct: 70  KEDVTEIILNIKGLVVSSEHDEPITAYLRKTGAGQVTAADISAPAGVEIHNPELVIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
             A   +ELT+ +G GYV A+ +R E    G I ID++YSP+ KV+Y VE+ R G+  D+
Sbjct: 130 DKAKFEVELTIERGRGYVSAQQNRNEYSEAGQIPIDSIYSPVLKVTYRVEATRAGERTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           D+L + ++T  +I+  D++A A R L +  G+        + ++          +  L  
Sbjct: 190 DRLVVDVETKPAISPRDAIASAGRTLVELFGLARELNSAAEGIEIGPAPVDQVLSSELSM 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L+LSVRS NCL+ E I  + +L+  +E  ++ + NFG+KS+ E+K  L  MGL L 
Sbjct: 250 PIEDLDLSVRSYNCLKREGINTVSELVSLSETQLMNIRNFGQKSVDEVKDKLTEMGLSLK 309

Query: 319 MNLPDWP 325
            ++P + 
Sbjct: 310 DSVPGFD 316


>gi|42812|emb|CAA37838.1| unnamed protein product [Escherichia coli]
          Length = 329

 Score =  343 bits (881), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALR +L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRCILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|94500967|ref|ZP_01307492.1| DNA-directed RNA polymerase alpha subunit [Oceanobacter sp. RED65]
 gi|94426907|gb|EAT11890.1| DNA-directed RNA polymerase alpha subunit [Oceanobacter sp. RED65]
          Length = 333

 Score =  343 bits (881), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 145/336 (43%), Positives = 220/336 (65%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  E + P +I+   +      +  +  EPL RGF HTLG ALRR+L+SS+ GAAI 
Sbjct: 1   MQRSVNEFLTPRHIQVEQVSN---TQAKVTLEPLERGFGHTLGAALRRILLSSMPGAAIV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ +I+LN+KG+ +++       +T+ K G G VTA DIQ 
Sbjct: 58  EVEIDGVLHEYSTIEGVQEDVIEILLNLKGVAVRLHERDEAFLTLHKTGAGQVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
            + +E+ NP+HVI NL     ++M + V+ G GY   +    +  E   IG + +DA YS
Sbjct: 118 DHGVEIANPEHVIANLSDKGELKMTIKVAAGRGYETVESRNQNEEETKAIGKLQLDATYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+K+V+Y VE+AR  Q  D DKL + ++T+G+I  E+++  ++ ILQ QL +F++    +
Sbjct: 178 PVKRVAYGVENARVEQRTDLDKLVIDLETNGTIEPEEAIRRSATILQQQLAVFVDL---E 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E + +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 235 NEAEPEPEEQEDEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM+L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMHLENWPPASLKKDDK 330


>gi|322388376|ref|ZP_08061979.1| DNA-directed RNA polymerase subunit alpha [Streptococcus infantis
           ATCC 700779]
 gi|321140689|gb|EFX36191.1| DNA-directed RNA polymerase subunit alpha [Streptococcus infantis
           ATCC 700779]
          Length = 311

 Score =  343 bits (881), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 135/313 (43%), Positives = 197/313 (62%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSIDIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILNIKGI +K      K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNIKGIAVKSYVKDEKTIELDVEGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A  +  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGASFKATMTVNTGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  K  +     
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSAEVMKEA 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            +   +  L + +EEL+LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E+K
Sbjct: 239 DTESDDRILERTIEELDLSVRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L   
Sbjct: 299 LKLIDLGLGLKDK 311


>gi|88812732|ref|ZP_01127978.1| DNA-directed RNA polymerase, alpha subunit [Nitrococcus mobilis
           Nb-231]
 gi|88789970|gb|EAR21091.1| DNA-directed RNA polymerase, alpha subunit [Nitrococcus mobilis
           Nb-231]
          Length = 333

 Score =  343 bits (881), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 141/337 (41%), Positives = 215/337 (63%), Gaps = 7/337 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q  +++ ++P  +    L    +   ++  EPL RGF HTLGNALRRVL+SS+ G A+ 
Sbjct: 1   MQGQFKDFLRPRLVGVEALS---DRHAMITLEPLERGFGHTLGNALRRVLLSSMPGYAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GVLHE ++I+GV ED+ DI+LN+K + +++       + + K+GPG+VTA DI  
Sbjct: 58  EVEIEGVLHEYTAIEGVQEDVVDILLNLKNLAVRLHSKDTATLHLSKQGPGLVTAADIGI 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSP 179
            +D+E+ NP+  I NL   + + M L +++G GY P        E  PIG + +DA YSP
Sbjct: 118 DHDVEIKNPELAIANLTKASEINMTLHIARGRGYEPVTTRGEHDEERPIGRLQLDASYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +++V+Y VESAR  Q  D DKL M I+T+G +  E++V  A+ +L+DQL +F++ E    
Sbjct: 178 VRRVAYNVESARVEQRTDLDKLVMDIETNGVLEPEEAVRFAAGLLRDQLSVFVDLE--GG 235

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           E  ED    +   +P LL+ +++LEL+VRS NCL+ ENI  +GDL+Q+TE ++L+  N G
Sbjct: 236 EEAEDQERTAPEVDPVLLRSIDDLELTVRSANCLKAENIHCVGDLVQKTEVELLKTPNLG 295

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKY 336
           +KSL EIK VL   GL LGM L +WPP   ++  +  
Sbjct: 296 KKSLNEIKEVLAQHGLALGMRLENWPPRGYDDKDRAI 332


>gi|296875379|ref|ZP_06899453.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           parasanguinis ATCC 15912]
 gi|312867033|ref|ZP_07727244.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           parasanguinis F0405]
 gi|322390685|ref|ZP_08064199.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           parasanguinis ATCC 903]
 gi|296433572|gb|EFH19345.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           parasanguinis ATCC 15912]
 gi|311097515|gb|EFQ55748.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           parasanguinis F0405]
 gi|321142658|gb|EFX38122.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           parasanguinis ATCC 903]
          Length = 312

 Score =  343 bits (881), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 132/313 (42%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++  + + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKDYGVFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILN+KGI +K      K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNVKGIAVKSYVQDEKIIELDVEGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A ++  LTV+ G GYVPA  ++ ++ P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGASLKATLTVNSGRGYVPADQNKKDDAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E          V
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLFTNLTEIAIATDVMKEV 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            +   +  L + +EEL+LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E+K
Sbjct: 239 DTTSDDRILERTIEELDLSVRSYNCLKRAGINTVYDLTEKSEAEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 IKLADLGLGLKND 311


>gi|310659474|ref|YP_003937195.1| RNA polymerase subunit alpha [Clostridium sticklandii DSM 519]
 gi|308826252|emb|CBH22290.1| RNA polymerase, alpha subunit [Clostridium sticklandii]
          Length = 313

 Score =  343 bits (881), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 129/311 (41%), Positives = 201/311 (64%), Gaps = 4/311 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP+    I + + +EN      EPL RGF  T+GN+LRRVL+SSL G A+T++++DG
Sbjct: 3   EIEKPS----IEVLELKENYGKFALEPLERGFGITVGNSLRRVLLSSLPGVAVTSIKVDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T++IL +K +++KM  D  + + I   G GV+ AGDI    D+E+
Sbjct: 59  VLHEFSTIPGVKEDVTELILTLKELSMKMDSDGARTLKIEHTGEGVIKAGDIICPPDVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D  I  L  DA + ME+ V KG GYV A+++++++ PIG+I +D++Y+P+ KVSY  
Sbjct: 119 LNKDLHIATLSEDAKLYMEINVDKGRGYVSAENNKSDDMPIGVIPVDSIYTPVHKVSYLT 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G   D+++L + + TDGSI  ++ V+L ++IL + L +FI+  +   EV+  +  
Sbjct: 179 ENTRVGTRTDFERLVLEVWTDGSIGAQEGVSLGAKILVEHLNLFIDLTDHLGEVELMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +      AL   +EEL+LSVRS NCL+   I  + +L ++TE DM+++ N G+KSL E+ 
Sbjct: 239 EEDKKEKALEMTIEELDLSVRSYNCLKRAGINTVEELTEKTEDDMMKVRNLGKKSLEEVI 298

Query: 308 GVLGTMGLFLG 318
             L  +G  L 
Sbjct: 299 QKLEELGFSLK 309


>gi|312862356|ref|ZP_07722599.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           vestibularis F0396]
 gi|322515893|ref|ZP_08068835.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           vestibularis ATCC 49124]
 gi|311101999|gb|EFQ60199.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           vestibularis F0396]
 gi|322125680|gb|EFX97007.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           vestibularis ATCC 49124]
          Length = 312

 Score =  343 bits (881), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 129/313 (41%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EFEKP----IITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKG+ +K   +  K + +  +GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGLAVKSYVEDEKTIELDVQGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A ++  +TV+   GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTISEGASLKATMTVATNRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  +  K        
Sbjct: 179 EPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTDVAKATDVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +     L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 EKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVHDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKND 311


>gi|320548029|ref|ZP_08042309.1| DNA-directed RNA polymerase subunit alpha [Streptococcus equinus
           ATCC 9812]
 gi|320447271|gb|EFW88034.1| DNA-directed RNA polymerase subunit alpha [Streptococcus equinus
           ATCC 9812]
          Length = 312

 Score =  343 bits (881), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 131/313 (41%), Positives = 198/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EFEKP----IITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI T +D+E+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDSDVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N DH +  +     ++  +TV+K  GYVPA+ ++ E+ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNTDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKEDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K        
Sbjct: 179 EPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKNTDVMKEA 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +     L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 EKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKND 311


>gi|29653615|ref|NP_819307.1| DNA-directed RNA polymerase subunit alpha [Coxiella burnetii RSA
           493]
 gi|154706094|ref|YP_001425157.1| DNA-directed RNA polymerase subunit alpha [Coxiella burnetii Dugway
           5J108-111]
 gi|161349357|ref|ZP_02096741.1| DNA-directed RNA polymerase, alpha subunit [Coxiella burnetii 'MSU
           Goat Q177']
 gi|161830881|ref|YP_001596210.1| DNA-directed RNA polymerase subunit alpha [Coxiella burnetii RSA
           331]
 gi|212213225|ref|YP_002304161.1| DNA-directed RNA polymerase subunit alpha [Coxiella burnetii
           CbuG_Q212]
 gi|212218099|ref|YP_002304886.1| DNA-directed RNA polymerase subunit alpha [Coxiella burnetii
           CbuK_Q154]
 gi|41688670|sp|Q83EQ2|RPOA_COXBU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|189043837|sp|A9KD06|RPOA_COXBN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|189043838|sp|A9NAZ5|RPOA_COXBR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238057755|sp|B6J5F7|RPOA_COXB1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238057756|sp|B6J238|RPOA_COXB2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|29540877|gb|AAO89821.1| DNA-directed RNA polymerase alpha chain [Coxiella burnetii RSA 493]
 gi|154355380|gb|ABS76842.1| DNA-directed RNA polymerase alpha chain [Coxiella burnetii Dugway
           5J108-111]
 gi|161762748|gb|ABX78390.1| DNA-directed RNA polymerase, alpha subunit [Coxiella burnetii RSA
           331]
 gi|164601573|gb|EDQ95164.1| DNA-directed RNA polymerase, alpha subunit [Coxiella burnetii 'MSU
           Goat Q177']
 gi|212011635|gb|ACJ19016.1| DNA-directed RNA polymerase alpha chain [Coxiella burnetii
           CbuG_Q212]
 gi|212012361|gb|ACJ19741.1| DNA-directed RNA polymerase alpha chain [Coxiella burnetii
           CbuK_Q154]
          Length = 327

 Score =  343 bits (881), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 149/332 (44%), Positives = 219/332 (65%), Gaps = 8/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q   +  + P NI+   +         ++ EPL RGF HTLGNALRR+L+SS+ GAAI 
Sbjct: 1   MQNVLKSFLTPKNIQVQTIS---PCHFRILLEPLERGFGHTLGNALRRILLSSMPGAAIV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE SSI+GV ED+ D++LN+KG+ +K+ G    ++T+ K+G G VTAGDIQT
Sbjct: 58  QAEIDGVLHEYSSIEGVREDVVDVLLNLKGVAIKLEGREDAKLTLHKKGAGTVTAGDIQT 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI--GLITIDALYSP 179
            + ++++NPDHVI ++  D  + M L  + G GY P+    T +     GL+ +DA YSP
Sbjct: 118 ESGVKIVNPDHVIAHITKDGEINMTLKAAMGRGYEPSSARSTGDQSRSVGLLLLDASYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I++V+Y+VE+AR  +  D DKL + ++TDG++  E+++  A+ +LQ QL  F++    K+
Sbjct: 178 IRRVTYSVENARVEKRTDLDKLIIDLETDGTLDPEEAIRFAAAVLQHQLAAFVDL---KQ 234

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           E   D   K    NP LL+ VE+LEL+VR+ NCL+ E+I Y+GDL+Q TE D+L+  N G
Sbjct: 235 ESDRDGGGKEGKVNPLLLRPVEDLELTVRAANCLKAESINYIGDLVQCTENDLLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +KSL+EIK VL   GL LGM+L  WPP  + +
Sbjct: 295 KKSLLEIKSVLAQKGLSLGMDLKGWPPADLTD 326


>gi|322374071|ref|ZP_08048605.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus sp. C150]
 gi|321277037|gb|EFX54108.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus sp. C150]
          Length = 312

 Score =  343 bits (881), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 128/313 (40%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EFEKP----IITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILN+KG+ +K   +  K + +  +GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNVKGLAVKSYVEDEKTIELDVQGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A ++  +TV+   GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIADGASLKATMTVATNRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  +  K        
Sbjct: 179 EPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTDVAKATDVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +     L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 EKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVHDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKND 311


>gi|294142908|ref|YP_003558886.1| DNA-directed RNA polymerase subunit alpha [Shewanella violacea
           DSS12]
 gi|12230609|sp|Q9S0Q8|RPOA_SHEVD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|5913932|dbj|BAA84525.1| RNA polymerase alpha subunit [Shewanella violacea]
 gi|293329377|dbj|BAJ04108.1| DNA-directed RNA polymerase, alpha subunit [Shewanella violacea
           DSS12]
          Length = 329

 Score =  343 bits (881), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 141/331 (42%), Positives = 213/331 (64%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E ++P  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLRPRLVD---IEQVNPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGLAVVIEGKDEAMLTLSKSGAGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
             D+ ++NP+HV+C+L  +  + M + V +G GYVPA        ++ PIG + +DA +S
Sbjct: 118 DGDVTIMNPEHVVCHLTGNNEISMRIRVERGRGYVPASARAQTEDDDRPIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VE+AR  Q  D DKL + + T+G++  E+++  A+ IL +QL  F+   +  
Sbjct: 178 PVARIAYNVEAARVEQRTDLDKLVIDMTTNGTLDPEEAIRRAATILAEQLDAFVELRDVT 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +        +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 EPE---QKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASL 325


>gi|145588267|ref|YP_001154864.1| DNA-directed RNA polymerase subunit alpha [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
 gi|189043841|sp|A4SUY6|RPOA_POLSQ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|145046673|gb|ABP33300.1| DNA-directed RNA polymerase subunit alpha [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
          Length = 326

 Score =  343 bits (881), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 151/333 (45%), Positives = 212/333 (63%), Gaps = 10/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N   L+KP  I    L     N+  ++ EP  RG+ HTLGNALRRVL+SS+ G A T
Sbjct: 1   MQTN---LLKPKIISVEAL---TANQAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GV+HE S++ GV ED+ +++LN+KGI  K+       + + K GPGVVTA DI  
Sbjct: 55  EVAIAGVVHEYSTLDGVQEDVVNLLLNLKGIVFKLQSRDEVTINLRKEGPGVVTAKDIDL 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYS 178
            +D+E++NPDHVI +L     + M++ V KG GYVP    +  ++     G I +DA +S
Sbjct: 115 PHDVEIMNPDHVIAHLSAGGKLDMQIKVEKGRGYVPGNVRQYNDETTKIIGRIVLDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +VSY VESAR  Q  D D+L MTI+T+G ++ E+++  A+ IL DQL +F    E  
Sbjct: 175 PVSRVSYAVESARVEQRTDLDRLVMTIETNGVLSPEEAIRQAASILVDQLVVFAAL-ESS 233

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +   +    +S   +P L++ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 234 EVSGDLAPSRSSMVDPMLMRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNL 293

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL   GL LGM L  WPP ++E+
Sbjct: 294 GRKSLNEIKDVLAARGLSLGMKLESWPPANLEK 326


>gi|322391224|ref|ZP_08064696.1| DNA-directed RNA polymerase subunit alpha [Streptococcus peroris
           ATCC 700780]
 gi|321145977|gb|EFX41366.1| DNA-directed RNA polymerase subunit alpha [Streptococcus peroris
           ATCC 700780]
          Length = 311

 Score =  343 bits (881), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 135/313 (43%), Positives = 197/313 (62%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSIDIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILNIKGI +K      K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNIKGIAVKSYVKDEKTIELDVEGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A  +  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGASFKATMTVNTGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  K  +     
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSTEVMKEA 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            +   +  L + +EEL+LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E+K
Sbjct: 239 DTESDDRILERTIEELDLSVRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L   
Sbjct: 299 LKLIDLGLGLKDK 311


>gi|157150884|ref|YP_001451209.1| DNA-directed RNA polymerase subunit alpha [Streptococcus gordonii
           str. Challis substr. CH1]
 gi|172045615|sp|A8AZJ9|RPOA_STRGC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|157075678|gb|ABV10361.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus gordonii
           str. Challis substr. CH1]
          Length = 312

 Score =  343 bits (881), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 132/313 (42%), Positives = 196/313 (62%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILNIKGI +K      K + +   GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNIKGIAVKSYVQDEKMIELDVEGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A  +  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGARFKAVMTVNSGRGYVPADQNKRDDAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F +  E  K       V
Sbjct: 179 EPARVGSNDGFDKLTLEIMTNGTIIPEDALGLSARILTEHLDLFTDLTEVAKATDVMKEV 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                +  L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 DKSSDDHVLERTIEELDLSVRSYNCLKRAGINTVYDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 IKLTDLGLGLKND 311


>gi|227883427|ref|ZP_04001232.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli 83972]
 gi|227839571|gb|EEJ50037.1| DNA-directed RNA polymerase subunit alpha [Escherichia coli 83972]
          Length = 329

 Score =  343 bits (880), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L + PP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENCPPASIAD 328


>gi|116493137|ref|YP_804872.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Pediococcus pentosaceus ATCC 25745]
 gi|122265399|sp|Q03EE2|RPOA_PEDPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116103287|gb|ABJ68430.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus
           ATCC 25745]
          Length = 314

 Score =  343 bits (880), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 137/312 (43%), Positives = 194/312 (62%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E +N    + EPL RG+  TLGN+LRR+L+SSL GAAIT+VQID 
Sbjct: 3   EFEKPK----IHKIDENDNYGRFVIEPLERGYGTTLGNSLRRILLSSLPGAAITSVQIDS 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +
Sbjct: 59  VLHEFSTIEGVVEDVTQIILNLKKVSLKIESDEDKTLEINVAGPANVTAGDIMGDGDVVI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSY 185
           LNP+  IC +         LT   G GY  A  ++    + PIG++ ID++Y+PI++V+Y
Sbjct: 119 LNPELPICTVAEGTTFHAVLTADTGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R GQ  DYDKL++ I TDGSIT  ++ +L+++IL + L +F+N  +  KE +  +
Sbjct: 179 QVENTRVGQRDDYDKLTLDIWTDGSITPSEATSLSAKILTEHLAIFVNLNDQAKETEIMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   +EEL+LSVRS NCL+   I  + +L  RT+A M+++ N GRKSLVE
Sbjct: 239 EKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINSVQELTDRTDAQMMKVRNLGRKSLVE 298

Query: 306 IKGVLGTMGLFL 317
           I+  L  +GL  
Sbjct: 299 IQEKLSLLGLGF 310


>gi|118595310|ref|ZP_01552657.1| DNA-directed RNA polymerase subunit alpha [Methylophilales
           bacterium HTCC2181]
 gi|118441088|gb|EAV47715.1| DNA-directed RNA polymerase subunit alpha [Methylophilales
           bacterium HTCC2181]
          Length = 328

 Score =  343 bits (880), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 213/334 (63%), Gaps = 9/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  +   ++  +   R  ++ EP+ RGF  TLGNALRRVL+SS+ G AIT
Sbjct: 1   MQNSPTEYLKPRIVNVDIVNSQ---RAKVVLEPMERGFGFTLGNALRRVLLSSIPGYAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGV+HE S+++GV ED+ D++LN+K + LK+   +   + + K   G VT  D   
Sbjct: 58  EVKIDGVVHEYSTLEGVQEDVVDVLLNLKKVALKIHEGTEATIRLSKSEEGPVTVADFDV 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYS 178
            +D+EV+NP+HVI +L+    + +E  V  G GY P    R    E+  IG I IDA +S
Sbjct: 118 GHDVEVVNPEHVIAHLNKGGKLNIEAKVEMGRGYQPVPQRRKGPQEDSTIGYIMIDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI KVSY VESAR  Q  D D+L + ++T+G +  E ++  A+RIL  QL +F N E   
Sbjct: 178 PINKVSYFVESARVEQRTDLDRLILDVETNGVVDAEQAIRDAARILMGQLSVFANLESEL 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            EV+     ++   +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQR E+D+L+  N 
Sbjct: 238 TEVEV---QQAPQIDPVLLRPVDDLELTVRSANCLKAESIYYIGDLIQRNESDLLKAPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEEL 332
           GRKSL EIK +L T GL LGM + +WPP  +E++
Sbjct: 295 GRKSLNEIKDILATKGLSLGMKVENWPPAGVEKV 328


>gi|323357346|ref|YP_004223742.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Microbacterium testaceum StLB037]
 gi|323273717|dbj|BAJ73862.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Microbacterium testaceum StLB037]
          Length = 329

 Score =  343 bits (880), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 123/307 (40%), Positives = 183/307 (59%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
              +  E R+  + EPL  GF +T+GNALRR L+SS+ GAA+T+++IDGVLHE S+I GV
Sbjct: 10  TEEKVGEFRSRFVIEPLEPGFGYTIGNALRRSLLSSIPGAAVTSIRIDGVLHEFSTIPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+IILNIK + +    D      + K G G VTA DI     +EV NPD VI  L+
Sbjct: 70  KEDVTEIILNIKQLVVSSERDEPITAYLRKTGSGEVTAADISAPAGVEVHNPDLVIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
             A   +ELT+ +G GYV A  +R E    G I ID++YSP+ KVSY VE+ R G+  D+
Sbjct: 130 DTAKFELELTIERGRGYVSATQNRNEYAEAGQIPIDSIYSPVLKVSYRVEATRAGERTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + +++  SI   D+VA A R L +  G+        + ++          +  L  
Sbjct: 190 DKLVLDVESKPSIAPRDAVASAGRTLTELFGLARELNVEAEGIEIGPAPVETVLSNELSM 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L+LSVRS NCL+ E I  + +L+  +E  ++ + NFG+KS+ E++  L ++GL L 
Sbjct: 250 PIEDLDLSVRSYNCLKREGINTVSELVALSETQLMNIRNFGQKSVDEVRDKLVSLGLSLK 309

Query: 319 MNLPDWP 325
            ++P + 
Sbjct: 310 DSVPGFD 316


>gi|110833283|ref|YP_692142.1| DNA-directed RNA polymerase subunit alpha [Alcanivorax borkumensis
           SK2]
 gi|119366659|sp|Q0VSH8|RPOA_ALCBS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|110646394|emb|CAL15870.1| DNA-directed RNA polymerase, alpha subunit [Alcanivorax borkumensis
           SK2]
          Length = 335

 Score =  343 bits (880), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 150/332 (45%), Positives = 221/332 (66%), Gaps = 9/332 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             + + P +I    +    +    ++ EPL RGF HTLG ALRR+L+SS+ G AIT V+I
Sbjct: 4   VNDFLTPRSI---AVNAINQTHAKVVLEPLERGFGHTLGTALRRILISSMPGCAITEVEI 60

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGV HE SSI+GV ED+ +I+LN+KG+ LKM       + + K+GPGVVTA DIQ  + +
Sbjct: 61  DGVQHEYSSIEGVQEDVINILLNLKGVALKMEDSEETTLELVKKGPGVVTANDIQRDHSV 120

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKK 182
           E++NPDH+IC +  D  +R++L V KG GYV A   ++E+D     G + +DA YSP+++
Sbjct: 121 EIVNPDHLICTITGDTELRVKLKVQKGRGYVAADSRQSEDDETRGIGRLQLDASYSPVRR 180

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+Y VE+AR  Q  D DKL + ++TDG+I  E+++  A+ ILQ Q+ +F++ E+  K   
Sbjct: 181 VAYVVEAARVEQRTDLDKLVIDLETDGTIEPEEAIRRAATILQQQIAVFVDLEQDAKP-- 238

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
            +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G+KS
Sbjct: 239 -EPKQEREEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLGKKS 297

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           L EIK VL + GL LGM L +WPP S+ +  +
Sbjct: 298 LTEIKDVLASKGLSLGMRLENWPPVSLRDDDR 329


>gi|90416841|ref|ZP_01224770.1| DNA-directed RNA polymerase alpha chain [marine gamma
           proteobacterium HTCC2207]
 gi|90331188|gb|EAS46432.1| DNA-directed RNA polymerase alpha chain [marine gamma
           proteobacterium HTCC2207]
          Length = 331

 Score =  343 bits (880), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 148/332 (44%), Positives = 213/332 (64%), Gaps = 8/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P NI+             ++ EPL RGF HTLGNALRR+L+SS+ G AI 
Sbjct: 1   MQNSANEFLTPRNIDVT---SYSPTHAKVVLEPLERGFGHTLGNALRRILLSSMSGCAIV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GV HE S+I+GVHED+  I+LN+KG+ + M G     V++  +GP VVTAGDI+ 
Sbjct: 58  EVEIEGVEHEYSAIEGVHEDVMGILLNLKGVAVVMEGRDETTVSLSVKGPCVVTAGDIEV 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSP 179
            + +EV+NPDHVI  +     + ++L + +G GY P+       +N  IG + +DA +SP
Sbjct: 118 DSHVEVINPDHVIATISDKCTLNIQLRIERGRGYQPSDARISDEDNRTIGRLQLDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I KVSY+VE+AR     D DKL + ++T+G+I  E+S+  A+ ILQ Q+ +F+N E    
Sbjct: 178 IHKVSYSVENARVENRTDLDKLVLELETNGTIDPEESIRRAATILQQQMAVFVNLEGETA 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
                   K    +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N G
Sbjct: 238 AE---PEEKEEEIDPILLRPVDDLELTVRSANCLKAESIYYIGDLIQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +KSL EIK VL + GL LGM L +WPP S++ 
Sbjct: 295 KKSLTEIKDVLASRGLSLGMRLENWPPASLKS 326


>gi|171462905|ref|YP_001797018.1| DNA-directed RNA polymerase, alpha subunit [Polynucleobacter
           necessarius subsp. necessarius STIR1]
 gi|238692836|sp|B1XSS7|RPOA_POLNS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|171192443|gb|ACB43404.1| DNA-directed RNA polymerase, alpha subunit [Polynucleobacter
           necessarius subsp. necessarius STIR1]
          Length = 326

 Score =  343 bits (880), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 151/333 (45%), Positives = 212/333 (63%), Gaps = 10/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N   L+KP  I    L     N+  ++ EP  RG+ HTLGNALRRVL+SS+ G A T
Sbjct: 1   MQTN---LLKPKIISVEAL---TANQAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GV+HE S++ GV ED+ +++LN+KGI  K+       + + K GPGVVTA DI  
Sbjct: 55  EVAIAGVVHEYSTLDGVQEDVVNLLLNLKGIVFKLQSRDEVIINLRKEGPGVVTAKDIDL 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYS 178
            +D+E++NPDHVI +L     + M++ V KG GYVP    +  ++     G I +DA +S
Sbjct: 115 PHDVEIMNPDHVIAHLSAGGKLDMQIKVEKGRGYVPGNVRQYNDEATKIIGHIVLDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +VSY VESAR  Q  D D+L MTI+T+G ++ E+++  A+ IL DQL +F    E  
Sbjct: 175 PVSRVSYAVESARVEQRTDLDRLVMTIETNGVLSPEEAIRQAASILVDQLVVFAAL-ESS 233

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +   +    +S   +P L++ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 234 EVSGDLAPSRSSMVDPMLMRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNL 293

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL   GL LGM L  WPP ++E+
Sbjct: 294 GRKSLNEIKDVLAARGLSLGMKLESWPPANLEK 326


>gi|158520750|ref|YP_001528620.1| DNA-directed RNA polymerase, alpha subunit [Desulfococcus
           oleovorans Hxd3]
 gi|238686889|sp|A8ZV82|RPOA_DESOH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158509576|gb|ABW66543.1| DNA-directed RNA polymerase, alpha subunit [Desulfococcus
           oleovorans Hxd3]
          Length = 339

 Score =  343 bits (880), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 151/333 (45%), Positives = 223/333 (66%), Gaps = 6/333 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++  NWQE+I+P+ I+   +          I EPL RGF  T+GNALRR+++SSL GAAI
Sbjct: 5   LMYMNWQEMIQPDKIQ---VEAATPFYGKFICEPLGRGFGITIGNALRRIIISSLHGAAI 61

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V+ID V+HE S+++GV ED+++IILN+K + LK S  + K + I   GPGVVTAGDI 
Sbjct: 62  TSVKIDNVMHEYSTVEGVLEDVSEIILNLKEVRLKTSTAAAKTIRIDAAGPGVVTAGDIA 121

Query: 121 TVND-IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
           + +  +E+LNP+  I  L   A ++ME+TV  G GY  A+ ++ E  P+  I IDA++SP
Sbjct: 122 SPDGRVEILNPESHIATLSEGATLKMEMTVKVGRGYALAEANKDEETPVNTIPIDAMFSP 181

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I++V+Y V ++R  Q  D+DKL++ + TDGS+  ED+VA A++I+++Q+ +FINF+E  +
Sbjct: 182 IRRVNYVVGNSRVKQKTDFDKLTLEVWTDGSVLPEDAVAFAAKIMKEQMNVFINFDESAE 241

Query: 240 EVKEDINVKS--LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
                    S    FN  L + V ELELSVRS+NCL+   I  +  L+Q+TE++ML+  N
Sbjct: 242 PEHAGRKDDSGGKVFNENLYRSVNELELSVRSSNCLKNAEIDKLYQLVQKTESEMLKTKN 301

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           FGRKSL EIK +L  MGL LGM+L  + P + +
Sbjct: 302 FGRKSLNEIKELLAEMGLSLGMDLEGFVPPAED 334


>gi|7388086|sp|P74963|RPOA_SHESP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|1565189|dbj|BAA11840.1| RNA polymerase alpha subunit [Shewanella sp. DB6705]
          Length = 328

 Score =  343 bits (880), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 149/333 (44%), Positives = 218/333 (65%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E ++P  ++   + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLRPRLVD---IEQISSTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SSI+GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI  
Sbjct: 58  EVEIDGVLHEYSSIEGVQEDVLEILLNLKGLAIKLEGKDEALLTLTKSGTGPVLAGDITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
             D+E++NP+HVI NL   A + M + V+KG GYVPA        E  PIG + +DA +S
Sbjct: 118 DGDVEIINPEHVIRNLTGQADISMRIRVAKGRGYVPASTRIQSDDEERPIGRLLVDAAFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y VESAR  Q  + DKL + ++T+G++  E+++  A+ IL +QL  F++  +  
Sbjct: 178 PVSRIAYNVESARVEQRTNLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVT 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +        +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 EPE---QKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 327


>gi|319945810|ref|ZP_08020060.1| DNA-directed RNA polymerase subunit alpha [Streptococcus australis
           ATCC 700641]
 gi|319747875|gb|EFW00119.1| DNA-directed RNA polymerase subunit alpha [Streptococcus australis
           ATCC 700641]
          Length = 312

 Score =  343 bits (880), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 130/313 (41%), Positives = 197/313 (62%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++  + + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKDYGVFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILN+KGI +K      K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNVKGIAVKSYVQDEKIIELDVEGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   +  +  LTV+ G GYVPA  ++ ++ P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGSSFKATLTVNSGRGYVPADQNKKDDAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E          V
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLFTNLTEIAIATDVMKEV 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            +   +  L + +EEL+LSVRS NCL+   I  + DL +++E +M+++ N GRKSL E+K
Sbjct: 239 DTASDDRVLERTIEELDLSVRSYNCLKRAGINTVYDLTEKSEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKND 311


>gi|317050555|ref|YP_004111671.1| DNA-directed RNA polymerase subunit alpha [Desulfurispirillum
           indicum S5]
 gi|316945639|gb|ADU65115.1| DNA-directed RNA polymerase, alpha subunit [Desulfurispirillum
           indicum S5]
          Length = 354

 Score =  343 bits (880), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 151/341 (44%), Positives = 214/341 (62%), Gaps = 5/341 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  NW E+I+P  +         ++    IAEPL RGF  TLGNALRRVL+SSL GAA+T
Sbjct: 1   MMMNWNEVIRPRAL-VCDTKTATDSYGKFIAEPLERGFGITLGNALRRVLLSSLEGAAVT 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           A++ID VLHE S++ GV ED+TDIILN+K +  K+     K +T+     G VTA  ++ 
Sbjct: 60  AIRIDNVLHEFSTVSGVVEDVTDIILNVKQLRFKLLSPGEKVLTLKASSVGPVTAASLEC 119

Query: 122 VNDIEVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             D++VLN D VI  L   DA + MEL V  G  Y  A+ ++  +D I +I +D+L++P+
Sbjct: 120 PPDVKVLNSDCVIATLGREDAELNMELRVDIGRAYRLAEENKKADDVIDMIPVDSLFNPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KV+YTVE AR  Q  ++DKL + + TDGS+  ED+VA A++I++DQL +FINFE+ ++ 
Sbjct: 180 VKVNYTVEQARVVQDTNFDKLILEVWTDGSVKPEDAVAFAAKIIKDQLAIFINFEDVEEP 239

Query: 241 VK-EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           V  E +   S      L K VEELELSVRS NCL   +I  + DL+ R+E ++L+  NFG
Sbjct: 240 VALESVEDGSEELFALLSKSVEELELSVRSYNCLNNIDIRTIADLVARSENELLKTKNFG 299

Query: 300 RKSLVEIKGVLGTMGLFLGMNLP--DWPPESIEELAKKYED 338
           +KSL+EIK +L  M L LGM+L    + P    E   + + 
Sbjct: 300 KKSLLEIKEILKEMNLTLGMDLDALGYQPVVAAESGDEQDS 340


>gi|225016257|ref|ZP_03705449.1| hypothetical protein CLOSTMETH_00160 [Clostridium methylpentosum
           DSM 5476]
 gi|224950932|gb|EEG32141.1| hypothetical protein CLOSTMETH_00160 [Clostridium methylpentosum
           DSM 5476]
          Length = 316

 Score =  343 bits (880), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 136/311 (43%), Positives = 200/311 (64%), Gaps = 3/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE   L + +      I EPL RGF  TLGN+LRRVL+SSL G A+T+++IDG
Sbjct: 3   EIEKPR-IETAEL-KSDGTYGRFILEPLERGFGTTLGNSLRRVLLSSLPGVAVTSIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE S+I GV ED+T+I+LNIKG+  K+ GD  K V I   G   VTAGDI+  +++E+
Sbjct: 61  VQHEFSTIPGVKEDVTEIVLNIKGLIAKVHGDVPKTVYIEAEGECEVTAGDIKADSEVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP-IGLITIDALYSPIKKVSYT 186
           L+P   I  LD  A + MEL + +G GYV +  ++    P IG+I ID++Y+P+ KV+Y+
Sbjct: 121 LDPGMHIATLDEGAKLYMELVIDRGRGYVSSDRNKQIMQPVIGVIPIDSIYTPVLKVNYS 180

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+ R GQ+ DYDKL++ I TDG+I+ +++V+LA+++L + L +F++  E     +  + 
Sbjct: 181 VENTRVGQITDYDKLTLEIWTDGTISAKEAVSLAAKVLNEHLNLFVDLSEEGYTEQIMVE 240

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
                    L   +EEL+LSVRS NCL+   I  + DL  +TE DM+++ N GRKSL E+
Sbjct: 241 KDDKCKEKVLEMTIEELDLSVRSFNCLKRAGINTVEDLTNKTEEDMMKVRNLGRKSLDEV 300

Query: 307 KGVLGTMGLFL 317
              L ++G  L
Sbjct: 301 VLKLKSLGYDL 311


>gi|22536269|ref|NP_687120.1| DNA-directed RNA polymerase subunit alpha [Streptococcus agalactiae
           2603V/R]
 gi|25010159|ref|NP_734554.1| DNA-directed RNA polymerase subunit alpha [Streptococcus agalactiae
           NEM316]
 gi|76798216|ref|ZP_00780466.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae 18RS21]
 gi|77412562|ref|ZP_00788854.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae CJB111]
 gi|77414960|ref|ZP_00791053.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae 515]
 gi|41688699|sp|Q8CX32|RPOA_STRA3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|41688702|sp|Q8E2B1|RPOA_STRA5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|22533090|gb|AAM98992.1|AE014195_11 DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae 2603V/R]
 gi|23094510|emb|CAD45729.1| RNA polymerase (alpha subunit) [Streptococcus agalactiae NEM316]
 gi|76586425|gb|EAO62933.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae 18RS21]
 gi|77158989|gb|EAO70207.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae 515]
 gi|77161385|gb|EAO72404.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae CJB111]
 gi|319743969|gb|EFV96349.1| DNA-directed RNA polymerase subunit alpha [Streptococcus agalactiae
           ATCC 13813]
          Length = 312

 Score =  343 bits (880), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 129/313 (41%), Positives = 200/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EFEKP----IITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKIIELDVEGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +     ++  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIAEGHSLKATMTVAKNRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K  +     
Sbjct: 179 EPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +     L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 EKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 IKLADLGLGLKND 311


>gi|302036693|ref|YP_003797015.1| DNA-directed RNA polymerase subunit alpha [Candidatus Nitrospira
           defluvii]
 gi|300604757|emb|CBK41089.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Nitrospira
           defluvii]
          Length = 333

 Score =  343 bits (880), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 144/325 (44%), Positives = 206/325 (63%), Gaps = 2/325 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + K  ++   P  +E                E   RGF  T+GN+LRRVL+SSL GAA+T
Sbjct: 1   MIKAMKDFQIPMRVEVDK-DTLSPTFGRFTTEAFERGFGTTVGNSLRRVLLSSLTGAAVT 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GVLHE S+I GV ED+T IILN+K + L + GD  K + + K+GPG     DI  
Sbjct: 60  TVKIEGVLHEFSTIPGVTEDVTSIILNVKSLRLALQGDKPKTIRLKKKGPGEAKGSDITH 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
             D+ +L PD  I  LD DA + +E+T+  G G+VPA+ ++ E  PIG+I +D+++SPIK
Sbjct: 120 DGDVTILTPDLHIATLDKDASLDLEMTIKHGRGFVPAERNKEEGLPIGVIAVDSIFSPIK 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE-PKKE 240
           +V++ VE+AR G++ DYDKL++ I TDG+I+  D+++ A+ IL++ L +FIN EE    +
Sbjct: 180 RVNFHVENARVGRMTDYDKLTLEIWTDGTISPRDALSNAAGILREHLDIFINPEERSDAK 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                   S   N  L + V ELELSVR+ NCL+  NI  + DL+Q+TEA+ML+  NFG+
Sbjct: 240 PAAGSEDLSDEVNKNLYRSVNELELSVRAANCLKNANIKTIADLVQKTEAEMLKTKNFGK 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL EIK +L  MGL LGM +   P
Sbjct: 300 KSLNEIKEILTEMGLSLGMKVDALP 324


>gi|15674313|ref|NP_268486.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           M1 GAS]
 gi|19745267|ref|NP_606403.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           MGAS8232]
 gi|50913465|ref|YP_059437.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           MGAS10394]
 gi|71902735|ref|YP_279538.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           MGAS6180]
 gi|71909884|ref|YP_281434.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           MGAS5005]
 gi|94987701|ref|YP_595802.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           MGAS9429]
 gi|94989582|ref|YP_597682.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           MGAS10270]
 gi|94991570|ref|YP_599669.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           MGAS2096]
 gi|94993470|ref|YP_601568.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           MGAS10750]
 gi|139472953|ref|YP_001127668.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           str. Manfredo]
 gi|209558653|ref|YP_002285125.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           NZ131]
 gi|306828235|ref|ZP_07461495.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           ATCC 10782]
 gi|54039279|sp|P66711|RPOA_STRP8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|54042189|sp|P66710|RPOA_STRP1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61215821|sp|Q5XEA9|RPOA_STRP6 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|90110873|sp|Q48VS3|RPOA_STRPM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366735|sp|Q1JE33|RPOA_STRPB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366736|sp|Q1JNZ1|RPOA_STRPC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366737|sp|Q1JJ35|RPOA_STRPD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366738|sp|Q1J8Y7|RPOA_STRPF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158512769|sp|A2RC40|RPOA_STRPG RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|13621394|gb|AAK33208.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pyogenes
           M1 GAS]
 gi|19747362|gb|AAL96902.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pyogenes
           MGAS8232]
 gi|50902539|gb|AAT86254.1| DNA-directed RNA polymerase alpha chain [Streptococcus pyogenes
           MGAS10394]
 gi|71801830|gb|AAX71183.1| DNA-directed RNA polymerase alpha chain [Streptococcus pyogenes
           MGAS6180]
 gi|71852666|gb|AAZ50689.1| DNA-directed RNA polymerase alpha chain [Streptococcus pyogenes
           MGAS5005]
 gi|94541209|gb|ABF31258.1| DNA-directed RNA polymerase alpha chain [Streptococcus pyogenes
           MGAS9429]
 gi|94543090|gb|ABF33138.1| DNA-directed RNA polymerase alpha chain [Streptococcus pyogenes
           MGAS10270]
 gi|94545078|gb|ABF35125.1| DNA-directed RNA polymerase alpha chain [Streptococcus pyogenes
           MGAS2096]
 gi|94546978|gb|ABF37024.1| DNA-directed RNA polymerase alpha chain [Streptococcus pyogenes
           MGAS10750]
 gi|134271199|emb|CAM29412.1| DNA-directed RNA polymerase alpha chain [Streptococcus pyogenes
           str. Manfredo]
 gi|209539854|gb|ACI60430.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pyogenes
           NZ131]
 gi|304429546|gb|EFM32595.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           ATCC 10782]
          Length = 312

 Score =  343 bits (880), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 130/313 (41%), Positives = 200/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EFEKP----IITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKIIELEVEGPAEVTAGDILTDSDIEL 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +     +R  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIAEGHSLRATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K  +     
Sbjct: 179 EPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +     L + +EEL+LSVRS NCL+   I  + DL +++E +M+++ N GRKSL E+K
Sbjct: 239 EKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKSEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKND 311


>gi|18311358|ref|NP_563292.1| DNA-directed RNA polymerase subunit alpha [Clostridium perfringens
           str. 13]
 gi|110799041|ref|YP_697065.1| DNA-directed RNA polymerase subunit alpha [Clostridium perfringens
           ATCC 13124]
 gi|110802435|ref|YP_699634.1| DNA-directed RNA polymerase subunit alpha [Clostridium perfringens
           SM101]
 gi|168205205|ref|ZP_02631210.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           E str. JGS1987]
 gi|168211876|ref|ZP_02637501.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           B str. ATCC 3626]
 gi|168215205|ref|ZP_02640830.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           CPE str. F4969]
 gi|168216660|ref|ZP_02642285.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           NCTC 8239]
 gi|169347112|ref|ZP_02866054.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           C str. JGS1495]
 gi|182626919|ref|ZP_02954652.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           D str. JGS1721]
 gi|119366675|sp|Q0TMS5|RPOA_CLOP1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366676|sp|Q0SQH3|RPOA_CLOPS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|124053359|sp|P0C2E6|RPOA_CLOPE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|7707686|dbj|BAA95357.1| RNA polymerase alpha subunit [Clostridium perfringens]
 gi|18146042|dbj|BAB82082.1| RNA polymerase alpha subunit [Clostridium perfringens str. 13]
 gi|110673688|gb|ABG82675.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           ATCC 13124]
 gi|110682936|gb|ABG86306.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           SM101]
 gi|169296795|gb|EDS78924.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           C str. JGS1495]
 gi|170663306|gb|EDT15989.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           E str. JGS1987]
 gi|170710183|gb|EDT22365.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           B str. ATCC 3626]
 gi|170713403|gb|EDT25585.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           CPE str. F4969]
 gi|177907709|gb|EDT70324.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           D str. JGS1721]
 gi|182381168|gb|EDT78647.1| DNA-directed RNA polymerase, alpha subunit [Clostridium perfringens
           NCTC 8239]
          Length = 315

 Score =  343 bits (880), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 131/313 (41%), Positives = 202/313 (64%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  +   V   +         EPL RG+  TLGNALRR+L+SSL G A T+V+ID 
Sbjct: 3   EIEKP--VIQCVESNDNGTYGKFEIEPLERGYGITLGNALRRILLSSLPGVAPTSVKIDS 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T+IILN+K + L M G+  K + I  +GPGVVT  DI+T  D+EV
Sbjct: 61  VLHEFSTITGVKEDVTEIILNLKMLALTMEGEGPKTIYIDAQGPGVVTGADIKTDGDVEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N D  I  LD D  + ME+ V++G GYV    ++TE+ P+  I ID++Y+P+K+V+++V
Sbjct: 121 VNKDLHIATLDNDGKLYMEIVVNRGRGYVTQNKNKTEDLPLSAIAIDSIYTPVKRVNFSV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ++ R GQ+ DYDKL++ I T+G+I  E++++L+++IL +   +F+   +   +V+  I  
Sbjct: 181 QNTRVGQITDYDKLTLEIWTNGTIRIEEAISLSAKILIEHFKLFMTLTDNANDVEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +      AL   +EEL+LSVRS NCL+   I  + +L  ++  DM+++ N G+KSL E++
Sbjct: 241 EEDKKEKALEMTIEELDLSVRSYNCLKRAGINTVQELAGKSMDDMMKVRNLGKKSLEEVE 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L +N
Sbjct: 301 RKLNELGLNLRLN 313


>gi|293390660|ref|ZP_06634994.1| DNA-directed RNA polymerase, alpha subunit [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290951194|gb|EFE01313.1| DNA-directed RNA polymerase, alpha subunit [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 329

 Score =  343 bits (879), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 150/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    E +KP  ++   + Q    +  +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGAVTEFLKPRLVD---IEQVSSTQAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVQNKDDVLLTLSKSGIGPVVAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+EV+NP+HVIC+L D  + + M + V +G GYVPA      + E  PIG + +DA Y
Sbjct: 118 DGDVEVINPEHVICHLTDESSSISMRIRVRRGRGYVPASVRAQIQDEERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPI++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPIERIAYNVEAARVEQRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|242278684|ref|YP_002990813.1| DNA-directed RNA polymerase subunit alpha [Desulfovibrio salexigens
           DSM 2638]
 gi|259494166|sp|C6C1B1|RPOA_DESAD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|242121578|gb|ACS79274.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio
           salexigens DSM 2638]
          Length = 346

 Score =  343 bits (879), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 157/337 (46%), Positives = 223/337 (66%), Gaps = 3/337 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW EL+KP  +  +   +  E     I EPL RGF  T+GN+LRRVL+SS++GAA  AV
Sbjct: 13  RNWAELVKPEQL--VRDPKSNELYGKFICEPLERGFGTTIGNSLRRVLLSSMQGAAAVAV 70

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+GV HE ++I+GV ED+T+I+LNIK I   M+ D  + +T+     GVVTA DIQ   
Sbjct: 71  KIEGVQHEFTTIEGVMEDVTEIVLNIKQIRFAMTTDEPQFLTLRVNKQGVVTAADIQENQ 130

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           +++VLNP+ +I  L     + M   +  G GYVPA  H    + IG I +D+ +SPI+KV
Sbjct: 131 NVKVLNPEQIIATLSEKMDMEMTFEIRMGKGYVPADMHEGLVNEIGHIILDSSFSPIRKV 190

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+VE AR GQ+ +YDKL + + TDGS+T ED++A +++IL+DQL +FINF+E   E +E
Sbjct: 191 AYSVEQARVGQMTNYDKLIIEVFTDGSVTPEDAIAYSAKILKDQLSVFINFDEMGSEQEE 250

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                 L  NP L K ++ELELSVR+TNCL+  NI  +G+L+QRTE  ML+  NFGRKSL
Sbjct: 251 SKE-SDLDLNPNLFKSIDELELSVRATNCLKAANIRIVGELVQRTEQTMLKTKNFGRKSL 309

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
            EI+ VL +M L  GM L D+  +  E L +K +++ 
Sbjct: 310 DEIRRVLDSMELKFGMVLEDFDKKHQEWLKRKEKNEA 346


>gi|325267151|ref|ZP_08133819.1| DNA-directed RNA polymerase subunit alpha [Kingella denitrificans
           ATCC 33394]
 gi|324981389|gb|EGC17033.1| DNA-directed RNA polymerase subunit alpha [Kingella denitrificans
           ATCC 33394]
          Length = 327

 Score =  343 bits (879), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 149/332 (44%), Positives = 216/332 (65%), Gaps = 8/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+   L      R  +  +P  RGF HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSTSEFLKPRQIDVDTLS---ATRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQ 120
            + I GVLHE S++ GV ED+ DI+LN+K +  K+ G+ +   +++ K G G V A D +
Sbjct: 58  EITIAGVLHEYSTLDGVQEDVVDILLNVKSVVFKLHGNRTEAVLSLKKTGAGPVYASDFE 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR-TENDPIGLITIDALYSP 179
             +D+E++NP  VIC+L  +  + ME+ V +G GY      R T+++ IG I +DA +SP
Sbjct: 118 LPHDVEIINPKQVICHLSDNGSIDMEVKVEQGRGYQTVSGRRVTKDNKIGAIQLDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I +VS+ VE+AR  Q  D D L + I+T+GSI  E++V +A+RIL DQ+ +F + E    
Sbjct: 178 ITRVSFDVEAARVEQRTDLDSLILDIETNGSIDPEEAVRMAARILIDQMSIFADLEGTPA 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           EV+E+   K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N G
Sbjct: 238 EVEEE---KAPPIDPVLLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           RKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 295 RKSLNEIKEVLASKGLTLGSRLESWPPAGLEK 326


>gi|251781544|ref|YP_002995845.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
 gi|242390172|dbj|BAH80631.1| DNA-directed RNA polymerase alpha subunit [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
 gi|322410884|gb|EFY01792.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           dysgalactiae subsp. dysgalactiae ATCC 27957]
          Length = 312

 Score =  343 bits (879), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 129/313 (41%), Positives = 200/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EFEKP----IITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKIIELEVEGPAEVTAGDILTDSDIEL 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +     +R  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIAEGHSLRATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  +  K  +     
Sbjct: 179 EPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTDVAKATEVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +     L + +EEL+LSVRS NCL+   I  + DL +++E +M+++ N GRKSL E+K
Sbjct: 239 EKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKSEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKND 311


>gi|21909602|ref|NP_663870.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           MGAS315]
 gi|28894980|ref|NP_801330.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pyogenes
           SSI-1]
 gi|25009138|sp|Q8K8W9|RPOA_STRP3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|21903783|gb|AAM78673.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pyogenes
           MGAS315]
 gi|28810225|dbj|BAC63163.1| putative DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pyogenes SSI-1]
          Length = 312

 Score =  343 bits (879), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 130/313 (41%), Positives = 200/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EFEKP----IITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKIIELEVEGPAEVTAGDILTDSDIEL 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +     +R  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIAEGHSLRATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K  +     
Sbjct: 179 EPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKSTEVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +     L + +EEL+LSVRS NCL+   I  + DL +++E +M+++ N GRKSL E+K
Sbjct: 239 EKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKSEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKND 311


>gi|281415637|ref|ZP_06247379.1| DNA-directed RNA polymerase subunit alpha [Micrococcus luteus NCTC
           2665]
          Length = 334

 Score =  343 bits (879), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 121/317 (38%), Positives = 194/317 (61%), Gaps = 4/317 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V     ++R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVLH
Sbjct: 8   RPTLTEEVV----SDHRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVLH 63

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T+IILNIK +++    D      + K+G GVVTA DI     +E+ NP
Sbjct: 64  EFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEIHNP 123

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+      MELT+ +G GYV A  +++ +  IG I +D++YSP+ KV++ VE+ 
Sbjct: 124 DLHIATLNAKGKFDMELTIERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEAT 183

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  ++   D+VA A   L +  G+  +     + +      + +
Sbjct: 184 RVEQRTDFDRLILDVETKENMLPRDAVASAGSTLVELFGLARSLNVEAEGIDLGDEPEVV 243

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +  L + +EELEL+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L
Sbjct: 244 EGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEKL 303

Query: 311 GTMGLFLGMNLPDWPPE 327
             +GL L  +   + P+
Sbjct: 304 QELGLSLKDSPAGYDPQ 320


>gi|300174006|ref|YP_003773172.1| DNA-directed RNA polymerase subunit alpha [Leuconostoc
           gasicomitatum LMG 18811]
 gi|299888385|emb|CBL92353.1| DNA-directed RNA polymerase, alpha subunit [Leuconostoc
           gasicomitatum LMG 18811]
          Length = 314

 Score =  343 bits (879), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 129/312 (41%), Positives = 190/312 (60%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E       + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDG
Sbjct: 3   EFEKPN----IHNIEEGARYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE S++ GV ED+T IILN+K + L +  D  + + +  +GP  VTA D+Q   D+EV
Sbjct: 59  VVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDEERSLEVDIQGPADVTAADLQAGADVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
           LNPD  I  +     + M +T  KG GY  A  ++   +  PIG++ +D++Y+PI++V+Y
Sbjct: 119 LNPDLHIATVAAGKSLHMTITAFKGRGYSSADENKQLRDEMPIGVLAVDSIYTPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R G   DYDKL+  I T+GSI   D+++L S+IL + L +F++      E    +
Sbjct: 179 HVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSLGSKILAEHLNLFMDISPVAAEANVMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            V+ +  + +    +E+L+LSVRS NCL+   I  + +L  RTEADM+++ N GRKSL E
Sbjct: 239 EVEPVAVSASDSAPIEDLDLSVRSYNCLKRAGINTIVELTDRTEADMMKVRNLGRKSLDE 298

Query: 306 IKGVLGTMGLFL 317
           I+  L  M L  
Sbjct: 299 IQEKLTEMSLGF 310


>gi|313889541|ref|ZP_07823186.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pseudoporcinus SPIN 20026]
 gi|313122050|gb|EFR45144.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pseudoporcinus SPIN 20026]
          Length = 312

 Score =  343 bits (879), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 130/313 (41%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EFEKPT----ITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILNIKG+ +K   +  K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNIKGLAVKSYVEDEKMIELDVEGPAEVTAGDILTDSDIEL 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +     ++  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K        
Sbjct: 179 EPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKATDVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +     L + +EEL+LSVRS NCL+   I  + DL +++E +M+++ N GRKSL E+K
Sbjct: 239 EKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKSEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKND 311


>gi|171778401|ref|ZP_02919580.1| hypothetical protein STRINF_00431 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171282932|gb|EDT48356.1| hypothetical protein STRINF_00431 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 312

 Score =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 132/313 (42%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EFEKP----IITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI T +D+E+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDSDVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +     ++  +TV+K  GYVPA+ ++ E+ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIAEGHSLKAIMTVAKKRGYVPAEGNKKEDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K        
Sbjct: 179 EPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKNTDVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +     L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 EKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKND 311


>gi|239918173|ref|YP_002957731.1| DNA-directed RNA polymerase, alpha subunit [Micrococcus luteus NCTC
           2665]
 gi|289706559|ref|ZP_06502909.1| DNA-directed RNA polymerase, alpha subunit [Micrococcus luteus
           SK58]
 gi|239839380|gb|ACS31177.1| DNA-directed RNA polymerase, alpha subunit [Micrococcus luteus NCTC
           2665]
 gi|289556694|gb|EFD50035.1| DNA-directed RNA polymerase, alpha subunit [Micrococcus luteus
           SK58]
          Length = 332

 Score =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 121/317 (38%), Positives = 194/317 (61%), Gaps = 4/317 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V     ++R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVLH
Sbjct: 6   RPTLTEEVV----SDHRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T+IILNIK +++    D      + K+G GVVTA DI     +E+ NP
Sbjct: 62  EFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEIHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+      MELT+ +G GYV A  +++ +  IG I +D++YSP+ KV++ VE+ 
Sbjct: 122 DLHIATLNAKGKFDMELTIERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  ++   D+VA A   L +  G+  +     + +      + +
Sbjct: 182 RVEQRTDFDRLILDVETKENMLPRDAVASAGSTLVELFGLARSLNVEAEGIDLGDEPEVV 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +  L + +EELEL+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L
Sbjct: 242 EGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEKL 301

Query: 311 GTMGLFLGMNLPDWPPE 327
             +GL L  +   + P+
Sbjct: 302 QELGLSLKDSPAGYDPQ 318


>gi|313123135|ref|YP_004033394.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           delbrueckii subsp. bulgaricus ND02]
 gi|312279698|gb|ADQ60417.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           delbrueckii subsp. bulgaricus ND02]
          Length = 312

 Score =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 125/310 (40%), Positives = 190/310 (61%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +E++    + EPL RGF  TLGN+LRRVL++S+ G  +  V+IDG
Sbjct: 3   EFKKPN----ITVVDQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSVPGTGLVKVKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           +LHE +++ GV ED+T IILN+K + L+   +  K + +   GP  VTA D++   D+EV
Sbjct: 59  ILHEFTTVPGVKEDVTKIILNLKKLVLRAYTEEVKTIELDVEGPATVTAEDLKADADVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + M + V  G GYVPA  +++    IG I +D+L+SPI+KV+Y V
Sbjct: 119 LNPDQYICTIAQGGHLHMWIDVCNGRGYVPASENKSAEMSIGDIPVDSLFSPIEKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL++ I T+GSI   D++  A+R+L +    F + +   +  +  +  
Sbjct: 179 ESTRVGKREDFDKLTLEIWTNGSIAPNDALNFAARVLVEHFKAFESADAAAEIGEVMVEQ 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           ++      L   +E+L+LSVRS NCL+   I  + DL  ++EA+M+R+ N GRKSL E+K
Sbjct: 239 ENDQKEKKLEMTIEDLDLSVRSYNCLKRAGINTLQDLTVKSEAEMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLADLGLSL 308


>gi|254517499|ref|ZP_05129555.1| RNA polymerase subunit alpha [Clostridium sp. 7_2_43FAA]
 gi|226911248|gb|EEH96449.1| RNA polymerase subunit alpha [Clostridium sp. 7_2_43FAA]
          Length = 315

 Score =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 133/313 (42%), Positives = 209/313 (66%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  I   +   E       + EPL RG+  TLGNALRR+L+SSL GAA T+V+IDG
Sbjct: 3   EIEKP--IIECIEANENGTYGKYVIEPLERGYGITLGNALRRILLSSLPGAAPTSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T+IILNIK + L M+G+  K + I  +GPGVVT  DI+T  D+EV
Sbjct: 61  VLHEFSTVQGVKEDVTEIILNIKSLALIMNGEGPKTIYIDAQGPGVVTGADIKTDGDVEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           ++ D  I  LD +A + ME+TV++G GYV    +++E+ P+  I +D++Y+P+K+V++TV
Sbjct: 121 VSKDLHIATLDDNAKLYMEITVNRGRGYVTQNKNKSEDLPLSAIAVDSIYTPVKRVNFTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ DYDKL++ I T+G+I  +++++L+++IL +   +F++  +   +V+  I  
Sbjct: 181 ENTRVGQITDYDKLTLEIWTNGTIKIDEAISLSAKILIEHFKLFMSLGDSTNDVEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   VEEL+LSVRS NCL+   I  + +L  ++  DM+++ N G+KSL E++
Sbjct: 241 EEDKKEKVLEMTVEELDLSVRSYNCLKRAGINTVQELAGKSMDDMMKVRNLGKKSLEEVE 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L +N
Sbjct: 301 RKLKELGLGLRLN 313


>gi|331702054|ref|YP_004399013.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus buchneri
           NRRL B-30929]
 gi|329129397|gb|AEB73950.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus buchneri
           NRRL B-30929]
          Length = 319

 Score =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 145/314 (46%), Positives = 203/314 (64%), Gaps = 8/314 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E  N   ++ EPL RG+  TLGN+LRR L+SSL GAA+T++QID 
Sbjct: 6   EFEKPN----IHKIEETNNFGEVVVEPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDD 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE S+IKGV ED+T IILN+K I+LK+ G  D  + + I   GP  VTAGDIQ  +D+
Sbjct: 62  VLHEFSTIKGVVEDVTQIILNVKKISLKLDGPEDEEENLEIDVIGPADVTAGDIQADSDV 121

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKV 183
            VLNPD  I  +   A   M LT +KG GYV A  ++      PIG++ +D++Y+PI++V
Sbjct: 122 TVLNPDLHIATVAEGATFHMRLTANKGRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERV 181

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VES R GQ  D+DKL++ I TDGSIT  ++V+LA++IL + L MF++  +  K  + 
Sbjct: 182 NYQVESTRVGQRDDFDKLTLDIWTDGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEI 241

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  +       L   +EEL+LSVRS NCL+   I  + +L ++TEADM+++ N GRKSL
Sbjct: 242 MVEKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTEKTEADMMKVRNLGRKSL 301

Query: 304 VEIKGVLGTMGLFL 317
            E+K  L  +GL L
Sbjct: 302 EEVKEKLAALGLSL 315


>gi|195977234|ref|YP_002122478.1| DNA-directed RNA polymerase subunit alpha [Streptococcus equi
           subsp. zooepidemicus MGCS10565]
 gi|225867691|ref|YP_002743639.1| DNA-directed RNA polymerase alpha chain [Streptococcus equi subsp.
           zooepidemicus]
 gi|225869562|ref|YP_002745509.1| DNA-directed RNA polymerase alpha chain [Streptococcus equi subsp.
           equi 4047]
 gi|195973939|gb|ACG61465.1| DNA-directed RNA polymerase alpha chain [Streptococcus equi subsp.
           zooepidemicus MGCS10565]
 gi|225698966|emb|CAW92015.1| DNA-directed RNA polymerase alpha chain [Streptococcus equi subsp.
           equi 4047]
 gi|225700967|emb|CAW97690.1| DNA-directed RNA polymerase alpha chain [Streptococcus equi subsp.
           zooepidemicus]
          Length = 312

 Score =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 128/313 (40%), Positives = 200/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EFEKP----IITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIRIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKIIELDVEGPAEVTAGDILTDSDIEL 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +     ++  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIADGYTLKASMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  +  K  +     
Sbjct: 179 EPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTDVAKATEVMKEA 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +     L + +EEL+LSVRS NCL+   I  + DL +++E +M+++ N GRKSL E+K
Sbjct: 239 EKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKSEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKND 311


>gi|117619246|ref|YP_854867.1| DNA-directed RNA polymerase subunit alpha [Aeromonas hydrophila
           subsp. hydrophila ATCC 7966]
 gi|145300910|ref|YP_001143751.1| DNA-directed RNA polymerase subunit alpha [Aeromonas salmonicida
           subsp. salmonicida A449]
 gi|158512292|sp|A0KF45|RPOA_AERHH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158514057|sp|A4SSY1|RPOA_AERS4 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|117560653|gb|ABK37601.1| DNA-directed RNA polymerase, alpha subunit [Aeromonas hydrophila
           subsp. hydrophila ATCC 7966]
 gi|142853682|gb|ABO92003.1| DNA-directed RNA polymerase, alpha subunit [Aeromonas salmonicida
           subsp. salmonicida A449]
          Length = 329

 Score =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 222/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +  + +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MLGSVTDFLKPRLVD---IEQVSPTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KGI +K+ G     +++ K G G VTAGDI  
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDILEILLNLKGIAVKLEGKDEVTLSLTKSGTGPVTAGDITH 117

Query: 122 VNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
            +++E++NP+HVIC+L   +A + M L V +G GYVPA    H+  E  PIG + +D+ +
Sbjct: 118 GDEVEIVNPEHVICHLTGANAEISMRLKVQRGRGYVPASARVHNDDEERPIGRLLLDSAF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPI +++Y VE+AR  Q  D DKL + ++T+G++  E+++  ++ IL +QL  F++  + 
Sbjct: 178 SPIVRIAYNVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRSATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
               K++   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 SVPEKKE---EKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|59710869|ref|YP_203645.1| DNA-directed RNA polymerase subunit alpha [Vibrio fischeri ES114]
 gi|197334008|ref|YP_002155021.1| DNA-directed RNA polymerase, alpha subunit [Vibrio fischeri MJ11]
 gi|75431853|sp|Q5E889|RPOA_VIBF1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238690301|sp|B5FGE1|RPOA_VIBFM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|59478970|gb|AAW84757.1| RNA polymerase, alpha subunit [Vibrio fischeri ES114]
 gi|197315498|gb|ACH64945.1| DNA-directed RNA polymerase, alpha subunit [Vibrio fischeri MJ11]
          Length = 329

 Score =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 148/334 (44%), Positives = 216/334 (64%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI  
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVIITLNKSGAGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E+ NP+HVIC+L  D A + M + V +G GYVP+    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIANPEHVICHLTDDNAEISMRIKVERGRGYVPSTARIHTEEDERPIGRLLVDATY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ K+SY VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDKISYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|148381392|ref|YP_001255933.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum A
           str. ATCC 3502]
 gi|153932349|ref|YP_001385767.1| DNA-directed RNA polymerase subunit alpha [Clostridium botulinum A
           str. ATCC 19397]
 gi|153936668|ref|YP_001389174.1| DNA-directed RNA polymerase subunit alpha [Clostridium botulinum A
           str. Hall]
 gi|153940858|ref|YP_001392805.1| DNA-directed RNA polymerase subunit alpha [Clostridium botulinum F
           str. Langeland]
 gi|168178861|ref|ZP_02613525.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           NCTC 2916]
 gi|168181893|ref|ZP_02616557.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           Bf]
 gi|170756437|ref|YP_001783092.1| DNA-directed RNA polymerase subunit alpha [Clostridium botulinum B1
           str. Okra]
 gi|170760187|ref|YP_001788792.1| DNA-directed RNA polymerase subunit alpha [Clostridium botulinum A3
           str. Loch Maree]
 gi|187776604|ref|ZP_02993077.1| hypothetical protein CLOSPO_00118 [Clostridium sporogenes ATCC
           15579]
 gi|226950904|ref|YP_002805995.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           A2 str. Kyoto]
 gi|237796913|ref|YP_002864465.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           Ba4 str. 657]
 gi|166229269|sp|A7FZ44|RPOA_CLOB1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|166229270|sp|A5I7H7|RPOA_CLOBH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|166229271|sp|A7GJ45|RPOA_CLOBL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|229564246|sp|B1IGC5|RPOA_CLOBK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238688736|sp|B1KSJ6|RPOA_CLOBM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|254765247|sp|C1FMS2|RPOA_CLOBJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|259494165|sp|C3KVM2|RPOA_CLOB6 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|148290876|emb|CAL85012.1| DNA-directed RNA polymerase alpha chain [Clostridium botulinum A
           str. ATCC 3502]
 gi|152928393|gb|ABS33893.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum A
           str. ATCC 19397]
 gi|152932582|gb|ABS38081.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum A
           str. Hall]
 gi|152936754|gb|ABS42252.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum F
           str. Langeland]
 gi|169121649|gb|ACA45485.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           B1 str. Okra]
 gi|169407176|gb|ACA55587.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           A3 str. Loch Maree]
 gi|182670092|gb|EDT82068.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           NCTC 2916]
 gi|182674826|gb|EDT86787.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           Bf]
 gi|187775263|gb|EDU39065.1| hypothetical protein CLOSPO_00118 [Clostridium sporogenes ATCC
           15579]
 gi|226842850|gb|ACO85516.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           A2 str. Kyoto]
 gi|229260648|gb|ACQ51681.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           Ba4 str. 657]
 gi|295320785|gb|ADG01163.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum F
           str. 230613]
 gi|322807777|emb|CBZ05352.1| DNA-directed RNA polymerase alpha subunit [Clostridium botulinum
           H04402 065]
          Length = 315

 Score =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 127/310 (40%), Positives = 204/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE  V   E+ +    + EPL RG+  TLGNALRR+L+SSL G A   ++ID 
Sbjct: 3   EIEKP-KIE-CVENAEDGSYGKFVIEPLERGYGITLGNALRRILLSSLPGVAADHIKIDS 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T++ILNIK + L M+G+  K + I + GP  VTA DI+T  D+EV
Sbjct: 61  VLHEFSTVQGVKEDVTELILNIKCLALTMNGEGPKTIYIDEVGPKEVTAADIKTDGDVEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N D  I  LD +  + ME+ V++G GYV    ++T++ PIG I +D++Y+P+K+V+++V
Sbjct: 121 INKDLHIATLDENGKMYMEINVNRGRGYVTQNKNKTKDMPIGSIAVDSIYTPVKRVNFSV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ DYDKL++ + T+G+I  E++V+L+++IL +   +F+   +   +++  +  
Sbjct: 181 ENTRVGQITDYDKLTIEVWTNGTIRPEEAVSLSAKILIEHFKLFMTLTDHADDMEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L +R+  DM+++ N G+KSL E++
Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELCERSMDDMMKVRNLGKKSLEEVE 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 QKLEALGLGL 310


>gi|323700832|ref|ZP_08112744.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio sp.
           ND132]
 gi|323460764|gb|EGB16629.1| DNA-directed RNA polymerase, alpha subunit [Desulfovibrio
           desulfuricans ND132]
          Length = 346

 Score =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 151/337 (44%), Positives = 224/337 (66%), Gaps = 3/337 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW +L+KP  +  +   +  +     I EPL RG+A T+GNA+RRVL+SS++G AI + 
Sbjct: 13  RNWSQLVKPEAL--VRDSKSSKTYGKFICEPLERGYATTIGNAMRRVLLSSMQGCAIVSA 70

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
            I+GV HE +++ GV ED+T+++LN+K + + M+ D  +R+ +     G VTAG IQ   
Sbjct: 71  SIEGVQHEFTTLPGVLEDMTEVVLNLKQVRIAMTTDEPQRLVLEANKKGQVTAGMIQENQ 130

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           ++ +LN D +I  L  +  ++MEL V  G GYVPA  H    D IG + +DA YSP+KKV
Sbjct: 131 NVTILNKDQLIATLTENRPLKMELEVRMGKGYVPADMHEGLTDEIGSMVLDASYSPVKKV 190

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+VE AR GQ+ +YDKL + + TDGS+T ED+ A +++IL+DQL +FINF+E   E  E
Sbjct: 191 AYSVEQARVGQMTNYDKLILEVWTDGSVTPEDACAYSAKILKDQLSVFINFDESSSETHE 250

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           + +  S+  NP L K ++ELELSVR+TNCL+  NI  +G+L+QRTE  ML+  NFGRKSL
Sbjct: 251 EED-NSIDLNPNLFKSIDELELSVRATNCLKAANIQLVGELVQRTEQTMLKTKNFGRKSL 309

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
            EI+ VL  M L  GM++ D+  +  E L +K +++ 
Sbjct: 310 DEIRRVLDGMALKFGMSVEDFDKKYQEWLKRKEKNEA 346


>gi|313808805|gb|EFS47259.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL087PA2]
          Length = 338

 Score =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 121/320 (37%), Positives = 184/320 (57%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                 E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV HE S+I+G 
Sbjct: 10  TEESISEFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQHEFSTIEGC 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+IILN+KG+ L    D    + + K G G VTA DI     + + NP+  I  L+
Sbjct: 70  VEDVTEIILNLKGLVLSSEEDEPVAMYLRKSGAGEVTAADITPPAGVTIHNPELHIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D    MEL V +G GYV +  +   N  IG I +D++YSP+ KV+Y VE+ R  Q  D+
Sbjct: 130 DDGRFEMELIVERGRGYVSSALNDDPNAEIGRIAVDSIYSPVLKVTYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  SI   D++A A + L +  G+        + ++         +  +L  
Sbjct: 190 DKLVVDVETKPSILPRDAIASAGKTLVELFGLTRELNAEAEGIEIGSGPVDEEYAESLGT 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  +GL L 
Sbjct: 250 PVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEKLTELGLALK 309

Query: 319 MNLPDWPPESIEELAKKYED 338
            + P + P +  E   +  D
Sbjct: 310 DSAPGFDPLAAAEAYDEAND 329


>gi|322386328|ref|ZP_08059958.1| DNA-directed RNA polymerase subunit alpha [Streptococcus cristatus
           ATCC 51100]
 gi|321269552|gb|EFX52482.1| DNA-directed RNA polymerase subunit alpha [Streptococcus cristatus
           ATCC 51100]
          Length = 312

 Score =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 130/310 (41%), Positives = 194/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E +N    + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKNYGKFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILNIKGI +K      K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTISGVREDVMQIILNIKGIAVKSYVQDEKMIELDVEGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A  + ++ V+ G GYVPA  ++ ++ P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTISEGARFKAKMAVNSGRGYVPADENKKDDAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F +  E           
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLFTDLTEVAISTDVMKEA 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    +  L + +EEL+LSVRS NCL+   I  + DL +++E +M+++ N GRKSL E+K
Sbjct: 239 EKSSDDRILERTIEELDLSVRSYNCLKRAGINTVFDLTEKSEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 VKLADLGLGL 308


>gi|15900172|ref|NP_344776.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           TIGR4]
 gi|15902259|ref|NP_357809.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           R6]
 gi|111658776|ref|ZP_01409407.1| hypothetical protein SpneT_02000073 [Streptococcus pneumoniae
           TIGR4]
 gi|116516293|ref|YP_815737.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           D39]
 gi|148983635|ref|ZP_01816954.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP3-BS71]
 gi|148987973|ref|ZP_01819436.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP6-BS73]
 gi|148992813|ref|ZP_01822456.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP9-BS68]
 gi|148996658|ref|ZP_01824376.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP11-BS70]
 gi|149001657|ref|ZP_01826630.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae SP14-BS69]
 gi|149005987|ref|ZP_01829716.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP18-BS74]
 gi|149011106|ref|ZP_01832411.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP19-BS75]
 gi|149017926|ref|ZP_01834385.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP23-BS72]
 gi|168483873|ref|ZP_02708825.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae CDC1873-00]
 gi|168485997|ref|ZP_02710505.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae CDC1087-00]
 gi|168489713|ref|ZP_02713912.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae SP195]
 gi|168492190|ref|ZP_02716333.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae CDC0288-04]
 gi|168493930|ref|ZP_02718073.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae CDC3059-06]
 gi|168576337|ref|ZP_02722220.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae MLV-016]
 gi|169834017|ref|YP_001693767.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           Hungary19A-6]
 gi|182683213|ref|YP_001834960.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           CGSP14]
 gi|194396717|ref|YP_002036935.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           G54]
 gi|221231138|ref|YP_002510290.1| DNA-directed RNA polymerase alpha chain [Streptococcus pneumoniae
           ATCC 700669]
 gi|225853841|ref|YP_002735353.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           JJA]
 gi|225856000|ref|YP_002737511.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           P1031]
 gi|225858089|ref|YP_002739599.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           70585]
 gi|225860277|ref|YP_002741786.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           Taiwan19F-14]
 gi|289168706|ref|YP_003446975.1| DNA-dependent RNA polymerase, alpha subunit [Streptococcus mitis
           B6]
 gi|298230392|ref|ZP_06964073.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           str. Canada MDR_19F]
 gi|298256013|ref|ZP_06979599.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           str. Canada MDR_19A]
 gi|298502049|ref|YP_003723989.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           TCH8431/19A]
 gi|303255069|ref|ZP_07341145.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           BS455]
 gi|303259287|ref|ZP_07345265.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           SP-BS293]
 gi|303261042|ref|ZP_07346991.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           SP14-BS292]
 gi|303263370|ref|ZP_07349293.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           BS397]
 gi|303265535|ref|ZP_07351435.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           BS457]
 gi|303267907|ref|ZP_07353709.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           BS458]
 gi|307066913|ref|YP_003875879.1| DNA-directed RNA polymerase subunit alpha/40 kD subunit
           [Streptococcus pneumoniae AP200]
 gi|307126454|ref|YP_003878485.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           670-6B]
 gi|307704090|ref|ZP_07641019.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus mitis
           SK597]
 gi|307708085|ref|ZP_07644553.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus mitis
           NCTC 12261]
 gi|307709936|ref|ZP_07646383.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus mitis
           SK564]
 gi|307711030|ref|ZP_07647452.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus mitis
           SK321]
 gi|54039278|sp|P66709|RPOA_STRR6 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|54042188|sp|P66708|RPOA_STRPN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|122279377|sp|Q04ML1|RPOA_STRP2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|14971705|gb|AAK74416.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae TIGR4]
 gi|15457760|gb|AAK99019.1| RNA polymerase alpha subunit [Streptococcus pneumoniae R6]
 gi|116076869|gb|ABJ54589.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae D39]
 gi|147757233|gb|EDK64272.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP11-BS70]
 gi|147760115|gb|EDK67104.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae SP14-BS69]
 gi|147762343|gb|EDK69304.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP18-BS74]
 gi|147764742|gb|EDK71672.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP19-BS75]
 gi|147923782|gb|EDK74894.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP3-BS71]
 gi|147926437|gb|EDK77510.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP6-BS73]
 gi|147928539|gb|EDK79554.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP9-BS68]
 gi|147931490|gb|EDK82468.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           SP23-BS72]
 gi|168996519|gb|ACA37131.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae Hungary19A-6]
 gi|172042844|gb|EDT50890.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae CDC1873-00]
 gi|182628547|gb|ACB89495.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           CGSP14]
 gi|183570913|gb|EDT91441.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae CDC1087-00]
 gi|183571834|gb|EDT92362.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae SP195]
 gi|183573577|gb|EDT94105.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae CDC0288-04]
 gi|183576079|gb|EDT96607.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae CDC3059-06]
 gi|183577825|gb|EDT98353.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae MLV-016]
 gi|194356384|gb|ACF54832.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae G54]
 gi|220673598|emb|CAR68084.1| DNA-directed RNA polymerase alpha chain [Streptococcus pneumoniae
           ATCC 700669]
 gi|225720212|gb|ACO16066.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae 70585]
 gi|225723399|gb|ACO19252.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae JJA]
 gi|225725259|gb|ACO21111.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae P1031]
 gi|225726707|gb|ACO22558.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae Taiwan19F-14]
 gi|288908273|emb|CBJ23115.1| DNA-dependent RNA polymerase, alpha subunit [Streptococcus mitis
           B6]
 gi|298237644|gb|ADI68775.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           TCH8431/19A]
 gi|301793507|emb|CBW35880.1| DNA-directed RNA polymerase alpha chain [Streptococcus pneumoniae
           INV104]
 gi|301799383|emb|CBW31918.1| DNA-directed RNA polymerase alpha chain [Streptococcus pneumoniae
           OXC141]
 gi|301801178|emb|CBW33851.1| DNA-directed RNA polymerase alpha chain [Streptococcus pneumoniae
           INV200]
 gi|302597899|gb|EFL64969.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           BS455]
 gi|302637879|gb|EFL68365.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           SP14-BS292]
 gi|302639705|gb|EFL70162.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           SP-BS293]
 gi|302642603|gb|EFL72948.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           BS458]
 gi|302644975|gb|EFL75222.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           BS457]
 gi|302647143|gb|EFL77367.1| DNA-directed RNA polymerase alpha subunit [Streptococcus pneumoniae
           BS397]
 gi|306408450|gb|ADM83877.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Streptococcus pneumoniae AP200]
 gi|306483516|gb|ADM90385.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae 670-6B]
 gi|307615870|gb|EFN95075.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus mitis
           NCTC 12261]
 gi|307616992|gb|EFN96170.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus mitis
           SK321]
 gi|307619307|gb|EFN98436.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus mitis
           SK564]
 gi|307622380|gb|EFO01388.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus mitis
           SK597]
 gi|327390653|gb|EGE88993.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae GA04375]
 gi|332075900|gb|EGI86367.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae GA17570]
 gi|332076680|gb|EGI87142.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae GA17545]
          Length = 311

 Score =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 133/313 (42%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  K  +     
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSTEVMKEA 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            +   +  L + +EEL+LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E+K
Sbjct: 239 DTESDDRILDRTIEELDLSVRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L   
Sbjct: 299 LKLIDLGLGLKDK 311


>gi|145596406|ref|YP_001160703.1| DNA-directed RNA polymerase subunit alpha [Salinispora tropica
           CNB-440]
 gi|145305743|gb|ABP56325.1| DNA-directed RNA polymerase, alpha subunit [Salinispora tropica
           CNB-440]
          Length = 354

 Score =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 121/310 (39%), Positives = 188/310 (60%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
                E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV 
Sbjct: 25  EESINETRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTIPGVK 84

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+ ++++NIK + +    D    + + K+GPG VTAGDIQ    + V NPD  +  L+ 
Sbjct: 85  EDVVELVMNIKELCVSSEHDEPVSMYLRKQGPGDVTAGDIQPPAGVSVHNPDLKLATLNG 144

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              + MELTV +G GYV A  ++     IG I +D++YSP+ +V+Y VE+ R  Q  D+D
Sbjct: 145 KGRLDMELTVERGRGYVTAAQNKQAGAEIGRIPVDSIYSPVLRVTYRVEATRVEQRTDFD 204

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           +L + +++  S+    ++A A   L +  G+    +E  + +    + +       L   
Sbjct: 205 RLIIDVESKPSMGPRTALASAGSTLVELFGLARELDETAEGIDIGPSPQDAQLAADLALP 264

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +EEL+L+VRS NCL+ E I  +G+LI RTEAD+L + NFG+KS+ E+K  L  MGL L  
Sbjct: 265 IEELDLTVRSYNCLKREGINTVGELIGRTEADLLDIRNFGQKSIDEVKMKLAGMGLGLKD 324

Query: 320 NLPDWPPESI 329
           + P++ P ++
Sbjct: 325 SAPNFDPANV 334


>gi|320352939|ref|YP_004194278.1| DNA-directed RNA polymerase subunit alpha [Desulfobulbus
           propionicus DSM 2032]
 gi|320121441|gb|ADW16987.1| DNA-directed RNA polymerase subunit alpha [Desulfobulbus
           propionicus DSM 2032]
          Length = 346

 Score =  342 bits (877), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 155/336 (46%), Positives = 214/336 (63%), Gaps = 4/336 (1%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
            KNW  LI P  +E    G         + +PL RGFA T+GN+LRR+++SS+RGAAIT+
Sbjct: 12  YKNWHSLISPEKLEVDE-GTLTSRYGKFVCQPLERGFATTIGNSLRRIMLSSIRGAAITS 70

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           V+I   LHE ++I GVHED+ +IILN+K + LK+ G   + V + K GPG V AGDI   
Sbjct: 71  VRIGNALHEFTTIDGVHEDVAEIILNLKQVRLKLHGPESRTVVLEKNGPGRVLAGDINGG 130

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
             +EV+NP+ VIC +  +   R EL V  G GYVPA+ ++ E   IG+I IDA +SPI +
Sbjct: 131 AYVEVMNPELVICTVTSETNFRAELEVHWGKGYVPAEQNKKEGQSIGVIPIDAAFSPIIR 190

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y V  AR GQ  DYD+L+M I+TDGS+  + ++A A++IL++Q+ +FINF E   +  
Sbjct: 191 VQYVVSQARVGQQTDYDRLTMEIETDGSVEPQSALAYAAKILKEQMTIFINFNEEIAKAP 250

Query: 243 E--DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           +  D +     + P L K VE+LELSVRS NCL+   I Y+G L+ +T+A+ML+  NFGR
Sbjct: 251 DSLDSDEDGKAYPPFLDKNVEDLELSVRSANCLKNAQIQYIGQLVNKTDAEMLKTKNFGR 310

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDW-PPESIEELAKK 335
           KSL EIK +L    L LGM    W  PE  EE  ++
Sbjct: 311 KSLNEIKALLAEHNLTLGMKYEGWVAPEKREEKLEE 346


>gi|332077536|gb|EGI87997.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae GA41301]
          Length = 311

 Score =  342 bits (877), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 132/313 (42%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  +  +     
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIARSTEVMKEA 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            +   +  L + +EEL+LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E+K
Sbjct: 239 DTESDDRILDRTIEELDLSVRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L   
Sbjct: 299 LKLIDLGLGLKDK 311


>gi|291613262|ref|YP_003523419.1| DNA-directed RNA polymerase subunit alpha [Sideroxydans
           lithotrophicus ES-1]
 gi|291583374|gb|ADE11032.1| DNA-directed RNA polymerase, alpha subunit [Sideroxydans
           lithotrophicus ES-1]
          Length = 323

 Score =  342 bits (877), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 152/331 (45%), Positives = 207/331 (62%), Gaps = 10/331 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  N   L+KP  I+     +    +  ++ EP  RG+ HTLGNALRRVL+SS+ G A+T
Sbjct: 1   MSNN--NLLKPRIIDVQ---RSSATQARVVMEPFERGYGHTLGNALRRVLLSSMPGYAVT 55

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I GVLHE SSI GV ED+ +I+LN+KG+ LK+       + + K G GVVTA DI+ 
Sbjct: 56  EVKIAGVLHEYSSIDGVQEDVVEILLNLKGLVLKLHNSREATLHLRKSGAGVVTAADIEV 115

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN--DPIGLITIDALYSP 179
             D EV+NP+HVI +L     + ME+ V +G GYV A          P+G I +DA +SP
Sbjct: 116 GADTEVINPNHVIAHLAAGGKLDMEIKVEQGRGYVSAISRMQPGATRPVGHIALDASFSP 175

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I +VSY VESAR  Q  D DKL M I+T+ +I  E+++  A+RIL DQL +F   E    
Sbjct: 176 ISRVSYAVESARVEQRTDLDKLIMDIETNSAIDPEEAIRYAARILMDQLSVFAALEGTPA 235

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            V++     +   +P LL+ V++LEL+ RS+NCL+ ++I Y+GDLIQ TEAD+LR  N G
Sbjct: 236 PVEKPQ---TPKVDPMLLRPVDDLELTPRSSNCLKAQSIHYIGDLIQNTEADLLRTPNLG 292

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           RKSL EIK VL   GL LGM L +W   S +
Sbjct: 293 RKSLNEIKQVLAEHGLSLGMKLENWTAMSEK 323


>gi|322377205|ref|ZP_08051697.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus sp. M334]
 gi|321281918|gb|EFX58926.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus sp. M334]
          Length = 311

 Score =  342 bits (877), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 133/313 (42%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  K  +     
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSTEVMKEA 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            +   +  L + +EEL+LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E+K
Sbjct: 239 DTESDDRILDRTIEELDLSVRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L   
Sbjct: 299 FKLIDLGLGLKDK 311


>gi|297242944|ref|ZP_06926882.1| DNA-directed RNA polymerase, alpha subunit [Gardnerella vaginalis
           AMD]
 gi|296889155|gb|EFH27889.1| DNA-directed RNA polymerase, alpha subunit [Gardnerella vaginalis
           AMD]
          Length = 331

 Score =  342 bits (877), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 123/312 (39%), Positives = 179/312 (57%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                   R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ GV
Sbjct: 10  TEESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTTLPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+I+LNIKGI L    D    + + K G G  TAGDI     + + NPD  I  L 
Sbjct: 70  EEDVTEILLNIKGIVLTSEYDEPVVMYLRKNGKGEATAGDITPPAGVTIANPDLHIATLA 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  + +E TV +G GYVPA+ ++ EN  IG I +D++YSP+ KVSY VE+ R  Q  D+
Sbjct: 130 EDGELEIEFTVERGRGYVPAQMNKQENSEIGRIPVDSIYSPVLKVSYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  +IT  D+VA A   L +  G+        + V+          +  L  
Sbjct: 190 DKLILDVETKPAITPRDAVASAGSTLVELFGLCRELNVDAEGVEVGPAPTHDEADSQLAI 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E++  + RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L TMGL L 
Sbjct: 250 PIEDMNFTQRSYNCLKREGIHTVGELVVHTEQDLLDIRNFGMKSIDEVKEKLQTMGLSLK 309

Query: 319 MNLPDWPPESIE 330
            +   +   ++E
Sbjct: 310 ASPIGFDANNLE 321


>gi|283782779|ref|YP_003373533.1| DNA-directed RNA polymerase, alpha subunit [Gardnerella vaginalis
           409-05]
 gi|283441001|gb|ADB13467.1| DNA-directed RNA polymerase, alpha subunit [Gardnerella vaginalis
           409-05]
          Length = 331

 Score =  342 bits (877), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 122/312 (39%), Positives = 178/312 (57%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                   R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ GV
Sbjct: 10  TEESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTTLPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+I+LNIKGI L    D    + + K G G  TAGDI     + + NPD  I  L 
Sbjct: 70  EEDVTEILLNIKGIVLTSEYDEPVVMYLRKNGKGEATAGDITPPAGVTIANPDLHIATLA 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  + +E TV +G GYVPA+ ++ EN  IG I +D++YSP+ KVSY VE+ R  Q  D+
Sbjct: 130 EDGELEIEFTVERGRGYVPAQMNKQENSEIGRIPVDSIYSPVLKVSYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  +IT  D+VA A   L +  G+        + V+          +  L  
Sbjct: 190 DKLILDVETKPAITPRDAVASAGSTLVELFGLCRELNVDAEGVEVGPAPTHDEADSQLAI 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E++  + RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L  MGL L 
Sbjct: 250 PIEDMNFTQRSYNCLKREGIHTVGELVVHTEQDLLDIRNFGMKSIDEVKEKLQAMGLSLK 309

Query: 319 MNLPDWPPESIE 330
            +   +   ++E
Sbjct: 310 ASPIGFDANNLE 321


>gi|294786438|ref|ZP_06751692.1| DNA-directed RNA polymerase, alpha subunit [Parascardovia
           denticolens F0305]
 gi|315226001|ref|ZP_07867789.1| DNA-directed RNA polymerase subunit alpha [Parascardovia
           denticolens DSM 10105]
 gi|294485271|gb|EFG32905.1| DNA-directed RNA polymerase, alpha subunit [Parascardovia
           denticolens F0305]
 gi|315120133|gb|EFT83265.1| DNA-directed RNA polymerase subunit alpha [Parascardovia
           denticolens DSM 10105]
          Length = 331

 Score =  342 bits (877), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 121/302 (40%), Positives = 179/302 (59%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
              Q    R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ GV
Sbjct: 10  TEEQINPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTALPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+ +I+LNIK + L    D    + + K G G  TA DI     + V NPD  I  L 
Sbjct: 70  KEDVAEILLNIKELVLTSEYDEPVVMYLRKSGEGEATAADITPPAGVVVANPDLHIATLA 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  + +E TV +G GYVPA+ ++ E D IG I +D++YSP+ KVSY V+  R  Q  D+
Sbjct: 130 EDGELEIEFTVERGRGYVPAQMNKQEGDEIGRIPVDSIYSPVLKVSYKVDPTRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL++ ++T  SI+  D+VA A   L +  G+F       + V+          +P +  
Sbjct: 190 DKLTVDVETKPSISPRDAVASAGSTLVELFGLFHELNNQAEGVEVGPAPVVEEVDPQMEI 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L L+ RS NCL+ E I  +G+L++R+E D+L + NFG+KS+ E+K  L +MGL L 
Sbjct: 250 PIEDLNLTQRSYNCLKREGIHTIGELVKRSEQDLLDIRNFGQKSIDEVKEKLDSMGLSLK 309

Query: 319 MN 320
            +
Sbjct: 310 QS 311


>gi|308235469|ref|ZP_07666206.1| DNA-directed RNA polymerase subunit alpha [Gardnerella vaginalis
           ATCC 14018]
 gi|311115142|ref|YP_003986363.1| DNA-directed RNA polymerase subunit alpha [Gardnerella vaginalis
           ATCC 14019]
 gi|310946636|gb|ADP39340.1| DNA-directed RNA polymerase subunit alpha [Gardnerella vaginalis
           ATCC 14019]
          Length = 331

 Score =  342 bits (877), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 122/312 (39%), Positives = 180/312 (57%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                   R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ GV
Sbjct: 10  TEESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTTLPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+I+LNIKGI L    D    + + K G G  TAGDI     + + NP+  I  L 
Sbjct: 70  EEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGVTIANPEMHIATLA 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  + +E TV +G GYVPA+ ++ EN  IG I +D++YSP+ KVSY VE+ R  Q  D+
Sbjct: 130 EDGELEIEFTVERGRGYVPAQMNKQENSEIGRIPVDSIYSPVLKVSYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  +IT  D+VA A   L +  G+        + V+          +  +  
Sbjct: 190 DKLILDVETKPAITPRDAVASAGSTLVELFGLCRELNVDAEGVEVGPAPVMGEVDSQMAT 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  L +MGL L 
Sbjct: 250 PIEDLNLTQRSYNCLKREGIHTVGELVVHTEQDLLDIRNFGMKSIDEVKEKLQSMGLSLK 309

Query: 319 MNLPDWPPESIE 330
            +   +   ++E
Sbjct: 310 ASPLGFDANNLE 321


>gi|319787901|ref|YP_004147376.1| DNA-directed RNA polymerase subunit alpha [Pseudoxanthomonas
           suwonensis 11-1]
 gi|317466413|gb|ADV28145.1| DNA-directed RNA polymerase, alpha subunit [Pseudoxanthomonas
           suwonensis 11-1]
          Length = 332

 Score =  342 bits (877), Expect = 6e-92,   Method: Composition-based stats.
 Identities = 143/326 (43%), Positives = 218/326 (66%), Gaps = 9/326 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            ++++P   +   L     NR  ++ EPL RG+ HTLGNALRRVL+SS+ G AIT V+ID
Sbjct: 6   NQVLRPRGPQIERLN---GNRAKIVIEPLERGYGHTLGNALRRVLLSSIPGFAITEVEID 62

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE ++++G+ ED+ +++LN+K + ++M       +++ K+GPGVVTAGDI+T + +E
Sbjct: 63  GVLHEYTTVEGLQEDVLEVLLNLKDVAIRMHTGESATLSLAKQGPGVVTAGDIKTDHSVE 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKV 183
           +LNP+HVIC+L  D  + M L + +G GY PA   R  ++     G + +DA +SP+++V
Sbjct: 123 ILNPEHVICHLTKDTALNMRLKIERGFGYQPATSRRRPDEETRAIGRLMLDASFSPVRRV 182

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+VE+AR  Q  D DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +
Sbjct: 183 AYSVEAARVEQRTDLDKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAK 242

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                    +P LL+ +++LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KSL
Sbjct: 243 PAQAG---VDPVLLRPIDDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSL 299

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESI 329
            EIK VL   GL LGM L +WPP  +
Sbjct: 300 TEIKEVLAQRGLSLGMKLENWPPAGV 325


>gi|282855170|ref|ZP_06264502.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           J139]
 gi|289427589|ref|ZP_06429301.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           J165]
 gi|295131352|ref|YP_003582015.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           SK137]
 gi|282581758|gb|EFB87143.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           J139]
 gi|289159080|gb|EFD07272.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           J165]
 gi|291375859|gb|ADD99713.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           SK137]
 gi|313773118|gb|EFS39084.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL074PA1]
 gi|313810401|gb|EFS48115.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL083PA1]
 gi|313812263|gb|EFS49977.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL025PA1]
 gi|313817984|gb|EFS55698.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL046PA2]
 gi|313819897|gb|EFS57611.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL036PA1]
 gi|313823388|gb|EFS61102.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL036PA2]
 gi|313824859|gb|EFS62573.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL063PA1]
 gi|313830101|gb|EFS67815.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL007PA1]
 gi|313832627|gb|EFS70341.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL056PA1]
 gi|314925754|gb|EFS89585.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL036PA3]
 gi|314960834|gb|EFT04935.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL002PA2]
 gi|314964876|gb|EFT08975.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL082PA2]
 gi|314973050|gb|EFT17146.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL053PA1]
 gi|314975546|gb|EFT19641.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL045PA1]
 gi|314979765|gb|EFT23859.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL072PA2]
 gi|314982217|gb|EFT26310.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL110PA3]
 gi|314984829|gb|EFT28921.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL005PA1]
 gi|314986088|gb|EFT30180.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL005PA2]
 gi|314988703|gb|EFT32794.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL005PA3]
 gi|315079863|gb|EFT51839.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL078PA1]
 gi|315083183|gb|EFT55159.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL027PA2]
 gi|315086863|gb|EFT58839.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL002PA3]
 gi|315089955|gb|EFT61931.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL072PA1]
 gi|315090477|gb|EFT62453.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL110PA4]
 gi|315093710|gb|EFT65686.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL060PA1]
 gi|315096723|gb|EFT68699.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL038PA1]
 gi|315104002|gb|EFT75978.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL050PA2]
 gi|327325137|gb|EGE66943.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL096PA3]
 gi|327325234|gb|EGE67039.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL096PA2]
 gi|327325530|gb|EGE67329.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL103PA1]
 gi|327444034|gb|EGE90688.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL043PA1]
 gi|327449338|gb|EGE95992.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL013PA2]
 gi|327449434|gb|EGE96088.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL043PA2]
 gi|328756317|gb|EGF69933.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL020PA1]
 gi|328761349|gb|EGF74876.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL099PA1]
          Length = 338

 Score =  342 bits (877), Expect = 6e-92,   Method: Composition-based stats.
 Identities = 121/320 (37%), Positives = 184/320 (57%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                 E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV HE S+I+G 
Sbjct: 10  TEESISEFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQHEFSTIEGC 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+IILN+KG+ L    D    + + K G G VTA DI     + + NP+  I  L+
Sbjct: 70  VEDVTEIILNLKGLVLSSEEDEPVAMYLRKSGAGEVTAADINPPAGVTIHNPELHIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D    MEL V +G GYV +  +   N  IG I +D++YSP+ KV+Y VE+ R  Q  D+
Sbjct: 130 DDGRFEMELIVERGRGYVSSALNDDPNAEIGRIAVDSIYSPVLKVTYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  SI   D++A A + L +  G+        + ++         +  +L  
Sbjct: 190 DKLVVDVETKPSILPRDAIASAGKTLVELFGLTRELNAEAEGIEIGSGPVDEEYAESLGT 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  +GL L 
Sbjct: 250 PVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEKLTELGLALK 309

Query: 319 MNLPDWPPESIEELAKKYED 338
            + P + P +  E   +  D
Sbjct: 310 DSAPGFDPLAAAEAYDEAND 329


>gi|76787566|ref|YP_328809.1| DNA-directed RNA polymerase subunit alpha [Streptococcus agalactiae
           A909]
 gi|90110872|sp|Q3K3U4|RPOA_STRA1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|76562623|gb|ABA45207.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae A909]
          Length = 312

 Score =  342 bits (877), Expect = 6e-92,   Method: Composition-based stats.
 Identities = 129/313 (41%), Positives = 200/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EFEKP----IITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKIIELDVEGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +     ++  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIAEGHSLKATMTVAKNRGYVPAEGNKKDDVPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K  +     
Sbjct: 179 EPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +     L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 EKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 IKLADLGLGLKND 311


>gi|293364322|ref|ZP_06611048.1| DNA-directed RNA polymerase subunit alpha [Streptococcus oralis
           ATCC 35037]
 gi|291317168|gb|EFE57595.1| DNA-directed RNA polymerase subunit alpha [Streptococcus oralis
           ATCC 35037]
          Length = 311

 Score =  342 bits (877), Expect = 6e-92,   Method: Composition-based stats.
 Identities = 132/313 (42%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  K  +     
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSTEVMKEA 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            +   +  L + +EEL+LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E+K
Sbjct: 239 DTESDDRILDRTIEELDLSVRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L   
Sbjct: 299 LKLIDLGLGLKDK 311


>gi|254429260|ref|ZP_05042967.1| DNA-directed RNA polymerase, alpha subunit [Alcanivorax sp. DG881]
 gi|196195429|gb|EDX90388.1| DNA-directed RNA polymerase, alpha subunit [Alcanivorax sp. DG881]
          Length = 335

 Score =  341 bits (876), Expect = 6e-92,   Method: Composition-based stats.
 Identities = 148/332 (44%), Positives = 220/332 (66%), Gaps = 9/332 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             + + P +I    +    +    ++ EPL RGF HTLG ALRR+L+SS+ G AIT V+I
Sbjct: 4   VNDFLTPRSI---AVNAINQTHAKVVLEPLERGFGHTLGTALRRILISSMPGCAITEVEI 60

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGV HE SSI+GV ED+ +I+LN+KG+ L+M       + + K+GPG VTA DIQ  + +
Sbjct: 61  DGVQHEYSSIEGVQEDVINILLNLKGVALQMEDREEATLELVKKGPGAVTANDIQRDHSV 120

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKK 182
           E++NPDH+IC +  D  +R++L V KG GYV A   ++E+D     G + +DA YSP+++
Sbjct: 121 EIVNPDHLICTITGDTELRVKLKVQKGRGYVAADSRQSEDDETRGIGRLQLDASYSPVRR 180

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+Y VE+AR  Q  D DKL + ++TDG+I  E+++  A+ ILQ Q+ +F++ E+  K   
Sbjct: 181 VAYVVEAARVEQRTDLDKLVIDLETDGTIDPEEAIRRAATILQQQIAVFVDLEQDAKP-- 238

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
            +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G+KS
Sbjct: 239 -EPKQEREEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLGKKS 297

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           L EIK VL + GL LGM L +WPP S+ +  +
Sbjct: 298 LTEIKDVLASKGLSLGMRLENWPPVSLRDDDR 329


>gi|94266328|ref|ZP_01290030.1| DNA-directed RNA polymerase, alpha subunit [delta proteobacterium
           MLMS-1]
 gi|93453082|gb|EAT03561.1| DNA-directed RNA polymerase, alpha subunit [delta proteobacterium
           MLMS-1]
          Length = 365

 Score =  341 bits (876), Expect = 6e-92,   Method: Composition-based stats.
 Identities = 152/331 (45%), Positives = 214/331 (64%), Gaps = 4/331 (1%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
            +NW +LI P ++E        E     + +PL RGFA T+GN+LRR+L+SS++G AIT+
Sbjct: 32  YRNWHDLIIPESLEVDQ-ENHSERFGKFVCQPLERGFATTIGNSLRRILLSSIQGVAITS 90

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
            +IDGVLHE+S+I GV ED T+IILN+K + L++  +  + V I K+  GV+TA DI   
Sbjct: 91  AKIDGVLHELSTIPGVKEDATEIILNLKEVRLRLHSEKPRMVKIDKKKKGVITAADIVGD 150

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
             +EV+NP+  IC +  D     EL V  G GYV A+ +++E   IG+I +DA+++PI+ 
Sbjct: 151 -QVEVMNPEQHICTITGDGHFVAELEVRWGKGYVSAERNKSEEQTIGVIALDAIFTPIRN 209

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK-KEV 241
           V      AR GQ  DYDKL + I TDGSI  ED++A  ++IL++QL +FINF+E +   V
Sbjct: 210 VKVITSQARVGQQTDYDKLILEITTDGSIRPEDALAYGAKILKEQLQVFINFDEERVVPV 269

Query: 242 KEDINVKSLPF-NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           K D      P  N  L + VE+LELSVRS NCLR   I ++G+L+Q++EA+ML+  NFGR
Sbjct: 270 KSDSEPGEKPKLNENLYRSVEDLELSVRSANCLRNAEINHIGELVQKSEAEMLKTKNFGR 329

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           KSL EIK +L  M L+LGM +  W P    E
Sbjct: 330 KSLNEIKQLLAEMDLYLGMKIDGWEPPPAAE 360


>gi|288942047|ref|YP_003444287.1| DNA-directed RNA polymerase subunit alpha [Allochromatium vinosum
           DSM 180]
 gi|288897419|gb|ADC63255.1| DNA-directed RNA polymerase, alpha subunit [Allochromatium vinosum
           DSM 180]
          Length = 337

 Score =  341 bits (876), Expect = 6e-92,   Method: Composition-based stats.
 Identities = 146/330 (44%), Positives = 211/330 (63%), Gaps = 5/330 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +KP  ++   +       + +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I G
Sbjct: 7   EFLKPRIVKVEQVDG-NPCHSRVSLEPLERGFGHTLGNALRRILLSSMDGYAVTEVEIQG 65

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE ++++GV ED+ +I+LN K + + + G       + KRGPG VTA DI   +  E+
Sbjct: 66  VLHEYTTLEGVQEDVLEILLNFKQLAIVLQGKDEATFALSKRGPGPVTAADIAIDHTAEI 125

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYSPIKKVS 184
            NP+ VI NL     + M LTV +G GY PA        E+ PIG + IDA +SP+++V+
Sbjct: 126 ANPELVIANLTTGGELSMTLTVRRGRGYEPASQRELEGAEDRPIGKLPIDASFSPVRRVA 185

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK-EVKE 243
             V+SAR  Q  D D+L + ++T+G+I  ++++  A+ IL+DQL  F+  E     E + 
Sbjct: 186 IEVQSARVEQRTDLDRLVIDLETNGTIDPKETIQRAATILRDQLSSFVALEGTAPAETQV 245

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             +    P++P LL+ V++LEL+VRS NCL+ ENI  +GDLIQRTE ++L+  N G+KSL
Sbjct: 246 QESRDESPYDPILLRPVDDLELTVRSANCLKAENIYLIGDLIQRTEVELLKTPNLGKKSL 305

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELA 333
            EIK VL T GL LGM L +WPPE+I EL+
Sbjct: 306 TEIKDVLATRGLSLGMRLENWPPENIAELS 335


>gi|21230388|ref|NP_636305.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas campestris
           pv. campestris str. ATCC 33913]
 gi|21241761|ref|NP_641343.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas axonopodis
           pv. citri str. 306]
 gi|58583181|ref|YP_202197.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas oryzae pv.
           oryzae KACC10331]
 gi|66769618|ref|YP_244380.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas campestris
           pv. campestris str. 8004]
 gi|78046579|ref|YP_362754.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas campestris
           pv. vesicatoria str. 85-10]
 gi|84625020|ref|YP_452392.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas oryzae pv.
           oryzae MAFF 311018]
 gi|166710857|ref|ZP_02242064.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas oryzae pv.
           oryzicola BLS256]
 gi|188575514|ref|YP_001912443.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas oryzae pv.
           oryzae PXO99A]
 gi|188992830|ref|YP_001904840.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas campestris
           pv. campestris str. B100]
 gi|289665161|ref|ZP_06486742.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas campestris
           pv. vasculorum NCPPB702]
 gi|294627862|ref|ZP_06706441.1| DNA-directed RNA polymerase alpha subunit [Xanthomonas fuscans
           subsp. aurantifolii str. ICPB 11122]
 gi|294664167|ref|ZP_06729553.1| DNA-directed RNA polymerase alpha subunit [Xanthomonas fuscans
           subsp. aurantifolii str. ICPB 10535]
 gi|325916511|ref|ZP_08178780.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas vesicatoria
           ATCC 35937]
 gi|325921505|ref|ZP_08183360.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas gardneri
           ATCC 19865]
 gi|325925363|ref|ZP_08186765.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas perforans
           91-118]
 gi|59800197|sp|P0A0Y1|RPOA_XANCP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|59800198|sp|P0A0Y2|RPOA_XANAC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|75434358|sp|Q5GWV9|RPOA_XANOR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|81304427|sp|Q4URG3|RPOA_XANC8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|90110876|sp|Q3BWV9|RPOA_XANC5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366750|sp|Q2P009|RPOA_XANOM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|229564281|sp|B0RU58|RPOA_XANCB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238689542|sp|B2SQT4|RPOA_XANOP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|7709421|gb|AAD00325.2| RNA polymerase ALPHA subunit [Xanthomonas campestris pv.
           campestris]
 gi|21107133|gb|AAM35879.1| RNA polymerase alpha subunit [Xanthomonas axonopodis pv. citri str.
           306]
 gi|21111945|gb|AAM40229.1| RNA polymerase alpha subunit [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|58427775|gb|AAW76812.1| RNA polymerase alpha subunit [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|66574950|gb|AAY50360.1| RNA polymerase alpha subunit [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|78035009|emb|CAJ22654.1| DNA directed RNA polymerase (alpha subunit) [Xanthomonas campestris
           pv. vesicatoria str. 85-10]
 gi|84368960|dbj|BAE70118.1| RNA polymerase alpha subunit [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|167734590|emb|CAP52800.1| DNA directed RNA polymerase (alpha subunit) [Xanthomonas campestris
           pv. campestris]
 gi|188519966|gb|ACD57911.1| DNA-directed RNA polymerase, alpha subunit [Xanthomonas oryzae pv.
           oryzae PXO99A]
 gi|292597776|gb|EFF41934.1| DNA-directed RNA polymerase alpha subunit [Xanthomonas fuscans
           subsp. aurantifolii str. ICPB 11122]
 gi|292606070|gb|EFF49335.1| DNA-directed RNA polymerase alpha subunit [Xanthomonas fuscans
           subsp. aurantifolii str. ICPB 10535]
 gi|325537300|gb|EGD09027.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas vesicatoria
           ATCC 35937]
 gi|325544241|gb|EGD15622.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas perforans
           91-118]
 gi|325548052|gb|EGD19051.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas gardneri
           ATCC 19865]
          Length = 332

 Score =  341 bits (876), Expect = 6e-92,   Method: Composition-based stats.
 Identities = 141/328 (42%), Positives = 217/328 (66%), Gaps = 9/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            ++++P   +   L    +NR  ++ EPL RG+ HTLGNALRRVL+SS+ G AIT V+ID
Sbjct: 6   NQVLRPRGPQIERL---TDNRAKVVIEPLERGYGHTLGNALRRVLLSSIPGFAITEVEID 62

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE ++++G+ ED+ D++LN+K + ++M       +++ K+GPG VTA DI+T +++E
Sbjct: 63  GVLHEYTTVEGLQEDVLDVLLNLKDVAIRMHSGDSATLSLSKQGPGTVTAADIRTDHNVE 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKV 183
           ++N DHVIC+L  D  + M L + +G GY PA   R  ++     G + +DA +SP+++V
Sbjct: 123 IINGDHVICHLTKDTALNMRLKIERGFGYQPAAARRRPDEETRTIGRLMLDASFSPVRRV 182

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +
Sbjct: 183 AYAVEAARVEQRTDLDKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAK 242

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                    +P LL+ +++LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KSL
Sbjct: 243 PAASG---VDPVLLRPIDDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSL 299

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL   GL LGM L +WPP  + +
Sbjct: 300 TEIKEVLAQRGLALGMKLENWPPAGVAQ 327


>gi|257095015|ref|YP_003168656.1| DNA-directed RNA polymerase subunit alpha [Candidatus
           Accumulibacter phosphatis clade IIA str. UW-1]
 gi|257047539|gb|ACV36727.1| DNA-directed RNA polymerase, alpha subunit [Candidatus
           Accumulibacter phosphatis clade IIA str. UW-1]
          Length = 324

 Score =  341 bits (876), Expect = 6e-92,   Method: Composition-based stats.
 Identities = 148/332 (44%), Positives = 209/332 (62%), Gaps = 10/332 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +   L KP  I+   L         ++ EP  RG+ HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQSS--GLFKPRIIDVQSLSPV---HARVVMEPFERGYGHTLGNALRRILLSSMPGYAPT 55

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V IDGVLHE S+I GV ED+ DI+LN+KG+  K+       + + K G GVV A DI+ 
Sbjct: 56  EVSIDGVLHEYSTIDGVQEDVVDILLNLKGVVFKLHNREEVVLHLRKEGKGVVRAADIEV 115

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN--DPIGLITIDALYSP 179
            +D+E++NP+H+I +L     + MEL V K  GY+        +    IG + +DA +SP
Sbjct: 116 SHDVEIINPEHIIAHLSAGGKLAMELKVEKSRGYLAGNLREFGDGGKSIGKLVLDASFSP 175

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +++VSY VESAR  Q  D DKL M I+T+G+I  E+++  A+RIL +QL +F +      
Sbjct: 176 VRRVSYAVESARVEQRTDLDKLIMDIETNGAIEPEEAIRTAARILMEQLSVFADLAGTAM 235

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            ++     K++  +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G
Sbjct: 236 PIEY---QKTVQVDPLLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLG 292

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           RKSL EIK VL   GL LGM L +WPP  +E+
Sbjct: 293 RKSLNEIKEVLAARGLTLGMKLENWPPAGLEK 324


>gi|295396439|ref|ZP_06806601.1| DNA-directed RNA polymerase subunit alpha [Brevibacterium
           mcbrellneri ATCC 49030]
 gi|294970741|gb|EFG46654.1| DNA-directed RNA polymerase subunit alpha [Brevibacterium
           mcbrellneri ATCC 49030]
          Length = 332

 Score =  341 bits (876), Expect = 6e-92,   Method: Composition-based stats.
 Identities = 121/329 (36%), Positives = 193/329 (58%), Gaps = 4/329 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V     + R+  I EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVLH
Sbjct: 6   RPTLNEEVV----SDYRSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T+ ILN+K + +    D      + K+GPG VTA DI     +EV NP
Sbjct: 62  EFSTVPGVKEDVTEFILNLKSLVVSSEFDEPVVAYLRKQGPGEVTAADISAPGGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I +L+ +  + +ELT+ +G GYV A  ++  +  IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLHIASLNDEGQLDIELTIERGRGYVSAAQNKNADAEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  SI   D+VA A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDRLIIDVETKPSILPRDAVASAGKTLVELFGLARELNVEAEGIDIGPSPVDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +E+L+L+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L
Sbjct: 242 ALAADLALAIEDLDLTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGSKSIDEVKQKL 301

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             + L L  +   +   +++      ED+
Sbjct: 302 NELNLSLKDSPNGFGEANLDSDESFVEDE 330


>gi|209693948|ref|YP_002261876.1| DNA-directed RNA polymerase subunit alpha [Aliivibrio salmonicida
           LFI1238]
 gi|238057754|sp|B6EPU9|RPOA_ALISL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|208007899|emb|CAQ78029.1| RNA polymerase alpha-subunit [Aliivibrio salmonicida LFI1238]
          Length = 329

 Score =  341 bits (876), Expect = 7e-92,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 217/334 (64%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSLTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI  
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVIITLNKSGAGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E+ NP+HVIC+L  D A + M + V +G GYVP+    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIANPEHVICHLTDDNAEISMRIKVERGRGYVPSTARIHTEEDERPIGRLLVDATY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ K+SY VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDKISYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|125717012|ref|YP_001034145.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK36]
 gi|323350965|ref|ZP_08086623.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           VMC66]
 gi|158513356|sp|A3CK90|RPOA_STRSV RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|125496929|gb|ABN43595.1| DNA-directed RNA polymerase, alpha chain, putative [Streptococcus
           sanguinis SK36]
 gi|322122947|gb|EFX94653.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           VMC66]
 gi|324989977|gb|EGC21918.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK353]
 gi|324991840|gb|EGC23765.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK405]
 gi|324996270|gb|EGC28178.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK678]
 gi|325686430|gb|EGD28460.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK72]
 gi|325689206|gb|EGD31212.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK115]
 gi|325695785|gb|EGD37682.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK150]
 gi|325698001|gb|EGD39884.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK160]
 gi|327458456|gb|EGF04812.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK1]
 gi|327463697|gb|EGF10013.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK1057]
 gi|327467360|gb|EGF12860.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK330]
 gi|327471717|gb|EGF17158.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK408]
 gi|327490438|gb|EGF22220.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK1058]
 gi|328945192|gb|EGG39346.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           SK1087]
          Length = 312

 Score =  341 bits (876), Expect = 7e-92,   Method: Composition-based stats.
 Identities = 130/313 (41%), Positives = 195/313 (62%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILN+KGI +K      K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTISGVREDVMQIILNVKGIAVKSYVQDEKIIELDVEGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A  +  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+ KV+Y V
Sbjct: 119 INPDHYLFTIGEGASFKATMTVNSGRGYVPADENKKDDAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E           
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLFTNLTEVAIAADVMKEA 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    +  L + +EEL+LSVRS NCL+   I  + DL +++E +M+++ N GRKSL E+K
Sbjct: 239 EKTSDDRILERTIEELDLSVRSYNCLKRAGINTVFDLTEKSEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKND 311


>gi|194364558|ref|YP_002027168.1| DNA-directed RNA polymerase subunit alpha [Stenotrophomonas
           maltophilia R551-3]
 gi|254523842|ref|ZP_05135897.1| DNA-directed RNA polymerase, alpha subunit [Stenotrophomonas sp.
           SKA14]
 gi|238693448|sp|B4SLH5|RPOA_STRM5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|194347362|gb|ACF50485.1| DNA-directed RNA polymerase, alpha subunit [Stenotrophomonas
           maltophilia R551-3]
 gi|219721433|gb|EED39958.1| DNA-directed RNA polymerase, alpha subunit [Stenotrophomonas sp.
           SKA14]
          Length = 332

 Score =  341 bits (876), Expect = 7e-92,   Method: Composition-based stats.
 Identities = 142/328 (43%), Positives = 216/328 (65%), Gaps = 9/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            ++++P   +   L    + R  ++ EPL RG+ HTLGNALRRVL+SS+ G AIT V+ID
Sbjct: 6   NQVLRPRGPQIERL---TDTRAKVVIEPLERGYGHTLGNALRRVLLSSIPGFAITEVEID 62

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE ++++G+ ED+ +++LN+K + ++M       +++ K+GPGVVTA DI+  +++E
Sbjct: 63  GVLHEYTTVEGLQEDVLEVLLNLKDVAIRMHSGDSATLSLSKQGPGVVTAADIKVDHNVE 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKV 183
           +LN DHVIC+L  D  V M L + +G GY PA   R  ++     G + +DA +SP+++V
Sbjct: 123 ILNGDHVICHLTKDTAVNMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRV 182

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +
Sbjct: 183 AYAVEAARVEQRTDLDKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAK 242

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             N      +P LL+ +++LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KSL
Sbjct: 243 PAN---NGVDPVLLRPIDDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSL 299

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL   GL LGM L +WPP  +  
Sbjct: 300 TEIKEVLAQRGLSLGMKLENWPPAGVAS 327


>gi|190572968|ref|YP_001970813.1| DNA-directed RNA polymerase subunit alpha [Stenotrophomonas
           maltophilia K279a]
 gi|229564258|sp|B2FQK8|RPOA_STRMK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|190010890|emb|CAQ44499.1| putative DNA-directed RNA polymerase alpha chain [Stenotrophomonas
           maltophilia K279a]
          Length = 332

 Score =  341 bits (876), Expect = 7e-92,   Method: Composition-based stats.
 Identities = 141/328 (42%), Positives = 216/328 (65%), Gaps = 9/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            ++++P   +   L    + R  ++ EPL RG+ HTLGNALRRVL+SS+ G AIT V+ID
Sbjct: 6   NQVLRPRGPQIERL---TDTRAKVVIEPLERGYGHTLGNALRRVLLSSIPGFAITEVEID 62

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE ++++G+ ED+ +++LN+K + ++M       +++ K+GPGVVTA DI+  +++E
Sbjct: 63  GVLHEYTTVEGLQEDVLEVLLNLKDVAIRMHSGDSATLSLSKQGPGVVTAADIKVDHNVE 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKV 183
           +LN DHVIC+L  D  + M L + +G GY PA   R  ++     G + +DA +SP+++V
Sbjct: 123 ILNGDHVICHLTKDTAINMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRV 182

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +
Sbjct: 183 AYAVEAARVEQRTDLDKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAK 242

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             N      +P LL+ +++LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KSL
Sbjct: 243 PAN---NGVDPVLLRPIDDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSL 299

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL   GL LGM L +WPP  +  
Sbjct: 300 TEIKEVLAQRGLSLGMKLENWPPAGVAS 327


>gi|327332743|gb|EGE74477.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL097PA1]
          Length = 338

 Score =  341 bits (876), Expect = 7e-92,   Method: Composition-based stats.
 Identities = 119/308 (38%), Positives = 180/308 (58%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                 E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV HE S+I+G 
Sbjct: 10  TEESISEFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQHEFSTIEGC 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+IILN+KG+ L    D    + + K G G VTA DI     + + NP+  I  L+
Sbjct: 70  VEDVTEIILNLKGLVLSSEEDEPVAMYLRKTGAGEVTAADINPPAGVTIHNPELHIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D    MEL V +G GYV +  +   N  IG I +D++YSP+ KV+Y VE+ R  Q  D+
Sbjct: 130 DDGRFEMELIVERGRGYVSSALNDDPNAEIGRIAVDSIYSPVLKVTYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  SI   D++A A + L +  G+        + ++         +  +L  
Sbjct: 190 DKLVVDVETKPSILPRDAIASAGKTLVELFGLTRELNAEAEGIEIGSGPVDEEYAESLGT 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  +GL L 
Sbjct: 250 PVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEKLTELGLALK 309

Query: 319 MNLPDWPP 326
            + P + P
Sbjct: 310 DSAPGFDP 317


>gi|152964684|ref|YP_001360468.1| DNA-directed RNA polymerase subunit alpha [Kineococcus
           radiotolerans SRS30216]
 gi|189043840|sp|A6W5W5|RPOA_KINRD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|151359201|gb|ABS02204.1| DNA-directed RNA polymerase, alpha subunit [Kineococcus
           radiotolerans SRS30216]
          Length = 337

 Score =  341 bits (876), Expect = 7e-92,   Method: Composition-based stats.
 Identities = 126/319 (39%), Positives = 195/319 (61%), Gaps = 4/319 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLTEDVV----DEYRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSLRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +S+ GV ED+T+I+LN+K + +    D    + + K+GPG VTA DI     +EV NP
Sbjct: 62  EFTSVPGVKEDVTEIVLNVKNLVVSSEHDEPVVMYLRKQGPGAVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+    + +ELTV +G GYV A  ++T    IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLHIATLNAKGKLELELTVERGRGYVSAAQNKTGEQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  +I+  D+VA A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDRLVVDVETKHAISPRDAVASAGKTLTELFGLARELNVEAEGIDMGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L  ++E L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  L
Sbjct: 242 ALAADLALEIEALDLTVRSYNCLKREGIHSVGELVSRSEADLLDIRNFGQKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPPESI 329
             MGL L  + P + P ++
Sbjct: 302 VGMGLHLKDSPPGFDPSAV 320


>gi|170780766|ref|YP_001709098.1| DNA-directed RNA polymerase subunit alpha [Clavibacter
           michiganensis subsp. sepedonicus]
 gi|189043834|sp|B0RB72|RPOA_CLAMS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|169155334|emb|CAQ00437.1| DNA-directed RNA polymerase alpha chain [Clavibacter michiganensis
           subsp. sepedonicus]
          Length = 331

 Score =  341 bits (876), Expect = 7e-92,   Method: Composition-based stats.
 Identities = 119/307 (38%), Positives = 184/307 (59%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                 E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S++ GV
Sbjct: 10  TEESISEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFSTVPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+IILNIKG+ +    D      + K+G G VTA DI     +E+ NP+ VI  L+
Sbjct: 70  KEDVTEIILNIKGLVVSSEHDEPITAYLRKQGAGQVTAADISAPAGVEIHNPELVIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
             A   +ELT+ +G GYV A  +R+E    G I +D++YSP+ KV+Y VE+ R G+  D+
Sbjct: 130 EKAKFELELTIERGRGYVSATQNRSEFSEAGQIPVDSIYSPVLKVTYRVEATRAGERTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           D+L + ++T  +IT  D++A A R L +  G+        + ++          +  L  
Sbjct: 190 DRLVVDVETKSAITPRDAIASAGRTLTELFGLARELNSAAEGIEIGPAPVDAVLSSELSM 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L+LSVRS NCL+ E I  + +L+  +E  ++ + NFG+KS+ E+K  L  +GL L 
Sbjct: 250 PIEDLDLSVRSYNCLKREGIHNVSELVALSETQLMNIRNFGQKSVDEVKDKLVELGLSLK 309

Query: 319 MNLPDWP 325
             +P + 
Sbjct: 310 DAVPGFD 316


>gi|310829556|ref|YP_003961913.1| DNA-directed RNA polymerase [Eubacterium limosum KIST612]
 gi|308741290|gb|ADO38950.1| DNA-directed RNA polymerase [Eubacterium limosum KIST612]
          Length = 319

 Score =  341 bits (876), Expect = 7e-92,   Method: Composition-based stats.
 Identities = 136/316 (43%), Positives = 201/316 (63%), Gaps = 2/316 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP  I  IV   E+E     + EPL RG+  TLGN+LRR+++SSL G A+T+V+IDG
Sbjct: 3   EFEKP--IIEIVEKSEDETYGKFVVEPLERGYGTTLGNSLRRIMLSSLPGVAVTSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+ +I+LN+KG+  ++  D  K V I   G G +TAGDI T  D+E+
Sbjct: 61  VLHEFSTIPGVREDVVEILLNMKGLAAEIFSDEPKTVRIEAEGEGEITAGDIITDADVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L   A + ME+ + KG GYV +  ++    PIG + +D+++SPI+KV++ V
Sbjct: 121 LNPDMHIATLAKGATLNMEMRLEKGRGYVASDKNKYPGMPIGTLPVDSIFSPIRKVNFLV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ+ D+DKL++ + TDG+ T E++++L++++L + L +FI+  +    V+  +  
Sbjct: 181 ENTRVGQITDFDKLTLEVWTDGTTTPEEALSLSAKVLNEHLNLFIDLTDHANSVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +           +EELELSVRS+NCLR  NI  +  L Q+TE DM+++ N GRKSL EIK
Sbjct: 241 EENEKERIREMSIEELELSVRSSNCLRRANIDTVEKLTQKTEEDMIKVRNLGRKSLNEIK 300

Query: 308 GVLGTMGLFLGMNLPD 323
             L  +GL L      
Sbjct: 301 HKLAEIGLSLSQEDEK 316


>gi|257440240|ref|ZP_05615995.1| DNA-directed RNA polymerase, alpha subunit [Faecalibacterium
           prausnitzii A2-165]
 gi|257197274|gb|EEU95558.1| DNA-directed RNA polymerase, alpha subunit [Faecalibacterium
           prausnitzii A2-165]
          Length = 332

 Score =  341 bits (876), Expect = 7e-92,   Method: Composition-based stats.
 Identities = 135/316 (42%), Positives = 203/316 (64%), Gaps = 5/316 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ +P  IE   L   +      +AEPL RGF  TLGN+LRRVL+SSL G A+T+V+IDG
Sbjct: 17  EIERP-KIETASLS-PDGRYGRFVAEPLERGFGITLGNSLRRVLLSSLPGVAVTSVKIDG 74

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE S+I+GV ED+T+I+LN+KGI  K+  D  K V +   GP  VTA +I+  +DIE+
Sbjct: 75  VVHEFSTIEGVKEDVTEIVLNLKGIAAKLYTDGPKTVRVEAVGPCEVTADNIKQGDDIEI 134

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVS 184
           LNP+  I  L     + MELT  KG GYVPA+ ++    E + I  + +D++Y+P+ KV+
Sbjct: 135 LNPEWHIATLGEGGKLVMELTFDKGRGYVPAERNKQAIVEKNDINTLPVDSIYTPVLKVN 194

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VES R GQ +DYDKL++ + TDG+I  +++V+LA+R+L + L +F+N  +     +  
Sbjct: 195 YNVESTRVGQAIDYDKLTIEVWTDGTINAQEAVSLAARVLTEHLNLFVNLSDEAAGTEIM 254

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +   +     AL   +EEL+LSVRS NCL+   I  + DL+ ++E +M+++ N GRKSL 
Sbjct: 255 VEKTNDDKEKALEMTIEELDLSVRSFNCLKRAGINTVEDLVSKSEDEMMKVRNLGRKSLE 314

Query: 305 EIKGVLGTMGLFLGMN 320
           E+   L ++G  L  +
Sbjct: 315 EVMAKLDSLGFKLNTD 330


>gi|30248443|ref|NP_840513.1| DNA-directed RNA polymerase subunit alpha [Nitrosomonas europaea
           ATCC 19718]
 gi|41688666|sp|Q82X69|RPOA_NITEU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|30138329|emb|CAD84337.1| Bacterial RNA polymerase, alpha chain [Nitrosomonas europaea ATCC
           19718]
          Length = 336

 Score =  341 bits (876), Expect = 7e-92,   Method: Composition-based stats.
 Identities = 147/338 (43%), Positives = 215/338 (63%), Gaps = 12/338 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  N    + P  +E   +         ++ EP   GF +TLGNALRRVL+SS+ G A T
Sbjct: 1   MSSN--SFLTPRIVEVHNISPL---HAKVVMEPFEHGFGYTLGNALRRVLLSSIPGCAPT 55

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQ 120
            V I GV+HE S+I G+ ED+ D+ILN+KG+ LK+  +  +  +T+ K   G+VTAGDI+
Sbjct: 56  KVSISGVVHEYSTIDGLQEDVVDLILNLKGVVLKLHNNKTQSVLTLKKSSEGIVTAGDIE 115

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN---DPIGLITIDALY 177
             +D+E++NPDHVI ++     +  ++TV KG GY P+ +   E+     IG I +DA +
Sbjct: 116 ATHDVEIVNPDHVIAHITSGGKIEAQITVEKGRGYWPSANRSKEDKSSSSIGDILLDASF 175

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPI++VSY VESAR  Q  D DKL + I+T+GS+  E+++  A+++L +Q   F + E  
Sbjct: 176 SPIRRVSYAVESARVEQRTDLDKLIIDIETNGSVDPEEAIRYAAKVLVEQFSFFADLEST 235

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
               ++    K+   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTEA++LR  N
Sbjct: 236 PLPTEQP---KAPVIDPILLRPVDDLELTVRSANCLKVENIFYIGDLIQRTEAELLRTPN 292

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
            GRKSL EIK VL +  L LGM L +WPP ++E   K+
Sbjct: 293 LGRKSLNEIKEVLASRDLSLGMKLENWPPANLENYIKE 330


>gi|222152291|ref|YP_002561466.1| DNA-directed RNA polymerase subunit alpha [Streptococcus uberis
           0140J]
 gi|222113102|emb|CAR40486.1| DNA-directed RNA polymerase alpha chain [Streptococcus uberis
           0140J]
          Length = 312

 Score =  341 bits (876), Expect = 8e-92,   Method: Composition-based stats.
 Identities = 129/313 (41%), Positives = 198/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++ DG
Sbjct: 3   EFEKPT----ITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKFDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILNIKG+ +K   +  K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNIKGLAVKSYVEDEKMIELEVEGPAEVTAGDILTDSDIEL 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +     ++  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K        
Sbjct: 179 EPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKATDVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +     L + +EEL+LSVRS NCL+   I  + DL +++E +M+++ N GRKSL E+K
Sbjct: 239 EKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKSEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKND 311


>gi|317505829|ref|ZP_07963674.1| DNA-directed RNA polymerase [Segniliparus rugosus ATCC BAA-974]
 gi|316255911|gb|EFV15136.1| DNA-directed RNA polymerase [Segniliparus rugosus ATCC BAA-974]
          Length = 350

 Score =  341 bits (875), Expect = 8e-92,   Method: Composition-based stats.
 Identities = 121/314 (38%), Positives = 192/314 (61%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            +      E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I 
Sbjct: 8   VLTEEVVSEYRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTIA 67

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+T+I+LN+KG+ +    D    + + K+GPG VTA DI   + + +  PD  I  
Sbjct: 68  GVKEDVTEIVLNVKGLEVSSVEDEPATLYLRKQGPGPVTAADIVAPSGVTITKPDTHIAT 127

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           L+    + MEL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  
Sbjct: 128 LNDKGKLEMELVVERGRGYVPAVQNKDSGAEIGRIPVDSIYSPVLKVTYQVEATRVEQRT 187

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           D+D+L + +++  SIT  D+VA A + L +  G+        + ++      S     +L
Sbjct: 188 DFDRLILDVESKSSITPRDAVASAGKTLVELFGLARELNLAAEGIEIGAVAASTNNIASL 247

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E+L L+VRS NCL+ E +  +G+L+ R+E+D+L + NFG+KS+ E+K  L T+GL 
Sbjct: 248 ALPIEDLHLTVRSYNCLKREGVHTIGELVARSESDLLDIRNFGQKSIDEVKLKLYTLGLA 307

Query: 317 LGMNLPDWPPESIE 330
           L  +  ++ P +I+
Sbjct: 308 LKDSPANFDPSNID 321


>gi|323126337|gb|ADX23634.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           dysgalactiae subsp. equisimilis ATCC 12394]
          Length = 312

 Score =  341 bits (875), Expect = 8e-92,   Method: Composition-based stats.
 Identities = 128/313 (40%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EFEKP----IITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKILELEVEGPAEVTAGDILTDSDIEL 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +     +R  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIAEGHSLRATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  +  K  +     
Sbjct: 179 EPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTDVAKATEVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +     L + +E L+LSVRS NCL+   I  + DL +++E +M+++ N GRKSL E+K
Sbjct: 239 EKVNDEKVLDRTIEVLDLSVRSYNCLKRAGINTVFDLTEKSEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKND 311


>gi|315127931|ref|YP_004069934.1| DNA-directed RNA polymerase subunit alpha [Pseudoalteromonas sp.
           SM9913]
 gi|315016445|gb|ADT69783.1| DNA-directed RNA polymerase subunit alpha [Pseudoalteromonas sp.
           SM9913]
          Length = 328

 Score =  341 bits (875), Expect = 8e-92,   Method: Composition-based stats.
 Identities = 148/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +      R+ ++ EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IDAINPTRSKVVLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DIQ 
Sbjct: 58  EVEIDGVLHEYSAKEGVQEDIIEILLNLKGLAVTLEGKDEVFLTLTKSGVGPVTAADIQH 117

Query: 122 VNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALY 177
             D+ + NPDHVICNL   ++ + M + V +G GYVPA    + +D   PIG + +DA +
Sbjct: 118 DGDVTIANPDHVICNLTTNNSEISMRIRVERGRGYVPASSRLSSDDDERPIGRLLLDASF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y+VESAR  Q  D DKL + ++T+G++  E+++  AS IL +QL  F++  + 
Sbjct: 178 SPVERIAYSVESARVEQRTDLDKLIIDMETNGTLDPEEAIRRASTILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +        +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 TEPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEQIQYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP S+ E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASLAE 328


>gi|261367774|ref|ZP_05980657.1| DNA-directed RNA polymerase, alpha subunit [Subdoligranulum
           variabile DSM 15176]
 gi|282570572|gb|EFB76107.1| DNA-directed RNA polymerase, alpha subunit [Subdoligranulum
           variabile DSM 15176]
          Length = 319

 Score =  341 bits (875), Expect = 9e-92,   Method: Composition-based stats.
 Identities = 133/319 (41%), Positives = 204/319 (63%), Gaps = 5/319 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ +P  IE   L   +      + EPL RGF  TLGN+LRRVL+SSL G A+T+V+IDG
Sbjct: 3   EIERP-KIETASLS-PDGRYGKFVVEPLERGFGTTLGNSLRRVLLSSLPGVAVTSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE S+I+GV ED+T+I+LN+KGI  K+ G+S K V +   GP  + AG I+  +D+E+
Sbjct: 61  VVHEFSTIEGVREDVTEIVLNLKGIAAKIYGESPKTVRVEAVGPCELIAGSIKGGDDLEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYSPIKKVS 184
           LNP+  I  L   A + MELT  KG GYVPA+ ++    E + I  + +D++Y+P+ K +
Sbjct: 121 LNPEWHIATLGEGAKLVMELTFDKGRGYVPAERNKLALIEKNDISTLPVDSIYTPVLKAN 180

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           YTV+  R GQ+ DYDKL + + TDG+   +++++LA+R+L + L +F+N  +   E +  
Sbjct: 181 YTVDHTRVGQITDYDKLIIEVWTDGTCNAQEALSLAARVLTEHLNLFVNLCDETGETEIM 240

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           ++        AL   +EEL+LSVRS NCL+   I  +GDLI ++E +M+++ N GRKSL 
Sbjct: 241 VDNDDQGREKALEMTIEELDLSVRSFNCLKRAGINTVGDLINKSEDEMMKVRNLGRKSLE 300

Query: 305 EIKGVLGTMGLFLGMNLPD 323
           E+   L ++G  L  +  +
Sbjct: 301 EVMAKLDSLGFSLTKDDEN 319


>gi|270292026|ref|ZP_06198241.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus sp. M143]
 gi|306828808|ref|ZP_07462000.1| DNA-directed RNA polymerase subunit alpha [Streptococcus mitis ATCC
           6249]
 gi|315612357|ref|ZP_07887270.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           ATCC 49296]
 gi|322375014|ref|ZP_08049528.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus sp. C300]
 gi|331267109|ref|YP_004326739.1| DNA-dependent RNA polymerase, alpha subunit [Streptococcus oralis
           Uo5]
 gi|270279554|gb|EFA25396.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus sp. M143]
 gi|304428986|gb|EFM32074.1| DNA-directed RNA polymerase subunit alpha [Streptococcus mitis ATCC
           6249]
 gi|315315338|gb|EFU63377.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sanguinis
           ATCC 49296]
 gi|321280514|gb|EFX57553.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus sp. C300]
 gi|326683781|emb|CBZ01399.1| DNA-dependent RNA polymerase, alpha subunit [Streptococcus oralis
           Uo5]
          Length = 311

 Score =  341 bits (875), Expect = 9e-92,   Method: Composition-based stats.
 Identities = 131/313 (41%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  K  +     
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSTEVMKEA 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            +   +  L + +EEL+LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E+K
Sbjct: 239 DTESDDRILDRTIEELDLSVRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L   
Sbjct: 299 LKLIDLGLGLKDK 311


>gi|71279611|ref|YP_267376.1| DNA-directed RNA polymerase subunit alpha [Colwellia
           psychrerythraea 34H]
 gi|90110833|sp|Q488Y8|RPOA_COLP3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|71145351|gb|AAZ25824.1| DNA-directed RNA polymerase, alpha subunit [Colwellia
           psychrerythraea 34H]
          Length = 329

 Score =  341 bits (875), Expect = 9e-92,   Method: Composition-based stats.
 Identities = 147/331 (44%), Positives = 213/331 (64%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E ++P  +    +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLRPRLVGIETVS---PRRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +I+LN+KG+ + + G +   +T+ K G G VTA DIQ 
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDIIEILLNLKGLAVILEGKNEAVLTVTKSGEGPVTAADIQH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYS 178
             D+ + NPDHVIC L  +  + M + V  G GYVPA   R    E+  IG + +DA +S
Sbjct: 118 DGDVTIANPDHVICTLTGEGSISMRIKVEMGRGYVPASARRDAEEEDRAIGRLLVDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ +++Y V+SAR  Q  D DKL + ++T+G++  E+++  AS IL +QL  F+   + K
Sbjct: 178 PVVRIAYDVDSARVEQRTDLDKLVLDMETNGTLDPEEAIRRASTILAEQLDAFVELRDIK 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              + +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QR E ++L+  N 
Sbjct: 238 ---EVEQVEEKPLFDPILLRPVDDLELTVRSANCLKAEAIQYIGDLVQRAEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L +WPPESI
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPESI 325


>gi|302877827|ref|YP_003846391.1| DNA-directed RNA polymerase, alpha subunit [Gallionella
           capsiferriformans ES-2]
 gi|302580616|gb|ADL54627.1| DNA-directed RNA polymerase, alpha subunit [Gallionella
           capsiferriformans ES-2]
          Length = 322

 Score =  341 bits (875), Expect = 9e-92,   Method: Composition-based stats.
 Identities = 149/326 (45%), Positives = 209/326 (64%), Gaps = 10/326 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  N  + +KP  IE   +    E +  ++ EP  RGF HTLGNALRR+L+SS+ GAA T
Sbjct: 1   MYNN--DFLKPRIIEVQKIS---ETQAKVVMEPFERGFGHTLGNALRRILLSSMAGAAPT 55

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V++ GVLHE ++I GV ED+ DI+LN+KG+ L++ G     +T+ K G GVVTA DI  
Sbjct: 56  EVKMSGVLHEYATIDGVQEDVVDILLNLKGVVLRLHGVKEVVLTLKKEGFGVVTAADISA 115

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI--GLITIDALYSP 179
             ++EVLNP+HVI +L     + M++ V +G GYV A   +  N+    G I +DA +SP
Sbjct: 116 NAEVEVLNPEHVIAHLTAGGKLDMQIKVEQGRGYVSAISRQLPNETRAVGHIALDASFSP 175

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           + +VSY VESAR  Q  D DKL MTI+T+G+I  E ++  A+RIL DQ  +F   E  + 
Sbjct: 176 VSRVSYAVESARVEQRTDLDKLIMTIETNGAIDPEQAIRNAARILVDQFSVFAALEGTEP 235

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            V+++        +P LL+ V++LEL+ RS+NCL+ ++I Y+GDLIQ +E D+LR  N G
Sbjct: 236 VVEKE---HVPQVDPILLRPVDDLELTPRSSNCLKAQSIHYIGDLIQYSENDLLRTPNLG 292

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWP 325
           RKSL EIK VL    L LGM L +WP
Sbjct: 293 RKSLNEIKQVLAEHNLSLGMKLENWP 318


>gi|302543333|ref|ZP_07295675.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces
           hygroscopicus ATCC 53653]
 gi|302460951|gb|EFL24044.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces
           himastatinicus ATCC 53653]
          Length = 340

 Score =  341 bits (875), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 128/316 (40%), Positives = 193/316 (61%), Gaps = 4/316 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNVDAEGIDMGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPP 326
             MGL L  + P + P
Sbjct: 302 AGMGLALKDSPPGFDP 317


>gi|306825961|ref|ZP_07459297.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sp. oral
           taxon 071 str. 73H25AP]
 gi|304431677|gb|EFM34657.1| DNA-directed RNA polymerase subunit alpha [Streptococcus sp. oral
           taxon 071 str. 73H25AP]
          Length = 311

 Score =  341 bits (874), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 131/313 (41%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  K  +     
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSTEVMKEA 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            +   +  L + +EEL+LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E+K
Sbjct: 239 DTESDDRILDRTIEELDLSVRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L   
Sbjct: 299 FKLIDLGLGLKDK 311


>gi|187933966|ref|YP_001884502.1| DNA-directed RNA polymerase subunit alpha [Clostridium botulinum B
           str. Eklund 17B]
 gi|188589874|ref|YP_001919701.1| DNA-directed RNA polymerase subunit alpha [Clostridium botulinum E3
           str. Alaska E43]
 gi|251778696|ref|ZP_04821616.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           E1 str. 'BoNT E Beluga']
 gi|238689634|sp|B2UYD9|RPOA_CLOBA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238691607|sp|B2TIK4|RPOA_CLOBB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|187722119|gb|ACD23340.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum B
           str. Eklund 17B]
 gi|188500155|gb|ACD53291.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           E3 str. Alaska E43]
 gi|243083011|gb|EES48901.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           E1 str. 'BoNT E Beluga']
          Length = 315

 Score =  341 bits (874), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 131/313 (41%), Positives = 206/313 (65%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  I   +   E+      + EPL RG+  TLGNALRR+L+SSL G A ++V+IDG
Sbjct: 3   EIEKP--IIECIEASEDGTYGKYVVEPLERGYGITLGNALRRILLSSLPGVATSSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T++ILNIK + L+M+G+  K + I  +GPG VT  DI+T  D+EV
Sbjct: 61  VLHEFSTVQGVKEDVTELILNIKSLALRMNGEGPKVIYIDAKGPGEVTGADIKTDGDVEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N D  I  LD +  + MELTV++G GYV    ++++  PI  I ID++Y+P+KKV++TV
Sbjct: 121 VNKDLHIATLDDNGRLYMELTVNRGRGYVTQNKNKSDELPISSIAIDSIYTPVKKVNFTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ++ R GQ+ DYDKL++ I T+G+I  +++++L+++IL +   +F++      +V+  I  
Sbjct: 181 DNTRVGQITDYDKLTLEIWTNGTIKIDEAISLSAKILIEHFKLFMSLTNNTNDVEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   VEEL+LSVRS NCL+   I  + +L  ++  DM+++ N G+KSL E++
Sbjct: 241 EEDKKEKVLEMTVEELDLSVRSYNCLKRAGINTVQELATKSMDDMMKVRNLGKKSLEEVE 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L +N
Sbjct: 301 RKLKELGLCLKLN 313


>gi|291442292|ref|ZP_06581682.1| RNA polymerase alpha subunit [Streptomyces ghanaensis ATCC 14672]
 gi|291345187|gb|EFE72143.1| RNA polymerase alpha subunit [Streptomyces ghanaensis ATCC 14672]
          Length = 336

 Score =  341 bits (874), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 126/316 (39%), Positives = 193/316 (61%), Gaps = 4/316 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 5   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 60

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 61  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 120

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 121 DLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEAT 180

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +    
Sbjct: 181 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNIGAEGIDMGPSPTDA 240

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EELEL+VRS NCL+ E +  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 241 ALAADLALPIEELELTVRSYNCLKREGVHSVGELLARSEADLLDIRNFGAKSIDEVKAKL 300

Query: 311 GTMGLFLGMNLPDWPP 326
             +GL L  + P + P
Sbjct: 301 AGLGLALKDSPPGFAP 316


>gi|332037268|gb|EGI73723.1| DNA-directed RNA polymerase alpha subunit [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 328

 Score =  341 bits (874), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 148/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +      R+ ++ EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IDAINPTRSKIVLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DIQ 
Sbjct: 58  EVEIDGVLHEYSAKEGVQEDIIEILLNLKGLAVTLEGKDEVFLTLTKSGVGPVTAADIQH 117

Query: 122 VNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALY 177
             D+ + NPDHVICNL   ++ + M + V +G GYVPA    + +D   PIG + +DA +
Sbjct: 118 DGDVTIANPDHVICNLTTNNSEISMRIRVERGRGYVPASSRLSSDDDERPIGRLLLDASF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y+VESAR  Q  D DKL + ++T+G++  E+++  AS IL +QL  F++  + 
Sbjct: 178 SPVERIAYSVESARVEQRTDLDKLIIDMETNGTLDPEEAIRRASTILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +        +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 TEPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEQIQYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP S+ E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASLAE 328


>gi|160932172|ref|ZP_02079563.1| hypothetical protein CLOLEP_01007 [Clostridium leptum DSM 753]
 gi|156868774|gb|EDO62146.1| hypothetical protein CLOLEP_01007 [Clostridium leptum DSM 753]
          Length = 317

 Score =  341 bits (874), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 129/315 (40%), Positives = 202/315 (64%), Gaps = 4/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  I+  VL   +      + EPL RGF  TLGN+LRRVL+SSL G A+T+++IDG
Sbjct: 3   EIEKPR-IDTEVLS-ADGTYGKFVVEPLERGFGTTLGNSLRRVLLSSLPGVAVTSIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T+I+LN+KG+  K+  D  K V I   GP  VTA  I+  +++E+
Sbjct: 61  VLHEFSTIPGVKEDVTEIVLNMKGLTAKLHCDGAKTVEISAEGPCEVTADSIKCDSEVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
           LNP+  I  L   A + ME+T+ KG GY+ A+ ++   +N+ IG++ ID++Y+P+ KV++
Sbjct: 121 LNPEMHIATLGDGARLYMEITLDKGRGYISAERNKANMQNNVIGILPIDSIYTPVLKVNF 180

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R GQ+ DYDKL++ + T+G I  +++V+LA+++L + L +F++  +     +  +
Sbjct: 181 GVENTRVGQITDYDKLTLEVWTNGVINAQEAVSLAAKVLTEHLNLFVDLSDKGYNTEIMV 240

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                     L   +EEL+LSVRS NCL+   I  + DLI ++E DM+++ N GRKSL E
Sbjct: 241 EKDDKGKEKVLEMTIEELDLSVRSFNCLKRAGINTVEDLINKSEDDMMKVRNLGRKSLEE 300

Query: 306 IKGVLGTMGLFLGMN 320
           +   L ++G  L  +
Sbjct: 301 VVYKLNSLGFSLRKD 315


>gi|329116068|ref|ZP_08244785.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           parauberis NCFD 2020]
 gi|326906473|gb|EGE53387.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           parauberis NCFD 2020]
          Length = 312

 Score =  341 bits (874), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 128/313 (40%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EFEKP----IITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKMIELDVEGPAEVTAGDILTDSDIEL 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +     ++  +TV+K  GY+PA+ ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIAEGHSLKATMTVAKKRGYIPAEGNKQDDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K        
Sbjct: 179 EPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKTTDVMKET 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +     L + +EEL+LSVRS NCL+   I  + DL +++E +M+++ N GRKSL E+K
Sbjct: 239 EKVNDEKILDRTIEELDLSVRSYNCLKRAGINTVFDLTEKSEPEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L  +
Sbjct: 299 VKLADLGLGLKND 311


>gi|114330598|ref|YP_746820.1| DNA-directed RNA polymerase subunit alpha [Nitrosomonas eutropha
           C91]
 gi|122314408|sp|Q0AIH1|RPOA_NITEC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|114307612|gb|ABI58855.1| DNA-directed RNA polymerase subunit alpha [Nitrosomonas eutropha
           C91]
          Length = 335

 Score =  341 bits (874), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 146/337 (43%), Positives = 219/337 (64%), Gaps = 11/337 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  N    + P  IE   L      R  ++ EP  RGF +TLGNALRRVL+SS+ G A T
Sbjct: 1   MSSN--SFLTPRIIEVHNLSPL---RAKVVMEPFERGFGYTLGNALRRVLLSSIPGCAPT 55

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            + I GV+HE S+I G+ ED+ D+ILN+KG+ LK+   +   +++ K   G+VTAGDI++
Sbjct: 56  KISISGVVHEYSTIDGLQEDIVDLILNLKGVVLKLHSKNSTVLSLKKDTEGIVTAGDIES 115

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN---DPIGLITIDALYS 178
            +D+E++NP+HVI ++     +  ++TV KG GY+P+ +   E+     IG I +DA +S
Sbjct: 116 SHDVEIVNPEHVIAHITSGGRIEAQITVEKGRGYLPSVNRSREDKSLSSIGDILLDASFS 175

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSYT+E+AR  Q  D DKL + I+T+GS+  E+++  A+R+L +Q   F + E   
Sbjct: 176 PVRRVSYTIENARVEQRTDLDKLIIDIETNGSVDPEEAIRYAARVLVEQFSFFADLESTL 235

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              ++    ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTEA++LR  N 
Sbjct: 236 LPTEQP---RAPAIDPILLRPVDDLELTVRSANCLKVENIFYIGDLIQRTEAELLRTPNL 292

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
           GRKSL EIK VL +  L LGM L +WPP ++E   K+
Sbjct: 293 GRKSLNEIKEVLASRDLSLGMKLENWPPANLENYVKE 329


>gi|269796227|ref|YP_003315682.1| DNA-directed RNA polymerase subunit alpha [Sanguibacter keddieii
           DSM 10542]
 gi|269098412|gb|ACZ22848.1| DNA-directed RNA polymerase subunit alpha [Sanguibacter keddieii
           DSM 10542]
          Length = 334

 Score =  341 bits (874), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 121/320 (37%), Positives = 196/320 (61%), Gaps = 4/320 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E ++     E+R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLTEEVI----SESRSRFSIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+T+IILN+K + +    D    + + K+G GVVTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTEIILNVKNLVVSSENDEPVVMYLRKQGSGVVTAADIVPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+    + +ELTV +G GYV A+ +++ +  IG + +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLHIATLNDKGKLEIELTVERGRGYVSAQQNKSFDAEIGRVPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  +I+  D++A A + L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +E+L+L++RS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEDLQLTIRSYNCLKREGIHAVGELVARSEADLLDIRNFGAKSINEVKDKL 301

Query: 311 GTMGLFLGMNLPDWPPESIE 330
             +GL L  +  D+ P + +
Sbjct: 302 AELGLSLKDSPLDFDPTTAD 321


>gi|149376659|ref|ZP_01894418.1| DNA-directed RNA polymerase subunit alpha [Marinobacter algicola
           DG893]
 gi|149359032|gb|EDM47497.1| DNA-directed RNA polymerase subunit alpha [Marinobacter algicola
           DG893]
          Length = 313

 Score =  341 bits (874), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 153/306 (50%), Positives = 213/306 (69%), Gaps = 6/306 (1%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
           R  +  EPL RGF HTLG+ALRR+L+SS+ G AIT  QIDGVLHE S+I+GV ED+ +I+
Sbjct: 2   RAKVTLEPLERGFGHTLGSALRRILLSSMPGCAITEAQIDGVLHEYSAIEGVQEDVIEIL 61

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+KG+ +KM G     VT+ K+GPGVVTAGDI+  +D+E+ NP+HVIC+L  +  V M 
Sbjct: 62  LNLKGVAVKMGGRDDAEVTLSKKGPGVVTAGDIKLDHDVEITNPEHVICHLSANGEVNMR 121

Query: 147 LTVSKGHGYVPAKHH---RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
           L V++G GY PA        E   IG + +DA +SP+++V+Y VESAR  Q  D DKL +
Sbjct: 122 LKVARGRGYEPADQRGLDEDETRAIGRLQLDATFSPVRRVAYAVESARVEQRTDLDKLVI 181

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T+G+I  E+++  A+ ILQ QL +F++F+  K+        +    +P LL+ V++L
Sbjct: 182 DLETNGTIDPEEAIRRAATILQQQLAVFVDFDHEKEPE---RVEEEEEIDPILLRPVDDL 238

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           EL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G+KSL EIK VL + GL LGM L +
Sbjct: 239 ELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLDN 298

Query: 324 WPPESI 329
           WPP S+
Sbjct: 299 WPPASL 304


>gi|104773568|ref|YP_618548.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC 11842]
 gi|119366691|sp|Q1GBJ2|RPOA_LACDA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|103422649|emb|CAI97257.1| DNA-directed RNA polymerase, alpha chain [Lactobacillus delbrueckii
           subsp. bulgaricus ATCC 11842]
 gi|325125200|gb|ADY84530.1| RNA-polymerase DNA-directed [Lactobacillus delbrueckii subsp.
           bulgaricus 2038]
          Length = 312

 Score =  340 bits (873), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 126/310 (40%), Positives = 190/310 (61%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +E++    + EPL RGF  TLGN+LRRVL++S+ G  +  V+IDG
Sbjct: 3   EFKKPN----ITVVDQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSVPGTGLVKVKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           +LHE +++ GV ED+T IILN+K + L+   +  K + +   GP  VTA D++   D+EV
Sbjct: 59  ILHEFTTVPGVKEDVTKIILNLKKLELRAYTEEVKTIELDVEGPATVTAEDLKADADVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + M + V  G GYVPA  ++T    IG I +D+L+SPI+KV+Y V
Sbjct: 119 LNPDQYICTIAQGGHLHMWIDVCNGRGYVPASENKTAEMSIGDIPVDSLFSPIEKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL++ I T+GSI   D++  A+R+L +    F + +   +  +  +  
Sbjct: 179 ESTRVGKREDFDKLTLEIWTNGSIAPNDALNFAARVLVEHFKAFESADAAAEIGEVMVEQ 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           ++      L   +E+L+LSVRS NCL+   I  + DL  ++EA+M+R+ N GRKSL E+K
Sbjct: 239 ENDQKEKKLEMTIEDLDLSVRSYNCLKRAGINTLQDLTVKSEAEMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLADLGLSL 308


>gi|50843283|ref|YP_056510.1| DNA-directed RNA polymerase subunit alpha [Propionibacterium acnes
           KPA171202]
 gi|289424833|ref|ZP_06426615.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           SK187]
 gi|61215892|sp|Q6A6R1|RPOA_PROAC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|50840885|gb|AAT83552.1| DNA-directed RNA polymerase alpha chain [Propionibacterium acnes
           KPA171202]
 gi|289154796|gb|EFD03479.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           SK187]
 gi|313763203|gb|EFS34567.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL013PA1]
 gi|313793292|gb|EFS41350.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL110PA1]
 gi|313801064|gb|EFS42332.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL110PA2]
 gi|313816540|gb|EFS54254.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL059PA1]
 gi|313828399|gb|EFS66113.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL063PA2]
 gi|313837983|gb|EFS75697.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL086PA1]
 gi|314914366|gb|EFS78197.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL005PA4]
 gi|314917686|gb|EFS81517.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL050PA1]
 gi|314919582|gb|EFS83413.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL050PA3]
 gi|314930172|gb|EFS94003.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL067PA1]
 gi|314957155|gb|EFT01259.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL027PA1]
 gi|314957796|gb|EFT01899.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL002PA1]
 gi|314963508|gb|EFT07608.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL082PA1]
 gi|314969909|gb|EFT14007.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL037PA1]
 gi|315077129|gb|EFT49196.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL053PA2]
 gi|315097951|gb|EFT69927.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL059PA2]
 gi|315100594|gb|EFT72570.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL046PA1]
 gi|315106083|gb|EFT78059.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL030PA1]
 gi|327451456|gb|EGE98110.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL087PA3]
 gi|327451856|gb|EGE98510.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL083PA2]
 gi|328752070|gb|EGF65686.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL087PA1]
 gi|328755532|gb|EGF69148.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL025PA2]
          Length = 338

 Score =  340 bits (873), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 120/320 (37%), Positives = 184/320 (57%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                 E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV HE S+I+G 
Sbjct: 10  TEESISEFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQHEFSTIEGC 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+IILN+KG+ L    D    + + K G G +TA DI     + + NP+  I  L+
Sbjct: 70  VEDVTEIILNLKGLVLSSEEDEPVAMYLRKTGAGEITAADINPPAGVTIHNPELHIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D    MEL V +G GYV +  +   N  IG I +D++YSP+ KV+Y VE+ R  Q  D+
Sbjct: 130 DDGRFEMELIVERGRGYVSSALNDDPNAEIGRIAVDSIYSPVLKVTYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  SI   D++A A + L +  G+        + ++         +  +L  
Sbjct: 190 DKLVVDVETKPSILPRDAIASAGKTLVELFGLTRELNVEAEGIEIGSGPVDEEYAESLGT 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  +GL L 
Sbjct: 250 PVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEKLTELGLALK 309

Query: 319 MNLPDWPPESIEELAKKYED 338
            + P + P +  E   +  D
Sbjct: 310 DSAPGFDPLAAAEAYDEAND 329


>gi|296130462|ref|YP_003637712.1| DNA-directed RNA polymerase, alpha subunit [Cellulomonas flavigena
           DSM 20109]
 gi|296022277|gb|ADG75513.1| DNA-directed RNA polymerase, alpha subunit [Cellulomonas flavigena
           DSM 20109]
          Length = 337

 Score =  340 bits (873), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 122/317 (38%), Positives = 191/317 (60%), Gaps = 4/317 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E ++     E+R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLTEEVI----SEHRSRFSIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S+I GV ED+T+IILNIK + +    D    + + K+G G VT  DI     +EV NP
Sbjct: 62  EFSTIPGVKEDVTEIILNIKNLVVSSENDEPVVMYLRKQGAGEVTGADIVPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           +  +  L+    + +ELTV +G GYV A  +++ +  IG I ID++YSP+ KV+Y VE+ 
Sbjct: 122 ELHLATLNEKGKLEIELTVERGRGYVSANQNKSFDAEIGRIPIDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + +++  +I+  D++A A R L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDKLIVDVESKPAISPRDALASAGRTLVELFGLARELNVEAEGIEIGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +E+L+L++RS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEDLQLTIRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSITEVKEKL 301

Query: 311 GTMGLFLGMNLPDWPPE 327
             +GL L  +  D+ P 
Sbjct: 302 AELGLTLKDSPLDFDPS 318


>gi|283457576|ref|YP_003362159.1| DNA-directed RNA polymerase subunit alpha [Rothia mucilaginosa
           DY-18]
 gi|283133574|dbj|BAI64339.1| DNA-directed RNA polymerase, alpha subunit [Rothia mucilaginosa
           DY-18]
          Length = 330

 Score =  340 bits (873), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 120/329 (36%), Positives = 192/329 (58%), Gaps = 9/329 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V      NR+    EPL  GF +T+GN+LRR L+SS+ GAA+T+V+IDGVLH
Sbjct: 6   RPTLTEEVV----APNRSRFTIEPLEPGFGYTMGNSLRRTLLSSIPGAAVTSVRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T+IILNIK +++    D      + K+G G +TAGDI+    +E+ NP
Sbjct: 62  EFSTVPGVTEDVTEIILNIKKLSISSENDEPVVAYLRKQGEGELTAGDIEVPAGVEIHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           +  +  L+  A    EL + +G GYV A  ++  +  IG I +D++YSP+ KV+++V + 
Sbjct: 122 ELHLATLNASANFNAELVIERGRGYVTAAQNKAGDSEIGRIPVDSIYSPVLKVTFSVNAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D L++ ++T  +I   D+VA A   L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDSLTLDVETKEAIAPRDAVASAGSTLVELFGLARELNIAAEGIEVGPSPADE 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +E+L +SVRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L
Sbjct: 242 SMAADLALPIEDLNMSVRSYNCLKREGIHTVGELVTRSEADLMDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             +GL L  + P + P      A+  +D+
Sbjct: 302 TELGLSLKDSPPGFEPA-----ARPLDDE 325


>gi|315109197|gb|EFT81173.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL030PA2]
          Length = 338

 Score =  340 bits (873), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 120/320 (37%), Positives = 184/320 (57%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                 E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV HE S+I+G 
Sbjct: 10  TEESISEFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQHEFSTIEGC 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+IILN+KG+ L    D    + + K G G +TA DI     + + NP+  I  L+
Sbjct: 70  VEDVTEIILNLKGLVLSSEEDEPVAMYLRKTGAGEITAADINPPAGVTIHNPELHIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D    MEL V +G GYV +  +   N  IG I +D++YSP+ KV+Y VE+ R  Q  D+
Sbjct: 130 DDGRFEMELIVERGRGYVSSALNDDPNAEIGRIAVDSIYSPVLKVTYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  SI   D++A A + L +  G+        + ++         +  +L  
Sbjct: 190 DKLVVDVETKPSILPRDAIASAGKTLVELFGLTRELNVEAEGIEIGSGPVDEEYAESLGT 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  +GL L 
Sbjct: 250 PVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEKLTELGLALK 309

Query: 319 MNLPDWPPESIEELAKKYED 338
            + P + P +  E   +  D
Sbjct: 310 DSAPGFDPLAAAEAYDEAND 329


>gi|260584442|ref|ZP_05852189.1| DNA-directed RNA polymerase, alpha subunit [Granulicatella elegans
           ATCC 700633]
 gi|260157960|gb|EEW93029.1| DNA-directed RNA polymerase, alpha subunit [Granulicatella elegans
           ATCC 700633]
          Length = 314

 Score =  340 bits (873), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 137/310 (44%), Positives = 202/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I + ++ +     + EPL RG+  TLGN+LRR+L+SSL G A+T +Q+DG
Sbjct: 3   EIEKP-KIETIEISEDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGTAVTDIQMDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+  IILNIK I LK   +  K + I   GP VVTAGDI+  +DIE+
Sbjct: 61  VLHEFSTIDGVVEDVAAIILNIKKIALKSFSEDDKVLEIDIVGPAVVTAGDIKHDSDIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +       + +    G GYV A +++++N PIG+I ID++Y+PI KV+Y V
Sbjct: 121 LNPDLYICTVAEGHRFHVRMNAKNGRGYVRADYNKSDNMPIGVIPIDSIYTPISKVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ   YDKL++ + TDGSI+ E++++LA+RIL + L +F+N  +  ++V+  +  
Sbjct: 181 ENTRIGQKNIYDKLTLDVWTDGSISPEEAISLAARILTEHLNIFVNLTDETRQVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EA+M+++ N GRKSL E+K
Sbjct: 241 EETQKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELTNKSEAEMIKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  + L L
Sbjct: 301 HKLIELNLDL 310


>gi|29826981|ref|NP_821615.1| DNA-directed RNA polymerase subunit alpha [Streptomyces avermitilis
           MA-4680]
 gi|41688664|sp|Q82QR5|RPOA2_STRAW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|29604078|dbj|BAC68150.1| putative RNA polymerase alpha subunit [Streptomyces avermitilis
           MA-4680]
          Length = 338

 Score =  340 bits (873), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 126/316 (39%), Positives = 194/316 (61%), Gaps = 4/316 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNIDAEGIDMGPSPVDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L+  +EELEL+VRS NCL+ E +  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLVMPIEELELTVRSYNCLKREGVHSVGELVARSEADLLDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPP 326
             MGL L  + P + P
Sbjct: 302 AGMGLGLKDSPPGFDP 317


>gi|289669368|ref|ZP_06490443.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas campestris
           pv. musacearum NCPPB4381]
          Length = 332

 Score =  340 bits (873), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 141/328 (42%), Positives = 217/328 (66%), Gaps = 9/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            ++++P   +   L    +NR  ++ EPL RG+ HTLGNALRRVL+SS+ G AIT V+ID
Sbjct: 6   NQVLRPRGPQIERL---TDNRAKVVIEPLKRGYGHTLGNALRRVLLSSIPGFAITEVEID 62

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE ++++G+ ED+ D++LN+K + ++M       +++ K+GPG VTA DI+T +++E
Sbjct: 63  GVLHEYTTVEGLQEDVLDVLLNLKDVAIRMHSGDSATLSLSKQGPGTVTAADIRTDHNVE 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKV 183
           ++N DHVIC+L  D  + M L + +G GY PA   R  ++     G + +DA +SP+++V
Sbjct: 123 IINGDHVICHLTKDTALNMRLKIERGFGYQPAAARRRPDEETRTIGRLMLDASFSPVRRV 182

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +
Sbjct: 183 AYAVEAARVEQRTDLDKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAK 242

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                    +P LL+ +++LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KSL
Sbjct: 243 PAASG---VDPVLLRPIDDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSL 299

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL   GL LGM L +WPP  + +
Sbjct: 300 TEIKEVLAQRGLALGMKLENWPPAGVAQ 327


>gi|159039805|ref|YP_001539058.1| DNA-directed RNA polymerase subunit alpha [Salinispora arenicola
           CNS-205]
 gi|157918640|gb|ABW00068.1| DNA-directed RNA polymerase, alpha subunit [Salinispora arenicola
           CNS-205]
          Length = 340

 Score =  340 bits (873), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 121/310 (39%), Positives = 188/310 (60%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
                E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV 
Sbjct: 11  EESINETRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTIPGVK 70

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+ ++++NIK + +    D    + + K+GPG VTAGDIQ    + V NPD  +  L+ 
Sbjct: 71  EDVVELVMNIKELCVSSEHDEPVSMYLRKQGPGDVTAGDIQPPAGVSVHNPDLKLATLNG 130

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              + MELTV +G GYV A  ++     IG I +D++YSP+ +V+Y VE+ R  Q  D+D
Sbjct: 131 KGRLDMELTVERGRGYVTAAQNKQAGAEIGRIPVDSIYSPVLRVTYRVEATRVEQRTDFD 190

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           +L + +++  S+    ++A A   L +  G+    +E  + +    + +       L   
Sbjct: 191 RLIIDVESKPSMGPRTALASAGSTLVELFGLARELDETAEGIDIGPSPQDAQLAADLALP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +EEL+L+VRS NCL+ E I  +G+LI RTEAD+L + NFG+KS+ E+K  L  MGL L  
Sbjct: 251 IEELDLTVRSYNCLKREGINSVGELIGRTEADLLDIRNFGQKSIDEVKMKLAGMGLGLKD 310

Query: 320 NLPDWPPESI 329
           + P++ P ++
Sbjct: 311 SAPNFDPANV 320


>gi|300812355|ref|ZP_07092790.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus
           delbrueckii subsp. bulgaricus PB2003/044-T3-4]
 gi|300496660|gb|EFK31747.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus
           delbrueckii subsp. bulgaricus PB2003/044-T3-4]
          Length = 312

 Score =  340 bits (873), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 125/310 (40%), Positives = 190/310 (61%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +E++    + EPL RGF  TLGN+LRRVL++S+ G  +  V+IDG
Sbjct: 3   EFKKPN----ITVVDQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSVPGTGLVKVKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           +LHE +++ GV ED+T IILN+K + L+   +  K + +   GP  VTA D++   D+EV
Sbjct: 59  ILHEFTTVPGVKEDVTKIILNLKKLELRAYTEEVKTIELDVEGPATVTAEDLKADADVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + M + V  G GYVPA  +++    IG I +D+L+SPI+KV+Y V
Sbjct: 119 LNPDQYICTIAQGGHLHMWIDVCNGRGYVPASENKSAEMSIGDIPVDSLFSPIEKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL++ I T+GSI   D++  A+R+L +    F + +   +  +  +  
Sbjct: 179 ESTRVGKREDFDKLTLEIWTNGSIAPNDALNFAARVLVEHFKAFESADAAAEIGEVMVEQ 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           ++      L   +E+L+LSVRS NCL+   I  + DL  ++EA+M+R+ N GRKSL E+K
Sbjct: 239 ENDQKEKKLEMTIEDLDLSVRSYNCLKRAGINTLQDLTVKSEAEMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLADLGLSL 308


>gi|302536278|ref|ZP_07288620.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. C]
 gi|302445173|gb|EFL16989.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. C]
          Length = 340

 Score =  340 bits (873), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 128/316 (40%), Positives = 193/316 (61%), Gaps = 4/316 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVLH
Sbjct: 6   RPSLTEEVV----DEYRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TDIILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDIILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNGKGKLEMELTVERGRGYVSAVQNKQLGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNIDAEGIDMGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPP 326
             MGL L  + P + P
Sbjct: 302 AGMGLALKDSPPGFDP 317


>gi|254391366|ref|ZP_05006569.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           clavuligerus ATCC 27064]
 gi|294814494|ref|ZP_06773137.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           clavuligerus ATCC 27064]
 gi|297192676|ref|ZP_06910074.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           pristinaespiralis ATCC 25486]
 gi|326442883|ref|ZP_08217617.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           clavuligerus ATCC 27064]
 gi|197705056|gb|EDY50868.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           clavuligerus ATCC 27064]
 gi|197721669|gb|EDY65577.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           pristinaespiralis ATCC 25486]
 gi|294327093|gb|EFG08736.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           clavuligerus ATCC 27064]
          Length = 340

 Score =  340 bits (873), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 128/316 (40%), Positives = 193/316 (61%), Gaps = 4/316 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPSLTEEVV----DEYRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNIDAEGIDMGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPP 326
             MGL L  + P + P
Sbjct: 302 AGMGLALKDSPPGFDP 317


>gi|167629496|ref|YP_001679995.1| DNA-directed RNA polymerase, alpha subunit [Heliobacterium
           modesticaldum Ice1]
 gi|238687877|sp|B0TC85|RPOA_HELMI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|167592236|gb|ABZ83984.1| DNA-directed RNA polymerase, alpha subunit [Heliobacterium
           modesticaldum Ice1]
          Length = 314

 Score =  340 bits (873), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 135/310 (43%), Positives = 200/310 (64%), Gaps = 3/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE +    ++      + EPL RG+  TLGN+LRR+L++SL GAA+T+V+I+G
Sbjct: 3   EIEKP-KIECVARS-DDATYGKFVVEPLERGYGVTLGNSLRRILLTSLFGAAVTSVKIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED TDIILN+K + +KM  +  + + +   G GVVTA DI T  D+E+
Sbjct: 61  VLHEFSTIPGVVEDTTDIILNLKQLAIKMHTEESRTIRVEFEGEGVVTAADILTDADVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD VI  +D    + ME+TV K  GY+ A  HR     IG+I IDA +SP++KV+Y V
Sbjct: 121 LNPDQVIATVDKG-RLFMEITVEKSRGYITATKHRKSEHAIGVIPIDANFSPVRKVNYRV 179

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R GQ+ +YD+L + + T+GS+T E++++ +++I+ D L +F+   E  + V+  +  
Sbjct: 180 EDTRVGQITNYDRLILEVWTNGSLTPEEAISWSAKIMNDYLKLFVALTENTENVEIMVET 239

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +  P +  L   +EEL+LSVRS NCL+   I  + DL  +TE DM+++ N GRKSL E+ 
Sbjct: 240 EERPQDKILEMTIEELDLSVRSYNCLKRAGINTVKDLTNKTEEDMIKVRNLGRKSLEEVD 299

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 300 AKLAALGLSL 309


>gi|167749410|ref|ZP_02421537.1| hypothetical protein EUBSIR_00364 [Eubacterium siraeum DSM 15702]
 gi|167657582|gb|EDS01712.1| hypothetical protein EUBSIR_00364 [Eubacterium siraeum DSM 15702]
          Length = 319

 Score =  340 bits (873), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 132/321 (41%), Positives = 207/321 (64%), Gaps = 7/321 (2%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M++K    + KP  IE + L + +    +   EPL  G+ +TLGN+LRRVL+SSL G A+
Sbjct: 1   MLEK----IEKP-VIETVKL-KPDGTYGMFTLEPLECGYGNTLGNSLRRVLLSSLPGVAV 54

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V+IDGV HE S+I GV ED+T+IILNIKG+  KM G+  + V I   G   VTAGDI+
Sbjct: 55  TSVKIDGVQHEFSTIPGVKEDVTEIILNIKGLIAKMYGECPQTVYIEAEGECDVTAGDIK 114

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP-IGLITIDALYSP 179
           T ++IE+L+P   I  L   A + ME+T+ KG GYV A+ ++ +  P IG+I +D++Y+P
Sbjct: 115 TDSEIEILDPGMHIATLGPGAKLYMEITLDKGRGYVSAEKNKQQLQPVIGIIAVDSIYTP 174

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           + KV+YTVE+ R GQ  DYDKL + + TDG+I+ +++V+ A+++L D L  F+   +   
Sbjct: 175 VLKVNYTVENTRVGQRTDYDKLILEVWTDGTISAKEAVSYAAKLLVDHLQPFVELSDEAI 234

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           + +   +      +  L   +++L+LSVRS NCL+  NI  + DLI +++ DM+++ N G
Sbjct: 235 QPELMADKSESGKDKLLEMTIDDLDLSVRSFNCLKRANINTVDDLINKSQGDMMKVRNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMN 320
           +KS  E++  L ++G  L  +
Sbjct: 295 KKSFEEVRAKLQSLGFDLASD 315


>gi|292492446|ref|YP_003527885.1| DNA-directed RNA polymerase, subunit alpha [Nitrosococcus
           halophilus Nc4]
 gi|291581041|gb|ADE15498.1| DNA-directed RNA polymerase, alpha subunit [Nitrosococcus
           halophilus Nc4]
          Length = 332

 Score =  340 bits (873), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 148/331 (44%), Positives = 214/331 (64%), Gaps = 9/331 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            +    +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G AI   
Sbjct: 1   MSVSNFLKPRIVDVQRVNDYT---AKVTLEPLERGFGHTLGNALRRILLSSMPGCAIVEA 57

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           QIDGVLHE ++ +GV ED+T+I+LN+KG+ +K+ G     + +  +GPG VTAG+IQ  +
Sbjct: 58  QIDGVLHEYTTKEGVQEDMTEILLNLKGVAIKLHGRDEVTLALNSKGPGAVTAGEIQLEH 117

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPI 180
           D+E++NP+HVI +L     + + + V +G GY PA        E  PIG + +DA +SPI
Sbjct: 118 DVEIINPEHVIAHLTKSGELNITMKVVRGRGYQPASVRIPKEEEERPIGYLILDASFSPI 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++V+Y V+SAR  Q  D DKL + I+T+G+I  +++V  A+ ILQDQL  F+  E   + 
Sbjct: 178 RRVTYEVDSARVEQRTDLDKLIIEIETNGTIASDEAVRKAATILQDQLTAFVELEGKTET 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            KE    K+   +P LL+ +++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G+
Sbjct: 238 AKE---KKTAEIDPVLLQPIDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNLGK 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           KSL EIK VL + GL LGM L +WPP  + E
Sbjct: 295 KSLTEIKDVLASRGLSLGMRLENWPPAGLHE 325


>gi|260893344|ref|YP_003239441.1| DNA-directed RNA polymerase, alpha subunit [Ammonifex degensii KC4]
 gi|260865485|gb|ACX52591.1| DNA-directed RNA polymerase, alpha subunit [Ammonifex degensii KC4]
          Length = 319

 Score =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 129/311 (41%), Positives = 189/311 (60%), Gaps = 4/311 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           + KP     +       +    + EPL RG+  TLGNALRRVL+SS+ GAA+T V+I+GV
Sbjct: 4   IEKPRV--SVDSLAPTGDYGRFVIEPLVRGYGITLGNALRRVLLSSIPGAAVTMVKIEGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S++ GV ED+ +IILN++G+ ++M  D  + + I   G   V A DI    D+E+L
Sbjct: 62  LHEFSTLPGVREDVVEIILNLRGLKIRMHTDEERILRIEAAGEREVRARDIIADADVEIL 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NPDH I +L  +  + ME+TV +G GYVPA   R  +  IG I +DA +SP+KKV+Y VE
Sbjct: 122 NPDHYIASLAPEGRLFMEMTVRRGRGYVPADRQR-HDHVIGAIPVDADFSPVKKVNYRVE 180

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK-EDINV 247
           +A  GQ  DYD+L + + T+G +  E++V+LA+RIL +   +          ++   +  
Sbjct: 181 NAWVGQNADYDRLILEVWTNGCVRPEEAVSLAARILCEHFQLLTGLSTSTGHLEKIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    N  L   +EEL+LSVRS NCL+   I  + DL QRTE +M+++ N G+KSL E+K
Sbjct: 241 EEDNKNRLLEMPIEELDLSVRSYNCLKRAGINTILDLTQRTEEEMMKVRNLGKKSLEEVK 300

Query: 308 GVLGTMGLFLG 318
             L  +GL L 
Sbjct: 301 QKLAELGLSLK 311


>gi|77361710|ref|YP_341285.1| DNA-directed RNA polymerase subunit alpha [Pseudoalteromonas
           haloplanktis TAC125]
 gi|90110860|sp|Q3IJI6|RPOA_PSEHT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|76876621|emb|CAI87843.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           (Transcriptase alpha chain) (RNA polymerase alpha
           subunit) [Pseudoalteromonas haloplanktis TAC125]
          Length = 328

 Score =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 148/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +      R+ ++ EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IDAINPTRSKIVLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ + + G     +T+ K G G VTA DIQ 
Sbjct: 58  EVEIDGVLHEYSAKEGVQEDIIEILLNLKGLAVTLEGKDEVFLTLAKSGVGPVTASDIQH 117

Query: 122 VNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALY 177
             D+ + NPDHVICNL   ++ + M + V +G GYVPA    + +D   PIG + +DA +
Sbjct: 118 DGDVTIANPDHVICNLTTNNSEISMRIRVERGRGYVPASSRLSSDDDERPIGRLLLDASF 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y+VESAR  Q  D DKL + ++T+G++  E+++  AS IL +QL  F++  + 
Sbjct: 178 SPVERIAYSVESARVEQRTDLDKLIIDMETNGTLDPEEAIRRASTILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +        +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 TEPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEQIQYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP S+ E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASLAE 328


>gi|313112850|ref|ZP_07798496.1| DNA-directed RNA polymerase, alpha subunit [Faecalibacterium cf.
           prausnitzii KLE1255]
 gi|310624755|gb|EFQ08064.1| DNA-directed RNA polymerase, alpha subunit [Faecalibacterium cf.
           prausnitzii KLE1255]
          Length = 333

 Score =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 135/316 (42%), Positives = 203/316 (64%), Gaps = 5/316 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ +P  IE   L   +      +AEPL RGF  TLGN+LRRVL+SSL G A+T+V+IDG
Sbjct: 17  EIERP-KIETASLS-PDGRYGKFVAEPLERGFGITLGNSLRRVLLSSLPGVAVTSVKIDG 74

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE S+I+GV ED+T+I+LN+KGI  K+  D  K V +   GP  VTA +I+  +DIE+
Sbjct: 75  VVHEFSTIEGVKEDVTEIVLNLKGIAAKLYTDGPKTVRVEAVGPCEVTADNIKQGDDIEI 134

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVS 184
           LNP+  I  L     + MELT  KG GYVPA+ ++    E + I  + +D++Y+P+ KV+
Sbjct: 135 LNPEWHIATLGEGGKLVMELTFDKGRGYVPAERNKQAIIEKNDINTLPVDSIYTPVLKVN 194

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VES R GQ +DYDKL++ + TDG+I  +++V+LA+R+L + L +F+N  +     +  
Sbjct: 195 YNVESTRVGQAIDYDKLTIEVWTDGTINAQEAVSLAARVLTEHLNLFVNLSDEAAGAEIM 254

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +   +     AL   +EEL+LSVRS NCL+   I  + DL+ ++E +M+++ N GRKSL 
Sbjct: 255 VEKTNDDKEKALEMTIEELDLSVRSFNCLKRAGINTVEDLVSKSEDEMMKVRNLGRKSLE 314

Query: 305 EIKGVLGTMGLFLGMN 320
           E+   L ++G  L  +
Sbjct: 315 EVMAKLDSLGFKLNTD 330


>gi|21223108|ref|NP_628887.1| DNA-directed RNA polymerase subunit alpha [Streptomyces coelicolor
           A3(2)]
 gi|29831496|ref|NP_826130.1| DNA-directed RNA polymerase subunit alpha [Streptomyces avermitilis
           MA-4680]
 gi|182436600|ref|YP_001824319.1| DNA-directed RNA polymerase subunit alpha [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|239929487|ref|ZP_04686440.1| DNA-directed RNA polymerase subunit alpha [Streptomyces ghanaensis
           ATCC 14672]
 gi|239943604|ref|ZP_04695541.1| DNA-directed RNA polymerase subunit alpha [Streptomyces roseosporus
           NRRL 15998]
 gi|239990057|ref|ZP_04710721.1| DNA-directed RNA polymerase subunit alpha [Streptomyces roseosporus
           NRRL 11379]
 gi|256785796|ref|ZP_05524227.1| DNA-directed RNA polymerase subunit alpha [Streptomyces lividans
           TK24]
 gi|282860838|ref|ZP_06269904.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. ACTE]
 gi|289769688|ref|ZP_06529066.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces lividans
           TK24]
 gi|290958124|ref|YP_003489306.1| DNA-directed RNA polymerase subunit alpha [Streptomyces scabiei
           87.22]
 gi|291437812|ref|ZP_06577202.1| RNA polymerase alpha subunit [Streptomyces ghanaensis ATCC 14672]
 gi|291447071|ref|ZP_06586461.1| RNA polymerase alpha subunit [Streptomyces roseosporus NRRL 15998]
 gi|294630920|ref|ZP_06709480.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. e14]
 gi|297201756|ref|ZP_06919153.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sviceus
           ATCC 29083]
 gi|302553569|ref|ZP_07305911.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces
           viridochromogenes DSM 40736]
 gi|302558967|ref|ZP_07311309.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces
           griseoflavus Tu4000]
 gi|326777222|ref|ZP_08236487.1| DNA-directed RNA polymerase subunit alpha [Streptomyces cf. griseus
           XylebKG-1]
 gi|329938205|ref|ZP_08287656.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           griseoaurantiacus M045]
 gi|41692291|sp|P60312|RPOA_STRCO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|41692292|sp|P60313|RPOA1_STRAW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238689027|sp|B1W3Y0|RPOA_STRGG RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|3449241|emb|CAA20385.1| DNA-directed RNA polymerase alpha chain [Streptomyces coelicolor
           A3(2)]
 gi|29608612|dbj|BAC72665.1| RNA polymerase alpha subunit [Streptomyces avermitilis MA-4680]
 gi|178465116|dbj|BAG19636.1| RNA polymerase alpha subunit [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|197710869|gb|EDY54903.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sviceus
           ATCC 29083]
 gi|260647650|emb|CBG70755.1| DNA-directed RNA polymerase alpha chain [Streptomyces scabiei
           87.22]
 gi|282564574|gb|EFB70110.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. ACTE]
 gi|289699887|gb|EFD67316.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces lividans
           TK24]
 gi|291340707|gb|EFE67663.1| RNA polymerase alpha subunit [Streptomyces ghanaensis ATCC 14672]
 gi|291350018|gb|EFE76922.1| RNA polymerase alpha subunit [Streptomyces roseosporus NRRL 15998]
 gi|292834253|gb|EFF92602.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sp. e14]
 gi|297159625|gb|ADI09337.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           bingchenggensis BCW-1]
 gi|302471187|gb|EFL34280.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces
           viridochromogenes DSM 40736]
 gi|302476585|gb|EFL39678.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces
           griseoflavus Tu4000]
 gi|320009075|gb|ADW03925.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces
           flavogriseus ATCC 33331]
 gi|326657555|gb|EGE42401.1| DNA-directed RNA polymerase subunit alpha [Streptomyces cf. griseus
           XylebKG-1]
 gi|328884454|emb|CCA57693.1| DNA-directed RNA polymerase alpha subunit [Streptomyces venezuelae
           ATCC 10712]
 gi|329302694|gb|EGG46584.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           griseoaurantiacus M045]
          Length = 340

 Score =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 128/316 (40%), Positives = 193/316 (61%), Gaps = 4/316 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNIDAEGIDMGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPP 326
             MGL L  + P + P
Sbjct: 302 AGMGLALKDSPPGFDP 317


>gi|312968380|ref|ZP_07782590.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           2362-75]
 gi|312287205|gb|EFR15115.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           2362-75]
 gi|327250943|gb|EGE62636.1| DNA-directed RNA polymerase, alpha subunit [Escherichia coli
           STEC_7v]
 gi|332090427|gb|EGI95525.1| DNA-directed RNA polymerase, alpha subunit [Shigella boydii
           3594-74]
          Length = 325

 Score =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 146/330 (44%), Positives = 218/330 (66%), Gaps = 10/330 (3%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I
Sbjct: 1   MTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEI 57

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI    D+
Sbjct: 58  DGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDV 117

Query: 126 EVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIK 181
           E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP++
Sbjct: 118 EIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVE 177

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++  
Sbjct: 178 RIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP- 236

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
             ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+K
Sbjct: 237 --EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKK 294

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           SL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 SLTEIKDVLASRGLSLGMRLENWPPASIAD 324


>gi|160942870|ref|ZP_02090109.1| hypothetical protein FAEPRAM212_00346 [Faecalibacterium prausnitzii
           M21/2]
 gi|158445771|gb|EDP22774.1| hypothetical protein FAEPRAM212_00346 [Faecalibacterium prausnitzii
           M21/2]
          Length = 332

 Score =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 136/316 (43%), Positives = 204/316 (64%), Gaps = 5/316 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ +P  IE   L   +      +AEPL RGF  TLGN+LRRVL+SSL G A+T+V+IDG
Sbjct: 17  EIERP-KIETASLS-PDGRYGKFVAEPLERGFGITLGNSLRRVLLSSLPGVAVTSVKIDG 74

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE S+I+GV ED+T+I+LN+KGI  K+  D  K V +   GP  VTA +I+  +DIE+
Sbjct: 75  VVHEFSTIEGVKEDVTEIVLNLKGIAAKLYTDGPKTVRVEAVGPCEVTADNIKQGDDIEI 134

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVS 184
           LNP+  I  L   A + MELT  KG GYVPA+ ++    E + I  + +D++Y+P+ KV+
Sbjct: 135 LNPEWHIATLGEGAKLVMELTFDKGRGYVPAERNKQAIIEKNDINTLPVDSIYTPVLKVN 194

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VES R GQ +DYDKL++ + TDG+I  +++V+LA+R+L + L +F+N  +     +  
Sbjct: 195 YNVESTRVGQAIDYDKLTIEVWTDGTINAQEAVSLAARVLTEHLNLFVNLSDEAAGAEIM 254

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +   +     AL   +EEL+LSVRS NCL+   I  + DL+ ++E +M+++ N GRKSL 
Sbjct: 255 VEKTNDDKEKALEMTIEELDLSVRSFNCLKRAGINTVEDLVSKSEDEMMKVRNLGRKSLE 314

Query: 305 EIKGVLGTMGLFLGMN 320
           E+   L ++G  L  +
Sbjct: 315 EVMAKLDSLGFKLNTD 330


>gi|148273768|ref|YP_001223329.1| DNA-directed RNA polymerase subunit alpha [Clavibacter
           michiganensis subsp. michiganensis NCPPB 382]
 gi|166229268|sp|A5CU80|RPOA_CLAM3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|147831698|emb|CAN02667.1| DNA-directed RNA polymerase alpha chain [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
          Length = 331

 Score =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 119/307 (38%), Positives = 184/307 (59%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                 E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S++ GV
Sbjct: 10  TEESISEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFSTVPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+IILNIKG+ +    D      + K+G G VTA DI     +E+ NP+ VI  L+
Sbjct: 70  KEDVTEIILNIKGLVVSSEHDEPITAYLRKQGAGQVTAADISAPAGVEIHNPELVIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
             A   +ELT+ +G GYV A  +R+E    G I +D++YSP+ KV+Y VE+ R G+  D+
Sbjct: 130 EKAKFELELTIERGRGYVSATQNRSEFSEAGQIPVDSIYSPVLKVTYRVEATRAGERTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           D+L + ++T  +IT  D++A A R L +  G+        + ++          +  L  
Sbjct: 190 DRLVVDVETKSAITPRDAIASAGRTLTELFGLARELNSAAEGIEIGPAPVDAVLSSELSM 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L+LSVRS NCL+ E I  + +L+  +E  ++ + NFG+KS+ E+K  L  +GL L 
Sbjct: 250 PIEDLDLSVRSYNCLKREGINNVSELVALSETQLMNIRNFGQKSVDEVKDKLVELGLSLK 309

Query: 319 MNLPDWP 325
             +P + 
Sbjct: 310 DAVPGFD 316


>gi|254383145|ref|ZP_04998499.1| DNA-directed RNA polymerase alpha subunit [Streptomyces sp. Mg1]
 gi|194342044|gb|EDX23010.1| DNA-directed RNA polymerase alpha subunit [Streptomyces sp. Mg1]
          Length = 340

 Score =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 129/316 (40%), Positives = 193/316 (61%), Gaps = 4/316 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVLH
Sbjct: 6   RPSLTEEVV----DEYRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TDIILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDIILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNGKGKLEMELTVERGRGYVSAVQNKQLGQEIGRIPIDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNIDAEGIDMGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPP 326
             MGL L  + P + P
Sbjct: 302 AGMGLALKDSPPGFDP 317


>gi|150015072|ref|YP_001307326.1| DNA-directed RNA polymerase subunit alpha [Clostridium beijerinckii
           NCIMB 8052]
 gi|189043835|sp|A6LPU0|RPOA_CLOB8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|149901537|gb|ABR32370.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           beijerinckii NCIMB 8052]
          Length = 315

 Score =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 130/313 (41%), Positives = 206/313 (65%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  I   +   E+      + EPL RG+  TLGNALRR+L+SSL G A T+V+IDG
Sbjct: 3   EIEKP--IIECIEANEDGTYGKYVVEPLERGYGITLGNALRRILLSSLPGVATTSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T++ILNIK + L+M+G+  K + I  +GPG VT  DI+T  D+EV
Sbjct: 61  VLHEFSTVQGVKEDVTELILNIKSLALRMNGEGPKVIYIDAKGPGEVTGADIKTDGDVEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N +  I  LD D  + MELTV+KG GYV    ++++  PI  I +D++Y+P+K+V++TV
Sbjct: 121 VNKNLHIATLDNDGRLYMELTVNKGRGYVTQNKNKSDELPISAIAVDSIYTPVKRVNFTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ++ R GQ+ DYDKL++ I T+G+I  +++++L+++IL +   +F++  +   +V+  I  
Sbjct: 181 DNTRVGQITDYDKLTLEIWTNGTIKIDEAISLSAKILIEHFKLFMSLTDNTNDVEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   VEEL+LSVRS NCL+   I  + +L  ++  DM+++ N G+KSL E++
Sbjct: 241 EDDKKEKVLEMTVEELDLSVRSYNCLKRAGINTVQELATKSMDDMMKVRNLGKKSLEEVE 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L + 
Sbjct: 301 RKLKELGLALKLT 313


>gi|307328058|ref|ZP_07607239.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces
           violaceusniger Tu 4113]
 gi|306886363|gb|EFN17368.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces
           violaceusniger Tu 4113]
          Length = 340

 Score =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 127/316 (40%), Positives = 193/316 (61%), Gaps = 4/316 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNVDAEGIDMGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPP 326
             MGL L  + P + P
Sbjct: 302 AGMGLALKDSPPGFDP 317


>gi|256390173|ref|YP_003111737.1| DNA-directed RNA polymerase subunit alpha [Catenulispora acidiphila
           DSM 44928]
 gi|256356399|gb|ACU69896.1| DNA-directed RNA polymerase, alpha subunit [Catenulispora
           acidiphila DSM 44928]
          Length = 341

 Score =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 130/329 (39%), Positives = 198/329 (60%), Gaps = 6/329 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E I+    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLTEEII----DEYRSRFLIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E ++I GV ED+TD+ILNIK + +    D    + + K+GPG VTA DI     +EV NP
Sbjct: 62  EFTTIPGVKEDVTDLILNIKQLVVSSEIDEPVTMYLRKQGPGTVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           + +I  L+    + MELTV +G GYV A  ++     IG I ID++YSP+ KV Y VE+ 
Sbjct: 122 ELIIATLNGKGKLEMELTVERGRGYVSAVQNKQAGQEIGRIPIDSIYSPVLKVKYDVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  S+   D+VA A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDRLVLDVETKQSMRPRDAVASAGKTLVELFGLARELNIEAEGIDMGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +E+LEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEDLELTVRSYNCLKREGIHTVGELVARSEADLLDIRNFGAKSIDEVKVKL 301

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +MGL L  + P + P  +  +  +Y+++
Sbjct: 302 MSMGLALKDSPPGFDPSLV--VDNQYDEE 328


>gi|298500605|ref|ZP_07010409.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae MAK
           757]
 gi|297540774|gb|EFH76831.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae MAK
           757]
          Length = 329

 Score =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 146/335 (43%), Positives = 219/335 (65%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E++NP+HVIC+L   +A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIVNPEHVICHLTSDNAAIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +SP+ K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 FSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|291532118|emb|CBK97703.1| DNA-directed RNA polymerase subunit alpha [Eubacterium siraeum
           70/3]
 gi|291558142|emb|CBL35259.1| DNA-directed RNA polymerase subunit alpha [Eubacterium siraeum
           V10Sc8a]
          Length = 319

 Score =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 133/321 (41%), Positives = 207/321 (64%), Gaps = 7/321 (2%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M++K    + KP  IE + L + +    +   EPL  G+ +TLGN+LRRVL+SSL G A+
Sbjct: 1   MLEK----IEKP-VIETVKL-KPDGTYGMFTLEPLECGYGNTLGNSLRRVLLSSLPGVAV 54

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V+IDGV HE S+I GV ED+T+IILNIKG+  KM G+  K V I   G   VTAGDI+
Sbjct: 55  TSVKIDGVQHEFSTIPGVKEDVTEIILNIKGLIAKMYGECPKTVYIEAEGECDVTAGDIK 114

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP-IGLITIDALYSP 179
           T ++IE+L+P   I  L   A + ME+T+ KG GYV A+ ++ +  P IG+I +D++Y+P
Sbjct: 115 TDSEIEILDPGMHIATLGPGAKLYMEITLDKGRGYVSAEKNKQQLQPVIGIIAVDSIYTP 174

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           + KV+YTVE+ R GQ  DYDKL + + TDG+I+ +++V+ A+++L D L  F+   +   
Sbjct: 175 VLKVNYTVENTRVGQRTDYDKLILEVWTDGTISAKEAVSYAAKLLVDHLQPFVELSDEAI 234

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           + +   +      +  L   +++L+LSVRS NCL+  NI  + DLI +++ DM+++ N G
Sbjct: 235 QPELMADKSESGKDKLLEMTIDDLDLSVRSFNCLKRANINTVDDLINKSQGDMMKVRNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMN 320
           +KS  E++  L ++G  L  +
Sbjct: 295 KKSFEEVRAKLQSLGFDLASD 315


>gi|7388098|sp|Q9X4V6|RPOA_STRGT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|4633288|gb|AAD26700.1|AF118449_1 DNA-dependent RNA polymerase alpha subunit [Streptomyces
           granaticolor]
          Length = 340

 Score =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 128/316 (40%), Positives = 193/316 (61%), Gaps = 4/316 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNAKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNIDAEGIDMGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPP 326
             MGL L  + P + P
Sbjct: 302 AGMGLALKDSPPGFDP 317


>gi|297204185|ref|ZP_06921582.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sviceus
           ATCC 29083]
 gi|197714127|gb|EDY58161.1| DNA-directed RNA polymerase, alpha subunit [Streptomyces sviceus
           ATCC 29083]
          Length = 335

 Score =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 123/314 (39%), Positives = 193/314 (61%), Gaps = 4/314 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNIDAEGIDMGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L+  +E+L+L+VRS NCL+ E +  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLVMPIEDLDLTVRSYNCLKREGVHSVGELVARSEADLLDIRNFGAKSIDEVKEKL 301

Query: 311 GTMGLFLGMNLPDW 324
             +GL L  + P +
Sbjct: 302 AGLGLGLKDSPPGF 315


>gi|297163220|gb|ADI12932.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           bingchenggensis BCW-1]
          Length = 337

 Score =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 121/316 (38%), Positives = 189/316 (59%), Gaps = 4/316 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +  R+  + EPL  GF +TLGN+LRR L+SS+  AA+T+++IDGVLH
Sbjct: 6   RPSLTEEVV----DAYRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPAAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILN+K + +    D    + + K+GPG+ TA DI     +EV NP
Sbjct: 62  EFTTVPGVREDITDLILNLKQLVVSSEHDEPVVMYLRKQGPGLATAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + +ELTV +G GYV A  +  +   IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNAKGKLEIELTVERGRGYVSAVQNTQQGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKPAMHPRDAIASAGKTLVELFGLARGLNIDAEGIDIGPSPTDT 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EELEL+VRS NCL+ E +  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALASDLALPIEELELTVRSYNCLKREGVHSVGELVARSEADLLDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPP 326
             MGL    + P + P
Sbjct: 302 AGMGLAFKDSPPGFDP 317


>gi|116513565|ref|YP_812471.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
 gi|122275665|sp|Q04BY9|RPOA_LACDB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116092880|gb|ABJ58033.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
          Length = 312

 Score =  340 bits (871), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 127/310 (40%), Positives = 190/310 (61%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +E++    + EPL RGF  TLGN+LRRVL++S+ G  +  V+IDG
Sbjct: 3   EFKKPN----ITVVDQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSVPGTGLVKVKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           +LHE +++ GV ED+T IILN+K + L+   +  K + +   GP  VTA D++   D+EV
Sbjct: 59  ILHEFTTVPGVKEDVTKIILNLKKLELRAYTEEVKTIELDVEGPATVTAEDLKADADVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + M + V  G GYVPA  ++T    IG I +D+L+SPI+KV+Y V
Sbjct: 119 LNPDQYICTIAQGGHLHMWIDVCNGRGYVPASENKTAEMSIGDIPVDSLFSPIEKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL+M I T+GSI   D++  A+R+L +    F + +   +  +  +  
Sbjct: 179 ESTRVGKREDFDKLTMEIWTNGSIAPNDALNFAARVLVEHFKAFESADAAAEIGEVMVEQ 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           ++      L   +E+L+LSVRS NCL+   I  + DL  ++EA+M+R+ N GRKSL E+K
Sbjct: 239 ENDQKEKKLEMTIEDLDLSVRSYNCLKRAGINTLQDLTVKSEAEMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLADLGLSL 308


>gi|285017344|ref|YP_003375055.1| DNA-directed RNA polymerase alpha chain (RNA polymerase alpha
           subunit) protein [Xanthomonas albilineans GPE PC73]
 gi|283472562|emb|CBA15067.1| probable dna-directed rna polymerase alpha chain (rna polymerase
           alpha subunit) protein [Xanthomonas albilineans]
          Length = 332

 Score =  340 bits (871), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 142/328 (43%), Positives = 217/328 (66%), Gaps = 9/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            ++++P   +   L    +NR  ++ EPL RG+ HTLGNALRRVL+SS+ G AIT V+ID
Sbjct: 6   NQVLRPRGPQIERL---TDNRAKVVIEPLERGYGHTLGNALRRVLLSSIPGFAITEVEID 62

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
            VLHE ++++G+ ED+ +++LN+K + ++M       +++ K+GPG VTA DI+T +++E
Sbjct: 63  NVLHEYTTVEGLQEDVLEVLLNLKDVAIRMHTGDSATLSLSKQGPGTVTATDIKTDHNVE 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKV 183
           +LN DHVIC+L  D  + M L + +G GY PA   R  ++     G + +DA +SP+++V
Sbjct: 123 ILNSDHVICHLTKDTALNMRLKIERGFGYQPAAARRRPDEETRTIGRLVLDASFSPVRRV 182

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VESAR  Q  D DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +    
Sbjct: 183 AYAVESARVEQRTDLDKLVLDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGA-- 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +   S   +P LL+ +++LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KSL
Sbjct: 241 -VKPASNGVDPVLLRPIDDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSL 299

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL   GL LGM L +WPP  + +
Sbjct: 300 TEIKEVLAQRGLSLGMKLENWPPAGVAQ 327


>gi|229829398|ref|ZP_04455467.1| hypothetical protein GCWU000342_01488 [Shuttleworthia satelles DSM
           14600]
 gi|229791829|gb|EEP27943.1| hypothetical protein GCWU000342_01488 [Shuttleworthia satelles DSM
           14600]
          Length = 320

 Score =  340 bits (871), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 130/314 (41%), Positives = 207/314 (65%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  +++     + EPL RG+  TLGN+LRR+++SS+ G A+T ++I+G
Sbjct: 3   DFKKPN-IEIAEIS-DDKKYGKFVVEPLERGYGITLGNSLRRIMLSSMPGVAVTQIKIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+I+LNIK + ++ +   D  K   I   G G VTA DIQ  +DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIVLNIKQLAIRSNSQTDEPKVAYIEYEGEGTVTAADIQVDSDI 120

Query: 126 EVLNPDHVICNLDV--DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E++NPD VI +L+   D+ + MELT+SKG GYV +  ++T++ PIG+I +D++Y+P+++V
Sbjct: 121 EIVNPDLVIAHLNGGSDSKLYMELTISKGRGYVSSDKNKTDDTPIGVIAVDSIYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +  VE+ R GQV D+DKL++ + T+G+I  +++ +LA+++L + L +FI+  E  +  + 
Sbjct: 181 NMNVENTRVGQVTDFDKLTLEVWTNGTIGPDEAASLAAKVLSEHLNLFIDLSENARNTEI 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +   S       +  ++ELELSVRS NCL+   I  + +L+ +T  DM+++ N GRKSL
Sbjct: 241 MVEKPSADTASMKMMNIDELELSVRSYNCLKRAGINTVEELVNKTPEDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFL 317
            E+   L  MGL L
Sbjct: 301 EEVLQKLQEMGLSL 314


>gi|222150471|ref|YP_002559624.1| DNA-directed RNA polymerase alpha chain [Macrococcus caseolyticus
           JCSC5402]
 gi|254765255|sp|B9E9L7|RPOA_MACCJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|222119593|dbj|BAH16928.1| DNA-directed RNA polymerase alpha chain [Macrococcus caseolyticus
           JCSC5402]
          Length = 314

 Score =  340 bits (871), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 125/310 (40%), Positives = 201/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + + ++ +     + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+G
Sbjct: 3   EIEKPR-IETVEISEDSKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVKNIEIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+ V ED+T II+NIK + LK+  D  K + I  +  GVVTA DI   +D+E+
Sbjct: 61  VLHEFSAIENVVEDVTSIIMNIKKLALKIYSDEDKTLEIDVKDEGVVTAKDIMHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  +     ++M L  + G GY  A+ + T + PIG+I +D++Y+P+++V+Y V
Sbjct: 121 LNPDLKIATVSKGGHLKMRLIANAGRGYTLAEDNNTSDLPIGVIPVDSIYTPVERVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  ++DKL++ + TDGSIT +++++L ++I+ + L +F++  +  +  +  I  
Sbjct: 181 ENTRVGQSTNFDKLTLDVWTDGSITPQEAISLGAKIMTEHLNIFVDLTDEAQNAEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+++ N GRKSL E+K
Sbjct: 241 EEDHKEKVLEMSIEELDLSVRSYNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 FKLEDLGLGL 310


>gi|15642566|ref|NP_232199.1| DNA-directed RNA polymerase subunit alpha [Vibrio cholerae O1
           biovar El Tor str. N16961]
 gi|121730283|ref|ZP_01682657.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae V52]
 gi|147674278|ref|YP_001218065.1| DNA-directed RNA polymerase subunit alpha [Vibrio cholerae O395]
 gi|153824205|ref|ZP_01976872.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae B33]
 gi|227082688|ref|YP_002811239.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae M66-2]
 gi|229507377|ref|ZP_04396882.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae BX
           330286]
 gi|229509699|ref|ZP_04399180.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae B33]
 gi|229513494|ref|ZP_04402958.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae TMA 21]
 gi|229516824|ref|ZP_04406270.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae RC9]
 gi|229521637|ref|ZP_04411055.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae TM
           11079-80]
 gi|229527499|ref|ZP_04416891.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae
           12129(1)]
 gi|229606883|ref|YP_002877531.1| DNA-directed RNA polymerase subunit alpha [Vibrio cholerae MJ-1236]
 gi|254292242|ref|ZP_04963005.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae
           AM-19226]
 gi|254851111|ref|ZP_05240461.1| DNA-directed RNA polymerase subunit alpha [Vibrio cholerae MO10]
 gi|255744460|ref|ZP_05418412.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholera CIRS 101]
 gi|258622737|ref|ZP_05717755.1| DNA-directed RNA polymerase alpha subunit [Vibrio mimicus VM573]
 gi|258625765|ref|ZP_05720644.1| DNA-directed RNA polymerase alpha subunit [Vibrio mimicus VM603]
 gi|261211126|ref|ZP_05925415.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. RC341]
 gi|262166592|ref|ZP_06034329.1| DNA-directed RNA polymerase alpha subunit [Vibrio mimicus VM223]
 gi|262170492|ref|ZP_06038170.1| DNA-directed RNA polymerase alpha subunit [Vibrio mimicus MB-451]
 gi|262401858|ref|ZP_06078423.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. RC586]
 gi|297581413|ref|ZP_06943336.1| DNA-directed RNA polymerase subunit alpha [Vibrio cholerae RC385]
 gi|12230593|sp|Q9KP08|RPOA_VIBCH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172047565|sp|A5F572|RPOA_VIBC3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|254765262|sp|C3LRN3|RPOA_VIBCM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|9657157|gb|AAF95712.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae O1
           biovar El Tor str. N16961]
 gi|121627963|gb|EAX60526.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae V52]
 gi|126518273|gb|EAZ75498.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae B33]
 gi|146316161|gb|ABQ20700.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae O395]
 gi|150421844|gb|EDN13828.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae
           AM-19226]
 gi|227010576|gb|ACP06788.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae M66-2]
 gi|227014460|gb|ACP10670.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae O395]
 gi|229335131|gb|EEO00616.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae
           12129(1)]
 gi|229341231|gb|EEO06235.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae TM
           11079-80]
 gi|229345887|gb|EEO10859.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae RC9]
 gi|229349371|gb|EEO14327.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae TMA 21]
 gi|229353173|gb|EEO18112.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae B33]
 gi|229354882|gb|EEO19803.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae BX
           330286]
 gi|229369538|gb|ACQ59961.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae MJ-1236]
 gi|254846816|gb|EET25230.1| DNA-directed RNA polymerase subunit alpha [Vibrio cholerae MO10]
 gi|255737985|gb|EET93378.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholera CIRS 101]
 gi|258582003|gb|EEW06873.1| DNA-directed RNA polymerase alpha subunit [Vibrio mimicus VM603]
 gi|258584925|gb|EEW09656.1| DNA-directed RNA polymerase alpha subunit [Vibrio mimicus VM573]
 gi|260839627|gb|EEX66238.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. RC341]
 gi|261891568|gb|EEY37554.1| DNA-directed RNA polymerase alpha subunit [Vibrio mimicus MB-451]
 gi|262026308|gb|EEY44976.1| DNA-directed RNA polymerase alpha subunit [Vibrio mimicus VM223]
 gi|262351830|gb|EEZ00961.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. RC586]
 gi|297534251|gb|EFH73089.1| DNA-directed RNA polymerase subunit alpha [Vibrio cholerae RC385]
 gi|327485053|gb|AEA79460.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae
           LMA3894-4]
          Length = 330

 Score =  340 bits (871), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 146/335 (43%), Positives = 219/335 (65%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E++NP+HVIC+L   +A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIVNPEHVICHLTSDNAAIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +SP+ K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 FSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|270284452|ref|ZP_05966137.2| DNA-directed RNA polymerase, alpha subunit [Bifidobacterium
           gallicum DSM 20093]
 gi|270276907|gb|EFA22761.1| DNA-directed RNA polymerase, alpha subunit [Bifidobacterium
           gallicum DSM 20093]
          Length = 351

 Score =  340 bits (871), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 122/312 (39%), Positives = 183/312 (58%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                   R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ GV
Sbjct: 30  TEESITPQRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTALPGV 89

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+I+LNIKGI L    D    + + K G G  TAGDI     I + NP+  I +L 
Sbjct: 90  EEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGITIANPEMHIASLA 149

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  + +E TV +G GYVPA+ ++ ++D IG I +D++YSP+ KVSY VE+ R  Q  D+
Sbjct: 150 EDGELEIEFTVERGRGYVPAQMNKQDSDEIGRIPVDSIYSPVLKVSYKVEATRVEQRTDF 209

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  +I+  D+VA A   L +  G+        + V+          NP L  
Sbjct: 210 DKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNMQAEGVEVGPAPVVEETNPELAV 269

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L L+ RS NCL+ E I  +G+L+   E D+L + NFG KS+ E+K  L ++GL L 
Sbjct: 270 PIEDLNLTQRSYNCLKREGIHTVGELVAHNEQDLLDIRNFGMKSIDEVKEKLQSLGLSLK 329

Query: 319 MNLPDWPPESIE 330
            +   +   ++E
Sbjct: 330 ASPLGFDTTNLE 341


>gi|295101439|emb|CBK98984.1| DNA-directed RNA polymerase subunit alpha [Faecalibacterium
           prausnitzii L2-6]
          Length = 318

 Score =  340 bits (871), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 135/316 (42%), Positives = 203/316 (64%), Gaps = 5/316 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ +P  IE   L   +      +AEPL RGF  TLGN+LRRVL+SSL G A+T+V+IDG
Sbjct: 3   EIERP-KIETASLS-PDGRYGKFVAEPLERGFGITLGNSLRRVLLSSLPGVAVTSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE S+I+GV ED+T+I+LN+KGI  K+  D  K V +   GP  VTA +I+  +DIE+
Sbjct: 61  VVHEFSTIEGVKEDVTEIVLNLKGIAAKLYTDGPKTVRVEAVGPCEVTADNIKQGDDIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVS 184
           LNP+  I  L     + MELT  KG GYVPA+ ++    E + I  + +D++Y+P+ KV+
Sbjct: 121 LNPEWHIATLGEGGKLVMELTFDKGRGYVPAERNKQAIIEKNDINTLPVDSIYTPVLKVN 180

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VES R GQ +DYDKL++ + TDG+I  +++V+LA+R+L + L +F+N  +     +  
Sbjct: 181 YNVESTRVGQAIDYDKLTIEVWTDGTINAQEAVSLAARVLTEHLNLFVNLSDEAAGAEIM 240

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +   +     AL   +EEL+LSVRS NCL+   I  + DL+ ++E +M+++ N GRKSL 
Sbjct: 241 VEKTNDDKEKALEMTIEELDLSVRSFNCLKRAGINTVEDLVSKSEDEMMKVRNLGRKSLE 300

Query: 305 EIKGVLGTMGLFLGMN 320
           E+   L ++G  L  +
Sbjct: 301 EVMAKLDSLGFKLNTD 316


>gi|325684745|gb|EGD26899.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 312

 Score =  340 bits (871), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 125/310 (40%), Positives = 189/310 (60%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +E++    + EPL R F  TLGN+LRRVL++S+ G  +  V+IDG
Sbjct: 3   EFKKPN----ITVVDQEDSYGKFVVEPLERRFGTTLGNSLRRVLLTSVPGTGLVKVKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           +LHE +++ GV ED+T IILN+K + L+   +  K + +   GP  VTA D++   D+EV
Sbjct: 59  ILHEFTTVPGVKEDVTKIILNLKKLVLRAYTEEVKTIELDVEGPATVTAEDLKADADVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + M + V  G GYVPA  ++T    IG I +D+L+SPI+KV+Y V
Sbjct: 119 LNPDQYICTIAQGGHLHMWIDVCNGRGYVPASENKTAEMFIGDIPVDSLFSPIEKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R G+  D+DKL++ I T+GSI   D++  A+R+L +    F + +   +  +  +  
Sbjct: 179 ESTRVGKREDFDKLTLEIWTNGSIAPNDALNFAARVLVEHFKAFESADAAAEIGEVMVEQ 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           ++      L   +E+L+LSVRS NCL+   I  + DL  ++EA+M+R+ N GRKSL E+K
Sbjct: 239 ENDQKEKKLEMTIEDLDLSVRSYNCLKRAGINTLQDLTVKSEAEMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLADLGLSL 308


>gi|295103950|emb|CBL01494.1| DNA-directed RNA polymerase subunit alpha [Faecalibacterium
           prausnitzii SL3/3]
          Length = 318

 Score =  340 bits (871), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 136/316 (43%), Positives = 204/316 (64%), Gaps = 5/316 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ +P  IE   L   +      +AEPL RGF  TLGN+LRRVL+SSL G A+T+V+IDG
Sbjct: 3   EIERP-KIETASLS-PDGRYGKFVAEPLERGFGITLGNSLRRVLLSSLPGVAVTSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE S+I+GV ED+T+I+LN+KGI  K+  D  K V +   GP  VTA +I+  +DIE+
Sbjct: 61  VVHEFSTIEGVKEDVTEIVLNLKGIAAKLYTDGPKTVRVEAVGPCEVTADNIKQGDDIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVS 184
           LNP+  I  L   A + MELT  KG GYVPA+ ++    E + I  + +D++Y+P+ KV+
Sbjct: 121 LNPEWHIATLGEGAKLVMELTFDKGRGYVPAERNKQAIIEKNDINTLPVDSIYTPVLKVN 180

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VES R GQ +DYDKL++ + TDG+I  +++V+LA+R+L + L +F+N  +     +  
Sbjct: 181 YNVESTRVGQAIDYDKLTIEVWTDGTINAQEAVSLAARVLTEHLNLFVNLSDEAAGAEIM 240

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +   +     AL   +EEL+LSVRS NCL+   I  + DL+ ++E +M+++ N GRKSL 
Sbjct: 241 VEKTNDDKEKALEMTIEELDLSVRSFNCLKRAGINTVEDLVSKSEDEMMKVRNLGRKSLE 300

Query: 305 EIKGVLGTMGLFLGMN 320
           E+   L ++G  L  +
Sbjct: 301 EVMAKLDSLGFKLNTD 316


>gi|307246714|ref|ZP_07528784.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|307248855|ref|ZP_07530868.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
 gi|307251083|ref|ZP_07533007.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
 gi|307253469|ref|ZP_07535340.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|307255699|ref|ZP_07537503.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|307257883|ref|ZP_07539639.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
 gi|307260151|ref|ZP_07541861.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
 gi|307262279|ref|ZP_07543928.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
 gi|307264488|ref|ZP_07546073.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
 gi|306852414|gb|EFM84649.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 1 str. 4074]
 gi|306854782|gb|EFM86972.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 2 str. S1536]
 gi|306856913|gb|EFM89045.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 4 str. M62]
 gi|306859148|gb|EFM91190.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 6 str. Femo]
 gi|306861376|gb|EFM93366.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 9 str. CVJ13261]
 gi|306863613|gb|EFM95540.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 10 str. D13039]
 gi|306865797|gb|EFM97675.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 11 str. 56153]
 gi|306868042|gb|EFM99869.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 12 str. 1096]
 gi|306870185|gb|EFN01944.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus
           pleuropneumoniae serovar 13 str. N273]
          Length = 325

 Score =  340 bits (871), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 151/330 (45%), Positives = 221/330 (66%), Gaps = 10/330 (3%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E +KP+ +    + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I
Sbjct: 1   MTEFLKPHLVN---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEI 57

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGVLHE SS +GV ED+ +++LN+KG+ +K+SG     +T+ K G G VTA DI    D+
Sbjct: 58  DGVLHEYSSKEGVQEDILEVLLNLKGLAVKVSGKDDIILTLNKSGIGPVTAADITHDGDV 117

Query: 126 EVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIK 181
           E++NP HVIC+L D DA + M + V +G GYVPA    H + E+ PIG + +DA +SP+ 
Sbjct: 118 EIVNPHHVICHLTDKDASISMRIRVQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVD 177

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++  
Sbjct: 178 RIAYNVEAARVEQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP- 236

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
             ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+K
Sbjct: 237 --EVKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKK 294

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           SL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 SLTEIKDVLASRGLSLGMRLENWPPASIAE 324


>gi|224477194|ref|YP_002634800.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus carnosus
           subsp. carnosus TM300]
 gi|222421801|emb|CAL28615.1| DNA-directed RNA polymerase alpha chain [Staphylococcus carnosus
           subsp. carnosus TM300]
          Length = 314

 Score =  340 bits (871), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 131/310 (42%), Positives = 201/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I + ++ +     + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+G
Sbjct: 3   EIEKPR-IETIEISEDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I  V ED++ II+NIK + LK+  +  K + I  +  G VTA DI   +D+E+
Sbjct: 61  VLHEFSAIDNVVEDVSTIIMNIKELALKIYSEEDKTLEIDVKDEGEVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  +     +++ L  +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTV
Sbjct: 121 LNPELKIATVSKGGHLKIRLVANKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  D+DKL++ + TDGSIT ++SV+LA++IL + L +F+   +  K  +  I  
Sbjct: 181 ENTRVGQSSDFDKLTLDVWTDGSITPQESVSLAAKILTEHLNIFVGLTDEAKNAEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMSIEELDLSVRSYNCLKRAGINTVQELADKSEADMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 YKLEDLGLGL 310


>gi|229524552|ref|ZP_04413957.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae bv.
           albensis VL426]
 gi|229338133|gb|EEO03150.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae bv.
           albensis VL426]
          Length = 330

 Score =  339 bits (870), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 146/335 (43%), Positives = 220/335 (65%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E++NP+HVIC+L   +A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIVNPEHVICHLTSDNAAIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +SP+ K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL +F++  +
Sbjct: 178 FSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDVFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|330470144|ref|YP_004407887.1| DNA-directed RNA polymerase subunit alpha [Verrucosispora maris
           AB-18-032]
 gi|328813115|gb|AEB47287.1| DNA-directed RNA polymerase subunit alpha [Verrucosispora maris
           AB-18-032]
          Length = 340

 Score =  339 bits (870), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 123/310 (39%), Positives = 187/310 (60%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
                E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV 
Sbjct: 11  EESINETRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTIPGVK 70

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+ ++++NIK + +    D    + + K+GPG VTAGDIQ    + V NPD  +  L+ 
Sbjct: 71  EDVVELVMNIKELCVSSEHDEPVSMYLRKQGPGDVTAGDIQPPAGVSVHNPDLKLATLNG 130

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D
Sbjct: 131 KGRLDMELTVERGRGYVTAAQNKQAGAEIGRIPVDSIYSPVLKVTYRVEATRVEQRTDFD 190

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           +L + ++T  S+    ++A A   L +  G+    +E  + +    + +       L   
Sbjct: 191 RLIIDVETKPSMGPRTALASAGSTLVELFGLARELDETAEGIDIGPSPQDAQLAADLALP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +EEL+L+VRS NCL+ E I  +G+LI RTEAD+L + NFG+KS+ E+K  L  MGL L  
Sbjct: 251 IEELDLTVRSYNCLKREGINSVGELIGRTEADLLDIRNFGQKSIDEVKMKLAGMGLGLKD 310

Query: 320 NLPDWPPESI 329
           + P++ P  +
Sbjct: 311 SAPNFDPAHV 320


>gi|28897056|ref|NP_796661.1| DNA-directed RNA polymerase subunit alpha [Vibrio parahaemolyticus
           RIMD 2210633]
 gi|153840230|ref|ZP_01992897.1| DNA-directed RNA polymerase, alpha subunit [Vibrio parahaemolyticus
           AQ3810]
 gi|260877974|ref|ZP_05890329.1| DNA-directed RNA polymerase, alpha subunit [Vibrio parahaemolyticus
           AN-5034]
 gi|262392491|ref|YP_003284345.1| DNA-directed RNA polymerase subunit alpha [Vibrio sp. Ex25]
 gi|269959713|ref|ZP_06174093.1| DNA-directed RNA polymerase alpha subunit [Vibrio harveyi 1DA3]
 gi|269964712|ref|ZP_06178950.1| DNA-directed RNA polymerase alpha subunit [Vibrio alginolyticus
           40B]
 gi|31076905|sp|Q87SZ0|RPOA_VIBPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|28805264|dbj|BAC58545.1| DNA-directed RNA polymerase, alpha subunit [Vibrio parahaemolyticus
           RIMD 2210633]
 gi|149746107|gb|EDM57237.1| DNA-directed RNA polymerase, alpha subunit [Vibrio parahaemolyticus
           AQ3810]
 gi|262336085|gb|ACY49880.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. Ex25]
 gi|269830611|gb|EEZ84832.1| DNA-directed RNA polymerase alpha subunit [Vibrio alginolyticus
           40B]
 gi|269835636|gb|EEZ89715.1| DNA-directed RNA polymerase alpha subunit [Vibrio harveyi 1DA3]
 gi|308089902|gb|EFO39597.1| DNA-directed RNA polymerase, alpha subunit [Vibrio parahaemolyticus
           AN-5034]
 gi|328471859|gb|EGF42736.1| DNA-directed RNA polymerase subunit alpha [Vibrio parahaemolyticus
           10329]
          Length = 330

 Score =  339 bits (870), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 148/335 (44%), Positives = 218/335 (65%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H+  +  PIG + +DA 
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHNEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|238061094|ref|ZP_04605803.1| DNA-directed RNA polymerase, alpha subunit [Micromonospora sp. ATCC
           39149]
 gi|302869942|ref|YP_003838579.1| DNA-directed RNA polymerase subunit alpha [Micromonospora
           aurantiaca ATCC 27029]
 gi|315501403|ref|YP_004080290.1| DNA-directed RNA polymerase, alpha subunit [Micromonospora sp. L5]
 gi|237882905|gb|EEP71733.1| DNA-directed RNA polymerase, alpha subunit [Micromonospora sp. ATCC
           39149]
 gi|302572801|gb|ADL49003.1| DNA-directed RNA polymerase, alpha subunit [Micromonospora
           aurantiaca ATCC 27029]
 gi|315408022|gb|ADU06139.1| DNA-directed RNA polymerase, alpha subunit [Micromonospora sp. L5]
          Length = 340

 Score =  339 bits (870), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 123/310 (39%), Positives = 187/310 (60%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
                E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV 
Sbjct: 11  EESINETRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTIPGVK 70

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+ ++++NIK + +    D    + + K+GPG VTAGDIQ    + V NPD  +  L+ 
Sbjct: 71  EDVVELVMNIKELCVSSEHDEPVSMYLRKQGPGDVTAGDIQPPAGVSVHNPDLKLATLNG 130

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+D
Sbjct: 131 KGRLDMELTVERGRGYVTAAQNKQAGAEIGRIPVDSIYSPVLKVTYRVEATRVEQRTDFD 190

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           +L + ++T  S+    ++A A   L +  G+    +E  + +    + +       L   
Sbjct: 191 RLIIDVETKPSMGPRTALASAGSTLVELFGLARELDETAEGIDIGPSPQDAQLAADLALP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +EEL+L+VRS NCL+ E I  +G+LI RTEAD+L + NFG+KS+ E+K  L  MGL L  
Sbjct: 251 IEELDLTVRSYNCLKREGINSVGELIGRTEADLLDIRNFGQKSIDEVKMKLAGMGLGLKD 310

Query: 320 NLPDWPPESI 329
           + P++ P  +
Sbjct: 311 SAPNFDPAHV 320


>gi|268316435|ref|YP_003290154.1| DNA-directed RNA polymerase, alpha subunit [Rhodothermus marinus
           DSM 4252]
 gi|262333969|gb|ACY47766.1| DNA-directed RNA polymerase, alpha subunit [Rhodothermus marinus
           DSM 4252]
          Length = 323

 Score =  339 bits (870), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 140/312 (44%), Positives = 208/312 (66%), Gaps = 3/312 (0%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           E + + +  E     + +PL RG+  T+GNALRRVL+SSL G AITAV+IDGV HE S+I
Sbjct: 6   EGVRVEEATETFGRFVVQPLERGYGVTIGNALRRVLLSSLPGVAITAVRIDGVQHEFSTI 65

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVI 134
            GV ED+ +IILN+KG+  K    +   + +  +GP V TA DI +  +  EVLNPDH I
Sbjct: 66  PGVTEDVAEIILNLKGVRFKAKDTTDANIRLSLKGPHVWTARDIGEATSHYEVLNPDHYI 125

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
             L   A V +EL + +G GYVPA+ ++  +DPIG+I IDA+++PIK V YT++  R GQ
Sbjct: 126 ATLAEGAEVNLELRMGRGRGYVPAEENKLPDDPIGVIAIDAIFTPIKNVRYTIKPTRVGQ 185

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EPKKEV-KEDINVKSLPF 252
            ++Y++L + I TDGS++ E+++  A+ IL+D + +FI  E EP+ EV K++++ +    
Sbjct: 186 KIEYERLELEITTDGSVSPEEALVQAATILRDHINLFITMESEPQPEVKKKEVDAEVQRI 245

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
              L + V+EL+LSVR+ NCL+  NI  +GDL++R E++ML+  NFGRKSL E+  VL  
Sbjct: 246 RELLSQPVDELDLSVRAQNCLKAANIRTIGDLVRRQESEMLKFRNFGRKSLQELIAVLEE 305

Query: 313 MGLFLGMNLPDW 324
            GL  GM++  +
Sbjct: 306 RGLHFGMDVDKY 317


>gi|260770938|ref|ZP_05879867.1| DNA-directed RNA polymerase alpha subunit [Vibrio furnissii CIP
           102972]
 gi|260614175|gb|EEX39365.1| DNA-directed RNA polymerase alpha subunit [Vibrio furnissii CIP
           102972]
 gi|315178983|gb|ADT85897.1| DNA-directed RNA polymerase subunit alpha - rpoA [Vibrio furnissii
           NCTC 11218]
          Length = 330

 Score =  339 bits (870), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 146/335 (43%), Positives = 219/335 (65%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E++NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIVNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +SP+ K++Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 FSPVDKIAYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|308272953|emb|CBX29557.1| DNA-directed RNA polymerase subunit alpha [uncultured
           Desulfobacterium sp.]
          Length = 340

 Score =  339 bits (870), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 149/327 (45%), Positives = 216/327 (66%), Gaps = 6/327 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++  NWQE+I P+ ++         N    + EPL RGF  T+GNALRR+++SSL GAAI
Sbjct: 6   LMYMNWQEMIMPDKVQVTT---NMPNYDKFVCEPLERGFGLTIGNALRRIMLSSLYGAAI 62

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
            +V+ID V HE S I GV ED+++IILN+K +  K + D  K V I   G   +TA DI 
Sbjct: 63  VSVKIDSVFHEFSVIPGVLEDVSEIILNLKCVRFKTADDEPKTVRIDATGECEITARDII 122

Query: 121 TVND-IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
           + +   EVLNPD  I +L  DAV++  +TV  G GY  ++ ++ E+DP+G I ID+++SP
Sbjct: 123 SDDGKCEVLNPDIHIASLSKDAVLKANMTVKVGKGYSLSESNKNEDDPVGTIPIDSVFSP 182

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +K+V+Y V +AR GQ  DYDKL++ + TDGS++  ++++ +++I+++Q+ +FINF+E  +
Sbjct: 183 VKRVNYVVGNARVGQRTDYDKLTIEVWTDGSLSPVEALSYSAKIIKEQMSIFINFDEKLE 242

Query: 240 EVKEDINVK--SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
              E  + K     FN  L + VEELELSVRS NCL+  NI  +  L+ +TEA+MLR  N
Sbjct: 243 PEVEKKSEKRQKPQFNENLYRSVEELELSVRSANCLKNANIFKIYQLVNKTEAEMLRTKN 302

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           FGRKSL EIK VL  MGL LGM L ++
Sbjct: 303 FGRKSLNEIKEVLSEMGLSLGMKLEEF 329


>gi|237649697|ref|ZP_04523949.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           CCRI 1974]
 gi|237821395|ref|ZP_04597240.1| DNA-directed RNA polymerase subunit alpha [Streptococcus pneumoniae
           CCRI 1974M2]
          Length = 311

 Score =  339 bits (870), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 132/313 (42%), Positives = 198/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K   +  K + +   G   VTAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGLAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  K  +     
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSTEVMKEA 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            +   +  L + +EEL+LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E+K
Sbjct: 239 DTESDDRILDRTIEELDLSVRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L   
Sbjct: 299 LKLIDLGLGLKDK 311


>gi|239933876|ref|ZP_04690829.1| DNA-directed RNA polymerase subunit alpha [Streptomyces ghanaensis
           ATCC 14672]
          Length = 329

 Score =  339 bits (870), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 123/309 (39%), Positives = 188/309 (60%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +     +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ G
Sbjct: 1   MTEEVVDEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPG 60

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV NPD V+  L
Sbjct: 61  VKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNPDLVLATL 120

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           +    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D
Sbjct: 121 NGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEATRVEQRTD 180

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL + ++T  ++   D++A A + L +  G+        + +    +         L 
Sbjct: 181 FDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNIGAEGIDMGPSPTDAALAADLA 240

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +EELEL+VRS NCL+ E +  +G+L+ R+EAD+L + NFG KS+ E+K  L  +GL L
Sbjct: 241 LPIEELELTVRSYNCLKREGVHSVGELLARSEADLLDIRNFGAKSIDEVKAKLAGLGLAL 300

Query: 318 GMNLPDWPP 326
             + P + P
Sbjct: 301 KDSPPGFAP 309


>gi|298531060|ref|ZP_07018461.1| DNA-directed RNA polymerase, alpha subunit [Desulfonatronospira
           thiodismutans ASO3-1]
 gi|298509083|gb|EFI32988.1| DNA-directed RNA polymerase, alpha subunit [Desulfonatronospira
           thiodismutans ASO3-1]
          Length = 347

 Score =  339 bits (869), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 150/337 (44%), Positives = 216/337 (64%), Gaps = 2/337 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW  L+KP+ ++      E+        EPL RGF +T GNALRR+L+SSL+GAAI A+
Sbjct: 13  RNWSSLVKPDQVQRDEKSTEQ--YGKFSCEPLERGFGNTFGNALRRILLSSLQGAAIVAI 70

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +ID   HE ++I GV ED+TDI+LN+K +  KMS D  +++ +     G VTA  IQT  
Sbjct: 71  KIDNAPHEFATITGVVEDVTDIVLNLKQVRFKMSRDEPQKLKLVANEKGQVTAKAIQTNQ 130

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           +I VLNPD  I  L  D  + + + V  G GYVP++ H   ++ IGLI +DA +SPI+KV
Sbjct: 131 NIAVLNPDQHIATLSQDIDLVINIEVRMGKGYVPSEQHEDLDEEIGLIPMDATFSPIRKV 190

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SYTVE AR GQ+ +YDKL + I TDGS+  ED++A +++IL+DQL +FINF+E + ++  
Sbjct: 191 SYTVEQARVGQMTNYDKLILEIHTDGSVLPEDALAYSAKILKDQLSVFINFDESQTDINV 250

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                    +P L K +EELEL VR+ NCLR   I  +G+LIQ++E D+LR  NFGRKSL
Sbjct: 251 IDTNSDEGLDPKLFKTIEELELPVRAGNCLRNAGIRLVGELIQQSENDLLRTKNFGRKSL 310

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
            +I+ V+  MG      + ++  +  E L +K +D+ 
Sbjct: 311 EDIRRVIEQMGYDFNTQIDNFDQKYQEWLKRKEDDEA 347


>gi|291542059|emb|CBL15169.1| DNA-directed RNA polymerase subunit alpha [Ruminococcus bromii
           L2-63]
          Length = 317

 Score =  339 bits (869), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 130/312 (41%), Positives = 203/312 (65%), Gaps = 4/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE   L  E+      + EPL RGF +TLGN+LRRVL+SSL G A+T+++IDG
Sbjct: 3   EIEKPR-IETEEL-TEDGKYGKFVVEPLERGFGNTLGNSLRRVLLSSLEGCAVTSIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T+I+LN+K +  K+   S K + I   GP  V A DI+  +++E+
Sbjct: 61  VLHEFSTIPGVKEDVTEIVLNMKSLVAKLHETSPKVIEIAAEGPCEVKAADIKCDDEVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSY 185
           LNP+  I  L   A + ME+TV KG GY+P++ ++  + N+ IG++ ID++Y+P+ KV+Y
Sbjct: 121 LNPELHIATLGEGAKLNMEITVDKGRGYIPSERNKQLSGNNVIGVLPIDSIYTPVLKVNY 180

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TV++ R GQ+ DYDKL++ + T+G I  +++V+LA+++L + L +F+N  +     +  +
Sbjct: 181 TVDNTRVGQITDYDKLTLDVWTNGVINAQEAVSLAAKVLTEHLNLFVNLSDKASSAEVMV 240

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                     L   +E+L+LSVRS NCL+   I  + DLI ++E DM+++ N GRKSL E
Sbjct: 241 EKDDKGKEKILEMTIEDLDLSVRSFNCLKRAGINTVEDLINKSEEDMMKVRNLGRKSLEE 300

Query: 306 IKGVLGTMGLFL 317
           +   L ++G  L
Sbjct: 301 VVQKLNSLGFSL 312


>gi|326803058|ref|YP_004320876.1| DNA-directed RNA polymerase, alpha subunit [Aerococcus urinae
           ACS-120-V-Col10a]
 gi|326651415|gb|AEA01598.1| DNA-directed RNA polymerase, alpha subunit [Aerococcus urinae
           ACS-120-V-Col10a]
          Length = 314

 Score =  339 bits (869), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 133/313 (42%), Positives = 204/313 (65%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KPN IE I   ++ +       EPL RG+  TLGN+LRRVL+SSL G A+T+++I+ 
Sbjct: 3   EIEKPN-IETIETSEDNKF-GKFAVEPLERGYGTTLGNSLRRVLLSSLPGTAVTSIKIEN 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T I+LNIK + LK+     K + +   GP  VTA DI    D +V
Sbjct: 61  VLHEFSTIPGVREDVTQIVLNIKQLALKLYDVDEKDIELDITGPAEVTAADITADADFDV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP   IC+L   A + M + V  G G+V A++++T++ PIG+I +D++Y+PIKKV+Y V
Sbjct: 121 LNPYLHICSLAEGAKIHMLMHVKNGRGFVRAENNKTDDMPIGVIPVDSIYTPIKKVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G+V +YDKL+  I TDG+I  +++++LA+++L + L +F++  +  +E +  +  
Sbjct: 181 ENTRIGEVNEYDKLTFDIWTDGTIAPKEALSLAAKVLTEHLAIFVSLTDEAQEAEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L Q+TEA+M+++ N GRKSL E+K
Sbjct: 241 EETQKEKMLEMTIEELDLSVRSYNCLKRAGINTVEELTQKTEAEMMKVRNLGRKSLDEVK 300

Query: 308 GVLGTMGLFLGMN 320
           G L  + L L  +
Sbjct: 301 GKLDALDLSLKDD 313


>gi|325678576|ref|ZP_08158186.1| RNA polymerase, alpha subunit C-terminal domain protein
           [Ruminococcus albus 8]
 gi|324109626|gb|EGC03832.1| RNA polymerase, alpha subunit C-terminal domain protein
           [Ruminococcus albus 8]
          Length = 326

 Score =  339 bits (869), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 128/315 (40%), Positives = 203/315 (64%), Gaps = 6/315 (1%)

Query: 9   LIKPNNIEYIVLGQEE----ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           L+    IE   +   E          I EPL RG+  TLGN+LRRVL+SSL G A+T+V+
Sbjct: 6   LLMLEKIEKPKIETPELKSNGTYGKFILEPLERGYGITLGNSLRRVLLSSLPGVAVTSVK 65

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           IDGV HE+S+I GV ED+T+IILN+KG+  K+ G+  K + I   G  VVTAGDI+  ++
Sbjct: 66  IDGVHHELSTIPGVKEDVTEIILNLKGLTAKLYGEGPKTIYIEAEGECVVTAGDIKADSE 125

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKK 182
           +++L PD  I  L   A + ME+T+ +G GYV A+ +++  +N PIG+I +D++YSP+ K
Sbjct: 126 VDILVPDMHIATLGAGAKLYMEITIDRGRGYVSAEKNKSLMQNAPIGIIAVDSIYSPVLK 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+YTV++ R G + D+DKL++ + TDG+I+ +++V++A+++L + L  F++  E    V+
Sbjct: 186 VNYTVDNTRVGHITDFDKLTLEVWTDGTISAKEAVSMAAKLLNEHLNPFVDLSEEANVVE 245

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
             +          L   +EEL+LSVRS NCL+   I  + DLI+++  +M+++ N G+KS
Sbjct: 246 IMVEKDDQSQAKVLEMTIEELDLSVRSFNCLKRAGINTVNDLIEKSAEEMMKVRNLGKKS 305

Query: 303 LVEIKGVLGTMGLFL 317
             E+K  L ++G  L
Sbjct: 306 FDEVKEKLHSLGYEL 320


>gi|311744778|ref|ZP_07718574.1| DNA-directed RNA polymerase subunit alpha [Aeromicrobium marinum
           DSM 15272]
 gi|311311895|gb|EFQ81816.1| DNA-directed RNA polymerase subunit alpha [Aeromicrobium marinum
           DSM 15272]
          Length = 336

 Score =  339 bits (869), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 123/333 (36%), Positives = 192/333 (57%), Gaps = 8/333 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T+IILN+K + +    D    + +     GVVT  +I+    +EV NP
Sbjct: 62  EFSTVPGVTEDVTEIILNLKNLVVSSENDEPVVMYLRADTAGVVTGANIEPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  +  L+    + +EL V +G GYV A  ++T ++ IG + ID++YSP+ KV+Y VE+ 
Sbjct: 122 DLHVATLNDKGRLEIELVVERGRGYVSAVQNKTGDEEIGRMPIDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  SI   D++A A   L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDRLVVDVETKKSILPRDAIASAGSTLVELFGLARELNVEAEGIDIGPSPVDE 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +E+L  +VRS NCL+ E I  +G+LI R+E D+L + NFG KS+ E+K  L
Sbjct: 242 QLAADLALPIEDLNFTVRSYNCLKREGIHTVGELITRSEQDLLDIRNFGSKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPPESI----EELAKKYEDK 339
             MGL L  +   + P ++    +E A   ED+
Sbjct: 302 AEMGLALKDSPAGFDPSAVIADYDEDASFAEDE 334


>gi|156973075|ref|YP_001443982.1| DNA-directed RNA polymerase subunit alpha [Vibrio harveyi ATCC
           BAA-1116]
 gi|166229282|sp|A7N0H8|RPOA_VIBHB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|156524669|gb|ABU69755.1| hypothetical protein VIBHAR_00754 [Vibrio harveyi ATCC BAA-1116]
          Length = 330

 Score =  339 bits (869), Expect = 5e-91,   Method: Composition-based stats.
 Identities = 147/335 (43%), Positives = 217/335 (64%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVI 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H+  +  PIG + +DA 
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHNEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|260779478|ref|ZP_05888368.1| DNA-directed RNA polymerase alpha subunit [Vibrio coralliilyticus
           ATCC BAA-450]
 gi|261250392|ref|ZP_05942967.1| DNA-directed RNA polymerase alpha subunit [Vibrio orientalis CIP
           102891]
 gi|323492144|ref|ZP_08097306.1| DNA-directed RNA polymerase subunit alpha [Vibrio brasiliensis LMG
           20546]
 gi|323495529|ref|ZP_08100603.1| DNA-directed RNA polymerase subunit alpha [Vibrio sinaloensis DSM
           21326]
 gi|260604287|gb|EEX30591.1| DNA-directed RNA polymerase alpha subunit [Vibrio coralliilyticus
           ATCC BAA-450]
 gi|260938961|gb|EEX94948.1| DNA-directed RNA polymerase alpha subunit [Vibrio orientalis CIP
           102891]
 gi|323313705|gb|EGA66807.1| DNA-directed RNA polymerase subunit alpha [Vibrio brasiliensis LMG
           20546]
 gi|323319410|gb|EGA72347.1| DNA-directed RNA polymerase subunit alpha [Vibrio sinaloensis DSM
           21326]
          Length = 330

 Score =  338 bits (868), Expect = 5e-91,   Method: Composition-based stats.
 Identities = 147/335 (43%), Positives = 217/335 (64%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|314924147|gb|EFS87978.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL001PA1]
          Length = 338

 Score =  338 bits (868), Expect = 5e-91,   Method: Composition-based stats.
 Identities = 119/320 (37%), Positives = 182/320 (56%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                 E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV HE S+I+G 
Sbjct: 10  TEESISEFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQHEFSTIEGC 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+IIL ++G  L    D    + + K G G VTA DI     + + NP+  I  L+
Sbjct: 70  VEDVTEIILTLRGFVLPSEEDEPVAMYLRKSGAGEVTAADINPPAGVTIHNPELHIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D    MEL V +G GYV +  +   N  IG I +D++YSP+ KV+Y VE+ R  Q  D+
Sbjct: 130 DDGRFEMELIVERGRGYVSSALNDDPNAEIGRIAVDSIYSPVLKVTYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  SI   D++A A + L +  G+        + ++         +  +L  
Sbjct: 190 DKLVVDVETKPSILPRDAIASAGKTLVELFGLTRELNAEAEGIEIGSGPVDEEYAESLGT 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  +GL L 
Sbjct: 250 PVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEKLTELGLALK 309

Query: 319 MNLPDWPPESIEELAKKYED 338
            + P + P +  E   +  D
Sbjct: 310 DSAPGFDPLAAAEAYDEAND 329


>gi|288870169|ref|ZP_06113169.2| DNA-directed RNA polymerase, alpha subunit [Clostridium hathewayi
           DSM 13479]
 gi|288868138|gb|EFD00437.1| DNA-directed RNA polymerase, alpha subunit [Clostridium hathewayi
           DSM 13479]
          Length = 347

 Score =  338 bits (868), Expect = 5e-91,   Method: Composition-based stats.
 Identities = 138/314 (43%), Positives = 206/314 (65%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 28  DFEKPN-IEIAEIS-EDKKYGKFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 85

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+NIK + +K + D    K   I   G GVVTA DIQ   DI
Sbjct: 86  VLHEFSSIPGVKEDVTEIIMNIKSLAIKNNSDTNEAKVAYIEFEGEGVVTAADIQADPDI 145

Query: 126 EVLNPDHVICNLDV--DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E++NPD VI  L    D+   MELT++KG GYV A  +++E+ PIG+I +D++Y+P+++V
Sbjct: 146 EIMNPDQVIATLSGGTDSKFYMELTITKGRGYVSADKNKSEDLPIGVIAVDSIYTPVERV 205

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + TV++ R GQV D+DKL++ + TDG++  +++V+LA+++L + L +FI+  E  K  + 
Sbjct: 206 NMTVQNTRVGQVTDFDKLTLDVYTDGTLAPDEAVSLAAKVLSEHLNLFIDLSENAKTAEV 265

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  +       L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL
Sbjct: 266 MVEKEDNEKEKVLEMNIDELELSVRSYNCLKRAGINTVEELCNRTSEDMMKVRNLGRKSL 325

Query: 304 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 326 EEVLAKLKELGLQL 339


>gi|260772121|ref|ZP_05881038.1| DNA-directed RNA polymerase alpha subunit [Vibrio metschnikovii CIP
           69.14]
 gi|260612988|gb|EEX38190.1| DNA-directed RNA polymerase alpha subunit [Vibrio metschnikovii CIP
           69.14]
          Length = 330

 Score =  338 bits (868), Expect = 6e-91,   Method: Composition-based stats.
 Identities = 144/335 (42%), Positives = 217/335 (64%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++        +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRLGENKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E++NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIVNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +SP+ K++Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 FSPVDKIAYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|331004894|ref|ZP_08328310.1| DNA-directed RNA polymerase alpha subunit [gamma proteobacterium
           IMCC1989]
 gi|330421281|gb|EGG95531.1| DNA-directed RNA polymerase alpha subunit [gamma proteobacterium
           IMCC1989]
          Length = 331

 Score =  338 bits (868), Expect = 6e-91,   Method: Composition-based stats.
 Identities = 144/333 (43%), Positives = 219/333 (65%), Gaps = 11/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    E + P +I+     +       ++ EPL RGF HTLGNALRR+L+SS+ G AI 
Sbjct: 1   MQSAVNEFLTPRHIDVT---EHSPTHAKVVLEPLERGFGHTLGNALRRILLSSMPGCAII 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDI 119
             +I+GV HE S+++GV ED+ +I+LN+KG+ + M      H  +++ K+GPGVVTA DI
Sbjct: 58  EAEIEGVEHEYSALEGVQEDIIEILLNLKGVAVVMHDQEKSHAMLSLKKKGPGVVTAADI 117

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDAL 176
              +++E+ NPDHVI  +  D  + M L++++G GY PA   R+++D     G + +DA 
Sbjct: 118 VVDHEVEIKNPDHVIATITGDVELNMSLSIARGRGYQPADARRSDDDETRAIGRLQLDAS 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +SP+K+++Y+VESAR  Q  D DKL + ++T+G+I  E+++  ++ ILQ QL +F++ E 
Sbjct: 178 FSPVKRLAYSVESARVEQRTDLDKLVLDLETNGTIDPEEAIRRSATILQQQLAVFVDLES 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            K    E+        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  
Sbjct: 238 EKSSEPEEKEED---VDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LG+ L +WPP S+
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGLRLENWPPASL 327


>gi|302023188|ref|ZP_07248399.1| DNA-directed RNA polymerase subunit alpha [Streptococcus suis
           05HAS68]
          Length = 300

 Score =  338 bits (868), Expect = 6e-91,   Method: Composition-based stats.
 Identities = 130/302 (43%), Positives = 197/302 (65%), Gaps = 4/302 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T+++IDG
Sbjct: 3   EFEKPT----ITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K   +  K++ +   GP  VTAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKKIELDVVGPAEVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDH +  +   A  +  LTV+ G GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y V
Sbjct: 119 VNPDHYLFTIADGATFKAVLTVNSGRGYVPAEDNKKDDAPVGTLAVDSIYTPVKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I+T+G+I  ED++ L++RIL + LG+F +  E  K  +     
Sbjct: 179 EPARVGSNDGFDKLTLEINTNGTIVPEDALGLSARILMEHLGLFTDLTEVAKSAEVMKEA 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    +  L + +EEL+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K
Sbjct: 239 EVASDDRMLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKTEPEMMKVRNLGRKSLEEVK 298

Query: 308 GV 309
             
Sbjct: 299 VK 300


>gi|237749540|ref|ZP_04580020.1| DNA-directed RNA polymerase subunit alpha [Oxalobacter formigenes
           OXCC13]
 gi|229380902|gb|EEO30993.1| DNA-directed RNA polymerase subunit alpha [Oxalobacter formigenes
           OXCC13]
          Length = 325

 Score =  338 bits (868), Expect = 6e-91,   Method: Composition-based stats.
 Identities = 151/326 (46%), Positives = 210/326 (64%), Gaps = 8/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  I    LG     R+++  EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   FLKPRIINVESLG---AGRSVVEMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S++ GV ED+ D++LN+KG+  K+       +T+ K G GVV A DI+  +D+E++
Sbjct: 62  VHEYSTLDGVQEDVVDLLLNLKGVVFKLHNRDSITLTLKKSGAGVVLASDIELPHDVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYSPIKKVSY 185
           NP+HVI NL  +  + M++ V KG GYVP    R     N  IG I +DA +SP+++VSY
Sbjct: 122 NPEHVIANLTDNGKLDMQIKVEKGRGYVPGNVRRLSEDANKTIGRIILDASFSPVRRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D DKL + I+T+G I+ E+++  ++RIL DQL +F   E    E   + 
Sbjct: 182 AVESARVEQRTDLDKLIINIETNGVISAEEAIRQSARILVDQLSVFAALE--GTETTSEA 239

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GRKSL E
Sbjct: 240 LTQVPAVDPILLRPVDDLELTVRSANCLKAENINYIGDLIQRSENELLKTPNLGRKSLNE 299

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP   E+
Sbjct: 300 IKEVLASRGLTLGMRLDNWPPAGFEK 325


>gi|327451569|gb|EGE98223.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL092PA1]
          Length = 338

 Score =  338 bits (868), Expect = 6e-91,   Method: Composition-based stats.
 Identities = 119/320 (37%), Positives = 183/320 (57%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                 E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV HE S+I+G 
Sbjct: 10  TEESISEFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQHEFSTIEGC 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+IILN+KG+ L    D    + + K G G + A DI     + + NP+  I  L+
Sbjct: 70  VEDVTEIILNLKGLVLSSEEDEPVAMYLRKTGAGEIPAADINPPAGVTIHNPELHIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D    MEL V +G GYV +  +   N  IG I +D++YSP+ KV+Y VE+ R  Q  D+
Sbjct: 130 DDGRFEMELIVERGRGYVSSALNDDPNAEIGRIAVDSIYSPVLKVTYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  SI   D++A A + L +  G+        + ++         +  +L  
Sbjct: 190 DKLVVDVETKPSILPRDAIASAGKTLVELFGLTRELNVEAEGIEIGSGPVDEEYAESLGT 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  +GL L 
Sbjct: 250 PVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEKLTELGLALK 309

Query: 319 MNLPDWPPESIEELAKKYED 338
            + P + P +  E   +  D
Sbjct: 310 DSAPGFDPLAAAEAYDEAND 329


>gi|309812375|ref|ZP_07706130.1| DNA-directed RNA polymerase, alpha subunit [Dermacoccus sp.
           Ellin185]
 gi|308433680|gb|EFP57557.1| DNA-directed RNA polymerase, alpha subunit [Dermacoccus sp.
           Ellin185]
          Length = 339

 Score =  338 bits (867), Expect = 7e-91,   Method: Composition-based stats.
 Identities = 128/330 (38%), Positives = 193/330 (58%), Gaps = 7/330 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V     E+R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGV H
Sbjct: 6   RPTLSEDVV----SESRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVQH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S+I GV ED+T++ILNIKG+ +    D    + + K+G GVVTA DI     +EV NP
Sbjct: 62  EFSTIPGVKEDVTEVILNIKGLVVSSEHDEPVVMYLRKQGAGVVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+    + MELTV +G GYV A  +++    IG I +D++YSP+  V+Y VE+ 
Sbjct: 122 DLEIATLNDKGSIEMELTVERGRGYVSAALNKSAEQEIGRIPVDSIYSPVLAVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  S+   D++A A   L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKNSMAPRDAMASAGSTLVELFGLARELNVEAEGIDMGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+   L
Sbjct: 242 ALAEDLALPIEDLDLTVRSYNCLKREGIHTVGELVSRSEADLLDIRNFGSKSIHEVADKL 301

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
             MGL L  + P +    I   A +Y++  
Sbjct: 302 RDMGLQLKDSPPGFDASVI---ADRYDEDA 328


>gi|309799084|ref|ZP_07693337.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus infantis
           SK1302]
 gi|308117319|gb|EFO54742.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus infantis
           SK1302]
          Length = 311

 Score =  338 bits (867), Expect = 7e-91,   Method: Composition-based stats.
 Identities = 130/313 (41%), Positives = 198/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K      K + +  +GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVKDEKIIELDVQGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NP H +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y V
Sbjct: 119 VNPGHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  K  +     
Sbjct: 179 EPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSAEVMKEA 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            +   +  L + +EEL+LSVRS NCL+   I  + DL +++EA+M+++ N GRKSL E+K
Sbjct: 239 DTESDDRILERTIEELDLSVRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L   
Sbjct: 299 VKLIDLGLGLKDK 311


>gi|269958607|ref|YP_003328394.1| DNA-directed RNA polymerase subunit alpha [Anaplasma centrale str.
           Israel]
 gi|269848436|gb|ACZ49080.1| DNA-directed RNA polymerase subunit alpha [Anaplasma centrale str.
           Israel]
          Length = 368

 Score =  338 bits (867), Expect = 7e-91,   Method: Composition-based stats.
 Identities = 164/348 (47%), Positives = 232/348 (66%), Gaps = 12/348 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           I  +W  L +P++I+ +  G        +I EPL  GFA TLGNALRRV+MSSLRG A+ 
Sbjct: 21  ISDHWDRLTRPSSIKVVGDGDVS-RSAELIVEPLESGFALTLGNALRRVMMSSLRGFAVY 79

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            ++++GV HE++S+ GV ED+ D++LN+  + +K+     + + +  +GPG VTA  I  
Sbjct: 80  GIEVEGVSHELTSLSGVREDVADLVLNLSMLRVKLLTSESRVLRLVAKGPGEVTAAAIGD 139

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR-------TENDPIGLITID 174
                +LN D  IC L  DA   M++ V+ G GYVPA  +R       T     G I  +
Sbjct: 140 SEGCVILNKDLHICTLGKDANFSMKIYVNSGKGYVPASEYRAASRSGATSEAGPGFIATN 199

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           ALYSP+KKV++ +ES+R GQ  DYDKL ++++TDGSI+ +++VA+++R+LQDQL  FI  
Sbjct: 200 ALYSPVKKVAFRIESSRIGQFTDYDKLVISVETDGSISPDEAVAVSARVLQDQLQAFIGS 259

Query: 235 EEPKKEV----KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
           EE + E     K D    +LP++  LL+KV+ELELSVRS NCL+ +NI Y+GDL+Q+TE+
Sbjct: 260 EEVEGESPVRKKVDKEEGALPYDHNLLRKVDELELSVRSHNCLKNDNITYIGDLVQKTES 319

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           DMLR  NFGRKSL EI  VL +M L LGM +P+WPPESIE L+K+Y +
Sbjct: 320 DMLRTPNFGRKSLNEINEVLASMNLHLGMKVPNWPPESIENLSKQYSE 367


>gi|119718095|ref|YP_925060.1| DNA-directed RNA polymerase subunit alpha [Nocardioides sp. JS614]
 gi|158513104|sp|A1SNI8|RPOA_NOCSJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119538756|gb|ABL83373.1| DNA-directed RNA polymerase subunit alpha [Nocardioides sp. JS614]
          Length = 338

 Score =  338 bits (867), Expect = 7e-91,   Method: Composition-based stats.
 Identities = 122/308 (39%), Positives = 183/308 (59%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
               +E R+  + EPL  GF +TLGN+LRR L+SS+ GA++T+++ID VLHE S+I+GV 
Sbjct: 11  EETVDEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIKIDNVLHEFSTIEGVK 70

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+T++ILN+KG+ +    D    + + K G G VTA DI     +EV NPD  I  L  
Sbjct: 71  EDVTEVILNLKGLVVSSEHDEPVTMYLRKSGAGDVTAADIAPPAGVEVHNPDLKIATLSD 130

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              + MEL V +G GYV A  ++  ++ IG + +D++YSP+ KV+Y VE+ R  Q  D+D
Sbjct: 131 KGKLEMELVVERGRGYVSAVQNKGADNEIGRMPVDSIYSPVLKVTYKVEATRVEQRTDFD 190

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + ++T  SI   D++A A + L +  G+        + +    +         L   
Sbjct: 191 KLVIDVETKPSIRPRDAIASAGKTLVELFGLARELNVEAEGIDIGPSPVDEQLAADLALP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           VE+L+L+VRS NCL+ E I  +G+LI R+E D+L + NFG KS+ E+K  L  MGL L  
Sbjct: 251 VEDLQLTVRSYNCLKREGIHTVGELISRSEQDLLDIRNFGAKSIDEVKAKLVEMGLSLKD 310

Query: 320 NLPDWPPE 327
           + P + P 
Sbjct: 311 SAPGFDPH 318


>gi|218135253|ref|ZP_03464057.1| hypothetical protein BACPEC_03158 [Bacteroides pectinophilus ATCC
           43243]
 gi|217990638|gb|EEC56649.1| hypothetical protein BACPEC_03158 [Bacteroides pectinophilus ATCC
           43243]
          Length = 319

 Score =  338 bits (867), Expect = 7e-91,   Method: Composition-based stats.
 Identities = 132/317 (41%), Positives = 205/317 (64%), Gaps = 6/317 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP  IE   +  +++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+I+G
Sbjct: 3   DFQKP-KIEIATIS-DDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+NIK + +K     D  K   I   G GVV A DIQT  DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNIKNLAIKNNSDSDEPKTAYIEFEGEGVVKASDIQTDGDI 120

Query: 126 EVLNPDHVICNLD--VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E++NPD VI +L+      + MELT++KG GYV +  ++TE+ P+G+I +D++Y+P+++V
Sbjct: 121 EIINPDLVIAHLNGGDGCKLSMELTITKGRGYVSSDKNKTEDTPVGVIAVDSIYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +  V++ R GQV DYDKL++ + T+G++  +++V+LA+++L + L +FI+  E  K  + 
Sbjct: 181 NMAVQNTRVGQVTDYDKLTLDVYTNGTLAPDEAVSLAAKVLSEHLNLFIDLSENAKTAEI 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +   +      L   ++ELELSVRS NCL+   I  + +L  +T  DM+++ N GRKSL
Sbjct: 241 MVEESTDEHEKVLEMTIDELELSVRSYNCLKRAGINTVEELCNKTPDDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFLGMN 320
            E+   L  +GL L  N
Sbjct: 301 EEVLAKLKELGLQLSPN 317


>gi|70725829|ref|YP_252743.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           haemolyticus JCSC1435]
 gi|90110870|sp|Q4L888|RPOA_STAHJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|68446553|dbj|BAE04137.1| DNA-directed RNA polymerase alpha chain [Staphylococcus
           haemolyticus JCSC1435]
          Length = 314

 Score =  338 bits (867), Expect = 7e-91,   Method: Composition-based stats.
 Identities = 131/310 (42%), Positives = 201/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I + ++ +     + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+G
Sbjct: 3   EIEKPR-IETIEISEDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I  V ED++ II+NIK + LK+  +  K + I  R  G VTA DI   +D+EV
Sbjct: 61  VLHEFSAIDNVVEDVSTIIMNIKKLALKIYSEEDKTLEIDVRDEGEVTASDITHDSDVEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  +     +++ L  +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTV
Sbjct: 121 LNPELKIATVSKGGHLKIRLVANKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  D+DKL++ + T+GSIT ++SV+LA++IL + L +F+   +  +  +  I  
Sbjct: 181 ENTRVGQSSDFDKLTLDVWTNGSITPQESVSLAAKILTEHLNIFVGLTDEAQNAEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMSIEELDLSVRSYNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 YKLEDLGLGL 310


>gi|292669831|ref|ZP_06603257.1| DNA-directed RNA polymerase subunit alpha [Selenomonas noxia ATCC
           43541]
 gi|292648628|gb|EFF66600.1| DNA-directed RNA polymerase subunit alpha [Selenomonas noxia ATCC
           43541]
          Length = 319

 Score =  338 bits (866), Expect = 9e-91,   Method: Composition-based stats.
 Identities = 130/319 (40%), Positives = 197/319 (61%), Gaps = 6/319 (1%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             ++ KP  IE   +  E+      + EPL  G+  T GN+LRR+L+SSL GAA+T++QI
Sbjct: 1   MTDIEKP-KIEIAEIS-EDGRYGRFVCEPLEPGYGTTFGNSLRRMLLSSLDGAAVTSIQI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGVLHE S+I GV +D+T I+L +K + ++M G     + I   G   VTA DI+  +DI
Sbjct: 59  DGVLHEFSTIPGVRDDVTSIVLALKQLCIRMQGSELHTLRIEAEGEREVTAADIECGSDI 118

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E+LNP+  I  L     +++E+TV +G GYVPA  ++   D IG+I ID+++SP+++V+Y
Sbjct: 119 EILNPELHIATLGATGKLKIEMTVERGRGYVPADKNKKSEDSIGVIPIDSIFSPVQRVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVE  R G V DYD+L + + T+GSI  E++V+ A+ IL   L +F N +    E +E++
Sbjct: 179 TVEDTRVGNVTDYDRLILDVWTNGSIRPEEAVSKAAAILVMHLRLFQNMDGTMLEEEEEV 238

Query: 246 ----NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
                 +       L   +++L+LSVRS NCL+   I  + DL Q+TE DM+++ N GRK
Sbjct: 239 PNFPPEEVDDSAKVLEMTIDDLDLSVRSFNCLKRAGINTVADLAQKTEDDMMKVRNLGRK 298

Query: 302 SLVEIKGVLGTMGLFLGMN 320
           SL E+K  L  +GL L  +
Sbjct: 299 SLDEVKKKLEELGLSLRQD 317


>gi|326332227|ref|ZP_08198507.1| DNA-directed RNA polymerase, alpha subunit [Nocardioidaceae
           bacterium Broad-1]
 gi|325949933|gb|EGD41993.1| DNA-directed RNA polymerase, alpha subunit [Nocardioidaceae
           bacterium Broad-1]
          Length = 338

 Score =  338 bits (866), Expect = 9e-91,   Method: Composition-based stats.
 Identities = 126/308 (40%), Positives = 183/308 (59%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
               EE R+  + EPL  GF +TLGN+LRR L+SS+ GA++T+++IDGVLHE S+I+GV 
Sbjct: 11  EESVEEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIKIDGVLHEFSTIEGVK 70

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+T+IILN+KG+ +    D    + + K G G VTA DI     +EV NPD  I  L  
Sbjct: 71  EDVTEIILNLKGLVVSSEHDEPVTMYLRKSGAGDVTAADIAPPAGVEVHNPDLKIATLSD 130

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              + +EL V +G GYV A  ++   + IG I +D++YSP+ KVSY VE+ R  Q  D+D
Sbjct: 131 KGKIELELVVERGRGYVSAVQNKGAENEIGRIPVDSIYSPVLKVSYKVEATRVEQRTDFD 190

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + ++T  SI   D++A A + L +  G+        + +    +         L   
Sbjct: 191 KLVIDVETKPSIAPRDAIASAGKTLVELFGLARELNVDAEGIDIGPSPVDEQLAADLALP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           VE+L+L+VRS NCL+ E I  +G+LI R+E D+L + NFG KS+ E+K  L  MGL L  
Sbjct: 251 VEDLQLTVRSYNCLKREGIHTVGELISRSEQDLLDIRNFGAKSIDEVKLKLHEMGLSLKD 310

Query: 320 NLPDWPPE 327
           + P + P 
Sbjct: 311 SAPGFDPS 318


>gi|255326871|ref|ZP_05367947.1| DNA-directed RNA polymerase, alpha subunit [Rothia mucilaginosa
           ATCC 25296]
 gi|255296088|gb|EET75429.1| DNA-directed RNA polymerase, alpha subunit [Rothia mucilaginosa
           ATCC 25296]
          Length = 330

 Score =  338 bits (866), Expect = 9e-91,   Method: Composition-based stats.
 Identities = 120/329 (36%), Positives = 192/329 (58%), Gaps = 9/329 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V      NR+    EPL  GF +T+GN+LRR L+SS+ GAA+T+V+IDGVLH
Sbjct: 6   RPTLTEEVV----APNRSRFTIEPLEPGFGYTMGNSLRRTLLSSIPGAAVTSVRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T+IILNIK +++    D      + K+G G +TAGDI+    +E+ NP
Sbjct: 62  EFSTVPGVTEDVTEIILNIKKLSISSENDEPVVAYLRKQGEGELTAGDIEVPAGVEIHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           +  +  L+  A    EL + +G GYV A  ++  +  IG I +D++YSP+ KV+++V + 
Sbjct: 122 ELHLATLNASANFNAELVIERGRGYVTAAQNKVGDGEIGRIPVDSIYSPVLKVTFSVNAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D L++ ++T  +I   D+VA A   L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDSLTLDVETKEAIAPRDAVASAGSTLVELFGLARELNIAAEGIEVGPSPADE 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +E+L +SVRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  L
Sbjct: 242 SMAADLALPIEDLNMSVRSYNCLKREGIHTVGELVTRSEADLMDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             +GL L  + P + P      A+  +D+
Sbjct: 302 IELGLALKDSPPGFEPA-----ARPLDDE 325


>gi|25027128|ref|NP_737182.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           efficiens YS-314]
 gi|259506741|ref|ZP_05749641.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           efficiens YS-314]
 gi|41688706|sp|Q8FS33|RPOA_COREF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|23492408|dbj|BAC17382.1| putative DNA-directed RNA polymerase alpha chain [Corynebacterium
           efficiens YS-314]
 gi|259165682|gb|EEW50236.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           efficiens YS-314]
          Length = 338

 Score =  338 bits (866), Expect = 9e-91,   Method: Composition-based stats.
 Identities = 132/307 (42%), Positives = 196/307 (63%), Gaps = 1/307 (0%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           + +R+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+V+IDGVLHE ++I G+ ED++
Sbjct: 15  DSSRSKFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVKIDGVLHEFTTINGIKEDVS 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           DIILNIKG+ L    D    + + K GPGVVTAGDI+   D+E+ NPD  I  L+ +A +
Sbjct: 75  DIILNIKGLVLSSDSDEPVIMHLSKEGPGVVTAGDIEPPADVEIHNPDLHIATLNENAKL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +EL V +G GYVPA    T  D IG I +D +YSP+ KVSY VE+ R  Q  D+DKL +
Sbjct: 135 DIELIVERGRGYVPATMTATGGD-IGRIPVDQIYSPVLKVSYKVEATRVEQRTDFDKLII 193

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T  SI+  D++A A + L +  G+        + ++   + +   +  A    +E+L
Sbjct: 194 DVETKNSISARDALASAGKTLVELFGLARELNVAAEGIEIGPSPQETEYIAAYSMPIEDL 253

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           + SVRS NCL+ E+I  +G+L +R E+D+L + NFG+KS+ E+K  L  +GL L     D
Sbjct: 254 DFSVRSYNCLKREDIHTVGELAERAESDLLDIRNFGQKSINEVKIKLAGLGLTLKDAPED 313

Query: 324 WPPESIE 330
           + P ++E
Sbjct: 314 FDPSTLE 320


>gi|304438389|ref|ZP_07398330.1| DNA-directed RNA polymerase subunit alpha [Selenomonas sp. oral
           taxon 149 str. 67H29BP]
 gi|304368755|gb|EFM22439.1| DNA-directed RNA polymerase subunit alpha [Selenomonas sp. oral
           taxon 149 str. 67H29BP]
          Length = 319

 Score =  338 bits (866), Expect = 9e-91,   Method: Composition-based stats.
 Identities = 129/319 (40%), Positives = 197/319 (61%), Gaps = 6/319 (1%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             ++ KP  IE   +  E+      I EPL  G+  T GN+LRR+L+SSL GAA+T++QI
Sbjct: 1   MTDIEKP-KIEIAEIS-EDGRYGRFICEPLEPGYGTTFGNSLRRMLLSSLDGAAVTSIQI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGVLHE S+I GV +D+T I+L +K + ++M     + + I   G   VTA DI+  +DI
Sbjct: 59  DGVLHEFSTIPGVRDDVTSIVLALKQLCIRMQDSEPRTIRIEAAGAREVTAADIECGSDI 118

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E+LNP+  I  +     +++E+TV +G GYVPA  ++  +D IG+I ID+++SP+++V+Y
Sbjct: 119 EILNPELHIATMGETGKLKIEMTVERGRGYVPADRNKKPDDVIGVIPIDSIFSPVQRVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVE  R G V DYD+L + + T+GSI  E++V+ A+ IL   L +F N +    E +E++
Sbjct: 179 TVEDTRVGNVTDYDRLILEVWTNGSIRPEEAVSKAAAILVMHLRLFQNMDGSVVEEEEEV 238

Query: 246 NVKS----LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
                         L   +++L+LSVRS NCL+   I  + DL Q+TE DM+++ N GRK
Sbjct: 239 PNFPPEEVDDSAKVLEMTIDDLDLSVRSFNCLKRAGINTVADLAQKTEDDMMKVRNLGRK 298

Query: 302 SLVEIKGVLGTMGLFLGMN 320
           SL E+K  L  +GL L  +
Sbjct: 299 SLDEVKKKLEELGLSLRQD 317


>gi|94676571|ref|YP_588801.1| DNA-directed RNA polymerase subunit alpha [Baumannia
           cicadellinicola str. Hc (Homalodisca coagulata)]
 gi|119366665|sp|Q1LTB3|RPOA_BAUCH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|94219721|gb|ABF13880.1| DNA-directed RNA polymerase, alpha subunit [Baumannia
           cicadellinicola str. Hc (Homalodisca coagulata)]
          Length = 327

 Score =  338 bits (866), Expect = 9e-91,   Method: Composition-based stats.
 Identities = 139/332 (41%), Positives = 216/332 (65%), Gaps = 8/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQLSLTHAKVILEPLERGFGHTLGNALRRILLSSIPGYAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDG+LHE S+ +G+ ED+ +I+LN+K + +K+    +  +T+ K G G VTA +I  
Sbjct: 58  EVEIDGILHEYSTKEGIREDIIEILLNLKELAVKVQSKDNVILTLNKSGLGPVTAANIIH 117

Query: 122 VNDIEVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKHH-RTENDPIGLITIDALYSP 179
            +D++++ P H++C+L   +A + M + V +G GYVPA       + PIG + +DA YSP
Sbjct: 118 DSDVQIIKPQHILCHLTEENASINMRIKVQRGRGYVPASARIHKYDRPIGRLLVDACYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           ++ +SY VE+AR  Q  D DKL + I+T+G+I  E+++  A+ IL +QL  F++  +  +
Sbjct: 178 VENISYNVEAARVEQRTDLDKLILEIETNGTIDPEEAIRRAATILAEQLEAFVDLRDISQ 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
               ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G
Sbjct: 238 P---EVKEEKPEFDPVLLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +KSL EIK VL + GL LGM L +WPP    +
Sbjct: 295 KKSLTEIKDVLASRGLSLGMRLENWPPLGFID 326


>gi|313836061|gb|EFS73775.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL037PA2]
 gi|314929597|gb|EFS93428.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL044PA1]
 gi|314970628|gb|EFT14726.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL037PA3]
 gi|328906195|gb|EGG25970.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium sp.
           P08]
          Length = 338

 Score =  338 bits (866), Expect = 9e-91,   Method: Composition-based stats.
 Identities = 117/308 (37%), Positives = 178/308 (57%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                 E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV HE S+I+G 
Sbjct: 10  TEETISEFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQHEFSTIEGC 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+T+IILN+KG+ L    D    + + K G G + A DI     + + NP   I  L+
Sbjct: 70  VEDVTEIILNLKGLVLSSEEDEPVAMYLRKSGTGEIIAADINPPAGVTIHNPGLHIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D    MEL V +G GYV +  +   +  IG I +D++YSP+ KV+Y VE+ R  Q  D+
Sbjct: 130 DDGRFEMELVVERGRGYVSSALNDDPSAEIGRIAVDSIYSPVLKVTYKVEATRVEQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  SI   D+VA A + L +  G+        + ++         +  +L  
Sbjct: 190 DKLVVDVETKPSILPRDAVASAGKTLVELFGLTRELNAEAEGIEIGAGPVDEEYAESLST 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  +GL L 
Sbjct: 250 PVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEKLTELGLALK 309

Query: 319 MNLPDWPP 326
            + P + P
Sbjct: 310 DSAPGFDP 317


>gi|312884678|ref|ZP_07744379.1| DNA-directed RNA polymerase subunit alpha [Vibrio caribbenthicus
           ATCC BAA-2122]
 gi|309367591|gb|EFP95142.1| DNA-directed RNA polymerase subunit alpha [Vibrio caribbenthicus
           ATCC BAA-2122]
          Length = 330

 Score =  338 bits (866), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 146/335 (43%), Positives = 217/335 (64%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +++LN+KG+ +++  G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEVLLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|255659529|ref|ZP_05404938.1| DNA-directed RNA polymerase, alpha subunit [Mitsuokella multacida
           DSM 20544]
 gi|260848082|gb|EEX68089.1| DNA-directed RNA polymerase, alpha subunit [Mitsuokella multacida
           DSM 20544]
          Length = 319

 Score =  338 bits (866), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 138/317 (43%), Positives = 205/317 (64%), Gaps = 6/317 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           ++ KP  IE   +  E+      I EPL RG+  T GN+LRR+L+SSL GAAIT+++IDG
Sbjct: 3   DIEKP-KIEIAEIS-EDNRYGKFICEPLERGYGTTFGNSLRRMLLSSLEGAAITSIRIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV +D+T+I+LN+K + LKM+G+  + + I   G   VTA DI    DIE+
Sbjct: 61  VLHEFSTIPGVRDDVTNIVLNLKELCLKMAGNEPRIIRIDVEGEKEVTAADIICDADIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  ++ D  +++E+TV +G GYVPA  ++  +D IG+I ID+++SP+K+V+YTV
Sbjct: 121 LNPDLHIATVNEDGKLKIEMTVERGRGYVPADKNKKPDDTIGVIPIDSIFSPVKRVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKKEVKE 243
           +  R G V DYD+L + + TDGS+  E++V+ A+ IL   L +F N +    E ++E   
Sbjct: 181 QDTRVGNVTDYDRLILEVWTDGSLRPEEAVSKAAGILVMHLKLFQNMDGLPEEEEEEEAT 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +    +  L   +E+L+LSVRS NCL+  NI  + DL ++TE DM+++ N GRKSL
Sbjct: 241 FPEEEEDDSSKVLDMTIEDLDLSVRSFNCLKRANINTVADLAEKTEDDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFLGMN 320
            E+K  L  +GL L  N
Sbjct: 301 EEVKKKLEELGLTLKQN 317


>gi|150392131|ref|YP_001322180.1| DNA-directed RNA polymerase, alpha subunit [Alkaliphilus
           metalliredigens QYMF]
 gi|166991520|sp|A6TWF3|RPOA_ALKMQ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|149951993|gb|ABR50521.1| DNA-directed RNA polymerase, alpha subunit [Alkaliphilus
           metalliredigens QYMF]
          Length = 315

 Score =  338 bits (866), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 131/310 (42%), Positives = 207/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  +E   +  +       + EPL RG+  TLGN+LRR+++SSL GAA+T+V+I+G
Sbjct: 3   EMEKP-KVEVFEISDDS-TYGKFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVTSVKIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           +LHE S+I GV ED+T+IILN+K +++ + G+  K + I   GPG VTAGDI    D+EV
Sbjct: 61  ILHEFSTIPGVKEDVTEIILNLKDLSIGIDGNEPKTLRIEMEGPGTVTAGDIIADADVEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  LD ++ + ME+ ++KG GYV A++++T   PIG+I +D++++P++KVSY V
Sbjct: 121 LNPDMYIATLDDNSKLNMEINIAKGRGYVSAENNKTAGMPIGVIPVDSIFTPVRKVSYFV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
            + R GQV DYDKL + + TDGSI  +++++LA++++ + L +FI  +E   +V+  +  
Sbjct: 181 GNTRVGQVTDYDKLEIEVFTDGSIKPDEAISLAAKVMSEHLNLFITLKEDVSDVEIMVQK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N G+KSL E+ 
Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVEELSLKSEEDMMKVRNLGKKSLEEVD 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 KKLEELGLGL 310


>gi|239980029|ref|ZP_04702553.1| DNA-directed RNA polymerase subunit alpha [Streptomyces albus
           J1074]
 gi|291451886|ref|ZP_06591276.1| DNA-directed RNA polymerase subunit alpha [Streptomyces albus
           J1074]
 gi|291354835|gb|EFE81737.1| DNA-directed RNA polymerase subunit alpha [Streptomyces albus
           J1074]
          Length = 340

 Score =  338 bits (866), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 126/316 (39%), Positives = 192/316 (60%), Gaps = 4/316 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG + +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNAKGKLEMELTVERGRGYVSAVQNKQAGQEIGRVPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNVDAEGIDMGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAKL 301

Query: 311 GTMGLFLGMNLPDWPP 326
             M L L  + P + P
Sbjct: 302 AGMSLALKDSPPGFDP 317


>gi|259047529|ref|ZP_05737930.1| DNA-directed RNA polymerase, alpha subunit [Granulicatella adiacens
           ATCC 49175]
 gi|259035720|gb|EEW36975.1| DNA-directed RNA polymerase, alpha subunit [Granulicatella adiacens
           ATCC 49175]
          Length = 315

 Score =  337 bits (865), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 138/311 (44%), Positives = 201/311 (64%), Gaps = 3/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I + ++ +     + EPL RG+  TLGN+LRR+L+SSL G A+T +Q+DG
Sbjct: 3   EIEKP-KIETIEVSEDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGTAVTDIQMDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           VLHE S+I GV ED+  IILNIK I LK  S D +K + I  +GP VVTAGDI+  +DI+
Sbjct: 61  VLHEFSTIDGVVEDVAAIILNIKKIALKSFSEDENKVLEIDVKGPAVVTAGDIKHDSDIQ 120

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           VLNPD  IC +       + +    G GYV + ++++EN PIG+I ID++Y+PI KV+Y 
Sbjct: 121 VLNPDLYICTVAEGHHFHVRMNAKNGRGYVRSDYNKSENMPIGVIPIDSIYTPISKVNYQ 180

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+ R GQ   YDKL++ + TDGSI  +D+++LA+RIL + L +F+N       ++  + 
Sbjct: 181 VENTRIGQKNVYDKLTLDVWTDGSIAPQDAISLAARILTEHLNIFVNLTNEALPMEIMVE 240

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L   +EEL+LSVRS NCL+   I  + +L  ++EA+M+++ N GRKSL E+
Sbjct: 241 KEETQKERLLEMTIEELDLSVRSYNCLKRAGINTVHELTSKSEAEMIKVRNLGRKSLEEV 300

Query: 307 KGVLGTMGLFL 317
           K  L  + L L
Sbjct: 301 KQKLIDLNLDL 311


>gi|295398314|ref|ZP_06808356.1| DNA-directed RNA polymerase subunit alpha [Aerococcus viridans ATCC
           11563]
 gi|294973453|gb|EFG49238.1| DNA-directed RNA polymerase subunit alpha [Aerococcus viridans ATCC
           11563]
          Length = 314

 Score =  337 bits (865), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 129/310 (41%), Positives = 203/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KPN IE I +  + +     + EPL RG+  TLGN+LRR+L+SSL G A+T++QID 
Sbjct: 3   EIEKPN-IETIEINDDSKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGTAVTSIQIDD 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T+I+LN+K ++LK+     K+V I   GP  VTA DI    D +V
Sbjct: 61  VLHEYSTVPGVREDVTEIVLNVKQLSLKLYDVEEKQVEIDITGPADVTAADIIADADFDV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPD  IC L   A   M + V  G G+V +++++ ++ PIG I +D++Y+PI KV+Y V
Sbjct: 121 MNPDLHICTLAEGARFHMIMNVKNGRGFVRSENNKVDSMPIGEIPVDSIYTPISKVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G++ +YDKL+M I TDG+I+ E++++LA++I+ + L +F+N  +  ++V+  +  
Sbjct: 181 ENTRIGEINEYDKLTMDIWTDGTISPEEALSLAAKIMTEHLEVFVNLTDEARQVEVMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E +M+++ N GRKSL E+K
Sbjct: 241 EETQKEKMLEMTIEELDLSVRSYNCLKRAGINTVEELTNKSEPEMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  + L L
Sbjct: 301 NKLAALDLSL 310


>gi|27364190|ref|NP_759718.1| DNA-directed RNA polymerase subunit alpha [Vibrio vulnificus CMCP6]
 gi|37678583|ref|NP_933192.1| DNA-directed RNA polymerase subunit alpha [Vibrio vulnificus YJ016]
 gi|320157576|ref|YP_004189955.1| DNA-directed RNA polymerase subunit alpha [Vibrio vulnificus
           MO6-24/O]
 gi|29611853|sp|Q8DE63|RPOA_VIBVU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|41688623|sp|Q7MPG4|RPOA_VIBVY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|27360308|gb|AAO09245.1| DNA-directed RNA polymerase, alpha subunit [Vibrio vulnificus
           CMCP6]
 gi|37197323|dbj|BAC93163.1| DNA-directed RNA polymerase, alpha subunit [Vibrio vulnificus
           YJ016]
 gi|319932888|gb|ADV87752.1| DNA-directed RNA polymerase alpha subunit [Vibrio vulnificus
           MO6-24/O]
          Length = 330

 Score =  337 bits (865), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 148/335 (44%), Positives = 217/335 (64%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|15925214|ref|NP_372748.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus Mu50]
 gi|15927804|ref|NP_375337.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus N315]
 gi|21283872|ref|NP_646960.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus MW2]
 gi|49484440|ref|YP_041664.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus MRSA252]
 gi|49487006|ref|YP_044227.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus MSSA476]
 gi|57650808|ref|YP_187023.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus COL]
 gi|87162055|ref|YP_494813.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus USA300_FPR3757]
 gi|88196136|ref|YP_500953.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus NCTC 8325]
 gi|148268664|ref|YP_001247607.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus JH9]
 gi|150394729|ref|YP_001317404.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus JH1]
 gi|151222338|ref|YP_001333160.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus str. Newman]
 gi|156980539|ref|YP_001442798.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus Mu3]
 gi|161510428|ref|YP_001576087.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus USA300_TCH1516]
 gi|221140174|ref|ZP_03564667.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus str. JKD6009]
 gi|253316985|ref|ZP_04840198.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus str. CF-Marseille]
 gi|253729890|ref|ZP_04864055.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus USA300_TCH959]
 gi|253734367|ref|ZP_04868532.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus TCH130]
 gi|255007004|ref|ZP_05145605.2| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus Mu50-omega]
 gi|257423709|ref|ZP_05600138.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus 55/2053]
 gi|257426387|ref|ZP_05602789.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus 65-1322]
 gi|257431673|ref|ZP_05608036.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus E1410]
 gi|257434633|ref|ZP_05610684.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus M876]
 gi|257794570|ref|ZP_05643549.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A9781]
 gi|258408828|ref|ZP_05681112.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A9763]
 gi|258422427|ref|ZP_05685339.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A9719]
 gi|258422671|ref|ZP_05685576.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A9635]
 gi|258439815|ref|ZP_05690561.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A9299]
 gi|258442629|ref|ZP_05691189.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A8115]
 gi|258446673|ref|ZP_05694828.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A6300]
 gi|258450209|ref|ZP_05698301.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A6224]
 gi|258450780|ref|ZP_05698839.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A5948]
 gi|258455419|ref|ZP_05703379.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A5937]
 gi|269203857|ref|YP_003283126.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus ED98]
 gi|282893663|ref|ZP_06301895.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A8117]
 gi|282902127|ref|ZP_06310020.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus C160]
 gi|282906567|ref|ZP_06314415.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus Btn1260]
 gi|282909537|ref|ZP_06317348.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus WW2703/97]
 gi|282911785|ref|ZP_06319581.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus WBG10049]
 gi|282915073|ref|ZP_06322850.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus M899]
 gi|282917569|ref|ZP_06325321.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus D139]
 gi|282920799|ref|ZP_06328517.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus C427]
 gi|282922093|ref|ZP_06329789.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A9765]
 gi|282925704|ref|ZP_06333352.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus C101]
 gi|282926770|ref|ZP_06334397.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A10102]
 gi|283767316|ref|ZP_06340231.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus H19]
 gi|283959002|ref|ZP_06376443.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus A017934/97]
 gi|284025250|ref|ZP_06379648.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus 132]
 gi|293497477|ref|ZP_06665331.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus 58-424]
 gi|293511052|ref|ZP_06669749.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus M809]
 gi|293549658|ref|ZP_06672330.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus M1015]
 gi|294848757|ref|ZP_06789502.1| DNA-directed RNA polymerase [Staphylococcus aureus A9754]
 gi|295404900|ref|ZP_06814713.1| DNA-directed RNA polymerase [Staphylococcus aureus A8819]
 gi|295428807|ref|ZP_06821431.1| DNA-directed RNA polymerase [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|296275985|ref|ZP_06858492.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus MR1]
 gi|297209963|ref|ZP_06926359.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus ATCC 51811]
 gi|297243958|ref|ZP_06927848.1| DNA-directed RNA polymerase [Staphylococcus aureus A8796]
 gi|297589707|ref|ZP_06948348.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus MN8]
 gi|300910975|ref|ZP_07128425.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus TCH70]
 gi|304379408|ref|ZP_07362143.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus ATCC BAA-39]
 gi|54039276|sp|P66706|RPOA_STAAN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|54039277|sp|P66707|RPOA_STAAW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|54042187|sp|P66705|RPOA_STAAM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|56749506|sp|Q6G797|RPOA_STAAS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|56749553|sp|Q6GEK9|RPOA_STAAR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|62287349|sp|Q5HDY4|RPOA_STAAC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366732|sp|Q2FER5|RPOA_STAA3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366733|sp|Q2FW32|RPOA_STAA8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|171769946|sp|A7X5C4|RPOA_STAA1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172049005|sp|A6QJ66|RPOA_STAAE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|13702024|dbj|BAB43316.1| DNA-directed RNA polymerase alpha chain [Staphylococcus aureus
           subsp. aureus N315]
 gi|14247997|dbj|BAB58386.1| DNA-directed RNA polymerase alpha chain [Staphylococcus aureus
           subsp. aureus Mu50]
 gi|21205314|dbj|BAB96008.1| DNA-directed RNA polymerase alpha chain [Staphylococcus aureus
           subsp. aureus MW2]
 gi|49242569|emb|CAG41290.1| DNA-directed RNA polymerase alpha chain [Staphylococcus aureus
           subsp. aureus MRSA252]
 gi|49245449|emb|CAG43926.1| DNA-directed RNA polymerase alpha chain [Staphylococcus aureus
           subsp. aureus MSSA476]
 gi|57284994|gb|AAW37088.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus COL]
 gi|87128029|gb|ABD22543.1| DNA-directed RNA polymerase alpha subunit [Staphylococcus aureus
           subsp. aureus USA300_FPR3757]
 gi|87203694|gb|ABD31504.1| DNA-directed RNA polymerase alpha chain, putative [Staphylococcus
           aureus subsp. aureus NCTC 8325]
 gi|147741733|gb|ABQ50031.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus JH9]
 gi|149947181|gb|ABR53117.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus JH1]
 gi|150375138|dbj|BAF68398.1| DNA-directed RNA polymerase alpha chain [Staphylococcus aureus
           subsp. aureus str. Newman]
 gi|156722674|dbj|BAF79091.1| DNA-directed RNA polymerase alpha chain [Staphylococcus aureus
           subsp. aureus Mu3]
 gi|160369237|gb|ABX30208.1| DNA-directed RNA polymerase alpha subunit [Staphylococcus aureus
           subsp. aureus USA300_TCH1516]
 gi|253726337|gb|EES95066.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus USA300_TCH959]
 gi|253727684|gb|EES96413.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus TCH130]
 gi|257272727|gb|EEV04829.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus 55/2053]
 gi|257276018|gb|EEV07469.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus 65-1322]
 gi|257282552|gb|EEV12684.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus E1410]
 gi|257285229|gb|EEV15345.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus M876]
 gi|257788542|gb|EEV26882.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A9781]
 gi|257840511|gb|EEV64971.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A9763]
 gi|257841858|gb|EEV66295.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A9719]
 gi|257847082|gb|EEV71091.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A9635]
 gi|257847591|gb|EEV71593.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A9299]
 gi|257851750|gb|EEV75684.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A8115]
 gi|257854741|gb|EEV77689.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A6300]
 gi|257856301|gb|EEV79210.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A6224]
 gi|257861563|gb|EEV84365.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A5948]
 gi|257862630|gb|EEV85398.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           A5937]
 gi|262076147|gb|ACY12120.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus ED98]
 gi|269941813|emb|CBI50223.1| DNA-directed RNA polymerase alpha chain [Staphylococcus aureus
           subsp. aureus TW20]
 gi|282312533|gb|EFB42937.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus C101]
 gi|282315214|gb|EFB45598.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus C427]
 gi|282318531|gb|EFB48889.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus D139]
 gi|282320794|gb|EFB51128.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus M899]
 gi|282323481|gb|EFB53797.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus WBG10049]
 gi|282326516|gb|EFB56818.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus WW2703/97]
 gi|282329466|gb|EFB58987.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus Btn1260]
 gi|282591221|gb|EFB96294.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A10102]
 gi|282593561|gb|EFB98554.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A9765]
 gi|282596586|gb|EFC01545.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus C160]
 gi|282763721|gb|EFC03849.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           A8117]
 gi|283461195|gb|EFC08279.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus H19]
 gi|283471446|emb|CAQ50657.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus ST398]
 gi|283788594|gb|EFC27421.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus A017934/97]
 gi|285817886|gb|ADC38373.1| DNA-directed RNA polymerase alpha subunit [Staphylococcus aureus
           04-02981]
 gi|290918705|gb|EFD95781.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus M1015]
 gi|291096408|gb|EFE26666.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus 58-424]
 gi|291466039|gb|EFF08568.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus M809]
 gi|294824136|gb|EFG40560.1| DNA-directed RNA polymerase [Staphylococcus aureus A9754]
 gi|294969845|gb|EFG45863.1| DNA-directed RNA polymerase [Staphylococcus aureus A8819]
 gi|295127156|gb|EFG56798.1| DNA-directed RNA polymerase [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|296885636|gb|EFH24573.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus ATCC 51811]
 gi|297178736|gb|EFH37981.1| DNA-directed RNA polymerase [Staphylococcus aureus A8796]
 gi|297578218|gb|EFH96931.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus MN8]
 gi|298695481|gb|ADI98703.1| DNA-directed RNA polymerase alpha chain [Staphylococcus aureus
           subsp. aureus ED133]
 gi|300887955|gb|EFK83150.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus TCH70]
 gi|302333860|gb|ADL24053.1| DNA-directed RNA polymerase alpha subunit [Staphylococcus aureus
           subsp. aureus JKD6159]
 gi|302752097|gb|ADL66274.1| DNA-directed RNA polymerase alpha subunit [Staphylococcus aureus
           subsp. aureus str. JKD6008]
 gi|304341940|gb|EFM07844.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus ATCC BAA-39]
 gi|312437365|gb|ADQ76436.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus TCH60]
 gi|312830573|emb|CBX35415.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus ECT-R 2]
 gi|315129696|gb|EFT85687.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus CGS03]
 gi|315193476|gb|EFU23872.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus CGS00]
 gi|315198246|gb|EFU28577.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus CGS01]
 gi|320140238|gb|EFW32097.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus MRSA131]
 gi|320143508|gb|EFW35289.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus MRSA177]
 gi|323440096|gb|EGA97811.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           O11]
 gi|323442770|gb|EGB00396.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           O46]
 gi|329723377|gb|EGG59906.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus 21172]
 gi|329730447|gb|EGG66837.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus 21193]
 gi|329732085|gb|EGG68440.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus aureus
           subsp. aureus 21189]
          Length = 314

 Score =  337 bits (865), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 128/310 (41%), Positives = 201/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I + ++ +     + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+G
Sbjct: 3   EIEKPR-IETIEISEDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++  V ED++ II+NIK + LK+  +  K + I  R  G VTA DI   +D+E+
Sbjct: 61  VLHEFSAVDNVVEDVSTIIMNIKQLALKIYSEEDKTLEIDVRDEGEVTASDITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  +     +++ L  +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTV
Sbjct: 121 LNPELKIATVSKGGHLKIRLVANKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  D+DKL++ + T+GSIT ++SV+LA++I+ + L +F+   +  +  +  I  
Sbjct: 181 ENTRVGQSSDFDKLTLDVWTNGSITPQESVSLAAKIMTEHLNIFVGLTDEAQNAEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMSIEELDLSVRSYNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 YKLEDLGLGL 310


>gi|228474561|ref|ZP_04059292.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus hominis
           SK119]
 gi|314935857|ref|ZP_07843209.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus hominis
           subsp. hominis C80]
 gi|228271224|gb|EEK12592.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus hominis
           SK119]
 gi|313656422|gb|EFS20162.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus hominis
           subsp. hominis C80]
          Length = 314

 Score =  337 bits (865), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 130/310 (41%), Positives = 201/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I + ++ +     + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+G
Sbjct: 3   EIEKPR-IETIEISEDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I  V ED++ II+NIK + LK+  +  K + I  R  G VTA DI   +D+EV
Sbjct: 61  VLHEFSAIDNVVEDVSTIIMNIKKLALKIYSEEDKTLEIDVRDEGEVTASDITHDSDVEV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  +     +++ L  +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTV
Sbjct: 121 LNPELKIATVSKGGHLKIRLVANKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  D+DKL++ + T+GSIT ++SV+LA++I+ + L +F+   +  +  +  I  
Sbjct: 181 ENTRVGQSSDFDKLTLDVWTNGSITPQESVSLAAKIMTEHLNIFVGLTDEAQNAEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMSIEELDLSVRSYNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 YKLEDLGLGL 310


>gi|88854650|ref|ZP_01129316.1| DNA-directed RNA polymerase alpha subunit [marine actinobacterium
           PHSC20C1]
 gi|88815811|gb|EAR25667.1| DNA-directed RNA polymerase alpha subunit [marine actinobacterium
           PHSC20C1]
          Length = 331

 Score =  337 bits (865), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 116/306 (37%), Positives = 184/306 (60%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
                E R+  + EPL  GF +TLGN++RR L+SS+ GAA+T+++IDGVLHE S++ GV 
Sbjct: 11  EENISEFRSRFVIEPLEPGFGYTLGNSIRRTLLSSIPGAAVTSIRIDGVLHEFSTVAGVK 70

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+T++ILNIK + +    D      + K+G G VTA DI     +E+ NP+ VI  L+ 
Sbjct: 71  EDVTEVILNIKNLVVSSEHDEPITAYLRKQGAGEVTAADISAPAGVEIHNPELVIATLND 130

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
            A   +ELT+ +G GYV A  +R+E    G I +D++YSP+ KV+Y VE+ R G+  D+D
Sbjct: 131 KAKFELELTIERGRGYVTATQNRSEFSEAGQIPVDSIYSPVLKVTYRVEATRAGERTDFD 190

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           +L + ++T  +IT  D++A A R L +  G+        + ++          +  L   
Sbjct: 191 RLVVDVETKSAITPRDAIASAGRTLTELFGLARELNTAAEGIEIGPAPVDAVLSTELSMP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +E+L+LSVRS NCL+ E I  + +L+  +E  ++ + NFG+KS+ E++  L  MGL L  
Sbjct: 251 IEDLDLSVRSYNCLKREGINTVSELVALSETQLMNIRNFGQKSVDEVRDKLVEMGLSLKD 310

Query: 320 NLPDWP 325
           ++P + 
Sbjct: 311 SVPGFD 316


>gi|289550169|ref|YP_003471073.1| DNA-directed RNA polymerase alpha subunit [Staphylococcus
           lugdunensis HKU09-01]
 gi|315659201|ref|ZP_07912065.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           lugdunensis M23590]
 gi|289179701|gb|ADC86946.1| DNA-directed RNA polymerase alpha subunit [Staphylococcus
           lugdunensis HKU09-01]
 gi|315495626|gb|EFU83957.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           lugdunensis M23590]
          Length = 314

 Score =  337 bits (865), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 129/310 (41%), Positives = 200/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I +  + +     + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+G
Sbjct: 3   EIEKPR-IETIEISDDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I  V ED++ II+NIK + LK+  +  K + I  R  G VTA DI   +D+E+
Sbjct: 61  VLHEFSAIDNVVEDVSTIIMNIKKLALKIYSEEDKTLEIDVRDEGEVTASDITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  +     +++ L  +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTV
Sbjct: 121 LNPELKIATVSKGGHLKIRLVANKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  D+DKL++ + T+GSIT ++SV+LA++I+ + L +F+   +  +  +  I  
Sbjct: 181 ENTRVGQSSDFDKLTLDVWTNGSITPQESVSLAAKIMTEHLNIFVGLTDEAQNAEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMSIEELDLSVRSYNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 YKLEDLGLGL 310


>gi|296394890|ref|YP_003659774.1| DNA-directed RNA polymerase subunit alpha [Segniliparus rotundus
           DSM 44985]
 gi|296182037|gb|ADG98943.1| DNA-directed RNA polymerase, alpha subunit [Segniliparus rotundus
           DSM 44985]
          Length = 350

 Score =  337 bits (865), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 120/314 (38%), Positives = 191/314 (60%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            +      E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I 
Sbjct: 8   VLTEEVVGEYRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTIA 67

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+T+I+LN+KG+ +    D    + + K+GPG VTA DI     + +  P+  I  
Sbjct: 68  GVKEDVTEIVLNVKGLEVSSVEDEPATLYLRKQGPGPVTAADIVAPAGVTITKPETHIAT 127

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           L+    + MEL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  
Sbjct: 128 LNDKGKLEMELVVERGRGYVPAVQNKDSGAEIGRIPVDSIYSPVLKVTYQVEATRVEQRT 187

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           D+D+L + ++T  SIT  D+VA A + L +  G+        + ++      +     +L
Sbjct: 188 DFDRLILDVETKSSITPRDAVASAGKTLVELFGLARELNLAAEGIEIGSVAAATNNIASL 247

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E+L L+VRS NCL+ E +  +G+L+ R+E+D+L + NFG+KS+ E+K  L T+GL 
Sbjct: 248 GLPIEDLHLTVRSYNCLKREGVHTIGELVARSESDLLDIRNFGQKSIDEVKLKLYTLGLA 307

Query: 317 LGMNLPDWPPESIE 330
           L  +  ++ P +I+
Sbjct: 308 LKDSPANFDPSNID 321


>gi|242371871|ref|ZP_04817445.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           epidermidis M23864:W1]
 gi|242350378|gb|EES41979.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           epidermidis M23864:W1]
          Length = 314

 Score =  337 bits (864), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 128/310 (41%), Positives = 201/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I + ++ +     + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+G
Sbjct: 3   EIEKPR-IETIEISEDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++  V ED++ II+NIK + LK+  +  K + I  +  G VTA DI   +D+E+
Sbjct: 61  VLHEFSAVDNVVEDVSTIIMNIKKLALKIYSEEDKTLEIDVKDEGEVTASDITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  +     +++ L  +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTV
Sbjct: 121 LNPELKIATVSKGGHLKVRLVANKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  DYDKL++ + T+GSIT ++SV+LA++I+ + L +F+   +  +  +  I  
Sbjct: 181 ENTRVGQSSDYDKLTLDVWTNGSITPQESVSLAAKIMTEHLNIFVGLTDEAQNAEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMSIEELDLSVRSYNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 YKLEDLGLGL 310


>gi|256831853|ref|YP_003160580.1| DNA-directed RNA polymerase, alpha subunit [Jonesia denitrificans
           DSM 20603]
 gi|256685384|gb|ACV08277.1| DNA-directed RNA polymerase, alpha subunit [Jonesia denitrificans
           DSM 20603]
          Length = 334

 Score =  337 bits (864), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 125/322 (38%), Positives = 193/322 (59%), Gaps = 4/322 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E ++     + R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPTLSEEVI----SDARSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S+I GV ED+T+IILN+K + L    D    + + K+G GVVTA DI     +EV NP
Sbjct: 62  EFSTITGVKEDVTEIILNVKNLVLSSENDEPVVMYLRKQGAGVVTAADIVPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+    + +ELTV +G GYV A+ +++ +  IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLHIATLNDKGKLEIELTVERGRGYVSAQQNKSMDAEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  SI   D++A A + L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDRLIVDVETKSSIVPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPTDA 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +E+L L++RS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 242 ALAADLALPIEDLNLTIRSYNCLKREGIHQVGELVARSEADLLDIRNFGAKSINEVKEKL 301

Query: 311 GTMGLFLGMNLPDWPPESIEEL 332
             +GL L  +  D+ P S  + 
Sbjct: 302 HELGLSLKDSPLDFQPSSESDY 323


>gi|225026391|ref|ZP_03715583.1| hypothetical protein EUBHAL_00640 [Eubacterium hallii DSM 3353]
 gi|224956280|gb|EEG37489.1| hypothetical protein EUBHAL_00640 [Eubacterium hallii DSM 3353]
          Length = 319

 Score =  337 bits (864), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 132/314 (42%), Positives = 205/314 (65%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP  IE   + ++ +     + EPL RG+  TLGN+LRR+++SSL GAA++AV+I G
Sbjct: 3   EFEKPR-IEIAEISEDNK-YGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSAVKIKG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+NIK + +K   S +  KR  I   G GVVTA DIQ  +DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNIKELAIKNNSSSNEPKRAFIEFSGEGVVTAADIQVDSDI 120

Query: 126 EVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E++NPD VI  L   A      ELT++KG GYV A  +++E+  I +I +D++Y+P+++V
Sbjct: 121 EIINPDLVIATLSGGADSHFEAELTITKGRGYVGADKNKSEDQSIDVIAVDSIYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + TV++ R GQ+ D+DKL++ + T+G++  +++V+LA+++L + L +FI+  E  ++ + 
Sbjct: 181 NLTVQNTRVGQITDFDKLTLDVFTNGTLAPDEAVSLAAKVLSEHLNLFIDLSENAQKAEV 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +     P +  L   ++ELELSVRS NCL+   I  + +L  +T  DM+++ N GRKSL
Sbjct: 241 MVETAQDPVDKVLEMNIDELELSVRSYNCLKRAGINTVEELTNKTPEDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 301 EEVLAKLKELGLSL 314


>gi|303256475|ref|ZP_07342489.1| DNA-directed RNA polymerase, alpha subunit [Burkholderiales
           bacterium 1_1_47]
 gi|302859966|gb|EFL83043.1| DNA-directed RNA polymerase, alpha subunit [Burkholderiales
           bacterium 1_1_47]
          Length = 346

 Score =  337 bits (864), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 152/347 (43%), Positives = 206/347 (59%), Gaps = 22/347 (6%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            +   L+KP +IE     +       +  EP   G+AHTLGNALRRVL+SS+ G A T  
Sbjct: 1   MSVNALLKPRSIEVET-AEGNPYSATVTMEPFETGYAHTLGNALRRVLLSSMVGFAPTEA 59

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           QI GV+HE S I GV ED+ DI+LN+KGI  K+       +T+ K G GVVTA D    +
Sbjct: 60  QIAGVVHEYSQIDGVKEDVVDILLNVKGIIFKLENRDEVTITLRKEGEGVVTAADFDLPH 119

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND----PIGLITIDALYSP 179
           D+++LNP+HVI NL     + M+L + KG GY P      ++D     IG I +DA +SP
Sbjct: 120 DVQILNPEHVIANLS-GGKLDMQLKIEKGRGYQPGDMRALKDDYSKGTIGRIIMDASFSP 178

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE---- 235
           I +V+Y VE+AR  Q  D DKL M I+T+G+I  E+++  A+ ILQDQL +F        
Sbjct: 179 ILRVAYRVENARVEQRTDLDKLVMNIETNGAILPEEALRQAAHILQDQLSVFGGLPTIGL 238

Query: 236 ------------EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGD 283
                       +P+  V+  +     P +P L + V++LEL+VRS NCL+ ENI Y+GD
Sbjct: 239 EPVAPQPAFGAMQPQAPVEAPMAKPQPPVDPILRRPVDDLELTVRSANCLKAENIYYIGD 298

Query: 284 LIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           LIQRTE ++L+  N GRKSL EIK VL   GL LGM L +WPP   +
Sbjct: 299 LIQRTENELLKTPNLGRKSLNEIKEVLAAHGLTLGMKLENWPPVGFD 345


>gi|331000670|ref|ZP_08324323.1| DNA-directed RNA polymerase, alpha subunit [Parasutterella
           excrementihominis YIT 11859]
 gi|329570882|gb|EGG52593.1| DNA-directed RNA polymerase, alpha subunit [Parasutterella
           excrementihominis YIT 11859]
          Length = 346

 Score =  337 bits (864), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 152/347 (43%), Positives = 207/347 (59%), Gaps = 22/347 (6%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            +   L+KP +IE     +       +  EP   G+AHTLGNALRRVL+SS+ G A T  
Sbjct: 1   MSVNALLKPRSIEVET-AEGNPYSATVTMEPFETGYAHTLGNALRRVLLSSMVGFAPTEA 59

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           QI GV+HE S I GV ED+ DI+LN+KGI  K+       +T+ K G GVVTA D    +
Sbjct: 60  QIAGVVHEYSQIDGVKEDVVDILLNVKGIIFKLENRDEVTITLRKEGEGVVTAADFDLPH 119

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND----PIGLITIDALYSP 179
           D+++LNP+HVI NL     + M+L + KG GY P      ++D     IG I +DA +SP
Sbjct: 120 DVQILNPEHVIANLS-GGKLDMQLKIEKGRGYQPGDMRALKDDYSKGTIGRIIMDASFSP 178

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE---- 235
           I +V+Y VE+AR  Q  D DKL M I+T+G+I  E+++  A+ ILQDQL +F        
Sbjct: 179 ILRVAYRVENARVEQRTDLDKLVMNIETNGAILPEEALRQAAHILQDQLSVFGGLPTIGL 238

Query: 236 ------------EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGD 283
                       +P+  V+  +     P +P L + V++LEL+VRS NCL+ ENI Y+GD
Sbjct: 239 EPVAPQPAFGAMQPQAPVEAPMAKPQPPVDPILRRPVDDLELTVRSANCLKAENIYYIGD 298

Query: 284 LIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           LIQRTE ++L+  N GRKSL EIK VL   GL LGM L +WPP  ++
Sbjct: 299 LIQRTENELLKTPNLGRKSLNEIKEVLAAHGLTLGMKLENWPPVGLD 345


>gi|260886903|ref|ZP_05898166.1| DNA-directed RNA polymerase, alpha subunit [Selenomonas sputigena
           ATCC 35185]
 gi|330839299|ref|YP_004413879.1| DNA-directed RNA polymerase, alpha subunit [Selenomonas sputigena
           ATCC 35185]
 gi|260863502|gb|EEX78002.1| DNA-directed RNA polymerase, alpha subunit [Selenomonas sputigena
           ATCC 35185]
 gi|329747063|gb|AEC00420.1| DNA-directed RNA polymerase, alpha subunit [Selenomonas sputigena
           ATCC 35185]
          Length = 319

 Score =  336 bits (863), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 132/315 (41%), Positives = 197/315 (62%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  E+      + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDG
Sbjct: 3   EIEKP-KIEIVEIS-EDNRYGKFVCEPLERGYGTTLGNSLRRILLSSLPGAAITSIRIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV +D+T+I+LN+K +  KM  +  + + +  +G   +TA DI T  D+E+
Sbjct: 61  VLHEFSTIPGVRDDVTNIVLNLKSLCFKMYSEEPRVLRLDVKGEKEITAADIITDPDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L+ D  + ME+ V +G GYV A+ ++  +  IG+I ID+++SPI++V+YTV
Sbjct: 121 LNPDLHIATLNEDGELHMEMIVERGKGYVAAEKNKKPDHVIGVIPIDSIFSPIQRVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF----EEPKKEVKE 243
           +  R G V DYDKL + + TDGSI  E+ V+ A+ IL     +F N     E  ++E   
Sbjct: 181 QDTRVGNVTDYDKLILDVWTDGSIRPEEGVSRAASILISHFKLFQNMAGIPEIEEEEEIA 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +    +  L   +++L+LSVRS NCL+  NI  + DL+ +TE DM+++ N GRKSL
Sbjct: 241 PPEPEEPDASKVLETTIDDLDLSVRSFNCLKRANINTVADLVSKTEEDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFLG 318
            E+K  L    L L 
Sbjct: 301 EEVKKKLEEYDLTLK 315


>gi|27468715|ref|NP_765352.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           epidermidis ATCC 12228]
 gi|57867752|ref|YP_189368.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           epidermidis RP62A]
 gi|242243973|ref|ZP_04798416.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           epidermidis W23144]
 gi|251812073|ref|ZP_04826546.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|282875368|ref|ZP_06284241.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus
           epidermidis SK135]
 gi|293368459|ref|ZP_06615083.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|33301647|sp|Q8CRI4|RPOA_STAES RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|71153723|sp|Q5HM25|RPOA_STAEQ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|27316263|gb|AAO05438.1|AE016750_43 DNA-directed RNA polymerase alpha chain [Staphylococcus epidermidis
           ATCC 12228]
 gi|57638410|gb|AAW55198.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus
           epidermidis RP62A]
 gi|242232606|gb|EES34918.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           epidermidis W23144]
 gi|251804407|gb|EES57064.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|281296133|gb|EFA88654.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus
           epidermidis SK135]
 gi|291317417|gb|EFE57839.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|319400599|gb|EFV88824.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus
           epidermidis FRI909]
 gi|329731206|gb|EGG67576.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus
           epidermidis VCU144]
 gi|329736451|gb|EGG72719.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus
           epidermidis VCU028]
 gi|329737076|gb|EGG73331.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus
           epidermidis VCU045]
          Length = 314

 Score =  336 bits (863), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 127/310 (40%), Positives = 202/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I + ++ +     + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+G
Sbjct: 3   EIEKPR-IETIEVSEDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++  V ED++ II+NIK + LK+  +  K + I  +  G VTA DI   +D+E+
Sbjct: 61  VLHEFSAVDNVVEDVSTIIMNIKKLALKIYSEEDKTLEIDVKDEGEVTASDITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  +     +++ L  +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTV
Sbjct: 121 LNPELKIATVSKGGHLKVRLVANKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  D+DKL++ + T+GSIT ++SV+LA++I+ + L +F++  +  +  +  I  
Sbjct: 181 ENTRVGQSSDFDKLTLDVWTNGSITPQESVSLAAKIMTEHLNIFVSLTDEAQNAEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMSIEELDLSVRSYNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 YKLEDLGLGL 310


>gi|313895218|ref|ZP_07828775.1| DNA-directed RNA polymerase, alpha subunit [Selenomonas sp. oral
           taxon 137 str. F0430]
 gi|320529823|ref|ZP_08030900.1| DNA-directed RNA polymerase, alpha subunit [Selenomonas artemidis
           F0399]
 gi|312976113|gb|EFR41571.1| DNA-directed RNA polymerase, alpha subunit [Selenomonas sp. oral
           taxon 137 str. F0430]
 gi|320137841|gb|EFW29746.1| DNA-directed RNA polymerase, alpha subunit [Selenomonas artemidis
           F0399]
          Length = 319

 Score =  336 bits (863), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 134/316 (42%), Positives = 197/316 (62%), Gaps = 6/316 (1%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             ++ KP  IE   +  E+      + EPL  G+  T GN+LRR+L+SSL GAA+T++QI
Sbjct: 1   MTDIEKP-KIEITEIS-EDGRYGRFVCEPLEPGYGTTFGNSLRRMLLSSLEGAAVTSIQI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGVLHE S+I GV +D+T I+LNIK + LKM G     + I   G   VTA DI+  +DI
Sbjct: 59  DGVLHEFSTIPGVRDDVTSIVLNIKQLCLKMQGSDPHTIRIDVAGEREVTAADIECGSDI 118

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E+LNP+  I  L+    +++E+TV +G GYVPA  ++  +D IG+I ID+++SP+ +V+Y
Sbjct: 119 EILNPELHIATLNATGKLKIEMTVERGRGYVPADKNKKPDDSIGVIPIDSIFSPVHRVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED- 244
           TVE  R G V DYD+L + + T+GSI  E++V+ A+ IL   L +F N +    E +E+ 
Sbjct: 179 TVEDTRVGNVTDYDRLILDVWTNGSIRPEEAVSKAAAILVMHLRLFQNMDGNVVEEEEEV 238

Query: 245 ---INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
                 +       L   +++L+LSVRS NCL+   I  + DL Q+TE DM+++ N GRK
Sbjct: 239 ANFPPEEVDDSAKVLEMTIDDLDLSVRSFNCLKRAGINSVADLTQKTEEDMMKVRNLGRK 298

Query: 302 SLVEIKGVLGTMGLFL 317
           SL E+K  L  +GL L
Sbjct: 299 SLDEVKKKLEELGLSL 314


>gi|220930993|ref|YP_002507901.1| DNA-directed RNA polymerase, alpha subunit [Halothermothrix orenii
           H 168]
 gi|219992303|gb|ACL68906.1| DNA-directed RNA polymerase, alpha subunit [Halothermothrix orenii
           H 168]
          Length = 314

 Score =  336 bits (863), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 136/312 (43%), Positives = 207/312 (66%), Gaps = 5/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE +   +  +N       PL RG+  TLGN+LRRVL+SSL GAAIT+V+I+G
Sbjct: 3   EIEKP-KIEKV---ECTDNYGKFEVAPLERGYGITLGNSLRRVLLSSLPGAAITSVKIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE S+I GV ED++++ILN+KG+ LK  G+  +++T+   G G VTAGD +T  DIEV
Sbjct: 59  VRHEFSTIPGVVEDVSEVILNLKGVVLKYKGEDIEKITLNCEGEGEVTAGDFKTSGDIEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSPIKKVSYT 186
           +NPDH I  L     +++E TV  G GYV A+ ++   +  IGLI ID+ +SPI++ ++ 
Sbjct: 119 INPDHHIATLAEGGKLQLEATVEFGRGYVTAEENKEHFDRVIGLIPIDSSFSPIERANFK 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+ R GQV DYD+L + + T+GSI+ ED+++LA++I+ + L +F+N  +   +V+  + 
Sbjct: 179 VENTRVGQVTDYDRLVLEVYTNGSISPEDAISLAAKIMVEHLELFLNLTDEVTDVEIMVE 238

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +    +  L   +EEL+LSVRS+NCL+   I  +G+LI +TE D++++ N G+KSL EI
Sbjct: 239 KEEEEKDKILDTTIEELDLSVRSSNCLKRAGINTVGELINKTEDDLMKVRNLGKKSLQEI 298

Query: 307 KGVLGTMGLFLG 318
           K  L  + L L 
Sbjct: 299 KEKLNELDLKLK 310


>gi|84394603|ref|ZP_00993305.1| DNA-directed RNA polymerase alpha subunit [Vibrio splendidus 12B01]
 gi|218710724|ref|YP_002418345.1| DNA-directed RNA polymerase subunit alpha [Vibrio splendidus LGP32]
 gi|254765263|sp|B7VLD2|RPOA_VIBSL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|84374777|gb|EAP91722.1| DNA-directed RNA polymerase alpha subunit [Vibrio splendidus 12B01]
 gi|218323743|emb|CAV20097.1| DNA-directed RNA polymerase, alpha subunit [Vibrio splendidus
           LGP32]
          Length = 330

 Score =  336 bits (863), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 148/335 (44%), Positives = 217/335 (64%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>gi|283796525|ref|ZP_06345678.1| DNA-directed RNA polymerase, alpha subunit [Clostridium sp. M62/1]
 gi|291075939|gb|EFE13303.1| DNA-directed RNA polymerase, alpha subunit [Clostridium sp. M62/1]
          Length = 319

 Score =  336 bits (862), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 134/314 (42%), Positives = 204/314 (64%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP  IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFEKP-KIEIAEIS-EDKRYGKFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+NIK + +K S +    K   I   G GVVTA DI   +DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNIKSLAIKNSSETNEPKTAYIEFEGEGVVTAADINADSDI 120

Query: 126 EVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E+LNPD VI  L   A     MELT++KG GY+ A  +++++ PIG+I +D++Y+P+++V
Sbjct: 121 EILNPDQVIATLSGGADSKFYMELTITKGRGYISADKNKSDDLPIGVIAVDSIYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + +VE+ R GQV DYDKL++ + T+G++  +++V+LA+++L + L +FI+  E  +  + 
Sbjct: 181 NMSVENTRVGQVTDYDKLTLDVFTNGTLAPDEAVSLAAKVLSEHLNLFIDLSENARTAEV 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  +       L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL
Sbjct: 241 MVEKEDNEKEKVLEMNIDELELSVRSYNCLKRAGINTVEELCNRTPEDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 301 EEVLAKLKELGLQL 314


>gi|56416980|ref|YP_154054.1| DNA-directed RNA polymerase subunit alpha [Anaplasma marginale str.
           St. Maries]
 gi|222475348|ref|YP_002563765.1| DNA-directed RNA polymerase alpha chain (rpoA) [Anaplasma marginale
           str. Florida]
 gi|254995156|ref|ZP_05277346.1| DNA-directed RNA polymerase subunit alpha [Anaplasma marginale str.
           Mississippi]
 gi|255003330|ref|ZP_05278294.1| DNA-directed RNA polymerase subunit alpha [Anaplasma marginale str.
           Puerto Rico]
 gi|255004454|ref|ZP_05279255.1| DNA-directed RNA polymerase subunit alpha [Anaplasma marginale str.
           Virginia]
 gi|81599123|sp|Q5PA81|RPOA_ANAMM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|56388212|gb|AAV86799.1| DNA-directed RNA polymerase alpha chain [Anaplasma marginale str.
           St. Maries]
 gi|222419486|gb|ACM49509.1| DNA-directed RNA polymerase alpha chain (rpoA) [Anaplasma marginale
           str. Florida]
          Length = 366

 Score =  336 bits (862), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 158/346 (45%), Positives = 233/346 (67%), Gaps = 10/346 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           I  +W +L +P++I+ +  G        +I EPL  GFA TLGNALRRV+MSSLRG A+ 
Sbjct: 21  ISDHWDKLTRPSSIKVVGDGDLS-RSAELIVEPLESGFALTLGNALRRVMMSSLRGFAVY 79

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            ++++GV HE++S+ GV ED+ D++LN+  + +K+     + + +  +GPG +TA  I  
Sbjct: 80  GIEVEGVSHELTSLSGVREDVADLVLNLSMLRVKLLTSESRVLRLVAKGPGEITAAAIGD 139

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP-------IGLITID 174
                VLN D  IC L  D    M++ V+ G GYVPA  +R  +          G I  +
Sbjct: 140 SEGCVVLNKDLHICTLGKDVDFSMKIYVNSGKGYVPASEYRAASRSGATSEVGPGFIATN 199

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           ALYSP+KKV++ +ES+R GQ  DYD+L ++++TDGSI+ +++VA+++R+LQDQL  FI  
Sbjct: 200 ALYSPVKKVAFRIESSRIGQFTDYDRLVISVETDGSISPDEAVAVSARVLQDQLQSFIGS 259

Query: 235 EEPKKEVKEDINVKSL--PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           EE + E ++ ++ +    P++  LL+KV+ELELSVRS NCL+ +NI Y+GDL+Q+TE+DM
Sbjct: 260 EEVEGESRKKVDKEEGALPYDHNLLRKVDELELSVRSHNCLKNDNITYIGDLVQKTESDM 319

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           LR  NFGRKSL EI  VL +M L LGM +P+WPPESIE L+K+Y +
Sbjct: 320 LRTPNFGRKSLNEINEVLASMNLHLGMKVPNWPPESIENLSKQYSE 365


>gi|319893174|ref|YP_004150049.1| DNA-directed RNA polymerase alpha subunit [Staphylococcus
           pseudintermedius HKU10-03]
 gi|317162870|gb|ADV06413.1| DNA-directed RNA polymerase alpha subunit [Staphylococcus
           pseudintermedius HKU10-03]
 gi|323463778|gb|ADX75931.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus
           pseudintermedius ED99]
          Length = 314

 Score =  336 bits (862), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 127/310 (40%), Positives = 198/310 (63%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I +  + +     + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+G
Sbjct: 3   EIEKPR-IETIEVSDDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I  V ED++ I++NIK + LK+  +  K + I  +  G VTA DI   +D+E+
Sbjct: 61  VLHEFSAIDHVVEDVSTIVMNIKKLALKIYSEEDKTLEIDIKEEGEVTAKDIMHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  +     +++ L  + G GY  A  + + + PIG+I +D+LYSP+++V+YTV
Sbjct: 121 LNPDLKIATVSKGGHLKLRLVANTGRGYALADQNNSSDLPIGVIPVDSLYSPVERVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  D+DKL++ + TDGSIT ++SV+LA++I+ + L +F+   +  +  +  I  
Sbjct: 181 ENTRVGQSSDFDKLTLDVWTDGSITPQESVSLAAKIMTEHLNIFVGLTDEAQNAEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMSIEELDLSVRSYNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 YKLEDLGLGL 310


>gi|314934272|ref|ZP_07841631.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus caprae
           C87]
 gi|313652202|gb|EFS15965.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus caprae
           C87]
          Length = 314

 Score =  336 bits (862), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 127/310 (40%), Positives = 201/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I + ++ +     + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+G
Sbjct: 3   EIEKPR-IETIEISEDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++  V ED++ II+NIK + LK+  +  K + I  +  G VTA DI   +D+E+
Sbjct: 61  VLHEFSAVDNVVEDVSTIIMNIKKLALKIYSEEDKTLEIDVKDEGEVTASDITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  +     +++ L  +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTV
Sbjct: 121 LNPELKIATVSKGGHLKVRLVANKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  D+DKL++ + T+GSIT ++SV+LA++I+ + L +F+   +  +  +  I  
Sbjct: 181 ENTRVGQSSDFDKLTLDVWTNGSITPQESVSLAAKIMTEHLNIFVGLTDEAQNAEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMSIEELDLSVRSYNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 YKLEDLGLGL 310


>gi|160941042|ref|ZP_02088380.1| hypothetical protein CLOBOL_05935 [Clostridium bolteae ATCC
           BAA-613]
 gi|158435991|gb|EDP13758.1| hypothetical protein CLOBOL_05935 [Clostridium bolteae ATCC
           BAA-613]
          Length = 320

 Score =  336 bits (862), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 133/314 (42%), Positives = 201/314 (64%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFEKPN-IEIAEIS-EDKRYGKFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+NIK + +K     D  K   I   G GV+TA DIQ   DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNIKSLAIKNNSDTDEPKVAYIEFEGEGVITAADIQADADI 120

Query: 126 EVLNPDHVICNLDV--DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E++NPD +I  L    D+   MELT++KG GY+ A  ++ ++ PIG+I +D++Y+P+++V
Sbjct: 121 EIMNPDQIIATLSGGTDSKFYMELTITKGRGYISADKNKNDDLPIGVIAVDSIYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +  V + R GQ  DYDKL++ I T+G++  +++V+LA+++L + L +FI+  E  K  + 
Sbjct: 181 NMAVANTRVGQQTDYDKLTLEIYTNGTLAPDEAVSLAAKVLSEHLNLFIDLSENAKTAEI 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  +       L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL
Sbjct: 241 MVEKEDNEKEKVLEMNIDELELSVRSYNCLKRAGINTVEELCNRTSEDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 301 EEVLAKLKELGLQL 314


>gi|145294735|ref|YP_001137556.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           glutamicum R]
 gi|158513584|sp|A4QBQ7|RPOA_CORGB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|140844655|dbj|BAF53654.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 338

 Score =  336 bits (862), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 133/313 (42%), Positives = 194/313 (61%), Gaps = 1/313 (0%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I     +  R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+IDGVLHE ++I G
Sbjct: 9   ITEEFVDNARSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVKIDGVLHEFTTISG 68

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED++DIILNIKG+ L    D    + + K GPGVVTAGDIQ    +E+ NPD  I  L
Sbjct: 69  VKEDVSDIILNIKGLVLSSDSDEPVVMQLVKEGPGVVTAGDIQPPAGVEIHNPDLHIATL 128

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           +  A + +EL V +G GYVPA    T  + IG I +D +YSP+ KVSY VE+ R  Q  D
Sbjct: 129 NETAKIEIELIVERGRGYVPATVTATGGE-IGRIPVDQIYSPVLKVSYKVEATRVEQRTD 187

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL + ++T  SIT  D++A A + L +  G+        + ++   + +   +  A  
Sbjct: 188 FDKLVIDVETKNSITARDALASAGKTLVELFGLARELNIAAEGIEIGPSPQETEYIAAYS 247

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +E+L+ SVRS NCL+ E+I  +G+L +R E+D+L + NFG+KS+ E+K  L  +GL L
Sbjct: 248 MPIEDLDFSVRSYNCLKREDIHTVGELAERAESDLLDIRNFGQKSINEVKIKLAGLGLTL 307

Query: 318 GMNLPDWPPESIE 330
                D+ P ++E
Sbjct: 308 KDAPEDFDPSTLE 320


>gi|300857809|ref|YP_003782792.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           pseudotuberculosis FRC41]
 gi|300685263|gb|ADK28185.1| DNA-directed RNA polymerase alpha subunit [Corynebacterium
           pseudotuberculosis FRC41]
 gi|302205544|gb|ADL09886.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           pseudotuberculosis C231]
 gi|302330099|gb|ADL20293.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           pseudotuberculosis 1002]
 gi|308275780|gb|ADO25679.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           pseudotuberculosis I19]
          Length = 338

 Score =  336 bits (862), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 127/312 (40%), Positives = 190/312 (60%), Gaps = 1/312 (0%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                +  R+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+V+IDGVLHE ++I GV
Sbjct: 10  TEEYVDSARSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVKIDGVLHEFTTINGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED++DIILNIKG+ L    D    + + K G GVV+AGDI+    +E+ NPD  I  L+
Sbjct: 70  KEDVSDIILNIKGLVLSSDSDEPVVMYLRKEGAGVVSAGDIEPPAGVEIHNPDLHIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +E+ V +G GYVPA  +   N+ IG I +D +YSP+ KVSY VE+ R  Q  D+
Sbjct: 130 EQGRLDIEMIVERGRGYVPASLYAGTNE-IGRIPVDQIYSPVLKVSYKVEATRVEQRTDF 188

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  SI   D++A A + L +  G+        + ++   + +   +  A   
Sbjct: 189 DKLIIDVETKNSIAPSDALASAGKTLVELFGLARELNTAAEGIEIGPSPQETEYIAAYSM 248

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L  SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L  +GLFL 
Sbjct: 249 PIEDLNFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKIKLAGLGLFLK 308

Query: 319 MNLPDWPPESIE 330
            +  D+ P  +E
Sbjct: 309 DSPEDFDPTQLE 320


>gi|73661998|ref|YP_300779.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus
           saprophyticus subsp. saprophyticus ATCC 15305]
 gi|90110871|sp|Q49ZE2|RPOA_STAS1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|72494513|dbj|BAE17834.1| DNA-directed RNA polymerase alpha chain [Staphylococcus
           saprophyticus subsp. saprophyticus ATCC 15305]
          Length = 314

 Score =  336 bits (861), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 129/310 (41%), Positives = 202/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I + ++ +     + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+G
Sbjct: 3   EIEKPR-IETIEISEDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I  V ED++ II+NIK + LK+  +  K + I  +  G VTA DI   +D+E+
Sbjct: 61  VLHEFSAIDNVVEDVSTIIMNIKKLALKIYSEEDKTLEIDVKDEGDVTASDITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  +     +++ L  +KG GY  A+ ++T + PIG+I +D+LYSP+++V+YTV
Sbjct: 121 LNPEIKIATVSKGGHLKIRLVANKGRGYALAEQNKTSDLPIGVIPVDSLYSPVERVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  D+DKL++ + T+GSIT ++SV+LA++IL + L +F+   +  +  +  I  
Sbjct: 181 ENTRVGQSSDFDKLTLDVWTNGSITPQESVSLAAKILTEHLNIFVGLTDEAQNAEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMSIEELDLSVRSYNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 YKLEDLGLGL 310


>gi|239623375|ref|ZP_04666406.1| DNA-directed RNA polymerase [Clostridiales bacterium 1_7_47_FAA]
 gi|239522341|gb|EEQ62207.1| DNA-directed RNA polymerase [Clostridiales bacterium 1_7_47FAA]
          Length = 320

 Score =  335 bits (860), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 133/314 (42%), Positives = 201/314 (64%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFEKPN-IEIAEIS-EDKRYGKFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+NIK + +K     D  K   I   G GV+TA DIQ   DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNIKSLAIKNNSDTDEPKVAYIEFEGEGVITAADIQADADI 120

Query: 126 EVLNPDHVICNLDV--DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E++NPD VI  L    D+   MELT++KG GY+ A  ++ ++ PIG+I +D++Y+P+++V
Sbjct: 121 EIMNPDQVIATLSGGTDSKFYMELTITKGRGYISADKNKNDDLPIGVIAVDSIYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +  V + R GQ  D+DKL++ I T+G++  +++V+LA+++L + L +FI+  E  K  + 
Sbjct: 181 NMAVTNTRVGQQTDFDKLTLEIYTNGTLAPDEAVSLAAKVLSEHLNLFIDLSENAKTAEI 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  +       L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL
Sbjct: 241 MVEKEDNEKEKVLEMNIDELELSVRSYNCLKRAGINTVEELCNRTSEDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 301 EEVLAKLKELGLQL 314


>gi|223042663|ref|ZP_03612712.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus capitis
           SK14]
 gi|222444326|gb|EEE50422.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus capitis
           SK14]
          Length = 314

 Score =  335 bits (860), Expect = 5e-90,   Method: Composition-based stats.
 Identities = 127/310 (40%), Positives = 201/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I + ++ +     + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+G
Sbjct: 3   EIEKPR-IETIEISEDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++  V ED++ II+NIK + LK+  +  K + I  +  G VTA DI   +D+E+
Sbjct: 61  VLHEFSAVDNVVEDVSTIIMNIKKLALKIYSEEDKTLEIDVKDEGEVTASDITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  +     +++ L  +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTV
Sbjct: 121 LNPELKIATVSKGGHLKVRLVANKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  D+DKL++ + T+GSIT ++SV+LA++I+ + L +F+   +  +  +  I  
Sbjct: 181 ENTRVGQSSDFDKLTLDVWTNGSITPKESVSLAAKIMTEHLNIFVGLTDEAQNAEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMSIEELDLSVRSYNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 YKLEDLGLGL 310


>gi|325261521|ref|ZP_08128259.1| DNA-directed RNA polymerase, alpha subunit [Clostridium sp. D5]
 gi|324032975|gb|EGB94252.1| DNA-directed RNA polymerase, alpha subunit [Clostridium sp. D5]
          Length = 319

 Score =  335 bits (860), Expect = 5e-90,   Method: Composition-based stats.
 Identities = 136/316 (43%), Positives = 204/316 (64%), Gaps = 6/316 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAAI++V+IDG
Sbjct: 3   DFNKPN-IEITEIS-EDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAISSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+N+K + +K     D  K   I   G GVVT  DIQ  +DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNLKSLAIKNTSESDEVKTAYIEFEGEGVVTGADIQADSDI 120

Query: 126 EVLNPDHVICNLD--VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E++NPD VI  L    D+ + MELT++KG GYV A  ++ E+ PIG+I ID++Y+P+++V
Sbjct: 121 EIMNPDQVIATLSGGKDSKLYMELTITKGRGYVSADKNKNEDLPIGVIPIDSIYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + TVE+ R GQ+ DYDKL++ + T G++  +++V+LA+++L + L +FI+  E  +  + 
Sbjct: 181 NLTVENTRVGQITDYDKLTLDVWTKGTLLPDEAVSLAAKVLSEHLKLFIDLSEVAQAAEV 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            I  +       L   ++ELELSVRS NCL+   I  + +L  +T  DM+++ N GRKSL
Sbjct: 241 MIEKEDDEKEKVLEMSIDELELSVRSYNCLKRAGINTVEELTNKTPEDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFLGM 319
            E+   L  + L L  
Sbjct: 301 EEVLAKLKELDLELNQ 316


>gi|307244752|ref|ZP_07526853.1| DNA-directed RNA polymerase, alpha subunit [Peptostreptococcus
           stomatis DSM 17678]
 gi|306491850|gb|EFM63902.1| DNA-directed RNA polymerase, alpha subunit [Peptostreptococcus
           stomatis DSM 17678]
          Length = 315

 Score =  335 bits (860), Expect = 5e-90,   Method: Composition-based stats.
 Identities = 125/313 (39%), Positives = 201/313 (64%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  ++ + L  E+      + EPL RGF  T+GNALRR+L+SSL G A+ AV+IDG
Sbjct: 3   EIEKP-KVDIVELS-EDYRYGKFVVEPLERGFGITIGNALRRILLSSLPGVAVYAVRIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T++IL++K ++  + G+  K + I   GP  VT  DI    ++E+
Sbjct: 61  VLHEFSTVPGVKEDVTEMILSLKELSATIDGEESKVLKIQAVGPCEVTGADIICPPEVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           ++ D  I  LD +A + ME+ V+KG GYV A+ ++ ++ PIG + +D++Y+PI+KVSY V
Sbjct: 121 VSKDLHIATLDENAKLNMEIHVNKGRGYVSAEENKNDSMPIGTLPVDSIYTPIEKVSYHV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  D+DKL++ + T+GSI  ++ ++LA+++L++ L +FI+  E    V+  +  
Sbjct: 181 ENTRVGQKTDFDKLTLEVLTNGSINPQEGMSLAAKVLEEHLKLFIDLSEHIGNVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N G+KSL E+ 
Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVEELSNKSEEDMMKVRNLGKKSLEEVI 300

Query: 308 GVLGTMGLFLGMN 320
             L  + L L  N
Sbjct: 301 QKLNELDLKLKPN 313


>gi|325288605|ref|YP_004264786.1| DNA-directed RNA polymerase subunit alpha [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324964006|gb|ADY54785.1| DNA-directed RNA polymerase subunit alpha [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 315

 Score =  335 bits (860), Expect = 5e-90,   Method: Composition-based stats.
 Identities = 134/310 (43%), Positives = 201/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KPN IE +    E+      + EPL RG+  TLGN+LRR+L+SSL G+A+T+V+I+G
Sbjct: 3   EIEKPN-IECVERS-EDNTYAKFVIEPLERGYGITLGNSLRRILLSSLPGSAVTSVKIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T++ILNIK + LK   D  + + +   G GVVTAGDI T  DIE+
Sbjct: 61  VLHEFSTIPGVLEDVTEVILNIKSLALKGYTDESRVLRLEYEGEGVVTAGDIITGPDIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  LD D  + ME+TV +  GYV A+ ++     IG+I ID++++PI KV+Y V
Sbjct: 121 LNPDLKIATLDKDGRLFMEMTVDRSRGYVSAEKNKKPEHAIGVIPIDSIFAPIYKVNYAV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R G + D+D+L++ + ++GSIT E++ +LA++IL + L +FI   +    V+  +  
Sbjct: 181 EDTRVGMMTDFDRLTLEVWSNGSITPEEATSLAAKILSEHLRLFIGLTDNLGNVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    +  L   +EEL+LSVRS NCL+   I  + +L Q+TE +M+++ N GRKSL E++
Sbjct: 241 EEEAKDKILEMTIEELDLSVRSYNCLKRAGINTVEELTQKTEEEMIKVRNLGRKSLEEVE 300

Query: 308 GVLGTMGLFL 317
             L  + L  
Sbjct: 301 NKLKELSLGF 310


>gi|19551799|ref|NP_599801.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           glutamicum ATCC 13032]
 gi|62389454|ref|YP_224856.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           glutamicum ATCC 13032]
 gi|23822074|sp|Q8NSV2|RPOA_CORGL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|21323330|dbj|BAB97958.1| DNA-directed RNA polymerase alpha subunit/40 kD subunit
           [Corynebacterium glutamicum ATCC 13032]
 gi|41324788|emb|CAF19270.1| DNA-DIRECTED RNA POLYMERASE ALPHA SUBUNIT [Corynebacterium
           glutamicum ATCC 13032]
          Length = 338

 Score =  335 bits (860), Expect = 5e-90,   Method: Composition-based stats.
 Identities = 133/313 (42%), Positives = 193/313 (61%), Gaps = 1/313 (0%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I        R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+IDGVLHE ++I G
Sbjct: 9   ITEEFVNNARSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVKIDGVLHEFTTISG 68

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED++DIILNIKG+ L    D    + + K GPGVVTAGDIQ    +E+ NPD  I  L
Sbjct: 69  VKEDVSDIILNIKGLVLSSDSDEPVVMQLVKEGPGVVTAGDIQPPAGVEIHNPDLHIATL 128

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           +  A + +EL V +G GYVPA    T  + IG I +D +YSP+ KVSY VE+ R  Q  D
Sbjct: 129 NETAKIEIELIVERGRGYVPATVTATGGE-IGRIPVDQIYSPVLKVSYKVEATRVEQRTD 187

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL + ++T  SIT  D++A A + L +  G+        + ++   + +   +  A  
Sbjct: 188 FDKLVIDVETKNSITARDALASAGKTLVELFGLARELNIAAEGIEIGPSPQETEYIAAYS 247

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +E+L+ SVRS NCL+ E+I  +G+L +R E+D+L + NFG+KS+ E+K  L  +GL L
Sbjct: 248 MPIEDLDFSVRSYNCLKREDIHTVGELAERAESDLLDIRNFGQKSINEVKIKLAGLGLTL 307

Query: 318 GMNLPDWPPESIE 330
                D+ P ++E
Sbjct: 308 KDAPEDFDPSTLE 320


>gi|82751814|ref|YP_417555.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           RF122]
 gi|119366734|sp|Q2YYM2|RPOA_STAAB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|82657345|emb|CAI81786.1| DNA-directed RNA polymerase alpha chain [Staphylococcus aureus
           RF122]
          Length = 314

 Score =  335 bits (859), Expect = 6e-90,   Method: Composition-based stats.
 Identities = 128/310 (41%), Positives = 201/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I + ++ +     + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+G
Sbjct: 3   EIEKPR-IETIEISEDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLSGAAVKYIEIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++  V ED++ II+NIK + LK+  +  K + I  R  G VTA DI   +D+E+
Sbjct: 61  VLHEFSAVDNVVEDVSTIIMNIKQLALKIYSEEDKTLEIDVRDEGEVTASDITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  +     +++ L  +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTV
Sbjct: 121 LNPELKIATVSKGGHLKIRLVANKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  D+DKL++ + T+GSIT ++SV+LA++I+ + L +F+   +  +  +  I  
Sbjct: 181 ENTRVGQSSDFDKLTLDVWTNGSITPQESVSLAAKIMTEHLNIFVGLTDEAQNAEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMSIEELDLSVRSYNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 YKLEDLGLGL 310


>gi|297618355|ref|YP_003703514.1| DNA-directed RNA polymerase, subunit alpha [Syntrophothermus
           lipocalidus DSM 12680]
 gi|297146192|gb|ADI02949.1| DNA-directed RNA polymerase, alpha subunit [Syntrophothermus
           lipocalidus DSM 12680]
          Length = 315

 Score =  335 bits (859), Expect = 6e-90,   Method: Composition-based stats.
 Identities = 137/311 (44%), Positives = 201/311 (64%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ +P  IE  V    +      + EPL RGF  TLGN+LRRVL+SSL GAAI+ ++IDG
Sbjct: 3   EIERPR-IE-CVERTPDNRYGKFVIEPLERGFGITLGNSLRRVLLSSLPGAAISTIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED T+IILN+K + L+   D  K V + +RGP  V AGDI    +IE+
Sbjct: 61  VLHEFSTIPGVVEDTTEIILNLKQVVLRYDYDQPKTVFVEQRGPKEVKAGDIIRDAEIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  L+ D  + ME+TV +G GYV A   + + + IGLI ID++++PI KV++TV
Sbjct: 121 LNPELHIATLNEDGRLAMEMTVERGRGYVSADQKKKDENVIGLIPIDSIFTPINKVNFTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+AR G+V DYD+L + + T+GSI+ E++V+L++ IL D L +F    +    V+  +  
Sbjct: 181 ENARVGRVTDYDRLMLEVWTNGSISPEEAVSLSAHILIDHLKLFTEINDSYSPVEILVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    +  L   +EELELSVR++N L+  NI  +GDL+++T  +M ++ N G+KSL EI+
Sbjct: 241 EEDQKDKILDMSIEELELSVRASNGLKRANINTVGDLVEKTREEMSKIRNLGQKSLDEIE 300

Query: 308 GVLGTMGLFLG 318
             L  +GL   
Sbjct: 301 RKLKELGLSFK 311


>gi|77165763|ref|YP_344288.1| DNA-directed RNA polymerase subunit alpha [Nitrosococcus oceani
           ATCC 19707]
 gi|254434921|ref|ZP_05048429.1| DNA-directed RNA polymerase, alpha subunit [Nitrosococcus oceani
           AFC27]
 gi|90110852|sp|Q3J8T8|RPOA_NITOC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|76884077|gb|ABA58758.1| DNA-directed RNA polymerase subunit alpha [Nitrosococcus oceani
           ATCC 19707]
 gi|207091254|gb|EDZ68525.1| DNA-directed RNA polymerase, alpha subunit [Nitrosococcus oceani
           AFC27]
          Length = 332

 Score =  335 bits (859), Expect = 6e-90,   Method: Composition-based stats.
 Identities = 147/333 (44%), Positives = 213/333 (63%), Gaps = 11/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q      +KP  ++   +    +  T +  EPL RGF HTLGNALRR+L+SS+ G AI 
Sbjct: 1   MQ--VSNFLKPRIVDVQRIN---DYATKVTLEPLERGFGHTLGNALRRILLSSMPGCAII 55

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             QIDGVLHE ++ +GV ED+T+I+LN+KG+ +K+ G     + +  +GP  VTAGDIQ 
Sbjct: 56  EAQIDGVLHEYTTKEGVQEDMTEILLNLKGVAVKLHGRDEVTLNLSSKGPVTVTAGDIQL 115

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYS 178
            +D+EV+NP+HVI +L     + + + V +G GY  A        +   IG + +DA +S
Sbjct: 116 EHDVEVINPEHVIAHLTKSGELNLTMKVVRGRGYQSASMRIPKEEDERSIGHLILDASFS 175

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI++V+Y V+SAR  Q  D DKL + I+T+G+I  +++V  A+ ILQDQL  F+  E   
Sbjct: 176 PIRRVTYEVDSARVEQRTDLDKLIIEIETNGTIAPDEAVRKAATILQDQLTAFVELEGKI 235

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +  KE    K+   +P LL+ +++LEL+VRS NCL+ ENI Y+GDLIQ+TE ++L+  N 
Sbjct: 236 ETAKE---KKAAEIDPVLLQPIDDLELTVRSANCLKAENIYYIGDLIQKTEVELLKTPNL 292

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL   GL LGM L +WPP  + E
Sbjct: 293 GKKSLTEIKDVLTLRGLSLGMRLENWPPAGLRE 325


>gi|320533222|ref|ZP_08033935.1| DNA-directed RNA polymerase, alpha subunit [Actinomyces sp. oral
           taxon 171 str. F0337]
 gi|320134562|gb|EFW26797.1| DNA-directed RNA polymerase, alpha subunit [Actinomyces sp. oral
           taxon 171 str. F0337]
          Length = 353

 Score =  335 bits (859), Expect = 6e-90,   Method: Composition-based stats.
 Identities = 128/314 (40%), Positives = 189/314 (60%), Gaps = 3/314 (0%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V+   E+ R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+IDGV H
Sbjct: 26  RPTLTEEVVV---EDRRSRFVLEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRIDGVPH 82

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E  +I GV ED+  IILNIK I L    D    + + K GP  VTAGDI     +E+ NP
Sbjct: 83  EFRTIPGVKEDVAQIILNIKEIVLSSENDEPVVMYLRKSGPSEVTAGDITPPAGVEIHNP 142

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           + VI  L+    + +ELTV +G GYV A  ++  N  I  I +D++YSP+KKVSY+VE+ 
Sbjct: 143 ELVIATLNEKGKLEIELTVERGRGYVSANQNKDPNAEISRIPVDSIYSPVKKVSYSVEAT 202

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  SIT  D++A A + L +  G+        + ++   +    
Sbjct: 203 RVEQRTDFDRLIVDVETKSSITPRDALASAGKTLVELFGLARELNVEAEGIEVGPSPIDE 262

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
            F   L   ++EL+L  RS+N L+ E I  +G+L+ R+EAD+L + NFG KS+ EIK  L
Sbjct: 263 AFQQDLALMIDELDLQARSSNALKREGIHTVGELVSRSEADLLDIRNFGAKSISEIKDKL 322

Query: 311 GTMGLFLGMNLPDW 324
             +GL L  +  D+
Sbjct: 323 AELGLSLKGSPVDY 336


>gi|315925227|ref|ZP_07921441.1| DNA-directed RNA polymerase subunit alpha [Pseudoramibacter
           alactolyticus ATCC 23263]
 gi|315621461|gb|EFV01428.1| DNA-directed RNA polymerase subunit alpha [Pseudoramibacter
           alactolyticus ATCC 23263]
          Length = 318

 Score =  335 bits (859), Expect = 7e-90,   Method: Composition-based stats.
 Identities = 135/313 (43%), Positives = 197/313 (62%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     +V   E+        EPL RG+  TLGN+LRR+++SSL G AIT V+IDG
Sbjct: 3   EFEKPFI--KLVDRSEDNTYGKFTVEPLERGYGTTLGNSLRRIMLSSLPGVAITTVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I G+ ED+ +I+LN+KG+   M  D  + V I  +G G VTAGDI    ++E+
Sbjct: 61  VLHEFSTIPGIKEDVIEILLNLKGLCAVMHTDELQTVRIEAKGAGEVTAGDIIAGPEVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +  DA + ME+ +  G GY P++ ++ +  PIG + +D+++SPI+KV + V
Sbjct: 121 LNPDMHICTMAGDAELTMEMALEVGRGYRPSEKNKYDGMPIGTLPMDSIFSPIRKVIFRV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R GQV D+DKL++ I TDG+ + E++++L+++++ D L +FI+  E    V+  +  
Sbjct: 181 EDTRVGQVTDFDKLTLEIWTDGTTSPEEALSLSAKVMNDHLRLFIDLTEEAGSVETIVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +           +EELELSVRS+NCLR  NI  +  L Q+TE DM+++ N GRKSL EIK
Sbjct: 241 EETERERIREMSIEELELSVRSSNCLRRANIDTVEKLTQKTEEDMMKVRNLGRKSLNEIK 300

Query: 308 GVLGTMGLFLGMN 320
             L  MGL L   
Sbjct: 301 HKLAEMGLSLSQE 313


>gi|197303839|ref|ZP_03168875.1| hypothetical protein RUMLAC_02578 [Ruminococcus lactaris ATCC
           29176]
 gi|197297132|gb|EDY31696.1| hypothetical protein RUMLAC_02578 [Ruminococcus lactaris ATCC
           29176]
          Length = 319

 Score =  335 bits (858), Expect = 8e-90,   Method: Composition-based stats.
 Identities = 133/314 (42%), Positives = 205/314 (65%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  +++     + EPL RG+  TLGN+LRR+++SSL GAAI++V+IDG
Sbjct: 3   DFNKPN-IEITDVS-DDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAISSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+N+K + +K     D  K   I   G GVVT  DIQ  +DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNLKSLAIKNTSESDEVKTAYIEYEGEGVVTGADIQADSDI 120

Query: 126 EVLNPDHVICNLD--VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E++NP+ VI  L    D+ + MELT++KG GYV +  ++TE+ PIG++ ID++Y+PI +V
Sbjct: 121 EIVNPEQVIATLSGGKDSKLYMELTITKGRGYVSSDKNKTEDMPIGVLPIDSIYTPIDRV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + TV++ R GQ+ DYDKL++ + T G++  +++V+LA+++L + L +FI+  E  ++ + 
Sbjct: 181 NLTVQNTRVGQITDYDKLTLDVWTKGTMAPDEAVSLAAKVLSEHLKLFIDLSEVAQQAEV 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            I  +       L   ++ELELSVRS NCL+   I  + +L  +T  DM+++ N GRKSL
Sbjct: 241 MIEKEDDEKEKVLEMSIDELELSVRSYNCLKRAGINTVEELTNKTPEDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFL 317
            E+   L  + L L
Sbjct: 301 EEVLAKLKELNLEL 314


>gi|169335657|ref|ZP_02862850.1| hypothetical protein ANASTE_02077 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258395|gb|EDS72361.1| hypothetical protein ANASTE_02077 [Anaerofustis stercorihominis DSM
           17244]
          Length = 315

 Score =  335 bits (858), Expect = 8e-90,   Method: Composition-based stats.
 Identities = 129/310 (41%), Positives = 200/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN IE   +   +      + EPL RG+  T+GN+LRR+++SSL GAA+T V+I+ 
Sbjct: 3   EFQKPN-IEIAEIS-ADRTYGKFVVEPLERGYGTTIGNSLRRIMLSSLPGAAVTNVKIEN 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE ++I GV ED+  IILN+K +++K+  D    V I   G G VTAGDI   +D+E+
Sbjct: 61  VLHEFATIDGVAEDVLQIILNLKDLSVKLHSDGPVDVHIHSEGEGEVTAGDIICDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPD  I +L  DAV+ M +T+  G GYVP++ ++ E+ PIG + +D++++P+KK ++ V
Sbjct: 121 VNPDLHIASLMADAVLDMTITIDGGTGYVPSEKNKKEDMPIGTLPVDSIFTPVKKANFAV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G V DYDKL++ + TDG+I+ E++V+LA++++ D L +FI+           +  
Sbjct: 181 ENTRVGNVTDYDKLTIEVWTDGTISPEEAVSLAAKVINDHLQLFIDMNANLPNASLMVER 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   ++ELELSVRS+NCL+  +I  + +LI R+E DM ++ N G+KSL EIK
Sbjct: 241 EENEKEKVLEMSIDELELSVRSSNCLKRTSINTVEELISRSEEDMSKVRNLGKKSLNEIK 300

Query: 308 GVLGTMGLFL 317
             L  +GL  
Sbjct: 301 KKLAEIGLSF 310


>gi|284033971|ref|YP_003383902.1| DNA-directed RNA polymerase subunit alpha [Kribbella flavida DSM
           17836]
 gi|283813264|gb|ADB35103.1| DNA-directed RNA polymerase, alpha subunit [Kribbella flavida DSM
           17836]
          Length = 341

 Score =  335 bits (858), Expect = 8e-90,   Method: Composition-based stats.
 Identities = 125/330 (37%), Positives = 192/330 (58%), Gaps = 5/330 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V     E+R+  + EPL  GF +TLGN++RR L+SS+ GAA+T++++DGVLH
Sbjct: 6   RPTLTEEVV----GEHRSRFVIEPLEPGFGYTLGNSIRRTLLSSIPGAAVTSIKVDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED T +ILN+K + +    D    + + K+GPG VTA DI     +EV NP
Sbjct: 62  EFSTVAGVKEDATQLILNLKDLVVSSEHDEPVTMYLRKQGPGDVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+    + MEL V +G GYV A  +++ +  IG + +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLKIATLNEKGRLEMELVVERGRGYVSAIQNKSADAEIGRMPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  S+   D+VA A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDRLVVDVETKPSMLPRDAVASAGKTLVELFGLARELNVEAEGIDIGPSPVDE 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   VE+L+L+VRS NCL+ E I  +G+LI R+E D+L + NFG KS+ E+K  L
Sbjct: 242 QMAADLALPVEDLQLTVRSYNCLKREGIHTVGELISRSEQDLLDIRNFGSKSIDEVKLKL 301

Query: 311 GTMGLFLGMNLPDWP-PESIEELAKKYEDK 339
             MGL L  + P +    + E      ED+
Sbjct: 302 AEMGLSLKDSPPGFDLRAAAEAYGDDAEDE 331


>gi|325068059|ref|ZP_08126732.1| DNA-directed RNA polymerase subunit alpha [Actinomyces oris K20]
 gi|326773990|ref|ZP_08233272.1| DNA-directed RNA polymerase, alpha subunit [Actinomyces viscosus
           C505]
 gi|329945757|ref|ZP_08293444.1| DNA-directed RNA polymerase, alpha subunit [Actinomyces sp. oral
           taxon 170 str. F0386]
 gi|326636129|gb|EGE37033.1| DNA-directed RNA polymerase, alpha subunit [Actinomyces viscosus
           C505]
 gi|328528205|gb|EGF55183.1| DNA-directed RNA polymerase, alpha subunit [Actinomyces sp. oral
           taxon 170 str. F0386]
          Length = 333

 Score =  335 bits (858), Expect = 9e-90,   Method: Composition-based stats.
 Identities = 129/314 (41%), Positives = 189/314 (60%), Gaps = 3/314 (0%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V+   E+ R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+IDGV H
Sbjct: 6   RPTLTEEVVV---EDRRSRFVLEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRIDGVPH 62

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E  +I GV ED+  IILNIK I L    D    + + K GP  VTAGDI     +E+ NP
Sbjct: 63  EFRTIPGVKEDVAQIILNIKEIVLSSENDEPVVMYLRKSGPSEVTAGDITPPAGVEIHNP 122

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D VI  L+    + +ELTV +G GYV A  ++  N  I  I +D++YSP+KKVSY+VE+ 
Sbjct: 123 DLVIATLNEKGKLEIELTVERGRGYVSANQNKDPNAEISRIPVDSIYSPVKKVSYSVEAT 182

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  SIT  D++A A + L +  G+        + ++   +    
Sbjct: 183 RVEQRTDFDRLIVDVETKSSITPRDALASAGKTLVELFGLARELNVEAEGIEVGPSPIDE 242

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
            F   L   ++EL+L  RS+N L+ E I  +G+L+ R+EAD+L + NFG KS+ EIK  L
Sbjct: 243 AFQQDLALMIDELDLQARSSNALKREGIHTVGELVSRSEADLLDIRNFGAKSISEIKDKL 302

Query: 311 GTMGLFLGMNLPDW 324
             +GL L  +  D+
Sbjct: 303 AELGLSLKGSPVDY 316


>gi|258513668|ref|YP_003189890.1| DNA-directed RNA polymerase subunit alpha [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257777373|gb|ACV61267.1| DNA-directed RNA polymerase, alpha subunit [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 315

 Score =  335 bits (858), Expect = 9e-90,   Method: Composition-based stats.
 Identities = 136/311 (43%), Positives = 203/311 (65%), Gaps = 3/311 (0%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           + KP  IE  V   E+      I EPL RG+  TLGN+LRR+L+SSL G A+T+V+IDGV
Sbjct: 3   IEKPR-IE-CVETNEDNTYGKFIVEPLERGYGITLGNSLRRILLSSLPGVAVTSVKIDGV 60

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S++ GV ED+TDIILN+K + LKM G+   K + I  +G G V AGDI   +D+E+
Sbjct: 61  LHEFSTVPGVREDVTDIILNLKSLRLKMHGEADEKILRIEAQGEGEVRAGDIVPDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  I  L  +  + M++T+++G GY  A+ ++     IG+I ID++++P+ KV+Y+V
Sbjct: 121 LNPDMYIATLAANGRLSMDITIARGRGYFSAERNKKGEPIIGVIPIDSIFTPVYKVNYSV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  DYDKLS+ I TDGSI  +++ +LA++I+ + L +FI   E  K+V+  +  
Sbjct: 181 ENTRVGQRTDYDKLSIEIWTDGSIHPDEAASLAAKIMSEHLQLFIGLTEETKDVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    +  +   +EEL+LSVRS NCL+   I  + +LIQR E DM+++ N G+KSL E+ 
Sbjct: 241 EEEKKDKIMEMTIEELDLSVRSYNCLKRACINTVEELIQRNEEDMMKVRNLGKKSLEEVI 300

Query: 308 GVLGTMGLFLG 318
             L  +G+ L 
Sbjct: 301 QKLNELGVSLK 311


>gi|227487074|ref|ZP_03917390.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           glucuronolyticum ATCC 51867]
 gi|227541762|ref|ZP_03971811.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           glucuronolyticum ATCC 51866]
 gi|227093148|gb|EEI28460.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           glucuronolyticum ATCC 51867]
 gi|227182468|gb|EEI63440.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           glucuronolyticum ATCC 51866]
          Length = 338

 Score =  334 bits (857), Expect = 9e-90,   Method: Composition-based stats.
 Identities = 123/314 (39%), Positives = 186/314 (59%), Gaps = 1/314 (0%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            +     +  R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I 
Sbjct: 8   VLTEEPIDSARSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTIT 67

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED++DI+LN+KGI L    D    + + K G G V AGDIQ    +E+ NPD  +  
Sbjct: 68  GVKEDVSDIVLNVKGIVLSSDSDEPVVMYLNKEGAGEVKAGDIQPPAGVEIHNPDLHLAT 127

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           L+ D  + MEL V +G GYVPA  +  +   IG I +D +YSP+ KVSY VE+ R  Q  
Sbjct: 128 LNDDGRLNMELVVERGRGYVPAAMNN-DVAEIGRIPVDQIYSPVLKVSYKVEATRVEQRT 186

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           D+DKL + ++T  SIT  D++A A + L +  G+        + ++   +        + 
Sbjct: 187 DFDKLVIDVETKNSITARDAMASAGKTLVELFGLARELNTAAEGIEIGASPLEGDHTASY 246

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E+L+ SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L  +GL 
Sbjct: 247 SMPIEDLDFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKVKLAGLGLT 306

Query: 317 LGMNLPDWPPESIE 330
           L     D+   ++E
Sbjct: 307 LKDAPEDFDVTTVE 320


>gi|225387210|ref|ZP_03756974.1| hypothetical protein CLOSTASPAR_00962 [Clostridium asparagiforme
           DSM 15981]
 gi|225046689|gb|EEG56935.1| hypothetical protein CLOSTASPAR_00962 [Clostridium asparagiforme
           DSM 15981]
          Length = 330

 Score =  334 bits (857), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 134/314 (42%), Positives = 201/314 (64%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 13  DFEKPN-IEIAEIS-EDKRYGKFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 70

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+NIK + +K     D  K   I   G GV+TA DIQ   DI
Sbjct: 71  VLHEFSSIAGVKEDVTEIIMNIKSLAIKNNSDTDEPKVAYIEFEGEGVITAADIQADADI 130

Query: 126 EVLNPDHVICNLDV--DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E++NPD +I  L    D+   MELT++KG GYV A  ++ ++ PIG+I +D++Y+P+++V
Sbjct: 131 EIMNPDQIIATLSGGTDSKFYMELTITKGRGYVSADKNKNDDLPIGVIAVDSIYTPVERV 190

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +  V + R GQ  DYDKL++ I T+G++  +++V+LA+++L + L +FI+  E  K  + 
Sbjct: 191 NMAVANTRVGQQTDYDKLTLEIYTNGTLAPDEAVSLAAKVLSEHLNLFIDLSENAKTAEI 250

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  +       L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL
Sbjct: 251 MVEKEDNEKEKVLEMNIDELELSVRSYNCLKRAGINTVEELCNRTSEDMMKVRNLGRKSL 310

Query: 304 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 311 EEVLAKLKELGLQL 324


>gi|302669991|ref|YP_003829951.1| DNA-directed RNA polymerase alpha subunit RpoA [Butyrivibrio
           proteoclasticus B316]
 gi|302394464|gb|ADL33369.1| DNA-directed RNA polymerase alpha subunit RpoA [Butyrivibrio
           proteoclasticus B316]
          Length = 319

 Score =  334 bits (857), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 135/316 (42%), Positives = 206/316 (65%), Gaps = 5/316 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  +PN IE   +  +++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+I+G
Sbjct: 3   DFERPN-IEVAEIS-DDKKYGKFVVEPLERGYGITLGNSLRRIMLSSLPGAAVSQVKIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+NIK +++K S D    K   I   G GVV A DIQ   DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNIKNLSIKNSSDTNEPKTAYIEYSGEGVVRASDIQVDQDI 120

Query: 126 EVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           E++NPD VI  L   DA + MELT++KG GYV +  ++  + PIG+I ID++Y+P+++V+
Sbjct: 121 EIMNPDQVIATLSGKDAKLYMELTITKGRGYVSSDKNKGGDLPIGVIAIDSIYTPVERVN 180

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
            TVE+ R GQV D+DKL++ + TDG++  +++V+LA+++L + L +FI+  E  K  +  
Sbjct: 181 VTVENTRVGQVTDFDKLTLDVHTDGTLAPDEAVSLAAKVLSEHLSLFIDLSENAKTAEVM 240

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +  +       L   ++ELELSVRS NCL+   I  + +L  +T  DM+++ N GRKSL 
Sbjct: 241 VEKEDDEKGKVLEMSIDELELSVRSFNCLKRAGINTVQELANKTSDDMMKVRNLGRKSLE 300

Query: 305 EIKGVLGTMGLFLGMN 320
           E+   L  +GL L  +
Sbjct: 301 EVLAKLDELGLSLRQD 316


>gi|239636207|ref|ZP_04677211.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus warneri
           L37603]
 gi|239598223|gb|EEQ80716.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus warneri
           L37603]
 gi|330685120|gb|EGG96784.1| DNA-directed RNA polymerase, alpha subunit [Staphylococcus
           epidermidis VCU121]
          Length = 314

 Score =  334 bits (857), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 126/310 (40%), Positives = 201/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I + ++ +     + EPL RG+  TLGN+LRR+L+SSL G+A+  ++I+G
Sbjct: 3   EIEKPR-IETIEISEDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGSAVKYIEIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++  V ED++ II+NIK + LK+  +  K + I  +  G VTA DI   +D+E+
Sbjct: 61  VLHEFSAVDNVVEDVSTIIMNIKKLALKIYSEEDKTLEIDVKDEGEVTASDITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  +     +++ L  +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTV
Sbjct: 121 LNPELKIATVSKGGHLKVRLVANKGRGYALAETNNTSDLPIGVIPVDSLYSPVERVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  D+DKL++ + T+GSIT ++SV+LA++I+ + L +F+   +  +  +  I  
Sbjct: 181 ENTRVGQSSDFDKLTLDVWTNGSITPQESVSLAAKIMTEHLNIFVGLTDEAQNAEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMSIEELDLSVRSYNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 YKLEDLGLGL 310


>gi|28493495|ref|NP_787656.1| DNA-directed RNA polymerase subunit alpha [Tropheryma whipplei str.
           Twist]
 gi|28572392|ref|NP_789172.1| DNA-directed RNA polymerase subunit alpha [Tropheryma whipplei
           TW08/27]
 gi|41688659|sp|Q820D4|RPOA_TROWT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|41688662|sp|Q820D8|RPOA_TROW8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|28410523|emb|CAD66909.1| DNA-directed RNA polymerase alpha chain [Tropheryma whipplei
           TW08/27]
 gi|28476537|gb|AAO44625.1| DNA-directed RNA polymerase alpha chain [Tropheryma whipplei str.
           Twist]
          Length = 327

 Score =  334 bits (857), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 121/321 (37%), Positives = 189/321 (58%), Gaps = 5/321 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P  IE  V     + R+  I EPL  GF +TLGN+LRR L+SS+ GAA+T++ I GV+H
Sbjct: 6   RPTLIEKKV----SDIRSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSINIQGVMH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S+I GV ED+T+I+LN+K + +    D    V ++K G G V A DI+    IE+ N 
Sbjct: 62  EFSTIPGVKEDVTEIVLNVKRLVISSEIDEPFTVRLYKTGEGEVLAKDIEVPTGIEIGNG 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP-IGLITIDALYSPIKKVSYTVES 189
           D VI  L  DAV  M+LT+ +G GYV A+ +R +     G I +D++YSP+ KV+Y VE+
Sbjct: 122 DLVIATLAKDAVFDMQLTIERGRGYVSAEQNRNDGMSLAGHIPVDSIYSPVHKVTYRVEA 181

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R G+  D+D+L + ++T  SI   D+VA A + L +  G+        + V+  ++   
Sbjct: 182 TRAGERTDFDRLIIDVETKPSILPRDAVASAGKTLCELFGLARELNSQAEGVEFGVDSMI 241

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              +  L   +E+L LSVRS NCL+ E + Y+ +L+  +E ++L + NFG+KS  E++  
Sbjct: 242 PESDEDLRIPIEDLGLSVRSYNCLKREGVNYVSELLGFSEQELLDIRNFGQKSADEVQEK 301

Query: 310 LGTMGLFLGMNLPDWPPESIE 330
           L  +G  L  ++P +     +
Sbjct: 302 LAELGHSLKGSVPGFDGSYFD 322


>gi|227505247|ref|ZP_03935296.1| DNA-directed RNA polymerase [Corynebacterium striatum ATCC 6940]
 gi|227198146|gb|EEI78194.1| DNA-directed RNA polymerase [Corynebacterium striatum ATCC 6940]
          Length = 336

 Score =  334 bits (857), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 127/307 (41%), Positives = 190/307 (61%), Gaps = 3/307 (0%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           + +R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV ED++
Sbjct: 15  DSSRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTINGVKEDVS 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           +IILN+KG+ L    D    + + K GPGVVTAGDIQ    +E+ NPD  I +L+  A +
Sbjct: 75  EIILNVKGLVLSSDSDEPVVMYLSKEGPGVVTAGDIQPPAGVEIHNPDLHIASLNDTAKL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            MEL V +G GYVPA     E   IG I +D +YSP+ +VSY VE+ R  Q  D+DKL +
Sbjct: 135 DMELVVERGRGYVPAAPTSGE---IGRIPVDQIYSPVLQVSYKVEATRVEQRTDFDKLII 191

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T  SI+  D++A A   L +  G+        + ++   + +   +  A    +E+L
Sbjct: 192 DVETKNSISARDALASAGGTLVELFGLARELNNAAEGIEIGPSPQETEYIAAYSMPIEDL 251

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
             SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L  +GL L     D
Sbjct: 252 NFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKIKLANLGLALKDTPED 311

Query: 324 WPPESIE 330
           + P  +E
Sbjct: 312 FDPTQLE 318


>gi|329314907|gb|AEB89320.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus T0131]
          Length = 314

 Score =  334 bits (857), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 127/310 (40%), Positives = 200/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I + ++ +     + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+G
Sbjct: 3   EIEKPR-IETIEISEDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++  V ED++ II+NIK + LK+  +  K + I  R  G VTA DI   +D+E+
Sbjct: 61  VLHEFSAVDNVVEDVSTIIMNIKQLALKIYSEEDKTLEIDVRDEGEVTASDITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  +     +++ L  +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTV
Sbjct: 121 LNPELKIATVSKGGHLKIRLVANKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+   GQ  D+DKL++ + T+GSIT ++SV+LA++I+ + L +F+   +  +  +  I  
Sbjct: 181 ENTCVGQSSDFDKLTLDVWTNGSITPQESVSLAAKIMTEHLNIFVGLTDEAQNAEIMIEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+++ N GRKSL E+K
Sbjct: 241 EEDQKEKVLEMSIEELDLSVRSYNCLKRAGINSVQELADKSEADMMKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 YKLEDLGLGL 310


>gi|259500918|ref|ZP_05743820.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus iners DSM
           13335]
 gi|302190629|ref|ZP_07266883.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus iners
           AB-1]
 gi|309803637|ref|ZP_07697727.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LactinV 11V1-d]
 gi|309804964|ref|ZP_07699022.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LactinV 09V1-c]
 gi|309806715|ref|ZP_07700710.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LactinV 03V1-b]
 gi|309808436|ref|ZP_07702335.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LactinV 01V1-a]
 gi|309809144|ref|ZP_07703017.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           SPIN 2503V10-D]
 gi|312871172|ref|ZP_07731270.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LEAF 3008A-a]
 gi|312872807|ref|ZP_07732872.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LEAF 2062A-h1]
 gi|312874040|ref|ZP_07734075.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LEAF 2052A-d]
 gi|312874841|ref|ZP_07734860.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LEAF 2053A-b]
 gi|315654000|ref|ZP_07906916.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus iners ATCC
           55195]
 gi|325913233|ref|ZP_08175602.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           UPII 60-B]
 gi|329920643|ref|ZP_08277330.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           SPIN 1401G]
 gi|259167612|gb|EEW52107.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus iners DSM
           13335]
 gi|308164235|gb|EFO66492.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LactinV 11V1-d]
 gi|308165724|gb|EFO67949.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LactinV 09V1-c]
 gi|308166895|gb|EFO69079.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LactinV 03V1-b]
 gi|308168264|gb|EFO70383.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LactinV 01V1-a]
 gi|308170589|gb|EFO72609.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           SPIN 2503V10-D]
 gi|311089586|gb|EFQ48011.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LEAF 2053A-b]
 gi|311090380|gb|EFQ48789.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LEAF 2052A-d]
 gi|311091849|gb|EFQ50228.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LEAF 2062A-h1]
 gi|311093186|gb|EFQ51532.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           LEAF 3008A-a]
 gi|315488696|gb|EFU78342.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus iners ATCC
           55195]
 gi|325477497|gb|EGC80640.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           UPII 60-B]
 gi|328935901|gb|EGG32361.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           SPIN 1401G]
          Length = 312

 Score =  334 bits (856), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 136/311 (43%), Positives = 200/311 (64%), Gaps = 4/311 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +EE+    + EPL RGF  TLGN+LRRVL++S+ G A++ + IDG
Sbjct: 3   EFEKPN----ITVIDQEESYGKFVVEPLERGFGTTLGNSLRRVLLTSISGTALSYIMIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILN+K + LK+  D  K V I   GP VVTA D++   D+E+
Sbjct: 59  VLHEFSTIPGVREDVTKIILNLKKLELKLLVDEEKMVEIDVEGPAVVTAADLKVDADVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + M + +  G GY+PA  +++++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMSIAIKNGRGYIPASENKSDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+AR G+  DYDKL++ + TDGSIT  D+++ A++IL++   +F++ +   +     I  
Sbjct: 179 ENARVGKRDDYDKLTLELWTDGSITPNDALSFAAKILEEHFKVFMSADMSDQFANVMIEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+R+ N GRKSL E+K
Sbjct: 239 EDKSNEKKLEMTIEELDLSVRSYNCLKRAGINTVQELNNKSEADMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLG 318
             L  +GL   
Sbjct: 299 NKLTELGLSFS 309


>gi|227832273|ref|YP_002833980.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           aurimucosum ATCC 700975]
 gi|262183871|ref|ZP_06043292.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           aurimucosum ATCC 700975]
 gi|227453289|gb|ACP32042.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           aurimucosum ATCC 700975]
          Length = 336

 Score =  334 bits (856), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 126/307 (41%), Positives = 188/307 (61%), Gaps = 3/307 (0%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           + +R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV ED++
Sbjct: 15  DSSRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTINGVKEDVS 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           +IILN+KG+ L    D    + + K GPG VTAGDIQ    +E+ N D  I +L+  A +
Sbjct: 75  EIILNVKGLVLSSDSDEPVVMYLSKEGPGEVTAGDIQPPAGVEIHNSDLHIASLNESAKL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            MEL V +G GYVPA     E   IG I +D +YSP+ KVSY VE+ R  Q  D+DKL +
Sbjct: 135 EMELVVERGRGYVPAAATSGE---IGRIPVDQIYSPVLKVSYKVEATRVEQRTDFDKLII 191

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T  SI+  D++A A   L +  G+        + ++   + +   +  A    +E+L
Sbjct: 192 DVETKNSISARDALASAGGTLVELFGLARELNTAAEGIEIGPSPQETEYIAAYSMPIEDL 251

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
             SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L  +GL L     D
Sbjct: 252 NFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKIKLANLGLALKDTPED 311

Query: 324 WPPESIE 330
           + P  +E
Sbjct: 312 FDPTQLE 318


>gi|325912373|ref|ZP_08174769.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           UPII 143-D]
 gi|325475844|gb|EGC79014.1| DNA-directed RNA polymerase, alpha subunit [Lactobacillus iners
           UPII 143-D]
          Length = 312

 Score =  334 bits (856), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 136/311 (43%), Positives = 200/311 (64%), Gaps = 4/311 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I +  +EE+    + EPL RGF  TLGN+LRRVL++S+ G A++ + IDG
Sbjct: 3   EFEKPN----ITVIDQEESYGKFVVEPLERGFGTTLGNSLRRVLLTSISGTALSYIMIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T IILN+K + LK+  D  K V I   GP VVTA D++   D+E+
Sbjct: 59  VLHEFSTIPGVREDVTKIILNLKKLELKLLVDEEKMVEIDVEGPAVVTAADLKVDADVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNPD  IC +     + M + +  G GY+PA  +++++ PIG+I +D+L+SPIKKV+Y V
Sbjct: 119 LNPDQYICTIAEGGHLHMSIAIKSGRGYIPASENKSDDMPIGVIPVDSLFSPIKKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+AR G+  DYDKL++ + TDGSIT  D+++ A++IL++   +F++ +   +     I  
Sbjct: 179 ENARVGKRDDYDKLTLELWTDGSITPNDALSFAAKILEEHFKVFMSADMSDQFANVMIEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++EADM+R+ N GRKSL E+K
Sbjct: 239 EDKSNEKKLEMTIEELDLSVRSYNCLKRAGINTVQELNNKSEADMMRVRNLGRKSLEEVK 298

Query: 308 GVLGTMGLFLG 318
             L  +GL   
Sbjct: 299 NKLTELGLSFS 309


>gi|237786334|ref|YP_002907039.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           kroppenstedtii DSM 44385]
 gi|237759246|gb|ACR18496.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           kroppenstedtii DSM 44385]
          Length = 337

 Score =  334 bits (856), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 127/312 (40%), Positives = 183/312 (58%), Gaps = 3/312 (0%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                + +R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I+GVLHE +++ GV
Sbjct: 10  TEEYIDSSRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRIEGVLHEFTTVPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED++DIILNIKG+ L    D    + I K GPG VTAGDI     +E+ NPD  I  L+
Sbjct: 70  TEDVSDIILNIKGLVLSSDSDDPVTMYIRKEGPGEVTAGDIMPPAGVEIHNPDMHIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL V +G GYVPA     E   IG I +D +YSP+ KVSY VE+ R  Q  D+
Sbjct: 130 EQGKLDIELVVERGRGYVPAAQATGE---IGRIPVDQIYSPVLKVSYKVEATRVEQRTDF 186

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           D+L + ++T  SIT  D++A A   L +  G+        + ++   + +      A   
Sbjct: 187 DRLVIDVETKNSITARDAMASAGGTLVELFGLARELNTAAEGIEIGPSPQESEHIQAYGM 246

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L  SVRS NCL+ E I  +G+L  RTE+D+L + NFG+KS+ E+K  L  +GL L 
Sbjct: 247 PIEDLNFSVRSYNCLKREEIHTVGELASRTESDLLDIRNFGQKSINEVKVKLAGLGLALK 306

Query: 319 MNLPDWPPESIE 330
                +    IE
Sbjct: 307 DAPEGYDVSEIE 318


>gi|154505141|ref|ZP_02041879.1| hypothetical protein RUMGNA_02654 [Ruminococcus gnavus ATCC 29149]
 gi|153794620|gb|EDN77040.1| hypothetical protein RUMGNA_02654 [Ruminococcus gnavus ATCC 29149]
          Length = 319

 Score =  334 bits (856), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 135/316 (42%), Positives = 206/316 (65%), Gaps = 6/316 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAAI++V+IDG
Sbjct: 3   DFNKPN-IEITEIS-EDKKYGKFVVEPLERGYGITLGNSLRRIMLSSLPGAAISSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+N+K + +K     D  K   I   G G+VT  DIQT +DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNLKSLAIKNTSESDEVKTAYIEFEGEGIVTGADIQTDSDI 120

Query: 126 EVLNPDHVICNLD--VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E++NP+ VI  L    D+ + MELT++KG GYV A  +++E+ PIG+I ID++Y+P+++V
Sbjct: 121 EIMNPEQVIATLSGGKDSKLYMELTITKGRGYVSADKNKSEDMPIGVIPIDSIYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + TV++ R GQV DYDKL++ + T G++  +++V+LA+++L + L +FI+  E  +  + 
Sbjct: 181 NMTVQNTRVGQVTDYDKLTLDVWTKGTLLPDEAVSLAAKVLSEHLKLFIDLSEVAQSAEV 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            I  +       L   ++ELELSVRS NCL+   I  + +L  +T  DM+++ N GRKSL
Sbjct: 241 MIEKEDDEKEKVLEMSIDELELSVRSYNCLKRAGINTVEELTNKTPEDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFLGM 319
            E+   L  + L L  
Sbjct: 301 EEVLAKLKELNLELNQ 316


>gi|1524340|emb|CAA63080.1| RNA polymerase alpha subunit [Streptomyces coelicolor A3(2)]
          Length = 339

 Score =  334 bits (856), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 127/316 (40%), Positives = 192/316 (60%), Gaps = 5/316 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLH
Sbjct: 6   RPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV NP
Sbjct: 62  EFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLSKQGPGLVTAADIAPPAGVEVHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ 
Sbjct: 122 DLVLATLNGKGKLEMELTVERGRGYVSAVQNKEVGQEIGRIPVDSIYSPVLKVTYKVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+DKL + ++T  ++    ++A A + L +  G+        + +    +    
Sbjct: 182 RVEQRTDFDKLIVDVETKQAMRPR-AMASAGKTLVELFGLARELNIDAEGIDMGPSPTDA 240

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L
Sbjct: 241 ALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAKL 300

Query: 311 GTMGLFLGMNLPDWPP 326
             MGL L  + P + P
Sbjct: 301 AGMGLALKDSPPGFDP 316


>gi|289423648|ref|ZP_06425447.1| DNA-directed RNA polymerase, alpha subunit [Peptostreptococcus
           anaerobius 653-L]
 gi|289155898|gb|EFD04564.1| DNA-directed RNA polymerase, alpha subunit [Peptostreptococcus
           anaerobius 653-L]
          Length = 315

 Score =  334 bits (856), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 120/311 (38%), Positives = 196/311 (63%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  ++ + L  E+      + EPL RGF  T+GNALRR+L+SSL G A+ A++IDG
Sbjct: 3   EIEKP-KVDIVELS-EDYRFGKFVVEPLERGFGITVGNALRRILLSSLPGVAVYAIRIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+T+IIL++K ++  +  +  K + I   GP  V   DI    ++ +
Sbjct: 61  VLHEFSTVPGVKEDVTEIILSLKELSATIDDEEPKVLRIQAIGPCEVKGSDIICPPEVNI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           ++ D  I  LD  A + ME+ V+KG GY+ A+ ++ E+ PIG++ +D++Y+P++KVSY V
Sbjct: 121 VSKDLHIATLDEGAKLNMEIYVNKGRGYISAEENKKESMPIGVLPVDSIYTPVEKVSYHV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  D+DKL++ + T+GSI  ++ ++LA+++L + L +FI+  E    V+  +  
Sbjct: 181 ENTRVGQRSDFDKLTLEVLTNGSINPQEGISLAAKVLDEHLKLFIDLTEHVGNVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N G+KSL E+ 
Sbjct: 241 EEDKKEKVLEMTIEELDLSVRSYNCLKRAGINTVEELSNKSEDDMMKVRNLGKKSLEEVI 300

Query: 308 GVLGTMGLFLG 318
             L  + L L 
Sbjct: 301 HKLEELELRLK 311


>gi|300114711|ref|YP_003761286.1| DNA-directed RNA polymerase subunit alpha [Nitrosococcus watsonii
           C-113]
 gi|299540648|gb|ADJ28965.1| DNA-directed RNA polymerase, alpha subunit [Nitrosococcus watsonii
           C-113]
          Length = 332

 Score =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 147/333 (44%), Positives = 214/333 (64%), Gaps = 11/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q      +KP  ++   +    +  T +  EPL RGF HTLGNALRR+L+SS+ G AI 
Sbjct: 1   MQ--VSNFLKPRIVDVQRIN---DYATKVTLEPLERGFGHTLGNALRRILLSSMPGCAII 55

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             QIDGVLHE ++ +GV ED+T+I+LN+KG+ +K+ G     +++  +GP  VTAGDIQ 
Sbjct: 56  EAQIDGVLHEYTTKEGVQEDMTEILLNLKGVAIKLHGRDEVTLSLSSKGPVTVTAGDIQL 115

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
            +D+EV+NP HVI +L     + + + V +G GY PA        +   IG + +DA +S
Sbjct: 116 EHDVEVINPKHVIAHLTKSGELNLTMKVVRGRGYQPASVRIPKEEDERSIGHLILDASFS 175

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI++V+Y V+SAR  Q  D DKL + I+T+G+I  +++V  A+ ILQDQL  F+  E   
Sbjct: 176 PIRRVTYEVDSARVEQRTDLDKLIIEIETNGTIAPDEAVRKAATILQDQLTAFVELEGRI 235

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +  KE    K+   +P LL+ +++LEL+VRS NCL+ ENI Y+GDLIQ+TE ++L+  N 
Sbjct: 236 ETAKE---KKAAEIDPVLLQPIDDLELTVRSANCLKAENIYYIGDLIQKTEVELLKTPNL 292

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL   GL LG+ L +WPP  + E
Sbjct: 293 GKKSLTEIKDVLTLRGLSLGIRLENWPPAGLRE 325


>gi|38233158|ref|NP_938925.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           diphtheriae NCTC 13129]
 gi|61215957|sp|Q6NJ63|RPOA_CORDI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|38199417|emb|CAE49060.1| DNA-directed RNA polymerase alpha chain [Corynebacterium
           diphtheriae]
          Length = 338

 Score =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 120/312 (38%), Positives = 186/312 (59%), Gaps = 1/312 (0%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                +  R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV
Sbjct: 10  TEEYVDSARSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTINGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED++DIILNIKG+ L    D    + + K G GV+TAGDI+    +E+ NPD  +  L+
Sbjct: 70  KEDVSDIILNIKGLVLSSDSDEPVVMYLRKEGAGVITAGDIEPPAGVEIHNPDLHLATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +E+ V +G GYVPA  +      IG I +D +YSP+ KVSY VE+ R  Q  D+
Sbjct: 130 EQGRLDIEMIVERGRGYVPATLYSGP-AEIGRIPVDQIYSPVLKVSYKVEATRVEQRTDF 188

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  S+   D++A A + L +  G+        + ++   + +   +  A   
Sbjct: 189 DKLIIDVETKNSMAPRDALASAGKTLVELFGLARELNTAAEGIEIGPSPQETEYIAAYGM 248

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L  SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L  +GL L 
Sbjct: 249 PIEDLNFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKIKLAGLGLTLK 308

Query: 319 MNLPDWPPESIE 330
               D+ P  ++
Sbjct: 309 DAPEDFDPTQLD 320


>gi|229815743|ref|ZP_04446068.1| hypothetical protein COLINT_02792 [Collinsella intestinalis DSM
           13280]
 gi|229808659|gb|EEP44436.1| hypothetical protein COLINT_02792 [Collinsella intestinalis DSM
           13280]
          Length = 313

 Score =  333 bits (854), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 121/316 (38%), Positives = 189/316 (59%), Gaps = 7/316 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E I+P     + + +  +    +  EPL RG+  TLGN+LRRVL+SSL GAA+ A+QI
Sbjct: 1   MSEFIRPQ----VHVEEISDTAARVSVEPLERGYGDTLGNSLRRVLLSSLEGAAVEAIQI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLK-MSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           DG  HE ++I  + ED+TDI+LN+KG+  + +        TI   GP  VT  D    ++
Sbjct: 57  DGAQHEFTTIPNMVEDVTDIVLNVKGLVFRTLGTTDEGTATISVDGPCEVTGADFFIPSE 116

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            E++NPD  I  L     + M + +  G GYV  + ++ +NDPIG+I +D+L+SP+K+ +
Sbjct: 117 FELVNPDQHIATLTEGGHLTMSMRIGYGRGYVSYEQNKRDNDPIGIIHVDSLFSPVKRCA 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF-EEPKKEVKE 243
             VE+ R GQ  DYD+L + I+T+G+I+  D+V  A+ I+   +  F+   +EP+ E + 
Sbjct: 177 KLVEACRVGQHTDYDRLVLEIETNGAISPRDAVVSAANIINQHMAAFMTLADEPEAEEEV 236

Query: 244 DINVKSLPFNPALLKK-VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
            I    +  + A L K +E+L+LSVRS NCL+   I  +  L++ +E D+L + NFG KS
Sbjct: 237 SIFAPEVTSDNAELDKQIEDLDLSVRSYNCLKRAGIHSVRQLVEFSENDLLNIRNFGVKS 296

Query: 303 LVEIKGVLGTMGLFLG 318
           + E+K  L +MGL L 
Sbjct: 297 IEEVKDKLESMGLSLK 312


>gi|255283705|ref|ZP_05348260.1| DNA-directed RNA polymerase, alpha subunit [Bryantella
           formatexigens DSM 14469]
 gi|255265770|gb|EET58975.1| DNA-directed RNA polymerase, alpha subunit [Bryantella
           formatexigens DSM 14469]
          Length = 375

 Score =  333 bits (854), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 129/314 (41%), Positives = 199/314 (63%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP  IE   +  E+      + EPL RG+  TLGN+LRR+++SSL GAA++ V+I+G
Sbjct: 59  DFNKPR-IEIAEIS-EDRKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIEG 116

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+++II+N+K + +K     +  K   I   G GVVTA DIQ   DI
Sbjct: 117 VLHEFSSIPGVKEDVSEIIMNLKSLAIKNTSKTNEPKVAYIEYDGEGVVTAADIQVDQDI 176

Query: 126 EVLNPDHVICNLDV--DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E+LN D +I  L    D+ + ME+T++KG GY+ A   +T + PIG+I +D++Y+P+++V
Sbjct: 177 EILNKDQIIATLSGGPDSKLYMEITITKGRGYISADEGKTPDMPIGVIAVDSIYTPVERV 236

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + TVE+ R  Q  D+DKL++ + T+G++  +++V+LA+++L + L +FI+  E  K  + 
Sbjct: 237 NMTVENTRVAQATDFDKLTLDVYTNGTLAPDEAVSLAAKVLSEHLSLFIDLSESAKTAEI 296

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            I  +       L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL
Sbjct: 297 MIEKEDNEKEKVLEMNIDELELSVRSYNCLKRAGINTVEELCNRTPEDMMKVRNLGRKSL 356

Query: 304 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 357 EEVLAKLKELGLQL 370


>gi|253580648|ref|ZP_04857912.1| DNA-directed RNA polymerase [Ruminococcus sp. 5_1_39B_FAA]
 gi|251848019|gb|EES75985.1| DNA-directed RNA polymerase [Ruminococcus sp. 5_1_39BFAA]
          Length = 319

 Score =  333 bits (854), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 135/314 (42%), Positives = 203/314 (64%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP  IE   L  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFNKP-KIEITELS-EDKKFGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED++DII+N+K + +K     +  K   I   G GVVTA DIQ   DI
Sbjct: 61  VLHEFSSIPGVKEDVSDIIMNLKSLAIKNHSTDNEPKTAYIECEGKGVVTAADIQADQDI 120

Query: 126 EVLNPDHVICNLD--VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E++NPD VI  L+   D  + MELT++KG GY+ A   ++++ PIG++ +DA+Y+P+ +V
Sbjct: 121 EIMNPDQVIATLNGGKDCRLAMELTITKGRGYISADKGKSDDMPIGVLAVDAIYTPVDRV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + TVE+ R GQV DYDKL++ + T+G++  +++V+LA+++L + L +FI+  E  K  + 
Sbjct: 181 NMTVENTRVGQVTDYDKLTLDVYTNGTLDPDEAVSLAAKVLSEHLSLFIDLSENAKTAEV 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            I  +       L   ++ELELSVRS NCL+   I  + +L  +T  DM+++ N GRKSL
Sbjct: 241 MIEKEDNEKEKVLEMSIDELELSVRSYNCLKRAGINTVEELCNKTSDDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 301 EEVLAKLKELGLQL 314


>gi|325663034|ref|ZP_08151484.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae
           bacterium 4_1_37FAA]
 gi|331086641|ref|ZP_08335718.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae
           bacterium 9_1_43BFAA]
 gi|325470488|gb|EGC73718.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae
           bacterium 4_1_37FAA]
 gi|330409807|gb|EGG89242.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae
           bacterium 9_1_43BFAA]
          Length = 319

 Score =  333 bits (854), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 138/315 (43%), Positives = 204/315 (64%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAAI+ V+IDG
Sbjct: 3   DFNKPN-IEITEIS-EDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAISHVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+N+K + +K     D  K   I   G GVVTA DIQ   DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNLKSLAIKNSSETDEPKTAYIEFEGEGVVTAADIQVDPDI 120

Query: 126 EVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E++NPD VI  L+  A   + MELT++KG GY+ A  ++ E  PIG+I ID++Y+P+++V
Sbjct: 121 EIMNPDAVIATLNGGADSKLYMELTITKGRGYISADKNKNEELPIGVIPIDSIYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + TVE+ R GQ+ DYDKL++ + T+G++  +++V+LA+++L + L +FI+  E  +  + 
Sbjct: 181 NLTVENTRVGQITDYDKLTLDVYTNGTLLPDEAVSLAAKVLNEHLKLFIDLSEVAQAAEV 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            I  +       L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL
Sbjct: 241 MIEKEDDEKEKVLEMSIDELELSVRSYNCLKRAGINTVEELTNRTPEDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFLG 318
            E+   L  +GL L 
Sbjct: 301 EEVLAKLKELGLELS 315


>gi|325981830|ref|YP_004294232.1| DNA-directed RNA polymerase, alpha subunit [Nitrosomonas sp. AL212]
 gi|325531349|gb|ADZ26070.1| DNA-directed RNA polymerase, alpha subunit [Nitrosomonas sp. AL212]
          Length = 335

 Score =  333 bits (853), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 147/332 (44%), Positives = 221/332 (66%), Gaps = 9/332 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            +L+ P  I+   +         ++ EP  RG+ HTLGNALRR+L+SS+ G A T ++I 
Sbjct: 4   TDLLTPRIIDVQNISPL---HAKVVMEPFERGYGHTLGNALRRILLSSMTGYAPTEIKIA 60

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE S++ GV ED+ DI++NIKGI LK+  +    +++ K G G+VTA DI+  +D+E
Sbjct: 61  GVLHEYSALDGVQEDVVDILMNIKGIVLKLHNNDEVILSLKKSGKGIVTAADIELSHDVE 120

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKV 183
           ++NP+HVI +L  +  + ++L V KG GY PA   ++   E + IG I +DA +SPI++V
Sbjct: 121 IINPEHVIAHLTSEGKIDVQLKVEKGRGYAPANIRKSGINEKNSIGTILLDASFSPIRRV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY+VESAR  Q  D DKL + I+T+G++  E+++  A+R+L  QL +F + E      ++
Sbjct: 181 SYSVESARVEQRTDLDKLIVDIETNGAVEPEEAIRFAARVLVQQLSVFADLESTPLPKEK 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                +   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTEA++LR  N GRKSL
Sbjct: 241 PQ---APQIDPILLRPVDDLELTVRSANCLKVENIYYIGDLIQRTEAELLRTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
            EIK VL +  L LGM L +WPP +++ ++K+
Sbjct: 298 NEIKEVLASRELTLGMKLDNWPPANLDSVSKE 329


>gi|71901056|ref|ZP_00683166.1| DNA-directed RNA polymerase [Xylella fastidiosa Ann-1]
 gi|71729183|gb|EAO31304.1| DNA-directed RNA polymerase [Xylella fastidiosa Ann-1]
          Length = 332

 Score =  333 bits (853), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 145/330 (43%), Positives = 221/330 (66%), Gaps = 9/330 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             ++++P   +   L    ENR  ++ EPL RG+AHTLGNALRRVL+SS+ G AIT V+I
Sbjct: 5   VSQVLRPRGPQIERL---TENRAKVVLEPLGRGYAHTLGNALRRVLLSSIPGFAITEVEI 61

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGVLHE ++++G+ ED+ +++LN+K + +++       +++FK+G GVVTA DI+T +++
Sbjct: 62  DGVLHEYTTVEGLQEDVLEVLLNLKDVAIRIHSGDTATLSLFKQGAGVVTAADIKTDHNV 121

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYSPIKK 182
           E++N  HVIC+L  D  + M L + +G GY PA   R    EN  IG + +DA +SP+++
Sbjct: 122 EIINDGHVICHLTKDTTINMRLKIERGFGYQPAVVRRRPDDENRTIGRLILDASFSPVRR 181

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+Y VE+AR  Q  D DKL + I+T+G+I  E+++  A+ IL DQL +F NF    +   
Sbjct: 182 VAYVVEAARVEQRTDLDKLIIDIETNGTIDAEEALRTAADILTDQLSVFGNFTHRDRGT- 240

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
             +   S   +P LL+ +++LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KS
Sbjct: 241 --VKPASSGVDPVLLRPIDDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKS 298

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEEL 332
           L EIK VLG  GL LG+ L +WPP  + + 
Sbjct: 299 LTEIKEVLGQRGLGLGVKLENWPPPGVSQY 328


>gi|260589249|ref|ZP_05855162.1| DNA-directed RNA polymerase, alpha subunit [Blautia hansenii DSM
           20583]
 gi|331082657|ref|ZP_08331780.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae
           bacterium 6_1_63FAA]
 gi|260540330|gb|EEX20899.1| DNA-directed RNA polymerase, alpha subunit [Blautia hansenii DSM
           20583]
 gi|330400276|gb|EGG79918.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae
           bacterium 6_1_63FAA]
          Length = 319

 Score =  332 bits (852), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 133/314 (42%), Positives = 198/314 (63%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP     I    +++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFNKPKI--QITEMSDDKRYGKFVVEPLERGYGITLGNSLRRIMLSSLPGAAVSQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+N+K + +K     +  K   I   G GVVT  DIQ   D+
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNLKNLAIKNVSDSNEPKTAYIEFEGEGVVTGADIQVDQDL 120

Query: 126 EVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E+LNPD VI  L+  A      ELT++KG GYV A   +T++ PIG+I +D++Y+P+++V
Sbjct: 121 EILNPDLVIATLNGGADCKFNAELTITKGRGYVSADKGKTDDMPIGMIAVDSIYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +  VE+ R GQV DYDKL++ I T+G++  +++V+LA+++L + L +FI+  E  K  + 
Sbjct: 181 NMAVENTRVGQVTDYDKLTLDIYTNGTLDADEAVSLAAKVLSEHLSLFIDLSESAKTAEV 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            I  +       L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL
Sbjct: 241 MIEKEDNEKEKVLEMNIDELELSVRSYNCLKRAGINTVEELCNRTSEDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 301 EEVLAKLKELGLQL 314


>gi|226323042|ref|ZP_03798560.1| hypothetical protein COPCOM_00814 [Coprococcus comes ATCC 27758]
 gi|225208609|gb|EEG90963.1| hypothetical protein COPCOM_00814 [Coprococcus comes ATCC 27758]
          Length = 319

 Score =  332 bits (852), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 135/316 (42%), Positives = 207/316 (65%), Gaps = 6/316 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  +++     + EPL RG+  TLGN+LRR+++SSL GAAI+ ++IDG
Sbjct: 3   DFNKPN-IEIAEIS-DDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAISQIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+N+K + +K     D  K   I   G GVVTA DIQ  +DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNLKTLAIKNSSETDEPKTAYIEFEGEGVVTAADIQADSDI 120

Query: 126 EVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E++NP+ VI  L+  A   + MELT++KG GYV +  ++TE+ PIG+I ID++Y+P+++V
Sbjct: 121 EIMNPETVIATLNGGADSKLYMELTITKGRGYVGSDKNKTEDMPIGVIPIDSIYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + TV++ R GQ+ DYDKL++ + T+G++  +++V+LA+++L + L +FI+  E  +  + 
Sbjct: 181 NLTVQNTRVGQITDYDKLTLDVYTNGTLAPDEAVSLAAKVLNEHLKLFIDLSEVAQSAEV 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            I  +       L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL
Sbjct: 241 MIEKEDDEKEKVLEMSIDELELSVRSYNCLKRAGINTVEELTNRTSEDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFLGM 319
            E+   L  +GL L  
Sbjct: 301 EEVLAKLKELGLELSQ 316


>gi|169350821|ref|ZP_02867759.1| hypothetical protein CLOSPI_01595 [Clostridium spiroforme DSM 1552]
 gi|169292407|gb|EDS74540.1| hypothetical protein CLOSPI_01595 [Clostridium spiroforme DSM 1552]
          Length = 314

 Score =  332 bits (852), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 112/297 (37%), Positives = 183/297 (61%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E +N    + EPL RGF  TLGN+LRRVL+SSL G+A+ A+++ G +HE S++ GV ED
Sbjct: 15  DETDNYGKFVIEPLERGFGTTLGNSLRRVLLSSLPGSAVYAIKVQGAIHEFSAVDGVVED 74

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILN+K +   +  D    + I   GP  VT  DIQ  +++ +++ D VI ++   A
Sbjct: 75  VTSIILNLKKLVFDVDSDESATMIIDVEGPATVTGADIQCPSEVTMISNDLVIAHVAQGA 134

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + MEL   K  GY+ A  ++ + + IG+I  D+++SP+++VSY VE  R G+   YD+L
Sbjct: 135 HLYMELYAKKDRGYISADQNKKDINTIGIIPTDSIFSPVERVSYAVEPTRVGESAKYDQL 194

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           ++ I+T+G++   ++++LA++IL + L MF+   +    ++     ++   N  L   +E
Sbjct: 195 TLEIETNGALKPYEAISLAAKILVEHLNMFVELTDMAVNMEVMSEAQNDTSNKVLDMTIE 254

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           EL+LSVRS NCL+   I  + DL  ++E DM+++ N G+KSL E+K  L  +GL   
Sbjct: 255 ELDLSVRSYNCLKRAGIQTVQDLAAKSEDDMIKVRNLGKKSLKEVKEKLVELGLGFK 311


>gi|291298742|ref|YP_003510020.1| DNA-directed RNA polymerase subunit alpha [Stackebrandtia
           nassauensis DSM 44728]
 gi|290567962|gb|ADD40927.1| DNA-directed RNA polymerase, alpha subunit [Stackebrandtia
           nassauensis DSM 44728]
          Length = 345

 Score =  332 bits (852), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 122/319 (38%), Positives = 186/319 (58%), Gaps = 3/319 (0%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
                + R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I G  
Sbjct: 11  EESLSDTRSRFSIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTIPGAK 70

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+ +++LN+K + +    D    + + K+GPG VTAGDIQ  + + V NP+  +  L+ 
Sbjct: 71  EDVVELVLNVKQLCVSSELDEPVTMYLRKQGPGDVTAGDIQPPSGVTVHNPELKLATLNG 130

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              + MEL V +G GYV A  ++     IG I +D++YSP+ KVSY VE+ R  Q  D+D
Sbjct: 131 KGRLDMELIVERGRGYVSAAQNKQAGAGIGRIPVDSIYSPVVKVSYRVEATRVEQRTDFD 190

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + ++T  S     ++A A   L +  G++   +   + +    +         L   
Sbjct: 191 KLIIDVETKPSTGPRTALASAGSTLVELFGLYRELDSAAEGIDVGPSPADAQLAADLALP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +EELEL+VRS NCL+ E +  +G+LI RTEAD+L + NFG+KS+ E+K  L  +GL L  
Sbjct: 251 IEELELTVRSYNCLKREGVDQVGELINRTEADLLDIRNFGQKSIDEVKMKLAGLGLALKD 310

Query: 320 NLPDWPPESIEELAKKYED 338
           +   + P    E A  Y+D
Sbjct: 311 SPGTFDPA---EAAAAYDD 326


>gi|15837778|ref|NP_298466.1| DNA-directed RNA polymerase subunit alpha [Xylella fastidiosa 9a5c]
 gi|28198377|ref|NP_778691.1| DNA-directed RNA polymerase subunit alpha [Xylella fastidiosa
           Temecula1]
 gi|182681018|ref|YP_001829178.1| DNA-directed RNA polymerase subunit alpha [Xylella fastidiosa M23]
 gi|54039280|sp|P66713|RPOA_XYLFT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|54042190|sp|P66712|RPOA_XYLFA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238691090|sp|B2I8J3|RPOA_XYLF2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|9106142|gb|AAF83986.1|AE003951_11 RNA polymerase alpha subunit [Xylella fastidiosa 9a5c]
 gi|28056447|gb|AAO28340.1| RNA polymerase, alpha subunit [Xylella fastidiosa Temecula1]
 gi|182631128|gb|ACB91904.1| DNA-directed RNA polymerase, alpha subunit [Xylella fastidiosa M23]
 gi|307579487|gb|ADN63456.1| DNA-directed RNA polymerase subunit alpha [Xylella fastidiosa
           subsp. fastidiosa GB514]
          Length = 332

 Score =  332 bits (852), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 144/330 (43%), Positives = 221/330 (66%), Gaps = 9/330 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             ++++P   +   L    ENR  ++ EPL RG+AHTLGNALRRVL+SS+ G AIT V+I
Sbjct: 5   VSQVLRPRGPQIERL---TENRAKVVLEPLGRGYAHTLGNALRRVLLSSIPGFAITEVEI 61

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGVLHE ++++G+ ED+ +++LN+K + +++       +++FK+G GVVTA DI+T +++
Sbjct: 62  DGVLHEYTTVEGLQEDVLEVLLNLKDVAIRIHSGDTATLSLFKQGAGVVTAADIKTDHNV 121

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYSPIKK 182
           E++N  HVIC+L  D  + M L + +G GY PA   R    EN  IG + +DA +SP+++
Sbjct: 122 EIINDGHVICHLTKDTTINMRLKIERGFGYQPAVVRRRPDDENRTIGRLILDASFSPVRR 181

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+Y VE+AR  Q  D DKL + I+T+G+I  E+++  A+ IL DQL +F +F    +   
Sbjct: 182 VAYVVEAARVEQRTDLDKLIIDIETNGTIDAEEALRTAADILTDQLSVFGDFTHRDRGT- 240

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
             +   S   +P LL+ +++LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KS
Sbjct: 241 --VKPASSGVDPVLLRPIDDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKS 298

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEEL 332
           L EIK VLG  GL LG+ L +WPP  + + 
Sbjct: 299 LTEIKEVLGQRGLGLGVKLENWPPPGVSQY 328


>gi|167771239|ref|ZP_02443292.1| hypothetical protein ANACOL_02597 [Anaerotruncus colihominis DSM
           17241]
 gi|167666490|gb|EDS10620.1| hypothetical protein ANACOL_02597 [Anaerotruncus colihominis DSM
           17241]
          Length = 319

 Score =  332 bits (851), Expect = 5e-89,   Method: Composition-based stats.
 Identities = 129/316 (40%), Positives = 203/316 (64%), Gaps = 5/316 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           ++I+P  IE + L + + +    +AEPL RGF  TLGN+LRRVL+SSL G A+ +V+IDG
Sbjct: 3   KIIEP-KIETVEL-KSDGSYGKFVAEPLDRGFGTTLGNSLRRVLLSSLPGVAVISVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           + HE S+I GV ED+T+IILNIKG+  K+  D  K V I  +G   VTAG I+  +++E+
Sbjct: 61  IQHEFSTIPGVKEDVTEIILNIKGLTAKLYCDEPKTVRIDAQGECEVTAGSIECDSEVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKVS 184
           L+P   I  LD  A + ME+T+ KG GYV A  ++    E  P+G I +D++Y+P+ KV+
Sbjct: 121 LDPSMHIATLDTGAKLAMEITLKKGQGYVSADRNKHTELEKAPVGTIAVDSIYTPVLKVN 180

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           YTVE+ R  Q+ DYDKL++ + TDG+I+ +++V+LA++IL  QL  F++  +     +  
Sbjct: 181 YTVENTRVEQITDYDKLTLEVWTDGTISAKEAVSLAAKILNRQLNHFVDLSDEVSATEIM 240

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +    +  L   +EEL+LSVR+ NCL+   +  + DLI ++  +M+++ N G+KSL 
Sbjct: 241 DKKEDTGKDKLLEMTIEELDLSVRAFNCLKRAGVNTVADLINKSPDEMMKVRNLGKKSLE 300

Query: 305 EIKGVLGTMGLFLGMN 320
           E+   L ++G  L  +
Sbjct: 301 EVIWKLQSLGFDLSKD 316


>gi|225376438|ref|ZP_03753659.1| hypothetical protein ROSEINA2194_02080 [Roseburia inulinivorans DSM
           16841]
 gi|225211814|gb|EEG94168.1| hypothetical protein ROSEINA2194_02080 [Roseburia inulinivorans DSM
           16841]
          Length = 319

 Score =  332 bits (851), Expect = 5e-89,   Method: Composition-based stats.
 Identities = 137/316 (43%), Positives = 207/316 (65%), Gaps = 6/316 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP  IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFQKP-KIEIAEIS-EDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+NIK + ++   S D  K   I   G GVVTA DIQ  +DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNIKELAIRNNSSSDEPKVAYIEFEGEGVVTAADIQVDSDI 120

Query: 126 EVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           ++LNPD VI NL+  A   + MELT++KG GYV +  ++TE+ PIG+I ID++Y+P+++V
Sbjct: 121 QILNPDLVIANLNGGADCKLYMELTITKGRGYVSSDKNKTEDTPIGVIAIDSIYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + ++E+ R GQ+ DYDKL++ + T+G++  +++V+LA+++L + L +FI+  E  ++   
Sbjct: 181 NLSIENTRVGQITDYDKLTLDVYTNGTLEPDEAVSLAAKVLSEHLNLFIDLSEAAQQADV 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            I          L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL
Sbjct: 241 MIEKADDAKEKVLEMNIDELELSVRSFNCLKRAGINTVEELTNRTPEDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFLGM 319
            E+   L  +GL L  
Sbjct: 301 EEVLAKLKELGLQLNQ 316


>gi|302388059|ref|YP_003823881.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           saccharolyticum WM1]
 gi|302198687|gb|ADL06258.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           saccharolyticum WM1]
          Length = 322

 Score =  332 bits (851), Expect = 5e-89,   Method: Composition-based stats.
 Identities = 137/314 (43%), Positives = 206/314 (65%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFEKPN-IEIAEIS-EDKKYGKFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+NIK +++K + D    K   I   G GV+TA DIQ   DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNIKSLSIKNNSDTNEAKVAYIEFEGEGVITAADIQADPDI 120

Query: 126 EVLNPDHVICNLDV--DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E++NP+ VI  L    D+   MELT++KG GYV A  +++E+ PIG+I +D++Y+P+++V
Sbjct: 121 EIMNPEQVIATLSGGTDSKFYMELTITKGRGYVSADKNKSEDLPIGVIAVDSIYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + TVE+ R GQV DYDKL++ + T+G+   +++V+LA+++L + L +FI+  E  K  + 
Sbjct: 181 NMTVENTRVGQVTDYDKLTLDVFTNGTSAPDEAVSLAAKVLSEHLNLFIDLSENAKTAEV 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  +       L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL
Sbjct: 241 MVEKEDNEKEKVLEMNIDELELSVRSYNCLKRAGINTVEELCNRTSEDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 301 EEVLAKLKELGLQL 314


>gi|317054795|ref|YP_004103262.1| DNA-directed RNA polymerase subunit alpha [Ruminococcus albus 7]
 gi|315447064|gb|ADU20628.1| DNA-directed RNA polymerase, alpha subunit [Ruminococcus albus 7]
          Length = 319

 Score =  332 bits (851), Expect = 5e-89,   Method: Composition-based stats.
 Identities = 128/313 (40%), Positives = 206/313 (65%), Gaps = 4/313 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           +++ KP  IE   L +        I EPL RG+  TLGN+LRRVL+SSL G A+T+V+ID
Sbjct: 3   EKIEKP-KIETPEL-KSNGTYGKFILEPLERGYGITLGNSLRRVLLSSLPGVAVTSVKID 60

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV HE+S+I GV ED+T+IILN+KG+  K+ G+  K + I   G  VVTAGDI+  ++++
Sbjct: 61  GVHHELSTIPGVKEDVTEIILNLKGLTAKLYGEGPKTIYIEAEGECVVTAGDIKADSEVD 120

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVS 184
           +L PD  I  L   A + ME+T+ +G GYV A+ +++  +N PIG+I +D++YSP+ KV+
Sbjct: 121 ILVPDMHIATLGAGAKLYMEITIDRGRGYVSAEKNKSLMQNAPIGIIAVDSIYSPVLKVN 180

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           YTV++ R G + D+DKL++ + TDG+I+ +++V++A+++L + L  F++  E    V+  
Sbjct: 181 YTVDNTRVGHITDFDKLTLEVWTDGTISAKEAVSMAAKLLNEHLNPFVDLSEETNVVELI 240

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +          L   +EEL+LSVRS NCL+   I  + DLI+++  +M+++ N G+KS  
Sbjct: 241 VEKDDQGKEKILEMTIEELDLSVRSFNCLKRAGINTVNDLIEKSAEEMMKVRNLGKKSFD 300

Query: 305 EIKGVLGTMGLFL 317
           E++  L ++G  L
Sbjct: 301 EVREKLHSLGYEL 313


>gi|71276504|ref|ZP_00652779.1| DNA-directed RNA polymerase [Xylella fastidiosa Dixon]
 gi|71900585|ref|ZP_00682712.1| DNA-directed RNA polymerase [Xylella fastidiosa Ann-1]
 gi|170729724|ref|YP_001775157.1| DNA-directed RNA polymerase subunit alpha [Xylella fastidiosa M12]
 gi|238687957|sp|B0U5M3|RPOA_XYLFM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|71162681|gb|EAO12408.1| DNA-directed RNA polymerase [Xylella fastidiosa Dixon]
 gi|71729642|gb|EAO31746.1| DNA-directed RNA polymerase [Xylella fastidiosa Ann-1]
 gi|167964517|gb|ACA11527.1| DNA-directed RNA polymerase [Xylella fastidiosa M12]
          Length = 332

 Score =  332 bits (851), Expect = 5e-89,   Method: Composition-based stats.
 Identities = 145/326 (44%), Positives = 220/326 (67%), Gaps = 9/326 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++P   +   L    ENR  ++ EPL RG+AHTLGNALRRVL+SS+ G+AIT V+IDGVL
Sbjct: 9   LRPRGPQIERL---TENRAKVVLEPLGRGYAHTLGNALRRVLLSSIPGSAITQVEIDGVL 65

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE ++++G+ ED+ +++LN+K + +++       +++FK+G GVVTA DI+T +++E++N
Sbjct: 66  HEYTTVEGLQEDVLEVLLNLKDVAIRIHSGDTATLSLFKQGAGVVTAADIKTDHNVEIIN 125

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYSPIKKVSYT 186
             HVIC+L  D  + M L V +G GY PA   R    EN  IG + +DA +SP+++V+Y 
Sbjct: 126 DGHVICHLTKDTTINMRLKVERGFGYQPAVVRRRPDDENRTIGRLILDASFSPVRRVAYV 185

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+AR  Q  D DKL + I+T+G+I  E+++  A+ IL DQL +F +F    +     + 
Sbjct: 186 VEAARVEQRTDLDKLIIDIETNGTIDAEEALRTAADILTDQLSVFGDFTHRDRGT---VK 242

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
             S   +P LL+ +++LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KSL EI
Sbjct: 243 PASSGVDPVLLRPIDDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSLTEI 302

Query: 307 KGVLGTMGLFLGMNLPDWPPESIEEL 332
           K VLG  GL LG+ L +WPP  + + 
Sbjct: 303 KEVLGQRGLGLGVKLENWPPPGVSQY 328


>gi|124514416|gb|EAY55929.1| DNA-directed RNA polymerase, alpha subunit [Leptospirillum rubarum]
          Length = 324

 Score =  332 bits (851), Expect = 6e-89,   Method: Composition-based stats.
 Identities = 139/324 (42%), Positives = 211/324 (65%), Gaps = 3/324 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            + ++   P ++ +     + +    +IAEP  RG+  TLGN+LRR+L+SS++GAAITAV
Sbjct: 2   NSVRDFQMPKSLSFDR-DTQTDRFLRVIAEPFERGYGTTLGNSLRRILLSSIKGAAITAV 60

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +  GV HE S+I GV ED++DIILN+K + +K        V +   G   VTAGDI T  
Sbjct: 61  RFRGVFHEFSNIPGVLEDVSDIILNLKEVRVKSHEPEPHWVHLKVSGQKYVTAGDISTGG 120

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            I++L+P H I  LD  A + M+L +  G GYV A+ ++TE+  +G+I IDA+++P+KKV
Sbjct: 121 VIDILDPGHHIATLDKGASLEMDLRIETGRGYVSAERNKTESLEVGVIPIDAVFTPLKKV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI--NFEEPKKEV 241
           ++TV+S R G++ DYDKL++ I+TDGS+T E++++ A++IL+D L MF+  + +    + 
Sbjct: 181 NFTVDSTRVGRMTDYDKLTLDIETDGSLTPEEALSQAAQILKDHLDMFVIEDTDHLIPDS 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            +         +  L + V +LELSVR++NCL+   I  +GDLIQ+TE ++L+  NFGRK
Sbjct: 241 PKPTMKVEEIGDDLLTRNVLDLELSVRASNCLKNAEIKTVGDLIQKTENELLKTKNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL EIK VL  MGL LGM L +  
Sbjct: 301 SLNEIKTVLSNMGLTLGMELTNKD 324


>gi|319938481|ref|ZP_08012875.1| DNA-directed RNA polymerase [Coprobacillus sp. 29_1]
 gi|319806397|gb|EFW03064.1| DNA-directed RNA polymerase [Coprobacillus sp. 29_1]
          Length = 314

 Score =  332 bits (851), Expect = 6e-89,   Method: Composition-based stats.
 Identities = 115/297 (38%), Positives = 178/297 (59%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E +N    + EPL RGF  TLGN+LRRVL+SS+ G A+ AV++ G +HE S++ GV ED
Sbjct: 15  DESDNYGKFVIEPLERGFGTTLGNSLRRVLLSSIPGCAVHAVKVQGAIHEFSAVDGVVED 74

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILNIK +   + GD    + I  +GP VVT  DIQ  +++ +++ D  I ++   A
Sbjct: 75  VTSIILNIKKLVFSIDGDDDVTMIIDVKGPAVVTGADIQCPSNVTMISNDLEIAHVAEGA 134

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              ME+   +  GY+ A  ++   + IG+I  D++YSP+ KV+Y  E  R GQ   YD+L
Sbjct: 135 HFYMEMYAHRDRGYMSADQNKKLINTIGVIATDSIYSPVVKVAYATEPTRVGQSAKYDQL 194

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           ++ I TDGS+   +++ALA++IL + L MF+   +    ++     +    N  L   +E
Sbjct: 195 TLEITTDGSVQPHEALALAAKILVEHLNMFVELTDMAMNMEVMSETEEDTSNKVLDMTIE 254

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           EL+LSVRS NCL+   I  + +L  ++E DM+++ N G+KSL E+K  L  +GL   
Sbjct: 255 ELDLSVRSYNCLKRAGIQTVQELAAKSEDDMIKVRNLGKKSLKEVKEKLVELGLGFK 311


>gi|210611154|ref|ZP_03288768.1| hypothetical protein CLONEX_00958 [Clostridium nexile DSM 1787]
 gi|210152141|gb|EEA83148.1| hypothetical protein CLONEX_00958 [Clostridium nexile DSM 1787]
          Length = 319

 Score =  331 bits (850), Expect = 7e-89,   Method: Composition-based stats.
 Identities = 137/316 (43%), Positives = 204/316 (64%), Gaps = 6/316 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAAI+ V+IDG
Sbjct: 3   DFNKPN-IEITEIS-EDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAISQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+I++N+K + +K     D  K   I   G GVVTA DIQ   DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIVMNLKSLAIKNTSETDEPKTAYIEFEGEGVVTAADIQVDPDI 120

Query: 126 EVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E++NPD VI  L+  A   + MELT++KG GYV A  ++ E+ PI +I ID++Y+P+++V
Sbjct: 121 EIMNPDAVIATLNGGADSKLYMELTITKGRGYVSADKNKKEDLPIAVIPIDSIYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + TVE+ R GQ+ DYDKL++ + T+G++  +++V+LA+++L + L +FI+  E  +  + 
Sbjct: 181 NLTVENTRVGQITDYDKLTLDVYTNGTLLPDEAVSLAAKVLNEHLKLFIDLSEVAQAAEV 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            I  +       L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL
Sbjct: 241 MIEKEDDEKEKVLEMSIDELELSVRSYNCLKRAGINTVEELTNRTPEDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFLGM 319
            E+   L  +GL L  
Sbjct: 301 EEVLAKLKELGLELSQ 316


>gi|206602703|gb|EDZ39184.1| DNA-directed RNA polymerase, alpha subunit [Leptospirillum sp.
           Group II '5-way CG']
          Length = 324

 Score =  331 bits (850), Expect = 7e-89,   Method: Composition-based stats.
 Identities = 138/324 (42%), Positives = 211/324 (65%), Gaps = 3/324 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            + ++   P ++ +     + +    +IAEP  RG+  TLGN+LRR+L+SS++GAAITAV
Sbjct: 2   NSVRDFQMPKSLSFDR-DTQTDRFLRVIAEPFERGYGTTLGNSLRRILLSSIKGAAITAV 60

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +  GV HE S+I GV ED++DIILN+K + +K        V +   G   VTAGDI T  
Sbjct: 61  RFRGVFHEFSNIPGVLEDVSDIILNLKEVRVKSHESEPHWVHLKVSGQKYVTAGDISTGG 120

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            I++L+P H I  LD  A + M+L +  G GYV A+ +++E+  +G+I IDA+++P+KKV
Sbjct: 121 VIDILDPGHHIATLDKGASLEMDLRIETGRGYVSAERNKSESLEVGVIPIDAVFTPLKKV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI--NFEEPKKEV 241
           ++TV+S R G++ DYDKL++ I+TDGS+T E++++ A++IL+D L MF+  + +    + 
Sbjct: 181 NFTVDSTRVGRMTDYDKLTLDIETDGSLTPEEALSQAAQILKDHLDMFVIEDTDHLIPDS 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            +         +  L + V +LELSVR++NCL+   I  +GDLIQ+TE ++L+  NFGRK
Sbjct: 241 PKPTMKVEEIGDDLLTRNVLDLELSVRASNCLKNAEIKTVGDLIQKTENELLKTKNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL EIK VL  MGL LGM L +  
Sbjct: 301 SLNEIKTVLSNMGLTLGMELTNKD 324


>gi|296119324|ref|ZP_06837892.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           ammoniagenes DSM 20306]
 gi|295967716|gb|EFG80973.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           ammoniagenes DSM 20306]
          Length = 335

 Score =  331 bits (850), Expect = 8e-89,   Method: Composition-based stats.
 Identities = 122/313 (38%), Positives = 187/313 (59%), Gaps = 3/313 (0%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +     + +R+  + EPL  GF +T+GN++RR L+SS+ GAA+T+++IDGVLHE ++I G
Sbjct: 9   VTEEYIDSSRSRFVFEPLEPGFGYTIGNSMRRTLLSSIPGAAVTSIKIDGVLHEFTTISG 68

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+++IILN+K + L    D    + + K GPG VTAGDIQ    +E+ NP+  I  L
Sbjct: 69  VKEDVSEIILNVKNLVLSSDSDEPVVMYLSKEGPGAVTAGDIQPPAGVEIHNPELHIATL 128

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           +  A + MEL V +G GYVPA     +   IG I ID +YSP+ KVSY VE+ R  Q  D
Sbjct: 129 NDTAKLDMELVVERGRGYVPAAPTSGD---IGRIPIDQIYSPVLKVSYKVEATRVEQRTD 185

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL + ++T  SI+  D++A A   L +  G+        + ++   + +   +  A  
Sbjct: 186 FDKLIIDVETKNSISARDALASAGGTLVELFGLARELNTAAEGIEIGPSPQESEYIAAYS 245

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +E+L  SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L  + L L
Sbjct: 246 MPIEDLNFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKIKLANLNLAL 305

Query: 318 GMNLPDWPPESIE 330
                D+ P  +E
Sbjct: 306 KDTPEDFDPTQLE 318


>gi|160881757|ref|YP_001560725.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           phytofermentans ISDg]
 gi|160430423|gb|ABX43986.1| DNA-directed RNA polymerase, alpha subunit [Clostridium
           phytofermentans ISDg]
          Length = 319

 Score =  331 bits (850), Expect = 8e-89,   Method: Composition-based stats.
 Identities = 129/317 (40%), Positives = 203/317 (64%), Gaps = 6/317 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP  IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFEKP-KIEIADIS-EDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           V+HE S I GV ED+T+II+NIK + +K     +  K   I   G GVV AGDIQ   DI
Sbjct: 61  VVHEFSPIPGVKEDVTEIIMNIKNLAIKNTSETNEPKTAYIEFEGEGVVRAGDIQADPDI 120

Query: 126 EVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E+LNP+ VI  L   A   + +ELT++KG GY+ A  ++ ++ PIG+I +D++Y+P+++V
Sbjct: 121 EILNPELVIATLSGGADSKLYIELTITKGRGYISADKNKNDDLPIGVIAVDSIYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + +VE+ R GQ+ D+DKL++ + T+G++  +++V+LA+++L + L  FI+  E  K  + 
Sbjct: 181 NLSVENTRVGQITDFDKLTLDVFTNGTLGPDEAVSLAAKVLSEHLNSFIDLSENAKTAEV 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  +       L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL
Sbjct: 241 MVEKEDNEKEKVLEMNIDELELSVRSYNCLKRAGINTVEELCNRTSEDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFLGMN 320
            E+   L  +GL L ++
Sbjct: 301 EEVLAKLKELGLSLNLS 317


>gi|227497208|ref|ZP_03927456.1| DNA-directed RNA polymerase [Actinomyces urogenitalis DSM 15434]
 gi|226833339|gb|EEH65722.1| DNA-directed RNA polymerase [Actinomyces urogenitalis DSM 15434]
          Length = 333

 Score =  331 bits (849), Expect = 8e-89,   Method: Composition-based stats.
 Identities = 132/308 (42%), Positives = 188/308 (61%), Gaps = 3/308 (0%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E +V   EE+ R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+IDGV H
Sbjct: 6   RPTLSEEVV---EEDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRIDGVPH 62

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E  +I GV ED+T IILNIK I L    D    + + K GPGVVTAGDI     +E+ NP
Sbjct: 63  EFRTIAGVKEDVTQIILNIKEIVLSSENDEPVVMYLRKSGPGVVTAGDITPPAGVEIHNP 122

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D VI NL+    + +ELTV +G GYV A  ++  N  I  I +D++YSP+KKVSY VE+ 
Sbjct: 123 DLVIANLNEKGKLEIELTVERGRGYVSANQNKDPNGEISRIPVDSIYSPVKKVSYAVEAT 182

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  SIT  D++A A + L +  G+        + ++   +    
Sbjct: 183 RVEQRTDFDRLVVDVETKASITPRDALASAGKTLVELFGLARELNVEAEGIEVGPSPMDQ 242

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   ++EL+L  RS+N L+ E I  +G+L+ R+EAD+L + NFG KS+ EIK  L
Sbjct: 243 ALQQDLALMIDELDLQARSSNALKREGIHTVGELVARSEADLLDIRNFGAKSISEIKEKL 302

Query: 311 GTMGLFLG 318
             +GL L 
Sbjct: 303 AELGLSLK 310


>gi|255324779|ref|ZP_05365893.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           tuberculostearicum SK141]
 gi|311740030|ref|ZP_07713864.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           pseudogenitalium ATCC 33035]
 gi|255298254|gb|EET77557.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           tuberculostearicum SK141]
 gi|311305103|gb|EFQ81172.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           pseudogenitalium ATCC 33035]
          Length = 336

 Score =  331 bits (849), Expect = 8e-89,   Method: Composition-based stats.
 Identities = 126/307 (41%), Positives = 189/307 (61%), Gaps = 3/307 (0%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           + +R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV ED++
Sbjct: 15  DSSRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTINGVKEDVS 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           +IILNIK + L    D    + + K GPG VTAGDIQ    +E+ NPD  I +L+  A +
Sbjct: 75  EIILNIKSMVLSSDSDEPVVMYLSKEGPGDVTAGDIQPPAGVEIHNPDLHIASLNDTAKL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +EL V +G GYVPA     E   IG I +D +YSP+ KVSY VE+ R  Q  D+DKL++
Sbjct: 135 DIELVVERGRGYVPAAPTSGE---IGRIPVDQIYSPVLKVSYKVEATRVEQRTDFDKLTI 191

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T  SI+  D++A A   L +  G+        + ++   + +   +  A    +E+L
Sbjct: 192 DVETKNSISARDALASAGGTLVELFGLARELNNAAEGIEIGPSPQETEYIAAYGMPIEDL 251

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
             SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L  +GL L     D
Sbjct: 252 NFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKIKLANLGLALKDTPED 311

Query: 324 WPPESIE 330
           + P  +E
Sbjct: 312 FDPTQLE 318


>gi|207744550|ref|YP_002260942.1| dna-directed rna polymerase alpha chain (rnap alphasubunit)
           (transcriptase alpha chain) (rna polymerase alpha
           subunit) protein [Ralstonia solanacearum IPO1609]
 gi|206595956|emb|CAQ62883.1| dna-directed rna polymerase alpha chain (rnap alphasubunit)
           (transcriptase alpha chain) (rna polymerase alpha
           subunit) protein [Ralstonia solanacearum IPO1609]
          Length = 302

 Score =  331 bits (849), Expect = 9e-89,   Method: Composition-based stats.
 Identities = 140/303 (46%), Positives = 200/303 (66%), Gaps = 4/303 (1%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
            EP  RG+ HTLGNALRRVL+SS+ G A T V I GV+HE S+I GV ED+ +++LN+KG
Sbjct: 1   MEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGVVHEYSTIDGVQEDVVNLLLNLKG 60

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           +  K+       V++ K G GVVTA DI+  +D+E++NP HVI +L     + M++ V +
Sbjct: 61  VVFKLHNRDEVTVSLRKEGEGVVTAADIELPHDVEIINPGHVIASLSAGGKLDMQIKVEQ 120

Query: 152 GHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVP    +  ++     G + +DA ++P+++VSY VESAR  Q  D DKL M I+T+
Sbjct: 121 GRGYVPGNVRKFGDESSKVIGRVVLDASFAPVRRVSYAVESARVEQRTDLDKLVMNIETN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G I+ E+++  ++RIL DQL +F   E   +   E    ++   +P LL+ V++LEL+VR
Sbjct: 181 GVISPEEAIRQSARILVDQLSVFAALEG-TESAAEAAAARAPQIDPILLRPVDDLELTVR 239

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPES 328
           S NCL+ ENI Y+GDLIQ TE ++L+  N GRKSL EIK VL + GL LGM L +WPP  
Sbjct: 240 SANCLKAENIYYIGDLIQLTENELLKTPNLGRKSLNEIKEVLASRGLTLGMKLENWPPAG 299

Query: 329 IEE 331
           +E+
Sbjct: 300 LEK 302


>gi|227502699|ref|ZP_03932748.1| DNA-directed RNA polymerase [Corynebacterium accolens ATCC 49725]
 gi|306835270|ref|ZP_07468302.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium accolens
           ATCC 49726]
 gi|227076429|gb|EEI14392.1| DNA-directed RNA polymerase [Corynebacterium accolens ATCC 49725]
 gi|304568863|gb|EFM44396.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium accolens
           ATCC 49726]
          Length = 336

 Score =  331 bits (849), Expect = 9e-89,   Method: Composition-based stats.
 Identities = 127/307 (41%), Positives = 189/307 (61%), Gaps = 3/307 (0%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           + +R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV ED++
Sbjct: 15  DSSRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTINGVKEDVS 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           +IILNIK + L    D    + + K GPG VTAGDIQ    +E+ NPD  I +L+  A +
Sbjct: 75  EIILNIKSMVLSSDSDEPVVMYLSKEGPGDVTAGDIQPPAGVEIHNPDLHIASLNDTAKL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +EL V +G GYVPA     E   IG I ID +YSP+ KVSY VE+ R  Q  D+DKL++
Sbjct: 135 DIELVVERGRGYVPAAATSGE---IGRIPIDQIYSPVLKVSYKVEATRVEQRTDFDKLTI 191

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T  SI+  D++A A   L +  G+        + ++   + +   +  A    +E+L
Sbjct: 192 DVETKNSISARDALASAGGTLVELFGLARELNNAAEGIEIGPSPQETEYIAAYGMPIEDL 251

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
             SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L  +GL L     D
Sbjct: 252 NFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKIKLANLGLALKDTPED 311

Query: 324 WPPESIE 330
           + P  +E
Sbjct: 312 FDPTQLE 318


>gi|323483272|ref|ZP_08088662.1| hypothetical protein HMPREF9474_00411 [Clostridium symbiosum
           WAL-14163]
 gi|323691229|ref|ZP_08105505.1| DNA-directed RNA polymerase [Clostridium symbiosum WAL-14673]
 gi|323403370|gb|EGA95678.1| hypothetical protein HMPREF9474_00411 [Clostridium symbiosum
           WAL-14163]
 gi|323504748|gb|EGB20534.1| DNA-directed RNA polymerase [Clostridium symbiosum WAL-14673]
          Length = 320

 Score =  331 bits (848), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 132/314 (42%), Positives = 202/314 (64%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP  IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFEKP-KIEIAEIS-EDKRYGKFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+NIK + +K     +  K   I   G GVVTA DIQ  +DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNIKSLAIKNLSETNEPKTAYIEFEGEGVVTAADIQVDSDI 120

Query: 126 EVLNPDHVICNLDV--DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E+LNP+ VI  L    D+   MEL ++KG GY+ A  ++ +  PIG+I +D++Y+P+++V
Sbjct: 121 EILNPEQVIATLSGGTDSKFYMELNITKGRGYISADKNKNDELPIGMIAVDSIYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + TVE+ R GQV D+DKL++ + T+G++  +++V+LA+++L + L +FI+  E  +  + 
Sbjct: 181 NMTVENTRVGQVTDFDKLTLDVFTNGTLAPDEAVSLAAKVLSEHLNLFIDLSENARTAEV 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  +       L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL
Sbjct: 241 MVEKEDNEKEKVLEMNIDELELSVRSYNCLKRAGINTVEELCNRTPEDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 301 EEVLAKLKELGLQL 314


>gi|326407604|gb|ADZ64675.1| DNA-directed RNA polymerase subunit alpha [Lactococcus lactis
           subsp. lactis CV56]
          Length = 312

 Score =  331 bits (848), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 127/311 (40%), Positives = 199/311 (63%), Gaps = 4/311 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP   ++     E EN    + EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+G
Sbjct: 3   EFEKPKITKF----DESENYGKFVVEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE ++I GV ED+  I+L +KGI +K   +S K++ +   GP  VTAGDI T +DIE+
Sbjct: 59  VQHEFATIPGVREDVIQIVLAVKGIAIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N DH + ++     +R  +TV KG+GYVPA  ++ +  PIG I +D++Y+P+ KV+Y V
Sbjct: 119 VNKDHYLFSIAEGHSIRAVMTVKKGYGYVPADENKVDGAPIGTIAVDSIYTPVSKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    YDKL++ I T+G+I  +++++L+++IL D L +F++  E   E +  +  
Sbjct: 179 EPARVGGDSSYDKLTLEITTNGTIVSDEALSLSAKILTDHLNLFVDLSEVASEAETLVVK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
             +     L K +EE++ SVR+ N L+   I  + D+++ +EADM+++ N G KS+ E+K
Sbjct: 239 DEVKTERVLDKIIEEMDFSVRAYNGLKRAGINTVADIVEMSEADMIKVKNLGHKSVEEVK 298

Query: 308 GVLGTMGLFLG 318
             L  +GL L 
Sbjct: 299 VKLTELGLSLK 309


>gi|225574733|ref|ZP_03783343.1| hypothetical protein RUMHYD_02810 [Blautia hydrogenotrophica DSM
           10507]
 gi|225038062|gb|EEG48308.1| hypothetical protein RUMHYD_02810 [Blautia hydrogenotrophica DSM
           10507]
          Length = 319

 Score =  331 bits (848), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 132/314 (42%), Positives = 202/314 (64%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP  IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFNKP-KIEITEIS-EDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+++II+N+K + +K   +    K   I   G GVVTA DIQ   DI
Sbjct: 61  VLHEFSSIPGVKEDVSEIIMNLKSLAIKNKSNDSEPKTAYIECEGKGVVTAADIQADQDI 120

Query: 126 EVLNPDHVICNLD--VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E++NP+ VI  L+   D  + MELT++KG GYV A   ++++ PIG+I +DA+Y+P+ +V
Sbjct: 121 EIMNPEQVIATLNGGKDCRLAMELTITKGRGYVSADKGKSDDMPIGVIAVDAIYTPVDRV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +  VE+ R GQ+ D+DKL++ + T+G++  +++V+LA+++L + L +FI+  E  K  + 
Sbjct: 181 NLVVENTRVGQITDFDKLTLDVYTNGTLDPDEAVSLAAKVLSEHLSLFIDLSENAKTAEV 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            I  +       L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL
Sbjct: 241 MIEKEDNEKEKVLEMSIDELELSVRSYNCLKRAGINTVEELCNRTSDDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 301 EEVLAKLKELGLQL 314


>gi|157100343|emb|CAP03337.1| RpoA protein [Vibrio aestuarianus]
          Length = 323

 Score =  330 bits (847), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 143/329 (43%), Positives = 214/329 (65%), Gaps = 11/329 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEITNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           N G+KSL EIK VL + GL LGM L +WP
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWP 323


>gi|221195350|ref|ZP_03568405.1| DNA-directed RNA polymerase, alpha subunit [Atopobium rimae ATCC
           49626]
 gi|221184537|gb|EEE16929.1| DNA-directed RNA polymerase, alpha subunit [Atopobium rimae ATCC
           49626]
          Length = 313

 Score =  330 bits (847), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 121/316 (38%), Positives = 192/316 (60%), Gaps = 7/316 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E I+P+    + + +   N   + AEPL RG+  TLGN+LRRVL+SSL G+A+ A+QI
Sbjct: 1   MSEFIRPS----VSVEEIGANAARVSAEPLERGYGDTLGNSLRRVLLSSLEGSAVEAIQI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVND 124
           DGV HE +++ GV+ED+TDI+LN+K +  +   D      +I   GP VVT  DI     
Sbjct: 57  DGVQHEFTTVDGVYEDVTDIVLNVKCLVFRSLEDIDEAEASITVDGPKVVTGADIDVPTG 116

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            E++NP+  IC L   A + M L + KG GYV  + +  ++DPIG I++D+++SP+++ +
Sbjct: 117 FELVNPEQHICTLSDGAHLAMRLRIGKGRGYVSGEDNERDDDPIGFISVDSIFSPVRRCA 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
             VE  R G+  DYD+L + ++T+G+I+  ++V  A+ I+   +G F+   E  + ++E 
Sbjct: 177 KAVEPCRVGRHTDYDRLVLEVETNGAISPREAVVEAANIINQHMGAFMGLSEVDESLEET 236

Query: 245 I--NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                + +  +  L K+VE+L+LSVRS NCL+   I  +  L+  +E D+L + NFG KS
Sbjct: 237 SIFASEDVQDDSELDKQVEDLDLSVRSYNCLKRAGIHSVRQLVDFSENDLLNIRNFGVKS 296

Query: 303 LVEIKGVLGTMGLFLG 318
           + E+K  L  MGL L 
Sbjct: 297 IEEVKEKLEAMGLSLK 312


>gi|281492732|ref|YP_003354712.1| DNA-directed RNA polymerase subunit alpha [Lactococcus lactis
           subsp. lactis KF147]
 gi|281376384|gb|ABX75652.2| DNA-directed RNA polymerase, alpha chain [Lactococcus lactis subsp.
           lactis KF147]
          Length = 312

 Score =  330 bits (847), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 127/311 (40%), Positives = 199/311 (63%), Gaps = 4/311 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP   ++     E EN    + EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+G
Sbjct: 3   EFEKPKITKF----DESENYGKFVVEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE ++I GV ED+  I+L +KGI +K   +S K++ +   GP  VTAGDI T +DIE+
Sbjct: 59  VQHEFATIPGVREDVIQIVLAVKGIAIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N DH + ++     +R  +TV KG+GYVPA  ++ +  PIG I +D++Y+P+ KV+Y V
Sbjct: 119 VNKDHYLFSIAEGHSMRAVMTVKKGYGYVPADENKVDGAPIGTIAVDSIYTPVSKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    YDKL++ I T+G+I  +++++L+++IL D L +F++  E   E +  +  
Sbjct: 179 EPARVGGDSSYDKLTLEITTNGTIVSDEALSLSAKILTDHLNLFVDLSEVAAEAETLVVK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
             +     L K +EE++ SVR+ N L+   I  + D+++ +EADM+++ N G KS+ E+K
Sbjct: 239 DEVKTERVLDKIIEEMDFSVRAYNGLKRAGINTVADIVEMSEADMIKVKNLGHKSVEEVK 298

Query: 308 GVLGTMGLFLG 318
             L  +GL L 
Sbjct: 299 VKLTELGLSLK 309


>gi|313673440|ref|YP_004051551.1| DNA-directed RNA polymerase subunit alpha [Calditerrivibrio
           nitroreducens DSM 19672]
 gi|312940196|gb|ADR19388.1| DNA-directed RNA polymerase subunit alpha [Calditerrivibrio
           nitroreducens DSM 19672]
          Length = 336

 Score =  330 bits (847), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 144/324 (44%), Positives = 210/324 (64%), Gaps = 4/324 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI  N++ LIKP  +E        +   + +AEPL RGF  T+GN+LRR+L+SS+ G A+
Sbjct: 1   MILMNFKSLIKPKKLE--TSPDNTDRFGVFVAEPLERGFGITIGNSLRRILLSSIEGTAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
             V+I+ V HE ++I GV ED+ +IILNIK + L ++    KRV I K+G GVV A DI 
Sbjct: 59  VGVKINDVTHEYTTIPGVLEDVVEIILNIKMLELNLNTHEQKRVYIKKKGEGVVKASDIF 118

Query: 121 TVNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
               ++VLNPD  I  +   +A + +EL V +G GYVP++  + +   I +I +DA+++P
Sbjct: 119 GDPLVQVLNPDQHIATITDPNAELNIELYVERGIGYVPSEDMKGKFSDIHIIPVDAIFTP 178

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK- 238
           IK+ ++ VE+AR GQ  DYDKL + ++TDGSI  ED++  +++IL+D L +FINF+EP  
Sbjct: 179 IKRANFRVENARVGQSTDYDKLILEVETDGSIAPEDAIGFSAKILKDHLDLFINFDEPDY 238

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E  E   +++      L K +EELELSVR+ NCL+   I  + +L  +T+ DML+  NF
Sbjct: 239 SEEAEKNEIRNDQILELLDKSIEELELSVRAYNCLKNAEIKTLAELCSKTDNDMLKTKNF 298

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLP 322
           GRKSL EIK VL  +GL LGM+L 
Sbjct: 299 GRKSLEEIKKVLSELGLSLGMDLE 322


>gi|167755938|ref|ZP_02428065.1| hypothetical protein CLORAM_01458 [Clostridium ramosum DSM 1402]
 gi|237733255|ref|ZP_04563736.1| DNA-directed RNA polymerase [Mollicutes bacterium D7]
 gi|167703930|gb|EDS18509.1| hypothetical protein CLORAM_01458 [Clostridium ramosum DSM 1402]
 gi|229383636|gb|EEO33727.1| DNA-directed RNA polymerase [Coprobacillus sp. D7]
          Length = 314

 Score =  330 bits (847), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 116/297 (39%), Positives = 182/297 (61%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E +N    + EPL RGF  TLGN+LRRVL+SSL G+A+ A+++ G +HE S++ GV ED
Sbjct: 15  DETDNYGKFVIEPLERGFGTTLGNSLRRVLLSSLPGSAVYAIKVQGAIHEFSAVDGVVED 74

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILN+K +   +  D    + I   GP  VT  DIQ  +++ +++ D  I ++   A
Sbjct: 75  VTSIILNLKKLVFDVDSDESATMIIDVEGPATVTGADIQCPSEVTMISNDMEIAHVAQGA 134

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + MEL   K  GYV A  ++ E + IG+I  D++YSP++KVSY VE  R G+   YD+L
Sbjct: 135 HLYMELYAKKDRGYVSADQNKKEINTIGIIPTDSIYSPVEKVSYAVEPTRVGESAKYDQL 194

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           ++ I+T+G++   ++++LA++IL + L MF+   +    ++     +S   N  L   +E
Sbjct: 195 TLEIETNGALKPYEAISLAAKILVEHLNMFVELTDMAVNMEVMSEAQSDTTNKVLDMTIE 254

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           EL+LSVRS NCL+   I  + DL  ++E DM+++ N G+KSL E+K  L  +GL   
Sbjct: 255 ELDLSVRSYNCLKRAGIQTVQDLAAKSEDDMIKVRNLGKKSLKEVKEKLVELGLGFK 311


>gi|319442995|ref|ZP_07992151.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           variabile DSM 44702]
          Length = 337

 Score =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 124/312 (39%), Positives = 180/312 (57%), Gaps = 3/312 (0%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                   R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++I+GVLHE ++I GV
Sbjct: 10  TEEYISPARSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIEGVLHEFTTIPGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED++DIILNIK + +    D    + I K G G VT  D+     +EV NPD  I  L+
Sbjct: 70  KEDVSDIILNIKALVISSDSDEPVTMYIRKEGLGEVTGADVVVPAGVEVHNPDLHIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL V +G GYVPA     E   IG I +D +YSP+ KVSY VE+ R  Q  D+
Sbjct: 130 EQGKLDIELVVERGRGYVPAAATTGE---IGRIPVDQIYSPVLKVSYKVEATRVEQRTDF 186

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  SIT  D++A A   L +  G+        + ++   + +      A   
Sbjct: 187 DKLVLDVETKNSITARDAIASAGGTLVELFGLARELNTEAEGIEIGPSPQETEHIAAYSL 246

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L+ SVRS NCL+ E+I  +G+L  RTE+D+L + NFG+KS+ E+K  L  +GL L 
Sbjct: 247 PIEDLDFSVRSYNCLKREDIHTVGELAARTESDLLDIRNFGQKSINEVKVKLAELGLGLK 306

Query: 319 MNLPDWPPESIE 330
                +   SIE
Sbjct: 307 DAPEGFDINSIE 318


>gi|73913591|gb|AAZ91712.1| RNA polymerase alpha subunit [Corynebacterium stationis]
          Length = 334

 Score =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 122/313 (38%), Positives = 187/313 (59%), Gaps = 3/313 (0%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +     + +R+  I EPL  GF +T+GN++RR L+SS+ GAA+T+++I+GVLHE +++ G
Sbjct: 9   VTEEFIDSSRSRFIFEPLEPGFGYTIGNSMRRTLLSSIPGAAVTSIKIEGVLHEFTTVNG 68

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+++IILN+K + L    D    + + K GPG VTAGDIQ    +E+ NPD  I  L
Sbjct: 69  VKEDVSEIILNVKSLVLSSDSDEPVVMYLSKEGPGAVTAGDIQPPAGVEIHNPDLHIATL 128

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           +  A + MEL V +G GYVPA     +   IG I ID +YSP+ KVSY VE+ R  Q  D
Sbjct: 129 NDTAKLDMELVVERGRGYVPAAPTSGD---IGRIPIDQIYSPVLKVSYKVEATRVEQRTD 185

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL + ++T  SI+  D++A A   L +  G+        + ++   + +   +  A  
Sbjct: 186 FDKLIIDVETKNSISARDALASAGGTLVELFGLARELNTAAEGIEIGPSPQESEYIAAYS 245

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +E+L  SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L  + L L
Sbjct: 246 MPIEDLNFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKIKLANLNLAL 305

Query: 318 GMNLPDWPPESIE 330
                D+ P  +E
Sbjct: 306 KDTPEDFDPTQLE 318


>gi|42520507|ref|NP_966422.1| DNA-directed RNA polymerase subunit alpha [Wolbachia endosymbiont
           of Drosophila melanogaster]
 gi|61215982|sp|Q73HA9|RPOA_WOLPM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|42410246|gb|AAS14356.1| DNA-directed RNA polymerase, alpha subunit [Wolbachia endosymbiont
           of Drosophila melanogaster]
          Length = 355

 Score =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 161/346 (46%), Positives = 238/346 (68%), Gaps = 12/346 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            N  +LIKP++++ +    +   ++ ++ EPL  GFA TLGNALRRV++SSL+G+A+  +
Sbjct: 11  SNLDKLIKPSSVKVV--SDDSSEKSDIVLEPLESGFALTLGNALRRVMLSSLKGSAVYGI 68

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+GV HE +SI+GV ED+TDI+LN+  +  K++G S+K + +  +GP  V AG I+T +
Sbjct: 69  KIEGVTHEFTSIQGVREDVTDIVLNMGMLRCKLNGASNKCLNLNAKGPCQVLAGMIETDD 128

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--------TENDPIGLITIDA 175
              ++N D +IC L  +  + M + V+ G GY+P   ++        +E D IG I ++A
Sbjct: 129 QCSIVNKDLLICTLGQNVELNMTIYVASGKGYLPVTKYKENELLKLMSEQDLIGFIPVNA 188

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI--N 233
           LYSP+ +VSY VE++R GQV D DKL ++I+TDG+I+   +V  A+RILQ+QL  FI  +
Sbjct: 189 LYSPVNRVSYRVENSRVGQVTDKDKLILSIETDGTISPSQAVDSAARILQEQLQPFISSD 248

Query: 234 FEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
               K +V      K L ++P LL+KV+E+ELSVRS NCL+ ENI Y+GDL+Q+TE +ML
Sbjct: 249 VSYKKSQVSSSSGAKDLGYDPVLLRKVDEMELSVRSHNCLKNENITYIGDLVQKTEGEML 308

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           R ANFGRKSL EIK VL   GL LGMN+ +WPP+ I+ELAK++ D+
Sbjct: 309 RTANFGRKSLNEIKAVLTNFGLSLGMNVLNWPPKDIDELAKQHTDE 354


>gi|68536848|ref|YP_251553.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium jeikeium
           K411]
 gi|260579206|ref|ZP_05847096.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           jeikeium ATCC 43734]
 gi|90110834|sp|Q4JTC2|RPOA_CORJK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|68264447|emb|CAI37935.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           jeikeium K411]
 gi|258602692|gb|EEW15979.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           jeikeium ATCC 43734]
          Length = 337

 Score =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 124/307 (40%), Positives = 184/307 (59%), Gaps = 3/307 (0%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           +++R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++I+GVLHE ++I GV ED++
Sbjct: 15  DDSRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSLRIEGVLHEFTTIPGVKEDVS 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           DIILNIK + L    D    + I K GPG VT  D++    +EV N D  I  L+    +
Sbjct: 75  DIILNIKSLVLSSDSDEPVSMFIRKEGPGEVTGADVEVPAGVEVHNQDLHIATLNEQGKL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +E+TV +G GYVPA    +E   IG I +D +YSP+ KVSY VE+ R  Q  D+DKL +
Sbjct: 135 EIEMTVERGRGYVPAATASSE---IGRIPVDQIYSPVLKVSYKVEATRVEQRTDFDKLIL 191

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T  SIT  D++A A + L +  G+        + ++   + +      A    +E+L
Sbjct: 192 DVETKNSITARDAMASAGKTLVELFGLAQELNHEAEGIEIGPSPQESEHIAAYSMPIEDL 251

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
             SVRS NCL+ E I  +G+L  RTE+D+L + NFG+KS+ E+K  L  +GL L      
Sbjct: 252 NFSVRSYNCLKREEIHTVGELAARTESDLLDIRNFGQKSINEVKVKLAGLGLGLKDAPEG 311

Query: 324 WPPESIE 330
           +    IE
Sbjct: 312 FDITDIE 318


>gi|300932966|ref|ZP_07148222.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           resistens DSM 45100]
          Length = 337

 Score =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 126/314 (40%), Positives = 183/314 (58%), Gaps = 3/314 (0%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            +     + +R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I+GVLHE ++I 
Sbjct: 8   VLTEEYIDASRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRIEGVLHEFTTIP 67

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED++DIILNIK + L    D    + + K GPG VT  DI     +EV NPD  I  
Sbjct: 68  GVKEDVSDIILNIKSLVLSSDSDEPVVMNLHKEGPGAVTGADIMPPAGVEVHNPDLHIAT 127

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           L+    + +EL V +G GYVPA    +E   IG I +D +YSP+ KVSY VE+ R  Q  
Sbjct: 128 LNEQGKLDIELVVERGRGYVPAATASSE---IGRIPVDQIYSPVLKVSYKVEATRVEQRT 184

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           D+DKL + ++T  SIT  D++A A + L +  G+        + ++   + +      A 
Sbjct: 185 DFDKLILDVETKNSITARDAMASAGKTLVELFGLAQELNNEAEGIEIGPSPQESEHIAAY 244

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E+L  SVRS NCL+ E I  +G+L  RTE+D+L + NFG+KS+ E+K  L  +GL 
Sbjct: 245 SMPIEDLNFSVRSYNCLKREEIHTVGELAARTESDLLDIRNFGQKSINEVKVKLAGLGLG 304

Query: 317 LGMNLPDWPPESIE 330
           L      +    IE
Sbjct: 305 LKDAPEGFDINDIE 318


>gi|238922857|ref|YP_002936370.1| DNA-directed RNA polymerase, alpha subunit [Eubacterium rectale
           ATCC 33656]
 gi|238874529|gb|ACR74236.1| DNA-directed RNA polymerase, alpha subunit [Eubacterium rectale
           ATCC 33656]
          Length = 319

 Score =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 134/317 (42%), Positives = 209/317 (65%), Gaps = 6/317 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP  IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFEKP-KIEIAEIS-EDKTYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+NIK + ++ +   +  K   I   G GVVTA DIQ  +DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNIKNLAIRNNSSTNEPKVAYIEFEGEGVVTAADIQVDSDI 120

Query: 126 EVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E+LNP+  I +L+  A   + MELT++ G GYV A+ ++ E+ PIG++ +D++Y+P+++V
Sbjct: 121 EILNPELEIAHLNGGADSKLYMELTITNGRGYVGAEKNKNEDTPIGVLAVDSIYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + TVE+ R GQV DYDKL++ + T+G++  +++V+LA+++L + L +FI+  E  ++V  
Sbjct: 181 NLTVENTRVGQVTDYDKLTLDVFTNGTLEPDEAVSLAAKVLSEHLNLFIDLSEAAQQVDV 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  ++      L   ++ELELSVRS NCL+   I  + +LI RT  DM+++ N GRKSL
Sbjct: 241 MVEKENDAQEKVLEMNIDELELSVRSYNCLKRAGINTVAELINRTPEDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFLGMN 320
            E+   L  +GL L   
Sbjct: 301 EEVLAKLKELGLELNQT 317


>gi|225630278|ref|YP_002727069.1| DNA-directed RNA polymerase alpha subunit [Wolbachia sp. wRi]
 gi|225592259|gb|ACN95278.1| DNA-directed RNA polymerase alpha subunit [Wolbachia sp. wRi]
          Length = 355

 Score =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 162/346 (46%), Positives = 238/346 (68%), Gaps = 12/346 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            N  +LIKP++++ I    +   ++ ++ EPL  GFA TLGNALRRV++SSL+G+A+  +
Sbjct: 11  SNLDKLIKPSSVKVI--SDDSSEKSDIVLEPLESGFALTLGNALRRVMLSSLKGSAVYGI 68

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+GV HE +SI+GV ED+TDI+LN+  +  K++G S+K + +  +GP  V AG I+T +
Sbjct: 69  KIEGVTHEFTSIQGVREDVTDIVLNMGMLRCKLNGASNKCLNLNAKGPCQVLAGMIETDD 128

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--------TENDPIGLITIDA 175
              ++N D +IC L  +  + M + V+ G GY+P   ++        +E D IG I ++A
Sbjct: 129 QCSIVNKDLLICTLGQNVELNMTIYVASGKGYLPVTKYKENELLKLMSEQDLIGFIPVNA 188

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI--N 233
           LYSP+ +VSY VE++R GQV D DKL ++I+TDG+I+   +V  A+RILQ+QL  FI  +
Sbjct: 189 LYSPVNRVSYRVENSRVGQVTDKDKLILSIETDGTISPSQAVDSAARILQEQLQPFISSD 248

Query: 234 FEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
               K +V      K L ++P LL+KV+E+ELSVRS NCL+ ENI Y+GDL+Q+TE +ML
Sbjct: 249 VSYKKSQVSSSSGAKDLGYDPVLLRKVDEMELSVRSHNCLKNENITYIGDLVQKTEGEML 308

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           R ANFGRKSL EIK VL   GL LGMN+ +WPP+ I+ELAK++ D+
Sbjct: 309 RTANFGRKSLNEIKAVLTNFGLSLGMNVLNWPPKDIDELAKQHTDE 354


>gi|148284191|ref|YP_001248281.1| DNA-directed RNA polymerase alpha chain [Orientia tsutsugamushi
           str. Boryong]
 gi|172047207|sp|A5CCI9|RPOA_ORITB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|146739630|emb|CAM79419.1| DNA-directed RNA polymerase alpha chain [Orientia tsutsugamushi
           str. Boryong]
          Length = 342

 Score =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 171/341 (50%), Positives = 233/341 (68%), Gaps = 5/341 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
            + KNW  LIKP  ++Y  +     N   M+ EPL RG   TLGN+LRRVL+SSLRGAAI
Sbjct: 4   FLAKNWSSLIKPTKVQYEAVDN-NPNIKTMVVEPLERGLGLTLGNSLRRVLLSSLRGAAI 62

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+++I GV HE+S + GV EDLTDIILNI+ + +KM       + +   GP VVTAG I 
Sbjct: 63  TSIKIPGVEHELSPVSGVKEDLTDIILNIRDVIVKMDSVQKCNLRLEVTGPAVVTAGMIT 122

Query: 121 TVN--DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
             +  D+ +LNP HVICNL     + M+L   +G GYVP       + PIG I +DAL++
Sbjct: 123 VTDKQDVTILNPQHVICNLSKGFNLEMDLICEQGKGYVPTSCLHNSDSPIGAIHLDALFN 182

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY VE++  GQ+ +YDKL +T++T+G +  + ++ LA+RIL DQL +FINF+E +
Sbjct: 183 PVRRVSYKVENSMVGQMTNYDKLIITVETNGVVNPDAALGLAARILLDQLQVFINFQEVE 242

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +E  E + ++++  NP LLKKV ELELSVRS NCL+ ENIVY+GDL+ RTE  ML+ ANF
Sbjct: 243 EEKPEKLELQTI--NPVLLKKVYELELSVRSQNCLKNENIVYVGDLVARTETQMLKTANF 300

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           GRKSL E+K VL    L  GM    WPP+++E LAKK+ED+
Sbjct: 301 GRKSLNELKKVLANFNLEFGMKDIGWPPDNLESLAKKHEDQ 341


>gi|189183975|ref|YP_001937760.1| DNA-directed RNA polymerase subunit alpha [Orientia tsutsugamushi
           str. Ikeda]
 gi|238692016|sp|B3CT29|RPOA_ORITI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|189180746|dbj|BAG40526.1| DNA-directed RNA polymerase alpha chain [Orientia tsutsugamushi
           str. Ikeda]
          Length = 342

 Score =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 172/341 (50%), Positives = 233/341 (68%), Gaps = 5/341 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
            + KNW  LIKP  ++Y  +     N   M+ EPL RG   TLGN+LRRVL+SSLRGAAI
Sbjct: 4   FLAKNWSSLIKPTKVQYEAVDN-NPNIKTMVVEPLERGLGLTLGNSLRRVLLSSLRGAAI 62

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+++I GV HE+S + GV EDLTDIILNI+ + +KM       + +   GP VVTAG I 
Sbjct: 63  TSIKIPGVEHELSPVSGVKEDLTDIILNIRDVIVKMDSVQKCNLRLEVTGPAVVTAGMIT 122

Query: 121 TVN--DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
             +  D+ +LNP HVICNL     + M+L   +G GYVP       + PIG I +DAL++
Sbjct: 123 VTDKQDVTILNPQHVICNLSKGFNLEMDLICEQGKGYVPTSCLHNSDSPIGAIHLDALFN 182

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY VE++  GQ+ +YDKL +T++T+G +  + ++ LA+RIL DQL +FINF+E +
Sbjct: 183 PVRRVSYKVENSMVGQMTNYDKLIITVETNGVVNPDAALGLAARILLDQLQVFINFQEVE 242

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +E  E + ++++  NP LLKKV ELELSVRS NCL+ ENIVY+GDL+ RTE  ML+ ANF
Sbjct: 243 EEKPEKLELQTI--NPVLLKKVYELELSVRSQNCLKNENIVYVGDLVARTETQMLKTANF 300

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           GRKSL E+K VL    L  GM    WPPE++E LAKK+ED+
Sbjct: 301 GRKSLNELKKVLANFNLEFGMKDIGWPPENLESLAKKHEDQ 341


>gi|317501801|ref|ZP_07959987.1| DNA-directed RNA polymerase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331088678|ref|ZP_08337588.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae
           bacterium 3_1_46FAA]
 gi|316896834|gb|EFV18919.1| DNA-directed RNA polymerase [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330407201|gb|EGG86704.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae
           bacterium 3_1_46FAA]
          Length = 320

 Score =  330 bits (845), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 133/317 (41%), Positives = 203/317 (64%), Gaps = 7/317 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL G+AI++V+IDG
Sbjct: 3   DFNKPN-IEITDVS-EDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGSAISSVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVND 124
           VLHE SSI GV ED+T+II+N+K + ++     D  K V I   G GVVT  DI     D
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNLKSLAIRNMSESDEPKTVYIEFEGEGVVTGADININDPD 120

Query: 125 IEVLNPDHVICNLD--VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           IE++NPD VI  L    D  + MELT++KG GYV +  ++TE+ PIG+I ID++Y+P+++
Sbjct: 121 IEIVNPDQVIATLSGGKDCRLNMELTITKGRGYVSSDKNKTEDMPIGVIAIDSIYTPVER 180

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+ TVE+ R GQ+ DYDKL++ + T G++  +++V+LA+++L + L +F++  E  +  +
Sbjct: 181 VNLTVENTRVGQITDYDKLTLDVWTKGTMLPDEAVSLAAKVLSEHLKLFVDLSEVAQVAE 240

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
             I  +       L   ++ELELSVRS NCL+   I  + +L  +T  DM+++ N GRKS
Sbjct: 241 VMIEKEDDEKEKVLEMSIDELELSVRSYNCLKRAGINTVEELTNKTPEDMMKVRNLGRKS 300

Query: 303 LVEIKGVLGTMGLFLGM 319
           L E+   L  + L L  
Sbjct: 301 LEEVLAKLKELNLELNQ 317


>gi|125625115|ref|YP_001033598.1| DNA-directed RNA polymerase subunit alpha [Lactococcus lactis
           subsp. cremoris MG1363]
 gi|158512804|sp|A2RNM7|RPOA_LACLM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|124493923|emb|CAL98918.1| RNA polymerase alpha subunit [Lactococcus lactis subsp. cremoris
           MG1363]
 gi|300071923|gb|ADJ61323.1| DNA-directed RNA polymerase subunit alpha [Lactococcus lactis
           subsp. cremoris NZ9000]
          Length = 312

 Score =  330 bits (845), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 127/311 (40%), Positives = 199/311 (63%), Gaps = 4/311 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP   ++     E EN    + EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+G
Sbjct: 3   EFEKPKITKF----DESENYGKFVVEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE ++I GV ED+  I+L +KGI +K   +S K++ +   GP  VTAGDI T +DIE+
Sbjct: 59  VQHEFATIPGVREDVIQIVLAVKGIAIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N DH + ++     +R  +TV KG+GYVPA  ++ +  PIG I +D++Y+P+ KV+Y V
Sbjct: 119 VNKDHYLFSIAEGHSMRAVMTVKKGYGYVPADENKVDGAPIGTIAVDSIYTPVSKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    YDKL++ I T+G+I  +++++L+++IL D L +F++  E   E +  +  
Sbjct: 179 EPARVGGDSSYDKLTLEITTNGTIVSDEALSLSAKILTDHLNLFVDLSEVAAEAETLVVK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
             +     L K +EE++ SVR+ N L+   I  + D+++ +EADM+++ N G KS+ E+K
Sbjct: 239 DEVKTERVLDKIIEEMDFSVRTYNGLKRAGINTVADIVEMSEADMIKVKNLGHKSVEEVK 298

Query: 308 GVLGTMGLFLG 318
             L  +GL L 
Sbjct: 299 VKLTELGLSLK 309


>gi|187735995|ref|YP_001878107.1| DNA-directed RNA polymerase, alpha subunit [Akkermansia muciniphila
           ATCC BAA-835]
 gi|187426047|gb|ACD05326.1| DNA-directed RNA polymerase, alpha subunit [Akkermansia muciniphila
           ATCC BAA-835]
          Length = 374

 Score =  330 bits (845), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 127/311 (40%), Positives = 190/311 (61%), Gaps = 5/311 (1%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P+ +E I     + N    +AEP   G+ HTLGN+LRRVL+ SL GAAIT+V+I G  HE
Sbjct: 23  PSRLEKIE-DPNDANHLTFVAEPFENGYGHTLGNSLRRVLLGSLEGAAITSVRIAGAQHE 81

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            SS+ GV ED+T+I+LN+K +  K +G   + +++     GVVTA DI      +V+NPD
Sbjct: 82  FSSLPGVVEDVTEIVLNLKKVKFKHNGKEPRLLSLRVHKQGVVTAADIADDTVYQVVNPD 141

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
            +IC LD D +   E  V  G G+     ++  + PIG+I ID+++SP+ +V Y+V++ R
Sbjct: 142 QIICTLDQDTMFECEFQVRVGRGFATGDENKVPDMPIGVIPIDSIFSPVTRVKYSVQNTR 201

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI----NV 247
            GQ+ DYDKL + + TDG I   D++  AS IL+  L +F+N+++ +   +E      + 
Sbjct: 202 VGQMTDYDKLILEVWTDGRIAPADAMLQASAILRHHLDVFVNYDDKQVNFEEAPSAVQDE 261

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           ++      L   V E+ELSVR+ NCL   NI  +G L  ++E++ML+  NFG+KSL EIK
Sbjct: 262 ETARLRKLLNMSVNEIELSVRAANCLNNANITTVGQLAMKSESEMLKYRNFGKKSLNEIK 321

Query: 308 GVLGTMGLFLG 318
             L  +GL LG
Sbjct: 322 DKLLELGLSLG 332


>gi|301168432|emb|CBW28022.1| DNA-directed RNA polymerase alpha chain [Bacteriovorax marinus SJ]
          Length = 337

 Score =  330 bits (845), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 147/324 (45%), Positives = 219/324 (67%), Gaps = 4/324 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
            + KNW  +I+P ++E       + N    +A+PL RG+  TLGN+LRR L+SSL+GA I
Sbjct: 4   FVAKNWTNMIRPVSLEADN-ESMKANYGKFVAKPLERGYGQTLGNSLRRALLSSLQGAGI 62

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
            A++I+GV HE  +I  V E++++IILN+K +  K+ G     +T+ K G G VTAGDI 
Sbjct: 63  VAIRIEGVEHEFGTINNVKEEVSEIILNLKEVFFKLKGKEDTVLTLEKSGEGPVTAGDIS 122

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSP 179
               +EVLNP+HVICN+     +++EL V++G GYV A  ++ E + P+G I +D L+SP
Sbjct: 123 ESASLEVLNPEHVICNISSGGSIKVELKVARGKGYVTASENKEEYDLPVGWIYVDTLFSP 182

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           + +V++TV ++R G+  D+DKL++ + T+  I  +D+VA +++IL+DQL +F+NFE+ ++
Sbjct: 183 VHRVNFTVTNSRVGKRTDFDKLTLEVWTNAGIQPQDAVAFSAKILRDQLAVFLNFEDEEE 242

Query: 240 EV--KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            V  ++     S P N ALLK V ELELSVRS NCL+  NI Y+ +L+ +TE +MLR  N
Sbjct: 243 VVRLEKAPAQASSPANSALLKPVSELELSVRSANCLQNANIKYIYELVSKTEGEMLRTKN 302

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNL 321
           FGRKSL EIK +L  MGL LGM +
Sbjct: 303 FGRKSLNEIKEILSNMGLGLGMKV 326


>gi|308171332|gb|ADO15985.1| RpoA [Vibrio ichthyoenteri ATCC 700023]
          Length = 323

 Score =  330 bits (845), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 142/329 (43%), Positives = 214/329 (65%), Gaps = 11/329 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++ +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MRGSVTEFLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEITNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYSVDAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           N G+KSL EIK VL + GL LGM L +WP
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWP 323


>gi|291544484|emb|CBL17593.1| DNA-directed RNA polymerase subunit alpha [Ruminococcus sp. 18P13]
          Length = 318

 Score =  330 bits (845), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 129/313 (41%), Positives = 196/313 (62%), Gaps = 3/313 (0%)

Query: 9   LIKPNNIEYIVLG-QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           L K    E   +  + +      +  PL RG+  TLGN+LRRVL+SSL G A+ +V+IDG
Sbjct: 2   LEKIEKPEIDTVELRSDGKYGKFVLAPLERGYGITLGNSLRRVLLSSLPGVAVNSVKIDG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE+S+I GV ED+T+IIL+IKG+  K+ GD  K V I   G   VTAGDI+T +++ +
Sbjct: 62  VHHELSTIPGVKEDVTEIILSIKGLTAKLYGDGPKTVYIEATGECEVTAGDIKTDSEVNI 121

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
           L+P   I  L  DA + ME+T+ KG GYV A+ ++    N PI +I +D++Y+P+ KV+Y
Sbjct: 122 LDPGMHIATLGKDASLYMEITLDKGRGYVSAERNKQLMPNLPIDVIAVDSIYTPVLKVNY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVE  R GQV DYDKL+M + TDG+I+ +++++ A+ +L + L +F++  E     +  +
Sbjct: 182 TVEDTRLGQVTDYDKLTMEVWTDGTISAKEALSQAANLLNEHLKLFVDLSEEASIAEVLV 241

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                     L   +EEL+LSVRS NCL+   I  + DLI ++E +M+++ N G+KS  E
Sbjct: 242 EKDDKGKEKILEMTIEELDLSVRSFNCLKRAGINTVDDLINKSEEEMMKVRNLGKKSFDE 301

Query: 306 IKGVLGTMGLFLG 318
           +K  L ++G  L 
Sbjct: 302 VKEKLQSLGFDLS 314


>gi|308171338|gb|ADO15988.1| RpoA [Vibrio caribbenthicus]
          Length = 323

 Score =  330 bits (845), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 141/329 (42%), Positives = 213/329 (64%), Gaps = 11/329 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++ +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MRGSVTEFLKPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +++LN+KG+ +++  G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEVLLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           N G+KSL EIK VL + GL LGM L +WP
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWP 323


>gi|167748457|ref|ZP_02420584.1| hypothetical protein ANACAC_03201 [Anaerostipes caccae DSM 14662]
 gi|317472010|ref|ZP_07931342.1| DNA-directed RNA polymerase [Anaerostipes sp. 3_2_56FAA]
 gi|167652449|gb|EDR96578.1| hypothetical protein ANACAC_03201 [Anaerostipes caccae DSM 14662]
 gi|316900414|gb|EFV22396.1| DNA-directed RNA polymerase [Anaerostipes sp. 3_2_56FAA]
          Length = 318

 Score =  330 bits (845), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 136/313 (43%), Positives = 202/313 (64%), Gaps = 5/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN IE   +  E+      + EPL RG+  TLGN+LRR+++SSL GAA++AV+I G
Sbjct: 3   EFEKPN-IEISEIS-EDNRFGRFVVEPLVRGYGTTLGNSLRRIMLSSLPGAAVSAVKIKG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SS+ GV ED+ +II+NIK + +K +   D  K+  I   G GVVTAGDI+  +DI
Sbjct: 61  VLHEFSSVPGVKEDVPEIIMNIKSLAIKNNSSTDEPKQAFIECSGSGVVTAGDIKADSDI 120

Query: 126 EVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           E+LNPD VI  L   DA + MELT++KG GYV A     E + I  I +DA+Y+P+++V+
Sbjct: 121 EILNPDMVIATLSGDDAHLDMELTITKGRGYVGADKADKEGNSIDEIAVDAIYTPVERVN 180

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
             VE+ R GQV DYDKL++ + T+G+++ +++V+LA+++L + L +F++  E  K  +  
Sbjct: 181 LKVENTRVGQVTDYDKLTLDVFTNGTLSPDEAVSLAAKVLCEHLNLFVDLSENAKTAEVM 240

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +  +       L   ++ELELSVRS NCL+   I  + +L  +T  DM+++ N GRKSL 
Sbjct: 241 VEKEDDEKEKVLEMSIDELELSVRSYNCLKRAGINTVEELTNKTSEDMMKVRNLGRKSLE 300

Query: 305 EIKGVLGTMGLFL 317
           E+   L  +GL L
Sbjct: 301 EVLAKLNELGLAL 313


>gi|225020484|ref|ZP_03709676.1| hypothetical protein CORMATOL_00491 [Corynebacterium matruchotii
           ATCC 33806]
 gi|305679751|ref|ZP_07402561.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           matruchotii ATCC 14266]
 gi|224946873|gb|EEG28082.1| hypothetical protein CORMATOL_00491 [Corynebacterium matruchotii
           ATCC 33806]
 gi|305660371|gb|EFM49868.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           matruchotii ATCC 14266]
          Length = 341

 Score =  329 bits (844), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 123/323 (38%), Positives = 189/323 (58%), Gaps = 7/323 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   EY V    + +R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+IDGVLH
Sbjct: 6   RPRLTEYPV----DNSRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVKIDGVLH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E ++I GV ED++DI+LNIKG+ +    D    + +   G G VTAG I+    +E+ NP
Sbjct: 62  EFTTITGVKEDVSDILLNIKGLAISSDSDEPVVMYLRAEGAGEVTAGTIEPPAGVEIHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVP---AKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           D  I  L+    + +E+ V +G GYVP   +    +    IG I +D +YSP+ KVSY V
Sbjct: 122 DLHIATLNDQGRLEIEMVVERGRGYVPVSSSTTTNSGTTEIGRIQVDQIYSPVLKVSYNV 181

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R  Q  D+DKL++ ++T  SI+  ++ A A + L +  G+        + ++   + 
Sbjct: 182 EATRVEQRTDFDKLTIDVETKNSISPRNAFASAGKTLVELFGLARELNVSAEGIEVGPSP 241

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +      A    +EEL  SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K
Sbjct: 242 QETEHIAAYGMPIEELRFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVK 301

Query: 308 GVLGTMGLFLGMNLPDWPPESIE 330
             L  +GL L     D+ P  +E
Sbjct: 302 IKLAGLGLTLKDAPEDFDPTQLE 324


>gi|315652326|ref|ZP_07905318.1| DNA-directed RNA polymerase subunit alpha [Eubacterium saburreum
           DSM 3986]
 gi|315485449|gb|EFU75839.1| DNA-directed RNA polymerase subunit alpha [Eubacterium saburreum
           DSM 3986]
          Length = 330

 Score =  329 bits (844), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 128/312 (41%), Positives = 198/312 (63%), Gaps = 5/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     I EPL RG+  TLGN+LRR+++SSL G+A++ V+IDG
Sbjct: 16  DFEKPN-IEIAEIS-EDKKFGRFICEPLERGYGTTLGNSLRRIMLSSLPGSAVSQVKIDG 73

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKM--SGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+N+K + +K     +  K   I   G GV+TA DIQ    I
Sbjct: 74  VLHEFSSIPGVKEDVTEIIMNVKSLAIKNSAEDNEPKIAYIDFDGEGVITAEDIQCDPCI 133

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++N D VI  +       MELT++ G GYV +  ++ E+ PIG+I ID++Y+P+++V+ 
Sbjct: 134 EIINKDQVIATVSEG-KFYMELTITNGRGYVSSDKNKGEDTPIGVIAIDSIYTPVERVNL 192

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R GQV D+DKL++ + T+G++  +++V+LA+++L + L +FI+  +  K +   +
Sbjct: 193 RVENTRVGQVTDFDKLTLDVTTNGTLEPDEAVSLAAKVLSEHLNLFIDLSDNAKTIDVMV 252

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL E
Sbjct: 253 EKEEDDKEKVLEMNIDELELSVRSYNCLKRAGINTVEELCSRTSDDMMKVRNLGRKSLEE 312

Query: 306 IKGVLGTMGLFL 317
           +   L  +GL L
Sbjct: 313 VLQKLEELGLHL 324


>gi|116513027|ref|YP_811934.1| DNA-directed RNA polymerase subunit alpha [Lactococcus lactis
           subsp. cremoris SK11]
 gi|122939924|sp|Q02W51|RPOA_LACLS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116108681|gb|ABJ73821.1| DNA-directed RNA polymerase subunit alpha [Lactococcus lactis
           subsp. cremoris SK11]
          Length = 312

 Score =  329 bits (844), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 127/311 (40%), Positives = 199/311 (63%), Gaps = 4/311 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP   ++     E EN    + EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+G
Sbjct: 3   EFEKPKITKF----DESENYGKFVVEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE ++I GV ED+  I+L +KGI +K   +S K++ +   GP  VTAGDI T +DIE+
Sbjct: 59  VQHEFATIPGVREDVIQIVLAVKGIAIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N DH + ++     +R  +TV KG+GYVPA  ++ +  PIG I +D++Y+P+ KV+Y V
Sbjct: 119 VNKDHYLFSIAEGHSMRAVMTVKKGYGYVPADENKVDGAPIGTIAVDSIYTPVSKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    YDKL++ I T+G+I  +++++L+++IL D L +F++  E   E +  +  
Sbjct: 179 EPARVGGDSSYDKLTLEITTNGTIVSDEALSLSAKILTDHLNLFVDLSEVAAEAETLVVK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
             +     L K +EE++ SVR+ N L+   I  + D+++ +EADM+++ N G KS+ E+K
Sbjct: 239 DEVKTERVLDKIIEEMDFSVRAYNGLKRAGINTVTDIVEMSEADMIKVKNLGHKSVEEVK 298

Query: 308 GVLGTMGLFLG 318
             L  +GL L 
Sbjct: 299 VKLTELGLSLK 309


>gi|289449938|ref|YP_003475756.1| DNA-directed RNA polymerase subunit alpha [Clostridiales genomosp.
           BVAB3 str. UPII9-5]
 gi|289184485|gb|ADC90910.1| DNA-directed RNA polymerase, alpha subunit [Clostridiales genomosp.
           BVAB3 str. UPII9-5]
          Length = 321

 Score =  329 bits (844), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 129/320 (40%), Positives = 200/320 (62%), Gaps = 9/320 (2%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI+ N     KP  +   V  +   +    + EPL RG+  TLGN+LRRVL+SSL GAA+
Sbjct: 1   MIETN-----KP--VISTVALESNGSYGKFVVEPLDRGYGVTLGNSLRRVLLSSLPGAAV 53

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR--GPGVVTAGD 118
           TA++++G  HE S+++GV ED+T+IILN+K I +K++ D  K + +       GVVTAGD
Sbjct: 54  TAIRVEGAFHEFSTVEGVIEDMTEIILNVKCIRVKLNADGPKTIYLNTEEGRTGVVTAGD 113

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           I T  +++++NP+  I  L+ DA + MELTV  G GY  A+ ++  N PIG+I +D++++
Sbjct: 114 IVTDEEVQIMNPEQPIATLNGDARLFMELTVCSGIGYNSAERNKWPNQPIGVIPVDSIFT 173

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+KKV+Y+VE+ R GQ  D+DKL++ + TD +I  + +V+ A+ IL D L  F++ +   
Sbjct: 174 PVKKVNYSVENTRVGQFTDFDKLTLEVWTDRTIAADTAVSNAANILMDHLQYFVDLQGGP 233

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                     S   N  L   +E++  SVR+ NCL+   I  +GDL+ R+E DM+++ N 
Sbjct: 234 TGTGTRSYDGSGESNELLETAIEDMNFSVRTYNCLKRAGINVIGDLVIRSEDDMMKVRNL 293

Query: 299 GRKSLVEIKGVLGTMGLFLG 318
           G+KSL E+  +L  MGL L 
Sbjct: 294 GKKSLEEVIQILDEMGLSLA 313


>gi|190571569|ref|YP_001975927.1| DNA-directed RNA polymerase, alpha subunit [Wolbachia endosymbiont
           of Culex quinquefasciatus Pel]
 gi|213018971|ref|ZP_03334778.1| DNA-directed RNA polymerase, alpha subunit [Wolbachia endosymbiont
           of Culex quinquefasciatus JHB]
 gi|190357841|emb|CAQ55297.1| DNA-directed RNA polymerase, alpha subunit [Wolbachia endosymbiont
           of Culex quinquefasciatus Pel]
 gi|212995080|gb|EEB55721.1| DNA-directed RNA polymerase, alpha subunit [Wolbachia endosymbiont
           of Culex quinquefasciatus JHB]
          Length = 355

 Score =  329 bits (844), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 160/346 (46%), Positives = 232/346 (67%), Gaps = 12/346 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            N   L KPN I+ I    +   ++ ++ EPL  GFA TLG+ALRRV++SSLRG+A+  +
Sbjct: 11  GNLDRLTKPNAIKVI--SGDSSKKSDIVLEPLESGFALTLGHALRRVMLSSLRGSAVYGI 68

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I+GV HE +SI+GV ED+TDI LN+  +  K++  S+K + +  +GP  V AG I+T +
Sbjct: 69  KIEGVNHEFTSIQGVREDITDIALNMGMLRCKLNNTSNKCLNLSAKGPCQVLAGMIETDD 128

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--------ENDPIGLITIDA 175
              ++N D VIC L  D  + + + ++ G GY+    ++         E D IG I ++A
Sbjct: 129 QCSIVNKDLVICTLGQDVELNITIYIASGKGYLSVNKYKENEFLKSMNEQDLIGFIPVNA 188

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI--N 233
           LYSP+++VSY VE++R GQV D DKL ++I+TDG+I+   +V  A+RILQ+Q   FI  +
Sbjct: 189 LYSPVERVSYRVENSRVGQVTDKDKLILSIETDGTISPSQAVDYAARILQEQFQPFISSD 248

Query: 234 FEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
               K +V      K L ++P LL+KV+E+ELSVRS NCL+ ENI Y+GDL+Q+TE +ML
Sbjct: 249 MSYKKSQVSLSSGAKDLGYDPVLLRKVDEMELSVRSHNCLKNENITYIGDLVQKTEVEML 308

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           R ANFGRKSL EIK +L   GL LGMN+P+WPP+ I+ELAK++ D+
Sbjct: 309 RTANFGRKSLNEIKAILNNSGLSLGMNIPNWPPKDIDELAKQHTDE 354


>gi|58584576|ref|YP_198149.1| DNA-directed RNA polymerase subunit alpha [Wolbachia endosymbiont
           strain TRS of Brugia malayi]
 gi|75497934|sp|Q5GSW7|RPOA_WOLTR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|58418892|gb|AAW70907.1| DNA-directed RNA polymerase alpha subunit/40 kD subunit, RpoA
           [Wolbachia endosymbiont strain TRS of Brugia malayi]
          Length = 355

 Score =  329 bits (843), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 161/345 (46%), Positives = 236/345 (68%), Gaps = 12/345 (3%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           +  +L KPN+++ +     E  +  ++ EPL  GFA TLGNALRRV++SSL G+A+  ++
Sbjct: 12  SLDKLTKPNSMKVVSSDSSE--KGDIVLEPLESGFALTLGNALRRVMLSSLIGSAVYGIK 69

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           IDG+ HE +SI+GV ED+TDI+LN+  +  K++G S+K +++  +GP  V AG I+T + 
Sbjct: 70  IDGITHEFTSIQGVREDVTDIVLNMGMLRCKLNGTSNKCLSLSAKGPCQVLAGMIETDDQ 129

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--------ENDPIGLITIDAL 176
             ++N D +IC L  D  + M + V+ G GY+P   ++         E D I  I ++AL
Sbjct: 130 CSIVNKDLLICTLGQDVELNMTIYVASGKGYLPVTKYKENEFLKPMNEQDLISFIPVNAL 189

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI--NF 234
           YSPI +VSY VE++R GQV D DKL ++++TDG+I+   +V  A+RILQ+QL  FI  + 
Sbjct: 190 YSPINRVSYRVENSRVGQVTDKDKLILSVETDGTISPSQAVDSAARILQEQLQPFISSDI 249

Query: 235 EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
              K +V      K L ++P LL+KV+E+ELSVRS NCL+ ENI Y+GDL+Q+TE++MLR
Sbjct: 250 SYKKSQVSSPSGYKDLGYDPILLRKVDEMELSVRSHNCLKNENITYIGDLVQKTESEMLR 309

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            ANFGRKSL EIK VL   GL LGM++PDWPP+ I+ELA+++ D+
Sbjct: 310 TANFGRKSLNEIKAVLNNFGLSLGMDIPDWPPKDIDELARQHTDE 354


>gi|323141382|ref|ZP_08076273.1| DNA-directed RNA polymerase, alpha subunit [Phascolarctobacterium
           sp. YIT 12067]
 gi|322414131|gb|EFY04959.1| DNA-directed RNA polymerase, alpha subunit [Phascolarctobacterium
           sp. YIT 12067]
          Length = 321

 Score =  329 bits (843), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 141/318 (44%), Positives = 194/318 (61%), Gaps = 7/318 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  +   V   E+      + EPL RG+  TLGN+LRRVL+SSL GAA+T V+IDG
Sbjct: 3   EIEKPKMVTSDV--SEDGRYGKFVWEPLERGYGITLGNSLRRVLLSSLPGAAVTYVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE ++I GV ED+ DIILNIK + LKM G+  K + I   G   VTA +I   +D+E+
Sbjct: 61  VLHEFATIPGVREDVADIILNIKALCLKMEGEGEKILRIECSGEQEVTAANIIADSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  LD DAV  ME+ + KG GYVPA  ++  + PIG+I +D++YSPI +V + V
Sbjct: 121 LNPELHIATLDKDAVFNMEIHIDKGRGYVPADKNKQPDQPIGVIPVDSIYSPITRVKFAV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK----- 242
              R G V +YDKL++ + TDGSI  +++V +AS IL D L +F   +     +      
Sbjct: 181 NDTRVGNVTNYDKLTLEVWTDGSIKPDEAVDMASTILIDYLKLFQTSDGKGSVITVAGGS 240

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           E    +           +++L+LSVRS NCLR   I  + +LIQ+TEADM+++ N G KS
Sbjct: 241 EPEAPEPSKQEGQNTMSIDDLDLSVRSNNCLRRAGINTVEELIQKTEADMIKVRNLGSKS 300

Query: 303 LVEIKGVLGTMGLFLGMN 320
           L EIK  L  MGL    N
Sbjct: 301 LEEIKKKLEDMGLHFRKN 318


>gi|240145849|ref|ZP_04744450.1| DNA-directed RNA polymerase, alpha subunit [Roseburia intestinalis
           L1-82]
 gi|257201997|gb|EEV00282.1| DNA-directed RNA polymerase, alpha subunit [Roseburia intestinalis
           L1-82]
          Length = 319

 Score =  329 bits (843), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 135/316 (42%), Positives = 206/316 (65%), Gaps = 6/316 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP  IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFQKP-KIEIAEIS-EDKKYGKFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+NIK + ++ +   +  K   I   G GVVTA DIQ  +DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNIKNLAIRNNSSTNEPKVAYIEFEGEGVVTAADIQVDSDI 120

Query: 126 EVLNPDHVICNLDV--DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           ++LNPD VI NL+   D  + MELT++ G GYV A  ++TE+ PIG+I ID++Y+P+++V
Sbjct: 121 QILNPDLVIANLNGGPDCKLYMELTITNGRGYVSADKNKTEDIPIGVIAIDSIYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +  +E+ R GQ+ DYDKL++ + T+G++  +++V+LA+++L + L +FI+  E  ++   
Sbjct: 181 NLLIENTRVGQITDYDKLTLDVYTNGTLEPDEAVSLAAKVLSEHLSLFIDLSEAAQQADV 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            I  +       L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL
Sbjct: 241 MIEKEDNAKEKVLEMNIDELELSVRSYNCLKRAGINTVEELTNRTPEDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFLGM 319
            E+   L  +GL L  
Sbjct: 301 EEVLAKLKELGLQLNQ 316


>gi|283780399|ref|YP_003371154.1| DNA-directed RNA polymerase subunit alpha [Pirellula staleyi DSM
           6068]
 gi|283438852|gb|ADB17294.1| DNA-directed RNA polymerase, alpha subunit [Pirellula staleyi DSM
           6068]
          Length = 330

 Score =  329 bits (843), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 124/325 (38%), Positives = 192/325 (59%), Gaps = 5/325 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +   W+    P+ +               +AEP  RGF  T+GN+LRR+L+SSL G+AIT
Sbjct: 1   MHIRWRGFELPSIVN-CDATTLTSTYGKFVAEPFERGFGTTIGNSLRRILLSSLEGSAIT 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            ++I G  HE ++I GV ED+TDI+LN+K + +K   +S + +T+ K   G++T  D+Q 
Sbjct: 60  QIKIRGAQHEFTTIPGVLEDVTDIVLNVKSLVVKNHSESTRVITVEKNTTGLITGADVQV 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +D+E++N +HV+  L  +    ME+ V  G GY+PA  H T +  IG+I IDA++SPI 
Sbjct: 120 DSDVEIINKNHVLATLTDNVPFMMEMVVENGRGYIPATEHSTGDHEIGIIPIDAVFSPIT 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +V Y VE  R GQ  +YD+L++ I T+GSI  E ++  +++IL+  L  F+ + E    V
Sbjct: 180 RVRYEVEETRVGQKTNYDRLTLEIWTNGSIHPEMALVESAKILRKHLNPFVQYSELGPRV 239

Query: 242 KED----INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
                    V     +  L   + EL+LSVR+ NCL  ENI  + DL+Q+TE  +L + N
Sbjct: 240 HAPSRGGSPVVDGALDGKLAMSLAELKLSVRAMNCLESENIHTVRDLVQKTEDQLLEVRN 299

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLP 322
           FG  +L E+K  L  +G++LGM +P
Sbjct: 300 FGETTLNEVKDKLHDLGMYLGMRVP 324


>gi|291286339|ref|YP_003503155.1| DNA-directed RNA polymerase, alpha subunit [Denitrovibrio
           acetiphilus DSM 12809]
 gi|290883499|gb|ADD67199.1| DNA-directed RNA polymerase, alpha subunit [Denitrovibrio
           acetiphilus DSM 12809]
          Length = 335

 Score =  329 bits (843), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 148/324 (45%), Positives = 220/324 (67%), Gaps = 4/324 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M+  N+ E+IKP  IE   +G+  +     +AEP  +GF  T+GNALRRVL++++ G A+
Sbjct: 1   MVIMNFHEIIKPRKIE--AVGEVTDRYGEYVAEPYEKGFGITIGNALRRVLLATIEGTAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
             V+IDGV +E ++++GV+ED+ DI++NIK ++LK+     +RV I K G G VTAGDI 
Sbjct: 59  VGVKIDGVSNEFATLEGVYEDVVDILMNIKMLDLKLHTHETRRVYIKKTGEGPVTAGDIT 118

Query: 121 TVNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
               +E+L PD  IC +   +  + ME  V +G GYVPA+    + D I ++++DA+++P
Sbjct: 119 GDTMVEILTPDQHICTITDPNKELNMEFVVQRGIGYVPAEELEKDYDEIDMLSVDAVFTP 178

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           IKKV+Y V++AR GQ  DYD+L++ ++TDGSI  ED++  A++I++DQ+ +FINF+EP  
Sbjct: 179 IKKVNYHVDNARVGQSTDYDRLTLEVETDGSINPEDAIGFAAKIIKDQMNLFINFDEPVV 238

Query: 240 EVKEDINVKSLPFNPALLKK-VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           EVK+D           LL K +EELELSVR+ NCL+  NI  + +L  +T+A+ML+  NF
Sbjct: 239 EVKQDEEENQNDQLLDLLDKSIEELELSVRAYNCLKNANIKTLAELCMKTDAEMLKTKNF 298

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLP 322
           GRKSL EIK VL  +GL LGM+L 
Sbjct: 299 GRKSLEEIKKVLQELGLSLGMDLE 322


>gi|302336353|ref|YP_003801560.1| DNA-directed RNA polymerase subunit alpha [Olsenella uli DSM 7084]
 gi|301320193|gb|ADK68680.1| DNA-directed RNA polymerase subunit alpha [Olsenella uli DSM 7084]
          Length = 313

 Score =  329 bits (843), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 127/316 (40%), Positives = 193/316 (61%), Gaps = 7/316 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E I+P     + + +  EN   + AEPL RG+  TLGN+LRRVL+SSL GAA+ A+QI
Sbjct: 1   MSEFIRPQ----VSVEEISENLARVSAEPLERGYGDTLGNSLRRVLLSSLEGAAVEAIQI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVND 124
           DGV HE ++++GV+ED+TDI+LN+KG+  +  G       +I   GP  VT GD +   +
Sbjct: 57  DGVQHEFTTVEGVYEDVTDIVLNVKGLVFRSMGTGDEATASISIDGPCTVTGGDFKVPAE 116

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            E++N D VIC L   A + M++ +  G GYV    +  + DPIG+I +D+LYSP+++ +
Sbjct: 117 FELVNEDQVICTLGEGAHLSMQMRIGTGRGYVAGDDNERDGDPIGIIHVDSLYSPVRRCA 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
             VE  R GQ  +YD+L + ++TDGSIT  D+V  A+ I+   +  F+   + ++ V++ 
Sbjct: 177 KAVEPCRVGQHTNYDRLVLEVETDGSITPRDAVVDAANIVNQHMSAFMALADEEEPVEDA 236

Query: 245 I--NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                     N  L K++E+L+LSVRS NCL+   I  +  L++ +E D+L + NFG KS
Sbjct: 237 SIFATGVEEDNTELDKQIEDLDLSVRSYNCLKRAGIHSVRQLVEFSENDLLNIRNFGVKS 296

Query: 303 LVEIKGVLGTMGLFLG 318
           + E+K  L TMGL L 
Sbjct: 297 IEEVKDKLETMGLGLK 312


>gi|227549868|ref|ZP_03979917.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           lipophiloflavum DSM 44291]
 gi|227078123|gb|EEI16086.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           lipophiloflavum DSM 44291]
          Length = 337

 Score =  328 bits (842), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 122/312 (39%), Positives = 188/312 (60%), Gaps = 2/312 (0%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                + NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I G+
Sbjct: 10  TEEYIDTNRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTINGI 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E++++IILN+K I L    D    + + K GPG VTAGDI+   D+ + NPD  I +L+
Sbjct: 70  KENVSEIILNVKNIVLSSDSDEPVVLYLSKEGPGDVTAGDIELTADVAIHNPDLHIASLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
             A + MEL V +G GYVPA  +       G I +D +YSP+ +V+Y VE+ R  Q  D+
Sbjct: 130 DSARLEMELVVERGRGYVPAMPYAGGEA--GRIPVDQIYSPVTRVAYKVEATRVEQRTDF 187

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  S+T  D++A A   L +  G+        + ++   + +   +  A   
Sbjct: 188 DKLIIDVETKNSMTARDALASAGSTLVELFGLARELNTAAEGLEIGPSPQETEYIAAYNL 247

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L  SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L ++GL L 
Sbjct: 248 PIEDLNFSVRSYNCLKRQEIHSVGELAEYTESDLLDIRNFGQKSINEVKIKLASLGLTLK 307

Query: 319 MNLPDWPPESIE 330
               D+ P  IE
Sbjct: 308 DAPEDFDPTQIE 319


>gi|167759833|ref|ZP_02431960.1| hypothetical protein CLOSCI_02196 [Clostridium scindens ATCC 35704]
 gi|167662452|gb|EDS06582.1| hypothetical protein CLOSCI_02196 [Clostridium scindens ATCC 35704]
          Length = 322

 Score =  328 bits (842), Expect = 6e-88,   Method: Composition-based stats.
 Identities = 134/315 (42%), Positives = 203/315 (64%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAAI+ V+IDG
Sbjct: 6   DFNKPN-IEITEIS-EDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAISQVKIDG 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+N+K + +K     D  K   I   G GVVTA DIQ   DI
Sbjct: 64  VLHEFSSIPGVKEDVTEIIMNLKSLAIKNTSETDEPKTAYIEFEGEGVVTAADIQVDQDI 123

Query: 126 EVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E++NP+ VI  L+  A   + MELT+++G GYV A  ++ +  PI +I ID++Y+P+++V
Sbjct: 124 EIMNPETVIATLNGGADSKLYMELTITRGRGYVSADKNKNDELPIAVIPIDSIYTPVERV 183

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + TVE+ R GQ+ D+DKL++ + T+G++  +++V+LA+++L + L +FI+  E  +  + 
Sbjct: 184 NLTVENTRVGQITDFDKLTLDVYTNGTLLPDEAVSLAAKVLSEHLKLFIDLSEVAQAAEV 243

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            I  +       L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL
Sbjct: 244 MIEKEDDEKEKVLEMSIDELELSVRSYNCLKRAGINTVEELTNRTPEDMMKVRNLGRKSL 303

Query: 304 VEIKGVLGTMGLFLG 318
            E+   L  +GL L 
Sbjct: 304 EEVLAKLDELGLSLS 318


>gi|15674050|ref|NP_268225.1| DNA-directed RNA polymerase subunit alpha [Lactococcus lactis
           subsp. lactis Il1403]
 gi|13878751|sp|Q9CDY3|RPOA_LACLA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|12725120|gb|AAK06166.1|AE006436_15 DNA-directed RNA polymerase alpha chain [Lactococcus lactis subsp.
           lactis Il1403]
          Length = 312

 Score =  328 bits (842), Expect = 6e-88,   Method: Composition-based stats.
 Identities = 126/311 (40%), Positives = 198/311 (63%), Gaps = 4/311 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP   ++     E EN    + EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+G
Sbjct: 3   EFEKPKITKF----DESENYGKFVVEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE ++I GV ED+  I+L +KGI +K   +S K++ +   GP  VTAGDI T +DIE+
Sbjct: 59  VQHEFATIPGVREDVIQIVLAVKGIAIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N DH + ++     +R  +TV KG+GYVP   ++ +  PIG I +D++Y+P+ KV+Y V
Sbjct: 119 VNKDHYLFSIAEGHSMRAVMTVKKGYGYVPDDENKVDGAPIGTIAVDSIYTPVSKVNYQV 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E AR G    YDKL++ I T+G+I  +++++L+++IL D L +F++  E   E +  +  
Sbjct: 179 EPARVGGDSSYDKLTLEITTNGTIVSDEALSLSAKILTDHLNLFVDLSEVAAEAETLVVK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
             +     L K +EE++ SVR+ N L+   I  + D+++ +EADM+++ N G KS+ E+K
Sbjct: 239 DEVKTERVLDKIIEEMDFSVRAYNGLKRAGINTVADIVEMSEADMIKVKNLGHKSVEEVK 298

Query: 308 GVLGTMGLFLG 318
             L  +GL L 
Sbjct: 299 VKLTELGLSLK 309


>gi|139438878|ref|ZP_01772338.1| Hypothetical protein COLAER_01342 [Collinsella aerofaciens ATCC
           25986]
 gi|133775589|gb|EBA39409.1| Hypothetical protein COLAER_01342 [Collinsella aerofaciens ATCC
           25986]
          Length = 313

 Score =  328 bits (841), Expect = 7e-88,   Method: Composition-based stats.
 Identities = 121/316 (38%), Positives = 185/316 (58%), Gaps = 7/316 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E I+P     + + +  E    +  EPL RG+  TLGN+LRRVL+SSL GAA+ A+QI
Sbjct: 1   MSEFIRPQ----VQVEEINETSARVSVEPLERGYGDTLGNSLRRVLLSSLEGAAVEAIQI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLK-MSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           DG  HE  +I  + ED+TDI+LN+KG+  + +        TI   GP  VT  D    ++
Sbjct: 57  DGAQHEFMTIPNMVEDVTDIVLNVKGLVFRALGTTDEATATISVDGPCEVTGADFFIPSE 116

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            E++NP+  I  L     + M + +  G GYV  + ++ +NDPIG+I +D+LYSP+ + +
Sbjct: 117 FELVNPEQHIATLTEGGHLTMSMRIGYGRGYVSGEANKRDNDPIGVIHVDSLYSPVSRCA 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
             VE+ R GQ  DYD+L + I+T+GSI   D+V  A+ I+   +  F+N  E  +  +E 
Sbjct: 177 KLVEACRVGQHTDYDRLVLEIETNGSIAPRDAVVQAANIINQHMAAFMNLAETPEVEEEA 236

Query: 245 I--NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                +    N  L K++E+L+LSVRS NCL+  +I  +  L++ +E D+L + NFG KS
Sbjct: 237 SIFAPEVTNDNAELDKQIEDLDLSVRSYNCLKRASIHSVRQLVEFSENDLLNIRNFGVKS 296

Query: 303 LVEIKGVLGTMGLFLG 318
           + E+K  L +MGL L 
Sbjct: 297 IEEVKDKLESMGLSLK 312


>gi|300779796|ref|ZP_07089652.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           genitalium ATCC 33030]
 gi|300533906|gb|EFK54965.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           genitalium ATCC 33030]
          Length = 337

 Score =  328 bits (841), Expect = 7e-88,   Method: Composition-based stats.
 Identities = 122/312 (39%), Positives = 186/312 (59%), Gaps = 2/312 (0%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                + NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++I+GVLHE ++I GV
Sbjct: 10  TEEYIDTNRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIEGVLHEFTTINGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E++++IILNIK + L    D    + +  +GP  VTA DI    D+ V NPD  I +L+
Sbjct: 70  KENVSEIILNIKNLVLSSDSDEPVVMYLSAQGPTDVTAADIDLPADVTVHNPDLHIASLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
             A + MEL V +G GYVPA  +      IG I +D +YSP+ KVSY VE+ R  Q  D+
Sbjct: 130 ESARLDMELVVERGRGYVPAMTNSGGE--IGRIPVDQIYSPVLKVSYKVEATRVEQRTDF 187

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  S++  D++A A   L +  G+        + ++   + +   +  A   
Sbjct: 188 DKLIIDVETKNSMSARDALASAGSTLVELFGLARELNTAAEGIEIGPSPQETEYIAAYNM 247

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E+L  SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L ++GL L 
Sbjct: 248 PIEDLNFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKIKLASLGLTLK 307

Query: 319 MNLPDWPPESIE 330
               D+ P  IE
Sbjct: 308 DAPEDFDPTQIE 319


>gi|157100341|emb|CAP03336.1| RpoA protein [Vibrio aestuarianus]
          Length = 323

 Score =  328 bits (840), Expect = 9e-88,   Method: Composition-based stats.
 Identities = 143/329 (43%), Positives = 214/329 (65%), Gaps = 11/329 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMAGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEITNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           N G+KSL EIK VL + GL LGM L +WP
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWP 323


>gi|210631180|ref|ZP_03296791.1| hypothetical protein COLSTE_00676 [Collinsella stercoris DSM 13279]
 gi|210160147|gb|EEA91118.1| hypothetical protein COLSTE_00676 [Collinsella stercoris DSM 13279]
          Length = 313

 Score =  328 bits (840), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 120/316 (37%), Positives = 189/316 (59%), Gaps = 7/316 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E I+P     + + +  +    +  EPL RG+  TLGN+LRRVL+SSL GAA+ A+QI
Sbjct: 1   MSEFIRPQ----VHVEEISDTAARVSVEPLERGYGDTLGNSLRRVLLSSLEGAAVEAIQI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLK-MSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           DG  HE ++I  + ED+TDI+LN+KG+  + +        TI   GP  VT  D    ++
Sbjct: 57  DGAQHEFTTIPNMVEDVTDIVLNVKGLVFRTLGTTDEGTATISVDGPCEVTGADFFIPSE 116

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            E++NP+  I  L     + M + +  G GYV  + ++ +NDPIG+I +D+L+SP+K+ +
Sbjct: 117 FELVNPEQHIATLTEGGHLTMSMRIGYGRGYVSYEQNKRDNDPIGIIHVDSLFSPVKRCA 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF-EEPKKEVKE 243
             VE+ R GQ  DYD+L + I+T+G+I   D+V  A+ I+   +  F+   +EP+ E + 
Sbjct: 177 KLVEACRVGQHTDYDRLVLEIETNGAINPRDAVVSAANIINQHMAAFMTLADEPEAEEEI 236

Query: 244 DINVKSLPFNPALLKK-VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
            I    +  + A L K +E+L+LSVRS NCL+  +I  +  L++ +E D+L + NFG KS
Sbjct: 237 SIFAPEVTSDNAELDKQIEDLDLSVRSYNCLKRASIHSVRQLVEFSENDLLNIRNFGVKS 296

Query: 303 LVEIKGVLGTMGLFLG 318
           + E+K  L +MGL L 
Sbjct: 297 IEEVKDKLESMGLSLK 312


>gi|328955885|ref|YP_004373218.1| DNA-directed RNA polymerase subunit alpha [Coriobacterium glomerans
           PW2]
 gi|328456209|gb|AEB07403.1| DNA-directed RNA polymerase subunit alpha [Coriobacterium glomerans
           PW2]
          Length = 313

 Score =  328 bits (840), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 122/316 (38%), Positives = 189/316 (59%), Gaps = 7/316 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E I+P     + + + +E    +  EPL RG+  TLGN+LRRVL+SSL GAA+ A+QI
Sbjct: 1   MSEFIRPQ----VQVEEIDEVSARVSVEPLERGYGDTLGNSLRRVLLSSLEGAAVEAIQI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVND 124
           DG  HE  +I  + ED+TDI+LN+KG+  +  G       TI   GPG VT  D    +D
Sbjct: 57  DGAQHEFMTIPNMVEDVTDIVLNVKGLVFRSLGTTDEATATISVDGPGEVTGADFFVPSD 116

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            E++NPD  I  L     + M + +  G GY+  + ++ +NDPIG+I +D+LYSP+++ +
Sbjct: 117 FELVNPDQHIATLTEGGHLTMSMRIGYGRGYISYEANKHDNDPIGIIHVDSLYSPVRRCA 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
             VE+ R GQ  DYD+L + I+T+G+++  D+V  A+ I+   +  F+N  E  +  +E 
Sbjct: 177 KLVEATRVGQHTDYDRLVLEIETNGALSPRDAVVSAANIINQHMASFMNLAEVPEVEEEV 236

Query: 245 I--NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                +    N  L K++E+L+LSVRS NCL+  +I  +  L++ +E D+L + NFG KS
Sbjct: 237 SIFAPEVTSDNAELDKQIEDLDLSVRSYNCLKRASIHSVRQLVEFSENDLLNIRNFGVKS 296

Query: 303 LVEIKGVLGTMGLFLG 318
           + E+K  L +MGL L 
Sbjct: 297 IEEVKDKLESMGLGLK 312


>gi|160894727|ref|ZP_02075502.1| hypothetical protein CLOL250_02278 [Clostridium sp. L2-50]
 gi|156863661|gb|EDO57092.1| hypothetical protein CLOL250_02278 [Clostridium sp. L2-50]
          Length = 318

 Score =  328 bits (840), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 132/316 (41%), Positives = 200/316 (63%), Gaps = 5/316 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP  IE + +  + +     + EPL RG+  TLGN+LRR+++SSL G A+T V+I G
Sbjct: 3   EFEKP-KIEIVEISDDNK-YGKFVVEPLERGYGTTLGNSLRRIMLSSLPGTAVTHVKIKG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+I++NIK + +K +   +  K+  I   G  VV A DI    DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIVMNIKSLVIKNNSLTNEPKQAYIDVAGDCVVRASDIHVDGDI 120

Query: 126 EVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           E++NPD VI NL   DA + MELT+  G GYV +  ++  + PI +I ID++Y+P+++V+
Sbjct: 121 EIINPDLVIANLSGPDARLEMELTIGNGRGYVGSDKNKEADAPIDVIAIDSIYTPVERVN 180

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
            TV++ R GQV DYDKL++ + T+G+I  +++V+LA+R+L + L +F++  E  K V   
Sbjct: 181 LTVQNTRVGQVTDYDKLTLDVFTNGAIAPDEAVSLAARVLVEHLNLFVDLSENAKSVDVM 240

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +   +      L   ++ELELSVRS NCL+   I  + +LI +T  DM+++ N GRKSL 
Sbjct: 241 VESVTDEKEKVLEMNIDELELSVRSYNCLKRAGINTVEELINKTPEDMMKVRNLGRKSLD 300

Query: 305 EIKGVLGTMGLFLGMN 320
           E+   L  +GL L  +
Sbjct: 301 EVLAKLKELGLSLNDS 316


>gi|257784935|ref|YP_003180152.1| DNA-directed RNA polymerase, alpha subunit [Atopobium parvulum DSM
           20469]
 gi|257473442|gb|ACV51561.1| DNA-directed RNA polymerase, alpha subunit [Atopobium parvulum DSM
           20469]
          Length = 313

 Score =  328 bits (840), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 119/316 (37%), Positives = 187/316 (59%), Gaps = 7/316 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E I+PN    + + +   N   +  EPL RG+  TLGN+LRRVL+SSL GAA+ A+QI
Sbjct: 1   MSEFIRPN----VSVDEIGANVARVSVEPLERGYGDTLGNSLRRVLLSSLEGAAVEAIQI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           DGV HE ++++GV+ED+TDI+LN+KG+  +  +       +I   GP  VT  D+     
Sbjct: 57  DGVQHEFTTVEGVYEDVTDIVLNVKGLVFRNTNNSDEAEASISVDGPCTVTGADLDVPMG 116

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            E++NP   IC L   A + M L +  G GYV  + +  ENDPIG I +D+++SP+++ +
Sbjct: 117 YELVNPAQHICALAEGAHLSMRLRIGNGRGYVSGEDNERENDPIGFIHVDSIFSPVRRCA 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
             VE  R G+  DYD+L + ++T+G+I+  ++V  A+ I+   +  F+   +  +  +E 
Sbjct: 177 KAVEPCRVGRHTDYDRLVLEVETNGAISPREAVVEAANIINQHMSAFMGLTDFDETQEEA 236

Query: 245 I--NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                  +  +  L K+VE+L+LSVRS NCL+   I  +  L+  +E D+L + NFG KS
Sbjct: 237 SIFAKADVEDDSELEKQVEDLDLSVRSYNCLKRAGIHSVRQLVDFSENDLLNIRNFGVKS 296

Query: 303 LVEIKGVLGTMGLFLG 318
           + E+K  L +MGL L 
Sbjct: 297 IEEVKEKLESMGLSLK 312


>gi|224542265|ref|ZP_03682804.1| hypothetical protein CATMIT_01440 [Catenibacterium mitsuokai DSM
           15897]
 gi|224524807|gb|EEF93912.1| hypothetical protein CATMIT_01440 [Catenibacterium mitsuokai DSM
           15897]
          Length = 314

 Score =  327 bits (839), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 119/297 (40%), Positives = 179/297 (60%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E+EN    I EPL RGF  TLGN+LRRVL+SS+ GAA+ AV+I+G +HE S++ GV ED
Sbjct: 15  NEDENYGKFIIEPLERGFGTTLGNSLRRVLLSSMPGAAVFAVKINGAIHEFSAVDGVLED 74

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILNIK +  ++  D    + I   GP  VT  DIQ  +++++++ D VI ++    
Sbjct: 75  VTAIILNIKKLVFELDSDEDVTMVIDVTGPATVTGADIQCPSEVKMISNDLVIAHVAEGQ 134

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              ME+   K  GY+ A  ++   + IG+I  D+++SP+  V+Y VE  R GQ   YD+L
Sbjct: 135 HFYMEMYAHKDRGYMSADQNKKYVNTIGVIPTDSIFSPVVNVAYLVEPTRVGQSAKYDQL 194

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           +M I TDGSI   + +A+A+++L + L MF+   +    +     V+    N  L   +E
Sbjct: 195 TMEITTDGSIKPHEVLAIAAKVLVEHLNMFVELTDQAMNMDVMSEVQQDTGNKVLDMTIE 254

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           EL+LSVRS NCL+   I  + +L  +TE DM+++ N G+KSL E+K  L  +GL   
Sbjct: 255 ELDLSVRSYNCLKRAGIQTVQELASKTEDDMIKVRNLGKKSLKEVKEKLNELGLGFK 311


>gi|256825858|ref|YP_003149818.1| DNA-directed RNA polymerase subunit alpha [Kytococcus sedentarius
           DSM 20547]
 gi|256689251|gb|ACV07053.1| DNA-directed RNA polymerase subunit alpha [Kytococcus sedentarius
           DSM 20547]
          Length = 340

 Score =  327 bits (839), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 118/310 (38%), Positives = 183/310 (59%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
             +  E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE S++ GV 
Sbjct: 11  EEKVSEARSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFSTVPGVK 70

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+T++ILNIK +      D      + K+G G +T  DI     +EV NPD  +  L+ 
Sbjct: 71  EDVTELILNIKSLVFSSEHDEPVVAYLRKQGSGEMTGADISCPAGVEVHNPDLYLGALND 130

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           +  + +ELT+ +G GYV A+ ++     IG I +D++YSP+  V+Y VE+ R  Q  D+D
Sbjct: 131 EGAIDLELTIERGRGYVSAQQNKGGEQEIGRIPVDSIYSPVLSVTYKVEATRVEQRTDFD 190

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + ++T  S++  D++A A + L +  G+  +     + ++             L   
Sbjct: 191 KLIVDVETKNSMSPADAMASAGKTLVELFGLARDLNVEAEGIEMGTVQTDASLAADLALP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           VEEL LSVRS NCL+ E I  +G+L+ R++AD+L + NFG KS+ E++  L  +GL L  
Sbjct: 251 VEELNLSVRSYNCLKREGIHTVGELVARSQADLLDIRNFGNKSIDEVQVELHKLGLALKD 310

Query: 320 NLPDWPPESI 329
              D+ P +I
Sbjct: 311 TPADFDPSTI 320


>gi|223936403|ref|ZP_03628315.1| DNA-directed RNA polymerase, alpha subunit [bacterium Ellin514]
 gi|223894921|gb|EEF61370.1| DNA-directed RNA polymerase, alpha subunit [bacterium Ellin514]
          Length = 333

 Score =  327 bits (839), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 131/322 (40%), Positives = 193/322 (59%), Gaps = 7/322 (2%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  +         E     +AEP   G+ HT+GN+LRRVL+SSL GAAI++++IDG +HE
Sbjct: 2   PKRL-TKDETTSTETYAKFVAEPFETGYGHTIGNSLRRVLLSSLEGAAISSIKIDGAMHE 60

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            +++ GV ED+TDI+LN+K +  K      + + +     G VTA DIQ   +IE++NP 
Sbjct: 61  FTTVDGVVEDVTDIVLNLKKVLFKAHNREPQTLLLSANKDGEVTAADIQVNQNIELVNPK 120

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             IC LD      +EL V  G G+ P   ++  N  IG+I ID+L+SP+ +V Y VESAR
Sbjct: 121 QHICTLDKKKKFEIELEVKVGRGFCPGDENKKPNQAIGVIAIDSLFSPVTRVRYAVESAR 180

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            GQ  DYD+L + + TDG I+ +D++  AS ILQ  L +F+ +++   E +E ++ +   
Sbjct: 181 VGQRTDYDRLILEVWTDGRISPDDALTQASAILQHHLDVFVGYDKNAVEFEEVVDKQDEE 240

Query: 252 FNPALL---KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                      V E+ELSVR+ NCL   NI  +G L  +TEA+ML+  NFG+KSL EIK 
Sbjct: 241 KTKLKKLLGMSVNEIELSVRAANCLNNANITTVGQLAMKTEAEMLKYRNFGKKSLNEIKE 300

Query: 309 VLGTMGLFLGMNLPDWPPESIE 330
            L  +GL LGM+   + PE+++
Sbjct: 301 KLTALGLSLGMS---FDPEALD 319


>gi|116490683|ref|YP_810227.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Oenococcus oeni PSU-1]
 gi|290890098|ref|ZP_06553181.1| hypothetical protein AWRIB429_0571 [Oenococcus oeni AWRIB429]
 gi|122277133|sp|Q04G60|RPOA_OENOB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116091408|gb|ABJ56562.1| DNA-directed RNA polymerase subunit alpha [Oenococcus oeni PSU-1]
 gi|290480289|gb|EFD88930.1| hypothetical protein AWRIB429_0571 [Oenococcus oeni AWRIB429]
          Length = 314

 Score =  327 bits (838), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 133/317 (41%), Positives = 192/317 (60%), Gaps = 6/317 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I   +E EN    +AEPL RG+  TLGN+LRRVL+SSL GAAI +VQIDG
Sbjct: 3   EFQKPT----ISTVEESENYGKFVAEPLERGYGTTLGNSLRRVLLSSLPGAAINSVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE ++I GV ED+T IILN+K + +++  D  K + +   G G +TAGDI++  D+E+
Sbjct: 59  VLHEFTTIDGVTEDVTQIILNLKKVAMRIDSDEQKTLEVDFSGAGELTAGDIKSDGDVEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSPIKKVSYT 186
           LNPD  I  +     + M LT  +G GY  A+ ++ +    IG++ ID++Y+PI KV+YT
Sbjct: 119 LNPDLHIATVSAGKSLHMALTAVRGRGYDSAEENKAKMELGIGVLAIDSIYTPISKVNYT 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE  R G   DYDKL++ + TDGS++  +S++L S+IL + L +FI+     K+ +  ++
Sbjct: 179 VEKTRVGHRDDYDKLTLEVWTDGSVSPSESLSLGSKILSEHLALFIDLSNAGKK-EMMLD 237

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
             ++       + +EELELSVRS NCL+   I  + DL  +T  DM  + N GRKSL EI
Sbjct: 238 PDAVETVMENKEPIEELELSVRSFNCLKRAGINTIEDLTDKTLHDMGEVRNLGRKSLEEI 297

Query: 307 KGVLGTMGLFLGMNLPD 323
              L   G        +
Sbjct: 298 IQKLAERGQSFKQETEN 314


>gi|284042830|ref|YP_003393170.1| DNA-directed RNA polymerase, subunit alpha [Conexibacter woesei DSM
           14684]
 gi|283947051|gb|ADB49795.1| DNA-directed RNA polymerase, alpha subunit [Conexibacter woesei DSM
           14684]
          Length = 333

 Score =  327 bits (838), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 132/329 (40%), Positives = 190/329 (57%), Gaps = 22/329 (6%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
            +  I     EENR     EPL RGF +T GN+LRRVL+SSL GAA+T+V+I+GV HE S
Sbjct: 5   QVPRITTETVEENRGSFTIEPLDRGFGYTFGNSLRRVLLSSLAGAAVTSVRIEGVAHEFS 64

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           +I GV ED+TDI+LN+KGI  +M  D +     +   GPG +TA DI   + +E+LNPD 
Sbjct: 65  TIPGVKEDVTDIVLNLKGIVCRMHSDATEIEAPLVVTGPGDITAKDIDLPSGVEILNPDA 124

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L+    + + LT+ +G GY PA+ +++ + PIG+I ID+++SP+++V+Y VE AR 
Sbjct: 125 HIATLEKKTKLEVYLTIGRGRGYRPAEENKSPDQPIGVIPIDSIFSPVRRVAYAVEQARV 184

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK------------- 239
           GQ  DYDKL++ I+TDGSI    ++  A+ IL  QL +F + +   +             
Sbjct: 185 GQKTDYDKLTLDIETDGSIDPHAALREAAEILISQLAIFTDADRVIELRDTGGLGALEPG 244

Query: 240 --------EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
                              P N      +EELEL VRS NCL+   I  +GDLI +TE +
Sbjct: 245 LAGGGVGGVGGHGAGPGGRPANAMDDILIEELELGVRSYNCLKRAGIQTVGDLISKTENE 304

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           +  + NFG+KS+ E+   L   GL L  +
Sbjct: 305 LNAIPNFGKKSIDEVIETLEGRGLHLRQD 333


>gi|308171334|gb|ADO15986.1| RpoA [Vibrio scophthalmi LMG 19158]
          Length = 321

 Score =  326 bits (837), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 142/327 (43%), Positives = 212/327 (64%), Gaps = 11/327 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V
Sbjct: 1   GSVTEFLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEV 57

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTV 122
           +I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI   
Sbjct: 58  EIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHD 117

Query: 123 NDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
            D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YS
Sbjct: 118 GDVEITNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ K++Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +
Sbjct: 178 PVDKIAYSVDAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVR 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                    +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 VPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           G+KSL EIK VL + GL LGM L +WP
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWP 321


>gi|319942198|ref|ZP_08016514.1| DNA-directed RNA polymerase subunit alpha [Sutterella
           wadsworthensis 3_1_45B]
 gi|319804251|gb|EFW01143.1| DNA-directed RNA polymerase subunit alpha [Sutterella
           wadsworthensis 3_1_45B]
          Length = 335

 Score =  326 bits (837), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 149/328 (45%), Positives = 209/328 (63%), Gaps = 9/328 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP +++ + + +   NR ++  EP  RG+ HTLGNALRR+L+SS+ G A T  QI G+
Sbjct: 6   LLKPTSVD-VSVDESNPNRAVITLEPFERGYGHTLGNALRRILLSSMVGFAPTEAQITGI 64

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S I GV ED+ DI+LN+KG+  K+       + + K G GVVTA D    +D+ VL
Sbjct: 65  VHEYSQIDGVLEDVVDILLNLKGVVFKLEKRDEVTIMLRKDGDGVVTAADFDLPHDVTVL 124

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND----PIGLITIDALYSPIKKVS 184
           NPDHVI +L     + M++ + KG GY P       +D     IG I +DA +SPI +V+
Sbjct: 125 NPDHVIAHLS-GGRLEMQVKIEKGRGYQPGDVRAFRDDYSKSSIGRIIMDASFSPILRVA 183

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF--INFEEPKKEVK 242
           Y V +AR  Q  D DKL MTI+T+G+I  E+++  + RILQDQL +F  I+ E+    +K
Sbjct: 184 YQVMAARVAQRTDLDKLEMTIETNGAIGPEEALRESVRILQDQLAVFGAIHPEQGTDGIK 243

Query: 243 -EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ED      P +P LL+ V++LEL+VRS NCL+ E+I ++GDLIQRTE ++L+  N GRK
Sbjct: 244 PEDAANNPPPLDPILLRPVDDLELTVRSANCLKAESIYFIGDLIQRTENELLKTPNLGRK 303

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           SL EIK VL   GL LG  L +WPP  +
Sbjct: 304 SLNEIKEVLAAHGLTLGSKLENWPPAGV 331


>gi|295093661|emb|CBK82752.1| DNA-directed RNA polymerase subunit alpha [Coprococcus sp. ART55/1]
          Length = 318

 Score =  326 bits (837), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 131/316 (41%), Positives = 199/316 (62%), Gaps = 5/316 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP  IE +    + +     + EPL RG+  TLGN+LRR+++SSL G A++ V+I G
Sbjct: 3   EFEKP-KIEIVETSDDNK-YGKFVIEPLERGYGITLGNSLRRIMLSSLPGTAVSHVKIKG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+NIK + +K + D    K+  I   G  VV AGDI+   DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNIKNVVIKNNSDTFEPKQAYIDVVGERVVKAGDIKVDGDI 120

Query: 126 EVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           E++NPD VI NL   DA + MELT+  G GYV    ++  + PI +I ID++++P+++V+
Sbjct: 121 EIVNPDLVIANLSGPDAKLEMELTIVNGRGYVSLDKNKEADAPIDVIAIDSIFTPVERVN 180

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
            TV++ R GQV DYDKL++ + T+G++  +++V+LA+ +L + L +F++  E  + V   
Sbjct: 181 LTVQNTRVGQVTDYDKLTLDVYTNGALAPDEAVSLAANLLVEHLKLFVDLSENARLVDVM 240

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +   +      L   ++ELELSVRS NCL+   I  + +LI +T  DM+++ N GRKSL 
Sbjct: 241 VESTTDEKEKVLEMNIDELELSVRSYNCLKRAGINTVQELINKTPEDMMKVRNLGRKSLD 300

Query: 305 EIKGVLGTMGLFLGMN 320
           E+   L  +GL L  N
Sbjct: 301 EVLAKLKELGLSLNQN 316


>gi|15617093|ref|NP_240306.1| DNA-directed RNA polymerase subunit alpha [Buchnera aphidicola str.
           APS (Acyrthosiphon pisum)]
 gi|219682400|ref|YP_002468784.1| DNA-directed RNA polymerase alpha subunit [Buchnera aphidicola str.
           Tuc7 (Acyrthosiphon pisum)]
 gi|11134569|sp|P57566|RPOA_BUCAI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|25288361|pir||H84987 DNA-directed RNA polymerase (EC 2.7.7.6) alpha chain [imported] -
           Buchnera sp. (strain APS)
 gi|10039158|dbj|BAB13192.1| DNA-directed RNA polymerase alpha chain [Buchnera aphidicola str.
           APS (Acyrthosiphon pisum)]
 gi|219622133|gb|ACL30289.1| DNA-directed RNA polymerase alpha subunit [Buchnera aphidicola str.
           Tuc7 (Acyrthosiphon pisum)]
 gi|311086221|gb|ADP66303.1| DNA-directed RNA polymerase subunit alpha [Buchnera aphidicola str.
           LL01 (Acyrthosiphon pisum)]
 gi|311086798|gb|ADP66879.1| DNA-directed RNA polymerase subunit alpha [Buchnera aphidicola str.
           TLW03 (Acyrthosiphon pisum)]
 gi|311087385|gb|ADP67465.1| DNA-directed RNA polymerase subunit alpha [Buchnera aphidicola str.
           JF99 (Acyrthosiphon pisum)]
 gi|311087882|gb|ADP67961.1| DNA-directed RNA polymerase subunit alpha [Buchnera aphidicola str.
           JF98 (Acyrthosiphon pisum)]
          Length = 329

 Score =  326 bits (837), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 144/332 (43%), Positives = 216/332 (65%), Gaps = 10/332 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  + ++P  ++   + Q     T +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQNSIMDFLRPRLVD---IEQISATHTKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+K + +K+ G     +T+ K G G +TA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDVLEILLNLKALAVKVYGKDETLLTLHKSGIGSITAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A ++M + V +G GY+PA        ++ PIG + +DA Y
Sbjct: 118 DGDVEIIKPQHVICHLTDENASIKMRIKVQRGRGYIPASSRVHLEEDSRPIGCLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPI ++SY VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPINRISYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDI 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++        +   F P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 REPE---FKEEKPEFEPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            G+KSL EIK VL +  L LGM L +WPP SI
Sbjct: 295 LGKKSLTEIKDVLASRSLSLGMRLENWPPSSI 326


>gi|293375416|ref|ZP_06621697.1| DNA-directed RNA polymerase, alpha subunit [Turicibacter sanguinis
           PC909]
 gi|325844489|ref|ZP_08168216.1| DNA-directed RNA polymerase, alpha subunit [Turicibacter sp. HGF1]
 gi|292645969|gb|EFF63998.1| DNA-directed RNA polymerase, alpha subunit [Turicibacter sanguinis
           PC909]
 gi|325489163|gb|EGC91547.1| DNA-directed RNA polymerase, alpha subunit [Turicibacter sp. HGF1]
          Length = 314

 Score =  326 bits (837), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 122/311 (39%), Positives = 188/311 (60%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE     + +E     + EPL RG+  TLGN+LRRVL+SSL GAA+T++ I+G
Sbjct: 3   EIEKPR-IEVEEYIK-DEFYGKFVIEPLKRGYGTTLGNSLRRVLLSSLPGAAVTSISIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE ++I GV ED+T IILN+K + L +  +  K + I     G VTA DI+   ++ +
Sbjct: 61  VQHEFTAIDGVVEDVTQIILNLKNLILSIDTEEVKELRIDVAREGAVTAADIECDEEVTI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NP+  I  L     +RM +   +G+GYV A  ++   +  G I ID++Y+P+ +VSY V
Sbjct: 121 INPELHIATLSATGRLRMTMKARRGNGYVGADDNKKLLESAGEIAIDSIYTPVTRVSYDV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R GQ   YDKL++ + T+GSI  ++++++AS+IL +   + +N  E  +     +  
Sbjct: 181 EKTRVGQDASYDKLTLEVWTNGSINPQEAISVASKILVEHFSILVNLNEAGQLASFIVER 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    N  L   +EEL+LSVRS NCLR   I  + +L + +E DM+++ N G+KSL E+K
Sbjct: 241 EDEEKNKVLEMPIEELDLSVRSYNCLRRAGINTVEELARHSEEDMMKVRNLGKKSLKEVK 300

Query: 308 GVLGTMGLFLG 318
             L  +GL LG
Sbjct: 301 DKLDELGLSLG 311


>gi|163816005|ref|ZP_02207375.1| hypothetical protein COPEUT_02185 [Coprococcus eutactus ATCC 27759]
 gi|158448815|gb|EDP25810.1| hypothetical protein COPEUT_02185 [Coprococcus eutactus ATCC 27759]
          Length = 318

 Score =  326 bits (836), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 131/316 (41%), Positives = 200/316 (63%), Gaps = 5/316 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP  IE +    + +     + EPL RG+  TLGN+LRR+++SSL G A++ V+I G
Sbjct: 3   EFEKP-KIEIVETSDDNK-YGKFVIEPLERGYGITLGNSLRRIMLSSLPGTAVSHVKIKG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+NIK + +K + D    K+  I   G  VV AGDI+   DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNIKNVVIKNNSDTFEPKQAYIDVVGERVVKAGDIKVDGDI 120

Query: 126 EVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           E++NPD VI NL   DA + MELT++ G GYV    ++  + PI +I ID++++P+++V+
Sbjct: 121 EIVNPDLVIANLSGPDAKLEMELTIANGRGYVSLDKNKEADAPIDVIAIDSIFTPVERVN 180

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
            TV++ R GQV DYDKL++ + T+G++  +++V+LA+ +L + L +F++  E  + V   
Sbjct: 181 LTVQNTRVGQVTDYDKLTLDVYTNGALAPDEAVSLAANLLVEHLKLFVDLSENARLVDVM 240

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +   +      L   ++ELELSVRS NCL+   I  + +LI +T  DM+++ N GRKSL 
Sbjct: 241 VESTTDEKEKVLEMNIDELELSVRSYNCLKRAGINTVQELINKTPEDMMKVRNLGRKSLD 300

Query: 305 EIKGVLGTMGLFLGMN 320
           E+   L  +GL L  N
Sbjct: 301 EVLAKLKELGLALNQN 316


>gi|87306331|ref|ZP_01088478.1| DNA-directed RNA polymerase alpha subunit [Blastopirellula marina
           DSM 3645]
 gi|87290510|gb|EAQ82397.1| DNA-directed RNA polymerase alpha subunit [Blastopirellula marina
           DSM 3645]
          Length = 328

 Score =  326 bits (836), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 132/328 (40%), Positives = 193/328 (58%), Gaps = 5/328 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +   W+ L  P+ +          N    IAEP  RGF  T+GN+LRR+L+SSL GAA+T
Sbjct: 1   MHIRWRGLELPSVVN-CEAESLSPNYGKFIAEPFERGFGVTIGNSLRRILLSSLEGAAVT 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            +++ G  HE +SI GV ED+T+I+LN K I +K   +  K VTI K+GP  +T  DIQ 
Sbjct: 60  QIKVRGAQHEFTSIPGVVEDMTEIVLNTKAIVVKKHSEMTKVVTIEKQGPCTITGADIQC 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
             +++++N D  IC +  D    ME+ V  G GY+PA  H T    IG+I +DA+YSP+ 
Sbjct: 120 DPEVDIINKDIHICTITGDIPFMMEMVVESGRGYIPATEHSTAEHEIGIIPVDAVYSPVT 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +V Y VE  R GQ  +YDKL++ I TDGSI  E S+  A++IL+  L  F+ + E   ++
Sbjct: 180 RVRYEVEETRVGQKTNYDKLTLEIWTDGSIHPEYSLVEAAKILRKHLNPFVQYNELGSKI 239

Query: 242 KEDINVKSLPFNPALLKKVE----ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
                 +S   +P L  K+     E+ LSVR++NCL  ENI  + DL++RTE  ++ + N
Sbjct: 240 SIPSRTQSSGLDPVLESKLNMSLAEMHLSVRASNCLESENINTVRDLVRRTEDQLMEVRN 299

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           FG  +L E++  L  +GL LGM +   P
Sbjct: 300 FGETTLTEVREKLKELGLHLGMRVQSAP 327


>gi|219681845|ref|YP_002468231.1| DNA-directed RNA polymerase alpha subunit [Buchnera aphidicola str.
           5A (Acyrthosiphon pisum)]
 gi|219624688|gb|ACL30843.1| DNA-directed RNA polymerase alpha subunit [Buchnera aphidicola str.
           5A (Acyrthosiphon pisum)]
          Length = 329

 Score =  326 bits (836), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 144/332 (43%), Positives = 215/332 (64%), Gaps = 10/332 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  + ++P  ++   + Q     T +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQNSIMDFLRPRLVD---IEQISATHTKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+K + +K+ G     +T+ K G G +TA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDVLEILLNLKALAVKVYGKDETLLTLHKSGIGSITAADIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A ++M + V +G GY+PA        +  PIG + +DA Y
Sbjct: 118 DGDVEIIKPQHVICHLTDENASIKMRIKVQRGRGYIPASSRVHLEEDARPIGCLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPI ++SY VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPINRISYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDI 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++        +   F P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 REPE---FKEEKPEFEPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            G+KSL EIK VL +  L LGM L +WPP SI
Sbjct: 295 LGKKSLTEIKDVLASRSLSLGMRLENWPPSSI 326


>gi|325108639|ref|YP_004269707.1| DNA-directed RNA polymerase subunit alpha [Planctomyces
           brasiliensis DSM 5305]
 gi|324968907|gb|ADY59685.1| DNA-directed RNA polymerase subunit alpha [Planctomyces
           brasiliensis DSM 5305]
          Length = 338

 Score =  326 bits (835), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 127/333 (38%), Positives = 198/333 (59%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++  W+ L  PN + +I       N    +AEP  RGF  T+GN+LRR+L+SSL G+++T
Sbjct: 1   MRIRWRGLELPNRL-FIDRETATPNYGKFVAEPFERGFGSTIGNSLRRILLSSLEGSSVT 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I G  HE ++I GV ED+TDI LN+K + +K      K + I K   GVVT  D+  
Sbjct: 60  RVKIQGAQHEFTTIPGVVEDVTDICLNLKSLIVKSYAAGPKTIRIEKHTRGVVTGADVIA 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            + +EV+N D VI  +  D  + +ELTV  G GY+PA  H   +  +G+I +DALYSP++
Sbjct: 120 DDQVEVINKDMVIATMTDDVPLSLELTVENGRGYIPASEHFDRDPEVGVIPLDALYSPVE 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +V++ VE  R GQ  +YDKL + I T+G+++ E ++  +++I++  L  FI + EP  EV
Sbjct: 180 RVNFQVEETRVGQRTNYDKLILEIWTNGTVSPEMALVESAKIMRKHLNPFITYREPGPEV 239

Query: 242 KEDINVK-----------SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
             D  ++            L     L + + EL LSVR+TNCL  E IV + DL+ ++E 
Sbjct: 240 SPDGGLQGMAEATGHSPIDLELEEKLNQSLAELNLSVRATNCLESEGIVTVRDLVSKSED 299

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            +L++ NFG  +L E++  L ++GL +GM +P 
Sbjct: 300 QLLQVRNFGETTLQEVRERLSSIGLRMGMKMPK 332


>gi|331004149|ref|ZP_08327629.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae oral
           taxon 107 str. F0167]
 gi|330411559|gb|EGG90969.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae oral
           taxon 107 str. F0167]
          Length = 317

 Score =  325 bits (834), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 128/312 (41%), Positives = 199/312 (63%), Gaps = 5/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     I EPL RG+  TLGN+LRR+++SSL G+A++ V+IDG
Sbjct: 3   DFEKPN-IEIAEIS-EDKKFGRFICEPLERGYGTTLGNSLRRIMLSSLPGSAVSQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+N+K + ++   + D  K   I   G GV+TA DIQ    I
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNVKSLAIRNTSNDDEPKVAYIDFDGEGVITAEDIQCDPSI 120

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++N D VI  +       MELT++ G GYV +  ++ E+ PIG+I ID++Y+P+++V+ 
Sbjct: 121 EIINKDQVIATVSEG-KFYMELTITNGRGYVSSDKNKGEDTPIGVIAIDSIYTPVERVNL 179

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R GQ+ D+DKL++ + T+G++  +++V+LA+++L + L +FI+  +  K +   I
Sbjct: 180 LVENTRVGQMTDFDKLTLDVTTNGTLEPDEAVSLAAKVLSEHLNLFIDLSDNAKTIDVMI 239

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL E
Sbjct: 240 EKEEDDKEKVLEMNIDELELSVRSYNCLKRAGINTVEELCSRTSDDMMKVRNLGRKSLEE 299

Query: 306 IKGVLGTMGLFL 317
           +   L  +GL L
Sbjct: 300 VLQKLEELGLRL 311


>gi|21672745|ref|NP_660812.1| DNA-directed RNA polymerase subunit alpha [Buchnera aphidicola str.
           Sg (Schizaphis graminum)]
 gi|22654275|sp|O69232|RPOA_BUCAP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|21623391|gb|AAM68023.1| DNA-directed RNA polymerase alpha chain [Buchnera aphidicola str.
           Sg (Schizaphis graminum)]
          Length = 329

 Score =  325 bits (834), Expect = 5e-87,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 216/334 (64%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +    +KP  +E   + Q     T +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQNSIIGFLKPRLVE---IEQITATHTKVTLEPLERGFGHTLGNALRRILLSSMPGYAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+K + +K+ G     +++ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKELAVKVHGKDEVFMSLNKSGIGSVTASDIIH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ PDH+IC+L D +A ++M + V +G GY+PA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIIKPDHLICHLTDENASIQMRIKVQRGRGYIPASSRIHMEDDLRPIGCLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPI ++SY VE+AR  Q  D DKL + + T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPINRISYNVEAARVEQRTDLDKLIIEMKTNGTIDPEEAIRRAATILSEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           K+     I  +   F P LL+ V++LEL+VRS NCL+ E+I Y+GDL+QRTE ++L+  N
Sbjct: 238 KEPE---IKEEKPEFEPILLRPVDDLELTVRSANCLKAESIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK +L    L LGM L  WPP SI E
Sbjct: 295 LGKKSLTEIKDILAARNLSLGMKLEKWPPSSILE 328


>gi|157100339|emb|CAP03335.1| RpoA protein [Vibrio aestuarianus]
          Length = 323

 Score =  325 bits (834), Expect = 5e-87,   Method: Composition-based stats.
 Identities = 142/329 (43%), Positives = 213/329 (64%), Gaps = 11/329 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGN LRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNXLRRILLSSMXGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEITNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           N G+KSL EIK VL + GL LGM L +WP
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWP 323


>gi|308171336|gb|ADO15987.1| RpoA [Vibrio sinaloensis DSM 21326]
          Length = 321

 Score =  325 bits (834), Expect = 5e-87,   Method: Composition-based stats.
 Identities = 141/327 (43%), Positives = 211/327 (64%), Gaps = 11/327 (3%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           + +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T 
Sbjct: 1   RGSVTEFLKPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTE 57

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQT 121
           V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI  
Sbjct: 58  VEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDW 324
            G+KSL EIK VL + GL LGM L +W
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENW 321


>gi|331091639|ref|ZP_08340473.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae
           bacterium 2_1_46FAA]
 gi|330403396|gb|EGG82955.1| DNA-directed RNA polymerase subunit alpha [Lachnospiraceae
           bacterium 2_1_46FAA]
          Length = 319

 Score =  325 bits (834), Expect = 5e-87,   Method: Composition-based stats.
 Identities = 131/316 (41%), Positives = 202/316 (63%), Gaps = 6/316 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL G+AI+ V+IDG
Sbjct: 3   DFNKPN-IEITEIS-EDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGSAISYVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+I++N+K + +K     D  K   I   G GVVT  DIQ  +DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIVMNLKSLAIKNTSETDEPKTAYIEFEGEGVVTGADIQVDSDI 120

Query: 126 EVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E++NP+ VI  L+  A   + MELT++ G GYV A  +++   PI +I ID++Y+P+++V
Sbjct: 121 EIMNPETVIATLNGGADSKLYMELTITNGRGYVSADKNKSSELPIAVIPIDSIYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + TVE+ R GQ+ D+DKL++ + T+G++  +++V+LA+++L + L +FI+  E  +  + 
Sbjct: 181 NLTVENTRVGQITDFDKLTLDVYTNGTLAPDEAVSLAAKVLNEHLKLFIDLSEVAQAAEV 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            I  +       L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL
Sbjct: 241 MIEKEDDEKEKVLEMSIDELELSVRSYNCLKRAGINTVEELTNRTSEDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFLGM 319
            E+   L  +GL L  
Sbjct: 301 EEVLAKLKELGLELSQ 316


>gi|172040041|ref|YP_001799755.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           urealyticum DSM 7109]
 gi|171851345|emb|CAQ04321.1| DNA-directed RNA polymerase, alpha subunit [Corynebacterium
           urealyticum DSM 7109]
          Length = 337

 Score =  325 bits (833), Expect = 6e-87,   Method: Composition-based stats.
 Identities = 122/307 (39%), Positives = 184/307 (59%), Gaps = 3/307 (0%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           +++R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED++
Sbjct: 15  DDSRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSLRIDGVLHEFTTVPGVKEDVS 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           DIILNIK + L    D    + + K G G VT  DI+T   +EV N D  I  L+    +
Sbjct: 75  DIILNIKSLVLSSDFDEPVTMYLRKEGAGAVTGADIETPAGVEVHNKDLHIATLNEQGKL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +EL V +G GYVPA     E   IG I +D +YSP+ KVSY VE+ R  Q  D+DKL +
Sbjct: 135 DIELVVERGRGYVPAATSTDE---IGRIPVDQIYSPVLKVSYKVEATRVEQRTDFDKLIL 191

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T  S++  D++A A + L +  G+        + ++   + +      A    +E+L
Sbjct: 192 DVETKSSMSARDAMASAGKTLVELFGLAQELNIEAEGIEIGPSPQESEHIAAYNMPIEDL 251

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           + SVRS NCL+ E I  +G+L  RTE+D+L + NFG+KS+ E+K  L  +GL L  +   
Sbjct: 252 DFSVRSYNCLKREEIHTVGELAARTESDLLDIRNFGQKSINEVKVKLAGLGLALKDSPEG 311

Query: 324 WPPESIE 330
           +    IE
Sbjct: 312 FDLSDIE 318


>gi|326792578|ref|YP_004310399.1| DNA-directed RNA polymerase subunit alpha [Clostridium lentocellum
           DSM 5427]
 gi|326543342|gb|ADZ85201.1| DNA-directed RNA polymerase subunit alpha [Clostridium lentocellum
           DSM 5427]
          Length = 321

 Score =  325 bits (833), Expect = 6e-87,   Method: Composition-based stats.
 Identities = 128/317 (40%), Positives = 195/317 (61%), Gaps = 8/317 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP  IE   L Q +      + EPL RG+  TLGN+LRR+L SSL G+AI++V++DG
Sbjct: 3   EFEKP-QIEIKELSQ-DGKYGCFVVEPLERGYGITLGNSLRRILSSSLPGSAISSVKVDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+ +IILN+KG+ ++    G   K + I K G G VT  DI+   +I
Sbjct: 61  VLHEFSSIPGVKEDVVEIILNLKGLAIRDTSQGTEPKVIYIEKSGEGPVTGADIKCGPEI 120

Query: 126 EVLNPDHVICNLDVDAV--VRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL--YSPIK 181
           E+LNP+H I  L+  A   + +E+TV+ G GY      +  + PIG+I +DA   Y+P++
Sbjct: 121 EILNPEHHIATLNGGANSNLSIEMTVTTGRGYEGVDKLKKTDLPIGVIPVDANANYTPVE 180

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +V++ VE  R GQ  DYDKL++ + T+G++  +++V+LA+++L + L +FI+  E  +  
Sbjct: 181 RVNFIVEDTRVGQQTDYDKLTLEVWTNGTLKPDEAVSLAAKVLSEHLNLFIDLSENARTT 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +  +  +       L   +EEL+LSVRS NCL+   I  + DL  +TE +M+++ N GRK
Sbjct: 241 EIMVTKEDDSKEKTLEMTIEELDLSVRSFNCLKRAGINTVEDLTNKTEEEMMKVRNLGRK 300

Query: 302 SLVEIKGVLGTMGLFLG 318
           SL E+   L  +G  L 
Sbjct: 301 SLEEVFQKLNELGFQLK 317


>gi|255020793|ref|ZP_05292851.1| DNA-directed RNA polymerase alpha subunit [Acidithiobacillus caldus
           ATCC 51756]
 gi|254969789|gb|EET27293.1| DNA-directed RNA polymerase alpha subunit [Acidithiobacillus caldus
           ATCC 51756]
          Length = 339

 Score =  325 bits (833), Expect = 6e-87,   Method: Composition-based stats.
 Identities = 147/324 (45%), Positives = 206/324 (63%), Gaps = 5/324 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            +L++P + +  VL      R  +   PL RGF HTLGNALRRVL+SSL+GAA+T V+I+
Sbjct: 5   SDLLRPEHYDLEVLS---PRRARISLGPLERGFGHTLGNALRRVLLSSLKGAAVTEVEIE 61

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE SSI+GV ED+ DI+LN+K + ++  G +   VT+ KRGPG+VT  DI   + IE
Sbjct: 62  GVLHEYSSIEGVQEDVVDILLNLKQLAVRAQGRNEVMVTLRKRGPGLVTGADIIAEHGIE 121

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVP-AKHHRTENDPIGLITIDALYSPIKKVSY 185
           V NP+ VI  L  D  + M L    G GY P A   ++    IG++ +DA YSP+ +VS+
Sbjct: 122 VANPEQVIATLTRDVELVMHLRFDTGRGYEPAATRRQSHEKRIGVLALDASYSPVHRVSF 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VESAR  Q  D D+L + ++T+G +    +V  A+RIL+ QL +F    E   E +   
Sbjct: 182 QVESARVEQRTDLDRLVLDVETNGVVEPLWAVQEAARILRQQLAVFGGA-EAATEREAHA 240

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                   P L + V++LEL+VRS NCL+ E+I Y+GDL+Q+TE ++L+  N GRKSL E
Sbjct: 241 APVHEDLLPLLARPVDDLELTVRSANCLKAEDIFYIGDLVQKTEQELLKAPNLGRKSLTE 300

Query: 306 IKGVLGTMGLFLGMNLPDWPPESI 329
           IK VL   GL LGM + +WPPE++
Sbjct: 301 IKEVLDKNGLTLGMRIENWPPENL 324


>gi|224370665|ref|YP_002604829.1| DNA-directed RNA polymerase subunit alpha [Desulfobacterium
           autotrophicum HRM2]
 gi|259494167|sp|C0Q9U7|RPOA_DESAH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|223693382|gb|ACN16665.1| RpoA [Desulfobacterium autotrophicum HRM2]
          Length = 340

 Score =  325 bits (833), Expect = 7e-87,   Method: Composition-based stats.
 Identities = 138/337 (40%), Positives = 210/337 (62%), Gaps = 7/337 (2%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++  NW+E+I P  +               + EPL +G+  T+GN+LRR+++SSL GAAI
Sbjct: 6   LVYMNWREIIMPEKVAVTT----TSTYGKFVCEPLEKGYGITIGNSLRRIILSSLYGAAI 61

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
            +V+    LHE S +  V ED+++II+N+K + LK+     K +TI  +G   VTA DI 
Sbjct: 62  VSVKFSEALHEYSVVSDVREDVSEIIMNLKEVKLKLDDPGDKILTINVKGEKFVTAADII 121

Query: 121 T-VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
           +    +E+LNP+  I  +     + M + V  G GY  A  ++    P+G I ID+++SP
Sbjct: 122 SGDGRVEILNPEQHIATVSKGGELMMTMLVKTGKGYALAASNKDPEAPVGTIPIDSVFSP 181

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           IK+V Y V ++R GQ  DYDKL+M I TDGS+T EDSVA A++IL++Q+  FINF+E  +
Sbjct: 182 IKRVKYVVGASRIGQKTDYDKLTMEIWTDGSVTPEDSVAYAAKILKEQMNPFINFDEDIE 241

Query: 240 E--VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
              V+++    +  FN  L + V+ELELSVRS+NCL+   I+ +  L+Q+T+ +ML+  N
Sbjct: 242 PELVEKEHEGAAKNFNENLYRSVDELELSVRSSNCLKNAQILKIYQLVQKTDNEMLKTKN 301

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           FGRKSL EIK VL +M L LGM+L  + P   +++ +
Sbjct: 302 FGRKSLNEIKEVLTSMDLSLGMDLEGFEPPEEDQIKE 338


>gi|225571582|ref|ZP_03780578.1| hypothetical protein CLOHYLEM_07680 [Clostridium hylemonae DSM
           15053]
 gi|225159659|gb|EEG72278.1| hypothetical protein CLOHYLEM_07680 [Clostridium hylemonae DSM
           15053]
          Length = 322

 Score =  324 bits (832), Expect = 8e-87,   Method: Composition-based stats.
 Identities = 133/315 (42%), Positives = 203/315 (64%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL G+AI+ V+IDG
Sbjct: 6   DFNKPN-IEITEIS-EDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGSAISQVKIDG 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+I++N+K + +K     D  K   I   G GVVTA DIQ   DI
Sbjct: 64  VLHEFSSIPGVKEDVTEIVMNLKSLAIKNTSETDEPKTAYIEFEGEGVVTAADIQVDQDI 123

Query: 126 EVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E++NP+ VI  L+  A   + MELT++KG GYV A  ++ +  PI +I ID++Y+P+++V
Sbjct: 124 EIMNPETVIATLNGGADSKLYMELTITKGRGYVSADKNKNDELPIAVIPIDSIYTPVERV 183

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + TVE+ R GQ+ D+DKL++ + T+G++  +++V+LA+++L + L +FI+  E  +  + 
Sbjct: 184 NLTVENTRVGQITDFDKLTLDVYTNGTLLPDEAVSLAAKVLSEHLKLFIDLSEVAQAAEV 243

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            I  +       L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL
Sbjct: 244 MIEKEDDEKEKVLEMSIDELELSVRSYNCLKRAGINTVEELTNRTPEDMMKVRNLGRKSL 303

Query: 304 VEIKGVLGTMGLFLG 318
            E+   L  +GL L 
Sbjct: 304 EEVLAKLDELGLCLS 318


>gi|308171330|gb|ADO15984.1| RpoA [Vibrio brasiliensis LMG 20546]
          Length = 318

 Score =  324 bits (832), Expect = 8e-87,   Method: Composition-based stats.
 Identities = 142/324 (43%), Positives = 210/324 (64%), Gaps = 11/324 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+
Sbjct: 1   TEFLKPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIE 57

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+
Sbjct: 58  GVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDV 117

Query: 126 EVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIK 181
           E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ 
Sbjct: 118 EIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVD 177

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   
Sbjct: 178 KIAYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE 237

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
                 +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+K
Sbjct: 238 ---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKK 294

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL EIK VL + GL LGM L +WP
Sbjct: 295 SLTEIKDVLASRGLSLGMRLENWP 318


>gi|260549815|ref|ZP_05824031.1| RNA polymerase alpha subunit [Acinetobacter sp. RUH2624]
 gi|260407065|gb|EEX00542.1| RNA polymerase alpha subunit [Acinetobacter sp. RUH2624]
          Length = 335

 Score =  324 bits (832), Expect = 8e-87,   Method: Composition-based stats.
 Identities = 140/330 (42%), Positives = 223/330 (67%), Gaps = 8/330 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +   E + P  I+   +         +I EPL RGF HTLGNALRR+L+SSL GAA+ 
Sbjct: 1   MTRTANEFLTPQAIKVEAVSGTS---AKVILEPLERGFGHTLGNALRRILLSSLPGAAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GV HE S+++G+ +D+ +++LN+KG+++K+   +   +T+ K+GPG +TA D++ 
Sbjct: 58  EVEIEGVEHEYSTLEGLQQDIVELLLNLKGLSIKLFDQNEAYLTLEKQGPGDITAADLRL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSP 179
            +++EV+NPDH+I  L     ++M L V++G GY  +     E +  P+G + +DA YSP
Sbjct: 118 PHNVEVVNPDHLIGTLSASGSLKMRLKVAQGRGYETSDSRFPEGETRPVGRLQLDASYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           IK+VSYTVE+AR  Q  D DKL + ++T+G++  E+++  A+ ILQ Q+ +F++ ++ + 
Sbjct: 178 IKRVSYTVENARVEQRTDLDKLVIDLETNGTVDPEEAIRKAATILQQQIAIFVDLQKDQT 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            V ++   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G
Sbjct: 238 PVAQEPREE---VDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 324


>gi|268609564|ref|ZP_06143291.1| DNA-directed RNA polymerase, alpha subunit [Ruminococcus
           flavefaciens FD-1]
          Length = 321

 Score =  324 bits (832), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 124/316 (39%), Positives = 199/316 (62%), Gaps = 6/316 (1%)

Query: 9   LIKPNNIEYIVLG-QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           L K N  +  ++  + +      +  PL RG+  TLGN+LRRVL+SSL G A+T+V++ G
Sbjct: 2   LEKINKPDIDIVELKSDGKYGKFVLAPLERGYGITLGNSLRRVLLSSLPGVAVTSVKLSG 61

Query: 68  ----VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
               V HE+S+I GV ED+T+IIL+IKG+  K+ G+  K V I   G   +TAGDI+T +
Sbjct: 62  KDGTVHHELSTIPGVKEDVTEIILSIKGLTAKLYGEGPKTVYIEAEGECEITAGDIKTDS 121

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSPIKK 182
           ++ +L+P   I  L  DA + ME+T+ +G GYV A+ ++ + N P+ +I +D++Y+P+ K
Sbjct: 122 EVNILDPGMHIATLGKDAKLYMEITIDRGRGYVSAERNKKQINLPVDVIAVDSIYTPVLK 181

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+YTVE  R GQV DYDKL+M + TDG+I+ +++++ A+ +L + L +FI+  E     +
Sbjct: 182 VNYTVEDTRLGQVTDYDKLTMEVWTDGTISAKEALSQAANLLGEHLKLFIDLSEEAGLAE 241

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
             +          L   +E+L+LSVRS NCL+   I  + DLI ++E +M+++ N G+KS
Sbjct: 242 VLVEKDEKGKEKILEMTIEDLDLSVRSFNCLKRAGINTVDDLINKSEEEMMKVRNLGKKS 301

Query: 303 LVEIKGVLGTMGLFLG 318
             E+K  L ++G  L 
Sbjct: 302 FDEVKEKLQSLGFDLS 317


>gi|313884601|ref|ZP_07818362.1| DNA-directed RNA polymerase, alpha subunit [Eremococcus coleocola
           ACS-139-V-Col8]
 gi|312620385|gb|EFR31813.1| DNA-directed RNA polymerase, alpha subunit [Eremococcus coleocola
           ACS-139-V-Col8]
          Length = 314

 Score =  324 bits (831), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 133/310 (42%), Positives = 204/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP      V   ++E    ++ EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKPEITTIQV--SDDEKYGKIVIEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE ++I GV ED+  IILNIK + LK+  +  K + +   GP +VTA DI   ND+++
Sbjct: 61  VVHEFATIDGVVEDVPTIILNIKNLALKLYTEEDKVLELNAVGPKIVTAADIIHDNDVQI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  IC L   A ++M L  S G GYV +  +++++  IG++ ID++Y+P+KKV+Y V
Sbjct: 121 LNPELEICTLAEGAEIKMLLNASTGRGYVRSDFNKSDDTTIGVLPIDSIYTPVKKVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ    DKL++ I TDGSI+ E S++LA++IL + L +F++  E  ++V+  +  
Sbjct: 181 ENTRIGQQNICDKLTLDIWTDGSISPEKSLSLAAKILIEYLNVFVDLNEEARDVEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L+  +EEL+LSVRS NCL+   I  + +L  +TEA+M+++ N GRKSL E+K
Sbjct: 241 EETEKEKVLVMTIEELDLSVRSYNCLKRAGINTIQELTNKTEAEMMKVRNLGRKSLTEVK 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 NKLNDLGLGL 310


>gi|328814015|gb|AEB52123.1| DNA-directed RNA polymerase alpha chain [Lactobacillus rhamnosus]
          Length = 273

 Score =  324 bits (831), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 117/271 (43%), Positives = 175/271 (64%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I    E  N    + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I G
Sbjct: 3   ITKVDESTNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDG 62

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+T IILNIK + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +
Sbjct: 63  VLEDVTQIILNIKKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTV 122

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
                  + +TV KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D
Sbjct: 123 ADGGHFHVRMTVKKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRND 182

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL++ + T+GSI+  ++++LA++IL + L +F+N  +  K  +  +  +       L 
Sbjct: 183 FDKLTLDVWTNGSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLE 242

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
             +EEL+LSVRS NCL+   I  + +L  +T
Sbjct: 243 MTIEELDLSVRSYNCLKRAGINTVQELTNKT 273


>gi|166031630|ref|ZP_02234459.1| hypothetical protein DORFOR_01330 [Dorea formicigenerans ATCC
           27755]
 gi|166028607|gb|EDR47364.1| hypothetical protein DORFOR_01330 [Dorea formicigenerans ATCC
           27755]
          Length = 322

 Score =  324 bits (831), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 134/315 (42%), Positives = 204/315 (64%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL G+AI+ V+IDG
Sbjct: 6   DFNKPN-IEITEIS-EDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGSAISQVKIDG 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+N+K + +K     D  K   I   G GVVTA DIQ   DI
Sbjct: 64  VLHEFSSIPGVKEDVTEIIMNLKSLAIKNTSETDEPKTAYIEFEGEGVVTAADIQVDQDI 123

Query: 126 EVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E++NP+ VI  L+  A   + MELT++KG GYV A+ ++ +  PI +I ID++Y+P+++V
Sbjct: 124 EIMNPETVIATLNGGADSKLYMELTITKGRGYVSAEKNKNDELPIAVIPIDSIYTPVERV 183

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + TVE+ R GQ+ D+DKL++ + T+G++  +++V+LA+++L + L +FI+  E  +  + 
Sbjct: 184 NLTVENTRVGQITDFDKLTLDVYTNGTLLPDEAVSLAAKVLSEHLKLFIDLSEVAQAAEV 243

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            I  +       L   ++ELELSVRS NCL+   I  + +L  RT  DM+++ N GRKSL
Sbjct: 244 MIEKEDDEKEKVLEMSIDELELSVRSYNCLKRAGINTVEELTNRTSEDMMKVRNLGRKSL 303

Query: 304 VEIKGVLGTMGLFLG 318
            E+   L  +GL L 
Sbjct: 304 EEVLAKLDELGLSLS 318


>gi|298345434|ref|YP_003718121.1| DNA-directed RNA polymerase subunit alpha [Mobiluncus curtisii ATCC
           43063]
 gi|304390990|ref|ZP_07372942.1| DNA-directed RNA polymerase subunit alpha [Mobiluncus curtisii
           subsp. curtisii ATCC 35241]
 gi|315656234|ref|ZP_07909125.1| DNA-directed RNA polymerase subunit alpha [Mobiluncus curtisii
           subsp. holmesii ATCC 35242]
 gi|298235495|gb|ADI66627.1| DNA-directed RNA polymerase subunit alpha [Mobiluncus curtisii ATCC
           43063]
 gi|304325873|gb|EFL93119.1| DNA-directed RNA polymerase subunit alpha [Mobiluncus curtisii
           subsp. curtisii ATCC 35241]
 gi|315493236|gb|EFU82836.1| DNA-directed RNA polymerase subunit alpha [Mobiluncus curtisii
           subsp. holmesii ATCC 35242]
          Length = 335

 Score =  324 bits (831), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 121/320 (37%), Positives = 187/320 (58%), Gaps = 8/320 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E ++  Q    R+    EPL  GF +TLGN+LRR L+SS+ G+A+T+++I+G LH
Sbjct: 13  QPKLTEEVINDQ----RSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGSAVTSIKIEGALH 68

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+T I+LNIK I L    D    + + K G G VT GDI     + + NP
Sbjct: 69  EFTTLPGVKEDVTQIVLNIKEIVLSSDNDEPVVMYLRKTGEGEVTVGDIMPPAGVVIHNP 128

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           +H I  L+ D  + +ELTV +G GYV A  ++     I  I +D++YSP+ KVSY VE+ 
Sbjct: 129 EHHIATLNKDGKLEIELTVERGRGYVSASQNKDPEAEISRIPVDSIYSPVLKVSYRVEAT 188

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  +I   D++A A + L +  G+  +     + ++   +    
Sbjct: 189 RVEQRTDFDRLVVDVETKKAILPRDAMASAGKTLVELFGLARDLNHDAEGIELGPSGNDA 248

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   VE+L+L+ R+ NCL  E I  +GDL+ R++AD+L + NFG+KS+ EIK  L
Sbjct: 249 ALAEDLAMSVEDLDLTSRALNCLTREGINTVGDLVARSQADLLDIRNFGQKSIDEIKEKL 308

Query: 311 GTMGLFLGMNLPDWPPESIE 330
             M    GM+L D P  ++E
Sbjct: 309 AGM----GMSLKDTPMPAVE 324


>gi|224585210|ref|YP_002639009.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Paratyphi C strain RKS4594]
 gi|224469738|gb|ACN47568.1| DNA-directed RNA polymerase alpha subunit [Salmonella enterica
           subsp. enterica serovar Paratyphi C strain RKS4594]
          Length = 304

 Score =  324 bits (830), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 142/305 (46%), Positives = 209/305 (68%), Gaps = 7/305 (2%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
             EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+K
Sbjct: 2   TLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLK 61

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTV 149
           G+ +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + V
Sbjct: 62  GLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKV 121

Query: 150 SKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            +G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + ++
Sbjct: 122 QRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEME 181

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+P LL+ V++LEL+
Sbjct: 182 TNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP---EVKEEKPEFDPILLRPVDDLELT 238

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP
Sbjct: 239 VRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPP 298

Query: 327 ESIEE 331
            SI +
Sbjct: 299 ASIAD 303


>gi|32477618|ref|NP_870612.1| DNA-directed RNA polymerase subunit alpha [Rhodopirellula baltica
           SH 1]
 gi|41688636|sp|Q7UIC5|RPOA_RHOBA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|32448172|emb|CAD77689.1| DNA-directed RNA polymerase alpha chain [Rhodopirellula baltica SH
           1]
 gi|327538948|gb|EGF25586.1| DNA-directed RNA polymerase subunit alpha [Rhodopirellula baltica
           WH47]
          Length = 331

 Score =  324 bits (830), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 128/328 (39%), Positives = 195/328 (59%), Gaps = 5/328 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +   W+ +  P+++E        +      AEP  RGF  ++GN++RRVL+SSL G+A+T
Sbjct: 3   MHIRWRGMELPSSLEVDR-DSLTQTYGKFSAEPFERGFGASIGNSMRRVLLSSLVGSAVT 61

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            ++I G  HE ++I GV ED+TDI+LN+K + +  + DS + +T+ +   GVVT  D+QT
Sbjct: 62  QIKIRGAQHEFTTIPGVLEDVTDIVLNVKSLIVNSNTDSTRVITVERNTAGVVTGADVQT 121

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
             D+E++N DHVIC L  D    ME+ V  G GYVP+  H + +  IG+I IDA++SPI 
Sbjct: 122 DADVEIINKDHVICTLTDDVPFMMEMVVETGRGYVPSTEHSSVDHEIGIIPIDAVFSPIV 181

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +V Y VE+ R GQ  +YD+L++ I TDG+I  E ++  A++IL+  L  F+ + E    +
Sbjct: 182 RVRYEVEATRVGQKTNYDRLNLEIWTDGTINPEMALTEAAKILRKHLNPFVQYRELGPSI 241

Query: 242 KE----DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
                             L   + +L LSVR+ NCL  ENI+ + DL+QRTE  +L + N
Sbjct: 242 FSAARGGAGSPEAQLEAKLNMTLADLRLSVRANNCLESENIMTVRDLVQRTEDSLLEVRN 301

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           FG  +L E++  L   GL LGM +P+ P
Sbjct: 302 FGDTTLNEVREKLSQYGLHLGMRVPNQP 329


>gi|309785617|ref|ZP_07680248.1| DNA-directed RNA polymerase, alpha subunit [Shigella dysenteriae
           1617]
 gi|308926737|gb|EFP72213.1| DNA-directed RNA polymerase, alpha subunit [Shigella dysenteriae
           1617]
          Length = 304

 Score =  324 bits (830), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 142/305 (46%), Positives = 209/305 (68%), Gaps = 7/305 (2%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
             EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+K
Sbjct: 2   TLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLK 61

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTV 149
           G+ +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + V
Sbjct: 62  GLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKV 121

Query: 150 SKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            +G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + ++
Sbjct: 122 RRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEME 181

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+P LL+ V++LEL+
Sbjct: 182 TNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP---EVKEEKPEFDPILLRPVDDLELT 238

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP
Sbjct: 239 VRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPP 298

Query: 327 ESIEE 331
            SI +
Sbjct: 299 ASIAD 303


>gi|224713514|gb|ACN62064.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus minor]
          Length = 309

 Score =  324 bits (830), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 141/315 (44%), Positives = 211/315 (66%), Gaps = 10/315 (3%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KP+ +    + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLH
Sbjct: 1   KPHLVN---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLH 57

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E SS +GV ED+ +++LN+KG+ +K+       +T+ K G G VTAGDI    D+E++NP
Sbjct: 58  EYSSKEGVQEDILEVLLNLKGLAVKVQSKDDVVLTLNKSGIGPVTAGDITHDGDVEIVNP 117

Query: 131 DHVICNL-DVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYSPIKKVSYT 186
           DHVIC+L D +A + M + V +G GYVPA      + ++ PIG + +DA +SP+ +++Y 
Sbjct: 118 DHVICHLTDKNASINMRIRVQRGRGYVPASARIHAQDDDRPIGRLLVDARFSPVDRIAYN 177

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++ 
Sbjct: 178 VEAARVEQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVK 234

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EI
Sbjct: 235 EEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEI 294

Query: 307 KGVLGTMGLFLGMNL 321
           K VL + GL LGM L
Sbjct: 295 KDVLASRGLSLGMRL 309


>gi|198282664|ref|YP_002218985.1| DNA-directed RNA polymerase subunit alpha [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218666577|ref|YP_002424857.1| DNA-directed RNA polymerase, alpha subunit [Acidithiobacillus
           ferrooxidans ATCC 23270]
 gi|198247185|gb|ACH82778.1| DNA-directed RNA polymerase, alpha subunit [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218518790|gb|ACK79376.1| DNA-directed RNA polymerase, alpha subunit [Acidithiobacillus
           ferrooxidans ATCC 23270]
          Length = 339

 Score =  324 bits (830), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 142/332 (42%), Positives = 209/332 (62%), Gaps = 5/332 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           EL++P  ++  V+      R  +   PL RGF HTLG+ LRRVL+SSL+GAA+T V+I+G
Sbjct: 6   ELLRPQGVDVEVIS---ARRARLALGPLERGFGHTLGSGLRRVLLSSLKGAAVTEVEIEG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE SSI+GV ED+ DI+LN+K + ++  G     VT+ KRGPG +T  DI + + IEV
Sbjct: 63  VLHEYSSIEGVQEDVVDILLNLKMLAVRAHGRGDAVVTLRKRGPGQMTGADIVSEHGIEV 122

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGY-VPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
            NP+ VI  L  D  + + L + +G GY   A   ++    IG++ +DA +SP+ +VSY 
Sbjct: 123 ANPEQVIATLTRDVELVLRLRIDEGRGYDAAATRRQSHEKRIGVMALDASFSPVLRVSYL 182

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+AR  Q  D D+L + ++T+G +    +V  A+RI + QLG+    E  +      + 
Sbjct: 183 VENARVEQRTDLDRLILDVETNGVVDPVWAVQEAARIFRSQLGVLAGAETREIPEASQVQ 242

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           V S    P L++ V++LEL+VRS NCL+ E+I Y+GDL+Q++E ++L+  N GRKSL EI
Sbjct: 243 V-SQSLTPLLIRPVDDLELTVRSANCLKAEDIFYIGDLVQKSEQELLKAPNLGRKSLNEI 301

Query: 307 KGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           K VL   GL LGM L  WPPE++  +  +  D
Sbjct: 302 KEVLVAHGLTLGMRLDSWPPENLPPVPGRAAD 333


>gi|238898902|ref|YP_002924584.1| RNA polymerase, alpha subunit [Candidatus Hamiltonella defensa 5AT
           (Acyrthosiphon pisum)]
 gi|229466662|gb|ACQ68436.1| RNA polymerase, alpha subunit [Candidatus Hamiltonella defensa 5AT
           (Acyrthosiphon pisum)]
          Length = 330

 Score =  324 bits (830), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 142/334 (42%), Positives = 218/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  +    + Q   +   +  EPL RGF HTLGNALRR+L+SS++G A+T
Sbjct: 1   MQGSEIEFLKPRLVN---IEQISPSHAKITLEPLERGFGHTLGNALRRILLSSMQGYAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +++LN+KG+ +K+ G +   VT+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEVLLNLKGLKVKVQGKNEVTVTLNKSGIGPVLAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALY 177
             D+E++ P HVIC L D +A + M++ + +G GYVPA        +  PIG + +DA Y
Sbjct: 118 NGDVEIVKPQHVICYLTDENASISMKIKIQRGRGYVPASSRMNLEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  ++ IL  QL  FI+    
Sbjct: 178 SPVERIAYVVEAARVEQRTDLDKLVIDMETNGTINPEEAIRFSATILAKQLEAFIDLHHV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---ELKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL +  L LGM L +WPP ++ +
Sbjct: 295 LGKKSLTEIKDVLASRALSLGMRLENWPPANLSD 328


>gi|303233188|ref|ZP_07319861.1| DNA-directed RNA polymerase, alpha subunit [Atopobium vaginae
           PB189-T1-4]
 gi|302480773|gb|EFL43860.1| DNA-directed RNA polymerase, alpha subunit [Atopobium vaginae
           PB189-T1-4]
          Length = 314

 Score =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 123/317 (38%), Positives = 189/317 (59%), Gaps = 8/317 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E I+P     +V+    EN   +  EPL RG+  TLGN++RRVL+SSL GAA+ A+ I
Sbjct: 1   MSEFIRPQ----VVVEDISENLARVNVEPLERGYGDTLGNSMRRVLLSSLEGAAVEAISI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS-HKRVTIFKRGPGVVTAGDIQTVND 124
           DGV HE S+I GV+ED+TDI+LN+KG+  + +G       +I   GP  V AGD     +
Sbjct: 57  DGVQHEFSTIPGVYEDVTDIVLNVKGLVFRSNGTGSEAEASISVDGPCTVVAGDFLIPAE 116

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +++N DH IC L   A + M + +  G  YV    +  E+DPIG+I +D+L+SP+ + +
Sbjct: 117 FDLINKDHHICTLCEGAHLSMRMRIGMGRSYVSGDDNEREDDPIGVIHVDSLFSPVTRCA 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
             VE  R GQ  +YD+L + ++T+GSI+  D+V  A+ I+   +  F++  E ++E  ED
Sbjct: 177 KVVEPCRVGQHTNYDRLILEVETNGSISPRDAVIQAADIINQHMCAFMDLAEDEQEPLED 236

Query: 245 INVK---SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++        N  L K++E+L+LSVRS NCL+   I  +  L++ +E D+L + NFG K
Sbjct: 237 ASIFSTVEEEDNTELDKQIEDLDLSVRSYNCLKRAGIHNVRQLVEFSENDLLNIRNFGVK 296

Query: 302 SLVEIKGVLGTMGLFLG 318
           S+ E++  L   GL L 
Sbjct: 297 SIEEVREKLEAAGLGLK 313


>gi|304413170|ref|ZP_07394643.1| RNA polymerase alpha subunit [Candidatus Regiella insecticola LSR1]
 gi|304284013|gb|EFL92406.1| RNA polymerase alpha subunit [Candidatus Regiella insecticola LSR1]
          Length = 335

 Score =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 144/335 (42%), Positives = 213/335 (63%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q + +E +KP+ I      +  +    +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVKEFLKPSLI----SEKISQTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 56

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV-TIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+  I+LN+K + +K+    ++ + T+ K G G VTA DI 
Sbjct: 57  EVEIEGVLHEYSTKEGVKEDILSILLNLKELAVKVQEKENEVILTLEKSGIGPVTAADIT 116

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDAL 176
           + + IE++ P+HVIC+L    A + M + V +G GYVPA        +  PIG + +DA 
Sbjct: 117 SDSKIEIIKPEHVICHLTDKSASINMRIKVQRGRGYVPASTRVHGEEDERPIGRLLVDAC 176

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSPI++++Y VE+ R     D DKL + ++T+G+I  E+++  AS IL +QL  F++   
Sbjct: 177 YSPIERIAYNVEATRYQDRTDLDKLIIEMETNGTIDPEEAIRHASTILSEQLTAFVDISH 236

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
                K  +     P  P LL+ V++LEL+VRS NCL+ E I ++GDL+QRTE ++L+  
Sbjct: 237 NVNTCKTSVEAPDFP--PILLRPVDDLELTVRSANCLKAEAIHFIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL   GL LGM L +WPP SI +
Sbjct: 295 NLGKKSLTEIKDVLAVHGLSLGMRLENWPPASIAD 329


>gi|332086261|gb|EGI91417.1| DNA-directed RNA polymerase, alpha subunit [Shigella dysenteriae
           155-74]
          Length = 304

 Score =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 141/305 (46%), Positives = 208/305 (68%), Gaps = 7/305 (2%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
             EPL RGF HTLGNALRR+L+SS+ G A+  V+IDGVLHE S+ +GV ED+ +I+LN+K
Sbjct: 2   TLEPLERGFGHTLGNALRRILLSSMPGCAVIEVEIDGVLHEYSTKEGVQEDILEILLNLK 61

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTV 149
           G+ +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + V
Sbjct: 62  GLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKV 121

Query: 150 SKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            +G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + ++
Sbjct: 122 QRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEME 181

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+P LL+ V++LEL+
Sbjct: 182 TNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP---EVKEEKPEFDPILLRPVDDLELT 238

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP
Sbjct: 239 VRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPP 298

Query: 327 ESIEE 331
            SI +
Sbjct: 299 ASIAD 303


>gi|262370553|ref|ZP_06063878.1| RNA polymerase [Acinetobacter johnsonii SH046]
 gi|262314353|gb|EEY95395.1| RNA polymerase [Acinetobacter johnsonii SH046]
          Length = 335

 Score =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 141/330 (42%), Positives = 223/330 (67%), Gaps = 8/330 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +   E + P  I+   +         +I EPL RGF HTLGNALRR+L+SSL GAA+ 
Sbjct: 1   MTRTANEFLTPQAIKVEAVSGTS---AKVILEPLERGFGHTLGNALRRILLSSLPGAAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GV HE S+++G+ +D+ +++LN+KG+++K+   +   +T+ K+GPG VTA D++ 
Sbjct: 58  EVEIEGVEHEYSTLEGLQQDIVELLLNLKGLSIKLFDQNEAYLTLEKQGPGDVTAADLRL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSP 179
            +++EV+NP+H+I  L     ++M L VS+G GY  +     E +  P+G + +DA YSP
Sbjct: 118 PHNVEVVNPEHLIGTLSASGSLKMRLKVSQGRGYETSDSRFPEGETRPVGRLQLDASYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           IK+VSYTVE+AR  Q  D DKL + ++T+G++  E+++  A+ ILQ Q+ +F++ ++ + 
Sbjct: 178 IKRVSYTVENARVEQRTDLDKLVIDLETNGTVDPEEAIRKAATILQQQIAIFVDLQKDQA 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            V ++   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G
Sbjct: 238 PVAQEPREE---VDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 324


>gi|291166852|gb|EFE28898.1| DNA-directed RNA polymerase, alpha subunit [Filifactor alocis ATCC
           35896]
          Length = 315

 Score =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 126/313 (40%), Positives = 199/313 (63%), Gaps = 6/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KPN    + + +   +      EPL RGF  T+GN+LRRVL+SSL G A+ +++I+G
Sbjct: 3   EIEKPN----VTVLEYRNDYGKFALEPLERGFGITVGNSLRRVLLSSLPGVAVNSIKIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGV--VTAGDIQTVNDI 125
           VLHE S+I GV ED+T+I+L +K + + M+ +  ++ T+     G   +TAGDI    D+
Sbjct: 59  VLHEFSTIPGVKEDVTEIMLTLKELAMVMNSEESRQRTLIIEQEGEGIITAGDIICPPDV 118

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD  I     D  + ME+ VSKG GYV ++ ++TE+ PIG+I +D++Y+P+KKV+Y
Sbjct: 119 EVLNPDLHIMTCSKDTKLYMEINVSKGRGYVSSEDNKTEDMPIGVIPMDSIYTPVKKVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           T+E  R G   + +KL+  I T+GS   +++V+L S+IL + L +F+N  +   E++  +
Sbjct: 179 TIEPTRVGARSNLEKLTFEIWTNGSFEVQEAVSLGSKILIEHLNLFLNLSDKLSEIELMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +      AL   +EEL+LSVRS NCL+  +I  + +L ++TE DM+++ N G+KSL E
Sbjct: 239 EKEEGKKEKALEMTIEELDLSVRSYNCLKRASINTVEELTKKTEDDMMKVRNLGKKSLEE 298

Query: 306 IKGVLGTMGLFLG 318
           + G L  +G  L 
Sbjct: 299 VVGKLHDLGFTLK 311


>gi|315655841|ref|ZP_07908739.1| DNA-directed RNA polymerase subunit alpha [Mobiluncus curtisii ATCC
           51333]
 gi|315489905|gb|EFU79532.1| DNA-directed RNA polymerase subunit alpha [Mobiluncus curtisii ATCC
           51333]
          Length = 335

 Score =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 121/320 (37%), Positives = 187/320 (58%), Gaps = 8/320 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E ++  Q    R+    EPL  GF +TLGN+LRR L+SS+ G+A+T+++I+G LH
Sbjct: 13  QPKLTEEVINEQ----RSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGSAVTSIKIEGALH 68

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+T I+LNIK I L    D    + + K G G VT GDI     + + NP
Sbjct: 69  EFTTLPGVKEDVTQIVLNIKEIVLSSDNDEPVVMYLRKTGEGEVTVGDIMPPAGVVIHNP 128

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           +H I  L+ D  + +ELTV +G GYV A  ++     I  I +D++YSP+ KVSY VE+ 
Sbjct: 129 EHHIATLNKDGKLEIELTVERGRGYVSASQNKDPEAEISRIPVDSIYSPVLKVSYRVEAT 188

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  +I   D++A A + L +  G+  +     + ++   +    
Sbjct: 189 RVEQRTDFDRLVVDVETKKAILPRDAMASAGKTLVELFGLARDLNHDAEGIELGPSGNDA 248

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   VE+L+L+ R+ NCL  E I  +GDL+ R++AD+L + NFG+KS+ EIK  L
Sbjct: 249 ALAEDLAMSVEDLDLTSRALNCLTREGINTVGDLVARSQADLLDIRNFGQKSIDEIKEKL 308

Query: 311 GTMGLFLGMNLPDWPPESIE 330
             M    GM+L D P  ++E
Sbjct: 309 AGM----GMSLKDTPMPAVE 324


>gi|189219450|ref|YP_001940091.1| DNA-directed RNA polymerase, alpha subunit [Methylacidiphilum
           infernorum V4]
 gi|189186308|gb|ACD83493.1| DNA-directed RNA polymerase, alpha subunit [Methylacidiphilum
           infernorum V4]
          Length = 337

 Score =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 129/327 (39%), Positives = 197/327 (60%), Gaps = 7/327 (2%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P +I               I EP   G+ HTLGN+LRR+L+SSL GAAI++V+I+GV+HE
Sbjct: 11  PRSI-VKDETVSNSTFGKYIIEPFESGYGHTLGNSLRRILLSSLEGAAISSVKIEGVMHE 69

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            ++++GV ED+ DI+LN+K + +KM     +   +     G VTAGDIQ    +E++NP+
Sbjct: 70  FTTMEGVVEDVVDIVLNLKKVLIKMPDRQTRVFRVDVFKEGAVTAGDIQVDPGVEIVNPE 129

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
            +IC LD    + MEL V  G G++  ++++ ++  IG+I ID L+SP++ V YTVE+ R
Sbjct: 130 QLICTLDKKQRLLMELEVKVGRGFLLGEYNKKQDQSIGVIPIDCLFSPVRHVKYTVENTR 189

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE---DINVK 248
            GQ  DYD+L   I TDG I  ++++  ++ ILQ  L +F+ + +   E ++    I  +
Sbjct: 190 VGQRTDYDRLIFEIWTDGRIGPDEALVQSAAILQHHLDIFVQYGKEPVEFEKPKPPIKEE 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L   V E+ELSVR+ NCL   NI  +G L  +TEA+ML+  NFG+KSL EIK 
Sbjct: 250 ENRLRKILNMSVNEIELSVRAANCLNNANITTVGQLAMKTEAEMLKYRNFGKKSLNEIKE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKK 335
            L ++GL LGM    + P  +++  +K
Sbjct: 310 KLASLGLSLGM---KFDPSLLDQTEEK 333


>gi|32423696|gb|AAP81239.1| RNA polymerase alpha subunit [Candidatus Portiera aleyrodidarum]
          Length = 329

 Score =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 143/327 (43%), Positives = 208/327 (63%), Gaps = 7/327 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            +  E ++P+ I    +     N  ++  EPL RGF HTLGNALRR+L+S + G A+   
Sbjct: 2   SSVNEFVRPSKINVEAISN---NHAIISLEPLERGFGHTLGNALRRILLSYMPGCAVVEA 58

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +I GV HE S I G+ ED+ +IILNIK I +K+ G     + + K G GVV AGDI+   
Sbjct: 59  EIKGVQHEYSVIDGIKEDVIEIILNIKEIAIKLYGIDEIELELKKIGSGVVKAGDIKARQ 118

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           D+EV+NPDHVI +L+    + M+L   +G GY PA      +   G I IDA +SP+K+V
Sbjct: 119 DVEVINPDHVIAHLNDHGELNMKLRFVRGRGYEPAYLRNKSDKNYGRIQIDAKFSPVKRV 178

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EPKKEVK 242
           +Y VESAR  Q  D+DKL + ++T+G++  E+++  +++IL++QL  F++   E KK V+
Sbjct: 179 AYFVESARVEQKTDFDKLIIELETNGTLDPEEAIRTSAKILRNQLDFFVDLSCENKKHVE 238

Query: 243 EDINVK---SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            ++          + ALL  VE+LEL+VRS NCL+ ENI Y+GDL++RTE ++L+  N G
Sbjct: 239 NEVEHDRRTDTKIDKALLLPVEDLELTVRSANCLKAENIFYIGDLVKRTEGELLKTPNLG 298

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           +KSL EIK VL   GL LGM++  WPP
Sbjct: 299 KKSLNEIKKVLKVRGLALGMHIDLWPP 325


>gi|261415794|ref|YP_003249477.1| DNA-directed RNA polymerase, alpha subunit [Fibrobacter
           succinogenes subsp. succinogenes S85]
 gi|261372250|gb|ACX74995.1| DNA-directed RNA polymerase, alpha subunit [Fibrobacter
           succinogenes subsp. succinogenes S85]
          Length = 324

 Score =  323 bits (828), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 139/328 (42%), Positives = 210/328 (64%), Gaps = 5/328 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M+   W+ L  P + + +  G E+      + E L RG+  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MM---WKSLQMPRSFQKVETG-EDGRYAKFVVEALERGWGITLGNALRRVLLSSLQGAAI 56

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
            +V+I+GV  E S+I GV ED+TDIILN+K I +K+  D  + + +   G G VTA D  
Sbjct: 57  VSVKIEGVDKEFSTIPGVKEDVTDIILNLKSIRVKLLSDHDETLHLDMSGDGEVTAKDFM 116

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              ++ +L PD  I  L+ +A + M++ +S G GYV A   + ++ PIG+I +DA ++P+
Sbjct: 117 DNPNVTILTPDVHIATLNGNASLSMDVKISCGRGYVVADELKDKDAPIGVIAMDANFNPV 176

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KV+  +   R GQ  DY++L + I TDGSI  ED++A A+++L D L +FINFE   + 
Sbjct: 177 QKVAMHISDTRVGQKTDYNRLELEITTDGSIDPEDALAYAAKLLVDHLEIFINFEGDLES 236

Query: 241 VKE-DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            +E +++ +       L  +V++LELSVRS+NCLR  NI  +G+L++  E DML+  NFG
Sbjct: 237 PEELEMDEERQRIANLLRMRVDDLELSVRSSNCLRMANIHTIGELVRNKENDMLKYKNFG 296

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           RKSLVE+  VL +MGL  GM++ D+  +
Sbjct: 297 RKSLVELNEVLTSMGLSFGMDVDDYLKD 324


>gi|262280200|ref|ZP_06057984.1| RNA polymerase [Acinetobacter calcoaceticus RUH2202]
 gi|299768691|ref|YP_003730717.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter sp. DR1]
 gi|262257978|gb|EEY76712.1| RNA polymerase [Acinetobacter calcoaceticus RUH2202]
 gi|298698779|gb|ADI89344.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter sp. DR1]
          Length = 335

 Score =  323 bits (828), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 139/330 (42%), Positives = 223/330 (67%), Gaps = 8/330 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +   E + P  I+   +         +I EPL RGF HTLGNALRR+L+SSL GAA+ 
Sbjct: 1   MTRTANEFLTPQAIKVEAVSGTS---AKVILEPLERGFGHTLGNALRRILLSSLPGAAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GV HE S+++G+ +D+ +++LN+KG+++K+   +   +T+ K+GPG +TA D++ 
Sbjct: 58  EVEIEGVEHEYSTLEGLQQDIVELLLNLKGLSIKLFDQNEAYLTLEKQGPGEITAADLRL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSP 179
            +++EV+NP+H+I  L     ++M L V++G GY  +     E +  P+G + +DA YSP
Sbjct: 118 PHNVEVVNPEHLIGTLSASGSLKMRLKVAQGRGYETSDSRFPEGETRPVGRLQLDASYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           IK+VSYTVE+AR  Q  D DKL + ++T+G++  E+++  A+ ILQ Q+ +F++ ++ + 
Sbjct: 178 IKRVSYTVENARVEQRTDLDKLVIDLETNGTVDPEEAIRKAATILQQQIAIFVDLQKDQT 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            V ++   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G
Sbjct: 238 PVAQEPREE---VDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 324


>gi|226953896|ref|ZP_03824360.1| RNA polymerase, alpha subunit [Acinetobacter sp. ATCC 27244]
 gi|294651609|ref|ZP_06728913.1| DNA-directed RNA polymerase [Acinetobacter haemolyticus ATCC 19194]
 gi|226835379|gb|EEH67762.1| RNA polymerase, alpha subunit [Acinetobacter sp. ATCC 27244]
 gi|292822458|gb|EFF81357.1| DNA-directed RNA polymerase [Acinetobacter haemolyticus ATCC 19194]
          Length = 335

 Score =  323 bits (828), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 140/330 (42%), Positives = 222/330 (67%), Gaps = 8/330 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +   E + P  I+   +         +I EPL RGF HTLGNALRR+L+SSL GAA+ 
Sbjct: 1   MTRTANEFLTPQAIKVEAVSGTS---AKVILEPLERGFGHTLGNALRRILLSSLPGAAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GV HE S+++G+ +D+ +++LN+KG+++K+   +   +T+ K+G G VTA D++ 
Sbjct: 58  EVEIEGVEHEYSTLEGLQQDIVELLLNLKGLSIKLFDQNEAYLTLEKQGAGDVTAADLRL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSP 179
            +++EV+NPDH+I  L     ++M L V++G GY  +     E +  P+G + +DA YSP
Sbjct: 118 PHNVEVVNPDHLIGTLSASGSLKMRLKVAQGRGYETSDSRFPEGETRPVGRLQLDASYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           IK+VSYTVE+AR  Q  D DKL + ++T+G++  E+++  A+ ILQ Q+ +F++ ++ + 
Sbjct: 178 IKRVSYTVENARVEQRTDLDKLVIDLETNGTVDPEEAIRKAATILQQQIAIFVDLQKDQT 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            V ++   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G
Sbjct: 238 PVAQEPREE---VDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 324


>gi|241888925|ref|ZP_04776229.1| DNA-directed RNA polymerase, alpha subunit [Gemella haemolysans
           ATCC 10379]
 gi|241864174|gb|EER68552.1| DNA-directed RNA polymerase, alpha subunit [Gemella haemolysans
           ATCC 10379]
          Length = 313

 Score =  323 bits (828), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 129/310 (41%), Positives = 189/310 (60%), Gaps = 2/310 (0%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           + KP     I+    ++     + EPL RG+  TLGN+LRR+L+SSL GAA  ++ I+GV
Sbjct: 4   IEKPKI--QIIEESSDKRFGRFVVEPLERGYGTTLGNSLRRMLISSLPGAAARSIDIEGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE  +IKGV ED+T+II+N+K I   +  +  K+V+I  +GP VVTA DI   +DIEV+
Sbjct: 62  QHEFQAIKGVVEDVTEIIMNVKNIAFVVHSEEEKQVSISVKGPAVVTAADIAIDSDIEVV 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           N D  I  +       M + V KG G+VPA  ++  + PIG+I ID++Y+P+ KV+YTVE
Sbjct: 122 NTDQHIATVSEGGQFEMIIYVGKGRGFVPADGNKKRDLPIGVIPIDSIYTPVSKVNYTVE 181

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
             R GQ  D+DKL + + T+GSIT  D++ALAS+IL   L +F+   E  K  +  +  +
Sbjct: 182 KTRVGQSTDFDKLILDVTTNGSITANDALALASKILISHLELFMEMSEEAKAAEILVAKE 241

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L   +EEL+LSVRS NCL+   I  + +L  +TE +M+++ N GRKSL E+K 
Sbjct: 242 EDNKVQMLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEQEMIKVRNLGRKSLEEVKI 301

Query: 309 VLGTMGLFLG 318
            L  + L   
Sbjct: 302 KLQELELGFK 311


>gi|169823878|ref|YP_001691489.1| DNA-directed RNA polymerase subunit alpha [Finegoldia magna ATCC
           29328]
 gi|303234800|ref|ZP_07321426.1| DNA-directed RNA polymerase, alpha subunit [Finegoldia magna
           BVS033A4]
 gi|167830683|dbj|BAG07599.1| DNA-directed RNA polymerase alpha subunit [Finegoldia magna ATCC
           29328]
 gi|302494141|gb|EFL53921.1| DNA-directed RNA polymerase, alpha subunit [Finegoldia magna
           BVS033A4]
          Length = 317

 Score =  323 bits (827), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 132/306 (43%), Positives = 197/306 (64%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           IV   E+ N    +  PL RG+  TLGN+LRRVL+SSL GAAI+ + I GV HE+S+IKG
Sbjct: 11  IVELDEQNNYGKFVIMPLERGYGTTLGNSLRRVLLSSLPGAAISKINIQGVAHEMSTIKG 70

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +IILN+KGI +K   +    + +  +GP V+TA DI    D+EV NPDH I  L
Sbjct: 71  VKEDVPEIILNLKGIAVKKYNEEPISLNVDIKGPCVLTAKDILVDTDLEVKNPDHYIATL 130

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + DA + M++TV  G GY  ++ ++T+ D IG I ID+L+SP+KKV++TV++AR GQV+D
Sbjct: 131 NEDASLEMQITVINGKGYKISEFNKTDEDIIGDIAIDSLFSPVKKVNFTVDNARVGQVID 190

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           YDKL++ + T+G+I  +D+++  S IL + L +F      +     D           ++
Sbjct: 191 YDKLTIEVWTNGTIRPQDALSEGSNILINCLELFSELPNYECNTNSDDEDNQKDKETQMV 250

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +EEL+ S+RS NCL+  NI  +GD++  T+ADM+++ NFG+KSL E++  L  MGL  
Sbjct: 251 INIEELDFSLRSFNCLKRANINTVGDIVSHTKADMMKIKNFGKKSLDEVEEKLQEMGLAF 310

Query: 318 GMNLPD 323
              + D
Sbjct: 311 KQEIKD 316


>gi|224713516|gb|ACN62065.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus minor]
          Length = 307

 Score =  323 bits (827), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 142/313 (45%), Positives = 211/313 (67%), Gaps = 10/313 (3%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KP+ +    + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLH
Sbjct: 1   KPHLVN---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLH 57

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E SS +GV ED+ +++LN+KG+ +K+       +T+ K G G VTAGDI    D+E++NP
Sbjct: 58  EYSSKEGVQEDILEVLLNLKGLAVKVQSKDDVVLTLNKSGIGPVTAGDITHDGDVEIVNP 117

Query: 131 DHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYT 186
           DHVIC+L D +A + M + V +G GYVPA    H + ++ PIG + +DA +SP+ +++Y 
Sbjct: 118 DHVICHLTDKNASINMRIRVQRGRGYVPASARVHTQDDDRPIGRLLVDARFSPVDRIAYN 177

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++ V   + 
Sbjct: 178 VEAARVEQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQPV---VK 234

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EI
Sbjct: 235 EEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEI 294

Query: 307 KGVLGTMGLFLGM 319
           K VL + GL LGM
Sbjct: 295 KDVLASRGLSLGM 307


>gi|293610849|ref|ZP_06693149.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292827193|gb|EFF85558.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|325123579|gb|ADY83102.1| RNA polymerase, alpha subunit [Acinetobacter calcoaceticus PHEA-2]
          Length = 335

 Score =  323 bits (827), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 139/330 (42%), Positives = 223/330 (67%), Gaps = 8/330 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +   E + P  I+   +         +I EPL RGF HTLGNALRR+L+SSL GAA+ 
Sbjct: 1   MTRTANEFLTPQAIKVEAVSGTS---AKVILEPLERGFGHTLGNALRRILLSSLPGAAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GV HE S+++G+ +D+ +++LN+KG+++K+   +   +T+ K+GPG +TA D++ 
Sbjct: 58  EVEIEGVEHEYSTLEGLQQDIVELLLNLKGLSIKLFDQNEAYLTLEKQGPGDITAADLRL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSP 179
            +++EV+NP+H+I  L     ++M L V++G GY  +     E +  P+G + +DA YSP
Sbjct: 118 PHNVEVVNPEHLIGTLSASGSLKMRLKVAQGRGYETSDSRFPEGETRPVGRLQLDASYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           IK+VSYTVE+AR  Q  D DKL + ++T+G++  E+++  A+ ILQ Q+ +F++ ++ + 
Sbjct: 178 IKRVSYTVENARVEQRTDLDKLVIDLETNGTVDPEEAIRKAATILQQQIAIFVDLQKDQT 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            V ++   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G
Sbjct: 238 PVAQEPREE---VDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 324


>gi|282882483|ref|ZP_06291104.1| DNA-directed RNA polymerase, alpha subunit [Peptoniphilus
           lacrimalis 315-B]
 gi|300814667|ref|ZP_07094918.1| DNA-directed RNA polymerase, alpha subunit [Peptoniphilus sp. oral
           taxon 836 str. F0141]
 gi|281297625|gb|EFA90100.1| DNA-directed RNA polymerase, alpha subunit [Peptoniphilus
           lacrimalis 315-B]
 gi|300511286|gb|EFK38535.1| DNA-directed RNA polymerase, alpha subunit [Peptoniphilus sp. oral
           taxon 836 str. F0141]
          Length = 315

 Score =  323 bits (827), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 129/311 (41%), Positives = 186/311 (59%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP     I    +       I EPL  G+  T+GN+LRRVL+SSL GAA++ + I G
Sbjct: 3   EIEKPKI--TIDKLDDSGKYGKFIVEPLESGYGITIGNSLRRVLLSSLPGAAVSFINIRG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE  +I GV ED+ +IILN+K I  KM  D   ++ I K G G +TAGDI     + V
Sbjct: 61  VEHEFDTIPGVLEDVPEIILNVKSIVFKMENDEPVKLIIEKSGKGEITAGDIILEPSVSV 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NP+H I  L+ DA V +E+TV KG GY P++  + E   IG+I +D+ YSP++KV++ V
Sbjct: 121 VNPNHHIATLNEDADVYIEMTVEKGRGYEPSELKKDEVTQIGIIPVDSNYSPVRKVNWKV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  DYD+L + + TDGS+  +++ +LA++IL + L +FI       EV   +  
Sbjct: 181 ENTRVGQRTDYDRLILEVTTDGSMKADEATSLAAKILTEHLDLFIGLINHVDEVNIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +           VEEL+LSVRS NCL+   I  +G+L  +TE DM+++ N G+KSL E+ 
Sbjct: 241 EEDQSEKVKEMTVEELDLSVRSFNCLKRAGINTVGELTNKTEEDMMKVRNLGKKSLEEVV 300

Query: 308 GVLGTMGLFLG 318
             L  M L L 
Sbjct: 301 SKLQEMNLSLK 311


>gi|262373496|ref|ZP_06066774.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter junii
           SH205]
 gi|262311249|gb|EEY92335.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter junii
           SH205]
          Length = 335

 Score =  323 bits (827), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 140/330 (42%), Positives = 222/330 (67%), Gaps = 8/330 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +   E + P  I+   +         +I EPL RGF HTLGNALRR+L+SSL GAA+ 
Sbjct: 1   MTRTANEFLTPQAIKVEAVSGTS---AKVILEPLERGFGHTLGNALRRILLSSLPGAAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GV HE S+++G+ +D+ +++LN+KG+++K+   +   +T+ K+G G VTA D++ 
Sbjct: 58  EVEIEGVEHEYSTLEGLQQDIVELLLNLKGLSIKLFDQNEAYLTLEKQGAGDVTAADLRL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSP 179
            +++EV+NPDH+I  L     ++M L V++G GY  +     E +  P+G + +DA YSP
Sbjct: 118 PHNVEVVNPDHLIGTLSSSGSLKMRLKVAQGRGYETSDSRFPEGETRPVGRLQLDASYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           IK+VSYTVE+AR  Q  D DKL + ++T+G++  E+++  A+ ILQ Q+ +F++ ++ + 
Sbjct: 178 IKRVSYTVENARVEQRTDLDKLVIDLETNGTVDPEEAIRKAATILQQQIAIFVDLQKDQT 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            V ++   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G
Sbjct: 238 PVAQEPREE---VDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 324


>gi|160914535|ref|ZP_02076750.1| hypothetical protein EUBDOL_00541 [Eubacterium dolichum DSM 3991]
 gi|158433693|gb|EDP11982.1| hypothetical protein EUBDOL_00541 [Eubacterium dolichum DSM 3991]
          Length = 319

 Score =  323 bits (827), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 127/302 (42%), Positives = 187/302 (61%), Gaps = 5/302 (1%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E +N    + EPL RGF  T+GNALRRVL+SSL GAA+ ++++DGV HE +SI G+ ED
Sbjct: 15  NEADNYGKFVFEPLERGFGTTIGNALRRVLLSSLPGAAVFSIKVDGVYHEFTSIPGIVED 74

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           ++ +ILNIK + +K+  D    + I K+GPG VT  DI     +EVL+ D  IC L+   
Sbjct: 75  VSAMILNIKTLVMKIQDDEIYTLRISKQGPGEVTGADIICPEGVEVLSKDLHICTLEEGG 134

Query: 142 VVRMELTVSKGHGYVPAKHHR----TENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           ++ MEL    G GYV A  ++    T N P+G+I  D++Y+PI++V+Y  E  R GQ   
Sbjct: 135 MLEMELQARNGRGYVSADTNKQLYQTPNQPLGIIYTDSIYTPIERVAYNAEPTRVGQNAH 194

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE-DINVKSLPFNPAL 256
           YDK+++ I TD SI+  +SVALA++IL D L +  N  E   +++      +    N  L
Sbjct: 195 YDKVTLEIWTDSSISPAESVALAAKILIDHLELLTNVHEAVNDMESLMKEAQGEVQNKGL 254

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
           +  +E+L+LSVRS NCL+   I  + +L QRTE +M+R+ N G+KSL E+K  +  +GL 
Sbjct: 255 VMMIEDLDLSVRSYNCLKRAGIQTVEELTQRTEDEMMRVRNLGKKSLKEVKDKIYDLGLS 314

Query: 317 LG 318
             
Sbjct: 315 FK 316


>gi|308233885|ref|ZP_07664622.1| DNA-directed RNA polymerase, alpha subunit [Atopobium vaginae DSM
           15829]
 gi|328943592|ref|ZP_08241057.1| DNA-directed RNA polymerase subunit alpha [Atopobium vaginae DSM
           15829]
 gi|327491561|gb|EGF23335.1| DNA-directed RNA polymerase subunit alpha [Atopobium vaginae DSM
           15829]
          Length = 314

 Score =  323 bits (827), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 124/317 (39%), Positives = 191/317 (60%), Gaps = 8/317 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E I+P     + +    EN   +  EPL RG+  TLGN++RRVL+SSL GAA+ A+ I
Sbjct: 1   MSEFIRPQ----VSVVDISENLARVNVEPLERGYGDTLGNSMRRVLLSSLEGAAVEAISI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQTVND 124
           DGV HE S++ GV+ED+TDI+LN+KG+    +G       +I   GP  VT GD +   +
Sbjct: 57  DGVQHEFSTVDGVYEDVTDIVLNVKGLVFHANGSGETAEASISIDGPCTVTGGDFKIPAE 116

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            E++N DHVIC L     + M + +  G GYV    +  + DPIG+I +D+LYSP+++ +
Sbjct: 117 FELINKDHVICTLGEGGHLAMRMRIGVGRGYVSGDDNERDEDPIGVIHVDSLYSPVRRCA 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
            TVE  R GQ  +YD+L + I+T+GSI+  D+V  A+ I+   +  F++  E ++E +ED
Sbjct: 177 KTVEPCRVGQHTNYDRLILEIETNGSISPRDAVIEAADIINQHMAAFMDLAEDEEEPQED 236

Query: 245 INVKSLPFNPAL---LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +++ S           K++E+L+LSVRS NCL+   I  +  L++ +E D+L + NFG K
Sbjct: 237 VSIFSNEEEEENTELDKQIEDLDLSVRSYNCLKRAGIHNVRQLVEFSENDLLNIRNFGVK 296

Query: 302 SLVEIKGVLGTMGLFLG 318
           S+ E++  L   GL L 
Sbjct: 297 SIEEVRDKLEDAGLGLK 313


>gi|293402527|ref|ZP_06646662.1| DNA-directed RNA polymerase, alpha subunit [Erysipelotrichaceae
           bacterium 5_2_54FAA]
 gi|291304041|gb|EFE45295.1| DNA-directed RNA polymerase, alpha subunit [Erysipelotrichaceae
           bacterium 5_2_54FAA]
          Length = 319

 Score =  323 bits (827), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 126/302 (41%), Positives = 191/302 (63%), Gaps = 5/302 (1%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E ++    + EPL RGF  T+GNALRRVL+SSL GAA+ ++++DGV HE +SI G+ ED
Sbjct: 15  DESKHYGKFVFEPLERGFGTTIGNALRRVLLSSLPGAAVFSIKVDGVYHEFTSIPGIVED 74

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T +ILNIK + +K+  D    + I K+GPG VT  DI     +EVL+ D  IC L+   
Sbjct: 75  VTTMILNIKTLVMKIQDDEIYTLRISKQGPGEVTGADIYCPEGVEVLSKDLHICTLEEGG 134

Query: 142 VVRMELTVSKGHGYVPAKHHR----TENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           ++ MEL    G GYV A  ++    T N P+G+I  D++Y+PI+KVSY+V+  R GQ  +
Sbjct: 135 MLEMELQARVGRGYVNADTNKQLYQTPNQPLGIIYTDSIYTPIEKVSYSVDPTRVGQNAN 194

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK-EDINVKSLPFNPAL 256
           YDK+++ + +D SI+  +S+AL+++IL D L +  N +E   +++      +    N  L
Sbjct: 195 YDKVTLEVWSDSSISPAESLALSAKILIDHLELLTNVDEAVNDMESVMKEAQGEVQNKGL 254

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
           +  +E+L+LSVRS NCL+   I  + +L QRTE +M+R+ N G+KSL E+K  L  +GL 
Sbjct: 255 VMMIEDLDLSVRSYNCLKRAGIQTVEELTQRTEDEMMRVRNLGKKSLKEVKDKLYDLGLN 314

Query: 317 LG 318
             
Sbjct: 315 FK 316


>gi|302379835|ref|ZP_07268319.1| DNA-directed RNA polymerase, alpha subunit [Finegoldia magna
           ACS-171-V-Col3]
 gi|302312423|gb|EFK94420.1| DNA-directed RNA polymerase, alpha subunit [Finegoldia magna
           ACS-171-V-Col3]
          Length = 317

 Score =  322 bits (826), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 133/306 (43%), Positives = 197/306 (64%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           IV   E+ N    +  PL RG+  TLGN+LRRVL+SSL GAAI+ + I GV HE+S+IKG
Sbjct: 11  IVELDEQNNYGKFVIMPLERGYGTTLGNSLRRVLLSSLPGAAISKINIQGVAHEMSTIKG 70

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +IILN+KGI +K   +    + +  +GP V+TA DI    D+EV NPDH I  L
Sbjct: 71  VKEDVPEIILNLKGIAVKKYNEEPISLNVDIKGPCVLTAKDILVDTDLEVKNPDHYIATL 130

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + DA + M++TV  G GY  ++ ++TE D IG I ID+L+SP+KKV++TV++AR GQV+D
Sbjct: 131 NEDASLEMQITVINGKGYKISEFNKTEEDIIGDIAIDSLFSPVKKVNFTVDNARVGQVID 190

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           YDKL++ + T+G+I  +D+++  S IL + L +F      +     D           ++
Sbjct: 191 YDKLTIEVWTNGTIRPQDALSEGSNILINCLELFSELPNYECNTNSDDEDNQKDKETQMV 250

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +EEL+ S+RS NCL+  NI  +GD++  T+ADM+++ NFG+KSL E++  L  MGL  
Sbjct: 251 INIEELDFSLRSFNCLKRANINTVGDIVSHTKADMMKIKNFGKKSLDEVEEKLQEMGLAF 310

Query: 318 GMNLPD 323
              + D
Sbjct: 311 KQEIKD 316


>gi|296120769|ref|YP_003628547.1| DNA-directed RNA polymerase, subunit alpha [Planctomyces
           limnophilus DSM 3776]
 gi|296013109|gb|ADG66348.1| DNA-directed RNA polymerase, alpha subunit [Planctomyces
           limnophilus DSM 3776]
          Length = 336

 Score =  322 bits (826), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 128/333 (38%), Positives = 196/333 (58%), Gaps = 12/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++  W+ L  P+ +                 EP  RGF  T+GN+LRR+L+SSL G+++T
Sbjct: 1   MRIRWRGLELPSRV-VPERETLSSTYGKFTVEPFERGFGSTIGNSLRRILLSSLEGSSVT 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+I GV HE ++I G+ ED+T+I+LN+K I +K    S K + I K   GVVTAGDI T
Sbjct: 60  SVKIQGVQHEFTTIPGIVEDVTEIVLNLKAIIVKNHSPSTKTLRIEKTSRGVVTAGDIIT 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            + +E+LN D VI  +  D  + +E+TV  G GY+PA  H      +G+I +DA++SP+ 
Sbjct: 120 DDQVEILNRDLVIATMTDDVPLYLEMTVENGRGYIPAADHHGPEQELGVIPLDAIFSPVV 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +V Y +E  R GQ  +YD+L + I T+G++T E ++  +++IL+  L  FI + EP  E+
Sbjct: 180 RVRYLIEETRVGQRTNYDRLILEIWTNGTVTPESALVESAKILRKHLNPFITYREPGPEM 239

Query: 242 KED-----------INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
             +                L     L + + EL LSVR+TNCL  E I ++ DL+ RTE 
Sbjct: 240 FPEGGLRNMLEATGYAPVDLELEEKLGQSLAELNLSVRATNCLESEGINFVRDLVTRTED 299

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            +L++ NFG  +L E++  LG +GL LGM LP+
Sbjct: 300 QLLQVRNFGETTLTEVRERLGLIGLRLGMKLPN 332


>gi|330827907|ref|YP_004390859.1| DNA-directed RNA polymerase subunit alpha [Aeromonas veronii B565]
 gi|328803043|gb|AEB48242.1| DNA-directed RNA polymerase subunit alpha [Aeromonas veronii B565]
          Length = 304

 Score =  322 bits (826), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 144/305 (47%), Positives = 211/305 (69%), Gaps = 7/305 (2%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
             EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ +I+LN+K
Sbjct: 2   TLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDILEILLNLK 61

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV-DAVVRMELTV 149
           GI +K+ G     +++ K G G VTAGDI   +++E++NP+HVIC+L   +A + M L V
Sbjct: 62  GIAVKLEGKDEVTLSLTKSGTGPVTAGDITYGDEVEIVNPEHVICHLTGANAEISMRLKV 121

Query: 150 SKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            +G GYVPA    H+  E  PIG + +D+ +SPI +++Y VE+AR  Q  D DKL + ++
Sbjct: 122 QRGRGYVPASARVHNDDEERPIGRLLLDSAFSPIVRIAYNVEAARVEQRTDLDKLVIDME 181

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+G++  E+++  ++ IL +QL  F++  +     K++   +   F+P LL+ V++LEL+
Sbjct: 182 TNGTLDPEEAIRRSATILAEQLEAFVDLRDVSVPEKKE---EKPEFDPILLRPVDDLELT 238

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP
Sbjct: 239 VRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPP 298

Query: 327 ESIEE 331
            SI +
Sbjct: 299 ASIAD 303


>gi|50086190|ref|YP_047700.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter sp. ADP1]
 gi|61215915|sp|Q6F7T7|RPOA_ACIAD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|49532166|emb|CAG69878.1| RNA polymerase, alpha subunit [Acinetobacter sp. ADP1]
          Length = 335

 Score =  322 bits (826), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 140/330 (42%), Positives = 223/330 (67%), Gaps = 8/330 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +   E + P  I+   +         +I EPL RGF HTLGNALRR+L+SSL GAA+ 
Sbjct: 1   MTRTANEFLTPQAIKVEAVSGTS---AKVILEPLERGFGHTLGNALRRILLSSLPGAAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GV HE S+++G+ +D+ +++LN+KG+++K+   +   +T+ K+GPG +TA D++ 
Sbjct: 58  EVEIEGVEHEYSTLEGLQQDIVELLLNLKGLSIKLFDQNEAYLTLEKQGPGDITAADLRL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSP 179
            +++EV+NP+H+I  L     ++M L VS+G GY  +     E +  P+G + +DA YSP
Sbjct: 118 PHNVEVVNPEHLIGTLSASGSIKMRLKVSQGRGYETSDSRFPEGETRPVGRLQLDASYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           IK+VSYTVE+AR  Q  D DKL + ++T+G++  E+++  A+ ILQ Q+ +F++ ++ + 
Sbjct: 178 IKRVSYTVENARVEQRTDLDKLVIDLETNGTVDPEEAIRKAATILQQQIAIFVDLQKDQA 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            V ++   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G
Sbjct: 238 PVAQEPREE---VDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 324


>gi|299143167|ref|ZP_07036247.1| DNA-directed RNA polymerase, alpha subunit [Peptoniphilus sp. oral
           taxon 386 str. F0131]
 gi|298517652|gb|EFI41391.1| DNA-directed RNA polymerase, alpha subunit [Peptoniphilus sp. oral
           taxon 386 str. F0131]
          Length = 315

 Score =  322 bits (826), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 137/310 (44%), Positives = 197/310 (63%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP+ IE + L  E       + EPL  G+  T+GN+LRRVL+SSL GAAI+ + I G
Sbjct: 3   EIEKPS-IEKLELD-ESGVYGKFVVEPLESGYGITIGNSLRRVLLSSLPGAAISFINIRG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE ++I GV ED+  IILNIKGI LK + D   +V I K+G G + A DIQT  D+E+
Sbjct: 61  VEHEFATIPGVLEDVPQIILNIKGIVLKTNEDEPVKVIIEKKGEGEILASDIQTGGDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N DH I  L+ DA V +ELT+ +G GY P++  + E   IG+I ID+ Y+PIKKV++ V
Sbjct: 121 INLDHHIATLNEDADVYIELTIERGRGYEPSELKKDEITEIGVIPIDSNYTPIKKVNWKV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R G   DYD+L + + TDGS+  +++ +LA++IL + L +FI   E    V   +  
Sbjct: 181 ENTRVGNRTDYDRLILEVTTDGSMKADEATSLAAKILTEHLNLFIGLTEHVNNVNIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   VEEL+LSVRS NCL+  NI  + +L Q++E DM+++ N G+KSL E++
Sbjct: 241 EEDQKEKVLEMTVEELDLSVRSFNCLKRANINTVEELTQKSEDDMMKVRNLGKKSLEEVE 300

Query: 308 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 NKLAELGLGL 310


>gi|329768299|ref|ZP_08259800.1| DNA-directed RNA polymerase subunit alpha [Gemella haemolysans
           M341]
 gi|328837498|gb|EGF87127.1| DNA-directed RNA polymerase subunit alpha [Gemella haemolysans
           M341]
          Length = 313

 Score =  322 bits (826), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 129/310 (41%), Positives = 189/310 (60%), Gaps = 2/310 (0%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           + KP     I+    ++     + EPL RG+  TLGN+LRR+L+SSL GAA  ++ I+GV
Sbjct: 4   IEKPKI--QIIEESSDKRFGRFVVEPLERGYGTTLGNSLRRMLISSLPGAAARSIDIEGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE  +IKGV ED+T+II+N+K I   +  +  K+V+I  +GP VVTA DI   +DIEV+
Sbjct: 62  QHEFQAIKGVVEDVTEIIMNVKNIAFVVHSEEEKQVSISVKGPAVVTAADIAIDSDIEVV 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           N D  I  +       M + V KG G+VPA  ++  + PIG+I ID++Y+P+ KV+YTVE
Sbjct: 122 NTDQHIATVSEGGQFEMIIYVGKGRGFVPADGNKKRDLPIGVIPIDSIYTPVSKVNYTVE 181

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
             R GQ  D+DKL + + T+GSIT  D++ALAS+IL   L +F+   E  K  +  +  +
Sbjct: 182 KTRVGQSTDFDKLILDVTTNGSITANDALALASKILISHLELFMEMSEEAKAAEILVAKE 241

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L   +EEL+LSVRS NCL+   I  + +L  +TE +M+++ N GRKSL E+K 
Sbjct: 242 EDNKVQMLEMTIEELDLSVRSYNCLKRAGINTVQELASKTEQEMIKVRNLGRKSLEEVKI 301

Query: 309 VLGTMGLFLG 318
            L  + L   
Sbjct: 302 KLQELELGFK 311


>gi|169632375|ref|YP_001706111.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter baumannii
           SDF]
 gi|169794619|ref|YP_001712412.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter baumannii
           AYE]
 gi|184159573|ref|YP_001847912.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter baumannii
           ACICU]
 gi|213158810|ref|YP_002320808.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter baumannii
           AB0057]
 gi|215482208|ref|YP_002324390.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter baumannii
           AB307-0294]
 gi|239503209|ref|ZP_04662519.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter baumannii
           AB900]
 gi|260557052|ref|ZP_05829269.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter baumannii
           ATCC 19606]
 gi|294839722|ref|ZP_06784405.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter sp.
           6013113]
 gi|294860400|ref|ZP_06798169.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter sp.
           6013150]
 gi|301345035|ref|ZP_07225776.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter baumannii
           AB056]
 gi|301512034|ref|ZP_07237271.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter baumannii
           AB058]
 gi|301595209|ref|ZP_07240217.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter baumannii
           AB059]
 gi|158513671|sp|A3M959|RPOA_ACIBT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|226699350|sp|B7GW27|RPOA_ACIB3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|226699351|sp|B7IA14|RPOA_ACIB5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238688116|sp|B0V6U7|RPOA_ACIBY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238688241|sp|B0VQU3|RPOA_ACIBS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238691002|sp|B2HZ83|RPOA_ACIBC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|169147546|emb|CAM85407.1| RNA polymerase, alpha subunit [Acinetobacter baumannii AYE]
 gi|169151167|emb|CAO99839.1| RNA polymerase, alpha subunit [Acinetobacter baumannii]
 gi|183211167|gb|ACC58565.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Acinetobacter baumannii ACICU]
 gi|193078462|gb|ABO13453.2| RNA polymerase alpha subunit [Acinetobacter baumannii ATCC 17978]
 gi|213057970|gb|ACJ42872.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter baumannii
           AB0057]
 gi|213988894|gb|ACJ59193.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter baumannii
           AB307-0294]
 gi|260409658|gb|EEX02959.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter baumannii
           ATCC 19606]
 gi|322509483|gb|ADX04937.1| RNA polymerase, alpha subunit [Acinetobacter baumannii 1656-2]
 gi|323519504|gb|ADX93885.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter baumannii
           TCDC-AB0715]
          Length = 335

 Score =  322 bits (826), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 140/330 (42%), Positives = 223/330 (67%), Gaps = 8/330 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +   E + P  I+   +         +I EPL RGF HTLGNALRR+L+SSL GAA+ 
Sbjct: 1   MTRTANEFLTPQAIKVEAVSGTS---AKVILEPLERGFGHTLGNALRRILLSSLPGAAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GV HE S+++G+ +D+ +++LN+KG+++K+   +   +T+ K+GPG +TA D++ 
Sbjct: 58  EVEIEGVEHEYSTLEGLQQDIVELLLNLKGLSIKLFDQNEAYLTLEKQGPGDITAADLRL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSP 179
            +++EV+NP+H+I  L     ++M L VS+G GY  +     E +  P+G + +DA YSP
Sbjct: 118 PHNVEVVNPEHLIGTLSATGSLKMRLKVSQGRGYETSDSRFPEGETRPVGRLQLDASYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           IK+VSYTVE+AR  Q  D DKL + ++T+G++  E+++  A+ ILQ Q+ +F++ ++ + 
Sbjct: 178 IKRVSYTVENARVEQRTDLDKLVIDLETNGTVDPEEAIRKAATILQQQIAIFVDLQKDQT 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            V ++   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G
Sbjct: 238 PVAQEPREE---VDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 324


>gi|114778797|ref|ZP_01453604.1| DNA-directed RNA polymerase, alpha subunit [Mariprofundus
           ferrooxydans PV-1]
 gi|114550928|gb|EAU53492.1| DNA-directed RNA polymerase, alpha subunit [Mariprofundus
           ferrooxydans PV-1]
          Length = 325

 Score =  322 bits (826), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 146/330 (44%), Positives = 219/330 (66%), Gaps = 7/330 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           LI P +I      +       ++ EPL RG+  T+GN+LRR+L+SSL GAA+T+V +DGV
Sbjct: 3   LINPRHISIE--EKVPGRAAKIVFEPLERGYGTTIGNSLRRMLLSSLPGAAVTSVLMDGV 60

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE  SIKGV ED+ DIIL++K ++L+M GD    +++  +G  +VTA DI+    + VL
Sbjct: 61  AHEYDSIKGVREDVMDIILSLKELDLRMEGDEAATISLEIKGSAIVTAADIKCPAGLSVL 120

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+ ++ +L+ DA +++E  V KG GY PA     +   +G + +DA YSPI++VS  VE
Sbjct: 121 NPELILAHLNDDAHLKIEAVVEKGRGYEPATDREVDERAVGSLLVDASYSPIRRVSTRVE 180

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +AR GQ  +YDKL M I+T+GS++ E+++  A++IL+ QL +F++FE     +  +    
Sbjct: 181 AARVGQRTNYDKLIMEIETNGSLSPEEALNSAAKILEAQLAVFVDFENV--SIVSEPEGP 238

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
               +  L++ +E L+LSVRS NCL+ +++  +GDL+QR+E +MLR  NFGRKSL EIK 
Sbjct: 239 DDTLDNLLIQPIEHLDLSVRSMNCLKSDDVFRVGDLVQRSEQEMLRTPNFGRKSLNEIKE 298

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           VL  MGL LGM+LP+WPP   +E A+  ED
Sbjct: 299 VLENMGLELGMDLPNWPP---QEDAEALED 325


>gi|317496164|ref|ZP_07954524.1| DNA-directed RNA polymerase [Gemella moribillum M424]
 gi|316913739|gb|EFV35225.1| DNA-directed RNA polymerase [Gemella moribillum M424]
          Length = 313

 Score =  322 bits (825), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 124/312 (39%), Positives = 186/312 (59%), Gaps = 2/312 (0%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           + KP     I+    ++     + EPL RG+  TLGN+LRR+L+SSL GAA  ++ I+GV
Sbjct: 4   IEKPKI--QIIEESSDKRFGRFVVEPLERGYGTTLGNSLRRMLISSLPGAAARSIDIEGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE  +IKGV ED+T+II+N+K I   +  +  K ++I  +GP VVTA DI   +D+EV+
Sbjct: 62  QHEFQAIKGVVEDVTEIIMNVKNIAFIIHSEEEKVLSINVKGPAVVTAADIAIDSDVEVV 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           N D  I  +       M + V  G G+VPA  ++  + PIG+I ID++Y+P+ KV+YTVE
Sbjct: 122 NVDQHIATVAEGGHFEMLIYVGTGRGFVPADGNKRRDLPIGVIPIDSIYTPVSKVNYTVE 181

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
             R GQ  D+DKL + + T+G+I+  D++ALAS+IL   L +F+   E  K     +  +
Sbjct: 182 KTRVGQSTDFDKLILDVTTNGTISANDALALASKILISHLELFMEMSEQAKAADILVAKE 241

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L   +EEL+LSVRS NCL+   I  + +L  +TE +M+++ N GRKSL E+K 
Sbjct: 242 EDNKVQMLEMTIEELDLSVRSYNCLKRAGINTVQELASKTEQEMIKVRNLGRKSLEEVKI 301

Query: 309 VLGTMGLFLGMN 320
            L  + L     
Sbjct: 302 KLQELELGFKDE 313


>gi|255319790|ref|ZP_05360995.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter
           radioresistens SK82]
 gi|262380323|ref|ZP_06073477.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter
           radioresistens SH164]
 gi|255303109|gb|EET82321.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter
           radioresistens SK82]
 gi|262297769|gb|EEY85684.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter
           radioresistens SH164]
          Length = 335

 Score =  322 bits (825), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 138/330 (41%), Positives = 223/330 (67%), Gaps = 8/330 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +   E + P  I+   +         +I EPL RGF HTLGNALRR+L+SSL GAA+ 
Sbjct: 1   MTRTANEFLTPQAIKVEAVSGTS---AKVILEPLERGFGHTLGNALRRILLSSLPGAAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GV HE S+++G+ +D+ +++LN+KG+++K+   +   +T+ K+GPG +TA D++ 
Sbjct: 58  EVEIEGVEHEYSTLEGLQQDIVELLLNLKGLSIKLFDQNEAYLTLEKQGPGDITAADLRL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSP 179
            +++EV+NP+H+I  L     ++M L V++G GY  +     E +  P+G + +DA YSP
Sbjct: 118 PHNVEVVNPEHLIGTLSASGSIKMRLKVAQGRGYETSDSRFPEGETRPVGRLQLDASYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I++VSYTVE+AR  Q  D DKL + ++T+G++  E+++  A+ ILQ Q+ +F++ ++ + 
Sbjct: 178 IQRVSYTVENARVEQRTDLDKLIIDLETNGTVDPEEAIRKAATILQQQIAIFVDLQKDQA 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            V ++   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G
Sbjct: 238 PVAQEPREE---VDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 324


>gi|294507076|ref|YP_003571134.1| DNA-directed RNA polymerase alpha chain [Salinibacter ruber M8]
 gi|158518577|sp|Q2S3N9|RPOA_SALRD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|294343404|emb|CBH24182.1| DNA-directed RNA polymerase alpha chain [Salinibacter ruber M8]
          Length = 328

 Score =  322 bits (825), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 138/315 (43%), Positives = 202/315 (64%), Gaps = 3/315 (0%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           E + + +  ++    +  PL RG+  T+GNALRRVL+SSLRG AITAV+IDGV HE S+I
Sbjct: 10  EGVHVEEVSDSEGQFVMGPLERGYGVTIGNALRRVLLSSLRGLAITAVKIDGVQHEFSTI 69

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVI 134
            GV ED+ D+ILN+K +  K        + +   GPG  TA DI +   + +VLNPD  +
Sbjct: 70  PGVTEDVADLILNLKEVRFKADEMQEGHLHLNLEGPGNWTAADIDEATAEYDVLNPDQHV 129

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
             L  DAVV ++L V  G GYVP++ ++ E+DPIG+I ID++++PIK V+Y V+  R GQ
Sbjct: 130 ATLAEDAVVNVDLRVGYGRGYVPSEENKREDDPIGVIAIDSIFTPIKNVNYEVKPTRVGQ 189

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF-- 252
            +DY++L + ++TDGS+T E+++   + IL+D +  FI  EE  + V E+  V       
Sbjct: 190 KIDYEELLLDVETDGSLTPEEAITQGASILRDHVSFFIQLEEEPEPVVEEQEVDEEVKRI 249

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
              L + V+EL+LSVRS NCL+  NI  +GDL++R E +ML+  NFGRKSL E+  VL  
Sbjct: 250 RELLAQPVDELDLSVRSHNCLKAANIKTIGDLVRREEDEMLKFRNFGRKSLQELVEVLDE 309

Query: 313 MGLFLGMNLPDWPPE 327
            GL  GM++ ++  E
Sbjct: 310 RGLQFGMDVEEYLEE 324


>gi|257471550|ref|ZP_05635549.1| DNA-directed RNA polymerase subunit alpha [Buchnera aphidicola str.
           LSR1 (Acyrthosiphon pisum)]
          Length = 324

 Score =  321 bits (824), Expect = 6e-86,   Method: Composition-based stats.
 Identities = 143/326 (43%), Positives = 212/326 (65%), Gaps = 10/326 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           + ++P  ++   + Q     T +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDG
Sbjct: 2   DFLRPRLVD---IEQISATHTKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+ +GV ED+ +I+LN+K + +K+ G     +T+ K G G +TA DI    D+E+
Sbjct: 59  VLHEYSTKEGVQEDVLEILLNLKALAVKVYGKDETLLTLHKSGIGSITAADIIHDGDVEI 118

Query: 128 LNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYSPIKKV 183
           + P HVIC+L D +A ++M + V +G GY+PA        +  PIG + +DA YSPI ++
Sbjct: 119 IKPQHVICHLTDENASIKMRIKVQRGRGYIPASSRVHLEEDARPIGCLLVDACYSPINRI 178

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    
Sbjct: 179 SYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDIREPE-- 236

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 237 -FKEEKPEFEPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 295

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESI 329
            EIK VL +  L LGM L +WPP SI
Sbjct: 296 TEIKDVLASRSLSLGMRLENWPPSSI 321


>gi|83815189|ref|YP_445192.1| DNA-directed RNA polymerase subunit alpha [Salinibacter ruber DSM
           13855]
 gi|83756583|gb|ABC44696.1| DNA-directed RNA polymerase, alpha subunit [Salinibacter ruber DSM
           13855]
          Length = 321

 Score =  321 bits (824), Expect = 7e-86,   Method: Composition-based stats.
 Identities = 138/315 (43%), Positives = 202/315 (64%), Gaps = 3/315 (0%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           E + + +  ++    +  PL RG+  T+GNALRRVL+SSLRG AITAV+IDGV HE S+I
Sbjct: 3   EGVHVEEVSDSEGQFVMGPLERGYGVTIGNALRRVLLSSLRGLAITAVKIDGVQHEFSTI 62

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVI 134
            GV ED+ D+ILN+K +  K        + +   GPG  TA DI +   + +VLNPD  +
Sbjct: 63  PGVTEDVADLILNLKEVRFKADEMQEGHLHLNLEGPGNWTAADIDEATAEYDVLNPDQHV 122

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
             L  DAVV ++L V  G GYVP++ ++ E+DPIG+I ID++++PIK V+Y V+  R GQ
Sbjct: 123 ATLAEDAVVNVDLRVGYGRGYVPSEENKREDDPIGVIAIDSIFTPIKNVNYEVKPTRVGQ 182

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF-- 252
            +DY++L + ++TDGS+T E+++   + IL+D +  FI  EE  + V E+  V       
Sbjct: 183 KIDYEELLLDVETDGSLTPEEAITQGASILRDHVSFFIQLEEEPEPVVEEQEVDEEVKRI 242

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
              L + V+EL+LSVRS NCL+  NI  +GDL++R E +ML+  NFGRKSL E+  VL  
Sbjct: 243 RELLAQPVDELDLSVRSHNCLKAANIKTIGDLVRREEDEMLKFRNFGRKSLQELVEVLDE 302

Query: 313 MGLFLGMNLPDWPPE 327
            GL  GM++ ++  E
Sbjct: 303 RGLQFGMDVEEYLEE 317


>gi|294842678|ref|ZP_06787361.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter sp.
           6014059]
          Length = 335

 Score =  321 bits (824), Expect = 7e-86,   Method: Composition-based stats.
 Identities = 140/330 (42%), Positives = 223/330 (67%), Gaps = 8/330 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +   E + P  I+   +         +I EPL RGF HTLGNALRR+L+SSL GAA+ 
Sbjct: 1   MTRTANEFLTPQAIKVEAVSGTS---ATVILEPLERGFGHTLGNALRRILLSSLPGAAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GV HE S+++G+ +D+ +++LN+KG+++K+   +   +T+ K+GPG +TA D++ 
Sbjct: 58  EVEIEGVEHEYSTLEGLQQDIVELLLNLKGLSIKLFDQNEAYLTLEKQGPGDITAADLRL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSP 179
            +++EV+NP+H+I  L     ++M L VS+G GY  +     E +  P+G + +DA YSP
Sbjct: 118 PHNVEVVNPEHLIGTLSATGSLKMRLKVSQGRGYETSDSRFPEGETRPVGRLQLDASYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           IK+VSYTVE+AR  Q  D DKL + ++T+G++  E+++  A+ ILQ Q+ +F++ ++ + 
Sbjct: 178 IKRVSYTVENARVEQRTDLDKLVIDLETNGTVDPEEAIRKAATILQQQIAIFVDLQKDQT 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            V ++   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G
Sbjct: 238 PVAQEPREE---VDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 324


>gi|329770014|ref|ZP_08261409.1| DNA-directed RNA polymerase subunit alpha [Gemella sanguinis M325]
 gi|328837325|gb|EGF86955.1| DNA-directed RNA polymerase subunit alpha [Gemella sanguinis M325]
          Length = 313

 Score =  321 bits (824), Expect = 7e-86,   Method: Composition-based stats.
 Identities = 128/309 (41%), Positives = 187/309 (60%), Gaps = 2/309 (0%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           + KP     I+    ++     + EPL RG+  TLGN+LRR+L+SSL GAA  ++ I GV
Sbjct: 4   IEKPKI--QIIEESSDKRFGRFVVEPLERGYGTTLGNSLRRMLISSLPGAAARSIDIQGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE  ++KGV ED+T+II+N+K I  K+  +  K V+I  +GP VVTA DI   +DIEV+
Sbjct: 62  QHEFQAVKGVVEDVTEIIMNVKNIAFKVHSEEEKVVSINVKGPAVVTAEDIAIDSDIEVI 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           N D  I  +       M + V KG G+VPA  ++  + PIG+I ID++Y+P+ KV+YTVE
Sbjct: 122 NTDQHIATVSEGGQFEMLIYVGKGRGFVPADGNKKRDLPIGVIPIDSIYTPVSKVNYTVE 181

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
             R GQ  D+DKL + + T+G+IT  D++ALAS+IL   L +F+   E  K     +  +
Sbjct: 182 KTRVGQSTDFDKLILDVTTNGTITANDALALASKILISHLELFMEMSEEAKAADILVAKE 241

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L   +EEL+LSVRS NCL+   I  + +L  +TE +M+++ N GRKSL E+K 
Sbjct: 242 EDNKVQMLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEQEMIKVRNLGRKSLEEVKI 301

Query: 309 VLGTMGLFL 317
            L  + L  
Sbjct: 302 KLQDLELGF 310


>gi|78484664|ref|YP_390589.1| DNA-directed RNA polymerase subunit alpha [Thiomicrospira crunogena
           XCL-2]
 gi|119366747|sp|Q31IV8|RPOA_THICR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|78362950|gb|ABB40915.1| DNA-directed RNA polymerase, alpha subunit [Thiomicrospira
           crunogena XCL-2]
          Length = 329

 Score =  321 bits (824), Expect = 7e-86,   Method: Composition-based stats.
 Identities = 146/329 (44%), Positives = 215/329 (65%), Gaps = 7/329 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q+  ++L+ P  ++   +       + +  EPL RGF HTLGNALRR+L+SS+ GAAI 
Sbjct: 1   MQEMLEQLLTPRLVDIKTVNGFN---SRVTLEPLERGFGHTLGNALRRILLSSMPGAAIV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             QIDGVLHE S+I+GV ED+ +I+LN+K + +K++  S   +T+ K+GP VVTA DIQ 
Sbjct: 58  EAQIDGVLHEYSAIEGVREDVLEIMLNLKEVAIKLNETSEAELTLSKKGPAVVTAADIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT-ENDPIGLITIDALYSPI 180
            +D E++NPD VI +L   A + M+L V KG GY  A      E+  IG++ +DA +SP+
Sbjct: 118 NHDTEIMNPDLVIAHLGEGAELSMKLKVEKGIGYRAAVQSSDSESANIGVLKLDASFSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K VSY V++AR  Q  D DKL + + TDG++  ED++  A+ +L  QL  F++ +  +  
Sbjct: 178 KTVSYEVQNARVEQRTDLDKLILNVVTDGTLDPEDAIKQAATVLHYQLIAFVDLKHKEIV 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V+E+   +   F+P  L+ V++LEL+VRS NCL+ E I Y+GDL+QR E+ +L+  N G+
Sbjct: 238 VQEE---EENEFDPIFLQPVDDLELTVRSANCLKAEQIYYIGDLVQRAESSLLKTPNLGK 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           KSL EIK VL   GL LG  L +WPP S+
Sbjct: 295 KSLQEIKDVLAQRGLGLGTKLENWPPSSL 323


>gi|171911662|ref|ZP_02927132.1| DNA-directed RNA polymerase subunit alpha [Verrucomicrobium
           spinosum DSM 4136]
          Length = 371

 Score =  321 bits (823), Expect = 9e-86,   Method: Composition-based stats.
 Identities = 132/328 (40%), Positives = 194/328 (59%), Gaps = 8/328 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
              PN +         +     +AEP  RG+ HT+GN+LRRVL+SSL GA+IT+V+I G 
Sbjct: 8   FEMPNRL-VKNEATATDYYAQFVAEPFDRGYGHTIGNSLRRVLLSSLEGASITSVRIKGA 66

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK-MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
            HE +++ GV ED+T I+LN+K +  +       + + +     GVVTAGDI+     +V
Sbjct: 67  EHEFTTLPGVLEDVTQIVLNLKKVKFRHFENKETRLLQVSVDKEGVVTAGDIKDDTSYQV 126

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N D VIC LD       EL V  G G+   + ++  + PIG+I ID+++SP+ +V Y V
Sbjct: 127 INKDQVICTLDRKGKFEAELEVKVGRGFATNEDNKRPDMPIGVIPIDSIFSPVTRVKYGV 186

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK---ED 244
           E+ R GQ  DYDKL + + TDG IT +D++  +S IL+  L +F+N+++ + E +   E 
Sbjct: 187 EATRVGQNTDYDKLLIDVWTDGRITPQDALLQSSAILRKHLDVFVNYDDNQVEFEVAPEA 246

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
            + ++L     L   V E+ELSVR+ NCL   NI  +G L  ++EA+MLR  NFG+KSL 
Sbjct: 247 QSEENLELRKLLNMSVNEIELSVRAANCLNNANITSVGQLAMKSEAEMLRYRNFGKKSLT 306

Query: 305 EIKGVLGTMGLFLGMNLPDWPPESIEEL 332
           EIK  L  +GL LGM L    P  +E L
Sbjct: 307 EIKEKLSELGLTLGMKL---DPSLLEPL 331


>gi|297588218|ref|ZP_06946862.1| DNA-directed RNA polymerase subunit alpha [Finegoldia magna ATCC
           53516]
 gi|297574907|gb|EFH93627.1| DNA-directed RNA polymerase subunit alpha [Finegoldia magna ATCC
           53516]
          Length = 317

 Score =  321 bits (823), Expect = 9e-86,   Method: Composition-based stats.
 Identities = 132/306 (43%), Positives = 196/306 (64%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           IV   E+ N    +  PL RG+  TLGN+LRRVL+SSL GAAI+ + I GV HE+S+IKG
Sbjct: 11  IVELDEQNNYGKFVIMPLERGYGTTLGNSLRRVLLSSLPGAAISKINIQGVAHEMSTIKG 70

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +IILN+KGI +K   +    + +  +GP V+TA DI    D+EV NPDH I  L
Sbjct: 71  VKEDVPEIILNLKGIAVKKYNEEPISLNVDIKGPCVLTAKDILVDTDLEVKNPDHYIATL 130

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + DA + M++TV  G GY  ++ ++T+ D IG I ID+L+SP+KKV++TV++AR GQV+D
Sbjct: 131 NEDASLEMQITVINGKGYKISEFNKTDEDIIGDIAIDSLFSPVKKVNFTVDNARVGQVID 190

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           YDKL++ + T+G+I  +D+++  S IL + L +F      +     D           + 
Sbjct: 191 YDKLTIEVWTNGTIRPQDALSEGSNILINCLELFSELPNYECNTNSDDEDNQKDKETQMG 250

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +EEL+ S+RS NCL+  NI  +GD++  T+ADM+++ NFG+KSL E++  L  MGL  
Sbjct: 251 INIEELDFSLRSFNCLKRANINTVGDIVSHTKADMMKIKNFGKKSLDEVEEKLQEMGLAF 310

Query: 318 GMNLPD 323
              + D
Sbjct: 311 KEEIKD 316


>gi|262377287|ref|ZP_06070511.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter lwoffii
           SH145]
 gi|262307740|gb|EEY88879.1| DNA-directed RNA polymerase, alpha subunit [Acinetobacter lwoffii
           SH145]
          Length = 335

 Score =  321 bits (823), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 139/330 (42%), Positives = 222/330 (67%), Gaps = 8/330 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +   E + P  I+   +         +I EPL RGF HTLGNALRR+L+SSL GAA+ 
Sbjct: 1   MTRTANEFLTPQAIK---VEAASGTSAKVILEPLERGFGHTLGNALRRILLSSLPGAAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GV HE S+++G+ +D+ +++LN+KG+++K+   +   +T+ K+G G VTA D++ 
Sbjct: 58  EVEIEGVEHEYSTLEGLQQDIVELLLNLKGLSIKLFDQNEAYLTLEKQGAGDVTAADLRL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSP 179
            +++EV+NP+H+I  L     ++M L V++G GY  +     E +  P+G + +DA YSP
Sbjct: 118 PHNVEVVNPEHLIGTLSASGSLKMRLKVAQGRGYETSDSRFPEGETRPVGRLQLDASYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           IK+VSYTVE+AR  Q  D DKL + ++T+G++  E+++  A+ ILQ Q+ +F++ ++ + 
Sbjct: 178 IKRVSYTVENARVEQRTDLDKLIIDLETNGTVDPEEAIRKAATILQQQIAIFVDLQKDQA 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            V ++   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G
Sbjct: 238 PVAQEPREE---VDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 324


>gi|190341325|gb|ACE74739.1| RpoA [Enterobacter cowanii]
          Length = 308

 Score =  321 bits (823), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 138/314 (43%), Positives = 208/314 (66%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI    D+E++
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLSKSGIGPVTAADITHDGDVEIV 117

Query: 129 NPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
            P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+++++
Sbjct: 118 KPQHVICHLTDENASINMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACYSPVERIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    +
Sbjct: 178 YNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP---E 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 VKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|320103642|ref|YP_004179233.1| DNA-directed RNA polymerase subunit alpha [Isosphaera pallida ATCC
           43644]
 gi|319750924|gb|ADV62684.1| DNA-directed RNA polymerase subunit alpha [Isosphaera pallida ATCC
           43644]
          Length = 335

 Score =  321 bits (822), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 127/328 (38%), Positives = 192/328 (58%), Gaps = 11/328 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++  W+ L  P+ +         ++    + EP  RGF HT+GN+LRR+L+SSL G+A+T
Sbjct: 1   MRIRWRGLEIPSRV-VPNRETLSDSFGEFVIEPFERGFGHTVGNSLRRILLSSLEGSAVT 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            ++I+GV HE SSI G+ ED+TD++LN+KG+ +K   D  K + I +   G+VTA DI  
Sbjct: 60  RIKIEGVQHEFSSIPGMVEDITDLVLNLKGLIVKNHSDQPKTIVIERDREGIVTAADIVH 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              IEV+NPDH++C L  DA + M +TV  G GY PA    TE+   G I IDA++SP++
Sbjct: 120 DETIEVVNPDHILCTLSGDARLHMRMTVENGRGYRPAAEGHTEDLEPGAIPIDAIFSPVQ 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +V Y VE  R GQ  ++DKL M I T G+I  + ++  A++IL+  L  F+ + EP   +
Sbjct: 180 RVEYRVEETRVGQKTNFDKLIMRIWTTGTIRPDMALVEAAKILRKHLNPFVQYFEPGPGL 239

Query: 242 KED----------INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
             +          +          L   + ELELSVR+TNCL  E I  + +L+ R+E  
Sbjct: 240 PAEGSGPADIGRGLEPHDAELERKLNMSLAELELSVRATNCLESEGITTIRELVSRSEEQ 299

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +L + NFG  +L E++  L  +G+ LGM
Sbjct: 300 LLTVRNFGETTLKEVRSKLNDLGIDLGM 327


>gi|190341389|gb|ACE74771.1| RpoA [Cronobacter dublinensis]
 gi|190341391|gb|ACE74772.1| RpoA [Cronobacter dublinensis]
 gi|190341393|gb|ACE74773.1| RpoA [Cronobacter dublinensis]
 gi|190341395|gb|ACE74774.1| RpoA [Cronobacter dublinensis]
 gi|190341397|gb|ACE74775.1| RpoA [Cronobacter dublinensis]
 gi|190341401|gb|ACE74777.1| RpoA [Cronobacter genomosp. 1]
 gi|190341403|gb|ACE74778.1| RpoA [Cronobacter malonaticus]
 gi|190341405|gb|ACE74779.1| RpoA [Cronobacter malonaticus]
 gi|190341407|gb|ACE74780.1| RpoA [Cronobacter malonaticus]
 gi|190341409|gb|ACE74781.1| RpoA [Cronobacter malonaticus]
 gi|190341411|gb|ACE74782.1| RpoA [Cronobacter malonaticus]
 gi|190341413|gb|ACE74783.1| RpoA [Cronobacter malonaticus]
 gi|190341415|gb|ACE74784.1| RpoA [Cronobacter malonaticus]
 gi|190341417|gb|ACE74785.1| RpoA [Cronobacter muytjensii]
 gi|190341419|gb|ACE74786.1| RpoA [Cronobacter muytjensii]
 gi|190341421|gb|ACE74787.1| RpoA [Cronobacter muytjensii]
 gi|190341423|gb|ACE74788.1| RpoA [Cronobacter muytjensii]
 gi|190341425|gb|ACE74789.1| RpoA [Cronobacter muytjensii]
 gi|190341427|gb|ACE74790.1| RpoA [Cronobacter sakazakii]
 gi|190341429|gb|ACE74791.1| RpoA [Cronobacter sakazakii]
 gi|190341431|gb|ACE74792.1| RpoA [Cronobacter sakazakii]
 gi|190341433|gb|ACE74793.1| RpoA [Cronobacter sakazakii]
 gi|190341435|gb|ACE74794.1| RpoA [Cronobacter sakazakii]
 gi|190341437|gb|ACE74795.1| RpoA [Cronobacter sakazakii]
 gi|190341439|gb|ACE74796.1| RpoA [Cronobacter sakazakii]
 gi|190341441|gb|ACE74797.1| RpoA [Cronobacter sakazakii]
 gi|190341443|gb|ACE74798.1| RpoA [Cronobacter sakazakii]
 gi|190341445|gb|ACE74799.1| RpoA [Cronobacter sakazakii]
 gi|190341447|gb|ACE74800.1| RpoA [Cronobacter sakazakii]
 gi|190341449|gb|ACE74801.1| RpoA [Cronobacter sakazakii]
 gi|190341451|gb|ACE74802.1| RpoA [Cronobacter sakazakii]
 gi|190341455|gb|ACE74804.1| RpoA [Cronobacter sakazakii]
 gi|190341457|gb|ACE74805.1| RpoA [Cronobacter sakazakii]
 gi|190341459|gb|ACE74806.1| RpoA [Cronobacter sakazakii]
 gi|190341463|gb|ACE74808.1| RpoA [Cronobacter sakazakii]
 gi|190341465|gb|ACE74809.1| RpoA [Cronobacter sakazakii]
 gi|190341467|gb|ACE74810.1| RpoA [Cronobacter sakazakii]
 gi|190341469|gb|ACE74811.1| RpoA [Cronobacter sakazakii]
 gi|190341471|gb|ACE74812.1| RpoA [Cronobacter sakazakii]
 gi|190341473|gb|ACE74813.1| RpoA [Cronobacter sakazakii]
 gi|190341475|gb|ACE74814.1| RpoA [Cronobacter sakazakii]
 gi|190341477|gb|ACE74815.1| RpoA [Cronobacter turicensis]
 gi|190341479|gb|ACE74816.1| RpoA [Cronobacter turicensis]
 gi|190341481|gb|ACE74817.1| RpoA [Cronobacter turicensis]
 gi|190341483|gb|ACE74818.1| RpoA [Cronobacter turicensis]
          Length = 308

 Score =  321 bits (822), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 138/314 (43%), Positives = 208/314 (66%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI    D+E++
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVVLTLNKSGIGPVTAADITHDGDVEIV 117

Query: 129 NPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
            P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+++++
Sbjct: 118 KPQHVICHLTDENASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACYSPVERIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    +
Sbjct: 178 YNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP---E 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 VKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|313904923|ref|ZP_07838294.1| DNA-directed RNA polymerase, alpha subunit [Eubacterium
           cellulosolvens 6]
 gi|313470180|gb|EFR65511.1| DNA-directed RNA polymerase, alpha subunit [Eubacterium
           cellulosolvens 6]
          Length = 320

 Score =  321 bits (822), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 130/315 (41%), Positives = 203/315 (64%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP  IE   +  E++     + EPL RG+  TLGN+LRR+++SSL G+A++ V+I+G
Sbjct: 3   DFNKP-KIEITEIS-EDKKFGRFVVEPLERGYGTTLGNSLRRIMLSSLPGSAVSQVKIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+N+K +++K   S D  K   I   G G+V A DIQ   DI
Sbjct: 61  VLHEFSSIPGVKEDVTEIIMNLKNLSIKNNSSSDEPKVAYIEYDGEGIVRASDIQVDQDI 120

Query: 126 EVLNPDHVICNLDV--DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E++NPD +I +L+   D  + MELT++ G GYV A   + E+ PIG+I +DA+Y+P+++V
Sbjct: 121 EIMNPDQIIAHLNGGPDCKLYMELTITNGRGYVGADKGKPEDLPIGVIAVDAIYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + TVE+ R GQ+ D+DKL++ + T+ ++  +++V+LA+++L + L +FI+  E  K  + 
Sbjct: 181 NMTVENTRVGQITDFDKLTLDVYTNKTLGPDEAVSLAAKVLSEHLKLFIDLSENAKTAEV 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            I  +       L   ++ELELSVRS NCL+   I  + +L  +T  DM+++ N GRKSL
Sbjct: 241 MIEHQDDEKEKVLEMNIDELELSVRSYNCLKRAGINTVEELCNKTSEDMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFLG 318
            E+   L  +GL L 
Sbjct: 301 EEVLAKLNELGLSLS 315


>gi|190341367|gb|ACE74760.1| RpoA [Enterobacter radicincitans]
          Length = 308

 Score =  320 bits (821), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 138/314 (43%), Positives = 208/314 (66%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI    D+E++
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVQGKDDVILTLNKSGIGPVTAADITHDGDVEIV 117

Query: 129 NPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
            P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+++++
Sbjct: 118 KPQHVICHLTDENASINMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACYSPVERIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    +
Sbjct: 178 YNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP---E 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 VKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|190341399|gb|ACE74776.1| RpoA [Cronobacter genomosp. 1]
          Length = 308

 Score =  320 bits (821), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 138/314 (43%), Positives = 208/314 (66%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI    D+E++
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVVLTLNKSGIGPVTAADINHDGDVEIV 117

Query: 129 NPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
            P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+++++
Sbjct: 118 KPQHVICHLTDENASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACYSPVERIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    +
Sbjct: 178 YNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP---E 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 VKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|190341311|gb|ACE74732.1| RpoA [Enterobacter aerogenes]
 gi|190341327|gb|ACE74740.1| RpoA [Enterobacter helveticus]
 gi|190341329|gb|ACE74741.1| RpoA [Enterobacter helveticus]
 gi|190341331|gb|ACE74742.1| RpoA [Enterobacter helveticus]
 gi|190341333|gb|ACE74743.1| RpoA [Enterobacter helveticus]
 gi|190341337|gb|ACE74745.1| RpoA [Enterobacter helveticus]
 gi|190341339|gb|ACE74746.1| RpoA [Enterobacter helveticus]
 gi|190341341|gb|ACE74747.1| RpoA [Enterobacter helveticus]
 gi|190341343|gb|ACE74748.1| RpoA [Enterobacter helveticus]
 gi|190341345|gb|ACE74749.1| RpoA [Enterobacter helveticus]
 gi|190341347|gb|ACE74750.1| RpoA [Enterobacter helveticus]
 gi|190341355|gb|ACE74754.1| RpoA [Enterobacter pulveris]
 gi|190341357|gb|ACE74755.1| RpoA [Enterobacter pulveris]
 gi|190341359|gb|ACE74756.1| RpoA [Enterobacter pulveris]
 gi|190341361|gb|ACE74757.1| RpoA [Enterobacter pulveris]
 gi|190341363|gb|ACE74758.1| RpoA [Enterobacter pulveris]
 gi|190341365|gb|ACE74759.1| RpoA [Enterobacter pulveris]
 gi|190341375|gb|ACE74764.1| RpoA [Escherichia hermannii]
 gi|190341377|gb|ACE74765.1| RpoA [Escherichia hermannii]
          Length = 308

 Score =  320 bits (821), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 138/314 (43%), Positives = 208/314 (66%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI    D+E++
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIV 117

Query: 129 NPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
            P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+++++
Sbjct: 118 KPQHVICHLTDENASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACYSPVERIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    +
Sbjct: 178 YNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP---E 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 VKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|260438188|ref|ZP_05792004.1| DNA-directed RNA polymerase, alpha subunit [Butyrivibrio crossotus
           DSM 2876]
 gi|292809378|gb|EFF68583.1| DNA-directed RNA polymerase, alpha subunit [Butyrivibrio crossotus
           DSM 2876]
          Length = 321

 Score =  320 bits (821), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 132/318 (41%), Positives = 205/318 (64%), Gaps = 10/318 (3%)

Query: 8   ELIKPN-NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           E  KP   IE I    E++     + EPL RG+  TLGN+LRR+++SSL G+A++ V+ID
Sbjct: 3   EFEKPTIRIEEI---SEDKRYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGSAVSQVKID 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG---PGVVTAGDIQTVN 123
           GVLHE S I GV ED++DII+NIK + +K S DS++    +       GVVTAGDI T +
Sbjct: 60  GVLHEFSPIPGVKEDVSDIIMNIKNLAIKNSSDSNEPKIAYIECDGREGVVTAGDIHTDS 119

Query: 124 DIEVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           DIE++NPD  I  L+      + MELT++ G GYV A+ ++ E+ PIG+++ID++Y+P++
Sbjct: 120 DIEIMNPDLPIATLNGGNDCKLFMELTITNGRGYVSAEKNKHEDTPIGVLSIDSIYTPVE 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +V+ TV++ R GQV D+DKL++ + T+G++  +D+V+LA+++L + L +F++  +  K+V
Sbjct: 180 RVNMTVQNTRVGQVTDFDKLTLEVYTNGTLAPDDAVSLAAKVLCEHLNLFVDLSDNTKDV 239

Query: 242 KED-INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
               I              ++ELELSVRS NCL+   I  + +L  +T  DM+++ N GR
Sbjct: 240 VGTFIEKPEDEKVKTGAINIDELELSVRSYNCLKRAGINTVEELCSKTAEDMMKVRNLGR 299

Query: 301 KSLVEIKGVLGTMGLFLG 318
           KSL E+   L  +GL L 
Sbjct: 300 KSLEEVLAKLKELGLELS 317


>gi|306821592|ref|ZP_07455190.1| DNA-directed RNA polymerase subunit alpha [Eubacterium yurii subsp.
           margaretiae ATCC 43715]
 gi|304550337|gb|EFM38330.1| DNA-directed RNA polymerase subunit alpha [Eubacterium yurii subsp.
           margaretiae ATCC 43715]
          Length = 313

 Score =  320 bits (820), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 110/311 (35%), Positives = 193/311 (62%), Gaps = 4/311 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  ++ + L ++         EPL RGFA T+GN+LRRVL+SSL G A+TA++ID 
Sbjct: 3   EIEKP-QVQVLALEED---YGKFALEPLERGFATTVGNSLRRVLLSSLPGVAVTAIKIDK 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE S++KGV ED+T+++L +K +++ M  +    + I  +G   +TAGDI     +E+
Sbjct: 59  VMHEFSTVKGVKEDVTELMLTLKELSMNMDSNGEAILRIDAQGECEITAGDIICPAGVEM 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N D  I  L  DA ++ME+ ++KG GYV +  ++ +  PIG+I +D++Y+P+KKV++T+
Sbjct: 119 VNKDLHIATLSEDADLKMEIYINKGRGYVSSDTNKQKGLPIGVIPMDSIYTPVKKVNFTI 178

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E     +   Y++L + I T  ++  +D++++A++I  + L +FI+  +    ++  +  
Sbjct: 179 EEVNVSEDEQYERLVLDIWTKKTVNPKDALSIAAKIFTEHLSLFIDLTDSVNAMEIMVEK 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +EEL+LSVRS NCL+  +I  + +L  +TE +M+++ N G+KSL E+ 
Sbjct: 239 EQDEKEKVLEMTIEELDLSVRSYNCLKRASINTVQELTSKTEDEMMKVRNLGKKSLEEVI 298

Query: 308 GVLGTMGLFLG 318
             L  +G  L 
Sbjct: 299 HKLHELGFTLK 309


>gi|190341315|gb|ACE74734.1| RpoA [Enterobacter asburiae]
 gi|190341317|gb|ACE74735.1| RpoA [Enterobacter asburiae]
 gi|190341319|gb|ACE74736.1| RpoA [Enterobacter cancerogenus]
 gi|190341321|gb|ACE74737.1| RpoA [Enterobacter cancerogenus]
 gi|190341323|gb|ACE74738.1| RpoA [Enterobacter cloacae]
 gi|190341349|gb|ACE74751.1| RpoA [Enterobacter hormaechei ATCC 49162]
 gi|190341351|gb|ACE74752.1| RpoA [Enterobacter kobei]
 gi|190341353|gb|ACE74753.1| RpoA [Enterobacter ludwigii]
 gi|190341371|gb|ACE74762.1| RpoA [Enterobacter sp. KM877_04]
 gi|190341373|gb|ACE74763.1| RpoA [Enterobacter sp. OD1121_04]
 gi|190341381|gb|ACE74767.1| RpoA [Escherichia vulneris]
 gi|190341383|gb|ACE74768.1| RpoA [Leclercia adecarboxylata ATCC 23216]
 gi|190341385|gb|ACE74769.1| RpoA [Leclercia adecarboxylata]
          Length = 308

 Score =  320 bits (820), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 138/314 (43%), Positives = 208/314 (66%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI    D+E++
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIV 117

Query: 129 NPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
            P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+++++
Sbjct: 118 KPQHVICHLTDENAAISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACYSPVERIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    +
Sbjct: 178 YNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP---E 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 VKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|190341307|gb|ACE74730.1| RpoA [Citrobacter koseri]
 gi|190341309|gb|ACE74731.1| RpoA [Citrobacter koseri]
          Length = 308

 Score =  320 bits (820), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 138/314 (43%), Positives = 208/314 (66%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI    D+E++
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIV 117

Query: 129 NPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
            P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+++++
Sbjct: 118 KPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    +
Sbjct: 178 YNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP---E 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 VKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|182412026|ref|YP_001817092.1| DNA-directed RNA polymerase subunit alpha [Opitutus terrae PB90-1]
 gi|177839240|gb|ACB73492.1| DNA-directed RNA polymerase, alpha subunit [Opitutus terrae PB90-1]
          Length = 333

 Score =  320 bits (820), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 133/333 (39%), Positives = 195/333 (58%), Gaps = 4/333 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + K   +   P+ +  +  G         IAEP   G+ HT+GN+LRRVL+SS+ GAAI+
Sbjct: 1   MPKRLGKFELPSKLTKVEEGS-TPTYAKFIAEPFEAGYGHTIGNSLRRVLLSSIEGAAIS 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++IDGV HE  SI GV ED+TDI+LN+K + L         + I     G+VTA DIQ 
Sbjct: 60  SIKIDGVNHEFQSIDGVVEDVTDIVLNLKKVLLVSQKRESINLAIRVNKAGIVTAADIQP 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
             +I+V+NP+ VIC LD       E+ +  G GY P + ++ E   IG+I ID+L+SP++
Sbjct: 120 DPNIQVINPEQVICTLDAKKTFDAEIEIKTGRGYCPGEANKKEEQAIGVIPIDSLFSPVR 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
            V Y VE+ R GQ+ DYDKL + + TDG IT +D++  A+ IL+  L +F    E   E 
Sbjct: 180 LVKYAVEATRVGQITDYDKLVLEVWTDGRITPDDALKQAASILKHHLDVFDRVSEETYEF 239

Query: 242 KE---DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +    +++ +       L   V E+ELSVR+ NCL   NI  +G+L  +TE +ML+  NF
Sbjct: 240 ENQQSEVSEEQNKLRKLLNMSVNEIELSVRAANCLNNANITTVGELAMKTEQEMLKYRNF 299

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK  L  +GL LGM   +   ++ +E
Sbjct: 300 GKKSLNEIKEKLEALGLSLGMKFDERLLDTKKE 332


>gi|190341299|gb|ACE74726.1| RpoA [Citrobacter freundii]
 gi|190341301|gb|ACE74727.1| RpoA [Citrobacter sp. NZ3872_90]
 gi|190341303|gb|ACE74728.1| RpoA [Citrobacter sp. OD1158_06]
          Length = 308

 Score =  320 bits (820), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 138/314 (43%), Positives = 208/314 (66%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI    D+E++
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVQGKDDVILTLNKSGIGPVTAADITHDGDVEIV 117

Query: 129 NPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
            P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+++++
Sbjct: 118 KPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    +
Sbjct: 178 YNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP---E 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 VKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|168701504|ref|ZP_02733781.1| DNA-directed RNA polymerase subunit alpha [Gemmata obscuriglobus
           UQM 2246]
          Length = 336

 Score =  320 bits (820), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 126/333 (37%), Positives = 189/333 (56%), Gaps = 13/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++  W+ L  PN ++        +      AEP  +GF  T+GN+LRR+L+SSL G+AIT
Sbjct: 1   MRVRWRGLELPNRVQADR-SNLSDTYGKFYAEPFEKGFGMTIGNSLRRILLSSLEGSAIT 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I GV HEIS+I GV ED+TDIILN+K + +K   D  K + I K   G V   D+Q 
Sbjct: 60  RVKIQGVQHEISTITGVVEDVTDIILNVKSLVVKNLSDQPKTIRIQKHEAGAVRGVDVQH 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              I+++NP+H I  L  D    ME+TV  G GY  A  +  ++  +G+I +D+ +SP+ 
Sbjct: 120 DETIQIINPEHHIATLTSDVPFVMEMTVENGRGYRTADDNAGKDREVGVIPVDSSFSPVV 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +V Y +E  R GQ  +YD+L M I T+G++  + ++  A++IL+  L  F+ + EP  E+
Sbjct: 180 RVKYDIEETRVGQKTNYDRLVMEIWTNGTLAPQMAIVEAAKILRKHLNPFVQYTEPGPEL 239

Query: 242 KEDI------------NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           + D             + +       L   + EL+LSVR+TNCL  E I  + DL+ RT 
Sbjct: 240 QLDDGPIEIGPNASVRDQQDAELERKLNMSLAELDLSVRATNCLETEGIQTVRDLVIRTS 299

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
            ++L + NFG  +L E+K  L   GL LGM LP
Sbjct: 300 EELLEVRNFGETTLREVKSKLEERGLALGMRLP 332


>gi|190341387|gb|ACE74770.1| RpoA [Pantoea sp. E147]
          Length = 308

 Score =  320 bits (820), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 138/314 (43%), Positives = 207/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI    D+E++
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIV 117

Query: 129 NPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
            P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+ +++
Sbjct: 118 KPQHVICHLTDENAAISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACYSPVDRIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    +
Sbjct: 178 YNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP---E 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 VKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|196234320|ref|ZP_03133149.1| DNA-directed RNA polymerase, alpha subunit [Chthoniobacter flavus
           Ellin428]
 gi|196221587|gb|EDY16128.1| DNA-directed RNA polymerase, alpha subunit [Chthoniobacter flavus
           Ellin428]
          Length = 329

 Score =  319 bits (819), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 126/314 (40%), Positives = 179/314 (57%), Gaps = 4/314 (1%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P ++         +     +AEP   G+ +T+GN+LRRVL+SSL GAAIT+V+I G  HE
Sbjct: 2   PKSL-VKDDASRTDTYAKFVAEPFEAGYGNTIGNSLRRVLLSSLEGAAITSVKITGAQHE 60

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
             ++  V +D+TDI+LN+K +  K +    + +TI     G VTAGDI+  +  EVLN D
Sbjct: 61  FQTLPHVVDDVTDIVLNLKKVKFKANDHEIRNLTINVNKEGAVTAGDIEDSSQCEVLNKD 120

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
            +IC LD       EL V  G G+     ++  + PIG+I ID+++SP+ +V YTV + R
Sbjct: 121 QIICTLDKKTKFEAELEVKVGRGFSTGDENKHPDQPIGVIAIDSIFSPVTRVKYTVGNTR 180

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            GQ  DYDKL + I TDG +T E+++  AS IL+     F  ++E   +  E    +S  
Sbjct: 181 VGQRTDYDKLELEIWTDGRLTPEEALVQASSILKKHFEPFYAYDENAVQFDETPQAQSQE 240

Query: 252 FNPAL---LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                      V E+ELSVR+ NCL   NI  +G L  +TEA+ML+  NFG+KSL EIK 
Sbjct: 241 NQKMKKLLNMSVNEIELSVRAANCLNNANITTVGQLAMKTEAEMLKYRNFGKKSLNEIKD 300

Query: 309 VLGTMGLFLGMNLP 322
            L  +GL LGM   
Sbjct: 301 KLTQLGLSLGMKFE 314


>gi|269218963|ref|ZP_06162817.1| DNA-directed RNA polymerase, alpha subunit [Actinomyces sp. oral
           taxon 848 str. F0332]
 gi|269212074|gb|EEZ78414.1| DNA-directed RNA polymerase, alpha subunit [Actinomyces sp. oral
           taxon 848 str. F0332]
          Length = 334

 Score =  319 bits (819), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 120/292 (41%), Positives = 176/292 (60%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            +   Q  E R+  I EPL  GF +TLGN++RR L+SS+ GAA+T+V+IDGVLHE S+I 
Sbjct: 8   VLTEEQVSEYRSRFILEPLEPGFGYTLGNSMRRTLLSSIPGAAVTSVRIDGVLHEFSTIA 67

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ DIILN+K + +    D    + + K+GPG VTA DI     +E+ NPD  I  
Sbjct: 68  GVKEDVADIILNLKELVVSSENDEPVLMYLHKQGPGEVTAADITPPAGVEIHNPDLHIAT 127

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           L+    + ++LTV +G GYV A  ++ E D IG I ID++YSP+ KVSY VE+ R  Q  
Sbjct: 128 LNDKGKIEIDLTVERGRGYVSAAQNKGEEDEIGRIPIDSIYSPVLKVSYKVEATRVAQRT 187

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           D+DKL + ++   S T  D++A A + L +  G+ +      + ++          +  L
Sbjct: 188 DFDKLVVDVEVKPSTTPRDALASAGKTLVELFGLCVELNNEVEGIELGPPPVVETQSSDL 247

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
            + +  L L  RS NCL+ E I  +G+LIQR+EAD+L + NFG KS+ ++K 
Sbjct: 248 QRPITILNLPARSQNCLQREGIRTIGELIQRSEADLLDIRNFGAKSIEDVKD 299


>gi|86609045|ref|YP_477807.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|119366741|sp|Q2JL74|RPOA_SYNJB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|86557587|gb|ABD02544.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 335

 Score =  319 bits (819), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 114/308 (37%), Positives = 174/308 (56%), Gaps = 11/308 (3%)

Query: 18  IVLGQEEEN---RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS 74
            V    ++N          PL RG   T+GNALRRVL+S+L G A+TAV+I GV HE S+
Sbjct: 28  CVESHRDDNGVHYGKFALGPLERGQGITVGNALRRVLLSNLEGTAVTAVRIAGVTHEFST 87

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           + GV ED+ +I+LN+K + L+ S    +   +  +GPG VTA  +Q  +D+EV+NP H I
Sbjct: 88  VPGVREDVMEILLNMKELVLRSSSPETQVGRLVAQGPGEVTAEKLQLPSDVEVINPRHHI 147

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
             L   A++ ME  + +GHGY    +  ++   I  + ID+++ P++KV+Y VE+AR GQ
Sbjct: 148 ATLAEGAILEMEFMIGRGHGYRAVDYSDSKAMAIDFLQIDSVFMPVRKVNYAVEAARVGQ 207

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
            L+ D+L + I T+GS+T +++++ A+RIL                    +  K    N 
Sbjct: 208 FLEKDRLVLEIWTNGSLTPQEALSQAARILVGLFAPLQEVS-----FDAPVPPKPDEDNQ 262

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +EEL+LSVR+ NCL+   I  + DL+  TE D+L + NFG+KS  E+   L    
Sbjct: 263 KNQIPIEELQLSVRAYNCLKRAQINTVADLLLYTEEDLLEIKNFGQKSAEEVVQALKA-- 320

Query: 315 LFLGMNLP 322
              G+ LP
Sbjct: 321 -RFGLTLP 327


>gi|190341305|gb|ACE74729.1| RpoA [Citrobacter koseri]
          Length = 308

 Score =  319 bits (819), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 138/314 (43%), Positives = 207/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI    D+E++
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIV 117

Query: 129 NPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
            P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+++++
Sbjct: 118 KPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    +
Sbjct: 178 YNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP---E 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +  +   F P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 VKEEKPEFAPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|227499168|ref|ZP_03929303.1| DNA-directed RNA polymerase [Acidaminococcus sp. D21]
 gi|226904615|gb|EEH90533.1| DNA-directed RNA polymerase [Acidaminococcus sp. D21]
          Length = 323

 Score =  319 bits (819), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 128/319 (40%), Positives = 192/319 (60%), Gaps = 9/319 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
            +E+ KP+ +  I     +      + EPL RG+  TLGN+LRRVL+SSL G A+T ++I
Sbjct: 1   MKEIEKPSLV--IDEISPDGRYGKFVWEPLERGYGITLGNSLRRVLLSSLSGMAVTGIKI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-----SHKRVTIFKRGPGVVTAGDIQ 120
           DGVLHE S+I+GV ED+ DI+LNIK +  K++ D       K   I K G G VT  DI 
Sbjct: 59  DGVLHEFSTIEGVREDVADIVLNIKALCFKVNLDDQGTYEPKTFYIKKSGEGEVTGADII 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T  D EVLNP+  I  LD +A + ME+ V  G GYV A  +++++ PIG I +D++YSPI
Sbjct: 119 TDQDTEVLNPELHIATLDKNANLNMEIYVDIGRGYVSADKNKSKDQPIGFIPVDSIYSPI 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            +V + V   R G V +YD+L++ + TDGS+  +++V  A+ IL + L +F     PK +
Sbjct: 179 TRVKFGVTDTRVGNVTNYDRLTLEVWTDGSLGPDEAVTSAAEILINYLALFKTTNVPKIQ 238

Query: 241 VKEDINV--KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
             E+     +    +  L   +++L+L+VRS NCLR   I  + D+I +TE +++ + N 
Sbjct: 239 GSEESGKPDEEGTKSSVLQMSIDDLDLTVRSNNCLRRAGINTVEDIINKTEDELICVRNL 298

Query: 299 GRKSLVEIKGVLGTMGLFL 317
           G KSL E+K  +  +GL L
Sbjct: 299 GSKSLEEVKNKIEELGLHL 317


>gi|71891999|ref|YP_277729.1| DNA-directed RNA polymerase subunit alpha [Candidatus Blochmannia
           pennsylvanicus str. BPEN]
 gi|90101573|sp|Q493I4|RPOA_BLOPB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|71796105|gb|AAZ40856.1| RNA polymerase, alpha subunit [Candidatus Blochmannia
           pennsylvanicus str. BPEN]
          Length = 330

 Score =  319 bits (818), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 143/333 (42%), Positives = 220/333 (66%), Gaps = 11/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q  E R  +  EPL RGF HTLGNALRR+L+SS+ G AIT
Sbjct: 1   MQNSVIEFLKPRLVD---IEQITETRAKVTLEPLERGFGHTLGNALRRILLSSMPGYAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +G+ ED+ +I+LN+K + +++ G     +T+ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYSTKEGIQEDVLEILLNLKKLAIRIEGKDSVTLTLKKSGIGPVIANDILY 117

Query: 122 VN-DIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
            +  ++++ P+H+IC++ D +  + M + V +G GYVPA    H  ++  PIG + +DA 
Sbjct: 118 DSNSVKIVTPNHIICHITDKNTSISMSIKVQRGRGYVPASSRFHSESDILPIGRLLLDAC 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP++++SY VE+AR  Q  D DKL + ++TDG+I  E+++  A+ IL +QL  FI+  +
Sbjct: 178 YSPVERISYNVEAARVEQRTDLDKLIIDMETDGTIEPEEAIRRAATILSEQLEAFIDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
             +   ++   +   F+P LL+ V++LEL+VRS NCL+ E+I Y+GDL+QRTE ++L+  
Sbjct: 238 IHQPEHKE---EKPEFDPILLRLVDDLELTVRSANCLKAESIHYIGDLVQRTEIELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LG  L +WPP +I
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGTRLENWPPTNI 327


>gi|190341453|gb|ACE74803.1| RpoA [Cronobacter sakazakii]
          Length = 308

 Score =  319 bits (818), Expect = 4e-85,   Method: Composition-based stats.
 Identities = 139/314 (44%), Positives = 208/314 (66%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI    D+E++
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVVLTLNKSGIGPVTAADITHDGDVEIV 117

Query: 129 NPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
            P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+++++
Sbjct: 118 KPQHVICHLTDENASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACYSPVERIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    +
Sbjct: 178 YNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP---E 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +  +   F+P LL+ V++LEL+VRS NCL+ E I YMGDL+QRTE ++L+  N G+KSL 
Sbjct: 235 VKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYMGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|257454071|ref|ZP_05619345.1| DNA-directed RNA polymerase, alpha subunit [Enhydrobacter
           aerosaccus SK60]
 gi|257448549|gb|EEV23518.1| DNA-directed RNA polymerase, alpha subunit [Enhydrobacter
           aerosaccus SK60]
          Length = 335

 Score =  319 bits (818), Expect = 4e-85,   Method: Composition-based stats.
 Identities = 139/330 (42%), Positives = 212/330 (64%), Gaps = 8/330 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  N  E + PN I    +    E    +  EPL RGF HTLGNALRR+L+SSL GAA+ 
Sbjct: 1   MMLNATEFLTPNAIHVDTVN---ETHAKVTLEPLERGFGHTLGNALRRILLSSLPGAAVI 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +I+GV HE S+++G+ ED+ D++LN+KG+ +++   +   +T+ K+GPG V A DI+ 
Sbjct: 58  EAEIEGVDHEYSTLEGLQEDVLDLLLNLKGLAIQLHDQNEVFLTLDKQGPGTVLASDIEL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSP 179
            +++E++NPD V+  L     ++M L V+ G GY PA   +   +N  IG + +DA YSP
Sbjct: 118 PHNVEIINPDLVLGTLSDRGHLKMRLRVAVGRGYEPANVRKDSGDNKVIGRLKLDASYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I +V+Y VE+AR  Q  D D+L + ++T+G+I  E+++  A+ ILQ Q+ +F++ E    
Sbjct: 178 ILRVAYQVENARVEQRTDLDRLVIELETNGTIDPEEAIRKAATILQQQIAVFVDLE---A 234

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           E   +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G
Sbjct: 235 EATPEPVKEKEEVDPVLLRPVDDLELTVRSANCLKAENIYYIGDLVQRTETELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL +  L LGM L +WPP  +
Sbjct: 295 KKSLTEIKDVLASKDLELGMRLENWPPADL 324


>gi|328813947|gb|AEB52089.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 267

 Score =  319 bits (817), Expect = 4e-85,   Method: Composition-based stats.
 Identities = 116/264 (43%), Positives = 171/264 (64%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I    E  N    + EPL RG+  TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I G
Sbjct: 3   ITKVDESTNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDG 62

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+T IILNIK + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +
Sbjct: 63  VLEDVTQIILNIKKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTV 122

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
                  + +TV KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D
Sbjct: 123 ADGGHFHVRMTVKKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRND 182

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL++ + T+GSI+  ++++LA++IL + L +F+N  +  K  +  +  +       L 
Sbjct: 183 FDKLTLDVWTNGSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLE 242

Query: 258 KKVEELELSVRSTNCLRGENIVYM 281
             +EEL+LSVRS NCL+   I  +
Sbjct: 243 MTIEELDLSVRSYNCLKRAGINTV 266


>gi|45644721|gb|AAS73109.1| predicted DNA-directed RNA polymerase alpha subunit [uncultured
           marine gamma proteobacterium EBAC20E09]
          Length = 321

 Score =  319 bits (817), Expect = 4e-85,   Method: Composition-based stats.
 Identities = 133/327 (40%), Positives = 204/327 (62%), Gaps = 6/327 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  +L+ P  I+   +       + +  EPL RGF HTLGNALRR+L+SS+ GAA+T
Sbjct: 1   MQTSVIDLLVPTEIQ---VDDVSPTLSKVTLEPLERGFGHTLGNALRRILLSSMPGAAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I+G+ HE S+I+GV ED+ DI+LNIK + +K+       + +   GP  V A     
Sbjct: 58  DVAIEGISHEYSTIEGVREDVIDILLNIKDMPIKLIEGDAAEIILDVTGPCDVLASSFAA 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
             ++E+++ D  I  +     ++M LTV  G GY PA     E+  +G + +DA YSP++
Sbjct: 118 PGNLELVDQDFHIATIVDKVNLKMTLTVKTGRGYEPADLREDEDRAVGALKVDASYSPVR 177

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +VSYTV++AR G+  D DKL + ++TDG++  + ++  ++ ILQ QLG F++ +      
Sbjct: 178 RVSYTVDNARSGKRTDLDKLVIELETDGTLDPKMAIEHSATILQQQLGAFVDLDAIA--- 234

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +++       F+P LL+ +EELEL+VRSTNCL+ E+I  +GDLI R+E D+L+  N G+K
Sbjct: 235 EQEAKKDQNDFDPILLRSIEELELTVRSTNCLKAESIFLIGDLIHRSEFDLLKTPNLGKK 294

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPES 328
           SL EIK VL +  L LGMN+ +WPP  
Sbjct: 295 SLNEIKDVLASKNLSLGMNVENWPPVG 321


>gi|32491317|ref|NP_871571.1| DNA-directed RNA polymerase subunit alpha [Wigglesworthia
           glossinidia endosymbiont of Glossina brevipalpis]
 gi|30173252|sp|Q8D1Y8|RPOA_WIGBR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|25166524|dbj|BAC24714.1| rpoA [Wigglesworthia glossinidia endosymbiont of Glossina
           brevipalpis]
          Length = 328

 Score =  319 bits (817), Expect = 4e-85,   Method: Composition-based stats.
 Identities = 148/330 (44%), Positives = 218/330 (66%), Gaps = 8/330 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +  E +KP  ++   + Q  +    +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MHNSATEFLKPRLVD---IEQISKTHAKITLEPLERGFGHTLGNALRRILLSSMPGYAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDG+LHE SS +GV ED+ +I+LN+K + L + G     +++FK G G VTA DI  
Sbjct: 58  EVEIDGILHEYSSKEGVQEDIVEILLNLKELALIIKGKDIAVLSLFKSGIGKVTASDIIH 117

Query: 122 VNDIEVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPA-KHHRTENDPIGLITIDALYSP 179
             ++E+ +P+HV+CNL   ++ + M + V KG GYVPA      E+ PIG + +DA YSP
Sbjct: 118 DGNVEICHPEHVLCNLTHENSSINMRIKVQKGRGYVPAISRMHIEDRPIGRLLLDACYSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I+++SY VE+AR  Q  D DKL + ++T+G+I  E ++  A+ IL +QL  FI+  + +K
Sbjct: 178 IERISYNVEAARVEQRTDLDKLIIEMETNGTIDPESAIRRAATILSEQLEAFIDLRDIRK 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
               +I  +   F+P LL+ V++LEL+VRS NCL+ E+I Y+GDL+QRTE ++L+  N G
Sbjct: 238 P---EIKEEKPEFDPVLLRPVDDLELTVRSANCLKAESIHYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL T  L LGM + +WPP SI
Sbjct: 295 KKSLTEIKDVLSTRNLTLGMRIENWPPVSI 324


>gi|33519683|ref|NP_878515.1| DNA-directed RNA polymerase subunit alpha [Candidatus Blochmannia
           floridanus]
 gi|41688649|sp|Q7VQC3|RPOA_BLOFL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|33517346|emb|CAD83731.1| DNA-directed RNA polymerase alpha chain [Candidatus Blochmannia
           floridanus]
          Length = 331

 Score =  319 bits (817), Expect = 5e-85,   Method: Composition-based stats.
 Identities = 142/336 (42%), Positives = 219/336 (65%), Gaps = 12/336 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q   +E +KP +I    + +     + +  EPL RGF HTLGNALRR+L+SS+ G AIT
Sbjct: 1   MQSFEKEFLKPRSINIEKISEI---HSKITLEPLERGFGHTLGNALRRILLSSMPGCAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I+GVLHE  + +GV ED+ +I+LN+K + + M       +T+ K G G V A DI+ 
Sbjct: 58  EVEIEGVLHEYGTKEGVREDVLEILLNLKTLAINMYVKDSIVLTLKKTGIGPVIASDIEY 117

Query: 122 VND-IEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTEND----PIGLITIDA 175
            +  I ++NP+H+IC +   D  + M + V +G GYVPA    + +D    PIG + +DA
Sbjct: 118 DSSIISIVNPNHIICCITDQDTSIIMRIKVQRGRGYVPAFSRFSSDDQHDLPIGRLLLDA 177

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
            YSP++++SYTVE+AR  +  D DKL + ++T+G+I  E+++  A+ IL DQL  FI+ +
Sbjct: 178 CYSPVERISYTVEAARVEKRTDLDKLIIDMETNGTIDPEEAIRRAATILSDQLSSFIDLK 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           +  +    ++  +   F+P+LL  V++LEL+VRS NCL+ E+I Y+GDL+Q+TE ++L+ 
Sbjct: 238 DVHQP---EVKEEKPEFDPSLLNLVDDLELTVRSANCLKAESIHYIGDLVQKTEVELLKT 294

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL + GL LGM L +WPP+ + E
Sbjct: 295 PNLGKKSLTEIKDVLASRGLSLGMRLDNWPPKHLSE 330


>gi|320094553|ref|ZP_08026319.1| DNA-directed RNA polymerase subunit alpha [Actinomyces sp. oral
           taxon 178 str. F0338]
 gi|319978468|gb|EFW10045.1| DNA-directed RNA polymerase subunit alpha [Actinomyces sp. oral
           taxon 178 str. F0338]
          Length = 331

 Score =  319 bits (817), Expect = 5e-85,   Method: Composition-based stats.
 Identities = 117/305 (38%), Positives = 177/305 (58%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            +   +  + R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGV HE  +I+
Sbjct: 8   ILTEEKVSDLRSRFTLEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVPHEFRTIE 67

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +IILNIK I L    D    + + K GPG V AGDI     +E+ NPD  +  
Sbjct: 68  GVKEDVAEIILNIKQIVLSSENDEPVVMYLRKAGPGPVVAGDITPPAGVEIHNPDLHLAT 127

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           L+    + +ELTV +G GYV A  ++     I  I ID++YSP+ KV+Y VE+ R  Q  
Sbjct: 128 LNEKGKLEIELTVERGRGYVSAAQNKDPQAEISRIPIDSIYSPVVKVTYKVEATRVEQRT 187

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           D+D+L + ++T  +IT  D++A A + L +  G+     E  + ++   +         L
Sbjct: 188 DFDRLVIDVETKPAITPRDAIASAGKTLVELFGLMRELNEEAEGIEVGPSTTDATLAADL 247

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E L L  RS N LR   I+ +G+L+  +EAD+L + NFG KS+ EIK  L T+G+ 
Sbjct: 248 ALPIENLNLQSRSYNALRRRGILTVGELVAHSEADLLDIRNFGTKSIEEIKESLATLGMT 307

Query: 317 LGMNL 321
           L  ++
Sbjct: 308 LKDSV 312


>gi|86606119|ref|YP_474882.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp.
           JA-3-3Ab]
 gi|119366740|sp|Q2JUJ5|RPOA_SYNJA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|86554661|gb|ABC99619.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus sp.
           JA-3-3Ab]
          Length = 331

 Score =  318 bits (816), Expect = 6e-85,   Method: Composition-based stats.
 Identities = 113/308 (36%), Positives = 175/308 (56%), Gaps = 11/308 (3%)

Query: 18  IVLGQEEEN---RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS 74
            V   +E N          PL RG   T+GNALRRVL+S+L G A+TAV+I GV HE S+
Sbjct: 26  CVESHQEANGVHYGKFALGPLERGQGITVGNALRRVLLSNLEGTAVTAVRIAGVTHEFST 85

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           + GV ED+ +I+LN+K + L+ +    +   +  +GPG VTA  +Q  +++EV+NP H I
Sbjct: 86  VPGVREDVMEILLNMKELVLRSNAPDTQVGRLVAQGPGEVTAEKLQLPSEVEVINPRHHI 145

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
             L   A++ ME  + +G GY    +  +++  I  + ID+++ P++KV+YTVE+AR GQ
Sbjct: 146 ATLAEGAILEMEFMIGRGRGYRAVDYSDSKSMAIDFLQIDSVFMPVRKVNYTVEAARVGQ 205

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
            L+ D+L + I T+GS+T +++++ A+RIL                       +    N 
Sbjct: 206 SLEKDRLILEIWTNGSLTPQEALSQAARILVGLFSPLQEVS-----FDTPPEPRQAEDNQ 260

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +EEL+LSVR+ NCL+   I  + DL+  TE D+L + NFG+KS  E+   L    
Sbjct: 261 KNQIPIEELQLSVRAYNCLKRAQINTVADLLVYTEEDLLEIKNFGQKSAEEVVQALKN-- 318

Query: 315 LFLGMNLP 322
             LG+ LP
Sbjct: 319 -RLGLTLP 325


>gi|227876167|ref|ZP_03994283.1| DNA-directed RNA polymerase [Mobiluncus mulieris ATCC 35243]
 gi|269976926|ref|ZP_06183900.1| DNA-directed RNA polymerase, alpha subunit [Mobiluncus mulieris
           28-1]
 gi|306819442|ref|ZP_07453149.1| DNA-directed RNA polymerase subunit alpha [Mobiluncus mulieris ATCC
           35239]
 gi|307701655|ref|ZP_07638671.1| DNA-directed RNA polymerase, alpha subunit [Mobiluncus mulieris
           FB024-16]
 gi|227843128|gb|EEJ53321.1| DNA-directed RNA polymerase [Mobiluncus mulieris ATCC 35243]
 gi|269934757|gb|EEZ91317.1| DNA-directed RNA polymerase, alpha subunit [Mobiluncus mulieris
           28-1]
 gi|304647734|gb|EFM45052.1| DNA-directed RNA polymerase subunit alpha [Mobiluncus mulieris ATCC
           35239]
 gi|307613158|gb|EFN92411.1| DNA-directed RNA polymerase, alpha subunit [Mobiluncus mulieris
           FB024-16]
          Length = 327

 Score =  318 bits (816), Expect = 7e-85,   Method: Composition-based stats.
 Identities = 121/329 (36%), Positives = 188/329 (57%), Gaps = 8/329 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +P   E ++  Q    R+    EPL  GF +TLGN+LRR L+SS+ G+A+T+++I+G LH
Sbjct: 6   QPQLTEEVINNQ----RSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGSAVTSIKIEGALH 61

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+T ++LNIK I L    D    + + K G G VT GDI     + + NP
Sbjct: 62  EFTTLPGVKEDVTQVVLNIKEIVLSSDNDEPVVMYLRKTGEGEVTVGDIMPPAGVVIHNP 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           +H I  L+ D  + +ELTV +G GYV A  ++     I  I +D++YSP+ KVSY VE+ 
Sbjct: 122 EHHIATLNKDGKLEIELTVERGRGYVSAAQNKDPEAEISRIPVDSIYSPVLKVSYHVEAT 181

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R  Q  D+D+L + ++T  +I+  D++A A + L +  G+        + ++   +    
Sbjct: 182 RVEQRTDFDRLIVDVETKKAISPRDAMASAGKTLVELFGLARALNADAEGIELGSSNTDS 241

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   VE+LEL+ R+ NCL  E I  +GDL+ R++AD+L + NFG KS+ EIK  L
Sbjct: 242 ALAEDLAMSVEDLELTSRALNCLNREGIKTVGDLVARSQADLLDIRNFGHKSIDEIKEKL 301

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            TM    GM+L D      +    ++ D+
Sbjct: 302 ATM----GMSLKDSQNPETDSGVPQFSDE 326


>gi|148793282|gb|ABR12705.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           kishitanii]
          Length = 308

 Score =  318 bits (816), Expect = 7e-85,   Method: Composition-based stats.
 Identities = 140/314 (44%), Positives = 205/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---IEQVSSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ 
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIA 117

Query: 129 NPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
           NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ +++
Sbjct: 118 NPEHVICHLTDDNAELSMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDRIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +      
Sbjct: 178 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE--- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|190341335|gb|ACE74744.1| RpoA [Enterobacter helveticus]
          Length = 307

 Score =  318 bits (815), Expect = 8e-85,   Method: Composition-based stats.
 Identities = 138/313 (44%), Positives = 208/313 (66%), Gaps = 10/313 (3%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVL
Sbjct: 1   LKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVL 57

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI    D+E++ 
Sbjct: 58  HEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVK 117

Query: 130 PDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSY 185
           P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+++++Y
Sbjct: 118 PQHVICHLTDENASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACYSPVERIAY 177

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++
Sbjct: 178 NVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP---EV 234

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 235 KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 294

Query: 306 IKGVLGTMGLFLG 318
           IK VL + GL LG
Sbjct: 295 IKDVLASRGLSLG 307


>gi|254701949|ref|ZP_05163777.1| DNA-directed RNA polymerase subunit alpha [Brucella suis bv. 5 str.
           513]
          Length = 267

 Score =  318 bits (815), Expect = 8e-85,   Method: Composition-based stats.
 Identities = 178/267 (66%), Positives = 222/267 (83%), Gaps = 1/267 (0%)

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           SSI GV ED+TDI+LNIK I ++M G+  KR+ + K GPGVVTAGDIQTV D+E+LNP+H
Sbjct: 1   SSIPGVREDVTDIVLNIKEIAIRMEGEGPKRMVVRKEGPGVVTAGDIQTVGDVEILNPEH 60

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           VIC LD  A +RME TV+ G GYVPA  +R E+ PIGLI +D+LYSP++KVSY +E+ RE
Sbjct: 61  VICTLDEGAEIRMEFTVNTGKGYVPADRNRAEDAPIGLIPVDSLYSPVRKVSYKIENTRE 120

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           GQVLDYDKL++ I+T+GS+TGED+VA A+RILQDQL +F+NFEEP+KE  ++  V  L F
Sbjct: 121 GQVLDYDKLTLNIETNGSVTGEDAVAYAARILQDQLSIFVNFEEPQKEAPQEQ-VAELAF 179

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           NPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGRKSL EIK VL +
Sbjct: 180 NPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRKSLNEIKEVLAS 239

Query: 313 MGLFLGMNLPDWPPESIEELAKKYEDK 339
           MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 240 MGLHLGMEIPAWPPENIEDLAKRYEDQ 266


>gi|328813951|gb|AEB52091.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 260

 Score =  318 bits (815), Expect = 8e-85,   Method: Composition-based stats.
 Identities = 114/260 (43%), Positives = 170/260 (65%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               + EPL RG+  TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T II
Sbjct: 1   YGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQII 60

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LNIK + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +       + 
Sbjct: 61  LNIKKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVR 120

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           +TV KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + 
Sbjct: 121 MTVKKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVW 180

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+GSI+  ++++LA++IL + L +F+N  +  K  +  +  +       L   +EEL+LS
Sbjct: 181 TNGSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLS 240

Query: 267 VRSTNCLRGENIVYMGDLIQ 286
           VRS NCL+   I  + +L  
Sbjct: 241 VRSYNCLKRAGINTVQELTN 260


>gi|229825289|ref|ZP_04451358.1| hypothetical protein GCWU000182_00643 [Abiotrophia defectiva ATCC
           49176]
 gi|229790661|gb|EEP26775.1| hypothetical protein GCWU000182_00643 [Abiotrophia defectiva ATCC
           49176]
          Length = 319

 Score =  318 bits (815), Expect = 8e-85,   Method: Composition-based stats.
 Identities = 124/314 (39%), Positives = 197/314 (62%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +   PN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA+T V+I+G
Sbjct: 3   DFKIPN-IEIAEIS-EDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVTTVKIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           + HE+SSI GV ED+T+II+NIK + ++     D  K   I   G GVVTA +IQ  +DI
Sbjct: 61  IKHELSSIPGVKEDVTEIIMNIKSLAIRNDSETDEPKTAYIEFEGEGVVTAANIQADSDI 120

Query: 126 EVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            + NPD VI  L+      + MEL + +GHGYV A  +++++  I +I ID++Y+P+++V
Sbjct: 121 TITNPDQVIATLNGGNNCRLYMELNIGRGHGYVSADKNKSDDLAIDVIPIDSIYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +  +E+ R G + DYDKL++ + T+G++  +++V+LA+R++ + L  FI+  E  K V  
Sbjct: 181 NINIENTRVGHMTDYDKLTLEVYTNGTMGPDEAVSLAARVMSEHLNSFIDLSENAKVVDV 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +          L   ++ELELSVR+ NCL+   I  + +L+ +T  DM+++ N G KSL
Sbjct: 241 MVAKPDNERGRVLEMSIDELELSVRAFNCLKRSGINTVQELVGKTHEDMMKVRNLGNKSL 300

Query: 304 VEIKGVLGTMGLFL 317
            EIK  +  +GL L
Sbjct: 301 EEIKAKIKALGLSL 314


>gi|179184384|gb|ACB78145.1| RNA polymerase alpha subunit [Aliivibrio finisterrensis]
 gi|179184823|gb|ACB78161.1| RNA polymerase alpha subunit [Aliivibrio finisterrensis]
          Length = 313

 Score =  318 bits (815), Expect = 8e-85,   Method: Composition-based stats.
 Identities = 141/319 (44%), Positives = 207/319 (64%), Gaps = 10/319 (3%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T 
Sbjct: 1   QGSVTEFLKPRLVD---IEQVSMTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTE 57

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI   
Sbjct: 58  VEIEGVLHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVIITLNKSGAGPVVAGDITHD 117

Query: 123 NDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
            D+E+ NP+HVIC+L  D A + M + V +G GYVP+    H   +  PIG + IDA YS
Sbjct: 118 GDVEIANPEHVICHLTDDNAEISMRIRVERGRGYVPSTARIHTEEDERPIGRLLIDATYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ K+SY+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +
Sbjct: 178 PVDKISYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVR 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                    +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 VPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFL 317
           G+KSL EIK VL + GL L
Sbjct: 295 GKKSLTEIKDVLASRGLSL 313


>gi|27904917|ref|NP_778043.1| DNA-directed RNA polymerase subunit alpha [Buchnera aphidicola str.
           Bp (Baizongia pistaciae)]
 gi|29427637|sp|P59455|RPOA_BUCBP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|27904315|gb|AAO27148.1| DNA-directed RNA polymerase alpha chain [Buchnera aphidicola str.
           Bp (Baizongia pistaciae)]
          Length = 331

 Score =  318 bits (814), Expect = 9e-85,   Method: Composition-based stats.
 Identities = 140/334 (41%), Positives = 213/334 (63%), Gaps = 12/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P  +    + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQSSVTEFLIPRLVN---IEQISMTHVKITLEPLERGFGHTLGNALRRILLSSMPGFAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDG+LHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G GVVTA DI  
Sbjct: 58  EVEIDGILHEYSTKEGVQEDIIEILLNLKGLAIRVYGKDQVYLTLVKTGIGVVTAADINH 117

Query: 122 VNDIEVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKHHR-----TENDPIGLITIDA 175
            ND+E++N DH+IC L   +A + M + V  G GYVP           + + +G + +DA
Sbjct: 118 GNDVEIINLDHIICTLTCKNASISMRIKVQCGRGYVPVISRTNVISDNKENYVGKLLVDA 177

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
            YSP++++ Y VE+AR  +  D DKL + ++T+G++  E+++  A+ IL +QL  F+   
Sbjct: 178 CYSPVERMIYKVEAARVEKRTDLDKLVIEMETNGTLDPEEAIRRAATILSNQLESFVYLR 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           + ++     I  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+Q+TE ++LR 
Sbjct: 238 DIREPE---IKEEKPEFDPILLRPVDDLELTVRSANCLKAEMIHYIGDLVQKTEVELLRT 294

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            N G+KSL EIK VL    L LGMNL +WPP++I
Sbjct: 295 PNLGKKSLTEIKDVLAAKNLSLGMNLENWPPDNI 328


>gi|148793272|gb|ABR12700.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           kishitanii]
 gi|148793274|gb|ABR12701.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           kishitanii]
 gi|148793280|gb|ABR12704.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           kishitanii]
          Length = 308

 Score =  318 bits (814), Expect = 9e-85,   Method: Composition-based stats.
 Identities = 138/314 (43%), Positives = 204/314 (64%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ 
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIA 117

Query: 129 NPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
           NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA +SP+ +++
Sbjct: 118 NPEHVICHLTDDNAELSMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDRIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +      
Sbjct: 178 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE--- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|309777158|ref|ZP_07672121.1| DNA-directed RNA polymerase, alpha subunit [Erysipelotrichaceae
           bacterium 3_1_53]
 gi|308915028|gb|EFP60805.1| DNA-directed RNA polymerase, alpha subunit [Erysipelotrichaceae
           bacterium 3_1_53]
          Length = 319

 Score =  318 bits (814), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 130/302 (43%), Positives = 187/302 (61%), Gaps = 5/302 (1%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E ++    + EPL RGF  T+GNALRRVL+SSL GAA+ ++++DGV HE +SI G+ ED
Sbjct: 15  DESQHYGKFVFEPLERGFGTTIGNALRRVLLSSLPGAAVFSIKVDGVYHEFTSIPGIVED 74

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILNIK + + +  D    + I K+GPG VT  DI     +EV++ D  IC L+   
Sbjct: 75  VTAIILNIKTLVMSIQDDEIYTLRISKQGPGAVTGADIICPEGVEVISKDLHICTLEEGG 134

Query: 142 VVRMELTVSKGHGYVPAKHHR----TENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           ++ MEL    G GYV A  ++    T N P+G+I  D++Y+PI+KVSY VE  R GQ   
Sbjct: 135 MLEMELQARIGRGYVSADTNKQLYQTPNQPLGIIYTDSIYTPIEKVSYNVEPTRVGQDAH 194

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK-EDINVKSLPFNPAL 256
           YDK+++ I TD S++  +SVALASRIL D L +  N  E   +++      +    N  L
Sbjct: 195 YDKVTLEIWTDSSLSPAESVALASRILIDHLELLTNVHEAVNDMESVMKEAQGEVQNKGL 254

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
           +  +E+L+LSVRS NCL+   I  + +L QRTE +M+R+ N G+KSL E+K  +  +GL 
Sbjct: 255 VMMIEDLDLSVRSYNCLKRAGIQTVEELTQRTEDEMMRVRNLGKKSLKEVKDKIYDLGLS 314

Query: 317 LG 318
             
Sbjct: 315 FK 316


>gi|190341379|gb|ACE74766.1| RpoA [Escherichia vulneris]
          Length = 308

 Score =  318 bits (814), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 137/313 (43%), Positives = 207/313 (66%), Gaps = 10/313 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI    D+E++
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVQGKDDVILTLNKSGIGPVTAADITHDGDVEIV 117

Query: 129 NPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
            P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+++++
Sbjct: 118 KPQHVICHLTDENASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACYSPVERIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    +
Sbjct: 178 YNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP---E 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 VKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFL 317
           EIK VL + GL L
Sbjct: 295 EIKDVLASRGLSL 307


>gi|58415724|emb|CAH57276.1| RNA polymerase alpha-subunit [Photobacterium iliopiscarium]
 gi|58415732|emb|CAH57280.1| RNA polymerase alpha-subunit [Photobacterium phosphoreum]
 gi|148536424|gb|ABQ85764.1| RNA polymerase alpha-subunit [Photobacterium iliopiscarium]
 gi|148793266|gb|ABR12697.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           phosphoreum]
 gi|148793268|gb|ABR12698.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           phosphoreum]
 gi|148793270|gb|ABR12699.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           iliopiscarium]
 gi|148793276|gb|ABR12702.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           kishitanii]
 gi|148793278|gb|ABR12703.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           kishitanii]
          Length = 308

 Score =  318 bits (814), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 139/314 (44%), Positives = 204/314 (64%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ 
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIA 117

Query: 129 NPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
           NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ +++
Sbjct: 118 NPEHVICHLTDDNAELSMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDRIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +      
Sbjct: 178 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE--- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|315605926|ref|ZP_07880957.1| DNA-directed RNA polymerase subunit alpha [Actinomyces sp. oral
           taxon 180 str. F0310]
 gi|315312208|gb|EFU60294.1| DNA-directed RNA polymerase subunit alpha [Actinomyces sp. oral
           taxon 180 str. F0310]
          Length = 331

 Score =  318 bits (814), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 116/305 (38%), Positives = 176/305 (57%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            +   +  + R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGV HE  +I+
Sbjct: 8   ILTEEKVSDLRSRFTLEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVPHEFRTIE 67

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +IILNIK I L    D    + + K GPG V AGDI     +E+ NPD  +  
Sbjct: 68  GVKEDVAEIILNIKQIVLSSENDEPVVMYLRKAGPGEVLAGDITPPAGVEIHNPDLHLAT 127

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           L+    + +ELTV +G GYV A  ++     I  I ID++YSP+ KV+Y VE+ R  Q  
Sbjct: 128 LNEKGKLEIELTVERGRGYVSAAQNKDPQAEISRIPIDSIYSPVVKVTYKVEATRVEQRT 187

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           D+D+L + ++T  +IT  D++A A + L +  G+     E  + ++   +         L
Sbjct: 188 DFDRLVIDVETKPAITPRDALASAGKTLVELFGLMRELNEEAEGIEVGPSTTDATLAADL 247

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E L L  RS N LR   I+ +G+L+  +EAD+L + NFG KS+ EIK  L  +G+ 
Sbjct: 248 ALPIENLNLQSRSYNALRRRGILTVGELVAHSEADLLDIRNFGTKSIEEIKESLAALGMT 307

Query: 317 LGMNL 321
           L  ++
Sbjct: 308 LKDSV 312


>gi|328813955|gb|AEB52093.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 261

 Score =  317 bits (813), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 116/261 (44%), Positives = 173/261 (66%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
             + EPL RG+  TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILN
Sbjct: 1   KFVVEPLERGYGTTLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILN 60

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           IK + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +       + +T
Sbjct: 61  IKKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMT 120

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+
Sbjct: 121 VKKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           GSI+  ++++LA++IL + L +F+N  +  K  +  +  +       L   +EEL+LSVR
Sbjct: 181 GSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSVR 240

Query: 269 STNCLRGENIVYMGDLIQRTE 289
           S NCL+   I  + +L  +TE
Sbjct: 241 SYNCLKRAGINTVQELTNKTE 261


>gi|90194010|gb|ABD92566.1| RpoA [Actinobacillus minor NM305]
          Length = 303

 Score =  317 bits (813), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 138/304 (45%), Positives = 206/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+       +T+ K G G VTAGDI    D+E++NPDHVIC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVQSKDDVVLTLNKSGIGPVTAGDITHDGDVEIVNPDHVICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D +A + M + V +G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR  
Sbjct: 122 TDKNASINMRIRVQRGRGYVPASARVHTQDDDRPIGRLLVDARFSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++ V   +  +   F+
Sbjct: 182 QRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQPV---VKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|119484809|ref|ZP_01619291.1| DNA-directed RNA polymerase alpha subunit [Lyngbya sp. PCC 8106]
 gi|119457627|gb|EAW38751.1| DNA-directed RNA polymerase alpha subunit [Lyngbya sp. PCC 8106]
          Length = 314

 Score =  317 bits (813), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 113/312 (36%), Positives = 174/312 (55%), Gaps = 10/312 (3%)

Query: 14  NIEYIVLGQEEEN--RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE I    + +       + EPL RG   T+GNALRRVL+S+L G A+TAV+I GV HE
Sbjct: 5   KIECIESNTDTDRSQYGKFVLEPLDRGQGTTVGNALRRVLLSNLEGTAVTAVRIAGVNHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            ++I GV ED+ +I+LN+K I L    +  +   +  +GP  VTAG     +++EV++ +
Sbjct: 65  FATIPGVREDVLEILLNLKEIVLNSYSNQRQIGRLLVQGPATVTAGHFDLPSEVEVVDKN 124

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             I  L   + + ME  V KG GY     +R E   +  + IDA++ P++KV+YTVE AR
Sbjct: 125 QYIATLSPGSTLEMEFQVEKGTGYRAIDRNRDEATAVDFLQIDAVFMPVRKVNYTVEDAR 184

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            G  L+ D+L + I T+GS+T +++++ A+ IL D      +      +  +  +V    
Sbjct: 185 VGGSLEKDRLILDIWTNGSLTPQEALSQAATILVDLFVPLKDITLESIKTDQTDDV---- 240

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL+LSVR+ NCL+   I  + DL   T+ D+L + NFG+KS  E+   L 
Sbjct: 241 -DPTSQIPIEELQLSVRAYNCLKRAQINSVADLRDYTQEDLLEIKNFGQKSAEEVIEAL- 298

Query: 312 TMGLFLGMNLPD 323
                LG+ LP 
Sbjct: 299 --QKRLGITLPQ 308


>gi|238916292|ref|YP_002929809.1| DNA-directed RNA polymerase subunit alpha [Eubacterium eligens ATCC
           27750]
 gi|238871652|gb|ACR71362.1| DNA-directed RNA polymerase subunit alpha [Eubacterium eligens ATCC
           27750]
          Length = 322

 Score =  317 bits (813), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 127/310 (40%), Positives = 204/310 (65%), Gaps = 4/310 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           K   IE +    E+      + EPL RG+  TLGN+LRR+++SSL G A+++++I+GVLH
Sbjct: 9   KMPKIE-MTEKSEDGKYGKFVVEPLERGYGLTLGNSLRRIMLSSLVGTAVSSIKIEGVLH 67

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           E SSI GV ED+T+I++NIK +++K +G+    K   I   G GVV A DIQ   DIE++
Sbjct: 68  EFSSIPGVKEDVTEIVMNIKQLSIKNNGNSVEPKEAHIDFVGEGVVRASDIQVDPDIEII 127

Query: 129 NPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           NPD VI +L+  D+ + MELT++ G GYV ++ ++ ++ P G+I ID++Y+P+++V+  V
Sbjct: 128 NPDLVIAHLNGADSKLTMELTITNGRGYVSSEKNKRDDQPAGVIAIDSIYTPVERVNMAV 187

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ++ R GQ  D+DKL++ I T+G+I  +++++LA+++L + L  FIN  E  ++V+  +  
Sbjct: 188 QNTRVGQDTDFDKLTLDIFTNGTIEPDEALSLAAKVLSEHLKGFINLSENAQKVEIMVEQ 247

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   +E+LELSVRS+NCLR   I  + +L  +T  DM+++ N G+KSL E+ 
Sbjct: 248 EEDETTKVLSMSIEDLELSVRSSNCLRRAGINTVEELCNKTSDDMMKVRNLGKKSLDEVL 307

Query: 308 GVLGTMGLFL 317
             L  MGL L
Sbjct: 308 LKLKEMGLHL 317


>gi|291280121|ref|YP_003496956.1| DNA-directed RNA polymerase subunit alpha [Deferribacter
           desulfuricans SSM1]
 gi|290754823|dbj|BAI81200.1| DNA-directed RNA polymerase, alpha subunit [Deferribacter
           desulfuricans SSM1]
          Length = 338

 Score =  317 bits (813), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 150/324 (46%), Positives = 217/324 (66%), Gaps = 4/324 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M+  ++++++KP  IE   +G+  +     + EP  RGF  T+GN+LRRVL+S++ G A+
Sbjct: 1   MVLMDFRKVMKPKKIE--QIGEATDRYAKFVIEPYERGFGITIGNSLRRVLLSTIEGTAV 58

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
             V+IDGV HE  +I GV ED+ DIILNIK + L +   + KRV I K+G G +TA DIQ
Sbjct: 59  VGVKIDGVHHEYDTINGVLEDVVDIILNIKQLELNLLEHTLKRVYIHKKGEGRITANDIQ 118

Query: 121 TVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
           +   + VLNPD  I  + + +  V MEL V +G GYVP++  + + D I +I +DA+Y+P
Sbjct: 119 SDGSVVVLNPDQHIATITNPETEVYMELYVERGIGYVPSEEIKDKFDDIDVIPVDAIYTP 178

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           IKKV+Y VE+AR GQ  DYDKL   ++TDGSI   D++A A++I++DQ+  FINF+EP  
Sbjct: 179 IKKVNYVVENARVGQSTDYDKLIFELETDGSIKPVDAIAFAAKIIKDQMEFFINFDEPVY 238

Query: 240 EVKEDINVKSLPFNPALLKK-VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           E  E+   +   +   LL K +EELELSVR+ NCL+  NI  + DL ++T+A++L+  NF
Sbjct: 239 EEVEEEEKEDNSYILELLDKSIEELELSVRAYNCLKNANIKTLADLCEKTDAELLKTKNF 298

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLP 322
           GR+SL EIK VL  +GL LGM+L 
Sbjct: 299 GRRSLEEIKKVLAELGLSLGMDLE 322


>gi|58416032|emb|CAH57430.1| RNA polymerase alpha-subunit [Vibrio sp. R-21419]
          Length = 308

 Score =  317 bits (813), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 138/314 (43%), Positives = 203/314 (64%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---IEQVNTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ 
Sbjct: 58  LHEYSTKEGVQEDVLEILLNLKGLAVKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIA 117

Query: 129 NPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
           NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA +SP+ +++
Sbjct: 118 NPEHVICHLTDDNADISMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDRIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + + T+G++  E+++  A+ IL +QL  F++  + +      
Sbjct: 178 YAVEAARVEQRTDLDKLVIDMQTNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE--- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|313897186|ref|ZP_07830730.1| DNA-directed RNA polymerase, alpha subunit [Clostridium sp. HGF2]
 gi|312957907|gb|EFR39531.1| DNA-directed RNA polymerase, alpha subunit [Clostridium sp. HGF2]
          Length = 319

 Score =  317 bits (813), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 128/302 (42%), Positives = 187/302 (61%), Gaps = 5/302 (1%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E ++    + EPL RGF  T+GNALRRVL+SSL GAA+ ++++DGV HE +SI G+ ED
Sbjct: 15  DESQHYGKFVFEPLERGFGTTIGNALRRVLLSSLPGAAVFSIKVDGVYHEFTSIPGIVED 74

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILNIK + + +  D    + I K+GPG VT  DI     +EV++ D  IC L+   
Sbjct: 75  VTAIILNIKTLVMSIQDDEIYTLRISKQGPGAVTGADIICPEGVEVISKDLHICTLEEGG 134

Query: 142 VVRMELTVSKGHGYVPAKHHR----TENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           ++ MEL    G GYV A  ++    T N P+G+I  D++Y+PI+KVSY VE  R GQ   
Sbjct: 135 MLEMELQARIGRGYVSADTNKQLYQTPNQPLGIIYTDSIYTPIEKVSYNVEPTRVGQDAH 194

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK-EDINVKSLPFNPAL 256
           YDK+++ I TD S++  ++VALAS+IL D L +  N  E   +++      +    N  L
Sbjct: 195 YDKVALEIWTDSSLSPAEAVALASKILIDHLELLTNVHEAVNDMESVMKEAQGEVQNKGL 254

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
           +  +E+L+LSVRS NCL+   I  + +L QRTE +M+R+ N G+KSL E+K  +  +GL 
Sbjct: 255 VMMIEDLDLSVRSYNCLKRAGIQTVEELTQRTEDEMMRVRNLGKKSLKEVKDKIYDLGLS 314

Query: 317 LG 318
             
Sbjct: 315 FK 316


>gi|71065084|ref|YP_263811.1| DNA-directed RNA polymerase subunit alpha [Psychrobacter arcticus
           273-4]
 gi|93005339|ref|YP_579776.1| DNA-directed RNA polymerase subunit alpha [Psychrobacter
           cryohalolentis K5]
 gi|90110862|sp|Q4FUD1|RPOA_PSYA2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366710|sp|Q1QDG1|RPOA_PSYCK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|71038069|gb|AAZ18377.1| DNA-directed RNA polymerase, 30-40 kDa subunit:RNA polymerase,
           alpha chain, bacterial and organelle [Psychrobacter
           arcticus 273-4]
 gi|92393017|gb|ABE74292.1| DNA-directed RNA polymerase, alpha subunit [Psychrobacter
           cryohalolentis K5]
          Length = 335

 Score =  317 bits (813), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 135/330 (40%), Positives = 209/330 (63%), Gaps = 8/330 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  N  E + PN I    +    E    +  EPL RGF HTLGNALRR+L+SSL GAA+ 
Sbjct: 1   MMLNATEFLTPNAINVDTVN---ETIAKVTLEPLERGFGHTLGNALRRILLSSLPGAAVI 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGV HE S+++G+ ED+ D++LN+KG+ + +   +   +T+ K+GPG +TA DI  
Sbjct: 58  EAEIDGVDHEYSTLEGLQEDVLDLLLNLKGLAITLHDQNEVFLTLDKQGPGTITAADITL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI--GLITIDALYSP 179
            ++++++NP+ V+  L     ++M L V  G GY PA   R + D    G + +DA +SP
Sbjct: 118 PHNVDIINPELVLGTLSDRGHLKMRLRVVMGRGYEPANQRREDGDTKAIGRLKLDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           + +V+Y VE+AR  Q  D D+L + ++T+G+I  E+++  A+ ILQ Q+ +F++ E    
Sbjct: 178 VLRVAYQVENARVEQRTDLDRLIIELETNGTIDPEEAIRKAATILQQQISIFVDLE---A 234

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           E   +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QR+E ++L+  N G
Sbjct: 235 EEAPEPVKEKEEVDPVLLRPVDDLELTVRSANCLKAENIYYIGDLVQRSETELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL +  L LGM L +WPP  +
Sbjct: 295 KKSLTEIKDVLASKDLELGMRLDNWPPADL 324


>gi|227494572|ref|ZP_03924888.1| DNA-directed RNA polymerase [Actinomyces coleocanis DSM 15436]
 gi|226832306|gb|EEH64689.1| DNA-directed RNA polymerase [Actinomyces coleocanis DSM 15436]
          Length = 339

 Score =  317 bits (812), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 119/303 (39%), Positives = 177/303 (58%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
              +  +NR+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGV HE S++ GV
Sbjct: 20  TEEKVSDNRSRFILEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVQHEFSTVPGV 79

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+ +IILNIK I L    D    + + K G GVVTAGDI     +E+ NP+  +  L 
Sbjct: 80  KEDVAEIILNIKNIVLSSENDEPVVMYLRKTGAGVVTAGDITPPAGVEIHNPELELATLS 139

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               V +ELTV +G GYV A  ++  N  I  I ID++YSP+ KV+Y VE+ R  Q  D+
Sbjct: 140 EKGKVEIELTVERGRGYVSAMQNKDPNAEISRIPIDSIYSPVLKVTYKVEATRVEQRTDF 199

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           D+L + ++T  +IT  D++A A + L +  G+        + ++   +         L  
Sbjct: 200 DRLIVDVETKPAITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSATDETLAADLAL 259

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E L L  RS N LR   I+ +G+L+  +EAD+L + NFG KS+ EIK  L  +G+ L 
Sbjct: 260 PIENLGLQSRSYNALRRRGILSVGELVAHSEADLLDIRNFGLKSIEEIKEKLAGLGMTLK 319

Query: 319 MNL 321
            ++
Sbjct: 320 DSV 322


>gi|154507837|ref|ZP_02043479.1| hypothetical protein ACTODO_00319 [Actinomyces odontolyticus ATCC
           17982]
 gi|293190232|ref|ZP_06608728.1| DNA-directed RNA polymerase, alpha subunit [Actinomyces
           odontolyticus F0309]
 gi|153797471|gb|EDN79891.1| hypothetical protein ACTODO_00319 [Actinomyces odontolyticus ATCC
           17982]
 gi|292821048|gb|EFF80001.1| DNA-directed RNA polymerase, alpha subunit [Actinomyces
           odontolyticus F0309]
          Length = 331

 Score =  317 bits (812), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 116/305 (38%), Positives = 176/305 (57%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            +   +  + R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGV HE  +I+
Sbjct: 8   ILTEEKVSDLRSRFTLEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVPHEFRTIE 67

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +IILNIK I L    D    + + K GPG V AGDI     +E+ NPD  +  
Sbjct: 68  GVKEDVAEIILNIKQIVLSSENDEPVVMYLRKAGPGEVLAGDITPPAGVEIHNPDLHLAT 127

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           L+    + +ELTV +G GYV A  ++     I  I ID++YSP+ KV+Y VE+ R  Q  
Sbjct: 128 LNEKGKLEIELTVERGRGYVSAAQNKDPQAEISRIPIDSIYSPVVKVTYKVEATRVQQRT 187

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           D+D+L + ++T  +IT  D++A A + L +  G+     E  + ++   +         L
Sbjct: 188 DFDRLVIDVETKPAITPRDALASAGKTLVELFGLMRELNEEAEGIEVGPSTTDATLAADL 247

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E L L  RS N LR   I+ +G+L+  +EAD+L + NFG KS+ EIK  L  +G+ 
Sbjct: 248 ALPIENLNLQSRSYNALRRRGILTVGELVAHSEADLLDIRNFGTKSIEEIKESLAALGMT 307

Query: 317 LGMNL 321
           L  ++
Sbjct: 308 LKDSV 312


>gi|148652262|ref|YP_001279355.1| DNA-directed RNA polymerase subunit alpha [Psychrobacter sp.
           PRwf-1]
 gi|172048491|sp|A5WCL4|RPOA_PSYWF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|148571346|gb|ABQ93405.1| DNA-directed RNA polymerase, alpha subunit [Psychrobacter sp.
           PRwf-1]
          Length = 335

 Score =  317 bits (812), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 134/330 (40%), Positives = 211/330 (63%), Gaps = 8/330 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  N  E + PN I    + +       +  EPL RGF HTLGNALRR+L+SSL GAA+ 
Sbjct: 1   MMLNATEFLTPNAINVDAVDETN---AKVTLEPLERGFGHTLGNALRRILLSSLPGAAVI 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +I+GV HE S+++G+ ED+ D++LN+KG+ + M   +   +T+ K+GPG++TA DI+ 
Sbjct: 58  EAEIEGVDHEYSTLEGLQEDVLDLLLNLKGLAITMHDQNEVFLTLDKKGPGIITAADIEL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI--GLITIDALYSP 179
            ++++++NP+ V+  L     ++M L V  G GY PA   R + D    G + +DA +SP
Sbjct: 118 PHNVDIVNPELVLGTLGDRGHLKMRLRVVMGRGYEPANLRREDGDTKAIGRLKLDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           + +V+Y VE+AR  Q  D D+L + ++T+G+I  E+++  A+ ILQ Q+ +F++ E    
Sbjct: 178 VSRVAYQVENARVEQRTDLDRLIIELETNGTIDPEEAIRKAATILQQQISIFVDLE---A 234

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           E   +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QR+E ++L+  N G
Sbjct: 235 EEAPEPVKEKEEVDPVLLRPVDDLELTVRSANCLKAENIYYIGDLVQRSETELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL L M L +WPP  +
Sbjct: 295 KKSLTEIKDVLASKGLELDMRLENWPPADL 324


>gi|58415734|emb|CAH57281.1| RNA polymerase alpha-subunit [Salinivibrio costicola subsp.
           costicola]
          Length = 308

 Score =  316 bits (811), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 136/314 (43%), Positives = 203/314 (64%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI     +E+ 
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVILTLTKSGAGPVVAGDITHDGGVEIA 117

Query: 129 NPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYSPIKKVS 184
           NP+HVIC+L   +A + M + V +G GYVPA        +  PIG + +DA +SP+ +++
Sbjct: 118 NPEHVICHLTDANAEISMRIKVERGRGYVPASARIDSEDDERPIGRLLVDATFSPVDRIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +      
Sbjct: 178 YNVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE--- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GLFLG
Sbjct: 295 EIKDVLASRGLFLG 308


>gi|90194012|gb|ABD92567.1| RpoA [Actinobacillus porcitonsillarum]
          Length = 303

 Score =  316 bits (811), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 136/304 (44%), Positives = 205/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+       +T+ K G G VTAGDI    D+E++NPDHVIC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVQSKDDVVLTLNKSGIGPVTAGDITHDGDVEIVNPDHVICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D +A + M + V +G GYVPA      + ++ PIG + +DA +SP+ +++Y VE+AR  
Sbjct: 122 TDKNASINMRIRVQRGRGYVPASARVHAQDDDRPIGRLLVDARFSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|58415706|emb|CAH57267.1| RNA polymerase alpha-subunit [Photobacterium angustum]
 gi|58415726|emb|CAH57277.1| RNA polymerase alpha-subunit [Photobacterium leiognathi subsp.
           leiognathi]
 gi|58415730|emb|CAH57279.1| RNA polymerase alpha-subunit [Photobacterium leiognathi subsp.
           leiognathi]
 gi|148793254|gb|ABR12691.1| DNA-directed RNA polymerase alpha subunit [Photobacterium angustum]
 gi|148793256|gb|ABR12692.1| DNA-directed RNA polymerase alpha subunit [Photobacterium angustum]
 gi|148793258|gb|ABR12693.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           leiognathi]
 gi|148793260|gb|ABR12694.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           leiognathi]
 gi|148793262|gb|ABR12695.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           leiognathi subsp. mandapamensis]
 gi|148793264|gb|ABR12696.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           leiognathi subsp. mandapamensis]
          Length = 308

 Score =  316 bits (811), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 137/314 (43%), Positives = 203/314 (64%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ 
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIA 117

Query: 129 NPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
           NP+HVIC++  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ +++
Sbjct: 118 NPEHVICHITDDNAELSMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDRIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +      
Sbjct: 178 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE--- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|189501184|ref|YP_001960654.1| DNA-directed RNA polymerase subunit alpha [Chlorobium
           phaeobacteroides BS1]
 gi|238692283|sp|B3EP34|RPOA_CHLPB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|189496625|gb|ACE05173.1| DNA-directed RNA polymerase, alpha subunit [Chlorobium
           phaeobacteroides BS1]
          Length = 328

 Score =  316 bits (811), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 129/322 (40%), Positives = 200/322 (62%), Gaps = 6/322 (1%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  I+       ++N  + IA+PL RG+  TLGNA+RRVL++SL G AIT ++IDGV HE
Sbjct: 8   PEKIDVDEGTHNDKN-GIFIAQPLERGYGVTLGNAMRRVLLASLPGTAITGIKIDGVFHE 66

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNP 130
            S+I GV ED+ DIILN+K +  + S     + T+   GP  VTAGDI     + EVLN 
Sbjct: 67  FSAIDGVREDVPDIILNLKKVRFRSSTKRSCKTTVTVDGPADVTAGDIVAQEGEFEVLNT 126

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  ++  + + M++ + +G GYVPA+ +R +  P+G I ID++++PIK V ++VE+ 
Sbjct: 127 DLHIATVNEGSRLSMDVYIGRGRGYVPAEDNRGDGMPLGFIAIDSIFTPIKNVKFSVENT 186

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI----N 246
           R GQ  DY+K+ + ++TDGS++ +DS++LA +I+ + + +F NF    +E  E+     +
Sbjct: 187 RVGQRTDYEKMILDVETDGSVSPDDSISLAGKIINEHVSLFANFSPTDEEFTEEEYKQQD 246

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       LL ++E+L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL E+
Sbjct: 247 DEFENMRKMLLTRIEDLDLSVRSHNCLRLAEIDTLGDLVSRKEDELLTYKNFGKKSLTEL 306

Query: 307 KGVLGTMGLFLGMNLPDWPPES 328
           K  L    L  GM++  +  + 
Sbjct: 307 KEQLEKFELKFGMDITKYQMKG 328


>gi|164608416|gb|ABY62511.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio wodanis]
 gi|164608418|gb|ABY62512.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio wodanis]
          Length = 308

 Score =  316 bits (811), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 140/314 (44%), Positives = 205/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQVSQ---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ 
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIA 117

Query: 129 NPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
           NP+HVIC+L  D A + M + V +G GYVP+    H+  +  PIG + IDA YSP+ K+S
Sbjct: 118 NPEHVICHLTDDNAEISMRIKVERGRGYVPSTARIHNEEDERPIGRLLIDATYSPVDKIS 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +      
Sbjct: 178 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE--- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|269217218|ref|ZP_06161072.1| DNA-directed RNA polymerase, alpha subunit [Slackia exigua ATCC
           700122]
 gi|269129355|gb|EEZ60440.1| DNA-directed RNA polymerase, alpha subunit [Slackia exigua ATCC
           700122]
          Length = 317

 Score =  316 bits (811), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 122/321 (38%), Positives = 188/321 (58%), Gaps = 11/321 (3%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E ++P     +   +  +     I EPL RGF +TLGN +RRVL+SSL GA  TA+QI
Sbjct: 1   MAEFMRPT----VTTEEVNDTIARFIVEPLERGFGYTLGNCMRRVLLSSLDGARATAIQI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +GV HE ++ +GV ED+TDI LN+KG+  +      +    T+   GP  VT  DIQ   
Sbjct: 57  EGVQHEFTTAEGVIEDVTDIALNVKGLVFQALSEDYTEATATVSVEGPCTVTGADIQVPT 116

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           +  ++NP+HVIC +     + M + +  G GYVPA+ ++   DPIG+I +D+L+SP+++ 
Sbjct: 117 EFTLVNPEHVICTVADGGTLNMTIRIGVGRGYVPAERNKRSEDPIGIIHVDSLFSPVQRC 176

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +  V S R GQ  D+DKL + + TDGSIT +++V  A+ I+   +G F+   +   E ++
Sbjct: 177 TADVSSTRVGQRTDFDKLVLEVATDGSITPDEAVCRAANIINQYMGSFMALADIAGEDED 236

Query: 244 DI-----NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                    +    N  L K++E+L+LSVRS NCL+   I  +  L++ +E D+L + NF
Sbjct: 237 GEIPSIFAPEGQESNAELDKQIEDLDLSVRSYNCLKRAGIHSVRQLVEFSENDLLNIRNF 296

Query: 299 GRKSLVEIKGVLGTMGLFLGM 319
           G KS+ E+K  L +MGL L  
Sbjct: 297 GAKSIEEVKDKLISMGLNLKQ 317


>gi|190341313|gb|ACE74733.1| RpoA [Enterobacter amnigenus]
          Length = 308

 Score =  316 bits (811), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 137/314 (43%), Positives = 207/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            + P  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLNPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI    D+E++
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIV 117

Query: 129 NPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
            P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+++++
Sbjct: 118 KPQHVICHLTDENAAISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACYSPVERIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    +
Sbjct: 178 YNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP---E 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 VKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|225165487|ref|ZP_03727313.1| DNA-directed RNA polymerase, alpha subunit [Opitutaceae bacterium
           TAV2]
 gi|224800264|gb|EEG18668.1| DNA-directed RNA polymerase, alpha subunit [Opitutaceae bacterium
           TAV2]
          Length = 334

 Score =  316 bits (811), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 129/333 (38%), Positives = 195/333 (58%), Gaps = 4/333 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + K   +   PN +  +  G   +     IAEP   G+ HT+GN+LRRVL+SS+ G+AI+
Sbjct: 1   MPKRLGKFELPNKLTKVEEGS-SDTYAKFIAEPFEAGYGHTIGNSLRRVLLSSIEGSAIS 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++I+GV HE  SI GV ED+TDI+LN+K + L  +      + I     G VTA DIQ 
Sbjct: 60  SIKIEGVNHEFQSIDGVVEDVTDIVLNLKKVLLISTKRDPITLQIRVNREGPVTAADIQA 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +++ V+NP+ VIC LD       E+ +  G GY P + ++ E   IG+I ID+L+SP+ 
Sbjct: 120 DSNVTVVNPNQVICTLDRARPFNAEIEIKTGRGYYPGEQNKKEEQAIGVIAIDSLFSPVT 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
            V Y VE+ R GQ+ DYDKL++ I TDG IT +D++  ++ IL+  + +F        E 
Sbjct: 180 LVKYAVENTRVGQITDYDKLNLEIWTDGRITPDDALKQSAAILKHHIDVFDRVSGENYEF 239

Query: 242 KE---DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +    +++ +       L   V E+ELSVR+ NCL   NI  +G+L  +TE +ML+  NF
Sbjct: 240 ENQQSEVSEEQNKLRKLLNMSVNEIELSVRAANCLNNANITTVGELAMKTEQEMLKYRNF 299

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK  L  +GL LGM   +   ++ +E
Sbjct: 300 GKKSLNEIKDKLEALGLSLGMKFDERLLDTKKE 332


>gi|58415690|emb|CAH57259.1| RNA polymerase alpha-subunit [Enterovibrio coralii]
 gi|58415692|emb|CAH57260.1| RNA polymerase alpha-subunit [Enterovibrio norvegicus]
 gi|58415694|emb|CAH57261.1| RNA polymerase alpha-subunit [Enterovibrio norvegicus]
 gi|58415696|emb|CAH57262.1| RNA polymerase alpha-subunit [Enterovibrio norvegicus]
 gi|58415698|emb|CAH57263.1| RNA polymerase alpha-subunit [Enterovibrio norvegicus]
 gi|58415700|emb|CAH57264.1| RNA polymerase alpha-subunit [Grimontia hollisae]
 gi|58415702|emb|CAH57265.1| RNA polymerase alpha-subunit [Grimontia hollisae]
 gi|58415704|emb|CAH57266.1| RNA polymerase alpha-subunit [Grimontia hollisae]
          Length = 308

 Score =  316 bits (810), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 136/314 (43%), Positives = 203/314 (64%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI     +E+ 
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVILTLNKSGAGPVVAGDITHDGGVEIA 117

Query: 129 NPDHVICNLDV-DAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
           NP+HVIC+L   +A + M + V +G GYVPA    H   +  PIG + +DA +SP+ +++
Sbjct: 118 NPEHVICHLTDSNAEISMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDRIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +      
Sbjct: 178 YNVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE--- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|328813991|gb|AEB52111.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 269

 Score =  316 bits (810), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 122/269 (45%), Positives = 178/269 (66%), Gaps = 2/269 (0%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E +N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+
Sbjct: 1   ENDNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDV 60

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A 
Sbjct: 61  TAIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGAH 120

Query: 143 VRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             M +T + G GYV A+ ++   ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DK
Sbjct: 121 FHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDK 180

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L++ + T+GSIT  ++++L+++IL D L +F+N  +  K     +  +       L   +
Sbjct: 181 LTLDVWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEMTI 240

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTE 289
           EEL+LSVRS NCL+   I  + +L  +TE
Sbjct: 241 EELDLSVRSYNCLKRAGINTVQELTNKTE 269


>gi|58415714|emb|CAH57271.1| RNA polymerase alpha-subunit [Photobacterium rosenbergii]
 gi|58415716|emb|CAH57272.1| RNA polymerase alpha-subunit [Photobacterium rosenbergii]
 gi|58415718|emb|CAH57273.1| RNA polymerase alpha-subunit [Photobacterium rosenbergii]
 gi|58415720|emb|CAH57274.1| RNA polymerase alpha-subunit [Photobacterium rosenbergii]
 gi|58415722|emb|CAH57275.1| RNA polymerase alpha-subunit [Photobacterium rosenbergii]
          Length = 308

 Score =  316 bits (810), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 138/314 (43%), Positives = 204/314 (64%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---IEQVNTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ 
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIA 117

Query: 129 NPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
           NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA +SP+ +++
Sbjct: 118 NPEHVICHLTDDNADISMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDRIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +      
Sbjct: 178 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE--- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|88606699|ref|YP_504915.1| DNA-directed RNA polymerase subunit alpha [Anaplasma
           phagocytophilum HZ]
 gi|119366662|sp|Q2GL36|RPOA_ANAPZ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|88597762|gb|ABD43232.1| DNA-directed RNA polymerase, alpha subunit [Anaplasma
           phagocytophilum HZ]
          Length = 344

 Score =  316 bits (810), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 164/345 (47%), Positives = 234/345 (67%), Gaps = 10/345 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +W +L +P++I+ +  G +E     ++ EPL  GFA TLGNALRRV+MSSLRG A+ 
Sbjct: 1   MADHWNKLTRPSSIKVV--GGKEPCVMELVIEPLESGFALTLGNALRRVMMSSLRGFAVY 58

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            ++I+G  HE++++ GV ED+ D++LN+  + +K+   + + + +  RGPG VTA  I  
Sbjct: 59  GIEIEGASHELTALSGVREDVADLVLNLSMLRVKLLNSNQRVLRLVARGPGEVTAASIVD 118

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP-------IGLITID 174
             D  VLN D  IC L  D    M++ V+ G GYVPA  +R  +          G I  +
Sbjct: 119 SADHVVLNKDLHICTLGKDVDFCMKIYVNSGKGYVPATEYRAASRSGGASEVGSGFIATN 178

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           ALYSP+KKV+  +ES+R GQ  DYD+L +T++TDGS+  +D+VA+A++ILQDQL  FI+F
Sbjct: 179 ALYSPVKKVALKIESSRIGQFTDYDRLMLTVETDGSVAPDDAVAVAAKILQDQLQSFISF 238

Query: 235 EEPKKEVK-EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           +E ++  K  D     LP++  LL+KV+ELELSVRS NCL+ +NI Y+GDL+QRTE+DML
Sbjct: 239 DEVEETRKSVDKEEGVLPYDHNLLRKVDELELSVRSHNCLKNDNITYIGDLVQRTESDML 298

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           R  NFGRKSL EI  VL +M L LGM +P+WPPESIE L+K+Y +
Sbjct: 299 RTPNFGRKSLNEINEVLASMNLHLGMKVPNWPPESIENLSKQYSE 343


>gi|297571895|ref|YP_003697669.1| DNA-directed RNA polymerase, subunit alpha [Arcanobacterium
           haemolyticum DSM 20595]
 gi|296932242|gb|ADH93050.1| DNA-directed RNA polymerase, alpha subunit [Arcanobacterium
           haemolyticum DSM 20595]
          Length = 334

 Score =  316 bits (810), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 113/306 (36%), Positives = 179/306 (58%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
              +  + R+     PL  GF +TLGN+LRR L+SS+ GAA+T++ IDGVLHE S+I+GV
Sbjct: 10  TEEKISDTRSRFTLNPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIHIDGVLHEFSTIEGV 69

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+  IILN+K + +    D   ++ + K GPG VTA DI     +E+ NP+ +I  L+
Sbjct: 70  KEDVAQIILNLKDLVVTSENDEPVQMYLRKAGPGQVTAEDITPPAGVEIHNPELLIATLN 129

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + ++LTV +G GYV A+ + + +  IG I +D++YSP+ KVSY VE+ R GQ  D+
Sbjct: 130 EKGKLEIDLTVERGRGYVSAQQNNSPDYEIGRIPVDSIYSPVVKVSYKVEATRVGQRTDF 189

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T  S+   D+ A A + L +  G+     +  + ++          +  L +
Sbjct: 190 DKLIVDVETKPSMAPRDAFASAGKTLVELFGLTTELNQEVEGLELKEAPVVEQQSSDLQR 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +  L L  RS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ ++K  L  + L L 
Sbjct: 250 PITILNLPARSQNCLQREGIHTIGELVLRSEADLLDIRNFGAKSIEDVKDELAKLDLRLK 309

Query: 319 MNLPDW 324
            +   +
Sbjct: 310 DSPAGF 315


>gi|119946252|ref|YP_943932.1| DNA-directed RNA polymerase subunit alpha [Psychromonas ingrahamii
           37]
 gi|158513118|sp|A1SXW8|RPOA1_PSYIN RecName: Full=DNA-directed RNA polymerase subunit alpha 1;
           Short=RNAP subunit alpha 1; AltName: Full=RNA polymerase
           subunit alpha 1; AltName: Full=Transcriptase subunit
           alpha 1
 gi|119864856|gb|ABM04333.1| DNA-directed RNA polymerase, alpha subunit [Psychromonas ingrahamii
           37]
          Length = 328

 Score =  316 bits (810), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 144/333 (43%), Positives = 218/333 (65%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q   ++ +KPN +    + Q    R  +  EPL RGF HTLGNALRR+L+SS+ GAAIT
Sbjct: 1   MQGFVKDFLKPNLV---GIEQINATRAKVTLEPLERGFGHTLGNALRRILLSSMPGAAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGV +E S  +GV E++ +I+LN+KG+ +K+ G +   V++ K G G V A DI  
Sbjct: 58  EVEIDGVQNEYSIKEGVQEEILEILLNLKGLAVKLEGKNEVLVSLTKSGAGPVIAADITH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
            +D+E++NP+HVIC+L  +  + M + +  G GYVPA    H   +    G + +DA +S
Sbjct: 118 DSDLEIVNPEHVICHLTGNTEISMRIKIELGRGYVPASSRIHSEEDKSANGRLFVDATFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++++Y+VESAR  Q  + DKL + ++TDG++  E+++  A+ IL  QL  F++     
Sbjct: 178 PVERIAYSVESARVEQRTNLDKLVIDMETDGTLEPEEAIRQAAMILAGQLDEFVDERIIS 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
             V+ +   +   F+P LL+ V +LEL+VRS NCL+ E+I Y+GDL+QRTE ++L+M N 
Sbjct: 238 APVEVE---EKPEFDPILLRPVNDLELTVRSANCLKAESIYYIGDLVQRTEVELLKMPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK  L + GL+LGM L +WPP S+ E
Sbjct: 295 GRKSLTEIKDDLVSRGLYLGMRLENWPPASLIE 327


>gi|58415708|emb|CAH57268.1| RNA polymerase alpha-subunit [Photobacterium damselae subsp.
           damselae]
 gi|58415710|emb|CAH57269.1| RNA polymerase alpha-subunit [Photobacterium damselae subsp.
           damselae]
 gi|58415712|emb|CAH57270.1| RNA polymerase alpha-subunit [Photobacterium damselae subsp.
           damselae]
          Length = 308

 Score =  316 bits (810), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 138/314 (43%), Positives = 204/314 (64%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---IEQVNSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ 
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIA 117

Query: 129 NPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
           NP+HVIC++  D A + M + V +G GYVPA    H   +  PIG + +DA +SP+ ++S
Sbjct: 118 NPEHVICHITDDNAELSMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDRIS 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +      
Sbjct: 178 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE--- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|312144220|ref|YP_003995666.1| DNA-directed RNA polymerase, alpha subunit [Halanaerobium sp.
           'sapolanicus']
 gi|311904871|gb|ADQ15312.1| DNA-directed RNA polymerase, alpha subunit [Halanaerobium sp.
           'sapolanicus']
          Length = 314

 Score =  316 bits (810), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 129/314 (41%), Positives = 201/314 (64%), Gaps = 5/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP     +   + ++N       PL RG+  TLGN+LRR+L+SSL GAA+T+V+++G
Sbjct: 3   EIEKPR----VERLESDDNYGRYEISPLERGYGTTLGNSLRRILLSSLPGAALTSVKVEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE S+I GV ED+TD+ILN+K + +K SG+    + I   G G VTAGD  T  D++V
Sbjct: 59  VKHEFSAISGVVEDMTDLILNLKEVVVKFSGEEQSTIRIEAEGEGEVTAGDFITSGDVQV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSPIKKVSYT 186
           +N DH I  L  D  + +E TV KG GY  A+ ++   +  IGLI ID+ +SPI++ ++ 
Sbjct: 119 INKDHHIATLAEDGRLLLEATVEKGRGYHTAEENKDHFDKVIGLIPIDSSFSPIERANFN 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           +E+ R GQV DYD+L + + T+GSI  +D+++LA++I+ + L +FIN  +  ++V+  + 
Sbjct: 179 IENTRVGQVTDYDRLILEVKTNGSIHPDDAISLAAKIMVEHLELFINLTDEIEDVEIMVE 238

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           V+    +  L   +EELELSVRS+NCL+   I  + +L+ +TE D++++ N G+KSL EI
Sbjct: 239 VEEEEKDKILDTTIEELELSVRSSNCLKRAGINTVEELVDKTEDDLMKVRNLGKKSLQEI 298

Query: 307 KGVLGTMGLFLGMN 320
           K  L  + L L   
Sbjct: 299 KDKLDELELELKDT 312


>gi|229823511|ref|ZP_04449580.1| hypothetical protein GCWU000282_00809 [Catonella morbi ATCC 51271]
 gi|229786955|gb|EEP23069.1| hypothetical protein GCWU000282_00809 [Catonella morbi ATCC 51271]
          Length = 314

 Score =  316 bits (810), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 133/313 (42%), Positives = 209/313 (66%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  I+ I +  + +    ++ EPL RG+  TLGN+LRR+L+SSL G+A+T++QIDG
Sbjct: 3   EIEKPE-IKTIEVSDDAKF-GKIVVEPLERGYGTTLGNSLRRILLSSLPGSAVTSIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE ++++G+ ED+  IILN+K + LK+     K + +   GP VVTA DI   ND+++
Sbjct: 61  VLHEFATVEGIVEDVPTIILNLKKLALKLHTQESKVIELNVTGPKVVTAADIMHDNDVQI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  IC L   A ++M L V+ G GYV ++H++ E+ PIG++ ID++Y+PIKKV+Y V
Sbjct: 121 LNPELYICTLADGAELKMRLNVANGRGYVRSEHNKREDMPIGVLPIDSIYTPIKKVNYQV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ   YDKL++ I TDGSI+ E S++LA++IL + L +F+N  +  ++ +  +  
Sbjct: 181 ENTRIGQKNVYDKLTLDIWTDGSISPEKSLSLAAKILTEHLNIFVNLNDEARQTEIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L+  +EEL+LSVRS NCL+   I  + +L  ++EA+M+++ N GRKSL E+K
Sbjct: 241 EEAEKEKMLIMTIEELDLSVRSYNCLKRAGINTIQELTNKSEAEMIKVRNLGRKSLEEVK 300

Query: 308 GVLGTMGLFLGMN 320
             L  + L L  +
Sbjct: 301 QKLANLELSLRQD 313


>gi|164608442|gb|ABY62524.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. MdR7]
 gi|164608444|gb|ABY62525.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. SA5]
 gi|164608446|gb|ABY62526.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. SA6]
          Length = 308

 Score =  316 bits (809), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 139/314 (44%), Positives = 204/314 (64%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQVSQ---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ 
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIA 117

Query: 129 NPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
           NP+HVIC+L    A + M + V +G GYVP+    H   +  PIG + IDA YSP+ K+S
Sbjct: 118 NPEHVICHLTDGNAEISMRIKVERGRGYVPSTARIHTEEDERPIGRLLIDATYSPVDKIS 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +      
Sbjct: 178 YSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE--- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|68171735|ref|ZP_00545087.1| DNA-directed RNA polymerase [Ehrlichia chaffeensis str. Sapulpa]
 gi|67998846|gb|EAM85546.1| DNA-directed RNA polymerase [Ehrlichia chaffeensis str. Sapulpa]
          Length = 307

 Score =  316 bits (809), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 160/306 (52%), Positives = 219/306 (71%), Gaps = 4/306 (1%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           GFA TLGNALRRV+MSSLRG A+  V+I+ VLHE +SI GV ED+TDI+LNI  + +K+S
Sbjct: 2   GFALTLGNALRRVMMSSLRGFAVYGVEIENVLHEFTSISGVREDVTDILLNISMMRVKLS 61

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
           G + K +++  +GP  V +G I   +D  +LN D +IC LD      +++ V+ G GYVP
Sbjct: 62  GMNSKVLSLKVKGPCEVRSGMIPDTDDCIILNKDLLICTLDQGVDFNIKMYVNAGKGYVP 121

Query: 158 AKH----HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           A      ++  + PI  I  +ALYSPIKK S+ VES+R GQ  DYD+L M+++TDGSI  
Sbjct: 122 AVKRKSVNKLGDIPINFIATNALYSPIKKASFKVESSRIGQFTDYDRLIMSVETDGSILP 181

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCL 273
           +++VALA+RILQDQ   FINF+E  +  K+     +LP++  LL+KV+ELELSVRS NCL
Sbjct: 182 DEAVALAARILQDQFQPFINFDETDEPHKKVDAKDTLPYDSNLLRKVDELELSVRSYNCL 241

Query: 274 RGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELA 333
           + +NI Y+GDL+Q+TE+DMLR  NFGRKSL EI  +L +M L LGM + +WPPESIE L+
Sbjct: 242 KNDNITYIGDLVQKTESDMLRTPNFGRKSLNEINELLASMNLHLGMKIANWPPESIESLS 301

Query: 334 KKYEDK 339
           K+Y ++
Sbjct: 302 KQYSEE 307


>gi|179184358|gb|ACB78144.1| RNA polymerase alpha subunit [Vibrio gallaecicus]
          Length = 315

 Score =  316 bits (809), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 140/321 (43%), Positives = 207/321 (64%), Gaps = 11/321 (3%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T 
Sbjct: 1   QGSVTEFLKPRLVD---IEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTE 57

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQT 121
           V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI  
Sbjct: 58  VEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLG 318
            G+KSL EIK VL + GL LG
Sbjct: 295 LGKKSLTEIKDVLASRGLSLG 315


>gi|319760354|ref|YP_004124292.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Blochmannia
           vafer str. BVAF]
 gi|318039068|gb|ADV33618.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Blochmannia
           vafer str. BVAF]
          Length = 334

 Score =  315 bits (808), Expect = 5e-84,   Method: Composition-based stats.
 Identities = 144/339 (42%), Positives = 212/339 (62%), Gaps = 15/339 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q   +E +KP  I    + +       +  EPL RGF HTLGNALRRVL+SS+ G A+T
Sbjct: 1   MQSPEKEFLKPRLINIEKISEV---HAKITLEPLERGFGHTLGNALRRVLLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE    +G+ ED+ +I+LN+K + + + G     +++ K G G V A DI  
Sbjct: 58  EVEIDGVLHEYGIKEGIREDVLEILLNLKTLAIAIEGKDSMILSLKKSGVGPVVASDILY 117

Query: 122 VND-IEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPA--KHHRTENDPIGLITI---- 173
            +  ++++NP HVIC +  D A++ M + V +G GYVPA  K +   ++    I I    
Sbjct: 118 DSSIVKIVNPAHVICVITDDHAILSMRIKVQRGRGYVPAFSKFNSILDEQQTAIPIGRLV 177

Query: 174 -DALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
            DA YSP+++VSYTVE+AR  +  D DKL + ++T+G+I  E+++  A+ IL DQL  FI
Sbjct: 178 LDACYSPVERVSYTVEAARVEKRTDLDKLIIDMETNGTIDPEEAIRRAATILSDQLSTFI 237

Query: 233 NFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +     +    +I      F+PALL  V++LEL+VRS NCL+ E+I Y+GDL+Q+TE ++
Sbjct: 238 DLNNVYQP---EIKEDKPEFDPALLHLVDDLELTVRSANCLKAESIHYIGDLVQKTEVEL 294

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           L+  N G+KSL EIK VL + GL LGM L  WPP+S  +
Sbjct: 295 LKTPNLGKKSLTEIKDVLASRGLSLGMCLEKWPPKSFTD 333


>gi|295315349|gb|ADF97760.1| RpoA [Vibrio sp. KTW-12]
          Length = 311

 Score =  315 bits (808), Expect = 6e-84,   Method: Composition-based stats.
 Identities = 137/316 (43%), Positives = 205/316 (64%), Gaps = 10/316 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           ++KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 2   ILKPRLVDIEQINNA---HAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 58

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ 
Sbjct: 59  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVILTLSKSGAGPVKAGDITHDGDVEIA 118

Query: 129 NPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
           NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA +SP+ +++
Sbjct: 119 NPEHVICHLTDDNAEISMRIKVERGRGYVPASARIHTDDDERPIGRLLVDATFSPVDRIA 178

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +      
Sbjct: 179 YAVEAARVEQRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE--- 235

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRT+ ++L+  N G+KSL 
Sbjct: 236 EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTDVELLKTPNLGKKSLT 295

Query: 305 EIKGVLGTMGLFLGMN 320
           EIK VL + GL LGM 
Sbjct: 296 EIKDVLASRGLSLGMR 311


>gi|284049230|ref|YP_003399569.1| DNA-directed RNA polymerase, alpha subunit [Acidaminococcus
           fermentans DSM 20731]
 gi|283953451|gb|ADB48254.1| DNA-directed RNA polymerase, alpha subunit [Acidaminococcus
           fermentans DSM 20731]
          Length = 323

 Score =  315 bits (807), Expect = 6e-84,   Method: Composition-based stats.
 Identities = 125/319 (39%), Positives = 189/319 (59%), Gaps = 9/319 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
            +E+ KP+ +  +     +      + EPL RG+  TLGN+LRRVL+SSL G A+T ++I
Sbjct: 1   MKEIEKPSLV--VDEISPDGRYGKFVWEPLERGYGITLGNSLRRVLLSSLSGMAVTGIKI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-----SHKRVTIFKRGPGVVTAGDIQ 120
           DGVLHE S+I+GV ED+ DI+LNIK +  K+  D       K   I K G G VT  D+ 
Sbjct: 59  DGVLHEFSTIEGVREDVADIVLNIKALCFKVGLDDQASFEPKTFYIKKAGEGEVTGADVI 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T  D EVLNP+  I  LD +  + ME+ V  G GYV A+ +++++ PIG I +D++YSPI
Sbjct: 119 TDQDTEVLNPELHIATLDKNGALNMEIYVDVGRGYVQAEKNKSKDQPIGFIPVDSIYSPI 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            +V + V   R G V +YD+L++ + TDGS+  +++V  A+ IL   L +F     P+ +
Sbjct: 179 TRVKFGVTDTRVGNVTNYDRLTLEVWTDGSLGPDEAVTSAAEILIKYLALFKTTNVPRIQ 238

Query: 241 VKEDINV--KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
             ED          +  L   +++L+L+VRS NCLR   I  + D+I +TE +++ + N 
Sbjct: 239 GDEDGTKTSDEGSKSSVLQMSIDDLDLTVRSNNCLRRAGINTVEDIINKTEDELICVRNL 298

Query: 299 GRKSLVEIKGVLGTMGLFL 317
           G KSL E+K  +  +GL L
Sbjct: 299 GSKSLEEVKNKIEELGLHL 317


>gi|164608420|gb|ABY62513.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio sp. ATCC
           33715]
 gi|164608422|gb|ABY62514.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. cann.1.1]
 gi|164608424|gb|ABY62515.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. cann.1.2]
 gi|164608426|gb|ABY62516.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. cann.1.3]
 gi|164608428|gb|ABY62517.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. cann.1.4]
 gi|164608430|gb|ABY62518.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. cann.2.1]
 gi|164608432|gb|ABY62519.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. cann.2.2]
 gi|164608434|gb|ABY62520.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. cann.2.3]
 gi|164608436|gb|ABY62521.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. cann.2.4]
 gi|164608438|gb|ABY62522.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. cann.2.5]
 gi|164608440|gb|ABY62523.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. cann.2.6]
          Length = 308

 Score =  315 bits (807), Expect = 7e-84,   Method: Composition-based stats.
 Identities = 140/314 (44%), Positives = 205/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQVSQ---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ 
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIA 117

Query: 129 NPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
           NP+HVIC+L  D A + M + V +G GYVP+    H   +  PIG + IDA YSP+ K+S
Sbjct: 118 NPEHVICHLTDDNAEISMRIKVERGRGYVPSTARIHTEEDERPIGRLLIDATYSPVDKIS 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +      
Sbjct: 178 YSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE--- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|206890328|ref|YP_002249220.1| DNA-directed RNA polymerase, alpha subunit [Thermodesulfovibrio
           yellowstonii DSM 11347]
 gi|206742266|gb|ACI21323.1| DNA-directed RNA polymerase, alpha subunit [Thermodesulfovibrio
           yellowstonii DSM 11347]
          Length = 343

 Score =  314 bits (806), Expect = 8e-84,   Method: Composition-based stats.
 Identities = 147/340 (43%), Positives = 206/340 (60%), Gaps = 14/340 (4%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           ++E   P  +E+       +    ++ EPL RG+  TLGN+LRRVL+SSL G A+ A++I
Sbjct: 4   YKEFQMPKKVEFDQ-ESLTDTYGKLVIEPLERGYGITLGNSLRRVLLSSLDGVAVYAIRI 62

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMS--GDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +  LHE SSIKGV ED+ DIILN+K +  K        K  TI  +GP  VTA  IQT  
Sbjct: 63  NDALHEFSSIKGVKEDILDIILNVKKLRFKYYAQDSDKKIATIKIKGPADVTAESIQTDG 122

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
             EVLN    IC+LD DA + M L + KG GYVP++  + +  P+  IT+DA++SP+KKV
Sbjct: 123 TYEVLNKSQYICSLDQDAQMEMVLYIRKGRGYVPSEAIKDDELPVDAITVDAIFSPVKKV 182

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           ++ VE  R G++ DYD+L + I TDGSIT E +++ AS IL       I F+E + + KE
Sbjct: 183 NFRVEKTRVGELTDYDRLILEIWTDGSITPERAISDASSILIKHFEYLIFFKEAELQNKE 242

Query: 244 DINVKSLPF--------NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
                  P         N  +LK +E+LELSVR+ NCL+   I  + +L+QRTE ++++ 
Sbjct: 243 IHETVPNPEEDLNFDLLNENILKPIEDLELSVRAYNCLKSAGINTIAELVQRTEGELMKT 302

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
            NFGR+SL EIK VL  MGL LGM +    PE +E+  +K
Sbjct: 303 KNFGRRSLEEIKEVLTNMGLKLGMRI---NPELLEKFKEK 339


>gi|58416108|emb|CAH57468.1| RNA polymerase alpha-subunit [Aliivibrio wodanis]
 gi|58416110|emb|CAH57469.1| RNA polymerase alpha-subunit [Aliivibrio wodanis]
 gi|148536422|gb|ABQ85763.1| RNA polymerase alpha-subunit [Aliivibrio wodanis]
          Length = 308

 Score =  314 bits (806), Expect = 9e-84,   Method: Composition-based stats.
 Identities = 140/314 (44%), Positives = 204/314 (64%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQVSQ---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ 
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIA 117

Query: 129 NPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
           NP+HVIC+L  D A + M + V +G GYVP+    H   +  PIG + IDA YSP+ K+S
Sbjct: 118 NPEHVICHLTDDNAEISMRIKVERGRGYVPSTARIHTEEDERPIGRLLIDATYSPVDKIS 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +      
Sbjct: 178 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE--- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|164608414|gb|ABY62510.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio wodanis]
          Length = 308

 Score =  314 bits (806), Expect = 9e-84,   Method: Composition-based stats.
 Identities = 140/314 (44%), Positives = 204/314 (64%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQVSQ---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ 
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIA 117

Query: 129 NPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
           NP+HVIC+L  D A + M + V +G GYVP+    H   +  PIG + IDA YSP+ K+S
Sbjct: 118 NPEHVICHLTDDNAEISMRIKVERGRGYVPSTARIHSEEDERPIGRLLIDATYSPVDKIS 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +      
Sbjct: 178 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE--- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|179184569|gb|ACB78152.1| RNA polymerase alpha subunit [Vibrio crassostreae]
          Length = 315

 Score =  314 bits (806), Expect = 9e-84,   Method: Composition-based stats.
 Identities = 138/321 (42%), Positives = 205/321 (63%), Gaps = 11/321 (3%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T 
Sbjct: 1   QGSVTEFLKPRLVDXEQINT---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTE 57

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQT 121
           V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI  
Sbjct: 58  VEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+  ++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDXIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLG 318
            G+KSL EIK VL + GL LG
Sbjct: 295 LGKKSLTEIKDVLASRGLSLG 315


>gi|108804947|ref|YP_644884.1| DNA-directed RNA polymerase subunit alpha [Rubrobacter xylanophilus
           DSM 9941]
 gi|119366722|sp|Q1AU56|RPOA_RUBXD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|108766190|gb|ABG05072.1| DNA-directed RNA polymerase, alpha subunit [Rubrobacter
           xylanophilus DSM 9941]
          Length = 313

 Score =  314 bits (805), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 123/298 (41%), Positives = 183/298 (61%), Gaps = 1/298 (0%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           + +E+E   + +AEPLPRG  HTLGNALRRV++S L GAA+T ++I+GV HE S+I+GV 
Sbjct: 12  VEEEDERHGIFVAEPLPRGLGHTLGNALRRVMLSGLPGAAVTKLRIEGVQHEFSTIEGVR 71

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+ DIILN+K +  ++  D    + I K GPG V   DI+   D+EV+NPD  I +L  
Sbjct: 72  EDVVDIILNVKQLKFRLERDEPIELQISKDGPGEVRGSDIELKADVEVVNPDAYIASLSE 131

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              + M LTV +G GYVPA+ ++++ DPIG+I +D+L+SP++KV Y V   R G  +D D
Sbjct: 132 GGHLDMTLTVERGQGYVPAEQNKSDADPIGVIAVDSLFSPVEKVQYRVSETRAGARVDLD 191

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
            L++ + TDG +   +++  ASR L D  G+F    +     +E       P      + 
Sbjct: 192 ALTLEVFTDGRLGPREALREASRKLIDFFGLFAEGYQGAGAAEEPGRSGGRPVI-TDERP 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +E+LEL+VRS NCL+ E +  +G L   TE +++ + N G KS+ EI+  L   G  L
Sbjct: 251 IEDLELTVRSYNCLKREGVDTIGQLATMTEEELMNIRNLGMKSVDEIRSKLEEYGYTL 308


>gi|160872598|ref|ZP_02062730.1| DNA-directed RNA polymerase, alpha subunit [Rickettsiella grylli]
 gi|159121397|gb|EDP46735.1| DNA-directed RNA polymerase, alpha subunit [Rickettsiella grylli]
          Length = 348

 Score =  314 bits (805), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 135/340 (39%), Positives = 208/340 (61%), Gaps = 9/340 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  N ++ + P  IE   +     NR+L+  +P   GF HTLGNALRRVL+SS+ G A+ 
Sbjct: 1   MSTNVKKFLTPQTIEVQTI---APNRSLITLQPFEAGFGHTLGNALRRVLLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +I+GVLHE SS++GV ED+ DI+LN+KG+  +M G     + + K   G V AGDI  
Sbjct: 58  EAKIEGVLHEYSSLEGVQEDIIDILLNLKGVAFQMHGKEEVTLELIKNTVGPVCAGDITL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYS 178
            +DIEV NPD VI +L      +M L V++G GY PA   + +      +G + +DA ++
Sbjct: 118 PSDIEVKNPDFVIAHLTKPKEFKMTLKVARGRGYQPASLRKADERFVSEVGALQLDARFN 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI + +Y+VE+AR  Q  D DKL + ++T+G+I  E+++  A+ I+Q+QL  F+     K
Sbjct: 178 PILRATYSVENARVEQRTDLDKLVIDLETNGTIDPEEAIRRAATIIQEQLRTFVEL---K 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E +E++  + +  NP LL  V+ELEL+VR+ NCL+ E+I  + DL+ +TE+++L   N 
Sbjct: 235 HETEEEVVDEFVDINPMLLLPVDELELTVRAANCLKAEHIYRIADLVTKTESELLSTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           G+ SL EIK  L   GL LGM +P     S+++  +  E+
Sbjct: 295 GKVSLWEIKTALQKRGLSLGMEVPIQQLASLKKSLEATEE 334


>gi|40063201|gb|AAR38038.1| DNA-directed RNA polymerase, alpha subunit [uncultured marine
           bacterium 562]
          Length = 321

 Score =  314 bits (805), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 133/327 (40%), Positives = 204/327 (62%), Gaps = 6/327 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  +L+ P  I+   +     N + +  EPL RGF HTLGNALRR+L+SS+ GAA+T
Sbjct: 1   MQISVIDLLVPTEIQ---VDDITPNLSKITLEPLERGFGHTLGNALRRILLSSMPGAAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V IDG+ HE S+I+GV ED+ DI+LNIK + + +   +   +T+   GP  V A     
Sbjct: 58  DVAIDGISHEYSTIEGVREDVIDILLNIKDMPVNIIEGNTAEITLDVTGPCDVLASSFDV 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
             ++E++N D  +  +     ++M LTV  G GY PA     E+  +G + +DA YSP++
Sbjct: 118 PGNVELVNQDFHVATIVDKVNLKMTLTVQTGRGYEPADTRDDEDRVVGALKVDASYSPVR 177

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +VSYTV++AR  +  D DKL + ++TDG++  + ++  ++ ILQ QL  F++ +      
Sbjct: 178 RVSYTVDNARFEKRTDLDKLVIELETDGTLDPKMAIEHSATILQQQLSSFVDLDAIA--- 234

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +++       F+P LL+ +EELEL+VRSTNCL+ E+I  +GDLI R+E D+L+  N G+K
Sbjct: 235 EQEAKKDQNDFDPFLLRSIEELELTVRSTNCLKAESIFLIGDLIHRSEFDLLKTPNLGKK 294

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPES 328
           SL EIK VL +  L LGMN+ +WPP  
Sbjct: 295 SLNEIKDVLASKELSLGMNVDNWPPVG 321


>gi|328814007|gb|AEB52119.1| DNA-directed RNA polymerase alpha chain [Lactobacillus rhamnosus]
          Length = 258

 Score =  314 bits (804), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 114/258 (44%), Positives = 172/258 (66%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED+T IILNIK
Sbjct: 1   VVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLEDVTQIILNIK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV 
Sbjct: 61  KLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVK 120

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GS
Sbjct: 121 KGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGS 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I+  ++++LA++IL + L +F+N  +  K  +  +  +       L   +EEL+LSVRS 
Sbjct: 181 ISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSVRSY 240

Query: 271 NCLRGENIVYMGDLIQRT 288
           NCL+   I  + +L  +T
Sbjct: 241 NCLKRAGINTVQELTNKT 258


>gi|58415862|emb|CAH57345.1| RNA polymerase alpha-subunit [Vibrio gazogenes]
          Length = 309

 Score =  314 bits (804), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 141/315 (44%), Positives = 208/315 (66%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
           +NP+HVIC+L+ D A V M + V +G GYVPA    H   ++ PIG + +DA YSP+ K+
Sbjct: 118 VNPEHVICHLNDDNAEVAMRIKVQRGRGYVPASARIHTDEDDRPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +YTVE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYTVEAARVEQRTDLDKLVIDMETNGTIEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|58415836|emb|CAH57332.1| RNA polymerase alpha-subunit [Aliivibrio fischeri]
 gi|58415838|emb|CAH57333.1| RNA polymerase alpha-subunit [Aliivibrio fischeri]
 gi|148536414|gb|ABQ85759.1| RNA polymerase alpha-subunit [Aliivibrio fischeri]
 gi|148536416|gb|ABQ85760.1| RNA polymerase alpha-subunit [Aliivibrio fischeri]
 gi|148536418|gb|ABQ85761.1| RNA polymerase alpha-subunit [Aliivibrio fischeri]
 gi|148793252|gb|ABR12690.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio fischeri]
 gi|164608402|gb|ABY62504.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio fischeri]
          Length = 308

 Score =  314 bits (804), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 138/314 (43%), Positives = 203/314 (64%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ 
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIA 117

Query: 129 NPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
           NP+HVIC+L  D A + M + V +G GYVP+    H   +  PIG + +DA YSP+ K+S
Sbjct: 118 NPEHVICHLTDDNAEISMRIKVERGRGYVPSTARIHTEEDERPIGRLLVDATYSPVDKIS 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +      
Sbjct: 178 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE--- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|168334324|ref|ZP_02692511.1| DNA-directed RNA polymerase, alpha subunit [Epulopiscium sp. 'N.t.
           morphotype B']
          Length = 319

 Score =  314 bits (804), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 122/314 (38%), Positives = 189/314 (60%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP+ IE   L  E+      + EPL RG+  TLGN LRR+L+S+L G+A++ V+ +G
Sbjct: 3   EFEKPS-IEIKALS-EDGKYGCFVIEPLERGYGMTLGNGLRRILLSTLPGSAVSNVKFEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE S+I GV ED+ +IILN+KG+ ++   +    K   I   G GVVTA DI+    +
Sbjct: 61  VLHEFSTIPGVKEDVLEIILNLKGLCIRDSSATQEPKIAYIEVTGEGVVTAEDIKCPLGV 120

Query: 126 EVLNPDHVICNLD--VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           E+LNP+  I  LD   +  +  ELT++ G GY      +     IG+I +DA Y+P+++V
Sbjct: 121 EILNPEMYIATLDGDKNTKLYAELTITNGRGYEGISKLKKSELLIGVIPVDASYTPVERV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           ++ VE  R GQ  D+D+L++ + T G+I  +++++LA+++L + L +FI+  E  K  + 
Sbjct: 181 NFKVEDTRVGQQTDFDRLTLEVFTKGTIRPDEAISLAAKVLSEHLSIFIDLSEHAKRAEI 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            I  +       L   +EEL+LSVRS NCL+   I  + DL  +TE +M+++ N GRKSL
Sbjct: 241 MITKEDDTKEKTLEMTIEELDLSVRSFNCLKRAGINNVQDLTNKTEEEMMKVRNLGRKSL 300

Query: 304 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 301 EEVFKKLEDLGLSL 314


>gi|161511875|emb|CAP16948.1| DNA-directed RNA polymerase subunit alpha [Pediococcus siamensis]
          Length = 275

 Score =  313 bits (803), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 119/266 (44%), Positives = 175/266 (65%), Gaps = 2/266 (0%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E EN    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED
Sbjct: 7   DENENYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVED 66

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILNIK ++LK+  D  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +    
Sbjct: 67  VTQIILNIKKVSLKIESDDEKSLEINVKGPATVTAGDIQGDSDVEILNPDQYICTVADGV 126

Query: 142 VVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
                LT   G GYV A  ++   ++ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYD
Sbjct: 127 TFHAVLTADTGRGYVSADENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRNDYD 186

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL++ + TDGSI+  ++ +L+++IL + L +F+N  +  +E +  +  +       L   
Sbjct: 187 KLTLDVWTDGSISPSEATSLSAKILTEHLALFVNLTDEAQEAEIMVEKEETHKEKMLEMS 246

Query: 260 VEELELSVRSTNCLRGENIVYMGDLI 285
           +EEL+LSVRS NCL+   I  + +L 
Sbjct: 247 IEELDLSVRSYNCLKRAGINTVQELT 272


>gi|328814021|gb|AEB52126.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 262

 Score =  313 bits (803), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 117/262 (44%), Positives = 173/262 (66%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+I GV ED+T II
Sbjct: 1   YGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIPGVREDVTQII 60

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LNIKG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D VIC++   A     
Sbjct: 61  LNIKGLALKLYAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLVICSVAEGATFHAR 120

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I 
Sbjct: 121 LTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIW 180

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           TDGSI  +++++LA++I+ + L +F+N  +  K  +  +  +       L   +EEL+LS
Sbjct: 181 TDGSIIPQEALSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEELDLS 240

Query: 267 VRSTNCLRGENIVYMGDLIQRT 288
           VRS NCL+   I  + +L  ++
Sbjct: 241 VRSYNCLKRAGINTVQELTNKS 262


>gi|179184592|gb|ACB78153.1| RNA polymerase alpha subunit [Vibrio breoganii]
          Length = 314

 Score =  313 bits (803), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 139/320 (43%), Positives = 207/320 (64%), Gaps = 11/320 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V
Sbjct: 1   GSVTEFLKPRLVD---IEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEV 57

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTV 122
           +I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI   
Sbjct: 58  EIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHD 117

Query: 123 NDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
            D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YS
Sbjct: 118 GDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +
Sbjct: 178 PVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVR 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                    +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 VPE---KEEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLG 318
           G+KSL EIK VL + GL LG
Sbjct: 295 GKKSLTEIKDVLASRGLSLG 314


>gi|251772518|gb|EES53084.1| DNA-directed RNA polymerase, alpha subunit [Leptospirillum
           ferrodiazotrophum]
          Length = 322

 Score =  313 bits (803), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 131/307 (42%), Positives = 190/307 (61%), Gaps = 2/307 (0%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +       + ++ EP  RGF  T+GNALRRVL+SS+ G AITA++   V HE S+I GV 
Sbjct: 15  VSHSSARSSRVVVEPFERGFGITVGNALRRVLLSSIPGVAITAIRAKNVFHEFSNIPGVV 74

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+TDIILN+K + +K        + +  +GP +V A DI TV  +E+++PDHVI  LD 
Sbjct: 75  EDVTDIILNLKSLRMKPLLQGEHWLHLKVKGPRIVKASDIDTVGAVEMMDPDHVIATLDE 134

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              + M+L    G GYVPA H R+    +G+I IDA+++PI KV+Y VES R G++ DYD
Sbjct: 135 GGHLDMDLKTEFGRGYVPADHSRSTETEVGIIPIDAIFTPINKVNYFVESTRVGRITDYD 194

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFI--NFEEPKKEVKEDINVKSLPFNPALL 257
           +L   I+TDGSIT  ++++ A++IL+  L +F+  +           +   S      + 
Sbjct: 195 RLIFEIETDGSITPGEALSEAAKILRTHLDLFVSSDLHLANDSSPLSLESNSSKEETIMD 254

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           K V ELELSVR+ NCL+  +I  +G+L+ RTE ++L+  NFG+KSL EIK  L  +GL L
Sbjct: 255 KSVNELELSVRAANCLKSSDIKKIGELVIRTEDELLQTKNFGKKSLDEIKEALENIGLSL 314

Query: 318 GMNLPDW 324
           GM+L   
Sbjct: 315 GMDLSKK 321


>gi|90194018|gb|ABD92570.1| RpoA [Actinobacillus ureae ATCC 25976]
          Length = 302

 Score =  313 bits (803), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 137/304 (45%), Positives = 206/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVKIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           + ED+ +++LN+KG+ +K+S      +T+ K G G VTA DI    D+E++NPDHVIC+L
Sbjct: 62  IQEDILEVLLNLKGLAVKVSNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPDHVICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D +A + M + V +G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  
Sbjct: 122 TDKNASINMCIRVQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|90194052|gb|ABD92587.1| RpoA [Mannheimia glucosida]
          Length = 304

 Score =  313 bits (803), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 135/304 (44%), Positives = 205/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VNIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+       +T+ K G G VTA DI    D+E++NPDHVIC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVQNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPDHVICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D +A + M + V +G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR  
Sbjct: 122 TDKNASINMRIRVQRGRGYVPASARLHTQNDDRPIGRLLVDARFSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|197288305|gb|ACH57435.1| RpoA [Aliivibrio finisterrensis]
          Length = 313

 Score =  313 bits (803), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 141/319 (44%), Positives = 206/319 (64%), Gaps = 10/319 (3%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E +K   ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I
Sbjct: 1   VTEFLKLRLVD---IEQVSMTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEI 57

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           +GVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+
Sbjct: 58  EGVLHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVIITLNKSGAGPVVAGDITHDGDV 117

Query: 126 EVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIK 181
           E+ NP+HVIC+L  D A + M + V +G GYVP+    H   +  PIG + IDA YSP+ 
Sbjct: 118 EIANPEHVICHLTDDNAEISMRIRVERGRGYVPSTARIHTEEDERPIGRLLIDATYSPVD 177

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           K+SY+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   
Sbjct: 178 KISYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE 237

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
                 +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+K
Sbjct: 238 ---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKK 294

Query: 302 SLVEIKGVLGTMGLFLGMN 320
           SL EIK VL + GL LGM 
Sbjct: 295 SLTEIKDVLASRGLSLGMR 313


>gi|114567812|ref|YP_754966.1| DNA-directed RNA polymerase [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|119366746|sp|Q0AUK9|RPOA_SYNWW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|114338747|gb|ABI69595.1| DNA-directed RNA polymerase [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
          Length = 316

 Score =  313 bits (803), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 128/311 (41%), Positives = 200/311 (64%), Gaps = 3/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP      V      N    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EMEKPRI--DCVEKNSSSNYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED T+IILNIK + L  +G   K + + ++GP  V A DI    ++E+
Sbjct: 61  VLHEFSTIPGVLEDTTEIILNIKKLVLSYTGSERKIIRLEQQGPKEVKASDITPDAEVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH-HRTENDPIGLITIDALYSPIKKVSYT 186
           LNPD  + +LD D  V +E+TV +G GYV +    +  +D +GLI ID++++P+ +V+YT
Sbjct: 121 LNPDLHLASLDEDGKVEIEMTVERGRGYVSSDQQPQKNDDIVGLIPIDSIFTPVSRVNYT 180

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+AR G+  DYD+L++ + T+GSI+ E++++L+++IL + L +F   ++   EV+  + 
Sbjct: 181 VENARVGKRTDYDRLNLEVWTNGSISPEEAISLSAQILIEYLKLFTEIDDTYAEVEILVE 240

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +    +  L   +EELELSVR++N L+  +I  +GDLI +   +M ++ N G+KSL EI
Sbjct: 241 KEEEKKDKILEMSIEELELSVRASNGLKRASINTVGDLIAKNREEMSKIRNLGQKSLEEI 300

Query: 307 KGVLGTMGLFL 317
           +  L  + L  
Sbjct: 301 ERKLKELNLSF 311


>gi|270157886|ref|ZP_06186543.1| DNA-directed RNA polymerase alpha subunit [Legionella longbeachae
           D-4968]
 gi|289163855|ref|YP_003453993.1| DNA-directed RNA polymerase alpha chain [Legionella longbeachae
           NSW150]
 gi|269989911|gb|EEZ96165.1| DNA-directed RNA polymerase alpha subunit [Legionella longbeachae
           D-4968]
 gi|288857028|emb|CBJ10842.1| DNA-directed RNA polymerase alpha chain [Legionella longbeachae
           NSW150]
          Length = 330

 Score =  313 bits (802), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 140/336 (41%), Positives = 212/336 (63%), Gaps = 12/336 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +     E++ PN ++      E   +  ++ EPL RGF HTLGNALRR+L+SS+ G+ IT
Sbjct: 1   MYTEINEMLTPNVLKVQA---ESPFKAKIVLEPLERGFGHTLGNALRRILLSSMPGSVIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
              I+GVLHE S+I+GV ED+ DI+LN+K + +KM+      +T+ K+GP  VTAGDIQ 
Sbjct: 58  EASIEGVLHEYSTIEGVQEDVVDILLNLKLVAIKMTVGEEALITLNKQGPCQVTAGDIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH------RTENDPIGLITIDA 175
            + +EV+NPD VI NL+    + M + V +G G+              E   +G + ID 
Sbjct: 118 SHGLEVVNPDLVIANLNEKGKLNMTMKVERGIGFHSTDSFIGHFDDEVERKSVGKLKIDN 177

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
            +SP++KV+Y V+SAR     D DKL++ ++T+G+I  E+++ +++ ILQ QL  F++  
Sbjct: 178 SFSPVRKVAYYVDSARVENRTDLDKLTIELETNGTIDSEEAIRISASILQRQLHAFVDMR 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
             +    +    +   F+P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+ 
Sbjct: 238 FEESRSDQ---KERNDFDPILLRSVDDLELTVRSANCLKAENIHYIGDLVQRTENELLKT 294

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL +  L LGM L +WPP ++ E
Sbjct: 295 PNLGKKSLTEIKDVLASRSLSLGMKLENWPPANLGE 330


>gi|323342814|ref|ZP_08083046.1| DNA-directed RNA polymerase subunit alpha [Erysipelothrix
           rhusiopathiae ATCC 19414]
 gi|322463926|gb|EFY09120.1| DNA-directed RNA polymerase subunit alpha [Erysipelothrix
           rhusiopathiae ATCC 19414]
          Length = 319

 Score =  313 bits (802), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 122/302 (40%), Positives = 183/302 (60%), Gaps = 5/302 (1%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E  +    + EPL RGF +T+GNALRRVL+SSL GAA+ +++I+GV HE +SI GV ED
Sbjct: 15  DETAHYGKFVIEPLERGFGNTIGNALRRVLLSSLPGAAVYSIKIEGVYHEFTSIAGVGED 74

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T I+LN+K + L +  +    + I ++GP VVTA DI+   ++E+LN DH+I  L   A
Sbjct: 75  VTGIVLNVKDLVLNVQDEEVYTLRISQKGPKVVTAADIECPANVEILNKDHIIATLAEGA 134

Query: 142 VVRMELTVSKGHGYVPAKHHR----TENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           V+ MEL    G GYV +  ++      +  IG I  D++Y+PI++V Y +E  R GQ   
Sbjct: 135 VLEMELKARNGRGYVSSDENKLIYQNASQGIGTIFTDSIYTPIERVKYHIEPTRVGQDSK 194

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK-SLPFNPAL 256
           YD+L M + T+GSI  + +++L S+IL D L   +  ++   E +  I    S   NP  
Sbjct: 195 YDRLIMEVWTNGSIQPQVALSLGSKILMDHLEQIVAIKDSVYETESVIKPDVSGVENPMA 254

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +E+L+LSVRS NCL+   I  + +L  +TE +M+R+ N G+KSL E+K  L  +GL 
Sbjct: 255 TMMIEDLDLSVRSYNCLKRAGIQTVEELTLKTEDEMMRIRNLGKKSLKEVKDKLHDLGLG 314

Query: 317 LG 318
             
Sbjct: 315 FK 316


>gi|223983946|ref|ZP_03634106.1| hypothetical protein HOLDEFILI_01387 [Holdemania filiformis DSM
           12042]
 gi|223964138|gb|EEF68490.1| hypothetical protein HOLDEFILI_01387 [Holdemania filiformis DSM
           12042]
          Length = 321

 Score =  313 bits (802), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 123/301 (40%), Positives = 180/301 (59%), Gaps = 5/301 (1%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E ++    + EPL RGF  TLGNALRRVL+SSL GAA+ +++++GV HE +SI GV ED+
Sbjct: 18  ESDHYGKFVVEPLERGFGTTLGNALRRVLLSSLPGAAVYSIKVEGVYHEFTSIPGVEEDV 77

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T +ILNIK + +K+  D    + I  +GP  VTAGDI     +EVLN D  I +L+  A 
Sbjct: 78  TMMILNIKNLIMKIDDDESYTLRIAAKGPMTVTAGDIICPTGVEVLNKDLEIAHLEEGAT 137

Query: 143 VRMELTVSKGHGYVPAKHHRT----ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
           + MEL    G GY+ A  ++      +  IG +  D++Y+PI ++SY VE  R GQ   Y
Sbjct: 138 LEMELKARNGRGYISADGNKALYQGSSQGIGTVYTDSIYTPIDRISYNVEPTRVGQDAKY 197

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK-EDINVKSLPFNPALL 257
           D+L   I T+GSIT + S+AL S+IL D L +  +  E   +++    +V          
Sbjct: 198 DRLIFEIWTNGSITPQMSLALGSKILIDHLDLLTHVNESVADMESVMKDVNGESPKNMQS 257

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +E+L+LSVRS NCL+   I  + +L QR+E +M+R+ N G+KSL E+K  +  +GL  
Sbjct: 258 MAIEDLDLSVRSYNCLKRAGIQTVEELTQRSEEEMMRVRNLGKKSLKEVKDKIYELGLSF 317

Query: 318 G 318
            
Sbjct: 318 K 318


>gi|58415916|emb|CAH57372.1| RNA polymerase alpha-subunit [Aliivibrio logei]
 gi|148536420|gb|ABQ85762.1| RNA polymerase alpha-subunit [Aliivibrio salmonicida]
 gi|164608404|gb|ABY62505.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio logei]
 gi|164608406|gb|ABY62506.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio logei]
 gi|164608408|gb|ABY62507.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio logei]
 gi|164608410|gb|ABY62508.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio salmonicida]
 gi|164608412|gb|ABY62509.1| DNA-directed RNA polymerase alpha subunit [Aliivibrio salmonicida]
          Length = 308

 Score =  313 bits (802), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 139/314 (44%), Positives = 204/314 (64%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQVSLTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ 
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIA 117

Query: 129 NPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
           NP+HVIC+L  D A + M + V +G GYVP+    H   +  PIG + +DA YSP+ K+S
Sbjct: 118 NPEHVICHLTDDNAEISMRIKVERGRGYVPSTARIHTEEDERPIGRLLVDATYSPVDKIS 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +      
Sbjct: 178 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE--- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|179184612|gb|ACB78154.1| RNA polymerase alpha subunit [Vibrio breoganii]
          Length = 314

 Score =  313 bits (802), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 139/320 (43%), Positives = 207/320 (64%), Gaps = 11/320 (3%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T 
Sbjct: 1   QGSVTEFLKPRLVD---IEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTE 57

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQT 121
           V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI  
Sbjct: 58  VEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPE---KEEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFL 317
            G+KSL EIK VL + GL L
Sbjct: 295 LGKKSLTEIKDVLASRGLSL 314


>gi|190341461|gb|ACE74807.1| RpoA [Cronobacter sakazakii]
          Length = 301

 Score =  313 bits (802), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 136/303 (44%), Positives = 203/303 (66%), Gaps = 7/303 (2%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV 
Sbjct: 2   IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQ 61

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-D 138
           ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI    D+E++ P HVIC+L D
Sbjct: 62  EDILEILLNLKGLAVRVQGKDEVVLTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTD 121

Query: 139 VDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
            +A + M + V +G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q 
Sbjct: 122 ENASISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQR 181

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+P 
Sbjct: 182 TDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP---EVKEEKPEFDPI 238

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL
Sbjct: 239 LLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGL 298

Query: 316 FLG 318
            LG
Sbjct: 299 SLG 301


>gi|256826600|ref|YP_003150559.1| DNA-directed RNA polymerase subunit alpha [Cryptobacterium curtum
           DSM 15641]
 gi|256582743|gb|ACU93877.1| DNA-directed RNA polymerase subunit alpha [Cryptobacterium curtum
           DSM 15641]
          Length = 316

 Score =  313 bits (802), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 119/320 (37%), Positives = 191/320 (59%), Gaps = 10/320 (3%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E ++P     I   +  +     + +PL RG+ +TLGN +RRVL++SL GAA TA+QI
Sbjct: 1   MTEFMRPT----ITTEEVSDTVARFVVDPLERGYGYTLGNTMRRVLLNSLDGAAATAIQI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQTVN 123
           DGV HE ++ +GV ED+TDI+LN+KG+   +  +        +   GP  VT  D+Q   
Sbjct: 57  DGVQHEFATAEGVIEDITDIVLNVKGLVFSVFAEDAIEATAHVSAEGPCTVTGADLQVPT 116

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           +  ++NPDHVI  +     + M + +  G GYV A+ ++   DPIG+I +D+L+SP+++ 
Sbjct: 117 EFTLVNPDHVIATVADGGQLDMTIRIGVGRGYVVAERNKRNEDPIGIIHVDSLFSPVRRC 176

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           + +V   R GQ  DYDKL + ++TDGS+T  D+V  A+ I+   +G F++  E ++E + 
Sbjct: 177 ALSVTDTRVGQSTDYDKLILEVETDGSLTPTDAVCQAANIVTQYMGAFLSLNESEEEEEG 236

Query: 244 DIN----VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           ++      +    N  L K++E+L+LSVRS NCL+   I  +  L++ +E D+L + NFG
Sbjct: 237 EVPSIFAPEGEETNAELDKQIEDLDLSVRSYNCLKRAGIHSVRQLVEYSENDLLNIRNFG 296

Query: 300 RKSLVEIKGVLGTMGLFLGM 319
            KS+ E+K  L +MGL L  
Sbjct: 297 AKSIEEVKDKLISMGLNLKQ 316


>gi|304438880|ref|ZP_07398803.1| DNA-directed RNA polymerase subunit alpha [Peptoniphilus duerdenii
           ATCC BAA-1640]
 gi|304372546|gb|EFM26129.1| DNA-directed RNA polymerase subunit alpha [Peptoniphilus duerdenii
           ATCC BAA-1640]
          Length = 315

 Score =  313 bits (802), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 124/313 (39%), Positives = 198/313 (63%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP+ IE   L  E+  + + + EPL  G+  T+GN+LRRVL+SSL GA+++ V I G
Sbjct: 3   EIEKPS-IEIQELS-EDGKKGIFVVEPLESGYGITIGNSLRRVLLSSLPGASVSFVNIRG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
             HE ++I GV ED+ +IILNIK + ++M+      VTI K+GPG +TA DI     + +
Sbjct: 61  AEHEFATIPGVLEDVPEIILNIKSVVIQMTEIDEALVTIEKKGPGEITAEDINCPLGVTI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NP+  I  L+ DA V +E+ + +G GYVP++  + E   IG+I ID+ ++P++ V++ V
Sbjct: 121 VNPEEHIATLNEDADVYIEMKIERGRGYVPSELKKDEVSTIGVIPIDSNFTPVRHVNWKV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  DYD+L + + TDGS+  +++ +LA++IL + L +FI   E   +V   +  
Sbjct: 181 ENTRVGQRTDYDRLVLDVTTDGSMKADEATSLAAKILTEHLKLFIGLTEHVSDVNIMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   VEEL+LSVRS NCL+  NI  + +L+ ++EA+M+++ N G+KSL E++
Sbjct: 241 EEDRKEKVLEMTVEELDLSVRSFNCLKRANINTVEELVDKSEAEMMKVRNLGKKSLEEVQ 300

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L   
Sbjct: 301 NKLAELGLGLKQE 313


>gi|179184539|gb|ACB78151.1| RNA polymerase alpha subunit [Vibrio gigantis]
          Length = 314

 Score =  313 bits (802), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 139/320 (43%), Positives = 206/320 (64%), Gaps = 11/320 (3%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T 
Sbjct: 1   QGSVTEFLKPRLVD---IEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTE 57

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQT 121
           V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI  
Sbjct: 58  VEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITH 117

Query: 122 VNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFL 317
            G+KSL EIK VL + GL L
Sbjct: 295 LGKKSLTEIKDVLASRGLSL 314


>gi|90194008|gb|ABD92565.1| RpoA [Bibersteinia trehalosi]
          Length = 302

 Score =  313 bits (802), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 136/304 (44%), Positives = 205/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VNIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+       +T+ K G G VTA DI    D+E++NPDHVIC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVQNKDDIILTLTKSGIGPVTAADITADADVEIVNPDHVICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D +A + M + V +G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  
Sbjct: 122 TDKNASISMRIRVQRGRGYVPASARVHSQHEDRPIGRLLVDARFSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|320526894|ref|ZP_08028084.1| DNA-directed RNA polymerase, alpha subunit [Solobacterium moorei
           F0204]
 gi|320132862|gb|EFW25402.1| DNA-directed RNA polymerase, alpha subunit [Solobacterium moorei
           F0204]
          Length = 319

 Score =  313 bits (802), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 115/301 (38%), Positives = 179/301 (59%), Gaps = 5/301 (1%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E EN    +  PL RGF  T+GNALRRVL+SSL GAA+ ++++DGV HE +SI GV ED+
Sbjct: 16  ESENYGKFVLSPLERGFGTTIGNALRRVLLSSLPGAAVFSIKVDGVYHEFTSIPGVREDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           + IIL +K + +K+  D    + I  +GP  +TAGDI     +EV+N D  I +L+ D  
Sbjct: 76  SMIILQLKQLVMKIEDDEVYTLQISAKGPCTITAGDIICPAQVEVINKDLEIAHLEKDVT 135

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI----GLITIDALYSPIKKVSYTVESAREGQVLDY 198
           + MEL    G GY+ A  ++  N       G +  D++Y+P++KV+Y VE  R G+ + Y
Sbjct: 136 LEMELKAKNGRGYISADLNKQLNQGSSQGIGTVFTDSIYTPVEKVAYNVEPTRVGEDVKY 195

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED-INVKSLPFNPALL 257
           D +++ + TDGSI  + ++A+A++IL D L +     +   ++ E      +   +    
Sbjct: 196 DAVTLEVWTDGSINPQKAIAMAAKILMDHLDIVAGINDEVLQMDEVLKEGNTEQPSKGQQ 255

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +E+L+LSVRS NCL+   I  + +L Q+TE +M+R+ N G+KSL E+K  L  +GL  
Sbjct: 256 MMIEDLDLSVRSYNCLKRAGIQTVDELTQKTEDEMMRVRNLGKKSLKEVKDKLIELGLGF 315

Query: 318 G 318
            
Sbjct: 316 K 316


>gi|54296390|ref|YP_122759.1| DNA-directed RNA polymerase subunit alpha [Legionella pneumophila
           str. Paris]
 gi|61215818|sp|Q5X834|RPOA_LEGPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|53750175|emb|CAH11567.1| DNA-directed RNA polymerase alpha chain [Legionella pneumophila
           str. Paris]
          Length = 330

 Score =  313 bits (802), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 142/336 (42%), Positives = 214/336 (63%), Gaps = 12/336 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +     E++ P  ++      E   +  ++ EPL RGF HTLGNALRR+L+SS+ G+AIT
Sbjct: 1   MYTEINEMLTPKVLKVQA---ESPYKARIVLEPLERGFGHTLGNALRRILLSSMPGSAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
              IDGVLHE S+I+GV ED+ D++LN+K + +K++  +  +VT+ K GP  VTAGDIQ 
Sbjct: 58  EASIDGVLHEYSTIEGVQEDVVDLLLNLKSVAIKLTVGNEAQVTLNKEGPCQVTAGDIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK------HHRTENDPIGLITIDA 175
            +  E++NP+ VI NL+    + M L V +G G+              E   +G + ID 
Sbjct: 118 THGQEIINPELVIANLNEKGKLNMTLKVERGIGFHNTDAFVRYHDDEIEKKTVGKLKIDN 177

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
            +SP+KKV+Y V+SAR     D DKL++ ++T+G+I  E+++ +++ ILQ QL  F++ +
Sbjct: 178 SFSPVKKVAYFVDSARVENRTDLDKLTIELETNGTIDAEEAIRISASILQRQLHAFVDMK 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
             +       N +   F+P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE+++L+ 
Sbjct: 238 FEESRAD---NKERNDFDPVLLRSVDDLELTVRSANCLKAENIHYIGDLVQRTESELLKT 294

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL +  L LGM L +WPP S+ E
Sbjct: 295 PNLGKKSLTEIKDVLASRSLSLGMKLENWPPASLGE 330


>gi|148361030|ref|YP_001252237.1| DNA-directed RNA polymerase subunit alpha RpoA [Legionella
           pneumophila str. Corby]
 gi|296105902|ref|YP_003617602.1| DNA-directed RNA polymerase subunit alpha [Legionella pneumophila
           2300/99 Alcoy]
 gi|166229273|sp|A5IHP1|RPOA_LEGPC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|148282803|gb|ABQ56891.1| DNA-directed RNA polymerase alpha subunit RpoA [Legionella
           pneumophila str. Corby]
 gi|295647803|gb|ADG23650.1| DNA-directed RNA polymerase subunit alpha [Legionella pneumophila
           2300/99 Alcoy]
          Length = 330

 Score =  313 bits (801), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 142/336 (42%), Positives = 214/336 (63%), Gaps = 12/336 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +     E++ P  ++      E   +  ++ EPL RGF HTLGNALRR+L+SS+ G+AIT
Sbjct: 1   MYTEINEMLTPKVLKVQA---ESPYKARIVLEPLERGFGHTLGNALRRILLSSMPGSAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
              IDGVLHE S+I+GV ED+ D++LN+K + +K++  +  +VT+ K GP  VTAGDIQ 
Sbjct: 58  EASIDGVLHEYSTIEGVQEDVVDLLLNLKSVAIKLTVGNEAQVTLNKEGPCQVTAGDIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK------HHRTENDPIGLITIDA 175
            +  E++NP+ VI NL+    + M L V +G G+              E   +G + ID 
Sbjct: 118 THGQEIINPELVIANLNEKGKLNMTLKVERGIGFHNTDAFVRYHEDEIEKKTVGKLKIDN 177

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
            +SP+KKV+Y V+SAR     D DKL++ ++T+G+I  E+++ +++ ILQ QL  F++ +
Sbjct: 178 SFSPVKKVAYFVDSARVENRTDLDKLTIELETNGTIDAEEAIRISASILQRQLHAFVDMK 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
             +       N +   F+P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE+++L+ 
Sbjct: 238 FEESRAD---NKERNDFDPVLLRSVDDLELTVRSANCLKAENIHYIGDLVQRTESELLKT 294

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL +  L LGM L +WPP S+ E
Sbjct: 295 PNLGKKSLTEIKDVLASRSLSLGMKLENWPPASLGE 330


>gi|90194054|gb|ABD92588.1| RpoA [Mannheimia varigena]
          Length = 302

 Score =  313 bits (801), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 136/304 (44%), Positives = 206/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTDVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+       +T+ K G G VTA DI    D+E++NPDHVICNL
Sbjct: 62  VQEDILEVLLNLKGLAVKVQNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPDHVICNL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D +A + M + V +G GYVPA    H ++++ PIG + +DA +SP+ +++Y VE+AR  
Sbjct: 122 TDKNASINMRIRVQRGRGYVPASARLHTQSDDRPIGRLLVDARFSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|58416068|emb|CAH57448.1| RNA polymerase alpha-subunit [Vibrio sp. R-23695]
          Length = 308

 Score =  313 bits (801), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 140/314 (44%), Positives = 205/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQVSMTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ 
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIA 117

Query: 129 NPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
           NP+HVIC+L  D A + M + V +G GYVP+    H   +  PIG + IDA YSP+ K+S
Sbjct: 118 NPEHVICHLTDDNAEISMRIKVERGRGYVPSTARIHTEEDERPIGRLLIDATYSPVDKIS 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +      
Sbjct: 178 YSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE--- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|90194062|gb|ABD92592.1| RpoA [Pasteurella multocida subsp. septica]
          Length = 304

 Score =  313 bits (801), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 137/305 (44%), Positives = 203/305 (66%), Gaps = 7/305 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 3   VDIEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 62

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+       +T+ K G G V A DI    D+E++NP+HVIC+L
Sbjct: 63  VQEDILEVLLNLKGLAVKVQNKDDVFLTLNKSGIGPVVAADITHDGDVEIVNPEHVICHL 122

Query: 138 -DVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D  A + M + V +G GYVPA      + E  PIG + +DA YSP+ +++Y VE+AR  
Sbjct: 123 TDESASINMRIRVQRGRGYVPASARVHAQDEERPIGRLLVDACYSPVDRIAYNVEAARVE 182

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 183 QRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEFD 239

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 240 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 299

Query: 314 GLFLG 318
           GL LG
Sbjct: 300 GLSLG 304


>gi|90194032|gb|ABD92577.1| RpoA [Actinobacillus lignieresii]
          Length = 302

 Score =  313 bits (801), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 139/304 (45%), Positives = 206/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VNIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+SG     +T+ K G G VTA DI    D+E++NP HVIC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVSGKDDIILTLNKSGIGPVTAADITHDGDVEIVNPHHVICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D DA + M + V +G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  
Sbjct: 122 TDKDASISMRIRVQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|193214826|ref|YP_001996025.1| DNA-directed RNA polymerase subunit alpha [Chloroherpeton
           thalassium ATCC 35110]
 gi|238692721|sp|B3QYF0|RPOA_CHLT3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|193088303|gb|ACF13578.1| DNA-directed RNA polymerase, alpha subunit [Chloroherpeton
           thalassium ATCC 35110]
          Length = 328

 Score =  313 bits (801), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 131/323 (40%), Positives = 204/323 (63%), Gaps = 6/323 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           Q++  P  +E              IA+PL RG+  T+GNA+RRVL+SSL G AIT ++I+
Sbjct: 3   QQMQMPEKLEVDEAS-YSNYYGKFIAQPLERGYGVTIGNAIRRVLLSSLPGTAITGIKIE 61

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV-NDI 125
           GVLHE S+I GV ED+ DI+LN+K I  +     +  VT+  RGP    AGDI +   D 
Sbjct: 62  GVLHEFSTIDGVKEDVPDIVLNLKQIRFRSISKRNAVVTLVLRGPKDFVAGDIVSPEGDF 121

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+H I  L+ DA ++++++V +G GY+PA+ ++ E  PIG I++D++++PI+ V Y
Sbjct: 122 EVLNPEHHIATLNEDATLKIDVSVGRGRGYMPAEDNKPETMPIGYISVDSIFTPIRNVKY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKKEV 241
           +VE+ R GQ  DY+KLS+ ++TDGSI  +++V++A +I+ D + +F  F     E  +E 
Sbjct: 182 SVENTRVGQRTDYEKLSLEVETDGSIAPDEAVSMAGKIINDHVRLFSLFSPTQEEEVEEE 241

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            +  + +       L+ ++E+LELSVRS NCLR   I  +G L+ + E ++L   NFG+K
Sbjct: 242 VQQEDEEFENMRKLLMTRIEDLELSVRSHNCLRSAEIDTLGQLVSKREDELLGYKNFGKK 301

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+K +L +  L  GM +  +
Sbjct: 302 SLAELKELLESKNLSFGMEVTKY 324


>gi|90194006|gb|ABD92564.1| RpoA [Mannheimia haemolytica]
          Length = 302

 Score =  313 bits (801), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 135/304 (44%), Positives = 205/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VNIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+       +T+ K G G VTA DI    D+E++NPDHVIC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVQNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPDHVICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D +A + M + V +G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR  
Sbjct: 122 TDKNASINMRIRVQRGRGYVPASARLHTQNDDRPIGRLLVDARFSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|90194056|gb|ABD92589.1| RpoA [Mannheimia ruminalis]
          Length = 302

 Score =  313 bits (801), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 136/304 (44%), Positives = 206/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VNIEQVSSTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+       +T+ K G G VTA DI    D+E++NPDH+IC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVQNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPDHIICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D +A + M + V +G GYVPA    H + ++ PIG + +DA YSP+ +++Y VE+AR  
Sbjct: 122 TDKNASISMRIRVQRGRGYVPASARLHTQNDDRPIGRLLVDARYSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|52840599|ref|YP_094398.1| DNA-directed RNA polymerase subunit alpha [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
 gi|54293346|ref|YP_125761.1| DNA-directed RNA polymerase subunit alpha [Legionella pneumophila
           str. Lens]
 gi|61215814|sp|Q5WZI7|RPOA_LEGPL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61215830|sp|Q5ZYL8|RPOA_LEGPH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|52627710|gb|AAU26451.1| DNA-directed RNA polymerase alpha subunit RpoA [Legionella
           pneumophila subsp. pneumophila str. Philadelphia 1]
 gi|53753178|emb|CAH14625.1| DNA-directed RNA polymerase alpha chain [Legionella pneumophila
           str. Lens]
 gi|307609162|emb|CBW98618.1| DNA-directed RNA polymerase alpha chain [Legionella pneumophila
           130b]
          Length = 330

 Score =  312 bits (800), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 141/336 (41%), Positives = 214/336 (63%), Gaps = 12/336 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +     E++ P  ++      E   +  ++ EPL RGF HTLGNALRR+L+SS+ G+AIT
Sbjct: 1   MYTEINEMLTPKVLKVQA---ESPYKARIVLEPLERGFGHTLGNALRRILLSSMPGSAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
              IDGVLHE S+I+GV ED+ D++LN+K + +K++  +  ++T+ K GP  VTAGDIQ 
Sbjct: 58  EASIDGVLHEYSTIEGVQEDVVDLLLNLKSVAIKLTVGNEAQITLNKEGPCQVTAGDIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK------HHRTENDPIGLITIDA 175
            +  E++NP+ VI NL+    + M L V +G G+              E   +G + ID 
Sbjct: 118 THGQEIINPELVIANLNEKGKLNMTLKVERGIGFHNTDAFVRYHDDEIEKKTVGKLKIDN 177

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
            +SP+KKV+Y V+SAR     D DKL++ ++T+G+I  E+++ +++ ILQ QL  F++ +
Sbjct: 178 SFSPVKKVAYFVDSARVENRTDLDKLTIELETNGTIDAEEAIRISASILQRQLHAFVDMK 237

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
             +       N +   F+P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE+++L+ 
Sbjct: 238 FEESRAD---NKERNDFDPVLLRSVDDLELTVRSANCLKAENIHYIGDLVQRTESELLKT 294

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL +  L LGM L +WPP S+ E
Sbjct: 295 PNLGKKSLTEIKDVLASRSLSLGMKLENWPPASLGE 330


>gi|328814009|gb|AEB52120.1| DNA-directed RNA polymerase alpha chain [Lactobacillus rhamnosus]
          Length = 257

 Score =  312 bits (800), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 113/257 (43%), Positives = 171/257 (66%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED+T IILNIK
Sbjct: 1   VVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLEDVTQIILNIK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV 
Sbjct: 61  KLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVK 120

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GS
Sbjct: 121 KGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGS 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I+  ++++LA++IL + L +F+N  +  K  +  +  +       L   +EEL+LSVRS 
Sbjct: 181 ISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSVRSY 240

Query: 271 NCLRGENIVYMGDLIQR 287
           NCL+   I  + +L  +
Sbjct: 241 NCLKRAGINTVQELTNK 257


>gi|254412021|ref|ZP_05025796.1| DNA-directed RNA polymerase, alpha subunit [Microcoleus
           chthonoplastes PCC 7420]
 gi|196180987|gb|EDX75976.1| DNA-directed RNA polymerase, alpha subunit [Microcoleus
           chthonoplastes PCC 7420]
          Length = 315

 Score =  312 bits (800), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 103/310 (33%), Positives = 168/310 (54%), Gaps = 9/310 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             +E   L  + +  +  + EPL RG   T+GNALRRVL+S+L G AITAV+I GV HE 
Sbjct: 7   ECVESKTLKNQSQ-YSKFVLEPLDRGQGTTVGNALRRVLLSNLEGTAITAVRIAGVNHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I G+ ED+ +I+LN+K + LK          +   GP  V +      +D+E ++P  
Sbjct: 66  ATIAGIREDVLEILLNMKEVVLKSYTPGPHIGRVMITGPSTVRSAQFDLPSDVEFVDPGQ 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L   A + ME  + +G GY   +  R E   +  + +DA++ P+ KV+Y+VE  R 
Sbjct: 126 YIATLADGAKLEMEFRIERGKGYRSVERGRDETSSVDFLQLDAVFMPVTKVNYSVEDTRV 185

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
              L+ D+L + + T+GS++ +++++ A+ IL D      + E   + V    +      
Sbjct: 186 DGSLEKDRLILDVWTNGSVSPQEALSQAANILVDLFNPLKDIELKPEPVGRPEDE----- 240

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P     +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L  
Sbjct: 241 DPTSQIPIEELQLSVRAYNCLKRAQINSVADLLDYSQEDLLEIKNFGQKSAEEVIDAL-- 298

Query: 313 MGLFLGMNLP 322
               LG+ LP
Sbjct: 299 -QKRLGITLP 307


>gi|91200694|emb|CAJ73745.1| strongly similar to DNA-directed RNA polymerase, alpha chain
           [Candidatus Kuenenia stuttgartiensis]
          Length = 338

 Score =  312 bits (800), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 126/330 (38%), Positives = 195/330 (59%), Gaps = 10/330 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++  W+ L  P  ++        +     IA P  RGF HT+GN+LRR+L+SSL G+A+ 
Sbjct: 1   MRIRWRGLELPVRVDVEN-ETLTDRYGKFIAAPFERGFGHTIGNSLRRILLSSLEGSAVV 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+I+GV HE +++ GV ED+ DIILNIK + +KM  D  K + I     G VT  DI T
Sbjct: 60  SVKIEGVAHEFTNVPGVIEDVADIILNIKNLIVKMHSDQPKIIKIEANKKGKVTGKDIIT 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
             ++EV+N D  I  L  D    +E+ V KG GYV A  +  E+  IGLI++D+ +SP++
Sbjct: 120 DENVEVVNDDLHIATLSEDMAFNVEMEVRKGRGYVTADENEAEDQEIGLISVDSFFSPVR 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
            V Y  E  R G+  +YD+L + I T+G++T E ++  A+ I +  L  FI + E  +E+
Sbjct: 180 NVRYVTEETRVGRRTNYDRLILEIWTNGTVTPEMALVEAAMITRKHLNPFIQYFEIGREL 239

Query: 242 KEDI---------NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           ++           ++ S  FN  L   + EL+LSVR++NCL   NIV +GDL+ +TE D+
Sbjct: 240 QQIEKNMSAECISDMSSEEFNRTLSMPIAELDLSVRASNCLETVNIVTVGDLVVKTEDDL 299

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           L++ NFG+ ++ E+K  L  + L +GM L 
Sbjct: 300 LQIKNFGKTTMKELKKKLSQLNLAIGMPLE 329


>gi|90194004|gb|ABD92563.1| RpoA [Lonepinella koalarum]
          Length = 302

 Score =  312 bits (800), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 138/304 (45%), Positives = 204/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE SS +G
Sbjct: 2   VDIEQISPTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+       +T+ K G G V A DI    D+E++NPDHVIC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVQNKDDVFLTLNKSGIGPVVAADITHDGDVEIVNPDHVICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D +A V M + V +G GYVPA    H + E  PIG + +DA YSP+ +++Y VE+AR  
Sbjct: 122 TDENASVNMRIRVQRGRGYVPASARVHTQDEERPIGRLLVDACYSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|90194046|gb|ABD92584.1| RpoA [Actinobacillus indolicus]
          Length = 303

 Score =  312 bits (800), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 136/304 (44%), Positives = 205/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+       +T+ K G G VTA DI    D+E++NPDHVICNL
Sbjct: 62  VQEDILEVLLNLKGLAVKVQNKDDIILTLTKSGIGPVTAADITHDGDVEIVNPDHVICNL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D +A + M + V +G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR  
Sbjct: 122 TDKNASINMRIRVQRGRGYVPASARVHTQDDDRPIGRLLVDARFSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|302390985|ref|YP_003826805.1| DNA-directed RNA polymerase subunit alpha [Acetohalobium arabaticum
           DSM 5501]
 gi|302203062|gb|ADL11740.1| DNA-directed RNA polymerase subunit alpha [Acetohalobium arabaticum
           DSM 5501]
          Length = 314

 Score =  312 bits (799), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 125/312 (40%), Positives = 192/312 (61%), Gaps = 5/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP  IE I   +  +        PL RG+  TLGN+LRR+++SSL G A T+V+I+G
Sbjct: 3   EFEKP-AIERI---ESTDTYGKFAITPLERGYGITLGNSLRRIMLSSLPGTAPTSVKIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE S+I GV ED+TDI+LN+K + L+M  +  + + +   G G VTA +     +IE+
Sbjct: 59  VEHEFSTISGVVEDVTDIVLNLKELVLRMESEEPEILRLNASGEGEVTADEFTVSGNIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP-IGLITIDALYSPIKKVSYT 186
           LNPD  I  L  D  + ME+TV  G GYV A+ ++ + +  IG+I +D+ +SPIK+V++ 
Sbjct: 119 LNPDQHIATLSDDGQLDMEVTVENGRGYVSAEENKDDEEHVIGVIPMDSSFSPIKRVNFD 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE    G   D DKL + I+TDGS+T E++++LA+++L + L + IN  E   +V   + 
Sbjct: 179 VEDVWVGNRTDLDKLVLEINTDGSLTPEEAISLAAKVLDEHLDLLINLNEEITDVDLMVE 238

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +    +  L   +EEL+LSVRS+NCL+   I  + +L ++TE D++++ N G+KSL EI
Sbjct: 239 KEEEEKDKVLETTIEELDLSVRSSNCLKRAGIDNVEELTEQTEDDLMKVRNLGKKSLQEI 298

Query: 307 KGVLGTMGLFLG 318
           K  L  + L L 
Sbjct: 299 KDKLDELDLSLK 310


>gi|90194024|gb|ABD92573.1| RpoA [Actinobacillus genomosp. 1]
          Length = 303

 Score =  312 bits (799), Expect = 6e-83,   Method: Composition-based stats.
 Identities = 139/304 (45%), Positives = 206/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+SG     +T+ K G G VTA DI    D+E++NP HVIC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVSGKDDIILTLNKSGIGPVTAADITHDGDVEIVNPHHVICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D DA + M + V +G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  
Sbjct: 122 TDKDAAISMRIRVQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|90193996|gb|ABD92559.1| RpoA [Volucribacter psittacicida]
          Length = 302

 Score =  312 bits (799), Expect = 6e-83,   Method: Composition-based stats.
 Identities = 138/304 (45%), Positives = 205/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VDIEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+       +T+ K G G V AGDI    D+E++NP+HVIC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVQNKDDVLLTLSKSGIGPVVAGDIIHDGDVEIVNPEHVICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D +A ++M + V +G GYVPA      + E  PIG + +DA YSP+ +++Y VE+AR  
Sbjct: 122 TDENASIQMRIRVQRGRGYVPASARVHAQDEERPIGRLLVDACYSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G+I  ED++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLVIELETNGTIDPEDAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|167767776|ref|ZP_02439829.1| hypothetical protein CLOSS21_02311 [Clostridium sp. SS2/1]
 gi|317497067|ref|ZP_07955394.1| DNA-directed RNA polymerase [Lachnospiraceae bacterium 5_1_63FAA]
 gi|167710515|gb|EDS21094.1| hypothetical protein CLOSS21_02311 [Clostridium sp. SS2/1]
 gi|291558883|emb|CBL37683.1| DNA-directed RNA polymerase subunit alpha [butyrate-producing
           bacterium SSC/2]
 gi|316895612|gb|EFV17767.1| DNA-directed RNA polymerase [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 318

 Score =  311 bits (798), Expect = 7e-83,   Method: Composition-based stats.
 Identities = 129/305 (42%), Positives = 194/305 (63%), Gaps = 5/305 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN IE   +  E+      + EPL RG+  TLGN+LRR+++SSL GAA+++V+I G
Sbjct: 3   EFEKPN-IEINEIS-EDNRFGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSSVKIKG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+ +II+NIK + +K +      K+  I   G GVVTAGDI+  +DI
Sbjct: 61  VLHEFSSIPGVKEDVPEIIMNIKSLAIKNNSSSAETKQAYIEFSGKGVVTAGDIKADSDI 120

Query: 126 EVLNPDHVICNLDVDA-VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           E+LNP+ VI  L  D+  + MELT++ G GYV A     E   I  I +DA+Y+P+++V+
Sbjct: 121 EILNPELVIATLSDDSSKLDMELTITNGRGYVGADKADKEGKAIDEIAVDAIYTPVERVN 180

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
             VE+ R GQ+ DYDKL++ + T+G++T ++SV+LA+++L + L +F++  E  K  +  
Sbjct: 181 LKVENTRVGQITDYDKLTLDVFTNGTLTPDESVSLAAKVLCEHLNLFVDLSENAKTAEVM 240

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +  +       L   ++ELELSVRS NCL+   I  + +L  +T  DM+++ N GRKSL 
Sbjct: 241 VEKEDDEKEKVLEMSIDELELSVRSYNCLKRAGINTVEELTNKTSEDMMKVRNLGRKSLE 300

Query: 305 EIKGV 309
           E+   
Sbjct: 301 EVLAK 305


>gi|300775039|ref|ZP_07084902.1| DNA-directed RNA polymerase subunit alpha [Chryseobacterium gleum
           ATCC 35910]
 gi|300506854|gb|EFK37989.1| DNA-directed RNA polymerase subunit alpha [Chryseobacterium gleum
           ATCC 35910]
          Length = 331

 Score =  311 bits (798), Expect = 7e-83,   Method: Composition-based stats.
 Identities = 124/324 (38%), Positives = 206/324 (63%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            IKP+ +   +L   +E +      PL  GF  T+GNALRRVL+SSL G AI++++I+GV
Sbjct: 6   FIKPDKV---ILLNSDEFKGQFEFRPLEPGFGLTIGNALRRVLLSSLEGYAISSIKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE S+I GV ED+T+IILN+K + LK + +   +++V     G  V+TAGD+ +++N  
Sbjct: 63  EHEFSTIPGVIEDVTEIILNLKQVRLKAAAEGQANEQVVAKVSGQTVITAGDLGKSINGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VICNL+ D    +   + KG GYVP++ +++ N P+G I ID++++PIKKV Y
Sbjct: 123 EVLNPDLVICNLNTDVTFEITFNIEKGRGYVPSEQNKSNNAPVGTIAIDSIFTPIKKVQY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL + I+TDGSI+ ++++  AS+IL     +F    I  E    + 
Sbjct: 183 SIENYRVEQKTDYEKLVLDIETDGSISPQNALTEASKILIYHFMLFSDERITLETEAVKA 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
               + ++L     L  K+ +++LSVR+ NCL+   +  +G+L+  +++D+++  NFG+K
Sbjct: 243 SIQYDEETLHTRQLLKSKLADMDLSVRALNCLKAAEVETLGELVSYSKSDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E++ ++ + GL  G ++  + 
Sbjct: 303 SLTELEELVHSKGLNFGFDVAKYK 326


>gi|256371243|ref|YP_003109067.1| DNA-directed RNA polymerase, alpha subunit [Acidimicrobium
           ferrooxidans DSM 10331]
 gi|256007827|gb|ACU53394.1| DNA-directed RNA polymerase, alpha subunit [Acidimicrobium
           ferrooxidans DSM 10331]
          Length = 312

 Score =  311 bits (798), Expect = 7e-83,   Method: Composition-based stats.
 Identities = 119/301 (39%), Positives = 174/301 (57%), Gaps = 1/301 (0%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
              LG E +NR      PL  GF H++GNALRRVL+SS+ GAAIT V+ D  LHE ++I 
Sbjct: 9   VESLGDEVDNRQRFAIGPLEPGFGHSIGNALRRVLISSVPGAAITQVRFDDALHEFTTIP 68

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ DIILN+K I  +   +    V +  RGP  VTAGD    +D+EV+N D  I +
Sbjct: 69  GVKEDVIDIILNLKDIVWRSWSEEPVTVRLDVRGPKEVTAGDFMLPSDVEVINRDLHIAS 128

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +     + ++  V +G GYV A+ ++     IG+I IDA++SP++ V+Y VE  R GQ  
Sbjct: 129 VSEHGRLGLDAVVEQGRGYVSAEGNKR-TTTIGIIAIDAIFSPVRHVNYRVEPVRVGQST 187

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           D+D++ + ++TDGS+T  ++VA A+R L    G+          ++              
Sbjct: 188 DFDQVVLEVETDGSVTPREAVASAARTLTSLFGLVAELATDVNALEVAATADDSVRPAEY 247

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +EELEL+ R  NCL+  +I  +GDL++RT  D+L + NFG+KSL E+   L   GL 
Sbjct: 248 DLPIEELELTERPRNCLKRASINTIGDLVERTPEDLLSITNFGQKSLDEVVERLTQRGLE 307

Query: 317 L 317
           L
Sbjct: 308 L 308


>gi|116515234|ref|YP_802863.1| DNA-directed RNA polymerase subunit alpha [Buchnera aphidicola str.
           Cc (Cinara cedri)]
 gi|122285370|sp|Q057C9|RPOA_BUCCC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116257088|gb|ABJ90770.1| RNA polymerase, a subunit [Buchnera aphidicola str. Cc (Cinara
           cedri)]
          Length = 329

 Score =  311 bits (798), Expect = 7e-83,   Method: Composition-based stats.
 Identities = 142/334 (42%), Positives = 211/334 (63%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q   ++ +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGFVEDFLKPRLVDIQQIS---ATHAKITLEPLERGFGHTLGNALRRILLSSISGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDG+LHE    +GV ED+ DI+LN+KG+++K+ G     + + K G G V A DI  
Sbjct: 58  EVEIDGILHEYMHKEGVKEDILDILLNLKGLSIKLFGKDEVTLYLKKSGIGPVLAKDINH 117

Query: 122 VNDIEVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALY 177
            N  E++N  H+ICNL   DA + + + V++G GY+ AK  +   D     G + +D  Y
Sbjct: 118 DNSTEIINNKHIICNLTCSDASIDIRMKVTRGRGYITAKSRKENYDNEHIIGKLFLDVTY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPI+++ YTVESAR  Q  D DKL + ++T+G+I  ED++  A+ IL  QL  F++    
Sbjct: 178 SPIERIMYTVESARVEQRTDLDKLIIEMETNGTIDPEDAIRKAATILAQQLEAFVDLRGV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++     I  +   F P LL+ V++LEL+VRS NCL+ E+I Y+GDL+Q+TE ++L+  N
Sbjct: 238 REPE---IKEEKPEFEPVLLRPVDDLELTVRSANCLKAESIHYIGDLVQKTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP+S+ E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMKLDNWPPKSLLE 328


>gi|300867111|ref|ZP_07111777.1| DNA-directed RNA polymerase subunit alpha [Oscillatoria sp. PCC
           6506]
 gi|300334866|emb|CBN56943.1| DNA-directed RNA polymerase subunit alpha [Oscillatoria sp. PCC
           6506]
          Length = 320

 Score =  311 bits (798), Expect = 7e-83,   Method: Composition-based stats.
 Identities = 105/317 (33%), Positives = 171/317 (53%), Gaps = 10/317 (3%)

Query: 14  NIEYIVLGQEEEN--RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE I    +++       I EPL RG   T+GNALRRV++S+L G A+T+V+I GV HE
Sbjct: 12  QIECIESNTDKDRSQYGKFILEPLDRGQGTTVGNALRRVMLSNLEGTAVTSVRIAGVNHE 71

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            ++I+GV ED+ +I+LN+K + LK      +   +   GP  VTA      ++++V++  
Sbjct: 72  FATIEGVREDVLEILLNMKEVVLKSHSSQPQIGRLRVEGPATVTADRFDVPSEVDVIDRS 131

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             I  L   + + ME  + +G GY      R +   +  + IDA++ P++KV+Y+VE AR
Sbjct: 132 QYIATLSPGSTLEMEFRIERGVGYRAVDRSRDDGGALDFLAIDAIFMPVRKVNYSVEDAR 191

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            G   + D+L M I T+GS+T +++++ A+ IL D      +            +     
Sbjct: 192 VGGSTEKDRLIMEIWTNGSLTPQEALSQAASILVDLFSPLKDITLESLRSDVGSDA---- 247

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL+LSVR+ NCL+   I  + DL+  T+ D+L + NFG+KS  E+   L 
Sbjct: 248 -DPTSQIPIEELQLSVRAYNCLKRAQINSVADLLDYTQEDLLEIKNFGQKSAEEVIEAL- 305

Query: 312 TMGLFLGMNLPDWPPES 328
                LG+ LP    ++
Sbjct: 306 --QKRLGITLPQEKAKT 320


>gi|209527118|ref|ZP_03275632.1| DNA-directed RNA polymerase, alpha subunit [Arthrospira maxima
           CS-328]
 gi|209492458|gb|EDZ92799.1| DNA-directed RNA polymerase, alpha subunit [Arthrospira maxima
           CS-328]
          Length = 314

 Score =  311 bits (798), Expect = 8e-83,   Method: Composition-based stats.
 Identities = 114/312 (36%), Positives = 175/312 (56%), Gaps = 10/312 (3%)

Query: 14  NIEYIV--LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE I   +  +       +  PL RG   T+GNALRRVL+S+L G AITAV+I GV HE
Sbjct: 5   KIECIESNISTDRSQYGKFVLGPLDRGQGITVGNALRRVLLSNLEGTAITAVRIAGVNHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            ++I+GV ED+ +I+LN+K   LK      +   +  +GP  VT G     +++EV+N +
Sbjct: 65  FATIEGVREDVLEIMLNLKEAVLKSHTYQKQIGRLLVQGPATVTVGHFDLPSEVEVVNKN 124

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             I  L   A + ME  + KG GY     HR ++  +  + IDA++ P++KV+YTVE AR
Sbjct: 125 QYIATLSPGATLEMECQIEKGTGYRAVDRHRDDSAALDFLQIDAIFMPVRKVNYTVEDAR 184

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           +G  L+ D+L++ I T GS+T +++++ A+ IL D  G   +       ++   + +   
Sbjct: 185 DGGSLEKDRLTLEIWTSGSLTPQEAISQAAAILVDLFGALKDI-----NLESITSDQRDD 239

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL+LSVR+ NCL+   I  + DL   TE D+L + NFG+KS  E+   L 
Sbjct: 240 IDPTSQIPIEELQLSVRAYNCLKRAQINSVADLRDYTEEDLLEIKNFGQKSAEEVIEALQ 299

Query: 312 TMGLFLGMNLPD 323
                LG+ LP 
Sbjct: 300 N---RLGITLPK 308


>gi|90194016|gb|ABD92569.1| RpoA [Actinobacillus hominis]
          Length = 302

 Score =  311 bits (798), Expect = 8e-83,   Method: Composition-based stats.
 Identities = 137/304 (45%), Positives = 206/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+S      +T+ K G G VTA DI    D+E++NP+HVIC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVSNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPNHVICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D +A + M + V +G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  
Sbjct: 122 TDKNASINMRIRVQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|90194022|gb|ABD92572.1| RpoA [Actinobacillus suis ATCC 33415]
          Length = 302

 Score =  311 bits (798), Expect = 8e-83,   Method: Composition-based stats.
 Identities = 138/304 (45%), Positives = 206/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + L Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VNLEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+S      +T+ K G G VTA DI    D+E++NP+HVIC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVSNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPNHVICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D +A + M + V +G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  
Sbjct: 122 TDKNASINMRIRVQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|328814013|gb|AEB52122.1| DNA-directed RNA polymerase alpha chain [Lactobacillus rhamnosus]
          Length = 260

 Score =  311 bits (798), Expect = 8e-83,   Method: Composition-based stats.
 Identities = 114/258 (44%), Positives = 169/258 (65%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I    E  N    + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I G
Sbjct: 3   ITKVDESTNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDG 62

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+T IILNIK + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +
Sbjct: 63  VLEDVTQIILNIKKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTV 122

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
                  + +TV KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D
Sbjct: 123 ADGGHFHVRMTVKKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRND 182

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL++ + T+GSI+  ++++LA++IL + L +F+N  +  K  +  +  +       L 
Sbjct: 183 FDKLTLDVWTNGSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLE 242

Query: 258 KKVEELELSVRSTNCLRG 275
             +EEL+LSVRS NCL+ 
Sbjct: 243 MTIEELDLSVRSYNCLKR 260


>gi|110598114|ref|ZP_01386392.1| DNA-directed RNA polymerase, alpha subunit [Chlorobium ferrooxidans
           DSM 13031]
 gi|110340246|gb|EAT58743.1| DNA-directed RNA polymerase, alpha subunit [Chlorobium ferrooxidans
           DSM 13031]
          Length = 327

 Score =  311 bits (798), Expect = 8e-83,   Method: Composition-based stats.
 Identities = 131/321 (40%), Positives = 196/321 (61%), Gaps = 6/321 (1%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  IE        ++    IA+PL RG+  TLGN +RRVL++SL G AIT ++IDGV HE
Sbjct: 8   PAKIEVDE-ANHTDSFGRFIAQPLERGYGVTLGNVMRRVLLASLPGTAITGLKIDGVFHE 66

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNP 130
            +++ GV ED+ +I+LN+K +  K +   + + T+   GP   TAGDI     + EVLN 
Sbjct: 67  FAAVDGVREDVPEIVLNLKRVRFKSTCKRNCKTTLAIVGPKEFTAGDIIAQEGEFEVLNK 126

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  ++  A ++++L V +G GYVPA+ +R E  PIG I IDA+Y+PI+ V +TVE+ 
Sbjct: 127 DMHIATVNAGATLKIDLYVGRGRGYVPAEENRPEGMPIGYIAIDAIYTPIRNVRFTVENT 186

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKKEVKEDIN 246
           R GQ  DY+K+ + ++TDGS+T +DS++LA +I+ D +  F NF     E  +E  +  +
Sbjct: 187 RVGQRTDYEKMILDVETDGSVTPDDSISLAGKIITDHVTFFANFSPTEEEFTEEEFKQQD 246

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L  K+E+L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL E+
Sbjct: 247 DEFETMRRLLHTKIEDLDLSVRSHNCLRLAEIDTIGDLVSRKEDELLNYKNFGKKSLTEL 306

Query: 307 KGVLGTMGLFLGMNLPDWPPE 327
           K  L    L  GM++  +  +
Sbjct: 307 KEQLEKFDLKFGMDITKYQMK 327


>gi|58415776|emb|CAH57302.1| RNA polymerase alpha-subunit [Vibrio cholerae]
 gi|58415778|emb|CAH57303.1| RNA polymerase alpha-subunit [Vibrio cholerae]
 gi|58415780|emb|CAH57304.1| RNA polymerase alpha-subunit [Vibrio cholerae]
 gi|58415782|emb|CAH57305.1| RNA polymerase alpha-subunit [Vibrio cholerae]
 gi|58415784|emb|CAH57306.1| RNA polymerase alpha-subunit [Vibrio cholerae]
 gi|58415786|emb|CAH57307.1| RNA polymerase alpha-subunit [Vibrio cholerae]
 gi|58415788|emb|CAH57308.1| RNA polymerase alpha-subunit [Vibrio cholerae]
 gi|58415790|emb|CAH57309.1| RNA polymerase alpha-subunit [Vibrio cholerae]
 gi|58415792|emb|CAH57310.1| RNA polymerase alpha-subunit [Vibrio cholerae]
 gi|58415936|emb|CAH57382.1| RNA polymerase alpha-subunit [Vibrio mimicus]
 gi|58415938|emb|CAH57383.1| RNA polymerase alpha-subunit [Vibrio mimicus]
 gi|58415940|emb|CAH57384.1| RNA polymerase alpha-subunit [Vibrio mimicus]
 gi|58415942|emb|CAH57385.1| RNA polymerase alpha-subunit [Vibrio mimicus]
          Length = 309

 Score =  311 bits (797), Expect = 9e-83,   Method: Composition-based stats.
 Identities = 136/315 (43%), Positives = 206/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLD-VDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
           +NP+HVIC+L   +A + M + V +G GYVPA    H   +  PIG + +DA +SP+ K+
Sbjct: 118 VNPEHVICHLTSDNAAIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|37523140|ref|NP_926517.1| DNA-directed RNA polymerase subunit alpha [Gloeobacter violaceus
           PCC 7421]
 gi|41688630|sp|Q7NFF5|RPOA_GLOVI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|35214143|dbj|BAC91512.1| RNA polymerase alpha subunit [Gloeobacter violaceus PCC 7421]
          Length = 314

 Score =  311 bits (797), Expect = 9e-83,   Method: Composition-based stats.
 Identities = 112/312 (35%), Positives = 179/312 (57%), Gaps = 8/312 (2%)

Query: 14  NIEYIVLGQEEEN--RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE +    E +N      + EPL RG   TLGNALRRVL+S+L G A+TAV+I GV HE
Sbjct: 5   TIECVETRTEADNGQYGKFVLEPLERGQGTTLGNALRRVLLSNLEGTAVTAVRITGVNHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            +++KG+ ED+ DI+LN+K + L+      +   +  +GP  VTA D++   +++V++P 
Sbjct: 65  FATMKGIREDVLDILLNMKELVLRSYTSDIQIGRLAVQGPKRVTAADLELPTEVQVVHPR 124

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
           H I  L  D  + ME  + +G GY   +    +   I  ++IDA++ P++KV++TVES R
Sbjct: 125 HYIATLAEDGQLEMEFQIERGKGYRAIERGSEDGAAIDYLSIDAIFMPVRKVNWTVESER 184

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
               ++ D+L++ I T GS++ +++++ A++IL DQL             +     +   
Sbjct: 185 SAANVEQDRLTLEIWTSGSLSPQEALSQAAKILVDQLRPLQEIT-----FEPPAEPQRSA 239

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL- 310
            N      +EEL+LSVR+ NCL+   I  + DL++ TE D+L + NFG+KS  E+   L 
Sbjct: 240 PNTVGQVPIEELQLSVRAYNCLKRAQINTVADLLEYTEEDLLEIKNFGQKSAEEVIEALQ 299

Query: 311 GTMGLFLGMNLP 322
             MGL L  + P
Sbjct: 300 DKMGLSLPKDKP 311


>gi|90194030|gb|ABD92576.1| RpoA [Actinobacillus equuli subsp. haemolyticus]
          Length = 303

 Score =  311 bits (797), Expect = 9e-83,   Method: Composition-based stats.
 Identities = 137/304 (45%), Positives = 206/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+S      +T+ K G G VTA DI    D+E++NP+HVIC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVSNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPNHVICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D +A + M + V +G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  
Sbjct: 122 TDKNASINMRIRVQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|119511155|ref|ZP_01630272.1| DNA-directed RNA polymerase alpha subunit [Nodularia spumigena
           CCY9414]
 gi|119464143|gb|EAW45063.1| DNA-directed RNA polymerase alpha subunit [Nodularia spumigena
           CCY9414]
          Length = 315

 Score =  311 bits (797), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 100/312 (32%), Positives = 168/312 (53%), Gaps = 10/312 (3%)

Query: 14  NIEYIVLGQEEEN--RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE +    EE     +  + EPL RG   T+GNALRRVL+S+L G A+TAV+I GV HE
Sbjct: 5   QIECVESNTEESRSHYSKFVLEPLERGQGTTVGNALRRVLLSNLEGTAVTAVRIAGVSHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            +++ GV ED+ +I++ +K + L+      +   +   GP  VT       +++EV++  
Sbjct: 65  FATVPGVREDVLEILMKMKEVILRSYSSQPQIGRLLVNGPATVTVAHFDLPSEVEVIDQT 124

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  L     + ME  + KG GY   +  R E   +  + ID+++ P++KV+Y+VE AR
Sbjct: 125 QYVATLAEGGKLEMEFRIEKGKGYRTVERGREEATSLDFLQIDSVFMPVRKVNYSVEEAR 184

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
               +  D+L + + T+GSI+ +++++ A+ IL +      +      E   ++     P
Sbjct: 185 GESSIPKDRLLLEVWTNGSISPQEALSSAAGILVELFNPLKDISLEPTETGAEV-----P 239

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL+LSVR+ NCL+   +  + DL+  T+ D+L + NFG+KS  E+   L 
Sbjct: 240 DDPTAQIPIEELQLSVRAYNCLKRAQVNSVADLLDFTQEDLLEIKNFGQKSAEEVVEALQ 299

Query: 312 TMGLFLGMNLPD 323
                LG+ LP 
Sbjct: 300 R---RLGITLPQ 308


>gi|309389906|gb|ADO77786.1| DNA-directed RNA polymerase subunit alpha [Halanaerobium praevalens
           DSM 2228]
          Length = 315

 Score =  311 bits (797), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 128/315 (40%), Positives = 202/315 (64%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP     +     +EN       PL RG+  TLGN+LRR+L+SSL GAA+T+V+++G
Sbjct: 3   EIEKPR----VERLGSDENYGRYEISPLERGYGTTLGNSLRRILLSSLPGAALTSVKVEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE S+I GV ED+TD+ILN+K + +K SG+    + +   G G +TAGD  +  D+EV
Sbjct: 59  VKHEFSAIPGVVEDMTDLILNLKEVVVKYSGEEQTTIRLEAEGEGEITAGDFISAGDVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
           +N +H +  L     + +E TV KG GY  A+ +    EN+ IGLI ID+ YSPI++ ++
Sbjct: 119 VNKEHHVATLAEGGRLVLEATVDKGRGYHTAEENEKLFENNVIGLIPIDSAYSPIERANF 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            +E+ R GQV D+D+L + ++T+GSI  +D+++LA++I+ + L +FIN  +  ++V+  +
Sbjct: 179 NIENTRVGQVTDFDRLVLEVNTNGSIHPDDAISLAAKIMVEHLELFINLTDEIEDVEIMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            V+    +  L   +EELELSVRS+NCL+   I  + +L+ RTE D++++ N G+KSL E
Sbjct: 239 EVEEEEKDEILDTTIEELELSVRSSNCLKRAGINTVEELVSRTEDDLMKVRNLGKKSLKE 298

Query: 306 IKGVLGTMGLFLGMN 320
           I+  L  + L L  N
Sbjct: 299 IEKKLDELELDLKEN 313


>gi|90194014|gb|ABD92568.1| RpoA [Actinobacillus genomosp. 2]
          Length = 303

 Score =  311 bits (797), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 139/304 (45%), Positives = 206/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+SG     +T+ K G G VTA DI    D+E++NP HVIC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVSGKDDIILTLNKSGIGPVTAADITHDGDVEIVNPHHVICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D DA + M + + +G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  
Sbjct: 122 TDKDASISMRIRIQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    +I  +   F+
Sbjct: 182 QRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EIKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|189347676|ref|YP_001944205.1| DNA-directed RNA polymerase subunit alpha [Chlorobium limicola DSM
           245]
 gi|238692198|sp|B3EGW3|RPOA_CHLL2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|189341823|gb|ACD91226.1| DNA-directed RNA polymerase, alpha subunit [Chlorobium limicola DSM
           245]
          Length = 328

 Score =  311 bits (797), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 121/322 (37%), Positives = 192/322 (59%), Gaps = 6/322 (1%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  IE        +     +A+PL RG+  TLGN +RR L++SL G AIT ++IDGV HE
Sbjct: 8   PAKIEVDE-ATHTDRFGRFVAQPLERGYGVTLGNVMRRALLASLPGTAITGLKIDGVFHE 66

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNP 130
            S+I GV ED+ +I+LN+K +  + +   + + ++   G    TAGDI     + EVLN 
Sbjct: 67  FSTINGVREDVPEIVLNLKKVRFRSNCKRNCKTSLVLNGQKEFTAGDIIAQEGEFEVLNK 126

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  ++  A +++++ V +G GY+P++ +R +  PIG I IDA+++PI+ V +TVE+ 
Sbjct: 127 DLHIATVNEGATLKIDIFVGRGRGYLPSEENRPDGMPIGFIAIDAIFTPIRNVKFTVENT 186

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKKEVKEDIN 246
           R GQ  DY+K+ + ++TDGSIT +DS++LA +I+ + +  F +F     E  +E  +  +
Sbjct: 187 RVGQRTDYEKMILDVETDGSITPDDSISLAGKIINEHVTFFADFSPTEEEFTEEEFKQQD 246

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +          K+E+L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL E+
Sbjct: 247 DEFENMRKLFNTKIEDLDLSVRSHNCLRLAEIDTIGDLVSRKEDELLNYKNFGKKSLTEL 306

Query: 307 KGVLGTMGLFLGMNLPDWPPES 328
           K  L    L  GM++  +  + 
Sbjct: 307 KEQLEKFDLKFGMDITKYQMKG 328


>gi|164608448|gb|ABY62527.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 309

 Score =  311 bits (797), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 136/315 (43%), Positives = 207/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLD-VDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
           +NP+HVIC+L   +A + M + V +G GYVPA    H   +  PIG + +DA +SP+ K+
Sbjct: 118 VNPEHVICHLTSDNAAIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL +F++  + +     
Sbjct: 178 AYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDVFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|58415740|emb|CAH57284.1| RNA polymerase alpha-subunit [Vibrio alginolyticus]
 gi|58415742|emb|CAH57285.1| RNA polymerase alpha-subunit [Vibrio alginolyticus]
 gi|58415746|emb|CAH57287.1| RNA polymerase alpha-subunit [Vibrio alginolyticus]
 gi|58415748|emb|CAH57288.1| RNA polymerase alpha-subunit [Vibrio alginolyticus]
 gi|58415760|emb|CAH57294.1| RNA polymerase alpha-subunit [Vibrio campbellii]
 gi|58415762|emb|CAH57295.1| RNA polymerase alpha-subunit [Vibrio campbellii]
 gi|58415764|emb|CAH57296.1| RNA polymerase alpha-subunit [Vibrio campbellii]
 gi|58415766|emb|CAH57297.1| RNA polymerase alpha-subunit [Vibrio campbellii]
 gi|58415768|emb|CAH57298.1| RNA polymerase alpha-subunit [Vibrio campbellii]
 gi|58415818|emb|CAH57323.1| RNA polymerase alpha-subunit [Vibrio diabolicus]
 gi|58415872|emb|CAH57350.1| RNA polymerase alpha-subunit [Vibrio harveyi]
 gi|58415874|emb|CAH57351.1| RNA polymerase alpha-subunit [Vibrio harveyi]
 gi|58415876|emb|CAH57352.1| RNA polymerase alpha-subunit [Vibrio harveyi]
 gi|58415878|emb|CAH57353.1| RNA polymerase alpha-subunit [Vibrio harveyi]
 gi|58415880|emb|CAH57354.1| RNA polymerase alpha-subunit [Vibrio communis]
 gi|58415882|emb|CAH57355.1| RNA polymerase alpha-subunit [Vibrio harveyi]
 gi|58415884|emb|CAH57356.1| RNA polymerase alpha-subunit [Vibrio harveyi]
 gi|58415886|emb|CAH57357.1| RNA polymerase alpha-subunit [Vibrio harveyi]
 gi|58415888|emb|CAH57358.1| RNA polymerase alpha-subunit [Vibrio harveyi]
 gi|58415890|emb|CAH57359.1| RNA polymerase alpha-subunit [Vibrio harveyi]
 gi|58415982|emb|CAH57405.1| RNA polymerase alpha-subunit [Vibrio parahaemolyticus]
 gi|58415984|emb|CAH57406.1| RNA polymerase alpha-subunit [Vibrio parahaemolyticus]
 gi|58416024|emb|CAH57426.1| RNA polymerase alpha-subunit [Vibrio sp. R-21410]
 gi|58416026|emb|CAH57427.1| RNA polymerase alpha-subunit [Vibrio sp. R-21413]
 gi|58416036|emb|CAH57432.1| RNA polymerase alpha-subunit [Vibrio sp. R-21426]
 gi|58416038|emb|CAH57433.1| RNA polymerase alpha-subunit [Vibrio sp. R-21427]
 gi|58416066|emb|CAH57447.1| RNA polymerase alpha-subunit [Vibrio sp. R-23694]
          Length = 309

 Score =  311 bits (797), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 138/315 (43%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H+  +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHNEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|78186095|ref|YP_374138.1| DNA-directed RNA polymerase subunit alpha [Chlorobium luteolum DSM
           273]
 gi|119366706|sp|Q3B6D6|RPOA_PELLD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|78165997|gb|ABB23095.1| DNA-directed RNA polymerase subunit alpha [Chlorobium luteolum DSM
           273]
          Length = 328

 Score =  311 bits (796), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 127/322 (39%), Positives = 193/322 (59%), Gaps = 6/322 (1%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  IE       ++     IA+PL RG+  TLGN +RRVL++SL G AIT +++DGV HE
Sbjct: 8   PAKIEVDEATHTDQ-YGRFIAQPLERGYGVTLGNMMRRVLLASLPGTAITGIKVDGVFHE 66

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNP 130
            SSI+GV ED+ +I+LN+K +  K +     + T+   GP   TAGDI     + EVLN 
Sbjct: 67  FSSIEGVREDVPEIVLNLKKVRFKSTCKRSCKTTLSIVGPKDFTAGDIVAQEGEFEVLNK 126

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  ++  + + +++ + +G GY PA+  R ++ PIG I IDA+Y+PI+ V + VE+ 
Sbjct: 127 DLYIATVNEGSTLNIDVYIGRGRGYTPAEESRPDSMPIGYIAIDAIYTPIRNVKFAVENT 186

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK----EDIN 246
           R GQ  DY+K+ + ++TDGSIT +DS++LA RI+ + +  F NF   ++E      +  +
Sbjct: 187 RVGQRTDYEKMVLDVETDGSITPDDSISLAGRIINEHVTFFANFSPTEEEFTEEEYKQQD 246

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L  K+E+L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL E+
Sbjct: 247 DEFETMRRLLNTKIEDLDLSVRSHNCLRLAEIDTIGDLVSRKEDELLNYKNFGKKSLTEL 306

Query: 307 KGVLGTMGLFLGMNLPDWPPES 328
           K  L    L  GM++  +  + 
Sbjct: 307 KEQLEKFELKFGMDITRYQMKG 328


>gi|313888838|ref|ZP_07822499.1| DNA-directed RNA polymerase, alpha subunit [Peptoniphilus harei
           ACS-146-V-Sch2b]
 gi|312845207|gb|EFR32607.1| DNA-directed RNA polymerase, alpha subunit [Peptoniphilus harei
           ACS-146-V-Sch2b]
          Length = 315

 Score =  311 bits (796), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 124/311 (39%), Positives = 191/311 (61%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP     I    E       + EPL  GF  T+GN+LRRVL+SSL GAA++ + I G
Sbjct: 3   EIEKPRI--SIEELDESGLYGKFVVEPLEAGFGITIGNSLRRVLLSSLPGAAVSFINIRG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE  +I GV ED+ +I+LNIK I LKM+ D   ++ I K+G G + A DI+ V  + +
Sbjct: 61  VEHEFDTIPGVLEDVPEIVLNIKSIVLKMTEDEPVKLVIEKKGKGEIKASDIELVPHVSI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPD  I  L+ DA   +E+ V KG GY P++  + E   IG+I +D+ ++P++KV++ V
Sbjct: 121 INPDQHIATLNDDADFYLEMMVEKGRGYEPSELKKDEISEIGIIPMDSNFTPVEKVNWKV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  D+D+L + + TDGS+  +++ +LA++IL + L +FI  +E   E+   +  
Sbjct: 181 ENTRVGQRTDFDRLILEVTTDGSMKADEATSLAAKILTEHLELFIGLKEHVSEINLMVEK 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   VEEL+LSVRS NCL+   I  + +L  +TE++M+++ N GRKSL+E+ 
Sbjct: 241 EEDQKEKVLEMTVEELDLSVRSFNCLKRAGINSVEELTNKTESEMMKVRNLGRKSLLEVT 300

Query: 308 GVLGTMGLFLG 318
             L  +GL L 
Sbjct: 301 EKLDELGLSLK 311


>gi|90194034|gb|ABD92578.1| RpoA [Actinobacillus pleuropneumoniae serovar 1]
 gi|90194036|gb|ABD92579.1| RpoA [Actinobacillus pleuropneumoniae serovar 2 str. S1536]
 gi|90194038|gb|ABD92580.1| RpoA [Actinobacillus pleuropneumoniae]
 gi|90194040|gb|ABD92581.1| RpoA [Actinobacillus pleuropneumoniae serovar 4 str. M62]
 gi|90194042|gb|ABD92582.1| RpoA [Actinobacillus pleuropneumoniae]
 gi|90194044|gb|ABD92583.1| RpoA [Actinobacillus pleuropneumoniae serovar 8 str. 405]
          Length = 301

 Score =  311 bits (796), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 138/303 (45%), Positives = 205/303 (67%), Gaps = 7/303 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VNIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+SG     +T+ K G G VTA DI    D+E++NP HVIC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVSGKDDIILTLNKSGIGPVTAADITHDGDVEIVNPHHVICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D DA + M + V +G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  
Sbjct: 122 TDKDASISMRIRVQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLF 316
           GL 
Sbjct: 299 GLS 301


>gi|90193994|gb|ABD92558.1| RpoA [Gallibacterium anatis]
          Length = 300

 Score =  311 bits (796), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 134/302 (44%), Positives = 201/302 (66%), Gaps = 5/302 (1%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VDIEQISPTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+       +T+ K G G V A DI    D+E++NPDH+IC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVQNKDDVFLTLTKSGIGPVVAADITHDGDVEIVNPDHIICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAKHH-RTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
            D +A + M + V +G GYVPA      E  PIG + +DA YSP+ +++Y VE+AR  Q 
Sbjct: 122 TDENASINMRIRVQRGRGYVPASSRTHDEERPIGRLLVDACYSPVDRIAYNVEAARVEQR 181

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F+P 
Sbjct: 182 TDLDKLVIEMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEFDPI 238

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL
Sbjct: 239 LLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGL 298

Query: 316 FL 317
            L
Sbjct: 299 SL 300


>gi|58415840|emb|CAH57334.1| RNA polymerase alpha-subunit [Vibrio fluvialis]
 gi|58415842|emb|CAH57335.1| RNA polymerase alpha-subunit [Vibrio fluvialis]
 gi|58415852|emb|CAH57340.1| RNA polymerase alpha-subunit [Vibrio furnissii]
 gi|58415854|emb|CAH57341.1| RNA polymerase alpha-subunit [Vibrio furnissii]
 gi|58415856|emb|CAH57342.1| RNA polymerase alpha-subunit [Vibrio furnissii]
 gi|58415858|emb|CAH57343.1| RNA polymerase alpha-subunit [Vibrio furnissii]
          Length = 309

 Score =  311 bits (796), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 136/315 (43%), Positives = 206/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
           +NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA +SP+ K+
Sbjct: 118 VNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|58415986|emb|CAH57407.1| RNA polymerase alpha-subunit [Vibrio pectenicida]
 gi|58415988|emb|CAH57408.1| RNA polymerase alpha-subunit [Vibrio pectenicida]
 gi|58415990|emb|CAH57409.1| RNA polymerase alpha-subunit [Vibrio pectenicida]
          Length = 309

 Score =  311 bits (796), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 136/315 (43%), Positives = 203/315 (64%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L    A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K+
Sbjct: 118 TNPEHVICHLTDGNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|90194002|gb|ABD92562.1| RpoA [Phocoenobacter uteri]
          Length = 302

 Score =  311 bits (796), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 134/304 (44%), Positives = 205/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VNIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+       +T+ K G G V A DI    D+E++NP+HVIC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVQNKDDIVLTLNKSGIGPVIAADITHDGDVEIVNPEHVICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D DA + M + V +G GYVPA    H ++++ PIG + +DA +SP+ +++Y VE+AR  
Sbjct: 122 TDKDASINMRIRVQRGRGYVPASARVHSQSDDRPIGRLLVDARFSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLIIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|90194020|gb|ABD92571.1| RpoA [Actinobacillus arthritidis]
          Length = 303

 Score =  311 bits (796), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 138/304 (45%), Positives = 206/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+SG     +T+ K G G VTA DI    D+E++NP H+IC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVSGKDDIILTLNKSGIGPVTAADITHDGDVEIVNPHHIICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D DA + M + + +G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  
Sbjct: 122 TDKDASISMRIRIQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    +I  +   F+
Sbjct: 182 QRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EIKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|90193998|gb|ABD92560.1| RpoA [Avibacterium gallinarum]
          Length = 302

 Score =  311 bits (796), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 136/304 (44%), Positives = 205/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VDIEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+    +  +T+ K G G V A DI    D+E++NP+HVIC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVQNKDNVFLTLSKSGIGPVVAADITYDGDVEIVNPEHVICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D +A + M + V +G GYVPA    H + E  PIG + +DA YSP+++++Y VE+ R  
Sbjct: 122 TDENASINMCIRVQRGRGYVPASARVHSQDEERPIGRLLVDACYSPVQRIAYNVEATRVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|179184326|gb|ACB78143.1| RNA polymerase alpha subunit [Vibrio breoganii]
          Length = 311

 Score =  310 bits (795), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 139/317 (43%), Positives = 206/317 (64%), Gaps = 11/317 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+
Sbjct: 1   TEFLKPRLVD---IEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIE 57

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+
Sbjct: 58  GVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDV 117

Query: 126 EVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIK 181
           E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ 
Sbjct: 118 EIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVD 177

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   
Sbjct: 178 KIAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE 237

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
                 +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+K
Sbjct: 238 ---KEEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKK 294

Query: 302 SLVEIKGVLGTMGLFLG 318
           SL EIK VL + GL LG
Sbjct: 295 SLTEIKDVLASRGLSLG 311


>gi|293393287|ref|ZP_06637601.1| DNA-directed RNA polymerase subunit alpha [Serratia odorifera DSM
           4582]
 gi|291424197|gb|EFE97412.1| DNA-directed RNA polymerase subunit alpha [Serratia odorifera DSM
           4582]
          Length = 334

 Score =  310 bits (795), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 130/310 (41%), Positives = 202/310 (65%), Gaps = 10/310 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENAAISMRIKVQRGRGYVPASARIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIK 307
            G+  L  +K
Sbjct: 295 LGKNLLPRLK 304


>gi|197288307|gb|ACH57436.1| RpoA [Vibrio gallaecicus]
          Length = 311

 Score =  310 bits (795), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 140/317 (44%), Positives = 206/317 (64%), Gaps = 11/317 (3%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVL
Sbjct: 1   LKPRLVD---IEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVL 57

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           HE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+ 
Sbjct: 58  HEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIA 117

Query: 129 NPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 184
           NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K++
Sbjct: 118 NPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +      
Sbjct: 178 YAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE--- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 235 EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLGMNL 321
           EIK VL + GL LGM L
Sbjct: 295 EIKDVLASRGLSLGMRL 311


>gi|90194064|gb|ABD92593.1| RpoA [Pasteurella canis]
          Length = 302

 Score =  310 bits (795), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 135/304 (44%), Positives = 202/304 (66%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VDIEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+       +T+ K G G V A DI    D+E++NP+H+IC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVQNKDDVFLTLNKSGIGPVVAADITHDGDVEIVNPEHIICHL 121

Query: 138 DVD-AVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYSPIKKVSYTVESAREG 193
             D A + M + V +G GYVPA      + E  PIG + +DA YSP+ +++Y VE+AR  
Sbjct: 122 TDDNASINMRIRVQRGRGYVPASARVHAQDEERPIGRLLVDACYSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|58415754|emb|CAH57291.1| RNA polymerase alpha-subunit [Vibrio brasiliensis]
 gi|58415756|emb|CAH57292.1| RNA polymerase alpha-subunit [Vibrio brasiliensis LMG 20546]
 gi|58415798|emb|CAH57313.1| RNA polymerase alpha-subunit [Vibrio coralliilyticus]
 gi|58415800|emb|CAH57314.1| RNA polymerase alpha-subunit [Vibrio coralliilyticus]
 gi|58415802|emb|CAH57315.1| RNA polymerase alpha-subunit [Vibrio coralliilyticus]
 gi|58415804|emb|CAH57316.1| RNA polymerase alpha-subunit [Vibrio coralliilyticus ATCC BAA-450]
 gi|58415806|emb|CAH57317.1| RNA polymerase alpha-subunit [Vibrio coralliilyticus]
 gi|58415808|emb|CAH57318.1| RNA polymerase alpha-subunit [Vibrio coralliilyticus]
 gi|58415810|emb|CAH57319.1| RNA polymerase alpha-subunit [Vibrio coralliilyticus]
 gi|58415892|emb|CAH57360.1| RNA polymerase alpha-subunit [Vibrio hepatarius]
 gi|58415956|emb|CAH57392.1| RNA polymerase alpha-subunit [Vibrio neptunius]
 gi|58415958|emb|CAH57393.1| RNA polymerase alpha-subunit [Vibrio neptunius]
 gi|58415960|emb|CAH57394.1| RNA polymerase alpha-subunit [Vibrio neptunius]
 gi|58415974|emb|CAH57401.1| RNA polymerase alpha-subunit [Vibrio orientalis]
 gi|58416052|emb|CAH57440.1| RNA polymerase alpha-subunit [Vibrio sp. R-23286]
 gi|58416070|emb|CAH57449.1| RNA polymerase alpha-subunit [Vibrio sp. R-23696]
 gi|58416098|emb|CAH57463.1| RNA polymerase alpha-subunit [Vibrio tubiashii]
 gi|58416100|emb|CAH57464.1| RNA polymerase alpha-subunit [Vibrio tubiashii]
 gi|58416102|emb|CAH57465.1| RNA polymerase alpha-subunit [Vibrio tubiashii]
 gi|58416112|emb|CAH57470.1| RNA polymerase alpha-subunit [Vibrio xuii]
 gi|58416114|emb|CAH57471.1| RNA polymerase alpha-subunit [Vibrio xuii]
 gi|58416116|emb|CAH57472.1| RNA polymerase alpha-subunit [Vibrio xuii]
          Length = 309

 Score =  310 bits (795), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 137/315 (43%), Positives = 204/315 (64%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|309789643|ref|ZP_07684224.1| DNA-directed RNA polymerase subunit alpha [Oscillochloris
           trichoides DG6]
 gi|308228379|gb|EFO82026.1| DNA-directed RNA polymerase subunit alpha [Oscillochloris
           trichoides DG6]
          Length = 330

 Score =  310 bits (795), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 129/323 (39%), Positives = 196/323 (60%), Gaps = 11/323 (3%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
            IE +   Q  EN      EPL  G+ HTLGNALRRVL+SS+ G+AIT ++IDGV HE S
Sbjct: 8   KIEVV---QAAENYGRFKIEPLDPGYGHTLGNALRRVLVSSIPGSAITKIKIDGVFHEFS 64

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           +I+GV ED+T+I+LNIKG+ L+   +   +V + KRGPG+VTA DI   ++IE++NP+H 
Sbjct: 65  TIEGVKEDVTEIVLNIKGVRLRSYAERPVKVLLTKRGPGIVTAKDIDVPSNIELVNPNHY 124

Query: 134 ICNLDVD-AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           IC LD + A + +E+TV +G GYV A     +  PIG I +DA+++P+ +V+Y VE+ R 
Sbjct: 125 ICTLDSEVARLEIEMTVERGRGYVSADQR--DILPIGEIPVDAIFTPVPRVNYVVENTRI 182

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP- 251
           GQ  D+D+L + I TDG++   D+++ A+++L        +F     E +E      L  
Sbjct: 183 GQATDFDRLLLEIWTDGTVKPGDALSHAAQVLVQYSQTIADFNRLAVEEEESPTPSGLTI 242

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +      +E+L+LS R+ NCL+  +I  +G ++Q  E  +L + N G+KS+ EI+  L 
Sbjct: 243 PSDIYDTPIEDLDLSTRTYNCLKRADITKVGQVLQMDEKALLSVRNLGQKSMEEIRDRLV 302

Query: 312 TMGLFLGM----NLPDWPPESIE 330
             G         +L D  P +IE
Sbjct: 303 ERGYISRQAGNGSLSDSEPVTIE 325


>gi|90194000|gb|ABD92561.1| RpoA [Nicoletella semolina]
          Length = 302

 Score =  310 bits (794), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 134/304 (44%), Positives = 203/304 (66%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VSIEQVSLTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+       +T+ K G G V A DI    D+E++NP+HVIC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVQNKDDVILTLTKSGIGPVIAADIVHDGDVEIVNPNHVICHL 121

Query: 138 DV-DAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
              +A + M + V +G GYVPA    H + +N PIG + +DA +SP+ ++SY VE+AR  
Sbjct: 122 TDNNASINMRIRVRRGRGYVPASALVHTQDDNRPIGRLLVDARFSPVDRISYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|328814017|gb|AEB52124.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 263

 Score =  310 bits (794), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 120/263 (45%), Positives = 172/263 (65%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T II
Sbjct: 1   YGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQII 60

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LNIKG+ LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     
Sbjct: 61  LNIKGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHAR 120

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I 
Sbjct: 121 LTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIW 180

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +EEL+LS
Sbjct: 181 TDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEELDLS 240

Query: 267 VRSTNCLRGENIVYMGDLIQRTE 289
           VRS NCL+   I  + +L  ++E
Sbjct: 241 VRSYNCLKRAGINTVQELTNKSE 263


>gi|58415844|emb|CAH57336.1| RNA polymerase alpha-subunit [Vibrio fluvialis]
          Length = 309

 Score =  310 bits (794), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 136/315 (43%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
           +NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA +SP+ K+
Sbjct: 118 VNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFGPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|90194048|gb|ABD92585.1| RpoA [Actinobacillus porcinus]
          Length = 303

 Score =  310 bits (794), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 136/304 (44%), Positives = 204/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE SS +G
Sbjct: 2   VNIEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+       +T+ K G G V A DI    D+E++NPDHV+C+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVQNKDDVFLTLNKSGIGPVVAADITHDGDVEIVNPDHVLCHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D +A + M + V +G GYVPA    H + E  PIG + +DA YSP+ +++Y VE+AR  
Sbjct: 122 TDENASINMRIRVQRGRGYVPASARAHTQDEERPIGRLLVDACYSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|257064662|ref|YP_003144334.1| DNA-directed RNA polymerase subunit alpha [Slackia
           heliotrinireducens DSM 20476]
 gi|256792315|gb|ACV22985.1| DNA-directed RNA polymerase subunit alpha [Slackia
           heliotrinireducens DSM 20476]
          Length = 316

 Score =  310 bits (794), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 118/320 (36%), Positives = 184/320 (57%), Gaps = 10/320 (3%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E ++P     +   +  +     + EPL RGF +TLGN +RRVL+SSL GA  TA+QI
Sbjct: 1   MAEFMRPT----VTTEEVSDTDARFVVEPLERGFGYTLGNCMRRVLLSSLDGARATAIQI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +GV HE ++ +GV ED+TDI+LN+KG+         +    TI   GP  VT  DIQ   
Sbjct: 57  EGVQHEFTTAEGVIEDVTDIVLNVKGLVFAALTEDYTEATATISVEGPCTVTGADIQVPT 116

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           +  ++NP+HVI  +     + M + +  G GYV A+ ++   DPIG+I +D+L+SP+++ 
Sbjct: 117 EFTLINPEHVIATVADGGTLNMSIRIGVGRGYVSAERNKRTEDPIGIIPVDSLFSPVRRC 176

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +  V   R GQ  D+D+L + ++TDGSI   ++V  A+ I+   +G F+   +   E + 
Sbjct: 177 TLAVNDTRVGQRTDFDQLLLEVETDGSIAPNEAVCRAANIINQYMGAFLTLADITDEDEG 236

Query: 244 DIN----VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           DI      +    N  L K++E+L+LSVRS NCL+   I  +  L++ +E D+L + NFG
Sbjct: 237 DIPSIFATEGQESNAELDKQIEDLDLSVRSYNCLKRAGIHSVRQLVEFSENDLLNIRNFG 296

Query: 300 RKSLVEIKGVLGTMGLFLGM 319
            KS+ E+K  L +M L L  
Sbjct: 297 AKSIEEVKDKLISMDLNLKQ 316


>gi|58415930|emb|CAH57379.1| RNA polymerase alpha-subunit [Vibrio metschnikovii]
 gi|58415932|emb|CAH57380.1| RNA polymerase alpha-subunit [Vibrio metschnikovii]
 gi|58415934|emb|CAH57381.1| RNA polymerase alpha-subunit [Vibrio metschnikovii]
          Length = 309

 Score =  310 bits (794), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 134/315 (42%), Positives = 204/315 (64%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++        +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRLGENKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
           +NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA +SP+ K+
Sbjct: 118 VNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|328813997|gb|AEB52114.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 270

 Score =  310 bits (794), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 123/273 (45%), Positives = 177/273 (64%), Gaps = 6/273 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KPN    I    E +N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLH
Sbjct: 2   KPN----IHKIDENDNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLH 57

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S+I+GV ED+T IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EVLNP
Sbjct: 58  EFSTIEGVTEDVTAIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEVLNP 117

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVE 188
           D  IC +   A   M +T + G GYV A+ ++   ++ PIG++ +D+LYSPI++V+Y VE
Sbjct: 118 DLPICTVADGAHFHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVE 177

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           + R GQ  D+DKL++ + T+GSIT  ++++L+++IL D L +F+N  +  K     +  +
Sbjct: 178 NTRVGQRDDFDKLTLDVWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMVEKE 237

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
                  L   +EEL+LSVRS NCL+   I  +
Sbjct: 238 ETHKEKMLEMTIEELDLSVRSYNCLKRAGINTV 270


>gi|326562118|gb|EGE12446.1| DNA-directed RNA polymerase subunit alpha [Moraxella catarrhalis
           7169]
 gi|326565701|gb|EGE15864.1| DNA-directed RNA polymerase subunit alpha [Moraxella catarrhalis
           12P80B1]
 gi|326566269|gb|EGE16421.1| DNA-directed RNA polymerase subunit alpha [Moraxella catarrhalis
           103P14B1]
 gi|326567079|gb|EGE17201.1| DNA-directed RNA polymerase subunit alpha [Moraxella catarrhalis
           BC1]
 gi|326568343|gb|EGE18423.1| DNA-directed RNA polymerase subunit alpha [Moraxella catarrhalis
           BC7]
 gi|326574842|gb|EGE24772.1| DNA-directed RNA polymerase subunit alpha [Moraxella catarrhalis
           101P30B1]
 gi|326576166|gb|EGE26081.1| DNA-directed RNA polymerase subunit alpha [Moraxella catarrhalis
           CO72]
          Length = 334

 Score =  310 bits (794), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 135/327 (41%), Positives = 207/327 (63%), Gaps = 8/327 (2%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           N  E + P+ I    + +       +  EPL RGF HTLGNALRR+L+SSL GAA+   +
Sbjct: 3   NATEFLTPSAINVDTVNETT---AKVTLEPLERGFGHTLGNALRRILLSSLSGAAVVEAE 59

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           I+GV HE S+++G+ ED+ D++LN+K + + +   +   +T+ KRG GVVTA D++  ++
Sbjct: 60  IEGVDHEYSTLEGLQEDVLDLLLNLKSLAIILHDQNEAYLTLDKRGAGVVTAADLELPHN 119

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI--GLITIDALYSPIKK 182
           +E+ NPD V+  L     ++M L V  G GY PA   R + +    G + +DA +SPI +
Sbjct: 120 VEIANPDLVLGTLSERGHLKMRLHVVTGRGYEPANQRREDANSKIIGRLKLDASFSPIIR 179

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ ILQ Q+ +F++ E    E  
Sbjct: 180 VAYDVENARVEQRTDLDKLIIELETNGTIDPEEAIRKAATILQQQIAIFVDLE---AEEA 236

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
            +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QR+E ++L+  N G+KS
Sbjct: 237 PEPIKEKEEIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLVQRSETELLKTPNLGKKS 296

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESI 329
           L EIK VL +  L LGM L +WPP  +
Sbjct: 297 LTEIKDVLASKNLELGMRLDNWPPSDL 323


>gi|296113773|ref|YP_003627711.1| DNA-directed RNA polymerase alpha subunit [Moraxella catarrhalis
           RH4]
 gi|295921467|gb|ADG61818.1| DNA-directed RNA polymerase alpha subunit [Moraxella catarrhalis
           RH4]
 gi|326564517|gb|EGE14743.1| DNA-directed RNA polymerase subunit alpha [Moraxella catarrhalis
           46P47B1]
 gi|326572244|gb|EGE22239.1| DNA-directed RNA polymerase subunit alpha [Moraxella catarrhalis
           BC8]
 gi|326574586|gb|EGE24526.1| DNA-directed RNA polymerase subunit alpha [Moraxella catarrhalis
           O35E]
          Length = 334

 Score =  310 bits (794), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 134/327 (40%), Positives = 207/327 (63%), Gaps = 8/327 (2%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           N  E + P+ I    + +       +  EPL RGF HTLGNALRR+L+SSL GAA+   +
Sbjct: 3   NATEFLTPSAINVDTVNETT---AKVTLEPLERGFGHTLGNALRRILLSSLSGAAVVEAE 59

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           I+GV HE S+++G+ ED+ D++LN+K + + +   +   +T+ K+G GVVTA D++  ++
Sbjct: 60  IEGVDHEYSTLEGLQEDVLDLLLNLKSLAIILHDQNEAYLTLDKQGAGVVTAADLELPHN 119

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI--GLITIDALYSPIKK 182
           +E+ NPD V+  L     ++M L V  G GY PA   R + +    G + +DA +SPI +
Sbjct: 120 VEIANPDLVLGTLSERGHLKMRLHVVTGRGYEPANQRREDANSKIIGRLKLDASFSPIIR 179

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ ILQ Q+ +F++ E    E  
Sbjct: 180 VAYDVENARVEQRTDLDKLIIELETNGTIDPEEAIRKAATILQQQIAIFVDLE---AEEA 236

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
            +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QR+E ++L+  N G+KS
Sbjct: 237 PEPIKEKEEIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLVQRSETELLKTPNLGKKS 296

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESI 329
           L EIK VL +  L LGM L +WPP  +
Sbjct: 297 LTEIKDVLASKNLELGMRLDNWPPSDL 323


>gi|58415758|emb|CAH57293.1| RNA polymerase alpha-subunit [Vibrio campbellii]
          Length = 309

 Score =  310 bits (794), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 138/315 (43%), Positives = 206/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+++++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLSVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H+  +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHNEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|58416062|emb|CAH57445.1| RNA polymerase alpha-subunit [Vibrio sp. R-23692]
          Length = 309

 Score =  310 bits (794), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 137/315 (43%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +++LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEVLLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H+  +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHNEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|90193990|gb|ABD92556.1| RpoA [Pasteurella multocida]
 gi|90194060|gb|ABD92591.1| RpoA [Pasteurella multocida subsp. gallicida]
          Length = 302

 Score =  309 bits (793), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 136/304 (44%), Positives = 202/304 (66%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VDIEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+       +T+ K G G V A DI    D+E++NP+HVIC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVQNKDDVFLTLNKSGIGPVVAADITHDGDVEIVNPEHVICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D  A + M + V +G GYVPA      + E  PIG + +DA YSP+ +++Y VE+AR  
Sbjct: 122 TDESASINMRIRVQRGRGYVPASARVHAQDEERPIGRLLVDACYSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|284053326|ref|ZP_06383536.1| DNA-directed RNA polymerase subunit alpha [Arthrospira platensis
           str. Paraca]
 gi|291567808|dbj|BAI90080.1| RNA polymerase alpha subunit [Arthrospira platensis NIES-39]
          Length = 314

 Score =  309 bits (793), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 112/312 (35%), Positives = 173/312 (55%), Gaps = 10/312 (3%)

Query: 14  NIEYIV--LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE I   +  +       +  PL RG   T+GNALRRVL+S+L G AITAV+I GV HE
Sbjct: 5   KIECIESNISTDRSQYGKFVLGPLDRGQGITVGNALRRVLLSNLEGTAITAVRIAGVNHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            ++I G  ED+ +I+LN+K   LK      +   +  +GP  VT G     +++EV++ +
Sbjct: 65  FATIDGAREDVLEIMLNLKEAVLKSHTHQKQIGRLLVQGPATVTVGHFDLPSEVEVVDKN 124

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             I  L   A + ME  + KG GY     HR ++  +  + IDA++ P++KV+YTVE AR
Sbjct: 125 QYIATLSPGATLEMECQIEKGTGYRAVDRHRDDSAALDFLQIDAIFMPVRKVNYTVEDAR 184

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           +G  L+ D+L++ I T GS+T +++++ A+ IL D  G   +       ++   + +   
Sbjct: 185 DGGSLEKDRLTLEIWTSGSLTPQEAISQAAAILVDLFGALKDI-----NLESITSDQRDD 239

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL+LSVR+ NCL+   I  + DL   TE D+L + NFG+KS  E+   L 
Sbjct: 240 IDPTSQIPIEELQLSVRAYNCLKRAQINSVADLRDYTEEDLLEIKNFGQKSAEEVIEALQ 299

Query: 312 TMGLFLGMNLPD 323
                LG+ LP 
Sbjct: 300 N---RLGITLPK 308


>gi|90194026|gb|ABD92574.1| RpoA [Actinobacillus capsulatus]
          Length = 303

 Score =  309 bits (793), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 135/304 (44%), Positives = 203/304 (66%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+S      +T+ K G G VTA DI    D+E++NP+HVIC+L
Sbjct: 62  VQEDILEVLLNLKGLAVKVSNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPNHVICHL 121

Query: 138 DVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
               A + M + V +G GYV A    H + E+ PIG + +DA +SP+ +++Y VE+AR  
Sbjct: 122 TDKSASINMRIRVQRGRGYVSASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|255536128|ref|YP_003096499.1| DNA-directed RNA polymerase alpha subunit [Flavobacteriaceae
           bacterium 3519-10]
 gi|255342324|gb|ACU08437.1| DNA-directed RNA polymerase alpha subunit [Flavobacteriaceae
           bacterium 3519-10]
          Length = 331

 Score =  309 bits (793), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 124/324 (38%), Positives = 202/324 (62%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            IKP+ +   +L   ++ +      PL +GF  T+GNALRRVL+SSL G AI++++I+GV
Sbjct: 6   FIKPDKV---ILLNSDDFKGKFEFRPLEQGFGLTIGNALRRVLLSSLEGYAISSIKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE S+I GV ED+T+IILN+K + LK   ++   + VT    G   VTAGD+ +++   
Sbjct: 63  EHEFSTIPGVIEDVTEIILNLKQLRLKAKSEASAAETVTAKVTGQTTVTAGDLGKSIQGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E+LNPD VICNL+ +    +   + KG GYVP+  ++T + PIG I ID++++PIKKV Y
Sbjct: 123 EILNPDLVICNLNKEVKFELTFNIEKGRGYVPSDQNKTGSAPIGTIAIDSIFTPIKKVQY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           +VE+ R  Q  DY+KL + I+TDGSI+ ++++  AS+IL     +F    I  E    + 
Sbjct: 183 SVENYRVEQKTDYEKLVLDIETDGSISPQNALTEASKILIYHFMLFSDERITLETEAVKA 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
               + ++L     L  K+ +++LSVR+ NCL+   +  +G+L+  T++D+++  NFG+K
Sbjct: 243 SIQYDEETLHTRQLLKSKLTDMDLSVRALNCLKAAEVETLGELVSYTKSDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E++ ++   GL  G ++  + 
Sbjct: 303 SLTELEELVHAKGLNFGFDVAKYK 326


>gi|58384667|gb|AAW72682.1| DNA-directed RNA polymerase alpha chain [Buchnera aphidicola
           (Cinara cedri)]
          Length = 329

 Score =  309 bits (793), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 142/334 (42%), Positives = 211/334 (63%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q   ++ +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGFVEDFLKPGLVDIQQIS---ATHAKITLEPLERGFGHTLGNALRRILLSSISGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDG+LHE    +GV ED+ DI+LN+KG+++K+ G     + + K G G V A DI  
Sbjct: 58  EVEIDGILHEYMHKEGVKEDILDILLNLKGLSIKLFGKDEVTLYLKKSGIGPVLAKDINH 117

Query: 122 VNDIEVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALY 177
            N  E++N  H+ICNL   DA + + + V++G GY+ AK  +   D     G + +D  Y
Sbjct: 118 DNSTEIINNKHIICNLTCSDASIDIRMKVTRGRGYITAKSRKENYDNEHIIGKLFLDVTY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPI+++ YTVESAR  Q  D DKL + ++T+G+I  ED++  A+ IL  QL  F++    
Sbjct: 178 SPIERIMYTVESARVEQRTDLDKLIIEMETNGTIDPEDAIRKAATILAQQLEAFVDLRGV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++     I  +   F P LL+ V++LEL+VRS NCL+ E+I Y+GDL+Q+TE ++L+  N
Sbjct: 238 REPE---IKEEKPEFEPVLLRPVDDLELTVRSANCLKAESIHYIGDLVQKTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP+S+ E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMKLDNWPPKSLLE 328


>gi|58415830|emb|CAH57329.1| RNA polymerase alpha-subunit [Vibrio ezurae]
 gi|58415832|emb|CAH57330.1| RNA polymerase alpha-subunit [Vibrio ezurae]
 gi|58415834|emb|CAH57331.1| RNA polymerase alpha-subunit [Vibrio ezurae]
          Length = 309

 Score =  309 bits (793), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 137/315 (43%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA        +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNADIAMRIKVERGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + + +   
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVQEPI 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 E---EKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|298491422|ref|YP_003721599.1| DNA-directed RNA polymerase subunit alpha ['Nostoc azollae' 0708]
 gi|298233340|gb|ADI64476.1| DNA-directed RNA polymerase, alpha subunit ['Nostoc azollae' 0708]
          Length = 314

 Score =  309 bits (793), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 105/312 (33%), Positives = 171/312 (54%), Gaps = 11/312 (3%)

Query: 14  NIEYIVLGQEEEN--RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE +    EE     +  + EPL RG   T+GNALRRVL+S+L G A+TAV+IDGV HE
Sbjct: 5   QIECVESNTEESRSHYSKFVLEPLERGQGITVGNALRRVLLSNLEGTAVTAVRIDGVSHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            +++ GV ED+ +I++ +K + LK      +   +   GP  VTA      +++EV++P 
Sbjct: 65  FATVPGVREDVLEILMRMKEVILKNYSSQPQIGRLLVNGPVTVTAAHFDLPSEVEVIDPT 124

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  +     + ME  + +G GY   +  R E   +  + ID+++ P++KV+Y+VE AR
Sbjct: 125 QYVATIADGGKLEMEFRIERGKGYRTVERGREEATSLDFLQIDSVFMPVRKVNYSVEEAR 184

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            G     D+L + + T+GSI+ +++++ A+ IL D      +      +   DI     P
Sbjct: 185 -GDGSLKDRLLLEVWTNGSISPQEALSSAAGILVDLFNPLKDISLEPTDTGSDI-----P 238

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL+LSVR+ NCL+   +  + DL+  T+ D+L + NFG+KS  E+   L 
Sbjct: 239 DDPTAQIPIEELQLSVRAYNCLKRAQVNSVADLLDYTQEDLLEIKNFGQKSAEEVVEALQ 298

Query: 312 TMGLFLGMNLPD 323
                LG+ LP 
Sbjct: 299 R---RLGITLPQ 307


>gi|149197867|ref|ZP_01874916.1| DNA-directed RNA polymerase subunit alpha [Lentisphaera araneosa
           HTCC2155]
 gi|149139088|gb|EDM27492.1| DNA-directed RNA polymerase subunit alpha [Lentisphaera araneosa
           HTCC2155]
          Length = 341

 Score =  309 bits (793), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 132/324 (40%), Positives = 188/324 (58%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            +      E     IAEP  +GF HTLGN LRRVL+ SL G A+T ++IDGVLHE +   
Sbjct: 15  VLDEATATEKYGKFIAEPFEKGFGHTLGNGLRRVLLHSLEGVAVTWIKIDGVLHEYAQAA 74

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
            V ED+T+I+LN K +     GD  +++ +     G VTA DI T    +V+NP+  IC 
Sbjct: 75  DVVEDVTEIVLNFKNVRFTAEGDLPRKLELRANTKGPVTAADIVTDGVTQVVNPEQYICT 134

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           LD D  +R+E  V+ G G+  A  ++    PIGLI +D+L+SPI++VSY V   R GQ+ 
Sbjct: 135 LDKDTPLRIEFEVASGRGWKSADDNKPSEAPIGLIPVDSLFSPIERVSYDVSDTRVGQMT 194

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           DYDKL + I TDG I+ ED++  ++ IL+D L +F +              +       +
Sbjct: 195 DYDKLELEIWTDGRISPEDALRKSAIILRDHLCVFTDDNPEDSTASLIQTPEDEAILSKM 254

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
           L  V  +ELSVR+ NCLR   I Y+G+LIQ++E++ML+  NFG+KSL EIK  +  MG+ 
Sbjct: 255 LIPVTSVELSVRAQNCLRNAEIKYLGELIQKSESEMLKYRNFGKKSLDEIKDKMLEMGIT 314

Query: 317 LGMNLPDWPPESIEELAKKYEDKC 340
           L M L D    +  +  +K E K 
Sbjct: 315 LNMKLKDEVRVAFNKKLEKEEMKS 338


>gi|58416086|emb|CAH57457.1| RNA polymerase alpha-subunit [Vibrio tapetis]
 gi|58416088|emb|CAH57458.1| RNA polymerase alpha-subunit [Vibrio tapetis]
 gi|58416090|emb|CAH57459.1| RNA polymerase alpha-subunit [Vibrio tapetis]
          Length = 309

 Score =  309 bits (792), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 137/315 (43%), Positives = 203/315 (64%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQVSATHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +K+  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA        +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  ++ IL +QL  F++  + +     
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRSATILAEQLDAFVDLRDIRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|58415898|emb|CAH57363.1| RNA polymerase alpha-subunit [Vibrio ichthyoenteri]
 gi|58415900|emb|CAH57364.1| RNA polymerase alpha-subunit [Vibrio ichthyoenteri]
 gi|58415902|emb|CAH57365.1| RNA polymerase alpha-subunit [Vibrio ichthyoenteri]
 gi|58416014|emb|CAH57421.1| RNA polymerase alpha-subunit [Vibrio scophthalmi LMG 19158]
 gi|58416016|emb|CAH57422.1| RNA polymerase alpha-subunit [Vibrio scophthalmi]
 gi|58416018|emb|CAH57423.1| RNA polymerase alpha-subunit [Vibrio scophthalmi]
          Length = 309

 Score =  309 bits (792), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 137/315 (43%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K+
Sbjct: 118 TNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYSVDAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|58415866|emb|CAH57347.1| RNA polymerase alpha-subunit [Vibrio halioticoli]
 gi|58415868|emb|CAH57348.1| RNA polymerase alpha-subunit [Vibrio halioticoli]
 gi|58415870|emb|CAH57349.1| RNA polymerase alpha-subunit [Vibrio halioticoli]
 gi|58415950|emb|CAH57389.1| RNA polymerase alpha-subunit [Vibrio neonatus]
 gi|58415952|emb|CAH57390.1| RNA polymerase alpha-subunit [Vibrio neonatus]
 gi|58415954|emb|CAH57391.1| RNA polymerase alpha-subunit [Vibrio neonatus]
          Length = 309

 Score =  309 bits (792), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 137/315 (43%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDDVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA        +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNADIAMRIKVERGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + + +   
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVQEPI 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 E---EKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|58415948|emb|CAH57388.1| RNA polymerase alpha-subunit [Vibrio navarrensis]
          Length = 309

 Score =  309 bits (792), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 137/315 (43%), Positives = 204/315 (64%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA +SP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|58415794|emb|CAH57311.1| RNA polymerase alpha-subunit [Vibrio cincinnatiensis]
          Length = 309

 Score =  309 bits (792), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 134/315 (42%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++        +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRLGENKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLD-VDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
           +NP+HVIC+L   +A + M + V +G GYVPA    H   +  PIG + +DA +SP+ K+
Sbjct: 118 VNPEHVICHLTSDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|58415962|emb|CAH57395.1| RNA polymerase alpha-subunit [Vibrio nereis]
          Length = 309

 Score =  309 bits (792), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 136/315 (43%), Positives = 204/315 (64%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +++LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEVLLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|58416028|emb|CAH57428.1| RNA polymerase alpha-subunit [Vibrio sp. R-21415]
          Length = 309

 Score =  309 bits (792), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 137/315 (43%), Positives = 203/315 (64%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEISMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|75906938|ref|YP_321234.1| DNA-directed RNA polymerase subunit alpha [Anabaena variabilis ATCC
           29413]
 gi|119366663|sp|Q3MF97|RPOA_ANAVT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|75700663|gb|ABA20339.1| DNA-directed RNA polymerase subunit alpha [Anabaena variabilis ATCC
           29413]
          Length = 315

 Score =  309 bits (792), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 103/312 (33%), Positives = 169/312 (54%), Gaps = 10/312 (3%)

Query: 14  NIEYIVLGQEEEN--RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE +    EE     +  I EPL RG   T+GNALRRVL+S+L G A+TAV+I GV HE
Sbjct: 5   QIECVESNTEESRNHYSKFILEPLERGQGTTVGNALRRVLLSNLEGTAVTAVRIAGVSHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            +++ GV ED+ +II+ +K + LK      +   +   GP  +TA      +++EV++P 
Sbjct: 65  FATVPGVREDVLEIIMRMKEVILKSYSSQAQIGRLLVNGPTTITASHFDLPSEVEVIDPT 124

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  +     + ME  + +G GY   +  R E   +  + ID+++ P++KV+Y+VE  R
Sbjct: 125 QYVATIAEGGKLEMEFRIERGKGYRTVERGREEATSLDFLQIDSIFMPVRKVNYSVEEVR 184

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
               +  D+L + + T+GSI+ +++++ A+ IL D      +      +   DI     P
Sbjct: 185 ADGSIPKDRLLLEVWTNGSISPQEALSSAAGILVDLFNPLKDISLEPTDTNSDI-----P 239

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL+LSVR+ NCL+   +  + DL+  T+ D+L + NFG+KS  E+   L 
Sbjct: 240 DDPTAQIPIEELQLSVRAYNCLKRAQVNSVADLLDYTQEDLLEIKNFGQKSAEEVVEALQ 299

Query: 312 TMGLFLGMNLPD 323
                LG+ LP 
Sbjct: 300 R---RLGITLPQ 308


>gi|58415744|emb|CAH57286.1| RNA polymerase alpha-subunit [Vibrio alginolyticus]
          Length = 309

 Score =  309 bits (792), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 137/315 (43%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +++LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEVLLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H+  +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHNEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASCGLSLG 309


>gi|58416006|emb|CAH57417.1| RNA polymerase alpha-subunit [Vibrio rotiferianus]
 gi|58416008|emb|CAH57418.1| RNA polymerase alpha-subunit [Vibrio rotiferianus]
 gi|58416030|emb|CAH57429.1| RNA polymerase alpha-subunit [Vibrio sp. R-21416]
 gi|58416034|emb|CAH57431.1| RNA polymerase alpha-subunit [Vibrio sp. R-21422]
 gi|58416104|emb|CAH57466.1| RNA polymerase alpha-subunit [Vibrio vulnificus]
 gi|58416106|emb|CAH57467.1| RNA polymerase alpha-subunit [Vibrio vulnificus]
          Length = 309

 Score =  309 bits (791), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 138/315 (43%), Positives = 204/315 (64%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|58415918|emb|CAH57373.1| RNA polymerase alpha-subunit [Vibrio mediterranei]
 gi|58415920|emb|CAH57374.1| RNA polymerase alpha-subunit [Vibrio mediterranei]
 gi|58415922|emb|CAH57375.1| RNA polymerase alpha-subunit [Vibrio mediterranei]
 gi|58415924|emb|CAH57376.1| RNA polymerase alpha-subunit [Vibrio mediterranei]
 gi|58415926|emb|CAH57377.1| RNA polymerase alpha-subunit [Vibrio mediterranei]
 gi|58415928|emb|CAH57378.1| RNA polymerase alpha-subunit [Vibrio mediterranei]
 gi|58416020|emb|CAH57424.1| RNA polymerase alpha-subunit [Vibrio shilonii AK1]
 gi|58416072|emb|CAH57450.1| RNA polymerase alpha-subunit [Vibrio sp. R-23697]
          Length = 309

 Score =  309 bits (791), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 138/315 (43%), Positives = 204/315 (64%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEISMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|17231683|ref|NP_488231.1| DNA-directed RNA polymerase subunit alpha [Nostoc sp. PCC 7120]
 gi|20139485|sp|Q8YPK3|RPOA_ANASP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|17133326|dbj|BAB75890.1| RNA polymerase alpha subunit [Nostoc sp. PCC 7120]
          Length = 315

 Score =  309 bits (791), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 103/312 (33%), Positives = 169/312 (54%), Gaps = 10/312 (3%)

Query: 14  NIEYIVLGQEEEN--RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE +    EE     +  I EPL RG   T+GNALRRVL+S+L G A+TAV+I GV HE
Sbjct: 5   QIECVESNTEESRNHYSKFILEPLERGQGTTVGNALRRVLLSNLEGTAVTAVRIAGVSHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            +++ GV ED+ +II+ +K + LK      +   +   GP  +TA      +++EV++P 
Sbjct: 65  FATVPGVREDVLEIIMRMKEVILKSYSSQAQIGRLLVNGPTTITASHFDLPSEVEVIDPT 124

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  +     + ME  + +G GY   +  R E   +  + ID+++ P++KV+Y+VE  R
Sbjct: 125 QYVATIAEGGKLEMEFRIERGKGYRTVERGREEATSLDFLQIDSIFMPVRKVNYSVEEVR 184

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
               +  D+L + + T+GSI+ +++++ A+ IL D      +      +   DI     P
Sbjct: 185 ADGSIPKDRLLLEVWTNGSISPQEALSSAAGILVDLFNPLKDISLEPTDTNSDI-----P 239

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL+LSVR+ NCL+   +  + DL+  T+ D+L + NFG+KS  E+   L 
Sbjct: 240 DDPTAQIPIEELQLSVRAYNCLKRAQVNSVADLLDYTQEDLLEIKNFGQKSAEEVVEALQ 299

Query: 312 TMGLFLGMNLPD 323
                LG+ LP 
Sbjct: 300 R---RLGITLPQ 308


>gi|90194028|gb|ABD92575.1| RpoA [Actinobacillus equuli subsp. equuli]
          Length = 300

 Score =  309 bits (791), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 136/300 (45%), Positives = 204/300 (68%), Gaps = 7/300 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
             +     +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED
Sbjct: 3   NNQFTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQED 62

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVD 140
           + +++LN+KG+ +K+S      +T+ K G G VTA DI    D+E++NP+HVIC+L D +
Sbjct: 63  ILEVLLNLKGLAVKVSNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPNHVICHLTDKN 122

Query: 141 AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           A + M + V +G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR  Q  D
Sbjct: 123 ASINMRIRVQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTD 182

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
            DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+P LL
Sbjct: 183 LDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEFDPILL 239

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 240 RPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 299


>gi|58416002|emb|CAH57415.1| RNA polymerase alpha-subunit [Vibrio proteolyticus]
 gi|58416004|emb|CAH57416.1| RNA polymerase alpha-subunit [Vibrio proteolyticus]
          Length = 309

 Score =  309 bits (791), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 138/315 (43%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|328813953|gb|AEB52092.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 250

 Score =  309 bits (791), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 112/250 (44%), Positives = 166/250 (66%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               + EPL RG+  TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T II
Sbjct: 1   YGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQII 60

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LNIK + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +       + 
Sbjct: 61  LNIKKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVR 120

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           +TV KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + 
Sbjct: 121 MTVKKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVW 180

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+GSI+  ++++LA++IL + L +F+N  +  K  +  +  +       L   +EEL+LS
Sbjct: 181 TNGSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLS 240

Query: 267 VRSTNCLRGE 276
           VRS NCL+  
Sbjct: 241 VRSYNCLKRA 250


>gi|58415996|emb|CAH57412.1| RNA polymerase alpha-subunit [Vibrio penaeicida]
          Length = 309

 Score =  309 bits (791), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 137/315 (43%), Positives = 203/315 (64%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +K+  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA        +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +YTVE+AR  Q  D DKL + ++T+G++  E+++  ++ IL +QL  F++  + +     
Sbjct: 178 AYTVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRSATILAEQLDAFVDLRDIRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|282898333|ref|ZP_06306324.1| DNA-directed RNA polymerase, alpha subunit [Raphidiopsis brookii
           D9]
 gi|281196864|gb|EFA71769.1| DNA-directed RNA polymerase, alpha subunit [Raphidiopsis brookii
           D9]
          Length = 314

 Score =  309 bits (791), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 101/312 (32%), Positives = 168/312 (53%), Gaps = 11/312 (3%)

Query: 14  NIEYIVLGQEEEN--RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE +    EE        + EPL RG   T+GNALRRVL+S+L G A+TAV+I GV HE
Sbjct: 5   QIECVESSTEESRNHYGRFVLEPLERGQGTTVGNALRRVLLSNLEGTAVTAVRIAGVTHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            +++ GV ED+ +II+ +K + LK      +   +   GP  VTA       ++EV++P 
Sbjct: 65  FATVPGVREDVMEIIMRMKEVILKSYSHQPQIGRLLVTGPTTVTAAHFDLPGEVEVIDPT 124

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  L     + ME  + +G GY   +  R E   +  + ID+++ P++KV+Y+VE +R
Sbjct: 125 QYVATLAEGGKLEMEFRIERGKGYRTVEKGREEATSLDFLQIDSVFMPVRKVNYSVEESR 184

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            G     D+L + + T+GSI+ +++++ ++ IL +      +       ++       +P
Sbjct: 185 -GDGSLKDRLLLEVWTNGSISPQEALSSSAAILVELFNPLKDIS-----LEPTDMGLDMP 238

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL+LSVR+ NCL+   +  + DL+  T+ D+L + NFG+KS  E+   L 
Sbjct: 239 DDPTAQIPIEELQLSVRAYNCLKRAQVNSVADLLDYTQEDLLEIKNFGQKSAEEVVEALQ 298

Query: 312 TMGLFLGMNLPD 323
                LG+ LP 
Sbjct: 299 R---RLGITLPQ 307


>gi|283768437|ref|ZP_06341349.1| DNA-directed RNA polymerase, alpha subunit [Bulleidia extructa
           W1219]
 gi|283104829|gb|EFC06201.1| DNA-directed RNA polymerase, alpha subunit [Bulleidia extructa
           W1219]
          Length = 319

 Score =  309 bits (791), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 121/301 (40%), Positives = 179/301 (59%), Gaps = 5/301 (1%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E EN    I  PL RGF  T+GNALRRVL+SSL GAA+ ++++D V HE +SI GV ED+
Sbjct: 16  ESENYGRFILTPLERGFGTTIGNALRRVLLSSLPGAAVFSIKVDQVYHEFTSIPGVREDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           + IILN+K + +K+  D    + I  +GPG V A D+     +E++N D VI NL+V A 
Sbjct: 76  SMIILNLKQLVMKIEDDEEYTLQISAKGPGTVKAADLIVPAQVEIVNKDLVIANLEVGAS 135

Query: 143 VRMELTVSKGHGYVPAKHHRTE----NDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
           + ME+ V  G GYV A  ++      +  IG +  D++Y+P+ KV+Y VE  R G+ + Y
Sbjct: 136 LEMEIKVQNGRGYVSADINKQLRSGVSQGIGTVYTDSIYTPVTKVAYHVEPTRVGENVKY 195

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-FNPALL 257
           D+L+M + TDGSI  + +++LA++IL D L +     +        I   +    N    
Sbjct: 196 DELTMEVTTDGSINPQKALSLAAKILVDHLEIVAGINDEVMISDSVIKQSTAEKPNKGHQ 255

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +E+L+LSVRS NCL+   I  + +L Q+TE +M+R+ N G+KSL E+K  L  MG   
Sbjct: 256 MMIEDLDLSVRSYNCLKRAGIQTVDELTQKTEDEMMRVRNLGKKSLKEVKDKLIEMGFGF 315

Query: 318 G 318
            
Sbjct: 316 K 316


>gi|58415822|emb|CAH57325.1| RNA polymerase alpha-subunit [Vibrio diazotrophicus]
          Length = 309

 Score =  309 bits (791), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 135/315 (42%), Positives = 204/315 (64%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDV-DAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L   +A + M + V +G GYVPA    H   +  PIG + +DA +SP+ K+
Sbjct: 118 ANPEHVICHLTDSNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+V+ AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYSVDPARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|328813987|gb|AEB52109.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 262

 Score =  308 bits (790), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 118/261 (45%), Positives = 171/261 (65%), Gaps = 2/261 (0%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
              +N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED
Sbjct: 2   DGNDNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTED 61

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A
Sbjct: 62  VTAIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGA 121

Query: 142 VVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              M +T + G GYV A+ ++   ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+D
Sbjct: 122 HFHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFD 181

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL++ + T+GSIT  ++++L+++IL D L +F+N  +  K     +  +       L   
Sbjct: 182 KLTLDVWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEMT 241

Query: 260 VEELELSVRSTNCLRGENIVY 280
           +EEL+LSVRS NCL+   I  
Sbjct: 242 IEELDLSVRSYNCLKRAGINT 262


>gi|146742342|gb|ABQ42692.1| RNA polymerase alpha subunit [Vibrio porteresiae]
 gi|156106873|gb|ABU49636.1| RNA polymerase alpha subunit [Vibrio porteresiae]
          Length = 307

 Score =  308 bits (790), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 135/313 (43%), Positives = 203/313 (64%), Gaps = 11/313 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T  +I+GVLHE
Sbjct: 1   PRLVD---IEQISATHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEAEIEGVLHE 57

Query: 72  ISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
            S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E++NP
Sbjct: 58  YSTKEGVQEDILEILLNLKGLAVRVADGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNP 117

Query: 131 DHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYT 186
           +HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA +SP+ K++Y+
Sbjct: 118 EHVICHLTDDNAEIAMRIKVQRGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYS 177

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           V +AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +        
Sbjct: 178 VAAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EK 234

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EI
Sbjct: 235 EEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEI 294

Query: 307 KGVLGTMGLFLGM 319
           K VL + GL LGM
Sbjct: 295 KDVLASRGLSLGM 307


>gi|300244653|gb|ADJ93835.1| RNA polymerase alpha subunit [Vibrio sp. G21]
          Length = 309

 Score =  308 bits (790), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 137/315 (43%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVYITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ +L +QL  F++  + +     
Sbjct: 178 AYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATVLAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|58415964|emb|CAH57396.1| RNA polymerase alpha-subunit [Vibrio nigripulchritudo]
          Length = 309

 Score =  308 bits (790), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 138/315 (43%), Positives = 204/315 (64%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +K+  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVKVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA        +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +YTVE+AR  Q  D DKL + ++T+G++  E+++  ++ IL +QL  F++  + +     
Sbjct: 178 AYTVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRSATILAEQLDAFVDLRDIRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|269925858|ref|YP_003322481.1| DNA-directed RNA polymerase, alpha subunit [Thermobaculum terrenum
           ATCC BAA-798]
 gi|269789518|gb|ACZ41659.1| DNA-directed RNA polymerase, alpha subunit [Thermobaculum terrenum
           ATCC BAA-798]
          Length = 367

 Score =  308 bits (790), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 125/320 (39%), Positives = 188/320 (58%), Gaps = 8/320 (2%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           +  EL  P  +E I +    +N       PL  G+  T+GNALRRVL+SSL GAAIT+VQ
Sbjct: 21  SVIELTTP-KVECIGI---ADNYGRFSISPLAPGYGLTIGNALRRVLLSSLEGAAITSVQ 76

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           I+G  HE  ++ GV ED+TDIILNIK I ++   D    + +   GP VVTA DI+   D
Sbjct: 77  IEGARHEFMALPGVKEDVTDIILNIKRIRVRSYSDRPVTLRLEATGPKVVTAADIRPHAD 136

Query: 125 IEVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           +++++ D  I  LD  DA + M+LTV KG GYVPA+    +   IG I +DA+YSP+ KV
Sbjct: 137 VDIVSLDQPIATLDSEDATLSMQLTVQKGRGYVPAES--QDFFEIGRIPVDAIYSPVTKV 194

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE  R GQ  DYD L + I TDG+I   ++++ A+ IL  Q  +   +   +     
Sbjct: 195 NYVVERTRVGQRTDYDNLIIEIWTDGTIAPGEALSQAASILVGQFQIIAAYANAETSFGI 254

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           ++  +++       + ++EL LS R+ N L+  +I  +G ++ +T+ D+L + NFG KSL
Sbjct: 255 ELPTETMSVPEVDNRSIDELGLSARTLNSLKRAHITTVGQVLSKTKDDLLSIRNFGDKSL 314

Query: 304 VEIKGVLGTMGLFLGMNLPD 323
            E++  L   G +L  +LP+
Sbjct: 315 HELEAKLKEFG-YLPSDLPE 333


>gi|58415976|emb|CAH57402.1| RNA polymerase alpha-subunit [Vibrio pacinii]
 gi|58415978|emb|CAH57403.1| RNA polymerase alpha-subunit [Vibrio pacinii]
 gi|58415980|emb|CAH57404.1| RNA polymerase alpha-subunit [Vibrio pacinii]
          Length = 309

 Score =  308 bits (790), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 136/315 (43%), Positives = 204/315 (64%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ + +  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVHVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L + +A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTNDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|282899976|ref|ZP_06307937.1| DNA-directed RNA polymerase, alpha subunit [Cylindrospermopsis
           raciborskii CS-505]
 gi|281195246|gb|EFA70182.1| DNA-directed RNA polymerase, alpha subunit [Cylindrospermopsis
           raciborskii CS-505]
          Length = 314

 Score =  308 bits (790), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 101/312 (32%), Positives = 168/312 (53%), Gaps = 11/312 (3%)

Query: 14  NIEYIVLGQEEEN--RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE +    EE        + EPL RG   T+GNALRRVL+S+L G A+TAV+I GV HE
Sbjct: 5   QIECVESSTEESRNHYGKFVLEPLERGQGTTVGNALRRVLLSNLEGTAVTAVRIAGVTHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            +++ GV ED+ +II+ +K + LK      +   +   GP  VTA       ++EV++P 
Sbjct: 65  FATVPGVREDVMEIIMRMKEVILKSYSHQPQIGRLLVTGPTTVTAAHFDLPGEVEVIDPT 124

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  L     + ME  + +G GY   +  R E   +  + ID+++ P++KV+Y+VE +R
Sbjct: 125 QYVATLAEGGKLEMEFRIERGKGYRTVEKGREEATSLDFLQIDSVFMPVRKVNYSVEESR 184

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            G     D+L + + T+GSI+ +++++ ++ IL +      +       ++       +P
Sbjct: 185 -GDGSLKDRLLLEVWTNGSISPQEALSSSAAILVELFNPLKDIS-----LEPTDMGLDMP 238

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL+LSVR+ NCL+   +  + DL+  T+ D+L + NFG+KS  E+   L 
Sbjct: 239 DDPTAQIPIEELQLSVRAYNCLKRAQVNSVADLLDYTQEDLLEIKNFGQKSAEEVVEALQ 298

Query: 312 TMGLFLGMNLPD 323
                LG+ LP 
Sbjct: 299 R---RLGITLPQ 307


>gi|58415860|emb|CAH57344.1| RNA polymerase alpha-subunit [Vibrio gallicus]
 gi|58416084|emb|CAH57456.1| RNA polymerase alpha-subunit [Vibrio superstes]
 gi|179184721|gb|ACB78158.1| RNA polymerase alpha subunit [Vibrio superstes]
 gi|179184755|gb|ACB78159.1| RNA polymerase alpha subunit [Vibrio gallicus]
          Length = 309

 Score =  308 bits (790), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 138/315 (43%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -KEEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|58415946|emb|CAH57387.1| RNA polymerase alpha-subunit [Vibrio natriegens]
          Length = 309

 Score =  308 bits (790), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 137/315 (43%), Positives = 204/315 (64%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GY+PA    H   +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYIPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|58415750|emb|CAH57289.1| RNA polymerase alpha-subunit [Listonella anguillarum]
 gi|58415752|emb|CAH57290.1| RNA polymerase alpha-subunit [Listonella anguillarum]
 gi|58415966|emb|CAH57397.1| RNA polymerase alpha-subunit [Vibrio ordalii]
 gi|58415968|emb|CAH57398.1| RNA polymerase alpha-subunit [Vibrio ordalii]
 gi|58415970|emb|CAH57399.1| RNA polymerase alpha-subunit [Vibrio ordalii]
 gi|58415972|emb|CAH57400.1| RNA polymerase alpha-subunit [Vibrio ordalii]
          Length = 309

 Score =  308 bits (790), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 137/315 (43%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +G+ ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGIQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K+
Sbjct: 118 TNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|120437149|ref|YP_862835.1| DNA-directed RNA polymerase subunit alpha [Gramella forsetii
           KT0803]
 gi|158512451|sp|A0M573|RPOA_GRAFK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|117579299|emb|CAL67768.1| DNA-directed RNA polymerase alpha subunit [Gramella forsetii
           KT0803]
          Length = 330

 Score =  308 bits (790), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 125/325 (38%), Positives = 194/325 (59%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT+V+I+G
Sbjct: 5   NFQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGFAITSVRIEG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VND 124
           V HE S+I GV ED+T+IILN+K +  K   D   ++ VTI   G   +TAG  Q  ++ 
Sbjct: 62  VDHEFSTIAGVVEDVTEIILNLKQVRFKRQIDEIDNESVTISVSGEEQLTAGHFQKFISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLNPD VIC++D    + ME+T+ KG GYVPA+ ++  N P+G I +D++Y+PIK V 
Sbjct: 122 FQVLNPDQVICHMDKKVSLNMEITIEKGRGYVPAEENKKANAPLGTIFVDSIYTPIKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y++E+ R  Q  DY+KL   I +DGSI  +D++  A++ L     +F    I  E  +  
Sbjct: 182 YSIENFRVEQKTDYEKLVFEIISDGSIHPKDALTEAAKTLIHHFMLFSDERITLEADEIA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+
Sbjct: 242 QTETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSYNKNDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E++ ++   GL  GM+L  + 
Sbjct: 302 KSLTELEELVSNKGLNFGMDLSKYK 326


>gi|58415820|emb|CAH57324.1| RNA polymerase alpha-subunit [Vibrio diazotrophicus]
 gi|58415824|emb|CAH57326.1| RNA polymerase alpha-subunit [Vibrio diazotrophicus]
          Length = 309

 Score =  308 bits (790), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 135/315 (42%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDV-DAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L   +A + M + V +G GYVPA    H   +  PIG + +DA +SP+ K+
Sbjct: 118 ANPEHVICHLTDSNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|58415738|emb|CAH57283.1| RNA polymerase alpha-subunit [Vibrio aestuarianus]
          Length = 309

 Score =  308 bits (790), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 137/315 (43%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K+
Sbjct: 118 TNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|186684486|ref|YP_001867682.1| DNA-directed RNA polymerase subunit alpha [Nostoc punctiforme PCC
           73102]
 gi|186466938|gb|ACC82739.1| DNA-directed RNA polymerase, alpha subunit RpoA [Nostoc punctiforme
           PCC 73102]
          Length = 315

 Score =  308 bits (789), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 102/311 (32%), Positives = 171/311 (54%), Gaps = 10/311 (3%)

Query: 14  NIEYIVLGQEEEN--RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE +    EE     +  + EPL RG   T+GNALRRVL+S+L G A+TAV+I GV HE
Sbjct: 5   QIECVESNTEESRNHYSKFVLEPLERGQGTTVGNALRRVLLSNLEGTAVTAVRIAGVSHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            +++ GV ED+ +I++ +K + LK      +   +   GP  +TA      +++EV++P 
Sbjct: 65  FATVPGVREDVLEILMRMKEVILKNYSSQPQIGRLLVSGPTTITAAHFDLPSEVEVIDPT 124

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  +     + ME  + KG GY   +  R E   +  + ID+++ P++KV+Y+VE +R
Sbjct: 125 QYVATIAEGGKLEMEFRIEKGKGYRTVERGREEATSLDFLQIDSIFMPVRKVNYSVEESR 184

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
              ++  D+L + + T+GSI+ +++++ A+ IL D      +      +   DI     P
Sbjct: 185 GEGLIPKDRLLLEVWTNGSISPQEALSSAAGILVDLFNPLKDISLEPTDTGSDI-----P 239

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL+LSVR+ NCL+   +  + DL+  T+ D+L + NFG+KS  E+   L 
Sbjct: 240 DDPTAQIPIEELQLSVRAYNCLKRAQVNSVADLLDYTQEDLLEIKNFGQKSAEEVVEALQ 299

Query: 312 TMGLFLGMNLP 322
                LG+ LP
Sbjct: 300 R---RLGITLP 307


>gi|295698626|ref|YP_003603281.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Riesia
           pediculicola USDA]
 gi|291157272|gb|ADD79717.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Riesia
           pediculicola USDA]
          Length = 344

 Score =  308 bits (789), Expect = 8e-82,   Method: Composition-based stats.
 Identities = 140/327 (42%), Positives = 219/327 (66%), Gaps = 9/327 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E IKP   +   + +    +  +  EPL RGF HT+GNALRR+L+SS+ G A+T V+IDG
Sbjct: 22  EFIKPKLADIQKISK---TQARITLEPLERGFGHTIGNALRRILLSSMPGFAVTEVEIDG 78

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           +LHE S+  GV ED+ +I+LN+K + +++ G     +++ K+G   VTA DI+   ++E+
Sbjct: 79  ILHEYSTKDGVQEDIVEILLNLKELGVRIYGKEEIVLSLVKKGICTVTAQDIERNENVEI 138

Query: 128 LNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVS 184
           +NP+HVIC++ D + V++M + ++KG GYVP     +E  N  IG + +DA YSP+++VS
Sbjct: 139 INPEHVICHITDENTVIKMRIKINKGRGYVPVSSRSSEEQNRSIGRLLVDACYSPVERVS 198

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+ R  Q  D DKL + I+T+G+I  ++++  ++ IL +QL  F+  +    E K++
Sbjct: 199 YKVEATRVEQRTDLDKLIIEIETNGTIDPKEAIHKSATILANQLESFVELQN---EDKKE 255

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +      F+P LLK V++LEL+VRS NCL+ E+I Y+GDL+QRTE ++L+  N G+KSL+
Sbjct: 256 VQEDHPKFDPMLLKTVDDLELTVRSANCLKTESIHYIGDLVQRTEVELLKTPNLGKKSLM 315

Query: 305 EIKGVLGTMGLFLGMNLPDWPPESIEE 331
           EIK +L + GL LGM L +WPP   +E
Sbjct: 316 EIKDILASRGLSLGMKLENWPPSKKDE 342


>gi|307154818|ref|YP_003890202.1| DNA-directed RNA polymerase subunit alpha [Cyanothece sp. PCC 7822]
 gi|306985046|gb|ADN16927.1| DNA-directed RNA polymerase, alpha subunit [Cyanothece sp. PCC
           7822]
          Length = 314

 Score =  308 bits (789), Expect = 8e-82,   Method: Composition-based stats.
 Identities = 101/302 (33%), Positives = 168/302 (55%), Gaps = 7/302 (2%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               I EPL RG   T+GNALRRVL+S+L GAA+TA++I GV HE ++I GV ED+ ++I
Sbjct: 20  YGKFILEPLDRGQGTTVGNALRRVLLSNLEGAAVTALRIAGVNHEFATISGVREDVMELI 79

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+K I LK      +   +   GP  VTAG     +++E+++P   +  L   + + ME
Sbjct: 80  LNMKEITLKSYTSQPQIGRLVATGPATVTAGQFDLPSEVEIVDPSQYVATLAEGSKLEME 139

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
             + KG GY   +  + ++  +  + ID+++ P+ KV+Y+VE  R       D+L++ I 
Sbjct: 140 FRIEKGKGYRAIERGKDDSTSLDFLQIDSVFMPVTKVNYSVEDVRVDGTSSKDRLTIEIW 199

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+GS+  +++++ A+ I+ D      +  E    ++   +      NP     +EEL+LS
Sbjct: 200 TNGSVNPKEALSEAAAIIVDLFSPLRDLNE----LEATQSDYPDEVNPESQIPIEELQLS 255

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           VR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L      LG+ LP    
Sbjct: 256 VRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEEVIEAL---QKRLGITLPQEKA 312

Query: 327 ES 328
           ++
Sbjct: 313 KT 314


>gi|58415770|emb|CAH57299.1| RNA polymerase alpha-subunit [Vibrio chagasii]
 gi|58415772|emb|CAH57300.1| RNA polymerase alpha-subunit [Vibrio chagasii]
 gi|58415774|emb|CAH57301.1| RNA polymerase alpha-subunit [Vibrio chagasii]
 gi|58415812|emb|CAH57320.1| RNA polymerase alpha-subunit [Vibrio cyclitrophicus]
 gi|58415814|emb|CAH57321.1| RNA polymerase alpha-subunit [Vibrio cyclitrophicus]
 gi|58415816|emb|CAH57322.1| RNA polymerase alpha-subunit [Vibrio cyclitrophicus]
 gi|58415846|emb|CAH57337.1| RNA polymerase alpha-subunit [Vibrio fortis]
 gi|58415848|emb|CAH57338.1| RNA polymerase alpha-subunit [Vibrio fortis]
 gi|58415850|emb|CAH57339.1| RNA polymerase alpha-subunit [Vibrio fortis]
 gi|58415904|emb|CAH57366.1| RNA polymerase alpha-subunit [Vibrio kanaloae]
 gi|58415906|emb|CAH57367.1| RNA polymerase alpha-subunit [Vibrio kanaloae]
 gi|58415908|emb|CAH57368.1| RNA polymerase alpha-subunit [Vibrio lentus]
 gi|58415910|emb|CAH57369.1| RNA polymerase alpha-subunit [Vibrio lentus]
 gi|58415912|emb|CAH57370.1| RNA polymerase alpha-subunit [Vibrio lentus]
 gi|58415914|emb|CAH57371.1| RNA polymerase alpha-subunit [Vibrio lentus]
 gi|58415992|emb|CAH57410.1| RNA polymerase alpha-subunit [Listonella pelagia]
 gi|58415994|emb|CAH57411.1| RNA polymerase alpha-subunit [Listonella pelagia]
 gi|58415998|emb|CAH57413.1| RNA polymerase alpha-subunit [Vibrio pomeroyi]
 gi|58416000|emb|CAH57414.1| RNA polymerase alpha-subunit [Vibrio pomeroyi]
 gi|58416022|emb|CAH57425.1| RNA polymerase alpha-subunit [Vibrio sp. R-21409]
 gi|58416040|emb|CAH57434.1| RNA polymerase alpha-subunit [Vibrio sp. R-21431]
 gi|58416054|emb|CAH57441.1| RNA polymerase alpha-subunit [Vibrio sp. R-23685]
 gi|58416056|emb|CAH57442.1| RNA polymerase alpha-subunit [Vibrio sp. R-23689]
 gi|58416058|emb|CAH57443.1| RNA polymerase alpha-subunit [Vibrio sp. R-23690]
 gi|58416060|emb|CAH57444.1| RNA polymerase alpha-subunit [Vibrio sp. R-23691]
 gi|58416064|emb|CAH57446.1| RNA polymerase alpha-subunit [Vibrio sp. R-23693]
 gi|58416074|emb|CAH57451.1| RNA polymerase alpha-subunit [Vibrio splendidus]
 gi|58416076|emb|CAH57452.1| RNA polymerase alpha-subunit [Vibrio splendidus]
 gi|58416078|emb|CAH57453.1| RNA polymerase alpha-subunit [Vibrio splendidus]
 gi|58416080|emb|CAH57454.1| RNA polymerase alpha-subunit [Vibrio splendidus]
 gi|58416082|emb|CAH57455.1| RNA polymerase alpha-subunit [Vibrio splendidus]
 gi|58416092|emb|CAH57460.1| RNA polymerase alpha-subunit [Vibrio tasmaniensis]
 gi|58416094|emb|CAH57461.1| RNA polymerase alpha-subunit [Vibrio tasmaniensis]
 gi|58416096|emb|CAH57462.1| RNA polymerase alpha-subunit [Vibrio tasmaniensis]
 gi|179184408|gb|ACB78146.1| RNA polymerase alpha subunit [Vibrio sp. CECT 7226]
 gi|179184453|gb|ACB78148.1| RNA polymerase alpha subunit [Vibrio sp. CECT 7224]
 gi|179184476|gb|ACB78149.1| RNA polymerase alpha subunit [Vibrio sp. CECT 7225]
          Length = 309

 Score =  308 bits (789), Expect = 8e-82,   Method: Composition-based stats.
 Identities = 138/315 (43%), Positives = 204/315 (64%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|254444876|ref|ZP_05058352.1| DNA-directed RNA polymerase, alpha subunit [Verrucomicrobiae
           bacterium DG1235]
 gi|198259184|gb|EDY83492.1| DNA-directed RNA polymerase, alpha subunit [Verrucomicrobiae
           bacterium DG1235]
          Length = 307

 Score =  308 bits (789), Expect = 9e-82,   Method: Composition-based stats.
 Identities = 128/307 (41%), Positives = 192/307 (62%), Gaps = 3/307 (0%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
           +  AEP   G+ HT+GN+LRR+L+SS+ GAAI++V+I+GV HE  S+ G+ ED+TDI+LN
Sbjct: 1   MFHAEPFEAGYGHTIGNSLRRILLSSIEGAAISSVKIEGVSHEFQSVDGIVEDITDIVLN 60

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           +K + L        ++ I     G +TA DIQ  +++EV+NPD +IC LD +     EL 
Sbjct: 61  LKKVLLVCHKREGVKLMINTNRSGAITAADIQPDSNVEVINPDQIICTLDREMPFTAELE 120

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           +  G GY P   ++ E DPIG+I ID+L+SP+  V Y VE+   GQ+ DYDKL + + TD
Sbjct: 121 IKVGRGYCPGDDNKDEEDPIGVIAIDSLFSPVSLVKYAVEATLVGQITDYDKLLLEVWTD 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKE---DINVKSLPFNPALLKKVEELEL 265
           G IT +D++  A+ IL+  L +F N  +   E ++   +++ +       L   V E+EL
Sbjct: 181 GRITPDDALKQAAAILKHHLDVFDNVSDENYEFEDEGGEVSEEQNKLRKLLNMSVNEIEL 240

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           SVR+ NCL   NI  +G+L  ++E +ML+  NFG+KSL EIK  L ++GL LGM   +  
Sbjct: 241 SVRAANCLNNANITTVGELAMKSEQEMLKYRNFGKKSLNEIKDKLESLGLSLGMKFDERL 300

Query: 326 PESIEEL 332
            +S +EL
Sbjct: 301 LDSKKEL 307


>gi|179184854|gb|ACB78162.1| RNA polymerase alpha subunit [Aliivibrio finisterrensis]
          Length = 306

 Score =  308 bits (788), Expect = 9e-82,   Method: Composition-based stats.
 Identities = 140/312 (44%), Positives = 204/312 (65%), Gaps = 10/312 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  ++   +    E    +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE
Sbjct: 1   PRLVDIEQVSMTHE---KVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHE 57

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ NP+
Sbjct: 58  YSTKEGVQEDILEILLNLKGLAVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIANPE 117

Query: 132 HVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTV 187
           HVIC+L  D A + M + V +G GYVP+    H   +  PIG + IDA YSP+ K+SY+V
Sbjct: 118 HVICHLTDDNAEISMRIRVERGRGYVPSTARIHTEEDERPIGRLLIDATYSPVDKISYSV 177

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         
Sbjct: 178 EAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKE 234

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK
Sbjct: 235 EKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIK 294

Query: 308 GVLGTMGLFLGM 319
            VL + GL LGM
Sbjct: 295 DVLASRGLSLGM 306


>gi|126643071|ref|YP_001086055.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter baumannii
           ATCC 17978]
          Length = 310

 Score =  308 bits (788), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 137/301 (45%), Positives = 214/301 (71%), Gaps = 5/301 (1%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           I EPL RGF HTLGNALRR+L+SSL GAA+  V+I+GV HE S+++G+ +D+ +++LN+K
Sbjct: 2   ILEPLERGFGHTLGNALRRILLSSLPGAAVVEVEIEGVEHEYSTLEGLQQDIVELLLNLK 61

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           G+++K+   +   +T+ K+GPG +TA D++  +++EV+NP+H+I  L     ++M L VS
Sbjct: 62  GLSIKLFDQNEAYLTLEKQGPGDITAADLRLPHNVEVVNPEHLIGTLSATGSLKMRLKVS 121

Query: 151 KGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           +G GY  +     E +  P+G + +DA YSPIK+VSYTVE+AR  Q  D DKL + ++T+
Sbjct: 122 QGRGYETSDSRFPEGETRPVGRLQLDASYSPIKRVSYTVENARVEQRTDLDKLVIDLETN 181

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ ILQ Q+ +F++ ++ +  V ++   +    +P LL+ V++LEL+VR
Sbjct: 182 GTVDPEEAIRKAATILQQQIAIFVDLQKDQTPVAQEPREE---VDPILLRPVDDLELTVR 238

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPES 328
           S NCL+ ENI Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP S
Sbjct: 239 SANCLKAENIYYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASKGLQLGMRLENWPPAS 298

Query: 329 I 329
           +
Sbjct: 299 L 299


>gi|220906743|ref|YP_002482054.1| DNA-directed RNA polymerase subunit alpha [Cyanothece sp. PCC 7425]
 gi|219863354|gb|ACL43693.1| DNA-directed RNA polymerase, alpha subunit [Cyanothece sp. PCC
           7425]
          Length = 314

 Score =  308 bits (788), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 109/310 (35%), Positives = 170/310 (54%), Gaps = 9/310 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             +E  V     +  +  + EPL RG   T+GNALRRVL+S+L+G A+TAV+I GV HE 
Sbjct: 6   ECVESRVEADYSQ-YSQFVLEPLERGQGTTVGNALRRVLLSNLKGTAVTAVRIAGVNHEF 64

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED  DI+L +K + L+      +   +F +GP  VTA + +   D+EV+N DH
Sbjct: 65  ATIPGVREDALDILLRMKELVLRSYSPDPQIGRLFIQGPATVTAINFEVSPDVEVINLDH 124

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L  DA + ME  + +G GY   +  + E+  +  + IDA++ P++KV+YTVE AR 
Sbjct: 125 YIATLSADATLEMEFKIEQGKGYRAIERGKDESASLDFLQIDAIFMPVRKVNYTVEDARS 184

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           G +++ D+L + I T+GS+T ++++   + IL D      +      E            
Sbjct: 185 GGLVEKDRLVLEIWTNGSLTPQEALNQGASILVDLFNPLKDVPFRSSEPSHSTEEDET-- 242

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                  +E L LSVR+ NCL+   I  + DL++ ++ D+L + NFG KS  E+   L  
Sbjct: 243 ---NQIPIESLNLSVRAYNCLKRAQINTVADLLEYSQEDLLEIKNFGAKSAEEVIEALH- 298

Query: 313 MGLFLGMNLP 322
               LG+ LP
Sbjct: 299 --KNLGITLP 306


>gi|148655310|ref|YP_001275515.1| DNA-directed RNA polymerase subunit alpha [Roseiflexus sp. RS-1]
 gi|172048077|sp|A5USG2|RPOA_ROSS1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|148567420|gb|ABQ89565.1| DNA-directed RNA polymerase, alpha subunit [Roseiflexus sp. RS-1]
          Length = 323

 Score =  308 bits (788), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 124/304 (40%), Positives = 182/304 (59%), Gaps = 7/304 (2%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
            IE +      EN      EPL  G+ HTLGNALRRVL+SS+ GAAIT ++I+GV HE S
Sbjct: 8   KIEVVT---AAENYGRFKIEPLDPGYGHTLGNALRRVLLSSIPGAAITKIKIEGVFHEFS 64

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           +I GV ED+T+I+LNIKGI L+   +   ++++ KRG GVV A DI   +++E++NP+H 
Sbjct: 65  TIPGVKEDVTEIVLNIKGIRLRSYAERPVKISLSKRGAGVVRAADIDAPSNVEIVNPNHY 124

Query: 134 ICNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           IC +D  DA + ME+TV +G GY+PA     +  PIG I IDA+++P+ KV+Y VE  R 
Sbjct: 125 ICTIDRDDAAIDMEMTVERGRGYLPADQR--DALPIGEIPIDAIFTPVPKVNYVVEHIRV 182

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP- 251
           GQ  D D L + I TDG+I   D+++ A+++L        +F     E +       L  
Sbjct: 183 GQATDIDSLLIEIWTDGTIKPGDALSHAAQVLVQYSQTIADFNRLSTEAEPTTAPNGLAI 242

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL+LS R+ NCL+  +I  +G +++  E  +L + N G+KS+ EI+  L 
Sbjct: 243 PADIYDTPIEELDLSTRTYNCLKRADITKVGQVLEMDEKALLSVRNLGQKSMEEIRDKLI 302

Query: 312 TMGL 315
             G 
Sbjct: 303 ERGY 306


>gi|90193992|gb|ABD92557.1| RpoA [Histophilus somni]
          Length = 302

 Score =  307 bits (787), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 137/304 (45%), Positives = 204/304 (67%), Gaps = 7/304 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VDIEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGYAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+    +  +T+ K G G V A DI    D+E++NPDHVIC+L
Sbjct: 62  VQEDIIEVLLNLKGLAVKVQNKDNVFLTLSKSGIGPVVAADITHDGDVEIVNPDHVICHL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D +A + M + V +G GYVPA    H   E  PIG + +DA YSP+ +++Y V++AR  
Sbjct: 122 TDENASINMRIRVQRGRGYVPASSRVHSLDEERPIGRLLVDACYSPVDRIAYNVQAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLVIELETNGTIEPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + 
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLVSR 298

Query: 314 GLFL 317
           GL L
Sbjct: 299 GLSL 302


>gi|194334834|ref|YP_002016694.1| DNA-directed RNA polymerase subunit alpha [Prosthecochloris
           aestuarii DSM 271]
 gi|238693316|sp|B4S5A1|RPOA_PROA2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|194312652|gb|ACF47047.1| DNA-directed RNA polymerase, alpha subunit [Prosthecochloris
           aestuarii DSM 271]
          Length = 328

 Score =  307 bits (787), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 127/322 (39%), Positives = 197/322 (61%), Gaps = 6/322 (1%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  IE        E+    +A+PL RG+  TLGNA+RRVL++SL G AIT ++IDGV HE
Sbjct: 8   PERIEVDE-ATHSESIGQFVAQPLERGYGVTLGNAMRRVLLASLPGTAITGIKIDGVFHE 66

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNP 130
            S+I GV ED+ +I+LN+K +  K +     + ++   GP    AGDI     + EVLN 
Sbjct: 67  FSTIDGVREDVPEIVLNLKKVRFKSTTKRSCKTSLSIEGPADFKAGDIVAQEGEFEVLNK 126

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  L+ DA + +++ + +G GYVPA+ +R E  PIG I ID++++PIK V ++VE+ 
Sbjct: 127 DMHIATLNGDAKLNIDIYIGRGRGYVPAEENRGEGMPIGFIAIDSIFTPIKNVKFSVENT 186

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK----EDIN 246
           R GQ  DY+K+ + ++TDGSI+ +DS++LA +++ + + +F NF   ++E      +  +
Sbjct: 187 RVGQRTDYEKMILDVETDGSISPDDSISLAGKVINEHVSLFANFSPTEEEFAEEEYKQQD 246

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L  ++E+L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL E+
Sbjct: 247 DEFENMRKLLQTRIEDLDLSVRSHNCLRLAEIDTLGDLVSRKEDELLTYKNFGKKSLTEL 306

Query: 307 KGVLGTMGLFLGMNLPDWPPES 328
           K  L    L  GM++  +  +S
Sbjct: 307 KEQLDKCELKFGMDITKYQMKS 328


>gi|258543844|ref|ZP_05704078.1| DNA-directed RNA polymerase, alpha subunit [Cardiobacterium hominis
           ATCC 15826]
 gi|258520933|gb|EEV89792.1| DNA-directed RNA polymerase, alpha subunit [Cardiobacterium hominis
           ATCC 15826]
          Length = 322

 Score =  307 bits (787), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 134/319 (42%), Positives = 196/319 (61%), Gaps = 7/319 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            EL+ P  ++   +G    N + +  EPL RGF +TLG ALRRVL+SS+ GAA+T  +ID
Sbjct: 4   SELLTPRIVKIQEMG---LNTSRVTLEPLERGFGYTLGTALRRVLLSSIEGAAVTECEID 60

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE S I+GV ED+ D++LN+KG+ L +       + +     G V A D    +++E
Sbjct: 61  GVLHEYSGIEGVSEDVIDVLLNLKGLALILHEGERAEMRLSVNKAGEVKASDFSAPSNVE 120

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH-RTENDPIGLITIDALYSPIKKVSY 185
           + NPDHVI +L  D    M + V KG GY  A     T      ++ +DA +SPIK+++Y
Sbjct: 121 ICNPDHVIAHLTQDVSFSMTVVVEKGRGYRVATQEIDTATHAPNVLRVDASFSPIKRIAY 180

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+AR  Q  D DKL + I+++G+I  E ++  A+ IL  Q+ +F+N E       E  
Sbjct: 181 RVEAARVEQHTDLDKLVIDIESNGTIDPEQAIREAATILHKQIAVFVNLE---STEVEAE 237

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             + +  +P LL+ V++LEL+VRS NCL+ ENI  +GDL++RTE ++L+  N G+KSL E
Sbjct: 238 YEEEVQVDPVLLRPVDDLELTVRSANCLKAENINNIGDLVRRTEVELLKTPNLGKKSLNE 297

Query: 306 IKGVLGTMGLFLGMNLPDW 324
           IK VL   GL LGM+L +W
Sbjct: 298 IKEVLAAHGLELGMDLENW 316


>gi|294055196|ref|YP_003548854.1| DNA-directed RNA polymerase, alpha subunit [Coraliomargarita
           akajimensis DSM 45221]
 gi|293614529|gb|ADE54684.1| DNA-directed RNA polymerase, alpha subunit [Coraliomargarita
           akajimensis DSM 45221]
          Length = 333

 Score =  307 bits (787), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 132/325 (40%), Positives = 191/325 (58%), Gaps = 4/325 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + K   +   PN +   V     +   +  AEP   G+ HT+GN+LRRVL+SS+ GAAI+
Sbjct: 1   MPKRLGKFELPNRL-VKVEETATDTFAVFQAEPFEAGYGHTIGNSLRRVLLSSIEGAAIS 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +++IDGV HE  SI+GV ED+TDI+LN+K + L         + I     G +TA DIQ 
Sbjct: 60  SIKIDGVQHEFQSIEGVVEDVTDIVLNLKKVLLVSESRESVNLIIDVTREGAITAADIQE 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
             +I+V+NPD VIC L+ +     EL V  G GY     ++    PIG+I ID+L+SP+K
Sbjct: 120 DANIQVVNPDQVICTLEKEQRFFAELEVRVGRGYCTGDDNKKAEQPIGVIAIDSLFSPVK 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
            V Y+VE+ R GQ +DYDKL + I TDG I+ +D++  ++ IL+  L +F    +   E 
Sbjct: 180 LVKYSVENTRVGQEMDYDKLVLEITTDGRISPDDALKQSAAILKHHLDVFDEVSQDDIEF 239

Query: 242 KEDINVKSLPFN---PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + +    S   N     L   V E+ELSVR+ NCL   NI  +G+L  ++E +ML+  NF
Sbjct: 240 ESESKEISEEQNRLRKLLNMSVNEIELSVRAANCLNNANITTVGELAMKSEQEMLKYRNF 299

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPD 323
           G+KSL EIK  L  +GL LGM + +
Sbjct: 300 GKKSLNEIKDKLEQLGLSLGMKIDE 324


>gi|21674971|ref|NP_663036.1| DNA-directed RNA polymerase subunit alpha [Chlorobium tepidum TLS]
 gi|25009133|sp|Q8KAJ8|RPOA_CHLTE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|21648203|gb|AAM73378.1| DNA-directed RNA polymerase, alpha subunit [Chlorobium tepidum TLS]
          Length = 328

 Score =  307 bits (787), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 130/322 (40%), Positives = 195/322 (60%), Gaps = 6/322 (1%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  I+         +    IA+PL RG+  TLGNA+RRVL++SL G AIT ++IDGV HE
Sbjct: 8   PTKIDVDE-ATHTGSFGRFIAQPLERGYGVTLGNAMRRVLLASLPGTAITGIKIDGVFHE 66

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNP 130
            S+I GV ED+ +I+LN+K +  K +     + T+   GP    AGDI     + EVLN 
Sbjct: 67  FSTIDGVREDVPEIVLNLKKVRFKSNCKRSCKTTLTLAGPKDFLAGDIVAQEGEFEVLNK 126

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  ++ +A V +++ + +G GYVPA+ +R++  PIG I ID++Y+PIK V  TVE+ 
Sbjct: 127 DLHIATINSEATVTIDIYIGRGRGYVPAEENRSDGMPIGFIAIDSIYTPIKNVKLTVENT 186

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI----N 246
           R GQ  DY+K+ + ++TDGSIT +D+++LA +I+ D +  F NF   ++E  E+     +
Sbjct: 187 RVGQKTDYEKMILDVETDGSITPDDAISLAGKIINDHITFFANFSPTEEEFSEEEYKQLD 246

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L  K+E+L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL E+
Sbjct: 247 DEFESMRKLLQTKIEDLDLSVRSHNCLRLAEIDSLGDLVSRREEELLNYKNFGKKSLTEL 306

Query: 307 KGVLGTMGLFLGMNLPDWPPES 328
           K  L    L  GM++  +  + 
Sbjct: 307 KEQLEKFNLKFGMDITRYQLKG 328


>gi|295135676|ref|YP_003586352.1| DNA-directed RNA polymerase subunit alpha [Zunongwangia profunda
           SM-A87]
 gi|294983691|gb|ADF54156.1| DNA-directed RNA polymerase subunit alpha [Zunongwangia profunda
           SM-A87]
          Length = 330

 Score =  307 bits (787), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 125/325 (38%), Positives = 193/325 (59%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT+V+I+G
Sbjct: 5   NFQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGFAITSVRIEG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VND 124
           V HE S+I GV ED+T+IILN+K +  K   D   ++ VTI   G   +TAG  Q  ++ 
Sbjct: 62  VDHEFSTIPGVVEDVTEIILNLKQVRFKRQIDEIDNEAVTISVSGEEELTAGHFQKFISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLNP+ VIC+LD    + ME+T+ KG GYVPA+ ++  N P+G I  D++Y+PIK V 
Sbjct: 122 FQVLNPELVICHLDSKVNINMEITIEKGRGYVPAEENKKANAPLGTIFTDSIYTPIKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y++E+ R  Q  DY+KL   I +DGSI  +D++  A++ L     +F    I  E  +  
Sbjct: 182 YSIENYRVEQKTDYEKLVFEIISDGSIHPKDALTEAAKTLIHHFMLFSDERITLEADEIA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+
Sbjct: 242 QTETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSYNKNDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E++ ++   GL  GM+L  + 
Sbjct: 302 KSLTELEELVSNKGLNFGMDLSKYK 326


>gi|218440647|ref|YP_002378976.1| DNA-directed RNA polymerase subunit alpha [Cyanothece sp. PCC 7424]
 gi|218173375|gb|ACK72108.1| DNA-directed RNA polymerase, alpha subunit [Cyanothece sp. PCC
           7424]
          Length = 314

 Score =  307 bits (787), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 107/317 (33%), Positives = 172/317 (54%), Gaps = 9/317 (2%)

Query: 14  NIEYIVL--GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE + L   + +      I EPL RG   T+GNALRRVL+S+L GAA+TA++I GV HE
Sbjct: 5   QIECVELKAQKNQGQYGKFILEPLDRGQGTTVGNALRRVLLSNLEGAAVTALRIAGVNHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            ++I GV ED+ ++ILN+K I LK      +   +   GP  VTA      ++IEV++P 
Sbjct: 65  FATISGVREDVMELILNMKEITLKSYTSQPQIGRLVATGPATVTAAQFDVPSEIEVVDPS 124

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  L   + + ME  V KG GY   +  + +   +  + ID+++ P+ KV+Y+VE  R
Sbjct: 125 QYVATLSDGSKLEMEFRVEKGKGYRAIERGKDDTTSLDFLQIDSVFMPVTKVNYSVEDVR 184

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  D+L++ I T+GSI  +++++ A+ I+ D      +  E    ++   +     
Sbjct: 185 VDGTGSKDRLTLEIWTNGSINPKEALSEAAAIIVDLFSPLKDLNE----LEATQSDYQDE 240

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            NP     +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L 
Sbjct: 241 VNPESQIPIEELQLSVRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEEVIEAL- 299

Query: 312 TMGLFLGMNLPDWPPES 328
                LG+ LP    ++
Sbjct: 300 --QKRLGITLPQEKAKT 314


>gi|58415894|emb|CAH57361.1| RNA polymerase alpha-subunit [Vibrio hispanicus]
          Length = 309

 Score =  307 bits (786), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 134/315 (42%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDV-DAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L   ++ + M + V +G GYVPA    H   +  PIG + +DA +SP+ K+
Sbjct: 118 ANPEHVICHLTDSNSEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|172038952|ref|YP_001805453.1| DNA-directed RNA polymerase subunit alpha [Cyanothece sp. ATCC
           51142]
 gi|171700406|gb|ACB53387.1| RNA polymerase alpha subunit [Cyanothece sp. ATCC 51142]
          Length = 314

 Score =  307 bits (786), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 111/311 (35%), Positives = 172/311 (55%), Gaps = 8/311 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             IE      + +  +  + EPL RG   T+GNALRRVL+++L G A+TA++I GV HE 
Sbjct: 7   ECIESKTQKNQSQ-YSKFVLEPLERGQGTTVGNALRRVLLANLEGTAVTAIRIGGVNHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ +I+LN+K I LK   D  +   +   G   VTAG     +++EV+NP  
Sbjct: 66  ATIPGVREDVLEIMLNMKEIVLKSYTDQPQIGRLVATGAAHVTAGQFDLPSEVEVINPTQ 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L   A + ME  + KG GYVP +    E   +  + IDA++ P+ KV+Y+VES R 
Sbjct: 126 PIATLTEGAKLEMEFRIEKGVGYVPVERSSDEPTALDFLQIDAVFMPVTKVNYSVESIRG 185

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            +    D+L + I T+GS   +++++ A+ IL D      +  + +  V E  + +    
Sbjct: 186 EEGEAKDRLMLEIWTNGSFNPKEALSRAADILVDLFNPLKDLNQLETAVPEYPDEE---- 241

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           NP     +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L  
Sbjct: 242 NPQSQIPIEELQLSVRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEEVIEAL-- 299

Query: 313 MGLFLGMNLPD 323
               LG+ LP 
Sbjct: 300 -QKRLGITLPQ 309


>gi|156743921|ref|YP_001434050.1| DNA-directed RNA polymerase subunit alpha [Roseiflexus castenholzii
           DSM 13941]
 gi|189043845|sp|A7NR36|RPOA_ROSCS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|156235249|gb|ABU60032.1| DNA-directed RNA polymerase, alpha subunit [Roseiflexus
           castenholzii DSM 13941]
          Length = 323

 Score =  307 bits (786), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 126/322 (39%), Positives = 190/322 (59%), Gaps = 10/322 (3%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
            IE +      EN      EPL  G+ HTLGNALRRVL+SS+ GAAIT ++IDGV HE S
Sbjct: 8   KIEVVT---AAENYGRFKIEPLDPGYGHTLGNALRRVLLSSIPGAAITKIKIDGVFHEFS 64

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           +I G+ ED+T+I+LNIKG+ L+   +   ++++ KRG G+V A DI   +++E++NP H 
Sbjct: 65  TISGIKEDVTEIVLNIKGVRLRSYAERPVKISLSKRGSGIVRAADIDAPSNVEIVNPFHY 124

Query: 134 ICNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           IC +D  DA++ ME+TV +G GY+PA     +  PIG I IDA+++P+ KV+Y VE+ R 
Sbjct: 125 ICTIDRDDAMLEMEMTVERGRGYLPADQR--DALPIGEIPIDAIFTPVPKVNYVVENIRV 182

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP- 251
           GQ  D+D L + I TDG+I   D+++ A+++L        +F     E +       L  
Sbjct: 183 GQATDFDSLLIEIWTDGTIKPGDALSHAAQVLVQYSQTIADFNRLSTETESTAAPNGLAI 242

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL+LS R+ NCL+  +I  +G +++  E  +L + N G+KS+ EI+  L 
Sbjct: 243 PADIYDTPIEELDLSTRTYNCLKRADITKVGQVLEMDEKALLSVRNLGQKSMEEIRDKLI 302

Query: 312 TMGL--FLGMNLPDWPPESIEE 331
             G    +G    +  P  IE 
Sbjct: 303 ERGYIPRIGQT-TNSSPAGIES 323


>gi|319827250|gb|ADV74824.1| RNA polymerase subunit A [Vibrio neptunius]
 gi|319827252|gb|ADV74825.1| RNA polymerase subunit A [Vibrio coralliilyticus]
          Length = 305

 Score =  306 bits (785), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 137/306 (44%), Positives = 200/306 (65%), Gaps = 8/306 (2%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
                    +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV E
Sbjct: 3   STVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQE 62

Query: 81  DLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           D+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+ NP+HVIC+L  
Sbjct: 63  DILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTD 122

Query: 140 D-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
           D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q 
Sbjct: 123 DNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQR 182

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P 
Sbjct: 183 TDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPI 239

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL
Sbjct: 240 LLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGL 299

Query: 316 FLGMNL 321
            LGM L
Sbjct: 300 SLGMRL 305


>gi|58415864|emb|CAH57346.1| RNA polymerase alpha-subunit [Vibrio halioticoli]
          Length = 309

 Score =  306 bits (785), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 136/315 (43%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDDVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA        +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNADIAMRIKVERGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + + +   
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVQEPI 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  + G+KSL
Sbjct: 238 E---EKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPSLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|255994834|ref|ZP_05427969.1| DNA-directed RNA polymerase, alpha subunit [Eubacterium saphenum
           ATCC 49989]
 gi|255993547|gb|EEU03636.1| DNA-directed RNA polymerase, alpha subunit [Eubacterium saphenum
           ATCC 49989]
          Length = 316

 Score =  306 bits (785), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 126/311 (40%), Positives = 194/311 (62%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
            + KP     ++   E+ +    + EPL RG+  TLGN+LRRVL+S+L GAA+T+++IDG
Sbjct: 3   NIEKPTI--KMLHDNEKASEGRFVIEPLERGYGITLGNSLRRVLLSTLPGAAVTSIRIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           +LHE S+I GV ED+T+IILNIK + ++   +     TI   GP  +TA DI   +++++
Sbjct: 61  ILHEFSTIPGVTEDVTEIILNIKRLAIRAWSEEPIVATIKASGPCEITAADIDCGSEVKI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
            N DH I  LD DA + MEL + +G GY  A+ ++ ++DPI  I ID+++SP++K ++ V
Sbjct: 121 FNEDHHIATLDKDAELDMELVIDRGRGYSSAEQNKGKDDPISTIAIDSIFSPVEKANFIV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
              R GQV D+DKL + + TDGSI+  D+VA+A+RI+Q+ L +F+   E   E    +  
Sbjct: 181 SDTRVGQVTDFDKLELEVRTDGSISANDAVAVAARIMQEHLALFVELSEEATEYSIMLEH 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           + +     L K +E+LEL+VRS N L    I  + DL+  TE ++  + N G+KSL EIK
Sbjct: 241 EDIEQTRVLEKNIEDLELTVRSLNALTQAGIDTVSDLVSMTEGELNSVKNLGKKSLSEIK 300

Query: 308 GVLGTMGLFLG 318
             +  +GL L 
Sbjct: 301 DKIRELGLSLS 311


>gi|67923562|ref|ZP_00517035.1| DNA-directed RNA polymerase [Crocosphaera watsonii WH 8501]
 gi|67854588|gb|EAM49874.1| DNA-directed RNA polymerase [Crocosphaera watsonii WH 8501]
          Length = 314

 Score =  306 bits (785), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 110/311 (35%), Positives = 175/311 (56%), Gaps = 8/311 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             IE      + +  +  + EPL RG   T+GN+LRRVL+++L GAA+TA++I GV HE 
Sbjct: 7   ECIESKTQKNQSQ-YSKFVLEPLERGQGTTVGNSLRRVLLANLEGAAVTAIRIGGVNHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ +I+LN+K I LK   +  +   +   G   VTAG  +  +++EV+NP  
Sbjct: 66  ATIPGVREDVLEIMLNMKEIVLKSYTEQPQIGRLVATGAAHVTAGQFELPSEVEVVNPTQ 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L   A + ME  + KG GYVP +    E   +  + IDA++ P+ KV+Y+VES R 
Sbjct: 126 PIATLTEGAKLEMEFRIEKGVGYVPVERSSEEPAALDFLQIDAVFMPVTKVNYSVESIRG 185

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            +    D+L + I T+GS   +++++ A+ IL D      +  + +  V+E  + +    
Sbjct: 186 EEGEAKDRLMLEIWTNGSFNPKEALSKAADILVDLFNPLKDLNQLETAVQEYPDEE---- 241

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           NP     +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L  
Sbjct: 242 NPQSQIPIEELQLSVRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEEVIEAL-- 299

Query: 313 MGLFLGMNLPD 323
               LG+ LP 
Sbjct: 300 -QKRLGITLPQ 309


>gi|163786164|ref|ZP_02180612.1| DNA-directed RNA polymerase alpha subunit [Flavobacteriales
           bacterium ALC-1]
 gi|159878024|gb|EDP72080.1| DNA-directed RNA polymerase alpha subunit [Flavobacteriales
           bacterium ALC-1]
          Length = 330

 Score =  306 bits (785), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 130/325 (40%), Positives = 195/325 (60%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT+V+I+G
Sbjct: 5   NFQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGFAITSVRIEG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VND 124
           V HE S+I GV ED+T++ILN+K +N K   D   ++ VTI   G   +TAGD Q  ++ 
Sbjct: 62  VDHEFSTISGVVEDVTEMILNLKQVNFKRQIDEVDNETVTISISGQEQITAGDFQKFISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLN D VICNLD    + MELT+ KG GYVPA+ ++  + PIG I  D++Y+PIK V 
Sbjct: 122 FQVLNTDLVICNLDPKVNINMELTIEKGRGYVPAEENKKASAPIGTIFTDSIYTPIKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y++E+ R  Q  DY+KL   I TDGSI  +D++  A++IL     +F    I  E  +  
Sbjct: 182 YSIENFRVEQKTDYEKLVFEIQTDGSINPKDALTEAAKILIHHFMLFSDERITLEADEIA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+
Sbjct: 242 QTETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E++ ++   GL  GM+L  + 
Sbjct: 302 KSLTELEELVNVKGLNFGMDLSKYK 326


>gi|119358164|ref|YP_912808.1| DNA-directed RNA polymerase subunit alpha [Chlorobium
           phaeobacteroides DSM 266]
 gi|158512605|sp|A1BJ07|RPOA_CHLPD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119355513|gb|ABL66384.1| DNA-directed RNA polymerase subunit alpha [Chlorobium
           phaeobacteroides DSM 266]
          Length = 327

 Score =  306 bits (784), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 127/321 (39%), Positives = 192/321 (59%), Gaps = 6/321 (1%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  IE        E     IA+PL RG+  T+GN +RRVL++SL G AIT V+I+GV HE
Sbjct: 8   PAKIEVDE-ATHTEMFGRFIAQPLERGYGVTIGNVMRRVLLASLPGTAITGVKIEGVYHE 66

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNP 130
            S+I+GV ED+ +I+LN+K +  K +     + ++   G    TAGDI     + EVLN 
Sbjct: 67  FSAIEGVREDVPEIVLNLKRVRFKSNCKRSCKTSLSIAGTKDFTAGDIIAKEGEFEVLNK 126

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  ++  +V+ +E+ + +G GY+PA+ +  E  PIG I IDA+++PI+ V +TVE+ 
Sbjct: 127 DLHIATVNDGSVLNIEIYIGRGRGYLPAEENHPEGMPIGFIAIDAIFTPIRNVKFTVENT 186

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKKEVKEDIN 246
           R GQ  DY+K+ + ++TDGSI  +DS++LA +I+ D +  F NF     E  +E  +  +
Sbjct: 187 RVGQRTDYEKMILDVETDGSIAPDDSISLAGKIINDHIMYFANFSPTEEEFTEEEFKQQD 246

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L  K+E+L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL E+
Sbjct: 247 DEFESMRKLLHTKIEDLDLSVRSHNCLRLAEIDTIGDLVSRKEDELLNYKNFGKKSLTEL 306

Query: 307 KGVLGTMGLFLGMNLPDWPPE 327
           K  L    L  GM++  +  +
Sbjct: 307 KEQLEKFDLKFGMDITRYQMK 327


>gi|126658013|ref|ZP_01729165.1| DNA-directed RNA polymerase subunit alpha [Cyanothece sp. CCY0110]
 gi|126620651|gb|EAZ91368.1| DNA-directed RNA polymerase subunit alpha [Cyanothece sp. CCY0110]
          Length = 314

 Score =  306 bits (784), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 110/311 (35%), Positives = 172/311 (55%), Gaps = 8/311 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             IE      + +  +  + EPL RG   T+GNALRRVL+++L G A+TA++I GV HE 
Sbjct: 7   ECIESKTQKNQSQ-YSKFVLEPLERGQGTTVGNALRRVLLANLEGTAVTAIRIGGVNHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ +I+LN+K I LK   +  +   +   G   VTAG     +++EV+NP  
Sbjct: 66  ATIPGVREDVLEIMLNMKEIVLKSYTEQPQIGRLVATGAAHVTAGQFDLPSEVEVINPTQ 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L   A + ME  + KG GYVP +    E   +  + IDA++ P+ KV+Y+VES R 
Sbjct: 126 PIATLTEGAKLEMEFRIEKGVGYVPVERSSDEPTALDFLQIDAVFMPVTKVNYSVESIRG 185

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            +    D+L + I T+GS   +++++ A+ IL D      +  + +  V E  + +    
Sbjct: 186 EEGEAKDRLMLEIWTNGSFNPKEALSRAADILVDLFNPLKDLNQLETAVPEYPDEE---- 241

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           NP     +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L  
Sbjct: 242 NPQSQIPIEELQLSVRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEEVIEAL-- 299

Query: 313 MGLFLGMNLPD 323
               LG+ LP 
Sbjct: 300 -QKRLGITLPQ 309


>gi|58415728|emb|CAH57278.1| RNA polymerase alpha-subunit [Photobacterium leiognathi subsp.
           leiognathi]
          Length = 292

 Score =  306 bits (783), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 135/295 (45%), Positives = 197/295 (66%), Gaps = 7/295 (2%)

Query: 28  TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIIL 87
             +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+L
Sbjct: 1   AKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILL 60

Query: 88  NIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRME 146
           N+KG+ +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC++  D A + M 
Sbjct: 61  NLKGLAVKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIANPEHVICHITDDNAELSMR 120

Query: 147 LTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
           + V +G GYVPA    H   +  PIG + +DA YSP+ +++Y VE+AR  Q  D DKL +
Sbjct: 121 IKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDRIAYAVEAARVEQRTDLDKLVI 180

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V++L
Sbjct: 181 DMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDL 237

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           EL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 238 ELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 292


>gi|58416010|emb|CAH57419.1| RNA polymerase alpha-subunit [Vibrio rumoiensis]
 gi|58416012|emb|CAH57420.1| RNA polymerase alpha-subunit [Vibrio rumoiensis]
          Length = 309

 Score =  306 bits (783), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 137/315 (43%), Positives = 203/315 (64%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ + +  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVSVAEGKDEVFITLKKSGSGPVVAGDIIHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVP+    H   +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDKAEIAMRIKVQRGRGYVPSSARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|163752891|ref|ZP_02160015.1| DNA-directed RNA polymerase subunit alpha [Kordia algicida OT-1]
 gi|161326623|gb|EDP97948.1| DNA-directed RNA polymerase subunit alpha [Kordia algicida OT-1]
          Length = 330

 Score =  306 bits (783), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 126/325 (38%), Positives = 193/325 (59%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++    E        PL  G+  T+GNALRRVL+SSL G AIT+V+ID 
Sbjct: 5   NFQKPDKV---IMIDSSEFDGKFEFRPLEPGYGLTIGNALRRVLLSSLEGFAITSVRIDK 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VND 124
           V HE S+I GV ED+T+IILN+K +  K   D   ++ V+I   G   +TAGD Q  ++ 
Sbjct: 62  VDHEFSTISGVVEDVTEIILNLKQVRFKRQIDDIDNESVSISVSGKEQLTAGDFQKFISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLNPD VICN+D    + ME+T+ KG GYVPA+ ++  N P+G I  D++Y+P+K V 
Sbjct: 122 FQVLNPDLVICNMDASVNINMEITIEKGRGYVPAEENKKSNAPLGTIFTDSIYTPVKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y++E+ R  Q  DY+KL   I TDGSI  ++++  A++ L     +F    I  E  +  
Sbjct: 182 YSIENYRVEQKTDYEKLVFEIITDGSIHPKEALTEAAKTLIHHFMLFSDERITLEADEIA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+
Sbjct: 242 QTETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSYNKNDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E++ ++   GL  GM+L  + 
Sbjct: 302 KSLTELEELVNVKGLSFGMDLSKYK 326


>gi|145219088|ref|YP_001129797.1| DNA-directed RNA polymerase subunit alpha [Prosthecochloris
           vibrioformis DSM 265]
 gi|189043842|sp|A4SCT6|RPOA_PROVI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|145205252|gb|ABP36295.1| DNA-directed RNA polymerase subunit alpha [Chlorobium
           phaeovibrioides DSM 265]
          Length = 328

 Score =  306 bits (783), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 125/322 (38%), Positives = 192/322 (59%), Gaps = 6/322 (1%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  IE        +     +A+PL RG+  TLGN +RRVL++SL G AIT +++DGV HE
Sbjct: 8   PAKIEVDET-THTDYFGRFVAQPLERGYGVTLGNMMRRVLLASLPGTAITGIKVDGVFHE 66

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNP 130
            S+I+GV ED+ +I+LN+K +  + +     + T+   GP   TAGDI     + +VLN 
Sbjct: 67  FSAIEGVREDVPEIVLNLKKVRFRSTCKRSCKTTLTITGPKDFTAGDIVAMEGEFDVLNK 126

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  ++  + + +++ V +G GY PA+ +R E+ PIG I IDA+Y+PI+ V   VE+ 
Sbjct: 127 DLHIATVNEGSTLNIDVFVGRGRGYTPAEDNRPESMPIGYIAIDAIYTPIRNVKVAVENT 186

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKKEVKEDIN 246
           R GQ  DY+K+ + ++TDGSIT +DS++LA RI+ + +  F +F     E  +E  +  +
Sbjct: 187 RVGQRTDYEKMVLDVETDGSITPDDSISLAGRIINEHVAFFADFSPTEEEFTEEEFKQQD 246

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L  K+E+L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL E+
Sbjct: 247 DEFEAMRKLLNTKIEDLDLSVRSHNCLRLAEIDSIGDLVSRKEDELLNYKNFGKKSLTEL 306

Query: 307 KGVLGTMGLFLGMNLPDWPPES 328
           K  L    L  GM++  +  + 
Sbjct: 307 KEQLEKFELKFGMDITKYQMKG 328


>gi|327402757|ref|YP_004343595.1| DNA-directed RNA polymerase subunit alpha [Fluviicola taffensis DSM
           16823]
 gi|327318265|gb|AEA42757.1| DNA-directed RNA polymerase subunit alpha [Fluviicola taffensis DSM
           16823]
          Length = 330

 Score =  306 bits (783), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 122/325 (37%), Positives = 203/325 (62%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP+ +   ++ Q +E +      PL  G+  T+GNALRR+L+SSL G AI++V+I+G
Sbjct: 5   DFQKPDKV---IMIQSDERKGQFEFRPLEPGYGITVGNALRRILLSSLEGYAISSVRIEG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVND 124
           V HE +++KGV ED+T+I+LN+K +  K  + G  ++ V +   G   +TAGD+ +  + 
Sbjct: 62  VDHEFATLKGVVEDVTEIVLNLKQVRFKQQIEGTDNETVVVSISGQDKLTAGDLGKFTSG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLNPD VICN++    + +ELT+ KG GY+PA+ +++ N P G I ID++++PI  V 
Sbjct: 122 FQVLNPDLVICNMESSVKLELELTIIKGRGYLPAEENKSGNAPFGTIAIDSIFTPIVNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           YT+E+ R  Q  DY+KL + + TDGSI  +D++  A++IL     +F    I  +   K 
Sbjct: 182 YTIENYRVEQKTDYEKLVLELTTDGSIHPKDALKEAAKILIHHFMLFSDERITLDSEVKS 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E+ +  SL     L  K+ +++LSVR+ NCL+  ++  +GDL+   + D+L+  NFG+
Sbjct: 242 ETEEFDETSLHMRQLLKTKLVDMDLSVRALNCLKAADVETLGDLVSYNKNDLLKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E++ ++ + GL  GMN+  + 
Sbjct: 302 KSLTELEDLVDSKGLNFGMNVAKYK 326


>gi|194335472|ref|YP_002017266.1| DNA-directed RNA polymerase, alpha subunit [Pelodictyon
           phaeoclathratiforme BU-1]
 gi|238693374|sp|B4SBX4|RPOA_PELPB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|194307949|gb|ACF42649.1| DNA-directed RNA polymerase, alpha subunit [Pelodictyon
           phaeoclathratiforme BU-1]
          Length = 327

 Score =  306 bits (783), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 124/321 (38%), Positives = 193/321 (60%), Gaps = 6/321 (1%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  IE        +     IA+PL RG+  TLGN +RRVL++SL G AIT ++IDGV HE
Sbjct: 8   PAKIEVDE-SSHTDCFGRFIAQPLERGYGVTLGNVMRRVLLASLPGTAITGIKIDGVFHE 66

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNP 130
            ++I GV ED+ +I+LN+K +  K +   + + ++   GP   TAGDI     + EVLN 
Sbjct: 67  FAAIDGVREDVPEIVLNLKKVRFKSTCKRNCKTSLTLVGPMDFTAGDIIAQEGEFEVLNK 126

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  +  ++  A V+++L + +G GY+PA+ +R E  PIG I +DA+Y+PI+ V +TVE+ 
Sbjct: 127 DMHVATINAGATVKIDLYIGRGRGYMPAEENRPEGMPIGYIAVDAIYTPIRNVKFTVENT 186

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKKEVKEDIN 246
           R GQ  DY+K+ + ++TDGS++ +DS++LA +I+ D +  F NF     E  +E  +  +
Sbjct: 187 RVGQRTDYEKMILDVETDGSVSPDDSISLAGKIITDHVTFFANFSPTEEEFTEEEFKQQD 246

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +          K+E+L+LSVRS NCLR   I  +G+L+   E ++L   NFG+KSL E+
Sbjct: 247 DEFETMRRLFHTKIEDLDLSVRSHNCLRLAEIDTIGELVSHKEDELLNYKNFGKKSLTEL 306

Query: 307 KGVLGTMGLFLGMNLPDWPPE 327
           K  L    L  GM++  +  +
Sbjct: 307 KEQLEKFDLKFGMDITKYQMK 327


>gi|328813969|gb|AEB52100.1| DNA-directed RNA polymerase alpha chain [Lactobacillus fermentum]
          Length = 275

 Score =  305 bits (782), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 119/270 (44%), Positives = 180/270 (66%), Gaps = 2/270 (0%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E +N    + EPL RG+  TLGN+LRRV+++SL GAAIT++QIDGVLHE S+++GV ED
Sbjct: 6   EETDNYGKFVVEPLERGYGTTLGNSLRRVMLASLPGAAITSIQIDGVLHEFSTVQGVTED 65

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILN+K + LK+  +  K + I  +GP  VTA DIQ   D+ +LN D  I  +   A
Sbjct: 66  VTQIILNLKQVALKIDSEDAKDLEIDVKGPAEVTAADIQGDGDVTILNSDLHIATVSDGA 125

Query: 142 VVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
            + +++T  KG GY  A  ++T  E   IG++ ID++Y+PI++V+YTVE+ R GQ  DYD
Sbjct: 126 ELHVKMTADKGRGYSSADDNKTRMEGLAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYD 185

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL++ + T+GS+T  ++++LA++IL + L MF+N  E  +  +  +  +       L K 
Sbjct: 186 KLTLDVWTNGSLTPTEAISLAAKILTEHLTMFVNLTEEAQVTQVMVEREETHQEKVLDKT 245

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +EEL+LSVRS NCL+  +I  + DL +RTE
Sbjct: 246 IEELDLSVRSYNCLKRADIQTVKDLTERTE 275


>gi|313206369|ref|YP_004045546.1| DNA-directed RNA polymerase subunit alpha [Riemerella anatipestifer
           DSM 15868]
 gi|312445685|gb|ADQ82040.1| DNA-directed RNA polymerase subunit alpha [Riemerella anatipestifer
           DSM 15868]
 gi|315023690|gb|EFT36694.1| DNA-directed RNA polymerase alpha subunit [Riemerella anatipestifer
           RA-YM]
 gi|325336185|gb|ADZ12459.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Riemerella anatipestifer RA-GD]
          Length = 331

 Score =  305 bits (782), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 125/325 (38%), Positives = 204/325 (62%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
             IKP+ +   +L    E +      PL  G+  T+G+ALRRVL+SSL G AIT+++I+G
Sbjct: 5   NFIKPDKV---ILLNSTEFQGQFEFRPLEPGYGLTVGHALRRVLLSSLEGYAITSIKIEG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVND 124
           V HE S+I GV ED+T+IILN+K + LK   ++   ++VT        +TAGD+ + ++ 
Sbjct: 62  VEHEFSTIPGVIEDVTEIILNLKQLRLKAKSENAPSEQVTAKIANLEQLTAGDLGKFISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            EVLNP+ VICNL  D  + M  +++KG GYVP++ +++ N PIG I ID++Y+PIKKV 
Sbjct: 122 FEVLNPELVICNLTKDVNLEMNFSINKGRGYVPSEQNKSNNAPIGTIAIDSIYTPIKKVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y+VE+ R  Q  DY+KL + I+TDGSI+ ++++  AS+IL     +F    I  E    +
Sbjct: 182 YSVENYRVEQKTDYEKLILDIETDGSISPQNALIEASKILIYHFMLFSDERITLETEAVK 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                + ++L     L  K+ E++LSVR+ NCL+   +  +G+L+  +++D+++  NFG+
Sbjct: 242 ASIQYDEETLHTRQLLKSKLAEMDLSVRALNCLKAAEVETLGELVSYSKSDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E++ ++ + GL  G ++  + 
Sbjct: 302 KSLTELEELVHSKGLNFGFDVSKYK 326


>gi|146329031|ref|YP_001210127.1| DNA-directed RNA polymerase, alpha subunit [Dichelobacter nodosus
           VCS1703A]
 gi|158513303|sp|A5EX94|RPOA_DICNV RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|146232501|gb|ABQ13479.1| DNA-directed RNA polymerase, alpha subunit [Dichelobacter nodosus
           VCS1703A]
          Length = 320

 Score =  305 bits (782), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 132/321 (41%), Positives = 201/321 (62%), Gaps = 8/321 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            EL+ P  ++   +G    N + +  EPL RGF +TLG ALRRVL+SS+ GAAIT  QID
Sbjct: 4   TELLTPRIVQIKEIGS---NTSRVTLEPLERGFGYTLGTALRRVLLSSIEGAAITECQID 60

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV HE S+I+GV ED+ D++LN+K I L M       + +     G +TAGD +    +E
Sbjct: 61  GVSHEYSAIEGVKEDVIDVLLNLKNIALLMPDLERAEIRLSVTEKGAITAGDFELPAGVE 120

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYSPIKKVS 184
           ++NPD VI +L  D    +   V KG GY  A      +E+    ++ +DA +SP+++++
Sbjct: 121 IVNPDCVIAHLTRDIPFSLTAVVEKGRGYRVAPQADDNSESTRSNVLRLDASFSPVRRIA 180

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE AR  Q  D DKL + I+++G+I  E ++  A+ IL +Q+ +F++ E  ++E +E+
Sbjct: 181 YRVEQARVEQRTDLDKLIIEIESNGTIDPEQAIRDAATILHNQIKVFVDLESTEEETEEE 240

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
             +     +P LL+ V++LEL+VRS NCL+ ENI  +GDL++RTE ++L+  N G+KSL 
Sbjct: 241 EEI---YIDPVLLRPVDDLELTVRSANCLKAENINNIGDLVRRTEVELLKTPNLGKKSLN 297

Query: 305 EIKGVLGTMGLFLGMNLPDWP 325
           EIK VL    L LGM++ +WP
Sbjct: 298 EIKEVLAAHNLELGMDIENWP 318


>gi|302337502|ref|YP_003802708.1| DNA-directed RNA polymerase, subunit alpha [Spirochaeta smaragdinae
           DSM 11293]
 gi|301634687|gb|ADK80114.1| DNA-directed RNA polymerase, alpha subunit [Spirochaeta smaragdinae
           DSM 11293]
          Length = 351

 Score =  305 bits (782), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 137/352 (38%), Positives = 206/352 (58%), Gaps = 13/352 (3%)

Query: 1   MIQKNW-QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M +KN  +   KP  I +    + + N    +A P  RGF  T+GN LRRVL+SS++G A
Sbjct: 1   MARKNLLKGFKKPRGITFE-HSELQSNYGKFVAYPFERGFGTTVGNTLRRVLLSSIQGYA 59

Query: 60  ITAVQI-----DGVLHEISS----IKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKR 109
           ++AV+I     +G  H +SS    +  V ED  +II N+K + +K+  +   K + I  +
Sbjct: 60  VSAVKITCYNEEGTPHMVSSEFEMVPEVVEDTPEIIANLKQLQIKLPEEVEQKTLLIECK 119

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GPG +T  D +  ND+E++N D  I  +   A   +E+ +  G GYVP++ +    + IG
Sbjct: 120 GPGEITGADFEKDNDVEIINKDWKILTMMEKANFDLEVQIDLGRGYVPSEVNEKYIEEIG 179

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            I IDA++SPIK+V+Y +E+ R GQ  DYDKL+M I TDG+I  ED++A A++I +D   
Sbjct: 180 TIPIDAVFSPIKRVTYGIENTRVGQRSDYDKLTMEIYTDGTIAPEDALAEAAKIAKDHFT 239

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +FINF+E   +  +D++ +       L   VEELELSVRS NCL+  NI  +GDL ++TE
Sbjct: 240 IFINFDEDAIDGDDDVDEEEERVRAVLDTPVEELELSVRSFNCLKSANIRTIGDLTRKTE 299

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE-ELAKKYEDKC 340
            ++ +  NFG+KSL EIK  L    L LGM        S +  + K+ ED+ 
Sbjct: 300 EEIAKTRNFGKKSLQEIKEKLKEWNLSLGMTDYSVLKTSTKLPMNKEEEDEA 351


>gi|218245116|ref|YP_002370487.1| DNA-directed RNA polymerase subunit alpha [Cyanothece sp. PCC 8801]
 gi|257058141|ref|YP_003136029.1| DNA-directed RNA polymerase subunit alpha [Cyanothece sp. PCC 8802]
 gi|218165594|gb|ACK64331.1| DNA-directed RNA polymerase, alpha subunit [Cyanothece sp. PCC
           8801]
 gi|256588307|gb|ACU99193.1| DNA-directed RNA polymerase, alpha subunit [Cyanothece sp. PCC
           8802]
          Length = 316

 Score =  305 bits (782), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 101/316 (31%), Positives = 171/316 (54%), Gaps = 8/316 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             IE      + +  +  + EPL RG   T+GNALRRVL+++L+GAA+TA++I GV HE 
Sbjct: 9   ECIESKTQKNQSQ-YSKFVLEPLARGQGTTVGNALRRVLLANLQGAAVTAIRIAGVNHEF 67

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ +I+LN+K I LK   D  +   +     G VTA + +  +++EV++P  
Sbjct: 68  ATIPGVREDVLEIMLNMKEIVLKSYSDQAQIGRLVATSAGTVTAANFELPSEVEVVDPTQ 127

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            +  L   + + ME  +  G GY   +  + +   +  + IDA++ P+ KV+Y VE  R 
Sbjct: 128 YVATLTEGSKLEMEFRIETGTGYKGVERGKDDGTSLDFLEIDAVFMPVTKVNYIVEDIRG 187

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
                 D+L + I T+GS   +++++ A+ I+ D      +  + +    +  + +    
Sbjct: 188 EHGEAQDRLILEIWTNGSFNPKEALSEAAEIVVDLFSPLKDLNQLETTTPDYQDDE---- 243

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           NP     +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L  
Sbjct: 244 NPQSQIPIEELQLSVRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEEVIEAL-- 301

Query: 313 MGLFLGMNLPDWPPES 328
               LG+ LP    +S
Sbjct: 302 -QKRLGITLPQEKAKS 316


>gi|179184433|gb|ACB78147.1| RNA polymerase alpha subunit [Vibrio sp. CECT 7223]
          Length = 308

 Score =  305 bits (782), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 137/314 (43%), Positives = 203/314 (64%), Gaps = 11/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFL 317
            EIK VL + GL L
Sbjct: 295 TEIKDVLASRGLSL 308


>gi|148244354|ref|YP_001219048.1| DNA-directed RNA polymerase subunit alpha [Candidatus
           Vesicomyosocius okutanii HA]
 gi|158514275|sp|A5CXI9|RPOA_VESOH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|146326181|dbj|BAF61324.1| DNA-directed RNA polymerase alpha subunit [Candidatus
           Vesicomyosocius okutanii HA]
          Length = 326

 Score =  305 bits (781), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 147/329 (44%), Positives = 211/329 (64%), Gaps = 7/329 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q + ++ +KP  +E     Q   N   +I EPL RGF HTLGNA+RR L+SS+ G A+T
Sbjct: 1   MQGSARDFLKPKLVES---SQTGVNEFKVILEPLERGFGHTLGNAIRRTLLSSMTGFAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V IDGV+HE S+I GV ED+ DI+LN+K +++ ++     +V I K+GP  +T  DI+T
Sbjct: 58  EVVIDGVMHEFSTIDGVQEDVLDILLNLKEVSVVLNTVETAQVVIDKKGPCEITVADIET 117

Query: 122 VN-DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DI   NPD VI  ++ +  +RM L ++ G GY  A     E   IG + +DA +SPI
Sbjct: 118 NGIDITTFNPDKVIATINDEGHMRMTLKITAGIGYDAAASRTDEASSIGGMQLDASFSPI 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+VS+TV++AR  Q ++ DKL++ I+T+GS+  E ++   + ILQ+QL  F+  E  ++E
Sbjct: 178 KRVSFTVDAARVKQKVNLDKLNIMIETNGSVNAEVAIKRVATILQEQLSSFVELELVEEE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V    +     F+P LL  V+ELEL+VRS NCL+ E I Y+GDLIQ++E D+LR  N GR
Sbjct: 238 VSLPTSED---FDPQLLAAVDELELTVRSANCLKAEQIYYIGDLIQKSEQDLLRTPNLGR 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           KSL EIK VL   GL LG N+ +WPP  +
Sbjct: 295 KSLNEIKEVLTEKGLSLGTNIENWPPVDL 323


>gi|311748487|ref|ZP_07722272.1| DNA-directed RNA polymerase, alpha subunit [Algoriphagus sp. PR1]
 gi|126577004|gb|EAZ81252.1| DNA-directed RNA polymerase, alpha subunit [Algoriphagus sp. PR1]
          Length = 329

 Score =  305 bits (781), Expect = 7e-81,   Method: Composition-based stats.
 Identities = 120/316 (37%), Positives = 194/316 (61%), Gaps = 6/316 (1%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           E +V+ + ++   L   +PL +G+  T+GNALRR+L+SSL G AIT+++I GVLHE S+I
Sbjct: 10  EKVVMEKADDFHGLFTFKPLEKGYGVTIGNALRRILLSSLEGYAITSIKIPGVLHEFSTI 69

Query: 76  KGVHEDLTDIILNIKGINLK-MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHV 133
           +GV ED+TDIILN+K +  K +      ++T+  +   V TAGDI +  +  E+LNPD V
Sbjct: 70  EGVVEDVTDIILNLKQVRFKKVHEAFDGKITVEIKNQSVFTAGDIAKFTSSFEILNPDLV 129

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           IC++D      +E+TV KG GY+PA+  + +    G I IDA+++PIK V Y+VE+ R  
Sbjct: 130 ICHIDESKNFEIEITVEKGRGYLPAEESKPKEQVFGQIAIDAIFTPIKNVKYSVENTRVE 189

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKS 249
           Q  D++KL + + TDGSI  E ++  +++IL     +F +     +       E I+ + 
Sbjct: 190 QKTDFEKLILEVSTDGSIHPEKALQESAKILIQHFMLFSDQTMVLDSTGIAEPEPIDEEF 249

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           L     L   + +L+LSVR+ NCL+  ++  +GDL +   +DM++  NFG+KSL E++ +
Sbjct: 250 LHMRKLLKTSLSDLDLSVRAFNCLKAADVKTLGDLAKLEISDMMKFRNFGKKSLAELEQL 309

Query: 310 LGTMGLFLGMNLPDWP 325
           +   GL  GM++  + 
Sbjct: 310 IQEKGLTFGMDISKYK 325


>gi|193211878|ref|YP_001997831.1| DNA-directed RNA polymerase subunit alpha [Chlorobaculum parvum
           NCIB 8327]
 gi|238692676|sp|B3QR98|RPOA_CHLP8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|193085355|gb|ACF10631.1| DNA-directed RNA polymerase, alpha subunit [Chlorobaculum parvum
           NCIB 8327]
          Length = 328

 Score =  305 bits (781), Expect = 7e-81,   Method: Composition-based stats.
 Identities = 129/322 (40%), Positives = 195/322 (60%), Gaps = 6/322 (1%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  I+         +    IA+PL RG+  TLGNA+RRVL++SL G AIT ++IDGV HE
Sbjct: 8   PAKIDVDE-ATHTGSFGRFIAQPLERGYGVTLGNAMRRVLLASLPGTAITGIKIDGVFHE 66

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNP 130
            S+I GV ED+ +I+LN+K +  K +     + T+   GP    AGDI     + EVLN 
Sbjct: 67  FSTIDGVREDVPEIVLNLKKVRFKSNCKRSCKTTLTLAGPKDFLAGDIVAQEGEFEVLNK 126

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  ++ +A V +++ + +G GYVPA+ +R++  PIG I ID++Y+PIK V  TVE+ 
Sbjct: 127 DLHIATINSEAAVTIDIYIGRGRGYVPAEENRSDGMPIGFIAIDSIYTPIKNVKLTVENT 186

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKKEVKEDIN 246
           R GQ  DY+K+ + ++TDGSI+ +D+++LA RI+ D +  F NF     E  +E  + ++
Sbjct: 187 RVGQKTDYEKMILDVETDGSISPDDAISLAGRIINDHVTFFANFSPTEEEYAEEEYKQLD 246

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L  K+E+L+LSVRS NCLR   I  + DL+ R E ++L   NFG+KSL E+
Sbjct: 247 EEFENMRKKLQTKIEDLDLSVRSHNCLRLAEIDTLADLVSRREDELLNYKNFGKKSLTEL 306

Query: 307 KGVLGTMGLFLGMNLPDWPPES 328
           +  L   GL  GM++  +  + 
Sbjct: 307 REALEKEGLKFGMDITRYQMKG 328


>gi|323436177|ref|ZP_01051163.2| DNA-directed RNA polymerase, alpha subunit [Dokdonia donghaensis
           MED134]
 gi|321496492|gb|EAQ37997.2| DNA-directed RNA polymerase, alpha subunit [Dokdonia donghaensis
           MED134]
 gi|332170585|gb|AEE19840.1| DNA-directed RNA polymerase, alpha subunit [Krokinobacter diaphorus
           4H-3-7-5]
          Length = 330

 Score =  305 bits (781), Expect = 8e-81,   Method: Composition-based stats.
 Identities = 123/325 (37%), Positives = 193/325 (59%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT+V+I+G
Sbjct: 5   NFQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGFAITSVRIEG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VND 124
           V HE S++ GV ED+T+IILN+K +  K   +   ++ VTI   G   +TAGD Q  ++ 
Sbjct: 62  VDHEFSTLAGVVEDVTEIILNLKQVRFKRQIEEIDNETVTISLSGVDQLTAGDFQKFISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLNPD VI N+D    + ME+T+ KG GYVPA+ ++  N P+G I  D++Y+PI+ V 
Sbjct: 122 FQVLNPDMVIANMDKKVNLNMEITIEKGRGYVPAEENKKSNAPLGTIFTDSIYTPIRNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y++E+ R  Q  DY+KL   I TDGSI  ++++  A++ L     +F    I  E  +  
Sbjct: 182 YSIENYRVEQKTDYEKLVFEIITDGSIHPKEALTEAAKTLIHHFMLFSDERITLEADEIA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+
Sbjct: 242 QTETYDEESLHMRQLLKTKLIDMDLSVRALNCLKAAEVETLGDLVSYNKNDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E++ ++   GL  GM+L  + 
Sbjct: 302 KSLTELEELVNVKGLSFGMDLAKYK 326


>gi|332042695|gb|EGI78895.1| DNA-directed RNA polymerase, alpha subunit [Lacinutrix algicola
           5H-3-7-4]
          Length = 330

 Score =  304 bits (780), Expect = 8e-81,   Method: Composition-based stats.
 Identities = 123/325 (37%), Positives = 194/325 (59%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT+++I+G
Sbjct: 5   NFQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGFAITSIRIEG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQT-VND 124
           V HE S++ GV ED+T+IILN+K +  K  +    ++ V+I   G   +TAGD Q  ++ 
Sbjct: 62  VDHEFSTVAGVVEDVTEIILNLKQMRFKRQIEDVDNESVSISISGQDKITAGDFQKFISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLN D VICNLD    + ME+T+ KG GYVPA+ ++  + PIG I  D++Y+PIK V 
Sbjct: 122 FQVLNSDLVICNLDPKVSITMEITIEKGRGYVPAEENKKASAPIGTIFTDSIYTPIKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y++E+ R  Q  DY+KL   I +DGSI+ +D++  A++ L     +F    I  E  +  
Sbjct: 182 YSIENYRVEQKTDYEKLVFEIQSDGSISPQDALTEAAKTLIHHFMLFSDERITLEADEIA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+
Sbjct: 242 QTETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E++ ++   GL  GM+L  + 
Sbjct: 302 KSLTELEELVNVKGLNFGMDLSKYK 326


>gi|56751897|ref|YP_172598.1| DNA-directed RNA polymerase subunit alpha [Synechococcus elongatus
           PCC 6301]
 gi|81301018|ref|YP_401226.1| DNA-directed RNA polymerase subunit alpha [Synechococcus elongatus
           PCC 7942]
 gi|6226041|sp|O24710|RPOA_SYNP6 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|119366742|sp|Q31L30|RPOA_SYNE7 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|2446913|dbj|BAA22472.1| DNA-dircted RNA polymerase alpha chain [Synechococcus elongatus PCC
           6301]
 gi|56686856|dbj|BAD80078.1| RNA polymerase alpha subunit [Synechococcus elongatus PCC 6301]
 gi|81169899|gb|ABB58239.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus elongatus
           PCC 7942]
          Length = 309

 Score =  304 bits (780), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 99/297 (33%), Positives = 161/297 (54%), Gaps = 6/297 (2%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
             ++        EPL RG   T+GNALRRVL+S+L G A+TAV+I GV HE ++I GV E
Sbjct: 13  EADQGQYGRFSIEPLARGQGTTVGNALRRVLLSNLEGTAVTAVRIGGVNHEFATIPGVRE 72

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+ DI+LN++ + +       +   +   GP  VTA D+    ++EV+NP+H I +L   
Sbjct: 73  DVLDILLNVRELVVHAHSPQPQIGRLRVVGPATVTAADVDFGPEVEVINPNHYIASLSEG 132

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
           A + MEL V  G GY        E   +  + +DA++ P+++V+Y+VE AR G+    D+
Sbjct: 133 ATLEMELKVEWGTGYRAIDRSHDETTALDFLQLDAVFMPVRRVNYSVEDARVGESTAIDR 192

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + + T+GS++ +++++ A+  L        N         +          P     +
Sbjct: 193 LVLEVWTNGSLSPQEALSQAASCLVALFEPLKNVSVGSTHTADP------EPTPESQTPI 246

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           E+L+LSVR+ NCL+   +  + DL+  T  D+L + NFG+KS  E+   L  +G+ L
Sbjct: 247 EDLQLSVRAYNCLKRAQVNSVADLLSYTYEDLLEIKNFGQKSAEEVVEALERIGIKL 303


>gi|16329917|ref|NP_440645.1| DNA-directed RNA polymerase subunit alpha [Synechocystis sp. PCC
           6803]
 gi|2500603|sp|P73297|RPOA_SYNY3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|1652403|dbj|BAA17325.1| RNA polymerase alpha subunit [Synechocystis sp. PCC 6803]
          Length = 314

 Score =  304 bits (780), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 109/311 (35%), Positives = 174/311 (55%), Gaps = 9/311 (2%)

Query: 14  NIEYIVLG--QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE +     + ++  +    EPL RG   T+GNALRRVL+S+L GAA+TA++I GV HE
Sbjct: 5   QIECVESSTRKNQQQYSKFSLEPLDRGQGTTVGNALRRVLLSNLPGAAVTAIRIAGVNHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            ++I GV ED+ +I+LN+K + LK   D  +   +   GPG VTA   +  +++EV++P+
Sbjct: 65  FATILGVREDVLEIMLNMKELVLKSYTDQPQIGRLTAIGPGTVTAAQFEVPSEVEVIDPN 124

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             I  L   A + ME  V +G GY   +  + EN  +  + ID+++ P+ KV+YTVE  R
Sbjct: 125 QYIATLAEGAKLEMEFRVERGVGYRVIERGKDENSSLDFLQIDSVFMPVTKVNYTVEDIR 184

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
              +   D+L + I T+GSI   ++++ AS I+ +      +  E    ++   +     
Sbjct: 185 ADGMSPKDRLILDIWTNGSIQPREALSEASDIIANLFIPLKDLNE----LEAAHSDYQDE 240

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            NP     +EEL+LSVR+ NCL+   I  + DL++ ++ D+L + NFG KS  E+   L 
Sbjct: 241 VNPESQIPIEELQLSVRAYNCLKRAQINSVADLLEYSQEDLLEIKNFGLKSAEEVIEAL- 299

Query: 312 TMGLFLGMNLP 322
                LG+ LP
Sbjct: 300 --QKRLGITLP 308


>gi|257792534|ref|YP_003183140.1| DNA-directed RNA polymerase, alpha subunit [Eggerthella lenta DSM
           2243]
 gi|317490400|ref|ZP_07948884.1| DNA-directed RNA polymerase [Eggerthella sp. 1_3_56FAA]
 gi|325833640|ref|ZP_08166089.1| DNA-directed RNA polymerase, alpha subunit [Eggerthella sp. HGA1]
 gi|257476431|gb|ACV56751.1| DNA-directed RNA polymerase, alpha subunit [Eggerthella lenta DSM
           2243]
 gi|316910535|gb|EFV32160.1| DNA-directed RNA polymerase [Eggerthella sp. 1_3_56FAA]
 gi|325485564|gb|EGC88033.1| DNA-directed RNA polymerase, alpha subunit [Eggerthella sp. HGA1]
          Length = 316

 Score =  304 bits (780), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 118/320 (36%), Positives = 185/320 (57%), Gaps = 10/320 (3%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E ++P     +   +  +     I EPL RG+ +TLGN +RRVL+SSL GA  TA+QI
Sbjct: 1   MTEFMRPT----VTTEEVNDTVARFIVEPLERGYGYTLGNCMRRVLLSSLDGAKATAIQI 56

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVN 123
           +GV HE ++ +GV ED+TDI+LN+KG+      D        +   GP  VT  D+    
Sbjct: 57  EGVQHEFTTAEGVIEDITDIVLNVKGLVFSALNDDIEEATAHVSAEGPCTVTGADLDIPT 116

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           +  ++NP+HVI  +     + M + +  G GYV A+ ++   DPIG+I +D+L+SP+++ 
Sbjct: 117 EFTLVNPEHVIATVADGGQLDMTVRIGVGRGYVSAERNKRTEDPIGVIHVDSLFSPVRRC 176

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +  V   R GQ  DYDKL + ++TDGSIT  ++V  AS I+   +G F++  +   E + 
Sbjct: 177 TLNVTDTRVGQRTDYDKLVLEVETDGSITPTEAVCRASNIINQYMGAFLSLSDVVDEEEG 236

Query: 244 DIN----VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           +I      +    N  L K++E+L+LSVRS NCL+   I  +  L++ +E D+L + NFG
Sbjct: 237 EIPSIFAPEGQESNAELDKQIEDLDLSVRSYNCLKRAGIHSVRQLVEFSENDLLNIRNFG 296

Query: 300 RKSLVEIKGVLGTMGLFLGM 319
            KS+ E+K  L +M L L +
Sbjct: 297 AKSIEEVKDKLISMDLNLKL 316


>gi|150025381|ref|YP_001296207.1| DNA-directed RNA polymerase subunit alpha [Flavobacterium
           psychrophilum JIP02/86]
 gi|172048610|sp|A6GZ73|RPOA_FLAPJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|149771922|emb|CAL43396.1| DNA-directed RNA polymerase alpha subunit RpoA [Flavobacterium
           psychrophilum JIP02/86]
          Length = 330

 Score =  304 bits (779), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 121/325 (37%), Positives = 191/325 (58%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++    +        PL  G+  T+GNALRRVL+S+L G AIT+++I+G
Sbjct: 5   NFQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSALEGYAITSIRIEG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQT-VND 124
           V HE S+I GV ED+T+IIL++K +  K  +    ++ VTI   G   +TAGD Q  ++ 
Sbjct: 62  VDHEFSTIPGVVEDVTEIILSLKQVRFKRQIEDIDNESVTIAISGKNQITAGDFQKYISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLNP+ VICNLD      ME+T+ KG GYVPA+ ++ +N  IG I  D++++P+K V 
Sbjct: 122 FQVLNPELVICNLDSKVNFNMEMTIEKGRGYVPAEENKKQNAAIGTIFTDSIFTPVKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y +E+ R  Q  DY+KL   I TDGSI  +D++  A+++L     +F    I  E  +  
Sbjct: 182 YAIENFRVEQKTDYEKLVFEIKTDGSINPKDALTEAAKVLIHHFMLFSDERITLEADEIA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+
Sbjct: 242 QTESYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E+  ++    L  GM+L  + 
Sbjct: 302 KSLTELDELVAIKNLTFGMDLAKYK 326


>gi|58415826|emb|CAH57327.1| RNA polymerase alpha-subunit [Vibrio diazotrophicus]
          Length = 309

 Score =  304 bits (779), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 134/315 (42%), Positives = 204/315 (64%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNAL R+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALHRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDV-DAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L   +A + M + V +G GYVPA    H   +  PIG + +DA +SP+ K+
Sbjct: 118 ANPEHVICHLTDSNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|125743179|gb|ABN54790.1| RpoA [Vibrio sp. RLUH-CZ]
          Length = 307

 Score =  304 bits (779), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 136/313 (43%), Positives = 202/313 (64%), Gaps = 11/313 (3%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T  +I+GVLH
Sbjct: 1   KPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEXEIEGVLH 57

Query: 71  EISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           E S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+ N
Sbjct: 58  EYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIAN 117

Query: 130 PDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSY 185
           P+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K++Y
Sbjct: 118 PEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAY 177

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           +VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +       
Sbjct: 178 SVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE---E 234

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 235 KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 294

Query: 306 IKGVLGTMGLFLG 318
           IK VL + GL LG
Sbjct: 295 IKDVLASRGLSLG 307


>gi|328813995|gb|AEB52113.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 254

 Score =  304 bits (779), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 117/254 (46%), Positives = 170/254 (66%), Gaps = 2/254 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTAIILNV 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK+  D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A   M +T 
Sbjct: 61  KKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGAHFHMRMTA 120

Query: 150 SKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           + G GYV A+ ++   ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T
Sbjct: 121 NTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +GSIT  ++++L+++IL D L +F+N  +  K     +  +       L   +EEL+LSV
Sbjct: 181 NGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEMTIEELDLSV 240

Query: 268 RSTNCLRGENIVYM 281
           RS NCL+   I  +
Sbjct: 241 RSYNCLKRAGINTV 254


>gi|90194050|gb|ABD92586.1| RpoA [Haemophilus parasuis]
          Length = 302

 Score =  304 bits (778), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 132/292 (45%), Positives = 198/292 (67%), Gaps = 7/292 (2%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
                 +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV ED+ 
Sbjct: 7   SSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQEDIL 66

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAV 142
           +++LN+KG+ +K+       +T+ K G G VTA DI    D+E++NPDHVICNL D +A 
Sbjct: 67  EVLLNLKGLAVKVQNKDDIILTLTKSGIGPVTAADITHDGDVEIVNPDHVICNLTDKNAS 126

Query: 143 VRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M + V +G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR  Q  D D
Sbjct: 127 ISMRIRVQRGRGYVPASARVHTQDDDRPIGRLLVDARFSPVDRIAYNVEAARVEQRTDLD 186

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F+P LL+ 
Sbjct: 187 KLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDVRQP---EVKEEKPEFDPILLRP 243

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
           V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL 
Sbjct: 244 VDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLA 295


>gi|312889340|ref|ZP_07748894.1| DNA-directed RNA polymerase subunit alpha [Mucilaginibacter paludis
           DSM 18603]
 gi|311298217|gb|EFQ75332.1| DNA-directed RNA polymerase subunit alpha [Mucilaginibacter paludis
           DSM 18603]
          Length = 330

 Score =  304 bits (778), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 130/324 (40%), Positives = 201/324 (62%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ +  +        PL  GF  T+GNALRR+L+SSL G AIT+V+  GV
Sbjct: 6   FQKPDKV---IMQKSNDFDGTFEFRPLEPGFGITIGNALRRILLSSLEGYAITSVRFSGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE S+IKGV ED+T+IILN+K + +K SG+    +++ +   G    +AGDI +  N+ 
Sbjct: 63  NHEFSTIKGVVEDVTEIILNLKQVRMKKSGESGDSEKIFVIINGQDTFSAGDITKFSNNF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
            VLNPD VICN+D    + +E+TV KG GYVP++ ++  +  +G+I ID++Y+PIK V Y
Sbjct: 123 TVLNPDLVICNMDSSVTLEIEITVGKGRGYVPSEENKNPDAMVGVIAIDSIYTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEV 241
           T+E+ R  Q  DY+KL + I TDGS+  ED++  A++IL     +F +     E   KE 
Sbjct: 183 TIENYRVEQKTDYEKLVLDIATDGSVHPEDALKEAAKILIQHFMLFSDENMMLEAQAKEE 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++++ + L     L  ++ +L+LSVR+ NCL+  +I  + DL+    ADML+  NFG+K
Sbjct: 243 TKEVDEEILHMRKILKTELVDLDLSVRALNCLKAADIRSLADLVSYDVADMLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL EI+ ++ + GL  GMNL  + 
Sbjct: 303 SLTEIQDLVKSKGLSFGMNLSKFK 326


>gi|256544533|ref|ZP_05471906.1| DNA-directed RNA polymerase, alpha subunit [Anaerococcus vaginalis
           ATCC 51170]
 gi|256399858|gb|EEU13462.1| DNA-directed RNA polymerase, alpha subunit [Anaerococcus vaginalis
           ATCC 51170]
          Length = 317

 Score =  304 bits (778), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 115/309 (37%), Positives = 194/309 (62%), Gaps = 5/309 (1%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             IE + + +E  N    +  PL RG+  T+GN++RR+L+SSL G++++ + IDGVLHE 
Sbjct: 7   TKIEILDIDEET-NYGKFVLYPLERGYGTTIGNSMRRMLLSSLPGSSVSKILIDGVLHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           S+I GV ED+ ++ILNIKGI++K        + +   GP +VTA DI+T   I+V NPDH
Sbjct: 66  STIPGVVEDVPELILNIKGIDIKKHTKEDITLFLDIEGPKIVTAKDIKTDAQIDVANPDH 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            +  ++    + + L V+ G GY  A+ ++ + DPIG I ID+ ++P+K V++TVE+ R 
Sbjct: 126 YLATVNDKGRLFIALDVTDGKGYRVAEQNKKDTDPIGAIAIDSSFTPVKSVNFTVENTRV 185

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF----EEPKKEVKEDINVK 248
           G+  DYDKL + + TDG+IT +++++  + IL + +  F +       P+ E +E   ++
Sbjct: 186 GESTDYDKLILEVWTDGTITPQEALSEGASILMEDIRFFKDLPGQQFPPEDEEEEIEEIE 245

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L K +EEL+LS+RS NCL+      +G++I+++E+++  + NFG+KSL E+  
Sbjct: 246 EDNNQMELSKTIEELDLSLRSFNCLKRAGYNTVGEIIEKSESELKDIKNFGKKSLEEVID 305

Query: 309 VLGTMGLFL 317
            + ++GL L
Sbjct: 306 KIHSLGLSL 314


>gi|261880855|ref|ZP_06007282.1| DNA-directed RNA polymerase subunit alpha [Prevotella bergensis DSM
           17361]
 gi|270332362|gb|EFA43148.1| DNA-directed RNA polymerase subunit alpha [Prevotella bergensis DSM
           17361]
          Length = 330

 Score =  304 bits (778), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 129/324 (39%), Positives = 197/324 (60%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  E+       PL  GF  T+GNALRR+L+SSL G AI  V+IDGV
Sbjct: 6   FQKPDKV---VMLEASESFGKFEFSPLEPGFGVTIGNALRRILLSSLEGYAINTVRIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVREDVTNIILNLKQVRFKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VIC+LD  A ++++LTV+KG GYVPA  +R     + ++ ID++Y+PI+ V Y
Sbjct: 123 EVLNPDLVICHLDSKASMQIDLTVNKGRGYVPADENRQFCTDVNVLPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           +VE  R  Q  DYDKL + I TDGSI  +D++  A++IL     +F    I  E+P K+ 
Sbjct: 183 SVEPTRVEQKTDYDKLCIEITTDGSIHPKDALNEAAKILIYHFMLFSDEKITLEDPNKDG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++ + + L     L  K+ +L LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NQEFDEEVLRMRQLLKTKLLDLNLSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLSELDDLLESLNLSFGTDISKYK 326


>gi|325955023|ref|YP_004238683.1| DNA-directed RNA polymerase subunit alpha [Weeksella virosa DSM
           16922]
 gi|323437641|gb|ADX68105.1| DNA-directed RNA polymerase subunit alpha [Weeksella virosa DSM
           16922]
          Length = 330

 Score =  304 bits (778), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 124/325 (38%), Positives = 195/325 (60%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
             IKP+ +   +L + +         PL  G+  T+GNALRRVL+SSL G AIT+++I+G
Sbjct: 5   NFIKPDKV---ILIESDTQFGQFEFRPLEPGYGITVGNALRRVLLSSLEGYAITSIKIEG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDI-QTVND 124
           V HE S+I GV ED+T+IILN+K +  K   D    + VT    G   +TAGD+ + ++ 
Sbjct: 62  VEHEFSTIPGVVEDVTEIILNLKKVRFKKQIDESDAENVTATISGQDQLTAGDLGKFISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLNP+ VI NLD    + +  T+ KG GYVPA+ ++  + PIG I ID++Y+PIK V 
Sbjct: 122 FQVLNPELVIANLDSKVNLTISFTIEKGRGYVPAEENKKASAPIGTIAIDSIYTPIKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y +E+ R  Q  DY+KL   I TDGSI+ +D++  A++IL     +F    I  E  +  
Sbjct: 182 YAIENYRVEQKTDYEKLVFEITTDGSISPQDALTEAAKILIHHFMLFSDERITLEAEEVA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + ++L     L  K+ +L+LSVR+ NCL+   +  +G+L+   ++D+++  NFG+
Sbjct: 242 SGEAYDEEALHMRQLLKTKLVDLDLSVRALNCLKAAEVETLGELVSFAKSDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E++ ++ + GL  GM+   + 
Sbjct: 302 KSLSELEELVDSKGLSFGMDTSKYK 326


>gi|170077662|ref|YP_001734300.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp. PCC
           7002]
 gi|169885331|gb|ACA99044.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus sp. PCC
           7002]
          Length = 313

 Score =  303 bits (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 104/311 (33%), Positives = 168/311 (54%), Gaps = 9/311 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             +E      + +  +  + EPL RG   TLGN+LRR+L+S+L G A+TA++I GV HE 
Sbjct: 7   ECVESKTHKNQSQ-YSKFVFEPLERGQGTTLGNSLRRILLSNLEGTAVTALRIGGVNHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED  +IILN+K I LK      +   +   GPG VTA      +++EV++P  
Sbjct: 66  ATIPGVREDALEIILNMKEIILKSYTHQPQIGRLTATGPGQVTAAQFDLPSEVEVVDPTQ 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L   A + ME  + KG  Y   + +R E   +  + IDA++ P+ KV+Y+V+S   
Sbjct: 126 YIATLADGAKLEMEFRIEKGKSYRAVQRNRDEATALDFLQIDAVFMPVTKVNYSVDSIHS 185

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
                 D+L++ I T+GSI  E++++ A+ I  +      +      + +   +      
Sbjct: 186 EGDAVRDRLTLEIWTNGSIKPEEALSQAAAIAVELFNPLKDLTLEAIQDELQEDE----- 240

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P     +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L T
Sbjct: 241 DPTSQIPIEELQLSVRAYNCLKRAQINSVADLLDYSQEDLLEIKNFGQKSAEEVIDALKT 300

Query: 313 MGLFLGMNLPD 323
               LG+ LP+
Sbjct: 301 ---RLGITLPE 308


>gi|281423812|ref|ZP_06254725.1| DNA-directed RNA polymerase, alpha subunit [Prevotella oris F0302]
 gi|299141174|ref|ZP_07034311.1| DNA-directed RNA polymerase, alpha subunit [Prevotella oris C735]
 gi|281402039|gb|EFB32870.1| DNA-directed RNA polymerase, alpha subunit [Prevotella oris F0302]
 gi|298577134|gb|EFI49003.1| DNA-directed RNA polymerase, alpha subunit [Prevotella oris C735]
          Length = 330

 Score =  303 bits (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 124/324 (38%), Positives = 194/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  E        PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---VMLEASEKFGKFEFRPLEPGFGVTIGNALRRILLSSLEGYAINTIRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VIC+LD  A ++++LT++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPDLVICHLDAKASMQIDLTINKGRGYVPADENREFCTDVNVIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           +VE  R  Q  DYDKL + + TDGSI  +D++  A++IL     +F    I  E P ++ 
Sbjct: 183 SVEPYRVEQKTDYDKLVIEVSTDGSIHPKDALKEAAKILIYHFMLFSDEKITLESPDQDG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++ + + L     L  K+ ++ LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NQEFDEEVLHMRQLLKTKLVDMNLSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLSELDDLLESLNLSFGTDISKYK 326


>gi|328813939|gb|AEB52085.1| DNA-directed RNA polymerase alpha chain [Lactobacillus brevis]
          Length = 265

 Score =  303 bits (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 117/265 (44%), Positives = 175/265 (66%), Gaps = 4/265 (1%)

Query: 28  TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIIL 87
              I EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T IIL
Sbjct: 1   GKFIVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVTQIIL 60

Query: 88  NIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           N+K I LK++G  D  + + I  +GP  +TAGDI    D+++LNPD  I  +   A   M
Sbjct: 61  NVKKIALKLNGSDDQEETMEINVKGPAQITAGDIVAGADVDILNPDLYIATVADGATFHM 120

Query: 146 ELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +T  KG GYV A  ++T   + PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++
Sbjct: 121 RMTADKGRGYVSADENKTRNTDMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTL 180

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            + T+GSI   +++ALA++IL + L MF++  +  K  +  +  +       L   +EEL
Sbjct: 181 DVWTNGSINPSEAIALAAKILTEHLAMFVDLTDEAKNAEIMVEKEETHKEKMLEMTIEEL 240

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRT 288
           +LSVRS NCL+   I  + +L  +T
Sbjct: 241 DLSVRSYNCLKRAGINTVQELNNKT 265


>gi|255530541|ref|YP_003090913.1| DNA-directed RNA polymerase subunit alpha [Pedobacter heparinus DSM
           2366]
 gi|255343525|gb|ACU02851.1| DNA-directed RNA polymerase, alpha subunit [Pedobacter heparinus
           DSM 2366]
          Length = 330

 Score =  303 bits (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 131/324 (40%), Positives = 200/324 (61%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ +  +        PL  GF  T+GNALRR+L+SSL G AIT+++  GV
Sbjct: 6   FQKPDKV---IMQKSTDFDGTFEFRPLEPGFGVTIGNALRRILLSSLEGYAITSIRFSGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE S+IKGV EDLT+IILN+K +  K SGD    ++V I   G     AGDI +  N+ 
Sbjct: 63  SHEFSTIKGVVEDLTEIILNLKQVRFKKSGDAGDSEKVFILVNGQEQFVAGDITKFSNNF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VICN++    + +ELT++KG GYVPA+ ++  +  +G+I ID++++P+K V Y
Sbjct: 123 EVLNPDFVICNMEKSVTLEVELTINKGRGYVPAEENKINDAVVGVIAIDSIFTPMKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEV 241
           T+E+ R  Q  DY+KL + I TDGSI  E+++  A++IL     +F +     E   KE 
Sbjct: 183 TIENYRVEQKTDYEKLILDISTDGSIHPEEALKEAAKILIQHFMLFSDENLVLESQAKEE 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++++ + L     L  ++ +L+LSVR+ NCL+  +I  + DL+    ADML+  NFG+K
Sbjct: 243 TKEVDEEILHMRKILKTELVDLDLSVRALNCLKAADIRTLADLVSYDVADMLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL EI+ ++ +  L  GMNL  + 
Sbjct: 303 SLTEIQELVKSKSLSFGMNLSKFK 326


>gi|328814003|gb|AEB52117.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 261

 Score =  303 bits (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 118/257 (45%), Positives = 171/257 (66%), Gaps = 2/257 (0%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E +N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED
Sbjct: 5   DENDNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTED 64

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A
Sbjct: 65  VTAIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGA 124

Query: 142 VVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              M +T + G GYV A+ ++   ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+D
Sbjct: 125 HFHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFD 184

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL++ + T+GSIT  ++++L+++IL D L +F+N  +  K     +  +       L   
Sbjct: 185 KLTLDVWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEMT 244

Query: 260 VEELELSVRSTNCLRGE 276
           +EEL+LSVRS NCL+  
Sbjct: 245 IEELDLSVRSYNCLKRA 261


>gi|328949253|ref|YP_004366590.1| DNA-directed RNA polymerase subunit alpha [Treponema succinifaciens
           DSM 2489]
 gi|328449577|gb|AEB15293.1| DNA-directed RNA polymerase subunit alpha [Treponema succinifaciens
           DSM 2489]
          Length = 348

 Score =  303 bits (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 126/331 (38%), Positives = 189/331 (57%), Gaps = 12/331 (3%)

Query: 1   MIQKNW-QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M +KN  +   KP  I +  L     N     A P   GF  T+GN LRRVL+SS++G A
Sbjct: 1   MARKNLLKGFKKPKGIIFEHLEN-NPNYGKFTAYPFEPGFGTTVGNTLRRVLLSSIQGYA 59

Query: 60  ITAVQI-----DGVLHEIS----SIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKR 109
           I++V+I     DGV H IS    +I  + ED  +++ ++K I L++  D   +      +
Sbjct: 60  ISSVRITSYDADGVPHVISSEFETIPNISEDTLEVLNSLKQIRLRLPRDVEQETFFYEFK 119

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GPG V + D+     +E+++ D  I  +   A + +E  V  G GYVPA+ +    + +G
Sbjct: 120 GPGTVKSDDLAKEGQLEIMSKDLEIFTMMEGAHLEIEFQVDLGRGYVPAEVNEHYIEIVG 179

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            I +D +++P+ KV Y++E  R GQ  DYDKL + I TDGSIT ED++A A++I +D   
Sbjct: 180 TIAMDCIFTPVPKVKYSIEPCRVGQRNDYDKLILEIWTDGSITPEDALAEAAKIAKDYFA 239

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +F+NF E +    ++++         L   VEELELSVRS+NCL+  NI  +G+L ++TE
Sbjct: 240 IFVNFNESEYSGSDELDEGDEKIRQLLNTSVEELELSVRSSNCLKNANIRTIGELTKKTE 299

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
            D+ +  NFG+KSL EIK  L   GL LGM 
Sbjct: 300 DDITKTRNFGKKSLEEIKAKLEEHGLTLGMT 330


>gi|22297649|ref|NP_680896.1| DNA-directed RNA polymerase subunit alpha [Thermosynechococcus
           elongatus BP-1]
 gi|34222870|sp|Q8DML0|RPOA_THEEB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|22293826|dbj|BAC07658.1| RNA polymerase alpha subunit [Thermosynechococcus elongatus BP-1]
          Length = 321

 Score =  303 bits (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 103/311 (33%), Positives = 168/311 (54%), Gaps = 16/311 (5%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           + +++         PL  G   T+GNALRRVL+S+L G+A+TAV+I GV HE S+I GV 
Sbjct: 12  VEEDQGQYGQFALHPLAPGQGITVGNALRRVLLSNLPGSAVTAVRIAGVNHEFSTIPGVR 71

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGV----VTAGDIQTVNDIEVLNPDHVIC 135
           ED+ DI+L +K + ++      +   +F + P      VTAG +Q  +++EV+NP+H I 
Sbjct: 72  EDVMDILLQMKQLVIRSHTSEPQMGRLFAQAPENEPLTVTAGMVQLGSEVEVVNPNHYIA 131

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR---- 191
            L   A + ME  + K  GY   +  R +   +  + +DA++ P+++V+YTV+S R    
Sbjct: 132 TLMPGATLEMEFKIEKDRGYRSVERVRDDRLALDYLQLDAVFMPVRRVNYTVDSVRSAGA 191

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           EG     D L + I T+GS+T +D++  A+ IL D        +E      E        
Sbjct: 192 EGDRQLQDYLKLEIWTNGSLTPQDALNQAATILVDLFSP---LKEVPLHTSEATATDD-- 246

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +      +E+L LSVR+ NCL+   +  + DL++ ++ ++L + NFG+KS  E+   L 
Sbjct: 247 HDETGQIPIEQLNLSVRAYNCLKRAQVNTVADLLEYSQEELLEIKNFGQKSAEEVIEAL- 305

Query: 312 TMGLFLGMNLP 322
                LG+ LP
Sbjct: 306 --QKHLGITLP 314


>gi|255038116|ref|YP_003088737.1| DNA-directed RNA polymerase subunit alpha [Dyadobacter fermentans
           DSM 18053]
 gi|254950872|gb|ACT95572.1| DNA-directed RNA polymerase, alpha subunit [Dyadobacter fermentans
           DSM 18053]
          Length = 322

 Score =  303 bits (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 128/315 (40%), Positives = 195/315 (61%), Gaps = 6/315 (1%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           + +V+ + ++   L   +PL +G+  T+GNALRR+L+SSL G AIT+V+  GVLHE SSI
Sbjct: 3   DKVVMEKADDFHGLFEFKPLEKGYGVTIGNALRRILLSSLEGYAITSVKFPGVLHEFSSI 62

Query: 76  KGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHV 133
           +G+ ED+T+IILN+K +  K   D S  R+ +  +   V+TAGDI +  +  EVLNPD V
Sbjct: 63  EGIVEDVTEIILNLKMVRFKKVSDLSESRIVVNLKNVSVITAGDIGKFTSAFEVLNPDQV 122

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           IC++D      MEL + KG GYVPA   R    P G I +D++Y+PIK V Y+VE+ R  
Sbjct: 123 ICHIDDQKEFEMELLLDKGRGYVPADEPRANELPFGYIAVDSIYTPIKNVKYSVENTRVE 182

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKS 249
           Q  DY++L + I TDGSI  ED++  A+ IL     +F +    FE+ K E    ++ + 
Sbjct: 183 QRTDYERLLIDIQTDGSIHPEDALKGAANILIQHFMLFSDQTMTFEKQKAEEDNQVDEEM 242

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           L     L   + EL+LSVR+ NCL+  ++  +GDL++   +DM++  NFG+KSL E++ +
Sbjct: 243 LRMRKLLKTSLSELDLSVRAYNCLKSADVKTLGDLVRLEISDMMKFRNFGKKSLTELEQL 302

Query: 310 LGTMGLFLGMNLPDW 324
           +    L  GM++  +
Sbjct: 303 VADKQLTFGMDVSKY 317


>gi|328813967|gb|AEB52099.1| DNA-directed RNA polymerase alpha chain [Lactobacillus fermentum]
          Length = 271

 Score =  303 bits (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 117/268 (43%), Positives = 178/268 (66%), Gaps = 2/268 (0%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E +N    + EPL RG+  TLGN+LRRV+++SL GAAIT++QIDGVLHE S+++GV ED
Sbjct: 4   EETDNYGKFVVEPLERGYGTTLGNSLRRVMLASLPGAAITSIQIDGVLHEFSTVQGVTED 63

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILN+K + LK+  +  K + I  +GP  VTA DIQ   D+ +LN D  I  +   A
Sbjct: 64  VTQIILNLKQVALKIDSEDAKDLEIDVKGPAEVTAADIQGDGDVTILNSDLHIATVSDGA 123

Query: 142 VVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
            + +++T  KG GY  A  ++T  E   IG++ ID++Y+PI++V+YTVE+ R GQ  DYD
Sbjct: 124 ELHVKMTADKGRGYSSADDNKTRMEGLAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYD 183

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL++ + T+GS+T  ++++LA++IL + L MF+N  E  +  +  +  +       L K 
Sbjct: 184 KLTLDVWTNGSLTPTEAISLAAKILTEHLTMFVNLTEEAQVTQVMVEREETHQEKVLDKT 243

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQR 287
           +EEL+LSVRS NCL+  +I  + DL +R
Sbjct: 244 IEELDLSVRSYNCLKRADIQTVKDLTER 271


>gi|288801125|ref|ZP_06406581.1| DNA-directed RNA polymerase, alpha subunit [Prevotella sp. oral
           taxon 299 str. F0039]
 gi|288332059|gb|EFC70541.1| DNA-directed RNA polymerase, alpha subunit [Prevotella sp. oral
           taxon 299 str. F0039]
          Length = 330

 Score =  303 bits (776), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 120/324 (37%), Positives = 197/324 (60%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  +        PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---VMLEANDKFGKFEFRPLEPGFGVTIGNALRRILLSSLEGFAINTIKIGGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +    +++V+I         AGD+ + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVDEFENEKVSITVENTTEFKAGDMGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VIC+LD  A +++++T++KG GYVPA  +R  +  + ++ ID++Y+PI+ V Y
Sbjct: 123 EVLNPDLVICHLDAKASMQIDITINKGRGYVPADENRQYSTDVNVLPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           +VE  R  Q  DYDKL + + TDGSI+ +D++  A++IL     +F    I  E P+++ 
Sbjct: 183 SVEPYRVEQKTDYDKLVLEVTTDGSISPKDALKEAAKILIYHFMLFSDEKITLENPEQDS 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++ + + L     L  K+ ++ LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NDEFDEEVLHMRQLLKTKLVDMNLSVRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLSELDDLLESLNLSFGTDISKYK 326


>gi|257067033|ref|YP_003153289.1| DNA-directed RNA polymerase subunit alpha [Anaerococcus prevotii
           DSM 20548]
 gi|256798913|gb|ACV29568.1| DNA-directed RNA polymerase, alpha subunit [Anaerococcus prevotii
           DSM 20548]
          Length = 318

 Score =  303 bits (776), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 112/304 (36%), Positives = 187/304 (61%), Gaps = 5/304 (1%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            EEEN       PL RG+  T+GN++RRVL+SSL G++++ + I+GVLHE S+I GV ED
Sbjct: 15  DEEENYGKFALYPLERGYGTTIGNSMRRVLLSSLPGSSVSKILIEGVLHEFSTIDGVVED 74

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + +I+LNIKG+++    D    + +   GP +VTA DI+  + +++ NPDH I  ++  +
Sbjct: 75  VPEIVLNIKGLDVTKHVDEDVTLFLDIEGPKIVTAKDIKADSSVDIANPDHYIATVNEKS 134

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + + + V+ G GY  +  ++ E+DPIG I ID+ ++P++KV++TVE+ R G+  DYDKL
Sbjct: 135 RLFIAMDVTDGKGYRVSDDNKKESDPIGAIAIDSSFTPVEKVNFTVENTRVGESTDYDKL 194

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK-----KEVKEDINVKSLPFNPAL 256
            M + T+G+IT ++++A  S IL +    F      +     +E + +   +    +  L
Sbjct: 195 VMEVWTNGTITPQEALAEGSSILIENFSFFNELPNQQFPPEVEEEEIEEVEEEDSLSEDL 254

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +EEL+LS+RS NCL+      +GD+I+ +E+++  + NFG+KSL E+   L  +GL 
Sbjct: 255 AMTIEELDLSLRSFNCLKRAGFDRVGDIIKVSESELKTIKNFGKKSLTEVIEKLDELGLS 314

Query: 317 LGMN 320
           L   
Sbjct: 315 LKDE 318


>gi|281357932|ref|ZP_06244417.1| DNA-directed RNA polymerase, alpha subunit [Victivallis vadensis
           ATCC BAA-548]
 gi|281315590|gb|EFA99618.1| DNA-directed RNA polymerase, alpha subunit [Victivallis vadensis
           ATCC BAA-548]
          Length = 338

 Score =  303 bits (776), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 133/322 (41%), Positives = 186/322 (57%), Gaps = 4/322 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
              P +I  +      E     IA P   GF HTLGN+LRRVL+SSL GAAI +V+IDG 
Sbjct: 7   FPMPKSI-VVDDATVTETYAKFIAAPFQSGFGHTLGNSLRRVLLSSLEGAAICSVRIDGA 65

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE  S+  V ED+T+I+LN+K + L +  +  K + I K   G VTA DI   + +EVL
Sbjct: 66  KHEFDSLDNVVEDVTEIVLNLKCVRLNLHAEGPKTLEIRKDKAGKVTAADIVCDSTVEVL 125

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NPD VIC LD     R E+ V KG GY+PA+ +      IG I +D L+SP+ +V+Y V 
Sbjct: 126 NPDQVICTLDKSLPFRAEIEVIKGKGYLPAEKNTAP-RSIGTIPVDCLFSPVTRVNYQVG 184

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +AR G+  + D L + I TDG I+ ++++  A+RIL+D L  F+       E    +  +
Sbjct: 185 AARVGEETEMDSLELEIWTDGRISPQNALEEAARILRDHLQPFMG--NQVVEKDVVLTEE 242

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L   VE L+LSVR+ NCL   NI  +G+L  +TE+ ML+  NFG+KSL EIK 
Sbjct: 243 ETKMFKLLSHDVEILDLSVRAMNCLNSANIKLIGELCTKTESRMLKYRNFGKKSLDEIKE 302

Query: 309 VLGTMGLFLGMNLPDWPPESIE 330
            +  +GL LGM+  D    ++E
Sbjct: 303 KIEKLGLELGMSFSDRLMAALE 324


>gi|90194058|gb|ABD92590.1| RpoA [Mannheimia granulomatis]
          Length = 303

 Score =  303 bits (776), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 132/296 (44%), Positives = 200/296 (67%), Gaps = 7/296 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +G
Sbjct: 2   VNIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +++LN+KG+ +K+       +T+ K G G VTA DI    D+E++NPDHVICNL
Sbjct: 62  VQEDILEVLLNLKGLAVKVQNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPDHVICNL 121

Query: 138 -DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            D +A + M + V +G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR  
Sbjct: 122 TDKNASINMRIRVQRGRGYVPASARLHTQNDDRPIGRLLVDARFSPVDRIAYNVEAARVE 181

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F+
Sbjct: 182 QRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDVRQP---EVKEEKPEFD 238

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK V
Sbjct: 239 PILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDV 294


>gi|212697280|ref|ZP_03305408.1| hypothetical protein ANHYDRO_01848 [Anaerococcus hydrogenalis DSM
           7454]
 gi|325848968|ref|ZP_08170478.1| DNA-directed RNA polymerase, alpha subunit [Anaerococcus
           hydrogenalis ACS-025-V-Sch4]
 gi|212675729|gb|EEB35336.1| hypothetical protein ANHYDRO_01848 [Anaerococcus hydrogenalis DSM
           7454]
 gi|325480612|gb|EGC83674.1| DNA-directed RNA polymerase, alpha subunit [Anaerococcus
           hydrogenalis ACS-025-V-Sch4]
          Length = 318

 Score =  303 bits (776), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 119/310 (38%), Positives = 196/310 (63%), Gaps = 6/310 (1%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             IE + + +E  N    +  PL RG+  T+GN++RR+L+SSL G++++ + IDGVLHE 
Sbjct: 7   TKIEILDIDEET-NYGKFVLYPLERGYGTTIGNSMRRMLLSSLPGSSVSKILIDGVLHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           S+I GV ED+ ++ILNIKGI++K        + +   GP +VTA DI+T   IEV NPDH
Sbjct: 66  STIPGVVEDVPELILNIKGIDIKKHTKEDLTLFLDIEGPKIVTAKDIKTDAQIEVANPDH 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            +  ++  A + + L V+ G GY  A+ ++ + DPIG I ID+ ++P+K V++TVE+ R 
Sbjct: 126 YLATVNDKARLFIALDVTDGKGYRVAELNKKDTDPIGAIAIDSSFTPVKSVNFTVENTRV 185

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF----EEPKKEVKEDINVK 248
           G+  DYDKL + + TDG+IT +++++  + IL + +  F +       P+ E +E   ++
Sbjct: 186 GESTDYDKLILEVWTDGTITPQEALSEGASILMEDIRFFKDLPGQQFPPEVEEEEVEEIE 245

Query: 249 SLPFNPALLKK-VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
               N   L K +EEL+LS+RS NCL+      +G++I+++EA++  + NFG+KSL E+ 
Sbjct: 246 EEDDNQVELSKTIEELDLSLRSFNCLKRAGYNTVGEIIEKSEAELKDIKNFGKKSLDEVI 305

Query: 308 GVLGTMGLFL 317
             + ++GL L
Sbjct: 306 DKIHSLGLSL 315


>gi|146298135|ref|YP_001192726.1| DNA-directed RNA polymerase subunit alpha [Flavobacterium
           johnsoniae UW101]
 gi|146152553|gb|ABQ03407.1| DNA-directed RNA polymerase, alpha subunit [Flavobacterium
           johnsoniae UW101]
          Length = 330

 Score =  303 bits (776), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 123/325 (37%), Positives = 191/325 (58%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++    +        PL  G+  T+GNALRRVL+S+L G AIT+V+I+G
Sbjct: 5   NFQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSALEGYAITSVRIEG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQT-VND 124
           V HE S+I GV ED+T+IILN+K +  K  +    ++ VTI   G   +TAGD Q  ++ 
Sbjct: 62  VDHEFSTISGVVEDVTEIILNLKQVRFKRQIEDIDNESVTISVSGKDQLTAGDFQKFISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLNPD VICNLD    +  +LT+ KG GYVPA+ ++ +N  IG I  D++++P+K V 
Sbjct: 122 FQVLNPDLVICNLDSKIKLNFDLTIEKGRGYVPAEENKKQNAAIGTIFTDSIFTPVKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y +E+ R  Q  DY+KL   I TDGSI  +D++  A+++L     +F    I  E  +  
Sbjct: 182 YAIENFRVEQKTDYEKLVFEIKTDGSINPKDALTEAAKVLIHHFMLFSDERITLEADEIA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+
Sbjct: 242 QTESYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E+  ++    L  GM+L  + 
Sbjct: 302 KSLTELDELVAVKNLTFGMDLAKYK 326


>gi|189308771|gb|ACD87087.1| RpoA [Vibrio sp. PP-200]
          Length = 302

 Score =  303 bits (776), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 135/304 (44%), Positives = 199/304 (65%), Gaps = 8/304 (2%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV 
Sbjct: 2   IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQ 61

Query: 80  EDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
           ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+ NP+HVIC+L 
Sbjct: 62  EDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEITNPEHVICHLT 121

Query: 139 VD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
              A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q
Sbjct: 122 DGNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQ 181

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
             D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P
Sbjct: 182 RTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDP 238

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
            LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + G
Sbjct: 239 ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRG 298

Query: 315 LFLG 318
           L LG
Sbjct: 299 LSLG 302


>gi|282880974|ref|ZP_06289665.1| DNA-directed RNA polymerase, alpha subunit [Prevotella timonensis
           CRIS 5C-B1]
 gi|281305197|gb|EFA97266.1| DNA-directed RNA polymerase, alpha subunit [Prevotella timonensis
           CRIS 5C-B1]
          Length = 330

 Score =  303 bits (775), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 121/324 (37%), Positives = 195/324 (60%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP  +   V+ + ++        PL  GF  T+GN+LRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPEKV---VMLEADDKFGKFEFRPLEPGFGITIGNSLRRILLSSLEGYAINTMRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VIC+LD  A ++++LT+++G GYVPA  +R     + ++ ID++Y+PI+ V Y
Sbjct: 123 EVLNPDLVICHLDAKASMQIDLTINQGRGYVPADENRQFCTDVNVLPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           TVE  R  Q  DYDKL + + TDGSI+ +D++  A++IL     +F    I  E P ++ 
Sbjct: 183 TVEPYRVEQKTDYDKLVIEVTTDGSISPKDALKEAAKILIYHFMLFSDEKITLENPDQDT 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++ + + L     L  K+ ++ LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NQEFDEEVLHMRQLLKTKLVDMNLSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLSELDDLLESLNLSFGTDISKYK 326


>gi|227501161|ref|ZP_03931210.1| DNA-directed RNA polymerase [Anaerococcus tetradius ATCC 35098]
 gi|227216746|gb|EEI82147.1| DNA-directed RNA polymerase [Anaerococcus tetradius ATCC 35098]
          Length = 318

 Score =  303 bits (775), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 118/313 (37%), Positives = 195/313 (62%), Gaps = 6/313 (1%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
            NI+ + + +EE         PL RG+  T+GN++RRVL+SSL G++++ + I+GVLHE 
Sbjct: 7   TNIQILDINEEEH-YGKFALYPLERGYGTTIGNSMRRVLLSSLPGSSVSKILIEGVLHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           S+I GV ED+ +I+LNIKG+++    D    + +   GP +VTA DI+  + +E+ NPDH
Sbjct: 66  STIDGVVEDVPEIVLNIKGLDVTKHTDEDVTLFLDIEGPKIVTAKDIKEDSSVEIANPDH 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  ++  + + + + V+ G GY  ++ ++ E+DPIG I ID+ ++P+KKV++TVE+ R 
Sbjct: 126 YIATVNEKSRLFIAMDVTDGKGYRISEENKKESDPIGAIAIDSSFTPVKKVNFTVENTRV 185

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK-----KEVKEDINV 247
           G+  DYDKL M + T+G+IT ++++A  S IL D    F      +     +EV+E++N 
Sbjct: 186 GESTDYDKLIMEVWTNGTITPQEALAEGSSILIDNFSFFTELPNQQFPPEVEEVEEEVND 245

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +    N  L   +EE++LS+RS NCL+      + D+I+ TE+++  + NFG+KSL E+ 
Sbjct: 246 EEENLNEDLAMTIEEMDLSLRSFNCLKRAGFNRVSDIIEVTESELKAIKNFGKKSLTEVI 305

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L   
Sbjct: 306 EKLDELGLSLKDE 318


>gi|158334432|ref|YP_001515604.1| DNA-directed RNA polymerase subunit alpha [Acaryochloris marina
           MBIC11017]
 gi|158304673|gb|ABW26290.1| DNA-directed RNA polymerase, alpha subunit [Acaryochloris marina
           MBIC11017]
          Length = 313

 Score =  303 bits (775), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 105/304 (34%), Positives = 172/304 (56%), Gaps = 8/304 (2%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            + ++    +  I EPL RG   T+GNALRRVL+++LRG A+TAV+I GV HE ++I GV
Sbjct: 12  TVEEDFSQYSRFILEPLDRGQGTTVGNALRRVLLANLRGTAVTAVRIAGVNHEFATIPGV 71

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+ DI+LN+K + L+   +  +   +F +GP  VT  D +   ++E++NP   +  L 
Sbjct: 72  REDVLDILLNMKQVVLRSHTNDPQIGRLFVQGPATVTTDDFELPTEVEIVNPTQYVATLS 131

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            DA + ME  + +G GY     +R E   +  + IDA+Y P+++V+Y VE AR G  L+ 
Sbjct: 132 SDATLEMEFRIEQGKGYHAVGKNRDEAAALDFLEIDAIYMPVRRVNYEVEDARVGGALEK 191

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           D+L + I T+G++T ++S++ A+ IL D      +            +++    +     
Sbjct: 192 DRLILDIWTNGNLTPQESLSQAATILVDLFNPLKD-----ATFNVVEDIELEEEDETNQI 246

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E L LSVR+ NCL+   I  + DL++ ++ D+L + NFG KS  E+   L      LG
Sbjct: 247 PIEGLNLSVRAYNCLKRAQINSVADLLEYSQEDLLEIKNFGAKSADEVIAALQD---HLG 303

Query: 319 MNLP 322
           + +P
Sbjct: 304 ITMP 307


>gi|88803724|ref|ZP_01119248.1| DNA-directed RNA polymerase alpha subunit [Polaribacter irgensii
           23-P]
 gi|88780457|gb|EAR11638.1| DNA-directed RNA polymerase alpha subunit [Polaribacter irgensii
           23-P]
          Length = 330

 Score =  303 bits (775), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 125/325 (38%), Positives = 196/325 (60%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++ +  +        PL  GF  T+GNALRRVL+SSL G AIT++++DG
Sbjct: 5   NFQKPDKV---IMIESTDFSGRFEFRPLEPGFGLTVGNALRRVLLSSLEGFAITSLRLDG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQT-VND 124
           V HE S++ GV ED+T+IILN+K +  K   +    + V+I   G    TAGD+Q  ++ 
Sbjct: 62  VEHEFSTVSGVVEDVTEIILNLKQVRFKKQIEETDRETVSISVSGQEQFTAGDLQKFISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLNPD VICN+D    +  E+T+ KG G+VPA+ ++  + PIG I  D++Y+PIK V 
Sbjct: 122 FQVLNPDLVICNMDKSVKLNAEITIEKGRGFVPAEENKKASAPIGTIFTDSIYTPIKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y VE+ R  Q  DY+KL   IDTDGSI+ +D++  A++IL     +F    I  E  +  
Sbjct: 182 YAVENFRVEQKTDYEKLVFDIDTDGSISPKDALTEAAKILIHHFMLFSDERITLEADEIA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + +SL     L  ++ +++LSVR+ NCL+   +  +GDL+   ++D+++  NFG+
Sbjct: 242 QTETYDEESLHMRQLLKTRLIDMDLSVRALNCLKAAEVDTLGDLVSFNKSDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E++ ++   GL  GM+L  + 
Sbjct: 302 KSLTELEELVIVKGLSFGMDLSKYK 326


>gi|300728416|ref|ZP_07061778.1| DNA-directed RNA polymerase, alpha subunit [Prevotella bryantii
           B14]
 gi|299774335|gb|EFI70965.1| DNA-directed RNA polymerase, alpha subunit [Prevotella bryantii
           B14]
          Length = 330

 Score =  303 bits (775), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 125/324 (38%), Positives = 195/324 (60%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  +        PL  GF  T+GNALRR+L+SSL G AI  V+I GV
Sbjct: 6   FQKPDKV---VMLEANDKFGRFEFRPLEPGFGVTVGNALRRMLLSSLEGYAINTVKIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K I  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQIRFKQVVEEFENEKVSIIVENSTEFKAGDISKHLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+ VIC+LD  A +R++LT++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPELVICHLDPKASMRIDLTINKGRGYVPADENRQFCTDVNVIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           +VE  R  Q  DYDKL++ + TDGSI  +D++  A++IL     +F    I  E P ++ 
Sbjct: 183 SVEPYRVEQKTDYDKLTIEVTTDGSIHPKDALKEAAKILIYHFMLFSDEKITLENPDQDG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++ + + L     L  K+ ++ LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NQEFDEEVLHMRQLLKTKLVDMNLSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLSELDDLLESLNLSFGTDISKYK 326


>gi|161511763|emb|CAP16892.1| DNA-directed RNA polymerase subunit alpha [Pediococcus parvulus]
          Length = 264

 Score =  303 bits (775), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 119/267 (44%), Positives = 174/267 (65%), Gaps = 6/267 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KPN    I    E  N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLH
Sbjct: 2   KPN----IHKIDENANYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLH 57

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S+I+GV ED+T IILNIK ++LK+  D  K + I  +GP  VTAGDIQ  +D+E+LNP
Sbjct: 58  EFSTIEGVVEDVTQIILNIKKVSLKIESDDEKSLEINVKGPATVTAGDIQGDSDVEILNP 117

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVE 188
           D  IC +         LT   G GYV A  ++   ++ PIG++ ID++Y+PI++V+Y VE
Sbjct: 118 DQYICTVADGVTFHAVLTADTGRGYVSADENKARKDDMPIGVLPIDSIYTPIERVNYQVE 177

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           + R GQ  DYDKL++ + TDGSI+  ++ +L+++IL + L +F+N  +  ++ +  +  +
Sbjct: 178 NTRVGQRDDYDKLTLDVWTDGSISPSEATSLSAKILTEHLALFVNLTDEAQDAEIMVEKE 237

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRG 275
                  L   +EEL+LSVRS NCL+ 
Sbjct: 238 ETHKEKMLEMSIEELDLSVRSYNCLKR 264


>gi|124003688|ref|ZP_01688536.1| DNA-directed RNA polymerase, alpha subunit [Microscilla marina ATCC
           23134]
 gi|123990743|gb|EAY30210.1| DNA-directed RNA polymerase, alpha subunit [Microscilla marina ATCC
           23134]
          Length = 329

 Score =  303 bits (775), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 124/316 (39%), Positives = 192/316 (60%), Gaps = 6/316 (1%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           E +V+ +  +   +   +PL  GF  T+GNA+RRVL+SSL G AIT ++I GV HE SSI
Sbjct: 10  EKVVMDKTTDFHGMFEFKPLEPGFGVTVGNAIRRVLLSSLEGYAITCIRIPGVQHEFSSI 69

Query: 76  KGVHEDLTDIILNIKGINLK-MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHV 133
           KGV +D+ +IILN+K +  K +S +   ++ +       +TAGDI +  +  E+LNPD V
Sbjct: 70  KGVMQDVAEIILNLKKVRFKKISENVDSKIVVEVSNQETLTAGDIGKFTSSFEILNPDLV 129

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           ICNLD    + +EL + KG GYV ++  +  +  IG I ID++++PIK V Y VE+ R  
Sbjct: 130 ICNLDESVDLEVELYIEKGRGYVSSEDQKLPDAAIGHIPIDSIFTPIKNVRYAVENTRVE 189

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKS 249
           Q  DY+KL + I TDGSI  E+++  A+ IL     +F +     E  KKE  ++++   
Sbjct: 190 QRTDYEKLLLDIQTDGSIHPEEALKGAANILIQHFMLFSDQNIILETAKKEEVQEVDEHF 249

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           L     L   + +L+LSVR+ NCL+  +I  +GDL++   ADM++  NFG+KSL E++ +
Sbjct: 250 LHMRKLLKTPISDLDLSVRAYNCLKSADIRTLGDLVKLDIADMMKFRNFGKKSLTELEQL 309

Query: 310 LGTMGLFLGMNLPDWP 325
           +   GL  GM++  + 
Sbjct: 310 VAEKGLSFGMDVSKYK 325


>gi|307718231|ref|YP_003873763.1| hypothetical protein STHERM_c05210 [Spirochaeta thermophila DSM
           6192]
 gi|306531956|gb|ADN01490.1| hypothetical protein STHERM_c05210 [Spirochaeta thermophila DSM
           6192]
          Length = 363

 Score =  303 bits (775), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 126/344 (36%), Positives = 193/344 (56%), Gaps = 13/344 (3%)

Query: 1   MIQKNW-QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M +KN  +  + P +I    L           A P  RG+  T+GN LRR+L+SS++G A
Sbjct: 1   MARKNLLKGFVLPTSITVEHLDTNAH-YGKFAAYPFERGYGVTIGNTLRRILLSSIQGYA 59

Query: 60  ITAVQI-----DGVLHEISS----IKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKR 109
           I+AV+I      G  H +SS    I GV ED  ++  N+K + +++  +   K V +  +
Sbjct: 60  ISAVRITWYDDQGTAHVLSSEYEQIPGVVEDTLELFANLKLLRVQLPDEMEQKTVMVEFK 119

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  VT  D +    +EV+N D  +  L  DA   ME+ V  G GYVPA+  +   + +G
Sbjct: 120 GPKEVTGADFEVD-QLEVMNKDFRVMTLMEDAHFEMEMQVDLGRGYVPAEVQKNYIEVVG 178

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            I +DALYSPI++V + VE+ R G   DYDKL + + TDGSI+ ED++  A+++ ++   
Sbjct: 179 TIPLDALYSPIQRVRFDVENTRVGHRSDYDKLILEVWTDGSISPEDALGEAAKLAKEHFT 238

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +FINF+E        ++ +       L   +EELELSVRS+NCL+  NI  +GDL+ ++E
Sbjct: 239 VFINFDEDAISHVRQLDHEEEQIRRLLETPIEELELSVRSSNCLKNANIRTIGDLVSKSE 298

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELA 333
            ++ +  NFG+KSL+EIK  L    L LGM  P     ++E + 
Sbjct: 299 EELSKTRNFGKKSLLEIKEKLKEWNLSLGMRDPSAYKAALERVR 342


>gi|213962766|ref|ZP_03391026.1| DNA-directed RNA polymerase, alpha subunit [Capnocytophaga
           sputigena Capno]
 gi|213954423|gb|EEB65745.1| DNA-directed RNA polymerase, alpha subunit [Capnocytophaga
           sputigena Capno]
          Length = 330

 Score =  303 bits (775), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 122/325 (37%), Positives = 189/325 (58%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++ +  +        PL  G+  T+GNALRRV++SSL G AIT+V+ D 
Sbjct: 5   NFQKPDKV---IMIESSDFEGRFEFRPLEPGYGLTIGNALRRVMLSSLEGFAITSVKFDK 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQ-TVND 124
           V HE S+I GV ED+T+IILN+K +  K   +    +  TI   G   +TAGD Q T++ 
Sbjct: 62  VDHEFSTIPGVREDVTEIILNLKQVRFKRQVEDVEDETATITVSGKKQLTAGDFQKTLSG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLNPD VICN++  A   ME+T+ KG GYV A+ +   N  IG+I  D++++PIK V 
Sbjct: 122 FQVLNPDLVICNMETSASFTMEITIEKGRGYVSAEENAKPNAAIGVIATDSIFTPIKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           YT+E+ R  Q  DY+KL   I TDGSI  + ++  A++ L     +F    I  E  +  
Sbjct: 182 YTIENYRVEQKTDYEKLVFEIKTDGSIHPKQALTEAAKTLIHHFMLFSDERITLEADEVA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             +  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   +AD+++  NFG+
Sbjct: 242 QTDAYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVETLGDLVSFNKADLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL+E+  ++   GL  GM+   + 
Sbjct: 302 KSLIELDELVANKGLVFGMDTSKYK 326


>gi|281422225|ref|ZP_06253224.1| DNA-directed RNA polymerase, alpha subunit [Prevotella copri DSM
           18205]
 gi|281403730|gb|EFB34410.1| DNA-directed RNA polymerase, alpha subunit [Prevotella copri DSM
           18205]
          Length = 331

 Score =  302 bits (774), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 121/324 (37%), Positives = 193/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ + +         PL  GF  T+GNALRR+L+SSL G A+  ++I GV
Sbjct: 6   FQKPDKV---VMLEADNKFGKFEFRPLEPGFGVTIGNALRRILLSSLEGYAVNTIRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VIC+LD  A ++++LT++KG GYVPA  +R     + ++ ID++Y+PI+ V Y
Sbjct: 123 EVLNPDLVICHLDAKASMQIDLTINKGRGYVPADENRQFCTDVNVLPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE  R  Q  DYDKL + I TDGSI+ +D++  A++IL     +F    I  E   +E 
Sbjct: 183 AVEPYRVEQKTDYDKLVLEITTDGSISPKDALKEAAKILIYHFMLFSDEKITLETQDQES 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++ + + L     L  ++ ++ LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NQEFDEEVLHMRQLLKTRLVDMNLSVRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLSELDDLLESLNLSFGTDISKYK 326


>gi|317503954|ref|ZP_07961962.1| DNA-directed RNA polymerase subunit alpha [Prevotella salivae DSM
           15606]
 gi|315664980|gb|EFV04639.1| DNA-directed RNA polymerase subunit alpha [Prevotella salivae DSM
           15606]
          Length = 330

 Score =  302 bits (774), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 121/324 (37%), Positives = 194/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  +        PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---VMLEANDKFGKFEFRPLEPGFGVTIGNALRRILLSSLEGYAINTIRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VIC+LD  A ++++LT++KG GY+PA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPDLVICHLDAKASMQIDLTINKGRGYIPADENREFCTDVNVIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           +VE  R  Q  DYDKL + + TDGSI  +D++  A++IL     +F    I  E P ++ 
Sbjct: 183 SVEPYRVEQKTDYDKLVIEVSTDGSIHPKDALKEAAKILIYHFMLFSDEKITLESPDQDG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++ + + L     L  ++ ++ LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NQEFDEEVLHMRQLLKTRLVDMNLSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLSELDDLLESLNLSFGTDISKYK 326


>gi|291334082|gb|ADD93755.1| DNA directed RNA polymerase alpha subunit [uncultured marine
           bacterium MedDCM-OCT-S05-C114]
          Length = 332

 Score =  302 bits (774), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 125/318 (39%), Positives = 188/318 (59%), Gaps = 4/318 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +   PN +         ++    IA+P   G+ HT+GNA RRVL+SS+ GAAI+++++DG
Sbjct: 7   KFELPNRL-VKEEDTSTDSYAKFIADPFESGYGHTIGNAFRRVLLSSIEGAAISSLKLDG 65

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE  SI GV ED+TDI+LN+K + +         +TI     G VTAGDI     IE+
Sbjct: 66  VQHEFQSIDGVVEDVTDIVLNLKKVLVISHKADPVTLTIDVEKDGEVTAGDISPAEGIEI 125

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NP+ +I   D    V  E+ V+ G G+   +  +++  PIG+I +DALYSP+K V Y V
Sbjct: 126 INPEQIILTTDRKLQVTGEMIVTVGRGFCLGEDSKSDEQPIGMINVDALYSPVKLVKYEV 185

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK---ED 244
           ++ R GQ+ DYDKL + + TDG IT +D++  ++ IL+  L +F    E + E +   ++
Sbjct: 186 QNTRVGQMTDYDKLLLEVTTDGRITPDDALKQSAAILRHHLDVFDQISEEQIEFESHTKE 245

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           ++ +       L   V E+ELSVR+ NCL   NI  +G+L  ++E +ML+  NFG+KSL 
Sbjct: 246 VSEEQNRLRNLLSMSVNEIELSVRAANCLNNANITTVGELATKSEPEMLKYRNFGKKSLN 305

Query: 305 EIKGVLGTMGLFLGMNLP 322
           EIK  L  +GL LGM   
Sbjct: 306 EIKAKLEQLGLSLGMKFE 323


>gi|149371655|ref|ZP_01891071.1| DNA-directed RNA polymerase subunit alpha [unidentified eubacterium
           SCB49]
 gi|149355282|gb|EDM43842.1| DNA-directed RNA polymerase subunit alpha [unidentified eubacterium
           SCB49]
          Length = 330

 Score =  302 bits (774), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 123/325 (37%), Positives = 193/325 (59%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT+++++G
Sbjct: 5   SFQKPDKV---IMINSTDFEGKFEFRPLEPGYGLTIGNALRRVLLSSLEGFAITSLRVEG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VND 124
           V HE S+I GV ED+T+IILN+K +  K   D   ++ VTI   G   V AGD Q  ++ 
Sbjct: 62  VDHEFSTIAGVVEDVTEIILNLKQLRFKRQIDEIDNETVTISVSGNDKVVAGDFQKFISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLNPD +ICN+D    + ME+T+ KG GYVPA+ ++  N P+G I  D++++PIK V 
Sbjct: 122 FQVLNPDLIICNMDSKVNLNMEITIEKGRGYVPAEENKKANAPLGTIFTDSIFTPIKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y++E+ R  Q  DY+KL   I +DGSI  +D++  A++ L     +F    I  E  +  
Sbjct: 182 YSIENFRVEQKTDYEKLVFEITSDGSIHPKDALTEAAKTLIHHFMLFSDERITLEADEIA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+
Sbjct: 242 QTETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E++ ++   GL  GM+L  + 
Sbjct: 302 KSLTELEELVLVKGLNFGMDLAKYK 326


>gi|254495367|ref|ZP_05108291.1| DNA-directed RNA polymerase, alpha subunit [Polaribacter sp.
           MED152]
 gi|85819721|gb|EAQ40878.1| DNA-directed RNA polymerase, alpha subunit [Polaribacter sp.
           MED152]
          Length = 330

 Score =  302 bits (774), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 125/325 (38%), Positives = 194/325 (59%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++ +  +        PL  GF  T+GNALRRVL+SSL G AIT+++IDG
Sbjct: 5   NFQKPDKV---IMIESTDFSGRFEFRPLEPGFGLTVGNALRRVLLSSLEGFAITSLRIDG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGV--VTAGDIQT-VND 124
           V HE S++ G+ ED+T+IILN+K +  K   D   R T+     G    TAGD+Q  ++ 
Sbjct: 62  VEHEFSTVSGIVEDVTEIILNLKQVRFKKQIDETDRETVSVSISGQEQFTAGDLQKFISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLNPD VICN+D    +  E+T+ KG G+VPA+ ++  + PIG I  D++Y+PIK V 
Sbjct: 122 FQVLNPDLVICNMDKSVKLNAEITIEKGRGFVPAEENKKASAPIGTIFTDSIYTPIKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y +E+ R  Q  DY+KL   IDTDGSI  +D++  A++IL     +F    I  E  +  
Sbjct: 182 YAIENFRVEQKTDYEKLVFDIDTDGSINPKDALTEAAKILIHHFMLFSDERITLEADEIA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + +SL     L  ++ +++LSVR+ NCL+   +  +GDL+   ++D+++  NFG+
Sbjct: 242 QTETYDEESLHMRQLLKTRLIDMDLSVRALNCLKAAEVDTLGDLVSFNKSDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E++ ++   GL  GM+L  + 
Sbjct: 302 KSLTELEELVIVKGLSFGMDLTKYK 326


>gi|328813993|gb|AEB52112.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 253

 Score =  302 bits (774), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 117/253 (46%), Positives = 170/253 (67%), Gaps = 2/253 (0%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T 
Sbjct: 1   DNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTA 60

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A   
Sbjct: 61  IILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGAHFH 120

Query: 145 MELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           M +T + G GYV A+ ++   ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL+
Sbjct: 121 MRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLT 180

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + + T+GSIT  ++++L+++IL D L +F+N  +  K     +  +       L   +EE
Sbjct: 181 LDVWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEMTIEE 240

Query: 263 LELSVRSTNCLRG 275
           L+LSVRS NCL+ 
Sbjct: 241 LDLSVRSYNCLKR 253


>gi|179184639|gb|ACB78155.1| RNA polymerase alpha subunit [Vibrio comitans]
          Length = 304

 Score =  302 bits (773), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 137/306 (44%), Positives = 202/306 (66%), Gaps = 9/306 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +G
Sbjct: 3   VDIEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEG 62

Query: 78  VHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           V ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+ NP+HVIC+
Sbjct: 63  VQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICH 122

Query: 137 LDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR 
Sbjct: 123 LTDDNADIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARV 182

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   KE    +   F
Sbjct: 183 EQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEKE----REPRF 238

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 239 DPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 298

Query: 313 MGLFLG 318
            G  LG
Sbjct: 299 RGWSLG 304


>gi|159901451|ref|YP_001547698.1| DNA-directed RNA polymerase subunit alpha [Herpetosiphon
           aurantiacus ATCC 23779]
 gi|238687089|sp|A9B437|RPOA_HERA2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|159894490|gb|ABX07570.1| DNA-directed RNA polymerase, alpha subunit [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 331

 Score =  302 bits (773), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 115/295 (38%), Positives = 182/295 (61%), Gaps = 4/295 (1%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
             EN      EPL  G+ HTLGNALRRVL+SS+ GAA+  ++IDG+ HE S I+GV ED 
Sbjct: 14  AAENYGRFKIEPLDPGYGHTLGNALRRVLLSSIPGAAVIKIKIDGIFHEFSPIQGVREDA 73

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDA 141
           T+I+LN+KGI L+   +   ++ + K GPGVV A DI+  +++E++NPDH I  LD  DA
Sbjct: 74  TEIVLNVKGIRLRSYAERPVKMILSKTGPGVVRASDIECPSNVEIVNPDHYIATLDSSDA 133

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + MELTV +  GY+PA++      PIG I +DA+++P+ KV+Y VE  R G + D+D+L
Sbjct: 134 RLDMELTVERHRGYLPAENRDP--VPIGEIPVDAIFTPVHKVNYVVEHTRIGGMTDFDRL 191

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS-LPFNPALLKKV 260
            + I TDG++   D+++ A+++L     +  +F     E ++  +    +  +      +
Sbjct: 192 LLEIWTDGTVKPGDALSYAAQVLVQYSSIIADFNRFDDEQEQVGDANGLVIPSEIYDMPI 251

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           E+L+LS R+ NCL+  +I  +G +++  E  +L + N G+KS+ EI+  L    L
Sbjct: 252 EDLDLSTRTYNCLKRADITKVGQVLEMDEKQLLAVRNLGQKSMDEIREKLIERNL 306


>gi|319952170|ref|YP_004163437.1| DNA-directed RNA polymerase subunit alpha [Cellulophaga algicola
           DSM 14237]
 gi|319420830|gb|ADV47939.1| DNA-directed RNA polymerase subunit alpha [Cellulophaga algicola
           DSM 14237]
          Length = 330

 Score =  302 bits (773), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 121/325 (37%), Positives = 191/325 (58%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT++++D 
Sbjct: 5   NFQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGFAITSIRVDK 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQT-VND 124
           V HE S I G+ ED+T+IILN+K +  K  +     + V++   G   +TAGD Q  ++ 
Sbjct: 62  VEHEFSVISGIVEDVTEIILNLKQVRFKRQIEDVDSETVSVSVSGKNQLTAGDFQKFISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLNPD VICN+D      MEL + KG GYVPA+ ++    PIG I ID++++PIK V 
Sbjct: 122 FQVLNPDLVICNMDAKVNFNMELVIEKGRGYVPAEENKKSGAPIGTIAIDSIFTPIKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y++E+ R  Q  DY+KL   I++DGSIT +D++   +++L     +F    I  E  +  
Sbjct: 182 YSIENFRVEQKTDYEKLVFEIESDGSITPKDALTEGAKVLIHHFMLFSDERITLEADEIA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+
Sbjct: 242 QTETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E++ ++   GL  GM+L  + 
Sbjct: 302 KSLTELEELVINKGLSFGMDLSKYK 326


>gi|179184786|gb|ACB78160.1| RNA polymerase alpha subunit [Vibrio gallaecicus]
          Length = 306

 Score =  302 bits (773), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 137/306 (44%), Positives = 200/306 (65%), Gaps = 8/306 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + L Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +G
Sbjct: 4   VGLEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEG 63

Query: 78  VHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           V ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+ NP+HVIC+
Sbjct: 64  VQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICH 123

Query: 137 LDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR 
Sbjct: 124 LTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARV 183

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F
Sbjct: 184 EQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEF 240

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 241 DPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 300

Query: 313 MGLFLG 318
            GL LG
Sbjct: 301 RGLSLG 306


>gi|149279637|ref|ZP_01885766.1| DNA-directed RNA polymerase subunit alpha [Pedobacter sp. BAL39]
 gi|149229673|gb|EDM35063.1| DNA-directed RNA polymerase subunit alpha [Pedobacter sp. BAL39]
          Length = 330

 Score =  301 bits (772), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 130/324 (40%), Positives = 201/324 (62%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ +  +   +    PL  GF  T+GNALRR+L+SSL G AIT+++  GV
Sbjct: 6   FQKPDKV---IMQKSTDFDGIFEFRPLEPGFGVTIGNALRRILLSSLEGYAITSIRFSGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE S++KGV EDLT+IILN+K +  K  GD    ++V I   G    TAGDI +  N+ 
Sbjct: 63  SHEFSTMKGVVEDLTEIILNLKQVRFKKVGDSGDSEKVFILVNGQDQFTAGDITKFSNNF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VICN++    + +ELT++KG GYVPA+ ++  +  +G+I ID++++P+K V Y
Sbjct: 123 EVLNPDFVICNMEKTVTLEVELTINKGRGYVPAEENKINDAVVGVIAIDSIFTPMKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEV 241
           T+E+ R  Q  DY+KL + I TDGSI  E+++  A++IL     +F +     E   KE 
Sbjct: 183 TIENYRVEQKTDYEKLILDISTDGSIHPEEALKEAAKILIQHFMLFSDENLVLESQAKEE 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++++ + L     L  ++ +L+LSVR+ NCL+  +I  + DL+    ADML+  NFG+K
Sbjct: 243 TKEVDEEILHMRKILKTELVDLDLSVRALNCLKAADIRTLADLVSYDVADMLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL EI+ ++ +  L  GMNL  + 
Sbjct: 303 SLTEIQELVKSKSLSFGMNLSKFK 326


>gi|116327251|ref|YP_796971.1| DNA-directed RNA polymerase subunit alpha [Leptospira
           borgpetersenii serovar Hardjo-bovis L550]
 gi|116327291|ref|YP_797011.1| DNA-directed RNA polymerase subunit alpha [Leptospira
           borgpetersenii serovar Hardjo-bovis L550]
 gi|116332095|ref|YP_801813.1| DNA-directed RNA polymerase subunit alpha [Leptospira
           borgpetersenii serovar Hardjo-bovis JB197]
 gi|122280175|sp|Q04PW5|RPOA_LEPBJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|122284902|sp|Q055B7|RPOA_LEPBL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116119995|gb|ABJ78038.1| DNA-directed RNA polymerase, alpha subunit [Leptospira
           borgpetersenii serovar Hardjo-bovis L550]
 gi|116120035|gb|ABJ78078.1| DNA-directed RNA polymerase, alpha subunit [Leptospira
           borgpetersenii serovar Hardjo-bovis L550]
 gi|116125784|gb|ABJ77055.1| DNA-directed RNA polymerase, alpha subunit [Leptospira
           borgpetersenii serovar Hardjo-bovis JB197]
          Length = 325

 Score =  301 bits (772), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 131/317 (41%), Positives = 203/317 (64%), Gaps = 4/317 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           +   +P  IE+        N    +AEP  RGFA T+GN+LRR LMSS+ GAAI+A++I+
Sbjct: 8   KGFKRPKKIEFNT-EASTPNYGKFVAEPFERGFATTIGNSLRRTLMSSIEGAAISAIRIE 66

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS---HKRVTIFKRGPGVVTAGDIQTVN 123
           GV HE S I+GV ED+T IILN+K + +K   +     K + +  +G G   AGD+   +
Sbjct: 67  GVNHEFSFIEGVAEDVTRIILNLKQVRIKYEPEEKDQSKIIHLELKGAGYFRAGDLAVDS 126

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            IE++NPD  I  L+ DA + M+L + +G GYVPA+  + + + +G I +D+++SP++KV
Sbjct: 127 SIEIMNPDLHIATLNEDANLVMDLEIQRGRGYVPAEEKKKDIEVLGTIPVDSIFSPVQKV 186

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
            + V   R  Q  DY+KL++ + TDGS++ +D+VA A++IL++ L +FINFEE  +E  +
Sbjct: 187 VFEVSETRVAQRSDYEKLTLEVWTDGSVSPDDAVAQAAKILKEHLTVFINFEEELEEEDD 246

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +++        +L K VEELELSVRS N LR   I ++GDL++R+E +M +  ++  + L
Sbjct: 247 ELDEADEKLKASLSKHVEELELSVRSLNVLRSLEIDFIGDLVKRSEEEMSKSKHYSDQCL 306

Query: 304 VEIKGVLGTMGLFLGMN 320
            E+KG L T+GL  GM 
Sbjct: 307 QELKGKLSTLGLSFGMR 323


>gi|298243941|ref|ZP_06967748.1| DNA-directed RNA polymerase, alpha subunit [Ktedonobacter racemifer
           DSM 44963]
 gi|297556995|gb|EFH90859.1| DNA-directed RNA polymerase, alpha subunit [Ktedonobacter racemifer
           DSM 44963]
          Length = 326

 Score =  301 bits (772), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 114/295 (38%), Positives = 175/295 (59%), Gaps = 3/295 (1%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           + + N      EPL  G+  TLGNALRRVL+SSL GAA+T+++I+GV HE   + GV ED
Sbjct: 13  KTQGNYASYDIEPLEAGYGQTLGNALRRVLLSSLPGAAVTSIRIEGVQHEFQDVPGVLED 72

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VD 140
           +TDI+LNIK + L+   +    + +   G   VTA DI   + +E++NP+  I +LD  +
Sbjct: 73  VTDIVLNIKKLRLRSFSEHPVTMRLEVNGEREVTAADIVAPSTVEIVNPELHIASLDNDN 132

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
           A + MEL V  G  YVPA     E+ PIG+I +DA+Y+P++KV+YTVE  R GQ+ +YDK
Sbjct: 133 AHLDMELVVETGRSYVPADS--KEDQPIGVIPVDAIYTPVQKVNYTVEHTRVGQMTNYDK 190

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           + + + TDG+IT ++++  ++ +L     +  N+     E ++                +
Sbjct: 191 IVLEVTTDGTITPDEALRQSADVLVRHFTLLANYRASLPEPEKAPLSSLPIPQKIYDTPI 250

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           EEL+LSVR+ NCL+  NI  +G ++   E D+L + NFG KSL E++  L     
Sbjct: 251 EELDLSVRAYNCLKRSNITKVGQVLSMNEEDLLGVRNFGEKSLQELRERLLARNF 305


>gi|126662238|ref|ZP_01733237.1| DNA-directed RNA polymerase subunit alpha [Flavobacteria bacterium
           BAL38]
 gi|126625617|gb|EAZ96306.1| DNA-directed RNA polymerase subunit alpha [Flavobacteria bacterium
           BAL38]
          Length = 330

 Score =  301 bits (772), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 127/325 (39%), Positives = 192/325 (59%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT+V+I+G
Sbjct: 5   NFQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGYAITSVRIEG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQT-VND 124
           V HE S+I GV ED+T+IILN+K +  K  +    ++ V+I   G   +TAGD Q  ++ 
Sbjct: 62  VEHEFSTISGVVEDVTEIILNLKQVRFKRQIEDIDNESVSISLSGKDKITAGDFQKFISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLNPD VICNLD    + MEL++ KG GYVPA+ ++  N PIG I  D++Y+P+K V 
Sbjct: 122 FQVLNPDLVICNLDSKTTLNMELSIEKGRGYVPAEENKKSNAPIGTIYTDSIYTPVKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           YT+E+ R  Q  DY+KL   I TDGSI  +D++  A++ L     +F    I  E  +  
Sbjct: 182 YTIENFRVEQKTDYEKLVFEIITDGSIHPKDALTEAAKTLIHHFMLFSDERITLEADEIA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+
Sbjct: 242 QTESYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E+  ++    L  GM+L  + 
Sbjct: 302 KSLTELDELVANKNLTFGMDLAKYK 326


>gi|298207753|ref|YP_003715932.1| DNA-directed RNA polymerase alpha subunit [Croceibacter atlanticus
           HTCC2559]
 gi|83850391|gb|EAP88259.1| DNA-directed RNA polymerase alpha subunit [Croceibacter atlanticus
           HTCC2559]
          Length = 317

 Score =  301 bits (772), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 122/311 (39%), Positives = 188/311 (60%), Gaps = 7/311 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
              +        PL  G+  T+GNALRRVL+SSL G AI++V+++GV HE S+I GV ED
Sbjct: 3   DSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGFAISSVRVEGVDHEFSTISGVVED 62

Query: 82  LTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLD 138
           +T+IILN+K +  K   D   ++ VT+   G   +TAGD Q  ++  +VLNPD VICN+D
Sbjct: 63  VTEIILNLKQVRFKRQIDEVDNETVTMNISGQEQLTAGDFQKFISGFQVLNPDMVICNMD 122

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +E+T+ KG GYVPA+ ++  N PIG I  D++++PIK V Y++E+ R  Q  DY
Sbjct: 123 KKVNLNIEITIEKGRGYVPAEENKKSNAPIGTIFTDSIFTPIKNVKYSIENYRVEQKTDY 182

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNP 254
           +KL   I TDGSI  +D++  A++ L     +F    I  E  +    E  + +SL    
Sbjct: 183 EKLVFEIQTDGSIHPKDALTEAAKTLIHHFMLFSDERITLEADEIAQTETYDEESLHMRQ 242

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
            L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+KSL E++ ++   G
Sbjct: 243 LLKTKLVDMDLSVRALNCLKAAEVDSLGDLVSYNKNDLMKFRNFGKKSLTELEELVNNKG 302

Query: 315 LFLGMNLPDWP 325
           L  GM+L  + 
Sbjct: 303 LNFGMDLSKYK 313


>gi|323344663|ref|ZP_08084887.1| DNA-directed RNA polymerase subunit alpha [Prevotella oralis ATCC
           33269]
 gi|323093933|gb|EFZ36510.1| DNA-directed RNA polymerase subunit alpha [Prevotella oralis ATCC
           33269]
          Length = 330

 Score =  301 bits (772), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 122/324 (37%), Positives = 195/324 (60%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ + ++        PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---VMVEADDKFGKFEFRPLEPGFGVTIGNALRRILLSSLEGYAINTIRIGGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VIC+LDV A +++++T++KG GYVPA  +R     + ++ ID++Y+PI+ V Y
Sbjct: 123 EVLNPDLVICHLDVKASMQIDITINKGRGYVPADENREFCTDVNVLPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           +VE  R  Q  DYDKL + + TDGSI  +D++  A++IL     +F    I  E   +E 
Sbjct: 183 SVEPYRVEQKTDYDKLVLEVTTDGSIYPKDALKEAAKILIYHFMLFSDEKITLESSDQEN 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++ + + L     L  K+ ++ LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NQEFDEEVLHMRQLLKTKLIDMNLSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLSELDDLLESLNLSFGTDISKYK 326


>gi|328813937|gb|AEB52084.1| DNA-directed RNA polymerase alpha chain [Lactobacillus brevis]
          Length = 263

 Score =  301 bits (772), Expect = 8e-80,   Method: Composition-based stats.
 Identities = 117/263 (44%), Positives = 175/263 (66%), Gaps = 4/263 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVTQIILNV 60

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K I LK++G  D  + + I  +GP  +TAGDI    D+++LNPD  I  +   A   M +
Sbjct: 61  KKIALKLNGSDDQEETMEINVKGPAQITAGDIVAGADVDILNPDLYIATVADGATFHMRM 120

Query: 148 TVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           T  KG GYV A  ++T   + PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ +
Sbjct: 121 TADKGRGYVSADENKTRNTDMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDV 180

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+GSI   +++ALA++IL + L MF++  +  K  +  +  +       L   +EEL+L
Sbjct: 181 WTNGSINPSEAIALAAKILTEHLAMFVDLTDEAKNAEIMVEKEETHKEKMLEMTIEELDL 240

Query: 266 SVRSTNCLRGENIVYMGDLIQRT 288
           SVRS NCL+   I  + +L  +T
Sbjct: 241 SVRSYNCLKRAGINTVQELNNKT 263


>gi|78189780|ref|YP_380118.1| DNA-directed RNA polymerase subunit alpha [Chlorobium
           chlorochromatii CaD3]
 gi|90110831|sp|Q3APK0|RPOA_CHLCH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|78171979|gb|ABB29075.1| DNA-directed RNA polymerase subunit alpha [Chlorobium
           chlorochromatii CaD3]
          Length = 327

 Score =  301 bits (771), Expect = 9e-80,   Method: Composition-based stats.
 Identities = 122/321 (38%), Positives = 192/321 (59%), Gaps = 6/321 (1%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  IE        ++    IA+PL RG+  TLGN +RRVL++SL G AIT ++I+ V HE
Sbjct: 8   PAKIELDE-SSHSDSFGKFIAQPLERGYGVTLGNLMRRVLLASLPGTAITGIKIENVYHE 66

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNP 130
            S+I+GV ED+ +I+LN+K +  +       + T+   GP   TAG IQ    + EVLN 
Sbjct: 67  FSTIQGVREDVPEIVLNLKKVRFRSQCKRSCKTTVTLVGPMEFTAGVIQPQEGEFEVLNK 126

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  ++    V +++ + +G GYVPA+ +R E  P+G I ID++++PI+ V +TVE+ 
Sbjct: 127 DLHIATINAGTTVTLDIFIGRGRGYVPAEENRAEGMPLGFIPIDSIFTPIRNVKFTVENT 186

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK----EDIN 246
           R GQ  DY+K+ + ++TDGSIT +DS++LA R++ D + +F +F   ++E      +  +
Sbjct: 187 RVGQRTDYEKMILEVETDGSITPDDSISLAGRVISDHVLLFADFSPAEEEYTEEEFKQQD 246

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L  K+E+L+LSVRS NCLR   I  +G+L+   E ++L   NFG+KSL E+
Sbjct: 247 DEFETMRRLLATKIEDLDLSVRSHNCLRLAEIDTLGELVSHKEDELLNYKNFGKKSLTEL 306

Query: 307 KGVLGTMGLFLGMNLPDWPPE 327
           K  L    L  GM++  +  +
Sbjct: 307 KEQLDKFDLKFGMDITRYQMK 327


>gi|328813965|gb|AEB52098.1| DNA-directed RNA polymerase alpha chain [Lactobacillus farraginis]
          Length = 270

 Score =  301 bits (771), Expect = 9e-80,   Method: Composition-based stats.
 Identities = 122/270 (45%), Positives = 178/270 (65%), Gaps = 4/270 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           +N   ++ EPL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T 
Sbjct: 1   KNYGEVVVEPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQ 60

Query: 85  IILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILN+K I+LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A 
Sbjct: 61  IILNVKKISLKLDGPEDEEENLEIDVIGPADVTAGDIQGDSDVTVLNPDLHIATVAEGAT 120

Query: 143 VRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             M LT ++G GYV A  ++      PIG++ +D++Y+PI++V+Y VES R GQ  D+DK
Sbjct: 121 FHMRLTANRGRGYVSAVENKKRATEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDK 180

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L++ + T+GSIT  ++V+LA++IL + L MF++  +  K  +  +  +       L   +
Sbjct: 181 LTLDVWTNGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEKEETHKEKMLEMTI 240

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEA 290
           EEL+LSVRS NCL+   I  + +L ++TEA
Sbjct: 241 EELDLSVRSYNCLKRAGINTVQELTEKTEA 270


>gi|325479152|gb|EGC82249.1| DNA-directed RNA polymerase, alpha subunit [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 318

 Score =  301 bits (771), Expect = 9e-80,   Method: Composition-based stats.
 Identities = 112/303 (36%), Positives = 195/303 (64%), Gaps = 5/303 (1%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           EEEN       PL RG+  T+GN++RRVL+SSL G++++ + I+GVLHE S+I GV ED+
Sbjct: 16  EEENYGKFALYPLERGYGTTIGNSMRRVLLSSLPGSSVSKILIEGVLHEFSTIDGVVEDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
            +I+LNIKG+++    D    + +   GP +VTA DI+  + +++ NPDH I  ++  + 
Sbjct: 76  PEIVLNIKGLDVTKHTDEDVTLFLDVEGPKIVTAKDIKADSLVDIANPDHYIATVNEKSR 135

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + + + V+ G GY  +++++ E+DPIG I ID+ ++P++KV+YTVE+ R G+  DYDKL 
Sbjct: 136 LFIAMDVTDGKGYRISENNKDESDPIGTIAIDSSFTPVEKVNYTVENTRVGESTDYDKLI 195

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK-----KEVKEDINVKSLPFNPALL 257
           + + T+G+I+ +++++L S IL + + +F N  + K     + ++E+ N +    +  L 
Sbjct: 196 LEVWTNGTISPQEALSLGSNILIEDVSLFNNLPDMKFPPEEEIIEEEENNEEEALSEDLS 255

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +EEL+LS+RS NCL+      + D+++ +E+++  + NFG+KSL E+   L  +GL L
Sbjct: 256 MTIEELDLSLRSFNCLKRAGFDKVADIVEVSESELKSIKNFGKKSLTEVMDKLDELGLSL 315

Query: 318 GMN 320
              
Sbjct: 316 KDE 318


>gi|113476555|ref|YP_722616.1| DNA-directed RNA polymerase subunit alpha [Trichodesmium erythraeum
           IMS101]
 gi|110167603|gb|ABG52143.1| DNA-directed RNA polymerase, alpha subunit [Trichodesmium
           erythraeum IMS101]
          Length = 321

 Score =  301 bits (771), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 111/312 (35%), Positives = 173/312 (55%), Gaps = 12/312 (3%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             +E     ++       I EPL RG   T+GNALRRVL+S+L G AIT+V+I GV HE 
Sbjct: 14  ECVESKT-DKDRSQYGKFIIEPLARGQGTTVGNALRRVLLSNLEGTAITSVRIAGVNHEF 72

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++IKGV ED+ +I+LN+K + LK   +  +   +   GP  VTA      +++EV++   
Sbjct: 73  ATIKGVREDVLEILLNMKEVVLKSYSEQPQIGRLRVEGPATVTADRFDVPSEVEVIDRSQ 132

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L   +++ ME  + KG GY      R +   +  + IDA++ P++KV+YT+E A  
Sbjct: 133 YIATLSPGSILEMEFRIEKGTGYKAVDRTRDDVATLDFLQIDAIFMPVRKVNYTIEDAHI 192

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP- 251
           G  L+ D+L M I T+GS T +D+++ A+ IL           EP K++    ++ S   
Sbjct: 193 GSSLEQDRLIMDIWTNGSYTPQDALSNAAGILMSLF-------EPLKDITNMADIPSGET 245

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L 
Sbjct: 246 TDPTSQIPIEELQLSVRAYNCLKRAQINSVADLLDYSQEDLLEIKNFGQKSAEEVIEAL- 304

Query: 312 TMGLFLGMNLPD 323
                LG+ LP 
Sbjct: 305 --QKRLGITLPQ 314


>gi|118602238|ref|YP_903453.1| DNA-directed RNA polymerase subunit alpha [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
 gi|158512574|sp|A1AVM5|RPOA_RUTMC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|118567177|gb|ABL01982.1| DNA-directed RNA polymerase subunit alpha [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
          Length = 326

 Score =  301 bits (771), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 146/329 (44%), Positives = 212/329 (64%), Gaps = 7/329 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q + +  +KP  +E     Q   N   +I EPL RGF HTLGNALRR L+SS+ G+A+T
Sbjct: 1   MQGSARNFLKPKLVES---SQTGVNEFKVILEPLERGFGHTLGNALRRTLLSSMTGSAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V IDGV+HE S+I+GV ED+ DI+LN+K +++ ++     +V I K+GP  +T  DI+ 
Sbjct: 58  EVAIDGVMHEFSTIEGVQEDVLDILLNLKEVSVMLNTAETAQVVIEKKGPCEITVADIEA 117

Query: 122 VN-DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              DI   NPD VI  ++ ++ +RM L +S G GY  A     E   IG + +DA +SPI
Sbjct: 118 NGIDITAFNPDKVIATINDESHMRMTLKISTGIGYDTATSRTDEASSIGGMQLDASFSPI 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VS+TV++AR  Q ++ DKL++TI+T+GS+  E ++  A+ ILQ+QL  F+  E  ++E
Sbjct: 178 RRVSFTVDAARVKQKVNLDKLNITIETNGSVNAEVAIKRAAIILQEQLSSFVELELVEEE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                +     F+P LL  V+ELEL+VRS NCL+ E I Y+GDLIQ++E D+LR  N GR
Sbjct: 238 EALPTSED---FDPQLLAAVDELELTVRSANCLKAEQIYYIGDLIQKSEQDLLRTPNLGR 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           KSL EIK VL   GL L  ++ +WPP  +
Sbjct: 295 KSLNEIKEVLTEKGLNLATSIENWPPVDL 323


>gi|91216884|ref|ZP_01253848.1| DNA-directed RNA polymerase alpha subunit [Psychroflexus torquis
           ATCC 700755]
 gi|91185045|gb|EAS71424.1| DNA-directed RNA polymerase alpha subunit [Psychroflexus torquis
           ATCC 700755]
          Length = 330

 Score =  301 bits (771), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 124/325 (38%), Positives = 193/325 (59%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT+V+I+G
Sbjct: 5   NFQKPDKV---IMIDSTDFEGTFEFRPLEPGYGLTVGNALRRVLLSSLEGFAITSVRIEG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VND 124
           V HE S+I+GV ED+T++ILN+K I  K   +   ++ V+I   G   +TAGD Q  +  
Sbjct: 62  VDHEFSTIEGVVEDVTEMILNLKQIRFKKRAEDVDNETVSISFSGNDKMTAGDFQKYLTG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            ++LNPD  IC +D    + +ELTV KG GYVPA+ ++T   PIG I  D++++PIK V 
Sbjct: 122 FDILNPDLEICTMDKKVSLNLELTVQKGRGYVPAEENKTSKAPIGTIFTDSVFTPIKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y++E+ R  Q  DY+KL   I +DGSI  +D++  A++ L     +F    I  E  +  
Sbjct: 182 YSIENFRVEQKTDYEKLIFEIISDGSIHPKDALTEAAKTLIHHFMLFSDERITLETEEMS 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + +SL     L  K+ +L+LSVR+ NCL+   +  +GDL+   ++D+++  NFG+
Sbjct: 242 QAETYDEESLHMRQLLKTKLVDLDLSVRALNCLKAAEVETLGDLVSHNKSDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E++ ++   GL  GM+L  + 
Sbjct: 302 KSLTELEELVENKGLDFGMDLSKYK 326


>gi|58415896|emb|CAH57362.1| RNA polymerase alpha-subunit [Vibrio ichthyoenteri ATCC 700023]
          Length = 297

 Score =  301 bits (770), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 134/300 (44%), Positives = 198/300 (66%), Gaps = 8/300 (2%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
                 +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ 
Sbjct: 1   STTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDIL 60

Query: 84  DIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-A 141
           +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+ NP+HVIC+L  D A
Sbjct: 61  EILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEITNPEHVICHLTDDNA 120

Query: 142 VVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M + V +G GYVPA    H   +  PIG + +DA YSP+ K++Y+V++AR  Q  D 
Sbjct: 121 EIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVDAARVEQRTDL 180

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+
Sbjct: 181 DKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLR 237

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 238 PVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 297


>gi|305665111|ref|YP_003861398.1| DNA-directed RNA polymerase subunit alpha [Maribacter sp. HTCC2170]
 gi|88709863|gb|EAR02095.1| DNA-directed RNA polymerase alpha subunit [Maribacter sp. HTCC2170]
          Length = 330

 Score =  301 bits (770), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 122/325 (37%), Positives = 190/325 (58%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT+V+ID 
Sbjct: 5   NFQKPDKV---IMIDSSDFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGHAITSVRIDK 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQT-VND 124
           V HE S I GV ED+T+IILN+K +  K  +     + V+I   G   +TAGD Q  ++ 
Sbjct: 62  VEHEFSVIPGVVEDVTEIILNLKQVRFKKQIEDSEAEVVSISVSGKDQLTAGDFQKFISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLNPD VICN+D    + ME+ + KG GYVPA+ ++  N  +G I +D++++PIK V 
Sbjct: 122 YQVLNPDLVICNMDSKVSINMEIVIDKGRGYVPAEENKKSNAALGTIAVDSIFTPIKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y++E+ R  Q  DY+KL   I TDGSI  +D++   +++L     +F    I  E  +  
Sbjct: 182 YSIENFRVEQKTDYEKLVFEIVTDGSIHPKDALTEGAKVLIHHFMLFSDERITLEADEIA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+
Sbjct: 242 QTETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E++ ++   GL  GM+L  + 
Sbjct: 302 KSLTELEELVINKGLSFGMDLSKYK 326


>gi|58415736|emb|CAH57282.1| RNA polymerase alpha-subunit [Vibrio aerogenes]
          Length = 293

 Score =  301 bits (770), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 135/296 (45%), Positives = 198/296 (66%), Gaps = 8/296 (2%)

Query: 28  TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIIL 87
             +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+L
Sbjct: 1   AKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILL 60

Query: 88  NIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRM 145
           N+KG+ +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M
Sbjct: 61  NLKGLAVRVAEGKDEVFITLHKSGSGPVVAGDITHDGDVEIVNPEHVICHLTDDNAEIAM 120

Query: 146 ELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
            + V +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL 
Sbjct: 121 RIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLV 180

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + ++T+G+I  E+++  A+ +L +QL  F++  + +         +   F+P LL+ V++
Sbjct: 181 IDMETNGTIEPEEAIRRAATVLAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDD 237

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 238 LELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 293


>gi|228472281|ref|ZP_04057047.1| DNA-directed RNA polymerase, alpha subunit [Capnocytophaga
           gingivalis ATCC 33624]
 gi|228276484|gb|EEK15208.1| DNA-directed RNA polymerase, alpha subunit [Capnocytophaga
           gingivalis ATCC 33624]
          Length = 330

 Score =  301 bits (770), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 126/327 (38%), Positives = 196/327 (59%), Gaps = 10/327 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++ +  E        PL  G+  T+GNALRRV++SSL G AIT+V+ID 
Sbjct: 5   NFQKPDKV---IMIESSEFEGKFEFRPLEPGYGLTIGNALRRVMLSSLEGYAITSVKIDS 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQT-VND 124
           V HE S+I GV ED+T+IILN+K +  K+  +   H++ +I   G   +TAGD Q  +  
Sbjct: 62  VEHEFSTITGVVEDVTEIILNLKQVRFKLQTEGTDHEKASISVTGKKQLTAGDFQKFITG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLNPD VICN++ D  ++M++T+ KG GYV A+ +   N P+G I  DA+++PIK V 
Sbjct: 122 FQVLNPDLVICNMEPDVAIKMDITIDKGMGYVFAEENTKPNMPMGTIPTDAIFTPIKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y++E+ R  Q  DY+KL   I TDGSI  +D++  A++ L     +F    I  E  +  
Sbjct: 182 YSIENYRVEQKTDYEKLIFEIKTDGSIHPKDALMEAAKTLIHHFMLFSDERITIEPEEVV 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+  T+ D+++  NFG+
Sbjct: 242 QPESYDEESLHMRQLLKTKLIDMDLSVRALNCLKAAEVDTLGDLVSFTKTDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           KSL E+  ++ + GL  GM+L  +  E
Sbjct: 302 KSLTELDELVESKGLTFGMDLSRYKLE 328


>gi|312880343|ref|ZP_07740143.1| DNA-directed RNA polymerase subunit alpha [Aminomonas paucivorans
           DSM 12260]
 gi|310783634|gb|EFQ24032.1| DNA-directed RNA polymerase subunit alpha [Aminomonas paucivorans
           DSM 12260]
          Length = 362

 Score =  300 bits (769), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 123/343 (35%), Positives = 190/343 (55%), Gaps = 20/343 (5%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I++ +   +   ++ EPL RG+  TLGNALRRVL+SS+ GA+I+AV+I+GVLHE S++ G
Sbjct: 19  IIVEEITPSYGRIVLEPLERGYGITLGNALRRVLLSSIPGASISAVRIEGVLHEFSTVPG 78

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ ++++N+K + L+      K + +   GP  VTA DIQ   D+E ++P+ VIC L
Sbjct: 79  VREDVIELLVNLKHVPLRCYNAELKTLHLEVEGPKTVTAADIQPDADVEYVDPEAVICTL 138

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           +    + M+L V +G GY      R    P+  + IDA++SP K+V Y V+  R GQ  D
Sbjct: 139 EAGHRISMDLYVEQGIGYAAIDRPRPAYLPVDALLIDAVFSPAKRVKYEVQDVRMGQRTD 198

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF------------EEPKKEVKEDI 245
           YD+L + + T+G +T +++VA AS IL+       N             E+      E +
Sbjct: 199 YDRLVLEVWTNGVVTPKEAVAKASAILEGYFRSLTNVLSSRPSQGGALPEDAISSEGEGV 258

Query: 246 NVKSLP--------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
             +  P         N  L + V +LELSVRS NCL    +  +GDL+ R   D+L++ N
Sbjct: 259 PAEGDPAEEPVRFFENALLARPVRDLELSVRSENCLLRGGVHVIGDLVGRAREDLLKIRN 318

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
            G+ SL EI+  L   GL LG        E+ ++L +  E++ 
Sbjct: 319 LGKISLKEIEEKLEKFGLSLGGEPLSDLGETEDDLPETKEEET 361


>gi|119366749|sp|Q110D1|RPOA_TRIEI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 314

 Score =  300 bits (769), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 111/312 (35%), Positives = 173/312 (55%), Gaps = 12/312 (3%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             +E     ++       I EPL RG   T+GNALRRVL+S+L G AIT+V+I GV HE 
Sbjct: 7   ECVESKT-DKDRSQYGKFIIEPLARGQGTTVGNALRRVLLSNLEGTAITSVRIAGVNHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++IKGV ED+ +I+LN+K + LK   +  +   +   GP  VTA      +++EV++   
Sbjct: 66  ATIKGVREDVLEILLNMKEVVLKSYSEQPQIGRLRVEGPATVTADRFDVPSEVEVIDRSQ 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L   +++ ME  + KG GY      R +   +  + IDA++ P++KV+YT+E A  
Sbjct: 126 YIATLSPGSILEMEFRIEKGTGYKAVDRTRDDVATLDFLQIDAIFMPVRKVNYTIEDAHI 185

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP- 251
           G  L+ D+L M I T+GS T +D+++ A+ IL           EP K++    ++ S   
Sbjct: 186 GSSLEQDRLIMDIWTNGSYTPQDALSNAAGILMSLF-------EPLKDITNMADIPSGET 238

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L 
Sbjct: 239 TDPTSQIPIEELQLSVRAYNCLKRAQINSVADLLDYSQEDLLEIKNFGQKSAEEVIEAL- 297

Query: 312 TMGLFLGMNLPD 323
                LG+ LP 
Sbjct: 298 --QKRLGITLPQ 307


>gi|86141166|ref|ZP_01059712.1| DNA-directed RNA polymerase alpha subunit [Leeuwenhoekiella
           blandensis MED217]
 gi|85831725|gb|EAQ50180.1| DNA-directed RNA polymerase alpha subunit [Leeuwenhoekiella
           blandensis MED217]
          Length = 317

 Score =  300 bits (769), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 122/311 (39%), Positives = 186/311 (59%), Gaps = 7/311 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
              +        PL  G+  T+GNALRRVL+SSL G AIT+V+++GV HE S+I GV ED
Sbjct: 3   DSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGFAITSVRVEGVDHEFSTIAGVVED 62

Query: 82  LTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLD 138
            T+IILN+K +  K   D   ++ VTI       +TAGD Q  ++  ++LNPD VI N++
Sbjct: 63  FTEIILNLKQVRFKRQIDEIDNETVTISVSDKEQLTAGDFQKFISGFQILNPDLVIANME 122

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + ME+TV KG GYVPA+ ++ +N P+G I  D++Y+PIK V Y++E+ R  Q  DY
Sbjct: 123 KSVNINMEITVEKGRGYVPAEENKKQNAPVGTIFTDSIYTPIKNVKYSIENYRVEQKTDY 182

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNP 254
           +KL   I TDGSI  +D++  A++ L     +F    I  E  +    E  + +SL    
Sbjct: 183 EKLVFEIITDGSIHPKDALTEAAKTLIHHFMLFSDERITLEADEIAQTETYDEESLHMRQ 242

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
            L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+KSL E++ ++   G
Sbjct: 243 LLKTKLVDMDLSVRALNCLKAAEVETLGDLVSYNKNDLMKFRNFGKKSLTELEELVNVKG 302

Query: 315 LFLGMNLPDWP 325
           L  GM+L  + 
Sbjct: 303 LNFGMDLSKYK 313


>gi|179184509|gb|ACB78150.1| RNA polymerase alpha subunit [Vibrio sp. RD 9.17]
          Length = 303

 Score =  300 bits (769), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 136/304 (44%), Positives = 199/304 (65%), Gaps = 8/304 (2%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV 
Sbjct: 3   IEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQ 62

Query: 80  EDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
           ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+ NP+HVIC+L 
Sbjct: 63  EDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLT 122

Query: 139 VD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
            D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q
Sbjct: 123 DDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQ 182

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
             D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P
Sbjct: 183 RTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDP 239

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
            LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + G
Sbjct: 240 ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRG 299

Query: 315 LFLG 318
           L LG
Sbjct: 300 LSLG 303


>gi|313204944|ref|YP_004043601.1| DNA-directed RNA polymerase subunit alpha [Paludibacter
           propionicigenes WB4]
 gi|312444260|gb|ADQ80616.1| DNA-directed RNA polymerase subunit alpha [Paludibacter
           propionicigenes WB4]
          Length = 330

 Score =  300 bits (769), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 121/324 (37%), Positives = 197/324 (60%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP  +   ++ + +  +      PL  G+  T+GNALRR+L+SSL G AIT+++I+G+
Sbjct: 6   FQKPEKV---IMLEADAFQGKFEFRPLEPGYGITIGNALRRILLSSLEGFAITSIKIEGI 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE S+I GV +D+T+IILN+K +  K  +    +++VTI   G     AGDI +     
Sbjct: 63  DHEYSTIPGVIDDVTNIILNLKQVRFKQIVEDIENEKVTINVSGTTSFKAGDIGKYFTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP  VIC LD  A  ++++TV+KG GY P++ ++  N  IGLI IDA+++PI+ V Y
Sbjct: 123 EVLNPKLVICELDPSASFQIDITVNKGRGYAPSEENKPANAEIGLIPIDAIFTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  QV DY+KL + I TDGSI  ++++  +++IL     +F    I+ E  + E 
Sbjct: 183 SIENYRVEQVTDYEKLVLEISTDGSIHPKEALKESAKILIHHFMLFSDEKISLEVTEGEG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++ + + L     L  K+ +LELSVR+ NCL+  ++  +G L    + D+L+  NFG+K
Sbjct: 243 SDEFDEEILHMRQLLKTKLTDLELSVRALNCLKAADVDTLGQLAGYHKHDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E++  L ++ L  GM++  + 
Sbjct: 303 SLTELEEKLESLNLSFGMDIAKYK 326


>gi|312130522|ref|YP_003997862.1| DNA-directed RNA polymerase subunit alpha [Leadbetterella
           byssophila DSM 17132]
 gi|311907068|gb|ADQ17509.1| DNA-directed RNA polymerase subunit alpha [Leadbetterella
           byssophila DSM 17132]
          Length = 329

 Score =  300 bits (768), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 122/323 (37%), Positives = 193/323 (59%), Gaps = 9/323 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
              P+ +   V+ + ++       +PL RG+  T+GNALRR+L+SSL G AIT+V+  GV
Sbjct: 6   FQMPDKV---VMEKADDFHGFFEFKPLERGYGVTIGNALRRILLSSLEGYAITSVRFPGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK-MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIE 126
           LHE S+I+GV +D+T+I+LN+K +  K ++     ++T+  +    +TAGDI +  +  E
Sbjct: 63  LHEFSAIEGVVDDVTEIVLNLKQVRFKKIADYVDNKITVKVKNQTEITAGDIGKYTSSFE 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +LNPD VI  LD    +  E+ V KG GYVP++  +T + PIG I ID++Y+PIK V Y+
Sbjct: 123 ILNPDLVIARLDSKKELEFEIIVDKGRGYVPSEEQKTADLPIGFIAIDSIYTPIKNVKYS 182

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVK 242
           +E+ R  Q  DY+KL + I TDGSI  E ++  AS IL      F +    F+    E  
Sbjct: 183 IENTRVEQRTDYEKLLLEIKTDGSIHPEKALQEASHILIQHFLKFTDENMVFDSKSDEED 242

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
             ++ + L     L   +++L+LSVR+ NCL+  +I  +GDL +   ADM++  NFG+KS
Sbjct: 243 NMVDEEFLHMRKLLKTPLQDLDLSVRAYNCLKSADIRTLGDLARLEVADMMKFRNFGKKS 302

Query: 303 LVEIKGVLGTMGLFLGMNLPDWP 325
           L E++ ++    L  GM++  + 
Sbjct: 303 LTELEQLIADKQLHFGMDVSKYK 325


>gi|294674744|ref|YP_003575360.1| DNA-directed RNA polymerase subunit alpha [Prevotella ruminicola
           23]
 gi|294472989|gb|ADE82378.1| DNA-directed RNA polymerase, alpha subunit [Prevotella ruminicola
           23]
          Length = 330

 Score =  300 bits (768), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 121/324 (37%), Positives = 194/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  +        PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---VMLEANDKFGKFEFRPLEPGFGVTIGNALRRILLSSLEGYAINTIRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +    +++V+I         AGDI + ++  
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQIVEEFENEKVSITVENSTEFKAGDISKYLSGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VIC+LD  A +++++T++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPDLVICHLDSKASMQIDITINKGRGYVPADENREFCTDVNVIAIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE  R  Q  DYDKL + + TDGSI  +D++  A++IL     +F    I+ E  + E 
Sbjct: 183 AVEPYRVEQKTDYDKLVLEVTTDGSIHPKDALKEAAKILIYHFMLFSDEKISLESSETES 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++ + + L     L  ++ ++ LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NQEFDEEILHMRQLLKTRLVDMNLSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLTELDDLLESLNLSFGTDISKYK 326


>gi|325104841|ref|YP_004274495.1| DNA-directed RNA polymerase subunit alpha [Pedobacter saltans DSM
           12145]
 gi|324973689|gb|ADY52673.1| DNA-directed RNA polymerase subunit alpha [Pedobacter saltans DSM
           12145]
          Length = 330

 Score =  300 bits (768), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 129/324 (39%), Positives = 199/324 (61%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ +  +        PL  GF  T+GNALRR+L+SSL G AIT+V+  GV
Sbjct: 6   FQKPDKV---IMQKSTDFDGTFEFRPLEPGFGVTIGNALRRILLSSLEGYAITSVRFSGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE S+IKGV ED+ DIILN+K +  K +G+    +++ +   G     AGDI +  N+ 
Sbjct: 63  SHEFSTIKGVAEDVVDIILNLKQVRFKKTGESGDSEKIFVIINGQESFKAGDITKFSNNF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD V+CN++    + +ELT++KG GYV A+ ++  +  +G+I ID++Y+PIK V Y
Sbjct: 123 EVLNPDFVVCNMESSVTLEIELTINKGRGYVAAEENKNADAAVGVIAIDSIYTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEV 241
           T+E+ R  Q  DY+KL + I TDGSI  ED++  A++IL     +F +     E   KE 
Sbjct: 183 TIENYRVEQKTDYEKLLLDISTDGSIHPEDALKEAAKILIQHFMLFSDENLILESQAKEE 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++++ + L     L  ++ +L+LSVR+ NCL+  +I  + DL+    ADML+  NFG+K
Sbjct: 243 TKEVDEEVLHMRKILKTELVDLDLSVRALNCLKAADIRSLADLVSYDVADMLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL EI+ ++ + GL  GMNL  + 
Sbjct: 303 SLTEIQELVKSKGLSFGMNLSKYK 326


>gi|326334519|ref|ZP_08200730.1| DNA-directed RNA polymerase subunit alpha [Capnocytophaga sp. oral
           taxon 338 str. F0234]
 gi|325693288|gb|EGD35216.1| DNA-directed RNA polymerase subunit alpha [Capnocytophaga sp. oral
           taxon 338 str. F0234]
          Length = 330

 Score =  300 bits (768), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 125/327 (38%), Positives = 196/327 (59%), Gaps = 10/327 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++ +  E        PL  G+  T+GNALRRV++SSL G AIT+V+ID 
Sbjct: 5   NFQKPDKV---IMIESSEFEGKFEFRPLEPGYGLTIGNALRRVMLSSLEGYAITSVKIDT 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQT-VND 124
           V HE S+I GV ED+T+IILN+K +  K+  +   H++ +I   G   +TAGD Q  +  
Sbjct: 62  VEHEFSTIAGVVEDVTEIILNLKQVRFKLQTEGTDHEKASISVTGKKQLTAGDFQKFITG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLNPD VICN++ +  ++M++T+ KG GYV A+ +   N P+G I  DA+++PIK V 
Sbjct: 122 FQVLNPDLVICNMEPEVEIKMDITIDKGMGYVSAEENAKPNMPVGTIPTDAIFTPIKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y++E+ R  Q  DY+KL   I TDGSI  +D++  A++ L     +F    I  E  +  
Sbjct: 182 YSIENYRVEQKTDYEKLIFEIKTDGSIHPKDALMEAAKTLIHHFMLFSDERITIEPEEVV 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+  T+ D+++  NFG+
Sbjct: 242 QPESYDEESLHMRQLLKTKLIDMDLSVRALNCLKAAEVDTLGDLVSFTKTDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           KSL E+  ++ + GL  GM+L  +  E
Sbjct: 302 KSLTELDELVESKGLTFGMDLSKYKLE 328


>gi|262383847|ref|ZP_06076983.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp.
           2_1_33B]
 gi|301312005|ref|ZP_07217927.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 20_3]
 gi|262294745|gb|EEY82677.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp.
           2_1_33B]
 gi|300830107|gb|EFK60755.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 20_3]
          Length = 330

 Score =  300 bits (768), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 121/324 (37%), Positives = 198/324 (61%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  G+  T+GNALRR+L+SSL G AIT+++IDGV
Sbjct: 6   FQKPDKV---LMLEADNFFGKFEFRPLEPGYGITIGNALRRILLSSLEGFAITSIKIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE  +I GV ED+T+IILN+K +  K  +    +++V+I   G  V  AGDI + +   
Sbjct: 63  DHEFGTIPGVIEDVTNIILNLKQVRFKHIVDDIENEKVSITVSGSEVFKAGDIGKQLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E+LNPD VIC LD  A  ++ELT++KG GYVPA  +R  N  + +I ID++++PI+ V Y
Sbjct: 123 EILNPDLVICRLDPTASFQIELTINKGRGYVPADENRDPNADMHVIAIDSIFTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEV 241
           ++E+ R  Q  DY+KL + I TDGSI  ++++  A++IL     +F +     E    E 
Sbjct: 183 SIENFRVEQKTDYEKLVLEIATDGSIHPKEALKEAAKILIHHFMLFSDEKIAIETADTEG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ +++LSVR+ NCL+  ++  +G+L++  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKSKLADMDLSVRALNCLKAADVETLGELVKFNKNDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  GM++  + 
Sbjct: 303 SLTELDELLESLNLSFGMDITKYK 326


>gi|24213465|ref|NP_710946.1| RNA polymerase subunit alpha [Leptospira interrogans serovar Lai
           str. 56601]
 gi|45658676|ref|YP_002762.1| DNA-directed RNA polymerase subunit alpha [Leptospira interrogans
           serovar Copenhageni str. Fiocruz L1-130]
 gi|26454665|sp|Q9XD09|RPOA_LEPIN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|59798772|sp|Q72NI8|RPOA_LEPIC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|24194237|gb|AAN47964.1| RNA polymerase alpha subunit [Leptospira interrogans serovar Lai
           str. 56601]
 gi|45601920|gb|AAS71399.1| DNA-directed RNA polymerase alpha chain [Leptospira interrogans
           serovar Copenhageni str. Fiocruz L1-130]
          Length = 325

 Score =  300 bits (768), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 130/317 (41%), Positives = 202/317 (63%), Gaps = 4/317 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           +   +P  IE+        N    +AEP  RGFA T+GN+LRR LMSS+ GAAI+A++I+
Sbjct: 8   KGFKRPKKIEFNT-EANTPNYGKFVAEPFERGFATTIGNSLRRTLMSSIEGAAISAIRIE 66

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS---HKRVTIFKRGPGVVTAGDIQTVN 123
           GV HE S I+GV ED+T IILN+K + +K   +     K + +  +G G   AGD+   +
Sbjct: 67  GVNHEFSFIEGVAEDVTRIILNLKQVRIKYEPEEKDQSKIIHLELKGAGYFRAGDLAVDS 126

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            IE++NPD  I  L+ DA + M+L + +G GYVPA+  + + + +G I +D+++SP++KV
Sbjct: 127 SIEIMNPDLHIATLNEDANLVMDLEIQRGRGYVPAEEKKKDIEVLGTIPVDSIFSPVQKV 186

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
            + V   R  Q  DY+KL++ + TDGS++ +D+VA A++IL++ L +FINFEE  +E  +
Sbjct: 187 VFEVSETRVAQRSDYEKLTLEVWTDGSVSPDDAVAQAAKILKEHLTVFINFEEELEEEDD 246

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +++        +L K VEELELSVRS N LR   I ++GDL++R+E +M +  ++  + L
Sbjct: 247 ELDEADEKLKASLSKHVEELELSVRSLNVLRSLEIDFIGDLVKRSEEEMSKSKHYSDQCL 306

Query: 304 VEIKGVLGTMGLFLGMN 320
            E+K  L T+GL  GM 
Sbjct: 307 QELKVKLSTLGLSFGMR 323


>gi|282878784|ref|ZP_06287552.1| DNA-directed RNA polymerase, alpha subunit [Prevotella buccalis
           ATCC 35310]
 gi|281299175|gb|EFA91576.1| DNA-directed RNA polymerase, alpha subunit [Prevotella buccalis
           ATCC 35310]
          Length = 330

 Score =  299 bits (767), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 120/324 (37%), Positives = 194/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ + ++        PL  GF  T+GN+LRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---VMLEADDKFGKFEFRPLEPGFGITIGNSLRRILLSSLEGYAINTIRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VIC+LD  A ++++LT+++G GYVPA  +R     + ++ ID++Y+PI+ V Y
Sbjct: 123 EVLNPDLVICHLDAKASMQIDLTINQGRGYVPADENRQFCTDVNVLPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           +VE  R  Q  DYDKL + + TDGS++ +D++  A++IL     +F    I  E P ++ 
Sbjct: 183 SVEPYRVEQKTDYDKLVIEVTTDGSLSPKDALKEAAKILIYHFMLFSDEKITLENPDQDD 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++ + + L     L  K+ +L LSVR+ NCL+   +  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NQEFDEEVLRMRQLLKTKLIDLNLSVRALNCLKAAEVETLGDLVQYNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G +   + 
Sbjct: 303 SLSELDDLLESLNLSFGTDTSKYK 326


>gi|150008958|ref|YP_001303701.1| DNA-directed RNA polymerase subunit alpha [Parabacteroides
           distasonis ATCC 8503]
 gi|255014788|ref|ZP_05286914.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. 2_1_7]
 gi|256841041|ref|ZP_05546548.1| DNA-directed RNA polymerase, alpha subunit [Parabacteroides sp.
           D13]
 gi|298375809|ref|ZP_06985765.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 3_1_19]
 gi|172048837|sp|A6LEG5|RPOA_PARD8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|149937382|gb|ABR44079.1| DNA-directed RNA polymerase alpha chain [Parabacteroides distasonis
           ATCC 8503]
 gi|256736884|gb|EEU50211.1| DNA-directed RNA polymerase, alpha subunit [Parabacteroides sp.
           D13]
 gi|298266846|gb|EFI08503.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 3_1_19]
          Length = 330

 Score =  299 bits (767), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 122/324 (37%), Positives = 198/324 (61%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  G+  T+GNALRR+L+SSL G AIT+++IDGV
Sbjct: 6   FQKPDKV---LMLEADNFFGKFEFRPLEPGYGITIGNALRRILLSSLEGFAITSIKIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE  +I GV ED+T+IILN+K +  K  +    +++V+I   G  V  AGDI + +   
Sbjct: 63  DHEFGTIPGVIEDVTNIILNLKQVRFKHIVDDIENEKVSITVSGSEVFKAGDIGKQLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E+LNPD VIC LD  A  ++ELT++KG GYVPA  +R  N  I +I ID++++PI+ V Y
Sbjct: 123 EILNPDLVICRLDPTASFQIELTINKGRGYVPADENRDPNADIHVIAIDSIFTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEV 241
           ++E+ R  Q  DY+KL + I TDGSI  ++++  A++IL     +F +     E    E 
Sbjct: 183 SIENFRVEQKTDYEKLVLEIATDGSIHPKEALKEAAKILIHHFMLFSDEKIAIETADTEG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ +++LSVR+ NCL+  ++  +G+L++  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKSKLADMDLSVRALNCLKAADVETLGELVKFNKNDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  GM++  + 
Sbjct: 303 SLTELDELLESLNLSFGMDITKYK 326


>gi|304384302|ref|ZP_07366713.1| DNA-directed RNA polymerase subunit alpha [Prevotella marshii DSM
           16973]
 gi|304334618|gb|EFM00900.1| DNA-directed RNA polymerase subunit alpha [Prevotella marshii DSM
           16973]
          Length = 330

 Score =  299 bits (767), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 123/324 (37%), Positives = 192/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  +        PL  GF  T+GNALRR+L+SSL G AI  ++I  V
Sbjct: 6   FQKPDKV---VMLEANDKFGKFEFRPLEPGFGVTIGNALRRILLSSLEGYAINTMRIGSV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SSI GV ED+T+IILN+K +  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFSSIPGVKEDVTNIILNLKQVRFKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VIC+LD  A ++++LT++KG GYV A  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPDLVICHLDAKASMQIDLTINKGRGYVTADENREFCTDVNVIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEV 241
           TVE  R  Q  DYDKL + +DTDGSI  +D++  A++IL     +F +     E P  E 
Sbjct: 183 TVEPYRVEQKTDYDKLVIEVDTDGSIQPKDALKEAAKILIYHFMLFSDEKIALESPDVEG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++ + + L     L  ++ ++ LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NQEFDEEVLHMRQLLKTRLVDMNLSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLSELDDLLESLNLTFGTDISKYK 326


>gi|206901886|ref|YP_002250728.1| DNA-directed RNA polymerase, alpha subunit [Dictyoglomus
           thermophilum H-6-12]
 gi|206740989|gb|ACI20047.1| DNA-directed RNA polymerase, alpha subunit [Dictyoglomus
           thermophilum H-6-12]
          Length = 324

 Score =  299 bits (766), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 116/319 (36%), Positives = 194/319 (60%), Gaps = 11/319 (3%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI++N +          +++ +  E+    + EPL RG+  T+GNALRR+L+SS+ GAA+
Sbjct: 1   MIEENVR----------VIVEKRSEDYGRFVIEPLERGYGWTIGNALRRILLSSIEGAAV 50

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
            +V+IDGV HE+  + G+ E++ ++++N+K + +K+  ++   + I  RGP VVTA D  
Sbjct: 51  VSVKIDGVRHELEVLPGLKEEILEVLMNLKKLVVKIEDNNSHILEIDTRGPKVVTAADFI 110

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             ++++++NPD VI  L  D    ME+ V KG GYV A+ ++ +N PIG++ +D+++SP+
Sbjct: 111 VPSNVKIVNPDLVIATLVEDMPFHMEVEVKKGKGYVSAEENKDQNYPIGVLVLDSIFSPV 170

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSYTVE  R G+  D D+L + I T+GSI+ E++   ASRIL +     +N +E +  
Sbjct: 171 KKVSYTVEKTRVGRRTDLDRLILEIWTNGSISPEEAFREASRILMEYF-RLLNEKEFQLP 229

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E     +          +E+L LS R+ N LR   I  + DL+ +T  +++++ NFG+
Sbjct: 230 YEEVKPENTYLEEEKKGLTLEDLGLSTRAYNSLRHAGIHTIEDLLSKTREELMKIKNFGQ 289

Query: 301 KSLVEIKGVLGTMGLFLGM 319
           KSL E++  L   GL L  
Sbjct: 290 KSLQELEEKLREKGLSLKD 308


>gi|256820008|ref|YP_003141287.1| DNA-directed RNA polymerase subunit alpha [Capnocytophaga ochracea
           DSM 7271]
 gi|256581591|gb|ACU92726.1| DNA-directed RNA polymerase, alpha subunit [Capnocytophaga ochracea
           DSM 7271]
          Length = 330

 Score =  299 bits (766), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 122/325 (37%), Positives = 190/325 (58%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++ +  +        PL  G+  T+GNALRRV++SSL G AIT+V+ D 
Sbjct: 5   NFQKPDKV---IMIESSDFEGRFEFRPLEPGYGLTIGNALRRVMLSSLEGFAITSVKFDK 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQ-TVND 124
           V HE S+I GV ED+T+IILN+K I  K  +    ++  TI   G   +TAGD Q  ++ 
Sbjct: 62  VGHEFSTISGVREDVTEIILNLKQIRFKRQIEDIENETATITVSGKRQLTAGDFQKALSG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLN D VICN+D  A   +E+T+ KG GYV A+ +   N PIG+I  DA+++PIK V 
Sbjct: 122 FQVLNTDLVICNMDSSASFTIEITIEKGRGYVSAEENAKPNAPIGVIATDAIFTPIKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y++E+ R  Q  DY+KL   I TDGSI  + ++  A++ L     +F    I  E  +  
Sbjct: 182 YSIENYRVEQKTDYEKLVFEIKTDGSIHPKQALTEAAKTLIHHFMLFSDERITLEADEIA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             +  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   +AD+++  NFG+
Sbjct: 242 QTDTYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVETLGDLVSFNKADLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL+E++ ++   GL  GM+   + 
Sbjct: 302 KSLIELEELVVNKGLVFGMDTSKYK 326


>gi|183221322|ref|YP_001839318.1| DNA-directed RNA polymerase subunit alpha [Leptospira biflexa
           serovar Patoc strain 'Patoc 1 (Paris)']
 gi|189911413|ref|YP_001962968.1| DNA-directed RNA polymerase subunit alpha [Leptospira biflexa
           serovar Patoc strain 'Patoc 1 (Ames)']
 gi|238687771|sp|B0SA20|RPOA_LEPBA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238687824|sp|B0SSF2|RPOA_LEPBP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|167776089|gb|ABZ94390.1| DNA-directed RNA polymerase, alpha subunit [Leptospira biflexa
           serovar Patoc strain 'Patoc 1 (Ames)']
 gi|167779744|gb|ABZ98042.1| DNA-directed RNA polymerase alpha chain [Leptospira biflexa serovar
           Patoc strain 'Patoc 1 (Paris)']
          Length = 325

 Score =  299 bits (766), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 136/317 (42%), Positives = 203/317 (64%), Gaps = 4/317 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           +   +P  IE+        N    +AEP  RG   T+GN+LRR LMSS+ GAAI+A++I+
Sbjct: 8   KGFKRPKKIEFTT-DVNTPNYGKFVAEPFERGIGTTIGNSLRRTLMSSIEGAAISAIRIE 66

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS---HKRVTIFKRGPGVVTAGDIQTVN 123
           GV HE S I+GV ED+T IILN+K + +K   +     K + +  +G G   A D+   +
Sbjct: 67  GVSHEFSYIEGVAEDVTRIILNLKQVRIKYEPEDKEASKVIHLELKGAGYFRAADLAVDS 126

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            IE++NPD  I  L+ DA + M+L + +G GYVPA+  + + + +G I ID+++SPI+KV
Sbjct: 127 SIEIMNPDLHIATLNEDANLIMDLEIQRGRGYVPAEDKKKDIEVLGTIPIDSIFSPIQKV 186

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
            + V   R  Q  DY+KL+M + TDGS++ ED+VA A++IL+D L +FINFEE  +E +E
Sbjct: 187 LFEVSETRVAQRSDYEKLTMEVWTDGSVSPEDAVAQAAKILKDHLTVFINFEEEIEEEEE 246

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +++        AL K VEELELSVRSTN LR   I ++G+L++R+E +M +  +F  +SL
Sbjct: 247 ELDEADEKLKAALSKHVEELELSVRSTNVLRSLEIDFIGELVKRSEDEMTKSKHFSEQSL 306

Query: 304 VEIKGVLGTMGLFLGMN 320
           +E+K  L +MGL  GM 
Sbjct: 307 LELKAKLSSMGLSFGMR 323


>gi|325287074|ref|YP_004262864.1| DNA-directed RNA polymerase subunit alpha [Cellulophaga lytica DSM
           7489]
 gi|324322528|gb|ADY29993.1| DNA-directed RNA polymerase subunit alpha [Cellulophaga lytica DSM
           7489]
          Length = 330

 Score =  299 bits (766), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 120/325 (36%), Positives = 190/325 (58%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++    +        PL  G+  T+GNALRRVL+S+L G AIT+V++D 
Sbjct: 5   NFQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSALEGFAITSVRMDK 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQT-VND 124
           V HE S I GV ED+T++ILN+K +  K  +     + V+I   G   +TAGD Q  ++ 
Sbjct: 62  VEHEFSVIPGVVEDVTEMILNLKQVRFKRQIEDVEAETVSISVSGKNQLTAGDFQKFISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLNPD VICN+D    + ME+ + KG GYVPA+ ++     IG I ID++++PIK V 
Sbjct: 122 YQVLNPDLVICNMDAKVSINMEIVIEKGRGYVPAEENKKPGAAIGTIPIDSIFTPIKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y++E+ R  Q  DY+KL   I +DGSI  +D++  A+++L     +F    I  E  +  
Sbjct: 182 YSIENYRVEQKTDYEKLVFEISSDGSINPKDALTEAAKVLIHHFMLFSDERITLEADEIA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+
Sbjct: 242 QTETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E++ ++   GL  GM+L  + 
Sbjct: 302 KSLTELEELVINKGLSFGMDLSKYK 326


>gi|315225426|ref|ZP_07867240.1| DNA-directed RNA polymerase subunit alpha [Capnocytophaga ochracea
           F0287]
 gi|314944699|gb|EFS96734.1| DNA-directed RNA polymerase subunit alpha [Capnocytophaga ochracea
           F0287]
          Length = 330

 Score =  299 bits (766), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 122/325 (37%), Positives = 189/325 (58%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++ +  +        PL  G+  T+GNALRRV++SSL G AIT+V+ D 
Sbjct: 5   NFQKPDKV---IMIESSDFEGRFEFRPLEPGYGLTIGNALRRVMLSSLEGFAITSVKFDK 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQ-TVND 124
           V HE S+I GV ED+T+IILN+K I  K  +    ++  TI   G   +TAGD Q  ++ 
Sbjct: 62  VGHEFSTISGVREDVTEIILNLKQIRFKRQIEDIENETATITVSGKRQLTAGDFQKALSG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLN D VICN+D  A   +E+T+ KG GYV A+ +   N PIG+I  DA+++PIK V 
Sbjct: 122 FQVLNTDLVICNMDSSASFTIEVTIEKGRGYVSAEENAKPNAPIGVIATDAIFTPIKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y++E+ R  Q  DY+KL   I TDGSI  + ++  A++ L     +F    I  E  +  
Sbjct: 182 YSIENYRVEQKTDYEKLVFEIKTDGSIHPKQALTEAAKTLIHHFMLFSDERITLEADEIA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             +  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   +AD+++  NFG+
Sbjct: 242 QTDTYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVETLGDLVSFNKADLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL+E+  ++   GL  GM+   + 
Sbjct: 302 KSLIELDELVVNKGLVFGMDTSKYK 326


>gi|5163231|gb|AAD40610.1|AF115283_29 RNA polymerase alpha-subunit [Leptospira interrogans]
          Length = 325

 Score =  299 bits (766), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 129/317 (40%), Positives = 201/317 (63%), Gaps = 4/317 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           +   +P  IE+        N    +AEP  RGFA T+GN+LRR LMSS+ GAAI+A++I+
Sbjct: 8   KGFKRPKKIEFNT-EANTPNYGKFVAEPFERGFATTIGNSLRRTLMSSIEGAAISAIRIE 66

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS---HKRVTIFKRGPGVVTAGDIQTVN 123
           GV HE S I+GV ED+T IILN+K + +K   +     K + +  +G G   AGD+   +
Sbjct: 67  GVNHEFSFIEGVAEDVTRIILNLKQVRIKYEPEEKDQSKIIHLELKGAGYFRAGDLAVDS 126

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            IE++NPD  I  L+ DA + M+L + +G GYVPA+  + + + +G I +D+++SP++KV
Sbjct: 127 SIEIMNPDLHIATLNEDANLVMDLEIQRGRGYVPAEEKKKDIEVLGTIPVDSIFSPVQKV 186

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
            + V   R  Q  DY+KL++ + TDGS++ +D+VA A++IL++ L +FINFEE  +E  +
Sbjct: 187 VFEVSETRVAQRSDYEKLTLEVWTDGSVSPDDAVAQAAKILKEHLTVFINFEEELEEEDD 246

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +++        +L K VEELELS RS N LR   I ++GDL++R+E +M +  ++  + L
Sbjct: 247 ELDEADEKLKASLSKHVEELELSARSLNVLRSLEIDFIGDLVKRSEEEMSKSKHYSDQCL 306

Query: 304 VEIKGVLGTMGLFLGMN 320
            E+K  L T+GL  GM 
Sbjct: 307 QELKVKLSTLGLSFGMR 323


>gi|326799155|ref|YP_004316974.1| DNA-directed RNA polymerase subunit alpha [Sphingobacterium sp. 21]
 gi|326549919|gb|ADZ78304.1| DNA-directed RNA polymerase subunit alpha [Sphingobacterium sp. 21]
          Length = 330

 Score =  299 bits (766), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 127/324 (39%), Positives = 198/324 (61%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ +  +        PL  GF  T+GNALRR+L+SSL G AIT+V+  GV
Sbjct: 6   FQKPDKV---IMQKSTDFDGTFEFRPLEPGFGVTIGNALRRILLSSLEGYAITSVRFSGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVND-I 125
            HE S+I GV ED+T+IILN+K +  K +G+    +++ +   G     AGDI + ++  
Sbjct: 63  SHEFSTITGVVEDVTEIILNLKQVRFKKTGESGDSEKIFVVINGQDQFKAGDITSHSNNF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
            VLNPD VICN++    + +ELTV+KG GYV A+ ++  +  +G+I ID++Y+PIK V Y
Sbjct: 123 TVLNPDLVICNMESSVTLEVELTVNKGRGYVNAEENKVADAAVGVIAIDSIYTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEV 241
           T+E+ R  Q  DY+KL + I TDGSI  ED++  A++IL     +F +     E   KE 
Sbjct: 183 TIENFRVEQKTDYEKLLLDISTDGSIHPEDALKEAAKILIHHFMLFSDENILLESQTKEE 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++++ + L     L  ++ +L+LSVR+ NCL+  +I  + +L+    ADML+  NFG+K
Sbjct: 243 TKEVDEEILHMRKILKTELVDLDLSVRALNCLKAADIRSLAELVSYDVADMLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL EI+ ++ + GL  GMNL  + 
Sbjct: 303 SLTEIQELVKSKGLSFGMNLSKYK 326


>gi|328813943|gb|AEB52087.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 250

 Score =  299 bits (765), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 112/250 (44%), Positives = 167/250 (66%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS 100
            TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNIK + LKM+ D 
Sbjct: 1   TTLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNTDE 60

Query: 101 HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
            K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV KG GYV A  
Sbjct: 61  DKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAADQ 120

Query: 161 HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA
Sbjct: 121 NKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLA 180

Query: 221 SRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVY 280
           ++IL + L +F+N  +  K  +  +  +       L   +EEL+LSVRS NCL+   I  
Sbjct: 181 AKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINT 240

Query: 281 MGDLIQRTEA 290
           + +L  +TEA
Sbjct: 241 VQELTNKTEA 250


>gi|225010542|ref|ZP_03701013.1| DNA-directed RNA polymerase, alpha subunit [Flavobacteria bacterium
           MS024-3C]
 gi|225005371|gb|EEG43322.1| DNA-directed RNA polymerase, alpha subunit [Flavobacteria bacterium
           MS024-3C]
          Length = 330

 Score =  299 bits (765), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 122/325 (37%), Positives = 193/325 (59%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++    +        PL  G+  T+GNALRRV++S+L G AIT+V++D 
Sbjct: 5   NFQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVMLSALEGFAITSVRMDK 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQT-VND 124
           V HE S I GV ED+T+IILN+K +  K  +    ++ ++I   G   +TAGD Q  ++ 
Sbjct: 62  VAHEFSVIPGVVEDVTEIILNLKQVRFKRQIEDVDNETISIALSGKQQLTAGDFQKFISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLNPD VICN+D    + MELT+ KG GYVPA+ ++    PIG I ID++++PIK V 
Sbjct: 122 FQVLNPDLVICNMDAKVNINMELTIEKGRGYVPAEENKKSGAPIGTIAIDSIFTPIKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y++E+ R  Q  DY+KL   I +DGSI  +D++  A+++L     +F    I  E  +  
Sbjct: 182 YSIENFRVEQKTDYEKLVFEIVSDGSIHPKDALTEAAKVLIHHFMLFSDERITLEADEIA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+
Sbjct: 242 QTETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E++ ++   GL  GM+L  + 
Sbjct: 302 KSLTELEELVINKGLSFGMDLSKYK 326


>gi|284040594|ref|YP_003390524.1| DNA-directed RNA polymerase, subunit alpha [Spirosoma linguale DSM
           74]
 gi|283819887|gb|ADB41725.1| DNA-directed RNA polymerase, alpha subunit [Spirosoma linguale DSM
           74]
          Length = 329

 Score =  298 bits (764), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 123/322 (38%), Positives = 196/322 (60%), Gaps = 9/322 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
              P+ +   V+ + ++   +   +PL +G+  T+GNALRR+L+SSL G AIT+V+  GV
Sbjct: 6   FQMPDKV---VVEKADDFHGVFEFKPLEKGYGVTIGNALRRILLSSLEGYAITSVKFPGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK-MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIE 126
           LHE SSI+GV ED+T+IILN+K +  K ++     ++T+  +   V+ AGDI +     E
Sbjct: 63  LHEFSSIEGVVEDVTEIILNLKMVRFKKINDMVDNKITVNIKKQSVLKAGDISKFSPSFE 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           VLNP+  IC++D    + ME+ V KG GYVP+   R    P G I IDA+Y+PIK V Y+
Sbjct: 123 VLNPELEICHIDDTRDLEMEIFVEKGRGYVPSDEPRVNELPFGHIPIDAIYTPIKNVKYS 182

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVK 242
           VE+ R  Q  DY++L + I+TDGSI  E+++  A+ IL     +F +    FE  K E +
Sbjct: 183 VENTRVEQKTDYERLLLDIETDGSIHPEEALKGAAYILIQHFMLFSDQTMTFETAKPEEE 242

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
             ++ + L     L   + +L+LSVR+ NCL+  ++  +GDL++   +DM++  NFG+KS
Sbjct: 243 NVVDEEVLHMRKLLKTSLADLDLSVRAYNCLKSADVRTLGDLVRLEISDMMKFRNFGKKS 302

Query: 303 LVEIKGVLGTMGLFLGMNLPDW 324
           L E++ ++    L  GM++  +
Sbjct: 303 LTELEQLVAEKNLTFGMDVAKY 324


>gi|226227379|ref|YP_002761485.1| DNA-directed RNA polymerase alpha subunit [Gemmatimonas aurantiaca
           T-27]
 gi|226090570|dbj|BAH39015.1| DNA-directed RNA polymerase alpha subunit [Gemmatimonas aurantiaca
           T-27]
          Length = 357

 Score =  298 bits (764), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 121/321 (37%), Positives = 193/321 (60%), Gaps = 7/321 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L++P  +E     ++  N      +PL RGF HTLGNA+RR+L+SSLRG+A+ A +IDGV
Sbjct: 9   LVRPQLVEA-TKREDSPNLAEFRLQPLERGFGHTLGNAMRRLLLSSLRGSAVWAFRIDGV 67

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV-TIFKRGPGVVTAGDIQTVNDIEV 127
           +HE  +I GV ED+  II N+K + L +  +  + V  I K GPG VTA DI     + +
Sbjct: 68  VHEHQTIGGVVEDVHQIIGNLKTLTLALPDEVEQTVLRISKSGPGTVTAADIIATGGVRI 127

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSPIKKVSYT 186
           ++P H I  +  +    +EL V+KG GY+ +  H  + N  + ++ IDA+YSP+++V++T
Sbjct: 128 IDPSHHIFTITGERDFNIELYVNKGRGYIESDQHPADKNLSVDVVRIDAIYSPVRRVNFT 187

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF----EEPKKEVK 242
           V   R GQ  DYD+L++T++T+G+++ E++V+ A+ + Q     F+ F            
Sbjct: 188 VAETRVGQRTDYDRLTLTVETNGTMSPEEAVSYAAALAQTHFQYFVGFGSSASAQPGTAG 247

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           +  N  ++         +++LELSVRS N L+  NI  +GDL+++TEA +L++ NFG+KS
Sbjct: 248 DGANSDAIRLAELFRTPIDDLELSVRSVNSLKNSNIRSLGDLVRQTEAQILQVKNFGKKS 307

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           L EI  +L   GL  GM   +
Sbjct: 308 LQEIAALLEKEGLNFGMRYEE 328


>gi|298253052|ref|ZP_06976844.1| DNA-directed RNA polymerase, alpha subunit [Gardnerella vaginalis
           5-1]
 gi|297532447|gb|EFH71333.1| DNA-directed RNA polymerase, alpha subunit [Gardnerella vaginalis
           5-1]
          Length = 290

 Score =  298 bits (764), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 108/280 (38%), Positives = 162/280 (57%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG 110
           ++SS+ GAA+T+V+I G LHE +++ GV ED+T+I+LNIKGI L    D    + + K G
Sbjct: 1   MLSSIPGAAVTSVRISGALHEFTTLPGVEEDVTEILLNIKGIVLTSEYDEPVVMYLRKNG 60

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
            G  TAGDI     + + NPD  I  L  D  + +E TV +G GYVPA+ ++ EN  IG 
Sbjct: 61  KGEATAGDITPPAGVTIANPDLHIATLAEDGELEIEFTVERGRGYVPAQMNKQENSEIGR 120

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           I +D++YSP+ KVSY VE+ R  Q  D+DKL + ++T  +IT  D+VA A   L +  G+
Sbjct: 121 IPVDSIYSPVLKVSYKVEATRVEQRTDFDKLILDVETKPAITPRDAVASAGSTLVELFGL 180

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
                   + V+          +  L   +E++  + RS NCL+ E I  +G+L+  TE 
Sbjct: 181 CRELNVDAEGVEVGPAPTHDEADSQLAIPIEDMNFTQRSYNCLKREGIHTVGELVVHTEQ 240

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           D+L + NFG KS+ E+K  L  MGL L  +   +   ++E
Sbjct: 241 DLLDIRNFGMKSIDEVKEKLQAMGLSLKASPIGFDANNLE 280


>gi|225011672|ref|ZP_03702110.1| DNA-directed RNA polymerase, alpha subunit [Flavobacteria bacterium
           MS024-2A]
 gi|225004175|gb|EEG42147.1| DNA-directed RNA polymerase, alpha subunit [Flavobacteria bacterium
           MS024-2A]
          Length = 330

 Score =  298 bits (763), Expect = 8e-79,   Method: Composition-based stats.
 Identities = 120/325 (36%), Positives = 192/325 (59%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++    E        PL  G+  T+GNALRRVL+SSL G AIT+V+++ 
Sbjct: 5   NFQKPDKV---IMIDSSEFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGFAITSVKLEN 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQT-VND 124
           V HE S+I GV ED+T+IILN+K +  K  +     ++VT+   G   + A D+Q  ++ 
Sbjct: 62  VEHEFSTIPGVVEDVTEIILNLKQVRFKRQIEDTEEEKVTVIIGGQEQLKAADLQKFISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLNPD VIC+L+    + ME+ + KG GYVPA+ ++  N  +G+I ID++++PIK V 
Sbjct: 122 FQVLNPDLVICHLEKSVQLNMEIAIEKGRGYVPAEENKKANAELGVIAIDSIFTPIKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y++E+ R  Q  DY+KL   I TDGSI  +D++  A++ L     +F    I  E  +  
Sbjct: 182 YSIENFRVEQKTDYEKLVFEIITDGSIHPKDALTEAAKTLIHHFLLFSDERITLEADEIA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+
Sbjct: 242 QTETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSYNKNDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E++ ++   GL  GM+L  + 
Sbjct: 302 KSLTELEELVVLKGLSFGMDLAKYK 326


>gi|325972636|ref|YP_004248827.1| DNA-directed RNA polymerase subunit alpha [Spirochaeta sp. Buddy]
 gi|324027874|gb|ADY14633.1| DNA-directed RNA polymerase subunit alpha [Spirochaeta sp. Buddy]
          Length = 350

 Score =  298 bits (763), Expect = 8e-79,   Method: Composition-based stats.
 Identities = 131/331 (39%), Positives = 195/331 (58%), Gaps = 13/331 (3%)

Query: 1   MIQKNW-QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M +KN  +   KP  I +      E N    IA P  RGF  T+GN LRRVL+SS++G A
Sbjct: 1   MARKNLLKGFKKPKGITFE-HSAVEPNYGKFIAYPFERGFGTTIGNTLRRVLLSSIQGYA 59

Query: 60  ITAVQI-----DGVLHEISS----IKGVHEDLTDIILNIKGINLKMSGDSHKR-VTIFKR 109
           +TAV+      DGV H ISS    + GV ED+ DII  +K + ++M  DS    + I  +
Sbjct: 60  VTAVKFTSFNEDGVPHLISSEYEQLPGVREDIADIIAALKKLQIRMPEDSEGTNLLIECK 119

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GPG+VT  + +    +E+ N D V+  +  DA + ME+ +  G GYVP++ +    + IG
Sbjct: 120 GPGIVTGANFERD-QVEITNKDLVLFTMMDDANIEMEVQIDLGRGYVPSEINEKYVEEIG 178

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            I IDA +SP+ +V Y++E  R G   DYDKL++ I TDG+I  ++++A A++I ++   
Sbjct: 179 TIPIDATFSPVTRVKYSIEPTRVGYRSDYDKLTLEIYTDGTIAPQNALAEAAKIAKEYFQ 238

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +FINF+E      ++++ +       L   VEELEL+VRS+NCL+  NI  +GDL ++TE
Sbjct: 239 IFINFDETLISNNDEVDEEEERVRKILNTSVEELELTVRSSNCLKNANIRTIGDLTKKTE 298

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
            ++ +  NFG+KSL EIK  L    L LGM 
Sbjct: 299 EEIAKTRNFGKKSLQEIKEKLKEWNLSLGMT 329


>gi|260895674|ref|ZP_05904170.1| DNA-directed RNA polymerase, alpha subunit [Vibrio parahaemolyticus
           Peru-466]
 gi|308089502|gb|EFO39197.1| DNA-directed RNA polymerase, alpha subunit [Vibrio parahaemolyticus
           Peru-466]
          Length = 318

 Score =  298 bits (763), Expect = 8e-79,   Method: Composition-based stats.
 Identities = 131/314 (41%), Positives = 201/314 (64%), Gaps = 11/314 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H+  +  PIG + +DA 
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHNEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVL 310
           N G+  L+ +K  L
Sbjct: 295 NLGKNLLLRLKTYL 308


>gi|288925688|ref|ZP_06419620.1| DNA-directed RNA polymerase, alpha subunit [Prevotella buccae D17]
 gi|315606477|ref|ZP_07881492.1| DNA-directed RNA polymerase subunit alpha [Prevotella buccae ATCC
           33574]
 gi|288337626|gb|EFC75980.1| DNA-directed RNA polymerase, alpha subunit [Prevotella buccae D17]
 gi|315251883|gb|EFU31857.1| DNA-directed RNA polymerase subunit alpha [Prevotella buccae ATCC
           33574]
          Length = 330

 Score =  298 bits (763), Expect = 9e-79,   Method: Composition-based stats.
 Identities = 119/324 (36%), Positives = 191/324 (58%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  +        PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---VMLEANDKFGKFEFRPLEPGFGVTIGNALRRILLSSLEGYAINTIKIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VIC+LD  A ++++L ++KG GYVPA+ +R     + ++ ID++Y+PI+ V Y
Sbjct: 123 EVLNPDLVICHLDTKASMQIDLNINKGRGYVPAEENREFCTDVNVLPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE  R  Q  DYDKL + + TDGSI  +D++  A++ L     +F    I  E P ++ 
Sbjct: 183 AVEPYRVEQKTDYDKLVIEVTTDGSIHPKDALKEAAKTLIYHFMLFSDEKITLENPDQDN 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++ + + L     L  ++ ++ LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NQEFDEEVLHMRQLLKTRLVDMNLSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L  + L  G ++  + 
Sbjct: 303 SLSELDDLLEGLNLSFGTDISKYK 326


>gi|328814019|gb|AEB52125.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 263

 Score =  298 bits (762), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 122/266 (45%), Positives = 172/266 (64%), Gaps = 4/266 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KP     I    EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLH
Sbjct: 2   KPR----IAKIDEEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLH 57

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S+IKGV ED+T IILNIKG+ LKM G   K + I   GP  VTAGDI   +D+E+LN 
Sbjct: 58  EFSTIKGVREDVTQIILNIKGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNK 117

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  IC++   A     LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ 
Sbjct: 118 DMYICSVSEGATFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENT 177

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R G   D+DKL+M I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +  
Sbjct: 178 RVGHREDFDKLTMEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEET 237

Query: 251 PFNPALLKKVEELELSVRSTNCLRGE 276
                L   +EEL+LSVRS NCL+  
Sbjct: 238 QKEKMLEMTIEELDLSVRSYNCLKRA 263


>gi|288803960|ref|ZP_06409383.1| DNA-directed RNA polymerase, alpha subunit [Prevotella
           melaninogenica D18]
 gi|302345101|ref|YP_003813454.1| DNA-directed RNA polymerase, alpha subunit [Prevotella
           melaninogenica ATCC 25845]
 gi|288333593|gb|EFC72045.1| DNA-directed RNA polymerase, alpha subunit [Prevotella
           melaninogenica D18]
 gi|302149271|gb|ADK95533.1| DNA-directed RNA polymerase, alpha subunit [Prevotella
           melaninogenica ATCC 25845]
          Length = 332

 Score =  298 bits (762), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 124/326 (38%), Positives = 195/326 (59%), Gaps = 12/326 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  ++       PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---VMLEANDHFGKFEFRPLEPGFGVTIGNALRRILLSSLEGFAINTIRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VIC+LD  A ++++LT++KG GYVPA+ +R     + ++ ID++Y+PI+ V Y
Sbjct: 123 EVLNPDLVICHLDSKASMQIDLTINKGRGYVPAEENREYCTDVNVLPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE  R  Q  DYDKL + + TDGSI  +D++  A++IL     +F    I  E P +E 
Sbjct: 183 AVEPYRVEQKTDYDKLVVEVTTDGSIHPKDALKEAAKILIYHFMLFSDEKITLENPDQEG 242

Query: 242 KEDINVKSLPFNPALLKKVEE--LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            ++ + + L     L  K+ +  L LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG
Sbjct: 243 NQEFDEEVLHMRQLLKTKLTDASLNLSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFG 302

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWP 325
           +KSL E+  +L ++ L  G ++  + 
Sbjct: 303 KKSLSELDDLLESLNLSFGTDITKYK 328


>gi|217967396|ref|YP_002352902.1| DNA-directed RNA polymerase, alpha subunit [Dictyoglomus turgidum
           DSM 6724]
 gi|217336495|gb|ACK42288.1| DNA-directed RNA polymerase, alpha subunit [Dictyoglomus turgidum
           DSM 6724]
          Length = 321

 Score =  298 bits (762), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 111/300 (37%), Positives = 185/300 (61%), Gaps = 1/300 (0%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +++ +  +     + EPL RG+  T+GN+LRR+L+SS+ GAA+ +V+I+GV HE+  + G
Sbjct: 8   VIIEKRSDEYGRFVIEPLERGYGWTIGNSLRRILLSSIEGAAVVSVKIEGVRHELEVLPG 67

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           + E++ +I++N+K + +K+  ++   + +  RGP VVTAGD     ++++LNPD VI  L
Sbjct: 68  LKEEILEILMNLKKLVVKIEDNNSHILELDVRGPKVVTAGDFIVPANVKILNPDLVIATL 127

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D    ME+ V KG GYV A+ ++ ++ PIG++ +D+++SP+KKVSYTVE  R G+  D
Sbjct: 128 VDDIPFHMEVEVRKGKGYVSAEENKDQSYPIGVLVLDSIFSPVKKVSYTVEKTRVGRRTD 187

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
            D+L + I T+ S+T E++   ASRIL +   +    E      +    + SL      L
Sbjct: 188 LDRLIIEIWTNKSVTPEEAFREASRILMEYFKLLSEREFQLPHEEVGQEITSLEEEKKGL 247

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +E+L LS R+ N LR   I  + DL+ ++  D++++ NFG+KSL E++  L   GL L
Sbjct: 248 -TLEDLGLSTRAYNSLRHAGIHTIEDLLSKSREDLMKIKNFGQKSLQELEEKLREKGLSL 306


>gi|208659512|gb|ACI31186.1| RpoA [Vibrio breoganii]
 gi|208659514|gb|ACI31187.1| RpoA [Vibrio breoganii]
 gi|208659516|gb|ACI31188.1| RpoA [Vibrio breoganii]
          Length = 302

 Score =  298 bits (762), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 134/308 (43%), Positives = 200/308 (64%), Gaps = 11/308 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -KEEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLG 311
            EIK VL 
Sbjct: 295 TEIKDVLA 302


>gi|284929584|ref|YP_003422106.1| DNA-directed RNA polymerase subunit alpha [cyanobacterium UCYN-A]
 gi|284810028|gb|ADB95725.1| DNA-directed RNA polymerase subunit alpha [cyanobacterium UCYN-A]
          Length = 314

 Score =  298 bits (762), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 105/309 (33%), Positives = 171/309 (55%), Gaps = 8/309 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             +E      + +  +  + EPL RG   T+GNALRRVL+++L G A+TA++I GV HE 
Sbjct: 7   ECVESKTQKNQSQ-YSKFVLEPLERGQGITVGNALRRVLLANLEGTAVTAIRIGGVNHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ +IILN+K I LK   D  +   +   G   VTA      +++E++NP  
Sbjct: 66  ATIPGVREDVLEIILNMKEIVLKSHTDQIQIGRLVAVGAAHVTAAQFDLPSEVEIINPTQ 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L   A + ME  + KG GYVP +  + +   +  + IDA++ P+ KV+Y+VE+ R 
Sbjct: 126 PIATLTDGAKLEMEFRIEKGMGYVPVERGKEKQGALDFLQIDAVFMPVTKVNYSVENIRG 185

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            +    D L + I T+GS+  +++++ A+ +L +      N  + +  V E  + +    
Sbjct: 186 ERNEVKDSLMLEIWTNGSVNPKEALSQATEVLVNLFSPLKNINQIETVVPEYPDEE---- 241

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           NP     +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L  
Sbjct: 242 NPQSQIPIEELQLSVRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEEVIEAL-- 299

Query: 313 MGLFLGMNL 321
               LG+ L
Sbjct: 300 -QKRLGITL 307


>gi|328814005|gb|AEB52118.1| DNA-directed RNA polymerase alpha chain [Lactobacillus rhamnosus]
          Length = 250

 Score =  298 bits (762), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 110/249 (44%), Positives = 164/249 (65%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E  N    + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED
Sbjct: 2   DESTNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLED 61

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILNIK + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +    
Sbjct: 62  VTQIILNIKKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGG 121

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + +TV KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL
Sbjct: 122 HFHVRMTVKKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKL 181

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           ++ + T+GSI+  ++++LA++IL + L +F+N  +  K  +  +  +       L   +E
Sbjct: 182 TLDVWTNGSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIE 241

Query: 262 ELELSVRST 270
           EL+LSVRS 
Sbjct: 242 ELDLSVRSY 250


>gi|332181991|gb|AEE17679.1| DNA-directed RNA polymerase subunit alpha [Treponema brennaborense
           DSM 12168]
          Length = 350

 Score =  297 bits (761), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 128/349 (36%), Positives = 198/349 (56%), Gaps = 13/349 (3%)

Query: 1   MIQKNW-QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M +KN  +   KP  I +  L     N     A P   GF  T+GN LRRVL+SS++G A
Sbjct: 1   MARKNLLKGFKKPKGITFEQLDS-NPNYGKFTAYPFETGFGTTVGNTLRRVLLSSIQGYA 59

Query: 60  ITAVQI-----DGVLHEIS----SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK-R 109
           IT+V+I     D V H IS    +I  V ED  +++ ++K I L++ GD+ +   +F+ +
Sbjct: 60  ITSVRITSYDADNVPHVISSEFETIPNVVEDTLEVLNSLKQIRLRLPGDAEQETFLFEFK 119

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GPG +T+ D      +E+L+ D ++  +  +A +  E+ V  G GY PA+ +    + +G
Sbjct: 120 GPGTITSNDFSRE-GLEILSKDMLVFTMMENAHLEFEVQVDLGRGYTPAEVNEHYIEIVG 178

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            I +DA+++PI KV Y +E  R GQ  DYDKL + I TDG+I+ ED++A A++I +D   
Sbjct: 179 TIPMDAIFTPIPKVKYAIEPCRVGQRNDYDKLVIEIWTDGTISPEDALAEAAKIAKDHFA 238

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +F+NF + +     +++         L   V+ELELSVRS+NCL+  NI  +G+L ++TE
Sbjct: 239 IFVNFNDSEIGHDGELDEGDERIRQLLNTPVDELELSVRSSNCLKNANIRTIGELTKKTE 298

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
            D+ +  NFG+KSL EIK  L    L LGM       +++    KK E 
Sbjct: 299 DDIAKTRNFGKKSLTEIKEKLLEWNLNLGMTDYSHLKDAVNLSKKKEES 347


>gi|89891130|ref|ZP_01202638.1| DNA-directed RNA polymerase alpha chain [Flavobacteria bacterium
           BBFL7]
 gi|89516774|gb|EAS19433.1| DNA-directed RNA polymerase alpha chain [Flavobacteria bacterium
           BBFL7]
          Length = 330

 Score =  297 bits (761), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 122/325 (37%), Positives = 188/325 (57%), Gaps = 10/325 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT+++I+G
Sbjct: 5   NFQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGFAITSIRIEG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGV--VTAGDIQT-VND 124
           V HE S+I+GV ED+T+IILN K I  +   D      +     G    TAGD+Q  ++ 
Sbjct: 62  VDHEFSTIEGVVEDVTEIILNFKQIRFRRQIDEVDSEVVNVSFSGKDTFTAGDMQKYISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +VLNP+ VICN +    + +ELT+ KG GYVPA+ ++  N  IG I ID++++PIK V 
Sbjct: 122 FQVLNPEMVICNTESSVSLNLELTIEKGRGYVPAEENKNPNAAIGTIAIDSIFTPIKNVK 181

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y++E+ R  Q  DY+KL   I TDGSI  + ++  A++ L     +F    I  E  +  
Sbjct: 182 YSIENYRVEQKTDYEKLVFEISTDGSIHPKQALTEAAKTLIHHFMLFSDERITLEADEIA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             E  + +SL     L  K+ ++ELSVR+ NCL+   +  +GDL+   + D+++  NFG+
Sbjct: 242 QTETYDEESLHMRQLLKTKLVDMELSVRALNCLKAAEVETLGDLVSYNKNDLMKFRNFGK 301

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL E++ ++   GL  GM+L  + 
Sbjct: 302 KSLTELEELVNVKGLNFGMDLSKYK 326


>gi|313292064|gb|ADR51221.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
 gi|313292066|gb|ADR51222.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
 gi|313292068|gb|ADR51223.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
 gi|313292070|gb|ADR51224.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
 gi|313292072|gb|ADR51225.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
 gi|313292074|gb|ADR51226.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
 gi|313292076|gb|ADR51227.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
          Length = 258

 Score =  297 bits (761), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 117/253 (46%), Positives = 169/253 (66%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E+++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED
Sbjct: 6   DEDKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVRED 65

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +  IILNIKG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  IC +   A
Sbjct: 66  VAQIILNIKGLALKMYGDEEKTLEIDISGPATVTAGDIIVDSDVEILNKDMYICTVSEGA 125

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
                LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL
Sbjct: 126 TFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKL 185

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           +M I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +E
Sbjct: 186 TMEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIE 245

Query: 262 ELELSVRSTNCLR 274
           EL+LSVRS NCL+
Sbjct: 246 ELDLSVRSYNCLK 258


>gi|179184696|gb|ACB78157.1| RNA polymerase alpha subunit [Vibrio inusitatus]
          Length = 294

 Score =  297 bits (761), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 132/297 (44%), Positives = 197/297 (66%), Gaps = 8/297 (2%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
               +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I
Sbjct: 1   THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEI 60

Query: 86  ILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVV 143
           +LN+KG+ +++  G     +T+ K G G V AGDI    D+E+ NP+HVIC+L    A +
Sbjct: 61  LLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDGNADI 120

Query: 144 RMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
            M + V +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DK
Sbjct: 121 AMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDK 180

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + ++T+G++  E+++  A+ IL +QL  F++  + + +   +   +   F+P LL+ V
Sbjct: 181 LVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVQEPIE---EKPEFDPILLRPV 237

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           ++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + G  L
Sbjct: 238 DDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGXSL 294


>gi|260592738|ref|ZP_05858196.1| DNA-directed RNA polymerase, alpha subunit [Prevotella veroralis
           F0319]
 gi|325269508|ref|ZP_08136124.1| DNA-directed RNA polymerase subunit alpha [Prevotella multiformis
           DSM 16608]
 gi|327313217|ref|YP_004328654.1| DNA-directed RNA polymerase subunit alpha [Prevotella denticola
           F0289]
 gi|260535269|gb|EEX17886.1| DNA-directed RNA polymerase, alpha subunit [Prevotella veroralis
           F0319]
 gi|324988127|gb|EGC20094.1| DNA-directed RNA polymerase subunit alpha [Prevotella multiformis
           DSM 16608]
 gi|326945436|gb|AEA21321.1| DNA-directed RNA polymerase, alpha subunit [Prevotella denticola
           F0289]
          Length = 332

 Score =  297 bits (761), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 124/326 (38%), Positives = 195/326 (59%), Gaps = 12/326 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  ++       PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---VMLEANDHFGKFEFRPLEPGFGVTIGNALRRILLSSLEGFAINTIRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VIC+LD  A ++++LT++KG GYVPA+ +R     + ++ ID++Y+PI+ V Y
Sbjct: 123 EVLNPDLVICHLDSKASMQIDLTINKGRGYVPAEENREFCTDVNVLPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE  R  Q  DYDKL + + TDGSI  +D++  A++IL     +F    I  E P +E 
Sbjct: 183 AVEPYRVEQKTDYDKLVVEVTTDGSIHPKDALKEAAKILIYHFMLFSDEKITLENPDQEG 242

Query: 242 KEDINVKSLPFNPALLKKVEE--LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            ++ + + L     L  K+ +  L LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG
Sbjct: 243 NQEFDEEVLHMRQLLKTKLTDASLNLSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFG 302

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWP 325
           +KSL E+  +L ++ L  G ++  + 
Sbjct: 303 KKSLSELDDLLESLNLSFGTDITKYK 328


>gi|328813961|gb|AEB52096.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 248

 Score =  297 bits (761), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 111/248 (44%), Positives = 166/248 (66%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNIK + LKM+ D  
Sbjct: 1   TLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNTDED 60

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV KG GYV A  +
Sbjct: 61  KNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAADQN 120

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           ++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA+
Sbjct: 121 KSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAA 180

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           +IL + L +F+N  +  K  +  +  +       L   +EEL+LSVRS NCL+   I  +
Sbjct: 181 KILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTV 240

Query: 282 GDLIQRTE 289
            +L  +TE
Sbjct: 241 QELTNKTE 248


>gi|219848267|ref|YP_002462700.1| DNA-directed RNA polymerase subunit alpha [Chloroflexus aggregans
           DSM 9485]
 gi|219542526|gb|ACL24264.1| DNA-directed RNA polymerase, alpha subunit [Chloroflexus aggregans
           DSM 9485]
          Length = 337

 Score =  297 bits (761), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 115/337 (34%), Positives = 183/337 (54%), Gaps = 12/337 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
            LI P     + L    EN       PL RG   +LGNALRRVL+SS+ GAA+T ++I G
Sbjct: 7   SLITPR----VTLLAAAENYGRFAIAPLQRGHGTSLGNALRRVLLSSIPGAAVTRIKITG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE ++I GV ED T ++LN+KGI L+   D    + + K+GPG V AGDI   + +E+
Sbjct: 63  VIHEFTAIPGVVEDGTQLVLNVKGIRLRSYSDRAVALQLVKQGPGPVFAGDIDAPSTVEI 122

Query: 128 LNPDHVICNLDVDA-VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +NP H +C +D +   + M+LTV +G G   A        PIG I +DAL+SPI +V++ 
Sbjct: 123 VNPQHYLCTIDDEHTTLEMQLTVERGRGVQLADT--VSGMPIGEIAVDALFSPIPRVNFL 180

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE      +  YD+L + I TDG+I   D+++ A++IL       ++  +P +E ++   
Sbjct: 181 VEEIGGDPLTGYDRLIIEIWTDGTIKPGDALSHAAQILTQYFSRIVSLNQP-EESEQQPT 239

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           +     +    + ++EL LS R+ N LR  +I  +G L++  +  ++ + N G K + EI
Sbjct: 240 LPPPIPDEIANRTIDELGLSTRTYNSLRRADIQTIGQLLRLDDRGLMSIRNLGAKGIEEI 299

Query: 307 KGVLGTMGLFLGMN----LPDWPPESIEELAKKYEDK 339
              L  +G   G      LPD   +++      Y ++
Sbjct: 300 HQRLAALGYRSGETTSGHLPDTTNQNVPSTHDSYPEE 336


>gi|154494406|ref|ZP_02033726.1| hypothetical protein PARMER_03761 [Parabacteroides merdae ATCC
           43184]
 gi|218262261|ref|ZP_03476784.1| hypothetical protein PRABACTJOHN_02458 [Parabacteroides johnsonii
           DSM 18315]
 gi|154085850|gb|EDN84895.1| hypothetical protein PARMER_03761 [Parabacteroides merdae ATCC
           43184]
 gi|218223484|gb|EEC96134.1| hypothetical protein PRABACTJOHN_02458 [Parabacteroides johnsonii
           DSM 18315]
          Length = 330

 Score =  297 bits (760), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 120/324 (37%), Positives = 199/324 (61%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  G+  T+GNALRR+L+SSL G AIT+++I+GV
Sbjct: 6   FQKPDKV---LMLEADNFFGKFEFRPLEPGYGITIGNALRRILLSSLEGFAITSIKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE  +I GV ED+T+IILN+K +  K  +    +++V+I   G  V  AGDI + +   
Sbjct: 63  DHEFGTIPGVIEDVTNIILNLKQVRFKHIVDDIENEKVSITVSGSEVFKAGDIGKQLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+ VIC LD +A  ++ELT++KG GYVPA  +R  N  + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPELVICRLDPNAGFQIELTINKGRGYVPADENRDPNADMHVIAIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEV 241
           ++E+ R  Q  DY+KL + I TDGSI  ++++  A++IL     +F +     E    + 
Sbjct: 183 SIENFRVEQKTDYEKLVLEIATDGSIHPKEALKEAAKILIHHFMLFSDEKIAIETVDTDG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ +++LSVR+ NCL+  ++  +G+L++  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKSKLSDMDLSVRALNCLKAADVETLGELVKFNKNDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  GM++  + 
Sbjct: 303 SLTELDELLESLNLSFGMDITKYK 326


>gi|328813957|gb|AEB52094.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 255

 Score =  297 bits (760), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 112/253 (44%), Positives = 165/253 (65%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I    E  N    + EPL RG+  TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I G
Sbjct: 3   ITKVDESTNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDG 62

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+T IILNIK + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +
Sbjct: 63  VLEDVTQIILNIKKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTV 122

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
                  + +TV KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D
Sbjct: 123 ADGGHFHVRMTVKKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRND 182

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL++ + T+GSI+  ++++LA++IL + L +F+N  +  K  +  +  +       L 
Sbjct: 183 FDKLTLDVWTNGSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLE 242

Query: 258 KKVEELELSVRST 270
             +EEL+LSVRS 
Sbjct: 243 MTIEELDLSVRSY 255


>gi|198273977|ref|ZP_03206509.1| hypothetical protein BACPLE_00113 [Bacteroides plebeius DSM 17135]
 gi|198273055|gb|EDY97324.1| hypothetical protein BACPLE_00113 [Bacteroides plebeius DSM 17135]
          Length = 330

 Score =  297 bits (760), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 119/324 (36%), Positives = 194/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AI  ++I+GV
Sbjct: 6   FQKPDKV---LMLEADSKFGKFEFRPLEPGFGITVGNALRRILLSSLEGYAINTIRIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE ++I GV ED+T+IILN+K +  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFATIPGVKEDVTNIILNLKQVRFKRVVEEFENEKVSITVENSTEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+ VIC+LD  A +++++T++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPELVICHLDSKATMQIDITINKGRGYVPADENREFCTDVNVIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE+ R  Q  DY+KL + I TDGSI  ++++  A++IL     +F    I  E    E 
Sbjct: 183 AVENYRVEQKTDYEKLVLEITTDGSIHPKEALKEAAKILIHHFMLFSDEKITLETSDAEG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ +++LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKTKLVDMDLSVRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLTELDDLLESLNLSFGTDISKYK 326


>gi|258648132|ref|ZP_05735601.1| DNA-directed RNA polymerase, alpha subunit [Prevotella tannerae
           ATCC 51259]
 gi|260852013|gb|EEX71882.1| DNA-directed RNA polymerase, alpha subunit [Prevotella tannerae
           ATCC 51259]
          Length = 330

 Score =  297 bits (760), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 121/324 (37%), Positives = 193/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + ++        PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---IMLENDDKFGKFEFRPLESGFGVTIGNALRRILLSSLEGFAINTIKIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE +SI GV ED+T+IILN+K +  K  +    +++V++         AGDI + ++  
Sbjct: 63  EHEFASIPGVREDVTNIILNLKQVRFKHIVEELENEKVSLTISNATEFRAGDIGKHLSGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+ VI +LD  A + +ELT++KG GYVPA+ +R     +  I ID++Y+PI+ V Y
Sbjct: 123 EVLNPELVIAHLDSKATISIELTINKGRGYVPAEENRDACVEVTQIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE  R  Q  DYDKL + + TDGSI  +D++  A++IL     +F    I  E+  +E 
Sbjct: 183 VVEPFRVEQKTDYDKLVLEVTTDGSIQPKDALKEAAKILIYHFMLFSDEKITMEDATQED 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L +K+ ++ LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQVLKQKLSDMNLSVRALNCLKAADVETLGDLVQFNKNDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L  + L  G ++  + 
Sbjct: 303 SLTELDDLLAGLNLQFGTDISKYK 326


>gi|303237482|ref|ZP_07324047.1| DNA-directed RNA polymerase, alpha subunit [Prevotella disiens
           FB035-09AN]
 gi|302482302|gb|EFL45332.1| DNA-directed RNA polymerase, alpha subunit [Prevotella disiens
           FB035-09AN]
          Length = 332

 Score =  297 bits (760), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 121/326 (37%), Positives = 192/326 (58%), Gaps = 12/326 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  +        PL  GF  T+GN+LRR+L+SSL G AI  V+I GV
Sbjct: 6   FQKPDKV---VMLEANDQFGKFEFRPLEPGFGVTIGNSLRRILLSSLEGYAINTVRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE S++ GV ED+T+IILN+K +  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFSTVPGVKEDVTNIILNLKQVRFKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VIC+LD  A ++++LT++KG GYV A  +R     + ++ ID++Y+PI+ V Y
Sbjct: 123 EVLNPDLVICHLDSKASMQIDLTINKGRGYVSADENREFCTDVNVLPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEV 241
            VE  R  Q  DYDKL + + TDGSI  +D++  A++IL     +F +     E P +E 
Sbjct: 183 AVEPYRVEQKTDYDKLVIEVATDGSIHPKDALKEAAKILIYHFMLFSDEKIMLESPDQEG 242

Query: 242 KEDINVKSLPFNPALLKKVEE--LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            ++ + + L     L  K+ +  L LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG
Sbjct: 243 NQEFDEEVLHMRQLLKTKLTDSSLNLSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFG 302

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWP 325
           +KSL E+  +L ++ L  G ++  + 
Sbjct: 303 KKSLSELDDLLESLNLTFGTDITKYK 328


>gi|325856023|ref|ZP_08171912.1| DNA-directed RNA polymerase, alpha subunit [Prevotella denticola
           CRIS 18C-A]
 gi|325483695|gb|EGC86659.1| DNA-directed RNA polymerase, alpha subunit [Prevotella denticola
           CRIS 18C-A]
          Length = 332

 Score =  297 bits (760), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 124/326 (38%), Positives = 195/326 (59%), Gaps = 12/326 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  ++       PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---VMLETNDHFGKFEFRPLEPGFGVTIGNALRRILLSSLEGFAINTIRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VIC+LD  A ++++LT++KG GYVPA+ +R     + ++ ID++Y+PI+ V Y
Sbjct: 123 EVLNPDLVICHLDSKASMQIDLTINKGRGYVPAEENREFCTDVNVLPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE  R  Q  DYDKL + + TDGSI  +D++  A++IL     +F    I  E P +E 
Sbjct: 183 AVEPYRVEQKTDYDKLVVEVTTDGSIHPKDALKEAAKILIYHFMLFSDEKITLENPDQEG 242

Query: 242 KEDINVKSLPFNPALLKKVEE--LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            ++ + + L     L  K+ +  L LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG
Sbjct: 243 NQEFDEEVLHMRQLLKTKLTDASLNLSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFG 302

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWP 325
           +KSL E+  +L ++ L  G ++  + 
Sbjct: 303 KKSLSELDDLLESLNLSFGTDITKYK 328


>gi|317016847|gb|ADU85964.1| DNA-directed RNA polymerase alpha chain [Lactobacillus sp. 3.1.1]
          Length = 249

 Score =  297 bits (760), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 116/249 (46%), Positives = 169/249 (67%), Gaps = 2/249 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVTEDVTAIILNV 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K I LK+S D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A   M +T 
Sbjct: 61  KKIALKLSSDETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLAICTVADGAHFHMRMTA 120

Query: 150 SKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           + G GYV A+ ++   ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T
Sbjct: 121 NTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +GSIT  ++++L+++IL D L +F+N  +  K     +  +       L   +EEL+LSV
Sbjct: 181 NGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEMTIEELDLSV 240

Query: 268 RSTNCLRGE 276
           RS NCL+  
Sbjct: 241 RSYNCLKRA 249


>gi|110639509|ref|YP_679718.1| DNA-directed RNA polymerase subunit alpha [Cytophaga hutchinsonii
           ATCC 33406]
 gi|119366677|sp|Q11QD8|RPOA_CYTH3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|110282190|gb|ABG60376.1| DNA-directed RNA polymerase subunit alpha [Cytophaga hutchinsonii
           ATCC 33406]
          Length = 329

 Score =  297 bits (760), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 120/316 (37%), Positives = 193/316 (61%), Gaps = 6/316 (1%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           E +V+ + ++   L   +PL +G+  T+GNALRR+L+SSL G AIT +++ GVLHE S+I
Sbjct: 10  EKVVMEKADDFHGLFEFKPLEKGYGVTIGNALRRILLSSLEGYAITGIKVPGVLHEFSTI 69

Query: 76  KGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHV 133
            GV ED+T+IILN+K +  K   D +  ++ +  +      AGDI +  +  ++LNP+ +
Sbjct: 70  PGVREDVTEIILNLKQVRFKKISDVNENKIVVSIKKQASFKAGDIAKFTSAYQILNPELL 129

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           ICN+D ++   +ELT+ KG GY+PA+ ++      G I IDA+++PIK V Y+VE+ R  
Sbjct: 130 ICNVDSNSNFDIELTLEKGRGYLPAEENKPAEQIFGYIPIDAIFTPIKNVKYSVENTRVE 189

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKS 249
           Q  DY+KL + I TDGSI  ED++  A+ IL     +F +    FE  K E +E ++ + 
Sbjct: 190 QRTDYEKLILEILTDGSIHPEDALKGAANILIKHFMLFSDQTMTFEAVKAEEEETVDEEF 249

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           L     L   + +L+LSVR+ NCL+  +I  +G+L     +DM++  NFG+KSL E++ +
Sbjct: 250 LHMRKLLKTSLADLDLSVRAYNCLKAADIKTLGELATLDISDMMKFRNFGKKSLNELEQL 309

Query: 310 LGTMGLFLGMNLPDWP 325
           +    L  GM+   + 
Sbjct: 310 IIDKNLSFGMDTAKYK 325


>gi|208659518|gb|ACI31189.1| RpoA [Vibrio breoganii]
          Length = 302

 Score =  296 bits (759), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 132/308 (42%), Positives = 199/308 (64%), Gaps = 11/308 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC++  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHITDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GD +QRTE ++L+  N G+KSL
Sbjct: 236 -KEEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDXVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLG 311
            EIK VL 
Sbjct: 295 TEIKDVLA 302


>gi|153805983|ref|ZP_01958651.1| hypothetical protein BACCAC_00228 [Bacteroides caccae ATCC 43185]
 gi|149130660|gb|EDM21866.1| hypothetical protein BACCAC_00228 [Bacteroides caccae ATCC 43185]
          Length = 330

 Score =  296 bits (759), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 121/324 (37%), Positives = 195/324 (60%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AIT ++IDGV
Sbjct: 6   FQKPDKV---LMLEADSRFGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIRIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +     ++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFESEKVSITVENSSEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+ VIC+LD  A +++++T++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPELVICHLDSKATMQIDITINKGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           +VE+ R  Q  DY+KL + I TDGSI  ++++  A++IL     +F    I  E    + 
Sbjct: 183 SVENFRVEQKTDYEKLVLEISTDGSIHPKEALKEAAKILIYHFMLFSDEKITLESNDTDG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ +++LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKTKLVDMDLSVRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLTELDDLLESLNLSFGTDISKYK 326


>gi|330997338|ref|ZP_08321189.1| DNA-directed RNA polymerase, alpha subunit [Paraprevotella
           xylaniphila YIT 11841]
 gi|329570712|gb|EGG52428.1| DNA-directed RNA polymerase, alpha subunit [Paraprevotella
           xylaniphila YIT 11841]
          Length = 330

 Score =  296 bits (759), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 122/324 (37%), Positives = 194/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + ++        PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---LMLEADDKYGKFEFRPLEPGFGITVGNALRRILLSSLEGYAINTMRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE +S+ GV ED+T+IILN+K I  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFASVPGVKEDVTNIILNLKQIRFKKIVEEFENEKVSITVENTTEFKAGDINKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+ VIC+LD  A +++EL+++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPELVICHLDAKATMQIELSINKGRGYVPADENRIFCTDVNVIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE+ R  Q  DY+KL + I TDGSI  +D++  A++IL     +F    I  E    E 
Sbjct: 183 AVENYRVEQKTDYEKLVLEISTDGSIHPKDALKEAAKILIYHFMLFSDEKITLENSDGEG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ +++LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKTKLVDMDLSVRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLTELDDLLESLNLSFGTDISKYK 326


>gi|260061923|ref|YP_003195003.1| DNA-directed RNA polymerase subunit alpha [Robiginitalea biformata
           HTCC2501]
 gi|88786056|gb|EAR17225.1| DNA-directed RNA polymerase alpha subunit [Robiginitalea biformata
           HTCC2501]
          Length = 317

 Score =  296 bits (759), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 121/311 (38%), Positives = 187/311 (60%), Gaps = 7/311 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
              +        PL  G+  T+GNALRRVL++SL G AIT+V+ID V HE S I+GV ED
Sbjct: 3   DSTDFEGKFEFRPLEPGYGLTVGNALRRVLLASLEGFAITSVRIDKVEHEFSVIEGVVED 62

Query: 82  LTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLD 138
           +T+IILN+K I  K   D    + V+I   G   +TAGD Q  ++  +VLNPD VICN+D
Sbjct: 63  VTEIILNLKQIRFKRQIDDVNEETVSISVSGKEQLTAGDFQKFISGFQVLNPDLVICNMD 122

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + ME+ + KG GYVPA+ ++  N P+G I +D++++P++ V Y++E+ R  Q  DY
Sbjct: 123 PKVSINMEIIIEKGRGYVPAEENKKSNAPLGSIAVDSIFTPVRNVKYSIENYRVEQKTDY 182

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNP 254
           +KL   I TDGSI  +D++  A+++L     +F    I  E  +    E  + +SL    
Sbjct: 183 EKLVFEILTDGSIHPKDALTEAAKVLIHHFMLFSDERITLEADEIAQTETYDEESLHMRQ 242

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
            L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+KSL E++ ++   G
Sbjct: 243 LLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKKSLTELEELVINKG 302

Query: 315 LFLGMNLPDWP 325
           L  GM+L  + 
Sbjct: 303 LNFGMDLSKYK 313


>gi|269792765|ref|YP_003317669.1| DNA-directed RNA polymerase, alpha subunit [Thermanaerovibrio
           acidaminovorans DSM 6589]
 gi|269100400|gb|ACZ19387.1| DNA-directed RNA polymerase, alpha subunit [Thermanaerovibrio
           acidaminovorans DSM 6589]
          Length = 342

 Score =  296 bits (758), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 123/333 (36%), Positives = 187/333 (56%), Gaps = 18/333 (5%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I++ +   +   ++ EPL RG+  TLGNALRRVL+SS+ GA I AV++DGVLHE S+I G
Sbjct: 8   IIVEEVTPSHGRVVLEPLERGYGTTLGNALRRVLLSSIPGAGIVAVRVDGVLHEFSTIPG 67

Query: 78  VHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
           V ED+ +++LN+K + +++SG     K + +   GP VV A DIQ   D+E ++P+ VIC
Sbjct: 68  VREDVIELLLNLKHVPVRVSGPGTDVKVLRLEAEGPKVVRAADIQGDADVEFVDPEAVIC 127

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
            LD    V M+L + +G GY P    R    P+  + IDA++SP+K+V Y V+  R GQ 
Sbjct: 128 TLDEGHRVSMDLYIERGVGYAPIDRPRPSYLPVDALLIDAIFSPVKRVRYEVQDVRSGQR 187

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF-INFEEPKKEVK------------ 242
            DYD+L + + T+G ++  D+VA AS IL         +       V             
Sbjct: 188 TDYDRLVLEVWTNGVVSFRDAVAEASSILSGYFRGLSTSLWGQSSAVTAGDEDFFEEKDE 247

Query: 243 ---EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
              +++       +  L + +++LELSVRS NCL    I  +GDL+ R + ++L++ N G
Sbjct: 248 EDLQEVPAVCGEDDSVLSRPIKDLELSVRSENCLLRGGIHRIGDLVSRPKEELLKIRNLG 307

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEEL 332
           + SL EI+  LG  GL L    P    +  E+L
Sbjct: 308 KISLREIEEKLGKFGLSLKGEEPSGEADQAEDL 340


>gi|29348110|ref|NP_811613.1| DNA-directed RNA polymerase subunit alpha [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|253569618|ref|ZP_04847028.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. 1_1_6]
 gi|298386206|ref|ZP_06995763.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 1_1_14]
 gi|41688697|sp|Q8A4A2|RPOA_BACTN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|29340013|gb|AAO77807.1| DNA-directed RNA polymerase alpha chain [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|251841637|gb|EES69718.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. 1_1_6]
 gi|298261434|gb|EFI04301.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 1_1_14]
          Length = 330

 Score =  296 bits (758), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 121/324 (37%), Positives = 194/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AIT ++IDGV
Sbjct: 6   FQKPDKV---LMLEADSRFGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIRIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +     ++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFESEKVSITVENSSEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+ VIC+LD  A +++++T++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPELVICHLDSKATMQIDITINKGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE+ R  Q  DY+KL + I TDGSI  ++++  A++IL     +F    I  E    + 
Sbjct: 183 AVENFRVEQKTDYEKLVLEISTDGSIHPKEALKEAAKILIYHFMLFSDEKITLESNDTDG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ +++LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKTKLVDMDLSVRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLTELDDLLESLNLSFGTDISKYK 326


>gi|224023645|ref|ZP_03642011.1| hypothetical protein BACCOPRO_00352 [Bacteroides coprophilus DSM
           18228]
 gi|224016867|gb|EEF74879.1| hypothetical protein BACCOPRO_00352 [Bacteroides coprophilus DSM
           18228]
          Length = 330

 Score =  296 bits (758), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 119/324 (36%), Positives = 192/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AI  + IDGV
Sbjct: 6   FQKPDKV---LMLEADSKFGKFEFRPLEPGFGITVGNALRRILLSSLEGYAINTIHIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE ++I GV ED+T+IILN+K +  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFATIPGVKEDVTNIILNLKQVRFKQVVEEFENEKVSITVENSTEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+ VIC+LD    ++M++T++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPELVICHLDSKTTMQMDITINKGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE+ R  Q  DY+KL + I TDGSI  ++++  A++IL     +F    I  E    + 
Sbjct: 183 AVENYRVEQKTDYEKLVLEITTDGSIHPKEALKEAAKILIYHFMLFSDEKITLETSDVDG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ +++LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKTKLVDMDLSVRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLTELDDLLESLNLSFGTDISKYK 326


>gi|189465444|ref|ZP_03014229.1| hypothetical protein BACINT_01797 [Bacteroides intestinalis DSM
           17393]
 gi|224537843|ref|ZP_03678382.1| hypothetical protein BACCELL_02730 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|189437718|gb|EDV06703.1| hypothetical protein BACINT_01797 [Bacteroides intestinalis DSM
           17393]
 gi|224520529|gb|EEF89634.1| hypothetical protein BACCELL_02730 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 330

 Score =  296 bits (758), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 121/324 (37%), Positives = 193/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AIT ++IDGV
Sbjct: 6   FQKPDKV---LMLEADSRFGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIKIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +     ++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFESEKVSITIENSSEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+ VIC+LD  A +++++T++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPELVICHLDSKATMQIDITINKGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            +E  R  Q  DYDKL + I TDGSI  ++++  A++IL     +F    I  E    + 
Sbjct: 183 QIEPFRVEQKTDYDKLVLEITTDGSIHPKEALKEAAKILIYHFMLFSDEKITLESNDVDG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ +++LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKTKLVDMDLSVRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLTELDDLLESLNLSFGTDISKYK 326


>gi|311990454|gb|ADQ26357.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 260

 Score =  296 bits (757), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 113/260 (43%), Positives = 163/260 (62%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+
Sbjct: 1   FVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK   D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V
Sbjct: 61  KKLELKSLSDERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDG
Sbjct: 121 QNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI   D+++ A++IL +   +F + +   K  +  +  +       L   +EEL+LSVRS
Sbjct: 181 SIKPNDALSFAAKILVEHFKVFESADADTKFSEVMVEKEDDKKEKKLEMTIEELDLSVRS 240

Query: 270 TNCLRGENIVYMGDLIQRTE 289
            NCL+   I  + +L   TE
Sbjct: 241 YNCLKRAGINTLQELTDMTE 260


>gi|328813971|gb|AEB52101.1| DNA-directed RNA polymerase alpha chain [Lactobacillus fermentum]
          Length = 257

 Score =  296 bits (757), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 114/257 (44%), Positives = 172/257 (66%), Gaps = 2/257 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRV+++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+
Sbjct: 1   FVVEPLERGYGTTLGNSLRRVMLASLPGAAITSIQIDGVLHEFSTVQGVTEDVTQIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  +GP  VTA DIQ   D+ +LN D  I  +   A + +++T 
Sbjct: 61  KQVALKIDSEDAKDLEIDVKGPAEVTAADIQGDGDVTILNSDLHIATVSDGAELHVKMTA 120

Query: 150 SKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GY  A  ++T  E   IG++ ID++Y+PI++V+YTVE+ R GQ  DYDKL++ + T
Sbjct: 121 DKGRGYSSADDNKTRMEGLAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +GS+T  ++++LA++IL + L MF+N  E  +  +  +  +       L K +EEL+LSV
Sbjct: 181 NGSLTPTEAISLAAKILTEHLTMFVNLTEEAQVTQVMVEREETHQEKVLDKTIEELDLSV 240

Query: 268 RSTNCLRGENIVYMGDL 284
           RS NCL+  +I  + DL
Sbjct: 241 RSYNCLKRADIQTVKDL 257


>gi|189460710|ref|ZP_03009495.1| hypothetical protein BACCOP_01357 [Bacteroides coprocola DSM 17136]
 gi|189432669|gb|EDV01654.1| hypothetical protein BACCOP_01357 [Bacteroides coprocola DSM 17136]
          Length = 330

 Score =  296 bits (757), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 118/324 (36%), Positives = 193/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AI  + I+GV
Sbjct: 6   FQKPDKV---LMLEADSKFGKFEFRPLEPGFGITVGNALRRILLSSLEGYAINTIHIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE +++ GV ED+T+IILN+K +  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFATVPGVKEDVTNIILNLKQVRFKQIVEEFENEKVSITVENSTEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+ VIC+LD  A ++++LT++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPELVICHLDSKATMQIDLTINKGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE+ R  Q  DY+KL + I TDGSI  ++++  A++IL     +F    I  E    + 
Sbjct: 183 AVENYRVEQKTDYEKLVLEITTDGSIHPKEALKEAAKILIYHFMLFSDEKITLETSDADG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ +++LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKTKLVDMDLSVRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLTELDDLLESLNLSFGTDISKYK 326


>gi|160888372|ref|ZP_02069375.1| hypothetical protein BACUNI_00785 [Bacteroides uniformis ATCC 8492]
 gi|270294725|ref|ZP_06200926.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. D20]
 gi|317477725|ref|ZP_07936918.1| DNA-directed RNA polymerase [Bacteroides sp. 4_1_36]
 gi|156862049|gb|EDO55480.1| hypothetical protein BACUNI_00785 [Bacteroides uniformis ATCC 8492]
 gi|270273972|gb|EFA19833.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. D20]
 gi|316906070|gb|EFV27831.1| DNA-directed RNA polymerase [Bacteroides sp. 4_1_36]
          Length = 330

 Score =  296 bits (757), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 119/324 (36%), Positives = 193/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AIT ++IDGV
Sbjct: 6   FQKPDKV---LMLEADSRFGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIKIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ G  ED+T+IILN+K +  K  +     ++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGAKEDVTNIILNLKQVRFKQVVEEFESEKVSITVENSSEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+ VIC+LD  + +++++T++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPELVICHLDSKSTMQIDITINKGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE+ R  Q  DY+KL + I TDGSI  ++++  A++IL     +F    I  E    + 
Sbjct: 183 QVENFRVEQKTDYEKLVLEITTDGSIHPKEALKEAAKILIYHFMLFSDEKITLETNDVDG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ +++LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKTKLVDMDLSVRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLTELDDLLESLNLSFGTDISKYK 326


>gi|254424496|ref|ZP_05038214.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus sp. PCC
           7335]
 gi|196191985|gb|EDX86949.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus sp. PCC
           7335]
          Length = 315

 Score =  295 bits (756), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 102/314 (32%), Positives = 173/314 (55%), Gaps = 9/314 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           N +E I+   + +  +  + EPL R    T+GNALRRVL+S+L G A+T+V+I G  HE 
Sbjct: 7   NCVESIIEDDQSQF-SRFVIEPLGRSQGTTVGNALRRVLLSNLEGTAVTSVRIAGASHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           S+I GV ED+ DI+LN+K   LK      +   +  +GP  VTA +    +++E+++ D 
Sbjct: 66  STIPGVREDVLDILLNMKETVLKSYSAQPQIGRLVVQGPAKVTAANFDLPSEVELISTDR 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I ++     + ME  + +G GY      R E   +  + IDA++ P++KV+Y+VE+  +
Sbjct: 126 YIASVAAGHKLEMEFRIERGKGYKAIDRSREETGGVEFMQIDAVFMPVRKVNYSVENFID 185

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            +    D+L M I T+GS+T + +++ A+ +L D      +       ++   +  +   
Sbjct: 186 PEGFPKDRLVMEIWTNGSLTAQQAMSEAAALLVDMFNPLKDVT-----LEPKRDEDTKEE 240

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P     +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L  
Sbjct: 241 DPTYQIPIEELQLSVRAYNCLKRAQINAVSDLLDYSQEDLLEIKNFGQKSAEEVVEAL-- 298

Query: 313 MGLFLGMNLPDWPP 326
             + LG+ LP   P
Sbjct: 299 -QIHLGIMLPLEKP 311


>gi|313292052|gb|ADR51215.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
 gi|313292054|gb|ADR51216.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
 gi|313292056|gb|ADR51217.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
 gi|313292058|gb|ADR51218.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
 gi|313292060|gb|ADR51219.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
 gi|313292062|gb|ADR51220.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
          Length = 258

 Score =  295 bits (756), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 120/253 (47%), Positives = 170/253 (67%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED
Sbjct: 6   DEEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVRED 65

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +  IILNIKG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  ICN+   A
Sbjct: 66  VAQIILNIKGLALKMYGDEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICNVSEGA 125

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
                LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL
Sbjct: 126 SFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKL 185

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           +M I TDGSI   ++++LA++I+ + L +F+N  +  K  +  +  +       L   +E
Sbjct: 186 TMEIWTDGSIEPLEAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIE 245

Query: 262 ELELSVRSTNCLR 274
           EL+LSVRS NCL+
Sbjct: 246 ELDLSVRSYNCLK 258


>gi|58415796|emb|CAH57312.1| RNA polymerase alpha-subunit [Vibrio coralliilyticus]
          Length = 287

 Score =  295 bits (756), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 134/290 (46%), Positives = 196/290 (67%), Gaps = 8/290 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ 
Sbjct: 1   PLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLA 60

Query: 94  LKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSK 151
           +++  G     +T+ K G G V AGDI    D+E+ NP+HVIC+L  D A + M + V +
Sbjct: 61  VRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVER 120

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T+
Sbjct: 121 GRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMETN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V++LEL+VR
Sbjct: 181 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVR 237

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LG
Sbjct: 238 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLG 287


>gi|150003362|ref|YP_001298106.1| DNA-directed RNA polymerase subunit alpha [Bacteroides vulgatus
           ATCC 8482]
 gi|212695279|ref|ZP_03303407.1| hypothetical protein BACDOR_04819 [Bacteroides dorei DSM 17855]
 gi|237711701|ref|ZP_04542182.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp.
           9_1_42FAA]
 gi|237725858|ref|ZP_04556339.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. D4]
 gi|254881349|ref|ZP_05254059.1| RNA polymerase subunit alpha [Bacteroides sp. 4_3_47FAA]
 gi|265753120|ref|ZP_06088689.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp.
           3_1_33FAA]
 gi|294777846|ref|ZP_06743290.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides vulgatus
           PC510]
 gi|319640350|ref|ZP_07995075.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. 3_1_40A]
 gi|172048639|sp|A6KYH0|RPOA_BACV8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|149931786|gb|ABR38484.1| DNA-directed RNA polymerase alpha chain [Bacteroides vulgatus ATCC
           8482]
 gi|212662189|gb|EEB22763.1| hypothetical protein BACDOR_04819 [Bacteroides dorei DSM 17855]
 gi|229435666|gb|EEO45743.1| DNA-directed RNA polymerase subunit alpha [Bacteroides dorei
           5_1_36/D4]
 gi|229454396|gb|EEO60117.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp.
           9_1_42FAA]
 gi|254834142|gb|EET14451.1| RNA polymerase subunit alpha [Bacteroides sp. 4_3_47FAA]
 gi|263236306|gb|EEZ21801.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp.
           3_1_33FAA]
 gi|294448300|gb|EFG16856.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides vulgatus
           PC510]
 gi|317388125|gb|EFV68979.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. 3_1_40A]
          Length = 330

 Score =  295 bits (756), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 119/324 (36%), Positives = 193/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AI  ++I+GV
Sbjct: 6   FQKPDKV---LMLEADSRFGKFEFRPLEPGFGITVGNALRRILLSSLEGFAINTIKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE +S+ GV ED+T+IILN+K +  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFASVPGVKEDVTNIILNLKQVRFKQVVEEFENEKVSITVENSSEFKAGDISKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+ VIC+LD  A ++M++T++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPELVICHLDSKATMQMDITINKGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE+ R  Q  DY+KL + I TDGSI  ++++  A++IL     +F    I  E    + 
Sbjct: 183 QVENFRVEQKTDYEKLVLEITTDGSIHPKEALKEAAKILIYHFMLFSDEKITLETSDVDG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ +++LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKTKLVDMDLSVRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L  + L  G ++  + 
Sbjct: 303 SLTELDDLLEGLNLSFGTDISKYK 326


>gi|325299105|ref|YP_004259022.1| DNA-directed RNA polymerase subunit alpha [Bacteroides salanitronis
           DSM 18170]
 gi|324318658|gb|ADY36549.1| DNA-directed RNA polymerase subunit alpha [Bacteroides salanitronis
           DSM 18170]
          Length = 330

 Score =  295 bits (756), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 118/324 (36%), Positives = 193/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AI  + I+GV
Sbjct: 6   FQKPDKV---LMLEADSKFGKFEFRPLEPGFGITVGNALRRILLSSLEGYAINTIHIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE +++ GV ED+T+IILN+K +  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFATVPGVKEDVTNIILNLKQVRFKQIVEEFENEKVSITVENSTEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+ VIC+LD  A ++++LT++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPELVICHLDSKATMQIDLTINKGRGYVPADENREFCTDVNVIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE+ R  Q  DY+KL + I TDGSI  ++++  A++IL     +F    I  E    + 
Sbjct: 183 AVENYRVEQKTDYEKLVLEITTDGSIHPKEALKEAAKILIYHFMLFSDEKITLETSDADG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ +++LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKTKLVDMDLSVRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLTELDDLLESLNLSFGTDISKYK 326


>gi|256420686|ref|YP_003121339.1| DNA-directed RNA polymerase, alpha subunit [Chitinophaga pinensis
           DSM 2588]
 gi|256035594|gb|ACU59138.1| DNA-directed RNA polymerase, alpha subunit [Chitinophaga pinensis
           DSM 2588]
          Length = 331

 Score =  295 bits (755), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 119/324 (36%), Positives = 194/324 (59%), Gaps = 11/324 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
              KP+ I   VL +  +        PL  G+  T+GNALRRVL+SSL G AI  ++I+G
Sbjct: 5   NFQKPDKI---VLQKSTDFEAQFEFRPLEPGYGVTVGNALRRVLLSSLEGYAIVGIKIEG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH---KRVTIFKRGPGVVTAGDIQ-TVN 123
             HE +++KG+ ED+T+IILN+K +  K   ++    +++ I  +G     A  I+   +
Sbjct: 62  ADHEFATLKGITEDVTEIILNLKQVRFKRIVENEVNNEKIQISIKGKTEFRADMIEKATS 121

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
             +++NP+ +IC LD  A + +ELT+ KG GYVPA+ ++ ++   G I ID++++PIK V
Sbjct: 122 AFQIMNPELLICTLDPSAKLDIELTIGKGRGYVPAEENKPKDAVFGYIAIDSIFTPIKNV 181

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKK 239
            Y++E+ R  Q  DY+KL M + TDG+I  E++V  ASRIL   L +  +    F+    
Sbjct: 182 KYSIENTRVEQKTDYEKLIMEVITDGTIHPEEAVKQASRILIQHLMIITDENISFDTKDT 241

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           E ++ ++ ++L     L   +E+L+LSVR+ NCL+   I  + +L+Q  + ++++  NFG
Sbjct: 242 EKEDVVDEQTLQLRKILKTPLEDLDLSVRAFNCLKAAKINSLSELVQYEQEELMKFRNFG 301

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPD 323
           +KSL EI+ VL   GL  GM+L  
Sbjct: 302 QKSLSEIEQVLNERGLHFGMDLSK 325


>gi|166367995|ref|YP_001660268.1| DNA-directed RNA polymerase subunit alpha [Microcystis aeruginosa
           NIES-843]
 gi|166090368|dbj|BAG05076.1| RNA polymerase alpha subunit [Microcystis aeruginosa NIES-843]
          Length = 313

 Score =  295 bits (755), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 96/302 (31%), Positives = 164/302 (54%), Gaps = 7/302 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           + +   +  + EPL RG   T+GNALRR+L+S+L GAA+TA++I GV HE ++++GV ED
Sbjct: 15  KNQSQYSKFVLEPLERGQGTTVGNALRRILISNLEGAAVTALRIAGVNHEFATVQGVRED 74

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + +++LN+K I LK   +  +   +   GP  V A      +++E+++ +  +  L   A
Sbjct: 75  VMELMLNMKEIILKSYTNQTQIGRLVATGPATVVAAQFDLPSEVEIVDRNQYVATLAEGA 134

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ME  V KG GY      + E   +  + ID+++ P+ KV+Y+VE  R       D+L
Sbjct: 135 KLEMEFRVEKGKGYRAIDRSKDEATSLDFLQIDSIFMPVTKVNYSVEDIRSESGQARDRL 194

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + I T+GSI  +++++ A+ +L +      +       ++   N      N      +E
Sbjct: 195 LLEIWTNGSINPKEALSQAADMLVNLFNPLKDLN----ALESSSNFDDQEINQENQIPIE 250

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           EL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L      LG+ L
Sbjct: 251 ELQLSVRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEEVIEAL---QKRLGITL 307

Query: 322 PD 323
           P 
Sbjct: 308 PQ 309


>gi|159027085|emb|CAO89270.1| rpoA [Microcystis aeruginosa PCC 7806]
          Length = 313

 Score =  295 bits (755), Expect = 8e-78,   Method: Composition-based stats.
 Identities = 96/302 (31%), Positives = 164/302 (54%), Gaps = 7/302 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           + +   +  + EPL RG   T+GNALRR+L+S+L GAA+TA++I GV HE ++++GV ED
Sbjct: 15  KNQSQYSKFVLEPLERGQGTTVGNALRRILISNLEGAAVTALRIAGVNHEFATVEGVRED 74

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + +++LN+K I LK   +  +   +   GP  V A      +++E+++ +  +  L   A
Sbjct: 75  VMELMLNMKEITLKSYTNQTQIGRLVATGPATVVAAQFDLPSEVEIVDRNQYVATLAEGA 134

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ME  V KG GY      + E   +  + ID+++ P+ KV+Y+VE  R       D+L
Sbjct: 135 KLEMEFRVEKGKGYRAIDRSKEEATSLDFLQIDSIFMPVTKVNYSVEDIRSESGQARDRL 194

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + I T+GSI  +++++ A+ +L +      +       ++   N      N      +E
Sbjct: 195 LLEIWTNGSINPKEALSQAADMLVNLFNPLKDLN----ALESSGNFDDQEINQENQIPIE 250

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           EL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L      LG+ L
Sbjct: 251 ELQLSVRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEEVIEAL---QKRLGITL 307

Query: 322 PD 323
           P 
Sbjct: 308 PQ 309


>gi|160883038|ref|ZP_02064041.1| hypothetical protein BACOVA_01001 [Bacteroides ovatus ATCC 8483]
 gi|237717426|ref|ZP_04547907.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. D1]
 gi|237718716|ref|ZP_04549197.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. 2_2_4]
 gi|255690030|ref|ZP_05413705.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides finegoldii
           DSM 17565]
 gi|260175443|ref|ZP_05761855.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. D2]
 gi|262406191|ref|ZP_06082741.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 2_1_22]
 gi|293372093|ref|ZP_06618484.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides ovatus SD
           CMC 3f]
 gi|294644084|ref|ZP_06721861.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides ovatus SD
           CC 2a]
 gi|294806544|ref|ZP_06765383.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides
           xylanisolvens SD CC 1b]
 gi|298483091|ref|ZP_07001272.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. D22]
 gi|299144597|ref|ZP_07037665.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 3_1_23]
 gi|315923672|ref|ZP_07919912.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. D2]
 gi|156111510|gb|EDO13255.1| hypothetical protein BACOVA_01001 [Bacteroides ovatus ATCC 8483]
 gi|229443409|gb|EEO49200.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. D1]
 gi|229451848|gb|EEO57639.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. 2_2_4]
 gi|260624637|gb|EEX47508.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides finegoldii
           DSM 17565]
 gi|262357066|gb|EEZ06156.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 2_1_22]
 gi|292632885|gb|EFF51472.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides ovatus SD
           CMC 3f]
 gi|292640608|gb|EFF58849.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides ovatus SD
           CC 2a]
 gi|294446239|gb|EFG14867.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides
           xylanisolvens SD CC 1b]
 gi|295085402|emb|CBK66925.1| DNA-directed RNA polymerase subunit alpha [Bacteroides
           xylanisolvens XB1A]
 gi|298270835|gb|EFI12415.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. D22]
 gi|298515088|gb|EFI38969.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 3_1_23]
 gi|313697547|gb|EFS34382.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. D2]
          Length = 330

 Score =  295 bits (755), Expect = 8e-78,   Method: Composition-based stats.
 Identities = 120/324 (37%), Positives = 194/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AIT ++IDGV
Sbjct: 6   FQKPDKV---LMLEADSRFGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIRIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +     ++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFESEKVSITVENSSEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+ VIC+LD  + +++++T++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPELVICHLDSKSTMQIDITINKGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE+ R  Q  DY+KL + I TDGSI  ++++  A++IL     +F    I  E    + 
Sbjct: 183 AVENFRVEQKTDYEKLVLEISTDGSIHPKEALKEAAKILIYHFMLFSDEKITLESNDTDG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ +++LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKTKLVDMDLSVRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLTELDDLLESLNLSFGTDISKYK 326


>gi|300770225|ref|ZP_07080104.1| DNA-directed RNA polymerase subunit alpha [Sphingobacterium
           spiritivorum ATCC 33861]
 gi|300762701|gb|EFK59518.1| DNA-directed RNA polymerase subunit alpha [Sphingobacterium
           spiritivorum ATCC 33861]
          Length = 330

 Score =  294 bits (754), Expect = 9e-78,   Method: Composition-based stats.
 Identities = 128/324 (39%), Positives = 199/324 (61%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +P+ +   ++ +  +        PL  GF  T+GNALRR+L+SSL G AIT+++  GV
Sbjct: 6   FQRPDKV---IMQKSTDFDGTFEFRPLEPGFGVTIGNALRRILLSSLEGYAITSIRFSGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE S+IKGV ED+T+IILN+K I  K +G+    +++ +   G     AGDI +  N+ 
Sbjct: 63  SHEFSTIKGVVEDVTEIILNLKQIRFKKTGEQGDSEKIFVVINGQEQFLAGDITKFSNNF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
            VLNPD V+CN+D    + +EL+V+KG GYV A+ ++  + P+GLI ID++++PIK V Y
Sbjct: 123 TVLNPDFVVCNMDSSVTIEVELSVAKGRGYVNAEENKVTDGPVGLIAIDSIFTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEV 241
           T+E+ R  Q  DY+KL + I TDGSI  ED++  A++IL     +F +     E   KE 
Sbjct: 183 TIENYRVEQKTDYEKLLLDITTDGSIHPEDALKEAAKILIQHFMLFSDENMLLESQTKEE 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            + ++ + L     L  ++ +L+LSVR+ NCL+  +I  + +L+    ADML+  NFG+K
Sbjct: 243 TKVVDEEILHMRKILKTELVDLDLSVRALNCLKAADIRTLAELVTYDVADMLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL EI+ ++ + GL  GMNL  + 
Sbjct: 303 SLSEIQELVKSKGLSFGMNLSKFK 326


>gi|227538692|ref|ZP_03968741.1| DNA-directed RNA polymerase [Sphingobacterium spiritivorum ATCC
           33300]
 gi|227241611|gb|EEI91626.1| DNA-directed RNA polymerase [Sphingobacterium spiritivorum ATCC
           33300]
          Length = 330

 Score =  294 bits (754), Expect = 9e-78,   Method: Composition-based stats.
 Identities = 127/324 (39%), Positives = 199/324 (61%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +P+ +   ++ +  +        PL  GF  T+GNALRR+L+SSL G AIT+++  GV
Sbjct: 6   FQRPDKV---IMQKSTDFDGTFEFRPLEPGFGVTIGNALRRILLSSLEGYAITSIRFSGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE S+IKGV ED+T+IILN+K +  K +G+    +++ +   G     AGDI +  N+ 
Sbjct: 63  SHEFSTIKGVVEDVTEIILNLKQVRFKKTGEQGDSEKIFVVINGQEQFLAGDITKFSNNF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
            VLNPD V+CN+D    + +EL+V+KG GYV A+ ++  + P+GLI ID++++PIK V Y
Sbjct: 123 TVLNPDFVVCNMDSSVTIEVELSVAKGRGYVNAEENKVTDGPVGLIAIDSIFTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEV 241
           T+E+ R  Q  DY+KL + I TDGSI  ED++  A++IL     +F +     E   KE 
Sbjct: 183 TIENYRVEQKTDYEKLLLDITTDGSIHPEDALKEAAKILIQHFMLFSDENMLLESQTKEE 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            + ++ + L     L  ++ +L+LSVR+ NCL+  +I  + +L+    ADML+  NFG+K
Sbjct: 243 TKVVDEEILHMRKILKTELVDLDLSVRALNCLKAADIRTLAELVTYDVADMLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL EI+ ++ + GL  GMNL  + 
Sbjct: 303 SLSEIQELVKSKGLSFGMNLSKFK 326


>gi|163848051|ref|YP_001636095.1| DNA-directed RNA polymerase subunit alpha [Chloroflexus aurantiacus
           J-10-fl]
 gi|222525940|ref|YP_002570411.1| DNA-directed RNA polymerase subunit alpha [Chloroflexus sp.
           Y-400-fl]
 gi|163669340|gb|ABY35706.1| DNA-directed RNA polymerase, alpha subunit [Chloroflexus
           aurantiacus J-10-fl]
 gi|222449819|gb|ACM54085.1| DNA-directed RNA polymerase, alpha subunit [Chloroflexus sp.
           Y-400-fl]
          Length = 335

 Score =  294 bits (754), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 118/321 (36%), Positives = 175/321 (54%), Gaps = 10/321 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
             I P     I L    EN       PL RG   +LGNALRRVL+SS+ GAA+T +++ G
Sbjct: 7   SFITPR----ITLVAAAENYGRFAIAPLQRGHGSSLGNALRRVLLSSIPGAAVTRIKVSG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE SSI GV ED T ++LNIKGI L+   D    + + K+GPG V A DI   + +E+
Sbjct: 63  VIHEFSSIPGVVEDGTQLVLNIKGIRLRSYSDRAVALQLIKQGPGPVFARDIDAPSTVEI 122

Query: 128 LNPDHVICNLDVDA-VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +NP H IC +D +     M+LTV +G G   A        PIG I +DAL+SPI +V++ 
Sbjct: 123 VNPQHYICTIDDEHTTFEMQLTVERGRGVQLADT--VSGMPIGEIAVDALFSPIPRVNFL 180

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE   +  +  YD+L + I TDG+I   D+++ A++IL    G  +N  +P +E +   +
Sbjct: 181 VEEMGDDPLTGYDRLILEIWTDGTIKPGDALSHAAQILAQYFGRIVNLNQP-EEPEPSAH 239

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           +          + ++EL LS R+ N LR   I  +G L++  +  ++ + N G K + EI
Sbjct: 240 LPPPIPEEIASRTIDELGLSTRTYNSLRRAEIHTIGQLLRLDDRGLMSIRNLGAKGIEEI 299

Query: 307 KGVLGTMGLFLGMN--LPDWP 325
              L  +G   G +  LP  P
Sbjct: 300 HQRLEALGYRSGSSSRLPAAP 320


>gi|313292020|gb|ADR51199.1| DNA-directed RNA polymerase alpha chain [Enterococcus viikkiensis]
 gi|313292022|gb|ADR51200.1| DNA-directed RNA polymerase alpha chain [Enterococcus viikkiensis]
 gi|313292024|gb|ADR51201.1| DNA-directed RNA polymerase alpha chain [Enterococcus viikkiensis]
 gi|313292026|gb|ADR51202.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
 gi|313292028|gb|ADR51203.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
 gi|313292030|gb|ADR51204.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
 gi|313292032|gb|ADR51205.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
 gi|313292034|gb|ADR51206.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
 gi|313292036|gb|ADR51207.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
 gi|313292038|gb|ADR51208.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
 gi|313292040|gb|ADR51209.1| DNA-directed RNA polymerase alpha chain [Enterococcus avium]
 gi|313292042|gb|ADR51210.1| DNA-directed RNA polymerase alpha chain [Enterococcus avium]
          Length = 258

 Score =  294 bits (754), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 118/257 (45%), Positives = 169/257 (65%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I    E+ +    + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKG
Sbjct: 2   ITKIDEDRDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+  IILNIKG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +
Sbjct: 62  VREDVVQIILNIKGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTV 121

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
              A     LTV  G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D
Sbjct: 122 AEGATFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDD 181

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL+M I TDGSI  +++++LA++IL + L +F+N  +  K  +  +  +       L 
Sbjct: 182 FDKLTMEIWTDGSIIAQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLE 241

Query: 258 KKVEELELSVRSTNCLR 274
             +EEL+LSVRS NCL+
Sbjct: 242 MTIEELDLSVRSYNCLK 258


>gi|179184670|gb|ACB78156.1| RNA polymerase alpha subunit [Vibrio rarus]
          Length = 301

 Score =  294 bits (754), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 130/303 (42%), Positives = 196/303 (64%), Gaps = 8/303 (2%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I  VLHE S+ +GV 
Sbjct: 2   IEQINATHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIGSVLHEYSTKEGVQ 61

Query: 80  EDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
           ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+ NP+HVIC+L 
Sbjct: 62  EDILEILLNLKGLAVRVAEGKDDVLITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLT 121

Query: 139 VD-AVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
            D A + M + V +G GYVPA        +  PIG + +DA YSP+ +++Y+V +AR  Q
Sbjct: 122 DDNADIAMRIKVERGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDQIAYSVAAARVEQ 181

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
             D DKL + ++T+G++  E+++  A+ IL +QL  F++  + + +   +   +   F+P
Sbjct: 182 RTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVQEPIE---EKPEFDP 238

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
            LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + G
Sbjct: 239 ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRG 298

Query: 315 LFL 317
             L
Sbjct: 299 XSL 301


>gi|307565140|ref|ZP_07627648.1| DNA-directed RNA polymerase, alpha subunit [Prevotella amnii CRIS
           21A-A]
 gi|307346171|gb|EFN91500.1| DNA-directed RNA polymerase, alpha subunit [Prevotella amnii CRIS
           21A-A]
          Length = 332

 Score =  294 bits (753), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 122/326 (37%), Positives = 191/326 (58%), Gaps = 12/326 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  E        PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---VMLEANETFGKFEFRPLEPGFGVTIGNALRRILLSSLEGFAINTIRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQT-VNDI 125
            HE SS+ GV ED+T+IILN+K +  +  +    +++V+I         AGDI   +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFRQVVEEFENEKVSITVENSTEFKAGDISNYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VIC+LD  A ++++LT++KG GYVPA  +R     + ++ ID++Y+PI+ V Y
Sbjct: 123 EVLNPDLVICHLDSKASMQIDLTINKGRGYVPADENREFCTDVNVLPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           +VE  R  Q  DYDKL + + TDGSI  ++++  A++ L     +F    I  E P +E 
Sbjct: 183 SVEPYRVEQKTDYDKLIIEVTTDGSIPPKEALKEAAKTLIHHFMLFSDEKITLESPDQEN 242

Query: 242 KEDINVKSLPFNPALLKKVEE--LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            ++ + + L     L  K+ +  L LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG
Sbjct: 243 NQEFDEEVLHMRQLLKTKLTDATLNLSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFG 302

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWP 325
           +KSL E+  +L  + L  G ++  + 
Sbjct: 303 KKSLSELDDLLEGLNLSFGTDITKYK 328


>gi|328813963|gb|AEB52097.1| DNA-directed RNA polymerase alpha chain [Lactobacillus farraginis]
          Length = 264

 Score =  294 bits (753), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 118/264 (44%), Positives = 173/264 (65%), Gaps = 4/264 (1%)

Query: 28  TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIIL 87
             ++ EPL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IIL
Sbjct: 1   GEVVVEPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIIL 60

Query: 88  NIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           N+K I+LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M
Sbjct: 61  NVKKISLKLDGPEDEEENLEIDVIGPADVTAGDIQGDSDVTVLNPDLHIATVAEGATFHM 120

Query: 146 ELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            LT ++G GYV A  ++      PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++
Sbjct: 121 RLTANRGRGYVSAVENKKRATEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTL 180

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            + T+GSIT  ++V+LA++IL + L MF++  +  K  +  +  +       L   +EEL
Sbjct: 181 DVWTNGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEKEETHKEKMLEMTIEEL 240

Query: 264 ELSVRSTNCLRGENIVYMGDLIQR 287
           +LSVRS NCL+   I  + +L ++
Sbjct: 241 DLSVRSYNCLKRAGINTVQELTEK 264


>gi|161511769|emb|CAP16895.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 262

 Score =  294 bits (753), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 115/256 (44%), Positives = 164/256 (64%), Gaps = 2/256 (0%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E +N    + EPL RG+  TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED
Sbjct: 7   DENDNYGRFVIEPLERGYGTTLGNSLRRILLSSLPGAAITSVQIDSVLHEFSTIEGVVED 66

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  IC +    
Sbjct: 67  VTQIILNLKKVSLKIESDEDKTLEINVAGPANVTAGDIMGDGDVVILNPELPICTVAEGT 126

Query: 142 VVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
                LT   G GY  A  ++    + PIG++ ID++Y+PI++V+Y VE+ R GQ  DYD
Sbjct: 127 TFHAVLTADTGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYD 186

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL++ I TDGSIT  ++ +L+++IL + L +F+N  +  KE +  +  +       L   
Sbjct: 187 KLTLDIWTDGSITPSEATSLSAKILTEHLAIFVNLNDQAKETEIMVEKEETHKEKMLEMT 246

Query: 260 VEELELSVRSTNCLRG 275
           +EEL+LSVRS NCL+ 
Sbjct: 247 IEELDLSVRSYNCLKR 262


>gi|53715439|ref|YP_101431.1| DNA-directed RNA polymerase subunit alpha [Bacteroides fragilis
           YCH46]
 gi|60683411|ref|YP_213555.1| DNA-directed RNA polymerase subunit alpha [Bacteroides fragilis
           NCTC 9343]
 gi|253566697|ref|ZP_04844150.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. 3_2_5]
 gi|255011673|ref|ZP_05283799.1| DNA-directed RNA polymerase subunit alpha [Bacteroides fragilis
           3_1_12]
 gi|265767575|ref|ZP_06095241.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 2_1_16]
 gi|313149509|ref|ZP_07811702.1| RNA polymerase subunit alpha [Bacteroides fragilis 3_1_12]
 gi|61215863|sp|Q64NN5|RPOA_BACFR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|81313537|sp|Q5L8D6|RPOA_BACFN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|52218304|dbj|BAD50897.1| DNA-directed RNA polymerase alpha chain [Bacteroides fragilis
           YCH46]
 gi|60494845|emb|CAH09652.1| putative DNA-directed RNA polymerase alpha chain [Bacteroides
           fragilis NCTC 9343]
 gi|251944869|gb|EES85344.1| DNA-directed RNA polymerase subunit alpha [Bacteroides sp. 3_2_5]
 gi|263252880|gb|EEZ24392.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides sp. 2_1_16]
 gi|301164896|emb|CBW24457.1| putative DNA-directed RNA polymerase alpha chain [Bacteroides
           fragilis 638R]
 gi|313138276|gb|EFR55636.1| RNA polymerase subunit alpha [Bacteroides fragilis 3_1_12]
          Length = 330

 Score =  294 bits (753), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 120/324 (37%), Positives = 194/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AIT ++I+GV
Sbjct: 6   FQKPDKV---LMLEADAKFGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIRIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +     ++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFESEKVSITIENSSEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+ VIC+LD  A +++++T++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPELVICHLDSKATMQIDITINKGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE+ R  Q  DY+KL + I TDGSI  ++++  A++IL     +F    I  E    + 
Sbjct: 183 AVENFRVEQKTDYEKLVLEITTDGSIHPKEALKEAAKILIYHFMLFSDEKITLESNDVDG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ +++LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKTKLVDMDLSVRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLTELDDLLESLNLSFGTDISKYK 326


>gi|328813979|gb|AEB52105.1| DNA-directed RNA polymerase alpha chain [Lactobacillus helveticus]
          Length = 263

 Score =  294 bits (752), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 114/267 (42%), Positives = 167/267 (62%), Gaps = 4/267 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGV
Sbjct: 1   FEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGV 56

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++VL
Sbjct: 57  LHEFSTVPGVREDVTKIILNLKKLELKSLSDERKVIELDVEGPATVTADDLKVDADVQVL 116

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NPD  IC +     + ME+ V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VE
Sbjct: 117 NPDQYICTIAEGGHLHMEIAVQNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVE 176

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   K  +  +  +
Sbjct: 177 STRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADADTKFSEVMVEKE 236

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRG 275
                  L   +EEL+LSVRS NCL+ 
Sbjct: 237 DDKKEKKLEMTIEELDLSVRSYNCLKR 263


>gi|157783870|gb|ABV72700.1| RNA polymerase alpha-subunit [Vibrio mangrovi]
 gi|163962991|gb|ABY50538.1| RNA polymerase alpha-subunit [Vibrio sp. MSSRF39]
          Length = 297

 Score =  294 bits (752), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 134/299 (44%), Positives = 197/299 (65%), Gaps = 8/299 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +G
Sbjct: 2   VDIEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEG 61

Query: 78  VHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           V ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+
Sbjct: 62  VQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICH 121

Query: 137 LDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L  D A V M + V +G GYVPA    H   ++ PIG + +DA YSP+ K++YTVE+AR 
Sbjct: 122 LTDDNAEVAMRIKVQRGRGYVPASARIHTDEDDRPIGRLLVDATYSPVDKIAYTVEAARV 181

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + +         +   F
Sbjct: 182 EQRTDLDKLVIDMETNGTIEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEF 238

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK  L 
Sbjct: 239 DPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDGLH 297


>gi|311990460|gb|ADQ26360.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus casei]
 gi|328813945|gb|AEB52088.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 245

 Score =  294 bits (752), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 109/245 (44%), Positives = 163/245 (66%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS 100
            TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNIK + LKM+ D 
Sbjct: 1   TTLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNTDE 60

Query: 101 HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
            K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV KG GYV A  
Sbjct: 61  DKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAADQ 120

Query: 161 HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA
Sbjct: 121 NKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLA 180

Query: 221 SRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVY 280
           ++IL + L +F+N  +  K  +  +  +       L   +EEL+LSVRS NCL+   I  
Sbjct: 181 AKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINT 240

Query: 281 MGDLI 285
           + +L 
Sbjct: 241 VQELT 245


>gi|295111400|emb|CBL28150.1| DNA-directed RNA polymerase, alpha subunit, bacterial and
           chloroplast-type [Synergistetes bacterium SGP1]
          Length = 333

 Score =  294 bits (752), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 117/331 (35%), Positives = 189/331 (57%), Gaps = 15/331 (4%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+++P     + L +       +  EPL RG+  TLGNALRRVL+SS+RGAAIT+V+IDG
Sbjct: 6   EILRP----VLKLEENTPTYGRLYLEPLERGYGMTLGNALRRVLLSSIRGAAITSVRIDG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++ GV ED+ +I++N+K I ++      + V++     G+VTAGDI    +IE 
Sbjct: 62  VLHEFSTVPGVREDVMEILMNLKHIPVRSKSKEVRVVSLDVERAGLVTAGDIPENGEIEF 121

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           ++P+  IC ++  A + MEL + +G GY+ A+  R    P+  +  DA++SP+ +V+Y V
Sbjct: 122 IDPNAKICTMEEGAHLSMELYIEQGTGYLSAERPRPAYLPVDALLTDAIFSPVLRVNYGV 181

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK--------- 238
           E+AR GQ  D+++L+M + T+G I  + +V  A++I++      +               
Sbjct: 182 EAARVGQRTDFERLAMDVWTNGIIAPDAAVGEAAQIIEKCFSYIVASVGQAGPDGVGGGA 241

Query: 239 --KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
              ++  D  +        L + V ELELS+RS NCL    +  +GDL+Q++  D+L++ 
Sbjct: 242 YDIDLGADRRIGPAGNEELLARPVRELELSIRSENCLLRGGVQTIGDLLQKSREDLLKIR 301

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           N G+ SL EI+  L + GL L         E
Sbjct: 302 NLGKISLTEIEEKLESAGLKLREKKEKAGKE 332


>gi|328813989|gb|AEB52110.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 264

 Score =  294 bits (752), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 121/266 (45%), Positives = 173/266 (65%), Gaps = 6/266 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E +N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EFEKPN----IHKIDENDNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EV
Sbjct: 59  VLHEFSTIEGVTEDVTAIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSY 185
           LNPD  IC +   A   M +T + G GYV A+ ++   ++ PIG++ +D+LYSPI++V+Y
Sbjct: 119 LNPDLPICTVADGAHFHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R GQ  D+DKL++ + T+GSIT  ++++L+++IL D L +F+N  +  K     +
Sbjct: 179 QVENTRVGQRDDFDKLTLDVWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTN 271
             +       L   +EEL+LSVRS N
Sbjct: 239 EKEETHKEKMLEMTIEELDLSVRSYN 264


>gi|282858348|ref|ZP_06267528.1| DNA-directed RNA polymerase, alpha subunit [Prevotella bivia
           JCVIHMP010]
 gi|282588796|gb|EFB93921.1| DNA-directed RNA polymerase, alpha subunit [Prevotella bivia
           JCVIHMP010]
          Length = 332

 Score =  294 bits (752), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 122/326 (37%), Positives = 190/326 (58%), Gaps = 12/326 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  +        PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---VMLEANDTFGKFEFRPLEPGFGVTIGNALRRILLSSLEGFAINTIRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQT-VNDI 125
            HE SS+ GV ED+T+IILN+K +  +  +    +++V+I         AGDI   +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFRQVVEEFENEKVSITVENSTEFKAGDISNYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VIC+LD  A +++ELT++KG GYVPA  +R     + ++ ID++Y+PI+ V Y
Sbjct: 123 EVLNPDLVICHLDSKASMQIELTINKGRGYVPADENREFCTDVNVLPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           +VE  R  Q  DYDKL + + TDGSI  +D++  A++ L     +F    I  E   +E 
Sbjct: 183 SVEPYRVEQKTDYDKLVIEVTTDGSIHPKDALKEAAKTLIYHFMLFSDEKITLESSDQEN 242

Query: 242 KEDINVKSLPFNPALLKKVEE--LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            ++ + + L     L  K+ +  L LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG
Sbjct: 243 NQEFDEEILHMRQLLKTKLTDASLNLSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFG 302

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWP 325
           +KSL E+  +L  + L  G ++  + 
Sbjct: 303 KKSLSELDDLLEGLNLSFGTDITKYK 328


>gi|83858542|ref|ZP_00952064.1| DNA-directed RNA polymerase alpha subunit [Oceanicaulis alexandrii
           HTCC2633]
 gi|83853365|gb|EAP91217.1| DNA-directed RNA polymerase alpha subunit [Oceanicaulis alexandrii
           HTCC2633]
          Length = 274

 Score =  293 bits (751), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 154/255 (60%), Positives = 197/255 (77%), Gaps = 1/255 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +I+KNWQELI+P   E I  G +   +  +IAEPL RGF  TLGNALRR+L+SSL+GA+I
Sbjct: 20  VIEKNWQELIRPMKPE-IQPGFDPVRQAKIIAEPLERGFGMTLGNALRRILLSSLQGASI 78

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQID VLHE SSIKGV ED+TDIILN+K + L+M G+  KR+T+ K+GPG VTAGDI+
Sbjct: 79  TAVQIDSVLHEFSSIKGVREDVTDIILNLKQVALRMHGEGPKRLTLKKQGPGEVTAGDIE 138

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              D+E++N DHVIC LD DA VRM LTV+ G GYVPA  +R E+ PIGLI +DALYSP+
Sbjct: 139 ETADVEIINKDHVICTLDEDADVRMVLTVNTGKGYVPADRNRPEDAPIGLIGVDALYSPV 198

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V+Y VE+ REGQVLDYDKL + ++T+G++T ED+VA A+RILQDQ  +F+NFEEP + 
Sbjct: 199 KRVAYRVENTREGQVLDYDKLILEVETNGAVTPEDAVAYAARILQDQFQIFVNFEEPSEA 258

Query: 241 VKEDINVKSLPFNPA 255
              + +   L FNPA
Sbjct: 259 RAAEDDKPELDFNPA 273


>gi|218131300|ref|ZP_03460104.1| hypothetical protein BACEGG_02911 [Bacteroides eggerthii DSM 20697]
 gi|317476330|ref|ZP_07935579.1| DNA-directed RNA polymerase [Bacteroides eggerthii 1_2_48FAA]
 gi|217986517|gb|EEC52853.1| hypothetical protein BACEGG_02911 [Bacteroides eggerthii DSM 20697]
 gi|316907356|gb|EFV29061.1| DNA-directed RNA polymerase [Bacteroides eggerthii 1_2_48FAA]
          Length = 330

 Score =  293 bits (751), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 120/324 (37%), Positives = 194/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AIT ++IDGV
Sbjct: 6   FQKPDKV---LMLEADSKFGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIKIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +     ++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFESEKVSITIENSSEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+ VIC+LD  + +++++T++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPELVICHLDSKSTMQIDITINKGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE+ R  Q  DY+KL + I TDGSI  ++++  A++IL     +F    I  E    + 
Sbjct: 183 QVENFRVEQKTDYEKLVLEITTDGSIHPKEALKEAAKILIYHFMLFSDEKITLETNDVDG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ +++LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKTKLVDMDLSVRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLTELDDLLESLNLSFGTDISKYK 326


>gi|153012268|gb|ABS50355.1| DNA-directed RNA polymerase alpha chain [Enterococcus thailandicus]
          Length = 250

 Score =  293 bits (751), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 117/248 (47%), Positives = 165/248 (66%)

Query: 28  TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIIL 87
              I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IIL
Sbjct: 3   GKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIIL 62

Query: 88  NIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           NIKG+ LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     L
Sbjct: 63  NIKGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARL 122

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           TV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I T
Sbjct: 123 TVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWT 182

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           DGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +EEL+LSV
Sbjct: 183 DGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEELDLSV 242

Query: 268 RSTNCLRG 275
           RS NCL+ 
Sbjct: 243 RSYNCLKR 250


>gi|167764346|ref|ZP_02436471.1| hypothetical protein BACSTE_02730 [Bacteroides stercoris ATCC
           43183]
 gi|167697751|gb|EDS14330.1| hypothetical protein BACSTE_02730 [Bacteroides stercoris ATCC
           43183]
          Length = 330

 Score =  293 bits (751), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 119/324 (36%), Positives = 194/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AIT ++I+GV
Sbjct: 6   FQKPDKV---LMLEADSKFGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +     ++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFESEKVSITIENSSEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+ VIC+LD  + +++++T++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPELVICHLDSKSTMQIDITINKGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE+ R  Q  DY+KL + I TDGSI  ++++  A++IL     +F    I  E    + 
Sbjct: 183 QVENFRVEQKTDYEKLVLEITTDGSIHPKEALKEAAKILIYHFMLFSDEKITLESNDADG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ +++LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKTKLVDMDLSVRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLTELDDLLESLNLSFGTDISKYK 326


>gi|218674111|ref|ZP_03523780.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli GR56]
          Length = 237

 Score =  293 bits (750), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 166/239 (69%), Positives = 196/239 (82%), Gaps = 3/239 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+         R  ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVEF---SSSSRTRATLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHE SSI GV ED+TDI+LNIK I +KM GD  KR+ + K+GPGVVTAGDIQ
Sbjct: 58  TAVQIDGVLHEFSSIPGVREDVTDIVLNIKEIAIKMDGDDAKRMVVRKQGPGVVTAGDIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +D+LYSP+
Sbjct: 118 TVGDIEILNPEHVICTLDEGAEIRMEFTVNNGKGYVPAERNRAEDAPIGLIPVDSLYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           KKVSY VE+ REGQVLDYDKL+MTI+TDGSITGED+VA A+RILQDQLG+F+NFE   +
Sbjct: 178 KKVSYKVENTREGQVLDYDKLNMTIETDGSITGEDAVAFAARILQDQLGVFVNFERAAE 236


>gi|261876120|gb|ACY04590.1| DNA-directed RNA polymerase [Lactobacillus sp. DCY 50T]
          Length = 251

 Score =  293 bits (750), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 117/251 (46%), Positives = 169/251 (67%), Gaps = 4/251 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNV 60

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K I LK++G  D  + + I  +GP  VTAGDI    D++VLNPD  I  +   A   M +
Sbjct: 61  KKIALKLNGSDDQEETMEINVKGPAQVTAGDIVAGADVDVLNPDLYIATVADGATFHMRM 120

Query: 148 TVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           T  KG GYV A  ++T   + PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ +
Sbjct: 121 TADKGRGYVSADENKTRNTDMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDV 180

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+GSI   +++ALA++IL + L MF++  +  K  +  +  +       L   +EEL+L
Sbjct: 181 WTNGSINPSEAIALAAKILTEHLAMFVDLTDEAKNAEIMVEKEETHKEKMLEMTIEELDL 240

Query: 266 SVRSTNCLRGE 276
           SVRS NCL+  
Sbjct: 241 SVRSYNCLKRA 251


>gi|329956729|ref|ZP_08297302.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides clarus YIT
           12056]
 gi|328524101|gb|EGF51177.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides clarus YIT
           12056]
          Length = 330

 Score =  293 bits (750), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 119/324 (36%), Positives = 194/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AIT ++I+GV
Sbjct: 6   FQKPDKV---LMLEADSKFGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +     ++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFESEKVSITIENSSEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+ VIC+LD  + +++++T++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPELVICHLDSKSTMQIDITINKGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE+ R  Q  DY+KL + I TDGSI  ++++  A++IL     +F    I  E    + 
Sbjct: 183 QVENFRVEQKTDYEKLVLEITTDGSIHPKEALKEAAKILIYHFMLFSDEKITLESNDVDG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ +++LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKTKLVDMDLSVRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLTELDDLLESLNLSFGTDISKYK 326


>gi|319900952|ref|YP_004160680.1| DNA-directed RNA polymerase subunit alpha [Bacteroides helcogenes P
           36-108]
 gi|319415983|gb|ADV43094.1| DNA-directed RNA polymerase subunit alpha [Bacteroides helcogenes P
           36-108]
          Length = 330

 Score =  293 bits (749), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 118/324 (36%), Positives = 193/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AIT ++I+GV
Sbjct: 6   FQKPDKV---LMLEADSRFGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +     ++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFESEKVSITIENSSEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+ VIC+LD  + +++++ ++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPELVICHLDSKSTMQIDIAINKGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE+ R  Q  DY+KL + I TDGSI  ++++  A++IL     +F    I  E    + 
Sbjct: 183 QVENFRVEQKTDYEKLVLEITTDGSIHPKEALKEAAKILIYHFMLFSDEKITLESNDVDG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ +++LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKTKLVDMDLSVRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLTELDDLLESLNLSFGTDISKYK 326


>gi|289523340|ref|ZP_06440194.1| DNA-directed RNA polymerase, alpha subunit [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
 gi|289503032|gb|EFD24196.1| DNA-directed RNA polymerase, alpha subunit [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
          Length = 340

 Score =  293 bits (749), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 112/307 (36%), Positives = 173/307 (56%), Gaps = 6/307 (1%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + +       +  EPL RG+  TLGNA+RRVL+SS+ GAA++A++IDGVLHE S++ G
Sbjct: 4   IHIEESSSGYGRIRIEPLERGYGVTLGNAIRRVLLSSIPGAAVSAIRIDGVLHEFSTVPG 63

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +IILNIK + +    D  + + +   GP VVT  DI   +++E  NP+  IC L
Sbjct: 64  VMEDVLEIILNIKKLAVVSHSDDVRMLRLEAEGPKVVTVADIIPDSEVEFSNPEAYICTL 123

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           +    + M+L V +G GY+     R    PI ++ +DA++SP+ +V+Y V +AR GQ  D
Sbjct: 124 EEGHKLEMDLYVERGVGYLTMDRPRPNYLPIDVLLVDAVFSPVLRVNYNVGAARVGQRTD 183

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF------EEPKKEVKEDINVKSLP 251
           Y+ L + + T+ ++    +   A +IL    G   +            EV E +      
Sbjct: 184 YESLLIELWTNETVEPAKAFLEAVKILNQYFGHIASLLLKEPVSPVAAEVPEAVVEAVAE 243

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P L + + +LELS+RS NCL    +  +GDL+Q T  D+L++ N G+ SL EI+  L 
Sbjct: 244 EDPILSRPIRDLELSIRSENCLLRAGVRTIGDLVQYTRDDLLKIRNLGKISLKEIEEKLD 303

Query: 312 TMGLFLG 318
             GL L 
Sbjct: 304 IFGLSLS 310


>gi|315186306|gb|EFU20067.1| DNA-directed RNA polymerase subunit alpha [Spirochaeta thermophila
           DSM 6578]
          Length = 363

 Score =  292 bits (748), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 125/344 (36%), Positives = 194/344 (56%), Gaps = 13/344 (3%)

Query: 1   MIQKNW-QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M +KN  +  + P +I    L           A P  RG+  T+GN LRR+L+SS++G A
Sbjct: 1   MARKNLLKGFVLPTSITVEHLDTNTH-YGKFAAYPFERGYGVTIGNTLRRILLSSIQGYA 59

Query: 60  ITAVQI-----DGVLHEISS----IKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKR 109
           I+AV+I      G  H +SS    I GV ED  +++ N+K + +++  +   K V +  +
Sbjct: 60  ISAVRITWYDDQGAAHVLSSEYEQIPGVVEDTLELLANLKLLRVQLPDEMEQKTVMVEFK 119

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  VT  D +    +EV+N D  +  L  DA   ME+ V  G GYVPA+  +   + +G
Sbjct: 120 GPKEVTGADFEVD-QLEVMNKDFRVMTLMEDAHFEMEMQVDLGRGYVPAEVQKNYIEVVG 178

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            I +DALYSP+++V + VE+ R G   DYDKL + + TDGSI+ ED++  A+++ ++   
Sbjct: 179 TIPLDALYSPVQRVRFNVENTRVGHRSDYDKLILEVWTDGSISPEDALGEAAKLAKEHFT 238

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +FINF+E        ++ +       L   +EELELSVRS+NCL+  NI  +GDL+ ++E
Sbjct: 239 VFINFDEDAISHVRQLDHEEEQIRRLLETPIEELELSVRSSNCLKNANIRTIGDLVSKSE 298

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELA 333
            ++ +  NFG+KSL+EIK  L    L LGM  P     ++E + 
Sbjct: 299 EELSKTRNFGKKSLLEIKEKLKEWNLSLGMRDPSAYKAALERVR 342


>gi|312271196|gb|ADQ57295.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 253

 Score =  292 bits (748), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 110/253 (43%), Positives = 159/253 (62%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           +    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T I
Sbjct: 1   SYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKI 60

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           ILN+K + LK   D  K + +   GP  VTA D++   D++VLNPD  IC +     + M
Sbjct: 61  ILNLKKLELKSFSDERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHM 120

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           E+ V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I
Sbjct: 121 EIAVQNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEI 180

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            TDGSI   D+++ A++IL +   +F + +   K  +  +  +       L   +EEL+L
Sbjct: 181 WTDGSIKPNDALSFAAKILVEHFKVFESADADTKFSEVMVEKEDDKKEKKLEMTIEELDL 240

Query: 266 SVRSTNCLRGENI 278
           SVRS NCL+   I
Sbjct: 241 SVRSYNCLKRAGI 253


>gi|161511759|emb|CAP16890.1| DNA-directed RNA polymerase subunit alpha [Pediococcus damnosus]
          Length = 265

 Score =  292 bits (748), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 115/268 (42%), Positives = 170/268 (63%), Gaps = 6/268 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KP     I    E+ N    + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDGVLH
Sbjct: 2   KPK----IHKVDEKSNYGRFVVEPLERGYGTTLGNSLRRILLSSLPGAALTSVQIDGVLH 57

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S+I+GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP
Sbjct: 58  EFSTIEGVVEDVTQIILNLKKVSLKVESDEEKSLEINVMGPANVTAGDIVGDGDVTILNP 117

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVE 188
           +  IC +         LT  KG GY  A  ++    + PIG++ ID++Y+PI++V+Y VE
Sbjct: 118 ELPICTVAEGTTFHAVLTAEKGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVE 177

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           + R GQ  DYDKL++ + TDGS+   ++++L+++IL + L +F+N ++  K+ +  +  +
Sbjct: 178 NTRVGQRDDYDKLTLDVWTDGSLAASEAISLSAKILTEHLTIFVNLDDQAKDTEIMVEKE 237

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGE 276
                  L   +EEL+LSVRS NCL+  
Sbjct: 238 ETHKEKMLEMTIEELDLSVRSYNCLKRA 265


>gi|313292044|gb|ADR51211.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
 gi|313292046|gb|ADR51212.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
 gi|313292048|gb|ADR51213.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
 gi|313292050|gb|ADR51214.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
          Length = 258

 Score =  292 bits (748), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 118/253 (46%), Positives = 169/253 (66%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED
Sbjct: 6   DEEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVRED 65

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILNIKG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A
Sbjct: 66  VTQIILNIKGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGA 125

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
                LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL
Sbjct: 126 TFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKL 185

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           +M I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +E
Sbjct: 186 TMEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIE 245

Query: 262 ELELSVRSTNCLR 274
           EL+LSVRS NCL+
Sbjct: 246 ELDLSVRSYNCLK 258


>gi|145577845|gb|ABP87373.1| RpoA [Vibrio ruber]
          Length = 294

 Score =  292 bits (748), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 132/295 (44%), Positives = 195/295 (66%), Gaps = 8/295 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +G
Sbjct: 3   VDIEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEG 62

Query: 78  VHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           V ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+
Sbjct: 63  VQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICH 122

Query: 137 LDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L    A V M + V +G GYVPA    H   ++ PIG + +DA YSP+ K++YTVE+AR 
Sbjct: 123 LTDGNAEVAMRIKVQRGRGYVPASARIHTDEDDRPIGRLLVDATYSPVDKIAYTVEAARV 182

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + +         +   F
Sbjct: 183 EQRTDLDKLVIDMETNGTIEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEF 239

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK
Sbjct: 240 DPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIK 294


>gi|34541514|ref|NP_905993.1| DNA-directed RNA polymerase subunit alpha [Porphyromonas gingivalis
           W83]
 gi|188995705|ref|YP_001929957.1| DNA-directed RNA polymerase subunit alpha [Porphyromonas gingivalis
           ATCC 33277]
 gi|41688626|sp|Q7MTP0|RPOA_PORGI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|34397831|gb|AAQ66892.1| DNA-directed RNA polymerase, alpha subunit [Porphyromonas
           gingivalis W83]
 gi|188595385|dbj|BAG34360.1| DNA-directed RNA polymerase alpha subunit [Porphyromonas gingivalis
           ATCC 33277]
          Length = 330

 Score =  292 bits (748), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 121/324 (37%), Positives = 193/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP N+   ++ +  ++      +PL  G+  T+GNALRR+L+SSL G AITA++I+GV
Sbjct: 6   FQKPENV---LMMETSDSIAKFEFKPLEPGYGITIGNALRRILLSSLEGFAITAIKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE ++I GV ED+T+IILN+K +  K  +     ++ TI      V  AGD+   +++ 
Sbjct: 63  EHEFATIPGVLEDVTNIILNLKQVRFKQIVPNADVEKATIVISNSEVFRAGDLNAQLSNF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLN + VIC+LD  A + ME +++KG GYV A+ +R E++ +  I ID++Y+PI+ V Y
Sbjct: 123 EVLNSNLVICHLDKSATLTMEFSINKGRGYVSAEENRAEHNELSTIAIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEV 241
            VE+ R  Q  DY+KL M + TDGSI   D++  A++IL     +F       E      
Sbjct: 183 AVENFRVEQKTDYEKLLMEVTTDGSIRPVDALREAAQILISHFSLFAENKIAIEYVDIVD 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++ +  SL     L  K+  L+LSVR+ NCL    +  +GDL+  + +D++++ NFG+K
Sbjct: 243 TDEFDEDSLHMRQLLKSKLSGLDLSVRALNCLNAAGVDTLGDLVSLSRSDLMKIRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L T+ L  GM++  + 
Sbjct: 303 SLTELDELLATLNLSFGMDISKYK 326


>gi|257456916|ref|ZP_05622097.1| DNA-directed RNA polymerase, alpha subunit [Treponema vincentii
           ATCC 35580]
 gi|257445625|gb|EEV20687.1| DNA-directed RNA polymerase, alpha subunit [Treponema vincentii
           ATCC 35580]
          Length = 351

 Score =  292 bits (748), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 123/352 (34%), Positives = 193/352 (54%), Gaps = 13/352 (3%)

Query: 1   MIQKNW-QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M +KN  +   KP  +E+       ++     A P   GF  T+GN LRRVL+SS++G A
Sbjct: 1   MARKNLLKGFKKPKGLEF-AADVSNDSYGKFTASPFETGFGTTIGNCLRRVLLSSIQGYA 59

Query: 60  ITAVQI-----DGVLHEISS----IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF-KR 109
           I+AV+I     D V H ISS    I  V ED  +++ N+K + L++  +  +   +F  +
Sbjct: 60  ISAVKITSYGADDVPHSISSEFEAIPNVTEDTMEVLNNLKQMRLRLPNEIEQDTFLFDFK 119

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  V A D      +E+L+ D  I  L  +A V +E+ V  G GYVPA+ +    + +G
Sbjct: 120 GPRSVKAADFAKPGQLEILSGDLHIMELMENAHVELEVQVDFGRGYVPAETNEKYVEVVG 179

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            I++D ++SP++KVSY ++  R GQ  DYDKL + I TDG+I  ED++A A++I ++   
Sbjct: 180 TISLDTIFSPVRKVSYEIQPCRVGQRNDYDKLVLEIWTDGTIRPEDALAEAAKIAKEHFT 239

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +F+NF E +    ++ +         L   + EL+LSVR++NCL+  N+  + DL   TE
Sbjct: 240 VFVNFNENELLSDDEADESDEMIKQLLDTPITELDLSVRASNCLKNANVSTIRDLTMMTE 299

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE-DKC 340
            ++ +  N G+KSL EI+  L    L LGM        SI+   +K E D+ 
Sbjct: 300 DEISKTRNVGKKSLQEIQEKLAERNLSLGMTDYSHLKNSIKLSRQKEETDEA 351


>gi|189308769|gb|ACD87086.1| RpoA [Vibrio sp. PP-203]
          Length = 295

 Score =  292 bits (747), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 131/298 (43%), Positives = 195/298 (65%), Gaps = 8/298 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +G
Sbjct: 1   VDIEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEG 60

Query: 78  VHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           V ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+ NP+HVIC+
Sbjct: 61  VQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEITNPEHVICH 120

Query: 137 LDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L    A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR 
Sbjct: 121 LTDGNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F
Sbjct: 181 EQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVL 295


>gi|189308773|gb|ACD87088.1| RpoA [Vibrio sp. PP-204]
          Length = 295

 Score =  292 bits (747), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 131/297 (44%), Positives = 194/297 (65%), Gaps = 8/297 (2%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV 
Sbjct: 2   IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQ 61

Query: 80  EDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
           ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+ NP+HVIC+L 
Sbjct: 62  EDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEITNPEHVICHLT 121

Query: 139 VD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
              A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q
Sbjct: 122 DGNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQ 181

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
             D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P
Sbjct: 182 RTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDP 238

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL 
Sbjct: 239 ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKNVLA 295


>gi|330837630|ref|YP_004412271.1| DNA-directed RNA polymerase subunit alpha [Spirochaeta coccoides
           DSM 17374]
 gi|329749533|gb|AEC02889.1| DNA-directed RNA polymerase subunit alpha [Spirochaeta coccoides
           DSM 17374]
          Length = 350

 Score =  292 bits (747), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 126/331 (38%), Positives = 192/331 (58%), Gaps = 13/331 (3%)

Query: 1   MIQKN-WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M +KN  +   +P  I        + +     A P  RGF  T+GN LRR+L+SS++G A
Sbjct: 1   MARKNLMKGFKRPKGI-IFEHSDVKPDYGKFTAYPFERGFGTTIGNTLRRILLSSIQGYA 59

Query: 60  ITAVQI-----DGVLHEISS----IKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKR 109
           ITAV+      DGV H ++S    + GV ED++DII  +K + L++  +S    + I  +
Sbjct: 60  ITAVKFTTFNQDGVPHLVTSEYESLPGVREDVSDIIAALKKLQLRLPEESESTTLLIECK 119

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GPG+++    +    +EV+N D  I  +  DA + ME+ +  G GYVPA+ +    + IG
Sbjct: 120 GPGILSGASFER-GQVEVINKDMEILTMMDDANIEMEVQIDLGRGYVPAEINEKYVEEIG 178

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            I +DA +SP+ +V Y +E  R GQ  DYDKL + + TDG+I+ E ++A A++I +D   
Sbjct: 179 TIPLDASFSPVTRVKYAIEPTRVGQRSDYDKLVIEVYTDGTISPESALAEAAKIAKDHFS 238

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +FINF+E      ++I+ +       L   VEELEL+VRS+NCL+  NI  +GDL ++TE
Sbjct: 239 IFINFDESLINSSDEIDEEEERVRKILNTSVEELELTVRSSNCLKNANIRTIGDLTKKTE 298

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
            ++ +  NFG+KSL EIK  L    L LGM 
Sbjct: 299 EEIAKTRNFGKKSLSEIKAKLAEWNLSLGMT 329


>gi|313677146|ref|YP_004055142.1| DNA-directed RNA polymerase subunit alpha [Marivirga tractuosa DSM
           4126]
 gi|312943844|gb|ADR23034.1| DNA-directed RNA polymerase subunit alpha [Marivirga tractuosa DSM
           4126]
          Length = 329

 Score =  292 bits (747), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 111/316 (35%), Positives = 188/316 (59%), Gaps = 6/316 (1%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           E + + + ++   L   +PL +G+  T+GNALRR+L+SSL G AIT ++I GVLHE S++
Sbjct: 10  EKVAMEKADDFHGLFTFKPLEKGYGVTVGNALRRILLSSLEGYAITGIKIPGVLHEFSAV 69

Query: 76  KGVHEDLTDIILNIKGINLKMSGDS-HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHV 133
           +GV ED++++ILN+K +  K   ++   ++ I  +      AGDI +     E+LNPD +
Sbjct: 70  EGVVEDVSELILNLKMVRFKKIAETADNKINISLKNTKEFKAGDINKFTTAFEILNPDLL 129

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           IC++D      +ELT+ KG GYV ++ +   +     I ID++++PIK V Y+VE+ R  
Sbjct: 130 ICHMDESINFEIELTIEKGRGYVSSEENTLVDQVADYIAIDSIFTPIKNVKYSVENTRVE 189

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKS 249
           Q  DY++L + I+TDGSI  E ++  A+ IL     +F +     +    +  E ++ + 
Sbjct: 190 QKTDYEQLVLDIETDGSIHPEVALKGAANILIKHFMLFSDQNMVLDAGGSDEPEAVDEEM 249

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           L     L   + +L+LSVR+ NCL+  ++  +GDL+    +DM++  NFG+KSL E++ +
Sbjct: 250 LHMRKLLKTALNDLDLSVRAYNCLKAADVKTLGDLVALEISDMMKFRNFGKKSLAELEQL 309

Query: 310 LGTMGLFLGMNLPDWP 325
           +   GL  GM+L  + 
Sbjct: 310 VADKGLTFGMDLSKYK 325


>gi|227485498|ref|ZP_03915814.1| DNA-directed RNA polymerase [Anaerococcus lactolyticus ATCC 51172]
 gi|227236497|gb|EEI86512.1| DNA-directed RNA polymerase [Anaerococcus lactolyticus ATCC 51172]
          Length = 316

 Score =  291 bits (746), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 113/311 (36%), Positives = 190/311 (61%), Gaps = 4/311 (1%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
            NIE + + +E+         PL RG+  T+GN++RRVL+SSL G++++ + IDGVLHE 
Sbjct: 7   TNIEILDINEEDH-YGKFALYPLERGYGTTIGNSMRRVLLSSLPGSSVSKILIDGVLHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           S I GV ED+ +IILNIKG+N+K   D    + +   GP +VTA DI+    +E+ NPDH
Sbjct: 66  SIIDGVVEDVPEIILNIKGLNVKKHSDEDVTLFLEIEGPKIVTAKDIKEDALVEIANPDH 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  ++  + + + + V+ G+GY  +  ++ + DPIG I ID+ ++P++KV+YTVE+ R 
Sbjct: 126 YIATVNDKSKLLIAMDVTNGNGYRISDDNKDDKDPIGTIAIDSSFTPVEKVNYTVENTRV 185

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK---KEVKEDINVKS 249
           G+  D+DKL + + T+G++T ++++A    IL ++   F    + K   +E++    + +
Sbjct: 186 GESTDFDKLIIEVWTNGTVTPQEALAEGLSILMNKFAFFKELPDKKFPPEEIETTEELAA 245

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              N  L + +EEL+LS+RS NCL+      + D+I+  EA++  + NFG+KSL E+   
Sbjct: 246 DDVNEDLERTIEELDLSLRSFNCLKRAGFNTVADIIKVPEAELKIIKNFGKKSLTEVIDK 305

Query: 310 LGTMGLFLGMN 320
           +  +G  L   
Sbjct: 306 IHDLGFTLKDE 316


>gi|325280941|ref|YP_004253483.1| DNA-directed RNA polymerase subunit alpha [Odoribacter splanchnicus
           DSM 20712]
 gi|324312750|gb|ADY33303.1| DNA-directed RNA polymerase subunit alpha [Odoribacter splanchnicus
           DSM 20712]
          Length = 330

 Score =  291 bits (746), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 115/324 (35%), Positives = 184/324 (56%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ +  +        PL  G+  T+GN LRR+L+SSL G AIT ++I GV
Sbjct: 6   FQKPDKV---IMLESTDKFGKFEFRPLEPGYGITIGNPLRRILLSSLEGFAITGIKIHGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE ++I GV ED+T+IILN+K +  K   +    +++T+   G     AGDI + +   
Sbjct: 63  EHEFATIPGVIEDVTEIILNLKQVRFKRKVEDVEDEKLTVLINGQEAFKAGDINKFLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLN + VIC++D     +ME+T+ KG GYVP+  +       G I IDA+Y+PI+ V Y
Sbjct: 123 EVLNTELVICHMDPSVNFQMEITIQKGRGYVPSTENMPAEAEAGFIPIDAIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            +E+ R     DY+KL   I+TDGSI   D++  A++IL     +F    I+ E   K  
Sbjct: 183 EIENYRVEGKTDYEKLLFEIETDGSIAPTDALKEAAKILIHHFMLFSDEKISLESEDKYG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ +++LSVR+ NCL+   +  +G+L +  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKTKLVDMDLSVRALNCLKAAEVETLGELCRFNKNDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E++ +L    L  GM++  + 
Sbjct: 303 SLTELEALLENNNLEFGMDVTKYK 326


>gi|161511757|emb|CAP16889.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 263

 Score =  291 bits (746), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 115/267 (43%), Positives = 170/267 (63%), Gaps = 6/267 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KP     I    E+ N    + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDGVLH
Sbjct: 1   KPK----IHKVDEKSNYGRFVVEPLERGYGTTLGNSLRRILLSSLPGAALTSVQIDGVLH 56

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S+I+GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP
Sbjct: 57  EFSTIEGVVEDVTQIILNLKKVSLKVESDEEKSLEINVMGPANVTAGDIVGDGDVTILNP 116

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVE 188
           +  IC +         LT  KG GY  A  ++    + PIG++ ID++Y+PI++V+Y VE
Sbjct: 117 ELPICTVAEGTTFHAVLTAEKGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVE 176

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           + R GQ  DYDKL++ + TDGS+   ++++L+++IL + L +F+N ++  K+ +  +  +
Sbjct: 177 NTRVGQRDDYDKLTLDVWTDGSLAASEAISLSAKILTEHLTIFVNLDDQAKDTEIMVEKE 236

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRG 275
                  L   +EEL+LSVRS NCL+ 
Sbjct: 237 ETHKEKMLEMTIEELDLSVRSYNCLKR 263


>gi|313891534|ref|ZP_07825144.1| DNA-directed RNA polymerase, alpha subunit [Dialister
           microaerophilus UPII 345-E]
 gi|329121855|ref|ZP_08250470.1| DNA-directed RNA polymerase subunit alpha [Dialister micraerophilus
           DSM 19965]
 gi|313119993|gb|EFR43175.1| DNA-directed RNA polymerase, alpha subunit [Dialister
           microaerophilus UPII 345-E]
 gi|327467793|gb|EGF13285.1| DNA-directed RNA polymerase subunit alpha [Dialister micraerophilus
           DSM 19965]
          Length = 324

 Score =  291 bits (746), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 133/314 (42%), Positives = 190/314 (60%), Gaps = 13/314 (4%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           IV   +++       EPL RGF  TLGN+LRRVL+SSL G AIT+++IDGVLHE ++I+G
Sbjct: 11  IVELSDDKRYGKFECEPLERGFGITLGNSLRRVLLSSLDGVAITSIKIDGVLHEFTTIEG 70

Query: 78  VHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
           V ED+TD+ILN+K I      ++    +V I     G+  AGD+Q  ++I+VLN D  IC
Sbjct: 71  VREDVTDMILNLKKIRFIAHDEAVFPIQVRIDIDKEGIFHAGDMQLPSEIDVLNTDLEIC 130

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
            LD DA + MELT+ +GHGYVP   ++  ND IG+I ID++++P+ K +Y V   R G  
Sbjct: 131 TLDADAHLGMELTIDRGHGYVPFNKNKK-NDEIGIIPIDSIFTPVVKCNYKVSDTRVGNE 189

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF------EEPKKEVKEDINVKS 249
           +DYDKL++ ++TDGS+  ED+VA A+ IL      F         E    E++ +I  K 
Sbjct: 190 MDYDKLTLELETDGSVKVEDAVAQAATILIKYFENFRRLATKQIPEIDVDEIEPEIEEKD 249

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              +   +  +EELELSVR+ NCL+   I  +  L  +TE ++ R+ N G+KS+ EIK  
Sbjct: 250 DSPD-LSVIPIEELELSVRAFNCLKRAEINMLDQLTDKTEDELTRVRNLGKKSVDEIKEK 308

Query: 310 LGTM---GLFLGMN 320
           L      GL L  N
Sbjct: 309 LAAYKGWGLHLKDN 322


>gi|189501627|ref|YP_001957344.1| DNA-directed RNA polymerase subunit alpha [Candidatus Amoebophilus
           asiaticus 5a2]
 gi|189497068|gb|ACE05615.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Amoebophilus
           asiaticus 5a2]
          Length = 329

 Score =  291 bits (745), Expect = 9e-77,   Method: Composition-based stats.
 Identities = 118/313 (37%), Positives = 190/313 (60%), Gaps = 6/313 (1%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + Q +E   +   +PL RG+  T+GNALRRV++SSL G AIT+++I G+ HE S+I+G
Sbjct: 12  ISVKQADEFHGIFTFKPLERGYGVTIGNALRRVILSSLEGYAITSIRIPGIYHEFSTIEG 71

Query: 78  VHEDLTDIILNIKGINLKMSGDS-HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVIC 135
           V EDL +IILN+K I  K  GD+   ++ I      ++TAGD  Q     E+ NP+ VIC
Sbjct: 72  VTEDLVEIILNLKQIRFKKIGDTTENKIFISINNKKILTAGDFAQATAAFEITNPELVIC 131

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
           ++D  A   +E+TV KG GYVPA+ ++ +    G+I ID++++P+K V Y VE+ R GQ 
Sbjct: 132 HIDESARFEIEVTVEKGRGYVPAEENKIDAQVKGVIPIDSIFTPVKNVKYHVENTRVGQK 191

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKSLP 251
            DY+ L  +++TDG+I  + ++  A+ I+     + I+     E    +  + ++  +L 
Sbjct: 192 TDYESLVFSVETDGTIHPQTAIERAADIMIKHFALLIDRNKMVETKDADEIDVLDESTLQ 251

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L   + E+ LSVR+ NCL+  +I  +GDL+Q   +DM +  NFG+KSL E++ ++ 
Sbjct: 252 MRKLLKTPLSEMGLSVRAFNCLKAADIKTLGDLVQLKVSDMAQFRNFGKKSLKELQDLVA 311

Query: 312 TMGLFLGMNLPDW 324
           +  L  GM+L  +
Sbjct: 312 SKDLTFGMDLSAY 324


>gi|315134694|dbj|BAJ41855.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus ozensis]
          Length = 264

 Score =  291 bits (745), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 120/258 (46%), Positives = 172/258 (66%), Gaps = 4/258 (1%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E +N   ++ EPL RG+  TLGN+LRR+L+SSL GAA+T++QID VLHE S++KGV ED
Sbjct: 7   DETDNYGEVVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDDVLHEFSTVKGVVED 66

Query: 82  LTDIILNIKGINLKMS--GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           +  IILN+K I+LK+    D  K + I   GP  VTAGDIQ   D+ VLNPD  IC +  
Sbjct: 67  VAQIILNVKKISLKLDIADDEEKSMEINVTGPAQVTAGDIQADGDVTVLNPDLKICTVAE 126

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLD 197
            A   M +T +KG GYV A  ++  ND  PIG++ +D++Y+PI++V+Y VE+AR GQ  D
Sbjct: 127 GATFHMRMTANKGRGYVSADENKARNDGMPIGVLPVDSIYTPIERVNYQVENARVGQRAD 186

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL++ + TDGSIT  ++V+LA++IL + L MF++  +  K  +  +  +       L 
Sbjct: 187 FDKLTLDVWTDGSITPSEAVSLAAKILSEHLSMFVDLTDEAKNAEVMVEKEETHKEKMLE 246

Query: 258 KKVEELELSVRSTNCLRG 275
             +EEL+LSVRS NCL+ 
Sbjct: 247 MTIEELDLSVRSYNCLKR 264


>gi|313292016|gb|ADR51197.1| DNA-directed RNA polymerase alpha chain [Enterococcus viikkiensis]
 gi|313292018|gb|ADR51198.1| DNA-directed RNA polymerase alpha chain [Enterococcus viikkiensis]
          Length = 258

 Score =  291 bits (744), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 117/257 (45%), Positives = 168/257 (65%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I    E+ +    + E L RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKG
Sbjct: 2   ITKIDEDRDYGKFVVESLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+  IILNIKG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +
Sbjct: 62  VREDVVQIILNIKGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTV 121

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
              A     LTV  G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D
Sbjct: 122 AEGATFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDD 181

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL+M I TDGSI  +++++LA++IL + L +F+N  +  K  +  +  +       L 
Sbjct: 182 FDKLTMEIWTDGSIIAQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLE 241

Query: 258 KKVEELELSVRSTNCLR 274
             +EEL+LSVRS NCL+
Sbjct: 242 MTIEELDLSVRSYNCLK 258


>gi|311990466|gb|ADQ26363.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 257

 Score =  291 bits (744), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 112/257 (43%), Positives = 161/257 (62%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
            EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K 
Sbjct: 1   VEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKK 60

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           + LK   D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V  
Sbjct: 61  LELKSLSDERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQN 120

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI
Sbjct: 121 GRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTN 271
              D+++ A++IL +   +F + +   K  +  +  +       L   +EEL+LSVRS N
Sbjct: 181 KPNDALSFAAKILVEHFKVFESADADTKFSEVMVEKEDDKKEKKLEMTIEELDLSVRSYN 240

Query: 272 CLRGENIVYMGDLIQRT 288
           CL+   I  + +L   T
Sbjct: 241 CLKRAGINTLQELTDMT 257


>gi|332176606|gb|AEE12296.1| DNA-directed RNA polymerase subunit alpha [Porphyromonas
           asaccharolytica DSM 20707]
          Length = 330

 Score =  290 bits (743), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 116/320 (36%), Positives = 190/320 (59%), Gaps = 7/320 (2%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           + +++    ++      +PL  G+A T+GNALRR+L+SSL G AI +++I+GV HE ++I
Sbjct: 10  DSVLMLDASDHYAKFEFKPLEPGYAMTIGNALRRILLSSLEGYAIASIRIEGVEHEFATI 69

Query: 76  KGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDH 132
            GV ED+T IILN+K I  K  +     + +T+   G     AGD+ Q +   +V NPD 
Sbjct: 70  PGVLEDVTHIILNLKQIRFKAAVEDPQEETITLHVTGRNTFQAGDLNQVLTSYKVQNPDL 129

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           VICNL  DA   +EL ++KG GYV ++ +R E+DP+  + ID +Y+PI+KV+ T E+ R 
Sbjct: 130 VICNLAEDADFTIELRINKGRGYVVSEENRREDDPVNTLPIDGIYTPIRKVNQTTEAYRV 189

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV----K 248
            Q  DY+KL + I+TDG+I   +++  A+ IL     +F + E   +  +E+ +     +
Sbjct: 190 DQRTDYEKLVLEIETDGTIHPREALRQAATILISHFALFTDKEFEVELPEEEPDQLLDNQ 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
           ++     L+  +   +LSVR+ NCL+   I  + DL+ R   ++L++ NFG+KSLVEI+ 
Sbjct: 250 TMKVRTQLMTDLATTDLSVRALNCLKAAGISTIADLLSRDRDELLKIKNFGKKSLVEIEQ 309

Query: 309 VLGTMGLFLGMNLPDWPPES 328
            L    L   M+L  +  ++
Sbjct: 310 FLADQDLDFDMDLTPYRLDN 329


>gi|270265489|emb|CBI68381.1| RNA polymerase alpha-subunit [Vibrio tapetis]
 gi|270265491|emb|CBI68382.1| RNA polymerase alpha-subunit [Vibrio tapetis]
          Length = 299

 Score =  290 bits (743), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 131/300 (43%), Positives = 194/300 (64%), Gaps = 8/300 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +G
Sbjct: 3   VDIEQVSATHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEG 62

Query: 78  VHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           V ED+ +I+LN+KG+ +K+  G     +T+ K G G V AGDI    D+E+ NP+HVIC+
Sbjct: 63  VQEDILEILLNLKGLAVKVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICH 122

Query: 137 LDVD-AVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L  D A + M + V +G GYVPA        +  PIG + +DA YSP+ K++Y VE+AR 
Sbjct: 123 LTDDNAEIAMRIKVERGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARV 182

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G++  E+++  ++ IL +QL  F++  + +         +   F
Sbjct: 183 EQRTDLDKLVIDMETNGTLDPEEAIRRSATILAEQLDAFVDLRDIRVPE---EKEEKPEF 239

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G KSL EIK VL +
Sbjct: 240 DPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGNKSLTEIKDVLAS 299


>gi|332144664|dbj|BAK19492.1| RNA polymerase alpha subunit [Lactobacillus sp. YIT 12363]
          Length = 251

 Score =  290 bits (743), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 107/251 (42%), Positives = 162/251 (64%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I    E  N    + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE +++ G
Sbjct: 1   ITKVDEGTNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFTTVDG 60

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+T IILNIK + LK+  D  K V I  +GP  VTA DI    D+EVLNP+  IC +
Sbjct: 61  VLEDVTQIILNIKKLALKLLTDDDKTVEIDVQGPATVTAADIVADGDVEVLNPEQYICTV 120

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
                  + +T+ KG GYV A  ++ ++ PIG++ ID++++PI +V+Y VES R G+  D
Sbjct: 121 AEGGHFHVRMTIKKGRGYVAADQNKVDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRND 180

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL++ + T+GSI   ++++LA++IL + L +F+N  +  K  +  +  +       L 
Sbjct: 181 FDKLTLDVWTNGSINPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLE 240

Query: 258 KKVEELELSVR 268
             +EEL+LSVR
Sbjct: 241 MTIEELDLSVR 251


>gi|219849860|ref|YP_002464293.1| DNA-directed RNA polymerase subunit alpha [Chloroflexus aggregans
           DSM 9485]
 gi|219544119|gb|ACL25857.1| DNA-directed RNA polymerase, alpha subunit [Chloroflexus aggregans
           DSM 9485]
          Length = 318

 Score =  290 bits (743), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 114/311 (36%), Positives = 175/311 (56%), Gaps = 9/311 (2%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
            IE +   +  E+      EPL  G+ HTLGNALRRVL++++ G+AIT V++ GV  E  
Sbjct: 8   KIEVV---EATESFGRFKIEPLDPGYGHTLGNALRRVLLTAIPGSAITHVRVTGVYQETD 64

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
            I GV ED+ ++ILN+KGI+L+   +     TI K+GPGVVTA D+     + V++PDH 
Sbjct: 65  RIPGVTEDMVELILNLKGIHLRGHHEGTVTATIRKQGPGVVTAADLVLPEGLAVVDPDHY 124

Query: 134 ICNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           IC L+   A + +  T+ +G GY+ A        P+G I IDA+++P+ +V+Y VE+ R 
Sbjct: 125 ICTLEHEQAQIELTATIERGRGYLSADQR--GILPLGEIPIDAIFTPVPRVNYIVENTRI 182

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           GQ  D+D+L + + T+G++   D++  A+R+L        NF     E +       L  
Sbjct: 183 GQATDFDRLILEVWTNGTVRPVDALDYAARVLVHYNTTIANFNRMAVEPEAQPETTGLEI 242

Query: 253 NP-ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            P      +E LELS R+ NCL+   I  +G ++Q  E  +L + N G+KS+ EI+  L 
Sbjct: 243 PPSVYDTSIETLELSTRTYNCLKRAEITKIGQVLQMDEKALLSVRNLGQKSMEEIRDKLI 302

Query: 312 TMGL--FLGMN 320
             G    L +N
Sbjct: 303 ERGYIPRLPIN 313


>gi|313887090|ref|ZP_07820789.1| DNA-directed RNA polymerase, alpha subunit [Porphyromonas
           asaccharolytica PR426713P-I]
 gi|312923501|gb|EFR34311.1| DNA-directed RNA polymerase, alpha subunit [Porphyromonas
           asaccharolytica PR426713P-I]
          Length = 330

 Score =  290 bits (742), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 115/320 (35%), Positives = 190/320 (59%), Gaps = 7/320 (2%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           + +++    ++      +PL  G+A T+GNALRR+L+SSL G AI +++I+GV HE ++I
Sbjct: 10  DSVLMLDASDHYAKFEFKPLEPGYAMTIGNALRRILLSSLEGYAIASIRIEGVEHEFATI 69

Query: 76  KGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDH 132
            GV ED+T IILN+K I  K  +     + +T+   G     AGD+ Q +   +V NPD 
Sbjct: 70  PGVLEDVTHIILNLKQIRFKAAVEDPQEETITLHVTGRNTFQAGDLNQVLTSYKVQNPDL 129

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           VICNL  DA   +E+ ++KG GYV ++ +R E+DP+  + ID +Y+PI+KV+ T E+ R 
Sbjct: 130 VICNLAEDADFTIEIRINKGRGYVVSEENRREDDPVNTLPIDGIYTPIRKVNQTTEAYRV 189

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV----K 248
            Q  DY+KL + I+TDG+I   +++  A+ IL     +F + E   +  +E+ +     +
Sbjct: 190 DQRTDYEKLVLEIETDGTIHPREALRQAATILISHFALFTDKEFEVELPEEEPDQLLDNQ 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
           ++     L+  +   +LSVR+ NCL+   I  + DL+ R   ++L++ NFG+KSLVEI+ 
Sbjct: 250 TMKVRTQLMTDLATTDLSVRALNCLKAAGISTIADLLSRDRDELLKIKNFGKKSLVEIEQ 309

Query: 309 VLGTMGLFLGMNLPDWPPES 328
            L    L   M+L  +  ++
Sbjct: 310 FLADQDLDFDMDLTPYRLDN 329


>gi|269997192|gb|ACZ57818.1| RNA polymerase alpha subunit [Vibrio owensii]
 gi|269997194|gb|ACZ57819.1| RNA polymerase alpha subunit [Vibrio owensii]
 gi|269997196|gb|ACZ57820.1| RNA polymerase alpha subunit [Vibrio sp. CAIM 994]
          Length = 294

 Score =  290 bits (742), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 129/300 (43%), Positives = 195/300 (65%), Gaps = 11/300 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H+  +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHNEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294


>gi|303231259|ref|ZP_07317997.1| DNA-directed RNA polymerase, alpha subunit [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302514166|gb|EFL56170.1| DNA-directed RNA polymerase, alpha subunit [Veillonella atypica
           ACS-049-V-Sch6]
          Length = 332

 Score =  290 bits (742), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 124/324 (38%), Positives = 189/324 (58%), Gaps = 18/324 (5%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
            IE + +  E       + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE S
Sbjct: 8   KIEKVDI-AEGGRYGKFVCEPLDRGYGITLGNSLRRILLSSLDGAAITSIKIDGVLHEFS 66

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGP--GVVTAGDI--QTVNDIEVLN 129
           +I G+ ED+TDIILN+K + +K+  D+   + +       GV+TA D+  Q   ++EVLN
Sbjct: 67  TIPGIREDVTDIILNLKQLCIKLEEDAEWPLEVHFDFQKDGVLTAADLAEQFPPEVEVLN 126

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+ VI  +D  A + M++ + +G GYVP+  ++ + D IG I ID+++SPI +  Y V  
Sbjct: 127 PELVIATMDETAHLVMDVVIERGKGYVPSTKNKKDTDVIGCIPIDSIFSPILRAKYEVSD 186

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK-EDINVK 248
            R G  +D+DKL++ + TDGSIT  D+VA ++ I+   LG F         V+ +D N++
Sbjct: 187 VRVGNEMDFDKLTLEVWTDGSITAADAVAKSAAIMIGYLGNFTKLAHSTSVVELDDQNLE 246

Query: 249 SLPFNPALLK----------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
               +P               ++ELELSVR+ NCL+   I  + DL+ +T  D+ ++ N 
Sbjct: 247 GDVVDPTPQDVQEDDGPAKISIDELELSVRAYNCLKRAGINTIADLLDKTIDDLGKVRNL 306

Query: 299 GRKSLVEIKGVLGTM--GLFLGMN 320
           G+KS+ EI   L     G  L   
Sbjct: 307 GKKSIDEIAEKLSNHPGGFSLKQK 330


>gi|258646025|ref|ZP_05733494.1| DNA-directed RNA polymerase, alpha subunit [Dialister invisus DSM
           15470]
 gi|260403397|gb|EEW96944.1| DNA-directed RNA polymerase, alpha subunit [Dialister invisus DSM
           15470]
          Length = 326

 Score =  289 bits (741), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 126/312 (40%), Positives = 184/312 (58%), Gaps = 14/312 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
             +         PL RG+  TLGN+LRRVL+SSL G AIT++ IDGV HE S++ GV ED
Sbjct: 15  SADGRYGKFECGPLERGYGITLGNSLRRVLLSSLDGVAITSINIDGVEHEFSTVPGVRED 74

Query: 82  LTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           +TD+ILN+K I      ++    +V +     GV+ AGD+Q  ++I+VLN D  +C LD 
Sbjct: 75  VTDMILNLKKIRFIAYEEAEFPIKVRVDVTKEGVLLAGDLQLPSEIDVLNGDLALCTLDT 134

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           +A + MELT+ +GHGYVP   +R E+DPIG I ID++YSP+ K +Y V   R G  +DYD
Sbjct: 135 EAHLGMELTIDRGHGYVPFTKNRREDDPIGSIPIDSIYSPVVKCNYNVSDTRVGNEMDYD 194

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINF-EEPKKEVKEDINVKSLPFNPALLK 258
           KL++ ++TDGSI   D+VA A+ IL +   +F      P  E ++  ++     +    +
Sbjct: 195 KLTLELETDGSIKASDAVATAATILMNCFELFRPLATGPILEARDGSDMARQSSDQQAEE 254

Query: 259 --------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                    +EELELSVR+ NCL+   I  +  L ++TE ++ R+ N G+KS+ EI   L
Sbjct: 255 EKIDLSGIPIEELELSVRAFNCLKRAEINTLDQLAEKTEEELGRVRNLGKKSIDEIIEKL 314

Query: 311 GT---MGLFLGM 319
                +GL L  
Sbjct: 315 AQFRGLGLHLKD 326


>gi|162446984|ref|YP_001620116.1| DNA-directed RNA polymerase subunit alpha [Acholeplasma laidlawii
           PG-8A]
 gi|161985091|gb|ABX80740.1| DNA-directed RNA polymerase, alpha subunit [Acholeplasma laidlawii
           PG-8A]
          Length = 330

 Score =  289 bits (739), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 119/332 (35%), Positives = 193/332 (58%), Gaps = 11/332 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP ++E I    +E N    + +PL RG+  TLGNALRRVL+SSL GAAI  V+I+G
Sbjct: 5   KFEKPTSVEEI---SQEGNLGRFLIKPLERGYGLTLGNALRRVLLSSLPGAAIVNVKIEG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDS---HKRVTIFKRGPGVVTAGDIQTVND 124
           V HE S+I+GV+ED+  I+LN+K +   +        +++ ++  GP V+TAGD    +D
Sbjct: 62  VEHEFSTIEGVYEDVMGIVLNLKKVVFSVDSQDPQYEQQLELYAEGPAVITAGDFNLADD 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT-ENDPIGLITIDALYSPIKKV 183
           IEV+N D  I  L   A   M +TV +G GYVPA  ++      + +I ID+LY+P+++V
Sbjct: 122 IEVVNKDQHIATLAEGAKFNMTVTVRRGIGYVPADQNKQYSKYELNVIPIDSLYTPVERV 181

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
            Y+VE  R     D D+L++ I+T+G+I  ++++ALAS++L D   + ++  E   E   
Sbjct: 182 IYSVEKTR----GDLDELTIEIETNGAILAKEALALASKMLVDHFQVLVDISEKASEFDF 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             +++  P +     K+E+L+LSVR  N L+   I  +G+L++ +E +++R+ + GRKS 
Sbjct: 238 IRDIEEEPASKKSDTKIEQLDLSVRLFNSLKRSGITTVGELLKLSEEEVMRLRSLGRKSF 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
            E+K  L   GL    +         +    K
Sbjct: 298 KELKEKLAEHGLEFEHSTSKEARFGFDSDEDK 329


>gi|303230143|ref|ZP_07316912.1| DNA-directed RNA polymerase, alpha subunit [Veillonella atypica
           ACS-134-V-Col7a]
 gi|302515204|gb|EFL57177.1| DNA-directed RNA polymerase, alpha subunit [Veillonella atypica
           ACS-134-V-Col7a]
          Length = 332

 Score =  289 bits (739), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 122/315 (38%), Positives = 187/315 (59%), Gaps = 16/315 (5%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
            IE + +  E       + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE S
Sbjct: 8   KIEKVDI-AEGGRYGKFVCEPLDRGYGITLGNSLRRILLSSLDGAAITSIKIDGVLHEFS 66

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGP--GVVTAGDI--QTVNDIEVLN 129
           +I G+ ED+TDIILN+K + +K+  D+   + +       GV+TA D+  Q   ++EVLN
Sbjct: 67  TIPGIREDVTDIILNLKQLCIKLEEDAEWPLEVHFDFQKDGVLTAADLAEQFPPEVEVLN 126

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+ VI  +D  A + M++ + +G GYVP+  ++ + D IG I ID+++SPI +  Y V  
Sbjct: 127 PELVIATMDETAHLVMDVVIERGKGYVPSTKNKKDTDVIGCIPIDSIFSPILRAKYEVSD 186

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK-EDINVK 248
            R G  +D+DKL++ + TDGSIT  D+VA ++ I+   LG F         V+ +D N++
Sbjct: 187 VRVGNEMDFDKLTLEVWTDGSITAADAVAKSAAIMIGYLGNFTKLAHSTSVVELDDQNLE 246

Query: 249 SLPFNPALLK----------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
               +P               ++ELELSVR+ NCL+   I  + DL+ +T  D+ ++ N 
Sbjct: 247 GDVVDPTPQDVQEDDGPAKISIDELELSVRAYNCLKRAGINTIADLLDKTIDDLGKVRNL 306

Query: 299 GRKSLVEIKGVLGTM 313
           G+KS+ EI   L   
Sbjct: 307 GKKSIDEIAEKLSNH 321


>gi|323144991|ref|ZP_08079551.1| DNA-directed RNA polymerase, alpha subunit [Succinatimonas hippei
           YIT 12066]
 gi|322415270|gb|EFY06044.1| DNA-directed RNA polymerase, alpha subunit [Succinatimonas hippei
           YIT 12066]
          Length = 329

 Score =  289 bits (739), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 134/331 (40%), Positives = 195/331 (58%), Gaps = 16/331 (4%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            +L++PN  E + L +   N + +I EP  + +A  LG ALRR+++SS+ G AIT V+ID
Sbjct: 5   TDLLRPNIKEVVTLSR---NVSRVILEPFEQHYAQVLGTALRRIMLSSIPGYAITEVEID 61

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVND 124
           GV+HE S+++GV ED+  I+LN+K + +  +        + I K G G VTA DIQ    
Sbjct: 62  GVVHEYSALEGVQEDILLILLNLKEVAVFSATIPQHDPVLEINKSGIGTVTAADIQCPGG 121

Query: 125 IEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHHRT----ENDPIGLITIDALYSP 179
           IE+ NP+ V+C++ D    +RM L V++G GYVPA  H      E+  IG + +DA Y P
Sbjct: 122 IEIRNPELVLCHITDEKTNLRMRLHVTRGRGYVPAVTHPHIEGAEDRFIGRLLLDASYCP 181

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +  V+       +G     ++L + I+T+G+I   D+V  A+ I  DQL  F++      
Sbjct: 182 VLNVAVHTAPLNDG----QEQLILDIETNGTIDPSDAVCSAATIFADQLNSFVDIRNSVA 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
               D        +P LL  VE+LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G
Sbjct: 238 PA--DDASFKPLIDPKLLCPVEDLELTVRSANCLKAEGIKYIGDLVQRTEVELLKTPNLG 295

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           +KSL EIK VL   GL LGM L +WPP  +E
Sbjct: 296 KKSLTEIKDVLAERGLSLGMRLENWPPADLE 326


>gi|288818044|ref|YP_003432391.1| DNA-directed RNA polymerase alpha subunit [Hydrogenobacter
           thermophilus TK-6]
 gi|288787443|dbj|BAI69190.1| DNA-directed RNA polymerase alpha subunit [Hydrogenobacter
           thermophilus TK-6]
 gi|308751645|gb|ADO45128.1| DNA-directed RNA polymerase, alpha subunit [Hydrogenobacter
           thermophilus TK-6]
          Length = 316

 Score =  289 bits (739), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 113/322 (35%), Positives = 181/322 (56%), Gaps = 10/322 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q+   E + P+ + +   G+        + EPL RGF  TLGN+LRR L+SS++G AIT
Sbjct: 1   MQR---EFLFPSKVYWEERGK---TYGRFVVEPLERGFGITLGNSLRRTLLSSIQGTAIT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           AV+I G+ HE S I+GV ED+ ++I N+K I   +     + + + K+G G VTA DI  
Sbjct: 55  AVKIYGIYHEFSPIEGVQEDVLEVIANLKKIRFNLKSSDVETLYLKKKGEGTVTAKDITC 114

Query: 122 VNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             +++++NPD  I  +   +  + ME+ + +G GY+  +      + +G I +DA +SP+
Sbjct: 115 PPNVDIINPDQKIATITDPNKELNMEIRIERGFGYMTTEEMEVIGE-VGWILVDADFSPV 173

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++VS+ VE  R  +  DYD+L M I T+G+ T E+ V  A  IL        +       
Sbjct: 174 RQVSFRVEKTRVEKRSDYDRLIMEIYTNGTKTPEEVVKEAISILVKYFSSLEHISYELPV 233

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V+E + V        L   VEEL++S R+ N ++   I  +GDL++ +E D+    N GR
Sbjct: 234 VEEPVIVDEFA--EKLSLPVEELDVSQRALNSIKRMGINTIGDLVRLSEEDLKGTKNVGR 291

Query: 301 KSLVEIKGVLGTMGLFLGMNLP 322
           K++ EIK  L  MGL+LGM++ 
Sbjct: 292 KAINEIKEALKQMGLYLGMDIE 313


>gi|114107164|ref|YP_740149.1| RNA polymerase alpha subunit [Daucus carota]
 gi|122239960|sp|Q0G9T0|RPOA_DAUCA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|113200939|gb|ABI32455.1| RNA polymerase alpha subunit [Daucus carota]
          Length = 353

 Score =  289 bits (739), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 89/348 (25%), Positives = 166/348 (47%), Gaps = 26/348 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +  + +N        I  PL +G A T+G ++RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESKADNKRLYYGRFILSPLMKGQADTIGISMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S++ G+ E + DI++N+K I L+ +       +I  RGPG VTA DI     +EV+
Sbjct: 71  PHEYSTLVGIQESVHDILMNLKEIVLRSNLYGTCDASICVRGPGYVTAQDIILPPYVEVV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY+    +   N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIELCIGLQIERNRGYLIKTPNN--NSKDGSYPIDAVFMPVRNANHSIH 188

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    +  + ++ 
Sbjct: 189 SYGNG-NDKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHTEEENLHLANNQHMV 247

Query: 249 SLPF----------------NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            LP                        +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 248 PLPPFTFHDKLDKLRKNKKKRALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDL 307

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
           +++ +F  K   ++K +LG +     +NL   P    E LA+  + K 
Sbjct: 308 MKIEHFRIK---DVKQILGILEKNFSINLGKKPKMGFESLAQLIDSKS 352


>gi|163783137|ref|ZP_02178131.1| DNA-directed RNA polymerase alpha subunit [Hydrogenivirga sp.
           128-5-R1-1]
 gi|159881471|gb|EDP74981.1| DNA-directed RNA polymerase alpha subunit [Hydrogenivirga sp.
           128-5-R1-1]
          Length = 316

 Score =  288 bits (738), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 130/317 (41%), Positives = 188/317 (59%), Gaps = 7/317 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E + PN I +    Q+E+N+ + + EPL RGF  TLGNALRRVL+SS+ G A+TAV+I 
Sbjct: 3   NEFVFPNKIYW---EQKEDNKGVFVVEPLERGFGTTLGNALRRVLLSSISGTAVTAVKIY 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV HE SS++GV ED+ +II NIKG+   +     + + + K+G G V AGDI    ++E
Sbjct: 60  GVYHEFSSLEGVAEDVVEIIANIKGVRFTLKDSDVEVLYLKKKGEGEVKAGDISLPPNVE 119

Query: 127 VLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           V NPD VI  +   +     E+ + +G GYV A+   T  +  G I +DA +SP+K VSY
Sbjct: 120 VANPDKVIATITDPEVEFNAEIRIERGKGYVLAEEMETIGE-TGWILLDADFSPVKLVSY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            +E  R G+  DY+KL++ + TDG+ + E  V  A  ILQ  L +  +       ++E I
Sbjct: 179 RIEQTRVGEKTDYEKLTVEVLTDGTKSPEAVVKEAVDILQRHLSLLEHISYEVPTLEEPI 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            V  L  +  L   +EEL++S R+ N L+   I  +GDL+Q TE ++    N GRK+L E
Sbjct: 239 PVDEL--SEKLTLSIEELDISQRALNSLKRMGITTIGDLVQMTEEELKSTKNIGRKALAE 296

Query: 306 IKGVLGTMGLFLGMNLP 322
           IK  L  MGL LG+N+ 
Sbjct: 297 IKEALKQMGLQLGINIE 313


>gi|58416046|emb|CAH57437.1| RNA polymerase alpha-subunit [Vibrio sp. R-21434]
 gi|58416048|emb|CAH57438.1| RNA polymerase alpha-subunit [Vibrio sp. R-21435]
 gi|58416050|emb|CAH57439.1| RNA polymerase alpha-subunit [Vibrio sp. R-21439]
          Length = 293

 Score =  288 bits (738), Expect = 7e-76,   Method: Composition-based stats.
 Identities = 128/299 (42%), Positives = 194/299 (64%), Gaps = 11/299 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H+  +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHNEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KS
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKS 293


>gi|328813981|gb|AEB52106.1| DNA-directed RNA polymerase alpha chain [Lactobacillus helveticus]
          Length = 249

 Score =  288 bits (738), Expect = 7e-76,   Method: Composition-based stats.
 Identities = 109/249 (43%), Positives = 157/249 (63%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T II
Sbjct: 1   YGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKII 60

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+K + LK   D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME
Sbjct: 61  LNLKKLELKSFSDERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHME 120

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           + V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I 
Sbjct: 121 IAVQNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIW 180

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           TDGSI   D+++ A++IL +   +F + +   K  +  +  +       L   +EEL+LS
Sbjct: 181 TDGSIKPNDALSFAAKILVEHFKVFESADADTKFSEVMVEKEDDKKEKKLEMTIEELDLS 240

Query: 267 VRSTNCLRG 275
           VRS NCL+ 
Sbjct: 241 VRSYNCLKR 249


>gi|58416044|emb|CAH57436.1| RNA polymerase alpha-subunit [Vibrio sp. R-21433]
          Length = 294

 Score =  288 bits (737), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 129/300 (43%), Positives = 194/300 (64%), Gaps = 11/300 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294


>gi|150036782|emb|CAM98034.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. dextranicum]
          Length = 248

 Score =  288 bits (737), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 104/248 (41%), Positives = 158/248 (63%), Gaps = 2/248 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T 
Sbjct: 61  KKVVLAIDSDDERSLEIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTA 120

Query: 150 SKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T
Sbjct: 121 VKGRGYTSADENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +GSI   D+++L ++IL + LG+F++      E    +  + +  + +    +E+L+LSV
Sbjct: 181 NGSIKPSDALSLGAKILAEHLGLFMDISPVAAEASVMVEAEPVAASASDSAPIEDLDLSV 240

Query: 268 RSTNCLRG 275
           RS NCL+ 
Sbjct: 241 RSYNCLKR 248


>gi|153812445|ref|ZP_01965113.1| hypothetical protein RUMOBE_02844 [Ruminococcus obeum ATCC 29174]
 gi|149831370|gb|EDM86458.1| hypothetical protein RUMOBE_02844 [Ruminococcus obeum ATCC 29174]
          Length = 276

 Score =  288 bits (737), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 114/271 (42%), Positives = 178/271 (65%), Gaps = 4/271 (1%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFK 108
           ++SSL GAA++ V+IDGVLHE SSI GV ED+++II+N+K + +K +   +  K   I  
Sbjct: 1   MLSSLPGAAVSQVKIDGVLHEFSSIPGVKEDVSEIIMNLKSLAIKNNSADNEPKTAYIEC 60

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLD--VDAVVRMELTVSKGHGYVPAKHHRTEND 166
            G GVVTA DIQ   DIE++NPD VI  L+   D  + MELT+++G GYV A   +T++ 
Sbjct: 61  EGKGVVTAADIQADQDIEIMNPDQVIATLNGGKDCRLAMELTITRGRGYVSADKGKTDDM 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           PIG++ +DA+Y+P+ +V+  V++ R GQ+ DYDKL++ + T+G++  +++V+LA+++L +
Sbjct: 121 PIGVLAVDAIYTPVDRVNMIVQNTRVGQITDYDKLTLDVYTNGTLDPDEAVSLAAKVLSE 180

Query: 227 QLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQ 286
            L +FI+  E  K  +  I  +       L   ++ELELSVRS NCL+   I  + +L  
Sbjct: 181 HLSLFIDLSENAKTAEVMIEKEDNEKEKVLEMSIDELELSVRSYNCLKRAGINTVEELCN 240

Query: 287 RTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +T  DM+++ N GRKSL E+   L  +GL L
Sbjct: 241 KTSDDMMKVRNLGRKSLEEVLAKLKELGLQL 271


>gi|225850763|ref|YP_002730997.1| DNA-directed RNA polymerase subunit alpha [Persephonella marina
           EX-H1]
 gi|225646203|gb|ACO04389.1| DNA-directed RNA polymerase, alpha subunit [Persephonella marina
           EX-H1]
          Length = 324

 Score =  288 bits (737), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 129/322 (40%), Positives = 185/322 (57%), Gaps = 6/322 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E I P+ I +     + E+   +  EPL RG+  TLGNALRRVL+SSL G A+TAV+I G
Sbjct: 5   EFITPSKIYWDE-SSKTESFGRLYVEPLERGYGITLGNALRRVLLSSLEGGAVTAVKIHG 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           V HE ++I+GV ED+++IILN+K I  KM          +  +G G VTA DI+    I+
Sbjct: 64  VAHEFTTIEGVIEDVSEIILNLKQIKFKMDEGIDSDFAILEFKGTGEVTAKDIKVPAGIK 123

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           ++NPD  I  +D +  +RMEL + KG GYV  +      + IG I ID  +SPIKK ++ 
Sbjct: 124 IVNPDVHIATVDKEIELRMELKIEKGRGYVMVEEMEPPTE-IGWIPIDTAFSPIKKCTFY 182

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV---KE 243
           VE  R G+  +YDKL + + TDGSIT E+++  A+ IL +   + +N    K EV    E
Sbjct: 183 VEPTRVGEKTNYDKLILEVTTDGSITPEEALTKATNILIEHFQLLLNPTVRKVEVIKKAE 242

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             ++        L   +EELE+S R+TN L+   I  +GDL++ TE D+    + GRK+L
Sbjct: 243 PESIAEKIEADKLSLAIEELEISSRATNTLKKLGIQTIGDLVKMTEEDLKEAKSIGRKAL 302

Query: 304 VEIKGVLGTMGLFLGMNLPDWP 325
            EIK  L  +GL L  +     
Sbjct: 303 KEIKEALAELGLELAPSPTKKD 324


>gi|11467399|ref|NP_043256.1| RNA polymerase alpha subunit [Cyanophora paradoxa]
 gi|1350840|sp|P48118|RPOA_CYAPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1016200|gb|AAA81287.1| alpha subunit of RNA polymerase [Cyanophora paradoxa]
          Length = 315

 Score =  288 bits (736), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 100/311 (32%), Positives = 167/311 (53%), Gaps = 10/311 (3%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             +E  V     +     I EPL  G   T+GN+LRRVL+S + G+AITAV+I GV HE 
Sbjct: 7   ECVESKVESSCNQ-YGRFIVEPLEPGQGITIGNSLRRVLLSDIEGSAITAVRIAGVNHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
            SI GV ED+ +++LN+K I LK   +  +   +  +G   VT  + +  +++E+++   
Sbjct: 66  CSIPGVKEDVLELLLNLKNIVLKSYTNEPQIGRLKIQGACKVTTANFELPSEVEIIHGTQ 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            +  +  +A++ ME  + KG GY      +TEN  I  + IDA++ P++KV+Y VE    
Sbjct: 126 YVATVAENAILEMEFKIEKGRGYKIIDKKQTEN-SIDFLPIDAIFMPVRKVNYMVEEIFL 184

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
                 ++L + I  +GS+T +DS++ A+ +L +    F      K   +   +      
Sbjct: 185 RNSEIKERLILEIWRNGSVTPQDSISQAAEVLLNLFNPF-----KKINFENTDDSTEQTE 239

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +      +EEL+LSVR+ NCL+   I  +GDL+  ++ ++L + NFG+KS  E+   L  
Sbjct: 240 DKISQIPIEELQLSVRAYNCLKRAQIHSIGDLLNVSQEELLEIRNFGQKSAKEVIDAL-- 297

Query: 313 MGLFLGMNLPD 323
               LG++LP 
Sbjct: 298 -QKRLGISLPK 307


>gi|313892870|ref|ZP_07826447.1| DNA-directed RNA polymerase, alpha subunit [Veillonella sp. oral
           taxon 158 str. F0412]
 gi|313442223|gb|EFR60638.1| DNA-directed RNA polymerase, alpha subunit [Veillonella sp. oral
           taxon 158 str. F0412]
          Length = 334

 Score =  288 bits (736), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 119/317 (37%), Positives = 183/317 (57%), Gaps = 18/317 (5%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
            IE + +          + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE S
Sbjct: 8   KIEKVDIADG-GRYGKFVCEPLDRGYGITLGNSLRRILLSSLDGAAITSIKIDGVLHEFS 66

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGP--GVVTAGDI--QTVNDIEVLN 129
           +I G+ ED+TDIILN+K + +K+  D+   + +       GV+TA D+  Q   ++EVLN
Sbjct: 67  TIPGIREDVTDIILNLKQLCIKVEEDAQLPLEVHFDFQKDGVLTAADLAEQFPPEVEVLN 126

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+ VI  +D  A + M++ + +G GYVP+  ++ + D IG I ID+++SPI +  Y V  
Sbjct: 127 PELVIATMDETAHLVMDVVIERGKGYVPSTKNKKDTDVIGCIPIDSIFSPILRAKYEVSD 186

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI---- 245
            R G  +D+DKL++ + TDGSIT  D+VA ++ I+   LG F         V  +     
Sbjct: 187 VRVGNEMDFDKLTLEVWTDGSITAADAVAKSAAIMIGYLGNFTKLAHSADVVDVNTGEGG 246

Query: 246 ---------NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
                    N +    +      ++ELELSVR+ NCL+   I  + DL+ +T  D+ ++ 
Sbjct: 247 IVVDPVGSDNEEPAVDDGPAKISIDELELSVRAYNCLKRAGINTIADLLDKTIDDLGKVR 306

Query: 297 NFGRKSLVEIKGVLGTM 313
           N G+KS+ EI+  L   
Sbjct: 307 NLGKKSIDEIEEKLNNH 323


>gi|313158337|gb|EFR57739.1| DNA-directed RNA polymerase, alpha subunit [Alistipes sp. HGB5]
          Length = 330

 Score =  288 bits (736), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 115/324 (35%), Positives = 184/324 (56%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP  +   ++ +   +       PL  GF  T+GNALRR+L+SSL G AIT V++ GV
Sbjct: 6   FQKPEKV---IMLESTSSFGKFEFRPLEPGFGMTVGNALRRILLSSLEGYAITTVKVAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINL--KMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDI 125
            HE ++I GV ED+  IILN+K +     +     ++V+I   G   +TAG I   ++  
Sbjct: 63  DHEFAAIPGVMEDMLKIILNLKQVRFIRTVDNQDAEKVSINVAGVTELTAGYISNYLSFF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNPD VIC+L     ++M LT+ KG GYVPA+ +       G + ID++++PIK V Y
Sbjct: 123 KVLNPDLVICHLAPGTKMQMTLTIGKGRGYVPAEENTPAECEFGTLPIDSIFTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL++ I TDGSI  ++++  A++IL     +F    I         
Sbjct: 183 SIENYRVEQKTDYEKLNLEITTDGSIHPKEALKEAAKILIQHFMLFSDEKITVNMEDTNG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ +   L     L  K+ + +LSVR+ NCL+  ++  +GDL++    D+L+  NFG+K
Sbjct: 243 AEEFDEDVLHMRQLLKTKLSDQDLSVRALNCLKAADVDTVGDLVKLNRNDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  GM++  + 
Sbjct: 303 SLTELDELLTSLNLKFGMDVSIYK 326


>gi|195952671|ref|YP_002120961.1| DNA-directed RNA polymerase subunit alpha [Hydrogenobaculum sp.
           Y04AAS1]
 gi|229564248|sp|B4U772|RPOA_HYDS0 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|195932283|gb|ACG56983.1| DNA-directed RNA polymerase, alpha subunit [Hydrogenobaculum sp.
           Y04AAS1]
          Length = 319

 Score =  288 bits (736), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 111/317 (35%), Positives = 181/317 (57%), Gaps = 7/317 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
            +E I P  I +    ++++N    + EPL RG+  T+GNALRRVL+SS+ G+AITAV+I
Sbjct: 1   MKEFIFPMKIYW---EEKDKNYGRFVVEPLERGYGTTIGNALRRVLLSSIYGSAITAVKI 57

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           +GV HE S+I+GV ED+  II N+K +   +     + + + K  PGVV A DI+T  ++
Sbjct: 58  EGVQHEFSTIEGVQEDVLQIIANLKNVRFDLKDSDLEILYLEKNAPGVVLASDIKTPPNV 117

Query: 126 EVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            ++N D  I  ++  +  ++ME+ + +G GYV +       +  G + +DA +SPIK  +
Sbjct: 118 TIINKDAYIATINSANTTLKMEIRIERGKGYVMSDEMEQIGE-AGWVVLDADFSPIKVAA 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + VE+ R G   DYDKL+  + T+G ++ + ++  A  ++   + M  N       + E 
Sbjct: 177 FRVEATRVGDRTDYDKLTFELTTNGVVSPDTAIQQAVELIVKHMNMLTNISYEVPTLPEP 236

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +    L     L   +EEL++S R+ N L+   +  +G+L+Q TE ++    N GRK+L 
Sbjct: 237 MPPDELM--EKLTFSIEELDISQRALNSLKRIGVTTIGELVQLTEDELKSSKNIGRKALT 294

Query: 305 EIKGVLGTMGLFLGMNL 321
           EIK  L  MG  LGMN+
Sbjct: 295 EIKEALKNMGFSLGMNI 311


>gi|329565841|gb|AEB92257.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
 gi|329565847|gb|AEB92260.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
 gi|329565849|gb|AEB92261.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
 gi|329565851|gb|AEB92262.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
 gi|329565859|gb|AEB92266.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
          Length = 250

 Score =  288 bits (736), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 109/250 (43%), Positives = 161/250 (64%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL+SSL GAA  +V+IDGVLHE S++ GV ED+ +IILN+K + +K+  D    
Sbjct: 1   GNSLRRVLLSSLPGAAPKSVKIDGVLHEFSTLPGVKEDVVEIILNLKEVAVKLHSDEPVV 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
             I   G G VTAG I+   DIE+LNPDH I  L  D  + ME+   KG GYVP+  ++ 
Sbjct: 61  GRIDVEGKGEVTAGHIKGSADIEILNPDHHIATLSDDGKLHMEIVFVKGKGYVPSDKNKE 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
            N PIG+I +D++++P+K+VSY V++ R G V DYDKL++ + T+G+IT ++++++AS +
Sbjct: 121 PNQPIGVIPVDSIFTPVKRVSYNVKNTRVGHVTDYDKLTLEVWTNGTITPKEAISMASDM 180

Query: 224 LQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGD 283
           L      FI+F    K     ++         L   +EEL+LSVRS NCL+   I  + +
Sbjct: 181 LIKYFQKFISFTGEYKSSDIFVDKPEKKVEKPLDMTIEELDLSVRSYNCLKRAGINTVQE 240

Query: 284 LIQRTEADML 293
           L Q+TE +M+
Sbjct: 241 LTQKTEEEMM 250


>gi|261752517|ref|ZP_05996226.1| DNA-directed RNA polymerase subunit alpha [Brucella suis bv. 5 str.
           513]
 gi|261742270|gb|EEY30196.1| DNA-directed RNA polymerase subunit alpha [Brucella suis bv. 5 str.
           513]
          Length = 244

 Score =  288 bits (736), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 163/244 (66%), Positives = 203/244 (83%), Gaps = 1/244 (0%)

Query: 96  MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY 155
           M G+  KR+ + K GPGVVTAGDIQTV D+E+LNP+HVIC LD  A +RME TV+ G GY
Sbjct: 1   MEGEGPKRMVVRKEGPGVVTAGDIQTVGDVEILNPEHVICTLDEGAEIRMEFTVNTGKGY 60

Query: 156 VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
           VPA  +R E+ PIGLI +D+LYSP++KVSY +E+ REGQVLDYDKL++ I+T+GS+TGED
Sbjct: 61  VPADRNRAEDAPIGLIPVDSLYSPVRKVSYKIENTREGQVLDYDKLTLNIETNGSVTGED 120

Query: 216 SVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRG 275
           +VA A+RILQDQL +F+NFEEP+KE  ++  V  L FNPALLKKV+ELELSVRS NCL+ 
Sbjct: 121 AVAYAARILQDQLSIFVNFEEPQKEAPQEQ-VAELAFNPALLKKVDELELSVRSANCLKN 179

Query: 276 ENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
           +NIVY+GDLIQ+TEA+MLR  NFGRKSL EIK VL +MGL LGM +P WPPE+IE+LAK+
Sbjct: 180 DNIVYIGDLIQKTEAEMLRTPNFGRKSLNEIKEVLASMGLHLGMEIPAWPPENIEDLAKR 239

Query: 336 YEDK 339
           YED+
Sbjct: 240 YEDQ 243


>gi|269837094|ref|YP_003319322.1| DNA-directed RNA polymerase, alpha subunit [Sphaerobacter
           thermophilus DSM 20745]
 gi|269786357|gb|ACZ38500.1| DNA-directed RNA polymerase, alpha subunit [Sphaerobacter
           thermophilus DSM 20745]
          Length = 340

 Score =  287 bits (735), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 121/321 (37%), Positives = 183/321 (57%), Gaps = 12/321 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ +P     +       N      EPL  G+  T+GNALRR+L+ SL G AI  V+I  
Sbjct: 3   EIARPR----VQQTHAGVNYGRFEIEPLEPGYGITIGNALRRILLRSLPGTAIVRVRIAD 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQTVNDI 125
           V HE S+I+GV ED+T+I+LN+K + LK   +S    R +++ +G GVV AGDI    D+
Sbjct: 59  VWHEFSTIEGVREDVTEIVLNLKRVRLKALTESFREGRASLYAQGEGVVRAGDIDWPGDV 118

Query: 126 EVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           EV+NP+HVI  LD  DA + M+L +++G GY PA+    E   IG I +DA+++PI+KV+
Sbjct: 119 EVVNPEHVIATLDNDDARLEMDLVIARGRGYQPAET--QEIYTIGEIPVDAIFTPIEKVN 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE  R GQ+ DYD+L + I TDG+I   D+++ A++IL D   +  +F     E +E+
Sbjct: 177 YVVEHTRVGQMTDYDRLIIEIITDGTIEPADALSEAAQILVDHARLIADFNREPSEPEEE 236

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
            +      +    + + EL LS R  N LR   I  +G ++   +  +L + NFG +SL 
Sbjct: 237 EDKTPSIVD---NRPLAELGLSPRVLNALRSRQIERVGQVLSLPQEQLLSIRNFGPRSLQ 293

Query: 305 EIKGVLGTMGLFLGMNLPDWP 325
           E++  L   G  L M+     
Sbjct: 294 ELRERLAEHGYTLAMDAEKKD 314


>gi|157493235|gb|ABV57983.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493237|gb|ABV57984.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 289

 Score =  287 bits (735), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 127/289 (43%), Positives = 192/289 (66%), Gaps = 8/289 (2%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
                 +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ 
Sbjct: 2   STTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDIL 61

Query: 84  DIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDA 141
           +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L   +A
Sbjct: 62  EILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNA 121

Query: 142 VVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M + V +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D 
Sbjct: 122 AIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDL 181

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+
Sbjct: 182 DKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLR 238

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK
Sbjct: 239 PVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIK 287


>gi|328813975|gb|AEB52103.1| DNA-directed RNA polymerase alpha chain [Lactobacillus fermentum]
          Length = 248

 Score =  287 bits (735), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 111/248 (44%), Positives = 167/248 (67%), Gaps = 2/248 (0%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRRV+++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K
Sbjct: 1   VVEPLERGYGTTLGNSLRRVMLASLPGAAITSIQIDGVLHEFSTVQGVTEDVTQIILNLK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            + LK+  +  K + I  +GP  VTA DIQ   D+ +LN D  I  +   A + +++T  
Sbjct: 61  QVALKIDSEDAKDLEIDVKGPAEVTAADIQGDGDVTILNSDLHIATVSDGAELHVKMTAD 120

Query: 151 KGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           KG GY  A  ++T  E   IG++ ID++Y+PI++V+YTVE+ R GQ  DYDKL++ + T+
Sbjct: 121 KGRGYSSADDNKTRMEGLAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYDKLTLDVWTN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           GS+T  ++++LA++IL + L MF+N  E  +  +  +  +       L K +EEL+LSVR
Sbjct: 181 GSLTPTEAISLAAKILTEHLTMFVNLTEEAQVTQVMVEREETHQEKVLDKTIEELDLSVR 240

Query: 269 STNCLRGE 276
           S NCL+  
Sbjct: 241 SYNCLKRA 248


>gi|255067433|ref|ZP_05319288.1| DNA-directed RNA polymerase, alpha subunit [Neisseria sicca ATCC
           29256]
 gi|255048228|gb|EET43692.1| DNA-directed RNA polymerase, alpha subunit [Neisseria sicca ATCC
           29256]
          Length = 278

 Score =  287 bits (735), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 134/280 (47%), Positives = 185/280 (66%), Gaps = 6/280 (2%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           + G A T V I GVLHE S++ GV ED+ DI+LN+KGI  K+ G    ++T+ K G GVV
Sbjct: 1   MNGFAPTEVAISGVLHEYSTVDGVQEDVVDILLNVKGIVFKLHGRGQVQLTLRKSGAGVV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLI 171
            AGDI+  +D+E+LNP+H+IC+L  +  + ME+ V +G GY         R EN  IG I
Sbjct: 61  VAGDIELPHDVEILNPEHIICHLAENGQIEMEIKVEQGRGYQSVSGRRVVRDENRQIGAI 120

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA +SPI +VS+ VE AR  Q  D DKL + I+TDGSI  E++V  A+RIL DQ+ +F
Sbjct: 121 QLDASFSPISRVSFEVEPARVEQRTDLDKLVLDIETDGSIDPEEAVRSAARILIDQMSIF 180

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
            +    +    E++  K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE +
Sbjct: 181 ADL---QGTPVEEVEEKAPPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETE 237

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +L+  N GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 238 LLKTPNLGRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 277


>gi|58415944|emb|CAH57386.1| RNA polymerase alpha-subunit [Vibrio mytili]
          Length = 294

 Score =  287 bits (735), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 128/300 (42%), Positives = 194/300 (64%), Gaps = 11/300 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GY+PA    H   +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYIPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294


>gi|260909777|ref|ZP_05916471.1| DNA-directed RNA polymerase subunit alpha [Prevotella sp. oral
           taxon 472 str. F0295]
 gi|260636202|gb|EEX54198.1| DNA-directed RNA polymerase subunit alpha [Prevotella sp. oral
           taxon 472 str. F0295]
          Length = 330

 Score =  287 bits (735), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 121/324 (37%), Positives = 192/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  +        PL  GF  T+GN+LRR+L+SSL G +I  V+I GV
Sbjct: 6   FQKPDKV---VMLEANDKFGRFEFRPLEPGFGVTIGNSLRRILLSSLEGFSINTVRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFENEKVSITVENTTEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VIC+LD  A ++++LT++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPDLVICHLDAKASLQIDLTINKGRGYVPADENREFCTDVNVIPIDSIYTPIRNVRY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEV 241
           +VE  R  Q  DYDKL + + TDGSI+ +D++  A++IL     +F +     E    + 
Sbjct: 183 SVEPYRVEQKTDYDKLIIDVTTDGSISPKDALKEAAKILIYHFMLFSDEKIAVENQDVDT 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ ++ LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKTKLVDMNLSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L  + L  G ++  + 
Sbjct: 303 SLTELDDLLLGLNLSFGTDISKYK 326


>gi|288929313|ref|ZP_06423158.1| DNA-directed RNA polymerase, alpha subunit [Prevotella sp. oral
           taxon 317 str. F0108]
 gi|288329415|gb|EFC68001.1| DNA-directed RNA polymerase, alpha subunit [Prevotella sp. oral
           taxon 317 str. F0108]
          Length = 330

 Score =  287 bits (735), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 121/324 (37%), Positives = 192/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  +        PL  GF  T+GN+LRR+L+SSL G +I  V+I GV
Sbjct: 6   FQKPDKV---VMLEANDKFGRFEFRPLEPGFGVTIGNSLRRILLSSLEGFSINTVRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +    +++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFENEKVSITVENTTEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNPD VIC+LD  A ++++LT++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPDLVICHLDAKASLQIDLTINKGRGYVPADENREFCTDVNVIPIDSIYTPIRNVRY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEV 241
           +VE  R  Q  DYDKL + + TDGSI+ +D++  A++IL     +F +     E    + 
Sbjct: 183 SVEPYRVEQKTDYDKLVIDVTTDGSISPKDALKEAAKILIYHFMLFSDEKIAVENQDVDT 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ ++ LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKTKLVDMNLSVRALNCLKAADVETLGDLVQYNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L  + L  G ++  + 
Sbjct: 303 SLTELDDLLLGLNLSFGTDISKYK 326


>gi|145577841|gb|ABP87371.1| RpoA [Vibrio rhizosphaerae]
 gi|162955840|gb|ABY25295.1| RNA polymerase alpha subunit [Vibrio sp. MSSRF6]
          Length = 286

 Score =  287 bits (734), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 131/289 (45%), Positives = 193/289 (66%), Gaps = 8/289 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED
Sbjct: 1   QISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQED 60

Query: 82  LTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           + +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L+ D
Sbjct: 61  ILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLNDD 120

Query: 141 -AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
            A V M + V +G GYVPA    H   ++ PIG + +DA YSP+ K++YTVE+AR  Q  
Sbjct: 121 NAEVAMRIKVQRGRGYVPASARIHTDEDDRPIGRLLVDATYSPVDKIAYTVEAARVEQRT 180

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + +         +   F+P L
Sbjct: 181 DLDKLVIDMETNGTIEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPIL 237

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           L+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 238 LRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 286


>gi|145577855|gb|ABP87378.1| RpoA [Vibrio sp. MSSRF10]
          Length = 286

 Score =  287 bits (734), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 129/287 (44%), Positives = 190/287 (66%), Gaps = 8/287 (2%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
                 +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ 
Sbjct: 3   STTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDIL 62

Query: 84  DIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-A 141
           +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L    A
Sbjct: 63  EILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTDGNA 122

Query: 142 VVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            V M + V +G GYVPA    H   ++ PIG + +DA YSP+ K++YTVE+AR  Q  D 
Sbjct: 123 EVAMRIKVQRGRGYVPASARIHTDEDDRPIGRLLVDATYSPVDKIAYTVEAARVEQRTDL 182

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T+G+I  E+++  A+ IL +QL  F++  + +         +   F+P LL+
Sbjct: 183 DKLVIDMETNGTIEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLR 239

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 240 PVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 286


>gi|312899071|ref|ZP_07758455.1| DNA-directed RNA polymerase, alpha subunit [Megasphaera
           micronuciformis F0359]
 gi|310619856|gb|EFQ03432.1| DNA-directed RNA polymerase, alpha subunit [Megasphaera
           micronuciformis F0359]
          Length = 334

 Score =  287 bits (734), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 113/317 (35%), Positives = 176/317 (55%), Gaps = 20/317 (6%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
             +      + +PL RG+  TLGN+LRR+L+SSL G AIT+++IDG+LHE ++I GV ED
Sbjct: 15  DGDGTFGKFVCKPLDRGYGITLGNSLRRILLSSLEGVAITSIKIDGILHEFTTIPGVRED 74

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGV--VTAGDIQTVNDIEVLNPDHVICNLDV 139
           +++IILN+K + +K   +      I     G    TA D+   +DIE+LNP   I  LD 
Sbjct: 75  VSEIILNLKQVRMKFHKEDQMEADIIVDISGECDFTAADLNVNSDIEILNPTLHIATLDE 134

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           DA +RM+  + +G GYVP+  ++ + D IG+I ID+++SPI +  Y V + R G  +DYD
Sbjct: 135 DAHIRMQCHIERGKGYVPSTKNKKDTDVIGVIPIDSIFSPILRAKYEVGNVRVGNEMDYD 194

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK----------------- 242
            L+M + TDGS+T ED++A ++ IL   L        P + ++                 
Sbjct: 195 SLTMEVLTDGSLTAEDAMAESASILSSYLEKIKQLAAPGRNLQQGKFTEDELGAGANGAN 254

Query: 243 -EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E              + ++ L+LSVR++NCL+  NI  + +LI  T++D+ ++ N G K
Sbjct: 255 AEGAGADGTDMGEGGDESIDTLQLSVRASNCLKRANIYTIKELISHTKSDLGKIRNLGSK 314

Query: 302 SLVEIKGVLGTMGLFLG 318
           S+ EI   L   G  L 
Sbjct: 315 SVEEIIEKLSQFGYKLK 331


>gi|269213694|ref|ZP_05982639.2| DNA-directed RNA polymerase, alpha subunit [Neisseria cinerea ATCC
           14685]
 gi|269145516|gb|EEZ71934.1| DNA-directed RNA polymerase, alpha subunit [Neisseria cinerea ATCC
           14685]
          Length = 278

 Score =  286 bits (733), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 136/280 (48%), Positives = 187/280 (66%), Gaps = 6/280 (2%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           + G A T V I GVLHE S++ GV ED+ DI+LN+KGI  K+ G S  ++T+ K G GVV
Sbjct: 1   MNGFAPTEVAITGVLHEYSTLDGVQEDVVDILLNVKGIVFKLHGRSQVQLTLKKSGSGVV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLI 171
           +AGDI+  +D+E+LNPDH+IC+L  +  + ME+ V +G GY         R EN  IG I
Sbjct: 61  SAGDIELPHDVEILNPDHIICHLADNGQIEMEIKVEQGRGYQSVSGRQVVRDENRQIGSI 120

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA +SPI +VS+ VE AR  Q  D DKL + I+TDGSI  E++V  A+RIL DQ+ +F
Sbjct: 121 QLDASFSPISRVSFEVEPARVEQRTDLDKLVLDIETDGSIDPEEAVRSAARILIDQMSIF 180

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
            +    +    E++  K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE +
Sbjct: 181 ADL---QGTPVEEVEEKAPPIDPVLLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETE 237

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +L+  N GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 238 LLKTPNLGRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 277


>gi|238018650|ref|ZP_04599076.1| hypothetical protein VEIDISOL_00485 [Veillonella dispar ATCC 17748]
 gi|237865121|gb|EEP66411.1| hypothetical protein VEIDISOL_00485 [Veillonella dispar ATCC 17748]
          Length = 337

 Score =  286 bits (733), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 120/317 (37%), Positives = 182/317 (57%), Gaps = 18/317 (5%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
            IE + +  E       + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE S
Sbjct: 11  KIEKVDI-AEGGRYGKFVCEPLDRGYGITLGNSLRRILLSSLDGAAITSIKIDGVLHEFS 69

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGP--GVVTAGDI--QTVNDIEVLN 129
           +I G+ ED+TDIILN+K + +K+  D    + +       GV+TA D+  Q   ++EVLN
Sbjct: 70  TIPGIREDVTDIILNLKQLCIKVEEDVQLPLEVHFDFQKDGVLTAADLAEQFPPEVEVLN 129

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+ VI  +D  A + M++ + +G GYVP+  ++ + D IG I ID+++SPI +  Y V  
Sbjct: 130 PELVIATMDETAHLVMDVVIERGKGYVPSTKNKKDTDVIGCIPIDSIFSPILRAKYEVSD 189

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI---- 245
            R G  +D+DKL++ + TDGSIT  D+VA ++ I+   LG F         V  +     
Sbjct: 190 VRVGNEMDFDKLTLEVWTDGSITAADAVAKSAAIMIGYLGNFTKLAHSADVVDVNTGEGG 249

Query: 246 ---------NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
                    N +           ++ELELSVR+ NCL+   I  + DL+ +T  D+ ++ 
Sbjct: 250 IVVDPVGSDNEEPAVDEGPAKISIDELELSVRAYNCLKRAGINTIADLLDKTIDDLGKVR 309

Query: 297 NFGRKSLVEIKGVLGTM 313
           N G+KS+ EI+  L   
Sbjct: 310 NLGKKSIDEIEEKLNNH 326


>gi|320160441|ref|YP_004173665.1| DNA-directed RNA polymerase alpha chain [Anaerolinea thermophila
           UNI-1]
 gi|319994294|dbj|BAJ63065.1| DNA-directed RNA polymerase alpha chain [Anaerolinea thermophila
           UNI-1]
          Length = 321

 Score =  286 bits (733), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 113/314 (35%), Positives = 179/314 (57%), Gaps = 10/314 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             ++ P     +    E  N    I  PL  G+  TLGNALRRVL+SSL GAA+T+++I 
Sbjct: 5   TNMVTPK----VEREAEARNYGKFIIGPLEGGYGVTLGNALRRVLLSSLEGAAVTSIRIS 60

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
            VLHE S I GV ED+  ++LNIK + L +       + +  RG G VTA DIQ   ++E
Sbjct: 61  DVLHEFSDIPGVREDVIQVMLNIKQLRLILHDVETTHMHLEVRGEGTVTAADIQAPAEVE 120

Query: 127 VLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           ++NP+  +  +D  +  + ++ TVS+G GY PA   R+   PIG + +DA++SP+K+V++
Sbjct: 121 IVNPELELFTVDDPNTRLEIDFTVSRGRGYSPASE-RSGRLPIGELPVDAIFSPVKRVNW 179

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           +V +AR GQ  +YD+L + I TDG+IT E++++ +++IL D L            V  + 
Sbjct: 180 SVTAARVGQSTNYDRLILEIWTDGTITPENALSTSAKILIDHLRYITGVSAESLAVTVEK 239

Query: 246 NVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDL---IQRTEADMLRMANFGRK 301
            V      + A    +E L+LSVR  N L+   I  +GD+   +++ E  ++ + NFG K
Sbjct: 240 EVAGGRLTSEAAETPIENLDLSVRVFNSLKRTGITTVGDVLELLEKGEDAVMSIRNFGEK 299

Query: 302 SLVEIKGVLGTMGL 315
           SL E++  +   G 
Sbjct: 300 SLDELRQKMREKGF 313


>gi|312386519|gb|ADQ74778.1| RNA polymerase alpha subunit [Lactobacillus sp. MWBPC 1-3-1]
          Length = 248

 Score =  286 bits (733), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 109/248 (43%), Positives = 157/248 (63%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T II
Sbjct: 1   YGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKII 60

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+K + LK   D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME
Sbjct: 61  LNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHME 120

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           L V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I 
Sbjct: 121 LAVKNGRGYVTASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIW 180

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           TDGSI   D+++ A++IL +   +F + +   +  +  +  +       L   +EEL+LS
Sbjct: 181 TDGSIKPNDALSFAAKILVEHFKVFESADANTQFSEVMVEKEDDKKEKKLEMTIEELDLS 240

Query: 267 VRSTNCLR 274
           VRS NCL+
Sbjct: 241 VRSYNCLK 248


>gi|218462761|ref|ZP_03502852.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli Kim 5]
          Length = 247

 Score =  286 bits (732), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 173/247 (70%), Positives = 210/247 (85%), Gaps = 1/247 (0%)

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +KM GD  KR+ + K+GPGVVTAGDIQTV DIE+LNP+HVIC LD  A +RME TV+ G
Sbjct: 1   AIKMDGDDAKRMVVRKQGPGVVTAGDIQTVGDIEILNPEHVICTLDEGAEIRMEFTVNNG 60

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYVPA+ +R E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKL+MTI+TDGSIT
Sbjct: 61  KGYVPAERNRAEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLNMTIETDGSIT 120

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
           GED+VA A+RILQDQLG+F+NF+EP+KE +E+  V  L FNPALLKKV+ELELSVRS NC
Sbjct: 121 GEDAVAFAARILQDQLGVFVNFDEPQKETEEEA-VTELAFNPALLKKVDELELSVRSANC 179

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEEL 332
           L+ +NIVY+GDLIQ+TEA+MLR  NFGRKSL EIK VL +MGL LGM +P WPPE+IE+L
Sbjct: 180 LKNDNIVYIGDLIQKTEAEMLRTPNFGRKSLNEIKEVLASMGLHLGMEVPAWPPENIEDL 239

Query: 333 AKKYEDK 339
           AK+YED+
Sbjct: 240 AKRYEDQ 246


>gi|288575869|ref|ZP_05977763.2| DNA-directed RNA polymerase, alpha subunit [Neisseria mucosa ATCC
           25996]
 gi|288566928|gb|EFC88488.1| DNA-directed RNA polymerase, alpha subunit [Neisseria mucosa ATCC
           25996]
          Length = 278

 Score =  286 bits (732), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 133/280 (47%), Positives = 184/280 (65%), Gaps = 6/280 (2%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           + G A T V I GVLHE S++ GV ED+ DI+LN+KGI  K+ G    ++T+ K G G V
Sbjct: 1   MNGFAPTEVAISGVLHEYSTVDGVQEDVVDILLNVKGIVFKLHGRGQVQLTLKKSGAGAV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLI 171
            AGDI+  +D+E+LNP+H+IC+L  +  + ME+ V +G GY         R EN  IG I
Sbjct: 61  VAGDIELPHDVEILNPEHIICHLAENGQIEMEIKVEQGRGYQSVSGRRVVRDENRQIGAI 120

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA +SPI +VS+ VE AR  Q  D DKL + I+TDGSI  E++V  A+RIL DQ+ +F
Sbjct: 121 QLDASFSPISRVSFEVEPARVEQRTDLDKLVLDIETDGSIDPEEAVRSAARILIDQMSIF 180

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
            +    +    E++  K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE +
Sbjct: 181 ADL---QGTPVEEVEEKAPPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETE 237

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +L+  N GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 238 LLKTPNLGRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 277


>gi|294794575|ref|ZP_06759711.1| DNA-directed RNA polymerase, alpha subunit [Veillonella sp. 3_1_44]
 gi|294454905|gb|EFG23278.1| DNA-directed RNA polymerase, alpha subunit [Veillonella sp. 3_1_44]
          Length = 334

 Score =  286 bits (731), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 117/317 (36%), Positives = 182/317 (57%), Gaps = 18/317 (5%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
            IE + +          + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE S
Sbjct: 8   KIEKVDIADG-GRYGKFVCEPLDRGYGITLGNSLRRILLSSLDGAAITSIKIDGVLHEFS 66

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGP--GVVTAGDI--QTVNDIEVLN 129
           +I G+ ED+TDIILN+K + +K+  ++   + +       G++TA D+  Q   ++EVLN
Sbjct: 67  TIPGIREDVTDIILNLKQLCIKVEEEAQLPLEVHFDFQKDGILTAADLAEQFPPEVEVLN 126

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+ VI  +D  A   M++ + +G GYVP+  ++ + D IG I ID+++SPI +  Y V  
Sbjct: 127 PELVIATMDETAHFVMDVVIERGKGYVPSTKNKKDTDVIGCIPIDSIFSPILRAKYEVSD 186

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI---- 245
            R G  +D+DKL++ + TDGSIT  D+VA ++ I+   LG F         V  +     
Sbjct: 187 VRVGNEMDFDKLTLEVWTDGSITAADAVAKSAAIMIGYLGNFTKLAHSADVVDVNTGEGG 246

Query: 246 ---------NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
                    N +    +      ++ELELSVR+ NCL+   I  + DL+ +T  D+ ++ 
Sbjct: 247 IVIDPVGSDNEEPAVDDGPAKISIDELELSVRAYNCLKRAGINTIADLLDKTIDDLGKVR 306

Query: 297 NFGRKSLVEIKGVLGTM 313
           N G+KS+ EI+  L   
Sbjct: 307 NLGKKSIDEIEEKLNNH 323


>gi|282849891|ref|ZP_06259274.1| DNA-directed RNA polymerase, alpha subunit [Veillonella parvula
           ATCC 17745]
 gi|282580328|gb|EFB85728.1| DNA-directed RNA polymerase, alpha subunit [Veillonella parvula
           ATCC 17745]
          Length = 334

 Score =  286 bits (731), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 117/317 (36%), Positives = 183/317 (57%), Gaps = 18/317 (5%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
            IE + +          + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE S
Sbjct: 8   KIEKVDIADG-GRYGKFVCEPLDRGYGITLGNSLRRILLSSLDGAAITSIKIDGVLHEFS 66

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGP--GVVTAGDI--QTVNDIEVLN 129
           +I G+ ED+TDIILN+K + +K+  ++   + +       G++TA D+  Q   ++EVLN
Sbjct: 67  TIPGIREDVTDIILNLKQLCIKVEEEAQLPLEVHFDFQKDGILTAADLAEQFPPEVEVLN 126

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+ VI  +D  A + M++ + +G GYVP+  ++ + D IG I ID+++SPI +  Y V  
Sbjct: 127 PELVIATMDETAHLVMDVVIERGKGYVPSTKNKKDTDVIGCIPIDSIFSPILRAKYEVSD 186

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI---- 245
            R G  +D+DKL++ + TDGSIT  D+VA ++ I+   LG F         V  +     
Sbjct: 187 VRVGNEMDFDKLTLEVWTDGSITAADAVAKSAAIMIGYLGNFTKLAHSADVVDVNTGEGG 246

Query: 246 ---------NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
                    N +    +      ++ELELSVR+ NCL+   I  + DL+ +T  D+ ++ 
Sbjct: 247 IVIDPVGSDNEEPAVDDGPAKISIDELELSVRAYNCLKRAGINTIADLLDKTIDDLGKVR 306

Query: 297 NFGRKSLVEIKGVLGTM 313
           N G+KS+ EI+  L   
Sbjct: 307 NLGKKSIDEIEEKLNNH 323


>gi|329565853|gb|AEB92263.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
 gi|329565855|gb|AEB92264.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
 gi|329565861|gb|AEB92267.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
          Length = 250

 Score =  286 bits (731), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 109/250 (43%), Positives = 160/250 (64%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL+SSL GAA  +V+IDGVLHE S++ GV ED+  IILN+K + +K+  D    
Sbjct: 1   GNSLRRVLLSSLPGAAPKSVKIDGVLHEFSTLPGVKEDVVKIILNLKEVAVKLHSDEPVV 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
             I   G G VTAG I+   DIE+LNPDH I  L  D  + ME+   KG GYVP+  ++ 
Sbjct: 61  GRIDVEGKGEVTAGHIKGSADIEILNPDHHIATLSDDGKLHMEIVFVKGKGYVPSDKNKE 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
            N PIG+I +D++++P+K+VSY V++ R G V DYDKL++ + T+G+IT ++++++AS +
Sbjct: 121 PNQPIGVIPVDSIFTPVKRVSYNVKNTRVGHVTDYDKLTLEVWTNGTITPKEAISMASDM 180

Query: 224 LQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGD 283
           L      FI+F    K     ++         L   +EEL+LSVRS NCL+   I  + +
Sbjct: 181 LIKYFQKFISFTGEYKSSDIFVDKPEKKVEKPLDMTIEELDLSVRSYNCLKRAGINTVQE 240

Query: 284 LIQRTEADML 293
           L Q+TE +M+
Sbjct: 241 LTQKTEEEMM 250


>gi|90994483|ref|YP_536973.1| RNA polymerase alpha subunit [Porphyra yezoensis]
 gi|109900623|sp|Q1XDJ5|RPOA_PORYE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|90819047|dbj|BAE92416.1| DNA directed RNA polymerase alpha subunit [Porphyra yezoensis]
 gi|116266126|gb|ABJ91301.1| DNA-directed RNA polymerase alpha subunit [Porphyra yezoensis]
          Length = 311

 Score =  285 bits (730), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 103/311 (33%), Positives = 165/311 (53%), Gaps = 10/311 (3%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             IE    G   +     + EPL +G   TLGNALRR ++S L G AI AV+I GV HE 
Sbjct: 7   ECIESRTDGARGQ-YGSFVIEPLNQGQGITLGNALRRSILSDLEGTAIVAVRIAGVNHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           S+I GV ED+ +I+LN+K +  K      +   I  +GP +VTAG  +  +DIEV++P  
Sbjct: 66  STIPGVREDVLEILLNLKEVVFKSYNKESQIGRIRVQGPAIVTAGLFELSSDIEVVDPRQ 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +  + +  ME  + K  GY  A+    +   +  + +D+++ P+ KV+Y VE  R 
Sbjct: 126 YIATICNNTIFEMEFKIEKNCGYRLAEK-AVDELSVDFLQVDSVFMPVNKVNYKVEEVRI 184

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           G     D+L + I T+GSI+ +++++  + +L +      N +      K   N +S   
Sbjct: 185 GSNSIKDRLIIQIWTNGSISPQEAISQGATVLTNLFCSLRNLD-----FKSADNYRSKED 239

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                  +EEL+LSVR+ NCL+   I  + DL+  ++ ++L + NFG+KS  E+   L  
Sbjct: 240 KKISQVLIEELQLSVRAYNCLKRAQIHSIADLLDYSQEELLEIKNFGQKSAEEVIYAL-- 297

Query: 313 MGLFLGMNLPD 323
               LG++LP 
Sbjct: 298 -QKKLGISLPK 307


>gi|163847950|ref|YP_001635994.1| DNA-directed RNA polymerase subunit alpha [Chloroflexus aurantiacus
           J-10-fl]
 gi|222525830|ref|YP_002570301.1| DNA-directed RNA polymerase subunit alpha [Chloroflexus sp.
           Y-400-fl]
 gi|163669239|gb|ABY35605.1| DNA-directed RNA polymerase, alpha subunit [Chloroflexus
           aurantiacus J-10-fl]
 gi|222449709|gb|ACM53975.1| DNA-directed RNA polymerase, alpha subunit [Chloroflexus sp.
           Y-400-fl]
          Length = 318

 Score =  285 bits (730), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 108/304 (35%), Positives = 168/304 (55%), Gaps = 7/304 (2%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
            IE +   +  E       EPL  G+ HTLGNALRRVL++++ G+AIT V+I GV  E  
Sbjct: 8   KIEVV---EATETFGRFKIEPLDPGYGHTLGNALRRVLLTAIPGSAITHVRIAGVYQETD 64

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
            I G+ ED+ ++ILN+KGI+L+   +   + TI K+GP +VTA D+     + V++P H 
Sbjct: 65  VIPGMTEDVVELILNLKGIHLRGRHEGTVQATIQKQGPAIVTAADLMLPEGLSVVDPTHY 124

Query: 134 ICNLDVD-AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           IC L+ D A + +  T+  G GY+ A        P+G   IDA+++P+ +V+Y VE+ R 
Sbjct: 125 ICTLEHDQARIEITATIEHGRGYLSADQR--GILPLGEFPIDAIFTPVPRVNYVVENTRI 182

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP- 251
           GQ  DYD+L + + T+G+I  ++++  A+R+L        NF     E         L  
Sbjct: 183 GQATDYDRLILEVWTNGTIRAQEALDYAARVLVHYYTTIANFNRLMVEPAAQPETNGLEI 242

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +E L+LS R+ NCL+   I  +G ++Q  E  +L + N G+KS+ EI+  L 
Sbjct: 243 PAHVYDTSIETLDLSTRTYNCLKRAEITKIGQVLQMDEKALLSVRNLGQKSMEEIRDKLI 302

Query: 312 TMGL 315
             G 
Sbjct: 303 ERGY 306


>gi|296840731|ref|ZP_06863331.2| DNA-directed RNA polymerase, alpha subunit [Neisseria polysaccharea
           ATCC 43768]
 gi|296840100|gb|EFH24038.1| DNA-directed RNA polymerase, alpha subunit [Neisseria polysaccharea
           ATCC 43768]
          Length = 278

 Score =  285 bits (730), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 137/280 (48%), Positives = 185/280 (66%), Gaps = 6/280 (2%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           + G A T V I GVLHE S++ GV ED+ DI+LNIKGI  K+ G S  ++ + K G GVV
Sbjct: 1   MNGFAPTEVAIAGVLHEYSTVDGVQEDVVDILLNIKGIVFKLHGRSQVQLVLKKSGSGVV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLI 171
           +AGDI+  +D+E+LNP HVIC+L  +  + ME+ V +G GY         R EN  IG I
Sbjct: 61  SAGDIELPHDVEILNPGHVICHLADNGQIEMEIKVEQGRGYQSVSGRQVVRDENRQIGAI 120

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +DA +SPI +VS+ VE AR  Q  D DKL + I+TDGSI  E++V  A+RIL DQ+ +F
Sbjct: 121 QLDASFSPISRVSFEVEPARVEQRTDLDKLVLDIETDGSIDPEEAVRSAARILIDQMSIF 180

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
            N    +    E++  K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE +
Sbjct: 181 ANL---QGTPVEEVEEKAPPIDPVLLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETE 237

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +L+  N GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 238 LLKTPNLGRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 277


>gi|291514968|emb|CBK64178.1| DNA-directed RNA polymerase subunit alpha [Alistipes shahii WAL
           8301]
          Length = 317

 Score =  285 bits (730), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 113/311 (36%), Positives = 180/311 (57%), Gaps = 7/311 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +   +       PL  GF  T+GNALRR+L+SSL G AIT V++ GV HE ++I GV ED
Sbjct: 3   ESTSSFGKFEFRPLEPGFGMTVGNALRRILLSSLEGYAITTVKVAGVDHEFAAIPGVMED 62

Query: 82  LTDIILNIKGINL--KMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLD 138
           + +IILN+K +     +     ++V+I   G   +TAG I   ++  +VLNPD VIC+L 
Sbjct: 63  MLNIILNLKQVRFIRTVDNQDAEKVSINVAGVTELTAGYISNYLSFFKVLNPDLVICHLA 122

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               ++M LT+ KG GYVPA+ +       G + ID++++PIK V Y++E+ R  Q  DY
Sbjct: 123 PGTKMQMTLTIGKGRGYVPAEENAPAESEFGTLPIDSIFTPIKNVKYSIENYRVEQKTDY 182

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNP 254
           +KL++ I TDGSI  ++++  A++IL     +F    I          E+ +   L    
Sbjct: 183 EKLNLEITTDGSIHPKEALKEAAKILIQHFMLFSDEKITVNMEDTNGAEEFDEDVLHMRQ 242

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
            L  K+ + +LSVR+ NCL+  ++  +GDL++    D+L+  NFG+KSL E+  +L ++ 
Sbjct: 243 LLKTKLSDQDLSVRALNCLKAADVDTVGDLVKLNRNDLLKFRNFGKKSLTELDELLTSLN 302

Query: 315 LFLGMNLPDWP 325
           L  GM++  + 
Sbjct: 303 LKFGMDVSIYK 313


>gi|329565845|gb|AEB92259.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
 gi|329565857|gb|AEB92265.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
          Length = 250

 Score =  285 bits (730), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 109/250 (43%), Positives = 160/250 (64%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL+SSL GAA  +V+IDGVLHE S++ GV ED+  IILN+K + +K+  D    
Sbjct: 1   GNSLRRVLLSSLPGAAPKSVKIDGVLHEFSTLPGVKEDVVKIILNLKEVAVKLHSDEPVV 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
             I   G G VTAG I+   DIE+LNPDH I  L  D  + ME+   KG GYVP+  ++ 
Sbjct: 61  GRIDVEGKGEVTAGHIKGSADIEILNPDHHIATLSDDGKLHMEIVFVKGKGYVPSNKNKE 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
            N PIG+I +D++++P+K+VSY V++ R G V DYDKL++ + T+G+IT ++++++AS +
Sbjct: 121 PNQPIGVIPVDSIFTPVKRVSYNVKNTRVGHVTDYDKLTLEVWTNGTITPKEAISMASDM 180

Query: 224 LQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGD 283
           L      FI+F    K     ++         L   +EEL+LSVRS NCL+   I  + +
Sbjct: 181 LIKYFQKFISFTGEYKSSDIFVDKPEKKVEKPLDMTIEELDLSVRSYNCLKRAGINTVQE 240

Query: 284 LIQRTEADML 293
           L Q+TE +M+
Sbjct: 241 LTQKTEEEMM 250


>gi|157493247|gb|ABV57989.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 286

 Score =  285 bits (729), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 126/288 (43%), Positives = 191/288 (66%), Gaps = 8/288 (2%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
                 +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ 
Sbjct: 2   STTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDIL 61

Query: 84  DIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDA 141
           +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L   +A
Sbjct: 62  EILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNA 121

Query: 142 VVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M + V +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D 
Sbjct: 122 AIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDL 181

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+
Sbjct: 182 DKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLR 238

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EI
Sbjct: 239 PVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEI 286


>gi|290489678|gb|ADD31223.1| RNA polymerase alpha subunit protein [Berberidopsis corallina]
          Length = 337

 Score =  285 bits (729), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 81/331 (24%), Positives = 163/331 (49%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  RGPG VTA DI +   +E++
Sbjct: 71  PHEYSTIVGIQESVHEILMNLKEIVLRSNLYGTCDASICVRGPGYVTAQDIISPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY     +  ++   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDLCIGLQIERNRGYRIKTLNNFQD---GSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLEDNQHKA 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           + P      +                 +++LEL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TFPLFTFHDRLAKLRKNKKEIALKYIFIDQLELPPRIYNCLKRSNIHTLSDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F    + ++K +LG +     ++LP 
Sbjct: 307 MKIEHFR---IEDVKQILGILEKHFTIDLPK 334


>gi|289548514|ref|YP_003473502.1| DNA-directed RNA polymerase subunit alpha [Thermocrinis albus DSM
           14484]
 gi|289182131|gb|ADC89375.1| DNA-directed RNA polymerase, alpha subunit [Thermocrinis albus DSM
           14484]
          Length = 317

 Score =  285 bits (729), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 115/317 (36%), Positives = 178/317 (56%), Gaps = 6/317 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           +E + P+ + +    ++ +     + EPL RGF  T+GNALRR L+SS+ G AIT V++ 
Sbjct: 3   REFVYPSKVYW---EEKTKTYGRFVVEPLERGFGITVGNALRRTLLSSIEGTAITGVKVY 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           G  HE S+++GV ED+ +II N+K +  ++     + + + KRG G V A DI     ++
Sbjct: 60  GAYHEFSTVEGVLEDVLEIIANLKRVRFRLRESHVEILYLKKRGEGEVYARDIILPPSVD 119

Query: 127 VLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           ++ PD  I  +   D  + +E+ V +G GYVP +   +  + +G I +DA +SP++ VSY
Sbjct: 120 LITPDVKIATITSPDTELHIEIRVERGFGYVPTEEMESFGE-VGWILVDADFSPVRHVSY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE  R  +  DYD+L M I TDGS T E+ V  A +IL        N  +    V E+ 
Sbjct: 179 RVEKTRVERRSDYDRLIMEIRTDGSKTPEEVVKEAVQILLRNFSSLENIAQEIPFVAEEP 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            V         L  +EEL++S RS N L+   I  +G+L++ TE D+    N GRK++ E
Sbjct: 239 VVVDELMEKLSL-PIEELDISQRSLNSLKRIGINTLGELVRLTEEDLKSTKNVGRKAINE 297

Query: 306 IKGVLGTMGLFLGMNLP 322
           IK  L  MGL+LGM++ 
Sbjct: 298 IKEALKQMGLYLGMDIE 314


>gi|260656836|gb|ACX47808.1| RNA polymerase alpha-subunit [Vibrio casei]
          Length = 295

 Score =  285 bits (729), Expect = 8e-75,   Method: Composition-based stats.
 Identities = 130/297 (43%), Positives = 193/297 (64%), Gaps = 8/297 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +G
Sbjct: 2   VDIEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEG 61

Query: 78  VHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           V ED+ +I+LN+KG+ + +  G     +T+ K G G V AGDI    D+E+ NP+HVIC+
Sbjct: 62  VQEDILEILLNLKGLAVSVAEGKDEVFITLKKSGSGPVVAGDIIHDGDVEIANPEHVICH 121

Query: 137 LDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L  D A + M + V +G GYVP+    H   +  PIG + +DA YSP+ K++Y VE+AR 
Sbjct: 122 LTDDKAEIAMRIKVQRGRGYVPSSARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARV 181

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F
Sbjct: 182 EQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEF 238

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK V
Sbjct: 239 DPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDV 295


>gi|328813949|gb|AEB52090.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 241

 Score =  284 bits (728), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 105/241 (43%), Positives = 159/241 (65%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           +LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNIK + LKM+ D  K + 
Sbjct: 1   SLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNTDEDKNIE 60

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
           I   GP  VTA DI    D+EVLNP+  IC +       + +TV KG GYV A  +++++
Sbjct: 61  IDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAADQNKSDD 120

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
            PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++IL 
Sbjct: 121 MPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKILT 180

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLI 285
           + L +F+N  +  K  +  +  +       L   +EEL+LSVRS NCL+   I  + +L 
Sbjct: 181 EHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVQELT 240

Query: 286 Q 286
            
Sbjct: 241 N 241


>gi|158148901|dbj|BAF81985.1| RNA polymerase alpha subunit [Lactobacillus parabrevis]
          Length = 246

 Score =  284 bits (728), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 114/246 (46%), Positives = 167/246 (67%), Gaps = 4/246 (1%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+K I 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVTQIILNVKKIA 60

Query: 94  LKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           LK++G  D  + + I  +GP  +TAGDI    D++VLNPD  I  +   A   M +T  K
Sbjct: 61  LKLNGSDDQEETMEINVKGPAQITAGDIVAGADVDVLNPDLYIATVADGATFHMRMTADK 120

Query: 152 GHGYVPAKHHRTEN--DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           G GYV A  H+ +N   PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ + T+G
Sbjct: 121 GRGYVSADEHKAQNTEMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDVWTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI   +++ALA++IL + L MF++  +  K  +  +  +       L   +EEL+LSVRS
Sbjct: 181 SINPSEAIALAAKILTEHLAMFVDLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSVRS 240

Query: 270 TNCLRG 275
            NCL+ 
Sbjct: 241 YNCLKR 246


>gi|325294424|ref|YP_004280938.1| DNA-directed RNA polymerase subunit alpha [Desulfurobacterium
           thermolithotrophum DSM 11699]
 gi|325064872|gb|ADY72879.1| DNA-directed RNA polymerase subunit alpha [Desulfurobacterium
           thermolithotrophum DSM 11699]
          Length = 318

 Score =  284 bits (728), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 115/315 (36%), Positives = 178/315 (56%), Gaps = 7/315 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E I P    +    +  EN    + EPL +G+  T+GNALRRVL+SS+ GAA TAV+ +G
Sbjct: 3   EFITPEKFLW---EEHTENYGRFVVEPLEKGYGTTVGNALRRVLLSSIEGAAPTAVKFEG 59

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
             HE +++ GV ED+T+I+LN+K +   + G+    + + KRGPG V A D +  + +E+
Sbjct: 60  AYHEFTTLPGVVEDVTEIVLNLKQLRFILHGEGPVFIELKKRGPGKVYAKDFELPSQVEL 119

Query: 128 LNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVS 184
           L PD  I  LD  ++ + + L + KG G+V ++  +   +   IG I +DA +SPIKKV+
Sbjct: 120 LTPDQEIATLDNENSEIEIYLRIDKGKGFVLSEDIQEIFDISTIGWIPLDADFSPIKKVA 179

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN-FEEPKKEVKE 243
           + VE  R G+  DY++L+M I TDGSIT +D+V  A+ IL +   M  +   E      +
Sbjct: 180 FRVEDTRVGRRTDYNRLTMEIWTDGSITPKDAVVRAANILIEHFSMVRDKLVEAIFATAQ 239

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
              VK         + +EE  L  R+   L    I  +GDL++ T+ ++  M   G+KSL
Sbjct: 240 PEEVKKEEVPEIYNQTLEEAGLKGRALKILGENGITTVGDLVKLTKKELESMKGLGKKSL 299

Query: 304 VEIKGVLGTMGLFLG 318
            EI+  L ++G  LG
Sbjct: 300 AEIENFLASLGFELG 314


>gi|157493243|gb|ABV57987.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 286

 Score =  284 bits (728), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 126/289 (43%), Positives = 191/289 (66%), Gaps = 8/289 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED
Sbjct: 1   QISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQED 60

Query: 82  LTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-V 139
           + +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L   
Sbjct: 61  ILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSD 120

Query: 140 DAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +A + M + V +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  
Sbjct: 121 NAAIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRT 180

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P L
Sbjct: 181 DLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPIL 237

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           L+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 238 LRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 286


>gi|225849517|ref|YP_002729682.1| DNA-directed RNA polymerase subunit alpha [Sulfurihydrogenibium
           azorense Az-Fu1]
 gi|225644691|gb|ACN99741.1| DNA-directed RNA polymerase, alpha subunit [Sulfurihydrogenibium
           azorense Az-Fu1]
          Length = 326

 Score =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 121/316 (38%), Positives = 179/316 (56%), Gaps = 7/316 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           + + P+ I +     + EN   +  EPL RG+  TLGNALRRVL+SSL   AITAV+I G
Sbjct: 6   DFVMPSKIYWDE-STKTENFGKLYVEPLERGYGITLGNALRRVLLSSLPSGAITAVKIVG 64

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR-VTIFKRGPGVVTAGDIQTVNDIE 126
           V HE +++KGV ED+++IILN+K I LK+  +  +    +   GPG V A DI+    IE
Sbjct: 65  VPHEFTTVKGVIEDVSEIILNLKQIRLKIDENIERDFAILEVEGPGKVFAKDIKAPPGIE 124

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           ++NPD  IC L  +  ++ME  + +G GY   +     N+ IG I ID  +SPIK+ ++ 
Sbjct: 125 IVNPDEYICTLSENVKLQMEFRIERGRGYKTVEELEDINE-IGWILIDTSFSPIKRCTFF 183

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE  R G   DYD+L + I+TDG+IT ++++  ++ IL +   +       K +V +   
Sbjct: 184 VEPVRVGDKTDYDRLILEIETDGTITPDEALEKSANILIEHFTLLQKPTVRKAQVIKKTV 243

Query: 247 VKSLPFNPALLKK----VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                       K    ++ELE+S R+ N LR   I  +GDL++ +E D+    + GRKS
Sbjct: 244 APKTEELKIEEDKLSLAIDELEISSRAINTLRKLGINTIGDLVKLSEDDLKEAKSIGRKS 303

Query: 303 LVEIKGVLGTMGLFLG 318
           L EIK  L  MGL L 
Sbjct: 304 LKEIKDALADMGLELA 319


>gi|269798523|ref|YP_003312423.1| DNA-directed RNA polymerase, subunit alpha [Veillonella parvula DSM
           2008]
 gi|294792821|ref|ZP_06757968.1| DNA-directed RNA polymerase, alpha subunit [Veillonella sp. 6_1_27]
 gi|269095152|gb|ACZ25143.1| DNA-directed RNA polymerase, alpha subunit [Veillonella parvula DSM
           2008]
 gi|294456720|gb|EFG25083.1| DNA-directed RNA polymerase, alpha subunit [Veillonella sp. 6_1_27]
          Length = 334

 Score =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 117/317 (36%), Positives = 183/317 (57%), Gaps = 18/317 (5%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
            IE + +          + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE S
Sbjct: 8   KIEKVDIADG-GRYGKFVCEPLDRGYGITLGNSLRRILLSSLDGAAITSIKIDGVLHEFS 66

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGP--GVVTAGDI--QTVNDIEVLN 129
           +I G+ ED+TDIILN+K + +K+  ++   + +       G++TA D+  Q   ++EVLN
Sbjct: 67  TIPGIREDVTDIILNLKQLCIKVEEEAQLPLEVHFDFQKDGILTATDLAEQFPPEVEVLN 126

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+ VI  +D  A + M++ + +G GYVP+  ++ + D IG I ID+++SPI +  Y V  
Sbjct: 127 PELVIATMDETAHLVMDVVIERGKGYVPSTKNKKDTDVIGCIPIDSIFSPILRAKYEVSD 186

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI---- 245
            R G  +D+DKL++ + TDGSIT  D+VA ++ I+   LG F         V  +     
Sbjct: 187 VRVGNEMDFDKLTLEVWTDGSITAADAVAKSAAIMIGYLGNFTKLAHSADVVDVNTGEGG 246

Query: 246 ---------NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
                    N +    +      ++ELELSVR+ NCL+   I  + DL+ +T  D+ ++ 
Sbjct: 247 IVIDPVGSDNEEPAVDDGPAKISIDELELSVRAYNCLKRAGINTIADLLDKTIDDLGKVR 306

Query: 297 NFGRKSLVEIKGVLGTM 313
           N G+KS+ EI+  L   
Sbjct: 307 NLGKKSIDEIEEKLNNH 323


>gi|269122553|ref|YP_003310730.1| DNA-directed RNA polymerase, subunit alpha [Sebaldella termitidis
           ATCC 33386]
 gi|268616431|gb|ACZ10799.1| DNA-directed RNA polymerase, alpha subunit [Sebaldella termitidis
           ATCC 33386]
          Length = 321

 Score =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 123/306 (40%), Positives = 188/306 (61%), Gaps = 4/306 (1%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
              + ++   +   EPL RG+  T+GNALRRVL+SS+ G+AI  V+IDGVL+E S+I+GV
Sbjct: 14  KEDKTDDFHAIYTLEPLYRGYGATIGNALRRVLLSSIPGSAIKGVKIDGVLNEFSTIEGV 73

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E +TDIILNIK I ++      K++++  +GP  +TA DI     ++++NPD VI  + 
Sbjct: 74  KEAVTDIILNIKEIVVESDEPGEKKMSLSVKGPREITARDIILEPGLKIINPDQVIATIT 133

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + ME  V  G G+V ++   TEN PIG I +DA+Y+PIKK+SY+VE    G+  DY
Sbjct: 134 TKREINMEFLVDSGEGFVVSEEIETENWPIGYIAVDAIYTPIKKISYSVEDTMVGRATDY 193

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKSLPFNP 254
           DKL++ I TDGSI   D+++ A  ++   L  F N     E+ + E + + +++ +  N 
Sbjct: 194 DKLTLDITTDGSIEIRDALSYAVELISFHLNPFTNIGNSMEKFRSEDEVESSIEVISENN 253

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
               K+EEL+ +VRS NCL+   +  +GDL + T A++L++ N GRKSL EI   +  +G
Sbjct: 254 MDDMKIEELDFTVRSYNCLKKAGVNTIGDLGKMTYAELLKIKNLGRKSLNEIIDKMKELG 313

Query: 315 LFLGMN 320
             L  N
Sbjct: 314 FDLNDN 319


>gi|153816223|ref|ZP_01968891.1| hypothetical protein RUMTOR_02472 [Ruminococcus torques ATCC 27756]
 gi|145846406|gb|EDK23324.1| hypothetical protein RUMTOR_02472 [Ruminococcus torques ATCC 27756]
          Length = 277

 Score =  284 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 115/274 (41%), Positives = 177/274 (64%), Gaps = 5/274 (1%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFK 108
           ++SSL G+AI++V+IDGVLHE SSI GV ED+T+II+N+K + ++     D  K V I  
Sbjct: 1   MLSSLPGSAISSVKIDGVLHEFSSIPGVKEDVTEIIMNLKSLAIRNMSESDEPKTVYIEF 60

Query: 109 RGPGVVTAGDI-QTVNDIEVLNPDHVICNLD--VDAVVRMELTVSKGHGYVPAKHHRTEN 165
            G GVVT  DI     DIE++NPD VI  L    D  + MELT++KG GYV +  ++TE+
Sbjct: 61  EGEGVVTGADININDPDIEIVNPDQVIATLSGGKDCRLNMELTITKGRGYVSSDKNKTED 120

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
            PIG+I ID++Y+P+++V+ TVE+ R GQ+ DYDKL++ + T G++  +++V+LA+++L 
Sbjct: 121 MPIGVIAIDSIYTPVERVNLTVENTRVGQITDYDKLTLDVWTKGTMLPDEAVSLAAKVLS 180

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLI 285
           + L +F++  E  +  +  I  +       L   ++ELELSVRS NCL+   I  + +L 
Sbjct: 181 EHLKLFVDLSEVAQVAEVMIEKEDDEKEKVLEMSIDELELSVRSYNCLKRAGINTVEELT 240

Query: 286 QRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
            +T  DM+++ N GRKSL E+   L  + L L  
Sbjct: 241 NKTPEDMMKVRNLGRKSLEEVLAKLKELNLELNQ 274


>gi|160947673|ref|ZP_02094840.1| hypothetical protein PEPMIC_01608 [Parvimonas micra ATCC 33270]
 gi|158446807|gb|EDP23802.1| hypothetical protein PEPMIC_01608 [Parvimonas micra ATCC 33270]
          Length = 313

 Score =  284 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 116/305 (38%), Positives = 183/305 (60%), Gaps = 2/305 (0%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
            NIE + +   E+N       PL RG+  TLGN++RRVL+ SL G+AI  V+IDGV HE 
Sbjct: 7   TNIEVLDID-LEKNYGKFAIMPLDRGYGTTLGNSMRRVLLGSLPGSAIATVKIDGVGHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++IKG   D+ +I++NIKGI LK   D    + +  +GP VVTAGDI    ++E+ N DH
Sbjct: 66  TTIKGSIADVPEILINIKGIALKKFNDEPVILELNVKGPKVVTAGDISENQNVEIANKDH 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L+ +  +RM+L V  G GY  +  ++   D I  I +D+ +SP+KKV++ V + R 
Sbjct: 126 YITTLNEEGEIRMDLLVLNGKGYRVSDLNKEYCD-INSIAVDSSFSPVKKVNFIVGNTRV 184

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           GQ +D+DKL + + T+G+IT +++++  + I  D L +F +  +   +     + K L  
Sbjct: 185 GQSIDFDKLEIEVWTNGTITPQEALSTGAGIFIDYLSLFRSLPDINLDNSSIKDGKILDA 244

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           N  L K VEEL+LS+RS NCL+  N+  + D+I +    + ++ NFG+KS+ E+   +  
Sbjct: 245 NGVLSKSVEELDLSLRSFNCLKRANLDTVKDIISQDIEQLKKIKNFGKKSVEEVVDKIHE 304

Query: 313 MGLFL 317
           +GL  
Sbjct: 305 LGLKF 309


>gi|167752412|ref|ZP_02424539.1| hypothetical protein ALIPUT_00656 [Alistipes putredinis DSM 17216]
 gi|167660653|gb|EDS04783.1| hypothetical protein ALIPUT_00656 [Alistipes putredinis DSM 17216]
          Length = 330

 Score =  284 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 113/324 (34%), Positives = 184/324 (56%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP  +   ++ +   +       PL  GF  T+GNALRR+L+SSL G AIT V++ GV
Sbjct: 6   FQKPEKV---IMLESTSSFGKFEFRPLEPGFGMTVGNALRRILLSSLEGYAITTVKVAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINL--KMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDI 125
            HE ++I GV E + DIILN+K +     +     ++V++   G   +TAG I   ++  
Sbjct: 63  DHEFAAIPGVMEGMIDIILNLKQVRFIRTVDNQDAEKVSVNVAGVTELTAGYISNYLSFF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNP+ VIC+L     +++ LT+ KG GYVPA+ +   +   G + ID++++PIK V Y
Sbjct: 123 KVLNPELVICHLAPGTKMQLTLTIGKGRGYVPAEENTPADCEFGTLPIDSIFTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL++ I TDGSI   D++  A++IL     +F    I         
Sbjct: 183 SIENYRVEQKTDYEKLNLEITTDGSIHPTDALKEAAKILIQHFMLFSDEKITVNMEDTNG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ +   L     L  K+ + +LSVR+ NCL+  ++  +GDL++    D+L+  NFG+K
Sbjct: 243 AEEFDEDILHMRQLLKTKLSDQDLSVRALNCLKAADVDTVGDLVKLNRNDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  GM++  + 
Sbjct: 303 SLTELDELLASLNLKFGMDVSIYK 326


>gi|151400011|gb|ABS11121.1| RpoA [Vibrio cholerae]
 gi|151400013|gb|ABS11122.1| RpoA [Vibrio cholerae]
 gi|151400015|gb|ABS11123.1| RpoA [Vibrio cholerae]
 gi|151400017|gb|ABS11124.1| RpoA [Vibrio cholerae]
 gi|151400019|gb|ABS11125.1| RpoA [Vibrio cholerae]
 gi|151400021|gb|ABS11126.1| RpoA [Vibrio cholerae]
 gi|151400023|gb|ABS11127.1| RpoA [Vibrio mimicus]
          Length = 283

 Score =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 125/285 (43%), Positives = 190/285 (66%), Gaps = 8/285 (2%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
               +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I
Sbjct: 2   THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEI 61

Query: 86  ILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVV 143
           +LN+KG+ +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L   +A +
Sbjct: 62  LLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAI 121

Query: 144 RMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
            M + V +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DK
Sbjct: 122 AMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDK 181

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V
Sbjct: 182 LVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPV 238

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           ++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 239 DDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 283


>gi|221632951|ref|YP_002522174.1| DNA-directed RNA polymerase subunit alpha [Thermomicrobium roseum
           DSM 5159]
 gi|221156271|gb|ACM05398.1| DNA-directed RNA polymerase, alpha subunit [Thermomicrobium roseum
           DSM 5159]
          Length = 326

 Score =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 118/313 (37%), Positives = 176/313 (56%), Gaps = 11/313 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  +P  I+              + EPL  G+  TLGNALRR+L+ SL GAAIT ++I G
Sbjct: 3   DFARPRVIQT----HAGPTYGRFVVEPLEPGYGTTLGNALRRILLRSLPGAAITRIRIAG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK-MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           V HE S+I+GV ED+T+I+LN+KG+ L+ ++     R T+F +G GVV AGD+    ++E
Sbjct: 59  VWHEFSTIEGVREDVTEIVLNLKGVRLRAVTEFRETRATLFAQGEGVVRAGDVDWPAEVE 118

Query: 127 VLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           V+NPDHVI  LD D A + M+L + +G GY+PA+    E   IG I IDA+++P  KV+Y
Sbjct: 119 VVNPDHVIATLDNDQARLEMDLWIGRGRGYLPAEA--QEIRSIGEIPIDAIFTPTLKVNY 176

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE  R G   DYD+L + I TDG++    ++  A+RIL         FE   +  +E +
Sbjct: 177 VVEHTRVGGATDYDRLILEIVTDGTVEPAKALVEAARILVQHARWIAEFE--SEGAEEPV 234

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
              S+       + + E+ LS R  N LR   I  +G ++      +L + NFG ++L E
Sbjct: 235 EEWSVAHVD-DTRLLSEIGLSQRVLNALRARGIERVGQVLAMRPDQLLGIRNFGPRALQE 293

Query: 306 IKGVLGTMGLFLG 318
           ++  L   G   G
Sbjct: 294 LRERLQENGYTEG 306


>gi|157493231|gb|ABV57981.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493233|gb|ABV57982.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493239|gb|ABV57985.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493241|gb|ABV57986.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493245|gb|ABV57988.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493249|gb|ABV57990.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493251|gb|ABV57991.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493253|gb|ABV57992.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493257|gb|ABV57994.1| RNA polymerase alpha subunit [Vibrio mimicus]
 gi|157493259|gb|ABV57995.1| RNA polymerase alpha subunit [Vibrio mimicus]
 gi|157493261|gb|ABV57996.1| RNA polymerase alpha subunit [Vibrio mimicus]
 gi|157493265|gb|ABV57998.1| RNA polymerase alpha subunit [Vibrio mimicus]
 gi|157493269|gb|ABV58000.1| RNA polymerase alpha subunit [Vibrio mimicus VM603]
 gi|157493271|gb|ABV58001.1| RNA polymerase alpha subunit [Vibrio mimicus]
 gi|157493289|gb|ABV58010.1| RNA polymerase alpha subunit [Vibrio mimicus]
 gi|157493291|gb|ABV58011.1| RNA polymerase alpha subunit [Vibrio mimicus]
 gi|157493293|gb|ABV58012.1| RNA polymerase alpha subunit [Vibrio mimicus]
          Length = 285

 Score =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 125/287 (43%), Positives = 190/287 (66%), Gaps = 8/287 (2%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
                 +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ 
Sbjct: 2   STTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDIL 61

Query: 84  DIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDA 141
           +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L   +A
Sbjct: 62  EILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNA 121

Query: 142 VVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M + V +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D 
Sbjct: 122 AIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDL 181

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+
Sbjct: 182 DKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLR 238

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 239 PVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 285


>gi|329565863|gb|AEB92268.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
          Length = 250

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 108/250 (43%), Positives = 159/250 (63%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL+SSL GAA  +V+IDGVLHE S++ GV ED+  IILN+K + +K+  D    
Sbjct: 1   GNSLRRVLLSSLPGAAPKSVKIDGVLHEFSTLPGVKEDVVKIILNLKEVAVKLHSDEPVV 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
             I   G G VTAG I+   DIE+LNPDH I  L  D  + ME+   KG GYVP+  ++ 
Sbjct: 61  GRIDVEGKGEVTAGHIKGSADIEILNPDHHIATLSDDGKLHMEIVFVKGKGYVPSDKNKE 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
            N PIG+I +D++++P+K+VSY V++ R G V DYDKL++ + T+G+IT ++++++AS +
Sbjct: 121 PNQPIGVIPVDSIFTPVKRVSYNVKNTRVGHVTDYDKLTLEVWTNGTITPKEAISMASDM 180

Query: 224 LQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGD 283
           L      FI+F    K     ++         L   +EEL+L VRS NCL+   I  + +
Sbjct: 181 LIKYFQKFISFTGEYKSSDIFVDKPEKKVEKPLDMTIEELDLFVRSYNCLKRAGINTVQE 240

Query: 284 LIQRTEADML 293
           L Q+TE +M+
Sbjct: 241 LTQKTEEEMM 250


>gi|52220841|ref|YP_086997.1| RNA polymerase alpha subunit [Panax ginseng]
 gi|68053096|sp|Q68RX5|RPOA_PANGI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|51235344|gb|AAT98540.1| RNA polymerase alpha subunit [Panax ginseng]
          Length = 353

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 88/360 (24%), Positives = 171/360 (47%), Gaps = 28/360 (7%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLR 56
           M+Q+  +  +    +++  +    ++        I  PL +G A T+G A+RR L+  + 
Sbjct: 1   MVQEKVR--VSTRTLQWKCVEARADSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIE 58

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           G  IT  + + + HE S++ G+ E + +I++N+K I LK +       +I  RGPG VTA
Sbjct: 59  GTCITRAKSEKIPHEYSTLVGIQESVHEILMNLKEIILKSNLYGTCDASICIRGPGYVTA 118

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
            DI +   +E+++    I +L     + + L + +  GY+    +   N   G   IDA+
Sbjct: 119 QDIISPPYVEIVDNTQHIASLAEPIDLCIGLQIERNRGYLIKTPNN--NFQDGSYPIDAV 176

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           + P++  ++++ S   G     + L + I T+GS+T ++++  ASR L D    F++ EE
Sbjct: 177 FMPVRNANHSIHSYGNG-NEKQEILFLEIWTNGSLTPKEALHQASRNLIDLFIPFLHTEE 235

Query: 237 PKKEVKEDINVKSLPFNPALLK----------------KVEELELSVRSTNCLRGENIVY 280
               + ++ +   LP      K                 +++ EL  R  NCL   NI  
Sbjct: 236 ENLHLADNQHTVPLPPFTFHEKLTKLRKNKKKIALKSIFIDQSELPPRIYNCLIRSNIYT 295

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
           + DL+  ++ D++++ +F    + ++K +LG +     ++LP       E LA+    + 
Sbjct: 296 LLDLLNNSQEDLMKIEHFR---IEDVKAILGILEKHFAIDLPKKLKIGFESLAQSIYSES 352


>gi|11465759|ref|NP_053903.1| RNA polymerase alpha subunit [Porphyra purpurea]
 gi|1710668|sp|P51293|RPOA_PORPU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1276759|gb|AAC08179.1| DNA directed RNA polymerase alpha subunit [Porphyra purpurea]
          Length = 311

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 97/297 (32%), Positives = 160/297 (53%), Gaps = 9/297 (3%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               + E L +G   TLGNALRR ++S L G AI AV+I GV HE S+I GV ED+ +I+
Sbjct: 20  YGSFVIEALNQGQGITLGNALRRSILSDLEGTAIVAVRIAGVNHEFSTIPGVREDVLEIL 79

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+K +  K +    +   I  +GP +VTAG  +  +DIEV++P   I  +  + +  ME
Sbjct: 80  LNLKEVVFKSNNQESQIGRIKVQGPAIVTAGLFELSSDIEVVDPRQYIATICNNTIFEME 139

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
             + K  GY  A+    +   +  + +D+++ P+ KV+Y VE  R G     D+L + I 
Sbjct: 140 FKIEKSCGYRLAEK-AVDELSLDFLQVDSVFMPVNKVNYKVEEVRVGTNSIKDRLILQIW 198

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+GSI+ +++++  + +L +      N +    +   +   K           +EEL+LS
Sbjct: 199 TNGSISPQEAISQGATVLTNLFCSLRNLDFKSVDTYRNKEDK-----KISQVLIEELQLS 253

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           VR+ NCL+   I  + DL+  ++ ++L + NFG+KS  E+   L      LG++LP 
Sbjct: 254 VRAYNCLKRAQIHSIADLLDYSQEELLEIKNFGQKSAEEVIYAL---QKTLGISLPK 307


>gi|148243238|ref|YP_001228395.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp.
           RCC307]
 gi|172047891|sp|A5GVY3|RPOA_SYNR3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|147851548|emb|CAK29042.1| DNA-directed RNA polymerase alpha chain [Synechococcus sp. RCC307]
          Length = 312

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 103/312 (33%), Positives = 169/312 (54%), Gaps = 14/312 (4%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + ++Y +   + ++  + +  PL RG A TLG ALRRVLMS L G A+TAV+I GV HE 
Sbjct: 7   DRVDYQIADDQSQS-GVFVIGPLDRGQATTLGTALRRVLMSGLEGTAVTAVRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           +++ GV ED+ DI+LN K + L       +   +   GP  VTAGD+Q  + + V+N D 
Sbjct: 66  ATVPGVREDVLDILLNCKELVLSSRSRDTEIGRLVVNGPASVTAGDLQFSSQVSVVNADC 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P +    +   + L+ IDA++ P+++V++TV+    
Sbjct: 126 PIATVADGHALELEVHVERGVGYRPVERTSEDAAALDLLQIDAVFMPVRRVNFTVDETAV 185

Query: 193 GQVLD-YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF---EEPKKEVKEDINVK 248
           G+     ++L + I+T+GSIT +D++A A+  L             EEP +E +     +
Sbjct: 186 GEGGSARERLRLEINTNGSITPDDALAYAANQLIALFQPLATVTLAEEPGQEPEPSAESQ 245

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                      +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+  
Sbjct: 246 ---------IPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGAKSADEVIE 296

Query: 309 VLGTMGLFLGMN 320
            L  +G+ L  +
Sbjct: 297 ALERIGISLPQS 308


>gi|300089409|gb|ADJ67856.1| RNA polymerase alpha-subunit [Photobacterium jeanii]
          Length = 274

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 125/277 (45%), Positives = 185/277 (66%), Gaps = 7/277 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+
Sbjct: 1   VTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDVLEILLNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELT 148
           KG+ +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L  D A + M + 
Sbjct: 61  KGLAVKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNADISMRIK 120

Query: 149 VSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           V +G GYVPA    H   +  PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + +
Sbjct: 121 VERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDRIAYAVEAARVEQRTDLDKLVIDM 180

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V++LEL
Sbjct: 181 QTNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLEL 237

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           +VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KS
Sbjct: 238 TVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKS 274


>gi|329565843|gb|AEB92258.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
          Length = 250

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 109/250 (43%), Positives = 159/250 (63%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL+SSL GAA  +V+IDGVLHE S++ GV ED+ +IILN+K   +K+  D    
Sbjct: 1   GNSLRRVLLSSLPGAAPKSVKIDGVLHEFSTLPGVKEDVVEIILNLKEGAVKLHSDEPVV 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
             I   G G VTAG I+   DIE+LNPDH I  L  D    ME+   KG GYVP+  ++ 
Sbjct: 61  GRIDVEGKGEVTAGHIKGSADIEILNPDHHIATLSDDGKPHMEIVFVKGKGYVPSDKNKE 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
            N PIG+I +D++++P+K+VSY V++ R G V DYDKL++ + T+G+IT ++++++AS +
Sbjct: 121 PNQPIGVIPVDSIFTPVKRVSYNVKNTRVGHVTDYDKLTLEVWTNGTITPKEAISMASDM 180

Query: 224 LQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGD 283
           L      FI+F    K     ++         L   +EEL+LSVRS NCL+   I  + +
Sbjct: 181 LIKYFQKFISFTGEYKSSDIFVDKPEKKVEKPLDMTIEELDLSVRSYNCLKRAGINTVQE 240

Query: 284 LIQRTEADML 293
           L Q+TE +M+
Sbjct: 241 LTQKTEEEMM 250


>gi|46143635|ref|ZP_00134832.2| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Actinobacillus pleuropneumoniae serovar 1 str. 4074]
          Length = 279

 Score =  282 bits (722), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 129/281 (45%), Positives = 192/281 (68%), Gaps = 7/281 (2%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           + G A+T V+IDGVLHE SS +GV ED+ +++LN+KG+ +K+SG     +T+ K G G V
Sbjct: 1   MPGCAVTEVEIDGVLHEYSSKEGVQEDILEVLLNLKGLAVKVSGKDDIILTLNKSGIGPV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGL 170
           TA DI    D+E++NP HVIC+L D DA + M + V +G GYVPA    H + E+ PIG 
Sbjct: 61  TAADITHDGDVEIVNPHHVICHLTDKDASISMRIRVQRGRGYVPASARVHSQDEDRPIGR 120

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  
Sbjct: 121 LLVDARFSPVDRIAYNVEAARVEQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDA 180

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
           F++  + ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE 
Sbjct: 181 FVDLRDVRQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEV 237

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           ++L+  N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 238 ELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 278


>gi|290489662|gb|ADD31215.1| RNA polymerase alpha subunit protein [Ilex cornuta]
          Length = 337

 Score =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 83/331 (25%), Positives = 162/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  RGPG VT  DI     +E++
Sbjct: 71  PHEYSTIVGIQESVHEILMNLKEIVLRSNLYGTCDASICVRGPGYVTTQDIILPPYVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY+    +  ++   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDLCIGLQIERNRGYLIKTPNNFQD---GSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S R G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYRNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEENLHLEDNQHTI 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            LP      K                 +++LEL  R  NCL+  NI  + DL+   + D+
Sbjct: 247 PLPPFNFHDKLAKLRKNKKKIALKSIFIDQLELPPRIYNCLKRSNIYTLLDLLNNVQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F    + ++K +LG +     ++LP 
Sbjct: 307 MKIEHFR---IEDVKQILGVLEKHFAIDLPK 334


>gi|260891349|ref|ZP_05902612.1| DNA-directed RNA polymerase, alpha subunit [Leptotrichia hofstadii
           F0254]
 gi|260858732|gb|EEX73232.1| DNA-directed RNA polymerase, alpha subunit [Leptotrichia hofstadii
           F0254]
          Length = 324

 Score =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 115/309 (37%), Positives = 178/309 (57%), Gaps = 4/309 (1%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
              +E+        EPL RG+ +T+GNALRR+L+SS+ G AI  ++I+GVL+E S+I+GV
Sbjct: 14  TEEKEDNYTAKYTLEPLYRGYGNTIGNALRRILLSSIPGTAIKGIKIEGVLNEFSTIEGV 73

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E +TDIILN+K I ++      K++T+  +GP V+TA DI     + ++NP+ VI  + 
Sbjct: 74  KEAVTDIILNVKEIVVEADEPGEKKMTLSVKGPAVITAADIHVEPGLRIINPEQVIMTVT 133

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  + +E  V  G G+V +    T+  PIG + +DA+Y+PIK+V+Y+VE    G+V +Y
Sbjct: 134 TDRQIDIEFLVDSGEGFVVSDEINTDGWPIGYLAVDAIYTPIKRVNYSVEDTMVGRVTNY 193

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK----EVKEDINVKSLPFNP 254
           DKL + I TDGSI  +D+++ A  +L   L  F N             E     +   N 
Sbjct: 194 DKLILEIATDGSIEIKDALSYAVELLTWHLEPFTNIGNSMSKYRDSEDELAEADAENENN 253

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
               K+EEL+ +VRS NCL+   +  + DL   T  ++L++ N G+KSL EI   +  +G
Sbjct: 254 IEDMKIEELDFTVRSYNCLKKAGVNTISDLTSMTYNELLKIKNLGKKSLNEIIDKMKELG 313

Query: 315 LFLGMNLPD 323
             LG N  +
Sbjct: 314 YDLGDNQSN 322


>gi|228470691|ref|ZP_04055542.1| DNA-directed RNA polymerase, alpha subunit [Porphyromonas uenonis
           60-3]
 gi|228307548|gb|EEK16544.1| DNA-directed RNA polymerase, alpha subunit [Porphyromonas uenonis
           60-3]
          Length = 317

 Score =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 113/314 (35%), Positives = 190/314 (60%), Gaps = 7/314 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
              ++      +PL  G+A T+GNALRR+L+SSL G AI +++I+GV HE ++I GV ED
Sbjct: 3   DASDHYAKFEFKPLEPGYAMTIGNALRRILLSSLEGYAIASIRIEGVEHEFATIPGVLED 62

Query: 82  LTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHVICNLD 138
           +T IILN+K I  + + +    + +T+   G     AGD+ + +   +V NPD VICNL 
Sbjct: 63  VTHIILNLKQIRFRATVEDPQEETITLHVTGRNSFKAGDLNKVLTSYKVQNPDLVICNLA 122

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            DA   +E+ ++KG GYV ++ +R E+DP+  + ID +Y+PI+KV+ T E+ R  Q  DY
Sbjct: 123 EDADFTIEIRINKGRGYVVSEENRREDDPVNTLPIDGIYTPIRKVNQTTEAYRVDQRTDY 182

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKSLPFNP 254
           +KL + I+TDG+I   +++  A++IL     +F +     E P++E ++ ++ + +    
Sbjct: 183 EKLVLEIETDGTIHPREALREAAKILISHFALFTDKEFEVELPEEEPEQLLDNQMMKVRS 242

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
            L+  +   +LSVR+ NCL+   I  + DL+ R   ++L++ NFG+KSLVE++  L    
Sbjct: 243 QLMTDLATTDLSVRALNCLKAAGISTIADLLSRDREELLKIKNFGKKSLVELEQFLTDQK 302

Query: 315 LFLGMNLPDWPPES 328
           L   M+L  +  ++
Sbjct: 303 LDFDMDLSPYRLDN 316


>gi|257126748|ref|YP_003164862.1| DNA-directed RNA polymerase subunit alpha [Leptotrichia buccalis
           C-1013-b]
 gi|257050687|gb|ACV39871.1| DNA-directed RNA polymerase, alpha subunit [Leptotrichia buccalis
           C-1013-b]
          Length = 324

 Score =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 113/309 (36%), Positives = 180/309 (58%), Gaps = 4/309 (1%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
              +E+        EPL RG+ +T+GNALRR+L+SS+ G AI  ++I+GVL+E S+I+GV
Sbjct: 14  TEEKEDNYTAKYTLEPLYRGYGNTIGNALRRILLSSIPGTAIKGIKIEGVLNEFSTIEGV 73

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E +TDIILN+K I ++      K++T+  +GP V+TA DI     ++++NP+ VI  + 
Sbjct: 74  KEAVTDIILNVKEIVVESDEPGEKKMTLSVKGPAVITAADIHVEPGLKIINPEQVIMTVT 133

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  + +E  V  G G+V +    T+  PIG + +DA+Y+PIK+V+Y+VE    G+V +Y
Sbjct: 134 TDKQIDIEFLVDSGEGFVVSDEINTDGWPIGYLAVDAIYTPIKRVNYSVEDTMVGRVTNY 193

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV----KSLPFNP 254
           DKL + I TDGSI  +D+++ A  +L   L  F N      + ++  +          N 
Sbjct: 194 DKLILEIATDGSIEIKDALSYAVELLTWHLEPFTNIGNSMSKYRDSEDELTVTAEENENN 253

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
               K+EEL+ +VRS NCL+   +  + DL   T  ++L++ N G+KSL EI   +  +G
Sbjct: 254 IEDMKIEELDFTVRSYNCLKKAGVNTISDLTSMTYNELLKIKNLGKKSLNEIIDKMKELG 313

Query: 315 LFLGMNLPD 323
             LG    +
Sbjct: 314 YDLGDTSSN 322


>gi|300521220|gb|ADK25829.1| RpoA [Vibrio vulnificus]
 gi|300521222|gb|ADK25830.1| RpoA [Vibrio vulnificus]
 gi|300521224|gb|ADK25831.1| RpoA [Vibrio vulnificus]
 gi|300521226|gb|ADK25832.1| RpoA [Vibrio vulnificus]
 gi|300521228|gb|ADK25833.1| RpoA [Vibrio vulnificus]
 gi|300521230|gb|ADK25834.1| RpoA [Vibrio vulnificus]
 gi|300521232|gb|ADK25835.1| RpoA [Vibrio vulnificus]
 gi|300521234|gb|ADK25836.1| RpoA [Vibrio vulnificus]
 gi|300521236|gb|ADK25837.1| RpoA [Vibrio vulnificus]
 gi|300521238|gb|ADK25838.1| RpoA [Vibrio vulnificus]
 gi|300521240|gb|ADK25839.1| RpoA [Vibrio vulnificus]
          Length = 286

 Score =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 128/289 (44%), Positives = 189/289 (65%), Gaps = 8/289 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED
Sbjct: 1   QISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQED 60

Query: 82  LTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           + +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+ NP+HVIC+L  D
Sbjct: 61  ILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDD 120

Query: 141 -AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
            A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  
Sbjct: 121 NAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRT 180

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P L
Sbjct: 181 DLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPIL 237

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           L+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 238 LRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 286


>gi|187251794|ref|YP_001876276.1| DNA-directed RNA polymerase subunit alpha [Elusimicrobium minutum
           Pei191]
 gi|186971954|gb|ACC98939.1| DNA-directed RNA polymerase, alpha subunit [Elusimicrobium minutum
           Pei191]
          Length = 329

 Score =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 124/327 (37%), Positives = 185/327 (56%), Gaps = 13/327 (3%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           + +L+ P  I+             +IAEP   G+ HT+GN+LRR+L+S L G+A+TAV++
Sbjct: 3   FNQLVLPTKIQLDEK-TVTPFYGRIIAEPYESGYGHTVGNSLRRILLSGLDGSAVTAVRV 61

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
            G +HE S+I  V ED+ +I+LN+K + +K+ G + + V +    PG VTA DI  V+ +
Sbjct: 62  RGAVHEYSTIPNVKEDVINILLNLKKLRVKLEGKNREYVYLTASKPGKVTAKDIAEVSGV 121

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++N D  I NL+    + +E+ +S+G GYVPA+       P G I +DA++SPI KV Y
Sbjct: 122 EIINKDLEIANLEQGGKLELEIEISQGKGYVPAEDLSKIQRPAGFIPVDAIFSPILKVHY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI----NFEEPKKEV 241
            VE AR GQ  DYD+L + I TDG++    ++  A+ +L   L +F            E 
Sbjct: 182 DVEPARVGQKTDYDRLVIQITTDGTLEPAKALHKAAVLLSQSLHIFTIEGEEVNAAAPET 241

Query: 242 KEDINVKSLPFNPALLKKVEEL--------ELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           +      S+    A+  KVEEL        ELS RS NCL+ E +  + DL+ +TE D+ 
Sbjct: 242 EPLSTTGSVSGVSAVNSKVEELLNQSVEFIELSSRSINCLKSEGVNTVKDLVSKTEDDLK 301

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMN 320
            + NFG +SL E+K  L  M L LGM 
Sbjct: 302 MIKNFGTRSLDEVKERLAEMNLSLGMK 328


>gi|37912970|gb|AAR05302.1| DNA-directed RNA polymerase alpha subunit [uncultured marine gamma
           proteobacterium EB000-45B06]
          Length = 283

 Score =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 119/286 (41%), Positives = 183/286 (63%), Gaps = 3/286 (1%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           +GNALRR+L+SS+ GAA+T V IDG+ HE S+I+GV ED+ DI+LNIK + + +   +  
Sbjct: 1   MGNALRRILLSSMPGAAVTDVAIDGISHEYSTIEGVREDVIDILLNIKDMPVNIIEGNTA 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            +T+   GP  V A       ++E++N D  +  +     ++M LTV  G GY PA    
Sbjct: 61  EITLDVTGPCDVLASSFDVPGNVELVNQDFHVATIVDKVNLKMTLTVQTGRGYEPADTRD 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            E+  +G + +DA YSP+++VSYTV++AR  +  D DKL + ++TDG++  + ++  ++ 
Sbjct: 121 DEDRVVGALKVDASYSPVRRVSYTVDNARFEKRTDLDKLVIELETDGTLDPKMAIEHSAT 180

Query: 223 ILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMG 282
           ILQ QL  F++ +      +++       F+P LL+ +EELEL+VRSTNCL+ E+I  +G
Sbjct: 181 ILQQQLSSFVDLDAIA---EQEAKKDQNDFDPFLLRSIEELELTVRSTNCLKAESIFLIG 237

Query: 283 DLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPES 328
           DLI R+E D+L+  N G+KSL EIK VL +  L LGMN+ +WPP  
Sbjct: 238 DLIHRSEFDLLKTPNLGKKSLNEIKDVLASKELSLGMNVDNWPPVG 283


>gi|58758770|gb|AAW81775.1| RNA polymerase alpha subunit [Oedipodium griffithianum]
          Length = 340

 Score =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 93/342 (27%), Positives = 162/342 (47%), Gaps = 27/342 (7%)

Query: 1   MIQKNWQ---ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRG 57
           MIQ       ++++   +E  V  +     +     P   G A+T+G A+RR L+  + G
Sbjct: 1   MIQNEISVSAQVLQWRCVESKVDSERLH-YSRFAISPFRCGQANTVGIAMRRALLGEVEG 59

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
             IT  +   V HE S+I G+ E + DI++N+K I L+ +    ++  I   GP  VTA 
Sbjct: 60  TCITCAKFKKVTHEYSTIAGIQESVHDILINLKEIVLRSNSYETQKAFISILGPKKVTAQ 119

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI     +++++    I  L     + +EL + K  GY      ++ +   G   IDA++
Sbjct: 120 DIILPPSVKIIDTTQYIATLTKTIHLDIELEIEKDCGYRIQDSIKSTD---GHFPIDAIF 176

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-- 235
            PI+  +Y+V S         + L + I T+GSIT ++++  ASR L D    F++ E  
Sbjct: 177 MPIRNANYSVHSFEHENKT-QEILFIEIWTNGSITPKEALYEASRSLIDLFIPFLHAEKK 235

Query: 236 ------EPKKEVKEDINVKSLPFNPALLKK--------VEELELSVRSTNCLRGENIVYM 281
                 E K E        S       + K        +++LEL  R+ NCL+  N+  +
Sbjct: 236 EIINGLENKYESNNMSYFSSFSPLADRITKEVTFKHIFIDQLELPARAYNCLKRVNVHTI 295

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            DL+  ++ D++++ NFG+KS+ ++   L  +     +NLP 
Sbjct: 296 SDLLNYSQDDLMKIKNFGKKSVEQV---LEALQKQFSINLPK 334


>gi|254431538|ref|ZP_05045241.1| DNA-directed RNA polymerase, alpha subunit [Cyanobium sp. PCC 7001]
 gi|197625991|gb|EDY38550.1| DNA-directed RNA polymerase, alpha subunit [Cyanobium sp. PCC 7001]
          Length = 312

 Score =  282 bits (721), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 105/309 (33%), Positives = 167/309 (54%), Gaps = 8/309 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ V     +   + +  PL RG A TLGNALRRVL+  L G+AITAV+I GV HE 
Sbjct: 7   DRIEHHVAEDRAQT-GVFLIGPLDRGQATTLGNALRRVLIGGLEGSAITAVRISGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           +++ GV ED+ DI+LN K + +       +   +   GP  VTA D+Q  + ++V++PD 
Sbjct: 66  ATVPGVREDVLDILLNCKQVAVSSRSRELEIGRLVVNGPATVTAADLQFSSQVQVIDPDR 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           +I  +     + ME+ V +G GY P   H  +   I L+ IDA++ P+K+V+YTV+    
Sbjct: 126 LIATVAEGFGLEMEVHVERGVGYRPVDRHSEDTSAIDLLQIDAVFKPVKRVNYTVDETAV 185

Query: 193 GQVLD-YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           G+     ++L + I+T+GSIT +D++A A+  L             ++  +E        
Sbjct: 186 GEGGSARERLRLEIETNGSITPDDAMAQAANQLIALFQPLATLSVVEEPGQEPEPSAE-- 243

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 244 ----AQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLFLGMN 320
            +G+ L  +
Sbjct: 300 RIGITLPQS 308


>gi|323149114|ref|YP_004222678.1| RNA polymerase alpha subunit [Anthriscus cerefolium]
 gi|289645607|gb|ADD13670.1| RNA polymerase alpha subunit [Anthriscus cerefolium]
          Length = 338

 Score =  282 bits (721), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 89/334 (26%), Positives = 163/334 (48%), Gaps = 23/334 (6%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +  + +N        I  PL +G A T+G A+RR L+  + G  IT  + D +
Sbjct: 11  RTLQWKCVESKADNKRLYYGRFIMSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFDKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S++ G+ E + DI++N+K I L+ +       +I  RGPG VTA DI     +EV+
Sbjct: 71  PHEYSTLMGIQESVHDILMNLKEIVLRSNLYGTCDASICVRGPGYVTAQDIILPPYVEVV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY+    +   N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIELCIGLQIERNRGYLIKTPNN--NSQDGSYPIDAVFMPVRNANHSIH 188

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    + ++ ++ 
Sbjct: 189 SYGNG-NDKQEILFLEIWTNGSLTPKEALHEASRNLIDLFITFLHTEEENLHLADNQHMV 247

Query: 249 SLPFNPALLK-------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
            LP      K              +++ EL  R  NCL+  NI  + DL+  ++ D++++
Sbjct: 248 PLPPFTFHDKLRKKQKKIALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQKDLMKI 307

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
             F  K   ++K +LG +   L ++LP  P    
Sbjct: 308 DRFRIK---DVKHILGILEKHLSIDLPKKPKMGF 338


>gi|156597913|gb|ABU85224.1| RNA polymerase alpha subunit [Anethum graveolens]
          Length = 338

 Score =  281 bits (720), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 86/333 (25%), Positives = 161/333 (48%), Gaps = 26/333 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +  + +N        I  PL +G A T+G A+RR L+  + G  IT  +   +
Sbjct: 11  RTLQWKCVESKADNKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSKKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S++ G+ E + DI++N+K I L+ +       +I  RGPG VTA DI     +EV+
Sbjct: 71  PHEYSTLVGIQESVHDILMNLKEIVLRSNLYGTCDASICVRGPGYVTAQDIILPPYVEVV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY+    +   N   G   IDA++ PI+  ++++ 
Sbjct: 131 DNTQHIASLTEPIELHIGLQIERSRGYLIKTPNN--NFQDGSYPIDAVFMPIRNANHSIH 188

Query: 189 SAREGQVLD-YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           S   G   D  + L + I T+GS+T ++++  ASR L D    F++ EE    + ++ ++
Sbjct: 189 SYGNGNGNDKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHTEEENLHLADNQHM 248

Query: 248 KSLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
             LP                        +++ EL  R  NCL+  NI  + DL+  ++ D
Sbjct: 249 VPLPPFTFHDNLDKLRKNKKKIALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQED 308

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           ++++ +F    + ++K +LG +     ++LP  
Sbjct: 309 LMKIEHFR---INDVKQILGILEKHFSIDLPKK 338


>gi|15605668|ref|NP_213043.1| DNA-directed RNA polymerase subunit alpha [Aquifex aeolicus VF5]
 gi|6226037|sp|O66483|RPOA_AQUAE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|2982817|gb|AAC06440.1| RNA polymerase alpha subunit [Aquifex aeolicus VF5]
          Length = 317

 Score =  281 bits (720), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 120/318 (37%), Positives = 186/318 (58%), Gaps = 8/318 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E I P+ I +    ++ +    ++ EPL RGF  T+GN+LRRVL+SS+ G AITAV+I 
Sbjct: 3   NEFIYPDKIFW---EEKTDTYGRLVVEPLERGFGTTVGNSLRRVLLSSISGTAITAVKIY 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQTVNDI 125
           G+ HE S+I+GV ED  ++I N+K I   M GDS  + + + K+G G V A DI+T  ++
Sbjct: 60  GIYHEFSAIEGVQEDAIELIANLKKIKFLMKGDSDVEILYLQKKGEGEVKASDIKTPPNV 119

Query: 126 EVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           E+LNPD  I  +   +  + +E+ V +G GYVP +      + +G I +DA +SP+KKV 
Sbjct: 120 EILNPDQYIATITDPNKELNIEIRVERGRGYVPVEEMEAIGE-VGWILVDADFSPVKKVG 178

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + V++ R G+   Y++L++ I T+G  T +  +  A  IL+    +  N    K  V + 
Sbjct: 179 FRVDNVRVGKKSTYERLTLEIFTNGIKTPDQCMQEAIEILKKHYELLENIFTEKPTVPQK 238

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           + V  L     L   +EEL++S R+ N L+   I  +GDL++ TE ++    N GRK+L 
Sbjct: 239 VAVDELA--EKLSLSIEELDISQRALNSLKRIGITTIGDLVRMTEDELKSTKNIGRKALA 296

Query: 305 EIKGVLGTMGLFLGMNLP 322
           EIK  L  +GL LGMN+ 
Sbjct: 297 EIKEALHKLGLELGMNIE 314


>gi|15644221|ref|NP_229272.1| DNA-directed RNA polymerase subunit alpha [Thermotoga maritima
           MSB8]
 gi|7388097|sp|Q9X1I2|RPOA_THEMA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|4982038|gb|AAD36540.1|AE001798_5 DNA-directed RNA polymerase, alpha subunit [Thermotoga maritima
           MSB8]
          Length = 336

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 117/331 (35%), Positives = 179/331 (54%), Gaps = 22/331 (6%)

Query: 8   ELIKPNNIEYIVLGQE-EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           E + P  ++     +E +   +     PL RG+A T+GNALRRVL+SS+   AI  V+  
Sbjct: 3   EFVIPKKLKVEEEREERDYYYSRFSLSPLERGYAITIGNALRRVLLSSIPSLAIVGVRFI 62

Query: 67  G--VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTV 122
                HE   I+GV ED+ DIILN+K +  +++       ++ + K+GPG + AGDI+T 
Sbjct: 63  KPEKYHEYDYIEGVKEDILDIILNLKKVQFRINVTVKGTIKMEVEKKGPGELVAGDIKTP 122

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
             IEV+NPD  I  L+  A +  E+    G G+VP    R E   +G I ID ++SP+ K
Sbjct: 123 AGIEVVNPDLHIATLNSKADLFFEVYAEVGKGFVPVSE-REERPDVGWIPIDGVFSPVIK 181

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM------------ 230
           V++  E+ R G+  DYDKL + I T  SI  E+++  A+ IL +   +            
Sbjct: 182 VNFLTENVRVGKRTDYDKLILEIWTKKSIRPEEALRKAADILINHFKIVTEGLPELKISE 241

Query: 231 ---FINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
                + EE  +    +   +    +    +K++ELELSVRS NCL+   I  +GDL+ +
Sbjct: 242 EYIITSEEEEAEVPASEHEEEHRENSDVYNRKIDELELSVRSLNCLKRAKIETIGDLLSK 301

Query: 288 TEADMLRMANFGRKSLVEIKGVLGT-MGLFL 317
           TE ++L++ NFG+KSL E+K  L    GL L
Sbjct: 302 TEEELLKIKNFGQKSLDEVKEKLKEKFGLEL 332


>gi|157493267|gb|ABV57999.1| RNA polymerase alpha subunit [Vibrio mimicus]
          Length = 283

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 124/285 (43%), Positives = 189/285 (66%), Gaps = 8/285 (2%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
                 +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ 
Sbjct: 2   STTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDIL 61

Query: 84  DIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDA 141
           +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L   +A
Sbjct: 62  EILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNA 121

Query: 142 VVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M + V +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D 
Sbjct: 122 AIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDL 181

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+
Sbjct: 182 DKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLR 238

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 239 PVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 283


>gi|282857336|ref|ZP_06266573.1| DNA-directed RNA polymerase, alpha subunit [Pyramidobacter
           piscolens W5455]
 gi|282584836|gb|EFB90167.1| DNA-directed RNA polymerase, alpha subunit [Pyramidobacter
           piscolens W5455]
          Length = 338

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 111/341 (32%), Positives = 187/341 (54%), Gaps = 21/341 (6%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+++P     I + +       ++  PL RG+  T+GNALRRVL+SS++GAAI+AV+++G
Sbjct: 2   EIMRPE----IQVEECSSTAARLVIGPLERGYGQTIGNALRRVLLSSIKGAAISAVRVEG 57

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
             HE ++I G+ ED+ +++LN+K + ++     ++ + +   G   VTA D Q  +DIE 
Sbjct: 58  AQHEFTTIPGMKEDVIELLLNLKHVPVRSHSAEYRTLKLDVEGGKKVTAADFQEDSDIEF 117

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           ++PD  IC L     + +E+ + +G GY      R    P+  + IDA+YSPI +V Y V
Sbjct: 118 IDPDAYICTLAEGHSLSLEVYIEQGVGYATVDRPRPSYLPVDALMIDAIYSPILRVKYEV 177

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI--------------- 232
           ++ R GQ  DY+K+ M + T+G +  + +VA A+++L++   + I               
Sbjct: 178 QNERVGQKTDYEKIVMNVTTNGVVAPDIAVAEAAKLLREYFDIVIQELRKLHPAEPGLFD 237

Query: 233 --NFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
             +  +P    +      + P N  L K V ELELS+RS NCL    I  +GDL+ R++ 
Sbjct: 238 DESASQPSGNGQAGDGADNPPENALLNKPVRELELSIRSENCLLRGGIHTIGDLVSRSKD 297

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           D+L++ N G+ SL EI+  +   G+ L  +       S E+
Sbjct: 298 DLLKIRNLGKISLREIEEKMTKYGIVLSDDKASAENSSKED 338


>gi|237736198|ref|ZP_04566679.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium mortiferum
           ATCC 9817]
 gi|229421751|gb|EEO36798.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium mortiferum
           ATCC 9817]
          Length = 325

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 119/309 (38%), Positives = 186/309 (60%), Gaps = 6/309 (1%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I   +E E +   I EPL RG+ HT+GNALRRVL+SS+ GAAI  V+I+GVL E S ++G
Sbjct: 13  ITEVKENEFKGQYIVEPLYRGYGHTVGNALRRVLLSSIPGAAIKGVRINGVLSEFSVMEG 72

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V E +T+IILNIK I +K      +++T+  +GP  VTA DI     IE++NP+ VIC +
Sbjct: 73  VKEAVTEIILNIKEIVVKAETSGERKMTLSVKGPKTVTAADIIPDVGIEIVNPEQVICTI 132

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSYT++    G++ D
Sbjct: 133 TTDRELDMEFLVDTGEGFVVSEDIERKDWPVDYIAVDAIYTPIRKVSYTIQDTMVGRMTD 192

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP------ 251
           +DKL++ I+TDGSI   D+++ A  +L+     F+      + ++ ++  +         
Sbjct: 193 FDKLTLEIETDGSIEIRDALSYAVELLKLHFDPFLELGNKMENLRAEVEDEEEDSTTHSK 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +  L  K+EEL+L+VRS NCL+   I  +  L + +  ++L++ N GRKSL EI   + 
Sbjct: 253 DDNILNTKIEELDLTVRSFNCLKKAGIEEVSQLAKLSLNELLKIKNLGRKSLDEILEKMK 312

Query: 312 TMGLFLGMN 320
            +G  L  N
Sbjct: 313 ELGYDLTQN 321


>gi|157493255|gb|ABV57993.1| RNA polymerase alpha subunit [Vibrio mimicus]
          Length = 285

 Score =  281 bits (718), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 124/287 (43%), Positives = 189/287 (65%), Gaps = 8/287 (2%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
                 +  EPL RGF HTLGNALRR+L+SS+ G  +T V+I+GVLHE S+ +GV ED+ 
Sbjct: 2   STTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCVVTEVEIEGVLHEYSTKEGVQEDIL 61

Query: 84  DIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDA 141
           +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L   +A
Sbjct: 62  EILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNA 121

Query: 142 VVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M + V +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D 
Sbjct: 122 AIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDL 181

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+
Sbjct: 182 DKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLR 238

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 239 PVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 285


>gi|318042541|ref|ZP_07974497.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp.
           CB0101]
          Length = 312

 Score =  281 bits (718), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 101/312 (32%), Positives = 167/312 (53%), Gaps = 14/312 (4%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + +E+ +     +   + +  PL RG A TLGN+LRRVLM +L G+AITAV+I GV HE 
Sbjct: 7   DRVEHQIADDRSQT-GVFVIGPLERGQAITLGNSLRRVLMGALEGSAITAVRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           +++ GV ED+ DI+LN K I +       +   +   GP  VTA D+Q  + + V++ D 
Sbjct: 66  ATVPGVREDVLDILLNCKDIAVSSRTRELEIGRLVANGPCTVTASDLQFSSQVSVIDGDR 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P      +   I L+ IDA++ P+++V+Y+V+    
Sbjct: 126 PIATVADGYSLELEVHVERGVGYRPVDRRSEDTSAIDLLQIDAVFMPVRRVNYSVDETAV 185

Query: 193 GQVLD-YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF---EEPKKEVKEDINVK 248
           G+     ++L + I+TDGS+T +D++A A+  L        +    +EP  E +     +
Sbjct: 186 GEGGSARERLRLEIETDGSVTPDDAMAQAANQLIALFQPLASLTMVDEPGLEPEPSAEAQ 245

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                      +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+  
Sbjct: 246 ---------IPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIE 296

Query: 309 VLGTMGLFLGMN 320
            L  +G+ L  +
Sbjct: 297 ALERIGISLPQS 308


>gi|300089407|gb|ADJ67855.1| RNA polymerase alpha-subunit [Photobacterium jeanii]
          Length = 270

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 124/273 (45%), Positives = 183/273 (67%), Gaps = 7/273 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+ 
Sbjct: 1   PLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDVLEILLNLKGLA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKG 152
           +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L  D A + M + V +G
Sbjct: 61  VKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNADISMRIKVERG 120

Query: 153 HGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            GYVPA    H   +  PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + + T+G
Sbjct: 121 RGYVPASARIHTEEDERPIGRLLVDATFSPVDRIAYAVEAARVEQRTDLDKLVIDMQTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           ++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V++LEL+VRS
Sbjct: 181 TLDPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRS 237

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
            NCL+ E I Y+GDL+QRTE ++L+  N G+KS
Sbjct: 238 ANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKS 270


>gi|730608|sp|Q01569|RPOA_PYRSA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|938275|emb|CAA46702.1| DNA-directed RNA polymerase alpha subunit [Pyrenomonas salina]
          Length = 314

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 100/311 (32%), Positives = 168/311 (54%), Gaps = 10/311 (3%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             IE    G  +   +    EPL +G   TLGNALRR L++ L G AI AV+I GV HE 
Sbjct: 7   ECIESTREGLRDH-YSKFCLEPLNQGQGTTLGNALRRTLLADLEGTAIVAVRIAGVSHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           S+I G+ ED+ +I+LN+K + LK    +     +  +GP +VT   ++  ++IE+++P+ 
Sbjct: 66  STIPGIREDVLEILLNLKEVVLKSQIGTSGVGRLRVQGPAIVTTNHLELPSEIELIDPNQ 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +  + ++ ME  +  G GY   +   ++   I  + +DA++ P+KKV+Y  +  R 
Sbjct: 126 YIATICGNNILEMEFRIETGKGYNLVER-DSDESSIDFLQVDAIFMPVKKVNYLSKDIRS 184

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
              L  ++L++ + T+GSI  +D+V+ A +IL + L             K D +   +  
Sbjct: 185 ENNLIQEQLTLEVWTNGSIDPQDAVSQAGKILTELLFPLKEI-----NFKPDDSESIIED 239

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +      +EEL+LSVR+ NCL+   I  + DL+  ++ D++ + NFG+KS  E+   L  
Sbjct: 240 SKINQILIEELQLSVRAYNCLKRAQIHSVADLLDYSQEDLIEIKNFGQKSAEEVIDAL-- 297

Query: 313 MGLFLGMNLPD 323
               LG+NLP 
Sbjct: 298 -QKRLGINLPK 307


>gi|329118621|ref|ZP_08247325.1| DNA-directed RNA polymerase subunit alpha [Neisseria bacilliformis
           ATCC BAA-1200]
 gi|327465356|gb|EGF11637.1| DNA-directed RNA polymerase subunit alpha [Neisseria bacilliformis
           ATCC BAA-1200]
          Length = 277

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 127/278 (45%), Positives = 180/278 (64%), Gaps = 5/278 (1%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           + G A T V I GVLHE S++ GV ED+ DI+LN+KG+  K+ G    R+ + K G G V
Sbjct: 1   MNGFAPTEVSISGVLHEYSTLDGVQEDVVDILLNLKGVVFKLHGREEIRLKLKKAGNGPV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLIT 172
           TA DI   +D++V+NP HVICNL  +  + ME+ V +G GY      R    +  IG+I 
Sbjct: 61  TAADIDLPHDVDVINPKHVICNLANNGSIEMEIVVEQGRGYQSVSGRRDVRSDTGIGVIQ 120

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           +DA +SPI +VS+ VE AR  Q  D D+L + ++T+GS+  E++V  A+RIL DQ+ +F 
Sbjct: 121 LDASFSPISRVSFEVEPARVEQRTDLDRLVLDVETNGSLDPEEAVRSAARILIDQMSVFA 180

Query: 233 NFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +    +    E++  K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++
Sbjct: 181 DL---QGTPVEEVEEKTPPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETEL 237

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           L+  N GRKSL EIK VL + GL LG  L  WPP  +E
Sbjct: 238 LKTPNLGRKSLNEIKEVLASKGLTLGSKLEAWPPAGLE 275


>gi|58415828|emb|CAH57328.1| RNA polymerase alpha-subunit [Vibrio diazotrophicus]
          Length = 285

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 124/285 (43%), Positives = 189/285 (66%), Gaps = 8/285 (2%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
               +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I
Sbjct: 4   THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEI 63

Query: 86  ILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV-DAVV 143
           +LN+KG+ +++  G     +T+ K G G V AGDI    D+E+ NP+HVIC+L   +A +
Sbjct: 64  LLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDSNAEI 123

Query: 144 RMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
            M + V +G GYVPA    H   +  PIG + +DA +SP+ K++Y+V++AR  Q  D DK
Sbjct: 124 AMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVDAARVEQRTDLDK 183

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V
Sbjct: 184 LVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPV 240

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           ++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 241 DDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 285


>gi|51209922|ref|YP_063586.1| RNA polymerase alpha subunit [Gracilaria tenuistipitata var. liui]
 gi|68053119|sp|Q6B8X4|RPOA_GRATL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|50657676|gb|AAT79661.1| RNA polymerase alpha subunit [Gracilaria tenuistipitata var. liui]
          Length = 314

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 95/311 (30%), Positives = 164/311 (52%), Gaps = 10/311 (3%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             +E       ++     I EPL +G   TLGN+LRR ++S L+GAAI AV+I G+ HE 
Sbjct: 7   ECVESKTESNRQQ-YGRFILEPLNKGQGITLGNSLRRTILSDLQGAAIVAVRIAGINHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           S+I GV ED+ +I+LN+K + LK   D+ +   I  +GP ++T G  +   +I +++P  
Sbjct: 66  STITGVREDVLEILLNLKKVVLKSHSDTPQIGRIRLQGPAIITTGLFEVPPEILIIDPQQ 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +  + +  ME  + KG GY        +   I  + IDA++ P+ K +YTVE  + 
Sbjct: 126 YIATICNNTIFEMEFRIEKGSGYKLVNKG-FDKKSIDFLQIDAVFMPVTKFNYTVEEKKI 184

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
             +L  +KL + + T+GS++ +++++  +++L        N         ++   +    
Sbjct: 185 SPILIQEKLFLEVWTNGSLSPQEAISEGAQVLHSLFYPLTNLNFQNANNTDNEYEEE--- 241

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                  +EEL+LSVR+ NCL+   I  + DL+  ++ ++L + NFG+KS  E+   L  
Sbjct: 242 --INQVLIEELQLSVRAYNCLKRAQINSISDLLDYSQDELLEIKNFGQKSAEEVIEALQN 299

Query: 313 MGLFLGMNLPD 323
               LG+ LP 
Sbjct: 300 K---LGIRLPK 307


>gi|153854998|ref|ZP_01996211.1| hypothetical protein DORLON_02217 [Dorea longicatena DSM 13814]
 gi|149752495|gb|EDM62426.1| hypothetical protein DORLON_02217 [Dorea longicatena DSM 13814]
          Length = 276

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 115/272 (42%), Positives = 176/272 (64%), Gaps = 4/272 (1%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFK 108
           ++SSL G+AI+ V+IDGVLHE SSI GV ED+T+II+N+K + +K     D  K   I  
Sbjct: 1   MLSSLPGSAISQVKIDGVLHEFSSIPGVKEDVTEIIMNLKSLAIKNTSESDEPKTAYIEF 60

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHRTEND 166
            G GVVTA DIQ   DIE++NP+ VI  L+  A   + MELT++ G GYV A  ++ +  
Sbjct: 61  EGEGVVTAADIQVDQDIEIMNPETVIATLNGGADSKLYMELTITNGRGYVSADKNKNDEL 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           PI +I ID++Y+P+++V+ TVE+ R GQ+ D+DKL++ + T+G++  +++V+LA+++L +
Sbjct: 121 PIAVIPIDSIYTPVERVNLTVENTRVGQITDFDKLTLDVYTNGTLLPDEAVSLAAKVLSE 180

Query: 227 QLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQ 286
            L +FI+  E  +  +  I  +       L   ++ELELSVRS NCL+   I  + +L  
Sbjct: 181 HLKLFIDLSEVAQAAEVMIEKEDDEKEKVLEMSIDELELSVRSYNCLKRAGINTVEELTN 240

Query: 287 RTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           RT  DM+++ N GRKSL E+   L  +GL L 
Sbjct: 241 RTPEDMMKVRNLGRKSLEEVLAKLDELGLSLS 272


>gi|188996211|ref|YP_001930462.1| DNA-directed RNA polymerase, alpha subunit [Sulfurihydrogenibium
           sp. YO3AOP1]
 gi|188931278|gb|ACD65908.1| DNA-directed RNA polymerase, alpha subunit [Sulfurihydrogenibium
           sp. YO3AOP1]
          Length = 324

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 121/316 (38%), Positives = 173/316 (54%), Gaps = 7/316 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           + + P  I +     + +    +  EPL RGF  T+GNALRRVL+SSL G AITAV+I G
Sbjct: 5   DFVMPTKIYWDE-ATKTDTYGKLYVEPLERGFGITIGNALRRVLLSSLPGGAITAVKIMG 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR-VTIFKRGPGVVTAGDIQTVNDIE 126
           V HE ++IKGV ED+ +I+LN+K I LK+  +  +    +     G V A DI+    IE
Sbjct: 64  VPHEFTTIKGVLEDVVEIVLNLKQIRLKIDENIERDFAILEAENVGKVYAKDIKFPAGIE 123

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           ++ PD  IC +     ++ME  V +G GY   +        IG I ID  +SPI+KV++ 
Sbjct: 124 LVTPDVHICTISEPTKLQMEFRVERGIGYKTVEELEP-ISEIGWIIIDTAFSPIRKVAFN 182

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK----KEVK 242
           VE  R G   DYDKL + I+TDG+IT ++++  AS IL D   +       K    K+  
Sbjct: 183 VEPTRVGDKTDYDKLILEIETDGTITPDEALTKASNILIDHFNILQKPTVKKVQVIKKTV 242

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              + +       L   ++ELE+S R+ N LR   I  +GDL++ +E D+    + GRKS
Sbjct: 243 APKSEEIKIEEDKLSLSIDELEISSRAINTLRKLGINTIGDLVRLSEEDLREAKSIGRKS 302

Query: 303 LVEIKGVLGTMGLFLG 318
           L EIK  L  MGL L 
Sbjct: 303 LKEIKDALAEMGLELA 318


>gi|237756134|ref|ZP_04584706.1| DNA-directed RNA polymerase, alpha subunit [Sulfurihydrogenibium
           yellowstonense SS-5]
 gi|237691698|gb|EEP60734.1| DNA-directed RNA polymerase, alpha subunit [Sulfurihydrogenibium
           yellowstonense SS-5]
          Length = 325

 Score =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 120/316 (37%), Positives = 172/316 (54%), Gaps = 7/316 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           + + P  I +     + +    +  EPL RGF  T+GNALRRVL+SSL G AITAV+I G
Sbjct: 5   DFVMPTKIYWDE-ATKTDTYGKLYVEPLERGFGITIGNALRRVLLSSLPGGAITAVKIMG 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR-VTIFKRGPGVVTAGDIQTVNDIE 126
           V HE ++IKGV ED+ +I+LN+K I LK+  +  +    +     G V A DI+    IE
Sbjct: 64  VPHEFTTIKGVIEDVAEIVLNLKQIRLKIDENIERDFAILEAENVGKVYAKDIKFPAGIE 123

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           ++ PD  IC +     ++ME  V +G GY   +        IG I ID  +SPIK+V++ 
Sbjct: 124 LVTPDVHICTISEPTKLQMEFRVERGIGYKTVEELEP-ISEIGWIIIDTAFSPIKRVAFN 182

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE  R G   DYDKL + I+TDG+IT ++++  AS IL D   +       K +V +   
Sbjct: 183 VEPTRVGDKTDYDKLILEIETDGTITPDEALTKASNILIDHFNILQKPTVKKVQVIKKTV 242

Query: 247 VKSLPFNPALLKK----VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                       K    ++ELE+S R+ N LR   I  +GDL++ +E D+    + GRKS
Sbjct: 243 APKPEEIKIEEDKLSLSIDELEISSRAINNLRKLGINTIGDLVRLSEEDLKEAKSIGRKS 302

Query: 303 LVEIKGVLGTMGLFLG 318
           + EIK  L  MGL L 
Sbjct: 303 IKEIKDALAEMGLELA 318


>gi|32487326|emb|CAE05901.1| OSJNBa0061C08.8 [Oryza sativa Japonica Group]
 gi|57834095|emb|CAE04760.3| OSJNBa0079C19.1 [Oryza sativa Japonica Group]
          Length = 446

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 95/332 (28%), Positives = 162/332 (48%), Gaps = 24/332 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+    G  IT  +   V 
Sbjct: 122 LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVP 180

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 181 HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRTASICVKGPRYITAQDIILPPSVEIVD 240

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL      R+EL + +  GY       T++   G   IDA+  P++ V+Y++ +
Sbjct: 241 TAQPIANLTEPTDFRIELRIKRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFA 297

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    Y+ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 298 CGNG-NAKYEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFT 356

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 357 SPLLSFQKRLTNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 416

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           R+ +F    + + K +  T+   L M+LP   
Sbjct: 417 RIDSFR---MQDGKQIWDTLEKHLPMDLPKNK 445


>gi|329962293|ref|ZP_08300299.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides fluxus YIT
           12057]
 gi|328530401|gb|EGF57278.1| DNA-directed RNA polymerase, alpha subunit [Bacteroides fluxus YIT
           12057]
          Length = 330

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 120/324 (37%), Positives = 194/324 (59%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AIT ++IDGV
Sbjct: 6   FQKPDKV---LMLEADSRFGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIKIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K  +     ++V+I         AGDI + +   
Sbjct: 63  EHEFSSVPGVKEDVTNIILNLKQVRFKQVVEEFESEKVSITIENSSEFKAGDIGKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EVLNP+ VIC+LD  + +++++T++KG GYVPA  +R     + +I ID++Y+PI+ V Y
Sbjct: 123 EVLNPELVICHLDSKSTMQIDITINKGRGYVPADENREYCTDVNVIPIDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE+ R  Q  DY+KL + I TDGSI  ++++  A++IL     +F    I  E    + 
Sbjct: 183 QVENFRVEQKTDYEKLVLEIATDGSIHPKEALKEAAKILIYHFMLFSDEKITLESNDVDG 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + + L     L  K+ +++LSVR+ NCL+  ++  +GDL+Q  + D+L+  NFG+K
Sbjct: 243 NEEFDEEVLHMRQLLKTKLVDMDLSVRALNCLKAADVETLGDLVQFNKTDLLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E+  +L ++ L  G ++  + 
Sbjct: 303 SLTELDDLLESLSLSFGTDISKYK 326


>gi|87300890|ref|ZP_01083732.1| DNA-directed RNA polymerase alpha subunit [Synechococcus sp. WH
           5701]
 gi|87284761|gb|EAQ76713.1| DNA-directed RNA polymerase alpha subunit [Synechococcus sp. WH
           5701]
          Length = 312

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 105/312 (33%), Positives = 166/312 (53%), Gaps = 14/312 (4%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + +E+ +     +   + +  PL RG A TLGNALRRVLM  + G+AITAV+I GV HE 
Sbjct: 7   DRVEHHIADDRSQT-GVFVIGPLDRGQAITLGNALRRVLMGGMEGSAITAVRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K + +       +   +   GP  VTA D+Q  + ++V++ D 
Sbjct: 66  ATIPGVREDVLDILLNCKEVVVNSRNRDLEIGRLIVNGPASVTAADLQFSSQVQVIDFDR 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V KG GY P   H  +   I L+ IDA++ P+++V+YTV+    
Sbjct: 126 PIATVAEGHSLELEVHVEKGVGYRPVDRHHEDTSAIDLLQIDAVFMPVRRVNYTVDETAV 185

Query: 193 GQVLD-YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF---EEPKKEVKEDINVK 248
           G+     ++L + I T GSIT +D++A A+  L        +    EEP  E +     +
Sbjct: 186 GEGGSARERLRLEIVTSGSITPDDAMAQAANQLIQLFQPLASLTMVEEPGLEPEPSAESQ 245

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                      +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+  
Sbjct: 246 ---------IPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIE 296

Query: 309 VLGTMGLFLGMN 320
            L  +G+ L  +
Sbjct: 297 ALERIGISLPQS 308


>gi|290489668|gb|ADD31218.1| RNA polymerase alpha subunit protein [Nelumbo nucifera]
          Length = 339

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 83/332 (25%), Positives = 166/332 (50%), Gaps = 26/332 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RR L+  + G  IT  + + + 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +    +   I  RGPG VTA DI +   +E+++
Sbjct: 72  HEYSTIVGIEESVHEILMNLKEIVLRSNLYGTRDAFICVRGPGYVTAQDIISPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I +L     + + L + +  GY     + +++   G   IDA++ P++  ++++ S
Sbjct: 132 TTQHIASLTEPIDLCIGLQIERNRGYRMKTPNNSQD---GSYPIDAVFMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L D    F++ +E   +++++ N  +
Sbjct: 189 YGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLDAQEEDIQLEDNQNKVT 247

Query: 250 LPFNPALLK------------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           LPF     +                   +++ EL  R+ NCL+  NI  + DL+  ++ D
Sbjct: 248 LPFFTFHDRLTKLRKNKKEKEIALKCIFIDQSELPPRTYNCLKRSNIHTLLDLLNNSQED 307

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++M +F    + ++K +L  +     ++LP 
Sbjct: 308 LMKMFHF---QIEDVKQILDILQKHFAIDLPK 336


>gi|290968216|ref|ZP_06559759.1| DNA-directed RNA polymerase, alpha subunit [Megasphaera genomosp.
           type_1 str. 28L]
 gi|290781698|gb|EFD94283.1| DNA-directed RNA polymerase, alpha subunit [Megasphaera genomosp.
           type_1 str. 28L]
          Length = 325

 Score =  279 bits (715), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 119/319 (37%), Positives = 185/319 (57%), Gaps = 11/319 (3%)

Query: 13  NNIEYIVLGQEEE-NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           N  +   + + ++      + EPL RG+  TLGN+LRRVL+SSL G AIT+++IDGVLHE
Sbjct: 5   NKFKVKTVERSDDGTYGKFVCEPLDRGYGITLGNSLRRVLLSSLDGVAITSIKIDGVLHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGV--VTAGDIQTVNDIEVLN 129
            S+I+GV ED+++IILN+K + L+ + D    + I     G    TA D+   +DIE+LN
Sbjct: 65  FSTIQGVREDVSEIILNLKQLRLRFTRDDVNELDISVDVNGECEFTAKDLDVNSDIEILN 124

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  +  LD DA + M   + +G GY+P+  ++ E D IG+I ID+++SP+ +  Y V +
Sbjct: 125 PELHLATLDADAHIYMTCHIERGKGYIPSTKNKKETDMIGVIPIDSIFSPVMRTKYEVGN 184

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK------- 242
            R G  +DYD L++ + TDGSI  E++VA A+ I+   L  F          +       
Sbjct: 185 IRVGNEMDYDSLTLEVKTDGSIAAENAVAKAASIMVSYLDYFQKIASDPVANEALAPFTT 244

Query: 243 -EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E    +          K++ L+LSVR++NCL+  NI  +GDL++RTE D+ ++ N G+K
Sbjct: 245 PEGEEPEVEEGPELSQVKIDVLDLSVRASNCLKRANIYTLGDLVERTEEDLSKIRNLGKK 304

Query: 302 SLVEIKGVLGTMGLFLGMN 320
           S+ EI   L   G  L  +
Sbjct: 305 SVDEIIEKLKDYGFDLKSD 323


>gi|254553679|gb|ACT67298.1| RNA polymerase alpha subunit [Joinvillea plicata]
          Length = 339

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 93/330 (28%), Positives = 165/330 (50%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLIKGQADTIGIAMRRALLGEIEGTCITRAKSGKVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI +   +E+++
Sbjct: 72  HEYSTIVGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIISPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL     + +EL + +  GY       +++   G   IDA+  P++ V+Y++ S
Sbjct: 132 TTQHIANLTEPIDLCIELQIKRDRGYHTEPRKNSQD---GSYPIDAVSMPVRNVNYSIYS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                   Y+ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNE-NEKYEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEEDTNFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           LP                  P     +++LEL  R+ NCL+  NI  + DL+ ++E D++
Sbjct: 248 LPLLTFQKRLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRSNIHTLLDLLSKSEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++ NF    + + K +L T+   L M+LP 
Sbjct: 308 KIENFR---MEDGKQILDTLQKHLSMDLPK 334


>gi|18767372|gb|AAL79338.1|AC099402_2 Putative RNA polymerase alpha subunit [Oryza sativa]
 gi|21327372|gb|AAM48277.1|AC122148_30 Putative RNA polymerase alpha subunit [Oryza sativa Japonica Group]
 gi|110288947|gb|ABB47310.2| DNA-directed RNA polymerase alpha chain, putative, expressed [Oryza
           sativa Japonica Group]
          Length = 446

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 95/332 (28%), Positives = 162/332 (48%), Gaps = 24/332 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+    G  IT  +   V 
Sbjct: 122 LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVP 180

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 181 HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRTASICVKGPRYITAQDIILPPSVEIVD 240

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL      R+EL + +  GY       T++   G   IDA+  P++ V+Y++ +
Sbjct: 241 TAQPIANLTEPTDFRIELRIKRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFA 297

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    Y+ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 298 CGNG-NARYEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFT 356

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 357 SPLLSFQKRLTNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 416

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           R+ +F    + + K +  T+   L M+LP   
Sbjct: 417 RIDSFR---MQDGKQIWDTLEKHLPMDLPKNK 445


>gi|290489670|gb|ADD31219.1| RNA polymerase alpha subunit protein [Nerium oleander]
          Length = 337

 Score =  279 bits (713), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 87/331 (26%), Positives = 162/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    E+        I  PL +G A T+G A+RR L+  + G  IT V+ D V
Sbjct: 11  RTLQWKCVESRTESKRLYYGRFILSPLLKGQADTIGIAMRRALLGEIEGTCITRVKFDKV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+IKG+ E + +I++N+K I L+ +       +I  RGPG VTA DI     +E++
Sbjct: 71  PHEYSTIKGIQESVHEILMNLKEIVLRSNLYGTCDASICVRGPGYVTAQDIVLPPYVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY+       +N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLMEPINLCIGLQIERNRGYLIQT---PQNFQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN-- 246
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEENSHLENNQHAV 246

Query: 247 --------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                         +K+          +++LEL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 PLFPFIFHDKLTKLIKNKKEIALKSIFIDQLELPPRIYNCLKRSNIYTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F    + ++K +L  +   L + LP 
Sbjct: 307 MKIEHFR---IEDVKQILVILEKHLAIFLPK 334


>gi|308522660|dbj|BAJ22941.1| RNA polymerase alpha subunit [Vibrio sagamiensis]
 gi|308522662|dbj|BAJ22942.1| RNA polymerase alpha subunit [Vibrio sagamiensis]
          Length = 282

 Score =  279 bits (713), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 126/285 (44%), Positives = 188/285 (65%), Gaps = 8/285 (2%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
                 +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ 
Sbjct: 1   SSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDIL 60

Query: 84  DIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-A 141
           +I+LN+KG+++++  G     +T+ K G G V AGDI    D+E+ NP+HVIC+L  D A
Sbjct: 61  EILLNLKGLSVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDSA 120

Query: 142 VVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M + V +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D 
Sbjct: 121 DIAMRIKVERGRGYVPASARIHTDEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDL 180

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+
Sbjct: 181 DKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLR 237

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 PVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 282


>gi|257470860|ref|ZP_05634950.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium ulcerans
           ATCC 49185]
 gi|317065063|ref|ZP_07929548.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium ulcerans
           ATCC 49185]
 gi|313690739|gb|EFS27574.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium ulcerans
           ATCC 49185]
          Length = 325

 Score =  279 bits (713), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 118/309 (38%), Positives = 184/309 (59%), Gaps = 6/309 (1%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I   +E E +   I EPL RG+ HT+GNALRRVL+SS+ GAAI  V+IDGVL E S + G
Sbjct: 13  ITEVKESEFKGQYIVEPLYRGYGHTVGNALRRVLLSSIPGAAIKGVRIDGVLSEFSVMDG 72

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           + E +T+IILNIK I +K      +++T+  +GP +VTA DI     IE++NP+ VIC +
Sbjct: 73  IKEAVTEIILNIKEIVVKAESTGERKMTLSVKGPKIVTAADIIPDVGIEIVNPEQVICTI 132

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + ME  V  G G+V ++    ++  +  I +DA+Y+PI+KVSY+V+    G++ D
Sbjct: 133 TTDRELDMEFLVDTGEGFVVSEEIERKDWAVDYIAVDAIYTPIRKVSYSVQDTMVGRMTD 192

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF----- 252
           +DKL++ I+TDGSI   D+++ A  +L+     F+      + ++ +   +         
Sbjct: 193 FDKLTLDIETDGSIEIRDALSYAVELLKLHFDPFLELGNKMENLRVEAEEEEENPVSHAK 252

Query: 253 -NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +  L  K+EEL+L+VRS NCL+   I  +  L + +  ++L++ N GRKSL EI   + 
Sbjct: 253 DDNILNTKIEELDLTVRSFNCLKKAGIEEVSQLAKLSLNELLKIKNLGRKSLDEILEKMK 312

Query: 312 TMGLFLGMN 320
            +G  L  N
Sbjct: 313 ELGYDLSQN 321


>gi|212550426|ref|YP_002308743.1| DNA-directed RNA polymerase subunit alpha [Candidatus
           Azobacteroides pseudotrichonymphae genomovar. CFP2]
 gi|212548664|dbj|BAG83332.1| DNA-directed RNA polymerase alpha subunit [Candidatus
           Azobacteroides pseudotrichonymphae genomovar. CFP2]
          Length = 328

 Score =  279 bits (713), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 116/324 (35%), Positives = 190/324 (58%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   +  +  +        PL  G+  T+GN+LRRVL+SSL G AIT+++I+GV
Sbjct: 6   FQKPDRV---IEVESGDKYGKFEFHPLESGYGITIGNSLRRVLLSSLEGYAITSIKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            +E + + GV ED+T+IIL +K +  K       ++RV +         A DI + ++  
Sbjct: 63  SNEFAVVPGVVEDVTNIILKLKQVRFKRINKDFEYERVVLTISETDKFKADDISKRLSGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EV+N D +I +LD  A + +ELT+ KG GYVP++ +  ++D +  I ID++++PI  V Y
Sbjct: 123 EVVNSDFIIAHLDKSANLNIELTIRKGRGYVPSEENYRDSDDVNQIAIDSVFTPIVNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VES R  Q  DY+KL++ I TDGS+  + ++  AS IL   L +F    I  E+ + E 
Sbjct: 183 NVESFRVEQKTDYEKLTIEIMTDGSVCPKIALKSASDILIQHLELFSEGRIRLEKDEIET 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            +D +   L     L  K+ ++ELSVR+ NCL+ E I  + DL++  ++D+++  NFG+K
Sbjct: 243 VKDFDEDVLRIRQLLKSKLSDMELSVRALNCLKAEAIETLEDLVKYQKSDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SLVE+  +L  + L  GM++  + 
Sbjct: 303 SLVELDELLAKLNLTFGMDIEKYK 326


>gi|297623302|ref|YP_003704736.1| DNA-directed RNA polymerase subunit alpha [Truepera radiovictrix
           DSM 17093]
 gi|297164482|gb|ADI14193.1| DNA-directed RNA polymerase, alpha subunit [Truepera radiovictrix
           DSM 17093]
          Length = 310

 Score =  279 bits (713), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 112/299 (37%), Positives = 172/299 (57%), Gaps = 5/299 (1%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
            +     I EPLPRG+  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED+ 
Sbjct: 12  TDQYGEFIVEPLPRGYGVTLGNPLRRILLSSVAGTAVTSVYIEDVLHEFSTIPGVKEDVM 71

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            IILN+K + +K+  D    +T+    PG VTA D +      ++NP+  +  L+    +
Sbjct: 72  QIILNLKELVVKLHDDEPVTLTLRAENPGRVTAADFEVPMGATLINPELYLATLNEGGKL 131

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            ME+ V  G GYVPA+ H T++  I  I +DA+++P+++V+Y VE  R GQ  D D+L +
Sbjct: 132 VMEVRVEPGIGYVPAEVHATKDR-INSIPVDAVFTPVRRVAYRVEDTRVGQKTDLDRLVL 190

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFIN--FEEPKKEVKEDINVKSLPFNPALLKKV- 260
            + TDGS++  +++  A  IL++QL +F     +EP   +         P + A   ++ 
Sbjct: 191 RVWTDGSVSPREALDSAVEILRNQLSVFSGGVIDEPLPVMAIPPRSADEPLSRAEPARIS 250

Query: 261 -EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            E LELS R  + L+ E I  +  L+  +E D+ ++   G KSL EIK  L   GL+L 
Sbjct: 251 LESLELSSRVLHSLQEEGIDSVDALLALSERDLKKVGGVGDKSLEEIKERLQAQGLYLK 309


>gi|290489702|gb|ADD31235.1| RNA polymerase alpha subunit protein [Trochodendron aralioides]
          Length = 337

 Score =  279 bits (713), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 86/330 (26%), Positives = 165/330 (50%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E      +       I  PL +G A T+G A+RR L+  + G  IT  + + + 
Sbjct: 13  LQWKCVES-RADSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +       +I  RGPG VTA DI +   +E+++
Sbjct: 72  HEYSTIVGIEESVQEILLNLKEIVLRSNLYGTLDASICVRGPGYVTAQDIISPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I +L     + + L + +  GY     + +++   G   IDA++ P++  S+++ S
Sbjct: 132 ATQHIASLTEPIDLCIGLQIERNRGYRMKTPNNSQD---GSYPIDAVFMPVRNASHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L D    F++ EE   +++++ N  S
Sbjct: 189 YGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEESIKLEDNQNGIS 247

Query: 250 LPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           LPF     +                 +++ EL  R+ NCL+  NI  + DL+  ++ D++
Sbjct: 248 LPFFAFHDRLANLKKKKKEIAFKCIFIDQSELPPRTYNCLKRSNIYTLLDLLNNSQEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++ +F    + ++K +L  +     ++LP 
Sbjct: 308 KIDHFH---IEDVKQILDILQKHFSIDLPK 334


>gi|288574689|ref|ZP_06393046.1| DNA-directed RNA polymerase, alpha subunit [Dethiosulfovibrio
           peptidovorans DSM 11002]
 gi|288570430|gb|EFC91987.1| DNA-directed RNA polymerase, alpha subunit [Dethiosulfovibrio
           peptidovorans DSM 11002]
          Length = 354

 Score =  278 bits (712), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 113/327 (34%), Positives = 184/327 (56%), Gaps = 21/327 (6%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E ++P     I + +       ++  PL RGF  T+GNALRRVL+SS++GAAIT+V+IDG
Sbjct: 16  EFMRPE----IRVEECSATSARIVVGPLERGFGVTIGNALRRVLLSSIKGAAITSVRIDG 71

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE S+I GV ED+ +++LN+K + ++      + + +   G   VTA D Q  ++IE 
Sbjct: 72  VVHEFSTIPGVGEDVIELLLNLKHVPIRSYSPEVRVLRLEAEGERRVTAADFQPDSEIEF 131

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           ++P+  IC L   A + +E+ + +G GY PA   +    P+  + IDA+++PI++V Y V
Sbjct: 132 VDPEAYICTLAEGARLSLEVYIEQGVGYAPADRPKPAYLPMDSLLIDAIFTPIQRVKYEV 191

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF-------EEPKKE 240
           ++ R GQ  DY+++ M +DT+G +  + +VA A+R+L+    + +         E    E
Sbjct: 192 QAERVGQRTDYERIVMDVDTNGVVKPDLAVAEAARLLRKYFTIVVEEIQKLHPSEHTDPE 251

Query: 241 VKEDINVK----------SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
           + E   +               N  L + V +LELS+RS NCL    I  +GDL+ R   
Sbjct: 252 IVESQEISVAEEETETEQESEENTLLSRGVRDLELSIRSENCLLRGGIHTIGDLVSRGRD 311

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFL 317
           D+L++ N G+ SL EI+  L  +G  L
Sbjct: 312 DLLKIRNLGKISLREIEEKLENLGFSL 338


>gi|297180261|gb|ADI16480.1| DNA-directed RNA polymerase, alpha subunit/40 kd subunit
           [uncultured bacterium HF4000_05M23]
          Length = 362

 Score =  278 bits (712), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 110/312 (35%), Positives = 180/312 (57%), Gaps = 10/312 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + + EE     +AEPL RG+  TLGN +RR L+++L G AIT V+IDG+ HE S++K 
Sbjct: 26  ITIQENEETYGRFVAEPLERGWGVTLGNPIRRSLLNALSGTAITWVRIDGIHHEYSTVKH 85

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           + E++ + +LN+KGI L+   D   R+ +   G G V AGDI    D E++NP+H +  L
Sbjct: 86  MREEVVEFLLNVKGIRLRSLADRPGRLRLEVDGEGEVRAGDIMATADFEIVNPEHHLATL 145

Query: 138 D-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           D   A + +E  V +G GY PA  +  E  PIG++ +DA+++P++K ++ VE+ R GQ  
Sbjct: 146 DNGGARLSVEFNVEQGVGYEPA--NHEEGLPIGVLPVDAIFTPVRKANFAVEATRVGQRS 203

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           D ++L + + TD +IT  D+V  A  +L ++  +F   ++P+ +  E++           
Sbjct: 204 DLERLVVEVWTDRTITPLDAVRAAGNLLMERFFLFKRLDKPQDD--EEVLGVPGVLPEVF 261

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              VE L LS R+ NCL+   I  +G+++   + ++L++ NFG+KSL E+   L      
Sbjct: 262 NTLVETLSLSARTLNCLKRAGINRVGEVLMMPKGELLKIRNFGQKSLDELYDKLAEKNY- 320

Query: 317 LGMNLPDWPPES 328
               LP+  PE 
Sbjct: 321 ----LPEENPEG 328


>gi|148270450|ref|YP_001244910.1| DNA-directed RNA polymerase subunit alpha [Thermotoga petrophila
           RKU-1]
 gi|170289155|ref|YP_001739393.1| DNA-directed RNA polymerase, alpha subunit [Thermotoga sp. RQ2]
 gi|172047882|sp|A5IMB1|RPOA_THEP1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|147735994|gb|ABQ47334.1| DNA-directed RNA polymerase, alpha subunit [Thermotoga petrophila
           RKU-1]
 gi|170176658|gb|ACB09710.1| DNA-directed RNA polymerase, alpha subunit [Thermotoga sp. RQ2]
          Length = 336

 Score =  278 bits (712), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 117/331 (35%), Positives = 177/331 (53%), Gaps = 22/331 (6%)

Query: 8   ELIKPNNIEYIVL-GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           E + P  ++      +++         PL RG+A T+GNALRRVL+SS+   AI  V+  
Sbjct: 3   EFVIPKKLKVEEEREEKDYYYARFSLSPLERGYAITIGNALRRVLLSSIPSLAIVGVRFI 62

Query: 67  G--VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTV 122
                HE   I+GV ED+ DIILN+K +  +++       ++ + K+GPG + AGDI+T 
Sbjct: 63  KPEKYHEYDYIEGVKEDILDIILNLKKVQFRVNVTVKGTIKMEVEKKGPGELVAGDIKTP 122

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
             IEV NPD  I  L+  A +  E+    G G+VP    R E   +G I ID ++SP+ K
Sbjct: 123 AGIEVANPDLHIATLNSKADLFFEVYAEVGKGFVPVSE-REERPDVGWIPIDGVFSPVIK 181

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM------------ 230
           V++  E+ R G+  DYDKL + I T  SI  E+++  A+ IL +   +            
Sbjct: 182 VNFLTENVRVGKRTDYDKLILEIWTKKSIRPEEALRKAADILINHFKIVTEGLPELKISE 241

Query: 231 ---FINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
                + EE  +    D   ++        +K++ELELSVRS NCL+   I  +GDL+ +
Sbjct: 242 EYIITSEEEEAEIPAVDHEEENRENLDVYNRKIDELELSVRSLNCLKRAKIETIGDLLSK 301

Query: 288 TEADMLRMANFGRKSLVEIKGVLGT-MGLFL 317
           TE ++L++ NFG+KSL E+K  L    GL L
Sbjct: 302 TEEELLKIKNFGQKSLDEVKEKLKEKFGLEL 332


>gi|161511761|emb|CAP16891.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           ethanolidurans]
          Length = 251

 Score =  278 bits (711), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 108/246 (43%), Positives = 162/246 (65%), Gaps = 2/246 (0%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E  N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED
Sbjct: 6   DENANYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVED 65

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILNIK ++LK+  D  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +    
Sbjct: 66  VTQIILNIKKVSLKIESDDEKSLEINVKGPATVTAGDIQGDSDVEILNPDQYICTVADGV 125

Query: 142 VVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
                LT   G GYV A  ++   ++ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYD
Sbjct: 126 TFHAVLTADTGRGYVSADENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYD 185

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL++ + TDGSI+  ++ +L+++IL + L +F+N  +  ++ +  +  +       L   
Sbjct: 186 KLTLDVWTDGSISPSEATSLSAKILTEHLALFVNLTDEAQDAEIMVEKEETHKEKMLEMS 245

Query: 260 VEELEL 265
           +EEL+L
Sbjct: 246 IEELDL 251


>gi|253581360|ref|ZP_04858586.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium varium
           ATCC 27725]
 gi|251836724|gb|EES65258.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium varium
           ATCC 27725]
          Length = 325

 Score =  278 bits (711), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 117/309 (37%), Positives = 185/309 (59%), Gaps = 6/309 (1%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I   +E E +   I EPL RG+ HT+GNALRRVL+SS+ GAAI  V+IDGVL E S ++G
Sbjct: 13  ITEVKESEFKGQYIVEPLYRGYGHTVGNALRRVLLSSIPGAAIKGVRIDGVLSEFSVMEG 72

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           + E +T+I+LNIK I +K      +++T+  +GP +VTA DI     IE++NP+ VIC +
Sbjct: 73  IKEAVTEIVLNIKEIVVKAESTGERKMTLSVKGPKIVTAADIIPDVGIEIVNPEQVICTI 132

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + ME  V  G G+V ++    ++  +  I +DA+Y+PI+KVSY+V+    G++ D
Sbjct: 133 TTDRELDMEFLVDTGEGFVVSEEIERKDWAVDYIAVDAIYTPIRKVSYSVQDTMVGRMTD 192

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF----- 252
           +DKL++ I+TDGSI   D+++ A  +L+     F+      + ++ +   +         
Sbjct: 193 FDKLTLDIETDGSIEIRDALSYAVELLKLHFDPFLELGNKMENLRVEAEEEEENPVSHAK 252

Query: 253 -NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +  L  K+EEL+L+VRS NCL+   I  +  L + +  ++L++ N GRKSL EI   + 
Sbjct: 253 DDNILNTKIEELDLTVRSFNCLKKAGIEEVSQLAKLSLNELLKIKNLGRKSLDEILEKMK 312

Query: 312 TMGLFLGMN 320
            +G  L  N
Sbjct: 313 ELGYDLSQN 321


>gi|319789266|ref|YP_004150899.1| DNA-directed RNA polymerase, alpha subunit [Thermovibrio
           ammonificans HB-1]
 gi|317113768|gb|ADU96258.1| DNA-directed RNA polymerase, alpha subunit [Thermovibrio
           ammonificans HB-1]
          Length = 316

 Score =  278 bits (711), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 112/314 (35%), Positives = 171/314 (54%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E I P   E     +        + EPL +G+  T+GNALRRVL+SS+ GAA TAV+ +G
Sbjct: 3   EFITP---ERFTWEEHTNTYGRFVVEPLEKGYGVTIGNALRRVLLSSIEGAAPTAVKFEG 59

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
             HE +++ GV EDLT+I+LNIK +   + G+    + + K+GPG V A D +  + +E+
Sbjct: 60  AYHEFTTLPGVVEDLTEIVLNIKKLRFVLHGEGPVFIELKKKGPGKVYAKDFELPSQLEL 119

Query: 128 LNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVS 184
           L PD  I  LD   + + + L V KG G+V ++  +   +   +G I +DA +SPIKKV+
Sbjct: 120 LTPDQEIATLDNESSEIEIHLRVDKGKGFVLSEDIQEIFDISTLGWIPLDADFSPIKKVT 179

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + VE  R G+  DY+KL+  I TDGSIT +D+V  AS IL D      +         E+
Sbjct: 180 FKVEDTRVGRRTDYNKLTFEIWTDGSITPKDAVVRASNILIDHFSQIRDRLVEALFAVEE 239

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
                   +  L + +EE  LS R+   L+   I  + DL+     ++  +   G+KS+ 
Sbjct: 240 AQEPKEEVSEVLNQTLEEAGLSGRALKVLKEHGIETVKDLVALDRKELESLKGLGKKSIA 299

Query: 305 EIKGVLGTMGLFLG 318
           +I+  L  +GL LG
Sbjct: 300 DIEAFLSQLGLELG 313


>gi|297180267|gb|ADI16486.1| DNA-directed RNA polymerase, alpha subunit/40 kd subunit
           [uncultured bacterium HF4000_05M23]
          Length = 328

 Score =  278 bits (711), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 111/317 (35%), Positives = 175/317 (55%), Gaps = 8/317 (2%)

Query: 2   IQKNWQELIKPNNIEY----IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRG 57
           +    QEL+ P   E     I + + EE     +AEPL RG   TLGNALRR L++SL G
Sbjct: 1   MIGTVQELLSPFTPEIPDLSIAIQENEEAYGRFVAEPLERGRGVTLGNALRRTLLNSLPG 60

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
            AIT V+IDG LHE S+I  + E++ + +L +KGI L+   D   R+ I   G G V AG
Sbjct: 61  TAITWVRIDGALHEYSTIPHMPEEVVEFLLKVKGIRLRSLADRPGRLRIEVDGEGEVRAG 120

Query: 118 DIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
           DI    D E++NP+H +  LD   A + +E  V +G GY PA   + E  PIG++ +DA+
Sbjct: 121 DIMATADFEIVNPEHHLATLDSAMARLSVEFNVEQGVGYQPA--IQEEGLPIGVLLVDAI 178

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           ++PI+K +++VE+ R G   D ++L + + TD +I   +++  AS++L D    F    E
Sbjct: 179 FTPIRKSNFSVEATRAGHRSDLERLIVEVWTDRTIMPLEAMKSASKLLMDCFFPFTQVGE 238

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           P     +   +  +         VE L LS R+ NCL+      +G+++   +++++++ 
Sbjct: 239 PVGGEDDKPGIDGVTPE-VFNTLVETLALSARTHNCLKRAGFNRVGEILLLPKSELMKIR 297

Query: 297 NFGRKSLVEIKGVLGTM 313
            FG+KSL E+   L   
Sbjct: 298 GFGQKSLDELYVKLAEK 314


>gi|58758781|gb|AAW81783.1| RNA polymerase alpha subunit [Polytrichastrum pallidisetum]
          Length = 338

 Score =  278 bits (711), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 89/340 (26%), Positives = 158/340 (46%), Gaps = 25/340 (7%)

Query: 1   MIQKNWQ---ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRG 57
           MIQ       + ++   +E  V  +     +     P   G A+T+G A+RR L+  + G
Sbjct: 1   MIQNEISVSAQALQWRCVESKVDSERLH-YSRFAISPFRCGQANTVGIAMRRALLGEIEG 59

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
             IT      V HE S+I G+ E + DI++N+K I LK +    ++  I   GP  +TA 
Sbjct: 60  TCITCAIFKKVTHEYSTIVGIQESVHDILINLKEIVLKSNSSETQKAFISILGPKKITAQ 119

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI     +++++    I  +     + +EL + K  GY      ++ +   G   IDA++
Sbjct: 120 DIILPPSVKIIDTTQYIATITKPIHLDIELEIEKDCGYRIQDSVKSID---GYFPIDAIF 176

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
            PI+  +Y+V S  E      + L + I T+GSIT ++++  ASR L D    F++ E+ 
Sbjct: 177 MPIRNANYSVHSF-ENNNKIQEILFIEIWTNGSITPKEALYEASRSLIDLFIPFLHPEKK 235

Query: 238 KK--------------EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGD 283
           +                    +  K           +++LEL  R+ NCL+  N   + D
Sbjct: 236 ETIDRLKYTPNDISDFSSFSPVTGKLTKEITFKHIFIDQLELPARAYNCLKRVNGHTISD 295

Query: 284 LIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           L+  ++ D++++ NFG+KS+ ++   L  +     +NLP 
Sbjct: 296 LLNYSQDDLMKIKNFGKKSVEQV---LEALEKQFSINLPK 332


>gi|298372561|ref|ZP_06982551.1| DNA-directed RNA polymerase, alpha subunit [Bacteroidetes oral
           taxon 274 str. F0058]
 gi|298275465|gb|EFI17016.1| DNA-directed RNA polymerase, alpha subunit [Bacteroidetes oral
           taxon 274 str. F0058]
          Length = 331

 Score =  278 bits (711), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 113/324 (34%), Positives = 188/324 (58%), Gaps = 10/324 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +PN +  +   +  E +      PL  G+  T+GNALRRVL+SSL G AIT+++I  V
Sbjct: 6   FQRPNQVYMV---EATEFKGRFEFAPLEPGYGITIGNALRRVLLSSLEGYAITSLKISEV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTV-NDI 125
           +HE  +I  V +D+T+IILN+K +  K     ++ + ++I      V+ A D++    + 
Sbjct: 63  VHEFDTIPNVIDDVTNIILNLKQVRFKHIAGAETSESISITVSNKEVLKAKDLEEGMANF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNPDHVIC++D  A   MEL + KG GY+PA  ++  +  IG I IDA+++PI  V Y
Sbjct: 123 KVLNPDHVICSMDKSAEFTMELKIEKGRGYLPADENKNVSKEIGWIGIDAIFTPIVNVMY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEV 241
           +VE  R  Q  DY+KL + I TDGS+  + ++  A++IL     +F +     E    + 
Sbjct: 183 SVEDERVEQKTDYNKLILEIQTDGSVHPKQALKEAAKILIQHFMLFTDEKITLEIEDIDD 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++ +   L     L  ++ +L+LSVR+ NCL+  N+  +GDL +  + ++L+  NFG+K
Sbjct: 243 NDEFDEDFLKKRQLLKTQLTDLDLSVRALNCLKSANLETLGDLARIPKPELLKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL E++  L ++ L  G+++  + 
Sbjct: 303 SLTELEQKLESLNLHFGIDIAKYK 326


>gi|260655357|ref|ZP_05860845.1| DNA-directed RNA polymerase, alpha subunit [Jonquetella anthropi
           E3_33 E1]
 gi|260629805|gb|EEX47999.1| DNA-directed RNA polymerase, alpha subunit [Jonquetella anthropi
           E3_33 E1]
          Length = 338

 Score =  278 bits (711), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 102/322 (31%), Positives = 175/322 (54%), Gaps = 19/322 (5%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + +    +  +I  PL RG+  T+GNALRRVL+SS++GA +TAV+++G LHE +++ G
Sbjct: 5   IRVEECTPTKARLIIGPLERGYGVTIGNALRRVLLSSIKGAGVTAVRVEGALHEFTTLPG 64

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ ++ LN+K I ++      + + +   GP  VT  DIQ  ++IE ++P+  IC L
Sbjct: 65  VREDIIELQLNLKHIPVRSHSVEVRVLRLEATGPKKVTVADIQPDSEIEFIDPNFYICTL 124

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
                + MEL + +G GY  A   R +  P+  + +D  ++PI +V Y V++ R G   D
Sbjct: 125 AEGHSISMELYIEQGVGYATADRPRPDYLPVDALMVDPNFAPISRVKYDVQAERVGHKTD 184

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI---------NFEEPKKEVKEDINV- 247
           Y+K+ M I ++G I  + +VA A+++L++   + +         + E     V+ +    
Sbjct: 185 YEKVVMDIYSNGVIAPDMAVAEAAKLLREYFSIVVKEILKRYPASAEMAASPVEMEQEQP 244

Query: 248 ---------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                         N  L   V +LELS+RS NCL    I  +G+L+ R++ ++L++ N 
Sbjct: 245 SLGQAIVHSDDGAENSLLGHGVRDLELSIRSENCLLRGGIHTIGELVSRSKEELLKIRNL 304

Query: 299 GRKSLVEIKGVLGTMGLFLGMN 320
           G+ SL EI+  +    L L  +
Sbjct: 305 GKISLREIEEKMAKYNLSLADD 326


>gi|225544155|ref|YP_002720144.1| rpoA [Jatropha curcas]
 gi|224979596|gb|ACN72723.1| rpoA [Jatropha curcas]
          Length = 339

 Score =  278 bits (711), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 83/334 (24%), Positives = 163/334 (48%), Gaps = 25/334 (7%)

Query: 10  IKPNNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           I    +++  +    +N        I  PL +G A T+G A+RR L+  + G  IT  + 
Sbjct: 8   ISTRTLQWKCVESRTDNKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKS 67

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           + + HE S+I G+ E + +I++N+K + LK +       +I+ +GPG VTA DI     +
Sbjct: 68  EKIPHEFSTIAGIQESIHEILMNLKNVVLKSNLYGTCDASIYVKGPGYVTAQDIILPPFV 127

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E+++    I +L     + + L + +  GY     +  ++   G   IDA++ P++  ++
Sbjct: 128 EIIDNTQHIASLTESIDLCIGLQIERNRGYRIKPTNNFQD---GSYPIDAVFMPVRNANH 184

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           +V S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + 
Sbjct: 185 SVHSYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLEINQ 243

Query: 246 NVKSLP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +  +LP                        +++ EL+ ++ NCL+  NI  + DL+ +++
Sbjct: 244 HKVTLPLFTFHGRLTKLRKNQKEIALKYIFIDQSELTPKTYNCLKRSNIHTLSDLLNKSQ 303

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            D++++ NF    +  I G+L  +     ++LP 
Sbjct: 304 EDLMKIENFRIDDVKHILGIL-EIEKHFAIDLPK 336


>gi|222099995|ref|YP_002534563.1| DNA-directed RNA polymerase subunit alpha [Thermotoga neapolitana
           DSM 4359]
 gi|221572385|gb|ACM23197.1| DNA-directed RNA polymerase subunit alpha [Thermotoga neapolitana
           DSM 4359]
          Length = 340

 Score =  278 bits (711), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 120/339 (35%), Positives = 182/339 (53%), Gaps = 25/339 (7%)

Query: 1   MIQKNWQELIKPNNIEYIVL-GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M++    E + P  ++      +++   T     PL RG+A T+GNALRRVL+SS+   A
Sbjct: 1   MMKM--VEFVMPKKLKVEEEREEKDYYYTRFSLSPLERGYAITIGNALRRVLLSSIPSLA 58

Query: 60  ITAVQIDG--VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVT 115
           I  V+       HE   I+GV ED+ DIILN+K +  +++       ++ + K+GPG + 
Sbjct: 59  IVGVRFIKPEKYHEYDYIEGVKEDILDIILNLKKVQFRVNVTVKDRIKMEVEKKGPGELV 118

Query: 116 AGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDA 175
           AGDI+T   IEV NPD  I  L+  A +  E+    G G+VP    R E   +G I ID 
Sbjct: 119 AGDIKTPAGIEVANPDLHIATLNSKADLFFEIYAEVGKGFVPVSE-RDERPEVGWIPIDG 177

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN-- 233
           ++SP+ KV++  E+ R G+  DYDKL + + T  SI  E+++  A+ IL +   + +   
Sbjct: 178 VFSPVMKVNFLTENVRVGKRTDYDKLILEVWTKKSIRPEEALRKAADILINHFRIVMEGL 237

Query: 234 --------------FEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIV 279
                          EE      E  + +S+       KK++ELELSVRS NCL+   I 
Sbjct: 238 PEMKISEEYIITEEDEEEALTAVEGEDQESVENLDVYSKKIDELELSVRSLNCLKRAKIE 297

Query: 280 YMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT-MGLFL 317
            +GDL+ +TE ++L++ NFG+KSL E+K  L    GL L
Sbjct: 298 TIGDLMSKTEDELLKIKNFGQKSLDEVKKKLKEKFGLEL 336


>gi|320451273|ref|YP_004203369.1| DNA-directed RNA polymerase subunit alpha [Thermus scotoductus
           SA-01]
 gi|320151442|gb|ADW22820.1| DNA-directed RNA polymerase, subunit alpha [Thermus scotoductus
           SA-01]
          Length = 313

 Score =  278 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 112/294 (38%), Positives = 163/294 (55%), Gaps = 3/294 (1%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED+ +II
Sbjct: 20  YGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEII 79

Query: 87  LNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           LN+K + ++          + +   GP VV AGD     D E+LNPD  I  LD    + 
Sbjct: 80  LNLKELVVRFLDPKMQTTTLVLKAEGPKVVRAGDFVVPPDAEILNPDLTIATLDKGGKLY 139

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           ME+ V +G GYVPA+ H  ++  I  I +DA++SP+++V++ VE  R GQ  D DKL++ 
Sbjct: 140 MEVRVDRGVGYVPAERHGIKDR-INSIPVDAIFSPVRRVAFQVEDTRLGQRTDLDKLTLR 198

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           I TDGS+T  +++  A  IL++ L  F N +       E  +V+       L   +EEL 
Sbjct: 199 IWTDGSVTPLEALNQAVEILKEHLSYFANPQATALPAPEPASVERAEGEEDLDLPLEELG 258

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS R  + L+ E I  +  L+     D+  +   G +SL EI+  L   G  L 
Sbjct: 259 LSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIREALAKKGFALK 312


>gi|218961406|ref|YP_001741181.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           (Transcriptase alpha chain) (RNA polymerase alpha
           subunit) [Candidatus Cloacamonas acidaminovorans]
 gi|167730063|emb|CAO80975.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           (Transcriptase alpha chain) (RNA polymerase alpha
           subunit) [Candidatus Cloacamonas acidaminovorans]
          Length = 391

 Score =  278 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 109/316 (34%), Positives = 175/316 (55%), Gaps = 2/316 (0%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L  PN ++Y                PL  G+  T+GN LRR+L+SS++GAA+  V+I+G+
Sbjct: 7   LQMPNEVDYDKAS-YSRTYGKFEIGPLEPGYGTTIGNTLRRILLSSIQGAAVRFVRIEGL 65

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE   I G + D  D+IL +K + +  S      + +  +G GV+TA  IQ    ++++
Sbjct: 66  HHEFCPIPGTNSDYIDLILRLKQLVISSSSVEEVPLVLEHKGKGVITASMIQETAYVKII 125

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           N D  +  +  D   R+E+ V  G GYV A     E   +G I +D++YSP+ KV+++V 
Sbjct: 126 NKDLYLLEVVDDIDFRLEMIVGIGRGYVSADRQNPEGKAVGFIPVDSIYSPVLKVNFSVS 185

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EPKKEVKEDINV 247
             R  + +++D+L M I T+G++    ++ LA++IL+D       FE EP+     +++ 
Sbjct: 186 HQRVKERMNFDRLIMEIYTNGAVEPSIALFLAAKILKDMAAKISLFEIEPQYIRDIELDP 245

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       L   V+E+ELSVR+ NCL    I  +GDL+ +TEA+ML+  NFG+KSL EI 
Sbjct: 246 ELEEKERILKTSVKEIELSVRAANCLAQAKIETIGDLVSKTEAEMLKFRNFGKKSLEEIV 305

Query: 308 GVLGTMGLFLGMNLPD 323
             L    L LGM++  
Sbjct: 306 QKLKKYDLHLGMDVEG 321


>gi|323144989|ref|ZP_08079549.1| DNA-directed RNA polymerase, alpha subunit [Succinatimonas hippei
           YIT 12066]
 gi|322415268|gb|EFY06042.1| DNA-directed RNA polymerase, alpha subunit [Succinatimonas hippei
           YIT 12066]
          Length = 329

 Score =  277 bits (709), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 125/332 (37%), Positives = 188/332 (56%), Gaps = 9/332 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            +  EL+KP  + +  +     N   ++ EPL RGF +T+G +L  +L+ +L G AI A 
Sbjct: 1   MSVCELLKPKPVSFTEV---APNCAHIVLEPLERGFGNTIGVSLSGILLKTLPGCAIDAF 57

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQT 121
           QIDGV  E S    + E + ++I+N+K I +      +S   +++ K G G V A DI  
Sbjct: 58  QIDGVSDENSVKADMVETVFELIMNLKTIAVASESPLNSPVWLSLVKSGEGEVKASDIVL 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHH-RTENDPIGLITIDALYSP 179
            + I   NPD  IC L    A + M++ VS G GYVPA             I IDA +SP
Sbjct: 118 ASGISFPNPDAHICTLKGAKAALSMKIRVSYGRGYVPASSDAHIPAQSENEILIDASFSP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +++  Y VESAR  Q  D D+L + I+TDG++  E  +   + +L+D L   ++ EE  +
Sbjct: 178 VRRFVYEVESARVEQRTDLDRLVINIETDGTVAPEAVLMQGADLLRDHLCELVDQEEVSE 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
             +          +P L++ V++LEL+VRS NCL+ E+I+Y+GDL+QRTE ++L+  N G
Sbjct: 238 --RSMAPAAPPMPDPVLMQLVDDLELTVRSANCLKAESIIYIGDLVQRTEVELLKTPNLG 295

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +KSL EIK VL   GL LGM L +WPP ++  
Sbjct: 296 KKSLTEIKDVLAQRGLSLGMRLTNWPPPNLRS 327


>gi|281412757|ref|YP_003346836.1| DNA-directed RNA polymerase, alpha subunit [Thermotoga naphthophila
           RKU-10]
 gi|281373860|gb|ADA67422.1| DNA-directed RNA polymerase, alpha subunit [Thermotoga naphthophila
           RKU-10]
          Length = 336

 Score =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 117/331 (35%), Positives = 178/331 (53%), Gaps = 22/331 (6%)

Query: 8   ELIKPNNIEYIVL-GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           E + P  ++      +++ +       PL RG+A T+GNALRRVL+SS+   AI  V+  
Sbjct: 3   EFVIPKKLKVEEEREEKDYHYARFSLSPLERGYAITIGNALRRVLLSSIPSLAIIGVRFI 62

Query: 67  G--VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTV 122
                HE   I+GV ED+ DIILN+K +  +++       ++ + K+GPG + AGDI+T 
Sbjct: 63  KPEKYHEYDYIEGVKEDILDIILNLKKVQFRVNVTVKGTIKMEVEKKGPGELVAGDIKTP 122

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
             IEV NPD  I  L+  A +  E+    G G+VP    R E   +G I ID ++SP+ K
Sbjct: 123 AGIEVANPDLHIATLNSKADLFFEVYAEVGKGFVPVSE-REERPDVGWIPIDGVFSPVIK 181

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM------------ 230
           V++  E+ R G+  DYDKL + I T  SI  E+++  A+ IL +   +            
Sbjct: 182 VNFLTENVRVGKRTDYDKLILEIWTKKSIRPEEALRKAADILINHFKIVTEGLPELKISE 241

Query: 231 ---FINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
                + EE  +    D   ++        +K++ELELSVRS NCL+   I  +GDL+ +
Sbjct: 242 EYIITSEEEEAEIPAVDHEEENRENLDVYNRKIDELELSVRSLNCLKRAKIETIGDLLSK 301

Query: 288 TEADMLRMANFGRKSLVEIKGVLGT-MGLFL 317
           TE ++L++ NFG+KSL E+K  L    GL L
Sbjct: 302 TEEELLKIKNFGQKSLDEVKEKLKEKFGLEL 332


>gi|75755691|ref|YP_319795.1| RNA polymerase alpha subunit [Acorus calamus]
 gi|161622341|ref|YP_001586213.1| RNA polymerase alpha subunit [Acorus americanus]
 gi|90101572|sp|Q3V502|RPOA_ACOCL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|69215818|gb|AAZ03865.1| RNA polymerase alpha chain [Acorus americanus]
 gi|74381741|emb|CAI53826.1| RNA polymerase alpha subunit [Acorus calamus]
 gi|160369884|gb|ABX38775.1| RNA polymerase alpha subunit [Acorus americanus]
          Length = 337

 Score =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 84/330 (25%), Positives = 159/330 (48%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E      +       I  PL +G A T+G A+RR L+  + G  IT  + + V 
Sbjct: 13  LQWKCVES-RADSKRLYYGRFILSPLLKGQADTIGIAMRRALLGEIEGTCITRAKSEKVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +    +  +I  RGP  VTA DI +   +EV++
Sbjct: 72  HEYSTIAGIEESVHEILMNLKEIVLRSNLYGTRDASICVRGPRCVTAQDIISPPSVEVVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I +L     + + L + +  GY       +++   G   IDA+  P++  ++++ S
Sbjct: 132 TTQHIASLTEPIDLCIGLQIQRDRGYRMKTTKNSQD---GSYPIDAVSMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 YGNG-NQKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEEDINFEENQNRFT 247

Query: 250 LPFN----------------PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           +P                        +++ EL  R+ NCL+  NI  + DL+  ++ D++
Sbjct: 248 VPPFTFPDRLANLKKNKKEIALKCIFIDQSELPPRTYNCLKRSNIHTLLDLLSNSQEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++  F    + ++K +L T+     ++LP 
Sbjct: 308 KIEYFR---IEDVKQILDTLQKHFAIDLPK 334


>gi|294101657|ref|YP_003553515.1| DNA-directed RNA polymerase, alpha subunit [Aminobacterium
           colombiense DSM 12261]
 gi|293616637|gb|ADE56791.1| DNA-directed RNA polymerase, alpha subunit [Aminobacterium
           colombiense DSM 12261]
          Length = 339

 Score =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 121/331 (36%), Positives = 184/331 (55%), Gaps = 19/331 (5%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           EL++P     I + +       +I EPL RG+  TLGNALRRVL+SS++GAAIT+V++DG
Sbjct: 6   ELMRPE----IRIEECSSTFGKVIVEPLERGYGVTLGNALRRVLLSSVKGAAITSVRVDG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+ +++LN+K I +       K + +   GP  V A DIQ  ++IE 
Sbjct: 62  VLHEFSTIPGVREDVIELMLNLKHIPVHSYSKDVKVLHLEAEGPKQVVAADIQPDSEIEF 121

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           ++PD  +C L+  A + M+L + +G GY      R    P   + IDA+YSP+ KV Y V
Sbjct: 122 IDPDAPVCVLEDGAQLSMDLYIEQGVGYATIDRPRPAYLPADALLIDAIYSPVLKVHYDV 181

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK----- 242
           E+AR GQ  DY++L + + T+G I  + +V  A++I++   G  +   +    ++     
Sbjct: 182 EAARVGQRTDYERLVLDVTTNGVIAPDVAVGEAAKIIRSYFGFIVEDVDKLHPLEGIDEE 241

Query: 243 ----------EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                      +    +   +  L + V ELELS+RS NCL    I  +GDL+ RT  D+
Sbjct: 242 EAALSADEAAAEAAEAAKEEDDLLSRPVRELELSIRSENCLLRGGIHTIGDLLTRTRDDL 301

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           L++ N G+ SL EI+  L   GL L     +
Sbjct: 302 LKIRNLGKISLREIEERLEKQGLRLSTEKSE 332


>gi|262038698|ref|ZP_06012058.1| DNA-directed RNA polymerase, alpha subunit [Leptotrichia
           goodfellowii F0264]
 gi|261747250|gb|EEY34729.1| DNA-directed RNA polymerase, alpha subunit [Leptotrichia
           goodfellowii F0264]
          Length = 322

 Score =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 116/304 (38%), Positives = 178/304 (58%), Gaps = 4/304 (1%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
              +E         EPL RG+ +T+GNALRR+L+SS+ G+AI  ++IDGVL+E S+I GV
Sbjct: 14  TEEKESRYTAKYTLEPLYRGYGNTIGNALRRILLSSIPGSAIKGLRIDGVLNEFSTIPGV 73

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E +TDIILN+K I +++     K++ +  +GP V+TA DI+    I+++NP+ VI  + 
Sbjct: 74  KEAVTDIILNVKEIVVELDEPGEKKMVLSVKGPKVITAADIKPDPGIKIINPEQVIATVT 133

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  + ME  V  G G+V +    TE  PIG + +DA+Y+PIK+V+Y+VE    G+V +Y
Sbjct: 134 TDKEINMEFLVDSGEGFVVSDEIDTEGWPIGYLAVDAIYTPIKRVTYSVEDTMVGRVTNY 193

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK----EVKEDINVKSLPFNP 254
           DKL + I TDGSI   D+++ A  +L   +  F N             E+ ++ S   + 
Sbjct: 194 DKLILEISTDGSIEIHDALSYAVELLILHVKPFTNIGNSMSKFRGNEDENSSLNSETESN 253

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
               K+EEL+ +VRS NCL+   +  + DL   T  ++L++ N GRKSL EI   +  +G
Sbjct: 254 IEDMKIEELDFTVRSYNCLKKAGVNTISDLTSMTYVELLKIKNLGRKSLNEIIDKMKELG 313

Query: 315 LFLG 318
             L 
Sbjct: 314 YDLS 317


>gi|283794999|ref|YP_003359390.1| RNA polymerase alpha subunit [Olea europaea]
 gi|330850774|ref|YP_004376452.1| RNA polymerase alpha subunit [Olea europaea subsp. europaea]
 gi|281428718|gb|ADA69957.1| RNA polymerase alpha subunit [Olea europaea]
 gi|291059284|gb|ADD72120.1| RNA polymerase alpha subunit [Olea europaea]
 gi|328795464|emb|CBR30346.1| RNA polymerase alpha subunit [Olea europaea subsp. europaea]
          Length = 337

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 83/333 (24%), Positives = 159/333 (47%), Gaps = 27/333 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +   E++        I  PL +G A T+G A+RR L+  + G  IT V+ + V
Sbjct: 11  RTLQWKCVESREDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRVKSENV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  RGPG VTA DI     +E++
Sbjct: 71  PHEYSTIAGIQESVHEILMNLKEIVLRSNLYGTCDASICVRGPGYVTAQDIILPPYVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY+    H  ++   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDLCIGLQIKRNRGYLIKMPHNFQD---GSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV- 247
           S   G     + L + I T+GS+T ++++  A R L D    F++ EE    ++++ +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEACRNLIDLFIPFLHKEEENLPLEDNQHTV 246

Query: 248 ---------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                          K+          +++ E S R  NCL+  NI  + DL+  +  D+
Sbjct: 247 PLSPLTFHDKLDKLRKNKKKIALKSIFIDQSEFSPRVYNCLKRSNIYTLLDLLNNSPEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           +++ +     L +IK +L  +     ++LP   
Sbjct: 307 MKIEHLR---LEDIKQILVILEKHFAIDLPKKK 336


>gi|110589176|gb|ABG77097.1| DNA-directed RNA polymerase alpha subunit [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 303

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 118/271 (43%), Positives = 177/271 (65%), Gaps = 4/271 (1%)

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +   VLHE ++I+GV ED+ +I+LN+K + L M       + + K+GPGVV+AGDI   +
Sbjct: 30  RFQDVLHEYTAIEGVQEDVLEILLNLKQVALVMHSRDEAVLRLQKKGPGVVSAGDITLDH 89

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPI 180
           DIE+ NPD  I  L     + M LTV +G GY P+   ++   E+ PIG++ +DA +SP+
Sbjct: 90  DIEIANPDLHIATLTKSGEINMTLTVKRGRGYQPSTARQSSAGEDRPIGMLQLDASFSPV 149

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++V+Y++ESAR  Q  + D+L + + TDG+I  E+++  ++ IL+DQL +F++ E     
Sbjct: 150 RRVAYSIESARVEQRTNMDRLVIELQTDGTIDPEEAIRRSAGILRDQLSVFVDLEG-GGA 208

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +     +    +P LL+ V++LEL+VRS NCL+ ENI  +GDLIQRTE ++L+  N G+
Sbjct: 209 AEATAEPEEPMIDPILLRPVDDLELTVRSANCLKAENIFLIGDLIQRTEVELLKTPNLGK 268

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           KSL EIK VL   GL LGM L  WPPESI+E
Sbjct: 269 KSLTEIKDVLARRGLSLGMRLEHWPPESIDE 299


>gi|291460345|ref|ZP_06599735.1| DNA-directed RNA polymerase, alpha subunit [Oribacterium sp. oral
           taxon 078 str. F0262]
 gi|291417100|gb|EFE90819.1| DNA-directed RNA polymerase, alpha subunit [Oribacterium sp. oral
           taxon 078 str. F0262]
          Length = 313

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 119/315 (37%), Positives = 187/315 (59%), Gaps = 10/315 (3%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KP  +E I L  E++        PL +G A  LGN+LRR+L+SS+ GAAI+ V+++ V H
Sbjct: 6   KPE-LEVIELS-EDKRFGRFSCAPLVKGEATVLGNSLRRILLSSMPGAAISEVKVESVYH 63

Query: 71  EISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           E SSI GV ED+++II+N+K + ++   S D      I   G GV+ A DI+  ++IE++
Sbjct: 64  EFSSIAGVKEDVSEIIMNLKKLAVRNTSSSDEAVMAYIDYAGEGVIRAADIRVSSEIEIV 123

Query: 129 NPDHVICNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           NP+ VI  L   DA + ME+ ++KG GY  A        PIG+I +DA+Y+P+ KV+ +V
Sbjct: 124 NPEQVIATLSGKDAKLYMEMKITKGRGYDGANTRDHSELPIGVIAVDAVYTPVTKVNVSV 183

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           +          ++L + + T+G++  +D+V+LA++I+Q  L +FI+ +   KE     N 
Sbjct: 184 KDLGRS-----ERLVLDVMTNGTLAPDDAVSLAAKIMQTHLQLFIDMDNTVKEPFLPGNT 238

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                   + K ++ELELSVRS NCL+   I  + DL ++T  D++++ N GRKSL EI 
Sbjct: 239 AVEDVQDEMNKSIDELELSVRSYNCLKRAGINTVEDLCEKTMDDLMKVRNMGRKSLDEIL 298

Query: 308 GVLGTMGLFLGMNLP 322
             L +MGL L   + 
Sbjct: 299 NKLESMGLSLASKVE 313


>gi|124112107|ref|YP_001019081.1| alpha subunit of RNA polymerase [Chlorokybus atmophyticus]
 gi|158512761|sp|A2CI44|RPOA_CHLAT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|124012216|gb|ABM87965.1| alpha subunit of RNA polymerase [Chlorokybus atmophyticus]
          Length = 318

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 101/311 (32%), Positives = 162/311 (52%), Gaps = 10/311 (3%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             IE  +  +        +  PL  G   T+GN  RRVL+  L GA IT+VQI GV HE 
Sbjct: 12  ECIESRIESRRNH-YGRFVIAPLEIGQGITVGNVFRRVLLGDLEGACITSVQIPGVNHEF 70

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           S+I GV E + DI+LN+K I LK      +R  +  +GP  V A D+Q  + IE+++PD 
Sbjct: 71  STIHGVREAVLDILLNLKEIVLKTQSQETQRGHLSVQGPSTVLARDLQLPSSIELVDPDQ 130

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + ME TV  G GY    + + +   + ++ IDA++ P+ KV+YTVE    
Sbjct: 131 YIATISGRVSLNMEFTVEVGKGYQLPDYEKKKTFQVDVLPIDAVFMPVTKVNYTVEENYG 190

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           G     +++ + + T+GSI    ++ L+   + +      N     + ++ +  VK    
Sbjct: 191 GDRS-QERVIIEVWTNGSINSRQAIDLSVNKIINLFSPLQNV----RSIEHEPLVKEKD- 244

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +      VEEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFGR+S  E+   +  
Sbjct: 245 SKMTEVLVEELDLSVRAYNCLKRAQIHTVSDLLSYSQEDLLEIKNFGRRSAEEV---IEG 301

Query: 313 MGLFLGMNLPD 323
           +   LG++LP 
Sbjct: 302 LQKRLGIHLPK 312


>gi|320335496|ref|YP_004172207.1| DNA-directed RNA polymerase subunit alpha [Deinococcus maricopensis
           DSM 21211]
 gi|319756785|gb|ADV68542.1| DNA-directed RNA polymerase subunit alpha [Deinococcus maricopensis
           DSM 21211]
          Length = 321

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 116/310 (37%), Positives = 172/310 (55%), Gaps = 15/310 (4%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           + N      EPL RG+  T+GN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED+ 
Sbjct: 13  DGNYGEFTLEPLKRGYGVTIGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVI 72

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            +ILN+K + +K      K +T+  +G GVVTAG  +  +D E++NPD VI NL  D  +
Sbjct: 73  QLILNLKELVVKFHAPGPKTLTLRAQGQGVVTAGAFEVPSDAEIVNPDLVIANLAEDGKL 132

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            ME+ V +G GYVPA  H T++  I  I +DA+YSP+++V+Y VE+ R GQ  D D+L +
Sbjct: 133 VMEVRVEEGEGYVPADKHATKDR-INSIPVDAVYSPVRRVAYHVENTRVGQQTDLDRLII 191

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---------- 253
            I TDGS   + ++ +A   L+D+L +F N E  + E         LP            
Sbjct: 192 RIWTDGSADPQSALDMAVDTLRDELSVFGNVETIQAETVVTPAAYDLPQPSALSINPQPY 251

Query: 254 ----PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                +    +E L L+ R  + L+ E I  +  L   ++ D+ ++   G +SL EIK  
Sbjct: 252 PADLDSPKVTLEGLGLTTRVLHSLKEEGIDSVDALCALSDRDLKKVPGIGERSLDEIKAQ 311

Query: 310 LGTMGLFLGM 319
           L   GL L  
Sbjct: 312 LAQFGLSLKD 321


>gi|157325562|ref|YP_001468340.1| RNA polymerase alpha subunit [Ipomoea purpurea]
 gi|171769953|sp|A7Y3I1|RPOA_IPOPU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|157056790|gb|ABV02380.1| RNA polymerase alpha subunit [Ipomoea purpurea]
          Length = 337

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 82/333 (24%), Positives = 160/333 (48%), Gaps = 27/333 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT V+ +  
Sbjct: 11  RTLQWKCVESRTDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRVKSEKA 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  +GPG VTA DI     +E++
Sbjct: 71  PHEYSTIAGIQESVHEILMNLKEIVLRSNLYGTCDASICVKGPGCVTAEDIILPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L       + L + +  GY+   HH  E+   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIAWLTEPIDFCIGLQIERNRGYILKTHHNFED---GSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV- 247
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    +++  +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEENLHLEDGEHTI 246

Query: 248 ---------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                          K+          +++LE   +  NCL+  NI  + DL+ +++ D+
Sbjct: 247 PLSPLSFHDKVAKLRKNKKKLALKSIFIDQLEFPPKIYNCLKKSNISTLLDLLNKSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           +++ +F    + ++K +LG +     ++LP   
Sbjct: 307 MKIEHFH---IEDVKQILGILEKHFAIDLPKNQ 336


>gi|330444134|ref|YP_004377120.1| DNA-directed RNA polymerase subunit alpha [Chlamydophila pecorum
           E58]
 gi|328807244|gb|AEB41417.1| DNA-directed RNA polymerase, alpha subunit [Chlamydophila pecorum
           E58]
          Length = 374

 Score =  276 bits (706), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 124/366 (33%), Positives = 195/366 (53%), Gaps = 28/366 (7%)

Query: 2   IQKNWQELIK-----PNNIEYIVLGQ-EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSL 55
           + +N Q L+      P +++ + +     +     +AEPL +G  HTLGNALRR L+  L
Sbjct: 1   MSENLQNLLYDKFELPESVKMLSMEGFSTDTHARFVAEPLEKGMGHTLGNALRRALLIGL 60

Query: 56  RGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLK---MSGDSHKRVTIF----- 107
              AI +  + GVLHE  +I+G+ ED+T+IILN+K   LK   M G    R T       
Sbjct: 61  EAPAIISFSMTGVLHEYMAIEGIIEDVTNIILNLKSALLKKHPMQGSEEGRSTQLLKSSI 120

Query: 108 ---------KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
                      G   VT GD+      E +NP+ VI  +     + + L V+ G GY  +
Sbjct: 121 SIDASDLAAVGGQKEVTLGDLLQEGGFEAVNPEQVIFTVTQPMQLDITLRVAFGRGYTTS 180

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           +    E+  +  I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG IT ++++A
Sbjct: 181 ERIVLEDKGVNEIVLDAAFSPVCLVNYYVEDTRVGQDTDFDRLILQVETDGRITPKEALA 240

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK---KVEELELSVRSTNCLRG 275
            +++IL     +F   +E +   +E ++++    +  L K    + E+ELSVRSTNCL  
Sbjct: 241 FSTQILTKHFSIFEKMDEKRIVFEEAVSIEKENKDDILHKLILGINEIELSVRSTNCLSN 300

Query: 276 ENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW--PPESIEELA 333
            NI  +G+L+   E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  
Sbjct: 301 ANIETIGELVIMPEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGIGLDNVKEKM 360

Query: 334 KKYEDK 339
           K Y +K
Sbjct: 361 KWYAEK 366


>gi|194477035|ref|YP_002049214.1| DNA-directed RNA polymerase alpha subunit [Paulinella
           chromatophora]
 gi|171192042|gb|ACB43004.1| DNA-directed RNA polymerase alpha subunit [Paulinella
           chromatophora]
          Length = 308

 Score =  276 bits (706), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 104/306 (33%), Positives = 162/306 (52%), Gaps = 8/306 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+       +   + +  PL RG A TLGN+LRRVLM SL G+AITAV+I GV HE 
Sbjct: 7   DRIEHNTADNRSQT-GVFLIGPLDRGHAITLGNSLRRVLMGSLEGSAITAVRIAGVSHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K +++       +   +   GP  VTA D Q  + ++V+    
Sbjct: 66  ATIPGVREDVLDILLNCKQVSISSRNQELEIGRLVVSGPANVTAADFQFSSQVQVVYGSS 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + ME+ V +G GY P   H  +   I L+ IDA++ P+++V+YT++    
Sbjct: 126 PIVTIAEGHSIEMEVHVERGVGYRPVNRHNEDTSAIDLLQIDAVFMPVRRVNYTIDETAV 185

Query: 193 GQVLD-YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           G+     ++L + I+T+GSIT ED++A A+  L        N    ++       +    
Sbjct: 186 GEGGSARERLRLEIETNGSITPEDAMAEAANQLISMFQPLANLTMVEEP------IPEPE 239

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 240 PPTEAQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLFL 317
            +GL L
Sbjct: 300 RIGLSL 305


>gi|257467163|ref|ZP_05631474.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|315918294|ref|ZP_07914534.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|313692169|gb|EFS29004.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium
           gonidiaformans ATCC 25563]
          Length = 326

 Score =  276 bits (706), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 116/310 (37%), Positives = 187/310 (60%), Gaps = 6/310 (1%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
           +I   +E E +   + EPL RG+ HTLGNALRRVL+SS+ GAAI  ++I+GVL E S + 
Sbjct: 12  HITEVRESEFKGQFVVEPLYRGYGHTLGNALRRVLLSSIPGAAIKGIRIEGVLSEFSVMD 71

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV E +T+IILN+K I +K      +++T+  +GP VVTA DI     +E++NPD  IC 
Sbjct: 72  GVKEAVTEIILNVKEIVVKSETAGERKMTLSVKGPKVVTAADIIPDIGLEIINPDQEICT 131

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +  D  + +E  V  G G+V ++    +   +  I +DA+Y+PI+KVSY ++    G++ 
Sbjct: 132 ITTDRELDIEFLVDTGEGFVVSEEIERDGWAVDYIAVDAIYTPIRKVSYDIQDTMVGRMT 191

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV------KSL 250
           D+DKL+++++TDGSI   D+++ A  +L+  L  F+      + ++ ++         S+
Sbjct: 192 DFDKLTLSVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRVEVEEEVENQSSSI 251

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +  L  K+EEL+L+VRS NCL+   I  +G L + +  ++L++ N GRKSL EI   +
Sbjct: 252 KDDINLNIKIEELDLTVRSFNCLKKAGIEEVGQLSKLSMNELLKIKNLGRKSLDEILEKM 311

Query: 311 GTMGLFLGMN 320
             +G  L  N
Sbjct: 312 KELGYDLAQN 321


>gi|34849417|gb|AAP58916.1| DNA-directed RNA polymerase alpha subunit [Spiroplasma kunkelii
           CR2-3x]
          Length = 317

 Score =  276 bits (706), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 107/317 (33%), Positives = 173/317 (54%), Gaps = 8/317 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
            ++ I+P     +    +  N    + EPL RGF  TLGNA+RR L+S+  GAA+ AV+I
Sbjct: 1   MKQFIRPEF--KLQAEDKANNYGKFLVEPLERGFGVTLGNAIRRTLLSATPGAAVFAVRI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-----SHKRVTIFKRGPGVVTAGDIQ 120
            G  HE ++I GV E +T IILNIK + LK++ D         + +F    G + A D+ 
Sbjct: 59  KGSSHEFTAIPGVVEHVTKIILNIKNLVLKINQDIIPDGESVILKVFSSKEGEIYARDLV 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               +EV+N D ++  +     + +EL      GY     ++ E     LI ID+ Y PI
Sbjct: 119 VPTGVEVINGDLLLATIAKGGELDLELHARNSRGYKSFTDNKKEKKYADLIVIDSNYCPI 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++V+Y VE  + G+  D +KL + I TD SIT  ++VA+A++++ + L  F+N  E  K 
Sbjct: 179 QRVAYNVEPTKVGKNADLEKLELEIQTDSSITPVNAVAMAAKVITEHLEFFVNLNEAIKA 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +  I+ ++      L + ++ELE + RS NCL+   I  + DL+ ++E ++  + N G+
Sbjct: 239 TQI-ISSEAEAEEDELDRSIDELEFTQRSQNCLKRAKIDTLRDLVSKSEDEIQEIRNLGK 297

Query: 301 KSLVEIKGVLGTMGLFL 317
           KSL EIK  +  +GL  
Sbjct: 298 KSLTEIKDKVAQLGLHF 314


>gi|262273354|ref|ZP_06051168.1| DNA-directed RNA polymerase alpha subunit [Grimontia hollisae CIP
           101886]
 gi|262222332|gb|EEY73643.1| DNA-directed RNA polymerase alpha subunit [Grimontia hollisae CIP
           101886]
          Length = 279

 Score =  276 bits (706), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 123/281 (43%), Positives = 184/281 (65%), Gaps = 7/281 (2%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           + G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +K+ G     +T+ K G G V
Sbjct: 1   MPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVKVEGKDEVILTLNKSGAGPV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAK---HHRTENDPIGL 170
            AGDI     +E+ NP+HVIC+L   +A + M + V +G GYVPA    H   +  PIG 
Sbjct: 61  VAGDITHDGGVEIANPEHVICHLTDSNAEISMRIKVERGRGYVPASARIHTEEDERPIGR 120

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           + +DA +SP+ +++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  
Sbjct: 121 LLVDATFSPVDRIAYNVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDA 180

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
           F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE 
Sbjct: 181 FVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEV 237

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           ++L+  N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 238 ELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 278


>gi|78211905|ref|YP_380684.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp.
           CC9605]
 gi|119366745|sp|Q3AMQ3|RPOA_SYNSC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|78196364|gb|ABB34129.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus sp.
           CC9605]
          Length = 312

 Score =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 101/305 (33%), Positives = 165/305 (54%), Gaps = 8/305 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ V     ++  + +  PL RG A TLGNALRRVLM  L G+A+TA++I GV HE 
Sbjct: 7   DRIEHQVADDRAQS-GVFLIGPLERGQATTLGNALRRVLMGGLEGSAVTAIRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           +++ GV ED+ DI+LN K + +       +   +   GP  V AGD+Q  + ++V++ D 
Sbjct: 66  ATVPGVREDVLDILLNCKELTVNSRSAELEIGRLVVAGPAEVKAGDLQFSSQVQVVDTDR 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +EL V +G GY P   H  E   I L+ IDA++ P+ +V++T++    
Sbjct: 126 PIATVADGHSLELELHVERGVGYRPVDRHNEETSAIDLLQIDAVFMPVTRVNFTIDETAV 185

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L M I TDGSIT ++++A ++  L +              + E++  +  P
Sbjct: 186 AEGGSARERLRMEIVTDGSITPDEALAQSANQLIELFQPLATVT-----LVEEVPAEPEP 240

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
              A +  +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 241 SAEAQI-PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIS 304


>gi|308522648|dbj|BAJ22935.1| RNA polymerase alpha subunit [Aliivibrio sifiae]
 gi|308522650|dbj|BAJ22936.1| RNA polymerase alpha subunit [Aliivibrio sifiae]
 gi|308522654|dbj|BAJ22938.1| RNA polymerase alpha subunit [Aliivibrio sp. ATCC 33715]
          Length = 271

 Score =  276 bits (705), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 126/274 (45%), Positives = 185/274 (67%), Gaps = 7/274 (2%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
            EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG
Sbjct: 1   LEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKG 60

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVS 150
           + +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L  D A + M + V 
Sbjct: 61  LAVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNAEISMRIKVE 120

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVP+    H   +  PIG + IDA YSP+ K+SY+VE+AR  Q  D DKL + ++T
Sbjct: 121 RGRGYVPSTARIHTEEDERPIGRLLIDATYSPVDKISYSVEAARVEQRTDLDKLVIDMET 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V++LEL+V
Sbjct: 181 NGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTV 237

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+K
Sbjct: 238 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKK 271


>gi|308522652|dbj|BAJ22937.1| RNA polymerase alpha subunit [Aliivibrio sp. LC2-088]
          Length = 271

 Score =  276 bits (705), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 126/274 (45%), Positives = 186/274 (67%), Gaps = 7/274 (2%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
            EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG
Sbjct: 1   LEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKG 60

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVS 150
           + +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L  D A + M + V 
Sbjct: 61  LAVKVEGKDEVIITLNKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNAEISMRIRVE 120

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVP+    H   +  PIG + IDA YSP+ K+SY+VE+AR  Q  D DKL + ++T
Sbjct: 121 RGRGYVPSTARIHTEEDERPIGRLLIDATYSPVDKISYSVEAARVEQRTDLDKLVIDMET 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL +F++  + +         +   F+P LL+ V++LEL+V
Sbjct: 181 NGTLDPEEAIRRAATILAEQLDVFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTV 237

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+K
Sbjct: 238 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKK 271


>gi|157493285|gb|ABV58008.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 272

 Score =  276 bits (705), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 123/275 (44%), Positives = 187/275 (68%), Gaps = 8/275 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ 
Sbjct: 1   PLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLA 60

Query: 94  LKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVVRMELTVSK 151
           +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L   +A + M + V +
Sbjct: 61  VRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVER 120

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T+
Sbjct: 121 GRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMETN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V++LEL+VR
Sbjct: 181 GTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVR 237

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 272


>gi|118572712|sp|Q60F88|RPOA_TAKLE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|99653933|dbj|BAD60944.2| DNA-dependent RNA polymerase alpha subunit [Takakia lepidozioides]
          Length = 341

 Score =  276 bits (705), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 84/331 (25%), Positives = 160/331 (48%), Gaps = 25/331 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +     + +     P   G A T+G A+RR L+  + G  IT  +   V 
Sbjct: 13  LQWRCVES-RVDSARLHYSRFAISPFRSGQASTVGIAMRRALLGEVEGTCITCAEFKRVT 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + D+++N+  I L+      ++  I   GP  VTA DI     +++++
Sbjct: 72  HEYSTILGIQESVHDVLINLGEIVLRSDSYETQKAFISILGPKKVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  +     + +EL + K  GY      ++ +   G   +DA++ PI+ V+Y+V S
Sbjct: 132 TTQYIATVTKAIHLDIELKIEKDFGYRIEDPIKSAD---GNFPVDAVFMPIRNVNYSVHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP------KKEVKE 243
              G     + L + I T+GS+T ++++  ASR L +    F++ E+       K   + 
Sbjct: 189 FENGNET-QEILFLEIWTNGSVTPKEALYEASRSLINLFIPFLHAEKKEFIYGLKNTYES 247

Query: 244 DINVKSLPFNPALLKK-----------VEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +++  S P   A + +           +++LEL  R+ NCL+  N   + DL+  ++ D+
Sbjct: 248 NMSYFSSPSLSADIDEMTKGVTFKHIFIDQLELPARAYNCLKRVNAHTISDLLNYSQDDL 307

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ NFG+KS+ ++   L  +     +NLP 
Sbjct: 308 MKIKNFGKKSVEQV---LEALQKRFSINLPK 335


>gi|260656834|gb|ACX47807.1| RNA polymerase alpha-subunit [Vibrio litoralis]
          Length = 276

 Score =  276 bits (705), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 127/279 (45%), Positives = 187/279 (67%), Gaps = 8/279 (2%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ 
Sbjct: 1   PLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLA 60

Query: 94  LKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSK 151
           + +  G     +T+ K G G V AGDI    D+E+ NP+HVIC+L  D A + M + V +
Sbjct: 61  VSVAEGKDEVFITLKKSGSGPVVAGDIIHDGDVEIANPEHVICHLTDDKAEIAMRIKVQR 120

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVP+    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+
Sbjct: 121 GRGYVPSSARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V++LEL+VR
Sbjct: 181 GTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVR 237

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK
Sbjct: 238 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIK 276


>gi|15618536|ref|NP_224822.1| DNA-directed RNA polymerase subunit alpha [Chlamydophila pneumoniae
           CWL029]
 gi|33241983|ref|NP_876924.1| DNA-directed RNA polymerase subunit alpha [Chlamydophila pneumoniae
           TW-183]
 gi|4376924|gb|AAD18765.1| RNA Polymerase Alpha [Chlamydophila pneumoniae CWL029]
 gi|33236493|gb|AAP98581.1| DNA-directed RNA polymerase alpha chain [Chlamydophila pneumoniae
           TW-183]
          Length = 374

 Score =  276 bits (705), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 127/366 (34%), Positives = 195/366 (53%), Gaps = 28/366 (7%)

Query: 2   IQKNWQELIK-----PNNIEYIVLGQEE-ENRTLMIAEPLPRGFAHTLGNALRRVLMSSL 55
           +  N   L+      P  ++ + +     +     IAEPL RG  HTLGNALRR L+  L
Sbjct: 1   MSDNAHNLLYDKFELPEAVKMLPVEGLPIDKHARFIAEPLERGMGHTLGNALRRALLIGL 60

Query: 56  RGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-------GDSHKRVTIFK 108
              AI +  + GVLHE  +I+GV ED+T+IILN+KG  LK         G + + +    
Sbjct: 61  EAPAIISFAMTGVLHEYMAIEGVIEDVTNIILNLKGALLKKYPMQDSSLGRTTQVLKASI 120

Query: 109 ----------RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
                      G   VT  D+    D E +NPD VI  +     + + L ++ G GY P+
Sbjct: 121 SIDASDLAAANGQKEVTLQDLLQEGDFEAVNPDQVIFTVTQPIQLEVVLRIAFGRGYTPS 180

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           +    E+  +  I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +T ++++A
Sbjct: 181 ERIVLEDKGVYEIVLDAAFSPVTLVNYFVEDTRVGQDTDFDRLVLIVETDGRVTPKEALA 240

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK---KVEELELSVRSTNCLRG 275
            +++IL     +F N +E K   +E I+++    +  L K    + E+ELSVRSTNCL  
Sbjct: 241 FSTQILTKHFSIFENMDEKKIVFEEAISIEKENKDDILHKLILGINEIELSVRSTNCLSN 300

Query: 276 ENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELA 333
            NI  +G+L+   E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  
Sbjct: 301 ANIETIGELVIMPEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLTQFGVGLDNVKEKM 360

Query: 334 KKYEDK 339
           K Y +K
Sbjct: 361 KWYAEK 366


>gi|16752414|ref|NP_444673.1| DNA-directed RNA polymerase subunit alpha [Chlamydophila pneumoniae
           AR39]
 gi|7189055|gb|AAF38004.1| DNA-directed RNA polymerase, alpha subunit [Chlamydophila
           pneumoniae AR39]
          Length = 391

 Score =  275 bits (704), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 127/366 (34%), Positives = 195/366 (53%), Gaps = 28/366 (7%)

Query: 2   IQKNWQELIK-----PNNIEYIVLGQEE-ENRTLMIAEPLPRGFAHTLGNALRRVLMSSL 55
           +  N   L+      P  ++ + +     +     IAEPL RG  HTLGNALRR L+  L
Sbjct: 18  MSDNAHNLLYDKFELPEAVKMLPVEGLPIDKHARFIAEPLERGMGHTLGNALRRALLIGL 77

Query: 56  RGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-------GDSHKRVTIFK 108
              AI +  + GVLHE  +I+GV ED+T+IILN+KG  LK         G + + +    
Sbjct: 78  EAPAIISFAMTGVLHEYMAIEGVIEDVTNIILNLKGALLKKYPMQDSSLGRTTQVLKASI 137

Query: 109 ----------RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
                      G   VT  D+    D E +NPD VI  +     + + L ++ G GY P+
Sbjct: 138 SIDASDLAAANGQKEVTLQDLLQEGDFEAVNPDQVIFTVTQPIQLEVVLRIAFGRGYTPS 197

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           +    E+  +  I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +T ++++A
Sbjct: 198 ERIVLEDKGVYEIVLDAAFSPVTLVNYFVEDTRVGQDTDFDRLVLIVETDGRVTPKEALA 257

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK---KVEELELSVRSTNCLRG 275
            +++IL     +F N +E K   +E I+++    +  L K    + E+ELSVRSTNCL  
Sbjct: 258 FSTQILTKHFSIFENMDEKKIVFEEAISIEKENKDDILHKLILGINEIELSVRSTNCLSN 317

Query: 276 ENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELA 333
            NI  +G+L+   E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  
Sbjct: 318 ANIETIGELVIMPEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLTQFGVGLDNVKEKM 377

Query: 334 KKYEDK 339
           K Y +K
Sbjct: 378 KWYAEK 383


>gi|313847669|emb|CBY16657.1| putative DNA-directed RNA polymerase alpha chain [Chlamydophila
           psittaci RD1]
 gi|325506783|gb|ADZ18421.1| DNA-directed RNA polymerase subunit alpha [Chlamydophila psittaci
           6BC]
 gi|328914306|gb|AEB55139.1| DNA-directed RNA polymerase, alpha subunit [Chlamydophila psittaci
           6BC]
          Length = 376

 Score =  275 bits (704), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 124/357 (34%), Positives = 191/357 (53%), Gaps = 25/357 (7%)

Query: 8   ELIKPNNIEYIVL---GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           +   P +++ + +   G   + +   IAEPL RG  HTLGNALRR L+  L   AI +  
Sbjct: 12  KFELPESVKMMAVEGSGGSVDKQASFIAEPLERGMGHTLGNALRRALLIGLEAPAIISFS 71

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMS---GDSHKRVTIFKRGP---------- 111
           + GVLHE  +I G+ ED+T+IILN+KG  LK        + R T   +            
Sbjct: 72  MTGVLHEYMAINGIIEDVTNIILNLKGALLKKYPFQDSENGRCTQLLKSKVSIDASDLAA 131

Query: 112 ----GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
                 VT  D+      E +NPDHVI  +     + + L V+ G GY  ++    E+  
Sbjct: 132 CGGQKAVTLADLLQEGGFESVNPDHVIFTVTQPMQLDITLRVAFGRGYTTSERIVLEDKG 191

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           +  I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG ++ ++++A +++IL   
Sbjct: 192 VNEIVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLILHVETDGRVSPKEALAFSTQILTKH 251

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLK---KVEELELSVRSTNCLRGENIVYMGDL 284
             +F   +E K   +E I+++    +  L K    + E+ELSVRSTNCL   NI  +G+L
Sbjct: 252 FSIFEKMDEKKIVFEEAISIEKENKDDILHKLVLGINEIELSVRSTNCLSNANIETIGEL 311

Query: 285 IQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           +   E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y DK
Sbjct: 312 VIMPEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYADK 368


>gi|68053044|sp|Q5QA74|RPOA_ACOGR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|56122468|gb|AAV74359.1| RpoA [Acorus gramineus]
          Length = 337

 Score =  275 bits (704), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 84/330 (25%), Positives = 159/330 (48%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E      +       I  PL +G A T+G A+RR L+  + G  IT  + + V 
Sbjct: 13  LQWKCVES-RADSKRLYYGRFILSPLLKGQADTIGIAMRRALLGEIEGTCITRAKSEKVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +    +  +I  RGP  VTA DI +   +EV++
Sbjct: 72  HEYSTIAGIEESVHEILMNLKEIVLRSNLYGTRDASICVRGPRCVTAQDIISPPSVEVVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I +L     + + L + +  GY       +++   G   IDA+  P++  ++++ S
Sbjct: 132 TTQHIASLTEPIDLCIGLQIQRDRGYRMKTTKNSQD---GSYPIDAVSMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 YGNG-NQKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEEDINFEENQNRFT 247

Query: 250 LPFN----------------PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           +P                        +++ EL  R+ NCL+  NI  + DL+  ++ D++
Sbjct: 248 VPPFTFPDRLANLKKNKKEIALKCIFIDQSELPPRTYNCLKRSNIHTLLDLLSNSQEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++  F    + ++K +L T+     ++LP 
Sbjct: 308 KIEYFR---IEDVKQILDTLRKHFAIDLPK 334


>gi|320538142|ref|ZP_08038037.1| DNA-directed RNA polymerase, alpha subunit [Treponema phagedenis
           F0421]
 gi|320144959|gb|EFW36680.1| DNA-directed RNA polymerase, alpha subunit [Treponema phagedenis
           F0421]
          Length = 351

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 120/352 (34%), Positives = 194/352 (55%), Gaps = 13/352 (3%)

Query: 1   MIQKNW-QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M +KN  +   KP  ++++     +E+    IA P   GF  T+GN LRRVL+SS++G A
Sbjct: 1   MARKNLLKGFKKPKGVDFVA-EVSDESHGKFIASPFETGFGTTIGNCLRRVLLSSIQGYA 59

Query: 60  ITAVQI-----DGVLHEISS----IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK-R 109
           IT+V+I     DGV H ISS    I  V ED  +I+ N+K I L +  +  +    F+ +
Sbjct: 60  ITSVRITTYDADGVGHSISSEFESIPHVREDTLEILNNLKQIRLLLPEEEEEGAFTFEFQ 119

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  +T  D++    +++L+ D  I  +   A V  E+ V  G GYVPA+ +    + +G
Sbjct: 120 GPCTITGADLEKEYQLQILSKDVHIMEMMEGAHVEFEVNVKFGRGYVPAETNEQYVEVVG 179

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            I +D+++SP+ KV Y ++  R GQ  DYDKL + I TDG++  ED++A A++I +D   
Sbjct: 180 TIPLDSIFSPVLKVRYEIQPCRVGQRNDYDKLVLEIWTDGTVRPEDALAEAAKIAKDHFS 239

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +F+NF+E     ++D +         L  K+ E++ SVR+ NCL    +  +G+L + +E
Sbjct: 240 IFVNFDESVLIGEDDADEDDAKIIDLLNTKISEVDFSVRARNCLANIGVKTLGELTKISE 299

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE-DKC 340
             +    N G+KSL EI+G L    L LGM       ++ + + +K E D+ 
Sbjct: 300 QTLASTRNVGKKSLSEIQGKLQEYNLRLGMTDYSHLKDTNKLVRQKEETDEA 351


>gi|329942432|ref|ZP_08291242.1| DNA-directed RNA polymerase, alpha subunit [Chlamydophila psittaci
           Cal10]
 gi|328815342|gb|EGF85330.1| DNA-directed RNA polymerase, alpha subunit [Chlamydophila psittaci
           Cal10]
          Length = 356

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 123/345 (35%), Positives = 184/345 (53%), Gaps = 22/345 (6%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
               G   + +   IAEPL RG  HTLGNALRR L+  L   AI +  + GVLHE  +I 
Sbjct: 4   VEGSGGSVDKQASFIAEPLERGMGHTLGNALRRALLIGLEAPAIISFSMTGVLHEYMAIN 63

Query: 77  GVHEDLTDIILNIKGINLKMS---GDSHKRVTIFKRGP--------------GVVTAGDI 119
           G+ ED+T+IILN+KG  LK        + R T   +                  VT  D+
Sbjct: 64  GIIEDVTNIILNLKGALLKKYPFQDSENGRCTQLLKSKVSIDASDLAACGGQKAVTLADL 123

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
                 E +NPDHVI  +     + + L V+ G GY  ++    E+  +  I +DA +SP
Sbjct: 124 LQEGGFESVNPDHVIFTVTQPMQLDITLRVAFGRGYTTSERIVLEDKGVNEIVLDAAFSP 183

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +  V+Y VE  R GQ  D+D+L + ++TDG ++ ++++A +++IL     +F   +E K 
Sbjct: 184 VVLVNYFVEDTRVGQDTDFDRLILHVETDGRVSPKEALAFSTQILTKHFSIFEKMDEKKI 243

Query: 240 EVKEDINVKSLPFNPALLK---KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
             +E I+++    +  L K    + E+ELSVRSTNCL   NI  +G+L+   E  +L+  
Sbjct: 244 VFEEAISIEKENKDDILHKLVLGINEIELSVRSTNCLSNANIETIGELVIMPEPRLLQFR 303

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y DK
Sbjct: 304 NFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYADK 348


>gi|291460745|ref|ZP_06600135.1| DNA-directed RNA polymerase, alpha subunit [Oribacterium sp. oral
           taxon 078 str. F0262]
 gi|291416704|gb|EFE90423.1| DNA-directed RNA polymerase, alpha subunit [Oribacterium sp. oral
           taxon 078 str. F0262]
          Length = 320

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 106/315 (33%), Positives = 184/315 (58%), Gaps = 9/315 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN    +V   E+E     + EPL RG+  TLGN+L+R+++S+L G+A++A +I+G
Sbjct: 3   DFEKPNI--RVVEISEDERFGRFVCEPLERGYGTTLGNSLKRIMLSALPGSALSAAKIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQT---V 122
              +  S+ GV E L+++I+N+K + ++     +  KR+ +   G GVV A  IQ     
Sbjct: 61  ADFQSGSVPGVKESLSELIMNLKSLAIRDLSDSEDAKRLILTAEGSGVVRASSIQAETAD 120

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
            +  + N +  I  L  +  +R+EL +S+G GYV A+    E  P G+  +D+ Y+P+++
Sbjct: 121 TEFVIANEEQSIATLTGEEALRIELLLSRGRGYVSAEE--QEELPEGMFALDSSYTPVER 178

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+ +VE+ R G + DYDKL++ + TDG++  +D+++L++R+L  +L +F++        +
Sbjct: 179 VNMSVENTRVGNMTDYDKLTVDVFTDGTLPPDDALSLSARLLSTELCLFVDLSANAAAAE 238

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
             +         AL   ++ELELSVRS NCL+   I  + +L  +T  DM+++ N GRKS
Sbjct: 239 VMVEKTDDEKGKALEMNIDELELSVRSYNCLKRAGINTVQELCSKTPEDMMKVRNLGRKS 298

Query: 303 LVEIKGVLGTMGLFL 317
           L E+   L  + L L
Sbjct: 299 LEEVLAKLKELNLSL 313


>gi|15836158|ref|NP_300682.1| DNA-directed RNA polymerase subunit alpha [Chlamydophila pneumoniae
           J138]
 gi|12644496|sp|Q9Z7S8|RPOA_CHLPN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|8978998|dbj|BAA98833.1| RNA polymerase alpha [Chlamydophila pneumoniae J138]
          Length = 374

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 127/366 (34%), Positives = 195/366 (53%), Gaps = 28/366 (7%)

Query: 2   IQKNWQELIK-----PNNIEYIVLGQEE-ENRTLMIAEPLPRGFAHTLGNALRRVLMSSL 55
           +  N   L+      P  ++ + +     +     IAEPL RG  HTLGNALRR L+  L
Sbjct: 1   MSDNAHNLLYDKFELPEAVKMLPVEGLPIDKHARFIAEPLERGMGHTLGNALRRALLIGL 60

Query: 56  RGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-------GDSHKRVTIFK 108
              AI +  + GVLHE  +I+GV ED+T+IILN+KG  LK         G + + +    
Sbjct: 61  EAPAIISFAMTGVLHEYMAIEGVIEDVTNIILNLKGALLKKYPMQDSSLGRTTQVLKASI 120

Query: 109 ----------RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
                      G   VT  D+    D E +NPD VI  +     + + L ++ G GY P+
Sbjct: 121 SIDASDLAAANGQKEVTLQDLLQEGDFEAVNPDQVIFTVTQPIQLEVVLRIAFGRGYTPS 180

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           +    E+  +  I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +T ++++A
Sbjct: 181 ERIVLEDKGVYEIVLDAAFSPVTLVNYFVEDTRVGQDTDFDRLVLIVETDGRVTPKEALA 240

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK---KVEELELSVRSTNCLRG 275
            +++IL     +F N +E K   +E I+++    +  L K    + E+ELSVRSTNCL  
Sbjct: 241 FSTQILTKHFSIFENMDEKKIVFEEAISIEKENKDDILHKLILGINEIELSVRSTNCLSN 300

Query: 276 ENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELA 333
            NI  +G+L+   E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  
Sbjct: 301 ANIETIGELVIMPEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLTQFGVGLDNVKEKM 360

Query: 334 KKYEDK 339
           K Y +K
Sbjct: 361 KWYAEK 366


>gi|290489654|gb|ADD31211.1| RNA polymerase alpha subunit protein [Antirrhinum majus]
          Length = 336

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 84/332 (25%), Positives = 163/332 (49%), Gaps = 26/332 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT V+ + +
Sbjct: 11  RTLQWKCVESRTDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRVKSENI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  RGPG VTA DI     +E++
Sbjct: 71  PHEYSTITGIQESVHEILMNLKEIVLRTNLYGTCDASICARGPGYVTAQDIILPPYVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L       + L + +  GY+    H  ++   G  +IDA++ P++ V++++ 
Sbjct: 131 DNTQHIASLTEPINFCIGLEIERNRGYLIKMPHNFQD---GSYSIDAVFMPVRNVNHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV- 247
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    + ++ +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHKEEENLPLDDNQHTI 246

Query: 248 --------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         +           +++ ELS R+ NCL+  NI  + DL+  ++ D++
Sbjct: 247 PLSPFSFHDKLDKLRKNKKIALKSIFIDQSELSPRAYNCLKRSNIYTLFDLLNNSQEDLM 306

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           ++ +F    L ++K +LG +     ++LP   
Sbjct: 307 KIEHFR---LKDVKEILGILEKHFAIDLPKKK 335


>gi|260434747|ref|ZP_05788717.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus sp. WH
           8109]
 gi|260412621|gb|EEX05917.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus sp. WH
           8109]
          Length = 312

 Score =  275 bits (703), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 102/305 (33%), Positives = 166/305 (54%), Gaps = 8/305 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ V     ++  + +  PL RG A TLGNALRRVLM  L G+A+TA++I GV HE 
Sbjct: 7   DRIEHQVAEDRAQS-GVFLIGPLERGQATTLGNALRRVLMGGLEGSAVTAIRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           +++ GV ED+ DI+LN K I++       +   +   GP  V AGD+Q  + ++V++ D 
Sbjct: 66  ATVPGVREDVLDILLNCKEISVNSRSAELQIGRLVVAGPAEVKAGDLQFSSQVQVVDADR 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P   H  E   I L+ IDA++ P+ +V++T++    
Sbjct: 126 SIATVADGHSLELEVHVERGVGYRPVDRHNEETSAIDLLQIDAVFMPVTRVNFTIDETAV 185

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L M I TDGSIT +D++A ++  L +              + E++  +  P
Sbjct: 186 AEGGSARERLRMEIVTDGSITPDDALAQSANQLIELFQPLATVT-----LVEEVPAEPEP 240

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
              A +  +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 241 SAEAQI-PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIS 304


>gi|332144686|dbj|BAK19503.1| RNA polymerase alpha subunit [Lactobacillus camelliae]
          Length = 228

 Score =  275 bits (703), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 103/226 (45%), Positives = 149/226 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA++ +QIDGVLHE S+I GV ED+T IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVSNIQIDGVLHEFSTIDGVLEDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM  D  K V I   GP  VTA DI T  D+EVLNP+  IC +       + +TV
Sbjct: 61  KKLALKMHSDEDKTVEIDVDGPATVTAADIVTDADVEVLNPEQYICTVAEGGHFHVRMTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++TEN PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+G
Sbjct: 121 RTGRGYVAADQNKTENMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           SI+  ++++LA++IL + L +F+N  +  K  +  +  +       
Sbjct: 181 SISPREAISLAAKILTEHLDIFVNLTDSAKNAEIMVEKEETHKEKM 226


>gi|58416042|emb|CAH57435.1| RNA polymerase alpha-subunit [Vibrio sp. R-21432]
          Length = 287

 Score =  275 bits (703), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 123/293 (41%), Positives = 188/293 (64%), Gaps = 11/293 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQVST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+
Sbjct: 58  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K+
Sbjct: 118 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +     
Sbjct: 178 AYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
               +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 236 -EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 287


>gi|290489690|gb|ADD31229.1| RNA polymerase alpha subunit protein [Heuchera sanguinea]
          Length = 337

 Score =  275 bits (703), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 80/331 (24%), Positives = 162/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +E+  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLEWKCVESRADSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K + L+ +    +  +I   GPG VTA DI +   +E++
Sbjct: 71  PHEYSTIVGIQESVHEILMNLKEVVLRSNLYGTRNASICVSGPGYVTAQDIISPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + K  GY     +  ++   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDLCIGLQIEKNRGYRIKTPNNFQD---GSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLEDNQHKV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP      +                 +++ EL  R   CL+  NI  + DL+  ++ D+
Sbjct: 247 TLPLFTFHDRLAKLRKNKKEIALKYIFIDQSELPPRIYTCLKRSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F    + ++K +LG +     ++LP 
Sbjct: 307 MKIEHFR---IEDVKEILGFLEKHFEIDLPK 334


>gi|110004254|emb|CAK98592.1| probable dna-directed rna polymerase alpha chain protein
           [Spiroplasma citri]
          Length = 317

 Score =  275 bits (703), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 106/317 (33%), Positives = 172/317 (54%), Gaps = 8/317 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
            ++ I+P     +    +  N    + EPL RGF  TLGNA+RR L+S+  GAA+ AV+I
Sbjct: 1   MKQFIRPEF--KLQAEDKANNYGKFLVEPLERGFGVTLGNAIRRTLLSATPGAAVFAVRI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-----SHKRVTIFKRGPGVVTAGDIQ 120
            G  HE ++I GV E +T IILNIK + LK++ D         + +     G + A D+ 
Sbjct: 59  KGASHEFTAIPGVVEHVTKIILNIKNLVLKINQDIIPDGESVILKVVSSKEGEIYARDLV 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               +EV+N D ++  +     + +EL      GY     ++ E     LI ID+ Y PI
Sbjct: 119 VPTGVEVINGDLLLATIAKGGELDLELYARNSRGYKSFTDNKKEKKYADLIVIDSNYCPI 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++V+Y VE  + G+  D +KL + I TD SIT  ++VA+A++++ + L  F+N  E  K 
Sbjct: 179 QRVAYNVEPTKVGKNADLEKLELEIQTDSSITPVNAVAMAAKVITEHLEFFVNLNEAIKA 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +  I+ ++      L + ++ELE + RS NCL+   I  + DL+ ++E ++  + N G+
Sbjct: 239 TQI-ISSEAEAEEDELERSIDELEFTQRSQNCLKRAKIDTLRDLVSKSEDEIQEIRNLGK 297

Query: 301 KSLVEIKGVLGTMGLFL 317
           KSL EIK  +  +GL  
Sbjct: 298 KSLTEIKDKVAQLGLNF 314


>gi|269302410|gb|ACZ32510.1| DNA-directed RNA polymerase, alpha subunit [Chlamydophila
           pneumoniae LPCoLN]
          Length = 374

 Score =  275 bits (703), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 127/366 (34%), Positives = 195/366 (53%), Gaps = 28/366 (7%)

Query: 2   IQKNWQELIK-----PNNIEYIVLGQEE-ENRTLMIAEPLPRGFAHTLGNALRRVLMSSL 55
           +  N   L+      P  ++ + +     +     IAEPL RG  HTLGNALRR L+  L
Sbjct: 1   MSDNAHNLLYDKFELPEAVKMLPVEGLPIDKHARFIAEPLERGMGHTLGNALRRALLIGL 60

Query: 56  RGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-------GDSHKRVTIFK 108
              AI +  + GVLHE  +I+GV ED+T+IILN+KG  LK         G + + +    
Sbjct: 61  EAPAIISFAMTGVLHEYMAIEGVIEDVTNIILNLKGALLKKYPMQDSSLGRTTQVLKASI 120

Query: 109 ----------RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
                      G   VT  D+    D E +NPD VI  +     + + L ++ G GY P+
Sbjct: 121 SIDASDLAAANGQKEVTLQDLLQEGDFEAVNPDQVIFTVTQPIQLEVVLRIAFGRGYTPS 180

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           +    E+  +  I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +T ++++A
Sbjct: 181 ERIVLEDKGVYEIILDAAFSPVTLVNYFVEDTRVGQDTDFDRLVLIVETDGRVTPKEALA 240

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK---KVEELELSVRSTNCLRG 275
            +++IL     +F N +E K   +E I+++    +  L K    + E+ELSVRSTNCL  
Sbjct: 241 FSTQILTKHFSIFENMDEKKIVFEEAISIEKENKDDILHKLILGINEIELSVRSTNCLSN 300

Query: 276 ENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELA 333
            NI  +G+L+   E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  
Sbjct: 301 ANIETIGELVIMPEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLTQFGVGLDNVKEKM 360

Query: 334 KKYEDK 339
           K Y +K
Sbjct: 361 KWYAEK 366


>gi|257453242|ref|ZP_05618541.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp.
           3_1_5R]
 gi|317059776|ref|ZP_07924261.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp.
           3_1_5R]
 gi|313685452|gb|EFS22287.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp.
           3_1_5R]
          Length = 326

 Score =  274 bits (702), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 115/310 (37%), Positives = 187/310 (60%), Gaps = 6/310 (1%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
           +I   +E E +   + EPL RG+ HTLGNALRRVL+SS+ GAAI  ++I+GVL E S + 
Sbjct: 12  HITEVRESEFKGQFVVEPLYRGYGHTLGNALRRVLLSSIPGAAIKGIRIEGVLSEFSVMD 71

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV E +T+IILN+K I +K      +++T+  +GP VVTA DI     +E++NP+  IC 
Sbjct: 72  GVKEAVTEIILNVKEIVVKSETAGERKMTLSVKGPKVVTAADIIPDIGLEIINPEQEICT 131

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +  D  + +E  V  G G+V ++    +   +  I +DA+Y+PI+KVSY ++    G++ 
Sbjct: 132 ITTDRELDIEFLVDTGEGFVVSEEIERDGWAVDYIAVDAIYTPIRKVSYDIQDTMVGRMT 191

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV------KSL 250
           D+DKL+++++TDGSI   D+++ A  +L+  L  F+      + ++ ++         S+
Sbjct: 192 DFDKLTLSVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRVEVEEEVENQSSSI 251

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +  L  K+EEL+L+VRS NCL+   I  +G L + +  ++L++ N GRKSL EI   +
Sbjct: 252 RDDINLNIKIEELDLTVRSFNCLKKAGIEEVGQLSKLSMNELLKIKNLGRKSLDEILEKM 311

Query: 311 GTMGLFLGMN 320
             +G  L  N
Sbjct: 312 KELGYDLAQN 321


>gi|119662349|emb|CAJ33163.1| RNA polymerase alpha subunit [Lactobacillus rhamnosus]
          Length = 223

 Score =  274 bits (702), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 99/222 (44%), Positives = 151/222 (68%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED+T IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLEDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV
Sbjct: 61  KKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+G
Sbjct: 121 KKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           SI+  ++++LA++IL + L +F+N  +  K  +  +  +   
Sbjct: 181 SISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETH 222


>gi|300431307|gb|ADK12618.1| RNA polymerase alpha subunit [Achnatherum chingii]
          Length = 339

 Score =  274 bits (702), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 160/328 (48%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY     +  ++   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIELQIKRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTTGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ NF    + + K +  T+   L ++L
Sbjct: 308 RIDNFR---MEDGKQIWDTLEKHLPIDL 332


>gi|86438808|emb|CAJ43369.1| RNA polymerase alpha subunit [Lactobacillus casei]
          Length = 233

 Score =  274 bits (702), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 102/233 (43%), Positives = 155/233 (66%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
             + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED+T IILN
Sbjct: 1   KFVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLEDVTQIILN 60

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           IK + LKM+ D  K + I   GP  VTA DI T  D+EVLNP+  IC +       + +T
Sbjct: 61  IKKLALKMNTDEDKNIEIDVNGPAKVTAADIVTDPDVEVLNPEQYICTVADGGHFHVRMT 120

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+
Sbjct: 121 VKKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           GSI+  ++++LA++IL + L +F+N  +  K  +  +  +       L   +E
Sbjct: 181 GSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMTIE 233


>gi|32480874|ref|NP_862785.1| RNA polymerase alpha subunit [Calycanthus floridus var. glaucus]
 gi|41688654|sp|Q7YJU6|RPOA_CALFG RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|32399410|emb|CAD28752.1| RNA polymerase alpha subunit [Calycanthus floridus var. glaucus]
          Length = 340

 Score =  274 bits (702), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 84/333 (25%), Positives = 161/333 (48%), Gaps = 29/333 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        +  PL +G A T+G A+R+ L+  + G  IT  + + V
Sbjct: 11  RTLQWKCVESRTDSNRLYYGRFVLSPLMKGQADTIGIAMRKALLGEIEGTCITRAKSEKV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I LK +    +  +I  RGP  VTA DI +   +E++
Sbjct: 71  PHEYSTIVGIEESVHEILMNLKEIVLKSNLYGTRDASICVRGPKYVTAQDIISPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + +EL + +  GY     +  ++   G   IDA+  P++  ++++ 
Sbjct: 131 DTTQHIASLTEPINLCIELQIERDRGYRMKAPNNYQD---GSYPIDAVSMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    +  + N  
Sbjct: 188 SYGSG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEQDIHLNLEDNQN 246

Query: 249 SLPFNPALLKK------------------VEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
               +P  L                    +++ EL  R+ NCL+  NI  + DL+  ++ 
Sbjct: 247 RFTVSPFTLHDRLGNIRKNKKEIALKCIFIDQSELPTRTYNCLKRSNIHTLLDLLNNSQE 306

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           D++R+ +F    + +IK +L  +    G++LP 
Sbjct: 307 DLMRIEHFR---IEDIKQILDILQKHFGIDLPK 336


>gi|149390571|ref|YP_001294216.1| RNA polymerase alpha subunit [Buxus microphylla]
 gi|172048681|sp|A6MM68|RPOA_BUXMI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|146762316|gb|ABQ45280.1| RNA polymerase alpha subunit [Buxus microphylla]
          Length = 337

 Score =  274 bits (702), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 82/331 (24%), Positives = 160/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    +N        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRADNKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITCAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +    +  +I  RGP  VTA DI +   +E++
Sbjct: 71  PHEYSNIVGIEESVHEILMNLKEIVLRSNLYGTRDASICVRGPRHVTAQDIISPPSVEII 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY        +N   G   IDA++ P++  ++++ 
Sbjct: 131 DTTQHIASLTEPIDLCIGLQIERNRGY---NMKTPKNSQDGRYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV- 247
           S   G     + L + I T+GS+T ++++  ASR L D    F++  E    +K++ N  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHANEENFILKDNQNKV 246

Query: 248 ---------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                          K+          +++ EL  R+ NCL+  NI  + DL+  ++ D+
Sbjct: 247 ALPLFTFHDRLAKQRKNKKEISFQCIFIDQSELPPRTYNCLKRSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F    + ++K +LG +     ++LP 
Sbjct: 307 MKIEHFR---IEDVKQILGILQKHFAIDLPK 334


>gi|20160832|dbj|BAB89772.1| Chloroplast RNA polymerase alpha chain [Oryza sativa Japonica
           Group]
          Length = 337

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 95/330 (28%), Positives = 162/330 (49%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+    G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRTASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL      R+EL + +  GY       T++   G   IDA+  P++ V+Y++ +
Sbjct: 132 TAQPIANLTEPTDFRIELRIKRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFA 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    Y+ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NAKYEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 SPLLSFQKRLTNLKKNKKRIPLSCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           R+ +F    + + K +  T+   L M+LP 
Sbjct: 308 RIDSFR---MQDGKQIWDTLEKHLPMDLPK 334


>gi|11466821|ref|NP_039417.1| RNA polymerase alpha subunit [Oryza sativa Japonica Group]
 gi|50234003|ref|YP_052781.1| RNA polymerase alpha subunit [Oryza nivara]
 gi|109156616|ref|YP_654235.1| RNA polymerase alpha subunit [Oryza sativa Indica Group]
 gi|68053137|sp|Q6ENE2|RPOA_ORYNI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|148839633|sp|P0C498|RPOA_ORYSA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|148839634|sp|P0C499|RPOA_ORYSI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|148839635|sp|P0C500|RPOA_ORYSJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|12018|emb|CAA33979.1| RNA polymerase alpha subunit [Oryza sativa Japonica Group]
 gi|40253573|dbj|BAD05519.1| RNA polymerase alpha chain [Oryza sativa Japonica Group]
 gi|42795508|gb|AAS46075.1| RNA polymerase alpha chain [Oryza sativa Indica Group]
 gi|42795575|gb|AAS46141.1| RNA polymerase alpha chain [Oryza sativa Japonica Group]
 gi|42795639|gb|AAS46204.1| RNA polymerase alpha chain [Oryza sativa Japonica Group]
 gi|49615027|dbj|BAD26810.1| RNA polymerase alpha chain [Oryza nivara]
 gi|290790595|gb|ADD62855.1| RNA polymerase alpha subunit [Oryza sativa Japonica Group]
 gi|290790664|gb|ADD62923.1| RNA polymerase alpha subunit [Oryza meridionalis]
 gi|226639|prf||1603356BN RNA polymerase alpha
          Length = 337

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 95/330 (28%), Positives = 162/330 (49%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+    G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRTASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL      R+EL + +  GY       T++   G   IDA+  P++ V+Y++ +
Sbjct: 132 TAQPIANLTEPTDFRIELRIKRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFA 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    Y+ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NAKYEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 SPLLSFQKRLTNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           R+ +F    + + K +  T+   L M+LP 
Sbjct: 308 RIDSFR---MQDGKQIWDTLEKHLPMDLPK 334


>gi|238021616|ref|ZP_04602042.1| hypothetical protein GCWU000324_01516 [Kingella oralis ATCC 51147]
 gi|237866230|gb|EEP67272.1| hypothetical protein GCWU000324_01516 [Kingella oralis ATCC 51147]
          Length = 278

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 131/280 (46%), Positives = 185/280 (66%), Gaps = 6/280 (2%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGV 113
           + G A T V I GVLHE S++ GV ED+ DI+LNIKG+  K+ G S +  +T+ K G GV
Sbjct: 1   MNGFAPTEVTIAGVLHEYSTLDGVQEDIVDILLNIKGVVFKLHGGSTEAVITLKKEGSGV 60

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLI 171
           VTA D +  +D+E++NP+ VIC+L  +  + ME+ V +G GY      +   E   IG I
Sbjct: 61  VTAADFELPHDVEIINPEQVICHLAANGNIDMEVKVEQGRGYQSVAGRKAAKEQTKIGSI 120

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +D+ +SPI +VS+ VE+AR  Q  D D L + I+T+GSI  E++V  A+RIL DQ+ +F
Sbjct: 121 QLDSSFSPISRVSFEVEAARVEQRTDLDSLVLDIETNGSIEPEEAVRAAARILIDQMSIF 180

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
            + E    EV+E+   K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE +
Sbjct: 181 ADLEGTPIEVEEE---KAPPIDPVLLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETE 237

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +L+  N GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 238 LLKTPNLGRKSLNEIKEVLASKGLTLGSKLESWPPAGLEK 277


>gi|326200311|gb|ADZ52350.1| RNA polymerase alpha subunit [Asclepias syriaca]
          Length = 340

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 87/333 (26%), Positives = 160/333 (48%), Gaps = 27/333 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    E+        I  PL +  A T+G A+RR L+  + G  IT V+ D +
Sbjct: 11  RTLQWKCVESRTESKRLYYGRFILSPLLKSQADTIGIAMRRALLGEIEGTCITHVKFDKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+IKG+ E + +I++N+K I L+ +        I  RGP  VTA DI     +E++
Sbjct: 71  PHEYSTIKGIQESVHEILMNLKEIVLRSNLYEPCDAYICVRGPRSVTAQDIVLPPYVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I NL     + + L + +  GY+       +N P G   IDA++ P++  +++V 
Sbjct: 131 DNTQHIANLTEPINLCIVLKIERNRGYLIQT---PQNVPDGSYPIDAVFMPVRNANHSVH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN-- 246
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEENSHLENNQHRV 246

Query: 247 --------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                         +K+          +++LEL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 PLFPFTFHDKLTKLIKNKKEIALKSIFIDQLELPPRIYNCLKRSNIYTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           +++ +F    + ++K +L  +   L + LP   
Sbjct: 307 MKIEHFR---IEDVKQILVVLEKHLAIFLPKKK 336


>gi|253729586|ref|YP_003029770.1| RpoA [Bambusa oldhamii]
 gi|255961413|ref|YP_003097606.1| RNA polymerase a-subunit [Dendrocalamus latiflorus]
 gi|246367096|gb|ACS94707.1| RpoA [Bambusa oldhamii]
 gi|255040290|gb|ACT99950.1| RNA polymerase a-subunit [Dendrocalamus latiflorus]
          Length = 339

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 91/330 (27%), Positives = 161/330 (48%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY       +++   G   IDA+  P++ V+Y++  
Sbjct: 132 MAQPIANLTEPIDFCIELQIKRDRGYHTELRKNSQD---GSYPIDAVSMPVRNVNYSIFY 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLLTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           R+ +F    + + K +  T+   L ++LP 
Sbjct: 308 RIDSFR---MEDGKQIWDTLEKHLPIDLPK 334


>gi|149390473|ref|YP_001294302.1| RNA polymerase alpha subunit [Illicium oligandrum]
 gi|172048708|sp|A6MMX6|RPOA_ILLOL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|147917426|gb|ABQ52550.1| RNA polymerase alpha subunit [Illicium oligandrum]
          Length = 331

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 79/328 (24%), Positives = 157/328 (47%), Gaps = 27/328 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        +  PL +G A T+G A+RR L+  + G  IT  + + V
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFVLSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I  +      +  +I  RGP  VTA DI +   ++++
Sbjct: 71  PHEYSTIVGIEESVHEILMNLKEIVFRSHLYGTRGASICVRGPRYVTAQDIISPPSVKIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + +EL + +  GY     +  ++   G   IDA+  P++  ++++ 
Sbjct: 131 DTTQYIASLTEPIDLCIELQIERDRGYRIKTPNNYQD---GSYPIDAVSMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS T ++++  ASR L D    F++ EE    V+++ N  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSFTPKEALYEASRNLIDLFLPFLHAEEQDINVEDNQNRA 246

Query: 249 SLPFNPALL----------------KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           + P                        +++ EL  R+ NCL+  NI  + DL+  ++ D+
Sbjct: 247 TAPLFTFHDGLTNIGKRKKGIALKRVFIDQSELPTRTYNCLKRSNIHTLLDLLSNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           +R+ +F    + ++K +LG +     ++
Sbjct: 307 MRIEHFR---IEDVKQILGILQKRFAID 331


>gi|119662385|emb|CAJ33181.1| RNA polymerase alpha subunit [Lactobacillus zeae]
          Length = 227

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 100/226 (44%), Positives = 152/226 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED+T IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLEDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM+ D  K + I   GP  VTA DI T  D+EVLNP+  IC +       + +TV
Sbjct: 61  KKLALKMNTDEDKNIEIDVNGPAKVTAADIVTDPDVEVLNPEQYICTVADGGHFHVRMTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+G
Sbjct: 121 KKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           SI+  ++++LA++IL + L +F+N  +  K  +  +  +       
Sbjct: 181 SISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKM 226


>gi|270265495|emb|CBI68384.1| RNA polymerase alpha-subunit [Vibrio tapetis]
          Length = 286

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 123/287 (42%), Positives = 185/287 (64%), Gaps = 8/287 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +G
Sbjct: 3   VDIEQVSATHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEG 62

Query: 78  VHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           V ED+ +I+LN+KG+ +K+  G     +T+ K G G V AGDI    D+E+ NP+HVIC+
Sbjct: 63  VQEDILEILLNLKGLAVKVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICH 122

Query: 137 LDVD-AVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L  D A + M + V +G GYVPA        +  PIG + +DA YSP+ K++Y VE+AR 
Sbjct: 123 LTDDNAEIAMRIKVERGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARV 182

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G++  E+++  ++ IL +QL  F++  + +         +   F
Sbjct: 183 EQRTDLDKLVIDMETNGTLDPEEAIRRSATILAEQLDAFVDLRDIRVPE---EKEEKPEF 239

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G
Sbjct: 240 DPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLG 286


>gi|300431278|gb|ADK12604.1| RNA polymerase alpha subunit [Piptochaetium montevidense]
          Length = 339

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 90/328 (27%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY     +  ++   G   IDA+  P++ V+Y++ S
Sbjct: 132 RAQPIANLTEPIDFCIELQIKRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           ++ +F    + + K +  T+   L ++L
Sbjct: 308 KIDSFR---MEDGKQIWDTLEKHLPIDL 332


>gi|328813959|gb|AEB52095.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 231

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 101/231 (43%), Positives = 153/231 (66%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
             + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED+T IILN
Sbjct: 1   KFVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLEDVTQIILN 60

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           IK + LKM+ D  K + I   GP  VTA DI T  D+EVLNP+  IC +       + +T
Sbjct: 61  IKKLALKMNTDEDKNIEIDVNGPAKVTAADIVTDPDVEVLNPEQYICTVADGGHFHVRMT 120

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+
Sbjct: 121 VKKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           GSI+  ++++LA++IL + L +F+N  +  K  +  +  +       L   
Sbjct: 181 GSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMT 231


>gi|311990462|gb|ADQ26361.1| RNA polymerase alpha subunit [Lactobacillus plantarum]
          Length = 252

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 112/254 (44%), Positives = 162/254 (63%), Gaps = 6/254 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E +N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EFEKPN----IHKIDENDNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EV
Sbjct: 59  VLHEFSTIEGVTEDVTAIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSY 185
           LNPD  IC +   A   M +T + G GYV A+ ++   ++ PIG++ +D+LYSPI++V+Y
Sbjct: 119 LNPDLPICTVADGAHFHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R GQ  D+DKL++ + T+GSIT  ++++L+++IL D L +F+N  +  K     +
Sbjct: 179 QVENTRVGQRDDFDKLTLDVWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMV 238

Query: 246 NVKSLPFNPALLKK 259
             +       L   
Sbjct: 239 EKEETHKEKMLEMT 252


>gi|290489660|gb|ADD31214.1| RNA polymerase alpha subunit protein [Ehretia acuminata]
          Length = 339

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 83/339 (24%), Positives = 165/339 (48%), Gaps = 29/339 (8%)

Query: 7   QELIKPNNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           + ++    +++  +    ++        I  PL +G A T+G A+RR L+  + G +IT 
Sbjct: 5   KVIVSTRTLQWKCVESRTDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTSITR 64

Query: 63  VQID--GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           V+ +   V HE S+I G+ E + +I++N+K I L+ +       +I  RGPG VTA DI 
Sbjct: 65  VKSESEKVPHEYSTISGIQESVHEILMNLKEIVLRSNLYGTCDASICVRGPGYVTAQDII 124

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               +E+++    I +L     + + L + +  GY+    H  ++   G   IDA++ P+
Sbjct: 125 LPPYVEIVDNTQHIASLTEPIDLCIGLQIERNRGYLIKTPHNFQD---GSYPIDAVFMPV 181

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +  ++++ S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    
Sbjct: 182 RNANHSIHSYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEENVH 240

Query: 241 VKEDINVKSLPFNPALLKK----------------VEELELSVRSTNCLRGENIVYMGDL 284
           ++++ +   L       K                 +++ EL  R  NCL+  NI  + DL
Sbjct: 241 LEDNQHTVPLSPFIFHDKLAKLRKKKKKIALKSIFIDQSELPPRIYNCLKRSNIYTLLDL 300

Query: 285 IQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +  ++ D++++ +F    + ++K +LG +     ++L  
Sbjct: 301 LNNSQEDLMKIEHFR---IEDVKQILGILEKHFAIDLSK 336


>gi|154249789|ref|YP_001410614.1| DNA-directed RNA polymerase subunit alpha [Fervidobacterium nodosum
           Rt17-B1]
 gi|171769360|sp|A7HM24|RPOA_FERNB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|154153725|gb|ABS60957.1| DNA-directed RNA polymerase, alpha subunit [Fervidobacterium
           nodosum Rt17-B1]
          Length = 328

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 117/312 (37%), Positives = 178/312 (57%), Gaps = 13/312 (4%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG--VLHEISSI 75
             +  E+         PL +G+A T+GN LRRVL+SS+   AIT V+       HE  +I
Sbjct: 13  EQVEHEDHYYARYSLSPLEKGYAVTVGNTLRRVLLSSIPSFAITDVRFVKPEKYHEFDTI 72

Query: 76  KGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           +G  ED+ DI+LN+K + L++    +S  ++TI K+GPGV+TAGDI+    + V+NP H 
Sbjct: 73  EGAKEDIMDILLNLKKVQLRVDTYVESPVKLTINKKGPGVLTAGDIECPAGVVVVNPGHY 132

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           +  L+ DA + +EL  + G G+VPA   R E   IG I +D +YSP+ KV++ VE+ R  
Sbjct: 133 LATLNEDADLEIELYATFGKGFVPAAD-RNERPEIGWIVLDGVYSPVIKVNWLVENVRVD 191

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEE---PKKEVKEDIN 246
           +  DY+KL + I T  SI   +++  + +I+ D          + EE   P  +    + 
Sbjct: 192 KRTDYEKLILEIWTKKSIKPSEALKHSLKIILDHFMFIEQSLSDVEELPIPIIQETAVVT 251

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       + KKVEELELS RS NCL+ + I  +GDL+ RTE +++++ NFG KSL E+
Sbjct: 252 EEIGSPEDVMSKKVEELELSARSLNCLKRDKIETIGDLLSRTEEELMKIKNFGLKSLEEV 311

Query: 307 KGVL-GTMGLFL 317
           +  L    GL L
Sbjct: 312 REKLRDKFGLSL 323


>gi|290790733|gb|ADD62991.1| RNA polymerase alpha subunit [Oryza australiensis]
          Length = 337

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 96/330 (29%), Positives = 162/330 (49%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+    G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRNASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL      R+EL + +  GY       T++   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPTDFRIELRIKRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    Y+ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NAKYEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 SPLLSFQKRLTNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           R+ +F    + + K +  T+   L M+LP 
Sbjct: 308 RIDSFR---MQDGKQIWDTLEKHLPMDLPK 334


>gi|290489666|gb|ADD31217.1| RNA polymerase alpha subunit protein [Meliosma aff. cuneifolia
           Moore 333]
          Length = 337

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 85/331 (25%), Positives = 168/331 (50%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFIMSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSETI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +    +  +I  RGPG VTA DI + + +E++
Sbjct: 71  PHEYSTIVGIEESVHEILMNLKEIVLRSNLYGTRDASICVRGPGYVTAQDIISPSSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + + HGY       +++   G   IDA++ P++  ++++ 
Sbjct: 131 DTTQHIASLTEPINLCIGLQIERNHGYRMKTPKNSQD---GSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ N  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHTEEEDIIIEDNQNRF 246

Query: 249 SLPFNPAL----------------LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           ++PF                       +++ EL  R+ NCL+  NI  + DL+ +++ D+
Sbjct: 247 TVPFFTFHDRLAKLRKNKKEIALKFIFIDQSELPPRTYNCLKRSNIHTLLDLLNKSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +R+ +F    + ++K +LG +     +NLP 
Sbjct: 307 MRIEHFR---IEDVKHILGILQKHFEINLPK 334


>gi|169788419|emb|CAP58131.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788421|emb|CAP58132.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788423|emb|CAP58133.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788425|emb|CAP58134.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788427|emb|CAP58135.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788429|emb|CAP58136.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788431|emb|CAP58137.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788433|emb|CAP58138.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788435|emb|CAP58139.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788437|emb|CAP58140.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788439|emb|CAP58141.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788441|emb|CAP58142.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788443|emb|CAP58143.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788445|emb|CAP58144.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788449|emb|CAP58146.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788451|emb|CAP58147.1| RNA polymerase [Lactobacillus rossiae]
 gi|169788453|emb|CAP58148.1| RNA polymerase [Lactobacillus rossiae]
          Length = 235

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 113/235 (48%), Positives = 165/235 (70%), Gaps = 2/235 (0%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+K ++LKM
Sbjct: 1   RGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVTQIILNMKKVSLKM 60

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
           + D  K + I  +GP  VTAGDIQT  D+EV+NPD  IC +   A   M LT +KG GYV
Sbjct: 61  ATDEEKGMDIDVKGPATVTAGDIQTDADVEVMNPDLYICTVADGATFHMHLTANKGRGYV 120

Query: 157 PAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A  ++   ++ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSIT  
Sbjct: 121 SADENKARQDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSITPS 180

Query: 215 DSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           ++++LA++IL + L MF++  +  K  +  +  +       L   +EEL+LSVRS
Sbjct: 181 EAISLAAKILTEHLAMFVDLTDTAKNAEIMVEKEETHKEKMLEMTIEELDLSVRS 235


>gi|289065121|ref|YP_003434007.1| RNA polymerase alpha subunit [Typha latifolia]
 gi|69215826|gb|AAZ03869.1| RNA polymerase alpha chain [Typha latifolia]
 gi|281371804|gb|ADA63731.1| RNA polymerase alpha subunit [Typha latifolia]
          Length = 339

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 92/330 (27%), Positives = 163/330 (49%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           I+   +E   +  +       I  PL +G A T+G A+RR L+  + G  IT  + + V 
Sbjct: 13  IQWKCVES-RVDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSERVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  RGP  VTA DI     +E+++
Sbjct: 72  HEYSTIIGIEESVHEILLNLKEIVLRSNLYGVRDASICVRGPRYVTAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P   I NL     + +EL + +  GY     + +++   G   IDA+  P++  ++++ S
Sbjct: 132 PTQHIANLTEPIDLYIELQIKRDRGYRMEPTNNSQD---GSYPIDAVSMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 YGNG-NEKQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEEDINFEENKNRFT 247

Query: 250 LPF----------------NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           LPF                 P     +++LEL  R+ NCL+  NI  + DL+   + D++
Sbjct: 248 LPFLTFQDRLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRSNIHTLLDLLSNGQEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           R+       + ++K +L T+     ++LP 
Sbjct: 308 RIEYLR---MEDVKQILDTLQKNFAIDLPK 334


>gi|69215824|gb|AAZ03868.1| RNA polymerase alpha chain [Ranunculus macranthus]
          Length = 339

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 80/333 (24%), Positives = 161/333 (48%), Gaps = 29/333 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +    +  +I  +GPG VTA DI +   +E++
Sbjct: 71  PHEYSTIVGIEESVHEILMNLKEIVLRSNLYGTRDASICVKGPGYVTAQDIISPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L       + L +    GY     +   N   G   IDA++ P++  ++++ 
Sbjct: 131 DTTQHIASLTEPVDFCIGLQIESNRGYRMKTPN---NAQKGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN-- 246
           S   G   + + L + I T+GS+T ++++  ASR L D    F++ EE  + +K++    
Sbjct: 188 SYGNG-NENQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEQDQNLKDNQKNG 246

Query: 247 ---------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
                           K+          +++ EL  R+ NCL+  NI  + DL+ +++ D
Sbjct: 247 VTLPFFTFHDGFDKLKKNKKEIELKCIFIDQSELPSRTYNCLKRANIHTLLDLLNKSQED 306

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFL-GMNLPD 323
           ++++ +F    + ++K +L  +      ++LP 
Sbjct: 307 LMKIEHFR---IEDVKQILDIIQKHFVVIDLPK 336


>gi|84874028|gb|ABC68037.1| RNA polymerase subunit [Oryza sativa]
          Length = 317

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 93/320 (29%), Positives = 157/320 (49%), Gaps = 23/320 (7%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +  +       I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+ 
Sbjct: 2   VDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGIE 61

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL  
Sbjct: 62  ESVQEILLNLKEIVLRSNLYGVRTASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTE 121

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
                +EL + +  GY       T++   G   IDA+  P++ V+Y++ +   G    Y+
Sbjct: 122 PTDFHIELRIKRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFACGNG-NAKYE 177

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-------- 251
            L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P        
Sbjct: 178 ILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKRL 237

Query: 252 --------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                     P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    +
Sbjct: 238 TNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSFR---M 294

Query: 304 VEIKGVLGTMGLFLGMNLPD 323
            + K +  T+   L M+LP 
Sbjct: 295 QDGKQIWDTLEKHLPMDLPK 314


>gi|169788447|emb|CAP58145.1| RNA polymerase [Lactobacillus rossiae]
          Length = 235

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 112/235 (47%), Positives = 164/235 (69%), Gaps = 2/235 (0%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+K ++LKM
Sbjct: 1   RGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVTQIILNMKKVSLKM 60

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
           + D  K + I  +GP  VTAGD QT  D+EV+NPD  IC +   A   M LT +KG GYV
Sbjct: 61  ATDEEKGMDIDVKGPATVTAGDFQTDADVEVMNPDLYICTVADGATFHMHLTANKGRGYV 120

Query: 157 PAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A  ++   ++ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSIT  
Sbjct: 121 SADENKARQDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSITPS 180

Query: 215 DSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           ++++LA++IL + L MF++  +  K  +  +  +       L   +EEL+LSVRS
Sbjct: 181 EAISLAAKILTEHLAMFVDLTDTAKNAEIMVEKEETHKEKMLEMTIEELDLSVRS 235


>gi|328951208|ref|YP_004368543.1| DNA-directed RNA polymerase subunit alpha [Marinithermus
           hydrothermalis DSM 14884]
 gi|328451532|gb|AEB12433.1| DNA-directed RNA polymerase subunit alpha [Marinithermus
           hydrothermalis DSM 14884]
          Length = 317

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 114/302 (37%), Positives = 168/302 (55%), Gaps = 8/302 (2%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           E N    + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+  LHE S++ GV ED+ 
Sbjct: 16  EGNYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDALHEFSTLPGVKEDVV 75

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            IILN+K + +K      K +T+   GP  + A D++   D E++NPD  I  L     +
Sbjct: 76  QIILNLKELVVKFHAPGSKILTLRAEGPRTIYARDLECPPDAEIINPDLYIATLGEGGKL 135

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            ME+ V +G GYVPA+ H  ++  I  I +DALYSP+++V+Y VE  R GQ  D DKL +
Sbjct: 136 VMEVRVDEGVGYVPAEKHGIKDR-INSIPVDALYSPVRRVAYHVEDTRLGQRTDLDKLIL 194

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMF-------INFEEPKKEVKEDINVKSLPFNPAL 256
            I TDGS++  D++  A  IL++ LG F           EP +   E   V +       
Sbjct: 195 RIWTDGSVSPLDALQSAVGILREHLGFFDQAAVVAEAEAEPVEAAPEVEAVGAEEAAERP 254

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +++L LS R  + L+ E I  + +L+  TE ++ ++   G +S+ EIK  L   GL 
Sbjct: 255 ALTLDDLGLSTRVLHNLKEEGIDSIENLLALTERELKKVPGIGERSVEEIKERLAEHGLS 314

Query: 317 LG 318
           L 
Sbjct: 315 LK 316


>gi|12230594|sp|Q9KWU8|RPOA_THEAQ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|21466003|pdb|1L9U|A Chain A, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 gi|21466004|pdb|1L9U|B Chain B, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 gi|21466009|pdb|1L9U|J Chain J, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 gi|21466010|pdb|1L9U|K Chain K, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 gi|21466016|pdb|1L9Z|A Chain A, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
           Promoter Dna Complex At 6.5 A Resolution
 gi|21466017|pdb|1L9Z|B Chain B, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
           Promoter Dna Complex At 6.5 A Resolution
 gi|62738680|pdb|1YNJ|A Chain A, Taq Rna Polymerase-Sorangicin Complex
 gi|62738681|pdb|1YNJ|B Chain B, Taq Rna Polymerase-Sorangicin Complex
 gi|62738686|pdb|1YNN|A Chain A, Taq Rna Polymerase-Rifampicin Complex
 gi|62738687|pdb|1YNN|B Chain B, Taq Rna Polymerase-Rifampicin Complex
 gi|109157854|pdb|2GHO|A Chain A, Recombinant Thermus Aquaticus Rna Polymerase For
           Structural Studies
 gi|109157855|pdb|2GHO|B Chain B, Recombinant Thermus Aquaticus Rna Polymerase For
           Structural Studies
 gi|7573271|emb|CAB65464.2| RNA polymerase, alpha subunit [Thermus aquaticus]
          Length = 314

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 109/297 (36%), Positives = 163/297 (54%), Gaps = 4/297 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ++    + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED+ +
Sbjct: 18  DHYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVE 77

Query: 85  IILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILN+K + ++          + +   GP  V AGD     D+E++NPD  I  L+    
Sbjct: 78  IILNLKELVVRFLDPKMASTTLILRAEGPKEVRAGDFTPSADVEIMNPDLHIATLEEGGK 137

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + ME+ V +G GYVPA+ H  ++  I  I +DA++SP+++V++ VE  R GQ  D DKL+
Sbjct: 138 LYMEVRVDRGVGYVPAERHGIKDR-INAIPVDAIFSPVRRVAFQVEDTRLGQRTDLDKLT 196

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK-KVE 261
           + I TDGS+T  +++  A  IL++ L  F N E       E    +        L   +E
Sbjct: 197 LRIWTDGSVTPLEALNQAVAILKEHLNYFANPEASLLPTPEVSKGEKRESAEEDLDLPLE 256

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           EL LS R  + L+ E I  +  L+     D+  +   G +SL EI+  L   G  L 
Sbjct: 257 ELGLSTRVLHSLKEEGIESVRALLALNLKDLRNIPGIGERSLEEIRQALAKKGFTLK 313


>gi|300431299|gb|ADK12614.1| RNA polymerase alpha subunit [Hesperostipa comata]
          Length = 339

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY     +  ++   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIELQIKRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LPFN----------------PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPRFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDGKQIWDTLEKHLPIDL 332


>gi|122894022|ref|YP_001004218.1| RNA polymerase alpha subunit [Ranunculus macranthus]
 gi|158514028|sp|A1XGS0|RPOA_RANMC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|85540836|gb|ABC70788.1| RNA polymerase alpha subunit [Ranunculus macranthus]
          Length = 346

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 80/333 (24%), Positives = 161/333 (48%), Gaps = 29/333 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +    +  +I  +GPG VTA DI +   +E++
Sbjct: 71  PHEYSTIVGIEESVHEILMNLKEIVLRSNLYGTRDASICVKGPGYVTAQDIISPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L       + L +    GY     +   N   G   IDA++ P++  ++++ 
Sbjct: 131 DTTQHIASLTEPVDFCIGLQIESNRGYRMKTPN---NAQKGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN-- 246
           S   G   + + L + I T+GS+T ++++  ASR L D    F++ EE  + +K++    
Sbjct: 188 SYGNG-NENQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEQDQNLKDNQKNG 246

Query: 247 ---------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
                           K+          +++ EL  R+ NCL+  NI  + DL+ +++ D
Sbjct: 247 VTLPFFTFHDGFDKLKKNKKEIELKCIFIDQSELPSRTYNCLKRANIHTLLDLLNKSQED 306

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFL-GMNLPD 323
           ++++ +F    + ++K +L  +      ++LP 
Sbjct: 307 LMKIEHFR---IEDVKQILDIIQKHFVVIDLPK 336


>gi|323148937|ref|YP_004222491.1| RNA polymerase alpha subunit [Smilax china]
 gi|308742628|gb|ADO33479.1| RNA polymerase alpha subunit [Smilax china]
          Length = 339

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 87/330 (26%), Positives = 159/330 (48%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RR L+  + G  IT  + + V 
Sbjct: 13  LQWKCVES-RIDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE  +I G+ E + +I++N+K I L+ +    +   I  RGP  VTA DI +   +E+++
Sbjct: 72  HEYFTIVGIKESVHEILINLKEIVLRSTLYGVRDAAICVRGPRYVTAQDIISPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L     + + L + +  GY     + +++   G   IDA+  P++  ++++ S
Sbjct: 132 TTQHIATLTEPIDLCIGLQIKRDRGYRMKPTNNSKD---GSYPIDAVSMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L D    F++ EE     KE+ N  +
Sbjct: 189 YGNG-NEKQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEEGINFKENENRFT 247

Query: 250 LPFN----------------PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           LP                  P     +++LEL  R+ NCL+  NI  + DL+  ++ D++
Sbjct: 248 LPPFTLQDRLINLKKTKKCIPLKCIFIDQLELPPRTYNCLKRSNIHTLLDLLSNSQEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           R+       + ++K +L T+   L  +LP 
Sbjct: 308 RIDYLR---IEDVKQILDTLQKHLASDLPK 334


>gi|300431329|gb|ADK12627.1| RNA polymerase alpha subunit [Achnatherum diegoense]
          Length = 339

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 162/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I+ +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY     +  ++   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIELQIQRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDGKQIWDTLEKHLPIDL 332


>gi|119668363|emb|CAK95475.1| RNA polymerase alpha subunit [Lactobacillus rhamnosus]
          Length = 228

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 99/226 (43%), Positives = 151/226 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED+T IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLEDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV
Sbjct: 61  KKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+G
Sbjct: 121 KKGRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           SI+  ++++LA++IL + L +F+N  +  K  +  +  +       
Sbjct: 181 SISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKM 226


>gi|310779568|ref|YP_003967901.1| DNA-directed RNA polymerase subunit alpha [Ilyobacter polytropus
           DSM 2926]
 gi|309748891|gb|ADO83553.1| DNA-directed RNA polymerase subunit alpha [Ilyobacter polytropus
           DSM 2926]
          Length = 325

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 123/309 (39%), Positives = 189/309 (61%), Gaps = 6/309 (1%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I   +E + +   I EPL RG+ HT+GNALRRVL+SS+ GAAI  ++IDGVL+E S I+G
Sbjct: 13  ISEVKENDFKAQYIVEPLYRGYGHTIGNALRRVLLSSIPGAAIKGLRIDGVLNEFSIIEG 72

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V E +TDIILN+K + +K      KR+ +  +GP +VTA DI   +++E++NPD VIC +
Sbjct: 73  VKEAVTDIILNVKEVIVKTETSGEKRMNLSVQGPKIVTAADINPDSELEIINPDQVICTV 132

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             +  + ME  V  G G+V A+    ++  +  IT+DA+Y+PIK+VSY+VE    G++ D
Sbjct: 133 TTEKEINMEFLVDTGEGFVVAEDIERKDWSVDYITVDAIYTPIKRVSYSVEDTMVGRMTD 192

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED------INVKSLP 251
           +DKL++ ++TDGSI   D+++ A  +L+     F++     + ++ D        V S  
Sbjct: 193 FDKLTLNVETDGSIVIRDAISYAVELLRLHFDPFLDIGNGMENLRGDLEEEEVEEVDSSK 252

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L  K+EEL+L+VRS NCL+   I  +G L   +  ++L++ N GRKSL EI   + 
Sbjct: 253 DEDVLNLKIEELDLTVRSFNCLKKAGIEEVGQLAILSLNELLKIKNLGRKSLDEILDKMK 312

Query: 312 TMGLFLGMN 320
            +G  L  N
Sbjct: 313 ELGFDLSQN 321


>gi|328813941|gb|AEB52086.1| DNA-directed RNA polymerase alpha chain [Lactobacillus brevis]
          Length = 248

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 109/248 (43%), Positives = 165/248 (66%), Gaps = 4/248 (1%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRV 104
           LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+K I LK++G  D  + +
Sbjct: 1   LRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVTQIILNVKKIALKLNGSDDQEETM 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            I  +GP  +TAGDI    D+++LNPD  I  +   A   M +T  KG GYV A  ++T 
Sbjct: 61  EINVKGPAQITAGDIVAGADVDILNPDLYIATVADGATFHMRMTADKGRGYVSADENKTR 120

Query: 165 --NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
             + PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ + T+GSI   +++ALA++
Sbjct: 121 NTDMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDVWTNGSINPSEAIALAAK 180

Query: 223 ILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMG 282
           IL + L MF++  +  K  +  +  +       L   +EEL+LSVRS NCL+   I  + 
Sbjct: 181 ILTEHLAMFVDLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSVRSYNCLKRAGINTVQ 240

Query: 283 DLIQRTEA 290
           +L  +TEA
Sbjct: 241 ELNNKTEA 248


>gi|189162303|ref|YP_001936549.1| RNA polymerase alpha subunit [Fagopyrum esculentum subsp.
           ancestrale]
 gi|166065389|gb|ABY79764.1| RNA polymerase alpha subunit [Fagopyrum esculentum subsp.
           ancestrale]
          Length = 337

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 86/333 (25%), Positives = 165/333 (49%), Gaps = 27/333 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRTDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  RGPG VTA DI +   +E++
Sbjct: 71  PHEYSTIVGIQESVHEILMNLKEIVLRSTFYGTCDASICVRGPGGVTAQDIISPPYVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I NL     +R+EL + +  GY     +  ++   G   ID ++ P++ V++++ 
Sbjct: 131 DTTQHIANLTEPIDLRIELQLERNRGYRIKTPNNFQD---GSYPIDVVFMPVRNVNHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F+  E+    ++++ +  
Sbjct: 188 SYSNG-NEKQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLYAEKENFHLEDNQDRV 246

Query: 249 SLP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP                        +++LEL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPLFLFHDRLIELRKNKKKIALKSIFIDQLELPPRIYNCLKNSNIHTLLDLLTNSQDDI 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           +++ +F   S+ ++K +L T+     +NLP   
Sbjct: 307 MKIEHF---SIEDVKQILDTLEKHFAINLPKKK 336


>gi|187233921|gb|ACD01207.1| RNA polymerase alpha subunit [Phyllostachys propinqua]
          Length = 339

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 92/330 (27%), Positives = 162/330 (49%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY       +++   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIELQIKRDRGYHTELRKNSQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLLTFQKRLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           R+ +F    + + K +  T+   L ++LP 
Sbjct: 308 RIDSFR---MEDGKQIWDTLEKHLPIDLPK 334


>gi|218294782|ref|ZP_03495636.1| DNA-directed RNA polymerase, alpha subunit [Thermus aquaticus
           Y51MC23]
 gi|218244690|gb|EED11214.1| DNA-directed RNA polymerase, alpha subunit [Thermus aquaticus
           Y51MC23]
          Length = 314

 Score =  273 bits (699), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 109/295 (36%), Positives = 161/295 (54%), Gaps = 4/295 (1%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED+ +II
Sbjct: 20  YGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEII 79

Query: 87  LNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           LN+K + ++          + +   GP  V AGD     D+E++NPD  I  L+    + 
Sbjct: 80  LNLKELVVRFLDPKMASTTLILRAEGPKEVRAGDFTPSADVEIMNPDLHIATLEEGGKLY 139

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           ME+ V +G GYVPA+ H  ++  I  I +DA++SP+++V++ VE  R GQ  D DKL++ 
Sbjct: 140 MEVRVDRGVGYVPAERHGIKDR-INAIPVDAIFSPVRRVAFQVEDTRLGQRTDLDKLTLR 198

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK-KVEEL 263
           I TDGS+T  +++  A  IL++ L  F N E       E    +        L   +EEL
Sbjct: 199 IWTDGSVTPLEALNQAVAILKEHLNYFANPEASLLPTPEVSKGEKRESAEEDLDLPLEEL 258

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            LS R  + L+ E I  +  L+     D+  +   G +SL EI+  L   G  L 
Sbjct: 259 GLSTRVLHSLKEEGIESVRALLALNLKDLRNIPGIGERSLEEIRQALAKKGFTLK 313


>gi|327399495|ref|YP_004340364.1| DNA-directed RNA polymerase subunit alpha [Hippea maritima DSM
           10411]
 gi|327182124|gb|AEA34305.1| DNA-directed RNA polymerase subunit alpha [Hippea maritima DSM
           10411]
          Length = 340

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 127/324 (39%), Positives = 194/324 (59%), Gaps = 3/324 (0%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + +          EPL  G+A T+GNALRRVL+SS+ G A+  V+I+GV HE S+I+G
Sbjct: 14  VNVEKNTPTYGRFSLEPLNEGYATTIGNALRRVLLSSIVGIAVVGVEIEGVEHEFSTIEG 73

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKR--VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
           V ED+ +IILN+K +  K   DS K   V I K GPG V +GDI+ + +IE++N D  I 
Sbjct: 74  VKEDVLNIILNLKQVRFKALNDSFKEGEVYIHKEGPGSVVSGDIEALGNIEIVNKDIYIA 133

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
            L   A +  ++ + +G GY  A  +   N  IG I +DAL+SPI +V+Y  + +     
Sbjct: 134 ELMDGAKLDAKIYLQRGIGYKQAN-YDAVNREIGFIPVDALFSPIVRVAYHTKKSTMKDY 192

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            D++KL + I+TDG+I  +D++  AS IL + + +F    +   + + + N   +  N  
Sbjct: 193 YDFEKLVLEIETDGTIMPQDALKQASYILGNYISIFSADFKETTQKEPEENKIDIQINEN 252

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           LLK VEELEL+VR++NCL   NI Y+ +L Q+T+ ++L   NFG++SL EIK  L  +GL
Sbjct: 253 LLKPVEELELNVRASNCLAAHNIKYIYELTQKTDTELLNTKNFGKQSLKEIKDSLKQLGL 312

Query: 316 FLGMNLPDWPPESIEELAKKYEDK 339
            LGM       E I++L ++ E +
Sbjct: 313 ELGMKFSQEQLERIQQLIEEKEGE 336


>gi|15639205|ref|NP_218652.1| DNA-directed RNA polymerase subunit alpha [Treponema pallidum
           subsp. pallidum str. Nichols]
 gi|189025446|ref|YP_001933218.1| DNA-directed RNA polymerase subunit alpha [Treponema pallidum
           subsp. pallidum SS14]
 gi|6094122|sp|O83242|RPOA_TREPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|3322481|gb|AAC65201.1| DNA-directed RNA polymerase, alpha subunit (rpoA) [Treponema
           pallidum subsp. pallidum str. Nichols]
 gi|189018021|gb|ACD70639.1| DNA-directed RNA polymerase, alpha subunit [Treponema pallidum
           subsp. pallidum SS14]
 gi|291059617|gb|ADD72352.1| DNA-directed RNA polymerase, alpha subunit [Treponema pallidum
           subsp. pallidum str. Chicago]
          Length = 351

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 117/350 (33%), Positives = 188/350 (53%), Gaps = 14/350 (4%)

Query: 1   MIQKNW-QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M ++N  +   +P  +E++      E      A P   GF  T+GN LRRVL+SS++G A
Sbjct: 1   MPRRNLLKGFKRPKVLEFLS-ENSSECYGKFTASPFETGFGTTVGNCLRRVLLSSIQGYA 59

Query: 60  ITAVQI-----DGVLHEISS----IKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKR 109
           +T V+I     DGV H ISS    I  V ED  +I+ N K +   +  G      T   R
Sbjct: 60  VTGVRITSFDADGVAHFISSEFEQIPHVREDTLEILNNFKRLRFLLPQGAESSTFTYEFR 119

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           G   +T  D      +EVL+ D +I  +   A V +EL V  G GYVPA+ H    D +G
Sbjct: 120 GAVSLTGKDFAKKFQLEVLSQDLLIMEMMDGAHVEVELHVEFGRGYVPAESHDRYADLVG 179

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           +I +DA++SP+ +V Y ++S R GQ  DYD+LS+ + TDG++  ED++A A++I+++   
Sbjct: 180 VIPVDAIFSPVLRVRYDIQSCRVGQRGDYDQLSLEVWTDGTVRPEDAIAEAAKIIKEHFT 239

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +F+NF+E   +++++           L  K+ +++ SVR+ NCL    I  +G+L + +E
Sbjct: 240 VFVNFDETALDLEDEPEEDDPAVLELLNTKIADVDFSVRARNCLLTMGIKTLGELTRISE 299

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             +    N G+KSL EI+G L    L LGM   D+    +     + +++
Sbjct: 300 QTLANTRNVGKKSLSEIQGKLQEYNLRLGM--ADYNHVGVVSRLMRQKEE 347


>gi|149072030|ref|YP_001293601.1| RNA polymerase alpha subunit [Rhodomonas salina]
 gi|172048721|sp|A6MW22|RPOA_RHDSA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134302981|gb|ABO70785.1| RNA polymerase alpha subunit [Rhodomonas salina]
          Length = 314

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 98/311 (31%), Positives = 164/311 (52%), Gaps = 10/311 (3%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             +E    G  +   +    EPL +G   TLGNALRR L+S L G AI AV+I GV HE 
Sbjct: 7   ECVESTTDGARDH-YSKFCLEPLEQGQGVTLGNALRRTLLSDLEGTAIVAVRIAGVSHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           S+I G+ ED+ +I+LN+K + LK    +     +  +GP +VT  +++  +++E+++P+ 
Sbjct: 66  STIPGIREDVLEILLNLKEVVLKSQTKNPSVGRLRVQGPAIVTTSNLELPSEVELIDPNQ 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +  + ++ ME  +  G GY   +    +   I  + +DA++ P+KKV+Y  +  R 
Sbjct: 126 YIATICGNNILEMEFRIETGKGYHLIE-RSIDETSIDFLQVDAIFMPVKKVNYLTKDIRS 184

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
              L  ++L + + T+GSI  +D+V+   +IL + L             K D        
Sbjct: 185 NDNLLQEQLLLEVWTNGSIDPQDAVSQGGKILTELLHPLKEI-----NFKSDEEDTVAED 239

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +      +EEL+LSVR+ NCL+   I  + DL+  ++ D++ + NFG+KS  E+   L  
Sbjct: 240 SKINQILIEELQLSVRAYNCLKRAQIHSVADLLDYSQEDLIEIKNFGQKSAEEVIDAL-- 297

Query: 313 MGLFLGMNLPD 323
               LG+NLP 
Sbjct: 298 -QKRLGINLPK 307


>gi|300431303|gb|ADK12616.1| RNA polymerase alpha subunit [Aciachne flagellifera]
          Length = 339

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY     +  ++   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIELQIKRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDGKQIWDTLEKHLPIDL 332


>gi|159161193|ref|YP_001542479.1| RNA polymerase alpha subunit [Ceratophyllum demersum]
 gi|172048124|sp|A8SED5|RPOA_CERDE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|148508476|gb|ABQ81483.1| RNA polymerase alpha subunit [Ceratophyllum demersum]
 gi|227481150|emb|CAP62529.1| RNA polymerase alpha subunit [Ceratophyllum demersum]
          Length = 337

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 84/330 (25%), Positives = 163/330 (49%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ++RR L+  + G  IT  + D V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLMKGQADTIGISMRRALLGEIEGTCITRAKFDKVT 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +       +I  RGP  VTA DI +   +E+++
Sbjct: 72  HEYSTIVGIEESVHEILMNLKEIVLRSNLYGTLDASICVRGPRSVTAQDIISPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL     + + L + +  GY     +  ++   G   ID ++ P++  ++++ S
Sbjct: 132 TTQHIANLTEPIDLCIGLQIERDRGYRLKTPNNYQD---GSYPIDTVFMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L +    F++ EE +  +++  N+ +
Sbjct: 189 YGNGTE-KQEILFLEIWTNGSLTPKEALYEASRNLINLFIPFLHAEEQEILLEDSENIST 247

Query: 250 LPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           +P      +                 +++LEL  R+ NCL+  NI  + DL+  ++ D++
Sbjct: 248 VPLFTFHNELANLKKNKKGIALKCIFIDQLELPSRTYNCLKRSNIHTLFDLLSNSKEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           R+ +F    + ++K +L  +     MNLP 
Sbjct: 308 RIEHFR---VEDVKQILDILQKNFAMNLPK 334


>gi|87124986|ref|ZP_01080833.1| Bacterial RNA polymerase, alpha chain [Synechococcus sp. RS9917]
 gi|86167306|gb|EAQ68566.1| Bacterial RNA polymerase, alpha chain [Synechococcus sp. RS9917]
          Length = 312

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 99/308 (32%), Positives = 165/308 (53%), Gaps = 14/308 (4%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ +     +   + +  PL RG A TLGNALRRVLM  L G+A+TAV+I GV HE 
Sbjct: 7   DRIEHQISDDRAQT-GVFLIGPLERGQATTLGNALRRVLMGGLEGSAVTAVRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           +++ GV ED+ DI+LN K +++       +   +   GP  V A D+Q  + ++V++P+ 
Sbjct: 66  ATVPGVREDVLDILLNCKQLSVNSRTSELEIGRLVVAGPAEVKARDLQFSSQVQVVDPER 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P   H  +   I L+ IDA++ P+++V+++++    
Sbjct: 126 PIATVSDGHSLELEVHVERGIGYRPVDRHNEDTSAIDLLQIDAVFMPVQRVNFSIDETAV 185

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF---INFEEPKKEVKEDINVK 248
                  ++L M + TDGSIT +D++A A+ +L +           EEP  E +     +
Sbjct: 186 AEGGSARERLRMEVVTDGSITPDDAIAQAANLLIELFQPLATVTMVEEPGLEPEPSAEAQ 245

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                      +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+  
Sbjct: 246 ---------IPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIE 296

Query: 309 VLGTMGLF 316
            L  +G+ 
Sbjct: 297 ALERIGIS 304


>gi|13096176|pdb|1HQM|A Chain A, Crystal Structure Of Thermus Aquaticus Core Rna
           Polymerase- Includes Complete Structure With Side-Chains
           (Except For Disordered Regions)-Further Refined From
           Original Deposition-Contains Additional Sequence
           Information
 gi|13096177|pdb|1HQM|B Chain B, Crystal Structure Of Thermus Aquaticus Core Rna
           Polymerase- Includes Complete Structure With Side-Chains
           (Except For Disordered Regions)-Further Refined From
           Original Deposition-Contains Additional Sequence
           Information
          Length = 313

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 108/296 (36%), Positives = 163/296 (55%), Gaps = 3/296 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ++    + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED+ +
Sbjct: 18  DHYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVE 77

Query: 85  IILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           IILN+K + ++      +  + +   GP  V A D     D+E++NPD  I  L+    +
Sbjct: 78  IILNLKELVVRFLDPRWRTTLILRAEGPKEVRAVDFTPSADVEIMNPDLHIATLEEGGKL 137

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            ME+ V +G GYVPA+ H  ++  I  I +DA++SP+++V++ VE  R GQ  D DKL++
Sbjct: 138 YMEVRVDRGVGYVPAERHGIKDR-INAIPVDAIFSPVRRVAFQVEDTRLGQRTDLDKLTL 196

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK-KVEE 262
            I TDGS+T  +++  A  IL++ L  F N E       E    +        L   +EE
Sbjct: 197 RIWTDGSVTPLEALNQAVAILKEHLNYFANPEASLLPTPEVSKGEKRESAEEDLDLPLEE 256

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           L LS R  + L+ E I  +  L+     D+  +   G +SL EI+  L   G  L 
Sbjct: 257 LGLSTRVLHSLKEEGIESVRALLALNLKDLRNIPGIGERSLEEIRQALAKKGFTLK 312


>gi|218282150|ref|ZP_03488449.1| hypothetical protein EUBIFOR_01031 [Eubacterium biforme DSM 3989]
 gi|218216860|gb|EEC90398.1| hypothetical protein EUBIFOR_01031 [Eubacterium biforme DSM 3989]
          Length = 318

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 116/306 (37%), Positives = 169/306 (55%), Gaps = 7/306 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +E       + EPL   +   LGNALRRVL+SS+ G AI +++IDGV HE + IKGV ED
Sbjct: 11  EETTKEGKFLFEPLEYRYGTPLGNALRRVLLSSIPGGAIFSIRIDGVYHEFTGIKGVKED 70

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT--AGDIQTVNDIEVLNPDHVICNLDV 139
           +  IILN+K + L +    ++  T+     G  T  AGDI+    + VLN D  IC L  
Sbjct: 71  VASIILNLKQLILDIDIHDNEVYTLRIDQEGPKTVVAGDIECPTGVTVLNKDLPICTLSE 130

Query: 140 DAVVRMELTVSKGHGYVPAKHHR----TENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
              + MEL    G G+V +  ++     E  P+G+I  D+LYSP+K VSY     +    
Sbjct: 131 GGSIHMELQARLGRGFVRSDVNKRMYQNEGQPLGIIYTDSLYSPVKNVSYVANPIKSEDG 190

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
             YD L + I TD +I   +++A+A++IL+D L +  + +E   EVKE     S      
Sbjct: 191 SMYDSLELEITTDETIKPSEALAVAAKILRDHLSILASVDEASLEVKEQEVEVSEEPVVH 250

Query: 256 LLKK-VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
              K +E+LELSVRS NCL+   I  + +L Q+TE +M+ + N G+KSL E+K  +  +G
Sbjct: 251 TTHKMIEDLELSVRSYNCLKRAGIATVDELTQKTEEEMIHVRNLGKKSLQEVKDKIKELG 310

Query: 315 LFLGMN 320
           L    N
Sbjct: 311 LSFRQN 316


>gi|300431276|gb|ADK12603.1| RNA polymerase alpha subunit [Nassella pampagrandensis]
 gi|300431282|gb|ADK12606.1| RNA polymerase alpha subunit [Nassella melanosperma]
 gi|300431318|gb|ADK12622.1| RNA polymerase alpha subunit [Amelichloa brachychaeta]
 gi|300431325|gb|ADK12625.1| RNA polymerase alpha subunit [Austrostipa nodosa]
          Length = 339

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 162/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I+ +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY     +  ++   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIELQIKRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDGKQIWDTLEKHLPIDL 332


>gi|300431309|gb|ADK12619.1| RNA polymerase alpha subunit [Achnatherum psilantherum]
          Length = 339

 Score =  272 bits (697), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 162/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I+ +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY     +  ++   G   IDA+  P++ V+Y++ S
Sbjct: 132 TGQPIANLTEPIDFCIELQIKRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDGKQIWDTLEKHLPIDL 332


>gi|300431297|gb|ADK12613.1| RNA polymerase alpha subunit [Anatherostipa brevis]
 gi|300431301|gb|ADK12615.1| RNA polymerase alpha subunit [Aciachne pulvinata]
 gi|300431327|gb|ADK12626.1| RNA polymerase alpha subunit [Lorenzochloa erectifolia]
          Length = 339

 Score =  272 bits (697), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDITLPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY     +  ++   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIELQIKRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDGKQIWDTLEKHLPIDL 332


>gi|300431270|gb|ADK12600.1| RNA polymerase alpha subunit [Piptochaetium medium]
          Length = 339

 Score =  272 bits (697), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 90/328 (27%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY     +  ++   G   IDA+  P++ V+Y++ S
Sbjct: 132 RAQPIANLTEPIDFCIELQIKRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTCFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           ++ +F    + + K +  T+   L ++L
Sbjct: 308 KIDSFR---MEDGKQIWDTLEKHLPIDL 332


>gi|290489694|gb|ADD31231.1| RNA polymerase alpha subunit protein [Oxalis latifolia]
          Length = 339

 Score =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 81/345 (23%), Positives = 167/345 (48%), Gaps = 27/345 (7%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLR 56
           M+++          +++  +    +         I  PL +G A T+G A+RR L+  + 
Sbjct: 1   MVREKVTVSTSTRTLQWKCVESRADGKRLYYGRFILSPLMKGQADTIGIAIRRALLGEIE 60

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           G  IT  + + + HE S++ G+ E + +I++N+K I L+ +       ++  +GPG VTA
Sbjct: 61  GTCITRAKSEKIPHEYSTLAGIQESIHEILMNLKEIVLRSNLYGTHDASLCVKGPGYVTA 120

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
            DI     +E+++    I +L     + + L + +  GY     +  ++   G   IDA+
Sbjct: 121 QDIILPPSVEIIDNTQHIASLTEPIELCIGLQIERNRGYHKKTPNNFQD---GSYPIDAV 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           + P++  ++++ S R G     + L + I T+GS+T ++++  ASR L D    F++ EE
Sbjct: 178 FMPVRNANHSIHSYRNG-NEKQEMLFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEE 236

Query: 237 PKKEVKEDINVKSLPFNPALLK----------------KVEELELSVRSTNCLRGENIVY 280
               ++ + +  +LP      +                 +++LEL+ R  NCL+  NI  
Sbjct: 237 ENSHLETNQHKVTLPLFTFHDRLAKLRKIKKKISLKYIFIDQLELTPRIYNCLKRSNIHT 296

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           + DL+  ++ D++ + +F    + ++K ++G +   L ++LP   
Sbjct: 297 LLDLLNNSQEDLMNIEHFH---IEDVKHIMGVLENNLAIDLPKKK 338


>gi|114107078|ref|YP_740234.1| RNA polymerase alpha subunit [Liriodendron tulipifera]
 gi|122239940|sp|Q0G9I7|RPOA_LIRTU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|113201026|gb|ABI32541.1| RNA polymerase alpha subunit [Liriodendron tulipifera]
          Length = 337

 Score =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 80/331 (24%), Positives = 161/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT V+ + V
Sbjct: 11  RTLQWKCVESRTDSKRLYYGRFILAPLMKGQADTIGIAMRRALLGEIEGTCITRVKSEKV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            +E  +I G+ E + +I++N+K I L+      +  +I  RGP  VTA DI     +E++
Sbjct: 71  PNEYYTIVGIEESVHEILMNLKEIVLRSHLYGTRDASICVRGPRYVTAQDIIPPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + +EL + +  GY     +  ++   G   IDA+  P++  ++++ 
Sbjct: 131 DTTQHIASLTEPIDLCIELQIERDRGYRMKTPNNYQD---GSYPIDAVSMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S    +    + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ N  
Sbjct: 188 SYGN-RNEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEQDIVLEDNPNRF 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           ++P      +                 +++ EL  R+ NCL+  NI  + DL+  ++ D+
Sbjct: 247 TVPLFTFHDRLANIRKNKKGIALKCIFIDQSELPPRTYNCLKRSNIHTLLDLLSNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +R+ +F    + ++K +L  +     ++LP 
Sbjct: 307 MRIEHFR---IEDVKQILDILQKHFTIDLPK 334


>gi|84874038|gb|ABC68042.1| RNA polymerase subunit [Oryza rhizomatis]
          Length = 317

 Score =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 95/320 (29%), Positives = 158/320 (49%), Gaps = 23/320 (7%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +  +       I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+ 
Sbjct: 2   VDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGIE 61

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL  
Sbjct: 62  ESVQEILLNLKEIVLRSNLYGVRNASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTE 121

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
               R+EL + +  GY       T++   G   IDA+  P++ V+Y++ S   G    Y+
Sbjct: 122 PTDFRIELRIKRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFSCGNG-NAKYE 177

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-------- 251
            L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P        
Sbjct: 178 ILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENQNRFTSPLLSFQKRL 237

Query: 252 --------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                     P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    +
Sbjct: 238 TNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSFR---M 294

Query: 304 VEIKGVLGTMGLFLGMNLPD 323
            + K +  T+   L M+LP 
Sbjct: 295 QDGKQIWDTLEKHLPMDLPK 314


>gi|167946610|ref|ZP_02533684.1| DNA-directed RNA polymerase subunit alpha [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 280

 Score =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 118/271 (43%), Positives = 177/271 (65%), Gaps = 4/271 (1%)

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +   VLHE ++I+GV ED+ +I+LN+K + L M       + + K+GPGVV+AGDI   +
Sbjct: 7   RFQDVLHEYTAIEGVQEDVLEILLNLKQVALVMHSRDEAVLRLQKKGPGVVSAGDITLDH 66

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPI 180
           DIE+ NPD  I  L     + M LTV +G GY P+   ++   E+ PIG++ +DA +SP+
Sbjct: 67  DIEIANPDLHIATLTKSGEINMTLTVKRGRGYQPSTARQSSAGEDRPIGMLQLDASFSPV 126

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           ++V+Y++ESAR  Q  + D+L + + TDG+I  E+++  ++ IL+DQL +F++ E     
Sbjct: 127 RRVAYSIESARVEQRTNMDRLVIELQTDGTIDPEEAIRRSAGILRDQLSVFVDLEG-GGA 185

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +     +    +P LL+ V++LEL+VRS NCL+ ENI  +GDLIQRTE ++L+  N G+
Sbjct: 186 AEATAEPEEPMIDPILLRPVDDLELTVRSANCLKAENIFLIGDLIQRTEVELLKTPNLGK 245

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           KSL EIK VL   GL LGM L  WPPESI+E
Sbjct: 246 KSLTEIKDVLARRGLSLGMRLEHWPPESIDE 276


>gi|84874024|gb|ABC68035.1| RNA polymerase subunit [Oryza sativa]
 gi|84874026|gb|ABC68036.1| RNA polymerase subunit [Oryza sativa]
 gi|84874030|gb|ABC68038.1| RNA polymerase subunit [Oryza nivara]
 gi|84874034|gb|ABC68040.1| RNA polymerase subunit [Oryza sp. IRGC 81916]
          Length = 317

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 94/320 (29%), Positives = 158/320 (49%), Gaps = 23/320 (7%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +  +       I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+ 
Sbjct: 2   VDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGIE 61

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL  
Sbjct: 62  ESVQEILLNLKEIVLRSNLYGVRTASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTE 121

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
               R+EL + +  GY       T++   G   IDA+  P++ V+Y++ +   G    Y+
Sbjct: 122 PTDFRIELRIKRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFACGNG-NAKYE 177

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-------- 251
            L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P        
Sbjct: 178 ILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKRL 237

Query: 252 --------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                     P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    +
Sbjct: 238 TNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSFR---M 294

Query: 304 VEIKGVLGTMGLFLGMNLPD 323
            + K +  T+   L M+LP 
Sbjct: 295 QDGKQIWDTLEKHLPMDLPK 314


>gi|85057775|ref|YP_456691.1| DNA-directed RNA polymerase subunit alpha [Aster yellows
           witches'-broom phytoplasma AYWB]
 gi|119366664|sp|Q2NIY1|RPOA_AYWBP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|84789880|gb|ABC65612.1| DNA-directed RNA polymerase alpha chain [Aster yellows
           witches'-broom phytoplasma AYWB]
          Length = 330

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 112/333 (33%), Positives = 185/333 (55%), Gaps = 11/333 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           + IKP  +E I    E         +PL RG+  T+GNALRRVL+SSL GAAI  V+I G
Sbjct: 5   KFIKPFFVEEI---DENPISGKFTIKPLERGYGITVGNALRRVLLSSLPGAAIVNVKIQG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDS---HKRVTIFKRGPGVVTAGDIQTVND 124
           V  E ++I GV+ED+  IILN+K I   +  +S    +++ +  +GP  +TA   +    
Sbjct: 62  VEQEFTTIPGVYEDVMTIILNLKKIVFAVDDESDDFEEKLELIAKGPQRLTAASFELPAG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSPIKKV 183
           ++++NPDH I  L  D    M +T+ KG GYV AK ++    + +G+I ID+L++P+  V
Sbjct: 122 VKIINPDHYITTLSDDVCFHMTVTIKKGIGYVGAKENKVHIENQVGVIAIDSLFTPVVNV 181

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VE     ++ + D+L++ I T+G++  ++++A A+ IL D   + +   +    V+ 
Sbjct: 182 SYQVE----KKLGNKDELTIEITTNGALLAKEALATAASILVDHFNVLVELSQKPAHVEF 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               K    N  L  ++E+L+LSVR  N L+   I  +  L++ +E +++++ + GRKS 
Sbjct: 238 VSESKKEAHNYVLDLEIEQLDLSVRLFNSLKRAGIDTVASLVKLSEKEVVKLKSLGRKSF 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKY 336
            E+K      GL     L +    S+EE   K+
Sbjct: 298 QELKDKFLEYGLEFNDYLKEALHHSVEEDKDKH 330


>gi|89898699|ref|YP_515809.1| DNA-directed RNA polymerase subunit alpha [Chlamydophila felis
           Fe/C-56]
 gi|119366672|sp|Q252X4|RPOA_CHLFF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|89332071|dbj|BAE81664.1| DNA-directed RNA polymerase alpha chain [Chlamydophila felis
           Fe/C-56]
          Length = 376

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 125/368 (33%), Positives = 197/368 (53%), Gaps = 30/368 (8%)

Query: 2   IQKNWQELIK-----PNNIEYIVL---GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMS 53
           +  N Q L+      P +++ + +   G   +     +AEPL RG  HTLGNALRR L+ 
Sbjct: 1   MSDNSQNLLYDKFELPKSVKMMTVEGSGGSIDKHARFVAEPLERGMGHTLGNALRRALLI 60

Query: 54  SLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM----SGDSHKRVTIFKR 109
            L   AI +  + GVLHE  +I+G+ ED+T+I+LN+KG  LK       +  +R  + K 
Sbjct: 61  GLEAPAIISFSMTGVLHEYMAIEGIIEDVTNIVLNLKGALLKKYPFQDSEDGRRPQLLKS 120

Query: 110 -------------GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
                        G   VT  D+      E +NP+HVI  +     V + L V+ G GY 
Sbjct: 121 MISIDASDLAACGGQRAVTLADLLQEGGFEAVNPEHVIFTVTQPMQVEVALRVAFGRGYS 180

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
            ++    E+  +  I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG ++ +++
Sbjct: 181 TSERIILEDKGVNEIVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLILYVETDGRVSPKEA 240

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK---KVEELELSVRSTNCL 273
           +A +++IL     +F   +E K   +E I+++    +  L K    + E+ELSVRSTNCL
Sbjct: 241 LAFSTQILTKHFSIFEKMDEKKIVFEEAISIEKENKDDILHKLVLGINEIELSVRSTNCL 300

Query: 274 RGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEE 331
              NI  +G+L+   E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E
Sbjct: 301 SNANIETIGELVIMPEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKE 360

Query: 332 LAKKYEDK 339
             K Y +K
Sbjct: 361 KMKWYAEK 368


>gi|62184758|ref|YP_219543.1| DNA-directed RNA polymerase subunit alpha [Chlamydophila abortus
           S26/3]
 gi|81313062|sp|Q5L6Z9|RPOA_CHLAB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|62147825|emb|CAH63571.1| putative DNA-directed RNA polymerase alpha chain [Chlamydophila
           abortus S26/3]
          Length = 376

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 123/357 (34%), Positives = 191/357 (53%), Gaps = 25/357 (7%)

Query: 8   ELIKPNNIEYIVL---GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           +   P +++ + +   G   + +   IAEPL RG  HTLGNALRR L+  L   AI +  
Sbjct: 12  KFELPESVKMMAVEGSGGSVDKQASFIAEPLERGMGHTLGNALRRALLIGLEAPAIISFS 71

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMS---GDSHKRVTIFKRGP---------- 111
           + GVLHE  +I G+ ED+T+IILN+KG  LK        + R T   +            
Sbjct: 72  MTGVLHEYMAINGIIEDVTNIILNLKGALLKKYPFQDSENGRCTQLLKSKVSIDASDLAA 131

Query: 112 ----GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
                 VT  D+      E +NPD+VI  +     + + L V+ G GY  ++    E+  
Sbjct: 132 CGGQKAVTLADLLQEGGFESVNPDYVIFTVTQPMQLDITLRVAFGRGYTTSERIVLEDKG 191

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           +  I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG ++ ++++A +++IL   
Sbjct: 192 VNEIVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLILHVETDGRVSPKEALAFSTQILTKH 251

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLK---KVEELELSVRSTNCLRGENIVYMGDL 284
             +F   +E K   +E I+++    +  L K    + E+ELSVRSTNCL   NI  +G+L
Sbjct: 252 FSIFEKMDEKKIVFEEAISLEKENKDDILHKLVLGINEIELSVRSTNCLSNANIETIGEL 311

Query: 285 IQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           +   E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y DK
Sbjct: 312 VIMPEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYADK 368


>gi|300431291|gb|ADK12610.1| RNA polymerase alpha subunit [Jarava plumosula]
          Length = 339

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 90/328 (27%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I+ +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY     +  ++   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIELQIKRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  AS  L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASHNLIDLFLPFLHAEEEGASFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDGKQIWDTLEKHLPIDL 332


>gi|114330001|ref|YP_740682.1| RNA polymerase alpha subunit [Nandina domestica]
 gi|122165930|sp|Q09FS9|RPOA_NANDO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|114054503|gb|ABI49896.1| RNA polymerase alpha subunit [Nandina domestica]
          Length = 338

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 83/329 (25%), Positives = 164/329 (49%), Gaps = 23/329 (6%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E      +       +  PL +G A T+G A+RR L+  + G  IT  + + + 
Sbjct: 13  LQWRCVESRT-DSKRLYYGRFVLSPLMKGQADTIGIAMRRALLGEIEGTCITHAKSEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +       +I  +GP  +TA DI +   +E+++
Sbjct: 72  HEYSTIVGIEESVHEILMNLKEIVLRSNLYGTCDASICVKGPINITAKDIISPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I +L     + + L + +  GY     ++ +N   G   IDA++ P++  ++++ S
Sbjct: 132 TTQHIASLTEPFDLCIGLQIERNRGYRMKTPNKAQN---GSYPIDAVFMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ N  +
Sbjct: 189 YGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEQDIILEDNQNRVT 247

Query: 250 LPFNPAL---------------LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           LPF                      +++ EL  R+ NCL+  NI  + DL+ +++ D+L+
Sbjct: 248 LPFFTFHDGLAKLKKKNEIALKFIFIDQSELPSRTYNCLKKSNINTLLDLLNKSQEDLLK 307

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           + +F    + ++K VLG +     ++LP 
Sbjct: 308 IEHFR---IEDVKRVLGILQKRFVIDLPK 333


>gi|300431284|gb|ADK12607.1| RNA polymerase alpha subunit [Nassella arcuata]
          Length = 339

 Score =  272 bits (696), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 162/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I+ +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY     +  ++   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPMDFCIELQIKRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDGKQIWDTLEKHLPIDL 332


>gi|294669850|ref|ZP_06734909.1| hypothetical protein NEIELOOT_01743 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291308243|gb|EFE49486.1| hypothetical protein NEIELOOT_01743 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 277

 Score =  272 bits (695), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 128/279 (45%), Positives = 183/279 (65%), Gaps = 5/279 (1%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           + G A T V I GVLHE S++ G+ ED+ D++LNIKGI  K+ G +  R+ + K G GVV
Sbjct: 1   MDGFAPTEVSITGVLHEYSTLDGIQEDVVDVLLNIKGIIFKLHGRNEVRLRLKKSGSGVV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLIT 172
            A DI+  +D EV+NP+H+IC+L  +A + ME+ V KG GY      +     + IG I 
Sbjct: 61  LASDIELPHDAEVINPNHIICHLSDNADIEMEIKVEKGRGYQSVVGRKKSGNENNIGSIQ 120

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           +DA +SPI +VS+ VE AR  Q  D D+L + I+TDGS+  E++V  A+RIL DQ+ +F 
Sbjct: 121 LDASFSPIARVSFDVEPARVEQRTDLDRLVLDIETDGSLEPEEAVRSAARILIDQMAVFA 180

Query: 233 NFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +    +    E++   + P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++
Sbjct: 181 DL---QGTPVEEVEEVAPPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETEL 237

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           L+  N GRKSL EIK VL + GL LG  L  WPP ++E+
Sbjct: 238 LKTPNLGRKSLNEIKEVLASKGLTLGSKLEAWPPVNLEK 276


>gi|313199607|ref|YP_004021222.1| RNA polymerase alpha subunit [Isoetes flaccida]
 gi|291575336|gb|ADE18049.1| RNA polymerase alpha subunit [Isoetes flaccida]
          Length = 341

 Score =  272 bits (695), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 86/330 (26%), Positives = 164/330 (49%), Gaps = 26/330 (7%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
              IE  +  +     +  I  PL  G A+TLG A+RR  +  L G  IT+ + + ++HE
Sbjct: 16  WKCIESKIENERLH-HSRFIISPLGIGQANTLGIAMRRASLGELEGTCITSAKFEKIIHE 74

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            S++ G+ E + D ++N+K I L+ +    ++  I   GPG +TA DI     IE+++P 
Sbjct: 75  YSTVVGIQESVHDTLINLKEIVLRSNSSEIQKAYISIIGPGEITAQDIILPPSIEIIDPA 134

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             I  L     + +EL + +  GY      ++++   G   ++A++ PI+ V+Y++    
Sbjct: 135 QHIATLTKKIHLNIELRIERDRGYRRQNIVKSQD---GNFPLNAVFMPIRNVNYSIHCFE 191

Query: 192 -EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
              + +  + L + I T+GSIT  +++  ASR L +    F++ E  +K        +S 
Sbjct: 192 SHDKKIMKEMLLLEIWTNGSITPREAIYEASRSLINLFIPFLHAENGEKIYGMGNINESN 251

Query: 251 PFNPALLKK------------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
             + ++L                    +++LEL  R+ NCL+  N+  + DL+  ++ D+
Sbjct: 252 ALSCSVLPPMSIQVDQMAKEVTFRHIFIDQLELPPRAYNCLKRINVHTISDLLDYSQDDL 311

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           +++ NFG KS+ ++   L  +    G++LP
Sbjct: 312 MKIKNFGIKSVEQV---LEALWKRFGISLP 338


>gi|295065759|ref|YP_003587699.1| RNA polymerase alpha subunit [Anomochloa marantoidea]
 gi|251765283|gb|ACT15437.1| RNA polymerase alpha subunit [Anomochloa marantoidea]
          Length = 339

 Score =  272 bits (695), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 92/330 (27%), Positives = 163/330 (49%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  + + V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLIKGQADTVGIALRRALLGEIEGTCITRAKSENVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI +   +E+++
Sbjct: 72  HEYSTIVGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIISPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       +EL + +  GY       ++++      IDA+  P++ V+Y++ S
Sbjct: 132 TAQHIATLTEPIDFCIELQIKRDRGYYTELRKNSQDES---YPIDAVSMPVQNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEESTNFEENKNRFT 247

Query: 250 LPF----------------NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++L+L  R+ NCL+  NI  + DL+ +TE D+L
Sbjct: 248 QPPLTLQKKLTNLKKNKKGVPLNSIFIDQLKLPSRTYNCLKRANIHTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           R+ NF    + + K +L T+   L ++LP 
Sbjct: 308 RIDNFR---MEDGKQILDTLEKDLPIDLPK 334


>gi|311990458|gb|ADQ26359.1| RNA polymerase alpha subunit [Lactobacillus fermentum]
          Length = 242

 Score =  272 bits (695), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 108/242 (44%), Positives = 163/242 (67%), Gaps = 2/242 (0%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRRV+++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K
Sbjct: 1   VVEPLERGYGTTLGNSLRRVMLASLPGAAITSIQIDGVLHEFSTVQGVTEDVTQIILNLK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            + LK+  +  K + I  +GP  VTA DIQ   D+ +LN D  I  +   A + +++T  
Sbjct: 61  QVALKIDSEDAKDLEIDVKGPAEVTAADIQGDGDVTILNSDLHIATVSDGAELHVKMTAD 120

Query: 151 KGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           KG GY  A  ++T  E   IG++ ID++Y+PI++V+YTVE+ R GQ  DYDKL++ + T+
Sbjct: 121 KGRGYSSADDNKTRMEGLAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYDKLTLDVWTN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           GS+T  ++++LA++IL + L MF+N  E  +  +  +  +       L K +EEL+LSVR
Sbjct: 181 GSLTPTEAISLAAKILTEHLTMFVNLTEEAQVTQVMVEREETHQEKVLDKTIEELDLSVR 240

Query: 269 ST 270
           S 
Sbjct: 241 SY 242


>gi|114329779|ref|YP_740597.1| RNA polymerase alpha subunit [Platanus occidentalis]
 gi|122166006|sp|Q09G14|RPOA_PLAOC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|114054417|gb|ABI49811.1| RNA polymerase alpha subunit [Platanus occidentalis]
          Length = 337

 Score =  272 bits (695), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 84/331 (25%), Positives = 165/331 (49%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFILSPLIKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +    +  +I  RGPG VTA DI +   +E +
Sbjct: 71  PHEYSTIVGIEESVHEILMNLKEIVLRSNLYGTRNASICIRGPGYVTAQDIISPPSVETV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I NL       +EL + +  GY     + +++   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIANLTEPIDFCIELEIERNRGYRMKTPNNSQD---GSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ +E    ++++ N  
Sbjct: 188 SYANG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAQEENILLEDNQNGV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LPF     +                 +++ EL  R+ NCL+  NI  + DL   ++ D+
Sbjct: 247 TLPFFTFHDRLAKIRKNEKEIALKYIFIDQSELPPRTYNCLKRSNIHTLLDLFNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F    + ++K +LG +     ++LP 
Sbjct: 307 MKIEDFR---IEDVKQILGILQKHFTVDLPK 334


>gi|33301631|sp|Q824N1|RPOA_CHLCV RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 376

 Score =  272 bits (695), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 123/368 (33%), Positives = 195/368 (52%), Gaps = 30/368 (8%)

Query: 2   IQKNWQELIK-----PNNIEYIVL---GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMS 53
           +  N Q L+      P +++ + +   G   + +   +AEPL RG  HTLGNALRR L+ 
Sbjct: 1   MSDNSQNLLYDKFELPESVKMMAVEGSGGSVDKQASFVAEPLERGMGHTLGNALRRALLI 60

Query: 54  SLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS---GDSHKRVTIFKRG 110
            L   AI +  + GVLHE  +I+G+ ED+T+I+LN+KG  LK          R T   + 
Sbjct: 61  GLEAPAIISFSMTGVLHEYMAIEGIVEDVTNIVLNLKGALLKKYPFQDSEDGRCTQLLKS 120

Query: 111 --------------PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
                            +T  D+      E +NPDHVI  +     + + L V+ G GY 
Sbjct: 121 TISVDASDLAACGGQKSITLADLLQEGGFESVNPDHVIFTVTQPMQLEIALRVAFGRGYS 180

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
            ++    E+  +  I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG ++ +++
Sbjct: 181 TSERIVLEDKGVNEIVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLILHVETDGRVSPKEA 240

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK---KVEELELSVRSTNCL 273
           +A +++IL     +F   +E K   +E I+++    +  L K    + E+ELSVRSTNCL
Sbjct: 241 LAFSTQILTKHFSIFEKMDEKKIVFEEAISIEKENKDDILHKLVLGINEIELSVRSTNCL 300

Query: 274 RGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEE 331
              NI  +G+L+   E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E
Sbjct: 301 SNANIETIGELVIMPEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKE 360

Query: 332 LAKKYEDK 339
             K Y +K
Sbjct: 361 KMKSYAEK 368


>gi|290489692|gb|ADD31230.1| RNA polymerase alpha subunit protein [Liquidambar styraciflua]
          Length = 338

 Score =  272 bits (695), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 77/332 (23%), Positives = 159/332 (47%), Gaps = 28/332 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K + L+ +    +  +I  RGPG VTA DI +   +E++
Sbjct: 71  PHEYSTIVGIQESVHEILMNLKEVVLRSNLYGTRDASICVRGPGYVTAQDIISPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY     +  ++       IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDLCIGLKMERNRGYRIKTPNNFQDRS---YPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S         + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYGNE-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLEDNQHKT 246

Query: 249 SLPFNPALLKK-----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
            LP      +                  +++ EL  R   CL+  NI  + DL+   + D
Sbjct: 247 ILPLFTFHDRLAKLKEKTKKKKALKSIFIDQSELPPRIYTCLKRSNIHTLLDLLNNNQED 306

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++++ +F    + ++K +LG +     ++LP 
Sbjct: 307 LMKIEHFR---IEDVKKILGILEKHFAIDLPK 335


>gi|84874036|gb|ABC68041.1| RNA polymerase subunit [Oryza officinalis]
 gi|84874042|gb|ABC68044.1| RNA polymerase subunit [Oryza australiensis]
          Length = 317

 Score =  272 bits (695), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 95/320 (29%), Positives = 158/320 (49%), Gaps = 23/320 (7%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +  +       I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+ 
Sbjct: 2   VDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGIE 61

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL  
Sbjct: 62  ESVQEILLNLKEIVLRSNLYGVRNASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTE 121

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
               R+EL + +  GY       T++   G   IDA+  P++ V+Y++ S   G    Y+
Sbjct: 122 PTDFRIELRIKRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFSCGNG-NAKYE 177

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-------- 251
            L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P        
Sbjct: 178 ILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKRL 237

Query: 252 --------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                     P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    +
Sbjct: 238 TNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSFR---M 294

Query: 304 VEIKGVLGTMGLFLGMNLPD 323
            + K +  T+   L M+LP 
Sbjct: 295 QDGKQIWDTLEKHLPMDLPK 314


>gi|71056814|emb|CAH58962.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 243

 Score =  272 bits (695), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 107/243 (44%), Positives = 159/243 (65%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E  +    + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+I GV ED
Sbjct: 1   DENRDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIPGVRED 60

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILNIKG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D VIC++   A
Sbjct: 61  VTQIILNIKGLALKLYAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLVICSVAEGA 120

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
                LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL
Sbjct: 121 TFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKL 180

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           +M I TDGSI  +++++LA++I+ + L +F+N  +  K  +  +  +       L   +E
Sbjct: 181 TMEIWTDGSIIPQEALSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIE 240

Query: 262 ELE 264
           E +
Sbjct: 241 ERD 243


>gi|300431322|gb|ADK12624.1| RNA polymerase alpha subunit [Amelichloa brevipes]
          Length = 339

 Score =  271 bits (694), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL     + +EL + +  GY     +  ++   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDLCIELQIKRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +   +   L +NL
Sbjct: 308 RIDSFR---MEDGKQIWDNLEKHLPINL 332


>gi|300431288|gb|ADK12609.1| RNA polymerase alpha subunit [Jarava leptostachya]
          Length = 339

 Score =  271 bits (694), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 90/328 (27%), Positives = 162/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I+ +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY     +  ++   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIELQIKRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +++ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEKNKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDGKQIWDTLEKHLPIDL 332


>gi|167391838|ref|YP_001671715.1| RNA polymerase alpha subunit [Carica papaya]
 gi|166344165|gb|ABY86815.1| RNA polymerase alpha chain [Carica papaya]
          Length = 327

 Score =  271 bits (694), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 81/321 (25%), Positives = 160/321 (49%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRTDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +    +   I  +GPG VTA DI     +E++
Sbjct: 71  PHEYSTIVGIQESVHEILMNLKEIVLRSNLYGTRDAFICVKGPGYVTAQDIVLPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     +R+ L + +  GY     +  ++   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDLRIGLQIERNRGYGIKTPNNFQD---GSYPIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE K  ++ + +  
Sbjct: 188 SYGTG-NEKQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHAEEEKFYLENNQHKV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LPF P   +                 +++LEL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPFFPFHDRLAKLRKKKTEIAFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTM 313
           +++ +F  + + +I  +L   
Sbjct: 307 MKIEHFRTEDVKQILSILEKK 327


>gi|29839882|ref|NP_828988.1| DNA-directed RNA polymerase subunit alpha [Chlamydophila caviae
           GPIC]
 gi|29834229|gb|AAP04866.1| DNA-directed RNA polymerase, alpha subunit [Chlamydophila caviae
           GPIC]
          Length = 393

 Score =  271 bits (694), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 123/368 (33%), Positives = 195/368 (52%), Gaps = 30/368 (8%)

Query: 2   IQKNWQELIK-----PNNIEYIVL---GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMS 53
           +  N Q L+      P +++ + +   G   + +   +AEPL RG  HTLGNALRR L+ 
Sbjct: 18  MSDNSQNLLYDKFELPESVKMMAVEGSGGSVDKQASFVAEPLERGMGHTLGNALRRALLI 77

Query: 54  SLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS---GDSHKRVTIFKRG 110
            L   AI +  + GVLHE  +I+G+ ED+T+I+LN+KG  LK          R T   + 
Sbjct: 78  GLEAPAIISFSMTGVLHEYMAIEGIVEDVTNIVLNLKGALLKKYPFQDSEDGRCTQLLKS 137

Query: 111 --------------PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
                            +T  D+      E +NPDHVI  +     + + L V+ G GY 
Sbjct: 138 TISVDASDLAACGGQKSITLADLLQEGGFESVNPDHVIFTVTQPMQLEIALRVAFGRGYS 197

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
            ++    E+  +  I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG ++ +++
Sbjct: 198 TSERIVLEDKGVNEIVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLILHVETDGRVSPKEA 257

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK---KVEELELSVRSTNCL 273
           +A +++IL     +F   +E K   +E I+++    +  L K    + E+ELSVRSTNCL
Sbjct: 258 LAFSTQILTKHFSIFEKMDEKKIVFEEAISIEKENKDDILHKLVLGINEIELSVRSTNCL 317

Query: 274 RGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEE 331
              NI  +G+L+   E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E
Sbjct: 318 SNANIETIGELVIMPEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKE 377

Query: 332 LAKKYEDK 339
             K Y +K
Sbjct: 378 KMKSYAEK 385


>gi|14278481|pdb|1I6V|A Chain A, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
 gi|14278482|pdb|1I6V|B Chain B, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
          Length = 314

 Score =  271 bits (694), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 108/297 (36%), Positives = 162/297 (54%), Gaps = 4/297 (1%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ++    + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED+ +
Sbjct: 18  DHYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVE 77

Query: 85  IILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           IILN+K + ++          + +   GP  V A D     D+E++NPD  I  L+    
Sbjct: 78  IILNLKELVVRFLDPKMASTTLILRAEGPKEVRAVDFTPSADVEIMNPDLHIATLEEGGK 137

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + ME+ V +G GYVPA+ H  ++  I  I +DA++SP+++V++ VE  R GQ  D DKL+
Sbjct: 138 LYMEVRVDRGVGYVPAERHGIKDR-INAIPVDAIFSPVRRVAFQVEDTRLGQRTDLDKLT 196

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK-KVE 261
           + I TDGS+T  +++  A  IL++ L  F N E       E    +        L   +E
Sbjct: 197 LRIWTDGSVTPLEALNQAVAILKEHLNYFANPEASSLPTPEVSKGEKRESAEEDLDLPLE 256

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           EL LS R  + L+ E I  +  L+     D+  +   G +SL EI+  L   G  L 
Sbjct: 257 ELGLSTRVLHSLKEEGIESVRALLALNLKDLRNIPGIGERSLEEIRQALAKKGFTLK 313


>gi|300431280|gb|ADK12605.1| RNA polymerase alpha subunit [Piptochaetium napostaense]
          Length = 339

 Score =  271 bits (694), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 89/328 (27%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY     +  ++   G   IDA+  P++ V+Y++ S
Sbjct: 132 RAQPIANLTEPIDFCIELQIKRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  ++ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSKTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           ++ +F    + + K +  T+   L ++L
Sbjct: 308 KIDSFR---MEDGKQIWDTLEKHLPIDL 332


>gi|149184060|ref|ZP_01862413.1| DNA-directed RNA polymerase subunit alpha [Bacillus sp. SG-1]
 gi|148848232|gb|EDL62529.1| DNA-directed RNA polymerase subunit alpha [Bacillus sp. SG-1]
          Length = 245

 Score =  271 bits (694), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 99/244 (40%), Positives = 153/244 (62%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+T II+NIK + LK+  D  K + I   G GVVTA DI   +D+EVLNP+  I  
Sbjct: 1   GVVEDVTTIIMNIKKLALKIYSDEEKTLEIDVNGEGVVTAADITHDSDVEVLNPELHIAT 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           L  ++  RM L   +G GY PA  ++ E+ PIG+I ID++Y+P+ +V+Y VE+ R GQ+ 
Sbjct: 61  LSANSNFRMRLAAQRGRGYTPADQNKREDLPIGVIPIDSIYTPVSRVNYQVENTRVGQLT 120

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           ++DKLS+ + TDGSI  +++++L ++IL + L +F+   +  +  +  +  +       L
Sbjct: 121 NFDKLSLDVWTDGSIGPKEAISLGAKILNEHLNIFVGLTDEAQNAEIMVEKEEDQKEKVL 180

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  +GL 
Sbjct: 181 EMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKVKLEDLGLG 240

Query: 317 LGMN 320
           L  +
Sbjct: 241 LRKD 244


>gi|290489682|gb|ADD31225.1| RNA polymerase alpha subunit protein [Cornus florida]
          Length = 337

 Score =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 81/329 (24%), Positives = 161/329 (48%), Gaps = 27/329 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  +GPG VTA DI +   +E++
Sbjct: 71  QHEYSTIVGIQESVHEILMNLKEIVLRSTLYGTCDASICVKGPGYVTAQDIISPPYVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY     +  ++   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQYIASLTEPIDLCIGLQIERNRGYRIKPPNNFQD---GNYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHTEEENLHLEDNQHKV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP      K                 +++ ELS R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPTFTFHDKLAKLRKNKKKIAFKYIFIDQSELSPRIYNCLKRSNIYTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           ++M +F    + ++K +L  +      +L
Sbjct: 307 MKMKDFR---IEDVKEILDILEKRFATDL 332


>gi|119662337|emb|CAJ33157.1| RNA polymerase alpha subunit [Lactobacillus paracasei subsp.
           tolerans]
          Length = 230

 Score =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 101/230 (43%), Positives = 152/230 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV
Sbjct: 61  KKLALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            KG GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+G
Sbjct: 121 KKGRGYVAADQNKSDDVPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           SI+  ++++LA++IL + L +F+N  +  K  +  +  +       L   
Sbjct: 181 SISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEMT 230


>gi|306486177|gb|ADM92734.1| RNA polymerase alpha subunit protein [Davidia involucrata]
          Length = 328

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 78/320 (24%), Positives = 155/320 (48%), Gaps = 24/320 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFERI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G  E + +I++N+K I L+ +       +I  +GPG VTA DI +   +E++
Sbjct: 71  PHEYSTIVGTQESVHEILMNLKEIVLRSNLYGTCDASICVKGPGYVTAQDIISPPYVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY     +  ++   G   IDA++ P++  ++++ 
Sbjct: 131 DSTQYIASLTEPIDLCIGLQIERNRGYRIKMPNNFQD---GSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHTEEENLHLEDNQHKV 246

Query: 249 SLP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP                        +++ EL  R  NCL+  NI  + D +  ++ D+
Sbjct: 247 TLPLFTFHEKLAKLRKNKKKIALKYIFIDQSELPTRIYNCLKRSNIYTLLDFLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGT 312
           +++ +F  + + EI G+L  
Sbjct: 307 MKIEHFRIEDVKEILGILEK 326


>gi|168042925|ref|XP_001773937.1| DNA-directed RNA polymerase alpha chain [Physcomitrella patens
           subsp. patens]
 gi|41688609|sp|P60315|RPOA_PHYPA RecName: Full=DNA-directed RNA polymerase subunit alpha,
           chloroplastic; AltName: Full=Plastid-encoded RNA
           polymerase subunit alpha; Short=PEP; Short=RNA
           polymerase subunit alpha; Flags: Precursor
 gi|34494700|dbj|BAC85012.1| DNA-dircted RNA polymerase alpha chain [Physcomitrella patens]
 gi|34494702|dbj|BAC85013.1| RNA polymerase alpha subunit [Physcomitrella patens]
 gi|162674781|gb|EDQ61285.1| DNA-directed RNA polymerase alpha chain [Physcomitrella patens
           subsp. patens]
          Length = 450

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 92/338 (27%), Positives = 165/338 (48%), Gaps = 20/338 (5%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++ N Q  ++   +E  V G+           P   G A+T+G ++++ L+  + GAA++
Sbjct: 117 LKSNAQSALQWKCVETQVEGERLH-YGRFAVSPFRSGQANTVGVSMQKALLGEVEGAAVS 175

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
                 V  E +++KGV E   DI++N+K + ++   D  ++  I   GPG VTAGDI  
Sbjct: 176 CATFKNVKSEYAAMKGVEETPMDILVNLKELVIRSDSDEPQKAIISAIGPGPVTAGDIVL 235

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              +EV +P   I  L  +  + +EL V KG GY    H ++ +   G   ID+++ P++
Sbjct: 236 PPSLEVTDPTQHIAYLTKEVSLDIELDVEKGCGYRMGDHTKSGD---GRFYIDSVFMPVR 292

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
             +Y+V S      +  + L + I T+GSIT E+++  A+R L D    F++ ++ +   
Sbjct: 293 NANYSVHSYESEPDVTQEILFLEIWTNGSITPEEALHEAARCLIDLFLPFLHPKKKEVTN 352

Query: 242 KEDINVKSLPFNPALLKK-------------VEELELSVRSTNCLRGENIVYMGDLIQRT 288
                 KS   +                   V++L +  ++ N L+  NI  + DL+  T
Sbjct: 353 SATKMHKSFTMSQFNSSAEMSAKEVDLRHVYVDQLRIPSKAYNSLKRANINTVSDLLDYT 412

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           + D+L + NFGRKS+ +I   L  +     ++LP+  P
Sbjct: 413 QDDLLSIPNFGRKSVDDI---LEALQAQFSIDLPENNP 447


>gi|158563962|sp|Q6YQZ5|RPOA_ONYPE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 330

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 112/333 (33%), Positives = 185/333 (55%), Gaps = 11/333 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           + IKP  +E I    E       I +PL RG+  T+GNALRRVL+SSL G AI  V+I G
Sbjct: 5   KFIKPFFVEEI---DENPISGKFIIKPLERGYGITVGNALRRVLLSSLPGTAIVNVKIQG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDS---HKRVTIFKRGPGVVTAGDIQTVND 124
           V  E ++I GV+ED+  IILN+K I   +  +S    +++ +  +GP  +TA   +    
Sbjct: 62  VEQEFTTIPGVYEDVMTIILNLKKIVFAVDDESDDFEEKLELIAKGPQRLTASSFELPAG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSPIKKV 183
           ++++NPDH I  L  D    M +T+ KG GYV AK ++    + +G+I ID+L++P+  V
Sbjct: 122 VKIINPDHYITTLSDDVCFHMTVTLKKGIGYVGAKDNKVHGENQVGVIAIDSLFTPVVNV 181

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VE     ++ + D+L++ I T+G++  ++++A A+ IL D   + +   +    V+ 
Sbjct: 182 SYQVE----KKLGNKDELTIEITTNGALLAKEALATAASILVDHFNVLVELSQKPAHVEF 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               K    N  L  ++E+L+LSVR  N L+   I  +  L++ +E +++++ + GRKS 
Sbjct: 238 VSESKKEAHNSVLDLEIEQLDLSVRLFNSLKRAGIDTVAALVKLSEKEVVKLKSLGRKSF 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKY 336
            E+K      GL     L +    S+EE   K+
Sbjct: 298 QELKDKFLEYGLEFNDYLKEVLHHSVEEDKDKH 330


>gi|213420654|ref|ZP_03353720.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E01-6750]
          Length = 271

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 115/277 (41%), Positives = 180/277 (64%), Gaps = 10/277 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLR 274
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLK 271


>gi|325473246|gb|EGC76441.1| DNA-directed RNA polymerase subunit alpha [Treponema denticola
           F0402]
          Length = 351

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 121/352 (34%), Positives = 184/352 (52%), Gaps = 13/352 (3%)

Query: 1   MIQKNW-QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M +KN  +   KP  +E+    +  E+     A P   GF  T+GN LRR+L+SS++G A
Sbjct: 1   MARKNLLKGFKKPKGLEFAQ-QESTESYGKFTASPFETGFGTTIGNCLRRILLSSIQGYA 59

Query: 60  ITAVQI-----DGVLHEISS----IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK-R 109
           I+AV I     DGV H ISS    I  V ED  +I+  +K I L++S +S +    F+ +
Sbjct: 60  ISAVLITSHDADGVPHTISSEFENIPNVSEDTLEILNKLKQIRLRLSDESEQGDFHFEFK 119

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  +T+ D      +E+L     +  L   A V  ++ V  G GYVPA+ +    + +G
Sbjct: 120 GPASITSKDFAVEGQLEILGEPFHVMELMKGANVSFDVQVDFGRGYVPAEVNEKYIEIVG 179

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            I +DA+Y P+ KVSY +E  R GQ  DYDKL + I TD ++  ED +  A++I +D   
Sbjct: 180 TIPMDAIYGPVLKVSYAIEPCRVGQRNDYDKLILEIWTDSTVRPEDVLGEAAKIAKDHFS 239

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +FINF E     +++ + +       L   +  L+ SVR+ NCL    I  +G+L Q++E
Sbjct: 240 IFINFNENDYLGEDEDDNEEAVIKQLLATSINTLDFSVRAKNCLDSAGIKTLGELAQKSE 299

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE-DKC 340
            ++  M N GR +L EI   L    L LGM        +I+   +K E D+ 
Sbjct: 300 DEIESMRNVGRMTLNEIHAKLAEYNLRLGMTDYSHLKNTIKVSRQKEETDEA 351


>gi|300431320|gb|ADK12623.1| RNA polymerase alpha subunit [Amelichloa caudata]
          Length = 339

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I+ +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY     +  ++   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIELQIKRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSSTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDGKQIWDTLEKHLPIDL 332


>gi|148238747|ref|YP_001224134.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp. WH
           7803]
 gi|158513313|sp|A5GIS2|RPOA_SYNPW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|147847286|emb|CAK22837.1| DNA-directed RNA polymerase alpha chain [Synechococcus sp. WH 7803]
          Length = 312

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 97/304 (31%), Positives = 158/304 (51%), Gaps = 8/304 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ +     +   + +  PL RG A TLGN+LRRVLM +L G A+TAV+I GV HE 
Sbjct: 7   DRIEHQIADDRSQT-GVFLIGPLERGQATTLGNSLRRVLMGNLEGTAVTAVRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K I +       +   +   GP  V A D+Q  + ++V++ + 
Sbjct: 66  ATIPGVREDVLDILLNCKQITVNSRTSELEIGRLVVAGPATVKARDLQFSSQVQVVDGER 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P   H  +   I L+ IDA++ P+ +V++T++    
Sbjct: 126 AIATVGEGYSLELEVHVERGIGYRPVDRHNEDTSAIDLLQIDAVFMPVHRVNFTIDETAV 185

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L M + TDGSIT +D++A A+  L +           ++   E        
Sbjct: 186 AEGGSARERLRMEVVTDGSITPDDAIAQAANQLIELFQPLATVTMVEEVSAEPEPTAE-- 243

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 244 ----AQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGL 315
            +G+
Sbjct: 300 RIGI 303


>gi|42526303|ref|NP_971401.1| DNA-directed RNA polymerase subunit alpha [Treponema denticola ATCC
           35405]
 gi|61215985|sp|Q73PK8|RPOA_TREDE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|41816415|gb|AAS11282.1| DNA-directed RNA polymerase, alpha subunit [Treponema denticola
           ATCC 35405]
          Length = 351

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 121/352 (34%), Positives = 184/352 (52%), Gaps = 13/352 (3%)

Query: 1   MIQKNW-QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M +KN  +   KP  +E+    +  E+     A P   GF  T+GN LRR+L+SS++G A
Sbjct: 1   MARKNLLKGFKKPKGLEFAQ-QESTESYGKFTASPFETGFGTTIGNCLRRILLSSIQGYA 59

Query: 60  ITAVQI-----DGVLHEISS----IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK-R 109
           I+AV I     DGV H ISS    I  V ED  +I+  +K I L++S +S +    F+ +
Sbjct: 60  ISAVLITSHDADGVPHTISSEFENIPNVSEDTLEILNKLKQIRLRLSDESEQGDFHFEFK 119

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  +T+ D      +E+L     +  L   A V  ++ V  G GYVPA+ +    + +G
Sbjct: 120 GPASITSKDFAVEGQLEILGEPFYVMELMKGANVSFDVQVDFGRGYVPAEVNEKYIEIVG 179

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            I +DA+Y P+ KVSY +E  R GQ  DYDKL + I TD ++  ED +  A++I +D   
Sbjct: 180 TIPMDAIYGPVLKVSYAIEPCRVGQRNDYDKLILEIWTDSTVRPEDVLGEAAKIAKDHFS 239

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +FINF E     +++ + +       L   +  L+ SVR+ NCL    I  +G+L Q++E
Sbjct: 240 IFINFNENDYLGEDEDDNEEAVIKQLLATSINTLDFSVRAKNCLDSAGIKTLGELAQKSE 299

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE-DKC 340
            ++  M N GR +L EI   L    L LGM        +I+   +K E D+ 
Sbjct: 300 DEIESMRNVGRMTLNEIHAKLAEYNLRLGMTDYSHLKNTIKVSRQKEETDEA 351


>gi|324985144|gb|ADY69170.1| RNA polymerase subunit A [Photobacterium halotolerans]
          Length = 270

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 121/272 (44%), Positives = 181/272 (66%), Gaps = 7/272 (2%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
               +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I
Sbjct: 2   THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDVLEI 61

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVR 144
           +LN+KG+ +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L  D A + 
Sbjct: 62  LLNLKGLAVKVEGKDEVILTLSKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNADIS 121

Query: 145 MELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           M + V +G GYVPA    H   +  PIG + +DA +SP+ +++Y+VE+AR  Q  D DKL
Sbjct: 122 MRIKVERGRGYVPASARIHSDEDERPIGRLLVDATFSPVDRIAYSVEAARVEQRTDLDKL 181

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V+
Sbjct: 182 VIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVD 238

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           +LEL+VRS NCL+ E I Y+GDL+QRTE ++L
Sbjct: 239 DLELTVRSANCLKAEAIHYIGDLVQRTEVELL 270


>gi|300431335|gb|ADK12628.1| RNA polymerase alpha subunit [Achnatherum eminens]
          Length = 339

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 90/328 (27%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I+ +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY     +  ++   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIELQIKRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+G +T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGRLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDGKQIWDTLEKHLPIDL 332


>gi|270307868|ref|YP_003329926.1| DNA-directed RNA polymerase alpha subunit/40 kD subunit
           [Dehalococcoides sp. VS]
 gi|270153760|gb|ACZ61598.1| DNA-directed RNA polymerase alpha subunit/40 kD subunit
           [Dehalococcoides sp. VS]
          Length = 330

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 119/322 (36%), Positives = 179/322 (55%), Gaps = 5/322 (1%)

Query: 15  IEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS 74
           I  I   + +      + EPL +GF  T+GN+LRR+L+S L G AIT V+IDG+ HE S+
Sbjct: 6   IPTISCTESDGKYGCFVVEPLEKGFGTTMGNSLRRILLSYLDGVAITRVRIDGIQHEFSA 65

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           +    ED  D +LN+K I ++        + +   G  VVTA DI+  ND  V+NP+  +
Sbjct: 66  LPKAKEDTLDFLLNLKNIRVESLSGLEGILYLRASGSKVVTAADIEPSNDFAVVNPELYL 125

Query: 135 CNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
             LD  DAV+ +EL V  G GY P +   TEN PIG I +DA+++PI+KV++T E    G
Sbjct: 126 LTLDSDDAVLNVELEVELGRGYRPPES--TENTPIGTIPVDAIFTPIRKVNFTTEPMHVG 183

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           +    ++L + + TDG++    +V+ ++ IL  Q    ++  +   EV+    VK     
Sbjct: 184 RETSLERLVLEVWTDGTVEPATAVSRSADILVKQFAALVSHSKVVAEVEASEPVKYAIPE 243

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +E+L+LSVR+ NCLR   I  +G++I R   ++L + NFG KSL E++  L T+
Sbjct: 244 EKYNMPIEQLDLSVRAVNCLRHAGITTVGEVINRGTKELLTLRNFGLKSLTELEDRLKTI 303

Query: 314 GLFLGMNLPDWPPESIEELAKK 335
           GL L  N  D   E  E   KK
Sbjct: 304 GLSL--NPEDELFEDAENTKKK 323


>gi|84874032|gb|ABC68039.1| RNA polymerase subunit [Oryza glumipatula]
          Length = 317

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 94/320 (29%), Positives = 157/320 (49%), Gaps = 23/320 (7%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +  +       I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+ 
Sbjct: 2   VDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGIE 61

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL  
Sbjct: 62  ESVQEILLNLKEIVLRSNLYGVRTASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTE 121

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
               R+EL + +  GY       T++   G   IDA+  P++ V+Y++ +   G    Y+
Sbjct: 122 PTDFRIELRIKRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFACGNG-NAKYE 177

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-------- 251
            L + I T+GS+T  +++  ASR L D    F++ EE     +E+ N  + P        
Sbjct: 178 ILFLEIWTNGSLTPMEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKRL 237

Query: 252 --------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                     P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    +
Sbjct: 238 TNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSFR---M 294

Query: 304 VEIKGVLGTMGLFLGMNLPD 323
            + K +  T+   L M+LP 
Sbjct: 295 QDGKQIWDTLEKHLPMDLPK 314


>gi|33866622|ref|NP_898181.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp. WH
           8102]
 gi|41688634|sp|Q7U4H7|RPOA_SYNPX RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|33633400|emb|CAE08605.1| RNA polymerase alpha subunit [Synechococcus sp. WH 8102]
          Length = 312

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 101/308 (32%), Positives = 164/308 (53%), Gaps = 14/308 (4%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ V     ++  + +  PL RG A TLGNALRRVLM  L G+A+TA++I GV HE 
Sbjct: 7   DRIEHQVEEDRSQS-GVFLIGPLERGQATTLGNALRRVLMGGLEGSAVTAIRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           +++ GV ED+ DI+LN K +++       +   +   GP  VTA D+Q  + +EV++ + 
Sbjct: 66  ATVPGVREDVLDILLNCKELSVNSRSPELEIGRLVVAGPAEVTAKDLQFSSQVEVVDGNR 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P   H  +   I L+ IDA++ P+ +V++T++    
Sbjct: 126 SIATVADGYSLELEVHVERGVGYRPVDRHSEDTSAIDLLQIDAVFMPVIRVNFTIDETAV 185

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN---FEEPKKEVKEDINVK 248
                  ++L M I TDGSIT +D++A ++  L +           EEP  E +     +
Sbjct: 186 AEGGSARERLRMEIVTDGSITPDDALAQSANYLIELFQPLATVTLVEEPGIEPEPSAEAQ 245

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                      +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+  
Sbjct: 246 ---------IPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIE 296

Query: 309 VLGTMGLF 316
            L  +G+ 
Sbjct: 297 ALERIGIS 304


>gi|91984023|ref|YP_567109.1| RNA polymerase alpha subunit [Vitis vinifera]
 gi|122230333|sp|Q0ZIY7|RPOA_VITVI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|91701681|gb|ABE47565.1| RNA polymerase alpha subunit [Vitis vinifera]
          Length = 331

 Score =  271 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 81/328 (24%), Positives = 161/328 (49%), Gaps = 27/328 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    +N        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRVDNKRLCYGRFILSPLIKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +    +   I  RGPG VTA DI +   +E++
Sbjct: 71  PHEYSTIVGIQESVHEILMNLKEIVLRSNLYGTRGAFICARGPGYVTAQDIISPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + + L + +  GY   + +  ++   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIARLMEPIDLCIGLQIERNRGYSIKRPNNFQD---GSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + +  
Sbjct: 188 SYGNG-NERQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEETLHLEYNQHKS 246

Query: 249 SLPF----------------NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP                        +++LEL  R  NCL+  NI  + DL+ +++ D+
Sbjct: 247 TLPPLTFHDRLAKLRKNKKEIELKYIFIDQLELPPRIYNCLKRSNIHTLLDLLNKSQKDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           +++ +F    + ++K +LG +     ++
Sbjct: 307 MKIEDFR---IEDVKQLLGILEKHFTID 331


>gi|317968839|ref|ZP_07970229.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp.
           CB0205]
          Length = 312

 Score =  271 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 96/309 (31%), Positives = 165/309 (53%), Gaps = 8/309 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + +E+ +     +   + +  PL RG A TLGN+LRR+LM +L G+AITAV+I GV HE 
Sbjct: 7   DRVEHQIADDRSQT-GVFVIGPLERGQATTLGNSLRRMLMGALEGSAITAVRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           +++ GV ED+ DI+LN K + +       +   +   GP  VTAGD+Q  + + V++P  
Sbjct: 66  ATVPGVREDVLDILLNCKDVAVNSRTRELEIGRLVVNGPATVTAGDLQFSSQVSVIDPAR 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P      +   + L+ IDA++ P+++ +YT++    
Sbjct: 126 PIATVAEGHSLELEVHVERGVGYRPVDRRVEDTSAVDLLQIDAVFMPVQRANYTIDETAV 185

Query: 193 GQVLD-YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           G+     ++L + I TDGS+T +D++A A+  L   +         +++ +E        
Sbjct: 186 GEGGSARERLRLEIQTDGSLTPDDAMAQAANQLITLIQPMATLTMEEEQGQEPEPSAE-- 243

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 244 ----AQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLFLGMN 320
            +G+ L  +
Sbjct: 300 RIGISLPQS 308


>gi|94985940|ref|YP_605304.1| DNA-directed RNA polymerase subunit alpha [Deinococcus geothermalis
           DSM 11300]
 gi|119366678|sp|Q1IX99|RPOA_DEIGD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|94556221|gb|ABF46135.1| DNA-directed RNA polymerase subunit alpha [Deinococcus geothermalis
           DSM 11300]
          Length = 331

 Score =  271 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 114/318 (35%), Positives = 172/318 (54%), Gaps = 25/318 (7%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           E +    + EPL RG+  T+GN +RR+LMSS+ G A+T+V I+ VLHE S+I GV ED+ 
Sbjct: 13  EGDYGEFVLEPLTRGYGVTIGNPIRRILMSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVI 72

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            IILN+K + +K      K +T+  +G GVV A   +  +D E++NPD  I  L  D  +
Sbjct: 73  RIILNLKELVVKFHAPGPKTLTLRAQGEGVVKASAFEVPSDAEIVNPDLTIATLAEDGKL 132

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            ME+ V +G GYVPA  H T++  I  I +DA++SP+++V+Y VE+ R GQ  D D+L +
Sbjct: 133 VMEVRVEEGEGYVPADKHATKDR-INSIPVDAVFSPVRRVAYHVENTRVGQQTDLDRLIL 191

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE-------------------- 243
            I TDGS+  ++++  A  IL+D+L +F N E       E                    
Sbjct: 192 RIWTDGSVGPQEALDRAVEILRDELTVFGNVETVSAAAPELPSVYTPAAPIVSGYDLPRQ 251

Query: 244 ---DINVKSLPFN-PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
               IN +  P +       +E L L+ R  + L+ E I  +  L   ++ D+ ++   G
Sbjct: 252 PELSINPQPYPADLDTPRVTLEGLGLTTRVLHSLKEEGIDSVDALCALSDRDLKKVPGIG 311

Query: 300 RKSLVEIKGVLGTMGLFL 317
            +SL EIK  L   GL L
Sbjct: 312 ERSLDEIKQQLAQFGLAL 329


>gi|113955543|ref|YP_729644.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp.
           CC9311]
 gi|119366743|sp|Q0ID28|RPOA_SYNS3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|113882894|gb|ABI47852.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus sp.
           CC9311]
          Length = 312

 Score =  271 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 99/308 (32%), Positives = 162/308 (52%), Gaps = 14/308 (4%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ +     +   + +  PL RG A TLGN+LRR+LM +L G A+TAV+I GV HE 
Sbjct: 7   DRIEHQITDDRSQT-GVFLIGPLERGQATTLGNSLRRMLMGNLAGTAVTAVRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K + +    D  +   +   GP VV A D+Q  + ++V++ + 
Sbjct: 66  ATIPGVREDVLDILLNCKQLTVTSRTDELEIGRLIVSGPAVVKAKDLQFSSQVQVVDGER 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P   H  +   I L+ IDA++ P+ +V++T +    
Sbjct: 126 PIATVSEGHSLELEVHVERGVGYRPVDRHNEDTSAIDLLQIDAVFMPVHRVNFTTDETAV 185

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF---INFEEPKKEVKEDINVK 248
                  ++L M + TDGS+T +D++A A+  L +           EEP  E +     +
Sbjct: 186 AEGGSARERLRMEVVTDGSMTPDDAIAQAANQLIELFQPLATVTMVEEPGIEPEPSAEAQ 245

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                      +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+  
Sbjct: 246 ---------IPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIE 296

Query: 309 VLGTMGLF 316
            L  +G+ 
Sbjct: 297 ALERIGIS 304


>gi|156598227|gb|ABU85377.1| RNA polymerase alpha subunit [Elaeis oleifera]
          Length = 339

 Score =  271 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 88/334 (26%), Positives = 163/334 (48%), Gaps = 24/334 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RR L+  + G  IT  + + V 
Sbjct: 13  LRWKCVES-RVDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKVA 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +       +I  RGP  VTA DI +   +E+++
Sbjct: 72  HEYSTIVGIEESVHEILLNLKEIILRSNLYGVIDASICVRGPRYVTAQDIISPPYVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL     + +EL + +  GY     + +++   G   IDA+  P++  ++++ S
Sbjct: 132 TTQHIANLTEPIDLCIELQIKRDRGYRMKSANNSQD---GSYPIDAVSMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G     + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N   
Sbjct: 189 YGNG-NEKQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEEDINFEENKNRFP 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         K+    P     +++ EL  R+ NCL+G NI  + DL+  ++ D++
Sbjct: 248 LPLFTFQNRLTNLKKNKKGIPLKCIFIDQSELPSRTYNCLKGSNIHTLSDLLSNSQEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           R+  F    + ++K +L T+  +  ++L     +
Sbjct: 308 RIKFFR---IEDVKQILDTLQKYFAIDLSKNKNK 338


>gi|116075744|ref|ZP_01473003.1| DNA-directed RNA polymerase alpha subunit [Synechococcus sp.
           RS9916]
 gi|116067059|gb|EAU72814.1| DNA-directed RNA polymerase alpha subunit [Synechococcus sp.
           RS9916]
          Length = 312

 Score =  271 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 99/308 (32%), Positives = 164/308 (53%), Gaps = 14/308 (4%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ +     +   + +  PL RG A TLGN+LRRVLM  L G+A+TAV+I GV HE 
Sbjct: 7   DRIEHQIADDRAQT-GVFLIGPLERGQATTLGNSLRRVLMGGLEGSAVTAVRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           +++ GV ED+ DI+LN K +++       +   +   GP  V A D+Q  + ++V++P+ 
Sbjct: 66  ATVPGVREDVLDILLNCKQLSVNSRSSELEIGRLVVAGPSEVKARDLQFSSQVQVVDPER 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +EL V +G GY P   H  + + I L+ IDA++ P+ +V+++++    
Sbjct: 126 TIATVSDGHSLELELHVERGIGYRPVDRHSEDTNAIDLLQIDAVFMPVHRVNFSIDETAV 185

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF---INFEEPKKEVKEDINVK 248
                  ++L M + TDGSIT +D++A A+  L +           EEP  E +     +
Sbjct: 186 AEGGSARERLRMEVVTDGSITPDDAIAEAANQLIELFQPLATVTMVEEPGLEPEPSAEAQ 245

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                      +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+  
Sbjct: 246 ---------IPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIE 296

Query: 309 VLGTMGLF 316
            L  +G+ 
Sbjct: 297 ALERIGIS 304


>gi|294785154|ref|ZP_06750442.1| DNA-directed RNA polymerase, alpha subunit [Fusobacterium sp.
           3_1_27]
 gi|294486868|gb|EFG34230.1| DNA-directed RNA polymerase, alpha subunit [Fusobacterium sp.
           3_1_27]
          Length = 332

 Score =  271 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 115/310 (37%), Positives = 185/310 (59%), Gaps = 7/310 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I   +E   +   I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + G
Sbjct: 19  ITEVKESNYKGQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDG 78

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V E +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ VIC +
Sbjct: 79  VKEAVTEIILNVKEIVVKAESSGERRMTLSIKGPKVVKAADIVADIGLEIVNPEQVICTV 138

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D
Sbjct: 139 TTDRTLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTD 198

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI-------NFEEPKKEVKEDINVKSL 250
           +DKL++ ++TDGSI   D+++ A  +L+  L  F+       N  +  +E+ E+     +
Sbjct: 199 FDKLTLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEIIEEPMDIQV 258

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +
Sbjct: 259 VDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKM 318

Query: 311 GTMGLFLGMN 320
             +G  L  N
Sbjct: 319 KDLGYDLEKN 328


>gi|57234751|ref|YP_181246.1| DNA-directed RNA polymerase subunit alpha [Dehalococcoides
           ethenogenes 195]
 gi|90110837|sp|Q3Z953|RPOA_DEHE1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|57225199|gb|AAW40256.1| DNA-directed RNA polymerase, alpha subunit [Dehalococcoides
           ethenogenes 195]
          Length = 330

 Score =  271 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 119/322 (36%), Positives = 179/322 (55%), Gaps = 5/322 (1%)

Query: 15  IEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS 74
           I  I   + +      + EPL +GF  T+GN+LRR+L+S L G AIT V+IDG+ HE S+
Sbjct: 6   IPTISCTESDGKYGRFVVEPLEKGFGTTMGNSLRRILLSYLDGVAITRVRIDGIQHEFSA 65

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           +    ED  D +LN+K I ++        + +   G  VVTA DI+  ND EV+NP+  +
Sbjct: 66  LPKAKEDTLDFLLNLKNIRVESLSGLEGILYLKASGAKVVTAADIEPSNDFEVVNPELYL 125

Query: 135 CNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
             LD  DAV+ +EL V  G GY   +   TEN PIG I +DA+++PI+KV++T E    G
Sbjct: 126 LTLDSDDAVLNVELEVELGRGYRAPES--TENTPIGTIPVDAIFTPIRKVNFTTEPMHVG 183

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           +    ++L + + TDG+I    +V+ ++ IL  Q    ++  +   EV+    VK     
Sbjct: 184 RETSLERLVLEVWTDGTIEPATAVSRSADILVKQFAALVSHNKVVAEVEASEPVKYAIPE 243

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +E+L+LSVR+ NCLR   I  +G++I R   ++L + NFG KSL E++  L T+
Sbjct: 244 EKYNMPIEQLDLSVRAVNCLRHAGITTVGEVINRGTKELLTLRNFGLKSLTELEDRLKTI 303

Query: 314 GLFLGMNLPDWPPESIEELAKK 335
           GL L  N  +   E  E   KK
Sbjct: 304 GLSL--NPEEELFEDAENSKKK 323


>gi|290489656|gb|ADD31212.1| RNA polymerase alpha subunit protein [Aucuba japonica]
          Length = 349

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 78/328 (23%), Positives = 158/328 (48%), Gaps = 27/328 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +  A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFILSPLMKSQADTIGIAMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  RGPG +TA DI     +E++
Sbjct: 71  PHEYSTIVGIQESIHEILMNLKEIVLRSNLYGTCDTSICVRGPGYITAQDIILPPYVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY+    +  ++   G   IDA++ P++ V+Y++ 
Sbjct: 131 DKTQHIASLTEPIDLCIGLQIERNRGYLIKTPNNFQD---GSYPIDAVFMPVRNVNYSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV- 247
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEENLHLEDNQHTV 246

Query: 248 ---------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                          K+          +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 PLSPFTFHDKLAKLRKNKNKIALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           +++  F    + ++K +LG +     ++
Sbjct: 307 MKIEQFR---IQDVKQILGILEKHFAID 331


>gi|34763720|ref|ZP_00144641.1| DNA-directed RNA polymerase alpha chain [Fusobacterium nucleatum
           subsp. vincentii ATCC 49256]
 gi|237742278|ref|ZP_04572759.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp.
           4_1_13]
 gi|27886499|gb|EAA23753.1| DNA-directed RNA polymerase alpha chain [Fusobacterium nucleatum
           subsp. vincentii ATCC 49256]
 gi|229429926|gb|EEO40138.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp.
           4_1_13]
          Length = 342

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 115/310 (37%), Positives = 185/310 (59%), Gaps = 7/310 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I   +E   +   I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + G
Sbjct: 29  ITEVKESNYKGQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDG 88

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V E +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ VIC +
Sbjct: 89  VKEAVTEIILNVKEIVVKAESSGERRMTLSIKGPKVVKAADIVADIGLEIVNPEQVICTV 148

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D
Sbjct: 149 TTDRTLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTD 208

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI-------NFEEPKKEVKEDINVKSL 250
           +DKL++ ++TDGSI   D+++ A  +L+  L  F+       N  +  +E+ E+     +
Sbjct: 209 FDKLTLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEIIEEPMDIQV 268

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +
Sbjct: 269 VDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKM 328

Query: 311 GTMGLFLGMN 320
             +G  L  N
Sbjct: 329 KDLGYDLEKN 338


>gi|156598421|gb|ABU85470.1| RNA polymerase alpha subunit [Musa acuminata]
          Length = 339

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 88/332 (26%), Positives = 160/332 (48%), Gaps = 24/332 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       +  PL +G A T+G A+RR L+  + G  IT    + V 
Sbjct: 13  LQWRCVES-RVDSKRLYYGRFVLSPLMKGQADTIGIAMRRALLGEIEGTCITRANSEKVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  RGP  VTA DI +   +E+++
Sbjct: 72  HEYSTIIGIEESVHEILLNLKEIVLRSNIYGVRDASICARGPKYVTAQDIISPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL     + + L + +  GY       ++N   G   IDA+  P++  ++++ S
Sbjct: 132 TTQHIANLTEPIDLCIGLQIRRDRGYRTKPTTNSQN---GSYPIDAVSMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L D    F++ EE     KE+ N  +
Sbjct: 189 YGNG-NEKQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEEDINFKENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           LP                  P     +++ EL  R+ NCL+  NI  + DL+ +++ D++
Sbjct: 248 LPIFTFQDRLTNLKKNKKEIPLKCIFIDQSELPSRTYNCLKRSNIHTLLDLLNKSQEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           R+  F    + ++K +  T+     ++LP   
Sbjct: 308 RIEYFR---IEDVKEISDTLQKHFAIDLPKNQ 336


>gi|303308474|gb|ADM14340.1| RNA polymerase alpha subunit [Punica granatum]
          Length = 337

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 80/319 (25%), Positives = 157/319 (49%), Gaps = 21/319 (6%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RR L+  + G  IT  + + + 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +       +I  +GPG VTA DI     +E+++
Sbjct: 72  HEYSTIVGIQESVHEILMNLKEIVLRSNLYGTCNASICVKGPGCVTAQDIILPPSVEIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I +L     + + L + +  GY     +  ++   G   IDA++ P++  ++++ S
Sbjct: 132 NTQHIASLMEPINLCIGLQIERNRGYHIKTPNNFQD---GSYPIDAVFMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L D L  F++ EE    ++ +    +
Sbjct: 189 YGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLLIPFLHAEEENLHLENNQYKVT 247

Query: 250 LPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           LP      +                 +++LEL  R  N L+  NI  + DL+ +++ D++
Sbjct: 248 LPLFTFHDRLTKLRKTKKGIALKYIFIDQLELPPRIYNFLKKSNIHTLLDLLNKSQEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGT 312
           ++ +F R+ + +I  +L  
Sbjct: 308 KIKHFRREDVKQILDILEI 326


>gi|165910447|gb|ABY73978.1| RNA polymerase alpha subunit [Cuscuta japonica]
          Length = 332

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 82/327 (25%), Positives = 157/327 (48%), Gaps = 26/327 (7%)

Query: 14  NIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +E+  +    ++        I  PL +G A T+G ALRR L++ + G  IT V+     
Sbjct: 12  KLEWECVESRTDSKRLYYGRFILSPLMKGQADTIGIALRRALLAEIEGTRITRVKFANAS 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +       +I  +GPG VTA DI     +E+++
Sbjct: 72  HEYSTIAGIQESVHEILMNLKEIVLRSNLYGTCDASISFKGPGYVTAEDIILPPHVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L     + + L + +  GY    H   E+   G   IDA++ P++  ++++ S
Sbjct: 132 STQHIAWLTEPIDLCIGLKIERNRGYFIKTHANFED---GSYPIDAVFMPVQNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV-- 247
                    + L + I T+GS+T ++++  ASR L D    F++ E+    +++  +   
Sbjct: 189 YGNE---KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEKENLPLEDADHTIP 245

Query: 248 -----------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
                      K+          +++LE   +  NCL+  NI  + DL+  ++ D++++ 
Sbjct: 246 LSPFTVYYKVAKNKKKLSLESLFIDQLEFPPKIYNCLKKSNIFTLLDLLNNSQEDLIKIE 305

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +F    L ++K +L  +G    ++LP 
Sbjct: 306 HFR---LEDVKQILAILGKHFALDLPK 329


>gi|33241138|ref|NP_876080.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           subsp. marinus str. CCMP1375]
 gi|41688642|sp|Q7V9Y5|RPOA_PROMA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|33238668|gb|AAQ00733.1| DNA-directed RNA polymerase alpha subunit/40 kD subunit
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
          Length = 312

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 100/305 (32%), Positives = 158/305 (51%), Gaps = 8/305 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ V     +   + +  PL RG A TLGN+LRRVLM  L G+A+TAV+I GV HE 
Sbjct: 7   DRIEHQVSDDRSQT-GIFLIGPLERGQATTLGNSLRRVLMGGLEGSAVTAVRISGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           +++ GV ED+ DI+LN K + +       +   +   GP  V A D+Q  + +++++ D 
Sbjct: 66  ATVPGVREDVLDILLNCKELTVNSRSQELEIGRLVVTGPAEVKARDLQFSSQVQIVDVDR 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +EL V +G GY P          I L+ IDA++ P+KKV++T++    
Sbjct: 126 PIATVHSGHSLELELHVERGVGYRPVDRRNEATTAIDLLQIDAVFMPVKKVNFTIDETAV 185

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L M I TDGSIT +D+VA A+  L +           ++  +E        
Sbjct: 186 SEGGSTRERLRMEIVTDGSITPDDAVAEAANQLIELFQPLATVTMVEEVPQEPEPTAE-- 243

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 244 ----AQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIS 304


>gi|157493273|gb|ABV58002.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493275|gb|ABV58003.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 270

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 121/273 (44%), Positives = 184/273 (67%), Gaps = 8/273 (2%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
            EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG
Sbjct: 1   LEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKG 60

Query: 92  INLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVVRMELTV 149
           + +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L   +A + M + V
Sbjct: 61  LAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKV 120

Query: 150 SKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++
Sbjct: 121 ERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDME 180

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V++LEL+
Sbjct: 181 TNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELT 237

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           VRS NCL+ E I Y+GDL+QRTE ++L+  N G
Sbjct: 238 VRSANCLKAEAIHYIGDLVQRTEVELLKTPNLG 270


>gi|256845557|ref|ZP_05551015.1| DNA-directed RNA polymerase, alpha subunit [Fusobacterium sp.
           3_1_36A2]
 gi|256719116|gb|EEU32671.1| DNA-directed RNA polymerase, alpha subunit [Fusobacterium sp.
           3_1_36A2]
          Length = 332

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 115/310 (37%), Positives = 185/310 (59%), Gaps = 7/310 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I   +E   +   I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + G
Sbjct: 19  ITEVKESNYKGQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDG 78

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V E +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ VIC +
Sbjct: 79  VKEAVTEIILNVKEIVVKAESSGERRMTLSIKGPKVVKAADIVADIGLEIVNPEQVICTV 138

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D
Sbjct: 139 TTDRTLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTD 198

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI-------NFEEPKKEVKEDINVKSL 250
           +DKL++ ++TDGSI   D+++ A  +L+  L  F+       N  +  +E+ E+     +
Sbjct: 199 FDKLTLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEIIEEPMDIQV 258

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +
Sbjct: 259 IDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKM 318

Query: 311 GTMGLFLGMN 320
             +G  L  N
Sbjct: 319 KDLGYDLEKN 328


>gi|71056830|emb|CAH58970.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
          Length = 243

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 108/241 (44%), Positives = 158/241 (65%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E+++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED
Sbjct: 3   DEDKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVRED 62

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +  IILNIKG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  IC +   A
Sbjct: 63  VAQIILNIKGLALKMYGDEEKTLEIDISGPATVTAGDIIVDSDVEILNKDMYICTVSEGA 122

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
                LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL
Sbjct: 123 TFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKL 182

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           +M I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +E
Sbjct: 183 TMEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIE 242

Query: 262 E 262
           E
Sbjct: 243 E 243


>gi|303308472|gb|ADM14339.1| RNA polymerase alpha subunit [Punica granatum]
          Length = 337

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 154/319 (48%), Gaps = 21/319 (6%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RR L+  + G  IT  + + + 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+         +I  +GPG VTA DI     +E+++
Sbjct: 72  HEYSTIVGIQESVHEILMNLKEIVLRSYLYGTCNASICVKGPGCVTAQDIILPPSVEIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I +L     + + L + +  GY     +  ++   G   IDA++ P++  ++++ S
Sbjct: 132 NTQHIASLMEPINLCIGLQIERNRGYHIKTPNNFQD---GSYPIDAVFMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV-- 247
              G     + L + I T+GS+T ++++  ASR L D L  F++ EE    ++ +     
Sbjct: 189 YGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLLIPFLHAEEENLHLENNQYKVT 247

Query: 248 --------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         K+          +++LEL  R  N L+  NI  + DL+ +++ D++
Sbjct: 248 LPLFTFHDRLTKLRKTKKEIALKYIFIDQLELPPRIYNFLKKSNIHTLLDLLNKSQEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGT 312
           ++ +F R+ + +I  +L  
Sbjct: 308 KIKHFRREDVEQILDILEI 326


>gi|317016849|gb|ADU85965.1| DNA-directed RNA polymerase alpha chain [Lactobacillus
           fabifermentans]
          Length = 235

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 103/235 (43%), Positives = 154/235 (65%), Gaps = 2/235 (0%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T II
Sbjct: 1   YGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVTEDVTAII 60

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+K + LK+  D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A   M 
Sbjct: 61  LNVKKVALKLDSDETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLAICTVADGAHFHMR 120

Query: 147 LTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +T + G GYV A+ ++   ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ 
Sbjct: 121 MTANTGRGYVSAEDNKHREDDMPIGVLPVDSLYSPIERVNYQVENTRVGQRDDFDKLTLD 180

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           + T+GSIT  ++++L+++IL D L +F+N  +  K     +  +       L   
Sbjct: 181 VWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEMT 235


>gi|307297367|ref|ZP_07577173.1| DNA-directed RNA polymerase, alpha subunit [Thermotogales bacterium
           mesG1.Ag.4.2]
 gi|306916627|gb|EFN47009.1| DNA-directed RNA polymerase, alpha subunit [Thermotogales bacterium
           mesG1.Ag.4.2]
          Length = 348

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 124/328 (37%), Positives = 182/328 (55%), Gaps = 25/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENR-TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           I P N+      +++ +  T  I  P+ RG+A T+GN+LRRVL+SS+   AIT ++I G 
Sbjct: 14  IMPKNLRIEEEREDDNSYFTRFILSPMERGYATTIGNSLRRVLLSSIPSMAITRLKIPGK 73

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
            HE   I GV ED+ +IILN K + LK  +      ++T+   GPGV+TAGDI+T   +E
Sbjct: 74  YHEYDVIDGVKEDILEIILNFKKVQLKPALEFSDAVKLTLETAGPGVITAGDIKTPTGVE 133

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           V+NP   I  L+ D+V+ +EL    G G+VP      E+D   +I ID ++SP+ KV++ 
Sbjct: 134 VVNPSQYIATLNTDSVIYIELFAEIGRGFVPVSEMEIEHDVE-MIYIDGIFSPVLKVNFQ 192

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN------------- 233
            E+ R G+  DYDKL + + T  SIT  D++  A+ IL     +F N             
Sbjct: 193 TENVRVGKRTDYDKLILDVWTKKSITPSDALLRATDILIRHFEVFSNGLGKPGQGLTSSA 252

Query: 234 --------FEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLI 285
                     E  +   E   V+    N    KKVEEL+LSVRS NCL+ + I  +GDL+
Sbjct: 253 LKQEEEEIISEEAEVTVETPQVEEQDSNSLGAKKVEELDLSVRSLNCLKRDKINTIGDLL 312

Query: 286 QRTEADMLRMANFGRKSLVEIKGVLGTM 313
            ++EAD+LR+ NFG KS++E+   L   
Sbjct: 313 DKSEADLLRIRNFGEKSMLEVVKKLREK 340


>gi|292559539|ref|YP_003540963.1| DNA-directed RNA polymerase alpha chain [Phoenix dactylifera]
 gi|290790947|gb|ADD63202.1| DNA-directed RNA polymerase alpha chain [Phoenix dactylifera]
 gi|294620609|gb|ADF28178.1| DNA-directed RNA polymerase alpha chain [Phoenix dactylifera]
          Length = 337

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 88/330 (26%), Positives = 162/330 (49%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RR L+  + G  IT  + + V 
Sbjct: 13  LRWKCVES-RVDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKVA 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +       +I  RGP  VTA DI +   +E+++
Sbjct: 72  HEYSTIVGIEESVHEILLNLKEIILRSNLYGVIDASICVRGPRYVTAKDIISPPYVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL     + +EL + +  GY     + +++   G   IDA+  P++  ++++ S
Sbjct: 132 TTQHIANLTEPIDLCIELQIKRDRGYRMKSANNSQD---GSYPIDAVSMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G     + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N   
Sbjct: 189 YGNG-NEKQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEEDINFEENKNRFP 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         K+    P     +++ EL  R+ NCL+G NI  + DL+  ++ D++
Sbjct: 248 LPLFTFQDRLTNLKKNKKGIPLKCIFIDQSELPSRTYNCLKGSNIHTLSDLLNNSQEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           R+  F    + ++K +L T+  +  ++L  
Sbjct: 308 RIEFFR---IEDVKQILDTLQKYFAIDLSK 334


>gi|84874040|gb|ABC68043.1| RNA polymerase subunit [Oryza punctata]
          Length = 317

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 95/320 (29%), Positives = 158/320 (49%), Gaps = 23/320 (7%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +  +       I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+ 
Sbjct: 2   VDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGIE 61

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL  
Sbjct: 62  ESVQEILLNLKEIVLRSNLYGVRNASICVKGPRYITAQDIILPPSVEIVDTAQPIANLTE 121

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
               R+EL + +  GY       T++   G   IDA+  P++ V+Y++ S   G    Y+
Sbjct: 122 PEDFRIELRIKRDRGYHTEVRKNTQD---GSYPIDAVSMPVRNVNYSIFSCGNG-NAKYE 177

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-------- 251
            L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P        
Sbjct: 178 ILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKRL 237

Query: 252 --------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                     P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    +
Sbjct: 238 TNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSFR---M 294

Query: 304 VEIKGVLGTMGLFLGMNLPD 323
            + K +  T+   L M+LP 
Sbjct: 295 QDGKQIWDTLEKHLPMDLPK 314


>gi|290489700|gb|ADD31234.1| RNA polymerase alpha subunit protein [Staphylea colchica]
          Length = 342

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 161/334 (48%), Gaps = 28/334 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    +         I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRADRKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +    +  +I  +GPG VTA DI     +E++
Sbjct: 71  PHEYSTIVGIQESVHEILMNLKEIVLRSNLYGTRDASICIKGPGYVTAQDIILPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY     +   +   G   IDA++ P++ V+Y++ 
Sbjct: 131 DNTQHIASLTEPMDLCIGLQIERNRGYSIKTPNNF-HFQDGSYPIDAVFMPVRNVNYSIH 189

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + +  
Sbjct: 190 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEDNGHLENNHHKL 248

Query: 249 SLPFNPALLKK-------------------VEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +LP      +                    +++ ELS R  NCL+  NI  + DL+  ++
Sbjct: 249 TLPLFTFHDRLAKLRKKKKEQKEIVLKYIFIDQSELSPRIYNCLKRSNIHTLLDLLNNSQ 308

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            D+L++ +     + ++K +L  + +   ++LP 
Sbjct: 309 EDLLKIEDLR---IEDVKQILDILEIENTIDLPK 339


>gi|300431295|gb|ADK12612.1| RNA polymerase alpha subunit [Aciachne acicularis]
          Length = 339

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 160/328 (48%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDITLPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY     +  ++   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIELQIKRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D+ 
Sbjct: 248 PPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLR 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDGKQIWDTLEKHLPIDL 332


>gi|116617139|ref|YP_817514.1| RNA polymerase alpha subunit [Coffea arabica]
 gi|122153651|sp|A0A367|RPOA_COFAR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|116242195|gb|ABJ89710.1| RNA polymerase alpha subunit [Coffea arabica]
          Length = 335

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 85/332 (25%), Positives = 158/332 (47%), Gaps = 27/332 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +E+  +    ++        I  PL +G A T+G A+RR L+  + G  IT V+ + V
Sbjct: 11  RTLEWKCVELRTDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRVKSEKV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I  + +       +I  RGPG VTA DI     +E++
Sbjct: 71  AHEYSTIAGIQESVHEILMNLKEIVFRSNLYGTCDASICVRGPGYVTAQDIVLPPYVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + + L + +  GY+       +N   G   IDA++ PI+  +Y++ 
Sbjct: 131 DNTQHIARLMEPINLCIRLEIERNRGYLIKT---PQNFQDGSYPIDAVFMPIRNANYSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV- 247
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHQASRNLIDLFIPFLHMEEQNSHLENNQHTV 246

Query: 248 ---------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                          K+          +++ EL  R  NCL+  NI  + DL+  ++ ++
Sbjct: 247 PLAPFFFHDKLDKLRKNKKEIALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQENL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           +++ +F    + ++K +LG +   L + LP  
Sbjct: 307 MKIEHFH---IEDVKEILGILEKQLVIFLPKK 335


>gi|71056838|emb|CAH58974.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
          Length = 237

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 107/236 (45%), Positives = 154/236 (65%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  II
Sbjct: 2   YGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQII 61

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LNIKG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     
Sbjct: 62  LNIKGLALKMYGDEEKTLEIDISGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHAR 121

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I 
Sbjct: 122 LTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIW 181

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 182 TDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEE 237


>gi|118430333|ref|YP_874768.1| RNA polymerase alpha subunit [Agrostis stolonifera]
 gi|125987636|sp|A1EA40|RPOA_AGRST RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|118201242|gb|ABK79611.1| RNA polymerase alpha subunit [Agrostis stolonifera]
          Length = 339

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 93/328 (28%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIELQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+  +L M+L
Sbjct: 308 RIESFR---MEDRKQIWDTLEKYLPMDL 332


>gi|157493263|gb|ABV57997.1| RNA polymerase alpha subunit [Vibrio mimicus]
          Length = 270

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 121/273 (44%), Positives = 185/273 (67%), Gaps = 8/273 (2%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM- 96
           GF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++ 
Sbjct: 1   GFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVA 60

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVVRMELTVSKGHGY 155
            G     +T+ K G G V AGDI    D+E++NP+HVIC+L   +A + M + V +G GY
Sbjct: 61  EGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVERGRGY 120

Query: 156 VPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           VPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T+G++ 
Sbjct: 121 VPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLE 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
            E+++  A+ IL +QL  F++  + +         +   F+P LL+ V++LEL+VRS NC
Sbjct: 181 PEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANC 237

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           L+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 238 LKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 270


>gi|88807908|ref|ZP_01123419.1| DNA-directed RNA polymerase alpha subunit [Synechococcus sp. WH
           7805]
 gi|88787947|gb|EAR19103.1| DNA-directed RNA polymerase alpha subunit [Synechococcus sp. WH
           7805]
          Length = 312

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 98/304 (32%), Positives = 159/304 (52%), Gaps = 8/304 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ +     +   + +  PL RG A TLGN+LRRVLM +L G A+TAV+I GV HE 
Sbjct: 7   DRIEHQIADDRSQT-GVFLIGPLERGQATTLGNSLRRVLMGNLEGTAVTAVRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K I +       +   +   GP  V A D+Q  + ++V++ + 
Sbjct: 66  ATIPGVREDVLDILLNCKQITVNSRTSELEIGRLVVAGPATVKARDLQFSSQVQVIDGER 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           VI  +     + +E+ V +G GY P   H  +   I L+ IDA++ P+ +V++T++    
Sbjct: 126 VIATVGESYSLELEVHVERGIGYRPVDRHNEDTSAIDLLQIDAVFMPVHRVNFTIDETAV 185

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L M + TDGSIT +D++A A+  L +           ++   E        
Sbjct: 186 AEGGSARERLRMEVVTDGSITPDDAIAQAANQLIELFQPLATVTMVEEVSAEPEPTAE-- 243

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 244 ----AQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGL 315
            +G+
Sbjct: 300 RIGI 303


>gi|84874044|gb|ABC68045.1| RNA polymerase subunit [Oryza granulata]
          Length = 317

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 94/320 (29%), Positives = 158/320 (49%), Gaps = 23/320 (7%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +  +       I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+ 
Sbjct: 2   VDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGIE 61

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL  
Sbjct: 62  ESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDMAQPIANLTE 121

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
               R+EL + +  GY        ++   G   IDA+  P++ V+Y++ S   G    Y+
Sbjct: 122 PMDFRIELRIKRDRGYHTEVRKNAQD---GSYPIDAVSMPVRNVNYSIFSCGNG-NAKYE 177

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-------- 251
            L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P        
Sbjct: 178 ILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKRL 237

Query: 252 --------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                     P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    +
Sbjct: 238 TNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSFR---M 294

Query: 304 VEIKGVLGTMGLFLGMNLPD 323
            + K +  T+  +L M+LP 
Sbjct: 295 QDGKQIWDTLEKYLPMDLPK 314


>gi|124020697|gb|ABM88794.1| DNA-directed RNA polymerase alpha chain [Enterococcus camelliae]
          Length = 223

 Score =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 104/222 (46%), Positives = 150/222 (67%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  II
Sbjct: 2   YGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVAQII 61

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LNIKG+ LK+ G+  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     
Sbjct: 62  LNIKGLALKLYGEDEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSDGATFHAR 121

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           LTV  G GYV A  ++ ++ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I 
Sbjct: 122 LTVKPGRGYVQADENKKDDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIW 181

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           TDGSI   D+++LA++I+ + L +F+N  +  K  +  +  +
Sbjct: 182 TDGSIEPLDAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKE 223


>gi|90110835|sp|Q49CA2|RPOA_CUSJA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|66876488|gb|AAY58033.1| RpoA [Cuscuta japonica]
          Length = 332

 Score =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 81/328 (24%), Positives = 157/328 (47%), Gaps = 26/328 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G ALRR L++ + G  IT V+    
Sbjct: 11  RTLQWKCVESRTDSKRLYYGRFILSPLMKGQADTIGIALRRALLAEIEGTRITRVKFANA 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  +GPG VTA DI     +E++
Sbjct: 71  SHEYSTIAGIQESVHEILMNLKEIVLRSNLYGTCDASISFKGPGYVTAEDIILPPHVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + + L + +  GY    H   E+   G   IDA++ P++  ++++ 
Sbjct: 131 DSTQHIAWLTEPIDLCIGLKIERNRGYFIKTHANFED---GSYPIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV- 247
           S         + L + I T+GS+T ++++  ASR L D    F++ E+    +++  +  
Sbjct: 188 SYGNE---KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEKENLPLEDADHTI 244

Query: 248 ------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
                       K+          +++LE   +  NCL+  NI  + DL+  ++ D++++
Sbjct: 245 PLSPFTVYYKVAKNKKKLSLESLFIDQLEFPPKIYNCLKKSNIFTLLDLLNNSQEDLIKI 304

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            +F    L ++K +L  +G    ++LP 
Sbjct: 305 EHFR---LEDVKQILAILGKHFALDLPK 329


>gi|12661177|gb|AAK01152.2|AF311314_2 RPoA [Marsilea quadrifolia]
          Length = 347

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 85/337 (25%), Positives = 165/337 (48%), Gaps = 22/337 (6%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E+I+   +E+ +  +        +  P  +G A+T+G A+RR L+  + GA+IT+ + +
Sbjct: 16  NEVIQWKCVEFRIESKRLH-YGRFVISPFKKGQANTVGIAMRRALLGEVGGASITSARFE 74

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV HE S++ G+ E + DI++N+K I L+   D +++  +   GP  VTAGDI     ++
Sbjct: 75  GVAHEYSTVAGIQETIHDILVNLKEIVLRSDSDGNQKAILSVTGPKRVTAGDISLPPSVK 134

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           V++    I  +     V +EL +    GY     +   +   G   +DA++ P++ V+Y+
Sbjct: 135 VIDDSQYIVTITQPISVNIELNIECDCGYRIESLNEYRD---GEFPVDAVFMPVRNVNYS 191

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED-- 244
           V     G+ +  + L + + T+GS+T  ++++ AS+   D L  F++ +       E   
Sbjct: 192 VHPFGSGKEM-REILFIEVWTNGSLTPTEAISKASKSSIDLLSPFLHTKHEDIPDFESNR 250

Query: 245 ------------INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                        +V     +      +++LEL  R+ NCL+   I  + DL+  +  D+
Sbjct: 251 DSSSLMKFSSRVDDVDKSEGDFFKNTFIDQLELPARAFNCLKRAEIHTISDLLSYSRDDL 310

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           L++ +FG+KS+ ++   L          LP+  P  +
Sbjct: 311 LKLKSFGKKSVDQVSRALWE---RFATELPNEKPRVV 344


>gi|226356865|ref|YP_002786605.1| DNA-directed RNA polymerase subunit alpha [Deinococcus deserti
           VCD115]
 gi|226318855|gb|ACO46851.1| putative DNA-directed RNA polymerase alpha chain (DNA-dependent RNA
           polymerase) [Deinococcus deserti VCD115]
          Length = 333

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 110/320 (34%), Positives = 171/320 (53%), Gaps = 27/320 (8%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           + N    + EPL RG+  T+GN +RR+LMSS+ G A+T+V I+ VLHE S+I GV ED+ 
Sbjct: 13  DGNYGEFVLEPLTRGYGVTIGNPIRRILMSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVI 72

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            +ILN+K + ++      K +T+  +G GVV A   +  +D E++NPD  I  L  D  +
Sbjct: 73  QLILNLKELVVRFHTSGPKTLTLRAQGEGVVKASAFEVPSDAEIVNPDLTIATLAEDGKL 132

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            ME+ V +G GYVPA  H T++  I  I +DA++SP+++V+Y VE+ R GQ  D D+L +
Sbjct: 133 VMEVRVEEGEGYVPADKHATKDR-INSIPVDAVFSPVRRVAYHVENTRVGQQTDLDRLIL 191

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEE-------------------------PK 238
            + TDGS   +D++  +  IL+D+L +F N E                          P 
Sbjct: 192 RVWTDGSTGPQDALDKSVEILRDELTVFGNVEALPALVSDVAPVYTPTPVPAHNVYDLPP 251

Query: 239 KEVKEDINVKSLPFN-PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
                ++N    P    +    +E L L+ R  + L+ E I  +  L   ++ D+ ++  
Sbjct: 252 TSGSVNLNPGDYPAELDSPRVTLEGLGLTTRVLHSLKEEGIDSVDALCALSDRDLKKVPG 311

Query: 298 FGRKSLVEIKGVLGTMGLFL 317
            G +SL EIK  L   GL L
Sbjct: 312 IGERSLDEIKQQLAQFGLAL 331


>gi|260494239|ref|ZP_05814370.1| DNA-directed RNA polymerase, alpha subunit [Fusobacterium sp.
           3_1_33]
 gi|260198385|gb|EEW95901.1| DNA-directed RNA polymerase, alpha subunit [Fusobacterium sp.
           3_1_33]
          Length = 332

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 113/310 (36%), Positives = 187/310 (60%), Gaps = 7/310 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I   +E   ++  I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + G
Sbjct: 19  ITEVKESNYKSQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDG 78

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V E +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ +IC +
Sbjct: 79  VKEAVTEIILNVKEIVVKAESSGERRMTLSIKGPKVVKAADIVADIGLEIVNPEQIICTV 138

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D
Sbjct: 139 TTDRTLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTD 198

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVK---SL 250
           +DKL++ ++TDGSI   D+++ A  +L+  L  F+      E  + +++E ++      +
Sbjct: 199 FDKLTLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEMVDEPMDIQV 258

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +
Sbjct: 259 IDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKM 318

Query: 311 GTMGLFLGMN 320
             +G  L  N
Sbjct: 319 KDLGYDLEKN 328


>gi|124024019|ref|YP_001018326.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. MIT 9303]
 gi|156637356|sp|A2CC51|RPOA_PROM3 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|123964305|gb|ABM79061.1| Bacterial RNA polymerase, alpha chain [Prochlorococcus marinus str.
           MIT 9303]
          Length = 312

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 100/308 (32%), Positives = 162/308 (52%), Gaps = 14/308 (4%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ V     +   + +  PL RG A TLGN+LRRVLM  L G+AITAV+I GV HE 
Sbjct: 7   DRIEHQVADDRAQT-GVFLIGPLERGQATTLGNSLRRVLMGGLEGSAITAVRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K +++       +   +   GP  V A D+Q  + ++V++ D 
Sbjct: 66  ATIPGVREDVLDILLNCKQLSVNSRTSELEIGRLVVTGPAQVKAKDLQFSSQVQVVDGDR 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P   H  +   I L+ IDA++ P+++V++T++    
Sbjct: 126 QIATVHEGHSLELEVHVERGIGYRPVDRHNEDISAIDLLQIDAVFMPVRRVNFTIDETAV 185

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF---INFEEPKKEVKEDINVK 248
                  ++L + I TDGS T +D++A ++  L +           EEP  E +     +
Sbjct: 186 AEGGSTRERLRIEIVTDGSTTPDDALAESANQLIELFQPLATVTMVEEPGLEPEPSAESQ 245

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                      +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+  
Sbjct: 246 ---------IPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIE 296

Query: 309 VLGTMGLF 316
            L  +G+ 
Sbjct: 297 ALERIGIS 304


>gi|33864022|ref|NP_895582.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. MIT 9313]
 gi|41688640|sp|Q7V523|RPOA_PROMM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|33635606|emb|CAE21930.1| Bacterial RNA polymerase, alpha chain [Prochlorococcus marinus str.
           MIT 9313]
          Length = 312

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 100/308 (32%), Positives = 162/308 (52%), Gaps = 14/308 (4%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ V     +   + +  PL RG A TLGN+LRRVLM  L G+AITAV+I GV HE 
Sbjct: 7   DRIEHQVADDRAQT-GVFLIGPLERGQATTLGNSLRRVLMGGLEGSAITAVRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K +++       +   +   GP  V A D+Q  + ++V++ D 
Sbjct: 66  ATIPGVREDVLDILLNCKQLSVNSRTSELEIGRLVVTGPAQVKAKDLQFSSQVQVVDGDR 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P   H  +   I L+ IDA++ P+++V++T++    
Sbjct: 126 QIATVHEGHSLELEVHVERGIGYRPVDRHNEDVSAIDLLQIDAVFMPVRRVNFTIDETAV 185

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF---INFEEPKKEVKEDINVK 248
                  ++L + I TDGS T +D++A ++  L +           EEP  E +     +
Sbjct: 186 AEGGSTRERLRIEIVTDGSTTPDDALAESANQLIELFQPLATVTMVEEPGLEPEPSAESQ 245

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                      +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+  
Sbjct: 246 ---------IPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIE 296

Query: 309 VLGTMGLF 316
            L  +G+ 
Sbjct: 297 ALERIGIS 304


>gi|78185545|ref|YP_377979.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp.
           CC9902]
 gi|119366744|sp|Q3AW70|RPOA_SYNS9 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|78169839|gb|ABB26936.1| DNA-directed RNA polymerase, alpha subunit [Synechococcus sp.
           CC9902]
          Length = 312

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 97/305 (31%), Positives = 164/305 (53%), Gaps = 8/305 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ +     +   + +  PL RG A TLGNALRRVLM  L G+A+TA++I GV HE 
Sbjct: 7   DRIEHQIAEDRAQT-GVFLIGPLERGQATTLGNALRRVLMGGLEGSAVTAIRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           +++ GV ED+ DI+LN K +++       +   +   GP  V A D+Q  + ++V++ + 
Sbjct: 66  ATVPGVREDVLDILLNCKELSVNSRSAELEIGRLVVAGPAEVKASDLQFSSQVQVIDGNR 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P   H  +   I L+ IDA++ P+K+V++ ++    
Sbjct: 126 TIATVADGHSLELEVHVERGIGYRPVDRHNEDTSAIDLLQIDAVFMPVKRVNFNIDETAV 185

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L + I TDGSIT +D++A  +  L +              + E++ V+  P
Sbjct: 186 AEGGSARERLRIEISTDGSITPDDALAQTANQLLELFQPLATVT-----LVEEVGVEPEP 240

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
              A +  +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 241 SAEAQI-PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIS 304


>gi|313199734|ref|YP_004021348.1| RNA polymerase alpha subunit [Theobroma cacao]
 gi|309321298|gb|ADO64841.1| RNA polymerase alpha subunit [Theobroma cacao]
 gi|328924811|gb|ADO64922.2| RNA polymerase alpha subunit [Theobroma cacao]
          Length = 327

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 77/320 (24%), Positives = 155/320 (48%), Gaps = 24/320 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRTDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +    +   I  +GPG VTA DI     +E++
Sbjct: 71  PHEYSTIVGIQESVHEILMNLKEIVLRSNLYGTRNAFICAKGPGYVTAQDIILPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY     +   +   G   +DA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDLCIGLQIERNRGYRIKTPNNFHD---GSYPLDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
                     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + +  
Sbjct: 188 CYGND-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLENNQHNV 246

Query: 249 SLPFNPALLKK----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LPF P   +                 +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPFFPFHDRLAKLRKKKKEIALKYIFIDQSELPPRIYNCLKKSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGT 312
           +++ +F  + + +I G+L  
Sbjct: 307 MKIEHFRIEDVKQILGILEK 326


>gi|256027710|ref|ZP_05441544.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp. D11]
          Length = 326

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 113/310 (36%), Positives = 186/310 (60%), Gaps = 7/310 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I   +E   ++  I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + G
Sbjct: 13  ITEVKESNYKSQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDG 72

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V E +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ +IC +
Sbjct: 73  VKEAVTEIILNVKEIVVKAESSGERRMTLSIKGPKVVKAADIVADIGLEIVNPEQIICTV 132

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D
Sbjct: 133 TTDRTLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTD 192

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI-------NFEEPKKEVKEDINVKSL 250
           +DKL++ ++TDGSI   D+++ A  +L+  L  F+       N  +  +E+ ++     +
Sbjct: 193 FDKLTLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEIVDEPMDIQV 252

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +
Sbjct: 253 IDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKM 312

Query: 311 GTMGLFLGMN 320
             +G  L  N
Sbjct: 313 KDLGYDLEKN 322


>gi|237744175|ref|ZP_04574656.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp. 7_1]
 gi|229431404|gb|EEO41616.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp. 7_1]
          Length = 342

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 113/310 (36%), Positives = 187/310 (60%), Gaps = 7/310 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I   +E   ++  I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + G
Sbjct: 29  ITEVKESNYKSQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDG 88

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V E +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ +IC +
Sbjct: 89  VKEAVTEIILNVKEIVVKAESSGERRMTLSIKGPKVVKAADIVADIGLEIVNPEQIICTV 148

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D
Sbjct: 149 TTDRTLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTD 208

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVK---SL 250
           +DKL++ ++TDGSI   D+++ A  +L+  L  F+      E  + +++E ++      +
Sbjct: 209 FDKLTLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEMVDEPMDIQV 268

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +
Sbjct: 269 IDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKM 328

Query: 311 GTMGLFLGMN 320
             +G  L  N
Sbjct: 329 KDLGYDLEKN 338


>gi|125987861|sp|Q9BBN0|RPOA_MARQU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
          Length = 341

 Score =  269 bits (689), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 85/337 (25%), Positives = 165/337 (48%), Gaps = 22/337 (6%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E+I+   +E+ +  +        +  P  +G A+T+G A+RR L+  + GA+IT+ + +
Sbjct: 10  NEVIQWKCVEFRIESKRLH-YGRFVISPFKKGQANTVGIAMRRALLGEVGGASITSARFE 68

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV HE S++ G+ E + DI++N+K I L+   D +++  +   GP  VTAGDI     ++
Sbjct: 69  GVAHEYSTVAGIQETIHDILVNLKEIVLRSDSDGNQKAILSVTGPKRVTAGDISLPPSVK 128

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           V++    I  +     V +EL +    GY     +   +   G   +DA++ P++ V+Y+
Sbjct: 129 VIDDSQYIVTITQPISVNIELNIECDCGYRIESLNEYRD---GEFPVDAVFMPVRNVNYS 185

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED-- 244
           V     G+ +  + L + + T+GS+T  ++++ AS+   D L  F++ +       E   
Sbjct: 186 VHPFGSGKEM-REILFIEVWTNGSLTPTEAISKASKSSIDLLSPFLHTKHEDIPDFESNR 244

Query: 245 ------------INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                        +V     +      +++LEL  R+ NCL+   I  + DL+  +  D+
Sbjct: 245 DSSSLMKFSSRVDDVDKSEGDFFKNTFIDQLELPARAFNCLKRAEIHTISDLLSYSRDDL 304

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           L++ +FG+KS+ ++   L          LP+  P  +
Sbjct: 305 LKLKSFGKKSVDQVSRALWE---RFATELPNEKPRVV 338


>gi|159904196|ref|YP_001551540.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. MIT 9211]
 gi|159889372|gb|ABX09586.1| Bacterial RNA polymerase, alpha chain [Prochlorococcus marinus str.
           MIT 9211]
          Length = 312

 Score =  269 bits (689), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 100/305 (32%), Positives = 160/305 (52%), Gaps = 8/305 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + I++ +     +   L +  PL RG A TLGN+LRRVLM  L G+A+TAV+I GV HE 
Sbjct: 7   DRIDHQISDDRSQT-GLFLIGPLERGQATTLGNSLRRVLMGGLEGSAVTAVRISGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K +++       +   +   GP  V A D+Q  + ++V++ D 
Sbjct: 66  ATIPGVREDVLDILLNCKQLSVNSRSPELEIGRLVVNGPAEVKARDVQFSSQVQVVDGDR 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +EL V +G GY P   H  E   I L+ IDA++ PIKKV++ ++    
Sbjct: 126 PIATVHSGHSLELELHVERGVGYRPVDRHNEETTSIDLLHIDAVFMPIKKVNFNIDETAV 185

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L M I TDGS++ +D++A A+  L +           ++  +E        
Sbjct: 186 AEGGSTRERLKMEIVTDGSMSPDDALAEAANQLIELFQPLATVTMVEEIPQEPEPSAE-- 243

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 244 ----AQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIS 304


>gi|46446067|ref|YP_007432.1| DNA-directed RNA polymerase subunit alpha [Candidatus
           Protochlamydia amoebophila UWE25]
 gi|81627550|sp|Q6ME42|RPOA_PARUW RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|46399708|emb|CAF23157.1| putative DNA-directed RNA polymerase alpha chain [Candidatus
           Protochlamydia amoebophila UWE25]
          Length = 371

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 118/349 (33%), Positives = 186/349 (53%), Gaps = 21/349 (6%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +   P+ I        E N    +AEP  RGF HT+GNALRR+++SSL   AI +V+++G
Sbjct: 7   KFEMPHKITVDQ-ESPESNFARYVAEPFERGFGHTIGNALRRMMLSSLEAPAIISVRVEG 65

Query: 68  VLHEISSIKGVHEDLTDIILNIKG-INLKMSGDSHKRVT--------------IFKRGPG 112
           + HE  +I+G+ ED+T+IILN KG +  K+  +   R T                 +G  
Sbjct: 66  IPHEYMAIEGISEDMTNIILNFKGALLRKLPTEETPRDTRILTKVVEVTQDDLDRNQGQY 125

Query: 113 VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT 172
            VT  D+    + E++NP+  +  +      +++L ++ G GYVP++ H   +     I 
Sbjct: 126 CVTLQDVVQEGNFEIVNPELHLFTVTKPMRRQVDLRIAFGRGYVPSERHVVRDKTSDEIL 185

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           +DA +SP++ ++Y +E+ R GQ  D+D+L M + TDG IT  ++++ A +I      +F 
Sbjct: 186 VDAAFSPVRLINYFIENTRVGQDTDFDRLIMEVTTDGRITPAEALSFAVQIGLKHFEVFN 245

Query: 233 NFEEPKKEVKE---DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
            F        E   D N         L   ++E+ELSVRS NCL G NI  + +L+   E
Sbjct: 246 QFNNYALSFDEKDGDRNGDQDELMDKLSLGIDEIELSVRSANCLTGANIETLAELVCIPE 305

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP--PESIEELAKKY 336
             ML   NFG+KSL EIK  L  M L LGM+L  +   P+++++  K+Y
Sbjct: 306 RRMLEFRNFGKKSLNEIKAKLHEMSLHLGMDLSRFGVSPDNVKDKIKQY 354


>gi|71056806|emb|CAH58958.1| DNA-directed RNA polymerase alpha chain [Enterococcus italicus DSM
           15952]
          Length = 234

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 105/233 (45%), Positives = 150/233 (64%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  II
Sbjct: 2   YGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVAQII 61

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LNIKG+ LK+ G+  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     
Sbjct: 62  LNIKGLALKLYGEDEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHAR 121

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           LTV  G GYV A  ++ ++ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I 
Sbjct: 122 LTVKPGRGYVQADENKKDDMPIGVLPVDSIYTPVRRVNYQVENTRVGHRDDFDKLTMEIW 181

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           TDGSI   D+++LA++I+ + L +F+N  +  K  +  +  +       L   
Sbjct: 182 TDGSIEPLDAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMT 234


>gi|34500945|ref|NP_904130.1| RNA polymerase alpha subunit [Amborella trichopoda]
 gi|41688608|sp|P60314|RPOA_AMBTC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|34481660|emb|CAD45138.1| RNA polymerase alpha subunit [Amborella trichopoda]
          Length = 334

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 82/330 (24%), Positives = 157/330 (47%), Gaps = 28/330 (8%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E      +       +  PL +G A T+G A+RR L+  + G  IT  + + V 
Sbjct: 13  LQWKCVESKA-DSKRLYYGRFVLSPLMKGQADTIGTAMRRSLLGEIEGTCITCAKSERVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I ++      +   I  RGP  VTA DI +   +++++
Sbjct: 72  HEYSTIVGIEESVHEILMNLKEIIVRSDLYGTRDAFICVRGPKYVTAQDIISPPSVKIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I ++       + L + +  GY     ++  +       IDA+  P++  +Y+++ 
Sbjct: 132 TTQHIASITEPINFCIGLEIERNRGYRTRTTNQDAS-----YPIDAVSMPVRNANYSIQC 186

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                    + L + I T+GS+T ++++  ASR L D    F++ EE    + +D N+ +
Sbjct: 187 YGNE-NEKQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEERDLHLDDDQNIFT 245

Query: 250 LPFNPALL------------------KKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
            PF P                       +++LELS R+ NCL+  NI  + DL+ +++ D
Sbjct: 246 APFFPFHEGLAYIGIGESKKRIALKRIFIDQLELSPRTYNCLKRSNIHTLLDLLSKSQED 305

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           + ++ +F    + ++K VL  +     MNL
Sbjct: 306 LRKIQHFR---VEDVKRVLDILKKRFAMNL 332


>gi|290489688|gb|ADD31228.1| RNA polymerase alpha subunit protein [Gunnera manicata]
          Length = 330

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 82/325 (25%), Positives = 163/325 (50%), Gaps = 27/325 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRTDSKRLYYGRFIMSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I LK +    +  +I  RGPG VTA DI +   +E++
Sbjct: 71  PHEYSTIVGIQESVHEILMNLKEIILKSNIYGTRDASICVRGPGYVTAQDIISPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + ++L + K  GY     +  ++   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDLCIQLQIEKNRGYRIKTPNTYQD---GSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G+    + L + I T+GS+T ++++  ASR L D    F++ EE    ++++    
Sbjct: 188 SYGNGKE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLEDNQYKV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LPF     +                 +++ EL  R+ NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPFFTFHDRLAKLRKNKKEIALKSIFIDQSELPSRTYNCLKSSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFL 317
           +++ +F   S+ ++K +L  +    
Sbjct: 307 MKIKHF---SIEDVKQILDILEKQF 328


>gi|289765669|ref|ZP_06525047.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp. D11]
 gi|289717224|gb|EFD81236.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp. D11]
          Length = 342

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 113/310 (36%), Positives = 186/310 (60%), Gaps = 7/310 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I   +E   ++  I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + G
Sbjct: 29  ITEVKESNYKSQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDG 88

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V E +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ +IC +
Sbjct: 89  VKEAVTEIILNVKEIVVKAESSGERRMTLSIKGPKVVKAADIVADIGLEIVNPEQIICTV 148

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D
Sbjct: 149 TTDRTLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTD 208

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI-------NFEEPKKEVKEDINVKSL 250
           +DKL++ ++TDGSI   D+++ A  +L+  L  F+       N  +  +E+ ++     +
Sbjct: 209 FDKLTLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEIVDEPMDIQV 268

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +
Sbjct: 269 IDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKM 328

Query: 311 GTMGLFLGMN 320
             +G  L  N
Sbjct: 329 KDLGYDLEKN 338


>gi|123966950|ref|YP_001012031.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. MIT 9515]
 gi|156637357|sp|A2BYR3|RPOA_PROM5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|123201316|gb|ABM72924.1| Bacterial RNA polymerase, alpha chain [Prochlorococcus marinus str.
           MIT 9515]
          Length = 312

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 94/305 (30%), Positives = 160/305 (52%), Gaps = 8/305 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + I++       +     +  PL RG A TLGN+LRRVLM  L G+A+TAV+I G+ HE 
Sbjct: 7   DRIDHQTANDRSQT-GTFLIGPLERGQATTLGNSLRRVLMGGLEGSAVTAVRIAGINHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K +++  S    +   +   GP  V A DIQ  + +E+++ D 
Sbjct: 66  ATIPGVREDVLDILLNCKQLSINSSNPELEIGRLVVSGPMEVKANDIQFSSQVEIVDGDK 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P      E   + L+ IDA++ P+K+V+++++    
Sbjct: 126 PIATIQEGHNLELEIHVERGVGYRPVDRRNQETTSVDLLQIDAVFMPVKRVNFSIDETAV 185

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L+M + TDGS + +D++A A+  L +           ++        +   
Sbjct: 186 AEGGTGRERLTMEVVTDGSTSPDDAIAEAANQLIELFQPLATVTMVEEI------PEEPE 239

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 240 PSPEAQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIS 304


>gi|300431293|gb|ADK12611.1| RNA polymerase alpha subunit [Piptatherum miliaceum]
          Length = 339

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 160/328 (48%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTLAGIEESVQEILLNLKEIVLRSNLYGVRDASISVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPVDFCIELQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDGKQIWDTLEKHLPIDL 332


>gi|326909424|ref|YP_004327694.1| RNA polymerase alpha subunit [Hevea brasiliensis]
 gi|308523538|gb|ADO33588.1| RNA polymerase alpha subunit [Hevea brasiliensis]
          Length = 341

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 163/334 (48%), Gaps = 23/334 (6%)

Query: 10  IKPNNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           I    +++  +    +N        I  PL +G A T+G A+RR L+  + G  IT  + 
Sbjct: 8   ISTRTLQWKCVESRTDNKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKS 67

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           + + HE S+I G+ E + +I++N+K I L+ +       +I   GPG VTA DI     +
Sbjct: 68  EKIPHEFSTIAGIQESIHEILMNLKEIVLRSNLYGTCNASICVEGPGYVTAQDIILPPFV 127

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E+++    I +L     + + L + +  GY     +  +    G  +IDA++ P++  ++
Sbjct: 128 EIIDNTQHIASLTEAIDLCIGLQIERNRGYRINPTNNFQ-VQDGSYSIDAVFMPVRNANH 186

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           +V S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ 
Sbjct: 187 SVHSYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDFFIPFLHAEEENLHLEKNQ 245

Query: 246 NVKSLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +  +LP      +                 +++ EL+ +  NCL+  NI  + DL+++++
Sbjct: 246 HKVTLPLFTFHDRLTKLRKNKKEIALKYIFIDQSELTPKIYNCLKRSNIHTLSDLLKKSQ 305

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            D++++ +F    +  I G+L  +     ++LP 
Sbjct: 306 EDLMKIEHFRIDDVKHILGIL-EIEKHFAIDLPK 338


>gi|159161282|ref|YP_001542560.1| RNA polymerase alpha subunit [Cuscuta exaltata]
 gi|172048134|sp|A8W3F3|RPOA_CUSEX RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|158938707|gb|ABW83724.1| RNA polymerase alpha subunit [Cuscuta exaltata]
          Length = 335

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 82/333 (24%), Positives = 157/333 (47%), Gaps = 29/333 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L++ + G  IT V+    
Sbjct: 11  RTLQWKCVESRTDSKRLYYGRFILSPLRKGQADTIGIAMRRALLAEIEGTRITRVKFAKA 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I +N+K I L+ +       +I  +GPG VTA DI     +E++
Sbjct: 71  SHEYSTIAGIQESVHEIFMNLKEIVLRSNLYGTCDASISIKGPGHVTAKDIILPPHVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + + L + +  GY    H   E+   G   IDA++ P++  ++++ 
Sbjct: 131 DSTQHIAWLTEPIDLCIGLKIERNRGYFIKTHPNFED---GSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV- 247
           S         + L + I T+GS+T ++++  ASR L D    F++ EE    +++  +  
Sbjct: 188 SYGNE---KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEENLHLEDADHTI 244

Query: 248 ---------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                          K+          +++LE   +  NCL+  NI  + DL+  ++ D+
Sbjct: 245 SLSPFTVYDKVAKLRKNKKKRSLESIFIDQLEFPPKIYNCLKKSNIFTLLDLLNNSQEDL 304

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           +++ +F    L ++K +LG +G    ++LP   
Sbjct: 305 IKIEHFR---LEDVKQILGILGKHFALDLPKKK 334


>gi|300431272|gb|ADK12601.1| RNA polymerase alpha subunit [Piptochaetium lasianthum]
          Length = 339

 Score =  269 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 88/328 (26%), Positives = 158/328 (48%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY     +  ++   G   IDA+  P++ V+Y    
Sbjct: 132 RAQPIANLTEPIDFCIELQIKRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYXXXX 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + + T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 XGNG-NEKHEILFLELWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           ++ +F    + + K +  T+   L ++L
Sbjct: 308 KIDSFR---MEDGKQIWDTLEKHLPIDL 332


>gi|150251505|ref|YP_001312238.1| RNA polymerase alpha chain [Cycas taitungensis]
 gi|172048628|sp|A6H5L3|RPOA_CYCTA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|149941555|dbj|BAF64979.1| RNA polymerase alpha chain [Cycas taitungensis]
 gi|156598071|gb|ABU85301.1| RNA polymerase alpha subunit [Cycas micronesica]
          Length = 340

 Score =  269 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 84/313 (26%), Positives = 147/313 (46%), Gaps = 23/313 (7%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
                  PL +G A T+G A+RR L+  + G  IT  +++ V HE S+I G+ E + DI+
Sbjct: 29  YGRFALSPLRKGQASTIGIAMRRALLGEIEGTCITHAKLEKVTHEYSAIIGIEESVHDIL 88

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           +N+K I L+      +  +I   GP  VTA DI     + +++    I +L       + 
Sbjct: 89  INLKEIVLRSDPYGTREASICIVGPRNVTAQDIILPPSVRIIDATQHIASLTKSITFDIR 148

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           L + K  GY        +N   G+  IDA++ P++  +Y++ S   G     + L + I 
Sbjct: 149 LWIEKDRGYRIQS---PKNYQDGIFPIDAVFMPVRNANYSIHSYGNG-NDIQEILFLEIW 204

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK------- 259
           T+GS+   +++  ASR L D    F+  EE   +  ++ N  ++P               
Sbjct: 205 TNGSLAPREALYRASRNLIDLFIPFLRAEEQNIDGMDNQNGSNMPSFSFSNISADMERME 264

Query: 260 ---------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                    +++ EL  R  NCL   NI  + DL+  ++ D++R+ +FG+KS+ ++  VL
Sbjct: 265 EEVAFKHIFIDQSELPPRVYNCLGRVNIHTLSDLLNYSQEDLMRIGHFGKKSVEQVSEVL 324

Query: 311 GTMGLFLGMNLPD 323
                   ++LP 
Sbjct: 325 ---QKHFAVDLPK 334


>gi|116072177|ref|ZP_01469445.1| DNA-directed RNA polymerase alpha subunit [Synechococcus sp. BL107]
 gi|116065800|gb|EAU71558.1| DNA-directed RNA polymerase alpha subunit [Synechococcus sp. BL107]
          Length = 312

 Score =  269 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 97/305 (31%), Positives = 164/305 (53%), Gaps = 8/305 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+ +     +   + +  PL RG A TLGNALRRVLM  L G+A+TA++I GV HE 
Sbjct: 7   DRIEHQIAEDRAQT-GVFLIGPLERGQATTLGNALRRVLMGGLEGSAVTAIRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           +++ GV ED+ DI+LN K +++       +   +   GP  V A D+Q  + ++V++ + 
Sbjct: 66  ATVPGVREDVLDILLNCKELSVNSRSAELEIGRLVVAGPAEVKASDLQFSSQVQVIDGNR 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P   H  +   I L+ IDA++ P+K+V++ ++    
Sbjct: 126 TIATVADGHSLELEVHVERGIGYRPVDRHNEDTSAIDLLQIDAVFMPVKRVNFNIDETAV 185

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L + I TDGSIT +D++A  +  L +              + E++ V+  P
Sbjct: 186 AEGGSARERLRIEICTDGSITPDDALAQTANQLLELFQPLATVT-----LVEEVGVEPEP 240

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
              A +  +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 241 SAEAQI-PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIS 304


>gi|73748344|ref|YP_307583.1| DNA-directed RNA polymerase subunit alpha [Dehalococcoides sp.
           CBDB1]
 gi|147669124|ref|YP_001213942.1| DNA-directed RNA polymerase subunit alpha [Dehalococcoides sp.
           BAV1]
 gi|289432392|ref|YP_003462265.1| DNA-directed RNA polymerase subunit alpha [Dehalococcoides sp. GT]
 gi|90110838|sp|Q3ZZP6|RPOA_DEHSC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|73660060|emb|CAI82667.1| DNA-directed RNA polymerase, alpha subunit [Dehalococcoides sp.
           CBDB1]
 gi|146270072|gb|ABQ17064.1| DNA-directed RNA polymerase subunit alpha [Dehalococcoides sp.
           BAV1]
 gi|288946112|gb|ADC73809.1| DNA-directed RNA polymerase, alpha subunit [Dehalococcoides sp. GT]
          Length = 330

 Score =  269 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 117/322 (36%), Positives = 178/322 (55%), Gaps = 5/322 (1%)

Query: 15  IEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS 74
           I  I   + +      + EPL +GF  T+GN+LRR+L+S L G AIT V+IDG+ HE  +
Sbjct: 6   IPTISCTESDGKYGRFVVEPLEKGFGTTMGNSLRRILLSYLDGVAITRVRIDGIQHEFCA 65

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           +    ED  D +LN+K I ++        + +   G  VVTA DI+  ND EV+NP+  +
Sbjct: 66  LPKAKEDTLDFLLNLKNIRVESLSGLEGILYLRASGSKVVTAADIEPSNDFEVVNPELYL 125

Query: 135 CNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
             LD  DAV+ +EL V  G GY P +    EN PIG I +DA+++PI+KV++T E    G
Sbjct: 126 LTLDSDDAVLNVELEVELGRGYRPPES--AENTPIGTIPVDAIFTPIRKVNFTTEPMHVG 183

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           +    ++L + + TDG++    +V+ ++ IL  Q    ++  +   E++    VK     
Sbjct: 184 RETSLERLVLEVWTDGTVEPATAVSRSADILVKQFASLVSHSKVVAEIEASEPVKYTIPE 243

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +E+L+LSVR+ NCLR   I  +G++I R   ++L + NFG KSL E++  L T+
Sbjct: 244 EKYNMPIEQLDLSVRAVNCLRHAGITTVGEVINRGTKELLTLRNFGLKSLTELEDRLKTI 303

Query: 314 GLFLGMNLPDWPPESIEELAKK 335
           GL L  N  D   E  E   KK
Sbjct: 304 GLSL--NPEDELFEEAENNKKK 323


>gi|69215828|gb|AAZ03870.1| RNA polymerase alpha chain [Yucca schidigera]
          Length = 337

 Score =  269 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 92/330 (27%), Positives = 161/330 (48%), Gaps = 26/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RR L+  + G  IT  + + V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I +N+K I   ++    +  +I  RGP  VTA DI +   +E+++
Sbjct: 72  HEYSTIVGIEESVHEIFINLKEIV--LNLYGVRDASICVRGPRYVTAQDIISPPSVEIVD 129

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL     +R+EL + +  GY     + T N   G   IDA+  P++  ++++ S
Sbjct: 130 TTQHIANLTEPIDLRIELQIKRDRGYRI---NPTNNSQDGSYPIDAVSMPVRNANHSIHS 186

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 187 YGNG-NEKQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEGDIHFEENKNRFT 245

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           LP                  P     +++LEL  R+ NCL+  NI  + DL+  ++ D++
Sbjct: 246 LPLFTFQNRLTNLKKNKKGIPLKCIFIDQLELPPRTYNCLKRSNIHTLLDLLSNSQEDLM 305

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           R+  F      ++K +L T+     +NLP 
Sbjct: 306 RIEYFRT---EDVKQILDTLQKHFAINLPK 332


>gi|295311758|ref|YP_003587497.1| RNA polymerase a-subunit [Oncidium Gower Ramsey]
 gi|254833135|gb|ACT83138.1| RNA polymerase a-subunit [Oncidium Gower Ramsey]
          Length = 339

 Score =  269 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 90/332 (27%), Positives = 163/332 (49%), Gaps = 24/332 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       +  PL +G A T+G A+RR L+  + G  IT    + VL
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFVLSPLMKGQADTIGIAMRRALLGRIEGTCITRATSENVL 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S I G+ E + DI++N+K I LK +    +  +I  RGP  +TA DI +   +++++
Sbjct: 72  HEYSMIAGIEESVHDILINLKEIVLKSNLYGVRDASICVRGPKYITAQDIISPPSVKIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL     + +EL + +G GY     + + +   G   ID +  P++  ++++ S
Sbjct: 132 TTQHIANLTEPIDLCIELQIKRGRGYHMKSTNESHD---GSYPIDIVSMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G     + L + I T+GS+T ++++  ASR L D L  F++ EE    ++E+     
Sbjct: 189 YGNG-NEKQEILFLEIWTNGSLTPKEALYEASRNLIDLLIPFLHAEEEDMNLEENEKRWN 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         K+    P     +++ ELS R+ NCL+  NI  + DL+  ++ D++
Sbjct: 248 LPLFSFQDRFTNLKKNKKGIPLTCIFIDQSELSSRTYNCLKRSNIHTLLDLLNHSQEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           +M  F    + ++K +LGT+     +NLP   
Sbjct: 308 KMEYFR---IEDVKQILGTLQKHFAINLPKKK 336


>gi|290489696|gb|ADD31232.1| RNA polymerase alpha subunit protein [Plumbago auriculata]
          Length = 333

 Score =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 80/329 (24%), Positives = 160/329 (48%), Gaps = 27/329 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    +N        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRTDNKRLSYGRFILFPLRKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S++ G+ E + +I++N+K I L+ +    +  +I  RGP  +TA DI     +E++
Sbjct: 71  AHEYSTLVGIQESVHEILMNLKEIVLRSNLYGTRDASICVRGPRCITAHDIILPPGVEII 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + + L + +  GY     +  ++   G   IDA++ P++ V++++ 
Sbjct: 131 DNTQHIATLTEPIDLCIGLQLERNRGYRIQTQNNFQD---GSYPIDAVFMPVRNVNHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE     + + +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEENLHFEANQHKV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP      K                 +++LE   R  NCL+  NI  + DL+ +++ D+
Sbjct: 247 TLPPFTFHDKLNELRKDKKKIALKSIFIDQLEFPPRIYNCLKNSNIHTLLDLLNKSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +++ +F    + ++K + GT+     ++L
Sbjct: 307 MQIEDFR---IEDLKQIWGTLEKNFSIDL 332


>gi|227873400|ref|ZP_03991657.1| DNA-directed RNA polymerase [Oribacterium sinus F0268]
 gi|227840761|gb|EEJ51134.1| DNA-directed RNA polymerase [Oribacterium sinus F0268]
          Length = 312

 Score =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 117/299 (39%), Positives = 184/299 (61%), Gaps = 9/299 (3%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           EE+     + + L +G A  LGN+LRR+L+SS+ G+A++ V++D V HE SSI GV ED+
Sbjct: 16  EEQGYARFVCDSLAKGEATVLGNSLRRILLSSMPGSAVSEVKLDSVYHEFSSIPGVKEDV 75

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRG--PGVVTAGDIQTVNDIEVLNPDHVICNLD-V 139
           ++II+N+K + L+ +G   + V  +      GVV A DI+  +++E++NPD V+ +L   
Sbjct: 76  SEIIMNLKNLALRYTGSGEEPVMAYVDYMGEGVVKASDIKVSSEVEIMNPDLVLAHLSGK 135

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           DA + ME+ VSKG GY  A      +  IG+I +DA+YSP+KKV+  VE        + +
Sbjct: 136 DAKIYMEMKVSKGKGYDGANTRDHSDLAIGVIAVDAIYSPVKKVNVFVEEQG-----NTE 190

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           +L + + TD ++  E++V+LA+RILQ  L +F++ +   KE    +  +    +    K 
Sbjct: 191 RLILDVTTDRTMMPEEAVSLAARILQTHLQLFMHMDTSAKEQGAAVANQEAGRDELN-KS 249

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           ++ELELSVRS NCL+   I  + DL  +T  D++++ N GRKSL EI   L +MGLFL 
Sbjct: 250 IDELELSVRSYNCLKRAGINTVEDLCAKTMDDLMKVRNMGRKSLDEILNKLESMGLFLS 308


>gi|282891929|ref|ZP_06300408.1| hypothetical protein pah_c200o089 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281498189|gb|EFB40529.1| hypothetical protein pah_c200o089 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 371

 Score =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 122/359 (33%), Positives = 187/359 (52%), Gaps = 27/359 (7%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +   P  I  +      +     IAEP  +GF HT+GN+LRR+++SSL   AI +V+I+G
Sbjct: 7   KFEIPQQI-SVDEETLSQTFGRFIAEPFEKGFGHTVGNSLRRMMLSSLEAPAIVSVRIEG 65

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKM-------SGDSHKRVT----------IFKRG 110
           + HE  +I+G+ ED+T+IILN+KG  ++        +    + VT              G
Sbjct: 66  ISHEYMAIEGIVEDMTNIILNLKGALIRKLPLDDAPNSRDDRIVTSILEITQDDLDKNHG 125

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
              VT GD+ T  + EV+NP   +  +      +++L V  G GYVP+            
Sbjct: 126 KYHVTLGDVFTEGNYEVVNPQLHLFTVTQPMKRQVDLRVVIGRGYVPSDRLDVHGKTSDE 185

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           I IDA +SP++ V+Y VE+ R GQ  D+D+L + I TDG +T  +++A A++I    + +
Sbjct: 186 ILIDAAFSPVRLVNYAVENTRVGQDTDFDRLLLEITTDGRVTPAEALAFAAQIGVKHMSV 245

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLK---KVEELELSVRSTNCLRGENIVYMGDLIQR 287
           F +         E  +      +  + K   +++E+ELSVRSTNCL G NI  + +L+  
Sbjct: 246 FTHINPHLLLFDEGQSRDDADQDAIMAKLALRIDEIELSVRSTNCLSGANIDTIAELVSI 305

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP------PESIEELAKKYEDKC 340
            E  ML   NFG+KSL EIK  L  MGL LGM+L  +        E I +  K+ +DK 
Sbjct: 306 PERRMLEFRNFGKKSLNEIKAKLTEMGLHLGMDLSKYGITADNVKEKIAQYHKEAKDKS 364


>gi|237739945|ref|ZP_04570426.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp.
           2_1_31]
 gi|229421962|gb|EEO37009.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp.
           2_1_31]
          Length = 342

 Score =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 113/310 (36%), Positives = 185/310 (59%), Gaps = 7/310 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I   +E   +   + EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GV+ E + + G
Sbjct: 29  ITEVKESNYKGQFVVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVMSEFTVMDG 88

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V E +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ VIC +
Sbjct: 89  VKEAVTEIILNVKEIVVKAESSGERRMTLSVKGPKVVKAADIVADIGLEIVNPEQVICTV 148

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D
Sbjct: 149 TTDRTLDMEFLVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRITD 208

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI-------NFEEPKKEVKEDINVKSL 250
           +DKL++ ++TDGSI   D+++ A  +L+  L  F+       N  +  +E+ E+     +
Sbjct: 209 FDKLTLNVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRDEIEEIIEEPIDIQV 268

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +
Sbjct: 269 IDDKSHDMKIEELDLTVRSFNCLKKAGIEDVSQLASLSLNELLKIKNLGKKSLDEILEKM 328

Query: 311 GTMGLFLGMN 320
             +G  L  N
Sbjct: 329 KDLGYDLEKN 338


>gi|290489676|gb|ADD31222.1| RNA polymerase alpha subunit protein [Ximenia americana]
          Length = 337

 Score =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 80/330 (24%), Positives = 157/330 (47%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RRVL+  + G  IT  + + V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLMKGRADTIGIAMRRVLLGEIEGTCITRAKSEQVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+  G+ E + +I++N+K I L+ +       +I  RGP  +TA DI +   +E+++
Sbjct: 72  HEYSTAIGIQESIHEILMNLKEIVLRSNLYGTCNASICVRGPRYITAQDIISPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I +L       +EL + +  GY     +  ++   G   IDA++ P++  ++++ S
Sbjct: 132 NTQYIASLTEPIDFCIELQIERNRGYHIKMPNNFQD---GSYPIDAVFMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV-- 247
              G     + L + I T+GS+T + ++  AS+ L D    F++ EE    ++++ +   
Sbjct: 189 YGNG-NEKQEILFLEIWTNGSLTPKKALYEASQNLIDLFIPFLHAEEENLHLEDNQHKVI 247

Query: 248 --------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         K+          +++ EL  R  NCL+  NI  + DL   ++ D++
Sbjct: 248 LPLFTPHDRLAKLRKNKEKIALKSIFIDQSELPSRIYNCLKRSNIHTLLDLFNNSQKDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++ +F    + + K +LG +     ++LP 
Sbjct: 308 KIEHFR---VEDGKQILGILEKHFAVDLPK 334


>gi|262341038|ref|YP_003283893.1| DNA-directed RNA polymerase subunit alpha [Blattabacterium sp.
           (Blattella germanica) str. Bge]
 gi|262272375|gb|ACY40283.1| DNA-directed RNA polymerase subunit alpha [Blattabacterium sp.
           (Blattella germanica) str. Bge]
          Length = 337

 Score =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 122/336 (36%), Positives = 199/336 (59%), Gaps = 12/336 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           + +KP+ I    + +  +N+ +   +PL  G+  TLGNALRRVL+ SL+G A+T+++I G
Sbjct: 5   DFVKPDRI---AMSEFSDNKGIFHLKPLEPGYGITLGNALRRVLLGSLKGFAVTSIRIKG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINL--KMSGDSHKRVTIFKRGPGVVTAGDI-QTVND 124
           V +E S+I+GV ED+T+I+LN K I L  K+SG   + V         VT G + + ++ 
Sbjct: 62  VKYEFSTIEGVVEDVTEIVLNFKKIRLKQKISGIHKETVNASIHHGKQVTGGYLNKFISG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP-IGLITIDALYSPIKKV 183
             +LN + VICN D    + +  T+ +G GYVPA+ ++  ND  IG I ID++Y+PI+ V
Sbjct: 122 FHILNENLVICNKDESIPLEISFTIEEGRGYVPAEENKKNNDHLIGTIPIDSIYTPIRNV 181

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
            YT+E+ R GQ  D++ LS+ I TDGSI  + ++  AS+IL     +F + +  KK+ +E
Sbjct: 182 KYTIENCRVGQKTDFENLSLEIQTDGSICPKSALMEASKILIQYFSIFSHEKIGKKKQEE 241

Query: 244 -----DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                  + + L     L  K+ +++LSVR+ NCL+  +I  + DL+     +ML+M NF
Sbjct: 242 INKDKKYDEEFLRMRTLLKSKLSDMDLSVRTKNCLKSASIESIADLVSCNRNNMLKMRNF 301

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL E++  +   GL  GM + ++   + E   +
Sbjct: 302 GKKSLDELESKMKEKGLCFGMEISEYRLNNKENNKE 337


>gi|313665551|ref|YP_004047422.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma leachii
           PG50]
 gi|312949424|gb|ADR24020.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma leachii
           PG50]
          Length = 317

 Score =  268 bits (686), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 111/318 (34%), Positives = 183/318 (57%), Gaps = 10/318 (3%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
            ++ ++P  I  ++   +++N       PL RGF  TLGNA+RR L+++  GA++ A++I
Sbjct: 1   MKQFVRPEFI--LLKEGQDKNYGKFSVSPLERGFGITLGNAIRRTLLAATPGASVYAIKI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMS-----GDSHKRVTIFKRGPGVVTAGDIQ 120
            G  HE +SI G+ E++T IILNIK + L++       D   ++ I     G V AGD++
Sbjct: 59  AGATHEFTSIPGIIENVTKIILNIKQLVLRIDTSIYGDDEVVQLKIRSDIQGPVYAGDLE 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSP 179
               +EVLN D +I  +    ++ + L      GY   K ++ E N   G+ITID+ YSP
Sbjct: 119 LPAGVEVLNQDLLIATISEGGILDLVLYAKNSRGYKTFKDNKNEKNIEPGMITIDSNYSP 178

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I KV+Y+V+SA+ G+ +D +KL + + TDGSIT  D++++AS+IL   L  FI+      
Sbjct: 179 IIKVAYSVDSAKIGRAIDLEKLELEVTTDGSITAIDAISIASKILVAHLEFFIDLNREIS 238

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            ++  +   +   +  L + VEEL+ + RS NCL+   I  + +L+ + E ++  + N G
Sbjct: 239 VLE--VIGVNQTDDKELDRTVEELDFTQRSLNCLKRAGINTLRELVTKNEDEIGSIRNLG 296

Query: 300 RKSLVEIKGVLGTMGLFL 317
           RKSL EIK  + ++GL  
Sbjct: 297 RKSLKEIKDKVASLGLAF 314


>gi|307697293|gb|ADN86101.1| RNA polymerase alpha subunit [Chasmanthium latifolium]
          Length = 339

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 92/330 (27%), Positives = 162/330 (49%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGNVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIVGIEESIQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY       +++   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLREPIDFCIELQIKRDRGYHTELRKNSQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGSSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLLTFQKRFTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           R+ +F    + + K +  T+   L ++LP 
Sbjct: 308 RIDSFR---MEDGKLIWDTLEKHLPIDLPQ 334


>gi|260677450|ref|YP_003208218.1| RNA polymerase alpha subunit [Coix lacryma-jobi]
 gi|209361388|gb|ACI43303.1| RNA polymerase alpha subunit [Coix lacryma-jobi]
          Length = 339

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 93/330 (28%), Positives = 163/330 (49%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LEWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGNVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIVGIEESIQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY       +++   G   IDA++ P++ V+Y++ S
Sbjct: 132 TTQPIANLREPIDFCIELQIKRDRGYHTELRKNSQD---GSYPIDAVFMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    FI+ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFIHTEEEGTSFEENKNRLT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLLTFQKRFTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRSNIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           R+ +F    + + K +  T+   L ++LP 
Sbjct: 308 RINSFR---MEDGKLIWDTLEKHLPIDLPK 334


>gi|294782963|ref|ZP_06748289.1| DNA-directed RNA polymerase, alpha subunit [Fusobacterium sp.
           1_1_41FAA]
 gi|294481604|gb|EFG29379.1| DNA-directed RNA polymerase, alpha subunit [Fusobacterium sp.
           1_1_41FAA]
          Length = 342

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 113/310 (36%), Positives = 185/310 (59%), Gaps = 7/310 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I   +E   +   + EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GV+ E + + G
Sbjct: 29  ITEVKESNYKGQFVVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVMSEFTVMDG 88

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V E +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ VIC +
Sbjct: 89  VKEAVTEIILNVKEIVVKAESSGERRMTLSVKGPKVVKAADIVADIGLEIVNPEQVICTV 148

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D
Sbjct: 149 TTDRTLDMEFLVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRITD 208

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI-------NFEEPKKEVKEDINVKSL 250
           +DKL++ ++TDGSI   D+++ A  +L+  L  F+       N  +  +E+ E+     +
Sbjct: 209 FDKLTLNVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRDEIEEIIEEPIDIQV 268

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +
Sbjct: 269 IDDKSHDMKIEELDLTVRSFNCLKKAGIEDVSQLASLSLNELLKIKNLGKKSLDEILEKM 328

Query: 311 GTMGLFLGMN 320
             +G  L  N
Sbjct: 329 KDLGYDLEKN 338


>gi|257463991|ref|ZP_05628376.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp. D12]
 gi|317061513|ref|ZP_07925998.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp. D12]
 gi|313687189|gb|EFS24024.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp. D12]
          Length = 314

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 115/303 (37%), Positives = 186/303 (61%), Gaps = 6/303 (1%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
           +I   +E   +   + EPL RG+ HTLGNALRRVL+SS+ GAAI  ++I+GVL E S + 
Sbjct: 12  HITEVRESAFKGQFVVEPLYRGYGHTLGNALRRVLLSSIPGAAIKGIRIEGVLSEFSVMD 71

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV E +T+IILN+K I +K      +++T+  +GP VVTA DI     +E++NP+  IC 
Sbjct: 72  GVKEAVTEIILNVKEIVVKSETAGERKMTLSVKGPKVVTAADIIPDIGLEIINPEQEICT 131

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +  D  + +E  V  G G+V ++    +   +  I +DA+Y+PI+KVSY ++    G++ 
Sbjct: 132 ITTDRSLDIEFLVDTGEGFVVSEEIERDGWVVDYIAVDAIYTPIRKVSYEIQDTMVGRMT 191

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKSLPF 252
           D+DKL+++++TDGSI   D+++ A  +L+  L  F+      E  + EV+E++  +S   
Sbjct: 192 DFDKLTLSVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRLEVEEEMENQSSSM 251

Query: 253 --NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +  L  K+EEL+L+VRS NCL+   I  +G L + +  ++L++ N GRKSL EI   +
Sbjct: 252 KDDINLNIKIEELDLTVRSFNCLKKAGIEEVGQLSKLSMNELLKIKNLGRKSLDEILEKM 311

Query: 311 GTM 313
             +
Sbjct: 312 KEL 314


>gi|331703690|ref|YP_004400377.1| DNA directed RNA polymerase subunit alpha [Mycoplasma mycoides
           subsp. capri LC str. 95010]
 gi|256384042|gb|ACU78612.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma mycoides
           subsp. capri str. GM12]
 gi|256384874|gb|ACU79443.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma mycoides
           subsp. capri str. GM12]
 gi|296455853|gb|ADH22088.1| DNA-directed RNA polymerase, alpha subunit [synthetic Mycoplasma
           mycoides JCVI-syn1.0]
 gi|328802245|emb|CBW54399.1| DNA directed RNA polymerase alpha chain [Mycoplasma mycoides subsp.
           capri LC str. 95010]
          Length = 317

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 113/318 (35%), Positives = 182/318 (57%), Gaps = 10/318 (3%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
            ++ ++P  I  ++   +++N       PL RGF  TLGNA+RR L+++  GA++ A++I
Sbjct: 1   MKQFVRPEFI--LLKEGQDKNYGKFSVSPLERGFGITLGNAIRRTLLAATPGASVYAIKI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMS-----GDSHKRVTIFKRGPGVVTAGDIQ 120
            G  HE +SI G+ E++T IILNIK + LK+       D   ++ I     G V AGD+ 
Sbjct: 59  AGATHEFTSIPGIIENVTKIILNIKQLVLKIDTSIYSDDEVVQLRIRSDIQGPVYAGDLD 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSP 179
               +E+LN D +I  +    V+ + L      GY   K ++ E N   G+ITID+ YSP
Sbjct: 119 IPAGVEILNKDLLIATISEGGVLDLVLYAKNSRGYKTFKDNKNEKNIEPGMITIDSNYSP 178

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I KV+Y+V+SA+ G+ +D +KL + + TDGSIT  D++++ASRIL   L  FI+      
Sbjct: 179 IIKVAYSVDSAKIGRAIDLEKLELEVTTDGSITAIDAISIASRILVAHLEFFIDLNREIS 238

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            ++     ++   +  L + VEEL+ + RS NCL+   I  + +L+ + E ++  + N G
Sbjct: 239 VLEVIGTNQTD--DKELDRTVEELDFTQRSLNCLKRAGINTLRELVSKNEDEIGSIRNLG 296

Query: 300 RKSLVEIKGVLGTMGLFL 317
           RKSL EIK  + ++GL  
Sbjct: 297 RKSLKEIKDKVASLGLAF 314


>gi|166154722|ref|YP_001654840.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           434/Bu]
 gi|166155597|ref|YP_001653852.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
 gi|301335996|ref|ZP_07224240.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           L2tet1]
 gi|238687389|sp|B0B881|RPOA_CHLT2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|238687487|sp|B0BCE6|RPOA_CHLTB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|165930710|emb|CAP04207.1| DNA-directed RNA polymerase alpha chain [Chlamydia trachomatis
           434/Bu]
 gi|165931585|emb|CAP07161.1| DNA-directed RNA polymerase alpha chain [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
          Length = 377

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 124/354 (35%), Positives = 190/354 (53%), Gaps = 24/354 (6%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +K + +E  V G   +     +A+PL +G  HTLG+ALRR L+  L   AI +  + G
Sbjct: 17  ESVKMSPVEGAVGGI--DKVARFVADPLEKGMGHTLGSALRRALLIGLEAPAIVSFSMTG 74

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK---------RVTIFKRG-------- 110
           VLHE  +++G+ ED+T+I+LN+KG  LK                R TI            
Sbjct: 75  VLHEYMAVEGIIEDVTNIVLNLKGSLLKKYPLQDCEGGRCSQKLRATISVDASDLAAAGG 134

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
              VT GD+      E +NP+HVI  +     + + L V+ G GY P++    E   +  
Sbjct: 135 QKEVTLGDLLQEGTFEAVNPEHVIFTVTRPMQLEVMLRVAFGRGYSPSERIVLEERGMNE 194

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +  +++VA A++IL     +
Sbjct: 195 IVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLVLQVETDGRVAPKEAVAFATQILSKHFSV 254

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLK---KVEELELSVRSTNCLRGENIVYMGDLIQR 287
           F   +E +   +E I+V+    +  L K    + E+ELSVRSTNCL   NI  +G+L+  
Sbjct: 255 FEKMDEKRIVFEEAISVEKENKDDILHKLVLGINEIELSVRSTNCLSNANIETIGELVIM 314

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
            E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 315 PEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYAEK 368


>gi|50346815|ref|YP_053186.1| RNA polymerase alpha subunit [Nymphaea alba]
 gi|68053159|sp|Q6EW20|RPOA_NYMAL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|50250360|emb|CAF28626.1| RNA polymerase alpha subunit [Nymphaea alba]
          Length = 341

 Score =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 81/328 (24%), Positives = 161/328 (49%), Gaps = 26/328 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        +  PL +G A T+G A+RR L+  L G  IT  + D V
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFVLSPLMKGQADTIGIAMRRALLGELEGTCITRAKSDKV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S++ G+ E + +I++N+K +  +         +I  RGP  VTA DI +   +E++
Sbjct: 71  PHEYSTVVGIEESVHEILMNLKKMVFRSDLYGTLDASICVRGPRHVTAQDIISPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + +EL + +G GY     +  ++   G   IDA+  P++  ++++ 
Sbjct: 131 DTTQHIAVLTEPVDLCIELKIERGRGYCTRTQNNYQD---GSYPIDAVSMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP--KKEVKEDIN 246
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    + +++++ 
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEQDINRNMEDNLK 246

Query: 247 VKSLPFNPALL-------------KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
             S+PF                    +++LEL  R+ NCL+  NI  + DL+ +++ D++
Sbjct: 247 RASVPFFAFDDGLDNIKREIILKRIFIDQLELPPRTYNCLKRSNIHTLLDLLSKSQEDLM 306

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + ++K +   +     ++L
Sbjct: 307 RIEHFR---VEDVKQIFDILQKGFTIDL 331


>gi|121720645|ref|YP_001001566.1| RNA polymerase alpha subunit [Nuphar advena]
 gi|69215822|gb|AAZ03867.1| RNA polymerase alpha chain [Nuphar advena]
 gi|84682236|gb|ABC60490.1| RNA polymerase alpha subunit [Nuphar advena]
          Length = 336

 Score =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 80/326 (24%), Positives = 159/326 (48%), Gaps = 24/326 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        +  PL +G A T+G A+RR L+  L G  IT  + D V
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFVLSPLMKGQADTIGIAMRRALLGELEGTCITRAKSDKV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I  +         +I  RGP  VTA DI +   +E++
Sbjct: 71  PHEYSTIVGIEESVHEILMNLKKIVFRSDLYGTLDASICVRGPRHVTAQDIISPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + +EL + +G GY     +  ++   G   IDA+  P++  ++++ 
Sbjct: 131 DTTQHIAILTEPVDLCIELKIERGRGYCMRTPNNYQD---GSYPIDAVSMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    +++++   
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEQDINIEDNLKRA 246

Query: 249 SLPFNPALL-------------KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           ++PF                    +++ EL  R+ NCL+  NI  + +L+ +++ D++R+
Sbjct: 247 TVPFFTFHDGLDNMKREIILKRIFIDQSELPPRTYNCLKKSNIHTLLNLLSKSQEDLMRI 306

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNL 321
            +F    + ++K +   +     ++L
Sbjct: 307 EHFR---VEDVKQIFDILQKGFTIDL 329


>gi|48478801|ref|YP_024408.1| RNA polymerase alpha subunit [Saccharum hybrid cultivar SP-80-3280]
 gi|50812559|ref|YP_054661.1| RNA polymerase alpha subunit [Saccharum officinarum]
 gi|68053147|sp|Q6ENT2|RPOA_SACOF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|75261480|sp|Q6L370|RPOA_SACHY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|48478703|gb|AAT44723.1| RNA polymerase alpha chain [Saccharum hybrid cultivar SP80-3280]
 gi|49659543|dbj|BAD27324.1| RNA polymerase alpha subunit [Saccharum hybrid cultivar NCo 310]
          Length = 339

 Score =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 93/330 (28%), Positives = 163/330 (49%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LEWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFWNVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIVGIEESIQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY       +++   G   IDA++ P++ V+Y++ S
Sbjct: 132 TTQPIANLREPVDFCIELQIKRDRGYHTELRKNSQD---GSYPIDAVFMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    FI+ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFIHTEEEGTSFEENKNRLT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLLTFQKRFTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           R+ +F    + + K +  T+   L ++LP 
Sbjct: 308 RINSFR---MEDGKLIWDTLEKHLPIDLPK 334


>gi|161513438|emb|CAP16862.1| DNA-directed RNA polymerase subunit alpha [Pediococcus damnosus]
          Length = 234

 Score =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 102/234 (43%), Positives = 154/234 (65%), Gaps = 2/234 (0%)

Query: 28  TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIIL 87
              + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IIL
Sbjct: 1   GKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIIL 60

Query: 88  NIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           NIK ++LK+  D  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         L
Sbjct: 61  NIKKVSLKIESDDEKSLEINVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAVL 120

Query: 148 TVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           T   G GYV A  ++   ++ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ +
Sbjct: 121 TADTGRGYVSADENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDV 180

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
            TDGSI+  ++ +L+++IL + L +F+N  +  ++ +  +  +       L   
Sbjct: 181 WTDGSISPSEATSLSAKILTEHLALFVNLTDEAQDAEIMVEKEETHKEKMLEMS 234


>gi|254302866|ref|ZP_04970224.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium nucleatum
           subsp. polymorphum ATCC 10953]
 gi|148323058|gb|EDK88308.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium nucleatum
           subsp. polymorphum ATCC 10953]
          Length = 326

 Score =  268 bits (685), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 113/310 (36%), Positives = 185/310 (59%), Gaps = 7/310 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I   +E   +   I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + G
Sbjct: 13  ITEVKESNYKGQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDG 72

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V E +T+IILN+K I +K      +R+++  +GP VV A DI     +E++NP+ +IC +
Sbjct: 73  VKEAVTEIILNVKEIVVKAESSGERRMSLSIKGPKVVKAADIVADIGLEIVNPEQIICTV 132

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D
Sbjct: 133 TTDRTLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTD 192

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI-------NFEEPKKEVKEDINVKSL 250
           +DKL++ ++TDGSI   D+++ A  +L+  L  F+       N  +  +E+ E+     +
Sbjct: 193 FDKLTLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEMIEEPMDIQV 252

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +
Sbjct: 253 IDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKM 312

Query: 311 GTMGLFLGMN 320
             +G  L  N
Sbjct: 313 KDLGYDLEKN 322


>gi|11467223|ref|NP_043055.1| RNA polymerase alpha subunit [Zea mays]
 gi|1173146|sp|P09562|RPOA_MAIZE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|902253|emb|CAA60317.1| RNA polymerase alpha subunit [Zea mays]
          Length = 339

 Score =  268 bits (685), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 90/330 (27%), Positives = 162/330 (49%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LEWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGNVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIVGIEESIQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +   Y       +++   G   IDA++ P++ V+Y++ S
Sbjct: 132 TTQPIANLREPVDFCIELQIKRDRAYHTELRKNSQD---GSYPIDAVFMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTSFEENKNRLT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLLTFQKRFTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++ +F    + + K +  T+   L ++LP 
Sbjct: 308 QINSFR---MEDGKLIWDTLEKHLPIDLPK 334


>gi|99024202|dbj|BAE94567.1| plastid DNA-dependent RNA polymerase subunit alpha [Takakia
           lepidozioides]
          Length = 341

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 82/331 (24%), Positives = 158/331 (47%), Gaps = 25/331 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +     + +     P   G A T+G A+RR L+  + G  IT  +   V 
Sbjct: 13  LQWRCVES-RVDSARLHYSRFAISPFRSGQASTVGIAMRRALLGEVEGTCITCAEFKRVT 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + D+++N+  I L+      ++  I   GP  VTA DI     +++++
Sbjct: 72  HEYSTILGIQESVHDVLINLGEIVLRSDSYETQKAFISILGPKKVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  +     + +EL + K  GY      ++ +   G   +DA++ PI+ V+Y+V S
Sbjct: 132 TTQYIATVXKAIHLDIELKIEKDFGYRIEDPIKSAD---GNFPVDAVFMPIRNVNYSVHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP------KKEVKE 243
              G     + L + I T+GS+T ++++  ASR L +    F++ E+       K   + 
Sbjct: 189 FENGNET-QEILFLEIWTNGSVTPKEALYEASRSLINLFIPFLHAEKKEFIYGLKNTYES 247

Query: 244 DINVKSLPFNPALLKK-----------VEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +++  S P   A + +           +++LEL  R+ NC +  N   + DL+  ++ D+
Sbjct: 248 NMSYFSSPSLSADIDEMTKGVTFKHIFIDQLELPARAYNCXKRVNXHTISDLLNYSQDDL 307

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ NFG+KS+ ++   L  +     +N P 
Sbjct: 308 MKIKNFGKKSVEQV---LEALQKRFSINXPK 335


>gi|58758777|gb|AAW81780.1| RNA polymerase alpha subunit [Dendroligotrichum dendroides]
          Length = 340

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 89/342 (26%), Positives = 160/342 (46%), Gaps = 27/342 (7%)

Query: 1   MIQKNWQ---ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRG 57
           MIQ       + ++   +E  V  +     +     P   G A+T+G A+RR L+  + G
Sbjct: 1   MIQNEISISAQALQWRCVESKVDSERLH-YSRFAISPFRCGQANTVGIAMRRALLGEIEG 59

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
             IT  +   V HE S+I G+ E   DI++N+K I LK +    ++  +   GP  +TA 
Sbjct: 60  TCITCARSKKVTHEYSTIVGIQESAHDILINLKEIVLKSNSYETQKAFLSILGPKKITAQ 119

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI     +++++    I  +     + +EL + K  GY      ++ +   G  +IDA++
Sbjct: 120 DIILPPSVKIIDTTQYIATITKPIHLDIELEIDKDCGYRIXDSVKSID---GYFSIDAIF 176

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
            PI+  +Y+V S  E      + L + I T+GSIT ++++  ASR L D    F++ E+ 
Sbjct: 177 MPIRNANYSVHSF-ENNNKIQEILFIEIWTNGSITPKEALYEASRSLIDLFIPFLHTEKK 235

Query: 238 KKEVKEDINVKSLPFN----------------PALLKKVEELELSVRSTNCLRGENIVYM 281
           +         KS   +                      +++LEL  R+ NCL+  N+  +
Sbjct: 236 ETINGLKTEYKSNDMSDFSSFSPLADKLTKEIKFKHIFIDQLELPARAYNCLKRVNVHPI 295

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            DL+   + D +++ NFG+KS+ ++   L  +     +NLP+
Sbjct: 296 SDLLNYXQDDFMKIKNFGKKSVEQV---LEALQKQFSINLPE 334


>gi|189485112|ref|YP_001956053.1| DNA-directed RNA polymerase alpha chain [uncultured Termite group 1
           bacterium phylotype Rs-D17]
 gi|170287071|dbj|BAG13592.1| DNA-directed RNA polymerase alpha chain [uncultured Termite group 1
           bacterium phylotype Rs-D17]
          Length = 323

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 112/316 (35%), Positives = 182/316 (57%), Gaps = 5/316 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +L K   +  +      +      A P  RG+ HT+GN+LRR+L+SSL GAAIT+V+I G
Sbjct: 5   DLEKLRKL-ILDEKTATKFYGHFSAGPFERGYGHTIGNSLRRILLSSLEGAAITSVKIAG 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
             HE + +KGV ED+  I+LN+K I +K+  +  +++ +  +  G VTA DI+    +E+
Sbjct: 64  AFHEFAVLKGVKEDVAQIVLNLKRIKVKLHSEGPEKLYLKVKKAGTVTAKDIEANASVEI 123

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NP+  I N+D    + MEL  S G GYV A+  ++     G I +D+L+SPI KV+Y V
Sbjct: 124 MNPEQEIANIDNGTTLEMELEASLGKGYVLAEEMKSNGYSSGTIILDSLFSPIIKVNYEV 183

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R  Q L+YDKL + I TDGS++ +D++  ++ IL+  L +F +         E+++ 
Sbjct: 184 ENTRVEQTLNYDKLIIEIWTDGSVSPKDALMRSAEILRKILVIFTD----NAFKTEEVSA 239

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                +  L K V  +++SV++   L+   I  + DL++  E D+L   N  ++S  EIK
Sbjct: 240 DKEEQDGILGKPVSIMDISVKTLKSLKSAGIETVEDLVKIKEEDLLNFNNLSKRSCEEIK 299

Query: 308 GVLGTMGLFLGMNLPD 323
             +  +GL LGM + D
Sbjct: 300 NRVKELGLSLGMKIED 315


>gi|237804858|ref|YP_002889012.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           B/TZ1A828/OT]
 gi|231273158|emb|CAX10071.1| DNA-directed RNA polymerase alpha chain [Chlamydia trachomatis
           B/TZ1A828/OT]
          Length = 377

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 124/354 (35%), Positives = 190/354 (53%), Gaps = 24/354 (6%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +K + +E  V G   +     +A+PL +G  HTLG+ALRR L+  L   AI +  + G
Sbjct: 17  ESVKMSPVEGAVGGI--DKVARFVADPLEKGMGHTLGSALRRALLIGLEAPAIVSFSMTG 74

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK---------RVTIFKRG-------- 110
           VLHE  +++G+ ED+T+I+LN+KG  LK                R TI            
Sbjct: 75  VLHEYMAVEGIIEDVTNIVLNLKGSLLKKYPLQDCEGGRCSQKLRATISIDASDLAAAGG 134

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
              VT GD+      E +NP+HVI  +     + + L V+ G GY P++    E   +  
Sbjct: 135 QKEVTLGDLLQEGTFEAVNPEHVIFTVTRPMQLEVMLRVAFGRGYSPSERIVLEERGMNE 194

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +  +++VA A++IL     +
Sbjct: 195 IVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLVLQVETDGRVAPKEAVAFATQILSKHFSV 254

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLK---KVEELELSVRSTNCLRGENIVYMGDLIQR 287
           F   +E +   +E I+V+    +  L K    + E+ELSVRSTNCL   NI  +G+L+  
Sbjct: 255 FEKMDEKRIVFEEAISVEKENKDDILHKLVLGINEIELSVRSTNCLSNANIETIGELVIM 314

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
            E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 315 PEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYAEK 368


>gi|42561246|ref|NP_975697.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma mycoides
           subsp. mycoides SC str. PG1]
 gi|61215950|sp|Q6MSP9|RPOA_MYCMS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|42492744|emb|CAE77339.1| DNA-directed RNA polymerase alpha chain [Mycoplasma mycoides subsp.
           mycoides SC str. PG1]
 gi|301321162|gb|ADK69805.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma mycoides
           subsp. mycoides SC str. Gladysdale]
          Length = 317

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 112/318 (35%), Positives = 182/318 (57%), Gaps = 10/318 (3%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
            ++ ++P  I  ++   +++N       PL RGF  TLGNA+RR L+++  GA++ A++I
Sbjct: 1   MKQFVRPEFI--LLKEGQDKNYGKFSVSPLERGFGITLGNAIRRTLLAATPGASVYAIKI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMS-----GDSHKRVTIFKRGPGVVTAGDIQ 120
            G  HE +SI G+ E++T IILNIK + LK+       D   ++ I     G + AGD+ 
Sbjct: 59  AGATHEFTSIPGIIENVTKIILNIKQLVLKIDTSIYSDDEVVQLRIRSDIQGPIYAGDLD 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSP 179
               +E+LN D +I  +    V+ + L      GY   K ++ E N   G+ITID+ YSP
Sbjct: 119 IPAGVEILNKDLLIATISEGGVLDLVLYAKNSRGYKTFKDNKNEKNIEPGMITIDSNYSP 178

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I KV+Y+V+SA+ G+ +D +KL + + TDGSIT  D++++ASRIL   L  FI+      
Sbjct: 179 IIKVAYSVDSAKIGRAIDLEKLELEVTTDGSITAIDAISIASRILVAHLEFFIDLNREIS 238

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            ++     ++   +  L + VEEL+ + RS NCL+   I  + +L+ + E ++  + N G
Sbjct: 239 VLEVIGTNQTD--DKELDRTVEELDFTQRSLNCLKRAGINTLRELVSKNEDEIGSIRNLG 296

Query: 300 RKSLVEIKGVLGTMGLFL 317
           RKSL EIK  + ++GL  
Sbjct: 297 RKSLKEIKDKVASLGLAF 314


>gi|83319728|ref|YP_424634.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma capricolum
           subsp. capricolum ATCC 27343]
 gi|119366699|sp|Q2SRH9|RPOA_MYCCT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|83283614|gb|ABC01546.1| DNA-directed RNA polymerase, alpha chain [Mycoplasma capricolum
           subsp. capricolum ATCC 27343]
          Length = 317

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 111/318 (34%), Positives = 183/318 (57%), Gaps = 10/318 (3%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
            ++ ++P  I  ++   +++N       PL RGF  TLGNA+RR L+++  GA++ A++I
Sbjct: 1   MKQFVRPEFI--LLKEGQDKNYGKFSVSPLERGFGITLGNAIRRTLLAATPGASVYAIKI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMS-----GDSHKRVTIFKRGPGVVTAGDIQ 120
            G  HE +SI G+ E++T IILNIK + L++       D   ++ I     G V AGD++
Sbjct: 59  AGATHEFTSIPGIIENVTKIILNIKQLVLRIDTSIYSDDEVVQLKIRSDIQGPVYAGDLE 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSP 179
               +EVLN D +I  +    ++ + L      GY   K ++ E N   G+ITID+ YSP
Sbjct: 119 LPAGVEVLNQDLLIATISEGGILDLVLYAKNSRGYKTFKDNKNEKNIEPGMITIDSNYSP 178

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I KV+Y+V+SA+ G+ +D +KL + + TDGSIT  D++++AS+IL   L  FI+      
Sbjct: 179 IIKVAYSVDSAKIGRAIDLEKLELEVTTDGSITAIDAISIASKILVAHLEFFIDLNREIS 238

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            ++  +   +   +  L + VEEL+ + RS NCL+   I  + +L+ + E ++  + N G
Sbjct: 239 VLE--VIGVNQTDDKELDRTVEELDFTQRSLNCLKRAGINTLRELVTKNEDEIGSIRNLG 296

Query: 300 RKSLVEIKGVLGTMGLFL 317
           RKSL EIK  + ++GL  
Sbjct: 297 RKSLKEIKDKVASLGLAF 314


>gi|28261749|ref|NP_783263.1| RNA polymerase alpha subunit [Atropa belladonna]
 gi|41688712|sp|Q8S8V9|RPOA_ATRBE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|20068363|emb|CAC88076.1| RNA polymerase alpha subunit [Atropa belladonna]
          Length = 337

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 82/331 (24%), Positives = 160/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT V+ + V
Sbjct: 11  RTLQWKCVESRTDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRVKFEKV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +II+N+K I L+ +       ++  +GPG VTA DI     +E++
Sbjct: 71  PHEYSTITGIQESVHEIIMNLKEIVLRSNLYGTSEASVCVKGPGYVTAQDIILPPYVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L       + L + +  GY+       +N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDFCIGLQIERNRGYLIKT---PQNFQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN-- 246
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEDNLYLQDNQHTV 246

Query: 247 --------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                         +K+          +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 PLSPFTFHDKLAKLIKNNKKIALKSIFIDQSELPSRIYNCLKMSNIYTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F      +IK +LG +  +  ++L  
Sbjct: 307 MKIEHFRS---EDIKQILGILEKYFVIDLAK 334


>gi|291461038|ref|ZP_06026582.2| DNA-directed RNA polymerase, alpha subunit [Fusobacterium
           periodonticum ATCC 33693]
 gi|291379318|gb|EFE86836.1| DNA-directed RNA polymerase, alpha subunit [Fusobacterium
           periodonticum ATCC 33693]
          Length = 342

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 113/310 (36%), Positives = 185/310 (59%), Gaps = 7/310 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I   +E   +   + EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GV+ E + + G
Sbjct: 29  ITEVKESNYKGHFVVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVMSEFTVMDG 88

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V E +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ VIC +
Sbjct: 89  VKEAVTEIILNVKEIVVKAESSGERRMTLSVKGPKVVKAADIVADIGLEIVNPEQVICTV 148

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D
Sbjct: 149 TTDRTLDMEFLVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRITD 208

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI-------NFEEPKKEVKEDINVKSL 250
           +DKL++ ++TDGSI   D+++ A  +L+  L  F+       N  +  +E+ E+     +
Sbjct: 209 FDKLTLNVETDGSIEIRDAISYAVELLRLHLDPFLEIGNKMENLRDEIEEIIEEPIDIQV 268

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +
Sbjct: 269 IDDKSHDMKIEELDLTVRSFNCLKKAGIEDVSQLASLSLNELLKIKNLGKKSLDEILEKM 328

Query: 311 GTMGLFLGMN 320
             +G  L  N
Sbjct: 329 KDLGYDLEKN 338


>gi|19704618|ref|NP_604180.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium nucleatum
           subsp. nucleatum ATCC 25586]
 gi|19714918|gb|AAL95479.1| DNA-directed RNA polymerase alpha chain [Fusobacterium nucleatum
           subsp. nucleatum ATCC 25586]
          Length = 342

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 113/310 (36%), Positives = 185/310 (59%), Gaps = 7/310 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I   +E   +   I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + G
Sbjct: 29  ITEVKESNYKGQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDG 88

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V E +T+IILN+K I +K      +R+++  +GP VV A DI     +E++NP+ VIC +
Sbjct: 89  VKEAVTEIILNVKEIVVKAESSGERRMSLSIKGPKVVKAADIVADIGLEIVNPEQVICTV 148

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + +E  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D
Sbjct: 149 TTDRTLDIEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTD 208

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVK---SL 250
           +DKL++ ++TDGSI   D+++ A  +L+  L  F+      E  + +++E I       +
Sbjct: 209 FDKLTLNVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRDDIEEMIEEPMDIQV 268

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +
Sbjct: 269 IDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKM 328

Query: 311 GTMGLFLGMN 320
             +G  L  N
Sbjct: 329 KDLGYDLEKN 338


>gi|71056876|emb|CAH58993.1| DNA-directed RNA polymerase alpha chain [Enterococcus canis]
          Length = 235

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 105/235 (44%), Positives = 154/235 (65%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
             + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILN
Sbjct: 1   KFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILN 60

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           IKG+ LK+     K + I   GP  VTAGDI   +D+E+LN D  +C +   A     LT
Sbjct: 61  IKGLALKLYAQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLYLCTVSEGATFHARLT 120

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V  G GYV A  ++TE+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TD
Sbjct: 121 VKPGRGYVQADENKTEDMPIGVLPVDSIYTPVRRVNYQVENTRVGNRQDFDKLTMEIWTD 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
           GSI  +++++L+++IL + L +F+N  +  K  +  +  +       L   +EEL
Sbjct: 181 GSIIPQEALSLSAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEEL 235


>gi|170784739|ref|YP_001718655.1| RNA polymerase alpha subunit [Trachelium caeruleum]
 gi|156598871|gb|ABU85688.1| RNA polymerase alpha subunit [Trachelium caeruleum]
 gi|157267487|gb|ABV26480.1| RNA polymerase alpha subunit [Trachelium caeruleum]
          Length = 337

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 77/329 (23%), Positives = 162/329 (49%), Gaps = 25/329 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A  +G A+RR L+  L G  IT  + + +
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFILSPLLKGQADIIGIAMRRALLGELEGTCITRAKSEKL 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S++ G+ E + +I++N+K I L+ +        I  +GPG VTA DI +   +E++
Sbjct: 71  PHEYSTLVGIQESVHEILMNLKEIVLRSNLYGTCDAAICVKGPGYVTAQDIISPPYVEII 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY+       ++   G   IDA++ P++ V++++ 
Sbjct: 131 DNTQHIASLTEPIELCIGLQIERNRGYLIKTAKNFQD---GSYPIDAVFMPVRNVNHSIY 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G    ++ L + I T+GS+T ++++  A+R L D    F++ EE   +++++ ++ 
Sbjct: 188 SYGTG-NDKHEILFLEIWTNGSLTPKEALHEAARNLIDLFIPFLHTEEENLDLEDNQHML 246

Query: 249 SLPFN--------------PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
               +                    +++ EL  R  NCL+  NI  + DL+  ++ D+++
Sbjct: 247 PFRPSILPEKFVKIKNKKISLKSIFIDQSELPPRVYNCLKRSNIYTLLDLLNNSQEDLMK 306

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           + +F    + ++K +L  +    G++LP 
Sbjct: 307 IEHFR---VEDLKRILDILEKNFGIDLPQ 332


>gi|194132131|gb|ACF33385.1| RNA polymerase alpha subunit [Gonystylus bancanus]
          Length = 329

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 82/320 (25%), Positives = 157/320 (49%), Gaps = 21/320 (6%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RR L+  + G  IT  + + + 
Sbjct: 15  LQWKCVES-RIDSKHLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIP 73

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S I G+ E + +I++N+K I L+ +    +   I  +GPG VTA DI     +E+++
Sbjct: 74  HEYSIIAGIQESVHEILMNLKEIVLRSNLYGTRNAFICAKGPGYVTAQDIILPPSVEIVD 133

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I +L     + + L + +  GY     +   +   G   ID ++ P++ V++++ S
Sbjct: 134 NTQHIASLTEPIDLCIGLQIERNRGYGIKTPNNFHD---GSYPIDVVFMPVRNVNHSIHS 190

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++   +  +
Sbjct: 191 YGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENSHLENSQHKVT 249

Query: 250 LPFNPALLKK----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           LPF P   K                 +++ EL  R  NCL+  NI  + DL+ +++ D++
Sbjct: 250 LPFFPFHDKLTKLRKKKKEIALKYFFIDQSELPPRIYNCLKTSNIHTLFDLLNKSQEDLM 309

Query: 294 RMANFGRKSLVEIKGVLGTM 313
           ++ +F R+ + +I G++   
Sbjct: 310 KIEHFHREDVKQILGIIENK 329


>gi|159106895|ref|YP_001531313.1| RNA polymerase alpha subunit [Lolium perenne]
 gi|172048163|sp|A8Y9B8|RPOA_LOLPR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|158934429|emb|CAO86007.1| RNA polymerase alpha subunit [Lolium perenne]
          Length = 341

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 91/330 (27%), Positives = 160/330 (48%), Gaps = 26/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  I   +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCIARAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TSQPIANLTEPIDFCIELQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP------------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
            P                    P     +++LEL  R+ NCL+  NI  + DL+ +TE D
Sbjct: 248 PPLFTFQKRLTNLNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEED 307

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           ++R+ +F    + + K +  T+  +L ++L
Sbjct: 308 LMRIDSFH---MEDGKQIWDTLEKYLPIDL 334


>gi|76789244|ref|YP_328330.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           A/HAR-13]
 gi|90110832|sp|Q3KLJ0|RPOA_CHLTA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|76167774|gb|AAX50782.1| DNA-directed RNA polymerase alpha chain [Chlamydia trachomatis
           A/HAR-13]
          Length = 377

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 124/354 (35%), Positives = 190/354 (53%), Gaps = 24/354 (6%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +K + +E  V G   +     +A+PL +G  HTLG+ALRR L+  L   AI +  + G
Sbjct: 17  ESVKMSPVEGAVGGI--DKVARFVADPLEKGMGHTLGSALRRALLIGLEAPAIVSFSMTG 74

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK---------RVTIFKRG-------- 110
           VLHE  +++G+ ED+T+I+LN+KG  LK                R TI            
Sbjct: 75  VLHEYMAVEGIIEDVTNIVLNLKGSLLKKYPLQDCEGGRCSQKLRATISIDASDLAAAGG 134

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
              VT GD+      E +NP+HVI  +     + + L V+ G GY P++    E   +  
Sbjct: 135 QKEVTLGDLLQEGTFEAVNPEHVIFTVTRPMQLEVMLRVAFGRGYSPSERIVLEERGMNE 194

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +  +++VA A++IL     +
Sbjct: 195 IVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLVLQVETDGRVAPKEAVAFATQILSKHFSV 254

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLK---KVEELELSVRSTNCLRGENIVYMGDLIQR 287
           F   +E +   +E I+V+    +  L K    + E+ELSVRSTNCL   NI  +G+L+  
Sbjct: 255 FEKMDEKRIVFEEAISVEKENKDDILHKLVLGINEIELSVRSTNCLSNANIETIGELVIM 314

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
            E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 315 PEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYAEK 368


>gi|15605236|ref|NP_220022.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           D/UW-3/CX]
 gi|237802936|ref|YP_002888130.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           B/Jali20/OT]
 gi|255311325|ref|ZP_05353895.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           6276]
 gi|255317626|ref|ZP_05358872.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           6276s]
 gi|255348884|ref|ZP_05380891.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           70]
 gi|255503424|ref|ZP_05381814.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           70s]
 gi|255507102|ref|ZP_05382741.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           D(s)2923]
 gi|290463292|sp|P0CE08|RPOA_CHLTR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|3328944|gb|AAC68108.1| RNA Polymerase Alpha [Chlamydia trachomatis D/UW-3/CX]
 gi|231274170|emb|CAX10964.1| DNA-directed RNA polymerase alpha chain [Chlamydia trachomatis
           B/Jali20/OT]
 gi|289525552|emb|CBJ15030.1| DNA-directed RNA polymerase alpha chain [Chlamydia trachomatis
           Sweden2]
 gi|296435112|gb|ADH17290.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           E/150]
 gi|296436040|gb|ADH18214.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           G/9768]
 gi|296436968|gb|ADH19138.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           G/11222]
 gi|296437901|gb|ADH20062.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           G/11074]
 gi|296438832|gb|ADH20985.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           E/11023]
 gi|297140401|gb|ADH97159.1| DNA-directed RNA polymerase subunit alpha [Chlamydia trachomatis
           G/9301]
          Length = 377

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 124/354 (35%), Positives = 190/354 (53%), Gaps = 24/354 (6%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +K + +E  V G   +     +A+PL +G  HTLG+ALRR L+  L   AI +  + G
Sbjct: 17  ESVKMSPVEGAVGGI--DKVARFVADPLEKGMGHTLGSALRRALLIGLEAPAIVSFSMTG 74

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK---------RVTIFKRG-------- 110
           VLHE  +++G+ ED+T+I+LN+KG  LK                R TI            
Sbjct: 75  VLHEYMAVEGIIEDVTNIVLNLKGSLLKKYPLQDCEGGRCSQKLRATISIDASDLAAAGG 134

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
              VT GD+      E +NP+HVI  +     + + L V+ G GY P++    E   +  
Sbjct: 135 QKEVTLGDLLQEGTFEAVNPEHVIFTVTRPMQLEVMLRVAFGRGYSPSERIVLEERGMNE 194

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +  +++VA A++IL     +
Sbjct: 195 IVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLVLQVETDGRVAPKEAVAFATQILSKHFSV 254

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLK---KVEELELSVRSTNCLRGENIVYMGDLIQR 287
           F   +E +   +E I+V+    +  L K    + E+ELSVRSTNCL   NI  +G+L+  
Sbjct: 255 FEKMDEKRIVFEEAISVEKENKDDILHKLVLGINEIELSVRSTNCLSNANIETIGELVIM 314

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
            E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 315 PEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYAEK 368


>gi|115604965|ref|YP_784418.1| RNA polymerase alpha subunit [Drimys granadensis]
 gi|122164409|sp|Q06GW5|RPOA_DRIGR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|112032693|gb|ABH88328.1| RNA polymerase alpha subunit [Drimys granadensis]
          Length = 339

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 79/331 (23%), Positives = 158/331 (47%), Gaps = 25/331 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A  +G A+RR L+  + G  IT  + D +
Sbjct: 11  RTLQWKCVESRTDSKRLSYGRFILSPLMKGQADMIGIAMRRALLGEIEGTCITRAKSDKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E +  I++N+K I L+ +       +IF RGP  VTA DI +   ++++
Sbjct: 71  PHEYSTIVGIEESVHQILMNLKEIVLRSNLYGTCDASIFVRGPRCVTAQDIISPPSVKMV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY     +  ++     I I+A+  P++  ++++ 
Sbjct: 131 DTTQHIASLTEPIDLCIGLQIERDRGYRMKTPNNDQD-GSYPIPIEAVSMPVRNANHSIH 189

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  AS  L D    F++ EE    +++ +N  
Sbjct: 190 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASHNLIDLFIPFLHGEEEDINLEDSLNRG 248

Query: 249 SLPFN----------------PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LPF                       +++ EL  R+ NCL+  NI  + DL+  ++ D+
Sbjct: 249 TLPFFTFQDKLANLRKNKKAIALECIFIDQSELPPRTYNCLKRSNIHTLLDLLSNSQEDL 308

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +R+ +     + ++K +L  +     ++LP 
Sbjct: 309 MRIEHLR---IEDVKRILDILQKHFTIDLPK 336


>gi|22257019|sp|Q8RE44|RPOA_FUSNN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 326

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 113/310 (36%), Positives = 185/310 (59%), Gaps = 7/310 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I   +E   +   I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + G
Sbjct: 13  ITEVKESNYKGQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDG 72

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V E +T+IILN+K I +K      +R+++  +GP VV A DI     +E++NP+ VIC +
Sbjct: 73  VKEAVTEIILNVKEIVVKAESSGERRMSLSIKGPKVVKAADIVADIGLEIVNPEQVICTV 132

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + +E  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D
Sbjct: 133 TTDRTLDIEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTD 192

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVK---SL 250
           +DKL++ ++TDGSI   D+++ A  +L+  L  F+      E  + +++E I       +
Sbjct: 193 FDKLTLNVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRDDIEEMIEEPMDIQV 252

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +
Sbjct: 253 IDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKM 312

Query: 311 GTMGLFLGMN 320
             +G  L  N
Sbjct: 313 KDLGYDLEKN 322


>gi|118614523|ref|YP_899439.1| RNA polymerase alpha subunit [Sorghum bicolor]
 gi|125987638|sp|A1E9V6|RPOA_SORBI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|118201157|gb|ABK79527.1| RNA polymerase alpha subunit [Sorghum bicolor]
          Length = 339

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 93/330 (28%), Positives = 162/330 (49%), Gaps = 27/330 (8%)

Query: 14  NIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +E+  +    ++        I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 12  KLEWKCVESRVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGNVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIVGIEESIQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY       +++   G   IDA++ P++ V+Y++ S
Sbjct: 132 TAQPIANLREPIDFCIELQIKRDRGYHTELRKNSQD---GSYPIDAVFMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    FI+ EE     +E  N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFIHTEEEGTSFEESKNRLT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLLTFQKRFTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           R+ +F    + + K +  T+   L ++LP 
Sbjct: 308 RINSFR---MEDGKLIWDTLEKHLPIDLPK 334


>gi|328813983|gb|AEB52107.1| DNA-directed RNA polymerase alpha chain [Lactobacillus
           parabuchneri]
          Length = 244

 Score =  267 bits (683), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 114/244 (46%), Positives = 162/244 (66%), Gaps = 4/244 (1%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRR L+SSL G+A+T++QID VLHE S+IKGV ED+T IILN+K
Sbjct: 1   VVEPLERGYGTTLGNSLRRTLLSSLPGSAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVK 60

Query: 91  GINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
            I+LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT
Sbjct: 61  KISLKLDGPEDEEENLEIDVIGPADVTAGDIQADSDVTVLNPDLHIATVAEGATFHMRLT 120

Query: 149 VSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            +KG GYV A  ++      PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ + 
Sbjct: 121 ANKGRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDVW 180

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           TDGSIT  ++V+LA++IL + L MF++  +  K  +  +  +       L   +EEL+LS
Sbjct: 181 TDGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEKEETHKEKMLEMTIEELDLS 240

Query: 267 VRST 270
           VRS 
Sbjct: 241 VRSY 244


>gi|33862091|ref|NP_893652.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           subsp. pastoris str. CCMP1986]
 gi|41688638|sp|Q7UZW6|RPOA_PROMP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|33634309|emb|CAE19994.1| Bacterial RNA polymerase, alpha chain [Prochlorococcus marinus
           subsp. pastoris str. CCMP1986]
          Length = 312

 Score =  267 bits (683), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 95/305 (31%), Positives = 161/305 (52%), Gaps = 8/305 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + I++ +     +     +  PL RG A TLGN+LRRVLM  L G+A+TAV+I G+ HE 
Sbjct: 7   DRIDHQISDDRSQT-GTFLIGPLERGQATTLGNSLRRVLMGGLEGSAVTAVRISGINHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K +++  S    +   +   GP  V A DIQ  + +E+++ + 
Sbjct: 66  ATIPGVREDVLDILLNCKQLSINSSNPETEIGRLVVNGPMEVKANDIQFSSQVEIVDGEK 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P      E   I L+ IDA++ P+K+V++T++    
Sbjct: 126 PIATIQEGHNLELEIHVERGVGYRPVDRRNQETTAIDLLQIDAVFMPVKRVNFTIDETAV 185

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L+M + TDGS + +D++A A+  L +           ++        +   
Sbjct: 186 AEGATGRERLTMEVVTDGSTSPDDAIAEAANQLIELFQPLATVTMVEEI------PEEPE 239

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 240 PSPEAQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIS 304


>gi|81301600|ref|YP_398896.1| RNA polymerase alpha subunit [Nicotiana tomentosiformis]
 gi|90110851|sp|Q33C00|RPOA_NICTO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|80750959|dbj|BAE48035.1| RNA polymerase alpha subunit [Nicotiana tomentosiformis]
          Length = 337

 Score =  267 bits (683), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 83/330 (25%), Positives = 160/330 (48%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           +K   +E      +       I  PL +G A T+G A+RR L+  + G  IT V+ + V 
Sbjct: 13  LKWKCVESRT-DSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRVKSEKVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +       +I  +GPG VTA DI     +E+++
Sbjct: 72  HEYSTIMGIQESVHEILMNLKEIVLRSNLYGTSDASICVKGPGYVTAQDIILPPYVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I +L       + L + +  GY+    H  ++   G   IDA++ P++  ++++ S
Sbjct: 132 NTQHIASLTETIDFCIGLQIKRNRGYLIKTPHNFQD---GSYPIDAVFMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +   
Sbjct: 189 YGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHIEEDNLYLQDNQHTVP 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                        +K+          +++ EL  R  NCL+  NI  + DL+  ++ D++
Sbjct: 248 LSPFTFHDKLAKLIKNKKKIALKSIFIDQSELPSRIYNCLKMSNIYTLLDLLNNSQEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++ +F      ++K +LG +  +  ++L  
Sbjct: 308 KIEHFRS---EDVKQILGILEKYFVIDLAK 334


>gi|313183854|ref|YP_004021697.1| RNA polymerase alpha subunit [Prunus persica]
 gi|309321466|gb|ADO65007.1| RNA polymerase alpha subunit [Prunus persica]
          Length = 326

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 78/320 (24%), Positives = 155/320 (48%), Gaps = 24/320 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFILAPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +    +  +I  +GPG VTA DI     +E++
Sbjct: 71  PHEYSTIIGIQESVHEILMNLKEIVLRSNLYGTRNASICIKGPGYVTAQDIILPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I NL     + +EL + +  GY     +  ++   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIANLTEPINLCIELQIERNRGYRIKTPNNFQD---GSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S         + L + I T+GS+T ++++  ASR L D    F++ EE   +++ + +  
Sbjct: 188 SY-VNGNEKQEILFLEIWTNGSLTPKEALHDASRNLIDLFIPFLHAEEENLQLENNQHKV 246

Query: 249 SLP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP                        +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPLFTFHGRLAKQRKNKKEIALQYIFIDQSELFPRVYNCLKRSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGT 312
           +++ +F  + +  I  +L  
Sbjct: 307 MKIKHFRIEDVKHILNILEI 326


>gi|71056822|emb|CAH58966.1| DNA-directed RNA polymerase alpha chain [Enterococcus avium]
          Length = 245

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 108/243 (44%), Positives = 158/243 (65%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E+ +    + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED
Sbjct: 3   DEDRDYGQFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVRED 62

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +  IILNIKG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A
Sbjct: 63  VVQIILNIKGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGA 122

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
                LTV  G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL
Sbjct: 123 TFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKL 182

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           +M I TDGSI  +++++LA++IL + L +F+N  +  K  +  +  +       L   +E
Sbjct: 183 TMEIWTDGSIIAQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIE 242

Query: 262 ELE 264
           E +
Sbjct: 243 ERD 245


>gi|296329035|ref|ZP_06871541.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium nucleatum
           subsp. nucleatum ATCC 23726]
 gi|296153839|gb|EFG94651.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium nucleatum
           subsp. nucleatum ATCC 23726]
          Length = 342

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 113/310 (36%), Positives = 185/310 (59%), Gaps = 7/310 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I   +E   +   I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + G
Sbjct: 29  ITEVKESNYKGQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMDG 88

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V E +T+IILN+K I +K      +R+++  +GP VV A DI     +E++NP+ VIC +
Sbjct: 89  VKEAVTEIILNVKEIVVKAESSGERRMSLSIKGPKVVKAADIVADIGLEIVNPEQVICTV 148

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + +E  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ D
Sbjct: 149 TTDRALDIEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMTD 208

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVK---SL 250
           +DKL++ ++TDGSI   D+++ A  +L+  L  F+      E  + +++E I       +
Sbjct: 209 FDKLTLNVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRDDIEEMIEEPMDIQV 268

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   +
Sbjct: 269 IDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEKM 328

Query: 311 GTMGLFLGMN 320
             +G  L  N
Sbjct: 329 KDLGYDLEKN 338


>gi|165910449|gb|ABY73979.1| RNA polymerase alpha subunit [Cuscuta lupuliformis]
          Length = 335

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 83/331 (25%), Positives = 156/331 (47%), Gaps = 29/331 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G ALRR L++ + G  IT V+    
Sbjct: 11  RTLQWKCVESRTDSKRLYYGRFILSPLMKGQADTIGIALRRALLAEIEGTRITRVKFANA 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  +GPG VTA DI     +EV+
Sbjct: 71  SHEYSTIAGIQESVHEILMNLKEIVLRSNLYGTCDASISIKGPGYVTAEDIILPPHVEVV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + + L + +  GY    H   E+   G   IDA++ P++  ++++ 
Sbjct: 131 DSTQHIAWLMEPIDLCIGLKIERNRGYFLKTHANFED---GSYPIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV- 247
           S         + L + I T+GS+T ++++  ASR L D    F++ E+    +++     
Sbjct: 188 SYGNE---KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHIEKENLHLEDADRTI 244

Query: 248 ---------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                          K+          +++LE      NCL+  NI  + DL+  ++ D+
Sbjct: 245 PLSPFTVYDKVAKLRKNKKKLALESLFIDQLEFPPNIYNCLKKSNIFTLLDLLNNSQEDL 304

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F    L ++K +LG +G    ++LP 
Sbjct: 305 MKIEHFR---LEDVKQILGILGKHFALDLPK 332


>gi|317046205|ref|YP_004072494.1| RNA polymerase alpha subunit [Corynocarpus laevigata]
 gi|309252922|gb|ADO60342.1| RNA polymerase alpha subunit [Corynocarpus laevigata]
          Length = 331

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 80/325 (24%), Positives = 153/325 (47%), Gaps = 22/325 (6%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           +K   +E      +       I  PL +G A T+G A+R+ L+  + G  IT  + + + 
Sbjct: 13  LKWKCVES-RADSKRLYYGRFILSPLMKGQADTIGIAMRKALLGEIEGTCITRAKSEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I +N+K I L+ +    +  +I  +GPG VTA DI     +E+++
Sbjct: 72  HEYSTIVGIQESVHEIFMNLKEIVLRSNLYGTRDASICVKGPGYVTAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL     + +EL + +  GY     +  ++   G   IDA++ P++  ++++ S
Sbjct: 132 NTQHIANLTEPINLCIELQIERNRGYRIKTPNNFQD---GSYPIDAVFMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                    + L + I T+GS+T ++++  ASR L D    F++ EE    +K + +  +
Sbjct: 189 Y-VNGNEKQEILFLEIWTNGSLTPKEALYEASRNLIDFFIPFLHAEEENFHLKNNQHKVT 247

Query: 250 LPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           LP      +                 +++ EL  R  NCL+  NI  + DL+  +  D++
Sbjct: 248 LPLFTFHDRLAKLRKNKKEIALKYIFIDQSELPPRIYNCLKRSNIHTLLDLLNNSPDDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLG 318
           ++ +F  + +  I  +L  +     
Sbjct: 308 KIKHFRIEDVKHILDIL-EIEKHFA 331


>gi|313292082|gb|ADR51230.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
          Length = 241

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 108/234 (46%), Positives = 155/234 (66%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED
Sbjct: 6   DEEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVRED 65

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +  IILNIKG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  ICN+   A
Sbjct: 66  VAQIILNIKGLALKMYGDEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICNVSEGA 125

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
                LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL
Sbjct: 126 SFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKL 185

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           +M I TDGSI   ++++LA++I+ + L +F+N  +  K  +  +  +       
Sbjct: 186 TMEIWTDGSIEPLEAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 239


>gi|297748637|gb|ADI51183.1| DNA-directed RNA polymerase alpha chain [Chlamydia trachomatis
           D-EC]
 gi|297749517|gb|ADI52195.1| DNA-directed RNA polymerase alpha chain [Chlamydia trachomatis
           D-LC]
          Length = 394

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 124/354 (35%), Positives = 190/354 (53%), Gaps = 24/354 (6%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +K + +E  V G   +     +A+PL +G  HTLG+ALRR L+  L   AI +  + G
Sbjct: 34  ESVKMSPVEGAVGGI--DKVARFVADPLEKGMGHTLGSALRRALLIGLEAPAIVSFSMTG 91

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK---------RVTIFKRG-------- 110
           VLHE  +++G+ ED+T+I+LN+KG  LK                R TI            
Sbjct: 92  VLHEYMAVEGIIEDVTNIVLNLKGSLLKKYPLQDCEGGRCSQKLRATISIDASDLAAAGG 151

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
              VT GD+      E +NP+HVI  +     + + L V+ G GY P++    E   +  
Sbjct: 152 QKEVTLGDLLQEGTFEAVNPEHVIFTVTRPMQLEVMLRVAFGRGYSPSERIVLEERGMNE 211

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +  +++VA A++IL     +
Sbjct: 212 IVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLVLQVETDGRVAPKEAVAFATQILSKHFSV 271

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLK---KVEELELSVRSTNCLRGENIVYMGDLIQR 287
           F   +E +   +E I+V+    +  L K    + E+ELSVRSTNCL   NI  +G+L+  
Sbjct: 272 FEKMDEKRIVFEEAISVEKENKDDILHKLVLGINEIELSVRSTNCLSNANIETIGELVIM 331

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
            E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 332 PEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYAEK 385


>gi|157493277|gb|ABV58004.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 269

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 120/272 (44%), Positives = 183/272 (67%), Gaps = 8/272 (2%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
            EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG
Sbjct: 1   LEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKG 60

Query: 92  INLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVVRMELTV 149
           + +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L   +A + M + V
Sbjct: 61  LAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKV 120

Query: 150 SKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++
Sbjct: 121 ERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDME 180

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V++LEL+
Sbjct: 181 TNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELT 237

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 VRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 269


>gi|119662335|emb|CAJ33156.1| RNA polymerase alpha subunit [Lactobacillus paracasei subsp.
           paracasei]
          Length = 213

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 100/213 (46%), Positives = 148/213 (69%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
            EPL RG+  TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNIK 
Sbjct: 1   VEPLERGYGTTLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNIKK 60

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           + LKM+ D  K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV K
Sbjct: 61  LALKMNTDEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVKK 120

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GYV A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI
Sbjct: 121 GRGYVAADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           +  ++++LA++IL + L +F+N  +  K  +  
Sbjct: 181 SPREAISLAAKILTEHLDIFVNLTDEAKNAEIM 213


>gi|68124013|emb|CAJ01914.1| DNA-directed RNA polymerase alpha chain [Chrysanthemum x
           morifolium]
          Length = 335

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 82/330 (24%), Positives = 161/330 (48%), Gaps = 26/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E      +       I  PL +G A T+G A+RR L+  + G  IT  + + + 
Sbjct: 13  LQWKCVES-AADSKRPFYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFEKIS 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +       +I  RGPG VTA DI     +E+++
Sbjct: 72  HEYSTIMGIQESVHEILMNLKEIVLRSNLYGTCEASICVRGPGYVTAQDIILPPYVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L     + + L + K  GY+    +  ++   G   ID ++ P++  ++++ S
Sbjct: 132 NTQHIATLTEPIELVIGLQIEKNRGYLIKAPNTFQD---GSYPIDPVFMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV-- 247
              G   + + L + I T+GS+T ++++  ASR L D L  F++ +E    ++++ ++  
Sbjct: 189 YENG---NKEILFLEIWTNGSLTPKEALHEASRNLIDLLIPFLHTKEENLNLEDNQHMIP 245

Query: 248 --------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         K+          +++ EL  R  NCL+  NI  + DL+  ++ D++
Sbjct: 246 LPPFTFYDKLAKLTKNKKKMALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQDDLM 305

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +M +F    + ++K +LG +     ++LP 
Sbjct: 306 KMEHFH---IEDVKQILGILEKNFVIDLPK 332


>gi|58491826|gb|AAW78552.1| RNA polymerase alpha subunit [Sphagnum fimbriatum]
          Length = 338

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 88/327 (26%), Positives = 160/327 (48%), Gaps = 21/327 (6%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E  V  +           P   G A+T+G A+RR L+  + G  IT  + + V 
Sbjct: 14  LQWRCVESKVDSERLH-YGRFAISPFRSGQANTVGIAVRRALLGGVEGTCITRAKSEKVT 72

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           HE S+I G+ E + DI++N+K I LK   +    ++  +   GP  VTA DI     +EV
Sbjct: 73  HEYSTILGIQESVRDILINLKEIVLKSKSNSCETQKAFLSIFGPKEVTARDIIFPPSVEV 132

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           ++    I  L     + +EL + K  GY      ++ +   G  ++DA+++PI+  +Y+V
Sbjct: 133 IDTTQYIATLTKAIHLDIELKIEKDCGYRTQDSIKSAD---GYFSVDAVFTPIRNANYSV 189

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EPKKEVKEDIN 246
            S         + L + I T+GS+T ++++  ASR L D    F++ E E     K + N
Sbjct: 190 HSFENKNET-QEILFIEIWTNGSVTPKEALYEASRSLIDLFIPFLHAEKEEVMHDKNESN 248

Query: 247 VKSLPFNPALLKK----------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
                 +P+  K           +++LEL  R+ NCL+  ++  + DL+  ++ D++++ 
Sbjct: 249 TLHFSSSPSENKMEKEMTFKHIFIDQLELPARAYNCLKRVDVHTISDLLSYSQDDLMKIK 308

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           NFG+KS+ ++   L  +     + LP 
Sbjct: 309 NFGKKSVEQV---LEALQKRFSIKLPK 332


>gi|157363470|ref|YP_001470237.1| DNA-directed RNA polymerase subunit alpha [Thermotoga lettingae
           TMO]
 gi|172045986|sp|A8F4T9|RPOA_THELT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|157314074|gb|ABV33173.1| DNA-directed RNA polymerase, alpha subunit [Thermotoga lettingae
           TMO]
          Length = 332

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 114/328 (34%), Positives = 175/328 (53%), Gaps = 18/328 (5%)

Query: 8   ELIKPNNIEYIVL-GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           E + P  ++      + E      +  P+ +G+  T+GNALRRVL+SS+   AI  ++  
Sbjct: 3   EYVIPKKLKIEEERSETEYYYARYVLSPMEKGYGTTIGNALRRVLLSSIPSVAIVGIRFI 62

Query: 67  G--VLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTV 122
                HE  ++ GV ED+ +IILN+K I L+         ++T+ KRGPG +TA DI+  
Sbjct: 63  KPEKYHEFDTLPGVKEDILEIILNLKRIQLRADVPVRERVKMTVEKRGPGNLTAADIKVP 122

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
              E+ NP   I  LD +A +  EL    G G+VPA+    ++  IG I ID ++SP+ K
Sbjct: 123 AGFEIANPSLKIATLDEEADLFFELYAQAGKGFVPAQEM-DDHPEIGWIPIDGVFSPVMK 181

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN--------- 233
           V++ VESAR  +  DYDK+ + I T  +I   +++  A  IL + L +  +         
Sbjct: 182 VNFRVESARVEKRTDYDKMILEIWTKKTIFPNEALKRAVDILMNHLQIITDSLPEGMPPL 241

Query: 234 --FEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
                P  + +  +            KK++ELEL++RS NCLR + I  +GDL++RTE D
Sbjct: 242 TTEFVPISQEEVKVEQTVSEEEAVYSKKIDELELTIRSLNCLRRDKIETIGDLLKRTEED 301

Query: 292 MLRMANFGRKSLVEIKGV-LGTMGLFLG 318
           +L++ NFG KSL E+K   L   GL L 
Sbjct: 302 LLKIKNFGPKSLDEVKQKLLEKFGLSLK 329


>gi|161513430|emb|CAP16858.1| DNA-directed RNA polymerase subunit alpha [Pediococcus parvulus]
          Length = 224

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 100/224 (44%), Positives = 153/224 (68%), Gaps = 2/224 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K ++LK+  +  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT 
Sbjct: 61  KKVSLKIESNDEKSLEINVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAVLTA 120

Query: 150 SKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             G GYV A  ++   ++ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + T
Sbjct: 121 DTGRGYVSADENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           DGSI+  ++ +L+++IL + L +F+N  +  ++ +  +  +   
Sbjct: 181 DGSISPSEATSLSAKILTEHLALFVNLTDEAQDAEIMVEKEETH 224


>gi|71056824|emb|CAH58967.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
          Length = 235

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 107/233 (45%), Positives = 152/233 (65%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  II
Sbjct: 3   YGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQII 62

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LNIKG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  ICN+   A     
Sbjct: 63  LNIKGLALKMYGDEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICNVSEGASFHAR 122

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I 
Sbjct: 123 LTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIW 182

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           TDGSI   ++++LA++I+ + L +F+N  +  K  +  +  +       L   
Sbjct: 183 TDGSIEPLEAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMT 235


>gi|71056884|emb|CAH58998.1| DNA-directed RNA polymerase alpha chain [Enterococcus pseudoavium]
          Length = 236

 Score =  266 bits (681), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 108/236 (45%), Positives = 156/236 (66%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
             + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILN
Sbjct: 1   KFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILN 60

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           IKG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LT
Sbjct: 61  IKGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLT 120

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V  G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TD
Sbjct: 121 VKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTD 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           GSI  +++++LA++IL + L +F+N  +  K  +  +  +       L   +EEL+
Sbjct: 181 GSIIAQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEELD 236


>gi|110227111|ref|YP_665590.1| RNA polymerase alpha subunit [Populus alba]
 gi|122243407|sp|Q14FC5|RPOA_POPAL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|109945549|dbj|BAE97237.1| RNA polymerase alpha chain [Populus alba]
          Length = 339

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 83/334 (24%), Positives = 164/334 (49%), Gaps = 25/334 (7%)

Query: 10  IKPNNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           I    +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + 
Sbjct: 8   ISTRTLQWKCVESRADSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKS 67

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
             + HE S+I G+ E + +I++N+K I L+ +       +I  +GPG VTA DI     +
Sbjct: 68  KKIPHEFSTITGIQESIHEILMNLKEIVLRSNLYGTHNASICVKGPGCVTAQDIILPPSV 127

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E+++    I +L     + + L + +  GY        ++   G  +IDA++ P++  ++
Sbjct: 128 EIIDNTQHIASLREPIDLHIGLEIERNRGYCMKPPKNFQD---GSYSIDAVFMPVRNANH 184

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           +V S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ 
Sbjct: 185 SVHSYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEESFHLEKNQ 243

Query: 246 NVKSLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +  +LP      +                 +++LEL+ +  NCL+  NI  + DL++ ++
Sbjct: 244 HKITLPLFAFHDRLAKLRKNQKEIALKSIFIDQLELAPKIYNCLKRSNIHTLWDLLKNSQ 303

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            D++++ +F  + +  I G+L  +     +NLP 
Sbjct: 304 EDLMKIEHFRIEDVKHIFGILK-IEKHFTINLPK 336


>gi|134093233|ref|YP_001109534.1| RNA polymerase alpha subunit [Populus trichocarpa]
 gi|158513819|sp|A4GYU3|RPOA_POPTR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|133712095|gb|ABO36738.1| RNA polymerase alpha subunit [Populus trichocarpa]
          Length = 339

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 83/334 (24%), Positives = 164/334 (49%), Gaps = 25/334 (7%)

Query: 10  IKPNNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           I    +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + 
Sbjct: 8   ISTRTLQWKCVESRADSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKS 67

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
             + HE S+I G+ E + +I++N+K I L+ +       +I  +GPG VTA DI     +
Sbjct: 68  KKIPHEFSTITGIQESIHEILMNLKEIVLRSNLYGTHDASICVKGPGCVTAQDIILPPSV 127

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E+++    I +L     + + L + +  GY        ++   G  +IDA++ P++  ++
Sbjct: 128 EIIDNTQHIASLREPIDLHIGLEIERNRGYCMKPPKNFQD---GSYSIDAVFMPVRNANH 184

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           +V S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ 
Sbjct: 185 SVHSYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENFHLEKNQ 243

Query: 246 NVKSLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +  +LP      +                 +++LEL+ +  NCL+  NI  + DL++ ++
Sbjct: 244 HKITLPLFAFHDRLAKLRKNQKEIALKSIFIDQLELAPKIYNCLKRSNIHTLWDLLKNSQ 303

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            D++++ +F  + +  I G+L  +     +NLP 
Sbjct: 304 EDLMKIEHFRIEDVKHIFGILK-IEKHFTINLPK 336


>gi|91209019|ref|YP_538881.1| RNA polymerase alpha subunit [Solanum bulbocastanum]
 gi|108773161|ref|YP_635671.1| RNA polymerase alpha subunit [Solanum tuberosum]
 gi|90110868|sp|Q2VEE8|RPOA_SOLTU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|109900624|sp|Q2MIF6|RPOA_SOLBU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|82754657|gb|ABB90071.1| RNA polymerase alpha chain [Solanum tuberosum]
 gi|84371926|gb|ABC56244.1| RNA polymerase alpha subunit [Solanum bulbocastanum]
 gi|88656835|gb|ABD47088.1| RNA polymerase alpha subunit [Solanum tuberosum]
          Length = 337

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 83/331 (25%), Positives = 162/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT V+ + V
Sbjct: 11  RTLQWKCVESRTDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRVKSEKV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  +GPG VTA DI     +E++
Sbjct: 71  PHEYSTITGIQESVHEILMNLKEIVLRSNLYGTSDASICVKGPGYVTAQDIILPPYVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L       + L + +  GY+    H  ++   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDFCIGLQIERNRGYLIKTPHNFQD---GSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN-- 246
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYGNG-NEKQEILFIEIWTNGSLTPKEALHDASRNLIDLFIPFLHMEEDNLYLQDNQHTV 246

Query: 247 --------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                         +K+          +++ ELS R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 PLSPFTFHDKLAKLIKNKKKIALKSIFIDQSELSSRIYNCLKMSNIYTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F      +IK +LG +  +  ++L  
Sbjct: 307 MKIEHFRS---EDIKQILGILEKYFVIDLAK 334


>gi|11466357|ref|NP_038360.1| RNA polymerase alpha subunit [Mesostigma viride]
 gi|12230597|sp|Q9MUV0|RPOA_MESVI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|7259500|gb|AAF43801.1|AF166114_13 alpha subunit of RNA polymerase [Mesostigma viride]
          Length = 316

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 99/316 (31%), Positives = 161/316 (50%), Gaps = 10/316 (3%)

Query: 10  IKPNNIEYIVLGQEEEN--RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           + P+ I  I    E         + EPL  G   T+GN LRR+L+  + GAAIT+V+I G
Sbjct: 6   LFPSTIYCIESKIESPRNLYGRFLIEPLAIGQGITVGNTLRRILLGDIEGAAITSVKIPG 65

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
             +E S + G+ E + +I+LN+K I  +      ++  +  +GP VV A ++Q    IEV
Sbjct: 66  ANNEFSILPGIRESVLEILLNLKEIVFRTKSLDVQKGYLSIQGPCVVKAANLQLPTSIEV 125

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           ++    I  L  +A + ME  ++ G GY  A +   +N  I  + +DA++ PI KV+Y V
Sbjct: 126 VDGGQYIATLSGNANLDMEFVINTGKGYQMADYAIKKNSYISSLPVDAIFMPIHKVNYMV 185

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E     + L  +++ + I T+GSI+  D++ +  + + D      +        K D + 
Sbjct: 186 EQDHTSKFLT-ERVILEIWTNGSISPRDALDIGIKKVIDLFNPLHHCSSEYSTNKNDFST 244

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +S          VEELELSVR+ NCL+   I  + DL+  ++ D+L + NFGR+S  E+ 
Sbjct: 245 ES----KINDILVEELELSVRAYNCLKRAQIHTISDLLAYSQEDLLEIKNFGRRSAEEVI 300

Query: 308 GVLGTMGLFLGMNLPD 323
             L      L + LP 
Sbjct: 301 EALE---KKLNIYLPK 313


>gi|270285588|ref|ZP_06194982.1| DNA-directed RNA polymerase subunit alpha [Chlamydia muridarum
           Nigg]
 gi|270289598|ref|ZP_06195900.1| DNA-directed RNA polymerase subunit alpha [Chlamydia muridarum
           Weiss]
 gi|301336984|ref|ZP_07225186.1| DNA-directed RNA polymerase subunit alpha [Chlamydia muridarum
           MopnTet14]
 gi|12230602|sp|Q9PJN4|RPOA_CHLMU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 377

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 119/359 (33%), Positives = 189/359 (52%), Gaps = 25/359 (6%)

Query: 6   WQELIKPNNIEYIVLGQEE---ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           + +   P +++   +       +     +A+PL +G  HTLG+ALRR L+  L   AI +
Sbjct: 10  YNKFELPESVKMSPVEGAAGGIDKVARFVADPLEKGMGHTLGSALRRALLIGLEAPAIVS 69

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK---------RVTIFKRG--- 110
             + GVLHE  +++G+ ED+T+I+LN+KG  LK                R TI       
Sbjct: 70  FSMTGVLHEYMAVEGIIEDVTNIVLNLKGSLLKKYPLQDCEGGRASQKLRATISIDASDL 129

Query: 111 -----PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
                   +T GD+      E +NP+HVI  +     + + L V+ G GY P++    E 
Sbjct: 130 AAAGGQKAITLGDLLQEGTFEAVNPEHVIFTVTRPMQLDVMLRVAFGRGYTPSERIVLEE 189

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
             +  I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +  +++VA A++IL 
Sbjct: 190 REMNEIVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLILQVETDGRVAPKEAVAFATQILS 249

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLK---KVEELELSVRSTNCLRGENIVYMG 282
               +F   +E +   +E I+V+    +  L K    + E+ELSVRSTNCL   NI  +G
Sbjct: 250 KHFSVFEKMDEKRIVFEEAISVEKENKDDILHKLVLGINEIELSVRSTNCLSNANIETIG 309

Query: 283 DLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           +L+   E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 310 ELVIMPEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYAEK 368


>gi|89280667|ref|YP_514884.1| RNA polymerase alpha subunit [Solanum lycopersicum]
 gi|109900622|sp|Q2MI69|RPOA_SOLLC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|84372014|gb|ABC56331.1| RNA polymerase alpha subunit [Solanum lycopersicum]
 gi|89241703|emb|CAJ32426.1| RNA polymerase alpha chain [Solanum lycopersicum]
          Length = 337

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 82/331 (24%), Positives = 161/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT V+ + V
Sbjct: 11  RTLQWKCVESRTDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRVKSEKV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  +GPG VTA DI     +E++
Sbjct: 71  PHEYSTITGIQESVHEILMNLKEIVLRSNLYGTSEASICVKGPGYVTAQDIILPPYVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L       + L + +  GY+    H  ++   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDFCIGLQIERNRGYLIKTPHNFQD---GSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN-- 246
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYGNG-NEKQEILFIEIWTNGSLTPKEALHDASRNLIDLFIPFLHMEEDNLYLQDNQHTV 246

Query: 247 --------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                         +K+          +++ ELS R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 PLSPFTFHDKLAKLIKNKKKIALKSIFIDQSELSSRIYNCLKMSNIYTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F      +IK +L  +  +  ++L  
Sbjct: 307 MKIEHFRS---EDIKQILDILEKYFVIDLAK 334


>gi|71056800|emb|CAH58955.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
          Length = 233

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 107/233 (45%), Positives = 154/233 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV
Sbjct: 61  KGLALKMYGDEEKTLEIDISGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           SI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 181 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEE 233


>gi|157493279|gb|ABV58005.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|157493281|gb|ABV58006.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 268

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 120/271 (44%), Positives = 183/271 (67%), Gaps = 8/271 (2%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 1   EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 60

Query: 93  NLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVVRMELTVS 150
            +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L   +A + M + V 
Sbjct: 61  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVE 120

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 121 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMET 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V++LEL+V
Sbjct: 181 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTV 237

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           RS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 RSANCLKAEAIHYIGDLVQRTEVELLKTPNL 268


>gi|71056828|emb|CAH58969.1| DNA-directed RNA polymerase alpha chain [Enterococcus sulfureus]
          Length = 234

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 108/234 (46%), Positives = 153/234 (65%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
             I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILN
Sbjct: 1   QFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILN 60

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           IKG+ LKM G+  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LT
Sbjct: 61  IKGLALKMYGEDEKTLEIDIAGPATVTAGDILVDSDVEILNKDMYICTVSEGATFNARLT 120

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TD
Sbjct: 121 VRPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHRDDFDKLTMEIWTD 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           GSI   D+++LA++I+ + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 181 GSIEPLDAMSLAAKIMTEHLDIFVNLTDEAKHAEIMVEKEETQKEKMLEMTIEE 234


>gi|313292086|gb|ADR51232.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
          Length = 241

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 106/238 (44%), Positives = 154/238 (64%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I    E+ +    + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKG
Sbjct: 2   ITKIDEDRDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+  IILNIKG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +
Sbjct: 62  VREDVVQIILNIKGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTV 121

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
              A     LTV  G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D
Sbjct: 122 AEGATFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDD 181

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           +DKL+M I TDGSI  +++++LA++IL + L +F+N  +  K  +  +  +       
Sbjct: 182 FDKLTMEIWTDGSIIAQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 239


>gi|71056941|emb|CAH59029.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
 gi|71056947|emb|CAH59033.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 230

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 104/230 (45%), Positives = 153/230 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+I GV ED+T IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIPGVREDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D VIC++   A     LTV
Sbjct: 61  KGLALKLYAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLVICSVAEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           SI  +++++LA++I+ + L +F+N  +  K  +  +  +       L   
Sbjct: 181 SIIPQEALSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMT 230


>gi|72534399|emb|CAH59014.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
          Length = 227

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 104/227 (45%), Positives = 150/227 (66%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
             I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILN
Sbjct: 1   KFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILN 60

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           IKG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LT
Sbjct: 61  IKGLALKMYGDEEKTLEIDISGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLT 120

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TD
Sbjct: 121 VKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTD 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           GSI   ++++L+++I+ + L +F+N  +  K  +  +  +       
Sbjct: 181 GSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 227


>gi|217077310|ref|YP_002335028.1| DNA-directed RNA polymerase subunit alpha [Thermosipho africanus
           TCF52B]
 gi|217037165|gb|ACJ75687.1| DNA-directed RNA polymerase, alpha subunit [Thermosipho africanus
           TCF52B]
          Length = 330

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 114/326 (34%), Positives = 178/326 (54%), Gaps = 16/326 (4%)

Query: 8   ELIKPNNIEYIV-LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI- 65
           E + P  ++       E+      +  PL +G+A T+GN LRRVL+SS+   AIT V+  
Sbjct: 2   EFVMPKRLKMEEHKESEDYYYARYVLSPLEKGYATTIGNTLRRVLLSSIPSLAITDVKFV 61

Query: 66  -DGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTV 122
                HE  +I+GV ED+ +I+LN+K + L M    +    +TI  +G G + AGDI   
Sbjct: 62  RPEKYHEFDTIEGVKEDILEILLNLKKVQLSMEDYVEDPVELTIQHKGAGEIKAGDIIVP 121

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
             + V NP+  I  L+ DA + ++L  + G G+VPA     + D IG I +D +Y+P+ K
Sbjct: 122 AGVSVTNPNLHIATLNEDADLEIKLYATIGKGFVPAAERNEKPD-IGWIVLDGVYNPVLK 180

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL----GMFINFEEPK 238
           V++  E+ R G+  DYDKL + I T  +I   D++  A +I+ D        F  F+E  
Sbjct: 181 VNWIAENVRVGKKTDYDKLVLEIWTKKNIKPSDALKKAVKIINDHFRIIEESFGEFDEEN 240

Query: 239 -----KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                 EV      + +  N  L +K++EL+LS+R+ NCL+ + I  +GDL+ R E ++L
Sbjct: 241 DIAEVSEVSTVEEEEVVDENDILSRKIDELDLSMRALNCLKRDKIETIGDLLSRGEEELL 300

Query: 294 RMANFGRKSLVEIKGVL-GTMGLFLG 318
           ++ NFG+KSL E+K  L    GL  G
Sbjct: 301 KIKNFGQKSLDEVKEKLMEKFGLSFG 326


>gi|71056912|emb|CAH59015.1| DNA-directed RNA polymerase alpha chain [Enterococcus raffinosus]
          Length = 235

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 108/235 (45%), Positives = 156/235 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV
Sbjct: 61  KGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           SI  +++++LA++IL + L +F+N  +  K  +  +  +       L   +EEL+
Sbjct: 181 SIIAQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEELD 235


>gi|153799480|gb|ABS50515.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
 gi|153799482|gb|ABS50516.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 240

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 102/242 (42%), Positives = 152/242 (62%), Gaps = 4/242 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGV
Sbjct: 1   FEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGV 56

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++VL
Sbjct: 57  LHEFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQVL 116

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NPD  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VE
Sbjct: 117 NPDQYICTIAEGGHLHMELAVKNGRGYVTASDNKSDDMPIGVIPVDSLFSPIKKVNYQVE 176

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   +  +  +  +
Sbjct: 177 STRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADANTQFSEVMVEKE 236

Query: 249 SL 250
             
Sbjct: 237 DD 238


>gi|115605053|ref|YP_784505.1| RNA polymerase alpha subunit [Piper cenocladum]
 gi|122164330|sp|Q06GM8|RPOA_PIPCE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|112253782|gb|ABI14503.1| RNA polymerase alpha subunit [Piper cenocladum]
          Length = 339

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 86/334 (25%), Positives = 161/334 (48%), Gaps = 26/334 (7%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +   +E   +  +    +  I  PL +G A  +G A+RR L+  + G  IT V+ + V H
Sbjct: 14  RWKCVES-RIDSKRLYYSRFILSPLMKGQADMIGIAMRRALLGEIEGTCITRVKSEKVPH 72

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S+I G+ E + +I++N+K I L+ +       +I  RGP  VTA DI     +E+++ 
Sbjct: 73  EFSTIVGIEESVHEIVMNLKEIVLRSNLYGTLDASICIRGPRYVTAQDIILPPSVEIVDA 132

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
              I NL     + ++L + +  GY     H  E+   G   IDA++ P++  +++V S 
Sbjct: 133 TQHIANLTERVDLCIKLQIERDRGYSMKTPHNDED---GSYPIDAIFMPVRNANHSVHSY 189

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN---- 246
             G     + L + I T+GS+T ++++  ASR L D    F++ EE +  ++++ N    
Sbjct: 190 GNG-NEKQEILFIEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEREIHLEDNANGVPL 248

Query: 247 --------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                          K+          +++ EL  ++ NCL+  NI  + DL+  ++ D+
Sbjct: 249 ALFTFHDEFAITNIRKNKKKMALKSIFIDQSELPSKTYNCLKKSNIHTLLDLLNNSQEDL 308

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           L++ +F    + ++K +L  +    G +LP    
Sbjct: 309 LKIEHF---CMEDVKRILDILQKHFGFDLPKNGK 339


>gi|11467449|ref|NP_043595.1| RNA polymerase alpha subunit [Odontella sinensis]
 gi|1350842|sp|P49465|RPOA_ODOSI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1185144|emb|CAA91627.1| RNA polymerase alpha-chain [Odontella sinensis]
          Length = 312

 Score =  266 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 100/297 (33%), Positives = 162/297 (54%), Gaps = 4/297 (1%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               + + L  G   T+GN  RRVL+S L G AIT V+I GV  E S+I G+ ED+ +I+
Sbjct: 20  YGQFVIKSLHPGQGITIGNLFRRVLLSDLGGTAITGVRIAGVRDEFSTIPGIREDILEIL 79

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+KGI LK   +  K   +  +GP VVTA  IQ  +++E++NP+H I  +    V+ +E
Sbjct: 80  LNLKGIVLKSKTNDLKFGRLKIKGPAVVTANCIQLPSEVEIVNPNHYIATITTSNVLEIE 139

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
             +  G GY  A     +      + IDA++ P++KV + +E+  +      ++L + I 
Sbjct: 140 FKIESGTGYKLAGQTFCK-KSQDYLQIDAIFMPVQKVDFKIENIYDNSNDLTERLFLDIW 198

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+GS++ E++V+ ASR +       +  + P++  + +    S P NP     +EEL LS
Sbjct: 199 TNGSMSPEEAVSSASRFIISFFSSLLENKLPQETKESENKTLSAPKNPHTNIAIEELHLS 258

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           VR+ NCL+   I  +GDL++ +   +  + NFGRKS  E+   L      LG+ L +
Sbjct: 259 VRAYNCLKRAQINTIGDLLKYSPEKLQELKNFGRKSADEVFTTLKNK---LGIVLSN 312


>gi|187918368|ref|YP_001883931.1| DNA-directed RNA polymerase subunit alpha [Borrelia hermsii DAH]
 gi|119861216|gb|AAX17011.1| DNA-directed RNA polymerase alpha chain [Borrelia hermsii DAH]
          Length = 344

 Score =  266 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 119/325 (36%), Positives = 181/325 (55%), Gaps = 16/325 (4%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           ++   P+ IE++  G+++ +    I  P  +GF  T+GN LRRVL+SS+ G AI+A++I 
Sbjct: 9   KDFTIPDRIEFLR-GEDDGSYGKFIIYPFEKGFGVTIGNTLRRVLLSSIEGYAISAMRIQ 67

Query: 67  G--------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT--- 115
                    V  E   I GV ED  ++I NIK I+LK+  +  K  TI     G  T   
Sbjct: 68  SNQGGSLKIVSSEFDLIPGVVEDTLEVIANIKNIHLKLD-EGVKSATISVSVNGKDTNVL 126

Query: 116 AGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDA 175
                    +EV N D VI  L  +A +  E  V  G GYV ++H+    + +  I +D+
Sbjct: 127 KAVHLEREGVEVCNKDLVIATLSSEANLDFEFQVDYGRGYVSSEHNAKYLEEVNTIALDS 186

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           ++SPI+KV+Y+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L   +NFE
Sbjct: 187 IFSPIEKVTYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREFLLPLVNFE 246

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           +   +V   ++      +  L   +E+L LSVRS NCL  EN+  +G+LI ++  ++ + 
Sbjct: 247 D---KVVHSVDDSEFRDSDILNMNIEKLNLSVRSLNCLTKENVKTLGELISKSAEELSKA 303

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMN 320
            NFG+KSL EI   L   GLFLGM+
Sbjct: 304 RNFGKKSLEEIVEKLSVYGLFLGMS 328


>gi|313292084|gb|ADR51231.1| DNA-directed RNA polymerase alpha chain [Enterococcus malodoratus]
          Length = 241

 Score =  266 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 106/238 (44%), Positives = 154/238 (64%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I    E+ +    + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKG
Sbjct: 2   ITKIDEDRDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+  IILNIKG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +
Sbjct: 62  VREDVVQIILNIKGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTV 121

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
              A     LTV  G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D
Sbjct: 122 SEGATFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDD 181

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           +DKL+M I TDGSI  +++++LA++IL + L +F+N  +  K  +  +  +       
Sbjct: 182 FDKLTMEIWTDGSIIAQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 239


>gi|15835408|ref|NP_297167.1| DNA-directed RNA polymerase subunit alpha [Chlamydia muridarum
           Nigg]
 gi|7190822|gb|AAF39597.1| DNA-directed RNA polymerase, alpha subunit [Chlamydia muridarum
           Nigg]
          Length = 394

 Score =  266 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 119/359 (33%), Positives = 189/359 (52%), Gaps = 25/359 (6%)

Query: 6   WQELIKPNNIEYIVLGQEE---ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           + +   P +++   +       +     +A+PL +G  HTLG+ALRR L+  L   AI +
Sbjct: 27  YNKFELPESVKMSPVEGAAGGIDKVARFVADPLEKGMGHTLGSALRRALLIGLEAPAIVS 86

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK---------RVTIFKRG--- 110
             + GVLHE  +++G+ ED+T+I+LN+KG  LK                R TI       
Sbjct: 87  FSMTGVLHEYMAVEGIIEDVTNIVLNLKGSLLKKYPLQDCEGGRASQKLRATISIDASDL 146

Query: 111 -----PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
                   +T GD+      E +NP+HVI  +     + + L V+ G GY P++    E 
Sbjct: 147 AAAGGQKAITLGDLLQEGTFEAVNPEHVIFTVTRPMQLDVMLRVAFGRGYTPSERIVLEE 206

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
             +  I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +  +++VA A++IL 
Sbjct: 207 REMNEIVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLILQVETDGRVAPKEAVAFATQILS 266

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLK---KVEELELSVRSTNCLRGENIVYMG 282
               +F   +E +   +E I+V+    +  L K    + E+ELSVRSTNCL   NI  +G
Sbjct: 267 KHFSVFEKMDEKRIVFEEAISVEKENKDDILHKLVLGINEIELSVRSTNCLSNANIETIG 326

Query: 283 DLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           +L+   E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 327 ELVIMPEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYAEK 385


>gi|71842332|ref|YP_277420.1| RNA polymerase alpha subunit [Emiliania huxleyi]
 gi|90110842|sp|Q4G347|RPOA_EMIHU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|60101575|gb|AAX13919.1| RNA polymerase alpha subunit [Emiliania huxleyi]
          Length = 309

 Score =  266 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 97/291 (33%), Positives = 163/291 (56%), Gaps = 1/291 (0%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
             EN      EPL +G   T+GNALRR L+S++ G AI   +I GV HE S I GV ED 
Sbjct: 14  ATENVAKFCIEPLSKGQGITIGNALRRTLLSNIPGTAIVGTRISGVDHEFSVIPGVKEDA 73

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
            +I+LN+K +  K + +      +  +GP +VTAGDI    D+E+++P   I  +   + 
Sbjct: 74  LEILLNLKQLVFKGNLNEPIITRLNIQGPCIVTAGDIDIPTDLELIDPQQYIATITDFSH 133

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + ME  + +G  YV ++   + N P G + +DA+++PIKKV++ VE++   + L+ ++L 
Sbjct: 134 LEMEFILEQGESYVLSEKTASNN-PRGFLAVDAVFTPIKKVNFFVETSSSKERLEKERLI 192

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + I+T+GSI   +++ LA+  L     +  + +   +   E  N+  +         +EE
Sbjct: 193 IEIETNGSILPLEALNLAAERLSSLFKLVNSADLTAEFPTEVENIVQVSQTDVTGVLIEE 252

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           LELSVR+ NCL+   I  +G+L++ ++ ++L   NFG+KS  E+   L   
Sbjct: 253 LELSVRAYNCLKRAQIHTLGELLKYSKENLLEFKNFGQKSANEVCENLHER 303


>gi|51859683|gb|AAU11121.1| RNA polymerase alpha subunit [Psathyrostachys fragilis subsp.
           secaliformis]
          Length = 339

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIXIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|328813973|gb|AEB52102.1| DNA-directed RNA polymerase alpha chain [Lactobacillus fermentum]
          Length = 243

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 106/243 (43%), Positives = 162/243 (66%), Gaps = 2/243 (0%)

Query: 48  RRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF 107
           RRV+++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K + LK+  +  K + I 
Sbjct: 1   RRVMLASLPGAAITSIQIDGVLHEFSTVQGVTEDVTQIILNLKQVALKIDSEDAKDLEID 60

Query: 108 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--EN 165
            +GP  VTA DIQ   D+ +LN D  I  +   A + +++T  KG GY  A  ++T  E 
Sbjct: 61  VKGPAEVTAADIQGDGDVTILNSDLHIATVSDGAELHVKMTADKGRGYSSADDNKTRMEG 120

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
             IG++ ID++Y+PI++V+YTVE+ R GQ  DYDKL++ + T+GS+T  ++++LA++IL 
Sbjct: 121 LAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYDKLTLDVWTNGSLTPTEAISLAAKILT 180

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLI 285
           + L MF+N  E  +  +  +  +       L K +EEL+LSVRS NCL+  +I  + DL 
Sbjct: 181 EHLTMFVNLTEEAQVTQVMVEREETHQEKVLDKTIEELDLSVRSYNCLKRADIQTVKDLT 240

Query: 286 QRT 288
           +RT
Sbjct: 241 ERT 243


>gi|41688710|sp|Q8MAJ0|RPOA_AEGUN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|22657234|gb|AAM97420.1| RNA polymerase alpha subunit [Aegilops uniaristata]
          Length = 339

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 93/328 (28%), Positives = 162/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + GA IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGACITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D+L
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|149390385|ref|YP_001294384.1| RNA polymerase alpha subunit [Dioscorea elephantipes]
 gi|172048699|sp|A6MMN9|RPOA_DIOEL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|148668077|gb|ABR01461.1| RNA polymerase alpha subunit [Dioscorea elephantipes]
          Length = 337

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 86/330 (26%), Positives = 163/330 (49%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ++RR L+  + G  IT  + + V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLMKGQADTIGISMRRALLGEIEGTCITRAKSEKVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ G+ E + +I+ N+K I L+ +    +  +I  RGP  VTA DI +   +E+++
Sbjct: 72  HEYSTVVGIEESVHEILFNLKEIVLRSNLYEIRDASICVRGPRYVTAQDIISPPYVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL     + +EL + +  GY       +++   G   IDA++ P++  ++++ S
Sbjct: 132 TTQYIANLTEPIDLCIELEIKRDRGYRMKPITNSQD---GSYPIDAVFMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 YGNG-NEKQEILFLEIWTNGSLTPKEALYEASRNLIDLFVPFLHAEEEDINFEENKNKFT 247

Query: 250 LPF----------------NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           LP                  P     +++LEL  R+ NCL+  NI  + DL+ + + +++
Sbjct: 248 LPPLTFQDRLSNLKKNKKGIPLKYIFIDQLELPSRTYNCLKRSNIHTLLDLLSKGQENLI 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +M  F    + ++K +L T+     ++LP 
Sbjct: 308 KMEYFH---IEDVKQILDTLQKHFAVDLPK 334


>gi|118430418|ref|YP_874684.1| RNA polymerase alpha subunit [Hordeum vulgare subsp. vulgare]
 gi|68053191|sp|Q7H6J0|RPOA_HORMA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|68053192|sp|Q7H6J1|RPOA_HORJU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|68053193|sp|Q7H6J2|RPOA_HORBU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|126302597|sp|P92392|RPOA_HORVU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1770313|emb|CAB01360.1| alpha subunit of RNA polymerase [Hordeum brachyantherum subsp.
           californicum]
 gi|1770331|emb|CAB01774.1| alpha subunit of RNA polymerase [Hordeum erectifolium]
 gi|1770339|emb|CAB01366.1| alpha subunit of RNA polymerase [Hordeum marinum subsp.
           gussoneanum]
 gi|22657246|gb|AAM97426.1| RNA polymerase alpha subunit [Hordeum brachyantherum]
 gi|22657250|gb|AAM97428.1| RNA polymerase alpha subunit [Hordeum bulbosum]
 gi|22657252|gb|AAM97429.1| RNA polymerase alpha subunit [Hordeum jubatum]
 gi|22657254|gb|AAM97430.1| RNA polymerase alpha subunit [Hordeum marinum]
 gi|22657260|gb|AAM97433.1| RNA polymerase alpha subunit [Hordeum pusillum]
 gi|118201072|gb|ABK79443.1| RNA polymerase alpha subunit [Hordeum vulgare subsp. vulgare]
 gi|317017394|gb|ADU86099.1| RNA polymerase alpha subunit [Elymus enysii]
 gi|317017404|gb|ADU86104.1| RNA polymerase alpha subunit [Stenostachys gracilis]
          Length = 339

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 160/328 (48%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E ++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVETVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|3122776|sp|P92439|RPOA_THIBE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1771793|emb|CAB01384.1| alpha subunit of RNA polymerase [Thinopyrum bessarabicum]
 gi|22657340|gb|AAM97473.1| RNA polymerase alpha subunit [Thinopyrum bessarabicum]
 gi|22657344|gb|AAM97475.1| RNA polymerase alpha subunit [Thinopyrum scirpeum]
          Length = 339

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LPFN----------------PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D+L
Sbjct: 248 PPPFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|71056812|emb|CAH58961.1| DNA-directed RNA polymerase alpha chain [Enterococcus hirae]
          Length = 237

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 107/236 (45%), Positives = 154/236 (65%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T II
Sbjct: 2   YGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQII 61

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LNIKG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     
Sbjct: 62  LNIKGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHAR 121

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I 
Sbjct: 122 LTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIW 181

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 182 TDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEE 237


>gi|300431286|gb|ADK12608.1| RNA polymerase alpha subunit [Nassella novarae]
          Length = 339

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 90/328 (27%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I+ +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY     +  ++   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIELQIKRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGXXFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTILDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
            + +F    + + K +  T+   L ++L
Sbjct: 308 XIDSFR---MEDGKQIWDTLEKHLPIDL 332


>gi|313292080|gb|ADR51229.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 241

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 107/234 (45%), Positives = 154/234 (65%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED
Sbjct: 6   DEEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVRED 65

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILNIKG+ LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A
Sbjct: 66  VTQIILNIKGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGA 125

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
                LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL
Sbjct: 126 TFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKL 185

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           +M I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       
Sbjct: 186 TMEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 239


>gi|108802673|ref|YP_636331.1| RNA polymerase alpha subunit [Eucalyptus globulus subsp. globulus]
 gi|309322478|ref|YP_003933992.1| RNA polymerase alpha subunit [Eucalyptus grandis]
 gi|90110843|sp|Q49KW6|RPOA_EUCGG RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|60460839|gb|AAX21059.1| RNA polymerase alpha subunit [Eucalyptus globulus subsp. globulus]
 gi|308223312|gb|ADO23620.1| RNA polymerase alpha subunit [Eucalyptus grandis]
          Length = 337

 Score =  265 bits (678), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 80/324 (24%), Positives = 159/324 (49%), Gaps = 27/324 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +    +  +I  +GPG VTA DI     +E++
Sbjct: 71  PHEYSTIVGIQESVHEILMNLKEIVLRSNLYGTRNASICVKGPGCVTAQDIILPTSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I NL     + + L + +  GY        ++   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQYIANLTEPINLCIGLQIERNRGYHIKTPKNFQD---GSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ +    
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLENNQYKV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LPF     +                 +++ EL  R+ NCL+  NI  + DL+ +++ D+
Sbjct: 247 TLPFFTFHDRLAKLRKTKKEIALKSIFIDQFELPPRTYNCLKRYNIHTLFDLLNKSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLF 316
           ++M  F    + ++K +L ++ + 
Sbjct: 307 MKMEYFR---IEDVKQILDSLEIE 327


>gi|325126897|ref|YP_004286134.1| RNA polymerase alpha subunit [Fragaria vesca subsp. vesca]
 gi|324022809|gb|ADY15383.1| RNA polymerase alpha subunit [Fragaria vesca subsp. vesca]
          Length = 331

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 80/324 (24%), Positives = 152/324 (46%), Gaps = 24/324 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFILAPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+  G+ E + +I++N+K I L+ +    +  +I  +GPG VTA DI     IE++
Sbjct: 71  PHEYSTFVGIQESVHEILMNLKEIVLRSNLYGTRNASICVKGPGYVTAQDIILPPSIEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I NL     + +EL + +  GY     +   N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIANLTEPINLCIELQIERNRGYRIKTPN---NFQEGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S         + L + I T+GS+T ++++  ASR L D    F++ EE     + + +  
Sbjct: 188 SY-VNGNEKQEILFIEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHFENNQHKV 246

Query: 249 SLP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP                 N      +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPLFTFHGKLANPKKIKKENTLKYIFIDQSELPPRVYNCLKRSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLF 316
           +++ +   + +  I  +L     F
Sbjct: 307 MKIKHLRIEDVKHILNILEIKKHF 330


>gi|68053188|sp|Q7H6F6|RPOA_PSAJU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1770335|emb|CAB01363.1| alpha subunit of RNA polymerase [Hordeum murinum subsp. glaucum]
 gi|1771433|emb|CAB01336.1| alpha subunit of RNA polymerase [Psathyrostachys fragilis]
 gi|22657248|gb|AAM97427.1| RNA polymerase alpha subunit [Hordeum brevisubulatum]
 gi|22657256|gb|AAM97431.1| RNA polymerase alpha subunit [Hordeum murinum]
 gi|22657258|gb|AAM97432.1| RNA polymerase alpha subunit [Hordeum murinum]
 gi|22657346|gb|AAM97476.1| RNA polymerase alpha subunit [Psathyrostachys fragilis]
 gi|22657348|gb|AAM97477.1| RNA polymerase alpha subunit [Psathyrostachys juncea]
 gi|51859675|gb|AAU11117.1| RNA polymerase alpha subunit [Psathyrostachys juncea]
 gi|51859677|gb|AAU11118.1| RNA polymerase alpha subunit [Psathyrostachys lanuginosa]
 gi|51859685|gb|AAU11122.1| RNA polymerase alpha subunit [Psathyrostachys fragilis subsp.
           villosus]
 gi|51859687|gb|AAU11123.1| RNA polymerase alpha subunit [Psathyrostachys fragilis subsp.
           villosus]
 gi|51859689|gb|AAU11124.1| RNA polymerase alpha subunit [Psathyrostachys huashanica]
 gi|51859693|gb|AAU11126.1| RNA polymerase alpha subunit [Psathyrostachys rupestris subsp.
           rupestris]
 gi|193885480|gb|ACF28432.1| RNA polymerase alpha subunit [Leymus angustus]
 gi|193885484|gb|ACF28435.1| RNA polymerase alpha subunit [Leymus chinensis]
 gi|193885488|gb|ACF28438.1| RNA polymerase alpha subunit [Leymus paboanus]
 gi|193885492|gb|ACF28441.1| RNA polymerase alpha subunit [Leymus racemosus]
 gi|193885496|gb|ACF28444.1| RNA polymerase alpha subunit [Leymus karelinii]
 gi|193885500|gb|ACF28447.1| RNA polymerase alpha subunit [Leymus sabulosus]
 gi|193885504|gb|ACF28450.1| RNA polymerase alpha subunit [Leymus mollis]
 gi|193885508|gb|ACF28453.1| RNA polymerase alpha subunit [Leymus secalinus]
 gi|307696913|gb|ADN85913.1| RNA polymerase alpha subunit [Leymus erianthus]
 gi|307696921|gb|ADN85919.1| RNA polymerase alpha subunit [Leymus arenarius]
 gi|307696925|gb|ADN85922.1| RNA polymerase alpha subunit [Leymus salinus]
 gi|307696929|gb|ADN85925.1| RNA polymerase alpha subunit [Leymus cinereus]
 gi|307696933|gb|ADN85928.1| RNA polymerase alpha subunit [Leymus pseudoracemosus]
 gi|307696937|gb|ADN85931.1| RNA polymerase alpha subunit [Leymus akmolinensis]
 gi|307696941|gb|ADN85934.1| RNA polymerase alpha subunit [Leymus karelinii]
 gi|307696945|gb|ADN85937.1| RNA polymerase alpha subunit [Leymus paboanus]
 gi|307696949|gb|ADN85940.1| RNA polymerase alpha subunit [Leymus angustus]
          Length = 339

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|161511773|emb|CAP16897.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 249

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 106/243 (43%), Positives = 153/243 (62%), Gaps = 2/243 (0%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E +N    + EPL RG+  TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED
Sbjct: 7   DENDNYGRFVIEPLERGYGTTLGNSLRRILLSSLPGAAITSVQIDSVLHEFSTIEGVVED 66

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  IC +    
Sbjct: 67  VTQIILNLKKVSLKIESDEDKTLEINVAGPANVTAGDIMGDGDVVILNPELPICTVAEGT 126

Query: 142 VVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
                LT   G GY  A  ++    + PIG++ ID++Y+PI++V+Y VE+ R GQ  DYD
Sbjct: 127 TFHAVLTADTGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYD 186

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL++ I TDGSIT  ++ +L+++IL + L +F+N  +  KE +  +  +       L   
Sbjct: 187 KLTLDIWTDGSITPSEATSLSAKILTEHLAIFVNLNDQAKETEIMVEKEETHKEKMLEMT 246

Query: 260 VEE 262
           +EE
Sbjct: 247 IEE 249


>gi|254796670|ref|YP_003081506.1| DNA-directed RNA polymerase, alpha subunit [Neorickettsia risticii
           str. Illinois]
 gi|254589917|gb|ACT69279.1| DNA-directed RNA polymerase, alpha subunit [Neorickettsia risticii
           str. Illinois]
          Length = 333

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 124/305 (40%), Positives = 179/305 (58%), Gaps = 6/305 (1%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
            E      + EPL  GF  T+GNA+RRVL+SSL G AI+AV I G+ HE S I GV ED 
Sbjct: 25  REGYSAEFVVEPLRGGFGLTIGNAMRRVLLSSLSGFAISAVGIKGLTHEFSCIPGVREDF 84

Query: 83  TDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
            D+ LN+K + LK  SG +   + +   G G V +  I   +D EV+N D +ICN+    
Sbjct: 85  ADLALNLKKVVLKSVSGATCGNLHLSVTGGGAVFSNMISPSHDFEVVNADLLICNVAEGV 144

Query: 142 VVRMELTVSKGHGYVPAKH-HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
            + ME+ VS G GYV +    + E D  G + IDA+Y+P++ V++TV+    G  + +DK
Sbjct: 145 SLEMEMKVSSGFGYVSSVSVRKDEYDLEGAVPIDAIYNPVRAVNFTVKPTSAGSFVGHDK 204

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK----EDINVKSLPFNPAL 256
           L + ++T+G++  + +V  AS+IL  Q   F+N  +P+  V               +  L
Sbjct: 205 LILYVETNGAMDPKTAVLEASKILSTQARCFLNIADPEHRVHGVPYSVSTSDRNDTSDLL 264

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
             +++ L LS R+  CL GENIVY+ DL+ RTEAD+L+  NFGR+SL E+K  L + GL 
Sbjct: 265 SARIDRLYLSARARKCLNGENIVYIRDLVSRTEADLLKAPNFGRRSLEEVKKELFSKGLS 324

Query: 317 LGMNL 321
           LGMNL
Sbjct: 325 LGMNL 329


>gi|169794105|ref|YP_001718469.1| RNA polymerase alpha subunit [Manihot esculenta]
 gi|157695917|gb|ABV66186.1| RNA polymerase alpha subunit [Manihot esculenta]
          Length = 343

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 82/336 (24%), Positives = 160/336 (47%), Gaps = 25/336 (7%)

Query: 10  IKPNNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           I    +++  +    +N        I  PL +G A T+G A+RR L+  + G  IT  + 
Sbjct: 8   ISTRTLQWKCIESRTDNKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKS 67

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           + + HE S+I G+ E + +I++N+K I L+ +       +I  +GPG VTA DI     +
Sbjct: 68  EKIPHEFSTIAGIQESIHEILMNLKEIVLRSNLYGTCDASICVKGPGYVTAQDIILPPFV 127

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E+++    I +L     + + L + +  GY     +  +    G  +IDA++ P++  ++
Sbjct: 128 EIIDNTQHIASLTKAIDLCIGLQIERNRGYRIKPTNNFQ-VQDGSYSIDAVFMPVRNANH 186

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           +V S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + 
Sbjct: 187 SVHSYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDFFIPFLHAEEENLHLEIEK 245

Query: 246 NV------------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
           N                   K+          +++ EL+ +  NCL+  NI  + DL+ +
Sbjct: 246 NQHKVTLPLFCFHDKLTKLRKNKKEIVLKYIFIDQSELTPKIYNCLKRSNIHTLSDLLNK 305

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++ D++++ +F    +  I G+L  +     ++LP 
Sbjct: 306 SQEDLMKIEHFRIDDVKHILGIL-EIEKHFTIDLPK 340


>gi|71056880|emb|CAH58996.1| DNA-directed RNA polymerase alpha chain [Enterococcus avium]
          Length = 235

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 108/235 (45%), Positives = 155/235 (65%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
             + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILN
Sbjct: 1   KFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILN 60

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           IKG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LT
Sbjct: 61  IKGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLT 120

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V  G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TD
Sbjct: 121 VKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTD 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
           GSI  +++++LA++IL + L +F+N  +  K  +  +  +       L   +EEL
Sbjct: 181 GSIIAQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEEL 235


>gi|11467738|ref|NP_050790.1| RNA polymerase alpha subunit [Guillardia theta]
 gi|3914811|sp|O46914|RPOA_GUITH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|3603063|gb|AAC35724.1| RNA polymerase a subunit [Guillardia theta]
          Length = 318

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 92/317 (29%), Positives = 165/317 (52%), Gaps = 15/317 (4%)

Query: 13  NNIEYIVLGQEEENR----TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
              E   L  +  N     +  + +PL  G   TLGNALRR L+S L G AITAV+I GV
Sbjct: 2   TQFEIECLDSKVYNARDHWSRFVIDPLKPGQGTTLGNALRRTLLSELEGLAITAVRIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ ED+ +I+LN+K I             +  +GP +VTA   +   +I+++
Sbjct: 62  SHEFSTINGIREDVLEILLNLKEIVFSGQLQESTIGRLTVQGPAIVTARSFELPPEIKLI 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +P+  I  +  +  + ME  +  G GY   +   +  +    + +D+++ P+KKV++ +E
Sbjct: 122 DPEQYIATICGNNTLEMEFKIEVGSGYKIVEKDNS-TEHFEFLQVDSVFMPVKKVNFRIE 180

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
             R    +  ++L + I T+GSI+ +++++ A+  L +        +      + + + +
Sbjct: 181 ETRGENNILNEQLILDIWTNGSISAKEAISNAADNLINLFSPLKTIDG-----ESETDYE 235

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRG--ENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           +   +      +EEL+LSVR+ NCL+    +I  + DL+  ++ D++ + NFG+KS  E+
Sbjct: 236 TNETSHINQILIEELQLSVRAYNCLKRGCAHIHSVADLLDYSQEDLIEIKNFGQKSAEEV 295

Query: 307 KGVLGTMGLFLGMNLPD 323
              L      LG+NLP 
Sbjct: 296 IDAL---QKRLGINLPK 309


>gi|297621699|ref|YP_003709836.1| DNA-directed RNA polymerase, alpha subunit [Waddlia chondrophila
           WSU 86-1044]
 gi|297377000|gb|ADI38830.1| DNA-directed RNA polymerase, alpha subunit [Waddlia chondrophila
           WSU 86-1044]
          Length = 370

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 129/351 (36%), Positives = 185/351 (52%), Gaps = 23/351 (6%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
              P+ I  +            IAEP  RGF HTLGN+LRR++++SL   AI  V+I+GV
Sbjct: 8   FEMPDEI-VVDEETATGTFARFIAEPFERGFGHTLGNSLRRLMLTSLEAPAIIGVRIEGV 66

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSH-----------------KRVTIFKRGP 111
            HE  +I G+ ED+T+IILNIKG  L+                       +      +G 
Sbjct: 67  AHEYMAIDGIVEDMTNIILNIKGAKLRKLPMEDTPNARNQRLLTKVLEITQEDIDNGKGQ 126

Query: 112 GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI 171
             V  GDI      EV+NP+H I  + V    +++L VS G GYVP++ H   +     I
Sbjct: 127 YEVRLGDIVEGGIFEVVNPNHHIFTVTVPMQKQVDLRVSFGRGYVPSERHVVNDKSTDEI 186

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            IDA ++P+K V+Y VE+ R GQ  D+D+L + + TDG +T  ++   AS+I      +F
Sbjct: 187 LIDAAFTPVKLVNYHVENTRVGQDTDFDRLVLEVTTDGRVTPTEAFGFASQIGLKHFEIF 246

Query: 232 INFEEPK---KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
              +       E+KED +         L  +++E+ELSVRSTNCL G NI  + +L+   
Sbjct: 247 KKVQTQMVSFDEIKEDSDSDDDEIMDKLALRIDEIELSVRSTNCLSGANIETIAELVSIP 306

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW--PPESIEELAKKYE 337
           E  ML   NFG+KSL EIK  L  MGL LGM+L  +    E++ E  K+Y+
Sbjct: 307 ERRMLEFRNFGKKSLTEIKAKLQEMGLGLGMDLSRYGITAENVREKIKEYQ 357


>gi|153799472|gb|ABS50511.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
 gi|153799474|gb|ABS50512.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
 gi|153799476|gb|ABS50513.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 240

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 102/240 (42%), Positives = 152/240 (63%), Gaps = 4/240 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGV
Sbjct: 1   FEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGV 56

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++VL
Sbjct: 57  LHEFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQVL 116

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NPD  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VE
Sbjct: 117 NPDQYICTIAEGGHLHMELAVKNGRGYVTASDNKSDDMPIGVIPVDSLFSPIKKVNYQVE 176

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   +  +  +  +
Sbjct: 177 STRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADANTQFSEVMVEKE 236


>gi|88608775|ref|YP_506180.1| DNA-directed RNA polymerase subunit alpha [Neorickettsia sennetsu
           str. Miyayama]
 gi|119366702|sp|Q2GEB6|RPOA_NEOSM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|88600944|gb|ABD46412.1| DNA-directed RNA polymerase, alpha subunit [Neorickettsia sennetsu
           str. Miyayama]
          Length = 333

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 122/305 (40%), Positives = 175/305 (57%), Gaps = 6/305 (1%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
            E      I EPL  GF  T+GNA+RRVL+SSL G AI+AV I G+ HE S I GV ED 
Sbjct: 25  REGYCAEFIVEPLRVGFGLTIGNAMRRVLLSSLSGFAISAVGIKGLTHEFSCIPGVREDF 84

Query: 83  TDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
            D+ LN+K + LK    +    + +     G V +  I   +D EV+N D +ICN+    
Sbjct: 85  ADLALNLKKVVLKSISGATCGNLHLSVTDGGAVFSNMISPSHDFEVVNGDLLICNVAEGV 144

Query: 142 VVRMELTVSKGHGYVPAKH-HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
            + ME+ VS G GYV +    + E D  G + IDA+Y+P++ V++TV+    G    +DK
Sbjct: 145 SLEMEMKVSSGFGYVSSVSVRKDEYDLEGAVPIDAIYNPVRAVNFTVKPTSAGSFAGHDK 204

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI----NVKSLPFNPAL 256
           L + ++T+G++  + +V  AS+IL  Q   F+N  +P+  V               +  L
Sbjct: 205 LILYVETNGAMDPKTAVLEASKILSTQARCFLNIADPEHRVHGVPCGVSTSDRNDASDLL 264

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
             +++ L LS R+  CL GENIVY+ DL+ RTEAD+L+  NFGR+SL E+K  L + GL 
Sbjct: 265 SARIDRLYLSARARKCLNGENIVYIRDLVSRTEADLLKAPNFGRRSLEEVKKELFSKGLS 324

Query: 317 LGMNL 321
           LGMNL
Sbjct: 325 LGMNL 329


>gi|311990464|gb|ADQ26362.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 243

 Score =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 102/243 (41%), Positives = 151/243 (62%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           +LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   D  K + 
Sbjct: 1   SLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLSDERKVIE 60

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
           +   GP  VTA D++   D++VLNPD  IC +     + ME+ V  G GYV A  +++++
Sbjct: 61  LDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNGRGYVAASDNKSDD 120

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
            PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++ A++IL 
Sbjct: 121 MPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILV 180

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLI 285
           +   +F + +   K  +  +  +       L   +EEL+LSVRS NCL+   I  + +L 
Sbjct: 181 EHFKVFESADADTKFSEVMVEKEDDKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELT 240

Query: 286 QRT 288
             T
Sbjct: 241 DMT 243


>gi|22657270|gb|AAM97438.1| RNA polymerase alpha subunit [Elymus canadensis]
 gi|22657294|gb|AAM97450.1| RNA polymerase alpha subunit [Elymus virginicus]
 gi|22657296|gb|AAM97451.1| RNA polymerase alpha subunit [Elymus virginicus]
 gi|22657298|gb|AAM97452.1| RNA polymerase alpha subunit [Elymus virginicus]
          Length = 339

 Score =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D+L
Sbjct: 248 PPLFTFQKRLTNPKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|307696909|gb|ADN85910.1| RNA polymerase alpha subunit [Leymus innovatus]
 gi|307696917|gb|ADN85916.1| RNA polymerase alpha subunit [Leymus triticoides]
          Length = 339

 Score =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFH---MEDRKHIWDTLEKHLPIDL 332


>gi|71056888|emb|CAH59000.1| DNA-directed RNA polymerase alpha chain [Enterococcus mundtii]
          Length = 238

 Score =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 107/236 (45%), Positives = 154/236 (65%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T II
Sbjct: 3   YGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQII 62

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LNIKG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     
Sbjct: 63  LNIKGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHAR 122

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I 
Sbjct: 123 LTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIW 182

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 183 TDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEE 238


>gi|14017603|ref|NP_114289.1| RNA polymerase alpha subunit [Triticum aestivum]
 gi|17380278|sp|P12073|RPOA_WHEAT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|68053005|sp|P92892|RPOA_AEGSP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|68053170|sp|Q6YLW2|RPOA_SECCE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|68053185|sp|Q7GED0|RPOA_TAECM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|68053186|sp|Q7GED9|RPOA_AEGCM RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1769857|emb|CAB01345.1| alpha subunit of RNA polymerase [Amblyopyrum muticum]
 gi|1770118|emb|CAB01303.1| alpha subunit of RNA polymerase [Aegilops comosa]
 gi|1770176|emb|CAB01348.1| alpha subunit of RNA polymerase [Triticum monococcum]
 gi|1771730|emb|CAB01375.1| alpha subunit of RNA polymerase [Aegilops speltoides]
 gi|1771811|emb|CAB01357.1| alpha subunit of RNA polymerase [Taeniatherum caput-medusae]
 gi|13928236|dbj|BAB47065.1| RNA polymerase alpha subunit [Triticum aestivum]
 gi|22657228|gb|AAM97417.1| RNA polymerase alpha subunit [Aegilops markgrafii]
 gi|22657230|gb|AAM97418.1| RNA polymerase alpha subunit [Aegilops speltoides]
 gi|22657332|gb|AAM97469.1| RNA polymerase alpha subunit [Secale montanum]
 gi|22657334|gb|AAM97470.1| RNA polymerase alpha subunit [Secale cereale]
 gi|22657336|gb|AAM97471.1| RNA polymerase alpha subunit [Secale montanum]
 gi|22657338|gb|AAM97472.1| RNA polymerase alpha subunit [Taeniatherum caput-medusae]
          Length = 339

 Score =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D+L
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|7388087|sp|P92220|RPOA_BROIN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1769950|emb|CAB01354.1| alpha subunit of RNA polymerase [Bromus inermis]
          Length = 339

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 90/328 (27%), Positives = 160/328 (48%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  I   +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCIARAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFKKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|290489658|gb|ADD31213.1| RNA polymerase alpha subunit protein [Dillenia indica]
          Length = 353

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 82/328 (25%), Positives = 162/328 (49%), Gaps = 22/328 (6%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RR L+  + G  IT  + + + 
Sbjct: 13  LQWKCVES-RIDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+++G+ E + +I++N+K I L+ +    +  +I  RGPG VTA DI     +E+++
Sbjct: 72  HEYSTMRGIQESVHEILMNLKEIVLRSNLYGTRNASICARGPGYVTAQDIILPPSVEIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I +L     + +EL + +  GY     +  +++      IDA++ P++  ++++ S
Sbjct: 132 NTQHIASLTEPINLYIELQIERNRGYHIKTPNNFQDES---YPIDAVFMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR   D    FI+ E+    + ++ +  +
Sbjct: 189 YGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNFIDLFIPFIHVEKENLYLGDNQDKDT 247

Query: 250 LPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P      +                 +++LEL  R  NCL+  NI  + DL+  ++ D++
Sbjct: 248 FPLFTFHDELAKLRKNKKEIALKYLFIDQLELPPRIYNCLKRSNIHTLLDLLNNSQEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGT-MGLFLGMN 320
           ++  F R+ + +I G+L   +  FL  N
Sbjct: 308 KIEYFRREDVKQIFGILEKHLNFFLTKN 335


>gi|228016583|gb|ACP51413.1| RNA polymerase alpha subunit [Abies firma]
          Length = 336

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 88/330 (26%), Positives = 157/330 (47%), Gaps = 25/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E     +           PL +G A T+G A+RR L+  + G  IT V++D + 
Sbjct: 13  LRWKCLESRAYSKRLH-YGRFALSPLCKGRADTIGIAMRRALLGEVEGTCITHVKLDNIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITFDIRLRIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED----- 244
              G  +  + L + I T+G +T  +++  ASR L D L  F++ EE   +   +     
Sbjct: 189 YGSGNEI-REVLFLEIWTNGGLTPREALYEASRNLIDLLIPFLHGEEQNIDGMNNRKGSS 247

Query: 245 ------------INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                          ++          +++LEL  R+ NCLR  NI  + DL+  +  D+
Sbjct: 248 NMPPFPLSHVFTDTGETKEKIAFQHIFIDQLELPPRTYNCLRRANIHTLLDLLNYSREDL 307

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           +R+ +FG++S+ ++  VL        +NLP
Sbjct: 308 MRIEHFGKESIEQVLEVLR---KRFAINLP 334


>gi|4379135|emb|CAA83722.1| DNA-directed RNA Polymerase (alpha) [Mycoplasma capricolum subsp.
           capricolum ATCC 27343]
          Length = 317

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 111/318 (34%), Positives = 183/318 (57%), Gaps = 10/318 (3%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
            ++ ++P  I  ++   +++N       PL RGF  TLGNA+RR L+++  GA++ A++I
Sbjct: 1   MKQFVRPEFI--LLKEGQDKNYGKXXVSPLERGFGITLGNAIRRTLLAATPGASVYAIKI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMS-----GDSHKRVTIFKRGPGVVTAGDIQ 120
            G  HE +SI G+ E++T IILNIK + L++       D   ++ I     G V AGD++
Sbjct: 59  AGATHEFTSIPGIIENVTKIILNIKQLVLRIDTSIYSDDEVVQLKIRSDIQGPVYAGDLE 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSP 179
               +EVLN D +I  +    ++ + L      GY   K ++ E N   G+ITID+ YSP
Sbjct: 119 LPAGVEVLNQDLLIATISEGGILDLVLYAKNSRGYKTFKDNKNEKNVEPGMITIDSNYSP 178

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I KV+Y+V+SA+ G+ +D +KL + + TDGSIT  D++++AS+IL   L  FI+      
Sbjct: 179 IIKVAYSVDSAKIGRAIDLEKLELEVTTDGSITAIDAISIASKILVAHLEFFIDLNREIS 238

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            ++  +   +   +  L + VEEL+ + RS NCL+   I  + +L+ + E ++  + N G
Sbjct: 239 VLE--VIGVNQTDDKELDRTVEELDFTQRSLNCLKRAGINTLRELVTKNEDEIGSIRNLG 296

Query: 300 RKSLVEIKGVLGTMGLFL 317
           RKSL EIK  + ++GL  
Sbjct: 297 RKSLKEIKDKVASLGLAF 314


>gi|311990563|gb|ADQ26408.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           helveticus]
          Length = 243

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 103/243 (42%), Positives = 151/243 (62%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   D  K + +
Sbjct: 1   LRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLSDERKVIEL 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
              GP  VTA D++   D++VLNPD  IC +     + ME+ V  G GYV A  +++++ 
Sbjct: 61  DVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNGRGYVAASDNKSDDM 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++ A++IL +
Sbjct: 121 PIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVE 180

Query: 227 QLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQ 286
              +F + +   K  +  +  +       L   +EEL+LSVRS NCL+   I  + +L  
Sbjct: 181 HFKVFESADADTKFSEVMVEKEDDKKEKKLEMTIEELDLSVRSYNCLKRAGINTLQELTD 240

Query: 287 RTE 289
            TE
Sbjct: 241 MTE 243


>gi|317016851|gb|ADU85966.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 238

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 93/238 (39%), Positives = 144/238 (60%), Gaps = 2/238 (0%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           +      + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T
Sbjct: 1   DARYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVT 60

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            IILN+K + L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     +
Sbjct: 61  QIILNLKKVVLAIDSDDERSLEIDVQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSL 120

Query: 144 RMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            M +T  KG GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL
Sbjct: 121 HMTVTAVKGRGYTSADENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGARDDYDKL 180

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           +  I T+GSI   D+++L ++IL + L +F++      E    +  + +  + +    
Sbjct: 181 TFDIWTNGSIKPSDALSLGAKILAEHLNLFMDISPVAAEAXVMVEAEPVAVSASDSAP 238


>gi|51859679|gb|AAU11119.1| RNA polymerase alpha subunit [Psathyrostachys lanuginosa]
          Length = 339

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGXVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 MAQPIANLTEPIDFCIDLRIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|32171671|sp|Q8MAI6|RPOA_LOPEL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|22657342|gb|AAM97474.1| RNA polymerase alpha subunit [Lophopyrum elongatum]
          Length = 339

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LPFN----------------PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D+L
Sbjct: 248 PPPFTFKKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|71056890|emb|CAH59001.1| DNA-directed RNA polymerase alpha chain [Enterococcus cecorum]
          Length = 235

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 105/233 (45%), Positives = 152/233 (65%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
             + I EPL RG+  TLGN+LRR+L+SSL GAAIT++QID V HE S+I GV ED++ II
Sbjct: 3   YGMFIVEPLERGYGTTLGNSLRRILLSSLPGAAITSIQIDTVQHEFSTIVGVREDVSQII 62

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LNIKG+ LK+ G   K + I   GP VVTAGDI   +D+E+LN D  IC +   A  R  
Sbjct: 63  LNIKGLALKLYGSEEKTLEIDITGPAVVTAGDIIVDSDVEILNKDMYICTVSEGATFRAR 122

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           L V  G GYV A  ++TE+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I 
Sbjct: 123 LKVKAGRGYVQADENKTEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIW 182

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           TDGSI   D+++LA++IL + L +F+N  +  +  +  +  +       L   
Sbjct: 183 TDGSIEPLDAMSLAAKILTEHLDIFVNLTDEARHAEIMVEKEETQKEKMLEMT 235


>gi|111115331|ref|YP_709949.1| DNA-directed RNA polymerase subunit alpha [Borrelia afzelii PKo]
 gi|119366667|sp|Q0SN05|RPOA_BORAP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|110890605|gb|ABH01773.1| DNA-directed RNA polymerase [Borrelia afzelii PKo]
          Length = 344

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 119/335 (35%), Positives = 185/335 (55%), Gaps = 19/335 (5%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +++  ++   P  IE++   Q++ +       P  RGF  T+GN LRRVL+SS+ G AIT
Sbjct: 3   MERFLKDFTIPEKIEFLK-SQDDGSYGKFTIYPFERGFGVTIGNTLRRVLLSSIEGYAIT 61

Query: 62  AVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
           A+++           V  E   I GV ED  ++I NIK I+LK+  +  +R TI     G
Sbjct: 62  AMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLEVIANIKNIHLKLR-EGEQRKTISFSVSG 120

Query: 113 ----VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
               V+ A   +    +EV N D VI  L  D  +  E  ++ G GYV ++ +    + +
Sbjct: 121 KDTNVLKASHFERD-GVEVFNKDLVIATLSHDVNLDFEFQINYGRGYVSSEQNSKYLEEV 179

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
            +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L
Sbjct: 180 NVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREFL 239

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
              ++FE+    V    +      +  L   +E+L+LSVRS NCL  EN+  +G+LI + 
Sbjct: 240 FPLVDFED---SVSVSFDKSKSESSNLLDMSIEKLDLSVRSLNCLAKENVRTLGELISKN 296

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
             ++ +  NFG+KSL EI   LG+  LFLGM+  D
Sbjct: 297 AEELSKARNFGKKSLEEIIEKLGSYQLFLGMSKED 331


>gi|229496135|ref|ZP_04389855.1| DNA-directed RNA polymerase, alpha subunit [Porphyromonas
           endodontalis ATCC 35406]
 gi|229316713|gb|EEN82626.1| DNA-directed RNA polymerase, alpha subunit [Porphyromonas
           endodontalis ATCC 35406]
          Length = 343

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 116/333 (34%), Positives = 187/333 (56%), Gaps = 17/333 (5%)

Query: 9   LIKPNNIEYIVL-------GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
             KP N+  + +        +  E       +PL  G+A T+GNALRR+L+SSL G AI 
Sbjct: 6   FQKPENVVKVEVPQYVLDECEPYELVGRFEFKPLEPGYAKTIGNALRRILLSSLEGYAIA 65

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM---SGDSHKRVTIFKRGPGVVTAGD 118
           +++IDGV HE ++I GV ED+T+IILN+K I  K    + D       F     V TA D
Sbjct: 66  SIRIDGVEHEFATIPGVTEDVTNIILNLKKIRFKQKVDNADEEVVTVAFPANKDVFTAED 125

Query: 119 I-QTVNDIEVLNPDHVICNLDV--DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDA 175
           +   + + E+ N D  IC+ D    + V++E  ++KG GYVP+  +  E DP+  I ID+
Sbjct: 126 LNAALGNFEITNLDQHICSFDPQVASNVKIEFRINKGRGYVPSDENAREGDPLNTIAIDS 185

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF---- 231
           +Y+PI++V    ES R  Q  DY+KL + + TDG+I  E ++  A++IL D   +F    
Sbjct: 186 IYTPIRRVMPKEESFRVEQKTDYEKLILEVVTDGTIEPEMALREAAKILIDLFSLFSDGE 245

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           ++ EE   E  + ++ ++L     L ++++   LSVR+ NCLR  N+  + DL++    +
Sbjct: 246 MHMEEAGDETGDVMDEETLRIRQMLRQELDSFNLSVRARNCLRSNNVFTLADLVKHNRQE 305

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           +L+  NFG+K+  E++G L  +GL    +L  +
Sbjct: 306 LLKFRNFGKKTFEELEGFLAEVGLEFATDLSKY 338


>gi|11465990|ref|NP_054532.1| RNA polymerase alpha subunit [Nicotiana tabacum]
 gi|78102570|ref|YP_358710.1| RNA polymerase alpha subunit [Nicotiana sylvestris]
 gi|133409|sp|P06269|RPOA_TOBAC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|90110850|sp|Q3C1M3|RPOA_NICSY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|11860|emb|CAA77376.1| RNA polymerase alpha subunit [Nicotiana tabacum]
 gi|10442805|gb|AAG15578.1| RNA polymerase alpha subunit [synthetic construct]
 gi|77799597|dbj|BAE46686.1| RNA polymerase alpha subunit [Nicotiana sylvestris]
 gi|225228|prf||1211235BK RNA polymerase alpha
          Length = 337

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 81/331 (24%), Positives = 161/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT V+ + V
Sbjct: 11  RTLQWKCVESRTDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRVKSEKV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  +GPG VTA DI     +E++
Sbjct: 71  PHEYSTITGIQESVHEILMNLKEIILRSNLYGTSDASICVKGPGSVTAQDIILPPYVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L       + L + +  GY+    H  ++   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDFCIGLQIERNRGYLIKTPHNFQD---GSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN-- 246
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEDNLYLQDNQHTV 246

Query: 247 --------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                         +K+          +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 PLSPFTFHDKLAKLIKNKKKIALKSIFIDQSELPSRIYNCLKMSNIYTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F      ++K +LG +  +  ++L  
Sbjct: 307 MKIEHFRS---EDVKRILGILEKYFVIDLAK 334


>gi|2500619|sp|P92418|RPOA_PSAFR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1771429|emb|CAB01333.1| alpha subunit of RNA polymerase [Psathyrostachys fragilis]
          Length = 339

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGXVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|7388079|sp|P92209|RPOA_AGRCR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1769834|emb|CAB01390.1| alpha subunit of RNA polymerase [Agropyron cristatum]
 gi|22657236|gb|AAM97421.1| RNA polymerase alpha subunit [Agropyron cristatum]
 gi|22657238|gb|AAM97422.1| RNA polymerase alpha subunit [Agropyron cristatum]
 gi|22657240|gb|AAM97423.1| RNA polymerase alpha subunit [Agropyron mongolicum]
          Length = 339

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 RAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D+L
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|290489686|gb|ADD31227.1| RNA polymerase alpha subunit protein [Ficus sp. Moore 315]
          Length = 323

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 82/329 (24%), Positives = 157/329 (47%), Gaps = 23/329 (6%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLR 56
           M+Q+      +P  +++  +    ++        I  PL RG A T+G A+RR L+  + 
Sbjct: 1   MVQEKVTVSTRP--LQWKCVESRADSKRLYYGRFILAPLMRGQADTIGIAMRRALLGEIE 58

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           G  IT V+ + + HE S+I G+ E + +I++N+K I L+ +    +  +I  +GP  VTA
Sbjct: 59  GTCITRVKFEKLPHEYSTIIGIQESVHEILMNLKEIVLRSNLYGTRDASICVKGPRYVTA 118

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
            DI     +E+++    I NL     + +EL + +  GY     +  +N   G   IDA+
Sbjct: 119 QDIILPPSVEIVDNTQHIANLTEPITLCIELQIKRDRGYRIKTPNNFQN---GSYPIDAV 175

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           + P++  ++++ S       + + L + I T+GS+T ++++  ASR L D    F + EE
Sbjct: 176 FMPVRNANHSIHSY-VNGNENQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFFHAEE 234

Query: 237 PKKEVKE-------------DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGD 283
             +  +                  K+          +++ EL+ R  NCL+  NI    D
Sbjct: 235 HLENNQHKGTLPLFNFHGRLAKPRKTKKEKALKYIYIDQSELTPRVYNCLKRSNINTFLD 294

Query: 284 LIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           L+  ++ +++++ +F  + +  I  VL  
Sbjct: 295 LLNNSQEELMKIKDFTIEDVKHILDVLEI 323


>gi|216263341|ref|ZP_03435336.1| DNA-directed RNA polymerase, alpha subunit [Borrelia afzelii ACA-1]
 gi|215980185|gb|EEC21006.1| DNA-directed RNA polymerase, alpha subunit [Borrelia afzelii ACA-1]
          Length = 342

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 119/335 (35%), Positives = 185/335 (55%), Gaps = 19/335 (5%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +++  ++   P  IE++   Q++ +       P  RGF  T+GN LRRVL+SS+ G AIT
Sbjct: 1   MERFLKDFTIPEKIEFLK-SQDDGSYGKFTIYPFERGFGVTIGNTLRRVLLSSIEGYAIT 59

Query: 62  AVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
           A+++           V  E   I GV ED  ++I NIK I+LK+  +  +R TI     G
Sbjct: 60  AMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLEVIANIKNIHLKLR-EGEQRKTISFSVSG 118

Query: 113 ----VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
               V+ A   +    +EV N D VI  L  D  +  E  ++ G GYV ++ +    + +
Sbjct: 119 KDTNVLKASHFERD-GVEVFNKDLVIATLSHDVNLDFEFQINYGRGYVSSEQNSKYLEEV 177

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
            +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L
Sbjct: 178 NVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREFL 237

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
              ++FE+    V    +      +  L   +E+L+LSVRS NCL  EN+  +G+LI + 
Sbjct: 238 FPLVDFED---SVSVSFDKSKSESSNLLDMSIEKLDLSVRSLNCLAKENVRTLGELISKN 294

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
             ++ +  NFG+KSL EI   LG+  LFLGM+  D
Sbjct: 295 AEELSKARNFGKKSLEEIIEKLGSYQLFLGMSKED 329


>gi|119953291|ref|YP_945500.1| DNA-directed RNA polymerase subunit alpha [Borrelia turicatae
           91E135]
 gi|119862062|gb|AAX17830.1| DNA-directed RNA polymerase alpha chain [Borrelia turicatae 91E135]
          Length = 344

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 119/325 (36%), Positives = 181/325 (55%), Gaps = 16/325 (4%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           ++   P+ IE++  G+++ +    I  P  +GF  T+GN LRRVL+SS+ G AI+A++I 
Sbjct: 9   KDFTIPDRIEFVR-GEDDSSYGKFIMYPFEKGFGVTIGNTLRRVLLSSIEGYAISAMRIQ 67

Query: 67  G--------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT--- 115
                    V  E   I GV ED  ++I NIK I+LK+  +     TI     G  T   
Sbjct: 68  SNQGGSLKIVSSEFDLIPGVVEDTLEVIANIKNIHLKLD-EGVNSTTISLSVNGKDTNVL 126

Query: 116 AGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDA 175
                    +EV N D VI  L  +A +  E  ++ G GYV ++ +    + +  I +D+
Sbjct: 127 KAVHLEREGVEVFNKDLVIATLSSEANLDFEFQINYGRGYVSSEQNAKYLEEVNTIALDS 186

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           ++SPI+KV+Y+VE  R GQ  DYDKL M I T G I+ +D++  A+ I++D L   +NFE
Sbjct: 187 IFSPIEKVTYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVRDFLLPLVNFE 246

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           +      E+  ++    +  L   +E+L LSVRS NCL  EN+  +G+LI ++  D+ + 
Sbjct: 247 DKVVHSVENSELRD---SDILSINIEKLNLSVRSLNCLTKENVKTLGELISKSAEDLSKA 303

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMN 320
            NFG+KSL EI   L T GLFLGM+
Sbjct: 304 RNFGKKSLEEIIEKLNTYGLFLGMS 328


>gi|68053189|sp|Q7H6G1|RPOA_PSEPI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|68053190|sp|Q7H6I5|RPOA_ELYCA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1769861|emb|CAB01378.1| alpha subunit of RNA polymerase [Australopyrum retrofractum]
 gi|1770228|emb|CAB01300.1| alpha subunit of RNA polymerase [Dasypyrum villosum]
 gi|1770247|emb|CAB01316.1| alpha subunit of RNA polymerase [Eremopyrum triticeum]
 gi|1770348|emb|CAB01321.1| alpha subunit of RNA polymerase [Henrardia persica]
 gi|1771184|emb|CAB01306.1| alpha subunit of RNA polymerase [Lophopyrum elongatum]
 gi|1771497|emb|CAB01309.1| alpha subunit of RNA polymerase [Pseudoroegneria spicata]
 gi|1771501|emb|CAB01324.1| alpha subunit of RNA polymerase [Peridictyon sanctum]
 gi|22657242|gb|AAM97424.1| RNA polymerase alpha subunit [Australopyrum retrofractum]
 gi|22657244|gb|AAM97425.1| RNA polymerase alpha subunit [Australopyrum velutinum]
 gi|22657264|gb|AAM97435.1| RNA polymerase alpha subunit [Dasypyrum villosum]
 gi|22657268|gb|AAM97437.1| RNA polymerase alpha subunit [Elymus canadensis]
 gi|22657272|gb|AAM97439.1| RNA polymerase alpha subunit [Elymus canadensis]
 gi|22657274|gb|AAM97440.1| RNA polymerase alpha subunit [Elymus ciliaris]
 gi|22657276|gb|AAM97441.1| RNA polymerase alpha subunit [Elymus elymoides]
 gi|22657278|gb|AAM97442.1| RNA polymerase alpha subunit [Elymus glaucus]
 gi|22657280|gb|AAM97443.1| RNA polymerase alpha subunit [Elymus glaucus]
 gi|22657282|gb|AAM97444.1| RNA polymerase alpha subunit [Elymus glaucus]
 gi|22657286|gb|AAM97446.1| RNA polymerase alpha subunit [Elymus lanceolatus]
 gi|22657288|gb|AAM97447.1| RNA polymerase alpha subunit [Elymus lanceolatus]
 gi|22657290|gb|AAM97448.1| RNA polymerase alpha subunit [Elymus trachycaulus]
 gi|22657292|gb|AAM97449.1| RNA polymerase alpha subunit [Elymus trachycaulus]
 gi|22657300|gb|AAM97453.1| RNA polymerase alpha subunit [Elymus wawawaiensis]
 gi|22657302|gb|AAM97454.1| RNA polymerase alpha subunit [Elymus wawawaiensis]
 gi|22657304|gb|AAM97455.1| RNA polymerase alpha subunit [Eremopyrum bonaepartis]
 gi|22657306|gb|AAM97456.1| RNA polymerase alpha subunit [Eremopyrum bonaepartis]
 gi|22657310|gb|AAM97458.1| RNA polymerase alpha subunit [Eremopyrum orientale]
 gi|22657312|gb|AAM97459.1| RNA polymerase alpha subunit [Henrardia persica]
 gi|22657316|gb|AAM97461.1| RNA polymerase alpha subunit [Peridictyon sanctum]
 gi|22657318|gb|AAM97462.1| RNA polymerase alpha subunit [Pseudoroegneria strigosa]
 gi|22657320|gb|AAM97463.1| RNA polymerase alpha subunit [Pseudoroegneria strigosa]
 gi|22657322|gb|AAM97464.1| RNA polymerase alpha subunit [Pseudoroegneria tauri subsp.
           libanotica]
 gi|22657324|gb|AAM97465.1| RNA polymerase alpha subunit [Pseudoroegneria spicata]
 gi|22657326|gb|AAM97466.1| RNA polymerase alpha subunit [Pseudoroegneria spicata]
 gi|22657328|gb|AAM97467.1| RNA polymerase alpha subunit [Pseudoroegneria spicata]
 gi|22657330|gb|AAM97468.1| RNA polymerase alpha subunit [Pseudoroegneria spicata]
 gi|34329585|gb|AAQ63942.1| RNA polymerase alpha subunit [Elymus repens]
 gi|34329587|gb|AAQ63943.1| RNA polymerase alpha subunit [Elymus repens]
 gi|34329589|gb|AAQ63944.1| RNA polymerase alpha subunit [Elymus repens]
 gi|34329591|gb|AAQ63945.1| RNA polymerase alpha subunit [Elymus repens]
 gi|34329593|gb|AAQ63946.1| RNA polymerase alpha subunit [Elymus repens]
 gi|34329595|gb|AAQ63947.1| RNA polymerase alpha subunit [Elymus repens]
 gi|73747864|gb|AAZ82833.1| RNA polymerase subunit a [Elymus abolinii]
 gi|73747866|gb|AAZ82834.1| RNA polymerase subunit a [Elymus caucasicus]
 gi|317017396|gb|ADU86100.1| RNA polymerase alpha subunit [Elymus caucasicus]
 gi|317017398|gb|ADU86101.1| RNA polymerase alpha subunit [Elymus canadensis]
 gi|317017400|gb|ADU86102.1| RNA polymerase alpha subunit [Elymus semicostatus]
 gi|317017402|gb|ADU86103.1| RNA polymerase alpha subunit [Elymus sibiricus]
          Length = 339

 Score =  264 bits (676), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D+L
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|261749445|ref|YP_003257131.1| DNA-directed RNA polymerase subunit alpha [Blattabacterium sp.
           (Periplaneta americana) str. BPLAN]
 gi|261497538|gb|ACX83988.1| DNA-directed RNA polymerase subunit alpha [Blattabacterium sp.
           (Periplaneta americana) str. BPLAN]
          Length = 332

 Score =  264 bits (676), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 117/327 (35%), Positives = 197/327 (60%), Gaps = 12/327 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           + +KP+ I    + +  + + +   +PL  G+  TLGNALRRVL+ SL+G A+T+++I G
Sbjct: 5   DFVKPDRI---TISEFTDQKGIFHLKPLEPGYGLTLGNALRRVLLGSLKGFAVTSIKIKG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINL--KMSGDSHKRVTIFKRGPGVVTAGDI-QTVND 124
           V +E S+I+GV ED+T+IILN K I    K+ G + + + +  +    VT   + + ++ 
Sbjct: 62  VKYEFSTIEGVVEDVTEIILNFKKIRFHRKIKGVTKETINVLIKNKEKVTGKILNEFISS 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT-ENDPIGLITIDALYSPIKKV 183
            +VLN D VIC+ +    + M  T+ +G GYVPA+ ++   ND IG I ID++Y+PIK V
Sbjct: 122 FQVLNTDVVICHKEKSIPLEMSFTIEEGRGYVPAEENKKNNNDLIGNIPIDSIYTPIKNV 181

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF-----EEPK 238
            YT+E+ R GQ  D++ LS+ I TDGS++ + ++  AS+IL     +F +      E  +
Sbjct: 182 KYTIENCRVGQKTDFESLSLEIITDGSMSPKTALMEASQILIKYFSIFSHEKIGKKEHEE 241

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              +   + + L     L  K+ +++LSVR+ NCL+  +I  + DL+    ++ML+M NF
Sbjct: 242 ISKERKYDEEFLRMRTLLKSKLTDMDLSVRTKNCLKSASIQSVADLVNCNRSNMLKMRNF 301

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           GRKSL E++  +   GL+ GM++ ++ 
Sbjct: 302 GRKSLEELESQMKEKGLYFGMDISEYK 328


>gi|1771084|emb|CAB01369.1| alpha subunit of RNA polymerase [Hordeum vulgare subsp. spontaneum]
          Length = 339

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 159/328 (48%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E ++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVETVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+  F    + + K +  T+   L ++L
Sbjct: 308 RIDXFR---MEDRKHIWDTLEKHLPIDL 332


>gi|22657232|gb|AAM97419.1| RNA polymerase alpha subunit [Aegilops tauschii]
          Length = 339

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D+L
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNSIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|203287946|ref|YP_002222961.1| DNA-directed RNA polymerase [Borrelia recurrentis A1]
 gi|201085166|gb|ACH94740.1| DNA-directed RNA polymerase [Borrelia recurrentis A1]
          Length = 343

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 114/325 (35%), Positives = 185/325 (56%), Gaps = 16/325 (4%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           ++   P+ IE++  G+++ +    +  P  +GF  T+GN LRRVL+SS+ G AI+A++I 
Sbjct: 8   KDFTIPDRIEFVR-GEDDGSYGKFVIYPFEKGFGVTIGNTLRRVLLSSIEGYAISAMRIQ 66

Query: 67  G--------VLHEISSIKGVHEDLTDIILNIKGINLKMSG---DSHKRVTIFKRGPGVVT 115
                    V  E   I GV ED  ++I NIK ++LK+     ++   +++  +   V+ 
Sbjct: 67  SNQEESLKIVSSEFDLIPGVMEDTLEVIANIKNVHLKLDEGVTNTTINLSVNGKDNNVLK 126

Query: 116 AGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDA 175
           AG ++    +EV N D VI  L  DA +  E  V+ G GYV ++ +    + +  I +D+
Sbjct: 127 AGHLERE-GVEVFNKDLVIATLSSDANLDFEFQVNYGRGYVSSEQNAKYLEEVNTIALDS 185

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           ++SPI+KV+Y+VE  R GQ  DYDKL M I T G I+ +D++  A+ ++++ L   +NFE
Sbjct: 186 IFSPIEKVTYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASVVREFLLPLVNFE 245

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           +        ++      +  L   VE+L LSVRS NCL  EN+  +G+LI ++  ++ + 
Sbjct: 246 DKVIH---SVDYAEFRDSDILSMNVEKLNLSVRSLNCLIKENVKTLGELISKSPVELSKA 302

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMN 320
            NFG+KSL EI   L   GLFLGM+
Sbjct: 303 RNFGKKSLEEIVEKLNAYGLFLGMS 327


>gi|41688709|sp|Q8MAI9|RPOA_ELYCL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|22657266|gb|AAM97436.1| RNA polymerase alpha subunit [Leymus californicus]
          Length = 339

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFWSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFH---MEDRKHIWDTLEKHLPIDL 332


>gi|309322375|ref|YP_003934455.1| RNA polymerase alpha chain [Cathaya argyrophylla]
 gi|307683301|dbj|BAJ19608.1| RNA polymerase alpha chain [Cathaya argyrophylla]
          Length = 335

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 90/329 (27%), Positives = 162/329 (49%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE  V  +        +  PL +G A T+G A+RR L+  ++G  IT V+++ + 
Sbjct: 13  LRWKCIESRVYSKRFH-YGRFVLSPLRKGRADTIGIAMRRALLGEVKGTCITHVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIQEASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITFDIRLRIEKNRGYLI---HSPTNYGDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK---EVKEDIN 246
              G  +  + L + I T+G +T  +++  ASR L +    F++ EE        ++  N
Sbjct: 189 YGSGNEI-REVLFLEIWTNGGLTPREALYEASRNLINFFIPFLHGEEQNIDGMNSRKGSN 247

Query: 247 VKSLPFNPALLKK-------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           + S P +  L                +++LEL  R  NCLR  NI  + DL+  ++ D++
Sbjct: 248 IPSFPLSHVLTNTGETKEIFEFQHIFIDQLELPSRIYNCLRRANIYTLLDLLNYSQEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+  FG+KS+ ++  +L        ++LP
Sbjct: 308 RIEQFGKKSVEQVLEILR---KRFAIDLP 333


>gi|297567256|ref|YP_003686228.1| DNA-directed RNA polymerase subunit alpha [Meiothermus silvanus DSM
           9946]
 gi|296851705|gb|ADH64720.1| DNA-directed RNA polymerase, alpha subunit [Meiothermus silvanus
           DSM 9946]
          Length = 319

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 107/302 (35%), Positives = 170/302 (56%), Gaps = 10/302 (3%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           + N    + EPL RGF  TLGN +RR+L+SS+ G A+T+V I+ VLHE S+I GV ED+ 
Sbjct: 16  DGNYGEFVLEPLERGFGVTLGNPIRRILLSSIPGTAVTSVYIEDVLHEFSTINGVKEDVV 75

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            +ILN+K + +K      K +T+  +GP  V A D++   D EV+NPD  +  L   A +
Sbjct: 76  QLILNLKELVVKFHTPGSKTLTLRAQGPRSVYARDLEVPADAEVVNPDLYLATLGEGARL 135

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            ME+ V +G GYVPA+ H  ++     I +DAL+SP+++V++ VE  R GQ  D DKL++
Sbjct: 136 VMEVRVDEGVGYVPAEKHGIKDRIS-SIPVDALFSPVRRVAFQVEDTRLGQRTDLDKLTL 194

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK----- 258
            I TDGS++  + +  +  IL++QL  F      + E ++   V + P            
Sbjct: 195 RIWTDGSVSPMEVLQRSVAILREQLSFFDQSPVIRVEKEKPAPVAAAPAPSPATPAAAAV 254

Query: 259 ----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +++L L+ R  + L+ E I  +  L+  +E ++ ++   G +SL EIK +L   G
Sbjct: 255 STGLTLDDLGLTTRVLHNLKEEGIESVESLLALSERELKKVPGIGERSLQEIKDILAQHG 314

Query: 315 LF 316
           L 
Sbjct: 315 LE 316


>gi|71056886|emb|CAH58999.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           saccharolyticus]
          Length = 231

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 105/231 (45%), Positives = 150/231 (64%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
             I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILN
Sbjct: 1   KFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILN 60

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           IKG+ LKM G+  K + I   GP  VTAGDI   +D+E+LN D  IC +         LT
Sbjct: 61  IKGLALKMYGEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGTTFHARLT 120

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TD
Sbjct: 121 VRPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTD 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           GSI   D+++LA++I+ + L +F+N  +  K  +  +  +       L   
Sbjct: 181 GSIEPLDAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMT 231


>gi|7388080|sp|P93993|RPOA_AUSVE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1769912|emb|CAB01381.1| alpha subunit of RNA polymerase [Australopyrum velutinum]
          Length = 339

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVXMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D+L
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|296936704|gb|ADH94376.1| RNA polymerase alpha subunit [Syzygium cumini]
          Length = 337

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 77/324 (23%), Positives = 156/324 (48%), Gaps = 27/324 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +    +  +I  +GPG VTA DI     +E++
Sbjct: 71  PHEYSTIVGIQESVHEILMNLKEIVLRSNLYGTRNASICVKGPGCVTAQDIILPTSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY        ++   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQYIASLTEPINLCIGLQIERNRGYHIKTPKNFQD---GSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV- 247
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ +    
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLENNQYKV 246

Query: 248 ---------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                          K+          +++ EL  R+ NCL+  NI  + DL+ +++ D+
Sbjct: 247 TLPLFTFHDRLVKLRKTKKEIALKSIFIDQFELPPRTYNCLKRYNIHTLFDLLNKSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLF 316
           ++M  F    + ++K +L ++ + 
Sbjct: 307 MKMEYFR---IEDVKQILNSLEIE 327


>gi|7388095|sp|P93974|RPOA_EREDI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1770241|emb|CAB01312.1| alpha subunit of RNA polymerase [Eremopyrum distans]
 gi|22657308|gb|AAM97457.1| RNA polymerase alpha subunit [Eremopyrum orientale]
          Length = 339

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D+L
Sbjct: 248 PPLFTFKKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|260656838|gb|ACX47809.1| RNA polymerase alpha-subunit [Vibrio casei]
          Length = 275

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 121/277 (43%), Positives = 181/277 (65%), Gaps = 8/277 (2%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
               +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I
Sbjct: 2   THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEI 61

Query: 86  ILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVV 143
           +LN+KG+ + +  G     +T+ K G G V AGDI    D+E+ NP+HVIC+L  D A +
Sbjct: 62  LLNLKGLAVSVAEGKDEVFITLKKSGSGPVVAGDIIHDGDVEIANPEHVICHLTDDKAEI 121

Query: 144 RMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
            M + V +G GYVP+    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DK
Sbjct: 122 AMRIKVQRGRGYVPSSARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDK 181

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V
Sbjct: 182 LVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPV 238

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 239 DDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 275


>gi|7388091|sp|P93960|RPOA_PSARU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1771473|emb|CAB01342.1| alpha subunit of RNA polymerase [Psathyrostachys rupestris]
          Length = 339

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGXVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TXQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNYIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|50364965|ref|YP_053390.1| DNA-directed RNA polymerase subunit alpha [Mesoplasma florum L1]
 gi|61215913|sp|Q6F1W7|RPOA_MESFL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|50363521|gb|AAT75506.1| DNA-directed RNA polymerase alpha chain [Mesoplasma florum L1]
          Length = 317

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 116/321 (36%), Positives = 169/321 (52%), Gaps = 10/321 (3%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
            ++  KP     IV     +      A PL RGFA TLGNALRR L+SS  GA++ A++I
Sbjct: 1   MKQFNKPEF--GIVKESPNKFYGKFEAAPLERGFAVTLGNALRRTLLSSTPGASVFAIKI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSG-----DSHKRVTIFKRGPGVVTAGDIQ 120
            G  HE +SI G+ E++T I+LN+K + L++       D    + +     G VTAG + 
Sbjct: 59  AGAQHEFTSISGIEENVTRIVLNVKKLILRIDSAIYNDDETVELKVGTSTIGPVTAGSLV 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT-ENDPIGLITIDALYSP 179
               +EVLN D VI N+     + + L      GY   K ++  ++   G+ITID+ YSP
Sbjct: 119 LPAGVEVLNKDLVIANVAEGGNLDLVLYAKNSRGYKTFKENKELKDVVPGMITIDSNYSP 178

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I KV+Y       G+  D++KL + ++TDGSI   D+V+LAS+IL     +F    E  +
Sbjct: 179 IIKVAYGSTPINLGKAQDFEKLILEVETDGSILASDAVSLASKILISHFDVFTTLAEEVE 238

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           EV              L K VEELE + RS NCL+   I  + +L+ +TE ++  + N G
Sbjct: 239 EVAIM--GVETVEEKELDKPVEELEFTQRSLNCLKRAGISTLRELVSKTEDEIQDIRNLG 296

Query: 300 RKSLVEIKGVLGTMGLFLGMN 320
           RKSL EIK  +  + L    N
Sbjct: 297 RKSLKEIKDKVAALELTFKQN 317


>gi|203284412|ref|YP_002222152.1| DNA-directed RNA polymerase [Borrelia duttonii Ly]
 gi|201083855|gb|ACH93446.1| DNA-directed RNA polymerase [Borrelia duttonii Ly]
          Length = 343

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 115/325 (35%), Positives = 185/325 (56%), Gaps = 16/325 (4%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           ++   P+ IE++  G+++ +    I  P  +GF  T+GN LRRVL+SS+ G AI+A++I 
Sbjct: 8   KDFTIPDRIEFVR-GEDDGSYGKFIIYPFEKGFGVTIGNTLRRVLLSSIEGYAISAMRIQ 66

Query: 67  G--------VLHEISSIKGVHEDLTDIILNIKGINLKMSG---DSHKRVTIFKRGPGVVT 115
                    V  E   I GV ED  ++I NIK ++LK+     ++   +++  +   V+ 
Sbjct: 67  SNQEESLKIVSSEFDLIPGVMEDTLEVIANIKNVHLKLDEGVTNTTINLSVNGKDNNVLK 126

Query: 116 AGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDA 175
           AG ++    +EV N D VI  L  DA +  E  V+ G GYV ++ +    + +  I +D+
Sbjct: 127 AGHLERE-GVEVFNKDLVIATLSSDANLDFEFQVNYGRGYVSSEQNAKYLEEVNTIALDS 185

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           ++SPI+KV+Y+VE  R GQ  DYDKL M I T G I+ +D++  A+ ++++ L   +NFE
Sbjct: 186 IFSPIEKVTYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASVVREFLLPLVNFE 245

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           +        ++      +  L   VE+L LSVRS NCL  EN+  +G+LI ++  ++ + 
Sbjct: 246 DKVIH---SVDYAEFRDSDILSMNVEKLNLSVRSLNCLIKENVKTLGELISKSPVELSKA 302

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMN 320
            NFG+KSL EI   L   GLFLGM+
Sbjct: 303 RNFGKKSLEEIVEKLNAYGLFLGMS 327


>gi|2500618|sp|P92429|RPOA_AEGTA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1771509|emb|CAB01351.1| alpha subunit of RNA polymerase [Aegilops tauschii]
          Length = 339

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D+L
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNSIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|7388090|sp|P93956|RPOA_FESSE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1770282|emb|CAB01778.1| alpha subunit of RNA polymerase [Festucopsis serpentini]
 gi|22657262|gb|AAM97434.1| RNA polymerase alpha subunit [Dasypyrum villosum]
          Length = 339

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFWSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D+L
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|313680487|ref|YP_004058226.1| DNA-directed RNA polymerase subunit alpha [Oceanithermus profundus
           DSM 14977]
 gi|313153202|gb|ADR37053.1| DNA-directed RNA polymerase subunit alpha [Oceanithermus profundus
           DSM 14977]
          Length = 322

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 114/312 (36%), Positives = 170/312 (54%), Gaps = 12/312 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           ++  + E N    + EPL RGF  TLGN LRR+LMSS+ G A+T+V I+  LHE +++ G
Sbjct: 11  VLTSRVEGNYGEFVLEPLERGFGVTLGNPLRRILMSSIPGTAVTSVYIEDALHEFATLPG 70

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           + ED+  I+LN+K + +K      K + +   GP  V A D+   +  E++NPD  I  L
Sbjct: 71  IKEDVVQIVLNLKELIVKFHEPGSKTLLLRVEGPREVYARDLVVPSSAELVNPDLYIATL 130

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
              A + ME+ V +G GYV A+ H  ++  I  I +DAL+SPIK+V++ VE  R GQ  D
Sbjct: 131 GEGAKLVMEVRVDEGVGYVAAEKHGIKDR-INSIPVDALFSPIKRVAFHVEDTRLGQRTD 189

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
            DKL + I TDGS+T + ++A A  IL+ QLG F           E     +    PA  
Sbjct: 190 LDKLILRIWTDGSVTPDAALAQAVEILRGQLGYFDQLAPQAAPEPEAAEAPAPEAAPAEP 249

Query: 258 KK-----------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           ++           +E+L LS R  + LR E I  + +L   TE ++ ++   G +S+ EI
Sbjct: 250 EEAAAEPGREGIALEDLGLSTRVLHNLREEGIDSVANLTALTERELKKVPGIGERSVEEI 309

Query: 307 KGVLGTMGLFLG 318
           K  L  +GL L 
Sbjct: 310 KERLAALGLALK 321


>gi|313292078|gb|ADR51228.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
          Length = 241

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 106/234 (45%), Positives = 154/234 (65%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED
Sbjct: 6   DEEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVRED 65

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +T IILNIKG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A
Sbjct: 66  VTQIILNIKGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGA 125

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
                LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL
Sbjct: 126 TFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKL 185

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           +M I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       
Sbjct: 186 TMEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 239


>gi|73747868|gb|AAZ82835.1| RNA polymerase subunit a [Elymus dentatus]
          Length = 339

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICIKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D+L
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|71056892|emb|CAH59003.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           phoeniculicola]
 gi|72534418|emb|CAH59045.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           phoeniculicola]
          Length = 230

 Score =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 106/230 (46%), Positives = 152/230 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV
Sbjct: 61  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLYICSVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 121 RPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           SI   ++++LA++I+ + L +F+N  +  +  +  +  +       L   
Sbjct: 181 SIEPLEAMSLAAKIMTEHLDIFVNLTDEARNAEIMVEKEETQKEKMLEMT 230


>gi|54144446|dbj|BAD60947.1| DNA-dependent RNA polymerase alpha subunit [Sphagnum girgensohnii]
          Length = 341

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 86/332 (25%), Positives = 161/332 (48%), Gaps = 24/332 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E  V  +           P   G A+T+G A+RR L+  + G  IT  + + V 
Sbjct: 14  LQWRCVESKVDSERLH-YGRFAISPFRSGQANTVGIAVRRALLGGVEGTCITRAKSEKVT 72

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           HE S+I G+ E + DI++N+K I LK   +    ++  +   GP  VTA DI     +EV
Sbjct: 73  HEYSTILGIQESVRDILINLKEIVLKSKSNSCETQKAFLSIFGPKEVTARDIVFPPSVEV 132

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           ++    I  L     + +EL + K  GY      ++ +   G  ++DA+++PI+  +Y+V
Sbjct: 133 IDTTQYIATLTKAIHLDIELKIEKDCGYRTQDSIKSAD---GYFSVDAVFTPIRNANYSV 189

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK-------KE 240
            S         + L + I T+GS+T ++++  ASR L D    F++ E+ +       K 
Sbjct: 190 HSFENKNET-QEILFIEIWTNGSVTPKEALYEASRSLIDLFIPFLHAEKEEVMHGLGNKN 248

Query: 241 VKEDINVKSLPFNPALLKK-------VEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
               ++  S P    + K+       +++LEL  R+ NC +  ++  + DL+  ++ D++
Sbjct: 249 ESNTLHFSSSPSENKMEKEMTFKHIFIDQLELPARAYNCPKRVDVHTISDLLSYSQDDLM 308

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           ++ NFG+KS+ ++   L  +     + LP   
Sbjct: 309 KIKNFGKKSVEQV---LEALQKRFSIKLPKKK 337


>gi|58758766|gb|AAW81772.1| RNA polymerase alpha subunit [Buxbaumia aphylla]
          Length = 340

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 90/342 (26%), Positives = 169/342 (49%), Gaps = 27/342 (7%)

Query: 1   MIQKNW---QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRG 57
           MIQ       ++++   +E   +  E  + +     P   G A+T+G A+RR L+  ++G
Sbjct: 1   MIQNEILISAQVLQWRCVESK-IDNERLHYSRFAISPFRCGQANTVGIAMRRALLGEVKG 59

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
            +IT  + + V HE S+I G+ E + DI +N K I L+ +    ++  I   GP  +TA 
Sbjct: 60  TSITCAKFEKVTHEYSTIAGIQESVHDISINSKEIVLESNSSETQKAFISILGPKKITAQ 119

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI     +++++    I  L     + +EL + K +GY     +++ N       IDA++
Sbjct: 120 DIILPPSVKIIDGKQYIATLTKAIQLDIELEIEKDYGYRIQNSNKSTNS---HFFIDAIF 176

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-- 235
            PI+  +Y+V S         + L + I T+GSIT +D++  ASR L D    F++ E  
Sbjct: 177 MPIRNANYSVHSFENENKT-QEMLFIEIWTNGSITPKDALYEASRSLIDLFIPFLHAERR 235

Query: 236 EPKKEVKEDINVKSLPFNPALLK--------------KVEELELSVRSTNCLRGENIVYM 281
           E   E++ +  + ++ +  +                  +++LEL  R+ NCL+  N+  +
Sbjct: 236 EIINELENEYKLSNISYFSSFSPLADKITKEVSFKHIFIDQLELPARAYNCLKRVNVNTL 295

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            DL+  ++ D++++ NFG+KS+ ++   L  +     +NLP 
Sbjct: 296 ADLLNYSQEDLMKIKNFGKKSVEQV---LEALQKQFSINLPK 334


>gi|71056908|emb|CAH59011.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
 gi|71056945|emb|CAH59032.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
          Length = 226

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 106/226 (46%), Positives = 151/226 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  ICN+   A     LTV
Sbjct: 61  KGLALKMYGDEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICNVSEGASFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           SI   ++++LA++I+ + L +F+N  +  K  +  +  +       
Sbjct: 181 SIEPLEAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 226


>gi|153799484|gb|ABS50517.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 240

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 102/240 (42%), Positives = 152/240 (63%), Gaps = 4/240 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLH
Sbjct: 3   KPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLH 58

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++VLNP
Sbjct: 59  EFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQVLNP 118

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES 
Sbjct: 119 DQYICTIAEGGHLHMELAVKNGRGYVTASDNKSDDMPIGVIPVDSLFSPIKKVNYQVEST 178

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   +  +  +  +  
Sbjct: 179 RVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADANTQFSEVMVEKEDD 238


>gi|224531785|ref|ZP_03672417.1| DNA-directed RNA polymerase, alpha subunit [Borrelia valaisiana
           VS116]
 gi|224511250|gb|EEF81656.1| DNA-directed RNA polymerase, alpha subunit [Borrelia valaisiana
           VS116]
          Length = 344

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 123/335 (36%), Positives = 187/335 (55%), Gaps = 19/335 (5%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++K  ++   P  IE++   Q++ +       P  RGF  T+GN LRRVL+SS+ G AIT
Sbjct: 3   VEKFLKDFTIPEKIEFLK-SQDDGSYGKFTIYPFERGFGVTIGNTLRRVLLSSIEGYAIT 61

Query: 62  AVQIDGVLHEISS---------IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
           A+++     + SS         I GV ED  ++I NIK I+LK+ G+  +R TI     G
Sbjct: 62  AMRVQSNNKDSSSKIVSSEFDLIPGVSEDTLEVIANIKNIHLKL-GEGEQRKTISFSISG 120

Query: 113 ----VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
               V+ A   +    +EV N D VI NL  DA +  E  ++ G GYV ++ +    + +
Sbjct: 121 KDTSVLKASHFERD-GVEVFNKDLVIANLSHDANLDFEFQINYGRGYVSSEQNSKYLEEV 179

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
            +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L
Sbjct: 180 NVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREFL 239

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
              ++FE+    V              L   +E+L+LSVRS NCL  EN+  +G+LI + 
Sbjct: 240 FPLVDFED---NVNISFEKSKSESYNLLDMSIEKLDLSVRSLNCLAKENVRTLGELISKN 296

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
             ++ +  NFG+KSL EI   LG+  LFLGM+  D
Sbjct: 297 AEELSKARNFGKKSLEEIIEKLGSYRLFLGMSKED 331


>gi|291296963|ref|YP_003508361.1| DNA-directed RNA polymerase subunit alpha [Meiothermus ruber DSM
           1279]
 gi|290471922|gb|ADD29341.1| DNA-directed RNA polymerase, alpha subunit [Meiothermus ruber DSM
           1279]
          Length = 321

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 113/303 (37%), Positives = 170/303 (56%), Gaps = 12/303 (3%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           + N    + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED  
Sbjct: 16  DGNYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDAI 75

Query: 84  DIILNIKGINLKM--SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
            +ILN+K + ++    G   K +T+   GP V+ A D++   D EV+NPD  I  L+   
Sbjct: 76  QLILNLKELVVRFANPGTGPKTLTLRASGPKVIYARDLECPPDAEVVNPDQYIATLEEKG 135

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ME+ V +G GYVPA+ H  ++     I +DALYSP+++V+Y VE  R GQ  D DKL
Sbjct: 136 KLVMEIRVDEGVGYVPAEKHGIKDRIS-SIPVDALYSPVRRVAYQVEDTRLGQRTDLDKL 194

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALL 257
           ++ I T+G+++  D++  A  IL++QLG F    +   EPK          +     A  
Sbjct: 195 TLRIWTNGAVSPMDALQQAVAILREQLGYFDQSPVMRVEPKSTPAPAPAAPATTAPAAPA 254

Query: 258 KK-----VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                  +++L L+ R  + L+ E I  +  L+  +E ++ R+   G +SL EIK  L  
Sbjct: 255 SPGVGLTLDDLGLTTRVLHNLKEEGIESVESLLALSEKELRRVPGIGDRSLQEIKDCLAQ 314

Query: 313 MGL 315
            GL
Sbjct: 315 HGL 317


>gi|300431268|gb|ADK12599.1| RNA polymerase alpha subunit [Poa holciformis]
          Length = 341

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 93/330 (28%), Positives = 161/330 (48%), Gaps = 26/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     IE+++
Sbjct: 72  HEYSTIGGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSIEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TSQPIANLTEPIDFCIELQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP------------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
            P                    P     +++LEL  R+ NCL+  NI  + DL+ +TE D
Sbjct: 248 PPLLTFQKRLTNLNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEED 307

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           ++R+ +F    + + K +  T+  +L ++L
Sbjct: 308 LMRIDSFR---MEDRKQIWDTLENYLPIDL 334


>gi|307683665|dbj|BAJ19811.1| RNA polymerase alpha chain [Picea morrisonicola]
          Length = 336

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 88/330 (26%), Positives = 154/330 (46%), Gaps = 25/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RRVL+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSERLH-YGRFALSPLRKGRADTIGIAMRRVLLGEVEGTCITHVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I   GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIRGASICIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE------------- 236
              G  +  + L + I T+G +T  ++++ ASRIL +    F++ EE             
Sbjct: 189 YGNGNEI-REVLFLEIWTNGGLTPREALSEASRILIELFIPFLHGEEQNIDGMNNRKGSN 247

Query: 237 ----PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
               P   V  D               +++LEL  R  NCLR  NI  + DL+  +  D+
Sbjct: 248 MPPFPLSHVLTDTGETKEKKIAFQHIFIDQLELPPRVYNCLRRANIHTLSDLLNYSREDL 307

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           +R+  FG++S+ ++  +L        ++ P
Sbjct: 308 MRIERFGKESVEQVFEILR---KRFAIDPP 334


>gi|227871774|ref|ZP_03990179.1| DNA-directed RNA polymerase [Oribacterium sinus F0268]
 gi|227842375|gb|EEJ52600.1| DNA-directed RNA polymerase [Oribacterium sinus F0268]
          Length = 314

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 97/312 (31%), Positives = 175/312 (56%), Gaps = 5/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE + +  E++     + EPL RG+  TLGN+LRR+++SSL GAAI+A++I+ 
Sbjct: 3   DFTKPN-IEILEIS-EDKRFGRFVCEPLERGYGSTLGNSLRRMMLSSLPGAAISAIKIEN 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           +  +   + G+ E   +++ N+K I + +  +     V++   G   + A D    ++++
Sbjct: 61  LSGD--KVSGIQESFPELLTNLKSIAVILPEEVESLEVSVDLSGKSEILAEDFIGESELK 118

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           + NP   I  ++  A   + L +S+G GY   K       P     IDALY+P+++V+ +
Sbjct: 119 LSNPTEHIATVEAGAQGSISLFISRGQGYSGEKAEGRVEAPKEYQDIDALYTPVERVNMS 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           +E+ R G + DYD+L++ + T+GS++ ED+++ A+++L   L +F+   E     +  ++
Sbjct: 179 IENTRVGNMTDYDRLTLDVYTNGSMSPEDAISKAAQMLFQHLDLFVALSEEVAATELMVD 238

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
                    +   ++ELELSVRS NCL+   I  + +L  +T  DM+++ N GRKSL E+
Sbjct: 239 KPEDEKGKVMEMNIDELELSVRSYNCLKRAGINTVSELTSKTPEDMMKVRNLGRKSLEEV 298

Query: 307 KGVLGTMGLFLG 318
              L  + L L 
Sbjct: 299 LAKLRDLNLGLS 310


>gi|71056840|emb|CAH58975.1| DNA-directed RNA polymerase alpha chain [Enterococcus hirae]
          Length = 235

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 105/233 (45%), Positives = 151/233 (64%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T II
Sbjct: 3   YGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQII 62

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LNIKG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     
Sbjct: 63  LNIKGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHAR 122

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I 
Sbjct: 123 LTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIW 182

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   
Sbjct: 183 TDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMT 235


>gi|302584003|gb|ADL57236.1| RNA polymerase A [Paralactobacillus selangorensis]
          Length = 222

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 99/222 (44%), Positives = 148/222 (66%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAA+T VQIDGVLHE S+I GV ED+T IILNIK + 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAVTDVQIDGVLHEFSTIDGVVEDVTQIILNIKKLA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +KM G+  + + +   GP  VTA DI T  D+E+LNPD  +C +     +   +TV KG 
Sbjct: 61  IKMEGEEDRTIELDVTGPAKVTAADIHTDADVEILNPDLYLCTVSDGGSIHARMTVKKGR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GY   K +++E+ PIG++ ID++Y+PI +V+Y VES R G+  DYDKL++ + T+GSI+ 
Sbjct: 121 GYDSWKENKSEDMPIGVLPIDSIYTPISRVNYQVESTRVGRRSDYDKLTLDVWTNGSISP 180

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            ++++LA++IL + L +F+N  +  K  +  +  +       
Sbjct: 181 REAISLAAKILTEHLAIFVNLTDEAKNAEIMVEKEETHKEKM 222


>gi|219684168|ref|ZP_03539112.1| DNA-directed RNA polymerase, alpha subunit [Borrelia garinii PBr]
 gi|219672157|gb|EED29210.1| DNA-directed RNA polymerase, alpha subunit [Borrelia garinii PBr]
          Length = 344

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 121/335 (36%), Positives = 184/335 (54%), Gaps = 19/335 (5%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++K  ++   P  IE++   Q + +       P  RGF  T+GN LRRVL+SS+ G AIT
Sbjct: 3   VEKFLKDFTIPEKIEFLK-SQGDGSYGKFTIYPFERGFGVTIGNTLRRVLLSSIEGYAIT 61

Query: 62  AVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
           A++I           V  E   I GV ED  ++I NIK I+LK+ G+  +R TI     G
Sbjct: 62  AMRIQSNNKDSSSKVVSSEFDLIPGVSEDTLEVIANIKNIHLKL-GEGEQRKTISFSVSG 120

Query: 113 ----VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
               V+ A   +    +EV N D VI  L  D  + +E  ++ G GYV ++ +    + +
Sbjct: 121 KDTKVLKASHFERD-GVEVFNRDLVIATLSQDVNLDLEFQINYGRGYVSSEQNSKYLEEV 179

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
            +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L
Sbjct: 180 NVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIIREFL 239

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
              ++FE+    V           +  L   +E+L+LSVRS NCL  EN+  +G+LI + 
Sbjct: 240 FPLVDFED---NVNTSFEKSKSESSNLLDMSIEKLDLSVRSLNCLAKENVRTLGELISKN 296

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
             ++ +  NFG+KSL EI   L +  LFLGM+  D
Sbjct: 297 AEELSKARNFGKKSLEEIIEKLSSYQLFLGMSKED 331


>gi|71056802|emb|CAH58956.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 234

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 108/234 (46%), Positives = 154/234 (65%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
             I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILN
Sbjct: 1   KFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILN 60

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           IKG+ LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LT
Sbjct: 61  IKGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLT 120

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TD
Sbjct: 121 VKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTD 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           GSI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 181 GSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEE 234


>gi|254527170|ref|ZP_05139222.1| DNA-directed RNA polymerase, alpha subunit [Prochlorococcus marinus
           str. MIT 9202]
 gi|221538594|gb|EEE41047.1| DNA-directed RNA polymerase, alpha subunit [Prochlorococcus marinus
           str. MIT 9202]
          Length = 311

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 95/305 (31%), Positives = 160/305 (52%), Gaps = 8/305 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + I++ +     +     +  PL RG A TLGN+LRRVLM  L G+A+TAV+I G+ HE 
Sbjct: 6   DRIDHQIADDRSQT-GTFLIGPLERGQATTLGNSLRRVLMGGLEGSAVTAVRIAGINHEY 64

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K +++  S    +   +   GP  V A DIQ  + +E+++ + 
Sbjct: 65  ATIPGVREDVLDILLNCKQLSINSSSPDLEIGRLVASGPMEVKANDIQFSSQVEIVDGEK 124

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P      E   I L+ IDA++ P+K+V++T++    
Sbjct: 125 PIATIQEGHNLELEIHVERGVGYRPVDRKSEETTAIDLLQIDAVFMPVKRVNFTIDETAV 184

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L M + TDGS + +D++A A+  L +           ++        +   
Sbjct: 185 AEGGTGRERLKMEVVTDGSTSPDDAIAEAANQLIELFQPLATVTMVEEI------PEEPE 238

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 239 PSPEAQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIDALE 298

Query: 312 TMGLF 316
            +G+ 
Sbjct: 299 RIGIS 303


>gi|73747870|gb|AAZ82836.1| RNA polymerase subunit a [Elymus mutabilis]
          Length = 339

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICIKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNGIE-KHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D+L
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|156618855|ref|YP_001430136.1| RNA polymerase alpha subunit [Cuscuta reflexa]
 gi|166209247|sp|Q8SKY1|RPOA_CUSRE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|156556040|emb|CAM98423.1| RNA polymerase alpha chain [Cuscuta reflexa]
 gi|165910451|gb|ABY73980.1| RNA polymerase alpha subunit [Cuscuta reflexa]
          Length = 335

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 84/331 (25%), Positives = 158/331 (47%), Gaps = 29/331 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L++ + G  IT V+    
Sbjct: 11  RTLQWKCVESRTDSKRLYYGRFILSPLTKGQADTIGIAMRRALLAEIEGTRITRVKFANT 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  +GPG VTA DI     +E++
Sbjct: 71  SHEYSTIAGIQESVHEILMNLKEIVLRSNLYGTCDASISIKGPGYVTAEDIILPPHVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L       + L + + HGY    H   E+   G   IDAL+ P++  ++++ 
Sbjct: 131 DSTQHIAWLTEPINFFIGLKIERNHGYFIKTHANFED---GSYPIDALFMPVRNANHSIN 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV- 247
           S         + L + I T+GS+T ++++  ASR L D    F++ EE    +++  +  
Sbjct: 188 SYGNE---KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEENLHLEDADHTI 244

Query: 248 ---------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                          K+          +++LE   +  NCL+  NI  + DL+  ++ D+
Sbjct: 245 PLSPFTVYDKVAKLRKNKKKLSLESIFIDQLEFPPKIYNCLKKSNIFTLLDLLNNSQEDL 304

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F    L ++K +LG +G    ++LP 
Sbjct: 305 IKIEHFH---LEDVKQILGILGKHFALDLPK 332


>gi|161511727|emb|CAP16874.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 235

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 107/235 (45%), Positives = 152/235 (64%), Gaps = 2/235 (0%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++LK+  D
Sbjct: 1   GTTLGNSLRRILLSSLPGAAITSVQIDSVLHEFSTIEGVVEDVTQIILNLKKVSLKIESD 60

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             K + I   GP  VTAGDI    D+ +LNP+  IC +         LT   G GY  A 
Sbjct: 61  EDKTLEINVAGPANVTAGDIMGDGDVVILNPELPICTVAEGTTFHAVLTADTGRGYTSAD 120

Query: 160 HHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
            ++    + PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ I TDGSIT  ++ 
Sbjct: 121 ENKARKVDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDIWTDGSITPSEAT 180

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
           +L+++IL + L +F+N  +  KE +  +  +       L   +EEL+LSVRS NC
Sbjct: 181 SLSAKILTEHLAIFVNLNDQAKETEIMVEKEETHKEKMLEMTIEELDLSVRSYNC 235


>gi|153799478|gb|ABS50514.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 240

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 102/242 (42%), Positives = 153/242 (63%), Gaps = 4/242 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           + KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGV
Sbjct: 1   IEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGV 56

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++VL
Sbjct: 57  LHEFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQVL 116

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NPD  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VE
Sbjct: 117 NPDQYICTIAEGGHLHMELAVKNGRGYVTASDNKSDDMPIGVIPVDSLFSPIKKVNYQVE 176

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   +  +  +  +
Sbjct: 177 STRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADANTQFSEVMVEKE 236

Query: 249 SL 250
             
Sbjct: 237 DD 238


>gi|51859695|gb|AAU11127.1| RNA polymerase alpha subunit [Psathyrostachys caduca]
          Length = 339

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKNLPIDL 332


>gi|219685166|ref|ZP_03539986.1| DNA-directed RNA polymerase, alpha subunit [Borrelia garinii Far04]
 gi|219673262|gb|EED30281.1| DNA-directed RNA polymerase, alpha subunit [Borrelia garinii Far04]
          Length = 344

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 121/335 (36%), Positives = 184/335 (54%), Gaps = 19/335 (5%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++K  ++   P  IE++   Q + +       P  RGF  T+GN LRRVL+SS+ G AIT
Sbjct: 3   VEKFLKDFTIPEKIEFLK-SQGDGSYGKFTIYPFERGFGVTIGNTLRRVLLSSIEGYAIT 61

Query: 62  AVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
           A++I           V  E   I GV ED  ++I NIK I+LK+ G+  +R TI     G
Sbjct: 62  AMRIQSNNKDSSSKVVSSEFDLIPGVSEDTLEVIANIKNIHLKL-GEGEQRKTISFSVSG 120

Query: 113 ----VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
               V+ A   +    +EV N D VI  L  D  + +E  ++ G GYV ++ +    + +
Sbjct: 121 KDTKVLKASHFERD-GVEVFNRDLVIATLSQDVNLDLEFQINYGRGYVSSEQNSKYLEEV 179

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
            +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L
Sbjct: 180 NVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIIREFL 239

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
              ++FE+    V           +  L   +E+L+LSVRS NCL  EN+  +G+LI + 
Sbjct: 240 YPLVDFED---NVNTSFEKSKSESSNLLDMSIEKLDLSVRSLNCLAKENVRTLGELISKN 296

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
             ++ +  NFG+KSL EI   L +  LFLGM+  D
Sbjct: 297 AEELSKARNFGKKSLEEIIEKLSSYQLFLGMSKED 331


>gi|183217772|ref|YP_001837392.1| RNA polymerase alpha subunit [Guizotia abyssinica]
 gi|179366287|gb|ACB86558.1| RNA polymerase alpha subunit [Guizotia abyssinica]
          Length = 335

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 82/331 (24%), Positives = 163/331 (49%), Gaps = 29/331 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + D +
Sbjct: 11  RTLQWKCVESAADSKRLLYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSDKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  RGPG VTA DI     +E++
Sbjct: 71  SHEYSTIMGIQESVHEILMNLKEIVLRSNLYGTYEASICVRGPGYVTAQDIILPPYVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + K  GY+    +  ++   G   ID ++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIELVIGLQIEKNRGYLIKAPNTFQD---GSYPIDPVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G   + + L + I T+GS+T ++++  ASR L D L  F++ +E    ++++ ++ 
Sbjct: 188 SYENG---NKEILFLEIWTNGSLTPKEALHEASRNLIDLLIPFLHTKEENLNLEDNQHIV 244

Query: 249 SLPF----------------NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            LP                        +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 245 PLPPFTFYDKLAKLTKNKKKMALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDL 304

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F    + ++K +LG +     ++LP 
Sbjct: 305 MKIEHFR---IEDVKQILGILEKNFVIDLPK 332


>gi|71056810|emb|CAH58960.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
          Length = 230

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 107/230 (46%), Positives = 152/230 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  ICN+   A     LTV
Sbjct: 61  KGLALKMYGDEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICNVSEGASFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           SI   ++++LA++I+ + L +F+N  +  K  +  +  +       L   
Sbjct: 181 SIEPLEAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMT 230


>gi|119662297|emb|CAJ33135.1| RNA polymerase alpha subunit [Lactobacillus curvatus]
          Length = 223

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 94/222 (42%), Positives = 148/222 (66%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L++SL G A+T +QIDGVLHE S+I GV ED+T IILNIK + 
Sbjct: 1   PLERGYGTTLGNSLRRILLASLPGTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNIKKLA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK+  +  K + I  +GP  VTA DI + +D+EVLN D  IC +       + +TV KG 
Sbjct: 61  LKLHVEEDKTIEIDVKGPATVTAADIISDDDVEVLNTDQYICTVAEGGNFHVRMTVKKGR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYV A  +++++ PIG++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+ 
Sbjct: 121 GYVAADQNKSDDMPIGVLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISP 180

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            ++++LA++I+ + L +F++  +  K  +  +  +       
Sbjct: 181 REAISLAAKIMTEHLAIFVDLTDEAKNAEIMVEKEETHKEKM 222


>gi|71056826|emb|CAH58968.1| DNA-directed RNA polymerase alpha chain [Tetragenococcus
           solitarius]
          Length = 226

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 100/223 (44%), Positives = 148/223 (66%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  II
Sbjct: 2   YGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVAQII 61

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LNIKG+ LK+  +  K++ I   GP  +TAGDI   +D+E+LN D  IC +         
Sbjct: 62  LNIKGLALKLYSEEEKKLEIDITGPATITAGDIIVDSDVEILNKDMYICTVAEGTRFHAR 121

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           L+V  G GY  A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  DYDKL+M + 
Sbjct: 122 LSVQPGRGYDQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDYDKLTMELW 181

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           TDGSI   D+++L+++IL + L +F+N  +  K  +  +  + 
Sbjct: 182 TDGSIEPLDALSLSAKILTEHLEIFVNMTDEAKNTEIMVEKEE 224


>gi|7388094|sp|P93968|RPOA_FESFE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1770264|emb|CAB01387.1| alpha subunit of RNA polymerase [Festucopsis festucoides]
          Length = 339

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 91/328 (27%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ ++Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNLNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D+L
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|72382944|ref|YP_292299.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. NATL2A]
 gi|124026686|ref|YP_001015801.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. NATL1A]
 gi|90110857|sp|Q46IT2|RPOA_PROMT RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|156637355|sp|A2C4X7|RPOA_PROM1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|72002794|gb|AAZ58596.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. NATL2A]
 gi|123961754|gb|ABM76537.1| Bacterial RNA polymerase, alpha chain [Prochlorococcus marinus str.
           NATL1A]
          Length = 312

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 98/305 (32%), Positives = 157/305 (51%), Gaps = 8/305 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + I++ V     +   + +  PL RG A TLGN+LRRVLM  L G+A+TAV+I GV HE 
Sbjct: 7   DRIDHQVSNDRSQT-GVFLIGPLERGQATTLGNSLRRVLMGGLEGSAVTAVRIAGVNHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K I++       +   +   GP  V A DIQ  + +EV++ D 
Sbjct: 66  ATIPGVREDVLDILLNCKQISVDSRSQELEIGRLVVTGPADVKAKDIQFSSQVEVVDGDR 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P      E   I L+ IDA++ PI +V++T++    
Sbjct: 126 PIATVQEGHNLELEIHVERGVGYRPVDRKNEETSAIDLLQIDAVFMPINRVNFTIDETAV 185

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L M + TDGS + +D++A A+  L +           ++        +   
Sbjct: 186 AEGGSTRERLKMELVTDGSTSPDDALAEAANQLIELFQPLATVSMVEEI------PEEPE 239

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 240 PAAEAQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIS 304


>gi|309322294|ref|YP_003934145.1| RNA polymerase alpha chain [Cedrus deodara]
 gi|228017091|gb|ACP51913.1| RNA polymerase alpha subunit [Cedrus deodara]
 gi|307683220|dbj|BAJ19528.1| RNA polymerase alpha chain [Cedrus deodara]
          Length = 335

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 87/329 (26%), Positives = 158/329 (48%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGVREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       ++L + K  GY+    H   N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIKLRIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE   +   +    +
Sbjct: 189 YGSGNEI-REVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNRKGSN 247

Query: 250 LPFNPA----------------LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           +P  P                     +++LEL  R+ NCLR  NI  + DL+  +  D++
Sbjct: 248 MPPFPLSHVLTDTGETKEKIAFQHIFIDQLELPPRTYNCLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ +FG++S+ ++  VL        ++ P
Sbjct: 308 RIEHFGKESVEQVLEVLR---KRFAIDPP 333


>gi|22657314|gb|AAM97460.1| RNA polymerase alpha subunit [Heteranthelium piliferum]
          Length = 339

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFWSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPKYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTEL---IKNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D+L
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|325282668|ref|YP_004255209.1| DNA-directed RNA polymerase subunit alpha [Deinococcus
           proteolyticus MRP]
 gi|324314477|gb|ADY25592.1| DNA-directed RNA polymerase subunit alpha [Deinococcus
           proteolyticus MRP]
          Length = 328

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 111/315 (35%), Positives = 174/315 (55%), Gaps = 22/315 (6%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           E N    + EPL RG+  T+GN +RR+LMSS++G A+T+V I+ VLHE S+I GV ED+ 
Sbjct: 13  EGNYGEFVLEPLKRGYGVTIGNPIRRILMSSIQGTAVTSVYIEDVLHEFSTIPGVKEDVI 72

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            +ILN+K + +K      K +T+  +G GV+ A D +  +D E++NPD  I NL     +
Sbjct: 73  RLILNLKELVVKFHAPGPKTLTLRAQGQGVIRASDFEVPSDAEIVNPDLEIANLADGGQL 132

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            ME+ V +G GYVPA  H T++  I  I +DA+++P+++V+Y VE+ R G+  D DKL +
Sbjct: 133 VMEVRVEEGEGYVPADKHATKDR-INSIPVDAMFNPVRRVAYHVENTRVGRQTDLDKLIL 191

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEE-------------------PKKEV--K 242
            I TDGS + +D +  A  IL+++L +F + EE                   P+ EV  +
Sbjct: 192 RIWTDGSASPQDVLDQAIDILREELLVFGSVEELEDSESSALDYTISAETVQPEAEVAPE 251

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                +    +      +E L L+ R  + L+ E I  +  L   ++ D+ ++   G +S
Sbjct: 252 SAAPAEESVSSGEPSVSLEGLGLTTRVLHSLKEEGIDNVDALCALSDRDLKKVPGIGERS 311

Query: 303 LVEIKGVLGTMGLFL 317
           L EIK  L   G  L
Sbjct: 312 LDEIKQQLAQFGKAL 326


>gi|114804296|ref|YP_762293.1| RNA polymerase alpha subunit [Morus indica]
 gi|122166773|sp|Q09WY5|RPOA_MORIN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|78100348|gb|ABB20989.1| RNA polymerase alpha subunit [Morus indica]
          Length = 323

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 80/329 (24%), Positives = 155/329 (47%), Gaps = 23/329 (6%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLR 56
           M Q+      +P  +++  +    ++        +  PL RG A T+G A+RR L+  + 
Sbjct: 1   MGQEKVTVSTRP--LQWKCVESRADSKRLYYGRFLLAPLMRGQADTIGIAMRRALLGEIE 58

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           G  IT  + + + HE S+I G+ E + +I++N+K I L+ +    +  +I  +GPG VTA
Sbjct: 59  GTCITRAKSEKIPHEYSTIVGIQESVHEILMNLKEIVLRSNLYGTRDASICVKGPGYVTA 118

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
            DI     +E+++    I NL     + +EL + +  GY     +  +N   G   IDA+
Sbjct: 119 QDIILPPSVEIVDNTQHIANLTEPITLCIELQIERNRGYRIKTPNNFQN---GSYPIDAV 175

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           + P++  ++++ S       + + L + I T+GS+T ++++  ASR L D    F + EE
Sbjct: 176 FMPVRNANHSIHSY-VNGNENQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFFHAEE 234

Query: 237 PKKEVKE-------------DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGD 283
             +  +                  K+          +++ EL  R  NCL+  NI    +
Sbjct: 235 HLENNQHKGTLPLFNFHGRLAKPRKTKKEIALKYIYIDQSELPPRVYNCLKRSNINTFLE 294

Query: 284 LIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           L+  ++ +++++ +F  + +  I  VL  
Sbjct: 295 LLNNSQEELMKIQDFRIEDVKHILDVLEI 323


>gi|296877834|ref|ZP_06901856.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           NAP07]
 gi|296431134|gb|EFH16959.1| DNA-directed RNA polymerase subunit alpha [Clostridium difficile
           NAP07]
          Length = 252

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 102/252 (40%), Positives = 161/252 (63%), Gaps = 2/252 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  ++ + L  E+      + EPL RG+  T+GNALRR+L+SSL G A+ A++IDG
Sbjct: 3   EIEKP-KVDIVELS-EDYRYGKFVIEPLERGYGITIGNALRRILLSSLPGVAVNAIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV ED+T+IIL +K ++  + G+  + + I  +GP  +T  DI    D+E+
Sbjct: 61  VLHEFSTIPGVKEDVTEIILTLKELSATIDGEGSRTLKIEAQGPCSITGADIICSPDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           L+ D  I  LD +A + ME+ V KG GYV A+ ++TEN PIG++ +D++Y+P++KVSY V
Sbjct: 121 LSKDLAIATLDDNAKLNMEIFVDKGRGYVSAEENKTENVPIGVLPVDSIYTPVEKVSYHV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  DYDKL + + T+GSI  ++ ++LA+++L + L +FI+  E    V+  +  
Sbjct: 181 ENTRVGQKTDYDKLVLEVWTNGSINPQEGISLAAKVLVEHLNLFIDLTEHVSSVEIMVEK 240

Query: 248 KSLPFNPALLKK 259
           +       L   
Sbjct: 241 EEDQKEKVLEMT 252


>gi|157414140|ref|YP_001485006.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. MIT 9215]
 gi|172047296|sp|A8G739|RPOA_PROM2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|157388715|gb|ABV51420.1| DNA-directed RNA polymerase, alpha subunit [Prochlorococcus marinus
           str. MIT 9215]
          Length = 312

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 95/305 (31%), Positives = 160/305 (52%), Gaps = 8/305 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + I++ +     +     +  PL RG A TLGN+LRRVLM  L G+A+TAV+I G+ HE 
Sbjct: 7   DRIDHQIADDRSQT-GTFLIGPLERGQATTLGNSLRRVLMGGLEGSAVTAVRIAGINHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K +++  S    +   +   GP  V A DIQ  + +E+++ + 
Sbjct: 66  ATIPGVREDVLDILLNCKQLSINSSSPDLEIGRLVASGPMDVKANDIQFSSQVEIVDGEK 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P      E   I L+ IDA++ P+K+V++T++    
Sbjct: 126 PIATIQEGHNLELEIHVERGVGYRPVDRKSEETTAIDLLQIDAVFMPVKRVNFTIDETAV 185

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L M + TDGS + +D++A A+  L +           ++        +   
Sbjct: 186 AEGGTGRERLKMEVVTDGSTSPDDAIAEAANQLIELFQPLATVTMVEEI------PEEPE 239

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 240 PSPEAQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIDALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIS 304


>gi|139389982|ref|YP_001123582.1| RNA polymerase alpha subunit [Draba nemorosa]
 gi|158513976|sp|A4QL51|RPOA_DRANE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134286784|dbj|BAF50406.1| RNA polymerase alpha subunit [Draba nemorosa]
          Length = 327

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 75/320 (23%), Positives = 153/320 (47%), Gaps = 21/320 (6%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E      +       I  PL +G A T+G A+RR L+  + G  IT  + + + 
Sbjct: 13  LQWRCVES-RRDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           H+ S+I G+ E + +I++N+  I L+ +    +   I  +GPG +TA DI     +E+++
Sbjct: 72  HDYSNIVGIQESVHEILMNLNEIVLRSNLYGTRNALICVQGPGYITARDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  +     + + L + +  GY     +  E+       IDA++ P++  ++++ S
Sbjct: 132 NTQHIATVTESIDLCIGLKIERNRGYSLKMSNNFEDRS---YPIDAVFMPVQNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  +
Sbjct: 189 YGNG-NGKQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFHLENNQHQVT 247

Query: 250 LPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           LP  P   +                 +++LEL  R  NCL+  NI  + DL+  ++ D++
Sbjct: 248 LPLFPFHNRLVNLRKKKKELAFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLI 307

Query: 294 RMANFGRKSLVEIKGVLGTM 313
           ++ +F  + + +I  +L   
Sbjct: 308 KIEHFHIEDVKKILDILEKK 327


>gi|153799470|gb|ABS50510.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 240

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 102/240 (42%), Positives = 153/240 (63%), Gaps = 4/240 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           + KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGV
Sbjct: 1   IEKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGV 56

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++VL
Sbjct: 57  LHEFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQVL 116

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NPD  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VE
Sbjct: 117 NPDQYICTIAEGGHLHMELAVKNGRGYVTASDNKSDDMPIGVIPVDSLFSPIKKVNYQVE 176

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   +  +  +  +
Sbjct: 177 STRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADANTQFSEVMVEKE 236


>gi|119663518|emb|CAK22330.1| RNA polymerase alpha subunit [Lactobacillus algidus]
          Length = 230

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 102/230 (44%), Positives = 153/230 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GA+IT +QIDGVLHE S+I+GV ED+T IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGASITNIQIDGVLHEFSTIEGVLEDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK++ D  + + I  +GP  VTAGDI   +D+EVLNPD  IC +   A   + +  
Sbjct: 61  KKVALKLAADEDQSIEIDVKGPAEVTAGDIIGNSDVEVLNPDLYICTVAEGASFHVRMNA 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           S G GYV A  ++ E+ PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T+G
Sbjct: 121 SNGRGYVSADQNKAEDMPIGVLPIDSIYTPIERVNYQVEKTRVGQKDDYDKLTLDVWTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           SIT  ++++L+++IL + L +F++  +  K  +  +  +       L   
Sbjct: 181 SITPSEAISLSAKILTEHLTLFVDLTDEAKNAEIMVEKEETHKEKMLEMT 230


>gi|78103281|ref|YP_358613.1| RNA polymerase alpha subunit [Phalaenopsis aphrodite subsp.
           formosana]
 gi|90110856|sp|Q3BAK5|RPOA_PHAAO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|58802811|gb|AAW82531.1| RNA polymerase alpha chain [Phalaenopsis aphrodite subsp.
           formosana]
          Length = 337

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 90/328 (27%), Positives = 160/328 (48%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       +  PL +G A T+G A+RR L+  + G  IT    + VL
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFVLSPLMKGQADTIGIAIRRALLGEIEGTCITRATSENVL 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  RGP  +TA DI +   +E+++
Sbjct: 72  HEYSTIAGIEESVHEILLNLKDIVLRSNLYGVRNASICVRGPKYITAQDIISPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL     + +EL + +  GY     +   +   G   ID +  P++  ++++ S
Sbjct: 132 TTQHIANLTEPINLCIELQIKRDRGYRMKSTN---DSHDGSYPIDIVSMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L D L  F++ EE     KE+ N  +
Sbjct: 189 YGNG-NEKQEILFIEIWTNGSLTPKEALYEASRNLIDLLIPFLHAEEEDMNFKENENRWN 247

Query: 250 LPFN----------------PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           LP                  P     +++ ELS R+ NCL+  NI  + DL+  ++ D++
Sbjct: 248 LPPFSFQDKFTNFKKNKKGIPLTCIFIDQSELSSRTYNCLKRSNIHTLLDLLSHSQEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +M  F      ++K +L T+     +NL
Sbjct: 308 KMEYFRT---EDVKQILSTVQKHFAINL 332


>gi|7388093|sp|P93964|RPOA_SECST RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1771726|emb|CAB01374.1| alpha subunit of RNA polymerase [Secale strictum]
          Length = 339

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 160/328 (48%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLXEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D+L
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+  F    + + K +  T+   L ++L
Sbjct: 308 RIDXFR---MEDRKHIWDTLEKHLPIDL 332


>gi|228017404|gb|ACP52221.1| RNA polymerase alpha subunit [Larix occidentalis]
          Length = 335

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 88/329 (26%), Positives = 158/329 (48%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLRIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G  +  + L + I T+G +T  +++  ASR L D L  F++ EE   +   +    +
Sbjct: 189 YGSGNEI-REVLFLEIWTNGGLTPREALYEASRNLIDLLIPFLHGEEQNIDGMNNRKGSN 247

Query: 250 LPFNPA----------------LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           +P  P                     +++LEL  R+ NCLR  NI  + DL+  +  D++
Sbjct: 248 MPPFPLSHVLTDTRETKEKIAFKHIFIDQLELPPRTYNCLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ +FG++S+ ++  VL        ++ P
Sbjct: 308 RIEHFGKESVEQVLEVL---QKRFAIDPP 333


>gi|161513428|emb|CAP16857.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           argentinicus]
          Length = 225

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 102/225 (45%), Positives = 150/225 (66%), Gaps = 2/225 (0%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
             + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQID VLHE S++KGV ED+T IILN
Sbjct: 1   RFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDDVLHEFSTVKGVVEDVTQIILN 60

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           +K ++LK+  D  K + I  +GP  VTAGDI   +D+ +LNPD  IC +   A     LT
Sbjct: 61  LKKVSLKIDSDDEKSMEIDVKGPATVTAGDISADSDVTILNPDLAICTVAEGATFHAHLT 120

Query: 149 VSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
             KG GY  A  ++    + PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ I 
Sbjct: 121 AEKGRGYTSADENKARKADMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDIW 180

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           TDGSIT  ++ +L+++IL + L +F+N  +  K+ +  +  +   
Sbjct: 181 TDGSITPSEATSLSAKILTEHLAIFVNLNDQAKDTEIMVEKEESH 225


>gi|71056882|emb|CAH58997.1| DNA-directed RNA polymerase alpha chain [Enterococcus malodoratus]
          Length = 227

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 104/227 (45%), Positives = 150/227 (66%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
             + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILN
Sbjct: 1   KFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILN 60

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           IKG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LT
Sbjct: 61  IKGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLT 120

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V  G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TD
Sbjct: 121 VKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTD 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           GSI  +++++LA++IL + L +F+N  +  K  +  +  +       
Sbjct: 181 GSIIAQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 227


>gi|51859681|gb|AAU11120.1| RNA polymerase alpha subunit [Psathyrostachys lanuginosa]
          Length = 339

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 90/328 (27%), Positives = 159/328 (48%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+   ++ V+Y++ S
Sbjct: 132 TXQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMXVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     + +LEL+ R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLLTFQKRLTNLKKNKKGIPLNCIFIXQLELTSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|41688708|sp|Q8MAI8|RPOA_ELYHY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|22657284|gb|AAM97445.1| RNA polymerase alpha subunit [Elymus hystrix]
          Length = 339

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 160/328 (48%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA   P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAESMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D+L
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|71056852|emb|CAH58981.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
          Length = 232

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 106/232 (45%), Positives = 153/232 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV
Sbjct: 61  KGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           SI  +++++LA++IL + L +F+N  +  K  +  +  +       L   +E
Sbjct: 181 SIIAQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIE 232


>gi|148982226|ref|ZP_01816652.1| DNA-directed RNA polymerase subunit alpha [Vibrionales bacterium
           SWAT-3]
 gi|145960588|gb|EDK25941.1| DNA-directed RNA polymerase subunit alpha [Vibrionales bacterium
           SWAT-3]
          Length = 278

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 118/284 (41%), Positives = 178/284 (62%), Gaps = 11/284 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  +    + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLV---YIEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  +
Sbjct: 178 YSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVY 280
            +         +   F+P LL+ V++LEL+VRS NCL+ E I Y
Sbjct: 238 VRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHY 278


>gi|72534397|emb|CAH59002.1| DNA-directed RNA polymerase alpha chain [Enterococcus cecorum]
          Length = 231

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 105/231 (45%), Positives = 151/231 (65%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
             I EPL RG+  TLGN+LRR+L+SSL GAAIT++QID V HE S+I GV ED++ IILN
Sbjct: 1   KFIVEPLERGYGTTLGNSLRRILLSSLPGAAITSIQIDTVQHEFSTIVGVREDVSQIILN 60

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           IKG+ LK+ G   K + I   GP VVTAGDI   +D+E+LN D  IC +   A  R  L 
Sbjct: 61  IKGLALKLYGSEEKTLEIDITGPAVVTAGDIIVDSDVEILNKDMYICTVSEGATFRARLK 120

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V  G GYV A  ++TE+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TD
Sbjct: 121 VKAGRGYVQADENKTEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTD 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           GSI   D+++LA++IL + L +F+N  +  +  +  +  +       L   
Sbjct: 181 GSIEPLDAMSLAAKILTEHLDIFVNLTDEARHAEIMVEKEETQKEKMLEMT 231


>gi|307683477|dbj|BAJ19717.1| RNA polymerase alpha chain [Pseudotsuga sinensis var. wilsoniana]
          Length = 335

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 90/329 (27%), Positives = 155/329 (47%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RRVL+  + G  IT VQ D + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRVLLGEVEGTCITHVQFDNIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILVNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLRIEKNRGYIM---HSPNNYKDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE   +   +    +
Sbjct: 189 YGSGNEI-REVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNRKGSN 247

Query: 250 LPFNPA----------------LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           +P  P                     +++LEL  R  NCLR  NI  + DL+  +  D++
Sbjct: 248 MPPFPLSHVLTDTRETIEKIAFQYIFIDQLELPPRIYNCLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ N G++S+ ++  VL        ++ P
Sbjct: 308 RIENLGKESVEQVLEVLR---KRFAIDPP 333


>gi|71056914|emb|CAH59016.1| DNA-directed RNA polymerase alpha chain [Enterococcus cecorum]
          Length = 229

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 104/227 (45%), Positives = 150/227 (66%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
             I EPL RG+  TLGN+LRR+L+SSL GAAIT++QID V HE S+I GV ED++ IILN
Sbjct: 1   KFIVEPLERGYGTTLGNSLRRILLSSLPGAAITSIQIDTVQHEFSTIVGVREDVSQIILN 60

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           IKG+ LK+ G   K + I   GP VVTAGDI   +D+E+LN D  IC +   A  R  L 
Sbjct: 61  IKGLALKLYGSEEKTLEIDITGPAVVTAGDIIVDSDVEILNKDMYICTVSEGATFRARLK 120

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V  G GYV A  ++TE+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TD
Sbjct: 121 VKAGRGYVQADENKTEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTD 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           GSI   D+++LA++IL + L +F+N  +  +  +  +  +       
Sbjct: 181 GSIEPLDAMSLAAKILTEHLDIFVNLTDEARHAEIMVEKEETQKEKM 227


>gi|237688485|ref|YP_002905104.1| RNA polymerase alpha subunit [Picea sitchensis]
 gi|226875313|gb|ACO89052.1| RNA polymerase alpha subunit [Picea sitchensis]
          Length = 336

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 87/330 (26%), Positives = 153/330 (46%), Gaps = 25/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RRVL+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSERLH-YGRFALSPLRKGRADTIGIAMRRVLLGEVEGTCITHVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I   GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIRGASICIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE------------- 236
              G  +  + L + I T+G +T  ++++ ASRIL +    F++ EE             
Sbjct: 189 YGSGNEI-REVLFLEIWTNGGLTPREALSEASRILIELFIPFLHGEEQNIDGMNNRKGSN 247

Query: 237 ----PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
               P   V  D               +++LE   R  NCLR  NI  + DL+  +  D+
Sbjct: 248 MPPFPLSHVLTDTGETKEKKIAFQHIFIDQLEFPPRVYNCLRRANIHTLSDLLNYSREDL 307

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           +R+  FG++S+ ++  +L        ++ P
Sbjct: 308 MRIERFGKESVEQVFEILR---KRFAIDPP 334


>gi|71056919|emb|CAH59018.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
 gi|71056935|emb|CAH59026.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 226

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 105/226 (46%), Positives = 150/226 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV
Sbjct: 61  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           SI   ++++L+++I+ + L +F+N  +  K  +  +  +       
Sbjct: 181 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 226


>gi|71056878|emb|CAH58995.1| DNA-directed RNA polymerase alpha chain [Enterococcus avium]
          Length = 231

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 105/231 (45%), Positives = 151/231 (65%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
             + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILN
Sbjct: 1   KFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILN 60

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           IKG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LT
Sbjct: 61  IKGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLT 120

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V  G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TD
Sbjct: 121 VKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTD 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           GSI  +++++LA++IL + L +F+N  +  K  +  +  +       L   
Sbjct: 181 GSIIAQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMT 231


>gi|71056818|emb|CAH58964.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 232

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 107/232 (46%), Positives = 153/232 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV
Sbjct: 61  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           SI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +E
Sbjct: 181 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIE 232


>gi|71833746|emb|CAH59013.1| DNA-directed RNA polymerase alpha chain [Enterococcus canintestini]
          Length = 233

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 108/233 (46%), Positives = 153/233 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT++QIDGVLHE S++KGV ED+  IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITSIQIDGVLHEFSTVKGVREDVAQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM     K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV
Sbjct: 61  KGLALKMYTQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG+I +D++Y+P+ +V+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 121 RPGRGYVQADENKREDMPIGVIPVDSIYTPVNRVNYQVENTRVGRRDDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           SI   ++++LA++I+ + L +F+N  +  K  +  I  +       L   +EE
Sbjct: 181 SIMPMEAMSLAAKIMTEHLDIFVNLTDEAKNAEIMIEKEETQKEKMLEMTIEE 233


>gi|254495738|ref|ZP_05108652.1| DNA-directed RNA polymerase subunit alpha [Legionella drancourtii
           LLAP12]
 gi|254355016|gb|EET13637.1| DNA-directed RNA polymerase subunit alpha [Legionella drancourtii
           LLAP12]
          Length = 280

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 123/283 (43%), Positives = 183/283 (64%), Gaps = 9/283 (3%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           + G+AIT   IDGVLHE S+I+GV ED+ D++LN+K + +K++     +VT+ K+GP  V
Sbjct: 1   MPGSAITEASIDGVLHEYSTIEGVQEDVVDLLLNLKLVAIKLTTGEEAQVTLSKQGPCQV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH------RTENDPI 168
           TAGDIQ  + ++V+NP+ VI NL+    + M L V +G G+              E   +
Sbjct: 61  TAGDIQLTHGVDVVNPELVIANLNEKGKLNMTLKVERGIGFHSTDSFIRHFDDEVERKSV 120

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           G + ID  +SP+KKV+Y V+SAR     D DKL++ ++T+G+I  E+++ +++ ILQ QL
Sbjct: 121 GKLKIDNSFSPVKKVAYYVDSARVENRTDLDKLTIELETNGTIDAEEAIRISASILQRQL 180

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
             F++    K E     N +   F+P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRT
Sbjct: 181 HAFVDM---KFEESRSDNKERNDFDPVLLRSVDDLELTVRSANCLKAENIHYIGDLVQRT 237

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           E ++L+  N G+KSL EIK VL +  L LGM L +WPP S+ E
Sbjct: 238 ENELLKTPNLGKKSLTEIKDVLASRSLSLGMKLENWPPASLGE 280


>gi|319827247|gb|ADV74823.1| RNA polymerase subunit A [Vibrio neptunius]
          Length = 275

 Score =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 120/277 (43%), Positives = 180/277 (64%), Gaps = 8/277 (2%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
                    +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV E
Sbjct: 2   STVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQE 61

Query: 81  DLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           D+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+ NP+HVIC+L  
Sbjct: 62  DILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTD 121

Query: 140 D-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
           D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q 
Sbjct: 122 DNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQR 181

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P 
Sbjct: 182 TDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPI 238

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++
Sbjct: 239 LLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVEL 275


>gi|319827245|gb|ADV74822.1| RNA polymerase subunit A [Vibrio coralliilyticus]
          Length = 276

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 120/277 (43%), Positives = 180/277 (64%), Gaps = 8/277 (2%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
                    +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV E
Sbjct: 3   STVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQE 62

Query: 81  DLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           D+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+ NP+HVIC+L  
Sbjct: 63  DILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTD 122

Query: 140 D-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
           D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR  Q 
Sbjct: 123 DNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQR 182

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P 
Sbjct: 183 TDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPI 239

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++
Sbjct: 240 LLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVEL 276


>gi|283945395|dbj|BAI66453.1| RNA polymerase alpha subunit [Lactobacillus odoratitofui]
          Length = 247

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 110/251 (43%), Positives = 162/251 (64%), Gaps = 7/251 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KPN    I   +E ++    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLH
Sbjct: 1   KPN----IHKIEESDDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLH 56

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           E S+I+GV ED+T IILN K I+LK+ G  D  + + I  +GP  VTAGDI   +D+ +L
Sbjct: 57  EFSTIEGVVEDVTQIILNTKKISLKLEGPDDEIESMEIDVKGPAQVTAGDITADSDVTIL 116

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR-TENDPIGLITIDALYSPIKKVSYTV 187
           NPD  I  +   A   M +T +KG GYV A  ++  E+ PIG++ ID++Y+PI++V+Y V
Sbjct: 117 NPDLYIATVAEGATFHMRMTANKGRGYVSADRNKAKEDMPIGVLPIDSIYTPIERVNYQV 176

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  DYDKL++ + TD SIT  +S++LA++IL + L MF++  +  K  +  +  
Sbjct: 177 ENTRVGQRDDYDKLTLDVWTDSSITPSESISLAAKILTEHLAMFVDLTDEAKNAEIMVEK 236

Query: 248 KSLPFNPALLK 258
           +       L  
Sbjct: 237 EETHKEKMLEM 247


>gi|71056870|emb|CAH58990.1| DNA-directed RNA polymerase alpha chain [Enterococcus malodoratus]
          Length = 231

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 105/231 (45%), Positives = 152/231 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV
Sbjct: 61  KGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           SI  +++++LA++IL + L +F+N  +  K  +  +  +       L   +
Sbjct: 181 SIIAQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTI 231


>gi|51598757|ref|YP_072945.1| DNA-directed RNA polymerase subunit alpha [Borrelia garinii PBi]
 gi|61215870|sp|Q661B8|RPOA_BORGA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|51573328|gb|AAU07353.1| DNA-directed RNA polymerase [Borrelia garinii PBi]
          Length = 344

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 120/335 (35%), Positives = 184/335 (54%), Gaps = 19/335 (5%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++K  ++   P  IE++   Q++ +       P  RGF  T+GN LRRVL+SS+ G AIT
Sbjct: 3   VEKFLKDFTIPEKIEFLK-SQDDGSYGKFTIYPFERGFGVTIGNTLRRVLLSSIEGYAIT 61

Query: 62  AVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
           A++I           V  E   I GV ED  ++I NIK I+LK+ G+  +R  I     G
Sbjct: 62  AMRIQSNNKDSSSKVVSSEFDLIPGVSEDTLEVIANIKNIHLKL-GEGEQRKIISFSVSG 120

Query: 113 ----VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
               V+ A   +    +EV N D VI  L  D  + +E  ++ G GYV ++ +    + +
Sbjct: 121 KDTKVLKASHFERD-GVEVFNRDLVIATLSQDVNLDLEFQINYGRGYVSSEQNSKYLEEV 179

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
            +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L
Sbjct: 180 NVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIIREFL 239

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
              I+FE+    +           +  L   +E+L+LSVRS NCL  EN+  +G+LI + 
Sbjct: 240 FPLIDFED---NINTSFEKSKSESSNLLDMSIEKLDLSVRSLNCLAKENVRTLGELISKN 296

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
             ++ +  NFG+KSL EI   L +  LFLGM+  D
Sbjct: 297 AEELSKARNFGKKSLEEIIEKLSSYQLFLGMSKED 331


>gi|71056906|emb|CAH59010.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 228

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 104/228 (45%), Positives = 152/228 (66%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
            EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+I GV ED+T IILNIKG
Sbjct: 1   VEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIPGVREDVTQIILNIKG 60

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           + LK+  +  K + I   GP  VTAGDI   +D+E+LN D VIC++   A     LTV  
Sbjct: 61  LALKLYAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLVICSVAEGATFHARLTVKP 120

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI
Sbjct: 121 GRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
             +++++LA++I+ + L +F+N  +  K  +  +  +       L   
Sbjct: 181 IPQEALSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMT 228


>gi|225548741|ref|ZP_03769788.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           94a]
 gi|225370771|gb|EEH00207.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           94a]
          Length = 344

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 119/336 (35%), Positives = 186/336 (55%), Gaps = 19/336 (5%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +++K  ++   P  IE++   Q + +       P  RGF  T+GN LRRVL+SS+ G AI
Sbjct: 2   LVEKFLKDFTIPEKIEFLK-SQGDGSYGKFTIYPFERGFGITIGNTLRRVLLSSIEGYAI 60

Query: 61  TAVQIDGVLHEISS---------IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGP 111
           TA+++     + SS         I GV ED  ++I NIK I+LK+ G+  ++ TI     
Sbjct: 61  TAMRVQSNNKDASSKVVSSEFDLIPGVSEDTLEVIANIKNIHLKL-GEGEQKKTISFSVS 119

Query: 112 G----VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
           G    V+ A   +    +EV N D VI  L  D  + +E  ++ G GYV ++ +    + 
Sbjct: 120 GKDTNVLKASHFERD-GVEVFNKDLVIATLSRDVNLDLEFQINYGRGYVSSEQNSKYLEE 178

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           + +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ 
Sbjct: 179 VNVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREF 238

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
           L   ++FE+    V           +  L   +E+L LSVRS NCL  EN+  +G+LI +
Sbjct: 239 LFPLVDFED---NVNTSFEKSKSESSNLLDMSIEKLNLSVRSLNCLAKENVRTLGELISK 295

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
              ++ +  NFG+KSL EI   LG+  L+LGM+  D
Sbjct: 296 NAEELSKARNFGKKSLEEIIEKLGSYRLYLGMSKED 331


>gi|139389450|ref|YP_001123147.1| RNA polymerase alpha subunit [Olimarabidopsis pumila]
 gi|158513629|sp|A4QJW3|RPOA_OLIPU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134286344|dbj|BAF49971.1| RNA polymerase alpha subunit [Olimarabidopsis pumila]
          Length = 327

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 77/321 (23%), Positives = 156/321 (48%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRRDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            H+ S+I G+ E + +I++N+  I L+ +    +   I  +GPG +TA DI     +E++
Sbjct: 71  PHDYSNIVGIQESVHEILMNLNEIVLRSNLYGTRNALICVQGPGYITARDIILPPSVEII 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + +EL + +  GY     +  E+       IDA++ P++  ++++ 
Sbjct: 131 DNTQHIATLTEPIDLCIELKIERNRGYSLKMSNNFEDRS---YPIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETVYLENNQHQV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LPF P   +                 +++LEL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPFFPFHNRLVNLRKKKKELAFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTM 313
           +++ +F  + + +I  +L   
Sbjct: 307 IKIEHFHIEDVKKILDILEKK 327


>gi|91214173|ref|YP_538797.1| RNA polymerase alpha subunit [Glycine max]
 gi|90110869|sp|Q2PMQ3|RPOA_SOYBN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|83595774|gb|ABC25155.1| RNA polymerase alpha subunit [Glycine max]
          Length = 333

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 82/327 (25%), Positives = 156/327 (47%), Gaps = 24/327 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RRVL+  + G  IT V+ + + 
Sbjct: 13  LQWKCVES-RIDSKRLYYGRFILSPLMKGQADTIGIAMRRVLLGEIEGTCITRVKSEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +    +  +I  +GPG VTA DI     +E+++
Sbjct: 72  HEYSTIIGIEESVHEILMNLKEIVLRSNLYGTRDASICFKGPGYVTAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I N+     + +EL + +  GY        ++   G   IDA + P++ V++++ S
Sbjct: 132 NTQHIANVTEPVNLCIELKIERNRGYRIKTLKNFQD---GSYPIDATFMPVRNVNHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                    + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + +  +
Sbjct: 189 Y-VNGNEKQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEDNFNLENNQHKVT 247

Query: 250 LP------------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           LP                          +++LEL  R  NCL+  NI  + +L+  ++ D
Sbjct: 248 LPLFTFHDILAKEKLRKKKKEIALKSIFIDQLELPPRIYNCLKRSNIHTLLELLNNSQED 307

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLG 318
           +L++ +F  + +  I   L  +     
Sbjct: 308 LLKIEHFRVEDVKYILDFL-EIEKHFA 333


>gi|71056898|emb|CAH59006.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           hermanniensis]
          Length = 234

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 106/234 (45%), Positives = 152/234 (64%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
             + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDG LHE S+IKGV ED+  IILN
Sbjct: 1   KFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGALHEFSTIKGVREDVVQIILN 60

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           IKG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LT
Sbjct: 61  IKGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLT 120

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V  G GYV A  ++ E+ PIG++ +D++Y+P+ KV+Y VE+ R G+  D+DKL+M I TD
Sbjct: 121 VKPGRGYVQADENKKEDMPIGVLPVDSIYTPVCKVNYQVENTRVGRRDDFDKLTMEIWTD 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           GSI  +++++LA++IL + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 181 GSIIAQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEE 234


>gi|71056896|emb|CAH59005.1| DNA-directed RNA polymerase alpha chain [Enterococcus italicus]
          Length = 223

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 103/223 (46%), Positives = 148/223 (66%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG+
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVAQIILNIKGL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LK+ G+  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G
Sbjct: 61  ALKLYGEDEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTVKPG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ ++ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI 
Sbjct: 121 RGYVQADENKKDDMPIGVLPVDSIYTPVRRVNYQVENTRVGHRDDFDKLTMEIWTDGSIE 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
             D+++LA++I+ + L +F+N  +  K  +  +  +       
Sbjct: 181 PLDAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 223


>gi|15807122|ref|NP_295851.1| DNA-directed RNA polymerase subunit alpha [Deinococcus radiodurans
           R1]
 gi|12230608|sp|Q9RSJ6|RPOA_DEIRA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|6459926|gb|AAF11678.1|AE002047_11 DNA-directed RNA polymerase, alpha subunit [Deinococcus radiodurans
           R1]
          Length = 341

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 111/328 (33%), Positives = 171/328 (52%), Gaps = 35/328 (10%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           + +    + EPL RG+  T+GN +RR+LMSS+ G A+T+V I+ VLHE S+I GV ED+ 
Sbjct: 13  DGDYGEFVLEPLARGYGVTIGNPIRRILMSSIPGTAVTSVYIEDVLHEFSTIPGVREDVI 72

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            +ILN+K + +K      K +T+  +G G V A   +   D E++NPD VI NL  D  +
Sbjct: 73  RLILNLKELVVKFHAPGPKTLTLRAQGEGEVRASAFEVPTDAEIVNPDLVIANLAEDGKL 132

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            ME+ V +G GYV A  H T++  I  I +DA++SP+++V+Y VE+ R GQ  D D+L +
Sbjct: 133 VMEVRVEEGEGYVSADKHATKDR-INSIPVDAMFSPVRRVAYHVENTRVGQQTDLDRLIL 191

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEE-PKKEVKEDINVKSLPFNPALLK---- 258
            + TDGS   ++++  A  IL+D+L +F N E  P  E        +  ++PA       
Sbjct: 192 RVWTDGSAGPQEALDKAVEILRDELSVFGNVEPMPALESSYAAATPAAVYDPATATLPAS 251

Query: 259 -----------------------------KVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
                                         +E L L+ R  + L+ E I  +  L   ++
Sbjct: 252 VYDSPRQPDLGSLSINPQPFPTDQDTPRVTLEGLGLTTRVLHSLKEEGIDSVDALCALSD 311

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            D+ ++   G +SL EIK  L   GL L
Sbjct: 312 RDLKKVPGIGERSLDEIKQQLAQFGLAL 339


>gi|222084117|ref|YP_002519569.1| RNA polymerase alpha chain [Keteleeria davidiana]
 gi|220983669|dbj|BAH11435.1| RNA polymerase alpha chain [Keteleeria davidiana]
          Length = 336

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 87/330 (26%), Positives = 155/330 (46%), Gaps = 25/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V ++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVTLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITFDIRLRIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED----- 244
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE   +   +     
Sbjct: 189 YGSGNEI-REVLFLEIWTNGGLTPREALYEASRNLIDFFIPFLHGEEQNIDGINNRKGSS 247

Query: 245 ------------INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                          ++          +++LEL  R+ NCLR  NI  + DL+  +  D+
Sbjct: 248 NMPPFPLLHVLTDTGETKEKIAFQHIFIDQLELPPRTYNCLRRANIHTLLDLLNYSREDL 307

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           +RM +FG++S+ ++  VL        ++LP
Sbjct: 308 MRMEHFGKESVEQVLEVLR---KRFAIDLP 334


>gi|123969275|ref|YP_001010133.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. AS9601]
 gi|123199385|gb|ABM71026.1| Bacterial RNA polymerase, alpha chain [Prochlorococcus marinus str.
           AS9601]
          Length = 340

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 95/305 (31%), Positives = 160/305 (52%), Gaps = 8/305 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + I++ +     +     +  PL RG A TLGN+LRRVLM  L G+A+TAV+I G+ HE 
Sbjct: 35  DRIDHQIADDRSQT-GTFLIGPLERGQATTLGNSLRRVLMGGLEGSAVTAVRIAGINHEY 93

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K +++  S    +   +   GP  V A DIQ  + +E+++ + 
Sbjct: 94  ATIPGVREDVLDILLNCKQLSINSSNPELEIGRLVASGPMEVKANDIQFSSQVEIVDGEK 153

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P      E   I L+ IDA++ P+K+V++T++    
Sbjct: 154 PIATIQEGHNLELEIHVERGVGYRPVDRKSEETTAIDLLQIDAVFMPVKRVNFTIDETAV 213

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L M + TDGS + +D++A A+  L +           ++        +   
Sbjct: 214 AEGATGRERLKMEVVTDGSTSPDDAIAEAANQLIELFQPLATVTMVEEI------PEEPE 267

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 268 PSPEAQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 327

Query: 312 TMGLF 316
            +G+ 
Sbjct: 328 RIGIS 332


>gi|156637358|sp|A2BTB5|RPOA_PROMS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
          Length = 312

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 95/305 (31%), Positives = 160/305 (52%), Gaps = 8/305 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + I++ +     +     +  PL RG A TLGN+LRRVLM  L G+A+TAV+I G+ HE 
Sbjct: 7   DRIDHQIADDRSQT-GTFLIGPLERGQATTLGNSLRRVLMGGLEGSAVTAVRIAGINHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K +++  S    +   +   GP  V A DIQ  + +E+++ + 
Sbjct: 66  ATIPGVREDVLDILLNCKQLSINSSNPELEIGRLVASGPMEVKANDIQFSSQVEIVDGEK 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P      E   I L+ IDA++ P+K+V++T++    
Sbjct: 126 PIATIQEGHNLELEIHVERGVGYRPVDRKSEETTAIDLLQIDAVFMPVKRVNFTIDETAV 185

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L M + TDGS + +D++A A+  L +           ++        +   
Sbjct: 186 AEGATGRERLKMEVVTDGSTSPDDAIAEAANQLIELFQPLATVTMVEEI------PEEPE 239

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 240 PSPEAQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIS 304


>gi|71056842|emb|CAH58976.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 215

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 103/215 (47%), Positives = 150/215 (69%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+I GV ED+T IILNIKG+
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIPGVREDVTQIILNIKGL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LK+  +  K + I   GP  VTAGDI   +D+E+LN D VIC++   A     LTV  G
Sbjct: 61  ALKLYAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLVICSVAEGATFHARLTVKPG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI 
Sbjct: 121 RGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSII 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
            +++++LA++I+ + L +F+N  +  K  +  +  
Sbjct: 181 PQEALSLAAKIMTEHLDIFVNLTDEAKNAEIMVEK 215


>gi|139387284|ref|YP_001123405.1| RNA polymerase alpha subunit [Capsella bursa-pastoris]
 gi|158513962|sp|A4QKM4|RPOA_CAPBU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134286605|dbj|BAF50229.1| RNA polymerase alpha subunit [Capsella bursa-pastoris]
          Length = 327

 Score =  262 bits (669), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 77/321 (23%), Positives = 156/321 (48%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRRDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            H+ S+I G+ E + +I++N+  I L+ +    +   I  +GPG +TA DI     +E++
Sbjct: 71  PHDYSNIVGIQESVHEILMNLNEIVLRSNLYGTRNALICVQGPGYITARDIILPPSVEII 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + +EL + +  GY     +  E+       IDA++ P++  ++++ 
Sbjct: 131 DNTQHIATLTEPIDLCIELKIERNRGYSLKMSNNFEDRS---YPIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LPF P   +                 +++LEL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPFFPFHNRLVNLRKKTKELAFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTM 313
           +++ +F  + + +I  +L   
Sbjct: 307 IKIEHFHVEDVKKILDILEKK 327


>gi|71056850|emb|CAH58980.1| DNA-directed RNA polymerase alpha chain [Enterococcus ratti]
 gi|72534395|emb|CAH58994.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 233

 Score =  262 bits (669), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 107/233 (45%), Positives = 154/233 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV
Sbjct: 61  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           SI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 181 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEE 233


>gi|149390299|ref|YP_001294130.1| RNA polymerase alpha subunit [Chloranthus spicatus]
 gi|172048690|sp|A6MMF4|RPOA_CHLSC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|146744219|gb|ABQ43291.1| RNA polymerase alpha subunit [Chloranthus spicatus]
          Length = 334

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 81/330 (24%), Positives = 160/330 (48%), Gaps = 29/330 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        +  PL +G A T+G A+RR L+  + G  IT  ++D V
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFMLSPLMKGQADTIGIAMRRALLGEIEGTCITRAKLDKV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I +N+K I L+ +    +  +I  RGP  VTA DI +   +E++
Sbjct: 71  PHEYSTIVGIEESIHEIFMNLKEIVLRSNLYGTRNASICVRGPRYVTAQDIISPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + +EL + +  GY     ++ +N   G   IDA+  P++  ++++ 
Sbjct: 131 DTTQHIASLTEPIDLCIELQIQRDRGYRMKTPNKYQN---GSYPIDAVSMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ N  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEEGIRLEDNPNRF 246

Query: 249 SLPFNPAL------------------LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
           ++PF                         +++ EL  R+ N L+  NI  + DL+  ++ 
Sbjct: 247 NIPFFTFHDGLANTNIRKKKKGIALKCIFIDQSELPPRTYNYLKRSNINTLLDLLSNSQE 306

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           D L++ +F    + ++K +L  +     ++
Sbjct: 307 DFLKIEHFR---IEDVKQILDILQKHFTID 333


>gi|81176283|ref|YP_398360.1| RNA polymerase alpha subunit [Lactuca sativa]
 gi|90110846|sp|Q332U5|RPOA_LACSA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|78675201|dbj|BAE47627.1| RNA polymerase alpha chain [Lactuca sativa]
          Length = 335

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 83/331 (25%), Positives = 162/331 (48%), Gaps = 29/331 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESAADSKRLLYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  RGPG VTA DI     +E+L
Sbjct: 71  SHEYSTIMGIQESVHEILMNLKEIVLRSNLYGTCEASICVRGPGYVTAQDIILPPYVEIL 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + K  GY+    +  ++   G   ID ++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIELVIGLQIEKNRGYLIKAPNTFQD---GSYPIDPVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G   + + L + I T+GS+T ++++  ASR L D L  F++ +E    ++ + ++ 
Sbjct: 188 SYENG---NKEILFLEIWTNGSLTPKEALYEASRNLIDLLIPFLHTKEENLNLEGNQHMV 244

Query: 249 SLPF----------------NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            LP                        +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 245 PLPPFTFYDKLAKLTKNKKKMALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDL 304

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++M +F    + ++K +LG +     ++LP 
Sbjct: 305 MKMEHFR---IEDVKQILGILEKNFVIDLPK 332


>gi|139389296|ref|YP_001123062.1| RNA polymerase alpha subunit [Aethionema grandiflorum]
 gi|158513623|sp|A4QJN1|RPOA_AETGR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134286258|dbj|BAF49886.1| RNA polymerase alpha subunit [Aethionema grandiflorum]
          Length = 333

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 76/320 (23%), Positives = 156/320 (48%), Gaps = 24/320 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRRDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEMEGTCITRAKSENI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            H+ S+I G+ E + +I++N++ I L+ +        I  +GPG +TA DI     +E++
Sbjct: 71  PHDYSNIVGIQESVHEILMNLQEIVLRSNLYGTCNALICVQGPGYITARDIILPPSVEIM 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + + L + +  GY     +  E+   G   IDAL+ P++  ++++ 
Sbjct: 131 DNTQHIATLTEPIDLCIGLQIERNRGYSLKMPNPFED---GSYPIDALFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G   + + L + I T+G++T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGTG-NENQEILFLEIWTNGNLTPKEALHEASRNLINLFIPFLHVEEETFYLENNEDKV 246

Query: 249 SLPFNPALLKK----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP  P   +                 +++LEL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPLFPFHNRLVKLRKKKKELVFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGT 312
           +++ +F  + + +I  +L  
Sbjct: 307 IKIEHFHIEDVKKILDILEK 326


>gi|126697065|ref|YP_001091951.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. MIT 9301]
 gi|156637354|sp|A3PF25|RPOA_PROM0 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|126544108|gb|ABO18350.1| Bacterial RNA polymerase, alpha chain [Prochlorococcus marinus str.
           MIT 9301]
          Length = 312

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 94/305 (30%), Positives = 159/305 (52%), Gaps = 8/305 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             I++ +     +     +  PL RG A TLGN+LRRVLM  L G+A+TAV+I G+ HE 
Sbjct: 7   ERIDHQIADDRSQT-GTFLIGPLERGQATTLGNSLRRVLMGGLEGSAVTAVRIAGINHEY 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K +++  +    +   +   GP  V A DIQ  + +E+++ + 
Sbjct: 66  ATIPGVREDVLDILLNCKQLSINSTNPELEIGRLVASGPMEVKANDIQFSSQVEIVDGEK 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P      E   I L+ IDA++ P+K+V++T++    
Sbjct: 126 PIATIQEGHNLELEIHVERGVGYRPVDRKSEETTAIDLLQIDAVFMPVKRVNFTIDETAV 185

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L M + TDGS + +D++A A+  L +           ++        +   
Sbjct: 186 AEGGTGRERLKMEVVTDGSTSPDDAIAEAANQLIELFQPLATVTMVEEI------PEEPE 239

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 240 PSPEAQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIS 304


>gi|124302938|ref|YP_001023733.1| RNA polymerase alpha subunit [Angiopteris evecta]
 gi|158512827|sp|A2T365|RPOA_ANGEV RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|110628336|gb|ABG79632.1| RNA polymerase alpha subunit [Angiopteris evecta]
          Length = 341

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 91/342 (26%), Positives = 160/342 (46%), Gaps = 28/342 (8%)

Query: 1   MIQKNW---QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRG 57
           MIQ       + I+   IE  +  +           P  +G A+T+G A+RR L+  + G
Sbjct: 1   MIQDEVPVSAQTIQWRCIESKIESKRLH-YGRFAISPFRKGQANTVGIAIRRSLLGEIEG 59

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
            AIT  +   V+HE S+I G+ E + DI++N K I L+      ++  I   GP  +TA 
Sbjct: 60  TAITYAKSKNVIHEYSTIIGIEESINDILINFKEIVLRSDSYETQKAYISITGPKDITAE 119

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI     ++ ++    I  +  D  + +E+ + K  GY       ++    G   IDA++
Sbjct: 120 DILLPPSVQAIDDSQHIATITKDITLDIEIEIQKDRGYRIQD---SKESQAGEFFIDAVF 176

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
            PI+K +Y+V S    +    + L + I TDGS+T ++++  ASR L D    F++ EE 
Sbjct: 177 MPIRKANYSVHSFGNNKKF-QEILFIEIWTDGSLTPKEALYEASRNLIDLFLPFLHTEEE 235

Query: 238 KKEVKEDINVKSLPFN-----------------PALLKKVEELELSVRSTNCLRGENIVY 280
           +     D   +S                           +++LEL  R+ NCL+  ++  
Sbjct: 236 EIISDRDEKSESNGNILLSNSISTDIDRMAKEVAFKHIFIDQLELPARAYNCLKKVDVHT 295

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           + DL++ ++ D+ ++ NFG+KS+ ++   L        +NLP
Sbjct: 296 ISDLLKYSQDDLRKIKNFGKKSVDQVLEALQE---RFAINLP 334


>gi|78780012|ref|YP_398124.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. MIT 9312]
 gi|119366708|sp|Q318K7|RPOA_PROM9 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|78713511|gb|ABB50688.1| DNA-directed RNA polymerase subunit alpha [Prochlorococcus marinus
           str. MIT 9312]
          Length = 311

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 94/305 (30%), Positives = 159/305 (52%), Gaps = 8/305 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             I++ +     +     +  PL RG A TLGN+LRRVLM  L G+A+TAV+I G+ HE 
Sbjct: 6   ERIDHQIADDRSQT-GTFLIGPLERGQATTLGNSLRRVLMGGLEGSAVTAVRIAGINHEY 64

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           ++I GV ED+ DI+LN K +++  S    +   +   GP  V A DIQ  + +E+++ + 
Sbjct: 65  ATIPGVREDVLDILLNCKQLSINSSNPELEIGRLVASGPLDVKANDIQFSSQVEIVDGEK 124

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +     + +E+ V +G GY P      E   I L+ IDA++ P+K+V+++++    
Sbjct: 125 PIATIQEGHNLELEIHVERGVGYRPVDRKNQETTAIDLLQIDAVFMPVKRVNFSIDETAV 184

Query: 193 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  ++L M + TDGS + +D++A A+  L +           ++        +   
Sbjct: 185 AEGGTGRERLKMEVVTDGSTSPDDAIAEAANQLIELFQPLATVTMVEEI------PEEPE 238

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 239 PSPEAQIPLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 298

Query: 312 TMGLF 316
            +G+ 
Sbjct: 299 RIGIS 303


>gi|71056894|emb|CAH59004.1| DNA-directed RNA polymerase alpha chain [Enterococcus italicus]
          Length = 229

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 105/229 (45%), Positives = 151/229 (65%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIK
Sbjct: 1   IVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVAQIILNIK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           G++LK+ G+  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV 
Sbjct: 61  GLSLKLYGEDEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTVK 120

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            G GYV A  ++ ++ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGS
Sbjct: 121 PGRGYVQADENKKDDMPIGVLPVDSIYTPVRRVNYQVENTRVGHRDDFDKLTMEIWTDGS 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           I   D+++LA++I+ + L +F+N  +  K  +  +  +       L   
Sbjct: 181 IEPLDAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMT 229


>gi|71056868|emb|CAH58989.1| DNA-directed RNA polymerase alpha chain [Enterococcus pseudoavium]
          Length = 229

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 105/229 (45%), Positives = 151/229 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNI
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV
Sbjct: 61  KGLALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           SI  +++++LA++IL + L +F+N  +  K  +  +  +       L  
Sbjct: 181 SIIAQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 229


>gi|312148520|gb|ADQ31179.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           JD1]
          Length = 344

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 119/336 (35%), Positives = 185/336 (55%), Gaps = 19/336 (5%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +++K  ++   P  IE++   Q + +       P  RGF  T+GN LRRVL+SS+ G AI
Sbjct: 2   LVEKFLKDFTIPEKIEFLK-SQGDGSYGKFTIYPFERGFGITIGNTLRRVLLSSIEGYAI 60

Query: 61  TAVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGP 111
           TA+++           V  E   I GV ED  ++I NIK I+LK+ G+  ++ TI     
Sbjct: 61  TAMRVQSNNKDASLKVVSSEFDLIPGVSEDTLEVIANIKNIHLKL-GEGEQKKTISFSVS 119

Query: 112 G----VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
           G    V+ A   +    +EV N D VI  L  D  + +E  ++ G GYV ++ +    + 
Sbjct: 120 GKDTNVLKASHFERD-GVEVFNKDLVIATLSRDVNLDLEFQINYGRGYVSSEQNSKYLEE 178

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           + +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ 
Sbjct: 179 VNVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREF 238

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
           L   ++FE+    V           +  L   +E+L LSVRS NCL  EN+  +G+LI +
Sbjct: 239 LFPLVDFED---NVNTSFEKSKSESSNLLDMSIEKLNLSVRSLNCLAKENVRTLGELISK 295

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
              ++ +  NFG+KSL EI   LG+  L+LGM+  D
Sbjct: 296 NAEELSKARNFGKKSLEEIIEKLGSYRLYLGMSKED 331


>gi|229021749|ref|ZP_04178329.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH1272]
 gi|228739536|gb|EEL89952.1| DNA-directed RNA polymerase subunit alpha [Bacillus cereus AH1272]
          Length = 233

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 91/232 (39%), Positives = 145/232 (62%)

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           +K + LK+  +  K + I  +G G+VTA DI   +D+E+LNPD  I  L  +A  RM LT
Sbjct: 1   MKKLALKIYSEEEKTLEIDVQGEGIVTAADITHDSDVEILNPDLHIATLAKNAHFRMRLT 60

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
             +G GY PA  +++E+ PIG+I ID++Y+P+ +V+Y VE  R GQV +YDKL++ + TD
Sbjct: 61  AKRGRGYTPADANKSEDQPIGVIPIDSIYTPVSRVTYQVEKTRVGQVANYDKLTLDVWTD 120

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           GSI  +++++L ++IL + L +F+   +  +  +  +  +       L   +EEL+LSVR
Sbjct: 121 GSIGPKEAISLGAKILTEHLNIFVGLTDEAQNAEIMVEKEEDQKEKVLEMTIEELDLSVR 180

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           S NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  +GL L  +
Sbjct: 181 SYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKHKLEELGLGLRKD 232


>gi|283945397|dbj|BAI66454.1| RNA polymerase alpha subunit [Lactobacillus similis]
          Length = 248

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 110/251 (43%), Positives = 162/251 (64%), Gaps = 7/251 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KPN    I   +E ++    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLH
Sbjct: 2   KPN----IHKIEESDDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLH 57

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           E S+++GV ED+T IILN K I+LK+ G  D  + + I  +GP  VTAGDI   +D+ VL
Sbjct: 58  EFSTVEGVVEDVTQIILNTKKISLKLEGPDDEIESMEIDVKGPAQVTAGDITADSDVTVL 117

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR-TENDPIGLITIDALYSPIKKVSYTV 187
           NPD  I  +   A   M +T +KG GYV A  ++  E+ PIG++ ID++Y+PI++V+Y V
Sbjct: 118 NPDLYIATVAEGATFHMRMTANKGRGYVSADRNKAKEDMPIGVLPIDSIYTPIERVNYQV 177

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  DYDKL++ + TD SIT  +S++LA++IL + L MF++  +  K  +  +  
Sbjct: 178 ENTRVGQRDDYDKLTLDVWTDSSITPSESISLAAKILTEHLAMFVDLTDEAKNAEIMVEK 237

Query: 248 KSLPFNPALLK 258
           +       L  
Sbjct: 238 EETHKEKMLEM 248


>gi|139389833|ref|YP_001123494.1| RNA polymerase alpha subunit [Crucihimalaya wallichii]
 gi|158513969|sp|A4QKW3|RPOA_CRUWA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134286695|dbj|BAF50318.1| RNA polymerase alpha subunit [Crucihimalaya wallichii]
          Length = 327

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 77/321 (23%), Positives = 156/321 (48%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT V+ + +
Sbjct: 11  RTLQWKCVESRRDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEMEGTCITRVKSENI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            H+ S+I G+ E + +I++N+  I L+ +    +   I  +GPG +TA DI     +E++
Sbjct: 71  PHDYSNIVGIQESVHEILMNLNEIVLRSNLYGTRNALICVQGPGYITARDIILPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + + L + +  GY     +  E+       IDA++ P++  ++++ 
Sbjct: 131 DNTQHIATLTEPIDLCIGLKIERNRGYSLKISNNLEDRS---YPIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LPF P   +                 +++LEL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPFFPFHNRFFNLRKKKKELAFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTM 313
           +++ +F  + + +I  +L   
Sbjct: 307 IKIEHFHVEDVKKILDILEKK 327


>gi|72534409|emb|CAH59041.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 229

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 106/229 (46%), Positives = 151/229 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV
Sbjct: 61  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           SI   ++++L+++I+ + L +F+N  +  K  +  +  +       L  
Sbjct: 181 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 229


>gi|290489680|gb|ADD31224.1| RNA polymerase alpha subunit protein [Bulnesia arborea]
          Length = 352

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 82/320 (25%), Positives = 158/320 (49%), Gaps = 24/320 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        +  PL +G A T+G A+RRVL+  + G +IT+ + + +
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFLLSPLKKGQADTIGIAMRRVLLGEIEGTSITSAKSENI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE SSI GV E + +I++N+K I L+         +I  +GPG VTA DI   + +E++
Sbjct: 71  PHEYSSIVGVEESVHEILMNLKEIVLRSHLYGICDASICVKGPGCVTAQDIILPSYVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I NL       + L + +  GY     ++ +    G+  IDA++ P++  ++++ 
Sbjct: 131 DNTQHIANLTEPIDFCIRLQIERNRGYRIKTPNQFQE---GIYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + N  
Sbjct: 188 SYGNGSET-QEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLENNQNKY 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP      +                 +++LEL+ +  NCL+  NI  + DL+   + D+
Sbjct: 247 TLPLFSFHDQFNQIKKNQKEIEFKSIFIDQLELTPKIYNCLKRSNIHTLFDLLNNRKEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGT 312
           +R+ +F  + +  I  +L  
Sbjct: 307 MRIEHFRIEDINHIFHILEK 326


>gi|154795220|ref|YP_588149.2| RNA polymerase alpha subunit [Helianthus annuus]
 gi|158518528|sp|Q1KXS7|RPOA_HELAN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
          Length = 335

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 81/331 (24%), Positives = 163/331 (49%), Gaps = 29/331 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESAADSKRLLYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE ++I G+ E + +I++N+K I L+ +       +I  RGPG VTA DI     +E++
Sbjct: 71  SHEYATIMGIQESVHEILMNLKEIVLRSNLYGTCEASICVRGPGYVTAQDIILPPYVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + K  GY+    +  ++   G   ID ++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIELVIGLQIEKNRGYLIKAPNTFQD---GSYPIDPVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G   + + L + I T+GS+T ++++  ASR L D L  F++ +E    ++++ ++ 
Sbjct: 188 SYENG---NKEILFLEIWTNGSLTPKEALHEASRNLIDLLIPFLHTKEENLSLEDNQHIV 244

Query: 249 SLPF----------------NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            LP                        +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 245 PLPPFTFYDKLAKLTKNKKKMALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDL 304

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++M +F    + ++K +LG +     ++LP 
Sbjct: 305 MKMEHFR---IEDVKQILGILEKNFVIDLPK 332


>gi|300431314|gb|ADK12620.1| RNA polymerase alpha subunit [Pappostipa vaginata]
          Length = 319

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 89/318 (27%), Positives = 154/318 (48%), Gaps = 23/318 (7%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +  +       I  PL +G A  +G ALRR L+  + G  IT  +   V HE S+I G+ 
Sbjct: 2   VDSKRLYYGRFILSPLRKGQADPVGIALRRALLXEIEGTCITRAKFGSVPHEYSTIAGIE 61

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+ +    I NL  
Sbjct: 62  ESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIXDTAQPIANLTE 121

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              + +EL + +  GY     +  ++   G   IDA+  P++ V+Y++ S   G     +
Sbjct: 122 PIDLCIELQIKRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFSCGNG-NEKPE 177

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-------- 251
            L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P        
Sbjct: 178 ILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKKL 237

Query: 252 --------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                     P     +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    +
Sbjct: 238 TNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSFR---M 294

Query: 304 VEIKGVLGTMGLFLGMNL 321
            + K +   +   L +NL
Sbjct: 295 EDGKQIWDNLEKHLPINL 312


>gi|139390380|ref|YP_001122978.1| RNA polymerase alpha subunit [Aethionema cordifolium]
 gi|158513605|sp|A4QJE7|RPOA_AETCO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134286173|dbj|BAF49802.1| RNA polymerase alpha subunit [Aethionema cordifolium]
          Length = 333

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 76/320 (23%), Positives = 155/320 (48%), Gaps = 24/320 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRRDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEMEGTCITRAKSENI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            H+ S+I G+ E + +I++N++ I L+ +        I  +GPG +TA DI     +E++
Sbjct: 71  PHDYSNIVGIQESVHEILMNLQEIVLRSNLYGTCNALICVQGPGSITARDIILPPSVEII 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + + L + +  GY     +  E+   G   IDAL+ P++  ++++ 
Sbjct: 131 DNTQHIATLTEPIDLCIGLQIERNRGYSLKMPNHFED---GSYPIDALFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+G++T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGTG-NEKQEILFLEIWTNGNLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHKV 246

Query: 249 SLPFNPALLKK----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP  P   +                 +++LEL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPLFPFHNRLVKLRKKKKELVFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGT 312
           +++ +F  + + +I  +L  
Sbjct: 307 IKIEHFHIEDVKKILEILEK 326


>gi|11497558|ref|NP_054966.1| RNA polymerase alpha subunit [Spinacia oleracea]
 gi|12644101|sp|P06505|RPOA_SPIOL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|7636139|emb|CAB88759.1| RNA polymerase alpha subunit [Spinacia oleracea]
          Length = 335

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 86/331 (25%), Positives = 162/331 (48%), Gaps = 25/331 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E     +        I  PL +G A T+G A+RR L+  + G  IT  + + + 
Sbjct: 13  LQWKCVESRTDSKCLH-YGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +       +I  RGP  VTA DI     +E+++
Sbjct: 72  HEYSTILGIQESVHEILMNLKEIVLRSNLYGTCEASICVRGPRGVTAQDIILPPYVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I +L     + + L + +  GY     +  ++   G   IDAL+ P++ V++++ S
Sbjct: 132 NTQHIASLTEPIDLCIGLQLERNRGYHIKAPNNFQD---GSFPIDALFMPVRNVNHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L D L  F++ EE    ++++ +  S
Sbjct: 189 YGNG-NEKQEILFLEIWTNGSLTPKEALYEASRNLIDLLIPFLHAEE-NVNLEDNQHKVS 246

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           LP                        +++LEL  R  NCL+  NI  + DL+  ++ D++
Sbjct: 247 LPLFTFHNRLAEIRKNKKKIALKFIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLI 306

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           +M +F    + ++K + GT+     ++L + 
Sbjct: 307 KMKHFR---IEDVKQIFGTLEKHFVIDLKNK 334


>gi|88657014|gb|ABD47264.1| RNA polymerase alpha subunit [Lactuca sativa]
          Length = 337

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 83/331 (25%), Positives = 162/331 (48%), Gaps = 29/331 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 13  RTLQWKCVESAADSKRLLYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 72

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  RGPG VTA DI     +E+L
Sbjct: 73  SHEYSTIMGIQESVHEILMNLKEIVLRSNLYGTCEASICVRGPGYVTAQDIILPPYVEIL 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + K  GY+    +  ++   G   ID ++ P++  ++++ 
Sbjct: 133 DNTQHIASLTEPIELVIGLQIEKNRGYLIKAPNTFQD---GSYPIDPVFMPVRNANHSIH 189

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G   + + L + I T+GS+T ++++  ASR L D L  F++ +E    ++ + ++ 
Sbjct: 190 SYENG---NKEILFLEIWTNGSLTPKEALYEASRNLIDLLIPFLHTKEENLNLEGNQHMV 246

Query: 249 SLPF----------------NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            LP                        +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 PLPPFTFYDKLAKLTKNKKKMALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++M +F    + ++K +LG +     ++LP 
Sbjct: 307 MKMEHFR---IEDVKQILGILEKNFVIDLPK 334


>gi|71056917|emb|CAH59017.1| DNA-directed RNA polymerase alpha chain [Enterococcus columbae]
          Length = 234

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 107/234 (45%), Positives = 155/234 (66%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
             I EPL RG+  TLGN+LRR+L+SSL GAAIT +QI+GVLHE S+IKGV ED+  IILN
Sbjct: 1   KFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIEGVLHEFSTIKGVREDVAQIILN 60

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           +KG+ LK+ G   K + I   GP VVTAGDI   +D+E+LN D  IC++   A  R  LT
Sbjct: 61  VKGLALKLYGSEEKTLEIDITGPAVVTAGDILVDSDVEILNKDMYICSVSEGATFRARLT 120

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           V  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+   +DKL+M I TD
Sbjct: 121 VKAGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDVFDKLTMEIWTD 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           GSI   D+++LA++I+ + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 181 GSIEPLDAMSLAAKIMTEHLDIFVNLTDEAKHAEIMVEKEETQKEKMLEMTIEE 234


>gi|118411080|ref|YP_874475.1| DNA-directed RNA polymerase alpha chain [Phaeodactylum tricornutum]
 gi|125987637|sp|A0T0K0|RPOA_PHATC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|116739827|gb|ABK20698.1| DNA-directed RNA polymerase alpha chain [Phaeodactylum tricornutum]
          Length = 311

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 95/296 (32%), Positives = 158/296 (53%), Gaps = 4/296 (1%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               +   L  G   T+GN LRRVL+  L G AI+AV+I G+ HE S+I GV ED+ +I+
Sbjct: 20  HGQFLINSLNPGQGITIGNQLRRVLLGDLGGVAISAVRIAGITHEFSTIPGVREDILEIL 79

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+KGI         +   +  +GP VVTA  IQ    +E++NP+H I  +    ++ +E
Sbjct: 80  LNLKGIICTSQIQDTQFGHLKVQGPSVVTADLIQLPPGVEIINPNHYIATISTSNILEIE 139

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
                G GY  A  +  E D    + +D ++ P++KV + +E+  +      ++L + I 
Sbjct: 140 FKFEYGSGYHLASQNFVEEDENY-LQLDTIFMPVQKVDFKIENIYDATNNISERLFLDIW 198

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+GSI+  D++  A++++ D   + IN +      + ++  +++   P     +EEL+LS
Sbjct: 199 TNGSISPNDALESAAQVIIDLFTLLINNKNINNNNRLELKPETISIEPYTNIAIEELQLS 258

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           VR+ NCL+   I  +GDL+Q +   +  + NFGRKS  E+   L      LG+ L 
Sbjct: 259 VRAYNCLKKAQINTVGDLLQYSPEKLQELKNFGRKSADEVFSTLKNK---LGIILK 311


>gi|119663520|emb|CAK22331.1| RNA polymerase alpha subunit [Lactobacillus hammesii]
          Length = 227

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 103/226 (45%), Positives = 154/226 (68%), Gaps = 4/226 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVTQIILNV 60

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K I LK++G  D  + + I  +GP  +TAGDI    D++VLNPD  I  +   A   M +
Sbjct: 61  KKIALKLNGSDDQEETMEINVKGPAQITAGDIVAGADVDVLNPDLYIATVADGATFHMRM 120

Query: 148 TVSKGHGYVPAKHHRTEN--DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           T  KG GYV A  H+ +N   PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ +
Sbjct: 121 TADKGRGYVSADEHKAQNTEMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDV 180

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            T+GSI   +++ALA++IL + L MF++  +  K  +  +  +   
Sbjct: 181 WTNGSINPSEAIALAAKILTEHLAMFVDLTDEAKNAEIMVEKEETH 226


>gi|139388126|ref|YP_001123318.1| RNA polymerase alpha subunit [Barbarea verna]
 gi|158513955|sp|A4QKD7|RPOA_BARVE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134286517|dbj|BAF50142.1| RNA polymerase alpha subunit [Barbarea verna]
          Length = 327

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 75/321 (23%), Positives = 154/321 (47%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRRDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            H+ S+I G+ E + +I++N+  I L+ +    +   I  +GPG +TA DI     +E++
Sbjct: 71  PHDYSNIVGIQESVHEILMNLNEIVLRSNLYGTRNALICVQGPGYITARDIILPPSVEII 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + + L + +  GY     +  E+       IDA++ P++  ++++ 
Sbjct: 131 DNTQHIATLTEPIDLCIGLKIERNRGYSLKMSNNFEDRS---YPIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP  P   +                 +++LEL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPLFPFHNRLVNLRKKKKEQGFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTM 313
           +++ +F  + + +I  +L   
Sbjct: 307 IKIEHFHIEDVKKILDILEKK 327


>gi|71056923|emb|CAH59020.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
          Length = 226

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 104/226 (46%), Positives = 150/226 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV
Sbjct: 61  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           SI   ++++L+++I+ + L +F+N  +  K  +  +  +       
Sbjct: 181 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 226


>gi|300431305|gb|ADK12617.1| RNA polymerase alpha subunit [Achnatherum inebrians]
          Length = 330

 Score =  261 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 88/328 (26%), Positives = 158/328 (48%), Gaps = 33/328 (10%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   + 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSLP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I+ +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY     +  ++   G   IDA+  P++ V+Y    
Sbjct: 132 TAQPIANLTEPIDFCIELQIKRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYR--- 185

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                   ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 186 -------KHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFT 238

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ NCL+  NI  + DL+ +TE D++
Sbjct: 239 PPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLM 298

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 299 RIDSFR---MEDGKQIWDTLEKHLPIDL 323


>gi|91208933|ref|YP_538968.1| RNA polymerase alpha subunit [Gossypium hirsutum]
 gi|325210961|ref|YP_004286036.1| RNA polymerase alpha subunit [Gossypium thurberi]
 gi|109900621|sp|Q2L938|RPOA_GOSHI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|85687447|gb|ABC73659.1| RNA polymerase alpha subunit [Gossypium hirsutum]
 gi|290775823|gb|ADD62319.1| RNA polymerase alpha subunit [Gossypium thurberi]
          Length = 329

 Score =  261 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 80/333 (24%), Positives = 158/333 (47%), Gaps = 24/333 (7%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLR 56
           M+++  +        ++  +    ++        I  PL +G A T+G A+RR L+  L 
Sbjct: 1   MVREKVKVSTSTRTRQWKCVESRTDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGELE 60

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           G  IT  + + + HE S+I G+ E + +I++N+K I L+ +    +   I  +GPG VTA
Sbjct: 61  GTCITRAKSEKIPHEYSTIVGIQESVHEILMNLKEIVLRGNLYGTRNAFICAKGPGYVTA 120

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
            DI     +E+++    + +L     + + L + +  GY        +N   G   IDA+
Sbjct: 121 QDIILPPSVEIVDNTQHVASLTEPIDLCIGLQIERNRGYGIKT---PKNFHDGSYPIDAV 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           + P++  ++++           + L + I T+GS+T ++++  ASR L D    F++ EE
Sbjct: 178 FMPVRNANHSIHCYGND-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHTEE 236

Query: 237 PKKEVKEDINVKSLPFNPALLK----------------KVEELELSVRSTNCLRGENIVY 280
               ++ + +  +LPF P   +                 +++ EL  R  NCL+  NI  
Sbjct: 237 ENLHLENNQHDVTLPFFPFHDRLVKLTKKKKEIALKYIFIDQSELPPRIYNCLKKSNIHT 296

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           + DL+  +  D++++ +F  + + +I G+L   
Sbjct: 297 LLDLLNNSREDLMKIEHFRIEDVKQILGILEKK 329


>gi|139389128|ref|YP_001123846.1| RNA polymerase alpha subunit [Nasturtium officinale]
 gi|158513997|sp|A4QLW5|RPOA_NASOF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134287051|dbj|BAF50670.1| RNA polymerase alpha subunit [Nasturtium officinale]
          Length = 327

 Score =  261 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 75/321 (23%), Positives = 154/321 (47%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRRDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            H+ S+I G+ E + +I++N+  I L+ +    +   I  +GPG +TA DI     +E++
Sbjct: 71  PHDYSNIVGIQESVHEILMNLNEIVLRSNLYGTRNALICVQGPGYITARDIILPPSVEII 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + + L + +  GY     +  E+       IDA++ P++  ++++ 
Sbjct: 131 DNTQHIATLTEPIDLCIGLKIERNRGYSLKMSNNFEDRS---YPIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP  P   +                 +++LEL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPLFPFHNRLVNLRKKKKELAFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTM 313
           +++ +F  + + +I  +L   
Sbjct: 307 IKIEHFHIEDVKKILDILEKK 327


>gi|68164836|ref|YP_247632.1| RNA polymerase alpha subunit [Cucumis sativus]
 gi|75317292|sp|Q4VZK3|RPOA_CUCSA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|67511431|emb|CAJ00791.1| RNA polymerase alpha chain [Cucumis sativus]
 gi|74027132|gb|AAZ94682.1| RNA polymerase alpha subunit [Cucumis sativus]
 gi|115432835|gb|ABI97448.1| RNA polymerase alpha subunit [Cucumis sativus]
 gi|115498335|gb|ABI98777.1| RNA polymerase alpha subunit [Cucumis sativus]
          Length = 333

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 78/327 (23%), Positives = 151/327 (46%), Gaps = 24/327 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           +K   +E      +       I  PL +G   T+G A+R+ L+  + G  IT  + + + 
Sbjct: 13  LKWKCVES-RADSKRLYYGRFILSPLMKGQGDTIGIAMRKALLGEIEGTCITRAKSEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +    +  +I  +GPG VTA DI     +E+++
Sbjct: 72  HEYSTIVGIQESVHEILMNLKEIVLRSNLYGTRDASICVKGPGCVTAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL     + +EL + +  GY     +  ++       +DA++ P++ V++++ S
Sbjct: 132 NTQHIANLMEPINLCIELKIERNRGYHIQTPNNFQDAS---YPMDAIFMPVRNVNHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                    + L + I T+GS+T ++++  ASR L D    F++ EE K+      N K 
Sbjct: 189 Y-VNGNEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEEKENFHLKNNKKK 247

Query: 250 LPFNPALLKK------------------VEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           +        +                  +++ EL  R  NCL+  NI  + DL+  +  +
Sbjct: 248 VTLPLFTFHEKLAKLRKKKKEIALKYIFIDQSELPPRIYNCLKRCNIHTLFDLLNNSPDE 307

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLG 318
           ++++ +F  + +  I  +L  M     
Sbjct: 308 LMKIKHFRIEDVKHILDIL-EMEKNFA 333


>gi|262400792|gb|ACY66281.1| RNA polymerase alpha subunit [Brassica napus]
          Length = 327

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 77/321 (23%), Positives = 154/321 (47%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRRDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            H+ S+I G+ E + +I++N+  I LK +    +   I  +GPG +TA DI     +E++
Sbjct: 71  PHDYSNIVGIQESVHEILMNLNEIVLKSNLYGTRNALICVQGPGYITARDIVLPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + + L + +  GY     +  E+       IDA++ P++  ++++ 
Sbjct: 131 DNTQHIATLTEPINLCIGLKIERNRGYSLKMSNNFEDRS---YPIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP  P   +                 +++LEL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPLFPFHNRLVNLRKKKKELAFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTM 313
           ++M +F  + + +I  +L   
Sbjct: 307 IKMEHFHIEDVKKILDILEKK 327


>gi|76665073|emb|CAJ17984.1| DNA-directed RNA polymerase alpha subunit [Candidatus Phytoplasma
           solani]
          Length = 318

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 102/321 (31%), Positives = 175/321 (54%), Gaps = 8/321 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
           ++    E       I +PL RG+  T+GNALRR+L+SSL GAAI  V+I+GV  E ++I 
Sbjct: 2   FVEELDENLTSGKFIIQPLERGYGVTIGNALRRILLSSLPGAAIVNVKIEGVEQEFTTIP 61

Query: 77  GVHEDLTDIILNIKGINLKMSGDS---HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           GV+ED+  IILN+K I  K+  +S    +++ I   GP  VTA   +    + ++NP H 
Sbjct: 62  GVYEDVMTIILNLKKIVFKVDDESDDFEEQLEINLTGPKKVTAACFELPAGVTIINPKHH 121

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHR-TENDPIGLITIDALYSPIKKVSYTVESARE 192
           I  +  +    M +T+ KG GYV AK ++    + IG+I ID+L++P+  V+Y V     
Sbjct: 122 ITTISDNINFHMTVTIKKGIGYVGAKDNKIHSENQIGVIAIDSLFTPVLDVAYQVG---- 177

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            ++ + D+L++ I T+G+   ++++  A++IL +   + +   +    ++     K    
Sbjct: 178 KKLGNKDELTIQITTNGAAVAKEALVTAAKILVEHFNVIVELSQKVANIEFIPETKEEAH 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           N  L  ++E+L+LSVR  N L+   I  +  L++ +E +++++ + GRKS  E+K     
Sbjct: 238 NYVLDLEIEQLDLSVRLFNSLKRAGINTVAALVKLSEKEVVKLKSLGRKSFQELKDKFVE 297

Query: 313 MGLFLGMNLPDWPPESIEELA 333
            GL     L +    S EE  
Sbjct: 298 YGLEFNDYLKEALHHSTEEDK 318


>gi|332178481|gb|AEE14170.1| DNA-directed RNA polymerase subunit alpha [Thermodesulfobium
           narugense DSM 14796]
          Length = 341

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 101/318 (31%), Positives = 174/318 (54%), Gaps = 14/318 (4%)

Query: 15  IEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS 74
           I+  +  +     +  + EPLP G+  T+GNALRRVL++S+ G+A+ AV++D   HE  +
Sbjct: 12  IKEQLEIENGGKYSKFVLEPLPPGYGATIGNALRRVLLTSIPGSAVIAVRVDDAPHEYMT 71

Query: 75  IKGVHEDLTDIILNIKGIN----LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           + G+ ED+ +  LN+K +       +S +  +++ +  +GP +V A DIQ   +++++N 
Sbjct: 72  LPGMVEDILEFHLNLKKLVVVVSPDISEEETRKLILDVKGPKIVKASDIQPNAEVQIINK 131

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP--IGLITIDALYSPIKKVSYTVE 188
           D  +  L+ +  +R E+TV KG GY+  +  +        G I +DA + PI +V+Y+VE
Sbjct: 132 DLYLATLEENGELRAEITVKKGKGYISIEKMKENTRWLSPGSIPLDANFLPITRVNYSVE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN---FEEPKKEVKEDI 245
           S R GQ  D+DKL   I T+G+I   +++ +A+  L     +F     F + +K V +  
Sbjct: 192 STRVGQETDWDKLIFEIWTNGAIEPVNALRIAAEDLISHFRIFAEYGTFLDSEKPVSDYK 251

Query: 246 NVKSLPF-----NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             K   +        L + +EE+ L  R  N L+   I  +GDLI +T  D+L + +FG+
Sbjct: 252 ETKKDSYLRSQAKMDLEQSIEEIGLQTRIANVLKRSGISTLGDLISKTREDILNVPSFGK 311

Query: 301 KSLVEIKGVLGTMGLFLG 318
           KSL E++ +L   G  L 
Sbjct: 312 KSLDELEEILHAKGYRLK 329


>gi|88656926|gb|ABD47177.1| RNA polymerase alpha subunit [Helianthus annuus]
          Length = 337

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 81/331 (24%), Positives = 163/331 (49%), Gaps = 29/331 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 13  RTLQWKCVESAADSKRLLYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 72

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE ++I G+ E + +I++N+K I L+ +       +I  RGPG VTA DI     +E++
Sbjct: 73  SHEYATIMGIQESVHEILMNLKEIVLRSNLYGTCEASICVRGPGYVTAQDIILPPYVEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + K  GY+    +  ++   G   ID ++ P++  ++++ 
Sbjct: 133 DNTQHIASLTEPIELVIGLQIEKNRGYLIKAPNTFQD---GSYPIDPVFMPVRNANHSIH 189

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G   + + L + I T+GS+T ++++  ASR L D L  F++ +E    ++++ ++ 
Sbjct: 190 SYENG---NKEILFLEIWTNGSLTPKEALHEASRNLIDLLIPFLHTKEENLSLEDNQHIV 246

Query: 249 SLPF----------------NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            LP                        +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 PLPPFTFYDKLAKLTKNKKKMALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++M +F    + ++K +LG +     ++LP 
Sbjct: 307 MKMEHFR---IEDVKQILGILEKNFVIDLPK 334


>gi|620029|gb|AAA74989.1| RNA polymerase alpha-subunit [Chlamydia trachomatis]
          Length = 380

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 122/357 (34%), Positives = 189/357 (52%), Gaps = 27/357 (7%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +K + +E  V     +     +A+PL +G  HTLG+ALRR L+  L   AI +  + G
Sbjct: 17  ESVKMSPVEGAVGSI--DKVARFVADPLEKGMGHTLGSALRRALLIGLEAPAIVSFSMTG 74

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK---------RVTIFKRG-------- 110
           VLHE  +++G+ ED+T+++LN+KG  LK                R TI            
Sbjct: 75  VLHEYMAVEGIIEDVTNMLLNLKGSLLKKYPLQDCEGGRCSQKLRATISVDASDLAAAGG 134

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
              VT GD+      E +NP+HVI  +     + + L V+ G GY P++    E   +  
Sbjct: 135 QKEVTLGDLLQEGTFEAVNPEHVIFTVTRPMQLEVMLRVAFGRGYSPSERIVLEERGMNE 194

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +  +++VA A++IL     +
Sbjct: 195 IVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLVLQVETDGRVAPKEAVAFATQILSKHFSV 254

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLK---KVEELELSV---RSTNCLRGENIVYMGDL 284
           F   +E +   +E I+V+    +  L K    + E+ELSV   RSTNCL   NI  +G+L
Sbjct: 255 FEKMDEKRIVFEEAISVEKENKDDILHKLVLGINEIELSVRLIRSTNCLSNANIETIGEL 314

Query: 285 IQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           +   E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 315 VIMPEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYAEK 371


>gi|224532905|ref|ZP_03673517.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           WI91-23]
 gi|224512181|gb|EEF82570.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           WI91-23]
          Length = 344

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 121/336 (36%), Positives = 185/336 (55%), Gaps = 19/336 (5%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +++K  ++   P  IE++   Q + +       P  RGF  T+GN LRRVL+SS+ G AI
Sbjct: 2   LVEKFLKDFTIPEKIEFLK-SQGDGSYGKFTIYPFERGFGITIGNTLRRVLLSSIEGYAI 60

Query: 61  TAVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGP 111
           TA+++           V  E   I GV ED  +II NIK I+LK+ G+  +R TI     
Sbjct: 61  TAMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLEIIANIKNIHLKL-GEGEQRKTISFSVS 119

Query: 112 G----VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
           G    V+ A   +    +EV N D VI  L  D  + +E  ++ G GYV ++ +    + 
Sbjct: 120 GKDTNVLKASHFERD-GVEVFNKDLVIATLSRDVNLDLEFQINYGRGYVSSEQNSKYLEE 178

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           + +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ 
Sbjct: 179 VNVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREF 238

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
           L   ++FE+    V           +  L   +E+L LSVRS NCL  EN+  +G+LI +
Sbjct: 239 LFPLVDFED---NVNTSFEKSKSESSNLLDMSIEKLNLSVRSLNCLAKENVRTLGELISK 295

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
              ++ +  NFG+KSL EI   LG+  L+LGM+  D
Sbjct: 296 NAEELSKARNFGKKSLEEIIEKLGSYRLYLGMSKED 331


>gi|328814001|gb|AEB52116.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 232

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 106/232 (45%), Positives = 156/232 (67%), Gaps = 2/232 (0%)

Query: 36  PRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLK 95
            RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK
Sbjct: 1   ERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTAIILNVKKIALK 60

Query: 96  MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY 155
           +  D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A   M +T + G GY
Sbjct: 61  LESDETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGAHFHMRMTANTGRGY 120

Query: 156 VPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           V A+ ++   ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T+GSIT 
Sbjct: 121 VSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWTNGSITP 180

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            ++++L+++IL D L +F+N  +  K     +  +       L   +EEL+L
Sbjct: 181 SEAISLSAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEMTIEELDL 232


>gi|224534741|ref|ZP_03675313.1| DNA-directed RNA polymerase, alpha subunit [Borrelia spielmanii
           A14S]
 gi|224513989|gb|EEF84311.1| DNA-directed RNA polymerase, alpha subunit [Borrelia spielmanii
           A14S]
          Length = 344

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 118/334 (35%), Positives = 185/334 (55%), Gaps = 17/334 (5%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++K  ++   P  IE++   Q++ +       P  RGF  T+GN LRRVL+SS+ G AIT
Sbjct: 3   VEKFLKDFTIPEKIEFLK-SQDDGSYGKFTIYPFERGFGVTIGNTLRRVLLSSIEGYAIT 61

Query: 62  AVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK---R 109
            +++           V  E   I GV ED  ++I NIK I+LK+     +++  F    +
Sbjct: 62  TMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLEVIANIKNIHLKLREGEQRKIISFSVSGK 121

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
              V+ A   +    +EV N D VI  L  DA +  E  ++ G GYV ++ +    + + 
Sbjct: 122 DTNVLKASHFEMD-GVEVFNKDLVIATLSHDANLDFEFQINYGRGYVSSEQNSKYLEEVN 180

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           +I +D+++SPI+KVSYTVE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L 
Sbjct: 181 VIALDSIFSPIEKVSYTVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAALIVREFLF 240

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
             ++FE+    V   ++      +  L   +E+L+LSVRS NCL  EN+  +G+LI +  
Sbjct: 241 PLVDFED---SVNTSVDKSKSENSNLLDMGIEKLDLSVRSLNCLAKENVKTLGELISKNA 297

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            ++ +  NFG+KSL EI   LG+  LFLGM+  D
Sbjct: 298 DELSKARNFGKKSLEEIIEKLGSYRLFLGMSKED 331


>gi|119662289|emb|CAJ33131.1| RNA polymerase alpha subunit [Lactobacillus casei]
          Length = 211

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 96/211 (45%), Positives = 147/211 (69%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           G+  TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED+T IILNIK + LKM+
Sbjct: 1   GYGTTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMN 60

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
            D  K + I   GP  VTA DI T  D+EVLNP+  IC +       + +TV KG GYV 
Sbjct: 61  TDEDKNIEIDVNGPAKVTAADIVTDPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVA 120

Query: 158 AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
           A  +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  +++
Sbjct: 121 ADQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAI 180

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +LA++IL + L +F+N  +  K  +  +  +
Sbjct: 181 SLAAKILTEHLDIFVNLTDEAKNAEIMVEKE 211


>gi|194033178|ref|YP_002000517.1| RNA polymerase alpha subunit [Brachypodium distachyon]
 gi|193075586|gb|ACF08669.1| RNA polymerase alpha subunit [Brachypodium distachyon]
          Length = 338

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 90/328 (27%), Positives = 159/328 (48%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLIKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +    +  +I  +GP  +TA DI     +EV++
Sbjct: 72  HEYSTIAGIEESVQEILVNLKEIVLRSNLYGVRDASICVKGPRCITAQDIILPPSVEVVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIQLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTGFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL  R+ N L+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKRLTNRKKNKKGIPLNFIFIDQLELPSRTYNYLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDGKQIWDTLEKHLPVDL 332


>gi|195941639|ref|ZP_03087021.1| DNA-directed RNA polymerase subunit alpha [Borrelia burgdorferi
           80a]
 gi|221218042|ref|ZP_03589508.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           72a]
 gi|223889037|ref|ZP_03623628.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           64b]
 gi|224533576|ref|ZP_03674165.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           CA-11.2a]
 gi|225549661|ref|ZP_03770627.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           118a]
 gi|221191990|gb|EEE18211.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           72a]
 gi|223885853|gb|EEF56952.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           64b]
 gi|224513249|gb|EEF83611.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           CA-11.2a]
 gi|225369938|gb|EEG99385.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           118a]
          Length = 344

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 121/336 (36%), Positives = 185/336 (55%), Gaps = 19/336 (5%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +++K  ++   P  IE++   Q + +       P  RGF  T+GN LRRVL+SS+ G AI
Sbjct: 2   LVEKFLKDFTIPEKIEFLK-SQGDGSYGKFTIYPFERGFGITIGNTLRRVLLSSIEGYAI 60

Query: 61  TAVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGP 111
           TA+++           V  E   I GV ED  +II NIK I+LK+ G+  +R TI     
Sbjct: 61  TAMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLEIIANIKNIHLKL-GEGEQRKTISFSVS 119

Query: 112 G----VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
           G    V+ A   +    +EV N D VI  L  D  + +E  ++ G GYV ++ +    + 
Sbjct: 120 GKDTNVLKASHFERD-GVEVFNKDLVIATLSHDVNLDLEFQINYGRGYVSSEQNSKYLEE 178

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           + +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ 
Sbjct: 179 VNVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREF 238

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
           L   ++FE+    V           +  L   +E+L LSVRS NCL  EN+  +G+LI +
Sbjct: 239 LFPLVDFED---NVNTSFEKSKSESSNLLDMSIEKLNLSVRSLNCLAKENVRTLGELISK 295

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
              ++ +  NFG+KSL EI   LG+  L+LGM+  D
Sbjct: 296 NAEELSKARNFGKKSLEEIIEKLGSYRLYLGMSKED 331


>gi|71056816|emb|CAH58963.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
 gi|71056836|emb|CAH58973.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
 gi|71056872|emb|CAH58991.1| DNA-directed RNA polymerase alpha chain [Enterococcus mundtii]
          Length = 230

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 105/230 (45%), Positives = 151/230 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV
Sbjct: 61  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           SI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   
Sbjct: 181 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMT 230


>gi|161513424|emb|CAP16855.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           dextrinicus]
          Length = 222

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 100/220 (45%), Positives = 151/220 (68%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL G+A++++QIDGVLHE S+I GV ED+T IILNIK I 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGSAVSSIQIDGVLHEFSTIDGVMEDVTQIILNIKKIA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +K   +  K + I   GP  VTA DI+  +DIEVLNP+  IC++     V M++TVS G 
Sbjct: 61  IKNHSEEQKVIEIDVDGPATVTAADIKADDDIEVLNPEQYICSIAEGGHVHMQMTVSNGR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYVPA  ++  + PIG+I +D++++PI +V+Y VES R G+  D+DKL++ + T+GSI+ 
Sbjct: 121 GYVPADQNKNGDMPIGVIAVDSIFTPINRVNYQVESTRVGKRNDFDKLTLDVWTNGSISP 180

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
            ++++LA++IL D L +FI+  +  K  +  +  +     
Sbjct: 181 REAISLAAKILSDHLNIFIDLSDEAKNTEIMVEKEETQKR 220


>gi|139390184|ref|YP_001123757.1| RNA polymerase alpha subunit [Lobularia maritima]
 gi|158513990|sp|A4QLM6|RPOA_LOBMA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134286961|dbj|BAF50581.1| RNA polymerase alpha subunit [Lobularia maritima]
          Length = 327

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 76/321 (23%), Positives = 156/321 (48%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +   +++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRKDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            H+ S+I G+ E + +I++N+  I L+ +    +   I  +GPG +TA DI     +E++
Sbjct: 71  PHDYSNIVGIQESVHEILMNLNEIVLRSNLYGTRNALICVQGPGYITAQDIILPPSVEII 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + +EL + +  GY     +  E+       IDA++ P++  ++++ 
Sbjct: 131 DNTQHIATLTEPIDLCIELKIERNRGYSLKMSNNFEDRS---YPIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP  P   +                 +++LEL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPLFPFHNRLVNLRKKKKELAFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTM 313
           +++ +F  + + +I  +L   
Sbjct: 307 IKIEHFHMEDVKKILDILEKK 327


>gi|71056804|emb|CAH58957.1| DNA-directed RNA polymerase alpha chain [Enterococcus italicus]
          Length = 224

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 102/222 (45%), Positives = 147/222 (66%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG+ 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVAQIILNIKGLA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK+ G+  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G 
Sbjct: 61  LKLYGEDEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTVKPGR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYV A  ++ ++ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI  
Sbjct: 121 GYVQADENKKDDMPIGVLPVDSIYTPVRRVNYQVENTRVGHRDDFDKLTMEIWTDGSIEP 180

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            D+++LA++I+ + L +F+N  +  K  +  +  +       
Sbjct: 181 LDAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 222


>gi|15594847|ref|NP_212636.1| DNA-directed RNA polymerase subunit alpha [Borrelia burgdorferi
           B31]
 gi|3914813|sp|O51455|RPOA_BORBU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|2688389|gb|AAC66840.1| DNA-directed RNA polymerase (rpoA) [Borrelia burgdorferi B31]
          Length = 345

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 121/336 (36%), Positives = 185/336 (55%), Gaps = 19/336 (5%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +++K  ++   P  IE++   Q + +       P  RGF  T+GN LRRVL+SS+ G AI
Sbjct: 3   LVEKFLKDFTIPEKIEFLK-SQGDGSYGKFTIYPFERGFGITIGNTLRRVLLSSIEGYAI 61

Query: 61  TAVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGP 111
           TA+++           V  E   I GV ED  +II NIK I+LK+ G+  +R TI     
Sbjct: 62  TAMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLEIIANIKNIHLKL-GEGEQRKTISFSVS 120

Query: 112 G----VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
           G    V+ A   +    +EV N D VI  L  D  + +E  ++ G GYV ++ +    + 
Sbjct: 121 GKDTNVLKASHFERD-GVEVFNKDLVIATLSHDVNLDLEFQINYGRGYVSSEQNSKYLEE 179

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           + +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ 
Sbjct: 180 VNVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREF 239

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
           L   ++FE+    V           +  L   +E+L LSVRS NCL  EN+  +G+LI +
Sbjct: 240 LFPLVDFED---NVNTSFEKSKSESSNLLDMSIEKLNLSVRSLNCLAKENVRTLGELISK 296

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
              ++ +  NFG+KSL EI   LG+  L+LGM+  D
Sbjct: 297 NAEELSKARNFGKKSLEEIIEKLGSYRLYLGMSKED 332


>gi|299830399|ref|YP_003734614.1| RNA polymerase alpha subunit [Kryptoperidinium foliaceum]
 gi|297385101|gb|ADI40399.1| RNA polymerase alpha subunit [Kryptoperidinium foliaceum]
          Length = 311

 Score =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 93/296 (31%), Positives = 156/296 (52%), Gaps = 4/296 (1%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               + + L  G   T+GN LRRVL++ L G AI+AV+I GV HE S+I GV ED+ +I+
Sbjct: 20  HGQFLIQTLRPGQGITIGNQLRRVLLNDLGGVAISAVRIAGVSHEFSTIPGVREDILEIL 79

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+K I L+    + +   +  +GP VVTA  IQ  + +E++NP+  I  +    ++ +E
Sbjct: 80  LNLKEIVLRSKTQTPQFGRLKIQGPAVVTADLIQLPSTVEIVNPNQYIMTISTSNILEIE 139

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
                G GY  A     E +    + +DA++ PI+KV + +E+  +      ++L + I 
Sbjct: 140 FKFDYGTGYRLASQTFLEENENY-LQLDAIFMPIQKVDFKIENVYDKANNITERLFLDIW 198

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+GSI+  +++  A++I  D     +  ++     +      ++   P     +EEL+LS
Sbjct: 199 TNGSISPTEAMKSAAQITIDVFTSLLENKDTNSSNEVPSKTSAISLEPYTNIAIEELQLS 258

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           VR+ NCL+   I  +GDL+  +   +  + NFGRKS  E+   L      LG+ L 
Sbjct: 259 VRAYNCLKKAQINTVGDLLHYSPEKLQELKNFGRKSADEVFSTLKNK---LGIILK 311


>gi|267798445|gb|ACY78903.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798461|gb|ACY78911.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 269

 Score =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 118/271 (43%), Positives = 179/271 (66%), Gaps = 8/271 (2%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
                 +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ 
Sbjct: 2   STTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDIL 61

Query: 84  DIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDA 141
           +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L   +A
Sbjct: 62  EILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNA 121

Query: 142 VVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M + V +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D 
Sbjct: 122 AIAMRIRVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDL 181

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+
Sbjct: 182 DKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLR 238

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
            V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 239 PVDDLELTVRSANCLKAEAIHYIGDLVQRTE 269


>gi|12265|emb|CAA27214.1| unnamed protein product [Spinacia oleracea]
          Length = 335

 Score =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 86/331 (25%), Positives = 162/331 (48%), Gaps = 25/331 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E     +        I  PL +G A T+G A+RR L+  + G  IT  + + + 
Sbjct: 13  LQWKCVESRTDSKCLH-YGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +       +I  RGP  VTA DI     +E+++
Sbjct: 72  HEYSTILGIQESVHEILMNLKEIVLRSNLYGACEASICVRGPRGVTAQDIILPPYVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I +L     + + L + +  GY     +  ++   G   IDAL+ P++ V++++ S
Sbjct: 132 NTQHIASLTEPIDLCIGLQLERNRGYHIKAPNNFQD---GSFPIDALFMPVRNVNHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L D L  F++ EE    ++++ +  S
Sbjct: 189 YGNG-NEKQEILFLEIWTNGSLTPKEALYEASRNLIDLLIPFLHAEE-NVNLEDNQHKVS 246

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           LP                        +++LEL  R  NCL+  NI  + DL+  ++ D++
Sbjct: 247 LPLFTFHNRLAEIRKNKKKIALKFIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLI 306

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           +M +F    + ++K + GT+     ++L + 
Sbjct: 307 KMKHFR---IEDVKQIFGTLEKHFVIDLKNK 334


>gi|216264217|ref|ZP_03436209.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           156a]
 gi|218249615|ref|YP_002375012.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           ZS7]
 gi|226320983|ref|ZP_03796528.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           29805]
 gi|226321812|ref|ZP_03797338.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           Bol26]
 gi|215980690|gb|EEC21497.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           156a]
 gi|218164803|gb|ACK74864.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           ZS7]
 gi|226233001|gb|EEH31754.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           Bol26]
 gi|226233584|gb|EEH32320.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           29805]
 gi|312149000|gb|ADQ29071.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           N40]
          Length = 344

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 120/336 (35%), Positives = 185/336 (55%), Gaps = 19/336 (5%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +++K  ++   P  IE++   Q + +       P  RGF  T+GN LRRVL+SS+ G AI
Sbjct: 2   LVEKFLKDFTIPEKIEFLK-SQGDGSYGKFTIYPFERGFGITIGNTLRRVLLSSIEGYAI 60

Query: 61  TAVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGP 111
           TA+++           V  E   I GV ED  +II NIK I+LK+ G+  ++ TI     
Sbjct: 61  TAMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLEIIANIKNIHLKL-GEGEQKKTISFSVS 119

Query: 112 G----VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
           G    V+ A   +    +EV N D VI  L  D  + +E  ++ G GYV ++ +    + 
Sbjct: 120 GKDTNVLKASHFERD-GVEVFNKDLVIATLSRDVNLDLEFQINYGRGYVSSEQNSKYLEE 178

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           + +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ 
Sbjct: 179 VNVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREF 238

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
           L   ++FE+    V           +  L   +E+L LSVRS NCL  EN+  +G+LI +
Sbjct: 239 LFPLVDFED---NVNTSFEKSKSESSNLLDMSIEKLNLSVRSLNCLAKENVRTLGELISK 295

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
              ++ +  NFG+KSL EI   LG+  L+LGM+  D
Sbjct: 296 NAEELSKARNFGKKSLEEIIEKLGSYRLYLGMSKED 331


>gi|7388092|sp|P93962|RPOA_PSAST RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1771505|emb|CAB01339.1| alpha subunit of RNA polymerase [Psathyrostachys stoloniformis]
          Length = 339

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 88/328 (26%), Positives = 158/328 (48%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +     
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSXP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   I  +  P++ V+Y++ S
Sbjct: 132 TXQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIXXVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D++
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|283794918|ref|YP_003359271.1| RNA polymerase alpha subunit [Cryptomonas paramecium]
 gi|253981890|gb|ACT46807.1| RNA polymerase alpha subunit [Cryptomonas paramecium]
          Length = 310

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 94/302 (31%), Positives = 162/302 (53%), Gaps = 9/302 (2%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
                    +PL  G   T+GNALRRVL+S L G AIT+ ++ G +HE S I G  ED+ 
Sbjct: 17  TSYYGRFTFQPLKLGQGLTIGNALRRVLLSDLEGIAITSARVSGSVHEFSEIPGTREDVL 76

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           +I+LN+K I LK S        +  +GP +VTA D +  + ++ ++P   I  +    V+
Sbjct: 77  EILLNLKKIVLKGSSKDAGIARLKVQGPCIVTASDFELPSFVKAVDPSQYIATICDSNVL 136

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +E+++S G GY      ++ +     + +DA++ P+ KV+YT+E       +  +KL++
Sbjct: 137 EIEVSISAGRGYKLVN-RQSLDSGKDSLELDAVFMPVNKVNYTIEEINTDFPIAEEKLTL 195

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            I T+GS+T E+S+  A+ +L D L         +  + ++ +  +          +E+L
Sbjct: 196 EIWTNGSLTPEESLMQAATVLTDILAPI-----QRIHLTDEEDFPADKEPEVKNLPIEDL 250

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +LSVR+ NCL+  NI Y  DL+ R++ ++L + NFG+K   E+   L  +   +G+ LP 
Sbjct: 251 KLSVRAYNCLKQINIDYTEDLLTRSQEELLEIKNFGKKCCEEVTQALKNI---VGLTLPK 307

Query: 324 WP 325
             
Sbjct: 308 KK 309


>gi|156598719|gb|ABU85614.1| RNA polymerase alpha subunit [Scaevola aemula]
          Length = 332

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 84/333 (25%), Positives = 160/333 (48%), Gaps = 26/333 (7%)

Query: 10  IKPNNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           + P  + +  +    +N        I  PL +G A T+G ALRR L++ + G AIT  + 
Sbjct: 8   VSPRGLHWRCVESRADNKRRLYGRFILSPLMKGQADTIGIALRRALLAEIEGTAITRAKF 67

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           + V HE S+I+G+ E + +I++N+K I L+ +       +I  +GPG VTA DI +   +
Sbjct: 68  EKVPHEYSTIRGIQESVHEILMNLKEIVLRSNLYGTCEASICVKGPGYVTAQDIISPPYV 127

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E+++    I +L     + + L + K       + +  ++   G   I A+  P++ ++Y
Sbjct: 128 EIVDNTQHIASLTEPIELIIRLQIEKNRFIQLKERNTFQD---GSYAIGAVLMPVRHMNY 184

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED- 244
           ++ S+  G     + L + I T+GS+T ++++  A R L D    F++ EE   E  +D 
Sbjct: 185 SIHSSGNG---KQEILFLEIWTNGSLTPKEALHEACRNLIDLFIPFLHKEEGNLENNQDR 241

Query: 245 ------------INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                         +K           +++ EL     NCL+  NI  + DL+  ++ D+
Sbjct: 242 IPFPSFTFYDKLSKLKKNKKMALKSIFIDQSELPPSIYNCLKRSNIYTLFDLLNNSQEDL 301

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           ++ A+     + ++K +LG +     ++LP  P
Sbjct: 302 MKKAHLH---IEDVKRILGLLEKNCVIDLPKNP 331


>gi|139388942|ref|YP_001123669.1| RNA polymerase alpha subunit [Lepidium virginicum]
 gi|158513983|sp|A4QLD8|RPOA_LEPVR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134286872|dbj|BAF50493.1| RNA polymerase alpha subunit [Lepidium virginicum]
          Length = 327

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 75/321 (23%), Positives = 154/321 (47%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRRDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            H+ S+I G+ E + +I++N+  I L+ +    +   I  +GPG +TA DI     +E++
Sbjct: 71  PHDYSNIVGIQESVHEILMNLNEIVLRSNLYGTRNALICVQGPGYITAQDIILPPSVEII 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + + L + +  GY     +  E+       IDA++ P++  ++++ 
Sbjct: 131 DNTQHIATLMEPIDLCIGLKIERNRGYSLKMSNNFEDRS---YPIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP  P   +                 +++LEL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPLFPFHNRLVNLRKKKKELAFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTM 313
           +++ +F  + + +I  +L   
Sbjct: 307 IKIEHFHIEDVKKILDILEKK 327


>gi|28202204|ref|NP_777445.1| RNA polymerase alpha subunit [Anthoceros formosae]
 gi|41688674|sp|Q85A01|RPOA_ANTFO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|27807906|dbj|BAC55381.1| RNA polymerase alpha subunit [Anthoceros formosae]
 gi|27808054|dbj|BAC55478.1| RNA polymerase alpha subunit [Anthoceros formosae]
          Length = 340

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 84/341 (24%), Positives = 162/341 (47%), Gaps = 26/341 (7%)

Query: 1   MIQKN---WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRG 57
           MIQ       E ++   IE  +  +           PL  G A+T+G A+RR L+  + G
Sbjct: 1   MIQNEIPIPAEALQWKCIESKIDSERLH-YGRFAISPLRPGQANTVGIAIRRALLGEIEG 59

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
             IT V+ + V HE S+I G+ E + DI++N+K I LK +    +  +I   GP  VTA 
Sbjct: 60  TCITYVKFEKVTHEYSTIMGIQESVHDILINLKEIVLKSNSYKTQEASISILGPKRVTAE 119

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI   + +EV++    I  +       ++L + K  GY      + E+   G   ++A +
Sbjct: 120 DIVLPSSVEVIDATQHIATITKAVYFNIKLGIRKDRGYRIENPVKYED---GNFAVNAAF 176

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           +PI+  +Y+V S    +    + L + + T+GS+T ++++  AS+ L +     ++ ++ 
Sbjct: 177 TPIRNANYSVHSFENEKE-KQEILFIEVWTNGSLTPKEALREASQSLINLFIPLLHEKKE 235

Query: 238 KKEVKEDINVKSLPFNPALLKK---------------VEELELSVRSTNCLRGENIVYMG 282
           ++  K +   +                          +++LEL  R+ N L+  ++  + 
Sbjct: 236 RENRKLENKDEYNVLRSCFSLTNIGEVRKEISFKHIFIDQLELPARAYNGLKKVDVHTIS 295

Query: 283 DLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           DL+  ++ D++++ NFG+KS   I+ V+  +     ++LP 
Sbjct: 296 DLLNYSQEDLMKIKNFGKKS---IQQVVEALQKHFAIHLPK 333


>gi|114329687|ref|YP_740508.1| RNA polymerase alpha subunit [Citrus sinensis]
 gi|122166151|sp|Q09ME5|RPOA_CITSI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|113952653|gb|ABI49051.1| RNA polymerase alpha subunit [Citrus sinensis]
          Length = 328

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 77/321 (23%), Positives = 154/321 (47%), Gaps = 23/321 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RRVL+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFILSPLMKGQADTIGIAMRRVLLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +        I  +GPG VTA DI     +E++
Sbjct: 71  PHEYSTIVGIQESVHEILMNLKDIVLRSNLYGTCDALICVKGPGYVTAQDILLPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY     +  ++       IDA++ P++  +++++
Sbjct: 131 DNTQHIASLTEPIDLSIGLQIERSRGYNIKTPNTFQD--GNCYPIDAVFMPVRNANHSIQ 188

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F+  E+    ++ +    
Sbjct: 189 SYGNG-NEKQEILFLEIWTNGSLTPKEALHEASRSLIDLFIPFLQAEDENLPLENNQYKV 247

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LPF     +                 +++ E+S R  NCL+  NI  + DL+   + D+
Sbjct: 248 TLPFFTFHDRLAKLTKKKKEIALKSIFIDQSEMSPRIYNCLKKSNIHTLFDLLNTRQEDL 307

Query: 293 LRMANFGRKSLVEIKGVLGTM 313
           +++ +F  + + +I  +L   
Sbjct: 308 MKIEHFRIEDVKQIMSILEKK 328


>gi|169142742|ref|YP_001687169.1| RNA polymerase alpha subunit [Oenothera argillicola]
 gi|169143063|ref|YP_001687483.1| RNA polymerase alpha subunit [Oenothera parviflora]
 gi|159792980|gb|ABW98736.1| RNA polymerase alpha subunit [Oenothera argillicola]
 gi|159895589|gb|ABX10153.1| RNA polymerase alpha subunit [Oenothera parviflora]
          Length = 366

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 152/319 (47%), Gaps = 21/319 (6%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RR L+  + G  IT  + + + 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +       +I  +GPG VTA DI     +E+++
Sbjct: 72  HEYSTIVGIQESVHEILMNLKEIVLRSNLYGTCNASICVKGPGCVTAQDILLPPSVEIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I +L     + + L + +  GY     +  ++   G   IDA++ P++  ++++ S
Sbjct: 132 NTQHIASLMEPIHLCIGLQIERNRGYHIKSPNNFQD---GSYPIDAVFMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
               Q    + L + I T+GS+T ++++  ASR L D    F++ EE    +  +    +
Sbjct: 189 YGN-QNEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFLPFLHAEEENLHLGNNKYNVT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                        +++LEL  R  N L+G  I  + DL+ +++ D++
Sbjct: 248 FPLFTFHKKLAKLRKPKNEIALKSIFIDQLELPPRIYNSLKGSKIHTLSDLLNKSQEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGT 312
           +M +F  + + +I  +L  
Sbjct: 308 KMKHFRIEDVKQILDILEI 326


>gi|164597832|ref|NP_084725.2| RNA polymerase alpha subunit [Oenothera elata subsp. hookeri]
 gi|169142892|ref|YP_001687315.1| RNA polymerase alpha subunit [Oenothera glazioviana]
 gi|169142977|ref|YP_001687399.1| RNA polymerase alpha subunit [Oenothera biennis]
 gi|172045760|sp|Q9MTJ3|RPOA_OENEH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|159793150|gb|ABW98904.1| RNA polymerase alpha subunit [Oenothera biennis]
 gi|159895504|gb|ABX10069.1| RNA polymerase alpha subunit [Oenothera glazioviana]
 gi|162423699|emb|CAB67191.2| RNA polymerase alpha subunit [Oenothera elata subsp. hookeri]
          Length = 366

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 153/319 (47%), Gaps = 21/319 (6%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RR L+  + G  IT  + + + 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +       +I  +GPG VTA DI     +E+++
Sbjct: 72  HEYSTIVGIQESVHEILMNLKEIVLRSNLYGTCNASICVKGPGCVTAQDILLPPSVEIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I +L     + + L + +  GY     +  ++   G   IDA++ P++  ++++ S
Sbjct: 132 NTQHIASLMEPIHLCIGLQIERNRGYHIKSPNNFQD---GSYPIDAVFMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
               Q    + L + I T+GS+T ++++  ASR L D    F++ EE    + ++    +
Sbjct: 189 YGN-QNEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFLPFLHAEEENLHLGKNKYNVT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                        +++LEL  R  N L+G  I  + DL+ +++ D++
Sbjct: 248 FPLFTFHKKLAKLRKPKNEIALKSIFIDQLELPPRIYNSLKGSKIHTLSDLLNKSQEDLM 307

Query: 294 RMANFGRKSLVEIKGVLGT 312
           +M +F  + + +I  +L  
Sbjct: 308 KMKHFRIEDVKQILDILEI 326


>gi|7388089|sp|P92389|RPOA_HETPI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1770352|emb|CAB01327.1| alpha subunit of RNA polymerase [Heteranthelium piliferum]
          Length = 339

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 161/328 (49%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFWSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPKYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTEL---IKNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D+L
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTXNCLKRANIHTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|151416840|emb|CAO78491.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gelidum]
          Length = 233

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 98/233 (42%), Positives = 149/233 (63%), Gaps = 2/233 (0%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  
Sbjct: 1   TLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDEE 60

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           + + +  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  +
Sbjct: 61  RSLEVDIQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTITAFKGRGYSSADEN 120

Query: 162 RT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           +   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L
Sbjct: 121 KQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSL 180

Query: 220 ASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
            S+IL + L +F++      E    + V+ +  + +    +E+L+LSVRS NC
Sbjct: 181 GSKILAEHLNLFMDISPVAAEANVMVEVEPVAVSASDSAPIEDLDLSVRSYNC 233


>gi|300088169|ref|YP_003758691.1| DNA-directed RNA polymerase subunit alpha [Dehalogenimonas
           lykanthroporepellens BL-DC-9]
 gi|299527902|gb|ADJ26370.1| DNA-directed RNA polymerase, alpha subunit [Dehalogenimonas
           lykanthroporepellens BL-DC-9]
          Length = 333

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 107/302 (35%), Positives = 169/302 (55%), Gaps = 3/302 (0%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            I   +   +      EPL +GF  TLGNALRRVL+SSL GAA+  V+I+GV HE S + 
Sbjct: 8   VIETKESGASFAHFTVEPLEKGFGTTLGNALRRVLLSSLSGAAVAQVRIEGVQHEFSPLP 67

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           G  ED  D +LN+K ++LK       R+ +  +GP  VTA DI+  ++ E+ NPD  +  
Sbjct: 68  GAKEDTMDFLLNLKNLHLKPLFGRPGRLILDVKGPREVTAADIEASSEYEIANPDLYLVT 127

Query: 137 LDV-DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
           LD  ++ + +E+ V  G G+V A     +N  IG I  DA+++P++KV+Y +E    GQ 
Sbjct: 128 LDDAESHLYVEMEVEVGRGFVEATS--ADNVAIGTIPQDAIFNPVEKVNYEIEPVHMGQE 185

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           + Y++L + I TDG++   D++A ++ IL +    F         ++E    K    +  
Sbjct: 186 MSYERLHLRIWTDGTLAPTDALAQSAAILVNHFQPFTAIGGSLPIIQEKKQEKLSIPDEK 245

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
               +E+L+LSVRS NCLR   +  +G+L+ +   +++ + NFG KSL E++  L   GL
Sbjct: 246 YNMPIEQLDLSVRSLNCLRHAGLNTVGELLSKGVDELMSLRNFGLKSLNELEERLQANGL 305

Query: 316 FL 317
             
Sbjct: 306 SF 307


>gi|267798443|gb|ACY78902.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798447|gb|ACY78904.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798449|gb|ACY78905.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798451|gb|ACY78906.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798453|gb|ACY78907.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798455|gb|ACY78908.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798459|gb|ACY78910.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798463|gb|ACY78912.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798465|gb|ACY78913.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798467|gb|ACY78914.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798469|gb|ACY78915.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798471|gb|ACY78916.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798473|gb|ACY78917.1| RNA polymerase alpha subunit [Vibrio cholerae]
 gi|267798475|gb|ACY78918.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 269

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 118/271 (43%), Positives = 179/271 (66%), Gaps = 8/271 (2%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
                 +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ 
Sbjct: 2   STTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDIL 61

Query: 84  DIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDA 141
           +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L   +A
Sbjct: 62  EILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNA 121

Query: 142 VVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M + V +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D 
Sbjct: 122 AIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDL 181

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+
Sbjct: 182 DKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLR 238

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
            V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 239 PVDDLELTVRSANCLKAEAIHYIGDLVQRTE 269


>gi|161511719|emb|CAP16870.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           acidilactici]
          Length = 235

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 108/235 (45%), Positives = 151/235 (64%), Gaps = 2/235 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAITSVQIDNVLHEFSTIEGVVEDVTQIILNLKKVS 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK+  D  K + I   GP  VTAGDI    D+ VLNPD  IC +         LT   G 
Sbjct: 61  LKIESDDEKTLDINVVGPANVTAGDIMGDGDVTVLNPDSPICTVAEGTTFHAVLTADTGR 120

Query: 154 GYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A  ++    + PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ I TDGSI
Sbjct: 121 GYTSADENKARKADMPIGVLPIDSIYTPIERVNYQVEKTRVGQRDDYDKLTLDIWTDGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T  ++ +L+++IL + L +F+N  +  KE +  +  +       L   +EEL+LS
Sbjct: 181 TPSEATSLSAKILTEHLAIFVNLNDQAKETEIMVEKEETHKEKMLEMTIEELDLS 235


>gi|330850862|ref|YP_004376612.1| DNA-directed RNA polymerase alpha chain [Fistulifera sp. JPCC
           DA0580]
 gi|328835682|dbj|BAK18978.1| DNA-directed RNA polymerase alpha chain [Fistulifera sp. JPCC
           DA0580]
          Length = 311

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 97/295 (32%), Positives = 161/295 (54%), Gaps = 4/295 (1%)

Query: 28  TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIIL 87
              +   L  G   T+GN LRRVL+  L G AI+AV+I G+ HE S+I GV ED+ +I+L
Sbjct: 21  GRFVINALRAGQGITIGNQLRRVLLGDLGGMAISAVRIAGITHEFSTIPGVREDILEILL 80

Query: 88  NIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           N+KGI LK   +  +   +  +GP VVTA  IQ  +++E++NP+H I  +    ++ +E 
Sbjct: 81  NLKGIVLKSEINDIQFGRLKVQGPAVVTADLIQLPSNLEIINPNHYIATISTSNILEIEF 140

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
               G GY  A    T++     + +D ++ PI+KV + +E+  +      ++L + I T
Sbjct: 141 KFEYGTGYKLATQTFTDDSENY-LQLDTVFMPIQKVDFKIENVYDSANNITERLLLDIWT 199

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +GSI+  +++  A++++ D   + IN +      + +   +S    P     +EEL+LSV
Sbjct: 200 NGSISPNEALESAAQVIVDLFTLLINNKNMVNTNQLESKPESSSIEPYTNIAIEELQLSV 259

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ NCL+   I  +GDL+Q +   +  + NFGRKS  E+   L      LG+ L 
Sbjct: 260 RAYNCLKKAQINTVGDLLQYSPEKLQELKNFGRKSADEVFSTLKNK---LGIILK 311


>gi|297837931|ref|XP_002886847.1| RNA polymerase alpha subunit [Arabidopsis lyrata subsp. lyrata]
 gi|297841001|ref|XP_002888382.1| RNA polymerase alpha subunit [Arabidopsis lyrata subsp. lyrata]
 gi|297332688|gb|EFH63106.1| RNA polymerase alpha subunit [Arabidopsis lyrata subsp. lyrata]
 gi|297334223|gb|EFH64641.1| RNA polymerase alpha subunit [Arabidopsis lyrata subsp. lyrata]
          Length = 327

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 78/320 (24%), Positives = 155/320 (48%), Gaps = 21/320 (6%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E      +       I  PL +G A T+G A+RR L+  + G  IT  + + + 
Sbjct: 13  LQWKCVESKR-DSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           H+ S+I G+ E + +I++N+  I L+ +    +   I  +GPG +TA DI     +E+++
Sbjct: 72  HDYSNIVGIQESVHEILMNLNEIVLRSNLYGTRNALICVQGPGYITARDIILPPSVEIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L     + +EL + +  GY     +  E+       IDA++ P++  ++++ S
Sbjct: 132 NTQHIATLTETIDLCIELKIERNRGYSLKMSNNFEDRS---YPIDAVFMPVENANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  +
Sbjct: 189 YGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQVT 247

Query: 250 LPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           LPF P   +                 +++LEL  R  NCL+  NI  + DL+  ++ D++
Sbjct: 248 LPFFPFHNRLVNLRKKTKELAFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLI 307

Query: 294 RMANFGRKSLVEIKGVLGTM 313
           ++ +F  + + +I  +L   
Sbjct: 308 KIEHFHVEDVKKILDILEKK 327


>gi|229577786|ref|YP_002836122.1| RNA polymerase alpha subunit [Megaleranthis saniculifolia]
 gi|226933914|gb|ACO92047.1| RNA polymerase alpha subunit [Megaleranthis saniculifolia]
          Length = 328

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 80/321 (24%), Positives = 161/321 (50%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRADSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +    +  +I  +GPG VTA DI +   +E++
Sbjct: 71  PHEYSTIVGIEESVHEILMNLKEIVLRSNLYGTRDASICVKGPGYVTAQDIISPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + +EL + +  GY     +  +        IDA++ P++  ++++ 
Sbjct: 131 DITQHIASLTEPIDLCIELQIERNRGYRMKTPNNAQERS---YPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I TDGS+T ++++  ASR L D    F++ EE   +++++ +  
Sbjct: 188 SYGNG-NEKQEILFLEIWTDGSLTPKEALYEASRNLIDLFIPFLHAEEQDTKLEDNQSRV 246

Query: 249 SLPFN----------------PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LPF                       +++ EL  R+ NCL+  NI  + DL+ +++ D+
Sbjct: 247 TLPFFTFHDGLDKVRKNKKEIELKCIFIDQSELPSRTYNCLKRFNIHTLLDLLNKSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTM 313
           ++M +F  + +  I G++  +
Sbjct: 307 MKMEHFRIEDVRRILGIIKNI 327


>gi|71056798|emb|CAH58954.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
          Length = 224

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 102/222 (45%), Positives = 148/222 (66%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNIKG+ 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNIKGLA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LKM GD  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G 
Sbjct: 61  LKMYGDEEKTLEIDISGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTVKPGR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI  
Sbjct: 121 GYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIEP 180

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            ++++L+++I+ + L +F+N  +  K  +  +  +       
Sbjct: 181 LEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 222


>gi|267798457|gb|ACY78909.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 269

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 118/271 (43%), Positives = 179/271 (66%), Gaps = 8/271 (2%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
                 +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ 
Sbjct: 2   STTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDIL 61

Query: 84  DIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDA 141
           +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L   +A
Sbjct: 62  EILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNA 121

Query: 142 VVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M + V +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D 
Sbjct: 122 AIAMRIIVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDL 181

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+
Sbjct: 182 DKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLR 238

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
            V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 239 PVDDLELTVRSANCLKAEAIHYIGDLVQRTE 269


>gi|71056921|emb|CAH59019.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
          Length = 226

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 104/226 (46%), Positives = 150/226 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDITQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV
Sbjct: 61  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           SI   ++++L+++I+ + L +F+N  +  K  +  +  +       
Sbjct: 181 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 226


>gi|228017032|gb|ACP51855.1| RNA polymerase alpha subunit [Pinus canariensis]
          Length = 335

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 84/329 (25%), Positives = 156/329 (47%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I  +      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVFRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H   N   G+  IDA++ P++ V+Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDVNYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE   +   +     
Sbjct: 189 YGSGNEI-REVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSN 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         ++       L  +++LEL  ++ N LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHVLTDTGETKEKIAFQLIFIDQLELPPKTYNSLRRANIHTLSDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ +FG++S+ ++  VL  +     ++ P
Sbjct: 308 RIEHFGKESVEQVLEVLQKL---FAIDPP 333


>gi|71056820|emb|CAH58965.1| DNA-directed RNA polymerase alpha chain [Enterococcus villorum]
 gi|71056844|emb|CAH58977.1| DNA-directed RNA polymerase alpha chain [Enterococcus villorum]
          Length = 230

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 105/230 (45%), Positives = 151/230 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNI
Sbjct: 1   FIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNI 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV
Sbjct: 61  KGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDG
Sbjct: 121 KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHCEDFDKLTMEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           SI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   
Sbjct: 181 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMT 230


>gi|150036806|emb|CAM98276.1| DNA-directed RNA polymerase alpha chain [Fructobacillus
           pseudoficulneus]
          Length = 242

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 102/242 (42%), Positives = 149/242 (61%), Gaps = 2/242 (0%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
            EPL RG+  TLGN+LRRVL+SSL G A+  VQIDGV+HE S++ GV ED+T +ILN+K 
Sbjct: 1   VEPLERGYGTTLGNSLRRVLLSSLPGVAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKK 60

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           +           + I  +GP  VTA D+    DIEVLNPD  I  L     + M +T  K
Sbjct: 61  VVFATDSAEEHALEIDVQGPKDVTAADLMGSADIEVLNPDLHIATLAAGKSLHMTVTAVK 120

Query: 152 GHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           G GY  A+ ++   +  PIG++T+D++Y+PI++V+Y VE+ R G   DYDKL+M + T+G
Sbjct: 121 GRGYSSAEENKQLRDEMPIGVLTVDSIYTPIERVNYHVENKRVGSRDDYDKLTMEVWTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           SI   D+++L S+IL + L +F +     ++ K  +  +      A    +E+L+LSVRS
Sbjct: 181 SIKPSDALSLGSKILTEHLNLFTDISPVAQDTKVMVESEPAANTAADAAPIEDLDLSVRS 240

Query: 270 TN 271
            N
Sbjct: 241 YN 242


>gi|19702212|emb|CAD28795.1| RNA polymerase alpha subunit [Cuscuta reflexa]
          Length = 335

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 84/330 (25%), Positives = 155/330 (46%), Gaps = 26/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E      +       I  PL +G A T+G A+RR L++ + G  IT V+     
Sbjct: 13  LQWKCVESRT-DSKRPYYGRFILSPLTKGQADTIGIAMRRALLAEIEGTRITRVKFANTS 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +       +I  +GPG VTA DI     +E+++
Sbjct: 72  HEYSTIAGIQESVHEILMNLKEIVLRSNLYGTCDASISIKGPGYVTAEDIILPPHVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + + HGY    H   E+   G   IDAL  P++  ++++ S
Sbjct: 132 STQHIAWLTEPINFFIGLKIERNHGYFIKTHANFED---GSYPIDALLMPVRNANHSINS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV-- 247
                    + L + I T+GS+T ++++  ASR L D    F++ EE    +++  +   
Sbjct: 189 YGNE---KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEENLHLEDADHTIP 245

Query: 248 --------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         K+          +++LE   +  NCL+  NI  + DL+  ++ D++
Sbjct: 246 LSPFTVYDKVAKLRKNKKKLSLESIFIDQLEFPPKIYNCLKKSNIFTLLDLLNNSQEDLI 305

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++ +F    L ++K +LG +G    ++ P 
Sbjct: 306 KIEHFH---LEDVKQILGILGKHFALDSPK 332


>gi|307683571|dbj|BAJ19764.1| RNA polymerase alpha chain [Larix decidua]
          Length = 335

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 87/329 (26%), Positives = 156/329 (47%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H   N   G+  IDA++ P+   +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLRIEKNRGYII---HSPNNYQDGIFPIDAVFMPVPDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
               +    + L + I T+G +T  +++  ASR L D L  F++ EE   +   +    +
Sbjct: 189 YG-SRNEIREVLFLEIWTNGGLTPREALYEASRNLIDLLIPFLHGEEQNIDGMNNRKGSN 247

Query: 250 LPFNPA----------------LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           +P  P                     +++LEL  R+ NCLR  NI  + DL+  +  D++
Sbjct: 248 MPPFPLSHVLTDTRETKEKIAFQHIFIDQLELPPRTYNCLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ +FG++S+ ++  VL        ++ P
Sbjct: 308 RIEHFGKESVEQVLEVL---QKRFAIDPP 333


>gi|328813977|gb|AEB52104.1| DNA-directed RNA polymerase alpha chain [Lactobacillus helveticus]
          Length = 237

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 100/237 (42%), Positives = 147/237 (62%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           +    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T I
Sbjct: 1   SYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKI 60

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           ILN+K + LK   D  K + +   GP  VTA D++   D++VLNPD  IC +     + M
Sbjct: 61  ILNLKKLELKSFSDERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHM 120

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           E+ V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I
Sbjct: 121 EIAVQNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEI 180

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
            TDGSI   D+++ A++IL +   +F + +   K  +  +  +       L   +EE
Sbjct: 181 WTDGSIKPNDALSFAAKILVEHFKVFESADADTKFSEVMVEKEDDKKEKKLEMTIEE 237


>gi|290489698|gb|ADD31233.1| RNA polymerase alpha subunit protein [Quercus nigra]
          Length = 331

 Score =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 81/319 (25%), Positives = 154/319 (48%), Gaps = 21/319 (6%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E              I  PL +G A T+G A+RR L+  + G  IT  + + + 
Sbjct: 13  LQWKCVES-RGDSNSLYYGRFILSPLMKGQADTIGIAVRRALLGEIEGTCITRAKSEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +       +I  +GP  VTA DI     +++++
Sbjct: 72  HEYSTIIGIQESVHEILMNLKEIVLRSNLYGISGASICVKGPRYVTAQDIILPPSVQIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL     + +EL + +  GY     + +++   G   IDA++ P++  ++++ S
Sbjct: 132 NTQHIANLTEPINLYIELQIERDRGYRIKTTNNSQD---GSYPIDAVFMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                    + L + I T+GS+T ++++  ASR L +    F++ EE K  ++ +    +
Sbjct: 189 Y-VNGNEKQEILFLEIWTNGSLTPKEALHEASRNLIELFIPFLHAEEEKLHLENNQQKVT 247

Query: 250 LPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           LPF     +                 +++ EL  R  NCL+G NI  + DL+  ++ D +
Sbjct: 248 LPFFTCHDRLAKLNKNSTEIALKSIFIDQSELPPRIYNCLKGSNIHTLLDLLNNSQTDFM 307

Query: 294 RMANFGRKSLVEIKGVLGT 312
           +M +F R+ +  I  +L  
Sbjct: 308 KMKHFRREDIKHILDILEI 326


>gi|72534405|emb|CAH59039.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 221

 Score =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 104/220 (47%), Positives = 149/220 (67%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
            EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG
Sbjct: 1   VEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKG 60

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           + LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV  
Sbjct: 61  LALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTVKP 120

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI
Sbjct: 121 GRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
              ++++L+++I+ + L +F+N  +  K  +  +  +   
Sbjct: 181 EPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQ 220


>gi|290489684|gb|ADD31226.1| RNA polymerase alpha subunit protein [Euonymus americanus]
          Length = 338

 Score =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 82/331 (24%), Positives = 159/331 (48%), Gaps = 26/331 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+RR L+  + G +IT  + + +
Sbjct: 11  RTLQWKCVESRTDSKRLFYGRFILSPLMKGQADTIGIAMRRALLGEIEGTSITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S++ G+ E + ++++N+K I L+ +    +  +I  +GPG VTA D+     +E++
Sbjct: 71  PHEYSTVVGIQETVHELLMNLKEIVLRGNLYGIQNGSICIKGPGYVTAQDLVLPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L       +EL + +  GY     +   N   G   IDA++ P++  +Y+++
Sbjct: 131 DNTQHIAILTEPIYFCIELQIERHRGYHIKTPN---NFQEGSFPIDAVFMPVRNTNYSIQ 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S R G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ D    
Sbjct: 188 SYRNGSE-KEEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLENDWYKV 246

Query: 249 SLP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP                        +++LEL+ R+ NCL+  NI  + DL+ ++   +
Sbjct: 247 TLPLFTFHDRLTKLKKNQKEMALKYIFIDQLELTSRTYNCLKRSNIHTLFDLLNKSHEYL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++M +F  + +  I  +L         +LP 
Sbjct: 307 MKMEHFHIEDVKHILNILEK--KKFATDLPK 335


>gi|7525065|ref|NP_051090.1| RNA polymerase alpha subunit [Arabidopsis thaliana]
 gi|6685903|sp|P56762|RPOA_ARATH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|5881726|dbj|BAA84417.1| RNA polymerase alpha subunit [Arabidopsis thaliana]
          Length = 329

 Score =  259 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 78/322 (24%), Positives = 155/322 (48%), Gaps = 23/322 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E      +       I  PL +G A T+G A+RR L+  + G  IT  + + + 
Sbjct: 13  LQWKCVESKR-DSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           H+ S+I G+ E + +I++N+  I L+ +    +   I  +GPG +TA DI     +E+++
Sbjct: 72  HDYSNIAGIQESVHEILMNLNEIVLRSNLYGTRNALICVQGPGYITARDIILPPAVEIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L     + +EL + +  GY     +  E+       IDA++ P++  ++++ S
Sbjct: 132 NTQHIATLTEPIDLCIELKIERNRGYSLKMSNNFEDRS---YPIDAVFMPVENANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  +
Sbjct: 189 YGNG-NEKQEILFLEIWTNGSLTPKEALHQASRNLINLFIPFLHVEEETFYLENNQHQVT 247

Query: 250 LPFNPALLK------------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           LPF P   +                   +++LEL  R  NCL+  NI  + DL+  ++ D
Sbjct: 248 LPFFPFHNRLVNLRKKKKTKELAFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQED 307

Query: 292 MLRMANFGRKSLVEIKGVLGTM 313
           ++++ +F  + + +I  +L   
Sbjct: 308 LIKIEHFHVEDVKKILDILEKK 329


>gi|313184025|ref|YP_004021182.1| RNA polymerase alpha subunit [Castanea mollissima]
 gi|309321552|gb|ADO65092.1| RNA polymerase alpha subunit [Castanea mollissima]
          Length = 331

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 81/319 (25%), Positives = 154/319 (48%), Gaps = 21/319 (6%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E              I  PL +G A T+G A+RR L+  + G  IT  + + + 
Sbjct: 13  LQWKCVES-RGDSNSLYYGRFILSPLMKGQADTIGIAVRRALLGEIEGTCITRAKSEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +       +I  +GP  VTA DI     +++++
Sbjct: 72  HEYSTIIGIQESVHEILMNLKEIVLRSNLYGISGASICVKGPRYVTAQDIILPPSVQIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL     + +EL + +  GY     + +++   G   IDA++ P++  ++++ S
Sbjct: 132 NTQHIANLTEPINLYIELQIERDRGYRIKTTNNSQD---GSYPIDAVFMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                    + L + I T+GS+T ++++  ASR L +    F++ EE K  ++ +    +
Sbjct: 189 Y-VNGNEKQEILFLEIWTNGSLTPKEALHEASRNLIELFIPFLHAEEEKLHLENNQQKVT 247

Query: 250 LPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           LPF     +                 +++ EL  R  NCL+G NI  + DL+  ++ D +
Sbjct: 248 LPFFTCHDRLAKLNKNSTEITLKSIFIDQSELPPRIYNCLKGSNIHTLLDLLNNSQTDFM 307

Query: 294 RMANFGRKSLVEIKGVLGT 312
           +M +F R+ +  I  +L  
Sbjct: 308 KMKHFRREDIKHILDILEI 326


>gi|72534411|emb|CAH59042.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 224

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 104/224 (46%), Positives = 149/224 (66%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
            EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG
Sbjct: 1   VEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKG 60

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           + LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV  
Sbjct: 61  LALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTVKP 120

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI
Sbjct: 121 GRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
              ++++L+++I+ + L +F+N  +  K  +  +  +       
Sbjct: 181 EPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 224


>gi|228016968|gb|ACP51792.1| RNA polymerase alpha subunit [Pinus banksiana]
          Length = 335

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 85/329 (25%), Positives = 155/329 (47%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE   +   +     
Sbjct: 189 YGSGNEI-REVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSN 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         ++       L  +++LEL  +  N LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHLLTDTGETKEKIAFQLIFIDQLELPPKIYNSLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ NFG++S+ ++  VL  +     ++ P
Sbjct: 308 RIKNFGKESVEQVLEVLQKL---FAIDPP 333


>gi|239618237|ref|YP_002941559.1| DNA-directed RNA polymerase, alpha subunit [Kosmotoga olearia TBF
           19.5.1]
 gi|239507068|gb|ACR80555.1| DNA-directed RNA polymerase, alpha subunit [Kosmotoga olearia TBF
           19.5.1]
          Length = 346

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 114/317 (35%), Positives = 174/317 (54%), Gaps = 23/317 (7%)

Query: 9   LIKPNNIEYIVL-GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
            + P +++      ++       +  P+ RG+A T+GNALRRVL+SS+   AIT ++I G
Sbjct: 12  FVMPKSLKIEEEREEQNSYYAKFVLSPMERGYAVTIGNALRRVLLSSIPSMAITRLKIPG 71

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
             HE  +I GV ED+ +IILN+K + LK  +      +++I K+GP ++TAGDI+    +
Sbjct: 72  KYHEYDTIDGVKEDILEIILNLKKVQLKPALEFSDPVKLSIEKKGPAILTAGDIKAPTGV 131

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           EV+NP   I  L+ DA V MEL    G G+VP      E D   +I ID ++SP+ KV++
Sbjct: 132 EVVNPSQYIATLNEDAAVYMELFAEIGKGFVPVSEMELEQDVE-MIYIDGIFSPVLKVNF 190

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI-NFEEPKKEVKED 244
             E+ R G+  DYDKL + + T  SI   +++  A+ IL     +   +  +        
Sbjct: 191 ISENVRVGKKTDYDKLILEVWTKKSIKPTEALLKATDILIKHFEVTTSSLNQVLDNSGIL 250

Query: 245 INVKS------------------LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQ 286
           +N  S                     +  L +++EELELSVRS NCL+ + I  +GDLI 
Sbjct: 251 VNSASIFEPEEPQPEEEPVEEPISEEDSVLSRRIEELELSVRSLNCLKRDKINTIGDLIS 310

Query: 287 RTEADMLRMANFGRKSL 303
           RTEAD+L++ NFG KS+
Sbjct: 311 RTEADLLKIRNFGDKSM 327


>gi|72534416|emb|CAH59044.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 217

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 104/217 (47%), Positives = 149/217 (68%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV  G
Sbjct: 61  ALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTVKPG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI 
Sbjct: 121 RGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIE 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
             ++++L+++I+ + L +F+N  +  K  +  +  + 
Sbjct: 181 PLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEE 217


>gi|197131698|gb|ACH47367.1| RNA polymerase alpha subunit [Sarcocaulon vanderietiae]
          Length = 333

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 79/310 (25%), Positives = 155/310 (50%), Gaps = 13/310 (4%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +   +E      +       I  PL +G A  +G A+RR L+  + G  IT  +   + H
Sbjct: 14  RWKCVES-RADDKRLYYGRFILSPLKKGQADIIGIAMRRALLVEIEGTCITHAKFAKIPH 72

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ G+ E + +I++N+K I L+ +    +  +I  RGP  VTA DI       +++ 
Sbjct: 73  EYTTMAGIKESIYEILMNLKEIVLRSNLYGTRDASICVRGPRDVTAQDIILPPSTAIVDN 132

Query: 131 DHVICNLDVDAVVRMELTVSKGHGY---VPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
              I  L       +EL + +G GY   +P   +   +D    I IDA++ P++ V++++
Sbjct: 133 TQHIVTLTEPIDFCVELKIERGRGYSIKIPMPTNPFHHDSGYPIPIDAVFMPVRNVNHSI 192

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK---KEVKED 244
            S + G     + L + I T+GS+T ++++  ASR L +    F++ EE      E  ++
Sbjct: 193 YSYKRGSR---EILFLEIWTNGSLTPKEALREASRKLINLFIPFLHAEEENFYLLENNQN 249

Query: 245 INVKSLPFNPALLKKV---EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            + + LP +   LK++   + +EL  R  NCL+   I  + DL+ ++  D++++ +F ++
Sbjct: 250 QHTEELPIDSCGLKEIYIDQLVELPPRFYNCLKRSGIHTVMDLLDKSRDDLMKITHFRQE 309

Query: 302 SLVEIKGVLG 311
            +  +  +L 
Sbjct: 310 DVERVMNILN 319


>gi|108792409|emb|CAJ33153.1| RNA polymerase alpha subunit [Lactobacillus murinus]
          Length = 222

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 102/221 (46%), Positives = 151/221 (68%), Gaps = 2/221 (0%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT VQIDGVLHE S++KGV ED+T IILN+K +
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAITDVQIDGVLHEFSTVKGVLEDVTAIILNLKKV 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LK+  +  + +     GP  VTAGDIQ  +D+E+LNPD  IC +   AV    +T +KG
Sbjct: 61  ALKLDSEDSQTLEFDVVGPKEVTAGDIQGSSDVEILNPDQYICTVADGAVFHARMTANKG 120

Query: 153 HGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            GYV A  +  + E+ PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T+GS
Sbjct: 121 RGYVSATENKAKAEDMPIGVLPIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWTNGS 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           IT  ++++L+++IL + L +F++  +  K  +  +  +   
Sbjct: 181 ITPSEAISLSAKILTEHLTLFVDLTDEAKNAEIMVEKEETH 221


>gi|46199602|ref|YP_005269.1| DNA-directed RNA polymerase subunit alpha [Thermus thermophilus
           HB27]
 gi|55981633|ref|YP_144930.1| DNA-directed RNA polymerase subunit alpha [Thermus thermophilus
           HB8]
 gi|7388103|sp|Q9Z9H6|RPOA_THETH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|61215969|sp|Q72I32|RPOA_THET2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|66773873|sp|Q5SHR6|RPOA_THET8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|7434691|pir||JE0397 DNA-directed RNA polymerase (EC 2.7.7.6) alpha chain - Thermus
           aquaticus (strain HB8)
 gi|21730337|pdb|1IW7|A Chain A, Crystal Structure Of The Rna Polymerase Holoenzyme From
           Thermus Thermophilus At 2.6a Resolution
 gi|21730338|pdb|1IW7|B Chain B, Crystal Structure Of The Rna Polymerase Holoenzyme From
           Thermus Thermophilus At 2.6a Resolution
 gi|21730343|pdb|1IW7|K Chain K, Crystal Structure Of The Rna Polymerase Holoenzyme From
           Thermus Thermophilus At 2.6a Resolution
 gi|21730344|pdb|1IW7|L Chain L, Crystal Structure Of The Rna Polymerase Holoenzyme From
           Thermus Thermophilus At 2.6a Resolution
 gi|49259055|pdb|1SMY|A Chain A, Structural Basis For Transcription Regulation By Alarmone
           Ppgpp
 gi|49259056|pdb|1SMY|B Chain B, Structural Basis For Transcription Regulation By Alarmone
           Ppgpp
 gi|49259061|pdb|1SMY|K Chain K, Structural Basis For Transcription Regulation By Alarmone
           Ppgpp
 gi|49259062|pdb|1SMY|L Chain L, Structural Basis For Transcription Regulation By Alarmone
           Ppgpp
 gi|78101157|pdb|1ZYR|A Chain A, Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Streptolydigin
 gi|78101158|pdb|1ZYR|B Chain B, Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Streptolydigin
 gi|78101163|pdb|1ZYR|K Chain K, Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Streptolydigin
 gi|78101164|pdb|1ZYR|L Chain L, Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Streptolydigin
 gi|78101219|pdb|2A68|A Chain A, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifabutin
 gi|78101220|pdb|2A68|B Chain B, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifabutin
 gi|78101225|pdb|2A68|K Chain K, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifabutin
 gi|78101226|pdb|2A68|L Chain L, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifabutin
 gi|78101231|pdb|2A69|A Chain A, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifapentin
 gi|78101232|pdb|2A69|B Chain B, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifapentin
 gi|78101237|pdb|2A69|K Chain K, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifapentin
 gi|78101238|pdb|2A69|L Chain L, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifapentin
 gi|78101243|pdb|2A6E|A Chain A, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme
 gi|78101244|pdb|2A6E|B Chain B, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme
 gi|78101249|pdb|2A6E|K Chain K, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme
 gi|78101250|pdb|2A6E|L Chain L, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme
 gi|78101255|pdb|2A6H|A Chain A, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Sterptolydigin
 gi|78101256|pdb|2A6H|B Chain B, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Sterptolydigin
 gi|78101261|pdb|2A6H|K Chain K, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Sterptolydigin
 gi|78101262|pdb|2A6H|L Chain L, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Sterptolydigin
 gi|78101757|pdb|2CW0|A Chain A, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme At 3.3 Angstroms Resolution
 gi|78101758|pdb|2CW0|B Chain B, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme At 3.3 Angstroms Resolution
 gi|78101763|pdb|2CW0|K Chain K, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme At 3.3 Angstroms Resolution
 gi|78101764|pdb|2CW0|L Chain L, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme At 3.3 Angstroms Resolution
 gi|83754372|pdb|2BE5|A Chain A, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Inhibitor Tagetitoxin
 gi|83754373|pdb|2BE5|B Chain B, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Inhibitor Tagetitoxin
 gi|83754378|pdb|2BE5|K Chain K, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Inhibitor Tagetitoxin
 gi|83754379|pdb|2BE5|L Chain L, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Inhibitor Tagetitoxin
 gi|151567769|pdb|2O5I|A Chain A, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Elongation Complex
 gi|151567770|pdb|2O5I|B Chain B, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Elongation Complex
 gi|151567774|pdb|2O5I|K Chain K, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Elongation Complex
 gi|151567775|pdb|2O5I|L Chain L, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Elongation Complex
 gi|151567785|pdb|2O5J|A Chain A, Crystal Structure Of The T. Thermophilus Rnap Polymerase
           Elongation Complex With The Ntp Substrate Analog
 gi|151567786|pdb|2O5J|B Chain B, Crystal Structure Of The T. Thermophilus Rnap Polymerase
           Elongation Complex With The Ntp Substrate Analog
 gi|151567790|pdb|2O5J|K Chain K, Crystal Structure Of The T. Thermophilus Rnap Polymerase
           Elongation Complex With The Ntp Substrate Analog
 gi|151567791|pdb|2O5J|L Chain L, Crystal Structure Of The T. Thermophilus Rnap Polymerase
           Elongation Complex With The Ntp Substrate Analog
 gi|152149351|pdb|2PPB|A Chain A, Crystal Structure Of The T. Thermophilus Rnap Polymerase
           Elongation Complex With The Ntp Substrate Analog And
           Antibiotic Streptolydigin
 gi|152149352|pdb|2PPB|B Chain B, Crystal Structure Of The T. Thermophilus Rnap Polymerase
           Elongation Complex With The Ntp Substrate Analog And
           Antibiotic Streptolydigin
 gi|152149356|pdb|2PPB|K Chain K, Crystal Structure Of The T. Thermophilus Rnap Polymerase
           Elongation Complex With The Ntp Substrate Analog And
           Antibiotic Streptolydigin
 gi|152149357|pdb|2PPB|L Chain L, Crystal Structure Of The T. Thermophilus Rnap Polymerase
           Elongation Complex With The Ntp Substrate Analog And
           Antibiotic Streptolydigin
 gi|209447473|pdb|3DXJ|A Chain A, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Myxopyronin
 gi|209447474|pdb|3DXJ|B Chain B, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Myxopyronin
 gi|209447479|pdb|3DXJ|K Chain K, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Myxopyronin
 gi|209447480|pdb|3DXJ|L Chain L, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Myxopyronin
 gi|210061064|pdb|3EQL|A Chain A, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Myxopyronin
 gi|210061065|pdb|3EQL|B Chain B, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Myxopyronin
 gi|210061070|pdb|3EQL|K Chain K, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Myxopyronin
 gi|210061071|pdb|3EQL|L Chain L, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Myxopyronin
 gi|313754163|pdb|3AOH|A Chain A, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
 gi|313754164|pdb|3AOH|B Chain B, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
 gi|313754168|pdb|3AOH|F Chain F, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
 gi|313754169|pdb|3AOH|G Chain G, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
 gi|313754173|pdb|3AOH|K Chain K, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
 gi|313754174|pdb|3AOH|L Chain L, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
 gi|313754183|pdb|3AOI|A Chain A, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
 gi|313754184|pdb|3AOI|B Chain B, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
 gi|313754188|pdb|3AOI|F Chain F, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
 gi|313754189|pdb|3AOI|G Chain G, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
 gi|313754193|pdb|3AOI|K Chain K, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
 gi|313754194|pdb|3AOI|L Chain L, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
 gi|4519423|dbj|BAA75549.1| RNA polymerase alpha subunit [Thermus thermophilus]
 gi|46197228|gb|AAS81642.1| DNA-directed RNA polymerase alpha chain [Thermus thermophilus HB27]
 gi|55773046|dbj|BAD71487.1| DNA-directed RNA polymerase alpha chain [Thermus thermophilus HB8]
          Length = 315

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 111/296 (37%), Positives = 162/296 (54%), Gaps = 5/296 (1%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED+ +II
Sbjct: 20  YGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEII 79

Query: 87  LNIKGINLKMSGDSHKRVT--IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           LN+K + ++    S + VT  +   GP  V A D   V D+E++NPD  I  L+    + 
Sbjct: 80  LNLKELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIMNPDLHIATLEEGGRLN 139

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           ME+ V +G GYVPA+ H  ++  I  I +DA++SP+++V++ VE  R GQ  D DKL++ 
Sbjct: 140 MEVRVDRGVGYVPAEKHGIKDR-INAIPVDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLR 198

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFIN--FEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           I TDGS+T  +++  A  IL++ L  F N          +             L   +EE
Sbjct: 199 IWTDGSVTPLEALNQAVEILREHLTYFSNPQAAAVAAPEEAKEPEAPPEQEEELDLPLEE 258

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           L LS R  + L+ E I  +  L+     D+  +   G +SL EIK  L   G  L 
Sbjct: 259 LGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEKKGFTLK 314


>gi|225552463|ref|ZP_03773403.1| DNA-directed RNA polymerase, alpha subunit [Borrelia sp. SV1]
 gi|225371461|gb|EEH00891.1| DNA-directed RNA polymerase, alpha subunit [Borrelia sp. SV1]
          Length = 344

 Score =  258 bits (659), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 118/335 (35%), Positives = 183/335 (54%), Gaps = 19/335 (5%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++   ++   P  IE++   Q + +       P  RGF  T+GN LRRVL+SS+ G AIT
Sbjct: 3   VENFLKDFTIPEKIEFLK-SQGDGSYGKFTIYPFERGFGITIGNTLRRVLLSSIEGYAIT 61

Query: 62  AVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
           A+++           V  E   I GV ED  ++I NIK I+LK+ G+  ++ TI     G
Sbjct: 62  AMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLEVIANIKNIHLKL-GEGEQKKTISFSVSG 120

Query: 113 ----VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
               V+ A   +    +EV N D VI  L  D  + +E  ++ G GYV ++ +    + +
Sbjct: 121 KDTNVLKASHFERD-GVEVFNKDLVIATLSRDVNLDLEFQINYGRGYVSSEQNSKYLEEV 179

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
            +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L
Sbjct: 180 NVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREFL 239

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
              ++FE+    V           +  L   +E+L LSVRS NCL  EN+  +G+LI + 
Sbjct: 240 FPLVDFED---NVNTSFEKSKSESSNLLDMSIEKLNLSVRSLNCLAKENVRTLGELISKN 296

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
             ++ +  NFG+KSL EI   LG+  L+LGM+  D
Sbjct: 297 AEELSKARNFGKKSLEEIIEKLGSYRLYLGMSKED 331


>gi|71056925|emb|CAH59021.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
 gi|71056927|emb|CAH59022.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
 gi|71056929|emb|CAH59023.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
 gi|71056931|emb|CAH59024.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 223

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 104/223 (46%), Positives = 149/223 (66%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV  G
Sbjct: 61  ALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTVKPG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI 
Sbjct: 121 RGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIE 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
             ++++L+++I+ + L +F+N  +  K  +  +  +       
Sbjct: 181 PLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 223


>gi|47679557|gb|AAT36722.1| RNA polymerase alpha subunit [Navicula salinicola]
          Length = 298

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 92/280 (32%), Positives = 152/280 (54%), Gaps = 1/280 (0%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               +   L  G   T+GN LRRVL+  L G AI+AV+I GV HE S+I GV ED+ +I+
Sbjct: 20  HGQFLINSLRPGQGITIGNQLRRVLLGDLGGVAISAVRIAGVSHEFSTIPGVREDILEIL 79

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+KGI L       +   +  +GP VVTA  IQ   ++E++NP+  I  +    ++ +E
Sbjct: 80  LNLKGIVLTSKTQETQFGRLKIQGPCVVTADLIQLPPNLEIVNPNQYIATITTSNIIEIE 139

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
                G GY  A    + ++    + +D ++ P+ KV + +E+  +      ++L + I 
Sbjct: 140 FKFEYGIGYKFASQTFS-DEADNFLQLDTVFMPVPKVDFKIENVYDTANNITERLFIDIW 198

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+GSI   D++  A++I+ D   + IN ++  +  +     +S+   P     +EEL+LS
Sbjct: 199 TNGSIPPNDALESAAQIIIDLFTLLINNKDTNESSQLKTKARSISMEPYTNIAIEELQLS 258

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           VR+ NCL+   I  +GDL+Q +   +  + NFGRKS  E+
Sbjct: 259 VRAYNCLKKAQINTVGDLLQYSPEKLQELKNFGRKSADEV 298


>gi|71056910|emb|CAH59012.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
 gi|72534413|emb|CAH59043.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 228

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 105/228 (46%), Positives = 150/228 (65%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
            EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG
Sbjct: 1   VEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKG 60

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           + LKM G   K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV  
Sbjct: 61  LALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTVKP 120

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI
Sbjct: 121 GRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
              ++++L+++I+ + L +F+N  +  K  +  +  +       L   
Sbjct: 181 EPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMT 228


>gi|119668343|emb|CAK95510.1| RNA polymerase alpha subunit [Lactobacillus paracasei subsp.
           paracasei]
          Length = 214

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 95/213 (44%), Positives = 145/213 (68%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNIK + LKM+ 
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNT 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV KG GYV A
Sbjct: 61  DEDKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++
Sbjct: 121 DQNKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAIS 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           LA++IL + L +F+N  +  K  +  +  +   
Sbjct: 181 LAAKILTEHLDIFVNLTDEAKNAEIMVEKEETH 213


>gi|228017468|gb|ACP52284.1| RNA polymerase alpha subunit [Pinus merkusii]
          Length = 335

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 83/329 (25%), Positives = 154/329 (46%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I  +      +  +I+  GP  VTA DI     ++ ++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVFRSDSYGIREASIYIVGPRNVTAQDIILPPSVKTID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE   +   +     
Sbjct: 189 YGSGNEI-REVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSN 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         ++       L  +++LEL  ++ N LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHVLTDTGETKEKIAFQLIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ +FG++S+ ++  VL  +     ++ P
Sbjct: 308 RIEHFGKESVEQVLEVLQKL---FAIDPP 333


>gi|12372|emb|CAA33618.1| unnamed protein product [Triticum aestivum]
          Length = 339

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 90/328 (27%), Positives = 159/328 (48%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L +   ++GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKLEILFLEYGSNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D+L
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|218282068|ref|ZP_03488367.1| hypothetical protein EUBIFOR_00938 [Eubacterium biforme DSM 3989]
 gi|218216942|gb|EEC90480.1| hypothetical protein EUBIFOR_00938 [Eubacterium biforme DSM 3989]
          Length = 321

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 95/299 (31%), Positives = 163/299 (54%), Gaps = 2/299 (0%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            EE N    I EPL RGF  T+GN + R L++S+ G  I   ++ G   + + + G+ ED
Sbjct: 20  NEENNTGSYIFEPLERGFGITIGNTICRTLLTSVPGTRIVGFKVSGFDGKATMVDGILED 79

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +  I LN+K + L   G+  + + I K+GP  + A DI     +EV++P+ VIC L+  A
Sbjct: 80  IYRISLNLKAVQLYNDGEGFQTLHISKKGPATIQAADIICPEAVEVVDPEQVICTLEKGA 139

Query: 142 VVRMELTVSKGHGYVPAKHHR-TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
            + ME+    G GY  +  ++ + +    ++ +DA ++PI+K  Y  E AR G    YDK
Sbjct: 140 SLEMEIYAVTGTGYKSSIENKVSYDFGEDVVVLDATFTPIRKADYLSEPARVGLDKKYDK 199

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF-NPALLKK 259
           + + ++TDG+IT   ++ +A+++  + L   +   + + E    +    +          
Sbjct: 200 VHINVETDGTITPLQAITMAAKVCMENLDEVLTVSDLELEESFMVQKPQVEDVKKVNTMM 259

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           +E+L+LSVRS NCL+   I  + +L Q+TE +M+ + N G+KSL E+K  +  +GLF  
Sbjct: 260 IEDLDLSVRSYNCLKRAGIQTVDELTQKTEDEMMHVKNLGKKSLKEVKDKMYQLGLFFK 318


>gi|71056808|emb|CAH58959.1| DNA-directed RNA polymerase alpha chain [Enterococcus raffinosus]
          Length = 228

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 105/228 (46%), Positives = 150/228 (65%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
            EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG
Sbjct: 1   VEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNIKG 60

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           + LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  
Sbjct: 61  LALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTVKP 120

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDGSI
Sbjct: 121 GRGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
             +++++LA++IL + L +F+N  +  K  +  +  +       L   
Sbjct: 181 IAQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMT 228


>gi|169142819|ref|YP_001687243.1| RNA polymerase alpha subunit [Aneura mirabilis]
 gi|153973845|gb|ABS54505.1| RNA polymerase alpha subunit [Aneura mirabilis]
          Length = 342

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 96/344 (27%), Positives = 161/344 (46%), Gaps = 29/344 (8%)

Query: 1   MIQK----NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLR 56
           MIQ+    + + L++   IE     +           P  +G A+T+G A+RR L++ + 
Sbjct: 1   MIQEEIEISTRTLLRWRCIESRTESKRLL-YGRFAISPFRKGQANTVGIAMRRALLNEIE 59

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GA+IT+  I G+ HE S+I G+ E + DI++N+K I L+      ++  I   GP  VTA
Sbjct: 60  GASITSATIRGIKHEYSAINGIRESIHDILINLKEIILRSDSPEPQKAYICVSGPSEVTA 119

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
            DIQ  + I V++    +  +     + +EL + K  GY      +      G   IDA+
Sbjct: 120 RDIQGSSLIHVIDNTQYVATITGKISLDIELDIEKDRGYRMENSRKYRE---GFFPIDAV 176

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF-- 234
           + PI+  +Y+V S    +    + L + I T+GS+T E ++  ASR L D     +N   
Sbjct: 177 FMPIRNANYSVHSFG-SREKTKEILLLEIWTNGSLTPEKALYEASRNLIDLFIPSMNPGG 235

Query: 235 EEPKKEVKEDINVKSLPFNPALLKK---------------VEELELSVRSTNCLRGENIV 279
           EE     KE             L                 +++LEL  R+ NCL+  N+ 
Sbjct: 236 EEKNSGTKEKPESDLSHSTVQFLSTDMEQMTRDVAPKHIFIDQLELPARAYNCLKRVNVH 295

Query: 280 YMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            + DL+   E D++++ NFG++S+ ++   L        +NLP 
Sbjct: 296 TVADLLDYGENDLMKIKNFGKESIKQVSEALK---KRFLVNLPK 336


>gi|323925214|gb|ADY11800.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 240

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 103/240 (42%), Positives = 161/240 (67%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +K
Sbjct: 1   VVEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           GI +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV 
Sbjct: 61  GIAIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSIRAVMTVK 120

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG+GYVPA  ++ +  PIG I +D++Y+P+ KV+Y VE AR G    YDKL++ I T+G+
Sbjct: 121 KGYGYVPADENKVDGAPIGTIAVDSIYTPVSKVNYQVEPARVGGDSSYDKLTLEITTNGT 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I  +++++L+++IL D L +F++  E   E +  +    +     L K +EE++ SVR+ 
Sbjct: 181 IVSDEALSLSAKILTDHLNLFVDLSEVASEAETLVVKDEVKTERVLDKIIEEMDFSVRAY 240


>gi|150036812|emb|CAM98039.1| DNA-directed RNA polymerase alpha chain [Fructobacillus
           pseudoficulneus]
          Length = 240

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 101/240 (42%), Positives = 148/240 (61%), Gaps = 2/240 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRVL+SSL G A+  VQIDGV+HE S++ GV ED+T +ILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRVLLSSLPGVAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVV 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
                     + I  +GP  VTA D+    DIEVLNPD  I  L     + M +T  KG 
Sbjct: 61  FATDSAEEHALEIDVQGPKDVTAADLMGSADIEVLNPDLHIATLAAGKALHMTVTAVKGR 120

Query: 154 GYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A+ ++   +  PIG++T+D++Y+PI++V+Y VE+ R G   DYDKL+M + T+GSI
Sbjct: 121 GYSSAEENKQLRDEMPIGVLTVDSIYTPIERVNYHVENKRVGSRDDYDKLTMEVWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTN 271
              D+++L S+IL + L +F +     ++ K  +  +      A    +E+L+LSVRS N
Sbjct: 181 KPSDALSLGSKILTEHLNLFTDISPVAQDTKVMVESEPAANTAADAAPIEDLDLSVRSYN 240


>gi|228016017|gb|ACP50856.1| RNA polymerase alpha subunit [Pinus resinosa]
          Length = 335

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 83/329 (25%), Positives = 155/329 (47%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I  +      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVFRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE   +   +     
Sbjct: 189 YGSGNEI-REVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSN 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         ++       L  +++LEL  ++ N LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHVLTDTGETKEKIAFQLIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ +FG++S+ ++  VL  +     ++ P
Sbjct: 308 RIEHFGKESVEQVLEVLQKL---FAIDPP 333


>gi|237688548|ref|YP_002905166.1| RNA polymerase alpha subunit [Pinus contorta]
 gi|226875376|gb|ACO89114.1| RNA polymerase alpha subunit [Pinus contorta]
          Length = 335

 Score =  257 bits (657), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 84/329 (25%), Positives = 155/329 (47%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE   +   +     
Sbjct: 189 YGSGNEI-REVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSN 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         ++       L  +++LEL  +  N LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHLLTDTGETKEKIAFQLIFIDQLELPPKIYNSLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ +FG++S+ ++  VL  +     ++ P
Sbjct: 308 RIKHFGKESVEQVLEVLQKL---FAIDPP 333


>gi|228016469|gb|ACP51301.1| RNA polymerase alpha subunit [Pinus torreyana subsp. insularis]
 gi|228016530|gb|ACP51361.1| RNA polymerase alpha subunit [Pinus torreyana subsp. torreyana]
          Length = 335

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 84/330 (25%), Positives = 156/330 (47%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE   +   +     
Sbjct: 189 YGSGNEI-REVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSN 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         ++       L  +++LEL  ++ N LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHLLTDTGETKEKIAFQLIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           R+ +FG++S+ ++  VL  +     ++ P 
Sbjct: 308 RIEHFGKESVEQVLEVLQKL---FAIDPPK 334


>gi|161513440|emb|CAP16863.1| DNA-directed RNA polymerase subunit alpha [Pediococcus inopinatus]
          Length = 229

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 102/229 (44%), Positives = 153/229 (66%), Gaps = 2/229 (0%)

Query: 35  LPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL 94
           L RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNIK ++L
Sbjct: 1   LERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNIKKVSL 60

Query: 95  KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHG 154
           K+  D  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G G
Sbjct: 61  KIESDDEKSLEIDVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAILTADTGRG 120

Query: 155 YVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           YV A  ++   ++ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSI+
Sbjct: 121 YVSADENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSIS 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
             ++ +L+++IL + L +F+N  +  K+ +  +  +       L   +E
Sbjct: 181 PSEATSLSAKILTEHLALFVNLTDEAKDAEIMVEKEETHKEKMLEMSIE 229


>gi|71056846|emb|CAH58978.1| DNA-directed RNA polymerase alpha chain [Enterococcus moraviensis]
          Length = 225

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 103/225 (45%), Positives = 152/225 (67%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+ 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGLA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK+  +  K + I   GP  VTAGDI   +D+E+LN D +IC++   A     LTV  G 
Sbjct: 61  LKLYAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLIICSVSEGATFHARLTVKPGR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI  
Sbjct: 121 GYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIIP 180

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           +++++LA++I+ + L +F+N  +  K  +  +  +       L  
Sbjct: 181 QEALSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 225


>gi|71056902|emb|CAH59008.1| DNA-directed RNA polymerase alpha chain [Enterococcus hirae]
          Length = 224

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 103/224 (45%), Positives = 149/224 (66%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
            EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG
Sbjct: 1   VEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKG 60

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           + LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV  
Sbjct: 61  LALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTVKP 120

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI
Sbjct: 121 GRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
              ++++L+++I+ + L +F+N  +  K  +  +  +       
Sbjct: 181 EPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 224


>gi|323925172|gb|ADY11786.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|323925175|gb|ADY11787.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|323925178|gb|ADY11788.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|323925181|gb|ADY11789.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|323925184|gb|ADY11790.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|323925190|gb|ADY11792.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|323925193|gb|ADY11793.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|323925199|gb|ADY11795.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|323925202|gb|ADY11796.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|323925208|gb|ADY11798.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|323925211|gb|ADY11799.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|323925217|gb|ADY11801.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|323925220|gb|ADY11802.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|323925223|gb|ADY11803.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|323925226|gb|ADY11804.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 240

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 103/240 (42%), Positives = 161/240 (67%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +K
Sbjct: 1   VVEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           GI +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV 
Sbjct: 61  GIAIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVK 120

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG+GYVPA  ++ +  PIG I +D++Y+P+ KV+Y VE AR G    YDKL++ I T+G+
Sbjct: 121 KGYGYVPADENKVDGAPIGTIAVDSIYTPVSKVNYQVEPARVGGDSSYDKLTLEITTNGT 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I  +++++L+++IL D L +F++  E   E +  +    +     L K +EE++ SVR+ 
Sbjct: 181 IVSDEALSLSAKILTDHLNLFVDLSEVAAEAETLVVKDEVKTERVLDKIIEEMDFSVRAY 240


>gi|299767525|gb|ADJ38428.1| RNA polymerase alpha-subunit [Vibrio communis]
 gi|299767527|gb|ADJ38429.1| RNA polymerase alpha-subunit [Vibrio communis]
 gi|299767529|gb|ADJ38430.1| RNA polymerase alpha-subunit [Vibrio communis]
 gi|299767531|gb|ADJ38431.1| RNA polymerase alpha-subunit [Vibrio communis]
 gi|299767533|gb|ADJ38432.1| RNA polymerase alpha-subunit [Vibrio communis]
 gi|299767535|gb|ADJ38433.1| RNA polymerase alpha-subunit [Vibrio communis]
 gi|299767537|gb|ADJ38434.1| RNA polymerase alpha-subunit [Vibrio communis]
          Length = 262

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 120/265 (45%), Positives = 179/265 (67%), Gaps = 8/265 (3%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ 
Sbjct: 1   PLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLA 60

Query: 94  LKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSK 151
           +++  G     +T+ K G G V AGDI    D+E+ NP+HVIC+L  D A + M + V +
Sbjct: 61  VRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVER 120

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H+  +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+
Sbjct: 121 GRGYVPASARIHNEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V++LEL+VR
Sbjct: 181 GTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVR 237

Query: 269 STNCLRGENIVYMGDLIQRTEADML 293
           S NCL+ E I Y+GDL+QRTE ++L
Sbjct: 238 SANCLKAEAIHYIGDLVQRTEVELL 262


>gi|139389674|ref|YP_001123231.1| RNA polymerase alpha subunit [Arabis hirsuta]
 gi|158513635|sp|A4QK50|RPOA_ARAHI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|134286429|dbj|BAF50055.1| RNA polymerase alpha subunit [Arabis hirsuta]
          Length = 337

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 76/320 (23%), Positives = 153/320 (47%), Gaps = 21/320 (6%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E      +       I  PL +G A T+G A+RR L+  + G  IT  + + + 
Sbjct: 13  LQWRCVES-RRDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           H+ S+I G+ E + +I++N+  I L+ +    +   I  +GPG +TA DI     +E+++
Sbjct: 72  HDYSNIVGIQESVHEILMNLNEIVLRSNLYGARNAIICVQGPGYITARDIILPPSVEIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L     + + L + +  GY     +  E+       IDA++ P++  ++++ S
Sbjct: 132 NTQHIATLTESIDLCIGLKIERNRGYSLKILNTFEDRS---YPIDAVFMPVQNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  +
Sbjct: 189 YGNG-NGKQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHHVT 247

Query: 250 LPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           LP  P   +                 +++LEL  R  NCL+  NI  + DL+  ++ D++
Sbjct: 248 LPLFPFHNRLVNLRKKKKELAFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLI 307

Query: 294 RMANFGRKSLVEIKGVLGTM 313
           ++ +F  + + +I  +L   
Sbjct: 308 KIEHFHIEDVKKILDILEKK 327


>gi|161511767|emb|CAP16894.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 219

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 101/219 (46%), Positives = 145/219 (66%), Gaps = 2/219 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+T IILN+
Sbjct: 1   FVIEPLERGYGTTLGNSLRRILLSSLPGAAITSVQIDSVLHEFSTIEGVVEDVTQIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  IC +         LT 
Sbjct: 61  KKVSLKIESDEDKTLEINVAGPANVTAGDIMGDGDVVILNPELPICTVAEGTTFHAVLTA 120

Query: 150 SKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             G GY  A  ++    + PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ I T
Sbjct: 121 DTGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDIWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           DGSIT  ++ +L+++IL + L +F+N  +  KE +  + 
Sbjct: 181 DGSITPSEATSLSAKILTEHLAIFVNLNDQAKETEIMVE 219


>gi|71056834|emb|CAH58972.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
          Length = 227

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 105/227 (46%), Positives = 150/227 (66%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG+
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNIKGL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G
Sbjct: 61  ALKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTVKPG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDGSI 
Sbjct: 121 RGYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDGSII 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
            +++++LA++IL + L +F+N  +  K  +  +  +       L   
Sbjct: 181 AQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMT 227


>gi|7524684|ref|NP_042438.1| RNA polymerase alpha subunit [Pinus thunbergii]
 gi|1173147|sp|P41629|RPOA_PINTH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1262678|dbj|BAA04395.1| RNA polymerase alpha subunit [Pinus thunbergii]
 gi|228016402|gb|ACP51235.1| RNA polymerase alpha subunit [Pinus thunbergii]
          Length = 335

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 83/329 (25%), Positives = 155/329 (47%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLHKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I  +      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVFRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE   +   +     
Sbjct: 189 YGSGNEI-REVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSN 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         ++       L  +++LEL  ++ N LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHVLTDTGETKEKIAFQLIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ +FG++S+ ++  VL  +     ++ P
Sbjct: 308 RIEHFGKESVEQVLEVLQKL---FAIDPP 333


>gi|158512705|sp|A0ZZ67|RPOA_GOSBA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
          Length = 330

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 77/334 (23%), Positives = 153/334 (45%), Gaps = 25/334 (7%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLR 56
           M+++  +        ++  +    ++        I  PL +G A T+G A+RR L+  L 
Sbjct: 1   MVREKVKVSTSTRTRQWKCVESRTDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGELE 60

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           G  IT  + + + HE S+I G+ E + +I++N+K I L+ +    +   I  +GPG VTA
Sbjct: 61  GTCITRAKSEKIPHEYSTIVGIQESVHEILMNLKEIVLRGNLYGTRNAFICAKGPGYVTA 120

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
            DI     +E+++    + +L     + + L + +  GY        +N   G   IDA+
Sbjct: 121 QDIILPPSVEIVDNTQHVASLTEPIDLCIGLQIERNRGYGIKT---PKNFHDGSYPIDAV 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           + P++  ++++           + L + I T+GS+T ++++  ASR L D    F++ +E
Sbjct: 178 FMPVRNANHSIHCYGND-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIHFLHAKE 236

Query: 237 PKKEVKEDIN-----------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIV 279
               ++ + +                  K           +++ EL  R  NCL+  NI 
Sbjct: 237 ENLHLENNQHDVTLHFFFPFHYRLVKLTKKKKEIALKYIFIDQSELPPRIYNCLKKSNIH 296

Query: 280 YMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
            + DL+  +  D+++M +F  + + +I G+L   
Sbjct: 297 TLLDLLNNSREDLMKMEHFRIEDVKQILGILEKK 330


>gi|150036758|emb|CAM98029.1| DNA-directed RNA polymerase alpha chain [Leuconostoc lactis KCTC
           3528]
          Length = 228

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 94/222 (42%), Positives = 140/222 (63%), Gaps = 2/222 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T 
Sbjct: 61  KKVVLAIDSDDERSLEIDVQGPAEVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTA 120

Query: 150 SKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GY  A  ++   E  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T
Sbjct: 121 VKGRGYSSADENKQLREEMPIGVLAVDSIYTPIERVNYHVENTRVGARDDYDKLTFDIWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           +GSI   D+++L ++IL + L +F++      E    +  + 
Sbjct: 181 NGSIKPSDALSLGAKILAEHLNLFMDISPVAAEANVMVEAEP 222


>gi|228015949|gb|ACP50789.1| RNA polymerase alpha subunit [Pinus ponderosa]
 gi|228016842|gb|ACP51668.1| RNA polymerase alpha subunit [Pinus attenuata]
          Length = 335

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 84/329 (25%), Positives = 156/329 (47%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE   +   +     
Sbjct: 189 YGSGNEI-REVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSN 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         ++       L  +++LEL  ++ N LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHLLTDTGETKEKIAFQLIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ +FG++S+ ++  VL  +     ++ P
Sbjct: 308 RIEHFGKESVEQVLEVLQKL---FAIDPP 333


>gi|150036764|emb|CAM98032.1| DNA-directed RNA polymerase alpha chain [Leuconostoc lactis]
          Length = 227

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 94/222 (42%), Positives = 140/222 (63%), Gaps = 2/222 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T 
Sbjct: 61  KKVVLAIDSDDERSLEIDVQGPAEVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTA 120

Query: 150 SKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GY  A  ++   E  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T
Sbjct: 121 VKGRGYSSADENKQLREEMPIGVLAVDSIYTPIERVNYHVENTRVGARDDYDKLTFDIWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           +GSI   D+++L ++IL + L +F++      E    +  + 
Sbjct: 181 NGSIKPSDALSLGAKILAEHLNLFMDISPVAAEANVMVAAEP 222


>gi|150020873|ref|YP_001306227.1| DNA-directed RNA polymerase subunit alpha [Thermosipho
           melanesiensis BI429]
 gi|172048670|sp|A6LLP1|RPOA_THEM4 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|149793394|gb|ABR30842.1| DNA-directed RNA polymerase, alpha subunit [Thermosipho
           melanesiensis BI429]
          Length = 328

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 113/324 (34%), Positives = 184/324 (56%), Gaps = 14/324 (4%)

Query: 8   ELIKPNNIEYIVLGQ-EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI- 65
           + I P N++     + +E      +  PL +G+A T+GN LRRVL+SS+   AIT V+  
Sbjct: 2   DFIMPKNLKMEDHSETDEHYYARFVLSPLEKGYATTIGNTLRRVLLSSIPSLAITDVKFV 61

Query: 66  -DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTV 122
                HE  +I+GV ED+ +I+LN+K + LKM     +   +TI  +G G + AGDI   
Sbjct: 62  RPEKYHEFDTIEGVKEDIIEILLNLKKVQLKMESYVNTPVELTIQHKGEGEIKAGDIVVP 121

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
             + V NP+  I  L+ DA + +++  + G G+VPA       D IG I +D +Y+PI K
Sbjct: 122 AGVTVTNPNLHIATLNEDADIEIKMYATVGKGFVPAAERNERPD-IGWIVLDGVYNPILK 180

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL----GMFINFEEPK 238
           V++ +E+ R G+  DYDKL + + T  +I   +++  A +I+ D        F + E+  
Sbjct: 181 VNWKIENVRVGKKTDYDKLILEVWTKKNIKPVEALKQAVKIINDHFKLIEESFGDMEDAG 240

Query: 239 ---KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
              +  K +I  + +  N  L KK++EL+LS+R+ NCL+ + I  +GDL++R E ++L++
Sbjct: 241 IVIETTKAEIVEEKIDENEILNKKIDELDLSMRALNCLKRDKIETIGDLLERGEEELLKI 300

Query: 296 ANFGRKSLVEIKGVL-GTMGLFLG 318
            NFG+KSL E+K  L    G+  G
Sbjct: 301 KNFGQKSLDEVKEKLMEKFGISFG 324


>gi|119662395|emb|CAJ33187.1| RNA polymerase alpha subunit [Lactobacillus aviarius subsp.
           aviarius]
          Length = 231

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 100/231 (43%), Positives = 150/231 (64%), Gaps = 2/231 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT VQIDGVLHE S+++GV ED+T IILN+
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAITDVQIDGVLHEFSTVEGVMEDVTTIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LKM  +  + + I   G   V AGDI    D+EVLNP+  IC +   A   + +T 
Sbjct: 61  KKVALKMDTEEPQILEIDVTGAKEVKAGDIHCGADVEVLNPELYICTVAEGASFHVRMTA 120

Query: 150 SKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +KG GYV A  +  + ++ PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T
Sbjct: 121 NKGRGYVSATENKAKADDMPIGVLAIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           +GSIT  ++++L+++IL + L +F+N  +  K  +  +  +       L  
Sbjct: 181 NGSITPSEAISLSAKILTEHLSIFVNLTDEAKNAEVMVEKEETHKEKMLEM 231


>gi|158564066|sp|Q06RA0|RPOA_JASNU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
          Length = 355

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 78/337 (23%), Positives = 156/337 (46%), Gaps = 31/337 (9%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +   E++        I  PL +G A T+   +RR L+  + G  IT V+   V
Sbjct: 11  RTLQWKCVESREDSKRLYYGRFILSPLRKGQADTIAIGIRRALLGEIEGTCITRVKSKNV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N K I L+ +       +I  RGPG VTA DI     +E++
Sbjct: 71  PHEYSTIAGIQESVHEILMNFKEIVLRSNLYGTCDASICVRGPGYVTAQDIILPPYVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY+    H +++   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDLCIGLQIERNRGYLMKMPHNSQD---GSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G    ++ L + I T+GS+T ++++  A R L D    F++ EE    ++++ +  
Sbjct: 188 SYGSG-NEKHEILFLEIWTNGSLTPKEALHEACRNLIDLFIPFLHKEEETSPLEDNHHTV 246

Query: 249 S--------------------LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
                                          +++ EL  +  NCL+G N+  + DL+ ++
Sbjct: 247 PLSPLTFHDKADKLRKRKKEIKKKIALKSIFIDQSELP-KVYNCLKGSNLYTLLDLLNKS 305

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           + D+++M +   + +  I  +L        + LP+  
Sbjct: 306 QEDLMKMEHLRLEDVNHILVILAR--KHFAIYLPNKK 340


>gi|323925205|gb|ADY11797.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 240

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 103/240 (42%), Positives = 161/240 (67%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +K
Sbjct: 1   VVEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           GI +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV 
Sbjct: 61  GIAIKSYVESEKQIELDVTGPIDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVK 120

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG+GYVPA  ++ +  PIG I +D++Y+P+ KV+Y VE AR G    YDKL++ I T+G+
Sbjct: 121 KGYGYVPADENKVDGAPIGTIAVDSIYTPVSKVNYQVEPARVGGDSSYDKLTLEITTNGT 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I  +++++L+++IL D L +F++  E   E +  +    +     L K +EE++ SVR+ 
Sbjct: 181 IVSDEALSLSAKILTDHLNLFVDLSEVAAEAETLVVKDEVKTERVLDKIIEEMDFSVRAY 240


>gi|323925169|gb|ADY11785.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|323925196|gb|ADY11794.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
          Length = 240

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 103/240 (42%), Positives = 161/240 (67%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +K
Sbjct: 1   VVEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           GI +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV 
Sbjct: 61  GIAIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVK 120

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG+GYVPA  ++ +  PIG I +D++Y+P+ KV+Y VE AR G    YDKL++ I T+G+
Sbjct: 121 KGYGYVPADENKVDGAPIGTIAVDSIYTPVSKVNYQVEPARVGGDSSYDKLTLEITTNGT 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I  +++++L+++IL D L +F++  E   E +  +    +     L K +EE++ SVR+ 
Sbjct: 181 IVSDEALSLSAKILTDHLNLFVDLSEVAAEAETLVVKDEVKTERVLDKIIEEMDFSVRTY 240


>gi|119662309|emb|CAJ33142.1| RNA polymerase alpha subunit [Lactobacillus gasseri]
          Length = 232

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 104/232 (44%), Positives = 152/232 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN+LRRVL++S+ G A++ +QIDGVLHE S++ GV ED+T IILN+
Sbjct: 1   FVVEPLERGFGTTLGNSLRRVLLTSIPGTALSYIQIDGVLHEFSTVPGVREDVTKIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK   D  K   I   GP +VTA D++  +DIEVLNPD  IC++     + M + +
Sbjct: 61  KKLELKSLSDEEKIAEIDVTGPAIVTAADLKVDSDIEVLNPDQYICSIADGGHLHMNVAI 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYVPA  ++T++ PIG+I +D+L+SPIKKV+Y VESAR G+  DYDKL++ I TDG
Sbjct: 121 KNGRGYVPASENKTDDMPIGVIPVDSLFSPIKKVNYQVESARVGKRDDYDKLTLEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           SIT  D+++ A++IL +   +F++ +   +     +  +       L   +E
Sbjct: 181 SITPNDALSFAAKILVEHFKVFMSTDMDAQFDDVMVEKEDDKNEKKLEMTIE 232


>gi|257429027|ref|ZP_05605414.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus 68-397]
 gi|257279508|gb|EEV10095.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus 68-397]
          Length = 253

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 98/248 (39%), Positives = 159/248 (64%), Gaps = 2/248 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I + ++ +     + EPL RG+  TLGN+LRR+L+SSL GAA+  ++I+G
Sbjct: 3   EIEKPR-IETIEISEDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVKYIEIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++  V ED++ II+NIK + LK+  +  K + I  R  G VTA DI   +D+E+
Sbjct: 61  VLHEFSAVDNVVEDVSTIIMNIKQLALKIYSEEDKTLEIDVRDEGEVTASDITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+  I  +     +++ L  +KG GY  A+ + T + PIG+I +D+LYSP+++V+YTV
Sbjct: 121 LNPELKIATVSKGGHLKIRLVANKGRGYALAEQNNTSDLPIGVIPVDSLYSPVERVNYTV 180

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  D+DKL++ + T+GSIT ++SV+LA++I+ + L +F+   +  +  +  I  
Sbjct: 181 ENTRVGQSSDFDKLTLDVWTNGSITPQESVSLAAKIMTEHLNIFVGLTDEAQNAEIMIEK 240

Query: 248 KSLPFNPA 255
           +       
Sbjct: 241 EEDQKEKV 248


>gi|49574614|ref|NP_848091.2| RNA polymerase alpha subunit [Adiantum capillus-veneris]
 gi|60393869|sp|Q85FJ1|RPOA_ADICA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|48476025|gb|AAP29422.2| RNA polymerase alpha chain [Adiantum capillus-veneris]
          Length = 345

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 87/346 (25%), Positives = 157/346 (45%), Gaps = 30/346 (8%)

Query: 2   IQKNW----QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRG 57
           ++KN     ++ I+   +E  +  +        +  P  RG A T+G A+RR L+  + G
Sbjct: 1   MRKNEMSTSKQAIQWKCLESKIESKRLH-YGRFLVSPFKRGQASTVGIAMRRALLQEIEG 59

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTA 116
            +IT  +  GV+HE S+I G+ E + D+++N+K I L+       +   +   GP  VTA
Sbjct: 60  TSITCARFCGVVHEYSTITGLQETIHDVLVNLKEIVLRGDSKEDIQEAFLSVTGPKEVTA 119

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
           GD+     +E ++    I  +     + +EL + K  GY      ++     G   IDA+
Sbjct: 120 GDLSLPPGVEAIDNSQYIATITQPISLTIELEIEKDCGYRIENLAKS---GKGQFPIDAV 176

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           + P++ V+Y++     G+    + L + I T+GS+T  +++  AS  L D L  F+    
Sbjct: 177 FMPVRNVNYSIHLFGSGRAT-QEILFIEIWTNGSLTPHEALRKASEKLMDLLTTFLYVRG 235

Query: 237 PKKEVKEDIN-----------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIV 279
               + E+                     +L       + +++LEL  R+ NCL+   I 
Sbjct: 236 GDVSLFENGEDSLDLTKSPSLQPQFGDTNNLEERVLENRFIDQLELPARAFNCLKRAEIY 295

Query: 280 YMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
            + DL+  +  D+ ++ NFGRKS+ ++   L          LPD  
Sbjct: 296 TIADLLNYSREDLSKLKNFGRKSVDQVSEALWD---RFAKELPDKK 338


>gi|323925187|gb|ADY11791.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
          Length = 240

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 103/240 (42%), Positives = 160/240 (66%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +K
Sbjct: 1   VVEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           GI +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV 
Sbjct: 61  GIAIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVK 120

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           KG+GYVPA  ++ +  PIG I +D++Y+P+ KV+Y VE AR G    YDKL++ I T+G+
Sbjct: 121 KGYGYVPADENKVDGAPIGTIAVDSIYTPVSKVNYQVEPARVGGDSSYDKLTLEITTNGT 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
           I  +++++L+++IL D L +F +  E   E +  +    +     L K +EE++ SVR+ 
Sbjct: 181 IVSDEALSLSAKILTDHLNLFXDLSEVAAEAETLVVKDEVKTERVLDKIIEEMDFSVRAY 240


>gi|71056953|emb|CAH59037.1| DNA-directed RNA polymerase alpha chain [Enterococcus sp. LMG
           14595]
          Length = 224

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 103/222 (46%), Positives = 148/222 (66%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG+ 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNIKGLA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK+  +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G 
Sbjct: 61  LKLFAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTVKPGR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYV A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDGSI  
Sbjct: 121 GYVQADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDGSIIA 180

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           +++++LA++IL + L +F+N  +  K  +  +  +       
Sbjct: 181 QEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 222


>gi|197294143|ref|YP_002149764.1| RNA polymerase alpha subunit [Cicer arietinum]
 gi|197089831|gb|ACH41101.1| RNA polymerase alpha subunit [Cicer arietinum]
          Length = 333

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 81/325 (24%), Positives = 162/325 (49%), Gaps = 26/325 (8%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RR+L+  + G  IT  + + + 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLMKGQADTIGIAMRRILLGEIEGTCITRAKSEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +    +  +I  +GPG VTA DI     +E+++
Sbjct: 72  HEYSTIVGIQESIHEILMNLKEIVLRSNLYGTRDASICFKGPGSVTAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL     + MEL + +  GY     +  +++     TIDA++ P++  ++++ S
Sbjct: 132 NTQHIANLTEPINLCMELKLERNRGYRIKTLNNIQDES---YTIDAVFMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L D    F++ EE K  ++ +    +
Sbjct: 189 YGNG-NEKQEILFLEIWTNGSLTPKEALFEASRNLIDLFIPFLHAEEDKLNLENNQQKVT 247

Query: 250 LP------------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           LP                          +++LEL  R  NCL+  NI  + +L+ +++ +
Sbjct: 248 LPLFTFHDRFVKDKLRKNKKEIALKSIFIDQLELPPRIYNCLKKSNIHTLLELLNKSQEE 307

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLF 316
           ++++ +F    + ++K +L  + + 
Sbjct: 308 LMKIEHFR---VEDVKNILNLLQIE 329


>gi|332144666|dbj|BAK19493.1| RNA polymerase alpha subunit [Lactobacillus sp. YIT 12364]
          Length = 239

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 109/239 (45%), Positives = 159/239 (66%), Gaps = 4/239 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR L+SSL GAAIT++QIDGVLHE S+IKGV ED+T IILN+K I
Sbjct: 1   EPLERGYGTTLGNSLRRTLLSSLPGAAITSIQIDGVLHEFSTIKGVVEDVTQIILNVKKI 60

Query: 93  NLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +LK+ G  +  + + I   GP  VTA DI   +D+ +LNPD  I  +   A   M LT +
Sbjct: 61  SLKLDGPDEEEENLEIDVIGPTEVTAADIVGGSDVTILNPDLHIATVADGASFHMNLTAN 120

Query: 151 KGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           KG GYV A  ++    + PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ + ++
Sbjct: 121 KGRGYVSAMENKKRSIDMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDVWSN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           GSIT  ++++LA++IL + L MF+N  +  K  +  +  +       L   +EEL+LSV
Sbjct: 181 GSITASEAISLAAKILTEHLEMFVNLTDEAKNAEIMVEKEETHKEKMLEMTIEELDLSV 239


>gi|330850661|ref|YP_004376542.1| RNA polymerase alpha subunit [Ptilidium pulcherrimum]
 gi|302024790|gb|ADK89636.1| RNA polymerase alpha subunit [Ptilidium pulcherrimum]
          Length = 336

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 91/335 (27%), Positives = 167/335 (49%), Gaps = 25/335 (7%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            ++++   IE   +  +          P  +G A+T+G A+RR L++ + GA+IT V+I 
Sbjct: 10  TQILQWRCIES-RMESKRLLYGRFAISPFRKGQANTIGIAMRRALLNEIEGASITYVEIK 68

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
            V HE S+I G+ E + DI++N+K I  K      ++  I   GP  +TA DI+  + I 
Sbjct: 69  KVKHEYSTITGIQESIHDILINLKEIVSKSDSYEPQKAYISIYGPKKITARDIKGTSSIR 128

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +++    I  L     + +EL + K HGY      +  +   G+ TIDA++ PI+ V+Y+
Sbjct: 129 IIDNTQYIATLTEAISLDIELNIEKDHGYRIENLQKYRD---GIFTIDAVFMPIRNVNYS 185

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK---- 242
           V S   G+    + L + I TDGS+T ++++  ASR L D     +N E  +        
Sbjct: 186 VHSFESGEKT-KEILFLEIWTDGSLTPKEALYEASRSLIDLFIPLMNSERKEINSGMKKK 244

Query: 243 ------------EDINVKSLPFNPALLKK-VEELELSVRSTNCLRGENIVYMGDLIQRTE 289
                         ++++ +  + A     +++LEL  R+ NCL+  N+  + D +  +E
Sbjct: 245 NELDIPCFPFRFISLDMEEMTKDIAFKHIFIDQLELPARAYNCLKRVNVHTIADSLNYSE 304

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
            D++++ NFG+KS+ ++   L  +     ++L   
Sbjct: 305 DDLVKIKNFGKKSIEQV---LEALKKRFSIDLQKK 336


>gi|71056874|emb|CAH58992.1| DNA-directed RNA polymerase alpha chain [Enterococcus ratti]
          Length = 227

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 104/227 (45%), Positives = 150/227 (66%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV  G
Sbjct: 61  ALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTVKPG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI 
Sbjct: 121 RGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIE 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
             ++++L+++I+ + L +F+N  +  K  +  +  +       L   
Sbjct: 181 PLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMT 227


>gi|71056943|emb|CAH59030.1| DNA-directed RNA polymerase alpha chain [Enterococcus hirae]
          Length = 225

 Score =  256 bits (653), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 103/223 (46%), Positives = 149/223 (66%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV  G
Sbjct: 61  ALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTVKPG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI 
Sbjct: 121 RGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIE 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
             ++++L+++I+ + L +F+N  +  K  +  +  +       
Sbjct: 181 PLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 223


>gi|119668287|emb|CAK95499.1| RNA polymerase alpha subunit [Lactobacillus brevis]
          Length = 228

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 101/227 (44%), Positives = 153/227 (67%), Gaps = 4/227 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+K I
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVTQIILNVKKI 60

Query: 93  NLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            LK++G  D  + + I  +GP  +TAGDI    D+++LNPD  I  +   A   M +T  
Sbjct: 61  ALKLNGSDDQEETMEINVKGPAQITAGDIVAGADVDILNPDLYIATVADGATFHMRMTAD 120

Query: 151 KGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           KG GYV A  ++T   + PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ + T+
Sbjct: 121 KGRGYVSADENKTRNTDMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDVWTN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           GSI   +++ALA++IL + L MF++  +  K  +  +  +       
Sbjct: 181 GSINPSEAIALAAKILTEHLAMFVDLTDEAKNAEIMVEKEETHKEKM 227


>gi|7388101|sp|Q9XQN8|RPOA_SINAL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|5541932|emb|CAB51131.1| putative RNA polymerase alpha subunit (PEP) [Sinapis alba]
          Length = 327

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 76/321 (23%), Positives = 153/321 (47%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+G A+ R L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRRDSKRLYYGRFILSPLMKGQADTIGIAMARALLGEIEGTCITRAKSENI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            H+ S+I G+ E + +I++N+  I LK +    +   I  +GPG +TA DI     +E++
Sbjct: 71  PHDYSNIVGIQESVHEILMNLNEIVLKSNLYGTRNPFICVQGPGYITARDIILPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + + L + +  GY     +  E+       IDA++ P++  ++++ 
Sbjct: 131 DNTQHIATLTEPINLCIGLKIERNRGYSLKMSNNFEDRS---YPIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNG-NEKQEILFIEIWTNGSLTPKEALYEASRNLINLFIPFLHVEEETFYLENNQHQV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP  P   K                 +++LEL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPVFPFHNKLVNLRQKKKELAFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTM 313
           ++M +F  + + ++  +L   
Sbjct: 307 IKMEHFHIEDVKKLLDILEKK 327


>gi|71056904|emb|CAH59009.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
          Length = 226

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 104/226 (46%), Positives = 150/226 (66%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV  G
Sbjct: 61  ALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTVKPG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI 
Sbjct: 121 RGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIE 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
             ++++L+++I+ + L +F+N  +  K  +  +  +       L  
Sbjct: 181 PLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 226


>gi|47679553|gb|AAT36720.1| RNA polymerase alpha subunit [Thalassionema frauenfeldii]
          Length = 298

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 94/296 (31%), Positives = 159/296 (53%), Gaps = 4/296 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KP   E +  G         + + L  G   T+GN LRRVL+  + G AI+AV+I G+ H
Sbjct: 7   KPLKSEKLQSG---GYYGQFLIDKLKLGQGITIGNQLRRVLLGEIGGTAISAVRIVGIRH 63

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E ++I GV ED+ +I+LN+KGI +K      K   +  +GP V+TA  I   + I+++NP
Sbjct: 64  EFATIPGVREDILEILLNLKGIVIKSDTTEIKFGRLKVQGPLVLTADSIDLPSGIKIVNP 123

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           +H I  +     + +E  +  G GY  A      ++    + ID+++ P++KV++ +E+ 
Sbjct: 124 NHYIATISTSINLELEFKIEHGIGYKLASQL-FNDENKNFLQIDSIFMPVQKVNFKIENL 182

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
            +      ++L + I T+GSI   +++  A +I+ +     +  +  K+  K+  N + L
Sbjct: 183 YDADNSISERLILEIWTNGSIEPIEALKKACKIIINCFNSLLKTQNTKETTKKTSNNRKL 242

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
              P     +EEL+LSVRS NCL+   I  +GDL+Q +   +  + NFGRKS  E+
Sbjct: 243 TIEPYTNIAIEELQLSVRSYNCLKKAKINTVGDLLQYSPDQLQELKNFGRKSADEV 298


>gi|324455908|gb|ADY39246.1| RNA polymerase alpha subunit [Vibrio variabilis]
 gi|324455910|gb|ADY39247.1| RNA polymerase alpha subunit [Vibrio sp. R-40493]
          Length = 262

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 120/265 (45%), Positives = 178/265 (67%), Gaps = 8/265 (3%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ 
Sbjct: 1   PLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLA 60

Query: 94  LKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSK 151
           +++  G     +T+ K G G V AGDI    D+E+ NP+HVIC+L  D A + M + V +
Sbjct: 61  VRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEISMRIKVER 120

Query: 152 GHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+
Sbjct: 121 GRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V++LEL+VR
Sbjct: 181 GTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVR 237

Query: 269 STNCLRGENIVYMGDLIQRTEADML 293
           S NCL+ E I Y+GDL+QRTE ++L
Sbjct: 238 SANCLKAEAIHYIGDLVQRTEVELL 262


>gi|86438804|emb|CAJ43367.1| RNA polymerase alpha subunit [Lactobacillus gallinarum]
 gi|119662307|emb|CAJ33141.1| RNA polymerase alpha subunit [Lactobacillus gallinarum]
          Length = 217

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 97/217 (44%), Positives = 141/217 (64%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+
Sbjct: 1   FVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK   D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V
Sbjct: 61  KKLELKSLSDERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDG
Sbjct: 121 QNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           SI   D+++ A++IL +   +F + +   K  +  + 
Sbjct: 181 SIKPNDALSFAAKILVEHFKVFESADADTKFSEVMVE 217


>gi|150036790|emb|CAM98272.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 223

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 93/223 (41%), Positives = 141/223 (63%), Gaps = 2/223 (0%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
            ++ EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN
Sbjct: 1   RVVIEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILN 60

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           +K + L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T
Sbjct: 61  LKKVVLAIDSDDERSLEIDVQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVT 120

Query: 149 VSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
             KG GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I 
Sbjct: 121 AVKGRGYTSADENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGARDDYDKLTFDIW 180

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           T+GSI   D+++L ++IL + L +F++      E    +  + 
Sbjct: 181 TNGSIKPSDALSLGAKILAEHLNLFMDISPVAAEASVMVEAEP 223


>gi|269784296|emb|CBH50793.1| alpha subunit of RNA polymerase [Vibrio sp. Cmj 13.4]
          Length = 270

 Score =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 119/273 (43%), Positives = 178/273 (65%), Gaps = 8/273 (2%)

Query: 56  RGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVV 114
            G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V
Sbjct: 1   PGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGL 170
            AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG 
Sbjct: 61  VAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGR 120

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  
Sbjct: 121 LLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDA 180

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
           F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE 
Sbjct: 181 FVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEV 237

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++L+  N G+KSL EIK VL + GL LGM L +
Sbjct: 238 ELLKTPNLGKKSLTEIKDVLASRGLSLGMRLEN 270


>gi|119668299|emb|CAK95504.1| RNA polymerase alpha subunit [Lactobacillus curvatus]
          Length = 212

 Score =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 91/212 (42%), Positives = 145/212 (68%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           G+  TLGN+LRR+L++SL G A+T +QIDGVLHE S+I GV ED+T IILNIK + LK+ 
Sbjct: 1   GYGTTLGNSLRRILLASLPGTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKLH 60

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
            +  K + I  +GP  VTA DI + +D+EVLN D  IC +       + +TV KG GYV 
Sbjct: 61  VEEDKTIEIDVKGPATVTAADIISDDDVEVLNTDQYICTVAEGGNFHVRMTVKKGRGYVA 120

Query: 158 AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
           A  +++++ PIG++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+  +++
Sbjct: 121 ADQNKSDDMPIGVLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAI 180

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           +LA++I+ + L +F++  +  K  +  +  + 
Sbjct: 181 SLAAKIMTEHLAIFVDLTDEAKNAEIMVEKEE 212


>gi|7388088|sp|P92225|RPOA_CRIDE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|1770151|emb|CAB01330.1| alpha subunit of RNA polymerase [Crithopsis delileana]
          Length = 339

 Score =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 89/328 (27%), Positives = 158/328 (48%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P     +++LEL+ R+ NC +      + DL+ +TE D+L
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCXKRXXXXTLLDLLSKTEEDLL 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + + K +  T+   L ++L
Sbjct: 308 RIDSFR---MEDRKHIWDTLEKHLPIDL 332


>gi|71056832|emb|CAH58971.1| DNA-directed RNA polymerase alpha chain [Enterococcus dispar]
          Length = 226

 Score =  255 bits (651), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 104/226 (46%), Positives = 149/226 (65%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAAIT++QIDGVLHE S++KGV ED+  IILNIKG+
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAITSIQIDGVLHEFSTVKGVREDVAQIILNIKGL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LKM     K + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV  G
Sbjct: 61  ALKMYTQEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTVRPG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  ++ E+ PIG++ +D++Y+P+ +V+Y VE+ R G+  D+DKL+M I TDGSI 
Sbjct: 121 RGYVQADENKREDMPIGVVPVDSIYTPVNRVNYQVENTRVGRRDDFDKLTMEIWTDGSIM 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
             ++++LA++I+ + L +F+N  +  K  +  I  +       L  
Sbjct: 181 PMEAMSLAAKIMTEHLDIFVNLTDEAKNAEIMIEKEETQKEKMLEM 226


>gi|324986527|ref|YP_004276397.1| RNA polymerase alpha subunit [Pinus nelsonii]
 gi|323522715|gb|ADX94963.1| RNA polymerase alpha subunit [Pinus nelsonii]
          Length = 335

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 84/329 (25%), Positives = 156/329 (47%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIKESVHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H + N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK---EVKEDIN 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE        K+  N
Sbjct: 189 YGNGNEI-QEVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNKKKGSN 247

Query: 247 V-------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           +             ++          +++LEL  ++ N LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHVLTDTGETKEKIAFQHIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ + G++S+ ++  VL        ++ P
Sbjct: 308 RIEHLGKESVEQVLEVLR---KRFAIDPP 333


>gi|228017724|gb|ACP52536.1| RNA polymerase alpha subunit [Pinus pinaster]
          Length = 335

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 83/329 (25%), Positives = 154/329 (46%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I  +      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVFRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE   +   +     
Sbjct: 189 YGSGNEI-REVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSN 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         ++       L  +++LEL  ++ N LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHVLTDTGETKEKIAFQLIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+  FG++S+ ++  VL  +     ++ P
Sbjct: 308 RIERFGKESVEQVLEVLQKL---FAIDPP 333


>gi|11466735|ref|NP_039331.1| RNA polymerase alpha subunit [Marchantia polymorpha]
 gi|133401|sp|P06270|RPOA_MARPO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|11706|emb|CAA28117.1| rpoA [Marchantia polymorpha]
          Length = 340

 Score =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 92/331 (27%), Positives = 164/331 (49%), Gaps = 25/331 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE  +  +     +     P  +G A+T+G A+RR L++ + GA+IT  +I  V 
Sbjct: 13  LQWKCIESKIESKRLL-YSRFAISPFRKGQANTVGIAMRRALLNEIEGASITYAKIKKVK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I LK      ++  I   GP  +TA DI+  + I+++ 
Sbjct: 72  HEYSTIIGLQESIHDILINLKEIVLKSESFEPQKAYISVLGPKKITAQDIKGPSCIKIMI 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L+ D ++ +EL + K  GY      +      GL  +DA++ PI+  +Y+V S
Sbjct: 132 IAQYIATLNKDILLEIELNIEKDRGYRIENLQK---YQEGLFPVDAVFMPIRNANYSVHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
               + +  + L + I TDGS+T ++++  ASR L D     IN E+ +K    +   +S
Sbjct: 189 FESEKKI-KEILFLEIWTDGSLTPKEALYEASRNLIDLFIPLINSEKKEKNFGIEKTNES 247

Query: 250 LPFN-----------------PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                                      +++LEL  R+ NCL+  N+  + DL+  +E D+
Sbjct: 248 NMSYFPFQSVSLDIEKMTKDVAFKHIFIDQLELPARAYNCLKKVNVHTIADLLHYSEDDL 307

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ NFG+KS+ ++   L  +     + LP 
Sbjct: 308 IKIKNFGKKSVEQV---LEALKKRFSIQLPK 335


>gi|165910441|gb|ABY73975.1| RNA polymerase alpha subunit [Cuscuta nitida]
          Length = 339

 Score =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 79/335 (23%), Positives = 154/335 (45%), Gaps = 25/335 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           +K   +E      +  +    I  PL +G A T+  A+RR L+S + G  IT V      
Sbjct: 13  LKWKCVESRT-DSKRLSYGRFILSPLMKGQADTIAIAMRRALLSEIEGTCITRVTFQNAS 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S I G+ E + DI++N+K I LK +       +++ +GP  VTA DI     +E+++
Sbjct: 72  HEYSIIAGIQESVHDILMNLKEIVLKSNLYGTCDASLYIKGPRYVTAQDIILPPHVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I +L     + + L + +  GY+   H   +N+     ++DA++ P+  V++++ S
Sbjct: 132 STQHIASLTEPINLCIGLKIERNRGYLIKAHPPFQNET---YSLDAVFMPVLNVNHSIYS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV-- 247
                    + L + I T+GS+T ++++  A++ L D    F+  EE    +++  +   
Sbjct: 189 YGNE---KKEILFLEIWTNGSLTPKEALHEAAQNLMDLFIPFLQMEEENLNLEDAEHQIP 245

Query: 248 -------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
                                    +++L    +  NCL   NI  + DL+ +++ D+L+
Sbjct: 246 FSPFTFYDKVSKLIKKKKRSLKSIFIDQLAFPPKIYNCLTKSNIFTLLDLLNKSQEDLLK 305

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           + +F    + ++K +LG +     ++LP    E  
Sbjct: 306 IEHFH---IEDVKQILGILEKNFALDLPKKKGEPF 337


>gi|119662313|emb|CAJ33144.1| RNA polymerase alpha subunit [Lactobacillus hilgardii]
          Length = 227

 Score =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 105/226 (46%), Positives = 152/226 (67%), Gaps = 4/226 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EPL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+
Sbjct: 1   VVVEPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNV 60

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K I+LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M L
Sbjct: 61  KKISLKLDGPEDEDENLEIDVIGPADVTAGDIQGDSDVTVLNPDLHIATVAEGATFHMRL 120

Query: 148 TVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           T ++G GYV A  ++      PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ I
Sbjct: 121 TANRGRGYVSAVENKKRATEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDI 180

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            T+GSIT  ++V+LA++IL + L MF++  +  K  +  +  +   
Sbjct: 181 WTNGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEKEETH 226


>gi|295136921|ref|YP_003587754.1| RNA polymerase alpha subunit [Lathyrus sativus]
 gi|293338643|gb|ADE43615.1| RNA polymerase alpha subunit [Lathyrus sativus]
          Length = 335

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 82/331 (24%), Positives = 158/331 (47%), Gaps = 25/331 (7%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            + ++   +E   +  +       I  PL +G A T+G A+RR+L+  + G  IT  + +
Sbjct: 10  TKTLQWKCVES-RVDSKRLYYGRFILSPLLKGQADTIGIAMRRILLGEIDGTCITRAKSE 68

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
            + HE S++ G+ E + +I++N+K I L+ +    +  +I  +GPG VTA DI     +E
Sbjct: 69  KIPHEYSTVVGIQESIHEILMNLKEIVLRSNLYGTREASISFKGPGYVTAQDIILPPSVE 128

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           V++    I NL     + +EL + +  GY     +  ++   G  TIDA++ P++  +Y+
Sbjct: 129 VIDKTQHIANLTEPINLCIELQIERKRGYRIKTLNNIQD---GSYTIDAVFMPVRNANYS 185

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           + S         D L + I T+GS T ++++  ASR L D    F++ EE    ++ + +
Sbjct: 186 IHSY-VNGNEKQDILFLEIWTNGSFTPKEALYEASRNLIDLFIPFLHAEEENFNLENNQH 244

Query: 247 VKSLPFNPALLKK--------------------VEELELSVRSTNCLRGENIVYMGDLIQ 286
             + P                            +++LEL  R  NCL+  NI  + + + 
Sbjct: 245 KMTWPLFTFHDHDRFVKDKLTNTQKEITLKSIFIDQLELPPRIYNCLKKSNIHTVFEFLN 304

Query: 287 RTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +++ D++++ +F  + L  I  +L     F+
Sbjct: 305 KSQEDLMKIEHFRVEDLKNILNILKIENHFV 335


>gi|153012181|ref|YP_001381697.1| RNA polymerase alpha subunit [Medicago truncatula]
          Length = 333

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 82/325 (25%), Positives = 161/325 (49%), Gaps = 26/325 (8%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RR+L+  + G  IT  + + + 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTIGIAMRRILLGEIEGTCITRAKSEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I LK +    +  +I  +GPG VTA DI     +E+++
Sbjct: 72  HEYSTIVGIQESIHEILMNLKEIVLKSNLYGTRDASICFKGPGYVTAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL     + +EL + +  GY     +  ++   G  TIDA++ P++  ++++ S
Sbjct: 132 NTQHIANLTEPINLCIELQIERKRGYRIKTLNNIQD---GSYTIDAVFMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                    + L + I T+GS+T ++++  ASR L D    F++ EE     + + +  +
Sbjct: 189 Y-VNGNEKQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEENLNFENNQHKVT 247

Query: 250 LP------------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           LP                          +++LELS R  NCL+  NI  + +L+ +++ D
Sbjct: 248 LPLFTFHDRLLKDKLRKNKKEIALKSIFIDQLELSPRIYNCLKKSNIHTLLELLNKSQED 307

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLF 316
           ++++ +F    + ++K +L  + + 
Sbjct: 308 LMKIEHFR---VEDVKNILNILQIE 329


>gi|228016331|gb|ACP51165.1| RNA polymerase alpha subunit [Pinus taeda]
          Length = 335

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 84/329 (25%), Positives = 154/329 (46%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+         +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKXIVLRSDSYGIXEASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE   +   +     
Sbjct: 189 YGSGNEI-REVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSN 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         ++       L  +++LEL  +  N LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHLLTDTGETKEKIAFQLIFIDQLELPPKIYNSLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ +FG++S+ ++  VL  +     ++ P
Sbjct: 308 RIEHFGKESVEQVLEVLQKL---FAIDPP 333


>gi|219674007|ref|YP_002456491.1| RNA polymerase alpha subunit [Trifolium subterraneum]
 gi|193788976|gb|ACF20572.1| RNA polymerase alpha subunit [Trifolium subterraneum]
          Length = 337

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 76/322 (23%), Positives = 154/322 (47%), Gaps = 24/322 (7%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
              +E   +  +       I  PL +G A T+G  +RR+L+  + G  IT  + + + HE
Sbjct: 15  WKCVES-RVDSKRLYYGRFILSPLMKGQADTIGITMRRILLGEIEGTCITRAKSEKIPHE 73

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            S+I G+ E + +I++N+K I L+ +    +  +I  +GPG VTA DI     +E+++  
Sbjct: 74  YSTIVGIQESIHEILMNLKQIVLRSNLYGTRDASICFKGPGYVTARDIILPPSVEIVDNT 133

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             I NL     + +EL + +  GY        ++     I +D ++ P+   +Y++ S  
Sbjct: 134 QHIANLTEPINLCIELQIERARGYRKKTIDNIQD-GSYTIDVDPVFMPVIHANYSIHSYL 192

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  + L + I T+GS+T ++++  A+R L D    F++ EE     + + +  +LP
Sbjct: 193 N-ANEKQEILFLEIWTNGSLTPKEALYEAARNLIDLFIPFLHAEEENFHFENNQHKVTLP 251

Query: 252 FNPALLK------------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                 +                   +++LEL  R  NCL+  +I  +  L+ +++ D++
Sbjct: 252 LFAFHDRLVKDKLRKNKKQIELKSVFIDQLELPPRIYNCLKKSDIHTLYQLLNKSQEDLM 311

Query: 294 RMANFGRKSLVEIKGVLGTMGL 315
           ++ +F   S+ ++K +L  + +
Sbjct: 312 KIEDF---SVEDVKNILNILQI 330


>gi|190411117|gb|ACE78313.1| RpoA [Vibrio parahaemolyticus]
 gi|190411119|gb|ACE78314.1| RpoA [Vibrio parahaemolyticus]
          Length = 263

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 117/266 (43%), Positives = 178/266 (66%), Gaps = 8/266 (3%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRV 104
           ALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +
Sbjct: 1   ALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---H 160
           T+ K G G V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H
Sbjct: 61  TLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIH 120

Query: 161 HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           +  +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A
Sbjct: 121 NEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRA 180

Query: 221 SRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVY 280
           + IL +QL  F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y
Sbjct: 181 ATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHY 237

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEI 306
           +GDL+QRTE ++L+  N G+KSL EI
Sbjct: 238 IGDLVQRTEVELLKTPNLGKKSLTEI 263


>gi|71056951|emb|CAH59036.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
          Length = 219

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 100/219 (45%), Positives = 146/219 (66%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNIKG+ LKM
Sbjct: 1   RGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNIKGLALKM 60

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
            GD  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G GYV
Sbjct: 61  YGDEEKTLEIDISGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTVKPGRGYV 120

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
            A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI   ++
Sbjct: 121 QADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIEPLEA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           ++L+++I+ + L +F+N  +  K  +  +  +       
Sbjct: 181 MSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 219


>gi|119668365|emb|CAK95514.1| RNA polymerase alpha subunit [Lactobacillus rhamnosus]
          Length = 205

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 94/205 (45%), Positives = 143/205 (69%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS 100
            TLGN+LRR+L+SSL GAA++++QIDGVLHE S+I GV ED+T IILNIK + LKM+ D 
Sbjct: 1   TTLGNSLRRILLSSLPGAAVSSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNTDE 60

Query: 101 HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
            K + I   GP  VTA DI    D+EVLNP+  IC +       + +TV KG GYV A  
Sbjct: 61  DKNIEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAADQ 120

Query: 161 HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           +++++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA
Sbjct: 121 NKSDDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLA 180

Query: 221 SRILQDQLGMFINFEEPKKEVKEDI 245
           ++IL + L +F+N  +  K  +  +
Sbjct: 181 AKILTEHLDIFVNLTDEAKNAEIMV 205


>gi|161513432|emb|CAP16859.1| DNA-directed RNA polymerase subunit alpha [Pediococcus parvulus]
          Length = 224

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 98/222 (44%), Positives = 149/222 (67%), Gaps = 2/222 (0%)

Query: 36  PRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLK 95
            RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNIK ++LK
Sbjct: 1   ERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNIKKVSLK 60

Query: 96  MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY 155
           +  D  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GY
Sbjct: 61  IESDDEKSLEINVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAVLTADTGRGY 120

Query: 156 VPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           V A  ++   ++ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSI+ 
Sbjct: 121 VSADENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSISP 180

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            ++ +L+++IL + L +F+N  +  ++ +  +  +       
Sbjct: 181 SEATSLSAKILTEHLALFVNLTDEAQDAEIMVEKEETNKEKM 222


>gi|57115498|gb|AAW33058.1| RNA polymerase alpha subunit [Plantago rugelii]
          Length = 308

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 81/315 (25%), Positives = 150/315 (47%), Gaps = 23/315 (7%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             +E     +        +  PL +G A T+G A+RR L+  ++G  IT V+ + V HE 
Sbjct: 1   KCVESRTDSKRLH-YGRFVLSPLMKGQADTIGIAMRRALLGEIQGTCITRVKSENVPHEY 59

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           S+I G+ E + +I++N+K I L+ +       +I  RGPG VTA DI     +E+ +   
Sbjct: 60  STIAGIQESVPEILMNLKEIVLRSNLYGTCGASICARGPGYVTAQDIILPPCVEIGDNTQ 119

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L       + L + +  GY+    H  ++       IDA++ P++ V++++ S   
Sbjct: 120 HIARLTEPISFCIGLEIERSRGYLIKSPHIFQDRS---YPIDAVFMPVRNVNHSIHSYGN 176

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV----- 247
                 + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + +      
Sbjct: 177 E---KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHKEEENLPLENNQDTVSFSP 233

Query: 248 -----------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
                      K+          +++ ELS R  NCL+  NI  + D + +++ D+++M 
Sbjct: 234 FSFHEKLDQFRKNKKKKALQSIFIDQFELSPRVYNCLKKSNIYTLFDFLTKSQEDLMKME 293

Query: 297 NFGRKSLVEIKGVLG 311
           +F  + L +  G+L 
Sbjct: 294 HFRLEDLKQTLGILE 308


>gi|108792407|emb|CAJ33136.1| RNA polymerase alpha subunit [Lactobacillus acidipiscis]
          Length = 224

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 102/224 (45%), Positives = 151/224 (67%), Gaps = 2/224 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAAIT VQIDGVLHE SSI GV ED+T IILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAITDVQIDGVLHEFSSIDGVLEDVTTIILNLKKVA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK++ +  + + I   GP  VTAGDIQ  +++EVLNPD  IC +   A     +T +KG 
Sbjct: 61  LKLNSEDVQTLEIDVTGPMEVTAGDIQGSSEVEVLNPDLYICTVADGASFHARMTANKGR 120

Query: 154 GYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GYV A  +  +TE+ PIG++ ID++Y+PI++V+Y VE  R GQ  D+DKL++ + T+GSI
Sbjct: 121 GYVSANENKAKTEDMPIGVLAIDSIYTPIERVNYQVEKTRVGQKSDFDKLTLDVWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           T  ++++L+++IL + L +F++  +  K  +  +  +       
Sbjct: 181 TPSEAISLSAKILTEHLTLFVDLTDEAKNAEIMVEKEETHKEKM 224


>gi|328813985|gb|AEB52108.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 228

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 104/228 (45%), Positives = 153/228 (67%), Gaps = 2/228 (0%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK+  D
Sbjct: 1   GTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTAIILNVKKIALKLESD 60

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             K + I  +GP  VTAGDI    D+EVLNPD  IC +   A   M +T + G GYV A+
Sbjct: 61  ETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGAHFHMRMTANTGRGYVSAE 120

Query: 160 HHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
            ++   ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T+GSIT  +++
Sbjct: 121 DNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWTNGSITPSEAI 180

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
           +L+++IL D L +F+N  +  K     +  +       L   +EEL+L
Sbjct: 181 SLSAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEMTIEELDL 228


>gi|150187102|emb|CAK30171.1| RNA polymerase alpha subunit [Streptococcus agalactiae]
          Length = 219

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 94/219 (42%), Positives = 148/219 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+
Sbjct: 1   FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNV 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +   GP  +TAGDI T +DIE++NPDH +  +     ++  +TV
Sbjct: 61  KGLAVKSYVEDEKIIELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIAEGHSLKATMTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 121 AKNRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +I  ED++ L++R+L + L +F +  E  K  +     +
Sbjct: 181 TIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKETE 219


>gi|150036766|emb|CAM98264.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides KCTC 3652]
          Length = 229

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 93/220 (42%), Positives = 139/220 (63%), Gaps = 2/220 (0%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
            EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K 
Sbjct: 1   IEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKK 60

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           + L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  K
Sbjct: 61  VVLAIDSDDERSLEIDVQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVK 120

Query: 152 GHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           G GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+G
Sbjct: 121 GRGYTSADENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGARDDYDKLTFDIWTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           SI   D+++L ++IL + L +F++      E    +  + 
Sbjct: 181 SIKPSDALSLGAKILAEHLNLFMDISPVAAEASVMVEAEP 220


>gi|190411121|gb|ACE78315.1| RpoA [Vibrio parahaemolyticus]
          Length = 263

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 117/266 (43%), Positives = 177/266 (66%), Gaps = 8/266 (3%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRV 104
           ALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +
Sbjct: 1   ALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---H 160
           T+ K G G V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H
Sbjct: 61  TLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIH 120

Query: 161 HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           +  +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A
Sbjct: 121 NEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRA 180

Query: 221 SRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVY 280
           + IL +QL  F++  + +         +   F+P LL+ V +LEL+VRS NCL+ E I Y
Sbjct: 181 ATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVNDLELTVRSANCLKAEAIHY 237

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEI 306
           +GDL+QRTE ++L+  N G+KSL EI
Sbjct: 238 IGDLVQRTEVELLKTPNLGKKSLTEI 263


>gi|86438814|emb|CAJ43372.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 226

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 97/216 (44%), Positives = 141/216 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+
Sbjct: 1   FVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK   D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V
Sbjct: 61  KKLELKSLSDERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDG
Sbjct: 121 QNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           SI   D+++ A++IL +   +F + +   K  +  +
Sbjct: 181 SIKPNDALSFATKILVEHFKVFESADADTKFSEVMV 216


>gi|139387483|ref|YP_001122838.1| RNA polymerase alpha subunit [Phaseolus vulgaris]
 gi|158513617|sp|A4GGD7|RPOA_PHAVU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|112031005|gb|ABH88117.1| RNA polymerase alpha subunit [Phaseolus vulgaris]
 gi|158187119|gb|ABW22752.1| RNA polymerase alpha subunit [Phaseolus vulgaris]
          Length = 333

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 80/327 (24%), Positives = 156/327 (47%), Gaps = 24/327 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RR+L+  + G  IT V+ + + 
Sbjct: 13  LQWKCVES-RIDSKRLYYGRFILSPLMKGQADTIGIAIRRILLGEIEGTCITCVKSEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I +N+K I LK +    +  +I  +GPG +TA DI     +E+++
Sbjct: 72  HEYSTIIGIEESVHEIFMNLKEIVLKSNMYGIQDASISFKGPGYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I N+     + +EL + +  GY        ++   G   IDA + P++ V+Y++ S
Sbjct: 132 NRQHIANVTEPVHLCIELKIERNRGYRIKTLKNFQD---GSYDIDARFMPVRNVNYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                    + L + I T+GS+T ++++  AS+ L +    F++ EE    ++++ +  +
Sbjct: 189 Y-VNGNEKQEILFLEIWTNGSLTPKEALYEASQNLIELFIPFLHAEEDNFHLEKNQHKVT 247

Query: 250 LP------------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           LP                          +++LEL  R  NCL+  NI  + +L+  ++ D
Sbjct: 248 LPLFTFHDILVKDKLRKNQKEIALKSIFIDQLELPPRIYNCLKRSNIHTLLELLSNSQED 307

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLG 318
           +L+  +F  +    I  +L  +  +  
Sbjct: 308 LLKFEHFHVEDGKSILDILK-IQKYFA 333


>gi|289524818|emb|CBJ94465.1| alpha subunit of RNA polymerase [Vibrio sp. Rd 16.2]
          Length = 267

 Score =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 118/270 (43%), Positives = 177/270 (65%), Gaps = 8/270 (2%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGV 113
           + G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G 
Sbjct: 1   MPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGP 60

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIG 169
           V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG
Sbjct: 61  VVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL 
Sbjct: 121 RLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLD 180

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
            F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
            ++L+  N G+KSL EIK VL + GL LGM
Sbjct: 238 VELLKTPNLGKKSLTEIKDVLASRGLSLGM 267


>gi|269123125|ref|YP_003305702.1| DNA-directed RNA polymerase, alpha subunit [Streptobacillus
           moniliformis DSM 12112]
 gi|268314451|gb|ACZ00825.1| DNA-directed RNA polymerase, alpha subunit [Streptobacillus
           moniliformis DSM 12112]
          Length = 322

 Score =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 110/303 (36%), Positives = 171/303 (56%), Gaps = 5/303 (1%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
              + ++       EPL RG+ +T+GNALRRVL+SS+ G+AI  V+IDGVL+E S I+GV
Sbjct: 14  TEEKIDQYSAKYTLEPLYRGYGNTIGNALRRVLLSSIPGSAIKGVRIDGVLNEFSMIEGV 73

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E +TDI+LNIK I +++     KR+ +   GP V+TA DI     I ++NP+ VI  + 
Sbjct: 74  KEAVTDIVLNIKEIVVELDEPVEKRMKLSVVGPKVITAADIVPEAGITIVNPEQVIATIT 133

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + ME  V  G G+V +    T       + +DA+Y+PI+KVSY VE    G+V +Y
Sbjct: 134 TKKAIDMEFIVDSGEGFVVSDEINTSGWEADFLAVDAIYTPIRKVSYQVEDTMVGRVTNY 193

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP---- 254
           DKL++T+ TDGSI   D+++ A  ++      F N      + + +  ++    N     
Sbjct: 194 DKLTLTVTTDGSIDIHDALSYAVELINIHTKPFANIGTAMAKFRSEEELELEVSNDSYPS 253

Query: 255 -ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                ++EEL L++RS NCL+  +I  +G+LI+ T+ D+ ++ N G KS  EI   +   
Sbjct: 254 LVEDTRIEELGLTIRSYNCLKKVDINTVGELIRLTKEDLKKIKNLGNKSAKEIIEKMKEY 313

Query: 314 GLF 316
           G  
Sbjct: 314 GYE 316


>gi|228016715|gb|ACP51543.1| RNA polymerase alpha subunit [Pinus aristata]
          Length = 335

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 84/329 (25%), Positives = 157/329 (47%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H + N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK---EVKEDIN 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE        K+  N
Sbjct: 189 YGSGNEI-QEVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNKKKGSN 247

Query: 247 V-------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           +             ++          +++LEL  ++ N LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHVLTDTGETKEKIAFQHIFIDQLELPPQTYNSLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ + G++S+ ++  VL  +     ++ P
Sbjct: 308 RIEHLGKESVEQVLEVLRKL---FAIDPP 333


>gi|58761465|gb|AAW82426.1| RNA polymerase alpha subunit [Takakia lepidozioides]
          Length = 382

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 79/331 (23%), Positives = 151/331 (45%), Gaps = 25/331 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +     + +     P   G A T+G A+RR  +  + G  IT  +   V 
Sbjct: 13  LQWRCVES-RVDSARLHYSRFAIPPFRSGQASTVGIAMRRASLGEVEGTCITCAESKRVT 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + D+ +N   I L+      ++  I   GP  VTA DI +   +++++
Sbjct: 72  HEYSTILGIQESVHDVSINSGEIVLRSDSYETQKAFISILGPKKVTAQDIISPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
                  +       +EL + K  GY      ++ +   G    DA++ PI+  +Y+V S
Sbjct: 132 TTQYTATVTKAIHSDIELKIEKDFGYRIEDPIKSAD---GNSPADAVFMPIRNANYSVHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP------KKEVKE 243
              G     + L + I T+GS+T ++++  ASR L +    F++ E+       K   + 
Sbjct: 189 FENGNET-QEILFLEIWTNGSVTPKEALYEASRSLINLFIPFLHAEKKEFIYGLKNTYES 247

Query: 244 DINVKSLPFNPALLKK-----------VEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +++  S P   A + +           +++LEL  R+ NC +  N   + D +  ++ D+
Sbjct: 248 NMSYFSSPSLSADIDEMTKGVTFKHIFIDQLELPARAYNCPKRVNAHTISDPLNYSQDDL 307

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ NFG+KS+ ++   L        +NLP 
Sbjct: 308 MKIKNFGKKSVEQV---LEASQKRFSINLPK 335


>gi|324986455|ref|YP_004276326.1| RNA polymerase alpha subunit [Pinus monophylla]
 gi|228016086|gb|ACP50924.1| RNA polymerase alpha subunit [Pinus rzedowskii]
 gi|323522550|gb|ADX94892.1| RNA polymerase alpha subunit [Pinus monophylla]
          Length = 335

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 84/329 (25%), Positives = 156/329 (47%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H + N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK---EVKEDIN 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE        K+  N
Sbjct: 189 YGSGNEI-QEVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNKKKGSN 247

Query: 247 V-------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           +             ++          +++LEL  ++ N LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHVLTDTGETKEKIAFQHIFIDQLELPPQTYNSLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ + G++S+ ++  VL        ++ P
Sbjct: 308 RIEHLGKESVEQVLEVLR---KRFAIDPP 333


>gi|154424845|emb|CAL18525.1| RNA polymerase alpha subunit [Streptococcus pyogenes]
          Length = 219

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 96/219 (43%), Positives = 148/219 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+
Sbjct: 1   FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNV 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     +R  +TV
Sbjct: 61  KGLAVKSYVEDEKIIELEVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLRATMTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 121 AKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +I  ED++ L++R+L + L +F +  E  K  +     +
Sbjct: 181 TIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKETE 219


>gi|332144696|dbj|BAK19508.1| RNA polymerase alpha subunit [Lactobacillus rapi]
          Length = 230

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 106/230 (46%), Positives = 152/230 (66%), Gaps = 4/230 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           ++ EPL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+
Sbjct: 1   VVVEPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNV 60

Query: 90  KGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           K I+LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M L
Sbjct: 61  KKISLKLDGPEDEEENLEIDVIGPADVTAGDIQGDSDVTVLNPDLHIATVADGATFHMRL 120

Query: 148 TVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           T +KG GYV A  ++      PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ +
Sbjct: 121 TANKGRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDV 180

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            TDGSIT  ++V+LA++IL + L MF++  +  K  +  +  +       
Sbjct: 181 WTDGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEKEETHKEKM 230


>gi|317016853|gb|ADU85967.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 228

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 92/228 (40%), Positives = 141/228 (61%), Gaps = 2/228 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVV 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG 
Sbjct: 61  LAIDSDDERSLEIDVQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGR 120

Query: 154 GYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI
Sbjct: 121 GYTSADENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGARDDYDKLTFDIWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
              D+++L ++IL + L +F++      E    +  + +  + +    
Sbjct: 181 KPSDALSLGAKILAEHLNLFMDISPVAAEASVMVEAEPVAVSASDSAP 228


>gi|47679551|gb|AAT36719.1| RNA polymerase alpha subunit [Thalassiosira sp. Cleve BA153110]
          Length = 300

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 92/280 (32%), Positives = 149/280 (53%), Gaps = 1/280 (0%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               + + L  G   T+GN LRRVL+  L+G AIT V+I GV  E S I GV ED+ +I+
Sbjct: 22  YGQFLIDSLSSGQGITIGNLLRRVLLGDLKGTAITGVRIAGVKDEFSLIPGVREDILEIL 81

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+KGI LK    + +   +   GP V+TA  IQ   D+E++NP+H I  L    ++ +E
Sbjct: 82  LNLKGIVLKSKNSTRQFARLRLHGPAVITASSIQLPPDVEIINPNHYIATLSSSHILEIE 141

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
             +  GH Y  A    + +     I  DA++ P +K  + VE+  +      +++ + + 
Sbjct: 142 FKIESGHDYRLANETFS-DKLSNFIETDAIFMPDQKDDFKVENVYDNSNNVKERVFLDVW 200

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+GSI+ E ++  AS ++ D        +  +++       ++ P +P     +EEL+LS
Sbjct: 201 TNGSISPEQAIFSASNLIIDLFKSITEHKINQEKESIKEKTQTKPVDPYTHIAIEELQLS 260

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           VR  NCL+   I  +GDL+  +   +L + NFGRKS  E+
Sbjct: 261 VRPYNCLKRAQINTIGDLLDYSPEKLLELKNFGRKSADEV 300


>gi|309322228|ref|YP_003934306.1| RNA polymerase alpha subunit [Monsonia speciosa]
 gi|197131696|gb|ACH47366.1| RNA polymerase alpha subunit [Monsonia speciosa]
 gi|300069321|gb|ADJ66441.1| RNA polymerase alpha subunit [Monsonia speciosa]
          Length = 331

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 77/308 (25%), Positives = 146/308 (47%), Gaps = 11/308 (3%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +   +E      +       I  PL +G A  +G A+RR L+  + G  IT  +   + H
Sbjct: 14  RWKCVES-RADDKRLFYGRFILSPLKKGQADIIGIAMRRALLGEIEGTCITHAKFAKIPH 72

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E ++I G+ E + +I++N+K I L+ +    +  +I  RGP  VTA DI       +++ 
Sbjct: 73  EYTTIAGIKESIYEILMNLKEIVLRSNLYGTRDASICVRGPRDVTAQDIILPPSTAIVDN 132

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL-ITIDALYSPIKKVSYTVES 189
              I  L       + L + +G GY       T+         IDA++ P++ V++++ S
Sbjct: 133 TQHIFTLTEPIDFCVGLKIERGRGYSIKIPMPTDLFHHDSAYPIDAVFMPVRNVNHSIHS 192

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L + L  F++ EE    + E+   + 
Sbjct: 193 YERGS---HEMLFLEIWTNGSLTPKEALREASRKLINLLMPFLHAEEENFYLVENNQNQD 249

Query: 250 LPFNPALLKKVEEL------ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               P  L  ++++      EL  R  NCL+   I  + DL+ +   D+++M +F ++ +
Sbjct: 250 TEELPIDLCGLKDIYIDQLVELPPRFYNCLKRSGIHTVMDLLDKNRDDLMKMTHFRQEDI 309

Query: 304 VEIKGVLG 311
             +  +L 
Sbjct: 310 EGVMNILN 317


>gi|332144694|dbj|BAK19507.1| RNA polymerase alpha subunit [Lactobacillus parafarraginis]
          Length = 236

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 110/236 (46%), Positives = 155/236 (65%), Gaps = 4/236 (1%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           I EPL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K
Sbjct: 1   IVEPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVK 60

Query: 91  GINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
            I+LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT
Sbjct: 61  KISLKLDGPEDEEENLEIDVIGPADVTAGDIQGDSDVTVLNPDLHIATVAEGATFHMRLT 120

Query: 149 VSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            +KG GYV A  ++      PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ + 
Sbjct: 121 ANKGRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDVW 180

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           TDGSIT  ++V+LA++IL + L MF++  +  K  +  +  +       L   +EE
Sbjct: 181 TDGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEKEETHKEKMLEMTIEE 236


>gi|300431316|gb|ADK12621.1| RNA polymerase alpha subunit [Lorenzochloa erectifolia]
          Length = 339

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 85/328 (25%), Positives = 149/328 (45%), Gaps = 24/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDITLPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +  GY     +  ++   G   IDA+  P++ V+Y++ S
Sbjct: 132 TAQPIANLTEPIDFCIELQIKRDRGYQTELRNNYQD---GSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F+           + N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLXXXXXXXXXXXNKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            P                  P       +LEL  R+ NCL+   I  + DL+ +TE  ++
Sbjct: 248 PPLFTFQKKLTNLXKNKKGIPXXCIFXXQLELPSRTYNCLKRAXIHTLLDLLSKTEEXLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
            + +F        K +  T+   L ++L
Sbjct: 308 XIDSFRX---EXGKQIWDTLEKHLPIDL 332


>gi|72534407|emb|CAH59040.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
          Length = 219

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 102/219 (46%), Positives = 147/219 (67%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNIKG+ LKM
Sbjct: 1   RGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNIKGLALKM 60

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
            GD  K + I   GP  VTAGDI   +D+E+LN D  ICN+   A     LTV  G GYV
Sbjct: 61  YGDEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICNVSEGASFHARLTVKPGRGYV 120

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
            A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI   ++
Sbjct: 121 QADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIEPLEA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           ++LA++I+ + L +F+N  +  K  +  +  +       
Sbjct: 181 MSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 219


>gi|150187156|emb|CAK30183.1| RNA polymerase alpha subunit [Streptococcus halichoeri]
          Length = 223

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 95/220 (43%), Positives = 148/220 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+
Sbjct: 1   FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNV 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV
Sbjct: 61  KGLAVKSYVEDEKIIELDVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLKATMTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 121 AKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           +I  ED++ L++R+L + L +F +  E  K        ++
Sbjct: 181 TIIPEDALGLSARVLIEHLNLFTDLTEVAKATDVMKETET 220


>gi|228017530|gb|ACP52345.1| RNA polymerase alpha subunit [Pinus monticola]
          Length = 335

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 80/329 (24%), Positives = 153/329 (46%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H + N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITFDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE   +   +     
Sbjct: 189 YGSGNEI-QEVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSN 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         ++          +++LEL  ++ N LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHVLTDTGETKEKIAFKHIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           ++ +  ++S+ ++  VL        ++ P
Sbjct: 308 KIEHLEKESVEQVLEVLR---KRFAIDPP 333


>gi|119662325|emb|CAJ33150.1| RNA polymerase alpha subunit [Lactobacillus intestinalis]
          Length = 211

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 97/210 (46%), Positives = 141/210 (67%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE +++ GV ED+T IILN+
Sbjct: 1   FVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFATVPGVREDVTKIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK   D  K + +   GP  VTA D++   D++VLNPD  IC +     + M++ V
Sbjct: 61  KKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMQIAV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYVPA  +++E+ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL++ I TDG
Sbjct: 121 KNGRGYVPASDNKSEDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTLEIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKK 239
           SI   D+++ A++IL +   +F + +   K
Sbjct: 181 SIKPNDALSFAAKILVEHFKVFESADANTK 210


>gi|47679559|gb|AAT36723.1| RNA polymerase alpha subunit [Phaeodactylum sp. Bohlin BA153065]
          Length = 298

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 90/280 (32%), Positives = 150/280 (53%), Gaps = 1/280 (0%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               +   L  G   T+GN LRRVL+  L G AI+AV+I G+ HE S+I GV ED+ +I+
Sbjct: 20  HGQFLINSLNPGQGITIGNQLRRVLLGDLGGVAISAVRIAGITHEFSTIPGVREDILEIL 79

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+KGI         +   +  +GP VVTA  IQ   ++E++NP+H I  +    ++ +E
Sbjct: 80  LNLKGIICTSQIQDTQFGHLKVQGPSVVTADLIQLPPEVEIINPNHYIATITTSNILEIE 139

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
                G GY  A       D    + +D ++ P++KV + +E+  +      ++L + I 
Sbjct: 140 FKFVYGGGYHLASQKFCREDENY-LQLDTIFMPVQKVDFKIENIYDATNNISERLFLDIW 198

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+GSI+  D++  A++++ D   + IN        +    ++++   P     +EEL+LS
Sbjct: 199 TNGSISPNDALESAAQVIIDLFTLLINNTNINNNNRLVKAIRAISIEPYTNIAIEELQLS 258

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           VR+ NCL+   I  +GDL+Q +   +  + NFGRKS  E+
Sbjct: 259 VRAYNCLKKAQINTVGDLLQYSPEKLQELKNFGRKSADEV 298


>gi|283945407|dbj|BAI66457.1| RNA polymerase alpha-subunit [Vibrio tapetis]
          Length = 260

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 119/262 (45%), Positives = 175/262 (66%), Gaps = 8/262 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 1   EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 60

Query: 93  NLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVS 150
            +K+  G     +T+ K G G V AGDI    D+E+ NP+HVIC+L  D A + M + V 
Sbjct: 61  AVKVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVE 120

Query: 151 KGHGYVPAKHH---RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA        +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T
Sbjct: 121 RGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMET 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  ++ IL +QL  F++  + +         +   F+P LL+ V++LEL+V
Sbjct: 181 NGTLDPEEAIRRSATILAEQLDAFVDLRDIRVPE---EKEEKPEFDPILLRPVDDLELTV 237

Query: 268 RSTNCLRGENIVYMGDLIQRTE 289
           RS NCL+ E I Y+GDL+QRTE
Sbjct: 238 RSANCLKAEAIHYIGDLVQRTE 259


>gi|323148861|ref|YP_004221953.1| RNA polymerase alpha subunit [Erodium carvifolium]
 gi|316926325|gb|ADU58178.1| RNA polymerase alpha subunit [Erodium carvifolium]
          Length = 324

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 80/306 (26%), Positives = 150/306 (49%), Gaps = 9/306 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +   +E    G+        I  PL +G A  +G A+RR L+  L G  IT  +   + H
Sbjct: 14  QWKCVESRADGKR-LYYGRFILSPLKKGQADIIGIAMRRALLGELEGTCITHAKFGKIPH 72

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E ++I G+ E + +I++N+K I L+ +    +  +I  RGP  VTA DI     + +++ 
Sbjct: 73  EYTTIVGIQESVYEILMNLKEIVLRSNLYGTRGASICVRGPRDVTAQDIVLPPSVAIVDN 132

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
              I  L       + L + +  GY       T +   G   IDA++ P+K V++++ S 
Sbjct: 133 TQHIVTLTEPIDFCVGLQIERNRGYSIKIPTATNSHNDGGYPIDAVFMPVKNVNHSIHSY 192

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV--K 248
             G    ++ L + I T+GS+T ++++  ASR L +    F+N EE    ++ + N   +
Sbjct: 193 ENGS---HEMLFLEIWTNGSLTPKEALREASRKLINLFIPFLNAEEENSHLENNQNEHTE 249

Query: 249 SLPFNPALLKKV---EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            L  +   LK +   + +EL  R  N L+G  I  + DL+ +   D++++ +F ++ + +
Sbjct: 250 ELSRDFCGLKDIYIDQLVELPPRLYNSLKGSGIHTVMDLLDKNPDDLMKITHFRQEDVEK 309

Query: 306 IKGVLG 311
           +  +L 
Sbjct: 310 VMNILN 315


>gi|119662353|emb|CAJ33165.1| RNA polymerase alpha subunit [Lactobacillus saerimneri]
          Length = 213

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 99/213 (46%), Positives = 144/213 (67%), Gaps = 2/213 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAAIT +QIDGVLHE S+++GV ED+T IILN+
Sbjct: 1   FVIEPLERGYGTTLGNSLRRVLLSSLPGAAITDIQIDGVLHEFSTVEGVLEDVTQIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L +  D    + I   GP  VTAGDIQ   D+E+ NPD  IC +   A   + +T 
Sbjct: 61  KKVALGIKSDDRVSLEIDVVGPMEVTAGDIQGSADVEIFNPDQYICTVADGASFHVRMTA 120

Query: 150 SKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           + G GYV AK ++   ++ PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T
Sbjct: 121 NTGRGYVSAKENKEMADDMPIGVLPIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           + SIT  ++V+L++++L + L +F+N  E    
Sbjct: 181 NKSITPSEAVSLSAKVLTEHLSLFVNLTEEAMN 213


>gi|332144698|dbj|BAK19509.1| RNA polymerase alpha subunit [Lactobacillus sunkii]
          Length = 235

 Score =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 108/235 (45%), Positives = 153/235 (65%), Gaps = 4/235 (1%)

Query: 28  TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIIL 87
             ++ EPL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IIL
Sbjct: 1   GEVVVEPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIIL 60

Query: 88  NIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           N+K I+LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M
Sbjct: 61  NVKKISLKLDGPEDEEENLEIDVIGPADVTAGDIQADSDVTVLNPDLHIATVAEGATFHM 120

Query: 146 ELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            LT +KG GYV A  ++      PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++
Sbjct: 121 RLTANKGRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTL 180

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
            I TDGSIT  ++V+LA++IL + L MF++  +  K  +  +  +       L  
Sbjct: 181 DIWTDGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEKEETHKEKMLEM 235


>gi|150036820|emb|CAM98279.1| DNA-directed RNA polymerase alpha chain [Fructobacillus ficulneus]
          Length = 238

 Score =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 99/238 (41%), Positives = 143/238 (60%), Gaps = 2/238 (0%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL G A+  VQIDGV+HE S++ GV ED+T +I N+K +
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGVAVNTVQIDGVVHEXSTVDGVVEDVTQLIXNLKKV 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
                      + I  +GP  VTA D+    DIEVLNPD  I  L     + M +T  KG
Sbjct: 61  VFATDSAEEHALEIDVQGPKDVTAADLAGSADIEVLNPDLHIATLAAGKSLHMTVTAVKG 120

Query: 153 HGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            GY  A+ ++   +  PIG++T+D++Y+PI++V+Y VE+ R G   DYDKL+M + T+GS
Sbjct: 121 RGYSSAEENKQLRDEMPIGVLTVDSIYTPIERVNYHVENKRVGSRDDYDKLTMEVWTNGS 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           I   D+++L S+IL + L +F       +E K  +              +E+L+LSVR
Sbjct: 181 INPSDALSLGSKILTEHLNLFTXISPVAQETKVMVETXQAASTATDAAPIEDLDLSVR 238


>gi|119668301|emb|CAK95453.1| RNA polymerase alpha subunit [Lactobacillus curvatus]
          Length = 212

 Score =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 90/212 (42%), Positives = 143/212 (67%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRR+L++SL G A+T +QIDGVLHE S+I GV ED+T IILNIK + LK+  +
Sbjct: 1   GTTLGNSLRRILLASLPGTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKLHVE 60

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             K + I  +GP  VTA DI + +D+EVLN D  IC +       + +TV KG GYV A 
Sbjct: 61  EDKTIEIDVKGPATVTAADIISDDDVEVLNTDQYICTVAEGGNFHVRMTVKKGRGYVAAD 120

Query: 160 HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
            +++++ PIG++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++L
Sbjct: 121 QNKSDDMPIGVLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISL 180

Query: 220 ASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           A++I+ + L +F++  +  K  +  +  +   
Sbjct: 181 AAKIMTEHLAIFVDLTDEAKNAEIMVEKEETH 212


>gi|197941213|gb|ACH78326.1| RNA polymerase [Streptococcus equi subsp. zooepidemicus]
          Length = 226

 Score =  252 bits (643), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 94/225 (41%), Positives = 149/225 (66%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+
Sbjct: 1   FVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIRIDGVLHEFDTIPGVREDVMQIILNV 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV
Sbjct: 61  KGLAVKSYVEDEKIIELDVEGPAEVTAGDILTDSDIELVNPDHYLFTIADGYTLKASMTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 121 AKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
           +I  ED++ L++R+L + L +F +  +  K  +     + +    
Sbjct: 181 TIIPEDALGLSARVLIEHLNLFTDLTDVAKATEVMKEAEKVNDEK 225


>gi|150036744|emb|CAM98026.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. mesenteroides]
          Length = 226

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 95/221 (42%), Positives = 141/221 (63%), Gaps = 2/221 (0%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           I EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K
Sbjct: 1   IVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            + L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  
Sbjct: 61  KVVLAIDSDDERSLEIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAV 120

Query: 151 KGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           KG GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+
Sbjct: 121 KGRGYTSADENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           GSI   D+++L ++IL + LG+F++      E    +  + 
Sbjct: 181 GSIKPSDALSLGAKILAEHLGLFMDISPVAAEASVMVEAEP 221


>gi|13518470|ref|NP_084829.1| RNA polymerase alpha subunit [Lotus japonicus]
 gi|22654080|sp|Q9BBQ4|RPOA_LOTJA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|13359011|dbj|BAB33228.1| RNA polymerase alpha subunit [Lotus japonicus]
          Length = 333

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 77/326 (23%), Positives = 156/326 (47%), Gaps = 24/326 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RR+L+  + G  IT  + + + 
Sbjct: 13  LQWKCVES-RIDSKRLYYGRFILSPLMKGQADTIGIAMRRILLGEMEGTCITRAKSEKIS 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I LK +    +  +I  +GPG VTA +I     + +++
Sbjct: 72  HEYSTIVGIQEPVHEILMNLKEIVLKSNLYGIRDASICFKGPGYVTAQNIILPPSVVIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I N+     + + L + +  GY     +  +N   G   IDA++ P++  ++++ S
Sbjct: 132 NTQHIANVTEPIQLCIGLQIERDRGYRI---NTLKNFQDGSYNIDAIFMPVRNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                    + L + I T+GS+T ++++  ASR L D    F++ EE K   + + +  +
Sbjct: 189 Y-VNGNEKQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEEKLNFENNEHKVT 247

Query: 250 LPFNPALLKK------------------VEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           LP                          +++LEL  +  NCL+  NI  + +L+ +++ D
Sbjct: 248 LPLFTCHDLLAKTKLKKKKKEIAFKSIFIDQLELPPKIYNCLKKSNIHTLLELLTKSKED 307

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFL 317
           ++++ +F  + +  I  +L  +    
Sbjct: 308 LMKIEHFRVEDVKHILDIL-EIEKHF 332


>gi|289066858|ref|YP_003434376.1| RNA polymerase alpha subunit [Vigna radiata]
 gi|259020045|gb|ACV90243.1| RNA polymerase alpha subunit [Vigna radiata]
          Length = 333

 Score =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 80/321 (24%), Positives = 154/321 (47%), Gaps = 23/321 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RR+L+  + G  IT V+ + + 
Sbjct: 13  LQWKCVES-RIESKRLYYGRFILSPLMKGQADTIGIAIRRILLGEIEGTCITRVKSEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I +N+K I LK +    +  +I  +GPG +TA DI     +E+++
Sbjct: 72  HEYSTIIGIEESVHEIFMNLKEIVLKSNMYGTQDASISFKGPGYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I N+       +EL + +  GY        +++      IDA + P++ V+Y++ S
Sbjct: 132 NRQHIANVTEPVNFCIELKIERNRGYRIKTLKNFQDESYD---IDARFMPVRNVNYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                    + L + I T+GS+T ++++  AS+ L D    F++ EE    ++++ +  +
Sbjct: 189 Y-VNGNEKQEILFLEIWTNGSLTPKEALYEASQNLIDLFIPFLHAEEENFNLEKNKDKVT 247

Query: 250 LP------------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           LP                          +++LEL  R  NCL+  NI  + +L+  ++ D
Sbjct: 248 LPLFTFHDILVKDKLRKNKKEIALKSIFIDQLELPPRIYNCLKRSNIHTLLELLNNSQED 307

Query: 292 MLRMANFGRKSLVEIKGVLGT 312
           +L++ +F  +    I  +L  
Sbjct: 308 LLKIEHFRVEDGKSILDILKI 328


>gi|161511771|emb|CAP16896.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 229

 Score =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 101/229 (44%), Positives = 146/229 (63%), Gaps = 2/229 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAITSVQIDSVLHEFSTIEGVVEDVTQIILNLKKVS 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK+  D  K + I   GP  VTAGDI    D+ +LNP+  IC +         LT   G 
Sbjct: 61  LKIESDEDKTLEINVAGPANVTAGDIMGDGDVVILNPELPICTVAEGTTFHAVLTADTGR 120

Query: 154 GYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A  ++    + PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ I TDGSI
Sbjct: 121 GYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDIWTDGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           T  ++ +L+++IL + L +F+N  +  KE +  +  +       L   +
Sbjct: 181 TPSEATSLSAKILTEHLAIFVNLNDQAKETEIMVEKEETHKEKMLEMTI 229


>gi|197294604|ref|YP_001799145.1| DNA-directed RNA polymerase subunit alpha [Candidatus Phytoplasma
           australiense]
 gi|171853931|emb|CAM11894.1| DNA-directed RNA polymerase alpha subunit [Candidatus Phytoplasma
           australiense]
          Length = 330

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 106/331 (32%), Positives = 181/331 (54%), Gaps = 11/331 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           + IKP  +E +    E+      I  PL +G A ++GN+LRR L+SSL G AI  V I+G
Sbjct: 5   KFIKPFFVEEL---DEKLTSGKFIFYPLVKGHATSIGNSLRRTLLSSLPGTAIVNVSIEG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDS---HKRVTIFKRGPGVVTAGDIQTVND 124
           V HE ++I GV+ED+  IILN+K I  K+  +S    +++ I   GP  +TA        
Sbjct: 62  VEHEFTTISGVYEDVMTIILNLKKIIFKVDDESNDFEEKLKISLSGPQKITAASFGLPEG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR-TENDPIGLITIDALYSPIKKV 183
           ++++NP+  I  +  D    M  T+ KG GYV AK ++    + +G+I ID+L++P+  V
Sbjct: 122 VKIINPEAPIATISSDINFNMTATIKKGIGYVSAKDNKVHSENQLGVIPIDSLFTPVVNV 181

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE     ++ + ++L+M I T+G++  ++++A A++IL +   +     +    V+ 
Sbjct: 182 AYQVE----KKIGNKEELTMEITTNGALLAKEALATAAKILVEHFNVVSELSQQTPNVEF 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               K    N  L  ++E+L+LSVR  N L+   I  + DL++ +E +++++ + GRKS 
Sbjct: 238 VSERKPEAHNYFLDLEIEQLDLSVRLFNSLKRAGINTVADLVKLSEREVVKLKSLGRKSF 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
            E+K      GL     L +    S EE  +
Sbjct: 298 QELKDKFVEYGLEFNDCLKEALHNSDEEEKE 328


>gi|119662383|emb|CAJ33180.1| RNA polymerase alpha subunit [Lactobacillus sakei subsp. carnosus]
          Length = 212

 Score =  251 bits (642), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 90/211 (42%), Positives = 144/211 (68%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L++SL G A+T +QIDGVLHE S+I GV ED+T IILNIK + LK+  
Sbjct: 1   YGTTLGNSLRRILLASLPGTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKLHV 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + I  +GP  VTA DI + +D+EVLN D  IC +       + +TV KG GYV A
Sbjct: 61  EEDKTIEIDVKGPATVTAADIISDDDVEVLNTDQYICTVAEGGNFHVRMTVKKGRGYVAA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++
Sbjct: 121 VQNKSDDMPIGVLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAIS 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           LA++I+ + L +F++  +  K  +  +  + 
Sbjct: 181 LAAKIMTEHLAIFVDLTDEAKNAEIMVEKEE 211


>gi|332144692|dbj|BAK19506.1| RNA polymerase alpha subunit [Lactobacillus otakiensis]
          Length = 233

 Score =  251 bits (642), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 108/233 (46%), Positives = 151/233 (64%), Gaps = 4/233 (1%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K
Sbjct: 1   VVEPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVK 60

Query: 91  GINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
            I+LK+ G  D  + + I   GP  VTAGDIQ   D+ VLNPD  I  +   A   M LT
Sbjct: 61  KISLKLDGPEDEEENLEIDVIGPADVTAGDIQADGDVTVLNPDLHIATVAEGATFHMRLT 120

Query: 149 VSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            +KG GYV A  ++      PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ I 
Sbjct: 121 ANKGRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDIW 180

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           TDGSIT  ++V+LA++IL + L MF++  +  K  +  +  +       L   
Sbjct: 181 TDGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEKEETHKEKMLEMT 233


>gi|119668297|emb|CAK95503.1| RNA polymerase alpha subunit [Lactobacillus curvatus]
          Length = 207

 Score =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 90/207 (43%), Positives = 143/207 (69%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L++SL G A+T +QIDGVLHE S+I GV ED+T IILNIK + LK+  
Sbjct: 1   YGTTLGNSLRRILLASLPGTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKLHV 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + I  +GP  VTA DI + +D+EVLN D  IC +       + +TV KG GYV A
Sbjct: 61  EEDKTIEIDVKGPATVTAADIISDDDVEVLNTDQYICTVAEGGNFHVRMTVKKGRGYVAA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++
Sbjct: 121 DQNKSDDMPIGVLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAIS 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDI 245
           LA++I+ + L +F++  +  K  +  +
Sbjct: 181 LAAKIMTEHLAIFVDLTDEAKNAEIMV 207


>gi|72534403|emb|CAH59034.1| DNA-directed RNA polymerase alpha chain [Enterococcus sp. LMG
           13603]
          Length = 226

 Score =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 104/226 (46%), Positives = 150/226 (66%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG+ LK+
Sbjct: 1   RGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNIKGLALKL 60

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G GYV
Sbjct: 61  FAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTVKPGRGYV 120

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
            A  ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDGSI  +++
Sbjct: 121 QADENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDGSIIAQEA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           ++LA++IL + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 181 LSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEE 226


>gi|299830620|ref|YP_003735068.1| DNA-directed RNA polymerase alpha subunit [Durinskia baltica]
 gi|297384984|gb|ADI40283.1| DNA-directed RNA polymerase alpha subunit [Durinskia baltica]
          Length = 311

 Score =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 97/296 (32%), Positives = 155/296 (52%), Gaps = 4/296 (1%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               +   L  G   T+GN LRRVL++ L G AI+AV+I G+ HE S+I GV ED+ +I+
Sbjct: 20  HGQFLINSLRPGQGITIGNQLRRVLLNDLGGVAISAVRIAGISHEFSTIPGVREDILEIL 79

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+K I LK    + +   +  +GP VVTA  IQ  + IE++N    I  +    +V +E
Sbjct: 80  LNLKEIVLKSKTQTPQFGRLKIQGPAVVTADLIQLPSTIEIVNSHQYIMTISTSNIVEIE 139

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
                G GY  A     E +    + +DA++ PI+KV + +E+  + +    ++L + I 
Sbjct: 140 FKFEYGTGYKLASQSFLEENENY-LQLDAIFMPIQKVDFKIENVYDNRNSLTERLLLDIW 198

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+GSI+  +++ +A+ I  D     +  +    + +      SL   P     +EEL+LS
Sbjct: 199 TNGSISPNEAIKMAAEITIDLFTALLENKATNSQEEVKSKTSSLSIEPYTNIAIEELQLS 258

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           VR+ NCL+   I  +GDL+Q +   +  + NFGRKS  E+   L      LG+ L 
Sbjct: 259 VRAYNCLKKAQINTVGDLLQYSPEKLQELKNFGRKSADEVFFTLKNK---LGIILK 311


>gi|108792411|emb|CAJ33183.1| RNA polymerase alpha subunit [Lactobacillus agilis]
          Length = 227

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 101/227 (44%), Positives = 150/227 (66%), Gaps = 2/227 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT VQIDGVLHE S+++GV ED+T IILN+
Sbjct: 1   FIIEPLERGYGTTLGNSLRRILLSSLPGAAITDVQIDGVLHEFSTVEGVLEDVTAIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  + + I   GP  VTAGDI   +D+E+LNPD  I  +   A   + +  
Sbjct: 61  KKVALKIDSEDAQALEINVVGPMDVTAGDINGSSDVEILNPDLHIATVAEGASFHVRMNA 120

Query: 150 SKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GYV A  ++ +ND  PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T
Sbjct: 121 DKGRGYVSASDNKAKNDEMPIGVLAIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
           +GSIT  ++++L+++IL + L +F++  +  K  +  I  +      
Sbjct: 181 NGSITPSEAISLSAKILTEHLTLFVDLTDEAKNAEIMIEKEETHKEK 227


>gi|161511765|emb|CAP16893.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           acidilactici]
          Length = 215

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 102/215 (47%), Positives = 142/215 (66%), Gaps = 2/215 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAITSVQIDNVLHEFSTIEGVVEDVTQIILNLKKVS 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK+  D  K + I   GP  VTAGDI    D+ VLNPD  IC +         LT   G 
Sbjct: 61  LKIESDDEKTLDINVVGPANVTAGDIMGDGDVTVLNPDSPICTVAEGTTFHAVLTADTGR 120

Query: 154 GYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A  ++    + PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ I TDGSI
Sbjct: 121 GYTSADENKARKADMPIGVLPIDSIYTPIERVNYQVEKTRVGQRDDYDKLTLDIWTDGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           T  ++ +L+++IL + L +F+N  +  KE +  + 
Sbjct: 181 TPSEATSLSAKILTEHLAIFVNLNDQAKETEIMVE 215


>gi|296126891|ref|YP_003634143.1| DNA-directed RNA polymerase, alpha subunit [Brachyspira murdochii
           DSM 12563]
 gi|296018707|gb|ADG71944.1| DNA-directed RNA polymerase, alpha subunit [Brachyspira murdochii
           DSM 12563]
          Length = 324

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 111/324 (34%), Positives = 180/324 (55%), Gaps = 5/324 (1%)

Query: 1   MIQKNWQELIK-PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M  K   E IK P+ + +             IA+P  RG+A T+GNALRRVL+SS+ G A
Sbjct: 1   MALKEILESIKHPHRVTFEKKD-LTPTYGKFIAQPFERGYAVTVGNALRRVLLSSIPGYA 59

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGD 118
           ITA++IDGV +E  ++ G+ ED   +I+++K + + +      K + + K GP  +TAGD
Sbjct: 60  ITAIKIDGVSNEFENVPGMKEDTIVMIMHLKNVVVSLPDRLETKTIHMKKEGPCTITAGD 119

Query: 119 IQT-VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           +    N+ +V NPD+ I  +       M++ +  G+ YVPA+ +    + +  I IDA+Y
Sbjct: 120 LVANDNEAQVHNPDYYIATIAEGYTFEMDIQIEGGYSYVPAEMNIELVEDVNAIAIDAIY 179

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPI  V Y V+  R GQ +DY KL++ I+T G+I  E +++ A++IL+D L  F++ EE 
Sbjct: 180 SPIVSVKYNVDPIRVGQRIDYGKLTLEIETKGNIAPEKALSQAAKILRDNLKHFMDPEEA 239

Query: 238 KKEVK-EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
             + +  +   K    +    K +EE+E SVR+ N L   ++  +  +  ++E+D+LR+ 
Sbjct: 240 NGDDEKIEETPKDSVLDSLKGKHIEEVEFSVRTANFLMASDLKTLDKVAVKSESDLLRLI 299

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMN 320
                 + EIK  L   G  LGM 
Sbjct: 300 GANEMIIEEIKEKLAEYGAHLGMR 323


>gi|332144688|dbj|BAK19504.1| RNA polymerase alpha subunit [Lactobacillus farraginis]
          Length = 218

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 104/218 (47%), Positives = 149/218 (68%), Gaps = 4/218 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K I
Sbjct: 1   EPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKI 60

Query: 93  NLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT +
Sbjct: 61  SLKLDGPEDEEENLEIDVIGPADVTAGDIQGDSDVTVLNPDLHIATVAEGATFHMRLTAN 120

Query: 151 KGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           +G GYV A  ++      PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ + T+
Sbjct: 121 RGRGYVSAVENKKRATEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDVWTN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           GSIT  ++V+LA++IL + L MF++  +  K  +  + 
Sbjct: 181 GSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVE 218


>gi|118411212|ref|YP_874606.1| DNA-directed RNA polymerase alpha chain [Thalassiosira pseudonana]
 gi|125987639|sp|A0T0Z4|RPOA_THAPS RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|116739959|gb|ABK20829.1| DNA-directed RNA polymerase alpha chain [Thalassiosira pseudonana]
          Length = 313

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 101/315 (32%), Positives = 159/315 (50%), Gaps = 10/315 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E IK   IE   +          + + L  G   T+GN LRRVL+  L+G AIT V+I G
Sbjct: 9   ECIKSEKIESGPM------YGQFLIDSLSSGQGITIGNLLRRVLLGDLQGTAITGVRIAG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V  E S I GV ED+ +I+LN+KGI LK    + +   +  +GP V+TA  IQ   +IE+
Sbjct: 63  VKDEFSLIPGVREDILEILLNLKGIVLKSKTPNRQFGRLRLQGPAVITASSIQLPPEIEI 122

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NP+H I  +    ++ +E  +  G  Y  A    + +     I  DA++ P++KV + V
Sbjct: 123 INPNHYIATISSSHILEIEFKIESGSKYRLANELFS-DKFEDFIETDAIFMPVQKVDFKV 181

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+  +      ++L + I T+GSI+ E ++   S ++ +        +  K++       
Sbjct: 182 ENVYDNSNNIKERLLIDIWTNGSISPEQAIFSGSNLIINLFKSIGEQKINKEKENIKEKN 241

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
              P +P     +EEL+LSVR  NCL+   I  +GDL+  +   +L + NFGRKS  E+ 
Sbjct: 242 HIKPIDPYTHIAIEELQLSVRPYNCLKRAQINTIGDLLDYSPEKLLELKNFGRKSADEVF 301

Query: 308 GVLGTMGLFLGMNLP 322
             L      LG+ L 
Sbjct: 302 ATLKNK---LGIVLK 313


>gi|228017657|gb|ACP52470.1| RNA polymerase alpha subunit [Pinus peuce]
          Length = 335

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 80/329 (24%), Positives = 153/329 (46%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H + N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE   +   +     
Sbjct: 189 YGSGNEI-QEVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSN 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         ++          +++LEL  ++ N LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHVLTDTGETKEKIAFQHIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           ++ +  ++S+ ++  VL        ++ P
Sbjct: 308 KIEHLEKESVEQVLEVLR---KRFAIDPP 333


>gi|218680479|ref|ZP_03528376.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli CIAT 894]
          Length = 208

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 147/208 (70%), Positives = 178/208 (85%), Gaps = 1/208 (0%)

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
           HVIC LD  A +RME TV+ G GYVPA+ +R E+ PIGLI +D+LYSP+KKVSY VE+ R
Sbjct: 1   HVICTLDEGAEIRMEFTVNNGKGYVPAERNRAEDAPIGLIPVDSLYSPVKKVSYKVENTR 60

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           EGQVLDYDKL+MTI+TDGSITGED+VA A+RILQDQLG+F+NF+EP+KE +E+  V  L 
Sbjct: 61  EGQVLDYDKLNMTIETDGSITGEDAVAFAARILQDQLGVFVNFDEPQKETEEEA-VTELA 119

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
           FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGRKSL EIK VL 
Sbjct: 120 FNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRKSLNEIKEVLA 179

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYEDK 339
           +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 180 SMGLHLGMEVPAWPPENIEDLAKRYEDQ 207


>gi|151416838|emb|CAO78490.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gelidum]
          Length = 220

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 94/220 (42%), Positives = 140/220 (63%), Gaps = 2/220 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+
Sbjct: 1   FVIEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L +  D  + + +  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T 
Sbjct: 61  KKVVLAIDSDEERSLEVDIQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTITA 120

Query: 150 SKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T
Sbjct: 121 FKGRGYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           +GSI   D+++L S+IL + L +F++      E    + V
Sbjct: 181 NGSIKPSDALSLGSKILAEHLNLFMDISPVAAEANVMVEV 220


>gi|119668315|emb|CAK95458.1| RNA polymerase alpha subunit [Lactobacillus gallinarum]
          Length = 214

 Score =  251 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 97/214 (45%), Positives = 140/214 (65%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
            EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K 
Sbjct: 1   VEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKK 60

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           + LK   D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V  
Sbjct: 61  LELKSLSDERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQN 120

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI
Sbjct: 121 GRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
              D+++ A++IL +   +F + +   K  +  +
Sbjct: 181 KPNDALSFAAKILVEHFKVFESADADTKFSEVMV 214


>gi|228016268|gb|ACP51103.1| RNA polymerase alpha subunit [Pinus strobus]
 gi|228016903|gb|ACP51728.1| RNA polymerase alpha subunit [Pinus ayacahuite]
 gi|228017272|gb|ACP52091.1| RNA polymerase alpha subunit [Pinus flexilis]
 gi|228017337|gb|ACP52155.1| RNA polymerase alpha subunit [Pinus lambertiana]
          Length = 335

 Score =  251 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 80/329 (24%), Positives = 153/329 (46%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H + N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE   +   +     
Sbjct: 189 YGSGNEI-QEVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSN 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         ++          +++LEL  ++ N LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHVLTDTGETKEKIAFQHIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           ++ +  ++S+ ++  VL        ++ P
Sbjct: 308 KIEHLEKESVEQVLEVLR---KRFAIDPP 333


>gi|269784302|emb|CBH50796.1| alpha subunit of RNA polymerase [Vibrio sp. C 2.4]
 gi|289524814|emb|CBJ94463.1| alpha subunit of RNA polymerase [Vibrio sp. Rd 14.14]
          Length = 266

 Score =  251 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 117/269 (43%), Positives = 176/269 (65%), Gaps = 8/269 (2%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGV 113
           + G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G 
Sbjct: 1   MPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGP 60

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIG 169
           V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG
Sbjct: 61  VVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL 
Sbjct: 121 RLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLD 180

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
            F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            ++L+  N G+KSL EIK VL + GL LG
Sbjct: 238 VELLKTPNLGKKSLTEIKDVLASRGLSLG 266


>gi|237688617|ref|YP_002905234.1| RNA polymerase alpha subunit [Pinus gerardiana]
 gi|226876077|gb|ACO89333.1| RNA polymerase alpha subunit [Pinus gerardiana]
          Length = 335

 Score =  251 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 82/329 (24%), Positives = 154/329 (46%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H + N   G+  IDA++ P++ V+Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDVNYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE   +   +     
Sbjct: 189 YGSGNEI-QEVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSN 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         ++          +++LEL  ++ N LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHVLTDTGETKEKIAFQHIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ +  ++S+ ++  VL        ++ P
Sbjct: 308 RIEHLEKESVEQVLEVLR---KRFAIDPP 333


>gi|29565639|ref|NP_817218.1| RNA polymerase alpha subunit [Pinus koraiensis]
 gi|324986384|ref|YP_004276256.1| RNA polymerase alpha subunit [Pinus lambertiana]
 gi|41688693|sp|Q85X01|RPOA_PINKO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|29469738|gb|AAO74066.1| RNA polymerase alpha subunit [Pinus koraiensis]
 gi|228016141|gb|ACP50978.1| RNA polymerase alpha subunit [Pinus sibirica]
 gi|228016779|gb|ACP51606.1| RNA polymerase alpha subunit [Pinus armandii]
 gi|228017149|gb|ACP51970.1| RNA polymerase alpha subunit [Pinus cembra]
 gi|228017593|gb|ACP52407.1| RNA polymerase alpha subunit [Pinus parviflora var. pentaphylla]
 gi|323514233|gb|ADX89780.1| RNA polymerase alpha subunit [Pinus lambertiana]
          Length = 335

 Score =  251 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 80/329 (24%), Positives = 153/329 (46%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H + N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE   +   +     
Sbjct: 189 YGSGNEI-QEVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSN 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         ++          +++LEL  ++ N LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHVLTDTGETKEKIAFKHIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           ++ +  ++S+ ++  VL        ++ P
Sbjct: 308 KIEHLEKESVEQVLEVLR---KRFAIDPP 333


>gi|162955838|gb|ABY25294.1| RNA polymerase alpha subunit [Vibrio sp. MSSRF28]
 gi|167077375|gb|ABZ10909.1| RNA polymerase alpha subunit [Vibrio sp. MSSRF2]
          Length = 256

 Score =  251 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 115/259 (44%), Positives = 170/259 (65%), Gaps = 8/259 (3%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
              +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+
Sbjct: 1   HAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEIL 60

Query: 87  LNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVR 144
           LN+KG+ +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L    A V 
Sbjct: 61  LNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTDGNAEVA 120

Query: 145 MELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           M + V +G GYVPA    H   ++ PIG + +DA YSP+ K++YTVE+AR  Q  D DKL
Sbjct: 121 MRIKVQRGRGYVPASARIHTDEDDRPIGRLLVDATYSPVDKIAYTVEAARVEQRTDLDKL 180

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + ++T+G+I  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V+
Sbjct: 181 VIDMETNGTIEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVD 237

Query: 262 ELELSVRSTNCLRGENIVY 280
           +LEL+VRS NCL+ E I Y
Sbjct: 238 DLELTVRSANCLKAEAIHY 256


>gi|165910445|gb|ABY73977.1| RNA polymerase alpha subunit [Cuscuta europaea]
          Length = 329

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 81/326 (24%), Positives = 151/326 (46%), Gaps = 26/326 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RR L+  + G  IT V+ +   
Sbjct: 13  LQWKCVES-RIDSKRLFYGRFILSPLIKGQADTIGIAMRRALLGEIEGTCITRVKSEKAS 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +       +I  +GP  VTA DI     +++++
Sbjct: 72  HEYSTIGGIQESVHEILMNLKEIVLRSNLYESCDASICIKGPRHVTAQDIILPPHVQIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + +  GY        ++   G   IDAL+ P++  ++++ S
Sbjct: 132 NTQHIAWLTEPIDFFIGLKIERNRGYFNKVDLHFDD---GSYPIDALFMPVQNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                    + L + I T+GS+T ++++  ++RIL D    F   EE    + +  +   
Sbjct: 189 YGNE---KQEILFLEIWTNGSLTPKEALHESARILIDFFIPFFQMEEENLYLADAKHTIP 245

Query: 250 LPF----------------NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           LP                     L  +++LE   +  NCL+  NI  + DL  + + D+L
Sbjct: 246 LPPLIFYNKVTTLIKKKKKLSLKLIFIDQLEFPPKIYNCLKKSNIFTLFDLFNQKQEDLL 305

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGM 319
           ++ +F    L +IK +LG +G +  +
Sbjct: 306 KIEHF---QLEDIKHILGILGKYFAL 328


>gi|332144690|dbj|BAK19505.1| RNA polymerase alpha subunit [Lactobacillus kisonensis]
          Length = 232

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 107/232 (46%), Positives = 151/232 (65%), Gaps = 4/232 (1%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
            EPL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K 
Sbjct: 1   VEPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKK 60

Query: 92  INLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           I+LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT 
Sbjct: 61  ISLKLDGPEDEEENLEIDVIGPADVTAGDIQGDSDVTVLNPDLHIATVADGATFHMRLTA 120

Query: 150 SKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +KG GYV A  ++      PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ + T
Sbjct: 121 NKGRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           DGSIT  ++V+LA++IL + L MF++  +  K  +  +  +       L   
Sbjct: 181 DGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEKEETHKEKMLEMT 232


>gi|119668289|emb|CAK95500.1| RNA polymerase alpha subunit [Lactobacillus buchneri]
          Length = 227

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 107/227 (47%), Positives = 150/227 (66%), Gaps = 4/227 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K I
Sbjct: 1   EPLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKI 60

Query: 93  NLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT +
Sbjct: 61  SLKLDGPEDEEENLEIDVIGPADVTAGDIQADSDVTVLNPDLHIATVAEGATFHMRLTAN 120

Query: 151 KGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           KG GYV A  ++      PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ I TD
Sbjct: 121 KGRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDIWTD 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           GSIT  ++V+LA++IL + L MF++  +  K  +  +  +       
Sbjct: 181 GSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEKEETHKEKM 227


>gi|161513426|emb|CAP16856.1| DNA-directed RNA polymerase subunit alpha [Pediococcus parvulus]
          Length = 223

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 97/223 (43%), Positives = 148/223 (66%), Gaps = 2/223 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNIK ++LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNIKKVSLKIES 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A
Sbjct: 61  DDEKSLEINVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAVLTADTGRGYVSA 120

Query: 159 KHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   ++ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSI+  ++
Sbjct: 121 DENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSISPSEA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
            +L+++IL + L +F+N  +  ++ +  +  +       L   
Sbjct: 181 TSLSAKILTEHLALFVNLTDEAQDAEIMVEKEETHKEKMLEMS 223


>gi|328814011|gb|AEB52121.1| DNA-directed RNA polymerase alpha chain [Lactobacillus rhamnosus]
          Length = 218

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 93/218 (42%), Positives = 143/218 (65%)

Query: 59  AITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGD 118
           A++++QIDGVLHE S+I GV ED+T IILNIK + LKM+ D  K + I   GP  VTA D
Sbjct: 1   AVSSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNTDEDKNIEIDVNGPAKVTAAD 60

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           I    D+EVLNP+  IC +       + +TV KG GYV A  +++++ PIG++ ID++++
Sbjct: 61  IVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAADQNKSDDMPIGVLPIDSIFT 120

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++IL + L +F+N  +  
Sbjct: 121 PISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKILTEHLDIFVNLTDEA 180

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGE 276
           K  +  +  +       L   +EEL+LSVRS NCL+  
Sbjct: 181 KNAEIMVEKEETHKEKMLEMTIEELDLSVRSYNCLKRA 218


>gi|228016207|gb|ACP51043.1| RNA polymerase alpha subunit [Pinus squamata]
          Length = 335

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 81/329 (24%), Positives = 153/329 (46%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H + N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE   +   +     
Sbjct: 189 YGSGNEI-QEVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSN 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         ++          +++LEL  ++ N LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHVLTDTRETKEKIAFQHIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ +  ++S+ ++  VL        ++ P
Sbjct: 308 RIEHLEKESVEQVLEVLR---KRFAIDPP 333


>gi|71056933|emb|CAH59025.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 221

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 99/221 (44%), Positives = 147/221 (66%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+I GV ED+T IILNIKG+ LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIPGVREDVTQIILNIKGLALKLYA 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + I   GP  VTAGDI   +D+E+LN D VIC++   A     LTV  G GYV A
Sbjct: 61  EEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLVICSVAEGATFHARLTVKPGRGYVQA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI  +++++
Sbjct: 121 DENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIIPQEALS 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           LA++I+ + L +F+N  +  K  +  +  +       L   
Sbjct: 181 LAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMT 221


>gi|47679549|gb|AAT36718.1| RNA polymerase alpha subunit [Chaetoceros gracilis]
          Length = 300

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 92/280 (32%), Positives = 151/280 (53%), Gaps = 1/280 (0%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               +   L  G   T+GN LRRVL+S L G  ITAV+I GV  E S I G+ ED+ +I+
Sbjct: 22  YGQFLINSLRPGQGITIGNLLRRVLLSDLEGTTITAVRIAGVQDEFSIIPGIREDILEIL 81

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+KG+ +K +        +  +GP VVTA  IQ   +IE++NP+H I  +    V+ +E
Sbjct: 82  LNLKGVVVKSATPDISFGRLKIKGPAVVTADSIQLPPNIEIINPNHYIATISTSNVLEIE 141

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
               +G GY  A      +     + IDA++ PI+KV + +E+  +      ++L + I 
Sbjct: 142 FKFERGTGYKLAGQTFC-DKSEDFLQIDAIFMPIQKVDFKIENVYDNSNSITERLFLDIW 200

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+GSI+ +D+++ AS+ + +     +  +  +     +        NP +   +EEL+LS
Sbjct: 201 TNGSISPDDAISYASKFIIEFFNSLLENKITQNLEIIEDTNSLTQLNPHINIAIEELQLS 260

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           VR+ NCL+   I  +GDL++ +   +  + NFGRKS  E+
Sbjct: 261 VRAYNCLKRAQINTIGDLLEYSPEKLQELKNFGRKSADEV 300


>gi|119668341|emb|CAK95468.1| RNA polymerase alpha subunit [Lactobacillus paracasei subsp.
           paracasei]
          Length = 209

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 93/208 (44%), Positives = 142/208 (68%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNIK + LKM+ D  K 
Sbjct: 1   GNSLRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNTDEDKN 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I   GP  VTA DI    D+EVLNP+  IC +       + +TV KG GYV A  +++
Sbjct: 61  IEIDVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAADQNKS 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           ++ PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++I
Sbjct: 121 DDMPIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKI 180

Query: 224 LQDQLGMFINFEEPKKEVKEDINVKSLP 251
           L + L +F+N  +  K  +  +  +   
Sbjct: 181 LTEHLDIFVNLTDEAKNAEIMVEKEETH 208


>gi|71056900|emb|CAH59007.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 219

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 98/217 (45%), Positives = 146/217 (67%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+I GV ED+T IILNIKG+ LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIPGVREDVTQIILNIKGLALKLYA 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + I   GP  VTAGDI   +D+E+LN D VIC++   A     LTV  G GYV A
Sbjct: 61  EEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLVICSVAEGATFHARLTVKPGRGYVQA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI  +++++
Sbjct: 121 DENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIIPQEALS 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           LA++I+ + L +F+N  +  K  +  +  +       
Sbjct: 181 LAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 217


>gi|269784256|emb|CBH50773.1| alpha subunit of RNA polymerase [Vibrio sp. Rd 6.8]
 gi|269784258|emb|CBH50774.1| alpha subunit of RNA polymerase [Vibrio sp. Rd2L5]
 gi|269784260|emb|CBH50775.1| alpha subunit of RNA polymerase [Vibrio sp. Rd 16.13]
          Length = 268

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 116/269 (43%), Positives = 175/269 (65%), Gaps = 8/269 (2%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGV 113
           + G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G 
Sbjct: 1   MPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGP 60

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIG 169
           V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG
Sbjct: 61  VVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL 
Sbjct: 121 RLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLD 180

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
            F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            ++L+  N G+KSL EIK VL + GL L 
Sbjct: 238 VELLKTPNLGKKSLTEIKDVLASRGLSLA 266


>gi|150036746|emb|CAM98260.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. mesenteroides]
          Length = 226

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 94/219 (42%), Positives = 139/219 (63%), Gaps = 2/219 (0%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K +
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKV 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG
Sbjct: 61  VLAIDSDDERSLEIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKG 120

Query: 153 HGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GS
Sbjct: 121 RGYTSADENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTNGS 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           I   D+++L ++IL + LG+F++      E    +    
Sbjct: 181 IKPSDALSLGAKILAEHLGLFMDISPVAAEASVMVEAGP 219


>gi|119668353|emb|CAK95471.1| RNA polymerase alpha subunit [Lactobacillus plantarum]
          Length = 219

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 99/219 (45%), Positives = 147/219 (67%), Gaps = 2/219 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTAIILNVKKIALKLES 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A   M +T + G GYV A
Sbjct: 61  DETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGAHFHMRMTANTGRGYVSA 120

Query: 159 KHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
           + ++   ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T+GSIT  ++
Sbjct: 121 EDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWTNGSITPSEA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           ++L+++IL D L +F+N  +  K     +  +       
Sbjct: 181 ISLSAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKM 219


>gi|161513436|emb|CAP16861.1| DNA-directed RNA polymerase subunit alpha [Pediococcus inopinatus]
          Length = 214

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 97/214 (45%), Positives = 146/214 (68%), Gaps = 2/214 (0%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNIK ++LK+  D
Sbjct: 1   GTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNIKKVSLKIESD 60

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A 
Sbjct: 61  DEKSLEIDVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAILTADTGRGYVSAD 120

Query: 160 HHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
            ++   ++ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSI+  ++ 
Sbjct: 121 ENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSISPSEAT 180

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           +L+++IL + L +F+N  +  K+ +  +  +   
Sbjct: 181 SLSAKILTEHLALFVNLTDEAKDAEIMVEKEETH 214


>gi|66876504|gb|AAY58043.1| RpoA [Cuscuta europaea]
          Length = 329

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 81/326 (24%), Positives = 151/326 (46%), Gaps = 26/326 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RR L+  + G  IT V+ +   
Sbjct: 13  LQWKCVES-RIDSKRLFYGRFILSPLIKGQADTIGIAMRRALLGEIEGTCITRVKSEKAS 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +       +I  +GP  VTA DI     +++++
Sbjct: 72  HEYSTIGGIQESVHEILMNLKEIVLRSNLYESCDASICIKGPRHVTAQDIILPPHVQIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + +  GY        ++   G   IDAL+ P++  ++++ S
Sbjct: 132 NTQHIAWLTEPIDFFIGLKIERNRGYFNKVDLHFDD---GSYPIDALFMPVQNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                    + L + I T+GS+T ++++  ++RIL D    F   EE    + +  +   
Sbjct: 189 YGNE---KQEILFLEIWTNGSLTPKEALHESARILIDFFIPFFQMEEENLYLADAKHTIX 245

Query: 250 LPF----------------NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           LP                     L  +++LE   +  NCL+  NI  + DL  + + D+L
Sbjct: 246 LPPLIFYNKVTTLIKKKKKLSLKLIFIDQLEFPPKIYNCLKKSNIFTLFDLFNQKQEDLL 305

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGM 319
           ++ +F    L +IK +LG +G +  +
Sbjct: 306 KIEHF---QLEDIKHILGILGKYFAL 328


>gi|71056949|emb|CAH59035.1| DNA-directed RNA polymerase alpha chain [Enterococcus hirae]
 gi|72534401|emb|CAH59031.1| DNA-directed RNA polymerase alpha chain [Enterococcus villorum]
          Length = 219

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 100/219 (45%), Positives = 146/219 (66%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+ LKM
Sbjct: 1   RGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGLALKM 60

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
            G   K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV  G GYV
Sbjct: 61  YGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTVKPGRGYV 120

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
            A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI   ++
Sbjct: 121 QADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIEPLEA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           ++L+++I+ + L +F+N  +  K  +  +  +       
Sbjct: 181 MSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 219


>gi|228016646|gb|ACP51475.1| RNA polymerase alpha subunit [Pinus albicaulis]
          Length = 335

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 84/329 (25%), Positives = 156/329 (47%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H + N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK---EVKEDIN 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE        K+  N
Sbjct: 189 YGSGNEI-QEVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNKKKGSN 247

Query: 247 VKSLPFNPALLKK-------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           +   P +  L                +++LEL  ++ N LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHVLTDTGETKEKIAFKHIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           ++ +  ++S+ ++  VL        ++ P
Sbjct: 308 KIEHLEKESVEQVLEVLR---KRFAIDPP 333


>gi|119672801|emb|CAK95516.1| RNA polymerase alpha subunit [Lactobacillus agilis]
          Length = 217

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 101/217 (46%), Positives = 148/217 (68%), Gaps = 2/217 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT VQIDGVLHE S+++GV ED+T IILN+
Sbjct: 1   FIIEPLERGYGTTLGNSLRRILLSSLPGAAITDVQIDGVLHEFSTVEGVLEDVTAIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  + + I   GP  VTAGDI   +D+E+LNPD  I  +   A   + +  
Sbjct: 61  KKVALKIDSEDAQALEINVVGPMDVTAGDINGSSDVEILNPDLHIATVAEGASFHVRMNA 120

Query: 150 SKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GYV A  ++ +ND  PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T
Sbjct: 121 DKGRGYVSASDNKAKNDEMPIGVLAIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           +GSIT  ++++L+++IL + L +F++  E  K  +  
Sbjct: 181 NGSITPSEAISLSAKILTEHLTLFVDLTEEAKNAEIM 217


>gi|161513442|emb|CAP16864.1| DNA-directed RNA polymerase subunit alpha [Pediococcus inopinatus]
          Length = 223

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 98/223 (43%), Positives = 148/223 (66%), Gaps = 2/223 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNIK ++LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNIKKVSLKIES 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A
Sbjct: 61  DDEKSLEIDVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAILTADTGRGYVSA 120

Query: 159 KHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   ++ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSI+  ++
Sbjct: 121 DENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSISPSEA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
            +L+++IL + L +F+N  +  K+ +  +  +       L   
Sbjct: 181 TSLSAKILTEHLALFVNLTDEAKDAEIMVEKEETHKEKMLEMS 223


>gi|255027946|ref|ZP_05299932.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL J2-003]
          Length = 219

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 89/219 (40%), Positives = 139/219 (63%)

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + I  +GPGVVTA DI   +D+E+LNPD  I  L  +A   + L  ++G GY PA
Sbjct: 1   DEEKTLEIDMQGPGVVTAADINYDSDVEILNPDLHIATLSDNAKFHVRLNATRGRGYTPA 60

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++ EN PIG++ +D+++SP+ +V+Y VE+ R GQ  +YDKL+  + TDGSI+ E++V+
Sbjct: 61  DQNKRENMPIGVLPVDSIFSPVIRVNYQVENTRVGQSTNYDKLTFDVLTDGSISPEEAVS 120

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENI 278
           L ++IL + L +F+N  +  ++ +  I  +       L   +EEL+LSVRS NCL+   I
Sbjct: 121 LGAKILSEHLSIFVNLTDEAQKAEIMIEKEESHKEKVLEMTIEELDLSVRSYNCLKRAGI 180

Query: 279 VYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             + +L  ++E DM+++ N GRKSL E+K  L  +GL L
Sbjct: 181 NTVQELADKSEDDMMKVRNLGRKSLEEVKVKLADLGLSL 219


>gi|150036736|emb|CAM98023.1| DNA-directed RNA polymerase alpha chain [Leuconostoc citreum]
          Length = 223

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 93/218 (42%), Positives = 138/218 (63%), Gaps = 2/218 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVV 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG 
Sbjct: 61  LAIDSDDERSLEIDVQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGR 120

Query: 154 GYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI
Sbjct: 121 GYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              D+++L S+IL + L +F++      E    +  + 
Sbjct: 181 KPSDALSLGSKILAEHLNLFMDISPVAAEANVMVEAEP 218


>gi|332144682|dbj|BAK19501.1| RNA polymerase alpha subunit [Lactobacillus buchneri]
          Length = 226

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 106/226 (46%), Positives = 149/226 (65%), Gaps = 4/226 (1%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K I+
Sbjct: 1   PLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKIS 60

Query: 94  LKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT +K
Sbjct: 61  LKLDGPEDEEENLEIDVIGPADVTAGDIQADSDVTVLNPDLHIATVAEGATFHMRLTANK 120

Query: 152 GHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           G GYV A  ++      PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ I TDG
Sbjct: 121 GRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDIWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           SIT  ++V+LA++IL + L MF++  +  K  +  +  +       
Sbjct: 181 SITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEKEETHKEKM 226


>gi|12467|emb|CAA30670.1| RNA polymerase alpha-subunit (AA 1-341) [Zea mays]
          Length = 341

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 90/332 (27%), Positives = 160/332 (48%), Gaps = 26/332 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LEWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGNVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+ +
Sbjct: 72  HEYSTIVGIEESIQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIDD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       +EL + +   Y       +++   G   IDA++ P++ V+Y++ S
Sbjct: 132 TTQPIANLREPVDFCIELQIKRDRAYHTELRKNSQD---GSYPIDAVFMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGED-SVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
              G    ++ L + I T+G +T ++  +  ASR L D    F++ EE     +E+ N  
Sbjct: 189 CGNG-NEKHEILFLEIWTNGKLTPKEGGIYEASRNLIDLFLPFLHTEEEGTSFEENKNRL 247

Query: 249 SLP----------------FNPALLKKVEELELSVRSTNCLRGENI-VYMGDLIQRTEAD 291
           + P                  P     +++LEL  R+ NCL+  NI   + DL+ +TE D
Sbjct: 248 TPPLLTFQKRFTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIPSALLDLLVKTEED 307

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++++ +FG   + + K +  T+   L ++LP 
Sbjct: 308 LIKINSFG---MEDGKLIWDTLEKHLPIDLPK 336


>gi|119668291|emb|CAK95501.1| RNA polymerase alpha subunit [Lactobacillus collinoides]
          Length = 209

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 104/209 (49%), Positives = 148/209 (70%), Gaps = 3/209 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN K I
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNTKKI 60

Query: 93  NLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           +LK+ G  D  + + I  +GP  VTAGDI   +D+ VLNPD  I  +   A   M +T +
Sbjct: 61  SLKLEGPDDEIESMEIDVKGPAQVTAGDITADSDVTVLNPDLYIATVAEGATFHMRMTAN 120

Query: 151 KGHGYVPAKHHR-TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           KG GYV A  ++  E+ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TD 
Sbjct: 121 KGRGYVSADRNKAKEDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDS 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPK 238
           SIT  +S++LA++IL + L MF++  +  
Sbjct: 181 SITPSESISLAAKILTEHLAMFVDLTDEA 209


>gi|150187107|emb|CAK30172.1| RNA polymerase alpha subunit [Streptococcus downei MFe28]
          Length = 219

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 97/217 (44%), Positives = 148/217 (68%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV+K 
Sbjct: 61  AVKSYVEDEKTIELDVTGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGHTLKATMTVAKN 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I 
Sbjct: 121 RGYVPAEGNKNDSAPVGTLAVDSIYTPVKKVNYQVEPARVGSNAGFDKLTIEIMTNGTII 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            ED++ L++R+L + L +F +  E  K  +     +S
Sbjct: 181 PEDALGLSARVLIEHLNLFTDLTEIAKTTEVMKETES 217


>gi|332144684|dbj|BAK19502.1| RNA polymerase alpha subunit [Lactobacillus diolivorans]
          Length = 216

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 106/216 (49%), Positives = 148/216 (68%), Gaps = 4/216 (1%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K I+
Sbjct: 1   PLERGYGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKIS 60

Query: 94  LKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           LK+ G  D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT +K
Sbjct: 61  LKLDGPEDEEENLEIDVIGPADVTAGDIQGDSDVTVLNPDLHIATVAEGATFHMRLTANK 120

Query: 152 GHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           G GYV A  ++      PIG++ +D++Y+PI++V+Y VES R GQ  DYDKL++ + TDG
Sbjct: 121 GRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDYDKLTLDVWTDG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           SIT  ++V+LA++IL + L MF++  +  K  +  +
Sbjct: 181 SITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMV 216


>gi|29427831|sp|Q8MC99|RPOA_PHAAN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|22725692|gb|AAN04898.1| RNA polymerase alpha subunit [Vigna angularis]
          Length = 333

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 80/321 (24%), Positives = 153/321 (47%), Gaps = 23/321 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RR+L+  + G  IT V+ + + 
Sbjct: 13  LQWKCVES-RIESKRLYYGRFILSPLMKGQADTIGIAIRRILLGEIEGTCITRVKSEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I +N+K I LK +    +  +I  +GPG +TA DI     +E+++
Sbjct: 72  HEYSTIIGIEESVHEIFMNLKEIVLKSNMYGTQDASISFKGPGYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I N+     + +EL + +  GY        ++   G   IDA + P++ V+Y++ S
Sbjct: 132 NRQHIANVTEPVNLCIELKIERNRGYRIKTLKNFQD---GSYDIDARFMPVRNVNYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                    + L + I T+GS+T ++++  AS+ L D    F++ EE    +++  +  +
Sbjct: 189 Y-VNGNEKQEILFLEIWTNGSLTPKEALYEASQNLIDLFIPFLHAEEENFNLEKKKHKVT 247

Query: 250 LP------------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           LP                          +++LEL  R  NCL+  NI  + +L+  ++  
Sbjct: 248 LPLFTFHDILVKDKLRKNKKEIALKSIFIDQLELPPRIYNCLKRSNIHTLLELLNNSQEX 307

Query: 292 MLRMANFGRKSLVEIKGVLGT 312
           +L++ +F  +    I  +L  
Sbjct: 308 LLKIEHFRVEDGKSILDILKI 328


>gi|117575075|emb|CAJ84777.1| RNA polymerase alpha subunit [Lactobacillus amylotrophicus]
          Length = 225

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 98/225 (43%), Positives = 146/225 (64%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRVL++SL G+A++ VQIDGVLHE S+I GV ED+T IILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRVLLASLPGSAVSYVQIDGVLHEFSTIPGVLEDVTQIILNLKKLT 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK      K   I   GP  VTAGD++  +++E+LNP+  I  +   A +RM + V +G 
Sbjct: 61  LKSIAADEKLAEIDVEGPATVTAGDLKVDDEVEILNPNQYIATVAEGAHLRMTVAVKQGR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYVPA  +++++ PIG++ +D+L+SPI+KV+Y VE  R G+  DYDKL+M + TDGSIT 
Sbjct: 121 GYVPADQNKSDDMPIGVVPVDSLFSPIEKVNYQVEGTRVGRNNDYDKLTMEVWTDGSITP 180

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
            D+++  ++IL + L +F+N     +     +  +       L  
Sbjct: 181 NDALSFGAKILTEHLNVFMNTNLETEFTDVMVEKEDTKKEKQLEM 225


>gi|161511749|emb|CAP16885.1| DNA-directed RNA polymerase subunit alpha [Pediococcus parvulus]
          Length = 214

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 96/212 (45%), Positives = 146/212 (68%), Gaps = 2/212 (0%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNIK ++LK+  D
Sbjct: 1   GTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNIKKVSLKIESD 60

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A 
Sbjct: 61  DEKSLEINVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAVLTADTGRGYVSAD 120

Query: 160 HHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
            ++   ++ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSI+  ++ 
Sbjct: 121 ENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSISPSEAT 180

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           +L+++IL + L +F+N  +  ++ +  +  + 
Sbjct: 181 SLSAKILTEHLALFVNLTDEAQDAEIMVEKEE 212


>gi|237688685|ref|YP_002905301.1| RNA polymerase alpha subunit [Pinus krempfii]
 gi|226951142|gb|ACO94205.1| RNA polymerase alpha subunit [Pinus krempfii]
          Length = 335

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 81/329 (24%), Positives = 153/329 (46%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +           PL +G A T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIREASIYIVGPKNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H + N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE   +   +     
Sbjct: 189 YGSGNEI-QEVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSN 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         ++          +++LEL  ++ N LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHVLTDTGETKEKIAFQHIFIDQLELPSKTYNSLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ +  ++S+ ++  VL        ++ P
Sbjct: 308 RIEHLEKESVEQVLEVLR---KRFAIDPP 333


>gi|119668359|emb|CAK95474.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
          Length = 221

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 98/220 (44%), Positives = 153/220 (69%), Gaps = 2/220 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRVL++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K ++
Sbjct: 1   PLERGYGTTLGNSLRRVLIASLPGAAITSMQIDGVLHEFSTVEGVTEDVTQIILNLKKVS 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK+  +  K + +  +GP  VTA DIQ  N++ +LNPD  I  +   A + ++LT  KG 
Sbjct: 61  LKLDSEDQKNLELDVKGPAEVTASDIQGDNEVTILNPDLHIATVADGAELHIKLTADKGR 120

Query: 154 GYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY+ A  ++   ++  IG++ ID++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+
Sbjct: 121 GYLSANDNKARMDDLAIGVLPIDSIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSL 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           T  ++V+L ++IL + L MF++  E  +  +  +  +   
Sbjct: 181 TPTEAVSLGAKILTEHLAMFVDLTETAQNAQVMVEKEETH 220


>gi|71056864|emb|CAH58987.1| DNA-directed RNA polymerase alpha chain [Enterococcus canis]
          Length = 217

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 96/217 (44%), Positives = 143/217 (65%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNIKG+ LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNIKGLALKLYA 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
              K + I   GP  VTAGDI   +D+E+LN D  +C +   A     LTV  G GYV A
Sbjct: 61  QEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLYLCTVSEGATFHARLTVKPGRGYVQA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++TE+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI  +++++
Sbjct: 121 DENKTEDMPIGVLPVDSIYTPVRRVNYQVENTRVGNRQDFDKLTMEIWTDGSIIPQEALS 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           L+++IL + L +F+N  +  K  +  +  +       
Sbjct: 181 LSAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKM 217


>gi|150187161|emb|CAK30184.1| RNA polymerase alpha subunit [Streptococcus equi subsp.
           ruminatorum]
          Length = 225

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 94/225 (41%), Positives = 148/225 (65%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG   TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+
Sbjct: 1   FVIEPLERGNGTTLGNSLRRVLLSSLPGAAVTSIRIDGVLHEFDTIPGVREDVMQIILNV 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV
Sbjct: 61  KGLAVKSYVEDEKIIELDVEGPAEVTAGDILTDSDIELVNPDHYLFTIADGYTLKASMTV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           +K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G
Sbjct: 121 AKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
           +I  ED++ L++R+L + L +F +  +  K  +     + +    
Sbjct: 181 TIIPEDALGLSARVLIEHLNLFTDLTDVAKATEVMKEAEKVNDEK 225


>gi|150036762|emb|CAM98031.1| DNA-directed RNA polymerase alpha chain [Leuconostoc carnosum]
          Length = 221

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 94/218 (43%), Positives = 138/218 (63%), Gaps = 2/218 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVV 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG 
Sbjct: 61  LAIDSDEERVLEIDVQGPSEVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGR 120

Query: 154 GYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A  ++   E  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI
Sbjct: 121 GYSSADENKQLREEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              D+++L S+IL + L +F++      E    +  + 
Sbjct: 181 KPSDALSLGSKILAEHLNLFMDISPVAAEANVMVEAEP 218


>gi|213584847|ref|ZP_03366673.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E98-0664]
          Length = 253

 Score =  249 bits (635), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 112/256 (43%), Positives = 176/256 (68%), Gaps = 7/256 (2%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           +GNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G    
Sbjct: 1   MGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEV 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK-- 159
            +T+ K G G VTA DI    D+E++ P HVIC+L D +A + M + V +G GYVPA   
Sbjct: 61  ILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTR 120

Query: 160 -HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
            H   +  PIG + +DA YSP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++ 
Sbjct: 121 IHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIR 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENI 278
            A+ IL +QL  F++  + ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I
Sbjct: 181 RAATILAEQLEAFVDLRDVRQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAI 237

Query: 279 VYMGDLIQRTEADMLR 294
            Y+GDL+QRTE ++L+
Sbjct: 238 HYIGDLVQRTEVELLK 253


>gi|161513422|emb|CAP16854.1| DNA-directed RNA polymerase subunit alpha [Pediococcus damnosus]
          Length = 222

 Score =  249 bits (635), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 100/222 (45%), Positives = 148/222 (66%), Gaps = 2/222 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+T++QIDGVLHE SSI+GV ED+T IILNIK ++LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSSIEGVVEDVTQIILNIKKVSLKIES 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A
Sbjct: 61  DDEKSLEIDVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAILTADTGRGYVSA 120

Query: 159 KHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   ++ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSIT  ++
Sbjct: 121 DENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSITPSEA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
            +L+++IL + L +F+N  +  K+ +  +  +       L  
Sbjct: 181 TSLSAKILTEHLALFVNLTDEAKDAEIMVEKEETHKEKMLEM 222


>gi|119662849|emb|CAJ33217.1| RNA polymerase alpha subunit [Lactobacillus suebicus]
          Length = 219

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 100/219 (45%), Positives = 153/219 (69%), Gaps = 2/219 (0%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRR+L++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K I+LK+
Sbjct: 1   RGYGTTLGNSLRRILLASLPGAAITSIQIDGVLHEFSTVEGVTEDVTQIILNMKKISLKI 60

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             +  K + I  +GP  VTAGDI+   D+EVLNPD  I  +   A + +++T + G GYV
Sbjct: 61  DSEEDKALEIDVKGPAAVTAGDIEADGDVEVLNPDLHIATVADGAELHIQMTANTGRGYV 120

Query: 157 PAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A  ++   ++ PIG++ ID++Y+PI++V+Y VE+AR GQ  DYDKL++ + TDGSIT  
Sbjct: 121 SADDNKARMDDLPIGVLPIDSIYTPIERVNYNVENARVGQRNDYDKLTLDVWTDGSITPS 180

Query: 215 DSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           +S++LA++IL + L MF++  +  K  +  +  +     
Sbjct: 181 ESISLAAKILTEHLSMFVDLTDTAKNAEIMVEKEETHKE 219


>gi|71056939|emb|CAH59028.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 220

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 99/220 (45%), Positives = 146/220 (66%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+I GV ED+T IILNIKG+ LK+  +
Sbjct: 1   GTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIPGVREDVTQIILNIKGLALKLYAE 60

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             K + I   GP  VTAGDI   +D+E+LN D VIC++   A     LTV  G GYV A 
Sbjct: 61  EEKTLEIDITGPATVTAGDIIVDSDVEILNKDLVICSVAEGATFHARLTVKPGRGYVQAD 120

Query: 160 HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
            ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI  +++++L
Sbjct: 121 ENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIIPQEALSL 180

Query: 220 ASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           A++I+ + L +F+N  +  K  +  +  +       L   
Sbjct: 181 AAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMT 220


>gi|13357817|ref|NP_078091.1| DNA-directed RNA polymerase subunit alpha [Ureaplasma parvum
           serovar 3 str. ATCC 700970]
 gi|170762312|ref|YP_001752340.1| DNA-directed RNA polymerase subunit alpha [Ureaplasma parvum
           serovar 3 str. ATCC 27815]
 gi|171920389|ref|ZP_02931716.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma parvum
           serovar 1 str. ATCC 27813]
 gi|183508783|ref|ZP_02958249.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma parvum
           serovar 14 str. ATCC 33697]
 gi|186701955|ref|ZP_02971592.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma parvum
           serovar 6 str. ATCC 27818]
 gi|225550927|ref|ZP_03771876.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 2 str. ATCC 27814]
 gi|12230604|sp|Q9PQN4|RPOA_UREPA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|11261081|pir||B82918 DNA-directed RNA polymerase alpha chain UU257 [imported] -
           Ureaplasma urealyticum
 gi|6899227|gb|AAF30666.1|AE002122_35 DNA-directed RNA polymerase alpha chain [Ureaplasma parvum serovar
           3 str. ATCC 700970]
 gi|168827889|gb|ACA33151.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma parvum
           serovar 3 str. ATCC 27815]
 gi|171902824|gb|EDT49113.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma parvum
           serovar 1 str. ATCC 27813]
 gi|182675728|gb|EDT87633.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma parvum
           serovar 14 str. ATCC 33697]
 gi|186700710|gb|EDU18992.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma parvum
           serovar 6 str. ATCC 27818]
 gi|225380081|gb|EEH02443.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 2 str. ATCC 27814]
          Length = 327

 Score =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 97/328 (29%), Positives = 172/328 (52%), Gaps = 14/328 (4%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
            ++ +K   ++   +  E++NRT++   PL  GF  TLGNALRR+ +SS+ GA++ AV+ 
Sbjct: 1   MRKFLK-YQLDVPSINSEDKNRTVVKIAPLEIGFGDTLGNALRRICLSSIPGASMFAVKF 59

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSG-------------DSHKRVTIFKRGPG 112
            G  HE    +GV ED+T IILN+K + +K+               D   ++ I  +GPG
Sbjct: 60  GGYSHEFQPYEGVKEDITHIILNLKNLAIKIDELIYSEDYFNNLLIDKWPKMKINFKGPG 119

Query: 113 VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT 172
           V+TA DI      E++N D  I  +     V +E+    G G V    ++     + +I 
Sbjct: 120 VITAKDIVCPVGFEIVNQDLYIAEVTKPIDVEIEIFAKTGRGRVDFNTNKDFVSTLHIIA 179

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
            D+ YSP+   +Y VE  ++ +    + L++ I T+G+I+G +++A+A++I+Q  L   +
Sbjct: 180 TDSNYSPVLHYAYNVEMIKDSKSSMSEILTIDIATNGTISGSEAIAIAAKIMQAHLEPIV 239

Query: 233 NFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           N ++   E+      +           +++L+L+VR+ N L+   I    +LI+ T++ +
Sbjct: 240 NIDKTINEMIIMREREEEEKRQNASISIDDLDLTVRAYNALKQSGINTTAELIELTKSQL 299

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMN 320
            ++ N GRKS+ EI   L    L L  +
Sbjct: 300 EKIKNLGRKSVTEIIQKLTERSLELKKD 327


>gi|18860343|ref|NP_569660.1| RNA polymerase alpha subunit [Psilotum nudum]
 gi|22654078|sp|Q8WHZ1|RPOA_PSINU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|18389496|dbj|BAB84248.1| RNA polymerase alpha subunit [Psilotum nudum]
          Length = 340

 Score =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 85/330 (25%), Positives = 158/330 (47%), Gaps = 24/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE    G+           P  +G A T+G A+RR L+  + G +IT  +   V+
Sbjct: 13  LQWKCIESKKEGKRLH-YGRFAVSPFRKGQASTVGVAMRRALLGEVEGTSITYAKFKNVV 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ G+ E + DI++N+K I L+      ++ +I   GP  VTAGDI     +++++
Sbjct: 72  HEYSTLVGIKESIHDILINLKEIVLQSDSYETQKASISILGPRDVTAGDILLPTSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  +     + +EL + +  GY        +    G   IDAL++PI+  +Y++ S
Sbjct: 132 ASQHIATITTAIPLDVELRIERDCGYRTLNL---KESQSGEFFIDALFTPIRNANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
             E      + L + + T+GS+T   +++ ASR L D   +F+N E+ +   + + N  +
Sbjct: 189 F-ESNNKVREILFLEVWTNGSLTPGAALSEASRDLIDLFIIFLNMEKEESIKEIENNELN 247

Query: 250 LPFNPALLKK----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           +   P+                    +++LEL  R+ NCL+   +  + DL++ T+ D+ 
Sbjct: 248 IKNFPSTSISVDIDRMAKEVAFKQIFIDQLELPARAYNCLKKMQVHTVSDLLKYTQYDLK 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++ NFG KS+ ++   L        + LP 
Sbjct: 308 KVKNFGNKSVEQVVEALQE---RFAIQLPK 334


>gi|119662351|emb|CAJ33164.1| RNA polymerase alpha subunit [Lactobacillus ruminis]
          Length = 203

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 99/203 (48%), Positives = 146/203 (71%), Gaps = 2/203 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAAIT VQIDGVLHE S++KGV ED+T+IILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAITDVQIDGVLHEFSTVKGVLEDVTEIILNLKKVA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK++ +  + +     GP  VTAGDI T +D+E+LNPD  IC +   A     +T +KG 
Sbjct: 61  LKLNSEEPQSLEFDIVGPKEVTAGDISTNSDVEILNPDLYICTVADGASFHARMTANKGR 120

Query: 154 GYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GYV A  +  + ++ PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T+GSI
Sbjct: 121 GYVSANENKAKADDMPIGVLAIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINF 234
           T  ++++L+++IL + L +F+N 
Sbjct: 181 TPSEAISLSAKILTEHLALFVNL 203


>gi|154424745|emb|CAL18475.1| RNA polymerase alpha subunit [Streptococcus salivarius]
          Length = 214

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 93/214 (43%), Positives = 144/214 (67%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILNIKG+ 
Sbjct: 1   PLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGLA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +K   +  K + +  +GP  VTAGDI T +DIE++NPDH +  +   A ++  +TV+   
Sbjct: 61  VKSYVEDEKTIELDVQGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGASLKATMTVATNR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  
Sbjct: 121 GYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIP 180

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ED++ L++R+L + L +F +  +  K        
Sbjct: 181 EDALGLSARVLIEHLNLFTDLTDVAKATDVMKET 214


>gi|289524822|emb|CBJ94467.1| alpha subunit of RNA polymerase [Vibrio sp. Cmf 5.9]
          Length = 265

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 116/268 (43%), Positives = 175/268 (65%), Gaps = 8/268 (2%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGV 113
           + G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G 
Sbjct: 1   MPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGP 60

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIG 169
           V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG
Sbjct: 61  VVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL 
Sbjct: 121 RLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLD 180

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
            F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            ++L+  N G+KSL EIK VL + GL L
Sbjct: 238 VELLKTPNLGKKSLTEIKDVLASRGLSL 265


>gi|197131690|gb|ACH47363.1| RNA polymerase alpha subunit [Geranium carolinianum]
          Length = 329

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 77/307 (25%), Positives = 148/307 (48%), Gaps = 11/307 (3%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +   +E    G+        I  PL +G A  +G A+RR L+  + G  IT  + + + H
Sbjct: 14  RWKCVESRADGKR-LYYGRFILSPLKKGQADIIGIAMRRALLGEIEGTCITHAKFEKIPH 72

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E ++I G+ E + +I++N+K I L+ + D  +  +I  RGP  VTA DI   N   +++ 
Sbjct: 73  EYTTIVGIQESIYEILMNLKEIVLRSNLDGTRDASICVRGPRDVTAQDIILPNSAAIVDN 132

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
              I  L       + L + +  GY       T         IDA++ P+K V++++ S 
Sbjct: 133 TQHIVTLTEPIDFCIGLQIDRNRGYSRKIPMPTNFHDDRGYPIDAVFLPVKNVNHSIHSY 192

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
             G    ++ L + I T+GS+T ++++  ASR L +    F++ EE     + + N  + 
Sbjct: 193 ENGS---HEMLFLEIWTNGSLTPKEALREASRKLINLFIPFLHAEEENFHFENNQNEHTD 249

Query: 251 PFNPALLKKVEEL------ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              P  L +++++      EL  R  NCL+   I  + DL+ +    ++++ +F ++ + 
Sbjct: 250 EL-PIDLCELKDIYIDQLVELPARFYNCLKRSGIHTVMDLLNKNTDGLMKITHFRQEDVE 308

Query: 305 EIKGVLG 311
           ++  +L 
Sbjct: 309 KVMNILN 315


>gi|119672799|emb|CAK95483.1| RNA polymerase alpha subunit [Lactobacillus agilis]
          Length = 214

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 100/214 (46%), Positives = 147/214 (68%), Gaps = 2/214 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRR+L+SSL GAAIT VQIDGVLHE S+++GV ED+T IILN+
Sbjct: 1   FIIEPLERGYGTTLGNSLRRILLSSLPGAAITDVQIDGVLHEFSTVEGVLEDVTAIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  + + I   GP  VTAGDI   +D+E+LNPD  I  +   A   + +  
Sbjct: 61  KKVALKIDSEDAQALEINVVGPMDVTAGDINGSSDVEILNPDLHIATVAEGASFHVRMNA 120

Query: 150 SKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GYV A  ++ +ND  PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T
Sbjct: 121 DKGRGYVSASDNKAKNDEMPIGVLAIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +GSIT  ++++L+++IL + L +F++  +  K  
Sbjct: 181 NGSITPSEAISLSAKILTEHLTLFVDLTDEAKNA 214


>gi|161511723|emb|CAP16872.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           acidilactici]
          Length = 229

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 104/229 (45%), Positives = 146/229 (63%), Gaps = 2/229 (0%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++LK+  D
Sbjct: 1   GTTLGNSLRRILLSSLPGAAITSVQIDNVLHEFSTIEGVVEDVTQIILNLKKVSLKIESD 60

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             K + I   GP  VTAGDI    D+ VLNPD  IC +         LT   G GY  A 
Sbjct: 61  DEKTLDINVVGPANVTAGDIMGDGDVTVLNPDSPICTVAEGTTFHAVLTADTGRGYTSAD 120

Query: 160 HHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
            ++    + PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ I TDGSIT  ++ 
Sbjct: 121 ENKARKADMPIGVLPIDSIYTPIERVNYQVEKTRVGQRDDYDKLTLDIWTDGSITPSEAT 180

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           +L+++IL + L +F+N  +  KE +  +  +       L   +EEL+LS
Sbjct: 181 SLSAKILTEHLAIFVNLNDQAKETEIMVEKEETHKEKMLEMTIEELDLS 229


>gi|150036814|emb|CAM98040.1| DNA-directed RNA polymerase alpha chain [Leuconostoc kimchii]
          Length = 226

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 92/226 (40%), Positives = 141/226 (62%), Gaps = 2/226 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVV 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L +  D  + + I  +GP  VTA D+Q   D+E+LNPD  +  +     + M +T  KG 
Sbjct: 61  LAIDSDDERSLEIDVQGPADVTAADLQAGADVEILNPDLHLATVAAGKSLHMTVTAVKGR 120

Query: 154 GYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI
Sbjct: 121 GYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
              D+++L S+IL + L +F++      E    +  + +  N +  
Sbjct: 181 KPSDALSLGSKILAEHLNLFMDISPVAAEASVMVEAEPVATNASDS 226


>gi|119668369|emb|CAK95477.1| RNA polymerase alpha subunit [Lactobacillus ruminis]
          Length = 201

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 98/201 (48%), Positives = 144/201 (71%), Gaps = 2/201 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAAIT VQIDGVLHE S++KGV ED+T+IILN+
Sbjct: 1   FVIEPLERGYGTTLGNSLRRILLSSLPGAAITDVQIDGVLHEFSTVKGVLEDVTEIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK++ +  + +     GP  VTAGDI T +D+E+LNPD  IC +   A     +T 
Sbjct: 61  KKVALKLNSEEPQSLEFDIVGPKEVTAGDISTNSDVEILNPDLYICTVADGASFHARMTA 120

Query: 150 SKGHGYVPAKHH--RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +KG GYV A  +  + ++ PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T
Sbjct: 121 NKGRGYVSANENKAKADDMPIGVLAIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQL 228
           +GSIT  ++++L+++IL + L
Sbjct: 181 NGSITPSEAISLSAKILTEHL 201


>gi|161511729|emb|CAP16875.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 229

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 102/229 (44%), Positives = 147/229 (64%), Gaps = 2/229 (0%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++LK+  D
Sbjct: 1   GTTLGNSLRRILLSSLPGAAITSVQIDSVLHEFSTIEGVVEDVTQIILNLKKVSLKIESD 60

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             K + I   GP  VTAGDI    D+ +LNP+  IC +         LT   G GY  A 
Sbjct: 61  EDKTLEINVAGPANVTAGDIMGDGDVVILNPELPICTVAEGTTFHAVLTADTGRGYTSAD 120

Query: 160 HHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
            ++    + PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ I TDGSIT  ++ 
Sbjct: 121 ENKARKVDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDIWTDGSITPSEAT 180

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           +L+++IL + L +F+N  +  KE +  +  +       L   +EEL+LS
Sbjct: 181 SLSAKILTEHLAIFVNLNDQAKETEIMVEKEETHKEKMLEMTIEELDLS 229


>gi|295137036|ref|YP_003587583.1| RNA polymerase alpha subunit [Pisum sativum]
 gi|133405|sp|P13911|RPOA_PEA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|12180|emb|CAA33668.1| RNA polymerase alpha subunit (AA 1-334) [Pisum sativum]
 gi|293338608|gb|ADE43581.1| RNA polymerase alpha subunit [Pisum sativum]
          Length = 334

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 82/328 (25%), Positives = 159/328 (48%), Gaps = 26/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G  +RR+L+  + G  IT  + + + 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLMKGQADTIGITMRRILLGEIEGTCITRAKSEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +    +  +I  +GPG VTA DI   + +EV++
Sbjct: 72  HEYSTIVGIQESIHEILMNLKEIVLRSNLYGTREASICFKGPGYVTAQDIILPS-VEVID 130

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL     + +EL + +  GY     +  ++   G  TIDA++ P++  ++++ S
Sbjct: 131 NTQHIANLTEPINLCIELQIERKRGYRIKTLNNIQD---GSYTIDAVFMPVRNANHSIHS 187

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                    + L + I T+GS+T ++++  ASR L D    F++ EE     + + +  +
Sbjct: 188 Y-VNGNQKQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEENLNFENNQHKMT 246

Query: 250 LPFNPALLKK--------------------VEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           LP                            +++LEL  R  NCL+  NI  + +L+ +++
Sbjct: 247 LPLFTFHDHDRFVKDKLRKNQKEITLKSIFIDQLELPPRIYNCLKKSNIHTVLELLNKSQ 306

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            D++++ +F  + L  I  +L     F+
Sbjct: 307 EDLMKIEHFRVEDLKFILNILQIENHFV 334


>gi|171920602|ref|ZP_02931853.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 13 str. ATCC 33698]
 gi|185179070|ref|ZP_02964804.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 5 str. ATCC 27817]
 gi|188024263|ref|ZP_02996959.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 7 str. ATCC 27819]
 gi|188518671|ref|ZP_03004106.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 11 str. ATCC 33695]
 gi|188524445|ref|ZP_03004458.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 12 str. ATCC 33696]
 gi|195867590|ref|ZP_03079592.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 9 str. ATCC 33175]
 gi|198273610|ref|ZP_03206145.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 4 str. ATCC 27816]
 gi|209554135|ref|YP_002284656.1| DNA-directed RNA polymerase subunit alpha [Ureaplasma urealyticum
           serovar 10 str. ATCC 33699]
 gi|225551180|ref|ZP_03772126.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 8 str. ATCC 27618]
 gi|171903312|gb|EDT49601.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 13 str. ATCC 33698]
 gi|184209067|gb|EDU06110.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 5 str. ATCC 27817]
 gi|188018926|gb|EDU56966.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 7 str. ATCC 27819]
 gi|188997781|gb|EDU66878.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 11 str. ATCC 33695]
 gi|195659713|gb|EDX53093.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 12 str. ATCC 33696]
 gi|195660647|gb|EDX53902.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 9 str. ATCC 33175]
 gi|198249638|gb|EDY74419.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 4 str. ATCC 27816]
 gi|209541636|gb|ACI59865.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 10 str. ATCC 33699]
 gi|225378995|gb|EEH01360.1| DNA-directed RNA polymerase, alpha subunit [Ureaplasma urealyticum
           serovar 8 str. ATCC 27618]
          Length = 327

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 97/328 (29%), Positives = 172/328 (52%), Gaps = 14/328 (4%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
            ++ +K   ++   +  E++NRT++   PL  GF  TLGNALRR+ +SS+ GA++ AV+ 
Sbjct: 1   MRKFLK-YQLDVPSINSEDKNRTVVKIAPLEIGFGDTLGNALRRICLSSIPGASMFAVKF 59

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSG-------------DSHKRVTIFKRGPG 112
            G  HE    +GV ED+T IILN+K + +K+               D   ++ I  +GPG
Sbjct: 60  GGYSHEFQPYEGVKEDITHIILNLKNLAIKIDELIYSEDYFNNLLIDKWPKMKINFKGPG 119

Query: 113 VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT 172
           V+TA DI      E++N D  I  +     V +E+    G G V    ++     + +I 
Sbjct: 120 VITAKDIVCPVGFEIVNQDLYIAEVTKPIDVEIEIFAKTGRGRVDFNTNKDFVSTLHIIA 179

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
            D+ YSP+   +Y VE  ++ +    + L++ I T+G+I+G +++A+A++I+Q  L   +
Sbjct: 180 TDSNYSPVLHYAYNVEMIKDSKSSMSEILTIDIATNGTISGSEAIAIAAKIMQAHLEPIM 239

Query: 233 NFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           N ++   E+      +           +++L+L+VR+ N L+   I    +LI+ T++ +
Sbjct: 240 NIDKTINEMIIMREREEEEKRQNASISIDDLDLTVRAYNALKQSGINTTAELIELTKSQL 299

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMN 320
            ++ N GRKS+ EI   L    L L  +
Sbjct: 300 EKIKNLGRKSVTEIIQKLTERSLELKKD 327


>gi|76563869|gb|ABA46366.1| RNA polymerase alpha subunit [Photobacterium halotolerans]
          Length = 252

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 111/253 (43%), Positives = 167/253 (66%), Gaps = 7/253 (2%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
             EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+K
Sbjct: 3   TLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDVLEILLNLK 62

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTV 149
           G+ +K+ G     +++ K G G V AGDI    D+E+ NP+HVIC+L  D A + M + V
Sbjct: 63  GLAVKVEGKDEVILSLSKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNADISMRIKV 122

Query: 150 SKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            +G GYVPA    H   +  PIG + +DA +SP+ +++Y+VE+AR  Q  D DKL + ++
Sbjct: 123 ERGRGYVPASARIHSDEDERPIGRLLVDATFSPVDRIAYSVEAARVEQRTDLDKLVIDME 182

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V++LEL+
Sbjct: 183 TNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELT 239

Query: 267 VRSTNCLRGENIV 279
           VRS NCL+ E I 
Sbjct: 240 VRSANCLKAEAIH 252


>gi|47679555|gb|AAT36721.1| RNA polymerase alpha subunit [Cylindrotheca fusiformis]
          Length = 291

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 93/281 (33%), Positives = 158/281 (56%), Gaps = 2/281 (0%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               +   L  G   T+GN LRRVL++ L G AI+A +I GV HE S+I GV ED+ +I+
Sbjct: 12  HGQFLINSLKPGQGITIGNQLRRVLLNDLGGVAISAARIAGVSHEFSTIPGVREDILEIL 71

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+KGI LK    + +   +  +GP VVTA  IQ  +D+E++NP+H +  +    V+ +E
Sbjct: 72  LNLKGIVLKSKTQTAQFGRLKIQGPTVVTADLIQLPSDLEIVNPNHYLMTISTSNVLEIE 131

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
                G GY         ++    + +D ++ P++KV++ +E+  +      +++ + I 
Sbjct: 132 FKFEYGTGYKLTSQ-AFLDESDNYLQLDTIFMPVQKVNFKIENVYDNNNNITEQVFLDIW 190

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK-EDINVKSLPFNPALLKKVEELEL 265
           T+GSI+  +++  A++I  D   + +  +E K++ K E   V S+   P     +EEL+L
Sbjct: 191 TNGSISPNEALKSAAQITIDLFELLLKNKETKEKNKLEATKVPSISIEPYTNIAIEELQL 250

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           SVR+ NCL+   I  +GDL++ +   +  + NFGRKS  E+
Sbjct: 251 SVRAYNCLKKAQINTVGDLLKYSPEKLQELKNFGRKSADEV 291


>gi|150036838|emb|CAM98284.1| DNA-directed RNA polymerase alpha chain [Leuconostoc lactis]
          Length = 228

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 92/228 (40%), Positives = 142/228 (62%), Gaps = 2/228 (0%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D
Sbjct: 1   GTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSD 60

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A 
Sbjct: 61  DERSLEIDVQGPAEVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSAD 120

Query: 160 HHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
            ++   E  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D++
Sbjct: 121 ENKQLREEMPIGVLAVDSIYTPIERVNYHVENTRVGARDDYDKLTFDIWTNGSIKPSDAL 180

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
           +L ++IL + L +F++      E    +  + +  + +    +E+L+L
Sbjct: 181 SLGAKILAEHLNLFMDISPVAAEANVMVEAEPVAVSASDSAPIEDLDL 228


>gi|315320586|ref|YP_004072643.1| DNA-directed RNA polymerase subunit alpha [Thalassiosira oceanica
           CCMP1005]
 gi|283569059|gb|ADB27596.1| DNA-directed RNA polymerase subunit alpha [Thalassiosira oceanica
           CCMP1005]
          Length = 332

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 99/298 (33%), Positives = 155/298 (52%), Gaps = 6/298 (2%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               + + L  G   T GN LRRVL+  L G AIT V+I GV  E S I GV ED+ +I+
Sbjct: 39  YGQFLIDSLNSGQGITNGNLLRRVLLGDLEGIAITGVRIAGVKDEFSLIPGVREDILEIL 98

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+KG+ LK +  + +   +  +GP V+TA  IQ   +IE +NP+H I  +    +V +E
Sbjct: 99  LNLKGVILKSNIVTRQFGRLRIQGPAVITASSIQLPPEIETINPNHYIATISTSDIVEIE 158

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
             +  G  Y  A    + +     I  DA++ P++KV + VE+  +      ++L + + 
Sbjct: 159 FKIESGRQYRLANELFS-DKFEDFIETDAIFMPVQKVDFKVENVYDNSNNIKERLFLDVW 217

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL--PFNPALLKKVEELE 264
           T+GSI  +D++  AS  +          +      KE+I  K+   P +P +   +EEL+
Sbjct: 218 TNGSIAPQDAIISASNSIIAFFQSISEQKVKNALEKENIIEKNQVKPIDPYIHIAIEELQ 277

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           LSVR  NCL+   I  +GDL++ +   +L + NFGRKS  E+   L      LG+ L 
Sbjct: 278 LSVRPYNCLKRARINTIGDLLEYSPEKLLELKNFGRKSADEVFATLKNK---LGIVLK 332


>gi|157493287|gb|ABV58009.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 259

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 115/267 (43%), Positives = 177/267 (66%), Gaps = 13/267 (4%)

Query: 35  LPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL 94
           L RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +
Sbjct: 1   LERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAV 60

Query: 95  KM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVVRMELTVSKG 152
           ++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L   +A + M + V +G
Sbjct: 61  RVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVERG 120

Query: 153 HGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
            GYVPA    H   +  PIG + +DA +SP+ K++Y+VE     Q  D DKL + ++T+G
Sbjct: 121 RGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVE-----QRTDLDKLVIDMETNG 175

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           ++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V++LEL+VRS
Sbjct: 176 TLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRS 232

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMA 296
            NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 233 ANCLKAEAIHYIGDLVQRTEVELLKTP 259


>gi|225621052|ref|YP_002722310.1| DNA-directed RNA polymerase subunit alpha [Brachyspira
           hyodysenteriae WA1]
 gi|225215872|gb|ACN84606.1| DNA-directed RNA polymerase alpha subunit [Brachyspira
           hyodysenteriae WA1]
          Length = 324

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 105/313 (33%), Positives = 174/313 (55%), Gaps = 4/313 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
            P+ + +             IA+P  RG+A T+GNALRRVL+SS+ G AIT ++IDGV +
Sbjct: 12  HPHRVTFEKKD-LTPTYGKFIAQPFERGYAVTVGNALRRVLLSSIPGYAITTIKIDGVSN 70

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVN-DIEVL 128
           E  ++ G+ ED   +I+++K + + +      K + + K GP V+TAGD+   + + +V 
Sbjct: 71  EFENVPGMKEDTIVMIMHLKNVVVSLPSHMDTKTIHMKKEGPCVITAGDLVADDTEAQVH 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NPD+ I  +       M++ +  G+ YVPA+ +    + I  I IDA+YSPI  V Y V+
Sbjct: 131 NPDYYIATIAEGYTFEMDIQIEGGYSYVPAEMNIELLEDINAIAIDAIYSPIVSVKYNVD 190

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK-EDINV 247
             R GQ +DY KL++ I+T G+I  + +++ A++IL+D L  F++ EE   + +  +   
Sbjct: 191 PIRVGQRIDYGKLTLEIETKGNIAPDKALSQAAKILRDNLKHFMDPEEANGDDEKIEETP 250

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           K    +    K +EE+E SVR+ N L   ++  +  +  +T+AD+LR+       + EIK
Sbjct: 251 KDSVLDSLKGKHIEEVEFSVRTANFLMASDLKTLDKVAVKTDADLLRLIGANEMIIEEIK 310

Query: 308 GVLGTMGLFLGMN 320
             L      LGM 
Sbjct: 311 EKLAEYNAHLGMR 323


>gi|150036810|emb|CAM98038.1| DNA-directed RNA polymerase alpha chain [Fructobacillus
           pseudoficulneus]
          Length = 235

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 97/235 (41%), Positives = 144/235 (61%), Gaps = 2/235 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL+SSL G A+  VQIDGV+HE S++ GV ED+T +ILN+K +      
Sbjct: 1   YGTTLGNSLRRVLLSSLPGVAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVVFATDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
                + I  +GP  VTA D+    DIEVLNPD  I  L     + M +T  KG GY  A
Sbjct: 61  AEEHALEIDVQGPKDVTAADLMGSADIEVLNPDLHIATLAAGKALHMTVTAVKGRGYSSA 120

Query: 159 KHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
           + ++   +  PIG++T+D++Y+PI++V+Y VE+ R G   DYDKL+M + T+GSI   D+
Sbjct: 121 EENKQLRDEMPIGVLTVDSIYTPIERVNYHVENKRVGSRDDYDKLTMEVWTNGSIKPSDA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTN 271
           ++L S+IL + L +F +     ++ K  +  +      A    +E+L+LSVRS N
Sbjct: 181 LSLGSKILTEHLNLFTDISPVAQDTKVMVESEPAANTAADAAPIEDLDLSVRSYN 235


>gi|300089411|gb|ADJ67857.1| RNA polymerase alpha-subunit [Photobacterium jeanii]
          Length = 248

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 111/251 (44%), Positives = 165/251 (65%), Gaps = 7/251 (2%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
           +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+
Sbjct: 1   VTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDVLEILLNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELT 148
           KG+ +K+ G     +T+ K G G V AGDI    D+E+ NP+HVIC+L  D A + M + 
Sbjct: 61  KGLAVKVEGKDEVILTLNKSGAGPVVAGDITHDGDVEIANPEHVICHLTDDNADISMRIK 120

Query: 149 VSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           V +G GYVPA    H   +  PIG + +DA +SP+ +++Y VE+AR  Q  D DKL + +
Sbjct: 121 VERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDRIAYAVEAARVEQRTDLDKLVIDM 180

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
            T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V++LEL
Sbjct: 181 QTNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLEL 237

Query: 266 SVRSTNCLRGE 276
           +VRS NCL+ E
Sbjct: 238 TVRSANCLKAE 248


>gi|308746019|ref|YP_003934590.1| RNA polymerase alpha subunit [Cheilanthes lindheimeri]
 gi|302375452|gb|ADL29826.1| RNA polymerase alpha subunit [Cheilanthes lindheimeri]
          Length = 342

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 81/330 (24%), Positives = 142/330 (43%), Gaps = 25/330 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           I+   +E     +        +  P  RG A T+G A+RR L   + G +IT  +  GV+
Sbjct: 13  IQWKCLESKTESKRLH-YGRFVVSPFKRGQASTVGIAMRRALSQEVGGTSITRAKFHGVV 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + D+++N+K I LK   +          GP  VTAGD      ++ ++
Sbjct: 72  HEYSTITGIQETIHDVLVNLKEIVLKSDSNDIWEAFPSVMGPKEVTAGDTSLPPRVKAID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  +       +EL + +  GY     +   +   G  +IDA++ P++ V+Y++  
Sbjct: 132 NSQYIATITQPISSNIELKIERDCGYRIENSNECRD---GQFSIDAVFMPVRNVNYSIHL 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G+    +   + I T+GS T  ++++ AS+ L D    F   +       ED    S
Sbjct: 189 FGNGRAT-QEISFIEIWTNGSPTPHEALSEASKKLIDLSTPFSGVKCRDVSFLEDHEDSS 247

Query: 250 LPFNPALL-----------------KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                  L                   +++LEL  R+ NCL+   I  + D +  +  D+
Sbjct: 248 DSTRSPFLQLQFGNACKLEGKLFENMFIDQLELPARAFNCLKRAEIHTIADSLNYSREDL 307

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
            ++ NFG+KS+ ++   L          LP
Sbjct: 308 SKIRNFGQKSVDQVSKALWE---RFSKELP 334


>gi|119662319|emb|CAJ33147.1| RNA polymerase alpha subunit [Lactobacillus kalixensis]
          Length = 208

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 95/207 (45%), Positives = 140/207 (67%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K +
Sbjct: 1   EPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LK   D  K + +   GP  VTA D++  +D++VLNPD  IC++     + M++ V  G
Sbjct: 61  ELKSLSDEQKVIELDVEGPATVTADDLKVDSDVQVLNPDQYICSIAEGGHLHMQIAVKNG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYV A  +++++ PIG+I +D+L+SPIKKV+Y VE+ R G+  D+DKL+  I TDGSI 
Sbjct: 121 RGYVAANDNKSDDMPIGVIPVDSLFSPIKKVNYQVEATRVGKRDDFDKLTFEIWTDGSIN 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKK 239
             D+++ A++IL +   +F + +   K
Sbjct: 181 PNDALSFAAKILVEHFKVFESADASTK 207


>gi|150036818|emb|CAM98041.1| DNA-directed RNA polymerase alpha chain [Leuconostoc fallax]
          Length = 222

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 94/220 (42%), Positives = 142/220 (64%), Gaps = 2/220 (0%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
            EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T +ILN+K 
Sbjct: 1   VEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKK 60

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           + L +  D  K + I  +GP  VTA D+Q   DIEVLNP+  +  +     + M +T  K
Sbjct: 61  VVLAIDSDEEKSLEIDVQGPAEVTAADLQGSADIEVLNPELHLATVAAGKSLHMTVTAVK 120

Query: 152 GHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           G GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R GQ  DYDKL+  I T+G
Sbjct: 121 GRGYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGQRDDYDKLTFDIWTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           SI   D+++L ++IL + L +F +      E +  ++V+ 
Sbjct: 181 SIKPSDALSLGAKILSEHLNLFTDISSVAAETEVMVDVEQ 220


>gi|60117163|ref|YP_209497.1| RNA polymerase alpha subunit [Huperzia lucidula]
 gi|68053058|sp|Q5SD25|RPOA_HUPLU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|50659971|gb|AAT80693.1| RNA polymerase alpha subunit [Huperzia lucidula]
          Length = 336

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 90/325 (27%), Positives = 162/325 (49%), Gaps = 22/325 (6%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
              +E   +  E    +  I  PL  G A+T+G  +RR L+  ++G  IT  + + + HE
Sbjct: 18  WRCVESK-VESERLFYSRFILSPLKVGQANTIGLVMRRALLGEIKGTCITCAKFENITHE 76

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            S++ G+ E + DI++N K I LK      ++  I   GP  VTA DI+    +EV++P 
Sbjct: 77  YSTMDGIQESVHDILINSKEIVLKSKSSEAQKAFISIVGPRRVTAQDIELPTSVEVIDPM 136

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             I  +     + +EL + K  GY        ++   G  T+DA+++PI+ V+Y++    
Sbjct: 137 QHIATITKKVKLNIELKIEKDSGYRRQNIVEYKD---GNFTVDAVFTPIRSVNYSIHCFE 193

Query: 192 -EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
              + +  + L   I ++GSIT E+++  ASR   +    F+  E+ K++ K +   +S 
Sbjct: 194 SHDKSIMKEMLLYEIWSNGSITPEEAIYEASRSSINLFLPFLQAEKEKEDFKGEDIHESN 253

Query: 251 PFNPA--------------LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
             +P+                  +E+LELS ++ N L+  N+  + DL+  ++ D+++M 
Sbjct: 254 ALHPSVSIVVDQMAKKVTFQHIFIEQLELSPKAYNFLKKINVHTISDLLDYSQDDLMKMK 313

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNL 321
           NFG+KS+ +I   L  +    GM L
Sbjct: 314 NFGKKSVEQI---LEALQKRFGMRL 335


>gi|165910443|gb|ABY73976.1| RNA polymerase alpha subunit [Cuscuta epilinum]
          Length = 330

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 82/328 (25%), Positives = 151/328 (46%), Gaps = 26/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +  +    I  PL +G A T+G A+RR L+  + G  IT V+ +   
Sbjct: 13  LQWKCVES-RIDSKRLSYGRFILSPLIKGQADTIGIAMRRALLGEIEGTCITRVKSEKAS 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +       +I  +GP  VTA DI     +++++
Sbjct: 72  HEYSTIGGIQESVHEILMNLKEIVLRSNLYGTCDASICIKGPRHVTAQDIILPPHVQIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + +  GY        ++   G+  IDAL+ P++  ++++ S
Sbjct: 132 NTQHIAWLTEPIDFFIGLKIERNRGYFNKVDLHFDD---GIYPIDALFMPVQNANHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV-- 247
                    + L + I T+GS+T ++++  A+RIL D    F + EE    + +  +   
Sbjct: 189 YGNE---KQEILFLEIWTNGSLTPKEALHEAARILIDFFIPFFHMEEENLYLADAEHTIP 245

Query: 248 --------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         K        L  +++LE   +  NCL   NI  + DL    E D+L
Sbjct: 246 LSSLIFYNKVTKLIKKKKKLSLKLIFIDQLEFPPKIYNCLTKSNIFTLFDLFNHKEEDLL 305

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           ++ +F    L +IK +LG +  +  + L
Sbjct: 306 KIEHF---QLEDIKKILGILAKYFALYL 330


>gi|119662343|emb|CAJ33160.1| RNA polymerase alpha subunit [Lactobacillus plantarum]
          Length = 204

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 99/204 (48%), Positives = 145/204 (71%), Gaps = 2/204 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTAIILNVKKIALKLES 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A   M +T + G GYV A
Sbjct: 61  DETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGAHFHMRMTANTGRGYVSA 120

Query: 159 KHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
           + ++   ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T+GSIT  ++
Sbjct: 121 EDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWTNGSITPSEA 180

Query: 217 VALASRILQDQLGMFINFEEPKKE 240
           ++L+++IL D L +F+N  +  K 
Sbjct: 181 ISLSAKILTDHLSIFVNLTDEAKN 204


>gi|119662295|emb|CAJ33134.1| RNA polymerase alpha subunit [Lactobacillus crispatus]
          Length = 212

 Score =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 96/212 (45%), Positives = 138/212 (65%)

Query: 35  LPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL 94
           L RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + L
Sbjct: 1   LERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLEL 60

Query: 95  KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHG 154
           K   D  K + +   GP  VTA D++   D++VLNPD  IC +     + MEL V  G G
Sbjct: 61  KSLSDEQKVIELDIEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMELAVKNGRG 120

Query: 155 YVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
           YV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   
Sbjct: 121 YVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPN 180

Query: 215 DSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           D+++ A++IL +   +F + +   K  +  + 
Sbjct: 181 DALSFAAKILVEHFKVFESADANAKFSEVMVE 212


>gi|150036808|emb|CAM98277.1| DNA-directed RNA polymerase alpha chain [Fructobacillus
           pseudoficulneus]
          Length = 235

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 97/235 (41%), Positives = 144/235 (61%), Gaps = 2/235 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRVL+SSL G A+  VQIDGV+HE S++ GV ED+T +ILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRVLLSSLPGVAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVV 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
                     + I  +GP  VTA D+    DIEVLNPD  I  L     + M +T  KG 
Sbjct: 61  FATDSAEEHALEIDVQGPKDVTAADLMGSADIEVLNPDLHIATLAAGKSLHMTVTAVKGR 120

Query: 154 GYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A+ ++   +  PIG++T+D++Y+PI++V+Y VE+ R G   DYDKL+M + T+GSI
Sbjct: 121 GYSSAEENKQLRDEMPIGVLTVDSIYTPIERVNYHVENKRVGSRDDYDKLTMEVWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
              D+++L S+IL + L +F +     ++ K  +  +      A    +E+L+LS
Sbjct: 181 KPSDALSLGSKILTEHLNLFTDISPVAQDTKVMVESEPAANTAADAAPIEDLDLS 235


>gi|51859691|gb|AAU11125.1| RNA polymerase alpha subunit [Psathyrostachys caduca]
          Length = 339

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 85/298 (28%), Positives = 145/298 (48%), Gaps = 21/298 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V 
Sbjct: 13  LQWKCVES-RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I NL       ++L + +  GY        +N   G   IDA+  P++ V+Y++ S
Sbjct: 132 XAQPIANLTEPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +
Sbjct: 189 CGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFT 247

Query: 250 LP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
            P                  P     +++LEL+ R+ NCL+  NI  + DL+ +TE D
Sbjct: 248 PPLFTFQKRLTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEED 305


>gi|11465443|ref|NP_045166.1| RNA polymerase alpha subunit [Cyanidium caldarium]
 gi|12230610|sp|Q9TLV2|RPOA_CYACA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|6466346|gb|AAF12928.1|AF022186_50 unknown [Cyanidium caldarium]
          Length = 310

 Score =  246 bits (627), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 102/310 (32%), Positives = 169/310 (54%), Gaps = 11/310 (3%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             +E +V+   E      + EPL  G A T+GNALRRVL+S + G  I +V+I G+ HE 
Sbjct: 11  ECLESMVINSREI-YGKFMIEPLSYGQAITVGNALRRVLLSDVPGVTIVSVRIAGINHEF 69

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           S++KGV ED+ +I+LN+K I LK +   ++   +  +GP +VT+G I+   DI V++P  
Sbjct: 70  STVKGVKEDVLEILLNLKNIVLKGNVLKNQIGRLKVQGPAIVTSGQIEFPLDITVVDPCQ 129

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +  +  + MEL V K  GY   +    +  P+  + ID+++ P+KKV+Y VE   +
Sbjct: 130 YIATISGNDYLEMELKVEKSSGYKLVETFSKK-SPLDFLPIDSIFMPVKKVNYYVEEILD 188

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            +V  Y+KL + + T+GS++ + S+  AS  L          +       ++ +      
Sbjct: 189 SKVA-YEKLILELWTNGSLSPQQSINYASDNLVKLFNPLRVLD-----FSKESSSVYEQN 242

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +    K +EEL LSVR+ NCL+   +  +GDL++ +  D+L + NFG+KS+ E+   L  
Sbjct: 243 SLIKQKLIEELCLSVRAYNCLKRVQVDSIGDLLEYSIGDLLEIKNFGQKSVEEVSKALY- 301

Query: 313 MGLFLGMNLP 322
                G+ L 
Sbjct: 302 --KKFGVKLK 309


>gi|119668303|emb|CAK95505.1| RNA polymerase alpha subunit [Lactobacillus curvatus]
          Length = 217

 Score =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 90/217 (41%), Positives = 143/217 (65%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRR+L++SL G A+T +QIDGVLHE S+I GV ED+T IILNIK + LK+  +  K
Sbjct: 1   LGNSLRRILLASLPGTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKLHVEEDK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + I  +GP  VTA DI + +D+EVLN D  IC +       + +TV KG GYV A  ++
Sbjct: 61  TIEIDVKGPATVTAADIISDDDVEVLNTDQYICTVAEGGNFHVRMTVKKGRGYVAADQNK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
           +++ PIG++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++
Sbjct: 121 SDDMPIGVLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAK 180

Query: 223 ILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           I+ + L +F++  +  K  +  +  +       L   
Sbjct: 181 IMTEHLAIFVDLTDEAKNAEIMVEKEETHKEKMLEMT 217


>gi|71056866|emb|CAH58988.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           hermanniensis]
          Length = 214

 Score =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 98/213 (46%), Positives = 143/213 (67%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAAIT +QIDG LHE S+IKGV ED+  IILNIKG+ LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAITNIQIDGALHEFSTIKGVREDVVQIILNIKGLALKLFA 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G GYV A
Sbjct: 61  EEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTVKPGRGYVQA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDGSI  +++++
Sbjct: 121 DENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDGSIIAQEALS 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           LA++IL + L +F+N  +  K  +  +  +   
Sbjct: 181 LAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQ 213


>gi|150036796|emb|CAM98274.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. mesenteroides]
          Length = 214

 Score =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 93/214 (43%), Positives = 138/214 (64%), Gaps = 2/214 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVV 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG 
Sbjct: 61  LAIDSDDERSLEIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGR 120

Query: 154 GYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI
Sbjct: 121 GYTSADENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
              D+++L ++IL + LG+F++      E    +
Sbjct: 181 KPSDALSLGAKILAEHLGLFMDISPVAAEASVMV 214


>gi|160902228|ref|YP_001567809.1| DNA-directed RNA polymerase subunit alpha [Petrotoga mobilis SJ95]
 gi|160359872|gb|ABX31486.1| DNA-directed RNA polymerase, alpha subunit [Petrotoga mobilis SJ95]
          Length = 353

 Score =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 113/331 (34%), Positives = 180/331 (54%), Gaps = 27/331 (8%)

Query: 9   LIKPNNIEYIV-LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           LIKP     +    Q+E N +     PL +G+A TLGNALRRVL+SS+   AIT ++I G
Sbjct: 4   LIKPEKFRIVQKEEQDEYNYSKYELFPLEKGYAITLGNALRRVLLSSIPSLAITGLRIPG 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG-------DSHKRVTIFKRGPG--VVTAGD 118
            LHE  +++G+ ED+ +I LN+K + LK+         D    +++ K+     V+ +GD
Sbjct: 64  KLHEYDTVEGIKEDIIEITLNLKKVQLKVDDIEKINEIDYPILLSLRKKYKAGQVIKSGD 123

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           I+T  ++EV NPD VI +++ D  V  EL    G G++PA+    ++D    I ID ++S
Sbjct: 124 IKTPAELEVANPDFVIAHVNKDMEVDFELYAQAGKGFIPAQELTFQSDIEY-IFIDGVFS 182

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ KV+Y  E+ R G+  DYDKL + I T  +IT  +++  A++IL +         E +
Sbjct: 183 PVLKVNYLTENIRVGRRTDYDKLILEIWTKKNITPTEALKEATKILMEHFDFISRLWERE 242

Query: 239 KEVKEDINVKSLP----------------FNPALLKKVEELELSVRSTNCLRGENIVYMG 282
            +V      +                       +  +++ L+L+ R+ NCL+ E I  +G
Sbjct: 243 GQVGAIEQTEVSVEKEEEEEEEEENIFGLPKDLMETQLDSLDLTKRAKNCLKREKIDTIG 302

Query: 283 DLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           +L++R  AD+L++ NFGRKSL EIK  L   
Sbjct: 303 ELLKRKPADLLKIKNFGRKSLDEIKNELKEK 333


>gi|289524816|emb|CBJ94464.1| alpha subunit of RNA polymerase [Vibrio sp. Rd 14.3]
 gi|289524826|emb|CBJ94469.1| alpha subunit of RNA polymerase [Vibrio sp. Cmf 11.16]
          Length = 267

 Score =  246 bits (627), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 116/270 (42%), Positives = 175/270 (64%), Gaps = 8/270 (2%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGV 113
           + G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G 
Sbjct: 1   MPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGP 60

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIG 169
           V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG
Sbjct: 61  VVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL 
Sbjct: 121 RLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLD 180

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
            F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
            ++L+  N G+KSL EIK V  + GL L M
Sbjct: 238 VELLKTPNLGKKSLTEIKDVHASRGLSLRM 267


>gi|119662303|emb|CAJ33139.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           indicus]
          Length = 223

 Score =  245 bits (626), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 90/222 (40%), Positives = 138/222 (62%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RGF  TLGN+LRRVL++S+ G  +  V+IDG+LHE +++ GV ED+T IILN+
Sbjct: 1   FVVEPLERGFGTTLGNSLRRVLLTSVPGTGLVKVKIDGILHEFTTVPGVKEDVTKIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L+   +  K + +   GP  VTA D++   D+EVLNPD  IC +     + M + V
Sbjct: 61  KKLELRAYTEEVKTIELDVEGPATVTAEDLKADADVEVLNPDQYICTIAQGGHLHMWIDV 120

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GYVPA  ++T    IG I +D+L+SPI+KV+Y VES R G+  D+DKL++ I T+G
Sbjct: 121 CNGRGYVPASENKTAEMSIGDIPVDSLFSPIEKVNYQVESTRVGKREDFDKLTLEIWTNG 180

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           SI   D++  A+R+L +    F + +   +  +  +  ++  
Sbjct: 181 SIAPNDALNFAARVLVEHFKAFESADAAAEIGEVMVEQENDQ 222


>gi|71056937|emb|CAH59027.1| DNA-directed RNA polymerase alpha chain [Enterococcus malodoratus]
          Length = 221

 Score =  245 bits (626), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 100/221 (45%), Positives = 145/221 (65%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG+ LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNIKGLALKLFA 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G GYV A
Sbjct: 61  EEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTVKPGRGYVQA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++ E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDGSI  +++++
Sbjct: 121 DENKKEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDGSIIAQEALS 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           LA++IL + L +F+N  +  K  +  +  +       L   
Sbjct: 181 LAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMT 221


>gi|172072879|ref|YP_001806640.1| RNA polymerase alpha subunit [Cryptomeria japonica]
 gi|171854898|dbj|BAG16638.1| RNA polymerase alpha subunit [Cryptomeria japonica]
 gi|239794267|dbj|BAH73264.1| RNA polymerase alpha subunit [Cryptomeria japonica]
 gi|239794349|dbj|BAH73345.1| RNA polymerase alpha subunit [Cryptomeria japonica]
          Length = 342

 Score =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 81/333 (24%), Positives = 152/333 (45%), Gaps = 28/333 (8%)

Query: 16  EYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           E   +    EN     +     PL +G A+T+G+A+RRVL+  + G  IT  +   + +E
Sbjct: 14  ELKCVESRTENKRFHYSRFTLSPLRKGQANTIGSAIRRVLLGEVEGTCITRAKFHNISNE 73

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            S I G+ E + +I++N+K I L+      +  +I   GP  VTA DI     + +++  
Sbjct: 74  YSVIIGIEESIHEILMNLKEIVLRSDAYGIREGSIHVVGPKKVTAQDIMLPPSVRIIDTT 133

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-------NDPIGLITIDALYSPIKKVS 184
             I N++    + + L + KG GY+    +           D   +  IDA ++P++ V+
Sbjct: 134 QHIANINKSITLDISLQIEKGRGYIIQNPNNYNPKDEIFAIDAAFVFPIDAAFAPVQNVN 193

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y++ S         + L + I T+G +  ++++  ASR L D    F+N +E   +    
Sbjct: 194 YSIHSYWSENET-QEILFLEIWTNGGLAPKEALYEASRNLIDFFLPFLNAKEENSDGTNS 252

Query: 245 INVKSLPFNPA------------LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           ++    P  P                 +++L  S R  NCL+  NI  + DL+  +  D+
Sbjct: 253 LSDDITPSLPILHISTDTKRIAFDQMYIDQLNFSTRVYNCLKKANINTVSDLLNYSREDL 312

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           +++ + G +S+ EI   +  +     ++ P  P
Sbjct: 313 MKIKHLGEQSVKEILEFIRNIQ----IDSPGNP 341


>gi|119668285|emb|CAK95451.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 217

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 94/215 (43%), Positives = 138/215 (64%)

Query: 36  PRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLK 95
            RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK
Sbjct: 1   ERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELK 60

Query: 96  MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY 155
              D  K + +   GP  VTA D++   D++VLNPD  IC +     + MEL V  G GY
Sbjct: 61  SLSDEQKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMELAVKNGRGY 120

Query: 156 VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
           V A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D
Sbjct: 121 VTASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPND 180

Query: 216 SVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           +++ A++IL +   +F + +   +  +  +  +  
Sbjct: 181 ALSFAAKILVEHFKVFESADANTQFSEVMVEKEDD 215


>gi|31544832|ref|NP_853410.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma gallisepticum
           str. R(low)]
 gi|31541678|gb|AAP56978.1| DNA-directed RNA polymerase subunit alpha (RpoA) [Mycoplasma
           gallisepticum str. R(low)]
 gi|284930906|gb|ADC30845.1| DNA-directed RNA polymerase subunit alpha (RpoA) [Mycoplasma
           gallisepticum str. R(high)]
 gi|284931662|gb|ADC31600.1| DNA-directed RNA polymerase subunit alpha (RpoA) [Mycoplasma
           gallisepticum str. F]
          Length = 340

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 105/309 (33%), Positives = 171/309 (55%), Gaps = 15/309 (4%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           ++    ++N    I +PL +GF  TLGNALRRV++S L G+++ A++I G+ HE   I G
Sbjct: 26  VIKEDNDKNYGKYIVKPLEKGFGITLGNALRRVMLSHLPGSSVFALKIKGISHEFGFIPG 85

Query: 78  VHEDLTDIILNIKGINLKMSG-------------DSHKRVTIFKRGPGVVTAGDIQTVND 124
           V ED+T IILNIK + + +S              +    +TI     G++ AGDI+    
Sbjct: 86  VKEDVTQIILNIKNLVVWISDNMITDETLSETPIEKWPVMTIRANKAGIIKAGDIECPLG 145

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            EV N D  IC L  DA V +++  ++G G+  A  +R+E   + +I ID+ ++PI KV 
Sbjct: 146 FEVFNKDLEICTLSEDAEVAIDIYATRGRGFKTAAENRSEIGSLSIIPIDSNFNPIIKVG 205

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE   E   +  DKL + + T+G I   D++A+AS+IL D L   I+  +   +++  
Sbjct: 206 YHVEE--ETSDVITDKLIIEVGTNGLIKSGDAIAIASKILSDHLKPLIDINKSLHDIQVL 263

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
                   N  L   +E+L+L+VRS NCL+   I  + +L+ R+++++  + N G+KS+ 
Sbjct: 264 NEKNVEEKNKKLSIPIEQLDLTVRSYNCLKRHGIQTVEELVTRSKSEIENIRNLGKKSVR 323

Query: 305 EIKGVLGTM 313
           EI   L  +
Sbjct: 324 EINKKLSEL 332


>gi|156788956|gb|ABU96049.1| RNA polymerase subunit A [Vibrio parahaemolyticus]
          Length = 258

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 112/260 (43%), Positives = 173/260 (66%), Gaps = 8/260 (3%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRV 104
           ALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +
Sbjct: 2   ALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFI 61

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---H 160
           T+ K G G V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H
Sbjct: 62  TLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIH 121

Query: 161 HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           +  +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A
Sbjct: 122 NEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRA 181

Query: 221 SRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVY 280
           + IL +QL  F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y
Sbjct: 182 ATILTEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHY 238

Query: 281 MGDLIQRTEADMLRMANFGR 300
           +GDL+QRTE ++L+  N G+
Sbjct: 239 IGDLVQRTEVELLKTPNLGK 258


>gi|309322061|ref|YP_003933879.1| RNA polymerase alpha subunit [Erodium texanum]
 gi|197131688|gb|ACH47362.1| RNA polymerase alpha subunit [Erodium texanum]
 gi|300069154|gb|ADJ66276.1| RNA polymerase alpha subunit [Erodium texanum]
          Length = 328

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 74/307 (24%), Positives = 148/307 (48%), Gaps = 9/307 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +   +E+   G+        I  PL +G A  +G A+RR L+  + G  IT  + + + H
Sbjct: 14  RWKCVEFRADGKR-LYYGRFILSPLKKGQADIIGIAMRRALLGEIEGTCITYAKFEKIPH 72

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ G+ E + +I++N+K I L+ +    +  +I  RGP  VTA DI     + +++ 
Sbjct: 73  EYTTLVGIQESVYEIVMNLKEIVLRSNLYGTRDASICVRGPRDVTAQDIILPPSVAIVDN 132

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
              I  L       + L + +  GY       T +       IDA++ P+K V++++ + 
Sbjct: 133 TQHIVTLTEPIDFCVGLQIERNRGYSMKIPMPTNSHDDRGYPIDAVFMPVKNVNHSIHAY 192

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--VK 248
             G    ++ L   I T+GS+T ++++  ASR L +    F++ EE    ++ + N   +
Sbjct: 193 ENGS---HEMLFFEIWTNGSLTPKEALREASRKLINLFIPFLHAEEENSHLENNQNQHTE 249

Query: 249 SLPFNPALLKKV---EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            L  +   LK +   + +EL  R  N L+G  I  + DL+ +    ++++ +F  + + +
Sbjct: 250 ELSIDLCGLKDIYIDQLVELPPRLYNSLKGSGIHTVMDLMDKNTDALMKIPHFRHEDVEK 309

Query: 306 IKGVLGT 312
           +  +L  
Sbjct: 310 VMNILNK 316


>gi|12230607|sp|Q9RDV6|RPOA_MYCGA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|16924180|gb|AAF19039.2| DNA-directed RNA polymerase alpha chain [Mycoplasma gallisepticum]
          Length = 325

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 105/309 (33%), Positives = 171/309 (55%), Gaps = 15/309 (4%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           ++    ++N    I +PL +GF  TLGNALRRV++S L G+++ A++I G+ HE   I G
Sbjct: 11  VIKEDNDKNYGKYIVKPLEKGFGITLGNALRRVMLSHLPGSSVFALKIKGISHEFGFIPG 70

Query: 78  VHEDLTDIILNIKGINLKMSG-------------DSHKRVTIFKRGPGVVTAGDIQTVND 124
           V ED+T IILNIK + + +S              +    +TI     G++ AGDI+    
Sbjct: 71  VKEDVTQIILNIKNLVVWISDNMITDETLSETPIEKWPVMTIRANKAGIIKAGDIECPLG 130

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            EV N D  IC L  DA V +++  ++G G+  A  +R+E   + +I ID+ ++PI KV 
Sbjct: 131 FEVFNKDLEICTLSEDAEVAIDIYATRGRGFKTAAENRSEIGSLSIIPIDSNFNPIIKVG 190

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE   E   +  DKL + + T+G I   D++A+AS+IL D L   I+  +   +++  
Sbjct: 191 YHVEE--ETSDVITDKLIIEVGTNGLIKSGDAIAIASKILSDHLKPLIDINKSLHDIQVL 248

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
                   N  L   +E+L+L+VRS NCL+   I  + +L+ R+++++  + N G+KS+ 
Sbjct: 249 NEKNVEEKNKKLSIPIEQLDLTVRSYNCLKRHGIQTVEELVTRSKSEIENIRNLGKKSVR 308

Query: 305 EIKGVLGTM 313
           EI   L  +
Sbjct: 309 EINKKLSEL 317


>gi|69215820|gb|AAZ03866.1| RNA polymerase alpha chain [Ginkgo biloba]
          Length = 337

 Score =  245 bits (625), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 85/332 (25%), Positives = 149/332 (44%), Gaps = 24/332 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE  V G+           PL +G A+T+G A+RR L+  + G  IT  + + + 
Sbjct: 13  LRWKCIESRVNGKRLH-YGRFALSPLQKGQANTIGIAMRRALLGEVEGTCITHAKFENMT 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI +N++GI L+      +  +I+  GP  VTA DI     + +++
Sbjct: 72  HEYSAIMGIEESVHDISINLRGIVLQSDPYGIREASIYSVGPRDVTAQDIILPPSVRIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I +L       +   + K  GY     + + +   G+ + DA+  P++  +Y++ S
Sbjct: 132 TTQHIASLKESITSDIRSQIGKDRGYRIQSPNNSRD---GIFSTDAVSMPVRNANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G  +  + L   I T+GS+   +++  ASR L D    F+  EE   +  ++ N   
Sbjct: 189 YGNGNEM-QEILFSEIWTNGSLAPGEALYEASRNLIDLFIPFMRAEEQNIDGIDNWNGYN 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         K           +++ EL  R  NCL+  NI  + DL+  +  D  
Sbjct: 248 MSLFPFSHISTDTEKMEEEIAFKHIFIDQSELPPRVYNCLKRVNIHTLSDLLNYSRDDPT 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           R+ NFG +S+ +I  VL        ++LP   
Sbjct: 308 RIENFGNQSVEQILEVL---QKRFAIDLPKKK 336


>gi|119668355|emb|CAK95472.1| RNA polymerase alpha subunit [Lactobacillus plantarum]
          Length = 214

 Score =  245 bits (625), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 98/214 (45%), Positives = 145/214 (67%), Gaps = 2/214 (0%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK+  D  
Sbjct: 1   TLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTAIILNVKKIALKLESDET 60

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I  +GP  VTA DI    D+EVLNPD  IC +   A   M +T + G GYV A+ +
Sbjct: 61  KTLEIDVKGPANVTASDIIGDADVEVLNPDLPICTVADGAHFHMRMTANTGRGYVSAEDN 120

Query: 162 R--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           +   ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T+GSIT  ++++L
Sbjct: 121 KHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWTNGSITPSEAISL 180

Query: 220 ASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           +++IL D L +F+N  +  K     +  +     
Sbjct: 181 SAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKE 214


>gi|119668283|emb|CAK95498.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 220

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 94/210 (44%), Positives = 137/210 (65%)

Query: 36  PRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLK 95
            RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK
Sbjct: 1   ERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELK 60

Query: 96  MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY 155
              D  K + +   GP  VTA D++   D++VLNPD  IC +     + MEL V  G GY
Sbjct: 61  SLSDEQKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMELAVKNGRGY 120

Query: 156 VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
           V A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D
Sbjct: 121 VTASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPND 180

Query: 216 SVALASRILQDQLGMFINFEEPKKEVKEDI 245
           +++ A++IL +   +F + +   +  +  +
Sbjct: 181 ALSFAAKILVEHFKVFESADANTQFSEVMV 210


>gi|72534420|emb|CAH59046.1| DNA-directed RNA polymerase alpha chain [Enterococcus canis]
          Length = 218

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 97/218 (44%), Positives = 143/218 (65%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNIKG+ LK+     
Sbjct: 1   TLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNIKGLALKLYAQEE 60

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + I   GP  VTAGDI   +D+E+LN D  +C +   A     LTV  G GYV A  +
Sbjct: 61  KTLEIDITGPATVTAGDIIVDSDVEILNKDLYLCTVSEGATFHARLTVKPGRGYVQADEN 120

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           +TE+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI  +++++L++
Sbjct: 121 KTEDMPIGVLPVDSIYTPVRRVNYQVENTRVGNRQDFDKLTMEIWTDGSIIPQEALSLSA 180

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           +IL + L +F+N  +  K  +  +  +       L   
Sbjct: 181 KILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMT 218


>gi|150036794|emb|CAM98273.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. mesenteroides]
          Length = 213

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 93/211 (44%), Positives = 138/211 (65%), Gaps = 2/211 (0%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K +
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKV 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG
Sbjct: 61  VLAIDSDDERSLEIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKG 120

Query: 153 HGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GS
Sbjct: 121 RGYTSADENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTNGS 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +   D+++L ++IL + LG+F++      E 
Sbjct: 181 VKPSDALSLGAKILAEHLGLFMDISPVAAEA 211


>gi|301633194|gb|ADK86748.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma pneumoniae
           FH]
          Length = 327

 Score =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 91/308 (29%), Positives = 160/308 (51%), Gaps = 13/308 (4%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
              N  +    PL  GF  T+GNA+RRVL+S + GA++ A+ I G   E ++++G+ ED+
Sbjct: 18  ANPNYGIFEVGPLESGFGITIGNAMRRVLLSCIPGASVFALSISGAKQEFAAVEGMKEDV 77

Query: 83  TDIILNIKGINLKMSG----DSHKR---------VTIFKRGPGVVTAGDIQTVNDIEVLN 129
           T+++LN K + +K+S     D             +T+     G V A D++     EV+N
Sbjct: 78  TEVVLNFKQLVVKISDLLFEDGEMVEPPLERWPLLTVTAEKAGPVYAKDLECPAGFEVVN 137

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
            D  + +L  D  V + + V +G G+V    +R   + +G+I  D+ +SP+    Y V+ 
Sbjct: 138 KDLYLFSLQTDKKVTVNVYVKQGRGFVTFLENREMINSLGIIATDSNFSPVLHCGYEVQE 197

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            +  +    D L+  I T+G+I+  D+ A+A++IL + L   +N  E  K +        
Sbjct: 198 LKTSKQKITDHLTFKIATNGAISAVDAFAMAAKILIEHLNPIVNVNESIKALNIIQEKAE 257

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                +  K++EEL+ +VR+ NCL+   I  + +L+ ++ AD+  + N G+KS  EI   
Sbjct: 258 ERRVRSFAKQIEELDFTVRTFNCLKRSGIHTLQELLSKSLADIREIRNLGKKSEREIIKK 317

Query: 310 LGTMGLFL 317
           +  +GL L
Sbjct: 318 VHELGLKL 325


>gi|242910197|ref|YP_002970676.1| RNA polymerase a-subunit [Alsophila spinulosa]
 gi|218454866|gb|ACK77203.1| RNA polymerase a-subunit [Alsophila spinulosa]
          Length = 338

 Score =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 82/330 (24%), Positives = 150/330 (45%), Gaps = 22/330 (6%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            ++I+   +E     +        +  P  RG  +T+G A+RR L+  + GA+IT  + +
Sbjct: 10  TQVIQWKCVESKTESKRLH-HGRSVISPFKRGQVNTVGIAMRRALLEEVGGASITCAKFE 68

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S+I G+ E + DI +N+K    +   +  K   +   GP  VTAGD      ++
Sbjct: 69  GVIHEYSTITGIQETIHDISVNLKETVPRSDSNDSKEAFLSVTGPKRVTAGDTSLPPSVK 128

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +++    I  +     V +E  + K  GY   + +   +   G   +DA+  P++ V+Y+
Sbjct: 129 IIDDSQYIVTITQPISVNIESRIEKDCGYRIEEFNGYRD---GEFPVDAVPMPVRNVNYS 185

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED-- 244
           V     G+ +  +   + I T+GS T  +++  AS+ L D L  F++ +       ED  
Sbjct: 186 VHPFGSGREM-REISFIEIWTNGSPTPNEALCEASKNLIDLLIPFLHMKHEDVPHFEDEQ 244

Query: 245 ------------INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
                       I V            +++LE   R+ NCL+   I  + DL+  +  D+
Sbjct: 245 DSSDLTILSSQLIGVGESEGEVLRNTFIDQLESPARAFNCLKRAEIHTITDLLNHSREDL 304

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           L++ +FG+KS+ ++   L          LP
Sbjct: 305 LKIKSFGKKSVDQVSRALWE---RFATELP 331


>gi|150036760|emb|CAM98030.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 223

 Score =  244 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 89/214 (41%), Positives = 135/214 (63%), Gaps = 2/214 (0%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           G+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L + 
Sbjct: 1   GYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAID 60

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
            D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  
Sbjct: 61  SDDERSLEIDVQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTS 120

Query: 158 AKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
           A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D
Sbjct: 121 ADENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGARDDYDKLTFDIWTNGSIKPSD 180

Query: 216 SVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           +++L ++IL + L +F++      E    +  + 
Sbjct: 181 ALSLGAKILAEHLNLFMDISPVAAEASVMVEAEP 214


>gi|86438812|emb|CAJ43371.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 213

 Score =  244 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 94/213 (44%), Positives = 137/213 (64%)

Query: 35  LPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL 94
           L RGF  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + L
Sbjct: 1   LERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLEL 60

Query: 95  KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHG 154
           K   D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V  G G
Sbjct: 61  KSLSDERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNGRG 120

Query: 155 YVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
           YV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   
Sbjct: 121 YVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPN 180

Query: 215 DSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           D+++ A++I  +   +F + +   K  +  +  
Sbjct: 181 DALSFAAKISVEHFKVFESADADTKFSEVMVEK 213


>gi|197131686|gb|ACH47361.1| RNA polymerase alpha subunit [Erodium chrysanthum]
          Length = 329

 Score =  244 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 79/307 (25%), Positives = 147/307 (47%), Gaps = 11/307 (3%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +   +E+   G+        I  PL +G A  +G A+RR L+  + G  IT  Q + + H
Sbjct: 14  RWKCVEFRADGKR-LYYGRFILSPLKKGQADIIGIAMRRALLGEIEGTCITHAQFEKIPH 72

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E ++  G+ E + +I++N+K I L+ S    +  +I  RGP  VTA DI     + +++ 
Sbjct: 73  EYTTRVGIQESVYEIVMNLKEIVLRSSLYGTRDASICVRGPRDVTAQDIILPPSVSIVDN 132

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
              I  L       + L + +  GY         +       IDA++ P+K V++++ S 
Sbjct: 133 TQHIVTLTEPIEFCVALQIERNRGYSLRIPTPNNSHDERGYPIDAVFMPVKNVNHSIHSY 192

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
             G    ++ L   I T+GS+T ++++  ASR L +    F++ EE K   + + N +  
Sbjct: 193 ENGS---HEMLFFEIWTNGSLTPKEALREASRKLINLFIPFLHAEEEKPHFENNQN-EPR 248

Query: 251 PFNPALLKKVEEL------ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
                 L +++E+      ELS R  N L+G  I  + DL+ +   D+L++ +F ++ + 
Sbjct: 249 DELLVDLCELKEIYIDQLVELSPRLYNILKGSGIHTVMDLLDKNPDDLLKLRHFRQEDVE 308

Query: 305 EIKGVLG 311
            +  +L 
Sbjct: 309 RVMNILN 315


>gi|309322147|ref|YP_003934062.1| RNA polymerase alpha subunit [Geranium palmatum]
 gi|197131694|gb|ACH47365.1| RNA polymerase alpha subunit [Geranium palmatum]
 gi|300069240|gb|ADJ66361.1| RNA polymerase alpha subunit [Geranium palmatum]
          Length = 329

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 73/307 (23%), Positives = 143/307 (46%), Gaps = 11/307 (3%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +   +E    G+        I  PL +G A  +G A+RR L+  + G  IT  + D + H
Sbjct: 14  RWKCVESRADGKR-LYYGRFILSPLKKGQADIIGIAMRRALLGEIEGTCITHAKFDKIPH 72

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ G+ E + +I++N+K I L+      +  +I  RGP  VTA DI       +++ 
Sbjct: 73  EYTTLVGIQESIYEILMNLKEIVLRSHLYGTRDASICVRGPRDVTAQDIILPTSATIVDN 132

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
              I  +       + L + +  GY       T         ID+++ P+K V++++ S 
Sbjct: 133 TQHIVTITEPIDFCVGLQIERNRGYFIQIPMLTNLHDDRGYPIDSVFMPVKNVNHSIHSY 192

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
             G    +  L + I T+GS+T ++++  ASR L +    F++ EE     + + N  + 
Sbjct: 193 ENG---IHAMLFLEIWTNGSLTPKEALREASRKLSNLFIPFLHAEEQNFHFENNQNEHTD 249

Query: 251 PFNPALLKKVEEL------ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              P     ++++      EL  R  NCL+   I  + DL+ +   D++++ +F ++ + 
Sbjct: 250 EL-PIDFCALKDIYIDQLVELPARFYNCLKISGIHTVMDLLNKNTEDLMKITHFRQQDIE 308

Query: 305 EIKGVLG 311
           ++  +L 
Sbjct: 309 KVMHILN 315


>gi|13507930|ref|NP_109879.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma pneumoniae
           M129]
 gi|2500601|sp|Q50295|RPOA_MYCPN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|1215697|gb|AAC43690.1| RpoA [Mycoplasma pneumoniae]
 gi|1674345|gb|AAB96288.1| RNA polymerase alpha core subunit [Mycoplasma pneumoniae M129]
          Length = 327

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 91/308 (29%), Positives = 160/308 (51%), Gaps = 13/308 (4%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
              N  +    PL  GF  T+GNA+RRVL+S + GA++ A+ I G   E ++++G+ ED+
Sbjct: 18  ANPNYGIFEVGPLESGFVITIGNAMRRVLLSCIPGASVFALSISGAKQEFAAVEGMKEDV 77

Query: 83  TDIILNIKGINLKMSG----DSHKR---------VTIFKRGPGVVTAGDIQTVNDIEVLN 129
           T+++LN K + +K+S     D             +T+     G V A D++     EV+N
Sbjct: 78  TEVVLNFKQLVVKISDLLFEDGEMVEPPLERWPLLTVTAEKAGPVYAKDLECPAGFEVVN 137

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
            D  + +L  D  V + + V +G G+V    +R   + +G+I  D+ +SP+    Y V+ 
Sbjct: 138 KDLYLFSLQTDKKVTVNVYVKQGRGFVTFLENREMINSLGIIATDSNFSPVLHCGYEVQE 197

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            +  +    D L+  I T+G+I+  D+ A+A++IL + L   +N  E  K +        
Sbjct: 198 LKTSKQKITDHLTFKIATNGAISAVDAFAMAAKILIEHLNPIVNVNESIKALNIIQEKAE 257

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                +  K++EEL+ +VR+ NCL+   I  + +L+ ++ AD+  + N G+KS  EI   
Sbjct: 258 ERRVRSFAKQIEELDFTVRTFNCLKRSGIHTLQELLSKSLADIREIRNLGKKSEREIIKK 317

Query: 310 LGTMGLFL 317
           +  +GL L
Sbjct: 318 VHELGLKL 325


>gi|161513434|emb|CAP16860.1| DNA-directed RNA polymerase subunit alpha [Pediococcus cellicola]
          Length = 214

 Score =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 96/202 (47%), Positives = 142/202 (70%), Gaps = 2/202 (0%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNIK ++LK+  D
Sbjct: 1   GTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNIKKVSLKIEND 60

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A 
Sbjct: 61  EEKSLEINVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAVLTADTGRGYVSAD 120

Query: 160 HHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
            ++   ++ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSI+  ++ 
Sbjct: 121 ENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSISPSEAT 180

Query: 218 ALASRILQDQLGMFINFEEPKK 239
           +L+++IL + L +F+N  +  +
Sbjct: 181 SLSAKILTEHLALFVNLTDEAQ 202


>gi|119662363|emb|CAJ33170.1| RNA polymerase alpha subunit [Lactobacillus spicheri]
          Length = 210

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 98/210 (46%), Positives = 145/210 (69%), Gaps = 4/210 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK++G
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNVKKIALKLNG 60

Query: 99  --DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             D  + + I  +GP  VTAGDI    D++VLNPD  I  +   A   M +T  KG GYV
Sbjct: 61  ADDQEETMEINVKGPAQVTAGDIVAGADVDVLNPDLYIATVADGATFHMRMTADKGRGYV 120

Query: 157 PAKHHRTEN--DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A  ++  N   PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ + T+GSI   
Sbjct: 121 SADENKARNTEMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDVWTNGSINPS 180

Query: 215 DSVALASRILQDQLGMFINFEEPKKEVKED 244
           ++++LA++IL + L MF++  +  K  +  
Sbjct: 181 EAISLAAKILTEHLAMFVDLTDEAKNAEIM 210


>gi|119662301|emb|CAJ33138.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           delbrueckii]
          Length = 215

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 90/215 (41%), Positives = 137/215 (63%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF  TLGN+LRRVL++S+ G  +  V+IDG+LHE +++ GV ED+T IILN+K +
Sbjct: 1   EPLERGFGTTLGNSLRRVLLTSVPGTGLVKVKIDGILHEFTTVPGVKEDVTKIILNLKKL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            L+   +  K + +   GP  VTA D++   D+EVLNPD  IC +     + M + V  G
Sbjct: 61  VLRAYTEEVKTIELDVEGPATVTAEDLKADADVEVLNPDQYICTIAQGGHLHMWIDVCNG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GYVPA  ++T+   IG I +D+L+SPI+KV+Y VES R G+  D+DKL++ I T+GSI 
Sbjct: 121 RGYVPASENKTDEMFIGDIPVDSLFSPIEKVNYQVESTRVGKREDFDKLTLEIWTNGSIA 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
             D++  A+R+L +   +F + +   +  +  +  
Sbjct: 181 PNDALNFAARVLVEHFKVFESADAAAEIGEVMVEQ 215


>gi|167957552|ref|ZP_02544626.1| DNA-directed RNA polymerase subunit alpha [candidate division TM7
           single-cell isolate TM7c]
          Length = 294

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 101/283 (35%), Positives = 154/283 (54%), Gaps = 3/283 (1%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +            EPL  G+ +TLGN+LRRVLMSS+ GAA+ + +I+G  HE +++ G+ 
Sbjct: 13  IEDYSSTSAAFTVEPLRGGYGNTLGNSLRRVLMSSIHGAAVISFKIEGATHEFTTVPGIK 72

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+ DI LN+K + +KM  D    + + K G G VTAGDIQ+  D+E++NP+ VIC +D 
Sbjct: 73  EDVVDISLNLKSVKIKMHTDDPIELRLEKHGAGQVTAGDIQSHADVEIINPEQVICTVDD 132

Query: 140 D-AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
             A   ++L +  G GY+  +           I +DA++SP+ +V Y VES R GQ  + 
Sbjct: 133 PSAKAVIDLVIDSGRGYLSIEDSSETRLHSDHIALDAVFSPVIRVRYKVESTRVGQETNL 192

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           +KL + IDTDGSIT  D+   A+ IL +Q          +         +       L  
Sbjct: 193 EKLIVVIDTDGSITPRDAFEEAAAILVNQYTALAGSTVVESAPALGQEREEESNE--LNT 250

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            +E+L+L+ R+ N L   +I  + DL+  TE D+  +  FG K
Sbjct: 251 SIEDLDLTARTANALINNDIRTVQDLVTLTEQDLRELKGFGSK 293


>gi|71056858|emb|CAH58984.1| DNA-directed RNA polymerase alpha chain [Enterococcus villorum]
          Length = 208

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 98/208 (47%), Positives = 142/208 (68%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+ LKM G 
Sbjct: 1   GTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGLALKMYGQ 60

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV  G GYV A 
Sbjct: 61  EEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTVKPGRGYVQAD 120

Query: 160 HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
            ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI   ++++L
Sbjct: 121 ENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHCEDFDKLTMEIWTDGSIEPLEAMSL 180

Query: 220 ASRILQDQLGMFINFEEPKKEVKEDINV 247
           +++I+ + L +F+N  +  K  +  +  
Sbjct: 181 SAKIMTEHLDIFVNLTDEAKNAEIMVEK 208


>gi|290489672|gb|ADD31220.1| RNA polymerase alpha subunit protein [Phoradendron serotinum]
          Length = 326

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 82/316 (25%), Positives = 158/316 (50%), Gaps = 22/316 (6%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           +K   +    +  +       I  PL +G A T+G A+RR L+  + G  IT  + D + 
Sbjct: 13  LKWKCV-ASRVDNKRFYYGRFILSPLIKGQADTIGIAMRRALLGEIEGTCITRAKSDQIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I+G+ E + DI++N+K I L+ +       +I+ +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIRGIQESVHDILINLKEIVLRSNLYGTCNASIYIKGPRYITAQDIILPPYVEIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
              +I +L       + L + K  GY        +N   G  +I+A++ P++  ++++ +
Sbjct: 132 HTQIIASLTEQIDFGIGLQIEKNRGYRIIT---PKNLQEGNFSIEAIFMPVRNANHSIHN 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
             E      + L + I T+GS+T ++++  A+R L D    F++ ++ K  V+++ +  S
Sbjct: 189 YNEKL----EILFLEIWTNGSLTPKEALHEAARNLIDLFIPFLHVKKEKLHVEDNQHKLS 244

Query: 250 LPFNPALLKK--------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           L      L+K              +++ ELS R  NCL+  NI  + DL+ +   D++++
Sbjct: 245 LFTFHDRLQKLRKTKEKIALKSIFIDQSELSPRIYNCLKSSNIQNILDLLNKNREDLMKI 304

Query: 296 ANFGRKSLVEIKGVLG 311
            +F  + L  I G+L 
Sbjct: 305 EHFRIEDLKHIWGILE 320


>gi|156752145|gb|ABU93823.1| RNA polymerase subunit A [Vibrio sp. 23023]
          Length = 256

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 113/259 (43%), Positives = 172/259 (66%), Gaps = 8/259 (3%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHK 102
           GNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G    
Sbjct: 1   GNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEV 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK-- 159
            +T+ K G G V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA   
Sbjct: 61  FITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEISMRIKVERGRGYVPASAR 120

Query: 160 -HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
            H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++ 
Sbjct: 121 IHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIR 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENI 278
            A+ IL +QL  F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I
Sbjct: 181 RAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAI 237

Query: 279 VYMGDLIQRTEADMLRMAN 297
            Y+GDL+QRTE ++L+  N
Sbjct: 238 HYIGDLVQRTEVELLKTPN 256


>gi|313683415|ref|YP_004061153.1| DNA-directed RNA polymerase subunit alpha [Sulfuricurvum kujiense
           DSM 16994]
 gi|313156275|gb|ADR34953.1| DNA-directed RNA polymerase subunit alpha [Sulfuricurvum kujiense
           DSM 16994]
          Length = 330

 Score =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 100/322 (31%), Positives = 171/322 (53%), Gaps = 7/322 (2%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
           V+ Q   N   +IA P   GFA +L + +RR L+SS  G A   ++I+G  HE  S++G+
Sbjct: 15  VVEQISANEANIIAYPFETGFAVSLAHPIRRFLLSSSVGFAPIGIKIEGAKHEFDSVRGM 74

Query: 79  HEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
            ED++D I+N+KGI  K+ +G   K +T    GP  +   D+    D+EV+ P+  +  L
Sbjct: 75  LEDISDFIINLKGIRFKLKNGLKEKEITYSFAGPCEIHGSDLDND-DVEVVTPNAFLATL 133

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + DA +   + + +G GY P++  R +    G I +DA ++P+++ +Y +E+       +
Sbjct: 134 NEDATLNFSVKIHQGIGYAPSEDVR-DILGDGYIALDAYFTPVRRATYAIENVLVEDNPN 192

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           ++K+ + I TDG I+  D+   A  ++  Q+ +F N E   K           P    L 
Sbjct: 193 FEKVVINIATDGQISPVDAFKNALEVMYAQMAVF-NSEVSIKAPAAAERGDEHPELKRLG 251

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            ++E+L LS RS NCL   NI Y+G+++  ++ D+  + N G+KS  EI   +   G  +
Sbjct: 252 ARIEDLGLSARSFNCLDRSNIKYIGEIVMMSQNDLKEVKNLGKKSFEEILEKITEYGYTV 311

Query: 318 GMNLPDWPPESIEELAKKYEDK 339
           G +L D   + I  + KK E +
Sbjct: 312 GQDLAD---DLISAIKKKIEAE 330


>gi|34558004|ref|NP_907819.1| DNA-directed RNA polymerase subunit alpha [Wolinella succinogenes
           DSM 1740]
 gi|41688621|sp|Q7M8F7|RPOA_WOLSU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|34483722|emb|CAE10719.1| RNA POLYMERASE ALPHA SUBUNIT [Wolinella succinogenes]
          Length = 331

 Score =  242 bits (618), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 102/327 (31%), Positives = 175/327 (53%), Gaps = 7/327 (2%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P +I    +G+   N+  + A P   G+A TL + LRR+L+ S  G A TA++I+G  HE
Sbjct: 11  PTDISIQEIGK---NKIKISAYPFESGYAITLAHPLRRLLLGSSVGFAPTALKIEGAAHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
             S++G+ ED+   I+N+K I  KM GD+ +  +    +GP  +   D+     ++V+ P
Sbjct: 68  FDSVRGIMEDVALFIVNLKSIRFKMRGDAERVTLDYSFKGPATIKGSDLVND-YVDVVTP 126

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           +  +  ++ DA +   L V KG GYVP++  R    P G I +DA ++P+KK +Y +E+ 
Sbjct: 127 NQHLATINEDATLTFSLIVQKGIGYVPSEETRNLI-PEGYIPLDAYFTPVKKATYEIENV 185

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
                  Y+K+ + I+TDG I    +   A  ++Q Q+ +F N E      +   + +  
Sbjct: 186 LVEDNPTYEKIVLEIETDGLIEPIAAFKDALGVMQKQMSVF-NSEWSVSSAESTSSDEED 244

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           P    LL+K+E L LS RS NCL    + ++G+L+   E ++  + N G+KS  EIK  L
Sbjct: 245 PELKPLLQKIEALNLSARSFNCLDRAGMKFVGELVLLGENELKEVKNLGKKSFDEIKDKL 304

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKYE 337
             +G  +G +L +    ++++   K +
Sbjct: 305 EEIGYPVGSDLAEEVSSALQKRLNKLK 331


>gi|71056856|emb|CAH58983.1| DNA-directed RNA polymerase alpha chain [Enterococcus villorum]
          Length = 219

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 99/219 (45%), Positives = 144/219 (65%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+ LKM G 
Sbjct: 1   GTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGLALKMYGQ 60

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             K + I   GP  VTAGDI   +++E+LN D  IC++   A     LTV  G GYV A 
Sbjct: 61  EEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFHARLTVKPGRGYVQAD 120

Query: 160 HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
            ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI   ++++L
Sbjct: 121 ENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHCEDFDKLTMEIWTDGSIEPLEAMSL 180

Query: 220 ASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           +++I+ + L +F+N  +  K  +  +  +       L  
Sbjct: 181 SAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 219


>gi|154424803|emb|CAL18504.1| RNA polymerase alpha subunit [Streptococcus hyovaginalis]
          Length = 212

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 89/212 (41%), Positives = 141/212 (66%)

Query: 35  LPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL 94
           L RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ +
Sbjct: 1   LERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNVKGLAV 60

Query: 95  KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHG 154
           K   +  K + +  +GP  VTAGDI T +D+E++N DH +  +   A  +  +TV+   G
Sbjct: 61  KSYVEDEKIIELDVQGPAEVTAGDILTDSDVEIVNSDHYLFTIAEGASFKASMTVATNRG 120

Query: 155 YVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
           YV A+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  E
Sbjct: 121 YVAAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPE 180

Query: 215 DSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           D++ L++R+L + L +F +  E  K       
Sbjct: 181 DALGLSARVLIEHLNLFTDLTEVAKTTDVMKE 212


>gi|119668361|emb|CAK95513.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
          Length = 211

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 97/210 (46%), Positives = 150/210 (71%), Gaps = 2/210 (0%)

Query: 35  LPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL 94
           L RG+  TLGN+LRRVL++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K ++L
Sbjct: 1   LERGYGTTLGNSLRRVLIASLPGAAITSMQIDGVLHEFSTVEGVTEDVTQIILNLKKVSL 60

Query: 95  KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHG 154
           K+  +  K + +  +GP  VTA DIQ  N++ +LNPD  I  +   A + ++LT  KG G
Sbjct: 61  KLDSEDQKNLELDVKGPAEVTASDIQGDNEVTILNPDLHIATVADGAELHIKLTADKGRG 120

Query: 155 YVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           Y+ A  ++   ++  IG++ ID++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T
Sbjct: 121 YLSANDNKARMDDLAIGVLPIDSIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLT 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVK 242
             ++V+L ++IL + L MF++  E  +  +
Sbjct: 181 PTEAVSLGAKILTEHLAMFVDLTETAQNAQ 210


>gi|30468203|ref|NP_849090.1| RNA polymerase alpha subunit [Cyanidioschyzon merolae strain 10D]
 gi|41688691|sp|Q85FU3|RPOA_CYAME RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|30409303|dbj|BAC76252.1| DNA-directed RNA polymerase alpha chain [Cyanidioschyzon merolae
           strain 10D]
          Length = 316

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 91/298 (30%), Positives = 152/298 (51%), Gaps = 12/298 (4%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +    +     I +PL    A T+GN+LRRVL+S L   +ITAV+I G  HE++++KGV
Sbjct: 18  TINHARDIYAKFILQPLSYTQALTMGNSLRRVLLSELESISITAVRIAGASHELATLKGV 77

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVT-IFKRGPGVVTAGDIQ--TVNDIEVLNPDHVIC 135
            ED+  I+LN+K I  +        +T +  +GP +VTA   Q    +   +++    I 
Sbjct: 78  REDVLQIMLNLKQIVWRGQLKKQPTITRLKVQGPAIVTAAAFQSEANSSANIIDTCQYIA 137

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
            +D   ++ ME  + +  GY  AK     +     + ID ++ P+K+V++ V+ A   +V
Sbjct: 138 TIDTQDILEMECQLEQSSGYRLAKPSEMID----WLPIDGVFMPVKRVNFWVDKALVDKV 193

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           L    L + I T+GSI+ ++++  A+RIL          E      K +           
Sbjct: 194 LVDKALHLEIWTNGSISPQEALHQAARILTHWFNPLQTLEWKTSHTKNEQ-----TMAQL 248

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
               +EEL+LSVR+ NCL+   I  + DL+Q T+ ++L + NFG+KS+ E+   L   
Sbjct: 249 SNMLIEELDLSVRAYNCLKRAQIHSVADLMQYTQEELLALKNFGQKSVEEVNKALEQK 306


>gi|119662841|emb|CAJ33213.1| RNA polymerase alpha subunit [Lactobacillus fructivorans KCTC 3543]
          Length = 220

 Score =  242 bits (617), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 101/220 (45%), Positives = 150/220 (68%), Gaps = 4/220 (1%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRRVL++SL GAA+T++QIDGVLHE S++KGV ED+T IILN+K INLK++ D
Sbjct: 1   GTTLGNSLRRVLLASLPGAAVTSIQIDGVLHEFSTVKGVVEDVTQIILNVKKINLKINSD 60

Query: 100 SHKR--VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
            ++   ++I   GP  VTAGDI T +D+E+LNPD  I  +   A   M +T +KG GYV 
Sbjct: 61  DNETKSMSINVTGPADVTAGDIVTDSDVEILNPDLHIATVADGATFHMNMTANKGRGYVS 120

Query: 158 AKHHRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
           A+ ++ +ND  PIG++ +D++Y+PI++V+Y VE AR GQ  DYDKL++ + T+GSIT  D
Sbjct: 121 AEENKAKNDGMPIGVLPVDSIYTPIERVNYQVEDARVGQRDDYDKLTLDVWTNGSITPSD 180

Query: 216 SVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           +++LA++IL     +FI+  +  K     +  +       
Sbjct: 181 AISLAAKILNQHFQLFIDLTDRAKNANVMVEKEESHKEKM 220


>gi|168026922|ref|XP_001765980.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162682886|gb|EDQ69301.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 438

 Score =  241 bits (616), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 89/339 (26%), Positives = 155/339 (45%), Gaps = 26/339 (7%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           Q + Q  ++   +E                 P  +G A T+GNALRR L+  ++GAAIT 
Sbjct: 105 QSSTQSPLQWRCVETFKENDHRH-YARFAVSPFRQGQAITVGNALRRALLGEVQGAAITC 163

Query: 63  VQI--DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
                 G++HE  ++ G+ E + DI+LN++ + +  +    ++  I   GP  V AGDI 
Sbjct: 164 ATFKDMGIVHEYQAVDGIQETVQDILLNVRDVAIGSNTHEPQKAFISVMGPRQVIAGDIL 223

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               + V +P   I  +       +E+ V K  GY      ++ N   G   ID+++ P+
Sbjct: 224 CPPSLVVPDPSQNIALVTAAIPFNVEIEVEKDVGYRIVDPGKSTN---GRFYIDSVFMPV 280

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            + +Y+V S     V   + L + I T+GSI+ E+++  A+R L D L   +  E  +  
Sbjct: 281 VQANYSVHSFEVEDVT-REILFLEIYTNGSISPEEALIEAARSLIDLLLPLLESEVIEVT 339

Query: 241 VKEDINVKSLPFNPALLKK----------------VEELELSVRSTNCLRGENIVYMGDL 284
              +    S   +                      +++L+L  R+ NCL+  NI  + DL
Sbjct: 340 NTTEKENGSRNISMLSSFLSSSDQITKEVTYKHVFIDQLKLPARAYNCLKRANIHTVSDL 399

Query: 285 IQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +  T+ D++R+ NFG+KS+ E+   L        ++LP 
Sbjct: 400 LDYTQDDLMRIKNFGKKSVEEVLEALRA---QFNISLPK 435


>gi|156752143|gb|ABU93822.1| RNA polymerase subunit A [Vibrio sp. 0908]
          Length = 257

 Score =  241 bits (616), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 109/258 (42%), Positives = 172/258 (66%), Gaps = 8/258 (3%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRV 104
           ALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +
Sbjct: 3   ALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFI 62

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---H 160
           T+ K G G V AGDI    D+E++NP+HVIC+L  D A + M + V +G GYVPA    H
Sbjct: 63  TLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIH 122

Query: 161 HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
              +  PIG + +DA +SP+ K++Y+V++AR  Q  D DKL + ++T+G++  E+++  A
Sbjct: 123 TEEDERPIGRLLVDATFSPVDKIAYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRA 182

Query: 221 SRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVY 280
           + IL +QL  F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y
Sbjct: 183 ATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHY 239

Query: 281 MGDLIQRTEADMLRMANF 298
           +GDL+QRTE ++L+  N 
Sbjct: 240 IGDLVQRTEVELLKTPNL 257


>gi|161511715|emb|CAP16868.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           acidilactici]
          Length = 225

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 102/225 (45%), Positives = 144/225 (64%), Gaps = 2/225 (0%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++LK+  D  K 
Sbjct: 1   GNSLRRILLSSLPGAAITSVQIDNVLHEFSTIEGVVEDVTQIILNLKKVSLKIESDDEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR- 162
           + I   GP  VTAGDI    D+ VLNPD  IC +         LT   G GY  A  ++ 
Sbjct: 61  LDINVVGPANVTAGDIMGDGDVTVLNPDSPICTVAEGTTFHAVLTADTGRGYTSADENKA 120

Query: 163 -TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
              + PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ I TDGSIT  ++ +L++
Sbjct: 121 RKADMPIGVLPIDSIYTPIERVNYQVEKTRVGQRDDYDKLTLDIWTDGSITPSEATSLSA 180

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           +IL + L +F+N  +  KE +  +  +       L   +EEL+LS
Sbjct: 181 KILTEHLAIFVNLNDQAKETEIMVEKEETHKEKMLEMTIEELDLS 225


>gi|313183899|ref|YP_004021753.1| RNA polymerase alpha subunit [Equisetum arvense]
 gi|281371619|gb|ADA63552.1| RNA polymerase alpha subunit [Equisetum arvense]
          Length = 337

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 89/328 (27%), Positives = 162/328 (49%), Gaps = 23/328 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E  +  +           P  +G A+T+G A+RR L+  + G +IT+ +  G  
Sbjct: 13  VQWKCVESRIESKRLH-YGRFAISPFQKGQANTVGIAIRRALLGEVGGTSITSAKFQGAA 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ G+ E + DI++N+K I L+ +    ++  I   GP  + AGDIQ  + +++++
Sbjct: 72  HEYSTMAGIQESIHDILMNLKEIVLENNSYEVQKGFIQVIGPKKILAGDIQVCSSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P   I  +     + +EL + K  GY        EN+      IDA++ PI+  +Y+V S
Sbjct: 132 PSQYIATITKSISLNIELKIEKDRGYRIKNTDLKENE----FPIDAIFMPIRNANYSVHS 187

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDI 245
            ++ + L Y+ L + I T+GS+T E +++ A+R L D +   I+      E       DI
Sbjct: 188 FQKNKQL-YEILFLEIWTNGSLTPEKAISEATRNLIDLVVPLIHIGDKLTENPINGTSDI 246

Query: 246 NVKSLPFNPALLKK----------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           N  S+     L K           +++LEL  R+ N L+  N+  + DL+  TE D+  +
Sbjct: 247 NFPSVSGTNDLNKIAQEVAFKNIFIDQLELPARAYNGLKKVNVHTVSDLLMYTETDLRNI 306

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            + G+KS+ +I   L  +     + L +
Sbjct: 307 RSLGKKSVEQI---LEALQKKFAIKLSE 331


>gi|154424747|emb|CAL18476.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
          Length = 216

 Score =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 94/215 (43%), Positives = 142/215 (66%)

Query: 36  PRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLK 95
            RG+  TLGN+LRRVL++SL GAA+T++ IDGVLHE  ++ GV ED+  IILNIKGI +K
Sbjct: 1   ERGYGTTLGNSLRRVLLASLPGAAVTSINIDGVLHEFDTVPGVREDVMQIILNIKGIAVK 60

Query: 96  MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY 155
              +  K + +   GP  VTAGDI T +DIE++NPDH +  +   + ++  +TV+ G GY
Sbjct: 61  SYVEDEKIIELDVEGPAEVTAGDILTDSDIEIVNPDHYLFTIGEGSSLKATMTVNSGRGY 120

Query: 156 VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
           VPA  ++ +N P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED
Sbjct: 121 VPADENKKDNAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPED 180

Query: 216 SVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           ++ L++RIL + L +F N  E  K  +      + 
Sbjct: 181 ALGLSARILTEHLDLFTNLTEIAKSTEVMKEADTE 215


>gi|162964321|dbj|BAF95589.1| DNA-directed RNA polymerase alpha chain [Physcomitrella patens]
 gi|162964323|dbj|BAF95590.1| DNA-directed RNA polymerase alpha chain [Physcomitrella patens]
          Length = 525

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 89/339 (26%), Positives = 155/339 (45%), Gaps = 26/339 (7%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           Q + Q  ++   +E                 P  +G A T+GNALRR L+  ++GAAIT 
Sbjct: 192 QSSTQSPLQWRCVETFKENDHRH-YARFAVSPFRQGQAITVGNALRRALLGEVQGAAITC 250

Query: 63  VQI--DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
                 G++HE  ++ G+ E + DI+LN++ + +  +    ++  I   GP  V AGDI 
Sbjct: 251 ATFKDMGIVHEYQAVDGIQETVQDILLNVRDVAIGSNTHEPQKAFISVMGPRQVIAGDIL 310

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               + V +P   I  +       +E+ V K  GY      ++ N   G   ID+++ P+
Sbjct: 311 CPPSLVVPDPSQNIALVTAAIPFNVEIEVEKDVGYRIVDPGKSTN---GRFYIDSVFMPV 367

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            + +Y+V S     V   + L + I T+GSI+ E+++  A+R L D L   +  E  +  
Sbjct: 368 VQANYSVHSFEVEDVT-REILFLEIYTNGSISPEEALIEAARSLIDLLLPLLESEVIEVT 426

Query: 241 VKEDINVKSLPFNPALLKK----------------VEELELSVRSTNCLRGENIVYMGDL 284
              +    S   +                      +++L+L  R+ NCL+  NI  + DL
Sbjct: 427 NTTEKENGSRNISMLSSFLSSSDQITKEVTYKHVFIDQLKLPARAYNCLKRANIHTVSDL 486

Query: 285 IQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +  T+ D++R+ NFG+KS+ E+   L        ++LP 
Sbjct: 487 LDYTQDDLMRIKNFGKKSVEEVLEALRA---QFNISLPK 522


>gi|157493283|gb|ABV58007.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 249

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 110/252 (43%), Positives = 168/252 (66%), Gaps = 8/252 (3%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+
Sbjct: 1   EPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGL 60

Query: 93  NLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVVRMELTVS 150
            +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L   +A + M + V 
Sbjct: 61  AVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVE 120

Query: 151 KGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T
Sbjct: 121 RGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMET 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V++LEL+V
Sbjct: 181 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTV 237

Query: 268 RSTNCLRGENIV 279
           RS NCL+ E I 
Sbjct: 238 RSANCLKAEAIH 249


>gi|26554440|ref|NP_758374.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma penetrans
           HF-2]
 gi|38372493|sp|Q8EUD7|RPOA_MYCPE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|26454450|dbj|BAC44778.1| RNA polymerase subunit alpha [Mycoplasma penetrans HF-2]
          Length = 331

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 99/320 (30%), Positives = 170/320 (53%), Gaps = 15/320 (4%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
           NI+      ++ +  + + +PL RGF HTLGN+LRRVL+S++ G ++ A++I  V HE  
Sbjct: 8   NIQIGKDQNKDADYGVFVFKPLERGFGHTLGNSLRRVLLSNIIGHSLFAIKIPNVSHEFQ 67

Query: 74  SIKGVHEDLTDIILNIKGINLKMS----GDSHKRVTIFKRGP---------GVVTAGDIQ 120
           SIKGV EDLT IILN+K + +K+     G+  ++ T  ++ P         GV+ A DI+
Sbjct: 68  SIKGVKEDLTQIILNLKRLVVKIDQEIFGEEEQKETSLEKWPTLKIDFSKGGVLKASDIE 127

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T    E++N D  I  ++     +MEL V  G G+     ++   + I +I +D+ +SP+
Sbjct: 128 TPVGFEIINKDMYIATIESGVKFKMELFVKTGRGFTTFSENKELINAINVIAVDSNFSPV 187

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN--FEEPK 238
            KV Y V   +  +    D L + + T+G+++  ++VA++++IL +     +   F+   
Sbjct: 188 LKVGYKVSDIKTTKNEINDVLELEVATNGAVSAAEAVAMSAKILLEHYKPIVTELFDNYN 247

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                +          +L   ++ELELSVRS NCL+   I  +  L  +T+ ++ ++ N 
Sbjct: 248 DLRIINEEATVSSSKSSLAISIDELELSVRSYNCLKRAGIHTITQLTDKTKGEIEKIRNL 307

Query: 299 GRKSLVEIKGVLGTMGLFLG 318
           G+KS  EI   +    L L 
Sbjct: 308 GKKSFKEIIKKIQDRNLKLK 327


>gi|269784300|emb|CBH50795.1| alpha subunit of RNA polymerase [Vibrio sp. C 14.7]
          Length = 261

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 113/264 (42%), Positives = 172/264 (65%), Gaps = 8/264 (3%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGV 113
           + G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G 
Sbjct: 1   MPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGP 60

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIG 169
           V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG
Sbjct: 61  VVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL 
Sbjct: 121 RLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLD 180

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
            F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMANFGRKSLVEIKGVLGTM 313
            ++L+  N G+KSL EIK VL + 
Sbjct: 238 VELLKTPNLGKKSLTEIKDVLASR 261


>gi|161511721|emb|CAP16871.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           acidilactici]
          Length = 225

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 101/225 (44%), Positives = 142/225 (63%), Gaps = 2/225 (0%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++LK+  D
Sbjct: 1   GTTLGNSLRRILLSSLPGAAITSVQIDNVLHEFSTIEGVVEDVTQIILNLKKVSLKIESD 60

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             K + I   GP  VTAGDI    D+ VLNPD  IC +         LT   G GY  A 
Sbjct: 61  DEKTLDINVVGPANVTAGDIMGDGDVTVLNPDSPICTVAEGTTFHAVLTADTGRGYTSAD 120

Query: 160 HHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
            ++    + PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ I TDGSIT  ++ 
Sbjct: 121 ENKARKADMPIGVLPIDSIYTPIERVNYQVEKTRVGQRDDYDKLTLDIWTDGSITPSEAT 180

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           +L+++IL + L +F+N  +  KE +  +  +       L   +EE
Sbjct: 181 SLSAKILTEHLAIFVNLNDQAKETEIMVEKEETHKEKMLEMTIEE 225


>gi|119668321|emb|CAK95507.1| RNA polymerase alpha subunit [Lactobacillus gasseri]
          Length = 214

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 98/212 (46%), Positives = 143/212 (67%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G A++ +QIDGVLHE S+I GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTALSYIQIDGVLHEFSTIPGVREDVTKIILNLKKLELKSLS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K   I   GP +VTA D++  +DIEVLNPD  IC++     + M + +  G GYVPA
Sbjct: 61  DEEKIAEIDVTGPAIVTAADLKVDSDIEVLNPDQYICSIADGGHLHMNVAIKNGRGYVPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++T++ PIG+I +D+L+SPIKKV+Y VESAR G+  DYDKL++ I TDGSIT  D+++
Sbjct: 121 SENKTDDMPIGVIPVDSLFSPIKKVNYQVESARVGKRDDYDKLTLEIWTDGSITPNDALS 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
            A++IL +   +F++ +   +     +  +  
Sbjct: 181 FAAKILVEHFKVFMSTDMDAQFDDVMVEKEDD 212


>gi|308125193|gb|ADO14945.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           saccharolyticus]
          Length = 204

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 96/204 (47%), Positives = 139/204 (68%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNIKG+ LKM G+  K 
Sbjct: 1   GNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNIKGLALKMYGEEEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I   GP  VTAGDI   +D+E+LN D  IC +         LTV  G GYV A  ++ 
Sbjct: 61  LEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGTTFHARLTVRPGRGYVQADENKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI   D+++LA++I
Sbjct: 121 EDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIEPLDAMSLAAKI 180

Query: 224 LQDQLGMFINFEEPKKEVKEDINV 247
           + + L +F+N  +  K  +  +  
Sbjct: 181 MTEHLDIFVNLTDEAKNAEIMVEK 204


>gi|150036834|emb|CAM98282.1| DNA-directed RNA polymerase alpha chain [Leuconostoc fallax]
          Length = 228

 Score =  241 bits (614), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 92/228 (40%), Positives = 143/228 (62%), Gaps = 2/228 (0%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T +ILN+K + L +  D
Sbjct: 1   GTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVVLAIDSD 60

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             K + I  +GP  VTA D+Q   DIEVLNP+  +  +     + M +T  KG GY  A 
Sbjct: 61  EEKSLEIDVQGPAEVTAADLQGSADIEVLNPELHLATVAAGKSLHMTVTAVKGRGYSSAD 120

Query: 160 HHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
            ++   +  PIG++ +D++Y+PI++V+Y VE+ R GQ  DYDKL+  I T+GSI   D++
Sbjct: 121 ENKQLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGQRDDYDKLTFDIWTNGSIKPSDAL 180

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
           +L ++IL + L +F +      E +  ++V+    +      +E+L+L
Sbjct: 181 SLGAKILSEHLNLFTDISSVAAETEVMVDVEQTVSSVQDSAPIEDLDL 228


>gi|119662317|emb|CAJ33146.1| RNA polymerase alpha subunit [Lactobacillus johnsonii]
          Length = 214

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 98/212 (46%), Positives = 143/212 (67%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G A++ +QIDGVLHE S+I GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTALSYIQIDGVLHEFSTIPGVREDVTKIILNLKKLELKSLS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K   I   GP +VTA D++  +DIEVLNPD  IC++     + M + +  G GYVPA
Sbjct: 61  DEEKIAEIDVTGPAIVTAADLKVDSDIEVLNPDQYICSIADGGHLHMNVAIKTGRGYVPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++T++ PIG+I +D+L+SPIKKV+Y VESAR G+  DYDKL++ I TDGSIT  D+++
Sbjct: 121 SENKTDDMPIGVIPVDSLFSPIKKVNYQVESARVGKRDDYDKLTLEIWTDGSITPNDALS 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
            A++IL +   +F++ +   +     +  +  
Sbjct: 181 FAAKILVEHFKVFMSTDMDAQFDDVMVEKEDD 212


>gi|193795092|gb|ACF21675.1| RpoA [Sinorhizobium sp. 206]
          Length = 212

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 150/212 (70%), Positives = 181/212 (85%), Gaps = 1/212 (0%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           KR+ + K+GPG VTAGDIQTV DIE+LNPDHVIC LD  A +RME TV+ G GYVPA  +
Sbjct: 1   KRMVVRKQGPGAVTAGDIQTVGDIEILNPDHVICTLDEGAEIRMEFTVNNGKGYVPADRN 60

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKL+MTI+TDGS+TGED+VA A+
Sbjct: 61  RAEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLTMTIETDGSVTGEDAVAFAA 120

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           RILQDQLG+F+NF+EP+KE +E+ +V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+
Sbjct: 121 RILQDQLGVFVNFDEPQKEAEEE-SVTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           GDLIQ+TEA+MLR  NFGRKSL EIK VL +M
Sbjct: 180 GDLIQKTEAEMLRTPNFGRKSLNEIKEVLASM 211


>gi|301353363|ref|YP_003795612.1| RNA polymerase alpha subunit [Pteridium aquilinum subsp. aquilinum]
 gi|301016281|gb|ADK47568.1| RNA polymerase alpha subunit [Pteridium aquilinum subsp. aquilinum]
          Length = 347

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 77/314 (24%), Positives = 147/314 (46%), Gaps = 19/314 (6%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            ++I+   +E     +        +  P  RG   T+G A+RR  +  + G +IT  +  
Sbjct: 10  TQVIQWKCVESKTESKRLH-YGRFVVSPFKRGQVSTVGIAMRRASLEEVEGTSITCARFH 68

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S+I G+ E + D+++N+K I  K   +  +       GP  VTAGD      ++
Sbjct: 69  GVVHEYSTITGIQETIRDVLVNLKEIAPKSDSNDIQEAVSSVTGPKKVTAGDTLLPPSVK 128

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
            ++    +  +     V +E  + K  GY     H       G   +DA+  P++ V+Y+
Sbjct: 129 AIDDSQYVVTITQPISVNIESKIEKDCGYRIENSH---GYGGGEFPVDAVSMPVRNVNYS 185

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EPKKEVKEDI 245
           V     G+ +  + L + I T+GS+T ++++  AS+ L D L  F++ + E      ++ 
Sbjct: 186 VHLFGSGKAM-RETLFIEIWTNGSLTPDEAICEASKKLIDLLTPFLHVKCEDVPHSGDNQ 244

Query: 246 NVKSLPFNPALLKK-------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +  +   +P+                 +++LEL  R+ NCL+   I  + DL+  +  D 
Sbjct: 245 DFSASTGSPSHFDDVSELEGKISKNTFIDQLELPARAFNCLKRAEIHTISDLLNYSREDS 304

Query: 293 LRMANFGRKSLVEI 306
            R+ +FG+KS+ ++
Sbjct: 305 SRIKSFGQKSVDQV 318


>gi|150187048|emb|CAK30159.1| RNA polymerase alpha subunit [Streptococcus australis ATCC 700641]
          Length = 217

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 92/217 (42%), Positives = 140/217 (64%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRRVL++SL GAA+T++ I+GVLHE  ++ GV ED+  IILN+KGI +K 
Sbjct: 1   RGYGTTLGNSLRRVLLASLPGAAVTSINIEGVLHEFDTVPGVREDVMQIILNVKGIAVKS 60

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
                K + +   GP  VTAGDI T +DIE++NPDH +  +   +  +  LTV+ G GYV
Sbjct: 61  YVQDEKIIELDVEGPAEVTAGDILTDSDIEIVNPDHYLFTIGEGSSFKATLTVNSGRGYV 120

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
           PA  ++ ++ P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED+
Sbjct: 121 PADQNKKDDAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           + L++RIL + L +F N  E          V +   +
Sbjct: 181 LGLSARILTEHLNLFTNLTEIAIATDVMKEVDTASDD 217


>gi|156752147|gb|ABU93824.1| RNA polymerase subunit A [Vibrio sp. 09022]
          Length = 256

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 111/259 (42%), Positives = 171/259 (66%), Gaps = 8/259 (3%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVT 105
           LRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T
Sbjct: 1   LRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFIT 60

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HH 161
           + K G G V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H 
Sbjct: 61  LNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHT 120

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
             +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+
Sbjct: 121 EEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAA 180

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
            IL +QL  F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+
Sbjct: 181 TILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYI 237

Query: 282 GDLIQRTEADMLRMANFGR 300
           GDL+QRTE ++L+  N G+
Sbjct: 238 GDLVQRTEVELLKTPNLGK 256


>gi|190411113|gb|ACE78311.1| RpoA [Vibrio campbellii]
          Length = 257

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 111/260 (42%), Positives = 172/260 (66%), Gaps = 8/260 (3%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRV 104
           ALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +
Sbjct: 1   ALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---H 160
           T+ K G G V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H
Sbjct: 61  TLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIH 120

Query: 161 HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           +  +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A
Sbjct: 121 NEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRA 180

Query: 221 SRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVY 280
           + IL +QL  F++  + +         +   F+P LL+ V++LEL+VRS NC + E I Y
Sbjct: 181 ATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCRKAEAIHY 237

Query: 281 MGDLIQRTEADMLRMANFGR 300
           +GDL+QRTE ++L+  N G+
Sbjct: 238 IGDLVQRTEVELLKTPNLGK 257


>gi|119662279|emb|CAJ33126.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 210

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 92/210 (43%), Positives = 136/210 (64%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + +   GP  VTA D++   D++VLNPD  IC +     + MEL V  G GYV A
Sbjct: 61  DEQKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMELAVKNGRGYVTA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++
Sbjct: 121 SDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALS 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVK 248
            A++IL +   +F + +   +  +  +  +
Sbjct: 181 FAAKILVEHFKVFESADANTQFSEVMVEKE 210


>gi|119668281|emb|CAK95497.1| RNA polymerase alpha subunit [Lactobacillus amylolyticus]
          Length = 217

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 93/207 (44%), Positives = 136/207 (65%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK + 
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSNS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + +   GP  VTA D++  +D+EVLNPD  IC +     + M++ V  G GYV A
Sbjct: 61  DEQKVIELDVEGPATVTADDLKVDSDVEVLNPDQYICTIAEGGHLHMQIAVKNGRGYVAA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++E+ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++
Sbjct: 121 SDNKSEDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSINPNDALS 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDI 245
            A+ IL +   +F + +   K  +  +
Sbjct: 181 FAANILVEHFKVFESADADNKFSEVMV 207


>gi|119662367|emb|CAJ33172.1| RNA polymerase alpha subunit [Lactobacillus ultunensis]
          Length = 212

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 93/212 (43%), Positives = 136/212 (64%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + +   GP  VTA D++   D++VLNPD  IC +     + MEL V  G GYV A
Sbjct: 61  DEQKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMELAVKNGRGYVTA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++
Sbjct: 121 SDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALS 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
            A++IL +   +F + +   K  +  +  +  
Sbjct: 181 FAAKILVEHFKVFESADANTKFSEVMVEKEDD 212


>gi|308125189|gb|ADO14943.1| DNA-directed RNA polymerase alpha chain [Enterococcus pallens]
          Length = 204

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 97/204 (47%), Positives = 140/204 (68%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNIKG+ LK+  +  K 
Sbjct: 1   GNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVVQIILNIKGLALKLFTEEEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G GYV A  ++ 
Sbjct: 61  LEIDITGPATVTAGDIIVDSDVEILNKDLYICTVSEGATFHARLTVRPGRGYVQADENKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           E+ PIG++ +D++Y+P++KV+Y VE+ R G+  DYDKL+M I TDGSI  +++++LA++I
Sbjct: 121 EDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDYDKLTMEIWTDGSIIAQEALSLAAKI 180

Query: 224 LQDQLGMFINFEEPKKEVKEDINV 247
           L + L +F+N  +  K  +  +  
Sbjct: 181 LTEHLDIFVNLTDEAKNAEIMVEK 204


>gi|254458753|ref|ZP_05072177.1| DNA-directed RNA polymerase, alpha subunit [Campylobacterales
           bacterium GD 1]
 gi|207084519|gb|EDZ61807.1| DNA-directed RNA polymerase, alpha subunit [Campylobacterales
           bacterium GD 1]
          Length = 332

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 97/328 (29%), Positives = 172/328 (52%), Gaps = 7/328 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
            P   +   + Q  EN   ++A P   G+A +L + LRR L+SS  G A  A++I+G  H
Sbjct: 7   TPLAPQEFEVEQISENEANIMAYPFETGYAISLAHPLRRFLLSSSVGYAPIAIKIEGAKH 66

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           E  S++G+ ED++D ILN+K I  K+  + S  +++    GP  +   D+ +  ++EV+ 
Sbjct: 67  EFDSVRGMLEDISDFILNLKEIRFKLKDEASEAKISYSFAGPCTIKGADLNSD-EVEVVT 125

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  +  L+ D+ +   + +++G GYVP++    E    G I +DA ++P++  +Y +E+
Sbjct: 126 PDAPLATLNEDSTLNFVIKIAQGIGYVPSEDTHDE-LEDGYIALDAYFTPVRSATYKIEN 184

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                  +++++ + I TDG I+  D+   +  ++  QL +F N E   K       V+ 
Sbjct: 185 VLVEDNPNFERVILNIRTDGQISPLDAFKNSLEVMYAQLAVF-NSEISIKAATTMERVEE 243

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
            P    L+  ++ L LS RS NCL   +I  +G++   ++ D+  + N G+KS  EI   
Sbjct: 244 NPDLKKLVTHIDSLGLSARSFNCLDRSSIKLVGEIALMSQNDLKNVKNLGKKSYDEIVDK 303

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYE 337
           L   G  +G +L D   + +  L KK E
Sbjct: 304 LLEFGFAVGADLAD---DVVSALKKKIE 328


>gi|308125199|gb|ADO14948.1| DNA-directed RNA polymerase alpha chain [Enterococcus termitis]
          Length = 204

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 97/204 (47%), Positives = 143/204 (70%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+ LK+  +  K 
Sbjct: 1   GNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGLALKLYAEEEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I   GP  VTAGDI   +D+E+LN D VIC++   A     LTV  G GYV A  ++ 
Sbjct: 61  LEIDITGPATVTAGDIIVDSDVEILNKDLVICSVSEGATFHARLTVKPGRGYVQADENKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI  +++++LA++I
Sbjct: 121 EDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIIPQEALSLAAKI 180

Query: 224 LQDQLGMFINFEEPKKEVKEDINV 247
           + + L +F+N  +  K  +  +  
Sbjct: 181 MTEHLDIFVNLTDEAKNAEIMVEK 204


>gi|308125183|gb|ADO14940.1| DNA-directed RNA polymerase alpha chain [Enterococcus aquimarinus]
          Length = 204

 Score =  240 bits (612), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 94/204 (46%), Positives = 139/204 (68%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  IILNIKG+ LKM G   K 
Sbjct: 1   GNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQIILNIKGLALKMYGQEEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I   GP  VTAGDI   +D+E+LN +  IC +   A     LTV  G GYV A  ++ 
Sbjct: 61  LEIDITGPATVTAGDIIVDSDVEILNKEMYICTVSEGATFHARLTVRPGRGYVQADENKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           ++ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL++ I TDGSI   D+++LA++I
Sbjct: 121 DDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTIEIWTDGSIEPLDAMSLAAKI 180

Query: 224 LQDQLGMFINFEEPKKEVKEDINV 247
           + + L +F+N  +  K  +  +  
Sbjct: 181 MTEHLDIFVNLTDEAKHAEIMVEK 204


>gi|295809868|emb|CBL85110.1| alpha subunit of RNA polymerase [Vibrio tapetis]
          Length = 263

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 112/263 (42%), Positives = 170/263 (64%), Gaps = 8/263 (3%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGV 113
           + G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +K+  G     +T+ K G G 
Sbjct: 1   MPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVKVAEGKDEVFITLNKSGSGP 60

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHH---RTENDPIG 169
           V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA        +  PIG
Sbjct: 61  VVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASSRIHTEEDERPIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  ++ IL +QL 
Sbjct: 121 RLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRSATILAEQLD 180

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
            F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDIRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMANFGRKSLVEIKGVLGT 312
            ++L+  N G KSL EIK VL +
Sbjct: 238 VELLKTPNLGNKSLTEIKDVLAS 260


>gi|150187035|emb|CAK30156.1| RNA polymerase alpha subunit [Streptococcus entericus]
          Length = 222

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 91/222 (40%), Positives = 143/222 (64%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ 
Sbjct: 1   PLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNLKGLA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +K   D  K + +   GP  VTAGDI T +DIE++N +H +  +   A  +  L V+   
Sbjct: 61  IKSHVDEEKTMELDIVGPAEVTAGDILTDSDIEIINTNHYLFTIAEGASFKAVLKVNTDR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYVPA++++  + P+G + IDA+Y+P+KKV+Y VE AR G    +DKL++ I+T+G+I  
Sbjct: 121 GYVPAENNKKGDAPVGTLAIDAIYTPVKKVNYQVEPARVGSNDGFDKLTIDIETNGTIIP 180

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           ED++ L++ +L + L +F +  +    +      + +     
Sbjct: 181 EDALGLSANVLINHLNLFTDLTDIANNMDVLKETEVVSDEKV 222


>gi|71056860|emb|CAH58985.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
          Length = 205

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 98/205 (47%), Positives = 141/205 (68%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG+ LK+  +  K
Sbjct: 1   LGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNIKGLALKLFAEEEK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G GYV A  ++
Sbjct: 61  TLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTVKPGRGYVQADENK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDGSI  +++++LA++
Sbjct: 121 KEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDGSIIAQEALSLAAK 180

Query: 223 ILQDQLGMFINFEEPKKEVKEDINV 247
           IL + L +F+N  +  K  +  +  
Sbjct: 181 ILTEHLDIFVNLTDEAKNAEIMVEK 205


>gi|193795085|gb|ACF21672.1| RpoA [Rhizobium tropici]
 gi|193795087|gb|ACF21673.1| RpoA [Rhizobium tropici]
          Length = 212

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 152/213 (71%), Positives = 183/213 (85%), Gaps = 1/213 (0%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           KR+ + K+GPGVVTAGDIQTV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +
Sbjct: 1   KRMVVRKQGPGVVTAGDIQTVGDIEILNPEHVICTLDEGAEIRMEFTVNNGKGYVPAERN 60

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKLSM+I+TDGSITGED+VA A+
Sbjct: 61  RAEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLSMSIETDGSITGEDAVAFAA 120

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           RILQDQLG+F+NF+EP+KE +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+
Sbjct: 121 RILQDQLGVFVNFDEPQKEAEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           GDLIQ+TEA+MLR  NFGRKSL EIK VL +MG
Sbjct: 180 GDLIQKTEAEMLRTPNFGRKSLNEIKEVLASMG 212


>gi|254368646|ref|ZP_04984661.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           holarctica FSC022]
 gi|157121554|gb|EDO65739.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           holarctica FSC022]
          Length = 323

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 108/317 (34%), Positives = 179/317 (56%), Gaps = 11/317 (3%)

Query: 13  NNIEYIVLGQEEENRTLMI----AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           + +E++   Q +E+           P+ +G AH LGN++RRVL+SSL GA+I  V I  V
Sbjct: 6   SKLEFVPNIQLKEDLGAFSYKVQLSPVEKGMAHILGNSIRRVLLSSLSGASIIKVNIANV 65

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+++ V ED+ +I+ N+K + +K+     +  + +     GVV AGD +T   +E+
Sbjct: 66  LHEYSTLEDVKEDVVEIVSNLKKVAIKLDTGIDRLDLELSVNKSGVVRAGDFKTTQGVEI 125

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N D  I  L       +  TVS G          TE + +G I +DA ++PIK+V++ V
Sbjct: 126 INKDQPIATLTNQRAFSLTATVSVGRNVGILSAIPTELERVGDIAVDADFNPIKRVAFEV 185

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
                    D + L + + T+G+I    +V  A     +Q+ +F++   P      D+ +
Sbjct: 186 FD-----NGDSETLEVFVKTNGTIGPLAAVTKALEYFCEQISVFVSLRVPSNGKTGDVLI 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            S   +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK
Sbjct: 241 DSN-IDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIK 299

Query: 308 GVLGTMGLFLGMNLPDW 324
            +L    L LG+ + ++
Sbjct: 300 QILIDNNLSLGVQIDNF 316


>gi|154173639|ref|YP_001409131.1| DNA-directed RNA polymerase subunit alpha [Campylobacter curvus
           525.92]
 gi|171769258|sp|A7H0Y9|RPOA_CAMC5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|112802250|gb|EAT99594.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter curvus
           525.92]
          Length = 338

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 107/338 (31%), Positives = 167/338 (49%), Gaps = 10/338 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++K       P  IE   +    EN   + A P   G+A TL + LRR+L +S  G A  
Sbjct: 1   MRKITTSAYMPTEIEVQSIS---ENVAKITAYPFETGYAVTLAHPLRRLLYTSTVGFAPI 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQ 120
            V+I GV HE  S++G+ ED+   I+N+K I  K+  DS  + V    +GP  +T  D+ 
Sbjct: 58  GVKIKGVSHEFDSMRGMLEDVAFFIINLKKIRFKLKNDSEREVVEYSFKGPKEITGADLN 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               +E++NPD  +  ++ DA +   + + KG GYVP++  R E +    I +DA ++P+
Sbjct: 118 ND-VVEIVNPDAYLATINEDAELNFSVIIQKGIGYVPSEEIREEIEDDY-IALDAFFTPV 175

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KK  Y +E+       DY+K+  TI TDG +   ++       +  Q+ +F    +    
Sbjct: 176 KKAVYELENVLVEDDPDYEKIVFTITTDGQVGPIEAFKHCLEAMYQQMSVFKGVLDIDVN 235

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                +          L  VEEL LS RS NCL    I Y+G+L    E ++  + N G+
Sbjct: 236 APMMSSSVGGEHAKL-LSSVEELNLSARSFNCLDKAEIRYIGELALMDENELKDLKNLGK 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK V+  +G  +G    D   +S E+L KK  +
Sbjct: 295 KSLEEIKAVMEEIGYPVG---SDVLKDSKEQLRKKIAE 329


>gi|193795065|gb|ACF21664.1| RpoA [Sinorhizobium sp. 72]
          Length = 212

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 147/213 (69%), Positives = 182/213 (85%), Gaps = 1/213 (0%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           KR+ + K+GPGVVTAGDIQTV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +
Sbjct: 1   KRMVVRKQGPGVVTAGDIQTVGDIEILNPNHVICTLDEGAEIRMEFTVNNGKGYVPAERN 60

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R+E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKL+M+I+TDGS+TGED++A A+
Sbjct: 61  RSEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLTMSIETDGSVTGEDAIAFAA 120

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           RILQDQL +F+NF+EP+KE +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+
Sbjct: 121 RILQDQLSVFVNFDEPQKEAEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           GDLIQ+TEA+MLR  NFGRKSL EIK VL + G
Sbjct: 180 GDLIQKTEAEMLRTPNFGRKSLNEIKEVLASSG 212


>gi|150036786|emb|CAM98270.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 221

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 88/212 (41%), Positives = 133/212 (62%), Gaps = 2/212 (0%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D
Sbjct: 1   GTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSD 60

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A 
Sbjct: 61  DERSLEIDVQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSAD 120

Query: 160 HHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
            ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D++
Sbjct: 121 ENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGARDDYDKLTFDIWTNGSIKPSDAL 180

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           +L ++IL + L +F++      E    +  + 
Sbjct: 181 SLGAKILAEHLNLFMDISPVAAEASVMVEAEP 212


>gi|119668373|emb|CAK95478.1| RNA polymerase alpha subunit [Lactobacillus sakei subsp. carnosus]
          Length = 203

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 87/203 (42%), Positives = 139/203 (68%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRR+L++SL G A+T +QIDGVLHE S+I GV ED+T IILNIK + LK+  +  K +
Sbjct: 1   NSLRRILLASLPGTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKLHVEEDKTI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            I  +GP  VTA DI + +D+EVLN D  IC +       + +TV KG GYV A  ++++
Sbjct: 61  EIDVKGPATVTAADIISDDDVEVLNTDQYICTVAEGGNFHVRMTVKKGRGYVAAVQNKSD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           + PIG++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++I+
Sbjct: 121 DMPIGVLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKIM 180

Query: 225 QDQLGMFINFEEPKKEVKEDINV 247
            + L +F++  +  K  +  +  
Sbjct: 181 TEHLAIFVDLTDEAKNAEIMVEK 203


>gi|255321746|ref|ZP_05362901.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter showae
           RM3277]
 gi|255301226|gb|EET80488.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter showae
           RM3277]
          Length = 328

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 105/322 (32%), Positives = 170/322 (52%), Gaps = 8/322 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I +    EN   + A P   G+A TL + LRR+L SS  G A T V+I+GV HE  S++G
Sbjct: 5   ISVESISENVARITAYPFETGYAVTLAHPLRRLLYSSTVGFAATGVKIEGVSHEFDSMRG 64

Query: 78  VHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           + ED+   I+N+K I  K+  +S  + V    +GP  + AGD+++   ++++N D  +  
Sbjct: 65  MLEDVAQFIINLKNIRFKLKNESEREVVEYSFKGPKEIKAGDLKSD-VVDIVNLDAYLAT 123

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           ++ DA ++  + + KG GYVP++  R +N   G I +DA ++P+KK  Y + +       
Sbjct: 124 INEDAELKFSVIIQKGIGYVPSEEIR-DNTEEGYIALDAFFTPVKKAVYELVNVLVEDNP 182

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           DY+K+  T+ TDG +   ++   A   +  Q+ +F            +    S   +  L
Sbjct: 183 DYEKIIFTVTTDGQVGAIEAFKHAIEAMYQQMSVFKGVLNIDVSAGLNAQT-SGSEHAKL 241

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
           L+ VEEL LS RS NCL    I ++G+L    E ++  + N G+KSL EIK V+  +G  
Sbjct: 242 LQSVEELNLSARSFNCLDKAEIRFIGELALMDENELKELKNLGKKSLDEIKAVMQEIGYP 301

Query: 317 LGMNLPDWPPESIEELAKKYED 338
           +G +L        E+L KK  D
Sbjct: 302 VGGDLGG----GKEQLKKKIAD 319


>gi|223038488|ref|ZP_03608782.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter rectus
           RM3267]
 gi|222880345|gb|EEF15432.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter rectus
           RM3267]
          Length = 328

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 105/322 (32%), Positives = 170/322 (52%), Gaps = 8/322 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I +    EN   + A P   G+A TL + LRR+L SS  G A T V+I+GV HE  S++G
Sbjct: 5   ISVESISENVARITAYPFETGYAVTLAHPLRRLLYSSTVGFAATGVKIEGVSHEFDSMRG 64

Query: 78  VHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           + ED+   I+N+K I  K+  +S  + V    +GP  + AGD+++   ++++NPD  +  
Sbjct: 65  MLEDVAQFIINLKNIRFKLKNESEREVVEYSFKGPKEIKAGDLKSD-VVDIVNPDAYLAT 123

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           ++ DA ++  + + KG GYVP++  R  +   G I +DA ++P+KK  Y + +       
Sbjct: 124 INEDAELKFSVIIQKGIGYVPSEEIR-GDTEEGYIALDAFFTPVKKAVYELVNVLVEDNP 182

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           DY+K+  T+ TDG +   ++   A   +  Q+ +F            +    S   +  L
Sbjct: 183 DYEKIIFTVTTDGQVGAIEAFKHAIEAMYQQMSVFKGVLNIDISAGLNAQT-SGSEHAKL 241

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
           L+ VEEL LS RS NCL    I ++G+L    E ++  + N G+KSL EIK V+  +G  
Sbjct: 242 LQSVEELNLSARSFNCLDKAEIRFIGELALMDENELKELKNLGKKSLEEIKAVMQEIGYP 301

Query: 317 LGMNLPDWPPESIEELAKKYED 338
           +G +L        E+L KK  D
Sbjct: 302 VGGDLGG----GKEQLKKKIAD 319


>gi|308125185|gb|ADO14941.1| DNA-directed RNA polymerase alpha chain [Enterococcus caccae]
 gi|308125191|gb|ADO14944.1| DNA-directed RNA polymerase alpha chain [Enterococcus sp.
           CCRI-16985]
 gi|308125197|gb|ADO14947.1| DNA-directed RNA polymerase alpha chain [Enterococcus silesiacus]
 gi|308125201|gb|ADO14949.1| DNA-directed RNA polymerase alpha chain [Enterococcus sp.
           CCRI-16620]
 gi|308125203|gb|ADO14950.1| DNA-directed RNA polymerase alpha chain [Enterococcus sp.
           CCRI-16986]
          Length = 204

 Score =  239 bits (611), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 96/204 (47%), Positives = 143/204 (70%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+ LK+  +  K 
Sbjct: 1   GNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGLALKLYAEEEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I   GP  VTAGDI   +D+E+LN D +IC++   A     LTV  G GYV A  ++ 
Sbjct: 61  LEIDITGPATVTAGDIIVDSDVEILNKDLIICSVSEGATFHARLTVKPGRGYVQADENKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI  +++++LA++I
Sbjct: 121 EDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIIPQEALSLAAKI 180

Query: 224 LQDQLGMFINFEEPKKEVKEDINV 247
           + + L +F+N  +  K  +  +  
Sbjct: 181 MTEHLDIFVNLTDEAKNAEIMVEK 204


>gi|5107487|pdb|1BDF|A Chain A, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit
           N-Terminal Domain
 gi|5107488|pdb|1BDF|B Chain B, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit
           N-Terminal Domain
 gi|5107489|pdb|1BDF|C Chain C, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit
           N-Terminal Domain
 gi|5107490|pdb|1BDF|D Chain D, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit
           N-Terminal Domain
          Length = 235

 Score =  239 bits (611), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 100/237 (42%), Positives = 153/237 (64%), Gaps = 7/237 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALR +L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRAILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++ 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDL 234


>gi|71056862|emb|CAH58986.1| DNA-directed RNA polymerase alpha chain [Enterococcus malodoratus]
          Length = 205

 Score =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 98/205 (47%), Positives = 141/205 (68%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG+ LK+  +  K
Sbjct: 1   LGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNIKGLALKLFAEEEK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G GYV A  ++
Sbjct: 61  TLEIDITGPATVTAGDIIVDSDVEILNKDMYICTVSEGATFHARLTVKPGRGYVQADENK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDGSI  +++++LA++
Sbjct: 121 KEDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDGSIIAQEALSLAAK 180

Query: 223 ILQDQLGMFINFEEPKKEVKEDINV 247
           IL + L +F+N  +  K  +  +  
Sbjct: 181 ILTEHLDIFVNLTDEAKNAEIMVEK 205


>gi|150187071|emb|CAK30164.1| RNA polymerase alpha subunit [Streptococcus equi subsp. equi]
          Length = 215

 Score =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 91/213 (42%), Positives = 144/213 (67%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K 
Sbjct: 1   RGYGTTLGNSLRRVLLSSLPGAAVTSIRIDGVLHEFDTIPGVREDVMQIILNVKGLAVKS 60

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             +  K + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV+K  GYV
Sbjct: 61  YVEDEKIIELDVEGPAEVTAGDILTDSDIELVNPDHYLFTIADGYTLKASMTVAKKRGYV 120

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
           PA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED+
Sbjct: 121 PAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           + L++R+L + L +F +  +  K  +     + 
Sbjct: 181 LGLSARVLIEHLNLFTDLTDVAKATEVMKEAEK 213


>gi|118496877|ref|YP_897927.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. novicida U112]
 gi|194324099|ref|ZP_03057873.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. novicida FTE]
 gi|254372234|ref|ZP_04987725.1| hypothetical protein FTCG_01300 [Francisella tularensis subsp.
           novicida GA99-3549]
 gi|158512418|sp|A0Q4K8|RPOA1_FRATN RecName: Full=DNA-directed RNA polymerase subunit alpha 1;
           Short=RNAP subunit alpha 1; AltName: Full=RNA polymerase
           subunit alpha 1; AltName: Full=Transcriptase subunit
           alpha 1
 gi|118422783|gb|ABK89173.1| DNA-directed RNA polymerase, alpha subunit [Francisella novicida
           U112]
 gi|151569963|gb|EDN35617.1| hypothetical protein FTCG_01300 [Francisella novicida GA99-3549]
 gi|194321546|gb|EDX19030.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. novicida FTE]
 gi|328676346|gb|AEB27216.1| DNA-directed RNA polymerase alpha subunit [Francisella cf. novicida
           Fx1]
          Length = 323

 Score =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 109/319 (34%), Positives = 178/319 (55%), Gaps = 11/319 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           QE + PN     +          +   P+ +G AH LGN++RRVL+SSL GA+I  V I 
Sbjct: 8   QEFV-PN---IQLKEDLGAFSYKVQLSPVEKGMAHILGNSIRRVLLSSLSGASIIKVNIA 63

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDI 125
            VLHE S+++ V ED+ +I+ N+K + +K+     +  + +     GVV+AGD +T   +
Sbjct: 64  NVLHEYSTLEDVKEDVVEIVSNLKKVAIKLDTAIDRLDLELSVNKSGVVSAGDFKTTQGV 123

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++N D  I  L       +  TVS G          TE + +G I +DA ++PIK+V++
Sbjct: 124 EIINKDQPIATLTNQRAFSLTATVSVGRNVGILSAIPTELERVGDIAVDADFNPIKRVAF 183

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            V         D + L + + T+G+I    +V  A     +Q+ +F++   P      D+
Sbjct: 184 EVFD-----NGDSETLEVFVKTNGTIEPLAAVTKALEYFCEQISVFVSLRVPSNGKTGDV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            + S   +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL E
Sbjct: 239 LIDSN-IDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLGKKSLNE 297

Query: 306 IKGVLGTMGLFLGMNLPDW 324
           IK +L    L LG+ + ++
Sbjct: 298 IKQILIDNNLSLGVQIDNF 316


>gi|319955882|ref|YP_004167145.1| DNA-directed RNA polymerase subunit alpha [Nitratifractor
           salsuginis DSM 16511]
 gi|319418286|gb|ADV45396.1| DNA-directed RNA polymerase subunit alpha [Nitratifractor
           salsuginis DSM 16511]
          Length = 332

 Score =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 98/305 (32%), Positives = 159/305 (52%), Gaps = 4/305 (1%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     + + +  + R  +IA P   G+A TL + LRR+L+ S  G A  +V+I+G  HE
Sbjct: 8   PFLPSEVEINEISDTRAQVIAYPFESGYAVTLAHPLRRLLLGSSIGYAPISVKIEGAAHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
             SI+G+HED+   I+++K I  K+        V+   +GP  V AGD+     +EV+NP
Sbjct: 68  FDSIRGMHEDIAVFIIHLKNIRFKIKEGLDRAVVSYSFKGPREVVAGDLNND-QVEVVNP 126

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  +  L+ D  +   L ++KG GYVP++  + E D    I +DA ++P++K +Y +E+ 
Sbjct: 127 DQPLATLNEDGELTFTLEIAKGIGYVPSEDLQEEVD-GDAIALDAFFTPVRKANYAIENV 185

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
                 DY+K+   I+TDG I+   + A A   +  Q+ +F        E     + ++ 
Sbjct: 186 LVEDNPDYEKIVFEIETDGQISPVAAFANALETMHKQMSVFGEVMNLDLERSSGNSAENS 245

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
              P  L  V+ L L  RS N L    I Y+G+L+  +E ++  + N G+KSL EI+ VL
Sbjct: 246 ELKP-FLVPVDALGLGARSFNSLDRAGIKYLGELVLMSENELKEIKNLGKKSLDEIQEVL 304

Query: 311 GTMGL 315
              G 
Sbjct: 305 AEHGF 309


>gi|254373716|ref|ZP_04989199.1| DNA-directed RNA polymerase [Francisella novicida GA99-3548]
 gi|151571437|gb|EDN37091.1| DNA-directed RNA polymerase [Francisella novicida GA99-3548]
          Length = 323

 Score =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 109/319 (34%), Positives = 178/319 (55%), Gaps = 11/319 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           QE + PN     +          +   P+ +G AH LGN++RRVL+SSL GA+I  V I 
Sbjct: 8   QEFV-PN---IQLKEDLGAFSYKVQLSPVEKGMAHILGNSIRRVLLSSLSGASIIKVNIS 63

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDI 125
            VLHE S+++ V ED+ +I+ N+K + +K+     +  + +     GVV+AGD +T   +
Sbjct: 64  NVLHEYSTLEDVKEDVVEIVSNLKKVAIKLDTGIDRLDLELSVNKSGVVSAGDFKTTQGV 123

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++N D  I  L       +  TVS G          TE + +G I +DA ++PIK+V++
Sbjct: 124 EIINKDQPIATLTNQRAFSLTATVSVGRNVGILSAIPTELERVGDIAVDADFNPIKRVAF 183

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            V         D + L + + T+G+I    +V  A     +Q+ +F++   P      D+
Sbjct: 184 EVFD-----NGDSETLEVFVKTNGTIEPLAAVTKALEYFCEQISVFVSLRVPSNGKTGDV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            + S   +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL E
Sbjct: 239 LIDSN-IDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLGKKSLNE 297

Query: 306 IKGVLGTMGLFLGMNLPDW 324
           IK +L    L LG+ + ++
Sbjct: 298 IKQILIDNNLSLGVQIDNF 316


>gi|119668339|emb|CAK95509.1| RNA polymerase alpha subunit [Lactobacillus kefiri]
          Length = 218

 Score =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 102/217 (47%), Positives = 144/217 (66%), Gaps = 4/217 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K I+LK+ G
Sbjct: 1   YGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKISLKLDG 60

Query: 99  --DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             D  + + I   GP  VTAGDIQ   D+ VLNPD  I  +   A   M LT +KG GYV
Sbjct: 61  PEDEEENLEIDVIGPADVTAGDIQADGDVTVLNPDLHIATVAEGATFHMRLTANKGRGYV 120

Query: 157 PAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A  ++      PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ I TDGSIT  
Sbjct: 121 SAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDIWTDGSITPS 180

Query: 215 DSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           ++V+LA++IL + L MF++  +  K  +  +  +   
Sbjct: 181 EAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEKEETH 217


>gi|208780325|ref|ZP_03247666.1| DNA-directed RNA polymerase, alpha subunit [Francisella novicida
           FTG]
 gi|208743693|gb|EDZ89996.1| DNA-directed RNA polymerase, alpha subunit [Francisella novicida
           FTG]
          Length = 323

 Score =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 109/319 (34%), Positives = 178/319 (55%), Gaps = 11/319 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           QE + PN     +          +   P+ +G AH LGN++RRVL+SSL GA+I  V I 
Sbjct: 8   QEFV-PN---IQLKEDLGAFSYKVQLSPVEKGMAHILGNSIRRVLLSSLSGASIIKVNIA 63

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDI 125
            VLHE S+++ V ED+ +I+ N+K + +K+     +  + +     GVV+AGD +T   +
Sbjct: 64  NVLHEYSTLEDVKEDVVEIVSNLKKVAIKLDAGIDRLDLELSVNKSGVVSAGDFKTTQGV 123

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++N D  I  L       +  TVS G          TE + +G I +DA ++PIK+V++
Sbjct: 124 EIINKDQPIATLTNQRAFSLTATVSVGRNVGILSAIPTELERVGDIAVDADFNPIKRVAF 183

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            V         D + L + + T+G+I    +V  A     +Q+ +F++   P      D+
Sbjct: 184 EVFD-----NGDSETLEVFVKTNGTIEPLAAVTKALEYFCEQISVFVSLRVPSNGKTGDV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            + S   +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL E
Sbjct: 239 LIDSN-IDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLGKKSLNE 297

Query: 306 IKGVLGTMGLFLGMNLPDW 324
           IK +L    L LG+ + ++
Sbjct: 298 IKQILIDNNLSLGVQIDNF 316


>gi|12045030|ref|NP_072840.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma genitalium
           G37]
 gi|255660326|ref|ZP_05405735.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma genitalium
           G37]
 gi|1350841|sp|P47423|RPOA_MYCGE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|3844773|gb|AAC71396.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma genitalium
           G37]
 gi|166078895|gb|ABY79513.1| DNA-directed RNA polymerase, alpha subunit [synthetic Mycoplasma
           genitalium JCVI-1.0]
          Length = 328

 Score =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 87/317 (27%), Positives = 157/317 (49%), Gaps = 13/317 (4%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
            +          N  +    PL  GF  T+GNA+RRVL+S + GA++ A+ I GV  E S
Sbjct: 10  KVNNNQPTNTNPNYGIFEVAPLESGFGITIGNAMRRVLLSCIPGASVFAIAISGVKQEFS 69

Query: 74  SIKGVHEDLTDIILNIKGINLKMSG-------------DSHKRVTIFKRGPGVVTAGDIQ 120
           +++GV ED+T+++LN K + +++S              +    + +     G V A D++
Sbjct: 70  NVEGVLEDVTEMVLNFKQLVVRISDLLFEDGEMIEPPLERWPVLKVTAEKKGAVYAKDLE 129

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
                EV+N D  + +L  D  + + + V +G G+     +R   + +G+I  DA +SP+
Sbjct: 130 CPAGFEVINKDLYLFSLQKDMKLTVSVYVKQGRGFTSFLENRELINSLGIIATDANFSPV 189

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
               Y V+  +  +    D L+  I T+G+I   D+ A+A++IL + L   ++  E  K 
Sbjct: 190 LHCGYEVQEVKTSKQKLTDHLTFKIATNGAIKAVDAFAMAAKILIEHLNPIVSVNESIKN 249

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           +             +  K++EEL+ +VR+ NCL+   I  + +L+ ++  D+  + N G+
Sbjct: 250 LTIIQEKAEERKVKSFAKQIEELDFTVRTFNCLKRSGIHTLQELLSKSLTDIREIRNLGK 309

Query: 301 KSLVEIKGVLGTMGLFL 317
           KS  EI   +  +GL  
Sbjct: 310 KSEREIIKKVQELGLKF 326


>gi|119668317|emb|CAK95459.1| RNA polymerase alpha subunit [Lactobacillus gallinarum]
          Length = 214

 Score =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 92/212 (43%), Positives = 136/212 (64%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V  G GYV A
Sbjct: 61  DERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNGRGYVAA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++
Sbjct: 121 SDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALS 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
            A++IL +   +F + +   K  +  +  +  
Sbjct: 181 FAAKILVEHFKVFESADADTKFSEVMVEKEDD 212


>gi|119668309|emb|CAK95455.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           delbrueckii]
          Length = 200

 Score =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 89/199 (44%), Positives = 130/199 (65%)

Query: 31  IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIK 90
           + EPL RGF  TLGN+LRRVL++S+ G  +  V+IDG+LHE +++ GV ED+T IILN+K
Sbjct: 1   VVEPLERGFGTTLGNSLRRVLLTSVPGTGLVKVKIDGILHEFTTVPGVKEDVTKIILNLK 60

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            + L+   +  K + +   GP  VTA D++   D+EVLNPD  IC +     + M + V 
Sbjct: 61  KLVLRAYTEEVKTIELDVEGPATVTAEDLKADADVEVLNPDQYICTIAQGGHLHMWIDVC 120

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            G GYVPA  ++T    IG I +D+L+SPI+KV+Y VES R G+  D+DKL++ I T+GS
Sbjct: 121 NGRGYVPASENKTAEMFIGDIPVDSLFSPIEKVNYQVESTRVGKREDFDKLTLEIWTNGS 180

Query: 211 ITGEDSVALASRILQDQLG 229
           I   D++  A+R+L +   
Sbjct: 181 IAPNDALNFAARVLVEHFK 199


>gi|119668319|emb|CAK95460.1| RNA polymerase alpha subunit [Lactobacillus gasseri]
          Length = 198

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 98/197 (49%), Positives = 140/197 (71%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G A++ +QIDGVLHE S+I GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTALSYIQIDGVLHEFSTIPGVREDVTKIILNLKKLELKSLS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K   I   GP +VTA D++  +DIEVLNPD  IC++     + M + +  G GYVPA
Sbjct: 61  DEEKIAEIDVTGPAIVTAADLKVDSDIEVLNPDQYICSIADGGHLHMNVAIKNGRGYVPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++T++ PIG+I +D+L+SPIKKV+Y VESAR G+  DYDKL++ I TDGSIT  D+++
Sbjct: 121 SENKTDDMPIGVIPVDSLFSPIKKVNYQVESARVGKRDDYDKLTLEIWTDGSITPNDALS 180

Query: 219 LASRILQDQLGMFINFE 235
            A++IL +   +F++ +
Sbjct: 181 FAAKILVEHFKVFMSTD 197


>gi|268680561|ref|YP_003304992.1| DNA-directed RNA polymerase, subunit alpha [Sulfurospirillum
           deleyianum DSM 6946]
 gi|268618592|gb|ACZ12957.1| DNA-directed RNA polymerase, alpha subunit [Sulfurospirillum
           deleyianum DSM 6946]
          Length = 337

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 106/328 (32%), Positives = 172/328 (52%), Gaps = 10/328 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  IE   +     N+  + A P   GFA TL + LRR+L+ S  G+A TAV+I+GV HE
Sbjct: 11  PTEIEVENIS---ANKVQISAYPFESGFAVTLAHPLRRLLLGSTIGSAPTAVKIEGVTHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKR-VTIFKRGPGVVTAGDIQTVNDIEVLNP 130
             S++G+ ED+   I+N+K I  K+ GD  +  V     GP  +   D+   + IE++ P
Sbjct: 68  FDSMRGMLEDVALFIINLKNIRFKIKGDEKRVEVNYSFSGPKEIKGSDL-ANSHIEIVTP 126

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  +  ++ DA     L + KG GYVP++ +  +      I +DA ++P+K+  Y +E+ 
Sbjct: 127 DTYLATINEDAEFNFSLIIEKGIGYVPSE-NIRDLLTDDYIALDAFFTPVKRAVYDIENV 185

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
                 +Y+K+  TI+TDG ++  ++   A   +  Q+ +F    +     K + +  ++
Sbjct: 186 LVEDNPNYEKIVFTIETDGLVSPIEAFKNALEAMYAQMSVFNGILDIAVAPKNETSHDNV 245

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 L+ VEEL LS RS NCL    + Y+G+L   +E ++  + N G+KSL EI+ V+
Sbjct: 246 ELGKL-LQSVEELNLSARSFNCLDRAEVKYIGELALMSETELKDLKNLGKKSLEEIRQVM 304

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKYED 338
              G  +G N  D   E+   L KK ED
Sbjct: 305 EESGYPVGYNFSD---ETASLLKKKIED 329


>gi|119662845|emb|CAJ33215.1| RNA polymerase alpha subunit [Lactobacillus hamsteri]
          Length = 212

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 95/212 (44%), Positives = 138/212 (65%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + +   GP  VTA D++  +D+EVLNPD  IC +     + M++ V  G GYV A
Sbjct: 61  DEQKVIELDVEGPATVTADDLKVDSDVEVLNPDQYICTIAEGGHLHMQIAVKNGRGYVAA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++E+ PIG+I +D+L+SPIKKV+Y VESAR G+  D+DKL+  I TDGSI   D+++
Sbjct: 121 SDNKSEDMPIGVIPVDSLFSPIKKVNYQVESARVGKRDDFDKLTFEIWTDGSIKPNDALS 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
            AS+IL +   +F + +   K  +  +  +  
Sbjct: 181 FASKILVEHFKVFESADANAKFSEVMVEKEDD 212


>gi|56707503|ref|YP_169399.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. tularensis SCHU S4]
 gi|89255695|ref|YP_513056.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica LVS]
 gi|110669974|ref|YP_666531.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. tularensis FSC198]
 gi|115314195|ref|YP_762918.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica OSU18]
 gi|134302561|ref|YP_001122531.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. tularensis WY96-3418]
 gi|156501643|ref|YP_001427708.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica FTNF002-00]
 gi|167010988|ref|ZP_02275919.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. holarctica FSC200]
 gi|187932118|ref|YP_001892103.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. mediasiatica FSC147]
 gi|224456566|ref|ZP_03665039.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. tularensis MA00-2987]
 gi|254370808|ref|ZP_04986813.1| hypothetical protein [Francisella tularensis subsp. tularensis
           FSC033]
 gi|254874323|ref|ZP_05247033.1| rpoA1, DNA-directed RNA polymerase, alpha subunit [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|290953188|ref|ZP_06557809.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica URFT1]
 gi|295313556|ref|ZP_06804145.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica URFT1]
 gi|81597921|sp|Q5NHU3|RPOA1_FRATT RecName: Full=DNA-directed RNA polymerase subunit alpha 1;
           Short=RNAP subunit alpha 1; AltName: Full=RNA polymerase
           subunit alpha 1; AltName: Full=Transcriptase subunit
           alpha 1
 gi|122325767|sp|Q0BNQ3|RPOA1_FRATO RecName: Full=DNA-directed RNA polymerase subunit alpha 1;
           Short=RNAP subunit alpha 1; AltName: Full=RNA polymerase
           subunit alpha 1; AltName: Full=Transcriptase subunit
           alpha 1
 gi|123094540|sp|Q2A5E5|RPOA1_FRATH RecName: Full=DNA-directed RNA polymerase subunit alpha 1;
           Short=RNAP subunit alpha 1; AltName: Full=RNA polymerase
           subunit alpha 1; AltName: Full=Transcriptase subunit
           alpha 1
 gi|123359594|sp|Q14J95|RPOA1_FRAT1 RecName: Full=DNA-directed RNA polymerase subunit alpha 1;
           Short=RNAP subunit alpha 1; AltName: Full=RNA polymerase
           subunit alpha 1; AltName: Full=Transcriptase subunit
           alpha 1
 gi|158513857|sp|A4IZQ9|RPOA1_FRATW RecName: Full=DNA-directed RNA polymerase subunit alpha 1;
           Short=RNAP subunit alpha 1; AltName: Full=RNA polymerase
           subunit alpha 1; AltName: Full=Transcriptase subunit
           alpha 1
 gi|171769926|sp|A7N9U9|RPOA1_FRATF RecName: Full=DNA-directed RNA polymerase subunit alpha 1;
           Short=RNAP subunit alpha 1; AltName: Full=RNA polymerase
           subunit alpha 1; AltName: Full=Transcriptase subunit
           alpha 1
 gi|56603995|emb|CAG44983.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. tularensis SCHU S4]
 gi|89143526|emb|CAJ78702.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. holarctica LVS]
 gi|110320307|emb|CAL08366.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. tularensis FSC198]
 gi|115129094|gb|ABI82281.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           holarctica OSU18]
 gi|134050338|gb|ABO47409.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. tularensis WY96-3418]
 gi|151569051|gb|EDN34705.1| hypothetical protein FTBG_00622 [Francisella tularensis subsp.
           tularensis FSC033]
 gi|156252246|gb|ABU60752.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. holarctica FTNF002-00]
 gi|187713027|gb|ACD31324.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. mediasiatica FSC147]
 gi|254840322|gb|EET18758.1| rpoA1, DNA-directed RNA polymerase, alpha subunit [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|282158647|gb|ADA78038.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. tularensis NE061598]
          Length = 323

 Score =  239 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 108/317 (34%), Positives = 180/317 (56%), Gaps = 11/317 (3%)

Query: 13  NNIEYIVLGQEEENRTLMI----AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           + +E++   Q +E+           P+ +G AH LGN++RRVL+SSL GA+I  V I  V
Sbjct: 6   SKLEFVPNIQLKEDLGAFSYKVQLSPVEKGMAHILGNSIRRVLLSSLSGASIIKVNIANV 65

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEV 127
           LHE S+++ V ED+ +I+ N+K + +K+     +  + +     GVV+AGD +T   +E+
Sbjct: 66  LHEYSTLEDVKEDVVEIVSNLKKVAIKLDTGIDRLDLELSVNKSGVVSAGDFKTTQGVEI 125

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +N D  I  L       +  TVS G          TE + +G I +DA ++PIK+V++ V
Sbjct: 126 INKDQPIATLTNQRAFSLTATVSVGRNVGILSAIPTELERVGDIAVDADFNPIKRVAFEV 185

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
                    D + L + + T+G+I    +V  A     +Q+ +F++   P      D+ +
Sbjct: 186 FD-----NGDSETLEVFVKTNGTIEPLAAVTKALEYFCEQISVFVSLRVPSNGKTGDVLI 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            S   +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK
Sbjct: 241 DSN-IDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIK 299

Query: 308 GVLGTMGLFLGMNLPDW 324
            +L    L LG+ + ++
Sbjct: 300 QILIDNNLSLGVQIDNF 316


>gi|154424781|emb|CAL18493.1| RNA polymerase alpha subunit [Streptococcus dysgalactiae subsp.
           equisimilis]
          Length = 205

 Score =  239 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 92/204 (45%), Positives = 142/204 (69%)

Query: 36  PRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLK 95
            RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K
Sbjct: 1   ERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVK 60

Query: 96  MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY 155
              +  K + +   GP  VTAGDI T +DIE++NPDH +  +     +R  +TV+K  GY
Sbjct: 61  SYVEDEKILELEVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLRATMTVAKKRGY 120

Query: 156 VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
           VPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED
Sbjct: 121 VPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPED 180

Query: 216 SVALASRILQDQLGMFINFEEPKK 239
           ++ L++R+L + L +F +  +  K
Sbjct: 181 ALGLSARVLIEHLNLFTDLTDVAK 204


>gi|193795063|gb|ACF21663.1| RpoA [Rhizobium giardinii]
          Length = 212

 Score =  239 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 150/213 (70%), Positives = 181/213 (84%), Gaps = 1/213 (0%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           KR+ + K+GPGVVTAGDIQTV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA  +
Sbjct: 1   KRMVVRKQGPGVVTAGDIQTVGDIEILNPNHVICTLDEGAEIRMEFTVNNGKGYVPADRN 60

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R+E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKLSM I+TDGS+TGED+VA A+
Sbjct: 61  RSEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLSMQIETDGSVTGEDAVAFAA 120

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           RILQDQLG+F+NF+EP+KE +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+
Sbjct: 121 RILQDQLGVFVNFDEPQKEAEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           GDLIQ+TEA+MLR  N GRKSL EIK VL +MG
Sbjct: 180 GDLIQKTEAEMLRTPNLGRKSLNEIKEVLASMG 212


>gi|308125195|gb|ADO14946.1| DNA-directed RNA polymerase alpha chain [Enterococcus sanguinicola]
          Length = 204

 Score =  239 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 97/204 (47%), Positives = 140/204 (68%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T IILNIKG+ LKM G   K 
Sbjct: 1   GNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGLALKMYGQEEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV  G GYV A  ++ 
Sbjct: 61  LEIDITGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTVKPGRGYVQADENKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI   ++++L+++I
Sbjct: 121 EDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIEPLEAMSLSAKI 180

Query: 224 LQDQLGMFINFEEPKKEVKEDINV 247
           + + L +F+N  +  K  +  +  
Sbjct: 181 MTEHLDIFVNLTDEAKNAEIMVEK 204


>gi|295809862|emb|CBL85107.1| alpha subunit of RNA polymerase [Vibrio tapetis]
          Length = 260

 Score =  239 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 112/263 (42%), Positives = 170/263 (64%), Gaps = 8/263 (3%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGV 113
           + G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +K+  G     +T+ K G G 
Sbjct: 1   MPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVKVAEGKDEVFITLNKSGSGP 60

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHH---RTENDPIG 169
           V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA        +  PIG
Sbjct: 61  VVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASSRIHTEEDERPIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  ++ IL +QL 
Sbjct: 121 RLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRSATILAEQLD 180

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
            F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDIRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMANFGRKSLVEIKGVLGT 312
            ++L+  N G KSL EIK VL +
Sbjct: 238 VELLKTPNLGNKSLTEIKDVLAS 260


>gi|161511747|emb|CAP16884.1| DNA-directed RNA polymerase subunit alpha [Pediococcus inopinatus]
          Length = 215

 Score =  239 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 94/213 (44%), Positives = 143/213 (67%), Gaps = 2/213 (0%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNIK ++LK+  D  K +
Sbjct: 1   NSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNIKKVSLKIESDDEKSL 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR-- 162
            I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A  ++  
Sbjct: 61  EIDVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAILTADTGRGYVSADENKAR 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            ++ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSI+  ++ +L+++
Sbjct: 121 KDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSISPSEATSLSAK 180

Query: 223 ILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           IL + L +F+N  +  K+ +  +  +       
Sbjct: 181 ILTEHLALFVNLTDEAKDAEIMVEKEETHKEKM 213


>gi|119662321|emb|CAJ33148.1| RNA polymerase alpha subunit [Lactobacillus kefiranofaciens subsp.
           kefirgranum]
          Length = 215

 Score =  239 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 93/215 (43%), Positives = 136/215 (63%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + +   GP  VTA D++   D++VLNPD  IC +     + MEL V  G GYV A
Sbjct: 61  DEQKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAKGGHLHMELAVKNGRGYVTA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++
Sbjct: 121 SDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALS 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
            A++IL +   +F + +   K  +  +  +     
Sbjct: 181 FAAKILVEHFKVFESADANTKFSEVMVEKEDDKKE 215


>gi|161511709|emb|CAP16865.1| DNA-directed RNA polymerase subunit alpha [Pediococcus inopinatus]
          Length = 204

 Score =  238 bits (608), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 94/204 (46%), Positives = 142/204 (69%), Gaps = 2/204 (0%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNIK ++LK+  D  K +
Sbjct: 1   NSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNIKKVSLKIESDDEKSL 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR-- 162
            I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A  ++  
Sbjct: 61  EIDVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAILTADTGRGYVSADENKAR 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            ++ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSI+  ++ +L+++
Sbjct: 121 KDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSISPSEATSLSAK 180

Query: 223 ILQDQLGMFINFEEPKKEVKEDIN 246
           IL + L +F+N  +  K+ +  + 
Sbjct: 181 ILTEHLALFVNLTDEAKDAEIMVE 204


>gi|71056854|emb|CAH58982.1| DNA-directed RNA polymerase alpha chain [Enterococcus asini]
          Length = 204

 Score =  238 bits (608), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 97/204 (47%), Positives = 141/204 (69%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAIT++QIDGVLHE S++KGV ED+  IILNIKG+ LKM     K 
Sbjct: 1   GNSLRRILLSSLPGAAITSIQIDGVLHEFSTVKGVREDVAQIILNIKGLALKMYTQEEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I   GP  VTAGDI   +D+E+LN D  IC++   A     LTV  G GYV A  ++ 
Sbjct: 61  LEIDIAGPATVTAGDIIVDSDVEILNKDMYICSVSEGATFHARLTVKPGRGYVQADENKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I TDGSI   ++++LA++I
Sbjct: 121 EDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWTDGSILPLEAMSLAAKI 180

Query: 224 LQDQLGMFINFEEPKKEVKEDINV 247
           + + L +F+N  +  K V+  I  
Sbjct: 181 MTEHLDIFVNLTDEAKNVEIMIEK 204


>gi|308125187|gb|ADO14942.1| DNA-directed RNA polymerase alpha chain [Enterococcus devriesei]
          Length = 204

 Score =  238 bits (608), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 97/204 (47%), Positives = 140/204 (68%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG+ LK+  +  K 
Sbjct: 1   GNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVVQIILNIKGLALKLFAEEEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I   GP  VTAGDI   +D+E+LN D  IC +   A     LTV  G GYV A  ++ 
Sbjct: 61  LEIDITGPATVTAGDIIVDSDVEILNKDMYICTVAEGATFHARLTVKPGRGYVQADENKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           E+ PIG++ +D++Y+P++KV+Y VE+ R G+  D+DKL+M I TDGSI  +++++LA++I
Sbjct: 121 EDMPIGVLPVDSIYTPVRKVNYQVENTRVGRRDDFDKLTMEIWTDGSIIAQEALSLAAKI 180

Query: 224 LQDQLGMFINFEEPKKEVKEDINV 247
           L + L +F+N  +  K  +  +  
Sbjct: 181 LTEHLDIFVNLTDEAKNAEIMVEK 204


>gi|328675432|gb|AEB28107.1| DNA-directed RNA polymerase alpha subunit [Francisella cf. novicida
           3523]
          Length = 323

 Score =  238 bits (608), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 109/319 (34%), Positives = 178/319 (55%), Gaps = 11/319 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           QE + PN     +          +   P+ +G AH LGN++RRVL+SSL GA+I  V I 
Sbjct: 8   QEFV-PN---IQLKEDLGAFSYKVELSPVEKGMAHILGNSIRRVLLSSLSGASIIKVNIA 63

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDI 125
            VLHE S+++ V ED+ +I+ N+K + +K+     +  + +     GVV+AGD +T   +
Sbjct: 64  NVLHEYSTLEDVKEDVVEIVSNLKKVAIKLDKGIDRLDLELSVNKSGVVSAGDFKTTQGV 123

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++N D  I  L       +  TVS G          TE + +G I +DA ++PIK+V++
Sbjct: 124 EIINKDQPIATLTNQRAFNLTATVSIGRNVGILSAIPTELERVGDIAVDADFNPIKRVAF 183

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            V         D + L + + T+G+I    +V  A     +Q+ +F++   P      D+
Sbjct: 184 EVFD-----NGDSETLEVFVKTNGTIEPLAAVTKALEYFCEQISVFVSLRVPSNGKTGDV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            + S   +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL E
Sbjct: 239 LIDSN-IDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLGKKSLNE 297

Query: 306 IKGVLGTMGLFLGMNLPDW 324
           IK +L    L LG+ + ++
Sbjct: 298 IKQILIDNNLSLGVQIDNF 316


>gi|193795081|gb|ACF21670.1| RpoA [Rhizobium gallicum]
          Length = 212

 Score =  238 bits (608), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 149/212 (70%), Positives = 182/212 (85%), Gaps = 1/212 (0%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           KR+ + K+GPGVVTAGDIQTV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +
Sbjct: 1   KRMVVRKQGPGVVTAGDIQTVGDIEILNPEHVICTLDEGAEIRMEFTVNNGKGYVPAERN 60

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKL+MTI+TDGS++GED+VA A+
Sbjct: 61  RAEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLTMTIETDGSVSGEDAVAFAA 120

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           RILQDQLG+F+NF+EP+KE +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+
Sbjct: 121 RILQDQLGVFVNFDEPQKEAEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           GDLIQ+TEA+MLR  NFGRKSL EIK VL +M
Sbjct: 180 GDLIQKTEAEMLRTPNFGRKSLNEIKEVLASM 211


>gi|193795090|gb|ACF21674.1| RpoA [Rhizobium tropici]
          Length = 212

 Score =  238 bits (608), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 151/213 (70%), Positives = 182/213 (85%), Gaps = 1/213 (0%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           KR+ + K+GPGVVTAGDIQTV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +
Sbjct: 1   KRMVVRKQGPGVVTAGDIQTVGDIEILNPEHVICTLDEGAEIRMEFTVNNGKGYVPAERN 60

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKLSM+I+TDGSITGED+VA A+
Sbjct: 61  RAEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLSMSIETDGSITGEDAVAFAA 120

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           RILQDQLG+F+NF+EP+KE +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+
Sbjct: 121 RILQDQLGVFVNFDEPQKEAEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           GDLIQ+TEA+MLR  N GRKSL EIK VL +MG
Sbjct: 180 GDLIQKTEAEMLRTPNLGRKSLNEIKEVLASMG 212


>gi|150036784|emb|CAM98269.1| DNA-directed RNA polymerase alpha chain [Leuconostoc lactis]
          Length = 211

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 89/211 (42%), Positives = 133/211 (63%), Gaps = 2/211 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A
Sbjct: 61  DDERSLEIDVQGPAEVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSA 120

Query: 159 KHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   E  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+
Sbjct: 121 DENKQLREEMPIGVLAVDSIYTPIERVNYHVENTRVGARDDYDKLTFDIWTNGSIKPSDA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ++L ++IL + L +F++      E    +  
Sbjct: 181 LSLGAKILAEHLNLFMDISPVAAEANVMVEA 211


>gi|119662361|emb|CAJ33169.1| RNA polymerase alpha subunit [Lactobacillus zymae]
          Length = 202

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 98/202 (48%), Positives = 143/202 (70%), Gaps = 4/202 (1%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG-- 98
            TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK++G  
Sbjct: 1   TTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNVKKIALKLNGAD 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  + + I  +GP  VTAGDI    D++VLNPD  I  +   A   M +T  KG GYV A
Sbjct: 61  DQEETMEINVKGPAQVTAGDIVAGADVDVLNPDLYIATVADGATFHMRMTADKGRGYVSA 120

Query: 159 KHHRTEN--DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++T N   PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ + T+GSI   ++
Sbjct: 121 DENKTRNTEMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDVWTNGSINPSEA 180

Query: 217 VALASRILQDQLGMFINFEEPK 238
           ++LA++IL + L MF++  +  
Sbjct: 181 ISLAAKILTEHLAMFVDLTDEA 202


>gi|118475267|ref|YP_891269.1| DNA-directed RNA polymerase subunit alpha [Campylobacter fetus
           subsp. fetus 82-40]
 gi|158512499|sp|A0RM36|RPOA_CAMFF RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|118414493|gb|ABK82913.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter fetus
           subsp. fetus 82-40]
          Length = 332

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 111/338 (32%), Positives = 179/338 (52%), Gaps = 10/338 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++K       P  IE + +    EN   +IA P   G+A TL + LRR+L +S  G A T
Sbjct: 1   MKKITTSAYMPTEIEVVNVS---ENVAKIIAYPFETGYAVTLAHPLRRLLYTSTVGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQ 120
           AV+IDGV HE  S++G+ ED+T  I+N+K +  K+  DS  + +    +GP  +T  D+ 
Sbjct: 58  AVKIDGVAHEFDSMRGMLEDVTLFIINLKNLRFKLKNDSKREVIEYSFKGPKEITGIDLN 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               +E++NPD  +  ++ DA ++  L V KG GYVP++  R   D    I +DA ++P+
Sbjct: 118 ND-IVEIVNPDSYLATINEDAELKFSLIVEKGIGYVPSEEIRDYIDSEY-IALDAFFTPV 175

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KK  Y +E+       DY+K+ +T+ TDG ++  ++   +   +  Q+ +F N       
Sbjct: 176 KKAVYEIENVLVEDNPDYEKIVLTVTTDGQVSPIEAFKHSIEAMYKQMSIFNNVLNIDVN 235

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           +    +  S   +   L+ VE L LS RS NCL   +I Y+G+L    E+++  + N G+
Sbjct: 236 MALTSSQNSNEHSKL-LESVENLNLSARSFNCLDKADIRYIGELALMEESELKDLKNLGK 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK V+  +G   G    +   +S E L KK  +
Sbjct: 295 KSLDEIKAVMAEIGYPFG---ENTLGDSKEALRKKISE 329


>gi|150036754|emb|CAM98262.1| DNA-directed RNA polymerase alpha chain [Fructobacillus durionis]
          Length = 220

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 94/219 (42%), Positives = 136/219 (62%), Gaps = 2/219 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRVL+SSL G AI  VQIDGV+HE S++ GV ED+T +ILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRVLLSSLPGVAINTVQIDGVVHEFSTVDGVAEDVTQLILNLKKVV 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
                     + I  +GP  VTA D     DIEVLNPD  I  L     + M +TV KG 
Sbjct: 61  FATDSAEEHTLEIDVQGPKDVTAADFVGSADIEVLNPDLHIATLAAGKSLHMTVTVVKGR 120

Query: 154 GYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A+ ++   +  PIG++T+D++Y+PI++V+Y VE  R G   D+DKL+M + T+GSI
Sbjct: 121 GYASAEENKQLRDEMPIGVLTVDSIYTPIERVNYHVEQKRVGSRDDFDKLTMEVWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
              D+++L S+IL + L +F +     +E K  +  ++ 
Sbjct: 181 KPSDALSLGSKILTEHLNLFTDISPVAQETKVMVEAEAP 219


>gi|119662323|emb|CAJ33149.1| RNA polymerase alpha subunit [Lactobacillus kimchii]
          Length = 213

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 87/213 (40%), Positives = 140/213 (65%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL++SL G A++ +QIDGVLHE S++ GV ED+T I+LN+K + LK   
Sbjct: 1   YGTTLGNSLRRVLLASLPGTAVSDIQIDGVLHEFSAVDGVIEDVTQIVLNVKKLKLKSYA 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D   +  I   GP  VTA DI+  +D+E+L+P+  IC +       M++TV  G GY PA
Sbjct: 61  DDSLKAEIDVVGPATVTANDIKADDDLEILDPEQFICTVAEGGHFHMQMTVINGRGYTPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           + ++T+  PIG++ +D++++P++KV+Y VE+ R G+  D+DKL++ I T+GSI   ++++
Sbjct: 121 EQNKTDETPIGVLPVDSIFTPVEKVNYQVENTRVGKRNDFDKLTIDIWTNGSIGPREAIS 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           L+++IL + L  F+N  E  K     I  +   
Sbjct: 181 LSAKILTEHLTSFVNLTEEAKSADMMIEKEETQ 213


>gi|150036822|emb|CAM98042.1| DNA-directed RNA polymerase alpha chain [Leuconostoc fallax KCTC
           3537]
          Length = 204

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 91/204 (44%), Positives = 135/204 (66%), Gaps = 2/204 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T +ILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVV 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L +  D  K + I  +GP  VTA D+Q   DIEVLNP+  +  +     + M +T  KG 
Sbjct: 61  LAIDSDEEKSLEIDVQGPAEVTAADLQGSADIEVLNPELHLATVAAGKSLHMTVTAVKGR 120

Query: 154 GYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R GQ  DYDKL+  I T+GSI
Sbjct: 121 GYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGQRDDYDKLTFDIWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFINFE 235
              D+++L ++IL + L +F +  
Sbjct: 181 KPSDALSLGAKILSEHLNLFTDIS 204


>gi|117575079|emb|CAJ84779.1| RNA polymerase alpha subunit [Lactobacillus amylotrophicus]
          Length = 202

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 93/201 (46%), Positives = 139/201 (69%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL++SL G+A++ VQIDGVLHE S+I GV ED+T IILN+K + LK   
Sbjct: 1   YGTTLGNSLRRVLLASLPGSAVSYVQIDGVLHEFSTIPGVLEDVTQIILNLKKLTLKSIA 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
              K   I   GP  VTAGD++  +++E+LNP+  I  +   A +RM + V +G GYVPA
Sbjct: 61  ADEKLAEIDVEGPATVTAGDLKVDDEVEILNPNQYIATVAEGAHLRMTVAVKQGRGYVPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG++ +D+L+SPI+KV+Y VE  R G+  DYDKL+M + TDGSIT  D+++
Sbjct: 121 DQNKSDDMPIGVVPVDSLFSPIEKVNYQVEGTRVGRNNDYDKLTMEVWTDGSITPNDALS 180

Query: 219 LASRILQDQLGMFINFEEPKK 239
             ++IL + L +F+N     +
Sbjct: 181 FGAKILTEHLNVFMNTNLETE 201


>gi|193795067|gb|ACF21665.1| RpoA [Rhizobium tropici]
          Length = 212

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 151/212 (71%), Positives = 182/212 (85%), Gaps = 1/212 (0%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           KR+ + K+GPGVVTAGDIQTV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +
Sbjct: 1   KRMVVRKQGPGVVTAGDIQTVGDIEILNPEHVICTLDEGAEIRMEFTVNNGKGYVPAERN 60

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKLSM+I+TDGSITGED+VA A+
Sbjct: 61  RAEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLSMSIETDGSITGEDAVAFAA 120

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           RILQDQLG+F+NF+EP+KE +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+
Sbjct: 121 RILQDQLGVFVNFDEPQKEAEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           GDLIQ+TEA+MLR  NFGRKSL EIK VL +M
Sbjct: 180 GDLIQKTEAEMLRTPNFGRKSLNEIKEVLASM 211


>gi|152989998|ref|YP_001355720.1| DNA-directed RNA polymerase subunit alpha [Nitratiruptor sp.
           SB155-2]
 gi|172048727|sp|A6Q1K4|RPOA_NITSB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|151421859|dbj|BAF69363.1| DNA-directed RNA polymerase, alpha subunit [Nitratiruptor sp.
           SB155-2]
          Length = 328

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 101/333 (30%), Positives = 176/333 (52%), Gaps = 12/333 (3%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           I P+   ++ + + +EN   +   P   G+A ++ + LRR+L+SS  G A   ++I+GV 
Sbjct: 6   ITPSVPTHMEVEKIKENAIRLHVYPYESGYAISVAHPLRRLLLSSTAGYAPIGLKIEGVQ 65

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG--VVTAGDIQTVNDIEV 127
           HE  S++G+ ED+   I+N+K +  K+     + VT+     G   +   D +    +EV
Sbjct: 66  HEFDSVRGMLEDVAAFIINLKNVRFKLRDSEQENVTLEYEFSGPKELFGKDFEND-LVEV 124

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           + PD  +  L+ DA ++M + V KG GYVP++  R +  P G I +DA ++P+KK  Y +
Sbjct: 125 VTPDAFLATLNEDAELKMSIIVQKGIGYVPSEMIR-DLLPQGYIPLDAFFTPVKKAVYEI 183

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E        +Y+K+   I+TDG +    ++ +A  ++Q Q+ +F N  E  + V ++I  
Sbjct: 184 EKVLVEDNPNYEKIVFDIETDGQVDPVSALKMAMNVMQSQMEIFTNDIEVTETVGQNIEN 243

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                     + ++ L+LS RS NCL    I Y+G+L+  +   +  + N G+KSL EI+
Sbjct: 244 SE-----IFYQPLDILDLSARSYNCLDKAGIKYVGELLLMSNEALKSIKNLGKKSLDEIQ 298

Query: 308 GVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
             L  + + LG  L D   E+I  L K  ++K 
Sbjct: 299 EKLSELNIDLG-KLSDQEKETI--LKKIEQNKS 328


>gi|119672807|emb|CAK95484.1| RNA polymerase alpha subunit [Lactobacillus fermentum]
          Length = 196

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 92/196 (46%), Positives = 139/196 (70%), Gaps = 2/196 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRRV+++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+
Sbjct: 1   FVVEPLERGYGTTLGNSLRRVMLASLPGAAITSIQIDGVLHEFSTVQGVTEDVTQIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + LK+  +  K + I  +GP  VTA DIQ   D+ +LN D  I  +   A + +++T 
Sbjct: 61  KQVALKIDSEDAKDLEIDVKGPAEVTAADIQGDGDVTILNSDLHIATVSDGAELHVKMTA 120

Query: 150 SKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GY  A  ++T  E   IG++ ID++Y+PI++V+YTVE+ R GQ  DYDKL++ + T
Sbjct: 121 DKGRGYSSADDNKTRMEGLAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRI 223
           +GS+T  ++++LA++I
Sbjct: 181 NGSLTPTEAISLAAKI 196


>gi|254779835|ref|YP_003057941.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori B38]
 gi|254001747|emb|CAX29978.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           (Transcriptase alpha chain) (RNA polymerase alpha
           subunit) [Helicobacter pylori B38]
          Length = 344

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 102/331 (30%), Positives = 170/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ + + IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSDH-IEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++ +  E  P G + +D  ++PIKKV Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMPEGYMPLDGSFTPIKKVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLNDLGYPVGTELSSEQRESLKKRLEKLEDK 340


>gi|242624287|ref|YP_003002205.1| DNA-directed RNA polymerase alpha chain [Aureoumbra lagunensis]
 gi|239997395|gb|ACS36917.1| DNA-directed RNA polymerase alpha chain [Aureoumbra lagunensis]
          Length = 303

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 95/293 (32%), Positives = 147/293 (50%), Gaps = 9/293 (3%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
            +  E  T      L +    T+GNALRRVL++ L G AITAV+I GV HE  +I GV E
Sbjct: 14  NENGEKTTRFCLAGLEQSQGITIGNALRRVLLTDLMGTAITAVRIYGVNHEYGTIPGVRE 73

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+ +I+LN+K I    +      +T+   GP ++TA DI   +++ V+N    I  +   
Sbjct: 74  DVLEILLNLKQIKFHGTCSDPVLITLEIEGPYLLTAVDITVPSNLNVINTKQYIATISEQ 133

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             +++EL +  G GY         +     + IDA+++P+K VSY V           + 
Sbjct: 134 TKLKLELQIESGCGYRLVTDELHRDSGT-FLNIDAIFTPVKNVSYKVLDLYRFDEKLLED 192

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + I TDGS+  +D++  A+ ILQ+  G           V E   +K      +    +
Sbjct: 193 LVLEITTDGSLNPKDALIQAANILQNMFGSLT--------VGEPKALKQTTTISSRQILI 244

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           EEL+LSVR+ NCL+  NI  + DL Q +  ++  + NFG+KS  E+   L   
Sbjct: 245 EELQLSVRAYNCLKRANIRTIDDLTQYSIKELKELKNFGQKSANEVIQKLQDR 297


>gi|158148899|dbj|BAF81984.1| RNA polymerase alpha subunit [Lactobacillus senmaizukei]
          Length = 199

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 97/199 (48%), Positives = 142/199 (71%), Gaps = 4/199 (2%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG- 98
             TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+K I LK++G 
Sbjct: 1   GTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVTQIILNVKKIALKLNGS 60

Query: 99  -DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
            D  + + I  +GP  VTAGDI T  D++VLNPD  I  +   A   M +T  KG GYV 
Sbjct: 61  DDQEETMEINVKGPAQVTAGDIVTGADVDVLNPDLYIATVADGATFHMRMTADKGRGYVS 120

Query: 158 AKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
           A  ++    + PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ + T+GSI   +
Sbjct: 121 ADENKARNTDMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDVWTNGSINPSE 180

Query: 216 SVALASRILQDQLGMFINF 234
           ++ALA++IL + L MF++ 
Sbjct: 181 AIALAAKILTEHLAMFVDL 199


>gi|154424751|emb|CAL18478.1| RNA polymerase alpha subunit [Streptococcus salivarius]
          Length = 216

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 89/216 (41%), Positives = 142/216 (65%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILNIKG+ +K   
Sbjct: 1   YGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGLAVKSYV 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + +  +GP  VTAGDI T +DIE++NPDH +  +   A ++  +TV+   GYVPA
Sbjct: 61  EDEKTIELDVQGPAEVTAGDILTDSDIEIVNPDHYLFTIADGASLKATMTVATNRGYVPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ 
Sbjct: 121 DENKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALG 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
           L++R+L + L +F +  +  K        + +    
Sbjct: 181 LSARVLIEHLNLFTDLTDVAKATDVMKETEKVNDEK 216


>gi|150036802|emb|CAM98037.1| DNA-directed RNA polymerase alpha chain [Fructobacillus
           pseudoficulneus]
          Length = 231

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 94/231 (40%), Positives = 141/231 (61%), Gaps = 2/231 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL+SSL G A+  VQIDGV+HE S++ GV ED+T +ILN+K +      
Sbjct: 1   YGTTLGNSLRRVLLSSLPGVAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVVFATDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
                + I  +GP  VTA D+    DIEVLNPD  I  L     + M +T  KG GY  A
Sbjct: 61  AEEHALEIDVQGPKDVTAADLMGSADIEVLNPDLHIATLAAGKALHMTVTAVKGRGYSSA 120

Query: 159 KHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
           + ++   +  PIG++T+D++Y+PI++V+Y VE+ R G   DYDKL+M + T+GSI   D+
Sbjct: 121 EENKQLRDEMPIGVLTVDSIYTPIERVNYHVENKRVGSRDDYDKLTMEVWTNGSIKPSDA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           ++L S+IL + L +F +     ++ K  +  +      A    +E+L+LSV
Sbjct: 181 LSLGSKILTEHLNLFTDISPVAQDTKVMVESEPAANTAADAAPIEDLDLSV 231


>gi|193795070|gb|ACF21666.1| RpoA [Rhizobium tropici CIAT 899]
 gi|193795078|gb|ACF21669.1| RpoA [Rhizobium tropici]
          Length = 212

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 150/212 (70%), Positives = 182/212 (85%), Gaps = 1/212 (0%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           KR+ + K+GPGVVTAGDIQTV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +
Sbjct: 1   KRMVVRKQGPGVVTAGDIQTVGDIEILNPEHVICTLDEGAEIRMEFTVNNGKGYVPAERN 60

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKLSM+I+TDGSI+GED+VA A+
Sbjct: 61  RAEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLSMSIETDGSISGEDAVAFAA 120

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           RILQDQLG+F+NF+EP+KE +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+
Sbjct: 121 RILQDQLGVFVNFDEPQKEAEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           GDLIQ+TEA+MLR  NFGRKSL EIK VL +M
Sbjct: 180 GDLIQKTEAEMLRTPNFGRKSLNEIKEVLASM 211


>gi|15612278|ref|NP_223931.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori J99]
 gi|7388104|sp|Q9ZJT5|RPOA_HELPJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|4155841|gb|AAD06815.1| RNA POLYMERASE ALPHA SUBUNIT [Helicobacter pylori J99]
          Length = 344

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 101/331 (30%), Positives = 169/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ + + IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSDH-IEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++ +  E  P G + +D  ++PIK V Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMPEGYMPLDGSFTPIKNVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|90567619|emb|CAJ31077.1| RNA polymerase alpha subunit [Lactobacillus helveticus R0052]
          Length = 197

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 91/193 (47%), Positives = 130/193 (67%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSFS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V  G GYV A
Sbjct: 61  DERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNGRGYVAA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++
Sbjct: 121 SDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALS 180

Query: 219 LASRILQDQLGMF 231
            A++IL +   +F
Sbjct: 181 FAAKILVEHFKVF 193


>gi|150036774|emb|CAN89786.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gasicomitatum]
          Length = 219

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 89/213 (41%), Positives = 135/213 (63%), Gaps = 2/213 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  + + +  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A
Sbjct: 61  DEERSLEVDIQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTITAFKGRGYSSA 120

Query: 159 KHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+
Sbjct: 121 DENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           ++L S+IL + L +F++      E    + V+ 
Sbjct: 181 LSLGSKILAEHLNLFMDISPVAAEANVMVEVEP 213


>gi|193795075|gb|ACF21668.1| RpoA [Rhizobium tropici]
 gi|193795083|gb|ACF21671.1| RpoA [Rhizobium tropici]
          Length = 212

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 150/212 (70%), Positives = 182/212 (85%), Gaps = 1/212 (0%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           KR+ + K+GPGVVTAGDIQTV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +
Sbjct: 1   KRMVVRKQGPGVVTAGDIQTVGDIEILNPEHVICTLDEGAEIRMEFTVNNGKGYVPAERN 60

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKLSM+I+TDGSI+GED+VA A+
Sbjct: 61  RAEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLSMSIETDGSISGEDAVAFAA 120

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           RILQDQLG+F+NF+EP+KE +E+  V  L FNPALLKKV+ELELSVRS NCL+ +NIVY+
Sbjct: 121 RILQDQLGVFVNFDEPQKETEEEA-VTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           GDLIQ+TEA+MLR  NFGRKSL EIK VL +M
Sbjct: 180 GDLIQKTEAEMLRTPNFGRKSLNEIKEVLASM 211


>gi|86438810|emb|CAJ43370.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 208

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 91/208 (43%), Positives = 134/208 (64%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V  G GYV A
Sbjct: 61  DERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNGRGYVAA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++
Sbjct: 121 SDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALS 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDIN 246
            A++I  +   +F + +   K  +  + 
Sbjct: 181 FAAKISVEHFKVFESADADTKFSEVMVE 208


>gi|154424851|emb|CAL18528.1| RNA polymerase alpha subunit [Streptococcus ratti]
          Length = 212

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 89/211 (42%), Positives = 141/211 (66%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ +K   
Sbjct: 1   YGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNLKGLAVKSYV 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + +   GP  +TAGDI T +DIE++NPDH +  +   A ++  LTV    GY+PA
Sbjct: 61  EEEKIIELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIAEGASLKATLTVGTNRGYIPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           + ++ ++ P+G + ID++Y+P+KKV+Y VE AR G   ++DKL++ I T+G+I  ED++ 
Sbjct: 121 EENKKDDAPVGTLAIDSIYTPVKKVNYQVEPARVGSNDNFDKLTIEIMTNGTIIPEDALG 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           L++R+L + L +F +  E  K        + 
Sbjct: 181 LSARVLIEHLNLFTDLTEVAKATDVMKETEQ 211


>gi|150036830|emb|CAM98044.1| DNA-directed RNA polymerase alpha chain [Leuconostoc kimchii]
          Length = 216

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 87/213 (40%), Positives = 134/213 (62%), Gaps = 2/213 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  + + I  +GP  VTA D+Q   D+E+LNPD  +  +     + M +T  KG GY  A
Sbjct: 61  DDERSLEIDVQGPADVTAADLQAGADVEILNPDLHLATVAAGKSLHMTVTAVKGRGYSSA 120

Query: 159 KHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+
Sbjct: 121 DENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           ++L S+IL + L +F++      E    +  + 
Sbjct: 181 LSLGSKILAEHLNLFMDISPVAAEASVMVEAEP 213


>gi|119662355|emb|CAJ33166.1| RNA polymerase alpha subunit [Lactobacillus salivarius]
          Length = 199

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 94/199 (47%), Positives = 141/199 (70%), Gaps = 2/199 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAAIT VQIDGVLHE S+I GV ED+T IILN+K + L M  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAITDVQIDGVLHEFSTIPGVLEDVTLIILNLKKVALSMES 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  + + I   GP  VTAGDIQ+ +D+EVLNP+  IC +   A + + +  +KG GYV A
Sbjct: 61  EDSQALEINVTGPMEVTAGDIQSNSDVEVLNPEQYICTVADGAELHVRMNANKGRGYVSA 120

Query: 159 KHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   ++ PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T+GSIT  ++
Sbjct: 121 NDNKALADDMPIGVLPIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWTNGSITPSEA 180

Query: 217 VALASRILQDQLGMFINFE 235
           ++L+++IL + L +F++  
Sbjct: 181 ISLSAKILTEHLALFVDLT 199


>gi|108773284|ref|YP_635780.1| RNA polymerase alpha subunit [Chara vulgaris]
 gi|122237365|sp|Q1ACG7|RPOA_CHAVU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|77157940|gb|ABA61981.1| alpha subunit of RNA polymerase [Chara vulgaris]
          Length = 358

 Score =  236 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 103/357 (28%), Positives = 172/357 (48%), Gaps = 27/357 (7%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQ    + I+   +E  +  Q           PL +G A+TLG  LRR L+S L G  I
Sbjct: 1   MIQNVTDDKIQWKCLESKIESQRIH-YGRFAIAPLKKGQANTLGITLRRTLLSDLDGICI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V+ID + HE  ++ GV E + DI+LN+K I  K   D  ++  IF +GP  +TA DIQ
Sbjct: 60  TSVKIDNIKHEYCTLTGVRESIQDILLNLKEIVFKGVCDKTQKGFIFVKGPKKITASDIQ 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               IE+L+ + +I +L      ++ELT+ K  G+      +   D     +IDA++ PI
Sbjct: 120 IEPCIEILDSNQIIAHLTEPIDFKVELTIEKSMGFRLQNATQISKDS---FSIDAIFMPI 176

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL------------ 228
           + V+Y++    +      + L + I T+GSIT +++   AS  + +              
Sbjct: 177 RNVNYSIHPVEKAGDWKSELLILEIWTNGSITPKEAFHQASEKIMNIFLSLSNSSDNQIQ 236

Query: 229 -GMFINFEEPKKEVKEDINVKSLPFNPALLK-------KVEELELSVRSTNCLRGENIVY 280
                NFEE ++ + ++I+         + +        + +LELS R+ NCL+ E I  
Sbjct: 237 EKSTKNFEEKEEFIFQNIDGFKQDKETKVQESLGWKKISINQLELSARAYNCLKNEKIST 296

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
           + DL+  ++ D+L++ NFG++S  ++   L        M L     +   E  K  E
Sbjct: 297 LFDLLNYSQEDLLKIKNFGKRSFEQVVNALE---KHFDMKLSKDSSKKFYEQLKNLE 350


>gi|308185045|ref|YP_003929178.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           SJM180]
 gi|308060965|gb|ADO02861.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           SJM180]
          Length = 344

 Score =  236 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 102/331 (30%), Positives = 170/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ + + IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLSSEH-IEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++ +  E  P G + +D  ++PIKKV Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMPEGYMPLDGSFTPIKKVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLNDLGYPVGTELSHEQRESLKKRLEKLEDK 340


>gi|150036778|emb|CAM98268.1| DNA-directed RNA polymerase alpha chain [Fructobacillus fructosus
           KCTC 3544]
          Length = 206

 Score =  236 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 92/206 (44%), Positives = 132/206 (64%), Gaps = 2/206 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            I EPL RG+  TLGN+LRRVL+SSL G AI  VQIDGV+HE S++ GV ED+T +ILN+
Sbjct: 1   FIVEPLERGYGTTLGNSLRRVLLSSLPGVAINTVQIDGVVHEFSTVDGVVEDVTQLILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K +           + +   GP  VTA D+    D+EVLNPD  I  L     + M +TV
Sbjct: 61  KKVVFATDSAEEHSLELDVTGPRDVTAADLVGSADVEVLNPDLHIATLAAGKSLHMTVTV 120

Query: 150 SKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GY  A+ ++   +  PIG++T+D++Y+PI++V+Y VE  R G   D+DKL+M + T
Sbjct: 121 VKGRGYASAEENKQLRDEMPIGVLTVDSIYTPIERVNYHVEQKRVGARDDFDKLTMEVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFIN 233
           +GSI   D+++L S+IL + L +F +
Sbjct: 181 NGSIKPSDALSLGSKILTEHLNLFTD 206


>gi|150036804|emb|CAM98275.1| DNA-directed RNA polymerase alpha chain [Fructobacillus
           pseudoficulneus]
          Length = 230

 Score =  236 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 93/230 (40%), Positives = 140/230 (60%), Gaps = 2/230 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL+SSL G A+  VQIDGV+HE S++ GV ED+T +ILN+K +      
Sbjct: 1   YGTTLGNSLRRVLLSSLPGVAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVVFATDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
                + I  +GP  VTA D+    DIEVLNPD  I  L     + M +T  KG GY  A
Sbjct: 61  AEEHALEIDVQGPKDVTAADLMGSADIEVLNPDLHIATLAAGKSLHMTVTAVKGRGYSSA 120

Query: 159 KHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
           + ++   +  PIG++T+D++Y+PI++V+Y VE+ R G   DYDKL+M + T+GSI   D+
Sbjct: 121 EENKQLRDEMPIGVLTVDSIYTPIERVNYHVENKRVGSRDDYDKLTMEVWTNGSIKPSDA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           ++L S+IL + L +F +     ++ K  +  +      A    +E+L+LS
Sbjct: 181 LSLGSKILTEHLNLFTDISPVAQDTKVMVESEPAANTAADAAPIEDLDLS 230


>gi|317009976|gb|ADU80556.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           India7]
          Length = 344

 Score =  236 bits (601), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 102/331 (30%), Positives = 170/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKESNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ + + IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSEH-IEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++ +  E  P G + +D  ++PIKKV Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMPEGYMPLDGSFTPIKKVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSTKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|119662837|emb|CAJ33211.1| RNA polymerase alpha subunit [Lactobacillus satsumensis]
          Length = 210

 Score =  235 bits (600), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 87/210 (41%), Positives = 142/210 (67%), Gaps = 2/210 (0%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAAIT++QIDGVLHE S+IKGV ED+T IILN+K + L++  +  + 
Sbjct: 1   GNSLRRILLSSLPGAAITSIQIDGVLHEFSTIKGVLEDVTQIILNLKKVALRIDSEEDQT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH-- 161
           + I   GP  V AGDIQ  +D+EVLNPD  +C +   A   + +  + G GYV A  +  
Sbjct: 61  LEISVNGPLEVKAGDIQGSSDVEVLNPDLYLCTVAEGASFHVRMNANTGRGYVSADENKI 120

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           + ++ PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T+G+++  ++++L++
Sbjct: 121 KADDMPIGVLPIDSIYTPIERVNYQVEKTRVGQRDDYDKLTLDVWTNGAVSPSEAISLSA 180

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           +IL + L +F++  +  K  +  +  +   
Sbjct: 181 KILTEHLTLFVDLTDEAKNAEIMVEKEETH 210


>gi|317013080|gb|ADU83688.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           Lithuania75]
          Length = 344

 Score =  235 bits (600), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 102/331 (30%), Positives = 170/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ + + IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSEH-IEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++ +  E  P G + +D  ++PIKKV Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMPEGYMPLDGSFTPIKKVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|197131692|gb|ACH47364.1| RNA polymerase alpha subunit [Geranium macrorrhizum]
          Length = 329

 Score =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 72/306 (23%), Positives = 141/306 (46%), Gaps = 9/306 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +   +E      +       I  PL +G A  +G A+RR L+  + G  IT  + D + H
Sbjct: 14  RWKCVES-RADSKRLYYGRFILSPLKKGQADMIGIAMRRALLGEIEGTCITHAKFDKIPH 72

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ G+ E + +I++N+K I L+      +  +I  RGP  VT+ DI       +++ 
Sbjct: 73  EYTTLVGIQESIYEILMNLKEIVLRSHLYGTRDASICVRGPRDVTSQDIILPTFATIVDN 132

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
              I  L       + L + +  GY       +         IDA++ P+K V++++ S 
Sbjct: 133 TQHIVTLTEPIDFCVGLQIERNRGYFIQIPMLSNLHDDRGYPIDAVFMPVKNVNHSIHSY 192

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
             G    +  L + I T+GS+T ++++  ASR L +    F++ EE     + + N  + 
Sbjct: 193 ENG---IHAMLFLEIWTNGSLTPKEALRGASRKLINLFIPFLHAEEQNCHFENNQNEHTD 249

Query: 251 PFN----PALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +          +++L EL  R   CL+G  I  + DL+ +   D++++  F ++ + +
Sbjct: 250 ELSIDFCALKDIYIDQLVELPARFYKCLKGSGIDTVMDLLNKNTDDLIKITQFCQQDVEK 309

Query: 306 IKGVLG 311
           +  +L 
Sbjct: 310 VMNILN 315


>gi|317014684|gb|ADU82120.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           Gambia94/24]
          Length = 344

 Score =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 101/331 (30%), Positives = 169/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ + + IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSEH-IEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++ +  E  P G + +D  ++PIK V Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMPEGYMPLDGSFTPIKNVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|188528081|ref|YP_001910768.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           Shi470]
 gi|188144321|gb|ACD48738.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           Shi470]
          Length = 344

 Score =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 100/331 (30%), Positives = 169/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ + + IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLSSEH-IEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           N +  +  ++ DA +   L + KG GYVP++ +  E  P G + +D  ++PIKKV Y +E
Sbjct: 133 NLEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMPEGYMPLDGSFTPIKKVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     E++++  +K EDK
Sbjct: 310 KLNDLGYPVGTELSPEQRENLKKRLEKLEDK 340


>gi|154424867|emb|CAL18536.1| RNA polymerase alpha subunit [Streptococcus uberis]
          Length = 210

 Score =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 90/210 (42%), Positives = 140/210 (66%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL+SSL GAA+T+++ DGVLHE  +I GV ED+  IILNIKG+ +K   
Sbjct: 1   YGTTLGNSLRRVLLSSLPGAAVTSIKFDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYV 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV+K  GYVPA
Sbjct: 61  EDEKMIELDVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLKATMTVAKKRGYVPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           + ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ 
Sbjct: 121 EGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALG 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVK 248
           L++R+L + L +F +  E  K        +
Sbjct: 181 LSARVLIEHLNLFTDLTEVAKATDVMKETE 210


>gi|119662371|emb|CAJ33174.1| RNA polymerase alpha subunit [Lactobacillus amylolyticus DSM 11664]
          Length = 208

 Score =  235 bits (600), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 91/208 (43%), Positives = 135/208 (64%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK + D  K
Sbjct: 1   LGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSNSDEQK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + +   GP  VTA D++  +D+EVLNPD  IC +     + M++ V  G GYV A  ++
Sbjct: 61  VIELDVEGPATVTADDLKVDSDVEVLNPDQYICTIAEGGHLHMQIAVKNGRGYVAASDNK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
           +E+ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++ A+ 
Sbjct: 121 SEDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSINPNDALSFAAN 180

Query: 223 ILQDQLGMFINFEEPKKEVKEDINVKSL 250
           IL +   +F + +   K  +  +  +  
Sbjct: 181 ILVEHFKVFESADADNKFSEVMVEKEDN 208


>gi|217033612|ref|ZP_03439040.1| hypothetical protein HP9810_899g48 [Helicobacter pylori 98-10]
 gi|216943958|gb|EEC23392.1| hypothetical protein HP9810_899g48 [Helicobacter pylori 98-10]
          Length = 344

 Score =  235 bits (599), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 101/331 (30%), Positives = 169/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ + + IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALIGQDSSLENQSVVVDYSFKGPMELKARDLSSEH-IEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++ +  E  P G + +D  ++PIK V Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMPEGYMPLDGSFTPIKNVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMGKQLGVFG--ERPITNTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLNDLGYPVGTELSSEQRESLKKRLEKLEDK 340


>gi|308064070|gb|ADO05957.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           Sat464]
          Length = 344

 Score =  235 bits (599), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 100/331 (30%), Positives = 169/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ + + IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKVLVGQDSSLENQSVVVDYSFKGPMELRARDLSSEH-IEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           N +  +  ++ DA +   L + KG GYVP++ +  E  P G + +D  ++PIKKV Y +E
Sbjct: 133 NLEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMPEGYMPLDGSFTPIKKVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     E++++  +K EDK
Sbjct: 310 KLNDLGYPVGTELSPEQRENLKKRLEKLEDK 340


>gi|241667362|ref|ZP_04754940.1| DNA-directed RNA polymerase subunit alpha [Francisella philomiragia
           subsp. philomiragia ATCC 25015]
 gi|254875912|ref|ZP_05248622.1| DNA-directed RNA polymerase alpha subunit [Francisella philomiragia
           subsp. philomiragia ATCC 25015]
 gi|158523432|gb|ABW70830.1| DNA-directed RNA polymerase alpha subunit 1 [Francisella
           philomiragia subsp. philomiragia ATCC 25015]
 gi|254841933|gb|EET20347.1| DNA-directed RNA polymerase alpha subunit [Francisella philomiragia
           subsp. philomiragia ATCC 25015]
          Length = 323

 Score =  235 bits (599), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 110/319 (34%), Positives = 180/319 (56%), Gaps = 11/319 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           QE + PN     +  +       +   P+ +G AH LGN++RR L+SSL GA+I  V ID
Sbjct: 8   QEFV-PN---IQLKEELGAFGYKIQVSPVEKGMAHILGNSIRRFLLSSLSGASIIKVNID 63

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR-VTIFKRGPGVVTAGDIQTVNDI 125
           GVLHE S+++ V ED+ +I+ N+K + +K+  +  K  + +     GVVTAGD +T   I
Sbjct: 64  GVLHEYSTLEDVKEDVVEIVSNLKKVAIKLDKNVSKVELELSVTKSGVVTAGDFKTTQGI 123

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++N D  I  L  +    +  TVS G          TE + +G I +D+ ++PIK+V++
Sbjct: 124 EIINKDQPIATLTNERKFSLTATVSVGRNVGILSALPTELEKVGDIAVDSDFNPIKRVAF 183

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            +           + L + + T+G+I    +V  A     +Q+ +F++   P      D 
Sbjct: 184 EIFDNGTN-----ETLEVFVKTNGTIEPLVAVTKALEYFCEQISVFVSLRVPSNGKTGDA 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            + S   +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL E
Sbjct: 239 LLDSN-IDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLGKKSLNE 297

Query: 306 IKGVLGTMGLFLGMNLPDW 324
           IK +L    L LG+ + ++
Sbjct: 298 IKQILIDNNLSLGVQIDNF 316


>gi|308062578|gb|ADO04466.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           Cuz20]
          Length = 344

 Score =  235 bits (599), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 102/331 (30%), Positives = 170/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRIKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ + + IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVNYSFKGPMELRARDLNSEH-IEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++ +  E  P G + +D  ++PIKKV Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMPEGYMPLDGSFTPIKKVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|22711961|ref|NP_683832.1| RNA polymerase alpha subunit [Chaetosphaeridium globosum]
 gi|25009134|sp|Q8M9V7|RPOA_CHAGL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|22416965|gb|AAM96565.1| alpha subunit of RNA polymerase [Chaetosphaeridium globosum]
          Length = 334

 Score =  235 bits (599), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 87/329 (26%), Positives = 159/329 (48%), Gaps = 26/329 (7%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +   +E   + +   +    I  PL +G A+T+G ALRR L+S + G  IT+V+I   +H
Sbjct: 14  QWRCLESK-IEKSTLHYGRFIISPLWKGQANTIGLALRRTLLSEVEGTCITSVKIKNAIH 72

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E SS+ GV E + DI++N+K I L  S        +   GP  V A D+   + I+++NP
Sbjct: 73  EYSSLSGVQESVHDILINLKKIILSSSFSGIFEGFLSVVGPKTVLASDLNLPSFIKIVNP 132

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  I  ++      +++ + KG GY        +    G   +D ++ PI+ V+Y++ S 
Sbjct: 133 DQYIATVNKPINFNLQIYIQKGKGYSLKNPISIK---QGFFLVDPVFIPIRSVNYSIHSF 189

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----------FEEPKKE 240
            + +    + L + + T+GSI  ++++  AS  L +     ++          F+E +K 
Sbjct: 190 EDEKAT-KEFLIVEVWTNGSIEPKEAIKEASYNLVNLFTPLVSQEYQQLKNQLFKEDEKN 248

Query: 241 VK--------EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            +          I+     +N      +++LELS R+ N L+  NI  + DL++ +  D+
Sbjct: 249 KELNFIETNSNAISDNENSYNLYNQIFLDQLELSSRAYNSLKKNNINTISDLLKYSYEDL 308

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           L++ NFG+KS  ++   L        + L
Sbjct: 309 LKIKNFGKKSADQVIEQLK---KRFKIQL 334


>gi|308183403|ref|YP_003927530.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           PeCan4]
 gi|308065588|gb|ADO07480.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           PeCan4]
          Length = 344

 Score =  235 bits (599), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 102/331 (30%), Positives = 169/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKESNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ +   IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSE-QIEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++ +  E  P G + +D  ++PIKKV Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMPEGYMPLDGSFTPIKKVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|317182539|dbj|BAJ60323.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori F57]
          Length = 344

 Score =  235 bits (599), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 101/331 (30%), Positives = 169/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ + + IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSEH-IEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++ +  E  P G + +D  ++PIK V Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMPEGYMPLDGSFTPIKNVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLNDLGYPVGTELSPDQRESLKKRLEKLEDK 340


>gi|150036816|emb|CAM98278.1| DNA-directed RNA polymerase alpha chain [Leuconostoc fallax]
          Length = 220

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 89/212 (41%), Positives = 136/212 (64%), Gaps = 2/212 (0%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T +ILN+K + L +  D
Sbjct: 1   GTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVVLAIDSD 60

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             K + I  +GP  VTA D+Q   DIEVLNP+  +  +     + M +T  KG GY  A 
Sbjct: 61  EEKSLEIDVQGPAEVTAADLQGSADIEVLNPELHLATVAAGKSLHMTVTAVKGRGYSSAD 120

Query: 160 HHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
            ++   +  PIG++ +D++Y+PI++V+Y VE+ R GQ  DYDKL+  I T+GSI   D++
Sbjct: 121 ENKQLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGQRDDYDKLTFDIWTNGSIKPSDAL 180

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           +L ++IL + L +F +      E +  ++V+ 
Sbjct: 181 SLGAKILSEHLNLFTDISSVAAETEVMVDVEQ 212


>gi|119662847|emb|CAJ33216.1| RNA polymerase alpha subunit [Lactobacillus kunkeei]
          Length = 202

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 97/202 (48%), Positives = 141/202 (69%), Gaps = 4/202 (1%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD--S 100
           LGN+LRR+L+SSL GAA+T++QID VLHE S++ GV ED+T IILN+K I+LK+  +   
Sbjct: 1   LGNSLRRILLSSLPGAAVTSIQIDDVLHEFSTVPGVVEDVTQIILNVKKISLKLDAEDGE 60

Query: 101 HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
            K + I   GP  VTAGDIQ   D+ VLNPD  I  +   +   M +T +KG GYV A  
Sbjct: 61  DKEMEINVTGPAQVTAGDIQADGDVTVLNPDLHIATVAEGSTFHMRMTANKGRGYVSADE 120

Query: 161 HRTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           ++  ND  PIG++ +D++Y+PI++V+Y VE+AR GQ  D+DKL++ + TDGSIT  ++++
Sbjct: 121 NKARNDGMPIGVLPVDSIYTPIERVNYQVENARVGQRSDFDKLTLDVWTDGSITPSEAIS 180

Query: 219 LASRILQDQLGMFINFEEPKKE 240
           LA++IL D L MF++  +  K 
Sbjct: 181 LAAKILNDHLAMFVDLTDEAKN 202


>gi|150036756|emb|CAM98263.1| DNA-directed RNA polymerase alpha chain [Leuconostoc inhae KCTC
           3774]
          Length = 214

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 89/212 (41%), Positives = 134/212 (63%), Gaps = 2/212 (0%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D
Sbjct: 1   GTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSD 60

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             + + +  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A 
Sbjct: 61  EERSLEVDIQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTITAVKGRGYSSAD 120

Query: 160 HHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
            ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D++
Sbjct: 121 ENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDAL 180

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           +L S+IL + L +F++      E    + V+ 
Sbjct: 181 SLGSKILAEHLNLFMDISPVAAEANVMVEVEP 212


>gi|15645906|ref|NP_208085.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           26695]
 gi|2500600|sp|P56001|RPOA_HELPY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|2314459|gb|AAD08336.1| DNA-directed RNA polymerase, alpha subunit (rpoA) [Helicobacter
           pylori 26695]
          Length = 344

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 102/331 (30%), Positives = 169/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ +   IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSE-QIEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++ +  E  P G + +D  ++PIKKV Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMPEGYMPLDGSFTPIKKVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|311990468|gb|ADQ26364.1| RNA polymerase alpha subunit [Lactobacillus fermentum]
          Length = 220

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 94/220 (42%), Positives = 146/220 (66%), Gaps = 2/220 (0%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRV+++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K + LK+  +  K 
Sbjct: 1   GNSLRRVMLASLPGAAITSIQIDGVLHEFSTVQGVTEDVTQIILNLKQVALKIDSEDAKD 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I  +GP  VTA DIQ   D+ +LN D  I  +   A + +++T  KG GY  A  ++T
Sbjct: 61  LEIDVKGPAEVTAADIQGDGDVTILNSDLHIATVSDGAELHVKMTADKGRGYSSADDNKT 120

Query: 164 --ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
             E   IG++ ID++Y+PI++V+YTVE+ R GQ  DYDKL++ + T+GS+T  ++++LA+
Sbjct: 121 RMEGLAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYDKLTLDVWTNGSLTPTEAISLAA 180

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           +IL + L MF+N  E  +  +  +  +       L K +E
Sbjct: 181 KILTEHLTMFVNLTEEAQVTQVMVEREETHQEKVLDKTIE 220


>gi|57504893|ref|ZP_00370868.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter coli
           RM2228]
 gi|57019321|gb|EAL56023.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter coli
           RM2228]
          Length = 337

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 98/321 (30%), Positives = 169/321 (52%), Gaps = 6/321 (1%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +    +    + A P   G+  TL + LRR+L +S  G A TA+ IDGV HE  S++G+
Sbjct: 15  TIENISDTVAKISAWPFEIGYGITLAHPLRRLLYTSTIGYAPTAIHIDGVAHEFDSMRGM 74

Query: 79  HEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
            ED+   I+N+K +  K+  DS+K  V    +GP  +   D+     +EV+N D  +  +
Sbjct: 75  LEDVALFIINLKKLRFKLKSDSNKEIVEFSFKGPKEIYGKDLNND-QVEVVNTDAYLATI 133

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + DA ++  L + KG GYVP++  +   +    I +DA ++P+++ +Y +E        D
Sbjct: 134 NEDAELKFTLIIEKGIGYVPSEEIKELLNDPKFIALDAFFTPVREATYDIEKVLFEDNPD 193

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           Y+K+ +T+ TDG IT  ++   A   +  QL +F      +  +K       L  N  LL
Sbjct: 194 YEKVVLTVTTDGQITPNEAFQNALEAMYKQLSVFDKITNVRSIIKSQATSNELE-NTKLL 252

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + + +L LS RS NCL    IVY+G+L   +  ++  + N G+KSL EIK ++ ++G  +
Sbjct: 253 QNITDLNLSARSYNCLEKAGIVYIGELALMSVNELAGLKNLGKKSLDEIKSIMESIGFPV 312

Query: 318 GMNLPDWPPESIEELAKKYED 338
           G +      ++ + L KK ++
Sbjct: 313 GTS---KLSDNKDLLKKKIDE 330


>gi|150186982|emb|CAK30141.1| RNA polymerase alpha subunit [Streptococcus suis]
          Length = 205

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 93/205 (45%), Positives = 142/205 (69%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRVL++SL GAA+T+++IDGVLHE  ++ GV ED+  IILNIKGI +K   +  K
Sbjct: 1   LGNSLRRVLLASLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
           ++ +   GP  VTAGDI T +DIE++NPDH +  +   A  +  LTV+ G GYVPA+ ++
Sbjct: 61  KIELDVVGPAEVTAGDILTDSDIEIVNPDHYLFTIADGATFKAVLTVNSGRGYVPAEDNK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I+T+G+I  ED++ L++R
Sbjct: 121 KDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTLEINTNGTIIPEDALGLSAR 180

Query: 223 ILQDQLGMFINFEEPKKEVKEDINV 247
           IL + LG+F +  E  K  +     
Sbjct: 181 ILMEHLGLFTDLTEVAKSAEVMKEA 205


>gi|307637964|gb|ADN80414.1| DNA-directed RNA polymerase alpha subunit [Helicobacter pylori 908]
 gi|325996569|gb|ADZ51974.1| DNA-directed RNA polymerase alpha subunit [Helicobacter pylori
           2018]
 gi|325998159|gb|ADZ50367.1| DNA-directed RNA polymerase alpha subunit [Helicobacter pylori
           2017]
          Length = 344

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 101/331 (30%), Positives = 168/331 (50%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ +   IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMEIRARDLNSE-QIEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++ +  E  P G + +D  ++PIK V Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMPEGYMPLDGSFTPIKNVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|307720213|ref|YP_003891353.1| DNA-directed RNA polymerase subunit alpha [Sulfurimonas
           autotrophica DSM 16294]
 gi|306978306|gb|ADN08341.1| DNA-directed RNA polymerase subunit alpha [Sulfurimonas
           autotrophica DSM 16294]
          Length = 333

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 94/328 (28%), Positives = 168/328 (51%), Gaps = 6/328 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
            P   +   + Q  +N   ++A P   G+A +L + LRR L+SS  G A  A++I+G  H
Sbjct: 7   TPLAPQEFEVEQISDNEANIMAYPFEVGYAISLAHPLRRFLLSSSVGYAPIAIKIEGAKH 66

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           E  S++G+ ED++D ILN+K I  K++ D+ +  +     GP  +   D+    ++EV+ 
Sbjct: 67  EFDSVRGMLEDISDFILNLKEIRFKLNNDATQAEINYSFAGPCTIKGADLSND-EVEVVT 125

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  +  L+ D+ +   L +++G GYV ++    E      I +DA ++P++  +Y +++
Sbjct: 126 PDAPLATLNEDSTLNFTLKIAQGIGYVASEDTAVEVADDDYIALDAYFTPVRSATYKIDN 185

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                  +++++ M I TDG I+  D+   +  ++  QL +F N E   K       V+ 
Sbjct: 186 VLVEDNPNFERVIMNIKTDGQISPIDAFRNSLEVMYAQLAVF-NSEISIKAPATIERVEE 244

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
            P    L   ++ L LS RS NCL   +I  +G+++  +  D+  + N G+KS  EI   
Sbjct: 245 SPDLKKLTTNIDSLGLSARSFNCLDRSSIKLIGEIVLMSTNDLKNVKNLGKKSYDEIVEK 304

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYE 337
           +   G  +G +L D   + +  L KK E
Sbjct: 305 IQEFGFEVGADLAD---DVVTALKKKIE 329


>gi|321310954|ref|YP_004193283.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma haemofelis
           str. Langford 1]
 gi|319802798|emb|CBY93444.1| DNA-directed RNA polymerase alpha subunit [Mycoplasma haemofelis
           str. Langford 1]
          Length = 326

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 107/318 (33%), Positives = 165/318 (51%), Gaps = 14/318 (4%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
           NI++ +L    +    ++  PL +GF  T+GNALRRVL+ S+ GAA+ A++IDGV HE  
Sbjct: 8   NIDFKLLES-SQYMASVVISPLKQGFGTTIGNALRRVLLGSIPGAAVFAIKIDGVDHEFM 66

Query: 74  SIKGVHEDLTDIILNIKGINLKMSG-------------DSHKRVTIFKRGPGVVTAGDIQ 120
           + +GV ED+T+IILN+K + + +                    + I K   GVV A DI+
Sbjct: 67  APEGVLEDVTNIILNVKKLVISIDEKVVDVQSLEEKSISEWPTMKIKKNKAGVVYANDIE 126

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               ++V+N D  IC L  D    MEL  +   GY     +R   D + +I+ID+L+SPI
Sbjct: 127 CPPGMKVINKDLKICELSKDVEFGMELYATLDRGYRSFSENRERLDTLKIISIDSLFSPI 186

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KV + V   +  +    DKL +T+ T+GS+   D+++LA+  L   L     F     +
Sbjct: 187 VKVEWKVVEEKTTKQGTTDKLHLTLVTNGSVKAADALSLAAHTLISLLEPISAFNPETSK 246

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            K     +      A+   ++ELEL++RS NCL+   I  + +L + T A+   + N G+
Sbjct: 247 RKLIGEAEVATKKVAMATPIDELELTMRSFNCLKQNGINTITELAEMTRAEAENIKNLGK 306

Query: 301 KSLVEIKGVLGTMGLFLG 318
           KSL EI   L   GL   
Sbjct: 307 KSLNEIIAKLAEKGLKFK 324


>gi|317178416|dbj|BAJ56204.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori F30]
          Length = 344

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 101/331 (30%), Positives = 169/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ + + IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLSSEH-IEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++ +  E  P G + +D  ++PIK V Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMPEGYMPLDGSFTPIKNVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMGKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKSVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLNDLGYPVGTELNPEQRESLKKRLEKLEDK 340


>gi|119662369|emb|CAJ33173.1| RNA polymerase alpha subunit [Lactobacillus versmoldensis]
          Length = 215

 Score =  234 bits (597), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 86/214 (40%), Positives = 141/214 (65%), Gaps = 1/214 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL++SL G A++ +QIDGVLHE  +I GV ED+T I+LNIK ++LK   
Sbjct: 1   YGTTLGNSLRRVLLASLPGTAVSDIQIDGVLHEFFAIDGVIEDVTQIVLNIKKLSLKSYA 60

Query: 99  DS-HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
           +    +  I   GP  +TA DIQ  +D+E+L+P+  IC +       M++T++ G GY P
Sbjct: 61  EEGSLKAEIDISGPATITAKDIQADDDLEILDPEQYICTVAEGGHFHMQMTITNGRGYTP 120

Query: 158 AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
           A+ ++T+  PIG++ +D++++P++KV+Y VE+ R G+  D+DKL++ I T+GSI   +++
Sbjct: 121 AEQNKTDETPIGVLPVDSIFTPVEKVNYQVENTRVGKRNDFDKLTIDIWTNGSIGPREAI 180

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           +L+++IL + L  F+N  E  K     I  +   
Sbjct: 181 SLSAKILTEHLTSFVNLTEEAKSADMMIEKEETQ 214


>gi|32266902|ref|NP_860934.1| DNA-directed RNA polymerase subunit alpha [Helicobacter hepaticus
           ATCC 51449]
 gi|41688644|sp|Q7VGB9|RPOA_HELHP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|32262954|gb|AAP78000.1| DNA-dependent RNA polymerase [Helicobacter hepaticus ATCC 51449]
          Length = 334

 Score =  234 bits (597), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 92/315 (29%), Positives = 157/315 (49%), Gaps = 3/315 (0%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           I+P     I + +   NR  + A P   G+A TL + +RR+L+SS  G A TA++I GV 
Sbjct: 6   IEPYIPTDISIEEISTNRIRISAYPFESGYAITLAHPIRRLLLSSSVGYAPTALRIQGVT 65

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT-AGDIQTVNDIEVL 128
           HE  SI+G+ ED++  I N+K I   +       V +     G +  + +    + + ++
Sbjct: 66  HEFDSIRGIVEDVSHFITNLKNIRFLIKDTESDNVQLHYEFKGPMVLSANELVNDMVGIV 125

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ +A +   L V KG GYVP++  R +      I +DA ++P+KK  Y +E
Sbjct: 126 NPEAYLATINENASLSFSLIVQKGIGYVPSESIRGKISEDY-IPLDAYFTPVKKAVYEIE 184

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A  I+  Q+ +F            +I+  
Sbjct: 185 NVLVEDNPNYEKIVFDIETDGQIEPITAFKEAIAIMHKQMSIFGVDLSTASSGTRNISED 244

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
           S      L+ K++ L LS R  NCL    + Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 245 SGEL-KTLMIKIDTLNLSARCFNCLDRSGLKYVGELVIMSENELKNIKNMGKKSYDEIAD 303

Query: 309 VLGTMGLFLGMNLPD 323
            L  +G  +G  + D
Sbjct: 304 KLEELGYPVGGEIAD 318


>gi|315639079|ref|ZP_07894247.1| DNA-directed RNA polymerase subunit alpha [Campylobacter
           upsaliensis JV21]
 gi|315480855|gb|EFU71491.1| DNA-directed RNA polymerase subunit alpha [Campylobacter
           upsaliensis JV21]
          Length = 337

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 101/321 (31%), Positives = 170/321 (52%), Gaps = 6/321 (1%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +    E    + A P   G+  TL + LRR+L +S  G A TA+ I+GV HE  S++G+
Sbjct: 15  TIENLSETSAKISAWPFEIGYGITLAHPLRRLLYTSTVGYAPTAIYIEGVAHEFDSMRGM 74

Query: 79  HEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
            ED+   I+N+K +  K+  DS+K  V  + +GP  +   D+     + V+N D  +  +
Sbjct: 75  LEDVALFIINLKKLRFKLKSDSNKEIVEFYFKGPKEIHGRDLDND-QVSVVNEDAYLATI 133

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + DA ++  L + KG GYVP++  +   D    I +DA ++PI++ +Y +E        D
Sbjct: 134 NEDAELKFTLIIEKGIGYVPSEEIKELLDDNKFIALDAFFTPIREATYDIEKVLFEDNPD 193

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           Y+K+ +TI TDG IT  ++   A   +  QL +F      +  +K   +   L  N  LL
Sbjct: 194 YEKVVLTITTDGQITPNEAFQNALEAMYKQLSVFDKITNVRSMIKTQASHNELE-NTKLL 252

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + + +L LS RS NCL    +VY+G+L   +  ++  + N G+KSL EIK V+ ++G  +
Sbjct: 253 QNITDLNLSARSYNCLEKAGVVYIGELALMSVNELAGLKNLGKKSLDEIKSVMESIGFAV 312

Query: 318 GMNLPDWPPESIEELAKKYED 338
           G +      ++ + L KK E+
Sbjct: 313 GTS---KLSDNKDLLKKKIEE 330


>gi|108563663|ref|YP_627979.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           HPAG1]
 gi|119366688|sp|Q1CRW7|RPOA_HELPH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|107837436|gb|ABF85305.1| DNA-directed RNA polymerase, alpha subunit [Helicobacter pylori
           HPAG1]
          Length = 344

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 102/331 (30%), Positives = 169/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPIGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +G   + A D+ + + IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGSMELRARDLNSDH-IEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++  R E  P G + +D  ++PIKKV Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSETTR-ELMPEGYMPLDGSFTPIKKVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|317181015|dbj|BAJ58801.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori F32]
          Length = 344

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 100/331 (30%), Positives = 170/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ + + IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSEH-IEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ +A +   L + KG GYVP++ +  E  P G + +D  ++PIKKV Y +E
Sbjct: 133 NPEMPLATINENAQLNFSLIICKGMGYVPSE-NTRELMPEGYMPLDGSFTPIKKVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     E++++  +K EDK
Sbjct: 310 KLNDLGYPVGTELNPEQRENLKKRLEKLEDK 340


>gi|119668279|emb|CAK95450.1| RNA polymerase alpha subunit [Lactobacillus amylolyticus]
          Length = 213

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 91/203 (44%), Positives = 134/203 (66%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK + D  K
Sbjct: 1   LGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSNSDEQK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + +   GP  VTA D++  +D+EVLNPD  IC +     + M++ V  G GYV A  ++
Sbjct: 61  VIELDVEGPATVTADDLKVDSDVEVLNPDQYICTIAEGGHLHMQIAVKNGRGYVAASDNK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
           +E+ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++ A+ 
Sbjct: 121 SEDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSINPNDALSFAAN 180

Query: 223 ILQDQLGMFINFEEPKKEVKEDI 245
           IL +   +F + +   K  +  +
Sbjct: 181 ILVEHFKVFESADADNKFSEVMV 203


>gi|119668325|emb|CAK95462.1| RNA polymerase alpha subunit [Lactobacillus hilgardii]
          Length = 200

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 99/200 (49%), Positives = 140/200 (70%), Gaps = 4/200 (2%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K I+LK+ G
Sbjct: 1   YGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKISLKLDG 60

Query: 99  --DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT ++G GYV
Sbjct: 61  PEDEDENLEIDVIGPADVTAGDIQGDSDVTVLNPDLHIATVAEGATFHMRLTANRGRGYV 120

Query: 157 PAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A  ++      PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ I T+GSIT  
Sbjct: 121 SAVENKKRATEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDIWTNGSITPS 180

Query: 215 DSVALASRILQDQLGMFINF 234
           ++V+LA++IL + L MF++ 
Sbjct: 181 EAVSLAAKILTEHLEMFVDL 200


>gi|57242509|ref|ZP_00370447.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter
           upsaliensis RM3195]
 gi|57016794|gb|EAL53577.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter
           upsaliensis RM3195]
          Length = 337

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 101/321 (31%), Positives = 170/321 (52%), Gaps = 6/321 (1%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +    E    + A P   G+  TL + LRR+L +S  G A TA+ I+GV HE  S++G+
Sbjct: 15  TIENLSETSAKISAWPFEIGYGITLAHPLRRLLYTSTVGYAPTAIYIEGVAHEFDSMRGM 74

Query: 79  HEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
            ED+   I+N+K +  K+  DS+K  V  + +GP  +   D+     + V+N D  +  +
Sbjct: 75  LEDVALFIINLKKLRFKLKSDSNKEIVEFYFKGPKEIHGRDLDND-QVSVVNEDAYLATI 133

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + DA ++  L + KG GYVP++  +   D    I +DA ++PI++ +Y +E        D
Sbjct: 134 NEDAELKFTLIIEKGIGYVPSEEIKELLDDNKFIALDAFFTPIREATYDIEKVLFEDNPD 193

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           Y+K+ +TI TDG IT  ++   A   +  QL +F      +  +K   +   L  N  LL
Sbjct: 194 YEKVVLTITTDGQITPNEAFQNALGAMYKQLSVFDKITNVRSMIKTQASHNELE-NTKLL 252

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + + +L LS RS NCL    +VY+G+L   +  ++  + N G+KSL EIK V+ ++G  +
Sbjct: 253 QNITDLNLSARSYNCLEKAGVVYIGELALMSVNELAGLKNLGKKSLDEIKSVMESIGFAV 312

Query: 318 GMNLPDWPPESIEELAKKYED 338
           G +      ++ + L KK E+
Sbjct: 313 GTS---KLSDNKDLLKKKIEE 330


>gi|149192395|ref|ZP_01870596.1| DNA-directed RNA polymerase subunit alpha [Vibrio shilonii AK1]
 gi|148833786|gb|EDL50822.1| DNA-directed RNA polymerase subunit alpha [Vibrio shilonii AK1]
          Length = 238

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 100/240 (41%), Positives = 152/240 (63%), Gaps = 8/240 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E ++P  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLRPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEISMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           Y P+ K++Y VE+AR  Q  D DKL + ++T G++  E++V  A+ IL +QL  F++  +
Sbjct: 178 YRPVDKIAYAVEAARVEQRTDLDKLVIDMETSGTLEPEEAVRRAATILAEQLDAFVDLRD 237


>gi|78776528|ref|YP_392843.1| DNA-directed RNA polymerase subunit alpha [Sulfurimonas
           denitrificans DSM 1251]
 gi|119366748|sp|Q30TS3|RPOA_SULDN RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|78497068|gb|ABB43608.1| DNA-directed RNA polymerase, alpha subunit [Sulfurimonas
           denitrificans DSM 1251]
          Length = 330

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 93/328 (28%), Positives = 166/328 (50%), Gaps = 7/328 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
            P   +   + Q  EN   ++A P   GFA +L + LRR L+SS  G A  A++I+G  H
Sbjct: 7   TPLAPQEFEVEQISENEANIMAYPFETGFAISLAHPLRRFLLSSSVGYAPIAIKIEGAKH 66

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           E  S++G+ ED++D ILN+K    K+  G +   +     GP  +   ++ + +++E++ 
Sbjct: 67  EFDSVRGMLEDISDFILNLKETRFKLLGGATEAEINYNFTGPCDIKGSNL-SNSEVEIVT 125

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  +  L+ D+ +   + +++G GYV ++    +    G I +DA ++P++  +Y +E+
Sbjct: 126 PNTHLATLNEDSTLNFSIRIAQGIGYVASED-TYDELQDGYIALDAYFTPVRSATYKIEN 184

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                  +++++ + I TDG IT  D+   +  ++  QL +F N E   K        + 
Sbjct: 185 VLVEDNPNFERVILNIKTDGQITPLDAFRNSLEVMYAQLAVF-NSEISVKAPATIERAEE 243

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
            P    L   ++ L LS RS NCL   NI  +G++   +  D+  + N G+KS  EI   
Sbjct: 244 SPDLKKLTAHIDSLGLSARSFNCLDRSNIKLIGEIALMSTNDLKNVKNLGKKSYDEIVEK 303

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYE 337
           L   G  +G +L D   + +  L KK E
Sbjct: 304 LQEFGYEVGGDLAD---DVVSALKKKIE 328


>gi|261838612|gb|ACX98378.1| alpha subunit of the DNA-dependent RNA polymerase core enzyme
           [Helicobacter pylori 51]
          Length = 344

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 100/331 (30%), Positives = 169/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ + + IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALIGQDSSLENQSVVVDYSFKGPMEIRARDLSSEH-IEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG G+VP++ +  E  P G + +D  ++PIK V Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGHVPSE-NTRELMPEGYMPLDGSFTPIKNVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|305432400|ref|ZP_07401562.1| DNA-directed RNA polymerase subunit alpha [Campylobacter coli JV20]
 gi|304444439|gb|EFM37090.1| DNA-directed RNA polymerase subunit alpha [Campylobacter coli JV20]
          Length = 337

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 98/321 (30%), Positives = 169/321 (52%), Gaps = 6/321 (1%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +    +    + A P   G+  TL + LRR+L +S  G A TA+ IDGV HE  S++G+
Sbjct: 15  TIENISDTVAKISAWPFEIGYGITLAHPLRRLLYTSTIGYAPTAIHIDGVAHEFDSMRGM 74

Query: 79  HEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
            ED+   I+N+K +  K+  DS+K  V    +GP  +   D+     +EV+N D  +  +
Sbjct: 75  LEDVALFIINLKKLQFKLKSDSNKEIVEFSFKGPKEIYGKDLNND-QVEVVNTDAYLATI 133

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + DA ++  L + KG GYVP++  +   +    I +DA ++P+++ +Y +E        D
Sbjct: 134 NEDAELKFTLIIEKGIGYVPSEEIKELLNDPKFIALDAFFTPVREATYDIEKVLFEDNPD 193

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           Y+K+ +T+ TDG IT  ++   A   +  QL +F      +  +K       L  N  LL
Sbjct: 194 YEKVVLTVTTDGQITPNEAFQNALEAMYKQLSVFDKITNVRSIIKSQATSNELE-NTKLL 252

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + + +L LS RS NCL    IVY+G+L   +  ++  + N G+KSL EIK ++ ++G  +
Sbjct: 253 QNITDLNLSARSYNCLEKAGIVYIGELALMSVNELAGLKNLGKKSLDEIKSIMESIGFPV 312

Query: 318 GMNLPDWPPESIEELAKKYED 338
           G +      ++ + L KK ++
Sbjct: 313 GTS---KLSDNKDLLKKKIDE 330


>gi|315587182|gb|ADU41563.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori 35A]
          Length = 344

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 101/331 (30%), Positives = 169/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ + + IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSEH-IEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++ +  E  P G + +D  ++PIK V Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMPEGYMPLDGSFTPIKNVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLNDLGYPVGTELNPEQRESLKKRLEKLEDK 340


>gi|119668345|emb|CAK95469.1| RNA polymerase alpha subunit [Lactobacillus paracasei subsp.
           paracasei]
          Length = 186

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 89/186 (47%), Positives = 133/186 (71%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNIK + LKM+ D  K + I
Sbjct: 1   LRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNTDEDKNIEI 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
              GP  VTA DI    D+EVLNP+  IC +       + +TV KG GYV A  +++++ 
Sbjct: 61  DVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAADQNKSDDM 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++IL +
Sbjct: 121 PIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKILTE 180

Query: 227 QLGMFI 232
            L +F+
Sbjct: 181 HLDIFV 186


>gi|210135452|ref|YP_002301891.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori P12]
 gi|210133420|gb|ACJ08411.1| DNA-directed RNA polymerase alpha subunit [Helicobacter pylori P12]
          Length = 344

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 102/331 (30%), Positives = 169/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKESNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPIGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ +   IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSE-QIEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++ +  E  P G + +D  ++PIKKV Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMPEGYMPLDGSFTPIKKVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYT 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|328813999|gb|AEB52115.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 215

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 95/215 (44%), Positives = 142/215 (66%), Gaps = 2/215 (0%)

Query: 48  RRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF 107
           RR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK+  D  K + I 
Sbjct: 1   RRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTAIILNVKKIALKLESDETKTLEID 60

Query: 108 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TEN 165
            +GP  VTAGDI    D+EVLNPD  IC +   A   M +T + G GYV A+ ++   ++
Sbjct: 61  VKGPANVTAGDIIGDADVEVLNPDLPICTVADGAHFHMRMTANTGRGYVSAEDNKHREDD 120

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
            PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T+GSIT  ++++L+++IL 
Sbjct: 121 MPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWTNGSITPSEAISLSAKILT 180

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           D L +F+N  +  K     +  +       L   +
Sbjct: 181 DHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEMTI 215


>gi|317178032|dbj|BAJ55821.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori F16]
          Length = 344

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 100/331 (30%), Positives = 169/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ + + IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSEH-IEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++ +  E  P G + +D  ++PIK V Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMPEGYMPLDGSFTPIKNVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEITE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     E++++  +K EDK
Sbjct: 310 KLNDLGYPVGTELNPEQRENLKKRLEKLEDK 340


>gi|86149413|ref|ZP_01067644.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni CF93-6]
 gi|88596039|ref|ZP_01099276.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni 84-25]
 gi|218563184|ref|YP_002344964.1| DNA-directed RNA polymerase subunit alpha [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|12230603|sp|Q9PM80|RPOA_CAMJE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|85840195|gb|EAQ57453.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni CF93-6]
 gi|88190880|gb|EAQ94852.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni 84-25]
 gi|112360891|emb|CAL35692.1| DNA-directed RNA polymerase alpha chain [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|284926790|gb|ADC29142.1| DNA-directed RNA polymerase alpha chain [Campylobacter jejuni
           subsp. jejuni IA3902]
 gi|315927659|gb|EFV06990.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni DFVF1099]
 gi|315929466|gb|EFV08663.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni 305]
          Length = 337

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 97/320 (30%), Positives = 166/320 (51%), Gaps = 4/320 (1%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +    +    + A P   G+  TL + LRR+L +S  G A TA+ IDGV HE  S++G+
Sbjct: 15  TIENISDTVAKISAWPFEIGYGITLAHPLRRLLYTSTIGYAPTAIHIDGVAHEFDSMRGM 74

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+   I+N+K +  K+ GDS+K +  F         G     + +EV+N D  +  ++
Sbjct: 75  LEDVALFIINLKKLRFKIKGDSNKEIVEFSFKGSKEIYGKDLNNDQVEVVNKDAYLATIN 134

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            DA ++  L V KG GYVP++  +   +    I +DA ++P+++ +Y +E        DY
Sbjct: 135 EDAELKFTLIVEKGIGYVPSEEIKELINDPKFIALDAFFTPVREATYDIEKVLFEDNPDY 194

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           +K+ +T+ TDG IT  ++   A   +  QL +F      +  +K       L  N  LL+
Sbjct: 195 EKVVLTVTTDGQITPNEAFQNALEAMYKQLSVFDKITNVRSVIKNQATSNELE-NTKLLQ 253

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            + +L LS RS NCL    +VY+G+L   + +++  + N G+KSL EIK ++ ++G  +G
Sbjct: 254 NITDLNLSARSYNCLEKAGVVYIGELALMSVSELAGLKNLGKKSLDEIKNIMESIGFPVG 313

Query: 319 MNLPDWPPESIEELAKKYED 338
            +      ++ E L  K  +
Sbjct: 314 TS---KLSDNKEILKNKIAE 330


>gi|121591860|ref|ZP_01679032.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae
           2740-80]
 gi|121546275|gb|EAX56569.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae
           2740-80]
          Length = 248

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 106/250 (42%), Positives = 162/250 (64%), Gaps = 8/250 (3%)

Query: 87  LNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVVR 144
           +N+KG+ +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L   +A + 
Sbjct: 1   MNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIA 60

Query: 145 MELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           M + V +G GYVPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL
Sbjct: 61  MRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKL 120

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V+
Sbjct: 121 VIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVD 177

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L
Sbjct: 178 DLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRL 237

Query: 322 PDWPPESIEE 331
            +WPP SI E
Sbjct: 238 ENWPPASIAE 247


>gi|261886106|ref|ZP_06010145.1| DNA-directed RNA polymerase subunit alpha [Campylobacter fetus
           subsp. venerealis str. Azul-94]
          Length = 326

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 105/316 (33%), Positives = 170/316 (53%), Gaps = 7/316 (2%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
            EN   +IA P    +A TL + LRR+L +S  G A TAV+IDGV HE  S++G+ ED+T
Sbjct: 14  SENVAKIIAYPFETVYAVTLAHPLRRLLYTSTVGFAPTAVKIDGVAHEFDSMRGMLEDVT 73

Query: 84  DIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
             I+N+K +  K+  DS  + +    +GP  +T  D+     +E++NPD  +  ++ DA 
Sbjct: 74  LFIINLKNLRFKLKNDSKREVIEYSFKGPKEITGIDLNND-IVEIVNPDSYLATINEDAE 132

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           ++  L V KG GYVP++  R   D    I +DA ++P+KK  Y +E+       DY+K+ 
Sbjct: 133 LKFSLIVEKGIGYVPSEEIRDYIDSEY-IALDAFFTPVKKAVYEIENVLVEDNPDYEKIV 191

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           +++ TDG ++  ++   +   +  Q+ +F N       +    +  S   +   L+ VE 
Sbjct: 192 LSVSTDGQVSPIEAFKHSIEAMYKQMSIFNNVLNIDVNMALTSSQNSNEHSKL-LESVEN 250

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           L LS RS NCL   +I Y+G+L    E+++  + N G+KSL EIK V+  +G   G    
Sbjct: 251 LNLSARSFNCLDKADIRYIGELALMEESELKDLKNLGKKSLDEIKAVMAEIGYPFG---E 307

Query: 323 DWPPESIEELAKKYED 338
           +   +S E L KK  +
Sbjct: 308 NTLGDSKEALRKKISE 323


>gi|217032047|ref|ZP_03437547.1| hypothetical protein HPB128_16g7 [Helicobacter pylori B128]
 gi|298735682|ref|YP_003728207.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori B8]
 gi|216946195|gb|EEC24803.1| hypothetical protein HPB128_16g7 [Helicobacter pylori B128]
 gi|298354871|emb|CBI65743.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori B8]
          Length = 344

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 101/331 (30%), Positives = 168/331 (50%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPIGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ +   IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSE-QIEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++ +  E    G + +D  ++PIKKV Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMSEGYMPLDGSFTPIKKVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLNDLGYPVGTELSHEQRESLKKRLEKLEDK 340


>gi|224417911|ref|ZP_03655917.1| DNA-directed RNA polymerase subunit alpha [Helicobacter canadensis
           MIT 98-5491]
 gi|253827250|ref|ZP_04870135.1| DNA-directed RNA polymerase alpha subunit [Helicobacter canadensis
           MIT 98-5491]
 gi|313141452|ref|ZP_07803645.1| DNA-directed RNA polymerase subunit alpha [Helicobacter canadensis
           MIT 98-5491]
 gi|253510656|gb|EES89315.1| DNA-directed RNA polymerase alpha subunit [Helicobacter canadensis
           MIT 98-5491]
 gi|313130483|gb|EFR48100.1| DNA-directed RNA polymerase subunit alpha [Helicobacter canadensis
           MIT 98-5491]
          Length = 329

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 100/328 (30%), Positives = 165/328 (50%), Gaps = 10/328 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  IE   +G    N+  + A P   G+A TL + LRR+L+ S  G A  A+ I GV HE
Sbjct: 11  PTKIEVKEVGV---NKVQITAYPFENGYAITLAHPLRRLLLGSSVGFAPVALHIAGVAHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
             S++GV ED++  I+N+K I  K+  DS    V     GP V+T  D+     +EV+ P
Sbjct: 68  FDSVRGVTEDVSQFIVNLKTIRFKIKDDSDSVSVDYTFNGPKVITGADLSND-LVEVVTP 126

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  +  ++ DA +   + + KG GYVP++  R  N P G + +DA ++P+   +Y  E+ 
Sbjct: 127 DVHLATINKDATLSFSIVIYKGIGYVPSEEIRA-NVPEGFMPLDAYFTPVTSATYATENM 185

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
                 +Y+K+   I TDG +    +   A  ++  Q+ +F N E   +  +  I+ +  
Sbjct: 186 LLEDDPNYEKVIFEIQTDGQVDPLTAFKNALSVMHKQMSIF-NSELNIEIPEVAISEEER 244

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           P    L + ++ L  S R  NCL    I Y+G+L+   E  +  + N G+KSL EI   L
Sbjct: 245 PELKVLSQTIDSLNFSARCFNCLDRSGIKYLGELVLLNEEQIKNIKNLGKKSLDEITAKL 304

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKYED 338
             +G  +   + +   + ++ L KK+ +
Sbjct: 305 DELGYPVNREISE---DLMQILKKKFSN 329


>gi|190411115|gb|ACE78312.1| RpoA [Vibrio parahaemolyticus]
          Length = 252

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 108/255 (42%), Positives = 168/255 (65%), Gaps = 8/255 (3%)

Query: 49  RVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIF 107
           R+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ 
Sbjct: 1   RILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLN 60

Query: 108 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRT 163
           K G G V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H+  
Sbjct: 61  KSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHNEE 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ I
Sbjct: 121 DERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATI 180

Query: 224 LQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGD 283
           L +QL  F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GD
Sbjct: 181 LAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGD 237

Query: 284 LIQRTEADMLRMANF 298
           L+QRTE ++L+  N 
Sbjct: 238 LVQRTEVELLKTPNL 252


>gi|119668273|emb|CAK95495.1| RNA polymerase alpha subunit [Lactobacillus kefiri]
          Length = 203

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 101/203 (49%), Positives = 140/203 (68%), Gaps = 4/203 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K I+LK+ G
Sbjct: 1   YGTTLGNSLRRTLLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKISLKLDG 60

Query: 99  --DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             D  + + I   GP  VTAGDIQ   D+ VLNPD  I  +   A   M LT +KG GYV
Sbjct: 61  PEDEEENLEIDVIGPADVTAGDIQADGDVTVLNPDLHIATVAEGATFHMRLTANKGRGYV 120

Query: 157 PAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A  ++      PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ I TDGSIT  
Sbjct: 121 SAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDIWTDGSITPS 180

Query: 215 DSVALASRILQDQLGMFINFEEP 237
           ++V+LA++IL + L MF++  + 
Sbjct: 181 EAVSLAAKILTEHLEMFVDLTDE 203


>gi|86438806|emb|CAJ43368.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 192

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 90/191 (47%), Positives = 128/191 (67%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   
Sbjct: 1   FGTTLGNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + +   GP  VTA D++   D++VLNPD  IC +     + ME+ V  G GYV A
Sbjct: 61  DERKVIELDVEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNGRGYVAA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++
Sbjct: 121 SDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALS 180

Query: 219 LASRILQDQLG 229
            A++IL +   
Sbjct: 181 FATKILVEHFK 191


>gi|261840008|gb|ACX99773.1| DNA-directed RNA polymerase alpha subunit [Helicobacter pylori 52]
          Length = 344

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 100/331 (30%), Positives = 168/331 (50%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ + + IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSEH-IEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++ +  E    G + +D  ++PIK V Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMHEGYMPLDGSFTPIKNVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLNDLGYPVGTELNPEQRESLKKRLEKLEDK 340


>gi|207721872|ref|YP_002252310.1| dna-directed rna polymerase alpha chain (partial sequence n
           terminus) protein [Ralstonia solanacearum MolK2]
 gi|206587039|emb|CAQ17623.1| probable dna-directed rna polymerase alpha chain (partial sequence
           n terminus) protein [Ralstonia solanacearum MolK2]
          Length = 230

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 103/231 (44%), Positives = 152/231 (65%), Gaps = 4/231 (1%)

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           +++ K G GVVTA DI+  +D+E++NP HVI +L     + M++ V +G GYVP    + 
Sbjct: 1   MSLRKEGEGVVTAADIELPHDVEIINPGHVIASLSAGGKLDMQIKVEQGRGYVPGNVRKF 60

Query: 164 ENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
            ++     G + +DA ++P+++VSY VESAR  Q  D DKL M I+T+G I+ E+++  +
Sbjct: 61  GDESSKVIGRVVLDASFAPVRRVSYAVESARVEQRTDLDKLVMNIETNGVISPEEAIRQS 120

Query: 221 SRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVY 280
           +RIL DQL +F   E   +   E    ++   +P LL+ V++LEL+VRS NCL+ ENI Y
Sbjct: 121 ARILVDQLSVFAALEG-TESAAEAAAARAPQIDPILLRPVDDLELTVRSANCLKAENIYY 179

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +GDLIQRTE ++L+  N GRKSL EIK VL + GL LGM L +WPP  +E+
Sbjct: 180 IGDLIQRTENELLKTPNLGRKSLNEIKEVLASRGLTLGMKLENWPPAGLEK 230


>gi|119668307|emb|CAK95506.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           delbrueckii]
          Length = 209

 Score =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 86/209 (41%), Positives = 131/209 (62%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           GF  TLGN+LRRVL++S+ G  +  V+IDG+LHE +++ GV ED+T IILN+K + L+  
Sbjct: 1   GFGTTLGNSLRRVLLTSVPGTGLVKVKIDGILHEFTTVPGVKEDVTKIILNLKKLVLRAY 60

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
            +  K + +   GP  VTA D++   D+EVLNPD  IC +     + M + V  G GYVP
Sbjct: 61  TEEVKTIELNVEGPATVTAEDLKADADVEVLNPDQYICTIAQGGHLHMWIDVCNGRGYVP 120

Query: 158 AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
           A  ++T    IG I +D+L+SPI+KV+Y VES R G+  D+DKL++ I T+GSI   D++
Sbjct: 121 ASENKTAEMFIGDIPVDSLFSPIEKVNYQVESTRVGKREDFDKLTLEIWTNGSIAPNDAL 180

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDIN 246
             A+R+L +    F + +   +  +  + 
Sbjct: 181 NFAARVLVEHFKAFESADAAAEIGEVMVE 209


>gi|242309345|ref|ZP_04808500.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pullorum
           MIT 98-5489]
 gi|239523916|gb|EEQ63782.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pullorum
           MIT 98-5489]
          Length = 329

 Score =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 95/327 (29%), Positives = 164/327 (50%), Gaps = 8/327 (2%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  IE    G    N+  + A P   G+A TL + LRR+L+ S  G A  A++I GV HE
Sbjct: 11  PTKIEVRETGN---NKVQITAYPFENGYAITLAHPLRRLLLGSSVGFAPIALRISGVAHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
             S++GV ED++  I+N+K I  ++  +S      +K     V  G   +   +EV+ PD
Sbjct: 68  FDSVRGVVEDVSQFIVNLKAIRFRIKDNSDNVSVDYKFNGSKVITGADLSNELVEVVTPD 127

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA +   + + KG GYVP++  R  + P G + +DA ++P+   +YT E+  
Sbjct: 128 IHLATINEDATLAFSIIIYKGIGYVPSEEIRA-SVPEGFMPLDAYFTPVTSATYTTENML 186

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I TDG +    +   A  ++  Q+ +F N E   +  +  ++ +  P
Sbjct: 187 LEDDPNYEKIIFDIQTDGQVDPLTAFKNALSVMHKQMSIF-NSELNIEMPETTVSEEERP 245

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L + ++ L  S R  NCL    I Y+G+L+   E  +  + N G+KSL EI   L 
Sbjct: 246 ELKVLSQTIDSLNFSARCFNCLDRSGIRYLGELVLLNEDQIKNIKNLGKKSLDEITAKLD 305

Query: 312 TMGLFLGMNLPDWPPESIEELAKKYED 338
            +G  +   +P+   + ++ L KK+ +
Sbjct: 306 ELGYPVNREIPE---DLLQILKKKFSN 329


>gi|300870622|ref|YP_003785493.1| DNA directed RNA polymerase subunit alpha [Brachyspira pilosicoli
           95/1000]
 gi|300688321|gb|ADK30992.1| DNA directed RNA polymerase alpha subunit [Brachyspira pilosicoli
           95/1000]
          Length = 325

 Score =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 103/301 (34%), Positives = 167/301 (55%), Gaps = 4/301 (1%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
             N    +A+P  RG+A T+GNALRRVL+SS+ G AITA++IDGV +E  ++ G+ ED  
Sbjct: 24  TPNYGKFVAQPFERGYATTIGNALRRVLLSSIPGYAITAIKIDGVTNEFENVPGMKEDTI 83

Query: 84  DIILNIKGINLKMSGD-SHKRVTIFKRGPGVVT-AGDIQTVNDIEVLNPDHVICNLDVDA 141
            +I+++K + + +  +   K + I K GP  VT A       D+ V NP+H I  +    
Sbjct: 84  VMIMHLKNVVVALPENVDAKTIHIKKEGPCTVTAADFASADADVSVFNPEHHIATIAEGY 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD-YDK 200
              M++ +  G+ YVPA+ +    + +  I IDA+YSPI  V + V+  R GQ ++ Y K
Sbjct: 144 TFEMDVQIESGYNYVPAEVNMELLEDVNAIAIDAIYSPIVSVKFAVDDVRVGQRINYYGK 203

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK-EDINVKSLPFNPALLKK 259
           L++ I+T G+I  E +++ A+++L+D L  F+  EE   + +  +   K    +    K 
Sbjct: 204 LTLEIETKGNIAPEKALSWAAKLLRDNLTPFMLPEEANGDDEKIEETPKDSVLDSLKDKH 263

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           VEE+E SVR+ N L   ++  +  +  +T+AD+LR+       + EIK  L      LGM
Sbjct: 264 VEEVEFSVRTANFLISSDLKTLDKVALKTDADLLRLIGANEMIIEEIKEKLAEYNAHLGM 323

Query: 320 N 320
            
Sbjct: 324 R 324


>gi|150036748|emb|CAM98027.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 210

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 86/208 (41%), Positives = 131/208 (62%), Gaps = 2/208 (0%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + 
Sbjct: 1   GNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERS 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++ 
Sbjct: 61  LEIDVQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSADENKK 120

Query: 164 --ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
             +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L +
Sbjct: 121 LRDEMPIGVLAVDSIYTPIERVNYQVENTRVGARDDYDKLTFDIWTNGSIKPSDALSLGA 180

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKS 249
           +IL + L +F++      E    +  + 
Sbjct: 181 KILAEHLNLFMDISPVAAEASVMVEAEP 208


>gi|257459220|ref|ZP_05624339.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter gracilis
           RM3268]
 gi|257443605|gb|EEV18729.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter gracilis
           RM3268]
          Length = 332

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 106/322 (32%), Positives = 168/322 (52%), Gaps = 6/322 (1%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I +    EN   +IA P   G+A TL + LRR+L +S  G A TAV+I+GV HE  S++G
Sbjct: 5   IKVENVSENVAKIIAYPFETGYAVTLAHPLRRLLYTSTVGFAPTAVKIEGVSHEFDSMRG 64

Query: 78  VHEDLTDIILNIKGINLKMSGDS-HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           + ED+   I+N+KG+  K+ GDS  + V    +GP  +   D+     +E++NP   +  
Sbjct: 65  MLEDMAAFIINLKGLRFKIKGDSLREVVEYSFKGPKEIYGSDLNNDA-VEIVNPSAYLAT 123

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           ++ DA ++  L + KG GYVP++  R EN     I +DA ++P+ K  Y +E+       
Sbjct: 124 INEDADLKFTLIIEKGIGYVPSEEIR-ENLDADFIALDAFFTPVTKAVYDIENVFVEDNP 182

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           DY+K+  TI TDG I+  D+   A   +  QL +F               + +      L
Sbjct: 183 DYEKVVFTITTDGQISAIDAFKNALEAMYQQLAVFKGIVNISAADTFGRAIPANSEFAKL 242

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
            + V  L LS RS NCL   +I ++G+L    E+++  + N G+KSL EIK V+  +G  
Sbjct: 243 FESVSNLSLSARSFNCLDRADIRFIGELAIMEESELKDLKNLGKKSLEEIKAVMEEIGYP 302

Query: 317 LGMNLPDWPPESIEELAKKYED 338
           +G        E  E+L +K ++
Sbjct: 303 IG---NQELGEKKEQLKRKLDE 321


>gi|153951055|ref|YP_001398875.1| DNA-directed RNA polymerase subunit alpha [Campylobacter jejuni
           subsp. doylei 269.97]
 gi|171769458|sp|A7H5U5|RPOA_CAMJD RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|152938501|gb|ABS43242.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. doylei 269.97]
          Length = 337

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 95/320 (29%), Positives = 163/320 (50%), Gaps = 4/320 (1%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +    +    + A P   G+  TL + LRR+L +S  G A TA+ IDGV HE  S++G+
Sbjct: 15  TIENISDTVAKISAWPFEIGYGITLAHPLRRLLYTSTVGYAPTAIHIDGVAHEFDSMRGM 74

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+   I+N+K +  K+  DS+K +  F         G     + +EV+N D  +  ++
Sbjct: 75  LEDVALFIINLKKLRFKIKSDSNKEIVEFSFKGSKEIYGKDLNNDQVEVVNKDAYLATIN 134

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            DA +   L V KG GY+P++  +   +    I +DA ++P+++ +Y +E        DY
Sbjct: 135 EDAELEFTLIVEKGIGYIPSEEIKEFLNDPKFIALDAFFTPVREATYDIEKVLFEDNPDY 194

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           +K+ +T+ TDG IT  ++   A   +  QL +F      +  +K       L  N  LL+
Sbjct: 195 EKVVLTVTTDGQITPNEAFQNALEAMYKQLSVFDKITNVRSVIKNQATSNELE-NTKLLQ 253

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            + +L LS RS NCL    +VY+G+L   + +++  + N G+KSL EIK ++  +G  +G
Sbjct: 254 NITDLNLSARSYNCLEKAGVVYIGELALMSVSELAGLKNLGKKSLDEIKNIMENIGFPVG 313

Query: 319 MNLPDWPPESIEELAKKYED 338
            +      ++ E L  K  +
Sbjct: 314 TS---KLSDNKEILKNKIAE 330


>gi|57238608|ref|YP_179739.1| DNA-directed RNA polymerase subunit alpha [Campylobacter jejuni
           RM1221]
 gi|86152271|ref|ZP_01070482.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni 260.94]
 gi|86152503|ref|ZP_01070708.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni HB93-13]
 gi|121612721|ref|YP_001001238.1| DNA-directed RNA polymerase subunit alpha [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|157415815|ref|YP_001483071.1| DNA-directed RNA polymerase subunit alpha [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|167006131|ref|ZP_02271889.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|205355609|ref|ZP_03222379.1| DNA-directed RNA polymerase alpha chain [Campylobacter jejuni
           subsp. jejuni CG8421]
 gi|315125003|ref|YP_004067007.1| DNA-directed RNA polymerase alpha subunit [Campylobacter jejuni
           subsp. jejuni ICDCCJ07001]
 gi|73621841|sp|Q5HSJ6|RPOA_CAMJR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|158513890|sp|A1W1J7|RPOA_CAMJJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|172047194|sp|A8FNQ7|RPOA_CAMJ8 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|57167412|gb|AAW36191.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           RM1221]
 gi|85840760|gb|EAQ58011.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni 260.94]
 gi|85843388|gb|EAQ60598.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni HB93-13]
 gi|87249974|gb|EAQ72933.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|157386779|gb|ABV53094.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|205346386|gb|EDZ33019.1| DNA-directed RNA polymerase alpha chain [Campylobacter jejuni
           subsp. jejuni CG8421]
 gi|307748452|gb|ADN91722.1| DNA-directed RNA polymerase subunit alpha [Campylobacter jejuni
           subsp. jejuni M1]
 gi|315018725|gb|ADT66818.1| DNA-directed RNA polymerase alpha subunit [Campylobacter jejuni
           subsp. jejuni ICDCCJ07001]
 gi|315059046|gb|ADT73375.1| DNA-directed RNA polymerase alpha subunit [Campylobacter jejuni
           subsp. jejuni S3]
 gi|315931274|gb|EFV10244.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter jejuni
           subsp. jejuni 327]
          Length = 337

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 96/320 (30%), Positives = 166/320 (51%), Gaps = 4/320 (1%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +    +    + A P   G+  TL + LRR+L +S  G A TA+ IDGV HE  S++G+
Sbjct: 15  TIENISDTVAKISAWPFEIGYGITLAHPLRRLLYTSTIGYAPTAIHIDGVAHEFDSMRGM 74

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+   I+N+K +  K+ G+S+K +  F         G     + +EV+N D  +  ++
Sbjct: 75  LEDVALFIINLKKLRFKIKGESNKEIVEFSFKGSKEIYGKDLNNDQVEVVNKDAYLATIN 134

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            DA ++  L V KG GYVP++  +   +    I +DA ++P+++ +Y +E        DY
Sbjct: 135 EDAELKFTLIVEKGIGYVPSEEIKELINDPKFIALDAFFTPVREATYDIEKVLFEDNPDY 194

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           +K+ +T+ TDG IT  ++   A   +  QL +F      +  +K       L  N  LL+
Sbjct: 195 EKVVLTVTTDGQITPNEAFQNALEAMYKQLSVFDKITNVRSVIKNQATSNELE-NTKLLQ 253

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            + +L LS RS NCL    +VY+G+L   + +++  + N G+KSL EIK ++ ++G  +G
Sbjct: 254 NITDLNLSARSYNCLEKAGVVYIGELALMSVSELAGLKNLGKKSLDEIKNIMESIGFPVG 313

Query: 319 MNLPDWPPESIEELAKKYED 338
            +      ++ E L  K  +
Sbjct: 314 TS---KLSDNKEILKNKIAE 330


>gi|297380475|gb|ADI35362.1| DNA-directed RNA polymerase, alpha subunit [Helicobacter pylori
           v225d]
          Length = 344

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 102/331 (30%), Positives = 169/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRIKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ +   IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLSSE-YIEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++ +  E  P G + +D  ++PIKKV Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMPEGYMPLDGSFTPIKKVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLNAKIENMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLNDLGYPVGTELNPEQRESLKKRLEKLEDK 340


>gi|150187066|emb|CAK30163.1| RNA polymerase alpha subunit [Streptococcus dysgalactiae subsp.
           equisimilis]
          Length = 208

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 90/208 (43%), Positives = 141/208 (67%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  
Sbjct: 1   TLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDE 60

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K + +   GP  VTAGDI T +DIE++NPDH +  +     +R  +TV+K  GYVPA+ +
Sbjct: 61  KILELEVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLRATMTVAKKRGYVPAEGN 120

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           + ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++
Sbjct: 121 KKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSA 180

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKS 249
           R+L + L +F +  +  K  +     + 
Sbjct: 181 RVLIEHLNLFTDLTDVAKATEVMKETEK 208


>gi|317011493|gb|ADU85240.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           SouthAfrica7]
          Length = 344

 Score =  232 bits (593), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 102/331 (30%), Positives = 169/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPIGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ +   IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSE-QIEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++  R E  P G + +D  ++PIK V Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSEITR-ELMPEGYMPLDGSFTPIKNVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E+P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--EKPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLSDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|193795072|gb|ACF21667.1| RpoA [Rhizobium tropici]
          Length = 212

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 149/213 (69%), Positives = 180/213 (84%), Gaps = 1/213 (0%)

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           KR+ + K+GPGVVTAGDIQTV DIE+LNP+HVIC LD  A +RME TV+ G GYVPA+ +
Sbjct: 1   KRMVVRKQGPGVVTAGDIQTVGDIEILNPEHVICTLDEGAEIRMEFTVNNGKGYVPAERN 60

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R E+ PIGLI +D+LYSP+KKVSY VE+ REGQVLDYDKLSM+I+TDGSITGED+VA A+
Sbjct: 61  RAEDAPIGLIPVDSLYSPVKKVSYKVENTREGQVLDYDKLSMSIETDGSITGEDAVAFAA 120

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           RILQDQLG+F+NF+EP+KE +E+  V  L FNPALLKKV+E E SVRS NCL+ +NIVY+
Sbjct: 121 RILQDQLGVFVNFDEPQKEAEEEA-VTELAFNPALLKKVDERERSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           GDLIQ+TEA+MLR  N GRKSL EIK VL +MG
Sbjct: 180 GDLIQKTEAEMLRTPNLGRKSLNEIKEVLASMG 212


>gi|283956979|ref|ZP_06374451.1| DNA-directed RNA polymerase alpha chain [Campylobacter jejuni
           subsp. jejuni 1336]
 gi|283791480|gb|EFC30277.1| DNA-directed RNA polymerase alpha chain [Campylobacter jejuni
           subsp. jejuni 1336]
          Length = 337

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 96/320 (30%), Positives = 166/320 (51%), Gaps = 4/320 (1%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +    +    + A P   G+  TL + LRR+L +S  G A TA+ IDGV HE  S++G+
Sbjct: 15  TIENISDTVAKISAWPFEIGYGITLAHPLRRLLYTSTIGYAPTAIHIDGVAHEFDSMRGM 74

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+   I+N+K +  K+ G+S+K +  F         G     + +EV+N D  +  ++
Sbjct: 75  LEDVALFIINLKKLRFKIKGESNKEIVEFSFKGSKEIYGKDLNNDQVEVVNKDTYLATIN 134

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            DA ++  L V KG GYVP++  +   +    I +DA ++P+++ +Y +E        DY
Sbjct: 135 EDAELKFTLIVEKGIGYVPSEEIKELINDPKFIALDAFFTPVREATYDIEKVLFEDNPDY 194

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           +K+ +T+ TDG IT  ++   A   +  QL +F      +  +K       L  N  LL+
Sbjct: 195 EKVVLTVTTDGQITPNEAFQNALEAMYKQLSVFDKITNVRSVIKNQATSNELE-NTKLLQ 253

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            + +L LS RS NCL    +VY+G+L   + +++  + N G+KSL EIK ++ ++G  +G
Sbjct: 254 NITDLNLSARSYNCLEKAGVVYIGELALMSVSELAGLKNLGKKSLDEIKNIMESIGFPVG 313

Query: 319 MNLPDWPPESIEELAKKYED 338
            +      ++ E L  K  +
Sbjct: 314 TS---KLSDNKEILKNKIAE 330


>gi|161367356|gb|ABX71083.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae O1]
          Length = 244

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 106/247 (42%), Positives = 164/247 (66%), Gaps = 8/247 (3%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM- 96
           GF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++ 
Sbjct: 1   GFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVA 60

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVVRMELTVSKGHGY 155
            G     +T+ K G G V AGDI    D+E++NP+HVIC+L   +A + M + V +G GY
Sbjct: 61  EGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVERGRGY 120

Query: 156 VPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           VPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T+G++ 
Sbjct: 121 VPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLE 180

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
            E+++  A+ IL +QL  F++  + +         +   F+P LL+ V++LEL+VRS NC
Sbjct: 181 PEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANC 237

Query: 273 LRGENIV 279
           L+ E I 
Sbjct: 238 LKAEAIH 244


>gi|118497985|ref|YP_899035.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. novicida U112]
 gi|134301520|ref|YP_001121488.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. tularensis WY96-3418]
 gi|194323208|ref|ZP_03056992.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. novicida FTE]
 gi|254374799|ref|ZP_04990280.1| DNA-directed RNA polymerase [Francisella novicida GA99-3548]
 gi|158512424|sp|A0Q7R6|RPOA2_FRATN RecName: Full=DNA-directed RNA polymerase subunit alpha 2;
           Short=RNAP subunit alpha 2; AltName: Full=RNA polymerase
           subunit alpha 2; AltName: Full=Transcriptase subunit
           alpha 2
 gi|158513850|sp|A4IWR6|RPOA2_FRATW RecName: Full=DNA-directed RNA polymerase subunit alpha 2;
           Short=RNAP subunit alpha 2; AltName: Full=RNA polymerase
           subunit alpha 2; AltName: Full=Transcriptase subunit
           alpha 2
 gi|118423891|gb|ABK90281.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Francisella novicida U112]
 gi|134049297|gb|ABO46368.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. tularensis WY96-3418]
 gi|151572518|gb|EDN38172.1| DNA-directed RNA polymerase [Francisella novicida GA99-3548]
 gi|194322572|gb|EDX20052.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. novicida FTE]
          Length = 318

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 103/323 (31%), Positives = 181/323 (56%), Gaps = 11/323 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I+
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKIN 60

Query: 67  -GVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVND 124
            G +  +  +    E + DIILN+K + + +  G     +T    G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLPVTLAEGVETGTITFELSGSEEEIFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG G+ PA+ +  +    G   +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQDNFKD----GEFLLDATFSPVVFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +   
Sbjct: 177 FEIKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGIF-- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +   +   NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL 
Sbjct: 235 VEDPTKDINPILLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLT 294

Query: 305 EIKGVLGTMGLFLGMNLPDWPPE 327
           EIK  L  +GL LG  + +WP +
Sbjct: 295 EIKDKLSELGLSLGTLIENWPQD 317


>gi|119668275|emb|CAK95496.1| RNA polymerase alpha subunit [Lactobacillus parabuchneri]
          Length = 216

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 99/216 (45%), Positives = 143/216 (66%), Gaps = 4/216 (1%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DS 100
           LGN+LRR L+SSL G+A+T++QID VLHE S+IKGV ED+T IILN+K I+LK+ G  D 
Sbjct: 1   LGNSLRRTLLSSLPGSAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKISLKLDGPEDE 60

Query: 101 HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
            + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT +KG GYV A  
Sbjct: 61  EENLEIDVIGPADVTAGDIQADSDVTVLNPDLHIATVAEGATFHMRLTANKGRGYVSAVE 120

Query: 161 HRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           ++      PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ + TDGSIT  ++V+
Sbjct: 121 NKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDVWTDGSITPSEAVS 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
           LA++IL + L MF++  +  K  +  +  +      
Sbjct: 181 LAAKILTEHLEMFVDLTDEAKNTEIMVEKEETHKEK 216


>gi|119662811|emb|CAJ33197.1| RNA polymerase alpha subunit [Lactobacillus psittaci]
          Length = 205

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 94/206 (45%), Positives = 141/206 (68%), Gaps = 1/206 (0%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL++S+ G A++ +QIDGVLHE S++ GV ED+T IILN+K + LK   D  K 
Sbjct: 1   GNSLRRVLLTSIPGTALSYIQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSVADEEKI 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + +   GP  VTAGD++  +D+ VLNPD  IC++     + M+L V  G GYV A  ++T
Sbjct: 61  IELDVEGPATVTAGDLKVDSDVTVLNPDQYICSIAEGGHLHMQLAVKTGRGYVSASENKT 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           E+ PIG+I +D+L+SPIKKV+Y VES R G+  DYDKL++ + TDGSIT  D+++ A++I
Sbjct: 121 EDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDYDKLTLEVWTDGSITPSDALSFAAKI 180

Query: 224 LQDQLGMFINFEEPKKEVKEDINVKS 249
           L +   +F  F + + +   ++ V+ 
Sbjct: 181 LVEHFKVF-EFSDAETDFGGEVMVEK 205


>gi|119662329|emb|CAJ33152.1| RNA polymerase alpha subunit [Lactobacillus mindensis]
          Length = 197

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 85/197 (43%), Positives = 136/197 (69%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRRVL++SL G A++ +QIDGVLHE S+I GV ED+T I+LN+K + LK   +  
Sbjct: 1   TLGNSLRRVLLASLPGTAVSDIQIDGVLHEFSAIDGVIEDVTQIVLNVKKLKLKSYAEDS 60

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
            +  I   GP  VTA DI+  +D+EVL+P+  IC +       M++T+  G GY PA+ +
Sbjct: 61  LKAEIDVVGPATVTAKDIKADDDLEVLDPEQFICTVAEGGHFHMQMTIKNGRGYTPAEQN 120

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           +T+  PIG++ +D++++P++KV+Y VE+ R G+  D+DKL++ I T+GSI   ++++L++
Sbjct: 121 KTDETPIGVLPVDSIFTPVEKVNYQVENTRVGKRNDFDKLTIDIWTNGSIGPREAISLSA 180

Query: 222 RILQDQLGMFINFEEPK 238
           +IL + L  F+N  E  
Sbjct: 181 KILTEHLNSFVNLTEEA 197


>gi|119662851|emb|CAJ33218.1| RNA polymerase alpha subunit [Lactobacillus fuchuensis]
          Length = 202

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 82/202 (40%), Positives = 134/202 (66%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           +L++SL G A+T +QIDGVLHE S+I GV ED+T IILN+K + LK+  +  K + I  +
Sbjct: 1   ILLASLPGTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNVKKLALKLHVEEDKTIEIDVK 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  VTA DI   +D+EVLN D  IC +       + +TV KG GYV A  +++++ PIG
Sbjct: 61  GPATVTAADIVADDDVEVLNTDQYICTVAEGGNFHVRMTVKKGRGYVAADQNKSDDMPIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           ++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++I+ + L 
Sbjct: 121 VLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKIMTEHLA 180

Query: 230 MFINFEEPKKEVKEDINVKSLP 251
           +F++  +  K  +  +  +   
Sbjct: 181 IFVDLTDEAKNAEIMVEKEETH 202


>gi|208779606|ref|ZP_03246951.1| DNA-directed RNA polymerase, alpha subunit [Francisella novicida
           FTG]
 gi|208744567|gb|EDZ90866.1| DNA-directed RNA polymerase, alpha subunit [Francisella novicida
           FTG]
          Length = 318

 Score =  232 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 104/323 (32%), Positives = 181/323 (56%), Gaps = 11/323 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I+
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKIN 60

Query: 67  -GVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVND 124
            G +  +  +    E + DIILN+K + + +  G     +T    G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLPVTLAEGVETGTITFELSGSEEEIFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG G+ PA+ +  E    G   +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQDNFKE----GEFLLDATFSPVVFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +   
Sbjct: 177 FEIKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGIF-- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +   +   NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL 
Sbjct: 235 VEDPTKDINPILLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLT 294

Query: 305 EIKGVLGTMGLFLGMNLPDWPPE 327
           EIK  L  +GL LG  + +WP +
Sbjct: 295 EIKDKLSELGLSLGTLIENWPQD 317


>gi|150036828|emb|CAM98281.1| DNA-directed RNA polymerase alpha chain [Leuconostoc lactis]
          Length = 208

 Score =  232 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 87/208 (41%), Positives = 131/208 (62%), Gaps = 2/208 (0%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + 
Sbjct: 1   GNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERS 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++ 
Sbjct: 61  LEIDVQGPAEVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSADENKQ 120

Query: 164 --ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
             E  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L +
Sbjct: 121 LREEMPIGVLAVDSIYTPIERVNYHVENTRVGARDDYDKLTFDIWTNGSIKPSDALSLGA 180

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKS 249
           +IL + L +F++      E    +  + 
Sbjct: 181 KILAEHLNLFMDISPVAAEANVMVEAEP 208


>gi|154424821|emb|CAL18513.1| RNA polymerase alpha subunit [Streptococcus mutans]
          Length = 200

 Score =  232 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 92/200 (46%), Positives = 140/200 (70%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
           TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   +  
Sbjct: 1   TLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVEEE 60

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           K V +   GP  +TAGDI T +DIE++NPDH +  +   A ++  +TV+   GYVPA+ +
Sbjct: 61  KIVELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIAEGANLKATMTVATNRGYVPAEKN 120

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           + ++ P+G + ID++Y+P+KKV+Y VE AR G   ++DKL++ I T+G+I  ED++ L++
Sbjct: 121 KRDDAPVGTLAIDSIYTPVKKVNYQVEPARVGSNDNFDKLTIEIMTNGTIIPEDALGLSA 180

Query: 222 RILQDQLGMFINFEEPKKEV 241
           R+L + L +F +  E  K  
Sbjct: 181 RVLIEHLNLFTDLTEVAKAT 200


>gi|119662375|emb|CAJ33176.1| RNA polymerase alpha subunit [Lactobacillus parabuchneri]
          Length = 201

 Score =  231 bits (590), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 99/201 (49%), Positives = 140/201 (69%), Gaps = 4/201 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR L+SSL G+A+T++QID VLHE S+IKGV ED+T IILN+K I+LK+ G
Sbjct: 1   YGTTLGNSLRRTLLSSLPGSAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKISLKLDG 60

Query: 99  --DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             D  + + I   GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT +KG GYV
Sbjct: 61  PEDEEENLEIDVIGPADVTAGDIQADSDVTVLNPDLHIATVAEGATFHMRLTANKGRGYV 120

Query: 157 PAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A  ++      PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ + TDGSIT  
Sbjct: 121 SAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDVWTDGSITPS 180

Query: 215 DSVALASRILQDQLGMFINFE 235
           ++V+LA++IL + L MF++  
Sbjct: 181 EAVSLAAKILTEHLEMFVDLT 201


>gi|208435191|ref|YP_002266857.1| DNA-directed RNA polymerase, alpha subunit [Helicobacter pylori
           G27]
 gi|208433120|gb|ACI27991.1| DNA-directed RNA polymerase, alpha subunit [Helicobacter pylori
           G27]
          Length = 336

 Score =  231 bits (590), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 101/330 (30%), Positives = 167/330 (50%), Gaps = 16/330 (4%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ + + IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSEH-IEIV 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ DA +   L + KG GYVP++ +  E  P G + +D  ++PIKKV Y +E
Sbjct: 133 NPEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTRELMPEGYMPLDGSFTPIKKVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--ERPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYED 338
            L  +G  +G  L     E  E L K+ E+
Sbjct: 310 KLNDLGYPVGTELS---HEQRESLKKRLEN 336


>gi|56708484|ref|YP_170380.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. tularensis SCHU S4]
 gi|110670955|ref|YP_667512.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. tularensis FSC198]
 gi|224457644|ref|ZP_03666117.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. tularensis MA00-2987]
 gi|254371109|ref|ZP_04987111.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           tularensis FSC033]
 gi|254875331|ref|ZP_05248041.1| rpoA2, DNA-directed RNA polymerase, alpha subunit [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|81597191|sp|Q5NF12|RPOA2_FRATT RecName: Full=DNA-directed RNA polymerase subunit alpha 2;
           Short=RNAP subunit alpha 2; AltName: Full=RNA polymerase
           subunit alpha 2; AltName: Full=Transcriptase subunit
           alpha 2
 gi|122970868|sp|Q14GG5|RPOA2_FRAT1 RecName: Full=DNA-directed RNA polymerase subunit alpha 2;
           Short=RNAP subunit alpha 2; AltName: Full=RNA polymerase
           subunit alpha 2; AltName: Full=Transcriptase subunit
           alpha 2
 gi|54113777|gb|AAV29522.1| NT02FT1997 [synthetic construct]
 gi|56604976|emb|CAG46075.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. tularensis SCHU S4]
 gi|110321288|emb|CAL09458.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. tularensis FSC198]
 gi|151569349|gb|EDN35003.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           tularensis FSC033]
 gi|254841330|gb|EET19766.1| rpoA2, DNA-directed RNA polymerase, alpha subunit [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|282159688|gb|ADA79079.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. tularensis NE061598]
          Length = 318

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 103/323 (31%), Positives = 181/323 (56%), Gaps = 11/323 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I+
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKIN 60

Query: 67  -GVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVND 124
            G +  +  +    E + DIILN+K + + +  G     +T    G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLPVTLAEGVETGTITFELSGSEEEIFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG G+ PA+ +  +    G   +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQDNFKD----GEFLLDATFSPVVFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +   
Sbjct: 177 FEIKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNILDIEEINKGIF-- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +   +   NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL 
Sbjct: 235 VEDPTKDINPILLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLT 294

Query: 305 EIKGVLGTMGLFLGMNLPDWPPE 327
           EIK  L  +GL LG  + +WP +
Sbjct: 295 EIKDKLSELGLSLGTLIENWPQD 317


>gi|154149371|ref|YP_001405812.1| DNA-directed RNA polymerase subunit alpha [Campylobacter hominis
           ATCC BAA-381]
 gi|166229267|sp|A7HZX1|RPOA_CAMHC RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|153805380|gb|ABS52387.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter hominis
           ATCC BAA-381]
          Length = 338

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 107/342 (31%), Positives = 178/342 (52%), Gaps = 11/342 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++K       P  IE   +    EN   +IA P   G+A TL + LRR+L +S  G A T
Sbjct: 1   MRKITTSAYMPTEIEVENVS---ENVAKIIAYPFETGYAVTLAHPLRRLLYTSTVGYAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQ 120
           AV+IDGV HE  S++G+ ED+   I+N+KGI  K+ GDS  + +     GP  +T  D+ 
Sbjct: 58  AVKIDGVSHEFDSMRGMLEDVAIFIINLKGIRFKIKGDSKREVIEYNFTGPKEITGKDLN 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               +E++NPD  +  ++ DA ++  + + KG GYVP++  R +      I +DA ++P+
Sbjct: 118 ND-IVEIVNPDAYLATINEDADLKFSVVIEKGIGYVPSESIR-DYVSSDYIALDAFFTPV 175

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            +  Y +E+       DY+K+  TI TDG ++  D+   A   +  Q+ +F    +    
Sbjct: 176 IRAIYDIENVFVEDNPDYEKIIFTITTDGQVSAVDAFKNALEAMYQQMSVFKGIVDIDTG 235

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                 + S   +    + +E L LS RS NCL   +I ++G+++   E+++  + N G+
Sbjct: 236 KSFTKQIPSGEHSKL-FESIENLNLSARSFNCLEKADIKFVGEIVIMDESELKGIKNLGK 294

Query: 301 KSLVEIKGVLGTMGLFLG----MNLPDWPPESIEELAKKYED 338
           KSL EIK V+  +G  +G     +  +   + I EL KK +D
Sbjct: 295 KSLEEIKSVMEEIGYPIGNEEIKDKKEVLSKKIAELKKKAKD 336


>gi|119662817|emb|CAJ33200.1| RNA polymerase alpha subunit [Lactobacillus homohiochii]
          Length = 205

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 98/205 (47%), Positives = 146/205 (71%), Gaps = 4/205 (1%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR- 103
           N+LRRVL++SL GAA+T++QIDGVLHE S++KGV ED+T IILN+K INLK++ D ++  
Sbjct: 1   NSLRRVLLASLPGAAVTSIQIDGVLHEFSTVKGVVEDVTQIILNVKKINLKINSDDNETK 60

Query: 104 -VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            ++I   GP  VTAGDI T +D+E+LNPD  I  +   A   M +T +KG GYV A+ ++
Sbjct: 61  SMSINVTGPADVTAGDIVTDSDVEILNPDLHIATVADGATFHMNMTANKGRGYVSAEENK 120

Query: 163 TEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
            +ND  PIG++ +D++Y+PI++V+Y VE AR GQ  DYDKL++ + T+GSIT  D+++LA
Sbjct: 121 AKNDGMPIGVLPVDSIYTPIERVNYQVEDARVGQRDDYDKLTLDVWTNGSITPSDAISLA 180

Query: 221 SRILQDQLGMFINFEEPKKEVKEDI 245
           ++IL     +FI+  +  K     +
Sbjct: 181 AKILNQHFQLFIDLTDRAKNANVMV 205


>gi|119672805|emb|CAK95518.1| RNA polymerase alpha subunit [Lactobacillus vaccinostercus]
          Length = 197

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 95/196 (48%), Positives = 145/196 (73%), Gaps = 2/196 (1%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRR+L++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K I+LK+  +  K
Sbjct: 1   LGNSLRRILLASLPGAAITSIQIDGVLHEFSTVEGVTEDVTQIILNMKQISLKIDSEEDK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + I  +GP  VTAGDI+   D+EVLNP+  I  +   A + +++T + G GYV A  ++
Sbjct: 61  TLEIDVKGPAAVTAGDIEADGDVEVLNPELHIATVADGAELHIQMTANTGRGYVSADDNK 120

Query: 163 T--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
              ++ PIG++ ID++Y+PI++V+YTVE+AR GQ  DYDKL++ + +DGSIT  +S++LA
Sbjct: 121 ARMDDLPIGVLPIDSIYTPIERVNYTVENARVGQRNDYDKLTLDVWSDGSITPSESISLA 180

Query: 221 SRILQDQLGMFINFEE 236
           ++IL + L MF+   +
Sbjct: 181 AKILTEHLAMFVVLTD 196


>gi|207721898|ref|YP_002252336.1| dna-directed rna polymerase alpha chain (partial sequence c
           terminus) protein [Ralstonia solanacearum MolK2]
 gi|206587066|emb|CAQ17650.1| probable dna-directed rna polymerase alpha chain (partial sequence
           c terminus) protein [Ralstonia solanacearum MolK2]
          Length = 215

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 93/214 (43%), Positives = 138/214 (64%), Gaps = 3/214 (1%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
            EP  RG+ HTLGNALRRVL+SS+ G A T V I GV+HE S+I GV ED+ +++LN+KG
Sbjct: 1   MEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGVVHEYSTIDGVQEDVVNLLLNLKG 60

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           +  K+       V++ K G GVVTA DI+  +D+E++NP HVI +L     + M++ V +
Sbjct: 61  VVFKLHNRDEVTVSLRKEGEGVVTAADIELPHDVEIINPGHVIASLSAGGKLDMQIKVEQ 120

Query: 152 GHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVP    +  ++     G + +DA ++P+++VSY VESAR  Q  D DKL M I+T+
Sbjct: 121 GRGYVPGNVRKFGDESSKVIGRVVLDASFAPVRRVSYAVESARVEQRTDLDKLVMNIETN 180

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           G I+ E+++  ++RIL DQL +F   E  +   +
Sbjct: 181 GVISPEEAIRQSARILVDQLSVFAALEGTESAAE 214


>gi|254373336|ref|ZP_04988824.1| DNA-directed RNA polymerase [Francisella tularensis subsp. novicida
           GA99-3549]
 gi|151571062|gb|EDN36716.1| DNA-directed RNA polymerase [Francisella novicida GA99-3549]
          Length = 318

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 104/323 (32%), Positives = 180/323 (55%), Gaps = 11/323 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I+
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKIN 60

Query: 67  -GVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVND 124
            G +  +  +    E + DIILN+K + + +  G     +T    G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLPVTLAEGVETGTITFELSGSEEEIFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG G+ PA     +N   G   +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGVGFRPA----QDNFKNGEFLLDATFSPVVFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +   
Sbjct: 177 FEIKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGIF-- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +   +   NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL 
Sbjct: 235 VEDPTKDINPILLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLT 294

Query: 305 EIKGVLGTMGLFLGMNLPDWPPE 327
           EIK  L  +GL LG  + +WP +
Sbjct: 295 EIKDKLSELGLSLGTLIENWPQD 317


>gi|149179437|ref|ZP_01857991.1| DNA-directed RNA polymerase subunit alpha [Planctomyces maris DSM
           8797]
 gi|148841748|gb|EDL56157.1| DNA-directed RNA polymerase subunit alpha [Planctomyces maris DSM
           8797]
          Length = 208

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 85/207 (41%), Positives = 129/207 (62%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
                + +AEP  RGF  T+ N+LRR+L+SSL G+++T V+I GV HE ++I GV ED+T
Sbjct: 2   TSTYGMFVAEPFERGFGATIANSLRRILLSSLEGSSVTRVKIQGVQHEFTTIPGVVEDIT 61

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           +I LN+K + +K S  + K + I K   GVVT  D+ T + +EV+N D VI  +  D  +
Sbjct: 62  EICLNLKSLIVKNSSSTSKTLRIEKHERGVVTGADVITDDQVEVINKDLVIATMTDDVPL 121

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            MELT+  G GY PA  H   +  +G+I +DA +SP+ +V Y +E  R GQ  +YDKL +
Sbjct: 122 NMELTIENGRGYSPASEHAQHDSEVGVIPLDATFSPVVRVRYKIEDTRVGQRTNYDKLIL 181

Query: 204 TIDTDGSITGEDSVALASRILQDQLGM 230
            I T+G++  + ++  AS+IL+  L  
Sbjct: 182 EIWTNGTVKPDMALVEASKILRKHLNP 208


>gi|150036798|emb|CAM98035.1| DNA-directed RNA polymerase alpha chain [Leuconostoc fallax]
          Length = 208

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 88/208 (42%), Positives = 133/208 (63%), Gaps = 2/208 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T +ILN+K + L +  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVVLAIDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + I  +GP  VTA D+Q   DIEVLNP+  +  +     + M +T  KG GY  A
Sbjct: 61  DEEKSLEIDVQGPAEVTAADLQGSADIEVLNPELHLATVAAGKSLHMTVTAVKGRGYSSA 120

Query: 159 KHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   +  PIG++ +D++Y+PI++V+Y VE+ R GQ  DYDKL+  I T+GSI   D+
Sbjct: 121 DENKQLRDEMPIGVLAVDSIYTPIERVNYQVENTRVGQRDDYDKLTFDIWTNGSIKPSDA 180

Query: 217 VALASRILQDQLGMFINFEEPKKEVKED 244
           ++L ++IL + L +F +      E +  
Sbjct: 181 LSLGAKILSEHLNLFTDISSVAAETEVM 208


>gi|119662815|emb|CAJ33199.1| RNA polymerase alpha subunit [Lactobacillus kefiranofaciens subsp.
           kefiranofaciens]
          Length = 203

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 90/203 (44%), Positives = 132/203 (65%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   D  K 
Sbjct: 1   GNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLSDEQKV 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + +   GP  VTA D++   D++VLNPD  IC +     + MEL V  G GYV A  +++
Sbjct: 61  IELDVEGPATVTADDLKVDADVQVLNPDQYICTIAKGGHLHMELAVKNGRGYVTASDNKS 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           ++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++ A++I
Sbjct: 121 DDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKI 180

Query: 224 LQDQLGMFINFEEPKKEVKEDIN 246
           L +   +F + +   K  +  + 
Sbjct: 181 LVEHFKVFESADANTKFSEVMVE 203


>gi|187932094|ref|YP_001892079.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. mediasiatica FSC147]
 gi|187713003|gb|ACD31300.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Francisella tularensis subsp. mediasiatica FSC147]
          Length = 318

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 102/323 (31%), Positives = 180/323 (55%), Gaps = 11/323 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I+
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKIN 60

Query: 67  -GVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVND 124
            G +  +  +    E + DIILN+K + + +  G     +T    G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLPVTLTEGVETGTITFELSGSEEEIFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG G+ PA+ +  +    G   +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQDNFKD----GEFLLDATFSPVVFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +   
Sbjct: 177 FEIKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGIF-- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +   +   NP LLK  EEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL 
Sbjct: 235 VEDPTKDINPILLKHAEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLT 294

Query: 305 EIKGVLGTMGLFLGMNLPDWPPE 327
           EIK  L  +GL LG  + +WP +
Sbjct: 295 EIKDKLSELGLSLGTLIENWPQD 317


>gi|119672813|emb|CAK95487.1| RNA polymerase alpha subunit [Lactobacillus gasseri]
          Length = 195

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 94/192 (48%), Positives = 137/192 (71%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL++S+ G A++ +QIDGVLHE S++ GV ED+T IILN+K + LK   D  K 
Sbjct: 1   GNSLRRVLLTSIPGTALSYIQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLSDEEKI 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
             I   GP +VTA D++  +DIEVLNPD  IC++     + M + +  G GYVPA  ++T
Sbjct: 61  AEIDVTGPAIVTAADLKVDSDIEVLNPDQYICSIADGGHLHMNVAIKNGRGYVPASENKT 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           ++ PIG+I +D+L+SPIKKV+Y VESAR G+  DYDKL++ I TDGSIT  D+++ A++I
Sbjct: 121 DDMPIGVIPVDSLFSPIKKVNYQVESARVGKRDDYDKLTLEIWTDGSITPNDALSFAAKI 180

Query: 224 LQDQLGMFINFE 235
           L +   +F++ +
Sbjct: 181 LVEHFKVFMSTD 192


>gi|119668295|emb|CAK95502.1| RNA polymerase alpha subunit [Lactobacillus crispatus]
          Length = 203

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 90/203 (44%), Positives = 132/203 (65%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   D  K 
Sbjct: 1   GNSLRRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLSDEQKV 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + +   GP  VTA D++   D++VLNPD  IC +     + MEL V  G GYV A  +++
Sbjct: 61  IELDIEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMELAVKNGRGYVAASDNKS 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           ++ PIG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++ A++I
Sbjct: 121 DDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKI 180

Query: 224 LQDQLGMFINFEEPKKEVKEDIN 246
           L +   +F + +   K  +  + 
Sbjct: 181 LVEHFKVFESADANAKFSEVMVE 203


>gi|89256013|ref|YP_513375.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica LVS]
 gi|115314492|ref|YP_763215.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica OSU18]
 gi|167010243|ref|ZP_02275174.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica FSC200]
 gi|254367357|ref|ZP_04983383.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. holarctica 257]
 gi|122325482|sp|Q0BMV6|RPOA2_FRATO RecName: Full=DNA-directed RNA polymerase subunit alpha 2;
           Short=RNAP subunit alpha 2; AltName: Full=RNA polymerase
           subunit alpha 2; AltName: Full=Transcriptase subunit
           alpha 2
 gi|122501012|sp|Q2A4H7|RPOA2_FRATH RecName: Full=DNA-directed RNA polymerase subunit alpha 2;
           Short=RNAP subunit alpha 2; AltName: Full=RNA polymerase
           subunit alpha 2; AltName: Full=Transcriptase subunit
           alpha 2
 gi|89143844|emb|CAJ79056.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. holarctica LVS]
 gi|115129391|gb|ABI82578.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           holarctica OSU18]
 gi|134253173|gb|EBA52267.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. holarctica 257]
          Length = 317

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 103/323 (31%), Positives = 182/323 (56%), Gaps = 12/323 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I+
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKIN 60

Query: 67  -GVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVND 124
            G +  +  +    E + DIILN+K +++ ++ D     +T    G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLSVTLAEDVETGTITFELSGSEEEIFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG G+ PA+ +  +    G   +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQDNFKD----GEFLLDATFSPVVFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +  +
Sbjct: 177 FEIKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGIFVE 236

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
                   NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL 
Sbjct: 237 ---DPKDINPILLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLT 293

Query: 305 EIKGVLGTMGLFLGMNLPDWPPE 327
           EIK  L  +GL LG  + +WP +
Sbjct: 294 EIKDKLSELGLSLGTLIENWPQD 316


>gi|283953793|ref|ZP_06371324.1| DNA-directed RNA polymerase alpha chain [Campylobacter jejuni
           subsp. jejuni 414]
 gi|283794834|gb|EFC33572.1| DNA-directed RNA polymerase alpha chain [Campylobacter jejuni
           subsp. jejuni 414]
          Length = 337

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 95/320 (29%), Positives = 165/320 (51%), Gaps = 4/320 (1%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +    +    + A P   G+  TL + LRR+L +S  G A TA+ IDGV HE  S++G+
Sbjct: 15  TIENISDTVAKISAWPFEIGYGITLAHPLRRLLYTSTIGYAPTAIHIDGVAHEFDSMRGM 74

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+   I+N+K +  K+ GDS+K +  F         G     + +EV+N D  +  ++
Sbjct: 75  LEDVALFIINLKKLRFKIKGDSNKEIVEFNFKGSKEIYGKDLNNDQVEVVNKDAYLATIN 134

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  ++  L + KG GYVP++  +   +    I +DA ++P+++ +Y +E        DY
Sbjct: 135 EDTELKFTLIIEKGIGYVPSEEIKELLNDPKFIALDAFFTPVREATYDIEKVLFEDNPDY 194

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           +K+ +T+ TDG IT  ++   A   +  QL +F      +  +K       L  N  LL+
Sbjct: 195 EKVVLTVTTDGQITPNEAFQNALEAMYKQLSVFDKITNVRSAIKNQATSNELE-NTKLLQ 253

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            + +L LS RS NCL    +VY+G+L   + +++  + N G+KSL EIK ++ ++G  +G
Sbjct: 254 NITDLNLSARSYNCLEKAGVVYIGELALMSVSELAGLKNLGKKSLDEIKNIMESIGFPVG 313

Query: 319 MNLPDWPPESIEELAKKYED 338
            +      ++ E L  K  +
Sbjct: 314 TS---KLSDNKEILKNKIVE 330


>gi|109946783|ref|YP_664011.1| DNA-directed RNA polymerase subunit alpha [Helicobacter acinonychis
           str. Sheeba]
 gi|123173594|sp|Q17ZB4|RPOA_HELAH RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|109714004|emb|CAJ99012.1| DNA-directed RNA polymerase alpha chain [Helicobacter acinonychis
           str. Sheeba]
          Length = 344

 Score =  231 bits (588), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 102/331 (30%), Positives = 171/331 (51%), Gaps = 13/331 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE  S++G
Sbjct: 14  IKVLEKEGNRIKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHEFDSLRG 73

Query: 78  VHEDLTDIILNIKGINLKMS---------GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           V ED++  I+N+K I               +    V    +GP  + A D+ + + IE++
Sbjct: 74  VTEDVSLFIMNLKNIRFIAKALVGQDSPLENQSVVVDYSFKGPMELRARDLNSEH-IEII 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+ ++  ++ DA +   L + KG GYVP++  R E  P G + +D  ++PIK V Y +E
Sbjct: 133 NPEMLLATINEDAQLNFSLIIYKGMGYVPSEITR-ELMPEGYMPLDGSFTPIKNVVYEIE 191

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A +++  QLG+F   E+P    +   +  
Sbjct: 192 NVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVFG--EKPIANTEYSGDYA 249

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 250 QRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKSYDEIAE 309

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            L  +G  +G  L     ES+++  +K EDK
Sbjct: 310 KLNDLGYPVGTELSLEQRESLKKRLEKLEDK 340


>gi|150036772|emb|CAN89785.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gasicomitatum
           LMG 18811]
          Length = 203

 Score =  231 bits (588), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 87/199 (43%), Positives = 131/199 (65%), Gaps = 2/199 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  + + +  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A
Sbjct: 61  DEERSLEVDIQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTITAFKGRGYSSA 120

Query: 159 KHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+
Sbjct: 121 DENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDA 180

Query: 217 VALASRILQDQLGMFINFE 235
           ++L S+IL + L +F++  
Sbjct: 181 LSLGSKILAEHLNLFMDIS 199


>gi|119662305|emb|CAJ33140.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           lactis]
          Length = 214

 Score =  231 bits (588), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 85/213 (39%), Positives = 132/213 (61%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  V+IDG+LHE +++ GV ED+T IILN+K + L+   
Sbjct: 1   FGTTLGNSLRRVLLTSVPGTGLVKVKIDGILHEFTTVPGVKEDVTKIILNLKKLVLRAYT 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + +   GP  VTA D++   D+EVLNPD  IC +     + M + V  G GYVPA
Sbjct: 61  EEVKTIELDVEGPATVTAEDLKADADVEVLNPDQYICTIAQGGHLHMWIDVCNGRGYVPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++T    IG I +D+L+SPI+KV+Y VES R G+  D+DKL++ I T+GSI   D++ 
Sbjct: 121 SENKTAEMFIGDIPVDSLFSPIEKVNYQVESTRVGKREDFDKLTLEIWTNGSIAPNDALN 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            A+R+L +    F + +   +  +  +  ++  
Sbjct: 181 FAARVLVEHFKAFESADAAAEIGEVMVEQENDQ 213


>gi|154424753|emb|CAL18479.1| RNA polymerase alpha subunit [Streptococcus agalactiae]
          Length = 213

 Score =  231 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 88/213 (41%), Positives = 141/213 (66%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K
Sbjct: 1   LGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + +   GP  +TAGDI T +DIE++NPDH +  +     ++  +TV+K  GYVPA+ ++
Sbjct: 61  IIELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIAEGHSLKATMTVAKNRGYVPAEGNK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R
Sbjct: 121 KDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSAR 180

Query: 223 ILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           +L + L +F +  E  K  +     + +     
Sbjct: 181 VLIEHLNLFTDLTEVAKATEVMKETEKVNDEKV 213


>gi|7388083|sp|O98462|RPOA_SPIMX RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|4007878|gb|AAC95318.1| RNA polymerase alpha subunit [Spirogyra maxima]
          Length = 344

 Score =  231 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 94/322 (29%), Positives = 157/322 (48%), Gaps = 36/322 (11%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
             L IA PL  G A TLG A+RR L+ S++G AI A +I G  HE S+++G+ E + DI+
Sbjct: 31  YMLFIASPLLAGQATTLGVAIRRTLLESIQGTAIVAAKIYGAAHEYSTLEGIQESIHDIL 90

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+K + +K      ++  I   GP  VTA DI+   +I + NP H I  +      ++E
Sbjct: 91  LNLKQVIIKNKICEFQKCLISIIGPKKVTAADIELSQNITISNPYHHIATITKPIRFQVE 150

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           L ++KG GY+    +  ++   G   +DAL++P++ V++++ +  E      + L + I 
Sbjct: 151 LIINKGRGYLIQDGNDVQD---GYFPVDALFNPVRNVNFSIHNLAE----QQEALILEIW 203

Query: 207 TDGSITGEDSVALASRILQDQL--------------------------GMFINFEEPKKE 240
           T+G+IT  D++   S  L                               +   FE    E
Sbjct: 204 TNGAITPLDALRQGSENLIHLFLPPFGLEDDTYMTSLGSQDYNIHIKNSLKEKFELHSIE 263

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ED ++    F       +E LELS R   CL+  NI  + DL++ ++ D+L+++N G 
Sbjct: 264 RIEDSHLIKDQFLEYSKTPIELLELSTRPFKCLKNANIYTINDLLKLSQQDLLKISNMGP 323

Query: 301 KSLVEIKGVLGTMGLFLGMNLP 322
            S   +K ++  +    G+NL 
Sbjct: 324 SS---VKQIVEALDKRFGINLK 342


>gi|154424871|emb|CAL18538.1| RNA polymerase alpha subunit [Streptococcus vestibularis]
          Length = 211

 Score =  231 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 88/211 (41%), Positives = 140/211 (66%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILNIKG+ +K   +  K
Sbjct: 1   LGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGLAVKSYVEDEK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + +  +GP  VTAGDI T +DIE++NPDH +  +   A ++  +TV+   GYVPA  ++
Sbjct: 61  TIELDVQGPAEVTAGDILTDSDIEIVNPDHYLFTISEGASLKATMTVATNRGYVPADENK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R
Sbjct: 121 KDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSAR 180

Query: 223 ILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           +L + L +F +  +  K        + +   
Sbjct: 181 VLIEHLNLFTDLTDVAKATDVMKETEKVNDE 211


>gi|148925739|ref|ZP_01809427.1| DNA-directed RNA polymerase alpha chain [Campylobacter jejuni
           subsp. jejuni CG8486]
 gi|145845749|gb|EDK22840.1| DNA-directed RNA polymerase alpha chain [Campylobacter jejuni
           subsp. jejuni CG8486]
          Length = 342

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 94/320 (29%), Positives = 166/320 (51%), Gaps = 1/320 (0%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +    +    + A P   G+  TL + LRR+L +S  G A TA+ IDGV HE  S++G+
Sbjct: 15  TIENISDTVAKISAWPFEIGYGITLAHPLRRLLYTSTIGYAPTAIHIDGVAHEFDSMRGM 74

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+   I+N+K +  K+ G+S+K +  F         G     + +EV+N D  +  ++
Sbjct: 75  LEDVALFIINLKKLRFKIKGESNKEIVEFSFKGSKEIYGKDLNNDQVEVVNKDAYLATIN 134

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            DA ++  L V KG GYVP++  +   +    I +DA ++P+++ +Y +E        DY
Sbjct: 135 EDAELKFTLIVEKGIGYVPSEEIKELINDPKFIALDAFFTPVREATYDIEKVLFEDNPDY 194

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           +K+ +T+ TDG IT  ++   A   +  QL +F      +  +K       L  N  LL+
Sbjct: 195 EKVVLTVTTDGQITPNEAFQNALEAMYKQLSVFDKITNVRSVIKNQATSNELE-NTKLLQ 253

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            + +L LS RS NCL    +VY+G+L   + +++  + N G+KSL EIK ++ ++G  +G
Sbjct: 254 NITDLNLSARSYNCLEKAGVVYIGELALMSVSELAGLKNLGKKSLDEIKNIMESIGFPVG 313

Query: 319 MNLPDWPPESIEELAKKYED 338
            +      E ++   ++ + 
Sbjct: 314 TSKLSDNKEILKNKNRRIKS 333


>gi|254368844|ref|ZP_04984857.1| hypothetical protein FTAG_00654 [Francisella tularensis subsp.
           holarctica FSC022]
 gi|157121765|gb|EDO65935.1| hypothetical protein FTAG_00654 [Francisella tularensis subsp.
           holarctica FSC022]
          Length = 317

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 103/323 (31%), Positives = 181/323 (56%), Gaps = 12/323 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I+
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKIN 60

Query: 67  -GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVND 124
            G +  +  +    E + DIILN+K + + ++ D     +T    G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLPVTLAEDVEMGTITFELSGSEEEIFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG G+ PA+ +  +    G   +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQDNFKD----GEFLLDATFSPVVFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +  +
Sbjct: 177 FEIKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGIFVE 236

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
                   NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL 
Sbjct: 237 ---DPKDINPILLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLT 293

Query: 305 EIKGVLGTMGLFLGMNLPDWPPE 327
           EIK  L  +GL LG  + +WP +
Sbjct: 294 EIKDKLSELGLSLGTLIENWPQD 316


>gi|150036844|emb|CAM98287.1| DNA-directed RNA polymerase alpha chain [Leuconostoc holzapfelii]
          Length = 199

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 89/198 (44%), Positives = 130/198 (65%), Gaps = 2/198 (1%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D
Sbjct: 1   GTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSD 60

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A 
Sbjct: 61  DERSLEIDVQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSAD 120

Query: 160 HHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
            ++   E  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D++
Sbjct: 121 ENKQLREEMPIGVLAVDSIYTPIERVNYHVENTRVGARDDYDKLTFDIWTNGSIKPSDAL 180

Query: 218 ALASRILQDQLGMFINFE 235
           +L S+IL + L +F++  
Sbjct: 181 SLGSKILAEHLNLFMDIS 198


>gi|157165509|ref|YP_001467695.1| DNA-directed RNA polymerase subunit alpha [Campylobacter concisus
           13826]
 gi|171855074|sp|A7ZFY7|RPOA_CAMC1 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|112800819|gb|EAT98163.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter concisus
           13826]
          Length = 338

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 104/338 (30%), Positives = 172/338 (50%), Gaps = 10/338 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++K       P  IE   +    EN   + A P   G+A TL + LRR+L +S  G A  
Sbjct: 1   MRKITTSAYMPTEIEVKSVS---ENVANITAYPFEAGYAVTLAHPLRRLLYTSTVGFAPI 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I GV HE  S++G+ ED+   I+N+K I  K+ SG   + +    +GP  +T  D+ 
Sbjct: 58  GVKIKGVSHEFDSMRGMLEDVAFFIINLKKIRFKLKSGSEREVIEYSFKGPKEITGADLN 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               +E++NPD  +  ++ DA +   + + KG GYVP++  R E +    I +DA ++P+
Sbjct: 118 ND-LVEIVNPDAYLATINEDAELNFSVIIQKGIGYVPSEEIREEIEDE-YIALDAFFTPV 175

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KK  Y +++       DY+K+  TI TDG +   ++       +  Q+ +F    +    
Sbjct: 176 KKAVYEIQNVLVEDDPDYEKIVFTITTDGQVGPVEAFKNCLEAMYQQMSVFKGILDIDVS 235

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                +  S  F+   L  VE+L LS RS NCL    I ++G+L    E ++  + N G+
Sbjct: 236 APVASSSASGEFSKL-LSSVEDLNLSARSFNCLDKAEIRFIGELALMDENELKELKNLGK 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK V+  +G  +G+++     +S E+L KK  +
Sbjct: 295 KSLEEIKAVMEEIGYPVGVDV---LKDSKEQLRKKITE 329


>gi|119662825|emb|CAJ33205.1| RNA polymerase alpha subunit [Lactobacillus fermentum]
          Length = 190

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 90/190 (47%), Positives = 135/190 (71%), Gaps = 2/190 (1%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRV+++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRVMLASLPGAAITSIQIDGVLHEFSTVQGVTEDVTQIILNLKQVA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK+  +  K + I  +GP  VTA DIQ   D+ +LN D  I  +   A + +++T  KG 
Sbjct: 61  LKIDSEDAKDLEIDVKGPAEVTAADIQGDGDVTILNSDLHIATVSDGAELHVKMTADKGR 120

Query: 154 GYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A  ++T  E   IG++ ID++Y+PI++V+YTVE+ R GQ  DYDKL++ + T+GS+
Sbjct: 121 GYSSADDNKTRMEGLAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYDKLTLDVWTNGSL 180

Query: 212 TGEDSVALAS 221
           T  ++++LA+
Sbjct: 181 TPTEAISLAA 190


>gi|167626782|ref|YP_001677282.1| DNA-directed RNA polymerase subunit alpha [Francisella philomiragia
           subsp. philomiragia ATCC 25017]
 gi|167596783|gb|ABZ86781.1| DNA-directed RNA polymerase, alpha subunit [Francisella
           philomiragia subsp. philomiragia ATCC 25017]
          Length = 325

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 110/321 (34%), Positives = 180/321 (56%), Gaps = 13/321 (4%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           QE + PN     +  +       +   P+ +G AH LGN++RR L+SSL GA+I  V ID
Sbjct: 8   QEFV-PN---IQLKEELGAFGYKIQVSPVEKGMAHILGNSIRRFLLSSLSGASIIKVNID 63

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR-VTIFKRGPGVV--TAGDIQTVN 123
           GVLHE S+++ V ED+ +I+ N+K + +K+  +  K  + +     GVV  TAGD +T  
Sbjct: 64  GVLHEYSTLEDVKEDVVEIVSNLKKVAIKLDKNVSKVELELSVTKSGVVVVTAGDFKTTQ 123

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            IE++N D  I  L  +    +  TVS G          TE + +G I +D+ ++PIK+V
Sbjct: 124 GIEIINKDQPIATLTNEREFSLTATVSVGRNVGILSALPTELEKVGDIAVDSDFNPIKRV 183

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           ++ +           + L + + T+G+I    +V  A     +Q+ +F++   P      
Sbjct: 184 AFEIFDNGTN-----ETLEVFVKTNGTIEPLVAVTKALEYFCEQISVFVSLRVPSNGKTG 238

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           D  + S   +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL
Sbjct: 239 DALLDSN-IDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLGKKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDW 324
            EIK +L    L LG+ + ++
Sbjct: 298 NEIKQILIDNNLSLGVQIDNF 318


>gi|222823139|ref|YP_002574712.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter lari
           RM2100]
 gi|222538360|gb|ACM63461.1| DNA-directed RNA polymerase, alpha subunit [Campylobacter lari
           RM2100]
          Length = 337

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 105/321 (32%), Positives = 163/321 (50%), Gaps = 8/321 (2%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +    +    + A P   G+A TL + LRR+L SS  G A T V+I GV HE  S++G+ 
Sbjct: 16  IENISDTVAKVSAWPFEIGYAITLAHPLRRLLYSSTVGFAPTGVKIKGVAHEFDSMRGML 75

Query: 80  EDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
           ED+   I+N+K +  K+  DS K  VT   +GP  +   D+     +EV+N D  +  ++
Sbjct: 76  EDVALFIINLKKLRFKLKTDSEKEIVTFSFKGPKEICGKDLDND-VVEVVNADSYLATIN 134

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            DA +   L + KG GYVP++  +   DP   I +DA ++P+K   Y +E        DY
Sbjct: 135 EDADLEFTLIIEKGIGYVPSEEVQNFLDPE-FIALDAFFTPVKHAVYDIEKVLFEDNPDY 193

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           +K+  TI TDG I+  D+   A   +  QL +F      +  V+       +      L+
Sbjct: 194 EKVVFTITTDGQISPSDAFKNALEAMYKQLSVFDKITNAQSVVRSQTQNNEVEHVKL-LQ 252

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            + EL L  RS NCL   N+VY+G+L     +++  + N G+KSL EIK V+ ++G  +G
Sbjct: 253 NITELNLGARSFNCLEKANVVYIGELALMNASELADLKNLGKKSLDEIKSVMESIGFPIG 312

Query: 319 -MNLPDWPPESIEELAKKYED 338
              L D   E+   L KK  +
Sbjct: 313 NSKLSDSAKET---LKKKITE 330


>gi|154424847|emb|CAL18526.1| RNA polymerase alpha subunit [Streptococcus pyogenes]
          Length = 202

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 90/202 (44%), Positives = 139/202 (68%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K
Sbjct: 1   LGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + +   GP  VTAGDI T +DIE++NPDH +  +     +R  +TV+K  GYVPA+ ++
Sbjct: 61  IIELEVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLRATMTVAKKRGYVPAEGNK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R
Sbjct: 121 KDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSAR 180

Query: 223 ILQDQLGMFINFEEPKKEVKED 244
           +L + L +F +  E  K  +  
Sbjct: 181 VLIEHLNLFTDLTEVAKATEVM 202


>gi|150187061|emb|CAK30162.1| RNA polymerase alpha subunit [Streptococcus didelphis]
          Length = 209

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 90/207 (43%), Positives = 139/207 (67%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           +GN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K
Sbjct: 1   IGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNLKGLAVKSYVEDEK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + +   GP  VTAGDI T +DIE++NPDH +  +     +R  +TV+K  GYVPA+ ++
Sbjct: 61  MIELDVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLRATMTVAKKRGYVPAEGNK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            ++ P+G + ID++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R
Sbjct: 121 KDDAPVGTLAIDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSAR 180

Query: 223 ILQDQLGMFINFEEPKKEVKEDINVKS 249
           +L + L +F +  E  K        + 
Sbjct: 181 VLIEHLNLFTDLTEVAKATDVMKETEK 207


>gi|150036740|emb|CAM98259.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. dextranicum]
          Length = 195

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 88/195 (45%), Positives = 130/195 (66%), Gaps = 2/195 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A
Sbjct: 61  DDERSLEIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSA 120

Query: 159 KHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+
Sbjct: 121 DENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTNGSIKPSDA 180

Query: 217 VALASRILQDQLGMF 231
           ++L ++IL + LG+F
Sbjct: 181 LSLGAKILAEHLGLF 195


>gi|167627502|ref|YP_001678002.1| DNA-directed RNA polymerase subunit alpha [Francisella philomiragia
           subsp. philomiragia ATCC 25017]
 gi|241668071|ref|ZP_04755649.1| DNA-directed RNA polymerase subunit alpha [Francisella philomiragia
           subsp. philomiragia ATCC 25015]
 gi|254876606|ref|ZP_05249316.1| DNA-directed RNA polymerase alpha subunit [Francisella philomiragia
           subsp. philomiragia ATCC 25015]
 gi|158523436|gb|ABW70833.1| DNA-directed RNA polymerase alpha subunit 2 [Francisella
           philomiragia subsp. philomiragia ATCC 25015]
 gi|167597503|gb|ABZ87501.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Francisella philomiragia subsp. philomiragia ATCC
           25017]
 gi|254842627|gb|EET21041.1| DNA-directed RNA polymerase alpha subunit [Francisella philomiragia
           subsp. philomiragia ATCC 25015]
          Length = 318

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 103/323 (31%), Positives = 180/323 (55%), Gaps = 11/323 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+V+I+
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGYALKQTMLYSIHGACVTSVKIN 60

Query: 67  -GVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVND 124
            G +  +  +    E + DIILN+K + + +  G     +T    G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLPVTLAEGVDTGVITFELSGSEEEVFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG GY  A+ +    +      +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGIGYRQAQENFKNEE----FLLDAAFSPVSFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y ++ AR G+  D DKL + I T+G+++ E+++ +A+  +Q+QL   ++ EE  K +   
Sbjct: 177 YEIKDARVGRRTDLDKLELNIKTNGNVSCEEALRIAATKIQNQLRNIVDVEEINKGIF-- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +   +   NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL 
Sbjct: 235 VEDPTKDINPLLLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLT 294

Query: 305 EIKGVLGTMGLFLGMNLPDWPPE 327
           EIK  L  +GL LG  + +WP +
Sbjct: 295 EIKDKLSELGLSLGTMIDNWPED 317


>gi|119662299|emb|CAJ33137.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           bulgaricus]
          Length = 214

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 85/213 (39%), Positives = 132/213 (61%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           F  TLGN+LRRVL++S+ G  +  V+IDG+LHE +++ GV ED+T IILN+K + L+   
Sbjct: 1   FGTTLGNSLRRVLLTSVPGTGLVKVKIDGILHEFTTVPGVKEDVTKIILNLKKLELRAYT 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + +   GP  VTA D++   D+EVLNPD  IC +     + M + V  G GYVPA
Sbjct: 61  EEVKTIELDVEGPATVTAEDLKADADVEVLNPDQYICTIAQGGHLHMWIDVCNGRGYVPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++T    IG I +D+L+SPI+KV+Y VES R G+  D+DKL++ I T+GSI   D++ 
Sbjct: 121 SENKTAEMSIGDIPVDSLFSPIEKVNYQVESTRVGKREDFDKLTLEIWTNGSIAPNDALN 180

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            A+R+L +    F + +   +  +  +  ++  
Sbjct: 181 FAARVLVEHFKAFESADAAAEIGEVMVEQENDQ 213


>gi|156502016|ref|YP_001428081.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica FTNF002-00]
 gi|290954162|ref|ZP_06558783.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica URFT1]
 gi|295312432|ref|ZP_06803209.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica URFT1]
 gi|171769927|sp|A7NAX2|RPOA2_FRATF RecName: Full=DNA-directed RNA polymerase subunit alpha 2;
           Short=RNAP subunit alpha 2; AltName: Full=RNA polymerase
           subunit alpha 2; AltName: Full=Transcriptase subunit
           alpha 2
 gi|156252619|gb|ABU61125.1| DNA-directed RNA polymerase, alpha subunit [Francisella tularensis
           subsp. holarctica FTNF002-00]
          Length = 317

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 102/323 (31%), Positives = 182/323 (56%), Gaps = 12/323 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I+
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKIN 60

Query: 67  -GVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVND 124
            G +  +  +    E + DIILN+K +++ ++ D     +T    G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLSVTLAEDVETGTITFELSGSEEEIFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG G+ PA+ +  + +      +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQDNFKDCE----FLLDATFSPVVFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +  +
Sbjct: 177 FEIKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGIFVE 236

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
                   NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL 
Sbjct: 237 ---DPKDINPILLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLT 293

Query: 305 EIKGVLGTMGLFLGMNLPDWPPE 327
           EIK  L  +GL LG  + +WP +
Sbjct: 294 EIKDKLSELGLSLGTLIENWPQD 316


>gi|161511755|emb|CAP16888.1| DNA-directed RNA polymerase subunit alpha [Pediococcus damnosus]
          Length = 187

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 93/186 (50%), Positives = 133/186 (71%), Gaps = 2/186 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+T++QIDGVLHE SSI+GV ED+T IILNIK ++LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSSIEGVVEDVTQIILNIKKVSLKIES 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A
Sbjct: 61  DDEKSLEIDVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAILTADTGRGYVSA 120

Query: 159 KHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   ++ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSIT  ++
Sbjct: 121 DENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSITPSEA 180

Query: 217 VALASR 222
            +L+++
Sbjct: 181 TSLSAK 186


>gi|296272962|ref|YP_003655593.1| DNA-directed RNA polymerase subunit alpha [Arcobacter nitrofigilis
           DSM 7299]
 gi|296097136|gb|ADG93086.1| DNA-directed RNA polymerase, alpha subunit [Arcobacter nitrofigilis
           DSM 7299]
          Length = 332

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 90/327 (27%), Positives = 169/327 (51%), Gaps = 7/327 (2%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  +E   + + E     + A P   GFA TL + LRR+L+SS  G +  AV+I+G  HE
Sbjct: 11  PTEVEIEAISETE---AKISAYPFESGFAITLAHPLRRLLLSSSVGYSPIAVKIEGASHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKR-VTIFKRGPGVVTAGDIQTVNDIEVLNP 130
             S++G+ ED+   I+N+K I  K+  D ++  V     GP  +   D+   +D+E+++P
Sbjct: 68  FDSLRGMLEDIAIFIINLKNIKFKILSDENQVEVEYSFNGPKEIKGSDL-VNSDVEIVSP 126

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           +  +  ++ D  +   + + KG GY+P++  R +      I +DA ++P+KKV Y +E  
Sbjct: 127 EAHLATINADCNLTFSVIIQKGIGYMPSEDIR-DMVSSDYIPLDAFFTPVKKVVYDIEKM 185

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
                 +++K   T+ T+G IT  ++   A  ++  Q+ +F    +   EV    + +  
Sbjct: 186 LVEDNPNFEKAVFTVQTNGQITPINAFKEAVSVMYSQMSVFNKVFD-LSEVTVSDSTEEP 244

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L+ K+++L LS RS N L    + Y+G+L+  +E ++  + N G+KS  EI   L
Sbjct: 245 VELKDLIVKIDDLNLSARSFNSLDRAGLKYLGELVLMSEVEVKNIKNLGKKSYDEIADKL 304

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKYE 337
            ++G  +   LP+    ++    ++++
Sbjct: 305 ASLGFPVENTLPENIASALRRKLEQFK 331


>gi|119662393|emb|CAJ33186.1| RNA polymerase alpha subunit [Lactobacillus plantarum]
          Length = 204

 Score =  229 bits (583), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 92/204 (45%), Positives = 138/204 (67%), Gaps = 2/204 (0%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           +L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK+  D  K + I  +
Sbjct: 1   ILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTAIILNVKKIALKLESDETKTLEIDVK 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDP 167
           GP  VTAGDI    D+EVLNPD  IC +   A   M +T + G GYV A+ ++   ++ P
Sbjct: 61  GPANVTAGDIIGDADVEVLNPDLPICTVADGAHFHMRMTANTGRGYVSAEDNKHREDDMP 120

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           IG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T+GSIT  ++++L+++IL D 
Sbjct: 121 IGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWTNGSITPSEAISLSAKILTDH 180

Query: 228 LGMFINFEEPKKEVKEDINVKSLP 251
           L +F+N  +  K     +  +   
Sbjct: 181 LSIFVNLTDEAKNTDVMVEKEETH 204


>gi|154424859|emb|CAL18532.1| RNA polymerase alpha subunit [Streptococcus sobrinus]
          Length = 203

 Score =  229 bits (583), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 89/203 (43%), Positives = 138/203 (67%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   +  K 
Sbjct: 1   GNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVEDEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV+K  GYVPA+ ++ 
Sbjct: 61  IELDVTGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGHSLKATMTVAKNRGYVPAEGNKN 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+
Sbjct: 121 DSAPVGTLAVDSIYTPVKKVNYQVEPARVGSNAGFDKLTIEIMTNGTIIPEDALGLSARV 180

Query: 224 LQDQLGMFINFEEPKKEVKEDIN 246
           L + L +F +  E  K  +    
Sbjct: 181 LIEHLNLFTDLTEIAKTTEVMKE 203


>gi|332184519|gb|AEE26773.1| DNA-directed RNA polymerase alpha subunit [Francisella cf. novicida
           3523]
          Length = 318

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 102/323 (31%), Positives = 180/323 (55%), Gaps = 11/323 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I+
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKIN 60

Query: 67  -GVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVND 124
            G +  +  +    E + DIILN+K + + +  G     +T    G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLPVTLAEGVETGIITFELSGSEEEIFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG G+ PA+ +  +    G   +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQDNFKD----GEFLLDATFSPVVFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +   
Sbjct: 177 FEIKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGIF-- 234

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +   +   NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL 
Sbjct: 235 VEDPTKDINPILLKHVEELNLTARSSNCLKAVNIKLIGELVQKTENELLKAPNFGKKSLT 294

Query: 305 EIKGVLGTMGLFLGMNLPDWPPE 327
           EIK  L  + L LG  + +WP +
Sbjct: 295 EIKDKLSELSLSLGTIIENWPQD 317


>gi|153217671|ref|ZP_01951352.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae 1587]
 gi|124113383|gb|EAY32203.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae 1587]
          Length = 244

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 103/239 (43%), Positives = 153/239 (64%), Gaps = 7/239 (2%)

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVVRMELTVSKGHGY 155
            G     +T+ K G G V AGDI    D+E++NP+HVIC+L   +A + M + V +G GY
Sbjct: 8   EGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVERGRGY 67

Query: 156 VPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           VPA    H   +  PIG + +DA +SP+ K++Y+VE+AR  Q  D DKL + ++T+G++ 
Sbjct: 68  VPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLE 127

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
            E+++  A+ IL +QL  F++  + +         +   F+P LL+ V++LEL+VRS NC
Sbjct: 128 PEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANC 184

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           L+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 185 LKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 243


>gi|150186952|emb|CAK30135.1| RNA polymerase alpha subunit [Streptococcus equi subsp.
           zooepidemicus]
          Length = 205

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 87/205 (42%), Positives = 139/205 (67%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K 
Sbjct: 1   GNSLRRVLLSSLPGAAVTSIRIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKI 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV+K  GYVPA+ ++ 
Sbjct: 61  IELDVEGPAEVTAGDILTDSDIELVNPDHYLFTIADGYTLKASMTVAKKRGYVPAEGNKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+
Sbjct: 121 DDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARV 180

Query: 224 LQDQLGMFINFEEPKKEVKEDINVK 248
           L + L +F +  +  K  +     +
Sbjct: 181 LIEHLNLFTDLTDVAKATEVMKEAE 205


>gi|119668371|emb|CAK95515.1| RNA polymerase alpha subunit [Lactobacillus sakei subsp. carnosus]
          Length = 196

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 83/196 (42%), Positives = 134/196 (68%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           +L++SL G A+T +QIDGVLHE S+I GV ED+T IILNIK + LK+  +  K + I  +
Sbjct: 1   ILLASLPGTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKLHVEEDKTIEIDVK 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  VTA DI + +D+EVLN D  IC +       + +TV KG GYV A  +++++ PIG
Sbjct: 61  GPATVTAADIISDDDVEVLNTDQYICTVAEGGNFHVRMTVKKGRGYVAAVQNKSDDMPIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           ++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++I+ + L 
Sbjct: 121 VLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKIMTEHLA 180

Query: 230 MFINFEEPKKEVKEDI 245
           +F++  +  K  +  +
Sbjct: 181 IFVDLTDEAKNAEIMV 196


>gi|157737266|ref|YP_001489949.1| DNA-directed RNA polymerase subunit alpha [Arcobacter butzleri
           RM4018]
 gi|315636983|ref|ZP_07892207.1| DNA-directed RNA polymerase subunit alpha [Arcobacter butzleri
           JV22]
 gi|172045649|sp|A8ETK6|RPOA_ARCB4 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|157699120|gb|ABV67280.1| DNA-directed RNA polymerase, alpha chain [Arcobacter butzleri
           RM4018]
 gi|315478813|gb|EFU69522.1| DNA-directed RNA polymerase subunit alpha [Arcobacter butzleri
           JV22]
          Length = 332

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 92/328 (28%), Positives = 167/328 (50%), Gaps = 12/328 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  +E   +    +N   + A P   GFA TL + LRR+L+SS  G A  AV+I+G  HE
Sbjct: 11  PTEVEIEAIS---DNEAKISAYPFEDGFAITLAHPLRRLLLSSSVGCAPIAVKIEGASHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
             S++G+ ED+   ++N+K I  K++GD  +  V     GP  +   D+   ++++V++ 
Sbjct: 68  FDSLRGMLEDVAIFVINLKNIKFKINGDKEQVVVEYSFNGPRDIKGEDLI-NSEVDVVSK 126

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  +  ++ D  +   + + KG GY+P++  R +      I IDA ++P+KKV Y +E  
Sbjct: 127 DAHLATINSDCNLTFSVILQKGIGYMPSEDIR-DIVGADYIPIDAFFTPVKKVVYDIEKM 185

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
                 +Y+K    + T+G I+   +   A  ++  Q+ +F    +   EV    + +  
Sbjct: 186 LVEDNPNYEKAVFRVQTNGQISPVTAFKEAVSVMYSQMSVFNKVFD-LSEVAVSDSGEEP 244

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L+ ++++L LS RS N L    + Y+G+L+  +E ++  + N G+KS  EI   L
Sbjct: 245 VELKELVIRIDDLNLSARSFNSLDRAGLKYLGELVLMSEVEVKNIKNLGKKSYDEIAEKL 304

Query: 311 GTMGLFLGMNLPDWPPESIEE-LAKKYE 337
            ++G      + +  PE++   L +K E
Sbjct: 305 ESLGYP----VENTLPENVASALRRKLE 328


>gi|150036788|emb|CAM98271.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 205

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 85/205 (41%), Positives = 129/205 (62%), Gaps = 2/205 (0%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + +
Sbjct: 1   NSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSL 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT- 163
            I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++  
Sbjct: 61  EIDVQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSADENKKL 120

Query: 164 -ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L ++
Sbjct: 121 RDEMPIGVLAVDSIYTPIERVNYQVENTRVGARDDYDKLTFDIWTNGSIKPSDALSLGAK 180

Query: 223 ILQDQLGMFINFEEPKKEVKEDINV 247
           IL + L +F++      E    +  
Sbjct: 181 ILAEHLNLFMDISPVAAEASVMVEA 205


>gi|195973794|gb|ACG63462.1| DNA-directed RNA polymerase subunit alpha [Francisella philomiragia
           subsp. philomiragia ATCC 25015]
          Length = 290

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 103/283 (36%), Positives = 166/283 (58%), Gaps = 7/283 (2%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
            +   P+ +G AH LGN++RR L+SSL GA+I  V IDGVLHE S+++ V ED+ +I+ N
Sbjct: 13  KIQVSPVEKGMAHILGNSIRRFLLSSLSGASIIKVNIDGVLHEYSTLEDVKEDVVEIVSN 72

Query: 89  IKGINLKMSGDSHKR-VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           +K + +K+  +  K  + +     GVVTAGD +T   IE++N D  I  L  +    +  
Sbjct: 73  LKKVAIKLDKNVSKVELELSVTKSGVVTAGDFKTTQGIEIINKDQPIATLTNERKFSLTA 132

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           TVS G          TE + +G I +D+ ++PIK+V++ +           + L + + T
Sbjct: 133 TVSVGRNVGILSALPTELEKVGDIAVDSDFNPIKRVAFEIFDNGTN-----ETLEVFVKT 187

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G+I    +V  A     +Q+ +F++   P      D  + S   +P LLK +++LEL+V
Sbjct: 188 NGTIEPLVAVTKALEYFCEQISVFVSLRVPSNGKTGDALLDSN-IDPILLKPIDDLELTV 246

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           RS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L
Sbjct: 247 RSSNCLRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQIL 289


>gi|119668313|emb|CAK95457.1| RNA polymerase alpha subunit [Lactobacillus fructivorans KCTC 3543]
          Length = 192

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 97/192 (50%), Positives = 142/192 (73%), Gaps = 4/192 (2%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL++SL GAA+T++QIDGVLHE S++KGV ED+T IILN+K INLK++ D ++ 
Sbjct: 1   GNSLRRVLLASLPGAAVTSIQIDGVLHEFSTVKGVVEDVTQIILNVKKINLKINSDDNET 60

Query: 104 --VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
             ++I   GP  VTAGDI T +D+E+LNPD  I  +   A   M +T +KG GYV A+ +
Sbjct: 61  KSMSINVTGPADVTAGDIVTDSDVEILNPDLHIATVADGATFHMNMTANKGRGYVSAEEN 120

Query: 162 RTEND--PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           + +ND  PIG++ +D++Y+PI++V+Y VE AR GQ  DYDKL++ + T+GSIT  D+++L
Sbjct: 121 KAKNDGMPIGVLPVDSIYTPIERVNYQVEDARVGQRDDYDKLTLDVWTNGSITPSDAISL 180

Query: 220 ASRILQDQLGMF 231
           A++IL     +F
Sbjct: 181 AAKILNQHFQLF 192


>gi|195973796|gb|ACG63463.1| DNA-directed RNA polymerase subunit alpha [Francisella
           philomiragia]
 gi|195973798|gb|ACG63464.1| DNA-directed RNA polymerase subunit alpha [Francisella
           philomiragia]
 gi|195973800|gb|ACG63465.1| DNA-directed RNA polymerase subunit alpha [Francisella
           philomiragia]
          Length = 290

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 103/283 (36%), Positives = 166/283 (58%), Gaps = 7/283 (2%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
            +   P+ +G AH LGN++RR L+SSL GA+I  V IDGVLHE S+++ V ED+ +I+ N
Sbjct: 13  KIQVSPVEKGMAHILGNSIRRFLLSSLSGASIIKVNIDGVLHEYSTLEDVKEDVVEIVSN 72

Query: 89  IKGINLKMSGDSHKR-VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           +K + +K+  +  K  + +     GVVTAGD +T   IE++N D  I  L  +    +  
Sbjct: 73  LKKVAIKLDKNVSKVELELSVTKSGVVTAGDFKTTQGIEIINKDQPIATLTNEREFSLTA 132

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           TVS G          TE + +G I +D+ ++PIK+V++ +           + L + + T
Sbjct: 133 TVSVGRNVGILSALPTELEKVGDIAVDSDFNPIKRVAFEIFDNGTN-----ETLEVFVKT 187

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G+I    +V  A     +Q+ +F++   P      D  + S   +P LLK +++LEL+V
Sbjct: 188 NGTIEPLVAVTKALEYFCEQISVFVSLRVPSNGKTGDALLDSN-IDPILLKPIDDLELTV 246

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           RS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L
Sbjct: 247 RSSNCLRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQIL 289


>gi|150036728|emb|CAM98255.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 194

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 87/193 (45%), Positives = 128/193 (66%), Gaps = 2/193 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A
Sbjct: 61  DDERSLEIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSA 120

Query: 159 KHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+
Sbjct: 121 DENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTNGSIKPSDA 180

Query: 217 VALASRILQDQLG 229
           ++L ++IL + LG
Sbjct: 181 LSLGAKILAEHLG 193


>gi|195973802|gb|ACG63466.1| DNA-directed RNA polymerase subunit alpha [Francisella
           philomiragia]
          Length = 290

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 102/283 (36%), Positives = 165/283 (58%), Gaps = 7/283 (2%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
            +   P+ +G AH LGN++RR L+SSL GA+I  V IDGVLHE S+++ V ED+ +I+ N
Sbjct: 13  KIQVSPVEKGMAHILGNSIRRFLLSSLSGASIIKVNIDGVLHEYSTLEDVKEDVVEIVSN 72

Query: 89  IKGINLKMSGDSHKR-VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           +K + +K+  +  K  + +     G VTAGD +T   IE++N D  I  L  +    +  
Sbjct: 73  LKKVAIKLDKNVSKVELELSVTKSGAVTAGDFKTTQGIEIINKDQPIATLTNEREFSLTA 132

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           TVS G          TE + +G I +D+ ++PIK+V++ +           + L + + T
Sbjct: 133 TVSVGRNVGILSALPTELEKVGDIAVDSDFNPIKRVAFEIFDNGTN-----ETLEVFVKT 187

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G+I    +V  A     +Q+ +F++   P      D  + S   +P LLK +++LEL+V
Sbjct: 188 NGTIEPLVAVTKALEYFCEQISVFVSLRVPSNGKTGDALLDSN-IDPILLKPIDDLELTV 246

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           RS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L
Sbjct: 247 RSSNCLRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQIL 289


>gi|77409855|ref|ZP_00786488.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae COH1]
 gi|77171535|gb|EAO74771.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae COH1]
          Length = 212

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 82/210 (39%), Positives = 135/210 (64%)

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
           P  +TAGDI T +DIE++NPDH +  +     ++  +TV+K  GYVPA+ ++ ++ P+G 
Sbjct: 2   PAEITAGDILTDSDIEIVNPDHYLFTIAEGHSLKATMTVAKNRGYVPAEGNKKDDAPVGT 61

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +
Sbjct: 62  LAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNL 121

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
           F +  E  K  +     + +     L + +EEL+LSVRS NCL+   I  + DL ++TE 
Sbjct: 122 FTDLTEVAKATEVMKETEKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVXDLTEKTEP 181

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           +M+++ N GRKSL E+K  L  +GL L  +
Sbjct: 182 EMMKVRNLGRKSLEEVKIKLADLGLGLKND 211


>gi|168805077|gb|ACA28617.1| DNA-directed RNA polymerase subunit alpha [Thiomonas arsenivorans]
          Length = 228

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 100/228 (43%), Positives = 154/228 (67%), Gaps = 3/228 (1%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           G+ ED+  ++LN+KG+  K+       +++ K G GVVTA DIQT +D+E++NP+HVI +
Sbjct: 1   GLQEDVIAVLLNLKGVVFKLHNRDEVTLSLRKEGEGVVTAADIQTPHDVEIINPEHVIAH 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSYTVESAREG 193
           L     + M++ V KG GYVP    R  ++    IG I +DA +SP+++VSY VE+AR  
Sbjct: 61  LSQQGKIDMQIKVEKGRGYVPGNLRRYADEGGKTIGRIVLDASFSPVRRVSYAVENARVE 120

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL M I+T+GSI+ E+++  ++RIL +QL +F + E  +K ++   +  +  F+
Sbjct: 121 QRTDLDKLVMEIETNGSISAEEAIRTSARILVEQLSVFASLEGAEKTLETGGSASAQQFD 180

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GRK
Sbjct: 181 PILLRPVDDLELTVRSANCLKAENIYYIGDLIQRSETELLKTPNLGRK 228


>gi|195973808|gb|ACG63469.1| DNA-directed RNA polymerase subunit alpha [Francisella noatunensis]
          Length = 290

 Score =  227 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 102/283 (36%), Positives = 165/283 (58%), Gaps = 7/283 (2%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
            +   P+ +G AH LGN++RR L+SSL GA+I  V I GVLHE S+++ V ED+ +I+ N
Sbjct: 13  KIQVSPVEKGMAHILGNSIRRFLLSSLSGASIIKVNISGVLHEYSTLEDVKEDVVEIVSN 72

Query: 89  IKGINLKMSGDSHKR-VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           +K + +K+  +  K  + +     GVVTAGD +T   IE++N D  I  L  +    +  
Sbjct: 73  LKKVAIKLDKNVSKVELELSVTKSGVVTAGDFKTTQGIEIINKDQPIATLTNEREFSLVA 132

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           TVS G           E + +G I +DA ++PIK+V++ +           + L + + T
Sbjct: 133 TVSVGRNVGILSALPIELEKVGDIAVDADFNPIKRVAFEIFDNGAS-----ETLEVFVKT 187

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G+I    +V  A     +Q+ +F++ + P      D  + S   +P LLK +++LEL+V
Sbjct: 188 NGTIEPLAAVTKALEYFCEQISVFVSLKVPSNGKTGDALLDSN-IDPILLKPIDDLELTV 246

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           RS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L
Sbjct: 247 RSSNCLRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQIL 289


>gi|150036792|emb|CAN89787.1| DNA-directed RNA polymerase alpha chain [Leuconostoc lactis]
          Length = 198

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 86/191 (45%), Positives = 125/191 (65%), Gaps = 2/191 (1%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  +
Sbjct: 1   LGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDER 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++
Sbjct: 61  SLEIDVQGPAEVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSADENK 120

Query: 163 T--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
              E  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L 
Sbjct: 121 QLREEMPIGVLAVDSIYTPIERVNYHVENTRVGARDDYDKLTFDIWTNGSIKPSDALSLG 180

Query: 221 SRILQDQLGMF 231
           ++IL + L   
Sbjct: 181 AKILAEHLNFV 191


>gi|119668347|emb|CAK95470.1| RNA polymerase alpha subunit [Lactobacillus paracasei subsp.
           paracasei]
          Length = 180

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 87/180 (48%), Positives = 129/180 (71%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRR+L+SSL GAAI+++QIDGVLHE S+I GV ED+T IILNIK + LKM+ D  K + I
Sbjct: 1   LRRILLSSLPGAAISSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNTDEDKNIEI 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
              GP  VTA DI    D+EVLNP+  IC +       + +TV KG GYV A  +++++ 
Sbjct: 61  DVNGPAKVTAADIVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAADQNKSDDM 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           PIG++ ID++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++IL +
Sbjct: 121 PIGVLPIDSIFTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKILTE 180


>gi|315451275|gb|ADU24722.1| RNA polymerase alpha subunit [Lactobacillus sp. YM 0181]
 gi|315451277|gb|ADU24723.1| RNA polymerase alpha subunit [Lactobacillus sp. YM 0188]
          Length = 213

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 83/202 (41%), Positives = 136/202 (67%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL++SL G A++ +QIDGVLHE S+I GV ED+T I+LN+K + LK   +   +
Sbjct: 1   GNSLRRVLLASLPGTAVSDIQIDGVLHEFSAIDGVIEDVTQIVLNVKKLKLKSYAEDSLK 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
             +   GP  VTA DI+  +D+E+L+P+  IC +       M++T+  G GY PA+ ++T
Sbjct: 61  AEVDIVGPATVTAKDIKADDDLEILDPEQFICTVAEGGHFHMQMTIKNGRGYTPAEQNKT 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           +  PIG++ +D++++P++KV+Y VE+ R G+  D+DKL++ I T+GSI   ++++L+++I
Sbjct: 121 DETPIGVLPVDSIFTPVEKVNYQVENTRVGKRNDFDKLTIDIWTNGSIGPREAISLSAKI 180

Query: 224 LQDQLGMFINFEEPKKEVKEDI 245
           L + L  F+N  E  K     I
Sbjct: 181 LTEHLNSFVNLTEEAKSADMMI 202


>gi|154424839|emb|CAL18522.1| RNA polymerase alpha subunit [Streptococcus pluranimalium]
          Length = 203

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 85/203 (41%), Positives = 135/203 (66%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ +K   +  K 
Sbjct: 1   GNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNVKGLAVKSYVEDEKI 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + +  +GP  VTAGDI T +DIE++N DH +  +   A  +  +TV+   GYV A+ ++ 
Sbjct: 61  IELDVQGPAEVTAGDILTDSDIEIVNSDHYLFTIAEGASFKASMTVATNRGYVAAEGNKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+
Sbjct: 121 DDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTVEIMTNGTIIPEDALGLSARV 180

Query: 224 LQDQLGMFINFEEPKKEVKEDIN 246
           L + L +F +  E  K       
Sbjct: 181 LIEHLNLFTDLTEVAKATDVMKE 203


>gi|194246759|ref|YP_002004398.1| DNA-directed RNA polymerase, alpha chain [Candidatus Phytoplasma
           mali]
 gi|193807116|emb|CAP18554.1| DNA-directed RNA polymerase, alpha chain [Candidatus Phytoplasma
           mali]
          Length = 331

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 106/308 (34%), Positives = 170/308 (55%), Gaps = 9/308 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E+ +    I + L   +  T+GN LRRVL+SSL GA I  V+I GV HE S+I GV+ED
Sbjct: 17  SEDLSFGRFIIQNLEPSYGVTIGNPLRRVLLSSLPGAGIVYVEIKGVDHEFSTIPGVYED 76

Query: 82  LTDIILNIKGINLK---MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL- 137
           +  I+LN+K + +    +  D  + + +F  G   VTA   + V  I+++NP+  I NL 
Sbjct: 77  VMSIVLNLKQVVISVDSIDDDFEQEMELFVTGKQKVTASCFEQVEGIKIINPEQEIANLV 136

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPI-GLITIDALYSPIKKVSYTVESAREGQVL 196
             +A ++M + + +G GYV A+ ++       GLI+ID LY+P+ KVSY +E     ++ 
Sbjct: 137 SENASLKMTVLIKRGIGYVSAEENKIYTKKKKGLISIDTLYTPVSKVSYDIE----KKLG 192

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           D ++L++ I T+ S T +D++  AS+IL D      N  E K ++      K    N +L
Sbjct: 193 DKEELAIEITTNKSTTAKDALTTASKILFDHFSFLANLNEKKDQISFIYKPKKELPNKSL 252

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
             ++++LELSVR  NCL+   I  + DL+   E ++ ++ + GRKS  E+K      GL 
Sbjct: 253 ELRIDQLELSVRLFNCLKKSGIEKVSDLVLLKEEEVFKLKSLGRKSFNELKEKFKQHGLE 312

Query: 317 LGMNLPDW 324
              +L   
Sbjct: 313 FQNDLEKK 320


>gi|150036768|emb|CAM98265.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. cremoris]
          Length = 212

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 86/207 (41%), Positives = 131/207 (63%), Gaps = 2/207 (0%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + +
Sbjct: 1   NSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIESDDERSL 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT- 163
            I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++  
Sbjct: 61  EIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSADENKKL 120

Query: 164 -ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L ++
Sbjct: 121 RDEMPIGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTNGSIKPSDALSLGAK 180

Query: 223 ILQDQLGMFINFEEPKKEVKEDINVKS 249
           IL + LG+F++      E    +  + 
Sbjct: 181 ILAEHLGLFMDISPVAAEASVMVEAEP 207


>gi|291277242|ref|YP_003517014.1| DNA-directed RNA polymerase subunit alpha [Helicobacter mustelae
           12198]
 gi|290964436|emb|CBG40286.1| DNA-directed RNA polymerase alpha chain [Helicobacter mustelae
           12198]
          Length = 336

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 91/331 (27%), Positives = 166/331 (50%), Gaps = 11/331 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  ++   LG    N+  ++A P   G+A TL + LRR+L+SS  G A  A++I+GV HE
Sbjct: 11  PTTVDVEELG---PNKVRVMAYPFESGYAVTLAHPLRRLLLSSSVGLAPIALKIEGVAHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL-----KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
             SI+G+ ED++  I+N+K I           +    +    +GP V++ G +     I+
Sbjct: 68  FDSIRGIVEDVSPFIVNLKNIRFLGKEGGFLEEEKVELHYSFQGPMVLSGGHLAND-QID 126

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           ++N +  +  ++ DAV+   + V KG GYVP++  R        I +DA ++P++K  Y 
Sbjct: 127 IVNKEAPLATINEDAVLNFSIIVQKGIGYVPSEDIRGLISEDY-IPLDAYFTPVRKAVYE 185

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           +E+        Y+K+   ++TDG +   ++   A  I+  Q+ +F N +       +   
Sbjct: 186 IENVLVEDNPTYEKIIFDVETDGQVDPYEAFKQAIAIMYSQMSIF-NADISSISTTQKQA 244

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           ++       LL K++ L L+ R  NCL    I Y+G+L+  +E+++  + N G+ S  EI
Sbjct: 245 IEDNFDFKDLLMKIDSLNLNARCFNCLDRIGIRYVGELVLMSESEIKGVKNLGKTSYNEI 304

Query: 307 KGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
              L  +G  +G  L +    ++ +   K +
Sbjct: 305 VEKLQEIGYPIGTELEEDKKIALTKKISKLK 335


>gi|195973806|gb|ACG63468.1| DNA-directed RNA polymerase subunit alpha [Francisella noatunensis]
 gi|198417145|gb|ACH87846.1| RpoA [Francisella noatunensis subsp. noatunensis]
          Length = 290

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 102/283 (36%), Positives = 165/283 (58%), Gaps = 7/283 (2%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
            +   P+ +G AH LGN++RR L+SSL GA+I  V I G+LHE S+++ V ED+ +I+ N
Sbjct: 13  KIQVSPVEKGMAHILGNSIRRFLLSSLSGASIIKVNISGILHEYSTLEDVKEDVVEIVSN 72

Query: 89  IKGINLKMSGDSHKR-VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           +K + +K+  +  K  + +     GVVTAGD +T   IE++N D  I  L  +    +  
Sbjct: 73  LKKVAIKLDKNVSKVELELSVTKSGVVTAGDFKTTQGIEIINKDQPIATLTNEREFSLVA 132

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           TVS G          TE + +G I +DA ++PIK+V++ +           + L + + T
Sbjct: 133 TVSVGRNVGILSALPTELEKVGDIAVDADFNPIKRVAFEIFDNGAS-----ETLEVFVKT 187

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G+I    +V  A     +Q+ +F++   P      D  + S   +P LLK +++LEL+V
Sbjct: 188 NGTIEPLAAVTKALEYFCEQISVFVSLRVPSNGKTGDALLDSN-IDPILLKPIDDLELTV 246

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           RS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L
Sbjct: 247 RSSNCLRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQIL 289


>gi|150186989|emb|CAK30143.1| RNA polymerase alpha subunit [Streptococcus gordonii]
          Length = 202

 Score =  226 bits (576), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 87/202 (43%), Positives = 132/202 (65%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL++SL GAA+T++ I+GVLHE  +I GV ED+  IILNIKGI +K      K +
Sbjct: 1   NSLRRVLLASLPGAAVTSINIEGVLHEFDTIPGVREDVMQIILNIKGIAVKSYVQDEKMI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  +TAGDI T +DIE++NPDH +  +   A  +  +TV+ G GYVPA  ++ +
Sbjct: 61  ELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIGEGARFKAVMTVNSGRGYVPADQNKRD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           + P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL
Sbjct: 121 DAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEIMTNGTIIPEDALGLSARIL 180

Query: 225 QDQLGMFINFEEPKKEVKEDIN 246
            + L +F +  E  K       
Sbjct: 181 TEHLDLFTDLTEVAKATDVMKE 202


>gi|237752997|ref|ZP_04583477.1| RNA polymerase alpha subunit [Helicobacter winghamensis ATCC
           BAA-430]
 gi|229375264|gb|EEO25355.1| RNA polymerase alpha subunit [Helicobacter winghamensis ATCC
           BAA-430]
          Length = 329

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 92/307 (29%), Positives = 156/307 (50%), Gaps = 5/307 (1%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  IE   +G    N+  + A P   G+A TL + LRR+L+ S  G A  A++I+GV HE
Sbjct: 11  PTKIEVKEVG---ANKIEITAYPFEAGYAITLAHPLRRLLLGSSVGFAPVALRIEGVAHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
             S++GV ED++  I+N+K I  K+  DS      +K     V  G+    + ++++ P+
Sbjct: 68  FDSVRGVVEDVSHFIVNLKTIRFKVKDDSESVSIDYKFIGPKVITGEDLKNDLVDIVTPN 127

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  ++ DA++   + V KG GYVP++  R      G + +DA ++P+  V+Y  E+  
Sbjct: 128 IHLATINEDAILNFSIIVRKGIGYVPSEDIRNLISE-GYMPLDAYFTPVTSVTYDTENVL 186

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                +Y+K+   I TDG I    +   A  ++  Q+ +F N E   +  +  +  +  P
Sbjct: 187 VEDDPNYEKVVFNIQTDGQIEPLTAFKNALSVMHKQMAIF-NSELNIEVPEVSLGEEDSP 245

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               L + ++ L  S R  NCL    I Y+G+L+  +E  +  + N G+KSL EI   L 
Sbjct: 246 EIRVLSQSIDSLNFSARCFNCLDRSGIKYLGELVLLSEDQIKNIKNLGKKSLDEITVKLE 305

Query: 312 TMGLFLG 318
            +G  +G
Sbjct: 306 ELGYPIG 312


>gi|119662347|emb|CAJ33162.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
          Length = 203

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 91/203 (44%), Positives = 144/203 (70%), Gaps = 2/203 (0%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K ++LK+  +  K +
Sbjct: 1   NSLRRVLIASLPGAAITSMQIDGVLHEFSTVEGVTEDVTQIILNLKKVSLKLDSEDQKNL 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT- 163
            +  +GP  VTA DIQ  N++ +LNPD  I  +   A + ++LT  KG GY+ A  ++  
Sbjct: 61  ELDVKGPAEVTASDIQGDNEVTILNPDLHIATVADGAELHIKLTADKGRGYLSANDNKAR 120

Query: 164 -ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            ++  IG++ ID++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T  ++V+L ++
Sbjct: 121 MDDLAIGVLPIDSIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLTPTEAVSLGAK 180

Query: 223 ILQDQLGMFINFEEPKKEVKEDI 245
           IL + L MF++  E  +  +  +
Sbjct: 181 ILTEHLAMFVDLTETAQNAQVMV 203


>gi|190411125|gb|ACE78317.1| RpoA [Vibrio parahaemolyticus]
          Length = 244

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 107/247 (43%), Positives = 164/247 (66%), Gaps = 8/247 (3%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVT 105
           LRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T
Sbjct: 1   LRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFIT 60

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HH 161
           + K G G V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H+
Sbjct: 61  LNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHN 120

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
             +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+
Sbjct: 121 EEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAA 180

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
            IL +QL  F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+
Sbjct: 181 TILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYI 237

Query: 282 GDLIQRT 288
           GDL+QRT
Sbjct: 238 GDLVQRT 244


>gi|119668293|emb|CAK95452.1| RNA polymerase alpha subunit [Lactobacillus collinoides]
          Length = 191

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 96/191 (50%), Positives = 137/191 (71%), Gaps = 3/191 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN K I+LK+ G
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNTKKISLKLEG 60

Query: 99  --DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             D  + + I  +GP  VTAGDI   +D+ VLNPD  I  +   A   M +T +KG GYV
Sbjct: 61  PDDEIESMEIDVKGPAQVTAGDITADSDVTVLNPDLYIATVAEGATFHMRMTANKGRGYV 120

Query: 157 PAKHHR-TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
            A  ++  E+ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TD SIT  +
Sbjct: 121 SADRNKAKEDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDSSITPSE 180

Query: 216 SVALASRILQD 226
           S++LA++IL +
Sbjct: 181 SISLAAKILTE 191


>gi|151416836|emb|CAO78489.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gelidum]
          Length = 193

 Score =  225 bits (575), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 87/193 (45%), Positives = 128/193 (66%), Gaps = 2/193 (1%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS 100
            TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D 
Sbjct: 1   TTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLXIDSDE 60

Query: 101 HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
            + + +  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  
Sbjct: 61  ERSLEVDIQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTITAFKGRGYSSADE 120

Query: 161 HRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++
Sbjct: 121 NKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDALS 180

Query: 219 LASRILQDQLGMF 231
           L S+IL + L +F
Sbjct: 181 LGSKILAEHLNLF 193


>gi|150036770|emb|CAM98266.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gasicomitatum]
          Length = 210

 Score =  225 bits (575), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 86/207 (41%), Positives = 131/207 (63%), Gaps = 2/207 (0%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + +
Sbjct: 1   NSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDEERSL 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT- 163
            +  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++  
Sbjct: 61  EVDIQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTITAFKGRGYSSADENKQL 120

Query: 164 -ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L S+
Sbjct: 121 RDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSLGSK 180

Query: 223 ILQDQLGMFINFEEPKKEVKEDINVKS 249
           IL + L +F++      E    + V+ 
Sbjct: 181 ILAEHLNLFMDISPVAAEANVMVEVEP 207


>gi|150187019|emb|CAK30152.1| RNA polymerase alpha subunit [Streptococcus sobrinus]
          Length = 202

 Score =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 88/202 (43%), Positives = 137/202 (67%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   +  K +
Sbjct: 1   NSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVEDEKTI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV+K  GYVPA+ ++ +
Sbjct: 61  ELDVTGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGHSLKATMTVAKNRGYVPAEGNKND 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           + P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L
Sbjct: 121 SAPVGTLAVDSIYTPVKKVNYQVEPARVGSNAGFDKLTIEIMTNGTIIPEDALGLSARVL 180

Query: 225 QDQLGMFINFEEPKKEVKEDIN 246
            + L +F +  E  K  +    
Sbjct: 181 IEHLNLFTDLTEIAKTTEVMKE 202


>gi|150187089|emb|CAK30168.1| RNA polymerase alpha subunit [Streptococcus alactolyticus]
          Length = 202

 Score =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 87/202 (43%), Positives = 135/202 (66%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K +
Sbjct: 1   NSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKII 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  VTAGDI T +D+E++N DH +  +     ++  +TV+K  GYVPA+ ++ +
Sbjct: 61  ELDVEGPAEVTAGDILTDSDVEIVNSDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           + P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L
Sbjct: 121 DAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVL 180

Query: 225 QDQLGMFINFEEPKKEVKEDIN 246
            + L +F +  E  K       
Sbjct: 181 IEHLNLFTDLTEVAKNTDVMKE 202


>gi|150187094|emb|CAK30169.1| RNA polymerase alpha subunit [Streptococcus constellatus subsp.
           constellatus]
 gi|154424831|emb|CAL18518.1| RNA polymerase alpha subunit [Streptococcus constellatus subsp.
           constellatus]
          Length = 202

 Score =  225 bits (574), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 88/202 (43%), Positives = 134/202 (66%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL++SL GAA+T++ I+GVLHE  ++ GV ED+  IILN+KGI +K   +  K +
Sbjct: 1   NSLRRVLLASLPGAAVTSINIEGVLHEFDTVPGVREDVMQIILNVKGIAVKSYVEDEKTI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  +TAGDI T +DIE++NPDH +  +   A ++  +TV+ G GYVPA  ++ +
Sbjct: 61  ELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIGEGASLKAIMTVNAGRGYVPADENKKD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           + P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I TDG+I  ED++ L++RIL
Sbjct: 121 DAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTLEIMTDGTIIPEDALGLSARIL 180

Query: 225 QDQLGMFINFEEPKKEVKEDIN 246
              L +F N  E  K       
Sbjct: 181 TQHLDLFTNLTEVAKSTDVMKE 202


>gi|242620061|ref|YP_003002065.1| DNA-directed RNA polymerase alpha chain [Aureococcus
           anophagefferens]
 gi|239997306|gb|ACS36829.1| DNA-directed RNA polymerase alpha chain [Aureococcus
           anophagefferens]
          Length = 305

 Score =  225 bits (574), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 88/289 (30%), Positives = 150/289 (51%), Gaps = 7/289 (2%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           E  +  + + L +G   T+GN LRRVL++ L G AITAV+I+G+ +E ++I GV ED+ +
Sbjct: 18  EQSSRFLLKELTQGQGLTIGNTLRRVLLTELEGTAITAVRINGINNEFATIPGVREDVLE 77

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           I+LN+K I             +  +GP +VTA +I   + + +LN +H I  +       
Sbjct: 78  ILLNLKQIKFTGLVTEPFFTHVSVQGPQLVTAANISLPDGLSLLNSNHYIAAVAEQTNFE 137

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +EL +  G GY               +++D++++P+K V+Y ++ + +      + L + 
Sbjct: 138 IELKIESGTGYNFTDEENRIC-SGDFLSLDSIFTPVKNVNYQIKDSYKIDEKITEILDLE 196

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           I T+GSIT  D++  A+ +LQ   G  +  E     V  +           L   +EEL+
Sbjct: 197 IITNGSITPNDALNKAALVLQTLFGSLVIDELQTNPVLPEQTETE------LDILIEELQ 250

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           LSVR+ NCL+  NI  + DL+Q +  ++  + NFG+KS  E+   L   
Sbjct: 251 LSVRAYNCLKRVNIKTIADLVQYSVKELKDIKNFGQKSANEVVEKLQDR 299


>gi|119672791|emb|CAK95479.1| RNA polymerase alpha subunit [Lactobacillus sakei subsp. sakei]
          Length = 176

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 85/176 (48%), Positives = 124/176 (70%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           G+  TLGN+LRR+L++SL G A+T +QIDGVLHE S+I GV ED+T IILNIK + LK+ 
Sbjct: 1   GYGTTLGNSLRRILLASLPGTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKLH 60

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
            +  K + I  +GP  VTA DI + +D+EVLN D  IC +       + +TV KG GYV 
Sbjct: 61  VEEDKTIEIDVKGPATVTAADIISDDDVEVLNTDQYICTVAEGGNFHVRMTVKKGRGYVA 120

Query: 158 AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           A  +++++ PIG++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+ 
Sbjct: 121 AVQNKSDDMPIGVLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISP 176


>gi|255023418|ref|ZP_05295404.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL J1-208]
          Length = 195

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 75/191 (39%), Positives = 121/191 (63%)

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +LNPD  I  L  +A   + L  ++G GY PA  ++ EN PIG++ +D+++SP+ +V+Y 
Sbjct: 1   MLNPDLHIATLSDNAKFHVRLNATRGRGYTPADQNKRENMPIGVLPVDSIFSPVIRVNYQ 60

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+ R GQ  +YDKL+  + TDGSI+ E++V+L ++IL + L +F+N  +  ++ +  I 
Sbjct: 61  VENTRVGQSTNYDKLTFDVLTDGSISPEEAVSLGAKILSEHLSIFVNLTDEAQKAEIMIE 120

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L   +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N GRKSL E+
Sbjct: 121 KEESHKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELADKSEDDMMKVRNLGRKSLEEV 180

Query: 307 KGVLGTMGLFL 317
           K  L  +GL L
Sbjct: 181 KVKLADLGLSL 191


>gi|150187125|emb|CAK30176.1| RNA polymerase alpha subunit [Streptococcus intermedius]
          Length = 202

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 89/202 (44%), Positives = 135/202 (66%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL++SL GAA+T++ I+GVLHE  ++ GV ED+  IILNIKGI +K   +  K +
Sbjct: 1   NSLRRVLLASLPGAAVTSINIEGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEGEKTI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  VTAGDI T +DIE++NP+H +  +   A ++  +TV+ G GYVPA  ++ +
Sbjct: 61  ELDVEGPAEVTAGDILTDSDIEIVNPNHYLFTIGEGASLKAVMTVNTGRGYVPADENKKD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           + P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I TDG+I  ED++ L++RIL
Sbjct: 121 DAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDSFDKLTLEIMTDGTIIPEDALGLSARIL 180

Query: 225 QDQLGMFINFEEPKKEVKEDIN 246
            + L +F N  E  K       
Sbjct: 181 TEHLDLFTNLTEMAKSTDVMKE 202


>gi|154424797|emb|CAL18501.1| RNA polymerase alpha subunit [Streptococcus gordonii]
          Length = 194

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 86/194 (44%), Positives = 131/194 (67%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL++SL GAA+T++ I+GVLHE  +I GV ED+  IILNIKGI +K      K +
Sbjct: 1   NSLRRVLLASLPGAAVTSINIEGVLHEFDTIPGVREDVMQIILNIKGIAVKSYVQDEKMI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  +TAGDI T +DIE++NPDH +  +   A  +  +TV+ G GYVPA  ++ +
Sbjct: 61  ELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIGEGARFKAVMTVNSGRGYVPADQNKRD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           + P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL
Sbjct: 121 DAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEIMTNGTIIPEDALGLSARIL 180

Query: 225 QDQLGMFINFEEPK 238
            + L +F +  E  
Sbjct: 181 TEHLDLFTDLTEVA 194


>gi|119668335|emb|CAK95508.1| RNA polymerase alpha subunit [Lactobacillus johnsonii]
          Length = 185

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 93/185 (50%), Positives = 131/185 (70%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRRVL++S+ G A++ +QIDGVLHE S+I GV ED+T IILN+K + LK   D  K   I
Sbjct: 1   LRRVLLTSIPGTALSYIQIDGVLHEFSTIPGVREDVTKIILNLKKLELKSLSDEEKIAEI 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
              GP +VTA D++  +DIEVLNPD  IC++     + M + +  G GYVPA  ++T++ 
Sbjct: 61  DVTGPAIVTAADLKVDSDIEVLNPDQYICSIADGGHLHMNVAIKTGRGYVPASENKTDDM 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           PIG+I +D+L+SPIKKV+Y VESAR G+  DYDKL++ I TDGSIT  D+++ A++IL +
Sbjct: 121 PIGVIPVDSLFSPIKKVNYQVESARVGKRDDYDKLTLEIWTDGSITPNDALSFAAKILVE 180

Query: 227 QLGMF 231
              +F
Sbjct: 181 HFKVF 185


>gi|190411123|gb|ACE78316.1| RpoA [Vibrio parahaemolyticus]
          Length = 243

 Score =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 106/246 (43%), Positives = 163/246 (66%), Gaps = 8/246 (3%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVT 105
           LRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T
Sbjct: 1   LRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFIT 60

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HH 161
           + K G G V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H+
Sbjct: 61  LNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHN 120

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
             +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+
Sbjct: 121 EEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAA 180

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
            IL +QL  F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+
Sbjct: 181 TILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYI 237

Query: 282 GDLIQR 287
           GDL+QR
Sbjct: 238 GDLVQR 243


>gi|86438816|emb|CAJ43373.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 203

 Score =  224 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 86/203 (42%), Positives = 129/203 (63%)

Query: 48  RRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF 107
           RRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   D  K + + 
Sbjct: 1   RRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSFSDERKVIELD 60

Query: 108 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
             GP  VTA D++   D++VLNPD  IC +     + ME+ V  G GYV A  +++++ P
Sbjct: 61  VEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNGRGYVAASDNKSDDMP 120

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           IG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++ A++IL + 
Sbjct: 121 IGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEH 180

Query: 228 LGMFINFEEPKKEVKEDINVKSL 250
             +F + +   K  +  +  +  
Sbjct: 181 FKVFESADADTKFSEVMVEKEDD 203


>gi|152993919|ref|YP_001359640.1| DNA-directed RNA polymerase subunit alpha [Sulfurovum sp. NBC37-1]
 gi|172048748|sp|A6QCS4|RPOA_SULNB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|151425780|dbj|BAF73283.1| DNA-directed RNA polymerase, alpha subunit [Sulfurovum sp. NBC37-1]
          Length = 333

 Score =  224 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 92/327 (28%), Positives = 159/327 (48%), Gaps = 6/327 (1%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  +E   + +   NR  ++A P   G+A TL + LRR+++ S  G A  +V+I+G  HE
Sbjct: 11  PTEVE---VNEISANRAEIVAYPFESGYAVTLAHPLRRLILGSSIGYAPISVKIEGAAHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
             +I+G+HED+   I+N+K I  K+  G     +     G   VTA D+     IEV+N 
Sbjct: 68  FDNIRGMHEDVAVFIINLKNIRFKIKDGSDRVELKYSFSGYKEVTAQDLNND-QIEVVNG 126

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  +  L+ DA +   + ++KG GYVP++  R E  P   I +DA ++P++K +Y +E  
Sbjct: 127 DLPLATLNEDAELNFTMVIAKGIGYVPSEDLRDEVAP-DSIALDAFFTPVRKANYKIEPV 185

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
                 +++K++  I+TD  I   ++   A  ++  QL +F    +              
Sbjct: 186 LVEDNPNFEKITFDIETDAQIGPVEAFTNALEVMNKQLSVFNGVLDVDISTTLPKRTNDD 245

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 L  V+ L LS RS N L    I ++G+L+  +E ++  + N G+KSL E    L
Sbjct: 246 NELKPFLAAVDALGLSARSFNSLDRAGIKFLGELVLMSENEIKNIKNLGKKSLDETNECL 305

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKYE 337
              G      L +    ++ +  ++ +
Sbjct: 306 VEHGFGPEFELKENTRANLVKKLEQLK 332


>gi|322378754|ref|ZP_08053183.1| DNA-directed RNA polymerase subunit alpha [Helicobacter suis HS1]
 gi|322380603|ref|ZP_08054755.1| DNA-directed RNA polymerase subunit alpha [Helicobacter suis HS5]
 gi|321146925|gb|EFX41673.1| DNA-directed RNA polymerase subunit alpha [Helicobacter suis HS5]
 gi|321148784|gb|EFX43255.1| DNA-directed RNA polymerase subunit alpha [Helicobacter suis HS1]
          Length = 337

 Score =  224 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 91/332 (27%), Positives = 163/332 (49%), Gaps = 12/332 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P +I    LG   +    +       G+A TL + LRR+L+ S  G A  A++I+GV HE
Sbjct: 12  PTDIRVERLG---DRGIRVSVSAFESGYAITLAHPLRRLLLQSSVGFAPIAIKIEGVAHE 68

Query: 72  ISSIKGVHEDLTDIILNIKGINLKM----SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
             S++G+ ED+   I N+K I L      + +    V     GP  ++  D+ T  ++EV
Sbjct: 69  FDSVRGMAEDVALFIANLKNIRLVAKNLENAEDQLVVHYSFNGPAKLSGKDLATE-EVEV 127

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           ++ +  +  ++ D  +   L + KG GYVP++  R        I +DA ++PIKK  Y +
Sbjct: 128 VDTETYLATINEDGQLGFSLIIQKGMGYVPSESIRGFISSDY-IPLDACFTPIKKAIYHI 186

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+       +++K+   I++DG +  + +   A + +  Q+ +F        + K   ++
Sbjct: 187 ENILVDGNPNFEKVIFEIESDGQVDPKQAFQEAIKTMHAQMHIF---STNLSDSKNAYHL 243

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           ++      L+KKVE+L+LS R  NCL    I Y+G+L+     ++  + N G+KS  EI 
Sbjct: 244 ENNLEIKELIKKVEDLDLSARCLNCLDKVGIKYIGELVLMDVYELKGIKNLGKKSYDEIA 303

Query: 308 GVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             L  +   +G  LP+    S++    K + +
Sbjct: 304 EKLEQLKYPVGQELPEGFKASLKARIDKLKSE 335


>gi|150186942|emb|CAK30133.1| RNA polymerase alpha subunit [Streptococcus canis]
          Length = 204

 Score =  224 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 86/204 (42%), Positives = 138/204 (67%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           +LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + 
Sbjct: 1   SLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKIIE 60

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
           +   GP  VTAGDI T +DIE++NPDH +  +     +R  +TV+K  GYVPA+ ++ ++
Sbjct: 61  LEVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLRATMTVAKKRGYVPAEGNKKDD 120

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
            P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L 
Sbjct: 121 APVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLI 180

Query: 226 DQLGMFINFEEPKKEVKEDINVKS 249
           + L +F +  +  K  +     ++
Sbjct: 181 EHLNLFTDLTDVAKATEVMKETET 204


>gi|162955842|gb|ABY25296.1| RNA polymerase alpha subunit [Vibrio sp. MSSRF7]
          Length = 240

 Score =  224 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 100/222 (45%), Positives = 149/222 (67%), Gaps = 5/222 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV ED
Sbjct: 1   QISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQED 60

Query: 82  LTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           + +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E++NP+HVIC+L+ D
Sbjct: 61  ILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLNDD 120

Query: 141 -AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
            A V M + V +G GYVPA    H   ++ PIG + +DA YSP+ K++YTVE+AR  Q  
Sbjct: 121 NAEVAMRIKVQRGRGYVPASARIHTDEDDRPIGRLLVDATYSPVDKIAYTVEAARVEQRT 180

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + +
Sbjct: 181 DLDKLVIDMETNGTIEPEEAIRRAATILAEQLDAFVDLRDVR 222


>gi|47679547|gb|AAT36717.1| RNA polymerase alpha subunit [Corethron hystrix]
          Length = 301

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 87/282 (30%), Positives = 143/282 (50%), Gaps = 3/282 (1%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
                   L  G   T+G  LRR L+S L   AIT V+I GV +E S I+GV ED+ +++
Sbjct: 21  YGQFQINDLNPGQGITIGTVLRRFLLSELNATAITGVRIAGVNNEFSIIEGVREDVLELL 80

Query: 87  LNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           LN++ I +K + D    K   +  +GP V+TA  IQ   ++E+LNP+  I  +    ++ 
Sbjct: 81  LNLRPIVIKNNSDNSEMKFGRLKVQGPAVITANAIQLPTELEILNPNQYIATISRSMILE 140

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           ME     G GY      + E      + IDA++ P++KV + VE+  +      + L + 
Sbjct: 141 MEFKFESGIGYRLVNQTKME-SSSDFLEIDAVFMPVQKVDFKVENIYDKNKHISENLIID 199

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           I T+GSI+ E ++  +S  + +     I  +  K+ ++       +         +EEL+
Sbjct: 200 IWTNGSISPETALYESSNNIIELFNSLIENKFKKEILEPLPENTRINSENHTNISIEELQ 259

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           LSVRS NCL+   I  + DL++ +   +  + NFGRKS  E+
Sbjct: 260 LSVRSYNCLKRAQINSISDLLKYSPEKLQEIKNFGRKSADEV 301


>gi|150187122|emb|CAK30175.1| RNA polymerase alpha subunit [Streptococcus lutetiensis]
          Length = 201

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 88/201 (43%), Positives = 135/201 (67%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           +LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + 
Sbjct: 1   SLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIE 60

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
           +   GP  VTAGDI T +D+E++NPDH +  +     ++  +TV+K  GYVPA+ ++ E+
Sbjct: 61  LDVEGPAEVTAGDILTDSDVEIVNPDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKED 120

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
            P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L 
Sbjct: 121 APVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLI 180

Query: 226 DQLGMFINFEEPKKEVKEDIN 246
           + L +F +  E  K       
Sbjct: 181 EHLNLFTDLTEVAKNTDVMKE 201


>gi|315451273|gb|ADU24721.1| RNA polymerase alpha subunit [Lactobacillus sp. YM 0097]
          Length = 212

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 82/201 (40%), Positives = 135/201 (67%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL++SL G A++ +QIDGVLHE S+I GV ED+T I+LN+K + LK   +   + 
Sbjct: 1   NSLRRVLLASLPGTAVSDIQIDGVLHEFSAIDGVIEDVTQIVLNVKKLKLKSYAEDSLKA 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  VTA DI+  +D+E+L+P+  IC +       M++T+  G GY PA+ ++T+
Sbjct: 61  EVDIVGPATVTAKDIKADDDLEILDPEQFICTVAEGGHFHMQMTIKNGRGYTPAEQNKTD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
             PIG++ +D++++P++KV+Y VE+ R G+  D+DKL++ I T+GSI   ++++L+++IL
Sbjct: 121 ETPIGVLPVDSIFTPVEKVNYQVENTRVGKRNDFDKLTIDIWTNGSIGPREAISLSAKIL 180

Query: 225 QDQLGMFINFEEPKKEVKEDI 245
            + L  F+N  E  K     I
Sbjct: 181 TEHLNSFVNLTEEAKSADMMI 201


>gi|119662357|emb|CAJ33167.1| RNA polymerase alpha subunit [Lactobacillus salivarius]
          Length = 194

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 90/194 (46%), Positives = 136/194 (70%), Gaps = 2/194 (1%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRR+L+SSL GAAIT VQIDGVLHE S+I GV ED+T IILN+K + L M  +  + + I
Sbjct: 1   LRRILLSSLPGAAITDVQIDGVLHEFSTIPGVLEDVTLIILNLKKVALSMESEDSQALEI 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TE 164
              GP  VTAGDIQ+ +D+EVLNP+  IC +   A + + +  +KG GYV A  ++   +
Sbjct: 61  NVTGPMEVTAGDIQSNSDVEVLNPEQYICTVADGAELHVRMNANKGRGYVSANDNKALAD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           + PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T+GSIT  ++++L+++IL
Sbjct: 121 DMPIGVLPIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWTNGSITPSEAISLSAKIL 180

Query: 225 QDQLGMFINFEEPK 238
            + L +F++  +  
Sbjct: 181 TEHLALFVDLTDEA 194


>gi|228017206|gb|ACP52026.1| RNA polymerase alpha subunit [Pinus leiophylla var. chihuahuana]
          Length = 335

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 77/329 (23%), Positives = 146/329 (44%), Gaps = 24/329 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   IE     +                   T+G A+RR L+  + G  IT V+++ + 
Sbjct: 13  LRWKCIESRAYSKRLH-YGRFXXXXXXXXXXDTIGIAMRRALLGEVEGTCITRVKLENIK 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++
Sbjct: 72  HEYSAIIGIEESVHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIID 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L       + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S
Sbjct: 132 TTQHIARLTKSITSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--- 246
              G  +  + L + I T+G +T  +++  ASR L D    F++ EE   +   +     
Sbjct: 189 YGSGNEI-REVLFLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSN 247

Query: 247 -------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                         ++       L  +++L         LR  NI  + DL+  +  D++
Sbjct: 248 MLPFPLSHLLTDTGETKEKIAFQLIFIDQLXXXXXXXXXLRRANIHTLLDLLNYSREDLM 307

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           R+ +FG++S+ ++  VL  +     ++ P
Sbjct: 308 RIEHFGKESVEQVLEVLQKL---FAIDPP 333


>gi|218176272|ref|YP_002364529.1| RNA polymerase alpha subunit [Festuca arundinacea]
 gi|215882356|gb|ACJ70786.1| RNA polymerase alpha subunit [Festuca arundinacea]
          Length = 346

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 82/301 (27%), Positives = 145/301 (48%), Gaps = 34/301 (11%)

Query: 48  RRVL-------MSSLRGAAITA--VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           RRVL       +  + G  + A   +   V HE S+I G+ E + +I+LN+K I L+ + 
Sbjct: 46  RRVLALGRGFNLEKIEGNNVLATRAKFGSVPHEYSTIAGIEESVQEILLNLKEIVLRSNL 105

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
              +  +I  +GP  +TA DI     +E+++    I NL       +EL + +  GY   
Sbjct: 106 YGVRDASISVKGPRYITAQDIILPPSVEIVDTSQPIANLTEPIDFCIELQIKRDRGYQTE 165

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
                +N   G   IDA+  P++ V+Y++ S   G    ++ L + I T+GS+T ++++ 
Sbjct: 166 LR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNG-NEKHEILFLEIWTNGSLTPKEALY 221

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLP------------------FNPALLKKV 260
            ASR L D    F++ EE     +E+ N  + P                    P     +
Sbjct: 222 EASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKRLTNLNLKKNKKGIPLNCIFI 281

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           ++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    + + K +  T+  +L ++
Sbjct: 282 DQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSFH---MEDGKQIWDTLEKYLPID 338

Query: 321 L 321
           L
Sbjct: 339 L 339


>gi|229915452|gb|ACQ90797.1| alpha subunit of RNA polymerase [Oocystis solitaria]
          Length = 356

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 85/341 (24%), Positives = 161/341 (47%), Gaps = 36/341 (10%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           + + +      I  P   G   TL N+LRR L+S + G AI A++I+G LHE S++ GV 
Sbjct: 19  IEENKNFYGRFILGPFEVGQGLTLANSLRRTLLSEISGLAIVAMEIEGALHEYSNLPGVQ 78

Query: 80  EDLTDIILNIKGINL--KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           E + DI+LN+K I L  +   D      +  +GPG+VTA D++  + I+ ++P   I  L
Sbjct: 79  ESILDILLNLKQIVLVSRFEMDQPVFGFLKVQGPGIVTASDLKLPSSIQCVDPHQYIATL 138

Query: 138 DVDAVVRMELTVSKGHGYV--------------------------PAKHHRTENDPIGLI 171
             +  + ++  V +   Y+                            K +   N    ++
Sbjct: 139 SYNGFLSIKFFVCQKKNYIFLKNASLKKKKIYKLKKNKIQSPILEKKKSNFLINKTSNVV 198

Query: 172 TIDALYSPIKKVSYTVESAREG-QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           +ID  +  + KV+Y +E+          +++ + I T+GS+    ++  A++ + +    
Sbjct: 199 SIDPNFFSVNKVNYLIETCSLFLFEKPKEQIFLEIWTNGSLHPRQAINEAAKRIVNIFSP 258

Query: 231 FIN---FEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
           F     ++  + +  +  ++K   F       +  L+LS+RS  CL+  NI  + +L+Q 
Sbjct: 259 FQETRFYKPGRLKSSKLFSLKRENFKKFTSLDIANLDLSLRSYTCLKRANIHTIDNLLQY 318

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPES 328
           +  ++L + NFG +SL E+  +L  +GL    NL D+  ++
Sbjct: 319 SSEELLLLKNFGTRSLEEVLNILQQIGL----NLRDFDKDT 355


>gi|168805075|gb|ACA28616.1| DNA-directed RNA polymerase subunit alpha [Thiomonas perometabolis]
          Length = 228

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 100/228 (43%), Positives = 149/228 (65%), Gaps = 3/228 (1%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           G+ ED+  ++LN+KG+ LK+       +++ K G GVVTA DIQT +D+E++NPDHVI +
Sbjct: 1   GLQEDVIGVLLNLKGVVLKLHNRDEVTLSLRKEGEGVVTAADIQTPHDVEIINPDHVIAH 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSYTVESAREG 193
           L     + M++ V KG GYVP        +    IG I +DA +SP+++VSY VESAR  
Sbjct: 61  LSQGGKLDMQIKVEKGRGYVPGTLRNFGEEGGKSIGHIVLDASFSPVRRVSYAVESARVE 120

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL M I+T+G I+ E+++  ++RIL +QL +F + E  +     +    +  ++
Sbjct: 121 QRTDLDKLVMEIETNGVISAEEAIRSSARILVEQLSVFASLEGAEATEAAEAAAGAQTYD 180

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GRK
Sbjct: 181 PILLRPVDELELTVRSANCLKAENIYYIGDLIQRSETELLKTPNLGRK 228


>gi|168805065|gb|ACA28611.1| DNA-directed RNA polymerase subunit alpha [Thiomonas sp. CB1]
 gi|168805067|gb|ACA28612.1| DNA-directed RNA polymerase subunit alpha [Thiomonas sp. 3As]
 gi|168805069|gb|ACA28613.1| DNA-directed RNA polymerase subunit alpha [Thiomonas sp. CB3]
 gi|168805071|gb|ACA28614.1| DNA-directed RNA polymerase subunit alpha [Thiomonas sp. CB6]
 gi|168805073|gb|ACA28615.1| DNA-directed RNA polymerase subunit alpha [Thiomonas sp. CB2]
          Length = 228

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 100/228 (43%), Positives = 148/228 (64%), Gaps = 3/228 (1%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           G+ ED+  ++LN+KG+ LK+       +++ K G GVVTA DIQT +D+E++NPDHVI +
Sbjct: 1   GLQEDVIGVLLNLKGVVLKLHNRDEVTLSLRKEGEGVVTAADIQTPHDVEIINPDHVIAH 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSYTVESAREG 193
           L     + M++ V KG GYVP        +    IG I +DA +SP+++VSY VESAR  
Sbjct: 61  LSQGGKLDMQIKVEKGRGYVPGTLRNFGEEGGKSIGHIVLDASFSPVRRVSYAVESARVE 120

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL M I+T+G I+ E+++  ++RIL +QL +F + E  +     +       ++
Sbjct: 121 QRTDLDKLVMEIETNGVISAEEAIRSSARILVEQLSVFASLEGAETTEAAEAAAGGQTYD 180

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GRK
Sbjct: 181 PILLRPVDELELTVRSANCLKAENIYYIGDLIQRSETELLKTPNLGRK 228


>gi|295809866|emb|CBL85109.1| alpha subunit of RNA polymerase [Vibrio tapetis]
          Length = 247

 Score =  222 bits (566), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 104/250 (41%), Positives = 161/250 (64%), Gaps = 8/250 (3%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGV 113
           + G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +K+  G     +T+ K G G 
Sbjct: 1   MPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVKVAEGKDEVFITLNKSGSGP 60

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHH---RTENDPIG 169
           V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA        +  PIG
Sbjct: 61  VVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASSRIHTEEDERPIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  ++ IL +QL 
Sbjct: 121 RLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRSATILAEQLD 180

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
            F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDIRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMANFG 299
            ++L+  N G
Sbjct: 238 VELLKTPNLG 247


>gi|150036722|emb|CAM98252.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. dextranicum]
          Length = 189

 Score =  222 bits (566), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 85/188 (45%), Positives = 125/188 (66%), Gaps = 2/188 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A
Sbjct: 61  DDERSLEIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSA 120

Query: 159 KHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+
Sbjct: 121 DENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTNGSIKPSDA 180

Query: 217 VALASRIL 224
           ++L ++IL
Sbjct: 181 LSLGAKIL 188


>gi|195973804|gb|ACG63467.1| DNA-directed RNA polymerase subunit alpha [Francisella noatunensis
           subsp. orientalis]
 gi|225624845|gb|ACN96557.1| RpoA [Francisella noatunensis subsp. orientalis]
          Length = 290

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 103/283 (36%), Positives = 166/283 (58%), Gaps = 7/283 (2%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
            +   P+ +G AH LGN++RR L+SSL GA+I  V I GVLHE S+++ V ED+ +I+ N
Sbjct: 13  KIQVSPVEKGMAHILGNSIRRFLLSSLSGASIIKVNISGVLHEYSTLEDVKEDVVEIVSN 72

Query: 89  IKGINLKMSGDSHKR-VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           +K + +K+  +  K  + +     GVVTAGD +T   IE++N D  I  L  +    +  
Sbjct: 73  LKKVAIKLDKNVSKVELELSVTKSGVVTAGDFKTTQGIEIINKDQPIATLTNEREFSLVA 132

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           TVS G          TE + +G I +DA ++PIK+V++ +           + L + + T
Sbjct: 133 TVSVGRNVGILSALPTELEKVGDIAVDADFNPIKRVAFEIFDNGAS-----ETLEVFVKT 187

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           +G+I    +V  A +   +Q+ +F++   P      D  + S   +P LLK +++LEL+V
Sbjct: 188 NGTIESLAAVTKALKYFCEQISVFVSLRVPSNGKTGDALLDSN-IDPILLKPIDDLELTV 246

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           RS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L
Sbjct: 247 RSSNCLRAENIKYLGDLVQYSESQLIKIPNLGKKSLNEIKQIL 289


>gi|154424829|emb|CAL18517.1| RNA polymerase alpha subunit [Streptococcus alactolyticus]
          Length = 200

 Score =  222 bits (565), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 86/200 (43%), Positives = 133/200 (66%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +
Sbjct: 1   LRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIEL 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
              GP  VTAGDI T +D+E++N DH +  +     ++  +TV+K  GYVPA+ ++ ++ 
Sbjct: 61  DVEGPAEVTAGDILTDSDVEIVNSDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKDDA 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L +
Sbjct: 121 PVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIE 180

Query: 227 QLGMFINFEEPKKEVKEDIN 246
            L +F +  E  K       
Sbjct: 181 HLNLFTDLTEVAKNTDVMKE 200


>gi|168805061|gb|ACA28609.1| DNA-directed RNA polymerase subunit alpha [Thiomonas sp. Ynys1]
          Length = 228

 Score =  222 bits (565), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 99/228 (43%), Positives = 150/228 (65%), Gaps = 3/228 (1%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           G+ ED+  ++LN+KG+ LK+       +++ K G GVVTA DIQT +D+E++NP+HVI +
Sbjct: 1   GLQEDVIGVLLNLKGVVLKLHNRDEVTLSLRKDGEGVVTAADIQTPHDVEIINPEHVIAH 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSYTVESAREG 193
           L     + M++ V KG GYVP       ++    IG I +DA +SP+++VSY VESAR  
Sbjct: 61  LSHGGKLDMQIKVEKGRGYVPGTLRNYGDEGGKSIGHIVLDASFSPVRRVSYAVESARVE 120

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL M I+T+G I+ E+++  ++RIL +QL +F + E  +     +    +  ++
Sbjct: 121 QRTDLDKLVMEIETNGVISAEEAIRSSARILVEQLSVFASLEGAETTETAEAAAGAQTYD 180

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GRK
Sbjct: 181 PILLRPVDELELTVRSANCLKAENIYYIGDLIQRSETELLKTPNLGRK 228


>gi|154424857|emb|CAL18531.1| RNA polymerase alpha subunit [Streptococcus sanguinis]
          Length = 194

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 87/194 (44%), Positives = 131/194 (67%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL++SL GAA+T++ I+GVLHE  +I GV ED+  IILN+KGI +K      K +
Sbjct: 1   NSLRRVLLASLPGAAVTSINIEGVLHEFDTISGVREDVMQIILNVKGIAVKSYVQDEKII 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  VTAGDI T +DIE++NPDH +  +   A  +  +TV+ G GYVPA  ++ +
Sbjct: 61  ELDVEGPAEVTAGDILTDSDIEIINPDHYLFTIGEGASFKATMTVNSGRGYVPADENKKD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           + P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL
Sbjct: 121 DAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARIL 180

Query: 225 QDQLGMFINFEEPK 238
            + L +F N  E  
Sbjct: 181 TEHLNLFTNLTEVA 194


>gi|154424837|emb|CAL18521.1| RNA polymerase alpha subunit [Streptococcus pluranimalium]
          Length = 204

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 84/203 (41%), Positives = 134/203 (66%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ +K   +  K + +
Sbjct: 1   LRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNVKGLAVKSYVEDEKIIEL 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
             +GP  VTAGDI T +DIE++N DH +  +   A  +  +TV+   GYV A+ ++ ++ 
Sbjct: 61  DVQGPAEVTAGDILTDSDIEIVNSDHYLFTIAEGASFKASMTVATNRGYVAAEGNKKDDA 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L +
Sbjct: 121 PVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTVEIMTNGTIIPEDALGLSARVLIE 180

Query: 227 QLGMFINFEEPKKEVKEDINVKS 249
            L +F +  E  K        +S
Sbjct: 181 HLNLFTDLTEVAKATDVMKETES 203


>gi|150036836|emb|CAM98283.1| DNA-directed RNA polymerase alpha chain [Leuconostoc fallax]
          Length = 215

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 85/205 (41%), Positives = 131/205 (63%), Gaps = 2/205 (0%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T +ILN+K + L +  D  K + I
Sbjct: 1   LRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVVLAIDSDEEKSLEI 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--E 164
             +GP  VTA D+Q   DIEVLNP+  +  +     + M +T  KG GY  A  ++   +
Sbjct: 61  DVQGPAEVTAADLQGSADIEVLNPELHLATVAAGKSLHMTVTAVKGRGYSSADENKQLRD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
             PIG++ +D++Y+PI++V+Y VE+ R GQ  DYDKL+  I T+GSI   D+++L ++IL
Sbjct: 121 EMPIGVLAVDSIYTPIERVNYQVENTRVGQRDDYDKLTFDIWTNGSIKPSDALSLGAKIL 180

Query: 225 QDQLGMFINFEEPKKEVKEDINVKS 249
            + L +F +      E +  ++V+ 
Sbjct: 181 SEHLNLFTDISSVAAETEVMVDVEQ 205


>gi|237751462|ref|ZP_04581942.1| DNA-directed RNA polymerase subunit alpha [Helicobacter bilis ATCC
           43879]
 gi|229372828|gb|EEO23219.1| DNA-directed RNA polymerase subunit alpha [Helicobacter bilis ATCC
           43879]
          Length = 337

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 90/333 (27%), Positives = 168/333 (50%), Gaps = 5/333 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++P   E + + +   N   + A P    +A T+ + +RR+L+SS  G A   ++I+GV 
Sbjct: 6   VRPYIPEKLEIEEIAPNHIRLHAYPFEPHYAVTIAHPVRRLLLSSSVGYAPIGIKIEGVR 65

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVT-AGDIQTVNDIE 126
           HE  +++GV ED+   I+NIK +  K++ D   H++  +     G +   G+  +  +I 
Sbjct: 66  HEFDTVRGVAEDVAPFIVNIKNLKFKVNEDMQQHEKFELHYEFNGPMELRGEHLSNENIT 125

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           VL+ D  + N++ DA ++  + + KG G+V ++  R E      I +DA ++P+K+  Y 
Sbjct: 126 VLSTDSHLANINSDAKLKFSILIHKGLGFVASETIREEIGSEY-IPLDADFTPVKRAVYD 184

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           +E+       +++K+   ++T+G I   ++   A  I+  Q+ +F   E           
Sbjct: 185 IENVLHESNPNFEKIVFEVETNGQIEPMEAFKEAVAIMHSQMSVF-GAELSDVPTSNGRL 243

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
               P    LL  VE L L  R +NCL+  NI Y+G+L+   E+D+  + N G++S  EI
Sbjct: 244 NDDSPELKVLLSSVEILNLEHRPSNCLQKSNIKYIGELVLMNESDLKNIKNLGKRSFDEI 303

Query: 307 KGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
              L  +G  +G +LP     ++ +   K + +
Sbjct: 304 TAKLNEVGYAVGADLPHELATTLSKRLAKLKGQ 336


>gi|289803215|ref|ZP_06533844.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. AG3]
          Length = 222

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 99/223 (44%), Positives = 149/223 (66%), Gaps = 7/223 (3%)

Query: 113 VVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPI 168
           VVTA DI    D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PI
Sbjct: 2   VVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPI 61

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           G + +DA YSP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL
Sbjct: 62  GRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQL 121

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
             F++  + ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRT
Sbjct: 122 EAFVDLRDVRQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRT 178

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           E ++L+  N G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 179 EVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 221


>gi|307128729|ref|YP_003880759.1| DNA-directed RNA polymerase subunit alpha [Candidatus Sulcia
           muelleri CARI]
 gi|306483191|gb|ADM90061.1| DNA-directed RNA polymerase subunit alpha [Candidatus Sulcia
           muelleri CARI]
          Length = 335

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 107/322 (33%), Positives = 177/322 (54%), Gaps = 12/322 (3%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           E +++ +          EPL  G+  T+GN+LRRVL+SSL G AI++V+I+GV +E S+I
Sbjct: 10  ENLIILKLTPEEGSFKIEPLYPGWGLTIGNSLRRVLLSSLEGYAISSVKIEGVNNEYSTI 69

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKRV-----TIFKRGPGVVTAGDI-QTVNDIEVLN 129
           KGV ED+T+IILN+K I  K   +           I       +TAGD+ + +N  E++N
Sbjct: 70  KGVIEDMTEIILNLKKIRFKKKIEDEDFESEEFHIIINNNKKEITAGDLGEFLNLFEIIN 129

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD +I N +    + + L + +G GY+P++ ++   + IG I ID +++PIKKV Y +++
Sbjct: 130 PDLIILNKEKLISLNITLVIKRGIGYLPSEKNKDMPNMIGTIPIDTIFTPIKKVKYKIDN 189

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDI 245
               +   Y+ + + I TDGSI    ++  AS +L        N     E  K + +   
Sbjct: 190 CSINKNPFYESIILKIKTDGSINPRKALTRASNLLIRHFQCLSNEKILLEYKKPKKRNKY 249

Query: 246 NVKSLPFNPALLKKVEEL--ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   L     L   +EE    LSVR+ NCL+   I   GDL++  ++D+L++ NFGRKSL
Sbjct: 250 DKNILKMRNLLKSSLEEEIDYLSVRTLNCLKSAKIFTWGDLVKSNKSDLLKLKNFGRKSL 309

Query: 304 VEIKGVLGTMGLFLGMNLPDWP 325
            E+   +  + ++ GM++  + 
Sbjct: 310 SELDKRMKKLNIYSGMDISIYK 331


>gi|119668349|emb|CAK95511.1| RNA polymerase alpha subunit [Lactobacillus paraplantarum]
          Length = 177

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 91/177 (51%), Positives = 127/177 (71%), Gaps = 2/177 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK+  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTAIILNVKKIALKLES 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A   M +T + G GYV A
Sbjct: 61  DETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGAHFHMRMTANTGRGYVSA 120

Query: 159 KHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           + ++   ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T+GSIT 
Sbjct: 121 EDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWTNGSITP 177


>gi|317447066|emb|CBX24362.1| DNA-directed RNA polymerase subunit alpha [Thiomonas perometabolis]
          Length = 201

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 94/201 (46%), Positives = 134/201 (66%), Gaps = 3/201 (1%)

Query: 28  TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIIL 87
           + ++ EP  RG+ HTLGNALRRV++SSL G A T V I+GVLHE S + G+ ED+  ++L
Sbjct: 1   SKVVLEPFERGYGHTLGNALRRVMLSSLVGYAPTEVSINGVLHEYSVVDGLQEDVIGVLL 60

Query: 88  NIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           N+KG+ LK+       +++ K G GVVTA DIQT +D+E++NPDHVI +L     + M++
Sbjct: 61  NLKGVVLKLHNRDEVTLSLRKEGEGVVTAADIQTPHDVEIINPDHVIAHLSQGGKLDMQI 120

Query: 148 TVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
            V KG GYVP        +    IG I +DA +SP+++VSY VESAR  Q  D DKL M 
Sbjct: 121 KVEKGRGYVPGTLRNFGEEGGKSIGHIVLDASFSPVRRVSYAVESARVEQRTDLDKLVME 180

Query: 205 IDTDGSITGEDSVALASRILQ 225
           I+T+G I+ E+++  ++RIL 
Sbjct: 181 IETNGVISAEEAIRSSARILV 201


>gi|150187043|emb|CAK30158.1| RNA polymerase alpha subunit [Streptococcus anginosus]
          Length = 203

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 86/202 (42%), Positives = 133/202 (65%)

Query: 48  RRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF 107
           RRVL++SL GAA+T++ I+GVLHE  ++ GV ED+  IILN+KGI +K   +  K + + 
Sbjct: 1   RRVLLASLPGAAVTSINIEGVLHEFDTVPGVREDVMQIILNVKGIAVKSYVEDEKTIELD 60

Query: 108 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
             GP  +TAGDI T +DIE++NPDH +  +   A ++  +TV+ G GYVPA  ++ ++ P
Sbjct: 61  VEGPAEITAGDILTDSDIEIVNPDHYLFTIGEGASLKAIMTVNTGRGYVPADENKKDDAP 120

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           +G + +D++Y+P+KKV+Y VE AR G    +DKL++ I TDG+I  ED++ L++RIL + 
Sbjct: 121 VGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTLEIMTDGTIIPEDALGLSARILTEH 180

Query: 228 LGMFINFEEPKKEVKEDINVKS 249
           L +F N  E  K        + 
Sbjct: 181 LDLFTNLTEVAKSTDVMKETEK 202


>gi|90567617|emb|CAJ31076.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
 gi|119662365|emb|CAJ33171.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 193

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 86/192 (44%), Positives = 126/192 (65%)

Query: 48  RRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF 107
           RRVL++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   D  K + + 
Sbjct: 1   RRVLLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSFSDERKVIELD 60

Query: 108 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
             GP  VTA D++   D++VLNPD  IC +     + ME+ V  G GYV A  +++++ P
Sbjct: 61  VEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNGRGYVAASDNKSDDMP 120

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           IG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++ A++IL + 
Sbjct: 121 IGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEH 180

Query: 228 LGMFINFEEPKK 239
             +F + +   K
Sbjct: 181 FKVFESADADTK 192


>gi|150186939|emb|CAK30132.1| RNA polymerase alpha subunit [Streptococcus equinus]
          Length = 185

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 87/185 (47%), Positives = 132/185 (71%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   
Sbjct: 1   YGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYV 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  K + +   GP  VTAGDI T +D+E++NPDH +  +     ++  +TV+K  GYVPA
Sbjct: 61  DDEKIIELDVEGPAEVTAGDILTDSDVEIVNPDHYLFTIAEGHSLKATMTVAKKRGYVPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           + ++ E+ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ 
Sbjct: 121 EGNKKEDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALG 180

Query: 219 LASRI 223
           L++R+
Sbjct: 181 LSARV 185


>gi|119668367|emb|CAK95476.1| RNA polymerase alpha subunit [Lactobacillus rhamnosus]
          Length = 198

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 82/198 (41%), Positives = 129/198 (65%)

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
           AA++++QIDGVLHE S+I GV ED+T IILNIK + LKM+ D  K + I   GP  VTA 
Sbjct: 1   AAVSSIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKMNTDEDKNIEIDVNGPAKVTAA 60

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI    D+EVLNP+  IC +       + +TV KG GYV A  +++++ PIG++ ID+++
Sbjct: 61  DIVADPDVEVLNPEQYICTVADGGHFHVRMTVKKGRGYVAADQNKSDDMPIGVLPIDSIF 120

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           +PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++IL + L +F+N  + 
Sbjct: 121 TPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKILTEHLDIFVNLTDE 180

Query: 238 KKEVKEDINVKSLPFNPA 255
            K  +  +  +       
Sbjct: 181 AKNAEIMVEKEETHKEKM 198


>gi|293363953|ref|ZP_06610689.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma alligatoris
           A21JP2]
 gi|292552443|gb|EFF41217.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma alligatoris
           A21JP2]
          Length = 334

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 87/330 (26%), Positives = 159/330 (48%), Gaps = 19/330 (5%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
            ++  K + +E        +     I +PL RGF  TLG ALRRVL+S++   A   V+I
Sbjct: 1   MEKFQKLDYLEVPSNSNTSDFENKFIIQPLERGFGTTLGVALRRVLLSNITSLAPFCVRI 60

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMS-----GDSHKRVTIFKRGPGVVTAGDIQ 120
           +GV HE   I+GV ED+  +I+N++ +           D   RV +     G + +  ++
Sbjct: 61  EGVTHEFRGIEGVVEDVPSLIMNLRKVRFSYDPELVKDDDIIRVELKADQVGEINSRYLE 120

Query: 121 TVN--DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR-----------TENDP 167
            V+  ++EV++ +  I  +  +  +R+EL +  G G+V ++ ++           T+   
Sbjct: 121 VVDNLNVEVIDHNVHIAEVSQENALRLELYLRPGRGFVSSEENKALVSKLEAQLETKIKK 180

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
              I +D+ +SP++KV+Y V       +   +KL   + TDG++  +D++  A+ IL   
Sbjct: 181 GKFIAVDSNFSPVEKVNYVVSELNSSSIKIEEKLEFNVYTDGTVKPKDAIKQAADILIAH 240

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
                N +E + ++ E  +   +  N      + +L LSVRS N LR      + D+ + 
Sbjct: 241 FKEIGNVDEIRNDIFETAD-DKITDNQETDIDITQLGLSVRSLNALRRIGRTKVSDISKM 299

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +  ++ +  N G+KSL EI   +   G  L
Sbjct: 300 SYEELEQTKNLGKKSLDEIVQKIKEHGFEL 329


>gi|161511753|emb|CAP16887.1| DNA-directed RNA polymerase subunit alpha [Pediococcus damnosus]
          Length = 211

 Score =  220 bits (561), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 92/211 (43%), Positives = 139/211 (65%), Gaps = 3/211 (1%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+   V +  + GAA+T++QIDGVLHE SSI+GV ED+T IILNIK ++LK+  D  K
Sbjct: 2   LGNSCV-VFVVIITGAAVTSIQIDGVLHEFSSIEGVVEDVTQIILNIKKVSLKIESDDEK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A  ++
Sbjct: 61  SLEIDVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAILTADTGRGYVSADENK 120

Query: 163 --TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
              ++ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSIT  ++ +L+
Sbjct: 121 ARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSITPSEATSLS 180

Query: 221 SRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           ++IL + L +F+N  +  K+ +  +  +   
Sbjct: 181 AKILTEHLALFVNLTDEAKDAEIMVEKEETH 211


>gi|72534426|emb|CAH59048.1| DNA-directed RNA polymerase alpha chain [Enterococcus sp. LMG
           22681]
          Length = 213

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 89/205 (43%), Positives = 130/205 (63%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           L GAAIT +QIDGVLHE S+IKGV ED+  IILNIKG+ LK+ G+  K + I   GP  V
Sbjct: 9   LPGAAITNIQIDGVLHEFSTIKGVREDVAQIILNIKGLALKLYGEDEKTLEIDITGPATV 68

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITID 174
           TAGDI   +D+E+LN D  IC +   A     LTV  G GYV A  ++ ++ PIG++ +D
Sbjct: 69  TAGDIIVDSDVEILNKDMYICTVSEGATFHARLTVKPGRGYVQADENKKDDMPIGVLPVD 128

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           ++Y+P+++V+Y VE+ R G   D+DKL+M I TDGSI   D+++LA++I+ + L +F+N 
Sbjct: 129 SIYTPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIEPLDAMSLAAKIMTEHLDIFVNL 188

Query: 235 EEPKKEVKEDINVKSLPFNPALLKK 259
            +  K  +  +  +       L   
Sbjct: 189 TDEAKNAEIMVEKEETQKEKMLEMT 213


>gi|150186968|emb|CAK30138.1| RNA polymerase alpha subunit [Streptococcus mutans]
          Length = 192

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 87/192 (45%), Positives = 134/192 (69%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   +  K V +
Sbjct: 1   LRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVEEEKIVEL 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
              GP  +TAGDI T +DIE++NPDH +  +   A ++  +TV+   GYVPA+ ++ ++ 
Sbjct: 61  DVEGPAEITAGDILTDSDIEIVNPDHYLFTIAEGANLKATMTVATNRGYVPAEKNKRDDA 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           P+G + ID++Y+P+KKV+Y VE AR G   ++DKL++ I T+G+I  ED++ L++R+L +
Sbjct: 121 PVGTLAIDSIYTPVKKVNYQVEPARVGSNDNFDKLTIEIMTNGTIIPEDALGLSARVLIE 180

Query: 227 QLGMFINFEEPK 238
            L +F +  E  
Sbjct: 181 HLNLFTDLTEVA 192


>gi|224373703|ref|YP_002608075.1| DNA-directed RNA polymerase subunit alpha [Nautilia profundicola
           AmH]
 gi|223588998|gb|ACM92734.1| DNA-directed RNA polymerase, alpha subunit [Nautilia profundicola
           AmH]
          Length = 330

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 96/332 (28%), Positives = 169/332 (50%), Gaps = 8/332 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E++ P+++ +    +EE N+  +   P   GF  ++ + +RR L++S  G A  A++I+
Sbjct: 6   TEVLIPSDVSF----KEEGNKATIEVYPFEAGFGVSVAHPIRRTLIASTPGFAPIALKIE 61

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV HE  S+KG+ ED+   I+N+K I  K+       V     GP  +   D+     ++
Sbjct: 62  GVKHEFDSLKGMLEDVASFIINLKNIRFKIKEGDEAVVDYVFVGPKEIKGSDLAND-LVD 120

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           ++ P+  I  L+ +A +++ L + KG G+V A  +  +  P G I +DA +SPIKKV Y 
Sbjct: 121 IVTPNEYIATLNEEAELKLTLIIRKGMGFV-AVENFRDEIPEGFIGLDAYFSPIKKVVYN 179

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           +E+       +++K+   ++TDG I+  D+   A     +Q  +F   +E K E K   +
Sbjct: 180 IENILVEDDPNFEKVIFEVETDGQISPIDAFKNAVNNYLNQFSVFS--KEFKLEQKTSQS 237

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           V+       L + +E L L  RS N L    I ++G+L+   +  +  + N G KSL EI
Sbjct: 238 VELDEVYNVLFEPIENLNLRSRSFNALDRAGIRFVGELVLMGKEKISNIKNLGTKSLEEI 297

Query: 307 KGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
              L  +G  L   LP    ++IE+   + ++
Sbjct: 298 FDKLEEIGFPLNKTLPLDIKKAIEDKLSQLKE 329


>gi|150036708|emb|CAM98019.1| DNA-directed RNA polymerase alpha chain [Leuconostoc carnosum]
          Length = 199

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 86/197 (43%), Positives = 126/197 (63%), Gaps = 2/197 (1%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + + I
Sbjct: 1   LRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDEERVLEI 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--E 164
             +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++   E
Sbjct: 61  DVQGPSEVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSADENKQLRE 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
             PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L S+IL
Sbjct: 121 EMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSLGSKIL 180

Query: 225 QDQLGMFINFEEPKKEV 241
            + L +F++      E 
Sbjct: 181 AEHLNLFMDISPVAAEA 197


>gi|161511717|emb|CAP16869.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           dextrinicus]
          Length = 205

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 87/192 (45%), Positives = 133/192 (69%)

Query: 54  SLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGV 113
           SL G+A++++QIDGVLHE S+I GV ED+T IILNIK I +K   +  K + I   GP  
Sbjct: 1   SLPGSAVSSIQIDGVLHEFSTIDGVMEDVTQIILNIKKIAIKNHSEEQKVIEIDVDGPAT 60

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITI 173
           VTA DI+  +DIEVLNP+  IC++     V M++TVS G GYVPA  ++  + PIG+I +
Sbjct: 61  VTAADIKADDDIEVLNPEQYICSIAEGGHVHMQMTVSNGRGYVPADQNKNGDMPIGVIAV 120

Query: 174 DALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           D++++PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++IL D L +FI+
Sbjct: 121 DSIFTPINRVNYQVESTRVGKRNDFDKLTLDVWTNGSISPREAISLAAKILSDHLNIFID 180

Query: 234 FEEPKKEVKEDI 245
             +  K  +  +
Sbjct: 181 LSDEAKNTEIMV 192


>gi|315453710|ref|YP_004073980.1| DNA-directed RNA polymerase alpha chain [Helicobacter felis ATCC
           49179]
 gi|315132762|emb|CBY83390.1| DNA-directed RNA polymerase alpha chain [Helicobacter felis ATCC
           49179]
          Length = 336

 Score =  219 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 89/333 (26%), Positives = 158/333 (47%), Gaps = 11/333 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + +  +    +       G+A TL + LRR L+ S  G A   ++++GV HE
Sbjct: 8   PQAPMDISVEKISDRHIKVCVSAFEAGYAITLAHPLRRFLLLSSVGYAPIGIKVEGVNHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINLK-----MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
             S++G+ ED+   I N+K I L       + +    V    +GP  ++  D++   +I 
Sbjct: 68  FDSLRGISEDMALFIANLKNIRLVGKHLDSAQNDQVVVHYTFKGPAKLSGKDLE-NEEIS 126

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           V+N D  +  ++ DA +   L V KG GYVP++  R        I +DA ++PIKKV Y 
Sbjct: 127 VVNHDAYLATINEDAHLEFSLIVQKGMGYVPSESIRGYISSDY-IPLDAYFTPIKKVVYN 185

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           +E+       +++KL   I++DG +  + +   A R +  Q+ +F        + K + +
Sbjct: 186 IENMLVDGNPNFEKLIFEIESDGQVDPQRAFQEAIRTMNAQMHIF---NTNIADYKGNAH 242

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           ++        L ++E L LS R  NCL    + Y+G+L+     ++  + N G+KS  EI
Sbjct: 243 LEEGLERDL-LMEIEGLNLSARCFNCLDKIGLKYVGELVLMDAYELKNIKNLGKKSYDEI 301

Query: 307 KGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
              L  +G  +G  +      S+E    K +++
Sbjct: 302 AEKLEGLGYPVGSEISAEFRASLETKLDKIKNQ 334


>gi|150036732|emb|CAM98257.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. mesenteroides]
          Length = 186

 Score =  219 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 83/186 (44%), Positives = 123/186 (66%), Gaps = 2/186 (1%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  
Sbjct: 1   YGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDS 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A
Sbjct: 61  DDERSLEIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSA 120

Query: 159 KHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+
Sbjct: 121 DENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTNGSIKPSDA 180

Query: 217 VALASR 222
           ++L ++
Sbjct: 181 LSLGAK 186


>gi|150187039|emb|CAK30157.1| RNA polymerase alpha subunit [Streptococcus agalactiae ATCC 13813]
          Length = 188

 Score =  219 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 84/188 (44%), Positives = 133/188 (70%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K +
Sbjct: 1   NSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKII 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  +TAGDI T +DIE++NPDH +  +     ++  +TV+K  GYVPA+ ++ +
Sbjct: 61  ELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIAEGHSLKATMTVAKNRGYVPAEGNKKD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           + P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L
Sbjct: 121 DAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVL 180

Query: 225 QDQLGMFI 232
            + L +F 
Sbjct: 181 IEHLNLFT 188


>gi|308190154|ref|YP_003923085.1| DNA-directed RNA polymerase alpha chain [Mycoplasma fermentans JER]
 gi|319777458|ref|YP_004137109.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma fermentans
           M64]
 gi|307624896|gb|ADN69201.1| DNA-directed RNA polymerase alpha chain [Mycoplasma fermentans JER]
 gi|318038533|gb|ADV34732.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma fermentans
           M64]
          Length = 337

 Score =  219 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 89/334 (26%), Positives = 158/334 (47%), Gaps = 25/334 (7%)

Query: 9   LIKPNNIEYIVL---GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           + K   +EY  +        N T    +PL RG   TLG ALRR+L+S++   A+ A++I
Sbjct: 1   MEKMTKLEYQKVTKLNNSTSNVTAFTLQPLERGMGQTLGVALRRILLSNITSLALFAIKI 60

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMS-----GDSHKRVTIFKRGPGVVTAGDIQ 120
           + V HE   + G  ED+  II+N++ +  + +      D   +VT+    PG VT+  ++
Sbjct: 61  EDVNHEFQVVDGCVEDVATIIMNLRKVKFQYNPEFVKDDEIIKVTLKADQPGEVTSRLLE 120

Query: 121 T-VNDIEVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHR-------------TE 164
              + IE+LN    I +L  +    + +EL +  G G++  + ++             ++
Sbjct: 121 VNNSSIEILNKSLEIAHLSANGKHKLNIELYLRPGRGFISNEENKKLLNNSSITTRMESK 180

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
                 I  D+ +SPI+KV+YTVE          ++L+ +  TDG++  + ++  A  IL
Sbjct: 181 IKNGIFIATDSNFSPIEKVNYTVEELNSSSNKIEERLTFSFQTDGTVDPKSALQQACEIL 240

Query: 225 QDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDL 284
                +  N +E K  V  + + ++   N      +  L LSVRS N L+      +  +
Sbjct: 241 VGHFKLIGNVDEMKVNVFAEESEQTQETNDND-VDINSLNLSVRSLNALKRIGKTKISQV 299

Query: 285 IQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            + +  ++ ++ N GRKSL EI+  L   G  L 
Sbjct: 300 AEMSLEELEQVKNLGRKSLDEIQQRLKEYGYELS 333


>gi|238810271|dbj|BAH70061.1| hypothetical protein [Mycoplasma fermentans PG18]
          Length = 339

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 89/334 (26%), Positives = 158/334 (47%), Gaps = 25/334 (7%)

Query: 9   LIKPNNIEYIVL---GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           + K   +EY  +        N T    +PL RG   TLG ALRR+L+S++   A+ A++I
Sbjct: 3   MEKMTKLEYQKVTKLNNSTSNVTAFTLQPLERGMGQTLGVALRRILLSNITSLALFAIKI 62

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMS-----GDSHKRVTIFKRGPGVVTAGDIQ 120
           + V HE   + G  ED+  II+N++ +  + +      D   +VT+    PG VT+  ++
Sbjct: 63  EDVNHEFQVVDGCVEDVATIIMNLRKVKFQYNPEFVKDDEIIKVTLKADQPGEVTSRLLE 122

Query: 121 T-VNDIEVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHR-------------TE 164
              + IE+LN    I +L  +    + +EL +  G G++  + ++             ++
Sbjct: 123 VNNSSIEILNKSLEIAHLSANGKHKLNIELYLRPGRGFISNEENKKLLNNSSITTRMESK 182

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
                 I  D+ +SPI+KV+YTVE          ++L+ +  TDG++  + ++  A  IL
Sbjct: 183 IKNGIFIATDSNFSPIEKVNYTVEELNSSSNKIEERLTFSFQTDGTVDPKSALQQACEIL 242

Query: 225 QDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDL 284
                +  N +E K  V  + + ++   N      +  L LSVRS N L+      +  +
Sbjct: 243 VGHFKLIGNVDEMKVNVFAEESEQTQETNDND-VDINSLNLSVRSLNALKRIGKTKISQV 301

Query: 285 IQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            + +  ++ ++ N GRKSL EI+  L   G  L 
Sbjct: 302 AEMSLEELEQVKNLGRKSLDEIQQRLKEYGYELS 335


>gi|150187022|emb|CAK30153.1| RNA polymerase alpha subunit [Streptococcus thoraltensis]
          Length = 184

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 82/184 (44%), Positives = 129/184 (70%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ +K   
Sbjct: 1   YGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNVKGLAVKSYV 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + +  +GP  VTAGDI T +DIE++N DH +  +   A  +  +TV+   GYV A
Sbjct: 61  EDEKIIELDVQGPAEVTAGDILTDSDIEIVNSDHYLFTIAEGASFKASMTVATNRGYVAA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           + ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ 
Sbjct: 121 EGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALG 180

Query: 219 LASR 222
           L++R
Sbjct: 181 LSAR 184


>gi|119662315|emb|CAJ33145.1| RNA polymerase alpha subunit [Lactobacillus iners DSM 13335]
          Length = 209

 Score =  218 bits (556), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 92/208 (44%), Positives = 141/208 (67%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRVL++S+ G A++ + IDGVLHE S+I GV ED+T IILN+K + LK+  D  K
Sbjct: 1   LGNSLRRVLLTSISGTALSYIMIDGVLHEFSTIPGVREDVTKIILNLKKLELKLLVDEEK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            V I   GP VVTA D++   D+E+LNPD  IC +     + M + +  G GY+PA  ++
Sbjct: 61  MVEIDVEGPAVVTAADLKVDADVEILNPDQYICTIAEGGHLHMSIAIKNGRGYIPASENK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
           +++ PIG+I +D+L+SPIKKV+Y VE+AR G+  DYDKL++ + TDGSIT  D+++ A++
Sbjct: 121 SDDMPIGVIPVDSLFSPIKKVNYQVENARVGKRDDYDKLTLELWTDGSITPNDALSFAAK 180

Query: 223 ILQDQLGMFINFEEPKKEVKEDINVKSL 250
           IL++   +F++ +   +     I  +  
Sbjct: 181 ILEEHFKVFMSADMSDQFANVMIEKEDK 208


>gi|154424861|emb|CAL18533.1| RNA polymerase alpha subunit [Streptococcus suis]
          Length = 203

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 86/203 (42%), Positives = 136/203 (66%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG 110
           L++SL GAA+T+++IDGVLHE  ++ GV ED+  IILNIKGI +K   +  K++ +   G
Sbjct: 1   LLASLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKKIELDVVG 60

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
           P  VTAGDI T +DIE++NPDH +  +   A  +  LTV+ G GYVPA+ ++ ++ P+G 
Sbjct: 61  PAEVTAGDILTDSDIEIVNPDHYLFTIADGATFKAVLTVNSGRGYVPAEGNKKDDAPVGT 120

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           + +D++Y+P+KKV+Y VE AR G    +DKL++ I+T+G+I  ED++ L++RIL + LG+
Sbjct: 121 LAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTLEINTNGTIIPEDALGLSARILMEHLGL 180

Query: 231 FINFEEPKKEVKEDINVKSLPFN 253
           F +  E  K  +     +    +
Sbjct: 181 FTDLTEVAKSAEVMKEAEVASDD 203


>gi|72080507|ref|YP_287565.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma hyopneumoniae
           7448]
 gi|90110848|sp|Q4A8J7|RPOA_MYCH7 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|71913631|gb|AAZ53542.1| DNA-directed RNA polymerase alpha subunit [Mycoplasma hyopneumoniae
           7448]
          Length = 332

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 83/311 (26%), Positives = 154/311 (49%), Gaps = 17/311 (5%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           + Q  E  T    +PL RG  +TLGNALRR ++SS+   A+  V+I+G+ HE + +  V 
Sbjct: 14  VEQVNEFETSFEIKPLERGLGNTLGNALRRTVLSSIPSCAVFGVKIEGIKHEFTVLDDVI 73

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFK-----RGPGVVTAGDIQTVNDIEVLNPDHVI 134
           ED+  I+ N+K +    +     + +I       +  G + A DI++ + ++++NPD  I
Sbjct: 74  EDVVTILNNLKRVRFFYNPSVFSQNSIHVASFLGQKAGQIYARDIESHSGLKIVNPDLYI 133

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRT---------ENDPIG-LITIDALYSPIKKVS 184
            ++     ++ EL ++ G G+V  + ++          E+   G ++ +D+ +SP+   +
Sbjct: 134 ADVSKVGALKFELFITNGKGFVDFETNKKYVNEVISRLESQIEGSVLAVDSDFSPVLNAN 193

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y          +  +KL+ +I TDGSI  +D+++  ++IL   L +  + E   K   + 
Sbjct: 194 YQAVEINSASPIIEEKLNFSIKTDGSIFAKDALSQGAKILIAHLNLLADVENLNKFSADF 253

Query: 245 INVKSLPFNPA--LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              + +   P       ++ L+LSVRS N LR      + D+ + ++ D   + N GRKS
Sbjct: 254 FGDQEIKEEPIRRFSNSIDALDLSVRSLNALRRAQYYKISDIEKLSQDDFENIKNLGRKS 313

Query: 303 LVEIKGVLGTM 313
           + EI   L   
Sbjct: 314 VQEIMEKLQNY 324


>gi|54020095|ref|YP_115726.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma hyopneumoniae
           232]
 gi|71893520|ref|YP_278966.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma hyopneumoniae
           J]
 gi|81603664|sp|Q601I9|RPOA_MYCH2 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|90110849|sp|Q4AAG6|RPOA_MYCHJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|53987268|gb|AAV27469.1| DNA-directed RNA polymerase alpha chain [Mycoplasma hyopneumoniae
           232]
 gi|71851647|gb|AAZ44255.1| DNA-directed RNA polymerase alpha subunit [Mycoplasma hyopneumoniae
           J]
 gi|312601096|gb|ADQ90351.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma hyopneumoniae
           168]
          Length = 332

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 83/311 (26%), Positives = 154/311 (49%), Gaps = 17/311 (5%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           + Q  E  T    +PL RG  +TLGNALRR ++SS+   A+  V+I+G+ HE + +  V 
Sbjct: 14  VEQVNEFETSFEIKPLERGLGNTLGNALRRTVLSSIPSCAVFGVKIEGIKHEFTVLDDVI 73

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFK-----RGPGVVTAGDIQTVNDIEVLNPDHVI 134
           ED+  I+ N+K +    +     + +I       +  G + A DI++ + ++++NPD  I
Sbjct: 74  EDVVTILNNLKRVRFFYNPSVFSQNSIHVASFLGQKAGQIYARDIESHSGLKIVNPDLYI 133

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRT---------ENDPIG-LITIDALYSPIKKVS 184
            ++     ++ EL ++ G G+V  + ++          E+   G ++ +D+ +SP+   +
Sbjct: 134 ADVSKVGALKFELFITNGKGFVDFETNKKYVNEVISLLESQIEGSVLAVDSDFSPVLNAN 193

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y          +  +KL+ +I TDGSI  +D+++  ++IL   L +  + E   K   + 
Sbjct: 194 YQAVEINSASPIIEEKLNFSIKTDGSIFAKDALSQGAKILIAHLNLLADVENLNKFSADF 253

Query: 245 INVKSLPFNPA--LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              + +   P       ++ L+LSVRS N LR      + D+ + ++ D   + N GRKS
Sbjct: 254 FGDQEIKEEPIRRFSNSIDALDLSVRSLNALRRAQYYKISDIEKLSQDDFENIKNLGRKS 313

Query: 303 LVEIKGVLGTM 313
           + EI   L   
Sbjct: 314 VQEIMEKLQNY 324


>gi|119662833|emb|CAJ33209.1| RNA polymerase alpha subunit [Lactobacillus ingluviei]
          Length = 180

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 85/180 (47%), Positives = 125/180 (69%), Gaps = 1/180 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRV+++SL GAAIT++ IDGVLHE S+++GV ED+T I+LN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRVMLASLPGAAITSIDIDGVLHEFSTVEGVTEDVTQIVLNLKKVA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           LK+  +  K + +  +GP  VTA DIQ   D+ +LNPD  I  +   A + M +T   G 
Sbjct: 61  LKIESEDAKNLELDVKGPAEVTAADIQADGDVTILNPDLHIATVADGAELHMRMTADTGR 120

Query: 154 GYVPAKHHRTE-NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           GY  A  ++   +  IG++ ID++Y+PI++V+YTVE+ R GQ  DYDKL++ + TDGS+T
Sbjct: 121 GYNSADVNKARMDLAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYDKLTLDVWTDGSLT 180


>gi|150036842|emb|CAM98286.1| DNA-directed RNA polymerase alpha chain [Leuconostoc carnosum]
          Length = 179

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 84/179 (46%), Positives = 119/179 (66%), Gaps = 2/179 (1%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + 
Sbjct: 1   PLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVV 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L +  D  + + I  +GP  VTA D+Q   D++VLNPD  I  +     + M +T  KG 
Sbjct: 61  LAIDSDEERVLEIDVQGPSEVTAADLQAGADVKVLNPDLHIATVAAGKSLHMTVTAVKGR 120

Query: 154 GYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           GY  A  ++   E  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GS
Sbjct: 121 GYSSADENKQLREEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGS 179


>gi|153820464|ref|ZP_01973131.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae NCTC
           8457]
 gi|126508991|gb|EAZ71585.1| DNA-directed RNA polymerase, alpha subunit [Vibrio cholerae NCTC
           8457]
          Length = 215

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 93/218 (42%), Positives = 142/218 (65%), Gaps = 8/218 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDAL 176
              D+E++NP+HVIC+L   +A + M + V +G GYVPA    H   +  PIG + +DA 
Sbjct: 118 HDGDVEIVNPEHVICHLTSDNAAIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
           +SP+ K++Y+VE+AR  Q  D DKL + ++T+G++  E
Sbjct: 178 FSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLEPE 215


>gi|154424833|emb|CAL18519.1| RNA polymerase alpha subunit [Streptococcus parauberis]
          Length = 194

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 84/194 (43%), Positives = 133/194 (68%)

Query: 48  RRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF 107
           RRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + + 
Sbjct: 1   RRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKMIELD 60

Query: 108 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
             GP  VTAGDI T +DIE++NPDH +  +     ++  +TV+K  GY+PA+ ++ ++ P
Sbjct: 61  VEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLKATMTVAKKRGYIPAEGNKQDDAP 120

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           +G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + 
Sbjct: 121 VGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEH 180

Query: 228 LGMFINFEEPKKEV 241
           L +F +  E  K  
Sbjct: 181 LNLFTDLTEVAKTT 194


>gi|149195168|ref|ZP_01872259.1| DNA-directed RNA polymerase subunit alpha [Caminibacter
           mediatlanticus TB-2]
 gi|149134720|gb|EDM23205.1| DNA-directed RNA polymerase subunit alpha [Caminibacter
           mediatlanticus TB-2]
          Length = 333

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 101/321 (31%), Positives = 163/321 (50%), Gaps = 7/321 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +E N+  +   P   GF  ++ + +RR L+++  G A   ++I+GV HE  S+KG+ ED
Sbjct: 17  NKEGNKASIEVYPFEAGFGVSVAHPIRRTLIAATTGFAPVGLKIEGVKHEFDSLKGMLED 76

Query: 82  LTDIILNIKGINLKM--SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           +   I+N+K I  K+  S      V  F  GP  +   D+    +I+V+ PD  I  L+ 
Sbjct: 77  VASFIINLKNIRFKIKNSSKDEVVVEYFFTGPKEIKGADLI-NEEIDVVTPDEYIATLNE 135

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           +  +++ L + KG G+V A  +  +  P G I +DA +SPIKK  Y +E+       +Y+
Sbjct: 136 EGELKLTLLIKKGMGFV-AVENFRDTLPEGFIGLDAYFSPIKKAVYNIENVLVEDDPNYE 194

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           K+   ++TDG I   D+   A     +Q G+F   +E K E K+  NV+       L K 
Sbjct: 195 KVIFEVETDGQIDPIDAFKNAVNNYLNQFGVFS--KEFKLETKKVENVELPDEYNILFKP 252

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +EEL L  RS N L    I ++G+L+   +  +  + N G KSL EI   L  +G  +  
Sbjct: 253 IEELNLRSRSFNALDRAGIKFIGELVLMGKEKISNIKNLGTKSLEEIFEKLEEIGFSINK 312

Query: 320 NLP-DWPPESIEELAKKYEDK 339
            LP D+     E+LAK   ++
Sbjct: 313 TLPLDFKKAIEEKLAKLKGEE 333


>gi|325989737|ref|YP_004249436.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma suis KI3806]
 gi|323574822|emb|CBZ40482.1| DNA-directed RNA polymerase subunit alpha (RNAP subunit alpha)
           [Mycoplasma suis]
          Length = 337

 Score =  217 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 89/322 (27%), Positives = 154/322 (47%), Gaps = 20/322 (6%)

Query: 15  IEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS 74
           IE  V+    E    ++  PL RG  +T+GN LRR+L+SS+   A+ A+++ G+ HE S 
Sbjct: 9   IETEVVDS-SETSASVVFYPLERGLGNTIGNTLRRLLLSSIPSPAVFAIRVAGLPHEFSP 67

Query: 75  IKGVHEDLTDIILNIKGINLKMSG-------------DSHKRVTIFKRGPGVVTAGDIQT 121
           IKGV ED+T +I+ IK + LK+               +    + I K   GVV A DI+ 
Sbjct: 68  IKGVAEDVTQLIIAIKKLVLKVDEKIADFEHLKDLPIEKWPFLKIRKSKVGVVQAKDIEC 127

Query: 122 VNDIEVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              +EV+NP+  +C +      + ++L      G+  +  +R     + LI ID  +SP+
Sbjct: 128 FAGVEVVNPELKLCEITEEGTSLEIDLYCMVDRGHRSSNENRERLSTLSLIPIDTTFSPV 187

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
             V + V   +  +    D+L + + T+GSI   D+V  A++IL          +    +
Sbjct: 188 LLVDWKVSEEKTTKYGISDRLRLNVSTNGSIKALDAVWYAAKILISMFTKIAEHDVELFK 247

Query: 241 V-----KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           +     K D   K    +      +E+LEL+ R+ N L+   I  + +L+  +  ++   
Sbjct: 248 LDSYAKKVDRKEKEEVHSSISSSPIEDLELTQRTFNILKNSGINTISELVAYSFDELAEF 307

Query: 296 ANFGRKSLVEIKGVLGTMGLFL 317
            N G+K+L+E++  L   G   
Sbjct: 308 RNLGKKALLEVQAKLEERGYKF 329


>gi|150187166|emb|CAK30185.1| RNA polymerase alpha subunit [Streptococcus marimammalium]
          Length = 210

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 89/210 (42%), Positives = 135/210 (64%)

Query: 49  RVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK 108
           RVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   +  K + +  
Sbjct: 1   RVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSHVEDEKTIELDV 60

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
           +GP  VTAGDI T +DIE++NPDH +  +   A  R  LTV+   GYVPA+ ++ EN P+
Sbjct: 61  QGPMEVTAGDILTDSDIEIVNPDHYLFTILEGASFRATLTVATKRGYVPAEENKKENAPV 120

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L
Sbjct: 121 GTLAVDSIYTPVKKVNYQVEPARVGSNDAFDKLTIEIMTNGTIIPEDALGLSARVLIEHL 180

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLK 258
            +F +  E  K  +     +         +
Sbjct: 181 NLFTDLTEIAKTTEVMKETEKASNEKVFDR 210


>gi|325973301|ref|YP_004250365.1| DNA-directed RNA polymerase, subunit alpha [Mycoplasma suis str.
           Illinois]
 gi|323651903|gb|ADX97985.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma suis str.
           Illinois]
          Length = 340

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 89/322 (27%), Positives = 154/322 (47%), Gaps = 20/322 (6%)

Query: 15  IEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS 74
           IE  V+    E    ++  PL RG  +T+GN LRR+L+SS+   A+ A+++ G+ HE S 
Sbjct: 12  IETEVVDS-SETSASVVFYPLERGLGNTIGNTLRRLLLSSIPSPAVFAIRVAGLPHEFSP 70

Query: 75  IKGVHEDLTDIILNIKGINLKMSG-------------DSHKRVTIFKRGPGVVTAGDIQT 121
           IKGV ED+T +I+ IK + LK+               +    + I K   GVV A DI+ 
Sbjct: 71  IKGVAEDVTQLIIAIKKLVLKVDEKIADFEHLKDLPIEKWPFLKIRKSKVGVVQAKDIEC 130

Query: 122 VNDIEVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              +EV+NP+  +C +      + ++L      G+  +  +R     + LI ID  +SP+
Sbjct: 131 FAGVEVVNPELKLCEITEEGTSLEIDLYCMVDRGHRSSNENRERLSTLSLIPIDTTFSPV 190

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
             V + V   +  +    D+L + + T+GSI   D+V  A++IL          +    +
Sbjct: 191 LLVDWKVSEEKTTKYGISDRLRLNVSTNGSIKALDAVWYAAKILISMFTKIAEHDVELFK 250

Query: 241 V-----KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           +     K D   K    +      +E+LEL+ R+ N L+   I  + +L+  +  ++   
Sbjct: 251 LDSYAKKVDRKEKEEVHSSISSSPIEDLELTQRTFNILKNSGINTISELVAYSFDELAEF 310

Query: 296 ANFGRKSLVEIKGVLGTMGLFL 317
            N G+K+L+E++  L   G   
Sbjct: 311 RNLGKKALLEVQAKLEERGYKF 332


>gi|304373166|ref|YP_003856375.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma hyorhinis
           HUB-1]
 gi|304309357|gb|ADM21837.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma hyorhinis
           HUB-1]
 gi|330723976|gb|AEC46346.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma hyorhinis
           MCLD]
          Length = 333

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 85/314 (27%), Positives = 152/314 (48%), Gaps = 20/314 (6%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
            +  T    +PL RGFA+TLGN+LRR ++SS+   A+  V+I+GV HE S I  V ED+ 
Sbjct: 18  SDFETTFELQPLERGFANTLGNSLRRTILSSVPSVAVFGVKIEGVEHEFSVIDKVREDVV 77

Query: 84  DIILNIKGINLKMSGD-----SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            I+ N+K +      +       +  +   R  G +T  DI   + +E++N D V+ N  
Sbjct: 78  TILNNLKKLRFSFKKEVFLQNEIQVASFDGRKVGKITGADILVNSALEIVNKDQVVANTS 137

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGL-----------ITIDALYSPIKKVSYTV 187
               ++ E+ ++ G G+V  + ++ +   +G            I +D+ +S ++ V ++ 
Sbjct: 138 EVGALKFEMFLTYGRGFVDFETNKRKIQELGPALESKLGYGQIIAVDSDFSAVENVKFSS 197

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF---INFEEPKKEVKED 244
                   +  +KL+ ++ TDG+I  +D++A A++IL   L +     N +       E+
Sbjct: 198 TELNSSNPIVEEKLTFSVKTDGTILAKDALAEAAKILIAHLKLVSDTANLDAEVDSFFEE 257

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +  K           +  L+L+VRS N LR      + DL++ T  ++  + N G+KS+ 
Sbjct: 258 VKQKEEAP-KKNSADLTTLDLTVRSLNALRRAQYYKISDLLELTLEELENIKNLGKKSVE 316

Query: 305 EIKGVLGTMGLFLG 318
           EI   L    L L 
Sbjct: 317 EIVEKLKEHNLELK 330


>gi|193216735|ref|YP_001999977.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma arthritidis
           158L3-1]
 gi|193002058|gb|ACF07273.1| DNA-directed RNA polymerase alpha subunit [Mycoplasma arthritidis
           158L3-1]
          Length = 350

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 79/308 (25%), Positives = 147/308 (47%), Gaps = 16/308 (5%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
            ++ +  T  + EPL RG+A+TLG  LRR L+SS+   A  A++I+ V HE  ++ GV E
Sbjct: 15  ERKTDFDTTFVIEPLMRGYANTLGTVLRRTLLSSITSVAPFAIKINNVQHEFETLPGVKE 74

Query: 81  DLTDIILNIKGINLKMSGDSHK-----RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
           D+  +I NI+ I      +  +     R++      G +TA DI   + +E++N D  IC
Sbjct: 75  DVVTLIANIRKIRFTYKPELFEKENLARISFKATHDGDITASDINEPSGLEIVNKDQHIC 134

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG-----------LITIDALYSPIKKVS 184
           +L     +  +L +  G GY+  + ++T     G            + ID+ +SP+K  +
Sbjct: 135 SLQKGTTLEFDLFLRVGRGYIDFEENKTIIQEYGPKLESKIKKGQFLAIDSDFSPVKNCA 194

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
              E          ++L +++ TDG++  + ++  A+ I+     +  N +        +
Sbjct: 195 IHFEELNTSAKNVEERLKISVQTDGTLDAKSAMQQAATIIVAHFQIIGNIDALGTINLFE 254

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
                      L   +E+L L++RS N LR  N   + +L++ +E ++  + N G+KS+ 
Sbjct: 255 EARDKKEKTTKLNLPIEKLNLTIRSLNALRRANYNTIDELLKLSEDELSNIKNLGKKSVQ 314

Query: 305 EIKGVLGT 312
           +I   L  
Sbjct: 315 DIIDKLVE 322


>gi|119662283|emb|CAJ33128.1| RNA polymerase alpha subunit [Lactobacillus antri]
          Length = 203

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 89/202 (44%), Positives = 139/202 (68%), Gaps = 2/202 (0%)

Query: 52  MSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGP 111
           ++SL GAAIT +QIDGVLHE S++KGV ED+T IILN+K ++LK++ +  K + +  +GP
Sbjct: 1   IASLPGAAITTMQIDGVLHEFSTVKGVTEDVTQIILNLKKVSLKINSEDQKDLELDVKGP 60

Query: 112 GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIG 169
             VTAGDIQ  +++ VLNPD  I  +   A + +++T  KG GY+ A  ++   E+  IG
Sbjct: 61  AEVTAGDIQGDSEVSVLNPDLHIATVADGAELHIKMTADKGRGYLSANDNKARMEDLAIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           ++ ID++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGSIT  ++V+L ++IL + L 
Sbjct: 121 VLPIDSIYTPIERVNYTVENARVGQRSDYDKLTLDVWTDGSITPTEAVSLGAKILTEHLA 180

Query: 230 MFINFEEPKKEVKEDINVKSLP 251
           MF+N  E  +  +  +  +   
Sbjct: 181 MFVNLTETAQNAQVMVEKEETH 202


>gi|47459096|ref|YP_015958.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma mobile 163K]
 gi|61215933|sp|Q6KI29|RPOA_MYCMO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|47458425|gb|AAT27747.1| DNA-directed RNA polymerase alpha chain [Mycoplasma mobile 163K]
          Length = 333

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 94/334 (28%), Positives = 155/334 (46%), Gaps = 26/334 (7%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
            I+ NW E  K   I         +  T  I +PL +G A TLG A+RRVL+SS+   A 
Sbjct: 4   FIKINWTE-NKTKRI--------NDFSTSFIVQPLEKGLATTLGTAIRRVLLSSISSVAP 54

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK------RGPGVV 114
            AV+I GV HE  +I  V ED+  I+L ++ I +  + +  +   I+K      +  G +
Sbjct: 55  FAVKIKGVEHEFMAINKVTEDVPQILLRLRDIKIAYNPEIFEDGKIYKLSLKSNKEAGDI 114

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI------ 168
            A D       E++NP  +I       V+ +++ V  G GYV  + ++   D I      
Sbjct: 115 YAKDFILPIGAEIVNPGLLIATTAAANVLEIDVFVRAGRGYVDFEENKKYIDEIKTNLTS 174

Query: 169 -----GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
                  I +D+ +SPI+KVS++        V+  +KL M I T G+I  ++++A A++I
Sbjct: 175 SISNGQYIAVDSNFSPIEKVSFSSSELNTSSVIVQEKLEMEIVTKGTIDAKNAIAQAAKI 234

Query: 224 LQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGD 283
           L   L +  +      +   +        +      ++ L+LS+RS N L+  N   +  
Sbjct: 235 LVAHLNIIGDVNSLNIKDIFEEGNTEKEHSKTQNILIQSLDLSIRSFNALKRANYTTVQQ 294

Query: 284 LIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L   +  D+  + N G KS+ EI   L    +FL
Sbjct: 295 LEALSLDDLKNIKNLGEKSINEIVEKLEKYNVFL 328


>gi|150187139|emb|CAK30179.1| RNA polymerase alpha subunit [Streptococcus peroris ATCC 700780]
          Length = 181

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 87/181 (48%), Positives = 126/181 (69%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR 103
           GN+LRRVL++SL GAA+T++ IDGVLHE  +I GV ED+  IILNIKGI +K      K 
Sbjct: 1   GNSLRRVLLASLPGAAVTSIDIDGVLHEFDTIPGVREDVMQIILNIKGIAVKSYVKDEKT 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + +   GP  VTAGDI T +DIE++NPDH +  +   A  +  +TV+ G GYVPA  ++ 
Sbjct: 61  IELDVEGPAEVTAGDILTDSDIEIVNPDHYLFTIGEGASFKATMTVNTGRGYVPADENKK 120

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
           +N P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RI
Sbjct: 121 DNAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARI 180

Query: 224 L 224
           L
Sbjct: 181 L 181


>gi|269784298|emb|CBH50794.1| alpha subunit of RNA polymerase [Vibrio sp. C 15.19]
          Length = 244

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 103/247 (41%), Positives = 160/247 (64%), Gaps = 8/247 (3%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGV 113
           + G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G 
Sbjct: 1   MPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGP 60

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIG 169
           V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG
Sbjct: 61  VVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL 
Sbjct: 121 RLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLD 180

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
            F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMA 296
            ++L+  
Sbjct: 238 VELLKTP 244


>gi|119662381|emb|CAJ33179.1| RNA polymerase alpha subunit [Lactobacillus sakei subsp. sakei]
          Length = 184

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 80/184 (43%), Positives = 127/184 (69%)

Query: 56  RGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT 115
            G A+T +QIDGVLHE S+I GV ED+T IILNIK + LK+  +  K + I  +GP  VT
Sbjct: 1   PGTAVTDIQIDGVLHEFSTIDGVLEDVTQIILNIKKLALKLHVEEDKTIEIDVKGPATVT 60

Query: 116 AGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDA 175
           A DI + +D+EVLN D  IC +       +++TV KG GYV A  +++++ PIG++ ID+
Sbjct: 61  AADIISDDDVEVLNTDQYICTVAEGGNFHVQMTVKKGRGYVAAVQNKSDDMPIGVLPIDS 120

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           +Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++I+ + L +F++  
Sbjct: 121 IYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKIMTEHLAIFVDLT 180

Query: 236 EPKK 239
           +  K
Sbjct: 181 DEAK 184


>gi|154424761|emb|CAL18483.1| RNA polymerase alpha subunit [Streptococcus equinus]
          Length = 183

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 85/183 (46%), Positives = 130/183 (71%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K +
Sbjct: 1   NSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKII 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  VTAGDI T +D+E++NPDH +  +     ++  +TV+K  GYVPA+ ++ E
Sbjct: 61  ELDVEGPAEVTAGDILTDSDVEIVNPDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKE 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           + P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L
Sbjct: 121 DAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVL 180

Query: 225 QDQ 227
            + 
Sbjct: 181 IEH 183


>gi|115391932|ref|YP_778521.1| RNA polymerase alpha subunit [Jasminum nudiflorum]
 gi|110456253|gb|ABG74658.1| RNA polymerase alpha subunit [Jasminum nudiflorum]
          Length = 270

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 63/236 (26%), Positives = 120/236 (50%), Gaps = 8/236 (3%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +   E++        I  PL +G A T+   +RR L+  + G  IT V+   V
Sbjct: 11  RTLQWKCVESREDSKRLYYGRFILSPLRKGQADTIAIGIRRALLGEIEGTCITRVKSKNV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N K I L+ +       +I  RGPG VTA DI     +E++
Sbjct: 71  PHEYSTIAGIQESVHEILMNFKEIVLRSNLYGTCDASICVRGPGYVTAQDIILPPYVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY+    H +++   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDLCIGLQIERNRGYLMKMPHNSQD---GSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           S   G    ++ L + I T+GS+T ++++  A R L D    F++ EE    ++++
Sbjct: 188 SYGSG-NEKHEILFLEIWTNGSLTPKEALHEACRNLIDLFIPFLHKEEETSPLEDN 242


>gi|295809864|emb|CBL85108.1| alpha subunit of RNA polymerase [Vibrio tapetis]
          Length = 244

 Score =  215 bits (548), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 102/247 (41%), Positives = 159/247 (64%), Gaps = 8/247 (3%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGV 113
           + G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +K+  G     +T+ K G G 
Sbjct: 1   MPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVKVAEGKDEVFITLNKSGSGP 60

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHH---RTENDPIG 169
           V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA        +  PIG
Sbjct: 61  VVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASSRIHTEEDERPIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  ++ IL +QL 
Sbjct: 121 RLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRSATILAEQLD 180

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
            F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDIRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMA 296
            ++L+  
Sbjct: 238 VELLKTP 244


>gi|161511725|emb|CAP16873.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           acidilactici]
          Length = 199

 Score =  215 bits (548), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 89/191 (46%), Positives = 125/191 (65%), Gaps = 2/191 (1%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           +L+SSL GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++LK+  D  K + I   
Sbjct: 9   ILLSSLPGAAITSVQIDNVLHEFSTIEGVVEDVTQIILNLKKVSLKIESDDEKTLDINVV 68

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDP 167
           GP  VTAGDI    D+ VLNPD  IC +         LT   G GY  A  ++    + P
Sbjct: 69  GPANVTAGDIMGDGDVTVLNPDSPICTVAEGTTFHAVLTADTGRGYTSADENKARKADMP 128

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           IG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ I TDGSIT  ++ +L+++IL + 
Sbjct: 129 IGVLPIDSIYTPIERVNYQVEKTRVGQRDDYDKLTLDIWTDGSITPSEATSLSAKILTEH 188

Query: 228 LGMFINFEEPK 238
           L +F+N  +  
Sbjct: 189 LAIFVNLNDQA 199


>gi|119668337|emb|CAK95467.1| RNA polymerase alpha subunit [Lactobacillus johnsonii]
          Length = 187

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 89/185 (48%), Positives = 130/185 (70%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG 110
           L++S+ G A++ +QIDGVLHE S+I GV ED+T IILN+K + LK   D  K   I   G
Sbjct: 1   LLTSIPGTALSYIQIDGVLHEFSTIPGVREDVTKIILNLKKLELKSLSDEEKIAEIDVTG 60

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
           P +VTA D++  +DIEVLNPD  IC++     + M + +  G GYVPA  ++T++ PIG+
Sbjct: 61  PAIVTAADLKVDSDIEVLNPDQYICSIADGGHLHMNVAIKTGRGYVPASENKTDDMPIGV 120

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           I +D+L+SPIKKV+Y VESAR G+  DYDKL++ I TDGSIT  D+++ A++IL +   +
Sbjct: 121 IPVDSLFSPIKKVNYQVESARVGKRDDYDKLTLEIWTDGSITPNDALSFAAKILVEHFKV 180

Query: 231 FINFE 235
           F++ +
Sbjct: 181 FMSTD 185


>gi|255645616|gb|ACU23302.1| unknown [Glycine max]
          Length = 269

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 67/242 (27%), Positives = 126/242 (52%), Gaps = 5/242 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E   +  +       I  PL +G A T+G A+RRVL+  + G  IT V+++ + 
Sbjct: 13  LQWKCVES-RIDSKRLYYGRFILSPLMKGQADTIGIAMRRVLLGEIEGTCITRVKLEKIP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +    +  +I  +GPG VTA DI     +E+++
Sbjct: 72  HEYSTIIGIEESVHEILMNLKEIVLRSNLYGTRDASICFKGPGYVTAQDIILPPSVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I N+     + +EL + +  GY        ++   G   IDA + P++ V++++ S
Sbjct: 132 NTQHIANVTEPVNLCIELKIERNRGYRIKTLKNFQD---GSYPIDATFMPVRNVNHSIHS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                    + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + +  +
Sbjct: 189 Y-VNGNEKQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEDNFNLENNQHKVT 247

Query: 250 LP 251
           LP
Sbjct: 248 LP 249


>gi|256370803|ref|YP_003108628.1| DNA-directed RNA polymerase subunit alpha [Candidatus Sulcia
           muelleri SMDSEM]
 gi|256009595|gb|ACU52955.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Sulcia
           muelleri SMDSEM]
          Length = 349

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 108/337 (32%), Positives = 175/337 (51%), Gaps = 24/337 (7%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +K    E + + +          EPL  G+  T+GN LRRVL+SSL G AI++V+I+GV
Sbjct: 3   FLKFTKKENLRVLKLTNYEGHFKIEPLYPGWGVTIGNTLRRVLLSSLEGYAISSVKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV---------------TIFKRGPGV 113
            HE ++IKGV ED+T+I+LN+K I  K   +  +                  I K     
Sbjct: 63  DHEFATIKGVKEDMTEILLNLKKIRFKKKMEMEEEEEEEEEEEEEEGEKFNIIIKNEKEE 122

Query: 114 VTAGDI-QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT 172
           +TAGD+ + ++  E++NPD +I N      + + + + KG GYVP++ +    +  G I+
Sbjct: 123 ITAGDLGEYIHLFEIINPDLIILNKKKFIYLNITIVIKKGIGYVPSEENEKHINTNGTIS 182

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           +D++++PIKKV YT+E+    +   Y++L   I TDG+I  +D++  AS ++   L +  
Sbjct: 183 MDSIFTPIKKVKYTIENCSVSKNSTYERLFFEIKTDGTINPKDALIKASNLVIRHLKLLS 242

Query: 233 N-----FEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
           N         K + K+  N   L     L   +E   LSVR+ NCL+   I   GDLI+ 
Sbjct: 243 NKKISLNYNKKYKKKKQTNENYLKLRNILNSSLERKNLSVRTLNCLKKAKIFTWGDLIKS 302

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
                      G+KSL E+  ++  + ++ GMNL D+
Sbjct: 303 NPT---NFKYLGKKSLEELDLIMKKLTIYYGMNLEDY 336


>gi|150036716|emb|CAM98021.1| DNA-directed RNA polymerase alpha chain [Fructobacillus durionis]
          Length = 197

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 87/195 (44%), Positives = 124/195 (63%), Gaps = 2/195 (1%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRVL+SSL G AI  VQIDGV+HE S++ GV ED+T +ILN+K +          
Sbjct: 1   LGNSLRRVLLSSLPGVAINTVQIDGVVHEFSTVDGVAEDVTQLILNLKKVVFATDSAEEH 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + I  +GP  VTA D     DIEVLNPD  I  L     + M +TV KG GY  A+ ++
Sbjct: 61  TLEIDVQGPKDVTAADFVGSADIEVLNPDLHIATLAAGKSLHMTVTVVKGRGYASAEENK 120

Query: 163 T--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
              +  PIG++T+D++Y+PI++V+Y VE  R G   D+DKL+M + T+GSI   D+++L 
Sbjct: 121 QLRDEMPIGVLTVDSIYTPIERVNYHVEQKRVGSRDDFDKLTMEVWTNGSIKPSDALSLG 180

Query: 221 SRILQDQLGMFINFE 235
           S+IL + L +F +  
Sbjct: 181 SKILTEHLNLFTDIS 195


>gi|154424855|emb|CAL18530.1| RNA polymerase alpha subunit [Streptococcus sanguinis]
          Length = 198

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 84/198 (42%), Positives = 127/198 (64%)

Query: 49  RVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK 108
           RVL++SL GAA+T++ I+GVLHE  +I GV ED+  IILN+KGI +K      K + +  
Sbjct: 1   RVLLASLPGAAVTSINIEGVLHEFDTISGVREDVMQIILNVKGIAVKSYVQDEKIIELDV 60

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
            GP  VTAGDI T +DIE++NPDH +  +   A  +  +TV+ G GYVPA  ++ ++ P+
Sbjct: 61  EGPAEVTAGDILTDSDIEIINPDHYLFTIGEGASFKATMTVNSGRGYVPADENKKDDAPV 120

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           G + +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L
Sbjct: 121 GTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHL 180

Query: 229 GMFINFEEPKKEVKEDIN 246
            +F N  E          
Sbjct: 181 NLFTNLTEVAIAADVMKE 198


>gi|150186960|emb|CAK30137.1| RNA polymerase alpha subunit [Streptococcus infantis ATCC 700779]
          Length = 173

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 84/172 (48%), Positives = 118/172 (68%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRVL++SL GAA+T++ IDGVLHE  +I GV ED+  IILNIKGI 
Sbjct: 1   PLERGYGTTLGNSLRRVLLASLPGAAVTSIDIDGVLHEFDTIPGVREDVMQIILNIKGIA 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           +K      K + +   GP  VTAGDI T +DIE++NPDH +  +   A  +  +TV+ G 
Sbjct: 61  VKSYVKDEKTIELDVEGPAEVTAGDILTDSDIEIVNPDHYLFTIGEGASFKATMTVNTGR 120

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           GYVPA  ++ +N P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ I
Sbjct: 121 GYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEI 172


>gi|119668327|emb|CAK95463.1| RNA polymerase alpha subunit [Lactobacillus hilgardii]
          Length = 198

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 93/198 (46%), Positives = 134/198 (67%), Gaps = 4/198 (2%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFK 108
           L+SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K I+LK+ G  D  + + I  
Sbjct: 1   LLSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKISLKLDGPEDEDENLEIDV 60

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--ND 166
            GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT ++G GYV A  ++      
Sbjct: 61  IGPADVTAGDIQDDSDVTVLNPDLHIATVAEGATFHMRLTANRGRGYVSAVENKKRATEM 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ I T+GSIT  ++V+LA++IL +
Sbjct: 121 PIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDIWTNGSITPSEAVSLAAKILTE 180

Query: 227 QLGMFINFEEPKKEVKED 244
            L MF++  +  K  +  
Sbjct: 181 HLEMFVDLTDEAKNTEIM 198


>gi|119662821|emb|CAJ33203.1| RNA polymerase alpha subunit [Lactobacillus parakefiri]
          Length = 203

 Score =  214 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 94/202 (46%), Positives = 135/202 (66%), Gaps = 4/202 (1%)

Query: 52  MSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKR 109
           +SSL GAA+T++QID VLHE S+IKGV ED+T IILN+K I+LK+ G  D  + + I   
Sbjct: 1   LSSLPGAAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKISLKLDGPEDEEENLEIDVI 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDP 167
           GP  VTAGDIQ  +D+ VLNPD  I  +   A   M LT +KG GYV A  ++      P
Sbjct: 61  GPADVTAGDIQADSDVTVLNPDLHIATVAEGATFHMRLTANKGRGYVSAVENKKRSSEMP 120

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           IG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ I TDGSIT  ++V+LA++IL + 
Sbjct: 121 IGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDIWTDGSITPSEAVSLAAKILTEH 180

Query: 228 LGMFINFEEPKKEVKEDINVKS 249
           L MF++  +  K  +  +  + 
Sbjct: 181 LEMFVDLTDEAKNTEIMVEKEE 202


>gi|119668333|emb|CAK95466.1| RNA polymerase alpha subunit [Lactobacillus intestinalis]
          Length = 191

 Score =  214 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 84/190 (44%), Positives = 126/190 (66%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           VL++S+ G  +  VQIDGVLHE +++ GV ED+T IILN+K + LK   D  K + +   
Sbjct: 1   VLLTSIPGTGLVYVQIDGVLHEFATVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVE 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  VTA D++   D++VLNPD  IC +     + M++ V  G GYVPA  +++E+ PIG
Sbjct: 61  GPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMQIAVKNGRGYVPASDNKSEDMPIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           +I +D+L+SPIKKV+Y VES R G+  D+DKL++ I TDGSI   D+++ A++IL +   
Sbjct: 121 VIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTLEIWTDGSIKPNDALSFAAKILVEHFK 180

Query: 230 MFINFEEPKK 239
           +F + +   K
Sbjct: 181 VFESADANTK 190


>gi|90567615|emb|CAJ31075.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
 gi|119662311|emb|CAJ33143.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 197

 Score =  214 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 83/197 (42%), Positives = 125/197 (63%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG 110
           L++S+ G  +  VQIDGVLHE S++ GV ED+T IILN+K + LK   D  K + +   G
Sbjct: 1   LLTSIPGTGLVYVQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLSDERKVIELDVEG 60

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
           P  VTA D++   D++VLNPD  IC +     + ME+ V  G GYV A  +++++ PIG+
Sbjct: 61  PATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMEIAVQNGRGYVAASDNKSDDMPIGV 120

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++ A++IL +   +
Sbjct: 121 IPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALSFATKILVEHFKV 180

Query: 231 FINFEEPKKEVKEDINV 247
           F + +   K  +  +  
Sbjct: 181 FESADADTKFSEVMVEK 197


>gi|119662285|emb|CAJ33129.1| RNA polymerase alpha subunit [Lactobacillus brevis]
          Length = 190

 Score =  213 bits (543), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 87/190 (45%), Positives = 133/190 (70%), Gaps = 4/190 (2%)

Query: 52  MSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKR 109
           +SSL GAA+T++QIDGVLHE S+++GV ED+T IILN+K I LK++G  D  + + I  +
Sbjct: 1   LSSLPGAAVTSIQIDGVLHEFSTVEGVVEDVTQIILNVKKIALKLNGSDDQEETMEINVK 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDP 167
           GP  +TAGDI    D+++LNPD  I  +   A   M +T  KG GYV A  ++T   + P
Sbjct: 61  GPAQITAGDIVAGADVDILNPDLYIATVADGATFHMRMTADKGRGYVSADENKTRNTDMP 120

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           IG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ + T+GSI   +++ALA++IL + 
Sbjct: 121 IGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDVWTNGSINPSEAIALAAKILTEH 180

Query: 228 LGMFINFEEP 237
           L MF++  + 
Sbjct: 181 LAMFVDLTDE 190


>gi|154424863|emb|CAL18534.1| RNA polymerase alpha subunit [Streptococcus thoraltensis]
          Length = 200

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 80/199 (40%), Positives = 130/199 (65%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           VL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ +K   +  K + +  +
Sbjct: 1   VLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNVKGLAVKSYVEDEKIIELDVQ 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  VTAGDI T +DIE++N DH +  +   A  +  +TV+   GYV A+ ++ ++ P+G
Sbjct: 61  GPAEVTAGDILTDSDIEIVNSDHYLFTIAEGASFKASMTVATNRGYVAAEGNKKDDAPVG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L 
Sbjct: 121 TLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLN 180

Query: 230 MFINFEEPKKEVKEDINVK 248
           +F +  E  K        +
Sbjct: 181 LFTDLTEVAKATDVMKETE 199


>gi|150187144|emb|CAK30180.1| RNA polymerase alpha subunit [Streptococcus phocae]
          Length = 204

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 83/204 (40%), Positives = 134/204 (65%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           VL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   
Sbjct: 1   VLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKTIELEVE 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  VTAGDI T +DIE++NPDH +  +     +R  +TV+K  GYVPA+ ++ ++ P+G
Sbjct: 61  GPATVTAGDILTDSDIELVNPDHYLFTIAEGHSLRATMTVAKKRGYVPAEGNKKDDAPVG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L 
Sbjct: 121 TLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTVEIMTNGTIIPEDALGLSARVLIEHLN 180

Query: 230 MFINFEEPKKEVKEDINVKSLPFN 253
           +F +  +  K  +     + +   
Sbjct: 181 LFTDLTDVAKATEVMKETEKVNDE 204


>gi|290489664|gb|ADD31216.1| RNA polymerase alpha subunit protein [Lonicera japonica]
          Length = 264

 Score =  213 bits (542), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 64/251 (25%), Positives = 126/251 (50%), Gaps = 10/251 (3%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLR 56
           M+Q+     +    +E+  +    ++        I  PL +G A T+G A+RR L+  + 
Sbjct: 1   MVQEKVT--VSTRTLEWKCVESRADSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIE 58

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           G  IT  + + + HE S+I G+ E + +I++N+K I L+ +       +I  RGPG VTA
Sbjct: 59  GTCITRAKSEKIPHEYSTIVGIQESVHEILMNLKEIVLRSNLYGTCDASICVRGPGNVTA 118

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
            DI +   +E+++    I +L       + L + +  GY+    +  ++   G   IDA+
Sbjct: 119 QDIISPPYVEIIDNTQHIVSLTEPIDFCIGLQIERNRGYLIKTPNHFQD---GSYPIDAV 175

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           + P++  ++++ S         + L + I T+GS+T ++++  ASR L D    F++ EE
Sbjct: 176 FMPVRNANHSIHSYGNE-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHTEE 234

Query: 237 PKKEVKEDINV 247
               ++++ + 
Sbjct: 235 ENLHLEDNQHT 245


>gi|154424865|emb|CAL18535.1| RNA polymerase alpha subunit [Streptococcus thoraltensis]
          Length = 203

 Score =  213 bits (542), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 80/199 (40%), Positives = 130/199 (65%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           VL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ +K   +  K + +  +
Sbjct: 1   VLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNVKGLAVKSYVEDEKIIELDVQ 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  VTAGDI T +DIE++N DH +  +   A  +  +TV+   GYV A+ ++ ++ P+G
Sbjct: 61  GPAEVTAGDILTDSDIEIVNSDHYLFTIAEGASFKASMTVATNRGYVAAEGNKKDDAPVG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L 
Sbjct: 121 TLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLN 180

Query: 230 MFINFEEPKKEVKEDINVK 248
           +F +  E  K        +
Sbjct: 181 LFTDLTEVAKATDVMKETE 199


>gi|150187007|emb|CAK30149.1| RNA polymerase alpha subunit [Streptococcus pluranimalium]
          Length = 200

 Score =  213 bits (542), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 80/199 (40%), Positives = 130/199 (65%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG 110
           L+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ +K   +  K + +  +G
Sbjct: 1   LLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNVKGLAVKSYVEDEKTIELDVQG 60

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
           P  VTAGDI T +DIE++N DH +  +   A  +  +TV+   GYV A+ ++ ++ P+G 
Sbjct: 61  PAEVTAGDILTDSDIEIVNSDHYLFTIAEGASFKASMTVATNRGYVAAEGNKKDDAPVGT 120

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +
Sbjct: 121 LAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTVEIMTNGTIIPEDALGLSARVLIEHLNL 180

Query: 231 FINFEEPKKEVKEDINVKS 249
           F +  E  K        +S
Sbjct: 181 FTDLTEVAKATDVMKETES 199


>gi|154424827|emb|CAL18516.1| RNA polymerase alpha subunit [Streptococcus parasanguinis]
          Length = 194

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 83/193 (43%), Positives = 127/193 (65%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           VL++SL GAA+T++ I+GVLHE  ++ GV ED+  IILN+KGI +K      K + +   
Sbjct: 1   VLLASLPGAAVTSINIEGVLHEFDTVPGVREDVMQIILNVKGIAVKSYVQDEKIIELDVE 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP  VTAGDI T +DIE++NPDH +  +   A ++  LTV+ G GYVPA  ++ ++ P+G
Sbjct: 61  GPAEVTAGDILTDSDIEIVNPDHYLFTIGEGASLKATLTVNSGRGYVPADQNKKDDAPVG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L 
Sbjct: 121 TLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLN 180

Query: 230 MFINFEEPKKEVK 242
           +F N  E      
Sbjct: 181 LFTNLTEIAIATD 193


>gi|161511731|emb|CAP16876.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 199

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 87/198 (43%), Positives = 127/198 (64%), Gaps = 2/198 (1%)

Query: 54  SLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGV 113
           SL GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++LK+  D  K + I   GP  
Sbjct: 1   SLPGAAITSVQIDSVLHEFSTIEGVVEDVTQIILNLKKVSLKIESDEDKTLEINVAGPAN 60

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLI 171
           VTAGDI    D+ +LNP+  IC +         LT   G GY  A  ++    + PIG++
Sbjct: 61  VTAGDIMGDGDVVILNPELPICTVAEGTTFHAVLTADTGRGYTSADENKARKVDMPIGVL 120

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            ID++Y+PI++V+Y VE+ R GQ  DYDKL++ I TDGSIT  ++ +L+++IL + L +F
Sbjct: 121 PIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDIWTDGSITPSEATSLSAKILTEHLAIF 180

Query: 232 INFEEPKKEVKEDINVKS 249
           +N  +  KE +  +  + 
Sbjct: 181 VNLNDQAKETEIMVEKEE 198


>gi|150187098|emb|CAK30170.1| RNA polymerase alpha subunit [Streptococcus criceti]
          Length = 181

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 83/181 (45%), Positives = 132/181 (72%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K
Sbjct: 1   LGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + +  +GP  VTAGD+ T +DIE++NPDH +  +     ++  +TV+K  GYVPA+ ++
Sbjct: 61  TIELDVQGPAEVTAGDVLTDSDIEIINPDHYLFTIAEGHSLKATMTVAKNRGYVPAEGNK 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
           +++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R
Sbjct: 121 SDSAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSAR 180

Query: 223 I 223
           +
Sbjct: 181 V 181


>gi|154424755|emb|CAL18480.1| RNA polymerase alpha subunit [Streptococcus alactolyticus]
          Length = 196

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 82/196 (41%), Positives = 129/196 (65%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG 110
           L+SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   G
Sbjct: 1   LLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEG 60

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL 170
           P  VTAGDI T +D+E++N DH +  +     ++  +TV+K  GYVPA+ ++ ++ P+G 
Sbjct: 61  PAEVTAGDILTDSDVEIVNSDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKDDAPVGT 120

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +
Sbjct: 121 LAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNL 180

Query: 231 FINFEEPKKEVKEDIN 246
           F +  E  K       
Sbjct: 181 FTDLTEVAKNTDVMKE 196


>gi|168805063|gb|ACA28610.1| DNA-directed RNA polymerase subunit alpha [Thiomonas sp. WJ68]
          Length = 228

 Score =  212 bits (539), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 96/228 (42%), Positives = 147/228 (64%), Gaps = 3/228 (1%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           G  + +  ++LN+KG+ LK+       +++ K G GVVTA DIQT +D+E++NP+HVI +
Sbjct: 1   GKRQRVIGVLLNLKGVVLKLHNRDEVTLSLRKEGEGVVTAADIQTPHDVEIINPEHVIAH 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALYSPIKKVSYTVESAREG 193
           L     + M++ V KG GYVP       ++    IG I +DA +SP+++VSY VESAR  
Sbjct: 61  LSHGGKLDMQIKVEKGRGYVPGTLRNYGDEGGKSIGHIVLDASFSPVRRVSYAVESARVE 120

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D DKL M I+T+G I+ E+++  ++RIL +QL +F + E  +     +    +  ++
Sbjct: 121 QRTDLDKLVMEIETNGVISAEEAIRSSARILVEQLSVFASLEGAETTEAAETAAGAQTYD 180

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           P LL+ V+ELEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N GR 
Sbjct: 181 PILLRPVDELELTVRSANCLKAENIYYIGDLIQRSETELLKTPNLGRM 228


>gi|161784224|ref|YP_001595540.1| RNA polymerase alpha subunit [Lemna minor]
 gi|88696802|gb|ABD48527.1| RNA polymerase alpha subunit [Lemna minor]
          Length = 284

 Score =  212 bits (539), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 69/275 (25%), Positives = 132/275 (48%), Gaps = 21/275 (7%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++   +E  V  +        +  PL +G A T+G A+RR L+  + G  IT  + + V 
Sbjct: 13  LQWKCVESRVDSKRLH-YGRFVLSPLMKGQADTIGIAMRRALLEEMEGTCITRAKSEKVP 71

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I G+ E + +I++N+K I L+ +    +  +I  +GP  +TA DI     +E+++
Sbjct: 72  HEYSTIVGIEESVHEILMNLKEIVLRSNLYGTREASICVKGPKTITAEDIILPASVEIVD 131

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L     + + L + +  GY     + +++   G   IDA++ P++  ++++ S
Sbjct: 132 TTQHIATLTEPLDLYIGLQIQRDRGYRMRPTNNSQD---GSYPIDAVFMPVRNANHSIYS 188

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++E+ +  +
Sbjct: 189 YGNG-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEKDINLEENKSRFT 247

Query: 250 LPFNPALLK----------------KVEELELSVR 268
           LP      K                 +++LEL  R
Sbjct: 248 LPLFTFHDKLVNLTKNKKEIGLKCIFIDQLELPSR 282


>gi|289524824|emb|CBJ94468.1| alpha subunit of RNA polymerase [Vibrio sp. Cmf 6.5]
          Length = 241

 Score =  212 bits (539), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 103/244 (42%), Positives = 158/244 (64%), Gaps = 8/244 (3%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGV 113
           + G A+T V+I+GVLHE S+ +GV ED+ +I+LN+KG+ + +  G     +T+ K G G 
Sbjct: 1   MPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVCVAEGKDEVFITLNKSGSGP 60

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIG 169
           V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG
Sbjct: 61  VVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL 
Sbjct: 121 RLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLD 180

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
            F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDVRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADML 293
            ++L
Sbjct: 238 VELL 241


>gi|222084158|ref|YP_002519753.1| RNA polymerase alpha chain [Gnetum parvifolium]
 gi|149941454|dbj|BAF64894.1| RNA polymerase alpha subunit [Brassica napus]
 gi|220983495|dbj|BAH11263.1| RNA polymerase alpha chain [Gnetum parvifolium]
          Length = 326

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 74/319 (23%), Positives = 141/319 (44%), Gaps = 13/319 (4%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV- 68
           ++   ++     +           PL +G A+T+  A+RR L+  + G +IT  +I+   
Sbjct: 13  LQWKCLDSKTESKRYH-YGRFSLSPLLKGQANTIAIAIRRTLLGEVEGTSITYAKIEKTT 71

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +H+ S++ G+ E + DI+LN+K I LK       + +I   GP  VTA DI   + I+++
Sbjct: 72  VHDYSTMSGIKESVHDILLNLKEIVLKSELYGIHKASICTVGPRNVTAQDIILPSSIKII 131

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L       + LT+ +  GY         +   GL  IDA   P++ V++++ 
Sbjct: 132 DGTQHIASLTKSVPFNVMLTIERNQGYAIPSQSSRRH-KNGLFPIDAPCMPVRNVNFSIH 190

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN-- 246
           S +       + L   I T+G +T  ++   A   L D +   ++ EE     K+     
Sbjct: 191 SYKSE-NDIREMLIFEIWTNGGLTPREAFYEACWKLIDLIVPLLHMEEDMNGAKDFFALP 249

Query: 247 ----VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
               +  L         + +LELS ++++C +   I  + D +  +  +     +  +KS
Sbjct: 250 ILTRMDKLGKALFQHLFMNQLELSSKNSSCFQQTFIYRLSDFLNYSRQNSKTFEDLDKKS 309

Query: 303 LVEIKGVLGTMGLFLGMNL 321
              IK ++       G+NL
Sbjct: 310 ---IKKIMEFFQKRFGINL 325


>gi|119662333|emb|CAJ33155.1| RNA polymerase alpha subunit [Lactobacillus oris]
          Length = 200

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 86/199 (43%), Positives = 136/199 (68%), Gaps = 2/199 (1%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           L G+AIT +QIDGVLHE S++KGV ED+T IILN+K ++LK++ +  K + +  +GP  V
Sbjct: 1   LPGSAITTMQIDGVLHEFSTVKGVTEDVTQIILNLKKVSLKINSEDQKDLELDVKGPAKV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLIT 172
           TAGDIQ  +++ VLNPD  I  +   A + +++T  KG GY+ A  ++   E+  IG++ 
Sbjct: 61  TAGDIQGDSEVSVLNPDLHIATVADGAELHIKMTADKGRGYLSANDNKARMEDLAIGVLP 120

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           ID++Y+PI++V+YTVE+AR GQ  D+DKL++ + TDGSIT  ++V+L ++IL + L MF+
Sbjct: 121 IDSIYTPIERVNYTVENARVGQRSDFDKLTLDVWTDGSITPTEAVSLGAKILTEHLAMFV 180

Query: 233 NFEEPKKEVKEDINVKSLP 251
           N  E  +  +  +  +   
Sbjct: 181 NLTETAQNAQVMVEKEETH 199


>gi|119368531|ref|YP_913219.1| RNA polymerase alpha subunit [Gossypium barbadense]
 gi|119224893|dbj|BAF41279.1| RNA polymerase alpha subunit [Gossypium barbadense]
          Length = 270

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 62/256 (24%), Positives = 124/256 (48%), Gaps = 8/256 (3%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLR 56
           M+++  +        ++  +    ++        I  PL +G A T+G A+RR L+  L 
Sbjct: 1   MVREKVKVSTSTRTRQWKCVESRTDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGELE 60

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           G  IT  + + + HE S+I G+ E + +I++N+K I L+ +    +   I  +GPG VTA
Sbjct: 61  GTCITRAKSEKIPHEYSTIVGIQESVHEILMNLKEIVLRGNLYGTRNAFICAKGPGYVTA 120

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
            DI     +E+++    + +L     + + L + +  GY        +N   G   IDA+
Sbjct: 121 QDIILPPSVEIVDNTQHVASLTEPIDLCIGLQIERNRGYGIKT---PKNFHDGSYPIDAV 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           + P++  ++++           + L + I T+GS+T ++++  ASR L D    F++ +E
Sbjct: 178 FMPVRNANHSIHCYGND-NEKQEILFLEIWTNGSLTPKEALHEASRNLIDLFIHFLHAKE 236

Query: 237 PKKEVKEDINVKSLPF 252
               ++ + +  +L F
Sbjct: 237 ENLHLENNQHDVTLHF 252


>gi|119672793|emb|CAK95480.1| RNA polymerase alpha subunit [Lactobacillus salivarius]
          Length = 199

 Score =  211 bits (537), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 84/198 (42%), Positives = 131/198 (66%), Gaps = 2/198 (1%)

Query: 56  RGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT 115
            GAAIT VQIDGVLHE S+I GV ED+T IILN+K + L M  +  + + I   GP  VT
Sbjct: 1   PGAAITDVQIDGVLHEFSTIPGVLEDVTLIILNLKKVALSMESEDSQALEINVTGPMEVT 60

Query: 116 AGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITI 173
           AGDIQ+ +D+EVLNP+  IC +   A + + +  +KG GYV A  ++   ++ PIG++ I
Sbjct: 61  AGDIQSNSDVEVLNPEQYICTVADGAELHVRMNANKGRGYVSANDNKALADDMPIGVLPI 120

Query: 174 DALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           D++Y+PI++V+Y VE  R GQ  DYDKL++ + T+GSIT  ++++L+++IL + L +F++
Sbjct: 121 DSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWTNGSITPSEAISLSAKILTEHLALFVD 180

Query: 234 FEEPKKEVKEDINVKSLP 251
             +  K  +  +  +   
Sbjct: 181 LTDEAKNAEIMVEKEETH 198


>gi|224437309|ref|ZP_03658281.1| DNA-directed RNA polymerase subunit alpha [Helicobacter cinaedi
           CCUG 18818]
 gi|313143764|ref|ZP_07805957.1| DNA-directed RNA polymerase subunit alpha [Helicobacter cinaedi
           CCUG 18818]
 gi|313128795|gb|EFR46412.1| DNA-directed RNA polymerase subunit alpha [Helicobacter cinaedi
           CCUG 18818]
          Length = 334

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 91/315 (28%), Positives = 157/315 (49%), Gaps = 3/315 (0%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           I+P     I + +   NR  + A P   G+A TL + LRR+L+ S  G A TA++I GV 
Sbjct: 6   IEPYIPTDISIEEVSSNRIKISAYPFESGYAITLAHPLRRLLLLSSVGYAPTALKIQGVT 65

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT-AGDIQTVNDIEVL 128
           HE  SI+G+ ED++  I N+K I   +  ++   V +     G +  + +      ++V+
Sbjct: 66  HEFDSIRGIVEDVSHFISNLKNIRFLIKDETLDSVQVHYEFKGPMVLSANELANESVDVV 125

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  +  ++ +A +   L V KG GYVP++  R +      I +DA ++P+KK  Y +E
Sbjct: 126 NPEAYLATINENASISFSLIVQKGIGYVPSESIRGKIAEDY-IPLDAYFTPVKKAIYEIE 184

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +       +Y+K+   I+TDG I    +   A  ++  Q+ +F           + I   
Sbjct: 185 NVLVEDNPNYEKIIFDIETDGQIEPLTAFKEAISVMHKQMSIFGVDLSATPNGSKSIAED 244

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
           S      L+ K++ L LS R  NCL    + Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 245 SGEL-KTLMIKIDTLNLSARCFNCLDRSGLKYVGELVIMSENELKNIKNMGKKSYDEITE 303

Query: 309 VLGTMGLFLGMNLPD 323
            L  +G  +G  + +
Sbjct: 304 KLEELGYPVGGEIAE 318


>gi|150036800|emb|CAM98036.1| DNA-directed RNA polymerase alpha chain [Leuconostoc fallax]
          Length = 196

 Score =  210 bits (535), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 82/195 (42%), Positives = 124/195 (63%), Gaps = 2/195 (1%)

Query: 49  RVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK 108
           R+L+SSL GAA+  VQIDGV+HE S++ GV ED+T +ILN+K + L +  D  K + I  
Sbjct: 2   RILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQLILNLKKVVLAIDSDEEKSLEIDV 61

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--END 166
           +GP  VTA D+Q   DIEVLNP+  +  +     + M +T  KG GY  A  ++   +  
Sbjct: 62  QGPAEVTAADLQGSADIEVLNPELHLATVAAGKSLHMTVTAVKGRGYSSADENKQLRDEM 121

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           PIG++ +D++Y+PI++V+Y VE+ R GQ  DYDKL+  I T+GSI   D+++L ++IL +
Sbjct: 122 PIGVLAVDSIYTPIERVNYQVENTRVGQRDDYDKLTFDIWTNGSIKPSDALSLGAKILSE 181

Query: 227 QLGMFINFEEPKKEV 241
            L +F +      E 
Sbjct: 182 HLNLFTDISSVAAET 196


>gi|150036776|emb|CAM98267.1| DNA-directed RNA polymerase alpha chain [Weissella viridescens]
          Length = 175

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 85/172 (49%), Positives = 119/172 (69%), Gaps = 2/172 (1%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRVL+SSL GAAI +VQIDGVLHE S+++GV ED+T IILN+K +++++  D  K
Sbjct: 4   LGNSLRRVLLSSLPGAAINSVQIDGVLHEFSTVEGVVEDVTQIILNLKKVSMRIDSDDEK 63

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + +   GP  VTAGD     D+EVLN D  I  +   A + M +T  +G GYV    ++
Sbjct: 64  TLEVNVNGPATVTAGDFVGDADVEVLNKDQYIATVAAGATLHMTVTAVRGRGYVSGDQNK 123

Query: 163 T--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
              E+ PIG++ ID++++PI++V+Y VE  R GQ  DYDKL+M I TDGS+T
Sbjct: 124 ELHEDTPIGVLAIDSIFTPIERVNYQVEETRVGQRNDYDKLTMDIWTDGSLT 175


>gi|119662831|emb|CAJ33208.1| RNA polymerase alpha subunit [Lactobacillus mucosae]
          Length = 180

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 86/180 (47%), Positives = 126/180 (70%), Gaps = 2/180 (1%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRRV+M+SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K ++LK+  +
Sbjct: 1   GTTLGNSLRRVMMASLPGAAITSIQIDGVLHEFSTVQGVTEDVTQIILNLKKVSLKIESE 60

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             K + +  +GP  VTAGDIQ   D+ +LNPD  I  +   A + + +T  KG GYVPA 
Sbjct: 61  DAKDLELDVKGPAEVTAGDIQGDGDVTILNPDLHIATVADGAELHIMMTADKGRGYVPAD 120

Query: 160 HHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
            ++       IG + ID++Y+PI++V+YTVE+ R GQ  D+DKL++ + TDGS+T   ++
Sbjct: 121 QNKLRLSGLEIGTLPIDSIYTPIERVNYTVENTRVGQSNDFDKLTLDVWTDGSLTPTAAI 180


>gi|240047283|ref|YP_002960671.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma conjunctivae
           HRC/581]
 gi|239984855|emb|CAT04845.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma conjunctivae]
          Length = 332

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 82/316 (25%), Positives = 147/316 (46%), Gaps = 17/316 (5%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           + Q  +  T    +PL RG  +T+GNALRR ++SS+  A++ A++I  + HE S +  V 
Sbjct: 14  IQQVSDFETTFELKPLERGLGNTIGNALRRTILSSVSSASVFAIKIANIDHEFSVLDNVV 73

Query: 80  EDLTDIILNIKGINLKMSG-----DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           ED+  I+ N+K I  +        D  ++V+      G + A DI     +E++N D  I
Sbjct: 74  EDVVSILNNLKKIRFRYHEELFDNDQIQKVSFSGDKAGNIYAKDIDNTGGLEIVNQDQYI 133

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTE----------NDPIGLITIDALYSPIKKVS 184
            ++     ++ E+ +  G G+   + ++            +    +I +D+ +SP+ KV 
Sbjct: 134 ASVGKVGALKFEMFIIGGKGFTDFETNKKRVSDLAGKLQSDLLGTIIAVDSDFSPVVKVH 193

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y          +  ++L + + TDG+I  +D++A A++IL   L +  N E   +     
Sbjct: 194 YEANELNSSNPIVEERLVLNLKTDGTIFAKDALAEAAKILIAHLQLVSNTENLDQIADNF 253

Query: 245 INVKSLPFN--PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                         L  +  L+LSVRS N LR      + D+   T+ ++  + N G+KS
Sbjct: 254 FEESRYHEEQPKKNLIDLSALDLSVRSLNALRRAQYYKVSDIQDLTQEELENIKNLGKKS 313

Query: 303 LVEIKGVLGTMGLFLG 318
           + EI   L   G+ L 
Sbjct: 314 VQEILDKLKEQGIELK 329


>gi|108796735|ref|YP_636498.1| alpha subunit of RNA polymerase [Zygnema circumcarinatum]
 gi|122226721|sp|Q32RM8|RPOA_ZYGCR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|61393719|gb|AAX45861.1| alpha subunit of RNA polymerase [Zygnema circumcarinatum]
          Length = 356

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 78/335 (23%), Positives = 148/335 (44%), Gaps = 47/335 (14%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
                  PL  G A T+G A+RR L+  +    IT+  + G  HE S++KG+ E + DI+
Sbjct: 26  YGRFAVYPLFPGQAITIGTAIRRALLGEVHSTCITSAYVVGASHEYSTLKGIRESIHDIL 85

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+K I  K      +   +   GPG+VTA  I+    ++V++    I  L++   + + 
Sbjct: 86  LNLKDIVFKSDTLERQEGILLFNGPGIVTAQHIKLPPVVQVVDNTQYIARLEMPTSIEIH 145

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           +T+             T     G   +DA   P++ ++Y++ S  EG +   + L + + 
Sbjct: 146 ITLENTKTCTSLNTMPT---TKGRFILDAALKPVRNMNYSIHSLGEGDMR-QEMLVLEVW 201

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFE----------------EPKKEVKEDINVKSL 250
           T+GS+T ++ ++ AS+ L D L   +  E                  + E      ++ +
Sbjct: 202 TNGSLTPQEVISQASQNLNDLLKPLLKVERYFQAKQNIHKKRMFTPTQSENLNMDQIEMI 261

Query: 251 PFNPALLKK--------------------------VEELELSVRSTNCLRGENIVYMGDL 284
             N  + +                           +++L++SVR++NCL+   I  +  L
Sbjct: 262 GGNKLIDQPLLPADSHLNSSLSLNIDNLVHLEGISIDDLQISVRASNCLKKVGIYTIRQL 321

Query: 285 IQRTEADMLRMANFGRKSLVEI-KGVLGTMGLFLG 318
           +  T+ D+ ++ N G+KS+ +I   +  + G  LG
Sbjct: 322 LSYTQQDLFQIKNLGKKSVEQIVIAIRKSYGHILG 356


>gi|121489391|emb|CAJ44676.1| RNA polymerase alpha subunit [Carnobacterium maltaromaticum]
 gi|145586275|emb|CAM91232.1| RNA polymerase alpha-subunit [Carnobacterium maltaromaticum]
          Length = 199

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 82/199 (41%), Positives = 130/199 (65%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T +QIDGVLHE S+I GV ED+T IILNIK + LK+     K + I  +GP VVTA DI
Sbjct: 1   VTTIQIDGVLHEFSTIDGVVEDVTSIILNIKKLALKLYSGEDKTIEIDVKGPAVVTAADI 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
              +D+E+LNPD  IC +   A   + LT  +G GY  A+H++ ++ PIG++ +D++Y+P
Sbjct: 61  TYDSDVEILNPDLYICTVAEGARFHVRLTAKQGRGYARAEHNKHDDMPIGVLPVDSIYTP 120

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           + +V+Y VE+ R GQ  ++DKL++ +  DGSI+ ED+V+LA++IL + L +F+N  +  +
Sbjct: 121 VSRVNYQVENTRVGQKDNFDKLTLDVWADGSISPEDAVSLAAKILTEHLDIFVNLSDEAR 180

Query: 240 EVKEDINVKSLPFNPALLK 258
           +V+  +  +       L  
Sbjct: 181 KVEIMVEKEETHKEKMLEM 199


>gi|119668331|emb|CAK95465.1| RNA polymerase alpha subunit [Lactobacillus iners]
          Length = 201

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 89/201 (44%), Positives = 136/201 (67%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRRVL++S+ G A++ + IDGVLHE S+I GV ED+T IILN+K + LK+  D  K V I
Sbjct: 1   LRRVLLTSISGTALSYIMIDGVLHEFSTIPGVREDVTKIILNLKKLELKLLVDEEKMVEI 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
              GP VVTA D++   D+E+LNPD  IC +     + M + +  G GY+PA  +++++ 
Sbjct: 61  DVEGPAVVTAADLKVDADVEILNPDQYICTIAEGGHLHMSIAIKNGRGYIPASENKSDDM 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           PIG+I +D+L+SPIKKV+Y VE+AR G+  DYDKL++ + TDGSIT  D+++ A++IL++
Sbjct: 121 PIGVIPVDSLFSPIKKVNYQVENARVGKRDDYDKLTLELWTDGSITPNDALSFAAKILEE 180

Query: 227 QLGMFINFEEPKKEVKEDINV 247
              +F++ +   +     I  
Sbjct: 181 HFKVFMSADMSDQFANVMIEK 201


>gi|150036710|emb|CAM98249.1| DNA-directed RNA polymerase alpha chain [Leuconostoc carnosum]
          Length = 189

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 82/188 (43%), Positives = 122/188 (64%), Gaps = 2/188 (1%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           +L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + + I  +
Sbjct: 1   ILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDEERVLEIDVQ 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDP 167
           GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++   E  P
Sbjct: 61  GPSEVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSADENKQLREEMP 120

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           IG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L S+IL + 
Sbjct: 121 IGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSLGSKILAEH 180

Query: 228 LGMFINFE 235
           L +F++  
Sbjct: 181 LNLFMDIS 188


>gi|161511713|emb|CAP16867.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 207

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 85/207 (41%), Positives = 131/207 (63%), Gaps = 2/207 (0%)

Query: 54  SLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGV 113
           SL GAA+T+VQIDGVLHE S+I+GV ED+T IILN+K ++LK+  D  K + I   GP  
Sbjct: 1   SLPGAALTSVQIDGVLHEFSTIEGVVEDVTQIILNLKKVSLKVESDEEKSLEINVMGPAN 60

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLI 171
           VTAGDI    D+ +LNP+  IC +         LT  KG GY  A  ++    + PIG++
Sbjct: 61  VTAGDIVGDGDVTILNPELPICTVAEGTTFHAVLTAEKGRGYTSADENKARKVDMPIGVL 120

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGS+   ++++L+++IL + L +F
Sbjct: 121 PIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSLAASEAISLSAKILTEHLTIF 180

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLK 258
           +N ++  K+ +  +  +       L  
Sbjct: 181 VNLDDQAKDTEIMVEKEETHKEKMLEM 207


>gi|187763133|ref|YP_001876608.1| RNA polymerase alpha subunit [Welwitschia mirabilis]
 gi|163311663|gb|ABY26821.1| RNA polymerase alpha subunit [Welwitschia mirabilis]
 gi|220983428|dbj|BAH11197.1| RNA polymerase alpha chain [Welwitschia mirabilis]
          Length = 340

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 74/326 (22%), Positives = 138/326 (42%), Gaps = 19/326 (5%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG--V 68
           +   +EY V  +           PL RG   T+G+ALRR L+  + G  +T V+     V
Sbjct: 14  QWKCLEYRVESKRSH-YGRFSLSPLLRGQGGTIGSALRRTLLRDVEGTNVTHVKFFNKRV 72

Query: 69  LHEIS--SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
            H  S  +I G+ E + DII+N++ I  +       +  I+  GP  VTA DI     I+
Sbjct: 73  KHLFSSSTILGIEESVHDIIMNLREIVFRCELHGIHKAYIYTVGPKNVTAQDIILPPFIQ 132

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +++    I ++     + + L + K  G      H         I  +  Y P++ V+Y 
Sbjct: 133 IVDGTQHIASITKPIHLHVTLKIEKNWGETTESIHPITKYFTRYIPTEIFYMPVRSVTYN 192

Query: 187 VESAREGQVL-DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN---FEEPKKEVK 242
           V   ++   +  YD L   + T+G +T ++++  A   L D +   ++          VK
Sbjct: 193 VYFYKDEYDIHIYDILIFELWTNGELTPKEALYEACWRLIDLIIPLLDVPLLHVEGSGVK 252

Query: 243 EDINVK-------SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           E I +        +          +++L L  + +  LR  +I  + D +  ++ D+  +
Sbjct: 253 ESIPLPIVSNMNRTQEDLFVQHLFIDQLGLPSKISKSLRESHIYRVSDFMNYSQQDLKNL 312

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNL 321
             + +K    I+  L  +  + G+NL
Sbjct: 313 E-YSKK--ESIEQTLEILHKYFGINL 335


>gi|150187001|emb|CAK30147.1| RNA polymerase alpha subunit [Streptococcus ovis]
          Length = 202

 Score =  209 bits (532), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 81/198 (40%), Positives = 128/198 (64%)

Query: 56  RGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT 115
            GAA+T+++IDGVLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  VT
Sbjct: 1   PGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKTIELDVVGPAEVT 60

Query: 116 AGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDA 175
           AGDI T +DIE++NPDH +  +   A  +  LTV+ G GYVPA+ ++ +  P+G + +D+
Sbjct: 61  AGDILTDSDIEIVNPDHYLFTISEGATFKATLTVNTGRGYVPAEGNKKDEAPVGTLAVDS 120

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           +Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + LG+F +  
Sbjct: 121 IYTPVVKVNYQVEPARVGSNDGFDKLTLEIMTNGTIIPEDALGLSARILMEHLGLFTDLT 180

Query: 236 EPKKEVKEDINVKSLPFN 253
           +  K  +     ++   +
Sbjct: 181 DVAKAAEVMKETETASDD 198


>gi|119662391|emb|CAJ33185.1| RNA polymerase alpha subunit [Lactobacillus amylophilus]
          Length = 174

 Score =  209 bits (532), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 82/174 (47%), Positives = 123/174 (70%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           +LRRVL++SL G+A++ +QIDGVLHE S+I GV ED+T IILN+K + LK      K   
Sbjct: 1   SLRRVLLASLPGSAVSYLQIDGVLHEFSTIPGVLEDVTQIILNLKKLTLKSIAADEKLAE 60

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
           I   GP  VTAGD++  +++++LNPD  I  +   A +RM + + +G GYVPA  +++++
Sbjct: 61  IDVEGPATVTAGDLKVDDEVQILNPDQYIATVAEGAHLRMTVAIKQGRGYVPADQNKSDD 120

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
            PIG++ +D+L+SPI+KV+Y VE  R G+  DYDKL+M + TDGSIT  D+++ 
Sbjct: 121 MPIGVVPVDSLFSPIEKVNYQVEGTRVGRNNDYDKLTMEVWTDGSITPNDALSF 174


>gi|119662377|emb|CAJ33177.1| RNA polymerase alpha subunit [Lactobacillus paraplantarum]
          Length = 176

 Score =  209 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 87/176 (49%), Positives = 127/176 (72%), Gaps = 2/176 (1%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG 110
           L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILN+K I LK+  D  K + I  +G
Sbjct: 1   LLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVTAIILNVKKIALKLESDETKTLEIDVKG 60

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPI 168
           P  VTAGDI    D+EVLNPD  IC +   A   M +T + G GYV A+ ++   ++ PI
Sbjct: 61  PANVTAGDIIGDADVEVLNPDLPICTVADGAHFHMRMTANTGRGYVSAEDNKHREDDMPI 120

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           G++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T+GSIT  ++++L+++IL
Sbjct: 121 GVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWTNGSITPSEAISLSAKIL 176


>gi|72534423|emb|CAH59047.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 190

 Score =  209 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 87/190 (45%), Positives = 127/190 (66%)

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
           AAIT +QIDGVLHE S+IKGV ED+T IILNIKG+ LKM G   K + I   GP  VTAG
Sbjct: 1   AAITNIQIDGVLHEFSTIKGVREDVTQIILNIKGLALKMYGQEEKTLEIDITGPATVTAG 60

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI   +D+E+LN D  IC++   A     LTV  G GYV A  ++ E+ PIG++ +D++Y
Sbjct: 61  DIIVDSDVEILNKDMYICSVSEGATFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIY 120

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           +P+++V+Y VE+ R G   D+DKL+M I TDGSI   ++++L+++I+ + L +F+N  + 
Sbjct: 121 TPVRRVNYQVENTRVGHREDFDKLTMEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDE 180

Query: 238 KKEVKEDINV 247
            K  +  +  
Sbjct: 181 AKNAEIMVEK 190


>gi|150036726|emb|CAM98254.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. dextranicum]
          Length = 189

 Score =  209 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 81/188 (43%), Positives = 123/188 (65%), Gaps = 2/188 (1%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           +L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + + I  +
Sbjct: 1   ILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDIQ 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDP 167
           GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++   +  P
Sbjct: 61  GPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSADENKKLRDEMP 120

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           IG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L ++IL + 
Sbjct: 121 IGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTNGSIKPSDALSLGAKILAEH 180

Query: 228 LGMFINFE 235
           LG+F++  
Sbjct: 181 LGLFMDIS 188


>gi|58699558|ref|ZP_00374269.1| dna-directed rna polymerase alpha chain [Wolbachia endosymbiont of
           Drosophila ananassae]
 gi|58533923|gb|EAL58211.1| dna-directed rna polymerase alpha chain [Wolbachia endosymbiont of
           Drosophila ananassae]
          Length = 220

 Score =  209 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 108/219 (49%), Positives = 150/219 (68%), Gaps = 10/219 (4%)

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--------TENDPIGLITIDALYSPIKK 182
           D +IC L  +  + M + V+ G GY+P   ++        +E D IG I ++ALYSP+ +
Sbjct: 1   DLLICTLGQNVELNMTIYVASGKGYLPVTKYKENELLKLMSEQDLIGFIPVNALYSPVNR 60

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI--NFEEPKKE 240
           VSY VE++R GQV D DKL ++I+TDG+I+   +V  A+RILQ+QL  FI  +    K +
Sbjct: 61  VSYRVENSRVGQVTDKDKLILSIETDGTISPSQAVDSAARILQEQLQPFISSDVSYKKSQ 120

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V      K L ++P LL+KV+E+ELSVRS NCL+ ENI Y+GDL+Q+TE +MLR ANFGR
Sbjct: 121 VSSSSGAKDLGYDPVLLRKVDEMELSVRSHNCLKNENITYIGDLVQKTEGEMLRTANFGR 180

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL   GL LGMN+ +WPP+ I+ELAK++ D+
Sbjct: 181 KSLNEIKAVLTNFGLSLGMNVLNWPPKDIDELAKQHTDE 219


>gi|161511775|emb|CAP16898.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 193

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 85/193 (44%), Positives = 124/193 (64%), Gaps = 2/193 (1%)

Query: 56  RGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT 115
            GAAIT+VQID VLHE S+I+GV ED+T IILN+K ++LK+  D  K + I   GP  VT
Sbjct: 1   PGAAITSVQIDSVLHEFSTIEGVVEDVTQIILNLKKVSLKIESDEDKTLEINVAGPANVT 60

Query: 116 AGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITI 173
           AGDI    D+ +LNP+  IC +         LT   G GY  A  ++    + PIG++ I
Sbjct: 61  AGDIMGDGDVVILNPELPICTVAEGTTFHAVLTADTGRGYTSADENKARKVDMPIGVLPI 120

Query: 174 DALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           D++Y+PI++V+Y VE+ R GQ  DYDKL++ I TDGSIT  ++ +L+++IL + L +F+N
Sbjct: 121 DSIYTPIERVNYQVENTRVGQRDDYDKLTLDIWTDGSITPSEATSLSAKILTEHLAIFVN 180

Query: 234 FEEPKKEVKEDIN 246
             +  KE +  + 
Sbjct: 181 LNDQAKETEIMVE 193


>gi|161511711|emb|CAP16866.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 209

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 88/209 (42%), Positives = 130/209 (62%), Gaps = 2/209 (0%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           IT+VQID VLHE S+I+GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI
Sbjct: 1   ITSVQIDSVLHEFSTIEGVVEDVTQIILNLKKVSLKIESDEDKTLEINVAGPANVTAGDI 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALY 177
               D+ +LNP+  IC +         LT   G GY  A  ++    + PIG++ ID++Y
Sbjct: 61  MGDGDVVILNPELPICTVAEGTTFHAVLTADTGRGYTSADENKARKVDMPIGVLPIDSIY 120

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           +PI++V+Y VE+ R GQ  DYDKL++ I TDGSIT  ++ +L+++IL + L +F+N  + 
Sbjct: 121 TPIERVNYQVENTRVGQRDDYDKLTLDIWTDGSITPSEATSLSAKILTEHLAIFVNLNDQ 180

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELS 266
            KE +  +  +       L   +EEL+LS
Sbjct: 181 AKETEIMVEKEETHKEKMLEMTIEELDLS 209


>gi|119662373|emb|CAJ33175.1| RNA polymerase alpha subunit [Lactobacillus panis]
          Length = 190

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 86/190 (45%), Positives = 134/190 (70%), Gaps = 2/190 (1%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           L GAAIT +QIDGVLHE S++KGV ED+T IILN+K ++LK++ +  K + +  +GP  V
Sbjct: 1   LPGAAITTMQIDGVLHEFSTVKGVTEDVTQIILNLKKVSLKLNSEDQKNLELDVKGPAEV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLIT 172
           TA DIQ  +++ +LNPD  I  +   A + +++T  KG GY+ A  ++   E+ PIG++ 
Sbjct: 61  TASDIQGDSEVTILNPDLHIATVADGAELHIKMTADKGRGYLSANDNKARMEDLPIGVLP 120

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           ID++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T  ++V+L ++IL + L MF+
Sbjct: 121 IDSIYTPIERVNYTVENARVGQRSDYDKLTLDVWTDGSLTPIEAVSLGAKILTEHLDMFV 180

Query: 233 NFEEPKKEVK 242
           N  E  +  +
Sbjct: 181 NLTETAQNAQ 190


>gi|313678392|ref|YP_004056132.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma bovis PG45]
 gi|312950669|gb|ADR25264.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma bovis PG45]
          Length = 336

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 91/333 (27%), Positives = 158/333 (47%), Gaps = 26/333 (7%)

Query: 9   LIKPNNIEYIVLGQE----EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           + + + ++Y+ +         N      +PL RGF +T+  ALRRVL+S++   A+ A++
Sbjct: 1   MERMSKLDYLQVSNSAINNNLNEVTFSLKPLERGFGNTVAVALRRVLLSNVTSLALFAIK 60

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-----SHKRVTIFKRGPGVVTAGDI 119
           I GV HE  +I G+ ED+T II+N++ +  K + +        + TI    PG+VT+  I
Sbjct: 61  ISGVSHEFQTIPGIVEDVTAIIMNLRKVKFKYNPEFVKDGEIIKATIKAEQPGIVTSKSI 120

Query: 120 Q-TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG--------- 169
           + T   +E++N    I N+     + +EL +  G G++  + ++                
Sbjct: 121 EITNPSVEIINKSQEIANIQKG-SLVIELFLRPGRGFISNESNKKFIQNDSLFASKIESN 179

Query: 170 -----LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
                 I +D+ +SP++K SYTV           ++L  TI TDG+I  + ++  A +IL
Sbjct: 180 IKKGLFIAVDSNFSPVEKCSYTVRELNTSSNKIEEELLFTIKTDGTIDAKSAINQACKIL 239

Query: 225 QDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDL 284
                   + +  K +V E+  VK+          + +L LSVRS N L+        ++
Sbjct: 240 VAHFMAVGDVDSMKLDVFEEEKVKNDEPIEND-VDINQLGLSVRSLNALKRIGKTKASEV 298

Query: 285 IQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
              T  ++ +  N GRKSL EI+  L   G  L
Sbjct: 299 AAMTWEELEQTKNLGRKSLDEIQECLKVNGFTL 331


>gi|150186935|emb|CAK30131.1| RNA polymerase alpha subunit [Streptococcus macedonicus]
          Length = 203

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 82/203 (40%), Positives = 129/203 (63%)

Query: 53  SSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
           SSL GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP 
Sbjct: 1   SSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPA 60

Query: 113 VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT 172
            VTAGDI T +D+E++NPDH +  +     ++  +TV+K  GYV A+ ++ E+ P+G + 
Sbjct: 61  EVTAGDILTDSDVEIVNPDHYLFTIAEGHSLKATMTVAKERGYVSAEGNKKEDAPVGTLA 120

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F 
Sbjct: 121 VDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFT 180

Query: 233 NFEEPKKEVKEDINVKSLPFNPA 255
           +  E  K        + +     
Sbjct: 181 DLTEVAKSTDVMKETEKVNDEKV 203


>gi|119662803|emb|CAJ33193.1| RNA polymerase alpha subunit [Lactobacillus mali]
          Length = 196

 Score =  207 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 79/195 (40%), Positives = 130/195 (66%), Gaps = 2/195 (1%)

Query: 59  AITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGD 118
           AIT +QIDGVLHE S+IKGV ED+T IILN+K + L++  + ++ + I   GP  VTAGD
Sbjct: 1   AITDIQIDGVLHEFSTIKGVLEDVTQIILNLKKVALRIDSEENQTLEINVAGPVEVTAGD 60

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDAL 176
           IQ  +D+EVLN D  IC +   A   + +T + G GYV A  ++   ++ PIG++ ID++
Sbjct: 61  IQGSSDVEVLNSDLYICTVAEGASFHVRMTANTGRGYVSADDNKARADDMPIGVLPIDSI 120

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           Y+PI++V+Y VE AR GQ  D+DKL++ + T+G++T  ++++L+++IL + L +F++  +
Sbjct: 121 YTPIERVNYQVEKARVGQKDDFDKLTLDVWTNGAVTPSEAISLSAKILTEHLTLFVDLTD 180

Query: 237 PKKEVKEDINVKSLP 251
             K  +  +  +   
Sbjct: 181 EAKNAEIMVEKEETH 195


>gi|148377782|ref|YP_001256658.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma agalactiae
           PG2]
 gi|148291828|emb|CAL59218.1| DNA directed RNA polymerase alpha chain (RNAPalpha subunit)
           (Transcriptase alpha chain) (RNApolymerase alpha
           subunit) [Mycoplasma agalactiae PG2]
          Length = 336

 Score =  207 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 90/333 (27%), Positives = 160/333 (48%), Gaps = 26/333 (7%)

Query: 9   LIKPNNIEYIVLGQE----EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           + + + ++Y+ +         N      +PL RGFA+T+  ALRRVL+S++   A+ A++
Sbjct: 1   MKRMSKLDYLQVSNSAINNNLNEVTFSLKPLERGFANTVAVALRRVLLSNITSLALFAIK 60

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-----SHKRVTIFKRGPGVVTAGDI 119
           I GV HE  +I G+ ED+T II+N++ +  K + +        + TI    PGVVT+  I
Sbjct: 61  ISGVSHEFQTIPGIVEDVTAIIMNLRKVKFKYNPEFVKDGEIIKATIKAEQPGVVTSKSI 120

Query: 120 Q-TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG--------- 169
           + +   +E++N    I N+   A + +EL +  G G++  + ++                
Sbjct: 121 EISNPSVEIINKSQEIANIQKGA-LVIELFLRPGRGFISNESNKKFIQNDSLFASKIESN 179

Query: 170 -----LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
                 I +D+ +SP++K SYTV+          ++L  TI TDG++  + ++  A +IL
Sbjct: 180 IKKGLFIAVDSNFSPVEKCSYTVKELNTSSNKIEEELLFTIKTDGTVDAKSAINQACKIL 239

Query: 225 QDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDL 284
                   + +  K +V E+  + +          + +L LSVRS N L+        ++
Sbjct: 240 VAHFMTVGDVDAMKIDVFEEEKINNDEPIEND-VDINQLGLSVRSLNALKRIGKTKASEV 298

Query: 285 IQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
              T  ++ +  N GRKSL EI+  L   G  L
Sbjct: 299 AAMTWEELEQTKNLGRKSLDEIQECLKLNGFTL 331


>gi|150036824|emb|CAM98043.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gasicomitatum]
          Length = 179

 Score =  207 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 80/179 (44%), Positives = 118/179 (65%), Gaps = 2/179 (1%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + +
Sbjct: 1   NSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDEERSL 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT- 163
            +  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++  
Sbjct: 61  EVDIQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTITAFKGRGYSSADENKQL 120

Query: 164 -ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
            +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L S
Sbjct: 121 RDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSLGS 179


>gi|291320469|ref|YP_003515733.1| DNA directed RNA polymerase subunit alpha (RNAPsubunit alpha)
           (Transcriptase subunit alpha) (RNApolymerase subunit
           alpha) [Mycoplasma agalactiae]
 gi|290752804|emb|CBH40779.1| DNA directed RNA polymerase alpha chain (RNAPalpha subunit)
           (Transcriptase alpha chain) (RNApolymerase alpha
           subunit) [Mycoplasma agalactiae]
          Length = 336

 Score =  206 bits (525), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 90/333 (27%), Positives = 160/333 (48%), Gaps = 26/333 (7%)

Query: 9   LIKPNNIEYIVLGQE----EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           + + + ++Y+ +         N      +PL RGFA+T+  ALRRVL+S++   A+ A++
Sbjct: 1   MERMSKLDYLQVSNSAINNNLNEVTFSLKPLERGFANTVAVALRRVLLSNITSLALFAIK 60

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-----SHKRVTIFKRGPGVVTAGDI 119
           I GV HE  +I G+ ED+T II+N++ +  K + +        + TI    PGVVT+  I
Sbjct: 61  ISGVSHEFQTIPGIVEDVTAIIMNLRKVKFKYNPEFVKDGEIIKATIKAEQPGVVTSKSI 120

Query: 120 Q-TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG--------- 169
           + +   +E++N    I N+   A + +EL +  G G++  + ++                
Sbjct: 121 EISNPSVEIINKSQEIANIQKGA-LVIELFLRPGRGFISNESNKRFIQNDSLFASKIESN 179

Query: 170 -----LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
                 I +D+ +SP++K SYTV+          ++L  TI TDG++  + ++  A +IL
Sbjct: 180 IKKGLFIAVDSNFSPVEKCSYTVKELNTSSNKIEEELLFTIKTDGTVDAKSAINQACKIL 239

Query: 225 QDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDL 284
                   + +  K +V E+  + +          + +L LSVRS N L+        ++
Sbjct: 240 VAHFMTVGDVDTMKIDVFEEERINNDEPIEND-VDINQLGLSVRSLNALKRIGKTKASEV 298

Query: 285 IQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
              T  ++ +  N GRKSL EI+  L   G  L
Sbjct: 299 AAMTWEELEQTKNLGRKSLDEIQECLKLNGFTL 331


>gi|119668357|emb|CAK95473.1| RNA polymerase alpha subunit [Lactobacillus pontis]
          Length = 179

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 84/178 (47%), Positives = 128/178 (71%), Gaps = 2/178 (1%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           G+  TLG++LR VL++SL GAAIT++QIDGVLHE S+ +GV ED+T IILN+K ++LK++
Sbjct: 1   GYGTTLGDSLRGVLLASLPGAAITSMQIDGVLHEFSTDEGVTEDVTQIILNLKKVSLKIN 60

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
            +  K + +  +GP  VTA DIQ   ++ +LNPD  I  +   A + +++T  KG GY+ 
Sbjct: 61  SEDQKDLELDVKGPAEVTAADIQGDGEVTILNPDLHIATVADGAELHIKMTADKGRGYLS 120

Query: 158 AKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           A  ++   E+  IG++ ID++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T 
Sbjct: 121 ANDNKARMEDLAIGVLPIDSIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLTP 178


>gi|71056848|emb|CAH58979.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           haemoperoxidus]
          Length = 199

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 85/199 (42%), Positives = 130/199 (65%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           IT +QIDGVLHE S+IKGV ED+T IILNIKG+ LK+  +  K + I   GP  VTAGDI
Sbjct: 1   ITNIQIDGVLHEFSTIKGVREDVTQIILNIKGLALKLYAEEEKTLEIDITGPATVTAGDI 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
              +D+E+LN D +IC++   A     LTV  G GYV A  ++ E+ PIG++ +D++Y+P
Sbjct: 61  IVDSDVEILNKDLIICSVSEGATFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTP 120

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +++V+Y VE+ R G+  D+DKL+M I TDGSI  +++++LA++I+ + L +F+N  +  K
Sbjct: 121 VRRVNYQVENTRVGRRDDFDKLTMEIWTDGSIIPQEALSLAAKIMTEHLDIFVNLTDEAK 180

Query: 240 EVKEDINVKSLPFNPALLK 258
             +  +  +       L  
Sbjct: 181 NAEIMVEKEETQKEKMLEM 199


>gi|294155443|ref|YP_003559827.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma crocodyli
           MP145]
 gi|291600072|gb|ADE19568.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma crocodyli
           MP145]
          Length = 333

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 87/318 (27%), Positives = 154/318 (48%), Gaps = 19/318 (5%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +      +       +PL RGFA TLG ALRRVL+S++   A   V+I+GV HE   I G
Sbjct: 12  VPSSTTSDFEGTFNLQPLERGFATTLGVALRRVLLSNITSLAPFCVRIEGVTHEFQGITG 71

Query: 78  VHEDLTDIILNIKGINLKMS-----GDSHKRVTIFKRGPGVVTAGDIQTVN--DIEVLNP 130
           V ED+  +I+N++ +           D   +V +     G + +  ++ V+  ++EV++ 
Sbjct: 72  VIEDVPSLIMNLRKVRFSYDPELVKDDEIIKVELKADQIGEINSRYLEVVDNLNVEVIDH 131

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHR-----------TENDPIGLITIDALYSP 179
           +  I ++ ++  +R+EL +  G G+V ++ ++           T+      I +D+ +SP
Sbjct: 132 NIHIADVALENSLRLELYLRPGRGFVSSEENKALVSKLETQLETKIKKGKFIAVDSNFSP 191

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           ++KV+Y V       V   +KL   + TDG++  +D++  A+ IL     +  N +E K 
Sbjct: 192 VEKVNYVVSELNSSSVKIEEKLEFNVITDGTVKPKDAIKQAAEILISHFKVIGNVDEIKD 251

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            + E    K L      +  + +L LSVRS N LR        ++ + T  ++ +  N G
Sbjct: 252 SIFETSEDKVLDVQEQDI-DINQLGLSVRSLNALRRIGKTKASEVAKMTYDELEQTKNLG 310

Query: 300 RKSLVEIKGVLGTMGLFL 317
           +KSL EI   +   G  L
Sbjct: 311 KKSLDEIITKIKEHGFEL 328


>gi|150186978|emb|CAK30140.1| RNA polymerase alpha subunit [Streptococcus sanguinis SK1]
          Length = 194

 Score =  205 bits (522), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 81/194 (41%), Positives = 123/194 (63%)

Query: 53  SSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
           +SL GAA+T++ I+GVLHE  +I GV ED+  IILN+KGI +K      K + +   GP 
Sbjct: 1   ASLPGAAVTSINIEGVLHEFDTISGVREDVMQIILNVKGIAVKSYVQDEKIIELDVEGPA 60

Query: 113 VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT 172
            VTAGDI T +DIE++NPDH +  +   A  +  +TV+ G GYVPA  ++ ++ P+G + 
Sbjct: 61  EVTAGDILTDSDIEIINPDHYLFTIGEGASFKATMTVNSGRGYVPADENKKDDAPVGTLA 120

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F 
Sbjct: 121 VDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLFT 180

Query: 233 NFEEPKKEVKEDIN 246
           N  E          
Sbjct: 181 NLTEVAIAADVMKE 194


>gi|12644248|sp|P38018|RPOA_MYCSP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|7330636|gb|AAA61685.2| RNA polymerase alpha subunit [Chlamydia muridarum]
          Length = 353

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 78/337 (23%), Positives = 156/337 (46%), Gaps = 16/337 (4%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
           V  +  +  T  + EPL RG+A+T+G  LRR L+SS+   A  A++I+ V HE  +I G+
Sbjct: 13  VAEKVNDFNTTFVIEPLARGYANTMGTVLRRTLLSSITSVAPFAIKINNVEHEFQTISGL 72

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFK-----RGPGVVTAGDIQTVNDIEVLNPDHV 133
            ED   ++ NI+ I    + +  ++  + K        G + A DI  V+ +E++N D  
Sbjct: 73  KEDAITLVRNIRNIRFVYNEEIFEKENLAKISFKTNKEGEIFASDIPEVSGLEIVNKDQY 132

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG-----------LITIDALYSPIKK 182
           I N+     +  +L + KG G++  + ++      G            + +D+ +SP+KK
Sbjct: 133 IANIAKGGSLEFDLFLRKGRGFIDFEENKNVISQYGSRLESSIKNGQFLAMDSDFSPVKK 192

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
            + + E       L  ++L + I+TD +++ ++++  A++I+     +  N    +    
Sbjct: 193 CAISFEELNSSSKLIEERLKIKIETDCTVSAKEAIEQAAKIIVAHFQIIGNINALETIEL 252

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
            + N +           + +L LSVRS N LR      + +++  ++ ++  + N G+KS
Sbjct: 253 FEENKEKKEREIKSTTPITKLGLSVRSENALRRAKYNTVEEVLGLSDEELSNIKNLGKKS 312

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           + +I          +G +        IE L +    +
Sbjct: 313 IQDIIEKRNEWKERIGYDDGQSDNFIIESLDQLNNSE 349


>gi|119662823|emb|CAJ33204.1| RNA polymerase alpha subunit [Lactobacillus coleohominis DSM 14060]
          Length = 173

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 81/173 (46%), Positives = 123/173 (71%), Gaps = 1/173 (0%)

Query: 34  PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN 93
           PL RG+  TLGN+LRRV+++SL GAAIT++ IDGVLHE S+++GV ED+T IILN+K ++
Sbjct: 1   PLERGYGTTLGNSLRRVMLASLPGAAITSINIDGVLHEFSTVEGVTEDVTQIILNLKKVS 60

Query: 94  LKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           L++  +  K + +  +GP  VTAGDIQ   D+ VLNPD  I  +   A + +++T  KG 
Sbjct: 61  LRIDSEDQKNLELNVKGPAEVTAGDIQGDGDVTVLNPDLHIATVADGAELHIQMTADKGR 120

Query: 154 GYVPAKHHRTE-NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           GY  A  ++   +  IG++ ID++Y+PI++V+YTVE+ R GQ  DY+KL++ +
Sbjct: 121 GYSSADDNKARMDLAIGVLPIDSIYTPIERVNYTVENTRVGQNNDYNKLTLDV 173


>gi|150186985|emb|CAK30142.1| RNA polymerase alpha subunit [Streptococcus gallolyticus subsp.
           gallolyticus]
          Length = 204

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 80/200 (40%), Positives = 127/200 (63%)

Query: 56  RGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT 115
            GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VT
Sbjct: 1   PGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVT 60

Query: 116 AGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDA 175
           AGDI T +D+E++NPDH +  +     ++  +TV+K  GYVPA+ ++ E+ P+G + +D+
Sbjct: 61  AGDILTDSDVEIVNPDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKEDAPVGTLAVDS 120

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           +Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  
Sbjct: 121 IYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLT 180

Query: 236 EPKKEVKEDINVKSLPFNPA 255
           E  K        + +     
Sbjct: 181 EVAKNTDVMKETEKVNDEKV 200


>gi|150036724|emb|CAM98253.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. mesenteroides]
          Length = 181

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 80/181 (44%), Positives = 118/181 (65%), Gaps = 2/181 (1%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG 110
           L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + + I  +G
Sbjct: 1   LLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDIQG 60

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPI 168
           P  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++   +  PI
Sbjct: 61  PADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSADENKKLRDEMPI 120

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           G++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L ++IL + L
Sbjct: 121 GVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTNGSIKPSDALSLGAKILAEHL 180

Query: 229 G 229
           G
Sbjct: 181 G 181


>gi|150036714|emb|CAM98250.1| DNA-directed RNA polymerase alpha chain [Leuconostoc citreum]
          Length = 186

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 80/185 (43%), Positives = 119/185 (64%), Gaps = 2/185 (1%)

Query: 53  SSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
           SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + + I  +GP 
Sbjct: 1   SSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDVQGPA 60

Query: 113 VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGL 170
            VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++   +  PIG+
Sbjct: 61  DVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSADENKQLRDEMPIGV 120

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           + +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L S+IL + L +
Sbjct: 121 LAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSLGSKILAEHLNL 180

Query: 231 FINFE 235
           F++  
Sbjct: 181 FMDIS 185


>gi|119663530|emb|CAK22336.1| RNA polymerase alpha subunit [Lactobacillus kitasatonis]
          Length = 171

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 81/171 (47%), Positives = 114/171 (66%)

Query: 48  RRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF 107
           RRVL++S+ G  +  VQIDGVL E S++ GV ED+T IILN+K + LK   D  K + + 
Sbjct: 1   RRVLLTSIPGTGLVYVQIDGVLPEFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELD 60

Query: 108 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
             GP  VTA D++   D++VLNPD  IC +     + MEL V  G GYV A  +++++ P
Sbjct: 61  VEGPATVTADDLKVDADVQVLNPDQYICTIAEGGHLHMELAVKNGRGYVTASDNKSDDMP 120

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           IG+I +D+L+SPIKKV+Y VES R G+  D+DKL+  I TDGSI   D+++
Sbjct: 121 IGVIPVDSLFSPIKKVNYQVESTRVGKRDDFDKLTFEIWTDGSIKPNDALS 171


>gi|119662835|emb|CAJ33210.1| RNA polymerase alpha subunit [Lactobacillus rossiae]
          Length = 173

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 86/173 (49%), Positives = 125/173 (72%), Gaps = 2/173 (1%)

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           QIDGVLHE S+++GV ED+T IILN+K ++LKM+ D  K + I  +GP  VTAGDIQT  
Sbjct: 1   QIDGVLHEFSTVEGVVEDVTQIILNMKKVSLKMATDEEKGMDIDVKGPATVTAGDIQTDA 60

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIK 181
           D+EV+NPD  IC +   A   M LT +KG GYV A  ++   ++ PIG++ ID++Y+PI+
Sbjct: 61  DVEVMNPDLYICTVADGATFHMHLTANKGRGYVSADENKARQDDMPIGVLPIDSIYTPIE 120

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           +V+Y VE+ R GQ  DYDKL++ + TDGSIT  ++++LA++IL + L MF++ 
Sbjct: 121 RVNYQVENTRVGQRDDYDKLTLDVWTDGSITPSEAISLAAKILTEHLAMFVDL 173


>gi|625804|pir||E49923 DNA-directed RNA polymerase (EC 2.7.7.6) alpha chain - Chlamydia
           trachomatis
          Length = 353

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 78/337 (23%), Positives = 156/337 (46%), Gaps = 16/337 (4%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
           V  +  +  T  + EPL RG+A+T+G  LRR L+SS+   A  A++I+ V HE  +I G+
Sbjct: 13  VAEKVNDFNTTFVIEPLARGYANTMGTVLRRTLLSSITSVAPFAIKINNVEHEFETISGL 72

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFK-----RGPGVVTAGDIQTVNDIEVLNPDHV 133
            ED   ++ NI+ I    + +  ++  + K        G + A DI  V+ +E++N D  
Sbjct: 73  KEDAITLVRNIRNIRFVYNEEIFEKENLAKISFKTNKEGEIFASDIPEVSGLEIVNKDQY 132

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG-----------LITIDALYSPIKK 182
           I N+     +  +L + KG G++  + ++      G            + +D+ +SP+KK
Sbjct: 133 IANIAKGGSLEFDLFLRKGRGFIDFEENKNVISQYGSRLESSIKNGQFLAMDSDFSPVKK 192

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
            + + E       L  ++L + I+TD +++ ++++  A++I+     +  N    +    
Sbjct: 193 CAISFEELNSSSKLIEERLKIKIETDCTVSAKEAIEQAAKIIVAHFQIIGNINALETIEL 252

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
            + N +           + +L LSVRS N LR      + +++  ++ ++  + N G+KS
Sbjct: 253 FEENKEKKEREIKSTTPITKLGLSVRSENALRRAKYNTVEEVLGLSDEELSNIKNLGKKS 312

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           + +I          +G +        IE L +    +
Sbjct: 313 IQDIIEKRNEWKERIGYDDGQSDNFIIESLDQLNNSE 349


>gi|108796837|ref|YP_636429.1| alpha subunit of RNA polymerase [Staurastrum punctulatum]
 gi|122245550|sp|Q32RU7|RPOA_STAPU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|61393605|gb|AAX45746.1| alpha subunit of RNA polymerase [Staurastrum punctulatum]
          Length = 383

 Score =  204 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 92/374 (24%), Positives = 158/374 (42%), Gaps = 72/374 (19%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
              ++         + +     PL    A T+G A+RR L+S + G +I +  I G +HE
Sbjct: 14  WKCVDDQPDHNRRLHYSRFALSPLLVDQAMTIGVAIRRALLSEVEGISIISANIVGAVHE 73

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMS--------GDSHKRVTIFKRGPGVVTAGDIQTVN 123
            S++ GV E + +I+LN+K I +K +             R +IF +GPGVVTA  I+  +
Sbjct: 74  YSTLDGVRESVDEILLNLKQIVIKGAKGASITPLDHKEYRASIFAQGPGVVTAEHIKFPS 133

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            I  ++PD  I  L  +  + +EL + +G     AK             IDA ++P++K 
Sbjct: 134 SILAVDPDQSIATLLNETQLCIELFIRQG----IAKQLTRTKKNHQGFFIDANFTPVQKA 189

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF------------ 231
           ++++ S  + + L    L + I T+ ++T  +++  A   L +                 
Sbjct: 190 NFSIHSVGDPKGLQQ-LLLLEIWTNKTLTPAEALYQAHASLLNLFHQISPPLLHKELSPS 248

Query: 232 --------------------------------INFEEPKKEVKEDINVKSLPFNPALLKK 259
                                            N     KE++  + +KS       + K
Sbjct: 249 KNILNQNSDSNSLGGSSFGRVVSLETRRDSTQTNNSSIPKEIQPSVRLKSYTDTNLSIDK 308

Query: 260 ------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                       ++ELELS R +NCL+  NI  + DL+  T+ D+L++ NFGRKS+ ++ 
Sbjct: 309 QMNDSVNKENLSIDELELSPRISNCLKKANINTIADLLNYTQEDLLKIKNFGRKSVEQVS 368

Query: 308 GVLGTMGLFLGMNL 321
            VL        M L
Sbjct: 369 LVLR---KRFNMEL 379


>gi|119662341|emb|CAJ33159.1| RNA polymerase alpha subunit [Lactobacillus parabuchneri]
          Length = 200

 Score =  204 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 89/199 (44%), Positives = 131/199 (65%), Gaps = 4/199 (2%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVV 114
           G+A+T++QID VLHE S+IKGV ED+T IILN+K I+LK+ G  D  + + I   GP  V
Sbjct: 1   GSAVTSIQIDDVLHEFSTIKGVVEDVTQIILNVKKISLKLDGPEDEEENLEIDVIGPADV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLIT 172
           TAGDIQ  +D+ VLNPD  I  +   A   M LT +KG GYV A  ++      PIG++ 
Sbjct: 61  TAGDIQADSDVTVLNPDLHIATVAEGATFHMRLTANKGRGYVSAVENKKRSSEMPIGVLP 120

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           +D++Y+PI++V+Y VES R GQ  D+DKL++ + TDGSIT  ++V+LA++IL + L MF+
Sbjct: 121 VDSIYTPIERVNYQVESTRVGQRDDFDKLTLDVWTDGSITPSEAVSLAAKILTEHLEMFV 180

Query: 233 NFEEPKKEVKEDINVKSLP 251
           +  +  K  +  +  +   
Sbjct: 181 DLTDEAKNTEIMVEKEETH 199


>gi|269115047|ref|YP_003302810.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma hominis]
 gi|268322672|emb|CAX37407.1| DNA-directed RNA polymerase alpha chain [Mycoplasma hominis ATCC
           23114]
          Length = 344

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 73/306 (23%), Positives = 149/306 (48%), Gaps = 16/306 (5%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
           V  +  +  T  + EPL RG+ +T+G  +RR L+SS+   A  A++I  V HE ++I+G+
Sbjct: 13  VAEKVSDFNTTFVIEPLMRGYGNTIGTVIRRTLLSSITSVAPFAIKISHVEHEFTAIEGL 72

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFK-----RGPGVVTAGDIQTVNDIEVLNPDHV 133
            ED   ++ NI+ I      +  ++  + K        G V A DI+T+  ++++N D  
Sbjct: 73  REDAITLVANIRKIRFAYDPELFEKDNLAKISFKSTKEGEVHASDIETIPGLDIVNKDQY 132

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG-----------LITIDALYSPIKK 182
           I  +  +  +  EL +  G GYV  + ++      G            + +D+ +SPIKK
Sbjct: 133 IATISKNGSLEFELYLRTGRGYVSFEDNKKTILEYGPKLESKIKNGQFLAMDSDFSPIKK 192

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+   E       +  ++L + ++TDG++  ++ +  A++I+     +  N +       
Sbjct: 193 VAILFEELNSTSNIIEERLKIKVETDGTVEAKNVMEEAAKIIVAHFQIIGNIDALGTIDL 252

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
            D   +     P +   +++L L++RS N LR      + ++++ ++ ++  + N G+KS
Sbjct: 253 FDDQKEKHEKTPKVSVSIDKLNLTIRSLNALRRAGFNNVDEIMKLSDEELSNIKNLGKKS 312

Query: 303 LVEIKG 308
           + +I  
Sbjct: 313 VQDIID 318


>gi|150187112|emb|CAK30173.1| RNA polymerase alpha subunit [Streptococcus equinus]
          Length = 191

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 79/191 (41%), Positives = 124/191 (64%)

Query: 56  RGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT 115
            GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VT
Sbjct: 1   PGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVT 60

Query: 116 AGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDA 175
           AGDI T +D+E++N DH +  +     ++  +TV+K  GYVPA+ ++ E+ P+G + +D+
Sbjct: 61  AGDILTDSDVEIVNTDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKEDAPVGTLAVDS 120

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           +Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  
Sbjct: 121 IYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLT 180

Query: 236 EPKKEVKEDIN 246
           E  K       
Sbjct: 181 EVAKNTDVMKE 191


>gi|639724|gb|AAA61684.1| RNA polymerase alpha subunit [Chlamydia muridarum]
          Length = 322

 Score =  202 bits (515), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 74/307 (24%), Positives = 148/307 (48%), Gaps = 16/307 (5%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
           V  +  +  T  + EPL RG+A+T+G  LRR L+SS+   A  A++I+ V HE  +I G+
Sbjct: 13  VAEKVNDFNTTFVIEPLARGYANTMGTVLRRTLLSSITSVAPFAIKINNVEHEFQTISGL 72

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFK-----RGPGVVTAGDIQTVNDIEVLNPDHV 133
            ED   ++ NI+ I    + +  ++  + K        G + A DI  V+ +E++N D  
Sbjct: 73  KEDAITLVRNIRNIRFVYNEEIFEKENLAKISFKTNKEGEIFASDIPEVSGLEIVNKDQY 132

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG-----------LITIDALYSPIKK 182
           I N+     +  +L + KG G++  + ++      G            + +D+ +SP+KK
Sbjct: 133 IANIAKGGSLEFDLFLRKGRGFIDFEENKNVISQYGSRLESSIKNGQFLAMDSDFSPVKK 192

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
            + + E       L  ++L + I+TD +++ ++++  A++I+     +  N    +    
Sbjct: 193 CAISFEELNSSSKLIEERLKIKIETDCTVSAKEAIEQAAKIIVAHFQIIGNINALETIEL 252

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
            + N +           + +L LSVRS N LR      + +++  ++ ++  + N G+KS
Sbjct: 253 FEENKEKKEREIKSTTPITKLGLSVRSENALRRAKYNTVEEVLGLSDEELSNIKNLGKKS 312

Query: 303 LVEIKGV 309
           + +I   
Sbjct: 313 IQDIIEK 319


>gi|119672797|emb|CAK95482.1| RNA polymerase alpha subunit [Lactobacillus animalis]
          Length = 190

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 79/189 (41%), Positives = 124/189 (65%), Gaps = 2/189 (1%)

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           IDGVLHE S++KGV ED+T IILN+K + LK+  +  + +     GP  VTAGDIQ  +D
Sbjct: 1   IDGVLHEFSTVKGVLEDVTAIILNLKKVALKLDSEDSQTLEFDVVGPKEVTAGDIQGSSD 60

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKK 182
           +E+LNPD  IC +   AV    +T +KG GYV A  ++   E+ PIG++ ID++Y+PI++
Sbjct: 61  VEILNPDQYICTVADGAVFHARMTANKGRGYVSATENKAKAEDMPIGVLPIDSIYTPIER 120

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+Y VE  R GQ  DYDKL++ + T+GSIT  ++++L+++IL + L +F++  +  K  +
Sbjct: 121 VNYQVEKTRVGQKNDYDKLTLDVWTNGSITPSEAISLSAKILTEHLTLFVDLTDEAKNAE 180

Query: 243 EDINVKSLP 251
             +  +   
Sbjct: 181 IMVEKEETH 189


>gi|154424853|emb|CAL18529.1| RNA polymerase alpha subunit [Streptococcus salivarius]
          Length = 199

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 77/199 (38%), Positives = 127/199 (63%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAA+T+++IDGVLHE  ++ GV ED+  IILNIKG+ +K   +  K + +  +GP  VTA
Sbjct: 1   GAAVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGLAVKSYVEDEKTIELDVQGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
           GDI T +DIE++NPDH +  +   A ++  +TV+   GYVPA  ++ ++ P+G + +D++
Sbjct: 61  GDILTDSDIEIVNPDHYLFTIADGASLKATMTVATNRGYVPADENKKDDAPVGTLAVDSI 120

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  +
Sbjct: 121 YTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTD 180

Query: 237 PKKEVKEDINVKSLPFNPA 255
             K        + +     
Sbjct: 181 VAKATDVMKETEKVNEEKV 199


>gi|150036832|emb|CAO03476.1| DNA-directed RNA polymerase alpha chain [Leuconostoc carnosum]
          Length = 174

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 79/170 (46%), Positives = 111/170 (65%), Gaps = 2/170 (1%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K + L +  D
Sbjct: 1   GTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSD 60

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG GY  A 
Sbjct: 61  EERVLEIDVQGPSEVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSAD 120

Query: 160 HHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            ++   E  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T
Sbjct: 121 ENKQLREEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTFDIWT 170


>gi|39938713|ref|NP_950479.1| DNA-directed RNA polymerase alpha subunit [Onion yellows
           phytoplasma OY-M]
 gi|39721822|dbj|BAD04312.1| DNA-directed RNA polymerase alpha subunit [Onion yellows
           phytoplasma OY-M]
          Length = 247

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 87/250 (34%), Positives = 141/250 (56%), Gaps = 11/250 (4%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           + IKP  +E I    E       I +PL RG+  T+GNALRRVL+SSL G AI  V+I G
Sbjct: 5   KFIKPFFVEEI---DENPISGKFIIKPLERGYGITVGNALRRVLLSSLPGTAIVNVKIQG 61

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDS---HKRVTIFKRGPGVVTAGDIQTVND 124
           V  E ++I GV+ED+  IILN+K I   +  +S    +++ +  +GP  +TA   +    
Sbjct: 62  VEQEFTTIPGVYEDVMTIILNLKKIVFAVDDESDDFEEKLELIAKGPQRLTASSFELPAG 121

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSPIKKV 183
           ++++NPDH I  L  D    M +T+ KG GYV AK ++    + +G+I ID+L++P+  V
Sbjct: 122 VKIINPDHYITTLSDDVCFHMTVTLKKGIGYVGAKDNKVHGENQVGVIAIDSLFTPVVNV 181

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SY VE     ++ + D+L++ I T+G++  ++++A A+ IL D   + +   +    V+ 
Sbjct: 182 SYQVE----KKLGNKDELTIEITTNGALLAKEALATAASILVDHFNVLVELSQKPAHVEF 237

Query: 244 DINVKSLPFN 253
               K    N
Sbjct: 238 VSESKKEAHN 247


>gi|119672795|emb|CAK95481.1| RNA polymerase alpha subunit [Lactobacillus saerimneri]
          Length = 170

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 84/170 (49%), Positives = 117/170 (68%), Gaps = 2/170 (1%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           G+  TLGN+LRRVL+SSL GAAIT +QIDGVLHE S+++GV ED+T IILN+K + L + 
Sbjct: 1   GYGTTLGNSLRRVLLSSLPGAAITDIQIDGVLHEFSTVEGVLEDVTQIILNLKKVALGIK 60

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
            D    + I   GP  VTAGDIQ   D+E+ NPD  IC +   A   + +T + G GYV 
Sbjct: 61  SDDRVSLEIDVVGPMEVTAGDIQGSADVEIFNPDQYICTVADGASFHVRMTANTGRGYVS 120

Query: 158 AKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           AK ++   ++ PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ +
Sbjct: 121 AKENKEMADDMPIGVLPIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDV 170


>gi|113170453|ref|YP_717245.1| RpoA [Ostreococcus tauri]
 gi|122241423|sp|Q0P3L0|RPOA_OSTTA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|112806860|emb|CAL36367.1| RpoA [Ostreococcus tauri]
          Length = 356

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 82/343 (23%), Positives = 154/343 (44%), Gaps = 51/343 (14%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
            +    +   P+  G   T+GN LRR+L++ L G  +   +I+GV  E S++ G+ E + 
Sbjct: 19  TDCYGRLSFGPVNPGQGLTIGNTLRRILLNDLPGIGVIGAEINGVQSEFSTLPGIRESVI 78

Query: 84  DIILNIKGINLKMSGDSHKRVTIFK--------------RGPGVVTAGDIQTVNDIEVLN 129
           +I LN++ +    +    ++V   K                P VVTA D+    + E ++
Sbjct: 79  EIFLNLRELIFTPTATCAQKVKQTKPFVYAKLNSELKIDNFPYVVTAKDLHIP-EYEFVD 137

Query: 130 PDHVICNL---DVDAVVRMELTVSKGHGYVPAKH-----------------HRTENDPIG 169
           P+  I  +         ++ L + +G GY   K                      N    
Sbjct: 138 PNQQIATILSPTAAENFKLTLLIGQGRGYQSWKKLPGVPQLMDQRFFEQFDSTQTNSKSV 197

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL- 228
              IDA++ PI++V++TV+       +D + +   + T+GSI   D+V  A+++    + 
Sbjct: 198 TFPIDAIFMPIRQVNFTVQ----EHSVDGEYIYFEVWTNGSINPFDAVKSAAKVGMKLMT 253

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKK-----------VEELELSVRSTNCLRGEN 277
                 ++ +  + E    ++  F      K           +E+LELS+R+ NCL+  N
Sbjct: 254 ACLTTLQDQQVYLDESKLPETPNFVQVNYNKMESESNFDQIFIEQLELSLRAYNCLKRAN 313

Query: 278 IVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           I+ + DL Q++  D++++ NFG+KS  E++  L T G+ L  +
Sbjct: 314 ILTLADLSQQSFRDLMKLRNFGQKSADEVRAALSTYGIELKED 356


>gi|119672815|emb|CAK95519.1| RNA polymerase alpha subunit [Lactobacillus gasseri]
          Length = 165

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 87/165 (52%), Positives = 118/165 (71%)

Query: 47  LRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
           LRRVL++S+ G A++ +QIDGVLHE S+I GV ED+T IILN+K + LK   D  K   I
Sbjct: 1   LRRVLLTSIPGTALSYIQIDGVLHEFSTIPGVREDVTKIILNLKKLELKSLSDEEKIAEI 60

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
              GP +VTA D++  +DIEVLNPD  IC++     + M + +  G GYVPA  ++T++ 
Sbjct: 61  DVTGPAIVTAADLKVDSDIEVLNPDQYICSIADGGHLHMNVAIKNGRGYVPASENKTDDM 120

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           PIG+I +D+L+SPIKKV+Y VESAR G+  DYDKL++ I TDGSI
Sbjct: 121 PIGVIPVDSLFSPIKKVNYQVESARVGKRDDYDKLTLEIWTDGSI 165


>gi|119662397|emb|CAJ33188.1| RNA polymerase alpha subunit [Lactobacillus vaccinostercus]
          Length = 174

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 84/174 (48%), Positives = 129/174 (74%), Gaps = 2/174 (1%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG 110
           L++SL GAAIT++QIDGVLHE S+++GV ED+T IILN+K I+LK+  +  K + I  +G
Sbjct: 1   LLASLPGAAITSIQIDGVLHEFSTVEGVTEDVTQIILNMKQISLKIDSEEDKTLEIDVKG 60

Query: 111 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPI 168
           P  VTAGDI+   D+EVLNP+  I  +   A + +++T + G GYV A  ++   ++ PI
Sbjct: 61  PAAVTAGDIEADGDVEVLNPELHIATVADGAELHIQMTANTGRGYVSADDNKARMDDLPI 120

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
           G++ ID++Y+PI++V+YTVE+AR GQ  DYDKL++ + +DGSIT  +S++LA++
Sbjct: 121 GVLPIDSIYTPIERVNYTVENARVGQRNDYDKLTLDVWSDGSITPSESISLAAK 174


>gi|150187056|emb|CAK30161.1| RNA polymerase alpha subunit [Streptococcus cristatus ATCC 51100]
          Length = 172

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 79/172 (45%), Positives = 118/172 (68%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL++SL GAA+T++ I+GVLHE  +I GV ED+  IILNIKGI +K      K +
Sbjct: 1   NSLRRVLLASLPGAAVTSINIEGVLHEFDTISGVREDVMQIILNIKGIAVKSYVQDEKMI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  VTAGDI T +DIE++NPDH +  +   A  + ++ V+ G GYVPA  ++ +
Sbjct: 61  ELDVEGPAEVTAGDILTDSDIEIVNPDHYLFTISEGARFKAKMAVNSGRGYVPADENKKD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
           + P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED+
Sbjct: 121 DAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDA 172


>gi|154424727|emb|CAL18466.1| RNA polymerase alpha subunit [Streptococcus gallolyticus]
          Length = 184

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 79/184 (42%), Positives = 124/184 (67%)

Query: 56  RGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT 115
            GAA+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VT
Sbjct: 1   PGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVT 60

Query: 116 AGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDA 175
           AGDI T +D+E++NPDH +  +     ++  +TV+K  GYV A+ ++ E+ P+G + +D+
Sbjct: 61  AGDILTDSDVEIVNPDHYLFTIAEGHSLKATMTVAKERGYVSAEGNKKEDAPVGTLAVDS 120

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           +Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  
Sbjct: 121 IYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLT 180

Query: 236 EPKK 239
           E  K
Sbjct: 181 EVAK 184


>gi|150187178|emb|CAK30188.1| RNA polymerase alpha subunit [Streptococcus acidominimus]
          Length = 174

 Score =  200 bits (509), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 78/174 (44%), Positives = 121/174 (69%)

Query: 56  RGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT 115
            GAA+T+++IDGVLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  +T
Sbjct: 1   PGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKTIELDVTGPAEIT 60

Query: 116 AGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDA 175
           AGDI T +DIE++NPDH +  +   A  +  +TV+ G GYVPA+ ++ ++ P+G + +D+
Sbjct: 61  AGDILTDSDIEIVNPDHYLFTISEGATFKAMMTVNTGRGYVPAEGNKKDDAPVGTLAVDS 120

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           +Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + LG
Sbjct: 121 IYTPVKKVNYQVEPARVGSNDGFDKLTLEIMTNGTIIPEDALGLSARILMEHLG 174


>gi|154424731|emb|CAL18468.1| RNA polymerase alpha subunit [Streptococcus thermophilus]
          Length = 179

 Score =  199 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 78/179 (43%), Positives = 123/179 (68%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAA+T+++IDGVLHE  ++ GV ED+  IILNIKG+ +K   +  K + +  +GP  VTA
Sbjct: 1   GAAVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGLAVKSYVEDEKTIELDVQGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
           GDI T +DIE++NPDH +  +   A  +  +TVS   GYVPA+ ++ ++ P+G + +D++
Sbjct: 61  GDILTDSDIEIVNPDHYLFTIAEGASFQATMTVSTNRGYVPAEENKKDDAPVGTLAVDSI 120

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F +  
Sbjct: 121 YTPVKKVNYQVEPARVGSNDGFDKLTIEIVTNGTIIPEDALGLSARILIEHLNLFTDLT 179


>gi|154424721|emb|CAL18463.1| RNA polymerase alpha subunit [Streptococcus thermophilus]
          Length = 169

 Score =  199 bits (505), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 78/169 (46%), Positives = 119/169 (70%)

Query: 49  RVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK 108
           RVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILNIKG+ +K   +  K + +  
Sbjct: 1   RVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGLAVKSYVEDEKTIELDV 60

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
           +GP  VTAGDI T +DIE++NPDH +  +   A  +  +TVS   GYVPA+ ++ ++ P+
Sbjct: 61  QGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGASFQATMTVSTNRGYVPAEENKKDDAPV 120

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
           G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++
Sbjct: 121 GTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIVTNGTIIPEDAL 169


>gi|150186992|emb|CAK30144.1| RNA polymerase alpha subunit [Streptococcus minor]
          Length = 189

 Score =  199 bits (505), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 77/189 (40%), Positives = 124/189 (65%)

Query: 59  AITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGD 118
           A+T+++IDGVLHE  ++ GV ED+  IILNIKGI +K   +  K++ +   GP  +TAGD
Sbjct: 1   AVTSIKIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKKIELDVVGPAEITAGD 60

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           I T +DIE++NPDH +  +   A  +  LTV++G GYVPA+ ++ +  P+G + +D++Y+
Sbjct: 61  ILTDSDIEIVNPDHYLFTIGEGASFKAILTVNRGRGYVPAEGNKKDEAPVGTLAVDSIYT 120

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ KV+Y VE AR G    +DKL++ I T+G+   ED++ L++RIL + LG+F +  +  
Sbjct: 121 PVVKVNYQVEPARVGSNDGFDKLTLEIMTNGTTNPEDALGLSARILMEHLGLFTDLTDVA 180

Query: 239 KEVKEDINV 247
           K  +     
Sbjct: 181 KSAEVMKEA 189


>gi|71056955|emb|CAH59038.1| DNA-directed RNA polymerase alpha chain [Enterococcus avium]
          Length = 177

 Score =  199 bits (505), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 82/175 (46%), Positives = 120/175 (68%)

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           +QIDGVLHE S+IKGV ED+  IILNIKG+ LK+  +  K + I   GP  VTAGDI   
Sbjct: 3   IQIDGVLHEFSTIKGVREDVVQIILNIKGLALKLFAEEEKTLEIDITGPATVTAGDIIVD 62

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           +D+E+LN D  IC +   A     LTV  G GYV A  ++ E+ PIG++ +D++Y+P++K
Sbjct: 63  SDVEILNKDMYICTVAEGATFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRK 122

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           V+Y VE+ R G+  D+DKL+M I TDGSI  +++++LA++IL + L +F+N  + 
Sbjct: 123 VNYQVENTRVGRRDDFDKLTMEIWTDGSIIAQEALSLAAKILTEHLDIFVNLTDE 177


>gi|154424795|emb|CAL18500.1| RNA polymerase alpha subunit [Streptococcus gordonii]
          Length = 183

 Score =  198 bits (504), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 78/182 (42%), Positives = 120/182 (65%)

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
           AA+T++ I+GVLHE  +I GV ED+  IILNIKGI +K      K + +   GP  +TAG
Sbjct: 1   AAVTSINIEGVLHEFDTIPGVREDVMQIILNIKGIAVKSYVQDEKMIELDVEGPAEITAG 60

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI T +DIE++NPDH +  +   A  +  +TV+ G GYVPA  ++ ++ P+G + +D++Y
Sbjct: 61  DILTDSDIEIVNPDHYLFTIGEGARFKAVMTVNSGRGYVPADQNKRDDAPVGTLAVDSIY 120

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           +P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F +  E 
Sbjct: 121 TPVTKVNYQVEPARVGSNDGFDKLTLEIMTNGTIIPEDALGLSARILTEHLDLFTDLTEV 180

Query: 238 KK 239
            K
Sbjct: 181 AK 182


>gi|145586271|emb|CAM91230.1| RNA polymerase alpha-subunit [Lactobacillus plantarum subsp.
           argentoratensis]
          Length = 176

 Score =  198 bits (504), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 82/176 (46%), Positives = 121/176 (68%), Gaps = 2/176 (1%)

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGVLHE S+I+GV ED+T IILN+K I LK+  D  K + I  +GP  VTAGDI    D+
Sbjct: 1   DGVLHEFSTIEGVTEDVTAIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADV 60

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKV 183
           EVLNPD  IC +   A   M +T + G GYV A+ ++   ++ PIG++ +D+LYSPI++V
Sbjct: 61  EVLNPDLPICTVADGAHFHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +Y VE+ R GQ  D+DKL++ + T+GSIT  ++++L+++IL D L +F+N  +  K
Sbjct: 121 NYQVENTRVGQRDDFDKLTLDVWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAK 176


>gi|154424805|emb|CAL18505.1| RNA polymerase alpha subunit [Streptococcus hyovaginalis]
          Length = 183

 Score =  198 bits (504), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 74/183 (40%), Positives = 123/183 (67%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ +K   +  K + +  +GP  VTA
Sbjct: 1   GAAVTSIKIDGVLHEFDTVPGVREDVMQIILNVKGLAVKSYVEDEKIIELDVQGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
           GDI T +D+E++N DH +  +   A  +  +TV+   GYV A+ ++ ++ P+G + +D++
Sbjct: 61  GDILTDSDVEIVNSDHYLFTIAEGASFKASMTVATNRGYVAAEGNKKDDAPVGTLAVDSI 120

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E
Sbjct: 121 YTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTE 180

Query: 237 PKK 239
             K
Sbjct: 181 VAK 183


>gi|119662827|emb|CAJ33206.1| RNA polymerase alpha subunit [Lactobacillus gastricus]
          Length = 172

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 81/172 (47%), Positives = 121/172 (70%), Gaps = 2/172 (1%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           LGN+LRRV+++SL GAAIT++QIDGVLHE S++ GV ED+T IILN+K + L++ GD  K
Sbjct: 1   LGNSLRRVMLASLPGAAITSIQIDGVLHEFSTVDGVTEDVTQIILNLKKVALRIDGDDAK 60

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
            + +  +GP  VTA DIQ   D+ +LNPD  +  +   A + +++T  KG GY  A  ++
Sbjct: 61  DLEVDVKGPTEVTAADIQGYGDVSILNPDLHLATVADGAELHIKMTADKGRGYSSADDNK 120

Query: 163 TENDPI--GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           +  D    G++ ID++Y+PI +V+YTVE+ R GQ  DYDKL++ + T+GS+T
Sbjct: 121 SNMDMSAIGVLPIDSIYTPIDRVNYTVENTRVGQSNDYDKLTLDVWTNGSLT 172


>gi|119668323|emb|CAK95461.1| RNA polymerase alpha subunit [Lactobacillus gasseri]
          Length = 166

 Score =  197 bits (500), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 84/166 (50%), Positives = 116/166 (69%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           VL++S+ G A++ +QIDGVLHE S++ GV ED+T IILN+K + LK   D  K   I   
Sbjct: 1   VLLTSIPGTALSYIQIDGVLHEFSTVPGVREDVTKIILNLKKLELKSLSDEEKIAEIDVT 60

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           GP +VTA D++  +DIEVLN D  IC++     + M + +  G GYVPA  ++T++ PIG
Sbjct: 61  GPAIVTAADLKVDSDIEVLNTDQYICSIADGGHLHMNVAIKNGRGYVPASENKTDDMPIG 120

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
           +I +D+L+SPIKKV+Y VESAR G+  DYDKL++ I TDGSIT  D
Sbjct: 121 VIPVDSLFSPIKKVNYQVESARVGKRDDYDKLTLEIWTDGSITPND 166


>gi|226968665|ref|YP_002808625.1| RNA polymerase alpha chain [Micromonas sp. RCC299]
 gi|226431143|gb|ACO55549.1| RNA polymerase alpha chain [Micromonas sp. RCC299]
          Length = 352

 Score =  197 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 83/351 (23%), Positives = 142/351 (40%), Gaps = 45/351 (12%)

Query: 8   ELIKPN---NIEYIV--LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
             I PN    +E +        ++   ++  PL  G   TLGN  RR+L++ L G AITA
Sbjct: 2   NFIVPNSSAKLECVEFRENNPRDHYARLVLGPLAPGQGVTLGNTFRRLLLNDLPGVAITA 61

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS----HKRVTI----------FK 108
            +++    E  ++ G+ E + +I LN++ I    +          +TI            
Sbjct: 62  AKLNETRTEFMTLPGIRESVVEIFLNLRDIVFFNTFPDVLAPQGTITISPRPQTDESKSF 121

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD---AVVRMELTVSKGHGYVPA------- 158
             P V+ AGD+Q    I  ++P   I  L        +   L  S G+            
Sbjct: 122 HTPRVICAGDMQLPEGITCVDPTQPIATLMNGDTAFNLTFILEQSTGYRVWKKPTQSYGT 181

Query: 159 --------KHHRTENDPIGLI-TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
                   +  + E    G+   ID  + P+K V++ V           + +   I T+G
Sbjct: 182 GFYPSPQIESVQIEQVKSGVFQPIDGNFMPVKNVNFAVHEV----QPHGEYIHFEITTNG 237

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKE---DINVKSLPFNPALLKKVEELELS 266
           SI   ++   A  IL +     +    P   + E    ++             +E+LELS
Sbjct: 238 SIHPHNAFKHAGAILTEITRATLQDPRPVVGIDEASTPVDTAVAQKAYFENIAIEQLELS 297

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +R+ NCL+   I+ + DL + + + +L + NFG+KS  E+   L T G+ L
Sbjct: 298 LRAYNCLKRAQILTLADLSRESYSSLLALRNFGQKSAEEVAKALETYGIEL 348


>gi|150187174|emb|CAK30187.1| RNA polymerase alpha subunit [Streptococcus devriesei]
          Length = 161

 Score =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 76/161 (47%), Positives = 113/161 (70%)

Query: 35  LPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL 94
           L RG+  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  ++ GV ED+  IILN+KG+ +
Sbjct: 1   LERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTVPGVREDVMQIILNLKGLAV 60

Query: 95  KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHG 154
           K   +  K + +   GP  +TAGDI T +DIE++NPDH +  +   A ++  LTV    G
Sbjct: 61  KSYVEEEKIIELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIAEGASLKATLTVDTNRG 120

Query: 155 YVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
           Y+PA+ ++ ++ P+G + ID++Y+P+KKV+Y VE AR G  
Sbjct: 121 YIPAEENKKDDAPVGTLAIDSIYTPVKKVNYQVEPARVGSN 161


>gi|290489674|gb|ADD31221.1| RNA polymerase alpha subunit protein [Rhododendron simsii]
          Length = 262

 Score =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 75/253 (29%), Positives = 122/253 (48%), Gaps = 11/253 (4%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLR 56
           M QKN +    P  +++  +    ++           PL RG A TLG A+RR L+  + 
Sbjct: 1   MSQKNRRGF--PRRLQWKCVESRVDSKRLYYGRFSLFPLRRGEAETLGIAMRRALLGEIE 58

Query: 57  GAAITAVQI--DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           G  IT  +     V HE SSI+G+ E + +I++N+K I LK +        I+ +GP  V
Sbjct: 59  GTCITRAKFGRVRVTHEYSSIEGIQESVNEILMNLKEIILKSNLYGPCSGLIWVQGPRDV 118

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITID 174
           TA DI     +E+++    I +L     + M+L + K  GY       T  D  G    D
Sbjct: 119 TARDIMVAPYVEIIDNTQHIASLTKRIDLYMKLEIQKNRGYQIKSPKNTLQD--GSYPTD 176

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           A++ P++  +Y + S    +V   + L   I T+GS+T ++++  ASR L D    F+N 
Sbjct: 177 AVFMPVRNANYNIYSY-LDRVAREEILFFEIWTNGSLTPKEALHEASRKLVDLFSPFLNT 235

Query: 235 EEPKKEVKEDINV 247
           EE    + E+ + 
Sbjct: 236 EEENVHLDENQHK 248


>gi|11467766|ref|NP_050817.1| RNA polymerase alpha chain [Nephroselmis olivacea]
 gi|24638188|sp|Q9TL28|RPOA_NEPOL RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|5880695|gb|AAD54788.1|AF137379_11 alpha subunit of RNA polymerase [Nephroselmis olivacea]
          Length = 495

 Score =  195 bits (496), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 94/376 (25%), Positives = 151/376 (40%), Gaps = 77/376 (20%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
            +IE   +             PLP G   TLGNALRR+L+  L G A T+  + G  HE 
Sbjct: 5   KHIETKRISART-YYGRFCVLPLPAGQGITLGNALRRILLGDLVGFAATSANLAGASHEF 63

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHK-------RVTIFKRGPGVVTAGDIQTVNDI 125
            ++ G+ E + +I+LNIK +  K      K       R ++   GP  VTA D+   + +
Sbjct: 64  DTLPGIRESVLEILLNIKQLVFKQISSRPKDTNRFAMRASLNLTGPATVTAKDLVLPSWM 123

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYV---------------PAKHHRTENDPI-- 168
           +V++P   I  L   A +  E+ +S+G GY                P      END    
Sbjct: 124 KVVDPSQYIATLASGASLEFEIQLSQGSGYRLRRTSLVPPGFTLPPPRDPLEPENDSKSE 183

Query: 169 --------------------------GLITIDALYSPIKKVSYTVESAREGQVLDY---- 198
                                      +I  D+  +  +K +  + S R+  +  +    
Sbjct: 184 TKSKSKGKSKNTSTSDVQLADTDVNAQIIDTDSNSTETEKEAPHIPSMRDDHMTLHIDAV 243

Query: 199 ---------------------DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
                                ++L + I T+GS++   ++  A+ IL   L         
Sbjct: 244 FFPVTRVNYRVEEEVINGRRREELVIDIWTNGSLSPRKALDQAAVILIRMLASLQAPPPL 303

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
             E ++    K++      L  +E L+LSVRS NCL+  NI  +G LI  T  ++L++ N
Sbjct: 304 LIEPEKKPTTKTIAKE-IALTPIESLDLSVRSFNCLKRANITNVGKLIAYTRQELLQLKN 362

Query: 298 FGRKSLVEIKGVLGTM 313
           FG KS  E+  VL + 
Sbjct: 363 FGTKSASEVVDVLNSR 378


>gi|154424813|emb|CAL18509.1| RNA polymerase alpha subunit [Streptococcus intermedius]
          Length = 177

 Score =  195 bits (496), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 78/177 (44%), Positives = 121/177 (68%)

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
           AA+T++ I+GVLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  VTAG
Sbjct: 1   AAVTSINIEGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEGEKTIELDVEGPAEVTAG 60

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI T +DIE++NP+H +  +   A ++  +TV+ G GYVPA  ++ ++ P+G + +D++Y
Sbjct: 61  DILTDSDIEIVNPNHYLFTIGEGASLKAVMTVNTGRGYVPADENKKDDAPVGTLAVDSIY 120

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           +P+KKV+Y VE AR G    +DKL++ I TDG+I  ED++ L++RIL + L +F N 
Sbjct: 121 TPVKKVNYQVEPARVGSNDSFDKLTLEIMTDGTIIPEDALGLSARILTEHLDLFTNL 177


>gi|119668311|emb|CAK95456.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           lactis]
          Length = 191

 Score =  195 bits (496), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 72/191 (37%), Positives = 115/191 (60%)

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
             +  V+IDG+LHE +++ GV ED+T IILN+K + L+   +  K + +   GP  VTA 
Sbjct: 1   TGLVKVKIDGILHEFTTVPGVKEDVTKIILNLKKLVLRAYTEEVKTIELDVEGPATVTAE 60

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           D++   D+EVLNPD  IC +     + M + V  G GYVPA  +++    IG I +D+L+
Sbjct: 61  DLKADADVEVLNPDQYICTIAQGGHLHMWIDVCNGRGYVPASENKSAEMSIGDIPVDSLF 120

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SPI+KV+Y VES R G+  D+DKL++ I T+GSI   D++  A+R+L +    F + +  
Sbjct: 121 SPIEKVNYQVESTRVGKREDFDKLTLEIWTNGSIAPNDALNFAARVLVEHFKAFESADAA 180

Query: 238 KKEVKEDINVK 248
            +  +  +  +
Sbjct: 181 AEIGEVMVEQE 191


>gi|108792429|emb|CAJ44677.1| RNA polymerase alpha subunit [Lactobacillus acidipiscis]
          Length = 187

 Score =  195 bits (496), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 77/186 (41%), Positives = 122/186 (65%), Gaps = 2/186 (1%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE SSI GV ED+T IILN+K + LK++ +  + + I   GP  VTAGDIQ  +++EV
Sbjct: 1   VLHEFSSIDGVLEDVTTIILNLKKVALKLNSEDVQTLEIDVTGPMEVTAGDIQGSSEVEV 60

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSY 185
           LNPD  IC +   A     +T +KG GYV A  ++  TE+ PIG++ ID++Y+PI++V+Y
Sbjct: 61  LNPDLYICTVADGASFHARMTANKGRGYVSANENKAKTEDMPIGVLAIDSIYTPIERVNY 120

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE  R GQ  D+DKL++ + T+GSIT  ++++L+++IL + L +F++  +  K  +  +
Sbjct: 121 QVEKTRVGQKSDFDKLTLDVWTNGSITPSEAISLSAKILTEHLTLFVDLTDEAKNAEIMV 180

Query: 246 NVKSLP 251
             +   
Sbjct: 181 EKEETH 186


>gi|108792431|emb|CAJ44678.1| RNA polymerase alpha subunit [Lactobacillus acidipiscis]
          Length = 196

 Score =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 79/196 (40%), Positives = 125/196 (63%), Gaps = 2/196 (1%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE SSI GV ED+T IILN+K + LK++ +  + + I   GP  VTAGDIQ  +++EV
Sbjct: 1   VLHEFSSIDGVLEDVTTIILNLKKVALKLNSEDVQTLEIDVTGPMEVTAGDIQGSSEVEV 60

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSY 185
           LNPD  IC +   A     +T +KG GYV A  ++  TE+ PIG++ ID++Y+PI++V+Y
Sbjct: 61  LNPDLYICTVADGASFHARMTANKGRGYVSANENKAKTEDMPIGVLAIDSIYTPIERVNY 120

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE  R GQ  D+DKL++ + T+GSIT  ++++L+++IL + L +F++  +  K  +  +
Sbjct: 121 QVEKTRVGQKSDFDKLTLDVWTNGSITPSEAISLSAKILTEHLTLFVDLTDEAKNAEIMV 180

Query: 246 NVKSLPFNPALLKKVE 261
             +       L   +E
Sbjct: 181 EKEETHKEKMLEMTIE 196


>gi|154424743|emb|CAL18474.1| RNA polymerase alpha subunit [Streptococcus salivarius]
          Length = 201

 Score =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 76/201 (37%), Positives = 127/201 (63%)

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+++IDGVLHE  ++ GV ED+  IILNIKG+ +K   +  K + +  +GP  VTAGDI 
Sbjct: 1   TSIKIDGVLHEFDTVPGVREDVMQIILNIKGLAVKSYVEDEKTIELDVQGPAEVTAGDIL 60

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIE++NPDH +  +   A ++  +TV+   GYVPA  ++ ++ P+G + +D++Y+P+
Sbjct: 61  TDSDIEIVNPDHYLFTIAEGASLKATMTVATNRGYVPADENKKDDAPVGTLAVDSIYTPV 120

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  +  K 
Sbjct: 121 KKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTDVAKA 180

Query: 241 VKEDINVKSLPFNPALLKKVE 261
                  + +     L + +E
Sbjct: 181 TDVMKETEKVNDEKVLDRTIE 201


>gi|213612397|ref|ZP_03370223.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E98-2068]
          Length = 195

 Score =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 83/197 (42%), Positives = 128/197 (64%), Gaps = 6/197 (3%)

Query: 138 DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
                + M + V +G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q
Sbjct: 1   MKTTSISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQ 60

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
             D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+P
Sbjct: 61  RTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP---EVKEEKPEFDP 117

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
            LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + G
Sbjct: 118 ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRG 177

Query: 315 LFLGMNLPDWPPESIEE 331
           L LGM L +WPP SI +
Sbjct: 178 LSLGMRLENWPPASIAD 194


>gi|119662281|emb|CAJ33127.1| RNA polymerase alpha subunit [Lactobacillus animalis KCTC 3501]
          Length = 167

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 83/167 (49%), Positives = 116/167 (69%), Gaps = 2/167 (1%)

Query: 53  SSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
           SSL GAAIT VQIDGVLHE S++KGV ED+T IILN+K + LK+  +  + +     GP 
Sbjct: 1   SSLPGAAITDVQIDGVLHEFSTVKGVLEDVTAIILNLKKVALKLDSEDSQTLEFDVVGPK 60

Query: 113 VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGL 170
            VTAGDIQ  +D+E+LNPD  IC +   AV    +T +KG GYV A  +  + E+ PIG+
Sbjct: 61  EVTAGDIQGSSDVEILNPDQYICTVADGAVFHARMTANKGRGYVSATENKAKAEDMPIGV 120

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
           + ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T+GSIT  +++
Sbjct: 121 LPIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWTNGSITPSEAI 167


>gi|150186998|emb|CAK30146.1| RNA polymerase alpha subunit [Streptococcus orisratti]
          Length = 199

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 74/197 (37%), Positives = 125/197 (63%)

Query: 59  AITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGD 118
           A+T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   +  K + +   GP  +TAGD
Sbjct: 1   AVTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVEDEKIIELDVEGPAEITAGD 60

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           I T +DIE++NP+H +  +     ++  +TV+   GYVPA+ ++ ++ P+G + +D++Y+
Sbjct: 61  ILTDSDIEIVNPNHYLFTIAEGHSLKATMTVNTNRGYVPAEGNKKDDAPVGTLAVDSIYT 120

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  +  
Sbjct: 121 PVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDAIGLSARVLIEHLNLFTDLTDVA 180

Query: 239 KEVKEDINVKSLPFNPA 255
           K       V+ +     
Sbjct: 181 KATDVMKEVEKVNDEKV 197


>gi|224178085|ref|YP_002600906.1| alpha subunit of RNA polymerase [Pyramimonas parkeae]
 gi|215882752|gb|ACJ71125.1| alpha subunit of RNA polymerase [Pyramimonas parkeae]
          Length = 351

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 84/314 (26%), Positives = 149/314 (47%), Gaps = 29/314 (9%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL---------HEISSIKG 77
             L    P   G   T+ N LRR L++++ G  IT+V+ +            HE S+I G
Sbjct: 47  YALFQLGPFSHGQGLTIANGLRRTLLNNIIGFGITSVKFEPKWVDISKEVFIHEYSTIPG 106

Query: 78  VHEDLTDIILNIKGINLKMSGD-----SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           + E + +II N+K I ++           + + I +  PGV+ A  I+    +++LN + 
Sbjct: 107 IWESIFEIIENLKKIKIRRENSPFEPFEKQVIRITQDKPGVLRADSIKLPPFLKILNQNQ 166

Query: 133 VICNL-DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
            I ++   + ++ + +T+           +   N+    I +  +  PIK V+Y +++  
Sbjct: 167 PIVSMMSSNLILDIIITIE------AQTGNHLCNNQ--FIHVSEVCLPIKWVNYVIKTDP 218

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE---EPKKEVKEDINVK 248
                  + L   I TDG+IT +++++ A+ I  D    F   +   E K  VKE +  +
Sbjct: 219 LLGSKSPESLFFEISTDGTITPQEALSKAADICIDLYSCFSTAQKELEVKSIVKEKVTEE 278

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                      +E L LSVR+ NCL+  NI  + DL+ ++++D+L M NFG+KS  E+  
Sbjct: 279 VKEEIITNKVTIENLGLSVRAYNCLKRANIYTVTDLLTKSKSDLLAMKNFGKKSADEVYE 338

Query: 309 VLGTMGLFLGMNLP 322
            L      LG++LP
Sbjct: 339 ALQN---RLGIDLP 349


>gi|108792433|emb|CAJ44679.1| RNA polymerase alpha subunit [Lactobacillus acidipiscis]
          Length = 194

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 78/194 (40%), Positives = 123/194 (63%), Gaps = 2/194 (1%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE SSI GV ED+T IILN+K + LK++ +  + + I   GP  VTAGDIQ  +++EV
Sbjct: 1   VLHEFSSIDGVLEDVTTIILNLKKVALKLNSEDVQTLEIDVTGPMEVTAGDIQGSSEVEV 60

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSY 185
           LNPD  IC +   A     +T +KG GYV A  ++  TE+ PIG++ ID++Y+PI++V+Y
Sbjct: 61  LNPDLYICTVADGASFHARMTANKGRGYVSANENKAKTEDMPIGVLAIDSIYTPIERVNY 120

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE  R GQ  D+DKL++ + T+GSIT  ++++L+++IL + L +F++  +  K  +  +
Sbjct: 121 QVEKTRVGQKSDFDKLTLDVWTNGSITPSEAISLSAKILTEHLTLFVDLTDEAKNAEIMV 180

Query: 246 NVKSLPFNPALLKK 259
             +       L   
Sbjct: 181 EKEETHKEKMLEMT 194


>gi|154424757|emb|CAL18481.1| RNA polymerase alpha subunit [Streptococcus anginosus]
          Length = 184

 Score =  194 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 77/184 (41%), Positives = 120/184 (65%)

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T++ I+GVLHE  ++ GV ED+  IILN+KGI +K   +  K + +   GP  +TAGDI 
Sbjct: 1   TSINIEGVLHEFDTVPGVREDVMQIILNVKGIAVKSYVEDEKTIELDVEGPAEITAGDIL 60

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIE++NPDH +  +   A ++  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+
Sbjct: 61  TDSDIEIVNPDHYLFTIGEGASLKAIMTVNTGRGYVPADENKKDDAPVGTLAVDSIYTPV 120

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKV+Y VE AR G    +DKL++ I TDG+I  ED++ L++RIL + L +F N  E  K 
Sbjct: 121 KKVNYQVEPARVGSNDGFDKLTLEIMTDGTIIPEDALGLSARILTEHLDLFTNLTEVAKS 180

Query: 241 VKED 244
               
Sbjct: 181 TDVM 184


>gi|150187117|emb|CAK30174.1| RNA polymerase alpha subunit [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 187

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 77/187 (41%), Positives = 122/187 (65%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI
Sbjct: 1   VTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDI 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
            T +D+E++NPDH +  +     ++  +TV+K  GYVPA+ ++ E+ P+G + +D++Y+P
Sbjct: 61  LTDSDVEIVNPDHYLFTIAEGHSLKAIMTVAKKRGYVPAEGNKKEDAPVGTLAVDSIYTP 120

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K
Sbjct: 121 VKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAK 180

Query: 240 EVKEDIN 246
                  
Sbjct: 181 NTDVMKE 187


>gi|150187170|emb|CAK30186.1| RNA polymerase alpha subunit [Streptococcus iniae]
          Length = 183

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 75/183 (40%), Positives = 123/183 (67%)

Query: 59  AITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGD 118
           A+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGD
Sbjct: 1   AVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKMIELDVEGPAEVTAGD 60

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           I T +DIE++NPDH +  +     ++  +TV+K  GY+PA+ ++ ++ P+G + +D++Y+
Sbjct: 61  ILTDSDIELVNPDHYLFTIAEGHSLKATMTVAKKRGYIPAEGNKKDDAPVGTLAVDSIYT 120

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  
Sbjct: 121 PVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVA 180

Query: 239 KEV 241
           K  
Sbjct: 181 KAT 183


>gi|150187135|emb|CAK30178.1| RNA polymerase alpha subunit [Streptococcus oralis ATCC 35037]
          Length = 177

 Score =  192 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 76/177 (42%), Positives = 119/177 (67%)

Query: 59  AITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGD 118
           A+T++ IDGVLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  +TAGD
Sbjct: 1   AVTSINIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEITAGD 60

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           I T +DIE++NPDH +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+
Sbjct: 61  ILTDSDIEIVNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYT 120

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N  
Sbjct: 121 PVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLT 177


>gi|154424765|emb|CAL18485.1| RNA polymerase alpha subunit [Streptococcus canis]
          Length = 188

 Score =  192 bits (488), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 75/188 (39%), Positives = 123/188 (65%)

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI 
Sbjct: 1   TSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKIIELEVEGPAEVTAGDIL 60

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIE++NPDH +  +     +R  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+
Sbjct: 61  TDSDIELVNPDHYLFTIAEGHSLRATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPV 120

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  +  K 
Sbjct: 121 KKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTDVAKA 180

Query: 241 VKEDINVK 248
            +     +
Sbjct: 181 TEVMKETE 188


>gi|150187076|emb|CAK30165.1| RNA polymerase alpha subunit [Streptococcus ferus]
          Length = 191

 Score =  192 bits (488), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 78/189 (41%), Positives = 124/189 (65%)

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI 
Sbjct: 1   TSIKIDGVLHEFDTIPGVREDVMQIILNLKGLAVKSYVEDEKTMELDVEGPAEVTAGDIL 60

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIE++NPDH +  +   A ++  LTV+   GYVPA+ ++ ++ P+G + ID++Y+P+
Sbjct: 61  TDSDIEIVNPDHYLFTIADGASMKATLTVATNRGYVPAEENKNDSAPVGTLAIDSIYTPV 120

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKV+Y VE AR G   +YDKL++ I T+G+I  ED++ L++R+L + L +F +  E  K 
Sbjct: 121 KKVNYQVEPARVGSKDNYDKLTIEIMTNGTIIPEDALGLSARVLMEHLNLFTDLTEVAKT 180

Query: 241 VKEDINVKS 249
            +     + 
Sbjct: 181 TEVMKETEK 189


>gi|226968553|ref|YP_002808506.1| RNA polymerase alpha chain [Micromonas pusilla CCMP1545]
 gi|226348848|gb|ACO50751.1| RNA polymerase alpha chain [Micromonas pusilla CCMP1545]
          Length = 358

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 85/358 (23%), Positives = 145/358 (40%), Gaps = 55/358 (15%)

Query: 9   LIKPN---NIEYIVLGQEEEN--RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            I PN    +E +   ++        ++  P+  G   TLGN  RR+L++ L G AITA 
Sbjct: 3   FIVPNSSAKLECVEFREKNPRTQYARLVLGPVAPGQGVTLGNTFRRLLLNDLPGVAITAA 62

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS----HKRVTIF------------ 107
           +++    E  ++ G+ E + +I LN++ I    +          +TI             
Sbjct: 63  KLNDARTEFVTLPGIRESVVEIFLNLRDIVFFNTFPDVLAPQGTITIDPSVHEGPTDAGE 122

Query: 108 ----KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV-VRMEL--------------T 148
                  P V+ AGD+Q    +  ++P   I  L        +                T
Sbjct: 123 GFELSTSPRVICAGDMQLPEGVYCVDPTQPIATLMNAHTPFHLSFILEQATGYRVWKKPT 182

Query: 149 VSKGHGYVPAKHH---RTENDPIGLI-TIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
              G G+ P +     + E    GL   ID  + P++ V++ V           + +   
Sbjct: 183 QPYGRGFYPPRQTAAPQMEQVKSGLFQPIDGNFMPVRTVNFKVHD----GPPHGEYIHFE 238

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKK-----EVKEDINVKSLPFNPALLKK 259
           I T+GSI    +   A  IL +        +EP+      EV +  +V +          
Sbjct: 239 ITTNGSIHPHAAFKHAGAILTEITR--ATLQEPRPLVGMDEVSQPADVPNNQMAYFETIA 296

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +E+LELS+R+ NCL+   I+ + DL + +   +L + NFG+KS  E+   L T G+ L
Sbjct: 297 IEQLELSLRAYNCLKRAQILTLADLSRESYQSLLALRNFGQKSAEEVAKALETYGIEL 354


>gi|150186920|emb|CAK30128.1| RNA polymerase alpha subunit [Streptococcus pasteurianus]
          Length = 177

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 75/177 (42%), Positives = 118/177 (66%)

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI T +
Sbjct: 1   KIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDS 60

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           D+E++NPDH +  +     ++  +T++K  GYVPA+ ++ E+ P+G + +D++Y+P+KKV
Sbjct: 61  DVEIVNPDHYLFTIAEGHSLKATMTIAKNRGYVPAEGNKKEDAPVGTLAVDSIYTPVKKV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K 
Sbjct: 121 NYQVEPARVGSNDGFDKLTLEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKN 177


>gi|119662389|emb|CAJ33184.1| RNA polymerase alpha subunit [Lactobacillus alimentarius]
          Length = 165

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 75/165 (45%), Positives = 113/165 (68%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG  + LGN+LRRVL++SL G A++ +QIDGVLHE S+I GV ED+T I+LN+K +
Sbjct: 1   EPLERGLWYNLGNSLRRVLLASLPGTAVSDIQIDGVLHEFSAIDGVIEDVTQIVLNVKKL 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            LK   D   +  I   GP  VTA DI+  +D+E+L+P+  IC +       M++TV  G
Sbjct: 61  KLKSYADDSLKAEIDVVGPATVTAKDIKADDDLEILDPEQFICTVAEGGHFHMQMTVING 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
            GY PA+ ++T+  PIG++ +D++++P++KV+Y VE+ R G+  D
Sbjct: 121 RGYTPAEQNKTDETPIGVLPVDSIFTPVEKVNYQVENTRVGKRND 165


>gi|150186996|emb|CAK30145.1| RNA polymerase alpha subunit [Streptococcus mitis]
          Length = 160

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 75/160 (46%), Positives = 110/160 (68%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
             TLGN+LRRVL++SL GAA+T++ IDGVLHE  ++ GV ED+  IILNIKGI +K   +
Sbjct: 1   GTTLGNSLRRVLLASLPGAAVTSINIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVE 60

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             K + +   GP  VTAGDI T +DIE++NPDH +  +   + ++  +TV+ G GYVPA 
Sbjct: 61  DEKIIELDVEGPAEVTAGDILTDSDIEIVNPDHYLFTIGEGSSLKATMTVNSGRGYVPAD 120

Query: 160 HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
            ++ +N P+G + +D++Y+P+ KV+Y VE AR G    +D
Sbjct: 121 ENKKDNAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDGFD 160


>gi|119663532|emb|CAK22337.1| RNA polymerase alpha subunit [Lactobacillus sharpeae]
          Length = 164

 Score =  191 bits (485), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 75/164 (45%), Positives = 111/164 (67%)

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+T IILNIK + LKM GD  K   I   GP  VTA DI+T  D++VLNP+  IC +  
Sbjct: 1   EDVTQIILNIKKLALKMHGDGEKTAEINIEGPATVTAADIKTDADVDVLNPEQYICTVAE 60

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
            A + M +TV  G GYVPA  ++T++ PIG+I +D++++PI +V+Y VESAR G+  D+D
Sbjct: 61  GAELHMRMTVKSGRGYVPAVQNKTDDMPIGVIAVDSIFTPISRVNYQVESARVGRRSDFD 120

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           KL++ + T+GSI   +++ALA++IL D L +F+N  +  K  + 
Sbjct: 121 KLTLDVWTNGSINPREAIALAAKILTDHLAIFVNLTDDAKNTEI 164


>gi|151416842|emb|CAO78492.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gelidum]
          Length = 164

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 75/163 (46%), Positives = 109/163 (66%), Gaps = 2/163 (1%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+K +
Sbjct: 1   EPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKV 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            L +  D  + + +  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T  KG
Sbjct: 61  VLAIDSDEERSLEVDIQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHMTITAFKG 120

Query: 153 HGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREG 193
            GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R G
Sbjct: 121 RGYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVG 163


>gi|150036712|emb|CAM98020.1| DNA-directed RNA polymerase alpha chain [Leuconostoc citreum]
          Length = 181

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 74/178 (41%), Positives = 113/178 (63%), Gaps = 2/178 (1%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+
Sbjct: 1   VNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDVQGPADVTAADL 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALY 177
           Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++   +  PIG++ +D++Y
Sbjct: 61  QAGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYSSADENKQLRDEMPIGVLAVDSIY 120

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           +PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L S+IL + L +F++  
Sbjct: 121 TPIERVNYHVENTRVGSRDDYDKLTFDIWTNGSIKPSDALSLGSKILAEHLNLFMDIS 178


>gi|154424773|emb|CAL18489.1| RNA polymerase alpha subunit [Streptococcus cristatus]
          Length = 182

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 75/182 (41%), Positives = 117/182 (64%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T++ I+GVLHE  +I GV ED+  IILNIKGI +K      K + +   GP  VTAGDI
Sbjct: 1   VTSINIEGVLHEFDTISGVREDVMQIILNIKGIAVKSYVQDEKMIELDVEGPAEVTAGDI 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
            T +DIE++NPDH +  +   A  + ++ V+ G GYVPA  ++ ++ P+G + +D++Y+P
Sbjct: 61  LTDSDIEIVNPDHYLFTISEGARFKAKMAVNSGRGYVPADENKKDDAPVGTLAVDSIYTP 120

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           + KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F +  E   
Sbjct: 121 VTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLFTDLTEVAI 180

Query: 240 EV 241
             
Sbjct: 181 ST 182


>gi|296044726|gb|ADG85772.1| RpoA [Vibrio sp. WH134]
          Length = 200

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 87/199 (43%), Positives = 134/199 (67%), Gaps = 5/199 (2%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKR 103
           NALRR+L+SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++  G     
Sbjct: 1   NALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVF 60

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK--- 159
           +T+ K G G V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    
Sbjct: 61  ITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARI 120

Query: 160 HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           H   +  PIG + +DA YSP+ K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  
Sbjct: 121 HTEEDERPIGRLLVDATYSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRR 180

Query: 220 ASRILQDQLGMFINFEEPK 238
           A+ IL +QL  F++  + +
Sbjct: 181 AATILAEQLDAFVDLRDVR 199


>gi|119663524|emb|CAK22333.1| RNA polymerase alpha subunit [Lactobacillus graminis]
          Length = 160

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 67/160 (41%), Positives = 109/160 (68%)

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           I GV ED+T IILNIK + LK+  +  K + I  +GP  VTA DI + +D+EVLN D  I
Sbjct: 1   IDGVLEDVTQIILNIKKLALKLHVEEDKTIEIDVKGPATVTAADIISDDDVEVLNTDQYI 60

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
           C +       + +TV KG GYV A  +++++ PIG++ ID++Y+PI +V+Y VES R G+
Sbjct: 61  CTVAEGGNFHVRMTVKKGRGYVAADQNKSDDMPIGVLPIDSIYTPISRVNYQVESTRVGR 120

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
             D+DKL++ + T+GSI+  ++++LA++I+ + L +F++ 
Sbjct: 121 RNDFDKLTLDVWTNGSISPREAISLAAKIMTEHLAIFVDL 160


>gi|154424779|emb|CAL18492.1| RNA polymerase alpha subunit [Streptococcus dysgalactiae subsp.
           equisimilis]
          Length = 179

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 74/179 (41%), Positives = 121/179 (67%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI
Sbjct: 1   VTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKILELEVEGPAEVTAGDI 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
            T +DIE++NPDH +  +     +R  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P
Sbjct: 61  LTDSDIELVNPDHYLFTIAEGHSLRATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTP 120

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           +KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  +  
Sbjct: 121 VKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLKLFTDLTDVA 179


>gi|150186909|emb|CAK30125.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
          Length = 171

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 76/171 (44%), Positives = 117/171 (68%)

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
           AA+T++ IDGVLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  VTAG
Sbjct: 1   AAVTSINIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEVTAG 60

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI T +DIE++NPDH +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y
Sbjct: 61  DILTDSDIEIVNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIY 120

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           +P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L
Sbjct: 121 TPVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHL 171


>gi|150036742|emb|CAM98025.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. dextranicum]
          Length = 178

 Score =  189 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 74/178 (41%), Positives = 114/178 (64%), Gaps = 2/178 (1%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +  VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+
Sbjct: 1   VNTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDIQGPADVTAADL 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALY 177
           Q   D+EVLNPD  I  +     + M +T  KG GY  A  ++   +  PIG++ +D++Y
Sbjct: 61  QGGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSADENKKLRDEMPIGVLAVDSIY 120

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           +PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L ++IL + LG+F++  
Sbjct: 121 TPIERVNYQVENTRIGARDDYDKLTFDIWTNGSIKPSDALSLGAKILAEHLGLFMDIS 178


>gi|119672811|emb|CAK95486.1| RNA polymerase alpha subunit [Lactobacillus farciminis]
          Length = 172

 Score =  189 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 69/172 (40%), Positives = 116/172 (67%)

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           QIDGVLHE S+I GV ED+T I+LN+K + LK   +   +  +   GP  VTA DI+  +
Sbjct: 1   QIDGVLHEFSAIDGVIEDVTQIVLNVKKLKLKSYAEDSLKAEVDIVGPATVTAKDIKADD 60

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           D+E+L+P+  IC +       M++T+  G GY PA+ ++T+  PIG++ +D++++P++KV
Sbjct: 61  DLEILDPEQFICTVAEGGHFHMQMTIKNGRGYTPAEQNKTDETPIGVLPVDSIFTPVEKV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           +Y VE+ R G+  D+DKL++ I T+GSI   ++++L+++IL + L  F+N  
Sbjct: 121 NYQVENTRVGKRNDFDKLTIDIWTNGSIGPREAISLSAKILTEHLNSFVNLT 172


>gi|154424809|emb|CAL18507.1| RNA polymerase alpha subunit [Streptococcus iniae]
          Length = 174

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 74/174 (42%), Positives = 121/174 (69%)

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
           AA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAG
Sbjct: 1   AAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKMIELDVEGPAEVTAG 60

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI T +DIE++NPDH +  +     ++  +TV+K  GY+PA+ ++ ++ P+G + +D++Y
Sbjct: 61  DILTDSDIELVNPDHYLFTIAEGHSLKATMTVAKKRGYIPAEGNKKDDAPVGTLAVDSIY 120

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           +P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F
Sbjct: 121 TPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLF 174


>gi|154424771|emb|CAL18488.1| RNA polymerase alpha subunit [Streptococcus cristatus]
          Length = 181

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 75/181 (41%), Positives = 116/181 (64%)

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T++ I+GVLHE  +I GV ED+  IILNIKGI +K      K + +   GP  VTAGDI 
Sbjct: 1   TSINIEGVLHEFDTISGVREDVMQIILNIKGIAVKSYVQDEKMIELDVEGPAEVTAGDIL 60

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIE++NPDH +  +   A  + ++ V+ G GYVPA  ++ ++ P+G + +D++Y+P+
Sbjct: 61  TDSDIEIVNPDHYLFTISEGARFKAKMAVNSGRGYVPADENKKDDAPVGTLAVDSIYTPV 120

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F +  E    
Sbjct: 121 TKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLFTDLTEVAIS 180

Query: 241 V 241
            
Sbjct: 181 T 181


>gi|150187152|emb|CAK30182.1| RNA polymerase alpha subunit [Streptococcus vestibularis ATCC
           49124]
          Length = 190

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 72/190 (37%), Positives = 118/190 (62%)

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGVLHE  ++ GV ED+  IILNIKG+ +K   +  K + +  +GP  VTAGDI T +DI
Sbjct: 1   DGVLHEFDTVPGVREDVMQIILNIKGLAVKSYVEDEKTIELDVQGPAEVTAGDILTDSDI 60

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++NPDH +  +   A ++  +TV+   GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y
Sbjct: 61  EIVNPDHYLFTISEGASLKATMTVATNRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNY 120

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  +  K      
Sbjct: 121 QVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTDVAKATDVMK 180

Query: 246 NVKSLPFNPA 255
             + +     
Sbjct: 181 ETEKVNDEKV 190


>gi|119668305|emb|CAK95454.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           bulgaricus]
          Length = 173

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 73/169 (43%), Positives = 108/169 (63%)

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           V+IDG+LHE +++ GV ED+T IILN+K + L+   +  K + +   GP  VTA D++  
Sbjct: 2   VKIDGILHEFTTVPGVKEDVTKIILNLKKLELRAYTEEVKTIELDVEGPATVTAEDLKAD 61

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
            D+EVLNPD  IC +     + M + V  G GYVPA  ++T    IG I +D+L+SPI+K
Sbjct: 62  ADVEVLNPDQYICTIAQGGHLHMWIDVCNGRGYVPASENKTAEMSIGDIPVDSLFSPIEK 121

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           V+Y VES R G+  D+DKL++ I T+GSI   D++  A+R+L +    F
Sbjct: 122 VNYQVESTRVGKREDFDKLTLEIWTNGSIAPNDALNFAARVLVEHFKAF 170


>gi|119662331|emb|CAJ33154.1| RNA polymerase alpha subunit [Lactobacillus nagelii]
          Length = 175

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 73/175 (41%), Positives = 120/175 (68%), Gaps = 2/175 (1%)

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGVLHE S+IKGV ED+T IILN+K + LK+  +  + + I   GP  VTA DIQ  +++
Sbjct: 1   DGVLHEFSTIKGVREDVTQIILNLKKVALKIDSEEDQALEIDVTGPLDVTASDIQGSSEV 60

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKV 183
           EVLN D  +C++   A + + +  +KG GYV A  ++T  ++ PIG++ ID++Y+PI++V
Sbjct: 61  EVLNKDLYLCSVAEGASLHVRMNANKGRGYVSADENKTKADDMPIGVLPIDSIYTPIERV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           +Y VE  R GQ  DYDKL++ + T+GSI+  ++++L+++IL + L +F++  +  
Sbjct: 121 NYQVEKTRVGQKNDYDKLTLDVWTNGSISPSEAISLSAKILTEHLTLFVDLTDEA 175


>gi|154424783|emb|CAL18494.1| RNA polymerase alpha subunit [Streptococcus equi subsp. equi]
          Length = 171

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 74/171 (43%), Positives = 119/171 (69%)

Query: 56  RGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT 115
            GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VT
Sbjct: 1   PGAAVTSIRIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKIIELDVEGPAEVT 60

Query: 116 AGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDA 175
           AGDI T +DIE++NPDH +  +     ++  +TV+K  GYVPA+ ++ ++ P+G + +D+
Sbjct: 61  AGDILTDSDIELVNPDHYLFTIADGYTLKASMTVAKKRGYVPAEGNKKDDAPVGTLAVDS 120

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           +Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L +
Sbjct: 121 IYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIE 171


>gi|154424823|emb|CAL18514.1| RNA polymerase alpha subunit [Streptococcus mutans]
          Length = 176

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 76/175 (43%), Positives = 118/175 (67%)

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           IDGVLHE  +I GV ED+  IILNIKG+ +K   +  K V +   GP  +TAGDI T +D
Sbjct: 1   IDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVEEEKIVELDVEGPAEITAGDILTDSD 60

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           IE++NPDH +  +   A ++  +TV+   GYVPA+ ++ ++ P+G + ID++Y+P+KKV+
Sbjct: 61  IEIVNPDHYLFTIAEGANLKATMTVATNRGYVPAEKNKRDDAPVGTLAIDSIYTPVKKVN 120

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           Y VE AR G   ++DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K
Sbjct: 121 YQVEPARVGSNDNFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAK 175


>gi|15829032|ref|NP_326392.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma pulmonis UAB
           CTIP]
 gi|20139643|sp|Q98Q08|RPOA_MYCPU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|14089976|emb|CAC13734.1| DNA-DIRECTED RNA POLYMERASE ALPHA CHAIN (TRANSCRIPTASE ALPHA CHAIN)
           (RNA POLYMERASE ALPHA SUBUNIT)rpo [Mycoplasma pulmonis]
          Length = 333

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 78/311 (25%), Positives = 143/311 (45%), Gaps = 17/311 (5%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
            +  T    EPL RGF  T+G ALRR L+SS+      A++I  V  E  +I  + ED+ 
Sbjct: 18  NDYETTFKIEPLERGFGSTIGTALRRTLLSSITSVVPFAIKIKDVDQEFDTISDIVEDVQ 77

Query: 84  DIILNIKGINLKMSGDSHKRVTIFK----RGPGVVTAGDIQTV--NDIEVLNPDHVICNL 137
            I+LN+K I+L    +  +   I++         +T+ D++     +IE++N D  I   
Sbjct: 78  MIMLNVKNIHLVYDENIFEDNKIYRGVIETKNEKITSSDLKFPENPEIEIVNKDLEIATN 137

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPI-----------GLITIDALYSPIKKVSYT 186
           +      ME+    G GY+  + ++   +               + ID+ +SP++KV   
Sbjct: 138 NGQKPFVMEVYFHVGRGYISFEDNKKLIEEKVALLNSTIKRGKFLAIDSDFSPVEKVKVK 197

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           V+      +   ++L + I T G+I  ++ ++ A++IL   L +  + +        +  
Sbjct: 198 VQEINSSSLNIEEELEIEIKTKGTIDTKNILSQAAQILIAHLQVIGDVKNLDAVDVFEQK 257

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +           +  L+LSVRS N L+ +    + D++  TE D++ + N G+KS+ EI
Sbjct: 258 KQEKVEPSIHSVDITSLDLSVRSINALKRQGYTKLADILTLTEDDLVAVKNLGKKSVEEI 317

Query: 307 KGVLGTMGLFL 317
              L    + L
Sbjct: 318 IQKLKEYNVTL 328


>gi|77406098|ref|ZP_00783172.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae H36B]
 gi|77175279|gb|EAO78074.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae H36B]
          Length = 179

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 68/178 (38%), Positives = 115/178 (64%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           ++  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL+
Sbjct: 1   MKATMTVAKNRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLT 60

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + I T+G+I  ED++ L++R+L + L +F +  E  K  +     + +     L + +EE
Sbjct: 61  IEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKETEKVNDEKVLDRTIEE 120

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           L+LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K  L  +GL L  +
Sbjct: 121 LDLSVRSYNCLKRAGINTIFDLTEKTEPEMMKVRNLGRKSLEEVKIKLADLGLGLKND 178


>gi|154424759|emb|CAL18482.1| RNA polymerase alpha subunit [Streptococcus anginosus]
          Length = 184

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 73/181 (40%), Positives = 114/181 (62%)

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE  ++ GV ED+  IILN+KGI +K   +  K + +   GP  +TAGDI T +DIE++
Sbjct: 1   LHEFDTVPGVREDVMQIILNVKGIAVKSYVEDEKTIELDVEGPAEITAGDILTDSDIEIV 60

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NPDH +  +   A ++  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y VE
Sbjct: 61  NPDHYLFTIGEGASLKAIMTVNTGRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQVE 120

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
            AR G    +DKL++ I TDG+I  ED++ L++RIL + L +F N  E  K        +
Sbjct: 121 PARVGSNDGFDKLTLEIMTDGTIIPEDALGLSARILTEHLDLFTNLTEVAKSTDVMKETE 180

Query: 249 S 249
            
Sbjct: 181 K 181


>gi|154424723|emb|CAL18464.1| RNA polymerase alpha subunit [Streptococcus gallolyticus]
          Length = 175

 Score =  187 bits (474), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 74/175 (42%), Positives = 118/175 (67%)

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI 
Sbjct: 1   TSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDIL 60

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +D+E++NPDH +  +     ++  +TV+K  GYV A+ ++ E+ P+G + +D++Y+P+
Sbjct: 61  TDSDVEIVNPDHYLFTIAEGHSLKATMTVAKERGYVSAEGNKKEDAPVGTLAVDSIYTPV 120

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  
Sbjct: 121 KKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLT 175


>gi|154424787|emb|CAL18496.1| RNA polymerase alpha subunit [Streptococcus ferus]
          Length = 177

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 77/177 (43%), Positives = 119/177 (67%)

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI T +
Sbjct: 1   KIDGVLHEFDTIPGVREDVMQIILNLKGLAVKSYVEDEKTMELDVEGPAEVTAGDILTDS 60

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIE++NPDH +  +   A ++  LTV+   GYVPA+ ++ ++ P+G + ID++Y+P+KKV
Sbjct: 61  DIEIVNPDHYLFTIADGASMKATLTVATNRGYVPAEENKNDSAPVGTLAIDSIYTPVKKV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +Y VE AR G   +YDKL++ I T+G+I  ED++ L++R+L + L +F +  E  K 
Sbjct: 121 NYQVEPARVGSKDNYDKLTIEIMTNGTIIPEDALGLSARVLMEHLNLFTDLTEVAKT 177


>gi|119662327|emb|CAJ33151.1| RNA polymerase alpha subunit [Lactobacillus lindneri]
          Length = 191

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 78/191 (40%), Positives = 120/191 (62%), Gaps = 4/191 (2%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE S++KGV ED+T IILN+K I LK+  D +    ++I   GP  VTAGDI T +D 
Sbjct: 1   VLHEFSTVKGVTEDVTKIILNLKKIKLKIESDDNDLHTMSINVTGPADVTAGDIVTDSDT 60

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKV 183
            +LNPD  I  +   A + M +T +KG GYV A+ ++   ++ PIG++ +D++Y+PI++V
Sbjct: 61  TILNPDLHIATVAEGATLHMTMTANKGRGYVSAEENKARNDDMPIGVLPVDSIYTPIERV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE  R GQ  D+DKL++ + TDGSIT  DS++LA++IL   L MF+   +  ++   
Sbjct: 121 NYQVEDTRVGQRDDFDKLTLDVWTDGSITPSDSISLAAKILSQHLDMFVGLTDRAQKANV 180

Query: 244 DINVKSLPFNP 254
            +  +      
Sbjct: 181 MVEKEESHKEK 191


>gi|154424791|emb|CAL18498.1| RNA polymerase alpha subunit [Streptococcus gallolyticus subsp.
           gallolyticus]
          Length = 172

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 74/172 (43%), Positives = 116/172 (67%)

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI T +
Sbjct: 1   KIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDS 60

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           D+E++NPDH +  +     ++  +TV+K  GYVPA+ ++ E+ P+G + +D++Y+P+KKV
Sbjct: 61  DVEIVNPDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKEDAPVGTLAVDSIYTPVKKV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           +Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  
Sbjct: 121 NYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLT 172


>gi|119662359|emb|CAJ33168.1| RNA polymerase alpha subunit [Lactobacillus sanfranciscensis]
          Length = 186

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 83/186 (44%), Positives = 130/186 (69%), Gaps = 4/186 (2%)

Query: 50  VLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIF 107
           +L++SL GAA+T+VQIDGVLHE S++KGV ED+T IILN+K + LK+  + +    ++I 
Sbjct: 1   ILLASLPGAAVTSVQIDGVLHEFSTVKGVTEDVTKIILNLKKLKLKIDSEDNDIHTLSIN 60

Query: 108 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TEN 165
             GP  VTA DI T ++  +LNPD  I  +   A + M +T +KG G+V A+ ++   ++
Sbjct: 61  VTGPADVTAADITTDSETTILNPDLHIATVAEGATLHMTMTANKGRGFVSAEENKARNDD 120

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
            PIG++ ID++Y+PI++V+Y VE  R GQ  D+DKL++ + T+GSI+  D+++LA++IL 
Sbjct: 121 MPIGVLPIDSIYTPIERVNYQVEDTRVGQRDDFDKLTLDVWTNGSISPSDAISLAAKILS 180

Query: 226 DQLGMF 231
             L MF
Sbjct: 181 QHLDMF 186


>gi|150186912|emb|CAK30126.1| RNA polymerase alpha subunit [Streptococcus lutetiensis]
 gi|154424793|emb|CAL18499.1| RNA polymerase alpha subunit [Streptococcus gallolyticus subsp.
           gallolyticus]
          Length = 171

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 74/171 (43%), Positives = 116/171 (67%)

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI T +
Sbjct: 1   KIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDS 60

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           D+E++NPDH +  +     ++  +TV+K  GYVPA+ ++ E+ P+G + +D++Y+P+KKV
Sbjct: 61  DVEIVNPDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKEDAPVGTLAVDSIYTPVKKV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           +Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F + 
Sbjct: 121 NYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDL 171


>gi|154424785|emb|CAL18495.1| RNA polymerase alpha subunit [Streptococcus ferus]
          Length = 175

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 76/175 (43%), Positives = 120/175 (68%)

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI 
Sbjct: 1   TSIKIDGVLHEFDTIPGVREDVMQIILNLKGLAVKSYVEDEKTMELDVEGPAEVTAGDIL 60

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T +DIE++NPDH +  +   A ++  LTV+   GYVPA+ ++ ++ P+G + ID++Y+P+
Sbjct: 61  TDSDIEIVNPDHYLFTIADGASMKATLTVATNRGYVPAEENKNDSAPVGTLAIDSIYTPV 120

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           KKV+Y VE AR G   +YDKL++ I T+G+I  ED++ L++R+L + L +F +  
Sbjct: 121 KKVNYQVEPARVGSKDNYDKLTIEIMTNGTIIPEDALGLSARVLMEHLNLFTDLT 175


>gi|150036720|emb|CAM98251.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. cremoris]
          Length = 176

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 74/176 (42%), Positives = 113/176 (64%), Gaps = 2/176 (1%)

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
             VQIDGV+HE S++ GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+Q
Sbjct: 1   NTVQIDGVVHEFSTVDGVVEDVTQIILNLKKVVLAIESDDERSLEIDIQGPADVTAADLQ 60

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYS 178
              D+EVLNPD  I  +     + M +T  KG GY  A  ++   +  PIG++ +D++Y+
Sbjct: 61  GGADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSADENKKLRDEMPIGVLAVDSIYT 120

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           PI++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L ++IL + LG+F++ 
Sbjct: 121 PIERVNYQVENTRIGARDDYDKLTFDIWTNGSIKPSDALSLGAKILAEHLGLFMDI 176


>gi|154424735|emb|CAL18470.1| RNA polymerase alpha subunit [Streptococcus pasteurianus]
          Length = 168

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 73/168 (43%), Positives = 115/168 (68%)

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI T +
Sbjct: 1   KIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDS 60

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           D+E++NPDH +  +     ++  +T++K  GYVPA+ ++ E+ P+G + +D++Y+P+KKV
Sbjct: 61  DVEIVNPDHYLFTIAEGHSLKATMTIAKNRGYVPAEGNKKEDAPVGTLAVDSIYTPVKKV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           +Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F
Sbjct: 121 NYQVEPARVGSNDGFDKLTLEIMTNGTIIPEDALGLSARVLIEHLNLF 168


>gi|154424811|emb|CAL18508.1| RNA polymerase alpha subunit [Streptococcus intermedius]
          Length = 168

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 74/168 (44%), Positives = 114/168 (67%)

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           I+GVLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  VTAGDI T +D
Sbjct: 1   IEGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEGEKTIELDVEGPAEVTAGDILTDSD 60

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           IE++NP+H +  +   A ++  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+KKV+
Sbjct: 61  IEIVNPNHYLFTIGEGASLKAVMTVNTGRGYVPADENKKDDAPVGTLAVDSIYTPVKKVN 120

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           Y VE AR G    +DKL++ I TDG+I  ED++ L++RIL + L +F 
Sbjct: 121 YQVEPARVGSNDSFDKLTLEIMTDGTIIPEDALGLSARILTEHLDLFT 168


>gi|119668329|emb|CAK95464.1| RNA polymerase alpha subunit [Lactobacillus iners]
          Length = 188

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 81/186 (43%), Positives = 123/186 (66%)

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           IDGVLHE S+I GV ED+T IILN+K + LK+  D  K V I   GP VVTA D++   D
Sbjct: 2   IDGVLHEFSTIPGVREDVTKIILNLKKLELKLLVDEEKMVEIDVEGPAVVTAADLKVDAD 61

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           +E+LNPD  IC +     + M + +  G GY+PA  +++++ PIG+I +D+L+SPIKKV+
Sbjct: 62  VEILNPDQYICTIAEGGHLHMSIAIKNGRGYIPASENKSDDMPIGVIPVDSLFSPIKKVN 121

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR G+  DYDKL++ + TDGSIT  D+++ A++IL++   +F++ +   +     
Sbjct: 122 YQVENARVGKRDDYDKLTLELWTDGSITPNDALSFAAKILEEHFKVFMSADMSDQFANVM 181

Query: 245 INVKSL 250
           I  +  
Sbjct: 182 IEKEDK 187


>gi|150187130|emb|CAK30177.1| RNA polymerase alpha subunit [Streptococcus macacae NCTC 11558]
          Length = 178

 Score =  185 bits (470), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 73/178 (41%), Positives = 115/178 (64%)

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +IDGVLHE  +I GV ED+  IILNIKG+ +K   +  K + +   GP  +TAGDI T +
Sbjct: 1   KIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVEEEKIIELDVEGPAEITAGDILTDS 60

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           DIE++N DH +  +   A ++  +TV    GY+PA+ ++ +  P+G + ID++Y+P+KKV
Sbjct: 61  DIEIVNSDHYLFTIAEGASLKATMTVETNRGYIPAEENKKDGAPVGTLAIDSIYTPVKKV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K  
Sbjct: 121 NYQVEPARVGSKDSFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKTT 178


>gi|154424835|emb|CAL18520.1| RNA polymerase alpha subunit [Streptococcus phocae]
          Length = 153

 Score =  185 bits (470), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 74/153 (48%), Positives = 110/153 (71%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG 98
           +  TLGN+LRRVL+SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   
Sbjct: 1   YGTTLGNSLRRVLLSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYV 60

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           +  K + +   GP  VTAGDI T +DIE++NPDH +  +     +R  +TV+K  GYVPA
Sbjct: 61  EDEKTIELEVEGPATVTAGDILTDSDIELVNPDHYLFTIAEGHSLRATMTVAKKRGYVPA 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
           + ++ ++ P+G + +D++Y+P+KKV+Y VE AR
Sbjct: 121 EGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPAR 153


>gi|23013214|ref|ZP_00053138.1| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Magnetospirillum magnetotacticum MS-1]
          Length = 159

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 99/153 (64%), Positives = 125/153 (81%), Gaps = 1/153 (0%)

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R GQV DYDKL+MT++T+G++T +D+VALA+RILQDQL +FINFEEP   V+E+ 
Sbjct: 6   KVENTRVGQVTDYDKLNMTVETNGAVTPDDAVALAARILQDQLQLFINFEEPTAVVEEE- 64

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
               LPFN  LL+KV+ELELSVRS NCL+ +NI+Y+GDL+Q+TEA+MLR  NFGRKSL E
Sbjct: 65  KKDELPFNKNLLRKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEMLRTPNFGRKSLNE 124

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           IK VL  MGL LGM + +WPPE+IEELAKK E+
Sbjct: 125 IKEVLAQMGLHLGMEIANWPPENIEELAKKLEE 157


>gi|150036752|emb|CAM98261.1| DNA-directed RNA polymerase alpha chain [Leuconostoc lactis]
          Length = 187

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 68/181 (37%), Positives = 107/181 (59%), Gaps = 2/181 (1%)

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+Q   D+EVLNP
Sbjct: 1   EFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDVQGPAEVTAADLQAGADVEVLNP 60

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVE 188
           D  I  +     + M +T  KG GY  A  ++   E  PIG++ +D++Y+PI++V+Y VE
Sbjct: 61  DLHIATVAAGKSLHMTVTAVKGRGYSSADENKQLREEMPIGVLAVDSIYTPIERVNYHVE 120

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           + R G   DYDKL+  I T+GSI   D+++L ++IL + L +F++      E    +  +
Sbjct: 121 NTRVGARDDYDKLTFDIWTNGSIKPSDALSLGAKILAEHLNLFMDISPVAAEANVMVEAE 180

Query: 249 S 249
            
Sbjct: 181 P 181


>gi|154424789|emb|CAL18497.1| RNA polymerase alpha subunit [Streptococcus gallolyticus subsp.
           gallolyticus]
          Length = 169

 Score =  184 bits (468), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 74/169 (43%), Positives = 115/169 (68%)

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI T +
Sbjct: 1   KIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDS 60

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           D+E++NPDH +  +     ++  +TV+K  GYVPA+ ++ E+ P+G + +D++Y+P+KKV
Sbjct: 61  DVEIVNPDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKEDAPVGTLAVDSIYTPVKKV 120

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           +Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F 
Sbjct: 121 NYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFT 169


>gi|154424825|emb|CAL18515.1| RNA polymerase alpha subunit [Streptococcus parasanguinis]
          Length = 167

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 72/167 (43%), Positives = 111/167 (66%)

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           +GVLHE  ++ GV ED+  IILN+KGI +K      K + +   GP  VTAGDI T +DI
Sbjct: 1   EGVLHEFDTVPGVREDVMQIILNVKGIAVKSYVQDEKIIELDVEGPAEVTAGDILTDSDI 60

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++NPDH +  +   A ++  LTV+ G GYVPA  ++ ++ P+G + +D++Y+P+ KV+Y
Sbjct: 61  EIVNPDHYLFTIGEGASLKATLTVNSGRGYVPADQNKKDDAPVGTLAVDSIYTPVTKVNY 120

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
            VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F 
Sbjct: 121 QVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLFT 167


>gi|270265493|emb|CBI68383.1| RNA polymerase alpha-subunit [Vibrio tapetis]
          Length = 200

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 86/203 (42%), Positives = 129/203 (63%), Gaps = 7/203 (3%)

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHH---RTENDPIG 169
           V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA        +  PIG
Sbjct: 1   VVAGDITHDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASSRIHTEEDERPIG 60

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +DA YSP+ K++Y VE+AR  Q  D DKL + ++T+G++  E+++  ++ IL +QL 
Sbjct: 61  RLLVDATYSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRSATILAEQLD 120

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
            F++  + +         +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 121 AFVDLRDIRVPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 177

Query: 290 ADMLRMANFGRKSLVEIKGVLGT 312
            ++L+  N G KSL EIK VL +
Sbjct: 178 VELLKTPNLGNKSLTEIKDVLAS 200


>gi|23012374|ref|ZP_00052476.1| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Magnetospirillum magnetotacticum MS-1]
          Length = 146

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 84/147 (57%), Positives = 111/147 (75%), Gaps = 1/147 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN + ++  G + +    ++AEPL RGF  TLGN+LRRVL+SSL+GAA+
Sbjct: 1   MIQKNWQELIKPNKL-HVEPGADAQRSATVVAEPLERGFGMTLGNSLRRVLLSSLQGAAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TA+QIDGVLHE SSI GV ED+TDIILNIK + L+M G+  KR+ +   GPG VTAG I+
Sbjct: 60  TAIQIDGVLHEFSSIPGVREDVTDIILNIKTLGLRMHGEGPKRMHLRAVGPGEVTAGLIE 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMEL 147
             +DIE+++P+ V+C LD  A + +E 
Sbjct: 120 VGHDIEIMDPELVLCTLDEGAKLNIEF 146


>gi|154424775|emb|CAL18490.1| RNA polymerase alpha subunit [Streptococcus dysgalactiae subsp.
           dysgalactiae]
          Length = 169

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 73/169 (43%), Positives = 116/169 (68%)

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           ++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI T 
Sbjct: 1   IKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKIIELEVEGPAEVTAGDILTD 60

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           +DIE++NPDH +  +     +R  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KK
Sbjct: 61  SDIELVNPDHYLFTIAEGHSLRATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKK 120

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           V+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F
Sbjct: 121 VNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLF 169


>gi|150036840|emb|CAM98285.1| DNA-directed RNA polymerase alpha chain [Leuconostoc argentinum
           KCTC 3773]
          Length = 190

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 65/186 (34%), Positives = 106/186 (56%), Gaps = 2/186 (1%)

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
             ED+T IILN+K + L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +
Sbjct: 5   CREDVTQIILNLKKVVLAIDSDDERSLEIDVQGPAEVTAADLQAGADVEVLNPDLHIATV 64

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
                + M +T  KG GY  A  ++   E  PIG++ +D++Y+PI++V+Y VE+ R G  
Sbjct: 65  AAGKSLHMTVTAVKGRGYSSADENKQLREEMPIGVLAVDSIYTPIERVNYHVENTRVGAR 124

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            DYDKL+  I T+GSI   D+++L ++IL + L +F++      E    +  + +  + +
Sbjct: 125 DDYDKLTFDIWTNGSIKPSDALSLGAKILAEHLNLFMDISPVAAEANVMVEAEPVAVSAS 184

Query: 256 LLKKVE 261
               +E
Sbjct: 185 DSAPIE 190


>gi|154424869|emb|CAL18537.1| RNA polymerase alpha subunit [Streptococcus uberis]
          Length = 170

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 72/170 (42%), Positives = 114/170 (67%)

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE  +I GV ED+  IILNIKG+ +K   +  K + +   GP  VTAGDI T +DIE
Sbjct: 1   GVLHEFDTIPGVREDVMQIILNIKGLAVKSYVEDEKMIELDVEGPAEVTAGDILTDSDIE 60

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           ++NPDH +  +     ++  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y 
Sbjct: 61  LVNPDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQ 120

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  E
Sbjct: 121 VEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTE 170


>gi|300379501|gb|ADK08381.1| DNA-directed RNA polymerase alpha subunit [Lactobacillus reuteri]
          Length = 166

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 77/166 (46%), Positives = 119/166 (71%), Gaps = 2/166 (1%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAA+T++QIDGVLHE S++KGV ED+T IILN+K ++LK+  +  K + +  +GP  VTA
Sbjct: 1   GAAVTSMQIDGVLHEFSTVKGVTEDVTQIILNLKKVSLKIDSEDQKDLELDVKGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITID 174
            DIQ  N++ +LNPD  I  +   A + ++LT  KG GY+ A  ++   ++  IG++ ID
Sbjct: 61  SDIQGDNEVTILNPDLHIATVADGAELHIKLTADKGRGYLSANDNKARMDDLAIGVLPID 120

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           ++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T  ++V+L 
Sbjct: 121 SIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLTPTEAVSLG 166


>gi|119662293|emb|CAJ33133.1| RNA polymerase alpha subunit [Lactobacillus coryniformis subsp.
           torquens KCTC 3535]
          Length = 161

 Score =  182 bits (463), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 62/161 (38%), Positives = 103/161 (63%)

Query: 88  NIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           NIK + LK+  D  K + I  +GP  VTAGDI+   D+E+LNPD  IC +       + +
Sbjct: 1   NIKKLALKLDSDDDKTLEIDVKGPATVTAGDIEADGDVEILNPDLYICTVAEGGRFHIRM 60

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           T  KG GYV A  ++ ++ PIG++ ID++Y+PI +V+Y VES R G+  D+DKL++ + T
Sbjct: 61  TAHKGRGYVAADGNKVDDMPIGVLPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWT 120

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +GSI+  ++++LA++IL + L +F+N  +  K  +  +  +
Sbjct: 121 NGSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKE 161


>gi|269929661|gb|ACZ53726.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929663|gb|ACZ53727.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929665|gb|ACZ53728.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929667|gb|ACZ53729.1| RNA polymerase alpha subunit [Lactobacillus reuteri ATCC 53608]
 gi|269929669|gb|ACZ53730.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929671|gb|ACZ53731.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929673|gb|ACZ53732.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929675|gb|ACZ53733.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929677|gb|ACZ53734.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929679|gb|ACZ53735.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929681|gb|ACZ53736.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929685|gb|ACZ53738.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929687|gb|ACZ53739.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929689|gb|ACZ53740.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929691|gb|ACZ53741.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929693|gb|ACZ53742.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929695|gb|ACZ53743.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929697|gb|ACZ53744.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929699|gb|ACZ53745.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929701|gb|ACZ53746.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929705|gb|ACZ53748.1| RNA polymerase alpha subunit [Lactobacillus reuteri ATCC 53608]
 gi|269929707|gb|ACZ53749.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929709|gb|ACZ53750.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929711|gb|ACZ53751.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929713|gb|ACZ53752.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929715|gb|ACZ53753.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929717|gb|ACZ53754.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929719|gb|ACZ53755.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929721|gb|ACZ53756.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929723|gb|ACZ53757.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929725|gb|ACZ53758.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929727|gb|ACZ53759.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929729|gb|ACZ53760.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929731|gb|ACZ53761.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929733|gb|ACZ53762.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929735|gb|ACZ53763.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929737|gb|ACZ53764.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929739|gb|ACZ53765.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929741|gb|ACZ53766.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929743|gb|ACZ53767.1| RNA polymerase alpha subunit [Lactobacillus reuteri DSM 20016]
 gi|269929745|gb|ACZ53768.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929747|gb|ACZ53769.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929749|gb|ACZ53770.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929751|gb|ACZ53771.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929753|gb|ACZ53772.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929755|gb|ACZ53773.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929757|gb|ACZ53774.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929759|gb|ACZ53775.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929761|gb|ACZ53776.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929763|gb|ACZ53777.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929765|gb|ACZ53778.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929767|gb|ACZ53779.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929769|gb|ACZ53780.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929771|gb|ACZ53781.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929773|gb|ACZ53782.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929775|gb|ACZ53783.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929777|gb|ACZ53784.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929779|gb|ACZ53785.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929781|gb|ACZ53786.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929783|gb|ACZ53787.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929785|gb|ACZ53788.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929787|gb|ACZ53789.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929789|gb|ACZ53790.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929791|gb|ACZ53791.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929793|gb|ACZ53792.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929795|gb|ACZ53793.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929797|gb|ACZ53794.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929799|gb|ACZ53795.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929801|gb|ACZ53796.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929803|gb|ACZ53797.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929805|gb|ACZ53798.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929807|gb|ACZ53799.1| RNA polymerase alpha subunit [Lactobacillus reuteri lpuph]
 gi|269929809|gb|ACZ53800.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929811|gb|ACZ53801.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929813|gb|ACZ53802.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929815|gb|ACZ53803.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929817|gb|ACZ53804.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929819|gb|ACZ53805.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929821|gb|ACZ53806.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929823|gb|ACZ53807.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929825|gb|ACZ53808.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929827|gb|ACZ53809.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929831|gb|ACZ53811.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929833|gb|ACZ53812.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929835|gb|ACZ53813.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929837|gb|ACZ53814.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929839|gb|ACZ53815.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929841|gb|ACZ53816.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929843|gb|ACZ53817.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929845|gb|ACZ53818.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929847|gb|ACZ53819.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929849|gb|ACZ53820.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929851|gb|ACZ53821.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929853|gb|ACZ53822.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929855|gb|ACZ53823.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929857|gb|ACZ53824.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929859|gb|ACZ53825.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929861|gb|ACZ53826.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929863|gb|ACZ53827.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929865|gb|ACZ53828.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929867|gb|ACZ53829.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929869|gb|ACZ53830.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929871|gb|ACZ53831.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929873|gb|ACZ53832.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929875|gb|ACZ53833.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929877|gb|ACZ53834.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929879|gb|ACZ53835.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929881|gb|ACZ53836.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929883|gb|ACZ53837.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929885|gb|ACZ53838.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929887|gb|ACZ53839.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929889|gb|ACZ53840.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
          Length = 166

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 77/166 (46%), Positives = 119/166 (71%), Gaps = 2/166 (1%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAAIT++QIDGVLHE S+++GV ED+T IILN+K ++LK+  +  K + +  +GP  VTA
Sbjct: 1   GAAITSMQIDGVLHEFSTVEGVTEDVTQIILNLKKVSLKLDSEDQKNLELDVKGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITID 174
            DIQ  N++ +LNPD  I  +   A + ++LT  KG GY+ A  ++   ++  IG++ ID
Sbjct: 61  SDIQGDNEVTILNPDLHIATVADGAELHIKLTADKGRGYLSANDNKARMDDLAIGVLPID 120

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           ++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T  ++V+L 
Sbjct: 121 SIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLTPTEAVSLG 166


>gi|117575081|emb|CAJ84780.1| RNA polymerase alpha subunit [Lactobacillus amylophilus]
          Length = 159

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 67/158 (42%), Positives = 105/158 (66%)

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            S+I GV ED+T IILN+K + LK      K   I   GP  VTAGD++  +++++LNPD
Sbjct: 1   FSTIPGVLEDVTQIILNLKKLTLKSIAADEKLAEIDVEGPATVTAGDLKVDDEVQILNPD 60

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             I  +   A ++M + + +G GYVPA  +++++ PIG++ +D+L+SPI+KV+Y VE  R
Sbjct: 61  QYIATVAEGAHLQMTVAIKQGRGYVPADQNKSDDMPIGVVPVDSLFSPIEKVNYQVEGTR 120

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            G+  DYDKL+M + TDGSIT  D+++  ++IL + L 
Sbjct: 121 VGRNNDYDKLTMEVWTDGSITPNDALSFGAKILTEHLN 158


>gi|269929659|gb|ACZ53725.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929703|gb|ACZ53747.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
          Length = 166

 Score =  182 bits (461), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 78/166 (46%), Positives = 119/166 (71%), Gaps = 2/166 (1%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAAIT++QIDGVLHE S++KGV ED+T IILN+K ++LK+  +  K + +  +GP  VTA
Sbjct: 1   GAAITSMQIDGVLHEFSTVKGVTEDVTQIILNLKKVSLKLDSEDQKNLELDVKGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITID 174
            DIQ  N++ +LNPD  I  +   A + ++LT  KG GY+ A  ++   ++  IG++ ID
Sbjct: 61  SDIQGDNEVTILNPDLHIATVADGAELHIKLTADKGRGYLSANDNKARMDDLAIGVLPID 120

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           ++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T  ++V+L 
Sbjct: 121 SIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLTPTEAVSLG 166


>gi|119663528|emb|CAK22335.1| RNA polymerase alpha subunit [Lactobacillus malefermentans]
          Length = 175

 Score =  182 bits (461), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 73/175 (41%), Positives = 112/175 (64%), Gaps = 4/175 (2%)

Query: 77  GVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           G+ ED+T IILN+K I+LK+ G  D  + + +  +GP  VTAGDI   +D+ VLNPD  I
Sbjct: 1   GIVEDVTQIILNVKKISLKLEGADDEVETLEVNVKGPAQVTAGDITADSDVTVLNPDLYI 60

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESARE 192
             +   A   M +T +KG GYV A  ++   E+ PIG++ ID++Y+PI++V+Y VE+ R 
Sbjct: 61  ATVAEGATFHMRMTANKGRGYVSADQNKVRDEDMPIGVLPIDSIYTPIERVNYQVENTRV 120

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           G   DYDKL++ + TDGSI   +S++LA++IL + L MF+N  +  K  +  +  
Sbjct: 121 GHKSDYDKLTLDVWTDGSINPSESISLAAKILMEHLDMFVNLTDEAKNAEIMVEK 175


>gi|161511741|emb|CAP16881.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 179

 Score =  182 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 69/177 (38%), Positives = 112/177 (63%), Gaps = 2/177 (1%)

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           +I+GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  
Sbjct: 1   TIEGVVEDVTQIILNLKKVSLKVESDEEKSLEINVMGPANVTAGDIVGDGDVTILNPELP 60

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAR 191
           IC +         LT  KG GY  A  ++    + PIG++ ID++Y+PI++V+Y VE+ R
Sbjct: 61  ICTVAEGTTFHAVLTAEKGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTR 120

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
            GQ  DYDKL++ + TDGS+   ++++L+++IL + L +F+N ++  K+ +  +  K
Sbjct: 121 VGQRDDYDKLTLDVWTDGSLAASEAISLSAKILTEHLTIFVNLDDQAKDTEIMVEKK 177


>gi|150036826|emb|CAM98280.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gasicomitatum]
          Length = 186

 Score =  182 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 67/180 (37%), Positives = 107/180 (59%), Gaps = 2/180 (1%)

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            S++ GV ED+T IILN+K + L +  D  + + +  +GP  VTA D+Q   D+EVLNPD
Sbjct: 1   FSTVDGVVEDVTQIILNLKKVVLAIDSDEERSLEVDIQGPADVTAADLQAGADVEVLNPD 60

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVES 189
             I  +     + M +T  KG GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+
Sbjct: 61  LHIATVAAGKSLHMTITAFKGRGYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYHVEN 120

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R G   DYDKL+  I T+GSI   D+++L S+IL + L +F++      E    + V+ 
Sbjct: 121 TRVGSRDDYDKLTFDIWTNGSIKPSDALSLGSKILAEHLNLFMDISPVAAEANVMVEVEP 180


>gi|150187014|emb|CAK30151.1| RNA polymerase alpha subunit [Streptococcus sinensis]
          Length = 171

 Score =  182 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 73/170 (42%), Positives = 113/170 (66%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T++ I+GVLHE  +I GV ED+  IILNIKGI +K      K + +   GP  VTAGDI
Sbjct: 1   VTSINIEGVLHEFDTISGVREDVMQIILNIKGIAVKSYVQDEKMIELDVEGPAAVTAGDI 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
            T +DIE++NPDH +  +   A  + ++ V+ G GYVPA  ++ ++ P+G + +D++Y+P
Sbjct: 61  LTDSDIEIINPDHYLFTISEGASFKAKMAVNSGRGYVPADENKKDDAPVGTLAVDSIYTP 120

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           + KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L 
Sbjct: 121 VTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLN 170


>gi|154424807|emb|CAL18506.1| RNA polymerase alpha subunit [Streptococcus lutetiensis]
          Length = 167

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 73/167 (43%), Positives = 116/167 (69%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T+++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI
Sbjct: 1   VTSIKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDI 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
            T +D+E++NPDH +  +     ++  +TV+K  GYVPA+ ++ E+ P+G + +D++Y+P
Sbjct: 61  LTDSDVEIVNPDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKEDAPVGTLAVDSIYTP 120

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           +KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L +
Sbjct: 121 VKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIE 167


>gi|269929683|gb|ACZ53737.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
          Length = 166

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 77/166 (46%), Positives = 120/166 (72%), Gaps = 2/166 (1%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAAIT++QIDGVLHE S+++GV ED+T IILN+K ++LK+  ++ K + +  +GP  VTA
Sbjct: 1   GAAITSMQIDGVLHEFSTVEGVTEDVTQIILNLKKVSLKLDSENQKNLELDVKGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITID 174
            DIQ  N++ +LNPD  I  +   A + ++LT  KG GY+ A  ++   ++  IG++ ID
Sbjct: 61  SDIQGDNEVTILNPDLHIATVADGAELHIKLTADKGRGYLSANDNKARMDDLAIGVLPID 120

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           ++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T  ++V+L 
Sbjct: 121 SIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLTPTEAVSLG 166


>gi|119668351|emb|CAK95512.1| RNA polymerase alpha subunit [Lactobacillus pentosus]
          Length = 160

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 73/160 (45%), Positives = 110/160 (68%), Gaps = 2/160 (1%)

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S+++GV ED+T IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EVLNP
Sbjct: 1   EFSTVEGVTEDVTAIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEVLNP 60

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVE 188
           D  IC +   A   M +T + G GYV A+ ++   ++ PIG++ +D+LYSPI++V+Y VE
Sbjct: 61  DLPICTVADGAHFHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVE 120

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           + R GQ  D+DKL++ + T+GSIT  ++++L+++IL D L
Sbjct: 121 TTRVGQRDDFDKLTLDVWTNGSITPSEAISLSAKILTDHL 160


>gi|150187149|emb|CAK30181.1| RNA polymerase alpha subunit [Streptococcus ratti]
          Length = 178

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 66/178 (37%), Positives = 111/178 (62%)

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
             ++ GV ED+  IILN+KG+ +K   +  K + +   GP  +TAGDI T +DIE++NPD
Sbjct: 1   FDTVPGVREDVMQIILNLKGLAVKSYVEEEKIIELDVEGPAEITAGDILTDSDIEIVNPD 60

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
           H +  +   A ++  LTV    GY+PA+ ++ ++ P+G + ID++Y+P+KKV+Y VE AR
Sbjct: 61  HYLFTIAEGASLKATLTVGTNRGYIPAEENKKDDAPVGTLAIDSIYTPVKKVNYQVEPAR 120

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            G   ++DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K        + 
Sbjct: 121 VGSNDNFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKATDVMKETEQ 178


>gi|154424799|emb|CAL18502.1| RNA polymerase alpha subunit [Streptococcus hyointestinalis]
          Length = 167

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 72/167 (43%), Positives = 116/167 (69%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           +T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI
Sbjct: 1   VTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKMIELDVEGPAEVTAGDI 60

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
            T +DIE++NPDH +  +     ++  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P
Sbjct: 61  LTDSDIEIVNPDHYLFTIAEGHSLKATMTVAKNRGYVPAEGNKKDDAPVGTLAVDSIYTP 120

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           +KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL +
Sbjct: 121 VKKVNYQVEPARVGSNDGFDKLTVEIMTNGTIIPEDALGLSARILIE 167


>gi|269929829|gb|ACZ53810.1| RNA polymerase alpha subunit [Lactobacillus reuteri mlc3]
          Length = 166

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 77/166 (46%), Positives = 119/166 (71%), Gaps = 2/166 (1%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAAIT++QIDGVLHE S+++GV ED+T IILN+K ++LK+  +  K + +  +GP  VTA
Sbjct: 1   GAAITSMQIDGVLHEFSTVEGVTEDVTQIILNLKKVSLKLDSEDQKNLELDVKGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITID 174
            DIQ  N++ +LNPD  I  +   A + ++LT  KG GY+ A  ++   ++  IG++ ID
Sbjct: 61  SDIQGDNEVTILNPDLHITTVADGAELHIKLTADKGRGYLSANDNKARMDDLAIGVLPID 120

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           ++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T  ++V+L 
Sbjct: 121 SIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLTPTEAVSLG 166


>gi|154424815|emb|CAL18510.1| RNA polymerase alpha subunit [Streptococcus minor]
          Length = 174

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 68/174 (39%), Positives = 111/174 (63%)

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           + GV ED+  IILNIKGI +K   +  K++ +   GP  +TAGDI T +DIE++NPDH +
Sbjct: 1   VPGVREDVMQIILNIKGIAVKSYVEDEKKIELDVVGPAEITAGDILTDSDIEIVNPDHYL 60

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
             +   A  +  LTV++G GYVPA+ ++ +  P+G + +D++Y+P+ KV+Y VE AR G 
Sbjct: 61  FTIGEGASFKAILTVNRGRGYVPAEGNKKDEAPVGTLAVDSIYTPVVKVNYQVEPARVGS 120

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
              +DKL++ I T+G+   ED++ L++RIL + LG+F +  +  K  +     +
Sbjct: 121 NDGFDKLTLEIMTNGTTNPEDALGLSARILMEHLGLFTDLTDVAKSAEVMKEAE 174


>gi|161511737|emb|CAP16879.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 171

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 71/171 (41%), Positives = 111/171 (64%), Gaps = 2/171 (1%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I+GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +
Sbjct: 1   VLHEFSTIEGVVEDVTQIILNLKKVSLKVESDEEKSLEINVMGPANVTAGDIVGDGDVTI 60

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSY 185
           LNP+  IC +         LT  KG GY  A  ++    + PIG++ ID++Y+PI++V+Y
Sbjct: 61  LNPELPICTVAEGTTFHAVLTAEKGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNY 120

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
            VE+ R GQ  DYDKL++ + TD S+   ++++L+++IL + L +F+N ++
Sbjct: 121 QVENTRVGQRDDYDKLTLDVWTDVSLAASEAISLSAKILTEHLTIFVNLDD 171


>gi|154424777|emb|CAL18491.1| RNA polymerase alpha subunit [Streptococcus dysgalactiae subsp.
           dysgalactiae]
          Length = 185

 Score =  180 bits (456), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 67/184 (36%), Positives = 113/184 (61%)

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
             +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPD
Sbjct: 1   FDTIPGVREDVMQIILNVKGLAVKSYVEDEKIIELEVEGPAEVTAGDILTDSDIELVNPD 60

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
           H +  +     +R  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR
Sbjct: 61  HYLFTIAEGHSLRATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPAR 120

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            G    +DKL++ I T+G+I  ED++ L++R+L + L +F +  +  K  +     + + 
Sbjct: 121 VGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTDVAKATEVMKETEKVN 180

Query: 252 FNPA 255
               
Sbjct: 181 DEKV 184


>gi|150187010|emb|CAK30150.1| RNA polymerase alpha subunit [Streptococcus pyogenes]
          Length = 184

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 68/182 (37%), Positives = 113/182 (62%)

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           +I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH 
Sbjct: 1   TIPGVREDVMQIILNVKGLAVKSYVEDEKIIELEVEGPAEVTAGDILTDSDIELVNPDHY 60

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           +  +     +R  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G
Sbjct: 61  LFTIAEGHSLRATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVG 120

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
               +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K  +     + +   
Sbjct: 121 SNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKETEKVNDE 180

Query: 254 PA 255
             
Sbjct: 181 KV 182


>gi|154424767|emb|CAL18486.1| RNA polymerase alpha subunit [Streptococcus constellatus subsp.
           constellatus]
          Length = 171

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 70/171 (40%), Positives = 107/171 (62%)

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
            GV ED+  IILN+KGI +K   +  K + +   GP  +TAGDI T +DIE++NPDH + 
Sbjct: 1   PGVREDVMQIILNVKGIAVKSYVEDEKTIELDVEGPAEITAGDILTDSDIEIVNPDHYLF 60

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
            +   A ++  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y VE AR G  
Sbjct: 61  TIGEGASLKAIMTVNAGRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSN 120

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
             +DKL++ I TDG+I  ED++ L++RIL   L +F N  E  K       
Sbjct: 121 DGFDKLTLEIMTDGTIIPEDALGLSARILTQHLDLFTNLTEVAKSTDVMKE 171


>gi|119662379|emb|CAJ33178.1| RNA polymerase alpha subunit [Lactobacillus pentosus]
          Length = 158

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 71/157 (45%), Positives = 107/157 (68%), Gaps = 2/157 (1%)

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+T IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EVLNPD  IC +  
Sbjct: 2   EDVTAIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVAD 61

Query: 140 DAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
            A   M +T + G GYV A+ ++   ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D
Sbjct: 62  GAHFHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVETTRVGQRDD 121

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           +DKL++ + T+GSIT  ++++L+++IL D L +F+N 
Sbjct: 122 FDKLTLDVWTNGSITPSEAISLSAKILTDHLSIFVNL 158


>gi|150186916|emb|CAK30127.1| RNA polymerase alpha subunit [Streptococcus oligofermentans]
          Length = 170

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 68/170 (40%), Positives = 106/170 (62%)

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
             +I GV ED+  IILNIKGI +K      K + +   GP  VTAGDI T +DIE++NPD
Sbjct: 1   FDTISGVREDVMQIILNIKGIAVKSYVQDEKMIELDVEGPAEVTAGDILTDSDIEIVNPD 60

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
           H +  +   A  + ++ V+ G GYVPA  ++ ++ P+G + +D++Y+P+ KV+Y VE AR
Sbjct: 61  HYLFTISEGARFKAKMAVNSGRGYVPADENKKDDAPVGTLAVDSIYTPVTKVNYQVEPAR 120

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
            G    +DKL++ I T+G+I  ED++ L++RIL + L +F +  E     
Sbjct: 121 VGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLFTDLTEVAIST 170


>gi|150036738|emb|CAM98024.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. dextranicum]
          Length = 171

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 68/170 (40%), Positives = 108/170 (63%), Gaps = 2/170 (1%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V+HE S++ GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+Q   D+EV
Sbjct: 1   VVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDIQGPADVTAADLQGGADVEV 60

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
           LNPD  I  +     + M ++  KG GY  A  ++   +  PIG++ +D++Y+PI++V+Y
Sbjct: 61  LNPDLHIATVAAGKSLHMTVSAVKGRGYTSADENKKLRDEMPIGVLAVDSIYTPIERVNY 120

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
            VE+ R G   DYDKL+  I T+GSI   D+++L ++IL + LG+F++  
Sbjct: 121 QVENTRIGARDDYDKLTFDIWTNGSIKPSDALSLGAKILAEHLGLFMDIS 170


>gi|154424819|emb|CAL18512.1| RNA polymerase alpha subunit [Streptococcus mitis]
          Length = 171

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 70/171 (40%), Positives = 108/171 (63%)

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
            GV ED+  IILNIKGI +K   +  K + +   GP  VTAGDI T +DIE++NPDH + 
Sbjct: 1   PGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEVTAGDILTDSDIEIVNPDHYLF 60

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
            +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y VE AR G  
Sbjct: 61  TIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQVEPARVGSN 120

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
             +DKL++ I T+G+I  ED++ L++RIL + L +F N  E  K  +    
Sbjct: 121 DGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSTEVMKE 171


>gi|119662807|emb|CAJ33195.1| RNA polymerase alpha subunit [Lactobacillus pantheris]
          Length = 165

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 83/165 (50%), Positives = 119/165 (72%), Gaps = 1/165 (0%)

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           HE S+I GV ED+T IILNIK + LK+ G+   K+ TI   GP VVTA DI+T  D+EVL
Sbjct: 1   HEFSTIDGVLEDVTQIILNIKKLALKVEGEEEDKKATILVEGPAVVTAADIKTDADVEVL 60

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NPD  IC +     + ME+T+  G GYVPA  +++++ PIG+I +D++++PI KV+YTVE
Sbjct: 61  NPDQYICTIAEGGRLEMEMTIKTGRGYVPADQNKSDDQPIGVIAVDSIFTPISKVNYTVE 120

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           SAR G+  D+DKL++ + T+GSIT   ++ALA++IL D L +F+N
Sbjct: 121 SARVGRRSDFDKLTLDVWTNGSITPSAAIALAAKILTDHLAIFVN 165


>gi|119662401|emb|CAJ33190.1| RNA polymerase alpha subunit [Lactobacillus frumenti]
          Length = 162

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 70/162 (43%), Positives = 111/162 (68%), Gaps = 2/162 (1%)

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            S++KGV ED+T IILN+K ++LK+  +  K + I  +GP  VTA DIQ   ++ VLNPD
Sbjct: 1   FSTVKGVTEDVTQIILNLKKVSLKIDSEEPKDLEIDVKGPAEVTASDIQGDGEVMVLNPD 60

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVES 189
             I  +   A + +++T  KG GY+ A  ++   ++  IG++ ID++Y+PI++V+YTVE+
Sbjct: 61  LYIATVADGAELHIKMTADKGRGYLSANDNKARMDDLAIGVLPIDSIYTPIERVNYTVEN 120

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           AR GQ  DYDKL++ + TDGS+T  ++V+L ++IL + L MF
Sbjct: 121 ARVGQRNDYDKLTLDVWTDGSLTPTEAVSLGAKILTEHLKMF 162


>gi|150036780|emb|CAM98033.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. cremoris]
          Length = 153

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 70/153 (45%), Positives = 100/153 (65%), Gaps = 2/153 (1%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
            + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDGV+HE S++ GV ED+T IILN+
Sbjct: 1   FVVEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDGVVHEFSTVDGVVEDVTQIILNL 60

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M +T 
Sbjct: 61  KKVVLAIESDDERSLEIDIQGPADVTAADLQGGADVEVLNPDLHIATVAAGKSLHMTVTA 120

Query: 150 SKGHGYVPAKHHRT--ENDPIGLITIDALYSPI 180
            KG GY  A  ++   +  PIG++ +D++Y+PI
Sbjct: 121 VKGRGYTSADENKKLRDEMPIGVLAVDSIYTPI 153


>gi|154424737|emb|CAL18471.1| RNA polymerase alpha subunit [Streptococcus oligofermentans]
          Length = 168

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 68/167 (40%), Positives = 106/167 (63%)

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
             +I GV ED+  IILNIKGI +K      K + +   GP  VTAGDI T +DIE++NPD
Sbjct: 1   FDTISGVREDVMQIILNIKGIAVKSYVQDEKMIELDVEGPAEVTAGDILTDSDIEIVNPD 60

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
           H +  +   A  + ++ V+ G GYVPA  ++ ++ P+G + +D++Y+P+ KV+Y VE AR
Sbjct: 61  HYLFTISEGARFKAKMAVNSGRGYVPADENKKDDAPVGTLAVDSIYTPVTKVNYQVEPAR 120

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
            G    +DKL++ I T+G+I  ED++ L++RIL + L +F +  E  
Sbjct: 121 VGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLFTDLTEVA 167


>gi|119662853|emb|CAJ33219.1| RNA polymerase alpha subunit [Lactobacillus farciminis KCTC 3681]
          Length = 164

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 66/163 (40%), Positives = 112/163 (68%)

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           +QIDGVLHE S+I GV ED+T I+LN+K + LK   +   +  +   GP  VTA DI+  
Sbjct: 2   IQIDGVLHEFSAIDGVIEDVTQIVLNVKKLKLKSYAEDSLKAEVDIVGPATVTAKDIKAD 61

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           +D+E+L+P+  IC +       M++T+  G GY PA+ ++T+  PIG++ +D++++P++K
Sbjct: 62  DDLEILDPEQFICTVAEGGHFHMQMTIKNGRGYTPAEQNKTDETPIGVLPVDSIFTPVEK 121

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
           V+Y VE+ R G+  D+DKL++ I T+GSI   ++++L+++IL 
Sbjct: 122 VNYQVENTRVGKRNDFDKLTIDIWTNGSIGPREAISLSAKILT 164


>gi|255961329|ref|YP_003097511.1| RNA polymerase alpha chain [Selaginella moellendorffii]
 gi|302824557|ref|XP_002993921.1| hypothetical protein SELMODRAFT_137778 [Selaginella moellendorffii]
 gi|254941501|gb|ACT89016.1| RNA polymerase alpha chain [Selaginella moellendorffii]
 gi|296399215|gb|ADH10390.1| RNA polymerase alpha subunit [Selaginella moellendorffii]
 gi|300138288|gb|EFJ05062.1| hypothetical protein SELMODRAFT_137778 [Selaginella moellendorffii]
          Length = 247

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 65/223 (29%), Positives = 100/223 (44%), Gaps = 8/223 (3%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV--QIDGVLH 70
             IE   +  E       I  P   G A+TLG A+RR L+  L GA IT      + + H
Sbjct: 14  RCIEPK-VDNERSYYGRFIISPPKIGQANTLGIAMRRALLGELEGACITPAGSPPERINH 72

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDS-HKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           E ++I GV E + DI++N+K I LK +  S  +   I   GP  VTA DI     +  ++
Sbjct: 73  EYTAIAGVRESVHDILMNLKEIVLKTNPFSAAQEAHIPIVGPRKVTAQDIVLPPSVGTMD 132

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P   I  +       + L V +G G+             G +  DA++ PI+  +Y++  
Sbjct: 133 PTQHIATITRKIHSSIGLRVERGCGFR---KRNMIEYQKGSLPPDAVFMPIRHANYSIHR 189

Query: 190 AR-EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
               G  +  + L +   TDGS T  +++  ASR L +    F
Sbjct: 190 LGSHGGGIMKEMLLLEARTDGSPTPREAIYEASRNLANLFSPF 232


>gi|161511733|emb|CAP16877.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 180

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 67/176 (38%), Positives = 110/176 (62%), Gaps = 2/176 (1%)

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           +I+GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  
Sbjct: 1   TIEGVVEDVTQIILNLKKVSLKVESDEEKSLEINVMGPANVTAGDIVGDGDVTILNPELP 60

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAR 191
           IC +         LT  KG GY  A  ++    + PIG++ ID++Y+PI++V+Y VE+ R
Sbjct: 61  ICTVAEGTTFHAVLTAEKGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTR 120

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
            GQ  DYDKL++ + TD S+   ++++L+++IL + L +F+N ++  K+ +  +  
Sbjct: 121 VGQRDDYDKLTLDVWTDXSLAASEAISLSAKILTEHLTIFVNLDDQVKDTEIMVET 176


>gi|42906|emb|CAA23646.1| unnamed protein product [Escherichia coli]
          Length = 159

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 72/161 (44%), Positives = 104/161 (64%), Gaps = 4/161 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHH 161
             D+E++ P HVIC+L D +A + M + V +G GYVPA   
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTR 158


>gi|311990456|gb|ADQ26358.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii]
          Length = 185

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 66/185 (35%), Positives = 105/185 (56%)

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
            GV ED+T IILN+K + L+   +  K + +   GP  VTA D++   D+EVLNPD  IC
Sbjct: 1   PGVKEDVTKIILNLKKLVLRAYTEEVKTIELDVEGPATVTAEDLKADADVEVLNPDQYIC 60

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
            +     + M + V  G GYVPA  +++    IG I +D+L+SPI+KV+Y VES R G+ 
Sbjct: 61  TIAQGGHLHMWIDVCNGRGYVPASENKSAEMSIGDIPVDSLFSPIEKVNYQVESTRVGKR 120

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            D+DKL++ I T+GSI   D++  A+R+L +    F + +   +  +  +  ++      
Sbjct: 121 EDFDKLTLEIWTNGSIAPNDALNFAARVLVEHFKAFESADAAAEIGEVMVEQENDQKEKK 180

Query: 256 LLKKV 260
           L   +
Sbjct: 181 LEMTI 185


>gi|117575083|emb|CAJ84781.1| RNA polymerase alpha subunit [Lactobacillus amylophilus]
          Length = 171

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 65/170 (38%), Positives = 107/170 (62%)

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+T IILN+K + LK      K   I   GP  VTAGD++  +++++LNPD  I  +  
Sbjct: 1   EDVTQIILNLKKLTLKSIAADEKLAEIDVEGPATVTAGDLKVDDEVQILNPDQYIATVAE 60

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
            A ++M + + +G GYVPA  +++++ PIG++ +D+L+SPI+KV+Y VE  R G+  DYD
Sbjct: 61  GAHLQMTVAIKQGRGYVPADQNKSDDMPIGVVPVDSLFSPIEKVNYQVEGTRVGRNNDYD 120

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           KL+M + TDGSIT  D+++  ++IL + L +F+N     +     +  + 
Sbjct: 121 KLTMEVWTDGSITPNDALSFGAKILTEHLNVFMNTNLETEFTDVMVEKED 170


>gi|150187052|emb|CAK30160.1| RNA polymerase alpha subunit [Streptococcus constellatus subsp.
           pharyngis]
          Length = 150

 Score =  177 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 69/149 (46%), Positives = 106/149 (71%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           N+LRRVL++SL GAA+T++ I+GVLHE  ++ GV ED+  IILN+KGI +K   +  K +
Sbjct: 1   NSLRRVLLASLPGAAVTSINIEGVLHEFDTVPGVREDVMQIILNVKGIAVKSYVEDEKTI 60

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            +   GP  +TAGDI T +DIE++NPDH +  +   A ++  +TV+ G GYVPA  ++ +
Sbjct: 61  ELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIGEGASLKAIMTVNAGRGYVPADENKKD 120

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREG 193
           + P+G + +D++Y+P+KKV+Y VE AR G
Sbjct: 121 DSPVGTLAVDSIYTPVKKVNYQVEPARVG 149


>gi|154424763|emb|CAL18484.1| RNA polymerase alpha subunit [Streptococcus canis]
          Length = 173

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 67/173 (38%), Positives = 110/173 (63%)

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +
Sbjct: 1   IPGVREDVMQIILNVKGLAVKSYVEDEKIIELEVEGPAEVTAGDILTDSDIELVNPDHYL 60

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
             +     +R  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G 
Sbjct: 61  FTIAEGHSLRATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGS 120

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
              +DKL++ I T+G+I  ED++ L++R+L + L +F +  +  K  +     
Sbjct: 121 NDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTDVAKATEVMKET 173


>gi|150036718|emb|CAM98022.1| DNA-directed RNA polymerase alpha chain [Fructobacillus durionis]
          Length = 178

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 71/178 (39%), Positives = 107/178 (60%), Gaps = 2/178 (1%)

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S++ GV ED+T +ILN+K +           + I  +GP  VTA D     DIE
Sbjct: 1   GVVHEFSTVDGVAEDVTQLILNLKKVVFATDSAEEHTLEIDVQGPKDVTAADFVGSADIE 60

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVS 184
           VLNPD  I  L     + M +TV KG GY  A+ ++   +  PIG++T+D++Y+PI++V+
Sbjct: 61  VLNPDLHIATLAAGKSLHMTVTVVKGRGYASAEENKQLRDEMPIGVLTVDSIYTPIERVN 120

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           Y VE  R G   D+DKL+M + T+GSI   D+++L S+IL + L +F +     +E K
Sbjct: 121 YHVEQKRVGSRDDFDKLTMEVWTNGSIKPSDALSLGSKILTEHLNLFTDISPVAQETK 178


>gi|307702711|ref|ZP_07639663.1| putative DNA-directed RNA polymerase, alpha subunit [Streptococcus
           oralis ATCC 35037]
 gi|307623827|gb|EFO02812.1| putative DNA-directed RNA polymerase, alpha subunit [Streptococcus
           oralis ATCC 35037]
          Length = 163

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 70/156 (44%), Positives = 100/156 (64%), Gaps = 4/156 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I    E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPN----ITKIDENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           +NPDH +  +   + ++  +TV+ G GYVPA  ++ 
Sbjct: 119 VNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKK 154


>gi|119662345|emb|CAJ33161.1| RNA polymerase alpha subunit [Lactobacillus pontis]
          Length = 160

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 66/160 (41%), Positives = 110/160 (68%), Gaps = 2/160 (1%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+T IILN+K ++LK++ +  K + +  +GP  VTA DIQ   ++ +LNPD  I  
Sbjct: 1   GVTEDVTQIILNLKKVSLKINSEDQKDLELDVKGPAEVTAADIQGDGEVTILNPDLHIAT 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
           +   A + +++T  KG GY+ A  ++   E+  IG++ ID++Y+PI++V+YTVE+AR GQ
Sbjct: 61  VADGAELHIKMTADKGRGYLSANDNKARMEDLAIGVLPIDSIYTPIERVNYTVENARVGQ 120

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
             DYDKL++ + TDGS+T  ++V+L ++IL + L +F++ 
Sbjct: 121 RNDYDKLTLDVWTDGSLTPTEAVSLGAKILTEHLAIFVDL 160


>gi|162751059|gb|ABY19884.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 72/146 (49%), Positives = 105/146 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R E+TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAEMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPADENKVDGAPIGTIAVDSIYT 146


>gi|162751067|gb|ABY19888.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 71/146 (48%), Positives = 104/146 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSIRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPADENKVDGAPIGTIAVDSIYT 146


>gi|254755535|ref|ZP_05207569.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           Vollum]
          Length = 150

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 56/149 (37%), Positives = 93/149 (62%)

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            ID++Y+P+ +V+Y VE  R GQV +YDKL++ + TDGSI  +++++L ++IL + L +F
Sbjct: 1   PIDSIYTPVSRVTYQVEKTRVGQVANYDKLTLDVWTDGSIGPKEAISLGAKILTEHLNIF 60

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           +   +  +  +  +  +       L   +EEL+LSVRS NCL+   I  + +L  +TE D
Sbjct: 61  VGLTDEAQNAEIMVEKEEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEED 120

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           M+++ N GRKSL E+K  L  +GL L  +
Sbjct: 121 MMKVRNLGRKSLEEVKHKLEELGLGLRKD 149


>gi|206896507|ref|YP_002247307.1| RNA-polymerase DNA-directed [Coprothermobacter proteolyticus DSM
           5265]
 gi|206739124|gb|ACI18202.1| RNA-polymerase DNA-directed [Coprothermobacter proteolyticus DSM
           5265]
          Length = 319

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 79/298 (26%), Positives = 130/298 (43%), Gaps = 4/298 (1%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
                 E +    +    LP G   TLGNALRRVL+  + G  +   +++G+ HE    +
Sbjct: 14  VDRESGELQRAAKLSVLNLPEGEGITLGNALRRVLLGQIGGTGVLGFRLEGLDHEFMVPE 73

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED   I LN+K +  K  GD  K + I  +GP  + A DI    D+EV N D  I  
Sbjct: 74  GVVEDGLTIGLNLKKVLFKYYGDGVKVLYIKAKGPAEIKAADIVPDADVEVFNLDQTILT 133

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRT-ENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
           +  D  + ME+ ++ G GY   + ++     P   I +D  +SP+++  Y V  A   + 
Sbjct: 134 VSTDREIYMEIYLTNGVGYRTVEDNKKLYQFPFRTIYLDTSFSPVRRAEYHVTPAIVDEP 193

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
             ++ L + + T+ ++   + +  A+  L ++       E  +    E +  +    +  
Sbjct: 194 GTFESLELIVYTNLAVDPVEVIRQAANFLSEEFR--KVAEAKEAAAGEVVVEEQAISDEK 251

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           L   VE L LS      L   NI  + DL+   E +   +   G   L EI+  L   
Sbjct: 252 LDASVEMLNLSRAVLTHLEKANINTIRDLVDVLEHN-ESIPGIGAVRLEEIRNKLAAY 308


>gi|119662839|emb|CAJ33212.1| RNA polymerase alpha subunit [Lactobacillus acidophilus]
          Length = 151

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 70/151 (46%), Positives = 99/151 (65%)

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++VLN
Sbjct: 1   HEFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQVLN 60

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES
Sbjct: 61  PDQYICTIAEGGHLHMELAVKNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVES 120

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
            R G+  D+DKL+  I TDGSI   D+++ A
Sbjct: 121 TRVGKRDDFDKLTFEIWTDGSIKPNDALSFA 151


>gi|162751159|gb|ABY19934.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
          Length = 146

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 72/146 (49%), Positives = 104/146 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R E+TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAEMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D+ Y+
Sbjct: 121 YGYVPADENKVDGAPIGTIAVDSNYT 146


>gi|162751111|gb|ABY19910.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 71/146 (48%), Positives = 104/146 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPADENKVDGWPIGTIAVDSIYT 146


>gi|162751008|gb|ABY19859.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751010|gb|ABY19860.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751012|gb|ABY19861.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751014|gb|ABY19862.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751016|gb|ABY19863.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751018|gb|ABY19864.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751020|gb|ABY19865.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751028|gb|ABY19869.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751030|gb|ABY19870.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis bv. diacetylactis]
 gi|162751034|gb|ABY19872.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis bv. diacetylactis]
 gi|162751036|gb|ABY19873.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751039|gb|ABY19874.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751041|gb|ABY19875.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751043|gb|ABY19876.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751045|gb|ABY19877.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751047|gb|ABY19878.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751049|gb|ABY19879.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751053|gb|ABY19881.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751055|gb|ABY19882.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751057|gb|ABY19883.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751061|gb|ABY19885.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751063|gb|ABY19886.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751065|gb|ABY19887.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751069|gb|ABY19889.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751071|gb|ABY19890.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751073|gb|ABY19891.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751075|gb|ABY19892.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751077|gb|ABY19893.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751079|gb|ABY19894.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751081|gb|ABY19895.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751083|gb|ABY19896.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751085|gb|ABY19897.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751087|gb|ABY19898.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751089|gb|ABY19899.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751091|gb|ABY19900.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751093|gb|ABY19901.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751095|gb|ABY19902.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751097|gb|ABY19903.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751099|gb|ABY19904.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751101|gb|ABY19905.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751103|gb|ABY19906.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751105|gb|ABY19907.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751107|gb|ABY19908.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751109|gb|ABY19909.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751113|gb|ABY19911.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751115|gb|ABY19912.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751117|gb|ABY19913.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751119|gb|ABY19914.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751123|gb|ABY19916.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751125|gb|ABY19917.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751127|gb|ABY19918.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751129|gb|ABY19919.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751131|gb|ABY19920.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751137|gb|ABY19923.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|162751139|gb|ABY19924.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|162751141|gb|ABY19925.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|162751143|gb|ABY19926.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751145|gb|ABY19927.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751149|gb|ABY19929.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751153|gb|ABY19931.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|162751157|gb|ABY19933.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|162751161|gb|ABY19935.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|162751163|gb|ABY19936.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|162751165|gb|ABY19937.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751169|gb|ABY19939.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751173|gb|ABY19941.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
 gi|162751175|gb|ABY19942.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis bv. diacetylactis]
 gi|162751177|gb|ABY19943.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis bv. diacetylactis]
 gi|164458717|gb|ABY57708.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 71/146 (48%), Positives = 104/146 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPADENKVDGAPIGTIAVDSIYT 146


>gi|162751024|gb|ABY19867.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751133|gb|ABY19921.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751181|gb|ABY19945.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis bv. diacetylactis]
          Length = 146

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 71/146 (48%), Positives = 104/146 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPADKNKVDGAPIGTIAVDSIYT 146


>gi|162751026|gb|ABY19868.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 70/146 (47%), Positives = 103/146 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           + YVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YAYVPADENKVDGAPIGTIAVDSIYT 146


>gi|162751022|gb|ABY19866.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 70/146 (47%), Positives = 103/146 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           + YVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YRYVPADENKVDGAPIGTIAVDSIYT 146


>gi|291533601|emb|CBL06714.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Megamonas
           hypermegale ART12/1]
          Length = 179

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 71/157 (45%), Positives = 101/157 (64%), Gaps = 2/157 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  E+      + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDG
Sbjct: 3   EIEKP-KIEIVEIS-EDNRYGKFVCEPLERGYGTTLGNSLRRILLSSLEGAAITSIKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+I GV +D+T+IILN+K + LKM  +    + I   G   VTA DI   +DIE+
Sbjct: 61  VLHEFSTIPGVRDDVTNIILNLKELCLKMHDEEPHTIRIDVTGEKEVTAADIIVDSDIEI 120

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
           LN D  I  +D    ++ME+ V +G GY PA  ++ +
Sbjct: 121 LNKDLHIATVDETGSLKMEMVVERGRGYTPADKNKNQ 157


>gi|119662843|emb|CAJ33214.1| RNA polymerase alpha subunit [Lactobacillus bifermentans]
          Length = 142

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 68/142 (47%), Positives = 95/142 (66%)

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            S+I GV ED+T IILNIK + LK+  D  K V I  +GP  VTAGDI+  +D+EVLNPD
Sbjct: 1   FSTIDGVTEDVTQIILNIKKLALKLESDDDKTVEIDVQGPATVTAGDIEADSDVEVLNPD 60

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             IC +         +TV KG GYV A+ ++ ++ PIG++ ID++Y+PI +V+Y VES R
Sbjct: 61  LYICTVAEGGHFHARMTVRKGRGYVAAEGNKVDDMPIGVLPIDSIYTPISRVNYQVESTR 120

Query: 192 EGQVLDYDKLSMTIDTDGSITG 213
            GQ  D+DKL++ + T+GSI  
Sbjct: 121 VGQRNDFDKLTLDVWTNGSINP 142


>gi|162751121|gb|ABY19915.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  174 bits (442), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 70/146 (47%), Positives = 103/146 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++ I+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIHIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPADENKVDGAPIGTIAVDSIYT 146


>gi|162751167|gb|ABY19938.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
          Length = 146

 Score =  174 bits (442), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 70/146 (47%), Positives = 104/146 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN++RRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSMRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPADENKVDGAPIGTIAVDSIYT 146


>gi|162751151|gb|ABY19930.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 71/146 (48%), Positives = 104/146 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQILLGVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPADENKVDGAPIGTIAVDSIYT 146


>gi|162751051|gb|ABY19880.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  173 bits (440), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 70/146 (47%), Positives = 103/146 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +   +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMLAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPADENKFDGAPIGTIAVDSIYT 146


>gi|153831468|ref|ZP_01984135.1| DNA-directed RNA polymerase alpha chain [Vibrio cholerae 623-39]
 gi|148873049|gb|EDL71184.1| DNA-directed RNA polymerase alpha chain [Vibrio cholerae 623-39]
          Length = 174

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 75/175 (42%), Positives = 111/175 (63%), Gaps = 8/175 (4%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLI 171
              D+E++NP+HVIC+L   +A + M + V +G GYVPA    H   +  PIG +
Sbjct: 118 HDGDVEIVNPEHVICHLTSDNAAIAMRIKVERGRGYVPASARIHTEEDERPIGRL 172


>gi|162751135|gb|ABY19922.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 70/146 (47%), Positives = 104/146 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +G+VPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGFVPADENKVDGAPIGTIAVDSIYT 146


>gi|162751171|gb|ABY19940.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 69/146 (47%), Positives = 104/146 (71%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +G+VPA  ++ +  PIG I ++++Y+
Sbjct: 121 YGFVPADENKVDGAPIGTIAVNSIYT 146


>gi|162751032|gb|ABY19871.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis bv. diacetylactis]
 gi|162751147|gb|ABY19928.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
 gi|162751179|gb|ABY19944.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis bv. diacetylactis]
          Length = 146

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 70/146 (47%), Positives = 103/146 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVP   ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPDDENKVDGAPIGTIAVDSIYT 146


>gi|119668277|emb|CAK95449.1| RNA polymerase alpha subunit [Lactobacillus acidophilus]
          Length = 150

 Score =  172 bits (437), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 69/150 (46%), Positives = 98/150 (65%)

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++VLNP
Sbjct: 1   EFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQVLNP 60

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES 
Sbjct: 61  DQYICTIAEGGHLHMELAVKNGRGYVAASDNKSDDMPIGVIPVDSLFSPIKKVNYQVEST 120

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           R G+  D+DKL+  I TDGSI   D+++ A
Sbjct: 121 RVGKRDDFDKLTFEIWTDGSIKPNDALSFA 150


>gi|154424801|emb|CAL18503.1| RNA polymerase alpha subunit [Streptococcus hyointestinalis]
          Length = 162

 Score =  172 bits (437), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 66/162 (40%), Positives = 107/162 (66%)

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E  +I GV ED+  IIL +KG+ +K   +  K + +   GP  VTAGDI T +DIE++NP
Sbjct: 1   EFDTIPGVREDVMQIILKVKGLAVKSYVEDEKMIELDVEGPAEVTAGDILTDSDIEIVNP 60

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           DH +  +     ++  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE A
Sbjct: 61  DHYLFTIAEGHSLKATMTVAKNRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPA 120

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           R G    +DKL++ I T+G+I  ED++ L++RIL + L +F 
Sbjct: 121 RVGSNDGFDKLTVEIMTNGTIIPEDALGLSARILIEHLNLFT 162


>gi|150187031|emb|CAK30155.1| RNA polymerase alpha subunit [Streptococcus urinalis 2285-97]
          Length = 169

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 65/169 (38%), Positives = 108/169 (63%)

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+  IILN+KG+ +K   D  K V +   GP  +TAGDI T +DIE++NPDH +  +  
Sbjct: 1   EDVMQIILNVKGLAVKSYVDDEKVVELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIAE 60

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              ++  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +D
Sbjct: 61  GHSLKATMTVAKDRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFD 120

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           KL++ I T+G+I  ED++ L++R+L + L +F +  E  K  +     +
Sbjct: 121 KLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKETE 169


>gi|162751006|gb|ABY19858.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 71/146 (48%), Positives = 103/146 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++N DH + ++     +R   TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVNKDHYLFSIAEGHSMRAVKTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +GYVPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGYVPADENKVDGAPIGTIAVDSIYT 146


>gi|150187084|emb|CAK30167.1| RNA polymerase alpha subunit [Streptococcus hyovaginalis]
          Length = 165

 Score =  172 bits (436), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 63/165 (38%), Positives = 106/165 (64%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+  IILN+KG+ +K   +  K + +  +GP  VTAGDI T +D+E++N DH +  
Sbjct: 1   GVREDVMQIILNVKGLAVKSYVEDEKIIELDVQGPAEVTAGDILTDSDVEIVNSDHYLFT 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +   A  +  +TV+   GYV A+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G   
Sbjct: 61  IAEGASFKASMTVATNRGYVAAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSND 120

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
            +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K  
Sbjct: 121 GFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKTT 165


>gi|119662399|emb|CAJ33189.1| RNA polymerase alpha subunit [Lactobacillus equi]
          Length = 170

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 62/170 (36%), Positives = 104/170 (61%), Gaps = 2/170 (1%)

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           ILN+K + LKM  +  + + I   GP  VTAGDI+  +D+EVLN D  I  +     + +
Sbjct: 1   ILNLKKVALKMDSEESQTLEIDVVGPLEVTAGDIKGPSDVEVLNDDLYIATVAEGHSLHV 60

Query: 146 ELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +T  KG GYV A  ++   ++ PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++
Sbjct: 61  RMTADKGRGYVSANENKAKNDDMPIGVLAIDSIYTPIERVNYQVEKTRVGQKNDYDKLTL 120

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
            + T+GSIT  ++++L+++IL + L +F +  +  K V+  +  +     
Sbjct: 121 DVWTNGSITPSEAISLSAKILTEHLTLFGDLTDEAKNVEIMVEKEESHKE 170


>gi|154424725|emb|CAL18465.1| RNA polymerase alpha subunit [Streptococcus gallolyticus]
          Length = 158

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 69/158 (43%), Positives = 107/158 (67%)

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           ++IDGVLHE  +I GV ED+  IILNIKG+ +K   D  K + +   GP  VTAGDI T 
Sbjct: 1   IKIDGVLHEFDTIPGVREDVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDILTD 60

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           +D+E++NPDH +  +     ++  +TV+K  GYV A+ ++ E+ P+G + +D++Y+P+KK
Sbjct: 61  SDVEIVNPDHYLFTIAEGHSLKATMTVAKERGYVSAEGNKKEDAPVGTLAVDSIYTPVKK 120

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           V+Y VE AR G    +DKL++ I T+G+I  ED++ L+
Sbjct: 121 VNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLS 158


>gi|119473466|ref|ZP_01614972.1| DNA-directed RNA polymerase subunit alpha [Alteromonadales
           bacterium TW-7]
 gi|119444456|gb|EAW25790.1| DNA-directed RNA polymerase subunit alpha [Alteromonadales
           bacterium TW-7]
          Length = 173

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 74/169 (43%), Positives = 114/169 (67%), Gaps = 3/169 (1%)

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            +  PIG + +DA +SP+++++Y+VESAR  Q  D DKL + ++T+G++  E+++  AS 
Sbjct: 8   DDERPIGRLLLDASFSPVERIAYSVESARVEQRTDLDKLIIDMETNGTLDREEAIRRAST 67

Query: 223 ILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMG 282
           IL +QL  F++  +  +        +   F+P LL+ V++LEL+VRS NCL+ E I Y+G
Sbjct: 68  ILAEQLDAFVDLRDVTEPE---EKEEKPEFDPILLRPVDDLELTVRSANCLKAEQIQYIG 124

Query: 283 DLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           DL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP S+ E
Sbjct: 125 DLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASLAE 173


>gi|71894584|ref|YP_278692.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma synoviae 53]
 gi|123747931|sp|Q4A5J0|RPOA_MYCS5 RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|71851372|gb|AAZ43981.1| DNA-directed RNA polymerase subunit alpha [Mycoplasma synoviae 53]
          Length = 333

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 75/315 (23%), Positives = 139/315 (44%), Gaps = 21/315 (6%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
            Q    + ++  + L RGF +TL  ALRR+L+S++ G A   V+I+GV HE ++++ V E
Sbjct: 17  SQNNSYKKVLKIKGLERGFGNTLAVALRRILLSNITGIAPFCVRIEGVEHEFTALEKVSE 76

Query: 81  DLTDIILNIKGINLKMSGDSHK-----RVTIFKRGPGVVTAGDIQTV--NDIEVLNPDHV 133
           D+  I+ N+K + L    D  K     ++++       +T+  +       +EV N D  
Sbjct: 77  DIVTILSNLKKVVLNYDEDYVKDNQIIKLSLNANEDNRITSNHLTVTNAPRVEVQNKDVE 136

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRT-------------ENDPIGLITIDALYSPI 180
           I  L    V+++E+ +  G GYV  + ++                     I +D+++SP+
Sbjct: 137 IATLSKPGVLKLEMFLRAGRGYVDFEDNKKFIEEKEKELKELSSLSKGAFIAMDSVFSPV 196

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
             V++ V       +   ++L + ++T   +T E ++ LA +IL        +  +   +
Sbjct: 197 VNVAWKVTELNTASLKIEEQLELELETKLGVTPESAIKLACKILVAHFQTIGDLTDLDSD 256

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +   + K          ++  L LS+RS N L    I  + +L       +  + N G 
Sbjct: 257 -EIFQSEKQSLEKEEDDMEIRLLNLSMRSQNALAKSGIKTLNELASYPIEKLKEIKNLGE 315

Query: 301 KSLVEIKGVLGTMGL 315
           KS  EI   L   G 
Sbjct: 316 KSREEIIRKLNEYGK 330


>gi|162751155|gb|ABY19932.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
          Length = 146

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 69/146 (47%), Positives = 103/146 (70%)

Query: 33  EPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           EPL RG+  TLGN+LRRVL+SSL GAA+T++QI+GV HE ++I GV ED+  I+L +KGI
Sbjct: 1   EPLERGYGTTLGNSLRRVLLSSLPGAAVTSIQIEGVQHEFATIPGVREDVIQIVLAVKGI 60

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
            +K   +S K++ +   GP  VTAGDI T +DIE++  DH + ++     +R  +TV KG
Sbjct: 61  AIKSYVESEKQIELDVTGPMDVTAGDILTDSDIEIVTKDHYLFSIAEGHSMRAVMTVKKG 120

Query: 153 HGYVPAKHHRTENDPIGLITIDALYS 178
           +G+VPA  ++ +  PIG I +D++Y+
Sbjct: 121 YGFVPADENKVDGAPIGTIAVDSIYT 146


>gi|222139917|ref|YP_002519985.1| RNA polymerase alpha chain [Ephedra equisetina]
 gi|220983586|dbj|BAH11353.1| RNA polymerase alpha chain [Ephedra equisetina]
          Length = 258

 Score =  170 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 64/261 (24%), Positives = 114/261 (43%), Gaps = 12/261 (4%)

Query: 6   WQELI------KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           W EL       +   +E     +           PL +G A+TL  A+R+ L+  ++G  
Sbjct: 3   WNELKTAESSPRWKCLESRTDSKRSH-YGRFSISPLFKGQANTLAIAIRKTLLQEVKGTY 61

Query: 60  ITAVQID-GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGD 118
           IT  +    +LHE SSI G+ E + DI++N+K I L+         +I   GP  VTA D
Sbjct: 62  ITYARFQKNILHEYSSIIGIKESVHDILMNLKQIVLRSELYGIHEASICTVGPKNVTAQD 121

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
           I   + I++++    I +L       + L + K   Y      + ++       ID +  
Sbjct: 122 IILPSSIQIIDDTQHIASLTKRIPFNVTLKIEKKKRYTIENMKQPKD---IFFPIDGVSL 178

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P++ V++++ S +    +  + L   I T+G +T  +++  A   L D +   +  E+  
Sbjct: 179 PVQNVNFSIHSYKSSDNI-QEMLIFEIWTNGGLTPRETIYEACWSLLDLIIPLLCVEQNI 237

Query: 239 KEVKEDINVKSLPFNPALLKK 259
           K  ++  N  SL       KK
Sbjct: 238 KNSQKKPNPLSLVTKDRNKKK 258


>gi|154424733|emb|CAL18469.1| RNA polymerase alpha subunit [Streptococcus pasteurianus]
          Length = 173

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 64/173 (36%), Positives = 107/173 (61%)

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+  IILNIKG+ +K   D  K + +   GP  VTAGDI T +D+E++NPDH +  +   
Sbjct: 1   DVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDSDVEIVNPDHYLFTIAEG 60

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             ++  +T++K  GYVPA+ ++ E+ P+G + +D++Y+P+KKV+Y VE AR G    +DK
Sbjct: 61  HSLKATMTIAKNRGYVPAEGNKKEDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDK 120

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           L++ I T+G+I  ED++ L++R+L + L +F +  E  K        + +   
Sbjct: 121 LTLEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKNTDVMKETEKVNDE 173


>gi|150186957|emb|CAK30136.1| RNA polymerase alpha subunit [Streptococcus hyointestinalis]
          Length = 171

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 64/169 (37%), Positives = 107/169 (63%)

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+  IILN+KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +   
Sbjct: 1   DVMQIILNVKGLAVKSYVEDEKMIELDVEGPAEVTAGDILTDSDIEIVNPDHYLFTIAEG 60

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             ++  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DK
Sbjct: 61  HSLKATMTVAKNRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDK 120

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           L++ I T+G+I  ED++ L++RIL + L +F +  E  K  +     + 
Sbjct: 121 LTVEIMTNGTIIPEDALGLSARILIEHLNLFTDLTEVAKTTEVMKEAEQ 169


>gi|326392491|ref|ZP_08213872.1| RNA polymerase insert [Thermoanaerobacter ethanolicus JW 200]
 gi|325991466|gb|EGD50077.1| RNA polymerase insert [Thermoanaerobacter ethanolicus JW 200]
          Length = 136

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 67/132 (50%), Positives = 87/132 (65%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91
            EPL RG+  TLGN+LRRVL+SSL GAA  +V+IDGVLHE S++ GV ED+ +IILN+K 
Sbjct: 1   MEPLERGYGITLGNSLRRVLLSSLPGAAPKSVKIDGVLHEFSTLPGVKEDVVEIILNLKE 60

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           + +K+  D      I   G G VTAG I+   DIE+LNPDH I  L  D  + ME+   K
Sbjct: 61  VAVKLHSDEPVVGRIDVEGKGEVTAGHIKGSADIEILNPDHHIATLSDDGKLHMEIVFVK 120

Query: 152 GHGYVPAKHHRT 163
           G GYVP+   ++
Sbjct: 121 GKGYVPSDKTKS 132


>gi|163804149|ref|ZP_02197920.1| DNA-directed RNA polymerase subunit alpha [Vibrio sp. AND4]
 gi|159172035|gb|EDP57006.1| DNA-directed RNA polymerase subunit alpha [Vibrio sp. AND4]
          Length = 174

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 72/162 (44%), Positives = 105/162 (64%), Gaps = 5/162 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQINSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
            V+I+GVLHE S+ +GV ED+ +I+LN+KG+++++  G     +T+ K G G V AGDI 
Sbjct: 58  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLSVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHH 161
              D+E+ NP+HVIC+L  D A + M + V +G GYVPA   
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASAR 159


>gi|161511735|emb|CAP16878.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 161

 Score =  168 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 65/161 (40%), Positives = 102/161 (63%), Gaps = 2/161 (1%)

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           S+I+GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+ 
Sbjct: 1   STIEGVVEDVTQIILNLKKVSLKVESDEEKSLEINVMGPANVTAGDIVGDGDVTILNPEL 60

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESA 190
            IC +         LT  KG GY  A  ++    + PIG++ ID++Y+PI++V+Y VE+ 
Sbjct: 61  PICTVAEGTTFHAVLTAEKGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENT 120

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           R GQ  DYDKL++ + TD S+   ++++ +++IL + L +F
Sbjct: 121 RVGQRDDYDKLTLDVWTDVSLAASEAISPSAKILTEHLTIF 161


>gi|154424741|emb|CAL18473.1| RNA polymerase alpha subunit [Streptococcus thermophilus]
          Length = 155

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 64/155 (41%), Positives = 104/155 (67%)

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
             ++ GV ED+  IILNIKG+ +K   +  K + +  +GP  VTAGDI T +DIE++NPD
Sbjct: 1   FDTVPGVREDVMQIILNIKGLAVKSYVEDEKTIELDVQGPAEVTAGDILTDSDIEIVNPD 60

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
           H +  +   A  +  +TVS   GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR
Sbjct: 61  HYLFTIAEGASFQATMTVSTNRGYVPAEENKKDDAPVGTLAVDSIYTPVKKVNYQVEPAR 120

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
            G    +DKL++ I T+G+I  ED++ L++R+L +
Sbjct: 121 VGSNDGFDKLTIEIVTNGTIIPEDALGLSARVLIE 155


>gi|154424849|emb|CAL18527.1| RNA polymerase alpha subunit [Streptococcus ratti]
          Length = 170

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 63/169 (37%), Positives = 106/169 (62%)

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+  IILN+KG+ +K   +  K + +   GP  +TAGDI T +DIE++NPDH +  +   
Sbjct: 1   DVMQIILNLKGLAVKSYVEEEKIIELDVEGPAEITAGDILTDSDIEIVNPDHYLFTIAEG 60

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
           A ++  LTV    GY+PA+ ++ ++ P+G + ID++Y+P+KKV+Y VE AR G   ++DK
Sbjct: 61  ASLKATLTVGTNRGYIPAEENKKDDAPVGTLAIDSIYTPVKKVNYQVEPARVGSNDNFDK 120

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           L++ I T+G+I  ED++ L++R+L + L +F +  E  K        + 
Sbjct: 121 LTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLPEVAKATDVMKETEQ 169


>gi|161511739|emb|CAP16880.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 166

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 63/166 (37%), Positives = 103/166 (62%), Gaps = 2/166 (1%)

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  IC +     
Sbjct: 1   TQIILNLKKVSLKVESDEEKSLEINVMGPANVTAGDIVGDGDVTILNPELPICTVAEGTT 60

Query: 143 VRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
               LT  KG GY  A  ++    + PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDK
Sbjct: 61  FHAVLTAEKGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDK 120

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           L++ + TDGS+   ++++L+++IL + L +F+N ++  K+ +  + 
Sbjct: 121 LTLDVWTDGSLAASEAISLSAKILTEHLTIFVNLDDQAKDTEIMVE 166


>gi|207092984|ref|ZP_03240771.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 235

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 72/234 (30%), Positives = 122/234 (52%), Gaps = 4/234 (1%)

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
              +GP  + A D+ + + IE++NP+  +  ++ DA +   L + KG GYVP++ +  E 
Sbjct: 2   YSFKGPMELRARDLNSEH-IEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSE-NTREL 59

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
            P G + +D  ++PIKKV Y +E+       +Y+K+   I+TDG I    +   A +++ 
Sbjct: 60  MPEGYMPLDGSFTPIKKVVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMS 119

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLI 285
            QLG+F   E P   ++   +         L  K+E + LS R  NCL    I Y+G+L+
Sbjct: 120 KQLGVFG--ERPIANMEYSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELV 177

Query: 286 QRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             +E ++  + N G+KS  EI   L  +G  +G  L     ES+++  +K EDK
Sbjct: 178 LMSEEELKGVKNMGKKSYDEIAEKLNDLGYPVGTELSLEQRESLKKRLEKLEDK 231


>gi|154424841|emb|CAL18523.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
          Length = 150

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 67/149 (44%), Positives = 101/149 (67%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAA+T++ IDGVLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  VTA
Sbjct: 1   GAAVTSINIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
           GDI T +DIE++NPDH +  +   + ++  +TV+ G GYVPA  ++ +N P+G + +D++
Sbjct: 61  GDILTDSDIEIVNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSI 120

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           Y+P+ KV+Y VE AR G    +DKL++ I
Sbjct: 121 YTPVTKVNYQVEPARVGSNDGFDKLTLEI 149


>gi|289524820|emb|CBJ94466.1| alpha subunit of RNA polymerase [Vibrio sp. C15.18]
          Length = 173

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 75/176 (42%), Positives = 113/176 (64%), Gaps = 6/176 (3%)

Query: 145 MELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           M + V +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q  D DKL
Sbjct: 1   MRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQRTDLDKL 60

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + ++T+G++  E+++  A+ IL +QL  F++  + +         +   F+P LL+ V+
Sbjct: 61  VIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE---EKEEKPEFDPILLRPVD 117

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 118 DLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 173


>gi|119663526|emb|CAK22334.1| RNA polymerase alpha subunit [Lactobacillus paracollinoides]
          Length = 154

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 71/154 (46%), Positives = 103/154 (66%), Gaps = 3/154 (1%)

Query: 77  GVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           GV ED+T IILN K I+LK+ G  D  + + I  +GP  VTAGDI   +D+ VLNPD  I
Sbjct: 1   GVVEDVTQIILNTKKISLKLEGPDDEIESMEIDVKGPAQVTAGDITADSDVTVLNPDLYI 60

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHR-TENDPIGLITIDALYSPIKKVSYTVESAREG 193
             +   A   M +T +KG GYV A  ++  E+ PIG++ ID++Y+PI++V+Y VE+ R G
Sbjct: 61  ATVAEGATFHMRMTANKGRGYVSADRNKAKEDMPIGVLPIDSIYTPIERVNYQVENTRVG 120

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           Q  DYDKL++ + TD SIT  +S++LA++IL + 
Sbjct: 121 QRDDYDKLTLDVWTDNSITPSESISLAAKILTEH 154


>gi|165932201|emb|CAP66258.1| RNA polymerase alpha subunit [Lactobacillus oligofermentans]
          Length = 151

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 69/151 (45%), Positives = 104/151 (68%), Gaps = 2/151 (1%)

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE SS++GV ED+T IILNIK I LK+  +  K + I  +GP VVTAGDIQ   D+ +LN
Sbjct: 1   HEFSSVEGVTEDVTQIILNIKKIALKIDSEDDKTLEIDVKGPAVVTAGDIQADGDVTILN 60

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTV 187
           PD  +  +     + M++T + G GYV A  +++  E+ PIG++ ID++Y+PI++V+Y V
Sbjct: 61  PDLQLATVADGVELHMQMTANTGRGYVSADDNKSRMEDLPIGVLPIDSIYTPIERVNYNV 120

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           E AR GQ  DYDKL++ + +DGSIT  ++++
Sbjct: 121 EDARVGQRNDYDKLTLDVWSDGSITPSEAIS 151


>gi|154424843|emb|CAL18524.1| RNA polymerase alpha subunit [Streptococcus porcinus]
          Length = 148

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 66/148 (44%), Positives = 102/148 (68%)

Query: 52  MSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGP 111
           +SSL GAA+T+++IDGVLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP
Sbjct: 1   LSSLPGAAVTSIKIDGVLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKMIELDVEGP 60

Query: 112 GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI 171
             VTAGDI T +DIE++NPDH +  +     ++  +TV+K  GYVPA+ ++ ++ P+G +
Sbjct: 61  AEVTAGDILTDSDIELVNPDHYLFTIAEGHSLKATMTVAKKRGYVPAEGNKKDDAPVGTL 120

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYD 199
            +D++Y+P+KKV+Y VE AR G    +D
Sbjct: 121 AVDSIYTPVKKVNYQVEPARVGSNDGFD 148


>gi|269991336|emb|CAX12520.1| DNA-directed RNA polymerase alpha chain [Fucus vesiculosus]
          Length = 368

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 77/347 (22%), Positives = 146/347 (42%), Gaps = 56/347 (16%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
              E     +   L +   +T+GN LRR L+S+L G  I  V+  G+ +E + ++GV ED
Sbjct: 16  NTNEFYGHFVFTALEKSQGNTIGNVLRRTLLSNLYGFRIVGVRFAGINNEFALLEGVRED 75

Query: 82  LTDIILNIKGINLKMSGDSHKRVT--IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           L +IILN+K I +  S    +     +   GP V+TAG ++  N++++LNP++ +  +  
Sbjct: 76  LFEIILNLKEIIILNSNRIDQTCYGRLKVYGPAVITAGSLELPNNVKILNPNNHLLTISD 135

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           ++++ +E+ +  G  Y+ AK  + E   +  I ID+ ++P+ KV++ + S  +      +
Sbjct: 136 ESLIEIEVKIEAGKSYILAKDQKLEGA-LDFIPIDSNFAPVLKVNWYIISLPQDGESINE 194

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA---- 255
           +L + I T+G++    ++  A  ++   L      E    +  E   +       +    
Sbjct: 195 ELHLEIYTNGTLLPHQALLQARTMIGYMLSPISTIEFSCLDTYEKEEIHDTNHIKSLTYI 254

Query: 256 -------------------------------------------------LLKKVEELELS 266
                                                              + ++ L LS
Sbjct: 255 TDPISRDQNKTVLRSNLIKNKSKFEKINLDKINQVSIDEQKLIKNIVDLEYESLKNLGLS 314

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
            R  N L   NI ++ DLI    + ++ +   G KS+ EIK  L   
Sbjct: 315 NRIINALNKVNINFISDLIHYPSSSLINIVGLGPKSVEEIKNKLNQF 361


>gi|154424729|emb|CAL18467.1| RNA polymerase alpha subunit [Streptococcus gallolyticus]
          Length = 167

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 64/167 (38%), Positives = 104/167 (62%)

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+  IILNIKG+ +K   D  K + +   GP  VTAGDI T +D+E++NPDH +  +   
Sbjct: 1   DVMQIILNIKGLAVKSYVDDEKIIELDVEGPAEVTAGDILTDSDVEIVNPDHYLFTIAEG 60

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             ++  +TV+K  GYV A+ ++ E+ P+G + +D++Y+P+KKV+Y VE AR G    +DK
Sbjct: 61  HSLKATMTVAKERGYVSAEGNKKEDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDK 120

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           L++ I T+G+I  ED++ L++R+L + L +F +  E  K        
Sbjct: 121 LTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKSTDVMKET 167


>gi|150186949|emb|CAK30134.1| RNA polymerase alpha subunit [Streptococcus dysgalactiae subsp.
           dysgalactiae]
          Length = 161

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 63/161 (39%), Positives = 105/161 (65%)

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+  IILN+KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +   
Sbjct: 1   DVMQIILNVKGLAVKSYVEDEKIIELEVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEG 60

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             +R  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DK
Sbjct: 61  HSLRATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDK 120

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           L++ I T+G+I  ED++ L++R+L + L +F +  +  K  
Sbjct: 121 LTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTDVAKAT 161


>gi|161833842|ref|YP_001598038.1| DNA-directed RNA polymerase subunit alpha [Candidatus Sulcia
           muelleri GWSS]
 gi|152206332|gb|ABS30642.1| DNA-directed RNA polymerase, alpha subunit [Candidatus Sulcia
           muelleri GWSS]
          Length = 239

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 84/230 (36%), Positives = 131/230 (56%), Gaps = 6/230 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +K    + + + +      L   EPL  G+  T+GN LRRVL+SSL G AI++V+I+GV
Sbjct: 3   FLKFKQSKNLRVLKLTPEEGLFKIEPLFPGWGVTIGNTLRRVLLSSLEGYAISSVKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNI-----KGINLKMSGDSHKRVTIFKRGPGVVTAGDI-QTV 122
            HE S+IKGV ED+T+IILN+     K    K + +S     I       +TAGD+ + +
Sbjct: 63  NHEFSTIKGVIEDMTEIILNLKKVRFKKNKKKENFESEVFNMIISNDKEEITAGDLGKYI 122

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           N  ++LNPD +I N      + + + + KG GYVP++ ++      G I +D++++PIK 
Sbjct: 123 NKFDILNPDLIILNKQKLISLDISIVIKKGIGYVPSEENKENLIGSGSIPMDSIFTPIKN 182

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           V Y +++    +  +Y+ L + I TDGSI   D++  AS IL   L MFI
Sbjct: 183 VKYKIDNCSINKNSNYESLLLEIKTDGSINPRDALTNASNILIQHLKMFI 232


>gi|119662809|emb|CAJ33196.1| RNA polymerase alpha subunit [Lactobacillus perolens]
          Length = 138

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 61/138 (44%), Positives = 94/138 (68%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+T IILNIK + LK++ D  K V I   GP  VTA +I T +D+E+LNP+  IC 
Sbjct: 1   GVLEDVTQIILNIKKLALKLNTDQEKTVEIDAEGPATVTAANIITDDDVEILNPEQYICT 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +     + M +TV  G GYVPA  +++++ PIG++ +D++++PI++V+Y VES R G+  
Sbjct: 61  IANGGHLHMRMTVKTGRGYVPADQNKSDDMPIGVLPVDSIFTPIERVNYQVESTRVGKRN 120

Query: 197 DYDKLSMTIDTDGSITGE 214
           D+DKL++ + T+GSI   
Sbjct: 121 DFDKLTLAVWTNGSIGPR 138


>gi|119672803|emb|CAK95517.1| RNA polymerase alpha subunit [Lactobacillus alimentarius]
          Length = 149

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 65/149 (43%), Positives = 101/149 (67%)

Query: 49  RVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK 108
           RVL++SL G A++ +QIDGVLHE S+I GV ED+T I+LN+K + LK   D   +  I  
Sbjct: 1   RVLLASLPGTAVSDIQIDGVLHEFSAIDGVIEDVTQIVLNVKKLKLKSYADDSLKAEIDV 60

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
            GP  VTA DI+  +D+E+L+P+  IC +       M++TV  G GY PA+ ++T+  PI
Sbjct: 61  VGPATVTAKDIKADDDLEILDPEQFICTVAEGGHFHMQMTVINGRGYTPAEQNKTDETPI 120

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLD 197
           G++ +D++++P++KV+Y VE+ R G+  D
Sbjct: 121 GVLPVDSIFTPVEKVNYQVENTRVGKRND 149


>gi|150036750|emb|CAM98028.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gelidum KCTC
           3527]
          Length = 153

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 62/153 (40%), Positives = 96/153 (62%), Gaps = 2/153 (1%)

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           ++ GV ED+T IILN+K + L +  D  + + +  +GP  VTA D+Q   D+EVLNPD  
Sbjct: 1   TVDGVVEDVTQIILNLKKVVLAIDSDEERSLEVDIQGPADVTAADLQAGADVEVLNPDLH 60

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAR 191
           I  +     + M +T  KG GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R
Sbjct: 61  IATVAAGKSLHMTITAFKGRGYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTR 120

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
            G   DYDKL+  I T+GSI   D+++L S+IL
Sbjct: 121 VGSRDDYDKLTFDIWTNGSIKPSDALSLGSKIL 153


>gi|293977954|ref|YP_003543384.1| DNA-directed RNA polymerase subunit alpha/40 kD subunit [Candidatus
           Sulcia muelleri DMIN]
 gi|292667885|gb|ADE35520.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Candidatus Sulcia muelleri DMIN]
          Length = 239

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 84/230 (36%), Positives = 131/230 (56%), Gaps = 6/230 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +K    + + + +      L   EPL  G+  T+GN LRRVL+SSL G AI++V+I+GV
Sbjct: 3   FLKFKQSKNLRVLKLTPEEGLFKIEPLFPGWGVTIGNTLRRVLLSSLEGYAISSVKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNI-----KGINLKMSGDSHKRVTIFKRGPGVVTAGDI-QTV 122
            HE S+IKGV ED+T+IILN+     K    K + +S     I       +TAGD+ + +
Sbjct: 63  NHEFSTIKGVIEDMTEIILNLKKVRFKKNKKKENFESEVFNMIISNDKEEITAGDLGKYI 122

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           N  ++LNPD +I N      + + + + KG GYVP++ ++      G I +D++++PIK 
Sbjct: 123 NKFDILNPDLIILNKQKLISLDISIVIKKGIGYVPSEENKENLIVSGSIPMDSIFTPIKN 182

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           V Y +++    +  +Y+ L + I TDGSI   D++  AS IL   L MFI
Sbjct: 183 VKYKIDNCSINKNSNYESLLLEIKTDGSINPRDALTNASNILIQHLKMFI 232


>gi|119662801|emb|CAJ33192.1| RNA polymerase alpha subunit [Lactobacillus kefiri]
          Length = 153

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 75/150 (50%), Positives = 99/150 (66%), Gaps = 4/150 (2%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE S+IKGV ED+T IILN+K I+LK+ G  D  + + I   GP  VTAGDIQ   D+
Sbjct: 3   VLHEFSTIKGVVEDVTQIILNVKKISLKLDGPEDEEENLEIDVIGPADVTAGDIQADGDV 62

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKV 183
            VLNPD  I  +   A   M LT +KG GYV A  ++      PIG++ +D++Y+PI++V
Sbjct: 63  TVLNPDLHIATVAEGATFHMRLTANKGRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERV 122

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           +Y VES R GQ  D+DKL++ I TDGSIT 
Sbjct: 123 NYQVESTRVGQRDDFDKLTLDIWTDGSITP 152


>gi|154424817|emb|CAL18511.1| RNA polymerase alpha subunit [Streptococcus minor]
          Length = 167

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 61/166 (36%), Positives = 103/166 (62%)

Query: 88  NIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           NIKGI +K   +  K++ +   GP  +TAGDI T +DIE++NPDH +  +   A  +  L
Sbjct: 1   NIKGIAVKSYVEDEKKIELDVVGPAEITAGDILTDSDIEIVNPDHYLFTIGEGASFKAIL 60

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           TV++G GYVPA+ ++ +  P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ I T
Sbjct: 61  TVNRGRGYVPAEGNKKDEAPVGTLAVDSIYTPVVKVNYQVEPARVGSNDGFDKLTLEIMT 120

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           +G+   ED++ L++RIL + LG+F +  +  K  +     +    +
Sbjct: 121 NGTTNPEDALGLSARILMEHLGLFTDLTDVAKSAEVMKEAEPASDD 166


>gi|154483160|ref|ZP_02025608.1| hypothetical protein EUBVEN_00861 [Eubacterium ventriosum ATCC
           27560]
 gi|149735968|gb|EDM51854.1| hypothetical protein EUBVEN_00861 [Eubacterium ventriosum ATCC
           27560]
          Length = 161

 Score =  162 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 55/152 (36%), Positives = 99/152 (65%)

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
              G+I +D++Y+P+++V+ +V++ R GQV D+DKL++ + T+G++  +++V+LAS++L 
Sbjct: 4   YQSGVIAVDSIYTPVERVNMSVQNTRVGQVTDFDKLTLDVYTNGTLDTDEAVSLASKVLC 63

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLI 285
           + L +FI+  E  K+++          +  L   ++ELELSVRS NCL+   I  + +L+
Sbjct: 64  EHLKLFIDLSETSKDIEVIAEPVDDEIDKVLEMNIDELELSVRSYNCLKRAGINTVEELV 123

Query: 286 QRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            +T  DM+++ N GRKSL E+   L  +GL L
Sbjct: 124 NKTSEDMMKVRNLGRKSLEEVLAKLKELGLGL 155


>gi|161511745|emb|CAP16883.1| DNA-directed RNA polymerase subunit alpha [Pediococcus inopinatus]
          Length = 141

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 70/141 (49%), Positives = 100/141 (70%), Gaps = 2/141 (1%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           +LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T IILNIK ++LK+  D  K + 
Sbjct: 1   SLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVVEDVTQIILNIKKVSLKIESDDEKSLE 60

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--T 163
           I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A  ++   
Sbjct: 61  IDVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAILTADTGRGYVSADENKARK 120

Query: 164 ENDPIGLITIDALYSPIKKVS 184
           ++ PIG++ ID++Y+PI++V+
Sbjct: 121 DDMPIGVLPIDSIYTPIERVN 141


>gi|58758774|gb|AAW81778.1| RNA polymerase alpha subunit [Andreaea rupestris]
          Length = 195

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 52/199 (26%), Positives = 92/199 (46%), Gaps = 7/199 (3%)

Query: 1   MIQKNW---QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRG 57
           MIQ       ++++   +E  V  +     +     P   G A+T+G A+RR L+  + G
Sbjct: 1   MIQNEIPISAQVLQWRCVESKVDSERLH-YSRFAISPFRCGQANTVGIAMRRALLGEIEG 59

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
             IT  +   V HE S+I G+ E + DI++N K I LK +    ++  I   GP  +TA 
Sbjct: 60  TCITCAKFKKVTHEYSTILGIQESVHDILINSKEIVLKSNSYETQKAFISILGPKKITAQ 119

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           DI     +++++    I  L     + +E  + K  GY      ++ +   GL  +DA++
Sbjct: 120 DIILPPSVKIIDTTQYIATLTKAIHLDIESEIEKDCGYRIQDSKKSTD---GLFFVDAVF 176

Query: 178 SPIKKVSYTVESAREGQVL 196
            PI+  +Y++ S       
Sbjct: 177 MPIRNANYSIHSFENKNKT 195


>gi|119663522|emb|CAK22332.1| RNA polymerase alpha subunit [Lactobacillus acetotolerans]
          Length = 140

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 62/140 (44%), Positives = 92/140 (65%)

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+  +ILN+K + LK   D  K + +   GP  VTA D++   D+EVLNPD  IC + 
Sbjct: 1   REDVAKMILNLKKLELKCLSDDQKIIELDVEGPATVTADDLKADADVEVLNPDQYICTIA 60

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + M++ V KG GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES R G+  D+
Sbjct: 61  EGGHLHMQIAVRKGRGYVTASDNKSDDMPIGVIPVDSLFSPIKKVNYQVESTRVGKRDDF 120

Query: 199 DKLSMTIDTDGSITGEDSVA 218
           DKL++ I TDGSI   D+++
Sbjct: 121 DKLTLEIWTDGSIKPNDALS 140


>gi|229915533|gb|ACQ90877.1| alpha subunit of RNA polymerase [Pedinomonas minor]
          Length = 365

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 70/353 (19%), Positives = 137/353 (38%), Gaps = 56/353 (15%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           + QE    +     P   G A T+ N+LRR L+S  +G  + AV+IDG +HE S ++G+ 
Sbjct: 14  MEQETSWYSRFEIGPFQAGQALTVANSLRRTLLSDQQGVFLAAVEIDGAIHEYSRLEGLK 73

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRG-----------PGVVTAGDIQTVNDIEVL 128
           E + DI+LN++ +++ ++ D+ K  + F              P  V A D++    IE  
Sbjct: 74  ESILDILLNLRQVSVLLTDDTSKTASEFANQETFVGYFDLQGPMEVKAKDLKFPKQIECG 133

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE----------------NDPIGLIT 172
           NP+  I  L  +   +    +    G         +                      + 
Sbjct: 134 NPNQHIATLTRNCTFQGRFLILTNPGLTFKNQSIGDPLLFTKQVAKLEIGNRLLEKNWLY 193

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           ++ + + I++V+Y VE   +      + + + + T+G+I  + ++  A   L        
Sbjct: 194 VNPITNAIRRVNYVVEQFGDVWE-QKEVVVLEVWTNGTIHPKQAIHSACTKLSTLFSSLS 252

Query: 233 NFEEPK-------------------------KEVKEDINVKSLPFNP---ALLKKVEELE 264
           +                              K + E    +S   +         +  L+
Sbjct: 253 SVNTTAFKFPASVARFKKVKTDSGADGNLTVKPMTEFSGQESPAGDKLTILFDLDIANLQ 312

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS+++   L+   I  +G+L+Q  ++D+ R+ N     + EI+  L   GL  
Sbjct: 313 LSLKTYLVLKNAKIQNIGNLLQYNKSDLTRLLNLANSQIEEIETALNVFGLAF 365


>gi|254751247|ref|ZP_05203285.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           Vollum]
          Length = 136

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 68/136 (50%), Positives = 92/136 (67%), Gaps = 2/136 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDG
Sbjct: 3   EIEKP-KIETVELN-EDAKYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K + LK+  +  K + I  +G G+VTA DI   +D+E+
Sbjct: 61  VLHEFSTVEGVVEDVTTIILNLKKLALKIYSEEEKTLEIDVQGEGIVTAADITHDSDVEI 120

Query: 128 LNPDHVICNLDVDAVV 143
           LNPD  I  L  DA  
Sbjct: 121 LNPDLHIATLAKDAHF 136


>gi|161511743|emb|CAP16882.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 158

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 61/154 (39%), Positives = 96/154 (62%), Gaps = 2/154 (1%)

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  IC +     
Sbjct: 1   TQIILNLKKVSLKVESDEEKSLEINVMGPANVTAGDIVGDGDVTILNPELPICTVAEGTT 60

Query: 143 VRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
               LT  KG GY  A  ++    + PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDK
Sbjct: 61  FHAVLTAEKGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDK 120

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           L++ + TDGS+   ++++L+++IL + L +F+  
Sbjct: 121 LTLDVWTDGSLAASEAISLSAKILTEHLXIFVTL 154


>gi|117575077|emb|CAJ84778.1| RNA polymerase alpha subunit [Lactobacillus amylophilus]
          Length = 138

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 61/138 (44%), Positives = 92/138 (66%)

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
            GV ED+T IILN+K + LK      K   I   GP  VTAGD++  +++++LNPD  I 
Sbjct: 1   PGVLEDVTQIILNLKKLTLKSIAADEKLAEIDVEGPATVTAGDLKVDDEVQILNPDQYIA 60

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
            +   A ++M + + +G GYVPA  +++++ PIG++ +D+L+SPI+KV+Y VE  R G+ 
Sbjct: 61  TVAEGAHLQMTVAIKQGRGYVPADQNKSDDMPIGVVPVDSLFSPIEKVNYQVEGTRVGRN 120

Query: 196 LDYDKLSMTIDTDGSITG 213
            DYDKL+M + TDGSIT 
Sbjct: 121 NDYDKLTMEVWTDGSITP 138


>gi|154424769|emb|CAL18487.1| RNA polymerase alpha subunit [Streptococcus criceti]
          Length = 168

 Score =  159 bits (402), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 60/168 (35%), Positives = 108/168 (64%)

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+KG+ +K   +  K + +  +GP  VTAGD+ T +DIE++NPDH +  +     ++  
Sbjct: 1   LNVKGLAVKSYVEDEKTIELDVQGPAEVTAGDVLTDSDIEIINPDHYLFTIAEGHSLKAT 60

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           +TV+K  GYVPA+ +++++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I 
Sbjct: 61  MTVAKNRGYVPAEGNKSDSAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIM 120

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
           T+G+I  ED++ L++R+L + L +F +  E  K  +     +S+  + 
Sbjct: 121 TNGTIIPEDALGLSARVLIEHLNLFTDLTEIAKTTEVMKETESVSNDQ 168


>gi|56807381|ref|ZP_00365362.1| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Streptococcus pyogenes M49 591]
          Length = 145

 Score =  158 bits (399), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 55/144 (38%), Positives = 90/144 (62%)

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +F  
Sbjct: 1   YTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDFFF 60

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
             K  +     + +     L + +EEL+LSVRS NCL+   I  + DL +++E +M+++ 
Sbjct: 61  VAKATEVMKETEKVNDEKVLDRTIEELDLSVRSYNCLKRAGINTVFDLTEKSEPEMMKVR 120

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMN 320
           N GR+SL E+K  L  +GL L  +
Sbjct: 121 NLGRRSLEEVKVKLADLGLGLKND 144


>gi|161511751|emb|CAP16886.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           dextrinicus]
          Length = 138

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 56/138 (40%), Positives = 92/138 (66%)

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITI 173
           VTA DI+  +DIEVLNP+  IC++     V M++TVS G GYVPA  ++  + PIG+I +
Sbjct: 1   VTAADIKADDDIEVLNPEQYICSIAEGGHVHMQMTVSNGRGYVPADQNKNGDMPIGVIAV 60

Query: 174 DALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           D++++PI +V+Y VES R G+  D+DKL++ + T+GSI+   +++LA++IL D L +FI+
Sbjct: 61  DSIFTPINRVNYQVESTRVGKRNDFDKLTLDVWTNGSISPRXAISLAAKILSDHLNIFID 120

Query: 234 FEEPKKEVKEDINVKSLP 251
             +  K  +  +  +   
Sbjct: 121 LSDEAKNTEIMVEKEETQ 138


>gi|189095413|ref|YP_001936426.1| DNA-directed RNA polymerase alpha subunit [Heterosigma akashiwo]
 gi|157694756|gb|ABV66032.1| DNA-directed RNA polymerase alpha subunit [Heterosigma akashiwo]
 gi|157777987|gb|ABV70173.1| DNA-directed RNA polymerase alpha subunit [Heterosigma akashiwo]
          Length = 402

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 69/227 (30%), Positives = 118/227 (51%), Gaps = 13/227 (5%)

Query: 14  NIEYIVLGQEEEN--RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE +   Q E N      +   L  G   T+G+ALRRVL++ L G AI  ++I  +  E
Sbjct: 3   KIEILESDQNEYNEQYGKFLINSLHPGQGTTVGSALRRVLLTDLPGLAIVGLRIANINTE 62

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT---IFKRGPGVVTAG--DIQTVNDIE 126
            SS+ GV ED+ +IILN+K I ++   +S K      +  +GPGVVTA   + +   +I+
Sbjct: 63  FSSLPGVREDILEIILNVKDIVIEGEFNSSKPWVLGRLKLKGPGVVTAALIEFEEDANIQ 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           ++NP   I  ++V++ + ME  V  G  Y   +   +       + IDA++ P+ KV++ 
Sbjct: 123 IINPSQYIATIEVNSSIEMEFLVQTGKNYRLVESENSITYSTDFLQIDAIFMPVTKVAFE 182

Query: 187 VESA------REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           V S           + D + L++ I T+GSI+   ++  ++ IL++ 
Sbjct: 183 VTSTKTNALENNSSIQDNENLTLEIWTNGSISPIKALVFSASILENL 229



 Score = 78.1 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 24/81 (29%), Positives = 41/81 (50%)

Query: 233 NFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +  + +  ++E     +          +EEL LSVR+ N L+  NI  + DL+Q +  D+
Sbjct: 316 DDSKSEPSIEEKRENVTSNERNLSQMPIEELILSVRAYNGLKRANIHSVSDLVQYSIKDL 375

Query: 293 LRMANFGRKSLVEIKGVLGTM 313
             + NFG+KSL E+   L  +
Sbjct: 376 KDIKNFGKKSLDEVVASLKNL 396


>gi|150036734|emb|CAM98258.1| DNA-directed RNA polymerase alpha chain [Leuconostoc citreum]
          Length = 145

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 59/145 (40%), Positives = 89/145 (61%), Gaps = 2/145 (1%)

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           + GV ED+T IILN+K + L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I
Sbjct: 1   VDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDVQGPADVTAADLQAGADVEVLNPDLHI 60

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESARE 192
             +     + M +T  KG GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R 
Sbjct: 61  ATVAAGKSLHMTVTAVKGRGYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRV 120

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSV 217
           G   DYDKL+  I T+GSI   D++
Sbjct: 121 GSRDDYDKLTFDIWTNGSIKPSDAL 145


>gi|262286213|gb|ACY41680.1| RNA polymerase alpha subunit [Streptococcus anginosus SK52]
          Length = 140

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 60/140 (42%), Positives = 94/140 (67%)

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+  IILN+KGI +K   +  K + +   GP  +TAGDI T +DIE++NPDH +  +
Sbjct: 1   VREDVMQIILNVKGIAVKSYVEDEKTIELDVEGPAEITAGDILTDSDIEIVNPDHYLFTI 60

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
              A ++  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    
Sbjct: 61  GEGASLKAIMTVNTGRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDG 120

Query: 198 YDKLSMTIDTDGSITGEDSV 217
           +DKL++ I TDG+I  ED++
Sbjct: 121 FDKLTLEIMTDGTIIPEDAL 140


>gi|262286211|gb|ACY41679.1| RNA polymerase alpha subunit [Streptococcus intermedius]
          Length = 140

 Score =  154 bits (390), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 60/140 (42%), Positives = 94/140 (67%)

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+  IILN+KGI +K   +  K + +   GP  +TAGDI T +DIE++NPDH +  +
Sbjct: 1   VREDVMQIILNVKGIAVKSYVEDEKTIELDVEGPAEITAGDILTDSDIEIVNPDHYLFTI 60

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
              A ++  +TV+ G GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    
Sbjct: 61  GEGASLKAIMTVNAGRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDG 120

Query: 198 YDKLSMTIDTDGSITGEDSV 217
           +DKL++ I TDG+I  ED++
Sbjct: 121 FDKLTLEIMTDGTIIPEDAL 140


>gi|119662339|emb|CAJ33158.1| RNA polymerase alpha subunit [Lactobacillus paralimentarius]
          Length = 134

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 51/134 (38%), Positives = 89/134 (66%)

Query: 108 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
             GP  VTA DI+  +D+E+L+P+  IC +       M++TV  G GY PA+ ++T+  P
Sbjct: 1   VVGPATVTANDIKADDDLEILDPEQFICTVAEGGHFHMQMTVINGRGYTPAEQNKTDETP 60

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           IG++ +D++++P++KV+Y VE+ R G+  D+DKL++ I T+GSI   ++++L+++IL + 
Sbjct: 61  IGVLPVDSIFTPVEKVNYQVENTRVGKRNDFDKLTIDIWTNGSIGPREAISLSAKILTEH 120

Query: 228 LGMFINFEEPKKEV 241
           L  F+N  E  K  
Sbjct: 121 LTSFVNLTEEAKSA 134


>gi|262286159|gb|ACY41653.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
 gi|262286161|gb|ACY41654.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
 gi|262286163|gb|ACY41655.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
 gi|262286167|gb|ACY41657.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
 gi|262286169|gb|ACY41658.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
 gi|262286171|gb|ACY41659.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
 gi|262286173|gb|ACY41660.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
 gi|262286175|gb|ACY41661.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
 gi|262286197|gb|ACY41672.1| RNA polymerase alpha subunit [Streptococcus mitis]
 gi|262286199|gb|ACY41673.1| RNA polymerase alpha subunit [Streptococcus mitis]
 gi|262286201|gb|ACY41674.1| RNA polymerase alpha subunit [Streptococcus mitis]
 gi|262286203|gb|ACY41675.1| RNA polymerase alpha subunit [Streptococcus mitis]
 gi|262286205|gb|ACY41676.1| RNA polymerase alpha subunit [Streptococcus mitis]
 gi|262286207|gb|ACY41677.1| RNA polymerase alpha subunit [Streptococcus mitis]
 gi|262286209|gb|ACY41678.1| RNA polymerase alpha subunit [Streptococcus mitis]
          Length = 140

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 60/140 (42%), Positives = 93/140 (66%)

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+  IILNIKGI +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +
Sbjct: 1   VREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEVTAGDILTDSDIEIVNPDHYLFTI 60

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
              + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y VE AR G    
Sbjct: 61  GEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDG 120

Query: 198 YDKLSMTIDTDGSITGEDSV 217
           +DKL++ I T+G+I  ED++
Sbjct: 121 FDKLTLEILTNGTIIPEDAL 140


>gi|284110424|ref|ZP_06386522.1| DNA-directed RNA polymerase subunit alpha [Candidatus Poribacteria
           sp. WGA-A3]
 gi|283829770|gb|EFC34077.1| DNA-directed RNA polymerase subunit alpha [Candidatus Poribacteria
           sp. WGA-A3]
          Length = 155

 Score =  153 bits (387), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 66/143 (46%), Positives = 97/143 (67%), Gaps = 1/143 (0%)

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           PIK+V++ VE+AR G+V DYDKL++ + TDGS+T  ++V+ ++ IL++ L + I  EE K
Sbjct: 1   PIKRVNFHVENARVGRVTDYDKLNLEVWTDGSVTPLEAVSSSASILREHLAICIPSEEMK 60

Query: 239 KEVKEDINVKSL-PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +   +    ++    N  L + V ELELSVR+ NCL+  NI  + DL+Q+TE +ML+  N
Sbjct: 61  EVEHDSAYEETQAELNKHLARSVNELELSVRAANCLKNANIKTIEDLVQKTEIEMLKTKN 120

Query: 298 FGRKSLVEIKGVLGTMGLFLGMN 320
           FG+KSL EIK VL  MGL LG+ 
Sbjct: 121 FGKKSLNEIKEVLAEMGLSLGLR 143


>gi|262286165|gb|ACY41656.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
 gi|262286177|gb|ACY41662.1| RNA polymerase alpha subunit [Streptococcus oralis]
 gi|262286179|gb|ACY41663.1| RNA polymerase alpha subunit [Streptococcus oralis]
 gi|262286181|gb|ACY41664.1| RNA polymerase alpha subunit [Streptococcus oralis]
 gi|262286183|gb|ACY41665.1| RNA polymerase alpha subunit [Streptococcus oralis]
 gi|262286185|gb|ACY41666.1| RNA polymerase alpha subunit [Streptococcus oralis]
 gi|262286187|gb|ACY41667.1| RNA polymerase alpha subunit [Streptococcus oralis]
 gi|262286189|gb|ACY41668.1| RNA polymerase alpha subunit [Streptococcus oralis]
 gi|262286191|gb|ACY41669.1| RNA polymerase alpha subunit [Streptococcus oralis]
 gi|262286193|gb|ACY41670.1| RNA polymerase alpha subunit [Streptococcus oralis]
 gi|262286195|gb|ACY41671.1| RNA polymerase alpha subunit [Streptococcus oralis]
          Length = 140

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 59/140 (42%), Positives = 93/140 (66%)

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+  IILNIKGI +K   +  K + +   GP  +TAGDI T +DIE++NPDH +  +
Sbjct: 1   VREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEITAGDILTDSDIEIVNPDHYLFTI 60

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
              + ++  +TV+ G GYVPA  ++ +N P+G + +D++Y+P+ KV+Y VE AR G    
Sbjct: 61  GEGSSLKATMTVNSGRGYVPADENKKDNAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDG 120

Query: 198 YDKLSMTIDTDGSITGEDSV 217
           +DKL++ I T+G+I  ED++
Sbjct: 121 FDKLTLEILTNGTIIPEDAL 140


>gi|150186925|emb|CAK30129.1| RNA polymerase alpha subunit [Streptococcus thermophilus]
          Length = 145

 Score =  153 bits (386), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 60/144 (41%), Positives = 97/144 (67%)

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           ILNIKG+ +K   +  K + +  +GP  VTAGDI T +DIE++NPDH +  +   A  + 
Sbjct: 1   ILNIKGLAVKSYVEDEKTIELDVQGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGASFQA 60

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
            +TVS   GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I
Sbjct: 61  TMTVSTNRGYVPAEENKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEI 120

Query: 206 DTDGSITGEDSVALASRILQDQLG 229
            T+G+I  ED++ L++R+L + L 
Sbjct: 121 VTNGTIIPEDALGLSARVLIEHLN 144


>gi|150036846|emb|CAM98288.1| DNA-directed RNA polymerase alpha chain [Fructobacillus
           pseudoficulneus]
          Length = 169

 Score =  153 bits (386), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 62/169 (36%), Positives = 98/169 (57%), Gaps = 2/169 (1%)

Query: 101 HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
              + I  +GP  VTA D+    DIEVLNPD  I  L     + M +T  KG GY  A+ 
Sbjct: 1   EHALEIDVQGPKDVTAADLMGSADIEVLNPDLHIATLAAGKALHMTVTAVKGRGYSSAEE 60

Query: 161 HRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           ++   +  PIG++T+D++Y+PI++V+Y VE+ R G   DYDKL+M + T+GSI   D+++
Sbjct: 61  NKQLRDEMPIGVLTVDSIYTPIERVNYHVENKRVGSRDDYDKLTMEVWTNGSIKPSDALS 120

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           L S+IL + L +F +     ++ K  +  +      A    +E+L+LSV
Sbjct: 121 LGSKILTEHLNLFTDISPVAQDTKVMVESEPAANTAADAAPIEDLDLSV 169


>gi|150186973|emb|CAK30139.1| RNA polymerase alpha subunit [Streptococcus porcinus]
          Length = 161

 Score =  153 bits (386), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 57/159 (35%), Positives = 98/159 (61%)

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
           G+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV+
Sbjct: 1   GLAVKSYVEDEKMIELDVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLKATMTVA 60

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+
Sbjct: 61  KKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGT 120

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           I  ED++ L++R+L + L +F +  E  K        + 
Sbjct: 121 IIPEDALGLSARVLIEHLNLFTDLTEVAKATDVMKETEK 159


>gi|150186930|emb|CAK30130.1| RNA polymerase alpha subunit [Streptococcus salivarius]
          Length = 141

 Score =  152 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 58/141 (41%), Positives = 95/141 (67%)

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+  IILNIKG+ +K   +  K + +  +GP  VTAGDI T +DIE++NPDH +  +   
Sbjct: 1   DVMQIILNIKGLAVKSYVEDEKTIELDVQGPAEVTAGDILTDSDIEIVNPDHYLFTIADG 60

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
           A ++  +TV+   GYVPA  ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DK
Sbjct: 61  ASLKATMTVATNRGYVPADENKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDK 120

Query: 201 LSMTIDTDGSITGEDSVALAS 221
           L++ I T+G+I  ED++ L++
Sbjct: 121 LTIEIMTNGTIIPEDALGLSA 141


>gi|289571691|ref|ZP_06451918.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis T17]
 gi|289545445|gb|EFD49093.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis T17]
          Length = 130

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 53/113 (46%), Positives = 77/113 (68%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
            +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T
Sbjct: 15  TDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVT 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           +IILN+K + +    D    + + K+GPG VTAGDI     + V NP   I +
Sbjct: 75  EIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIAH 127


>gi|48374282|gb|AAT41971.1| putative RNA polymerase alpha subunit [Fremyella diplosiphon Fd33]
          Length = 155

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 50/156 (32%), Positives = 87/156 (55%), Gaps = 8/156 (5%)

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           +  + ID+++ P++KV+Y+VE AR    +  D+L + + T+GSI+ +++++ A+ IL D 
Sbjct: 1   MDFLQIDSVFMPVRKVNYSVEEARGDGSITKDRLLLEVWTNGSISPQEALSSAAGILVDL 60

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
                +      +   DI     P +P     +EEL+LSVR+ NCL+   +  + DL+  
Sbjct: 61  FNPLKDISLEPTDTGSDI-----PDDPTAQIPIEELQLSVRAYNCLKRAQVNSVADLLDY 115

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           T+ D+L + NFG+KS  E+   L      LG+ LP 
Sbjct: 116 TQEDLLEIKNFGQKSAEEVVEALQR---RLGITLPQ 148


>gi|161511777|emb|CAP16899.1| DNA-directed RNA polymerase subunit alpha [Pediococcus stilesii]
          Length = 141

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 61/141 (43%), Positives = 86/141 (60%), Gaps = 2/141 (1%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  IC 
Sbjct: 1   GVVEDVTQIILNLKKVSLKIESDDEKTLDINVVGPANVTAGDIMGDGDVTILNPEAPICT 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQ 194
           +         LT   G GY  A  ++    + PI ++ ID++Y+PI++V+Y VE+ R GQ
Sbjct: 61  VAEGTTFHAVLTADTGRGYTSADENKARKVDMPISVLPIDSIYTPIERVNYQVENTRVGQ 120

Query: 195 VLDYDKLSMTIDTDGSITGED 215
             DYDKL++ I TDGSIT  +
Sbjct: 121 RDDYDKLTLDIWTDGSITPSE 141


>gi|150187079|emb|CAK30166.1| RNA polymerase alpha subunit [Streptococcus parasanguinis ATCC
           15912]
          Length = 150

 Score =  150 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 58/149 (38%), Positives = 92/149 (61%)

Query: 101 HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
            K + +   GP  VTAGDI T +DIE++NPDH +  +   A ++  LTV+ G GYVPA  
Sbjct: 1   EKIIELDVEGPAEVTAGDILTDSDIEIVNPDHYLFTIGEGASLKATLTVNSGRGYVPADQ 60

Query: 161 HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           ++ ++ P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L+
Sbjct: 61  NKKDDAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLS 120

Query: 221 SRILQDQLGMFINFEEPKKEVKEDINVKS 249
           +RIL + L +F N  E          V +
Sbjct: 121 ARILTEHLNLFTNLTEIAIATDVMKEVDT 149


>gi|116335037|ref|YP_802532.1| RNA polymerase alpha subunit [Candidatus Carsonella ruddii PV]
 gi|123126152|sp|Q05FK5|RPOA_CARRP RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|116235318|dbj|BAF35166.1| RNA polymerase alpha subunit [Candidatus Carsonella ruddii PV]
          Length = 322

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 79/314 (25%), Positives = 147/314 (46%), Gaps = 8/314 (2%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
            ++ I +      R+++  E     F  +LGN ++RV+  +     I  ++I  +  E  
Sbjct: 9   TLKKISIKNISFFRSIIRIETFNNSFCDSLGNFIKRVIFLTTNSYKIIYLKIYKIKSEFY 68

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
            + G+ E+   I+ N+  I +K++ D+   + I K+GP ++TA DI +  +I + NP+ +
Sbjct: 69  DLPGIIENTQTILKNLDNIIIKINNDNVANLIIKKKGPCIITAKDIFSDKNITIFNPNKI 128

Query: 134 ICNLDVDAVVRMELTVSK--GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
           I N+  + V    +         Y   +  + +     +I ++   SPI  ++Y +    
Sbjct: 129 IANVSNNIVFYCIMKCVNSLFKNY-TDEFFQFKIFKENIIFLNNFKSPIISLNYYINKKI 187

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL- 250
             + L   KL   I+T+GSI   D        ++    +  +F   KK  K ++  K+  
Sbjct: 188 FNKKLK--KLFFDIETNGSIKPVDCFKNCIFYIKKYFDLIFSFIGFKKYKKINVEKKNNL 245

Query: 251 --PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
               N   L  +  L+LS+RS NCL+  NI  +GDLI+ ++ +++ + N G+KS  EI  
Sbjct: 246 NLKINSVYLNSINNLKLSIRSLNCLKNNNIFLIGDLIKISKNNLINIPNLGKKSYNEILN 305

Query: 309 VLGTMGLFLGMNLP 322
            L   GL L   + 
Sbjct: 306 SLKNFGLNLNSKIE 319


>gi|119662829|emb|CAJ33207.1| RNA polymerase alpha subunit [Lactobacillus ingluviei]
          Length = 132

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 54/130 (41%), Positives = 83/130 (63%), Gaps = 1/130 (0%)

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-N 165
             +GP  VTA DIQ   D+ +LNPD  I  +   A + M +T   G GY  A  ++   +
Sbjct: 1   DVKGPAEVTAADIQADGDVTILNPDLHIATVADGAELHMRMTADTGRGYNSADVNKARMD 60

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
             IG++ ID++Y+PI++V+YTVE+ R GQ  DYDKL++ + TDGS+T  ++++LA++IL 
Sbjct: 61  LAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYDKLTLDVWTDGSLTPTEAISLAAKILT 120

Query: 226 DQLGMFINFE 235
             L MF+N  
Sbjct: 121 SHLTMFVNLT 130


>gi|108792413|emb|CAJ33201.1| RNA polymerase alpha subunit [Lactobacillus acidipiscis]
          Length = 133

 Score =  148 bits (375), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 53/133 (39%), Positives = 89/133 (66%), Gaps = 2/133 (1%)

Query: 116 AGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITI 173
           AGDIQ  +++EVLNPD  IC +   A     +T +KG GYV A  ++  TE+ PIG++ I
Sbjct: 1   AGDIQGSSEVEVLNPDLYICTVADGASFHARMTANKGRGYVSANENKAKTEDMPIGVLAI 60

Query: 174 DALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           D++Y+PI++V+Y VE  R GQ  D+DKL++ + T+GSIT  ++++L+++IL + L +F++
Sbjct: 61  DSIYTPIERVNYQVEKTRVGQKSDFDKLTLDVWTNGSITPSEAISLSAKILTEHLTLFVD 120

Query: 234 FEEPKKEVKEDIN 246
             +  K  +  + 
Sbjct: 121 LTDEAKNAEIMVE 133


>gi|260780686|ref|YP_003227042.1| RNA polymerase alpha subunit [Bryopsis hypnoides]
 gi|260176764|gb|ACX33773.1| RNA polymerase alpha subunit [Bryopsis hypnoides]
          Length = 363

 Score =  148 bits (375), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 68/339 (20%), Positives = 143/339 (42%), Gaps = 35/339 (10%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             I+   +    +          P+    T+ NALRR L++     +IT V I+ + HE 
Sbjct: 21  TRIDENTVDHTPQLYACFQLGLFPKNQGLTIANALRRTLLTESTECSITGVLIEDIKHEY 80

Query: 73  SSIKGVHEDLTDIILNIKGINLKM--SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           S++KG+ E + DI++N+K I      S    +   + ++GP V+ A +++  + +  +NP
Sbjct: 81  SNLKGIKETVFDILMNLKKIIFFSGQSFFKTQVSFLSEKGPIVLKAKNLKLPSFLFCINP 140

Query: 131 DHVICNLDVDAVVRMELTVSK---------GHGYVPA----------KHHRTENDPIGLI 171
           D  I  L+ ++ + M + + +          H Y             K + T+N     +
Sbjct: 141 DQYITTLETNSKINMTIFIDQSTPKNFSYFTHCYYSNFSNNFFPFKLKKNFTQNQQSNFL 200

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +D  + PI  ++Y ++     +    + L   I T+GS+     +  A + L   L  F
Sbjct: 201 FLDTQFCPISNLNYKIK----KKESQKEILFFEIWTNGSVHPNFILKKAIKNLLLNLIPF 256

Query: 232 INFEEPKKEVK--EDINVKSLPFNPALLKKVEELEL-----SVRSTNCLRGENIVYMGDL 284
            +    K E +  E+  ++ +      ++K+ +L+L     S+ +   L+  NI+ +GDL
Sbjct: 257 HSLRNSKIEFEDYENKKIQKIVSQKKFIQKLIKLDLTNFPISLETYQSLKKLNILTIGDL 316

Query: 285 IQRTEADMLRM-ANFGRKSLVEIKGVLGTMGLFLGMNLP 322
            +        +     ++  +E+  +   +  +    L 
Sbjct: 317 YRLKMQ--KNIPKTLTKQEFLEVHRLFKYLKFYFSNKLK 353


>gi|119029438|gb|ABL59935.1| DNA-directed RNA polymerase alpha subunit [uncultured bacterium]
          Length = 219

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 78/205 (38%), Positives = 124/205 (60%), Gaps = 7/205 (3%)

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF-KRGPGVVTAGD 118
           +  ++IDGVLH+ S++ G+ ED+ +++LN+K +   ++ D +     F K  PG V A D
Sbjct: 16  LHRIKIDGVLHDYSALDGLQEDVVEVLLNLKELAFNIASDENTVAINFEKSSPGPVLASD 75

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDAL 176
               ++IEV NP+ VICN+     ++MELT  +G GY  A +   +     IG++ +DA 
Sbjct: 76  FADQSNIEVFNPNLVICNVTSGV-LKMELTAQRGRGYELAVNRDVDRNEKSIGVLQLDAS 134

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+KKVSY VE AR G   D DKL + ++T+G+I+ ED++ ++S ILQ QL  F+N + 
Sbjct: 135 YSPVKKVSYNVEVARFGGRADLDKLVIDLETNGAISPEDAIRISSTILQQQLLAFVNLD- 193

Query: 237 PKKEVKEDINVKSLPFNPALLKKVE 261
              ++ ++   K   F+P L  K E
Sbjct: 194 --SKLLKEPTKKEEEFDPILCDKGE 216


>gi|284103857|ref|ZP_06386117.1| DNA-directed RNA polymerase subunit alpha [Candidatus Poribacteria
           sp. WGA-A3]
 gi|283830235|gb|EFC34482.1| DNA-directed RNA polymerase subunit alpha [Candidatus Poribacteria
           sp. WGA-A3]
          Length = 137

 Score =  147 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 62/138 (44%), Positives = 84/138 (60%), Gaps = 1/138 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + K  ++   P  +E         +     AEP  RGF  T+GN+LRRVL+SSL GAA+T
Sbjct: 1   MSKGIKDFQLPMRLELEK-ETASSSYGKFTAEPFERGFGTTVGNSLRRVLLSSLTGAAVT 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           +V+I+G  HE S++ GV ED+T IILNIK + LK+  D  K + + K+GPG V A DIQ 
Sbjct: 60  SVKIEGAFHEFSTLPGVTEDVTIIILNIKNLRLKLHTDKSKAMQLKKKGPGKVRAADIQH 119

Query: 122 VNDIEVLNPDHVICNLDV 139
             DI +LNP+  I  LD 
Sbjct: 120 DADITILNPELHIATLDK 137


>gi|150187003|emb|CAK30148.1| RNA polymerase alpha subunit [Streptococcus parauberis]
          Length = 161

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 54/160 (33%), Positives = 95/160 (59%)

Query: 96  MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY 155
              +  K + +   GP  VTAGDI T +DIE++NPDH +  +     ++  +TV+K  GY
Sbjct: 1   SYVEDEKMIELDVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSLKATMTVAKKRGY 60

Query: 156 VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
           +PA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED
Sbjct: 61  IPAEGNKQDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPED 120

Query: 216 SVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           ++ L++R+L + L +F +  E  K        + +     
Sbjct: 121 ALGLSARVLIEHLNLFTDLTEVAKTTDVMKETEKVNDEKI 160


>gi|150186905|emb|CAK30124.1| RNA polymerase alpha subunit [Streptococcus gallinaceus]
          Length = 138

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 56/138 (40%), Positives = 92/138 (66%)

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILNIKGI +K   +  K + +   GP  +TAGDI T +DIE++NPDH +  +   A  +
Sbjct: 1   IILNIKGIAVKSYVEDEKTIELDVVGPAEITAGDILTDSDIEIVNPDHYLFTIAAGATFK 60

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
             +TV+ G GY+PA+ ++ ++ P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ 
Sbjct: 61  AVMTVNTGRGYIPAEGNKKDDAPVGTLAVDSIYTPVVKVNYQVEPARVGSNDGFDKLTLE 120

Query: 205 IDTDGSITGEDSVALASR 222
           I T+G+   ED++ L++R
Sbjct: 121 IMTNGTTIPEDALGLSAR 138


>gi|119662291|emb|CAJ33132.1| RNA polymerase alpha subunit [Lactobacillus collinoides]
          Length = 135

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 62/135 (45%), Positives = 88/135 (65%), Gaps = 3/135 (2%)

Query: 79  HEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
            ED+T IILN K I+LK+ G  D  + + I  +GP  VTAGDI   +D+ VLNPD  I  
Sbjct: 1   VEDVTQIILNTKKISLKLEGPDDEIESMEIDVKGPAQVTAGDITADSDVTVLNPDLYIAT 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHR-TENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
           +   A   M +T +KG GYV A  ++  E+ PIG++ ID++Y+PI++V+Y VE+ R GQ 
Sbjct: 61  VAEGATFHMRMTANKGRGYVSADRNKAKEDMPIGVLPIDSIYTPIERVNYQVENTRVGQR 120

Query: 196 LDYDKLSMTIDTDGS 210
            DYDKL++ + TD S
Sbjct: 121 DDYDKLTLDVWTDSS 135


>gi|289445057|ref|ZP_06434801.1| LOW QUALITY PROTEIN: probable DNA-directed RNA polymerase rpoa
           [Mycobacterium tuberculosis T46]
 gi|289417976|gb|EFD15216.1| LOW QUALITY PROTEIN: probable DNA-directed RNA polymerase rpoa
           [Mycobacterium tuberculosis T46]
          Length = 173

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 37/128 (28%), Positives = 71/128 (55%)

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + ++T  SI+  D++A A + L +  G+        + ++   +        +    ++
Sbjct: 19  ILDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALPID 78

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           +L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  + 
Sbjct: 79  DLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSP 138

Query: 322 PDWPPESI 329
           P + P  +
Sbjct: 139 PSFDPSEV 146


>gi|154424739|emb|CAL18472.1| RNA polymerase alpha subunit [Streptococcus oligofermentans]
          Length = 136

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 57/136 (41%), Positives = 89/136 (65%)

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILNIKGI +K      K + +   GP  VTAGDI T +DIE++NPDH +  +   A  +
Sbjct: 1   IILNIKGIAVKSYVQDEKMIELDVEGPAEVTAGDILTDSDIEIVNPDHYLFTISEGARFK 60

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
            ++ V+ G GYVPA  ++ ++ P+G + +D++Y+P+ KV+Y VE AR G    +DKL++ 
Sbjct: 61  AKMAVNSGRGYVPADENKKDDAPVGTLAVDSIYTPVTKVNYQVEPARVGSNDGFDKLTLE 120

Query: 205 IDTDGSITGEDSVALA 220
           I T+G+I  ED++ L+
Sbjct: 121 ILTNGTIIPEDALGLS 136


>gi|13560647|gb|AAK30140.1|AF346704_1 DNA-directed RNA polymerase [Fucus vesiculosus]
          Length = 226

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 57/212 (26%), Positives = 113/212 (53%), Gaps = 3/212 (1%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
              E     +   L +   +T+GN LRR L+S+L G  I  V+  G+ +E + ++GV ED
Sbjct: 16  NTNEFYGHFVFTALKKSQGNTIGNVLRRTLLSNLYGFRIVGVRFAGINNEFALLEGVRED 75

Query: 82  LTDIILNIKGINLKMSGDSHKRVT--IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           L +IILN+K I +  S    +     +   GP V+TAG ++  N++++LNP++ +  +  
Sbjct: 76  LFEIILNLKEIIILNSNRIDQTCYGRLKVYGPAVITAGSLELPNNVKILNPNNHLLTISD 135

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           ++++ +E+ +  G  Y+ AK  + E   +  I ID+ ++P+ KV++ + S  +      +
Sbjct: 136 ESLIEIEVKIEAGKSYILAKDQKLEGA-LDFIPIDSNFAPVLKVNWYIISLPQDGESINE 194

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           +L + I T+G++    ++  A  ++   L   
Sbjct: 195 ELHLEIYTNGTLLPHQALLQARTMIGYMLSPI 226


>gi|215400751|ref|YP_002327512.1| RNA polyperase alpha-chain [Vaucheria litorea]
 gi|194441201|gb|ACF70929.1| RNA polyperase alpha-chain [Vaucheria litorea]
          Length = 230

 Score =  143 bits (361), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 65/233 (27%), Positives = 119/233 (51%), Gaps = 13/233 (5%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q+N  E I  N +E       +EN    I +PL  G   ++GN  RR+L++ +    IT
Sbjct: 1   MQENL-EFI--NLLEV-----PDENFGKYIIKPLNLGMGVSIGNLFRRILLTQMPRTNIT 52

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ- 120
            V+  G+ +E S+IKGV ED+ +I+LN+K I  K   +    V I   GP V+T+  +Q 
Sbjct: 53  GVRFAGITNEFSTIKGVREDVLEILLNLKQIIFKGFKEEKTYVRIKITGPTVITSSCLQS 112

Query: 121 -TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
              ++I ++NP   I  +  D+ +  EL +        A  ++   +    + +D + SP
Sbjct: 113 ALPDEITLVNPSQYIATITNDSTLEFELKIESEKKSNLAN-NQAIFESSDFLEVDKITSP 171

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           I+++ + V   ++ +    ++L + I TDGSIT  D++  + +++Q+      
Sbjct: 172 IRQILFDV--YKKSETETQEELVLQIWTDGSITPIDALITSVKLVQNLFTQIT 222


>gi|167010108|ref|ZP_02275039.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica FSC200]
          Length = 224

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 61/228 (26%), Positives = 122/228 (53%), Gaps = 9/228 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           + L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I+
Sbjct: 4   ENLLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKIN 60

Query: 67  -GVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVND 124
            G +  +  +    E + DIILN+K +++ ++ D     +T    G       +   +++
Sbjct: 61  DGKVTSLEDVIPCDETVADIILNVKSLSVTLAEDVETGTITFELSGSEEEIFSEEAKLSE 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
              +  +  IC+ +    +++E  V KG G+ PA+ +  +    G   +DA +SP+    
Sbjct: 121 GLAITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQDNFKD----GEFLLDATFSPVVFCD 176

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           + ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   +
Sbjct: 177 FEIKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIV 224


>gi|21039418|gb|AAM33638.1| RpoA [Pseudomonas putida]
          Length = 127

 Score =  142 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 58/130 (44%), Positives = 86/130 (66%), Gaps = 3/130 (2%)

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
             Q  D DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   + V  +   +   
Sbjct: 1   VEQRTDLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDSEPVVVEQEDE--- 57

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G+KSL EIK VL 
Sbjct: 58  IDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNLGKKSLTEIKDVLA 117

Query: 312 TMGLFLGMNL 321
           + GL LGM L
Sbjct: 118 SRGLSLGMRL 127


>gi|21039420|gb|AAM33639.1| RpoA [Escherichia coli]
          Length = 127

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 55/130 (42%), Positives = 87/130 (66%), Gaps = 3/130 (2%)

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
             Q  + DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   
Sbjct: 1   VEQRTNLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP---EVKEEKPE 57

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
           F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL 
Sbjct: 58  FDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLA 117

Query: 312 TMGLFLGMNL 321
           + GL LGM L
Sbjct: 118 SRGLSLGMRL 127


>gi|115350008|ref|YP_764409.1| alpha subunit of RNA polymerase [Stigeoclonium helveticum]
 gi|122165139|sp|Q06SF7|RPOA_STIHE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|98990222|gb|ABF60189.1| alpha subunit of RNA polymerase [Stigeoclonium helveticum]
          Length = 517

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 55/166 (33%), Positives = 88/166 (53%), Gaps = 2/166 (1%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
           ++  ++         PL  G   TL NALRR L+S L G AIT V+I+GV HE S++ GV
Sbjct: 27  IMENKKSFYGRFYIGPLEVGQGITLANALRRALLSELNGLAITTVEIEGVSHEYSTLMGV 86

Query: 79  HEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
            E + DI+LN+K I LK        +   I+ +GPGV+ AGDI   + I+ ++P+  I  
Sbjct: 87  RESVLDILLNLKQIVLKSKKSVKRAQTAYIYCQGPGVIRAGDIILPSSIQCVDPEQYIAT 146

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           L  D +++M++ + +G  Y+    +    D +    +D      K+
Sbjct: 147 LSSDGILKMKVIIRQGKNYLVQTPNSLFFDEVSEFVLDKNNLAEKR 192



 Score = 39.2 bits (90), Expect = 0.98,   Method: Composition-based stats.
 Identities = 13/61 (21%), Positives = 23/61 (37%)

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
            D + + I T+GSI    ++  A++ L +    F N +  K    E     +        
Sbjct: 453 KDIIILEIWTNGSILPRTALKHATQNLSNLFIKFQNAKMMKNSFFETNKTYTQTIRQLYE 512

Query: 258 K 258
           K
Sbjct: 513 K 513


>gi|313622252|gb|EFR92762.1| DNA-directed RNA polymerase subunit alpha [Listeria innocua FSL
           J1-023]
          Length = 129

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 53/123 (43%), Positives = 82/123 (66%)

Query: 101 HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
            K + I  +GPGVVTA DI   +D+E+LNPD  I  L  +A   + L  ++G GY PA  
Sbjct: 1   EKTLEIDMQGPGVVTAADINYDSDVEILNPDLHIATLSDNAKFHVRLNATRGRGYTPADQ 60

Query: 161 HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           ++ EN PIG++ +D+++SP+ +V+Y VE+ R GQ  +YDKL+  + TDGSI+ E++V+L 
Sbjct: 61  NKRENMPIGVLPVDSIFSPVIRVNYQVENTRVGQSTNYDKLTFDVLTDGSISPEEAVSLG 120

Query: 221 SRI 223
           +  
Sbjct: 121 ANS 123


>gi|213612396|ref|ZP_03370222.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E98-2068]
          Length = 117

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 54/120 (45%), Positives = 78/120 (65%), Gaps = 3/120 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITL 117


>gi|218755235|ref|ZP_03534031.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis GM 1503]
          Length = 118

 Score =  139 bits (351), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 49/100 (49%), Positives = 71/100 (71%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
            +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T
Sbjct: 15  TDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVT 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           +IILN+K + +    D    + + K+GPG VTAGDI    
Sbjct: 75  EIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPP 114


>gi|254798672|ref|YP_003058319.1| alpha subunit of RNA polymerase [Parachlorella kessleri]
 gi|229915620|gb|ACQ90963.1| alpha subunit of RNA polymerase [Parachlorella kessleri]
          Length = 275

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 70/257 (27%), Positives = 103/257 (40%), Gaps = 43/257 (16%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +  + E           RG A T+ NALRR L+  L    +T V IDGV+HE SSI GV 
Sbjct: 16  IQSQGEMYARFHLGTFFRGQALTVANALRRTLLGELPYLIVTKVHIDGVVHEFSSIPGVQ 75

Query: 80  EDLTDIILNIKGINLKMSGDSHK---------RVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E + DI+LN+K +   +S              +V +  RGP  VTA D++    +  + P
Sbjct: 76  ESVLDILLNLKRLTFTISNKKFNIFSNSWLKTKVFLKIRGPAKVTAADLKLPPHLACVWP 135

Query: 131 DHVICNLDVDAVVRMELT-------------------------------VSKGHGYVPAK 159
           +H I  L  +A +   L                                  KG G    K
Sbjct: 136 NHYIATLSSNAELACVLELAVVHPKQKISIAKNEVGSKNKIFGKVTNDVFEKGKGTESKK 195

Query: 160 HHRTENDPIGLI-TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
                 +    I ++D  YSPI+KV+Y +      +  +Y  L + I TDGSI  + ++ 
Sbjct: 196 ILTDSIEKNKKIFSLDTNYSPIRKVNYVIYELDSKKNSEY--LVLEIVTDGSIEPKQALR 253

Query: 219 LASRILQDQLGMFINFE 235
            A + L      F    
Sbjct: 254 FAFKQLTKLFYEFTQIS 270


>gi|119662387|emb|CAJ33182.1| RNA polymerase alpha subunit [Lactobacillus acidifarinae]
          Length = 132

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 61/132 (46%), Positives = 87/132 (65%), Gaps = 4/132 (3%)

Query: 84  DIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
            IILN+K I LK++G  D  + + I  +GP  VTAGDI    D++VLNPD  I  +   A
Sbjct: 1   QIILNVKKIALKLNGADDQEETMEINVKGPAQVTAGDIVAGADVDVLNPDLYIATVADGA 60

Query: 142 VVRMELTVSKGHGYVPAKHHRTEN--DPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              M +T  KG GYV A  ++T N   PIG++ +D++Y+PI++V+Y VE+AR GQ  DYD
Sbjct: 61  TFHMRMTADKGRGYVSADENKTRNTEMPIGVLAVDSIYTPIERVNYQVENARVGQRADYD 120

Query: 200 KLSMTIDTDGSI 211
           KL++ + T+GSI
Sbjct: 121 KLTLDVWTNGSI 132


>gi|150036730|emb|CAM98256.1| DNA-directed RNA polymerase alpha chain [Leuconostoc citreum]
          Length = 133

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 53/133 (39%), Positives = 80/133 (60%), Gaps = 2/133 (1%)

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           ILN+K + L +  D  + + I  +GP  VTA D+Q   D+EVLNPD  I  +     + M
Sbjct: 1   ILNLKKVVLAIDSDDERSLEIDVQGPADVTAADLQAGADVEVLNPDLHIATVAAGKSLHM 60

Query: 146 ELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +T  KG GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+ 
Sbjct: 61  TVTAVKGRGYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGSRDDYDKLTF 120

Query: 204 TIDTDGSITGEDS 216
            I T+GSI   D+
Sbjct: 121 DIWTNGSIKPSDA 133


>gi|218755234|ref|ZP_03534030.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis GM 1503]
          Length = 153

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 37/126 (29%), Positives = 71/126 (56%)

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
           +++T  SI+  D++A A + L +  G+        + ++   +        +    +++L
Sbjct: 1   SVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALPIDDL 60

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  + P 
Sbjct: 61  DLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPPS 120

Query: 324 WPPESI 329
           + P  +
Sbjct: 121 FDPSEV 126


>gi|269101036|ref|YP_003289184.1| DNA-directed RNA polymerase subunit alpha [Ectocarpus siliculosus]
 gi|266631544|emb|CAV31215.1| DNA-directed RNA polymerase subunit alpha [Ectocarpus siliculosus]
 gi|270118674|emb|CAT18735.1| DNA-directed RNA polymerase subunit alpha [Ectocarpus siliculosus]
          Length = 361

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 88/355 (24%), Positives = 148/355 (41%), Gaps = 52/355 (14%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
            Q + K   ++  +L   E      +   L +    T+GN LRRVL+S+L G  IT V++
Sbjct: 1   MQNMSKCKCVDSDLLSPSEL-YGHFVFTSLEQSEGSTIGNMLRRVLLSNLYGLKITGVRL 59

Query: 66  DGVLH-EISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTV 122
             V H E + + GV ED  ++ILN+K I LK            +  +GP VVTAG I+  
Sbjct: 60  PDVTHNEFNLLDGVREDFLEVILNLKEIILKDENKYGQSYHGLLKIQGPAVVTAGSIKFS 119

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
             I+VLNP++ +  +  D+ V + L +  G  YV AK  + E      + ID+ ++P+ K
Sbjct: 120 KGIKVLNPNNYLLTISDDSFVEIHLKLEHGKAYVLAKDQKLEG-STYFLPIDSNFAPVLK 178

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+  V++  +       +L + I T+GS+    ++  A  ++   L      E P     
Sbjct: 179 VNSYVKTLPQHIENTDVELHLEIFTNGSLLPHQALLQAKNMIGYMLSTVNKMEFPCLSQV 238

Query: 243 EDIN------------------------------------VKSLPFNPALLKKVEELE-- 264
                                                   ++       LLK+V E++  
Sbjct: 239 VSEETKSIVKIENIQKKIYKKKEKTVQAKIFQSGEKKAKCIEEPTPEELLLKRVNEMDSG 298

Query: 265 ------LSVRSTNCLRGENIVYMGDLIQRTEA---DMLRMANFGRKSLVEIKGVL 310
                 LS R    L+  NI +  +L+    +    ++ +   G KS+ EI+  L
Sbjct: 299 SLDCLKLSDRIVKALKKANINFTWELMDYDSSGPPYLIDIKGLGPKSVAEIEKSL 353


>gi|260202639|ref|ZP_05770130.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis T46]
 gi|289763639|ref|ZP_06523017.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis GM 1503]
 gi|289711145|gb|EFD75161.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis GM 1503]
          Length = 152

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 37/125 (29%), Positives = 70/125 (56%)

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           ++T  SI+  D++A A + L +  G+        + ++   +        +    +++L+
Sbjct: 1   METKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHIASFALPIDDLD 60

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
           L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  L  +GL L  + P +
Sbjct: 61  LTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPPSF 120

Query: 325 PPESI 329
            P  +
Sbjct: 121 DPSEV 125


>gi|194033308|ref|YP_002000450.1| alpha subunit of RNA polymerase [Oedogonium cardiacum]
 gi|156619050|gb|ABU88203.1| RNA polymerase alpha subunit [Oedogonium cardiacum]
 gi|186968925|gb|ACC97248.1| alpha subunit of RNA polymerase [Oedogonium cardiacum]
          Length = 442

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 59/269 (21%), Positives = 105/269 (39%), Gaps = 70/269 (26%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
                  P   G   T+ NALRR L+S L   A+T++QI  V+H+  +I+G+ E + D++
Sbjct: 109 YGQFYIGPFFIGQGLTIANALRRTLLSELSSLAVTSIQIQDVVHQYQTIQGLQESVFDLL 168

Query: 87  LNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           LN+K I LK        +   +  +GP ++ A D+     I+ ++P+  I  L  D ++ 
Sbjct: 169 LNMKDIVLKSKTTIPVPQIGYLQVQGPCIIKAKDLLLPPFIQCVDPEQYIATLSEDGILN 228

Query: 145 MELTVSKGHGY---------------------------VPAKHHRTE----NDPIGLITI 173
           M+  + +G                              V +  +R      N     + I
Sbjct: 229 MKFVIRQGKHSLTHVTPGYDSFTQKYDQHSYNSTCDTNVHSNKNRNSLSLLNTYSKHLII 288

Query: 174 DALYSPIKKVSYTVESAREGQVLDYDKLSMTI---------------------------- 205
           DA ++P+ KV+Y +E      VLD+D+L                                
Sbjct: 289 DASFNPVIKVNYIIE------VLDFDQLFFEKDSVKLESNDSNNFYCNEEKTLIKKEIII 342

Query: 206 ---DTDGSITGEDSVALASRILQDQLGMF 231
               T+GSI+   ++ ++ + L       
Sbjct: 343 LEIWTNGSISPITALKVSIQKLISVFLKI 371


>gi|119672809|emb|CAK95485.1| RNA polymerase alpha subunit [Lactobacillus mucosae]
          Length = 121

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 49/121 (40%), Positives = 77/121 (63%), Gaps = 2/121 (1%)

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALY 177
           Q   D+ +LNPD  I  +   A + + +T  KG GYVPA  ++       IG + ID++Y
Sbjct: 1   QGDGDVTILNPDLHIATVADGAELHIMMTADKGRGYVPADQNKLRLSGLEIGTLPIDSIY 60

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           +PI++V+YTVE+ R GQ  D+DKL++ + TDGS+T   +++LA++IL + L MF+N  E 
Sbjct: 61  TPIERVNYTVENTRVGQSNDFDKLTLDVWTDGSLTPTAAISLAAKILTEHLEMFVNLTEE 120

Query: 238 K 238
            
Sbjct: 121 A 121


>gi|119662287|emb|CAJ33130.1| RNA polymerase alpha subunit [Lactobacillus buchneri]
          Length = 125

 Score =  136 bits (342), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 48/124 (38%), Positives = 76/124 (61%), Gaps = 2/124 (1%)

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTV 187
           PD  I  +   A   M LT +KG GYV A  ++      PIG++ +D++Y+PI++V+Y V
Sbjct: 1   PDLHIATVAEGATFHMRLTANKGRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERVNYQV 60

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ES R GQ  D+DKL++ I TDGSIT  ++V+LA++IL + L MF++  +  K  +  +  
Sbjct: 61  ESTRVGQRDDFDKLTLDIWTDGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEK 120

Query: 248 KSLP 251
           +   
Sbjct: 121 EETH 124


>gi|119672817|emb|CAK95488.1| RNA polymerase alpha subunit [Lactobacillus johnsonii]
          Length = 115

 Score =  135 bits (341), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 57/114 (50%), Positives = 78/114 (68%)

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             K   I   GP +VTA D++  +DIEVLNPD  IC++     + M + +  G GYVPA 
Sbjct: 1   EEKIAEIDVTGPAIVTAADLKVDSDIEVLNPDQYICSIADGGHLHMNVAIKTGRGYVPAS 60

Query: 160 HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
            ++T++ PIG+I +D+L+SPIKKV+Y VESAR G+  DYDKL++ I TDGSIT 
Sbjct: 61  ENKTDDMPIGVIPVDSLFSPIKKVNYQVESARVGKRDDYDKLTLEIWTDGSITP 114


>gi|324533916|gb|ADY49343.1| DNA-directed RNA polymerase subunit alpha [Ascaris suum]
          Length = 179

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 52/179 (29%), Positives = 100/179 (55%), Gaps = 5/179 (2%)

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           MELT   G GY  A  +R +     +I +D++Y+P+K  SY VE  R G + +YD+L + 
Sbjct: 1   MELTARTGIGYKLADENRGKEKKANVIYVDSIYTPVKVFSYRVEDTRVGDITNYDRLLID 60

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE----VKEDINVKSLPFNPALLKK- 259
           I+T+G+I+ E++++ ++ I+++ + +  N EE   +    ++  + V +   N    +  
Sbjct: 61  IETNGTISPEEALSYSAHIMKEHMMLVENIEEAINQSQVFIESKVEVDTQIVNETDNQNA 120

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           +E L++S R+ N L+   I  + DL  +T+ ++  + N G K++ EI+  L  +G  L 
Sbjct: 121 IETLDISNRAYNGLKKAGIDTIEDLCNKTKKEIAAVDNIGAKTVDEIQKQLQELGYVLK 179


>gi|7524918|ref|NP_045920.1| RNA polymerase alpha chain [Chlorella vulgaris]
 gi|3024560|sp|P56298|RPOA_CHLVU RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|2224512|dbj|BAA57996.1| RNA polymerase alpha subunit [Chlorella vulgaris]
          Length = 278

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 59/268 (22%), Positives = 103/268 (38%), Gaps = 48/268 (17%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE  V  Q              RG A T GN++RR L+S + G  +T V+I G  HE 
Sbjct: 10  SCIESRVQDQGSL-YARFHIGTFFRGQALTFGNSIRRALLSEMPGFLMTDVRIQGATHEF 68

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRV-------TIFKRGPGVVTAGDIQTVNDI 125
           + +  V E + +I+LN+K          +++         +   GPG V A DI+    +
Sbjct: 69  AVLPDVEETVLEILLNLKKTVFVPRIPKNQKFETFQGFGFLKNNGPGKVRAADIRLPETV 128

Query: 126 EVLNPDHVICNLDVDAVVRMEL-------------------------TVSKG-------- 152
           + ++P+  I  L   A + +                               G        
Sbjct: 129 QCVSPEVHIATLTSGAELSLRFNLQFRNFSQLEKREGTFKSKTVAQAKTEDGNVQDTTNE 188

Query: 153 -----HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
                   +  +  + + +    + +D +  P++KV+Y ++S       +Y  + + I T
Sbjct: 189 LPTLEKNSLFFQQLQNKRNSKDQLFLDTVPMPVQKVNYVIKSLNAKNGSEY--IILEIWT 246

Query: 208 DGSITGEDSVALASRILQDQLGMFINFE 235
           DGS+  ++SV  A R L D    F N  
Sbjct: 247 DGSLYPQESVEFALRNLTDLFFQFANIS 274


>gi|207109275|ref|ZP_03243437.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           HPKX_438_CA4C1]
          Length = 176

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 54/179 (30%), Positives = 87/179 (48%), Gaps = 5/179 (2%)

Query: 160 HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
            +  E  P G + +D  ++PIKKV Y +E+       +Y+K+   I+TDG I    +   
Sbjct: 3   ENTRELMPEGYMPLDGSFTPIKKVVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLS 62

Query: 220 ASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIV 279
           A +++  QLG+F   E P   ++   +         L  K+E + LS R  NCL    I 
Sbjct: 63  AVKVMSKQLGVFG--ERPIANMEYSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIK 120

Query: 280 YMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           Y+G+L+  +E ++  + N G+KS  EI   L  +G  +G  L     E  E L K+ E+
Sbjct: 121 YVGELVLMSEEELKGVKNMGKKSYDEIAEKLNDLGYPVGTELS---LEQRESLKKRLEN 176


>gi|154424749|emb|CAL18477.1| RNA polymerase alpha subunit [Streptococcus pyogenes]
          Length = 128

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 54/128 (42%), Positives = 86/128 (67%)

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            IILN+KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +  +     +
Sbjct: 1   QIILNVKGLAVKSYVEDEKIIELEVEGPAEVTAGDILTDSDIELVNPDHYLFTIAEGHSL 60

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
           R  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++
Sbjct: 61  RATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTI 120

Query: 204 TIDTDGSI 211
            I T+G+I
Sbjct: 121 EIMTNGTI 128


>gi|222446775|gb|ACM51431.1| RNA polymerase alpha subunit [Caulerpa filiformis]
          Length = 301

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 55/242 (22%), Positives = 97/242 (40%), Gaps = 21/242 (8%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            + +  +        P       T  N+LRR L+          +QI GV HE SS+ GV
Sbjct: 9   KIEKTGQFYGCFKIGPFQTHSGMTFANSLRRTLLEDNSRYIFDTIQISGVEHEYSSLIGV 68

Query: 79  HEDLTDIILNIKGINLKMSGD--------SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
            E + DII N++ +  ++S            +   +   GPG++ A  I    D   + P
Sbjct: 69  RESVIDIIFNLQKLIFEVSDKVHLVGKDPKPQIAFLNFTGPGILRAQHIHLPKDFHFVYP 128

Query: 131 DHVICNLDVDAVVRMEL-----TVSKGHGYVPAKHHRTENDPI-----GLITIDALYSPI 180
           D  I  L+VD  +  +L        K +  + +K       P        + +D+ +  I
Sbjct: 129 DQYIATLEVDGKLNFKLFFSPKIFQKKYKSLHSKSGSGRQMPPSVLLENYLFLDSDFCSI 188

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR-ILQDQLGMFINFEEPKK 239
           ++V+YT++S    Q    + +   I T+GSI  + ++      IL D        ++  K
Sbjct: 189 ERVNYTIQSGN--QNPKEEFILFEIWTNGSIHPQKAIYQGINEILLDFFPYSFEIQKRNK 246

Query: 240 EV 241
            +
Sbjct: 247 NL 248


>gi|11466523|ref|NP_044772.1| RNA polymerase subunit alpha [Reclinomonas americana]
 gi|7388081|sp|O21260|RPOA_RECAM RecName: Full=DNA-directed RNA polymerase subunit alpha,
           mitochondrial; Short=RNA polymerase subunit alpha;
           AltName: Full=Transcriptase alpha chain
 gi|2258353|gb|AAD11887.1| RNA polymerase subunit alpha [Reclinomonas americana]
          Length = 222

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 60/217 (27%), Positives = 113/217 (52%), Gaps = 12/217 (5%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV--LHEISS 74
            I + + + N   ++  PL + F+ +  N LR+++     G +I  ++I+G+  LH  S 
Sbjct: 11  IIHVLKHDFNSIQVLIGPLEKNFSGSFANLLRKIIFRYTSGVSIIGLKINGIDSLHSYSL 70

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRV--TIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           I GV ED+ +++ N+K + +++    +K +  TI K+GP ++ + DI   ++I++LN D 
Sbjct: 71  IPGVKEDVLNVLNNLKHLLIQIDDYDYKPILLTIQKKGPYIIKSKDIICPSNIKILNDDL 130

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            IC L+ D+ + + L    G GYV + +     +   ++  D  + PIK VSY V S   
Sbjct: 131 YICTLENDSQIDLTLIGDIGCGYVLSTYF---GNRKSIVYSDTNFCPIKHVSYYVRSY-- 185

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
                Y++L   I T+G+      +  A   L+D++ 
Sbjct: 186 ---TTYEELIFYIKTNGTCNPLFVMKNAFSFLKDKIN 219


>gi|119662855|emb|CAJ33220.1| RNA polymerase alpha subunit [Lactobacillus vaginalis]
          Length = 120

 Score =  132 bits (332), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 50/118 (42%), Positives = 77/118 (65%)

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           KG+ LK+  +  K + I   GP  VTAGDI   +D+E+LN D +IC++   A     LTV
Sbjct: 3   KGLALKLYAEEEKTLEIDITGPATVTAGDIIVDSDVEILNKDLIICSVSEGATFHARLTV 62

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M I T
Sbjct: 63  KPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTMEIWT 120


>gi|108773381|ref|YP_635843.1| alpha subunit of RNA polymerase [Oltmannsiellopsis viridis]
 gi|122238319|sp|Q20F02|RPOA_OLTVI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|82541963|gb|ABB82004.1| alpha subunit of RNA polymerase [Oltmannsiellopsis viridis]
          Length = 508

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 48/154 (31%), Positives = 73/154 (47%), Gaps = 2/154 (1%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +       +     P   G   T+GNA RR L+S L G  IT ++IDGV HE S++ GV 
Sbjct: 13  IEHNRSFYSRFQLGPFDLGQGLTVGNAFRRTLLSELSGVGITLIEIDGVCHEYSTLPGVR 72

Query: 80  EDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           E + DI+LN+K + L         +   +   GPGVVTA D++    +  ++PD  I  L
Sbjct: 73  ESVLDILLNLKQLVLTSDTTFTVPQVGYLNFTGPGVVTAKDLKLPVSVYCVDPDQPIATL 132

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI 171
             DA +  +  V +G  Y+        ++    I
Sbjct: 133 SADATLNFKFLVCQGKNYIIQTPVDKFHEYQKKI 166



 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 30/156 (19%), Positives = 56/156 (35%), Gaps = 41/156 (26%)

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           + +D L+ PIKKV+Y ++   +    D + + + I T+GSI    +V  A++ L      
Sbjct: 318 LPVDTLFMPIKKVNYMIDI--DPAEPDRESVVLEIWTNGSIHPRQAVHEAAKQLIHLFSP 375

Query: 231 FI------------------------NFEEPKKEVKEDI---------------NVKSLP 251
           F+                        +  E   E  +D                N +   
Sbjct: 376 FLQTHLVPTTLQSTPYSKAASKTQEFSLNETSTEKVKDELGKVAFGSENNTAALNQQKNL 435

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
                   +  L  S+R+   L+ ENI  + +L++ 
Sbjct: 436 VTAIQTLDIANLNFSLRTFTFLKKENINTVSELVEF 471


>gi|58618634|gb|AAW80815.1| RNA polymerase alpha subunit [Polytrichadelphus purpureus]
          Length = 165

 Score =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 43/163 (26%), Positives = 79/163 (48%), Gaps = 20/163 (12%)

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           + PI+  +Y+V S  E      + L + I T+GSIT ++++  ASR L D    F++ E+
Sbjct: 1   FMPIRNANYSVHSF-ENNNKIQEILFIEIWTNGSITPKEALYEASRSLXDLFIPFLHTEK 59

Query: 237 PKKEVKEDINVKSLPFNPALLKK----------------VEELELSVRSTNCLRGENIVY 280
            +         KS   +                      +++LELS R+ NCL+  N+  
Sbjct: 60  KETIDGLKTEYKSNDMSDFSSFSPLANKSTKEITFKHIFIDQLELSARAYNCLKRVNVHT 119

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           + DL+  ++ D++++ NFG+KS+ ++   L  +     +NLP 
Sbjct: 120 ISDLLNYSQDDLMKIKNFGKKSVEQV---LEALXKXFSINLPK 159


>gi|304323004|ref|YP_003795543.1| alpha subunit of RNA polymerase [Floydiella terrestris]
 gi|270048203|gb|ACZ58498.1| alpha subunit of RNA polymerase [Floydiella terrestris]
          Length = 316

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 48/150 (32%), Positives = 70/150 (46%), Gaps = 2/150 (1%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
                 +         P   G + T+ NALRR L+S + G  +T+V+I+GV HE S+I G
Sbjct: 29  EEKENNQTFYGRFYIGPFEIGQSLTMANALRRSLLSEVPGLGLTSVEIEGVAHEYSTIPG 88

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT--AGDIQTVNDIEVLNPDHVIC 135
           V E + DI+LNIK I  K +    K    + R  G  T  A D+     I+ +NPD  I 
Sbjct: 89  VQETVFDILLNIKNIVFKSTTYLKKAEIGYCRASGPKTLRAKDLLLPAHIQCVNPDQYIA 148

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
            L  D  + M+L + +G  Y+         
Sbjct: 149 TLKSDGTLNMKLKIRQGTHYLVNTPFEQSE 178



 Score = 45.0 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 30/63 (47%)

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           + +D ++ P+ K +Y +E          + + + I T+GSI+   ++  A + L   LG 
Sbjct: 249 LLLDPVFMPVTKANYVLELDERVHNSPKELIVLEIWTNGSISPHGALQTAIKKLVRLLGN 308

Query: 231 FIN 233
             N
Sbjct: 309 VKN 311


>gi|119662799|emb|CAJ33191.1| RNA polymerase alpha subunit [Lactobacillus jensenii]
          Length = 117

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 55/117 (47%), Positives = 79/117 (67%)

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE S++ GV ED+T I+LN+K + LK   D  K V +   GP  VTAGD++  +++ 
Sbjct: 1   GVLHEFSTVPGVREDVTKIVLNLKKLELKSIADEEKIVELDVEGPATVTAGDLKVDSEVT 60

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           VLNPD  IC +     + M++ V  G GYVPA  ++T++ PIG+I +D+L+SPIKKV
Sbjct: 61  VLNPDQYICTVAEGGHLHMQIAVKNGRGYVPASENKTDDMPIGVIPVDSLFSPIKKV 117


>gi|331268154|ref|YP_004347803.1| alpha subunit of RNA polymerase [Chlorella variabilis]
 gi|325296331|gb|ADZ05051.1| alpha subunit of RNA polymerase [Chlorella variabilis]
          Length = 239

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 54/218 (24%), Positives = 98/218 (44%), Gaps = 11/218 (5%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
                     +G A T  NALRR L+S + G  +T + ++G  HE + + GV E + DII
Sbjct: 23  YARFHLGTFIQGQALTFANALRRTLLSEIPGIIMTDILVEGASHEFAILPGVEETVLDII 82

Query: 87  LNIKGINL-----KMSGDSHKRVTIFKRG--PGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           LN+K +       K+    + + T F +   P  ++  D++    ++ + P   I  +  
Sbjct: 83  LNLKKLVFAPSTSKLINLENFQATGFLKSCGPRKLSGADVKLPLTLKCVEPKAHIATITN 142

Query: 140 DAVV--RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
            A    R  L +      V  K +    +    + +D +  PI+KV+Y +++    Q L+
Sbjct: 143 GAEFALRFNLELRNPQQSVTNKIYYPVENKTRKLVLDNVPMPIQKVNYVIKALNGKQGLE 202

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           Y  + + + TDGS+  ++SV  A + L +    F    
Sbjct: 203 Y--IVLEVWTDGSVLPQESVQFALKNLTNFFFQFAEMS 238


>gi|300431274|gb|ADK12602.1| RNA polymerase alpha subunit [Pappostipa vaginata]
          Length = 167

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 45/164 (27%), Positives = 82/164 (50%), Gaps = 20/164 (12%)

Query: 174 DALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           DA+  P++ V+Y++ S   G    ++ L + I T+GS+T ++++  ASR L D    F++
Sbjct: 1   DAVSMPVRNVNYSIFSCGNG-NEKHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLH 59

Query: 234 FEEPKKEVKEDINVKSLP----------------FNPALLKKVEELELSVRSTNCLRGEN 277
            EE     +E+ N  + P                  P     +++LEL  R+ NCL+  N
Sbjct: 60  AEEEGTSFEENKNRFTPPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRAN 119

Query: 278 IVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           I  + DL+ +TE D++R+ +F    + + K +   +   L +NL
Sbjct: 120 IHTLLDLLSKTEEDLMRIDSFR---MEDGKQIWDNLEKHLPINL 160


>gi|323149183|ref|YP_004222012.1| alpha subunit of RNA polymerase [Coccomyxa sp. C-169]
 gi|317467239|gb|ADV29860.1| alpha subunit of RNA polymerase [Coccomyxa sp. C-169]
          Length = 624

 Score =  127 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 44/133 (33%), Positives = 66/133 (49%), Gaps = 2/133 (1%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               +  P   G   T+  ALRR L+S L+G AI+AV+I G  H+ SSI GV E   DI+
Sbjct: 20  YGRFLLGPFKVGQGTTVATALRRTLLSELQGIAISAVEIKGATHQYSSIAGVRESTLDIV 79

Query: 87  LNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           LN+K I L     +       +  +GP    A D++  N I  ++ D  I ++  +  + 
Sbjct: 80  LNLKQIVLTGDVRNGLPAVGYLAVQGPKAARARDLKLPNGIRCVDGDQYIASVSANGSLT 139

Query: 145 MELTVSKGHGYVP 157
           M+  +S G  YV 
Sbjct: 140 MKFVISAGKNYVS 152



 Score = 58.4 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 23/201 (11%), Positives = 63/201 (31%), Gaps = 58/201 (28%)

Query: 165 NDPIGLITIDALYSPIKKVSYT--VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
                 + IDA++ P+ KV+++  ++   +      +++ + I T+GS+    ++  A+ 
Sbjct: 427 EMDSSPLPIDAVFMPVNKVNFSLQIDDQWQEPR---ERVILEIWTNGSLHPRQAIGEAAS 483

Query: 223 ILQDQLGMFINFEEP--------------------------------------------- 237
            L     +    +                                               
Sbjct: 484 YLVYLFSLLRQGDASPAATVQPSPQLRGLGWGTADQRGRTNLQSVEGGGREGEGSSGGMS 543

Query: 238 --KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
             +  +K                 + +L+LS+++   L+   +    D++  +   +  +
Sbjct: 544 SYRATIKHPSPRALPGPGRDRSTDIADLDLSIQAYALLKRAGVHTFRDVMSLS---LNSI 600

Query: 296 ANFGRKS---LVEIKGVLGTM 313
              G  S   L+EI  ++  +
Sbjct: 601 KGGGLASPAILLEIDALIKRL 621


>gi|156619301|gb|ABU88330.1| RNA polymerase alpha subunit [Chlamydomonas moewusii]
          Length = 633

 Score =  126 bits (317), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 44/141 (31%), Positives = 73/141 (51%), Gaps = 2/141 (1%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +             P     + T+ N LRR L+S + G AI +V+I+G  HE SS+ GVH
Sbjct: 13  IENNRSFYGCFELGPFEPSQSLTIANTLRRTLLSEIYGLAIVSVEIEGASHEYSSLPGVH 72

Query: 80  EDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           E + DI+LN+K I LK  +   + +   +  RGPGVVT   ++    I+ ++PD  I  L
Sbjct: 73  ESVLDILLNLKEIVLKKSIKNFTPQIGYLRARGPGVVTGSHLRLPPFIQCVDPDQYIATL 132

Query: 138 DVDAVVRMELTVSKGHGYVPA 158
             +  + ++  V  G+ ++ +
Sbjct: 133 SHNGFLNIKFVVQYGNKWLAS 153



 Score = 36.1 bits (82), Expect = 8.1,   Method: Composition-based stats.
 Identities = 21/120 (17%), Positives = 47/120 (39%), Gaps = 9/120 (7%)

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE----VKEDINVKSLPFNPAL 256
           +++ I T+GS+   D++  A + L        N +           + +++ +L     +
Sbjct: 474 ITLEIWTNGSLHPRDALNQAFKNLIKTFLQLKNVQPYGLNNLLFNSQSLSINALGETLQV 533

Query: 257 LKKVEELELSVRSTN--CLRGENIVYMGDLIQRTEADMLRMANFG--RKSLVEIKGVLGT 312
               EE EL++  TN   L+     + G   +  +  + ++   G  +K  +E    L  
Sbjct: 534 SNISEENELALDPTNKKNLKRGKNDFSGQQSKLEQILLKKIR-MGVFKKDFIETLSPLNE 592


>gi|2951864|gb|AAC05400.1| RNA polymerase alpha subunit [Buchnera aphidicola]
 gi|448401|prf||1917188B RNA polymerase:SUBUNIT=alpha
          Length = 113

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 52/116 (44%), Positives = 75/116 (64%), Gaps = 3/116 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +    +KP  +E   + Q     T +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQNSIIGFLKPRLVE---IEQITATHTKVTLEPLERGFGHTLGNALRRILLSSMPGYAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
            V+IDGVLHE S+ +GV ED+ +I+LN+K + +K+ G     +++ K G G VTA 
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKELAVKVHGKDEVFMSLNKSGIGSVTAS 113


>gi|225466312|ref|XP_002271159.1| PREDICTED: similar to Os04g0237300, partial [Vitis vinifera]
          Length = 274

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 38/130 (29%), Positives = 69/130 (53%), Gaps = 4/130 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRG 57
           I+++ +  +    +++  +    +N        I  PL +G A T+G A+RR L+  + G
Sbjct: 145 IRRSEKVTVSTRTLQWKCVESRVDNKRLCYGRFILSPLIKGQADTIGIAMRRALLGEIEG 204

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
             IT  + + + HE S+I G+ E + +I++N+K I L+ +    +   I  RGPG VTA 
Sbjct: 205 TCITRAKSEKIPHEYSTIVGIQESVHEILMNLKEIVLRSNLYGTRGAFICARGPGYVTAQ 264

Query: 118 DIQTVNDIEV 127
           DI +   +E+
Sbjct: 265 DIISPPSVEI 274


>gi|153805627|ref|YP_001382211.1| alpha subunit of RNA polymerase [Leptosira terrestris]
 gi|134270158|gb|ABO69347.1| alpha subunit of RNA polymerase [Leptosira terrestris]
          Length = 537

 Score =  125 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 41/173 (23%), Positives = 75/173 (43%), Gaps = 2/173 (1%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
                        P   G   T+ N LRR L+S L G AITAV+I    HE  ++ G+ E
Sbjct: 20  ETNRSFYGRFEIGPFAHGQGITVANMLRRTLLSELSGLAITAVEIKEASHEYMTLPGISE 79

Query: 81  DLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            + DIILN+K +  + + D    +   +  +GP ++ A   +  + I+ ++P+  I  L 
Sbjct: 80  SVQDIILNLKQLIFRSNFDLKQPEFGFLSIQGPAIIKASHFRLPSFIKCVDPNQYIATLA 139

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
            +  + +++ + +G  Y             G ++     +  +K  Y   + R
Sbjct: 140 FNGQLNLKVQICQGKNYKFQTPLDLNWPGSGFLSSIHNSNSKQKSFYIKNNTR 192



 Score = 47.3 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 18/82 (21%), Positives = 39/82 (47%), Gaps = 1/82 (1%)

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           L + K       +          ++ +DA+++P+ KV+Y +    E      +++ + I 
Sbjct: 448 LNLDKKQALSIKEIENKLIKTDNILPVDAIFTPVTKVNYLI-CLDEKVKPFKEQILLEIW 506

Query: 207 TDGSITGEDSVALASRILQDQL 228
           T+GSIT + ++  A+  + D L
Sbjct: 507 TNGSITPKTAIYKAADCILDLL 528


>gi|61676006|gb|AAX51668.1| DNA dependent RNA polymerase alpha subunit [Waddlia chondrophila
           WSU 86-1044]
          Length = 174

 Score =  125 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 64/174 (36%), Positives = 93/174 (53%), Gaps = 17/174 (9%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           G  HTLGN+LRR++++SL   AI  V+I+GV HE  +I  + ED+T+IILNIKG  L+  
Sbjct: 1   GMGHTLGNSLRRLMLTSLEAPAIIGVRIEGVAHEYMAIDSIVEDMTNIILNIKGAKLRKL 60

Query: 98  GDSH-----------------KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
                                +      +G   V  GDI      EV+NP+H +  + V 
Sbjct: 61  PMEDTPNARNRGLLTKVLEITQEDIDNGKGQYEVRLGDIVEGGIFEVVNPNHHVFTVTVP 120

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
              +++L VS G GYVP++ H   +     I IDA ++P+K V+Y VE+ R GQ
Sbjct: 121 MQKQVDLRVSFGRGYVPSERHVVNDKSTDEILIDAAFTPVKLVNYHVENTRVGQ 174


>gi|75764945|ref|ZP_00744283.1| DNA-directed RNA polymerase alpha chain [Bacillus thuringiensis
           serovar israelensis ATCC 35646]
 gi|74487569|gb|EAO51447.1| DNA-directed RNA polymerase alpha chain [Bacillus thuringiensis
           serovar israelensis ATCC 35646]
          Length = 119

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 54/107 (50%), Positives = 75/107 (70%), Gaps = 2/107 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDG
Sbjct: 3   EIEKP-KIETVELN-EDAKYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           VLHE S+++GV ED+T IILN+K + LK+  +  K + I  +G G+V
Sbjct: 61  VLHEFSTVEGVVEDVTTIILNLKKLALKIYSEEEKTLEIDVQGEGIV 107


>gi|156099322|ref|XP_001615663.1| DNA-directed RNA polymerase, alpha subunit [Plasmodium vivax SaI-1]
 gi|148804537|gb|EDL45936.1| DNA-directed RNA polymerase, alpha subunit, putative [Plasmodium
           vivax]
          Length = 843

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 53/272 (19%), Positives = 96/272 (35%), Gaps = 34/272 (12%)

Query: 12  PNNIEYIVLGQEEEN------RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           PN+I+        +              PL     HT G  L+ V  + L G AI A++I
Sbjct: 416 PNDIKVEEATDIIKYPQNGRLYQKFYIGPLNITDGHTFGTLLKYVCQTQLYGYAIVAIKI 475

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSG-DSHKRVTIFKRGPGVVTAGDIQTVND 124
              ++E + I  V EDL +I LN+  + +     +    + +  +GP ++ AG I   + 
Sbjct: 476 HN-MNEDTRIDNVQEDLLEIALNLSDVCIYSKEVNIETNIRLIFKGPLMLVAGMIPLPSH 534

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYV------------------PAKHHRTEND 166
           ++V+N +  IC L  D  + + + +  G G+                     K    E  
Sbjct: 535 LQVVNKEQYICTLKEDGHLDISIKIEYGKGHWLTYEKGLYKRELGSDNECMKKRQVKEVV 594

Query: 167 PIGLITIDALYSPIKKVSYTVESA--------REGQVLDYDKLSMTIDTDGSITGEDSVA 218
               + I A +   + V   V           R         L M I TD  +  ++ + 
Sbjct: 595 EKNYMPISASFGTCRMVRMAVHKIATKYWCEDRCEFTDPKQMLVMEIWTDCRMLPKNVLL 654

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
              + ++  L  F        +   D   + +
Sbjct: 655 YGIKNIKKILRKFREMIISDSDFPSDAEDEEM 686


>gi|307702712|ref|ZP_07639664.1| DNA-directed RNA polymerase alpha chain domain protein
           [Streptococcus oralis ATCC 35037]
 gi|307623828|gb|EFO02813.1| DNA-directed RNA polymerase alpha chain domain protein
           [Streptococcus oralis ATCC 35037]
          Length = 115

 Score =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 44/114 (38%), Positives = 69/114 (60%)

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELS 266
           T+G+I  ED++ L++RIL + L +F N  E  K  +      +   +  L + +EEL+LS
Sbjct: 2   TNGTIIPEDALGLSARILTEHLDLFTNLTEIAKSTEVMKEADTESDDRILDRTIEELDLS 61

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           VRS NCL+   I  + DL +++EA+M+++ N GRKSL E+K  L  +GL L   
Sbjct: 62  VRSYNCLKRAGINTVHDLTEKSEAEMMKVRNLGRKSLEEVKLKLIDLGLGLKDK 115


>gi|83858541|ref|ZP_00952063.1| DNA-directed RNA polymerase alpha subunit [Oceanicaulis alexandrii
           HTCC2633]
 gi|83853364|gb|EAP91216.1| DNA-directed RNA polymerase alpha subunit [Oceanicaulis alexandrii
           HTCC2633]
          Length = 81

 Score =  122 bits (306), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 57/80 (71%), Positives = 70/80 (87%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           ++ELELSVRS NCL+ +NIVY+GDLIQ++EA+MLR  NFGRKSL EIK VL  MGL LGM
Sbjct: 1   MDELELSVRSANCLKNDNIVYIGDLIQKSEAEMLRTPNFGRKSLNEIKEVLAQMGLHLGM 60

Query: 320 NLPDWPPESIEELAKKYEDK 339
           + P+WPPE+IE+LAKKYED+
Sbjct: 61  DAPNWPPENIEDLAKKYEDQ 80


>gi|108796892|ref|YP_636190.1| alpha subunit of RNA polymerase [Pseudendoclonium akinetum]
 gi|122245934|sp|Q3ZJ77|RPOA_PSEAK RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|56159590|gb|AAV80614.1| alpha subunit of RNA polymerase [Pseudendoclonium akinetum]
          Length = 577

 Score =  121 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 50/200 (25%), Positives = 89/200 (44%), Gaps = 6/200 (3%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +    +        P   G A T+ NALRR L+S L G +IT V++ G  +E   I GV 
Sbjct: 49  VENLTKFYGRFELGPFAPGQALTVANALRRSLLSQLPGTSITLVEVRGASNEYEIITGVR 108

Query: 80  EDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           E + DI+LN+K I L    +  S +   +   GPGV+ A D++  + I  ++P+  I  L
Sbjct: 109 ESILDILLNLKQIVLTSDFEIFSPQIGFLSVEGPGVIRANDLKLPSFIYAVDPNQYIATL 168

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS-YTVESAREGQVL 196
                + M+  +  G  Y+    +  ++     +++     P+ K +   +        +
Sbjct: 169 SNSGRLNMKFLICCGKNYITYNPN--DSQYFEWLSLLKKSKPLIKSNSPKLNKGNINSEI 226

Query: 197 DYDKLSMTIDTDGSITGEDS 216
           D D  S+    D  I  +++
Sbjct: 227 DSDI-SIDKKNDEVIFFQNA 245



 Score =  112 bits (281), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 50/198 (25%), Positives = 90/198 (45%), Gaps = 33/198 (16%)

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
            Y    +   ++  IG   IDA++ PI +V+Y +ES  + ++   D++ + + T+GSI  
Sbjct: 380 DYDSDFNLDHKSTKIGYFPIDAIFMPINRVNYLIESTEDIKLKIKDRVILEVWTNGSIHP 439

Query: 214 EDSVALASRILQDQLGMF-------------INFEEPKKEVKEDIN-------------- 246
             ++  A++ L                     +FEE + ++K+ I+              
Sbjct: 440 RHAIHKAAKALIQLFLPLQQIRTNLFLISDNSHFEEGQDKIKKRIDNFKKEALLKANPQI 499

Query: 247 ------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                  K    +  L   +  LEL+ R  +CL+  NI  + DLI  ++ D+L + NFGR
Sbjct: 500 QANPQLKKRNFDHRLLELDIANLELTARPYSCLKLANINTIEDLISYSQEDLLSIKNFGR 559

Query: 301 KSLVEIKGVLGTMGLFLG 318
           +SL+E++  L  M L L 
Sbjct: 560 RSLIEVQKALQLMKLTLK 577


>gi|213517416|gb|ACJ50122.1| RNA polymerase alpha subunit [Chlamydomonas reinhardtii]
          Length = 737

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 41/156 (26%), Positives = 75/156 (48%), Gaps = 11/156 (7%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +             P     + TL N LRR L+S L G AIT+++I+GVLH+ S++ G+ 
Sbjct: 28  IENNTNFYGCFYLGPFDESLSQTLANDLRRTLLSELTGLAITSIEIEGVLHKFSTLTGMK 87

Query: 80  EDLTDIILNIKGINLKMSGDSHKRV-----------TIFKRGPGVVTAGDIQTVNDIEVL 128
           E + D+I N++ I L+    S   +            +   GP V+ A D++    ++ +
Sbjct: 88  EPVLDLICNLQNIVLRKETISSTNMNYRATKKTYIGFLSVNGPRVIKAADLKLPAGLQCV 147

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
           +P+  I  L  D  + M+  +++G  Y+  K +  +
Sbjct: 148 DPNQYIATLAEDGFLNMKFNINEGKNYIKQKPYNLD 183



 Score = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 20/62 (32%), Positives = 36/62 (58%)

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +  L++S+RS   L+   I  + DLI+ ++ D+  + N G+KS+ EI+  L  +GL L 
Sbjct: 676 PIGILKISLRSYTALKKAGITTLKDLIKYSKKDLFAIKNLGQKSVFEIEQNLALLGLTLV 735

Query: 319 MN 320
            +
Sbjct: 736 TD 737


>gi|41179033|ref|NP_958389.1| RNA polymerase alpha subunit [Chlamydomonas reinhardtii]
 gi|32699675|sp|Q8HUH2|RPOA_CHLRE RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|23307781|gb|AAN17816.1| RNA polymerase alpha subunit [Chlamydomonas reinhardtii]
 gi|28269756|tpg|DAA00934.1| TPA_inf: RNA polymerase alpha subunit [Chlamydomonas reinhardtii]
          Length = 550

 Score =  121 bits (304), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 41/156 (26%), Positives = 75/156 (48%), Gaps = 11/156 (7%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +             P     + TL N LRR L+S L G AIT+++I+GVLH+ S++ G+ 
Sbjct: 28  IENNTNFYGCFYLGPFDESLSQTLANDLRRTLLSELTGLAITSIEIEGVLHKFSTLTGMK 87

Query: 80  EDLTDIILNIKGINLKMSGDSHKRV-----------TIFKRGPGVVTAGDIQTVNDIEVL 128
           E + D+I N++ I L+    S   +            +   GP V+ A D++    ++ +
Sbjct: 88  EPVLDLICNLQNIVLRKETISSTNMNYRATKKTYIGFLSVNGPRVIKAADLKLPAGLQCV 147

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
           +P+  I  L  D  + M+  +++G  Y+  K +  +
Sbjct: 148 DPNQYIATLAEDGFLNMKFNINEGKNYIKQKPYNLD 183


>gi|154483161|ref|ZP_02025609.1| hypothetical protein EUBVEN_00862 [Eubacterium ventriosum ATCC
           27560]
 gi|149735969|gb|EDM51855.1| hypothetical protein EUBVEN_00862 [Eubacterium ventriosum ATCC
           27560]
          Length = 127

 Score =  120 bits (302), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 57/125 (45%), Positives = 83/125 (66%), Gaps = 4/125 (3%)

Query: 51  LMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFK 108
           ++SSL G+A++ ++IDGVLHE SS+ GV ED+T+I+LNIK + +K +   D  K   I  
Sbjct: 1   MLSSLPGSAVSQIKIDGVLHEFSSVPGVKEDVTEIVLNIKQLEIKNNSTTDEPKVAHIDV 60

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHRTEND 166
            G  VVTA DIQ  +DIE+LNPD VI  L+  A   + MEL ++KG GYV ++ ++ ++ 
Sbjct: 61  TGDCVVTAADIQVDSDIEILNPDLVIATLNGGADSKLSMELIITKGRGYVSSEKNKNDSL 120

Query: 167 PIGLI 171
           PI   
Sbjct: 121 PIRCY 125


>gi|67968322|dbj|BAE00222.1| RNA polymerase alpha chain like [Selaginella uncinata]
          Length = 245

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 53/221 (23%), Positives = 79/221 (35%), Gaps = 6/221 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV-QIDGVLHE 71
             IE   +  E    +  I  P   G A TLG A+RR       GA  T     + + HE
Sbjct: 14  RCIEPK-VDNERPCHSRSIIPPPKIGQASTLGIAMRRAPPGESEGACTTPAGSPERINHE 72

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
             +I GV E + +  +N+K I L     + +   I   GPG V A D    + I ++ P 
Sbjct: 73  YPAIAGVRESVHETSMNLKEIALTAHPSAAQEAHIPIVGPGKVAARDTVPPSSIGIIYPA 132

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
                +           V  G GY             G    DA+  PI+  +Y++    
Sbjct: 133 QHAATVTRKIRSSTGSRVEGGCGYR---RRNMVEYQKGSPPPDAVSMPIRNANYSIHRLE 189

Query: 192 -EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
                +  +       TDGS T  ++   ASR   +     
Sbjct: 190 SHSGGIMKEMPPPEARTDGSPTPGEATYEASRDSANLFSPV 230


>gi|108773091|ref|YP_636000.1| alpha subunit of RNA polymerase [Scenedesmus obliquus]
 gi|115311625|sp|P19587|RPOA_SCEOB RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|88696657|gb|ABD48283.1| alpha subunit of RNA polymerase [Scenedesmus obliquus]
          Length = 478

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 45/135 (33%), Positives = 72/135 (53%), Gaps = 2/135 (1%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
            +L             P     + T+ NALRR L++ L   AIT ++I+GV HE S++ G
Sbjct: 15  CILENPRSFYGSFSLGPFKNSQSLTVANALRRTLLAELSNIAITHLEIEGVTHEYSTLVG 74

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVT--IFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
           V E + D++LN KGI LK +    K +   +  RGPGVV A D++    I+ ++PD  I 
Sbjct: 75  VRESVLDLLLNFKGIALKNTSPVTKPLFGYLQVRGPGVVRASDLKFPPMIQCVDPDQYIA 134

Query: 136 NLDVDAVVRMELTVS 150
            L+ +  + ++  +S
Sbjct: 135 TLNENGKLILKFRIS 149



 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 38/228 (16%), Positives = 77/228 (33%), Gaps = 56/228 (24%)

Query: 147 LTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKVSYTVESA-REGQVLDYDKLS 202
             + K         +   +        + +D L++PI KV+Y +E+     + +  + + 
Sbjct: 244 FRIEKNQQDFNKNKNGNFDSQKNKTNSLWVDPLFNPILKVNYIIETIEPMQKNIPNEIVF 303

Query: 203 MTIDTDGSITGEDSVALASRILQDQLG-------------------------MFINFE-- 235
           + + T+GSI    +   A   L+                              F  FE  
Sbjct: 304 IELWTNGSIHPRKAFYTALLYLKTMFDKLDCMRLLNYEFSNTMLESEKTSTKFFKTFEYD 363

Query: 236 -----------------------EPKKEVKEDI--NVKSLPFNPALLKKVEELELSVRST 270
                                  E  ++V++D   N+K+   N      +  L L  R T
Sbjct: 364 FRFYNSREDKTMKSFTPEKFFLPEEIEDVEKDYLLNLKNQADNTWNDLPLTNLNLPYRIT 423

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
             L   N   +GDL++ +  ++ +++  G   +  ++     +GL LG
Sbjct: 424 KILAKNNFFVVGDLLKISPNELKKLSGIGNYCVFILQKRFEKLGLKLG 471


>gi|55274199|gb|AAV48981.1| DNA-directed RNA polymerase [Leuconostoc pseudomesenteroides]
          Length = 101

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 47/103 (45%), Positives = 65/103 (63%), Gaps = 4/103 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E+      + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDG
Sbjct: 3   EFEKPN----IHNIEEDARYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG 110
           V+HE S++ GV ED+T IILN+K + L +  D  + + I  + 
Sbjct: 59  VVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDVQE 101


>gi|313616947|gb|EFR89580.1| DNA-directed RNA polymerase subunit alpha [Listeria innocua FSL
           S4-378]
 gi|313622258|gb|EFR92767.1| DNA-directed RNA polymerase subunit alpha [Listeria innocua FSL
           J1-023]
          Length = 107

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 37/103 (35%), Positives = 62/103 (60%)

Query: 215 DSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLR 274
           ++V+L ++IL + L +F+N  +  ++ +  I  +       L   +EEL+LSVRS NCL+
Sbjct: 1   EAVSLGAKILSEHLSIFVNLTDEAQKAEIMIEKEESHKEKVLEMTIEELDLSVRSYNCLK 60

Query: 275 GENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
              I  + +L  ++E DM+++ N GRKSL E+K  L  +GL L
Sbjct: 61  RAGINTVQELADKSEDDMMKVRNLGRKSLEEVKVKLADLGLSL 103


>gi|221058981|ref|XP_002260136.1| DNA-directed RNA polymerase, alpha subunit,truncated [Plasmodium
           knowlesi strain H]
 gi|193810209|emb|CAQ41403.1| DNA-directed RNA polymerase, alpha subunit,truncated, putative
           [Plasmodium knowlesi strain H]
          Length = 805

 Score =  118 bits (295), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 52/271 (19%), Positives = 96/271 (35%), Gaps = 34/271 (12%)

Query: 12  PNNIEYIVLGQEEEN------RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           PN+I+        +              PL     HT G  L+ V  + + G AI A+++
Sbjct: 393 PNDIKVEEATDIIKYPQNGRLYQKFYIGPLNITDGHTFGTLLKYVCQTQVYGYAIVAIKV 452

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSG-DSHKRVTIFKRGPGVVTAGDIQTVND 124
              ++E + I  V EDL +I LN+  + +     +    V +  +GP +V AG I   + 
Sbjct: 453 HN-MNEDTRIDNVQEDLLEIALNLSDVCIYSKEINIETNVRLIFKGPLMVVAGMIPLPSH 511

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYV------------------PAKHHRTEND 166
           ++V+N +  IC L  D  + + + +  G G+                     K    E  
Sbjct: 512 LQVVNKEQYICTLKEDGYLDISIKIEYGKGHWLTYEKGLYKREVGSDNECMKKRQVKEVV 571

Query: 167 PIGLITIDALYSPIKKVSYTVESA--------REGQVLDYDKLSMTIDTDGSITGEDSVA 218
               + I A +   + V   V           R         L M I +D  +  ++ + 
Sbjct: 572 EKNYMPISASFGSCRMVRMAVHKIATKYWCEDRCEFTDPKQMLVMEIWSDCRMLPKNVLL 631

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              + ++  L  F        +   D+  + 
Sbjct: 632 YGIKNIKKILRKFREMIISDTDFPSDVEDEE 662


>gi|208751315|gb|ACI31270.1| RNA polymerase alpha subunit [Volvox carteri]
 gi|261888190|gb|ACY06045.1| alpha subunit of RNA polymerase [Volvox carteri f. nagariensis]
          Length = 768

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 41/156 (26%), Positives = 78/156 (50%), Gaps = 11/156 (7%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +             P     + T+ N +RR L+S L   AIT+++I+G+LH+ SS+ G+ 
Sbjct: 28  IENNTSFYGCFYLGPFDDSLSQTIANDIRRTLLSELTSLAITSIEIEGILHKYSSLPGMK 87

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIF-----------KRGPGVVTAGDIQTVNDIEVL 128
           E + D+I N++ I LK    S   +T+              GP V+ A D++  + ++ +
Sbjct: 88  ETVLDLICNLQSIVLKKQEISFTNITLRSTKKTYRGFLNVSGPRVIKAMDLKLPSGLQCV 147

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
           +P+  I  L  D ++ M+L +++G  ++  K H  +
Sbjct: 148 DPNQYIATLAEDGLLNMKLNINEGKNFIKQKPHNLD 183



 Score = 60.7 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 23/73 (31%), Positives = 41/73 (56%)

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           N        AL   +  L++S+R+   L+   I+ + DL++ ++ D+L++ N G+KSLV 
Sbjct: 693 NQMKFYSQAALKAPIGILKISLRAYTALKKAGILTINDLVKCSKNDLLKINNLGKKSLVL 752

Query: 306 IKGVLGTMGLFLG 318
           I+  L  +GL L 
Sbjct: 753 IETSLSYLGLTLK 765


>gi|119662813|emb|CAJ33198.1| RNA polymerase alpha subunit [Lactobacillus vaccinostercus]
          Length = 114

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 49/114 (42%), Positives = 77/114 (67%), Gaps = 2/114 (1%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K I+LK+  +  K + I  +GP  VTAGDI+   D+EV
Sbjct: 1   VLHEFSTVEGVTEDVTQIILNMKQISLKIDSEEDKTLEIDVKGPAAVTAGDIEADGDVEV 60

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSP 179
           LNP+  I  +   A + +++T + G GYV A  ++   ++ PIG++ ID++Y+P
Sbjct: 61  LNPELHIATVADGAELHIQMTANTGRGYVSADDNKARMDDLPIGVLPIDSIYTP 114


>gi|152218428|gb|ABS31648.1| RpoA [Francisella noatunensis subsp. noatunensis]
 gi|152218430|gb|ABS31649.1| RpoA [Francisella noatunensis subsp. noatunensis]
 gi|152218432|gb|ABS31650.1| RpoA [Francisella noatunensis subsp. noatunensis]
 gi|152218434|gb|ABS31651.1| RpoA [Francisella noatunensis subsp. noatunensis]
 gi|152218436|gb|ABS31652.1| RpoA [Francisella noatunensis subsp. noatunensis]
 gi|152218438|gb|ABS31653.1| RpoA [Francisella noatunensis subsp. noatunensis]
 gi|152218440|gb|ABS31654.1| RpoA [Francisella noatunensis subsp. noatunensis]
          Length = 167

 Score =  116 bits (290), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 54/171 (31%), Positives = 92/171 (53%), Gaps = 6/171 (3%)

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            IE++N D  I  L  +    +  TVS G          TE + +G I +DA ++PIK+V
Sbjct: 3   GIEIINKDQPIATLTNEREFSLVATVSVGRNVGILSALPTELEKVGDIAVDADFNPIKRV 62

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           ++ +           + L + + T+G+I    +V  A     +Q+ +F++   P      
Sbjct: 63  AFEIFDNGAS-----ETLEVFVKTNGTIEPLAAVTKALEYFCEQISVFVSLRVPSNGKTG 117

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           D  + S   +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ +++
Sbjct: 118 DALLDSN-IDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMK 167


>gi|152218442|gb|ABS31655.1| RpoA [Francisella philomiragia]
 gi|152218444|gb|ABS31656.1| RpoA [Francisella philomiragia]
 gi|152218446|gb|ABS31657.1| RpoA [Francisella philomiragia]
          Length = 167

 Score =  115 bits (289), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 53/171 (30%), Positives = 92/171 (53%), Gaps = 6/171 (3%)

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
            IE++N D  I  L  +    +  TVS G          TE + +G I +D+ ++PIK+V
Sbjct: 3   GIEIINKDQPIATLTNEREFSLTATVSVGRNVGILSALPTELEKVGDIAVDSDFNPIKRV 62

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           ++ +           + L + + T+G+I    +V  A     +Q+ +F++   P      
Sbjct: 63  AFEIFDNGTN-----ETLEVFVKTNGTIEPLVAVTKALEYFCEQISVFVSLRVPSNGKTG 117

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           D  + S   +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ +++
Sbjct: 118 DALLDSN-IDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMK 167


>gi|221060799|ref|XP_002261969.1| dna-directed rna polymerase alpha chain [Plasmodium knowlesi strain
           H]
 gi|193811119|emb|CAQ41847.1| dna-directed rna polymerase alpha chain,putative [Plasmodium
           knowlesi strain H]
          Length = 674

 Score =  115 bits (288), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 50/244 (20%), Positives = 96/244 (39%), Gaps = 9/244 (3%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
            T           +    NA RRV M  L+G  +TA++I  + HE   I GV E+  D+ 
Sbjct: 304 YTYFFMHSHEVELSPIFLNAFRRVAMKHLKGGRVTALRIPNMKHEFYCIVGVRENFFDLA 363

Query: 87  LNIKGINLK-----MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
            N++ I  K     +  D++       +GP +V AG +Q    IE++N +  IC++   +
Sbjct: 364 QNLRQITFKNVPENIDMDNYITGKFRIKGPMIVVAGHMQLPKGIEIVNKNQYICSVSAGS 423

Query: 142 VVRMELTVSKGHGYVPAK----HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
            + M++ +     YV  +        +      I   +  +P++   +  +         
Sbjct: 424 YLEMDVKIESIEEYVMPEYGSQSRNRDICKDNFIHFSSSCTPVEYFGFMGQRRGINLDTL 483

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
            +   + + TDGSIT + ++      + +      N         +D +V+    NP   
Sbjct: 484 GEINIVEMHTDGSITPKSALLKTIDYISENFQYMENALYNNCHTCDDGSVEEEFRNPEFY 543

Query: 258 KKVE 261
              +
Sbjct: 544 MDKD 547


>gi|152218448|gb|ABS31658.1| RpoA [Francisella philomiragia subsp. philomiragia ATCC 25015]
          Length = 167

 Score =  115 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 53/170 (31%), Positives = 92/170 (54%), Gaps = 6/170 (3%)

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           IE++N D  I  L  +    +  TVS G          TE + +G I +D+ ++PIK+V+
Sbjct: 4   IEIINKDQPIATLTNERKFSLTATVSVGRNVGILSALPTELEKVGDIAVDSDFNPIKRVA 63

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           + +           + L + + T+G+I    +V  A     +Q+ +F++   P      D
Sbjct: 64  FEIFDNGTN-----ETLEVFVKTNGTIEPLVAVTKALEYFCEQISVFVSLRVPSNGKTGD 118

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
             + S   +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ +++
Sbjct: 119 ALLDSN-IDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMK 167


>gi|246880788|gb|ACS95100.1| alpha subunit of RNA polymerase [Dunaliella salina]
          Length = 547

 Score =  115 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 43/165 (26%), Positives = 71/165 (43%), Gaps = 25/165 (15%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +   +             G + T+ NALRR L+S   G AI +V+ID V HE S++ GV 
Sbjct: 6   IENNKSFYGCFYLGSFDSGQSITVANALRRSLLSDCTGLAIISVKIDAVQHEYSTLPGVR 65

Query: 80  EDLTDIILNIKGINLK-------------------------MSGDSHKRVTIFKRGPGVV 114
           + + DI+LN K I LK                          +        +  +GPG++
Sbjct: 66  DSVLDILLNFKEIVLKKVKNPFGGPNGYKNKGLSSVYDKVGSTFFKPVVGYLKVKGPGII 125

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
            A D++    I+ ++P+  I  L  D V+ ++  + +G  Y   K
Sbjct: 126 RAKDLRLPPFIQCVDPNQYIATLAEDGVLNVKFVIMEGKSYYVQK 170


>gi|228311784|pdb|2JZB|A Chain A, Solution Structure Of The Complex Between E.Coli Nusa-Ar2
           And Rnap-Actd
          Length = 99

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 46/90 (51%), Positives = 65/90 (72%)

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           + ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+K
Sbjct: 9   QPEVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKK 68

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           SL EIK VL + GL LGM L +WPP SI +
Sbjct: 69  SLTEIKDVLASRGLSLGMRLENWPPASIAD 98


>gi|70945266|ref|XP_742471.1| DNA-directed RNA polymerase alpha chain [Plasmodium chabaudi
           chabaudi]
 gi|56521474|emb|CAH79423.1| DNA-directed RNA polymerase alpha chain, putative [Plasmodium
           chabaudi chabaudi]
          Length = 529

 Score =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 52/244 (21%), Positives = 97/244 (39%), Gaps = 9/244 (3%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
            T           +    NA RRV +  L+G   TA++I G+ HE   I GV E+  D+ 
Sbjct: 237 YTYFFMHSHEVELSPIFLNAFRRVAIKHLKGGRATALRIPGMKHEYYCIVGVRENFFDLS 296

Query: 87  LNIKGINLKM---SGDSHKRVTIFKRGPGVVT--AGDIQTVNDIEVLNPDHVICNLDVDA 141
            N++ I  K    + D +  +T   R  G +   AG +Q   +IE++N +  IC +   +
Sbjct: 297 QNLRQITFKNVPENADMNNYITGKFRIKGPMIVVAGHMQLPKNIEIINKNQYICYVAAGS 356

Query: 142 VVRMELTVSKGHGYVPAK----HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
            + M++ +     YV  +        +      I   +  +P++   +T +       + 
Sbjct: 357 YLEMDVKIESIEEYVMPEYGSQSRNRDICKDNFIHFCSSCTPVEHFGFTGQRRGINLDVL 416

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
            +   + + TDGSIT + ++      + +      N         ED +++    NP   
Sbjct: 417 GEINIVEMHTDGSITPKTALLKTIDYMSENFQYMENALHNNCHSCEDGSLEEEFRNPEFY 476

Query: 258 KKVE 261
              E
Sbjct: 477 MDKE 480


>gi|83314615|ref|XP_730437.1| DNA-directed RNA polymerase subunit alpha [Plasmodium yoelii yoelii
           str. 17XNL]
 gi|23490159|gb|EAA22002.1| DNA-directed RNA polymerase alpha chain [Plasmodium yoelii yoelii]
          Length = 656

 Score =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 54/245 (22%), Positives = 100/245 (40%), Gaps = 9/245 (3%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           + T           +    NA RRV +  L+G  +TA++I G+ HE   I GV E+  D+
Sbjct: 285 SYTYFFMHSHEVELSPIFLNAFRRVAIKHLKGGRVTALRIPGMKHEYYCIVGVRENFFDL 344

Query: 86  ILNIKGINLK-MSGDSHKRVTI----FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
             N++ I  K +  D+     I      +GP +V AG +Q   +IE++N +  IC +   
Sbjct: 345 SQNLRQITFKNVPEDADMNNYIIGKFRIKGPMIVVAGHMQLPKNIEIINKNQYICYVAAG 404

Query: 141 AVVRMELTVSKGHGYVPAK----HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           + + M++ +     YV  +        +      I   +  +P++   +T +       +
Sbjct: 405 SYLEMDVKIESIEEYVMPEYGSQSRNRDICKDNFIHFCSSCTPVEYFGFTGQRRGINLDI 464

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
             +   + + TDGSIT + ++      + +      N         ED +V+    NP  
Sbjct: 465 LGEINIVEMHTDGSITPKTALLKTIDYMSENFQYIENALHNNCHSCEDGSVEEEFRNPEF 524

Query: 257 LKKVE 261
               E
Sbjct: 525 YMDKE 529


>gi|56554702|pdb|1XS9|D Chain D, A Model Of The Ternary Complex Formed Between Mara, The
           Alpha-Ctd Of Rna Polymerase And Dna
          Length = 84

 Score =  113 bits (282), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 46/81 (56%), Positives = 61/81 (75%)

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
            F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL
Sbjct: 3   HFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVL 62

Query: 311 GTMGLFLGMNLPDWPPESIEE 331
            + GL LGM L +WPP SI +
Sbjct: 63  ASRGLSLGMRLENWPPASIAD 83


>gi|156102625|ref|XP_001617005.1| hypothetical protein [Plasmodium vivax SaI-1]
 gi|148805879|gb|EDL47278.1| hypothetical protein, conserved [Plasmodium vivax]
          Length = 668

 Score =  112 bits (281), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 49/244 (20%), Positives = 94/244 (38%), Gaps = 9/244 (3%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
            T           +    NA RRV +  L+G  +TA++I  + HE   I GV E+  D+ 
Sbjct: 298 YTYFFMHSHEVELSPIFLNAFRRVAIKHLKGGRVTALRIPNMKHEFYCIVGVRENFFDLA 357

Query: 87  LNIKGINLKM-----SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
            N++ I  K        D++       +GP +V AG +Q    IE++N +  IC++   +
Sbjct: 358 QNLRHITFKNVPEEADIDNYITGKFRIKGPMIVVAGHMQLPKGIEIVNKNQYICSVSAGS 417

Query: 142 VVRMELTVSKGHGYVPAK----HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
            + M++ +     YV  +        +      I   +  +P++   +  +         
Sbjct: 418 YLEMDVKIESIEEYVMPEYGSQSRNRDICKDNFIHFSSSCTPVEYFGFMGQRRGINLDTL 477

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
            +   + + TDGSIT + ++      + +      N         +D  V+    NP   
Sbjct: 478 GEINIVEMHTDGSITPKSALLKTIDYISENFQYMENALYNNCHTCDDGTVQEEFRNPEFY 537

Query: 258 KKVE 261
              +
Sbjct: 538 MDKD 541


>gi|68076655|ref|XP_680247.1| DNA-directed RNA polymerase alpha chain [Plasmodium berghei strain
           ANKA]
 gi|56501153|emb|CAH98242.1| DNA-directed RNA polymerase alpha chain, putative [Plasmodium
           berghei]
          Length = 573

 Score =  112 bits (280), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 52/244 (21%), Positives = 98/244 (40%), Gaps = 8/244 (3%)

Query: 26  NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI 85
           + T           +    NA RRV +  L+G  +TA++I G+ HE   I GV E+  D+
Sbjct: 203 SYTYFFMHSHEVELSPIFLNAFRRVAIKHLKGGRVTALRIPGMKHEYYCIVGVRENFFDL 262

Query: 86  ILNIKGINLKM---SGDSHKRVTIFKRGPGVVT--AGDIQTVNDIEVLNPDHVICNLDVD 140
             N++ I  K    + D +  +    R  G +   AG +Q   +IE++N +  IC +   
Sbjct: 263 SQNLRQITFKNVPENADMNNYIIGKFRIKGPMIVVAGHMQLPKNIEIINKNQYICYVAAG 322

Query: 141 AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + + M++ +     YV  +     R  +         +  +P++   +T +       + 
Sbjct: 323 SYLEMDVKIESIEEYVMPEYGSQSRNRDICKDNFIFCSSCTPVEYFGFTGQRRGINLDIL 382

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
            +   + + TDGSIT + ++      + +      N         ED +V+    NP   
Sbjct: 383 GEINIVEMHTDGSITPKTALLKTIDYMSENFQYIENALHNNCHSCEDGSVEEEFRNPEFY 442

Query: 258 KKVE 261
              E
Sbjct: 443 MDKE 446


>gi|68075539|ref|XP_679688.1| DNA-directed RNA polymerase, alpha subunit, truncated, [Plasmodium
           berghei strain ANKA]
 gi|56500488|emb|CAH98184.1| DNA-directed RNA polymerase, alpha subunit, truncated, putative
           [Plasmodium berghei]
          Length = 727

 Score =  111 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 45/235 (19%), Positives = 88/235 (37%), Gaps = 28/235 (11%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
                  PL     HT G+ ++ V  S + G AI  ++I   ++E + I+   EDL +I 
Sbjct: 336 YQKFYIGPLNITDGHTFGSLIKYVCQSQIYGYAIVGIKIHN-MNEDTKIENTQEDLLEIA 394

Query: 87  LNIKGINLKMSG-DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           LN+  + +     +    + +  +GP ++ AG I   + ++V+N +  IC +  +  + +
Sbjct: 395 LNLSDVCIYSKEINIETNIRLIFKGPLMLVAGMIPLPSHLKVVNKEQYICTIKENGYIDI 454

Query: 146 ELTVSKGHGYVPAKHHRTENDPIG------------------LITIDALYSPIKKVSYTV 187
            + +  G G+            IG                     + A +SP + V  TV
Sbjct: 455 SIKIEYGKGHWITYDKGLYKREIGSDNECMKKRQIKEVVNNNYTPLTASFSPCRMVRITV 514

Query: 188 ESA--------REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
                      R         L + I TD  +  ++ +    + ++  L  F   
Sbjct: 515 HKIATKYWCEDRCEFTDPKQMLVVEIWTDPRMLPKNVLLYGIKNIKKILNKFREM 569


>gi|24158833|pdb|1LB2|B Chain B, Structure Of The E. Coli Alpha C-Terminal Domain Of Rna
           Polymerase In Complex With Cap And Dna
 gi|24158834|pdb|1LB2|E Chain E, Structure Of The E. Coli Alpha C-Terminal Domain Of Rna
           Polymerase In Complex With Cap And Dna
          Length = 84

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 46/83 (55%), Positives = 61/83 (73%)

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
              F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK 
Sbjct: 1   KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKD 60

Query: 309 VLGTMGLFLGMNLPDWPPESIEE 331
           VL + GL LGM L +WPP SI +
Sbjct: 61  VLASRGLSLGMRLENWPPASIAD 83


>gi|157830665|pdb|1COO|A Chain A, The Cooh-Terminal Domain Of Rna Polymerase Alpha Subunit
          Length = 98

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 46/80 (57%), Positives = 61/80 (76%)

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
           F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL 
Sbjct: 18  FDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLA 77

Query: 312 TMGLFLGMNLPDWPPESIEE 331
           + GL LGM L +WPP SI +
Sbjct: 78  SRGLSLGMRLENWPPASIAD 97


>gi|254701950|ref|ZP_05163778.1| DNA-directed RNA polymerase subunit alpha [Brucella suis bv. 5
          str. 513]
          Length = 70

 Score =  110 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 50/72 (69%), Positives = 57/72 (79%), Gaps = 2/72 (2%)

Query: 1  MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
          MIQKNWQELIKPN +++I  G        ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1  MIQKNWQELIKPNKVDFITHGSRTH--ATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61 TAVQIDGVLHEI 72
          TAVQIDGVLHE 
Sbjct: 59 TAVQIDGVLHEF 70


>gi|124512894|ref|XP_001349803.1| DNA-directed RNA polymerase alpha chain, putative [Plasmodium
           falciparum 3D7]
 gi|23615220|emb|CAD52210.1| DNA-directed RNA polymerase alpha chain, putative [Plasmodium
           falciparum 3D7]
          Length = 619

 Score =  110 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 47/226 (20%), Positives = 96/226 (42%), Gaps = 9/226 (3%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLK-----MSGD 99
           NA RRV +  L+G  +TA++I  + HE   I GV E+  D+  N++ I  K     +  D
Sbjct: 267 NAFRRVAIKHLKGGRVTALRIPNMKHEFYCIVGVRENFFDLAQNLRQITFKNVPEDVDMD 326

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
           ++       +GP +V AG +Q   ++E++N +  IC++   + + M++ +     YV  +
Sbjct: 327 NYMIGKFRIKGPMIVVAGHMQLPKNVEIVNRNQYICSVAAGSYLSMDVKIESIEEYVMPE 386

Query: 160 ----HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
                   +      I   +  +P++   +T +          +   + + TDGSIT + 
Sbjct: 387 YGSQSRNRDICKDNFIHFSSSCTPVEHFVFTGQRRGINLDTLGEINIVEMHTDGSITPKS 446

Query: 216 SVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           ++      + +      N       + +D ++     NP      +
Sbjct: 447 ALLKTIDYISENFQYIENALYNNCHICDDGSLDEEFRNPEFYMDKD 492


>gi|156083567|ref|XP_001609267.1| DNA-directed RNA polymerase, alpha subunit [Babesia bovis T2Bo]
 gi|154796518|gb|EDO05699.1| DNA-directed RNA polymerase, alpha subunit, putative [Babesia
           bovis]
          Length = 676

 Score =  109 bits (272), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 55/296 (18%), Positives = 111/296 (37%), Gaps = 42/296 (14%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
                  P P     TLG+ L+ + +S   G  + AV++   ++E ++I GV +DL +I 
Sbjct: 257 YQKFYMGPYPITMGWTLGSLLKVLALSRSPGHGVVAVKVHN-MNEDTTIDGVTDDLMNIA 315

Query: 87  LNIKGINL-KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           LN+  + L  +      RV    +GP  V AG I+  + +++  PD  I N++    + +
Sbjct: 316 LNLNEVALETLEPGGEARVRTVIKGPAQVCAGSIEWPSFVKIATPDAYITNVEEGGTLDI 375

Query: 146 ELTVSKGHGYVPAK------------------HHRTENDPIGLITIDALYSPIKKVSYTV 187
           E+ +  G G   A                       E D      I   +   + V   V
Sbjct: 376 EIKIEWGRGLWLADYKGLYRHEDAADAVCMRRRRIKEVDEEDFHPITTFFGGCRMVRLAV 435

Query: 188 ESAREGQVLD---------YDKLSMTIDTDGSITGEDS----VALASRILQDQLGMFINF 234
                G+  D          ++L + + TD S T + +    ++ +   +++     I  
Sbjct: 436 HKL-IGERWDLITSSCPDPREQLVVEVWTDRSTTPKAALEFGLSESIAWIRELKRQLIQD 494

Query: 235 EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTN--------CLRGENIVYMG 282
            +   E ++  +          L++ +++     + N         L+  +  Y+G
Sbjct: 495 ADFDGEDEQLRDTWEKIDKYKSLQQRQQMMGGPPTYNLHDTNAIPGLKESDCQYVG 550


>gi|153820406|ref|ZP_01973073.1| DNA-directed RNA polymerase alpha chain [Vibrio cholerae NCTC 8457]
 gi|126509049|gb|EAZ71643.1| DNA-directed RNA polymerase alpha chain [Vibrio cholerae NCTC 8457]
          Length = 75

 Score =  108 bits (271), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 43/74 (58%), Positives = 56/74 (75%)

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL L
Sbjct: 1   RPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL 60

Query: 318 GMNLPDWPPESIEE 331
           GM L +WPP SI E
Sbjct: 61  GMRLENWPPASIAE 74


>gi|82540505|ref|XP_724565.1| DNA-directed RNA polymerase [Plasmodium yoelii yoelii str. 17XNL]
 gi|23479250|gb|EAA16130.1| DNA-directed RNA polymerase [Plasmodium yoelii yoelii]
          Length = 803

 Score =  106 bits (265), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 45/235 (19%), Positives = 88/235 (37%), Gaps = 28/235 (11%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
                  PL     HT G+ ++ V  S + G AI  ++I   ++E + I+   EDL +I 
Sbjct: 412 YQKFYIGPLNITDGHTFGSLIKYVCQSQIYGYAIVGIKIHN-MNEDTKIENTQEDLLEIA 470

Query: 87  LNIKGINLKMSG-DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           LN+  + +     +    + +  +GP ++ AG I   + ++V+N +  IC +  +  + +
Sbjct: 471 LNLSDVCIYSKEINIETNIRLIFKGPLMLVAGMIPLPSHLKVVNKEQYICTIKENGYIDI 530

Query: 146 ELTVSKGHGYVPAKHHRTENDPIG------------------LITIDALYSPIKKVSYTV 187
            + +  G G+            IG                     + A +SP + V  TV
Sbjct: 531 SIKIEYGKGHWITYDKGLYKREIGSDNECMKKRQIKEVVNNNYTPLTASFSPCRMVRTTV 590

Query: 188 ESA--------REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
                      R         L + I TD  +  ++ +    + ++  L  F   
Sbjct: 591 HKIATKYWCEDRCEFTDPKQMLVVEIWTDPRMLPKNVLLYGIKNIKKILKKFREM 645


>gi|150187027|emb|CAK30154.1| RNA polymerase alpha subunit [Streptococcus uberis]
          Length = 101

 Score =  106 bits (264), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 41/101 (40%), Positives = 65/101 (64%)

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           +I GV ED+  IILNIKG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH 
Sbjct: 1   TIPGVREDVMQIILNIKGLAVKSYVEDEKMIELDVEGPAEVTAGDILTDSDIELVNPDHY 60

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITID 174
           +  +     ++  +TV+K  GYVPA+ ++ ++ P+G + +D
Sbjct: 61  LFTIAEGHSLKATMTVAKKRGYVPAEGNKKDDAPVGTLAVD 101


>gi|85717255|ref|ZP_01048210.1| DNA-directed RNA polymerase alpha subunit [Nitrobacter sp. Nb-311A]
 gi|85695896|gb|EAQ33799.1| DNA-directed RNA polymerase alpha subunit [Nitrobacter sp. Nb-311A]
          Length = 317

 Score =  106 bits (264), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 38/69 (55%), Positives = 54/69 (78%)

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
           L++V++LELSVRS NCL+ + I ++G+L+Q++E +MLR  NFGR+SL EIK +L   GL 
Sbjct: 241 LERVDDLELSVRSANCLKKDGINHVGELVQKSEDEMLRTPNFGRRSLNEIKDLLAASGLH 300

Query: 317 LGMNLPDWP 325
           LGM+L  WP
Sbjct: 301 LGMDLSGWP 309



 Score =  104 bits (259), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 36/78 (46%), Positives = 62/78 (79%)

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + ++ELELSVR++ CL+ +++  +GD  + +EA++LR+ NFGRKSL E+K +LG +GL L
Sbjct: 159 RSIDELELSVRTSLCLKNDDVRLVGDFARNSEAELLRIPNFGRKSLNELKEILGQVGLQL 218

Query: 318 GMNLPDWPPESIEELAKK 335
           G+ LP+WPP +++ L+++
Sbjct: 219 GLALPEWPPPNVDFLSQQ 236


>gi|115443569|ref|YP_778588.1| RNA polymerase alpha subunit [Bigelowiella natans]
 gi|122221272|sp|Q06J39|RPOA_BIGNA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=RNAP
           subunit alpha; AltName: Full=RNA polymerase subunit
           alpha; AltName: Full=Transcriptase subunit alpha
 gi|110810214|gb|ABG91420.1| RNA polymerase alpha subunit [Bigelowiella natans]
          Length = 358

 Score =  105 bits (263), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 62/351 (17%), Positives = 124/351 (35%), Gaps = 52/351 (14%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE  + G+     +     P  +  A    N LRRVL+S      ITAV I G  HE 
Sbjct: 7   SCIESRLRGKRN-YYSRFYIGPFLKNQAFLYSNVLRRVLLSDSSNIVITAVNIVGAKHEY 65

Query: 73  SSIKGVHEDLTDIILN------IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           S + GV E   D++LN      +K I  K +        +   GP ++   DI   N I 
Sbjct: 66  SLLPGVRESSLDLLLNLKELVFVKDIYTKFNKSYF--AYLKSNGPKIIRCSDIILPNTIY 123

Query: 127 VLNPDHVICNLDVDAVVRMELT-----VSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            ++    I  +  +  + +++      ++  +  +  + +   +     I     +S I 
Sbjct: 124 AVDSTQYIATISNNKSLILKMKLTANLLNNFYSNLNYELNSLLSYYTNDILEKTNFSLII 183

Query: 182 KVSYTVESAREGQVLDYDKLS-------MTIDTDGSITGEDSVALASRILQDQLGMFINF 234
             +++  +     ++  D L        + + T+ S +    +  + + + +      + 
Sbjct: 184 DPNFSCVNKVNSSLISLDNLENYNDSISLEVWTNSSYSPRIIIQNSIKSMVNLFLSIYDT 243

Query: 235 EEPKKEVKEDINVKSLP-------------------------------FNPALLKKVEEL 263
                +++   N                                         L  ++EL
Sbjct: 244 SFIDIKLENSDNFLENHLVSLSNRATFFKKSFFNICTEFNTVKYKTSFDKNLTLISIDEL 303

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           +LS+ S   L+  NI+ + DL +  +  + R  N   K+L  I+  +   G
Sbjct: 304 DLSIYSKFLLKRHNILTLYDLFKIDKRVLERFYNISYKTLQSIERKMVKYG 354


>gi|119662857|emb|CAJ33221.1| RNA polymerase alpha subunit [Lactobacillus coryniformis subsp.
           coryniformis KCTC 3167]
          Length = 98

 Score =  105 bits (262), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 36/97 (37%), Positives = 64/97 (65%)

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           + ID++Y+PI +V+Y VES R G+  D+DKL++ + T+GSI+  ++++LA++IL + L +
Sbjct: 2   LPIDSIYTPISRVNYQVESTRVGRRNDFDKLTLDVWTNGSISPREAISLAAKILTEHLDI 61

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           F+N  +  K  +  +  +  P    L   +EEL+LSV
Sbjct: 62  FVNLTDEAKNAEIMVEKEETPKEKMLEMTIEELDLSV 98


>gi|258597949|ref|XP_001348869.2| DNA-directed RNA polymerase, alpha subunit, putative [Plasmodium
           falciparum 3D7]
 gi|255528941|gb|AAN37308.2| DNA-directed RNA polymerase, alpha subunit, putative [Plasmodium
           falciparum 3D7]
          Length = 861

 Score =  104 bits (260), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 45/261 (17%), Positives = 97/261 (37%), Gaps = 28/261 (10%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           + I   Q  +        PL     HT G+ ++ V  + + G AI  +++   ++E + I
Sbjct: 468 DIIKYPQNGKLYQKFYIGPLNITDGHTFGSLIKYVCQTQIYGYAIVGIKVHN-MNEDTKI 526

Query: 76  KGVHEDLTDIILNIKGINLKMSG-DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
             V EDL +I LNI  + +     +    + +  +GP ++ AG I   + ++++N +H I
Sbjct: 527 NNVQEDLLEIALNISDVCIYSKEINLESNIRLIFKGPLMLVAGMIPLPSHLKIINKEHYI 586

Query: 135 CNLDVDAVVRMELTVSKGHGYVP-------AKHHRTEND-----------PIGLITIDAL 176
           C +  D  + + + +  G G+          +   ++ND               + I + 
Sbjct: 587 CTIKEDGFIDISIKIEYGKGHWLTYDKGLYKRERGSDNDCMKKREIKEVVHKNYMPISSS 646

Query: 177 YSPIKKVSYTVESA--------REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           +   + +  TV           R         L + I TD  +  ++ +    + ++  L
Sbjct: 647 FGACRMIRLTVHKIATKFWCEDRCEFTDPKQMLVVEIWTDCRMLPKNVLLYGIKNIKKIL 706

Query: 229 GMFINFEEPKKEVKEDINVKS 249
             F        +       + 
Sbjct: 707 RKFREMIVKDTDFTFQEEEQE 727


>gi|169835538|ref|ZP_02868726.1| hypothetical protein cdivTM_00193 [candidate division TM7
           single-cell isolate TM7a]
          Length = 96

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 35/90 (38%), Positives = 54/90 (60%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +            EPL  G+ +TLGN+LRRVLMSS+ GAA+ + +I+G  HE +++ G+ 
Sbjct: 6   IEDYSSTSAAFTVEPLRGGYGNTLGNSLRRVLMSSIHGAAVISFKIEGATHEFTTVPGIK 65

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           ED+ DI LN+K + +KM  D    + + K 
Sbjct: 66  EDVVDISLNLKSVKIKMHTDDPIELRLEKH 95


>gi|81301|pir||S05342 DNA-directed RNA polymerase (EC 2.7.7.6) alpha chain - green alga
           KS3/2 chloroplast (fragment)
          Length = 129

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 41/115 (35%), Positives = 62/115 (53%), Gaps = 2/115 (1%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
            +L             P     + T+ NALRR L++ L   AIT ++I+GV HE S++ G
Sbjct: 15  CILENPRSFYGSFSLGPFKNSQSLTVANALRRTLLAELSNIAITHLEIEGVTHEYSTLVG 74

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVT--IFKRGPGVVTAGDIQTVNDIEVLNP 130
           V E + D++LN KGI LK +    K +   +  RGPGVV A D++    I+ ++P
Sbjct: 75  VRESVLDLLLNFKGIALKNTSPVTKPLFGYLQVRGPGVVRASDLKFPPMIQCVDP 129


>gi|84999732|ref|XP_954587.1| DNA-directed RNA polymerase alpha chain [Theileria annulata]
 gi|65305585|emb|CAI73910.1| DNA-directed RNA polymerase alpha chain, putative [Theileria
           annulata]
          Length = 680

 Score =  102 bits (255), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 53/256 (20%), Positives = 99/256 (38%), Gaps = 37/256 (14%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
                  P P     T+G+ L+ +  S   G A+ AV+I   +++ +++ GV +DL +I 
Sbjct: 262 YQKFYMGPYPVTMGWTIGSLLKVMTQSRCPGHAVVAVKIHN-MNKDTTVDGVADDLLNIA 320

Query: 87  LNIKGINL-KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           LN K + L  +      RV    +GP +V AG ++    +++ NP+  I  L+  A + +
Sbjct: 321 LNFKMVALQTLEPGKEARVRTKIKGPAMVCAGALEWPPFVKICNPESYITKLEEGAELDL 380

Query: 146 ELTVSKGHGYVPAKHHR------------------TENDPIGLITIDALYSPIKKVSYTV 187
           E+ +  G G+  A                       E    G      ++   + +   V
Sbjct: 381 EIKIEWGRGFWMADSKGLYRVEEGANSLCQKRRDIKEVKEEGFYPTSCVFGGCRMIRLAV 440

Query: 188 ESAREGQVL---------DYDKLSMTIDTDGSITGEDSVALA-------SRILQDQLGMF 231
                GQ             D+L + I TD S T +  +             L+ Q+   
Sbjct: 441 HKL-MGQRWCSLTYTCPDPMDQLVVEIWTDVSTTPKHVLEFGLCEVIAWLTELKRQVSHD 499

Query: 232 INFEEPKKEVKEDINV 247
           ++FE   +++K+    
Sbjct: 500 VDFENEDEQLKDIWEK 515


>gi|62361814|gb|AAX81443.1| RNA polymerase alpha subunit [Simkania negevensis]
          Length = 159

 Score =  102 bits (255), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 51/159 (32%), Positives = 82/159 (51%), Gaps = 17/159 (10%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-----------------S 97
           L   AI +++I+G  HE ++I+GV ED+T IILN+KG  L+                   
Sbjct: 1   LEAPAIISIKIEGAPHEYTAIEGVIEDMTHIILNLKGTLLRKIPLVENKDTRAPTIISQD 60

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
            D  + +     G  VV    I   ++ E++NPDH I  +      R++L ++ G GYVP
Sbjct: 61  LDVTQDMLDTGGGQFVVKFKHIMGESNFEMINPDHHIFTITKPMRKRIDLKIAIGRGYVP 120

Query: 158 AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           ++ H   +  +  I ID+ +SP++ V+Y VE+ R GQ  
Sbjct: 121 SERHELPDKVVDEIVIDSAFSPVRLVNYFVENTRVGQDT 159


>gi|119662819|emb|CAJ33202.1| RNA polymerase alpha subunit [Lactobacillus diolivorans]
          Length = 98

 Score =  102 bits (254), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 49/96 (51%), Positives = 61/96 (63%), Gaps = 2/96 (2%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE S+IKGV ED+T IILN+K I+LK+ G  D  + + I   GP  VTAGDIQ  +D+
Sbjct: 3   VLHEFSTIKGVVEDVTQIILNVKKISLKLDGPEDEEENLEIDVIGPADVTAGDIQGDSDV 62

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
            VLNPD  I  +   A   M LT +KG GYV A  +
Sbjct: 63  TVLNPDLHIATVAEGATFHMRLTANKGRGYVSAVEN 98


>gi|289804411|ref|ZP_06535040.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
          subsp. enterica serovar Typhi str. AG3]
          Length = 74

 Score =  102 bits (254), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 37/77 (48%), Positives = 51/77 (66%), Gaps = 3/77 (3%)

Query: 2  IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
          +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1  MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62 AVQIDGVLHEISSIKGV 78
           V+IDGVLHE S+ +GV
Sbjct: 58 EVEIDGVLHEYSTKEGV 74


>gi|183397279|gb|ACC62186.1| RpoA1 [Francisella noatunensis]
          Length = 154

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 50/160 (31%), Positives = 84/160 (52%), Gaps = 6/160 (3%)

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L  +    +  TVS G          TE + +G I +DA ++PIK+V++ +     
Sbjct: 1   PIATLTNEREFSLVATVSVGRNVGILSALPTELEKVGDIAVDADFNPIKRVAFEIFDNGA 60

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
                 + L + + T+G+I    +V  A     +Q+ +F++   P      D  + S   
Sbjct: 61  S-----ETLEVFVKTNGTIEPLAAVTKALEYFCEQISVFVSLRVPSNGKTGDALLDSN-I 114

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ +
Sbjct: 115 DPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQL 154


>gi|183397285|gb|ACC62189.1| RpoA1 [Francisella philomiragia]
          Length = 154

 Score =  101 bits (252), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 49/160 (30%), Positives = 84/160 (52%), Gaps = 6/160 (3%)

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L  +    +  TVS G          TE + +G I +D+ ++PIK+V++ +     
Sbjct: 1   PIATLTNEREFSLTATVSVGRNVGILSALPTELEKVGDIAVDSDFNPIKRVAFEIFDNGT 60

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
                 + L + + T+G+I    +V  A     +Q+ +F++   P      D  + S   
Sbjct: 61  N-----ETLEVFVKTNGTIEPLVAVTKALEYFCEQISVFVSLRVPSNGKTGDALLDSN-I 114

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ +
Sbjct: 115 DPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQL 154


>gi|183397281|gb|ACC62187.1| RpoA1 [Francisella noatunensis]
          Length = 154

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 49/160 (30%), Positives = 84/160 (52%), Gaps = 6/160 (3%)

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L  +    +  TVS G           E + +G I +DA ++PIK+V++ +     
Sbjct: 1   PIATLTNEREFSLVATVSVGRNVGILSALPIELEKVGDIAVDADFNPIKRVAFEIFD--- 57

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
                 + L + + T+G+I    +V  A     +Q+ +F++ + P      D  + S   
Sbjct: 58  --NSASETLEVFVKTNGTIEPLAAVTKALEYFCEQISVFVSLKVPSNGKTGDALLDSN-I 114

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ +
Sbjct: 115 DPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQL 154


>gi|300193165|pdb|3K4G|A Chain A, Crystal Structure Of E. Coli Rna Polymerase Alpha Subunit
           C-Terminal Domain
 gi|300193166|pdb|3K4G|B Chain B, Crystal Structure Of E. Coli Rna Polymerase Alpha Subunit
           C-Terminal Domain
 gi|300193167|pdb|3K4G|C Chain C, Crystal Structure Of E. Coli Rna Polymerase Alpha Subunit
           C-Terminal Domain
 gi|300193168|pdb|3K4G|D Chain D, Crystal Structure Of E. Coli Rna Polymerase Alpha Subunit
           C-Terminal Domain
 gi|300193169|pdb|3K4G|E Chain E, Crystal Structure Of E. Coli Rna Polymerase Alpha Subunit
           C-Terminal Domain
 gi|300193170|pdb|3K4G|F Chain F, Crystal Structure Of E. Coli Rna Polymerase Alpha Subunit
           C-Terminal Domain
 gi|300193171|pdb|3K4G|G Chain G, Crystal Structure Of E. Coli Rna Polymerase Alpha Subunit
           C-Terminal Domain
 gi|300193172|pdb|3K4G|H Chain H, Crystal Structure Of E. Coli Rna Polymerase Alpha Subunit
           C-Terminal Domain
          Length = 86

 Score =  100 bits (249), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 44/85 (51%), Positives = 58/85 (68%)

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           ++   F+P LL+ V++LEL+VRS NCL  E I Y+GDL+QRTE ++L   N G  SL EI
Sbjct: 1   MEXPEFDPILLRPVDDLELTVRSANCLXAEAIHYIGDLVQRTEVELLXTPNLGXXSLTEI 60

Query: 307 KGVLGTMGLFLGMNLPDWPPESIEE 331
             VL + GL LGM L +WPP SI +
Sbjct: 61  XDVLASRGLSLGMRLENWPPASIAD 85


>gi|156089709|ref|XP_001612261.1| hypothetical protein [Babesia bovis T2Bo]
 gi|154799515|gb|EDO08693.1| hypothetical protein BBOV_III011410 [Babesia bovis]
          Length = 610

 Score =  100 bits (248), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 49/232 (21%), Positives = 91/232 (39%), Gaps = 26/232 (11%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ++ T      L       L N+LRRV    L    ITA++I G+ +E  SI G+ ED  D
Sbjct: 219 KSFTFYYVHSLHTNVIPVLLNSLRRVAKRHLGAGRITALRIPGMKNEFYSIVGLREDFFD 278

Query: 85  IILNIKGINLKM-----SGDSHKRVTIFKRGPGVVTAGDIQTVND--------------- 124
           +  N+  +  +      +        +  +GP +  AG I+                   
Sbjct: 279 LSRNLTKVIFRNVPMTATFHRPLIGRLRLKGPIIAVAGHIELDQTFQKEGVGSSSGSKDD 338

Query: 125 --IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH----RTENDPIGLITIDALYS 178
             IE++N +  IC L  DA + ME+ +     YV  +        +  P G I   +  +
Sbjct: 339 RRIEIVNKNQYICALSRDAYLDMEVKIEYIANYVMPEKGPESLNRDITPDGFIHFSSSCT 398

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           PI+  ++  +     +    + +++ + TDGS T   ++   +  ++     
Sbjct: 399 PIEVFAFDGDRRGIDEESTSEIVTLELHTDGSTTPRLALLNCATFIETWFER 450


>gi|119662805|emb|CAJ33194.1| RNA polymerase alpha subunit [Lactobacillus manihotivorans]
          Length = 89

 Score = 99.7 bits (247), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 36/89 (40%), Positives = 55/89 (61%)

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             K V I   GP  VTA DI + +D+EVLNP+  IC +       + +TV  G GYV A 
Sbjct: 1   EDKTVEIDVAGPATVTAADIVSDSDVEVLNPEQYICTVAEGGRFHVRMTVKTGRGYVAAD 60

Query: 160 HHRTENDPIGLITIDALYSPIKKVSYTVE 188
            ++ ++ PIG++ ID++++PI +V+Y VE
Sbjct: 61  QNKVDDMPIGVLPIDSIFTPISRVNYQVE 89


>gi|237749604|ref|ZP_04580084.1| RpoA [Helicobacter bilis ATCC 43879]
 gi|229374800|gb|EEO25191.1| RpoA [Helicobacter bilis ATCC 43879]
          Length = 88

 Score = 98.5 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 30/87 (34%), Positives = 47/87 (54%)

Query: 234 FEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
             +  +  +  +  +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+
Sbjct: 1   MTDEAQHAEIMVEKEEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMM 60

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMN 320
           ++ N GRKSL E+K  L  +GL L  +
Sbjct: 61  KVRNLGRKSLEEVKAKLEELGLGLRKD 87


>gi|183397277|gb|ACC62185.1| RpoA1 [Francisella sp. PQ1104]
 gi|183397283|gb|ACC62188.1| RpoA1 [Francisella sp. PQ1105]
          Length = 154

 Score = 98.5 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 50/160 (31%), Positives = 85/160 (53%), Gaps = 6/160 (3%)

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L  +    +  TVS G          TE + +G I +DA ++PIK+V++ +     
Sbjct: 1   PIATLTNEREFSLVATVSVGRNVGILSALPTELEKVGDIAVDADFNPIKRVAFEIFDNGA 60

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
                 + L + + T+G+I    +V  A +   +Q+ +F++   P      D  + S   
Sbjct: 61  S-----ETLEVFVKTNGTIESLAAVTKALKYFCEQISVFVSLRVPSNGKTGDALLDSN-I 114

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ +
Sbjct: 115 DPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQL 154


>gi|77406111|ref|ZP_00783185.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae H36B]
 gi|77175292|gb|EAO78087.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           agalactiae H36B]
          Length = 110

 Score = 97.3 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 47/107 (43%), Positives = 66/107 (61%), Gaps = 4/107 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E ++    + EPL RG+  TLGN+LRR L+SSL GAA+T+++IDG
Sbjct: 3   EFEKP----IITKIDENKDYGRFVIEPLERGYGTTLGNSLRRXLLSSLPGAAVTSIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           VLHE  +I GV ED+  IILN+KG+ +K   +  K + +   GP  +
Sbjct: 59  VLHEFDTIPGVREDVMQIILNVKGLAVKSYVEDEKIIELDVEGPAEI 105


>gi|221487600|gb|EEE25832.1| hypothetical protein TGGT1_089410 [Toxoplasma gondii GT1]
          Length = 1082

 Score = 97.0 bits (240), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 55/291 (18%), Positives = 107/291 (36%), Gaps = 60/291 (20%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH------ 70
             ++ +       +   P+P     T+G+ ++        G AI A+++           
Sbjct: 602 VTIIPETGHLYQKLYIGPVPVTTGWTMGSLIKAFAAQRCPGHAIVALKLHAPRKPNAGGR 661

Query: 71  ---------------------EISSIKGVHEDLTDIILNIKGINL-KMSGDSHKRVTIFK 108
                                 ++ +  V EDL +I LN+KG+    +       V +  
Sbjct: 662 RGRKKTGEGEPQSAGGEAEAPMVTQLPNVREDLLEIALNLKGVAFETLRPRESACVRVKA 721

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTEN 165
            GP ++ AG I   + + V NP+H I  ++   V+ +E+ +  G G   A  H   R E 
Sbjct: 722 VGPQLLVAGMIDWPSFVRVGNPEHFIAKVEEGGVLDLEMKLEWGRGAWLADLHGLYREEE 781

Query: 166 ---------------DPIGLITIDALYSPIKKVSYTVESA--------REGQVLDYDKLS 202
                          D  G      ++     +   V           R+      ++L 
Sbjct: 782 GVDTRCYKRRRIWEVDHRGFYPTSCIFGACTMMRLAVHKLMGTRFCQDRQASTNPTEQLV 841

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           + I TD S + ++ +A A   LQD L  F++    ++++ ED++ K+   +
Sbjct: 842 LEIWTDASKSPKEVLAFA---LQDMLAWFVDL---RRQLVEDVDWKTEDED 886


>gi|71904766|gb|AAZ52664.1| DNA-dependent RNA polymerase alpha chain [Mycoplasma hominis ATCC
           23114]
          Length = 180

 Score = 97.0 bits (240), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 29/139 (20%), Positives = 70/139 (50%)

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +D+ +SPIKKV+   E       +  ++L + ++TDG++  ++ +  A++I+     
Sbjct: 16  FLAMDSDFSPIKKVAILFEELNSTSNIIEERLKIKVETDGTVEAKNVMEEAAKIIVAHFQ 75

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +  N +        D   +     P +   +++L L++RS N LR      + ++++ ++
Sbjct: 76  IIGNIDALGTIDLFDDQKEKHEKTPKVSVSIDKLNLTIRSLNALRRAGFNNVDEIMKLSD 135

Query: 290 ADMLRMANFGRKSLVEIKG 308
            ++  + N G+KS+ +I  
Sbjct: 136 EELSNIKNLGKKSVQDIID 154


>gi|166714638|gb|ABY88044.1| RpoA [Pseudoxanthomonas dokdonensis]
          Length = 122

 Score = 95.8 bits (237), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 43/124 (34%), Positives = 72/124 (58%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R  +D     G + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   LNMRLKIERGFGYQPAAARRHPDDETRTIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + I+T+G+I  E++V  A+ IL DQL +F +F   ++    +        +P LL+ 
Sbjct: 62  KLVLDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRQRG---EAKPSPTGVDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|166714704|gb|ABY88077.1| RpoA [Stenotrophomonas sp. ICB220]
          Length = 122

 Score = 95.8 bits (237), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 43/124 (34%), Positives = 72/124 (58%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R  +D     G + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   LNMRLKIERGFGYQPAAARRHPDDETRTIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + I+T+G+I  E++V  A+ IL DQL +F +F   ++    +        +P LL+ 
Sbjct: 62  KLVLDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRQRG---EAKPSKTGVDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|94502224|ref|ZP_01308710.1| DNA-directed RNA polymerase alpha chain [Candidatus Sulcia
          muelleri str. Hc (Homalodisca coagulata)]
 gi|94451195|gb|EAT14134.1| DNA-directed RNA polymerase alpha chain [Candidatus Sulcia
          muelleri str. Hc (Homalodisca coagulata)]
          Length = 92

 Score = 95.4 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 40/89 (44%), Positives = 58/89 (65%)

Query: 9  LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           +K    + + + +      L   EPL  G+  T+GN LRRVL+SSL G AI++V+I+GV
Sbjct: 3  FLKFKQSKNLRVLKLTPEEGLFKIEPLFPGWGVTIGNTLRRVLLSSLEGYAISSVKIEGV 62

Query: 69 LHEISSIKGVHEDLTDIILNIKGINLKMS 97
           HE S+IKGV ED+T+IILN+K +  K +
Sbjct: 63 NHEFSTIKGVIEDMTEIILNLKKVRFKKN 91


>gi|315283810|ref|ZP_07871881.1| DNA-directed RNA polymerase subunit alpha [Listeria marthii FSL
           S4-120]
 gi|313612547|gb|EFR86618.1| DNA-directed RNA polymerase subunit alpha [Listeria marthii FSL
           S4-120]
          Length = 86

 Score = 95.0 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 30/82 (36%), Positives = 47/82 (57%)

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           +  ++ +  I  +       L   +EEL+LSVRS NCL+   I  + +L  ++E DM+++
Sbjct: 1   DEAQKAEIMIEKEESHKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELADKSEDDMMKV 60

Query: 296 ANFGRKSLVEIKGVLGTMGLFL 317
            N GRKSL E+K  L  +GL L
Sbjct: 61  RNLGRKSLEEVKVKLADLGLSL 82


>gi|253795635|ref|YP_003038731.1| putative DNA-directed RNA polymerase, alpha subunit [Candidatus
           Hodgkinia cicadicola Dsem]
 gi|253739943|gb|ACT34278.1| putative DNA-directed RNA polymerase, alpha subunit [Candidatus
           Hodgkinia cicadicola Dsem]
          Length = 228

 Score = 95.0 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 63/193 (32%), Positives = 95/193 (49%), Gaps = 6/193 (3%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD 99
           AHTL  ALRR LM+ + G A+  + +DG  H ++  +GV ED+  +  N   I  +    
Sbjct: 25  AHTLAVALRRTLMARVEGWAVVGLCVDGAAHALARAEGVIEDVLGVAANAARIVFEGECG 84

Query: 100 SHKRVTIFKR-GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           S + V    R   GVVTAG +     + V+N +  +C++    V R E  V++G GY+ A
Sbjct: 85  SRRVVKAVVRASAGVVTAGQLVLPEGLRVVNTNERVCSVGAGCVFRAEFVVARGVGYMRA 144

Query: 159 KHHRTENDP--IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
              R        G   +DA +SP+K+VSY V SA        D+  + I+T+G + G  +
Sbjct: 145 AQARARWSRVLAGYTVVDAHFSPVKRVSYKVSSA--EDDRSCDRAQLVIETNG-VDGAHA 201

Query: 217 VALASRILQDQLG 229
           V  A R L     
Sbjct: 202 VVDACRELSRCFQ 214


>gi|166714644|gb|ABY88047.1| RpoA [Stenotrophomonas sp. LMG 10857]
          Length = 122

 Score = 95.0 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 44/124 (35%), Positives = 73/124 (58%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R  ++     G + +DA +SP+++V+Y+VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYSVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL M I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ 
Sbjct: 62  KLVMDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPAN---NGVDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|85000353|ref|XP_954895.1| DNA-directed RNA polymerase D subunit [Theileria annulata strain
           Ankara]
 gi|65303041|emb|CAI75419.1| DNA-directed RNA polymerase D subunit, putative [Theileria
           annulata]
          Length = 587

 Score = 95.0 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 51/255 (20%), Positives = 95/255 (37%), Gaps = 52/255 (20%)

Query: 28  TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIIL 87
           T      L       L N+LRRV    L    ITA++I G+ +E  S+ G+ ED  +++ 
Sbjct: 166 TFFYIHSLHTDVIPVLLNSLRRVAKRHLGSGRITALRIPGMENEFYSVVGLREDFFELVR 225

Query: 88  NIKGINLKM-----SGDSHKRVTIFKRGPGVVTAGDIQTV-------------------- 122
           N++G+  K      +       T+  +GP +  AG ++                      
Sbjct: 226 NLRGVIFKNVPKTATFHRPVIATLRLKGPIIAVAGHLKFDNKRSTKTASDIDNKTENKND 285

Query: 123 -----------------------NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
                                   +IEV+N +H IC+L     + M++ +     YV  +
Sbjct: 286 NTDTKADNEEGVINDYVYDKKYTGEIEVINKNHYICSLSQGCYLTMDVKIEYISNYVIPE 345

Query: 160 ----HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
                   +  P G I   +  +P++   +T E     +    + +S+ + TDGS T   
Sbjct: 346 FGPESLNRDITPDGFIHFCSSCNPVEIFGFTGERRGLDEQSTSEIVSLELHTDGSATPRV 405

Query: 216 SVALASRILQDQLGM 230
           ++  ++  L +    
Sbjct: 406 ALLRSATFLLNWFDR 420


>gi|166714628|gb|ABY88039.1| RpoA [Stenotrophomonas maltophilia]
          Length = 122

 Score = 95.0 bits (235), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 42/124 (33%), Positives = 74/124 (59%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M + + +G+GY PA   R+ ++     G + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMAVKIERGYGYQPAAARRSPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ 
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFNHRDRGAAKPAN---NGVDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|221507397|gb|EEE33001.1| RNA polymerase Rpb3/Rpb11 dimerisation domain-containing protein,
           putative [Toxoplasma gondii VEG]
          Length = 1084

 Score = 95.0 bits (235), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 53/291 (18%), Positives = 106/291 (36%), Gaps = 60/291 (20%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH------ 70
             ++ +       +   P+P     T+G+ ++        G A+ A+++           
Sbjct: 604 VTIIPETGHLYQKLYIGPVPVTTGWTMGSLIKAFAAQRCPGHAVVALKLHAPRKPNAGGR 663

Query: 71  ---------------------EISSIKGVHEDLTDIILNIKGINL-KMSGDSHKRVTIFK 108
                                 ++ +  V EDL +I LN+KG+    +       V +  
Sbjct: 664 RGRKKTGEGEPQSAGGEAEAPMVTQLPNVREDLLEIALNLKGVAFETLRPRESACVRVKA 723

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTEN 165
            GP ++ AG I   + + V NP+H I  ++   V+ +E+ +  G G   A  H   R E 
Sbjct: 724 VGPQLLVAGMIDWPSFVRVGNPEHFIAKVEEGGVLDLEMKLEWGRGAWLADLHGLYREEE 783

Query: 166 ---------------DPIGLITIDALYSPIKKVSYTVESA--------REGQVLDYDKLS 202
                          D  G      ++     +   V           R+      ++L 
Sbjct: 784 GVDTRCYKRRRIWEVDHRGFYPTSCIFGACTMMRLAVHKLMGTRFCQDRQASTNPTEQLV 843

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           + I TD S + ++ +A A   LQD L   ++    ++++ ED++ K+   +
Sbjct: 844 LEIWTDASKSPKEVLAFA---LQDMLAWLVDL---RRQLVEDVDWKTEDED 888


>gi|237830453|ref|XP_002364524.1| RNA polymerase Rpb3/Rpb11 dimerization domain-containing protein
           [Toxoplasma gondii ME49]
 gi|211962188|gb|EEA97383.1| RNA polymerase Rpb3/Rpb11 dimerization domain-containing protein
           [Toxoplasma gondii ME49]
          Length = 623

 Score = 95.0 bits (235), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 53/291 (18%), Positives = 106/291 (36%), Gaps = 60/291 (20%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH------ 70
             ++ +       +   P+P     T+G+ ++        G A+ A+++           
Sbjct: 143 VTIIPETGHLYQKLYIGPVPVTTGWTMGSLIKAFAAQRCPGHAVVALKLHAPRKPNAGGR 202

Query: 71  ---------------------EISSIKGVHEDLTDIILNIKGINL-KMSGDSHKRVTIFK 108
                                 ++ +  V EDL +I LN+KG+    +       V +  
Sbjct: 203 RGRKKTGEGEPQSAGGEAEAPMVTQLPNVREDLLEIALNLKGVAFETLRPRESACVRVKA 262

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTEN 165
            GP ++ AG I   + + V NP+H I  ++   V+ +E+ +  G G   A  H   R E 
Sbjct: 263 VGPQLLVAGMIDWPSFVRVGNPEHFIAKVEEGGVLDLEMKLEWGRGAWLADLHGLYREEE 322

Query: 166 ---------------DPIGLITIDALYSPIKKVSYTVESA--------REGQVLDYDKLS 202
                          D  G      ++     +   V           R+      ++L 
Sbjct: 323 GVDTRCYKRRRIWEVDHRGFYPTSCIFGACTMMRLAVHKLMGTRFCQDRQASTNPTEQLV 382

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           + I TD S + ++ +A A   LQD L   ++    ++++ ED++ K+   +
Sbjct: 383 LEIWTDASKSPKEVLAFA---LQDMLAWLVDL---RRQLVEDVDWKTEDED 427


>gi|166714682|gb|ABY88066.1| RpoA [Stenotrophomonas sp. LMG 981]
          Length = 122

 Score = 94.6 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 43/125 (34%), Positives = 73/125 (58%), Gaps = 6/125 (4%)

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M L + +G GY PA   R  ++     G + +DA +SP+++V+Y+VE+AR  Q  D 
Sbjct: 1   SINMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYSVEAARVEQRTDL 60

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+
Sbjct: 61  DKLVIEIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPAN---NGVDPVLLR 117

Query: 259 KVEEL 263
            +++L
Sbjct: 118 PIDDL 122


>gi|166714720|gb|ABY88085.1| RpoA [Stenotrophomonas sp. ICB141]
 gi|166714722|gb|ABY88086.1| RpoA [Stenotrophomonas sp. ICB129]
 gi|166714724|gb|ABY88087.1| RpoA [Stenotrophomonas sp. ICB133]
          Length = 122

 Score = 94.6 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 43/124 (34%), Positives = 72/124 (58%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R  ++     G + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ 
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRARGAAKPAN---NGVDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|166714634|gb|ABY88042.1| RpoA [Stenotrophomonas nitritireducens]
          Length = 122

 Score = 94.6 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 44/124 (35%), Positives = 72/124 (58%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L V +G GY PA   R  ++     G + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKVERGFGYQPAASRRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ 
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPAN---NGVDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|166714684|gb|ABY88067.1| RpoA [Stenotrophomonas sp. LMG 10874]
 gi|166714696|gb|ABY88073.1| RpoA [Stenotrophomonas sp. LMG 11111]
 gi|166714698|gb|ABY88074.1| RpoA [Stenotrophomonas sp. ICB130]
 gi|166714700|gb|ABY88075.1| RpoA [Stenotrophomonas sp. ICB134]
 gi|166714702|gb|ABY88076.1| RpoA [Stenotrophomonas sp. ICB209]
          Length = 122

 Score = 93.9 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 43/124 (34%), Positives = 72/124 (58%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R  ++     G + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ 
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPAN---NGVDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|166714668|gb|ABY88059.1| RpoA [Stenotrophomonas sp. LMG 10888]
 gi|166714670|gb|ABY88060.1| RpoA [Stenotrophomonas sp. LMG 10883]
 gi|166714688|gb|ABY88069.1| RpoA [Stenotrophomonas sp. LMG 10882]
          Length = 122

 Score = 93.9 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 44/124 (35%), Positives = 72/124 (58%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L V +G GY PA   R  ++     G + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKVERGFGYQPAAARRRPDEESRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ 
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPAN---NGVDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|166714636|gb|ABY88043.1| RpoA [Stenotrophomonas koreensis]
          Length = 122

 Score = 93.9 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 45/124 (36%), Positives = 72/124 (58%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L V +G GY PA   R  ++     G + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   LNMRLKVERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + IDT+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ 
Sbjct: 62  KLVLDIDTNGTIDAEEAVRTAADILTDQLSVFGDFTHRDRGAAKPTN---NGVDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|166714656|gb|ABY88053.1| RpoA [Stenotrophomonas sp. LMG 11114]
          Length = 122

 Score = 93.9 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 43/124 (34%), Positives = 71/124 (57%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R  ++     G + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + I+T+G+I  ED+V   + IL DQL +F +F    +   +  N      +P LL+ 
Sbjct: 62  KLVIDIETNGTIDAEDAVRTGADILSDQLSVFGDFTHRDRGAAKPAN---NGVDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|166714654|gb|ABY88052.1| RpoA [Stenotrophomonas sp. LMG 1108]
 gi|166714658|gb|ABY88054.1| RpoA [Stenotrophomonas sp. LMG 6608]
 gi|166714672|gb|ABY88061.1| RpoA [Stenotrophomonas sp. ICB91]
 gi|166714674|gb|ABY88062.1| RpoA [Stenotrophomonas sp. ICB194]
 gi|166714676|gb|ABY88063.1| RpoA [Stenotrophomonas pavanii]
 gi|166714686|gb|ABY88068.1| RpoA [Stenotrophomonas sp. LMG 10879]
 gi|166714690|gb|ABY88070.1| RpoA [Stenotrophomonas sp. LMG 10989]
 gi|166714694|gb|ABY88072.1| RpoA [Stenotrophomonas sp. LMG 11087]
          Length = 122

 Score = 93.5 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 44/124 (35%), Positives = 72/124 (58%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           V M L + +G GY PA   R  ++     G + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   VNMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ 
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPAN---NGVDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|166714650|gb|ABY88050.1| RpoA [Stenotrophomonas sp. LMG 10890]
          Length = 122

 Score = 93.5 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 44/124 (35%), Positives = 72/124 (58%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           V M L + +G GY PA   R  ++     G + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   VNMRLKIDRGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ 
Sbjct: 62  KLVIDIETNGTIDAEEAVQTAADILSDQLSVFGDFTHRDRGAAKPAN---NGVDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|166714692|gb|ABY88071.1| RpoA [Stenotrophomonas sp. LMG 11000]
          Length = 122

 Score = 93.5 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 42/124 (33%), Positives = 71/124 (57%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G  Y PA   R  ++     G + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFAYQPAALRRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ 
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPAN---NGVDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|166714680|gb|ABY88065.1| RpoA [Stenotrophomonas sp. ICB207]
          Length = 122

 Score = 93.5 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 42/124 (33%), Positives = 71/124 (57%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R  ++     G + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   LNMRLKIERGFGYQPAAARRRPDEETRTIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +         +   +P LL+ 
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGA---PKPATGGVDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|285803273|pdb|3IHQ|B Chain B, Crystal Structure Of Reduced C10s Spx In Complex With The
           Alpha C-Terminal Domain Of Rna Polymeras
          Length = 75

 Score = 93.5 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 31/72 (43%), Positives = 43/72 (59%)

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
           S      L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K 
Sbjct: 2   SHMKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKA 61

Query: 309 VLGTMGLFLGMN 320
            L  +GL L  +
Sbjct: 62  KLEELGLGLRKD 73


>gi|166714648|gb|ABY88049.1| RpoA [Stenotrophomonas sp. LMG 10887]
          Length = 122

 Score = 93.1 bits (230), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 42/124 (33%), Positives = 71/124 (57%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY P    R  ++     G + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFGYQPVAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ 
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPAN---NGVDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|166714642|gb|ABY88046.1| RpoA [Stenotrophomonas sp. LMG 10992]
          Length = 122

 Score = 93.1 bits (230), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 42/124 (33%), Positives = 73/124 (58%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M + + +G GY PA   R+ ++     G + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMAVKIERGFGYQPAAARRSPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ 
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFNHRDRGAAKPAN---NGVDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|166714646|gb|ABY88048.1| RpoA [Stenotrophomonas sp. LMG 10881]
          Length = 122

 Score = 93.1 bits (230), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 44/125 (35%), Positives = 71/125 (56%), Gaps = 6/125 (4%)

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + M L V +G GY PA   R  ++     G + +DA +SP+++V+Y VE+AR  Q  D 
Sbjct: 1   DINMRLKVERGFGYQPAASRRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDL 60

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL + I+T+G+I  E++V  A  IL DQL +F +F    +   +  N      +P LL+
Sbjct: 61  DKLVIDIETNGTIDAEEAVRTAGDILSDQLSVFGDFTHRDRGAAKPAN---NGVDPVLLR 117

Query: 259 KVEEL 263
            +++L
Sbjct: 118 PIDDL 122


>gi|166714632|gb|ABY88041.1| RpoA [Stenotrophomonas acidaminiphila]
          Length = 119

 Score = 92.7 bits (229), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 44/122 (36%), Positives = 71/122 (58%), Gaps = 6/122 (4%)

Query: 145 MELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           M L V +G GY PA   R  ++     G + +DA +SP+++V+Y VE+AR  Q  D DKL
Sbjct: 1   MRLKVERGFGYQPAASRRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLDKL 60

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ ++
Sbjct: 61  VIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPAN---NGVDPVLLRPID 117

Query: 262 EL 263
           +L
Sbjct: 118 DL 119


>gi|224983719|pdb|3GFK|B Chain B, Crystal Structure Of Bacillus Subtilis SpxRNA POLYMERASE
           Alpha Subunit C-Terminal Domain Complex
          Length = 79

 Score = 92.7 bits (229), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 30/74 (40%), Positives = 43/74 (58%)

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+
Sbjct: 5   KEEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEV 64

Query: 307 KGVLGTMGLFLGMN 320
           K  L  +GL L  +
Sbjct: 65  KAKLEELGLGLRKD 78


>gi|75764303|ref|ZP_00743839.1| DNA-directed RNA polymerase alpha chain [Bacillus thuringiensis
           serovar israelensis ATCC 35646]
 gi|74488206|gb|EAO51886.1| DNA-directed RNA polymerase alpha chain [Bacillus thuringiensis
           serovar israelensis ATCC 35646]
          Length = 78

 Score = 92.7 bits (229), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 30/77 (38%), Positives = 44/77 (57%)

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL
Sbjct: 1   MVEKEEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSL 60

Query: 304 VEIKGVLGTMGLFLGMN 320
            E+K  L  +GL L  +
Sbjct: 61  EEVKHKLEELGLGLRKD 77


>gi|166714678|gb|ABY88064.1| RpoA [Stenotrophomonas sp. ICB128]
          Length = 122

 Score = 92.3 bits (228), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 42/124 (33%), Positives = 72/124 (58%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           ++M L + +G GY P    R  ++     G + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   IKMRLKIERGFGYQPGAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ 
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPAN---NGVDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|166714630|gb|ABY88040.1| RpoA [Stenotrophomonas maltophilia]
          Length = 107

 Score = 91.6 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 38/106 (35%), Positives = 63/106 (59%), Gaps = 3/106 (2%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G+GY PA   R  ++     G + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGYGYQPAAARRCPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPA 107


>gi|166714706|gb|ABY88078.1| RpoA [Stenotrophomonas sp. LMG 11108]
          Length = 122

 Score = 90.8 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 44/124 (35%), Positives = 69/124 (55%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L   +G GY PA   R  ++     G + +DA +SP+++V+Y+VE+AR  Q  D D
Sbjct: 2   INMRLKSERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYSVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL M I+T+G+I  +++V  A  IL DQL  F +F    +      N      +P LL+ 
Sbjct: 62  KLVMDIETNGTIDAQEAVRTAPDILNDQLSAFGDFPHRHRGAPIPAN---NGMDPVLLRP 118

Query: 260 VEEL 263
           +E+L
Sbjct: 119 IEDL 122


>gi|82407558|pdb|1Z3E|B Chain B, Crystal Structure Of Spx In Complex With The C-Terminal
           Domain Of The Rna Polymerase Alpha Subunit
          Length = 73

 Score = 90.8 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 30/71 (42%), Positives = 43/71 (60%)

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           +     L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K  
Sbjct: 1   MEKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAK 60

Query: 310 LGTMGLFLGMN 320
           L  +GL L  +
Sbjct: 61  LEELGLGLRKD 71


>gi|166714664|gb|ABY88057.1| RpoA [Stenotrophomonas sp. LMG 10853]
          Length = 122

 Score = 90.4 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 42/124 (33%), Positives = 71/124 (57%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R  ++     G + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + I+T+G+I  E++V  A+ I  DQL +F +F    +   +  N      +P LL+ 
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADIPSDQLSVFGDFTHRDRGAAKPAN---NGVDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|166714666|gb|ABY88058.1| RpoA [Stenotrophomonas sp. LMG 10991]
          Length = 122

 Score = 89.6 bits (221), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 42/124 (33%), Positives = 70/124 (56%), Gaps = 6/124 (4%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R  ++    I    +DA +SP+++V+Y VE+A   Q  D D
Sbjct: 2   INMRLKIERGFGYQPAAARRRPDEETRAIGRRVLDASFSPVRRVAYAVEAALVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ 
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPAN---NGVDPVLLRP 118

Query: 260 VEEL 263
           +++L
Sbjct: 119 IDDL 122


>gi|302858180|ref|XP_002960035.1| hypothetical protein VOLCADRAFT_72193 [Volvox carteri f.
           nagariensis]
 gi|300253491|gb|EFJ38900.1| hypothetical protein VOLCADRAFT_72193 [Volvox carteri f.
           nagariensis]
          Length = 136

 Score = 88.9 bits (219), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 33/122 (27%), Positives = 60/122 (49%), Gaps = 11/122 (9%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +             P     + T+ N +RR L+S L   AIT+++I+G+LH+ SS+ G+ 
Sbjct: 15  IENNTSFYGCFYLGPFDDSLSQTIANDIRRTLLSELTSLAITSIEIEGILHKYSSLPGMK 74

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIF-----------KRGPGVVTAGDIQTVNDIEVL 128
           E + D+I N++ I LK    S   +T+              GP V+ A D++  + ++ +
Sbjct: 75  ETVLDLICNLQSIVLKKQEISFTNITLRSTKKTYRGFLNVSGPRVIKAMDLKLPSGLQCV 134

Query: 129 NP 130
           +P
Sbjct: 135 DP 136


>gi|255018323|ref|ZP_05290449.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL F2-515]
          Length = 62

 Score = 88.9 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 28/58 (48%), Positives = 40/58 (68%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +EEL+LSVRS NCL+   I  + +L  ++E DM+++ N GRKSL E+K  L  +GL L
Sbjct: 1   MEELDLSVRSYNCLKRAGINTVQELADKSEDDMMKVRNLGRKSLEEVKVKLADLGLSL 58


>gi|166714708|gb|ABY88079.1| RpoA [Stenotrophomonas sp. LMG 10878]
          Length = 116

 Score = 88.5 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 41/119 (34%), Positives = 69/119 (57%), Gaps = 6/119 (5%)

Query: 148 TVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
            + +G GY PA   R  ++     G + +DA +SP+++V+Y VE+AR  Q  D DKL + 
Sbjct: 1   KIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLDKLVID 60

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
           I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N      +P LL+ +++L
Sbjct: 61  IETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPAN---NGVDPVLLRPIDDL 116


>gi|166714652|gb|ABY88051.1| RpoA [Stenotrophomonas sp. LMG 11004]
          Length = 98

 Score = 88.1 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 39/97 (40%), Positives = 59/97 (60%), Gaps = 3/97 (3%)

Query: 143 VRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA        E   IG + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFGYQPAAARCRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           KL + I+T+G+I  E++V  A+ IL DQL +F +F  
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTH 98


>gi|325106907|ref|YP_004267975.1| RNA polymerase subunit alpha domain protein [Planctomyces
           brasiliensis DSM 5305]
 gi|324967175|gb|ADY57953.1| RNA polymerase alpha subunit domain protein [Planctomyces
           brasiliensis DSM 5305]
          Length = 436

 Score = 87.7 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 31/98 (31%), Positives = 46/98 (46%)

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+   +       L   + + ELS RS NCL    I  + DL + +E  +L   NFG  
Sbjct: 271 DEEAARRDKQLEQILSIPMSDFELSARSRNCLERAGIDRLEDLTKMSEEQLLAGKNFGET 330

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           SL EIK +L   GL LG N+    PE + +  +   ++
Sbjct: 331 SLKEIKAILEMHGLKLGQNVHKKQPEPLYKPEELTPEE 368



 Score = 81.2 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 31/105 (29%), Positives = 48/105 (45%), Gaps = 1/105 (0%)

Query: 214 EDSVALASRILQDQ-LGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
           E S+     IL+   L +  N  + + E        +          V +LELSVR+  C
Sbjct: 329 ETSLKEIKAILEMHGLKLGQNVHKKQPEPLYKPEELTPEERMIHEMTVSDLELSVRARKC 388

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L    I  +G+L+ R+  ++L + NFG  SL EI+  LG   + L
Sbjct: 389 LARLGINTVGELVSRSADELLSVRNFGVTSLNEIREKLGEKNIRL 433


>gi|20451756|emb|CAD30546.1| DNA-directed RNA polymerase alpha subunit [Listonella
          anguillarum]
          Length = 61

 Score = 87.7 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 28/64 (43%), Positives = 39/64 (60%), Gaps = 3/64 (4%)

Query: 2  IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
          +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1  MQGSVTEFLKPRLVD---IEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62 AVQI 65
           V I
Sbjct: 58 EVVI 61


>gi|86148803|ref|ZP_01067070.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. MED222]
 gi|85833393|gb|EAQ51584.1| DNA-directed RNA polymerase alpha subunit [Vibrio sp. MED222]
          Length = 82

 Score = 87.3 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 30/77 (38%), Positives = 47/77 (61%), Gaps = 4/77 (5%)

Query: 2  IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
          +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1  MQGSVTEFLKPRLVD---IEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62 AVQIDGVLHEISSIKGV 78
           V+I+ V +  +++K  
Sbjct: 58 EVEIE-VCYTNTALKKA 73


>gi|71032023|ref|XP_765653.1| DNA-directed RNA polymerase, subunit alpha [Theileria parva strain
           Muguga]
 gi|68352610|gb|EAN33370.1| DNA-directed RNA polymerase, alpha subunit, putative [Theileria
           parva]
          Length = 746

 Score = 87.3 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 48/305 (15%), Positives = 98/305 (32%), Gaps = 75/305 (24%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
                  P P     T+G+ L+ +  S   G A+ AV+I   +++ +++ GV +DL +I 
Sbjct: 284 YQKFYMGPYPVTMGWTIGSLLKVMTQSRCPGHAVVAVKIHN-MNKDTTVNGVADDLLNIA 342

Query: 87  LNIKGINL---------------------------KMSGDS------------------- 100
           LN+K ++                             +   +                   
Sbjct: 343 LNLKMVSYTHFYTIYTHFTHLHIYTFTHLHIYTFTHLHTYTFLQIFTQFIVSLQTLEYGK 402

Query: 101 HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
             RV    +GP ++ AG ++  + +++ NP+  I  L+  A + +E+ +  G G+  A  
Sbjct: 403 EARVRTVIKGPAMLCAGALEWPSFVKLCNPECYITKLEEGAELDLEIKIEWGRGFWMADS 462

Query: 161 --------------HRTEN----DPIGLITIDALYSPIKKVSYTVESAREGQVL------ 196
                         H+  +       G      ++   + +   V     GQ        
Sbjct: 463 KGLYRLEEGANSLCHKRRDIKEVKEEGFYPTSCVFGGCRMIRLAVHKL-MGQRWCSLTYT 521

Query: 197 ---DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
                D+L + I TD S T +  +      +   L  F        + + +       + 
Sbjct: 522 CPDPMDQLVVEIWTDVSTTPKHVLEFGLSEVIAWLTEFKRQVSHDVDFEHEDEQLKDIWE 581

Query: 254 PALLK 258
                
Sbjct: 582 KIDKY 586



 Score = 36.1 bits (82), Expect = 8.1,   Method: Composition-based stats.
 Identities = 16/84 (19%), Positives = 28/84 (33%), Gaps = 5/84 (5%)

Query: 235 EEPKKEVKEDINVKSLPFNPALLKKVEELE---LSVRS--TNCLRGENIVYMGDLIQRTE 289
           EE  ++ + +           +    E  +   L V S   + LR      M DL+  + 
Sbjct: 659 EEYNEKSEINAKNFEKFIPKPVEDTFENKDIDLLPVNSDIISSLRMSGFNVMADLMDYSV 718

Query: 290 ADMLRMANFGRKSLVEIKGVLGTM 313
            ++    N   +S   IK  L   
Sbjct: 719 EELSHFPNLSIESAKIIKNFLTEH 742


>gi|320103200|ref|YP_004178791.1| RNA polymerase subunit alpha domain-containing protein [Isosphaera
           pallida ATCC 43644]
 gi|319750482|gb|ADV62242.1| RNA polymerase alpha subunit domain protein [Isosphaera pallida
           ATCC 43644]
          Length = 448

 Score = 87.3 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 33/115 (28%), Positives = 51/115 (44%), Gaps = 4/115 (3%)

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVK----EDINVKSLPFNPALLKKVEELELSVR 268
            E        I  +     +  ++ +   +    E+   +       L   V + ELSVR
Sbjct: 245 AEQCFRRVLDIYPNHPRARLYLKDVRASKEMYYDEEAERRYDHLRQVLEIPVTDFELSVR 304

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           S NCL+   I  +GDL + TE+ +L   NFG  SL EIK ++    L LGM + +
Sbjct: 305 SRNCLKKMGIRTLGDLTRITESQLLSSKNFGETSLTEIKAMMEAKSLRLGMAIEN 359



 Score = 76.2 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 27/83 (32%), Positives = 39/83 (46%)

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           K  V+      S      L   + EL LSVR+  C+    I  +G+LI  T+  +L   N
Sbjct: 366 KVAVEPVDEPISPEERAKLAMPITELNLSVRARKCMNKLGITTVGELIAHTQDQLLECKN 425

Query: 298 FGRKSLVEIKGVLGTMGLFLGMN 320
           FG  SL E++  L  +GL L  +
Sbjct: 426 FGVTSLNEVRDKLSELGLKLKND 448


>gi|218672329|ref|ZP_03521998.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli GR56]
          Length = 57

 Score = 86.9 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 40/56 (71%), Positives = 48/56 (85%)

Query: 284 LIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           LIQ+TEA+MLR  NFGRKSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 1   LIQKTEAEMLRTPNFGRKSLNEIKEVLASMGLHLGMEVPAWPPENIEDLAKRYEDQ 56


>gi|87307747|ref|ZP_01089890.1| probable DNA-directed RNA polymerase alpha chain [Blastopirellula
           marina DSM 3645]
 gi|87289361|gb|EAQ81252.1| probable DNA-directed RNA polymerase alpha chain [Blastopirellula
           marina DSM 3645]
          Length = 455

 Score = 85.8 bits (211), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 38/99 (38%), Positives = 51/99 (51%), Gaps = 1/99 (1%)

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+   K       L   V + ELSVRS NCL+   I  +GDL + +E ++L   NFG  
Sbjct: 289 DEEAQKKRDRIAQVLSIPVTDFELSVRSRNCLQKMGIQTLGDLSRCSEQELLSSKNFGET 348

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW-PPESIEELAKKYEDK 339
           SLVEI+ +L + GL LG    D   PE   E+A    D+
Sbjct: 349 SLVEIREMLNSKGLELGQFSSDKGQPEPTIEVAGLSPDE 387



 Score = 69.2 bits (168), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 25/80 (31%), Positives = 40/80 (50%)

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           + E   ++   S      L + + EL LSVR+  C+    I  +G+L++RT  ++L   N
Sbjct: 373 QPEPTIEVAGLSPDEQALLDRPISELNLSVRARKCMVRLGISTIGELVRRTGDELLECKN 432

Query: 298 FGRKSLVEIKGVLGTMGLFL 317
           FG  SL E++  L    L L
Sbjct: 433 FGVTSLNEVREKLTASNLKL 452


>gi|149173495|ref|ZP_01852125.1| probable DNA-directed RNA polymerase alpha chain [Planctomyces
           maris DSM 8797]
 gi|148847677|gb|EDL62010.1| probable DNA-directed RNA polymerase alpha chain [Planctomyces
           maris DSM 8797]
          Length = 415

 Score = 85.8 bits (211), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 32/82 (39%), Positives = 46/82 (56%)

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+           L + V + ELSVRS NCL   +I  +GDL + +E D+L   NFG+ 
Sbjct: 249 DEETARNEARMKQLLDRPVTDFELSVRSRNCLHAMDIHTLGDLTRVSENDLLAGKNFGQT 308

Query: 302 SLVEIKGVLGTMGLFLGMNLPD 323
           SL EI+ +L + GL +G NL +
Sbjct: 309 SLDEIREMLSSFGLHIGQNLHE 330



 Score = 74.6 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 28/71 (39%), Positives = 39/71 (54%)

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
              L  NPA  K + +L LSVRS  C+    I  +G+L++R+  ++L   NFG  SL EI
Sbjct: 342 PPELADNPATEKPISDLGLSVRSRKCMSRLGIGTIGELLRRSPDELLASRNFGVTSLNEI 401

Query: 307 KGVLGTMGLFL 317
           +  L  M L L
Sbjct: 402 REKLTEMNLKL 412


>gi|166714660|gb|ABY88055.1| RpoA [Stenotrophomonas sp. LMG 957]
          Length = 97

 Score = 85.4 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 38/96 (39%), Positives = 59/96 (61%), Gaps = 3/96 (3%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R  ++     G + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFGYQPAAWRRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           KL + I+T+G+I  E++V  A  IL DQL +F +F 
Sbjct: 62  KLVIDIETNGTIDAEEAVRTADDILSDQLSVFGDFT 97


>gi|260903552|ref|ZP_05911947.1| DNA-directed RNA polymerase, alpha subunit [Vibrio
          parahaemolyticus AQ4037]
 gi|308109055|gb|EFO46595.1| DNA-directed RNA polymerase, alpha subunit [Vibrio
          parahaemolyticus AQ4037]
          Length = 58

 Score = 85.4 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 26/60 (43%), Positives = 37/60 (61%), Gaps = 3/60 (5%)

Query: 2  IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
          +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1  MQGSVTEFLKPRLVD---IEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57


>gi|85713167|ref|ZP_01044199.1| DNA-directed RNA polymerase alpha subunit [Idiomarina baltica
          OS145]
 gi|85693037|gb|EAQ31003.1| DNA-directed RNA polymerase alpha subunit [Idiomarina baltica
          OS145]
          Length = 70

 Score = 85.0 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 27/65 (41%), Positives = 40/65 (61%), Gaps = 3/65 (4%)

Query: 2  IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
          +Q +  E +KP  ++   + Q       +  EPL RGF +TL NALRR+L+SS+ G A+T
Sbjct: 1  MQGSVTEFLKPRLVD---IEQISTTHAKVTLEPLERGFGYTLRNALRRILLSSMPGCAVT 57

Query: 62 AVQID 66
           V+ID
Sbjct: 58 EVEID 62


>gi|325119669|emb|CBZ55222.1| putative RNA polymerase Rpb3/Rpb11 dimerisation domain-containing
           protein [Neospora caninum Liverpool]
          Length = 980

 Score = 85.0 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 41/194 (21%), Positives = 76/194 (39%), Gaps = 30/194 (15%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINL-KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
               ++ +  V ED+ +I LN+KG+    ++      + +   GP ++ AG I   + + 
Sbjct: 548 TQPMVTKLPSVREDILEIALNLKGVAFETLAPRESACIRVKVVGPQLLVAGMIGWPSFVR 607

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTEN---------------DPI 168
           V NP+H I  ++   V+ +E+ +  G G   A  H   R E                D  
Sbjct: 608 VANPEHFIAKVEEGGVLDLEIKLEWGRGAWLADLHGLYREEEGVDTRCYKRRRIWEVDNR 667

Query: 169 GLITIDALYSPIKKVSYTVESA--------REGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           G      ++     +   V           R+      ++L + I TD S + ++ +A A
Sbjct: 668 GFYPTSCVFGACTMMRLAVHKLMGTRFCQDRQVSTNPTEQLVVEIWTDASKSPKEVLAFA 727

Query: 221 SRILQDQLGMFINF 234
              LQD L   ++ 
Sbjct: 728 ---LQDMLAWLLDL 738


>gi|115531954|ref|YP_784109.1| putative rpoA-like protein [Pelargonium x hortorum]
 gi|115531992|ref|YP_784147.1| putative rpoA-like protein [Pelargonium x hortorum]
 gi|122164250|sp|Q06FN4|RPAL2_PELHO RecName: Full=Putative DNA-directed RNA polymerase subunit
           alpha-like 2; Short=Putative PEP 2; AltName:
           Full=Putative plastid-encoded RNA polymerase subunit
           alpha 2; Short=Putative RNA polymerase subunit alpha 2
 gi|112382108|gb|ABI17301.1| putative rpoA-like protein [Pelargonium x hortorum]
 gi|112382146|gb|ABI17339.1| putative rpoA-like protein [Pelargonium x hortorum]
          Length = 322

 Score = 84.2 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 46/235 (19%), Positives = 78/235 (33%), Gaps = 23/235 (9%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
              +E   L             PL    A  L   L   L++ +     T  +I      
Sbjct: 10  WQQVEADQLDSG-LYYGRFALSPLTAKQASLLKKGLPEALLTEILCLRFTHAKIQNECVN 68

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHK-----RVTIFKRGPGVVTAGDIQTVNDIE 126
           + +I G+ E L +I+ N   I L    +           +  RGP    A DI+    I+
Sbjct: 69  LMNIVGIQESLDEILKNFGKIILTGKLEEFVGKGPFVAILDVRGPLNAMAVDIELPPGIK 128

Query: 127 VLNPDHVICNLDVDAVVRMELTVS------KGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           V      I  +       +EL +       KG   +  +   + +       I  + + I
Sbjct: 129 VEIETQHIATITEPIPFVVELKIELVSSTSKGETGITDEEGFSID---PNPPIQKVDTSI 185

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           +   Y  E         +  L + I TD +I   +++A ASR +   L +    E
Sbjct: 186 QCYDYQGEP--------FQTLFLDIWTDRTIHPHEALAQASRKIFGLLSLVFQAE 232


>gi|307069669|ref|YP_003878146.1| putative DNA-directed RNA polymerase subunit alpha [Candidatus
           Zinderia insecticola CARI]
 gi|306482929|gb|ADM89800.1| putative DNA-directed RNA polymerase, alpha subunit [Candidatus
           Zinderia insecticola CARI]
          Length = 224

 Score = 83.9 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 51/202 (25%), Positives = 101/202 (50%), Gaps = 9/202 (4%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
            I   +  +   N +L   + L  G A+ + N ++++ ++ ++G  +  +    + +EIS
Sbjct: 2   KINKFIEKKIGINYSLFYLKNLKNGIANIIANFIKKISLNQIKGFCVYKIIFKNIKNEIS 61

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN-DIEVLNPDH 132
            IKG+ ED+ DI+LNIK +  K+  +      +     G + A +I+T+N +I++LNP H
Sbjct: 62  YIKGIKEDIIDIVLNIKNVIFKIKNNKT-TFFLKNYFLGPIYAYNIKTLNKNIKILNPSH 120

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRT-----ENDPIGLITIDALYSPIKKVSYTV 187
           +I N  +   + + + V KG GY+     +      +     +I +D  Y+P+KK     
Sbjct: 121 LIANAIIKTKLNILIKVKKGKGYINNNEKKKFKYYNKEKKKIVIYLDTNYTPVKKF--FF 178

Query: 188 ESAREGQVLDYDKLSMTIDTDG 209
           +  ++     Y+ L + I T+G
Sbjct: 179 KIKKKIIKKKYEDLKIYIKTNG 200


>gi|91203075|emb|CAJ72714.1| hypothetical protein kustd1969 [Candidatus Kuenenia
           stuttgartiensis]
          Length = 380

 Score = 83.5 bits (205), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 34/90 (37%), Positives = 47/90 (52%), Gaps = 3/90 (3%)

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+ + K       L   + + ELSVRS NCL   NI  + DL + +E D+L   NFG  
Sbjct: 280 DEEASKKQGHEGDVLNIPISDFELSVRSRNCLEKMNIHTLRDLTRISEPDLLTFKNFGET 339

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           SL EIK +L   GL LG +   +   +IE+
Sbjct: 340 SLNEIKAILIQKGLQLGQS---YDGHNIEK 366


>gi|168704678|ref|ZP_02736955.1| probable DNA-directed RNA polymerase alpha chain [Gemmata
           obscuriglobus UQM 2246]
          Length = 458

 Score = 82.3 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 30/78 (38%), Positives = 43/78 (55%)

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +    +      L   + + ELSVRS NCL+  NI  +GDL + TE  +L   NFG  SL
Sbjct: 293 EDEQLTQANRVVLEIPITDFELSVRSRNCLKRMNIRTLGDLTRVTEPQLLASKNFGETSL 352

Query: 304 VEIKGVLGTMGLFLGMNL 321
            EI+ ++ T GL +G +L
Sbjct: 353 DEIRAIMVTKGLRIGQSL 370



 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 27/69 (39%), Positives = 38/69 (55%)

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
           S      L K V +L LSVR+  C+   NI  +G+L+QRT  ++L   NFG+ SL E++ 
Sbjct: 387 SPEEQATLGKPVSDLNLSVRARKCMNRLNIGTLGELVQRTADELLEAKNFGQTSLTEVRE 446

Query: 309 VLGTMGLFL 317
            L    L L
Sbjct: 447 RLQQFNLKL 455


>gi|68000767|ref|XP_669714.1| hypothetical protein [Plasmodium berghei strain ANKA]
 gi|56484216|emb|CAI01628.1| hypothetical protein PB300311.00.0 [Plasmodium berghei]
          Length = 212

 Score = 81.5 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 28/122 (22%), Positives = 58/122 (47%), Gaps = 2/122 (1%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
                  PL     HT G+ ++ V  S + G AI  ++I   ++E + I+   EDL +I 
Sbjct: 92  YQKFYIGPLNITDGHTFGSLIKYVCQSQIYGYAIVGIKIHN-MNEDTKIENTQEDLLEIA 150

Query: 87  LNIKGINLKMSG-DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           LN+  + +     +    + +  +GP ++ AG I   + ++V+N +  IC +  +  + +
Sbjct: 151 LNLSDVCIYSKEINIETNIRLIFKGPLMLVAGMIPLPSHLKVVNKEQYICTIKENGYIDI 210

Query: 146 EL 147
            +
Sbjct: 211 SI 212


>gi|213420797|ref|ZP_03353863.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E01-6750]
          Length = 56

 Score = 81.5 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 31/54 (57%), Positives = 40/54 (74%)

Query: 278 IVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 2   IHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 55


>gi|296120871|ref|YP_003628649.1| RNA polymerase subunit alpha domain protein [Planctomyces
           limnophilus DSM 3776]
 gi|296013211|gb|ADG66450.1| RNA polymerase alpha subunit domain protein [Planctomyces
           limnophilus DSM 3776]
          Length = 451

 Score = 81.5 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 32/80 (40%), Positives = 47/80 (58%)

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            +D+          L + V + ELSVRS NCL   +I  +GDL + +E+D+L+  NFG  
Sbjct: 275 DDDMARNEARMAQLLSRPVTDFELSVRSRNCLASMDIHTLGDLTRVSESDLLQGKNFGET 334

Query: 302 SLVEIKGVLGTMGLFLGMNL 321
           SLVEI+ ++   GL +G NL
Sbjct: 335 SLVEIRDLMQQHGLKVGQNL 354



 Score = 68.5 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 26/81 (32%), Positives = 38/81 (46%)

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           P        N  S      L + V +L LSVR+  C+    I  +G+L+Q++  ++L   
Sbjct: 368 PASAFAPIGNDLSPQEQALLSRPVSDLNLSVRARKCMARLQIGTLGELVQKSADELLATK 427

Query: 297 NFGRKSLVEIKGVLGTMGLFL 317
           NFG  SL EI+  L    L L
Sbjct: 428 NFGVTSLNEIRAQLTEHNLKL 448


>gi|32471678|ref|NP_864671.1| DNA-directed RNA polymerase alpha chain [Rhodopirellula baltica SH
           1]
 gi|32397049|emb|CAD72353.1| probable DNA-directed RNA polymerase alpha chain [Rhodopirellula
           baltica SH 1]
 gi|327539093|gb|EGF25725.1| RNA polymerase alpha subunit domain protein [Rhodopirellula baltica
           WH47]
          Length = 500

 Score = 81.2 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 31/78 (39%), Positives = 42/78 (53%)

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+   ++      L   V   ELSVRS NCL+   I  +GDL + +E ++L   NFG  
Sbjct: 334 DEEAQRRNDRLAQTLNMPVANFELSVRSRNCLQKMGIETIGDLTRHSEQELLSSKNFGET 393

Query: 302 SLVEIKGVLGTMGLFLGM 319
           SLVEI+ +L   GL LG 
Sbjct: 394 SLVEIREMLSQKGLSLGQ 411



 Score = 70.4 bits (171), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 31/104 (29%), Positives = 50/104 (48%), Gaps = 2/104 (1%)

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL--KKVEELELSVRSTN 271
           E S+     +L  +      F   KK     ++   +  +   L  + + +L LSVR+  
Sbjct: 392 ETSLVEIREMLSQKGLSLGQFAGEKKSNDPPVDTSHMSPDEQALLERPIADLNLSVRARK 451

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           C+    I  +G+LI++T  DML   NFG  SL E++  LG +GL
Sbjct: 452 CMTRLQINSIGELIRKTGDDMLECKNFGVTSLNEVREKLGDLGL 495


>gi|143452|gb|AAA22708.1| RNA polymerase alpha subunit [Bacillus subtilis]
          Length = 65

 Score = 81.2 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 33/65 (50%), Positives = 46/65 (70%), Gaps = 2/65 (3%)

Query: 8  ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
          E+ KP  IE + +  + +     + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3  EIEKP-KIETVEISDDAKF-GKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 60

Query: 68 VLHEI 72
          VLHE 
Sbjct: 61 VLHEF 65


>gi|283781750|ref|YP_003372505.1| RNA polymerase subunit alpha [Pirellula staleyi DSM 6068]
 gi|283440203|gb|ADB18645.1| RNA polymerase alpha subunit domain protein [Pirellula staleyi DSM
           6068]
          Length = 440

 Score = 81.2 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 30/78 (38%), Positives = 44/78 (56%)

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+   ++      L   V + ELSVRS NCL+   +  +GDL + +E ++L   NFG  
Sbjct: 274 DEEAQRRNDRLAQVLSIPVTDFELSVRSRNCLQKMGVRTLGDLTRTSEQELLASKNFGET 333

Query: 302 SLVEIKGVLGTMGLFLGM 319
           SLVEI+ +L + GL LG 
Sbjct: 334 SLVEIRDMLHSKGLELGQ 351



 Score = 72.7 bits (177), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 29/106 (27%), Positives = 53/106 (50%), Gaps = 2/106 (1%)

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL--KKVEELELSVRSTN 271
           E S+     +L  +      F   K   +  +++ S+  +   L  + + EL LSVR+  
Sbjct: 332 ETSLVEIRDMLHSKGLELGQFAAEKAVAEPVLDLASMSPDEQALLERPISELNLSVRARK 391

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           C+    +  +G+L+++T  D+L   NFG  SL E++  L T+G+ L
Sbjct: 392 CMARLGLTLIGELVRKTGDDLLECKNFGVTSLNEVREKLTTLGIKL 437


>gi|213585431|ref|ZP_03367257.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E98-0664]
          Length = 54

 Score = 81.2 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 30/53 (56%), Positives = 39/53 (73%)

Query: 279 VYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 1   HYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 53


>gi|166714710|gb|ABY88080.1| RpoA [Stenotrophomonas sp. LMG 10851]
 gi|166714712|gb|ABY88081.1| RpoA [Stenotrophomonas sp. LMG 10877]
          Length = 93

 Score = 80.8 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 35/95 (36%), Positives = 59/95 (62%), Gaps = 3/95 (3%)

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           G + +DA +SP+++V+Y VE+AR  Q  D DKL + I+T+G+I  E++V  A+ IL DQL
Sbjct: 2   GRLVLDASFSPVRRVAYAVEAARVEQRTDLDKLVIDIETNGTIDAEEAVRTAADILSDQL 61

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            +F +F    +   +  N      +P LL+ +++L
Sbjct: 62  SVFGDFTHRDRGAAKPAN---NGVDPVLLRPIDDL 93


>gi|291533600|emb|CBL06713.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Megamonas
           hypermegale ART12/1]
          Length = 85

 Score = 80.4 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 25/62 (40%), Positives = 40/62 (64%)

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +    +  +   +E+L+LSVRS NCL+   I  + DL+Q++E DM+++ N GRKSL E+
Sbjct: 18  PEEDNTSKVMEMTIEDLDLSVRSYNCLKRAEINTVADLMQKSEDDMIKVRNLGRKSLEEV 77

Query: 307 KG 308
           K 
Sbjct: 78  KK 79


>gi|207092544|ref|ZP_03240331.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
          HPKX_438_AG0C1]
          Length = 126

 Score = 78.5 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 30/85 (35%), Positives = 51/85 (60%), Gaps = 3/85 (3%)

Query: 10 IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
          + P+ I+ +   ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV 
Sbjct: 9  LIPSEIKVL---EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPIGLKIEGVH 65

Query: 70 HEISSIKGVHEDLTDIILNIKGINL 94
          HE  S++GV ED++  I+N+K I  
Sbjct: 66 HEFDSLRGVTEDVSLFIMNLKNIRF 90


>gi|326392492|ref|ZP_08213873.1| RNA polymerase dimerization [Thermoanaerobacter ethanolicus JW 200]
 gi|325991467|gb|EGD50078.1| RNA polymerase dimerization [Thermoanaerobacter ethanolicus JW 200]
          Length = 85

 Score = 78.5 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 27/82 (32%), Positives = 45/82 (54%)

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           L+   K+VSY VE+ R G V DYDKL++ + T+G+IT ++++++AS +L      FI+F 
Sbjct: 3   LFYTSKRVSYNVENTRVGHVTDYDKLTLEVWTNGTITPKEAISMASDMLIKYFQKFISFT 62

Query: 236 EPKKEVKEDINVKSLPFNPALL 257
              K     ++          L
Sbjct: 63  GEYKSSDIFVDKPEKKSRETYL 84


>gi|224179501|ref|YP_002601032.1| alpha subunit of RNA polymerase [Monomastix sp. OKE-1]
 gi|217314544|gb|ACK36887.1| alpha subunit of RNA polymerase [Monomastix sp. OKE-1]
          Length = 324

 Score = 78.5 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 53/292 (18%), Positives = 93/292 (31%), Gaps = 83/292 (28%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------VL 69
                  +        L +G   T+ NALRRVL+  + G  IT V+ +           L
Sbjct: 34  TFENSSLHYGKFYLSGLKKGQGITVANALRRVLLYDIMGLGITKVKFNSKNNENLSSQKL 93

Query: 70  HEISSIKGVHEDLTDIILNIKGINL---------KMSGDS-------HKRVTIFKRGPGV 113
           HE S+I G+ E + ++++N++ +           K+SGDS       H+ + I       
Sbjct: 94  HEFSTISGIRESILELLMNLRLLVWTTSPLDSNQKVSGDSSSDPLLVHEELDISSSPSLT 153

Query: 114 VTAGDIQTVNDIEVLN---------------------------------------PDHVI 134
              G        +  +                                       P+  +
Sbjct: 154 SYLGQFSLPEYFKSKDWLSEKNKNNQSSVFVLRGKHLISADQRTNQNPNFAQLINPEQYL 213

Query: 135 CN----------LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
                       L       +E  + KG+ +          +    +     + P+KKV+
Sbjct: 214 ATILPIQKTATGLSKFPEFEIEYKIGKGNLFENLDLQSNNEE---FLLNSGPFFPVKKVN 270

Query: 185 YTVESAREGQVLDY------DKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           YTVE  +             + +   I TDGS+  E +++ A  IL D    
Sbjct: 271 YTVEDIKNSTNNFLWERGFSECVFFEIWTDGSLHPEKALSQAFDILLDFFQQ 322


>gi|68062152|ref|XP_673079.1| hypothetical protein [Plasmodium berghei strain ANKA]
 gi|56490663|emb|CAI02138.1| hypothetical protein PB300573.00.0 [Plasmodium berghei]
          Length = 299

 Score = 78.1 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 30/159 (18%), Positives = 62/159 (38%), Gaps = 4/159 (2%)

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK----HHR 162
             +GP +V AG +Q   +IE++N +  IC +   + + M++ +     YV  +       
Sbjct: 14  RIKGPMIVVAGHMQLPKNIEIINKNQYICYVAAGSYLEMDVKIESIEEYVMPEYGSQSRN 73

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            +      I   +  +P++   +T +       +  +   + + TDGSIT + ++     
Sbjct: 74  RDICKDNFIHFCSSCTPVEYFGFTGQRRGINLDILGEINIVEMHTDGSITPKTALLKTID 133

Query: 223 ILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + +      N         ED +V+    NP      E
Sbjct: 134 YMSENFQYIENALHNNCHSCEDGSVEEEFRNPEFYMDKE 172


>gi|207108315|ref|ZP_03242477.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           HPKX_438_CA4C1]
          Length = 130

 Score = 77.7 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 35/123 (28%), Positives = 62/123 (50%), Gaps = 12/123 (9%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           + P+ I+ +   ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV 
Sbjct: 9   LIPSEIKVL---EKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPIGLKIEGVH 65

Query: 70  HEISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           HE  S++GV ED++  I+N+K I               +    V    +GP  + A D+ 
Sbjct: 66  HEFDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLN 125

Query: 121 TVN 123
           + +
Sbjct: 126 SEH 128


>gi|239933877|ref|ZP_04690830.1| DNA-directed RNA polymerase subunit alpha [Streptomyces ghanaensis
           ATCC 14672]
          Length = 88

 Score = 74.2 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 24/76 (31%), Positives = 43/76 (56%)

Query: 160 HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
            ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL + ++T  ++   D++A 
Sbjct: 2   QNKQVGQEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLIVDVETKQAMRPRDAMAS 61

Query: 220 ASRILQDQLGMFINFE 235
           A + L +  G+     
Sbjct: 62  AGKTLVELFGLARELN 77


>gi|71027147|ref|XP_763217.1| DNA-directed RNA polymerase subunit alpha [Theileria parva strain
           Muguga]
 gi|68350170|gb|EAN30934.1| DNA-directed RNA polymerase, alpha subunit, putative [Theileria
           parva]
          Length = 377

 Score = 74.2 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 48/270 (17%), Positives = 94/270 (34%), Gaps = 63/270 (23%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKM-----SGDSHKRVTIFKRGPGVVTAGDIQTV 122
           + +E  S+ G+ ED  +++ N++G+  K      +  +    T+  +GP +  AG ++  
Sbjct: 1   MDNEFYSVVGLREDFFELVRNLRGVIFKNVPKTATFTNPVIATLRLKGPIIAVAGHLKFD 60

Query: 123 --------------------------------------------NDIEVLNPDHVICNLD 138
                                                        +IEV+N +H IC+L 
Sbjct: 61  NKKSSKTNPNSTDESTDKNADNTDAKVENAENVINDYVYDKKYTGEIEVINKNHYICSLS 120

Query: 139 VDAVVRMELTVSKGHGYVPAKHH----RTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
               + M++ +     YV  +H       +  P G I   +  +P++   +T E     +
Sbjct: 121 QGCYLTMDVKIEYISNYVIPEHGPESLNRDITPDGFIHFCSSVNPVEVFGFTGERRGLDE 180

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
               + +++ + TDGS T   ++  ++  L +     +               K   FN 
Sbjct: 181 QSTSEIVTLEVHTDGSATPRVALLKSATFLLNWFDRTLYALRTNLSRDFYALKKENMFNT 240

Query: 255 ALLKKVEELE--------LSV--RSTNCLR 274
           + L    EL         LS   R  N L+
Sbjct: 241 SPLMLNHELNRNLPWNPYLSPEQRVANKLK 270


>gi|166714662|gb|ABY88056.1| RpoA [Stenotrophomonas sp. LMG 978]
          Length = 81

 Score = 73.5 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 29/79 (36%), Positives = 48/79 (60%), Gaps = 3/79 (3%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPI---GLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R  ++     G + +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVA 218
           KL + I+ +G+I  E++V 
Sbjct: 62  KLVIDIENNGTIDAEEAVR 80


>gi|115531956|ref|YP_784111.1| putative rpoA-like protein [Pelargonium x hortorum]
 gi|115531990|ref|YP_784145.1| putative rpoA-like protein [Pelargonium x hortorum]
 gi|122164251|sp|Q06FN6|RPAL3_PELHO RecName: Full=Putative DNA-directed RNA polymerase subunit
           alpha-like 3; Short=Putative PEP 3; AltName:
           Full=Putative plastid-encoded RNA polymerase subunit
           alpha 3; Short=Putative RNA polymerase subunit alpha 3
 gi|112382110|gb|ABI17303.1| putative rpoA-like protein [Pelargonium x hortorum]
 gi|112382144|gb|ABI17337.1| putative rpoA-like protein [Pelargonium x hortorum]
          Length = 365

 Score = 73.1 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 38/216 (17%), Positives = 77/216 (35%), Gaps = 10/216 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            ++         PL    +  L   L   L++ +     T  +I      + +I G+ E 
Sbjct: 28  HKDFAYGRFALSPLTAKESRLLKKGLFEALLTEILCLRFTHAKIQNECVNLMNIVGIQES 87

Query: 82  LTDIILNIKGINLKMSGDSHK-----RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           L +I+ N   I L    +           +  RGP    A DI+    I+V      I  
Sbjct: 88  LDEILKNFGKIILTGKLEEFVGKGPFVAILDVRGPLNAMAVDIELPPGIKVEIETQHIAT 147

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +       +EL +               ++    I  +    PI+KV+ +++    G   
Sbjct: 148 ITEPIPFVVELRIEL-VSSTSKGETGITDEEGFSIDPNP---PIRKVNSSIQGYEYGGQT 203

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
            +++LS+ + T   I   +++ L S  + +   + +
Sbjct: 204 -FERLSIEMLTSLPIIPNEALLLGSMKIMNLFQIVL 238



 Score = 44.6 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 17/106 (16%), Positives = 42/106 (39%), Gaps = 12/106 (11%)

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           I  +  DA     L +  G  +        ++       ID+ ++P++ +   +ES  E 
Sbjct: 270 IKTILEDA-----LYMVGGRKHQGPLTDEEDDS------IDSNFTPVQNLDCRIESYEEE 318

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
               + +L + I T      ++++  AS  + +   +F+   +  +
Sbjct: 319 GQT-FQRLFLEIWTKSPTEPQEALWEASAKILELFSLFLQTSKENE 363


>gi|110004169|emb|CAK98507.1| hypothetical protein with alpha rna polymerase domain pd001179
           [Spiroplasma citri]
          Length = 111

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 24/85 (28%), Positives = 44/85 (51%)

Query: 233 NFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           N  E ++++   + +     N  L   +++LE++ R+  CL    I  + DL+ +TE ++
Sbjct: 25  NSNEIQEQITIWLEMDETERNQLLNHSIDDLEITQRTQICLEKAKIYRLSDLVSKTENEI 84

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFL 317
             + N G KSL EIK  +  +GL  
Sbjct: 85  KNIKNLGEKSLTEIKEKMHELGLHF 109


>gi|255027531|ref|ZP_05299517.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
          FSL J2-003]
          Length = 55

 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 26/55 (47%), Positives = 37/55 (67%), Gaps = 2/55 (3%)

Query: 8  ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
          E+ KP  IE I +  ++      + EPL RG+  TLGN+LRR+L+SSL GAA+T+
Sbjct: 3  EIEKP-KIETIEIS-DDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTS 55


>gi|94502342|ref|ZP_01308812.1| DNA-directed RNA polymerase alpha chain [Candidatus Sulcia muelleri
           str. Hc (Homalodisca coagulata)]
 gi|94451097|gb|EAT14052.1| DNA-directed RNA polymerase alpha chain [Candidatus Sulcia muelleri
           str. Hc (Homalodisca coagulata)]
          Length = 87

 Score = 70.8 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 29/79 (36%), Positives = 47/79 (59%)

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYVP++ ++      G I +D++++PIK V Y +++    +  +Y+ L + I TDGSI  
Sbjct: 2   GYVPSEENKENLIGSGSIPMDSIFTPIKNVKYKIDNCSINKNSNYESLLLEIKTDGSINP 61

Query: 214 EDSVALASRILQDQLGMFI 232
            D++  AS IL   L MFI
Sbjct: 62  RDALTNASNILIQHLKMFI 80


>gi|166714640|gb|ABY88045.1| RpoA [Stenotrophomonas rhizophila]
          Length = 79

 Score = 68.1 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 30/82 (36%), Positives = 49/82 (59%), Gaps = 3/82 (3%)

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +V+Y VE+AR  Q  D DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +  
Sbjct: 1   RVAYAVEAARVEQRTDLDKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGA 60

Query: 242 KEDINVKSLPFNPALLKKVEEL 263
            +  N      +P LL+ +++L
Sbjct: 61  AKPAN---NGVDPVLLRPIDDL 79


>gi|115531952|ref|YP_784107.1| putative rpoA-like protein [Pelargonium x hortorum]
 gi|115531994|ref|YP_784149.1| putative rpoA-like protein [Pelargonium x hortorum]
 gi|122164248|sp|Q06FN2|RPAL1_PELHO RecName: Full=Putative DNA-directed RNA polymerase subunit
           alpha-like 1; Short=Putative PEP 1; AltName:
           Full=Putative plastid-encoded RNA polymerase subunit
           alpha 1; Short=Putative RNA polymerase subunit alpha 1
 gi|112382106|gb|ABI17299.1| putative rpoA-like protein [Pelargonium x hortorum]
 gi|112382148|gb|ABI17341.1| putative rpoA-like protein [Pelargonium x hortorum]
          Length = 574

 Score = 67.7 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 37/213 (17%), Positives = 71/213 (33%), Gaps = 12/213 (5%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI--SSIKGVHEDLTD 84
                  PL    +  L   LR  L++ +     T  +I      +   +I G+ E L +
Sbjct: 24  YGRFALSPLTAKESRLLKKGLREALLTGILCLRFTHAKIQNACKNLNLMNIVGIQESLDE 83

Query: 85  IILNIKGINLKMSGDSHK-----RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           I+ N   I L    +           +  RGP    A DI+    I+V      I  +  
Sbjct: 84  ILKNFGKIILTGKLEEFVGKGPFVAILDVRGPLNAMAVDIELPPGIKVEIETQHIATITE 143

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
                +EL +               ++    I  +    PI+KV+ +++    G    + 
Sbjct: 144 PIPFVVELRIEL-VSSTSKGETGITDEEGFSIDPNP---PIQKVNSSIQGYEYGGQT-FQ 198

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
            L + I +        ++ L S  + +   + +
Sbjct: 199 TLFIEILSTSPTVPNKALLLVSMKIMNLFQIVL 231



 Score = 43.8 bits (102), Expect = 0.041,   Method: Composition-based stats.
 Identities = 17/106 (16%), Positives = 42/106 (39%), Gaps = 12/106 (11%)

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           I  +  DA     L +  G  +        ++       ID+ ++P++ +   +ES  E 
Sbjct: 263 IKTILEDA-----LYMVGGRKHQGPLTDEEDDS------IDSNFTPVQNLDCRIESYEEE 311

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
               + +L + I T      ++++  AS  + +   +F+   +  +
Sbjct: 312 GQT-FQRLFLEIWTKSPTEPQEALWEASAKILELFSLFLQTSKENE 356


>gi|32474617|ref|NP_867611.1| DNA-directed RNA polymerase alpha chain [Rhodopirellula baltica SH
           1]
 gi|32445156|emb|CAD75158.1| probable DNA-directed RNA polymerase alpha chain [Rhodopirellula
           baltica SH 1]
 gi|327540701|gb|EGF27273.1| DNA-directed RNA polymerase, alpha subunit [Rhodopirellula baltica
           WH47]
          Length = 92

 Score = 66.5 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 21/58 (36%), Positives = 36/58 (62%)

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
            + E+ L+VR+TNCL    I+ + DL+  T   +L+++NFG K+L E+   L  +G +
Sbjct: 24  SIAEMGLTVRTTNCLEETGILTVRDLLNATPRRLLKISNFGEKTLEEVYDALEQLGFY 81


>gi|313906563|ref|ZP_07839891.1| RNA polymerase alpha subunit domain protein [Eubacterium
           cellulosolvens 6]
 gi|313468593|gb|EFR63967.1| RNA polymerase alpha subunit domain protein [Eubacterium
           cellulosolvens 6]
          Length = 976

 Score = 66.5 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 21/62 (33%), Positives = 33/62 (53%)

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 ++ + LS RSTN L  E I  +GD++  TE  +L++ N G+KS+ EI   +   
Sbjct: 2   NIEALSIDTIGLSARSTNALHREEIHTVGDMLGFTEESLLQVKNLGKKSVEEIVEKIKKY 61

Query: 314 GL 315
            L
Sbjct: 62  KL 63


>gi|213580698|ref|ZP_03362524.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
          subsp. enterica serovar Typhi str. E98-0664]
          Length = 46

 Score = 65.8 bits (159), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 20/49 (40%), Positives = 28/49 (57%), Gaps = 3/49 (6%)

Query: 2  IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRV 50
          +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+
Sbjct: 1  MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRRI 46


>gi|108773408|ref|YP_635927.1| PEP RNA polymerase alpha subunit [Helicosporidium sp. ex Simulium
           jonesii]
 gi|122197336|sp|Q2EEW7|RPOA_HELSJ RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|87242983|gb|ABD33975.1| RNA polymerase alpha chain [Helicosporidium sp. ex Simulium jonesi]
          Length = 246

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 92/240 (38%), Gaps = 31/240 (12%)

Query: 21  GQEEENRT-LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
            +   N     +  PLP G A +LG  +R VL+      A+  ++ +   +   +  G  
Sbjct: 11  NEYNNNYAASFLIGPLPEGIAQSLGFNIRSVLLKEFPYFAVKNIRFNPENNNYKTHIGTK 70

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGP----------------------GVVTAG 117
           E +  II  I GI+   S D +K + ++K  P                      G++ A 
Sbjct: 71  ESIETIINTILGIDFNYSFDFYKAMGLYKSKPKALFQENLSKAKFLCSAKQVGEGILYAK 130

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           D+     I+   P  +I ++     +    T   G  +    + + EN            
Sbjct: 131 DLMLPVGIKCTTPYKIIAHVTKQNFL--GFTFELGFLFGLNNNIKFENKLY-----SIKT 183

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA-LASRILQDQLGMFINFEE 236
            PI+ ++  + ++++   L+ + + ++  T  S+   D +  L+  +L   L +   F++
Sbjct: 184 YPIQNINIEIINSKKSFNLNSESIILSFTTKSSLQPIDVIKILSYLLLNKHLILIKAFQQ 243


>gi|87309222|ref|ZP_01091359.1| probable DNA-directed RNA polymerase alpha chain [Blastopirellula
           marina DSM 3645]
 gi|87288213|gb|EAQ80110.1| probable DNA-directed RNA polymerase alpha chain [Blastopirellula
           marina DSM 3645]
          Length = 93

 Score = 64.6 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 26/70 (37%), Positives = 39/70 (55%)

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +S      L     E+ L+VR+TNCL    I  + DL+  T AD+L ++NFG K+L E+
Sbjct: 11  QESESLMSKLEMSTAEIGLTVRTTNCLEERGIFTVRDLLNCTRADLLSISNFGEKTLDEV 70

Query: 307 KGVLGTMGLF 316
              L ++G F
Sbjct: 71  YSSLESIGFF 80


>gi|315651633|ref|ZP_07904644.1| conserved hypothetical protein [Eubacterium saburreum DSM 3986]
 gi|315486087|gb|EFU76458.1| conserved hypothetical protein [Eubacterium saburreum DSM 3986]
          Length = 596

 Score = 63.4 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 17/66 (25%), Positives = 34/66 (51%)

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                     ++ LEL VRS N L+  NI+ +  L++ ++ ++L++ N G++ + EI+  
Sbjct: 217 EMQQKVDEDSIDNLELGVRSYNVLKRANIISIKKLLKMSDDELLKIRNLGKRQVAEIRTQ 276

Query: 310 LGTMGL 315
           L     
Sbjct: 277 LIEKNY 282


>gi|1491730|emb|CAA67855.1| orf [Musa balbisiana]
          Length = 67

 Score = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 19/66 (28%), Positives = 34/66 (51%)

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           +LN+K I L+ +    +  +I  RGP  VTA DI +   +E+++    I NL     + +
Sbjct: 1   LLNLKEIVLRSNIYGVRDASICARGPKYVTAQDIISPPSVEIVDTTQHIANLTEPIDLCI 60

Query: 146 ELTVSK 151
            L + +
Sbjct: 61  GLQIRR 66


>gi|301500891|ref|YP_003795303.1| RNA polymerase alpha subunit [Chromera velia]
 gi|300069437|gb|ADJ66545.1| RNA polymerase alpha subunit [Chromera velia]
          Length = 238

 Score = 61.9 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 24/105 (22%), Positives = 47/105 (44%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           NALRR   S   G  ++ ++    L+E   + G  E + D +  +K +  +    +    
Sbjct: 36  NALRRTFYSRTGGYQVSRIKTSSHLNEYLPLWGFQESIFDFLAALKMLIFRGKDYNSYIG 95

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           ++   GP ++ A  IQ   +I ++N +H +  L      R+ L +
Sbjct: 96  SLQSSGPILLIAAFIQLHPNICLVNKNHYLGTLLPGFKFRLYLEI 140


>gi|150389913|ref|YP_001319962.1| RNA polymerase subunit alpha [Alkaliphilus metalliredigens QYMF]
 gi|149949775|gb|ABR48303.1| RNA polymerase, alpha subunit domain protein [Alkaliphilus
           metalliredigens QYMF]
          Length = 912

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 19/66 (28%), Positives = 31/66 (46%)

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +      +  L LS RS N LR E I    DL+  ++ D++   + G KSL EI   +
Sbjct: 1   MHSHNYSDSISTLNLSTRSYNTLRREGIHTTNDLLNCSKDDIINFRSVGVKSLEEIVNAI 60

Query: 311 GTMGLF 316
            ++  +
Sbjct: 61  DSLNKY 66



 Score = 50.3 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 18/50 (36%), Positives = 33/50 (66%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           +E L LSVR+ NCL+  ++ Y   LI   + +++ + N GRK+L+E++ +
Sbjct: 98  IENLNLSVRAFNCLKSTSVDYYSQLIDVLDEELIAIPNMGRKTLLELEHI 147


>gi|224088404|ref|XP_002335097.1| predicted protein [Populus trichocarpa]
 gi|222832850|gb|EEE71327.1| predicted protein [Populus trichocarpa]
          Length = 54

 Score = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 13/47 (27%), Positives = 31/47 (65%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           +++LEL+ +  NCL+  NI  + DL++ ++ D++++ +F  + +  I
Sbjct: 6   IDQLELAPKIYNCLKRSNIHTLWDLLKNSQEDLMKIEHFRIEDVKHI 52


>gi|295091278|emb|CBK77385.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Clostridium cf. saccharolyticum K10]
          Length = 1539

 Score = 60.4 bits (145), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 25/115 (21%), Positives = 50/115 (43%), Gaps = 3/115 (2%)

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN---PALLK 258
              +   G ++ E+       I+Q    ++   EE  K + E     S            
Sbjct: 136 IFELRNVGVLSREEITKAIESIVQSGKIVYHEREEESKTIIETAPESSRLSELLPEIESI 195

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           +++++  SVR+ N L+  NI    +L+Q +E D++ + N G ++  EI  V+  +
Sbjct: 196 RLDDVPFSVRARNALKRANIQTADELVQMSEKDIMGLRNVGAQTRDEILAVINAI 250



 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 23/92 (25%), Positives = 39/92 (42%)

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
            +LQ+  G+  + +      +E                +E L L  R+TN LR   I  +
Sbjct: 66  DVLQELNGVIAHSDVIISFFEERAKRIKEILPNVQDAPIESLGLGTRATNALRRGGIHTV 125

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           G LIQ ++ D+  + N G  S  EI   + ++
Sbjct: 126 GALIQMSQKDIFELRNVGVLSREEITKAIESI 157


>gi|31580946|dbj|BAC77576.1| RNA polymerase alpha subunit [Nicotiana tomentosiformis]
          Length = 77

 Score = 60.4 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 14/48 (29%), Positives = 30/48 (62%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F  + + +I 
Sbjct: 29  IDQLELPSRIYNCLKMSNIYTLLDLLNNSQEDLMKIEHFRSEDVKQIL 76


>gi|310658943|ref|YP_003936664.1| RNA polymerase subunit alpha domain-containing protein [Clostridium
           sticklandii DSM 519]
 gi|308825721|emb|CBH21759.1| RNA polymerase, alpha subunit domain protein [Clostridium
           sticklandii]
          Length = 911

 Score = 60.0 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 22/64 (34%), Positives = 37/64 (57%)

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
             L  ++E+L LSVR+ NCL+ + I Y   L+ +   +++ + N G+KSLVEI+    + 
Sbjct: 92  KYLDVEIEKLCLSVRAYNCLKSDGIEYYSQLVDKLVEELITIPNMGQKSLVEIEEKRASF 151

Query: 314 GLFL 317
              L
Sbjct: 152 QPEL 155



 Score = 53.8 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 20/63 (31%), Positives = 30/63 (47%)

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                 L  +  L+ S RS N L    I  +GDL+  T+ D+  +   G KS+ EI GV+
Sbjct: 1   MNTHHHLDSISVLKFSARSYNALMRVGICSIGDLLSCTKDDISGIRQLGAKSIEEITGVI 60

Query: 311 GTM 313
             +
Sbjct: 61  DEL 63


>gi|31580902|dbj|BAC77553.1| RNA polymerase alpha subunit [Nicotiana sylvestris]
          Length = 79

 Score = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 14/48 (29%), Positives = 29/48 (60%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F  + +  I 
Sbjct: 31  IDQLELPSRIYNCLKMSNIYTLLDLLNNSQEDLMKIEHFRSEDVKRIL 78


>gi|301060344|ref|ZP_07201207.1| bacterial RNA polymerase, alpha chain C-terminal domain protein
           [delta proteobacterium NaphS2]
 gi|300445540|gb|EFK09442.1| bacterial RNA polymerase, alpha chain C-terminal domain protein
           [delta proteobacterium NaphS2]
          Length = 772

 Score = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 25/70 (35%), Positives = 41/70 (58%), Gaps = 1/70 (1%)

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGEN-IVYMGDLIQRTEADMLRMANFGRKSL 303
           I  K L  +     K+E++ LS R+ + L  +  +  +GD++  T  D+L + NFGRKSL
Sbjct: 128 ITAKDLHPDFQGAVKLEDIRLSHRTFHTLLNQGQMETIGDVMLTTCTDLLSLKNFGRKSL 187

Query: 304 VEIKGVLGTM 313
            EIK V+ ++
Sbjct: 188 NEIKEVIRSL 197



 Score = 38.8 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 27/73 (36%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           V E   SVR+TN L  +N+       Q T  D+    N GRK+++EI   L  +GL   +
Sbjct: 37  VMESGFSVRATNVLI-DNVKSFRAFEQLTAEDLAVFPNCGRKTVLEIMNFLNRIGLQREI 95

Query: 320 NLPDWPPESIEEL 332
                 P SIEEL
Sbjct: 96  E----APVSIEEL 104


>gi|224126651|ref|XP_002319890.1| predicted protein [Populus trichocarpa]
 gi|222858266|gb|EEE95813.1| predicted protein [Populus trichocarpa]
          Length = 62

 Score = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 31/53 (58%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +++LEL+ +  NCL+   I  + D ++ ++ D+++  +F  + +  I G+L  
Sbjct: 10  IDQLELAPKIYNCLKRSVIHTLWDFLKNSQEDLMKTEHFRIEDVKHIFGILKI 62


>gi|325120592|emb|CBZ56146.1| putative DNA-directed RNA polymerase alpha chain [Neospora caninum
           Liverpool]
          Length = 941

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 23/103 (22%), Positives = 39/103 (37%), Gaps = 4/103 (3%)

Query: 101 HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP--- 157
             R  +  RGP V  AG IQ    +EV+N +  +  ++    V M+  + +   YV    
Sbjct: 388 PLRAKLRVRGPLVAVAGHIQLPEGVEVVNKNQYLFTVNSGYYVNMDFKIERIREYVMPEF 447

Query: 158 -AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
                  + D  G +      +P+   +Y  E   E     +D
Sbjct: 448 GYDSLERDRDEEGFMYFTNHVAPVPIFAYAAERRGEAVHTKWD 490



 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 22/69 (31%), Positives = 32/69 (46%), Gaps = 1/69 (1%)

Query: 28  TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT-DII 86
                       A    NALRR  +S +   A+ AV+I+G  HE  S+ G+ ED+  DI 
Sbjct: 166 AFFYFHTCFSSLAPAFLNALRRTSLSRIESLAVAAVKIEGAKHEFYSLPGIREDIVDDIF 225

Query: 87  LNIKGINLK 95
            N+  I  +
Sbjct: 226 NNLGKIVFR 234


>gi|221484912|gb|EEE23202.1| DNA-directed RNA polymerase alpha chain, putative [Toxoplasma
           gondii GT1]
          Length = 837

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 23/103 (22%), Positives = 39/103 (37%), Gaps = 4/103 (3%)

Query: 101 HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP--- 157
             R  +  RGP V  AG IQ    +EV+N +  +  ++    V M+  + +   YV    
Sbjct: 281 PLRAKLRVRGPLVAVAGHIQLPEGVEVVNKNQYLFTVNAGYYVNMDFKIERIREYVMPEF 340

Query: 158 -AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
                  + D  G +      +P+   +Y  E   E     +D
Sbjct: 341 GYDSLERDRDKEGFMYFTNYVAPVPIFAYAAERRGEAVHTKWD 383



 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 23/52 (44%), Positives = 32/52 (61%), Gaps = 1/52 (1%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT-DIILNIKGINLK 95
           NALRR  +S L   AI+AV+I+G  HE  S+ G+ ED+  DI  N+  I  +
Sbjct: 74  NALRRTSLSRLESLAISAVKIEGAKHEFYSLPGIREDIVDDIFNNLGKIVFR 125


>gi|237835983|ref|XP_002367289.1| DNA-directed RNA polymerase alpha chain, putative [Toxoplasma
           gondii ME49]
 gi|211964953|gb|EEB00149.1| DNA-directed RNA polymerase alpha chain, putative [Toxoplasma
           gondii ME49]
 gi|221506032|gb|EEE31667.1| DNA-directed RNA polymerase alpha chain, putative [Toxoplasma
           gondii VEG]
          Length = 836

 Score = 58.1 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 23/103 (22%), Positives = 39/103 (37%), Gaps = 4/103 (3%)

Query: 101 HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP--- 157
             R  +  RGP V  AG IQ    +EV+N +  +  ++    V M+  + +   YV    
Sbjct: 281 PLRAKLRVRGPLVAVAGHIQLPEGVEVVNKNQYLFTVNAGYYVNMDFKIERIREYVMPEF 340

Query: 158 -AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
                  + D  G +      +P+   +Y  E   E     +D
Sbjct: 341 GYDSLERDRDKEGFMYFTNYVAPVPIFAYAAERRGEAVHTKWD 383



 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 23/52 (44%), Positives = 32/52 (61%), Gaps = 1/52 (1%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT-DIILNIKGINLK 95
           NALRR  +S L   AI+AV+I+G  HE  S+ G+ ED+  DI  N+  I  +
Sbjct: 74  NALRRTSLSRLESLAISAVKIEGAKHEFYSLPGIREDIVDDIFNNLGKIVFR 125



 Score = 36.1 bits (82), Expect = 7.7,   Method: Composition-based stats.
 Identities = 17/119 (14%), Positives = 37/119 (31%), Gaps = 16/119 (13%)

Query: 152 GHGYVPAKHHRTEN-DPIGLITIDALYSPIKKVSYTV----ESAREGQVLDY-------- 198
           G      +    +       +   +     +  +Y +    E  RE    DY        
Sbjct: 485 GKDAKVNEEGSPDRPASHSSLPFASKKPEDRYNAYRLLEPSEEMREAYRRDYLENDLPYQ 544

Query: 199 ---DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
              + +++ + TDGS+T  ++V      L  Q+    +       +  D   +    +P
Sbjct: 545 NLGEVVTLEVQTDGSLTPREAVLHCCDDLIKQVLDIQHALYHNCHIGVDGTEEEEFNDP 603


>gi|296329094|ref|ZP_06871599.1| hypothetical protein HMPREF0397_1792 [Fusobacterium nucleatum
           subsp. nucleatum ATCC 23726]
 gi|296153813|gb|EFG94626.1| hypothetical protein HMPREF0397_1792 [Fusobacterium nucleatum
           subsp. nucleatum ATCC 23726]
          Length = 979

 Score = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/129 (21%), Positives = 55/129 (42%), Gaps = 5/129 (3%)

Query: 215 DSVALASRILQDQLGMFINFEEPKKEVKEDINVK---SLPFNPALLKKVEELELSVRSTN 271
           +  +      + +       EE  ++  + I  K       N      ++ L LSVR+ N
Sbjct: 116 ECYSELLTKTEKEFESIKYSEEIIQKEIKSIRKKPNIETAINLEKDIPIDFLGLSVRAKN 175

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           CL+  NI Y   LI +TE +++ + + G  +L E++ +   +  + G   P    E+ E 
Sbjct: 176 CLKSANIEYYSQLISKTEEELMTIKHMGVTTLKELQRLKFLIFFYFG--FPVVDTENKES 233

Query: 332 LAKKYEDKC 340
             +K  ++ 
Sbjct: 234 KEEKISNES 242



 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 17/59 (28%), Positives = 29/59 (49%)

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                ++ L LS RS N L+  NI+ + DL+  ++ D+      G KS+ EI   +  +
Sbjct: 2   KKDTSIQILHLSKRSYNVLKKFNIITIQDLLTISKEDIKNFRGIGEKSIQEILSKIEIL 60


>gi|295106723|emb|CBL04266.1| DNA-directed RNA polymerase subunit beta' [Gordonibacter pamelaeae
            7-10-1-b]
          Length = 1473

 Score = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 22/69 (31%), Positives = 32/69 (46%)

Query: 248  KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
              L    A L   ++L +S R  N      I  + DL+  TE D+LR+   G K++ E+K
Sbjct: 1309 PQLTDEDARLYIYDDLGVSQRWANKFSEAGIETVADLVGHTEEDLLRIEGIGVKAIEELK 1368

Query: 308  GVLGTMGLF 316
              L   GL 
Sbjct: 1369 EGLAERGLS 1377


>gi|166714718|gb|ABY88084.1| RpoA [Stenotrophomonas sp. LMG 11002]
          Length = 65

 Score = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 28/65 (43%), Positives = 45/65 (69%)

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           G + +DA +SP+++V+Y VE+A   Q  D DKL + I+T+G+I  E++V  A+ IL DQL
Sbjct: 1   GRLVLDASFSPVRRVAYAVEAAAVEQRTDLDKLVIDIETNGTIDAEEAVRTAADILSDQL 60

Query: 229 GMFIN 233
            +F +
Sbjct: 61  SVFGD 65


>gi|317121288|ref|YP_004101291.1| sigma-70 region 4 domain protein [Thermaerobacter marianensis DSM
           12885]
 gi|315591268|gb|ADU50564.1| sigma-70 region 4 domain protein [Thermaerobacter marianensis DSM
           12885]
          Length = 1063

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 30/63 (47%)

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +      +++L LS R+   LR   +  +G L++  EA + R+   G +SL EI   L 
Sbjct: 155 PDAVRNLAIDDLGLSQRAYRALRRAGVQTVGQLLELGEAGLRRLRGLGPRSLDEICHRLD 214

Query: 312 TMG 314
            + 
Sbjct: 215 ALQ 217


>gi|302671247|ref|YP_003831207.1| RNA polymerase alpha subunit C terminal domain-containing protein
           [Butyrivibrio proteoclasticus B316]
 gi|302395720|gb|ADL34625.1| RNA polymerase alpha subunit C terminal domain-containing protein
           [Butyrivibrio proteoclasticus B316]
          Length = 125

 Score = 56.9 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 2/67 (2%)

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR--TEADMLRMANFGRKSLVEIKGV 309
            +      +E LEL VR+ N L+      +G+L +   +  ++ ++ N G KS  EI   
Sbjct: 36  NSQMSETPIESLELGVRAYNSLKRAGYSTIGELAESIASGTEISKIRNCGTKSCREIMEK 95

Query: 310 LGTMGLF 316
           L      
Sbjct: 96  LFLYQYS 102


>gi|269216200|ref|ZP_06160054.1| DNA-directed RNA polymerase, beta subunit [Slackia exigua ATCC
            700122]
 gi|269130459|gb|EEZ61537.1| DNA-directed RNA polymerase, beta subunit [Slackia exigua ATCC
            700122]
          Length = 1458

 Score = 56.5 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 23/69 (33%), Positives = 33/69 (47%)

Query: 248  KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            K L    A L   ++L +S R  N      I  +GDL+  TE ++LR+   G K+L E+K
Sbjct: 1297 KKLSDEDARLYLYDDLGVSQRWANKFSEAGIDTVGDLVGYTEDELLRIEGIGAKALEELK 1356

Query: 308  GVLGTMGLF 316
              L    L 
Sbjct: 1357 AGLEEHELS 1365


>gi|325972213|ref|YP_004248404.1| RNA polymerase subunit alpha domain protein [Spirochaeta sp. Buddy]
 gi|324027451|gb|ADY14210.1| RNA polymerase alpha subunit domain protein [Spirochaeta sp. Buddy]
          Length = 395

 Score = 56.5 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 26/125 (20%), Positives = 51/125 (40%), Gaps = 2/125 (1%)

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP--ALLK 258
           L + ++   +      +     IL      FIN  +     + ++  K++   P    L 
Sbjct: 263 LQVNLEKKNTSKALYFLKRQLNILVPWGATFINLSDYLSSSELEVIKKAIQTLPGAIYLI 322

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            ++ L+L+ R+ NC     I  +G   + T  D+    NFG+KSL E++     +  +  
Sbjct: 323 PIQFLDLTNRANNCCLNAEITTVGMFSKMTLFDIASSRNFGKKSLEELQSKTKNLIDYFN 382

Query: 319 MNLPD 323
           +   D
Sbjct: 383 ITGED 387


>gi|257064681|ref|YP_003144353.1| DNA-directed RNA polymerase subunit beta' [Slackia heliotrinireducens
            DSM 20476]
 gi|256792334|gb|ACV23004.1| DNA-directed RNA polymerase subunit beta' [Slackia heliotrinireducens
            DSM 20476]
          Length = 1463

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 23/69 (33%), Positives = 34/69 (49%)

Query: 248  KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            + L    A L   ++L +S R  N      I  +GDL+  TE ++LR+   G K+L E+K
Sbjct: 1298 QKLSDEDARLYLYDDLGVSQRWANKFSEAGIETVGDLVGYTEDELLRIEGIGAKALEELK 1357

Query: 308  GVLGTMGLF 316
              L   GL 
Sbjct: 1358 AGLQDHGLE 1366


>gi|4140424|gb|AAD04047.1| DNA-directed RNA polymerase [Chlamydia trachomatis]
          Length = 62

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 19/46 (41%), Positives = 27/46 (58%)

Query: 25 ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
          +     +A+PL +G  HTLG+ALRR L+  L   AI +  + GVL 
Sbjct: 8  DKVARFVADPLEKGMGHTLGSALRRALLIGLEAPAIVSFSMTGVLQ 53


>gi|256826829|ref|YP_003150788.1| DNA-directed RNA polymerase subunit beta' [Cryptobacterium curtum DSM
            15641]
 gi|256582972|gb|ACU94106.1| DNA-directed RNA polymerase subunit beta' [Cryptobacterium curtum DSM
            15641]
          Length = 1463

 Score = 55.7 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 21/63 (33%), Positives = 31/63 (49%)

Query: 253  NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
              A L   ++L +S R  N      I  +GDLI  +E D+LR+   G K++ E+K  L  
Sbjct: 1312 EDARLYIYDDLGVSQRWANKFSEAGIETVGDLIGYSEEDLLRIEGIGAKAIEELKEGLEK 1371

Query: 313  MGL 315
              L
Sbjct: 1372 HDL 1374


>gi|257784971|ref|YP_003180188.1| DNA-directed RNA polymerase, beta' subunit [Atopobium parvulum DSM
            20469]
 gi|257473478|gb|ACV51597.1| DNA-directed RNA polymerase, beta' subunit [Atopobium parvulum DSM
            20469]
          Length = 1475

 Score = 55.7 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 34/125 (27%), Positives = 54/125 (43%), Gaps = 7/125 (5%)

Query: 213  GEDSVALASRI---LQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
             + + A    I   L  QL       E         N ++L    A L   ++L +S R 
Sbjct: 1286 PDWAPAELKDIEEQLPKQLDW---VNEDYNGGVYSKNGRTLSSEDAKLYLFDDLGVSQRW 1342

Query: 270  TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            TN      I  +GDLI +TE D+LR+   G K++ E++  L    L L +  P+      
Sbjct: 1343 TNKFSEVGIETVGDLIGKTEEDLLRIDGIGAKAIEELRDGLEARNL-LYILEPEEDEADS 1401

Query: 330  EELAK 334
            E+L++
Sbjct: 1402 EDLSQ 1406


>gi|149176313|ref|ZP_01854928.1| Serine/threonine protein kinase [Planctomyces maris DSM 8797]
 gi|148844915|gb|EDL59263.1| Serine/threonine protein kinase [Planctomyces maris DSM 8797]
          Length = 1405

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/105 (24%), Positives = 46/105 (43%), Gaps = 4/105 (3%)

Query: 229 GMFINFEEPK--KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQ 286
             F   +EP    +  ++  ++ L  +     ++ EL L  RS N L   NI+ + DL+ 
Sbjct: 784 NCFEGIDEPGALSDHADETRLQELLADAEFETQIPELGLGSRSANALDRANILTVEDLLT 843

Query: 287 RTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
                ++R+   G K+  EI   +  +   LG   PD  P S+ +
Sbjct: 844 VPMRRLMRLRGVGNKTRREITSAVKILRDRLGK--PDRDPSSLSD 886


>gi|308233483|ref|ZP_07664220.1| DNA-directed RNA polymerase subunit beta' [Atopobium vaginae DSM
            15829]
 gi|328943547|ref|ZP_08241012.1| DNA-directed RNA polymerase subunit beta' [Atopobium vaginae DSM
            15829]
 gi|327491516|gb|EGF23290.1| DNA-directed RNA polymerase subunit beta' [Atopobium vaginae DSM
            15829]
          Length = 1485

 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/125 (26%), Positives = 54/125 (43%), Gaps = 6/125 (4%)

Query: 213  GEDS---VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
             + +   +      L  QL      E+         N +SL    A L   ++L +S R 
Sbjct: 1288 PDWAPDELKDIEEQLPKQLDWIG--EDYSNNGVYSKNGRSLSTEDAKLYLFDDLGVSQRW 1345

Query: 270  TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            TN      I  +GDLI +TE ++LR+   G K++ E++  L    L L +  PD      
Sbjct: 1346 TNKFSEVGIETVGDLIGKTEDELLRIDGIGAKAIEELREGLEARNL-LYILEPDEDEADS 1404

Query: 330  EELAK 334
            E+L++
Sbjct: 1405 EDLSQ 1409


>gi|221194869|ref|ZP_03567926.1| DNA-directed RNA polymerase, beta' subunit [Atopobium rimae ATCC
            49626]
 gi|221185773|gb|EEE18163.1| DNA-directed RNA polymerase, beta' subunit [Atopobium rimae ATCC
            49626]
          Length = 1480

 Score = 55.0 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 34/127 (26%), Positives = 55/127 (43%), Gaps = 6/127 (4%)

Query: 211  ITGEDSVALASRI---LQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
            +  + +      I   L  QL    +  E         N ++L    A L   ++L +S 
Sbjct: 1285 VLPDWAPQSLKDIEEKLPKQLDWVGD--EYGNGSIFSKNGRTLSSEDAKLYLFDDLGVSQ 1342

Query: 268  RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
            R TN      I  +GDLI +TE D+LR+   G K++ E++  L    L L +  PD    
Sbjct: 1343 RWTNKFSEVGIETVGDLIGKTEEDLLRIDGIGSKAIEELRQGLDARNL-LYILEPDEDEA 1401

Query: 328  SIEELAK 334
              E+L++
Sbjct: 1402 DAEDLSQ 1408


>gi|196229137|ref|ZP_03128002.1| RNA polymerase alpha subunit domain protein [Chthoniobacter flavus
           Ellin428]
 gi|196226369|gb|EDY20874.1| RNA polymerase alpha subunit domain protein [Chthoniobacter flavus
           Ellin428]
          Length = 145

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/101 (22%), Positives = 41/101 (40%), Gaps = 4/101 (3%)

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGEN 277
            L +  + + +         +     D   + LP +      + +L L  R  N LR   
Sbjct: 43  KLVAEAVAEHIAKITEIAATRALAALDRPSRVLPNH----TPIRDLPLPTRIANGLRRMG 98

Query: 278 IVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           +  +G+L      D+L   N G +SL +++ VLG +G  L 
Sbjct: 99  VRTLGELTALHAEDILLSPNLGERSLDQLRHVLGLIGRSLS 139


>gi|325297639|ref|YP_004257556.1| hypothetical protein Bacsa_0485 [Bacteroides salanitronis DSM
           18170]
 gi|324317192|gb|ADY35083.1| hypothetical protein Bacsa_0485 [Bacteroides salanitronis DSM
           18170]
          Length = 243

 Score = 55.0 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 21/108 (19%), Positives = 45/108 (41%)

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCL 273
            D++    + + +           K+ ++  +  K     P L + +  L +   + N L
Sbjct: 123 RDAIVQDGQAVVELEQRIDTLRRIKEGLEIAVENKPAEEVPYLSQPLFSLGIQPSAQNHL 182

Query: 274 RGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
               + Y+GDL++R E  ++ +   G  ++  IK  L   G  L M++
Sbjct: 183 TAYGLRYVGDLVRRDEQYLMEIWGIGPATVERIKTKLNENGACLDMDV 230


>gi|328955919|ref|YP_004373252.1| DNA-directed RNA polymerase subunit beta' [Coriobacterium glomerans
            PW2]
 gi|328456243|gb|AEB07437.1| DNA-directed RNA polymerase subunit beta' [Coriobacterium glomerans
            PW2]
          Length = 1497

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 25/106 (23%), Positives = 46/106 (43%), Gaps = 3/106 (2%)

Query: 213  GEDS---VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
             + +   +      L  QL      E    +     N +++  + A L   ++L +S R 
Sbjct: 1292 PDWAPPELKELDEELPQQLDWAGFDEFGVGDGSFTRNGRTISADDAKLYLFDDLGVSQRW 1351

Query: 270  TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
            TN      I  +GDL+ ++E D+LR+   G K++ E++  L    L
Sbjct: 1352 TNKFSEVGIETVGDLVGKSEEDLLRIDGIGAKAIEELRDGLEAHNL 1397


>gi|24638176|sp|Q8SL86|RPOA_EUGVI RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|19168446|gb|AAL83368.1| RNA polymerase alpha subunit [Euglena viridis]
          Length = 214

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/201 (17%), Positives = 76/201 (37%), Gaps = 39/201 (19%)

Query: 23  EEENRTLM-IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ-----------IDGVLH 70
            +   +L  I  P     +    N LRR+L+    G     +            +   ++
Sbjct: 15  RDTFYSLFDIIYP-RSENSLIFANQLRRILLGKSEGLRFLKISGFIANKNSKFSVYQKIN 73

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKR---VTIFKRGPGVVTAGDIQTVNDIEV 127
           E S  + ++E +  + LNIK I+L        +    T+    P   +  DI    +I++
Sbjct: 74  EFSEFEEINESVFQLFLNIKNIDLYYRSCDANKRFFGTLEAYYPKTYSQDDIILSKNIKL 133

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +  +  I +L     ++M+  +    G                    + ++P+K+V+Y +
Sbjct: 134 IKKNQHIFSLSS-LKLKMKFILEAKKGI------------------GSFFTPVKRVNYII 174

Query: 188 ESAREGQVLDYDKLSMTIDTD 208
           E       L + ++ + ++TD
Sbjct: 175 E----ENKLSFSRVVLELETD 191


>gi|218508353|ref|ZP_03506231.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli Brasil
          5]
          Length = 37

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 22/40 (55%), Positives = 26/40 (65%), Gaps = 3/40 (7%)

Query: 1  MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFA 40
          MIQKNWQELIKPN +E+         R  ++AEPL RGF 
Sbjct: 1  MIQKNWQELIKPNKVEF---SSSSRTRATLVAEPLERGFG 37


>gi|170694673|ref|ZP_02885824.1| RNA polymerase alpha subunit domain protein [Burkholderia graminis
           C4D1M]
 gi|170140304|gb|EDT08481.1| RNA polymerase alpha subunit domain protein [Burkholderia graminis
           C4D1M]
          Length = 77

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 22/63 (34%), Positives = 33/63 (52%)

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                ++ L+L+ R TN L    I  +GDL   + +D+L+M  FG KSL E++  L   G
Sbjct: 9   KSDAPLDLLDLNFRVTNRLASAGIFRVGDLCVCSASDLLKMPGFGVKSLQEVERSLQRAG 68

Query: 315 LFL 317
             L
Sbjct: 69  RSL 71


>gi|139438557|ref|ZP_01772073.1| Hypothetical protein COLAER_01071 [Collinsella aerofaciens ATCC
            25986]
 gi|133776096|gb|EBA39916.1| Hypothetical protein COLAER_01071 [Collinsella aerofaciens ATCC
            25986]
          Length = 1373

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 26/106 (24%), Positives = 44/106 (41%), Gaps = 3/106 (2%)

Query: 213  GEDS---VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
             E +   +      L  QL      E    +     N  ++    A L   ++L +S R 
Sbjct: 1173 PEWAPVELKDLDEQLPQQLDWAGYDEFGGADGSFTRNGHTISAEKARLYLFDDLGVSQRW 1232

Query: 270  TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
            TN      I  +GDL+ ++E D+LR+   G K++ E++  L    L
Sbjct: 1233 TNKFSEVGIETVGDLVGKSEEDLLRIDGIGAKAIEELRDGLEAHDL 1278


>gi|325829977|ref|ZP_08163435.1| DNA-directed RNA polymerase, beta' subunit [Eggerthella sp. HGA1]
 gi|325488144|gb|EGC90581.1| DNA-directed RNA polymerase, beta' subunit [Eggerthella sp. HGA1]
          Length = 1470

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 21/69 (30%), Positives = 31/69 (44%)

Query: 248  KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
              L    A L   ++L +S R  N      I  + DL+  TE D+LR+   G K++ E+K
Sbjct: 1309 PQLSDEDARLYIYDDLGVSQRWANKFSEAGIETVADLVGHTEEDLLRIEGIGVKAIEELK 1368

Query: 308  GVLGTMGLF 316
              L    L 
Sbjct: 1369 EGLEAHDLT 1377


>gi|257790478|ref|YP_003181084.1| DNA-directed RNA polymerase, beta' subunit [Eggerthella lenta DSM
            2243]
 gi|317490022|ref|ZP_07948513.1| DNA-directed RNA polymerase [Eggerthella sp. 1_3_56FAA]
 gi|257474375|gb|ACV54695.1| DNA-directed RNA polymerase, beta' subunit [Eggerthella lenta DSM
            2243]
 gi|316910863|gb|EFV32481.1| DNA-directed RNA polymerase [Eggerthella sp. 1_3_56FAA]
          Length = 1470

 Score = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 21/69 (30%), Positives = 31/69 (44%)

Query: 248  KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
              L    A L   ++L +S R  N      I  + DL+  TE D+LR+   G K++ E+K
Sbjct: 1309 PQLSDEDARLYIYDDLGVSQRWANKFSEAGIETVADLVGHTEEDLLRIEGIGVKAIEELK 1368

Query: 308  GVLGTMGLF 316
              L    L 
Sbjct: 1369 EGLEAHDLT 1377


>gi|210630991|ref|ZP_03296716.1| hypothetical protein COLSTE_00601 [Collinsella stercoris DSM 13279]
 gi|210160207|gb|EEA91178.1| hypothetical protein COLSTE_00601 [Collinsella stercoris DSM 13279]
          Length = 1490

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 21/70 (30%), Positives = 37/70 (52%)

Query: 246  NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            N +++    A L   ++L +S R TN      I  +GDL+ ++E D+LR+   G K++ E
Sbjct: 1331 NGRTISAEDARLYLFDDLGVSQRWTNKFSEVGIETVGDLVGKSEEDLLRIDGIGAKAIEE 1390

Query: 306  IKGVLGTMGL 315
            ++  L    L
Sbjct: 1391 LRDGLEEHNL 1400


>gi|302336390|ref|YP_003801597.1| DNA-directed RNA polymerase subunit beta' [Olsenella uli DSM 7084]
 gi|301320230|gb|ADK68717.1| DNA-directed RNA polymerase subunit beta' [Olsenella uli DSM 7084]
          Length = 1476

 Score = 53.4 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 33/120 (27%), Positives = 54/120 (45%), Gaps = 3/120 (2%)

Query: 215  DSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLR 274
            +S+      L  QL    +  +         N ++L    A L   ++L +S R TN   
Sbjct: 1291 ESLKGVEEQLPKQLDWIGD--DYGYGGVYSKNGRTLSSEDAKLYLFDDLGVSQRWTNKFS 1348

Query: 275  GENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
               I  +GDLI +TE D+LR+   G K++ E++  L    L L +  PD      E+L++
Sbjct: 1349 EVGIETVGDLIGKTEDDLLRIDGIGAKAIEELRDGLEARNL-LYILEPDDDEADSEDLSQ 1407


>gi|313902029|ref|ZP_07835443.1| sigma-70 region 4 domain protein [Thermaerobacter subterraneus DSM
           13965]
 gi|313467696|gb|EFR63196.1| sigma-70 region 4 domain protein [Thermaerobacter subterraneus DSM
           13965]
          Length = 1070

 Score = 53.0 bits (126), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 17/67 (25%), Positives = 28/67 (41%)

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                     + V++L L  R+   LR   I  +G L++  E  + R+   G +SL EI 
Sbjct: 155 PQRFPEAVRRRPVDDLGLGQRAYRALRRAGIQTVGQLLELGEPGLQRLRGLGPRSLAEIC 214

Query: 308 GVLGTMG 314
             L  + 
Sbjct: 215 HRLDALQ 221



 Score = 45.0 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 17/86 (19%), Positives = 28/86 (32%), Gaps = 6/86 (6%)

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF-- 316
            +  L L  R    L+   +  +G L   T+  + R+   G   +  +   L        
Sbjct: 247 PIGALLLPRRVVTALQRAGLHTVGALAGFTQEGLRRLRGLGESGVAAVLQSLHQYRQECS 306

Query: 317 ----LGMNLPDWPPESIEELAKKYED 338
                   L DW  E IE L  +  +
Sbjct: 307 RRGAFPRRLEDWLQELIEPLPDRERE 332


>gi|149175722|ref|ZP_01854341.1| hypothetical protein PM8797T_31393 [Planctomyces maris DSM 8797]
 gi|148845441|gb|EDL59785.1| hypothetical protein PM8797T_31393 [Planctomyces maris DSM 8797]
          Length = 69

 Score = 53.0 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 29/49 (59%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           +SVR+ N L+   +  +GDL++  + D+L + NFG ++L E   +   +
Sbjct: 1   MSVRTVNYLKEHKVHTIGDLVKLKQEDLLSIPNFGEQTLQECIDLFDRL 49


>gi|229815794|ref|ZP_04446119.1| hypothetical protein COLINT_02843 [Collinsella intestinalis DSM
            13280]
 gi|229808710|gb|EEP44487.1| hypothetical protein COLINT_02843 [Collinsella intestinalis DSM
            13280]
          Length = 1490

 Score = 53.0 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 29/130 (22%), Positives = 56/130 (43%), Gaps = 11/130 (8%)

Query: 211  ITGEDS---VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSV 267
            +  E +   +     +L  QL  F   +          N +++    A L   ++L +S 
Sbjct: 1294 VLPEWAPEELKELDTVLPQQLD-FGGGDFSADGGHITRNGRTISAEDARLYLFDDLGVSQ 1352

Query: 268  RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
            R TN      I  +GDL+ ++E D+LR+   G K++ E++  L    L        +  E
Sbjct: 1353 RWTNKFSEVGIEVVGDLVGKSEEDLLRIDGIGAKAIEELRDGLEEHNLL-------YILE 1405

Query: 328  SIEELAKKYE 337
            + E++A + +
Sbjct: 1406 NTEDVADEED 1415


>gi|303232376|ref|ZP_07319068.1| DNA-directed RNA polymerase, beta' subunit [Atopobium vaginae
            PB189-T1-4]
 gi|302481460|gb|EFL44528.1| DNA-directed RNA polymerase, beta' subunit [Atopobium vaginae
            PB189-T1-4]
          Length = 1484

 Score = 52.7 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 31/125 (24%), Positives = 52/125 (41%), Gaps = 6/125 (4%)

Query: 213  GEDS---VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
             E +   +      L  QL    +  +         N + L    A L   ++L +S R 
Sbjct: 1287 PEWAPDSLKEIEEKLPKQLDWIGD--DYSNGGVYSKNGRCLSSEDAKLYLFDDLGVSQRW 1344

Query: 270  TNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            TN      I  +GDLI +TE ++LR+   G K++ E++  L    L   +  PD      
Sbjct: 1345 TNKFSEVGIETVGDLIGKTEDELLRIDGIGAKAIEELREGLEARNLLYLLE-PDEDEADS 1403

Query: 330  EELAK 334
            E+L++
Sbjct: 1404 EDLSQ 1408


>gi|297831708|ref|XP_002883736.1| hypothetical protein ARALYDRAFT_899418 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297329576|gb|EFH59995.1| hypothetical protein ARALYDRAFT_899418 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 79

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 18/62 (29%), Positives = 34/62 (54%)

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
            L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  +LPF P   + 
Sbjct: 3   ILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQVTLPFFPFHNRL 62

Query: 260 VE 261
           V 
Sbjct: 63  VN 64


>gi|168697904|ref|ZP_02730181.1| protein kinase [Gemmata obscuriglobus UQM 2246]
          Length = 1390

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 20/90 (22%), Positives = 36/90 (40%)

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
             F     P      +  +++          V EL L  R+TN L   N++ + D++  +
Sbjct: 772 DCFAAIGPPDAGELNEEELRARLEGATFDSSVHELGLGTRATNALDRANMLTVEDMLSVS 831

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
              +LR+   G K+  EI   +  +   LG
Sbjct: 832 MRRLLRLRGVGNKTRREIASAVKILRARLG 861


>gi|195035209|ref|XP_001989070.1| GH11517 [Drosophila grimshawi]
 gi|193905070|gb|EDW03937.1| GH11517 [Drosophila grimshawi]
          Length = 333

 Score = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 46/300 (15%), Positives = 90/300 (30%), Gaps = 78/300 (26%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           N ++ +++  +EEN           G    + NA RR+++S +   AI  V I      I
Sbjct: 38  NKLQVVIVRNDEENGLEFDL----IGVYPAIANAFRRLMLSEVPSMAIEKVYIYNNTSII 93

Query: 73  ---------------------------SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
                                      S+ +G  +D  +  L +K    K +        
Sbjct: 94  QDEVLAHRMGLLPLRADPRLFAYRSEESTEQGSEQDTLEYELKVKCTRRKDATKEQSNFD 153

Query: 106 IFKRGPGVVTA----------GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG--- 152
              +   V +           G I + + +  ++ D +I  L     + + L   KG   
Sbjct: 154 DIYKNHKVYSGHLKWLPKGKQGQIYSESSVNCIHDDILIAQLRPGHELDLRLIAVKGIGK 213

Query: 153 ------------HGYVPAKHHRTENDPIGLITIDALYSP------------IKKVSYTVE 188
                       +  +P      E        +   +SP            +K   Y   
Sbjct: 214 DHAKFSPVATAFYRLLPQITLTREVSGKDAYLLQNCFSPGVIGIDENECAYVKDARYDSC 273

Query: 189 SAREGQVLD----------YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           S    +              D    ++++ G++  E     A ++L+ +   FI+  E K
Sbjct: 274 SRNVYRYPQLADAVIMARVRDHYIFSVESVGALKPEVIFLEAVKVLKKKCRAFIDEIEAK 333


>gi|166714716|gb|ABY88083.1| RpoA [Stenotrophomonas sp. LMG 980]
          Length = 66

 Score = 51.9 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 3/69 (4%)

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
             D DKL + I+T+G+I  E++V  A+ I  DQL +F +F    +   +  N      +P
Sbjct: 1   RTDLDKLVIDIETNGTIDAEEAVRTAADITSDQLSVFGDFTHRDRGAAKPAN---NGVDP 57

Query: 255 ALLKKVEEL 263
            LL+ +++L
Sbjct: 58  VLLRPIDDL 66


>gi|301500977|ref|YP_003795442.1| RNA polymerase alpha subunit [Alveolata sp. CCMP3155]
 gi|300069523|gb|ADJ66630.1| RNA polymerase alpha subunit [Chromerida sp. RM11]
          Length = 233

 Score = 51.5 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 30/149 (20%), Positives = 60/149 (40%), Gaps = 5/149 (3%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEI--SSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           NA+RR L+S      +  V+I+   +        G  +   D+I  ++ +++++   S  
Sbjct: 36  NAVRRTLLSFSTQLKLVGVKINSSRNTYPWCMFSGCRDSYLDLISRLQRLSVRIRETSLC 95

Query: 103 -RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-- 159
             + +   GP VV AG + T   +E+L P+  + +L     + MEL  S     VP    
Sbjct: 96  YVLQLKSSGPLVVVAGHMITPPTLEILTPNKYLTSLAAKCALDMELIFSSYVLAVPVSYW 155

Query: 160 HHRTENDPIGLITIDALYSPIKKVSYTVE 188
              T++         + +       + + 
Sbjct: 156 EKTTDSHASPCGPFSSSHVTCSFYGFRLN 184


>gi|186683568|ref|YP_001866764.1| RNA polymerase subunit alpha [Nostoc punctiforme PCC 73102]
 gi|186466020|gb|ACC81821.1| RNA polymerase, alpha subunit domain protein [Nostoc punctiforme
           PCC 73102]
          Length = 258

 Score = 51.5 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/105 (23%), Positives = 40/105 (38%), Gaps = 5/105 (4%)

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
              +          E+IN  + P        +E L L   +   L+   +  + DL +  
Sbjct: 158 NQLVEVANSNVHPVEEINGDNKPNGVVDENSIESLNLKRNTYTALKDAKVNTIEDLNKYG 217

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP-PESIEEL 332
              +  + N G KS+ +I   L    LF G+ LP+ P PE    L
Sbjct: 218 VTGLRTLKNLGNKSVSQIVEAL----LFRGIELPELPDPEHTPSL 258


>gi|118595065|ref|ZP_01552412.1| hypothetical protein MB2181_05315 [Methylophilales bacterium
           HTCC2181]
 gi|118440843|gb|EAV47470.1| hypothetical protein MB2181_05315 [Methylophilales bacterium
           HTCC2181]
          Length = 808

 Score = 51.5 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 3/83 (3%)

Query: 234 FEEPKKEVKEDINV---KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
             E ++ V+  I     +    N  L   V  L+L +RSTNCLR   I  + DL++ ++ 
Sbjct: 115 LNEIEQNVEFPIGSLGSRFNMSNNKLELDVVVLDLDIRSTNCLRSRGIDKIEDLLKLSDT 174

Query: 291 DMLRMANFGRKSLVEIKGVLGTM 313
           ++LR+ N GR+SL  I   +  +
Sbjct: 175 ELLRIDNLGRRSLKLIIDSISKL 197


>gi|242093528|ref|XP_002437254.1| hypothetical protein SORBIDRAFT_10g023655 [Sorghum bicolor]
 gi|241915477|gb|EER88621.1| hypothetical protein SORBIDRAFT_10g023655 [Sorghum bicolor]
          Length = 66

 Score = 51.5 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 17/51 (33%), Positives = 28/51 (54%)

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            + I T+GS+T ++++   SR L D    FI+ EE     +E+ N  + PF
Sbjct: 7   FLEIWTNGSLTPKEALYETSRNLIDLFLPFIHTEEEGTNFEENKNRLTPPF 57


>gi|166714714|gb|ABY88082.1| RpoA [Stenotrophomonas sp. LMG 10996]
          Length = 67

 Score = 51.1 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 3/70 (4%)

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
              D DKL + I+T+G+I  E++V  A+ I  DQL +F +F    +   +  N      +
Sbjct: 1   HRTDLDKLVIDIETNGTIDAEEAVRTAADIPSDQLSVFGDFTHRDRGAAKPAN---NGVD 57

Query: 254 PALLKKVEEL 263
           P LL+ +++L
Sbjct: 58  PVLLRPIDDL 67


>gi|313891416|ref|ZP_07825032.1| RNA polymerase, alpha subunit C-terminal domain protein [Dialister
           microaerophilus UPII 345-E]
 gi|313120191|gb|EFR43367.1| RNA polymerase, alpha subunit C-terminal domain protein [Dialister
           microaerophilus UPII 345-E]
          Length = 897

 Score = 51.1 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 1/56 (1%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTE-ADMLRMANFGRKSLVEIKGVLGTMG 314
           ++ LELS R+ NCLR   +  +G LI+  +  D+  +   GR S+ E++ VL  + 
Sbjct: 10  IDVLELSTRTNNCLRRAEVHTIGSLIEYAKNNDLSMIYGMGRLSVEEVERVLKELE 65


>gi|18978019|ref|NP_579376.1| DNA-directed RNA polymerase subunit D [Pyrococcus furiosus DSM
           3638]
 gi|23822102|sp|Q8U0E4|RPOD_PYRFU RecName: Full=DNA-directed RNA polymerase subunit D
 gi|18893802|gb|AAL81771.1| DNA-directed RNA polymerase subunit d [Pyrococcus furiosus DSM
           3638]
          Length = 261

 Score = 50.7 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 29/149 (19%), Positives = 60/149 (40%), Gaps = 9/149 (6%)

Query: 15  IEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH-EIS 73
           IE  +L ++E++    +     +G   +  NALRR ++  +   A+  V+          
Sbjct: 4   IEVQILEKKEDS-IKFVL----KGVHVSFANALRRTILGEVPTFAVDEVEFYENDSALFD 58

Query: 74  SIKGVHEDLTDIILNIK--GINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNP 130
            I      +  +   +    ++     D    +++   GPG+V +GD+++   D++ +NP
Sbjct: 59  EIIAHRLAMIPLTTPVDRFELDALELDDYTVTLSLEAEGPGIVYSGDLKSDDPDVKPVNP 118

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAK 159
           +  I  L     +        G G   AK
Sbjct: 119 NIPIVKLAEGQRLVFNAYAKLGRGKDHAK 147


>gi|329121465|ref|ZP_08250089.1| RNA polymerase subunit alpha [Dialister micraerophilus DSM 19965]
 gi|327469380|gb|EGF14850.1| RNA polymerase subunit alpha [Dialister micraerophilus DSM 19965]
          Length = 899

 Score = 50.7 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 1/56 (1%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTE-ADMLRMANFGRKSLVEIKGVLGTMG 314
           ++ LELS R+ NCLR   +  +G LI+  +  D+  +   GR S+ E++ VL  + 
Sbjct: 12  IDVLELSTRTNNCLRRAEVHTIGSLIEYAKNNDLSMIYGMGRLSVEEVERVLKELE 67


>gi|297745992|emb|CBI16048.3| unnamed protein product [Vitis vinifera]
          Length = 110

 Score = 50.7 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 13/59 (22%), Positives = 23/59 (38%), Gaps = 4/59 (6%)

Query: 7  QELIKPNNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
          + ++    +++  +     N        I  P   G A T+G  +RR L   + G  IT
Sbjct: 5  KVIVSTRTLQWKCVESRVNNKRLCYGRFILSPFIIGQADTIGIVMRRTLFGEIEGTCIT 63


>gi|195386486|ref|XP_002051935.1| GJ24400 [Drosophila virilis]
 gi|194148392|gb|EDW64090.1| GJ24400 [Drosophila virilis]
          Length = 333

 Score = 50.3 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 46/300 (15%), Positives = 91/300 (30%), Gaps = 78/300 (26%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + ++ +++  +EEN           G    + NA RR+++S +   AI  V I      I
Sbjct: 38  SKLQVVIVRNDEENGLEFDL----IGVYPAIANAFRRLMLSEVPSMAIEKVYIYNNTSII 93

Query: 73  ---------------------------SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
                                      S+ +G  +D  +  L +K    K +        
Sbjct: 94  QDEVLAHRMGLLPLRADPRLFAYRTEESTEQGTEQDTLEYELKVKCTRRKDASKDQSNFD 153

Query: 106 IFKRGPGVVTA----------GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKG--- 152
              +   V +           G I T N +  ++ D +I  L     + + L   KG   
Sbjct: 154 DIYKNHKVYSGHLKWLPKGKQGQIYTENSVGCIHEDILIAQLRPGHELDLRLIAVKGLGK 213

Query: 153 ------------HGYVPAKHHRTENDPIGLITIDALYSP------------IKKVSYTVE 188
                       +  +P  +   E        + + +SP            +K   Y   
Sbjct: 214 DHAKFSPVATAYYRLLPQINLTREVTGKDAYLLQSCFSPGVIGIDENECAYVKDARYDSC 273

Query: 189 SAREGQVLD----------YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           S    +              D     +++ G++  E     A ++L+ +   FI+  E +
Sbjct: 274 SRNVYRYPHLADAVTMARVRDHYIFNVESVGALKPEVIFLEAVKVLKKKCRSFIDEIEAE 333


>gi|327312665|ref|YP_004328102.1| hypothetical protein HMPREF9137_0370 [Prevotella denticola F0289]
 gi|326944759|gb|AEA20644.1| hypothetical protein HMPREF9137_0370 [Prevotella denticola F0289]
          Length = 488

 Score = 50.3 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 27/124 (21%), Positives = 59/124 (47%), Gaps = 4/124 (3%)

Query: 200 KLSMTIDTDGSITGEDS-VALASRILQDQLGMFINF--EEPKKEVKEDINVKSLPFNPAL 256
            L   +  +  +  +++ +   +++  +++    +   +E  +E +  +   +      L
Sbjct: 343 ILINEVHKNEQLRKDNAQLHAQAQLYIEEIQRLRSVVKDESLRETRNQVVDINSHVAELL 402

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA-DMLRMANFGRKSLVEIKGVLGTMGL 315
              V+ L LSVR+ N L    I   G++ +   A  +L++ N GRK++ +I+  +G  GL
Sbjct: 403 NTPVQNLNLSVRAINVLNVIGISTFGEIPKIDAAVTLLKVRNSGRKTVHDIEVFIGKFGL 462

Query: 316 FLGM 319
            LGM
Sbjct: 463 QLGM 466


>gi|241765300|ref|ZP_04763279.1| hypothetical protein AcdelDRAFT_2510 [Acidovorax delafieldii 2AN]
 gi|241365019|gb|EER59924.1| hypothetical protein AcdelDRAFT_2510 [Acidovorax delafieldii 2AN]
          Length = 222

 Score = 50.3 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 1/79 (1%)

Query: 247 VKSLPFNPALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                 +P L + + E+ EL+      L    +  +GDL+Q +   ++R+  F   ++  
Sbjct: 132 APEALLDPILFRPISEIYELTDPVIALLVAAGVHRLGDLVQMSPTALMRIRGFDVLAMER 191

Query: 306 IKGVLGTMGLFLGMNLPDW 324
           I+  L   GL +GM LP W
Sbjct: 192 IEEGLTIFGLKVGMALPGW 210


>gi|315607208|ref|ZP_07882212.1| DNA-directed RNA polymerase subunit alpha [Prevotella buccae ATCC
           33574]
 gi|315251262|gb|EFU31247.1| DNA-directed RNA polymerase subunit alpha [Prevotella buccae ATCC
           33574]
          Length = 488

 Score = 50.3 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 27/124 (21%), Positives = 59/124 (47%), Gaps = 4/124 (3%)

Query: 200 KLSMTIDTDGSITGEDS-VALASRILQDQLGMFINF--EEPKKEVKEDINVKSLPFNPAL 256
            L   +  +  +  +++ +   +++  +++    +   +E  +E +  +   +      L
Sbjct: 343 ILINEVHKNEQLRKDNAQLHAQAQLYIEEIQRLRSVVKDESLRETRNQVVDINSHVAELL 402

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA-DMLRMANFGRKSLVEIKGVLGTMGL 315
              V+ L LSVR+ N L    I   G++ +   A  +L++ N GRK++ +I+  +G  GL
Sbjct: 403 NTPVQNLNLSVRAINVLNVIGISTFGEIPKIDAAVTLLKVRNSGRKTVHDIEVFIGKFGL 462

Query: 316 FLGM 319
            LGM
Sbjct: 463 QLGM 466


>gi|269925713|ref|YP_003322336.1| sigma-70 region 4 domain protein [Thermobaculum terrenum ATCC
           BAA-798]
 gi|269789373|gb|ACZ41514.1| sigma-70 region 4 domain protein [Thermobaculum terrenum ATCC
           BAA-798]
          Length = 785

 Score = 50.0 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 11/87 (12%)

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +  +   +E L+LS R    LR   I     L + T+ ++L++   G+ +L EIK V   
Sbjct: 155 SHEVDNSLENLQLSPRIRGILRRAGIFTADQLYRLTDEELLKLKGIGKAALEEIKAV--- 211

Query: 313 MGLFLGMNLPDWP-PESIEELAKKYED 338
                   L D     SIEE  ++ +D
Sbjct: 212 -------KLGDADNKRSIEEEKQRLDD 231


>gi|195114368|ref|XP_002001739.1| GI17014 [Drosophila mojavensis]
 gi|193912314|gb|EDW11181.1| GI17014 [Drosophila mojavensis]
          Length = 333

 Score = 50.0 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 42/301 (13%), Positives = 92/301 (30%), Gaps = 80/301 (26%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + ++ +++  +EE+           G    + NA RR+++S +   AI  V I      I
Sbjct: 38  SKLQVVIVRNDEEHGLEFDL----IGVYPAIANAFRRLMLSEVPSMAIEKVYIYNNTSII 93

Query: 73  ---------------------------SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
                                      S+ +G  +D  +  L +K    +      +   
Sbjct: 94  QDEVLAHRMGLLPLRADPRLFAYRTDESTDQGTEQDTLEYELKVKCTR-RKDASKDQSNF 152

Query: 106 IFKRGPGVVTAGDIQ-----------TVNDIEVLNPDHVICNLDVDAVVRMELTVSKG-- 152
                   V +G ++           + + +  ++ D +I  L     + + L   KG  
Sbjct: 153 DDIYRNHKVYSGHLKWLPKGKQAQIYSESSVGCIHEDILIAQLRPGHELDLRLIAVKGIG 212

Query: 153 -------------HGYVPAKHHRTENDPIGLITIDALYSP------------IKKVSYTV 187
                        +  +P  +   E        + + +SP            +K   Y  
Sbjct: 213 KDHAKFSPVATAYYRLLPQINLTREVRGKDAYLLQSCFSPGVIGIDENECAYVKDARYDS 272

Query: 188 ESAREGQVLD----------YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
            S    +              D    ++++ G++  E     A R+L+ +   FI+  E 
Sbjct: 273 CSRNVFRYPHLADAVTMGRVRDHYIFSVESVGALKPEVIFLEAVRVLKKKCRSFIDEIEA 332

Query: 238 K 238
           +
Sbjct: 333 E 333


>gi|198276334|ref|ZP_03208865.1| hypothetical protein BACPLE_02529 [Bacteroides plebeius DSM 17135]
 gi|218129455|ref|ZP_03458259.1| hypothetical protein BACEGG_01032 [Bacteroides eggerthii DSM 20697]
 gi|254881373|ref|ZP_05254083.1| conserved hypothetical protein [Bacteroides sp. 4_3_47FAA]
 gi|255008156|ref|ZP_05280282.1| hypothetical protein Bfra3_03391 [Bacteroides fragilis 3_1_12]
 gi|313145873|ref|ZP_07808066.1| conserved hypothetical protein [Bacteroides fragilis 3_1_12]
 gi|198270776|gb|EDY95046.1| hypothetical protein BACPLE_02529 [Bacteroides plebeius DSM 17135]
 gi|217988185|gb|EEC54508.1| hypothetical protein BACEGG_01032 [Bacteroides eggerthii DSM 20697]
 gi|254834166|gb|EET14475.1| conserved hypothetical protein [Bacteroides sp. 4_3_47FAA]
 gi|313134640|gb|EFR52000.1| conserved hypothetical protein [Bacteroides fragilis 3_1_12]
          Length = 136

 Score = 50.0 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 5/77 (6%)

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM---NLPD 323
            R     R  +I  + DL Q    D++R+ + GRKS+ EI+ VL    L LGM    L +
Sbjct: 21  ARIQRIFREFDIKTIRDLCQWPGKDLVRVRDMGRKSIEEIEDVLERYNLRLGMLGKELDE 80

Query: 324 WPPESIEELAKKYEDKC 340
           +    IE   +  E++ 
Sbjct: 81  Y--AGIENSVQDEEEEA 95


>gi|317476176|ref|ZP_07935427.1| hypothetical protein HMPREF1016_02410 [Bacteroides eggerthii
           1_2_48FAA]
 gi|316907587|gb|EFV29290.1| hypothetical protein HMPREF1016_02410 [Bacteroides eggerthii
           1_2_48FAA]
          Length = 135

 Score = 49.6 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 5/77 (6%)

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM---NLPD 323
            R     R  +I  + DL Q    D++R+ + GRKS+ EI+ VL    L LGM    L +
Sbjct: 21  ARIQRIFREFDIKTIRDLCQWPGKDLVRVRDMGRKSIEEIEEVLERYNLRLGMLGKELDE 80

Query: 324 WPPESIEELAKKYEDKC 340
           +    IE   +  E++ 
Sbjct: 81  Y--AGIENSVQDEEEEA 95


>gi|4140450|gb|AAD04060.1| DNA-directed RNA polymerase alpha chain [Chlamydia trachomatis]
          Length = 46

 Score = 49.2 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 20/45 (44%), Positives = 28/45 (62%), Gaps = 2/45 (4%)

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 1   NFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYAEK 45


>gi|84687559|ref|ZP_01015435.1| RNA polymerase sigma factor [Maritimibacter alkaliphilus HTCC2654]
 gi|84664468|gb|EAQ10956.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2654]
          Length = 562

 Score = 48.8 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 25/59 (42%), Positives = 31/59 (52%), Gaps = 4/59 (6%)

Query: 275 GENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELA 333
            E IV +G  +Q T  D+LR    G+KS  E +  L  +GL LGM L  W     EELA
Sbjct: 3   KEGIVLVGSFVQLTAGDILRKQGLGKKSYREARATLEALGLSLGMELCGWD----EELA 57


>gi|13124813|sp|O59303|RPOD_PYRHO RecName: Full=DNA-directed RNA polymerase subunit D
          Length = 259

 Score = 48.0 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 52/264 (19%), Positives = 91/264 (34%), Gaps = 63/264 (23%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++ E+    I E    G +    NALRR ++  +   A+  V+       +     
Sbjct: 4   IKILKKTEDSITFILE----GVSVAFANALRRTILGEVPTFAVDEVEFYENDSAL----- 54

Query: 78  VHEDLTDIILN-IKGINLKMSGDS-----------HKRVTIFKRGPGVVTAGDIQT-VND 124
                 +II + +  I LK   D               +++   GPG+V +GD+++   D
Sbjct: 55  ----FDEIIAHRLAMIPLKTPTDRFELDALELDDYTVTLSLEAEGPGIVYSGDLKSDDPD 110

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK------------------------- 159
           ++ + PD  I  L     +        G G   AK                         
Sbjct: 111 VKPVTPDIPIVKLAKGQRLVFNAYAKLGRGKDHAKWQPGFTYYKYFTRVHISKKINGWEK 170

Query: 160 ----------HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
                       +   + + + TI   Y P +   Y  +   E  V   D     ++T+G
Sbjct: 171 LAKLAKKRGLPTKENEEEVIVETIKPFYIPKEFEEYEGKEIWEEIVP--DTYVFVVETNG 228

Query: 210 SITGEDSVALASRILQDQLGMFIN 233
            +  E+ V +A RIL  +   FIN
Sbjct: 229 ELPVEEIVKIALRILMRKADRFIN 252


>gi|189461065|ref|ZP_03009850.1| hypothetical protein BACCOP_01712 [Bacteroides coprocola DSM 17136]
 gi|265753971|ref|ZP_06089326.1| conserved hypothetical protein [Bacteroides sp. 3_1_33FAA]
 gi|189432155|gb|EDV01140.1| hypothetical protein BACCOP_01712 [Bacteroides coprocola DSM 17136]
 gi|263235685|gb|EEZ21209.1| conserved hypothetical protein [Bacteroides sp. 3_1_33FAA]
          Length = 136

 Score = 47.7 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 20/53 (37%), Positives = 28/53 (52%)

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
            R     R  +I  + DL Q    D++R+ + GRKS+ EI+ VL    L LGM
Sbjct: 21  ARIQRIFREFDIKTIRDLCQWPGKDLVRVRDMGRKSIEEIEDVLERYNLRLGM 73


>gi|255560816|ref|XP_002521421.1| conserved hypothetical protein [Ricinus communis]
 gi|223539320|gb|EEF40911.1| conserved hypothetical protein [Ricinus communis]
          Length = 111

 Score = 47.7 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 16/40 (40%), Positives = 23/40 (57%)

Query: 36 PRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           +G A T+G A RR L+  + G  IT  Q + + HE S+I
Sbjct: 1  MKGQADTIGIATRRALIGEIEGTCITRAQSEKIPHEFSTI 40


>gi|328853564|gb|EGG02702.1| hypothetical protein MELLADRAFT_72730 [Melampsora larici-populina
           98AG31]
          Length = 359

 Score = 47.7 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 41/270 (15%), Positives = 84/270 (31%), Gaps = 60/270 (22%)

Query: 12  PNNIE----YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           P +I+     + + + +E     + E    G    L N+LRR +M+ L   AI +V+ + 
Sbjct: 11  PQSIDGSNLQVKVTELDERHAAFVVE----GVDLALANSLRRTIMADLTTVAIHSVEFEE 66

Query: 68  ---------VLHEISSIKGVHEDL---------------------TDIILNIKGINLKMS 97
                    + H +  +  + EDL                      +++L++K      +
Sbjct: 67  NTSVLPDEMIAHRLGLMPLMSEDLDKYLKNWQRDCTCLSFCDDCSIELVLSVKSTLPGET 126

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV---ICNLDVDAVVRMELTVSKGHG 154
            +   +  +          GD+       + N +     I  L     V+++    KG  
Sbjct: 127 LEVTSKDLVITPREDGGDRGDVGKPVQFTLPNGEQPGVLITKLRKGQEVKLKCRAIKGIA 186

Query: 155 YVPAK-----HHRTENDPIGLI-----------TIDALYSPIKKVSYT---VESAREGQV 195
              AK         E DP   +              A +   K   +    ++       
Sbjct: 187 QEHAKWSAVSTIGFEYDPHNRLGHTDLWYEVGTDARAEWPLTKNAKFERPPLDDEPVDFT 246

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQ 225
               +    +++ G++  ED V      L 
Sbjct: 247 TKPSRFYFDVESAGNLRPEDIVVKGIESLI 276


>gi|14591408|ref|NP_143488.1| DNA-directed RNA polymerase subunit D [Pyrococcus horikoshii OT3]
 gi|3258066|dbj|BAA30749.1| 261aa long hypothetical DNA-directed RNA polymerase subunit D
           [Pyrococcus horikoshii OT3]
          Length = 261

 Score = 47.7 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 52/264 (19%), Positives = 91/264 (34%), Gaps = 63/264 (23%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++ E+    I E    G +    NALRR ++  +   A+  V+       +     
Sbjct: 6   IKILKKTEDSITFILE----GVSVAFANALRRTILGEVPTFAVDEVEFYENDSAL----- 56

Query: 78  VHEDLTDIILN-IKGINLKMSGDS-----------HKRVTIFKRGPGVVTAGDIQT-VND 124
                 +II + +  I LK   D               +++   GPG+V +GD+++   D
Sbjct: 57  ----FDEIIAHRLAMIPLKTPTDRFELDALELDDYTVTLSLEAEGPGIVYSGDLKSDDPD 112

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK------------------------- 159
           ++ + PD  I  L     +        G G   AK                         
Sbjct: 113 VKPVTPDIPIVKLAKGQRLVFNAYAKLGRGKDHAKWQPGFTYYKYFTRVHISKKINGWEK 172

Query: 160 ----------HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
                       +   + + + TI   Y P +   Y  +   E  V   D     ++T+G
Sbjct: 173 LAKLAKKRGLPTKENEEEVIVETIKPFYIPKEFEEYEGKEIWEEIVP--DTYVFVVETNG 230

Query: 210 SITGEDSVALASRILQDQLGMFIN 233
            +  E+ V +A RIL  +   FIN
Sbjct: 231 ELPVEEIVKIALRILMRKADRFIN 254


>gi|310794498|gb|EFQ29959.1| RNA polymerase Rpb3/RpoA insert domain-containing protein
           [Glomerella graminicola M1.001]
          Length = 339

 Score = 47.3 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 86/240 (35%), Gaps = 51/240 (21%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDII----- 86
            +  N+LRRV+ + +   AI  V+I+          + H +  I    +D+  ++     
Sbjct: 36  LSFANSLRRVIQAEVPVIAIDLVEIEANTSVLADEFIAHRLGLIPLQSKDVNSLLYTRDC 95

Query: 87  --------LNIK-GINLKMSGDSHKRVT----IFKRGPGVVTAGD--IQTVNDIEVLNPD 131
                    ++K  ++ + S D   +V     I        T G+  I        L   
Sbjct: 96  DCEQYCDNCSVKLTLHARCSSDDTMKVYASDLIVDSFRQNGTVGNPVILDPEGQGSL--- 152

Query: 132 HVICNLDVDAVVRMELTVSKGH-----GYVPAKHHRTENDPIGLITIDALYS-------- 178
             IC L     +++     KG       ++P      E DP   +    ++         
Sbjct: 153 --ICKLRKGQELKISCIAKKGIAKEHAKWMPTSAVGFEYDPHNKLHHLDMWYEEDAKAEW 210

Query: 179 PIKKVSYTVESAREGQVLDYD----KLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           P  K +   +  +EG   DYD    K    ++  GS+  +  +    +ILQ++L + ++ 
Sbjct: 211 PDSKYAKMEDPPQEGDPFDYDAVPGKFYFEVEGVGSLEPDQIIQEGIKILQEKLALTLHI 270


>gi|320161915|ref|YP_004175140.1| 50S ribosomal protein L31 [Anaerolinea thermophila UNI-1]
 gi|319995769|dbj|BAJ64540.1| 50S ribosomal protein L31 [Anaerolinea thermophila UNI-1]
          Length = 158

 Score = 47.3 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 3/77 (3%)

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDL---IQRTEADMLRMANFGR 300
           +          +L + +  L L  R T  L    I  +G +   +++ EA +L +  FGR
Sbjct: 73  EQKKAREEARTSLERPIASLNLGTRPTEALAKAGITTVGQVIALLEQGEAALLNVEGFGR 132

Query: 301 KSLVEIKGVLGTMGLFL 317
           K+L+++K  L  +G  L
Sbjct: 133 KALIDLKKTLRGLGYQL 149


>gi|331084582|ref|ZP_08333680.1| hypothetical protein HMPREF0992_02604 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330400652|gb|EGG80259.1| hypothetical protein HMPREF0992_02604 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 917

 Score = 47.3 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 23/85 (27%), Positives = 39/85 (45%), Gaps = 5/85 (5%)

Query: 235 EEPKKEVKEDINVKS----LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR-TE 289
            E  K ++ED  +         +      +EEL LSVR+ N  R  NI  +  LI+    
Sbjct: 65  SEELKYLEEDFEITEADLIEEKDVQEDFPIEELGLSVRALNAFRRVNIHTLNSLIEFLAT 124

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMG 314
            D+  + N G K++ E + ++  +G
Sbjct: 125 NDISEIKNVGAKTIQETEELMRRVG 149


>gi|332157864|ref|YP_004423143.1| DNA-directed RNA polymerase subunit D [Pyrococcus sp. NA2]
 gi|331033327|gb|AEC51139.1| DNA-directed RNA polymerase subunit D [Pyrococcus sp. NA2]
          Length = 259

 Score = 47.3 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 29/155 (18%), Positives = 59/155 (38%), Gaps = 26/155 (16%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++ E+    + E    G +    N+LRR ++  +   A+  V+       +     
Sbjct: 4   IKILKKTEDSITFLLE----GVSVAFANSLRRTILGEVPTFAVDEVEFYENDSAL----- 54

Query: 78  VHEDLTDIILN------IKGINLKMS------GDSHKRVTIFKRGPGVVTAGDIQT-VND 124
                 +II +      +K    +         D    +++   GPG+V +GD+++   D
Sbjct: 55  ----FDEIIAHRLAMIPLKTPVDRFELDALELDDYTVTLSLKAEGPGIVYSGDLESDDPD 110

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
           ++ +NP+  I  L     +        G G   AK
Sbjct: 111 VKPVNPNIPIVKLAKGQKLVFNAYARLGRGKDHAK 145


>gi|6633993|dbj|BAA88567.1| C-terminal domain of the RNA polymerase alpha subunit [synthetic
           construct]
          Length = 85

 Score = 46.9 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 16/53 (30%), Positives = 23/53 (43%)

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           S R  + L+ E I  +  L+     D+  +   G +SL EIK  L   G  L 
Sbjct: 32  STRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEKKGFTLK 84


>gi|145308100|gb|AAR05652.2| hypothetical protein bst011 [Bacteroides uniformis]
          Length = 137

 Score = 46.9 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 27/79 (34%), Positives = 36/79 (45%), Gaps = 9/79 (11%)

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM---NLPDW 324
           R     RG NI  + DL +    D++R+   G KS+ EI+ VL    L LGM    L  +
Sbjct: 22  RIQQVCRGFNIKTIRDLCKWPGRDLVRLRGIGGKSIDEIEDVLKKYNLRLGMFNEELDKY 81

Query: 325 ------PPESIEELAKKYE 337
                  PE  EE AK  +
Sbjct: 82  AGIGNTTPEDKEEEAKWEQ 100


>gi|168184418|ref|ZP_02619082.1| bacterial RNA polymerase, alpha chain C domain superfamily
           [Clostridium botulinum Bf]
 gi|182672578|gb|EDT84539.1| bacterial RNA polymerase, alpha chain C domain superfamily
           [Clostridium botulinum Bf]
          Length = 69

 Score = 46.9 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 27/63 (42%)

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                  ++ EL LS+R+ N LR   I  + DL   ++  + +    G  SL +I+  L 
Sbjct: 1   MRKNKRDELRELNLSIRAYNSLRNMGINTLEDLSTYSKKQLYQFKGIGIVSLRKIEKGLD 60

Query: 312 TMG 314
              
Sbjct: 61  KKN 63


>gi|224025038|ref|ZP_03643404.1| hypothetical protein BACCOPRO_01772 [Bacteroides coprophilus DSM
           18228]
 gi|224018274|gb|EEF76272.1| hypothetical protein BACCOPRO_01772 [Bacteroides coprophilus DSM
           18228]
          Length = 251

 Score = 46.5 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 20/108 (18%), Positives = 47/108 (43%)

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCL 273
            + +      ++D      + +  K  ++  +N       P L + + +L ++  +   L
Sbjct: 122 REDIRQREDTIRDMANYVDSIKSIKTGLEIAVNNIDAEEIPFLSRAITDLGITPSARERL 181

Query: 274 RGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
             E I+Y+G+LI   E  ++ +   G  ++  IK  L    ++ GM++
Sbjct: 182 AKEGILYVGELIHLNEDYLMDIWGVGPVTIDRIKNKLNENSVWFGMDV 229


>gi|57641438|ref|YP_183916.1| DNA-directed RNA polymerase subunit D [Thermococcus kodakarensis
           KOD1]
 gi|73917880|sp|Q5JJF4|RPOD_PYRKO RecName: Full=DNA-directed RNA polymerase subunit D
 gi|57159762|dbj|BAD85692.1| DNA-directed RNA polymerase, subunit D [Thermococcus kodakarensis
           KOD1]
          Length = 259

 Score = 46.5 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 32/151 (21%), Positives = 56/151 (37%), Gaps = 13/151 (8%)

Query: 15  IEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH-EIS 73
           +E+ +L +  ++    I      G      NALRR ++S +   A+  V+          
Sbjct: 2   VEFKILEKRPDS-IKFIVS----GVDVPFANALRRTILSEVPTFAVDEVEFLENDSALFD 56

Query: 74  SIKGVHEDLTDIILNIKGINLKMS----GDSHKRVTIFKRGPGVVTAGDIQ-TVNDIEVL 128
            I      L  I L        +      D    +++   GPG+V +GD++ +  D++  
Sbjct: 57  EIIAHR--LAMIPLTTPHERFSLDALELDDYTVTLSLEAEGPGMVYSGDLKSSDGDVKPA 114

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
           NP+  I  L     +        G G   AK
Sbjct: 115 NPNIPIVKLAEGQRLTFNAYARLGRGKDHAK 145


>gi|169834663|ref|YP_001693317.1| DNA-directed RNA polymerase subunit alpha [Clostridium botulinum B1
           str. Okra]
 gi|169835032|ref|YP_001715849.1| DNA-directed RNA polymerase subunit alpha [Clostridium botulinum A3
           str. Loch Maree]
 gi|229587412|ref|YP_002860450.1| dna-directed rna polymerase alpha chain [Clostridium botulinum Ba4
           str. 657]
 gi|169123211|gb|ACA47046.1| dna-directed rna polymerase alpha chain (rnap alphasubunit)
           (transcriptase alpha chain) (rna polymerase subunit
           alpha) [Clostridium botulinum B1 str. Okra]
 gi|169409139|gb|ACA57549.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           A3 str. Loch Maree]
 gi|229260347|gb|ACQ51384.1| DNA-directed RNA polymerase, alpha subunit [Clostridium botulinum
           Ba4 str. 657]
          Length = 69

 Score = 46.5 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 27/63 (42%)

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                  ++ EL LS+R+ N LR   I  + DL   ++  + +    G  SL +I+  L 
Sbjct: 1   MRKNKRDELRELNLSIRAYNSLRNMGINTLEDLSMYSKKQLYQFKGIGIVSLRKIEKGLD 60

Query: 312 TMG 314
              
Sbjct: 61  KKN 63


>gi|159162213|pdb|1DOQ|A Chain A, The C-Terminal Domain Of The Rna Polymerase Alpha Subunit
           From Thermus Thermophilus
          Length = 69

 Score = 46.1 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 16/53 (30%), Positives = 23/53 (43%)

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           S R  + L+ E I  +  L+     D+  +   G +SL EIK  L   G  L 
Sbjct: 16  STRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEKKGFTLK 68


>gi|87307624|ref|ZP_01089768.1| DNA-directed RNA polymerase, alpha subunit [Blastopirellula marina
           DSM 3645]
 gi|87289794|gb|EAQ81684.1| DNA-directed RNA polymerase, alpha subunit [Blastopirellula marina
           DSM 3645]
          Length = 124

 Score = 46.1 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 18/73 (24%), Positives = 30/73 (41%), Gaps = 7/73 (9%)

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +  L L  +  N L    I  +GDL   T  D+L + N G+    E++  +  +     
Sbjct: 57  PLARLNLEPQILNALEYCEINTVGDLQGVTYEDLLSVPNLGQSRASEVRDSVRQL----- 111

Query: 319 MNLPDWPPESIEE 331
             L D+   S E+
Sbjct: 112 --LRDFKTRSFEK 122


>gi|195437356|ref|XP_002066606.1| GK24584 [Drosophila willistoni]
 gi|194162691|gb|EDW77592.1| GK24584 [Drosophila willistoni]
          Length = 332

 Score = 46.1 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 42/270 (15%), Positives = 78/270 (28%), Gaps = 74/270 (27%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEI---------------------------SSI 75
           + NA RR+++S +   AI  V I      I                           S  
Sbjct: 63  IANAFRRLMLSEVPSMAIEKVYIYNNTSIIQDEVLAHRMGLLPLKADPRLFTYRTEESPE 122

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA----------GDIQTVNDI 125
            G  +D  +  L +K    K +           +   V +           G I T + +
Sbjct: 123 NGTEQDTLEYELKVKCTRRKDASKDQSTFDEIYKNHKVFSGHLKWLPKGKQGQIYTESSV 182

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKG---------------HGYVPAKHHRTENDPIGL 170
             ++ D +I  L     + + L   KG               +  +P      E      
Sbjct: 183 GCIHEDILIAQLRPGHEMDLRLIAVKGLGKDHAKFSPVATAYYRLLPLIKLNREVSGKDA 242

Query: 171 ITIDALYSP------------IKKVSYTVESAREGQVLD----------YDKLSMTIDTD 208
             + + +SP            +K   Y   S    +              D    T+++ 
Sbjct: 243 YLLQSCFSPGVIGIDENENAYVKDARYDSGSRNVYRYSHLADAVTLARVRDHYIFTVESV 302

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPK 238
           G++  E     A ++L+ +   FI+  E +
Sbjct: 303 GALKPEVIFIEAVKVLKKKCRSFIDEIEAE 332


>gi|14520746|ref|NP_126221.1| DNA-directed RNA polymerase subunit D [Pyrococcus abyssi GE5]
 gi|13124531|sp|Q9V198|RPOD_PYRAB RecName: Full=DNA-directed RNA polymerase subunit D
 gi|5457962|emb|CAB49452.1| rpoD DNA-directed RNA polymerase, subunit D [Pyrococcus abyssi GE5]
          Length = 259

 Score = 46.1 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 32/158 (20%), Positives = 59/158 (37%), Gaps = 27/158 (17%)

Query: 15  IEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS 74
           +E  +L + +++    I E    G      NALRR ++  +   A+  V+       +  
Sbjct: 2   VEIKILKKTDDS-ITFILE----GVDVAFANALRRTILGEVPTFAVDEVEFYENDSAL-- 54

Query: 75  IKGVHEDLTDIILN------IKGINLKMS------GDSHKRVTIFKRGPGVVTAGDIQT- 121
                    +II +      +K    +         D    +++   GPG+V +GD+++ 
Sbjct: 55  -------FDEIIAHRLAMIPLKTPVDRFELDALELDDYTVTLSLEAEGPGIVYSGDLKSD 107

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             D++  NPD  I  L     +        G G   AK
Sbjct: 108 DPDVKPANPDIPIVKLAKGQRLVFNAFAKLGRGKDHAK 145


>gi|160886752|ref|ZP_02067755.1| hypothetical protein BACOVA_04765 [Bacteroides ovatus ATCC 8483]
 gi|298383577|ref|ZP_06993138.1| conserved hypothetical protein [Bacteroides sp. 1_1_14]
 gi|156107163|gb|EDO08908.1| hypothetical protein BACOVA_04765 [Bacteroides ovatus ATCC 8483]
 gi|298263181|gb|EFI06044.1| conserved hypothetical protein [Bacteroides sp. 1_1_14]
          Length = 248

 Score = 45.7 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 19/92 (20%), Positives = 43/92 (46%)

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
              + +  K+ ++  ++         L + +  ++++    + L    I+Y+GDLIQ  E
Sbjct: 140 YINSVQRVKEGLEIALDNIQAEEVHYLSQPIFSMKMTPIVRSKLESHGILYVGDLIQLNE 199

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
             ++ +   G  +L  IK  L   G++ GM++
Sbjct: 200 EYLMEIWGLGPVALERIKTKLNENGVWFGMDV 231


>gi|24638177|sp|Q8SL88|RPOA_EUGST RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|19168443|gb|AAL83366.1| RNA polymerase alpha subunit [Euglena stellata]
          Length = 213

 Score = 45.7 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 41/180 (22%), Positives = 69/180 (38%), Gaps = 41/180 (22%)

Query: 44  GNALRRVLMSSLRGAAI-----------TAVQIDGVLHEISSIKGVHEDLTDIILNIKGI 92
           GN LRR L+  L G              + +     ++E S I+ V+  L  +  N + +
Sbjct: 38  GNLLRRTLLKDLEGLRFGNSSIFISRSFSKIPYYHRVNEYSDIEQVNPSLLQVFSNFRNL 97

Query: 93  NLKMSGDSHKRVT---IFKRGPGVVTAGDIQTVNDIEVLNPDHVICN-LDVDAVVRMELT 148
           ++  S   +++ +   I         + DI   N++ V+NPD  +   L     +R+   
Sbjct: 98  HIFSSKPFYRKTSYSMIKVLTSRSYFSKDILLPNNLYVVNPDVQLFEFLSKRYKLRIISE 157

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           + KG                        +SPIKKV+Y VE       + Y  L + I TD
Sbjct: 158 ICKG--------------------SGKSFSPIKKVNYVVE------GIPYASLLLEIYTD 191


>gi|289809444|ref|ZP_06540073.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. AG3]
          Length = 45

 Score = 45.0 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 18/45 (40%), Positives = 30/45 (66%)

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
           S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA 
Sbjct: 1   STKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAA 45


>gi|242398333|ref|YP_002993757.1| DNA-directed RNA polymerase subunit D [Thermococcus sibiricus MM
           739]
 gi|242264726|gb|ACS89408.1| DNA-directed RNA polymerase subunit D [Thermococcus sibiricus MM
           739]
          Length = 271

 Score = 45.0 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 29/151 (19%), Positives = 54/151 (35%), Gaps = 9/151 (5%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH-E 71
             ++  +L + ++     I E    G      NALRR ++  +   AI  V+        
Sbjct: 12  RKMQIKILEKRDD-AIRFILE----GMDIAFANALRRTIIGEVPTFAIDEVEFYENDSAL 66

Query: 72  ISSIKGVHEDLTDIILNIK--GINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVL 128
              I      L  +        +      D    +++   GP +V +GD+++   D++ +
Sbjct: 67  FDEIIAHRLSLIPLTTPFDRFELESMELEDYTVTLSLEAEGPAIVYSGDLKSDDPDVKPV 126

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
           NP+  I  L     +        G G   AK
Sbjct: 127 NPNIPIVKLAEGQRLVFNAYAKMGKGKDHAK 157


>gi|228984312|ref|ZP_04144493.1| hypothetical protein bthur0001_10190 [Bacillus thuringiensis
           serovar tochigiensis BGSC 4Y1]
 gi|228775429|gb|EEM23814.1| hypothetical protein bthur0001_10190 [Bacillus thuringiensis
           serovar tochigiensis BGSC 4Y1]
          Length = 95

 Score = 45.0 bits (105), Expect = 0.019,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 26/54 (48%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  + N L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 42  LSSPARNALENHGIHTIEELSKYSEKEILKLHGMGPASLPKLRKALEENGLSFK 95


>gi|75760174|ref|ZP_00740232.1| Hypothetical cytosolic protein [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|228899820|ref|ZP_04064066.1| hypothetical protein bthur0014_10330 [Bacillus thuringiensis IBL
           4222]
 gi|74492338|gb|EAO55496.1| Hypothetical cytosolic protein [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|228859839|gb|EEN04253.1| hypothetical protein bthur0014_10330 [Bacillus thuringiensis IBL
           4222]
          Length = 95

 Score = 45.0 bits (105), Expect = 0.019,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 27/54 (50%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  + N L+   I  + +L + +E ++L++   G  S+ +++  L   GL   
Sbjct: 42  LSSPARNALQHHGIHTIEELSKYSEKEILKLHGMGPASMPKLRKALEERGLSFK 95


>gi|24638179|sp|Q8SL92|RPOA_EUGGA RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|19168437|gb|AAL83362.1| RNA polymerase alpha subunit [Euglena granulata]
          Length = 216

 Score = 44.6 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 34/194 (17%), Positives = 72/194 (37%), Gaps = 36/194 (18%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLH------------EISSIKGVHEDLTDIILNIK 90
           LGN  R+ L+ S  G  I   +   V H            E S ++ V E   D+     
Sbjct: 36  LGNIFRQFLLGSFEGLVINEKRFY-VSHTNSLYKDFYLVNEFSLLEEVLEPFYDVWTVFD 94

Query: 91  GINLKMSGDSHKR--VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
            +  K      KR    +   G G + + DI   +++ +L    +   +     + + L 
Sbjct: 95  NLRFKEKFSLSKRYYARLLTYGSGEINSKDIIVPSNLSLLENKSLFTLITDSLCIDVILQ 154

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           +                         + ++ +++V+Y +E++  G  ++Y+KL + I T 
Sbjct: 155 ILS--------------------KNGSPFNGVERVNYILENSNSG-NINYNKLYLDISTR 193

Query: 209 GSITGEDSVALASR 222
             ++  +++    R
Sbjct: 194 YFLSPMEALFECFR 207


>gi|289742757|gb|ADD20126.1| RNA polymerase I and III subunit rPA40/rPC40 [Glossina morsitans
           morsitans]
          Length = 330

 Score = 44.6 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 40/266 (15%), Positives = 80/266 (30%), Gaps = 72/266 (27%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIK----------------- 76
           + NA RR+++S +   AI  V I           + H +  I                  
Sbjct: 63  IANAFRRLMLSEVPSMAIEKVYIHNNTSIIQDEVLAHRLGLIPLKADPRLFEYRGDESDQ 122

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV---------TAGDIQTVNDIEV 127
           G  +D  D  L +K    K   +S    +I+K                   I + +D+  
Sbjct: 123 GTEQDTLDFELKVKCSRRKDVKESSNFDSIYKNHKIYSGQIKWLPKGKQAQIYSESDVGP 182

Query: 128 LNPDHVICNLDVDAVVRMELTVSKG---------------HGYVPAKHHRTENDPIGLIT 172
           ++ D +I  +     + + L   KG               +  +P    + +        
Sbjct: 183 IDDDILITQMRPGHELDIRLAAVKGIGKDHAKFSPVATAFYRLLPEVKLKKDVVGKDAFL 242

Query: 173 IDALYSP------------IKKVSYTVESAR----------EGQVLDYDKLSMTIDTDGS 210
           +   +SP            +K   Y   S                   D    T+++ G+
Sbjct: 243 LQKCFSPGVIGLDENDRAYVKNARYDTCSRNVYRYPQLADVVEMARIRDHYIFTVESLGA 302

Query: 211 ITGEDSVALASRILQDQLGMFINFEE 236
           +  +     A ++L+ +   F++  E
Sbjct: 303 LKPDVIFIEAVKLLKSKCRKFLDEIE 328


>gi|222094864|ref|YP_002528924.1| hypothetical protein BCQ_1202 [Bacillus cereus Q1]
 gi|221238922|gb|ACM11632.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Bacillus
           cereus Q1]
          Length = 95

 Score = 44.6 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 26/54 (48%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  + N L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 42  LSSPARNALEQHGIHTIEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSFK 95


>gi|229171887|ref|ZP_04299456.1| hypothetical protein bcere0006_10040 [Bacillus cereus MM3]
 gi|228611597|gb|EEK68850.1| hypothetical protein bcere0006_10040 [Bacillus cereus MM3]
          Length = 95

 Score = 44.6 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 27/54 (50%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  + N L+   I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 42  LSSPARNALQHHGIHTIEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSFK 95


>gi|254573314|ref|XP_002493766.1| RNA polymerase II third largest subunit B44, part of central core
           [Pichia pastoris GS115]
 gi|238033565|emb|CAY71587.1| RNA polymerase II third largest subunit B44, part of central core
           [Pichia pastoris GS115]
 gi|328354411|emb|CCA40808.1| DNA-directed RNA polymerase II subunit RPB3 .5 [Pichia pastoris CBS
           7435]
          Length = 304

 Score = 44.6 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 44/235 (18%), Positives = 80/235 (34%), Gaps = 42/235 (17%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDIILNIK 90
             +L N+LRR +++ +   AI  V+I           + H +  I  V ED+ ++  +  
Sbjct: 25  NLSLANSLRRTMLAEVPTLAIDLVEIKMNTSVLADEFISHRLGLIPLVSEDVEEMKYSRD 84

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL--------------NPDHVI-- 134
                   +    + +  R  G     D+ + + I+V               + D  I  
Sbjct: 85  CTCEDYCDECSVVLELSARHEGEEGTTDVYSSSLIKVSGPGNLNVGEPVRRDDYDQGILL 144

Query: 135 CNLDVDAVVRMELTVSKGHGYVPA------------KHHRTENDPIGLITIDALYS-PIK 181
           C L     + +     KG     A              H           +DA    P  
Sbjct: 145 CKLRNHQELNIRCIAKKGIAKEHAKWSPCSAIAFEYDPHNKLKHTDFWFEVDAKKEWPDS 204

Query: 182 KVSYTVESAREGQVLDYD----KLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           K +   E  + G+V DY     +  MT++T GS+      +   + LQ++L   +
Sbjct: 205 KYATWEEPPKPGEVFDYKAKPNRFYMTVETTGSLKANQVFSRGIKTLQEKLANVL 259


>gi|229154810|ref|ZP_04282925.1| hypothetical protein bcere0010_10050 [Bacillus cereus ATCC 4342]
 gi|228628758|gb|EEK85470.1| hypothetical protein bcere0010_10050 [Bacillus cereus ATCC 4342]
          Length = 95

 Score = 44.6 bits (104), Expect = 0.024,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 26/54 (48%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  + N L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 42  LSSPARNALEHHGIHTIEELSKYSEKEILKLHGMGPASLPKLRKALEEQGLSFK 95


>gi|159905734|ref|YP_001549396.1| RNA polymerase insert [Methanococcus maripaludis C6]
 gi|159887227|gb|ABX02164.1| RNA polymerase insert [Methanococcus maripaludis C6]
          Length = 180

 Score = 44.2 bits (103), Expect = 0.029,   Method: Composition-based stats.
 Identities = 47/199 (23%), Positives = 82/199 (41%), Gaps = 32/199 (16%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           ALRR+++S +   AI  V      +  S    V      +I  IKG+ +  SGD    +T
Sbjct: 14  ALRRIMISEVPTYAIENVYFY--ENTSSMYDEVLAHRLGLI-PIKGVPV--SGDEVIVLT 68

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
           I K GP +V + DI++ +  E    +  I  L     + +E     G G + AK      
Sbjct: 69  ISKEGPCMVYSSDIKSESG-EPAFENIPIVKLAEGQKLELETEALVGTGKIHAK------ 121

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
                   +A+Y  I                  D++   I++ G++  ED V  +  IL+
Sbjct: 122 ----WQPCNAVYKQISN----------------DEVEFKIESFGNMDAEDIVRSSLEILK 161

Query: 226 DQLGMFINFEEPKKEVKED 244
           ++   F++  E ++   E+
Sbjct: 162 NKAEKFLSELEGRELSDEN 180


>gi|134045316|ref|YP_001096802.1| DNA-directed RNA polymerase subunit D [Methanococcus maripaludis
           C5]
 gi|132662941|gb|ABO34587.1| DNA-directed RNA polymerase, subunit D [Methanococcus maripaludis
           C5]
          Length = 180

 Score = 44.2 bits (103), Expect = 0.032,   Method: Composition-based stats.
 Identities = 45/199 (22%), Positives = 82/199 (41%), Gaps = 32/199 (16%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           ALRR+++S +   AI  V      +  S    V      ++  IKG+ +  SGD    +T
Sbjct: 14  ALRRIMISEVPTYAIENVYFY--ENTSSMYDEVLAHRLGLV-PIKGVPV--SGDEVIVLT 68

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
           I K GP +V + DI++ +  E    +  I  L     + +E     G G + AK      
Sbjct: 69  ISKEGPCMVYSSDIKSESG-EPAFENIPIVKLAEGQKLELEAEALVGTGKIHAK------ 121

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
                   +A+Y  I                  D++   I++ G++  ED +  +  IL+
Sbjct: 122 ----WQPCNAVYKQISN----------------DEVEFKIESFGNMDAEDIIRSSLEILK 161

Query: 226 DQLGMFINFEEPKKEVKED 244
           ++   F++  E ++   E+
Sbjct: 162 NKAEKFLSELEGQELSDEN 180


>gi|6172230|dbj|BAA85898.1| RNA-polymerase D [Halobacterium salinarum]
          Length = 249

 Score = 43.8 bits (102), Expect = 0.033,   Method: Composition-based stats.
 Identities = 43/256 (16%), Positives = 85/256 (33%), Gaps = 35/256 (13%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
             ++     +     R       N +RR ++  +   +I  V+       +         
Sbjct: 12  DRDDREARFVV----RNITPAFANGIRRAILVDVPTLSIDTVRFVENSSVMFD------- 60

Query: 82  LTDIILNIKGINLKMSGD---SHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNL 137
              + L +  + L    D       + +   GPG    GD+ +   ++E  + +  I  L
Sbjct: 61  -EQLGLRLGLVPLTTPEDYPAGEVTLALDVEGPGTAYPGDLVSNDPEVEAADENIPIIEL 119

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + +E     GHG   AKH        G + +   +  +++V + V  + E    D
Sbjct: 120 KDDQRLELEADAVDGHGRDHAKH-------QGGVAVGYRHLQLQRV-HVVGDSPEYADDD 171

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
              L   I+ D  +              D     +    P KEV+ +    +  F+    
Sbjct: 172 PQMLRGVIEEDDELVP-----------TDDFDNDLTTRYPGKEVEIEDVDGAFVFHVESD 220

Query: 258 KKVEELELSVRSTNCL 273
             +   EL +R+ + L
Sbjct: 221 GSMPVEELVLRAVDTL 236


>gi|206976556|ref|ZP_03237462.1| conserved domain protein [Bacillus cereus H3081.97]
 gi|206745239|gb|EDZ56640.1| conserved domain protein [Bacillus cereus H3081.97]
          Length = 95

 Score = 43.8 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 26/54 (48%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  + N L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 42  LSSPARNALEHHGIHTIEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSFK 95


>gi|240104023|ref|YP_002960332.1| DNA-directed RNA polymerase subunit D [Thermococcus gammatolerans
           EJ3]
 gi|239911577|gb|ACS34468.1| DNA-directed RNA polymerase subunit D (rpoD) [Thermococcus
           gammatolerans EJ3]
          Length = 260

 Score = 43.8 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 49/259 (18%), Positives = 90/259 (34%), Gaps = 61/259 (23%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEI 72
           +  E+    I     RG      NALRR +++ +   A+  V+            + H +
Sbjct: 9   ERREDAIKFIL----RGVDVPFANALRRTILAEVPTFAVDEVEFFENDSALFDEIIAHRL 64

Query: 73  SSIKGV--HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN-DIEVLN 129
           + I      E  +   L +         D    +++   GPG+V +GD+++ +  ++  N
Sbjct: 65  AMIPLTTPVERFSLDALEL--------DDYTVTLSLQAEGPGMVYSGDLKSDDEGVKPAN 116

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAK-----------------------HHRTEND 166
           P+  I  L     +        G G   AK                           E  
Sbjct: 117 PNIPIVKLAEGQKLTFNAYAKLGRGKDHAKWQPGFVYYKYLTEIHVSKEVPDWEELKELA 176

Query: 167 PIGLITID------------ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
               + ++            A Y P K  +Y  +  RE  +        T++T+G +  E
Sbjct: 177 ERRGLPVEEKKDEIIIKTIKAFYLPRKFEAYEGDKIREEIIPG--AFVFTVETNGELPVE 234

Query: 215 DSVALASRILQDQLGMFIN 233
           + V++A +IL  +   FIN
Sbjct: 235 EIVSIALKILMRKSDRFIN 253


>gi|255316715|ref|ZP_05358298.1| hypothetical protein CdifQCD-7_20312 [Clostridium difficile
           QCD-76w55]
          Length = 70

 Score = 43.8 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 19/56 (33%), Positives = 28/56 (50%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           + +L+LS +  N L   NI  +  L   T  D+L++   G KSL EIK  L  +  
Sbjct: 1   MNQLKLSKKIVNHLIKANIDSIESLKTMTSNDLLKINGIGPKSLEEIKQALSLLTK 56


>gi|218896178|ref|YP_002444589.1| hypothetical protein BCG9842_B4147 [Bacillus cereus G9842]
 gi|218543350|gb|ACK95744.1| conserved domain protein [Bacillus cereus G9842]
          Length = 95

 Score = 43.8 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 26/54 (48%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  + N L    I  + +L + +E ++L++   G  S+ +++  L   GL   
Sbjct: 42  LSSPARNALEHHGIHTIEELSKYSEKEILKLHGMGPASMPKLRKALEERGLSFK 95


>gi|150402492|ref|YP_001329786.1| RNA polymerase insert [Methanococcus maripaludis C7]
 gi|150033522|gb|ABR65635.1| RNA polymerase insert [Methanococcus maripaludis C7]
          Length = 180

 Score = 43.8 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 46/199 (23%), Positives = 82/199 (41%), Gaps = 32/199 (16%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           ALRR+++S +   AI  V      +  S    V      +I  IKG+ +  SGD    +T
Sbjct: 14  ALRRIMISEVPTYAIENVYFY--ENTSSMYDEVLAHRLGLI-PIKGVPV--SGDEVIVLT 68

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
           I K GP +V + D+++ +  E    +  I  L     + +E     G G + AK      
Sbjct: 69  ISKEGPCMVYSSDLKSESG-EPAFENIPIVKLAEGQKLELEAEALVGTGKIHAK------ 121

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
                   +A+Y  I                  D++   I++ G++  ED V  +  IL+
Sbjct: 122 ----WQPCNAVYKQISN----------------DEVEFKIESFGNMDAEDIVRSSLEILK 161

Query: 226 DQLGMFINFEEPKKEVKED 244
           ++   F++  E ++   E+
Sbjct: 162 NKAEKFLSELEGRELSDEN 180


>gi|157962130|ref|YP_001502164.1| sigma-70 region 4 domain-containing protein [Shewanella pealeana
           ATCC 700345]
 gi|157847130|gb|ABV87629.1| sigma-70 region 4 domain protein [Shewanella pealeana ATCC 700345]
          Length = 930

 Score = 43.4 bits (101), Expect = 0.054,   Method: Composition-based stats.
 Identities = 20/57 (35%), Positives = 27/57 (47%)

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
            K +EEL L VR  N         + DL   T+  ML   NFGRKS  ++  +L  +
Sbjct: 282 EKPLEELNLPVRLFNVFNVNGFTSLNDLKDITDKTMLSWPNFGRKSARDLYSLLLEI 338


>gi|292656898|ref|YP_003536795.1| DNA-directed RNA polymerase subunit D [Haloferax volcanii DS2]
 gi|291371468|gb|ADE03695.1| DNA-directed RNA polymerase subunit D [Haloferax volcanii DS2]
          Length = 259

 Score = 43.0 bits (100), Expect = 0.058,   Method: Composition-based stats.
 Identities = 29/149 (19%), Positives = 55/149 (36%), Gaps = 13/149 (8%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEI 72
            +E+I   + E+ R   +A    RG    L N +RR +++ +   +I  V+  +      
Sbjct: 6   QVEFI---EREDRRARFVA----RGLTPALANGIRRAMVADVPTFSIDTVRFVENTSVMF 58

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPD 131
             + G+   L  +   +              V +   GP    +GDI+   + +   + +
Sbjct: 59  DEMIGLRLGLVPLTTPLDD----FEPGDTVTVALEVDGPATAYSGDIESADDMVVPADEN 114

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKH 160
             I  L     +  E     GHG   AK+
Sbjct: 115 IPIIELKEGQRLEFEADAVLGHGKDHAKN 143


>gi|160944373|ref|ZP_02091601.1| hypothetical protein FAEPRAM212_01883 [Faecalibacterium prausnitzii
           M21/2]
 gi|158444155|gb|EDP21159.1| hypothetical protein FAEPRAM212_01883 [Faecalibacterium prausnitzii
           M21/2]
          Length = 1010

 Score = 43.0 bits (100), Expect = 0.064,   Method: Composition-based stats.
 Identities = 15/43 (34%), Positives = 23/43 (53%)

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            LS R+ N L   NI+ +  L + +E ++  M   G K+L EI
Sbjct: 10  NLSTRAINILARNNILTLSQLKECSEKELRSMRGLGGKTLDEI 52



 Score = 41.1 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 12/56 (21%), Positives = 25/56 (44%)

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
           N     ++ E+++S R  + L       +  L++    D  + AN G K++  I+ 
Sbjct: 85  NSLSYHQITEIDMSARGFHYLTLMGCTTIAQLVRLKREDFQKTANIGEKTIEIIEE 140



 Score = 38.4 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 16/94 (17%), Positives = 31/94 (32%), Gaps = 6/94 (6%)

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
           S          V EL LS R+ N L   N   +  + + +   +      G  ++ +I  
Sbjct: 180 SEMRTSLSFHNVSELNLSSRAANALIRGNYTTLDKIAELSIPKLTATKGIGLNTVNDIIT 239

Query: 309 ------VLGTMGLFLGMNLPDWPPESIEELAKKY 336
                  + +       N+ D   +  E+L   +
Sbjct: 240 QTRNWLTVNSYYESENFNISDNEKDLFEKLHSAF 273


>gi|169836384|ref|ZP_02869572.1| DNA-directed RNA polymerase alpha chain [candidate division TM7
           single-cell isolate TM7a]
          Length = 74

 Score = 43.0 bits (100), Expect = 0.068,   Method: Composition-based stats.
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 3/71 (4%)

Query: 117 GDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHHRTEND--PIGLITI 173
           GDIQ+  D+E++NP+ VIC +D   A   ++L +  G GY+  +            +I +
Sbjct: 1   GDIQSHADVEIINPEQVICTVDDPSAKAVIDLVIDSGRGYLSIEDSSETRLTISRSIIAL 60

Query: 174 DALYSPIKKVS 184
           DA  SP+ +V+
Sbjct: 61  DASISPVIRVT 71


>gi|194766065|ref|XP_001965145.1| GF21532 [Drosophila ananassae]
 gi|190617755|gb|EDV33279.1| GF21532 [Drosophila ananassae]
          Length = 333

 Score = 43.0 bits (100), Expect = 0.071,   Method: Composition-based stats.
 Identities = 41/270 (15%), Positives = 76/270 (28%), Gaps = 74/270 (27%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISS---------------------------I 75
           + NA RR+++S +   AI  V I      I                              
Sbjct: 64  IANAFRRLMLSDVPSMAIEKVYIYNNTSIIQDEVLAHRMGLLPLRADPRLFAYRTEESTE 123

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA----------GDIQTVNDI 125
            G  +D  +  L +K    K +G          +   V +             I T   +
Sbjct: 124 TGTEQDTLEFELKVKCTRRKDAGKDQSNFDDIYKNHKVYSGHLKWLPKGKQAQIYTETGV 183

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKG---------------HGYVPAKHHRTENDPIGL 170
             ++ D +I  L     + + L   KG               +  +P      E      
Sbjct: 184 GCIHDDILIAQLRPGHELDLRLVAVKGLGRDHAKFSPVATATYRLLPQIKLNREVSGKDA 243

Query: 171 ITIDALYSP------------IKKVSYTVESAREGQVLD----------YDKLSMTIDTD 208
             + + +SP            +K   Y   S    +              D    T+++ 
Sbjct: 244 YLLQSCFSPGVIGIDENECAYVKDARYDSCSRNVYRYPQINDSVTLARVRDHYIFTVESV 303

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPK 238
           G++  E     A ++L+ +   FI+  E +
Sbjct: 304 GALKPEVIFLEAVKVLKKKCRSFIDEIEAE 333


>gi|24638178|sp|Q8SL90|RPOA_EUGMY RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|19168440|gb|AAL83364.1| RNA polymerase alpha subunit [Euglena myxocylindracea]
          Length = 207

 Score = 43.0 bits (100), Expect = 0.072,   Method: Composition-based stats.
 Identities = 33/193 (17%), Positives = 78/193 (40%), Gaps = 42/193 (21%)

Query: 45  NALRRVLMSSLRGAAITAV--------QIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           N +RR+L+  +    ++ +        +    +HE + ++ V  +L   ++ +K I  + 
Sbjct: 38  NLIRRILLKEIYNFKVSTISIFLFNSNKFCYKIHEFTKVEEVKNNLVSFLILLKEIKFRS 97

Query: 97  SGDSHKRVT---IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV-DAVVRMELTVSKG 152
                 + T   +  +    V   DI   N+ ++L+ D+ +  L+  D  +++ L + K 
Sbjct: 98  YYKLKTKRTFALLKIKQFTQVFLTDIILPNNFKILSIDNNLIKLNSLDINLKVLLELHKS 157

Query: 153 HGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
            GY                     ++P+KKV+Y  E+           +   I T+ + T
Sbjct: 158 KGY--------------------NFNPVKKVNYIEENN----------VYFEIYTNQTST 187

Query: 213 GEDSVALASRILQ 225
             + +  + +I++
Sbjct: 188 PLEVLVKSLKIIK 200


>gi|212223251|ref|YP_002306487.1| DNA-directed RNA polymerase subunit D [Thermococcus onnurineus NA1]
 gi|212008208|gb|ACJ15590.1| DNA-directed RNA polymerase, subunit D [Thermococcus onnurineus
           NA1]
          Length = 260

 Score = 43.0 bits (100), Expect = 0.072,   Method: Composition-based stats.
 Identities = 30/150 (20%), Positives = 58/150 (38%), Gaps = 24/150 (16%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEI 72
           ++ E+    I E    G      NALRR +++ +   A+  V+            + H +
Sbjct: 9   EKREDSIKFIVE----GIDIPFANALRRTILAEVPTFAVDEVEFFENDSALFDEIIAHRL 64

Query: 73  SSIKGV--HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN-DIEVLN 129
           + I      E  +   L +         D    +++   GPG+V +GD+++ +  ++  N
Sbjct: 65  AMIPLTTPVERFSLDALEL--------DDYTVTLSLEAEGPGMVYSGDLKSDDEGVKPAN 116

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
           P+  I  L     + +      G G   AK
Sbjct: 117 PNIPIVKLAEGQNLTLNAYAKLGRGKDHAK 146


>gi|229028912|ref|ZP_04185013.1| hypothetical protein bcere0028_10160 [Bacillus cereus AH1271]
 gi|228732483|gb|EEL83364.1| hypothetical protein bcere0028_10160 [Bacillus cereus AH1271]
          Length = 95

 Score = 42.6 bits (99), Expect = 0.081,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 26/54 (48%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  + N L    I  + +L + +E ++L++   G  S+ +++  L   GL   
Sbjct: 42  LSSPARNALEHHGIHTIEELSKYSEKEILKLHGMGPASMPKLRKALEEAGLSFK 95


>gi|298483974|ref|ZP_07002144.1| conserved hypothetical protein [Bacteroides sp. D22]
 gi|298269883|gb|EFI11474.1| conserved hypothetical protein [Bacteroides sp. D22]
          Length = 245

 Score = 42.6 bits (99), Expect = 0.083,   Method: Composition-based stats.
 Identities = 22/105 (20%), Positives = 44/105 (41%)

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGE 276
           +     ++Q       + +  K  ++  +N         L + V  L ++    + L   
Sbjct: 124 IQQDELVIQKMQERLDSLKRIKVGLEIALNNIQAEEVHYLSEPVFSLGITPSIKSHLESH 183

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
            I+Y+GDLI   E  ++ +   G  +L +IK  L   G + GM++
Sbjct: 184 GILYIGDLIHLNEQYLMEIWGIGPVTLDKIKTKLNENGAWFGMDV 228


>gi|53714106|ref|YP_100098.1| hypothetical protein BF2814 [Bacteroides fragilis YCH46]
 gi|224026975|ref|ZP_03645341.1| hypothetical protein BACCOPRO_03734 [Bacteroides coprophilus DSM
           18228]
 gi|253567368|ref|ZP_04844817.1| conserved hypothetical protein [Bacteroides sp. 3_2_5]
 gi|255009127|ref|ZP_05281253.1| hypothetical protein Bfra3_08296 [Bacteroides fragilis 3_1_12]
 gi|256840343|ref|ZP_05545851.1| conserved hypothetical protein [Parabacteroides sp. D13]
 gi|293371316|ref|ZP_06617753.1| conserved hypothetical protein [Bacteroides ovatus SD CMC 3f]
 gi|294645285|ref|ZP_06723001.1| conserved hypothetical protein [Bacteroides ovatus SD CC 2a]
 gi|294808748|ref|ZP_06767481.1| conserved hypothetical protein [Bacteroides xylanisolvens SD CC 1b]
 gi|313146878|ref|ZP_07809071.1| conserved hypothetical protein [Bacteroides fragilis 3_1_12]
 gi|52216971|dbj|BAD49564.1| hypothetical protein [Bacteroides fragilis YCH46]
 gi|224020211|gb|EEF78209.1| hypothetical protein BACCOPRO_03734 [Bacteroides coprophilus DSM
           18228]
 gi|251943937|gb|EES84465.1| conserved hypothetical protein [Bacteroides sp. 3_2_5]
 gi|256737615|gb|EEU50941.1| conserved hypothetical protein [Parabacteroides sp. D13]
 gi|292633676|gb|EFF52231.1| conserved hypothetical protein [Bacteroides ovatus SD CMC 3f]
 gi|292639364|gb|EFF57666.1| conserved hypothetical protein [Bacteroides ovatus SD CC 2a]
 gi|294444045|gb|EFG12779.1| conserved hypothetical protein [Bacteroides xylanisolvens SD CC 1b]
 gi|313135645|gb|EFR53005.1| conserved hypothetical protein [Bacteroides fragilis 3_1_12]
          Length = 245

 Score = 42.6 bits (99), Expect = 0.083,   Method: Composition-based stats.
 Identities = 22/105 (20%), Positives = 44/105 (41%)

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGE 276
           +     ++Q       + +  K  ++  +N         L + V  L ++    + L   
Sbjct: 124 IQQDELVIQKMQERLDSLKRIKVGLEIALNNIQAEEVHYLSEPVFSLGITPSIKSHLESH 183

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
            I+Y+GDLI   E  ++ +   G  +L +IK  L   G + GM++
Sbjct: 184 GILYIGDLIHLNEQYLMEIWGIGPVTLDKIKTKLNENGAWFGMDV 228


>gi|315229895|ref|YP_004070331.1| DNA-directed RNA polymerase subunit D [Thermococcus barophilus MP]
 gi|315182923|gb|ADT83108.1| DNA-directed RNA polymerase subunit D [Thermococcus barophilus MP]
          Length = 258

 Score = 42.6 bits (99), Expect = 0.086,   Method: Composition-based stats.
 Identities = 32/155 (20%), Positives = 59/155 (38%), Gaps = 26/155 (16%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + ++ E+    I E    G      NALRRV++  +   A+  V+       +     
Sbjct: 3   IKVLEKREDAIRFILE----GVDAAFANALRRVIIGEVPTFAVDEVEFYENDSAL----- 53

Query: 78  VHEDLTDIILN-IKGINLKMS-----------GDSHKRVTIFKRGPGVVTAGDIQT-VND 124
                 +II + +  I L               +    +++   GPGVV +GD+++   D
Sbjct: 54  ----FDEIIAHRLAMIPLTTPYDRFELDALELDEYTVTLSLEAEGPGVVYSGDLKSDDPD 109

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
           ++ + P+  I  L     + +      G G   AK
Sbjct: 110 VKPVTPNIPIVKLAEGQKLTLNAYAKLGRGKDHAK 144


>gi|265763613|ref|ZP_06092181.1| conserved hypothetical protein [Bacteroides sp. 2_1_16]
 gi|263256221|gb|EEZ27567.1| conserved hypothetical protein [Bacteroides sp. 2_1_16]
          Length = 245

 Score = 42.6 bits (99), Expect = 0.087,   Method: Composition-based stats.
 Identities = 22/105 (20%), Positives = 45/105 (42%)

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGE 276
           +     ++Q       + +  K  ++  +N         L + V  L ++    + L   
Sbjct: 124 IQQDELVIQKMQERLDSLKRIKVGLEIALNNIQAEEVHYLSEPVFSLGITPSIKSHLESH 183

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
            I+Y+GDLI   E  ++ + + G  +L +IK  L   G + GM++
Sbjct: 184 GILYIGDLIHLNEQYLMEIWDIGPVTLDKIKTKLNENGAWFGMDV 228


>gi|126460700|ref|YP_001056978.1| DNA-directed RNA polymerase, subunit D [Pyrobaculum calidifontis
           JCM 11548]
 gi|166229320|sp|A3MXZ5|RPOD_PYRCJ RecName: Full=DNA-directed RNA polymerase subunit D
 gi|126250421|gb|ABO09512.1| DNA-directed RNA polymerase, subunit D [Pyrobaculum calidifontis
           JCM 11548]
          Length = 258

 Score = 42.6 bits (99), Expect = 0.090,   Method: Composition-based stats.
 Identities = 47/252 (18%), Positives = 82/252 (32%), Gaps = 39/252 (15%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT-AVQIDGVLHEISSIKGVHEDLTDI 85
           ++   A+ +  G   +L N+LRRV++S L   AI   V ++        +      L  +
Sbjct: 9   KSQFFAKAVVEGVPPSLINSLRRVIISELPVLAIDSVVVVNNTSVMYDEMLAHRLGLIPL 68

Query: 86  ILNIKGINLKMS--------GDSHKRVTIFKRGPG--VVTAGDIQTV-NDIEVLNPDHVI 134
              +K +              +   R+T+     G  VV AGD+     D+  +  D  I
Sbjct: 69  TTPLKDLPPIEDCESGLVDPSECTVRLTLQVNATGDVVVYAGDLVADRPDVAPVYKDIPI 128

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI----------------------T 172
             L     V +E     G     AK                                   
Sbjct: 129 VKLVEGQSVVVEAYAKLGRARDHAKWQAALASYYYYPKVVVKREECREMCKEVCRNLENP 188

Query: 173 IDALYSPIKKVSYTVESAREGQ--VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           ++  ++         E    G     + DK    I++ G+   E ++  A RIL+ +   
Sbjct: 189 LECTFNKATTCK---EMCGGGIVVEWEKDKYVFWIESFGNYDAETALREAFRILKKKFED 245

Query: 231 FINFEEPKKEVK 242
           F++    K E K
Sbjct: 246 FLDALSRKAEAK 257


>gi|84489668|ref|YP_447900.1| DNA-directed RNA polymerase subunit D [Methanosphaera stadtmanae
           DSM 3091]
 gi|121731854|sp|Q2NFZ6|RPOD_METST RecName: Full=DNA-directed RNA polymerase subunit D
 gi|84372987|gb|ABC57257.1| RpoD [Methanosphaera stadtmanae DSM 3091]
          Length = 270

 Score = 42.6 bits (99), Expect = 0.092,   Method: Composition-based stats.
 Identities = 43/275 (15%), Positives = 88/275 (32%), Gaps = 60/275 (21%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL-HEISSIK 76
           I + ++++ R + + E    G   T  N +RR+ +  +   AI  V I          + 
Sbjct: 3   IEIREKDDERAVFVVE----GVDDTFINTIRRICLVEIPTLAIEDVNIYKNDAKMFDEVL 58

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFK------------RGPGVVTAGDIQT-VN 123
                L  I+ ++    +    D        +                +V + D+++   
Sbjct: 59  AHRLGLIPIVTDLDSYVMPSECDCESGCQHCRVSFLLKEKCEEGNDSKIVYSKDLKSDDP 118

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK------------------------ 159
            ++ +     I  L     V +E     G G   AK                        
Sbjct: 119 AVKPVYDTIPIVRLREGEEVELEAIAELGLGSEHAKWQATTTCGYKYYPKIEIDTEKVND 178

Query: 160 -------------HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD--KLSMT 204
                            +   +G I   +     +++S   ++A     +D++  K    
Sbjct: 179 LEEYVEECPRNVLQIEDDTLVVGNIENCSTCRTCQRLSEKDDNAIV---VDFEESKYIFK 235

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I+TDGS+   D + +A  IL ++    INF   ++
Sbjct: 236 IETDGSLKPFDVLTIACDILSEKADNIINFVNEEE 270


>gi|228919963|ref|ZP_04083317.1| hypothetical protein bthur0011_9830 [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228964187|ref|ZP_04125310.1| hypothetical protein bthur0004_10400 [Bacillus thuringiensis
           serovar sotto str. T04001]
 gi|228795537|gb|EEM43021.1| hypothetical protein bthur0004_10400 [Bacillus thuringiensis
           serovar sotto str. T04001]
 gi|228839676|gb|EEM84963.1| hypothetical protein bthur0011_9830 [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 95

 Score = 42.6 bits (99), Expect = 0.094,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 27/54 (50%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  + N L+   I  + +L + +E ++L+M   G  SL +++  L   GL   
Sbjct: 42  LSSPARNALQHHGIQTIEELSKYSEKEILKMHGMGPASLPKLRRALEESGLSFK 95


>gi|254173028|ref|ZP_04879702.1| RNA polymerase Rpb3/Rpb11 dimerisation domain [Thermococcus sp.
           AM4]
 gi|214033184|gb|EEB74012.1| RNA polymerase Rpb3/Rpb11 dimerisation domain [Thermococcus sp.
           AM4]
          Length = 260

 Score = 42.6 bits (99), Expect = 0.095,   Method: Composition-based stats.
 Identities = 47/244 (19%), Positives = 86/244 (35%), Gaps = 57/244 (23%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGV--HEDLTDI 85
           RG      NALRR +++ +   A+  V+            + H ++ I      E  +  
Sbjct: 20  RGVDVPFANALRRTILAEVPTFAVDEVEFFENDSALFDEIIAHRLAMIPLTTPVERFSLD 79

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN-DIEVLNPDHVICNLDVDAVVR 144
            L++         D    +++   GPG+V +GD+++ +  ++  NP+  I  L     + 
Sbjct: 80  SLDL--------DDYTVTLSLQAEGPGMVYSGDLKSDDEGVKPANPNIPIVKLAEGQKLT 131

Query: 145 MELTVSKGHGYVPAK-----------------------HHRTENDPIGLITID------- 174
                  G G   AK                           E      + ++       
Sbjct: 132 FNAYARLGRGKDHAKWQPGFVYYKYLTEIHVSKEVPDWEELKELAERRGLPVEEKEDEIV 191

Query: 175 -----ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
                A Y P K   Y  +  RE  +        T++T+G +  E+ V++A +IL  +  
Sbjct: 192 IKTTKAFYLPRKFEEYEGDKIREEIIPG--AFVFTVETNGELPVEEIVSIALKILMRKSD 249

Query: 230 MFIN 233
            FIN
Sbjct: 250 RFIN 253


>gi|45358885|ref|NP_988442.1| DNA-directed RNA polymerase subunit D [Methanococcus maripaludis
           S2]
 gi|45047751|emb|CAF30878.1| DNA-directed RNA polymerase, subunit D [Methanococcus maripaludis
           S2]
          Length = 180

 Score = 42.3 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 46/199 (23%), Positives = 81/199 (40%), Gaps = 33/199 (16%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           ALRR+++S +   AI  V      +  S    V      +I  IKG+ +  SGD    +T
Sbjct: 14  ALRRIMISEVPTYAIENVYFY--ENTSSMYDEVLAHRLGLI-PIKGVPV--SGDEVIVLT 68

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
           I K GP  V + D+++ +  E    +  I  L  D  + +E     G G + AK      
Sbjct: 69  ISKEGPCTVYSSDLKSESG-EPAFENIPIVKLAEDQKLELETEALVGTGKIHAK------ 121

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
                   +A Y  I                  D++   I++ G++  ED +  +  IL+
Sbjct: 122 ----WQPCNASYKQISN----------------DEVEFKIESFGNMDAEDIIRSSLEILK 161

Query: 226 DQLGMFINFEEPKKEVKED 244
           ++   F+  E   +E+ ++
Sbjct: 162 NKAEKFL-LELEGQELSDE 179


>gi|116624612|ref|YP_826768.1| RNA polymerase subunit alpha [Candidatus Solibacter usitatus
           Ellin6076]
 gi|116227774|gb|ABJ86483.1| RNA polymerase, alpha subunit domain protein [Candidatus Solibacter
           usitatus Ellin6076]
          Length = 130

 Score = 42.3 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 21/79 (26%), Positives = 34/79 (43%), Gaps = 5/79 (6%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADM-LRMANFGRKSLVEIKGVLGTMGLFLG 318
           VE+L LSVR+ N LR      + +++     D+   +   GRK+  E+   L   G    
Sbjct: 24  VEDLGLSVRTRNALRAIGCDTVENVLAL---DLGSSVRGLGRKTKEELLVALELKGFRHP 80

Query: 319 MNLPDWPPESIEELAKKYE 337
             L   P   I+ L +  +
Sbjct: 81  -ALEQQPASEIQVLERSLD 98


>gi|224025021|ref|ZP_03643387.1| hypothetical protein BACCOPRO_01755 [Bacteroides coprophilus DSM
           18228]
 gi|224018257|gb|EEF76255.1| hypothetical protein BACCOPRO_01755 [Bacteroides coprophilus DSM
           18228]
          Length = 89

 Score = 42.3 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 16/48 (33%), Positives = 25/48 (52%)

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           L    IV + DL ++TE ++  +     K+L  IK +L   GL  GM+
Sbjct: 27  LMQAGIVTVEDLCRKTEEELSSIPFIKGKNLQAIKDMLAEKGLHTGMS 74


>gi|15790216|ref|NP_280040.1| DNA-directed RNA polymerase II [Halobacterium sp. NRC-1]
 gi|169235945|ref|YP_001689145.1| DNA-directed RNA polymerase subunit D [Halobacterium salinarum R1]
 gi|13124517|sp|Q9HQJ4|RPOD_HALSA RecName: Full=DNA-directed RNA polymerase subunit D
 gi|229564264|sp|B0R4Y2|RPOD_HALS3 RecName: Full=DNA-directed RNA polymerase subunit D
 gi|10580674|gb|AAG19520.1| DNA-directed RNA polymerase II [Halobacterium sp. NRC-1]
 gi|167727011|emb|CAP13797.1| DNA-directed RNA polymerase subunit D [Halobacterium salinarum R1]
          Length = 248

 Score = 42.3 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 25/144 (17%), Positives = 49/144 (34%), Gaps = 17/144 (11%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
             ++     +     R       N +RR ++  +   +I  V+       +         
Sbjct: 12  DRDDREARFVV----RNITPAFANGIRRAILVDVPTLSIDTVRFVENSSVMFD------- 60

Query: 82  LTDIILNIKGINLKMSGD----SHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICN 136
              + L +  + L    D        + +   GPG   +GD+ +   ++E  + +  I  
Sbjct: 61  -EQLGLRLGLVPLTTPEDYAAGEAVTLALDVEGPGTAYSGDLVSNDPEVEAADENIPIIE 119

Query: 137 LDVDAVVRMELTVSKGHGYVPAKH 160
           L  D  + +E     GHG   AKH
Sbjct: 120 LKDDQRLELEADAVMGHGRDHAKH 143


>gi|196004242|ref|XP_002111988.1| hypothetical protein TRIADDRAFT_24132 [Trichoplax adhaerens]
 gi|190585887|gb|EDV25955.1| hypothetical protein TRIADDRAFT_24132 [Trichoplax adhaerens]
          Length = 274

 Score = 42.3 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 81/248 (32%), Gaps = 51/248 (20%)

Query: 28  TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGV 78
              I E        ++ N+LRR+ ++++   AI  VQ            + H +  I   
Sbjct: 19  VKFILE----NTDLSVANSLRRIFIANVPTLAIDWVQFVNNTSVLSDEFIAHRLGLIPLT 74

Query: 79  HEDLTDIILNIKGINLKMSGDS-HKRVTIFKRGP-----GVVTAGDIQTVNDIEVLN--- 129
            +++ D +   +  N            T+  R        V T   I + + +  +    
Sbjct: 75  CDEVIDRLQYSRDCNCVEHCPECSVEFTLDVRCNDDQTRHVTTRDLISSDSRVVPVTTRY 134

Query: 130 -----------PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL-- 176
                       D +I  L     ++++    KG G   AK + T +        +A+  
Sbjct: 135 GEDDTVYGDQEDDILIAKLRRGQEIKIKAYAKKGLGTEHAKWNPTASVAFEYDPDNAMRH 194

Query: 177 -------------YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
                        YS + + +Y             DK  + ++T GS+  E+ V      
Sbjct: 195 TTYPKPEEWPKSEYSNLPEDNYEASY---DPQTVADKFYLNVETSGSLRPENIVLSGIST 251

Query: 224 LQDQLGMF 231
           L+++L   
Sbjct: 252 LKNKLSEL 259


>gi|312213137|emb|CBX93219.1| hypothetical protein [Leptosphaeria maculans]
          Length = 336

 Score = 41.9 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 39/254 (15%), Positives = 74/254 (29%), Gaps = 47/254 (18%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEI 72
           Q +  R   I +     F     N+LRRV++S +   AI  V++           V H +
Sbjct: 16  QADNQRAHFIVQ----NFNLETANSLRRVMLSEIPTLAIDVVEVLDNTSVLADEFVCHRL 71

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
             I    + + D++ +          +    +T+  +  G            +E + P+ 
Sbjct: 72  GLIPLCSKGVDDLLYSRDCDCEGYCSNCSVVLTLNAKCTGNEIMKVYARDLVVESMTPND 131

Query: 133 V---------------ICNLDVDAVVRMELTVSKGH---------------GYVPAKHHR 162
                           I  L     + M     KG                 Y PA    
Sbjct: 132 EVGRPVITDADGTGSCIVKLRRGQAIHMRCIAKKGIAKEHAKWAPSAAIGFEYDPANKLH 191

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD----KLSMTIDTDGSITGEDSVA 218
             +                +++     A   +  DY+    +    ++T G +  +  V 
Sbjct: 192 HLDYWHEEDPDKEWPKDEDRINLDGGPANPDEPFDYNAAPTRFFYDVETVGGLDPDQIVG 251

Query: 219 LASRILQDQLGMFI 232
               +LQ +L   I
Sbjct: 252 KGITVLQHKLAGII 265


>gi|302348806|ref|YP_003816444.1| DNA-directed RNA polymerase subunit D [Acidilobus saccharovorans
           345-15]
 gi|302329218|gb|ADL19413.1| DNA-directed RNA polymerase subunit D [Acidilobus saccharovorans
           345-15]
          Length = 287

 Score = 41.9 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 48/270 (17%), Positives = 85/270 (31%), Gaps = 72/270 (26%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           GF    GNALRR+ +S +   A+  V      +E S    +      I   +  + L+  
Sbjct: 22  GFPVAYGNALRRLALSEVPTMAVDFVYFY--DNESSVYDEI------IAHRLGLLVLRSD 73

Query: 98  G-----------------DSHKRVTIFKRGP--------GVVTAGDIQ-TVNDIEVLNPD 131
                             DSH    ++              V A D++ +  DI  + P+
Sbjct: 74  EALRKYGSPEECSNASENDSHCFAQVYLEYEVPQDAASGVYVKASDLKFSDPDIRPIYPE 133

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAK-----------HHRTENDPIGLITIDALYSPI 180
             I  L     + +      G GY   K               E DP  + +        
Sbjct: 134 TPIVYLAPGQRIHLVGYARLGRGYEHGKWSPASVAVLRYSVHVEYDPSKVTSECLECISA 193

Query: 181 ---------------KKVSYTV----------ESAREGQVLDYD--KLSMTIDTDGSITG 213
                           +++Y V          ES +    + YD  KL +T+++ G++  
Sbjct: 194 YQDLVGAIKGGSAGRLELNYKVNTSALRYCEEESCKGAIKVVYDPSKLYLTVESTGALEP 253

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKE 243
              +  A+  L  +    +   E  + V+E
Sbjct: 254 ARIIWEATNCLARKADKLLKELEEAQVVEE 283


>gi|237719951|ref|ZP_04550432.1| conserved hypothetical protein [Bacteroides sp. 2_2_4]
 gi|229450503|gb|EEO56294.1| conserved hypothetical protein [Bacteroides sp. 2_2_4]
          Length = 245

 Score = 41.9 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 22/105 (20%), Positives = 43/105 (40%)

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGE 276
           +     ++Q       + +  K  ++  +N         L + V  L ++      L   
Sbjct: 124 IQQNELVIQKMQERLDSLKRIKVGLEIALNNIQAEEVHYLSEPVFSLGITPSIKRHLESH 183

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
            I+Y+GDLI   E  ++ +   G  +L +IK  L   G + GM++
Sbjct: 184 GILYIGDLIHLNEQYLMEIWGIGPVTLDKIKTKLNENGTWFGMDV 228


>gi|297623200|ref|YP_003704634.1| hypothetical protein Trad_0961 [Truepera radiovictrix DSM 17093]
 gi|297164380|gb|ADI14091.1| conserved hypothetical protein [Truepera radiovictrix DSM 17093]
          Length = 72

 Score = 41.9 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 9/46 (19%), Positives = 19/46 (41%)

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           L+      +      +E ++L++   G K+L  ++  L   GL   
Sbjct: 19  LKRAGYTRLEQFAGVSETELLKLHGVGPKALAVLREALAERGLAFA 64


>gi|261403745|ref|YP_003247969.1| RNA polymerase insert [Methanocaldococcus vulcanius M7]
 gi|261370738|gb|ACX73487.1| RNA polymerase insert [Methanocaldococcus vulcanius M7]
          Length = 191

 Score = 41.9 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 42/196 (21%), Positives = 76/196 (38%), Gaps = 40/196 (20%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN-IKGINLK---M 96
            +  NA+RR+++S +   AI  V I      +           +I+ + +  I +K   +
Sbjct: 24  ISFSNAIRRIMISEVPTFAIEDVYIYENSSSMDD---------EILAHRLGLIPIKGKPL 74

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
                   T+ K GP  V + D+++ N  EV   +  I  L     +++E     G G V
Sbjct: 75  LDTEIITFTLEKEGPCTVYSSDLKSENG-EVAFKNIPIVKLGKGQRIKIECEAVPGIGKV 133

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
            AK              +A+Y                + L  D++   ++T G I  E  
Sbjct: 134 HAK----------WQPCNAVY----------------KQLSEDEVEFFVETFGQIDAEQI 167

Query: 217 VALASRILQDQLGMFI 232
           +  A +IL+D+   F+
Sbjct: 168 LKEAVKILRDKADSFL 183


>gi|312194760|ref|YP_004014821.1| hypothetical protein FraEuI1c_0873 [Frankia sp. EuI1c]
 gi|311226096|gb|ADP78951.1| hypothetical protein FraEuI1c_0873 [Frankia sp. EuI1c]
          Length = 282

 Score = 41.5 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 26/142 (18%), Positives = 52/142 (36%), Gaps = 12/142 (8%)

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            +   G +   + + L      DQ+   +     +        +  LP   A +  +  L
Sbjct: 59  EVTLYGLVRAREVLVLGQSQFADQVREVL-----RAGQVPGWGLHELPAERAPVSALYAL 113

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL-FLGMNL- 321
            LSVR+ N L+    ++  ++    +  +      G + L EI+  L    L    ++L 
Sbjct: 114 -LSVRTANILKRAPFLFAQEVAALPDEVLREFRGLGPRVLAEIRAALADPALANFRIDLA 172

Query: 322 -PDWPPESI---EELAKKYEDK 339
            P+    S    E+LA +   +
Sbjct: 173 SPESDASSEDLPEDLASRLRPE 194


>gi|328768461|gb|EGF78507.1| hypothetical protein BATDEDRAFT_20338 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 285

 Score = 41.5 bits (96), Expect = 0.21,   Method: Composition-based stats.
 Identities = 40/250 (16%), Positives = 84/250 (33%), Gaps = 44/250 (17%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS---------IKGVHEDLTDII----L 87
            ++ NALRR +++ +   AI  V+ +     ++          I    E +  I      
Sbjct: 36  LSVANALRRTMIAEVPTVAIDLVEFESNSSVLTDEFLAHRLGLIPLNSEQVGTITYTRDC 95

Query: 88  NIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND--IEVLNPD----HVICNLDVDA 141
           +      + S + H  V   +     VT+ D+ + +   + +++ D     +I  L    
Sbjct: 96  SCTQYCPQCSVELHLNVRCDEEFTREVTSRDLISSHSSIMPIIHGDDDSGIMIAKLRKGQ 155

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES------------ 189
            + +     KG     AK                 ++ ++  +Y VE             
Sbjct: 156 EINLRCIAKKGTAKEHAKWSPCAGIAFEYDP----HNRLRHTTYWVEDDIKSEWPVSANG 211

Query: 190 ---------AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
                             DK  MT++  G+I  ++ V  A RI+Q +L +     +   +
Sbjct: 212 LLEPEVVDDEPFDFNAKPDKFYMTVEGTGAIDPKEIVTTALRIMQTKLSLVQMLIKEISD 271

Query: 241 VKEDINVKSL 250
             +D +   +
Sbjct: 272 DNDDSSRAQM 281


>gi|52144187|ref|YP_082641.1| hypothetical protein BCZK1040 [Bacillus cereus E33L]
 gi|51977656|gb|AAU19206.1| conserved hypothetical protein [Bacillus cereus E33L]
          Length = 95

 Score = 41.1 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 42  LSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRAALEKKGLSFK 95


>gi|229101825|ref|ZP_04232540.1| hypothetical protein bcere0019_9910 [Bacillus cereus Rock3-28]
 gi|228681618|gb|EEL35780.1| hypothetical protein bcere0019_9910 [Bacillus cereus Rock3-28]
          Length = 92

 Score = 41.1 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 39  LSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEECGLSFK 92


>gi|254884141|ref|ZP_05256851.1| conserved hypothetical protein [Bacteroides sp. 4_3_47FAA]
 gi|255013657|ref|ZP_05285783.1| hypothetical protein B2_07100 [Bacteroides sp. 2_1_7]
 gi|254836934|gb|EET17243.1| conserved hypothetical protein [Bacteroides sp. 4_3_47FAA]
          Length = 245

 Score = 41.1 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 21/89 (23%), Positives = 40/89 (44%)

Query: 233 NFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           + +  K  ++  +N         L + V  L ++    + L    I+Y+GDLI   E  +
Sbjct: 140 SLKRIKVGLEIALNNIQAEEVHYLSEPVFSLGITPSIKSHLESHGILYIGDLIHLNEQYL 199

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           + +   G  +L +IK  L   G + GM++
Sbjct: 200 MEIWGVGPVTLEKIKTKLNENGAWFGMDV 228


>gi|30261250|ref|NP_843627.1| hypothetical protein BA_1143 [Bacillus anthracis str. Ames]
 gi|47526412|ref|YP_017761.1| hypothetical protein GBAA_1143 [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49184082|ref|YP_027334.1| hypothetical protein BAS1062 [Bacillus anthracis str. Sterne]
 gi|65318521|ref|ZP_00391480.1| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Bacillus anthracis str. A2012]
 gi|165873095|ref|ZP_02217713.1| conserved domain protein [Bacillus anthracis str. A0488]
 gi|167635403|ref|ZP_02393717.1| conserved domain protein [Bacillus anthracis str. A0442]
 gi|167640197|ref|ZP_02398463.1| conserved domain protein [Bacillus anthracis str. A0193]
 gi|170688124|ref|ZP_02879336.1| conserved domain protein [Bacillus anthracis str. A0465]
 gi|170707653|ref|ZP_02898105.1| conserved domain protein [Bacillus anthracis str. A0389]
 gi|177655489|ref|ZP_02936932.1| conserved domain protein [Bacillus anthracis str. A0174]
 gi|190566674|ref|ZP_03019591.1| conserved domain protein [Bacillus anthracis Tsiankovskii-I]
 gi|196036241|ref|ZP_03103640.1| conserved domain protein [Bacillus cereus W]
 gi|227816012|ref|YP_002816021.1| hypothetical protein BAMEG_3438 [Bacillus anthracis str. CDC 684]
 gi|228913818|ref|ZP_04077443.1| hypothetical protein bthur0012_10560 [Bacillus thuringiensis
           serovar pulsiensis BGSC 4CC1]
 gi|228926281|ref|ZP_04089355.1| hypothetical protein bthur0010_10010 [Bacillus thuringiensis
           serovar pondicheriensis BGSC 4BA1]
 gi|229602118|ref|YP_002865673.1| hypothetical protein BAA_1226 [Bacillus anthracis str. A0248]
 gi|254682689|ref|ZP_05146550.1| hypothetical protein BantC_02400 [Bacillus anthracis str.
           CNEVA-9066]
 gi|254725482|ref|ZP_05187264.1| hypothetical protein BantA1_23996 [Bacillus anthracis str. A1055]
 gi|254734107|ref|ZP_05191820.1| hypothetical protein BantWNA_02898 [Bacillus anthracis str. Western
           North America USA6153]
 gi|254740249|ref|ZP_05197941.1| hypothetical protein BantKB_04364 [Bacillus anthracis str. Kruger
           B]
 gi|254753589|ref|ZP_05205625.1| hypothetical protein BantV_14033 [Bacillus anthracis str. Vollum]
 gi|254758686|ref|ZP_05210713.1| hypothetical protein BantA9_10299 [Bacillus anthracis str.
           Australia 94]
 gi|30254864|gb|AAP25113.1| conserved domain protein [Bacillus anthracis str. Ames]
 gi|47501560|gb|AAT30236.1| conserved domain protein [Bacillus anthracis str. 'Ames Ancestor']
 gi|49178009|gb|AAT53385.1| conserved domain protein [Bacillus anthracis str. Sterne]
 gi|164711149|gb|EDR16708.1| conserved domain protein [Bacillus anthracis str. A0488]
 gi|167511798|gb|EDR87178.1| conserved domain protein [Bacillus anthracis str. A0193]
 gi|167529231|gb|EDR91984.1| conserved domain protein [Bacillus anthracis str. A0442]
 gi|170127428|gb|EDS96303.1| conserved domain protein [Bacillus anthracis str. A0389]
 gi|170668019|gb|EDT18770.1| conserved domain protein [Bacillus anthracis str. A0465]
 gi|172080088|gb|EDT65184.1| conserved domain protein [Bacillus anthracis str. A0174]
 gi|190562226|gb|EDV16194.1| conserved domain protein [Bacillus anthracis Tsiankovskii-I]
 gi|195991216|gb|EDX55185.1| conserved domain protein [Bacillus cereus W]
 gi|227004702|gb|ACP14445.1| conserved domain protein [Bacillus anthracis str. CDC 684]
 gi|228833378|gb|EEM78941.1| hypothetical protein bthur0010_10010 [Bacillus thuringiensis
           serovar pondicheriensis BGSC 4BA1]
 gi|228845757|gb|EEM90783.1| hypothetical protein bthur0012_10560 [Bacillus thuringiensis
           serovar pulsiensis BGSC 4CC1]
 gi|229266526|gb|ACQ48163.1| conserved domain protein [Bacillus anthracis str. A0248]
          Length = 95

 Score = 41.1 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 42  LSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSFK 95


>gi|158293560|ref|XP_314897.4| AGAP008771-PA [Anopheles gambiae str. PEST]
 gi|157016767|gb|EAA10097.5| AGAP008771-PA [Anopheles gambiae str. PEST]
          Length = 261

 Score = 41.1 bits (95), Expect = 0.27,   Method: Composition-based stats.
 Identities = 38/263 (14%), Positives = 77/263 (29%), Gaps = 55/263 (20%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV---- 68
             ++ +V+ + +EN           G +  + N  RR+++S +   AI  V I       
Sbjct: 4   RKLQIVVV-RYDENELEFDM----IGVSCAIANVFRRLMLSEVPSMAIEKVHIYNNTSII 58

Query: 69  ----------------------LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI 106
                                      +      D  +  L +K    K    +      
Sbjct: 59  QDEVLAHRLGLIPLRADPRMFEYKANETDPPSALDTLEFELKVKCTR-KNKDSTEVTNNE 117

Query: 107 FKRGPGVVTAGDIQ-----------TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY 155
                  + +G I+           T   +  ++ D +I  +       ++L   KG G 
Sbjct: 118 NMYKNHSIYSGQIKWVPIGNQATIYTEAAVGPIDDDILISKMRPGHEFDIKLFAVKGVGK 177

Query: 156 VPAKHHRTENDPIGLITIDALYSP--IKKVSYTVESAREGQVLD----------YDKLSM 203
             AK          L+    L  P  +K   Y   S    +              +    
Sbjct: 178 DHAKFSPVATVSYRLLPDIKLNRPAYVKDARYDSCSRNVYRYPQLADAVTIARVRNHFIF 237

Query: 204 TIDTDGSITGEDSVALASRILQD 226
           T+++ G++  E     A+++L+ 
Sbjct: 238 TVESLGALKPEVIFVEAAKVLKK 260


>gi|324325259|gb|ADY20519.1| hypothetical protein YBT020_06365 [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 95

 Score = 41.1 bits (95), Expect = 0.28,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 26/54 (48%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  + N L    I  + +L + +E ++L++   G  S+ +++  L   GL   
Sbjct: 42  LSSPARNALEHHGIQTIEELSKYSEKEILKLHGMGPTSMPKLRKALEESGLSFK 95


>gi|315044489|ref|XP_003171620.1| DNA-directed RNA polymerase I and III subunit RPAC1 [Arthroderma
           gypseum CBS 118893]
 gi|311343963|gb|EFR03166.1| DNA-directed RNA polymerase I and III subunit RPAC1 [Arthroderma
           gypseum CBS 118893]
          Length = 380

 Score = 40.7 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 36/200 (18%), Positives = 57/200 (28%), Gaps = 52/200 (26%)

Query: 33  EPLPRGFAHT-----LGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIK-- 76
           +PL   F+       + NA RR+L++ +   AI  V I           + H +  I   
Sbjct: 60  DPLEASFSLIGVDAAIANAFRRILLAEIPALAIEYVYIQNNTSVIQDEVLAHRLGLIPLK 119

Query: 77  -----------------------GVHEDLTDIILNIKGINLKM----SGDSHKRVTIF-- 107
                                    HED   I+L +     K      G+    +     
Sbjct: 120 GSLEGLNWLRWFKAPKEGDPDSGSTHEDSNTIVLRLVKECTKNRSAPPGEEDPTILYNNA 179

Query: 108 -------KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
                     P             I+  NPD ++  L     + +E+   KG G   AK 
Sbjct: 180 HIYAKDLVFEPQGRQEKYFHGDGAIQSCNPDILLAKLRPGQKIDIEMHCIKGIGADHAKF 239

Query: 161 HRTENDPIGLITIDALYSPI 180
                    L+    +  PI
Sbjct: 240 SPVATASYRLLPDIKILRPI 259


>gi|319641231|ref|ZP_07995930.1| hypothetical protein HMPREF9011_01527 [Bacteroides sp. 3_1_40A]
 gi|317387104|gb|EFV67984.1| hypothetical protein HMPREF9011_01527 [Bacteroides sp. 3_1_40A]
          Length = 159

 Score = 40.7 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 26/53 (49%)

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           R  N     +I  + +L   +  D++   + G +S+  ++ +LG  GL LGM 
Sbjct: 22  RIRNVCNSHDIATIRELCLHSNWDLIHFRHLGERSIAHMEEMLGNFGLRLGMT 74


>gi|83646207|ref|YP_434642.1| serine/threonine protein kinase [Hahella chejuensis KCTC 2396]
 gi|83634250|gb|ABC30217.1| Serine/threonine protein kinase [Hahella chejuensis KCTC 2396]
          Length = 1385

 Score = 40.7 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 21/119 (17%), Positives = 49/119 (41%), Gaps = 8/119 (6%)

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK-VEELELSVRSTNCLRG 275
            A A+ +L+    +F+   +  +       V + P   A     +  LELS ++ + L  
Sbjct: 741 FATAADMLRAWRQVFLQASKESRHPTVHGEVPTCPVEEAQQDTQIGLLELSPQALDALSR 800

Query: 276 ENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
            N+  + DL+++  + +      G K+  E+  ++  +          WP E  + +++
Sbjct: 801 RNLNTVADLLKQNRSKVRAWPGVGIKTRNEVSELIRKLQ-------EKWPNEVAQPVSQ 852


>gi|269837799|ref|YP_003320027.1| hypothetical protein Sthe_1771 [Sphaerobacter thermophilus DSM
           20745]
 gi|269787062|gb|ACZ39205.1| hypothetical protein Sthe_1771 [Sphaerobacter thermophilus DSM
           20745]
          Length = 193

 Score = 40.7 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 13/58 (22%), Positives = 26/58 (44%)

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
              L   +EEL+LS R    L    +  +  + +  EA ++ + NF  ++  E+   +
Sbjct: 89  RCRLQPPIEELDLSPRVLRLLHRYGLHTIAAVERVDEATLMLLPNFDARARHEVLRAI 146


>gi|229195443|ref|ZP_04322211.1| hypothetical protein bcere0001_10120 [Bacillus cereus m1293]
 gi|228587983|gb|EEK46033.1| hypothetical protein bcere0001_10120 [Bacillus cereus m1293]
          Length = 95

 Score = 40.7 bits (94), Expect = 0.35,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 26/54 (48%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LSV +   L    I  + +L + +E ++L++   G  S+ +++  L   GL   
Sbjct: 42  LSVPARRALEHHGIHTVEELSKYSEKEVLKLHGMGPASMPKLRKALEEQGLSFK 95


>gi|224025020|ref|ZP_03643386.1| hypothetical protein BACCOPRO_01754 [Bacteroides coprophilus DSM
           18228]
 gi|224018256|gb|EEF76254.1| hypothetical protein BACCOPRO_01754 [Bacteroides coprophilus DSM
           18228]
          Length = 146

 Score = 40.7 bits (94), Expect = 0.35,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 25/54 (46%)

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           VR     +   I  + DL  +++ ++       +KS+  I+ +LG   L LGM 
Sbjct: 21  VRVQRIFQTNGIFTVRDLCSQSKQELRHTRYLSKKSISMIEKILGKYALRLGMT 74


>gi|218902339|ref|YP_002450173.1| hypothetical protein BCAH820_1221 [Bacillus cereus AH820]
 gi|228932518|ref|ZP_04095399.1| hypothetical protein bthur0009_9960 [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228944851|ref|ZP_04107214.1| hypothetical protein bthur0007_10180 [Bacillus thuringiensis
           serovar monterrey BGSC 4AJ1]
 gi|229120766|ref|ZP_04250009.1| hypothetical protein bcere0016_10750 [Bacillus cereus 95/8201]
 gi|218538056|gb|ACK90454.1| conserved domain protein [Bacillus cereus AH820]
 gi|228662771|gb|EEL18368.1| hypothetical protein bcere0016_10750 [Bacillus cereus 95/8201]
 gi|228814879|gb|EEM61137.1| hypothetical protein bthur0007_10180 [Bacillus thuringiensis
           serovar monterrey BGSC 4AJ1]
 gi|228827208|gb|EEM72961.1| hypothetical protein bthur0009_9960 [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
          Length = 95

 Score = 40.7 bits (94), Expect = 0.36,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 42  LSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSFK 95


>gi|85082680|ref|XP_956964.1| DNA-directed RNA polymerase II 33 kDa polypeptide [Neurospora
           crassa OR74A]
 gi|7801032|emb|CAB91428.1| probable DNA-directed RNA polymerase II chain RPB3 [Neurospora
           crassa]
 gi|28918046|gb|EAA27728.1| DNA-directed RNA polymerase II 33 kDa polypeptide [Neurospora
           crassa OR74A]
          Length = 337

 Score = 40.3 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 46/279 (16%), Positives = 91/279 (32%), Gaps = 51/279 (18%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG--------- 67
            + + Q +  R           F     N+LRRV+++ +   AI  V+I+          
Sbjct: 17  VVKISQADNTRVKFELSNTELSF----ANSLRRVMLAEIPTIAIDLVEIEANSSVLADEF 72

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG----VVTAGDIQTVN 123
           + H +  I    E +  ++ +      +        + +  +  G     V A D+  V 
Sbjct: 73  IAHRLGLIPLNAEGIEQLLYSRDCDCDEYCEHCSVTLNLHAKCTGDDIMQVCARDLVPVG 132

Query: 124 DIEVLNPDH-------------VICNLDVDAVVRMELTVSKGH-----GYVPAKHHRTEN 165
           D   +N                +I  L     ++++    KG       + P+     E 
Sbjct: 133 D--RVNQVLGSPIINDPEGQGPLILKLRHGQEIKLQCIAKKGIAKEHSKWAPSAAIGFEY 190

Query: 166 DPIGLIT---------IDALYSPIKKVSYTVESAREGQVLDYD----KLSMTIDTDGSIT 212
           DP   +              + P +   +  E  +EG+  DYD    +    ++T G I 
Sbjct: 191 DPHNKLHHLDLWYEQDPKKEWPPSEYADWE-EPPQEGEPFDYDAVPQRFYYNVETAGPIP 249

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            +  V    +++Q +L   I+        +   N    P
Sbjct: 250 PDAIVTEGIKVIQQKLAGLIHELTESDGGENGYNGPRSP 288


>gi|229114676|ref|ZP_04244090.1| hypothetical protein bcere0017_9730 [Bacillus cereus Rock1-3]
 gi|228668741|gb|EEL24169.1| hypothetical protein bcere0017_9730 [Bacillus cereus Rock1-3]
          Length = 95

 Score = 40.3 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 42  LSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSFK 95


>gi|229095726|ref|ZP_04226705.1| hypothetical protein bcere0020_9780 [Bacillus cereus Rock3-29]
 gi|228687559|gb|EEL41458.1| hypothetical protein bcere0020_9780 [Bacillus cereus Rock3-29]
          Length = 92

 Score = 40.3 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 39  LSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEEGGLSFK 92


>gi|217958720|ref|YP_002337268.1| hypothetical protein BCAH187_A1298 [Bacillus cereus AH187]
 gi|229137930|ref|ZP_04266529.1| hypothetical protein bcere0013_10550 [Bacillus cereus BDRD-ST26]
 gi|217066098|gb|ACJ80348.1| conserved domain protein [Bacillus cereus AH187]
 gi|228645587|gb|EEL01820.1| hypothetical protein bcere0013_10550 [Bacillus cereus BDRD-ST26]
          Length = 95

 Score = 40.3 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 42  LSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSFK 95


>gi|24638473|sp|P34778|RPOA_ASTLO RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
          Length = 220

 Score = 40.3 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 33/225 (14%), Positives = 89/225 (39%), Gaps = 47/225 (20%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGA-AITAVQ---------------ID 66
           + +N   +  +P      +  GN +RR L+ +++    IT ++               I 
Sbjct: 15  KNQNINFLKIKPFNCPNYNFFGNEIRRSLLLNIKKTMTITNIKFFISKSKSKHPKKLKIF 74

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR----VTIFKRGPGVVTAGDIQTV 122
             ++E   I+ + E+L++I +N+K +  K +  ++K     + +        +A DI   
Sbjct: 75  HPVNEFFDIEEIKENLSNICINLKKLRFKFNPKNNKEKKTFIILNSFNKKSFSAKDIIIP 134

Query: 123 --NDIEVLNPDHVICN-LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
             ++++++N    + N +     +++ + +     Y                     Y+P
Sbjct: 135 STSNLKIVNLKEHLFNKISQKINLKVLIKIENNENY--------------------FYNP 174

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           IK++++ +E            + + +++D +I    +   + + L
Sbjct: 175 IKRINFILE----KNNNIGKYIILDLNSDININPFKAFIESLKYL 215


>gi|262384570|ref|ZP_06077704.1| predicted protein [Bacteroides sp. 2_1_33B]
 gi|262293863|gb|EEY81797.1| predicted protein [Bacteroides sp. 2_1_33B]
          Length = 193

 Score = 40.3 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 4/72 (5%)

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD----MLRMANFGRKSLV 304
               N   L  V + +L  R+ N LR   I  + DL++ T+      +L+   FG  SL 
Sbjct: 109 DDIMNVLSLSLVSDFDLDTRTINMLRKMEIYTLEDLLRYTKDKGLQVLLKYRGFGAHSLA 168

Query: 305 EIKGVLGTMGLF 316
            +K  L   G+F
Sbjct: 169 LLKESLIKKGVF 180


>gi|50555259|ref|XP_505038.1| YALI0F05566p [Yarrowia lipolytica]
 gi|49650908|emb|CAG77845.1| YALI0F05566p [Yarrowia lipolytica]
          Length = 314

 Score = 40.3 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 38/242 (15%), Positives = 79/242 (32%), Gaps = 43/242 (17%)

Query: 35  LPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDI 85
           LP     TL N+LRRV+++ +   AI  V+I           + H +  I    +D+ D+
Sbjct: 14  LPVCLGITLANSLRRVMLAEIPTLAIDLVEISTNTSVLADEFISHRLGLIPLDSQDVNDL 73

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG----DI------QTVNDIEVLNPD---- 131
             +   +  +        + +     G  T      D+      +     + +  D    
Sbjct: 74  EYSRDCVCDEYCDKCSVVLMLDATCTGDDTMDIYSRDLMVHTTPERPELGKPIYTDPAKK 133

Query: 132 -HVICNLDVDAVVRMELTVSKGH---------------GYVPAKHHRTENDPIGLITIDA 175
             +IC L  +  +R++    KG                 Y P    +  +        + 
Sbjct: 134 GILICKLRKNQSLRIKCIAKKGIAKEHAKWSPCAAIGFEYDPWNKLKHTDYWYEENAEEE 193

Query: 176 LYSPIKKVSYTV---ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
                K   +     E+         +K  + ++  G++T  + V    ++LQ +L   +
Sbjct: 194 WPLS-KNADWEEPPKENEPFDYNAKPNKFYINVEATGALTQYEVVLRGMQVLQKKLAEVV 252

Query: 233 NF 234
             
Sbjct: 253 MI 254


>gi|85822798|gb|ABC84857.1| RNA polymerase gamma subunit [Peanut witches'-broom phytoplasma]
          Length = 1379

 Score = 40.3 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 13/59 (22%), Positives = 26/59 (44%), Gaps = 2/59 (3%)

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
             K+E+  L+ R+   L+   I  +GD+      ++  + +   +S  E   +L   GL
Sbjct: 3   NMKIEDFALTKRTLKNLKSIGINSLGDINNYHLNEL--ITSLNEESFEEFVIILKKYGL 59


>gi|163939036|ref|YP_001643920.1| hypothetical protein BcerKBAB4_1042 [Bacillus weihenstephanensis
           KBAB4]
 gi|163861233|gb|ABY42292.1| conserved hypothetical protein [Bacillus weihenstephanensis KBAB4]
          Length = 92

 Score = 40.3 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 39  LSAPARRALEHHGIHTLEELSKYSEKEILKLHGIGPASLPKLRAALEDKGLSFK 92


>gi|222480231|ref|YP_002566468.1| RNA polymerase insert [Halorubrum lacusprofundi ATCC 49239]
 gi|222453133|gb|ACM57398.1| RNA polymerase insert [Halorubrum lacusprofundi ATCC 49239]
          Length = 250

 Score = 40.3 bits (93), Expect = 0.47,   Method: Composition-based stats.
 Identities = 24/131 (18%), Positives = 47/131 (35%), Gaps = 18/131 (13%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           + ++    ++     RG      N +RR +++ +   +I  V+   V +       +   
Sbjct: 12  ERDDRSARVLI----RGLTPAFANGIRRAMIADVPTFSIDTVRF--VENSSVMFDEM--- 62

Query: 82  LTDIILNIKGINLKMSGD-----SHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDHVIC 135
              I L +  I LK   D         + +   GP    +GDI+     +EV + +  I 
Sbjct: 63  ---IGLRLGLIPLKTPLDDFEVGDEVTLALDVEGPATAYSGDIESADPLVEVADDNIPII 119

Query: 136 NLDVDAVVRME 146
            L     +  E
Sbjct: 120 ELKEGQRLEFE 130


>gi|226287322|gb|EEH42835.1| DNA-directed RNA polymerases I and III subunit RPAC1
           [Paracoccidioides brasiliensis Pb18]
          Length = 380

 Score = 39.9 bits (92), Expect = 0.48,   Method: Composition-based stats.
 Identities = 39/201 (19%), Positives = 60/201 (29%), Gaps = 53/201 (26%)

Query: 33  EPLPRGFAH-----TLGNALRRVLMSSLRGAAITAVQIDGVLHEISS-----------IK 76
           EP    F+      ++ NA RR+L+S +   AI  V I      I             + 
Sbjct: 60  EPYEASFSLIGVDASIANAFRRILISEIPSLAIETVYIHNNTSVIQDEVLAHRLGLVPLT 119

Query: 77  GVHE-----------------------DLTDIILNIK---GINLKMSGDSHKRVTIFKRG 110
           G  E                       D   I+L++      N K S D    + ++   
Sbjct: 120 GSPEGINWLRWFRQPNEGDPSSGSELADYNTIVLHLNVECKKNPKASPDEQDPLKLYSHA 179

Query: 111 P-----------GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
                       G   A   +    I   NPD ++  L     + +E+   KG G   AK
Sbjct: 180 HVYAKDITFQPVGRQEAYFPEPDGGIRPTNPDILLAKLRPGQKIDIEMHCVKGIGADHAK 239

Query: 160 HHRTENDPIGLITIDALYSPI 180
                     L+    +  PI
Sbjct: 240 FSPVATASYRLLPDIRILRPI 260


>gi|159897791|ref|YP_001544038.1| hypothetical protein Haur_1262 [Herpetosiphon aurantiacus ATCC
           23779]
 gi|159890830|gb|ABX03910.1| hypothetical protein Haur_1262 [Herpetosiphon aurantiacus ATCC
           23779]
          Length = 75

 Score = 39.9 bits (92), Expect = 0.48,   Method: Composition-based stats.
 Identities = 11/56 (19%), Positives = 22/56 (39%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           LS  +   L       +G L Q +  ++ ++   G K + +++  L   GL     
Sbjct: 15  LSQPALRALHNAGYHSLGQLTQVSARELGKLHGMGPKGIRQLREALAAKGLAFADE 70


>gi|49480015|ref|YP_035379.1| hypothetical protein BT9727_1042 [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|49331571|gb|AAT62217.1| conserved hypothetical protein [Bacillus thuringiensis serovar
           konkukian str. 97-27]
          Length = 95

 Score = 39.9 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 42  LSAPARRALEYHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSFK 95


>gi|304399092|ref|ZP_07380960.1| hypothetical protein PanABDRAFT_4221 [Pantoea sp. aB]
 gi|304353332|gb|EFM17711.1| hypothetical protein PanABDRAFT_4221 [Pantoea sp. aB]
          Length = 429

 Score = 39.9 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 10/54 (18%), Positives = 20/54 (37%)

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
            V EL +  R  N L       + D       ++ ++      S +EI+  + +
Sbjct: 353 PVSELAIPTRLLNVLTKAGYETVADAGGELPDELAKVRGLSEASAIEIRAAVNS 406


>gi|302655859|ref|XP_003019711.1| hypothetical protein TRV_06253 [Trichophyton verrucosum HKI 0517]
 gi|291183453|gb|EFE39066.1| hypothetical protein TRV_06253 [Trichophyton verrucosum HKI 0517]
          Length = 388

 Score = 39.9 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 36/200 (18%), Positives = 57/200 (28%), Gaps = 52/200 (26%)

Query: 33  EPLPRGFAHT-----LGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIK-- 76
           +PL   F+       + NA RR+L++ +   AI  V I           + H +  I   
Sbjct: 68  DPLEASFSLIGVDAAIANAFRRILLAEIPALAIEYVYIQNNTSVIQDEVLAHRLGLIPLK 127

Query: 77  -----------------------GVHEDLTDIILNIKGINLKMSG---DSHKRVTIF--- 107
                                    HED   I+L +     K      D      ++   
Sbjct: 128 GSLEGLNWLRWFKIPKEGDPDSGSTHEDSNTIVLRLVKECTKNRNAAPDEEDPTVLYNNA 187

Query: 108 -------KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
                     P             I+  NPD ++  L     + +E+   KG G   AK 
Sbjct: 188 HIYAKDLVFEPQGRQEKYFHGDGVIQPCNPDILLAKLRPGQKIDIEMHCIKGIGADHAKF 247

Query: 161 HRTENDPIGLITIDALYSPI 180
                    L+    +  PI
Sbjct: 248 SPVATASYRLLPDIKILRPI 267


>gi|289580107|ref|YP_003478573.1| RNA polymerase insert [Natrialba magadii ATCC 43099]
 gi|289529660|gb|ADD04011.1| RNA polymerase insert [Natrialba magadii ATCC 43099]
          Length = 249

 Score = 39.9 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 35/238 (14%), Positives = 78/238 (32%), Gaps = 47/238 (19%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           + EE     + +    G      N +RR +++ +   AI  V+       +         
Sbjct: 11  EREERDARFLVQ----GITPAFANGIRRAMLADVPTMAIDTVRFVENSSVMFD------- 59

Query: 82  LTDIILNIKGINLKMS------GDSHKRVTIFKRGPGVVTAGDIQTVND-IEVLNPDHVI 134
              + L +  + L          D    ++I   GP    +GD+ + +D ++  + +  I
Sbjct: 60  -EQLALRLGLVPLTTPPVGEFVEDDTVTLSIDVEGPATAYSGDLVSSDDLVQPADENVPI 118

Query: 135 CNLDVDAVVRMELTV--SKGHGY----------------------VPAKHHRTENDPIGL 170
            +L     +  E      +G  +                      +P           G+
Sbjct: 119 IDLKDGQRLEAEADAVLDRGKDHAKHQGGVAVGYRHLQRVAAVEDLPEFEDPDRRIVRGV 178

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKL----SMTIDTDGSITGEDSVALASRIL 224
           I  D    P  +  + + +   G+ +  + +       ++TDGS + E+ V  A+  +
Sbjct: 179 IEEDGELVPTSEFDHDLSNRYPGKEVTLEDVPNSFVFHVETDGSFSVEELVTRAADTI 236


>gi|195472723|ref|XP_002088649.1| GE18688 [Drosophila yakuba]
 gi|194174750|gb|EDW88361.1| GE18688 [Drosophila yakuba]
          Length = 275

 Score = 39.9 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 37/259 (14%), Positives = 91/259 (35%), Gaps = 52/259 (20%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS--- 74
           + + +  ++    + E        ++ N+LRRV ++     AI  VQ++     +S    
Sbjct: 9   VQITELTDDNVKFVLEDTE----LSVANSLRRVFIAETPTLAIDWVQLEANSTVLSDEFL 64

Query: 75  ------IKGVHEDLTDIILNIKG-INLKMSGDSHKRVTIFKRGPGV----VTAGDIQT-- 121
                 I  + +D+ + +   +  I L    +     T+  +        VT  D+++  
Sbjct: 65  AHRIGLIPLISDDVVERLQYTRDCICLDFCPECSVEFTLDVKCSEEQTRHVTTADLKSSN 124

Query: 122 --------------VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---- 163
                          N+    N + +I  L     +++     KG G   AK + T    
Sbjct: 125 AKVLPVTSRNQGEEDNEYGESNDEILIIKLRKGQELKLRAYAKKGFGKEHAKWNPTAGVC 184

Query: 164 -----ENDPIGLIT------IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
                +N     +         + ++ ++   Y      E +   +      +++ G++ 
Sbjct: 185 FEYDPDNSMRHTLYPKPDEWPKSEHTELEDDQYEAPYNWEAKPNKF---FFNVESSGALK 241

Query: 213 GEDSVALASRILQDQLGMF 231
            E+ V +  ++L+++L   
Sbjct: 242 PENIVVMGVQVLKNKLSNL 260


>gi|50307587|ref|XP_453773.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|49642907|emb|CAH00869.1| KLLA0D16170p [Kluyveromyces lactis]
          Length = 307

 Score = 39.9 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 49/265 (18%), Positives = 91/265 (34%), Gaps = 49/265 (18%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDII----LNI 89
           L N+LRRV++S +   AI +V+I+          + H +  I     D+  ++       
Sbjct: 29  LANSLRRVMISEIPTLAIDSVEIETNTTVLADEFIAHRLGLIPLQSADIDQVVYCRDCYC 88

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV-----------ICNLD 138
           +    + S +              V A D+Q  +D++  N  H            IC L 
Sbjct: 89  EDHCDRCSVELILHAIGESESTTNVYAKDLQITSDLKGRNIGHPIIQDREANGVLICKLR 148

Query: 139 VDAVVRMELTVSKGH-----GYVPAKHHRTENDP-------IGLITIDAL--YSPIKKVS 184
               +R++    KG       + P+     E DP             DA   +   K   
Sbjct: 149 KGQEIRVKCIAKKGISKEHAKWSPSAAIEFEYDPWNKLKHTDYWYEQDARDEWPQSKNCE 208

Query: 185 Y-------TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           +            R      Y    + +++ GSIT E  V    + LQD++   +   + 
Sbjct: 209 FEDPPNEDEDFDYRAKPNTFY----INVESVGSITSEQVVVRGIKTLQDKVADILFSLKK 264

Query: 238 KKEVKEDINVKSLPFNPALLKKVEE 262
             + K +    ++  + +    +EE
Sbjct: 265 MDQEKVNFAAGAVSTHVSQQVPMEE 289


>gi|302511159|ref|XP_003017531.1| hypothetical protein ARB_04413 [Arthroderma benhamiae CBS 112371]
 gi|291181102|gb|EFE36886.1| hypothetical protein ARB_04413 [Arthroderma benhamiae CBS 112371]
          Length = 362

 Score = 39.9 bits (92), Expect = 0.58,   Method: Composition-based stats.
 Identities = 36/200 (18%), Positives = 58/200 (29%), Gaps = 52/200 (26%)

Query: 33  EPLPRGFAHT-----LGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIK-- 76
           +PL   F+       + NA RR+L++ +   AI  V I           + H +  I   
Sbjct: 42  DPLEASFSLIGVDAAIANAFRRILLAEIPALAIEYVYIQNNTSVIQDEVLAHRLGLIPLK 101

Query: 77  -----------------------GVHEDLTDIILNIKGINLK---MSGDSHKRVTIF--- 107
                                    HED   I+L +     K    + D      ++   
Sbjct: 102 GSLEGLNWLRWFKIPKEGDPDSGSTHEDSNTIVLRLVKECTKNRNSAPDEEDPTVLYNNA 161

Query: 108 -------KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
                     P             I+  NPD ++  L     + +E+   KG G   AK 
Sbjct: 162 HIYAKDLVFEPQGRQEKYFHGDGVIQPCNPDTLLAKLRPGQKIDIEMHCIKGIGADHAKF 221

Query: 161 HRTENDPIGLITIDALYSPI 180
                    L+    +  PI
Sbjct: 222 SPVATASYRLLPDIKILRPI 241


>gi|167044977|gb|ABZ09642.1| putative RNA polymerase Rpb3/RpoA insert domain protein [uncultured
           marine crenarchaeote HF4000_APKG8G2]
          Length = 214

 Score = 39.9 bits (92), Expect = 0.58,   Method: Composition-based stats.
 Identities = 35/209 (16%), Positives = 69/209 (33%), Gaps = 44/209 (21%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           +G +    NALRR+ ++ +   AI  V    V+   S I         I   +  I LK 
Sbjct: 34  KGISLHYANALRRICLNGVPIFAIDTV---DVIENSSVIPDE-----GIAHTLGMIPLKT 85

Query: 97  S----GDSHKRVTIF-----KRGPGVVTAGDIQ-TVNDIEVLNPDHVICNLDVDAVVRME 146
                 +S+ RV +           +VT+ +++     ++ ++    I +L     +++E
Sbjct: 86  ELNGFDESNSRVILVLDSEAAENTKIVTSAELESKDQVVKPISKQIPIVHLAPGQRIKLE 145

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY-DKLSMTI 205
                G G                          +   +   +       D  D+  +T+
Sbjct: 146 AYARLGRG-------------------------TEHAKWNSANISVLTNTDKEDERILTV 180

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINF 234
           +T GS+     +      L  +L  F   
Sbjct: 181 ETTGSLEPRQIILAGIEELSKRLEEFKEI 209


>gi|229056868|ref|ZP_04196264.1| hypothetical protein bcere0026_9850 [Bacillus cereus AH603]
 gi|228720396|gb|EEL71969.1| hypothetical protein bcere0026_9850 [Bacillus cereus AH603]
          Length = 92

 Score = 39.9 bits (92), Expect = 0.60,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 39  LSAPARRALEHHGIHTLEELSKYSEKEILKLHGIGPASLPKLRTALEDKGLSFK 92


>gi|229160195|ref|ZP_04288194.1| hypothetical protein bcere0009_9900 [Bacillus cereus R309803]
 gi|228623156|gb|EEK79983.1| hypothetical protein bcere0009_9900 [Bacillus cereus R309803]
          Length = 92

 Score = 39.9 bits (92), Expect = 0.61,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 24/54 (44%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L +   G  SL +++  L   GL   
Sbjct: 39  LSAPARRALEHHGIHTVEELSKYSEKEILNLHGMGPASLPKLRKALEENGLSFK 92


>gi|167044506|gb|ABZ09181.1| putative RNA polymerase Rpb3/RpoA insert domain protein [uncultured
           marine crenarchaeote HF4000_APKG6J21]
          Length = 200

 Score = 39.6 bits (91), Expect = 0.62,   Method: Composition-based stats.
 Identities = 42/213 (19%), Positives = 67/213 (31%), Gaps = 46/213 (21%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           G +    NALRR+ ++ +   AI  V I     E SS+         + L +  I LK  
Sbjct: 20  GISLHYANALRRICLNGVPIFAIDTVDII----ENSSVIPDE----GLALTLGMIPLKTE 71

Query: 98  G---DSHKRVTIFKRGPGVVTAGDIQTVNDIEV-------LNPDHVICNLDVDAVVRMEL 147
               D      I            I T  ++E        ++    I +L     +++E 
Sbjct: 72  LNGFDESNSRVILVLDSEAAETTKIVTSAELESKDQVVKPISKQIPIVHLAPGQRIKLEA 131

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
               G G   AK +             A  S +       E              +T++T
Sbjct: 132 YARLGRGTEHAKWN------------SANISVLTNADKEGEH------------ILTVET 167

Query: 208 DGSITGEDSVALASRILQDQLGMF----INFEE 236
            GS+     +      L  +L  F    +N EE
Sbjct: 168 TGSLEPRQIILAGIEELSKRLEEFKEILVNLEE 200


>gi|326475646|gb|EGD99655.1| DNA-directed RNA polymerase I and III [Trichophyton tonsurans CBS
           112818]
 gi|326485520|gb|EGE09530.1| DNA-directed RNA polymerase I and III subunit RPAC1 [Trichophyton
           equinum CBS 127.97]
          Length = 380

 Score = 39.6 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 36/200 (18%), Positives = 57/200 (28%), Gaps = 52/200 (26%)

Query: 33  EPLPRGFAHT-----LGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIK-- 76
           +PL   F+       + NA RR+L++ +   AI  V I           + H +  I   
Sbjct: 60  DPLEASFSLIGVDAAIANAFRRILLAEIPALAIEYVYIQNNTSVIQDEVLAHRLGLIPLK 119

Query: 77  -----------------------GVHEDLTDIILNIKGINLKMSG---DSHKRVTIF--- 107
                                    HED   I+L +     K      D      ++   
Sbjct: 120 GSLEGLNWLRWFKIPKEGDPDSGSTHEDSNTIVLRLVKECTKNRNAAPDEEDPTVLYNNA 179

Query: 108 -------KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
                     P             I+  NPD ++  L     + +E+   KG G   AK 
Sbjct: 180 HIYAKDLVFEPQGRQEKYFHGDGVIQPCNPDILLAKLRPGQKIDIEMHCIKGIGADHAKF 239

Query: 161 HRTENDPIGLITIDALYSPI 180
                    L+    +  PI
Sbjct: 240 SPVATASYRLLPDIKILRPI 259


>gi|150401521|ref|YP_001325287.1| RNA polymerase insert [Methanococcus aeolicus Nankai-3]
 gi|150014224|gb|ABR56675.1| RNA polymerase insert [Methanococcus aeolicus Nankai-3]
          Length = 197

 Score = 39.6 bits (91), Expect = 0.71,   Method: Composition-based stats.
 Identities = 44/174 (25%), Positives = 67/174 (38%), Gaps = 23/174 (13%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQID-GVLHEISSIKGVHEDLTDIILNIKGINLK- 95
           G   +  +ALRR+++SS+   AI  V            I           L +  I  K 
Sbjct: 22  GAPISFSSALRRIMVSSVPTYAIENVYFYENSSSMYDEILAHR-------LALIPITGKP 74

Query: 96  MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY 155
           +  D   R +I K GP  V + D+++ +D  V   +  I  L     + +E     G G 
Sbjct: 75  VISDEVVRFSIMKEGPCTVYSADLESESDSMVAFDNIPIVKLKEGQKLELECEALVGVGK 134

Query: 156 VPAKHHRTENDPIGLITIDALYSPIK--KVSYTVESAREGQVLDYDKLSMTIDT 207
             AK              +A Y  IK  +V ++VES   GQ+   D L   I+ 
Sbjct: 135 NHAK----------WQPCNASYKLIKDNEVEFSVES--HGQMDSEDILISAIEV 176


>gi|228906867|ref|ZP_04070736.1| hypothetical protein bthur0013_10430 [Bacillus thuringiensis IBL
           200]
 gi|228852871|gb|EEM97656.1| hypothetical protein bthur0013_10430 [Bacillus thuringiensis IBL
           200]
          Length = 95

 Score = 39.6 bits (91), Expect = 0.74,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 42  LSAPARRALEHHGIQTVEELSKYSEKEILKLHGMGPASLPKLRKALEERGLSFK 95


>gi|327297236|ref|XP_003233312.1| DNA-directed RNA polymerase I and III [Trichophyton rubrum CBS
           118892]
 gi|326464618|gb|EGD90071.1| DNA-directed RNA polymerase I and III [Trichophyton rubrum CBS
           118892]
          Length = 380

 Score = 39.6 bits (91), Expect = 0.75,   Method: Composition-based stats.
 Identities = 36/200 (18%), Positives = 57/200 (28%), Gaps = 52/200 (26%)

Query: 33  EPLPRGFAHT-----LGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIK-- 76
           +PL   F+       + NA RR+L++ +   AI  V I           + H +  I   
Sbjct: 60  DPLEASFSLIGVDAAIANAFRRILLAEIPALAIEYVYIQNNTSVIQDEVLAHRLGLIPLK 119

Query: 77  -----------------------GVHEDLTDIILNIKGINLKMSG---DSHKRVTIF--- 107
                                    HED   I+L +     K      D      ++   
Sbjct: 120 GSLEGLNWLRWFKIPKEGDPDSGSTHEDSNTIVLRLVKECTKNRNAAPDEEDPTVLYNNA 179

Query: 108 -------KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
                     P             I+  NPD ++  L     + +E+   KG G   AK 
Sbjct: 180 HIYAKDLVFEPQGRQEKYFHGDGVIQPCNPDILLAKLRPGQKIDIEMHCIKGIGADHAKF 239

Query: 161 HRTENDPIGLITIDALYSPI 180
                    L+    +  PI
Sbjct: 240 SPVATASYRLLPDIKILRPI 259


>gi|298674771|ref|YP_003726521.1| DNA-directed RNA polymerase [Methanohalobium evestigatum Z-7303]
 gi|298287759|gb|ADI73725.1| DNA-directed RNA polymerase [Methanohalobium evestigatum Z-7303]
          Length = 265

 Score = 39.6 bits (91), Expect = 0.75,   Method: Composition-based stats.
 Identities = 26/139 (18%), Positives = 48/139 (34%), Gaps = 14/139 (10%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS--------- 74
            E     +       F     N++RR +++ +   AI  + I      +           
Sbjct: 11  SERSARFVLSNTTPAF----ANSIRRAMLADVPTFAIDDLNIYNNTSVLYDEQLGLRLAL 66

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGD-IQTVNDIEVLNPDHV 133
           I    E++ D     +    +        +T+   GP +V +GD I +   I+  + +  
Sbjct: 67  IPLATENIDDYTTQDECTCEEGCPSCEVSITLSAEGPKMVYSGDLISSDPGIQPADTNIP 126

Query: 134 ICNLDVDAVVRMELTVSKG 152
           I  L  D  V +E    KG
Sbjct: 127 IIELKEDQRVVLEALAHKG 145


>gi|300711111|ref|YP_003736925.1| DNA-directed RNA polymerase subunit D [Halalkalicoccus jeotgali B3]
 gi|299124794|gb|ADJ15133.1| DNA-directed RNA polymerase subunit D [Halalkalicoccus jeotgali B3]
          Length = 248

 Score = 39.6 bits (91), Expect = 0.77,   Method: Composition-based stats.
 Identities = 38/245 (15%), Positives = 75/245 (30%), Gaps = 50/245 (20%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + + ++         L RG      N +RR +++ +   +I +V+       +     
Sbjct: 7   VEIIERDDRSARF----LVRGATPAFANGIRRAMLADVPTLSIDSVRFIENSSVM----- 57

Query: 78  VHEDLTDIILNIKGINLKMSGD----SHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDH 132
            +E    + L +  + L    D        + +   GP    +GD+  +   +E  + + 
Sbjct: 58  FNE---QLALRLGLVPLSTPEDYELGEDVTLALDVEGPATAYSGDLVSSDEQVEPADRNV 114

Query: 133 VICNLDVDAVVRMELTV--SKGHG-----------YVPAKHHRTEND------------- 166
            I  L     + +E       G             Y        E D             
Sbjct: 115 PIIELKEGQRLELEADAVLDVGREHAKHQGGVAVGYRHLVRVNIEGDREEFADEEANIVR 174

Query: 167 -----PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
                  G + +   +       Y  +  R   V   D     ++TDGS+T  + V  A+
Sbjct: 175 GVVETDEGELVLTDEFDHDLTNRYPGKELRLEDVP--DAFVFHVETDGSMTASELVDRAA 232

Query: 222 RILQD 226
             L D
Sbjct: 233 ASLGD 237


>gi|167044152|gb|ABZ08834.1| putative RNA polymerase Rpb3/RpoA insert domain protein [uncultured
           marine crenarchaeote HF4000_APKG5E24]
          Length = 200

 Score = 39.6 bits (91), Expect = 0.80,   Method: Composition-based stats.
 Identities = 42/213 (19%), Positives = 68/213 (31%), Gaps = 46/213 (21%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           G +    NALRR+ ++ +   AI  V I     E SS+         + L +  I LK  
Sbjct: 20  GISLHYANALRRICLNGVPIFAIDTVDII----ENSSVIPDE----GLALTLGMIPLKTE 71

Query: 98  G---DSHKRVTIFKRGPGVVTAGDIQTVNDIEV-------LNPDHVICNLDVDAVVRMEL 147
               D      I            I T  ++E        ++    I +L     +++E 
Sbjct: 72  LNGFDESNSRVILVLDSEAAETTKIVTSAELESKDQVVKPISKQIPIVHLAPGQRIKLEA 131

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
               G G   AK +             A  S +       E              +T++T
Sbjct: 132 YARLGRGTEHAKWN------------SANISVLTNADKEGEH------------ILTVET 167

Query: 208 DGSITGEDSVALASRILQDQLGMF----INFEE 236
            GS+  +  +      L  +L  F    +N EE
Sbjct: 168 TGSLEPKQIILAGIEELSKRLEEFKEILVNLEE 200


>gi|24638474|sp|P48337|RPOA_EUGGR RecName: Full=DNA-directed RNA polymerase subunit alpha; Short=PEP;
           AltName: Full=Plastid-encoded RNA polymerase subunit
           alpha; Short=RNA polymerase subunit alpha
 gi|15526343|emb|CAC69148.1| RNA polymerase subunit [Euglena gracilis]
          Length = 216

 Score = 39.2 bits (90), Expect = 0.85,   Method: Composition-based stats.
 Identities = 32/211 (15%), Positives = 74/211 (35%), Gaps = 40/211 (18%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID-----------GVLHE 71
           ++ N      + L     +     +RR L+  L    IT V               V+H 
Sbjct: 15  KDGNLAFFKVKNLQFFDKNFFVTEIRRYLLLDLESWNITNVMFFVTNNLKNTSTFHVVHN 74

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKR----VTIFKRGPGVVTAGDIQTVNDIEV 127
              ++ + + L +I    K +  K+   S++       +         +GDI     +++
Sbjct: 75  FLGLEELKQSLLEITKKFKLLRFKLCSKSYQGNKFFAVLNAFEVKDFLSGDIIFPPHLKL 134

Query: 128 LNPDHVICN-LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           LN   ++   +  +  +++ L +                         +   PIK+++  
Sbjct: 135 LNSRELLFTKISFNITLKILLKIEAKKA--------------------SFQKPIKRLNLI 174

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
           +E  ++    +Y  +   + TDGS+T  ++ 
Sbjct: 175 IE--KDEFFDNY--MIFDLTTDGSVTPFNAF 201


>gi|15668364|ref|NP_247160.1| DNA-directed RNA polymerase subunit D [Methanocaldococcus
           jannaschii DSM 2661]
 gi|2500626|sp|Q57648|RPOD_METJA RecName: Full=DNA-directed RNA polymerase subunit D
 gi|1590937|gb|AAB98172.1| DNA-directed RNA polymerase, subunit D (rpoD) [Methanocaldococcus
           jannaschii DSM 2661]
          Length = 191

 Score = 39.2 bits (90), Expect = 0.89,   Method: Composition-based stats.
 Identities = 40/196 (20%), Positives = 77/196 (39%), Gaps = 40/196 (20%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN-IKGINLK---M 96
            +  NA+RR+++S +   AI  V I      +           +I+ + +  I +K   +
Sbjct: 24  ISFSNAIRRIMISEVPTFAIEDVYIYENSSSMDD---------EILAHRLGLIPIKGKPL 74

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             +     T+ K GP  V + D+++ N  EV   +  I  L     +++E     G G V
Sbjct: 75  LENEVITFTLEKEGPCTVYSSDLKSENG-EVAFKNIPIVKLGKGQRIQIECEAIPGIGKV 133

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
            AK              +A+Y  I                  D++   ++T G +  E+ 
Sbjct: 134 HAK----------WQPCNAVYKQIAD----------------DEVEFFVETFGQMEAEEI 167

Query: 217 VALASRILQDQLGMFI 232
           +  A +IL+++   F+
Sbjct: 168 LEEAVKILKNKAESFL 183


>gi|126650396|ref|ZP_01722624.1| hypothetical protein BB14905_18620 [Bacillus sp. B14905]
 gi|126593046|gb|EAZ87028.1| hypothetical protein BB14905_18620 [Bacillus sp. B14905]
          Length = 107

 Score = 39.2 bits (90), Expect = 0.92,   Method: Composition-based stats.
 Identities = 16/54 (29%), Positives = 27/54 (50%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  + N L  E I  + +L + TE D+L++   G  S+  ++ +L   GL   
Sbjct: 49  LSSPARNALIHEGIDTLHELSKYTEKDVLKIHGIGPASIPMMRALLEEEGLSFK 102


>gi|126666550|ref|ZP_01737528.1| Serine/threonine protein kinase [Marinobacter sp. ELB17]
 gi|126628938|gb|EAZ99557.1| Serine/threonine protein kinase [Marinobacter sp. ELB17]
          Length = 1393

 Score = 39.2 bits (90), Expect = 0.94,   Method: Composition-based stats.
 Identities = 24/107 (22%), Positives = 45/107 (42%), Gaps = 1/107 (0%)

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK-VEELELSVRST 270
              +  A A  +L++   +F       +        +S P N A L   +  LELS ++ 
Sbjct: 736 DARERFASAGDMLREWRKIFHQARTDTQHSTVHPGQRSCPINEARLDTQIGLLELSPQAL 795

Query: 271 NCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + L   NI  + +LI+   + +  +   G K+  E+  V+G +   L
Sbjct: 796 DTLSRRNINTVAELIKLNRSRVRVLTGVGVKTRNELSEVIGQLQERL 842


>gi|270010836|gb|EFA07284.1| hypothetical protein TcasGA2_TC014519 [Tribolium castaneum]
          Length = 335

 Score = 39.2 bits (90), Expect = 0.95,   Method: Composition-based stats.
 Identities = 44/259 (16%), Positives = 78/259 (30%), Gaps = 76/259 (29%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEIS--------------------------SIK 76
           L N  RR+++S +   AI  V I      I                           + +
Sbjct: 66  LANTFRRLMLSDVPTMAIEKVHILNNTSIIQDEVLAHRLGLIPLKADPRLFEMKTDPTAE 125

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV---------NDIEV 127
           G  +D  +  L IK  N K S     R          V +  I+ V         +D+  
Sbjct: 126 GTEQDTLEFALKIKCTNNKDSSKDSLRAE-DMYKNNNVYSKHIKWVPIGKQKERFSDVGP 184

Query: 128 LNPDHVICNLDVDAVVRMELTVSK--GHGYVP------------------------AKHH 161
           ++PD +I  +     + ++L   K  G  +                          A   
Sbjct: 185 IHPDILIAKMRPGHELDLKLLAVKSNGRDHAKFSPVATAFYRLLPDIKLLREVEGEAAER 244

Query: 162 RTENDPIGLITI----DALYSPIKKVSYTVESAREGQVLD----------YDKLSMTIDT 207
             +    G+I+I       Y+ +    Y   S    +  D           D    T+++
Sbjct: 245 LQKCFSPGVISIRHEKGRKYAVVANARYDTGSRNVFRYEDLKDAVAMTKIQDHFIFTVES 304

Query: 208 DGSITGEDSVALASRILQD 226
            G++  +     A +IL+D
Sbjct: 305 VGALPPDVIFMEAVKILKD 323


>gi|17137650|ref|NP_477419.1| RNA polymerase II 33kD subunit [Drosophila melanogaster]
 gi|4490379|emb|CAB38635.1| RNA polymerase II p33 subunit [Drosophila melanogaster]
 gi|7298103|gb|AAF53342.1| RNA polymerase II 33kD subunit [Drosophila melanogaster]
 gi|16767948|gb|AAL28192.1| GH07456p [Drosophila melanogaster]
 gi|220944002|gb|ACL84544.1| RpII33-PA [synthetic construct]
 gi|220953902|gb|ACL89494.1| RpII33-PA [synthetic construct]
          Length = 275

 Score = 39.2 bits (90), Expect = 0.95,   Method: Composition-based stats.
 Identities = 37/259 (14%), Positives = 91/259 (35%), Gaps = 52/259 (20%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS--- 74
           + + +  ++    + E        ++ N+LRRV ++     AI  VQ++     +S    
Sbjct: 9   VQITELTDDNVKFVLEDTE----LSVANSLRRVFIAETPTLAIDWVQLEANSTVLSDEFL 64

Query: 75  ------IKGVHEDLTDIILNIKG-INLKMSGDSHKRVTIFKRGPGV----VTAGDIQT-- 121
                 I  + +D+ + +   +  I L    +     T+  +        VT  D+++  
Sbjct: 65  AHRIGLIPLISDDVVERLQYTRDCICLDFCPECSVEFTLDVKCSEEQTRHVTTADLKSSN 124

Query: 122 --------------VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---- 163
                          N+    N + +I  L     +++     KG G   AK + T    
Sbjct: 125 AKVLPVTSRNQGEEDNEYGESNDEILIIKLRKGQELKLRAYAKKGFGKEHAKWNPTAGVC 184

Query: 164 -----ENDPIGLIT------IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
                +N     +         + ++ ++   Y      E +   +      +++ G++ 
Sbjct: 185 FEYDPDNSMRHTLYPKPDEWPKSEHTELEDDQYEAPYNWEAKPNKF---FFNVESAGALK 241

Query: 213 GEDSVALASRILQDQLGMF 231
            E+ V +  ++L+++L   
Sbjct: 242 PENIVVMGVQVLKNKLSNL 260


>gi|78777616|ref|YP_393931.1| glycosyl transferase, group 1 [Sulfurimonas denitrificans DSM 1251]
 gi|78498156|gb|ABB44696.1| Glycosyl transferase, group 1 [Sulfurimonas denitrificans DSM 1251]
          Length = 365

 Score = 39.2 bits (90), Expect = 0.99,   Method: Composition-based stats.
 Identities = 13/51 (25%), Positives = 28/51 (54%), Gaps = 2/51 (3%)

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           ELSV+  + ++  NI  +G+++ R E+ + ++     K+L  IK ++    
Sbjct: 35  ELSVKDYDNIKNINIKTLGEILSRDESTLSKLKYL--KALSAIKEIIKEFQ 83


>gi|118088012|ref|XP_001234462.1| PREDICTED: similar to RNA polymerase I subunit hRPA39 isoform 1
           [Gallus gallus]
          Length = 300

 Score = 38.8 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 22/144 (15%), Positives = 50/144 (34%), Gaps = 14/144 (9%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGIN-----LKMS 97
           + NA RR+L++ +   A+  V +      +           +I+ +  G+       ++ 
Sbjct: 66  IANAFRRILLAEVPTMAVEKVFVYNNTSIVQD---------EILAHRLGLIPIRADPRLF 116

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
              ++  +       +    D+    D   ++ D +I  L     + + +   KG G   
Sbjct: 117 EYRNQVYSKHMTWVPLGNQTDLFPDADFRPVHDDILIALLRPGQEIDVLMHCVKGIGKDH 176

Query: 158 AKHHRTENDPIGLITIDALYSPIK 181
           AK          L+    L  P++
Sbjct: 177 AKFSPVATASYRLLPDITLLQPVE 200


>gi|187921976|ref|YP_001893565.1| Conjugal transfer protein TrbG/VirB9/CagX [Burkholderia
           phytofirmans PsJN]
 gi|187720414|gb|ACD21636.1| Conjugal transfer protein TrbG/VirB9/CagX [Burkholderia
           phytofirmans PsJN]
          Length = 302

 Score = 38.8 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 17/141 (12%), Positives = 37/141 (26%), Gaps = 4/141 (2%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
            L   S +    +D        K    +          +    P    A        ++ 
Sbjct: 112 ALKTNSFVTPSRDDDAQPTSRYKKTAGRPKTYLPTTWQLNIDYPPAEVAKIAAEDPAVKA 171

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGH----GYVPAKHHRTENDPIGLITIDALYSPIKKV 183
               H I +    A +   L    G+      +P   +        ++ I      + + 
Sbjct: 172 AKTKHEIVSAFDQAKMEGRLDADYGYIGDDELLPTAAYNNGKQTFIVLPIGTALPTVYEK 231

Query: 184 SYTVESAREGQVLDYDKLSMT 204
           +      R G  +D+D + + 
Sbjct: 232 TPDGTEVRVGAHMDHDMMVIH 252


>gi|126179746|ref|YP_001047711.1| DNA-directed RNA polymerase subunit D [Methanoculleus marisnigri
           JR1]
 gi|125862540|gb|ABN57729.1| DNA-directed RNA polymerase, subunit D [Methanoculleus marisnigri
           JR1]
          Length = 276

 Score = 38.8 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 40/271 (14%), Positives = 75/271 (27%), Gaps = 55/271 (20%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID-GVLHEISSIK 76
           I   + +E            G + +  N LRR ++S +   AI  V+I          + 
Sbjct: 3   IAFSRLDERVAKFTLS----GVSMSFANMLRRAMISEVPTLAIEDVRIYDNTSVLFDEML 58

Query: 77  GVHEDLTDIILNIKGINLKMSGDSH--------KRVTIFKRGPGVVTAGDIQT-VNDIEV 127
                L  +  ++K    +                 T+   GP  V + D+     D   
Sbjct: 59  AHRLGLIPLRTDLKRYKPRSECTCEDAGCPVCTATYTLSVEGPKTVYSSDLIPQDPDAAP 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY-------SPI 180
            +    I  L  D  + +E     G G   AK   T         + A+          I
Sbjct: 119 ADEKIPIIELARDQKLVLEAQAIVGTGKEHAKWQATTACGYKNYPVIAIDERCDGCGMCI 178

Query: 181 KKVSYTVESAREGQ----------------------------------VLDYDKLSMTID 206
            +   +V    +G+                                    D ++    ++
Sbjct: 179 DECPRSVLETAQGKIRVVEERQELCSLCRLCERACLAGGIGTEPAIHIGTDAERFIFVVE 238

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEP 237
            DGSI   + +  A + +Q      ++    
Sbjct: 239 GDGSIPVREIIERALQYIQKSSDDLVDVMNE 269


>gi|90417484|ref|ZP_01225407.1| chaperone protein HscA [marine gamma proteobacterium HTCC2207]
 gi|90330725|gb|EAS46004.1| chaperone protein HscA [marine gamma proteobacterium HTCC2207]
          Length = 623

 Score = 38.8 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 27/180 (15%), Positives = 54/180 (30%), Gaps = 16/180 (8%)

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
                D    M + V +G   + +         +  I        I +VSY V++     
Sbjct: 424 FTTFKDGQTAMAIHVLQGERELASDSRSLARFELRDIPPMVAGGAIIRVSYQVDADGLLS 483

Query: 195 VLDYDKLSMTIDTDGSITGEDSVAL--ASRILQDQLGMFIN------FEEPKKEVKEDIN 246
           V   +     +++   +     ++    + +LQD      +        E + E    I 
Sbjct: 484 VNAREM-ISGVESHIEVKPSYGLSENDITSMLQDSFSYAKDDMKARALREQQVEADRMIE 542

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGE--NIVYMGDLIQRTEADMLRMANFGRKSLV 304
                     L  ++E E      NCL      +  + D        M ++ + G+ S  
Sbjct: 543 DLGAALAKDGLALLDEAE-----YNCLEVAVKELQIVRDSSTEHRVLMRQIESVGKVSEE 597


>gi|210610456|ref|ZP_03288413.1| hypothetical protein CLONEX_00603 [Clostridium nexile DSM 1787]
 gi|210152449|gb|EEA83455.1| hypothetical protein CLONEX_00603 [Clostridium nexile DSM 1787]
          Length = 60

 Score = 38.8 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 10/52 (19%), Positives = 24/52 (46%)

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +++E+S R  N LR      +  + +  +   ++  N G+ +L E+  +   
Sbjct: 9   DDIEMSSRLRNVLRRNGFESLEGVREYPKEYFIKFRNMGQATLQELYQICEE 60


>gi|269928870|ref|YP_003321191.1| helix-hairpin-helix motif protein [Sphaerobacter thermophilus DSM
           20745]
 gi|269788227|gb|ACZ40369.1| helix-hairpin-helix motif protein [Sphaerobacter thermophilus DSM
           20745]
          Length = 72

 Score = 38.8 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 24/51 (47%)

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           L G     + DL + TE  +L++   G K+L +++  L   GL    +  D
Sbjct: 22  LLGAGYTRLEDLTRVTEDQLLQLHGIGPKALAQLREALAARGLAFAADTDD 72


>gi|162455957|ref|YP_001618324.1| protein kinase [Sorangium cellulosum 'So ce 56']
 gi|161166539|emb|CAN97844.1| Protein kinase [Sorangium cellulosum 'So ce 56']
          Length = 1477

 Score = 38.8 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 13/56 (23%), Positives = 23/56 (41%)

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               VE L L  R  N L    IV + +L+   +  +  +   GR++   I+  + 
Sbjct: 794 EATPVEALPLGAREKNALDRSGIVTVRELLALPQNQLSAIRGVGRETARAIQDFVE 849


>gi|228957512|ref|ZP_04119264.1| hypothetical protein bthur0005_10310 [Bacillus thuringiensis
           serovar pakistani str. T13001]
 gi|228802104|gb|EEM48969.1| hypothetical protein bthur0005_10310 [Bacillus thuringiensis
           serovar pakistani str. T13001]
          Length = 95

 Score = 38.8 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 42  LSAPARRALEQRGIQTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSFK 95


>gi|229143848|ref|ZP_04272267.1| hypothetical protein bcere0012_10130 [Bacillus cereus BDRD-ST24]
 gi|296501841|ref|YP_003663541.1| hypothetical protein BMB171_C1005 [Bacillus thuringiensis BMB171]
 gi|228639609|gb|EEK96020.1| hypothetical protein bcere0012_10130 [Bacillus cereus BDRD-ST24]
 gi|296322893|gb|ADH05821.1| hypothetical protein BMB171_C1005 [Bacillus thuringiensis BMB171]
          Length = 95

 Score = 38.8 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 26/54 (48%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL +++ VL   GL   
Sbjct: 42  LSAPARRALEHRGIQTVEELSKYSEKEILKLHGMGPASLPKLRKVLEESGLSFK 95


>gi|170291194|ref|YP_001738010.1| DNA-directed RNA polymerase subunit D [Candidatus Korarchaeum
           cryptofilum OPF8]
 gi|170175274|gb|ACB08327.1| DNA-directed RNA polymerase subunit D [Candidatus Korarchaeum
           cryptofilum OPF8]
          Length = 251

 Score = 38.8 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 40/253 (15%), Positives = 89/253 (35%), Gaps = 43/253 (16%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIK 76
           + + +  + RTL++ E    G + +  N++RR +++ +   AI  V   +          
Sbjct: 3   VRVIELSDQRTLLVLE----GVSPSFANSIRRAIIAEVPTFAIDEVIFFENTTPFFDEYI 58

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT---AGDIQT-VNDIEVLNPDH 132
                L  I L      L++  +    + + K+    +    +G++++    I   N   
Sbjct: 59  AHR--LAMIPLRTSLDVLRVDPNRTVVLELSKKAKDPIEVVYSGELKSSDPLIYPANDKI 116

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK----------- 181
            I  +     +R +     G G   +K           + I  L  P++           
Sbjct: 117 PIIKMRKGQKLRFQAIARIGRGKDHSKWSPAAAVGYSYMPIYELKDPVECDLSQCSNCIE 176

Query: 182 ------KVSYTV---------ESARE------GQVLDYDKLSMTIDTDGSITGEDSVALA 220
                 +V Y V         E  R        +  D  ++ ++ ++ GS+  E+  + A
Sbjct: 177 SDGGISRVDYPVLCEGCLEALERCRVRNPDKIIRRWDESRIIISYESTGSLRPEEIFSEA 236

Query: 221 SRILQDQLGMFIN 233
              ++ +LG  +N
Sbjct: 237 LNQVKGKLGELLN 249


>gi|196037707|ref|ZP_03105018.1| conserved domain protein [Bacillus cereus NVH0597-99]
 gi|196044418|ref|ZP_03111654.1| conserved domain protein [Bacillus cereus 03BB108]
 gi|225863094|ref|YP_002748472.1| hypothetical protein BCA_1183 [Bacillus cereus 03BB102]
 gi|229183445|ref|ZP_04310670.1| hypothetical protein bcere0004_10180 [Bacillus cereus BGSC 6E1]
 gi|301052779|ref|YP_003790990.1| hypothetical protein BACI_c11710 [Bacillus anthracis CI]
 gi|196025057|gb|EDX63728.1| conserved domain protein [Bacillus cereus 03BB108]
 gi|196031949|gb|EDX70545.1| conserved domain protein [Bacillus cereus NVH0597-99]
 gi|225786045|gb|ACO26262.1| conserved domain protein [Bacillus cereus 03BB102]
 gi|228600029|gb|EEK57624.1| hypothetical protein bcere0004_10180 [Bacillus cereus BGSC 6E1]
 gi|300374948|gb|ADK03852.1| conserved hypothetical protein [Bacillus cereus biovar anthracis
           str. CI]
          Length = 95

 Score = 38.8 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 42  LSAPARRALEHHGIHNVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSFK 95


>gi|302911227|ref|XP_003050446.1| hypothetical protein NECHADRAFT_84788 [Nectria haematococca mpVI
           77-13-4]
 gi|256731383|gb|EEU44733.1| hypothetical protein NECHADRAFT_84788 [Nectria haematococca mpVI
           77-13-4]
          Length = 136

 Score = 38.8 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 34/97 (35%), Gaps = 8/97 (8%)

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS--PIKKVSYTVESAREGQ 194
           +  D   ++E  V  G         + E+  +G +  + L     +    Y +      +
Sbjct: 20  ILDDGEKKIEEKVFSGMSNTSDFVLKKEDHTLGNLLSEHLKMHPNVYMAGYKIAHPNVPE 79

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
                 L + + TDG+IT  D        L +QL M 
Sbjct: 80  ------LFIRVQTDGTITPRDVFTSVCEKLINQLEML 110


>gi|307594234|ref|YP_003900551.1| RNA polymerase insert [Vulcanisaeta distributa DSM 14429]
 gi|307549435|gb|ADN49500.1| RNA polymerase insert [Vulcanisaeta distributa DSM 14429]
          Length = 302

 Score = 38.8 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 77/248 (31%), Gaps = 37/248 (14%)

Query: 45  NALRRVLMSSLRGAAITAVQI-DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK- 102
           N+LRRVL+S +   AI  V I D        +      +  I  +++ +  K+     + 
Sbjct: 27  NSLRRVLISDVPVLAIDEVIILDNTSVLYDEVLAHRLSMMPIKTDLRKL-PKIEECEQEL 85

Query: 103 ----------RVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
                      + +  + P +V + D+++   ++  +  D  I  L     + +E     
Sbjct: 86  VDPSLCQVRFELNVEAKEPMIVYSRDLKSDDPEVRPVYEDIPIVKLVPGQKIVLEAYAKL 145

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G     AK             +  +     K    +E              + I  DGSI
Sbjct: 146 GRARNHAKWQAGLASYYYYPKVSVVGKADDKCRVCLEVCNGA---------LEIKEDGSI 196

Query: 212 TGEDSVALA--SRILQDQLGMFINFEEPKK------------EVKEDINVKSLPFNPALL 257
              D +          +QL   +  +  +              V++ +            
Sbjct: 197 IINDVLKCTFNKWKTCEQLCPALKVDWDENKYVFWVESFGNMPVEDMVREGFRILKGKFQ 256

Query: 258 KKVEELEL 265
           + V ELEL
Sbjct: 257 EFVNELEL 264


>gi|256810443|ref|YP_003127812.1| RNA polymerase insert [Methanocaldococcus fervens AG86]
 gi|256793643|gb|ACV24312.1| RNA polymerase insert [Methanocaldococcus fervens AG86]
          Length = 191

 Score = 38.8 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 40/196 (20%), Positives = 78/196 (39%), Gaps = 40/196 (20%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN-IKGINLK---M 96
            +  NA+RR+++S +   AI  V I      +           +II + +  I +K   +
Sbjct: 24  ISFSNAIRRIMISEVPTYAIEDVYIFENSSSMDD---------EIIAHRLGLIPIKGKPL 74

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
             +     T+ K GP  V + D+++ N  EV   +  I  L     +++E     G G V
Sbjct: 75  LENEIITFTLEKEGPCTVYSSDLKSENG-EVAFKNIPIVKLGNGQKIQIECEAVPGIGKV 133

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
            AK              +A+Y                + +  D++   ++T G +  E+ 
Sbjct: 134 HAK----------WQPCNAVY----------------KQISEDEVEFFVETFGQMEAEEI 167

Query: 217 VALASRILQDQLGMFI 232
           +  A +IL+++   F+
Sbjct: 168 LEEAVKILKNKAESFL 183


>gi|118476727|ref|YP_893878.1| hypothetical protein BALH_1007 [Bacillus thuringiensis str. Al
           Hakam]
 gi|118415952|gb|ABK84371.1| conserved hypothetical protein [Bacillus thuringiensis str. Al
           Hakam]
          Length = 97

 Score = 38.8 bits (89), Expect = 1.4,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 44  LSAPARRALEHHGIHNVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSFK 97


>gi|195338303|ref|XP_002035764.1| GM15286 [Drosophila sechellia]
 gi|194129644|gb|EDW51687.1| GM15286 [Drosophila sechellia]
          Length = 275

 Score = 38.4 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 37/259 (14%), Positives = 91/259 (35%), Gaps = 52/259 (20%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS--- 74
           + + +  ++    + E        ++ N+LRRV ++     AI  VQ++     +S    
Sbjct: 9   VQITELTDDNVKFVLEDTE----LSVANSLRRVFIAETPTLAIDWVQLEANSTVLSDEFL 64

Query: 75  ------IKGVHEDLTDIILNIKG-INLKMSGDSHKRVTIFKRGPGV----VTAGDIQT-- 121
                 I  + +D+ + +   +  I L    +     T+  +        VT  D+++  
Sbjct: 65  AHRIGLIPLISDDVVERLQYTRDCICLDFCPECSVEFTLDVKCSEEQTRHVTTADLKSSN 124

Query: 122 --------------VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---- 163
                          N+    N + +I  L     +++     KG G   AK + T    
Sbjct: 125 AKVLPVTSRHQGEEDNEYGESNDEILIIKLRKGQELKLRAYAKKGFGKEHAKWNPTAGVC 184

Query: 164 -----ENDPIGLIT------IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
                +N     +         + ++ ++   Y      E +   +      +++ G++ 
Sbjct: 185 FEYDPDNSMRHTLYPKPDEWPKSEHTELEDDQYEAPYNWEAKPNKF---FFNVESAGALK 241

Query: 213 GEDSVALASRILQDQLGMF 231
            E+ V +  ++L+++L   
Sbjct: 242 PENIVIMGVQVLKNKLSNL 260


>gi|325968486|ref|YP_004244678.1| RNA polymerase insert [Vulcanisaeta moutnovskia 768-28]
 gi|323707689|gb|ADY01176.1| RNA polymerase insert [Vulcanisaeta moutnovskia 768-28]
          Length = 317

 Score = 38.4 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 40/234 (17%), Positives = 70/234 (29%), Gaps = 32/234 (13%)

Query: 45  NALRRVLMSSLRGAAITAVQI-DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK- 102
           NALRRV +S +   AI  V I D        +      +  I  ++K +  K+     + 
Sbjct: 44  NALRRVFISDVPVLAIDEVIILDNTSVLYDEVLAHRLSMIPIKTDLKKL-PKIEECEQEL 102

Query: 103 ----------RVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
                      + +  + P VV   D+++   ++  +  D  I  L     + +E     
Sbjct: 103 VDPSLCQVRFELNVEAKEPVVVYGRDLKSDDPEVRPVYEDVPIVKLVPGQKIVLEAYAKL 162

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G     AK             +  +     K     E              + I  DGSI
Sbjct: 163 GRARNHAKWQAGLAAYYYYPKVSVVDKANDKCMTCTEICNGA---------LEIKDDGSI 213

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF--NPALLKKVEEL 263
              D +             +   E+    +K D +     F         VE++
Sbjct: 214 MIHDVLKCT-------FNKWKTCEQVCSALKVDWDENKYVFWVESFGNMPVEDM 260


>gi|159041731|ref|YP_001540983.1| RNA polymerase insert [Caldivirga maquilingensis IC-167]
 gi|157920566|gb|ABW01993.1| RNA polymerase insert [Caldivirga maquilingensis IC-167]
          Length = 305

 Score = 38.4 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 29/156 (18%), Positives = 55/156 (35%), Gaps = 19/156 (12%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIK 76
           + + Q  ++    + E    G   +L N+LRR+L++ +   AI  V + D        + 
Sbjct: 7   VKVLQYSDDYLKFVVE----GVKPSLINSLRRILITDVPVLAIDRVIVLDNTTVMYDEVL 62

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIF---KRGPGVVTAGD----------IQTVN 123
                +  +  N++ +  K+     + V       R    + A D          I    
Sbjct: 63  AHRLSMIPLKTNLEKL-PKIEECEDELVDPSLCQVRYQLSIKANDQVVSVYAKDLIPDDP 121

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
           D   + PD +I  +    V+ +E     G     AK
Sbjct: 122 DFAPVYPDTLIVKMSKGQVLSIEAYAKLGRARDHAK 157


>gi|115649661|ref|XP_795508.2| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
 gi|115971068|ref|XP_001177736.1| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
          Length = 335

 Score = 38.4 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 32/168 (19%), Positives = 52/168 (30%), Gaps = 40/168 (23%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIK----------------- 76
           + NA RR+L++ +   AI  V I           + H +  I                  
Sbjct: 57  VANAFRRILLAEVPTMAIEKVSIFNNTSIIQDEILAHRLGLIPIKADPRIFEYREEGDET 116

Query: 77  GVHEDLTDIILNIKGI-NLKMSGDSHKRVTIFKRGPGVVTAGDIQ-----------TVND 124
           G  ED  +  L +K   N   S D+     ++K     VT    +               
Sbjct: 117 GTGEDTIEFQLKVKCTKNPNASKDATDPDELYKNAK--VTTEHFKWIPLENQEETYGPKA 174

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT 172
              +N D +I  L     + +++   KG G   AK          L+ 
Sbjct: 175 FAPVNKDILIAKLRPGQEIDLKMHCVKGIGKDHAKFSPVATASYRLMP 222


>gi|171689616|ref|XP_001909748.1| hypothetical protein [Podospora anserina S mat+]
 gi|170944770|emb|CAP70881.1| unnamed protein product [Podospora anserina S mat+]
          Length = 334

 Score = 38.4 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 41/259 (15%), Positives = 92/259 (35%), Gaps = 47/259 (18%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG--------- 67
            + + Q +  R     +     F     N+LRRV+++ +   AI  V+I+          
Sbjct: 17  VVKISQADSVRVKFELQNADISF----ANSLRRVMLAEIPTIAIDLVEIESNSSVLADEF 72

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG--VVTAGDIQTVNDI 125
           + H +  I    E +  ++ +      +   +   ++T+  +  G   ++      V   
Sbjct: 73  IAHRLGLIPLNAEGVEHLLYSRDCDCEEYCENCSVKLTLHAKCTGYENMSVSARDLVPVG 132

Query: 126 EVLNPDH-------------VICNLDVDAVVRMELTVSKGH-----GYVPAKHHRTENDP 167
           E +N                +I  L  +  +++E    KG       + P+     E DP
Sbjct: 133 ERINQSLGTPVINDKDGTGPLILKLRPEQEIKLECIAKKGIAKEHAKWAPSAAIGFEYDP 192

Query: 168 IGLI---------TIDALYSPIKKVSYTVESAREGQVLDYDKLS----MTIDTDGSITGE 214
              +            + + P +   +  E   EG+  D+D +       ++T G++  +
Sbjct: 193 HNKLRHLDLWYEKDPKSEWPPSEYAKWE-EPPVEGEPFDFDAVPNHFYYNVETAGNLPPD 251

Query: 215 DSVALASRILQDQLGMFIN 233
             V    +++Q +L   I+
Sbjct: 252 GIVTEGIKVIQQKLAGLIH 270


>gi|195579088|ref|XP_002079394.1| GD23930 [Drosophila simulans]
 gi|194191403|gb|EDX04979.1| GD23930 [Drosophila simulans]
          Length = 275

 Score = 38.4 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 37/259 (14%), Positives = 91/259 (35%), Gaps = 52/259 (20%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS--- 74
           + + +  ++    + E        ++ N+LRRV ++     AI  VQ++     +S    
Sbjct: 9   VQITELTDDNVKFVLEDTE----LSVANSLRRVFIAETPTLAIDWVQLEANSTVLSDEFL 64

Query: 75  ------IKGVHEDLTDIILNIKG-INLKMSGDSHKRVTIFKRGPGV----VTAGDIQT-- 121
                 I  + +D+ + +   +  I L    +     T+  +        VT  D+++  
Sbjct: 65  AHRIGLIPLISDDVVERLQYTRDCICLDFCPECSVEFTLDVKCSEEQTRHVTTADLKSSN 124

Query: 122 --------------VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---- 163
                          N+    N + +I  L     +++     KG G   AK + T    
Sbjct: 125 AKVLPVTSRNQGEEDNEYGESNDEILIIKLRKGQELKLRAYAKKGFGKEHAKWNPTAGVC 184

Query: 164 -----ENDPIGLIT------IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
                +N     +         + ++ ++   Y      E +   +      +++ G++ 
Sbjct: 185 FEYDPDNSMRHTLYPKPDEWPKSEHTELEDDQYEAPYNWEAKPNKF---FFNVESAGALK 241

Query: 213 GEDSVALASRILQDQLGMF 231
            E+ V +  ++L+++L   
Sbjct: 242 PENIVIMGVQVLKNKLSNL 260


>gi|222112349|ref|YP_002554613.1| sigma-70 region 4 domain-containing protein [Acidovorax ebreus
           TPSY]
 gi|221731793|gb|ACM34613.1| sigma-70 region 4 domain protein [Acidovorax ebreus TPSY]
          Length = 893

 Score = 38.4 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 11/47 (23%), Positives = 24/47 (51%)

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             K++ L  +VR  N  +G N+  +  +  +    +L++ N G+ S+
Sbjct: 226 NDKLQNLNTTVRMANVFKGHNLSTVAHIAAKGYNGLLKLPNLGQGSV 272


>gi|118576727|ref|YP_876470.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Cenarchaeum symbiosum A]
 gi|118195248|gb|ABK78166.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Cenarchaeum symbiosum A]
          Length = 212

 Score = 38.4 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 32/220 (14%), Positives = 70/220 (31%), Gaps = 48/220 (21%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIIL 87
           RG      NALRR+ ++ +   A+  V I         +G+ H +  I  +  D ++   
Sbjct: 19  RGVPLQYANALRRICLNGVPVFAVDTVDIVENTSVLADEGLAHRLGLIP-LRTDSSEF-- 75

Query: 88  NIKGINLKMSGDSHKRVTIFKRGPGV-------VTAGDIQTVNDIEVLNPDHVICNLDVD 140
             K +  ++  D      +     G        +++  +   + ++ ++    I  L   
Sbjct: 76  --KNLA-EIDPDDPINRVMLTLDSGEAAETRTVLSSELVSEDSSVKPISDTIPIVELAPG 132

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY-D 199
             +++E     G G                          +   +   +       D  D
Sbjct: 133 QRIKVEAYARLGRG-------------------------TEHAKWNSSNVSVLTATDKED 167

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +  +TI++ G++     V      L  +L  F    +  K
Sbjct: 168 ERILTIESTGAMDPAQLVLEGVTELSRRLADFRTMLDEMK 207


>gi|291230540|ref|XP_002735226.1| PREDICTED: polymerase (RNA) I polypeptide C, 30kDa-like, partial
           [Saccoglossus kowalevskii]
          Length = 202

 Score = 38.4 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 33/182 (18%), Positives = 64/182 (35%), Gaps = 32/182 (17%)

Query: 76  KGVHEDLTDIILNIKGIN-LKMSGDSHKRVTIFKRGPGVVT---------AGDIQTVNDI 125
           +G  ED  +  L +K         D+     +++                 GDI + +DI
Sbjct: 3   EGTTEDTIEFQLKVKCTRNPHAPKDATDPDEMYRHWRVTTKDLKWVPFGNQGDIYSGDDI 62

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI----- 180
             ++ D +I  L     + +++   KG G   AK          L+    L  P+     
Sbjct: 63  YSVHDDILIAKLRPGQEIDVKVHCVKGLGKDHAKFSPVATASYRLLPEMKLTKPVVGEQA 122

Query: 181 ----KKVSYTVESARE-GQVLDYD-----KL-------SMTIDTDGSITGEDSVALASRI 223
               K  S  V   ++ G +   D     KL         ++++ G++  +  V+ A ++
Sbjct: 123 ERLAKTFSPRVIEVQDIGGISSQDLKDCVKLSKVRNHFIFSVESTGALKPDVLVSEAIKV 182

Query: 224 LQ 225
           L 
Sbjct: 183 LI 184


>gi|229090185|ref|ZP_04221433.1| hypothetical protein bcere0021_10170 [Bacillus cereus Rock3-42]
 gi|228693121|gb|EEL46834.1| hypothetical protein bcere0021_10170 [Bacillus cereus Rock3-42]
          Length = 95

 Score = 38.4 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 42  LSAPARRALEHHGIHNVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSFK 95


>gi|228938360|ref|ZP_04100971.1| hypothetical protein bthur0008_10260 [Bacillus thuringiensis
           serovar berliner ATCC 10792]
 gi|228971239|ref|ZP_04131868.1| hypothetical protein bthur0003_10190 [Bacillus thuringiensis
           serovar thuringiensis str. T01001]
 gi|228977848|ref|ZP_04138230.1| hypothetical protein bthur0002_10550 [Bacillus thuringiensis Bt407]
 gi|228781866|gb|EEM30062.1| hypothetical protein bthur0002_10550 [Bacillus thuringiensis Bt407]
 gi|228788474|gb|EEM36424.1| hypothetical protein bthur0003_10190 [Bacillus thuringiensis
           serovar thuringiensis str. T01001]
 gi|228821306|gb|EEM67320.1| hypothetical protein bthur0008_10260 [Bacillus thuringiensis
           serovar berliner ATCC 10792]
 gi|326938869|gb|AEA14765.1| hypothetical protein CT43_CH1076 [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 95

 Score = 38.4 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 42  LSAPARRALEHHGIQTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSFK 95


>gi|218232408|ref|YP_002365927.1| hypothetical protein BCB4264_A1194 [Bacillus cereus B4264]
 gi|229042984|ref|ZP_04190715.1| hypothetical protein bcere0027_10400 [Bacillus cereus AH676]
 gi|218160365|gb|ACK60357.1| conserved domain protein [Bacillus cereus B4264]
 gi|228726324|gb|EEL77550.1| hypothetical protein bcere0027_10400 [Bacillus cereus AH676]
          Length = 95

 Score = 38.4 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 42  LSAPARRALEHHGIQTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSFK 95


>gi|206968409|ref|ZP_03229365.1| conserved domain protein [Bacillus cereus AH1134]
 gi|228951607|ref|ZP_04113711.1| hypothetical protein bthur0006_10240 [Bacillus thuringiensis
           serovar kurstaki str. T03a001]
 gi|229068797|ref|ZP_04202093.1| hypothetical protein bcere0025_10070 [Bacillus cereus F65185]
 gi|229078430|ref|ZP_04210991.1| hypothetical protein bcere0023_10990 [Bacillus cereus Rock4-2]
 gi|229177657|ref|ZP_04305034.1| hypothetical protein bcere0005_10240 [Bacillus cereus 172560W]
 gi|206737329|gb|EDZ54476.1| conserved domain protein [Bacillus cereus AH1134]
 gi|228605847|gb|EEK63291.1| hypothetical protein bcere0005_10240 [Bacillus cereus 172560W]
 gi|228704852|gb|EEL57277.1| hypothetical protein bcere0023_10990 [Bacillus cereus Rock4-2]
 gi|228714305|gb|EEL66184.1| hypothetical protein bcere0025_10070 [Bacillus cereus F65185]
 gi|228808068|gb|EEM54583.1| hypothetical protein bthur0006_10240 [Bacillus thuringiensis
           serovar kurstaki str. T03a001]
          Length = 95

 Score = 38.4 bits (88), Expect = 1.8,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 42  LSAPARRALEHHGIQTVEELSKYSEKEILKLHGMGPASLPKLRRALEESGLSFK 95


>gi|255714803|ref|XP_002553683.1| KLTH0E04598p [Lachancea thermotolerans]
 gi|238935065|emb|CAR23246.1| KLTH0E04598p [Lachancea thermotolerans]
          Length = 328

 Score = 38.0 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 44/229 (19%), Positives = 81/229 (35%), Gaps = 45/229 (19%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDII----L 87
            T+ N+LRRV+++ +   AI +V+++          + H +  I     D+ D+I     
Sbjct: 27  ITMANSLRRVMIAEIPTLAIDSVEVETNTSVLADEFISHRLGLIPLQSSDINDLIYCRDC 86

Query: 88  NIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV-----------ICN 136
             +    + S     +          V A D+  V+++   N  H            IC 
Sbjct: 87  YCEDHCDRCSVVLTLQAVGESESTTNVYAKDLVIVSNLMGRNIGHPIIQDKDGNGVLICK 146

Query: 137 LDVDAVVRMELTVSKGH---------------GYVPAKHHRTENDPIGLITIDALYSPIK 181
           L     ++++    KG                 Y P    +  +         A +   K
Sbjct: 147 LRKGQELKLKCVAKKGISKEHAKWSPAAAIEFEYDPWNKLKHTDYWHET-DAAAEWPQSK 205

Query: 182 KVSYTVESAREGQVLDYD-KLS---MTIDTDGSITGEDSVALASRILQD 226
              Y  +   E +  DY+ K +   M ++T GS+T +  V    + LQD
Sbjct: 206 NCEYE-DPPNEDEAFDYNAKPTTFYMNVETVGSLTVDQVVIRGMKTLQD 253


>gi|195433589|ref|XP_002064793.1| GK15011 [Drosophila willistoni]
 gi|194160878|gb|EDW75779.1| GK15011 [Drosophila willistoni]
          Length = 275

 Score = 38.0 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 40/257 (15%), Positives = 91/257 (35%), Gaps = 48/257 (18%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS--- 74
           + + +  ++    I E        ++ N+LRRV ++     AI  VQ++     +S    
Sbjct: 9   VQITELTDDNVKFILEDTE----LSVANSLRRVFIAETPTLAIDWVQLEANSTVLSDEFL 64

Query: 75  ------IKGVHEDLTDIILNIKG-INLKMSGDSHKRVTIFKRGPGV----VTAGDIQT-- 121
                 I  + +D+ + +   +  I L    +     T+  +        VT  D+++  
Sbjct: 65  AHRIGLIPLISDDVVERLQYTRDCICLDFCPECSVEFTLDVKCNEEQTRHVTTADLKSSN 124

Query: 122 --------------VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---- 163
                          N+    N + +I  L     +++     KG G   AK + T    
Sbjct: 125 AKVLPVTSRNQGEEDNEYGESNDEILIIKLRKGQELKLRAYAKKGFGKEHAKWNPTAGVC 184

Query: 164 -----ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD----KLSMTIDTDGSITGE 214
                +N     +       P K     +E  +     +++    K    +++ G++  E
Sbjct: 185 FEYDPDNSMRHTLYPKPDEWP-KSEHSELEDEQFEAPYNWEAKPNKFFFNVESSGALKPE 243

Query: 215 DSVALASRILQDQLGMF 231
           + V +  ++L+++L   
Sbjct: 244 NIVVMGVQVLKNKLSNL 260


>gi|229149445|ref|ZP_04277681.1| hypothetical protein bcere0011_10070 [Bacillus cereus m1550]
 gi|228634087|gb|EEK90680.1| hypothetical protein bcere0011_10070 [Bacillus cereus m1550]
          Length = 95

 Score = 38.0 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 42  LSAPARRALEHHGIQTVEELSKYSEKEILKLHGMGHASLPKLRRALEESGLSFK 95


>gi|229108700|ref|ZP_04238310.1| hypothetical protein bcere0018_9810 [Bacillus cereus Rock1-15]
 gi|228674730|gb|EEL29964.1| hypothetical protein bcere0018_9810 [Bacillus cereus Rock1-15]
          Length = 95

 Score = 38.0 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL   
Sbjct: 42  LSAPARRALEHRGIQTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSFK 95


>gi|289191580|ref|YP_003457521.1| RNA polymerase insert [Methanocaldococcus sp. FS406-22]
 gi|288938030|gb|ADC68785.1| RNA polymerase insert [Methanocaldococcus sp. FS406-22]
          Length = 191

 Score = 38.0 bits (87), Expect = 2.3,   Method: Composition-based stats.
 Identities = 38/196 (19%), Positives = 75/196 (38%), Gaps = 40/196 (20%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN-IKGINLK---M 96
            +  NA+RR+++S +   AI  V I      +           +I+ + +  I +K   +
Sbjct: 24  ISFSNAIRRIMISEVPTYAIEDVYIYENSSSMDD---------EILAHRLGLIPIKGKPL 74

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
                   T+ K GP  V + D+++ N  EV   +  I  L     +++E     G G  
Sbjct: 75  IESEVITFTLEKEGPCTVYSSDLKSENG-EVAFKNIPIVKLGRGQKIKIECEAVPGIGKT 133

Query: 157 PAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
            AK              +A+Y  +                  D++   ++T G +  E+ 
Sbjct: 134 HAK----------WQPCNAVYKQV----------------AEDEVEFFVETFGQMEAEEI 167

Query: 217 VALASRILQDQLGMFI 232
           +  A +IL+++   F+
Sbjct: 168 LEEAVKILKNKAESFL 183


>gi|123469797|ref|XP_001318108.1| hypothetical protein [Trichomonas vaginalis G3]
 gi|121900859|gb|EAY05885.1| hypothetical protein TVAG_353250 [Trichomonas vaginalis G3]
          Length = 739

 Score = 37.6 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 21/99 (21%), Positives = 42/99 (42%), Gaps = 1/99 (1%)

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCL 273
           ++ +A  ++I+ DQ    +  +E     K     K         +  +EL LS+     L
Sbjct: 574 DEKIANYNKIIADQQTTVMKLKEEINARKNMKGKKEK-VTAIEDELKQELNLSISELESL 632

Query: 274 RGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +  N     +L  + E D+ ++ N G+KSL ++   +  
Sbjct: 633 KITNAKKDKELRLQHEKDIQKIQNTGQKSLEKLTKRIKE 671


>gi|6635392|gb|AAF19808.1|AF185048_1 acyl-CoA oxidase [Sus scrofa]
          Length = 142

 Score = 37.6 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 17/109 (15%), Positives = 39/109 (35%), Gaps = 10/109 (9%)

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           E    + +     +          + +L+L     N L       +   ++++   + ++
Sbjct: 2   ELLTHILDGSPENTRRRREIENMILSDLDLQHEDLNFLSRSQRYEVA--VKKSATTVKKI 59

Query: 296 ANFGRKSLVEI---KGVLGT-----MGLFLGMNLPDWPPESIEELAKKY 336
             FG     EI   K  +       + L +GM LP    ++ EE  +++
Sbjct: 60  REFGLADPDEILWFKNFVQRGHPGPLDLHVGMFLPTLLHQATEEQQERF 108


>gi|321475674|gb|EFX86636.1| hypothetical protein DAPPUDRAFT_313021 [Daphnia pulex]
          Length = 274

 Score = 37.6 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 42/232 (18%), Positives = 77/232 (33%), Gaps = 46/232 (19%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIK-GVHEDLTDIILNIK 90
            ++ N+LRRV ++     AI  VQ +          + H +  I     E +  +  +  
Sbjct: 28  LSVANSLRRVFIAETPTLAIDWVQFEANSTVLFDEFLAHRVGLIPLTSDESVEKMQYSRD 87

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAG--------------------DIQTVNDIEVLNP 130
                   D     T+  +    VT                      D +  +D    + 
Sbjct: 88  CTCPDFCVDCSVEFTLDVKCSEDVTRNVTTADLKSTDPRVVPATSKRDEEPPDD---NDN 144

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT-----ENDPIGLITIDALYSPIK--KV 183
           + +I  L     ++M     KG G   AK + T     E DP   +       P +  + 
Sbjct: 145 EILIVKLRKGQELKMRAYAKKGFGKEHAKWNPTAGVAFEYDPDNSLRHTLFPKPEEWPRS 204

Query: 184 SYTVESAREGQVLDYD------KLSMTIDTDGSITGEDSVALASRILQDQLG 229
            Y+     +     YD      K  + +++ GS+  E+ V +   IL+ +L 
Sbjct: 205 EYSELGESDQHQAPYDPDGKPNKFFVNVESCGSLRPENIVLMGIAILKKKLS 256


>gi|71031382|ref|XP_765333.1| DNA-directed RNA polymerase I [Theileria parva strain Muguga]
 gi|68352289|gb|EAN33050.1| DNA-directed RNA polymerase I, putative [Theileria parva]
          Length = 303

 Score = 37.6 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 32/198 (16%), Positives = 70/198 (35%), Gaps = 32/198 (16%)

Query: 7   QELIKPNNIEYIVLGQEEEN----------RTLMIAEPLP------RGFAHTLGNALRRV 50
           +  ++P+ I+      ++ N          +   + +          G   +L NALRR+
Sbjct: 4   RVFLEPSGIKPCYEESDDNNIPILEKVKNLQVKFLKKTPEFSVVEIVGLDVSLANALRRI 63

Query: 51  LMSSLRGAAITAVQID---GV------LHEISSIKGVHE-DLTDIILNIKGINLKMSGDS 100
           L+S +   A+  VQI    GV       H +  I    + DL +   N K    +++  +
Sbjct: 64  LISEVPTLAVETVQIYQNTGVIQDELLAHRLGLIPFAIDPDLFNFKSNFKTNCEEINDKN 123

Query: 101 HKRVTIFKRGPGVVTAGDIQTVNDI------EVLNPDHVICNLDVDAVVRMELTVSKGHG 154
                +  +      +  + + + +      + +  D +I  L     + + + + KG G
Sbjct: 124 SVCFKLKVKYNKFDQSDYLSSNSLMFKDNPPKPVYDDILITKLAPGQEIDLNMYLEKGIG 183

Query: 155 YVPAKHHRTENDPIGLIT 172
            V +K           + 
Sbjct: 184 KVHSKWSPVSTAVYKFMP 201


>gi|289615067|emb|CBI58137.1| unnamed protein product [Sordaria macrospora]
          Length = 311

 Score = 37.6 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 4/50 (8%)

Query: 17 YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           + + Q +  R           F     N+LRRV+++ +   AI  V+I+
Sbjct: 17 VVKISQADSTRVKFELSNTELCF----ANSLRRVMLAEIPTIAIDLVEIE 62


>gi|171186411|ref|YP_001795330.1| RNA polymerase insert [Thermoproteus neutrophilus V24Sta]
 gi|229564213|sp|B1YC30|RPOD_THENV RecName: Full=DNA-directed RNA polymerase subunit D
 gi|170935623|gb|ACB40884.1| RNA polymerase insert [Thermoproteus neutrophilus V24Sta]
          Length = 262

 Score = 37.6 bits (86), Expect = 3.1,   Method: Composition-based stats.
 Identities = 36/225 (16%), Positives = 79/225 (35%), Gaps = 33/225 (14%)

Query: 42  TLGNALRRVLMSSLRGAAITAVQIDGVLH-EISSIKGVHEDLTDIILNIKGINLKMS--- 97
           +L N+LRRV++S L   AI  V +          +      L  +   ++ +        
Sbjct: 24  SLVNSLRRVIISELPVMAIDTVIVVNNTSVMYDEMLAHRLGLIPLTTPLQSLPPIEDCES 83

Query: 98  -----GDSHKRVTIFKRGPGVVT--AGDIQTV-NDIEVLNPDHVICNLDVDAVVRMELTV 149
                 +   R T+     G VT  +GD+ +   D+  ++ D  I  L     + +E   
Sbjct: 84  GLADPSECTVRFTLQVNADGEVTVYSGDLVSERPDVVPVHKDIPIVKLVKGQSIVLEAYA 143

Query: 150 SKGHG--------------YVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA----- 190
             G                Y P    R E+       +    +   + ++          
Sbjct: 144 KLGRARGHAKWQAALASYYYYPRVEVRDESCRERCREVCRDLTNPLECTFNKAMTCRDLC 203

Query: 191 REGQVLDYDKL--SMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
            +   +D+++      +++ G+   + ++  A RIL+ +  +F++
Sbjct: 204 GDKLHVDWERNKYVFWVESFGNYDVDTALREAFRILKRKYSLFLD 248


>gi|46124881|ref|XP_386994.1| hypothetical protein FG06818.1 [Gibberella zeae PH-1]
          Length = 239

 Score = 37.6 bits (86), Expect = 3.1,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 33/97 (34%), Gaps = 8/97 (8%)

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS--PIKKVSYTVESAREGQ 194
           L  +   ++E  V  G           E+  +G +  + L     +    Y +      +
Sbjct: 123 LLGEGEKKIEEKVFSGMSNTSDFVLMKEDHTLGNLLSEHLKMHPNVHMAGYKIAHPNVPE 182

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
                 L + + TDG+IT  D        L +QL M 
Sbjct: 183 ------LFIRVQTDGTITPRDVFTSVCEKLINQLEML 213


>gi|221114057|ref|XP_002158521.1| PREDICTED: similar to predicted protein [Hydra magnipapillata]
          Length = 273

 Score = 37.3 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 42/243 (17%), Positives = 77/243 (31%), Gaps = 44/243 (18%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIK-GV 78
             I E        ++ N+LRR+ ++ +   AI  VQI+          + H I  I    
Sbjct: 20  KFILE----NTDLSVANSLRRIFIAEVPTIAIDWVQIENNTSVLHDEFIAHRIGLIPLTS 75

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT------------------AGDIQ 120
            E +  +  +      +   +   + T+  +  G  T                     I+
Sbjct: 76  DEKVDKMCYSRDCTCSEFCDECSVKFTLDVKCTGETTRHVTSRDLISEDPKVIPVTSRIK 135

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
             +       + VI  L     +++     KG G   AK + T          +AL    
Sbjct: 136 DDDTGYGETDEIVIVKLRKGQELKLHAFAKKGFGKEHAKWNPTAGVSFEYDPDNALRHTT 195

Query: 181 -------KKVSYTV--ESAREGQVLDY---DKLSMTIDTDGSITGEDSVALASRILQDQL 228
                   K  Y+   E   E     +   DK    +++ GS+  E+ V     +L+ +L
Sbjct: 196 FARPDQWPKSEYSQLDEDQYEAPYDIHAKADKFYFNVESCGSLKPENIVMTGISVLKKKL 255

Query: 229 GMF 231
              
Sbjct: 256 SEL 258


>gi|282889932|ref|ZP_06298467.1| hypothetical protein pah_c008o015 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281500125|gb|EFB42409.1| hypothetical protein pah_c008o015 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 422

 Score = 37.3 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 12/57 (21%), Positives = 24/57 (42%)

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
            + +  L LS  +  CL       + DL++    D++ +   G+  + EI+  L   
Sbjct: 135 DEPIHILGLSQHAEKCLEKNGKCLIQDLLKADTQDLIFLKGMGQGHIDEIQQTLKKY 191


>gi|302414524|ref|XP_003005094.1| DNA-directed RNA polymerases I and III subunit RPAC1 [Verticillium
           albo-atrum VaMs.102]
 gi|261356163|gb|EEY18591.1| DNA-directed RNA polymerases I and III subunit RPAC1 [Verticillium
           albo-atrum VaMs.102]
          Length = 375

 Score = 37.3 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 37/211 (17%), Positives = 65/211 (30%), Gaps = 55/211 (26%)

Query: 23  EEENRTLMIAEPLPRGFAH-----TLGNALRRVLMSSLRGAAITAVQID----------- 66
           E          P    F+      ++ NALRR+L+S +   AI  V I            
Sbjct: 51  ENFRVRYHQLSPSESSFSLIGVDASIANALRRILISEIPTLAIETVYIYNNTSVIQDEVL 110

Query: 67  ----GVLHEISSIKGVHE--------------DLTDIILNIKGINLKMSGDSHKRVTIFK 108
               G++   ++  G+ +              D+ D   N   + L++    +      +
Sbjct: 111 AHRLGLVPFTANKAGLRDFLRWRKKNPDGTPGDIFDY--NTVQLRLRIECTRNPDAAPGE 168

Query: 109 RGPGVVTAGDIQTVNDIEVL-------------------NPDHVICNLDVDAVVRMELTV 149
                         +DIE +                   NPD ++  L    V+ M++ +
Sbjct: 169 IDSTKAFRNAHVHASDIEYVPSGRQLEYFDGPLNTVRPTNPDILLAKLRPGQVLEMDMHM 228

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
            KG G   AK          L+    +  PI
Sbjct: 229 HKGIGSDHAKFSPVATASYRLLPTITITRPI 259


>gi|257094932|ref|YP_003168573.1| serine/threonine protein kinase [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257047456|gb|ACV36644.1| serine/threonine protein kinase [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
          Length = 1413

 Score = 37.3 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 14/82 (17%), Positives = 27/82 (32%)

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLI 285
           D L  +    +           + +         + EL+ SV + N L    I  + +L+
Sbjct: 773 DMLRDWRKIFDQADTQTAADPFEVIALRATRETAIGELDYSVEAQNVLDRMGIHSVRELL 832

Query: 286 QRTEADMLRMANFGRKSLVEIK 307
                    + + G K   EI+
Sbjct: 833 AVDRVRFRYLKSVGDKVRKEIR 854


>gi|88604132|ref|YP_504310.1| DNA-directed RNA polymerase subunit D [Methanospirillum hungatei
           JF-1]
 gi|88189594|gb|ABD42591.1| DNA-directed RNA polymerase, subunit D [Methanospirillum hungatei
           JF-1]
          Length = 272

 Score = 37.3 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 34/152 (22%), Positives = 52/152 (34%), Gaps = 14/152 (9%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID-GVLHEISSIK 76
           I     EEN    +    P  F     NALRR ++S +   AI  V+I          I 
Sbjct: 3   IEFSSLEENAASFVLSDAPIAF----ANALRRAMVSEVMTFAIEDVKIYDNTSALFDEIL 58

Query: 77  GVHEDLTDIILNIKGINLKMSGDSH--------KRVTIFKRGPGVVTAGD-IQTVNDIEV 127
                L  ++ +      +     +          +T+   GPGVV +GD I     +  
Sbjct: 59  THRLGLIPLVTDPDSFVPRSQCSCNGAGCPRCTVTLTMSVEGPGVVMSGDLISQDAVVRP 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
              +  I  L+ +  V +E       G   AK
Sbjct: 119 AEDNIPIVKLEKNQKVVIEAQAYMERGMEHAK 150


>gi|183220911|ref|YP_001838907.1| transcription elongation factor NusA [Leptospira biflexa serovar
           Patoc strain 'Patoc 1 (Paris)']
 gi|189911007|ref|YP_001962562.1| transcription elongation factor NusA [Leptospira biflexa serovar
           Patoc strain 'Patoc 1 (Ames)']
 gi|167775683|gb|ABZ93984.1| Transcription elongation factor [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167779333|gb|ABZ97631.1| N utilization substance protein A [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
          Length = 466

 Score = 37.3 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 15/110 (13%), Positives = 35/110 (31%)

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           + I T      E +   A   L           E  ++            +       E 
Sbjct: 349 IDIKTVSQYNQELASPEAREKLDRLFNAQQEAMEESEDGYNQSGQDEEEEDSGFTPLSEI 408

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
             L+ R    L    I  +  L++ ++ ++ +++  G+ +  +I  +L  
Sbjct: 409 PGLTPRIVGLLEAGGIKNVETLLEFSQEELSKISGIGKTTAEQILRLLRE 458


>gi|261404088|ref|YP_003240329.1| helix-hairpin-helix motif protein [Paenibacillus sp. Y412MC10]
 gi|261280551|gb|ACX62522.1| helix-hairpin-helix motif protein [Paenibacillus sp. Y412MC10]
          Length = 72

 Score = 37.3 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 14/71 (19%), Positives = 26/71 (36%), Gaps = 4/71 (5%)

Query: 252 FNPALLKKVEELELSVRSTN----CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                     E +  V++ N     L       + DL + TE ++L +   G K++  ++
Sbjct: 1   MRDNPPATAAESDFPVKAGNPARRALIVAGYHRLADLTRATEKELLALHGVGPKAIGVLR 60

Query: 308 GVLGTMGLFLG 318
             L   GL   
Sbjct: 61  AALAEKGLAFK 71


>gi|189203213|ref|XP_001937942.1| DNA-directed RNA polymerases I and III subunit RPAC1 [Pyrenophora
          tritici-repentis Pt-1C-BFP]
 gi|187985041|gb|EDU50529.1| DNA-directed RNA polymerases I and III subunit RPAC1 [Pyrenophora
          tritici-repentis Pt-1C-BFP]
          Length = 376

 Score = 37.3 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 5/49 (10%)

Query: 23 EEENRTLMIAEPLPRGFAHT-----LGNALRRVLMSSLRGAAITAVQID 66
          +  N      +PL   F+ T     + NA RR+L+S +   AI  V I 
Sbjct: 48 DNFNVVFHKNDPLDAQFSLTGIDTSVANAFRRILLSEIPTLAIEDVYIY 96


>gi|313889958|ref|ZP_07823596.1| fibronectin-binding repeat protein [Streptococcus pseudoporcinus
           SPIN 20026]
 gi|313121674|gb|EFR44775.1| fibronectin-binding repeat protein [Streptococcus pseudoporcinus
           SPIN 20026]
          Length = 749

 Score = 37.3 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 20/101 (19%), Positives = 36/101 (35%), Gaps = 5/101 (4%)

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
            +  Y  I   +Y V+S       D +KL++     G+ T          IL    G  +
Sbjct: 460 TEESYYQITDTNYKVKSQLTEAQFDTEKLTLMA---GTNTAAKGEKRVGGILFSLFGNSV 516

Query: 233 NFEEPKKEVKEDIN--VKSLPFNPALLKKVEELELSVRSTN 271
              E  K         ++     P     +E+ +LS+++ N
Sbjct: 517 KLNEVVKPEPPVYETVIEPKVPTPPQTIVIEKPKLSLKTFN 557


>gi|319776580|ref|YP_004139068.1| putative trimeric autotransporter adhesin [Haemophilus influenzae
           F3047]
 gi|317451171|emb|CBY87404.1| Putative trimeric autotransporter adhesin [Haemophilus influenzae
           F3047]
          Length = 1016

 Score = 37.3 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 31/216 (14%), Positives = 67/216 (31%), Gaps = 26/216 (12%)

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             N + +     VI  +D    +       +G   V       +   +     I    L 
Sbjct: 466 ADNSVSIGTYSQVI--IDGGVALGDHSIADRGENSVGVDFSGKYTGIDANNHYILKGELK 523

Query: 178 SPIKKVSYTVESAREGQVLDYDK--------LSMTIDTDGSITGEDSVALASRILQDQLG 229
           +  + +   + +A+E    D +K          +  +   + +  +S       LQ+Q+ 
Sbjct: 524 TESEAMQTDINNAKERFKTDVEKYSELSELRNLIEGEIPAANSTFNSRNNTYTQLQNQMN 583

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
              N +   ++V++    K          K    EL           +I    D     +
Sbjct: 584 SSNNSKPKAEDVQKAKEAKEKAEANLNKLKARRSELET-------KHSITMTSDAANNND 636

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           ++     N  +K L EI+  L  +   L  +  ++ 
Sbjct: 637 SE----KN--KKELEEIENKLTALDKQLVTDEGNFK 666


>gi|257093661|ref|YP_003167302.1| Cupin 2 barrel domain-containing protein [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257046185|gb|ACV35373.1| Cupin 2 conserved barrel domain protein [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
          Length = 230

 Score = 37.3 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 12/44 (27%), Positives = 24/44 (54%), Gaps = 1/44 (2%)

Query: 265 LSVRSTNCLRGENIVYMGDLI-QRTEADMLRMANFGRKSLVEIK 307
           +S R    L  E +  + +++ +     + +M +FGRKS+ EI+
Sbjct: 56  ISPRLRTLLLKEGLTTVNEVVGRYRSKALFQMRSFGRKSIQEIE 99


>gi|329124094|ref|ZP_08252641.1| Hep_Hag superfamily protein [Haemophilus aegyptius ATCC 11116]
 gi|327467519|gb|EGF13017.1| Hep_Hag superfamily protein [Haemophilus aegyptius ATCC 11116]
          Length = 1103

 Score = 37.3 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 31/216 (14%), Positives = 67/216 (31%), Gaps = 26/216 (12%)

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             N + +     VI  +D    +       +G   V       +   +     I    L 
Sbjct: 466 ADNSVSIGTYSQVI--IDGGVALGDHSIADRGENSVGVDFSGKYTGIDANNHYILKGELK 523

Query: 178 SPIKKVSYTVESAREGQVLDYDK--------LSMTIDTDGSITGEDSVALASRILQDQLG 229
           +  + +   + +A+E    D +K          +  +   + +  +S       LQ+Q+ 
Sbjct: 524 TESEAMQTDINNAKERFKTDVEKYSELSELRNLIEGEIPAANSTFNSRNNTYTQLQNQMN 583

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
              N +   ++V++    K          K    EL           +I    D     +
Sbjct: 584 SSNNSKPKAEDVQKAKEAKEKAEANLNKLKARRSELET-------KHSITMTSDAANNND 636

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           ++     N  +K L EI+  L  +   L  +  ++ 
Sbjct: 637 SE----KN--KKELEEIENKLTALDKQLVTDEGNFK 666


>gi|284165822|ref|YP_003404101.1| RNA polymerase insert [Haloterrigena turkmenica DSM 5511]
 gi|284015477|gb|ADB61428.1| RNA polymerase insert [Haloterrigena turkmenica DSM 5511]
          Length = 249

 Score = 37.3 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 36/225 (16%), Positives = 76/225 (33%), Gaps = 43/225 (19%)

Query: 35  LPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL 94
           L RG      N +RR +++ +   AI  V+       +            + L +  + L
Sbjct: 20  LVRGVTPGFANGIRRAMLADVPTMAIDTVRFVENSSVMFD--------EQLALRLGLVPL 71

Query: 95  KMS------GDSHKRVTIFKRGPGVVTAGDIQTVND-IEVLNPDHVICNLDVDAVVRMEL 147
                     D    ++I   GP    +GD+ + +D ++  + +  I +L  D  +  E 
Sbjct: 72  TTPPEGEFGEDETVTLSIDVEGPATAYSGDLVSSDDLVQPADENVPIIDLKDDQRLEAEA 131

Query: 148 TV--SKGHGY----------------------VPAKHHRTENDPIGLITIDALYSPIKKV 183
                 G  +                      +P           G+I  D    P  + 
Sbjct: 132 DAVLDYGKDHAKHQGGVAVGYRHLQRVEVVGDLPEFEEEESRIVRGVIEDDGELVPTSEF 191

Query: 184 SYTVESAREGQVLDYDKL----SMTIDTDGSITGEDSVALASRIL 224
            + + +   G+ ++ + +       ++TDGS + E+ V  A+  +
Sbjct: 192 DHDLSNRYPGKEVEIEDVPNAFVFHVETDGSFSVEELVTRAADSI 236


>gi|116328714|ref|YP_798434.1| transcription elongation factor NusA [Leptospira borgpetersenii
           serovar Hardjo-bovis L550]
 gi|116330628|ref|YP_800346.1| transcription elongation factor NusA [Leptospira borgpetersenii
           serovar Hardjo-bovis JB197]
 gi|116121458|gb|ABJ79501.1| Transcription elongation factor [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116124317|gb|ABJ75588.1| Transcription elongation factor [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 462

 Score = 37.3 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 1/70 (1%)

Query: 244 DINVKSLPFNPALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           +    + P     L  +E+L  LS R    L+ E I  +  LI+ ++ D+ ++   G  +
Sbjct: 385 EEAKVAAPQEEEELTPLEDLPGLSARIVGILKSEGIKDLETLIEYSQDDLAKLQGIGHTT 444

Query: 303 LVEIKGVLGT 312
             +I  +L  
Sbjct: 445 AGQILKLLRE 454


>gi|148253101|ref|YP_001237686.1| hypothetical protein BBta_1564 [Bradyrhizobium sp. BTAi1]
 gi|146405274|gb|ABQ33780.1| hypothetical protein BBta_1564 [Bradyrhizobium sp. BTAi1]
          Length = 88

 Score = 36.9 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 26/62 (41%)

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                      +  +EL +R    L    +  +G++ +  + ++LR+ + G  SL  ++ 
Sbjct: 3   DPSPELPDDTPILNVELPLRVREALVAAGLTTIGEIRETPDKEILRIQHLGTSSLALLRK 62

Query: 309 VL 310
            L
Sbjct: 63  TL 64


>gi|76802059|ref|YP_327067.1| DNA-directed RNA polymerase subunit D [Natronomonas pharaonis DSM
           2160]
 gi|121723150|sp|Q3IQT6|RPOD_NATPD RecName: Full=DNA-directed RNA polymerase subunit D
 gi|76557924|emb|CAI49508.1| DNA-directed RNA polymerase subunit D [Natronomonas pharaonis DSM
           2160]
          Length = 247

 Score = 36.9 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 27/144 (18%), Positives = 52/144 (36%), Gaps = 17/144 (11%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
             +E         L RG      N LRR +++ +   +I  +++      +         
Sbjct: 11  DRDERSARF----LVRGVTPAFANGLRRAMIADVPTLSIDTLRVVENSSVMFD------- 59

Query: 82  LTDIILNIKGINLKMSGD----SHKRVTIFKRGPGVVTAGDIQTVND-IEVLNPDHVICN 136
              + L +  + L    D        + I   GP    +GD+ + +D ++  + +  I  
Sbjct: 60  -EQLALRLGLVPLTTPDDYEPGETVTLAIDVEGPATAYSGDLVSSDDKVQPADENIPIIE 118

Query: 137 LDVDAVVRMELTVSKGHGYVPAKH 160
           L  D  + +E   + G G   AKH
Sbjct: 119 LKDDQQLELEADATLGRGKDHAKH 142


>gi|115963733|ref|XP_001176308.1| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
 gi|115977296|ref|XP_001176467.1| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
          Length = 275

 Score = 36.9 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 47/258 (18%), Positives = 89/258 (34%), Gaps = 57/258 (22%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID---GVLH--EI 72
           I L +  ++    I E        ++ N++RR +++ +   AI  V+I     VLH   I
Sbjct: 9   IQLTELTDDNVKFIIE----DTDLSVANSIRRTILAEVPTIAIDWVEIQANSSVLHDEFI 64

Query: 73  SSIKGVHEDLTDIILNIKGINLKMS-----------GDSHKRVTIFKRGPG----VVTAG 117
           S   G+      I L    +  K++            D    +++  +        VT+ 
Sbjct: 65  SHRVGL------IPLTSDEVVDKLNFNRDCGCEEFCSDCSVELSLDVKCTDDQTRHVTSR 118

Query: 118 DI--------------QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGH-----GYVPA 158
           D+              Q  +D   ++ D +I  L     +R+     KG       +VP 
Sbjct: 119 DLLSSNQKVVPVPSRNQESSDYGEVD-DILIVKLRKGQELRLRAYAKKGFGKDHAKWVPT 177

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ-VLDYD------KLSMTIDTDGSI 211
                E DP  ++       P +          E      +D      K    +++ G++
Sbjct: 178 AAIAFEYDPDNIMRHTVYPKPEEWPKSEFTEVDEDTAQGKFDGDAVPNKFFFNVESIGAL 237

Query: 212 TGEDSVALASRILQDQLG 229
           T E+ V     +L+ +L 
Sbjct: 238 TPENIVFSGLSVLKKKLS 255


>gi|118352484|ref|XP_001009513.1| Guanylate-binding protein, N-terminal domain containing protein
           [Tetrahymena thermophila]
 gi|89291280|gb|EAR89268.1| Guanylate-binding protein, N-terminal domain containing protein
           [Tetrahymena thermophila SB210]
          Length = 1132

 Score = 36.9 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 13/63 (20%), Positives = 29/63 (46%), Gaps = 5/63 (7%)

Query: 281 MGDLIQRTEADMLRMANFGRKSL---VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
           + DL  +   ++  + NF +KS+    E+K     +         D+  ++ E L ++++
Sbjct: 356 IHDLKAKVREEL--IKNFKKKSIASEEELKEFYEQLDRQFAEKFRDFKKKNKERLQERFQ 413

Query: 338 DKC 340
           D C
Sbjct: 414 DMC 416


>gi|170033286|ref|XP_001844509.1| DNA-directed RNA polymerase I 40 kDa polypeptide [Culex
           quinquefasciatus]
 gi|167873916|gb|EDS37299.1| DNA-directed RNA polymerase I 40 kDa polypeptide [Culex
           quinquefasciatus]
          Length = 335

 Score = 36.9 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 33/197 (16%), Positives = 61/197 (30%), Gaps = 43/197 (21%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG----- 67
             ++ +V+ + EEN           G +  + NA RR+++S +   AI  V I       
Sbjct: 42  RQLQIVVV-RYEENELEFDM----IGVSPAIANAFRRLMLSEVPSMAIEKVHIYNNTSII 96

Query: 68  ----VLHEISSIK----------GVHE-------DLTDIILNIKGINLKMSGDSHKRVTI 106
               + H +  I             +E       D  +  L +K    K    +      
Sbjct: 97  QDEVLAHRLGLIPLKADPRLFEYKTNEGDAANAQDTLEFELKVKCTK-KNKDSTEVTNND 155

Query: 107 FKRGPGVVTAGDIQ-----------TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY 155
                  + +G I+              D+  ++ D +I  +       ++L   KG G 
Sbjct: 156 SMYKNHSIYSGQIKWVPVGNQASIYKEADVGPIDDDILISRMRPGHEFDIKLFAVKGVGK 215

Query: 156 VPAKHHRTENDPIGLIT 172
             AK          L+ 
Sbjct: 216 DHAKFSPVATASYRLLP 232


>gi|320108355|ref|YP_004183945.1| NusA antitermination factor [Terriglobus saanensis SP1PR4]
 gi|319926876|gb|ADV83951.1| NusA antitermination factor [Terriglobus saanensis SP1PR4]
          Length = 562

 Score = 36.9 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 15/81 (18%), Positives = 28/81 (34%)

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLI 285
             LG  I+ +  +++ +E     S           +  EL       L    I  +  L 
Sbjct: 333 KLLGWKIDIKSEEEKRQEVEQQMSAMQGAPQTPIEQVTELGESVLEKLIAAGITTVESLA 392

Query: 286 QRTEADMLRMANFGRKSLVEI 306
             T  ++  +   G KS+ +I
Sbjct: 393 DMTAEELEEVPGIGEKSVEKI 413


>gi|30019294|ref|NP_830925.1| hypothetical protein BC1139 [Bacillus cereus ATCC 14579]
 gi|29894837|gb|AAP08126.1| hypothetical Cytosolic Protein [Bacillus cereus ATCC 14579]
          Length = 95

 Score = 36.9 bits (84), Expect = 5.2,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 25/54 (46%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++L++   G  SL ++K VL    L   
Sbjct: 42  LSAPARRALEHRGIQTVEELSKYSEKEILKLHGMGPASLPKLKKVLEESWLSFK 95


>gi|124486064|ref|YP_001030680.1| DNA-directed RNA polymerase subunit D [Methanocorpusculum labreanum
           Z]
 gi|124363605|gb|ABN07413.1| DNA-directed RNA polymerase, subunit D [Methanocorpusculum
           labreanum Z]
          Length = 275

 Score = 36.5 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 25/154 (16%), Positives = 51/154 (33%), Gaps = 16/154 (10%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID-GVLHEISSIKG 77
           V  + +++           G      NALRR ++  +   AI  ++I          +  
Sbjct: 4   VFSRLDDSVARFTI----HGATPAFANALRRSMIGEVPTLAIEDIRIYDNTSVLFDEMLA 59

Query: 78  VHEDLTDIILNIKGINLKMSGD--------SHKRVTIFKRGPGVVTAGD-IQTVNDIEVL 128
               L  I  ++     +                 T+   GP +VT+GD I    ++  +
Sbjct: 60  HRLGLIPIKTDLSQYVPRSECSCGGEGCPHCTVMFTLSVEGPKMVTSGDLISMDENVVPV 119

Query: 129 NPDHVICNL--DVDAVVRMELTVSKGHGYVPAKH 160
           + +  I  L  +   V+     V+ G  +   + 
Sbjct: 120 HNNIPIVKLWENQKVVLEAVAEVNYGKEHAKWQP 153


>gi|125984946|ref|XP_001356237.1| GA20659 [Drosophila pseudoobscura pseudoobscura]
 gi|195164762|ref|XP_002023215.1| GL21238 [Drosophila persimilis]
 gi|54644558|gb|EAL33299.1| GA20659 [Drosophila pseudoobscura pseudoobscura]
 gi|194105300|gb|EDW27343.1| GL21238 [Drosophila persimilis]
          Length = 275

 Score = 36.5 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 42/261 (16%), Positives = 92/261 (35%), Gaps = 47/261 (18%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           N     +    ++N    + E        ++ N+LRRV ++     AI  VQ++     +
Sbjct: 5   NQPNVQITELTDDN-VKFVLEDTE----LSVANSLRRVFIAETPTLAIDWVQLEANSTVL 59

Query: 73  SS---------IKGVHEDLTDIILNIKG-INLKMSGDSHKRVTIFKRGPGV----VTAGD 118
           S          I  + +D+ + +   +  I L    +     T+  +        VT  D
Sbjct: 60  SDEFLAHRIGLIPLISDDVVERLQYTRDCICLDFCPECSVEFTLDVKCSEEQTRHVTTAD 119

Query: 119 IQT----------------VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
           ++T                 N+    + + +I  L     +++     KG G   AK + 
Sbjct: 120 LKTSNPKVLPVTSRNQGEEDNEYGESSDEILIIKLRKGQELKLRAYAKKGFGKEHAKWNP 179

Query: 163 T-----ENDPIGLITIDALYSPIKKVS---YTVESAREGQVLDYD----KLSMTIDTDGS 210
           T     E DP   +       P +        +E  +     +++    K    +++ G+
Sbjct: 180 TAGVCFEYDPDNCMRHTLYPKPDEWPKSEHTELEDDQFEAPYNWEAKPNKFFFNVESSGA 239

Query: 211 ITGEDSVALASRILQDQLGMF 231
           +  E+ V +  ++L+++L   
Sbjct: 240 LKPENIVIMGVQVLKNKLSNL 260


>gi|319790038|ref|YP_004151671.1| PHP domain protein [Thermovibrio ammonificans HB-1]
 gi|317114540|gb|ADU97030.1| PHP domain protein [Thermovibrio ammonificans HB-1]
          Length = 575

 Score = 36.5 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 29/140 (20%), Positives = 52/140 (37%), Gaps = 16/140 (11%)

Query: 185 YTVESAREGQVLD----YDKLSMTIDTDGSITGEDSVALASRILQDQ-LGMFINFEEPKK 239
           Y V + R    L      D   +  +   S        L ++IL+    G    FE+ K+
Sbjct: 25  YHVRAYRNAARLINDLSEDIEVLAREGKLSQLPGIGQRLQAKILEFLRTGKIEEFEKLKQ 84

Query: 240 EVKEDI-NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +V + I  +  +P       K+   EL +RS   L+                ++L++  F
Sbjct: 85  QVPDTIFTLLDIPGVGPKTVKLLYEELGIRSIEDLKRA----------IERGELLKLPGF 134

Query: 299 GRKSLVEIKGVLGTMGLFLG 318
           G K + +IK  +  +    G
Sbjct: 135 GPKRVEKIKKGIELLEKSGG 154


>gi|110678161|ref|YP_681168.1| RNA polymerase sigma factor, putative [Roseobacter denitrificans
           OCh 114]
 gi|109454277|gb|ABG30482.1| RNA polymerase sigma factor, putative [Roseobacter denitrificans
           OCh 114]
          Length = 1005

 Score = 36.5 bits (83), Expect = 5.8,   Method: Composition-based stats.
 Identities = 17/111 (15%), Positives = 43/111 (38%), Gaps = 8/111 (7%)

Query: 211 ITGEDSVALASRILQDQ-LGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
           +   D+   A R L++         ++  ++    ++        +++  V E + SVR 
Sbjct: 190 MRAPDAAREAFRQLENFGEKTATELDDLVRKFARKVDQDRQDAADSIVDVVREADCSVRL 249

Query: 270 TNCL----RGENIVYMGDLIQ---RTEADMLRMANFGRKSLVEIKGVLGTM 313
            N +        +  + + ++         L++ N GRKS  E+  ++ + 
Sbjct: 250 LNAISAHSHRLPVTTVSEYMKAPAHARQAFLKLPNLGRKSADELDLIMRSF 300


>gi|47567602|ref|ZP_00238313.1| hypothetical protein cytosolic protein [Bacillus cereus G9241]
 gi|47555797|gb|EAL14137.1| hypothetical protein cytosolic protein [Bacillus cereus G9241]
          Length = 95

 Score = 36.5 bits (83), Expect = 5.8,   Method: Composition-based stats.
 Identities = 12/54 (22%), Positives = 24/54 (44%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++ ++   G  SL +++  L   GL   
Sbjct: 42  LSAPARRALEHHGIQTVEELSKYSEKEISKLHGMGPASLPKLRKALEESGLSFK 95


>gi|167045221|gb|ABZ09881.1| putative RNA polymerase Rpb3/RpoA insert domain protein [uncultured
           marine crenarchaeote HF4000_APKG8O8]
          Length = 201

 Score = 36.5 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 34/205 (16%), Positives = 73/205 (35%), Gaps = 37/205 (18%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDI--ILNIKGINL 94
           +G      NALRR+ ++   G AI A+    ++   S +    E +T    ++ +K    
Sbjct: 19  KGVTLQYANALRRICLN---GVAIYAIDTVDMIENSSVLAD--EGITHRLGLIPLKTDLS 73

Query: 95  KMSGDSHKRVT-----IFKRGPGVVTAGDIQTVNDIEVLNPDHV-ICNLDVDAVVRMELT 148
           +      + +             +VT+ ++ + + +   + D + I +L     ++ E  
Sbjct: 74  RSDESDSRIMLTLDSGDDTETGRMVTSAELLSDDKVVKPSSDQIPIIHLTPGQKLKFEAY 133

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
              G G   AK + +           A+    KK                D+  +T++T 
Sbjct: 134 ARLGRGTEHAKWNSSNI---------AVLLDTKK---------------EDEHILTVETT 169

Query: 209 GSITGEDSVALASRILQDQLGMFIN 233
           G++   + +      L  +L  F  
Sbjct: 170 GALKPGEIIIGGINELTKRLEEFKE 194


>gi|332017912|gb|EGI58566.1| DNA-directed RNA polymerase II subunit RPB3 [Acromyrmex echinatior]
          Length = 256

 Score = 36.5 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 33/215 (15%), Positives = 73/215 (33%), Gaps = 27/215 (12%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH---------EDLTDIILNIKG 91
            ++ N++RRV ++     AI  +Q++     +  I+            E   +  L++K 
Sbjct: 28  LSVANSMRRVFIAETPTMAIDWIQLEANSTVVDRIQYTRDCQCMDFCPECSVEFTLDVKC 87

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
              +    +             VT+   +          + +I  L     +++     K
Sbjct: 88  TEEQTRHVTTADFKSSDPRVLPVTSRHREDDASEYGETDEILIVKLRKGQELKLRAYAKK 147

Query: 152 GHGYVPAKHHRT---------ENDPIGLITIDAL------YSPIKKVSYTVESAREGQVL 196
           G G   AK + T         +N     +   A       YS +++  Y      E +  
Sbjct: 148 GFGKEHAKWNPTAGVSFEYDPDNTMRHTLFPKADEWPKSEYSELEEDQYEASFNWEAKPN 207

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            Y      +++ G++  E+ V +    L+++L   
Sbjct: 208 KY---YFNVESSGALKPENIVMMGIAALKNKLSNL 239


>gi|229189332|ref|ZP_04316352.1| hypothetical protein bcere0002_10140 [Bacillus cereus ATCC 10876]
 gi|228594126|gb|EEK51925.1| hypothetical protein bcere0002_10140 [Bacillus cereus ATCC 10876]
          Length = 95

 Score = 36.5 bits (83), Expect = 6.3,   Method: Composition-based stats.
 Identities = 12/54 (22%), Positives = 24/54 (44%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           LS  +   L    I  + +L + +E ++ ++   G  SL +++  L   GL   
Sbjct: 42  LSAPARRALEHHGIQTVEELSKYSEKEISKLHGMGPASLPKLRKALEESGLSFK 95


>gi|32564376|ref|NP_492732.2| yeast SEC homolog family member (sec-8) [Caenorhabditis elegans]
 gi|30179897|sp|Q9XWS2|EXOC4_CAEEL RecName: Full=Exocyst complex component 4; AltName: Full=Exocyst
           complex component Sec8
 gi|25005036|emb|CAA21575.2| C. elegans protein Y106G6H.7, partially confirmed by transcript
           evidence [Caenorhabditis elegans]
          Length = 893

 Score = 36.5 bits (83), Expect = 6.5,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 26/57 (45%), Gaps = 7/57 (12%)

Query: 264 ELSVRSTNCLRGEN-----IVYMGDLIQRTEADMLRM--ANFGRKSLVEIKGVLGTM 313
           ++S + +NC    +     +  +  L++    D+ ++   N  +KS+ EI   L  +
Sbjct: 87  DVSSKISNCRERIHNVRNALHTVKSLLELRRDDLKKLWHENAQQKSVCEIMAKLEEL 143


>gi|195031522|ref|XP_001988351.1| GH11119 [Drosophila grimshawi]
 gi|195115860|ref|XP_002002474.1| GI12561 [Drosophila mojavensis]
 gi|195397712|ref|XP_002057472.1| GJ18149 [Drosophila virilis]
 gi|193904351|gb|EDW03218.1| GH11119 [Drosophila grimshawi]
 gi|193913049|gb|EDW11916.1| GI12561 [Drosophila mojavensis]
 gi|194141126|gb|EDW57545.1| GJ18149 [Drosophila virilis]
          Length = 275

 Score = 36.5 bits (83), Expect = 6.5,   Method: Composition-based stats.
 Identities = 36/259 (13%), Positives = 90/259 (34%), Gaps = 52/259 (20%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS--- 74
           + + +  ++    + E        ++ N+LRRV ++     AI  VQ++     +S    
Sbjct: 9   VQITELTDDNVKFVLEDTE----LSVANSLRRVFIAETPTLAIDWVQLEANSTVLSDEFL 64

Query: 75  ------IKGVHEDLTDIILNIKG-INLKMSGDSHKRVTIFKRGPGV----VTAGDIQT-- 121
                 I  + +D+ + +   +  I L    +     T+  +        VT  D+++  
Sbjct: 65  AHRIGLIPLISDDVVERLQYTRDCICLDFCPECSVEFTLDVKCNEEQTRHVTTADLKSSN 124

Query: 122 --------------VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---- 163
                          N+      + +I  L     +++     KG G   AK + T    
Sbjct: 125 AKVLPVTSRNQGEEDNEYGESTDEILIIKLRKGQELKLRAYAKKGFGKEHAKWNPTAGVC 184

Query: 164 -----ENDPIGLIT------IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
                +N     +         + ++ ++   Y      E +   +      +++ G++ 
Sbjct: 185 FEYDPDNSMRHTLYPKPDEWPKSEHTELEDDQYEAPYNWEAKPNKF---FFNVESSGALK 241

Query: 213 GEDSVALASRILQDQLGMF 231
            E+ V +  ++L+++L   
Sbjct: 242 PENIVIMGVQVLKNKLSNL 260


>gi|322436508|ref|YP_004218720.1| NusA antitermination factor [Acidobacterium sp. MP5ACTX9]
 gi|321164235|gb|ADW69940.1| NusA antitermination factor [Acidobacterium sp. MP5ACTX9]
          Length = 534

 Score = 36.1 bits (82), Expect = 7.2,   Method: Composition-based stats.
 Identities = 16/90 (17%), Positives = 38/90 (42%), Gaps = 4/90 (4%)

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGE 276
           V LA+++LQ ++ +    E+ ++  ++   +   P  P         EL  +    L   
Sbjct: 328 VRLAAKLLQWKIDIKSEEEKRQEVEQQMQAMSGGPTTPIEQVT----ELGEQILEKLIAA 383

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            I  +  +   T  ++ ++   G K++ +I
Sbjct: 384 GITTVEAVADMTAEELEQIPGIGEKTIEKI 413


>gi|308499521|ref|XP_003111946.1| CRE-SEC-8 protein [Caenorhabditis remanei]
 gi|308268427|gb|EFP12380.1| CRE-SEC-8 protein [Caenorhabditis remanei]
          Length = 893

 Score = 36.1 bits (82), Expect = 7.3,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 26/57 (45%), Gaps = 7/57 (12%)

Query: 264 ELSVRSTNCLRGEN-----IVYMGDLIQRTEADMLRM--ANFGRKSLVEIKGVLGTM 313
           ++S + +NC    +     +  +  L++    D+ ++   N  +KS+ EI   L  +
Sbjct: 87  DVSSKISNCRERIHNVRNALHTVKSLLELRRDDLKKLWHENAQQKSVCEIMAKLEEL 143


>gi|71894578|ref|YP_278686.1| DNA ligase [Mycoplasma synoviae 53]
 gi|123734274|sp|Q4A5J6|DNLJ_MYCS5 RecName: Full=DNA ligase; AltName: Full=Polydeoxyribonucleotide
           synthase [NAD+]
 gi|71851366|gb|AAZ43975.1| DNA ligase [Mycoplasma synoviae 53]
          Length = 697

 Score = 36.1 bits (82), Expect = 7.5,   Method: Composition-based stats.
 Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 3/62 (4%)

Query: 278 IVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
           I  + DL   T+ D+L +  FG KS+  +K  L +       +L  +  E++  L  K  
Sbjct: 562 ITKLSDLNNLTDEDLLSIDTFGEKSIENLKEFLSSEK---NQDLIKFLDENLNYLNSKKS 618

Query: 338 DK 339
            K
Sbjct: 619 SK 620


>gi|212530122|ref|XP_002145218.1| DNA-directed RNA polymerase I and III subunit Rpc40, putative
           [Penicillium marneffei ATCC 18224]
 gi|210074616|gb|EEA28703.1| DNA-directed RNA polymerase I and III subunit Rpc40, putative
           [Penicillium marneffei ATCC 18224]
          Length = 373

 Score = 36.1 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 23/105 (21%), Positives = 42/105 (40%), Gaps = 11/105 (10%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS 97
           G   ++ NA RR+L++ +   AI  V I   L+  S I+        +   +  I LK S
Sbjct: 70  GLDASVANAFRRILIAEVPTLAIEFVYI---LNNTSVIQDEV-----LASRLGLIPLKGS 121

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI-CNLDVDA 141
            +    +  FK+      +      +D   +  +  I C ++  A
Sbjct: 122 IEGLNWMQWFKKATEEDPSS--SEPSDFNTVVLNLNIECTVNEKA 164


>gi|146165282|ref|XP_001014723.2| AFR650Wp, putative [Tetrahymena thermophila]
 gi|146145525|gb|EAR94451.2| AFR650Wp, putative [Tetrahymena thermophila SB210]
          Length = 267

 Score = 36.1 bits (82), Expect = 7.6,   Method: Composition-based stats.
 Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 3/65 (4%)

Query: 278 IVYMGDLIQRTEADMLRM-ANFGRKSLVEIKGVLGTMGLFLGMNLP--DWPPESIEELAK 334
           +  +   I  T   ML +  NFG+K    I+  L        + LP   +P +SIE  AK
Sbjct: 5   VKRIDQPIIFTYNVMLNVYKNFGQKHFEHIENHLSKQTNMKAIVLPIISYPEDSIESRAK 64

Query: 335 KYEDK 339
           +   K
Sbjct: 65  QASQK 69


>gi|194246783|ref|YP_002004422.1| DNA-directed RNA polymerase beta\' chain [Candidatus Phytoplasma
           mali]
 gi|193807140|emb|CAP18578.1| DNA-directed RNA polymerase beta\' chain [Candidatus Phytoplasma
           mali]
          Length = 1352

 Score = 36.1 bits (82), Expect = 8.2,   Method: Composition-based stats.
 Identities = 13/58 (22%), Positives = 25/58 (43%), Gaps = 3/58 (5%)

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
            K++ + +S R  N L+   I Y+ +       D+    N  ++  V+I  +L    L
Sbjct: 6   TKIKNINISDRIINKLKLLGINYLEEFNTFNLDDL---KNLLKEDFVDIIPILKEYSL 60


>gi|198422271|ref|XP_002119444.1| PREDICTED: similar to polymerase (RNA) II (DNA directed)
           polypeptide C isoform 2 [Ciona intestinalis]
 gi|198422273|ref|XP_002119542.1| PREDICTED: similar to polymerase (RNA) II (DNA directed)
           polypeptide C isoform 3 [Ciona intestinalis]
 gi|198422275|ref|XP_002119306.1| PREDICTED: similar to polymerase (RNA) II (DNA directed)
           polypeptide C isoform 1 [Ciona intestinalis]
          Length = 277

 Score = 36.1 bits (82), Expect = 8.7,   Method: Composition-based stats.
 Identities = 38/258 (14%), Positives = 77/258 (29%), Gaps = 53/258 (20%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------V 68
           + + +  E+    + E        +  N++RRV ++ +   AI  +QI+          +
Sbjct: 9   VSITELTEDNVKFVVE----DTDLSTANSVRRVFIAEVPTLAIDWIQIEENSSVLNDEFL 64

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSG-DSHKRVTIFKRGPGV-----VTAGDIQTV 122
            H I  I    +D+ D I   +         D      +  +  G       T   I   
Sbjct: 65  SHRIGLIPLTSDDVVDKIQYSRDCMCDDFCQDCSVEFYLDVKCTGEGTRQVTTRDLISMN 124

Query: 123 NDIEVLN--------------PDHVICNLDVDAVVRMELTVSKGHGYVPAK--------- 159
             +  +                D +I  L     ++ +    KG G   AK         
Sbjct: 125 PKVVPITSRSRGDSSKSFGEQDDILIAKLRKGQSLKFKAFAKKGFGKEHAKWQCVSAVAF 184

Query: 160 --------HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
                    H T   P      +       +  Y  +    G+   +      +++ G++
Sbjct: 185 EYDPDNALRHTTYPKPEEWPKSEYSELADDEDKYQADFDPHGKPNKF---FFNVESTGAL 241

Query: 212 TGEDSVALASRILQDQLG 229
             E+ V     +L+ +L 
Sbjct: 242 RPENIVLNGLAVLKKKLS 259


>gi|303244308|ref|ZP_07330645.1| RNA polymerase insert [Methanothermococcus okinawensis IH1]
 gi|302485435|gb|EFL48362.1| RNA polymerase insert [Methanothermococcus okinawensis IH1]
          Length = 197

 Score = 36.1 bits (82), Expect = 8.8,   Method: Composition-based stats.
 Identities = 39/166 (23%), Positives = 63/166 (37%), Gaps = 26/166 (15%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLK---MSGDSHK 102
           ALRR+++S     AI  V      +  S    +      I   +  I +K   +S D   
Sbjct: 29  ALRRIMISETPTYAIENVYFY--ENTSSMYDEL------IAHRLGLIPIKGKPVSNDEVI 80

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
              + K GP VV +GD+++    EV+     I  L     + +E     G G   AK   
Sbjct: 81  IFALIKEGPCVVYSGDLESETG-EVVFKHIPIVKLKEGQKLELECEALVGTGKTHAK--- 136

Query: 163 TENDPIGLITIDALYSPIKK--VSYTVESAREGQVLDYDKLSMTID 206
                      +A+Y  +    V + VES   G +   D L  +++
Sbjct: 137 -------WQPCNAVYKLLNNDEVEFLVESY--GNMDSEDLLISSVE 173


>gi|193216369|ref|YP_001997568.1| Alg9 family protein mannosyltransferase [Chloroherpeton thalassium
           ATCC 35110]
 gi|193089846|gb|ACF15121.1| Alg9 family protein mannosyltransferase [Chloroherpeton thalassium
           ATCC 35110]
          Length = 494

 Score = 35.7 bits (81), Expect = 9.0,   Method: Composition-based stats.
 Identities = 20/112 (17%), Positives = 39/112 (34%), Gaps = 2/112 (1%)

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDP--IGLITIDALYSPIKKVSYTVESAREGQV 195
            ++ ++    T            +   N P    +I   A   PI  +   VE  R    
Sbjct: 356 TINIILLFAFTFHYSKKSRVETVYYFHNKPDVHAIIFDHARQPPIFYMDKWVEYYRVENS 415

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
            D+ KL   I     I    +V L  + +++++         K E++++I  
Sbjct: 416 EDWHKLKTKIQNKEIIKPNYAVFLGQKNIEERVKTMNEVLNVKTEIEKEIEP 467


>gi|269784633|ref|NP_001161428.1| DNA-directed RNA polymerase II subunit RPB3 [Danio rerio]
 gi|28278474|gb|AAH46047.1| Polymerase (RNA) II (DNA directed) polypeptide C [Danio rerio]
 gi|122890481|emb|CAM14256.1| polymerase (RNA) II (DNA directed) polypeptide C [Danio rerio]
          Length = 275

 Score = 35.7 bits (81), Expect = 9.0,   Method: Composition-based stats.
 Identities = 48/258 (18%), Positives = 84/258 (32%), Gaps = 46/258 (17%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG----- 67
           N     +    +EN    + E         + N++RRV MS +   AI  VQID      
Sbjct: 5   NQPTVKITELSDEN-VKFVIE----NTDLAVANSIRRVFMSEVPTIAIDWVQIDANSSVL 59

Query: 68  ----VLHEISSIKGVHEDLTDII-----LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGD 118
               V H +  I    +D+ D +             + S +    V   +     VT+ D
Sbjct: 60  HDEFVAHRVGLIPLTSDDIVDKMQYSRDCTCDDFCPECSVELTLDVRCTEDQTRHVTSRD 119

Query: 119 IQT---------------VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           + +                 +  V   D ++  L     +R+     KG G   AK + T
Sbjct: 120 LLSNNPRVIPVTSRSRDNDPNDYVEQDDILLVKLRKGQELRLRAYAKKGFGKEHAKWNPT 179

Query: 164 ENDPIGLITIDALYSPIK-------KVSYT-VESARE----GQVLDYDKLSMTIDTDGSI 211
                     +AL   +        K  Y+ +E              ++    +++ GS+
Sbjct: 180 AGVAFEYDPDNALRHTVYPIPQEWPKSEYSEIEEDGVQAQYDPNGKPERFYYNVESCGSL 239

Query: 212 TGEDSVALASRILQDQLG 229
             E  V  A  +L+ +L 
Sbjct: 240 RPETIVMSALAMLKKKLS 257


>gi|57241993|ref|ZP_00369933.1| protein-export membrane protein SecD [Campylobacter upsaliensis
           RM3195]
 gi|57017185|gb|EAL53966.1| protein-export membrane protein SecD [Campylobacter upsaliensis
           RM3195]
          Length = 527

 Score = 35.7 bits (81), Expect = 9.1,   Method: Composition-based stats.
 Identities = 17/105 (16%), Positives = 49/105 (46%), Gaps = 7/105 (6%)

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE--VKEDINVKSLPFNPALLKKVEELELSVRSTN 271
           +++V    + +   L   IN E    +  + +D +++    +   + K++ L   ++  N
Sbjct: 56  KEAVKSKMKSVASSLHYSINKENILIDQLIVKDEDLEFSLLDEGDMTKMQALLNEIKGLN 115

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFG-RKSLVEIKGVLGTMGL 315
            ++ +N+ ++   +  T+ ++  + NF   +++  I+  L   GL
Sbjct: 116 -VQKDNLHFV---VSFTQEELKNIENFALLQAVETIRNRLDEFGL 156


  Database: nr
    Posted date:  May 13, 2011  4:10 AM
  Number of letters in database: 999,999,932
  Number of sequences in database:  2,987,209
  
  Database: /data/usr2/db/fasta/nr.01
    Posted date:  May 13, 2011  4:17 AM
  Number of letters in database: 999,998,956
  Number of sequences in database:  2,896,973
  
  Database: /data/usr2/db/fasta/nr.02
    Posted date:  May 13, 2011  4:23 AM
  Number of letters in database: 999,999,979
  Number of sequences in database:  2,907,862
  
  Database: /data/usr2/db/fasta/nr.03
    Posted date:  May 13, 2011  4:29 AM
  Number of letters in database: 999,999,513
  Number of sequences in database:  2,932,190
  
  Database: /data/usr2/db/fasta/nr.04
    Posted date:  May 13, 2011  4:33 AM
  Number of letters in database: 792,586,372
  Number of sequences in database:  2,260,650
  
Lambda     K      H
   0.314    0.144    0.390 

Lambda     K      H
   0.267   0.0436    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,963,657,102
Number of Sequences: 13984884
Number of extensions: 241525915
Number of successful extensions: 821593
Number of sequences better than 10.0: 3690
Number of HSP's better than 10.0 without gapping: 6410
Number of HSP's successfully gapped in prelim test: 469
Number of HSP's that attempted gapping in prelim test: 803942
Number of HSP's gapped (non-prelim): 7352
length of query: 340
length of database: 4,792,584,752
effective HSP length: 139
effective length of query: 201
effective length of database: 2,848,685,876
effective search space: 572585861076
effective search space used: 572585861076
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.4 bits)
S2: 82 (36.1 bits)